Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009216.1 Corchorus capsularis cultivar CVL-1 contig09237, 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: 129507
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:204 original size:22 final size:22
Alignment explanation
Indices: 176--315 Score: 104
Period size: 22 Copynumber: 6.3 Consensus size: 22
166 TGTCTCTATG
*
176 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* * *
198 TGGTTATTATAAGTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* *
221 -GGTTATCAAAATTCCGTAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
242 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * * *
264 TCAAGTTATTAAAAATTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
**
288 TGGTTATTGAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
310 TGGTTA
1 TGGTTA
316 ATTATCACAA
Statistics
Matches: 89, Mismatches: 23, Indels: 12
0.72 0.19 0.10
Matches are distributed among these distances:
21 3 0.03
22 67 0.75
23 3 0.03
24 16 0.18
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:536 original size:23 final size:23
Alignment explanation
Indices: 508--587 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
498 CAGAAGAAAG
508 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
531 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
554 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
576 TTATCACAATTT
1 TTATCAAAATTT
588 CATTGTGTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 11 0.22
23 39 0.78
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:586 original size:22 final size:21
Alignment explanation
Indices: 507--790 Score: 90
Period size: 22 Copynumber: 12.8 Consensus size: 21
497 TCAGAAGAAA
*
507 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATA-GGAG
*
529 GTTTATCAAAATTTTATAGGAAG
1 G-TTATCAAAATTTCATAGG-AG
*
552 ATTTATCAAAATTTCATAGCGAG
1 -GTTATCAAAATTTCATAG-GAG
* * *
575 GTTATCACAATTTCATTGTGTG
1 GTTATCAAAATTTCATAG-GAG
** * *
597 ACTATCAAAATTTCAGAGTGTG
1 GTTATCAAAATTTCATAG-GAG
*
619 ATTA-CTAACAA-TTCATATGGAG
1 GTTATC-AA-AATTTCATA-GGAG
* * * *
641 GTTTTTAAATTTTCATAACGTA-
1 GTTATCAAAATTTCAT-A-GGAG
* * * *
663 ATTATCAATATATCATATAGAG
1 GTTATCAAAATTTCATA-GGAG
* * *
685 GTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATAG-G-AG
* * *
708 GTTATCAAAATTTTATTGGGAA
1 GTTATCAAAATTTCA-TAGGAG
*
730 GTTATCAAAATTTCATATTGAG
1 GTTATCAAAATTTCATA-GGAG
* * *
752 GTCT-TAAAAATTCCTTAGGGAG
1 GT-TATCAAAATTTCATA-GGAG
* *
774 GTTAACCAAATTTCATA
1 GTTATCAAAATTTCATA
791 AGAAGATTAA
Statistics
Matches: 190, Mismatches: 55, Indels: 34
0.68 0.20 0.12
Matches are distributed among these distances:
21 6 0.03
22 124 0.65
23 57 0.30
24 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGAG
Found at i:5037 original size:22 final size:22
Alignment explanation
Indices: 5012--6010 Score: 253
Period size: 22 Copynumber: 45.7 Consensus size: 22
5002 ATGATCCCAT
5012 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** *
5034 TATGAAATTTT-ATTAACGATAC
1 TATGAAATTTTGA-TAACCTTCC
* * * **
5056 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** ** *
5078 TAT-AAATTTTTTTTAATGTTCT
1 TATGAAA-TTTTGATAACCTTCC
*
5100 TATGAAATTTTGTTAACCTTTCC
1 TATGAAATTTTGATAACC-TTCC
* *
5123 TATAGGAATTTTGA-AGACC-TCAA
