Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_035979
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: 161960
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Found at i:12821 original size:21 final size:21
Alignment explanation
Indices: 12794--12877 Score: 123
Period size: 21 Copynumber: 4.0 Consensus size: 21
12784 CCCTTGCCTT
* * *
12794 AATCTCTTGATTTATAGATTT
1 AATCTCTCGATTTATGGATTC
* *
12815 ACTCTCTCGACTTATGGATTC
1 AATCTCTCGATTTATGGATTC
12836 AATCTCTCGATTTATGGATTC
1 AATCTCTCGATTTATGGATTC
12857 AATCTCTCGATTTATGGATTC
1 AATCTCTCGATTTATGGATTC
12878 GTCGTATATG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (21 bp):
AATCTCTCGATTTATGGATTC
Left flanking sequence: Indices 12294 -- 12793
AACTTACGAGGTTTCAGATACATTATCTGAAACCTTGTAGGCAAAAGGGGTAAGACTGGAAGCGG
AAAAGGAGCGCGTCTGCCGTATAATGGGAATCATTGATGGCGCTTCGAAAGATGGAGATTTGGTT
AGAGTTTTTACATATCTCATTACGAACATATATCGTCACGAGTCTCTATTTTGTTTTTCAAATAG
CCATAAAAATCAAAGGGTCCAAGGTCTGTCCGACCATCTGACCTCAGCAAAGAGGCGGAAGTACC
ACCCGCGCAGGAATAGCTAATCCAACCGGTTACGGTCCGTGAAGTCTTCTCTAACGGGCCACAAG
ATTAGATGAATGGTTAAATCCTGACGATTTTCATCCATTCATCTAATGTGGTGGCCCATTCCCAC
CCATTTATCTAATATGGTGGTCGAGAACTCCTGTCGGATCTCTTACTTCGTGAACTCATATGATT
AAATATTATTATTTGCTCCAAATTTCCGGATTTAACCCTTGCCTT
Right flanking sequence: Indices 12878 -- 13377
GTCGTATATGCATATATAATGATTATAATTTGCTCCCACCCAAATTTATTGATTTATGTATTATT
ATTTCCGTATACACAAAATAGAAGCCTTATGTTATCCGTGCTCCATTACGCTTCCCTCTTCCATT
ATCTCTTTACCCGGCTCGGTCTTCCGTTTCATATTATTCTTTCCCCCAAATAGCATCTCATATGC
GTTTGTGCCGACGCTGTTGCGAAAATATTTCATCTGCCGCGGGTCCGGTTCCTTATTGGACGATT
TTATTGACTCGATATAATTGGCTGCATCCACCTTGTTCCTAATGGTTTGCCCCTGGTCGAGTCCT
CCATCGAATAATACAACGCTTAAATCCGGTAGACATTCGCGGATGCTGGATGATTGCCGATGTGA
GCTGTCGCATAACCCCGATCTACGAAGTATTCCACAAATTGCTTTGTCACTACCTCGAGGGAAGC
GCAAGGGCTAGAATTAGGCCTAGAACGTATCAACTGCAAACTGCG
Found at i:31110 original size:23 final size:24
Alignment explanation
Indices: 31060--31104 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
31050 CGGAGAAGAA
31060 AAAACTGCATAATCTTTCGGTTAT
1 AAAACTGCATAATCTTTCGGTTAT
*
31084 AAAA-TGCATAATCTTTTGGTT
1 AAAACTGCATAATCTTTCGGTT
31105 TCAAAAGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (24 bp):
AAAACTGCATAATCTTTCGGTTAT
Left flanking sequence: Indices 30560 -- 31059
GGATGTTCGACACCTTATCAATTAGAGTATTTCACGCAATTTTTTTGATTTCCCCATTGCGTTGA
CCCACTCGAAACCGGCCGTATTGAAATCCGATTATCCGACTCGGCGGGGATCGCCAGGCCGCCGG
TCAACGACCTTTGCCGAACCTCTTTTGGCGAAGGCCAAACACATAACCTATGGTCCATTGAGCAC
GGGGGGGGTATAGGTGGCACCACCTAGTGCGCAGGGAGCATATTCGGGTATCGTGCGCGGTAAAG
CCATTTCTGGCCGGGCCGGGGGACCTGGGACAAAGAAGTGTGCCCTTTGGCCCTAAGAGTTTTGA
TTCGGCGATTCGCCATCGCTAGTTCGGTTCGGTCGTTTTTCGGCCGATTACGTTTCGCCTCCTTC
GGACCGACCCTACGGGCCTGTGTTTTACGTAATGTGATGTCGTATGGGGGGGCCACGGGCCTTGT
GCTTTTTCTTTACCCGATACACTGCTCTAAATATACGGAGAAGAA
Right flanking sequence: Indices 31105 -- 31604
TCAAAAGCTGCTGAATCGGAAGATGATGCAGCGTATGCGACGAAGGCGGGGTTTTTAAAGTTGAT
GGAGAACAAGGTCCGGAGGAGGGTTTTAGGCATTTTGATGGAAAATAAGAACCTTTGGTCCTTAT
