Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015221.1 Corchorus capsularis cultivar CVL-1 contig15242, 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: 36327
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Found at i:775 original size:69 final size:66
Alignment explanation
Indices: 639--791 Score: 180
Period size: 69 Copynumber: 2.3 Consensus size: 66
629 AAGTTCATAG
*** *
639 GAGGTTATCAAAATTTCATTTGAAGGCTATAAAAATTTCATAGTGCGGTTATCAAAATCTCACAA
1 GAGGTTATCAAAATTTCATGCCAAGGCTATAAAAATTTCATAATGCGGTTATCAAAATCTCACAA
704 T
66 T
* * * * *
705 GAGCTGGTTATCAAAATTTCATGCCAAGGTTATAAAAATTTTATAATGTGGTTATCAAAATTTGA
1 GA---GGTTATCAAAATTTCATGCCAAGGCTATAAAAATTTCATAATGCGGTTATCAAAATCTCA
*
770 TAAT
63 CAAT
*
774 GAGATTATCAAAATTTCA
1 GAGGTTATCAAAATTTCA
792 CACTATGGTT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
66 17 0.23
69 56 0.77
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (66 bp):
GAGGTTATCAAAATTTCATGCCAAGGCTATAAAAATTTCATAATGCGGTTATCAAAATCTCACAA
T
Found at i:930 original size:44 final size:43
Alignment explanation
Indices: 620--944 Score: 207
Period size: 44 Copynumber: 7.4 Consensus size: 43
610 TTGGTATGGA
* * * *
620 GGTTATAAAAAGTTCATAGGAGGTTATCAAAATTTCAT-TTGAA
1 GGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGTG-T
* * * * * *
663 GGCTATAAAAATTTCATAGTGCGGTTATCAAAATCTCACAATGAGCT
1 GGTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCA-TA-GTG-T
* * * *
710 GGTTATCAAAATTTCAT-GCCAAGGTTATAAAAATTTTATAATGT
1 GGTTATCAAAATTTCATAG--GAGGTTATCAAAATTTCATAGTGT
* * * * * *
754 GGTTATCAAAATTTGATAATGAGATTATCAAAATTTCACACTAT
1 GGTTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGTGT
*
798 GGTTATCAAAATTCCATATGGAGGTTA-CAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATA-GGAGGTTATCAAAATTTCATAGTGT
* * * * * *
841 -G---TCAAAATTTAATAGAGAGGGTTCA-CGAAATTACTTAGAGA
1 GGTTATCAAAATTTCATAG-GA-GGTT-ATCAAAATTTCATAGTGT
*
882 GATTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGTGT
* *
926 GATTATCAAAATTTTATAG
1 GGTTATCAAAATTTCATAG
945 TGTTGTTTTT
Statistics
Matches: 214, Mismatches: 51, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
38 1 0.00
39 13 0.06
40 4 0.02
41 12 0.06
42 1 0.00
43 34 0.16
44 102 0.48
45 14 0.07
46 4 0.02
47 29 0.14
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGTGT
Found at i:947 original size:22 final size:22
Alignment explanation
Indices: 541--947 Score: 108
Period size: 22 Copynumber: 18.6 Consensus size: 22
531 ATGTTCTTAT
* *
541 AATTTTATAGTGTGGTTA-CTAA
1 AATTTCATAGTGTGATTATC-AA
**
563 AATTTCATACG-AAGATTATCAA
1 AATTTCATA-GTGTGATTATCAA
* * *
585 AATTTCATGGTGTGCTTACCAA
1 AATTTCATAGTGTGATTATCAA
** *
607 AATTTGGTA-TG-GAGGTTATAAA
1 AATTTCATAGTGTGA--TTATCAA
