Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008649.1 Corchorus capsularis cultivar CVL-1 contig08670, 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: 21381
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:523 original size:2 final size:2
Alignment explanation
Indices: 516--546 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
506 ACTTTGAGAG
516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
547 TGATTAGTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2062 original size:22 final size:22
Alignment explanation
Indices: 2036--2380 Score: 340
Period size: 22 Copynumber: 15.4 Consensus size: 22
2026 AAGTTTCAGG
* *
2036 TACTGTTTTATGGTTAATTTGG
1 TACTGTTTTATGCTTAATTTGC
*
2058 TACTGTTTGT-TGATTGAATTTGC
1 TACTGTTT-TATGCTT-AATTTGC
* * *
2081 TTCTGTTTTATGATTGAATATGC
1 TACTGTTTTATGCTT-AATTTGC
* *
2104 TACTGTTTTATGATTGAATATGC
1 TACTGTTTTATGCTT-AATTTGC
2127 TACTGTTTCT-TGCTTATAATTTGC
1 TACTGTTT-TATGC-T-TAATTTGC
2151 TACTGTTTTATGCTTAATTTGC
1 TACTGTTTTATGCTTAATTTGC
*
2173 TACTGTTTTATGCTCAATTTGC
1 TACTGTTTTATGCTTAATTTGC
* * * *
2195 TACTGTTTTAGGGTTCATGTAGC
1 TACTGTTTTATGCTTAAT-TTGC
2218 TACTGTTTTATGCTTAAATTT-C
1 TACTGTTTTATGCTT-AATTTGC
* * *
2240 TACTGTTTTAGGGTTCATTTGC
1 TACTGTTTTATGCTTAATTTGC
2262 TACTGTTTTATGCTTAAATTT-C
1 TACTGTTTTATGCTT-AATTTGC
* * *
2284 TACTGTTTTAGGGTTCATTTGC
1 TACTGTTTTATGCTTAATTTGC
2306 TACTGTTTTATGCTTAATTTGC
1 TACTGTTTTATGCTTAATTTGC
* * *
2328 TACTGTTTTAGGGC-TCATGTAGC
1 TACTGTTTTA-TGCTTAAT-TTGC
2351 TACTGTTTTATGCTTAATTTGC
1 TACTGTTTTATGCTTAATTTGC
*
2373 TTCTGTTT
1 TACTGTTT
2381 GTTTGATGCT
Statistics
Matches: 272, Mismatches: 36, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
21 8 0.03
22 143 0.53
23 99 0.36
24 21 0.08
25 1 0.00
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.52
Consensus pattern (22 bp):
TACTGTTTTATGCTTAATTTGC
Found at i:2202 original size:44 final size:44
Alignment explanation
Indices: 2036--2380 Score: 383
Period size: 44 Copynumber: 7.7 Consensus size: 44
2026 AAGTTTCAGG
* * * * *
2036 TACTGTTTTATGGTTAATTTGGTACTGTTTGT-TGATTGAATTTGC
1 TACTGTTTTATGCTTAATTTGCTACTGTTT-TAGGGTT-CATTTGC
* * * * * * *
2081 TTCTGTTTTATGATTGAATATGCTACTGTTTTATGATTGAATATGC
1 TACTGTTTTATGCTT-AATTTGCTACTGTTTTAGGGTT-CATTTGC
* * *
2127 TACTGTTTCT-TGCTTATAATTTGCTACTGTTTTATGCTTAATTTGC
1 TACTGTTT-TATGC-T-TAATTTGCTACTGTTTTAGGGTTCATTTGC
* *
2173 TACTGTTTTATGCTCAATTTGCTACTGTTTTAGGGTTCATGTAGC
1 TACTGTTTTATGCTTAATTTGCTACTGTTTTAGGGTTCAT-TTGC
2218 TACTGTTTTATGCTTAAATTT-CTACTGTTTTAGGGTTCATTTGC
1 TACTGTTTTATGCTT-AATTTGCTACTGTTTTAGGGTTCATTTGC
2262 TACTGTTTTATGCTTAAATTT-CTACTGTTTTAGGGTTCATTTGC
1 TACTGTTTTATGCTT-AATTTGCTACTGTTTTAGGGTTCATTTGC
* *
2306 TACTGTTTTATGCTTAATTTGCTACTGTTTTAGGGCTCATGTAGC
1 TACTGTTTTATGCTTAATTTGCTACTGTTTTAGGGTTCAT-TTGC
*
2351 TACTGTTTTATGCTTAATTTGCTTCTGTTT
1 TACTGTTTTATGCTTAATTTGCTACTGTTT
2381 GTTTGATGCT
Statistics
Matches: 270, Mismatches: 20, Indels: 20
0.87 0.06 0.06
Matches are distributed among these distances:
43 5 0.02
44 102 0.38
45 84 0.31
46 56 0.21
47 22 0.08
