Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold442
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: 36049
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Found at i:3044 original size:25 final size:26
Alignment explanation
Indices: 2969--3098 Score: 74
Period size: 25 Copynumber: 5.0 Consensus size: 26
2959 TATTCCAAAA
* *
2969 AAAATTAT-TTTAATAATTTTAATGTT
1 AAAATTATATTTATTAA-TTTAATATT
* * * *
2995 AAATTTA-ATTTAAT-ACTT-ATCTT
1 AAAATTATATTTATTAATTTAATATT
*
3018 AAAAATAT-TTTATTAATTTAATATT
1 AAAATTATATTTATTAATTTAATATT
* *
3043 AAATTGATTATCTTAATATTAAATTAA-ATT
1 AAA---ATTATATT--TATTAATTTAATATT
*
3073 AAAATTTTATTTATTAATTTAATATT
1 AAAATTATATTTATTAATTTAATATT
3099 TAGCTTGATA
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
23 14 0.17
24 5 0.06
25 18 0.22
26 15 0.19
27 6 0.08
28 4 0.05
29 2 0.03
30 6 0.08
31 10 0.12
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
AAAATTATATTTATTAATTTAATATT
Found at i:3139 original size:56 final size:56
Alignment explanation
Indices: 3026--3141 Score: 130
Period size: 57 Copynumber: 2.1 Consensus size: 56
3016 TTAAAAATAT
* * *
3026 TTTATTAATTTAATATTAAATTGATTATCTTAATATTAAATTAAATTAAAATTTTA
1 TTTATTAATTTAATATTAAATTGATAATATTAATATTAAATTAAATTAAAATGTTA
** *
3082 TTTATTAATTTAATATTTAGCTTGATAAGTATT-ATATTAATTTAATATT-AAA-GTTA
1 TTTATTAATTTAATA-TTAAATTGATAA-TATTAATATTAAATTAA-ATTAAAATGTTA
3138 TTTA
1 TTTA
3142 GTGTCACACC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
56 22 0.43
57 23 0.45
58 6 0.12
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (56 bp):
TTTATTAATTTAATATTAAATTGATAATATTAATATTAAATTAAATTAAAATGTTA
Found at i:7722 original size:40 final size:41
Alignment explanation
Indices: 7676--7792 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
7666 TCAAACACAG
*
7676 AGCAATAGCGGCGTCTTA-CAAAAAATGCCGCTAAAAACAA
1 AGCAATAGCGGCGTCTTAGCAAAAAACGCCGCTAAAAACAA
* * *
7716 AGCAATAGCGGCGTTTTAGTAAAAAACGCCGCTAAAAACAG
1 AGCAATAGCGGCGTCTTAGCAAAAAACGCCGCTAAAAACAA
* * *
7757 AGCATTAGCGGCG-CTTTTG-ATAAAACGCCGCTAAAA
1 AGCAATAGCGGCGTC-TTAGCAAAAAACGCCGCTAAAA
7793 GTCATATAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
40 33 0.49
41 34 0.51
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (41 bp):
AGCAATAGCGGCGTCTTAGCAAAAAACGCCGCTAAAAACAA
Found at i:7752 original size:41 final size:40
Alignment explanation
Indices: 7676--7792 Score: 155
Period size: 40 Copynumber: 2.9 Consensus size: 40
7666 TCAAACACAG
* * *
7676 AGCAATAGCGGCGTCTTACAAAAAATGCCGCTAAAAACAA
1 AGCAATAGCGGCGTTTTAGAAAAAACGCCGCTAAAAACAA
*
7716 AGCAATAGCGGCGTTTTAGTAAAAAACGCCGCTAAAAACAG
1 AGCAATAGCGGCGTTTTAG-AAAAAACGCCGCTAAAAACAA
* *
7757 AGCATTAGCGGCGCTTTT-GATAAAACGCCGCTAAAA
1 AGCAATAGCGGCG-TTTTAGAAAAAACGCCGCTAAAA
7793 GTCATATAAC
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.48
41 32 0.46
42 4 0.06
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (40 bp):
AGCAATAGCGGCGTTTTAGAAAAAACGCCGCTAAAAACAA
Found at i:8696 original size:80 final size:81
Alignment explanation
Indices: 8601--8770 Score: 252
Period size: 81 Copynumber: 2.1 Consensus size: 81
8591 CTGGCGTTTA
*
8601 TTTAAAAAACGCCGCAAAAAACATAGCAG-TTAACAAAAACGGCGTCGTTTTAATTGGATATTTA
1 TTTAAAAAACGCCGCAAAAAACATAGCAGTTTAACAAAAACGGCGTCGTTTTAATTAGATATTTA
*
8665 GGAGAGTAGCGGCATT
66 GGAGAGTACCGGCATT
* * * * *
8681 TTTTAAAAACGCCGCAAAAAACATAGCAGTTTAACGAAAACGTCGTCGTTTTTATTAGATTTTTA
1 TTTAAAAAACGCCGCAAAAAACATAGCAGTTTAACAAAAACGGCGTCGTTTTAATTAGATATTTA
* *
8746 GGGGAGTACCGGCGTT
66 GGAGAGTACCGGCATT
8762 TTTAAAAAA
1 TTTAAAAAA
8771 AAAACGCCAC
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 28 0.35
81 51 0.65
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (81 bp):
TTTAAAAAACGCCGCAAAAAACATAGCAGTTTAACAAAAACGGCGTCGTTTTAATTAGATATTTA
GGAGAGTACCGGCATT
Found at i:14140 original size:240 final size:241
Alignment explanation
Indices: 13717--14202 Score: 866
Period size: 240 Copynumber: 2.0 Consensus size: 241
13707 ATGAATTAAT
13717 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAACTGACATTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAACTGACATTCTCTCCAACCTT
*
13782 ATTTTAAATATTTTAAATATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
* *
13847 TTGTAAGATATAATGGATCCTTCCTAGGTGTAACAACGCCACGCATGATGAATCTT-AAAAATTC
131 GTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGCATGATGAATCTTAAAAAATTC
13911 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
* * * *
13957 TTTATTACTATGTAGCTTGCTTGTTCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAACTGACATTCTCTCCAACCTT
*
14022 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAATCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
*
14087 GTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 GTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGCATGATGAATCTTAAAAAATTC
* *
