Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019795.1 Corchorus olitorius cultivar O-4 contig19828, 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: 97481
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:1746 original size:11 final size:11
Alignment explanation
Indices: 1730--1754 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1720 TTGAGTCAGG
1730 AAACTCTTCAA
1 AAACTCTTCAA
1741 AAACTCTTCAA
1 AAACTCTTCAA
1752 AAA
1 AAA
1755 AAATTTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (11 bp):
AAACTCTTCAA
Found at i:1827 original size:21 final size:20
Alignment explanation
Indices: 1785--1832 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1775 AACCACGTTA
*
1785 TTTTTTTTTACCCATCAGAT
1 TTTTTTTTTACCCATCAAAT
1805 TTATTTTTTTACCCA-CTAAAT
1 TT-TTTTTTTACCCATC-AAAT
1826 TTTTTTT
1 TTTTTTT
1833 CCCTAACCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.21, C:0.17, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTTTTTACCCATCAAAT
Found at i:2182 original size:31 final size:31
Alignment explanation
Indices: 2123--2182 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2113 GGCGAACCAC
* *
2123 ATCCGGCGCTGCAAACCCGATCTCATCTCCG
1 ATCCGGCGCCGCAAACCCGAACTCATCTCCG
*
2154 ATCCGGCGCCGCTATACCCGAACT-ATCTC
1 ATCCGGCGCCGC-AAACCCGAACTCATCTC
2183 TCTCCTCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.20, C:0.42, G:0.18, T:0.20
Consensus pattern (31 bp):
ATCCGGCGCCGCAAACCCGAACTCATCTCCG
Found at i:11710 original size:16 final size:16
Alignment explanation
Indices: 11689--11721 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11679 AGATACAAAA
11689 TAGTGATGATCAGTCC
1 TAGTGATGATCAGTCC
11705 TAGTGATGATCAGTCC
1 TAGTGATGATCAGTCC
11721 T
1 T
11722 CAGTCCTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (16 bp):
TAGTGATGATCAGTCC
Found at i:14938 original size:28 final size:28
Alignment explanation
Indices: 14909--14963 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
14899 ATGTTTTGCT
* *
14909 TTTGGG-ACAAAATAATCTCTTATGTTC
1 TTTGGGAACAAAATAATCCCTTACGTTC
*
14936 TTTGGGAACAAATTAATCCCTTACGTTC
1 TTTGGGAACAAAATAATCCCTTACGTTC
14964 CAAAAATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (28 bp):
TTTGGGAACAAAATAATCCCTTACGTTC
Found at i:15157 original size:31 final size:31
Alignment explanation
Indices: 15097--15200 Score: 140
Period size: 30 Copynumber: 3.4 Consensus size: 31
15087 CCAGGTCAGC
** *
15097 AAGGGATTAATTTGTCCCATAA-AAAAACAT
1 AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
*
15127 AAGGGATTTTTTTGTCCGAAAAGAAAAACAT
1 AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
*
15158 AA-GGATTTTTTTGTCCCAAAAGAAAAATAT
1 AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
*
15188 ATGGGATTTTTTT
1 AAGGGATTTTTTT
15201 AGTATTTAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
30 45 0.69
31 20 0.31
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (31 bp):
AAGGGATTTTTTTGTCCCAAAAGAAAAACAT
Found at i:15847 original size:185 final size:184
Alignment explanation
Indices: 15643--15990 Score: 536
Period size: 185 Copynumber: 1.9 Consensus size: 184
15633 TTTTTCGATT
* * * * *
15643 ATATTTCTTAAATGTCATTGTTTAAATTTTTATAGTTTTACTCAACTAAAAGCTCTA-TTTTATT
1 ATATTTCTTAAATGTCATTGATTAAACTTTTACACTTTTACTCAACTAAAAACTCTATTTTTATT
** *
15707 TAATTTAATCTAACATATTCATAAATATTTTATTTTTACAATTTTACTATTTTAATTTAAAAACT
