Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013587.1 Corchorus capsularis cultivar CVL-1 contig13608, 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: 52122
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:431 original size:29 final size:30
Alignment explanation
Indices: 384--442 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
374 AAACAAAGAA
*
384 GGTTATACCAATCTTCTTATTCAAGTTTAC
1 GGTTATACCAATCTTCTTATTCAAGGTTAC
*
414 GGTT-TACCATTCTTCTTATTCAAGGTTAC
1 GGTTATACCAATCTTCTTATTCAAGGTTAC
443 CAAAAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (30 bp):
GGTTATACCAATCTTCTTATTCAAGGTTAC
Found at i:2389 original size:100 final size:100
Alignment explanation
Indices: 2216--2415 Score: 364
Period size: 100 Copynumber: 2.0 Consensus size: 100
2206 TCACTTCGGT
* * *
2216 TATCAAATTTCACATTTATGATTAGTTAAGAAAGATAAACTATAATCAAAGAAGTGTGTTATATT
1 TATCAAATTTCACATTTACGATTACTTAAGAAAGATAAACTATAATCAAAGAAATGTGTTATATT
*
2281 AAGAAACGCAGTTGATAAAATCCTTATAGAGAAGC
66 AAGAAACGCAGTCGATAAAATCCTTATAGAGAAGC
2316 TATCAAATTTCACATTTACGATTACTTAAGAAAGATAAACTATAATCAAAGAAATGTGTTATATT
1 TATCAAATTTCACATTTACGATTACTTAAGAAAGATAAACTATAATCAAAGAAATGTGTTATATT
2381 AAGAAACGCAGTCGATAAAATCCTTATAGAGAAGC
66 AAGAAACGCAGTCGATAAAATCCTTATAGAGAAGC
2416 AAAAGGTAAA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.30
Consensus pattern (100 bp):
TATCAAATTTCACATTTACGATTACTTAAGAAAGATAAACTATAATCAAAGAAATGTGTTATATT
AAGAAACGCAGTCGATAAAATCCTTATAGAGAAGC
Found at i:4233 original size:31 final size:31
Alignment explanation
Indices: 4198--4263 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
4188 AACTTTATGT
* *
4198 TTTCCGATTGTACCCTTATT-TTTAAAATATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
4229 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
4260 TTTC
1 TTTC
4264 TAAATTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:4568 original size:19 final size:20
Alignment explanation
Indices: 4541--4578 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
4531 TACTATTATT
4541 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
4561 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
4579 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:4825 original size:22 final size:22
Alignment explanation
Indices: 4800--4929 Score: 95
Period size: 22 Copynumber: 5.9 Consensus size: 22
4790 GTTTATCAAA
*
4800 GAGGTTATCAAAATGTCATAGC
1 GAGGTTATCAAAATTTCATAGC
*
4822 GAGGTTAT-AAGAATTTCATAGT
1 GAGGTTATCAA-AATTTCATAGC
* *
4844 GTGGTTAACAAAATTTCATTAG-
1 GAGGTTATCAAAATTTCA-TAGC
* * * * *
4866 AAGGTTA-CTAATATTTGATGGG
1 GAGGTTATC-AAAATTTCATAGC
* * *
4888 GAGGTTTTCAAAATTTTATAGT
1 GAGGTTATCAAAATTTCATAGC
*
4910 GTGGTTATCAAAATTTCATA
1 GAGGTTATCAAAATTTCATA
4930 TGAAGGTTAT
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
21 5 0.06
22 73 0.87
23 6 0.07
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGC
Found at i:5187 original size:22 final size:22
Alignment explanation
Indices: 5159--5717 Score: 176
Period size: 22 Copynumber: 25.7 Consensus size: 22
5149 TCAGGGAGGA
5159 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
5181 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
5203 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
5225 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * *
5246 AGATCAAAATTTCATAGGAAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