* * *
629 AAGTTCATAG-GAGGTTATCAA
1 AATTTCATAGTGTGATTATCAA
* * ** *
650 AATTTCAT-TTGAAGGCTATAAA
1 AATTTCATAGTG-TGATTATCAA
* *
672 AATTTCATAGTGCGGTTATCAA
1 AATTTCATAGTGTGATTATCAA
* * * *
694 AATCTCACAATGAGCTGGTTATCAA
1 AATTTCA-TA-GTG-TGATTATCAA
*** * *
719 AATTTCAT-GCCAAGGTTATAAA
1 AATTTCATAG-TGTGATTATCAA
* * *
741 AATTTTATAATGTGGTTATCAA
1 AATTTCATAGTGTGATTATCAA
* * *
763 AATTTGATAATGAGATTATCAA
1 AATTTCATAGTGTGATTATCAA
* * * *
785 AATTTCACACTATGGTTATCAA
1 AATTTCATAGTGTGATTATCAA
*
807 AATTCCATA-TG-GAGGTTA-CAA
1 AATTTCATAGTGTGA--TTATCAA
828 AATTTCATAGTGTG----TCAA
1 AATTTCATAGTGTGATTATCAA
* * * * *
846 AATTTAATAGAGAGGGTTCA-CGA
1 AATTTCATAGTG-TGATT-ATCAA
* * * *
869 AATTACTTAGAGAGATTATCAA
1 AATTTCATAGTGTGATTATCAA
* *
891 AATTTCATAAG-GAGGTTATCAA
1 AATTTCAT-AGTGTGATTATCAA
913 AATTTCATAGTGTGATTATCAA
1 AATTTCATAGTGTGATTATCAA
*
935 AATTTTATAGTGT
1 AATTTCATAGTGT
948 TGTTTTTCAG
Statistics
Matches: 282, Mismatches: 74, Indels: 58
0.68 0.18 0.14
Matches are distributed among these distances:
18 13 0.05
19 1 0.00
20 2 0.01
21 32 0.11
22 197 0.70
23 20 0.07
24 2 0.01
25 15 0.05
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
AATTTCATAGTGTGATTATCAA
Found at i:1309 original size:22 final size:21
Alignment explanation
Indices: 1292--1376 Score: 100
Period size: 23 Copynumber: 3.9 Consensus size: 21
1282 AAATTTCCTA
1292 AGGAGGTTATCAAAA-TTTAT
1 AGGAGGTTATCAAAATTTTAT
*
1312 AGGGAGGTTTATCATAATTTTAT
1 A-GGAGG-TTATCAAAATTTTAT
1335 AGGAAGGTTTATCAAAATTTTAT
1 AGG-AGG-TTATCAAAATTTTAT
*
1358 AGTGAGGTTATCACAATTT
1 AG-GAGGTTATCAAAATTT
1377 CCTAGTGTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.02
21 5 0.09
22 21 0.37
23 29 0.51
24 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (21 bp):
AGGAGGTTATCAAAATTTTAT
Found at i:1383 original size:22 final size:21
Alignment explanation
Indices: 1272--1377 Score: 88
Period size: 22 Copynumber: 4.7 Consensus size: 21
1262 CAAAATTTGT
*
1272 GGTTATCAGAAAATTTCCTAAGGA
1 GGTTATC--AAAATTTCAT-AGGA
1296 GGTTATCAAAATTT-ATAGGGA
1 GGTTATCAAAATTTCATA-GGA
* *
1317 GGTTTATCATAATTTTATAGGAA
1 GG-TTATCAAAATTTCATAGG-A
*
1340 GGTTTATCAAAATTTTATAGTGA
1 GG-TTATCAAAATTTCATAG-GA
*
1363 GGTTATCACAATTTC
1 GGTTATCAAAATTTC
1378 CTAGTGTGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.01
21 6 0.08
22 31 0.43
23 26 0.36
24 8 0.11
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:1511 original size:22 final size:22
Alignment explanation
Indices: 1476--1555 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
1466 CATCTCACAG
1476 GTTATCAAAATTTCATAGTGAA
1 GTTATCAAAATTTCATAGTGAA
* *
1498 GTTATTAAAGTTTCATAGT---
1 GTTATCAAAATTTCATAGTGAA
*
1517 GTTATCAAAATTCCAT--TGAA
1 GTTATCAAAATTTCATAGTGAA