66 TAATCAAATCTAACATATTCATAAATATTTTATTTTTACAATTTTACTATTTTAA-TTAAAAAAT
*
15772 TAGATATATTAGAATTTTTTTAAATATATTTCTTACCCTTATTTTTCAAATTTCAA
130 TAGATATATTAGAA-TTTCTTAAATATATTTCTTACCCTTATTTTTCAAATTTCAA
**
15828 ATATTTCTTAAATGTCATTGATTAAACTTTTACACTTTTACTCAGTTAAAAACTCTATTTTTATT
1 ATATTTCTTAAATGTCATTGATTAAACTTTTACACTTTTACTCAACTAAAAACTCTATTTTTATT
* * * *
15893 TAATCAAATCTAATATATTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAATT
66 TAATCAAATCTAACATATTCATAAATATTTTATTTTTACAATTTTACTATTTTAATTAAAAAATT
15958 AGATATATTAGAATTTCTTAAATATATTTCTTA
131 AGATATATTAGAATTTCTTAAATATATTTCTTA
15991 AATGACTTTA
Statistics
Matches: 147, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
184 19 0.13
185 72 0.49
186 56 0.38
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (184 bp):
ATATTTCTTAAATGTCATTGATTAAACTTTTACACTTTTACTCAACTAAAAACTCTATTTTTATT
TAATCAAATCTAACATATTCATAAATATTTTATTTTTACAATTTTACTATTTTAATTAAAAAATT
AGATATATTAGAATTTCTTAAATATATTTCTTACCCTTATTTTTCAAATTTCAA
Found at i:16287 original size:31 final size:30
Alignment explanation
Indices: 16222--16315 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 30
16212 TTTGAAAATT
* *
16222 AAAAAATTCCTTATGTTTCTTTTTGAGACAA
1 AAAAAATCCCTTATGTTT-TTTTTGGGACAA
*
16253 AAAAAATCCCTTATGTTTTTCTTATGGGA-TA
1 AAAAAATCCCTTATGTTTTT-TT-TGGGACAA
*
16284 AAAAAATCCCTTATATTTTTTTGTGGGACAA
1 AAAAAATCCCTTATGTTTTTTT-TGGGACAA
16315 A
1 A
16316 TTAGTCCCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
30 9 0.17
31 41 0.76
32 4 0.07
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (30 bp):
AAAAAATCCCTTATGTTTTTTTTGGGACAA
Found at i:16464 original size:31 final size:30
Alignment explanation
Indices: 16402--16495 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
16392 AAAGGACTAA
* * *
16402 TTTGTCCCATAA-AAAAACATATGGAAATTT
1 TTTGTCCCA-AAGAAAAACATAAGGGATTTT
16432 TTTGTCCCAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAGAAAAACATAAGGGATTTT
16462 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCC-AAAGAAAAACATAAGGGATTTT
16493 TTT
1 TTT
16496 AGTATTTAGT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
29 2 0.03
30 32 0.54
31 25 0.42
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (30 bp):
TTTGTCCCAAAGAAAAACATAAGGGATTTT
Found at i:18517 original size:182 final size:180
Alignment explanation
Indices: 18300--18663 Score: 525
Period size: 182 Copynumber: 2.0 Consensus size: 180
18290 TTGATGATTA
* * *
18300 TACCCTTATTTTTCGATTATATTTCTTAAATGTCATTGATTAAACTTTTATAGA-ATTACTCAAC
1 TACCCTTATTTTTCAAATATATTTCTTAAATGTCATTGATTAAACTTTTACA-ATATTACTCAAC
* * * *
18364 TAAAAGCTCTATTTTTATTTAATCTAATCTAACATATTCGTAAATATTTTATTTTTACGA-TTTT
65 TAAAAACTCTATTTTTATTTAATCAAATCTAACATATTCATAAATATTTTATTTTTACCATTTTT
* *
18428 ACTATTTTAATTAAAAAAACTTAGTTATATTAAAATTTTTTTAAATATATTTCT
130 ACTATTTTAATT-AAAAAA-TTAGATATATTAAAA-TTTCTTAAATATATTTCT
* **
18482 TACCCTTATTTTTCAAATATATTTCTTAAATGTCATTGATTAAACTTTTACAATTTTACTCAGTT
1 TACCCTTATTTTTCAAATATATTTCTTAAATGTCATTGATTAAACTTTTACAATATTACTCAACT
* * * *
18547 AAAAACTCTATTTTTATTTAATCAAATCTAATATATTTATAACTATTTTATTTTTACCATTTTTG
66 AAAAACTCTATTTTTATTTAATCAAATCTAACATATTCATAAATATTTTATTTTTACCATTTTTA
*
18612 CTATTTTAATTAAAAAATTAGATATATTAGAATTTCTTAAATATATTTCT
131 CTATTTTAATTAAAAAATTAGATATATTAAAATTTCTTAAATATATTTCT
18662 TA
1 TA
18664 AATGACATTA
Statistics
Matches: 163, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