5269 TAACAAAATTTCATAATTAA-GT
1 TATCAAAATTTCAT-ATGAAGGT
*** * * *
5291 TATCAAAACACCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGT
*
5313 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * **
5329 TATCAAGATTTCATAAGAAATT
1 TATCAAAATTTCATATGAAGGT
* * *
5351 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
5374 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
5397 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
5419 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
5441 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
5463 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
5485 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * * *
5507 TATCAATATATCATATGGAGAT
1 TATCAAAATTTCATATGAAGGT
* * **
5529 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
5552 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
*
5574 TATCAAAATTTCATATTG-AGCT
1 TATCAAAATTTCATA-TGAAGGT
* * *
5596 CT-TCAAAATTCCTTA-GAATGT
1 -TATCAAAATTTCATATGAAGGT
* ** *
5617 TAACCGAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
5639 TA-AAAAAATT-ATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
5659 TCTCGAAATTCCATAGTG-TCGT
1 TATCAAAATTTCATA-TGAAGGT
*
5681 TATTAAAATTTCATA-GAAAGGT
1 TATCAAAATTTCATATG-AAGGT
5703 TATCAAAATTTCATA
1 TATCAAAATTTCATA
5718 ATGGAGTCAT
Statistics
Matches: 389, Mismatches: 111, Indels: 74
0.68 0.19 0.13
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
20 14 0.04
21 33 0.08
22 261 0.67
23 67 0.17
24 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:5226 original size:44 final size:44
Alignment explanation
Indices: 5159--5717 Score: 203
Period size: 44 Copynumber: 12.8 Consensus size: 44
5149 TCAGGGAGGA
*
5159 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
* * *
5203 TTTCAAAATTTCACAAGAGGGTTATCAAAATTTCATAGTATGTAG-
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGT-T-TAGT
* * * * *
5248 -ATCAAAATTTCATAGGAAGATTAACAAAATTTCATAATTAAGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
*** * * *
5291 TATCAAAACACCATAGGGAGATTATCAAAA-TT--T-G--TAGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
* ** * **
5329 TATCAAGATTTCATAAGAAATTTATCAAAATTTTATAG-GGAGGTT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTA-G-T
* * * *
5374 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAG-TGAGGT
1 TATCAAAATTTCATAAGAAG-GTTATCAAAATTTCATAGTTTA-GT
* * * *
5419 TATCACAATTTCAT-AG-TGTGATTATCAAAATTTCAGAGTGT-GAT
1 TATCAAAATTTCATAAGAAG-G-TTATCAAAATTTCATAGTTTAG-T
* * * * * *** *
5463 TA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGTGGT
1 TATC-AA-AATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
* * * * * * * *
5507 TATCAATATATCATATGGAGATTATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGT-TTAGT
** *
5552 TATCAAAATTTCATTGGGAA-GTTATCAAAATTTCATA-TTGAGCT
1 TATCAAAATTTCA-TAAGAAGGTTATCAAAATTTCATAGTTTAG-T
* * * * ** *
5596 CT-TCAAAA-TTCCTTAGAATGTTAACCGAATTTCATAAG--AAGGT
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTTCAT-AGTTTA-GT
* * * * * * * *
5639 TA-AAAAAATT-ATAAAAAGGTTCTCGAAATTCCATAGTGTCGT
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
*
5681 TATTAAAATTTCAT-AGAAAGGTTATCAAAATTTCATA
1 TATCAAAATTTCATAAG-AAGGTTATCAAAATTTCATA
5718 ATGGAGTCAT
Statistics
Matches: 380, Mismatches: 98, Indels: 74
0.69 0.18 0.13
