Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014148.1 Corchorus capsularis cultivar CVL-1 contig14169, 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: 70272
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1469 original size:3 final size:3
Alignment explanation
Indices: 1461--1485 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1451 ACATTAGTCC
1461 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1486 AAAGAACCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5539 original size:27 final size:27
Alignment explanation
Indices: 5498--5555 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
5488 GGCTGTTTTG
*
5498 TTTCCTTTGCCTCTGGTTTAGAAGTTA
1 TTTCCTTTGCCTCTGGTTTAGAAGTCA
5525 TTTCCTTT-CCTTCTGGTTTAGAAGTCA
1 TTTCCTTTGCC-TCTGGTTTAGAAGTCA
5552 TTTC
1 TTTC
5556 AACACCAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.14, C:0.21, G:0.16, T:0.50
Consensus pattern (27 bp):
TTTCCTTTGCCTCTGGTTTAGAAGTCA
Found at i:7628 original size:15 final size:15
Alignment explanation
Indices: 7608--7654 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
7598 TCTTGCTTCT
7608 ACTTTTTTGTTGGAA
1 ACTTTTTTGTTGGAA
**
7623 ACTTTTTTGGTTTCAAA
1 ACTTTTTT-G-TTGGAA
7640 AC-TTTTTGTTGGAA
1 ACTTTTTTGTTGGAA
7654 A
1 A
7655 TGGACAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 5 0.19
15 9 0.35
16 6 0.23
17 6 0.23
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (15 bp):
ACTTTTTTGTTGGAA
Found at i:9547 original size:71 final size:71
Alignment explanation
Indices: 9464--9742 Score: 465
Period size: 71 Copynumber: 4.0 Consensus size: 71
9454 TAGTGCAACT
*
9464 AGTTTGTAATTCCTGTATTAACATACCCAATGATCAATGAAAATATAACTTTTCTGAATTCAAGA
1 AGTTTGTAATTCCTGTATTAGCATACCCAATGATCAATGAAAATATAACTTTTCTGAATTCAAGA
9529 AACTCC
66 AACTCC
9535 AGTTTGTAATTCCTGTATTAGCATACCCAATGATCAATGAAAATATAACTTTTCTGAATTCAAGA
1 AGTTTGTAATTCCTGTATTAGCATACCCAATGATCAATGAAAATATAACTTTTCTGAATTCAAGA
9600 AACTCC
66 AACTCC
* * *
9606 AGTTTGTAATTCCTGTATTAGCATACCCAATGATTAATGAAAATACAACTTTTCTGAATTCTAGA
1 AGTTTGTAATTCCTGTATTAGCATACCCAATGATCAATGAAAATATAACTTTTCTGAATTCAAGA
9671 AACTCC
66 AACTCC
** * *
9677 AGTTTGTAAAACCTGTATTAGCAT---TAATGATCAATGAAAATGTAACTTTTCTGAATTCAAGA
1 AGTTTGTAATTCCTGTATTAGCATACCCAATGATCAATGAAAATATAACTTTTCTGAATTCAAGA
9739 AACT
66 AACT
9743 TCAATTAAAG
Statistics
Matches: 197, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
68 37 0.19
71 160 0.81
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (71 bp):
AGTTTGTAATTCCTGTATTAGCATACCCAATGATCAATGAAAATATAACTTTTCTGAATTCAAGA
AACTCC
Found at i:14738 original size:21 final size:21
Alignment explanation
Indices: 14709--14748 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14699 ATTTTACGCA
14709 TGGGATTATCGAAATAAGCAC
1 TGGGATTATCGAAATAAGCAC
* *
14730 TGGGCTTATTGAAATAAGC
1 TGGGATTATCGAAATAAGC
14749 CTCCACATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (21 bp):
TGGGATTATCGAAATAAGCAC
Found at i:15585 original size:31 final size:31
Alignment explanation
Indices: 15533--15651 Score: 116
Period size: 31 Copynumber: 3.9 Consensus size: 31
15523 TTATTAAGTC
*
15533 CATAACATTGCAAAGTCGGCTAAAATCAATT