180 19 0.12
181 14 0.09
182 115 0.71
183 15 0.09
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (180 bp):
TACCCTTATTTTTCAAATATATTTCTTAAATGTCATTGATTAAACTTTTACAATATTACTCAACT
AAAAACTCTATTTTTATTTAATCAAATCTAACATATTCATAAATATTTTATTTTTACCATTTTTA
CTATTTTAATTAAAAAATTAGATATATTAAAATTTCTTAAATATATTTCT
Found at i:18952 original size:31 final size:31
Alignment explanation
Indices: 18915--18978 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
18905 ACTAAATACT
* * *
18915 AAAAAATTCCTTATG-TTTTTCTTTTGGGACA
1 AAAAAATCCCGTATGCTTTTT-TTATGGGACA
18946 AAAAAATCCCGTATGCTTTTTTTATGGGACA
1 AAAAAATCCCGTATGCTTTTTTTATGGGACA
18977 AA
1 AA
18979 TTAGTCCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (31 bp):
AAAAAATCCCGTATGCTTTTTTTATGGGACA
Found at i:19065 original size:31 final size:31
Alignment explanation
Indices: 19029--19091 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
19019 GTTGACGTGG
*
19029 ATTTTCCACGTCAGCAAATCTGACGGCCGTT
1 ATTTTCCACATCAGCAAATCTGACGGCCGTT
*
19060 ATTTTCCACATCAGCAAATCTGACGGTCGTT
1 ATTTTCCACATCAGCAAATCTGACGGCCGTT
19091 A
1 A
19092 GTCACGTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.30
Consensus pattern (31 bp):
ATTTTCCACATCAGCAAATCTGACGGCCGTT
Found at i:22125 original size:182 final size:182
Alignment explanation
Indices: 21814--22182 Score: 686
Period size: 182 Copynumber: 2.0 Consensus size: 182
21804 GAATGTCTGA
**
21814 ATTT-GACTCAACTAGAGACATTGTATTAGATTGTGAGGAAAGAGTCGAGCTGATGTTGCTGAAT
1 ATTTAGACTCAACTAGAGACACCGTATTAGATTGTGAGGAAAGAGTCGAGCTGATGTTGCTGAAT
*
21878 GGAAACTGGAATTCATCAAATAGAACATGCCGAGAGGTGTAAATCTTTGTGATTTTGGTTCATAG
66 GGAAACTGGAATTCATCAAATAGAACATGCCGAGAGGTGTAAATCTTTATGATTTTGGTTCATAG
21943 CAGAAATAGGCACTTTGCTTTTTTGAATATCCAAGGAAGACACATGGCTTGG
131 CAGAAATAGGCACTTTGCTTTTTTGAATATCCAAGGAAGACACATGGCTTGG
21995 ATTTAGACTCAACTAGAGACACCGTATTAGATTGTGAGGAAAGAGTCGAGCTGATGTTGCTGAAT
1 ATTTAGACTCAACTAGAGACACCGTATTAGATTGTGAGGAAAGAGTCGAGCTGATGTTGCTGAAT
*
22060 GGAAACTGGAATTCATCAAATAGAACATGCCGAGAGGTGTAGATCTTTATGATTTTGGTTCATAG
66 GGAAACTGGAATTCATCAAATAGAACATGCCGAGAGGTGTAAATCTTTATGATTTTGGTTCATAG
*
22125 CAGAAATAGGCACTTTGGTTTTTTGAATATCCAAGGAAGACACATGGCTTGG
131 CAGAAATAGGCACTTTGCTTTTTTGAATATCCAAGGAAGACACATGGCTTGG
22177 ATTTAG
1 ATTTAG
22183 GTTCAAGTTT
Statistics
Matches: 182, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
181 4 0.02
182 178 0.98
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (182 bp):
ATTTAGACTCAACTAGAGACACCGTATTAGATTGTGAGGAAAGAGTCGAGCTGATGTTGCTGAAT
GGAAACTGGAATTCATCAAATAGAACATGCCGAGAGGTGTAAATCTTTATGATTTTGGTTCATAG
CAGAAATAGGCACTTTGCTTTTTTGAATATCCAAGGAAGACACATGGCTTGG
Found at i:25161 original size:46 final size:44
Alignment explanation
Indices: 25045--25258 Score: 144
Period size: 44 Copynumber: 4.8 Consensus size: 44
25035 AAGAACAACA
* *
25045 CAAAATGTCATTGGGAGGTTATCGAAATTTCATAATGTAATTAT
1 CAAAATTTCATTGGGAGGTTATCAAAATTTCATAATGTAATTAT
* * * **
25089 CCAAATTTCA-TGGAAAGGTTATCAAAATTTCATAGTGTGTGGTTAT
1 CAAAATTTCATTGG-GAGGTTATCAAAATTTCATA--ATGTAATTAT
* * * *
25135 CAAAATTTCATTGGGAGATTAACAAAATTTCA-AATGGAGGTTAT
1 CAAAATTTCATTGGGAGGTTATCAAAATTTCATAATGTA-ATTAT
* ** ** ** * * *
25179 AAAAAAATCAAAGGGAGACTATCAAAATTTTATAAGGATATTTAT
1 CAAAATTTCATTGGGAGGTTATCAAAATTTCATAATG-TAATTAT
** * *
25224 CAAAATTTCATAAGGATGTTATCAAAATTTTATAA
1 CAAAATTTCATTGGGAGGTTATCAAAATTTCATAA