Matches are distributed among these distances:
38 25 0.07
39 2 0.01
41 4 0.01
42 31 0.08
43 37 0.10
44 186 0.49
45 67 0.18
46 28 0.07
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAGT
Found at i:5824 original size:25 final size:25
Alignment explanation
Indices: 5790--5840 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5780 TAAATATTTT
5790 ATTTAAACACGTTGCGCCACGTGCA
1 ATTTAAACACGTTGCGCCACGTGCA
5815 ATTTAAACACGTTGCGCCACGTGCA
1 ATTTAAACACGTTGCGCCACGTGCA
5840 A
1 A
5841 CGCACGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (25 bp):
ATTTAAACACGTTGCGCCACGTGCA
Found at i:5882 original size:2 final size:2
Alignment explanation
Indices: 5875--5904 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5865 AAGTATAAAG
5875 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
5905 GTATGTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14539 original size:83 final size:82
Alignment explanation
Indices: 14400--14557 Score: 280
Period size: 83 Copynumber: 1.9 Consensus size: 82
14390 ATAATTGAAC
14400 CGGGATGGCCAAACCGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCTGGTTTACA
1 CGGGATGGCCAAACCGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCT-GTTTACA
14465 AAAGCATATGTGTATTAT
65 AAAGCATATGTGTATTAT
* * *
14483 CGGGATGGCCTAACTGGTCATGCCAAATAATAAACATAATGCAATCAATAAACTTCTGTTTACAA
1 CGGGATGGCCAAACCGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCTGTTTACAA
14548 AAGCATATGT
66 AAGCATATGT
14558 TTCAATCTTA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 18 0.25
83 54 0.75
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (82 bp):
CGGGATGGCCAAACCGGTCATGCCAAACAATAAACATAATGCAATCAATAAACTTCTGTTTACAA
AAGCATATGTGTATTAT
Found at i:14849 original size:35 final size:35
Alignment explanation
Indices: 14802--14899 Score: 151
Period size: 35 Copynumber: 2.8 Consensus size: 35
14792 AACAATATTA
* *
14802 GCTCTTCCGGAGCCTTCAATTAAATTTGAATACTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTGAATACTG
* * *
14837 GCTCTTCTGGAGCCTTTAATCAATTTTAAATACTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTGAATACTG
14872 GCTCTTCTGGAGCCTTCAATCAAATTTG
1 GCTCTTCTGGAGCCTTCAATCAAATTTG
14900 CACAATCTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (35 bp):
GCTCTTCTGGAGCCTTCAATCAAATTTGAATACTG
Found at i:16447 original size:36 final size:34
Alignment explanation
Indices: 16364--16464 Score: 136
Period size: 33 Copynumber: 3.0 Consensus size: 34
16354 ATACTATTTC
*
16364 TTTG-ATGTGACAACTTCAGGTGGCACTAATATG
1 TTTGCATGTGACAACTTCAGGTGCCACTAATATG
*
16397 TTTGC-TGTGACAACTTCAAGTGCCACTAATAT-
1 TTTGCATGTGACAACTTCAGGTGCCACTAATATG
16429 TCTTGATCATGTGACAACTTCAGGTGCCACTAATAT
1 T-TTG--CATGTGACAACTTCAGGTGCCACTAATAT
16465 ACAAGGTAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
32 1 0.02
33 32 0.53
35 1 0.02
36 26 0.43
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (34 bp):
TTTGCATGTGACAACTTCAGGTGCCACTAATATG
Found at i:16561 original size:32 final size:33
Alignment explanation
Indices: 16497--16569 Score: 121
Period size: 32 Copynumber: 2.2 Consensus size: 33
16487 ATAATTTTTA
*
16497 ATGATAAAGAAAGGTAGAAGGAGGAGATTATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATTATGC
16530 ATGATAAAGAAAGGTAGAA-GAAGAGATTATGC
1 ATGATAAAGAAAGGTAGAAGGAAGAGATTATGC
*
16562 ATGTTAAA
1 ATGATAAA
16570 TAAACTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 19 0.50