1 CATAACATTGCAAAATCGGCTAAAATCAATT
* * * *
15564 CATAGCGTTGCAAAATTGGCTAAAATCAGTT
1 CATAACATTGCAAAATCGGCTAAAATCAATT
* * * *
15595 CCTAACATTGCAAAATCGACT-AAAT-TATA
1 CATAACATTGCAAAATCGGCTAAAATCAATT
* * *
15624 CCTAACGTTGCAAAATCGGCTTAAATCA
1 CATAACATTGCAAAATCGGCTAAAATCA
15652 GTACCTGATG
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
29 20 0.29
30 8 0.11
31 42 0.60
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (31 bp):
CATAACATTGCAAAATCGGCTAAAATCAATT
Found at i:16437 original size:51 final size:50
Alignment explanation
Indices: 16372--16568 Score: 304
Period size: 51 Copynumber: 3.9 Consensus size: 50
16362 ATTTTGTTGT
* * *
16372 TAAAATCACCAAGACTCTACCTTTATCATCCAAAGATTCAATTTTTGTCAT
1 TAAAATCACCAAGACTCTACCTTTATGATCCAAAGATTTAA-TTTTGTCAA
*
16423 TAAAATCACCAAGACTCTACCTTTATGATCCAAAGATTTAACTTTTATCAA
1 TAAAATCACCAAGACTCTACCTTTATGATCCAAAGATTTAA-TTTTGTCAA
* * *
16474 TAAAATCAACAAGACTCTACCTTTATGATCCAAATATTTAATTTTCTCAA
1 TAAAATCACCAAGACTCTACCTTTATGATCCAAAGATTTAATTTTGTCAA
*
16524 TAAAATCAACAAGACTCTACCTTTATGATCCAAAGATTTAATTTT
1 TAAAATCACCAAGACTCTACCTTTATGATCCAAAGATTTAATTTT
16569 ATAATCAAAG
Statistics
Matches: 137, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 52 0.38
51 85 0.62
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (50 bp):
TAAAATCACCAAGACTCTACCTTTATGATCCAAAGATTTAATTTTGTCAA
Found at i:16556 original size:101 final size:101
Alignment explanation
Indices: 16372--16570 Score: 319
Period size: 101 Copynumber: 2.0 Consensus size: 101
16362 ATTTTGTTGT
* * * *
16372 TAAAATCACCAAGACTCTACCTTTATCATCCAAAGATTCAATTTTTGTCATTAAAATCACCAAGA
1 TAAAATCAACAAGACTCTACCTTTATCATCCAAAGATTCAATTTTTCTCAATAAAATCAACAAGA
16437 CTCTACCTTTATGATCCAAAGATTTAACTTTTATCAA
66 CTCTACCTTTATGATCCAAAGATTTAA-TTTTATCAA
* * *
16474 TAAAATCAACAAGACTCTACCTTTATGATCCAAATATTTAA-TTTTCTCAATAAAATCAACAAGA
1 TAAAATCAACAAGACTCTACCTTTATCATCCAAAGATTCAATTTTTCTCAATAAAATCAACAAGA
16538 CTCTACCTTTATGATCCAAAGATTTAATTTTAT
66 CTCTACCTTTATGATCCAAAGATTTAATTTTAT
16571 AATCAAAGTC
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
100 6 0.07
101 47 0.52
102 37 0.41
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (101 bp):
TAAAATCAACAAGACTCTACCTTTATCATCCAAAGATTCAATTTTTCTCAATAAAATCAACAAGA
CTCTACCTTTATGATCCAAAGATTTAATTTTATCAA
Found at i:19164 original size:25 final size:21
Alignment explanation
Indices: 19140--19180 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
19130 AACTTAGCTA
19140 GCTATGGAAAGAAAGGTGATG
1 GCTATGGAAAGAAAGGTGATG
19161 GCTATGGAAAGAAAGGTGAT
1 GCTATGGAAAGAAAGGTGAT
19181 AAACAACGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.37, T:0.20
Consensus pattern (21 bp):
GCTATGGAAAGAAAGGTGATG
Found at i:27424 original size:32 final size:33
Alignment explanation
Indices: 27359--27426 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
27349 CATATTTTTA
* *
27359 ATGATAAAGAAAGGTAGAAGGAGGAGATTATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
27392 ATGATAAAGAAAGGTAGAA-GAAGAGATCATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
27424 ATG
1 ATG
27427 TTCAATAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.47, C:0.04, G:0.31, T:0.18
