Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold234
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: 732544
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18906 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:666498 original size:6 final size:6
Alignment explanation
Indices: 666482--666523 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
666472 TGCAAATGGA
* * *
666482 TCATTT CCATTT TCATTT TCATTT CCATTT CCATTT TCATTT
1 TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT
666524 CTAGAAACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.60
Consensus pattern (6 bp):
TCATTT
Found at i:666499 original size:12 final size:12
Alignment explanation
Indices: 666482--666524 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
666472 TGCAAATGGA
666482 TCATTTCCATTT
1 TCATTTCCATTT
*
666494 TCATTTTCATTT
1 TCATTTCCATTT
*
666506 CCATTTCCATTT
1 TCATTTCCATTT
666518 TCATTTC
1 TCATTTC
666525 TAGAAACCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:666505 original size:18 final size:18
Alignment explanation
Indices: 666482--666524 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
666472 TGCAAATGGA
*
666482 TCATTTCCATTTTCATTT
1 TCATTTCCATTTCCATTT
666500 TCATTTCCATTTCCATTT
1 TCATTTCCATTTCCATTT
666518 TCATTTC
1 TCATTTC
666525 TAGAAACCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTTCCATTTCCATTT
Found at i:669968 original size:24 final size:25
Alignment explanation
Indices: 669922--669968 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
669912 TGGCTCTTAT
* * *
669922 GAGCTTTCCGTTATATGGTTCTTGC
1 GAGCTTCCCGTTATATAGCTCTTGC
669947 GAGCTTCCCGTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
669969 TGGAACATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGC
Found at i:670071 original size:25 final size:25
Alignment explanation
Indices: 670043--670114 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
670033 CCCGTTATAT
670043 GGCTCTTCGGAGCTTTCCGATTAAA
1 GGCTCTTCGGAGCTTTCCGATTAAA
** * *
670068 GGCTCTTTATGAGC-TTCTTGATTAAT
1 GGCTC-TTCGGAGCTTTC-CGATTAAA
*
670094 GGCTCTTCGGAGCTTCCCGAT
1 GGCTCTTCGGAGCTTTCCGAT
670115 ATTGGCTTGC
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
25 17 0.47
26 19 0.53
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (25 bp):
GGCTCTTCGGAGCTTTCCGATTAAA
Found at i:670157 original size:24 final size:24
Alignment explanation
Indices: 670074--670157 Score: 57
Period size: 24 Copynumber: 3.5 Consensus size: 24
670064 TAAAGGCTCT
* *
670074 TTATGAGCTTCTTGATTAATGGCTC
1 TTATGAGCTTCTCGATT-ATGGTTC
** *
670099 TTCGGAGCTTCCCGA-TATTGGCTTGC
1 TTATGAGCTTCTCGATTA-TGG-TT-C
*
670125 -T-TGAACTTCTCGATTATGGTTC
1 TTATGAGCTTCTCGATTATGGTTC
670147 TTATGAGCTTC
1 TTATGAGCTTC
670158 CCGTTATAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 13
0.67 0.14 0.20
Matches are distributed among these distances:
22 1 0.02
23 4 0.09
24 23 0.52
25 15 0.34
26 1 0.02
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (24 bp):
TTATGAGCTTCTCGATTATGGTTC
Found at i:677339 original size:27 final size:26
Alignment explanation
Indices: 677293--677357 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
677283 TTATATGGTT
*
677293 TTTCAGAGCTTCCCGGTTAAAGGCTC
1 TTTCAGAGCTTCCCGATTAAAGGCTC
* *
677319 TTTCATGAGCTTCCTGATTAATGGCTC
1 TTTCA-GAGCTTCCCGATTAAAGGCTC
*
677346 -TTCGGAGCTTCC
1 TTTCAGAGCTTCC
677358 AAATATTGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.24
26 8 0.24
27 18 0.53
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (26 bp):
TTTCAGAGCTTCCCGATTAAAGGCTC
