Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4434.1
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: 60016
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 226 characters in sequence are not A, C, G, or T
Found at i:1041 original size:40 final size:40
Alignment explanation
Indices: 1009--1316 Score: 431
Period size: 40 Copynumber: 7.7 Consensus size: 40
999 CCAGCATGAT
* * * * *
1009 TGCTCTTTGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * *
1049 TGCTCTTCGAGG-TTTAGCACGGATATATTACTAGCACGAA
1 TGCTCTTCG-GGACTTAGCCCGGATACATCACTAGCACGAA
* * *
1089 TGCTCTTCGGAACTTAGCTCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
1129 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
1169 TGCTCTTCGGGACTTAGCCCGGGTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
1209 TGCTCTTCGGGACTTAGCCCGAATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
1249 TGCTCTTCGGGACTTAGTCCGGGTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1289 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGGACTTAGCCCGGATACATC
1317 GTCGAGACCT
Statistics
Matches: 238, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 5 0.02
40 231 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:3619 original size:47 final size:47
Alignment explanation
Indices: 3541--3754 Score: 313
Period size: 47 Copynumber: 4.6 Consensus size: 47
3531 CCCTTCGGGA
* * * * * *
3541 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
3587 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
3635 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
3682 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
3729 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
3755 CACAATTATC
Statistics
Matches: 152, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
46 2 0.01
47 148 0.97
48 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:7381 original size:40 final size:40
Alignment explanation
Indices: 7349--7610 Score: 380
Period size: 40 Copynumber: 6.5 Consensus size: 40
7339 CCAGCATGAT
* * *
7349 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATAACACTAGCACGAA
* *
7389 TGCTCTTCGGAACTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATAACACTAGCACGAA
* *
7429 TGCTCTTCGGAACTTAGTCCGGATACAACACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATAACACTAGCACGAA
* * *
7469 TGCTCTTCGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATAACACTAGCACGAA
* *
7509 TGCTCTTCGGAACTTAGTCCGGATACAACACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATAACACTAGCACGAA
* * *
7549 TGCTCTTCGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATAACACTAGCACGAA
*
7589 TGCTCTTCGGAACTTAGTCCGG
1 TGCTCTTCGGAACTTAGCCCGG
7611 TCGGAACTTA
Statistics
Matches: 195, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 195 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCCCGGATATAACACTAGCACGAA
Found at i:7459 original size:80 final size:80
Alignment explanation
Indices: 7349--7610 Score: 452
Period size: 80 Copynumber: 3.3 Consensus size: 80
7339 CCAGCATGAT
* * * * * * * *
7349 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAACTTAGCACGGATA
1 TGCTCTTCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATA
7414 TATCACTAGCACGAA
66 TATCACTAGCACGAA
7429 TGCTCTTCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATA
1 TGCTCTTCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATA
7494 TATCACTAGCACGAA
66 TATCACTAGCACGAA
7509 TGCTCTTCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATA
1 TGCTCTTCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATA
7574 TATCACTAGCACGAA
66 TATCACTAGCACGAA
7589 TGCTCTTCGGAACTTAGTCCGG
1 TGCTCTTCGGAACTTAGTCCGG
7611 TCGGAACTTA
Statistics
Matches: 174, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 174 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (80 bp):
TGCTCTTCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATA
TATCACTAGCACGAA
Found at i:7616 original size:16 final size:16
Alignment explanation
Indices: 7595--7626 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
7585 CGAATGCTCT
7595 TCGGAACTTAGTCCGG
1 TCGGAACTTAGTCCGG
7611 TCGGAACTTAGTCCGG
1 TCGGAACTTAGTCCGG
7627 ATACAACACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (16 bp):
TCGGAACTTAGTCCGG
Found at i:7678 original size:40 final size:40
Alignment explanation
Indices: 7611--7862 Score: 292
