Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021416.1 Corchorus olitorius cultivar O-4 contig21449, 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: 95504
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:12272 original size:14 final size:13
Alignment explanation
Indices: 12236--12274 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
12226 TATATATTAG
12236 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
12249 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
12263 AATTTTTTAAAT
1 AATTTTTTAAAT
12275 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:12379 original size:85 final size:85
Alignment explanation
Indices: 12289--12458 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 85
12279 CAATTTTTTT
* *
12289 AGAAATAAACTTTTACAGTTATTCTACTAAAAAATCTATTTTTATTTAATTAAATTCAATATTAT
1 AGAAATAAACTTTTACAATTATTCTACTAAAAAATCTAATTTTATTTAATTAAATTCAATATTAT
12354 TATAAATATTTTATTTTTAC
66 TATAAATATTTTATTTTTAC
12374 AGAAATAAACTTTTACAATTATTCTACTAAAAAATCTAATTTTATTTAATTAAATTCAATATTAT
1 AGAAATAAACTTTTACAATTATTCTACTAAAAAATCTAATTTTATTTAATTAAATTCAATATTAT
*
12439 TATAACTATTTTATTTTTAC
66 TATAAATATTTTATTTTTAC
12459 CATTTTAATT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.48
Consensus pattern (85 bp):
AGAAATAAACTTTTACAATTATTCTACTAAAAAATCTAATTTTATTTAATTAAATTCAATATTAT
TATAAATATTTTATTTTTAC
Found at i:18328 original size:29 final size:28
Alignment explanation
Indices: 18256--18336 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
18246 GGATTAATGT
* * *
18256 CCAAATTTGGCCTAAATCTTTTCAAACTTG
1 CCAAATTGGGCCTAAA-CCTTT-AAACATG
* *
18286 CTCAATTTGAGCCTAAACCTTTAAACATG
1 C-CAAATTGGGCCTAAACCTTTAAACATG
18315 ACCAAATTGGGCCTAAA-CTTTA
1 -CCAAATTGGGCCTAAACCTTTA
18337 GCAAATTGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
28 5 0.12
29 19 0.45
30 6 0.14
31 12 0.29
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (28 bp):
CCAAATTGGGCCTAAACCTTTAAACATG
Found at i:18744 original size:4 final size:4
Alignment explanation
Indices: 18737--18763 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18727 TATATATATA
18737 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
18764 ATAAACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:24298 original size:28 final size:28
Alignment explanation
Indices: 24258--24315 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
24248 TCGGGTTCCA
24258 CAGCCAAGTATTCGACCCAAGTGGCAGC
1 CAGCCAAGTATTCGACCCAAGTGGCAGC
*
24286 CAGCCAAGTATTCGGCCCAAGTGGCAGC
1 CAGCCAAGTATTCGACCCAAGTGGCAGC
24314 CA
1 CA
24316 CCGATGGATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.33, G:0.26, T:0.14
Consensus pattern (28 bp):
CAGCCAAGTATTCGACCCAAGTGGCAGC
Found at i:25889 original size:28 final size:28
Alignment explanation
Indices: 25858--25913 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
25848 TTTTTTGGCC
*
25858 TTATAAAGTTTTTTAGCC-ACCTTATTAT
1 TTATAAAGTGTTTTA-CCAACCTTATTAT
*
25886 TTATTAAGTGTTTTACCTAACCTTATTA
1 TTATAAAGTGTTTTACC-AACCTTATTA
25914 AGAGTTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 13 0.54
29 9 0.38
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (28 bp):
TTATAAAGTGTTTTACCAACCTTATTAT
