Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011905.1 Corchorus capsularis cultivar CVL-1 contig11926, 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: 14655
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:55 original size:22 final size:22
Alignment explanation
Indices: 27--115 Score: 67
Period size: 22 Copynumber: 4.0 Consensus size: 22
17 TGTCTCTATG
27 TGGTTATCAAAATTTAATAAGA
1 TGGTTATCAAAATTTAATAAGA
* * * *
49 TGGTTATTACAATTTCATGAGGA
1 TGGTTATCAAAATTTAAT-AAGA
*
72 -GGTTATCAAAA-TTACAT-AGTG
1 TGGTTATCAAAATTTA-ATAAG-A
* *
93 TGGTTACCAAAATTTCATAAGA
1 TGGTTATCAAAATTTAATAAGA
115 T
1 T
116 CAGGTTATGA
Statistics
Matches: 49, Mismatches: 12, Indels: 12
0.67 0.16 0.16
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 39 0.80
23 7 0.14
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTAATAAGA
Found at i:181 original size:19 final size:20
Alignment explanation
Indices: 154--191 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
144 TACTATTATT
154 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
174 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
192 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:382 original size:22 final size:22
Alignment explanation
Indices: 357--459 Score: 68
Period size: 22 Copynumber: 4.6 Consensus size: 22
347 TGTCTCTATG
357 TGGTTATCAAAATTTAATAAGA
1 TGGTTATCAAAATTTAATAAGA
* * * *
379 TGGTTATTACAATTTCATGAGGA
1 TGGTTATCAAAATTTAAT-AAGA
*
402 -GGTTATCAAAA-TTACAT-AGTG
1 TGGTTATCAAAATTTA-ATAAG-A
* *
423 TGGTTACCAAAATTTCATAAGA
1 TGGTTATCAAAATTTAATAAGA
*
445 TCAGGTTATTAAAAT
1 T--GGTTATCAAAAT
460 CTCTTAGGTC
Statistics
Matches: 59, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
20 1 0.02
21 2 0.03
22 39 0.66
23 7 0.12
24 10 0.17
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTAATAAGA
Found at i:476 original size:22 final size:21
Alignment explanation
Indices: 356--495 Score: 66
Period size: 22 Copynumber: 6.3 Consensus size: 21
346 TTGTCTCTAT
* * *
356 GTGGTTATCAAAATTTAATAAG
1 GTGGTTATTAAAATCTCAT-AG
* * *
378 ATGGTTATTACAATTTCATGAG
1 GTGGTTATTAAAATCTCAT-AG
* *
400 GAGGTTATCAAAAT-TACATAG
1 GTGGTTATTAAAATCT-CATAG
** *
421 TGTGGTTACCAAAATTTCATAAG
1 -GTGGTTATTAAAATCTCAT-AG
* *
444 ATCAGGTTATTAAAATCTCTTAG
1 GT--GGTTATTAAAATCTCATAG
* *
467 GTCGGTTATTGAAATTTCATAG
1 GT-GGTTATTAAAATCTCATAG
489 GTGGTTA
1 GTGGTTA
496 ATTATCACAA
Statistics
Matches: 91, Mismatches: 21, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
21 8 0.09
22 64 0.70
23 6 0.07
24 13 0.14
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.37
Consensus pattern (21 bp):
GTGGTTATTAAAATCTCATAG
Found at i:577 original size:56 final size:56
Alignment explanation
Indices: 517--645 Score: 138
Period size: 56 Copynumber: 2.3 Consensus size: 56
507 TTTACAGAAA
517 GGTTATCAAAGAGATT-ATCAAA-ATGTCATAGCGAGGTTAT-AAGAATTTCATAGTGT
1 GGTTATCAAA-A-ATTCATCAAATATGTCATAGCGAGGTTATCAA-AATTTCATAGTGT
* * * * * * *
