Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014978.1 Corchorus capsularis cultivar CVL-1 contig14999, 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: 71547
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3724 original size:6 final size:6
Alignment explanation
Indices: 3713--3737 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3703 CATGTAGATT
3713 GTAGAA GTAGAA GTAGAA GTAGAA G
1 GTAGAA GTAGAA GTAGAA GTAGAA G
3738 AATAAGAATC
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:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GTAGAA
Found at i:4266 original size:210 final size:202
Alignment explanation
Indices: 3904--4287 Score: 547
Period size: 210 Copynumber: 1.9 Consensus size: 202
3894 CCATAATAAG
* **
3904 AAAAAAAGTAATTATTTGATACACCGGCAGTTTAAATTTTGGATTCCATAAGCGGATTGTGGAGT
1 AAAAAAAGTAATTATTTGATACACCGGCAGTGTAAATTTTGGATTCCATAAGCGGATCATGGAGT
* * *
3969 TGACACATGTCCATTTTCTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACAC
66 TGACACATGTCCATTTTCTTAATTAATTAAATTTTAAATATTTCAATATAATCCCTAGAGGACAC
* *
4034 ATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGCTAAACTCCACTGAAGGTGTATTGTATAATTT
131 ATGTCACCCTTCAAGACCCGCTTGTGCAGTCTGCTAAACTCCACTGAAGGTGTATTGTATAATTT
4099 GCCTAAT
196 GCCTAAT
* *
4106 AAAAAAAGGTAATTATTTGATACACCGG-TGATGTAAATTTTGGATTCCAATTTCCACAAGCGGG
1 AAAAAAA-GTAATTATTTGATACACCGGCAG-TGTAAATTTTGGATTCC-A--T----AAGCGGA
* *
4170 TCATGGAGTTGACACATGTCCATTTTCTTAATTAATTAAATTTTATATATTTCAATATAATCTCT
57 TCATGGAGTTGACACATGTCCATTTTCTTAATTAATTAAATTTTAAATATTTCAATATAATCCCT
*
4235 A-AGGGACACATGTCACCCTTCAAGTCCCGCTTGTGCAGTCTGCTAAACTCCAC
122 AGA-GGACACATGTCACCCTTCAAGACCCGCTTGTGCAGTCTGCTAAACTCCAC
4288 CGCCGGTATA
Statistics
Matches: 159, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
202 8 0.05
203 36 0.23
204 1 0.01
206 1 0.01
209 1 0.01
210 112 0.70
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (202 bp):
AAAAAAAGTAATTATTTGATACACCGGCAGTGTAAATTTTGGATTCCATAAGCGGATCATGGAGT
TGACACATGTCCATTTTCTTAATTAATTAAATTTTAAATATTTCAATATAATCCCTAGAGGACAC
ATGTCACCCTTCAAGACCCGCTTGTGCAGTCTGCTAAACTCCACTGAAGGTGTATTGTATAATTT
GCCTAAT
Found at i:6158 original size:23 final size:23
Alignment explanation
Indices: 6100--6173 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
6090 TTCTCTGTTT
* *
6100 TTTTTGGAATTCCTTGGTGAGAG
1 TTTTTGGAACTCCTTTGTGAGAG
*
6123 TTTTCGGAACTCCTTTGTGAGAG
1 TTTTTGGAACTCCTTTGTGAGAG
** * *
6146 TTTTTGGGGCTCCTTTATAAGAG
1 TTTTTGGAACTCCTTTGTGAGAG
6169 TTTTT
1 TTTTT
6174 TCTACTGTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.46
Consensus pattern (23 bp):
TTTTTGGAACTCCTTTGTGAGAG
Found at i:16709 original size:10 final size:11
Alignment explanation
Indices: 16681--16707 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16671 AAGGTTTTGG
16681 GTTTTTAATGA
1 GTTTTTAATGA
16692 GTTTTTAATGA
1 GTTTTTAATGA
16703 GTTTT
1 GTTTT
16708 AAGTCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (11 bp):
GTTTTTAATGA
Found at i:30330 original size:33 final size:35
Alignment explanation
Indices: 30279--30350 Score: 103
Period size: 33 Copynumber: 2.1 Consensus size: 35
30269 TTTCCTTATT
*
30279 GCTGTCTCCTATCCCCTGTTGAT-A-CTCTGTTTG
1 GCTGCCTCCTATCCCCTGTTGATGACCTCTGTTTG
