Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 79 of 79
Found at i:26504990 original size:263 final size:262
Alignment explanation
Indices: 26504484--26505678 Score: 1843
Period size: 263 Copynumber: 4.6 Consensus size: 262
26504474 TGATCCTAAA
* * *
26504484 CAGGTGTTGTTGTACATTAGTCTCTTAAAGTGCTA-CCCTATTCCCCCGAA-TCTGGTTTTCTTT
1 CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTC-GGTTTTCTTT
* * *
26504547 GGACCGATTTCGGTGATGAATTGGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACA
65 GGACCGATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAA-AAATATTATTACATTGACA
* *
26504612 AATGCTTTAAATTGGATATGTAGATTCAGCTATGAGAATGCATACATTTATTTATATATGTGTGT
129 AATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGT
26504677 GATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTC
194 GATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTC
26504742 CTAG
259 CTAG
*
26504746 CAGGTGGTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTT-TTTG
1 CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTTCTTTG
* * *
26504810 GACCGATTTTGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAGTATTATTACATTGACAAT
66 GACCGATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAA
* * * *
26504875 TGCTTTAAAATGGATATGTACATTCAGCTGTTAGAATGCATATATTTATTTTTATAAGTGTGTGT
131 TGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATAT-A-TGTGTGT
* *
26504940 GATGCAGTGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTA
194 GATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTC
26505005 CTAG
259 CTAG
* *
26505009 CAGATG-T--TGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAA-TCTGGTTTTCTTC
1 CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTC-GGTTTTCTTT
*
26505070 GGACCGATTTCGGGGATGAATC-AGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGAC
65 GGACCGATTTCGGCGATGAATCGA-AACTCTTTGTTACCTTGAAAA-AAATATTATTACATTGAC
*
26505134 AAATGCTTTAAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTG
128 AAATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTG
*
26505199 TGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTT
193 TGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTT
26505264 CCTAG
258 CCTAG
* * * * * *
26505269 CAGGTGTTGGTGTACTTTAGTTTCTTAAAGTGCTATCCCCATTCGCCCTAATCCTGTTTCCTTTG
1 CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTTCTTTG
*
26505334 GACCGATTTCGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAGAATATTATTACATTGACAA
66 GACCGATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAA-AATATTATTACATTGACAA
* * *
26505399 ATGCTTTAAATTGGATATATACGTTCAGCTGTGAGAATGCATACATTTATTTATATATGCGTGTG
130 ATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTG
* * * *
26505464 ATGCAATGTTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCTCATCTCCAAGCTTGTTTCC
195 ATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCC
26505529 TAG
260 TAG
* * *
26505532 CAGGTGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTG
1 CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTTCTTTG
* * * *
26505597 GACCGATTTCGACAATGAAT-TAGAATTCTTTGTTACCTT-AAAAAAATATTATTACATTGACAA
66 GACCGATTTCGGCGATGAATCGA-AACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAA
26505660 ATGCTTTAAATTGGATATG
130 ATGCTTTAAATTGGATATG
26505679 CTTGTTTTTT
Statistics
Matches: 854, Mismatches: 64, Indels: 31
0.90 0.07 0.03
Matches are distributed among these distances:
259 2 0.00
260 126 0.15
261 150 0.18
262 153 0.18
