Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015725.1 Corchorus olitorius cultivar O-4 contig15758, 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: 45594
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:660 original size:76 final size:76
Alignment explanation
Indices: 534--678 Score: 175
Period size: 76 Copynumber: 1.9 Consensus size: 76
524 ACAAGGACCC
** * *
534 CGACTCCACCTGGGCGCCCACATGGTTGCCTTTAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTGAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
599 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * * * **
610 CGACTCTAGCTGGGTGCCCACATGGTTTGTCTGAAG-ACCCATGTGTTTTGCCTGATCACCCAGA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTGAAGCACCCATGTGGTTTGCCTGAGAACCCAGA
674 TGGGC
65 TGGGC
679 TGTTTCATAG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
76 50 0.88
77 7 0.12
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTGAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:5374 original size:5 final size:6
Alignment explanation
Indices: 5344--5371 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5334 CACCTAAACG
5344 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
5372 TAACGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:11662 original size:19 final size:19
Alignment explanation
Indices: 11640--11691 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
11630 GGGCTGAAAT
11640 TAATTAATTATTAAATAAA
1 TAATTAATTATTAAATAAA
* * *
11659 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAAATAAA
11678 TAATT-ATTATTAAA
1 TAATTAATTATTAAA
11692 AATCTCACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATTAATTATTAAATAAA
Found at i:13228 original size:21 final size:21
Alignment explanation
Indices: 13204--13270 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
13194 AATTCTCTGT
13204 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
13225 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
13246 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
13267 AAAT
1 AAAT
13271 CCTAATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:13250 original size:42 final size:42
Alignment explanation
Indices: 13191--13271 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
13181 GCTAAGTCTT
13191 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
13233 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
13272 CTAATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:13425 original size:57 final size:56
Alignment explanation
Indices: 13337--13447 Score: 195
Period size: 57 Copynumber: 2.0 Consensus size: 56
13327 TTTATTTTGT
*
13337 AGAATAATTAAGTAGAGATAAGGGGATATGATTTATTATAACATTTATTGTGTGGA
1 AGAATAATTAAGTAGAAATAAGGGGATATGATTTATTATAACATTTATTGTGTGGA
*
13393 AGAATAATTAAGTAGAAATAGGGGGGATATGATTTATTATAACATTTATTGTGTG
1 AGAATAATTAAGTAGAAATA-AGGGGATATGATTTATTATAACATTTATTGTGTG
13448 AAAGGAAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
56 19 0.37
57 33 0.63
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (56 bp):
AGAATAATTAAGTAGAAATAAGGGGATATGATTTATTATAACATTTATTGTGTGGA
Found at i:21863 original size:18 final size:19
Alignment explanation
Indices: 21833--21868 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21823 TTTTGCTGTA
*
21833 AAATTCGTTTCTTCTTTCT
1 AAATTCGTTTCTTATTTCT
21852 AAATTC-TTTCTTATTTC
1 AAATTCGTTTCTTATTTC
21869 CAGTTAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.19, C:0.19, G:0.03, T:0.58
Consensus pattern (19 bp):
AAATTCGTTTCTTATTTCT
Found at i:22315 original size:26 final size:26
Alignment explanation