1537 TGATTATCAAAATTTCATA
1 -G-TTATCAAAATTTCATA
1556 AGAAAGTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
17 1 0.02
19 13 0.28
21 1 0.02
22 31 0.67
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAA
Found at i:1553 original size:41 final size:40
Alignment explanation
Indices: 1476--1555 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 40
1466 CATCTCACAG
* * *
1476 GTTATCAAAATTTCATAGTGAAGTTATTAAAGTTTCATAGT
1 GTTATCAAAATTCCATA-TGAAGTTATCAAAATTTCATAGT
1517 GTTATCAAAATTCCAT-TGAATGATTATCAAAATTTCATA
1 GTTATCAAAATTCCATATGAA-G-TTATCAAAATTTCATA
1556 AGAAAGTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 4 0.12
40 1 0.03
41 29 0.85
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (40 bp):
GTTATCAAAATTCCATATGAAGTTATCAAAATTTCATAGT
Found at i:2377 original size:32 final size:33
Alignment explanation
Indices: 2341--2418 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
2331 TGAGGTAGAT
*
2341 AAACGCCGCTATTTAGTGGCG-TTTGAGTACAG
1 AAACGCCGCTATTTAGCGGCGTTTTGAGTACAG
* ** ** *
2373 AAACGCCACTAAATAGCGGCGTTTTTTGTACGG
1 AAACGCCGCTATTTAGCGGCGTTTTGAGTACAG
2406 AAACGCCGCTATT
1 AAACGCCGCTATT
2419 CCAAAATCAA
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
32 17 0.49
33 18 0.51
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (33 bp):
AAACGCCGCTATTTAGCGGCGTTTTGAGTACAG
Found at i:3739 original size:145 final size:146
Alignment explanation
Indices: 3510--3790 Score: 474
Period size: 145 Copynumber: 1.9 Consensus size: 146
3500 TAAATGAAGA
* * *
3510 AGGTTATACTAATCTTCTTATTCAAGGTTACTAAAAAAAATGCTATAGTTAACAATTAGAAGATT
1 AGGTTATACCAATCTTCTTATTCAAGGTTACTAAAAAAAATGCAATAGTTAACAATTAAAAGATT
* * *
3575 GAGATACTAGCTATTAGCTAATTTAATTTGTATCCTTACATTAGTTACCAATTTTTTTATATAAG
66 GAGATACTAGCTATTAGCTAAGTTAATTTGTAACCTTACATTAGTTACCAATTTTCTTATATAAG
3640 ATTATTCAGAAACTGT
131 ATTATTCAGAAACTGT
* *
3656 AGGTTATACCAATCTTCTTATTCAAGGTTACTAAAAAAAA-GCAATGGTTAACATTTAAAAGATT
1 AGGTTATACCAATCTTCTTATTCAAGGTTACTAAAAAAAATGCAATAGTTAACAATTAAAAGATT
*
3720 GAGATGCTAGCTATTAGCTAAGTTAATTTGTAACCTTACATTAGTTACCAATTTTCTTATATAAG
66 GAGATACTAGCTATTAGCTAAGTTAATTTGTAACCTTACATTAGTTACCAATTTTCTTATATAAG
3785 ATTATT
131 ATTATT
3791 AAAAAATTGT
Statistics
Matches: 126, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
145 87 0.69
146 39 0.31
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (146 bp):
AGGTTATACCAATCTTCTTATTCAAGGTTACTAAAAAAAATGCAATAGTTAACAATTAAAAGATT
GAGATACTAGCTATTAGCTAAGTTAATTTGTAACCTTACATTAGTTACCAATTTTCTTATATAAG
ATTATTCAGAAACTGT
Found at i:4996 original size:21 final size:21
Alignment explanation
Indices: 4961--5003 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4951 TTTTCTATCT
*
4961 AAGGTTACTAAAAAAGTAATA
1 AAGGTTACTAAAAAAATAATA
