Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012233.1 Corchorus capsularis cultivar CVL-1 contig12254, whole genome shotgun sequence
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: 79660
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:6936 original size:56 final size:57
Alignment explanation
Indices: 6823--6938 Score: 198
Period size: 56 Copynumber: 2.0 Consensus size: 57
6813 GGCCAACAAA
* *
6823 TTATGCTCAATCGGTCTTTCAACTTTTTTTTTTTTTGTATATTTACAAGTTAACCTTG
1 TTATGCTCAATCGGTCTTTCAAC-TTCTTTTTTTTGGTATATTTACAAGTTAACCTTG
6881 TTATGCTCAATCGGTCTTTCAAC-TCTTTTTTTTGGTATATTTACAAGTTAACCTTG
1 TTATGCTCAATCGGTCTTTCAACTTCTTTTTTTTGGTATATTTACAAGTTAACCTTG
6937 TT
1 TT
6939 TGAGCCTGGT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
56 33 0.59
58 23 0.41
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.52
Consensus pattern (57 bp):
TTATGCTCAATCGGTCTTTCAACTTCTTTTTTTTGGTATATTTACAAGTTAACCTTG
Found at i:7435 original size:20 final size:18
Alignment explanation
Indices: 7393--7428 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
7383 ACACGGGTTA
*
7393 ATTTAGCCACGTGGATTT
1 ATTTAGCCACATGGATTT
7411 ATTTAGCCACATGGATTT
1 ATTTAGCCACATGGATTT
7429 TTATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (18 bp):
ATTTAGCCACATGGATTT
Found at i:7516 original size:11 final size:11
Alignment explanation
Indices: 7500--7529 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
7490 CTCTGAAACC
7500 TTTTTTCTTTT
1 TTTTTTCTTTT
7511 TTTTTTCTTTT
1 TTTTTTCTTTT
*
7522 TCTTTTCT
1 TTTTTTCT
7530 CCTTCTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:11572 original size:55 final size:56
Alignment explanation
Indices: 11487--11646 Score: 162
Period size: 55 Copynumber: 2.8 Consensus size: 56
11477 CAAACCTTCT
* * * **
11487 AGTACAGGACAATGCGTCAATATCAACATTAACCTTTGCAAGTCTCAGTAGACTTC
1 AGTACAGGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTAGACCAC
* * *
11543 -GTACAGGACATTGCATCAATTTCAACATTAATCTTTGCGAGTC-CAGTGGACCAC
1 AGTACAGGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTAGACCAC
* * * *
11597 AAATTATTCGGGACATTGCATCAATTTCAATATTAACCTTTACAAGTCTC
1 --AGTA--CAGGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTC
11647 GTGGACCGCA
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
54 8 0.10
55 38 0.45
57 2 0.02
59 35 0.42
60 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (56 bp):
AGTACAGGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTAGACCAC
Found at i:11622 original size:59 final size:60
Alignment explanation
Indices: 11493--11796 Score: 253
Period size: 59 Copynumber: 5.0 Consensus size: 60
11483 TTCTAGTACA
* * * * ** * *
11493 GGACAATGCGTCAATATCAACATTAACCTTTGCAAGTCTCAGTAGACTTC---GTA--CA
1 GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAATTATTCG
* * *
11548 GGACATTGCATCAATTTCAACATTAATCTTTGCGAGTC-CAGTGGACCACAAATTATTCG
1 GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAATTATTCG
* *
11607 GGACATTGCATCAATTTCAATATTAACCTTTACAAGTCTC-GTGGACCGCAAATTATTCATATG
1 GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAATTATTC----G
* * * ** *
11670 GGGCATTTCATCAATTTCATCAACAACCTTTGCAAGTCCCAGTGGACCGCAAATTAATATCCGTA
1 GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAA-T--TAT---T-
11735 CG
59 CG
* * * *
11737 GGACATTGCATCAATTTCACCGTTAATCTTTGCAAGTCTCAGTGGACTGCAAATTATTCG
1 GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAATTATTCG
11797 TAAGCCACAA
Statistics
Matches: 199, Mismatches: 32, Indels: 31