1 TAT-GAAATTTTGATA-ACCTTC-C
5146 TATGAAATTTTGATAA-CTTCTC
1 TATGAAATTTTGATAACCTTC-C
* * **
5168 AATAAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
5191 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
5212 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
5235 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
5256 ATATG-AATTGTT-AGTAATCACATT--
1 -TATGAAATT-TTGA-TAA-C-C-TTCC
5280 T-TGAAATTTTGATAATCAC-T-C
1 TATGAAATTTTGATAA-C-CTTCC
* *
5301 TGTGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
5323 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
5346 TATAAAATTTTGATAAACTTTCCC
1 TATGAAATTTTGAT-AACCTT-CC
* * *
5370 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
5392 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
5409 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
5430 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* *
5452 TATGAAATTTTGTTAA-TTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * *
5474 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
5496 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
5518 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
5540 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
5562 TATGAAA-TTT-ATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
5581 -CTGAAATTTTGATTA-C-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
5600 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* *
5624 T-T---A-TTTGGTAA-CTATAC
1 TATGAAATTTTGATAACCT-TCC
*
5641 TATGAAATTTTGATAACC-TCTT
1 TATGAAATTTTGATAACCTTC-C
* *
5663 TATAAAATTTTGTTAACC--CC
1 TATGAAATTTTGATAACCTTCC
** *
5683 TTTATGAAATTCCGATAATCACAT--
1 --TATGAAATTTTGATAA-C-CTTCC
*
5707 TAT-ATAATTTTGATTACC-TCGC
1 TATGA-AATTTTGATAACCTTC-C
* **
5729 TTTGAAATTTTGATAA-CAACGC
1 TATGAAATTTTGATAACCTTC-C
* *
5751 TATGAAA-TTTGATAATCTTTC
1 TATGAAATTTTGATAACCTTCC
**
5772 TAT-AAATTTTGATAATTCGATCTC
1 TATGAAATTTTGATAA--CCTTC-C
* *
5796 TGTGAAATTTCGATAATCAC-T-C
1 TATGAAATTTTGATAA-C-CTTCC
5818 TATGAAA-TTTGATAACCTT-C
1 TATGAAATTTTGATAACCTTCC
* *
5838 TATCAAATTTTGGT-A--TTCC
1 TATGAAATTTTGATAACCTTCC
* **
5857 TTATGAAATTGGGACTTTATAACCTTTA
1 -TATGAAATT-----TTGATAACCTTCC
* *
5885 TATGAAATTTTGATAACCATAC
1 TATGAAATTTTGATAACCTTCC
* *
5907 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
5929 CATGAAATATT-AGTAAAC-TCC
1 TATGAAATTTTGA-TAACCTTCC
* * * *
5950 TAATGAAATTTTGTTTACCATAC
1 T-ATGAAATTTTGATAACCTTCC
*
5973 TATGAAATTCTT-ATAACC-TCGT
1 TATGAAATT-TTGATAACCTTC-C
*
5995 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
6011 TCTCTTTGAT
Statistics
Matches: 717, Mismatches: 165, Indels: 190
0.67 0.15 0.18
Matches are distributed among these distances:
16 13 0.02
17 11 0.02
18 9 0.01
19 12 0.02
20 32 0.04
21 67 0.09
22 421 0.59
23 85 0.12
24 40 0.06
25 14 0.02
26 2 0.00
27 9 0.01
28 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:5376 original size:24 final size:23
Alignment explanation
Indices: 5322--5407 Score: 104
Period size: 23 Copynumber: 3.7 Consensus size: 23
5312 GATAACCTCG
*
5322 CTATGAAATTTTGATAAA-TCTTC
1 CTATAAAATTTTGATAAACT-TTC
5345 CTATAAAATTTTGATAAACTTTCC
1 CTATAAAATTTTGATAAACTTT-C
5369 CTATAAAATTTTGAT-AACTTTC
1 CTATAAAATTTTGATAAACTTTC
* * *
5391 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