48 1 0.00
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.52
Consensus pattern (44 bp):
TACTGTTTTATGCTTAATTTGCTACTGTTTTAGGGTTCATTTGC
Found at i:2325 original size:133 final size:135
Alignment explanation
Indices: 2083--2380 Score: 415
Period size: 133 Copynumber: 2.2 Consensus size: 135
2073 GAATTTGCTT
* * *
2083 CTGTTTTATGATTGAATATGCTACTGTTTTATGATTGAATATGCTACTGTTTCTTGCTTATAATT
1 CTGTTTTATGCTT-AAT-TTCTACTGTTTTAGGATTGAATATGCTACTGTTTCTTGCTTATAATT
* *
2148 TGCTACTGTTTTATGCTTAATTTGCTACTGTTTTATGCTCAATTTGCTACTGTTTTAGGGTTCAT
64 TGCTACTGTTTTAGGCTTAATTTGCTACTGTTTTATGCTCAATTTGCTACTGTTTTAGGGCTCAT
2213 GTAGCTA
129 GTAGCTA
* * *
2220 CTGTTTTATGCTTAAATTTCTACTGTTTTAGGGTT-CATTTGCTACTGTTT-TATGCTTA-AATT
1 CTGTTTTATGCTT-AATTTCTACTGTTTTAGGATTGAATATGCTACTGTTTCT-TGCTTATAATT
* * *
2282 T-CTACTGTTTTAGGGTTCATTTGCTACTGTTTTATGCTTAATTTGCTACTGTTTTAGGGCTCAT
64 TGCTACTGTTTTAGGCTTAATTTGCTACTGTTTTATGCTCAATTTGCTACTGTTTTAGGGCTCAT
2346 GTAGCTA
129 GTAGCTA
*
2353 CTGTTTTATGCTTAATTTGCTTCTGTTT
1 CTGTTTTATGCTTAATTT-CTACTGTTT
2381 GTTTGATGCT
Statistics
Matches: 146, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
132 5 0.03
133 86 0.59
134 6 0.04
135 19 0.13
136 15 0.10
137 15 0.10
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (135 bp):
CTGTTTTATGCTTAATTTCTACTGTTTTAGGATTGAATATGCTACTGTTTCTTGCTTATAATTTG
CTACTGTTTTAGGCTTAATTTGCTACTGTTTTATGCTCAATTTGCTACTGTTTTAGGGCTCATGT
AGCTA
Found at i:2468 original size:22 final size:22
Alignment explanation
Indices: 2442--2511 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
2432 CTAATTCTGT
2442 AATTCTGTTTTTGCTTAAGGTC
1 AATTCTGTTTTTGCTTAAGGTC
*
2464 AATTCTGTTTTTGCTTAAAGTC
1 AATTCTGTTTTTGCTTAAGGTC
*
2486 AATTCTGTTTTTGCTTAAGTTC
1 AATTCTGTTTTTGCTTAAGGTC
2508 AATT
1 AATT
2512 ATATTTATGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.21, C:0.13, G:0.14, T:0.51
Consensus pattern (22 bp):
AATTCTGTTTTTGCTTAAGGTC
Found at i:2522 original size:22 final size:22
Alignment explanation
Indices: 2442--2531 Score: 121
Period size: 22 Copynumber: 4.1 Consensus size: 22
2432 CTAATTCTGT
*
2442 AATTCTGTTTTTGCTTAAGGTC
1 AATTCTGTTTTTGCTTAAGTTC
2464 AATTCTGTTTTTGCTTAAAG-TC
1 AATTCTGTTTTTGCTT-AAGTTC
2486 AATTCTGTTTTTGCTTAAGTTC
1 AATTCTGTTTTTGCTTAAGTTC
* * *
2508 AATTATATTTATGCTT-AGTTC
1 AATTCTGTTTTTGCTTAAGTTC
2529 AAT
1 AAT
2532 ATTAGTTGAG
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.17
22 49 0.78
23 3 0.05
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.51
Consensus pattern (22 bp):
AATTCTGTTTTTGCTTAAGTTC
Found at i:4673 original size:16 final size:15
Alignment explanation
Indices: 4654--4707 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
4644 GAATCCACCC
4654 GACCCGAGATCCGAAT
1 GACCCGAGA-CCGAAT
*
4670 GACCCGCA-ACCCAGAT
1 GACCCG-AGACCGA-AT
4686 GACCCGAGACCCGAAT
1 GACCCGAGA-CCGAAT
4702 GACCCG
1 GACCCG
4708 TCCCAGATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 4 0.12
16 24 0.75
17 4 0.12
ACGTcount: A:0.30, C:0.39, G:0.24, T:0.07
Consensus pattern (15 bp):
GACCCGAGACCGAAT
Found at i:4690 original size:32 final size:31
