Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_042873
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 178019
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Found at i:3623 original size:14 final size:14
Alignment explanation
Indices: 3589--3625 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3579 CAAAAAAAAT
3589 AAAAAAAAACTGAC
1 AAAAAAAAACTGAC
**
3603 ACGAAAAAACTGAC
1 AAAAAAAAACTGAC
3617 AAAAAAAAA
1 AAAAAAAAA
3626 TAGAAAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.73, C:0.14, G:0.08, T:0.05
Consensus pattern (14 bp):
AAAAAAAAACTGAC
Left flanking sequence: Indices 3089 -- 3588
TATTTCCTTTTTTGTAACATGGGATTTCATGCCATAACTGTTATTTGTATTTTAGTGTTTATTGG
CGCTGTTGGAAAATCTGCACAGATTGGATTGCATACTTGGTTACCCGATGCAATGGAGGGTTTTA
TAATATTTGAGGGCTCTCATGTGCCATTAGGTACATTCCAACAATCTCACTGTATGCTGGAATCG
TCGACCAAATGAGAGTCCCTATCGGAAAAATATCTCATTTTGACCAATCAGCAGGAAACCTATCA
GGGTAAAATCCACCCGGCGAAGTAAAGGCCGAAGGAGCTCTATAGGATCCCCAGAGACTGTACGT
AAGACCTCTTGTTCGAAATTTAATCTCTCCCGAACCCGCTGGCCCAAAGGGCACGAAGACCAGAG
GGAGAGGCCCGGAGGGCAGGGGACTTGGGTTGTCTGACAGGGCCCCGGACTGTCAGACAAACAAG
GAAAAAAAACTGAAAAAAAAGGGGGGACTGTCAGACAAAAAAAAT
Right flanking sequence: Indices 3626 -- 4125
TAGAAAAAAACAGGGCAGAAACTTCTAAGGAAAAATCTATATTTTTGGCGTCAAGTCTATTCATG
TATGAAAAAACCACATCTTAGTTTTTAAGGGTACAGCGGCCACCCGTAAGACTATTGGGAGAGCC
TATATTTAATAAGTGGAAGATCCAGTCCCTACTCTTGCCAAAGGTAGACTCACCAACCAATTACC
CAATGCTGTGGAAAAAAAATATATACATTTTCCGGCCTTGTGAAATCGTAAAAGGTTATGCGAGA
GTAGCCCACTCCAGTATCCGCTTTGATTCATGCAGCTACTATGGTAACAGCAGGCGTTTTTATGA
TAGCAAGGTGCTCCCCTTTATTTGAATACTCACCCAATGCTTTAATTGTTATTACTTTTGTAGGC
GCTATGACGTCATTCTTCGCGGCAACCACCGGAATATTACAAAACGATTTAAAAAGGGTTATAGC
TTATTCAACTTGTAGTCAGTTAGGCTATATGATCTTTGCTTGCGG
Found at i:9645 original size:2 final size:2
Alignment explanation
Indices: 9638--9686 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
9628 ACCTATAAAT
* * *
9638 TA TA TA TA TA TA TA GA TA TA TA TA AA TA TA TC TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9680 TA TA TA T
1 TA TA TA T
9687 CTATTGCAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 9138 -- 9637
TGCCAGATTATCCTAAAAGGTATGCCAAGGCTGTAGAGGTCGTAAGTGCCCTTTGTTTTGTCGGA
CAGTATTTTGGTTTTGTGGTGTCCGACAAAACCAAGTACCCCGCCCTCCAACAAACAAATAGAAT
TCTGGATCTTCGGAATATAGCGGACACCGTTTACAAACTGCATAAGGACGAGATGCTTACAGGAC
CTACAGGACGTACGTACCGCGTAACCGAAAAAACGTTCCCCTCGGGTTATGCTTCCTATTTTCAG
TCCTATTAGTTTGGACTCCTGGCGGAAGCGTCCCTAAGGTTCTATGAGAAGTGACATGACTCCCG
ACCGGAGTTCCTATGTCATTTCCATGATGGAAGTCTTTGGGCGTTCCCGAAGGAAAACTAGAGGC
CTATATAACAGATCTCAAGAACATGGTAACCCAACCCAAGTAGGGGAAGATCTAGGCCTTCAGGA
TCCTCAAAGGTTAGAGGTCAAGGCTATCTTCCCTGACCTATAAAT
Right flanking sequence: Indices 9687 -- 10186
CTATTGCAGCTCATCCTCTTCTTCGAAGAAGAAAAATAGTAGCTCATTTTCTTTTGGAAGATGAG
CGAAGAATAAACATGGATTAAAAAGTCTCTTCTATAAATAATAGAATCTATTTTATTTATGCATT
TCTTCTATTATATATAAATATATATATATATATTTGAATTTCTTTTATTTATGAATTTATTAATT
TATTCTATTTATTTTAATTTAATTTATTAACCCTTTTTAATTATATAGAATTATTCTATATTCCA
TATATAATTCTATTATATATTACCTTCCCCACCCTTTAATTCCATATTAAAGGGTATTCCTCTAT
ATTATACTACAGATCCTCAACAAGTTTAGTCATATTAGCTAAATATGCGTCATTTCGCGAAGGTG
TCATTAGCGATGAGGATTCCAGAGTATTAATTCTCTATATTTATCTACAAATCCTCGCAATTTAG
TCATATTAGCGAAATTTAGTCATTTAGCAATGCTTCCTTCATGCT
Found at i:11467 original size:15 final size:15
Alignment explanation
Indices: 11447--11478 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
11437 TAAAGACGTA
11447 ATGGCATATGCTATC
1 ATGGCATATGCTATC
11462 ATGGCATATGCTATC
1 ATGGCATATGCTATC
11477 AT
1 AT
11479 AGAAACAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (15 bp):
ATGGCATATGCTATC
Left flanking sequence: Indices 10947 -- 11446
CGTCCTCAAGCAAATTGTGATAACTTGTCTCCGTGTGCTTAAACGGTTTCATTTTAAGCTCTAAT
GCCACGCCATATTGACCAAATTTTGTTGATATTCCTTCAGCGCCATTTTTTACTTTTGGATTTCT
TCGTTTGAGTTCGCGATCATCTTAGTGGTTGCAATGTTGACCGCCCCTCCAGCCACAACTGCGGA
GGCTAGTCTGCCCGTACCCGTAGCGGCGGCTGACAATGTTTCCGGGGCAGGGTTAGGCGCTGCGT
TTGCTATCCTACAGCTCCTCATGTTACGTTTGGGTATCCGGTTGCCACTGAAATCCAAAGGATTT
TAAAGGGTGCGGTTGGCATTATTCAAACCGCCTGCGCCCCAAGAATCCTTATAAGTTCTATAAAA
TTTGAGTTGATTCTCATTTAGAATTTTATATCTGAGTCTTATATAGTAAACTGATGCTATATGTA
TGAATAACTTCATTTTGTCCCCCGGATTCAACAAATAAAGACGTA
Right flanking sequence: Indices 11479 -- 11978
AGAAACAAGTATAAATCTCCCGTAATAGTTATCCCGTAACCATTCCTCGAGCCGGAGAGGTAATA
ATACAAGTAGTACTGAAAGAATCTAGTTTTGCAAAAGGACAAAAAAGCGGAATCCGTTTTTACCC
AGTGATCTATTAAATATAAAACCATGCTTGCCGTGACGACCCACGGGCTATAAAATAGGGGTGTT
ATGGGGCCAGTAGATTAGCTTAGGCAATAGAACCAAAATGGGTAACCAGATGAAAAAGTACAAAT
TCATATAGTAAACTACTCTTTTTGGCTTTTGTTTCAAATGAAAATAGAAACTTCCGGCGAGCTCC
CGTGCTTACAATGCTTGAGGGCTTGTCAAACCCCAATCATTCAAGGGCAGCCTTCGGCTGGCTAC