Indices: 22282--22336 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
22272 TAGTCAGAAT
22282 TTAATGTGACTATAAGATATCTTGAA
1 TTAATGTGACTATAAGATATCTTGAA
22308 TTAATGTGACTATAAGATATCTTGAA
1 TTAATGTGACTATAAGATATCTTGAA
22334 TTA
1 TTA
22337 GTGTAGTCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (26 bp):
TTAATGTGACTATAAGATATCTTGAA
Found at i:23220 original size:14 final size:13
Alignment explanation
Indices: 23201--23239 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
23191 AAATTGTAAA
23201 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
23214 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
23228 ATTTAAAAAATT
1 ATTTAAAAAATT
23240 CTAATATATA
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:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:23468 original size:122 final size:127
Alignment explanation
Indices: 23225--23478 Score: 392
Period size: 122 Copynumber: 2.0 Consensus size: 127
23215 ATTTAAGAAA
23225 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---
* * *
23290 ATAGGTATAAGGATATTAGATTTAATTAAAAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 ATA-GTATAAGGATATTAGATTTAATTAAAAAAAATAGAGTTTTTAATTGAATAAAACTATAAAA
23355 G
127 G
23356 TATATTTAAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATA
* *
23419 -TA-AA-GATATTAGATTTAATTAAATAAATTAGAGTTTTTAATTGAATAAAACTATAAAAG
66 GTATAAGGATATTAGATTTAATTAAAAAAAATAGAGTTTTTAATTGAATAAAACTATAAAAG
23478 T
1 T
23479 TTAAACAATA
Statistics
Matches: 118, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
122 51 0.43
123 2 0.02
124 2 0.02
126 2 0.02
130 32 0.27
131 29 0.25
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATA
GTATAAGGATATTAGATTTAATTAAAAAAAATAGAGTTTTTAATTGAATAAAACTATAAAAG
Found at i:23589 original size:6 final size:6
Alignment explanation
Indices: 23574--23607 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
23564 ATATAGTATA
*
23574 TATATC TATATT TATATC TATATC TATA-C TATAT
1 TATATC TATATC TATATC TATATC TATATC TATAT
23608 ATAAAAGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (6 bp):
TATATC
Found at i:25314 original size:20 final size:20
Alignment explanation
Indices: 25277--25315 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25267 TTACTATTTT
25277 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
25297 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
25316 AATGTGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:25533 original size:22 final size:21
Alignment explanation
Indices: 25481--25708 Score: 143
Period size: 22 Copynumber: 10.3 Consensus size: 21
25471 CTGTGTGGAA
*
25481 ATCAAAATTTCATAAGATGGTT
1 ATCAAAATTTCATAGGA-GGTT
* *
25503 ATTATAATTTCATGAGGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* *
25525 ATCAAAATTCCATAGTGTGGTT
1 ATCAAAATTTCATAG-GAGGTT
* *
25547 AACAAAATTTCATATGGAAGTT
1 ATCAAAATTTCATA-GGAGGTT
* *
25569 GTCAAAATTTCATGGGAAGGTT
1 ATCAAAATTTCATAGG-AGGTT
* *
25591 ATCAAAATTTCAAAGTGTGGTT
1 ATCAAAATTTCATAG-GAGGTT
* *
25613 ACCAGAATTTCATAGGATCAGGTT
1 ATCAAAATTTCATAGG---AGGTT
* *
25637 ATTAAAATTT-TTAAGGAAGGTT
1 ATCAAAATTTCAT-AGG-AGGTT
** *
25659 ATTGAAATTTCATAGTGTGGTT
1 ATCAAAATTTCATAG-GAGGTT
* * *
25681 ATCACAATTTTATAGAAAGGTT
1 ATCAAAATTTCATAG-GAGGTT
25703 ATCAAA
1 ATCAAA
25709 GAGATTATCA
Statistics
Matches: 156, Mismatches: 39, Indels: 22
0.72 0.18 0.10
Matches are distributed among these distances:
21 5 0.03
22 129 0.83
23 8 0.05
24 14 0.09
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:25758 original size:22 final size:21
Alignment explanation
Indices: 25733--25860 Score: 105