5408 CTACAAATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.23
23 26 0.46
24 17 0.30
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACTTTC
Found at i:5774 original size:21 final size:21
Alignment explanation
Indices: 5750--5847 Score: 92
Period size: 21 Copynumber: 4.5 Consensus size: 21
5740 GATAACAACG
*
5750 CTATGAAATTTGATAATCTTT
1 CTATGAAATTTGATAATCTCT
5771 CTAT-AAATTTTGATAATTCGATCT
1 CTATGAAA-TTTGATAA-TC--TCT
* *
5795 CTGTGAAATTTCGATAATCACT
1 CTATGAAATTT-GATAATCTCT
*
5817 CTATGAAATTTGATAACCT-T
1 CTATGAAATTTGATAATCTCT
*
5837 CTATCAAATTT
1 CTATGAAATTT
5848 TGGTATTCCT
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
20 14 0.22
21 18 0.28
22 14 0.22
24 10 0.16
25 8 0.12
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (21 bp):
CTATGAAATTTGATAATCTCT
Found at i:6074 original size:25 final size:23
Alignment explanation
Indices: 6046--6096 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
6036 TTGTGATAAT
6046 TAACCACATCCCTATGAAATTTTGG
1 TAACC-CA-CCCTATGAAATTTTGG
*
6071 TAA-CCACGCTATGAAATTTTGG
1 TAACCCACCCTATGAAATTTTGG
6093 TAAC
1 TAAC
6097 TACCTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 18 0.75
23 2 0.08
24 1 0.04
25 3 0.12
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (23 bp):
TAACCCACCCTATGAAATTTTGG
Found at i:8712 original size:20 final size:18
Alignment explanation
Indices: 8675--8721 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
8665 TTATTAGTAA
8675 ATTAGTAAATATTTATTT
1 ATTAGTAAATATTTATTT
*
8693 ATTAGTATATACTATTATTT
1 ATTAGTAAATA-T-TTATTT
8713 ATTAGTAAA
1 ATTAGTAAA
8722 ACATATCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.40
19 1 0.04
20 14 0.56
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (18 bp):
ATTAGTAAATATTTATTT
Found at i:10481 original size:2 final size:2
Alignment explanation
Indices: 10474--10507 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10464 TTACTTTGTC
10474 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
10508 TCAATTGACT
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:16352 original size:23 final size:23
Alignment explanation
Indices: 16322--16368 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
16312 ATAAAGAGCT
*
16322 TTATTTAATGCCTACATGCAAAA
1 TTATTTAATGCCTACAAGCAAAA
*
16345 TTATTTAATGGCTACAAGCAAAA
1 TTATTTAATGCCTACAAGCAAAA
16368 T
1 T
16369 CAAATTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (23 bp):
TTATTTAATGCCTACAAGCAAAA
Found at i:26357 original size:13 final size:14
Alignment explanation
Indices: 26333--26368 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
26323 AAAAACTTGG
26333 TTTTGAAGAAGTG-T
1 TTTTGAA-AAGTGTT
26347 TTTTGAAAAGTGTT
1 TTTTGAAAAGTGTT
26361 TTTTGAAA
1 TTTTGAAA
26369 TTGAGCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TTTTGAAAAGTGTT
Found at i:37990 original size:7 final size:7
Alignment explanation
Indices: 37975--38008 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
37965 CTGCAAAGTC
*
37975 CAAAGTT
1 CAAACTT
37982 CAAACTT
1 CAAACTT
37989 CAAACTT
1 CAAACTT
37996 CAAACTT
1 CAAACTT
38003 CAAACT
1 CAAACT
38009 ATTACTAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.44, C:0.26, G:0.03, T:0.26
Consensus pattern (7 bp):
CAAACTT
Found at i:37992 original size:21 final size:21
Alignment explanation