ATGCCTTAGGCCGGCTAGGCCCACAAGCAGCAGGCCGGCAGCCCAAGGGCGAAGCCGAAGGCCCA
GGGCCTCTGCCGAAAGCCCAAGGCCGGGAGGCCTTCAGGGCGGAA
Found at i:21752 original size:14 final size:14
Alignment explanation
Indices: 21733--21762 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21723 GAGGGGCCGG
*
21733 TTAAAAAAAATAGA
1 TTAAAAAAAAGAGA
21747 TTAAAAAAAAGAGA
1 TTAAAAAAAAGAGA
21761 TT
1 TT
21763 TGGCCGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (14 bp):
TTAAAAAAAAGAGA
Left flanking sequence: Indices 21233 -- 21732
ATATTGACGAATCCCACATATTATTAAGAAAATAGTACCTATAATGACATGAAATTGAGATAGGT
AGGCTCTTTCAAGCTTCCCCCCCCTAAGAACCGCACGTGCGAGTTTGCCCGCATGCGGCTCAAGC
AACGAAGAGTTTAGGCCCCCCAAGCGATGGCCCCGCGACTTGACCTCCGGCTGTTGGTGCGCTTT
GCGCCCATGATGCACTATGCTATCACTAAAGTGTTCTGTAACTCTGCGAGTTGCTTATGTCGCAA
CTGCGCGATTGGCCAATATTTACGCGCGCACTGCTTGCAGTTATTCACCTGAATTTCGCGTGGTG
AGTGGCTTTTTTAGTGTTTCGTCACTCAAGATTCAAGTCAGCACCAAAGACAAAATGTAGATTGT
TCCAAACCTGTAGAACCAGCCCTCCGGCCCTCCGGTGGAGAATGTGGCGCCGGGAGGGGGCCTCC
CTACGGGGGGCCGGGAGCCGAAATGGTTGAGAAAGGAGGGGCCGG
Right flanking sequence: Indices 21763 -- 22262
TGGCCGACTTCGCTTGGCTTTTTGAATCGTCTTCTGCCCACTGGACGGTATCCGATCTCACGACC
AAACCTCCCGACGCCGGGGAGCCCATTGGGTTTACCTTGTTGACATTTTGACTCTAATGCAAGGT
TTTAGACCCTGTGCTATACTCCGGTGATTATTTTCCGATCGGGGCACGCACCGATTCATCGTGTC
CCAAATCACATCCGGCCCTACTCAATGAAAACTCGTCGTAGGTGCGGTTTTACGAAACGTCCTTG
CACAGTTCACTTGCGTTGATCAGTAGCCTTGTCACTCCTAGCAGGTTGTATGCTGTATCATAAAC
TTCTTACTTTGTCCCTCACGCTTCAAGCCCTCTCCGTTTCCAGGAGCGCAAGGGGAGGTAGGAGC
ATCCCGTCGGTGGGGATGGCAATATAGTCCGGTGGACTATACGCATTGTCTTATGTCCTTCAAGT
CGCACAACCATGAAACCCTGTAGCTAAAAAAAACGTAGAACCATA
Found at i:40019 original size:27 final size:27
Alignment explanation
Indices: 39989--40044 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
39979 AGTTGATTGA
*
39989 ATATAAGTAATACAGTGTTTTTTTTGC
1 ATATAAGTAATACAGTGCTTTTTTTGC
* *
40016 ATATTAGTAATACCGTGCTTTTTTTGC
1 ATATAAGTAATACAGTGCTTTTTTTGC
40043 AT
1 AT
40045 GAGTGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (27 bp):
ATATAAGTAATACAGTGCTTTTTTTGC
Left flanking sequence: Indices 39489 -- 39988
TTGTGGGTCCGAAGGGCCGAAGGCCAGACATGGCTTGTAGATTTCGTTCTTTGCCTTTACGAAAA
AAGGGTTAAGCCCTGTAAAGCCAAAGAAATCTCCTTCGGACCCTAAAAAAATTTTTTTTACTCTT
GAACCTCAATTTCCCATTTTATGATGACATAGGATTTTATGATGATATTTAAACACGACGTTTTT
TAGGGGGTCGGCATCCATTATGTGGCGTTGGGGTTACATCGCGAATTTTGGTAATAATAAGACCT
CCTAGTTTTAAACCACGTAGCGAAGATTCCTTTCCATAACCTAATCCTTTGATTCTCACTTCAAC
AAACTTAAATCCAAGTTGAATGGCAACTCGCGCGGCATTTTCTGCAGTTGCTTGAGCAGCATAAT
TGGTTGAGCGACGAGATCCCTTAAACCCCACTGAACCTGAGGAGGACCAAGTTTTTGTATTTCCG
TTATAATCTGTTAAAGTAATAATTGTATTACCAAAAGTTGATTGA
Right flanking sequence: Indices 40045 -- 40544
GAGTGTTTATTGAATGTTTTTGGTGTTGTTTGATATCATCGATTTTGTTTTTTTATGATCCATCT
AATCCGTTGACTAATTACAAAGATATTTTGTACAAACTGAAAAAAAAAATAAATTTTTTATCAAC
TTCTAATCGAAACGTATCTTAATTTGCGACAAGTCTTAGCATTAGTATGAGTTCGTTGGCCACGT
AAGGGCAATCCTGCATTATGGCGAAACCCACGATAACAACCAATACTAATTAATCGTTTGATGTC
TCTCTGAATGACTCTCTTCAATTCTGAATCAACTAAAAAATTTTGACTTATTATTTTTAGAATTT
TGTCAAATTGATATTTAGTTAACTTATTAACCTTAATGGTATCGCTGAGGCCTAATTGATCACAA
ACTTGAATTGCCTTTTTAGGGCCAATTCCAAAGATTCGAGTTAAGGCAATTTTTACTTGTTTATT
CGAATTTAAATTAGTTCCTAAAATATATGACATGATTTATTTTTT
Found at i:45707 original size:27 final size:27
Alignment explanation
Indices: 45653--45708 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
45643 TCTTGATTGT
* **
45653 AGGTGCGTAGCACGAGACCAGAGGGAG
1 AGGTGCATAGCACGAGACCAGAAAGAG
**
45680 AGGTGCATAGCACTCGACCAGAAAGAG
1 AGGTGCATAGCACGAGACCAGAAAGAG
45707 AG
1 AG
45709 CGTTCGGAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.38, T:0.09
Consensus pattern (27 bp):
AGGTGCATAGCACGAGACCAGAAAGAG
Left flanking sequence: Indices 45153 -- 45652
ACCTTTCGTTCCTCGGGTTGTACGATGAACCGCTTTAAGTAATTCTGTTTTGTATTCATACATGG
CCAGAGTAGCTTTGGCCTCGGCAGCTCTTGCTTTCGCCTCATTACTAGCTGCAATAAATTTTGCT
TGCTCAGTGACCGAGCGCCCGATTTGTCGGATTCCTCCCCAATTCCCAAGGGATTCCCGGTCGGC
GGCACCGCTTTACCTAAGATATAAGTGACCCCCGTGAACATAGCAAGGTCTGCTCCTACTATCAG
GGTCGATGTCGAACCCTGCAATATAAAATCATATTAATCTATAGAAGAAAGGGCCCGGACTCTGT
TTTGTCGGACACCACAAAACCAAAATACTGTCCGCCCCGCGACTGTCTGACAGAATACGAGCCGA
CACAAGGGGCCGTCGGAACAATAAAACGCAGTAATAAACTAAGTAAAGGCGCGAAACGCCATTAA
ACATATACATAAGGATGATCGGAACATAAAAAACATCTTGATTGT
Right flanking sequence: Indices 45709 -- 46208
CGTTCGGAATGCCACTTTTGTCTTGAGGGCGGACTTCTTTAATAGAGCTAAATAACGTAACGAAG
GTTACAAGCTAATTTTTACTTTTTGCCATATTTATTTCTTTTTTTTATGACCACTTAAAAAACTT
TATCGACAACCCCAGTTTATGCGCGGCTAATGTAGCAGCTTGTTGAGCATTTGACAAACTAACAC
AATCAATTTCAAATAAGATTTGTCCCTTCAACACACGAGCAATCCAACCTTTAGTATTTCCCTTG
CCCTTTCCCATTCGCACTTCAGCCGGTTTACTGGTAATAGGAATATCTGCGAAAACTCTTACCCA
TATTTTAGAATTTCTTCGAAATTTTCTGCTTATAGCACGACGCGCTGCTTCAATTGCTTGATATG