33 19 0.50
ACGTcount: A:0.48, C:0.03, G:0.29, T:0.21
Consensus pattern (33 bp):
ATGATAAAGAAAGGTAGAAGGAAGAGATTATGC
Found at i:17778 original size:50 final size:51
Alignment explanation
Indices: 17709--17805 Score: 178
Period size: 50 Copynumber: 1.9 Consensus size: 51
17699 ATCATACCAC
*
17709 TTTTTTTTAAAAGGTAATTAGATTATAACCATACCACTTTAACATGATCTG
1 TTTTTTTTAAAAGGCAATTAGATTATAACCATACCACTTTAACATGATCTG
17760 TTTTTTTT-AAAGGCAATTAGATTATAACCATACCACTTTAACATGA
1 TTTTTTTTAAAAGGCAATTAGATTATAACCATACCACTTTAACATGA
17806 ACATGAACCG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 37 0.82
51 8 0.18
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (51 bp):
TTTTTTTTAAAAGGCAATTAGATTATAACCATACCACTTTAACATGATCTG
Found at i:20273 original size:28 final size:26
Alignment explanation
Indices: 20216--20276 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
20206 AATATTGTTT
*
20216 AAGAGGTTGGTTGAGATTAAAATTAG
1 AAGAGTTTGGTTGAGATTAAAATTAG
20242 --GAGTTTGGTTGAGATTAAAATTAG
1 AAGAGTTTGGTTGAGATTAAAATTAG
20266 TCAAGAGTTTG
1 --AAGAGTTTG
20277 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 23 0.77
28 7 0.23
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (26 bp):
AAGAGTTTGGTTGAGATTAAAATTAG
Found at i:21669 original size:21 final size:18
Alignment explanation
Indices: 21644--21686 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
21634 TATTATCATG
21644 TTAATTAAAAATCAAATTCTA
1 TTAA-TAAAAAT-AAATTC-A
*
21665 TTAATCAAAATAAATTCA
1 TTAATAAAAATAAATTCA
21683 TTAA
1 TTAA
21687 ACGTAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 6 0.29
21 4 0.19
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAATAAAAATAAATTCA
Found at i:22203 original size:486 final size:486
Alignment explanation
Indices: 21180--22511 Score: 2248
Period size: 486 Copynumber: 2.8 Consensus size: 486
21170 AAACGGTTCC
21180 TTAATTAAAAATCAAATCCTATTAATCAAAATAAATTCATTAAACG-----TAATAT--AATTAT
1 TTAATTAAAAATCAAATCCTATTAATCAAAATAAATTCATTAAACGTAATATAATATAAAATTAT
*
21238 CGTGTGCTTTTCAATTTATATATATCTCACACACTAG----------TA---T-TTCGATTTGTA
66 CGTGTGCTTTTCAATTTATATATATCTCACACACTAGTATTAACTTATATTGTATTCAATTTGTA
* *
21289 AAAAAATATCAAGTATATTTTCTAATTTGTTGAAATTTTGTATTTTGATCCTTATTTGAGAAAAT
131 AAAAAATATTAAGTATATTTTCTAATTTGTTGAAATTTTATATTTTGATCCTTATTTGAGAAAAT
* * *
21354 CTTGAAACATTTAGTCCTTATTTTAGCATTTACTCGCAACAACCGGGCTTATTTGGA-TTTTTTT
196 CTTGAAACATTTAGTCCTTATTTTAGCATTTAGTCGCAGCAACAGGGCTTATTTGGACTTTTTTT
21418 AAGA-TTT-CAGGAGCTTATTTGGCCAAAATAAAAGTTTAGGGGCTTATTTGATGGTTCGATGTA
261 AAGAGTTTAC-GG-GCTTATTTGGCCAAAATAAAAGTTTAGGGGCTTATTTGATGGTTCGATGTA
* *
21481 AGTTTAGGGGCATTTTTGCTCGTTAAGCCATTTTATAAATGTTACAAGTAATTTCTTATAGAACA
324 AGTTTAGGAGCCTTTTTGCTCGTTAAGCCATTTTATAAATGTTACAAGTAATTTCTTATAGAACA
21546 CATACTTAGCAAATTTTTACAAATTAGGGAATCCTTAAATGAAAACCAATGCTTTTCATGCATAC
389 CATACTTAGCAAATTTTTACAAATTAGGGAATCCTTAAATGAAAACCAATGCTTTTCATGCATAC
*
21611 ACGTTAAATTTGATAGAAAATGATATTATCATG
454 ACATTAAATTTGATAGAAAATGATATTATCATG
* *
21644 TTAATTAAAAATCAAATTCTATTAATCAAAATAAATTCATTAAACGTAATATAATATAAAACTAT
1 TTAATTAAAAATCAAATCCTATTAATCAAAATAAATTCATTAAACGTAATATAATATAAAATTAT
*
21709 CATGTGCTTTTCAATTTATATATATCTCACACACTAGTATTAACTTATATTGTATTCAATTTGTA
66 CGTGTGCTTTTCAATTTATATATATCTCACACACTAGTATTAACTTATATTGTATTCAATTTGTA
21774 AAAAAATATTAAGTATATTTTCTAATTTGTTGAAATTTTATATTTTGATCCTTATTTGAGAAAAT
