Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012607.1 Corchorus capsularis cultivar CVL-1 contig12628, 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: 43127
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Found at i:5189 original size:36 final size:36
Alignment explanation
Indices: 5141--5248 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
5131 GATCTCCAGA
5141 ACCTTGGCTACCCCAACCTCCACCAGAGCTCTGTCC
1 ACCTTGGCTACCCCAACCTCCACCAGAGCTCTGTCC
*
5177 GCCTTGGCTACCCCAACCTCCACCAGAGCTCTGTCC
1 ACCTTGGCTACCCCAACCTCCACCAGAGCTCTGTCC
5213 ACCTTGGCTACCCCAACCTCCACCAGAGCTCTGTCC
1 ACCTTGGCTACCCCAACCTCCACCAGAGCTCTGTCC
5249 TTGGTCCTTC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.19, C:0.47, G:0.15, T:0.19
Consensus pattern (36 bp):
ACCTTGGCTACCCCAACCTCCACCAGAGCTCTGTCC
Found at i:5533 original size:30 final size:30
Alignment explanation
Indices: 5403--5532 Score: 224
Period size: 30 Copynumber: 4.3 Consensus size: 30
5393 CCTTCCACGT
* *
5403 CCTCTACCTCCAAATCCTCCCCCGTCGCCA
1 CCTCTACCTCCAAATCCTCCCCTGTCACCA
5433 CCTCTACCTCCAAATCCTCCCCTGTCACCA
1 CCTCTACCTCCAAATCCTCCCCTGTCACCA
*
5463 CCTCTACCTCCAAATCCTCCCCTGTCGCCA
1 CCTCTACCTCCAAATCCTCCCCTGTCACCA
*
5493 CCTCTACCTCTAAATCCTCCCCTGTCACCA
1 CCTCTACCTCCAAATCCTCCCCTGTCACCA
5523 CCTCTACCTC
1 CCTCTACCTC
5533 TGTAGCCACC
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 95 1.00
ACGTcount: A:0.18, C:0.54, G:0.05, T:0.24
Consensus pattern (30 bp):
CCTCTACCTCCAAATCCTCCCCTGTCACCA
Found at i:5556 original size:18 final size:18
Alignment explanation
Indices: 5520--5556 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5510 TCCCCTGTCA
**
5520 CCACCTCTACCTCTGTAG
1 CCACCTCTACCTCCATAG
5538 CCACCTCTACCTCCATAG
1 CCACCTCTACCTCCATAG
5556 C
1 C
5557 TTTCTCCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.49, G:0.08, T:0.24
Consensus pattern (18 bp):
CCACCTCTACCTCCATAG
Found at i:5573 original size:30 final size:30
Alignment explanation
Indices: 5537--5608 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
5527 TACCTCTGTA
5537 GCCACCTCTACCTCCATAGCTTTCTCCATC
1 GCCACCTCTACCTCCATAGCTTTCTCCATC
5567 GCCACCTCTACCTCCATAGCTTTCTCCATC
1 GCCACCTCTACCTCCATAGCTTTCTCCATC
*
5597 GCCATCTCTACC
1 GCCACCTCTACC
5609 GCCAAAACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.17, C:0.47, G:0.07, T:0.29
Consensus pattern (30 bp):
GCCACCTCTACCTCCATAGCTTTCTCCATC
Found at i:5850 original size:57 final size:57
Alignment explanation
Indices: 5762--5889 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
5752 CATTTCCACT
* * *
5762 TCCCGAGTTCCAATTGCTTTTCTGGCCCCAACCTGAACCCTGGCTTGCACCTCCAGG
1 TCCCGAGTTCCAATCGCTTTTCTGGCCCCAACCTGAACCCTGGCCTGCACCACCAGG
* * * *
5819 TCCCGAGTTCCAGTCGCTTTTCTTGCCCCAACCTGAATCCTGGCCTGCACCACCAGA
1 TCCCGAGTTCCAATCGCTTTTCTGGCCCCAACCTGAACCCTGGCCTGCACCACCAGG
* *
5876 ACCAGAGTTCCAAT
1 TCCCGAGTTCCAAT
5890 TCCCCTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.19, C:0.38, G:0.18, T:0.25