AAATACGGCCAGCTTCACAACTTTTAATGCCATATTTTCCAAAACAAAGTTGTGTACTGTCTGCT
TTGCAACCTTTACATCTGCCTTTTTGATATTTACGAAATTTTGTA
Found at i:59445 original size:32 final size:32
Alignment explanation
Indices: 59409--59472 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
59399 CTTGTTCCAT
59409 GTGTAAAATGGCAAGTTAAGTGTTACGGGTGA
1 GTGTAAAATGGCAAGTTAAGTGTTACGGGTGA
59441 GTGTAAAATGGCAAGTTAAGTGTTACGGGTGA
1 GTGTAAAATGGCAAGTTAAGTGTTACGGGTGA
59473 ACCCGCAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.06, G:0.34, T:0.28
Consensus pattern (32 bp):
GTGTAAAATGGCAAGTTAAGTGTTACGGGTGA
Left flanking sequence: Indices 58909 -- 59408
TTATCCGGCCCGCGCTGAACTTTGTGGGTCTGGAAAGTGCTTACGCACCTTCGGACCCTTCGTAC
CCCCAAAATGCGTAGCACCTCTCCCTACAGTCTCGCGTCCCTTGGACCATGGGGTTCGGGTTGAG
CCCCGCCCCCCGAAGCCAAATTAAGGTGCGAAGCATAACGAGATCTCCCGCAGGTTTTAGAAAGT
TGCATTCTTACAAGTATTTATTCTATTTTTTTCCAGTAGATTGTGGAGACGATCGGATTTGAACC
GACAGCTTTATGCTTGCAAAACATACGCTCTACCAATTGAGCTACGTCCCCTACGGAGGAAATGG
GATTTGAACCCATGATACAATATTGTTGTATTTGTCGGGATAGGTAGGCCCTCTCAAGCTTTCCC
CCCTAAGAACCGTACGTGCGAGTTTTCCCGCATACGGCTCAAGCAACCTGTCCAAAATGTAAACC
CGCAAGAGTCATGTTTAAATCATTGGCTACTAGAACTTGTTCCAT
Right flanking sequence: Indices 59473 -- 59972
ACCCGCAGCTCTAAGCCCCGTTCCTTGTTTTGTCGGACAGTCTTTTGGTTTTGTGGTGTCCTCGG
GTCCTTGTGCCAATAAAAAAAAATGAATTTTATATCCTTTTTATCAAAGTCTCAAGATAGTACAA
GTCACCCATGCTCAAGTCTGCCACCTTTCGGTGTAGATCACAAGATCCTATCCCATCAATTACAG
ACGGGCTTTTGCTTTTTGAGCTGTCCTTTACCCGCATTGCGTTACTCTGCATTACCACAGAGCCT
CCCGAAAGGAGCGATACGGGTTTACCAAGTTCCGCGCAATGTACCATTTCTCTCAATAGGAAGAA
CCTAAAAAAACCCCGATGGAAATCTGAACCCACGGTGATATCAAAATCAGAAATACCACCCCTTC
CACGGCAGGCTTCCTGCTCGGGATACCTACCATTCCAATTTTGAACCTACGATATTCCATCCAGA
AGATCTTTTGGTTCCGCCTTGGATTGTTTTTTACGAGGTCTCTGT
Found at i:61782 original size:60 final size:59
Alignment explanation
Indices: 61598--61842 Score: 283
Period size: 60 Copynumber: 4.3 Consensus size: 59
61588 AATGGTTAAA
*
61598 ATATACTATATGTCAGGGTGAATATTCATAAAAGCACTGG-T----TA-ACTATATGTAC
1 ATATACTATATTTCAGGGTGAATATTCATAAAAGCA-TGGTTAAAATATACTATATGTAC
* **
61652 ATATACTATATTTCAGGCTGAATATTCGCAAAA--ATGGTTAAAATATACTATATGTAC
1 ATATACTATATTTCAGGGTGAATATTCATAAAAGCATGGTTAAAATATACTATATGTAC
61709 ATATACTATATTTCAGGGTGAATATTCATAAAAGCACTGGTTAAAATATACTATATGTAC
1 ATATACTATATTTCAGGGTGAATATTCATAAAAGCA-TGGTTAAAATATACTATATGTAC
* * * * * * * *
61769 TTATACTAGATTTCAGGGCGAATATTCA-GAGACCTATGGTTAAGATCTACTATATGTAC
1 ATATACTATATTTCAGGGTGAATATTCATAAAAGC-ATGGTTAAAATATACTATATGTAC
*
61828 ATATACTAGATTTCA
1 ATATACTATATTTCA
61843 TGGGGGGTAT
Statistics
Matches: 165, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
51 3 0.02
52 2 0.01
54 29 0.18
56 2 0.01
57 41 0.25
59 39 0.24
60 49 0.30
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (59 bp):
ATATACTATATTTCAGGGTGAATATTCATAAAAGCATGGTTAAAATATACTATATGTAC
Left flanking sequence: Indices 61098 -- 61597
CAGTGACGGAAAGGCCTCCGCCAGAGTCTCAAGTTGAACCTGCATTGGGTAAAATGAAATTAGAA
AGCAGAATAGTGAAAGCTTTTTTTCTGGCACCCAAAGTCATAGCATACATAACTGCGGGGATTTG
TACTATAATAAAGCATAAAGGGCCCTTTAAAGTAAATTGGGATTGGTTCGAATTGCAGAATAAAA
ATACAAGCCGCGCGACAGAAGTCATAAAACTCGGAAATTTTAGAATCAATTGGAGCAAGCTCCGT
GTCTTCTCAAGTGAAATACACCTTTCATTAGGTGCATTTGAGCGGAAAAGATAAAAAGTATACGC
ATCGGACAGAACGTGGGAGGGGACTCGCCCCATACGAGTAACAAAAGGGGAAATGCCAGAACCAA
ATTCCGAGTTAACTGCAACTCTGTTTAATTTAAAAGACTAGAAAACTAGTAATAAAAAGCAACCA
TAAGGCCCAGGCTATTTCATGCTGAATATTCACAAAATGGTTAAA
Right flanking sequence: Indices 61843 -- 62342
TGGGGGGTATTCATATGGTTAAAATAGACTCTATGTACTGATACATATACTAGATATCATTCGAT
CCAATAAAGAGATAAACCTACTTTAATAGATCTTCACGTAGGTAAGGAGCAAACAAAGGGTACCC
TTTAGGAGTTTTCGTGTAGGATATATGTAGGAAGTGTAGGATATAGGGGTACGCACCTAGGTAAC
CTTTTGGGAGTGAGATGTATGATATGTATGATATGTATGATAAATGAAAAAAAAGTAATATTGTA
TACTTAAAGGTTATACTTTATTGTAGGCAATTGCTTATGTGTATTTATGCTCGAAGATTAATAAG
GTGCGTCCCTGGCTTCTAAAGGGCGCACCCCCCCACCCCGTCATATTACTATAATTTAAAGGAAA
GAGAAGATACTTCTTTAGAATAGGCCATCTTAATTTGACGTTTTGGGAGTTAAACTGAATAGGAG
CAGGACTAGTCTTTCTCCTTGAGGGCAACCATCCAGAAAATTAAG
Found at i:61857 original size:119 final size:111
Alignment explanation
Indices: 61598--61842 Score: 305
Period size: 111 Copynumber: 2.1 Consensus size: 111
61588 AATGGTTAAA
* * *
61598 ATATACTATATGTCAGGGTGAATATTCATAAAAGCACTGGTTAACTATATGTACATATACTATAT
1 ATATACTAGATTTCAGGGTGAATATTCATAAAAGCACTGGTTAACTATATGTACATATACTAGAT
61663 TTCAGGCTGAATATTCGCAAAAATGGTTAAAATATACTATATGTAC
66 TTCAGGCTGAATATTCGCAAAAATGGTTAAAATATACTATATGTAC
* *
61709 ATATACTATATTTCAGGGTGAATATTCATAAAAGCACTGGTTAAAATATACTATATGTACTTATA
1 ATATACTAGATTTCAGGGTGAATATTCATAAAAGCACTGG-T----TA-ACTATATGTACATATA
** * *
61774 CTAGATTTCAGGGC-GAATATTCAG-AGACCTATGGTTAAGATCTACTATATGTAC