TGATTGCGGAACCCAGATAAGTGCGCCAGCCTCGGTGCATCGTGGACTTGTACTTTTTCTCGCGC
AGGACCCATACCGGTTATCGGTCGTCCAGGCGCGCATATCAGGCGTCGGAAGGGACATACGCCTC
CGTCCTCGCCGCCCCGAGGCGCTGTCTGAGCTTCTTACTCGGGCAGATTGGCCCGGTACGGTTCG
TAAGAGACGACGGCCCCCCGGCCGGCCCCTGTCTGACGGTCCAACCTCTCAGGGGGCCTGTCAGC
CGCCAGTCCCCGGCCCTTCGGACGGACCCACAAAGTTTCTCGTGTTCCTTGGTCAGTTGTTCCTT
CCCGCTCCTCTGTTGTCTATTTAGCACTCTCCGCCGCGGTTGTAT
Found at i:38297 original size:2 final size:2
Alignment explanation
Indices: 38290--38347 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
38280 CCGGAAAGAA
38290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38332 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
38348 GCTGCGCCCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 37790 -- 38289
GTCCAGCCAGATGAGCGCCGGCCAAGGCGGCGGGTTGGAAGTCAGAAGGCCCGCAGTACCCGGCT
AAACCTCCGCTTCGGGAAAGGGAAGGCACTGGAAACACCAGTAATCGGGAAGGGGCCTAGGTATC
TGCTTGGTCTAAGCGGATTTAACTCTACACAGCTTATCAAAGCAACTCTGACGGATCTCAGATTG
GCTATGACCGACACGGTACGGTATGCGGTTTGCTCCCTGTCAGCCCCTTGGATCTCTAGCTATGA
GAAAAAGCGAACAGGCGGACAAAGCGGCGGCGTGAAAGTCCTCTAGCTTCTCCAGCGAGCTATGG
GGTACGGCGCAGCACAAAATAGTTTTAATTCACTTGGTCCACCTGCCCTGGCTCCCCCGGCGAAA
CTTCCCAAGGATGCTCGAACTCTGCAAGGCGATAAGTATAAACTCTGGAATCGCTGGAAAAACGG
AGCAACCCGAAGAGCAGATCATTGGTTTTCGAGAACCGGAAAGAA
Right flanking sequence: Indices 38348 -- 38847
GCTGCGCCCGTAGTGAAAGAGGGACCAAAGTAAGTAGAGTTAGTGAGCCGTGTAATGGGCAACTA
TTTCGCACGGTTCGGAGGGCACTTCAGTAGGCCCTACATGGGCTGAAGTCCTGACCCCTATTCCT
TTTGATGATGCCAGAAGTCGTTTCGATATACGATTTTATCTCGTTTCTATTTTATTTATCATATC
CGATCCGGAAGTCACCTTTTTATTTCCCTGGGCAGTTTCTCTTAACAAGATTGGTTCGTTTGGAT
TCTGGTCTATGATGGTATTTTCACTTATTTCGACGATTGGATTTGTATATGAATGGAAAAAGGGC
GCTTTAGATCGGGAGTAACTCTTCATTCGCGAAAGCGAATGGAGTGGAAAGAAAAAATATAGGCC
CGTAGGGCTGAAGCTCTCATCGCTCTCTTTCTCCCTCTCCGGACACTTTTTTGGCTTGCCCCCGA
CCCGCTCGGCGGTTCAATTAATCCTCCGGATTGTAAGTATATAAA
Found at i:43118 original size:12 final size:12
Alignment explanation
Indices: 43101--43127 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43091 GTTGCATCTC
43101 TCGCTTCATGTT
1 TCGCTTCATGTT
43113 TCGCTTCATGTT
1 TCGCTTCATGTT
43125 TCG
1 TCG
43128 ATGGACGGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.26, G:0.19, T:0.48
Consensus pattern (12 bp):
TCGCTTCATGTT
Left flanking sequence: Indices 42601 -- 43100
TAGTATTCGATTCCAATGCAGCTTTATCGAAAGCTGCCGAAATTTCATGTCTGGGTTTTTCCCTA
GCCAATAAATAGGCAATCTCTACCTCTAATTCAGCGATATAATTGCCGTTGGGCGAACGCTGTGT
CCGTGAACTTCCGTTTATCGAAATCATTTTTACATAATGGGAAGTCTACAGCGTAACTAATAGTC
TTCGGGCGAAATTCGGAAAGGGTTGGGGTGTCAGGTAATGGTGCATCATTATCCTTTTCTCGTTC
GGTGCTTTAATTGGATCCGTAACCTTGCGCGGCAGGAACTCCTTTAGGCTCAGAACCTTTCTTAT
TTGGGCCACGAGGCTGGACTCTCTATGTCATCTAGCTCACGATAACCCGTTTGAAATTTCCTTGT
GCCAGCCATATGACAAATGTAGTAAACGAAGCTCGGTATAAGTCCCGGAATCATACGCAAACAAC
CCTTGGCTCTACTTCCTTTTTTTCGGCACAAGTAAGTTGCATCTC
Right flanking sequence: Indices 43128 -- 43627
ATGGACGGCGTAGGAACCTACGAAAGAGCCTGTATTGAAACGGCTTCGGCCTCCTCCACGGTTTT
ACAGAACTATGGAGCTGGAGCCGGTTTGAAGGAAGCCATGTTAATTACGATGAAGTTGCGTTCTG