131 AAAAAATATTAAGTATATTTTCTAATTTGTTGAAATTTTATATTTTGATCCTTATTTGAGAAAAT
* *
21839 CTTGAAACATTTAGTCCTTATTTTACCATTTAGTCACAGCAACAGGGCTTATTTGGACTTTTTTT
196 CTTGAAACATTTAGTCCTTATTTTAGCATTTAGTCGCAGCAACAGGGCTTATTTGGACTTTTTTT
*
21904 AAGAGTTTACGGGCTTATTTGACCAAAATAAAAGTTTAGGGGCTTATTTGATGGTTCGATGTAAG
261 AAGAGTTTACGGGCTTATTTGGCCAAAATAAAAGTTTAGGGGCTTATTTGATGGTTCGATGTAAG
21969 TTTAGGAGCCTTTTTGCTCGTTAAGCCATTTTATAAATGTTACAAGTAATTTCTTATAGAACACA
326 TTTAGGAGCCTTTTTGCTCGTTAAGCCATTTTATAAATGTTACAAGTAATTTCTTATAGAACACA
22034 TACTTAGCAAATTTTTACAAATTAGGGAATCCTTAAATGAAAACCAATGCTTTTCATGCATACAC
391 TACTTAGCAAATTTTTACAAATTAGGGAATCCTTAAATGAAAACCAATGCTTTTCATGCATACAC
22099 ATTAAATTTGATAGAAAATGATATTATCATG
456 ATTAAATTTGATAGAAAATGATATTATCATG
22130 TTAATTAAAAATCAAATCCTATTAATCAAAATAAATTCATTAAACGTAATATAATATAAAATTAT
1 TTAATTAAAAATCAAATCCTATTAATCAAAATAAATTCATTAAACGTAATATAATATAAAATTAT
22195 CGTGTGCTTTTCAATTTATATATATCTCACACACTAGTATTAACTTATATTGTATTCAATTTGTA
66 CGTGTGCTTTTCAATTTATATATATCTCACACACTAGTATTAACTTATATTGTATTCAATTTGTA
* *
22260 AAAAAATATTAAGTATATTTTCTAATTTGTTGAAATTTTTTATTTTAATCCTTATTTGAGAAAAT
131 AAAAAATATTAAGTATATTTTCTAATTTGTTGAAATTTTATATTTTGATCCTTATTTGAGAAAAT
*
22325 CTTGAAAGATTTAGTCCTTATTTTAGCATTTAGTCGCAGCAACAGGGCTTATTTGGAC-TTTTTT
196 CTTGAAACATTTAGTCCTTATTTTAGCATTTAGTCGCAGCAACAGGGCTTATTTGGACTTTTTTT
* * * * *
22389 AAGTGTTCAGGGGCTTATTTGGCCAAAATAAAAGTTTAGGGGCTTATTTGATGATTTGATGTAAG
261 AAGAGTTTACGGGCTTATTTGGCCAAAATAAAAGTTTAGGGGCTTATTTGATGGTTCGATGTAAG
22454 TTTA-GAGGCCTTTTTGCTCGTTAAGCCATTTTATAAATGTTACAAGTAATTTCTTATA
326 TTTAGGA-GCCTTTTTGCTCGTTAAGCCATTTTATAAATGTTACAAGTAATTTCTTATA
22512 TATACAATAT
Statistics
Matches: 814, Mismatches: 29, Indels: 29
0.93 0.03 0.03
Matches are distributed among these distances:
464 45 0.06
469 6 0.01
471 41 0.05
481 2 0.00
484 3 0.00
485 245 0.30
486 466 0.57
487 5 0.01
488 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (486 bp):
TTAATTAAAAATCAAATCCTATTAATCAAAATAAATTCATTAAACGTAATATAATATAAAATTAT
CGTGTGCTTTTCAATTTATATATATCTCACACACTAGTATTAACTTATATTGTATTCAATTTGTA
AAAAAATATTAAGTATATTTTCTAATTTGTTGAAATTTTATATTTTGATCCTTATTTGAGAAAAT
CTTGAAACATTTAGTCCTTATTTTAGCATTTAGTCGCAGCAACAGGGCTTATTTGGACTTTTTTT
AAGAGTTTACGGGCTTATTTGGCCAAAATAAAAGTTTAGGGGCTTATTTGATGGTTCGATGTAAG
TTTAGGAGCCTTTTTGCTCGTTAAGCCATTTTATAAATGTTACAAGTAATTTCTTATAGAACACA
TACTTAGCAAATTTTTACAAATTAGGGAATCCTTAAATGAAAACCAATGCTTTTCATGCATACAC
ATTAAATTTGATAGAAAATGATATTATCATG
Found at i:24030 original size:12 final size:12
Alignment explanation
Indices: 24013--24070 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
24003 TTTATATAAA
*
24013 ATATAATTATAT
1 ATATAAATATAT
* *
24025 ATATAAATAAAA
1 ATATAAATATAT
*
24037 ATATAATTATTAT
1 ATATAAATA-TAT
24050 ATATATAATATAT
1 ATATA-AATATAT
24063 AATATAAA
1 -ATATAAA
24071 CGAACATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
12 17 0.47
13 11 0.31
14 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATAAATATAT
Found at i:24066 original size:27 final size:27
Alignment explanation
Indices: 24006--24069 Score: 98
Period size: 24 Copynumber: 2.5 Consensus size: 27
23996 TTTAATATTT
24006 ATATAAAATATAATTA-TATATATA-A
1 ATATAAAATATAATTATTATATATATA
24031 ATA-AAAATATAATTATTATATATATA
1 ATATAAAATATAATTATTATATATATA
*
24057 ATATATAATATAA
1 ATATAAAATATAA
24070 ACGAACATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