Period size: 40 Copynumber: 6.6 Consensus size: 40
7601 CTTAGTCCGG
* * *
7611 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* *
7651 TCGGGATTTAGCCCGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* ** * *
7691 TTGAAACTTAGTCCGGATACAACACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* *
7731 TCGGGATTTAGCCCGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
* *
7771 TCGGAACTTAGTCCGG-------A-TA-CA-GAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
7801 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
*
7841 TCGGGAATTAGCCCGGAT-CATC
1 TCGGGACTTAGCCCGGATACATC
7863 GTCGAGACCT
Statistics
Matches: 177, Mismatches: 25, Indels: 21
0.79 0.11 0.09
Matches are distributed among these distances:
30 23 0.13
31 2 0.01
32 2 0.01
33 1 0.01
37 1 0.01
38 2 0.01
39 6 0.03
40 140 0.79
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
TCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCT
Found at i:7679 original size:96 final size:96
Alignment explanation
Indices: 7515--7706 Score: 366
Period size: 96 Copynumber: 2.0 Consensus size: 96
7505 CGAATGCTCT
7515 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
*
7580 TAGCACGAATGCTCTTCGGAACTTAGTCCGG
66 TAGCACGAATGCTCTTCGAAACTTAGTCCGG
7611 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
*
7676 TAGCACGAATGCTCTTTGAAACTTAGTCCGG
66 TAGCACGAATGCTCTTCGAAACTTAGTCCGG
7707 ATACAACACT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (96 bp):
TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
TAGCACGAATGCTCTTCGAAACTTAGTCCGG
Found at i:7729 original size:176 final size:176
Alignment explanation
Indices: 7435--7786 Score: 686
Period size: 176 Copynumber: 2.0 Consensus size: 176
7425 CGAATGCTCT
7435 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
*
7500 TAGCACGAATGCTCTTCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTA
66 TAGCACGAATGCTCTTCGAAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTA
7565 GCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGG
131 GCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGG
7611 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
1 TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
*
7676 TAGCACGAATGCTCTTTGAAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTA
66 TAGCACGAATGCTCTTCGAAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTA
7741 GCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGG
131 GCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGG
7787 ATACAGAATG
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 174 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (176 bp):
TCGGAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCAC
TAGCACGAATGCTCTTCGAAACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTA
GCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGG
Found at i:7748 original size:80 final size:80
Alignment explanation
Indices: 7615--7843 Score: 352
Period size: 80 Copynumber: 3.0 Consensus size: 80
7605 GTCCGGTCGG
7615 AACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCACTAGC
1 AACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCACTAGC
*
7680 ACGAATGCTCTTTGA
66 ACGAATGCTCTTCGA
7695 AACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCACTAGC
1 AACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCACTAGC
*
7760 ACGAATGCTCTTCGG
66 ACGAATGCTCTTCGA
* *
7775 AACTTAGTCCGG-------A-TA-CA-GAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGC
1 AACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCACTAGC
7830 ACGAATGCTCTTCG
66 ACGAATGCTCTTCG
7844 GGAATTAGCC
Statistics
Matches: 145, Mismatches: 4, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
70 50 0.34
71 2 0.01
72 2 0.01
73 1 0.01
80 90 0.62
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (80 bp):
AACTTAGTCCGGATACAACACTAGCACGAATGCTCTTCGGGATTTAGCCCGGATATATCACTAGC
ACGAATGCTCTTCGA
Found at i:7796 original size:30 final size:30
Alignment explanation
Indices: 7762--7821 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
7752 TCACTAGCAC
*
7762 GAATGCTCTTCGGAACTTAGTCCGGATACA
1 GAATGCTCTTCGGAACTTAGCCCGGATACA
*
7792 GAATGCTCTTCGGGACTTAGCCCGGATACA
1 GAATGCTCTTCGGAACTTAGCCCGGATACA
7822 TCACTAGCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (30 bp):
GAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:7835 original size:70 final size:70
Alignment explanation