Consensus pattern (57 bp):
TCCCGAGTTCCAATCGCTTTTCTGGCCCCAACCTGAACCCTGGCCTGCACCACCAGG
Found at i:5905 original size:57 final size:57
Alignment explanation
Indices: 5787--5906 Score: 134
Period size: 57 Copynumber: 2.1 Consensus size: 57
5777 GCTTTTCTGG
* * ** * * * *
5787 CCCCAACCTGAACCCTGGCTTGCACCTCCAGGTCCCGAGTTCCAGTCGCTTTTCTTG
1 CCCCAACCTGAACCCTGGCCTGCACCACCAGAACCAGAGTTCCAGTCCCCTTTCTTA
* *
5844 CCCCAACCTGAATCCTGGCCTGCACCACCAGAACCAGAGTTCCAATTCCCCTTT-TTA
1 CCCCAACCTGAACCCTGGCCTGCACCACCAGAACCAGAGTTCC-AGTCCCCTTTCTTA
5901 CCCCAA
1 CCCCAA
5907 GAGTCTTGGC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
57 45 0.87
58 7 0.13
ACGTcount: A:0.20, C:0.42, G:0.15, T:0.23
Consensus pattern (57 bp):
CCCCAACCTGAACCCTGGCCTGCACCACCAGAACCAGAGTTCCAGTCCCCTTTCTTA
Found at i:6369 original size:333 final size:333
Alignment explanation
Indices: 5758--6498 Score: 1139
Period size: 333 Copynumber: 2.2 Consensus size: 333
5748 TCTTCATTTC
* *
5758 CACTTCCCGAGTTCCAATTGCTTTTCTGGCCCCAACCTGAACCCTGGCTTGCACCTCCAGGTCCC
1 CACTTCCCGAGTTCCAATTGCTTTTCTGGCCCCAACCTGAACCCTGGCTTGCATCTCCAGGTCCT
* *
5823 GAGTTCCAGTCGCTTTTCTTGCCCCAACCTGAATCCTGGCCTGCACCACCAGAACCAGAGTTCCA
66 GAGTTCCAATCGCTTTTCTTGCCCCAACCTGAATCATGGCCTGCACCACCAGAACCAGAGTTCCA
* *
5888 ATTCCCCTTTTTACCCCAAGAGTCTTGGCCAGAATCACTGGTTCCAGCACCCCAGCTACTTTTTG
131 ATTCCCCTTTTTACCCCAAGAGTCTTGGCCAGAATCACCGGTTCCAGCACCCCAACTACTTTTTG
* * * *
5953 TGCCCCAGTTTGAATTCTGATTTGCATCTCCAGTTCCTGAATCAGAGTCATTTTTCTTTCCCCAA
196 TACCCCAGTTTGAATTCTGATTTGCATCTCCAGATCCTGAATCACAGTCATTTTTCCTTCCCCAA
** * * *
6018 CTAGAATCTTTTGTTGCATCATCAGATCCAAAATCTGAATTATTTTTCTTGGCC-CAACCTTGAT
261 CTAGAATCTTCGGTTGCATCATCAGATCCAAAATCTGAATCATTTTTCTT-ACCGCAACCTGGAT
6082 CCTGGTTTG
325 CCTGGTTTG
* * * * *
6091 CACTTCCCAAGTTCCAATTGCTTTTCTGGCCCCAACCCGACCCCTGGCTTGCATCTCCAGCTTCT
1 CACTTCCCGAGTTCCAATTGCTTTTCTGGCCCCAACCTGAACCCTGGCTTGCATCTCCAGGTCCT
* *
6156 GATTTCCAATCGCTTTTCTTGCCCCACCCTGAATCATGGCCTGCACCACCAGAACCAGAGTTCCA
66 GAGTTCCAATCGCTTTTCTTGCCCCAACCTGAATCATGGCCTGCACCACCAGAACCAGAGTTCCA
*
6221 ATTCCCCTTTTTACCCCCAGAGTCTTGGCCAGAATCACCGGTTCCAGCACCCCAACTACTTTTCT
131 ATTCCCCTTTTTACCCCAAGAGTCTTGGCCAGAATCACCGGTTCCAGCACCCCAACTACTTTT-T
* *
6286 -TACCCCAGTTTGAATTCTGATTTGCATCTGCAGATCCTGATTTC-CAGTCATTTTTCCTTCCCC
195 GTACCCCAGTTTGAATTCTGATTTGCATCTCCAGATCCTGA-ATCACAGTCATTTTTCCTTCCCC
* * *
6349 AACTAGAATCTTCGGTTGCATTATCAGATCCAAAGTTTGAATCATTTTTCTTACCGCAACCTGGA
259 AACTAGAATCTTCGGTTGCATCATCAGATCCAAAATCTGAATCATTTTTCTTACCGCAACCTGGA
6414 TCCTGGTTTG
324 TCCTGGTTTG
* **
6424 CAC-TCCCTGAGTTCCAATTGCTTTTCTTGCCCCAACCTGAATTCTGGCTTGCATCTCCAGGTCC
1 CACTTCCC-GAGTTCCAATTGCTTTTCTGGCCCCAACCTGAACCCTGGCTTGCATCTCCAGGTCC
6488 TGAGTTCCAAT
65 TGAGTTCCAAT
6499 TAGAATCCTT
Statistics
Matches: 367, Mismatches: 37, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
332 6 0.02
333 358 0.98
334 3 0.01
ACGTcount: A:0.20, C:0.33, G:0.15, T:0.32
Consensus pattern (333 bp):
CACTTCCCGAGTTCCAATTGCTTTTCTGGCCCCAACCTGAACCCTGGCTTGCATCTCCAGGTCCT
