Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_067638
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: 515187
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:23807 original size:11 final size:11
Alignment explanation
Indices: 23780--23813 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
23770 CAGACGGTCT
*
23780 TTTATAAGGAAG
1 TTTATAAGG-CG
23792 TTTATAAGGCG
1 TTTATAAGGCG
23803 TTTATAAGGCG
1 TTTATAAGGCG
23814 AAGGAGGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (11 bp):
TTTATAAGGCG
Left flanking sequence: Indices 23280 -- 23779
TACGCTCGAACCTCGTTCTATCAAAGCAGCTTGTAAACTCCTTGTGATGAGCTTGAAACTAGCTT
ACTTAAGAGCATAGGCTAGGCAAGGAAGCTCTCCAACAACTCTCAAATACTCGACGCCCTTTTCA
CGCTTAACATGGGAAAGAGATAGGGGTGGTAAATAAAGAGGGGAGGACAGTCATTCATGGAAATG
AAATAGGATATGCTGTCAAACTGGGTTCCTCGCCAACTGGCACTATCAATACTGTTCTCTTGTTT
AATACATTCCCCTTTTATTGTAAAGGCCTTTTTTTCTTTTCGATTCCGTGTGAATTTCATTTCCA
GTTGGAGTTGCTTTGCCCTTTGAGCCAGTGGGAGACATAAGAGAATCTCTTGCCTTCTATAAAAG
CAGTTCATTTTCATTGCATTTTGAGAAAAAGTCCATCAAGTTCAAGTTCAGTCCTACGTTCCACC
CTGCCGAGGGAAAGGGAAAAGAGGGAGTCCTATGACAGACGGTCT
Right flanking sequence: Indices 23814 -- 24313
AAGGAGGATATATACCCTTCAAAGGAGTTGGAGAGCGTCGAAGTTCTAATCTTACTATTCTTACC
CTCGTTACGGTGTGACGGATAAATCCCAATATACGAGTGTCTCACAGTTCTTGTTCACCTGATAG
TATACTCGTATCAGTAGTTGTCCCACGAAAGCCATATGAGTTGTGAATGAATAGTTTCATTCTTG
GCGGCAGTATTCGTTCCCGTGGTTGCATTTCCTTTTTTTTTTCCTCGAATGACTGCTAGCAAGTC
AATTGTGATAGAGCTCACAGACGCCAAACCTAAGGCGCTTTCAAAAGCATCAGTAGACGCAGAAA
GAGATCCTATCCCCTACGCCCTTTGCTATCGCTTGAAGCTTCCTATCGCCTGCTATCGACAGCCT
GGAATGAAAGGGAGGGCACCGACTAGCCAACCAGAAATGCTGGACCAAAGAAAACTAATTACCTT
CTCGCTACCCGTTTACTCTTCTTTCAGAGGTCGGCAAGAAAAGAT
Found at i:35296 original size:15 final size:15
Alignment explanation
Indices: 35276--35305 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35266 ATTTTTTTTT
35276 AATAATAATAATCAA
1 AATAATAATAATCAA
35291 AATAATAATAATCAA
1 AATAATAATAATCAA
35306 TAAAAGGCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATAATAATCAA
Left flanking sequence: Indices 34776 -- 35275
AAAATATGGACGTGGCTTGGGCTTGGCAAGATCCAGATCCAGGGTACTCAACTAACCCCGCGGAC
TATATTCAACCGCAAGTCAACGAGGAGGAGGGGGTCCCCCCTATTATACCTCCGGACATTCCTGT
ATTGGAGCAGCCCTTAATTCACGATGAACTAAGACGGGTCCAACTTTATAATAGACTAGGTCCGC
ATTCTTTCGTGCGGGAGTTTAACCTGAGGACTCTCGTTGACATCGTCTATCAACAGGCGGAGGTA
GAAAAAAAGATAGAGGCTGCCCTTGTTCTCGACGGGATTCCTCCAATCCGAGTTTTAAATGAATT