Found at i:29023 original size:15 final size:14
Alignment explanation
Indices: 29000--29034 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
28990 CTCTTCCCGC
*
29000 TTTTCTTTTCTTTCT
1 TTTTTTTTTCTTT-T
29015 TTTTTTTTTCTTTT
1 TTTTTTTTTCTTTT
29029 TTTTTT
1 TTTTTT
29035 CTAGTAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTCTTTT
Found at i:29024 original size:11 final size:11
Alignment explanation
Indices: 29005--29036 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28995 CCCGCTTTTC
*
29005 TTTTCTTTCTT
1 TTTTTTTTCTT
29016 TTTTTTTTCTT
1 TTTTTTTTCTT
29027 TTTTTTTTCT
1 TTTTTTTTCT
29037 AGTAAAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:29343 original size:22 final size:25
Alignment explanation
Indices: 29317--29374 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 25
29307 ATTTAAGTAG
*
29317 GGATCAAACCATTTTT-TT-T-AAA
1 GGATCCAACCATTTTTGTTATGAAA
29339 GGATCCAACCATTTTTGTTATGAAA
1 GGATCCAACCATTTTTGTTATGAAA
29364 GGATCCAACCA
1 GGATCCAACCA
29375 AATTTGGTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 15 0.47
23 2 0.06
24 1 0.03
25 14 0.44
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (25 bp):
GGATCCAACCATTTTTGTTATGAAA
Found at i:30095 original size:178 final size:181
Alignment explanation
Indices: 29666--30133 Score: 477
Period size: 182 Copynumber: 2.6 Consensus size: 181
29656 CAAAATAACA
* * * * * *
29666 AATTTTTCAGAAAC-TTTTTGATACTTGAAACATCAAATTTAACTTTGGAATCCTTCATGAAAGT
1 AATTTTTCGGAAACATTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGT
* * * * *
29730 TGTAGATTATGCAACAACCTTTTAATAGACATTTGAATCA-CTTCAATCGGACATCTGGAGCAAA
66 TGTAGATAATGGAACAACCTTTTAATAGACACTTGAATCACCTTCAATCAGACATCTGGAACAAA
*
29794 AATTATGCAATATTTAAGTACACCGTCATTTCCCGTTAACCGTAAACAACT
131 AATTAAGCAATATTTAAGTACACCGTCATTTCCCGTTAACCGTAAACAACT
* * * * *
29845 TATTTCTT--GAAATCGATTTTTTTATATTTGGAATATTAAA-TTAGCTTTCGAGTCCTTAATTG
1 AATTT-TTCGGAAA-C-A-TTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCA-TG
* * * * *
29907 AAAGTTGTAGATAATGGAACAATCTTTTAAGAGACACTTGAATCACCTT-AATTATACATGTGGA
61 AAAGTTGTAGATAATGGAACAACCTTTTAATAGACACTTGAATCACCTTCAATCAGACATCTGGA
* *** ** *
29971 ACAAAAGTTAAGTGTTA-TTAAGTGGAGCGTCCA-TTCCCGTTAACCG-AAACAACT
126 ACAAAAATTAAGCAATATTTAAGTACACCGT-CATTTCCCGTTAACCGTAAACAACT
* * * *
30025 AATTTTTCGGAAGCATTTTTTATACTTGAAACATTAAATTTAGTTTTCGAGTTCTCCATGAAAGT
1 AATTTTTCGGAAACATTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGT
* * * * *
30090 TGTAGATCATGGGATAACCTTTAAATAGACACTCGAATCACCTT
66 TGTAGATAATGGAACAACCTTTTAATAGACACTTGAATCACCTT
30134 GATCGGATAT
Statistics
Matches: 234, Mismatches: 44, Indels: 23
0.78 0.15 0.08
Matches are distributed among these distances:
178 68 0.29
179 23 0.10
180 15 0.06
181 41 0.18
182 84 0.36
183 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (181 bp):
AATTTTTCGGAAACATTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGT
TGTAGATAATGGAACAACCTTTTAATAGACACTTGAATCACCTTCAATCAGACATCTGGAACAAA
AATTAAGCAATATTTAAGTACACCGTCATTTCCCGTTAACCGTAAACAACT
Found at i:30284 original size:24 final size:23
Alignment explanation
Indices: 30257--30301 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