Indices: 37968--38008 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
37958 GAGTACACTG
* *
37968 CAAAGTCCAAAGTTCAAACTT
1 CAAACTCCAAACTTCAAACTT
*
37989 CAAACTTCAAACTTCAAACT
1 CAAACTCCAAACTTCAAACT
38009 ATTACTAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (21 bp):
CAAACTCCAAACTTCAAACTT
Found at i:42639 original size:36 final size:36
Alignment explanation
Indices: 42592--42663 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
42582 CCTCTTTTTC
42592 TTTTTCTTCCTTTTGAGTTTAATGGTTATAGTGGAA
1 TTTTTCTTCCTTTTGAGTTTAATGGTTATAGTGGAA
42628 TTTTTCTTCCTTTTGAGTTTAATGGTTATAGTGGAA
1 TTTTTCTTCCTTTTGAGTTTAATGGTTATAGTGGAA
42664 GATATTTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.53
Consensus pattern (36 bp):
TTTTTCTTCCTTTTGAGTTTAATGGTTATAGTGGAA
Found at i:45156 original size:19 final size:20
Alignment explanation
Indices: 45115--45158 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
45105 CCTTAACGTG
*
45115 TAATTATTTTATTTGACTTA
1 TAATTAATTTATTTGACTTA
45135 TAATTAATTT-TTTG-CTTGA
1 TAATTAATTTATTTGACTT-A
45154 TAATT
1 TAATT
45159 GTAACTCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 10 0.45
20 9 0.41
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (20 bp):
TAATTAATTTATTTGACTTA
Found at i:63769 original size:36 final size:36
Alignment explanation
Indices: 63722--63793 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
63712 ATATATATGG
63722 GGAAAGGAATAGAAACCAAACCATTACATCAATTAA
1 GGAAAGGAATAGAAACCAAACCATTACATCAATTAA
63758 GGAAAGGAATAGAAACCAAACCATTACATCAATTAA
1 GGAAAGGAATAGAAACCAAACCATTACATCAATTAA
63794 TATTTATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.17
Consensus pattern (36 bp):
GGAAAGGAATAGAAACCAAACCATTACATCAATTAA
Found at i:65195 original size:27 final size:29
Alignment explanation
Indices: 65141--65195 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
65131 TTACTCAACT
**
65141 AAAAACTCTATTTTTATTTTTCTGTAAAA
1 AAAAACTCTATTTTTATTTTAATGTAAAA
65170 AAAAACTCTATTTTTA-TTTAAT-TAAA
1 AAAAACTCTATTTTTATTTTAATGTAAA
65196 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 4 0.17
29 16 0.67
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (29 bp):
AAAAACTCTATTTTTATTTTAATGTAAAA
Found at i:73614 original size:12 final size:13
Alignment explanation
Indices: 73576--73619 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
73566 TGGAGTGAGT
73576 GGAAAAGAAGAAA
1 GGAAAAGAAGAAA
* *
73589 GGAAGA-AAGCAA
1 GGAAAAGAAGAAA
*
73601 GGAAAAGAAGAAG
1 GGAAAAGAAGAAA
73614 GGAAAA
1 GGAAAA
73620 CTGAAAAGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (13 bp):
GGAAAAGAAGAAA
Found at i:74229 original size:21 final size:22
Alignment explanation
Indices: 74194--74234 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
74184 GGCATTCAAG
*
74194 TTACAGTGGACAATTTTAAAGT
1 TTACAGTGGACAATTGTAAAGT
*
74216 TTACAGTGTA-AATTGTAAA
1 TTACAGTGGACAATTGTAAA
74235 ATGAGTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (22 bp):
TTACAGTGGACAATTGTAAAGT
Found at i:84661 original size:50 final size:50
Alignment explanation
Indices: 84602--84704 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
84592 TAGCCCAACA
84602 AAATATTTACTATTGTCGTGTTGCATTTCCCCTGTTTTCTTCAGCCAAGG
1 AAATATTTACTATTGTCGTGTTGCATTTCCCCTGTTTTCTTCAGCCAAGG
84652 AAATATTTACTATTGTCGTGTTGCATTTCCCCTGTTTTCTTCAGCCAAGG