GAACCGCTTAAGGGGAGTTCTTTTTTATCCCCGAGGGACCCCCCTTTCGCCAGCCACTTTAGCTC
GTTATATACAACAAATTGCCCAAAGTGGCACCCGTCAAAGCATTCCTTACCGACGGGTCATAAGG
GCAATTCAAAACTATGAATTGTTCATTGATTTAATATTTTTTTTT
Right flanking sequence: Indices 35306 -- 35805
TAAAAGGCGTATATGTTGTTCAGGCCGATTAGAAGGCGCTTCCAATACTTGCTTGCTGAAAATCA
AAGATTTAAGGTCAATTTTTTTCCCACGTAGTTCGTCGGTCAAACCAACGATTTTCTTCTCAAAG
TAATAGAGAGATCTTTTTCTAGTTAGACTTCTATCAATGCAATGAAAGAACCATCCCTTCCTATT
TTTTGTCCTGTCAGATAGAAAGAAGATTATACCCCATTAAGTCCTTCTTTACCACTTTAGGGGGT
GGGGGTGAAGGGGGGGTTTACATACAACTGAGGCAAAGTGGTTTATGATTGAATCTCAAAGGCAT
TCTTTTCATTTGGTAGATCCAAGTCCATGGCCTATTTCGGGTTCACTCGGAGCTTTGGCAACCAC
CGTAGGAGGTGTGATGTACATGCACTCATTTCAAGGGGGTGCAACACTTCTAAGTTTGGGCCTTC
TTTTTATCCTATATACCATGTTTGTATGGTGGCGTGATGTTCTAC
Found at i:50062 original size:17 final size:17
Alignment explanation
Indices: 50040--50073 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
50030 CCGTATGTTC
* *
50040 TTATTTCTTTCTATTAT
1 TTATTTATTTCAATTAT
50057 TTATTTATTTCAATTAT
1 TTATTTATTTCAATTAT
50074 GAGAAGGGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTTATTTCAATTAT
Left flanking sequence: Indices 49540 -- 50039
ATTCATTCCCACCCGTGGCTTGCTACCAATTCAATGAAAGCTCGCTCCGTGGGACGCTGATGGAA
GGGCAGTGGCTTGACCCGAGGAGATGAAGGTGACTGAAGTTCCTGTGAATACAACCTATTCTTTG
TGACTGCTCTGCGGGCTTGACTTCCATAGTGACAAAGGCTTGCTCCTTCCTAACCTAACTTCAGT
GAAAAAGAAAGGAAACAAGGCGAAGAAAGGCGATGAATCTCATGTGCCTGTGCCGATTCATCCCT
ATTACCAGTACCAGCTGACTCGCTTTCTTTCTGTCTTATCTTCTAATACAGAAATAGGAGATAGA
GAATTACAGAGACAGAGGTTGAGGTTATAAGTGTTGGTTCGGTAAGGGGTGATTATGCCTTTGCT
TGTGTGCCCACGGGCTTTCCTAGTGCAACCATCCTTTCTATTGAAAACTTCAGTATAGAAGTAGC
TGACAGGCAGGGTAGCTGACTTGCGATTCCTACTCCCGTATGTTC
Right flanking sequence: Indices 50074 -- 50573
GAGAAGGGCTTGCGTAACCCCTGGCTCAAAACCACCCGTTAGAGCAGCGAGCTGGTTACTGCTTG
AAGTCGAAGGCGGGAAAGGGGTAATGGATAGAGGATTGGACGGGCTTGCTTTAACCGAAGGGGAG
AGTGACGCTTAAGTCGAACAAGCAGTTCACCACTAGAACGAAGGGCTTACACGAGACCTAGTCCC
CTCTCATTGGCCAGTCGGTACTAAACTTCCTCGTCTTCCTTATTCGCCTCTCTCATCAGATCCTA
CTAGTCCAGTCCGTTCCTCATCGTATCAGATCGACGACTAGACAAAGAAAGTACAGCGTCATGCT
GGTTCGCTGGCTGGCCTTTTGCTATAGCTTCTATATCACAGTAGGCTCAACCAACGTAGCGCTGC
GCTTGATTGGATATTGCTTGCTAGTTTTTTTTGGATGAAATTTTTAGTGGCACTCAAGGTCTTGC
CAATTGAGATTACTCATTTTCTTCATAAAGCAGAAGCGCCTTTGC
Found at i:138636 original size:33 final size:30
Alignment explanation