4982 AAGGTTA-TAAAAAAAATAATA
1 AAGGTTACT-AAAAAAATAATA
5003 A
1 A
5004 TGCTATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGGTTACTAAAAAAATAATA
Found at i:4999 original size:18 final size:20
Alignment explanation
Indices: 4961--5000 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4951 TTTTCTATCT
4961 AAGGTTACTAAAAAAGTAATA
1 AAGGTTACTAAAAAAG-AATA
4982 AAGGTTA-TAAAAAA-AATA
1 AAGGTTACTAAAAAAGAATA
5000 A
1 A
5001 TAATGCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.23
Consensus pattern (20 bp):
AAGGTTACTAAAAAAGAATA
Found at i:8682 original size:166 final size:166
Alignment explanation
Indices: 8476--8791 Score: 533
Period size: 166 Copynumber: 1.9 Consensus size: 166
8466 TTTTCTTTTA
*
8476 TAATATGTAAAAGCTTTATGAATTACGAATTACTAATTTTTTTCCATTTATTAAAGCTAAATAAA
1 TAATATGTAAAAGCTTTATGAATTACGAATTACCAATTTTTTTCCATTTATTAAAGCTAAATAAA
* * *
8541 AGTTCCCCACCAATTAAAATTTAAAATTTAAAGTTAAATAAAAGTTTAAGAAGAAGTATATTACT
66 AGTTCCCCACCAATGAAAATTTAAAACTTAAAGTTAAATAAAAGTTTAAGAAGAAGTAAATTACT
8606 TATTAACCATTAAAACTTAACAAGTTTTGAATCTTT
131 TATTAACCATTAAAACTTAACAAGTTTTGAATCTTT
* * * * * *
8642 TAATATGTAAAAGTTTTATGAATTATGGATTACCAATTTTTTTTCATTTTTTAAAGTTAAATAAA
1 TAATATGTAAAAGCTTTATGAATTACGAATTACCAATTTTTTTCCATTTATTAAAGCTAAATAAA
*
8707 AGTTCCCCGCCAATGAAAATTTAAAACTTAAAGTTAAATAAAAGTTTAAGAAGAAGTAAATTACT
66 AGTTCCCCACCAATGAAAATTTAAAACTTAAAGTTAAATAAAAGTTTAAGAAGAAGTAAATTACT
8772 TATTAACCATTAAAACTTAA
131 TATTAACCATTAAAACTTAA
8792 TAGGTTTTAA
Statistics
Matches: 139, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
166 139 1.00
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.38
Consensus pattern (166 bp):
TAATATGTAAAAGCTTTATGAATTACGAATTACCAATTTTTTTCCATTTATTAAAGCTAAATAAA
AGTTCCCCACCAATGAAAATTTAAAACTTAAAGTTAAATAAAAGTTTAAGAAGAAGTAAATTACT
TATTAACCATTAAAACTTAACAAGTTTTGAATCTTT
Found at i:8935 original size:12 final size:13
Alignment explanation
Indices: 8918--8951 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
8908 CCACCAATTA
8918 AAATTTAAAAC-T
1 AAATTTAAAACTT
8930 AAATTTAAAACTT
1 AAATTTAAAACTT
8943 AAAGTTTAA
1 AAA-TTTAA
8952 GAAGAAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.55
13 4 0.20
14 5 0.25
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (13 bp):
AAATTTAAAACTT
Found at i:9084 original size:196 final size:195
Alignment explanation
Indices: 8692--9084 Score: 639
Period size: 197 Copynumber: 2.0 Consensus size: 195
8682 TTTTCATTTT
* *
8692 TTAAAGTTAAATAAAAGTTCCCCGCCAATGAAAATTTAAAACTTAAAGTTAAATAAAAGTTTAAG
1 TTAAAGTTAAATAAAAATTCCCCACCAATGAAAATTTAAAACTTAAAGTTAAATAAAAGTTTAAG
* * *
8757 AAGAAGTAAATTACTTATTAACCATTAAAACTTAATAGGTTTTAATGAAATAAAAATATATGTTT
66 AAGAAGTAAATTACGTATTAACCATTAAAACTTAACAGGTTTTAATGAAATAAAAATACATGTTT