Period size: 22 Copynumber: 5.8 Consensus size: 21
25723 ATCTTAATGA
25733 GGTTATAAGAATTTCATAGTGT
1 GGTTATAA-AATTTCATAGTGT
* *
25755 GGTTAACAAAATTTCATAAG-GA
1 GGTT-ATAAAATTTCAT-AGTGT
* * * *
25777 GGTTTCTAATATTTCATAGGGA
1 GG-TTATAAAATTTCATAGTGT
25799 GGTTATCAAAATTTCATAGTGT
1 GGTTAT-AAAATTTCATAGTGT
* **
25821 GGTTATTGAAATTTTTTAGTGT
1 GGTTA-TAAAATTTCATAGTGT
25843 GGTTATCAAAATTTCATA
1 GGTTAT-AAAATTTCATA
25861 CGAAGGTTAT
Statistics
Matches: 84, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
21 6 0.07
22 70 0.83
23 8 0.10
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.41
Consensus pattern (21 bp):
GGTTATAAAATTTCATAGTGT
Found at i:25779 original size:44 final size:44
Alignment explanation
Indices: 25713--25872 Score: 146
Period size: 44 Copynumber: 3.6 Consensus size: 44
25703 ATCAAAGAGA
* * *
25713 TTATCAAAATATCTTAATGAGGTTATAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAAGGAGGTTATAAGAATTTCATAGTGTGG
* * * * *
25757 TTAACAAAATTTCATAAGGAGGTTTCTAA-TATTTCATAGGGAGG
1 TTATCAAAATTTCATAAGGAGG-TTATAAGAATTTCATAGTGTGG
* * **
25801 TTATCAAAATTTCAT-AGTGTGGTTAT-TGAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAAG-GAGGTTATAAG-AATTTCATAGTGTGG
* *
25845 TTATCAAAATTTCATACGAAGGTTATAA
1 TTATCAAAATTTCATAAGGAGGTTATAA
25873 AAGTCTCAAC
Statistics
Matches: 89, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
43 5 0.06
44 78 0.88
45 6 0.07
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.39
Consensus pattern (44 bp):
TTATCAAAATTTCATAAGGAGGTTATAAGAATTTCATAGTGTGG
Found at i:25857 original size:66 final size:65
Alignment explanation
Indices: 25713--25874 Score: 157
Period size: 66 Copynumber: 2.5 Consensus size: 65
25703 ATCAAAGAGA
* * *
25713 TTATCAAAATATCTTAATGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAG
1 TTATCAAAATTTCATAAGGAGGTTATAA-AATTTCATAGTGTGGTTAACAAAATTTCATAAGGAG
25778 G
65 G
* * *** * *
25779 TT-TCTAATATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATTGAAATTT-TTTAGTG
1 TTATC-AAAATTTCATAAGGAGGTTAT-AAAATTTCATAGTGTGGTTAACAAAATTTCATAAG-G
*
25842 TGG
63 AGG
* *
25845 TTATCAAAATTTCATACGAAGGTTATAAAA
1 TTATCAAAATTTCATAAGGAGGTTATAAAA
25875 GTCTCAACTT
Statistics
Matches: 78, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
65 9 0.12
66 65 0.83
67 4 0.05
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (65 bp):
TTATCAAAATTTCATAAGGAGGTTATAAAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAGG
Found at i:26006 original size:22 final size:22
Alignment explanation
Indices: 25914--26020 Score: 103
Period size: 22 Copynumber: 4.8 Consensus size: 22
25904 TGGTAGAACG
* *
25914 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGATTGA
* * *
25935 TCATCGAAATTTCATAGAGATCGGA
1 TTATCAAAATTTCAT--AGAT-TGA
*
25960 TTATCAAAATTT-ATAGGTTGA
1 TTATCAAAATTTCATAGATTGA
25981 TTATCAAAATTTCATAGTATTG-
1 TTATCAAAATTTCATAG-ATTGA
26003 TTATCAAAATTTCATAGA
1 TTATCAAAATTTCATAGA
26021 GGGGTCAACA
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
21 19 0.27
22 32 0.45
23 3 0.04
24 5 0.07
25 12 0.17
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGATTGA
Found at i:26213 original size:22 final size:22
Alignment explanation
Indices: 26188--26323 Score: 107
Period size: 22 Copynumber: 6.2 Consensus size: 22
26178 TTATGGAGTA
26188 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
26210 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
26232 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * * *
26254 ATCGAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
26276 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