30247 TCTAAGGTTT
30257 GTGAGAATAAC-AAAAATACCAAAA
1 GTGA-AATAACTAAAAA-ACCAAAA
*
30281 GTGAAATGACTAAAAAACCAA
1 GTGAAATAACTAAAAAACCAA
30302 GATGTAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (23 bp):
GTGAAATAACTAAAAAACCAAAA
Found at i:31180 original size:18 final size:18
Alignment explanation
Indices: 31145--31181 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31135 ACTATTTTTC
*
31145 ATTAAAAAATTTGGATAT
1 ATTAAAAAATTTGAATAT
*
31163 ATTAAAAAATTTTAATAT
1 ATTAAAAAATTTGAATAT
31181 A
1 A
31182 CAATTTTATT
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:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATTAAAAAATTTGAATAT
Found at i:32312 original size:2 final size:2
Alignment explanation
Indices: 32305--32338 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
32295 CAAACATGTA
32305 AT AT AT 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 AT AT AT
32339 CTCATAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35971 original size:219 final size:218
Alignment explanation
Indices: 35580--35996 Score: 545
Period size: 219 Copynumber: 1.9 Consensus size: 218
35570 ACAATATGTA
* **
35580 GTGAAAGACTGAAGCATCAGGGGAATCCATTAATAACATAATAGATTCAGATTTGTAAAGATAAT
1 GTGAAAGACTGAAGCATCAGGGGAATCCATTAATAACATAATAAATTCAGATTTCCAAAGATAAT
** * * * * ** ** *
35645 TGTCTGGAAATTGGTTTCATATTAGATATGAGTTGTCATGGAGATGTTAGTTTGTCTTGAATATA
66 AATCTGCAAATTGGGTTCATATTAGATATGAGTTATCATAGAGAAATTAGTTTGTCTCAAACATA
* * * *
35710 GTATATAACAATAACAAATAGCTGTTAACATCAGCGACATACATTAAATTA-TCAATAGTGTTTA
131 GTATATAACAATAACAAATAGCTATGAACATCAGCAACATACATTAAATTAGT-AATAGTATTTA
35774 CAGAAAGTAAAGAGCGGTAATCCT
195 CAGAAAGTAAAGAGCGGTAATCCT
* * *
35798 GTGAAAGACTGAAGTATCAAGGGG-ATCCATTAATAATATCAATAAATTCAGATTTCCAAATATA
1 GTGAAAGACTGAAGCATC-AGGGGAATCCATTAATAACAT-AATAAATTCAGATTTCCAAAGATA
35862 ATAATCTGCAAATTGGGTTCAT-TGTA-ATCATGAGTTATCATAGAGAAATTAGTTTGTCTCAAA
64 ATAATCTGCAAATTGGGTTCATAT-TAGAT-ATGAGTTATCATAGAGAAATTAGTTTGTCTCAAA
* * *
35925 CATAGTATGTAACAATAGCAAATAGCTATGAATATCAGCAACATACATTAAATTAGTAATAGTAT
127 CATAGTATATAACAATAACAAATAGCTATGAACATCAGCAACATACATTAAATTAGTAATAGTAT
35990 TTACAGA
192 TTACAGA
35997 TGGCTTAATC
Statistics
Matches: 170, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
218 34 0.20
219 135 0.79
220 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (218 bp):
GTGAAAGACTGAAGCATCAGGGGAATCCATTAATAACATAATAAATTCAGATTTCCAAAGATAAT
AATCTGCAAATTGGGTTCATATTAGATATGAGTTATCATAGAGAAATTAGTTTGTCTCAAACATA
GTATATAACAATAACAAATAGCTATGAACATCAGCAACATACATTAAATTAGTAATAGTATTTAC
AGAAAGTAAAGAGCGGTAATCCT
Found at i:40780 original size:15 final size:14
Alignment explanation
Indices: 40760--40816 Score: 78
Period size: 15 Copynumber: 3.9 Consensus size: 14
40750 TTCAACACCA
40760 TGCTCAGAATTCAGT
1 TGCTCAGAATT-AGT
40775 TGCTCAGAATTGAGT
1 TGCTCAGAATT-AGT
*
40790 TGCTCAGAATTGGCT
1 TGCTCAGAATTAG-T
40805 TGCTCAGAATTA
1 TGCTCAGAATTA
40817 CCCTCCTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 1 0.03
15 37 0.97
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (14 bp):
TGCTCAGAATTAGT
Found at i:48472 original size:57 final size:57
Alignment explanation
Indices: 48402--48511 Score: 202
