Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007205.1 Corchorus capsularis cultivar CVL-1 contig07226, 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: 47513
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Found at i:383 original size:43 final size:42
Alignment explanation
Indices: 329--522 Score: 149
Period size: 43 Copynumber: 4.7 Consensus size: 42
319 GTAATTAGTA
*
329 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGA-AGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGCAA-ATA-GTAATCAAC
* **
372 AAGAGTAAAATAGTAGTCAGTAAAAAGCAAATAGTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGCAAATAGTAATCAAC
* * *
414 AAGAGTAAAATGGTAATAAGT-AAAAGGAAATCAG---T----
1 AAGAGTAAAATAGTAATCAGTAAAAAGCAAAT-AGTAATCAAC
* * * *
449 AAGAGTAAAA-AGGTGATCAGTAAAGAGTAAAAAGCTAATCAAC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGCAAATAG-TAATCAAC
*
492 AAGAAGTAAAA-GGTAATCAGTAAAAAGCAAA
1 AAG-AGTAAAATAGTAATCAGTAAAAAGCAAA
523 AGGCAATTAG
Statistics
Matches: 120, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
35 19 0.16
36 7 0.06
39 2 0.02
41 9 0.08
42 28 0.23
43 48 0.40
44 7 0.06
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGCAAATAGTAATCAAC
Found at i:424 original size:21 final size:20
Alignment explanation
Indices: 287--514 Score: 108
Period size: 22 Copynumber: 10.9 Consensus size: 20
277 GTCAGTAAAA
*
287 AGTAAAAAGGTAATCAATAAAGG
1 AGTAAAAA-GTAATCAGT-AA-G
* * *
310 GGTAAAATGGTAATTAGTAAAG
1 AGTAAAA-AGTAATCAGT-AAG
*
332 AGTAAAATAGTAATCAGTAAAA
1 AGTAAAA-AGTAATCAGT-AAG
* **
354 AGTAAGAAGGTAATCAACAAG
1 AGTAA-AAAGTAATCAGTAAG
* *
375 AGTAAAATAGTAGTCAGTAAAA
1 AGTAAAA-AGTAATCAGT-AAG
* *
397 AGCAAATAGTAATCAGTAAG
1 AGTAAAAAGTAATCAGTAAG
*
417 AGTAAAATGGT-A--A-T-A-
1 AGTAAAA-AGTAATCAGTAAG
* *
432 AGTAAAAGGAAATCAGTAAG
1 AGTAAAAAGTAATCAGTAAG
*
452 AGTAAAAAGGTGATCAGTAAAG
1 AGTAAAAA-GTAATCAGT-AAG
**
474 AGTAAAAAGCTAATCAACAAG
1 AGTAAAAAG-TAATCAGTAAG
*
495 AAGTAAAAGGTAATCAGTAA
1 -AGTAAAAAGTAATCAGTAA
515 AAAGCAAAAG
Statistics
Matches: 156, Mismatches: 34, Indels: 32
0.70 0.15 0.14
Matches are distributed among these distances:
14 2 0.01
15 8 0.05
16 1 0.01
17 2 0.01
18 2 0.01
19 1 0.01
20 17 0.11
21 43 0.28
22 62 0.40
23 18 0.12
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.20
Consensus pattern (20 bp):
AGTAAAAAGTAATCAGTAAG
Found at i:450 original size:42 final size:41
Alignment explanation
Indices: 314--450 Score: 132
Period size: 42 Copynumber: 3.2 Consensus size: 41
304 TAAAGGGGTA
* * *
314 AAATGGTAATTAGTAAAGAGTAAAATAGTAATCAGTAAAAAGT
1 AAATAGTAATCAGT-AAGAGTAAAATAGTAATCAGT-AAAAGG
** * *
357 AAGA-AGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGC
1 AA-ATA-GTAATCAGTAAGAGTAAAATAGTAATCAGT-AAAAGG
* *
400 AAATAGTAATCAGTAAGAGTAAAATGGTAATAAGTAAAAGG
1 AAATAGTAATCAGTAAGAGTAAAATAGTAATCAGTAAAAGG
441 AAATCAGTAA
1 AAAT-AGTAA
451 GAGTAAAAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
41 9 0.12
42 31 0.40
43 31 0.40
44 7 0.09
