Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3770
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: 69734
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:1582 original size:27 final size:27
Alignment explanation
Indices: 1551--1728 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
1541 TAAATTGTAC
1551 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
1578 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1604 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
1632 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
1660 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1687 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
1714 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
1729 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:1665 original size:82 final size:81
Alignment explanation
Indices: 1552--1707 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
1542 AAATTGTACA
* *
1552 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
1616 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
1633 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
1698 TGCGAGTTGA
65 TGCGAATTGA
1708 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:1719 original size:82 final size:81
Alignment explanation
Indices: 1548--1728 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
1538 GATTAAATTG
* *
1548 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
1613 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
1629 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
1693 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
1711 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
1729 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:9639 original size:27 final size:27
Alignment explanation
Indices: 9572--9748 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
9562 TAAATTGTAC
9572 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
9599 TGCA-TAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
9624 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
9652 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
9680 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
9707 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
9734 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
9749 GACTCAATAT
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
26 21 0.17
27 83 0.65
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:9693 original size:55 final size:54
Alignment explanation
Indices: 9572--9748 Score: 205
Period size: 55 Copynumber: 3.3 Consensus size: 54
9562 TAAATTGTAC
* **
9572 AGCACTAAGTGTGCGATTTGACTATGTTGCA-TAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
* * ** *
9624 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAG-TTGAATATGT
* * * *
9680 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
*
9734 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
9749 GACTCAATAT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
52 1 0.01
53 26 0.25
54 33 0.31
55 44 0.42
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
Found at i:9714 original size:82 final size:80
Alignment explanation
Indices: 9573--9727 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 80
9563 AAATTGTACA
* *
9573 GCACTAAGTGTGCGATTTGACTATGTTGCATAAGTGTGCGAAATGAATATGATGCACTAAGTGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCATAAGTGTGCGAAATGAATACGATGCACTAAGTGTG
9638 CGAATTGACCATGCG
66 CGAATTGACCATGCG
** *
9653 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCA-TAAGTGTGCGAAATGAATACGAT-GCACTAAGT
*
9717 GTGCGAGTTGA
63 GTGCGAATTGA
9728 TTATATAGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 15 0.23
81 15 0.23
82 36 0.55
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (80 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCATAAGTGTGCGAAATGAATACGATGCACTAAGTGTG
CGAATTGACCATGCG
Found at i:9739 original size:82 final size:80
Alignment explanation
Indices: 9569--9748 Score: 218
Period size: 82 Copynumber: 2.2 Consensus size: 80
9559 GGATAAATTG
* *
9569 TACAGCACTAAGTGTGCGATTTGACTATGTTGCATAAGTGTGCGAAATGAATATGATGCACTAAG
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCATAAGTGTGCGAAATGAATACGATGCACTAAG
9634 TGTGCGAATTGACCA
66 TGTGCGAATTGACCA
* * ** *
9649 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCA-TAAGTGTGCGAAATGAATACGAT-GCACT
* **
9713 AAGTGTGCGAGTTGATTA
63 AAGTGTGCGAATTGACCA
* *
9731 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
9749 GACTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 17 0.20
81 15 0.18
82 51 0.61
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (80 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCATAAGTGTGCGAAATGAATACGATGCACTAAG
TGTGCGAATTGACCA
Found at i:24439 original size:79 final size:80
Alignment explanation
Indices: 24282--24506 Score: 262
Period size: 79 Copynumber: 2.8 Consensus size: 80
24272 TTGAATGATG
* * * * * *
24282 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGA-T-ACTATAACCGGGCTAAG-TCCCGAAGGCA
24344 TTTGTGCAAGTTACTAAA
63 TTTGTGCAAGTTACTAAA
* **
24362 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA-ATTTCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTATA-ACCGGGCTAAGTCCCGAAGGCATT
*
24425 TGTGCGAGTTACTAAA
65 TGTGCAAGTTACTAAA
* * *
24441 TCTGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTT
24506 G
66 G
24507 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