Alignment explanation
Indices: 4654--4770 Score: 130
Period size: 32 Copynumber: 3.7 Consensus size: 31
4644 GAATCCACCC
* *
4654 GACCCGAGATCCGAATGACCCGCAACCCAGAT
1 GACCCGAAACCCGAATGACCCG-AACCCAGAT
* *
4686 GACCCGAGACCCGAATGACCCG-TCCCAGAT
1 GACCCGAAACCCGAATGACCCGAACCCAGAT
* *
4716 AACCCGAAACCCGAATGACACGTAACCC-GAGT
1 GACCCGAAACCCGAATGACCCG-AACCCAGA-T
*
4748 GACCCGAAACCCGAATAACCCGA
1 GACCCGAAACCCGAATGACCCGA
4771 GAAGTTAACC
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
30 26 0.36
31 3 0.04
32 44 0.60
ACGTcount: A:0.33, C:0.38, G:0.21, T:0.09
Consensus pattern (31 bp):
GACCCGAAACCCGAATGACCCGAACCCAGAT
Found at i:4768 original size:16 final size:16
Alignment explanation
Indices: 4714--4770 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
4704 CCCGTCCCAG
4714 ATAACCCGAAACCCGA
1 ATAACCCGAAACCCGA
* * *
4730 ATGACACGTAACCCGA
1 ATAACCCGAAACCCGA
* *
4746 GTGACCCGAAACCCGA
1 ATAACCCGAAACCCGA
4762 ATAACCCGA
1 ATAACCCGA
4771 GAAGTTAACC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.39, C:0.35, G:0.18, T:0.09
Consensus pattern (16 bp):
ATAACCCGAAACCCGA
Found at i:5605 original size:7 final size:7
Alignment explanation
Indices: 5593--5734 Score: 52
Period size: 7 Copynumber: 18.1 Consensus size: 7
5583 GAACCCTCCC
5593 AACCCGA
1 AACCCGA
5600 AACCCGGTA
1 AACCC-G-A
*
5609 GACCCGA
1 AACCCGA
*
5616 GACCCGA
1 AACCCGA
*
5623 GACCCGA
1 AACCCGA
*
5630 ATGACCCGG
1 A--ACCCGA
5639 AACCCGTA
1 AACCCG-A
* * *
5647 TGATCTGA
1 -AACCCGA
5655 AACCCGTA
1 AACCCG-A
5663 TAACCCGA
1 -AACCCGA
5671 AACCCGTA
1 AACCCG-A
5679 TAACCCGA
1 -AACCCGA
*
5687 GACCCGA
1 AACCCGA
5694 ATGACCCGAA
1 A--ACCCG-A
5704 TAACCC-A
1 -AACCCGA
*
5711 AACCCAAA
1 AACCC-GA
5719 TAACCCGA
1 -AACCCGA
5727 AACCCGA
1 AACCCGA
5734 A
1 A
5735 TGATTCGAGA
Statistics
Matches: 105, Mismatches: 13, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
6 5 0.05
7 49 0.47
8 9 0.09
9 40 0.38
10 1 0.01
11 1 0.01
ACGTcount: A:0.37, C:0.37, G:0.18, T:0.09
Consensus pattern (7 bp):
AACCCGA
Found at i:5635 original size:16 final size:16
Alignment explanation
Indices: 5608--5702 Score: 88
Period size: 16 Copynumber: 6.1 Consensus size: 16
5598 GAAACCCGGT
5608 AGACCCG-A-GACCCG
1 AGACCCGTATGACCCG
*
5622 AGACCCGAATGACCCG
1 AGACCCGTATGACCCG
* *
5638 -GAACCCGTATGATCTG
1 AG-ACCCGTATGACCCG
* *
5654 AAACCCGTATAACCCG
1 AGACCCGTATGACCCG
* *
5670 AAACCCGTATAACCCG
1 AGACCCGTATGACCCG
*
5686 AGACCCGAATGACCCG
1 AGACCCGTATGACCCG
5702 A
1 A
5703 ATAACCCAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
14 7 0.10
15 2 0.03
16 58 0.87
ACGTcount: A:0.33, C:0.36, G:0.21, T:0.11
Consensus pattern (16 bp):
AGACCCGTATGACCCG
Found at i:5660 original size:32 final size:32
Alignment explanation
Indices: 5617--5703 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
5607 TAGACCCGAG
* * *
5617 ACCCGAGACCCGAATGACCCGGAACCCGTATG
1 ACCCGAAACCCGAATGACCCGAAACCCGTATA
* * * *
5649 ATCTGAAACCCGTATAACCCGAAACCCGTATA
1 ACCCGAAACCCGAATGACCCGAAACCCGTATA
*
5681 ACCCGAGACCCGAATGACCCGAA
1 ACCCGAAACCCGAATGACCCGAA