263 420 0.49
264 3 0.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (262 bp):
CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTTCTTTG
GACCGATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAA
TGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGA
TGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCCT
AG
Found at i:26505503 original size:523 final size:524
Alignment explanation
Indices: 26504491--26505678 Score: 1956
Period size: 523 Copynumber: 2.3 Consensus size: 524
26504481 AAACAGGTGT
*
26504491 TGTTGTACATTAGTCTCTTAAAGTGCTA-CCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGAT
1 TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGAT
* *
26504555 TTCGGTGATGAATTGGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
66 TTCGGCGATGAATTAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
26504620 AAATTGGATATGTAGATTCAGCTATGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
131 AAATTGGATATGTAGATTCAGCTATGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
*
26504685 GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCCTAGCAGG
196 GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGG
* * *
26504750 TGGTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTTTTTGGACCG
261 TGGTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCCATTCCCCCTAATCCGGTTTCTTTGGACCG
* * *
26504815 ATTTTGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAGTATTATTACATTGACAATTGCTT
326 ATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTT
* * * * *
26504880 TAAAATGGATATGTACATTCAGCTGTTAGAATGCATATATTTATTTTTATAAGTGTGTGTGATGC
391 TAAAATGGATATATACATTCAGCTGTGAGAATGCATACATTTATTTATATAAGTGCGTGTGATGC
* * * *
26504945 AGTGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTACTAGC
456 AATGCTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCTCATCTCCAAGCTTGTTTACTAGC
26505010 A-GA
521 AGGA
* *
26505013 TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATCTGGTTTTCTTCGGACCGAT
1 TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGAT
* *
26505078 TTCGGGGATGAATCAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
66 TTCGGCGATGAATTAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
*
26505143 AAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
131 AAATTGGATATGTAGATTCAGCTATGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
26505208 GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGG
196 GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGG
* * * *
26505273 TGTTGGTGTACTTTAGTTTCTTAAAGTGCTATCCCCATTCGCCCTAATCCTGTTTCCTTTGGACC
261 TGGTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCCATTCCCCCTAATCCGGTTT-CTTTGGACC
*
26505338 GATTTCGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAGAATATTATTACATTGACAAATGC
325 GATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAA-AATATTATTACATTGACAAATGC
* *
26505403 TTTAAATTGGATATATACGTTCAGCTGTGAGAATGCATACATTTATTTATAT-A-TGCGTGTGAT
389 TTTAAAATGGATATATACATTCAGCTGTGAGAATGCATACATTTATTTATATAAGTGCGTGTGAT
* *
26505466 GCAATGTTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCTCATCTCCAAGCTTGTTTCCTA
454 GCAATGCTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCTCATCTCCAAGCTTGTTTACTA
*
26505531 GCAGGTGT
519 GCA-G-GA
*
26505539 TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACCGAT
1 TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGAT
* * *
26505604 TTCGACAATGAATTAGAATTCTTTGTTACCTT-AAAA-AAATATTATTACATTGACAAATGCTTT
66 TTCGGCGATGAATTAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
26505667 AAATTGGATATG
131 AAATTGGATATG
26505679 CTTGTTTTTT
Statistics
Matches: 619, Mismatches: 41, Indels: 10
0.92 0.06 0.01
Matches are distributed among these distances:
522 27 0.04
523 344 0.56
524 87 0.14
525 71 0.11
526 90 0.15
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (524 bp):
TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGAT
TTCGGCGATGAATTAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
AAATTGGATATGTAGATTCAGCTATGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGG
TGGTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCCATTCCCCCTAATCCGGTTTCTTTGGACCG
ATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTT
TAAAATGGATATATACATTCAGCTGTGAGAATGCATACATTTATTTATATAAGTGCGTGTGATGC
AATGCTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCTCATCTCCAAGCTTGTTTACTAGC
AGGA
Found at i:26510614 original size:39 final size:39
Alignment explanation
Indices: 26510571--26510688 Score: 236
Period size: 39 Copynumber: 3.0 Consensus size: 39
26510561 ACGCTGAAAT
26510571 AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
1 AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
26510610 AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
1 AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
26510649 AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
1 AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
26510688 A
1 A
26510689 TATTAAACCG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (39 bp):
AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
Found at i:26511471 original size:51 final size:51
Alignment explanation
Indices: 26511412--26511515 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 51
26511402 TCGGTGACAA
* * * * *
26511412 TAACAGTAACAGTATTTGGCGCACAAACTGTTGAATCGGTAACAGTAACAG
1 TAACAGTAACAGTATTCGACACACAAACTATCGAATCGGTAACAGTAACAG
* *
26511463 TAACAGTAATAGTATTCGACACACAAAGTATCGAATCGGTAACAGTAACAG
1 TAACAGTAACAGTATTCGACACACAAACTATCGAATCGGTAACAGTAACAG
26511514 TA
1 TA
26511516 GTCAGCACGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (51 bp):
TAACAGTAACAGTATTCGACACACAAACTATCGAATCGGTAACAGTAACAG
Found at i:26511505 original size:45 final size:46
Alignment explanation
Indices: 26511313--26511515 Score: 162
Period size: 45 Copynumber: 4.4 Consensus size: 46
26511303 TAATCAGTAA
* * * *
26511313 CGGTAGCAGTAACAGTAACAGTATTCAACACACAAAGT-GCTGAAT
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGGAAT
* * * * * * *
26511358 CTGTAATAGTAACGGTAATAGAATTCGACACACAAAGT-GCCGAAT
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGGAAT
* * * * *
26511403 CGGTGACAATAACAGTAACAGTATTTGGCGCACAAACTGTTGAATCGGTAA-
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAA--G-T--ATCGG-AAT
* *
26511454 CAGTAACAGTAACAGTAATAGTATTCGACACACAAAGTATC-GAAT
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGGAAT
26511499 CGGTAACAGTAACAGTA
1 CGGTAACAGTAACAGTA
26511516 GTCAGCACGT
Statistics
Matches: 122, Mismatches: 28, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
44 2 0.02
45 80 0.66
46 3 0.02
47 1 0.01
48 2 0.02
49 1 0.01
51 31 0.25
52 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (46 bp):
CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGGAAT
Found at i:26514598 original size:73 final size:73
Alignment explanation
Indices: 26514481--26514642 Score: 236
Period size: 73 Copynumber: 2.2 Consensus size: 73