573 GGTTAACAAAATTTCATTAAATATTTCATGGGGAGGTTATCAAAATTTTATAGTGT
1 GGTTATCAAAAATTCATCAAATATGTCATAGCGAGGTTATCAAAATTTCATAGTGT
*
629 GGTTATCAAAATTTCAT
1 GGTTATCAAAAATTCAT
646 ATGAAGGTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
54 2 0.03
55 6 0.10
56 52 0.84
57 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (56 bp):
GGTTATCAAAAATTCATCAAATATGTCATAGCGAGGTTATCAAAATTTCATAGTGT
Found at i:654 original size:22 final size:22
Alignment explanation
Indices: 595--940 Score: 73
Period size: 22 Copynumber: 15.5 Consensus size: 22
585 TTCATTAAAT
* *
595 ATTTCATGGGGAGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
* *
617 ATTTTATAGTGTGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
639 ATTTCATA-TGAAGGTTAT-AAA
1 ATTTCATAGTG-AGGTTATCAAA
* * * *
660 AGTCTCAATTTCA-TAAGGAGTACCAAA
1 A-TTTC-A--T-AGTGAGG-TTATCAAA
* * *
687 ATTTGATA-TAAGGTTATC-CA
1 ATTTCATAGTGAGGTTATCAAA
* * * * *
707 ATCTCATAGAGTGATTATCGAA
1 ATTTCATAGTGAGGTTATCAAA
*
729 ATTTCATAGAGATCGGATTATCAAA
1 ATTTCATAGTGA--GG-TTATCAAA
* *
754 ATTT-ATAG-GAAGATTGTCAAA
1 ATTTCATAGTG-AGGTTATCAAA
* *
775 AGTTTCATAG-CATTGTTATCAAA
1 A-TTTCATAGTGA-GGTTATCAAA
* * *
798 ATTTCAAAGCGAGATTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
* * * *
820 ATTACATAATGTGATTAT-AAGA
1 ATTTCATAGTGAGGTTATCAA-A
** * * *
842 ATTTCATAAAGGGGTCAACAAA
1 ATTTCATAGTGAGGTTATCAAA
* ** *
864 ATTTTATAAAGAGGTCATCAAA
1 ATTTCATAGTGAGGTTATCAAA
* ** *
886 TTTTCATAAAGAGGTTACCAAA
1 ATTTCATAGTGAGGTTATCAAA
* * * * *
908 TTTTCAAAATGTGATTA-CAAAA
1 ATTTCATAGTGAGGTTATC-AAA
930 ATTTCATAGTG
1 ATTTCATAGTG
941 GTATTTCTGA
Statistics
Matches: 242, Mismatches: 61, Indels: 42
0.70 0.18 0.12
Matches are distributed among these distances:
20 7 0.03
21 26 0.11
22 159 0.66
23 18 0.07
24 6 0.02
25 16 0.07
26 6 0.02
27 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
ATTTCATAGTGAGGTTATCAAA
Found at i:1048 original size:19 final size:19
Alignment explanation
Indices: 1018--1065 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1008 TTATGGAGTA
1018 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
*
1038 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
1057 ATCAAAATT
1 ATCAAAATT
1066 TCATGTGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:1084 original size:22 final size:22
Alignment explanation
Indices: 1018--1505 Score: 271
Period size: 22 Copynumber: 22.5 Consensus size: 22
1008 TTATGGAGTA
*
1018 ATCAAAATTTCA-AG-GAGGAT
1 ATCAAAATTTCATAGTGAGGTT
* *
1038 ATCAAAA-TTC--AGGGAGGAT
1 ATCAAAATTTCATAGTGAGGTT
1057 ATCAAAATTTCAT-GTGAAGGTT
1 ATCAAAATTTCATAGTG-AGGTT
*
1079 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-TGAGGTT
* * *
1101 TTCAAAATTTCACA-AGAGGGTT
1 ATCAAAATTTCATAGTGA-GGTT
* *
1123 ATCAAAATTTCATAGT-ATGTAG
1 ATCAAAATTTCATAGTGAGGT-T
* * *
1145 ATCAAAATGTCATAGGGAGATT
1 ATCAAAATTTCATAGTGAGGTT
* *
1167 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
** *
1189 ATCAAAAAAATCATAGGGAGGTT