0.76 0.12 0.12
Matches are distributed among these distances:
54 8 0.04
55 33 0.17
57 2 0.01
59 52 0.26
60 3 0.02
61 1 0.01
63 33 0.17
64 15 0.08
65 1 0.01
66 1 0.01
67 48 0.24
70 1 0.01
71 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (60 bp):
GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAATTATTCG
Found at i:11768 original size:67 final size:65
Alignment explanation
Indices: 11548--11792 Score: 263
Period size: 67 Copynumber: 3.9 Consensus size: 65
11538 ACTTCGTACA
* * *
11548 GGACATTGCATCAATTTCAACATTAATCTTTGCGAGTC-CAGTGGACCACAAATT-A-T--T-CG
1 GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAATTAATTCATACG
* * *
11607 GGACATTGCATCAATTTCAATATTAACCTTTACAAGTCTC-GTGGACCGCAAATT-ATTCATATG
1 GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAATTAATTCATACG
* * * ** * *
11670 GGGCATTTCATCAATTTCATCAACAACCTTTGCAAGTCCCAGTGGACCGCAAATTAATATCCGTA
1 GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAATTAAT-T-CATA
11735 CG
64 CG
* * * *
11737 GGACATTGCATCAATTTCACCGTTAATCTTTGCAAGTCTCAGTGGACTGCAAATTA
1 GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAATTA
11793 TTCGTAAGCC
Statistics
Matches: 152, Mismatches: 25, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
59 48 0.32
60 2 0.01
62 1 0.01
63 33 0.22
64 14 0.09
65 2 0.01
66 1 0.01
67 51 0.34
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (65 bp):
GGACATTGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTGGACCGCAAATTAATTCATACG
Found at i:12506 original size:75 final size:74
Alignment explanation
Indices: 12375--12517 Score: 232
Period size: 75 Copynumber: 1.9 Consensus size: 74
12365 AATGAAACAC
* * * *
12375 GCATGTAGAAACGAAGTTAAAGGAACTATCACCGTCACAGAAACAATGAGTGTCAAAAAGCCAAA
1 GCATGTAGAAACGAAGTTAAAGGAACCATCACCGTCACAGAAAAAACGAGTCTC-AAAAGCCAAA
12440 GCAAAAATAT
65 GCAAAAATAT
*
12450 GCATGTAGAAACGAAGTTAAAGGAACCATCACCGTCATAGAAAAAACGAGTCTCAAAAGCCAAAG
1 GCATGTAGAAACGAAGTTAAAGGAACCATCACCGTCACAGAAAAAACGAGTCTCAAAAGCCAAAG
12515 CAA
66 CAA
12518 TATAAACAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 14 0.22
75 49 0.78
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.15
Consensus pattern (74 bp):
GCATGTAGAAACGAAGTTAAAGGAACCATCACCGTCACAGAAAAAACGAGTCTCAAAAGCCAAAG
CAAAAATAT
Found at i:16441 original size:16 final size:17
Alignment explanation
Indices: 16405--16440 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
16395 ACAAAAACAG
*
16405 AACAATATATTCTTTGAA
1 AACAATATATTCTAT-AA
16423 AACAATATATTCTATAA
1 AACAATATATTCTATAA
16440 A
1 A
16441 CTGGCAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (17 bp):
AACAATATATTCTATAA
Found at i:17189 original size:61 final size:61
Alignment explanation
Indices: 17073--17215 Score: 182
Period size: 61 Copynumber: 2.3 Consensus size: 61
17063 TTTTCTAATA
* * * *
17073 AGGGACCA-TGCATCAATTTCAACATTAAACTTTGCAAGTCTTAGTGGACTACAAATTGTTC
1 AGGGA-CATTGCATCAATTCCAACAATAAACTTTGCAAGTCTCAGTGGACTACAAATTATTC
*
17134 -GGGACATTGCATCAATTCCAACAATAAACCTTTGCAAGTCTCAGTGGACTCCAAATTATTC
1 AGGGACATTGCATCAATTCCAACAATAAA-CTTTGCAAGTCTCAGTGGACTACAAATTATTC
17195 AAATGGGACATTGCATCAATT
1 --A-GGGACATTGCATCAATT
17216 TGCAAGTCCA
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
59 2 0.03
60 23 0.32
61 29 0.41
65 17 0.24
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (61 bp):
AGGGACATTGCATCAATTCCAACAATAAACTTTGCAAGTCTCAGTGGACTACAAATTATTC
Found at i:17488 original size:16 final size:18
Alignment explanation