26298 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
26320 ATCA
1 ATCA
26324 GGGAGGTTAT
Statistics
Matches: 87, Mismatches: 22, Indels: 10
0.73 0.18 0.08
Matches are distributed among these distances:
21 3 0.03
22 77 0.89
23 7 0.08
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:26237 original size:44 final size:44
Alignment explanation
Indices: 26188--26311 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 44
26178 TTATGGAGTA
*
26188 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGT-T-TAG
1 ATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAG
* * *
26230 TTTTCAAAATTTCATAAGAGGGTTATCGAAATTTCATAGTATGTAG
1 --ATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAG
* * * *
26276 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
1 ATCAAAATTTCATAAGAAGGTTATCAAAATTTCATA
26312 ATGAGGTTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 63 0.94
45 1 0.01
46 3 0.04
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAG
Found at i:26424 original size:23 final size:23
Alignment explanation
Indices: 26346--26452 Score: 73
Period size: 23 Copynumber: 4.7 Consensus size: 23
26336 AAATTTGCAG
* *
26346 TTATCAATATTTCATAAGG-AGG-
1 TTATCAAAATTTTAT-AGGAAGGT
*
26368 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGGT
26391 TTA--AATTAATTTTATAGGAAGGT
1 TTATCAA--AATTTTATAGGAAGGT
* *
26414 TTATCCAAATTTCATAGCG-AGG-
1 TTATCAAAATTTTATAG-GAAGGT
* *
26436 TTATCACAATTTCATAG
1 TTATCAAAATTTTATAG
26453 TGTGATTATC
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.07
22 31 0.44
23 33 0.46
24 1 0.01
25 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:26452 original size:22 final size:21
Alignment explanation
Indices: 26345--26659 Score: 116
Period size: 22 Copynumber: 14.2 Consensus size: 21
26335 AAAATTTGCA
*
26345 GTTATCAATATTTCATAAGGAG
1 GTTATCAAAATTTCAT-AGGAG
*
26367 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATA-GGAG
* *
26389 GTT-TAAATTAATTTTATAGGAAG
1 GTTATCAA--AATTTCATAGG-AG
*
26412 GTTTATCCAAATTTCATAGCGAG
1 G-TTATCAAAATTTCATAG-GAG
* *
26435 GTTATCACAATTTCATAGTGTG
1 GTTATCAAAATTTCATAG-GAG
* * *
26457 ATTATCAAAATTTCAGAGTGTG
1 GTTATCAAAATTTCATAG-GAG
* *
26479 ATTA-CTAACAA-TTCATGTGGAG
1 GTTATC-AA-AATTTCAT-AGGAG
* * * * *
26501 ATTTTTAAATTTTCATAAGGTG
1 GTTATCAAAATTTCAT-AGGAG
* * *
26523 GTTATCAATATATCGTATGGAG
1 GTTATCAAAATTTCATA-GGAG
* * *
26545 GTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATAG-G-AG
* * * *
26568 GTTATGAAAATTTTATTCGGAA
1 GTTATCAAAATTTCA-TAGGAG
*
26590 GTTATCAAAATTTCATATTGAG
1 GTTATCAAAATTTCATA-GGAG
* *
26612 GTCT-TCAAAATTCCTTAGGGAG
1 GT-TATCAAAATTTCATA-GGAG
* * *
26634 GTTAACGAAATTTCATAAGAAG
1 GTTATCAAAATTTCAT-AGGAG
26656 GTTA
1 GTTA
26660 AAAAAAATTT
Statistics
Matches: 218, Mismatches: 55, Indels: 40
0.70 0.18 0.13
Matches are distributed among these distances:
21 10 0.05
22 159 0.73
23 42 0.19
24 5 0.02
25 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGAG
Found at i:27016 original size:15 final size:16
Alignment explanation
Indices: 26990--27019 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
26980 GCAGAGAGTT
26990 AAGAAGAACAATTAAG
1 AAGAAGAACAATTAAG
27006 AAGAA-AACAATTAA
1 AAGAAGAACAATTAA
27020 ACTAGAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (16 bp):
AAGAAGAACAATTAAG
Found at i:33551 original size:15 final size:15
Alignment explanation
Indices: 33533--33566 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
33523 TGAAAAACAC
33533 AAAACACAAAAATTA
1 AAAACACAAAAATTA
*
33548 AAAACGCAAAAATTA
1 AAAACACAAAAATTA
33563 AAAA
1 AAAA