26514471 ATTTCATCCT
* * *
26514481 TTTATATTTGTTTTATCTATTTATTTATTTATTTGTTATTCTTTTA-CTTTTCAAACATTTAAAT
1 TTTATATTTGTTTTATCTATCTATTTATTTATTTATTATTCTTTTACCTTTT-AAACACTTAAAT
* *
26514545 TTGATATTA
65 TTAATATCA
* **
26514554 TTTAAATTTGTTTTATCTATCTATTTATTTATTTATTATTCTTTTACCTTTTAAATGCTTAAATT
1 TTTATATTTGTTTTATCTATCTATTTATTTATTTATTATTCTTTTACCTTTTAAACACTTAAATT
26514619 TAATATCA
66 TAATATCA
26514627 TTTATATTTGTTTTAT
1 TTTATATTTGTTTTAT
26514643 TTATTTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 74 0.94
74 5 0.06
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (73 bp):
TTTATATTTGTTTTATCTATCTATTTATTTATTTATTATTCTTTTACCTTTTAAACACTTAAATT
TAATATCA
Found at i:26514877 original size:13 final size:12
Alignment explanation
Indices: 26514846--26514894 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
26514836 GAGTATGACT
26514846 TTTTTATTTTATC
1 TTTTTA-TTTATC
*
26514859 TTTTTATTTATT
1 TTTTTATTTATC
*
26514871 TTCTTTATTAATC
1 TT-TTTATTTATC
*
26514884 TATTTATTTAT
1 TTTTTATTTAT
26514895 TTATGTCATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 15 0.50
13 15 0.50
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATTTATC
Found at i:26515295 original size:32 final size:32
Alignment explanation
Indices: 26515253--26515318 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
26515243 GTGTCCTAAT
26515253 TTACGAGACATGATCCTTCATTCTCGATTAAC
1 TTACGAGACATGATCCTTCATTCTCGATTAAC
* *
26515285 TTACGGGACATGATCCTTCATTCTTGATTAAC
1 TTACGAGACATGATCCTTCATTCTCGATTAAC
26515317 TT
1 TT
26515319 GAAATAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (32 bp):
TTACGAGACATGATCCTTCATTCTCGATTAAC
Found at i:26519432 original size:33 final size:32
Alignment explanation
Indices: 26519374--26519438 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
26519364 TAGAGTGTGA
26519374 ATTAAATTAGAAAAGTAAATAAATTTAGATAGG
1 ATTAAATTAG-AAAGTAAATAAATTTAGATAGG
*
26519407 ATTAAATTAG-AATTAAAGTATAATTTAGATAG
1 ATTAAATTAGAAAGTAAA-TA-AATTTAGATAG
26519439 AAATTCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 6 0.21
32 2 0.07
33 21 0.72
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (32 bp):
ATTAAATTAGAAAGTAAATAAATTTAGATAGG
Found at i:26520153 original size:21 final size:21
Alignment explanation
Indices: 26520079--26520189 Score: 107
Period size: 23 Copynumber: 5.1 Consensus size: 21
26520069 CGGCTTTGCC
*
26520079 TATCAGGCACTTTATGTGTTG
1 TATCAGGCACTTTATGTGTCG
*
26520100 TACATCAGACACTTTATGTGTCG
1 T--ATCAGGCACTTTATGTGTCG
26520123 TATCTCAGGCACTTTATGTGTCG
1 TA--TCAGGCACTTTATGTGTCG
* ** *
26520146 TATCAGGCACCTCGTGTGTCA
1 TATCAGGCACTTTATGTGTCG
* *
26520167 TTTCAGGCA-TTTATATGTCG
1 TATCAGGCACTTTATGTGTCG
26520187 TAT
1 TAT
26520190 ACTGATCAGG
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
20 8 0.11
21 25 0.35
23 39 0.54
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (21 bp):
TATCAGGCACTTTATGTGTCG
Found at i:26522843 original size:9 final size:9
Alignment explanation
Indices: 26522814--26522850 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
26522804 TGAGTTTTCG
26522814 AATTCGAAT
1 AATTCGAAT
*
26522823 AACTCGAAT
1 AATTCGAAT
26522832 AATTCGAAT
1 AATTCGAAT
*
26522841 AATTCAAAT
1 AATTCGAAT
26522850 A
1 A
26522851 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:26523254 original size:17 final size:18
Alignment explanation
Indices: 26523227--26523287 Score: 72
Period size: 17 Copynumber: 3.4 Consensus size: 18