24 12 0.34
25 11 0.31
26 4 0.11
27 8 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATAAAATATAATTATTATATATATA
Found at i:30364 original size:21 final size:20
Alignment explanation
Indices: 30322--30364 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
30312 ATACTTATTG
* *
30322 AAAAGAAAGCAATTAAACTA
1 AAAACAAAGCAAGTAAACTA
*
30342 AAAACAAAGCAAAGTAAATTA
1 AAAACAAAGC-AAGTAAACTA
30363 AA
1 AA
30365 TCTAAATCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.14
Consensus pattern (20 bp):
AAAACAAAGCAAGTAAACTA
Found at i:33312 original size:93 final size:90
Alignment explanation
Indices: 33176--33362 Score: 275
Period size: 93 Copynumber: 2.0 Consensus size: 90
33166 GTTTTCAGAT
* * * *
33176 GTGGCAGAGTACGATAAAAGATGTGTTAGTACAACAACGATTGGGAGATGCGTTTGAGACTGATA
1 GTGGCAAAGTACCATAAAAGATGTATTAGTACAACAACGATTGGGAGATGCGTTTGAAACTGATA
*
33241 AGCCTACAGTGCTAAACGAGAACAA
66 AGCCTACAGGGCTAAACGAGAACAA
33266 GTGGCAAAGTACCATAAAAGATGTAATATTAGTACAACAACGATTGGGAGATGCGTTTGAAACTG
1 GTGGCAAAGTACCATAAAAGATG---TATTAGTACAACAACGATTGGGAGATGCGTTTGAAACTG
* * *
33331 ATAAGCCTGCAGGGCTGAACGAGAACAG
63 ATAAGCCTACAGGGCTAAACGAGAACAA
33359 GTGG
1 GTGG
33363 AGAGATATTC
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 21 0.24
93 65 0.76
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.21
Consensus pattern (90 bp):
GTGGCAAAGTACCATAAAAGATGTATTAGTACAACAACGATTGGGAGATGCGTTTGAAACTGATA
AGCCTACAGGGCTAAACGAGAACAA
Found at i:34983 original size:26 final size:26
Alignment explanation
Indices: 34932--34985 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
34922 CTTTGTTGTT
34932 TTCATTTTAATTATTTGTTTGGTTAA
1 TTCATTTTAATTATTTGTTTGGTTAA
34958 TTCATTTTAATTATTTGTTTGGTTAA
1 TTCATTTTAATTATTTGTTTGGTTAA
34984 TT
1 TT
34986 TCTGGAATAT
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:0.22, C:0.04, G:0.11, T:0.63
Consensus pattern (26 bp):
TTCATTTTAATTATTTGTTTGGTTAA
Found at i:36457 original size:7 final size:7
Alignment explanation
Indices: 36445--36471 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
36435 TCATTTAATT
36445 TTTGCAA
1 TTTGCAA
36452 TTTGCAA
1 TTTGCAA
36459 TTTGCAA
1 TTTGCAA
36466 TTTGCA
1 TTTGCA
36472 TGCATGTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (7 bp):
TTTGCAA
Found at i:41417 original size:6 final size:6
Alignment explanation
Indices: 41408--41433 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41398 ATAGTTAGGG
41408 TTTGGC TTTGGC TTTGGC TTTGGC TT
1 TTTGGC TTTGGC TTTGGC TTTGGC TT
41434 GGAAGGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.31, T:0.54
Consensus pattern (6 bp):
TTTGGC
Found at i:42631 original size:14 final size:14
Alignment explanation
Indices: 42596--42633 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
42586 GAATCTTAGA
*
42596 TGTTTGAGCCAGTT
1 TGTTTGAGTCAGTT
42610 TAGTTTGAGTCAGTT
1 T-GTTTGAGTCAGTT
42625 TGTTTGAGT
1 TGTTTGAGT
42634 TTACAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.16, C:0.08, G:0.29, T:0.47
Consensus pattern (14 bp):
TGTTTGAGTCAGTT
Found at i:43744 original size:39 final size:39
Alignment explanation
Indices: 43655--43744 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 39
43645 ACCAAGACAC
* * *
43655 AACACCAAGGACCAGGCCAGCACACCCCAGGAACCAACA
1 AACACCAAGTACCAGCCCAGCACACCCCAGGAAACAACA
**
43694 AACACTGAGTACCAGCCCAGCACACCCCAGGAAACAACA