25259 AGAGTTTCTC
Statistics
Matches: 130, Mismatches: 33, Indels: 13
0.74 0.19 0.07
Matches are distributed among these distances:
43 5 0.04
44 55 0.42
45 35 0.27
46 32 0.25
47 3 0.02
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (44 bp):
CAAAATTTCATTGGGAGGTTATCAAAATTTCATAATGTAATTAT
Found at i:25258 original size:22 final size:23
Alignment explanation
Indices: 25198--25258 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
25188 AAAGGGAGAC
*
25198 TATCAAAATTTTATAAGGATATT
1 TATCAAAATTTTATAAGGATAGT
*
25221 TATCAAAATTTCATAAGGAT-GT
1 TATCAAAATTTTATAAGGATAGT
25243 TATCAAAATTTTATAA
1 TATCAAAATTTTATAA
25259 AGAGTTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (23 bp):
TATCAAAATTTTATAAGGATAGT
Found at i:25290 original size:44 final size:45
Alignment explanation
Indices: 25198--25296 Score: 130
Period size: 44 Copynumber: 2.2 Consensus size: 45
25188 AAAGGGAGAC
*
25198 TATCAAAATTTTATAAGGATATTTATCAAAATTTCATAAGGATGT
1 TATCAAAATTTTATAAAGATATTTATCAAAATTTCATAAGGATGT
* * * *
25243 TATCAAAATTTTATAAAGA-GTTTCTCACAATTTCATAATG-TGAT
1 TATCAAAATTTTATAAAGATATTTATCAAAATTTCATAAGGATG-T
25287 TATCAAAATT
1 TATCAAAATT
25297 CCATAGTAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 2 0.04
44 28 0.58
45 18 0.38
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (45 bp):
TATCAAAATTTTATAAAGATATTTATCAAAATTTCATAAGGATGT
Found at i:25296 original size:22 final size:22
Alignment explanation
Indices: 25063--25301 Score: 112
Period size: 22 Copynumber: 10.7 Consensus size: 22
25053 CATTGGGAGG
* * *
25063 TTATCGAAATTTCATAATGTAA
1 TTATCAAAATTTCATAAGGTGA
* *
25085 TTATCCAAATTTCATGGAAAG-G-
1 TTATCAAAATTTCAT--AAGGTGA
* *
25107 TTATCAAAATTTCATAGTGTGTGG
1 TTATCAAAATTTCATA-AG-GTGA
** *
25131 TTATCAAAATTTCATTGGGAGA
1 TTATCAAAATTTCATAAGGTGA
* * *
25153 TTAACAAAATTTCA-AATGGAGG
1 TTATCAAAATTTCATAA-GGTGA
* ** *
25175 TTATAAAAAAATCA-AAGGGAGA
1 TTATCAAAATTTCATAA-GGTGA
* *
25197 CTATCAAAATTTTATAAGGAT-A
1 TTATCAAAATTTCATAAGG-TGA
25219 TTTATCAAAATTTCATAAGGATG-
1 -TTATCAAAATTTCATAAGG-TGA
* * * *
25242 TTATCAAAATTTTATAAAGAGT
1 TTATCAAAATTTCATAAGGTGA
* * *
25264 TTCTCACAATTTCATAATGTGA
1 TTATCAAAATTTCATAAGGTGA
*
25286 TTATCAAAATTCCATA
1 TTATCAAAATTTCATA
25302 GTAAGGTTAA
Statistics
Matches: 165, Mismatches: 40, Indels: 24
0.72 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 122 0.74
23 23 0.14
24 18 0.11
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGTGA
Found at i:33796 original size:12 final size:12
Alignment explanation
Indices: 33779--33805 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33769 GGGGTTGAGT
33779 AGCACCAGCAGC
1 AGCACCAGCAGC
33791 AGCACCAGCAGC
1 AGCACCAGCAGC
33803 AGC
1 AGC
33806 GGCAGTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.41, G:0.26, T:0.00
Consensus pattern (12 bp):
AGCACCAGCAGC
Found at i:35355 original size:29 final size:29
Alignment explanation
Indices: 35295--35356 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
35285 GGTAAACGTT
** * *
35295 CAAAATTGAAAGTTTAAGGGTAAAATGTC
1 CAAAATTGAAAGTTTAAGGACAAAACGAC
35324 CAAAATTG-AAGTTTAAGGAACAAAACGAC
1 CAAAATTGAAAGTTTAAGG-ACAAAACGAC
35353 CAAA
1 CAAA
35357 CACTATAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (29 bp):
CAAAATTGAAAGTTTAAGGACAAAACGAC
Found at i:37275 original size:27 final size:25
Alignment explanation