26523217 CTCCCCCCAA
26523227 TTTACTTTCCCTCAAACT
1 TTTACTTTCCCTCAAACT
*
26523245 TTTA-TTTCCC-AAAACTT
1 TTTACTTTCCCTCAAAC-T
*
26523262 TTTATTTTCCCTCTAAACT
1 TTTACTTTCCCTC-AAACT
26523281 TTTACTT
1 TTTACTT
26523288 CTCACCCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 4 0.11
17 11 0.31
18 10 0.28
19 7 0.19
20 4 0.11
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTACTTTCCCTCAAACT
Found at i:26524495 original size:23 final size:23
Alignment explanation
Indices: 26524463--26524559 Score: 140
Period size: 23 Copynumber: 4.2 Consensus size: 23
26524453 TAAGTGTCAT
* *
26524463 ACTGATATGTAGTCGAAGCTACC
1 ACTGAAATGTAGCCGAAGCTACC
*
26524486 ACTGAAATGTAGCCGTAGCTACC
1 ACTGAAATGTAGCCGAAGCTACC
*
26524509 ACTGAAATGTAGCTGAAGCTACC
1 ACTGAAATGTAGCCGAAGCTACC
* *
26524532 GCTGAAATGTAGCCGAAACTACC
1 ACTGAAATGTAGCCGAAGCTACC
26524555 ACTGA
1 ACTGA
26524560 TCAATAACAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (23 bp):
ACTGAAATGTAGCCGAAGCTACC
Found at i:26530895 original size:32 final size:32
Alignment explanation
Indices: 26530830--26530895 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
26530820 TTTTTTTAAA
* **
26530830 TTTCGAATAAATCAAATCAAGTTATTCGGTTT
1 TTTCGAATAAATCAAATCAAGTAATTCAATTT
*
26530862 TTTCGAATTAACTCAAAT-AAGTAATTCAATTT
1 TTTCGAA-TAAATCAAATCAAGTAATTCAATTT
26530894 TT
1 TT
26530896 CGAGTTCGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (32 bp):
TTTCGAATAAATCAAATCAAGTAATTCAATTT
Found at i:26534370 original size:20 final size:21
Alignment explanation
Indices: 26534324--26534370 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
26534314 AAAAATAAAA
26534324 ATAAAAATCAATAAAAGTTAT
1 ATAAAAATCAATAAAAGTTAT
* *
26534345 AGAAAAAT-TATAAAATGTT-T
1 ATAAAAATCAATAAAA-GTTAT
26534365 ATAAAA
1 ATAAAA
26534371 TTTTATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (21 bp):
ATAAAAATCAATAAAAGTTAT
Found at i:26534411 original size:18 final size:17
Alignment explanation
Indices: 26534390--26534469 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 17
26534380 ATTTTCCTAT
26534390 ATTTTATATTTTTTACGA
1 ATTTTATATTTTTTAC-A
*
26534408 ATTTTATATAATTTTACA
1 ATTTTATAT-TTTTTACA
*
26534426 ATTTTTATATTTTATTAAA
1 A-TTTTATATTTT-TTACA
* * *
26534445 ATTTAATAGTTTTTATA
1 ATTTTATATTTTTTACA
26534462 ACTTTTAT
1 A-TTTTAT
26534470 TGATTTTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 5 0.10
18 27 0.53
19 19 0.37
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTTTATATTTTTTACA
Found at i:26534422 original size:19 final size:17
Alignment explanation
Indices: 26534369--26534439 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 17
26534359 ATGTTTATAA
*
26534369 AATTTTATAATATTTTCC
1 AATTTTAT-ATATTTTAC
*
26534387 TATATTTTATATTTTTTAC
1 -A-ATTTTATATATTTTAC
26534406 GAATTTTATATAATTTTAC
1 -AATTTTATAT-ATTTTAC
26534425 AATTTT-TATATTTTA
1 AATTTTATATATTTTA
26534440 TTAAAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
16 6 0.13
17 3 0.07
18 15 0.33
19 15 0.33
20 7 0.15
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (17 bp):
AATTTTATATATTTTAC
Found at i:26534447 original size:19 final size:18
Alignment explanation
Indices: 26534391--26534448 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
26534381 TTTTCCTATA
*
26534391 TTTTATATTTTTTACGAA-
1 TTTTATATTTTTTA-AAAT
* *
26534409 TTTTATATAATTTTACAAT
1 TTTTATAT-TTTTTAAAAT
26534428 TTTTATATTTTATTAAAAT
1 TTTTATATTTT-TTAAAAT
26534447 TT
1 TT