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (41 bp):
AAATAGTAATCAGTAAGAGTAAAATAGTAATCAGTAAAAGG
Found at i:523 original size:21 final size:21
Alignment explanation
Indices: 426--560 Score: 119
Period size: 21 Copynumber: 6.3 Consensus size: 21
416 GAGTAAAATG
* *
426 GTAATAAGTAAAAGGAAATCA
1 GTAAAAAGTAAAAGGTAATCA
* *
447 GT-AAGAGTAAAAAGGTGATCA
1 GTAAAAAGT-AAAAGGTAATCA
* *
468 GTAAAGAGTAAAAAGCTAATCA
1 GTAAAAAGT-AAAAGGTAATCA
** *
490 ACAAGAAGTAAAAGGTAATCA
1 GTAAAAAGTAAAAGGTAATCA
* * *
511 GTAAAAAGCAAAAGGCAATTA
1 GTAAAAAGTAAAAGGTAATCA
*
532 GTAAAAAGTAAAAGAGTAATTA
1 GTAAAAAGTAAAAG-GTAATCA
554 GTAAAAA
1 GTAAAAA
561 AAAAGAGCAG
Statistics
Matches: 92, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
20 4 0.04
21 53 0.58
22 35 0.38
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (21 bp):
GTAAAAAGTAAAAGGTAATCA
Found at i:2879 original size:2 final size:2
Alignment explanation
Indices: 2872--2897 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2862 CTTGACAGCC
2872 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2898 TAAAGCTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4959 original size:59 final size:59
Alignment explanation
Indices: 4867--4984 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
4857 CCTGGGTTAA
*
4867 AGGGTTAAACTTGAAGAGAAGATTGAAATGAATTTGAATCCAATTTAAACAAAGAAAAT
1 AGGGTTAAACTTGAAGAGAAGATTAAAATGAATTTGAATCCAATTTAAACAAAGAAAAT
4926 AGGGTTAAACTTGAAGAGAAGATTAAAATGAATTTGAATCCAATTTAAACAAAGAAAAT
1 AGGGTTAAACTTGAAGAGAAGATTAAAATGAATTTGAATCCAATTTAAACAAAGAAAAT
4985 GGAAAGTGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (59 bp):
AGGGTTAAACTTGAAGAGAAGATTAAAATGAATTTGAATCCAATTTAAACAAAGAAAAT
Found at i:5338 original size:62 final size:62
Alignment explanation
Indices: 5265--5625 Score: 564
Period size: 62 Copynumber: 5.8 Consensus size: 62
5255 TCCATTTCCA
* * * * * *
5265 TGAACTATCTTCAGATTCACTCTCAAATA-TCATTAAGGAATTGTCTTCAGAACCTATCTTCG
1 TGAACTGTCTTCAGATTCACTCTTAAATACT-TTTTAGGAACTGTCTTCAGAACCCATCTTCG
5327 TGAACTGTCTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCG
1 TGAACTGTCTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCG
*
5389 TGAACTGTCTTTAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCG
1 TGAACTGTCTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCG
*
5451 TGAACTGTCTTCAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAGAACCCATCTTCG
1 TGAACTGTCTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCG
* * *
5513 TGAACTATTTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTTAGAACCCATCTTCG
1 TGAACTGTCTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCG
* * *
5575 TGAACTGTCTTCAGATTCACTCTCAAATA-TCTTTCAGAAACTGTCTTCAGA
1 TGAACTGTCTTCAGATTCACTCTTAAATACT-TTTTAGGAACTGTCTTCAGA
5626 TCCCTATATG
Statistics
Matches: 278, Mismatches: 19, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
61 1 0.00
62 276 0.99
63 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (62 bp):
TGAACTGTCTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCG
Found at i:5430 original size:36 final size:36
Alignment explanation
Indices: 5390--5501 Score: 109
Period size: 36 Copynumber: 3.4 Consensus size: 36
5380 CCATCTTCGT
*
5390 GAACTGTCTTTAGATTCACTCTTAAATACTTTTTAG
1 GAACTGTCTTCAGATTCACTCTTAAATACTTTTTAG
* **
5426 GAACTGTCTTCAGA---AC-C---CAT-CTTCGT--
1 GAACTGTCTTCAGATTCACTCTTAAATACTTTTTAG
*
5452 GAACTGTCTTCAGATTCACTCTTAAATACCTTTTAG
1 GAACTGTCTTCAGATTCACTCTTAAATACTTTTTAG
5488 GAACTGTCTTCAGA
1 GAACTGTCTTCAGA
5502 ACCCATCTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
26 14 0.24
28 4 0.07
29 4 0.07
30 1 0.02
32 1 0.02
33 4 0.07
34 3 0.05
36 27 0.47
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (36 bp):
GAACTGTCTTCAGATTCACTCTTAAATACTTTTTAG
Found at i:5593 original size:186 final size:183
Alignment explanation
Indices: 5264--5683 Score: 585
Period size: 186 Copynumber: 2.3 Consensus size: 183
5254 ATCCATTTCC
* * * * *
5264 ATGAACTATCTTCAGATTCACTCTCAAATATCATTAAGGAATTGTCTTCAGAACCTATCTTCGTG
1 ATGAACTGTCTTCAGATTCACTCTTAAATATCTTTAAGGAACTGTCTTCAGAACCCATCTTCGTG
*
5329 AACTGTCTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCGTGAAC
66 AACTATCTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCGTGAAC
* * * * *
5394 TGTCTTTAGATTCACTCTTAAATA-CTTTTTAGGAACTGTCTTCAGAACCCATCTT
131 TGTCTTCAGATTCACTCTCAAATATC-TTTCAGAAACTGTCTTCAGAACCC-T-AT
* * *
5449 CGTGAACTGTCTTCAGATTCACTCTTAAATACCTTTTAGGAACTGTCTTCAGAACCCATCTTCGT
1 -ATGAACTGTCTTCAGATTCACTCTTAAATATCTTTAAGGAACTGTCTTCAGAACCCATCTTCGT
* *
5514 GAACTATTTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTTAGAACCCATCTTCGTGAA
65 GAACTATCTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCGTGAA
*
5579 CTGTCTTCAGATTCACTCTCAAATATCTTTCAGAAACTGTCTTCAGATCCCTAT
130 CTGTCTTCAGATTCACTCTCAAATATCTTTCAGAAACTGTCTTCAGAACCCTAT
* * * *
5633 ATGAGCAGTCTTCATACTT-ACTCTT-AATATCTTTCAGGAACTGTCTTCAGA
1 ATGAACTGTCTTCAGA-TTCACTCTTAAATATCTTTAAGGAACTGTCTTCAGA
5684 TCCCTGGACT
Statistics
Matches: 209, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
182 24 0.11
183 18 0.09
184 3 0.01
185 1 0.00
186 162 0.78
187 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (183 bp):
ATGAACTGTCTTCAGATTCACTCTTAAATATCTTTAAGGAACTGTCTTCAGAACCCATCTTCGTG
AACTATCTTCAGATTCACTCTTAAATACTTTTTAGGAACTGTCTTCAGAACCCATCTTCGTGAAC
TGTCTTCAGATTCACTCTCAAATATCTTTCAGAAACTGTCTTCAGAACCCTAT
Found at i:6159 original size:10 final size:10
Alignment explanation
Indices: 6144--6171 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6134 TTACCCTTAT
6144 TTCTTTTGAA
1 TTCTTTTGAA
6154 TTCTTTTGAA
1 TTCTTTTGAA
6164 TTCTTTTG
1 TTCTTTTG
6172 CTGATTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.64
Consensus pattern (10 bp):
TTCTTTTGAA
Found at i:6307 original size:10 final size:10
Alignment explanation
Indices: 6292--6319 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6282 TTACCCTTAT
6292 TTCTTTTGAA
1 TTCTTTTGAA
6302 TTCTTTTGAA
1 TTCTTTTGAA
6312 TTCTTTTG
1 TTCTTTTG