GCATGTTAAGGCCTGTCCCAACAACGCCAGCCGCGATATGCCACAGGTCGCCGGGCCTCACTCAC
CTTACCACCGAGAGTCATTTCATTACTACTCCCGATAGGTCCCAACCTGACAAATGGGTTTTTGC
GAGTTACATACATAATTGTCAAACATGCGGGCTGATGGGAACCCCATGGCGCGGCGGCTCCGGGA
GCATGTTCTTATAACGCTATCCTAGAAAGCCTTATCCATTATATTGAACCAGTTGGAGAGGGTCA
GGATAACCTGGTAATCCAACACTTTATTTTATTTTCCTTCTATAAAAAATTTGTGTTTTTGCTGC
CCTGCCGAAACACACTTTTATCCGAGTTATAAGGTGGATCGACCA
Found at i:43769 original size:17 final size:17
Alignment explanation
Indices: 43747--43783 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
43737 ATAATTTGCG
43747 TATTCGTTGAGTTCCAT
1 TATTCGTTGAGTTCCAT
*
43764 TATTCGTTGAGTTTCAT
1 TATTCGTTGAGTTCCAT
43781 TAT
1 TAT
43784 CTTACCACGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (17 bp):
TATTCGTTGAGTTCCAT
Left flanking sequence: Indices 43247 -- 43746
GTTGCGTTCTGGCATGTTAAGGCCTGTCCCAACAACGCCAGCCGCGATATGCCACAGGTCGCCGG
GCCTCACTCACCTTACCACCGAGAGTCATTTCATTACTACTCCCGATAGGTCCCAACCTGACAAA
TGGGTTTTTGCGAGTTACATACATAATTGTCAAACATGCGGGCTGATGGGAACCCCATGGCGCGG
CGGCTCCGGGAGCATGTTCTTATAACGCTATCCTAGAAAGCCTTATCCATTATATTGAACCAGTT
GGAGAGGGTCAGGATAACCTGGTAATCCAACACTTTATTTTATTTTCCTTCTATAAAAAATTTGT
GTTTTTGCTGCCCTGCCGAAACACACTTTTATCCGAGTTATAAGGTGGATCGACCACACGTTCGA
ACATGTAAAACCGCAGAAGTTAATGGAACTGCGCCGCGTGCAACGCATGGCGCCTCCTCGTCGCA
GTCGGGTTGCCTTCCGCCAGCCTTCTTCGGGAGCGATAATTTGCG
Right flanking sequence: Indices 43784 -- 44283
CTTACCACGCGCTTCGTCGAAAGGTCTGTGGAACACGACACAGGGCCTGTAACCGGGACCAAGAA
TAAATATTTGCTATTTAATATGTCGCGGGTAAATTCGGCATTTGGATTCGGGAATCATCTTGACT
TGGCTGATTCAATATACGTTCGAAAATTTTGTCCGGACTCACAGGCATTGTACGGGGTTTGCACT
GGGGAGCCAAGTAGTGCTTGGCTTTAATTAACTAAAATTTGCTTGACATATGATGTTGAGCTGAG
CTCGACTTTGTTATCTTCAAGCTTCAATTTGTACGTGCACTTCGGATACCCCGCGTGCAGCGTTT
GAACAGGGTTTTGGTAGTGATAGATGAAGAAGACCTCACCCTCGGTTTTCCGAAACCGGGGGGGG
AAATCACATCAGCGAGTGAGCGCGCTTGTTTGATGCCCTCCTGCATGCTCCAGTAGCAATCCCTC
GCCACGCGCACGATCCGATTAGTTGATGTACTTCATCGACGTATA
Found at i:62969 original size:27 final size:27
Alignment explanation
Indices: 62939--62994 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
62929 ATAAACAATC
* * *
62939 ATGCAAGAAAAGCAGGGTATTACTGAT
1 ATGCAAAAAAAACACGGTATTACTGAT
* *
62966 ATGCAAAAAAAACACTGTATTACTTAT
1 ATGCAAAAAAAACACGGTATTACTGAT
62993 AT
1 AT
62995 TCAATCAACT
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:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (27 bp):
ATGCAAAAAAAACACGGTATTACTGAT
Left flanking sequence: Indices 62439 -- 62938
AGGGAAAAAAAAATAAATCATGTCATATATTTTAGGAACCAATCTGAATTCCAATAAACAGGTGA
AAATTGCCTTAACTCGAATCTTCGGAATCGGGCCCAAAAAGGCAATTCAAGTTTGTGATCGATTA
GGCCTCAGCGATAACATTAAGGTTAATAAGTTAACTAAATATCAATTTGACCAAATTCTGGAAAT
AATAAGTCAAAATTATTTAGTCGATTCGGAATTGGAGAGAGTCATTCAGAGGGACATCAAACGAT
TAATTAGTATTGGTTGTTATCGCGGGTTTCGCCATAATGCAGGATTGCCCTTACGCGGCCAACGG
ACTCATACTAATGCTAAGACTTCTCGCAAATTTAGAAACATTTCGATCAGAAGTTGAGAAAAGTT
TTTTTCCAGTTCGTACAAAATATCTTTGTAATTAGTGAACGGATTGGATGGATCATAAAAAAACG
AAATCGATGATATCGAGCAACACCAAAAACATTCAATAAACAATC