Indices: 138568--138640 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
138558 CAGAATGGTC
138568 CCTACTACTCAAAACTAAGAAGGGATGCCA
1 CCTACTACTCAAAACTAAGAAGGGATGCCA
*
138598 CCTACTACTCAAAACTAAGAAGGGATGCCG
1 CCTACTACTCAAAACTAAGAAGGGATGCCA
138628 CCTACTACT-AAAA
1 CCTACTACTCAAAA
138641 TCCCGGTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 4 0.10
30 38 0.90
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.18
Consensus pattern (30 bp):
CCTACTACTCAAAACTAAGAAGGGATGCCA
Left flanking sequence: Indices 138068 -- 138567
AGAGAACTTACAATAATACAACGCCGCATTCTCCGAAAATTGAGAAAGAAGAAAAGATATATTAA
GAAAAAGATTTATCCGAGAAAAAATCGTAACAGTTACATCCAATTACAAACTACACGAAAGTTGC
CCCTTTTTCATGGGAATTTACCCATCACAAAGATGCACAGAGGAACAAAACGAACTTCATATATC
CCTTTTCTACTCAATCCAGAAACAAGATTGGACGTTATTCCGGTTCGTCTCCATTTTTGTGAAAC
TATTCCTCAAGCAAGGCAGCCGATAAGTCATCGAAAAGTGTGTGTGAATAATTCCATACTAAACA
TTACTCATTTTAAAGTTTCCCACGGTGATATAATATCTTTTCAAGAAAATTACGCGAGAACCCGC
GGTGAAGAAATAAGGAGATCTTTCTATATCAAAATCTCAGTTGAAAAAATAATAGGAAAATACCT
GGGTCACCGGGTAAGAATGCGGGGAAGAGCCAAAACAGAATGGTC
Right flanking sequence: Indices 138641 -- 139140
TCCCGGTTTTTGCAAAAGTTACGTTCTTCTATGCTTAAAGAAGACTTAGAAAGGACAAAGAAGTT
TGGATCCGAAAAAGTATGCTTAGGCAGTTCCTTCGCGGAGCACAGTAGAATGAAGAGGAATTTGT
ATCAGTATCATTTCAAATCCTTATTCTTATGGAAGAAGAGAAGGAACGAGAAAAACCGATATCTT
CCTATTATAGATCCAAGAAGTTCTATAGTTTACAACTCTTCTTTATATAGTAAAAAGATCTATTG
CTCTGCATACTCCCATCAGTTTACTATGAAGAGAAGGAAGAGAAGAATCAAAAGGATCGAACTAC
CTACTCATTATTCGGAGGTCAATCATAGAACACTAAAAGCTGTGGTATCTTATGGACCTAACATA
GATCACATCCCTCACGACATAAGATTGAAAGATCCAAACCTTCCTCTTCGGAGCGGAAACGGACG
TGGCCAAAACATATAAAGATCGGCGTAGTCGCTCATAGGGACATA
Found at i:199571 original size:18 final size:18
Alignment explanation
Indices: 199548--199590 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
199538 CGCCAAAGTT
199548 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
199566 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
199584 GACTATG
1 GACTATG
199591 GTAGGTTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 199048 -- 199547
CGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGAGAC
AGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTACCTT
AGGACAGTTAGAGTTACTGCCGCCGTTTACTGGGGCTTCCATTCAAAGCTTATAACACTTTTCCT
TCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGTCCT
GTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGAGAG
CACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAGCGC
CCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGATCGC
CCTCCCAATTCGAAGTTTTTTCCTGGAAGCCTAAACGCCAAAGTT
Right flanking sequence: Indices 199591 -- 200090
GTAGGTTCTGCAAGGCTTTGATGACTCAAGGTTCATCAACGGGAAAGGAGAGTGAGGGGAAGAGG
CGACGAGAGTCGGCCCGATCATCCAATTCGCTCCTTAAGACAGGCATGGTTCTGTAGTCAAAGCA
ACTTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTCGGGGGTTCCTTAGGGACCGATTCA
CTCTGCGTAGATTGACTGAACGCAGAAAGCCTTCCACTGGCAGGCGATCGTGTTTTTCACAGGAT
TTATCGTTACTCATGTCAGCATTCTCACTTCTGATATCTCCAGGTCTTGTCACCAAAAACCTTCC
CCGATTGACAGAACGTCCCGCTACTGACACTTGAAAAAGCAGCTTTCAAGGTCTCGTCGCTTCGG
TGAATCACTTGAGCCCTGATACATTTTCGGTGCCATGGAGCTAGACCAGTGAGCTATTACGCTTT
CTTCAAAGGATGGCTGCTTCCAAGCCCACCTCCTGGTTGTCATCG
Found at i:333577 original size:23 final size:25
Alignment explanation
Indices: 333551--333602 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
333541 TTTTTTGACT
*
333551 ATTATCCATTT-TTCTCTTT-CTTC
1 ATTATCCATTTATTCGCTTTGCTTC
*
333574 ATTATTCATTTCATTCGCTTTGCTTC
1 ATTATCCATTT-ATTCGCTTTGCTTC
333600 ATT
1 ATT
333603 TTTGAACTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.42
25 7 0.29
26 7 0.29
ACGTcount: A:0.15, C:0.23, G:0.04, T:0.58
Consensus pattern (25 bp):
ATTATCCATTTATTCGCTTTGCTTC
Left flanking sequence: Indices 333051 -- 333550
TAACCAAGCGGACAATGAGTTTTTTGAATTCCTTTTCTTCCCAAGAACGTCAGGGTCTACGGGCA
AGCGCTAGTGCTTTTGCTCAGACAGCCTTTCCTACCGAGGTGAGTAAGCGTCAGCTCCCTCCTTG
ATTCCATTCTTCGTTCCTTCCTACTGGCTACTGGTAGGGACATTTCCCTAAAATAAATCCTAAAC
TGCTTCTATTTTCATAGGGTCGTAAGAGAAAGAAGTTCAGGCACAGAGGTGTCCTCGAAGACAAA
TGAACAATGCCATATTTATTTGAATAAGGCTAATGTTAGCAAATAAGAAAATGAAAAATGGAAAG
GAAAGCATAACATACCCAACTCGAATGAATAAAAGGGAAATAAAAAAGAATTCTGCAAGTGGCAC
AAGACTTTTGCACATGTCACTAATAACCGTGTAGTTTTCCGAAGCCTTATTCTTTCCCCTCATTT
TTTTTTTGCCAATAATCAGTGATCATATCACTGATTTTTTTGACT
Right flanking sequence: Indices 333603 -- 334102
TTTGAACTGCTCTGCTCCTCCCAACAAGAGGAAAGACTTGTTTGTTGTCAATCGCTGGTTGGGTT
TACCAATCGAGAAAGACATGGGAAAAAGGCTTTTGTCCAACAAAGAAATGGGATTTTTTCTCGCA
CGTCGCACCTAATTGTCTGTGACTACACTACGCTATTTTAATCGATACAGTAATTAAGATTCCAT
TGTGACAATAGCTTTTAAGCAAGCAGCTTGTATTCGTATAATAAAATGTGGTGCTCAGTCAAGTG
AGGCACTACAGGTATTGGATTCAGCTTGAACTAGAAGTTGTTCCCAGTGAAAAGGAACGAAGTCA
CTCGACCAACAGGAAAGCAATTTATTGCTTACTTGATTAGAGTAAGGAAGGAGCTCTATCTTATT
TAAGTAATATGTCAGGTCAGAGTTCATTCTTACCCGTTCTCTAGGAACTTGCATTCGATGCCATC