1 AACACCAAGTACCAGCCCAGCACACCCCAGGAAACAACA
43733 AACACCAAGTAC
1 AACACCAAGTAC
43745 TAGGGGACCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.42, C:0.39, G:0.16, T:0.03
Consensus pattern (39 bp):
AACACCAAGTACCAGCCCAGCACACCCCAGGAAACAACA
Found at i:45899 original size:43 final size:43
Alignment explanation
Indices: 45852--45939 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
45842 AATTCAATGA
* * *
45852 TTATTTGTGTAATTTACTCGTTATTCCTCTATCTTCAAAATCT
1 TTATTTGTGTAATTTACTCGCTATTCCTCCACCTTCAAAATCT
*
45895 TTATTTGTGTAATTTACTCGCTATTCCTCCACCTTTAAAATCT
1 TTATTTGTGTAATTTACTCGCTATTCCTCCACCTTCAAAATCT
45938 TT
1 TT
45940 GAAAAAAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (43 bp):
TTATTTGTGTAATTTACTCGCTATTCCTCCACCTTCAAAATCT
Found at i:46557 original size:17 final size:17
Alignment explanation
Indices: 46509--46559 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
46499 ATTTTTGGAT
*
46509 TATATATAAAAATATAA
1 TATATATAATAATATAA
*
46526 T-TGATAGT-ATCATATAA
1 TAT-ATA-TAATAATATAA
46543 TATATATAATAATATAA
1 TATATATAATAATATAA
46560 ATAGATCGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
16 2 0.07
17 23 0.85
18 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (17 bp):
TATATATAATAATATAA
Found at i:46703 original size:206 final size:208
Alignment explanation
Indices: 46331--46741 Score: 729
Period size: 214 Copynumber: 2.0 Consensus size: 208
46321 ATTATATATA
46331 ATATATAATATATAAATAGATCGTCAACTCTACTTTCAAAATACAATAAAATCTCATGACAAGTA
1 ATATATAATATATAAATAGATCGTCAACTCTACTTTCAAAATACAATAAAATCTCATGACAAGTA
*
46396 AGTAATATTTGCACTTCGAATTAATCTAATTTTCTAAGCCATTAGTTAGGTACTCATGCATTCTT
66 AGTAATATTTGCACTTCGAATTAATCGAATTTTCTAAGCC--TAG-T--GTACTCATGCATTCTT
46461 CATTAGATATTAAAATAAAAGAATAATTAGGAGTATCAATTTTTGGATTATATATAAAAATATAA
126 CATTAGATATTAAAATAAAAGAATAATTAGGAGTATCAATTTTTGGATTATATATAAAAATATAA
46526 TTGATAGTATCATATAAT
191 TTGATAGTATCATATAAT
46544 ATATATAATAATATAAATAGATCGTCAACTCTACTTTCAAAATACAATAAAATCTCATGACAAGT
1 ATATATAAT-ATATAAATAGATCGTCAACTCTACTTTCAAAATACAATAAAATCTCATGACAAGT
*
46609 AAGTAATATTTGCACTTCGACTTAATCGAATTTTCTAAGCC-A-T-TACTCATGCATTCTTCATT
65 AAGTAATATTTGCACTTCGAATTAATCGAATTTTCTAAGCCTAGTGTACTCATGCATTCTTCATT
46671 AGATATTAAAATAAAAGAATAATTAGGAGTATCAATTTTTGGATTATATATAAAAATATAATTGA
130 AGATATTAAAATAAAAGAATAATTAGGAGTATCAATTTTTGGATTATATATAAAAATATAATTGA
46736 TAGTAT
195 TAGTAT
46742 GATTGTAATT
Statistics
Matches: 195, Mismatches: 2, Indels: 9
0.95 0.01 0.04
Matches are distributed among these distances:
206 90 0.46
209 1 0.01
211 1 0.01
213 9 0.05
214 94 0.48
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (208 bp):
ATATATAATATATAAATAGATCGTCAACTCTACTTTCAAAATACAATAAAATCTCATGACAAGTA
AGTAATATTTGCACTTCGAATTAATCGAATTTTCTAAGCCTAGTGTACTCATGCATTCTTCATTA
GATATTAAAATAAAAGAATAATTAGGAGTATCAATTTTTGGATTATATATAAAAATATAATTGAT
AGTATCATATAAT
Found at i:49585 original size:20 final size:20
Alignment explanation
Indices: 49562--49605 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
49552 GTTATAGGTC
**
49562 ATGGCTTGAGGGTTTAGGAA
1 ATGGCTTGAGGAATTAGGAA
*
49582 ATGGCTTTAGGAATTAGGAA
1 ATGGCTTGAGGAATTAGGAA
49602 ATGG
1 ATGG
49606 GTATTGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (20 bp):
ATGGCTTGAGGAATTAGGAA
Found at i:50704 original size:21 final size:22
Alignment explanation
Indices: 50678--50785 Score: 74