79 70 0.55
80 47 0.37
81 9 0.07
82 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCAAGTTACTAAA
Found at i:24513 original size:40 final size:40
Alignment explanation
Indices: 24282--24506 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
24272 TTGAATGATG
* * * *
24282 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
24322 TCCGGACTAAGAT-CCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
24362 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24402 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
24441 TCTGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
24482 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
24507 AACGAGTAGC
Statistics
Matches: 159, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 35 0.22
40 114 0.72
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:24528 original size:79 final size:78
Alignment explanation
Indices: 24335--24539 Score: 243
Period size: 79 Copynumber: 2.6 Consensus size: 78
24325 GGACTAAGAT
* *
24335 CCGAAGGCATTTGTGCAAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGTGCGAGTTACTAAATCC-GGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
**
24400 ATTTCGGGCTAAGC
65 ATACCGGGCTAAGC
* *
24414 CCGAAGGCATTTGTGCGAGTTACTAAATCTGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-
1 CCGAAGGCATTTGTGCGAGTTACTAAATC-CGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTA
*
24478 ATAACCGGGCTATGTC
65 AT-ACCGGGCTAAG-C
** * * *
24494 CCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAAATTCCGAAGG
1 CCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGTTAAGTCCCGAAGG
24540 TACGTGATTT
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
78 2 0.02
79 83 0.76
80 24 0.22
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGTTAAGTCCCGAAGGCAATTGTGCGAGATACTAA
TACCGGGCTAAGC
Found at i:26227 original size:85 final size:85
Alignment explanation
Indices: 26084--26239 Score: 208
Period size: 85 Copynumber: 1.8 Consensus size: 85
26074 GTCCTGGACG
* * * *
26084 TGGTCTTACATGTAATTCAATATCGATGCCTCTATCCCAGACAGGGTCTTACATGAAATCAGATA
1 TGGTCTTACATGTAATTCAATATCGAGGCCTCTATCCCAGACACGCTCTTACACGAAATCAGATA
26149 AGATGCTGATATTCCAGACA
66 AGATGCTGATATTCCAGACA
* * *
26169 TGGTCTTATATGTAAATCTC-A-ATCGAGGCCTGTGTCCCAGACACGCTCTTACACGAAATCAGA
1 TGGTCTTACATGT-AAT-TCAATATCGAGGCCTCTATCCCAGACACGCTCTTACACGAAATCAGA
*
26232 TATGATGC
64 TAAGATGC
26240 CGGTTATAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 55 0.90
86 4 0.07
87 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (85 bp):
TGGTCTTACATGTAATTCAATATCGAGGCCTCTATCCCAGACACGCTCTTACACGAAATCAGATA
AGATGCTGATATTCCAGACA
Found at i:26306 original size:40 final size:40
Alignment explanation
Indices: 26246--26482 Score: 291
Period size: 40 Copynumber: 6.0 Consensus size: 40
26236 ATGCCGGTTA
*
26246 TAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
* * *
26286 TAGTAACTCGCACAAATGCCTTCGAG-CTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
* *
26325 TAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
* * *
26365 TAGTATCTCGCACAAATGCCTTCGGGATTTAACCCAGATT
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
** *
26405 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATA
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATT
* * * *
26445 TGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGA
26483 CATCATTCAA
Statistics
Matches: 173, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 38 0.22
40 124 0.72
41 11 0.06
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
Found at i:26377 original size:79 final size:80
Alignment explanation
Indices: 26246--26429 Score: 280
Period size: 79 Copynumber: 2.3 Consensus size: 80
26236 ATGCCGGTTA
* *
26246 TAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGA
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCTTCGA
* *
26311 G-CTTAGCCCGGAAT
66 GACTTAACCCAGAAT
* * *
26325 TAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCTTCGA
* *
26390 GATTTAACCCAGATT
66 GACTTAACCCAGAAT
26405 TAGTAACTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGG
26430 ATCTTAGTCC
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
79 61 0.65
80 33 0.35
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCTTCGA
GACTTAACCCAGAAT
Found at i:37102 original size:17 final size:18
Alignment explanation
Indices: 37068--37113 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
37058 CCGTTATGTC
37068 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
37083 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
37100 CGCGACCGCGACCG
1 CGCGACCGCGACCG
37114 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:38303 original size:43 final size:43
Alignment explanation
Indices: 38194--38306 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 43
38184 ATATCATACA
* * * *
38194 ATGCCAACGTCCCGGACATGGTCTTACATGCAATCACATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGCAATCACATATCG
** *
38237 ATGCCATTATCCTAGACAG-GGTCTTACACGCAATCACATATCG
1 ATGCCAACATCCCAGAC-GTGGTCTTACACGCAATCACATATCG
38280 ATGCCAACATCCCAGACGTGGTCTTAC
1 ATGCCAACATCCCAGACGTGGTCTTAC
38307 TCAAAAACAC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
42 1 0.02
43 57 0.98
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACATCCCAGACGTGGTCTTACACGCAATCACATATCG
Found at i:48052 original size:59 final size:60
Alignment explanation
Indices: 47907--48052 Score: 168
Period size: 59 Copynumber: 2.4 Consensus size: 60
