Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007469.1 Corchorus capsularis cultivar CVL-1 contig07490, 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: 51349
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4542 original size:70 final size:70
Alignment explanation
Indices: 4459--4694 Score: 260
Period size: 70 Copynumber: 3.2 Consensus size: 70
4449 TTGTTTAGGT
* *
4459 TTTTA-TAGTTTTACTCAACTAAAAACTTTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTTTATTTTTATATAATTAAATCTAATATCTTTATAATT
4523 ATTTTA
65 ATTTTA
4529 TTTTACTATTTTACTCAACTAAAAA-TTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
1 TTTTACTATTTTACTCAACTAAAAACTT-TATTTTTATATAATTAAATCTAATAT-CTT-T-A-T
4593 ATTATTATGTTTTACCA
61 A--ATTA--TTTT---A
** * * *
4610 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTAATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTTTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
4675 TTATA
66 TTTTA
*
4680 TTTTACAATTTTACT
1 TTTTACTATTTTACT
4695 ATTTTAATTA
Statistics
Matches: 143, Mismatches: 9, Indels: 28
0.79 0.05 0.16
Matches are distributed among these distances:
69 2 0.01
70 61 0.43
71 5 0.03
72 1 0.01
73 4 0.03
74 2 0.01
75 3 0.02
76 4 0.03
77 2 0.01
78 5 0.03
80 2 0.01
81 51 0.36
82 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTTTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:4613 original size:81 final size:78
Alignment explanation
Indices: 4528--4700 Score: 283
Period size: 81 Copynumber: 2.2 Consensus size: 78
4518 TAATTATTTT
* * *
4528 ATTTTACTATTTTACTCAACTAAAAATTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
1 ATTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTAATAACT
*
4593 ATTATTATGTTTTACC
66 ATTA-TA--TTTTACA
4609 ATTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTAATAACT
1 ATTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTAATAACT
4674 ATTATATTTTACA
66 ATTATATTTTACA
4687 ATTTTACTATTTTA
1 ATTTTACTATTTTA
4701 ATTAAAAAAC
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
78 20 0.23
80 2 0.02
81 66 0.75
ACGTcount: A:0.38, C:0.13, G:0.01, T:0.49
Consensus pattern (78 bp):
ATTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTAATAACT
ATTATATTTTACA
Found at i:5399 original size:11 final size:12
Alignment explanation
Indices: 5385--5413 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
5375 AAATTTACCC
5385 AAAAAAGGAA-A
1 AAAAAAGGAACA
5396 AAAAAAGGAACA
1 AAAAAAGGAACA
5408 AAAAAA
1 AAAAAA
5414 TACAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGGAACA
Found at i:6523 original size:40 final size:40
Alignment explanation
Indices: 6474--6553 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
6464 ATTTGATTTG
* * *
6474 ATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTG-ACGACTTGATCTTGAATTGATA
6514 ATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGAT
1 ATTTAATTCAAGGGTC-TGACGACTTGATCTTGAATTGAT
6554 GACTTGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 15 0.43
41 19 0.54
42 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (40 bp):
ATTTAATTCAAGGGTCTGACGACTTGATCTTGAATTGATA
Found at i:6542 original size:67 final size:66
Alignment explanation
Indices: 6406--6547 Score: 153
Period size: 67 Copynumber: 2.1 Consensus size: 66
6396 ATGTTTTCAA
* * ** * *
6406 GATTTGTTTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAGTTTGATTTGAT
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATAATAATTCAAGAGTTTGA-TCGAC
6471 TT
65 TT
* *
6473 GATTTGATTCAAGGGTCGAATGACTTGGTCTTGAA-TTGATAATTTAATTCAAGGGTCTTGA-CG
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATAA--TAATTCAAGAGT-TTGATCG
6536 ACTT
