Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011326.1 Corchorus capsularis cultivar CVL-1 contig11347, 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: 59132
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:286 original size:22 final size:22
Alignment explanation
Indices: 261--597 Score: 160
Period size: 22 Copynumber: 15.6 Consensus size: 22
251 ATGATCCCAT
261 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
283 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
305 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** *
327 TATAAAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
349 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
371 TAAGAAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
393 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * *
415 AATAAAATTTTGATAA-CTAACAC
1 TATGAAATTTTGATAACCT-TC-C
* * * *
438 TATGAGATGTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
460 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
477 TA-AAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
498 TATGATTTTTTGAT-ATC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* **
519 TATGAAATTTTGTTAATTTTCC
1 TATGAAATTTTGATAACCTTCC
* * *
541 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
563 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
585 TATGAAATTTTGA
1 TATGAAATTTTGA
598 AAACTAAACT
Statistics
Matches: 230, Mismatches: 66, Indels: 38
0.69 0.20 0.11
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
20 1 0.00
21 20 0.09
22 176 0.77
23 19 0.08
24 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:451 original size:45 final size:45
Alignment explanation
Indices: 393--479 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
383 AAGACCTCAA
* *
393 TATGAAATTTTGATAACTTCCCAATAAAATTTTGATAACTAACAC
1 TATGAAATGTTGATAACTTCCCAATAAAATCTTGATAACTAACAC
* * ** *
438 TATGAGATGTTGATAACTTTCTTATGAAATCTTGATAACTAA
1 TATGAAATGTTGATAACTTCCCAATAAAATCTTGATAACTAA
480 AAATTTTGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (45 bp):
TATGAAATGTTGATAACTTCCCAATAAAATCTTGATAACTAACAC
Found at i:873 original size:31 final size:31
Alignment explanation
Indices: 838--896 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
828 TGGTAATTTA
838 GAAATATGTTTTAAAAAAAAAGATACAATTG
1 GAAATATGTTTTAAAAAAAAAGATACAATTG
* *
869 GAAATATGTTTTAAAAATAAAGGTACAA
1 GAAATATGTTTTAAAAAAAAAGATACAA
897 ACAGAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAAAAAAAGATACAATTG
Found at i:1177 original size:2 final size:2
Alignment explanation
Indices: 1170--1198 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1160 AGAATATAGA
1170 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
1199 GAATAAAAGT
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:2427 original size:156 final size:156
Alignment explanation
Indices: 2161--2525 Score: 357
Period size: 156 Copynumber: 2.3 Consensus size: 156
2151 TCATCTCAAA
* * * * *
2161 CAGACTTAGCATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACACTTTGAGGAGTCAAACCAAC
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTAGAGGAGACAAACCAAC
* * * * * * * * **
2226 TTCTCTATGCTAGAGAGTTCGGTTTTACTTAGATTTTTTCCCATAG-CTGTATGGTGATAATCTA
66 TTCCCCATCCAAGAGAGTACGGTTTCACTTAGAATTTTTCCCATAGTCT-CATGGAAATAATCTA
* * *
2290 AGT-CTATTGGTGGAAAA-CT-AGC-CTTGT
130 AGTACT-TT-G-GCAAAATCTCAACTCAT-T
** * *
2317 TGGCCTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATATAG-GGAGACAAACCTA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAAT-TAGAGGAGACAAACCAA
* * * * *
2381 GTTCCCCA-CCAAGGGAAGTACGGTTTCACTTGGAATTTTTCTCATAGTCTCATGGAAATATTCT
65 CTTCCCCATCCAAGAG-AGTACGGTTTCACTTAGAATTTTTCCCATAGTCTCATGGAAATAATCT
*