Period size: 57 Copynumber: 1.9 Consensus size: 57
48392 AAACACGATT
48402 AGCAGCGACAATTCCACCACGCAATTGGGAATTAATGTACCATAAAGACAGCCCATC
1 AGCAGCGACAATTCCACCACGCAATTGGGAATTAATGTACCATAAAGACAGCCCATC
* *
48459 AGCAGCGGCAATTCCACCATGCAATTGGGAATTAATGTACCATAAAGACAGCC
1 AGCAGCGACAATTCCACCACGCAATTGGGAATTAATGTACCATAAAGACAGCC
48512 AGGACGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (57 bp):
AGCAGCGACAATTCCACCACGCAATTGGGAATTAATGTACCATAAAGACAGCCCATC
Found at i:55829 original size:24 final size:24
Alignment explanation
Indices: 55802--55852 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
55792 GGAAAAAAGA
*
55802 AAAAACTTGCACTAGGGCAAGACT
1 AAAAACTTGCAATAGGGCAAGACT
*
55826 AAAAACTTGCAATATGGCAAGACT
1 AAAAACTTGCAATAGGGCAAGACT
55850 AAA
1 AAA
55853 GCTCTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (24 bp):
AAAAACTTGCAATAGGGCAAGACT
Found at i:59776 original size:11 final size:11
Alignment explanation
Indices: 59760--59794 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
59750 CAGGGTTTGC
59760 TTTCTTTACTT
1 TTTCTTTACTT
*
59771 TTTCTTTTCTT
1 TTTCTTTACTT
*
59782 TTTATTTACTT
1 TTTCTTTACTT
59793 TT
1 TT
59795 CAAAGTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTTACTT
Found at i:73156 original size:17 final size:17
Alignment explanation
Indices: 73134--73167 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
73124 TGTCACGGTC
73134 CACACCAACTTGTGAGG
1 CACACCAACTTGTGAGG
73151 CACACCAACTTGTGAGG
1 CACACCAACTTGTGAGG
73168 TATTGTCCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (17 bp):
CACACCAACTTGTGAGG
Found at i:74046 original size:22 final size:22
Alignment explanation
Indices: 74021--74069 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
74011 AAATTTCGAG
* *
74021 AACCTTTTTATAAAATTTTTTT
1 AACCTTCTTATAAAATTTTGTT
*
74043 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATAAAATTTTGTT
74065 AACCT
1 AACCT
74070 CCCTAAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (22 bp):
AACCTTCTTATAAAATTTTGTT
Found at i:74069 original size:44 final size:45
Alignment explanation
Indices: 73961--74069 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 45
73951 TTATGATCTC
* *
73961 CTTATGAAATTTTGATAATCTTTCTATGAAATTTTAATAACGATA
1 CTTATGAAATTTTGATAACCTTTCTATAAAATTTTAATAACGATA
* * * ** * *
74006 C-TATGAAATTTCGAGAACCTTTTTATAAAATTTTTTTAAC-CTT
1 CTTATGAAATTTTGATAACCTTTCTATAAAATTTTAATAACGATA
*
74049 CTTATGAAATTTTGTTAACCT
1 CTTATGAAATTTTGATAACCT
74070 CCCTAAGGAA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
43 2 0.04
44 48 0.94
45 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (45 bp):
CTTATGAAATTTTGATAACCTTTCTATAAAATTTTAATAACGATA
Found at i:74118 original size:23 final size:22
Alignment explanation
Indices: 74092--74540 Score: 141
Period size: 22 Copynumber: 20.8 Consensus size: 22
74082 GTAAAGACCT
74092 CACTATGAAATTTTGATAACCAA
1 CACTATGAAATTTTGATAACC-A
* * *
74115 CACTATGAGATGTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* *
74137 C-CATATGATATATTGATAACCA
1 CAC-TATGAAATTTTGATAACCA
** * * * * *
74159 CGTTATAAAAATTTAAAAACCTT
1 CACTATGAAATTTTGATAACC-A
* *
74182 CA-TATG-AATTGTT-AGTGATCA
1 CACTATGAAATT-TTGA-TAACCA
* *