63 ACTT
6540 GATCTTGA
1 GAT-TTGA
6548 ATTGATGACT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
66 6 0.10
67 40 0.63
68 13 0.21
69 4 0.06
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (66 bp):
GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATAATAATTCAAGAGTTTGATCGACT
T
Found at i:6626 original size:99 final size:93
Alignment explanation
Indices: 6469--6646 Score: 225
Period size: 94 Copynumber: 1.8 Consensus size: 93
6459 GTTTGATTTG
* *
6469 ATTTGATTTGATTCAAGGGTCGAATGACTTGGTCTTGAATTGATAATTTAATTCAAGGGTCTTG-
1 ATTTGATTTGATTCAAGGGTCGAATGACTTGATCTCGAATTGATAATTTAATTCAAGGGTC--GA
6533 ACGACTTGATCTTGAATTGATGACTTGGGA
64 ACGACTTGATCTTGAATTGATGACTTGGGA
* *
6563 ATTTGATTTGATTCGAGGGTCTTTG-ATGACTTGATCTCGAATTGATGATAATTTGATTCAAGGG
1 ATTTGATTTGATTCAAGGGTC---GAATGACTTGATCTCGAA-T--TGATAATTTAATTCAAGGG
*
6627 TCGAATGACTTGATCTTGAA
60 TCGAACGACTTGATCTTGAA
6647 CGAACACAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
94 20 0.28
96 14 0.19
97 3 0.04
98 15 0.21
99 20 0.28
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (93 bp):
ATTTGATTTGATTCAAGGGTCGAATGACTTGATCTCGAATTGATAATTTAATTCAAGGGTCGAAC
GACTTGATCTTGAATTGATGACTTGGGA
Found at i:6949 original size:16 final size:16
Alignment explanation
Indices: 6928--6959 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6918 GAAATATTTC
6928 AGAGCTTTTCTGCTTT
1 AGAGCTTTTCTGCTTT
6944 AGAGCTTTTCTGCTTT
1 AGAGCTTTTCTGCTTT
6960 CTGAATTGTG
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:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (16 bp):
AGAGCTTTTCTGCTTT
Found at i:7808 original size:59 final size:60
Alignment explanation
Indices: 7723--7841 Score: 186
Period size: 59 Copynumber: 2.0 Consensus size: 60
7713 TTTTTTGGTG
* * * *
7723 CTCTAAGTTTTGCCTAAGTCGTCCTTTTCAGGATTTTCAACTTAGCGAGC-CCTTTTTTT
1 CTCTAACTTTTGCCTAAGCCGTCCTTTGCAGAATTTTCAACTTAGCGAGCTCCTTTTTTT
*
7782 CTCTAACTTTTGCCTAAGCCGTCCTTTGCAGAATTTTCAACTTAGCGAGCTTCTTTTTTT
1 CTCTAACTTTTGCCTAAGCCGTCCTTTGCAGAATTTTCAACTTAGCGAGCTCCTTTTTTT
7842 TTTTGGGTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
59 46 0.85
60 8 0.15
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.44
Consensus pattern (60 bp):
CTCTAACTTTTGCCTAAGCCGTCCTTTGCAGAATTTTCAACTTAGCGAGCTCCTTTTTTT
Found at i:9715 original size:40 final size:40
Alignment explanation
Indices: 9666--9745 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
9656 ATTTGATTTG
* * *
9666 ATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTG-ACGACTTGATCTTGAATTGATA
9706 ATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGAT
1 ATTTAATTCAAGGGTC-TGACGACTTGATCTTGAATTGAT
9746 GACTTGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 15 0.43
41 19 0.54
42 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (40 bp):
ATTTAATTCAAGGGTCTGACGACTTGATCTTGAATTGATA
Found at i:9734 original size:67 final size:66
Alignment explanation
Indices: 9598--9739 Score: 153
Period size: 67 Copynumber: 2.1 Consensus size: 66
9588 TATGCTTCAA
* * ** * *
9598 GATTTGTTTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAGTTTGATTTGAT
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATAATAATTCAAGAGTTTGA-TCGAC
9663 TT
65 TT
* *
9665 GATTTGATTCAAGGGTCGAATGACTTGGTCTTGAA-TTGATAATTTAATTCAAGGGTCTTGA-CG
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATAA--TAATTCAAGAGT-TTGATCG
9728 ACTT
63 ACTT
9732 GATCTTGA
1 GAT-TTGA
9740 ATTGATGACT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
66 6 0.10
67 40 0.63
68 13 0.21
69 4 0.06
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (66 bp):
GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATAATAATTCAAGAGTTTGATCGACT