GAGTTCCAATCGCTTTTCTTGCCCCAACCTGAATCATGGCCTGCACCACCAGAACCAGAGTTCCA
ATTCCCCTTTTTACCCCAAGAGTCTTGGCCAGAATCACCGGTTCCAGCACCCCAACTACTTTTTG
TACCCCAGTTTGAATTCTGATTTGCATCTCCAGATCCTGAATCACAGTCATTTTTCCTTCCCCAA
CTAGAATCTTCGGTTGCATCATCAGATCCAAAATCTGAATCATTTTTCTTACCGCAACCTGGATC
CTGGTTTG
Found at i:10468 original size:15 final size:15
Alignment explanation
Indices: 10448--10477 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10438 TGAGCCCTCG
10448 CCTTTTTCACCTCCT
1 CCTTTTTCACCTCCT
10463 CCTTTTTCACCTCCT
1 CCTTTTTCACCTCCT
10478 TTATCAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.47, G:0.00, T:0.47
Consensus pattern (15 bp):
CCTTTTTCACCTCCT
Found at i:14872 original size:6 final size:6
Alignment explanation
Indices: 14839--14875 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
14829 CTTTATTTAA
*
14839 AAAAAA AAAAAG -AAAAG -AAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
14876 TAGTATTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:18027 original size:3 final size:3
Alignment explanation
Indices: 18013--18045 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
18003 GCCAATAACC
*
18013 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
18046 GAAAATCTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:31945 original size:92 final size:92
Alignment explanation
Indices: 31788--31972 Score: 370
Period size: 92 Copynumber: 2.0 Consensus size: 92
31778 TCTAAAGTTG
31788 ATAGTAATTAATGAAACATGTTCCTCTGTGAAAACTGAAAATGAAAAACTTAATAGGATGCCATA
1 ATAGTAATTAATGAAACATGTTCCTCTGTGAAAACTGAAAATGAAAAACTTAATAGGATGCCATA
31853 GCACGATCAGTACTGTTAGCTATATCA
66 GCACGATCAGTACTGTTAGCTATATCA
31880 ATAGTAATTAATGAAACATGTTCCTCTGTGAAAACTGAAAATGAAAAACTTAATAGGATGCCATA
1 ATAGTAATTAATGAAACATGTTCCTCTGTGAAAACTGAAAATGAAAAACTTAATAGGATGCCATA
31945 GCACGATCAGTACTGTTAGCTATATCA
66 GCACGATCAGTACTGTTAGCTATATCA
31972 A
1 A
31973 CGAGAATACA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (92 bp):
ATAGTAATTAATGAAACATGTTCCTCTGTGAAAACTGAAAATGAAAAACTTAATAGGATGCCATA
GCACGATCAGTACTGTTAGCTATATCA
Found at i:36821 original size:11 final size:12
Alignment explanation
Indices: 36785--36821 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
36775 TCACAAAGGA
36785 AAATCATTGTAC
1 AAATCATTGTAC
*
36797 AAAT-AATGTAC
1 AAATCATTGTAC
36808 AAATCATTGT-C
1 AAATCATTGTAC
36819 AAA
1 AAA
36822 AGTAGAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (12 bp):
AAATCATTGTAC
Found at i:39379 original size:19 final size:19
Alignment explanation
Indices: 39357--39393 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
39347 ACTATTAGTT
39357 TTTTAATTT-AATATTTTAC
1 TTTTAATTTCAAT-TTTTAC
39376 TTTTAATTTCAATTTTTA
1 TTTTAATTTCAATTTTTA
39394 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATTTCAATTTTTAC
Found at i:39616 original size:22 final size:21
Alignment explanation
Indices: 39560--39735 Score: 127
Period size: 22 Copynumber: 8.0 Consensus size: 21
39550 GTCTCTATAT
*