*
30312 GCTGCCTCCTATCTCCTGTTGATGACTCTCTGTTTG
1 GCTGCCTCCTATCCCCTGTTGATGAC-CTCTGTTTG
30348 GCT
1 GCT
30351 TCTGAAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 21 0.62
34 1 0.03
36 12 0.35
ACGTcount: A:0.08, C:0.31, G:0.19, T:0.42
Consensus pattern (35 bp):
GCTGCCTCCTATCCCCTGTTGATGACCTCTGTTTG
Found at i:37092 original size:2 final size:2
Alignment explanation
Indices: 37085--37115 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
37075 GATATGAAGA
37085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37116 GTATGAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39987 original size:28 final size:26
Alignment explanation
Indices: 39918--39993 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 26
39908 TAGGGTCACA
*
39918 TAGGAGCATTTTGGTCATTTTCACGTT
1 TAGGGGCATTTTGGTCATTTTCAC-TT
39945 TAGGGGCATTTTGGTCATGTTTGCA-TT
1 TAGGGGCATTTTGGTCAT-TTT-CACTT
*
39972 TAGGGGGTATTTTGGTACATTT
1 TA-GGGGCATTTTGGT-CATTT
39994 AACTTAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 21 0.49
28 17 0.40
29 5 0.12
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.45
Consensus pattern (26 bp):
TAGGGGCATTTTGGTCATTTTCACTT
Found at i:42109 original size:30 final size:31
Alignment explanation
Indices: 42073--42145 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
42063 AGTAAAAAGG
42073 GCAATCAGTAATTAAGTTCAATAAGGAAA-A-
1 GCAATCAGTAATTAAGTTCAATAA-GAAAGAT
* *
42103 GTAATCAGTGATTTAAGTTCAATAAGAAAGAT
1 GCAATCAGT-AATTAAGTTCAATAAGAAAGAT
42135 GCAATCAGTAA
1 GCAATCAGTAA
42146 AAGGTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 12 0.33
31 16 0.44
32 8 0.22
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.26
Consensus pattern (31 bp):
GCAATCAGTAATTAAGTTCAATAAGAAAGAT
Found at i:42187 original size:44 final size:45
Alignment explanation
Indices: 42137--42517 Score: 217
Period size: 44 Copynumber: 8.8 Consensus size: 45
42127 AGAAAGATGC
*
42137 AATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAGTGA-T
1 AATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATGAGT
* ** * *
42181 AATCAGT-AAAGAGTAATA-GAAAATCAGT-AAGA--AGCAAT-TGT
1 AATCAGTAAAAG-GTAAAATGGTAATCAGTAAAGAGTA-AAATGAGT
* * *
42222 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAT-AGT
1 AATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATGAGT
* ** *
42266 AATTAG-AAAAGAGTAAAATGGTAAAGAGTAAAGAGTAACCAGTAGAAGAGT
1 AATCAGTAAAAG-GTAAAATGGTAATCAGTAAAGAGT-A--A--A-ATGAGT
** * *
42317 AATCAGT-AAAGACAAAAATGATAA--AG-AAAGAGT--GAT-AGT
1 AATCAGTAAAAG-GTAAAATGGTAATCAGTAAAGAGTAAAATGAGT
*
42356 AA-GAGTAAAAAGGTAAAATGG---T-A--AAA-AGTAAAA-G-GT
1 AATCAGT-AAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATGAGT
* * * *
42392 AATCAATAAAGGGTAAAATGGTAATTAGTAAAAAGTAAAATG-GT
1 AATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATGAGT
* * *
42436 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAT-AGT
1 AATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATGAGT
*
42480 AATTAG-AAAAGAGTAAAATGGTAATCAGTAAAGAGTAA
1 AATCAGTAAAAG-GTAAAATGGTAATCAGTAAAGAGTAA
42518 TCAGCAAAGG
Statistics
Matches: 260, Mismatches: 43, Indels: 68
0.70 0.12 0.18
Matches are distributed among these distances:
35 3 0.01
36 20 0.08
37 4 0.02
38 3 0.01