Indices: 7722--7858 Score: 231
Period size: 70 Copynumber: 2.0 Consensus size: 70
7712 ACACTAGCAC
* * *
7722 GAATGCTCTTCGGGATTTAGCCCGGATATATCACTAGCACGAATGCTCTTC-GGAACTTAGTCCG
1 GAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAA-TTAGCCCG
7786 GATACA
65 GATACA
7792 GAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAATTAGCCCGG
1 GAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAATTAGCCCGG
7857 AT
66 AT
7859 CATCGTCGAG
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 59 0.94
71 4 0.06
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (70 bp):
GAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAATTAGCCCGG
ATACA
Found at i:7959 original size:38 final size:38
Alignment explanation
Indices: 7917--7990 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
7907 AATTTTAATT
*
7917 CGGACATAATCTCTGT-ACATAGCCATCGGGTCTTTACC
1 CGGACATAATCTCT-TCACATAGCCAGCGGGTCTTTACC
* *
7955 CGGACATAATCTCTTCATATAGTCAGCGGGTCTTTA
1 CGGACATAATCTCTTCACATAGCCAGCGGGTCTTTA
7991 AACTCGGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (38 bp):
CGGACATAATCTCTTCACATAGCCAGCGGGTCTTTACC
Found at i:20158 original size:12 final size:13
Alignment explanation
Indices: 20135--20183 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
20125 CCCTAATGTT
20135 ATAAAAGAAAAATA
1 ATAAAAG-AAAATA
20149 A-AAAAGAAAATA
1 ATAAAAGAAAATA
* *
20161 ATAATA-ATAATA
1 ATAAAAGAAAATA
20173 ATAAAAGAAAA
1 ATAAAAGAAAA
20184 AAAGAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 17 0.59
13 11 0.38
14 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (13 bp):
ATAAAAGAAAATA
Found at i:23167 original size:20 final size:21
Alignment explanation
Indices: 23130--23168 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
23120 TTTCAAATAT
* *
23130 AAATAACTAAAATGTAACTTA
1 AAATAAATAAAATATAACTTA
23151 AAATAAATAAAA-ATAACT
1 AAATAAATAAAATATAACT
23169 ATTTTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.26
Consensus pattern (21 bp):
AAATAAATAAAATATAACTTA
Found at i:23510 original size:7 final size:7
Alignment explanation
Indices: 23498--23529 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
23488 TTGGAGACAC
23498 AAAATTA
1 AAAATTA
23505 AAAATTA
1 AAAATTA
23512 AAAATTA
1 AAAATTA
23519 AAAATTA
1 AAAATTA
23526 AAAA
1 AAAA
23530 AAAGGGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATTA
Found at i:30280 original size:5 final size:6
Alignment explanation
Indices: 30264--30289 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30254 AACACTTTGG
30264 ATTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT
30290 CAAGAACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:40227 original size:24 final size:24
Alignment explanation
Indices: 40195--40240 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
40185 TAGTCGGAAC
40195 AGTGGTCTCGAGACCACAAATTCG
1 AGTGGTCTCGAGACCACAAATTCG
40219 AGTGGTCTCGAGACCACAAATT
1 AGTGGTCTCGAGACCACAAATT
40241 TGAAGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (24 bp):
AGTGGTCTCGAGACCACAAATTCG
Found at i:41094 original size:47 final size:44
Alignment explanation
Indices: 40943--41158 Score: 152
Period size: 47 Copynumber: 4.7 Consensus size: 44
40933 TGATTTGTGC
** *
40943 GCCAGTGTAAGACATGTCTGGGACATGTTTCGGCC-ACATTATGA-GA
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GCCTA-A-GA-GATGA
* * * *
40989 GCCAGTGTAAGACCATGTCTGGCACATGGTATCGGC-ACAGAGATGGGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGCCTA-AGAGAT--GA
**
41037 GCCAAAGTAAGACATGTCTGGGACATGCATCGACCTCGACAGAGAT-A
1 GCCAGTGTAAGACATGTCTGGGACATGCATCG-CCT--A-AGAGATGA
* * * * *
41084 GCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAGAGTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGCCTAAGAGATGA
*
41128 GCTAGTGTAAGACATGTCTGGGACATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
41159 AGCATGCATA
Statistics
Matches: 139, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
43 5 0.04
44 29 0.21
45 2 0.01
46 20 0.14
47 60 0.43
48 15 0.11
50 8 0.06
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (44 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGCCTAAGAGATGA
Found at i:47631 original size:5 final size:6
Alignment explanation
Indices: 47617--47641 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47607 CATTTTTAAT
47617 AAAAGA AAAAGA AAAAGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA A