6320 CCCCAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.64
Consensus pattern (10 bp):
TTCTTTTGAA
Found at i:6319 original size:148 final size:148
Alignment explanation
Indices: 6051--6320 Score: 531
Period size: 148 Copynumber: 1.8 Consensus size: 148
6041 CTCTTGACCT
6051 GACATCTTCCTCTTTTAAACCCTTATTTGCCCTCTTAGCTCAATTTTCCTCTAATTTCATGCCCC
1 GACATCTTCCTCTTTTAAACCCTTATTTGCCCTCTTAGCTCAATTTTCCTCTAATTTCATGCCCC
6116 CACATCCCTATCAATCTTTTACCCTTATTTCTTTTGAATTCTTTTGAATTCTTTTGCTGATTTAT
66 CACATCCCTATCAATCTTTTACCCTTATTTCTTTTGAATTCTTTTGAATTCTTTTGCTGATTTAT
6181 GTTTCTTTGTATCTTTTA
131 GTTTCTTTGTATCTTTTA
*
6199 GACATCTTCCTCTTTTAAACCCTTATTTGCCCTCTTAGCTCAATTTTCCTCTAATTTCGTGCCCC
1 GACATCTTCCTCTTTTAAACCCTTATTTGCCCTCTTAGCTCAATTTTCCTCTAATTTCATGCCCC
6264 CACATCCCTATCAATCTTTTACCCTTATTTCTTTTGAATTCTTTTGAATTCTTTTGC
66 CACATCCCTATCAATCTTTTACCCTTATTTCTTTTGAATTCTTTTGAATTCTTTTGC
6321 CCCAAATGAT
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 121 1.00
ACGTcount: A:0.18, C:0.27, G:0.07, T:0.48
Consensus pattern (148 bp):
GACATCTTCCTCTTTTAAACCCTTATTTGCCCTCTTAGCTCAATTTTCCTCTAATTTCATGCCCC
CACATCCCTATCAATCTTTTACCCTTATTTCTTTTGAATTCTTTTGAATTCTTTTGCTGATTTAT
GTTTCTTTGTATCTTTTA
Found at i:6993 original size:17 final size:17
Alignment explanation
Indices: 6959--6993 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6949 TTTTTTGTTT
*
6959 CTCTTTCTTTTTGCGGC
1 CTCTTTCTTTTTGAGGC
*
6976 CTCTTTCTTTTTTAGGC
1 CTCTTTCTTTTTGAGGC
6993 C
1 C
6994 CAGTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.29, G:0.14, T:0.54
Consensus pattern (17 bp):
CTCTTTCTTTTTGAGGC
Found at i:22913 original size:40 final size:40
Alignment explanation
Indices: 22836--22939 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
22826 ATTTTATTAA
* * *
22836 TTTCCAAAAGT-GTCTCTTGGATTTCTAAAAACTTTTTAT
1 TTTCCAAAAGTCTTCTCTTGAATTACTAAAAACTTTTTAT
22875 TTTCCAAAAGTCTTCTCTTGAAATTACTAAAAAC-TTTTAT
1 TTTCCAAAAGTCTTCTCTTG-AATTACTAAAAACTTTTTAT
*
22915 TTTCCAAAAGTCTTCTATTGGAATT
1 TTTCCAAAAGTCTTCTCTT-GAATT
22940 GCTTAAATAG
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
39 11 0.19
40 35 0.60
41 12 0.21
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (40 bp):
TTTCCAAAAGTCTTCTCTTGAATTACTAAAAACTTTTTAT
Found at i:27615 original size:59 final size:59
Alignment explanation
Indices: 27523--27640 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
27513 CCTGGGTTAA
*
27523 AGGGTTAAACTTGAAGAGAAGATTGAAATGAATTTGAATCCAATTTGAACAAAGAAAAT
1 AGGGTTAAACTTGAAGAGAAGATTGAAATGAATTTGAATCCAATTTAAACAAAGAAAAT
27582 AGGGTTAAACTTGAAGAGAAGATTGAAATGAATTTGAATCCAATTTAAACAAAGAAAAT
1 AGGGTTAAACTTGAAGAGAAGATTGAAATGAATTTGAATCCAATTTAAACAAAGAAAAT
27641 GGAAAGTGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.25
Consensus pattern (59 bp):
AGGGTTAAACTTGAAGAGAAGATTGAAATGAATTTGAATCCAATTTAAACAAAGAAAAT
Found at i:34032 original size:11 final size:10
Alignment explanation
Indices: 34014--34047 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