2445 AAGTACTTTGGCAAAATTTCAACTCATT
129 AAGTACTTTGGCAAAATCTCAACTCATT
*
2473 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGG
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTAGAGG
2526 TGAGAAGTCC
Statistics
Matches: 169, Mismatches: 32, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
154 5 0.03
155 8 0.05
156 148 0.88
157 8 0.05
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (156 bp):
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTAGAGGAGACAAACCAAC
TTCCCCATCCAAGAGAGTACGGTTTCACTTAGAATTTTTCCCATAGTCTCATGGAAATAATCTAA
GTACTTTGGCAAAATCTCAACTCATT
Found at i:5780 original size:2 final size:2
Alignment explanation
Indices: 5773--5801 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5763 CAATGATGTC
5773 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 T
5802 CTTATTTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8183 original size:4 final size:4
Alignment explanation
Indices: 8165--8250 Score: 52
Period size: 4 Copynumber: 20.5 Consensus size: 4
8155 TTTTATTGTT
* *
8165 TTTC TTCTC TCTC TTTC TTTAC TTTG TTT- TTTC ATTTC ATTTC ATTTC
1 TTTC TT-TC TTTC TTTC TTT-C TTTC TTTC TTTC -TTTC -TTTC -TTTC
* *
8213 GTTC ATTCTC TTTC TATC TTT- TTTC -TTC TTTC TTTC TT
1 TTTC -TT-TC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
8251 CTTCTGTGTT
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
3 9 0.13
4 32 0.48
5 24 0.36
6 2 0.03
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.67
Consensus pattern (4 bp):
TTTC
Found at i:8248 original size:11 final size:11
Alignment explanation
Indices: 8221--8253 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
8211 TCGTTCATTC
8221 TCTTTCTATCTT
1 TCTTTCT-TCTT
8233 T-TTTCTTCTT
1 TCTTTCTTCTT
8243 TCTTTCTTCTT
1 TCTTTCTTCTT
8254 CTGTGTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 14 0.70
12 1 0.05
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (11 bp):
TCTTTCTTCTT
Found at i:11958 original size:30 final size:30
Alignment explanation
Indices: 11922--11978 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
11912 ATGGGGATGT
11922 AATTGAAACCTGAAACGAGCATGTTAGGGG
1 AATTGAAACCTGAAACGAGCATGTTAGGGG
*
11952 AATTGAAACCTGAAATGAGCATGTTAG
1 AATTGAAACCTGAAACGAGCATGTTAG
11979 ATGGGGATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.23
Consensus pattern (30 bp):
AATTGAAACCTGAAACGAGCATGTTAGGGG
Found at i:15594 original size:2 final size:2
Alignment explanation
Indices: 15587--15630 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
15577 AAATTAAGAG
* * *
15587 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15629 TA
1 TA
15631 GTAAACTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15747 original size:2 final size:2
Alignment explanation
Indices: 15742--15769 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15732 TGTTGAAGTA
15742 AT 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 AT
15770 TGATTACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16559 original size:28 final size:29
Alignment explanation
Indices: 16503--16561 Score: 93
Period size: 28 Copynumber: 2.0 Consensus size: 29
16493 AAAATTATCA
*
16503 GTCAATGGTTGAAAAACTTTTGTAGAACTG
1 GTCAATGGTTG-AAAACTTTTGTAAAACTG
16533 GTCAATGGTTG-AAACTTTTGTAAAACTG
1 GTCAATGGTTGAAAACTTTTGTAAAACTG
16561 G
1 G
16562 GCAACTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 17 0.61
30 11 0.39
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (29 bp):
GTCAATGGTTGAAAACTTTTGTAAAACTG
Found at i:21011 original size:40 final size:40
Alignment explanation
Indices: 20967--21043 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
20957 GGTCATGATT
*
20967 TTACAGTGTGTTTGGATTGAGGGACCAGTAAGGACTGAGA