T
Found at i:9819 original size:99 final size:93
Alignment explanation
Indices: 9661--9838 Score: 225
Period size: 94 Copynumber: 1.8 Consensus size: 93
9651 GTTTGATTTG
* *
9661 ATTTGATTTGATTCAAGGGTCGAATGACTTGGTCTTGAATTGATAATTTAATTCAAGGGTCTTG-
1 ATTTGATTTGATTCAAGGGTCGAATGACTTGATCTCGAATTGATAATTTAATTCAAGGGTC--GA
9725 ACGACTTGATCTTGAATTGATGACTTGGGA
64 ACGACTTGATCTTGAATTGATGACTTGGGA
* *
9755 ATTTGATTTGATTCGAGGGTCTTTG-ATGACTTGATCTCGAATTGAGGATAATTTGATTCAAGGG
1 ATTTGATTTGATTCAAGGGTC---GAATGACTTGATCTCGAATT---GATAATTTAATTCAAGGG
*
9819 TCGAATGACTTGATCTTGAA
60 TCGAACGACTTGATCTTGAA
9839 CGAACACAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
94 20 0.28
96 16 0.22
97 2 0.03
98 15 0.21
99 19 0.26
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (93 bp):
ATTTGATTTGATTCAAGGGTCGAATGACTTGATCTCGAATTGATAATTTAATTCAAGGGTCGAAC
GACTTGATCTTGAATTGATGACTTGGGA
Found at i:10977 original size:371 final size:371
Alignment explanation
Indices: 10294--11019 Score: 1443
Period size: 371 Copynumber: 2.0 Consensus size: 371
10284 ACACAACAGT
10294 GATTTCTGATTGGTTAATGCTTGAAACCTTGAGATTTGATTGGCCAGATAATGCAATTTATTTAC
1 GATTTCTGATTGGTTAATGCTTGAAACCTTGAGATTTGATTGGCCAGATAATGCAATTTATTTAC
10359 CAATTATCTCAATTTAATTAGAGATAAAAGGTGATGACTCACAACTTAATTTTGATTGGTGAAAC
66 CAATTATCTCAATTTAATTAGAGATAAAAGGTGATGACTCACAACTTAATTTTGATTGGTGAAAC
10424 CATTAAACACTGAAATTTAATTGGTTAGACCATGTGTCATATTTATCTACCATTTTTCCTTAGAA
131 CATTAAACACTGAAATTTAATTGGTTAGACCATGTGTCATATTTATCTACCATTTTTCCTTAGAA
10489 AATATCCAATAAATTTAAGGATAAATTCTCAAAAGAAATTTGTAGGAAATTTCTGATTGGCCGAA
196 AATATCCAATAAATTTAAGGATAAATTCTCAAAAGAAATTTGTAGGAAATTTCTGATTGGCCGAA
10554 ATTTCTTGCTCTACAGAATAAAATAAAATTTATATGAATTTAGTCGTATAGTCATTATATACATT
261 ATTTCTTGCTCTACAGAATAAAATAAAATTTATATGAATTTAGTCGTATAGTCATTATATACATT
10619 ATCAAGTAAGTGGTTGGTACATCAATTATAATGCTTGAAACCTTGA
326 ATCAAGTAAGTGGTTGGTACATCAATTATAATGCTTGAAACCTTGA
*
10665 GATTTCTGATTGGTTAATGCTTGAAACCTTGAGATTTGATTGGCCAGATGATGCAATTTATTTAC
1 GATTTCTGATTGGTTAATGCTTGAAACCTTGAGATTTGATTGGCCAGATAATGCAATTTATTTAC
10730 CAATTATCTCAATTTAATTAGAGATAAAAGGTGATGACTCACAACTTAATTTTGATTGGTGAAAC
66 CAATTATCTCAATTTAATTAGAGATAAAAGGTGATGACTCACAACTTAATTTTGATTGGTGAAAC
10795 CATTAAACACTGAAATTTAATTGGTTAGACCATGTGTCATATTTATCTACCATTTTTCCTTAGAA
131 CATTAAACACTGAAATTTAATTGGTTAGACCATGTGTCATATTTATCTACCATTTTTCCTTAGAA
10860 AATATCCAATAAATTTAAGGATAAATTCTCAAAAGAAATTTGTAGGAAATTTCTGATTGGCCGAA
196 AATATCCAATAAATTTAAGGATAAATTCTCAAAAGAAATTTGTAGGAAATTTCTGATTGGCCGAA
10925 ATTTCTTGCTCTACAGAATAAAATAAAATTTATATGAATTTAGTCGTATAGTCATTATATACATT
261 ATTTCTTGCTCTACAGAATAAAATAAAATTTATATGAATTTAGTCGTATAGTCATTATATACATT
10990 ATCAAGTAAGTGGTTGGTACATCAATTATA
326 ATCAAGTAAGTGGTTGGTACATCAATTATA
11020 TATGATATAA
Statistics
Matches: 354, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
371 354 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (371 bp):
GATTTCTGATTGGTTAATGCTTGAAACCTTGAGATTTGATTGGCCAGATAATGCAATTTATTTAC
CAATTATCTCAATTTAATTAGAGATAAAAGGTGATGACTCACAACTTAATTTTGATTGGTGAAAC
CATTAAACACTGAAATTTAATTGGTTAGACCATGTGTCATATTTATCTACCATTTTTCCTTAGAA
AATATCCAATAAATTTAAGGATAAATTCTCAAAAGAAATTTGTAGGAAATTTCTGATTGGCCGAA
ATTTCTTGCTCTACAGAATAAAATAAAATTTATATGAATTTAGTCGTATAGTCATTATATACATT
ATCAAGTAAGTGGTTGGTACATCAATTATAATGCTTGAAACCTTGA
Found at i:11343 original size:109 final size:109
Alignment explanation
Indices: 11147--11442 Score: 441
Period size: 109 Copynumber: 2.7 Consensus size: 109
11137 ACTATTATAG
* * *
11147 TTTTATTCCACTAGAAACTCTATTTTTATTTAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTATTTTCA--T--TT-AATTAAATCTAATATCTTTATAATTACTT
*
11212 TATTTTTACTAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