Indices: 17452--17487 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17442 ACAAAAACAT
*
17452 AACAATATATTCTTTTAA
1 AACAATATATTCTTGTAA
17470 AACAATATATT-TTGTAA
1 AACAATATATTCTTGTAA
17487 A
1 A
17488 CTAGCAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (18 bp):
AACAATATATTCTTGTAA
Found at i:17781 original size:25 final size:25
Alignment explanation
Indices: 17747--17801 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
17737 ATTCGGGACA
17747 TTGCATCAATTCCAACAATAAACCT
1 TTGCATCAATTCCAACAATAAACCT
17772 TTGCATCAATTCCAACAATAAACCT
1 TTGCATCAATTCCAACAATAAACCT
17797 TTGCA
1 TTGCA
17802 AGTCTCAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.29
Consensus pattern (25 bp):
TTGCATCAATTCCAACAATAAACCT
Found at i:32974 original size:168 final size:168
Alignment explanation
Indices: 32689--33019 Score: 572
Period size: 168 Copynumber: 2.0 Consensus size: 168
32679 CAGGGTCCAA
* *
32689 GTATGCTGGAACTAAGAGTTCAGTACTCTACCACCAGGCCAAATGTCCGATGACTATGTAACCAA
1 GTATGCCGGAACTAAGAGTCCAGTACTCTACCACCAGGCCAAATGTCCGATGACTATGTAACCAA
*
32754 CATCTTTGGCCGTAAGAAAAAAAATGGCATTGATACCAACTAGACCTGTTCAAGGGTCAGGTTAC
66 CATCTTTGGCCGTAAGAAAAAAAATGGCATTGATACCAACTAGACCTGTTCAAGGGCCAGGTTAC
* *
32819 CCGCCCAAGCCCGTAAGCACGCCCGATATTTGGTCAAT
131 CCGCCCAAACCCGTAAGCACGCCAGATATTTGGTCAAT
* *
32857 GTATGCCGGAACTAAGAGTCCAGTACTCTACCACCAGGTCAAATGTCCGATGGCTATGTAACCAA
1 GTATGCCGGAACTAAGAGTCCAGTACTCTACCACCAGGCCAAATGTCCGATGACTATGTAACCAA
* *
32922 CATCTTTGGCCGTAAGAAAAAAAATGGCATTGATACCAACTAGACTTGTTCAAGGGCCGGGTTAC
66 CATCTTTGGCCGTAAGAAAAAAAATGGCATTGATACCAACTAGACCTGTTCAAGGGCCAGGTTAC
*
32987 CCGCCCAAACCCGTAAGCCCGCCAGATATTTGG
131 CCGCCCAAACCCGTAAGCACGCCAGATATTTGG
33020 GAGGGTTTGG
Statistics
Matches: 153, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
168 153 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (168 bp):
GTATGCCGGAACTAAGAGTCCAGTACTCTACCACCAGGCCAAATGTCCGATGACTATGTAACCAA
CATCTTTGGCCGTAAGAAAAAAAATGGCATTGATACCAACTAGACCTGTTCAAGGGCCAGGTTAC
CCGCCCAAACCCGTAAGCACGCCAGATATTTGGTCAAT
Found at i:33304 original size:25 final size:25
Alignment explanation
Indices: 33273--33321 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
33263 TCTTAGATAT
*
33273 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
33298 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
33322 GATTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:33351 original size:25 final size:23
Alignment explanation
Indices: 33271--33351 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 23
33261 TATCTTAGAT
33271 ATAATATATATTATTAAATAAAT-A
1 ATAA-ATATATT-TTAAATAAATAA
33295 ATAAATATATTTTAAAT-AATAA
1 ATAAATATATTTTAAATAAATAA
**
33317 AT-AATGAT-TTCAAAATAAATAA
1 ATAAAT-ATATTTTAAATAAATAA
33339 ATAATATATATTT
1 ATAA-ATATATTT
33352 AATTATTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
21 12 0.25
22 18 0.38
23 10 0.21
24 8 0.17
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
ATAAATATATTTTAAATAAATAA
Found at i:41167 original size:30 final size:30
Alignment explanation
Indices: 41131--41194 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
41121 AACATGGTAT
41131 GGAGATGGTTGCTGCGGGGCGCCATAAGGG
1 GGAGATGGTTGCTGCGGGGCGCCATAAGGG
41161 GGAGATGGTTGCTGCGGGGCGCCATAAGGG
1 GGAGATGGTTGCTGCGGGGCGCCATAAGGG
41191 GGAG
1 GGAG
41195 GATGATGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.17, C:0.16, G:0.52, T:0.16
Consensus pattern (30 bp):
GGAGATGGTTGCTGCGGGGCGCCATAAGGG