Indices: 37245--37301 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 25
37235 ACACAATCCA
37245 ATTTTGTTGGTTTTGATTCAAAACTTC
1 ATTTTGTTGG--TTGATTCAAAACTTC
37272 A--TT-TT-GTTGATTCAAAACTTC
1 ATTTTGTTGGTTGATTCAAAACTTC
37293 ATTTTGTTG
1 ATTTTGTTG
37302 ATACCCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
21 16 0.62
23 3 0.12
24 4 0.15
25 2 0.08
27 1 0.04
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.53
Consensus pattern (25 bp):
ATTTTGTTGGTTGATTCAAAACTTC
Found at i:37282 original size:21 final size:21
Alignment explanation
Indices: 37257--37303 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
37247 TTTGTTGGTT
37257 TTGATTCAAAACTTCATTTTG
1 TTGATTCAAAACTTCATTTTG
37278 TTGATTCAAAACTTCATTTTG
1 TTGATTCAAAACTTCATTTTG
37299 TTGAT
1 TTGAT
37304 ACCCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.49
Consensus pattern (21 bp):
TTGATTCAAAACTTCATTTTG
Found at i:43846 original size:140 final size:140
Alignment explanation
Indices: 43594--43876 Score: 548
Period size: 140 Copynumber: 2.0 Consensus size: 140
43584 TGACATTATA
* *
43594 AGTCTCATGCACTACTTTGGTTTATTGATATGGCCTCTGATCATATACTTTTAGCACCTGTGTTG
1 AGTCTCATGCACTACTTTGGTTTATTGATATGGCCTCTGATCATATACTTTTAGCACCTGGGATG
43659 GTCTATTCCATTAACCTTTTGGTATCTATGTTGCGGTGAAATAAACTCACTTATAGGAGTACAGA
66 GTCTATTCCATTAACCTTTTGGTATCTATGTTGCGGTGAAATAAACTCACTTATAGGAGTACAGA
43724 AGATTACTCC
131 AGATTACTCC
43734 AGTCTCATGCACTACTTTGGTTTATTGATATGGCCTCTGATCATATACTTTTAGCACCTGGGATG
1 AGTCTCATGCACTACTTTGGTTTATTGATATGGCCTCTGATCATATACTTTTAGCACCTGGGATG
43799 GTCTATTCCATTAACCTTTTGGTATCTATGTTGCGGTGAAATAAACTCACTTATAGGAGTACAGA
66 GTCTATTCCATTAACCTTTTGGTATCTATGTTGCGGTGAAATAAACTCACTTATAGGAGTACAGA
43864 AGATTACTCC
131 AGATTACTCC
43874 AGT
1 AGT
43877 TGTTGCTAAG
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 141 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (140 bp):
AGTCTCATGCACTACTTTGGTTTATTGATATGGCCTCTGATCATATACTTTTAGCACCTGGGATG
GTCTATTCCATTAACCTTTTGGTATCTATGTTGCGGTGAAATAAACTCACTTATAGGAGTACAGA
AGATTACTCC
Found at i:48082 original size:2 final size:2
Alignment explanation
Indices: 48077--48113 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
48067 ATAAAAGTAA
48077 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
48114 AACTACAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53968 original size:21 final size:21
Alignment explanation
Indices: 53944--54010 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
53934 AATTCTCTGT
53944 AAATTAAGAAATACTCAGCTC
1 AAATTAAGAAATACTCAGCTC
* * **
53965 AAATCATAGAAAATTCTTTG-T-
1 AAATTA-AG-AAATACTCAGCTC
*
53986 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAGCTC
54007 AAAT
1 AAAT
54011 CCTGATCCTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
19 6 0.18
20 3 0.09
21 14 0.42
22 3 0.09
23 7 0.21
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAGCTC
Found at i:53991 original size:42 final size:42
Alignment explanation
Indices: 53932--54011 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
53922 TAAGTCTTCA
*
53932 AAAATTCTCTGTAAATTAAGAAATACTCAGCTCAAATCATAG
1 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAG
*
53974 AAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
54012 CTGATCCTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAG
Found at i:54550 original size:31 final size:31
Alignment explanation