39560 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
39581 TGATTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
39604 GGTTATCAAAATTCCATAGCGT
1 GGTTATCAAAATTTCATAG-GA
* *
39626 GTTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
39648 AGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
39670 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* * *
39694 GGTTATTAAAATTTCTTAGGTT
1 GGTTATCAAAATTTCATAGG-A
**
39716 GGTTATTGAAATTTCATAGG
1 GGTTATCAAAATTTCATAGG
39736 GTGGTTAATT
Statistics
Matches: 120, Mismatches: 27, Indels: 14
0.75 0.17 0.09
Matches are distributed among these distances:
21 4 0.03
22 95 0.79
23 4 0.03
24 17 0.14
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:39719 original size:46 final size:43
Alignment explanation
Indices: 39591--39735 Score: 148
Period size: 44 Copynumber: 3.3 Consensus size: 43
39581 TGATTATTAT
* * * *
39591 AATTTCATGAGGAGGTTATCAAAATTCCATAGCGTGTTTACCAA
1 AATTTCAT-AGGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
39635 AATTTCATATGGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
1 AATTTCATA-GGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
* * ***
39679 AATTTCATAGGATCAGGTTATTAAAATTTCTTAG-GTTGGTTATTGA
1 AATTTCATAGGA--A-GTTATCAAAATTTCATAGTG-TGGTTACCAA
39725 AATTTCATAGG
1 AATTTCATAGG
39736 GTGGTTAATT
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
43 4 0.05
44 47 0.54
45 2 0.02
46 34 0.39
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (43 bp):
AATTTCATAGGAAGTTATCAAAATTTCATAGTGTGGTTACCAA
Found at i:39803 original size:22 final size:22
Alignment explanation
Indices: 39778--40169 Score: 120
Period size: 22 Copynumber: 17.6 Consensus size: 22
39768 ATCAAAGAGA
*
39778 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* * * *
39800 TTATAAAAATTTCATAGTGTGC
1 TTATCAAAATTTCATAGCGAGG
* *
39822 TCAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGCGAGG
* * *
39844 TTAGT-AATATTTCATGGGGAGG
1 TTA-TCAAAATTTCATAGCGAGG
* *
39866 TTATCAAAATTTTATAGCGTGG
1 TTATCAAAATTTCATAGCGAGG
*
39888 TTATCAAAATTTCATATG-AAGG
1 TTATCAAAATTTCATA-GCGAGG
* **
39910 TTATAAAAGTCTTAATTTCATAAGGA-G
1 TTAT-CAA-----AATTTCATAGCGAGG
* * *
39937 -TACCAAAATTTGATAG-AAGG
1 TTATCAAAATTTCATAGCGAGG
* * * *
39957 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGCGAGG
* * * *
39978 TTATCGAAATTCCATAGAGATCAGA
1 TTATCAAAATTTCATAGCG---AGG
*
40003 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGCG-AGG
** **
40024 TTATCAAAATTTCATAATGTTG
1 TTATCAAAATTTCATAGCGAGG
* * *
40046 TTATCAAAATTCCAAAGTGAGG
1 TTATCAAAATTTCATAGCGAGG
* ** * *
40068 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGCGAGG
* **
40090 TTATCATAATTTCATAAAG-GG
1 TTATCAAAATTTCATAGCGAGG
* * * **
40111 ATCAACAAAATTTTATAAAGAGG
1 -TTATCAAAATTTCATAGCGAGG
* **
40134 TTATCAAAATTTCAGAAAGAGG
1 TTATCAAAATTTCATAGCGAGG
*
40156 TTATCAAATTTTCA
1 TTATCAAAATTTCA
40170 GAATGTGATT
Statistics
Matches: 278, Mismatches: 69, Indels: 46
0.71 0.18 0.12