74203 CACTCTGAAATTTTGATAATCA
1 CACTATGAAATTTTGATAACCA
* * *
74225 CACTATGAAATTGTAATAACCT
1 CACTATGAAATTTTGATAACCA
* *
74247 CGCTATGAAATTTTGATAAACCTT
1 CACTATGAAATTTTGAT-AACC-A
* * *
74271 C-CTATAAAATTTTGATAAAACT
1 CACTATGAAATTTTGAT-AACCA
* * *
74293 CCCTATAAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
*
74315 C-CTAATGAAATCTTGAT----A
1 CACT-ATGAAATTTTGATAACCA
* *
74333 -ACTA-CAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* ** *
74353 CCCTATGATTTTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* *
74375 CATTATGAAACTTTG-T-----
1 CACTATGAAATTTTGATAACCA
* * * * *
74391 TATTATGAAATTTTGTTAATCT
1 CACTATGAAATTTTGATAACCA
* * *
74413 CCCTATGAAATTTTGATCTA-TA
1 CACTATGAAATTTTGAT-AACCA
* * *
74435 TACTATGAAATTTTGATCTA-TA
1 CACTATGAAATTTTGAT-AACCA
*
74457 TACTATGAAATTTTGATAACC-
1 CACTATGAAATTTTGATAACCA
* * *
74478 CTCCTATGAAATTTTGAAAACTA
1 C-ACTATGAAATTTTGATAACCA
* * *
74501 AACTATGCAATTTTGATAACCTT
1 CACTATGAAATTTTGATAACC-A
74524 CA-TATGAAATTTTGATA
1 CACTATGAAATTTTGATA
74541 TCCTGCCTGA
Statistics
Matches: 322, Mismatches: 74, Indels: 61
0.70 0.16 0.13
Matches are distributed among these distances:
16 22 0.07
17 2 0.01
18 2 0.01
21 14 0.04
22 216 0.67
23 64 0.20
24 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:74152 original size:22 final size:23
Alignment explanation
Indices: 74092--74158 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
74082 GTAAAGACCT
*
74092 CACTATGAAATTTTGATAACCAA
1 CACTATGAAATATTGATAACCAA
* * **
74115 CACTATGAGATGTTGATAACCTC
1 CACTATGAAATATTGATAACCAA
*
74138 CA-TATGATATATTGATAACCA
1 CACTATGAAATATTGATAACCA
74159 CGTTATAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (23 bp):
CACTATGAAATATTGATAACCAA
Found at i:74397 original size:16 final size:16
Alignment explanation
Indices: 74376--74408 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
74366 TGATAACCTC
74376 ATTATGAAACTTTGTT
1 ATTATGAAACTTTGTT
*
74392 ATTATGAAATTTTGTT
1 ATTATGAAACTTTGTT
74408 A
1 A
74409 ATCTCCCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (16 bp):
ATTATGAAACTTTGTT
Found at i:74402 original size:60 final size:60
Alignment explanation
Indices: 74277--74429 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
74267 CCTTCCTATA
* *
74277 AAATTTTGATAAAACTCCCTATAAAATTTTGATAACCTCCTAATGAAATCTTGATAACTAC
1 AAATTTTGAT-AAACTCCCTATGAAATTTTGATAACCTCATAATGAAATCTTGATAACTAC
* ** * * * *
74338 AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAA-CTTTG-TTATTATG
1 AAATTTTGATAAACTCCCTATGAAATTTTGATAACCTCATAATGAAATC-TTGATAACTA-C
* *
74398 AAATTTTGTTAATCTCCCTATGAAATTTTGAT
1 AAATTTTGATAAACTCCCTATGAAATTTTGAT
74430 CTATATACTA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 5 0.06
60 62 0.81
61 10 0.13
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (60 bp):
AAATTTTGATAAACTCCCTATGAAATTTTGATAACCTCATAATGAAATCTTGATAACTAC
Found at i:74506 original size:66 final size:66
Alignment explanation
Indices: 74394--74517 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
74384 ACTTTGTTAT
* * *
74394 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTATATACTATGAAATTTTGATCTATATA
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGAACTATATACTATGAAATTTTGATCTATATA