Right flanking sequence: Indices 62995 -- 63494
TCAATCAACTTTTGGTAATACGATTATTACTCTAACGGATCATGACGGAAATACAAAAACTTGGT
CCTCCTCGGGTTCAGTGGGGTTTAAGGGATCTCGTCGCTCAACCAATTATGCTGCTCAAGCAACC
GCAGAAAATGCCGCGCGAGCTGCCATTCAACTTGGATTTAAGTTTGTTGAAGTGAGAATCAAAGG
ATTGGGTTATGGAAAGGAATCTTCGCTACGTGGTTCAAAACTAGGAGGTCTTATTATTACCAAAA
TTCGCGATGTAACCCCAGCGCCACATAATGGATGCCGACCCCCTAAAAAACGTCGTGTTTAAATA
TCATCATAAAGTGCTATGTCATCATAAAATGGTAAATTGAGGTTCAAGAGTAGAAACAATTTTTT
TAGGGTCCGAGGGAGACTTCTTTGGGATACTTCTTTGGCTTCACGGGGCGGGGCTTAACCCGTCC
CTCGTAAAGGCGAAGAAGGAGATCTACAAGCCATGTCTGGCCCTC
Found at i:71924 original size:2 final size:2
Alignment explanation
Indices: 71911--71948 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
71901 GAAAGAACAA
* *
71911 AT AT AT AA AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71949 TTATCCACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 71411 -- 71910
TTCTTTCCCTACTCGGCACAGGGGAAGGGGCTTAAGCGTCTGCTATATTTCAGCAGATCGGATTC
AACCAAGTCCTCATCAAATAAGGATCCCAGGGACCCCGCCGGACGGGTCGATACACGGAAAAAGA
ATATTTGGGCGCGGATCTTTGGATTTTTGGATTTTGGGAAAAAAATACGCTACGCGCCTCGTTTC
GTAAATGCACCATGTTCGGCGGGGTCTCAAGGACGAGGGGGGCTCATATAAGAGAATGCTTGGTT
TTATTCCTTCCCACCCACTAGAATCTCACATGAGCGCTATAGTGAGAAAGCAAGTTACTTCATGT
AACTCACGCCACTTGTAGGCCCACATAGGTCACTGAAAAAACAAGCCAAGACCTTGCGACAGAAG
CAAATCCAAAGTAAGGTTGAATCGGAGAGCCGTATGATGGGCGACCATCTCGTACGGTTCGGAGA
GGGCTCGAGTACCAATGCATTCAATATGTGTCTGGGAAAGAACAA
Right flanking sequence: Indices 71949 -- 72448
TTATCCACTCTATTCAATTGCATGAAGGGTTAAGCACAAAACATGTGCTTCGCCTCCAGTTCTCA
AATACGAAGTATAGTTGGGAGAGGCAGGATTCGAACCTACGTAGAAAACCTTCAGCAGATTTACA
GTCTGTCGCTTTTAACCACTCGGCCACTCTCCCTATGATAAGTAAGCTTCTATTTTCCGGCGGTG
CAACGGGACTCTGACGAAAAATGGGTCAATCCACGCGTGTACCGTTGTTCCCATGGACTAATCGA
ACAAGTAAAAGGATGTACCGTTGATATATATTATTCATTGCACACTTTACGCATCCTACAGGATT
TGAACCTGTGACCTTCAACTTAGAAGGTTGTTGCTCTATCCAACTGAGCTAAGAATGCGGCACAT
TACTAACCATTTCGCAAAAAAAAAGTGAATTCCAGAGAAGAAAGAAGCTTGCTTCTTTCTTCTCT
CCCGCTTTATTCGCATCGCGAATGGAGGCCGAAAGAGAAGAAAGG
Found at i:92770 original size:10 final size:10
Alignment explanation
Indices: 92755--92858 Score: 129
Period size: 10 Copynumber: 10.3 Consensus size: 10
92745 GCTGCAATAG
*
92755 ATATCTAGAT
1 ATATCTATAT
92765 ATATCTATAT
1 ATATCTATAT
* *
92775 ATATATCTAT
1 ATATCTATAT
92785 ATATCTATAT
1 ATATCTATAT
92795 ATATCTATAT
1 ATATCTATAT
* *
92805 GTA-CTAGAT
1 ATATCTATAT
92814 ATATCTATAT
1 ATATCTATAT
92824 ATATCTATAT
1 ATATCTATAT
92834 ATCTATCTATAT
1 A--TATCTATAT
*
92846 ATATATATAT
1 ATATCTATAT
92856 ATA
1 ATA
92859 GATATATAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
9 7 0.09
10 64 0.79
12 10 0.12
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (10 bp):
ATATCTATAT
Left flanking sequence: Indices 92255 -- 92754
AAATGACTAAATTTCGCTAATATGGCTAAATCCCGAGGATTTGTAGATAAATATATGTAATTAAT
ACTCCAGAAGCCTCATCGCTAATGACACCTTCGCTAAATGACGCATATTTACCTAATATGACCAA
ACCCGTTGGGGATCTGTAGTATGATACGGAGAGGAATACCCCTTAATTAATATGTAATTAAAGGG
TCGGGAAAGGAATATATAATAGGAATCTATATGGGATATGGAAGAATTCCATATAATTGGGAAGA