39 12 0.05
40 7 0.03
41 15 0.06
42 18 0.07
43 30 0.12
44 112 0.43
45 2 0.01
47 1 0.00
48 7 0.03
49 3 0.01
50 1 0.00
51 22 0.08
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.20
Consensus pattern (45 bp):
AATCAGTAAAAGGTAAAATGGTAATCAGTAAAGAGTAAAATGAGT
Found at i:42245 original size:8 final size:7
Alignment explanation
Indices: 42226--42481 Score: 58
Period size: 7 Copynumber: 35.7 Consensus size: 7
42216 AATTGTAATC
42226 AGTAAAA
1 AGTAAAA
42233 AGTAAAA
1 AGTAAAA
**
42240 AGGTAATC
1 A-GTAAAA
42248 AGTAAAA
1 AGTAAAA
42255 AGTAAAA
1 AGTAAAA
**
42262 TAGTAATT
1 -AGTAAAA
42270 AG-AAAA
1 AGTAAAA
42276 GAGTAAAA
1 -AGTAAAA
* *
42284 TGGTAAAG
1 -AGTAAAA
*
42292 AGTAAAG
1 AGTAAAA
**
42299 AGTAACC
1 AGTAAAA
*
42306 AGTAGAAG
1 AGTA-AAA
**
42314 AGTAATC
1 AGTAAAA
*
42321 AGTAAAG
1 AGTAAAA
*
42328 A-CAAAA
1 AGTAAAA
*
42334 A-TGATAA
1 AGT-AAAA
*
42341 AG-AAAG
1 AGTAAAA
* *
42347 AGT-GAT
1 AGTAAAA
*
42353 AGTAAGA
1 AGTAAAA
42360 -GTAAAA
1 AGTAAAA
42366 AGGTAAAA
1 A-GTAAAA
*
42374 TGGTAAAA
1 -AGTAAAA
42382 AGTAAAA
1 AGTAAAA
* *
42389 GGTAATCA
1 AGTAA-AA
*
42397 A-TAAAG
1 AGTAAAA
*
42403 GGTAAAA
1 AGTAAAA
* **
42410 TGGTAATT
1 -AGTAAAA
42418 AGTAAAA
1 AGTAAAA
42425 AGTAAAA
1 AGTAAAA
* **
42432 TGGTAATC
1 -AGTAAAA
42440 AGTAAAA
1 AGTAAAA
42447 AGTAAAA
1 AGTAAAA
**
42454 AGGTAATC
1 A-GTAAAA
42462 AGTAAAA
1 AGTAAAA
42469 AGTAAAA
1 AGTAAAA
42476 TAGTAA
1 -AGTAA
42482 TTAGAAAAGA
Statistics
Matches: 175, Mismatches: 56, Indels: 35
0.66 0.21 0.13
Matches are distributed among these distances:
6 19 0.11
7 100 0.57
8 56 0.32
ACGTcount: A:0.57, C:0.03, G:0.21, T:0.20
Consensus pattern (7 bp):
AGTAAAA
Found at i:42298 original size:22 final size:22
Alignment explanation
Indices: 42137--42303 Score: 144
Period size: 22 Copynumber: 7.7 Consensus size: 22
42127 AGAAAGATGC
*
42137 AATCAGTAAAAGGTAAAATGGT
1 AATCAGTAAAAAGTAAAATGGT
* * *
42159 AATCAGTAAAGAGTAAAGTGAT
1 AATCAGTAAAAAGTAAAATGGT
* * **
42181 AATCAGTAAAGAGTAATA-GAA
1 AATCAGTAAAAAGTAAAATGGT
* * *
42202 AATCAGTAAGAAG--CAATTGT
1 AATCAGTAAAAAGTAAAATGGT
*
42222 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAATGGT
*
42244 AATCAGTAAAAAGTAAAATAGT
1 AATCAGTAAAAAGTAAAATGGT
*
42266 AATTAG-AAAAGAGTAAAATGGT
1 AATCAGTAAAA-AGTAAAATGGT
** *
42288 AAAGAGTAAAGAGTAA
1 AATCAGTAAAAAGTAA
42304 CCAGTAGAAG
Statistics
Matches: 115, Mismatches: 25, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
19 1 0.01
20 12 0.10
21 17 0.15
22 82 0.71
23 3 0.03
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.21
Consensus pattern (22 bp):
AATCAGTAAAAAGTAAAATGGT
Found at i:42314 original size:15 final size:14
Alignment explanation
Indices: 42292--42328 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
42282 AATGGTAAAG
42292 AGTAAAGAGTAACC
1 AGTAAAGAGTAACC
*
42306 AGTAGAAGAGTAATC
1 AGTA-AAGAGTAACC
42321 AGTAAAGA
1 AGTAAAGA
42329 CAAAAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.51, C:0.08, G:0.24, T:0.16
Consensus pattern (14 bp):
AGTAAAGAGTAACC
Found at i:42414 original size:22 final size:22
Alignment explanation
Indices: 42376--42517 Score: 189
Period size: 22 Copynumber: 6.5 Consensus size: 22
42366 AGGTAAAATG
42376 GTAAAAAGTAAAA-GGTAATCA
1 GTAAAAAGTAAAATGGTAATCA