74459 C
66 C
*
74460 TATGAAATTTTGATAACC-CTCCTATGAAATTTTGAAAACTA-A-ACTATGCAATTTTGAT
1 TATGAAATTTTGATAACCTC-CCTATGAAATTTTG--AACTATATACTATGAAATTTTGAT
74518 AACCTTCATA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
65 1 0.02
66 45 0.88
67 1 0.02
68 4 0.08
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (66 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGAACTATATACTATGAAATTTTGATCTATATA
C
Found at i:74825 original size:43 final size:41
Alignment explanation
Indices: 74733--74849 Score: 130
Period size: 43 Copynumber: 2.8 Consensus size: 41
74723 CCCCTCTATG
* * *
74733 AAATTTTGATAATCAC-ATTAATTTTGATAACCTCGCTTTT
1 AAATTTTGATAATCACTATAAATTTTGATAATCTCGCTTAT
*
74773 AAATTTTGATAATAACACTATAAAATTTTGATAATCT-TCTTAT
1 AAATTTTGATAAT--CACTAT-AAATTTTGATAATCTCGCTTAT
* *
74816 AAATTTTGATAATCTCTATGAAATTTCGATAATC
1 AAATTTTGATAATCACTAT-AAATTTTGATAATC
74850 ACTCTATGAG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
40 13 0.20
41 18 0.27
42 3 0.05
43 19 0.29
44 13 0.20
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.44
Consensus pattern (41 bp):
AAATTTTGATAATCACTATAAATTTTGATAATCTCGCTTAT
Found at i:74857 original size:22 final size:21
Alignment explanation
Indices: 74640--74885 Score: 127
Period size: 22 Copynumber: 11.6 Consensus size: 21
74630 AAAAATACCA
*
74640 CTATGAAATTTTGGTAATCACAT
1 CTATGAAATTTTGATAATC-C-T
* *
74663 -TTTGAAAATTTGATAA-CCT
1 CTATGAAATTTTGATAATCCT
*
74682 CTTTATGAAATTTTAATAA-CCT
1 C--TATGAAATTTTGATAATCCT
* * **
74704 CTTTATAAAATTTTGTTGACCCCT
1 C--TATGAAATTTTGAT-AATCCT
*
74728 CTATGAAATTTTGATAAT-CA
1 CTATGAAATTTTGATAATCCT
*
74748 C-AT-TAATTTTGATAA-CCT
1 CTATGAAATTTTGATAATCCT
* * * *
74766 CGCTTTTAAATTTTGATAATAACA
1 --CTATGAAATTTTGATAAT-CCT
* *
74790 CTATAAAATTTTGATAATCTT
1 CTATGAAATTTTGATAATCCT
74811 CTTAT-AAATTTTGATAAT-CT
1 C-TATGAAATTTTGATAATCCT
*
74831 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATC-CT
*
74853 CTATGAGA-TTTGATAA-CCTT
1 CTATGAAATTTTGATAATCC-T
*
74873 CTATCAAATTTTG
1 CTATGAAATTTTG
74886 GTACTCCTTA
Statistics
Matches: 173, Mismatches: 32, Indels: 38
0.71 0.13 0.16
Matches are distributed among these distances:
18 12 0.07
19 7 0.04
20 26 0.15
21 28 0.16
22 94 0.54
23 1 0.01
24 5 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.43
Consensus pattern (21 bp):
CTATGAAATTTTGATAATCCT
Found at i:76257 original size:539 final size:539
Alignment explanation
Indices: 75229--76306 Score: 1741
Period size: 539 Copynumber: 2.0 Consensus size: 539
75219 TAAGCTTGTT
* * *
75229 TGAGTTCATGAAGTCCAAATTGTCAAGTCAGATGTTTTGAAATCTAAATCTGATATTTTTAGACC
1 TGAGTCCATGAAGTCCAAATTGTCAAGGCAGATGTTTTGAAATCTAAATCTGATATTCTTAGACC
* *
75294 CAATTCGTTAATATGGAAGCCCAAAGAAGGAATCCAAGTCCAATCAGTAATTATGATGCAGTAAT
66 CAAATCGTTAATATGGAAGCCCAAAGAAGGAATCCAAATCCAATCAGTAATTATGATGCAGTAAT
75359 GATTCAGCCCTGATGCAACATTGTTAAATCCTATTTAAAGGAGGACTTCACAAGAGCAGTTTGGG
131 GATTCAGCCCTGATGCAACATTGTTAAATCCTATTTAAAGGAGGACTTCACAAGAGCAGTTTGGG
* * * * *
75424 AAGAAATTTCATAACTTTTGATTCAGAGCTCAGAAAAATGCAAATGAGGTACCGTTGGAAAGAGG
196 AAGAAAATTCATAACTCTTGATCCAGAACTCAGAAAAATGCAAATGAGATACCGTTGGAAAGAGG