1 ATC-AAAATTTCATAGTGAGGTT
1212 ATCAAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGTGAGGTT
* * *
1228 ATCAAGATTTCATAAG-AAAGTT
1 ATCAAAATTTCAT-AGTGAGGTT
* *
1250 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGTGAGG-TT
*
1273 ATCAAAATTTCATAG-GAAGATTT
1 ATCAAAATTTCATAGTG-AG-GTT
*
1296 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* * *
1318 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
* * *
1340 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
* *
1362 ACTGACAA-TTCATA-TGGAGGTT
1 A-TCAAAATTTCATAGT-GAGGTT
* * * ** *
1384 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGTGAGGTT
* **
1406 ATCAATATACCATA-TGGAGGTT
1 ATCAAAATTTCATAGT-GAGGTT
* * *
1428 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGTG-AGGTT
* * *
1451 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGTGAGGTT
*
1473 ATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATAGTGAGGT-T
1496 -TCAAAATTTC
1 ATCAAAATTTC
1506 GAGGTTAACT
Statistics
Matches: 359, Mismatches: 76, Indels: 64
0.72 0.15 0.13
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 3 0.01
19 18 0.05
20 11 0.03
21 13 0.04
22 218 0.61
23 82 0.23
24 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGAGGTT
Found at i:1218 original size:45 final size:44
Alignment explanation
Indices: 1119--1221 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 44
1109 TTCACAAGAG
* * **
1119 GGTTATCAAAATTTCATAGTATGTAGATCAAAATGTCATAGGGA
1 GGTTATCAAAATTTCATAATAGGTAGATCAAAAAATCATAGGGA
* * *
1163 GATTAACAAAATTTCATAATGAGGT-TATCAAAAAAATCATAGGGA
1 GGTTATCAAAATTTCATAAT-AGGTAGATC-AAAAAATCATAGGGA
1208 GGTTATCAAAATTT
1 GGTTATCAAAATTT
1222 GTAGTTATCA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
44 20 0.42
45 28 0.58
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATAGGTAGATCAAAAAATCATAGGGA
Found at i:1320 original size:45 final size:45
Alignment explanation
Indices: 955--1505 Score: 271
Period size: 44 Copynumber: 12.8 Consensus size: 45
945 TTCTGAGGAG
955 GTTATCAAAATTTCATAGT-ATGGTTATC-AAA--T--TAGGAAG-
1 GTTATCAAAATTTCATAGTGA-GGTTATCAAAATTTCATAGGAAGA
* * *
994 GTTAT-AAACTTTTATTA-TG-GAGTAATCAAAATTTCA-AGG-AG-
1 GTTATCAAAATTTCA-TAGTGAG-GTTATCAAAATTTCATAGGAAGA
* * *
1035 GATATCAAAA-TTC--AGGGAGGATATCAAAATTTCAT-GTGAAG-
1 GTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAG-GAAGA
* * * * *
1076 GTTATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCACAAG-AGG
1 GTTATCAAAATTTCATAG-TGAGGTTATCAAAATTTCATAGGAAGA
* * * *
1120 GTTATCAAAATTTCATAGT-ATGTAGATCAAAATGTCATAGGGAGA
1 GTTATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAGGAAGA
* * ** *
1165 -TTAACAAAATTTCATAATGAGGTTATCAAAAAAATCATAGGGAG-
1 GTTATCAAAATTTCATAGTGAGGTTATC-AAAATTTCATAGGAAGA
* *
1209 GTTATCAAAA-TT--T-GT-A-GTTATCAAGATTTCATAAGAA-A
1 GTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAGA
* *
1247 GTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTCATAGGAAGA
1 GTTATCAAAATTTCATAGTGAGG-TTATCAAAATTTCATAGGAAGA