33567 AAAAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.12, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAACACAAAAATTA
Found at i:33665 original size:45 final size:44
Alignment explanation
Indices: 33575--33663 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
33565 AAAAAAACTT
* *
33575 TTTTTTTTAGATCAAAAACGCAGAAAAGAAAAATAAAAGAAAAA
1 TTTTTTTTAGATCAAAAACACAGAAAAGAAAAACAAAAGAAAAA
* * *
33619 TTTTTTTTAGATGAAAAACACAGAAACGCAGAAACAAAGAGAAAA
1 TTTTTTTTAGATCAAAAACACAGAAAAG-AAAAACAAA-AGAAAA
33664 TTCCCAGGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 25 0.66
45 7 0.18
46 6 0.16
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.21
Consensus pattern (44 bp):
TTTTTTTTAGATCAAAAACACAGAAAAGAAAAACAAAAGAAAAA
Found at i:33907 original size:15 final size:16
Alignment explanation
Indices: 33881--33922 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
33871 GCAGAGAGTT
33881 AAGAAGAACAATTAAA-
1 AAGAA-AACAATTAAAC
33897 AAGAAAACAATTAAAC
1 AAGAAAACAATTAAAC
*
33913 TAGAAAACAA
1 AAGAAAACAA
33923 AGCAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.12
Consensus pattern (16 bp):
AAGAAAACAATTAAAC
Found at i:35337 original size:19 final size:18
Alignment explanation
Indices: 35304--35339 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35294 TTGAAATAGT
35304 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
35322 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
35340 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:36008 original size:20 final size:20
Alignment explanation
Indices: 35971--36009 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35961 TACTATTATT
35971 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
35991 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
36010 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:36238 original size:22 final size:21
Alignment explanation
Indices: 36186--36400 Score: 117
Period size: 22 Copynumber: 9.7 Consensus size: 21
36176 CTGTATGGTA
* *
36186 ATCAAAATTTTATAAGATGGTT
1 ATCAAAATTTCATAGGA-GGTT
* *
36208 ATTATAATTTCATGAGGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* * *
36230 ATCAAAATTCCATAGTATGATT
1 ATCAAAATTTCATAGGA-GGTT
* *
36252 ACCAAAATTTCATATGGAAGTT
1 ATCAAAATTTCATA-GGAGGTT
*
36274 AT-AACAATTTCATGGGAAGGTT
1 ATCAA-AATTTCATAGG-AGGTT
* *
36296 ATCAAAATTTCATAATGTGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* *
36318 ACCAAAATTTCATAGAATTAGGTT
1 ATCAAAATTTCATAG---GAGGTT
** *
36342 ATTTAAATTTCTTAGGAAGGTT
1 ATCAAAATTTCATAGG-AGGTT
** *
36364 ATTGAAATTTCATAGTGTGGTT
1 ATCAAAATTTCATAG-GAGGTT
* *
36386 ATCACAATTTTATAG
1 ATCAAAATTTCATAG
36401 AAATGTTATC
Statistics
Matches: 145, Mismatches: 36, Indels: 24
0.71 0.18 0.12
Matches are distributed among these distances:
21 8 0.06
22 113 0.78
23 9 0.06
24 15 0.10
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:36472 original size:22 final size:22
Alignment explanation
Indices: 36418--36858 Score: 170
Period size: 22 Copynumber: 19.9 Consensus size: 22
36408 ATCAAAGAGA
* * * *
36418 TTATCAAAATGTCATAGCGAGA
1 TTATCAAAATTTCATAGTGTGG
36440 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGTGG
* * *
36462 TTAACAAAATTTCATA-TGAAGA
1 TTATCAAAATTTCATAGTG-TGG
* * * *
36484 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGTGG
36506 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
**
36528 TTATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
*
36550 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-TGG
* *
36572 TTATAAAAGTCTCAATTTCATA-AG-GAG
1 TTAT-CAA-----AATTTCATAGTGTG-G
* * * **
36599 -TACCAAAATCTGATAG-AAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