60 CTAGATTTCA-GGCTGAATATTC-GCA-A-AAATGGTTAAAATATACTATATGTAC
61828 ATATACTAGATTTCA
1 ATATACTAGATTTCA
61843 TGGGGGGTAT
Statistics
Matches: 116, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
111 39 0.34
112 1 0.01
116 2 0.02
117 33 0.28
118 5 0.04
119 36 0.31
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (111 bp):
ATATACTAGATTTCAGGGTGAATATTCATAAAAGCACTGGTTAACTATATGTACATATACTAGAT
TTCAGGCTGAATATTCGCAAAAATGGTTAAAATATACTATATGTAC
Left flanking sequence: Indices 61098 -- 61597
CAGTGACGGAAAGGCCTCCGCCAGAGTCTCAAGTTGAACCTGCATTGGGTAAAATGAAATTAGAA
AGCAGAATAGTGAAAGCTTTTTTTCTGGCACCCAAAGTCATAGCATACATAACTGCGGGGATTTG
TACTATAATAAAGCATAAAGGGCCCTTTAAAGTAAATTGGGATTGGTTCGAATTGCAGAATAAAA
ATACAAGCCGCGCGACAGAAGTCATAAAACTCGGAAATTTTAGAATCAATTGGAGCAAGCTCCGT
GTCTTCTCAAGTGAAATACACCTTTCATTAGGTGCATTTGAGCGGAAAAGATAAAAAGTATACGC
ATCGGACAGAACGTGGGAGGGGACTCGCCCCATACGAGTAACAAAAGGGGAAATGCCAGAACCAA
ATTCCGAGTTAACTGCAACTCTGTTTAATTTAAAAGACTAGAAAACTAGTAATAAAAAGCAACCA
TAAGGCCCAGGCTATTTCATGCTGAATATTCACAAAATGGTTAAA
Right flanking sequence: Indices 61843 -- 62342
TGGGGGGTATTCATATGGTTAAAATAGACTCTATGTACTGATACATATACTAGATATCATTCGAT
CCAATAAAGAGATAAACCTACTTTAATAGATCTTCACGTAGGTAAGGAGCAAACAAAGGGTACCC
TTTAGGAGTTTTCGTGTAGGATATATGTAGGAAGTGTAGGATATAGGGGTACGCACCTAGGTAAC
CTTTTGGGAGTGAGATGTATGATATGTATGATATGTATGATAAATGAAAAAAAAGTAATATTGTA
TACTTAAAGGTTATACTTTATTGTAGGCAATTGCTTATGTGTATTTATGCTCGAAGATTAATAAG
GTGCGTCCCTGGCTTCTAAAGGGCGCACCCCCCCACCCCGTCATATTACTATAATTTAAAGGAAA
GAGAAGATACTTCTTTAGAATAGGCCATCTTAATTTGACGTTTTGGGAGTTAAACTGAATAGGAG
CAGGACTAGTCTTTCTCCTTGAGGGCAACCATCCAGAAAATTAAG
Found at i:62066 original size:9 final size:9
Alignment explanation
Indices: 62052--62079 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
62042 TGGGAGTGAG
62052 ATGTATGAT
1 ATGTATGAT
62061 ATGTATGAT
1 ATGTATGAT
62070 ATGTATGAT
1 ATGTATGAT
62079 A
1 A
62080 AATGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (9 bp):
ATGTATGAT
Left flanking sequence: Indices 61552 -- 62051
ATAAGGCCCAGGCTATTTCATGCTGAATATTCACAAAATGGTTAAAATATACTATATGTCAGGGT
GAATATTCATAAAAGCACTGGTTAACTATATGTACATATACTATATTTCAGGCTGAATATTCGCA
AAAATGGTTAAAATATACTATATGTACATATACTATATTTCAGGGTGAATATTCATAAAAGCACT
GGTTAAAATATACTATATGTACTTATACTAGATTTCAGGGCGAATATTCAGAGACCTATGGTTAA
GATCTACTATATGTACATATACTAGATTTCATGGGGGGTATTCATATGGTTAAAATAGACTCTAT
GTACTGATACATATACTAGATATCATTCGATCCAATAAAGAGATAAACCTACTTTAATAGATCTT
CACGTAGGTAAGGAGCAAACAAAGGGTACCCTTTAGGAGTTTTCGTGTAGGATATATGTAGGAAG
TGTAGGATATAGGGGTACGCACCTAGGTAACCTTTTGGGAGTGAG
Right flanking sequence: Indices 62080 -- 62579
AATGAAAAAAAAGTAATATTGTATACTTAAAGGTTATACTTTATTGTAGGCAATTGCTTATGTGT
ATTTATGCTCGAAGATTAATAAGGTGCGTCCCTGGCTTCTAAAGGGCGCACCCCCCCACCCCGTC
ATATTACTATAATTTAAAGGAAAGAGAAGATACTTCTTTAGAATAGGCCATCTTAATTTGACGTT
TTGGGAGTTAAACTGAATAGGAGCAGGACTAGTCTTTCTCCTTGAGGGCAACCATCCAGAAAATT
AAGGAAACTATGAAATTAGATCCGGAACAACTAATAAATAAAGGATCCCTTACAGTACAGGGATC
TATTCACGGAGAGTGACAGACTAAAAACACCGTGGGAGGTAACGGAGGTATTTAAGAGGAAGACC
TTCTTACATGATTCGAGATCGTTTCCCAAGATGAATCTCATATACATATATGACCCAGATCAGGG
CATCTATAGAGAGTATACAGAAAACGAGCTTATCTTAATTATAAC
Found at i:90763 original size:62 final size:60
Alignment explanation
Indices: 90692--90873 Score: 237
Period size: 58 Copynumber: 3.0 Consensus size: 60
90682 TTCAGTTTCG
* * *
90692 TATACATATA-AATAATTGAAAATAGCCTATATC-TATACAGAAACTTCAGTTTCGTATATA
1 TATATATATATAATAATT-CAAATAGCATATA-CATATACAGAAACTTCAGTTTCGTATATA
* * *
90752 TATATATATAT-A-ACTTCAAATAGAATATACATATACAGTAACTTCAGTTTCGTATATA
1 TATATATATATAATAATTCAAATAGCATATACATATACAGAAACTTCAGTTTCGTATATA
*
90810 TATATATATATATATAACTTCAAATAGCATATACATATACAGAAACTTCAGTTTCGTTTATA
1 TATATATATATA-ATAA-TTCAAATAGCATATACATATACAGAAACTTCAGTTTCGTATATA
90872 TA
1 TA
90874 ATCGCTTTTC
Statistics
Matches: 106, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
57 1 0.01
58 47 0.44
59 3 0.03
60 11 0.10
61 1 0.01
62 43 0.41
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (60 bp):
TATATATATATAATAATTCAAATAGCATATACATATACAGAAACTTCAGTTTCGTATATA
Left flanking sequence: Indices 90192 -- 90691
TATATATTATTCATTGTGCACTTTACGCATTCTACAGGATTTGAACCTGTGACCTTCAACTTAGA
AGGTTGTTGCTCTATCCAACTGAGCTAAGAATGCAGTACATTACTAACCACTTCGCAAAAAAAGA
GTGAATTCCGGAGAAGCTTGCTTCTGCCCTCTCTCCCGCTTTATTCGCATCGCGAATGAAGGCTG
AAAGAGAAAGGGTCGAATAGAATAAAACGAACAAAAAATCTATATATTTTTTTTTGCTTTGCGTT
TTCTTGGGTTTGATCAAGTTCAACACACGACGAAATATAATGCATTTTGTATTAAAAACAATTCT
GGAGGAAATTATAATTCGTGTTTTTTGTATATTGATTTGCTTTAGTTTTACATAGTTTACGTGTT
ATTGGTTCTCAGAAGCCTAAGACGGCCCCGGGGCGTGGCGCAGAGTGCGGCATAACGCATAGCAT
ATAGGACTTGTGATATCATATAGAATACACGAAACTTCAGTTTCG
Right flanking sequence: Indices 90874 -- 91373