47642 GGAAAGAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:48127 original size:47 final size:46
Alignment explanation
Indices: 48017--48289 Score: 273
Period size: 47 Copynumber: 5.8 Consensus size: 46
48007 TGATTTGTGT
* * *
48017 GCCAGTGTAAGA-CATGTCTGGGACATGCTTCGGCCACATTATGAGA
1 GCCAGAGTAAGACCATGTCTGGGACATGCATCGG-CACAATATGAGA
* * * * *
48063 GCTAGCGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGATGAGT
1 GCCAGAGTAAGACCATGTCTGGGACAT-GCATCGGCACA-ATATGAGA
* *
48111 GCCAGAGTAAGA-CATGTCTGGGACATGCTTCGGCCACATTATGAGA
1 GCCAGAGTAAGACCATGTCTGGGACATGCATCGG-CACAATATGAGA
* * * * *
48157 GCTAGCGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGATGAGT
1 GCCAGAGTAAGACCATGTCTGGGACAT-GCATCGGCACA-ATATGAGA
*
48205 GCCAGAGTAAGA-CATGTCTGGGACATGCATCAGCACGCATATATGAGA
1 GCCAGAGTAAGACCATGTCTGGGACATGCATCGGCA--CA-ATATGAGA
* *
48253 GCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCA
1 GCCAGAGTAAGACCATGTCTGGGACAT-GCATCGGCA
48290 ATTTATCCCA
Statistics
Matches: 185, Mismatches: 31, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
46 39 0.21
47 65 0.35
48 60 0.32
49 13 0.07
50 8 0.04
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (46 bp):
GCCAGAGTAAGACCATGTCTGGGACATGCATCGGCACAATATGAGA
Found at i:48176 original size:94 final size:94
Alignment explanation
Indices: 48015--48289 Score: 469
Period size: 94 Copynumber: 2.9 Consensus size: 94
48005 GGTGATTTGT
*
48015 GTGCCAGTGTAAGACATGTCTGGGACATGCTTCGGCCACATTATGAGAGCTAGCGTAAGACCATG
1 GTGCCAGAGTAAGACATGTCTGGGACATGCTTCGGCCACATTATGAGAGCTAGCGTAAGACCATG
48080 TCTGGGACATGGCATCGGCATAGAGATGA
66 TCTGGGACATGGCATCGGCATAGAGATGA
48109 GTGCCAGAGTAAGACATGTCTGGGACATGCTTCGGCCACATTATGAGAGCTAGCGTAAGACCATG
1 GTGCCAGAGTAAGACATGTCTGGGACATGCTTCGGCCACATTATGAGAGCTAGCGTAAGACCATG
48174 TCTGGGACATGGCATCGGCATAGAGATGA
66 TCTGGGACATGGCATCGGCATAGAGATGA
* * * * *
48203 GTGCCAGAGTAAGACATGTCTGGGACATGCATCAGCACGCATATATGAGAGCCAGTGTAAGACCA
1 GTGCCAGAGTAAGACATGTCTGGGACATGCTTCGGC-CACAT-TATGAGAGCTAGCGTAAGACCA
*
48268 TGTTTGGGACATGGCATCGGCA
64 TGTCTGGGACATGGCATCGGCA
48290 ATTTATCCCA
Statistics
Matches: 172, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
94 127 0.74
95 4 0.02
96 41 0.24
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (94 bp):
GTGCCAGAGTAAGACATGTCTGGGACATGCTTCGGCCACATTATGAGAGCTAGCGTAAGACCATG
TCTGGGACATGGCATCGGCATAGAGATGA
Found at i:48712 original size:105 final size:105
Alignment explanation
Indices: 48582--48794 Score: 426
Period size: 105 Copynumber: 2.0 Consensus size: 105
48572 TCTTCTTTCA
48582 ATATCTCTAGGCTAGCTTAAGGATTCCATAAAGTCAGAGATATTGGTCACACTATCAGCCGTAGT
1 ATATCTCTAGGCTAGCTTAAGGATTCCATAAAGTCAGAGATATTGGTCACACTATCAGCCGTAGT
48647 GCTTGGTATAGTTTGATTTATATTTTTGAAGGTGGCATGT
66 GCTTGGTATAGTTTGATTTATATTTTTGAAGGTGGCATGT
48687 ATATCTCTAGGCTAGCTTAAGGATTCCATAAAGTCAGAGATATTGGTCACACTATCAGCCGTAGT
1 ATATCTCTAGGCTAGCTTAAGGATTCCATAAAGTCAGAGATATTGGTCACACTATCAGCCGTAGT
48752 GCTTGGTATAGTTTGATTTATATTTTTGAAGGTGGCATGT
66 GCTTGGTATAGTTTGATTTATATTTTTGAAGGTGGCATGT
48792 ATA
1 ATA
48795 GGGCTAGAGT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 108 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (105 bp):
ATATCTCTAGGCTAGCTTAAGGATTCCATAAAGTCAGAGATATTGGTCACACTATCAGCCGTAGT
GCTTGGTATAGTTTGATTTATATTTTTGAAGGTGGCATGT
Found at i:53452 original size:27 final size:27
Alignment explanation
Indices: 53422--53599 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
53412 ATATTGAGTC
* * * *
53422 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
53449 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53476 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
53504 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
53531 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
53558 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53585 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53600 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:53561 original size:82 final size:81
Alignment explanation
Indices: 53443--53598 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
53433 TGCTATATAA
* *
53443 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
53508 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
53525 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
53589 CACTTAGTGC
65 CACTTAGTGC
53599 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.