36619 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGTGG
* **
36640 TTATCGAAATTTCATAAAGATCGG
1 TTATCAAAATTTCATAGTG-T-GG
* *
36664 ATTATCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-TGG
*
36686 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGTGG
* * *
36708 TTACCAAAATTTCA-AATCGAGG
1 TTATCAAAATTTCATAGT-GTGG
* * *
36730 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGTGG
* * *
36752 TCATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGTGG
* * * * *
36774 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGTGG
***
36796 TTATCAAAATTTCATAAAAAT-G
1 TTATCAAAATTTCAT-AGTGTGG
* * * *
36818 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGTGG
*
36840 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
36859 GTATTTTTGG
Statistics
Matches: 317, Mismatches: 74, Indels: 56
0.71 0.17 0.13
Matches are distributed among these distances:
20 18 0.06
21 34 0.11
22 219 0.69
23 15 0.05
24 4 0.01
25 13 0.04
26 3 0.01
27 1 0.00
28 10 0.03
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:36986 original size:22 final size:22
Alignment explanation
Indices: 36958--37530 Score: 153
Period size: 22 Copynumber: 26.4 Consensus size: 22
36948 TCAGGGAGGA
*
36958 TATCAAAATTTCTTATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
36980 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
37002 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
37024 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
37045 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
37068 TAACAAATTTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* *
37090 CATCAAACA-TTCATAGGGAA-GT
1 TATCAAA-ATTTCATA-TGAAGGT
* * *
37112 TGTCAGAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
37128 TATCAAGATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * *
37150 TATCAAAATTTTATAAGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
37173 TATCAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATATGAAGG-T
37196 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
37218 TATCACAATTTTATA-GTATGAT
1 TATCAAAATTTCATATG-AAGGT
*
37240 TATCAAAATTTCAGAGTGTAA--T
1 TATCAAAATTTCATA-TG-AAGGT
*
37262 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
** * *
37284 T-TTTAAATTATCATAACG-TGGT
1 TATCAAAATT-TCAT-ATGAAGGT
* * *
37306 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
37328 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
*
37351 CATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
37373 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* *
37395 CT-TCAAAA-TTCCTCATGGAGGT
1 -TATCAAAATTTCAT-ATGAAGGT
37417 TAAT-AAAATTTC--AT-AAGGT
1 T-ATCAAAATTTCATATGAAGGT
** ** **
37436 TAAAAAAATTT-ATAAAAATAT
1 TATCAAAATTTCATATGAAGGT
* ** * **
37457 TCTTGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* *
37479 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
* *
37501 TATCAAAATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
37523 CATCAAAA
1 TATCAAAA
37531 ATAGTGTAAT
Statistics
Matches: 407, Mismatches: 95, Indels: 98
0.68 0.16 0.16
Matches are distributed among these distances:
16 9 0.02
18 3 0.01
19 12 0.03
20 9 0.02
21 32 0.08
22 259 0.64
23 78 0.19
24 5 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:37195 original size:45 final size:44
Alignment explanation
Indices: 36953--37530 Score: 217
Period size: 44 Copynumber: 13.3 Consensus size: 44
36943 AAATTTCAGG
* *
36953 GAGGATATCAAAATTTCT-TATGAAGGTTATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTT-TATAGGAAGGTTATCAAAATTTCATAG-T