Indices: 54512--54590 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
54502 TGATAAAGTT
** *
54512 AATATCAGGATCAATTGTTGGGTCCTGATGG
1 AATATCAGGATCAATTGTTCAGTCCTGACGG
54543 AATATCAGGATCAATTGTTCAGTCCTGACGG
1 AATATCAGGATCAATTGTTCAGTCCTGACGG
* *
54574 TATATCGGGATCAATTG
1 AATATCAGGATCAATTG
54591 ACAAGCTCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (31 bp):
AATATCAGGATCAATTGTTCAGTCCTGACGG
Found at i:57347 original size:31 final size:31
Alignment explanation
Indices: 57269--57347 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
57259 AGGAGCTTGT
* * *
57269 CAATTGATCCCGATATACCGTCAGGACCCAA
1 CAATTGATCCTGATATTCCATCAGGACCCAA
* *
57300 CAATCGATTCTGATATTCCATCAGGACCCAA
1 CAATTGATCCTGATATTCCATCAGGACCCAA
57331 CAATTGATCCTGATATT
1 CAATTGATCCTGATATT
57348 AACTTTATCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (31 bp):
CAATTGATCCTGATATTCCATCAGGACCCAA
Found at i:61292 original size:21 final size:21
Alignment explanation
Indices: 61267--61309 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
61257 GAGGAATTTC
*
61267 AAGTTGATA-GCAAGATTTCTG
1 AAGTTGA-ACGCAAGATTACTG
61288 AAGTTGAACGCAAGATTACTG
1 AAGTTGAACGCAAGATTACTG
61309 A
1 A
61310 TCTTCAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (21 bp):
AAGTTGAACGCAAGATTACTG
Found at i:61823 original size:46 final size:46
Alignment explanation
Indices: 61770--62101 Score: 583
Period size: 46 Copynumber: 7.2 Consensus size: 46
61760 GCAATGTCAC
* * *
61770 CCATCCTGTTAGTATAAATTTCTTCACACCAGCAGGACCAATTTCT
1 CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTCT
*
61816 CCATCCTGATGGTATAAATTTCTTCACACCATCAAGACCAATTTCT
1 CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTCT
*
61862 CCATCCTGATGGTATAAATTTCTTCACACCATTAGGACCAATTTCT
1 CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTCT
*
61908 CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAAATTCT
1 CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTCT
61954 CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTCT
1 CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTCT
*
62000 CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAAATTCT
1 CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTCT
* *
62046 CCATCCTGATGGTATAAATTTCTCCACACCATCAGGACCAAATTCT
1 CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTCT
62092 CCATCCTGAT
1 CCATCCTGAT
62102 TAGAGATTTT
Statistics
Matches: 275, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 275 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.32
Consensus pattern (46 bp):
CCATCCTGATGGTATAAATTTCTTCACACCATCAGGACCAATTTCT
Found at i:62091 original size:23 final size:23
Alignment explanation
Indices: 61927--62094 Score: 75
Period size: 23 Copynumber: 7.3 Consensus size: 23
61917 TGGTATAAAT
*
61927 TTCTTCACACCATCAGGACCAAA
1 TTCTCCACACCATCAGGACCAAA
* * *
61950 TTCTCCA-TCC-TGATGGTA-TAAA
1 TTCTCCACACCATCA-GG-ACCAAA
* *
61972 TTTCTTCACACCATCAGGACCAAT
1 -TTCTCCACACCATCAGGACCAAA
* * *
61996 TTCTCCA-TCC-TGATGGTA-TAAA
1 TTCTCCACACCATCA-GG-ACCAAA
*
62018 TTTCTTCACACCATCAGGACCAAA
1 -TTCTCCACACCATCAGGACCAAA
* * *
62042 TTCTCCA-TCC-TGATGGTA-TAAA
1 TTCTCCACACCATCA-GG-ACCAAA
62064 TTTCTCCACACCATCAGGACCAAA
1 -TTCTCCACACCATCAGGACCAAA
62088 TTCTCCA
1 TTCTCCA
62095 TCCTGATTAG
Statistics
Matches: 102, Mismatches: 25, Indels: 36
0.63 0.15 0.22