5704 TAACCCAAAC
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.33, C:0.36, G:0.20, T:0.11
Consensus pattern (32 bp):
ACCCGAAACCCGAATGACCCGAAACCCGTATA
Found at i:5720 original size:15 final size:16
Alignment explanation
Indices: 5697--5731 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5687 GACCCGAATG
*
5697 ACCCGAATAACCC-AA
1 ACCCAAATAACCCGAA
5712 ACCCAAATAACCCGAA
1 ACCCAAATAACCCGAA
5728 ACCC
1 ACCC
5732 GAATGATTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.46, C:0.43, G:0.06, T:0.06
Consensus pattern (16 bp):
ACCCAAATAACCCGAA
Found at i:5725 original size:40 final size:41
Alignment explanation
Indices: 5656--5737 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 41
5646 ATGATCTGAA
* ** *
5656 ACCCGTATAACCCGAAACCCGTATAACCCGAGACCCGAATG
1 ACCCGAATAACCCGAAACCCAAATAACCCGAAACCCGAATG
5697 ACCCGAATAACCC-AAACCCAAATAACCCGAAACCCGAATG
1 ACCCGAATAACCCGAAACCCAAATAACCCGAAACCCGAATG
5737 A
1 A
5738 TTCGAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 25 0.68
41 12 0.32
ACGTcount: A:0.40, C:0.37, G:0.13, T:0.10
Consensus pattern (41 bp):
ACCCGAATAACCCGAAACCCAAATAACCCGAAACCCGAATG
Found at i:8547 original size:22 final size:21
Alignment explanation
Indices: 8505--8547 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
8495 TTGCTTTTCT
* *
8505 TTTTCCTTTTTCTACTGATAG
1 TTTTCCTTCTTCCACTGATAG
*
8526 TTTTCTCTTCTTCCACTTATAG
1 TTTTC-CTTCTTCCACTGATAG
8548 CATACTCAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.23, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTCCTTCTTCCACTGATAG
Found at i:11350 original size:35 final size:35
Alignment explanation
Indices: 11304--11711 Score: 548
Period size: 35 Copynumber: 11.7 Consensus size: 35
11294 AAACTTCTCT
*
11304 GAAAACTTCTTGAAATAAGATCAACTCTGATCTTC
1 GAAAACTTCTTGAAATGAGATCAACTCTGATCTTC
*
11339 GAAAACTTCTTGGAATGAGATCAACTCTG--CGTT-
1 GAAAACTTCTTGAAATGAGATCAACTCTGATC-TTC
* * *
11372 GGAAACTTTTTGAAATGAGATCAACTCTGATCGTTA
1 GAAAACTTCTTGAAATGAGATCAACTCTGATC-TTC
*
11408 G-AAACTTCTTGAAATGAGATCAACTCTGA-CCTC
1 GAAAACTTCTTGAAATGAGATCAACTCTGATCTTC
11441 TGAAAACTTCTTGAAATGAGATCAACTCTGATCTTC
1 -GAAAACTTCTTGAAATGAGATCAACTCTGATCTTC
* *
11477 GAAAAATTCTTGGAATGAGATCAACTCTGATCGTT-
1 GAAAACTTCTTGAAATGAGATCAACTCTGATC-TTC
* *
11512 GGAAACTTCTTGAAATGAAATCAACTCTGATC-TC
1 GAAAACTTCTTGAAATGAGATCAACTCTGATCTTC
*
11546 TGAAAAATTCTTGAAATGAGATCAACTCTGATCTTC
1 -GAAAACTTCTTGAAATGAGATCAACTCTGATCTTC
*
11582 GAAAACTTCTTGGAATGAGATCAACTCTGATCGTT-
1 GAAAACTTCTTGAAATGAGATCAACTCTGATC-TTC
* *
11617 GGAAACTTCTTGAAATGAGATCAACTCTGATATTC
1 GAAAACTTCTTGAAATGAGATCAACTCTGATCTTC
*
11652 GAAAACTTCTTGGAATGAGATCAACTCTGATCGTT-
1 GAAAACTTCTTGAAATGAGATCAACTCTGATC-TTC
11687 G-AAACTTCTTGAAATGAGATCAACT
1 GAAAACTTCTTGAAATGAGATCAACT
11712 TGACCATTGA
Statistics
Matches: 332, Mismatches: 27, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
33 29 0.09
34 29 0.09
35 262 0.79
36 12 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (35 bp):
GAAAACTTCTTGAAATGAGATCAACTCTGATCTTC
Found at i:11787 original size:54 final size:53