TAGTTAGCTAGTTAACATTCGATCTCCCCAGAACATCATTCTGCT
Found at i:361319 original size:39 final size:39
Alignment explanation
Indices: 361264--361339 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
361254 CCCATCCTTC
*
361264 AATATCATGATTGGGTCAACCAGGCCAGATCATGAGTCA
1 AATATCATGATCGGGTCAACCAGGCCAGATCATGAGTCA
*
361303 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGT
1 AATATCATGATCGGGTCAACCAGGCCAGATCATGAGT
361340 GAATTGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (39 bp):
AATATCATGATCGGGTCAACCAGGCCAGATCATGAGTCA
Left flanking sequence: Indices 360764 -- 361263
CAATGGGTTGTAGCATTTTCGCACTTTTTGTCGTCAGGATGTAAAAGAGGGCTTTCTCGTCTAAA
GGCAGGGGTGAGCTTTCTCGCTATAGAATTCGAACTACGAACGAAAGACCAACGAGGATTCAGGA
GGAGAAGGAGTAGGAGCTAGCTTTCATTGAAGCAGAGGCACGAAGTAGCGAAGAAATTCGATTAA
TTAAAAGAAAGGGGCGTTCACTTACTGTTTGCTTGCATTAAGGTTTTTTCTCGACCAGAGTCCTA
AGTGTGAAGAACTCAAATTGAAAATCGTTTCTATCCCACGAATCCAAAACGCATTTTGGAAAGCC
GAGGTTACTGGAAGTAACCACGCCACTGATTTATCCAACGAAAGCAATCGACATGATGATTCGTA
GCGAAAACTCTAAAAATCCTGAAGGAAGAAAAGATTGAAGAGATTCGATGAAGCACCTGAATCCA
CTTTTATCGAGATCCGGAGTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 361340 -- 361839
GAATTGAAAATCGAAAACGTACATAGCTGTTCCAGCTGAAATACTTGGAATAATTCTACCACTTC
TACTAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAG
GGTCCTGATGTAGTGGGATCGTTCGGATTGTTACAACCTCTAGCAGATGGTTCGAAATTGATTCT
AAAAGAACCTATTTCACCAAGTAGTGCTAATTTCTCCCTTTTTAGAATGGCTCCAGTCACTACAT
TTATGCTAAGTCTGGTTGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATCCG
AACATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGG
TTGGTCTAGTAATTATAGGGGGCGGCCGTTCGGTCGCCTATGATAAACGGACCAATAGGTCAAAA
ATTGCTTTGTGCCGCAGGTGTTGAACGATCTACTCTACACAGGTG
Found at i:363956 original size:18 final size:18
Alignment explanation
Indices: 363933--363967 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
363923 CCCTTGTTAT
363933 AAATATTTAATTAAAAAA
1 AAATATTTAATTAAAAAA
*
363951 AAATATTTATTTAAAAA
1 AAATATTTAATTAAAAA
363968 GTTCAGAGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATATTTAATTAAAAAA
Left flanking sequence: Indices 363433 -- 363932
AGGTGAAAATGTCATTCTCTCCGAGCCTTGCTTGTCCTCATAGATGCGGATATTAGCTTAGGTAA
CGTCAAAGAAAAGATCATAAGAGAAGCGTTATGCAGATATCAGTCTCGGTAATCGACTTCAGTGG
TGGGGCAAGTATCTTAACGAATAGGAAGAACATTTCTTCCCAGAGTACGAGATAGCTACTCAGAC
CCCCAGTCGACGTATCGACTTCAGGAGACCACCTACAAAGTTGTCAGGAATAGCGGCCTTAAGGG