*
8822 ACCCTTTAAAGGAATACTAAAATTTTAAAATTAAAAAAGGTAAATTTAGATATTTCAGGTCAAGG
131 ACCCTTTAAAGAAATACTAAAATTTTAAAATTAAAAAAGGTAAATTTAGATATTTCAGGTCAAGG
* * *
8887 TTAAAGTTAAATAAAAATTCCCCACCAATTAAAATTTAAAAC-TAAATTTAAAACTTAAAGTTTA
1 TTAAAGTTAAATAAAAATTCCCCACCAATGAAAATTTAAAACTTAAAGTT-AAA-TAAAAGTTTA
*
8951 AGAAGAAGTAAATTACGTATTAAACCATTAAAACTTAACAGGTTTTGATGAAATAAAAATACATG
64 AGAAGAAGTAAATTACGTATT-AACCATTAAAACTTAACAGGTTTTAATGAAATAAAAATACATG
9016 TTTACCCTTTAAAGAAATACTAAAATTTTAAAATT-AAAAAGG-ATAATTTAGATATTTCAGGTC
128 TTTACCCTTTAAAGAAATACTAAAATTTTAAAATTAAAAAAGGTA-AATTTAGATATTTCAGGTC
9079 AAGG
192 AAGG
9083 TT
1 TT
9085 TTTGAAGTTT
Statistics
Matches: 184, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
194 6 0.03
195 43 0.23
196 61 0.33
197 74 0.40
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.32
Consensus pattern (195 bp):
TTAAAGTTAAATAAAAATTCCCCACCAATGAAAATTTAAAACTTAAAGTTAAATAAAAGTTTAAG
AAGAAGTAAATTACGTATTAACCATTAAAACTTAACAGGTTTTAATGAAATAAAAATACATGTTT
ACCCTTTAAAGAAATACTAAAATTTTAAAATTAAAAAAGGTAAATTTAGATATTTCAGGTCAAGG
Found at i:9875 original size:176 final size:178
Alignment explanation
Indices: 9557--9878 Score: 411
Period size: 177 Copynumber: 1.8 Consensus size: 178
9547 GCAGATCACG
* *
9557 AAACAACCTTTTAACAAACACTTGAATCACATCAATCAGACATCTAAAGCAAAAATTATGTATTA
1 AAACAACCTTTTAACAAACACTTGAATCACATCAATCAGACATCCAAAGCAAAAATAATGTATTA
* * * * *
9622 TTAAGTGGACTGTCCATTCTCGCTAAACTAAACAACTATTTTTTTAGAAGCATTTTTTTATACTT
66 TTAAATGGACTGTCCATTCCCGCTAAACGAAACAACTATTTTTTCAGAAGCATTTTTTGATACTT
*
9687 GAAACGTTAAATTTAGATCATAAAACACTTTAAAATTTGTAGATCATA
131 GAAACATTAAATTTAGATCATAAAACACTTTAAAATTTGTAGATCATA
* * * * * *
9735 AAACAACCTTTTAAGAGACACTTTAATCACCTCAAT-AGACATCCAGAGCAAAAGTAATGTGA-T
1 AAACAACCTTTTAACAAACACTTGAATCACATCAATCAGACATCCAAAGCAAAAATAATGT-ATT
* * * * *
9798 ATTAAATGGA-TCGTTCATTCCCGTTAACCGAAACAAGTCA-TTTTTCGGAAGC-TTTTTTGATA
65 ATTAAATGGACT-GTCCATTCCCGCTAAACGAAACAACT-ATTTTTTCAGAAGCATTTTTTGATA
9860 CTTGAAACATTAAATTTAG
128 CTTGAAACATTAAATTTAG
9879 TTTTCTGAGT
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
176 28 0.23
177 60 0.49
178 34 0.28
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (178 bp):
AAACAACCTTTTAACAAACACTTGAATCACATCAATCAGACATCCAAAGCAAAAATAATGTATTA
TTAAATGGACTGTCCATTCCCGCTAAACGAAACAACTATTTTTTCAGAAGCATTTTTTGATACTT
GAAACATTAAATTTAGATCATAAAACACTTTAAAATTTGTAGATCATA
Found at i:11450 original size:42 final size:43
Alignment explanation
Indices: 11399--11492 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
11389 AGTGCATTAC
* * *
11399 CTAA-ATTCTA-CTCCATCTCTAGGTAATTGATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
11440 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