Matches are distributed among these distances:
21 6 0.06
22 20 0.20
23 50 0.49
24 20 0.20
25 6 0.06
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (23 bp):
TTCTCCACACCATCAGGACCAAA
Found at i:72607 original size:31 final size:31
Alignment explanation
Indices: 72529--72607 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
72519 AGGAGCTTGT
* * *
72529 CAATTGATCCCGATATACCGTCAGGACCCAA
1 CAATTGATCCTGATATTCCATCAGGACCCAA
72560 CAATTGATCCTGATATTCCATCAGGACCCAA
1 CAATTGATCCTGATATTCCATCAGGACCCAA
72591 CAATTGATCCTGATATT
1 CAATTGATCCTGATATT
72608 AACTTTATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (31 bp):
CAATTGATCCTGATATTCCATCAGGACCCAA
Found at i:74108 original size:203 final size:202
Alignment explanation
Indices: 73781--74163 Score: 497
Period size: 203 Copynumber: 1.9 Consensus size: 202
73771 ATACACTATT
***
73781 AGTGGAGTTTAGCAGACTGCACGTGCGGGTCTAAAAGGGTGACATGTGTCACCTTAGGAACTAGA
1 AGTGGAGTTTAGCAGACTGCACAAACGGGTCTAAAAGGGTGACATGTGTCACCTTAGGAACTAGA
* * * ***
73846 TTGAAATATTAGAAATCTAATTAATTCTGAAATGAAGTGCTTGTCAACCTTTGAACCCGCTTGTG
66 TTGAAATATTAGAAATCTAATTAATTCAGAAATAAAAT-CTTGTCAACCTCACAACCCGCTTGTG
* *
73911 GAATCCAAAAACTACACTGACGGTGTATCAAATAATAACACTTTATATTAAGGGTTTATATATAA
130 GAATCCAAAAACTACACCGACGGTGTATCAAATAATAAC-CCTTATATTAAGGGTTTATATATAA
73976 TACACGGTC
194 TACACGGTC
** *
73985 AGTGGAGTTTAGCAGACTGCACAAACGGGTCTTGAAGGGTGACATGTTTCACC-TA-GAGACTAG
1 AGTGGAGTTTAGCAGACTGCACAAACGGGTCTAAAAGGGTGACATGTGTCACCTTAGGA-ACTAG
*
74048 ATTGAAATATTTA-AAATTTAATTAATTCAGAAAATAAACAT-TTGTCAA-CTCCACAACCCGCT
65 ATTGAAATA-TTAGAAATCTAATTAATTCAG-AAATAAA-ATCTTGTCAACCT-CACAACCCGCT
* * * *
74110 TGTGGAGTCCAAAATCTACACCGCCGGTGTATCAAATAATTACCCTTATATTAA
126 TGTGGAATCCAAAAACTACACCGACGGTGTATCAAATAATAACCCTTATATTAA
74164 TGCACTTATA
Statistics
Matches: 155, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
202 14 0.09
203 84 0.54
204 56 0.36
205 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (202 bp):
AGTGGAGTTTAGCAGACTGCACAAACGGGTCTAAAAGGGTGACATGTGTCACCTTAGGAACTAGA
TTGAAATATTAGAAATCTAATTAATTCAGAAATAAAATCTTGTCAACCTCACAACCCGCTTGTGG
AATCCAAAAACTACACCGACGGTGTATCAAATAATAACCCTTATATTAAGGGTTTATATATAATA
CACGGTC
Found at i:78386 original size:85 final size:82
Alignment explanation
Indices: 78225--78388 Score: 231
Period size: 85 Copynumber: 1.9 Consensus size: 82
78215 GTTAATCTAC
*
78225 TAGATCTGAATAAATTTCTGTGAAGCAAATACCAAACTGATTTTTTGCATCTTTGAGTATTTTTT
1 TAGATCTGAATAAATTTCTCTGAAG---ATACCAAACTGATTTTTTGCATCTTTGAGTATTTTTT
*
78290 TCAACTTTTACACCTGATAA
63 TCAAATTTTACACCTGATAA
*
78310 TAGATCTGAATAAATTTCTCTGAAG-TACCAAACTGATTTTTTGCTTCTTTGAGTATTATTCTTT
1 TAGATCTGAATAAATTTCTCTGAAGATACCAAACTGATTTTTTGCATCTTTGAGTA-T-TT-TTT
78374 TCAAGATTTTACACC
63 TCAA-ATTTTACACC
78389 AAATAAAGTA
Statistics
Matches: 72, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
81 29 0.40
82 1 0.01
83 2 0.03
84 7 0.10
85 33 0.46
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.43
Consensus pattern (82 bp):
TAGATCTGAATAAATTTCTCTGAAGATACCAAACTGATTTTTTGCATCTTTGAGTATTTTTTTCA
AATTTTACACCTGATAA
Found at i:83374 original size:57 final size:57
Alignment explanation
Indices: 83286--83400 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
83276 ATAGAAATAC
83286 TGTTATAACTTTTGTTACTATTTCGTTGTCACAGACGTAATCACGGGATTGTGACAG
1 TGTTATAACTTTTGTTACTATTTCGTTGTCACAGACGTAATCACGGGATTGTGACAG