Found at i:46799 original size:1 final size:1
Alignment explanation
Indices: 46793--46823 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
46783 GCGTTGTGCC
46793 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46824 GTCCAAGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:46881 original size:4 final size:4
Alignment explanation
Indices: 46872--46933 Score: 56
Period size: 4 Copynumber: 15.5 Consensus size: 4
46862 TTATTTTTAA
* * * *
46872 AAAT AAAT AAAT -ATT ATTAT AAAT AAAT AAAT AAAT -ATT ATTAT AAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT
46920 AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AA
46934 GTTCCCTTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
3 4 0.09
4 38 0.83
5 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (4 bp):
AAAT
Found at i:46903 original size:24 final size:24
Alignment explanation
Indices: 46872--46932 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
46862 TTATTTTTAA
46872 AAATAAATAAATATTATTATAAAT
1 AAATAAATAAATATTATTATAAAT
46896 AAATAAATAAATATTATTATAAAT
1 AAATAAATAAATATTATTATAAAT
46920 AAATAAATAAATA
1 AAATAAATAAATA
46933 AGTTCCCTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AAATAAATAAATATTATTATAAAT
Found at i:47609 original size:1 final size:1
Alignment explanation
Indices: 47603--47638 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
47593 TTGTATTAGG
47603 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
47639 AAGATAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:55988 original size:1 final size:1
Alignment explanation
Indices: 55982--56008 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
55972 CCCAAAAGGA
55982 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
56009 CTCTGGGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:61575 original size:16 final size:15
Alignment explanation
Indices: 61554--61594 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
61544 TTTTTTTTAA
61554 TAATTATATTAAGAAT
1 TAATTATATTAA-AAT
61570 TAATTATATT--AAT
1 TAATTATATTAAAAT
61583 TAATTATATTAA
1 TAATTATATTAA
61595 TATAATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 13 0.57
16 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TAATTATATTAAAAT
Found at i:61585 original size:13 final size:13
Alignment explanation
Indices: 61567--61601 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
61557 TTATATTAAG
61567 AATTAATTATATT
1 AATTAATTATATT
61580 AATTAATTATATT
1 AATTAATTATATT
61593 AATATAATT
1 AAT-TAATT
61602 GTAAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AATTAATTATATT
Found at i:70742 original size:31 final size:31
Alignment explanation
Indices: 70706--70773 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
70696 AAAAAGGGGC
70706 AATCAGCAATTAAAGTTCAATAAGAAA-AAGT
1 AATCAGCAATT-AAGTTCAATAAGAAAGAAGT
** *
70737 AATCAGTGATTAAGTTCAATAAGAAAGATGT
1 AATCAGCAATTAAGTTCAATAAGAAAGAAGT
70768 AATCAG
1 AATCAG
70774 TAAAAGGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (31 bp):
AATCAGCAATTAAGTTCAATAAGAAAGAAGT
Found at i:70793 original size:22 final size:23
Alignment explanation
Indices: 70768--70827 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
70758 AGAAAGATGT
*
70768 AATCAGTAAAAG-GTAAAGCGGC
1 AATCAGTAAAAGAGTAAAGCGAC
* *
70790 AATCAGT-AAAGAGTAAAGTGAT
1 AATCAGTAAAAGAGTAAAGCGAC
70812 AATCAGT-AAAGAGTAA
1 AATCAGTAAAAGAGTAA
70828 TAAAAATCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.18