* * * *
1293 TTTATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTG-TGA
1 GTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAG-GAAGA
* * * * *
1338 -TTATCAAAATTTCAGAGTGTGATTACTGACAA-TTCATATGG-AG-
1 GTTATCAAAATTTCATAGTGAGGTTA-TCAAAATTTCATA-GGAAGA
* * * ** * * **
1381 GTTTTTAAATTTTCATAACGTGGTTATCAATATACCATATGG-AG-
1 GTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA-GGAAGA
* * * * *
1425 GTTATCAACATCTCATAGTGTTGGTTATCAAAATTTCATTGGGA-A
1 GTTATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATAGGAAGA
*
1470 GTTATCAAAATTTCATATTGAGGTCT-TCAAAATTTC
1 GTTATCAAAATTTCATAGTGAGGT-TATCAAAATTTC
1506 GAGGTTAACT
Statistics
Matches: 392, Mismatches: 76, Indels: 83
0.71 0.14 0.15
Matches are distributed among these distances:
37 1 0.00
38 34 0.09
39 33 0.08
40 3 0.01
41 22 0.06
42 12 0.03
43 9 0.02
44 152 0.39
45 104 0.27
46 22 0.06
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (45 bp):
GTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAGA
Found at i:1638 original size:158 final size:159
Alignment explanation
Indices: 1470--1802 Score: 616
Period size: 159 Copynumber: 2.1 Consensus size: 159
1460 TCATTGGGAA
1470 GTTATCAAAATTTCATATTGAGGTCTTCAAAATTTCGAGGTTAACTAAATTTCATAAGAAGGTTA
1 GTTATCAAAATTTCATATTGAGGTCTTCAAAATTTCGAGGTTAACTAAATTTCATAAGAAGGTT-
1535 AAAAAAAATTATAACAATTCATAT-G-GGTTTTTAAATTTTCATAACGTGGTTATCAATATACCA
65 AAAAAAAATTATAACAATTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATACCA
1598 TATGGAAGTTATCAACATCTCATAGTGTTG
130 TATGGAAGTTATCAACATCTCATAGTGTTG
1628 GTTATCAAAATTTCATATTGAGGTCTTCAAAATTTCGAGGTTAACTAAATTTCATAAGAAGGTTA
1 GTTATCAAAATTTCATATTGAGGTCTTCAAAATTTCGAGGTTAACTAAATTTCATAAGAAGGTTA
* *
1693 AAAAAATTTATAACAATTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTATTAATATACCAT
66 AAAAAAATTATAACAATTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATACCAT
1758 ATGGAAGTTATCAACATCTCATAGTGTTG
131 ATGGAAGTTATCAACATCTCATAGTGTTG
*
1787 GTTATTAAAATTTCAT
1 GTTATCAAAATTTCAT
1803 TGGAAAGTTA
Statistics
Matches: 170, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
157 23 0.14
158 65 0.38
159 82 0.48
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (159 bp):
GTTATCAAAATTTCATATTGAGGTCTTCAAAATTTCGAGGTTAACTAAATTTCATAAGAAGGTTA
AAAAAAATTATAACAATTCATATGGAGGTTTTTAAATTTTCATAACGTGGTTATCAATATACCAT
ATGGAAGTTATCAACATCTCATAGTGTTG
Found at i:1699 original size:22 final size:21
Alignment explanation
Indices: 1665--1705 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1655 CAAAATTTCG
**
1665 AGGTTAACTAAATTTCATAAGA
1 AGGTTAAAAAAATTT-ATAAGA
1687 AGGTTAAAAAAATTTATAA
1 AGGTTAAAAAAATTTATAA
1706 CAATTCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (21 bp):
AGGTTAAAAAAATTTATAAGA
Found at i:1811 original size:45 final size:45
Alignment explanation
Indices: 1740--1825 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
1730 TTTCATAACG
* *
1740 TGGTTATTAATATACCATATGGAAGTTATCAACATCTCATAGTGT