ATCGCTTTTCACATTCGTTGTCGAGGTGCAAATTGAAAGAATTTATGGAAAGAAGCCGCTGAAGT
TACTATCTAGTTGCAGCAGTCAAAGGCTTTTATGCGCTAATCCGCGTTTATTATACCTATGTGAT
TACCCTAAAATTTTGTTTAAAAGTTATGCATTTTTTCGGAGTGCCCAATTTAGGCCGTGTATTGT
ACACGTTTATGTTTTTATTTTCGTACGCGGAACGACAGCGCGTACTGGACTTTTCTGAGCCTTTC
ATTTATTTATAAATAGTCTGCGCAGTTTGCAGTTGATACGTTCTAGGCTTAATTATAGCCTTTGC
GGTTCTTTTGAGGTTTTCAATGATAAAGCAATTTGTAGAACACTTTGTAGATCGGGGTTATGTGA
CAGCTCACATCGGCGATCATCGAGCAGCCGCGAATGTCGTGCTGCCGGCTTTAAGTGTTGTATTA
TTTGATAGAGGACTCGGGCAGGCCATCAAGAACAAGATGAATGCA
Found at i:90789 original size:58 final size:58
Alignment explanation
Indices: 90663--90873 Score: 247
Period size: 62 Copynumber: 3.6 Consensus size: 58
90653 CTTGTGATAT
* * *
90663 CATATAGA-ATACACGAAACTTCAGTTTCG--TATACATATA-A-ATAA-TTGAAAATAG
1 CATATACATATACA-GAAACTTCAGTTTCGTATATATATATATATATAACTT-CAAATAG
*
90717 CCTATATC-TATACAGAAACTTCAGTTTCGTATATATATATATATATAACTTCAAATAG
1 CATATA-CATATACAGAAACTTCAGTTTCGTATATATATATATATATAACTTCAAATAG
* *
90775 AATATACATATACAGTAACTTCAGTTTCGTATATATATATATATATATATAACTTCAAATAG
1 CATATACATATACAGAAACTTCAGTTTCG----TATATATATATATATATAACTTCAAATAG
*
90837 CATATACATATACAGAAACTTCAGTTTCGTTTATATA
1 CATATACATATACAGAAACTTCAGTTTCGTATATATA
90874 ATCGCTTTTC
Statistics
Matches: 135, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
54 20 0.15
55 5 0.04
56 9 0.07
57 2 0.01
58 41 0.30
59 2 0.01
62 56 0.41
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (58 bp):
CATATACATATACAGAAACTTCAGTTTCGTATATATATATATATATAACTTCAAATAG
Left flanking sequence: Indices 90163 -- 90662
AATTAAACAAGTAGAAGGATTACCGTTGGTATATATTATTCATTGTGCACTTTACGCATTCTACA
GGATTTGAACCTGTGACCTTCAACTTAGAAGGTTGTTGCTCTATCCAACTGAGCTAAGAATGCAG
TACATTACTAACCACTTCGCAAAAAAAGAGTGAATTCCGGAGAAGCTTGCTTCTGCCCTCTCTCC
CGCTTTATTCGCATCGCGAATGAAGGCTGAAAGAGAAAGGGTCGAATAGAATAAAACGAACAAAA
AATCTATATATTTTTTTTTGCTTTGCGTTTTCTTGGGTTTGATCAAGTTCAACACACGACGAAAT
ATAATGCATTTTGTATTAAAAACAATTCTGGAGGAAATTATAATTCGTGTTTTTTGTATATTGAT
TTGCTTTAGTTTTACATAGTTTACGTGTTATTGGTTCTCAGAAGCCTAAGACGGCCCCGGGGCGT
GGCGCAGAGTGCGGCATAACGCATAGCATATAGGACTTGTGATAT
Right flanking sequence: Indices 90874 -- 91373
ATCGCTTTTCACATTCGTTGTCGAGGTGCAAATTGAAAGAATTTATGGAAAGAAGCCGCTGAAGT
TACTATCTAGTTGCAGCAGTCAAAGGCTTTTATGCGCTAATCCGCGTTTATTATACCTATGTGAT
TACCCTAAAATTTTGTTTAAAAGTTATGCATTTTTTCGGAGTGCCCAATTTAGGCCGTGTATTGT
ACACGTTTATGTTTTTATTTTCGTACGCGGAACGACAGCGCGTACTGGACTTTTCTGAGCCTTTC
ATTTATTTATAAATAGTCTGCGCAGTTTGCAGTTGATACGTTCTAGGCTTAATTATAGCCTTTGC
GGTTCTTTTGAGGTTTTCAATGATAAAGCAATTTGTAGAACACTTTGTAGATCGGGGTTATGTGA
CAGCTCACATCGGCGATCATCGAGCAGCCGCGAATGTCGTGCTGCCGGCTTTAAGTGTTGTATTA
TTTGATAGAGGACTCGGGCAGGCCATCAAGAACAAGATGAATGCA
Found at i:99129 original size:14 final size:15
Alignment explanation
Indices: 99099--99130 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
99089 GTTTTTGCCC
*
99099 TTTTTTTTTCTGTTT
1 TTTTTTTTTCAGTTT
99114 TTTTTTTTTCAGTTT
1 TTTTTTTTTCAGTTT
99129 TT
1 TT
99131 GGATAATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.84
Consensus pattern (15 bp):
TTTTTTTTTCAGTTT
Left flanking sequence: Indices 98599 -- 99098
TATCATATATTCTTTTTTATAACTTTTGACGCTATAAAAGCCAACAAGAATACAAATAGGAGTTA
AAAACGTGGTCAAGATCACAAAGAATAAAGAGATACCATCTATACCTATATAAAAATTTATATTT
GAATACGGAAGCCATCGAATAGTTTCCACAAACTGAAATTTTGCTGTATCATTCTCAAAGCGTAT
CCAAAAAAAAAGAGAATATAAAAAAGTGATCAAAGAGGTCCAAATTGTGATACCTCGTATCAGAC
GTACTCTTGAATTCGGGATCACCAAAATAATAAGGCTTCCTAGCAAAGGAAGCAAAATAAGACCA
CTTAAATTGGAATAAAATGGAGCTAAAACTTGGAACATATACGTTTACTCTTTTTCCTAGAAATC
CCGAAAAAAAATATATATATTTTTGCTGCGAAAAATATATATGCTGCGAAAAGGCCCGTAGCGCA
GCGCTACGGGCCGGAGGCCTGCGCTTGTTAGGCAAGTTTTTGCCC
Right flanking sequence: Indices 99131 -- 99630
GGATAATAGATAGTTATTCACAATGAAATCAGGATGCGCTAATTATTATAAAAAATGACAGTACA
ATAATAGCCTAAAGCAAAGAATTAGCATTTGATACTAAAAATCTGTTGACCCGATCTGTTTTTGG
CGAATTAAGTTTATTATTTTCATCGGGCGACCGGTCTAGATCCCGCACGATAAAAAGCACAAGTC
CATTTCTGTGCAAAGGCGTTGCACTCATTCTTGTTCGGCAACGAACACGGAGACCTTAGCATGTG
CAAGAAGCTCTGTTGAGGGGGTTTCATTTACCCTCCCCCCCCCGGGGGGGGGGTCACCCAAAAGT
ATGGAGCAAGCCGGTTTTCTTGTATTTAAGATGAGGTTCTGTACTGGCGAATCGGAGACTCTTTC
GGTCCTTGTCAACCAGCAATTAACCATTGGCACCTGAGCTCTGCAAATGGTGAAGCGCATGAACG
TACGTTGCTCGCTCCATGCCTATTGATGGTATATATCAACCAGGT
Found at i:119589 original size:21 final size:22
Alignment explanation
Indices: 119557--119599 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
119547 TTAAAGTAAG
119557 AAAAACCACTAC-AAAGAAACA
1 AAAAACCACTACTAAAGAAACA
*
119578 AAAAATCC-CTACTACAGAAACA
1 AAAAA-CCACTACTAAAGAAACA
119600 TATGAGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.60, C:0.26, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAAACCACTACTAAAGAAACA
Left flanking sequence: Indices 119057 -- 119556