Found at i:677443 original size:25 final size:24
Alignment explanation
Indices: 677385--677443 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
677375 AACATCCCGA
* *
677385 TTATGGCTCTCATGAGCTTTCAAT
1 TTATGGCTCACATGAGCTTCCAAT
* *
677409 TACATGGCTCACATGAGCTTCCCAT
1 T-TATGGCTCACATGAGCTTCCAAT
677434 TTATGTGCTC
1 TTATG-GCTC
677444 GTATGAGCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (24 bp):
TTATGGCTCACATGAGCTTCCAAT
Found at i:680210 original size:35 final size:37
Alignment explanation
Indices: 680169--680241 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 37
680159 AATATTTGTA
*
680169 TGATTGCAC-GTG-CCCTGTTTGTACTTCGGTACCTC
1 TGATTGCACAGTGCCCCTGTTTGTACTTCGATACCTC
680204 TGATTGCACATAGGTGCCCCTGTTTGTACTTCGATACC
1 TGATTGCAC--A-GTGCCCCTGTTTGTACTTCGATACC
680242 CTTGAAATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 9 0.28
39 3 0.09
40 20 0.62
ACGTcount: A:0.15, C:0.27, G:0.22, T:0.36
Consensus pattern (37 bp):
TGATTGCACAGTGCCCCTGTTTGTACTTCGATACCTC
Found at i:683454 original size:38 final size:38
Alignment explanation
Indices: 683378--683462 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 38
683368 CTGGATGACT
* *
683378 AGTAGATAACCGTCGTCACAGTGTCACCTCGAATGACC
1 AGTAGATAACCATCGTCACAGTGTCACCTCGAAAGACC
* *
683416 AGTAGATAACCATTGTCACGGTGTTGC-CCT-GAAAGACC
1 AGTAGATAACCATCGTCACAGTG-T-CACCTCGAAAGACC
*
683454 AGAAGATAA
1 AGTAGATAA
683463 TCGTTCCACA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 35 0.88
39 4 0.10
40 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (38 bp):
AGTAGATAACCATCGTCACAGTGTCACCTCGAAAGACC
Found at i:690033 original size:35 final size:35
Alignment explanation
Indices: 689969--690036 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
689959 GAATGACATG
* *
689969 TATATCGTTTACATGGTGTTACCCTAAAGGACCTA
1 TATATCGTTTACACGGTGATACCCTAAAGGACCTA
690004 TATATCGTTTACACGGT-AT-CGCCTCAAAGGACC
1 TATATCGTTTACACGGTGATAC-CCT-AAAGGACC
690037 AATAGTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 1 0.03
34 4 0.14
35 24 0.83
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (35 bp):
TATATCGTTTACACGGTGATACCCTAAAGGACCTA
Found at i:693830 original size:30 final size:30
Alignment explanation
Indices: 693794--693899 Score: 169
Period size: 30 Copynumber: 3.5 Consensus size: 30
693784 TAAATTGTAT
*
693794 AAGGTATGATATGTAATTGAAAATGATTAG
1 AAGGTATGATATGTAATTGAAAATCATTAG
*
693824 AAGGTATGATATGTAATTGGAAATCATTAG
1 AAGGTATGATATGTAATTGAAAATCATTAG
*
693854 AAGGTATGATATGTAATT-AGAAATTATTAG
1 AAGGTATGATATGTAATTGA-AAATCATTAG
693884 AAGGTATGATATGTAA
1 AAGGTATGATATGTAA
693900 CTATGAATGA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.42, C:0.01, G:0.23, T:0.34
Consensus pattern (30 bp):
AAGGTATGATATGTAATTGAAAATCATTAG
Found at i:695341 original size:41 final size:41
Alignment explanation
Indices: 695279--695387 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 41
695269 TTTAACATAT
*
695279 TCACCGGCACTTAGCCTGCTAGGCTTATAGCATGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACATGATT-CAGA
* * *
695320 TCACTGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACATGATTCAGA
* *
695361 TCACCGGTACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
695388 AAGTCTGAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
40 2 0.03
41 57 0.97
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACATGATTCAGA
Found at i:697162 original size:33 final size:33
Alignment explanation
Indices: 697120--697186 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
697110 GAACTTACTA