GATTGGGAAGAGTTAATCAATTGAATTGGAATAAATAGAATGGATTGATAAATAAAATAAATTCA
AATATATATATACATATTATATATTTGTGTATAACGGAGAAAATGCATAAATCAAATAGATTCTA
TTATTTATAGGAGAGACTATTAAATTCATGTTTATTCTTTCTTCGCCCATCTCCCGAAAGAAAAT
GAGCTACTATTTTTCTTATTCGAGAGAGACGATGAGCTGCAATAG
Right flanking sequence: Indices 92859 -- 93358
GATATATAATTTATGGGTCAGGGGAGGAGATAGCCTTGACCTCCAACCTCCGAAGATACTAAGGA
CCTGGATCTTCCCTGGGTTACCACGTTCTTGAGATCTGTTACATAGGCCCCTAGTTTTCCCTTGG
GAACGTCCAGAGACTTTCATCGTGGAAGTGGCATAGGAACTCCGGGCGGGGATCATGGCACTTCT
ACTAGAACCTTAGGTACGCTTTCGCTAGGAGCTCGAACTGGACTGAAGATAGGAAGCATAGATCG
AGGGGGCACAAGGGAACTATTTTTTCGGTCACGCGGTACGTACCGCCTGTAGGTCCCGTAAGCAT
CTCGTCTTTATGGGGTTTGTAAACGGTGTCCGCTACATTCCGAAGATCAAGAATTATATCTGGTT
GTTGGGTGCGGGGCGGGGGACTCGGTTCTGTCGGCTACCACAAAACCGGGAAACTGTCCGACAAA
ACAAAGGGCACTTACGACCAACTCTGCCTCGGAATACCTTTCAGT
Found at i:92779 original size:4 final size:4
Alignment explanation
Indices: 92763--92866 Score: 100
Period size: 4 Copynumber: 25.8 Consensus size: 4
92753 AGATATCTAG
* * * * * *
92763 ATAT ATCT ATAT ATAT ATCT ATAT ATCT ATAT ATAT CTAT ATGT ACTAG
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A-TAT
* * * * *
92812 ATAT ATCT ATAT ATAT CTAT ATAT CTAT CTAT ATAT ATAT ATAT ATAG
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
92860 ATAT ATA
1 ATAT ATA
92867 ATTTATGGGT
Statistics
Matches: 79, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
4 77 0.97
5 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (4 bp):
ATAT
Left flanking sequence: Indices 92263 -- 92762
AAATTTCGCTAATATGGCTAAATCCCGAGGATTTGTAGATAAATATATGTAATTAATACTCCAGA
AGCCTCATCGCTAATGACACCTTCGCTAAATGACGCATATTTACCTAATATGACCAAACCCGTTG
GGGATCTGTAGTATGATACGGAGAGGAATACCCCTTAATTAATATGTAATTAAAGGGTCGGGAAA
GGAATATATAATAGGAATCTATATGGGATATGGAAGAATTCCATATAATTGGGAAGAGATTGGGA
AGAGTTAATCAATTGAATTGGAATAAATAGAATGGATTGATAAATAAAATAAATTCAAATATATA
TATACATATTATATATTTGTGTATAACGGAGAAAATGCATAAATCAAATAGATTCTATTATTTAT
AGGAGAGACTATTAAATTCATGTTTATTCTTTCTTCGCCCATCTCCCGAAAGAAAATGAGCTACT
ATTTTTCTTATTCGAGAGAGACGATGAGCTGCAATAGATATCTAG
Right flanking sequence: Indices 92867 -- 93366
ATTTATGGGTCAGGGGAGGAGATAGCCTTGACCTCCAACCTCCGAAGATACTAAGGACCTGGATC
TTCCCTGGGTTACCACGTTCTTGAGATCTGTTACATAGGCCCCTAGTTTTCCCTTGGGAACGTCC
AGAGACTTTCATCGTGGAAGTGGCATAGGAACTCCGGGCGGGGATCATGGCACTTCTACTAGAAC
CTTAGGTACGCTTTCGCTAGGAGCTCGAACTGGACTGAAGATAGGAAGCATAGATCGAGGGGGCA
CAAGGGAACTATTTTTTCGGTCACGCGGTACGTACCGCCTGTAGGTCCCGTAAGCATCTCGTCTT
TATGGGGTTTGTAAACGGTGTCCGCTACATTCCGAAGATCAAGAATTATATCTGGTTGTTGGGTG
CGGGGCGGGGGACTCGGTTCTGTCGGCTACCACAAAACCGGGAAACTGTCCGACAAAACAAAGGG
CACTTACGACCAACTCTGCCTCGGAATACCTTTCAGTAACCTGTG
Found at i:110555 original size:21 final size:22
Alignment explanation
Indices: 110523--110564 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
110513 TTAGAGTAAG
110523 AAAAACCACTAC-AAAGAAACA
1 AAAAACCACTACTAAAGAAACA
*
110544 AAAAATCC-CTACTACAGAAAC
1 AAAAA-CCACTACTAAAGAAAC
110565 GTATGAGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.60, C:0.26, G:0.05, T:0.10