* ** *
42397 ATAAAGGGTAAAATGGTAATTA
1 GTAAAAAGTAAAATGGTAATCA
42419 GTAAAAAGTAAAATGGTAATCA
1 GTAAAAAGTAAAATGGTAATCA
*
42441 GTAAAAAGTAAAAAGGTAATCA
1 GTAAAAAGTAAAATGGTAATCA
* *
42463 GTAAAAAGTAAAATAGTAATTA
1 GTAAAAAGTAAAATGGTAATCA
42485 G-AAAAGAGTAAAATGGTAATCA
1 GTAAAA-AGTAAAATGGTAATCA
*
42507 GTAAAGAGTAA
1 GTAAAAAGTAA
42518 TCAGCAAAGG
Statistics
Matches: 103, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.14
22 86 0.83
23 3 0.03
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.22
Consensus pattern (22 bp):
GTAAAAAGTAAAATGGTAATCA
Found at i:42437 original size:66 final size:68
Alignment explanation
Indices: 42356--42517 Score: 203
Period size: 66 Copynumber: 2.5 Consensus size: 68
42346 GAGTGATAGT
* * ** *
42356 AAGAGTAAAAAGGTAAAAT-GGTAAAAAGT-AAAAGGTAATCAATAAAGGGTAAAATGGTAATTA
1 AAGAGTAAAATGGTAAAATCAGTAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAATAGTAATTA
42419 GTAA
66 G-AA
*
42423 AA-AGTAAAATGGT--AATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAATAGTAATTA
1 AAGAGTAAAATGGTAAAATCAGTAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAATAGTAATTA
42485 GAA
66 GAA
*
42488 AAGAGTAAAATGGT--AATCAGTAAAGAGTAA
1 AAGAGTAAAATGGTAAAATCAGTAAAAAGTAA
42518 TCAGCAAAGG
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 3 0.04
65 13 0.15
66 67 0.79
67 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.21
Consensus pattern (68 bp):
AAGAGTAAAATGGTAAAATCAGTAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAATAGTAATTA
GAA
Found at i:42497 original size:8 final size:7
Alignment explanation
Indices: 42359--42481 Score: 59
Period size: 7 Copynumber: 16.7 Consensus size: 7
42349 TGATAGTAAG
42359 AGTAAAA
1 AGTAAAA
42366 AGGTAAAA
1 A-GTAAAA
*
42374 TGGTAAAA
1 -AGTAAAA
42382 AGTAAAA
1 AGTAAAA
* *
42389 GGTAATCA
1 AGTAA-AA
*
42397 A-TAAAG
1 AGTAAAA
*
42403 GGTAAAA
1 AGTAAAA
* **
42410 TGGTAATT
1 -AGTAAAA
42418 AGTAAAA
1 AGTAAAA
42425 AGTAAAA
1 AGTAAAA
* **
42432 TGGTAATC
1 -AGTAAAA
42440 AGTAAAA
1 AGTAAAA
42447 AGTAAAA
1 AGTAAAA
**
42454 AGGTAATC
1 A-GTAAAA
42462 AGTAAAA
1 AGTAAAA
42469 AGTAAAA
1 AGTAAAA
42476 TAGTAA
1 -AGTAA
42482 TTAGAAAAGA
Statistics
Matches: 84, Mismatches: 24, Indels: 15
0.68 0.20 0.12
Matches are distributed among these distances:
7 52 0.62
8 32 0.38
ACGTcount: A:0.57, C:0.02, G:0.20, T:0.21
Consensus pattern (7 bp):
AGTAAAA
Found at i:42570 original size:7 final size:7
Alignment explanation
Indices: 42554--42605 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
42544 AGAAAAAATC
42554 GTAAAGA
1 GTAAAGA
*
42561 GTAAAAA
1 GTAAAGA
**
42568 GTAATCA
1 GTAAAGA
42575 GTAAAGA
1 GTAAAGA
42582 G-AAAGA
1 GTAAAGA
42588 GTAAAGA
1 GTAAAGA
42595 GTAAAGA
1 GTAAAGA
42602 GTAA
1 GTAA
42606 CCAGCAAAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 6 0.15
7 33 0.85
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (7 bp):
GTAAAGA
Found at i:42590 original size:20 final size:20
Alignment explanation
Indices: 42509--42602 Score: 78
Period size: 20 Copynumber: 5.0 Consensus size: 20
42499 GGTAATCAGT
*
42509 AAAGAGTAATCAGCAAAG-G
1 AAAGAGTAATCAGTAAAGAG
42528 AAATG-GTAATCAGT-AA-AG
1 AAA-GAGTAATCAGTAAAGAG
42546 AAA-A--AATC-GTAAAGAG
1 AAAGAGTAATCAGTAAAGAG
*