Consensus pattern (33 bp):
ATGATAAAGAAAGGTAGAAGGAAGAGATCATGC
Found at i:27580 original size:35 final size:36
Alignment explanation
Indices: 27521--27589 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
27511 TTTTCAATCC
*
27521 GATCTTTTTGAGCTTCTTGATCGTCACTTAAACTCG
1 GATCTTTTTGAACTTCTTGATCGTCACTTAAACTCG
27557 GATCTTTTTGAAC-TCTTGATCGTCACTTAAACT
1 GATCTTTTTGAACTTCTTGATCGTCACTTAAACT
27590 TGTACGATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.62
36 12 0.38
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (36 bp):
GATCTTTTTGAACTTCTTGATCGTCACTTAAACTCG
Found at i:28419 original size:30 final size:29
Alignment explanation
Indices: 28383--28450 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
28373 TAGCAGAAGA
28383 GCTTATTTGGCCAAAATT-AATAGTTTTA-GG
1 GCTTATTTGGCCAAAATTGAA-A--TTTAGGG
*
28413 GCTTATTTGGTCAAAATTGAAATTTAGGG
1 GCTTATTTGGCCAAAATTGAAATTTAGGG
28442 GCTTATTTG
1 GCTTATTTG
28451 ACCATTGACT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 4 0.11
29 11 0.31
30 18 0.51
31 2 0.06
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (29 bp):
GCTTATTTGGCCAAAATTGAAATTTAGGG
Found at i:28747 original size:26 final size:25
Alignment explanation
Indices: 28716--28780 Score: 96
Period size: 26 Copynumber: 2.6 Consensus size: 25
28706 TTATGCATGG
28716 TTGATGATAAAAAAATTAGTTTCATT
1 TTGATGATAAAAAAATTAGTTTCA-T
*
28742 TTGATGATAAAAGAATTAGTTTCAT
1 TTGATGATAAAAAAATTAGTTTCAT
*
28767 TTGGTG-TAAAAAAA
1 TTGATGATAAAAAAA
28781 AAAGAATTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 7 0.19
25 6 0.17
26 23 0.64
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.38
Consensus pattern (25 bp):
TTGATGATAAAAAAATTAGTTTCAT
Found at i:34386 original size:22 final size:22
Alignment explanation
Indices: 34359--34426 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
34349 AGAAGGATAA
34359 AAATAAATTTAA-AATATTATTT
1 AAATAAATTTAATAATATT-TTT
* *
34381 AAATAAAATTAATTATATTTTT
1 AAATAAATTTAATAATATTTTT
* *
34403 AAATAAA-TAAATTATATTTTT
1 AAATAAATTTAATAATATTTTT
34424 AAA
1 AAA
34427 ATCTAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 16 0.38
22 21 0.50
23 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATAAATTTAATAATATTTTT
Found at i:34428 original size:22 final size:22
Alignment explanation
Indices: 34372--34426 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
34362 TAAATTTAAA
*
34372 ATATTATTTAAATAAAATTAATT
1 ATATT-TTTAAATAAAATAAATT
34395 ATATTTTTAAAT-AAATAAATT
1 ATATTTTTAAATAAAATAAATT
34416 ATATTTTTAAA
1 ATATTTTTAAA
34427 ATCTAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 19 0.61
22 7 0.23
23 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTTTTAAATAAAATAAATT
Found at i:37505 original size:35 final size:35
Alignment explanation
Indices: 37457--37526 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
37447 ATTGCCGAAG
*
37457 CAAGAGTAGACCTTGTAAAAACAAGGGTGATGAAA
1 CAAGAGTACACCTTGTAAAAACAAGGGTGATGAAA
*
37492 CAAGATTACACCTTGTAAAAACAAGGGTGATGAAA
1 CAAGAGTACACCTTGTAAAAACAAGGGTGATGAAA
37527 AGTAAAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.19
Consensus pattern (35 bp):
CAAGAGTACACCTTGTAAAAACAAGGGTGATGAAA