1 TTACAGTGTATTTGGATTGAGGGACCAGTAAGGACTGAGA
21007 TTACAGTGTATTTGGATTGAGGGACCAGTAAGGACTG
1 TTACAGTGTATTTGGATTGAGGGACCAGTAAGGACTG
21044 GGACGGGACG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.27, C:0.10, G:0.34, T:0.29
Consensus pattern (40 bp):
TTACAGTGTATTTGGATTGAGGGACCAGTAAGGACTGAGA
Found at i:25666 original size:43 final size:43
Alignment explanation
Indices: 25531--25666 Score: 102
Period size: 43 Copynumber: 3.1 Consensus size: 43
25521 TTGATTAGTA
*
25531 TTATTAAGGTTAAATTACAAGTCACTTTTGTTGTAATGAGTTT
1 TTATTAAGGTTAAATTACAAGTCACTTTAGTTGTAATGAGTTT
** * * * * *
25574 TTATTTTGGTCACTCAATTATGAAAATTAAC--TA-TT-TAAT-AATTT
1 TTATTAAGGT---T-AA--ATTACAAGTCACTTTAGTTGTAATGAGTTT
25618 ATTATTAAGGTTAAATTACAAGTCACTTTAGTTGTAATGAGTTT
1 -TTATTAAGGTTAAATTACAAGTCACTTTAGTTGTAATGAGTTT
25662 TTATT
1 TTATT
25667 TTGGTCACTC
Statistics
Matches: 66, Mismatches: 15, Indels: 24
0.63 0.14 0.23
Matches are distributed among these distances:
39 8 0.12
41 4 0.06
42 3 0.05
43 17 0.26
44 8 0.12
45 12 0.18
46 3 0.05
47 3 0.05
49 8 0.12
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (43 bp):
TTATTAAGGTTAAATTACAAGTCACTTTAGTTGTAATGAGTTT
Found at i:25678 original size:88 final size:88
Alignment explanation
Indices: 25529--25706 Score: 338
Period size: 88 Copynumber: 2.0 Consensus size: 88
25519 ATTTGATTAG
*
25529 TATTATTAAGGTTAAATTACAAGTCACTTTTGTTGTAATGAGTTTTTATTTTGGTCACTCAATTA
1 TATTATTAAGGTTAAATTACAAGTCACTTTAGTTGTAATGAGTTTTTATTTTGGTCACTCAATTA
25594 TGAAAATTAACTATTTAATAATT
66 TGAAAATTAACTATTTAATAATT
25617 TATTATTAAGGTTAAATTACAAGTCACTTTAGTTGTAATGAGTTTTTATTTTGGTCACTCAATTA
1 TATTATTAAGGTTAAATTACAAGTCACTTTAGTTGTAATGAGTTTTTATTTTGGTCACTCAATTA
*
25682 TGAAAATTAACTATTTAATCATT
66 TGAAAATTAACTATTTAATAATT
25705 TA
1 TA
25707 AATGTAATAA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.46
Consensus pattern (88 bp):
TATTATTAAGGTTAAATTACAAGTCACTTTAGTTGTAATGAGTTTTTATTTTGGTCACTCAATTA
TGAAAATTAACTATTTAATAATT
Found at i:34554 original size:23 final size:23
Alignment explanation
Indices: 34526--34577 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
34516 ATAAATAATT
**
34526 ATAAAAATATTGAATTTAATTAA
1 ATAAAAATAGAGAATTTAATTAA
* *
34549 ATAAAAATAGAGATTTTAGTTAA
1 ATAAAAATAGAGAATTTAATTAA
34572 ATAAAA
1 ATAAAA
34578 CTTTGAAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (23 bp):
ATAAAAATAGAGAATTTAATTAA
Found at i:41130 original size:31 final size:28
Alignment explanation
Indices: 41066--41144 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
41056 CTAACTTTTG
* *
41066 AAACGTAAGGGATTAATTTGTCCCAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAA
41094 AAACATAAGGGATTATTTTGTCCCAAAAGAA
1 AAACATAAGGGATTATTTTGTCCC--AA-AA
41125 AAACATAAGGGATT-TTTTGT
1 AAACATAAGGGATTATTTTGT
41145 GGGTATTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 22 0.48
30 8 0.17
31 16 0.35
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (28 bp):
AAACATAAGGGATTATTTTGTCCCAAAA
Found at i:41604 original size:25 final size:25
Alignment explanation
Indices: 41570--41620 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
41560 AGAGATCTCA
41570 CCTTCTGCTATCTACTTGCAAAAAC
1 CCTTCTGCTATCTACTTGCAAAAAC
41595 CCTTCTGCTATCTACTTGCAAAAAC
1 CCTTCTGCTATCTACTTGCAAAAAC
41620 C
1 C
41621 TAAAGTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.33, G:0.08, T:0.31
Consensus pattern (25 bp):
CCTTCTGCTATCTACTTGCAAAAAC
Found at i:53881 original size:37 final size:37
Alignment explanation
Indices: 53786--53881 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 37
53776 AATTTGACTT
*
53786 TTTGTTTCCAAAGTCCTATTTAATTTTAACTTTTGTC
1 TTTGTTTCCAATGTCCTATTTAATTTTAACTTTTGTC
* ** *
53823 TTTGTTTCTAATTGTTGTATTTAATTTT-GCTTTTTGTC