11485 CTAATATT
1 CTAATATT
11493 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:13072 original size:2 final size:2
Alignment explanation
Indices: 13065--13090 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13055 AGTACTATCC
13065 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
13091 TAATTAGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17842 original size:132 final size:131
Alignment explanation
Indices: 17698--17961 Score: 379
Period size: 132 Copynumber: 2.0 Consensus size: 131
17688 GTTTAAGAAA
* * * *
17698 TATATTTTAAAATTCTAATATATCTATGTTTTTTTAATTAAATTAGTAAAATGATAAAA-ATAA-
1 TATATTTAAAAATTCTAATATATATAAG--TTTTTAATTAAAATAGTAAAATGATAAAAGATAAT
*
17761 AATAGGTATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTATA
64 AATAGGTATAAGGATATTAGATTTAATTAAAT-AAAAATAGAGTTCTTAGTTGAGTAAAACTATA
17826 AAAG
128 AAAG
* * * *
17830 TATATTTAAAAATTCTAATATATATAAGTTTTTAATTAAAATAGTAATATGGTAAAAGTTAATTA
1 TATATTTAAAAATTCTAATATATATAAGTTTTTAATTAAAATAGTAAAATGATAAAAGATAATAA
* * *
17895 TAGTTATAAGGATATTATATTTAATTAAATAAAAATAGAGTTCTTCGTTGAGTAAAACTATAAAA
66 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTCTTAGTTGAGTAAAACTATAAAA
17960 G
131 G
17961 T
1 T
17962 TTAAATAATG
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
130 26 0.22
131 38 0.32
132 54 0.46
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.40
Consensus pattern (131 bp):
TATATTTAAAAATTCTAATATATATAAGTTTTTAATTAAAATAGTAAAATGATAAAAGATAATAA
TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTCTTAGTTGAGTAAAACTATAAAA
G
Found at i:25060 original size:108 final size:108
Alignment explanation
Indices: 24871--25091 Score: 424
Period size: 108 Copynumber: 2.0 Consensus size: 108
24861 GAATTCTTCG
24871 AATTCTTCACTCCTTTCATCACAATCATCGAACCTTTGGTGATCTTAAAGCCTCCACCTCGGCAA
1 AATTCTTCACTCCTTTCATCACAATCATCGAACCTTTGGTGATCTTAAAGCCTCCACCTCGGCAA
*
24936 GAATATCCATAACCCAGTCTATCCAACTTTCCAAGTAAAATCA
66 GAATATCCATAACCCAGTCTATCCAACTTTCCAAGTAAAAACA
*
24979 AATTCTTCACTCCTTTCATCACAATCATCGAACCTTTGGTGATCTTCAAGCCTCCACCTCGGCAA
1 AATTCTTCACTCCTTTCATCACAATCATCGAACCTTTGGTGATCTTAAAGCCTCCACCTCGGCAA
25044 GAATATCCATAACCCAGTCTATCCAACTTTCCAAGTAAAAACA
66 GAATATCCATAACCCAGTCTATCCAACTTTCCAAGTAAAAACA
25087 AATTC
1 AATTC
25092 CTTGTAAAGT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 111 1.00
ACGTcount: A:0.32, C:0.31, G:0.09, T:0.29
Consensus pattern (108 bp):
AATTCTTCACTCCTTTCATCACAATCATCGAACCTTTGGTGATCTTAAAGCCTCCACCTCGGCAA
GAATATCCATAACCCAGTCTATCCAACTTTCCAAGTAAAAACA
Found at i:27011 original size:12 final size:12
Alignment explanation
Indices: 26996--27031 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
26986 GAAAGAAAGA
26996 AAGAAAAAGAAG
1 AAGAAAAAGAAG
*
27008 AAGAATAAGAAG