Found at i:40789 original size:2 final size:2
Alignment explanation
Indices: 40782--40819 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
40772 ATTCTTTACT
40782 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
40820 TTTTCTTGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:53268 original size:16 final size:16
Alignment explanation
Indices: 53244--53274 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53234 TTGTGGTAGT
*
53244 TGGATTGATGTTTTCA
1 TGGAATGATGTTTTCA
53260 TGGAATGATGTTTTC
1 TGGAATGATGTTTTC
53275 TGTTGATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.48
Consensus pattern (16 bp):
TGGAATGATGTTTTCA
Found at i:55619 original size:28 final size:30
Alignment explanation
Indices: 55560--55624 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
55550 TCATTCTGAT
* *
55560 AAAAACAATTTGCTTATAATCCTCTTTGAA
1 AAAAAAAATTTACTTATAATCCTCTTTGAA
55590 AAAAAAAATTTACTTATGAAT-CTC-TT-AA
1 AAAAAAAATTTACTTAT-AATCCTCTTTGAA
55618 AAAAAAA
1 AAAAAAA
55625 TTGATACCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 9 0.28
29 2 0.06
30 18 0.56
31 3 0.09
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (30 bp):
AAAAAAAATTTACTTATAATCCTCTTTGAA
Found at i:58792 original size:2 final size:2
Alignment explanation
Indices: 58785--58819 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
58775 AGGGACTATT
*
58785 TA TA TA TA TA CA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58820 AAATGTAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:59808 original size:2 final size:2
Alignment explanation
Indices: 59765--59800 Score: 54
Period size: 2 Copynumber: 17.0 Consensus size: 2
59755 TAATGGTATC
59765 AT AT AGT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
59801 CGATATATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 28 0.88
3 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:59808 original size:10 final size:9
Alignment explanation
Indices: 59761--59798 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
59751 ACAATAATGG
59761 TATCATATA
1 TATCATATA
59770 GTATCATATA
1 -TATCATATA
59780 TAT-ATATA
1 TATCATATA
59788 TAT-ATATA
1 TATCATATA
59796 TAT
1 TAT
59799 ATCGATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 16 0.57
9 3 0.11
10 9 0.32
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (9 bp):
TATCATATA
Found at i:65299 original size:17 final size:17
Alignment explanation
Indices: 65254--65299 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
65244 TAATTAATGG
*
65254 TACTAATCAAGTTGAGT
1 TACTAATCAAGTTAAGT
65271 TAGCT--TCAAAGTTAAGT
1 TA-CTAATC-AAGTTAAGT
65288 TACTAATCAAGT
1 TACTAATCAAGT
65300 GCTTTTAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (17 bp):
TACTAATCAAGTTAAGT
Found at i:66231 original size:2 final size:2
Alignment explanation
Indices: 66226--66271 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
66216 AAAATATATA
66226 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
66268 TG TG
1 TG TG
66272 AGTACTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:66753 original size:22 final size:22
Alignment explanation
Indices: 66728--66827 Score: 71