TAAATATCCCTTCAGCTTTCCTTGTCTTAGTAACTGAAAACTCTTCATCTTTGAAAACTCGGGGA
AACCGTCCCAAAGGCGCGTAGCGGAAGGAAAGGAAGGTCTACGGGCATAGATTGTAAAAAGATAT
GATAGATACATAAAATATGACATTGTCATCAAATATACAAATACAACTCAAAGGAGTACCAAATA
CAGGAAGGGGGTAGGCGGGGGAGGCTGGCGCCTACCCCGAAAAAGAGGGCCTGGCTCGGTCAAGT
CCCTAACTACAACTTTCGGGGCGGGCTCCGCCCTATAAGGACTAGGTCTGTATAGGGCGGAGCGG
GTCAGTGCTTAAGTTGCACAAATTGCTAAGACGTCTAAATGCTTTCCTTGATAGCTGGAAGTTCT
TCAAAAGTATGAAATGCCGGAGGGCTTGGGACCATCCATTCAAGTGTCGTTGAATTCTGTTCAAC
AGCCCAAGGACTTGGAGCACACTTGTTTTCACTAGTTAAAGTAAG
Right flanking sequence: Indices 119600 -- 120099
TATGAGCCAAAACTACTAAAGGCATTCCATCCAGCGTAAGCATCTGGATAATCAGGAATGCGACG
TGGCATACCTGCAAGCGGTTTTTTCCTTATTTATCAAATGTTAATGGATTGTGACTAAATATTTT
TCCTTTGTAAACTTCATCTGAAATTAGTCTTTTAGACTTTTCAGTGTGTTTAAATCCCAATGTTG
AATTAGTTCTTTTATTGATATTAAGAACTGGTTTATAAAGATTTAAATAGTACTGTTCTCGAGCT
AAATAATCCTTTTTAGTCATAGTACCTGTTGAACCACATAACTCAATAATAACTAAACTAAAATT
GTCATGACCATATTTCCAAATAGAATTATAAATATATCTGTTATCAGATAATTTAGGAGGGTGAT
AGTATTCAGCAAGTCTATCGCTTTATTTATAACCACTACCTACATATTGTTTACCATTAACTAAA
TTATGCCAAAGATAGATTCCAGTTTCCGTTAGATAATCAGAAACG
Found at i:124128 original size:16 final size:16
Alignment explanation
Indices: 124107--124141 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
124097 GTAATTGCCC
*
124107 TTTTTTGTCTGTTTTT
1 TTTTTTGTCAGTTTTT
*
124123 TTTTTTTTCAGTTTTT
1 TTTTTTGTCAGTTTTT
124139 TTT
1 TTT
124142 CCCTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.06, G:0.09, T:0.83
Consensus pattern (16 bp):
TTTTTTGTCAGTTTTT
Left flanking sequence: Indices 123607 -- 124106
TTACTTCACAGCTTATATATCCAGCCTTTTCAATGGAAAAACCTCCATCCCAGCTAACCCATTTT
TAAATTGATCCTCATCATTTCTTGTTTCAATAGGAGATGCGCTGCGTGTAGTCTCTGAGGATCCT
TCACCTGTTTGTAAAGTCAAAATATTTCTTTCATTCATTTACATTTTTTTTTTGAAGTTTCCTGC
TGATTGTGCATTGCCTATAGAACTGAAGATCTAATTCAGATCTATACATAAGCTTTTCACAGGTT
CGGGCGTAAAAAAATATATTTTTTCGCGCACTTATGAACCGAGTACTTAATGGCATTTAGCCTTT
CCAGCAAATAGCGGCATTATTCAATTTGAGATTGCTCTCAAATGCGGCCATCCTGTGGTTATTTT
TTGACCGAAGAACCAAAAAAGATGCTGGTATAAAATGGGATCCCCGCCACCAGCAGGATCAAAAA
AGGTTGTATTAAAGTTTCTATCAGTTAATAACATGGTAATTGCCC
Right flanking sequence: Indices 124142 -- 124641
CCCTTTTTTTTCTGACAGTCCTGGGGCCTTGTCGGACAGTATTTTGGTTTTGTGGTGTCCGACAA
GACAAAGTCCGGGCCCTGTCTGACAAGAAAAAAAAAAGTGCTTACACCGGAAACTAATAGATTTT
TTTCATGCCCGGCGTGGTTTTGGACTATATCTTCATCTCTTTCTATTCATACCTGCTTTGATGCG
CACAATTTCAGCAAACCCCGCATTGGTCAGATGTGCTTTGTGTAAGATCATGTCATAGATGCATC
GCCAGTCACGCCAATCCGCGGCTTTTGCCCGAAGAAAGGCATCAAAGTAAGCAACCACATGGGCA
TGCCTGCCATGCTGCATGTGCGACTACGCCAATTTACTCTAGAAGCACTAACCTTGGAAAGTATA
ACTTGTGCCCCAATTTGCTCAAGCGTCGGTCTAGTATCTATTTTCGTTTGTTTCTGCAGCTTACT
CTATTCTAGCTCAAACGAAATGTAAACGCGCCGATATCTACTGGA
Found at i:137238 original size:24 final size:24
Alignment explanation
Indices: 137184--137238 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
137174 TTGTTTATCG
*
137184 CCTT-TTATTTATCTATGATGATT
1 CCTTATTATTTATCTATGATAATT
* * * *
137207 CATCATTATTTCTTTATGATAATT
1 CCTTATTATTTATCTATGATAATT
137231 CCTTATTA
1 CCTTATTA
137239 ATGAGGATTC
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (24 bp):
CCTTATTATTTATCTATGATAATT
Left flanking sequence: Indices 136684 -- 137183
ACAAAACTTAAAGCTACAATAACTTCTTCATTATATATTAAGATTTTTTTTGAACTTAAAACGCT
AAAGCTTAAAATTGCAAATATTAATACTTCACGCATTTGTATTTTTCCTTTTTTTTATTGCAATA
AGGATTTAATTATAATAAATCATGATAAAAAATGTGTCACCACGAAACTCCAATAAAGGAGTTTA
ATGGATGATAAATCAGAACTTATCAATATATATCGTCCTACAGCTTTGTGTACCTGACCCATTAT
CATTTGCATGCCCGAGAGGGGAGACACAATCAAAACCTTTGTTTTGTCGGACAGTTTTTTGGTTT
TGTGGGTGGGTTGTTCATTTTTTGCTTTTTTTTTTTCTCCCCCGTTTTATCACCTTTTTTTGTTT
GGCGGGAGTCGGATTCGAACCCACAACATTCAGATTATGAGCCTGACGAGTTACCAATTACTCTA
TCCCGCGAACAGCCAACAAAAAAAGAAATATATTTTTGTTTATCG
Right flanking sequence: Indices 137239 -- 137738
ATGAGGATTCATCATTATTTATCTACGATAATTCATAATGAGGATTCATCATTATTTATCTACGA
TAATTCATCCAGATTTTCTATTAGAAATTTTTCTAGATTTAACCCAGATTTGTCTAGGTTCAAAG
GGAAAAAGGGGGCGCGCTGCAGCCCGCGCCAGCCCACTGAGTTGAAGTGACGGATCAAAATTTGG
TGTTTACCCAACCAAAGCAATTGACTAGAGACAAAACCACGGTGGCTTCCCCGCCCACAGGCTAT
AGGGATGTTATGGAGGCACGTAGATTACCTTAGGCAACAGTCCCGCAATCGGTAACATAATTCAA
AAGTACACAGGCACTACGTGCTTCTTTGGCTTTACCGGGACATCCTTTTTTTGAGTTTTTTGCCG
GAGCGAAATAACCAATTTTATGGAATACAGGAAGCGAGAAGGAGGCTGCAGGGTAGTTTATAGAA
GGGATTGAGCTACGGGGTTTATAGAAATATGGGGCATTCCCTCGT
Found at i:137278 original size:37 final size:37
Alignment explanation
Indices: 137198--137311 Score: 156
Period size: 37 Copynumber: 3.0 Consensus size: 37
137188 TTATTTATCT
* * * *
137198 ATGATGATTCATCATTATTTCTTTATGATAATTCCTTATTA
1 ATGAGGATTCATCATTATTTATCTACGATAATT-C--A-TA
137239 ATGAGGATTCATCATTATTTATCTACGATAATTCATA
1 ATGAGGATTCATCATTATTTATCTACGATAATTCATA