1 AAATATTTACTATTGTCGTGTTGCATTTCCCCTGTTTTCTTCAGCCAAGG
84702 AAA
1 AAA
84705 GCAGAAGACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (50 bp):
AAATATTTACTATTGTCGTGTTGCATTTCCCCTGTTTTCTTCAGCCAAGG
Found at i:90406 original size:3 final size:3
Alignment explanation
Indices: 90398--90428 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
90388 CCAGGGCTTA
*
90398 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
90429 GCAACAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:92125 original size:66 final size:66
Alignment explanation
Indices: 92014--92292 Score: 364
Period size: 66 Copynumber: 4.2 Consensus size: 66
92004 TTATCGGTTT
* * * * * **
92014 ATGTTGGTTTTGTGGCCTAAAAGATTTGAAATTG-GTGCACAATTTGCAGTCCACTAAGACTTGC
1 ATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGAG-GCATAATTTGCAGTCCACCGAGACTTGC
92078 AA
65 AA
92080 ATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGAGGCATAATTTGCAGTCCACCGAGACTTGCA
1 ATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGAGGCATAATTTGCAGTCCACCGAGACTTGCA
92145 A
66 A
* * * *
92146 ATGTCGGTTTTGTGGGTTAAGAGGTTTGAAACTGAATGCATAATTTGCAGTCCAACCGAGACCTG
1 ATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTG-AGGCATAATTTGCAGTCC-ACCGAGACTTG
92211 CAA
64 CAA
* * * *
92214 ATGTTGGGTTTT-TGGCTTAAGAGGTTTAAAATTGATGCATAATTTGCAGTCCACTGAGACTTGC
1 ATG-TCGGTTTTGTGGCTTAAGAGGTTTGAAATTGAGGCATAATTTGCAGTCCACCGAGACTTGC
92278 AA
65 AA
*
92280 ATGTCGATTTTGT
1 ATGTCGGTTTTGT
92293 TTGCAGTCCA
Statistics
Matches: 189, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
65 6 0.03
66 105 0.56
67 36 0.19
68 35 0.19
69 7 0.04
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (66 bp):
ATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGAGGCATAATTTGCAGTCCACCGAGACTTGCA
A
Found at i:92238 original size:134 final size:132
Alignment explanation
Indices: 92014--92292 Score: 380
Period size: 134 Copynumber: 2.1 Consensus size: 132
92004 TTATCGGTTT
* * * * *
92014 ATGTTGGTTTTGTGGCCTAAAAGATTTGAAATTGGTGCACAATTTGCAGTCCACTAAGACTTGCA
1 ATGTCGGTTTTGTGGCCTAAAAGATTTGAAACTGATGCACAATTTGCAGTCCACCAAGACCTGCA
*
92079 AATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGAGGCATAATTTGCAGTCCACCGAGACTTGC
66 AATGTCGGTTTTGTGGCTTAAGAGGTTTAAAATTGAGGCATAATTTGCAGTCCACCGAGACTTGC
92144 AA
131 AA
** * * * *
92146 ATGTCGGTTTTGTGGGTTAAGAGGTTTGAAACTGAATGCATAATTTGCAGTCCAACCGAGACCTG
1 ATGTCGGTTTTGTGGCCTAAAAGATTTGAAACTG-ATGCACAATTTGCAGTCC-ACCAAGACCTG
* * *
92211 CAAATGTTGGGTTTT-TGGCTTAAGAGGTTTAAAATTGATGCATAATTTGCAGTCCACTGAGACT
64 CAAATG-TCGGTTTTGTGGCTTAAGAGGTTTAAAATTGAGGCATAATTTGCAGTCCACCGAGACT
92275 TGCAA
128 TGCAA
*
92280 ATGTCGATTTTGT
1 ATGTCGGTTTTGT
92293 TTGCAGTCCA
Statistics
Matches: 128, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
132 28 0.22
133 16 0.12
134 77 0.60
135 7 0.05
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (132 bp):
ATGTCGGTTTTGTGGCCTAAAAGATTTGAAACTGATGCACAATTTGCAGTCCACCAAGACCTGCA
AATGTCGGTTTTGTGGCTTAAGAGGTTTAAAATTGAGGCATAATTTGCAGTCCACCGAGACTTGC
AA
Found at i:92303 original size:36 final size:36
Alignment explanation
Indices: 92256--92328 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
92246 TGATGCATAA
92256 TTTGCAGTCCACTGAGACTTGCAAATGTCGATTTTG
1 TTTGCAGTCCACTGAGACTTGCAAATGTCGATTTTG
*