CTAACAAAATAGTAGAGGCCAACTATTCTCTTTCAAACTTCCGTCATTGATCCCTTTCGTGAGGC
AAGGTAGCCGTACTGGAAGGTGCGGCTGGATCACCTCCTTTTTCAGGGAGAGCTAATGCTTGTTG
GGTATTTTGCTTTGACACTGCTTCACACCCAAAAAGAAGCGAGCGACGTCTGAGTTAAAGAAAGA
GATGGAAGTCTTCTTTCCTTTCTCGCTTGTAGCAGCCCTTGTTAT
Right flanking sequence: Indices 363968 -- 364467
GTTCAGAGGCCTCTACGTCAGCCGGATCCCAGGCTCCAGATAAATTCTCAGCCTCTACTACAGTT
AACCTTCATTTTATAGGTGGTATAGCTTATTACCAACCTCGGCCGTGCGACCTGCCTATTTGGGA
CGAGTCCGCGGACGAATCCTGAAAGAGACATGATAATAGGAGGGAAGAACATATTATATATATAA
ATATACGGAGCTAAACGCTTAACCTGAGCTAATACGCTCAAACTGACGAATCTGTAAAAGTTTTG
TTGTCCCGGATAGGGTCGAAACCATGGGCCCGCTTACCACAAGAGAAGTCCGGAATAGACGCGCA
ATTCGTTTGCACTTCAAGGCGAAATGAAGATCAGTCGCAATTCCCGCATCATTTGGATGTAGAAA
GAGAGAAGTCCCTTGGTTGGAGAATTCTTTACTTTGAGTTCAACGCGAGATAACGCGCTTAGCTA
AGTGAAAAGGGGAAGCGGAGCTATTCTCATAAAAATATTGAATTG
Found at i:364208 original size:19 final size:18
Alignment explanation
Indices: 364170--364208 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
364160 TAAATATACG
* *
364170 GAGCTAAACGCTTAACCT
1 GAGCTAAACGCTCAAACT
364188 GAGCTAATACGCTCAAACT
1 GAGCTAA-ACGCTCAAACT
364207 GA
1 GA
364209 CGAATCTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.21
Consensus pattern (18 bp):
GAGCTAAACGCTCAAACT
Left flanking sequence: Indices 363670 -- 364169
GTCAGGAATAGCGGCCTTAAGGGCTAACAAAATAGTAGAGGCCAACTATTCTCTTTCAAACTTCC
GTCATTGATCCCTTTCGTGAGGCAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCACCTCCTTTT
TCAGGGAGAGCTAATGCTTGTTGGGTATTTTGCTTTGACACTGCTTCACACCCAAAAAGAAGCGA
GCGACGTCTGAGTTAAAGAAAGAGATGGAAGTCTTCTTTCCTTTCTCGCTTGTAGCAGCCCTTGT
TATAAATATTTAATTAAAAAAAAATATTTATTTAAAAAGTTCAGAGGCCTCTACGTCAGCCGGAT
CCCAGGCTCCAGATAAATTCTCAGCCTCTACTACAGTTAACCTTCATTTTATAGGTGGTATAGCT
TATTACCAACCTCGGCCGTGCGACCTGCCTATTTGGGACGAGTCCGCGGACGAATCCTGAAAGAG
ACATGATAATAGGAGGGAAGAACATATTATATATATAAATATACG
Right flanking sequence: Indices 364209 -- 364708
CGAATCTGTAAAAGTTTTGTTGTCCCGGATAGGGTCGAAACCATGGGCCCGCTTACCACAAGAGA
AGTCCGGAATAGACGCGCAATTCGTTTGCACTTCAAGGCGAAATGAAGATCAGTCGCAATTCCCG
CATCATTTGGATGTAGAAAGAGAGAAGTCCCTTGGTTGGAGAATTCTTTACTTTGAGTTCAACGC
GAGATAACGCGCTTAGCTAAGTGAAAAGGGGAAGCGGAGCTATTCTCATAAAAATATTGAATTGG
TCCAACAGGGAGTCCGGGCCGTGTCTCAGTCCCAGTGTGGCTGATCATCCGAAAAGACCAGCTAC
TGATCATCGCCTTGGTAAGCTATTGCCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTCGGG
CGGATTCCTCCTTTTGCTCCTCAGCCTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCT
CCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGA
Found at i:410908 original size:36 final size:36
Alignment explanation
Indices: 410847--410918 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
410837 TTTATACCTC
* * *
410847 ACTGTGGCCACAATTATTGAGAAGATATCTGATTTG
1 ACTGTGGCCACAATAATGGAAAAGATATCTGATTTG
*
410883 ACTGTGGCCACTATAATGGAAAAGATATCTGATTTG
1 ACTGTGGCCACAATAATGGAAAAGATATCTGATTTG
410919 TAGGACCTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (36 bp):
ACTGTGGCCACAATAATGGAAAAGATATCTGATTTG
Left flanking sequence: Indices 410347 -- 410846
GATAGTGCCGGTAGAAGGCATAATGCAGCGGATCTACTGAGCAATGCAAAACCTTCAAACATAAA
GGTTTCTGTTCCTGCAAGTGTGGAGAGGTTTCTACTTGCTACTTCCTCTTCCTCTGCAGTAGATA
ACTCAAAATTATCAGCAATTGGAGTGGTGTACCGTGATGCTTTTGGTCACTATCATCACAGAATG
GTGCGTGATAATGGAGGAGAGGTTAGACTTTCATCCGGTGCAATGGGCAGTCCTCAGCTTCTGCT
ATTGAGTGGTATTGGTTGACGGCCATACCTTTCTGAATGAGGCATTTCCCTTGCCCTGCACTTGC
CATATGTGGGTCAATTCCTCTATGACAACCCAAGAAATGGTATAACCCTTCTTCCTCCAAAGCCT
GACGAGCATTGGCTTATTCAGGTGGTGGGTATAACTGAATCTTGGTCCTACCTTTTTCCTCCCCT
GCCCACTCGCACTTCATTAGACAACCATCTTCTCCTTTATACCTC
Right flanking sequence: Indices 410919 -- 411418
TAGGACCTACATTGCCCATTGATCAATCAAATGATATGCTAATGAGTGATTTCTTTCTGCCGCCG
GACAGTGAGCACCATTTGGCATTACCACAGGGGCTGCCTTGTGGATAAAGTTGTAGACAGTGACC
TCCGGGTGATCGGTATTAATGCCCTCCGAGTTGTTGATGGCTCAATATTCACAGTGTCTCCAGGA
ACCAATCCCCAGGCTACTCTGATGATGCTTGGCGGGTGAGTTGTTGCAGTAAATTTTATTCATAG
TTATTTTGTGTATCCCTTTTTTTTTCATTTGTGTTCTCTATGTCCGGCTTCTCAAAGCTAATACA
TTCTGCACCTGCCATGAGAAAATTACTACGATTACATAATAGTTGGAGGTGGCACGGCTGGGTGT
CCATTAGCAGAAACGATGAACTGAACCAAGAGGGCTTCTTGCCCACCCTCTTGCAGGTGGATACA
TTTGACTCCCCAGCACAAGCATTTACTTCAGAAGATGGTGTGCCT
Found at i:481474 original size:18 final size:18
Alignment explanation
Indices: 481451--481493 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
481441 CGCCAAAGTT
481451 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
481469 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
481487 GACTATG
1 GACTATG
481494 GTAGGTTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 480951 -- 481450
CGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGAGAC
AGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTACCTT
AGGACAGTTAGAGTTACTGCCGCCGTTTACTGGGGCTTCCATTCAAAGCTTATAACACTTTTCCT
TCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGTCCT
GTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGAGAG
CACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAGCGC
CCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGATCGC
CCTCCCAATTCGAAGTTTTTTCCTGGAAGCCTAAACGCCAAAGTT
Right flanking sequence: Indices 481494 -- 481993
GTAGGTTCTGCAAGGCTTTGATGACTCAAGGTTCATCAACGGGAAAGGAGAGTGAGGGGAAGAGG
CGACGAGAGTCGGCCCGATCATCCAATTCGCTCCTTAAGACAGGCATGGTTCTGTAGTCAAAGCA
ACTTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTCGGGGGTTCCTTAGGGACCGATTCA
CTCTGCGTAGATTGACTGAACGCAGAAAGCCTTCCACTGGCAGGCGATCGTGTTTTTCACAGGAT
TTATCGTTACTCATGTCAGCATTCTCACTTCTGATATCTCCAGGTCTTGTCACCAAAAACCTTCC
CCGATTGACAGAACGTCCCGCTACTGACACTTGAAAAAGCAGCTTTCAAGGTCTCGTCGCTTCGG
TGAATCACTTGAGCCCTGATACATTTTCGGTGCCATGGAGCTAGACCAGTGAGCTATTACGCTTT
CTTCAAAGGATGGCTGCTTCCAAGCCCACCTCCTGGTTGTCATCG
Found at i:514383 original size:16 final size:16
Alignment explanation
Indices: 514362--514399 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
514352 TAGTACATAA
*
514362 TCACTGATAGCATCAT
1 TCACTGAGAGCATCAT
*
514378 TCACTGAGAGGATCAT
1 TCACTGAGAGCATCAT
514394 TC-CTGA
1 TCACTGA
514400 AATTCACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (16 bp):
TCACTGAGAGCATCAT
Left flanking sequence: Indices 513862 -- 514361
TACTGACAGAGAACTTAAGAACTACCAATAAGCCTGACGGCAGACAGCTAACATGGTAAATGTCG
TCTTCCTTTACAATGACTTCTTCCTTTCCTCTTCACCATACGAAATTCGAGCTCACCCTCGGATC
AGGGATACCTTAAGTCAGCAGCTTCCTTTGAAGATAGGGCATTTACATAAACTCCGAAGCCGTAC
CCAGGGAGCTTACATCAGGAAACTCCCAAGCTTGCCGAGGAAGGAACAAAAGAGAGAAAGACACC
GTCCAACCGCTTATATATGTGCGCGTACCACTTTCGTCTATCTTTACACTCTGCGCTCCCTTAGA
TCATTGGCTACCAGAAAGAAGCAAACTCAGGAACATCAATATGGTTAGGGATCATTAAGGTACGG
CCCGACGCCTATTCCTTTCTGCCTTTTGAACGAATCGTCAACCTCAATTAGCAGATTCATTAGAA
ACCCTTCTTGGAAGACTCAATTCATTAGATAAGCCTAGTACATAA
Right flanking sequence: Indices 514400 -- 514899
AATTCACAAAGAAATTAATGGGCATTTTGAAGCAAGTTGATCTGCGAAGACTAACCTCGTAGCTC
ACTTATATCAATCAGTTCAAGCATTGACAAACCCGCCTTCCTTCTGTGTTCAGGACGGAGAAGAC
TCTTTCTGCCTTTGTCGAACTGCCTTGACGCGCAGGCTTTGACCTGCTTTCAAAAGCTTACCGGA
GAGCAGATTCTTTATTACTGACTTTTCGCGGTTGATCGCACCTCGCACCTAAATCGGTCCTTGTG
AGGAGGAGGTTCCAAGGGGCATACATTTCTCCGACCAGGTCAAGTTGCACTTTAGATTATGGATG
GAGATAAAGTTTTCATCAGCAGACCGCCAATGACCCACATAGATTCCCTGCCAGCACTTTTTAGA
AGATAAAACCTATAATATGTGGGCCCTTGAGTGCCCACTTTGATGGTGATTGCATTCGCCTATTC
TATCCCCAGTCCCTTGCTGCAAGAGCAGAAGTCTTTAAGCTTTTC
Done.