137276 ATGAGGATTCATCATTATTTATCTACGATAATTCAT
1 ATGAGGATTCATCATTATTTATCTACGATAATTCAT
137312 CCAGATTTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
37 38 0.55
38 1 0.01
40 1 0.01
41 29 0.42
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (37 bp):
ATGAGGATTCATCATTATTTATCTACGATAATTCATA
Left flanking sequence: Indices 136698 -- 137197
TACAATAACTTCTTCATTATATATTAAGATTTTTTTTGAACTTAAAACGCTAAAGCTTAAAATTG
CAAATATTAATACTTCACGCATTTGTATTTTTCCTTTTTTTTATTGCAATAAGGATTTAATTATA
ATAAATCATGATAAAAAATGTGTCACCACGAAACTCCAATAAAGGAGTTTAATGGATGATAAATC
AGAACTTATCAATATATATCGTCCTACAGCTTTGTGTACCTGACCCATTATCATTTGCATGCCCG
AGAGGGGAGACACAATCAAAACCTTTGTTTTGTCGGACAGTTTTTTGGTTTTGTGGGTGGGTTGT
TCATTTTTTGCTTTTTTTTTTTCTCCCCCGTTTTATCACCTTTTTTTGTTTGGCGGGAGTCGGAT
TCGAACCCACAACATTCAGATTATGAGCCTGACGAGTTACCAATTACTCTATCCCGCGAACAGCC
AACAAAAAAAGAAATATATTTTTGTTTATCGCCTTTTATTTATCT
Right flanking sequence: Indices 137312 -- 137811
CCAGATTTTCTATTAGAAATTTTTCTAGATTTAACCCAGATTTGTCTAGGTTCAAAGGGAAAAAG
GGGGCGCGCTGCAGCCCGCGCCAGCCCACTGAGTTGAAGTGACGGATCAAAATTTGGTGTTTACC
CAACCAAAGCAATTGACTAGAGACAAAACCACGGTGGCTTCCCCGCCCACAGGCTATAGGGATGT
TATGGAGGCACGTAGATTACCTTAGGCAACAGTCCCGCAATCGGTAACATAATTCAAAAGTACAC
AGGCACTACGTGCTTCTTTGGCTTTACCGGGACATCCTTTTTTTGAGTTTTTTGCCGGAGCGAAA
TAACCAATTTTATGGAATACAGGAAGCGAGAAGGAGGCTGCAGGGTAGTTTATAGAAGGGATTGA
GCTACGGGGTTTATAGAAATATGGGGCATTCCCTCGTTCAGAAGGGGAGTCTGTGACCCCTAAAC
CAGCTTGCCGAGAAGACCTTAAACAAAGATACATTGAGTTGCTGT
Found at i:143634 original size:10 final size:10
Alignment explanation
Indices: 143607--143647 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
143597 AAAGGCCTTG
143607 TCAGTTTTTT
1 TCAGTTTTTT
**
143617 TCTTTTTTTT
1 TCAGTTTTTT
*
143627 TCAGTTTTTG
1 TCAGTTTTTT
143637 TCAGTTTTTT
1 TCAGTTTTTT
143647 T
1 T
143648 GCCTTTTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.07, C:0.10, G:0.10, T:0.73
Consensus pattern (10 bp):
TCAGTTTTTT
Left flanking sequence: Indices 143107 -- 143606
TTTTGGTCGTATATATATATTTTTTTTTGATCAAGTGCGTTGTCCGGGCGTGGACCATGTCTCCC
GAAATTGATGAATCAGTACATATGGTCTAAGACGATTTCACATATCGAGGTCGAAATGGGATCGG
GTGTTTTCACATCTTACCATAGTGCCCGGCTCTCCAAATTTTTCTTTTTATTTTTTCAAATAAAT
AAATAATCTAATTTATTTTATTATTATATTATTTATAAAATAATTTATTATTATTTTTTTGCCGA
TTTTCATTAATTATATTAAAATGTGTACTAATTTGTACAAAGATAAAAGGCCAAAGGGCCTGAGC
GTCTAGTGGAGGATATCATAGGACCACCAGACCACCCATAAGGCACTGTAAGCTTGCACTTGAAT
TTGCTACTGAAAGGCAAGCTACACTTGCTACTTGCACTTAAAAAGAACAAGTTTAAGGCATGCCA
GGCCGAACGCATAAAGCATAAAAAAAATAGATAAAAAAGGCCTTG
Right flanking sequence: Indices 143648 -- 144147
GCCTTTTTTTGTCTGACAGGCCCCCCTGGGGGCCGAGGCCCTTCGCCCCGAATCTTCAAGCTAGT
CAAACTATCGGCGCGCTGTGCACGACGTCTTTGTAAGGTTGGATTCTCAAATGGCCCGATTGCCT
TAGGTGACTTGCCAAAGGGCACTCCGTGCCTTGTAATTGGTGGACTATTAAGATTTAAAAATGAA
GTAGAGAGGTAGAAACTTCACGGTGATCGAAACCCCGAAATCAAAGTGCCAAGCTTCGCAAGGTT
CTGGCATCTAAAAGTTTCCAGTGTTTCGTGAGTTAAGAAATGAATCCTCTAAAATGATTTATAAC
TCATTTATAACCGGACAGCTTTTTGAAGCTAATTTTCTACACTTTGTTAACAAAAGTACGTAGAT
ATTATGGGGTATAGCGGTCGTTTATATACTTTGTGAACAAAGTATATAATGAAAACTCAAGGTGC
ATTGTATATGATATTGATCGCTTTGTCAATACAACATACAGTATA
Found at i:156208 original size:8 final size:8
Alignment explanation
Indices: 156195--156219 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
156185 GCCATTTCTA
156195 GCCTTCGG
1 GCCTTCGG
156203 GCCTTCGG
1 GCCTTCGG
156211 GCCTTCGG
1 GCCTTCGG
156219 G
1 G
156220 GCCACTCGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.36, G:0.40, T:0.24
Consensus pattern (8 bp):
GCCTTCGG
Left flanking sequence: Indices 155695 -- 156194
AGCTAACTAAACGAGTAGCACATCGTATATTGTATGGGCAATTCTGTCCTGCGGCATGCTTCTAT
AGCCTGTAGGGCGAAGCTTGAATGAAAAAAAGCAAACCCGCAAAGTAAGCAAAGCACAGAGCATA
AAACTGTTATGCGAGAGGCTAAAGCACAAGTCTAGCTACTGAGAGAAAGTGGAGCTATTTTCACT
GATTACCTTATTCTTGCCAGAGAGTCCTTCGATCTGCTACACCCCCTATGCTAATAGAGCTAATA
AAGCTCCGGGCTGCTTGCGCGTCTACGCTGTTTATTTTTGAGTAGAGGGCGCACTTTGATCCTCT
GCCGCTGACAGCAGCTCTTGTAGATTTTGAACAGTCATATTTAGTAAGTTACTTACGCGAAGCCC
CGTGGAGTACGGAATAGCCAAGGCTACTCTGACTGTAGCTTGAACGCAAGAGTTCCCGCCAAGCC
CTCTCCTTCTGGTGCTCGTGTGCGGAAATCGTCAAGCCATTTCTA
Right flanking sequence: Indices 156220 -- 156719
GCCACTCGGGTCGCTTCCTCCGTGCTTTGGGCCCTTCGGGTCGAGCCTTACAAACCTAGCCAAAC
AAAACAAAAATTTTTGTTTATTCTCTGAACTTTAATTTACATAGTAATTGAATATTAGGTTTATT
ATTGTTTGCTTCAAGTTTAAGAGCTGATTACGAAAAGGATGGATGTCTGAGCGGTTGAAAGAGTC
GGTCTTGAAAACCGAAGTATTCTTAATACCGGGGGTTCGAATCCCTCTCCATCCGTGAGTATGTT
AATAAGTTAACTGCATTCTCTTCAATGCGTTTTACCGAACCCTAGGGCTCTTCGGGCACTCGACC
GAGAGGGTCGAGCCGCCTCTGGTGTTCGTGCGCGGAAATCGTCAAGCCATTTCAGGCCTTCGGGC
CTTCGGACGCCCCGAAGGATACTGCTTTGGCTTTCCGAAAAAAAAAAGGGCGCAGAAACTTTCCA
GTATCTGCCCGCAGGCACGTAATGCGAAGGGGTCCCGTACTTTTT
Found at i:159743 original size:18 final size:18