42562 TAAAAAGTAATCAGTAAAGAG
1 -AAAGAGTAATCAGTAAAGAG
**
42583 AAAGAGTAAAGAGTAAAGAG
1 AAAGAGTAATCAGTAAAGAG
42603 TAACCAGCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
14 2 0.03
15 6 0.10
16 2 0.03
17 3 0.05
18 7 0.11
19 11 0.18
20 22 0.36
21 8 0.13
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAAGAGTAATCAGTAAAGAG
Found at i:42598 original size:88 final size:87
Alignment explanation
Indices: 42506--42712 Score: 274
Period size: 88 Copynumber: 2.4 Consensus size: 87
42496 AATGGTAATC
*
42506 AGTAAAGAGTAATCAGCAAAGGAAATGGTAATCAGTAAAGAAAAAATCGTAAAGAGTAAAAAGTA
1 AGTAAAGAGTAATCAGCAAAGGAAATGGTAATCAGCAAAG-AAAAATCGTAAAGAGTAAAAAG-A
42571 A-TCAGTAAAG-AGAAAGAGTAAAG
64 AGTCAGTAAAGAAGAAAG-GTAAAG
* * * * *
42594 AGTAAAGAGTAACCAGCAAAGGAAATGGTAATCAGCAAAGGAAAATGGTAAAGAGTGAAGAGAAG
1 AGTAAAGAGTAATCAGCAAAGGAAATGGTAATCAGCAAAGAAAAATCGTAAAGAGTAAAAAGAAG
* *
42659 TCAGTAAAGAAGAATGGTGAAG
66 TCAGTAAAGAAGAAAGGTAAAG
* *
42681 AGTAAAGAGTAATCAACAAAGAAAAATGGTAA
1 AGTAAAGAGTAATCAGCAAAG-GAAATGGTAA
42713 AGAGTAAAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
86 2 0.02
87 51 0.49
88 52 0.50
ACGTcount: A:0.54, C:0.06, G:0.25, T:0.15
Consensus pattern (87 bp):
AGTAAAGAGTAATCAGCAAAGGAAATGGTAATCAGCAAAGAAAAATCGTAAAGAGTAAAAAGAAG
TCAGTAAAGAAGAAAGGTAAAG
Found at i:42629 original size:19 final size:20
Alignment explanation
Indices: 42602--42644 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
42592 AGAGTAAAGA
42602 GTAACCAGCAAAGG-AAATG
1 GTAACCAGCAAAGGAAAATG
*
42621 GTAATCAGCAAAGGAAAATG
1 GTAACCAGCAAAGGAAAATG
42641 GTAA
1 GTAA
42645 AGAGTGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.49, C:0.12, G:0.26, T:0.14
Consensus pattern (20 bp):
GTAACCAGCAAAGGAAAATG
Found at i:42682 original size:34 final size:34
Alignment explanation
Indices: 42621--42720 Score: 121
Period size: 34 Copynumber: 2.9 Consensus size: 34
42611 AAAGGAAATG
* * *
42621 GTAATCAGCAAAGGAAAATGGTAAAGAGTGAAGA
1 GTAATCAACAAAGAAAAATGGTAAAGAGTAAAGA
** * *
42655 G-AAGTCAGTAAAGAAGAATGGTGAAGAGTAAAGA
1 GTAA-TCAACAAAGAAAAATGGTAAAGAGTAAAGA
42689 GTAATCAACAAAGAAAAATGGTAAAGAGTAAA
1 GTAATCAACAAAGAAAAATGGTAAAGAGTAAA
42721 ATATTAATCA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 2 0.04
34 51 0.93
35 2 0.04
ACGTcount: A:0.53, C:0.05, G:0.27, T:0.15
Consensus pattern (34 bp):
GTAATCAACAAAGAAAAATGGTAAAGAGTAAAGA
Found at i:42742 original size:22 final size:22
Alignment explanation
Indices: 42717--42777 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
42707 TGGTAAAGAG
*
42717 TAAAATATTAATCAGTAAAAAA
1 TAAAATAATAATCAGTAAAAAA
*** *
42739 T-AAATGGCAATCAGTAAAGAA
1 TAAAATAATAATCAGTAAAAAA
*
42760 TAAAATAATAATTAGTAA
1 TAAAATAATAATCAGTAA
42778 TCAGTACAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.26
Consensus pattern (22 bp):
TAAAATAATAATCAGTAAAAAA
Found at i:42801 original size:21 final size:21
Alignment explanation
Indices: 42760--42826 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
42750 CAGTAAAGAA
*
42760 TAAAATAATAATTAGTAATCAG
1 TAAAATAGTAA-TAGTAATCAG
*
42782 TACAA-AGTAA-AGAATAATCAG
1 TAAAATAGTAATAG--TAATCAG
42803 TAAAATAGTAATAGTAATCAG
1 TAAAATAGTAATAGTAATCAG
42824 TAA
1 TAA
42827 TTCAGTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.05