11261 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
11326 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
11370 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
11434 TTTTTACCA
63 TTTTTACCA
11443 TTTTAATTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
108 1 0.01
109 122 0.71
110 7 0.04
111 15 0.09
112 1 0.01
114 25 0.15
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:12894 original size:2 final size:2
Alignment explanation
Indices: 12887--12926 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12877 AATTACCTAC
12887 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12927 CACATTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15650 original size:3 final size:3
Alignment explanation
Indices: 15642--15678 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
15632 CTTGTAAAGA
*
15642 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
15679 TATTATAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:22527 original size:12 final size:12
Alignment explanation
Indices: 22486--22528 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
22476 ACTAATATAC
22486 TAATTTTAATAT
1 TAATTTTAATAT
**
22498 TAATTGAAATAT
1 TAATTTTAATAT
22510 TAATTTTAATAT
1 TAATTTTAATAT
22522 TAATTTT
1 TAATTTT
22529 TATTGACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TAATTTTAATAT
Found at i:23269 original size:2 final size:2
Alignment explanation
Indices: 23262--23290 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23252 TTTATATTAA
23262 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 A
23291 GTGTTTGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24638 original size:25 final size:25
Alignment explanation
Indices: 24604--24654 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
24594 CTATTTGAGC
*
24604 AGTTTAAAATATTAAAAAATAAAAA
1 AGTTCAAAATATTAAAAAATAAAAA
*
24629 AGTTCAAAATATTTAAAAATAAAAA
1 AGTTCAAAATATTAAAAAATAAAAA
24654 A
1 A
24655 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (25 bp):
AGTTCAAAATATTAAAAAATAAAAA
Found at i:26154 original size:19 final size:20
Alignment explanation
Indices: 26130--26174 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
26120 ATTTTTGCCC
26130 TTGCTATATGA-TGAAAA-TT
1 TTGCTATAT-ATTGAAAATTT
*
26149 TTGCTATGTATTGAAAATTT
1 TTGCTATATATTGAAAATTT
26169 TTGCTA
1 TTGCTA
26175 AGTAATGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 14 0.61
20 8 0.35
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.47
Consensus pattern (20 bp):
TTGCTATATATTGAAAATTT
Found at i:26183 original size:20 final size:19
Alignment explanation
Indices: 26140--26183 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
26130 TTGCTATATG
*
26140 ATGAAAATTTTGCTATGTA
1 ATGAAAATTTTGCTAAGTA
*
26159 TTGAAAATTTTTGCTAAGTA
1 ATGAAAA-TTTTGCTAAGTA
26179 ATGAA
1 ATGAA
26184 GGGAAACTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.41
Consensus pattern (19 bp):
ATGAAAATTTTGCTAAGTA
Found at i:26711 original size:46 final size:45
Alignment explanation
Indices: 26583--26732 Score: 210
Period size: 45 Copynumber: 3.3 Consensus size: 45
26573 AAACCAAGTT
* **
26583 TGTTCAAACTAAACTAAAACAGCCATGAAAGACTATTTGAAACCA
1 TGTTCAAACTAAACTAAAATAGCCATGAAAGACTATTTGTTACCA
* * *
26628 TGTTCAAACTAAAATCAAATAGCCATGAAAGACTATTTGTTAGCA
1 TGTTCAAACTAAACTAAAATAGCCATGAAAGACTATTTGTTACCA
* *
26673 TGTTCAAACTAAACTAAAAGTAGCCATTAAAGACTATTTGTTACCT
1 TGTTCAAACTAAACTAAAA-TAGCCATGAAAGACTATTTGTTACCA
*
26719 TGTTCAAAATAAAC
1 TGTTCAAACTAAAC
26733 GAAACAGCCT
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
45 56 0.61
46 36 0.39
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (45 bp):