Alignment explanation
Indices: 159720--159763 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
159710 GGGGCGCGAA
*
159720 GACCAAAGAGAGA-AGGTC
1 GACCAAAGAGAGACA-CTC
*
159738 GACCAAAGCGAGACACTC
1 GACCAAAGAGAGACACTC
159756 GACCAAAG
1 GACCAAAG
159764 GAAGAGAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.43, C:0.25, G:0.27, T:0.05
Consensus pattern (18 bp):
GACCAAAGAGAGACACTC
Left flanking sequence: Indices 159220 -- 159719
GCAAACAAAGCAATAGCTTCAGTTAAAGCAAAACCTAAAATGGCATAACCAAATAATTGCTTAGC
CAATGATGGATTTCGCGCAACAGAAATAATCAAAGAATACCGATAGGGTTCTTCCCCCCGGTCAG
AACCACACGTGCAAGTTTCCCTGCATGTGGCTCGTCCATGGCAATTTCTTCAGCTTTTGTGGTTT
GGCCGTATAAGTGCTACTAGCCCTCCCGGGACGCGCGACTACTGTGCAATCCCCCCCCCTTCCCT
GCACCTTGTAACTAAGTCATTGTAGGCATAGCGTGATCCGCTTTCTCGATTTGGCTATGGTTGCC
CTAGCAAGAGCGCCGAGACCGGGATATATTGAAAAGATCTCAAGTGATACAGTTAAAGTTGCAAA
AAAAATTTTTAACTAGTCTAAATGGTTGAGAAAGAAGGGTCCGCAGGCTGGAAATGGCTTGACGA
TTTCCACGCACGAGTGCTATAGGAAGAAGAGGGGAGGGGCGCGAA
Right flanking sequence: Indices 159764 -- 160263
GAAGAGAGCCTAAACATATTTTTTTTGCCGGAGGCGCGGGATAGAGCCTTTTGTTGTGAGTAGTC
TGTCCGCTCTATCCACGCCACTCCATCACAGGGTTCCTCGAATATAGTCACCTGACTCCATAATA
TGGTTCCTCGAGTATAGTAACCTGACTGAACCTAGTAGCGTGGAACTTTCCTGTAGTTTTTAGAG
AGGTGGGGTAGTATAGTGACGCAACCTCCTTGCCTTTTTCTATGATCCGCAGGTTTGGACCAAAC
TTGAGTAAAGCAGCTTTGGCTGACCGTAGGCCGTGTTTTCTGGCCAAAGTTAGCGCGCAAGACTT
TTTATAGATGGACACAACTTTCCACAGGGAAGAGCGCTTGTTCACAAAGGAATAGTAGTTAACAA
TGCCGCGTATCACCGATGAGAAGTGGGTAACAATGTGTTTGTCCCCTGAGGAACCCAATCGTGGA
TTGGAGGTTGCTCGAGCTAAGCCCTTGGCGTTTTTTTTCGCGTAT
Found at i:160694 original size:19 final size:21
Alignment explanation
Indices: 160672--160714 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
160662 AAAAAACAAA
160672 TTTT-CAAAAAAATATTTTTT
1 TTTTACAAAAAAATATTTTTT
* *
160692 TTTTACTAAAATATATTTTTT
1 TTTTACAAAAAAATATTTTTT
160713 TT
1 TT
160715 GTTGTTCGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTACAAAAAAATATTTTTT
Left flanking sequence: Indices 160172 -- 160671
AGAAGTGGGTAACAATGTGTTTGTCCCCTGAGGAACCCAATCGTGGATTGGAGGTTGCTCGAGCT
AAGCCCTTGGCGTTTTTTTTCGCGTATCCAAGTTCCAAGGCTTTAGTTATTAAGTCCTTTATGGG
AGCTATTAGTTGTGGACGAGATCGGAGTCTTATTTGTTTGACATCGGAGACCTTGTCAGTGCTTA
AGATTTCCACACTTCCGGTGCCGTAATATATTACTAATGCGCCTAAGTATTTGGCCATCTCGGAC
TTTGCGTGTAAGATTTGACTTTTCTGTTCGTTTATGTCCAACTTCAGTTCTTCCTGCAGGAAGTT
TTGCACAGCTTTTCTAATATCTAGAGCATCTTGTTTGCTGCCTATAACACCTAAAATTATGTTAT
CCGCGTACCGGAGGTACTTAAGTCTTTTTAATTCTTCTTTCTCAGCCATTTCTAGAAGCATCCTT
CGGCCCAAAGGGCACGAAACTTTAGGGTTTCGAAAAAAAAACAAA
Right flanking sequence: Indices 160715 -- 161214
GTTGTTCGCGGTTTATCCACTTTAGGTGTTTGATGTTTTTGATGGCCTGCTCTAATTCTGTATAA
TATTTGAAGAACGCTTTGTCCTTTGAATGGATATTAAGCCTTTTTTTCTTATATTCCGCCGACGC
GGGGCGCATATTCCCTACATTGTATTTGGGTATGAGTATGTCTTCGACATAACAATCCAATTTAT
GTAGGAAGATATTGGCACAAAGCGGGGAGATTATAGAGCCCTGCGGAACGTCCTCTGTGTTGTAT
TGCGTTCGATCTGTAAGGTTATATACATCTATGTATCCTGCGTTAAGTAGCTTTCGCATAAGATC
CTGTAGTGCTTTAGATCGCAGTACTGATTGCATTTTCTTAATAAGCAGGTCATGATGAATCTTGT
CAAAGTCTTTCTTAATATCAATTTGTACAAGCCAAGTCAGTGCCGTCCACGAGTAACGGAGGTCT
CGGAGGGCTTTATGACAGCTTCTCCCAGGGCGGAACCCGTGGCTT
Found at i:163420 original size:21 final size:17
Alignment explanation
Indices: 163377--163413 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
163367 ATATTCAAAC
163377 ATTTTGATTGAACATAT
1 ATTTTGATTGAACATAT
163394 ATTTTGATTGAACATAT
1 ATTTTGATTGAACATAT
163411 ATT
1 ATT
163414 GCATTTGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (17 bp):
ATTTTGATTGAACATAT
Left flanking sequence: Indices 162877 -- 163376
CTAGAAATACAACCTCGCCGTCGGTCAACTCTTTGGCTTTTTATTCCAAATCACAATAATAAATG
ACGTGACCGAAAGGATAACCAAGTAAGCCCGATAGAACCATCGGTCTTGCTATACTTATATGGAA
CTAGAGAAGAAGTTATACATACCATGAGTTGGGCTATTTGACTGGCTATATCTCGGAAATCCTTA
GTATTCGTAATAGAAATTCAAAGGTATCGCGTACTTGTTCCGTGATGTTGTGAAAATCGATGTTT
CCGTGTAGAATAAGCGGTGGTGGGGCGAAGACTACGGCCTAAAGGGTTCGGGTCGAGCACTACGT
GCCTTCAATCTACAAGCCCTCTCCCTAAGGTCTTCGTCACCCTCGGGGCCTTCTCCCGCTACCCG
CGCACTCCGTGCCTATGGGTCCAAAGGAGACTTTCTTTGGCTTTACGAAAGAAGGACCTGAAGGG
CGCGAGACTATAGGGAGAGGTTTCTTTTTTACGTAATATTCAAAC
Right flanking sequence: Indices 163414 -- 163913
GCATTTGGTAATGTTCGATATAATAAAAACTATGGAATCCCCGGAATTCCGAATTGACAACAGCT
TCAATAAAATGAAGTAGGTTGCAATGACCATCATATATGAAAAAATGGAGCTCCTTCCACAAGGT
TAAACTAAGTAAAAGGGGATAGATGGCTATCAAATACCAATCGGTAGTTTAATATCTTGCTGTAT
TCTCCACTATCGAGGTGATATTAAAAAATGATGTCATAAAAACAGTCTGTTGGTCAAATTGAGTC
ATATTAATGGTTGTGACAAAGTGTTTTTGGCTTACGCCAATCTTGTTGTTTTTCATATTTTTTTT
TATTTTGATTCAAAAAGTATAAGAAATGGCTAAGTAACATAAGGGTAATGTATTGGATTGCAAAT
CCTATAAAGATGGTTCGAATCCGTCCTTAGCCTACTTTACGATTCTATTGTTCCTGGAAATACCC
TATTATCTAATAAGTACAAAGATCTTGACCACCCTTTAGACTTAC
Done.