21 25 0.66
22 9 0.24
23 2 0.05
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (21 bp):
TAAAATAGTAATAGTAATCAG
Found at i:45943 original size:10 final size:10
Alignment explanation
Indices: 45928--45952 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
45918 GTTGGTGCAC
45928 AATTCCAGAA
1 AATTCCAGAA
45938 AATTCCAGAA
1 AATTCCAGAA
45948 AATTC
1 AATTC
45953 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:46901 original size:6 final size:6
Alignment explanation
Indices: 46890--46916 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46880 TATAATCTGT
46890 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
46917 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:51456 original size:28 final size:28
Alignment explanation
Indices: 51416--51473 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
51406 ATATGCATAA
51416 AATTGATAAAATTGGAATAATTTTTTCG
1 AATTGATAAAATTGGAATAATTTTTTCG
51444 AATTGATAAAATTGGAATAATTTTTTCG
1 AATTGATAAAATTGGAATAATTTTTTCG
51472 AA
1 AA
51474 AATTTTGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.41
Consensus pattern (28 bp):
AATTGATAAAATTGGAATAATTTTTTCG
Found at i:52956 original size:10 final size:10
Alignment explanation
Indices: 52941--52965 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52931 GTTGCTGCAC
52941 AATTCCAGAA
1 AATTCCAGAA
52951 AATTCCAGAA
1 AATTCCAGAA
52961 AATTC
1 AATTC
52966 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:53914 original size:6 final size:6
Alignment explanation
Indices: 53903--53929 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53893 TATAATCTGT
53903 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
53930 TCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:59736 original size:25 final size:27
Alignment explanation
Indices: 59682--59736 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 27
59672 TAGAATTTTT
59682 GTTAAGGACATAATATTTTTTTGGGTACAA
1 GTTAAGGACATAATA---TTTTGGGTACAA
59712 GTTAAGGACATAATA-TTT-GGTACAA
1 GTTAAGGACATAATATTTTGGGTACAA
59737 ATTTAATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.28
26 3 0.12
30 15 0.60
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.36
Consensus pattern (27 bp):
GTTAAGGACATAATATTTTGGGTACAA
Found at i:66532 original size:32 final size:32
Alignment explanation
Indices: 66495--66566 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 32
66485 CAAATTGATA
* *
66495 GACAAAATAACCCTCAAATTTTGACATAGA-AG
1 GACAAAATAACCCTCAAACTTTGACA-AAATAG
66527 GACAAAATAACCCTCAAACTTTGACAAAATAG
1 GACAAAATAACCCTCAAACTTTGACAAAATAG
66559 GACAAAAT
1 GACAAAAT
66567 GTTCTTTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 2 0.05
32 35 0.95
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.19
Consensus pattern (32 bp):
GACAAAATAACCCTCAAACTTTGACAAAATAG
Found at i:66928 original size:16 final size:16
Alignment explanation
Indices: 66909--66942 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
66899 TTTAGAAGCA
*
66909 TGTTTATTTGTTTGTT
1 TGTTTATTTGGTTGTT
*
66925 TGTTTTTTTGGTTGTT
1 TGTTTATTTGGTTGTT
66941 TG
1 TG
66943 GTATGTAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.24, T:0.74
Consensus pattern (16 bp):
TGTTTATTTGGTTGTT
Done.