** * *
75489 ATTCCGAAATCTACAACTTTTATGTTTATCTCGAGACGTAATTCTGTTGTTTCGGTGGATGATTT
261 ATTCCGAAATCTACAACTTTTATGTTTATCTCGAGACGTAATTCTGCCGTTTCAGTGGACGATTT
*
75554 TACCCTTGAAAATTCTTGACAGAATTGATCTTCTCCTAAACCGACTTTGAGAATGTTTTAGACGA
326 TACCCTTGAAAATTCTTAACAGAATTGATCTTCTCCTAAACCGACTTTGAGAATGTTTTAGACGA
*
75619 AAATTCAGATGCTAAAAATGATGTGGGGCATCCTTATTGACCATGTTGGATTCTAATTAATGAGG
391 AAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGACCATGTTGGATTCTAATTAATGAGG
**
75684 ATAATCTAAATTTCCATTATTTTAATAGTGGAATAATTAAAAGATTATTTAATAATGGCAATTTA
456 ATAATCTAAATTTCCATTATTTTAATAGTGGAATAATTAAAAGATTATTTAATAACAGCAATTTA
75749 GAAATATATTTGAAAAAAA
521 GAAATATATTTGAAAAAAA
* *
75768 TGAGTCCATGAAGTCCAAATTGTCAAGGCAGAT-TTATTGAAGTCTAAATCTGATATTCTTAGCC
1 TGAGTCCATGAAGTCCAAATTGTCAAGGCAGATGTT-TTGAAATCTAAATCTGATATTCTTAGAC
* *
75832 CCAAATCGTTAATATGGAAGCCCAAAGAAGGAGTTCAAATCCAATCAGTAATTATGATGCAGTAA
65 CCAAATCGTTAATATGGAAGCCCAAAGAAGGAATCCAAATCCAATCAGTAATTATGATGCAGTAA
* * * *
75897 TGATTCAGCCCTGATGCAGCATTGTTAAATCCTATTTAAAGGAGGACTTTAGAAGAGCAGTTTTG
130 TGATTCAGCCCTGATGCAACATTGTTAAATCCTATTTAAAGGAGGACTTCACAAGAGCAGTTTGG
75962 GAAGAAAATTCATAACTCTTGATCCAGAACTCAGAAAAATGCAAATGAGATACCGTTGGAAAGAG
195 GAAGAAAATTCATAACTCTTGATCCAGAACTCAGAAAAATGCAAATGAGATACCGTTGGAAAGAG
*
76027 GATTCCGAGATCTACAACTTTTATGTTTATCTCGAGATC-TAATTCTGCCGTTTCAGTGGACGAT
260 GATTCCGAAATCTACAACTTTTATGTTTATCTCGAGA-CGTAATTCTGCCGTTTCAGTGGACGAT
* * * *
76091 TTTGCCCTT-AAAATTTTTTAACAGAATTGATCTTCTTCTAAACCGAC-TTGAAGAATGTTTTGG
324 TTTACCCTTGAAAA-TTCTTAACAGAATTGATCTTCTCCTAAACCGACTTTG-AGAATGTTTTAG
* * ** * *
76154 ACGAAAATTCAGATGTTAAAGATTTTGTGGGGCATCCCTATTGGCCATGTTGGATTTTAATTAAT
387 ACGAAAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGACCATGTTGGATTCTAATTAAT
* *
76219 GAGGATAATCTAAATTTCCATTATTTTAATATTGGAATAATTAAAATATTATTTAATAACAGCAA
452 GAGGATAATCTAAATTTCCATTATTTTAATAGTGGAATAATTAAAAGATTATTTAATAACAGCAA
76284 TTTAGAAATATATTTGAAAAAAA
517 TTTAGAAATATATTTGAAAAAAA
76307 GGATACAATC
Statistics
Matches: 496, Mismatches: 39, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
538 9 0.02
539 486 0.98
540 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (539 bp):
TGAGTCCATGAAGTCCAAATTGTCAAGGCAGATGTTTTGAAATCTAAATCTGATATTCTTAGACC
CAAATCGTTAATATGGAAGCCCAAAGAAGGAATCCAAATCCAATCAGTAATTATGATGCAGTAAT
GATTCAGCCCTGATGCAACATTGTTAAATCCTATTTAAAGGAGGACTTCACAAGAGCAGTTTGGG
AAGAAAATTCATAACTCTTGATCCAGAACTCAGAAAAATGCAAATGAGATACCGTTGGAAAGAGG
ATTCCGAAATCTACAACTTTTATGTTTATCTCGAGACGTAATTCTGCCGTTTCAGTGGACGATTT
TACCCTTGAAAATTCTTAACAGAATTGATCTTCTCCTAAACCGACTTTGAGAATGTTTTAGACGA
AAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGACCATGTTGGATTCTAATTAATGAGG
ATAATCTAAATTTCCATTATTTTAATAGTGGAATAATTAAAAGATTATTTAATAACAGCAATTTA
GAAATATATTTGAAAAAAA
Found at i:77957 original size:12 final size:12
Alignment explanation
Indices: 77940--77964 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
77930 GCCTACTCGA
77940 ACTTGCTCGGTT
1 ACTTGCTCGGTT
77952 ACTTGCTCGGTT
1 ACTTGCTCGGTT
77964 A
1 A
77965 GCTCATTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (12 bp):
ACTTGCTCGGTT
Found at i:81818 original size:16 final size:16
Alignment explanation
Indices: 81797--81836 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 16