Consensus pattern (22 bp):
AAAAACCACTACTAAAGAAACA
Left flanking sequence: Indices 110023 -- 110522
CCCCAAATAAACTTGCCGTATTATCTCCGCGAAAGAGACAAGAGCCTATGAACTCTGTATCAGAG
TCTTATTCCGGTATAAGTGCGAATTGAAACCGAGTGTTTAACCATTATTTCGCTATTCCCGATAT
TATAGCGACGGAGGCCCTTGATCCAATCCAGCGAGTTTTCTGTTATGTTTGTTTCTTCGGTGAAA
ATGAAAGAAAGGGGGAGGGGTAGACGCCAGCCTAACCCAGGAGGGCCTGGTGGCTCCTCGGTCAA
GTCCCTAACTTTCAGGGCGGGCTCCGCCCTATAAGGACTAGGTCTGTATAGGGCGGAGCGGATCG
GTGCTTAAGTAAGCTGCACAAATTGCTGAGACGTCTAAATGCTTTCCTTGATAGCTGGAAGTTCT
TCAAAAGTATGAAATGCCGGAGGGCTTGGGACCATCCATTCAAGTGTCGTTGAATTCTGTTCAAC
AGCCCAAGGACTTGGAGCACACTTGTTTTCACTAGTTAGAGTAAG
Right flanking sequence: Indices 110565 -- 111064
GTATGAGCCAAAACTACTAAAGGCATTCCATCCAGCGTAAGCATCTGGATAATCAGGAATGCGAC
GTGGCATACCCGCAAGCGGTTTTTTCCTTATTTATCAAATGTTAATGGATTGTGACTAAATATTT
TTCTTTTGTAAACTTCTTCATCTGGAATTAGTCCTTCAGACGTTTCGGTGTGTTTAAATCCCAAT
GTTGAATCAGTTATTTTATTGGTATTAAGAACTGGTTCATAGAGATCGAAATAGTACTGTTCCCG
AGCTAAATAATCCTTTTCATTCAGTAATAGTACCTGTTGAACCACCCACATGACTCAATAATAAC
TAAAATTGTCATGACCATATTTCCAACTGGAATTATAAATATATCTGTTATCGGATAATTTGGAA
GGGTGATAGTATTCAGCAAGTCTATCGCTTAATTTATAACCACTACCTACATATTGTTTCCCATT
AACTAAATTATGCCAAAGATAGATTCCAGTTTCCGTTAGATAATC
Found at i:125620 original size:24 final size:24
Alignment explanation
Indices: 125588--125634 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
125578 TCATTGCCTT
* *
125588 TTATTTATCTATGATGATTCATCA
1 TTATTTATCTACGATAATTCATCA
125612 TTATTTATCTACGATAATTCATC
1 TTATTTATCTACGATAATTCATC
125635 CAGATTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (24 bp):
TTATTTATCTACGATAATTCATCA
Left flanking sequence: Indices 125088 -- 125587
ATATAAACAGTGAAGAAATAACACACTTGATTTTCGGTGAGCAATTATTATATAATGATACGTAA
AAGGTAATATAATAAATACCATAATACGTGATACAAAAAATGATATAAAGCACGCATAACCGAAC
GAATTGTGTCAGATACGTAAAGTGATTTAGTTGAGTCCGAAGATGTAAGACGTTAGTTCTACCTA
ACATTTTTTTTCTACCTGCAAGAGAAATGTAAAAAGTTGGAATATAAGGTACTTCTATATAATTT
TTGGAAATATGGACTAAAGCCCTGCCGGGCGGGAGAGGAGATCGGAAAAGTTATATCTAGAGCCG
GACCTCGTGTTTCGTGGGTCGCTCCCTTCTCGCCCATTTTTTTGTTTTCTCACCCGTTTTTGGCG
GGAGTCGGATTCGAACCCACAACATTCAGATTATGAGCCTGACGAGTTACCAATTACTCTATCCC
GCGAACGGCCAACGAAAAAAGAGATATATTTTTGTTCATTGCCTT
Right flanking sequence: Indices 125635 -- 126134
CAGATTTTCTATTAGGAATTAGACTAGATTCGAACCAGATTTGTCTAGGTTCAAAAGGAAAAAGG
GGCGCGCCGCAGCCCGCGCTAGCCCACTGGGTTAAAATGACGGATACAATTTTGGTGTTCACCCA
ACTAAAGCGATTGGCTGGAGACAAAACCACGGTAGCTTCCCTACCCGCGCACAGGTCATGAATTA
GGGGTGTTATGAAGGAGGCAGGTAGATTACCCACCCTAGGCAACAACGGGCCCGCCGGTAACATA
ATGAAAAAGTACACAGGCACTACGTGCTTCTGGAACATACTTCTTTTAGTTTATGTCCGGAGCGA
GAATTTTTCATGGAATACGGGAAGCGATAAGGAAGCAGGAAAGTTTATAGAGGGGGTTGAGCTAC
GGGTTTTGAACCAACCGTAGCTCCACCTCGTTAGTAGGAGTCTGTGACCCCTAAACCAGCTTGCC
GAGAAGACCTTACACAAAGATACATTGAGGAGTTGCTGTCCCCCC
Found at i:126259 original size:15 final size:15
Alignment explanation
Indices: 126239--126269 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
126229 TCCTTCAGAG
126239 AATTATATATAAATA
1 AATTATATATAAATA