14152 AAAAAGACTTGGAAAAAGTTCTATCGATCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
14198 TTTAT
1 TTTAT
14203 ATAACCTTAA
Statistics
Matches: 234, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
240 177 0.76
241 57 0.24
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (241 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAACTGACATTCTCTCCAACCTT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
GTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGCATGATGAATCTTAAAAAATTC
AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:14409 original size:9 final size:9
Alignment explanation
Indices: 14382--14509 Score: 112
Period size: 9 Copynumber: 13.6 Consensus size: 9
14372 ATTGATCATT
*
14382 ACTTAAATA
1 ACTTACATA
*
14391 AATTACATA
1 ACTTACATA
*
14400 ACTTAAATA
1 ACTTACATA
* *
14409 ACTCATATA
1 ACTTACATA
14418 ACTTACATA
1 ACTTACATA
*
14427 ATTTACATAACA
1 ACTTACAT---A
14439 ACTTACATA
1 ACTTACATA
*
14448 ACTCACATA
1 ACTTACATA
14457 ACTTACATA
1 ACTTACATA
*
14466 ATTTACATA
1 ACTTACATA
*
14475 ACTCACATA
1 ACTTACATA
*
14484 ACGTACATAACA
1 ACTTACAT---A
14496 ACTTACATA
1 ACTTACATA
14505 ACTTA
1 ACTTA
14510 ACTAATACAT
Statistics
Matches: 95, Mismatches: 18, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
9 79 0.83
12 16 0.17
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:14452 original size:39 final size:39
Alignment explanation
Indices: 14399--14476 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
14389 TAAATTACAT
*
14399 AACTTAAATAACTCATATAACTTACATAATTTACATAAC
1 AACTTAAATAACTCACATAACTTACATAATTTACATAAC
*
14438 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTAAATAACTCACATAACTTACATAATTTACATAAC
14477 TCACATAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTAAATAACTCACATAACTTACATAATTTACATAAC
Found at i:14476 original size:57 final size:57
Alignment explanation
Indices: 14395--14507 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 57
14385 TAAATAAATT
* * **
14395 ACATAACTTAAATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTAAATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* * *
14452 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACATAACTTAAATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
14508 TAACTAATAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.30
Consensus pattern (57 bp):
ACATAACTTAAATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:17307 original size:54 final size:54
Alignment explanation
Indices: 17225--17336 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
17215 GGCAGAGGAG
17225 AGTATGACATTCTGTTCTAGATATTTAGATGTTGAAACAAGATTGAATAGACCA
1 AGTATGACATTCTGTTCTAGATATTTAGATGTTGAAACAAGATTGAATAGACCA
17279 AGTATGACATTCTGTTCTAGATATTTAGATGTTGAAACAAGATTGAATAGACCA
1 AGTATGACATTCTGTTCTAGATATTTAGATGTTGAAACAAGATTGAATAGACCA
17333 AGTA
1 AGTA
17337 GAAATGCCGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (54 bp):
AGTATGACATTCTGTTCTAGATATTTAGATGTTGAAACAAGATTGAATAGACCA
Found at i:20125 original size:21 final size:21
Alignment explanation
Indices: 20101--20144 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
20091 TCAACTTAGA
20101 GCGGAGGCAGCAACGAGGGAG
1 GCGGAGGCAGCAACGAGGGAG
*
20122 GCGGAGGCAGCAGCGAGGGAG
1 GCGGAGGCAGCAACGAGGGAG
20143 GC
1 GC
20145 AGAGCAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.20, G:0.55, T:0.00
Consensus pattern (21 bp):
GCGGAGGCAGCAACGAGGGAG
Found at i:20490 original size:43 final size:43
Alignment explanation
Indices: 20442--20593 Score: 250
Period size: 43 Copynumber: 3.5 Consensus size: 43
20432 ACTGGGCAAA
* * *
20442 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGATCCTGGTCT
1 TTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCT
* *
20485 GTAGCGGTGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCT
1 TTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCT
20528 TTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCT
1 TTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCT
*
20571 TTAGCGGCATTTTTTGAAGAAGC
1 TTAGCGGCGTTTTTTGAAGAAGC
20594 AGTCTTTAGC
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCT
Found at i:20599 original size:28 final size:28
Alignment explanation
Indices: 20567--20621 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
20557 AAAGGTCCTG
20567 GTCTTTAGCGGCATTTTTTGAAGAAGCA
1 GTCTTTAGCGGCATTTTTTGAAGAAGCA
* *
20595 GTCTTTAGCGGCGTTTTTTGTAGAAGC
1 GTCTTTAGCGGCATTTTTTGAAGAAGC
20622 GCCGCTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.38
Consensus pattern (28 bp):
GTCTTTAGCGGCATTTTTTGAAGAAGCA
Found at i:20640 original size:71 final size:71
Alignment explanation
Indices: 20524--20664 Score: 255
Period size: 71 Copynumber: 2.0 Consensus size: 71
20514 AAAGGTCCTG
*
20524 GTCTTTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTTTGAA
1 GTCTTTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTATGAA
20589 GAAGCA
66 GAAGCA
* *
20595 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTATGTA
1 GTCTTTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTATGAA
20660 GAAGC
66 GAAGC
20665 GCCGCTAAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.33
Consensus pattern (71 bp):
GTCTTTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTATGAA
GAAGCA
Found at i:20686 original size:114 final size:114
Alignment explanation
Indices: 20481--20707 Score: 373
Period size: 114 Copynumber: 2.0 Consensus size: 114
20471 AAAGATCCTG
* * *
20481 GTCTGTAGCGGTGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTTTTGAA
1 GTCTGTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTATGAA
*
20546 GAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTTTGAAGAAGCA
66 GAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTTTTGAAGAAGCA
* * *
20595 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTATGTA
1 GTCTGTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTATGAA
* *
20660 GAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTTGTAGAAGC
66 GAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTTTTGAAGAAGC
20708 GCCGCTAAAG
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (114 bp):
GTCTGTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTATGAA
GAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTTTTGAAGAAGCA
Found at i:20728 original size:157 final size:158
Alignment explanation
Indices: 20442--20752 Score: 489
Period size: 157 Copynumber: 2.0 Consensus size: 158
20432 ACTGGGCAAA
** *
20442 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGATCCTGGTCTGTAGCGGTGTTTTTTGAAGAAG
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGATCCTGGTCTGTAGCGGCATTTTATGAAGAAG
*
20507 CGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTT
66 CGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTT
20572 TAGCGGCATTTTTTGA-AGAAGCAGTCT
131 TAGCGGCATTTTTTGATAGAAGCAGTCT
** * * * *
20599 TTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCATTTTATGTAGAAG
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGATCCTGGTCTGTAGCGGCATTTTATGAAGAAG
*
20664 CGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTGGTCTT
66 CGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTT
** *
20729 TAGCGGTGTTTTTTTATAGAAGCA
131 TAGCGGCATTTTTTGATAGAAGCA
20753 CCGCTAAAGG
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
157 132 0.95
158 7 0.05
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (158 bp):
TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGATCCTGGTCTGTAGCGGCATTTTATGAAGAAG
CGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCTT
TAGCGGCATTTTTTGATAGAAGCAGTCT
Found at i:20757 original size:44 final size:43
Alignment explanation
Indices: 20595--20786 Score: 312
Period size: 43 Copynumber: 4.4 Consensus size: 43
20585 TGAAGAAGCA
20595 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
* * *
20638 GTCTTTAGCGGCATTTTATGTAGAAGCGCCGCTAAAGGTCATG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
20681 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
* * *
20724 GTCTTTAGCGGTGTTTTTTTATAGAAGCACCGCTAAAGGTCCTG
1 GTCTTTAGCGGCG-TTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
*
20768 GTCTTTAGCGACGTTTTTT
1 GTCTTTAGCGGCGTTTTTT
20787 CTGAAAAACG
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
43 98 0.72
44 39 0.28
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (43 bp):
GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
Found at i:28845 original size:40 final size:40
Alignment explanation
Indices: 28762--29024 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
28752 TTGAATGCTG
* * * * * *
28762 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
28802 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
28842 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
28882 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
28922 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28962 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
29001 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29025 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:29044 original size:79 final size:80
Alignment explanation
Indices: 28801--29059 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
28791 AAGTGAATAT
* * * * * * *
28801 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
28865 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
28881 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
28946 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
28961 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
29025 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
29040 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
29060 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Done.