1 TGGTTATTAAAATACCATATGGAAGTTATCAAAATCTCATAGTGT
** *
1785 TGGTTATTAAAATTTCAT-TGGAAAGTTATCAAAATTTCATA
1 TGGTTATTAAAATACCATATGG-AAGTTATCAAAATCTCATA
1826 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (45 bp):
TGGTTATTAAAATACCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:3501 original size:112 final size:112
Alignment explanation
Indices: 3304--3527 Score: 421
Period size: 112 Copynumber: 2.0 Consensus size: 112
3294 TAGCGCGAAG
* *
3304 TAACCGTCTTGTAGTAATATTATTATTAACCCCTTACAACAAGGACAAGGAAGGCAACATTATAA
1 TAACCCTCTTGTAGTAATATTATTATTAACCCCTTAAAACAAGGACAAGGAAGGCAACATTATAA
3369 ATCATCATGGATCAATATTGCCTTTTATTCCAACATCAAAAGCAAAC
66 ATCATCATGGATCAATATTGCCTTTTATTCCAACATCAAAAGCAAAC
*
3416 TAACCCTCTTGTAGTACTATTATTATTAACCCCTTAAAACAAGGACAAGGAAGGCAACATTATAA
1 TAACCCTCTTGTAGTAATATTATTATTAACCCCTTAAAACAAGGACAAGGAAGGCAACATTATAA
3481 ATCATCATGGATCAATATTGCCTTTTATTCCAACATCAAAAGCAAAC
66 ATCATCATGGATCAATATTGCCTTTTATTCCAACATCAAAAGCAAAC
3528 AAAGGACGAC
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (112 bp):
TAACCCTCTTGTAGTAATATTATTATTAACCCCTTAAAACAAGGACAAGGAAGGCAACATTATAA
ATCATCATGGATCAATATTGCCTTTTATTCCAACATCAAAAGCAAAC
Found at i:4448 original size:3 final size:3
Alignment explanation
Indices: 4442--4476 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4432 ATTTTTTTTA
4442 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4477 ATTTAATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4633 original size:24 final size:23
Alignment explanation
Indices: 4580--4634 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
4570 GCTATATTAT
* *
4580 ATATATATATATATTATTTAGAA
1 ATATATAGATATATTATTTACAA
4603 ATAATATAGATATATGTA-TTACATA
1 AT-ATATAGATATAT-TATTTACA-A
4628 ATATATA
1 ATATATA
4635 TACCATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 2 0.07
24 20 0.74
25 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
ATATATAGATATATTATTTACAA
Found at i:4970 original size:23 final size:23
Alignment explanation
Indices: 4940--4985 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
4930 ATACCTTACT
4940 ATTAAAAGTATCCTCAAATTGCA
1 ATTAAAAGTATCCTCAAATTGCA
4963 ATTAAAAGTATCCTCAAATTGCA
1 ATTAAAAGTATCCTCAAATTGCA
4986 TGCTGACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (23 bp):
ATTAAAAGTATCCTCAAATTGCA
Found at i:6591 original size:16 final size:16
Alignment explanation
Indices: 6572--6618 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
6562 GTCAGGTTCA
6572 GGTTAAATTTGGGTCG
1 GGTTAAATTTGGGTCG
* *
6588 GGTT-GATTCGGGTTCG
1 GGTTAAATTTGGG-TCG
*
6604 AGTTAAATTTGGGTC
1 GGTTAAATTTGGGTC
6619 AAATTGATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.17, C:0.09, G:0.36, T:0.38
Consensus pattern (16 bp):
GGTTAAATTTGGGTCG
Found at i:6609 original size:32 final size:32
Alignment explanation
Indices: 6573--6667 Score: 118
Period size: 32 Copynumber: 3.0 Consensus size: 32
6563 TCAGGTTCAG
*
6573 GTTAAATTTGGGTCGGGTTGATTCGGGTTCGA