Matches are distributed among these distances:
19 1 0.00
20 18 0.06
21 28 0.10
22 190 0.68
23 10 0.04
24 4 0.01
25 14 0.05
26 2 0.01
27 1 0.00
28 10 0.04
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:40012 original size:25 final size:21
Alignment explanation
Indices: 39976--40039 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 21
39966 CTCATAGAGT
*
39976 GATTATCGAAATTCCATAGAGATCA
1 GATTATCAAAATT-CATAG-GA--A
*
40001 GATTATCAAAATTTATAGGAA
1 GATTATCAAAATTCATAGGAA
40022 GATTATCAAAATTTCATA
1 GATTATCAAAA-TTCATA
40040 ATGTTGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 12 0.34
22 5 0.14
23 2 0.06
24 4 0.11
25 12 0.34
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (21 bp):
GATTATCAAAATTCATAGGAA
Found at i:40120 original size:88 final size:88
Alignment explanation
Indices: 40028--40193 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 88
40018 GGAAGATTAT
* ** * *
40028 CAAAATTTCATAATGTTGTTATCAAAATTCCA-AAGTGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAAAGAGGTTATCAAAATTCCAGAA-AGAGGTTATCAAAATTACAGAATGTGATT
*
40092 ATC-ATAATTTCATAAAGGGATCAA
65 A-CAAAAATTTCATAAAGGGATCAA
* * * *
40116 CAAAATTTTATAAAGAGGTTATCAAAATTTCAGAAAGAGGTTATCAAATTTTCAGAATGTGATTA
1 CAAAATTTCATAAAGAGGTTATCAAAATTCCAGAAAGAGGTTATCAAAATTACAGAATGTGATTA
40181 CAAAAATTTCATA
66 CAAAAATTTCATA
40194 GTGGTATTTC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
87 1 0.02
88 63 0.95
89 2 0.03
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (88 bp):
CAAAATTTCATAAAGAGGTTATCAAAATTCCAGAAAGAGGTTATCAAAATTACAGAATGTGATTA
CAAAAATTTCATAAAGGGATCAA
Found at i:40190 original size:22 final size:22
Alignment explanation
Indices: 40000--40191 Score: 97
Period size: 22 Copynumber: 8.8 Consensus size: 22
39990 CATAGAGATC
* *
40000 AGATTATCAAAATTT-A-TAGG
1 AGATTATCAAAATTTCAGAAAG
* *
40020 AAGATTATCAAAATTTCATAATG
1 -AGATTATCAAAATTTCAGAAAG
* * *
40043 TTG-TTATCAAAATTCCA-AAGTG
1 -AGATTATCAAAATTTCAGAA-AG
* * * *
40065 AGGTTATCAAAATTACATAATG
1 AGATTATCAAAATTTCAGAAAG
* * *
40087 TGATTATCATAATTTCATAAAG
1 AGATTATCAAAATTTCAGAAAG
* * * * *
40109 GGATCAACAAAATTTTATAAAG
1 AGATTATCAAAATTTCAGAAAG
*
40131 AGGTTATCAAAATTTCAGAAAG
1 AGATTATCAAAATTTCAGAAAG
* * *
40153 AGGTTATCAAATTTTCAGAATG
1 AGATTATCAAAATTTCAGAAAG
*
40175 TGATTA-CAAAAATTTCA
1 AGATTATC-AAAATTTCA
40192 TAGTGGTATT
Statistics
Matches: 137, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
21 19 0.14
22 113 0.82
23 5 0.04
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (22 bp):
AGATTATCAAAATTTCAGAAAG
Found at i:40344 original size:22 final size:22
Alignment explanation
Indices: 40319--40567 Score: 139
Period size: 22 Copynumber: 11.5 Consensus size: 22
40309 AGTTTAGTTT
40319 TCAAAATTTCATAAGAGGATTA
1 TCAAAATTTCATAAGAGGATTA
* *
40341 TCAAAATTTCAT-AGTATGCA-GA
1 TCAAAATTTCATAAG-A-GGATTA
*
40363 TCAAAATTTCAT-AGGGAGATTA
1 TCAAAATTTCATAAGAG-GATTA
*
40385 ACAAAATTTCATAATGAGG-TTA
1 TCAAAATTTCATAA-GAGGATTA