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAGCGAC
Found at i:70844 original size:28 final size:28
Alignment explanation
Indices: 70812--70902 Score: 95
Period size: 28 Copynumber: 3.3 Consensus size: 28
70802 GTAAAGTGAT
70812 AATCAGTAAAGAGTAATAAAAATCAGTA
1 AATCAGTAAAGAGTAATAAAAATCAGTA
70840 AATCAGTAATTA-AGTGAA-AAGAAAT---T-
1 AATCAGTAA--AGAGT-AATAA-AAATCAGTA
*
70866 AATCAGTAAAGAGTAATAGAAATCAGTA
1 AATCAGTAAAGAGTAATAAAAATCAGTA
70894 AATCAGTAA
1 AATCAGTAA
70903 TTAAGTAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 20
0.71 0.01 0.27
Matches are distributed among these distances:
24 7 0.13
25 4 0.08
26 9 0.17
27 2 0.04
28 18 0.35
29 5 0.10
30 7 0.13
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23
Consensus pattern (28 bp):
AATCAGTAAAGAGTAATAAAAATCAGTA
Found at i:70869 original size:26 final size:25
Alignment explanation
Indices: 70840--70925 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 25
70830 AAAATCAGTA
70840 AATCAGTAATTAAGTGAAAAGAAATT
1 AATCAGTAATTAAGT-AAAAGAAATT
*
70866 AATCAGTAA--AGAGTAATAGAAATCAGT
1 AATCAGTAATTA-AGTAAAAGAAAT---T
*
70893 AAATCAGTAATTAAGTAAAAAGAGATT
1 -AATCAGTAATTAAGT-AAAAGAAATT
70920 AATCAG
1 AATCAG
70926 AGTCAAAGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
24 9 0.18
25 3 0.06
26 15 0.31
27 2 0.04
28 9 0.18
29 3 0.06
30 8 0.16
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.24
Consensus pattern (25 bp):
AATCAGTAATTAAGTAAAAGAAATT
Found at i:70961 original size:55 final size:54
Alignment explanation
Indices: 70811--70962 Score: 218
Period size: 54 Copynumber: 2.8 Consensus size: 54
70801 AGTAAAGTGA
* *
70811 TAATCAGTAAAGAGTAATAAAAATCAGTAAATCAGTAATTAAGTGAAAAGAAAT
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAAAT
*
70865 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAAAT
* *
70919 TAATCAGAGTCAA-AGTAATAGTAATCAGTAAATC-GATAATTAAG
1 TAATC--AGTAAAGAGTAATAGAAATCAGTAAATCAG-TAATTAAG
70963 AGTTAAAATG
Statistics
Matches: 90, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
54 57 0.63
55 28 0.31
56 5 0.06
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.25
Consensus pattern (54 bp):
TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAAAT
Found at i:71226 original size:22 final size:21
Alignment explanation
Indices: 71148--71555 Score: 233
Period size: 21 Copynumber: 19.5 Consensus size: 21
71138 AATAGCAGGC
71148 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAAA-GT
* * **
71170 -ACCTG-AAAGGGTAAAAAG-
1 AATCAGTAAAAAGTAAAAAGT
*
71188 AGTTCAGTAAAAGAGTAAAATAGT
1 A-ATCAGTAAAA-AGTAAAA-AGT
*
71212 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGTAAAAAGTAA-AAAGT
*
71234 AATCA--ACAAGAGTAAAATAGT
1 AATCAGTA-AAAAGTAAAA-AGT
* *
71255 AGTCAGTAAAAAGTAAATAGT
1 AATCAGTAAAAAGTAAAAAGT
*
71276 AAACAGT----A--AAAAAGT
1 AATCAGTAAAAAGTAAAAAGT
* * * *
71291 AATAAGTAAGAAGTAAAAGGA
1 AATCAGTAAAAAGTAAAAAGT
* * *** *
71312 AATCGGTAAGAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAAAGT
* *
71333 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAAAGTAAAAAG-T
*
71355 AATCAGCAAAAAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAAA-GT
* * *
71377 AATCAGTAAAAAGCAAAAGGC
1 AATCAGTAAAAAGTAAAAAGT
*
71398 AATCATTAAAAAGTAAAAGAGT
1 AATCAGTAAAAAGTAAAA-AGT
71420 AATCAGT-AAAA--AAAAAG-
1 AATCAGTAAAAAGTAAAAAGT
* * *
71437 GAGCAG-AAAATAGTAAAGAGT
1 AATCAGTAAAA-AGTAAAAAGT
71458 AATCAGTAAAAGAGTAAAACAGT
1 AATCAGTAAAA-AGTAAAA-AGT
*
71481 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGTAAAAAGTAA-AAAGT