26534449 AATAGTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 12 0.36
19 21 0.64
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATATTTTTTAAAAT
Found at i:26534448 original size:37 final size:38
Alignment explanation
Indices: 26534362--26534448 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 38
26534352 TTATAAAATG
* *
26534362 TTTA-TAAAATTTTATAATATTTTCCTATATTTTATAT
1 TTTATTAAAATTTTATAATATTTTACAATATTTTATAT
*
26534399 TTT-TTACGAATTTTAT-ATAATTTTACAAT-TTTTATAT
1 TTTATTA-AAATTTTATAAT-ATTTTACAATATTTTATAT
26534436 TTTATTAAAATTT
1 TTTATTAAAATTT
26534449 AATAGTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
37 23 0.55
38 19 0.45
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (38 bp):
TTTATTAAAATTTTATAATATTTTACAATATTTTATAT
Found at i:26534864 original size:46 final size:45
Alignment explanation
Indices: 26534789--26534887 Score: 137
Period size: 46 Copynumber: 2.2 Consensus size: 45
26534779 CTTGAACTTT
* *
26534789 TTTTTTTTATTTTTATGTTGGGTTTTATTTAGATTTTGGGCCAGA
1 TTTTATTTATTTTTATGTTGGGTTCTATTTAGATTTTGGGCCAGA
* *
26534834 TTTTATTTATTTATT-TGGTTGGGTTCTATTTAGATTTTGGGGCAGG
1 TTTTATTTATTT-TTAT-GTTGGGTTCTATTTAGATTTTGGGCCAGA
26534880 TTTTATTT
1 TTTTATTT
26534888 TGGGCGTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
45 12 0.25
46 36 0.75
ACGTcount: A:0.15, C:0.04, G:0.21, T:0.60
Consensus pattern (45 bp):
TTTTATTTATTTTTATGTTGGGTTCTATTTAGATTTTGGGCCAGA
Found at i:26538730 original size:13 final size:13
Alignment explanation
Indices: 26538712--26538739 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
26538702 ACAAAATTGG
26538712 AAAGATGATAAAT
1 AAAGATGATAAAT
26538725 AAAGATGATAAAT
1 AAAGATGATAAAT
26538738 AA
1 AA
26538740 TAAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:26543983 original size:17 final size:17
Alignment explanation
Indices: 26543963--26544036 Score: 67
Period size: 17 Copynumber: 4.0 Consensus size: 17
26543953 ATATGGGAGT
26543963 TTTTAAAATTTTTTAAA
1 TTTTAAAATTTTTTAAA
26543980 TTTTAAAATTTTTTTAAAATA
1 TTTTAAAA-TTTTTT--AA-A
** *
26544001 CTTTTTTAATTTTTTTAA
1 -TTTTAAAATTTTTTAAA
26544019 TTTTAAAATATTTTTAAA
1 TTTTAAAAT-TTTTTAAA
26544037 ATACTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
17 15 0.33
18 14 0.31
19 1 0.02
20 2 0.04
21 7 0.16
22 6 0.13
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATTTTTTAAA
Found at i:26544017 original size:40 final size:40
Alignment explanation
Indices: 26543969--26544072 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 40
26543959 GAGTTTTTAA
* *
26543969 AATTTTTTAAATTTTAAAATTTTTTTAAAATAC-TTTTTT
1 AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
26544008 AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
1 AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
26544048 AATTTTTGTTTTAATTTTTAAAATA
1 AA--TTT-TTTTAA-TTTTAAAATA
26544073 AATTTTTGGT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
39 31 0.53
40 8 0.14
42 3 0.05
43 6 0.10
44 10 0.17
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.62
Consensus pattern (40 bp):
AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
Found at i:26544044 original size:28 final size:28
Alignment explanation
Indices: 26543991--26544044 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
26543981 TTTAAAATTT
* **
26543991 TTTTAAAATACTTTTTTAATTTTTTTAA
1 TTTTAAAATACTTTTTAAATACTTTTAA
26544019 TTTTAAAATA-TTTTTAAAATACTTTT
1 TTTTAAAATACTTTTT-AAATACTTTT