83343 TGTTATAACTTTTGTTACTATTTCGTTGTCACAGACGTAATCACGGGATTGTGACAG
1 TGTTATAACTTTTGTTACTATTTCGTTGTCACAGACGTAATCACGGGATTGTGACAG
83400 T
1 T
83401 ATATATTTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (57 bp):
TGTTATAACTTTTGTTACTATTTCGTTGTCACAGACGTAATCACGGGATTGTGACAG
Found at i:87248 original size:2 final size:2
Alignment explanation
Indices: 87227--87270 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
87217 AAATTGTAAT
* *
87227 TA TA CTA TA TA CA TA CA 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 TA
87270 T
1 T
87271 GTCTTTTGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:90501 original size:15 final size:14
Alignment explanation
Indices: 90481--90557 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 14
90471 ATAATTGAAT
90481 AATATACAAAGCAAA
1 AATATACAAAG-AAA
* * *
90496 AATATATAATTGAAT
1 AATATACAA-AGAAA
90511 AATATACAAAGTAAA
1 AATATACAAAG-AAA
* **
90526 AATATATAATTAAA
1 AATATACAAAGAAA
90540 TAATATACAAAGTAAA
1 -AATATACAAAG-AAA
90556 AA
1 AA
90558 AAAAACCACA
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 4 0.09
15 38 0.83
16 4 0.09
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (14 bp):
AATATACAAAGAAA
Found at i:90504 original size:30 final size:30
Alignment explanation
Indices: 90470--90557 Score: 158
Period size: 30 Copynumber: 2.9 Consensus size: 30
90460 CAAAAGTTTG
*
90470 TATAATTGAATAATATACAAAGCAAAAATA
1 TATAATTGAATAATATACAAAGTAAAAATA
90500 TATAATTGAATAATATACAAAGTAAAAATA
1 TATAATTGAATAATATACAAAGTAAAAATA
*
90530 TATAATTAAATAATATACAAAGTAAAAA
1 TATAATTGAATAATATACAAAGTAAAAA
90558 AAAAACCACA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (30 bp):
TATAATTGAATAATATACAAAGTAAAAATA
Found at i:91668 original size:24 final size:24
Alignment explanation
Indices: 91641--91688 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
91631 ACTAAATAAA
91641 CCCACCAATCATCAAATTCATATT
1 CCCACCAATCATCAAATTCATATT
* *
91665 CCCACCGATCATCAAATTTATATT
1 CCCACCAATCATCAAATTCATATT
91689 TAGGTTTGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (24 bp):
CCCACCAATCATCAAATTCATATT
Found at i:94403 original size:22 final size:22
Alignment explanation
Indices: 94377--94446 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
94367 AGGAAGTTTG
94377 GAATGTTATCAAAATTTTATAA
1 GAATGTTATCAAAATTTTATAA
* *
94399 GAATGTTATCGAAATTTCAT-A
1 GAATGTTATCAAAATTTTATAA
* *
94420 GTATGATTATCAAAATTTTACAA
1 GAATG-TTATCAAAATTTTATAA
94443 GAAT
1 GAAT
94447 ATTTAATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 5 0.13
22 30 0.77
23 4 0.10
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (22 bp):
GAATGTTATCAAAATTTTATAA
Found at i:96443 original size:58 final size:58
Alignment explanation
Indices: 96352--96461 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
96342 TCAAATATCA
*
96352 AGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTCCGGACCGAGGCTTATGG
1 AGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTCAGGACCGAGGCTTATGG
* * *
96410 AGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACCGAGGC
1 AGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTCAGGACCGAGGC
96462 ATGATGCTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 32 0.68
59 15 0.32
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (58 bp):
AGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTCAGGACCGAGGCTTATGG
Done.