*
71503 AATCA--ACAAGAGTAAAATAGT
1 AATCAGTA-AAAAGTAAAA-AGT
*
71524 AATCAGTACAAAGTAAAGAA-T
1 AATCAGTAAAAAGTAAA-AAGT
71545 AATCAGTAAAA
1 AATCAGTAAAA
71556 TAGTGATGCT
Statistics
Matches: 291, Mismatches: 62, Indels: 67
0.69 0.15 0.16
Matches are distributed among these distances:
15 11 0.04
17 8 0.03
18 3 0.01
19 6 0.02
20 23 0.08
21 109 0.37
22 97 0.33
23 33 0.11
24 1 0.00
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.17
Consensus pattern (21 bp):
AATCAGTAAAAAGTAAAAAGT
Found at i:71227 original size:64 final size:64
Alignment explanation
Indices: 71148--71292 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 64
71138 AATAGCAGGC
* * *
71148 AATCAGTAAAAAGTAAAAAGGT-ACCTGA-AAGGGTAAAA-AG-AGTTCAGTAAAAGAGTAAAAT
1 AATCAGTAAAAAGTAAAAAGGTAATC-AACAAGAGTAAAATAGTAG-TCAGTAAAA-AGT-AAAT
71209 AGT
62 AGT
*
71212 AATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGTAAATAGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGTAAATAGT
*
71276 AAACAGTAAAAAAGTAA
1 AATCAGT-AAAAAGTAA
71293 TAAGTAAGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
64 35 0.49
65 23 0.32
66 11 0.15
67 2 0.03
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (64 bp):
AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGTAAATAGT
Found at i:71247 original size:43 final size:41
Alignment explanation
Indices: 71198--71485 Score: 177
Period size: 43 Copynumber: 7.0 Consensus size: 41
71188 AGTTCAGTAA
71198 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAA-AGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
*
71241 AAGAGTAAAATAGTAGTCAGTAAAAAGTAAATA-GT-A--AAC
1 AAGAGTAAAA-AGTAATCAGTAAAAAGTAAA-AGGTAATCAAC
* * * ***
71280 ---AGTAAAAAAGTAATAAGTAAGAAGTAAAAGGAAATCGGT
1 AAGAGT-AAAAAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
* * * *
71319 AAGAGTAAAAAGGTGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAAA-GTAATCAGTAAAAAGT-AAAAGGTAATCAAC
* * *
71362 AAAAAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGCAATCATTA-
1 -AAGAGTAAAAA-GTAATCAGTAAAAAGTAAAAGGTAATCA--AC
* * *
71406 AAAAGTAAAAGAGTAATCAGTAAAAA--AAAAGG--AGCAGAA
1 AAGAGTAAAA-AGTAATCAGTAAAAAGTAAAAGGTAATCA-AC
* * *
71445 AATAGTAAAGAGTAATCAGTAAAAGAGTAAAACAGTAATCA
1 AAGAGTAAAAAGTAATCAGTAAAA-AGTAAAA-GGTAATCA
71486 GTAAAAAGTA
Statistics
Matches: 194, Mismatches: 29, Indels: 43
0.73 0.11 0.16
Matches are distributed among these distances:
35 1 0.01
36 21 0.11
37 5 0.03
38 15 0.08
39 15 0.08
41 16 0.08
42 19 0.10
43 74 0.38
44 28 0.14
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (41 bp):
AAGAGTAAAAAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
Found at i:71269 original size:7 final size:7
Alignment explanation
Indices: 71259--71308 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
71249 AATAGTAGTC
71259 AGTAAAA
1 AGTAAAA
*
71266 AGTAAAT
1 AGTAAAA
*
71273 AGTAAAC
1 AGTAAAA
71280 AGTAAAAA
1 AGT-AAAA
*
71288 AGTAATA
1 AGTAAAA
*
71295 AGTAAGA
1 AGTAAAA
71302 AGTAAAA
1 AGTAAAA
71309 GGAAATCGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
7 30 0.83
8 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.16, T:0.18
Consensus pattern (7 bp):
AGTAAAA
Found at i:71476 original size:104 final size:104
Alignment explanation
Indices: 71344--71531 Score: 258
Period size: 104 Copynumber: 1.8 Consensus size: 104
71334 ATCAGTAAAG
71344 AGTAAAAAGCTAATCAGCAAAAAGTAAAA-AGGTAATCAGTAAAAAGCAA-AAGGCAATCATTA-