** *
40407 TCAAAAAATCATAGGGAGG-TTA
1 TCAAAATTTCATA-AGAGGATTA
*
40429 TCAAAATTT-GT---A-G-TTA
1 TCAAAATTTCATAAGAGGATTA
* *
40445 TCAAGATTTCATAAGA-AAGTTA
1 TCAAAATTTCATAAGAGGA-TTA
* * * *
40467 TCAAAATTTTATAGGGATGTTTA
1 TCAAAATTTCATA-AGAGGATTA
* * *
40490 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAAGAGGA-TTA
*
40513 TCAAAATTTCATAGCGAGG-TTA
1 TCAAAATTTCATA-AGAGGATTA
*
40535 TCAAAATTTCAT-AGTGTGATTA
1 TCAAAATTTCATAAGAG-GATTA
40557 TCAAAATTTCA
1 TCAAAATTTCA
40568 GAGTATAATT
Statistics
Matches: 179, Mismatches: 29, Indels: 38
0.73 0.12 0.15
Matches are distributed among these distances:
16 12 0.07
17 2 0.01
20 4 0.02
21 5 0.03
22 114 0.64
23 37 0.21
24 5 0.03
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGATTA
Found at i:40578 original size:22 final size:22
Alignment explanation
Indices: 40532--40578 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
40522 CATAGCGAGG
* * *
40532 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTATAA
40554 TTATCAAAATTTCAGAGTATAA
1 TTATCAAAATTTCAGAGTATAA
40576 TTA
1 TTA
40579 CTAACAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTATAA
Found at i:40753 original size:22 final size:22
Alignment explanation
Indices: 40663--40835 Score: 95
Period size: 22 Copynumber: 7.9 Consensus size: 22
40653 TCATAGTGTT
**
40663 GGTTATCAAAATTTCATTGGGAA
1 GGTTATCAAAATTTCA-TAAGAA
*
40686 -GTTATCAAAATTTCATACTG-A
1 GGTTATCAAAATTTCATA-AGAA
* * * * *
40707 GGACT-TCAAAATTCCTTAGGGA
1 GG-TTATCAAAATTTCATAAGAA
*
40729 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
** * *
40751 GGTTAAAAAAAAATT-ATAAAAA
1 GGTT-ATCAAAATTTCATAAGAA
* *
40773 GGTTCTCAAAATTTCAT-AGTAT
1 GGTTATCAAAATTTCATAAG-AA
** * *
40795 CATTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAAGAA
40817 GGTTATCAAAATTTCATAA
1 GGTTATCAAAATTTCATAA
40836 TGGGATTATA
Statistics
Matches: 110, Mismatches: 31, Indels: 19
0.69 0.19 0.12
Matches are distributed among these distances:
21 11 0.10
22 89 0.81
23 10 0.09
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Found at i:40844 original size:44 final size:44
Alignment explanation
Indices: 40243--40837 Score: 252
Period size: 44 Copynumber: 13.6 Consensus size: 44
40233 GTTACCAAAT
* * * * *
40243 TAGGAAGGTTATTAAACTTTTATTATGGAGGATATCAAAATTTC-
1 TAGGAAGGTTATCAAAATTTCATAAT-GAGGTTATCAAAATTTCA
* * * * * *
40287 -AGGGAGGATATCAAAATTTTATAGTTTA-GTTTTCAAAATTTCA
1 TAGGAAGGTTATCAAAATTTCATA-ATGAGGTTATCAAAATTTCA
*
40330 TAAG-AGGATTATCAAAATTTCATAGTATGCA-G--ATCAAAATTTCA
1 TAGGAAGG-TTATCAAAATTTCATA--ATG-AGGTTATCAAAATTTCA
* * * **
40374 TAGGGAGATTAACAAAATTTCATAATGAGGTTATCAAAAAATCA
1 TAGGAAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTCA
* * *
40418 TAGGGAGGTTATCAAAA-TT--T-GT-A-GTTATCAAGATTTCA
1 TAGGAAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTCA
* * * ** * *
40456 TAAGAAAGTTATCAAAATTTTATAGGGATGTTTATCAAAATTTTA
1 TAGGAAGGTTATCAAAATTTCATAATGA-GGTTATCAAAATTTCA
* **
40501 TAGGAAGATTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCA
1 TAGGAAG-GTTATCAAAATTTCATAATGAGGTTATCAAAATTTCA
* * * *
40546 TAGTG-TGATTATCAAAATTTCAGAGTAT-A-ATTA-CTAACAA-TTCA
1 TAG-GAAGGTTATCAAAATTTCATA--ATGAGGTTATC-AA-AATTTCA
* * * * * * * *
40590 TATGG-AGGTTTTTAAATTTTCATAACGTGGTTACCAATATATCA
1 TA-GGAAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTCA
* * * * *
40634 TATGG-AGGTTATGAACATCTCATAGTGTTGGTTATCAAAATTTCA
1 TA-GGAAGGTTATCAAAATTTCATAATG-AGGTTATCAAAATTTCA
* * * * *
40679 TTGGGAA-GTTATCAAAATTTCATACTGAGGACT-TCAAAATTCCT
1 -TAGGAAGGTTATCAAAATTTCATAATGAGG-TTATCAAAATTTCA
* * ** *
40723 TAGGGAGGTTAACAAAATTTCATAA-GAAGGTTAAAAAAAAATT-A
1 TAGGAAGGTTATCAAAATTTCATAATG-AGGTT-ATCAAAATTTCA
** * * *
40767 TAAAAAGGTTCTCAAAATTTCATAGTATCA--TTATTAAAATTTCA
1 TAGGAAGGTTATCAAAATTTCATA--ATGAGGTTATCAAAATTTCA
40811 TAGGAAGGTTATCAAAATTTCATAATG
1 TAGGAAGGTTATCAAAATTTCATAATG
40838 GGATTATAAA
Statistics
Matches: 411, Mismatches: 100, Indels: 82
0.69 0.17 0.14
Matches are distributed among these distances:
38 26 0.06
39 3 0.01
40 1 0.00
41 3 0.01
42 20 0.05
43 40 0.10
44 212 0.52
45 81 0.20
46 25 0.06
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (44 bp):
TAGGAAGGTTATCAAAATTTCATAATGAGGTTATCAAAATTTCA
Found at i:42554 original size:21 final size:21
Alignment explanation
Indices: 42528--42572 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42518 AGAAACTGGA
*
42528 TTGCTAAACACCGCCTCATTT
1 TTGCTAAACACCGCCCCATTT
**
42549 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
42570 TTG
1 TTG
42573 ACGCTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:42840 original size:32 final size:32
Alignment explanation
Indices: 42786--42904 Score: 116
Period size: 32 Copynumber: 3.7 Consensus size: 32
42776 TACCGTGGCG
*
42786 AAGCCGCCCCACTT-GGGAGGCTTCGCCACGGC
1 AAGCCGCCCCA-TTGGGGCGGCTTCGCCACGGC
* * * **
42818 AAGTCGCCCCA-TGAGGGCGGCTTCCCCATGAA
1 AAGCCGCCCCATTG-GGGCGGCTTCGCCACGGC
42850 AAGGCCGCCCCATTGGGGCGGCTTCGCCACGGC
1 AA-GCCGCCCCATTGGGGCGGCTTCGCCACGGC
* **
42883 AGGCCGCCCCGGTGGGGCGGCT
1 AAGCCGCCCCATTGGGGCGGCT
42905 CGGCTACTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
30 1 0.01
32 43 0.62
33 23 0.33
34 2 0.03
ACGTcount: A:0.14, C:0.38, G:0.35, T:0.13
Consensus pattern (32 bp):
AAGCCGCCCCATTGGGGCGGCTTCGCCACGGC
Found at i:43015 original size:33 final size:31
Alignment explanation
Indices: 42970--43086 Score: 91
Period size: 33 Copynumber: 3.6 Consensus size: 31
42960 CCCCACCGGT
42970 GCCGTCCC-CCTGGGGCGGCTGAGCCATGGCCAA
1 GCCG-CCCTCCTGGGGCGGCT-A-CCATGGCCAA
*
43003 GCCGCCCTCCTGGGGCGGCACTACCATGGCCAG
1 GCCGCCCTCCTGGGGCGG--CTACCATGGCCAA
*
43036 GCCG-CCTCCCTAGGGCGGCCCTACCATGG--ATA
1 GCCGCCCT-CCTGGGGCGG--CTACCATGGCCA-A
43068 GACCGCCC-CCTGGGGCGGC
1 G-CCGCCCTCCTGGGGCGGC
43087 ACCGGTACTA
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 16 0.22
33 49 0.68
34 3 0.04
35 2 0.03
ACGTcount: A:0.12, C:0.42, G:0.34, T:0.12
Consensus pattern (31 bp):
GCCGCCCTCCTGGGGCGGCTACCATGGCCAA
Done.