47897 TATGTCATAA
* * * * *
47907 AGGATTTAGCCTAGACTAGTAATCTTGACTAAGCTCTATTCAGTATATATATATTGGAGGC
1 AGGATTTAGCCTGGACTGGTAATCCTCACTAAGCTCTATTCAG-ATATATATATTGGAGAC
* * * *
47968 AGGATTTAGCCTGGACTGGTTATCCTCACTAAGGTCTATTGAG-TATATATGTTGGAGAC
1 AGGATTTAGCCTGGACTGGTAATCCTCACTAAGCTCTATTCAGATATATATATTGGAGAC
* * *
48027 ATGATTTAGCTTGGATTGGTAATCCT
1 AGGATTTAGCCTGGACTGGTAATCCT
48053 GTTGTATATA
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 36 0.50
61 36 0.50
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (60 bp):
AGGATTTAGCCTGGACTGGTAATCCTCACTAAGCTCTATTCAGATATATATATTGGAGAC
Found at i:49676 original size:24 final size:24
Alignment explanation
Indices: 49649--49703 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
49639 TCACATGACA
49649 ATTGATATATGAAAATATGAGATG
1 ATTGATATATGAAAATATGAGATG
** *
49673 ATTGATATATGGCAATATGGGATG
1 ATTGATATATGAAAATATGAGATG
49697 A-TGATAT
1 ATTGATAT
49704 TTGTACATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.35
Consensus pattern (24 bp):
ATTGATATATGAAAATATGAGATG
Found at i:51842 original size:27 final size:26
Alignment explanation
Indices: 51794--51853 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
51784 GCGAAGCTGC
*
51794 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
51821 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
51847 CAGATAT
1 CAGATAT
51854 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:58989 original size:59 final size:60
Alignment explanation
Indices: 58845--58989 Score: 177
Period size: 59 Copynumber: 2.4 Consensus size: 60
58835 TATGTCATAA
* * * *
58845 AGGATTTA-CCTGGACTAGTAATCTTGACTAAGCTCTATTCAGTATATATATATTGGAGGC
1 AGGATTTAGCCTGGACTGGTAATCCTCACTAAGCTCTATTCAG-ATATATATATTGGAGAC
* * * *
58905 GGGATTTAGCCTAGACTGGTTATCCTCACTAAGCTCTATTGAG-TATATATATTGGAGAC
1 AGGATTTAGCCTGGACTGGTAATCCTCACTAAGCTCTATTCAGATATATATATTGGAGAC
* *
58964 AGGATTTAGGCTGGATTGGTAATCCT
1 AGGATTTAGCCTGGACTGGTAATCCT
58990 ATTGTATATA
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 36 0.51
60 7 0.10
61 28 0.39
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (60 bp):
AGGATTTAGCCTGGACTGGTAATCCTCACTAAGCTCTATTCAGATATATATATTGGAGAC
Found at i:60130 original size:43 final size:43
Alignment explanation
Indices: 60080--60419 Score: 403
Period size: 43 Copynumber: 7.9 Consensus size: 43
60070 CATGGATGTA
*
60080 TATGTGTAAGACCACGTCTGGGGCGTTGGCATCGATATGTGAT
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGAT
* * *
60123 TATGTGTAAGACCACATCTGGAACGTTGGCATCGATATGTGGT
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGAT
* * * *
60166 TATGTGTAAGACTATGTTTGGGACGTTGACATCGATATGTGAT
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGAT
** * * *
60209 TACATGTACGACCACATCTGGGACGTTGGAATCGATATGTGAT
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGAT
*
60252 TATGTGTAAGACCACGTCTGGGATGTTGGCATCGATATGTGAT
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGAT
* * * * *
60295 TACGTGTAAGACCACATTTGGGACGTTGGAATTGATATGTGAT
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGAT
* * * *
60338 TATGTGTAAGACCACGTCTAGGATGTTGGCATAGATATGTGTT
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGAT
*** ** *
60381 TACAAGTAAGACCTTGTCTGGGACAG-TGGCATCAATATG
1 TATGTGTAAGACCACGTCTGGGAC-GTTGGCATCGATATG
60420 AGGTTACATG
Statistics
Matches: 247, Mismatches: 49, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
43 246 1.00
44 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.31
Consensus pattern (43 bp):
TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGAT
Found at i:60419 original size:86 final size:86
Alignment explanation
Indices: 60080--60393 Score: 448
Period size: 86 Copynumber: 3.7 Consensus size: 86
60070 CATGGATGTA
* ** *
60080 TATGTGTAAGACCACGTCTGGGGCGTTGGCATCGATATGTGATTATGTGTAAGACCACATCTGGA
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACATGTAAGACCACATCTGGG
* *
60145 ACGTTGGCATCGATATGTGGT
66 ACGTTGGAATCGATATGTGAT
* * * * *
60166 TATGTGTAAGACTATGTTTGGGACGTTGACATCGATATGTGATTACATGTACGACCACATCTGGG
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACATGTAAGACCACATCTGGG
60231 ACGTTGGAATCGATATGTGAT
66 ACGTTGGAATCGATATGTGAT
* * *
60252 TATGTGTAAGACCACGTCTGGGATGTTGGCATCGATATGTGATTACGTGTAAGACCACATTTGGG
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACATGTAAGACCACATCTGGG
*
60317 ACGTTGGAATTGATATGTGAT
66 ACGTTGGAATCGATATGTGAT
* * * * *
60338 TATGTGTAAGACCACGTCTAGGATGTTGGCATAGATATGTGTTTACAAGTAAGACC
1 TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACATGTAAGACC
60394 TTGTCTGGGA
Statistics
Matches: 203, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 203 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (86 bp):
TATGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACATGTAAGACCACATCTGGG
ACGTTGGAATCGATATGTGAT
Found at i:62888 original size:40 final size:40
Alignment explanation
Indices: 62804--63027 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
62794 TTGAATGATG
* * * *
62804 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
62844 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
62884 TCCGGGCTAAG--CCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
62922 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
62962 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
63003 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
63028 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
38 34 0.21
40 120 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.