81787 AGTAGTTACA
81797 TTGAATTTCGATTAAT
1 TTGAATTTCGATTAAT
81813 TTGAATTTCGATTAAT
1 TTGAATTTCGATTAAT
81829 TTGGAATT
1 TT-GAATT
81837 GAGTTGCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (16 bp):
TTGAATTTCGATTAAT
Found at i:91432 original size:26 final size:26
Alignment explanation
Indices: 91396--91449 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
91386 CAAGCCACAT
91396 TGATCAAATCAACCGGAAATATAAAA
1 TGATCAAATCAACCGGAAATATAAAA
91422 TGATCAAATCAACCGGAAATATAAAA
1 TGATCAAATCAACCGGAAATATAAAA
91448 TG
1 TG
91450 TTAATTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.20
Consensus pattern (26 bp):
TGATCAAATCAACCGGAAATATAAAA
Found at i:92210 original size:24 final size:24
Alignment explanation
Indices: 92178--92275 Score: 160
Period size: 24 Copynumber: 4.1 Consensus size: 24
92168 TGTCGATGAC
* *
92178 TCTGGTTTTGACGACCGTGATTTT
1 TCTGCTTTTGACGACTGTGATTTT
* *
92202 TCTGGTTTTGACGATTGTGATTTT
1 TCTGCTTTTGACGACTGTGATTTT
92226 TCTGCTTTTGACGACTGTGATTTT
1 TCTGCTTTTGACGACTGTGATTTT
92250 TCTGCTTTTGACGACTGTGATTTT
1 TCTGCTTTTGACGACTGTGATTTT
92274 TC
1 TC
92276 GGATTTTTCG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.12, C:0.15, G:0.22, T:0.50
Consensus pattern (24 bp):
TCTGCTTTTGACGACTGTGATTTT
Found at i:94038 original size:78 final size:78
Alignment explanation
Indices: 93949--94109 Score: 286
Period size: 78 Copynumber: 2.1 Consensus size: 78
93939 AGATTTATAG
* * *
93949 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTGTAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
94014 TACCATTTTACTA
66 TACCATTTTACTA
*
94027 TTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCTTTATAACTATTTCAGTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
94092 TACCATTTTACTA
66 TACCATTTTACTA
94105 TTTTA
1 TTTTA
94110 AGTAGAAAAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (78 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
TACCATTTTACTA
Found at i:95165 original size:132 final size:131
Alignment explanation
Indices: 94949--95213 Score: 399
Period size: 132 Copynumber: 2.0 Consensus size: 131
94939 TTATTTAAAC
*
94949 TTTTATAATTTTTCTCAACTAAAAGCTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAATTTTACTCAACTAAAAGCTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
* * * * * *
95014 TTTAATTTTTTACCATTTTACTATTTTGATTAAAGAATTTATATATATTAGAATTATTTAAATAT
66 TTTAATTTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATT-TTTAAAAAT
95079 AT
130 AT
*
95081 TTTTATAGTTTTACTCAACTAGAAA-CTCTATTTTTTATTTAATTAAATCTAATATCCTTATACC
1 TTTTATAATTTTACTCAACTA-AAAGCTCTA-TTTTTATTTAATTAAATCTAATATCCTTATACC
* *
95145 TATTTTA-TTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTATAATTTTTAAAAA
64 TATTTAATTTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAAA
95209 TAT
129 TAT
95212 TT
1 TT
95214 CTTAAATGAA
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
131 12 0.10
132 67 0.55
133 42 0.35
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (131 bp):
TTTTATAATTTTACTCAACTAAAAGCTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
TTTAATTTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAAATA
T
Done.