TGTTCAAACTAAACTAAAATAGCCATGAAAGACTATTTGTTACCA
Found at i:28390 original size:19 final size:19
Alignment explanation
Indices: 28354--28391 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28344 AAATCAACTT
*
28354 GTATTTTTTAAAATTTTTA
1 GTATTTTTTAAAACTTTTA
*
28373 GTATTTTTTAAACCTTTTA
1 GTATTTTTTAAAACTTTTA
28392 ATTACATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (19 bp):
GTATTTTTTAAAACTTTTA
Found at i:39471 original size:17 final size:16
Alignment explanation
Indices: 39449--39506 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
39439 CCATCTCCCT
39449 TTCCTTCTTTTATCTTC
1 TTCCTTCTTTT-TCTTC
39466 TTCCTTCTTTTTTCCTTC
1 TTCCTTC-TTTTT-CTTC
**
39484 TTATTTCTTTTTCTT-
1 TTCCTTCTTTTTCTTC
39499 TT-CTTCTT
1 TTCCTTCTT
39507 CTTCCTCCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.14
15 2 0.06
16 3 0.08
17 13 0.36
18 13 0.36
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCCTTCTTTTTCTTC
Found at i:39483 original size:18 final size:17
Alignment explanation
Indices: 39449--39509 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
39439 CCATCTCCCT
*
39449 TTCCTTCTTTTATCTTC
1 TTCCTTCTTTTTTCTTC
39466 TTCCTTCTTTTTTCCTTC
1 TTCCTTCTTTTTT-CTTC
** *
39484 TTATTTCTTTTTCTTTTC
1 TTCCTTCTTTTT-TCTTC
39502 TT-CTTCTT
1 TTCCTTCTT
39510 CCTCCTTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 17 0.46
18 19 0.51
19 1 0.03
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCCTTCTTTTTTCTTC
Found at i:39518 original size:21 final size:21
Alignment explanation
Indices: 39450--39522 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
39440 CATCTCCCTT
*
39450 TCCTTCTTTT-ATCTTCTTCC
1 TCCTTCTTTTCTTCTTCTTCC
* * *
39470 TTCTT-TTTTCCTTCTTATTTC
1 TCCTTCTTTT-CTTCTTCTTCC
**
39491 TTTTTCTTTTCTTCTTCTTCC
1 TCCTTCTTTTCTTCTTCTTCC
39512 TCCTTCTTTTC
1 TCCTTCTTTTC
39523 CTCAACCTGA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 4 0.10
20 4 0.10
21 29 0.71
22 4 0.10
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (21 bp):
TCCTTCTTTTCTTCTTCTTCC
Found at i:41413 original size:27 final size:27
Alignment explanation
Indices: 41345--41415 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
41335 AAGTGGCCCT
* *
41345 AAAATGACTAAAATACCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAATGTA
* *
41372 AAAATGACCAAAATGCCCCTTAATGTG
1 AAAATGACCAAAATGCCCCTGAATGTA
*
41399 AAAACGACCAAAATGCC
1 AAAATGACCAAAATGCC
41416 ACCTAGGCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGTA
Found at i:50341 original size:57 final size:58
Alignment explanation
Indices: 50271--50387 Score: 182
Period size: 58 Copynumber: 2.0 Consensus size: 58
50261 AGCTTTAGAT
* * *
50271 TTAATGTTGGAAGAGTGG-TTTTGTGTCTTTCGTTTTTGCGCCTTGGGTTTTTGATGC
1 TTAATGCTGGAAGAGTGGTTTTTGTGTCTTTCGTTCTTGCGCCTTGAGTTTTTGATGC
* *
50328 TTAATGCTGGAAGAGTGGTTTTTTTGTCTTTCGTTCTTGCGCGTTGAGTTTTTGATGC
1 TTAATGCTGGAAGAGTGGTTTTTGTGTCTTTCGTTCTTGCGCCTTGAGTTTTTGATGC
50386 TT
1 TT
50388 GAAGACTTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 17 0.31
58 37 0.69
ACGTcount: A:0.11, C:0.11, G:0.28, T:0.50
Consensus pattern (58 bp):
TTAATGCTGGAAGAGTGGTTTTTGTGTCTTTCGTTCTTGCGCCTTGAGTTTTTGATGC
Found at i:50688 original size:17 final size:19
Alignment explanation
Indices: 50666--50707 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
50656 AAATAAGTAC
50666 AATTTTTCTTTCA-T-TTT
1 AATTTTTCTTTCATTCTTT
50683 AATTTTTCTTTCATTCTTT
1 AATTTTTCTTTCATTCTTT
50702 AATTTT
1 AATTTT
50708 ACTTCTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.57
18 1 0.04
19 9 0.39
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (19 bp):
AATTTTTCTTTCATTCTTT
Done.