1 TTTGTTTCCAA-TGTCCTATTTAATTTTAAC-TTTTGTC
*
53861 TTTGTCTCCAATGTCCTATTT
1 TTTGTTTCCAATGTCCTATTT
53882 GGACTTAGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
37 19 0.40
38 29 0.60
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.58
Consensus pattern (37 bp):
TTTGTTTCCAATGTCCTATTTAATTTTAACTTTTGTC
Found at i:54974 original size:118 final size:119
Alignment explanation
Indices: 54739--54977 Score: 340
Period size: 118 Copynumber: 2.0 Consensus size: 119
54729 AGTACGAATA
* *
54739 ATGGAAAACTTTATGTTTTTCGATTGTACCCTTTTTTCAATTACATTTCTAAATTGACATTATTA
1 ATGGAAAACTTTATGTTTTCCGATTGTACCCTTTTTTCAAATACATTTCTAAATTGACATTATT-
* *
54804 AAATTTATTACTTAAAAATTAATTATAAAATTTCAATTTAGATCGAATTATAAGTT
65 -AATTTATTACTTAAAAATTAATTAAAAAATTTCAATTTAGACCGAATTATAAGTT
* * **
54860 ATGGGAAACTTTATGTTTTCCGA-T-TACACCTTTTTTCCAAATATATTTCTAAATTTCCATTAT
1 ATGGAAAACTTTATGTTTTCCGATTGTAC-CCTTTTTT-CAAATACATTTCTAAATTGACATTAT
*
54923 T-ATTTATTATTTAAAAATTAATTAAAAAATTTCAATTTAGACCGAATTATAAGTT
64 TAATTTATTACTTAAAAATTAATTAAAAAATTTCAATTTAGACCGAATTATAAGTT
54978 TGTCAAATTG
Statistics
Matches: 107, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
118 51 0.48
119 3 0.03
120 9 0.08
121 44 0.41
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (119 bp):
ATGGAAAACTTTATGTTTTCCGATTGTACCCTTTTTTCAAATACATTTCTAAATTGACATTATTA
ATTTATTACTTAAAAATTAATTAAAAAATTTCAATTTAGACCGAATTATAAGTT
Found at i:55055 original size:19 final size:20
Alignment explanation
Indices: 55028--55065 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
55018 TACTATTATT
55028 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAA-ATTTTAC
55048 TTTT-AATTTCAAATTTTA
1 TTTTGAATTTCAAATTTTA
55066 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTGAATTTCAAATTTTAC
Found at i:55259 original size:22 final size:22
Alignment explanation
Indices: 55231--55414 Score: 106
Period size: 22 Copynumber: 8.3 Consensus size: 22
55221 TGTCTCTATG
*
55231 TGGTTATCAAAATTTCACAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
55253 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
55276 -GGTTATCAAAATTCCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
* * *
55297 TAGTTA-CTAAAATTTAATATGA
1 TGGTTATC-AAAATTTCATAAGA
** *
55319 AAGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
55341 TGGTTACCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
55363 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
55387 TGGTTATTTAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
55409 TGGTTA
1 TGGTTA
55415 ATTATCACAA
Statistics
Matches: 124, Mismatches: 28, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
21 4 0.03
22 97 0.78
23 6 0.05
24 17 0.14
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:55311 original size:44 final size:44
Alignment explanation
Indices: 55232--55380 Score: 140
Period size: 44 Copynumber: 3.3 Consensus size: 44
55222 GTCTCTATGT
* * * *
55232 GGTTATCAAAATTTCACAA-GATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCATAATG-TGGTTACTAAAATTTCAT-ATGAA
* * *
55276 GGTTATCAAAATTCCATAATGTAGTTACTAAAATTTAATATGAA
1 GGTTATCAAAATTTCATAATGTGGTTACTAAAATTTCATATGAA
* * * *
55320 AGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAAGATCA
1 GGTTATCAAAATTTCATAATGTGGTTACTAAAATTTCATATGA--A
*
55366 GGTTATTAAAATTTC
1 GGTTATCAAAATTTC
55381 TTAGGTTGGT
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
43 1 0.01
44 69 0.81
45 1 0.01
46 14 0.16
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATGTGGTTACTAAAATTTCATATGAA
Found at i:55475 original size:22 final size:22
Alignment explanation
Indices: 55450--56069 Score: 193
Period size: 22 Copynumber: 28.4 Consensus size: 22
55440 ATCAAAGATA
* *