92292 TTTGCAGTCCACTGAGACTTGCAAATGTCGGTTTTG
1 TTTGCAGTCCACTGAGACTTGCAAATGTCGATTTTG
92328 T
1 T
92329 GGCTTAAGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (36 bp):
TTTGCAGTCCACTGAGACTTGCAAATGTCGATTTTG
Found at i:92379 original size:102 final size:103
Alignment explanation
Indices: 92189--92394 Score: 335
Period size: 102 Copynumber: 2.0 Consensus size: 103
92179 GAATGCATAA
*
92189 TTTGCAGTCCAACCGAGACCTGCAAATGTTGGGTTTTTGGCTTAAGAGGTTTAAAATTGATGCAT
1 TTTGCAGTCCAACCGAGACCTGCAAATGTTCGGTTTTTGGCTTAAGAGGTTTAAAATTGATGCAT
92254 AATTTGCAGTCCACTGAGACTTGCAAATGTCGATTTTG
66 AATTTGCAGTCCACTGAGACTTGCAAATGTCGATTTTG
* * *
92292 TTTGCAGTCC-ACTGAGACTTGCAAATG-TCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCA
1 TTTGCAGTCCAACCGAGACCTGCAAATGTTCGGTTTT-TGGCTTAAGAGGTTTAAAATTGATGCA
* *
92355 TAATTTGCAGTCCACTGAGACTTGCAATTGTCGGTTTTG
65 TAATTTGCAGTCCACTGAGACTTGCAAATGTCGATTTTG
92394 T
1 T
92395 GGCTTAAGAG
Statistics
Matches: 96, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
101 7 0.07
102 79 0.82
103 10 0.10
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (103 bp):
TTTGCAGTCCAACCGAGACCTGCAAATGTTCGGTTTTTGGCTTAAGAGGTTTAAAATTGATGCAT
AATTTGCAGTCCACTGAGACTTGCAAATGTCGATTTTG
Found at i:92398 original size:66 final size:66
Alignment explanation
Indices: 92292--92705 Score: 596
Period size: 66 Copynumber: 6.3 Consensus size: 66
92282 GTCGATTTTG
92292 TTTGCAGTCCACTGAGACTTGCAAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATA
1 TTTGCAGTCCACTGAGACTTGCAAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATA
92357 A
66 A
*
92358 TTTGCAGTCCACTGAGACTTGCAATTGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATA
1 TTTGCAGTCCACTGAGACTTGCAAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATA
92423 A
66 A
* * * * * * *
92424 TTTGCAGTACAATAAGACTTGCAATTGTCGGTTTTGTGGCCTACGAGGTTTGACATTGATGCATA
1 TTTGCAGTCCACTGAGACTTGCAAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATA
*
92489 G
66 A
* **
92490 TTTGCAGTCCACTGAGACTTGCCAATGTCGGTTTTGTGGCTTAAGATCTTTGAAATTGATGCATA
1 TTTGCAGTCCACTGAGACTTGCAAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATA
92555 A
66 A
* * * * * * * *
92556 TTTGCA-TACACTAAGACTTGCAAATGTTGGTTTTGTGACCTATGAAGTTTGAAATTGATGCACA
1 TTTGCAGTCCACTGAGACTTGCAAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATA
92620 A
66 A
* * * *
92621 TTTGCAGTCCACTTAGACTTGCAAAAGTCAGTTTTGTGGCTTAAGAGGTTTAAAATTGATGCATA
1 TTTGCAGTCCACTGAGACTTGCAAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATA
92686 A
66 A
92687 TTTGCAGTCCACTTGAGAC
1 TTTGCAGTCCAC-TGAGAC
92706 ATACAAAGCT
Statistics
Matches: 305, Mismatches: 41, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
65 55 0.18
66 245 0.80
67 5 0.02
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.35
Consensus pattern (66 bp):
TTTGCAGTCCACTGAGACTTGCAAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATA
A
Found at i:95232 original size:66 final size:66
Alignment explanation
Indices: 95126--95792 Score: 1001
Period size: 66 Copynumber: 10.0 Consensus size: 66
95116 TCTGGCATCA
**
95126 AAATGTCAATTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
1 AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
95191 C
66 C
** *
95192 AAATGTTTGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTGCACCGAGACTTG
1 AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
95257 C
66 C
* *
95258 AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATCGAGGCATAATTTGCAGTCCACCGAGACTTG
1 AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
95323 C
66 C
* * *
95324 GAATGTCGGTTTTGTGGCTTAAGAGGTAGAGGTTTGAAATTGAGGCATAATTTGCAGTCCACCAA
1 AAATGTCGGTTTTGTGGCTT---A---AGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGA
95389 GACTTGC
60 GACTTGC
* *
95396 AAATGTCAGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAGTTTGCAGTCCACCGAGACTTG
1 AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
95461 C
66 C
*
95462 AAATGTCAGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
1 AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
95527 C
66 C
* * *
95528 AAATGTGGGTTTTCTGGCTTAAGAGGTTTAAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
1 AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
95593 C
66 C
* ** *
95594 AAATGTCGGTTTTGTGGCATAAGAGGTTTGAAATTGATTTATAATTTGCAGTCCACTGAGACTTG
1 AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
95659 C
66 C
* ** **
95660 AAATGTCAGTTTTGTGGCTTAAGAGGTTTGAAATTGATTTATAATTTGCAGTCCACTAAGACTTG
1 AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
95725 C
66 C
* ** * * *
95726 AAATGTCGGTTTTGTGGCCTAAGAGGGCTGAAGTAGATGCATAATTTGCAGTCCACTGAGACTTG
1 AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
95791 C
66 C
95792 A
1 A
95793 TAGGTTAATG
Statistics
Matches: 554, Mismatches: 41, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
66 491 0.89
69 2 0.00
72 61 0.11
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.33
Consensus pattern (66 bp):
AAATGTCGGTTTTGTGGCTTAAGAGGTTTGAAATTGATGCATAATTTGCAGTCCACCGAGACTTG
C
Found at i:118298 original size:19 final size:19
Alignment explanation
Indices: 118274--118310 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
118264 TATATTATTT
118274 TGGCAAGAAAACGTGCTCC
1 TGGCAAGAAAACGTGCTCC
* *
118293 TGGCAAGGAAATGTGCTC
1 TGGCAAGAAAACGTGCTC
118311 TTCATGGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.19
Consensus pattern (19 bp):
TGGCAAGAAAACGTGCTCC
Found at i:119483 original size:16 final size:15
Alignment explanation
Indices: 119456--119486 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
119446 CAGATTGAGA
119456 TATTATTATGATTAT
1 TATTATTATGATTAT
119471 TATTATATATGATTAT
1 TATTAT-TATGATTAT
119487 ATTCATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
TATTATTATGATTAT
Found at i:124133 original size:42 final size:43
Alignment explanation
Indices: 124063--124145 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
124053 CTTAAACGTG
*
124063 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATT
1 TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATT
*
124106 TTAATCGTGT-TCGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATTAC-GACACGAAACACGATAA
124146 GCCAAACACG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 1 0.03
42 26 0.70
43 10 0.27
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATT
Found at i:125514 original size:2 final size:2
Alignment explanation
Indices: 125507--125539 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
125497 TGGAGTAATC
125507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
125540 GCAATGTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.