34004 AATGGTCTTC
34014 AAATCTTCAA
1 AAATCTTCAA
34024 AATATCTTCAA
1 AA-ATCTTCAA
34035 GAAATCTTCAA
1 -AAATCTTCAA
34046 AA
1 AA
34048 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:37322 original size:42 final size:41
Alignment explanation
Indices: 37248--37328 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 41
37238 GGATCGAATA
*
37248 GCCGGTTGTGCCCGGATGGCGCATGCGTTGACCCGTGCGATG
1 GCCGGTTGTGCCCGGATGGCGCA-GCGATGACCCGTGCGATG
*
37290 GCCGGTTGTGGCCGGATGGCTTGC-GCGATGACCCGTGCG
1 GCCGGTTGTGCCCGGATGGC--GCAGCGATGACCCGTGCG
37329 GTGTCCCATG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 33 0.94
44 2 0.06
ACGTcount: A:0.09, C:0.28, G:0.42, T:0.21
Consensus pattern (41 bp):
GCCGGTTGTGCCCGGATGGCGCAGCGATGACCCGTGCGATG
Found at i:39257 original size:33 final size:33
Alignment explanation
Indices: 39211--39318 Score: 137
Period size: 33 Copynumber: 3.3 Consensus size: 33
39201 TTCTTCTCAC
* *
39211 CCAAAACAAAATTATTTTCAATGCTATGATCAT
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
*
39244 CCAAAACAGAATTATTTGT-AATACTATGATCAA
1 CCAAAACAGAATTATTT-TCAATGCTATGATCAA
* * * *
39277 CCACAACATAATTATTTGCAATGCAATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
39310 CCAAAACAG
1 CCAAAACAG
39319 GTTTGTTTTC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
33 62 0.98
34 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.28
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATGATCAA
Found at i:40805 original size:14 final size:15
Alignment explanation
Indices: 40786--40814 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40776 CTAGTCGAAA
40786 ATTTTTTTAT-TTTT
1 ATTTTTTTATATTTT
40800 ATTTTTTTATATTTT
1 ATTTTTTTATATTTT
40815 TCGATATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
ATTTTTTTATATTTT
Found at i:46787 original size:107 final size:107
Alignment explanation
Indices: 46601--46922 Score: 626
Period size: 107 Copynumber: 3.0 Consensus size: 107
46591 GCGGGATTTA
46601 GATATTATTTGGATATTAAGCCCACATATTGGGATTTTAACTCCAATTGTTGACTTATATGGGCT
1 GATATTATTTGGATATTAAGCCCACATATTGGGATTTTAACTCCAATTGTTGACTTATATGGGCT
46666 AAGTATTATCTCATATAAATTATCCAAAAATCCTTAACTTCC
66 AAGTATTATCTCATATAAATTATCCAAAAATCCTTAACTTCC
*
46708 GATATTATTTGGATATTAAGCCCACATATTGGGATTTTAACTCCAATTATTGACTTATATGGGCT
1 GATATTATTTGGATATTAAGCCCACATATTGGGATTTTAACTCCAATTGTTGACTTATATGGGCT
46773 AAGTATTATCTCATATAAATTATCCAAAAATCCTTAACTTCC
66 AAGTATTATCTCATATAAATTATCCAAAAATCCTTAACTTCC
*
46815 GATATTATTTGGATATTAAGCCCACATATTGGGATTTTAACTCCAATTGTTTACTTATATGGGCT
1 GATATTATTTGGATATTAAGCCCACATATTGGGATTTTAACTCCAATTGTTGACTTATATGGGCT
46880 AAGTATTATCTCATATAAATTATCCAAAAATCCTTAACTTCC
66 AAGTATTATCTCATATAAATTATCCAAAAATCCTTAACTTCC
46922 G
1 G
46923 GGCTTCTTCT
Statistics
Matches: 212, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 212 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (107 bp):
GATATTATTTGGATATTAAGCCCACATATTGGGATTTTAACTCCAATTGTTGACTTATATGGGCT
AAGTATTATCTCATATAAATTATCCAAAAATCCTTAACTTCC
Done.