126254 AATTATATATAAATA
1 AATTATATATAAATA
126269 A
1 A
126270 TGAAACCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATTATATATAAATA
Left flanking sequence: Indices 125739 -- 126238
ACGGATACAATTTTGGTGTTCACCCAACTAAAGCGATTGGCTGGAGACAAAACCACGGTAGCTTC
CCTACCCGCGCACAGGTCATGAATTAGGGGTGTTATGAAGGAGGCAGGTAGATTACCCACCCTAG
GCAACAACGGGCCCGCCGGTAACATAATGAAAAAGTACACAGGCACTACGTGCTTCTGGAACATA
CTTCTTTTAGTTTATGTCCGGAGCGAGAATTTTTCATGGAATACGGGAAGCGATAAGGAAGCAGG
AAAGTTTATAGAGGGGGTTGAGCTACGGGTTTTGAACCAACCGTAGCTCCACCTCGTTAGTAGGA
GTCTGTGACCCCTAAACCAGCTTGCCGAGAAGACCTTACACAAAGATACATTGAGGAGTTGCTGT
CCCCCCCCTCTCGAGATAGGAATGGACCAACGAGGGACGGACTTCGATGATCCCGATGGCGTTTT
CGAGTAAATCCTGGCTGGAAAATATAGATCATACTTCCTTCAGAG
Right flanking sequence: Indices 126270 -- 126769
TGAAACCTTATTAACGAATTAACGAGGTTGAGCGGATAATGACTTATTCTTACAAAGGGGTTGGG
ACCGGAATTGTAACCGTAAGTAACCATTTCAACTGGGTAACGGCGCGCGTAAGGGCTCAGTCCCT
AATAAATAACCTTAGACTAAGAATTTATAAGGGATATCGTCCCGTATAGATCAGGTGTTTATGAT
ACTCTACGAGCCCCGGACCCGTATTTGAAGTGAAGGTCTTCGGTGAAGGAAATGCCTTCGTTGAA
GGAAGCCTGGAAGCCGGGAGTATTCGGTTATGTTCGTAAGGAATTTCCCCAAGCACAACAAAGGT
TTTGGATATTTATATAATTAGCCAGCTTTAGATATTGCAATCCAATCCTCTCTTTTCCGAGGAGG
GAATAAAGCTATTATGATTCGAGGAATTCTTGGAGTTGATAGGAAAGGTCTAGCCATTTCCATCA
ATGAGTTGAAGGAGTTGCCACAGGTTACTGAAAGGTATTTCGAGG
Found at i:138321 original size:22 final size:22
Alignment explanation
Indices: 138296--138339 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
138286 GAGCCCCGAT
138296 AATAAACATAGGCTACAATAAG
1 AATAAACATAGGCTACAATAAG
*
138318 AATAAACATAGGCTATAATAAG
1 AATAAACATAGGCTACAATAAG
138340 CCCCTCGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (22 bp):
AATAAACATAGGCTACAATAAG
Left flanking sequence: Indices 137796 -- 138295
CGAACATATTCCGAATCGAGACAGAAACTTCTAATATATTTTTCATGGGTCCATCGTTGGTTGCA
CCGATCGGCTTCGCTATTCCTCCAAGTCACTTTACTGTAATCTGTTAACTCATCTATCACAGGCC
TCATCAAATTTACTATTAAAATATTTAACCCTATTAGTACTATAACAATATGCGTTGGTTACAAT
CTCCTTAACTAAATCTTTAGAAATTAAGGTTTGTGAAGAAGACTTCAAATTTGAATACATGAATT
TCGGTTGATAAACCGGAGGAGTATAATCCGAAAGGTTTGATTCATAAATATATTTATTAAAACCG
GTCCCTAGCAGCCTGCATATGAATCCTGAATTTTATTTGCAAGTGTACACAGATGATTTCTGTGA
GCTATGCCGTATCCTGTTCGCAGTTCCAGTGAGCTCTTAGCTGTAAGCTGCGAACATACAGCAGC
CGCGAGCGCATAACCAACTTCCTCGCGGAGAGCAGGAGCCCCGAT
Right flanking sequence: Indices 138340 -- 138839
CCCCTCGCATCGGGGAGGCACCTCCTTCGGTGCCTCTACCACTCGAATGTAGTAAATCAATTATT
TCATGGAATAATAATAGTAATATACAAAAGCATATATGGATAGAGAAAGCACAGCTTAATAATAG
AAGATACGTATATAATAAGAAAACCATAGGGCGCATAGGGTGTCACTACTAATAAATGAATTTAG
TAGTGACTTTTAATTATTTAGGAGAAATAAACGCGTTGGAATTTTTATTTAATGGGGGGGCCGCC
GGCCGTGGGCGTGAATCCACGAGCCGGCCGTATCGGCTGGCGGAGAAGCCATTTCAGGTCCATTA
CAAAGGACCTTTCTTTCGGGGAACCAAAGAAGTATCCTTTGGGCCCTTCCGATGAAACAAAAAAT
TCTTTTTTTCCCATCATATATTTTAACTCTTTCTTTCGTCATAACGCATTATTCCACCACCCATC
TCGGATCGTCAGGATGATAATTCATCTGGTTTTCGACCACAACAT
Found at i:144978 original size:21 final size:21
Alignment explanation
Indices: 144954--144996 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