697120 AGCATTTGTATACTTACTTTAGTTGCTTCTCTT
1 AGCATTTGTATACTTACTTTAGTTGCTTCTCTT
697153 AGCATTTGTATACTTACTTTAGTTGCTTCTCTT
1 AGCATTTGTATACTTACTTTAGTTGCTTCTCTT
697186 A
1 A
697187 CTTAGATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.19, C:0.18, G:0.12, T:0.51
Consensus pattern (33 bp):
AGCATTTGTATACTTACTTTAGTTGCTTCTCTT
Found at i:697191 original size:37 final size:35
Alignment explanation
Indices: 697113--697191 Score: 117
Period size: 33 Copynumber: 2.3 Consensus size: 35
697103 TCCATTTGAA
*
697113 CTTACTAAGCATTTGTATACTTACTTTAGTTGCTT
1 CTTACTTAGCATTTGTATACTTACTTTAGTTGCTT
697148 C-T-CTTAGCATTTGTATACTTACTTTAGTTGCTTCT
1 CTTACTTAGCATTTGTATACTTACTTTAGTTGC-T-T
697183 CTTACTTAG
1 CTTACTTAG
697192 ATCTTCAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
33 28 0.72
34 2 0.05
35 3 0.08
36 1 0.03
37 5 0.13
ACGTcount: A:0.20, C:0.19, G:0.11, T:0.49
Consensus pattern (35 bp):
CTTACTTAGCATTTGTATACTTACTTTAGTTGCTT
Found at i:698053 original size:20 final size:20
Alignment explanation
Indices: 698028--698067 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
698018 CGTAAAATGA
*
698028 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
698048 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
698068 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:698057 original size:34 final size:35
Alignment explanation
Indices: 698013--698079 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
698003 CAGTATAATG
*
698013 TTTTCCGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
698047 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
698080 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:700681 original size:14 final size:13
Alignment explanation
Indices: 700654--700684 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
700644 CAGGAAAGGG
700654 AAGGGGTAGGGAA
1 AAGGGGTAGGGAA
*
700667 AAGGGGTAGGGGA
1 AAGGGGTAGGGAA
700680 AAGGG
1 AAGGG
700685 AAGGAGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.58, T:0.06
Consensus pattern (13 bp):
AAGGGGTAGGGAA
Found at i:700710 original size:18 final size:18
Alignment explanation
Indices: 700676--700710 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
700666 AAAGGGGTAG
*
700676 GGGAAAGGGAAGGAGAAA
1 GGGAAAGGGAAGAAGAAA
*
700694 GGGAAAGGGGAGAAGAA
1 GGGAAAGGGAAGAAGAA
700711 TGGGTCATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (18 bp):
GGGAAAGGGAAGAAGAAA
Found at i:710013 original size:20 final size:20
Alignment explanation
Indices: 709988--710034 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
709978 TAAAAAATAG
709988 TAAAAATAGT-AAATATTATT
1 TAAAAATAGTGAAA-ATTATT
710008 TAAAAAT-GTGAAAATTATT
1 TAAAAATAGTGAAAATTATT
710027 TAAAAATA
1 TAAAAATA
710035 ATAATTNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (20 bp):
TAAAAATAGTGAAAATTATT
Found at i:710329 original size:20 final size:20
Alignment explanation
Indices: 710301--710373 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
710291 ATAATTATTG
*
710301 TAAACTTATTTAAAAA-TTAA
1 TAAAATTATTTAAAAAGTT-A
*
710321 TAAAATTA-TTAAAAAGTTG
1 TAAAATTATTTAAAAAGTTA
710340 TAAAAGTTATTT---AAGTTA
1 TAAAA-TTATTTAAAAAGTTA
* *
710358 TAAAAATATATAAAAA
1 TAAAATTATTTAAAAA
710374 ATTTAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
17 4 0.10
18 10 0.24
19 12 0.29
20 14 0.33
21 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.37
Consensus pattern (20 bp):
TAAAATTATTTAAAAAGTTA
Found at i:713625 original size:91 final size:91
Alignment explanation
Indices: 713462--713638 Score: 219