55450 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
55472 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
55494 TTAACAAAATTTCGTTAG-GAGG
1 TTATCAAAATTTC-ATAGTGAGG
* * * *
55516 TTA-CTAATATTTCATGGGGAAG
1 TTATC-AAAATTTCATAGTGAGG
*
55538 TTATCAAAATCTT-ATAGTGTGG
1 TTATCAAAAT-TTCATAGTGAGG
55560 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
55582 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * * *
55607 AGTACCAAAATTTGATAG-AAAG
1 -TTATCAAAATTTCATAGTGAGG
* * *
55629 TTATC-AAATCTT-ATAGAGTGA
1 TTATCAAAAT-TTCATAGTGAGG
* * *
55650 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCAT--AG-TGAGG
*
55675 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGTG-AGG
*
55696 TTATCAAAATTTCATAGT-ATTG
1 TTATCAAAATTTCATAGTGA-GG
* * * *
55718 TTATCGAAATTTTAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
55740 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
55762 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * ** *
55784 TTAACAAAATTTTATAAAGAGA
1 TTATCAAAATTTCATAGTGAGG
**
55806 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
55828 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
55850 TTA-AAAAATTTCATAGT-ATGG
1 TTATCAAAATTTCATAGTGA-GG
* *
55871 TTA-CCAAA--T--TAG-GAACG
1 TTATCAAAATTTCATAGTG-AGG
* * *
55888 TTATTAAACTTTTATTA-TG-GAG
1 TTATCAAAATTTCA-TAGTGAG-G
* *
55910 TAATCAAAATTTC--AGAGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
55930 ATATCAAAATTTCATA-TGAAGA
1 TTATCAAAATTTCATAGTG-AGG
*
55952 TTATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG-TGAGG
* *
55974 TT-TTAAGAATTTCATAAG-AAGG
1 TTATCAA-AATTTCAT-AGTGAGG
*
55996 TTATCAAAATTTCATAGT-ATG
1 TTATCAAAATTTCATAGTGAGG
* *
56017 TAGATCAAAATTTCATAGGGAGG
1 T-TATCAAAATTTCATAGTGAGG
* * *
56040 TTAACAAAATTTCATAATGGGG
1 TTATCAAAATTTCATAGTGAGG
56062 TTATCAAA
1 TTATCAAA
56070 CAGAATACTA
Statistics
Matches: 437, Mismatches: 107, Indels: 108
0.67 0.16 0.17
Matches are distributed among these distances:
17 7 0.02
18 3 0.01
19 2 0.00
20 22 0.05
21 69 0.16
22 278 0.64
23 23 0.05
24 5 0.01
25 18 0.04
26 6 0.01
27 4 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:55937 original size:20 final size:22
Alignment explanation
Indices: 55912--55965 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
55902 TTATGGAGTA
*
55912 ATCAAAATTTCAGA-GAGGA-T
1 ATCAAAATTTCAGATGAAGATT
*
55932 ATCAAAATTTCATATGAAGATT
1 ATCAAAATTTCAGATGAAGATT
55954 ATCAAAATTTCA
1 ATCAAAATTTCA
55966 TAGTTTAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.43
21 4 0.13
22 13 0.43
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (22 bp):
ATCAAAATTTCAGATGAAGATT
Found at i:57589 original size:2 final size:2
Alignment explanation
Indices: 57582--57608 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57572 TTAAAACTAG
57582 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 T
57609 GTGTGGCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58933 original size:25 final size:25
Alignment explanation
Indices: 58905--58957 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
58895 TTTTATAATT
*
58905 TTTGACATTTTTGCCTTTTGTTCCA
1 TTTGACACTTTTGCCTTTTGTTCCA
58930 TTTGACACTTTTGCCTTTTGTTCCA
1 TTTGACACTTTTGCCTTTTGTTCCA
58955 TTT
1 TTT
58958 TATAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.11, C:0.21, G:0.11, T:0.57
Consensus pattern (25 bp):
TTTGACACTTTTGCCTTTTGTTCCA
Found at i:59088 original size:19 final size:19
Alignment explanation
Indices: 59064--59100 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
59054 AAATCTTTTA
**
59064 AAAAAATTTTAAAAAAATT
1 AAAAAATTAAAAAAAAATT
59083 AAAAAATTAAAAAAAAAT
1 AAAAAATTAAAAAAAAAT
59101 GGCGGAGCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAATTAAAAAAAAATT
Done.