144944 AAAGAATAAA
*
144954 TTTACAAAAAAATCTTTTTTT
1 TTTACAAAAAAATATTTTTTT
* *
144975 TTTACGAAAATATATTTTTTT
1 TTTACAAAAAAATATTTTTTT
144996 T
1 T
144997 GTTGCTCGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTACAAAAAAATATTTTTTT
Left flanking sequence: Indices 144454 -- 144953
CCGATGAGAAGTGGGTAACAATGTGTTTGTCCTCCGAGGAAGCCAATCGTGGATTGGAGGTTGCC
CGAGCCAAGCCCTTGGCGTTTTTTTTCGCATATCCAGGTTCCAAGGCTTCAGTTATTAAGTCCGT
TATGGGAGCAATTAGTTGTGGACGAGATCGGAGTCTTACTTGGTTGACACCGGATATCTTGCCAG
TGCTTGAGATTTCCACACTTCGGGTGCCGTAATATATTACTAATGCGCCCAAGTATTTGGCCATC
CCGGACTCTGCGTGTAAGATTTTATGTTCGTTTATGTCCAACTTCAGTTCTTCCTGCGGGAAGTT
TTGCACGGCTTTTATAATATCCAGGGCATCTCGTTTGGTGCCTATAACACCTAAAATTATGTTAT
CCGCGTACCGTAGGTACTTAAGTCTTTCTAATCCTTCTTTCTCAGCCATTTCTGGAAGCGTCTCT
CGGCCCAAGGGGCACAAAACTTTAGGGTTTCGAAAAAAGAATAAA
Right flanking sequence: Indices 144997 -- 145496
GTTGCTCGCGGTTCATCCATTCTAGGTGTTTGATGTTTTTGATGGCCTGCCCCAATTCTGTATAG
TACTTGAAGAAGGCTTTGTATTTTGAATGGATATCAACCCTTTTCCTACTATATTCTCCCGACGC
GAGGCGCATATTCGCTACATTGTATTTGGGTATGAGTATGTCTTCGACGTAGCAATCCAACTTAT
GTAGGAAGATATTGGTACAAAGCGGGGATATTATAGAGCCCTGCGGAACGCCCTCTGTGTTGTAT
CCCGTTCGATCCGTAAGGTTATATACATCTATGTATCCTGCGTTAAGTAGCTTCCGCATAAGATC
CTGCAGTGCTTTAGATCGCAGTACTGGTCCCATCTCCTTAATAAGCAGGTCGTGATGAATCTTGT
CAAAGTCTTTCTTAATATCAATTTGTACAAGCCAAGTCGGTGCCGTCCACGAGTAACGTGGGTCT
CGCAGGGCTTCATGACAGCTTCTCCCGGGGCGGAACCCGTGGCTT
Found at i:161326 original size:32 final size:32
Alignment explanation
Indices: 161287--161351 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
161277 TTGAATCGCT
161287 AAAATTTATATAAATGGATTCACTACAGCATA
1 AAAATTTATATAAATGGATTCACTACAGCATA
161319 AAAATTTATATAAATGGATTCACTACAGCATA
1 AAAATTTATATAAATGGATTCACTACAGCATA
161351 A
1 A
161352 TTGGAGCCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAAATTTATATAAATGGATTCACTACAGCATA
Left flanking sequence: Indices 160787 -- 161286
CTATTCGTTACGTGAAAGAAAGGTGAGGATCTAATAGGGGGGCTACTTGGTCCACGGGGAATAAC
CAAGTGACGGGGCCTCACTTTGACAATCGAGCCCGTAGGCTTGATTGGCGTAGTTCGGTGGCTTA
GTTCATGACAAAAAGCTTTCTGGGTACATGAAACACCAGGTCCCGTAAAATCTATTCTTTCTCAG
CAATTTCGGCGAAGTAAATCGTAGAGCCGGCCCGAAACCCAACAACCCCCGAAGCCAAAGAAGCA
CATAGTGCCTGTAGAGGCAAAGAAGTATCCTTTCCCGAATTAGCTGGTGAACGTGTAATGCGGGA
GCCGAACGACACAGTACCTAAAACCTTCTGCATAGGTAGCGCTGAGTTAGGCAGGGCCCAAGTCC
TAGCCTGGGATAGCAATGGGCAAATTTTTCAGTGGCTGAGACCGTACATAGTTGTACAAGGTACT
ATCCGTGTCTCACCATGAACCGCTCCGGACGGCAGTTGAATCGCT
Right flanking sequence: Indices 161352 -- 161851
TTGGAGCCACTGGGGTTGGTTCCCAGCGCCTCGTATCATTAATCTAGTCTTTATGGTAGCCTGGC
GCTACGCGAACAAAAAAAAATCTTTTTTTTGCTCTGCATCTTTCTAGCACTCCATGGGCAGGGCC
CTAAGGGGACTTTATTTTGTCGGACACCACAATATTGAAATACTGTCCGACAAAACAAAGGGCTA
AATTCAGGCCGAAAGTCGGCGGCCTGATCGCAGCCTCTAAGCTCTCTGCCTCTTAAGGAATCCTC
CGCAATTTCACAAAAAACTTTAGAGTATGGCCCACGAAAAAAGATATATTTGCGAAATATATCTT
TTTTATGCATAAATATTCAAGCTAAGGGATGAGGGCCGCAGGCAAAATGAAATATATATTTTATG
ACAAAAGATTTAATTCTTTCGGCGAATAACGGGATTCGAACCCGTGTTTTCAGAGCCACAATCTG
CAACTTTGACCCCTAAGTTATATCCGCCCCTATTTATAAATGAGA
Done.