1 GTTAAATTTGGGTCAGGTTGATTCGGGTTCGA
** *
6605 GTTAAATTTGGGTCAAATTGATTCGGGTTCGG
1 GTTAAATTTGGGTCAGGTTGATTCGGGTTCGA
* * * *
6637 GTCAATTTTAGGTCAGGTTAATTCGGGTTCG
1 GTTAAATTTGGGTCAGGTTGATTCGGGTTCG
6668 GACTCGGATT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.19, C:0.11, G:0.33, T:0.38
Consensus pattern (32 bp):
GTTAAATTTGGGTCAGGTTGATTCGGGTTCGA
Found at i:6844 original size:20 final size:20
Alignment explanation
Indices: 6811--6849 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6801 CATATATGAA
*
6811 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
6831 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
6850 GAATTCAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:6880 original size:22 final size:22
Alignment explanation
Indices: 6852--6895 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6842 TTAGTATTGA
6852 ATTCAGGCTTTTTCAGGTTCGG
1 ATTCAGGCTTTTTCAGGTTCGG
* *
6874 ATTCAGGTTTTTTCGGGTTCGG
1 ATTCAGGCTTTTTCAGGTTCGG
6896 GTTTCTTCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.30, T:0.43
Consensus pattern (22 bp):
ATTCAGGCTTTTTCAGGTTCGG
Found at i:6898 original size:16 final size:16
Alignment explanation
Indices: 6869--6956 Score: 61
Period size: 16 Copynumber: 5.5 Consensus size: 16
6859 CTTTTTCAGG
* *
6869 TTCGGATTCAGGTTTT
1 TTCGGGTTCGGGTTTT
*
6885 TTCGGGTTCGGGTTTC
1 TTCGGGTTCGGGTTTT
* *
6901 TTCGGGTTTC-AGATTT
1 TTCGGG-TTCGGGTTTT
* *
6917 TTCGGGTTCTGATTTT
1 TTCGGGTTCGGGTTTT
* * * *
6933 TTTGAGTTTGGGCTTT
1 TTCGGGTTCGGGTTTT
6949 TTCGGGTT
1 TTCGGGTT
6957 TGGGCGGGTT
Statistics
Matches: 53, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
15 3 0.06
16 47 0.89
17 3 0.06
ACGTcount: A:0.07, C:0.12, G:0.30, T:0.51
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:7532 original size:66 final size:67
Alignment explanation
Indices: 7418--7577 Score: 241
Period size: 66 Copynumber: 2.4 Consensus size: 67
7408 TTGCCCGTAA
* * *
7418 AATACTAGCAAACTCCCACGTGATCAGACATCTAGAGACTTGTGTAAGAATTGATGGGCAATTCA
1 AATACTAGCAAACTCCCA--TG-TGAGACACCTAGAGACTTGTCTAAGAATTGATGGGCAATTCA
7483 GATAT
63 GATAT
*
7488 AAT-GTAGCAAACTCCCATGTGAGACACCTAGAGACTTGTCTAAGAATTGATGGGCAATTCAGAT
1 AATACTAGCAAACTCCCATGTGAGACACCTAGAGACTTGTCTAAGAATTGATGGGCAATTCAGAT
7552 AT
66 AT
*
7554 AATACTAGCAGACTCCCATGTGAG
1 AATACTAGCAAACTCCCATGTGAG
7578 TTGTGACACC
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
66 47 0.57
67 20 0.24
69 13 0.16
70 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (67 bp):
AATACTAGCAAACTCCCATGTGAGACACCTAGAGACTTGTCTAAGAATTGATGGGCAATTCAGAT
AT
Found at i:14407 original size:17 final size:17
Alignment explanation
Indices: 14385--14421 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
14375 TACTGCCTCC
14385 GATTCATAATTTTAAGT
1 GATTCATAATTTTAAGT
14402 GATTCATAATTTTAAGT
1 GATTCATAATTTTAAGT
14419 GAT
1 GAT
14422 ACACTACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (17 bp):
GATTCATAATTTTAAGT
Done.