* * * * *
36998 TA-GTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTTATAGGAAGGTTATCAAAATTTCATAGT
* * * * * * * *
37041 -ATGTAGATCAAAATTTCATAGGGAGATTAACAAATTTTCATAAT
1 GAGGT-TATCAAAATTTTATAGGAAGGTTATCAAAATTTCATAGT
* * * *
37085 GAGGTCATCAAACA-TTCATAGGGAA-GTTGTCAGAA-TT--T-GT
1 GAGGTTATCAAA-ATTTTATA-GGAAGGTTATCAAAATTTCATAGT
* * *
37125 -A-GTTATCAAGATTTCATAAGG-AGGTTATCAAAATTTTATAAG-
1 GAGGTTATCAAAATTTTAT-AGGAAGGTTATCAAAATTTCAT-AGT
37167 GAGGTTTATCAAAATTTTATAGGAAGGTTTATCAAAATTTCATAGT
1 GAGG-TTATCAAAATTTTATAGGAAGG-TTATCAAAATTTCATAGT
* * * * *
37213 GAGGTTATCACAATTTTATAGTATGATTATCAAAATTTCAGAGT
1 GAGGTTATCAAAATTTTATAGGAAGGTTATCAAAATTTCATAGT
* * ** **
37257 GTA-ATTA-CTAACAA-TTCATATGG-AGGTT-TTTAAATTATCATAAC
1 G-AGGTTATC-AA-AATTTTATA-GGAAGGTTATCAAAATT-TCATAGT
* * * * * *
37301 GTGGTTATCAATATATCATATGG-AGGTTATCAACATCTCATAGT
1 GAGGTTATCAAAATTTTATA-GGAAGGTTATCAAAATTTCATAGT
* * * *
37345 GTTGGTCATCAAAATTTCATTGGGAA-GTTATCAAAATTTCATAGT
1 G-AGGTTATCAAAATTTTA-TAGGAAGGTTATCAAAATTTCATAGT
*
37390 GAGGTCT-TCAAAATTCCTCAT-GG-AGGTTAAT-AAAATTTCATA--
1 GAGGT-TATCAAAATT--TTATAGGAAGGTT-ATCAAAATTTCATAGT
* * ** ** * ** *
37432 -AGGTTA-AAAAAATTTATAAAAATATTCTTGAAATTCCATAGT
1 GAGGTTATCAAAATTTTATAGGAAGGTTATCAAAATTTCATAGT
* * *
37474 -ATCGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCATAAG-
1 GA-GGTTATCAAAATTTTATAGGAAGGTTATCAAAATTTCAT-AGT
*
37518 GAGGTCATCAAAA
1 GAGGTTATCAAAA
37531 ATAGTGTAAT
Statistics
Matches: 396, Mismatches: 90, Indels: 95
0.68 0.15 0.16
Matches are distributed among these distances:
37 2 0.01
38 25 0.06
39 5 0.01
40 19 0.05
41 6 0.02
42 2 0.01
43 20 0.05
44 201 0.51
45 93 0.23
46 23 0.06
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
GAGGTTATCAAAATTTTATAGGAAGGTTATCAAAATTTCATAGT
Found at i:37450 original size:18 final size:19
Alignment explanation
Indices: 37413--37450 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
37403 TTCCTCATGG
*
37413 AGGTTAATAAAATTTCATA
1 AGGTTAAAAAAATTTCATA
37432 AGGTTAAAAAAATTT-ATA
1 AGGTTAAAAAAATTTCATA
37450 A
1 A
37451 AAATATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (19 bp):
AGGTTAAAAAAATTTCATA
Found at i:45031 original size:57 final size:56
Alignment explanation
Indices: 44957--45077 Score: 206
Period size: 57 Copynumber: 2.1 Consensus size: 56
44947 TAATTAACCT
* * *
44957 AAATGAAATAAAATACATGTTTATCTTCTAACATTAAAATTTTAAAATTATAAATG
1 AAATAAAATAAAATACATGTTTATCTTCTAACACTAAAATTTAAAAATTATAAATG
45013 AAATAAAATTAAAATACATGTTTATCTTCTAACACTAAAATTTAAAAATTATAAATG
1 AAATAAAA-TAAAATACATGTTTATCTTCTAACACTAAAATTTAAAAATTATAAATG
45070 AAATAAAA
1 AAATAAAA
45078 ATACATGTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
56 7 0.11
57 54 0.89
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (56 bp):
AAATAAAATAAAATACATGTTTATCTTCTAACACTAAAATTTAAAAATTATAAATG
Found at i:45109 original size:57 final size:52
Alignment explanation
Indices: 44956--45090 Score: 200
Period size: 57 Copynumber: 2.5 Consensus size: 52
44946 TTAATTAACC
* *
44956 TAAATGAAAT-AAAATACATGTTTATCTTCTAACATTAAAATTTTAAAATTA
1 TAAATGAAATAAAAATACATGTTTATCTTCTAACACTAAAATTTAAAAATTA
45007 TAAATGAAATAAAATTAAAATACATGTTTATCTTCTAACACTAAAATTTAAAAATTA
1 TAAATGAAAT---A--AAAATACATGTTTATCTTCTAACACTAAAATTTAAAAATTA
45064 TAAATGAAATAAAAATACATGTTTATC
1 TAAATGAAATAAAAATACATGTTTATC
45091 CTTTAAAAGA
Statistics
Matches: 76, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
51 10 0.13
52 16 0.21
54 1 0.01
57 49 0.64
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.36
Consensus pattern (52 bp):
TAAATGAAATAAAAATACATGTTTATCTTCTAACACTAAAATTTAAAAATTA
Done.