Alignment explanation
Indices: 11706--11807 Score: 186
Period size: 54 Copynumber: 1.9 Consensus size: 53
11696 TGAAATGAGA
*
11706 TCAACTTGACCATTGAATACTTTTTGGAATGACCGCACTGGATCATCTGGGGG
1 TCAACTTGACCATTGAATACTTCTTGGAATGACCGCACTGGATCATCTGGGGG
11759 TCAACTATGACCATTGAATACTTCTTGGAATGACCGCACTGGATCATCT
1 TCAACT-TGACCATTGAATACTTCTTGGAATGACCGCACTGGATCATCT
11808 AAAGATCAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 6 0.13
54 41 0.87
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (53 bp):
TCAACTTGACCATTGAATACTTCTTGGAATGACCGCACTGGATCATCTGGGGG
Found at i:11817 original size:54 final size:53
Alignment explanation
Indices: 11703--11819 Score: 180
Period size: 54 Copynumber: 2.2 Consensus size: 53
11693 TCTTGAAATG
* **
11703 AGATCAACTTGACCATTGAATACTTTTTGGAATGACCGCACTGGATCATCTGG
1 AGATCAACTTGACCATTGAATACTTCTTGGAATGACCGCACTGGATCATCTAA
* *
11756 GGGTCAACTATGACCATTGAATACTTCTTGGAATGACCGCACTGGATCATCTAA
1 AGATCAACT-TGACCATTGAATACTTCTTGGAATGACCGCACTGGATCATCTAA
11810 AGATCAACTT
1 AGATCAACTT
11820 AGATCTCTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 8 0.14
54 48 0.86
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (53 bp):
AGATCAACTTGACCATTGAATACTTCTTGGAATGACCGCACTGGATCATCTAA
Found at i:12866 original size:17 final size:18
Alignment explanation
Indices: 12846--12886 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12836 CATTTCCTTC
12846 TCTTTTTTC-CTCTTTTT
1 TCTTTTTTCTCTCTTTTT
* *
12863 TCTTTTTTCTTTTTTTTT
1 TCTTTTTTCTCTCTTTTT
12881 TCTTTT
1 TCTTTT
12887 CTTTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TCTTTTTTCTCTCTTTTT
Found at i:12877 original size:16 final size:16
Alignment explanation
Indices: 12846--12896 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
12836 CATTTCCTTC
*
12846 TCTTTTTTCCTCTTTTT
1 TCTTTTTT-CTTTTTTT
12863 TCTTTTTTCTTTTTTT
1 TCTTTTTTCTTTTTTT
12879 T-TTCTTTTCTTTGTTTT
1 TCTT-TTTTCTTT-TTTT
12896 T
1 T
12897 TTCCGCCACA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 2 0.06
16 16 0.52
17 13 0.42
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (16 bp):
TCTTTTTTCTTTTTTT
Found at i:13038 original size:37 final size:38
Alignment explanation
Indices: 12968--13039 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 38
12958 AAACATTTTT
** **
12968 TTTTTCTCTTTTGAAAAGATTTCTTTTTAAGGAAAACA
1 TTTTTCTCTTTTGAAAAGATCACACTTTAAGGAAAACA
*
13006 TTTTT-TCTTTTGAAAAGATCACACTTTGAGGAAA
1 TTTTTCTCTTTTGAAAAGATCACACTTTAAGGAAA
13040 GATTCATTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 24 0.83
38 5 0.17
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (38 bp):
TTTTTCTCTTTTGAAAAGATCACACTTTAAGGAAAACA
Found at i:19831 original size:22 final size:22
Alignment explanation
Indices: 19806--19849 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
19796 GAGACAATCG
19806 TATACGGTGGAAATGGAATGGT
1 TATACGGTGGAAATGGAATGGT
19828 TATACGGTGGAAATGGAATGGT
1 TATACGGTGGAAATGGAATGGT
19850 GCTTGATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.27
Consensus pattern (22 bp):
TATACGGTGGAAATGGAATGGT
Done.