Period size: 22 Copynumber: 4.5 Consensus size: 22
66718 GAAAGATTAT
*
66728 CAAAACTTCATAGTGTGGTTAC
1 CAAAACTTCATAGTGAGGTTAC
*
66750 C-AAACTTTCATA-TAGAGGTTAT
1 CAAAAC-TTCATAGT-GAGGTTAC
* * *
66772 CAAGACTTCATAGGGTA-GTTAT
1 CAAAACTTCATAGTG-AGGTTAC
* **
66794 CAAAATTTCATACAGAGGTTAC
1 CAAAACTTCATAGTGAGGTTAC
*
66816 CAAAATTTCATA
1 CAAAACTTCATA
66828 AAAAGGTTAG
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
21 6 0.10
22 53 0.84
23 4 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (22 bp):
CAAAACTTCATAGTGAGGTTAC
Found at i:66772 original size:44 final size:44
Alignment explanation
Indices: 66704--66827 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
66694 TGACAATCAA
* * * * * *
66704 ACCAAAATTACATAGAAAGATTATCAAAACTTCATAGTGTGGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAACTTCATAGGGTAGTT
* * *
66748 ACCAAACTTTCATATAGAGGTTATCAAGACTTCATAGGGTAGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAACTTCATAGGGTAGTT
* * *
66792 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATA
1 ACCAAAATTTCATACAGAGGTTATCAAAACTTCATA
66828 AAAAGGTTAG
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (44 bp):
ACCAAAATTTCATACAGAGGTTATCAAAACTTCATAGGGTAGTT
Found at i:66834 original size:22 final size:22
Alignment explanation
Indices: 66789--66846 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
66779 TCATAGGGTA
* * *
66789 GTTATCAAAATTTCATACAGAG
1 GTTACCAAAATTTCATAAAAAG
66811 GTTACCAAAATTTCATAAAAAG
1 GTTACCAAAATTTCATAAAAAG
* *
66833 GTTAGCACAATTTC
1 GTTACCAAAATTTC
66847 TTAGGGATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (22 bp):
GTTACCAAAATTTCATAAAAAG
Found at i:67208 original size:22 final size:22
Alignment explanation
Indices: 67183--67240 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
67173 TTCACAGTAT
*
67183 GGTTATCAAATTTTCATAGGGA
1 GGTTATCAAATTTTCATAAGGA
* **
67205 GGTTATCGAAA-TCTCATAATTA
1 GGTTATC-AAATTTTCATAAGGA
67227 GGTTATCAAATTTT
1 GGTTATCAAATTTT
67241 TAAAATGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 3 0.10
22 23 0.79
23 3 0.10
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (22 bp):
GGTTATCAAATTTTCATAAGGA
Found at i:68229 original size:21 final size:21
Alignment explanation
Indices: 68190--68229 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
68180 GTTGATGCAT
*
68190 ATATAACTTTTTTAATAACCG
1 ATATAACTTTTTCAATAACCG
*
68211 ATATAACTTTTTCAGTAAC
1 ATATAACTTTTTCAATAAC
68230 TAAAGTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATATAACTTTTTCAATAACCG
Found at i:69192 original size:66 final size:66
Alignment explanation
Indices: 69086--69215 Score: 251
Period size: 66 Copynumber: 2.0 Consensus size: 66
69076 TAATAGAAGA
*
69086 ATTAGACAGCCCATAATGACCATGTTAATGCTCACATAAAATTTTTATACAATTTACCAAATAAT
1 ATTAGACAACCCATAATGACCATGTTAATGCTCACATAAAATTTTTATACAATTTACCAAATAAT
69151 T
66 T
69152 ATTAGACAACCCATAATGACCATGTTAATGCTCACATAAAATTTTTATACAATTTACCAAATAA
1 ATTAGACAACCCATAATGACCATGTTAATGCTCACATAAAATTTTTATACAATTTACCAAATAA
69216 ATTTAGAATG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.32
Consensus pattern (66 bp):
ATTAGACAACCCATAATGACCATGTTAATGCTCACATAAAATTTTTATACAATTTACCAAATAAT
T
Done.