Period size: 22 Copynumber: 4.5 Consensus size: 22
50668 AAAAAGTTAA
* *
50678 AAAAGAGAGAGAG-AGAAAAAT
1 AAAAGAAAGAAAGTAGAAAAAT
50699 AAAAGAAAGAAAGTAGAAAAAGTT
1 AAAAGAAAGAAAGTAGAAAAA--T
50723 AAAAAGAAAGAAAGAGATTGAGAAAAAAT
1 -AAAAGAAAG-AA-AG--T-AG-AAAAAT
* *
50752 AAAACAAAGAAAGTACAAAAAGTT
1 AAAAGAAAGAAAGTAGAAAAA--T
50776 AAAAGAAAGA
1 AAAAGAAAGA
50786 GAAAGAGAGA
Statistics
Matches: 70, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
21 11 0.16
22 12 0.17
23 1 0.01
24 12 0.17
25 9 0.13
26 4 0.06
27 4 0.06
28 8 0.11
29 2 0.03
30 2 0.03
31 5 0.07
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (22 bp):
AAAAGAAAGAAAGTAGAAAAAT
Found at i:50726 original size:29 final size:29
Alignment explanation
Indices: 50694--50802 Score: 88
Period size: 29 Copynumber: 3.9 Consensus size: 29
50684 GAGAGAGAGA
50694 AAAATAAAAGAAAGAAAGTAGAAAAAGTT
1 AAAATAAAAGAAAGAAAGTAGAAAAAGTT
* * *
50723 AAAA-AGAAAGAAAGAGA-TTG-AGAA---
1 AAAATA-AAAGAAAGAAAGTAGAAAAAGTT
* *
50747 AAAATAAAACAAAGAAAGTACAAAAAGTT
1 AAAATAAAAGAAAGAAAGTAGAAAAAGTT
* *
50776 AAAAGAAAGAGAAAGAGAG-AGAAAAAG
1 AAAATAAA-AGAAAGAAAGTAGAAAAAG
50803 AGAGAGAGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
24 13 0.22
25 2 0.03
26 3 0.05
27 3 0.05
28 3 0.05
29 28 0.47
30 8 0.13
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (29 bp):
AAAATAAAAGAAAGAAAGTAGAAAAAGTT
Found at i:50778 original size:24 final size:24
Alignment explanation
Indices: 50661--50785 Score: 107
Period size: 25 Copynumber: 5.0 Consensus size: 24
50651 ACTAAAAACA
50661 AAAGTAGAAAAAGTTAAAA-AAGAG
1 AAAGTAGAAAAAGTTAAAAGAA-AG
50685 AGAGAG-AGAAAAA--TAAAAGAAAG
1 A-A-AGTAGAAAAAGTTAAAAGAAAG
50708 AAAGTAGAAAAAGTTAAAAAGAAAG
1 AAAGTAGAAAAAGTT-AAAAGAAAG
* *
50733 AAAGAGATTGAGAAAAA-ATAAAACAAAG
1 -AA-AG--T-AGAAAAAGTTAAAAGAAAG
*
50761 AAAGTACAAAAAGTTAAAAGAAAG
1 AAAGTAGAAAAAGTTAAAAGAAAG
50785 A
1 A
50786 GAAAGAGAGA
Statistics
Matches: 83, Mismatches: 5, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
21 2 0.02
22 8 0.10
23 14 0.17
24 15 0.18
25 17 0.20
26 6 0.07
27 4 0.05
28 8 0.10
29 2 0.02
30 7 0.08
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.10
Consensus pattern (24 bp):
AAAGTAGAAAAAGTTAAAAGAAAG
Found at i:50780 original size:52 final size:50
Alignment explanation
Indices: 50661--50801 Score: 189
Period size: 53 Copynumber: 2.8 Consensus size: 50
50651 ACTAAAAACA
* *
50661 AAAGTAGAAAAAGTT-AAA-AAAGAGAGAGAGAG-AAAAATAAAAGAAAG
1 AAAGTAGAAAAAGTTAAAAGAAAGAAAGAGAGAGAAAAAATAAAACAAAG
50708 AAAGTAGAAAAAGTTAAAAAGAAAGAAAGAGATTGAGAAAAAATAAAACAAAG
1 AAAGTAGAAAAAGTT-AAAAGAAAGAAAGAGA--GAGAAAAAATAAAACAAAG
*
50761 AAAGTACAAAAAGTTAAAAGAAAGAGAAAGAGAGAGAAAAA
1 AAAGTAGAAAAAGTTAAAAG-AA-AGAAAGAGAGAGAAAAA
50802 GAGAGAGAGA
Statistics
Matches: 83, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
47 15 0.18
49 3 0.04
50 10 0.12
52 16 0.19
53 30 0.36
54 9 0.11
ACGTcount: A:0.68, C:0.01, G:0.21, T:0.09
Consensus pattern (50 bp):
AAAGTAGAAAAAGTTAAAAGAAAGAAAGAGAGAGAAAAAATAAAACAAAG
Found at i:50798 original size:16 final size:17
Alignment explanation
Indices: 50778--50816 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
50768 AAAAAGTTAA
*
50778 AAGAAAGAGAAAGAGAG
1 AAGAAAAAGAAAGAGAG
*
50795 -AGAAAAAGAGAGAGAG
1 AAGAAAAAGAAAGAGAG
50811 AAGAAA
1 AAGAAA
50817 CAAAAAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAGAGAG
Done.