Period size: 91 Copynumber: 1.9 Consensus size: 91
713452 TGGGATGGGA
** * *
713462 CACACGGCCGTGTAAGCAAGCTGTGCAATAGATTGATCTCATGTGGAGTTAGAGTCACAAGACTG
1 CACACGGCCGTGTAAGCAAGCCATGCAACAGATTGATCTCATGTGGAGTTAGAGTCACAAGACCG
713527 TGCGAACAACCATGTACACTCGGGGT
66 TGCGAACAACCATGTACACTCGGGGT
* * * * * * * *
713553 CACACGGTCGTGTAGGCAAGCCATGCAACAGATTGATGTCGTGTGGGGTTGGAGTCACATGGCCG
1 CACACGGCCGTGTAAGCAAGCCATGCAACAGATTGATCTCATGTGGAGTTAGAGTCACAAGACCG
* * *
713618 TGTGAACAATCGTGTACACTC
66 TGCGAACAACCATGTACACTC
713639 ACCAAGGCCG
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
91 71 1.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (91 bp):
CACACGGCCGTGTAAGCAAGCCATGCAACAGATTGATCTCATGTGGAGTTAGAGTCACAAGACCG
TGCGAACAACCATGTACACTCGGGGT
Found at i:724291 original size:51 final size:51
Alignment explanation
Indices: 724215--724386 Score: 308
Period size: 51 Copynumber: 3.4 Consensus size: 51
724205 TTTGAGTACT
*
724215 TCTGATCAGTGACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
724266 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
724317 TCTGATCAGTGACAAATAACAAGTGATAAATGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
724368 TCTGATCAGTGACAAGTGA
1 TCTGATCAGTGACAAGTGA
724387 TTAAGGATGG
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 115 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (51 bp):
TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:725715 original size:19 final size:20
Alignment explanation
Indices: 725691--725740 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
725681 GATACTATTT
725691 TATCGATATT-TTTGAAAAA-
1 TATCGATATTATTT-AAAAAG
725710 TATCGATACTTATTTAAAAAG
1 TATCGATA-TTATTTAAAAAG
*
725731 TATTGATATT
1 TATCGATATT
725741 CATCTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.30
20 9 0.33
21 10 0.37
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (20 bp):
TATCGATATTATTTAAAAAG
Found at i:729355 original size:18 final size:19
Alignment explanation
Indices: 729334--729371 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
729324 ATGTGGAAAG
*
729334 TGTATATGTGT-TATAAAA
1 TGTATATGTATATATAAAA
729352 TGTATATGTATATATAAAA
1 TGTATATGTATATATAAAA
729371 T
1 T
729372 ATAAAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (19 bp):
TGTATATGTATATATAAAA
Found at i:729537 original size:16 final size:15
Alignment explanation
Indices: 729510--729548 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
729500 ACAACAAAAA
729510 AAATAAAAAATAACT
1 AAATAAAAAATAACT
729525 AAATAATAAAATAACT
1 AAATAA-AAAATAACT
729541 AAA-AAAAA
1 AAATAAAAA
729549 GGACTAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.13
15 8 0.35
16 12 0.52
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAAAAAATAACT
Found at i:731959 original size:35 final size:35
Alignment explanation
Indices: 731918--731986 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
731908 ACACTATCAT
* *
731918 AAATATAATAAATGTTTTATTATATTAAAAATAAA
1 AAATATAAAAAATATTTTATTATATTAAAAATAAA
* *
731953 AAATATAAAAAATATTTTATTGTATTAAATATAA
1 AAATATAAAAAATATTTTATTATATTAAAAATAA
731987 TTTTTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (35 bp):
AAATATAAAAAATATTTTATTATATTAAAAATAAA
Found at i:732154 original size:18 final size:19
Alignment explanation
Indices: 732117--732156 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
732107 ATAAATACAA
*
732117 ATATATAATTATTATTTAAC
1 ATATATAATTA-TATATAAC
732137 ATATATAATTA-ATATAAC
1 ATATATAATTATATATAAC
732155 AT
1 AT
732157 TTTTTATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATATAATTATATATAAC
Done.