1 AGTAAAAAGCTAATCAGCAAAAAGTAAAACA-GTAATCAGTAAAAAGCAAGAAGGCAATCA--AC
71406 AAAAGTAAAAGAGTAATCAGTAAAAAAAAAGGAGCAGAAAAT
63 AAAAGTAAAAGAGTAATCAGTAAAAAAAAAGGAGCAGAAAAT
* * * *
71448 AGTAAAGAG-TAATCAGTAAAAGAGTAAAACAGTAATCAGTAAAAAGTAAGAAGGTAATCAACAA
1 AGTAAAAAGCTAATCAGCAAAA-AGTAAAACAGTAATCAGTAAAAAGCAAGAAGGCAATCAACAA
* *
71512 GAGTAAAATAGTAATCAGTA
65 AAGTAAAAGAGTAATCAGTA
71532 CAAAGTAAAG
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
103 12 0.16
104 52 0.70
105 10 0.14
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.16
Consensus pattern (104 bp):
AGTAAAAAGCTAATCAGCAAAAAGTAAAACAGTAATCAGTAAAAAGCAAGAAGGCAATCAACAAA
AGTAAAAGAGTAATCAGTAAAAAAAAAGGAGCAGAAAAT
Found at i:72963 original size:26 final size:26
Alignment explanation
Indices: 72911--72959 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
72901 GTCCATATTT
72911 ATCTTTTAAAATAAAATAATAATTAA
1 ATCTTTTAAAATAAAATAATAATTAA
72937 ATCTTTTAATAA-AAAATAA-AATT
1 ATCTTTTAA-AATAAAATAATAATT
72960 TAAACATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 16 0.73
27 2 0.09
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (26 bp):
ATCTTTTAAAATAAAATAATAATTAA
Found at i:73095 original size:26 final size:28
Alignment explanation
Indices: 73064--73131 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 28
73054 AATTAATGTA
73064 TATATATAAATT-ATTCA-ATTCTATTATT
1 TATATAT-AATTAATT-ATATTCTATTATT
73092 TATAAATATAATTAATTATATTCTATTATT
1 TAT--ATATAATTAATTATATTCTATTATT
73122 TATATATAAT
1 TATATATAAT
73132 ACGGGTCAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
28 10 0.28
29 5 0.14
30 21 0.58
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (28 bp):
TATATATAATTAATTATATTCTATTATT
Found at i:76695 original size:11 final size:12
Alignment explanation
Indices: 76680--76722 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
76670 AAGAAATGAC
76680 CTTTTCTTTTC-
1 CTTTTCTTTTCT
*
76691 CTTTTTTTTTCTT
1 CTTTTCTTTTC-T
76704 CTTTTC-TTTCT
1 CTTTTCTTTTCT
76715 CTTTTCTT
1 CTTTTCTT
76723 CTTCAACCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 17 0.63
12 5 0.19
13 5 0.19
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
CTTTTCTTTTCT
Found at i:76707 original size:19 final size:19
Alignment explanation
Indices: 76683--76725 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
76673 AAATGACCTT
*
76683 TTCTTTTCCTTT-TTTTTTC
1 TTCTTTT-CTTTCTCTTTTC
76702 TTCTTTTCTTTCTCTTTTC
1 TTCTTTTCTTTCTCTTTTC
76721 TTCTT
1 TTCTT
76726 CAACCCGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTCTTTTCTTTCTCTTTTC
Found at i:76817 original size:21 final size:20
Alignment explanation
Indices: 76788--76826 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
76778 ACAGTCGCCA
*
76788 TTTCTCTTTTCTTCTTCTTCG
1 TTTCACTTTTCTT-TTCTTCG
*
76809 TTTCACTTTTGTTTTCTT
1 TTTCACTTTTCTTTTCTT
76827 TCCTTACTGC
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:0.03, C:0.23, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTCACTTTTCTTTTCTTCG
Found at i:79639 original size:33 final size:33
Alignment explanation
Indices: 79587--79654 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
79577 GCTGATGACC
*
79587 GTGCCGCCCCAGGAGGGCGGCATGCCGTGGCTA
1 GTGCCGCCCCAGGAGGGCGGCATGCCATGGCTA
* *
79620 GTGCTGCCCTAGGAGGGCGGCATGCCATGGCTA
1 GTGCCGCCCCAGGAGGGCGGCATGCCATGGCTA
79653 GT
1 GT
79655 AGGGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.13, C:0.29, G:0.41, T:0.16
Consensus pattern (33 bp):
GTGCCGCCCCAGGAGGGCGGCATGCCATGGCTA
Done.