26544045 TTTAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAAAATACTTTTTAAATACTTTTAA
Found at i:26547027 original size:164 final size:164
Alignment explanation
Indices: 26546731--26547033 Score: 471
Period size: 164 Copynumber: 1.8 Consensus size: 164
26546721 AAGTAGTTAG
* * *
26546731 GCACATCAACTCCAATAGCCTTTAGTTAAGCCCTAATATCCCTCATTTCCATGATGGCATTAAAT
1 GCACATCAACTCCAATAGCCTTTAGTTAAGCCCTAATATCCATCATTTCCATGATGACATTAAAC
* * ** * * *
26546796 TAGTGAACTTCATTGATGGTATTTTTCTCATTATGGTATTATCTAGGGTTTTATCTGAAGGTTCA
66 TAGTGAACTTCATTGATGATATTTTTCTCATTATGGTACTATCTAGAATTTCATATGAAGATTCA
26546861 AATTATTCATCAATGGCGTCTTGTTAAATAAAGT
131 AATTATTCATCAATGGCGTCTTGTTAAATAAAGT
* * *
26546895 GCACGTCAACTTCAATAGCCTTTAGTTAAGCCGTAATATCCATCATTTCCATGATGACATTAAAC
1 GCACATCAACTCCAATAGCCTTTAGTTAAGCCCTAATATCCATCATTTCCATGATGACATTAAAC
*
26546960 TAGTGAACTTCATTGATGATATTTTTCTCATTATGGTGCTATCTAGAATTTCATATGAAGATTCA
66 TAGTGAACTTCATTGATGATATTTTTCTCATTATGGTACTATCTAGAATTTCATATGAAGATTCA
*
26547025 AATTGTTCA
131 AATTATTCA
26547034 ACATTCAATA
Statistics
Matches: 124, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
164 124 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (164 bp):
GCACATCAACTCCAATAGCCTTTAGTTAAGCCCTAATATCCATCATTTCCATGATGACATTAAAC
TAGTGAACTTCATTGATGATATTTTTCTCATTATGGTACTATCTAGAATTTCATATGAAGATTCA
AATTATTCATCAATGGCGTCTTGTTAAATAAAGT
Found at i:26547591 original size:16 final size:16
Alignment explanation
Indices: 26547561--26547591 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26547551 AAAAATTATA
*
26547561 AAAATATTCAAAAAAT
1 AAAATATTAAAAAAAT
26547577 AAAATATTAAAAAAA
1 AAAATATTAAAAAAA
26547592 GATAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATATTAAAAAAAT
Found at i:26553221 original size:77 final size:77
Alignment explanation
Indices: 26553109--26553418 Score: 487
Period size: 77 Copynumber: 4.0 Consensus size: 77
26553099 TGATCGGGGG
* * *
26553109 AATTGGGAATTAGGGTTTTTTATTTGAAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGC
1 AATTGAGAATTAGGGTTTTTGA-TTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGC
26553174 CTTTGATAAGGAT
65 CTTTGATAAGGAT
* *
26553187 AACTGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAGTTATATTGACCAAAGGAATAGCC
1 AATTGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCC
26553252 TTTGATAAGGAT
66 TTTGATAAGGAT
* *
26553264 ATTTGAGAATTAGGGTTTTTAATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCC
1 AATTGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCC
*
26553329 TTTGATCAGGAT
66 TTTGATAAGGAT
* * * *
26553341 AATTGGGAATTAGGGTTTTTGATTTGTGTTCAATTTGTGT-ATTTTAATTGACCAAAGGAATAGC
1 AATTGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAATTAT-ATTGACCAAAGGAATAGC
26553405 CTTTGATAAGGAT
65 CTTTGATAAGGAT
26553418 A
1 A
26553419 GACTTTAAAG
Statistics
Matches: 214, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
76 4 0.02
77 191 0.89
78 19 0.09
ACGTcount: A:0.31, C:0.07, G:0.23, T:0.39
Consensus pattern (77 bp):
AATTGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCC
TTTGATAAGGAT
Found at i:26557288 original size:21 final size:22
Alignment explanation
Indices: 26557256--26557297 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
26557246 AAAAATAGTT
*
26557256 AAAATAGTTAAATACTAAATTA
1 AAAATAGTTAAAAACTAAATTA
*
26557278 AAAATAG-TAAAAATTAAATT
1 AAAATAGTTAAAAACTAAATT
26557298 TTAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (22 bp):
AAAATAGTTAAAAACTAAATTA
Done.