1 AAGAAAAAGAAG
27020 AAGAGAAAAGAA
1 AAGA-AAAAGAA
27032 AAATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (12 bp):
AAGAAAAAGAAG
Found at i:29957 original size:12 final size:12
Alignment explanation
Indices: 29940--29970 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29930 TACTAAACCA
29940 ATCCTCCTCAAG
1 ATCCTCCTCAAG
*
29952 ATCCTCCTCAAT
1 ATCCTCCTCAAG
29964 ATCCTCC
1 ATCCTCC
29971 AAAACTCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.45, G:0.03, T:0.29
Consensus pattern (12 bp):
ATCCTCCTCAAG
Found at i:30249 original size:87 final size:86
Alignment explanation
Indices: 30084--30280 Score: 220
Period size: 87 Copynumber: 2.3 Consensus size: 86
30074 CAGGCACAAA
* * * *
30084 ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCATCATTACTAACTAAAACTCCATTAGGAAGAT
1 ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGAT
* *
30149 CATTGAAATTTGAATTCAAATT
66 CA-TCAAAATTGAATTCAAATT
* * * *
30171 ATCCTCTACCATAAT-ATTTTCCAAAGATTTTGCACCATAACCACCCATAACTCCATTAGGAAGA
1 ATCCTCCACCA-AATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGA
30235 TCA-CAATCAATTGAATTCAAATT
65 TCATCAA--AATTGAATTCAAATT
* *
30258 ATTCTCCAGCC-TATCAGTTTCCA
1 ATCCTCCA-CCAAATCAGTTTCCA
30281 CAGAATTTAC
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
85 2 0.02
86 2 0.02
87 82 0.90
88 5 0.05
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.31
Consensus pattern (86 bp):
ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCACCATAACCAACCAAAACTCCATTAGGAAGAT
CATCAAAATTGAATTCAAATT
Found at i:34919 original size:21 final size:21
Alignment explanation
Indices: 34893--35524 Score: 709
Period size: 21 Copynumber: 30.8 Consensus size: 21
34883 TAGTCAAAGA
*
34893 CCAAAGTTTAATAGTCAATCC
1 CCAAAGTTTGATAGTCAATCC
** *
34914 ATAAAGTTTGATATTCAATCC
1 CCAAAGTTTGATAGTCAATCC
*
34935 CCAAAGTTTGATAGTCAAACC
1 CCAAAGTTTGATAGTCAATCC
*
34956 CCAAAGTTTGATATTCAATCC
1 CCAAAGTTTGATAGTCAATCC
* *
34977 CC-AAGTTTGAGAGTCAAACC
1 CCAAAGTTTGATAGTCAATCC
* * *
34997 CCAAATTTTGATACTCAAACC
1 CCAAAGTTTGATAGTCAATCC
* *
35018 CCAAAATTTGATAATCAATCC
1 CCAAAGTTTGATAGTCAATCC
* * *
35039 CGAAAGTTTGATAGTAAATTC
1 CCAAAGTTTGATAGTCAATCC
* * ** *
35060 ACAAAATTTGATTTTCAAACC
1 CCAAAGTTTGATAGTCAATCC
*
35081 CTAAAGTTTGATAGTCAATCC
1 CCAAAGTTTGATAGTCAATCC
*
35102 CCAAAGTTTGATAGTCAAACC
1 CCAAAGTTTGATAGTCAATCC
* * *
35123 CCAAAGTTTTATAGTAAAACC
1 CCAAAGTTTGATAGTCAATCC
*
35144 CCAAAGTTTGATAGTTAATCC
1 CCAAAGTTTGATAGTCAATCC
* * *
35165 CAAAAGTTTGATTGTCAAACC
1 CCAAAGTTTGATAGTCAATCC
35186 CCAAAGTTTGATAGTCAATCC
1 CCAAAGTTTGATAGTCAATCC
* *
35207 CCAAACATTT-ATAGTAAATCC
1 CCAAA-GTTTGATAGTCAATCC
* *
35228 CCAAAGTTTGATTGTCAAACC
1 CCAAAGTTTGATAGTCAATCC
*
35249 CCAAAGTTTGATAGTCAAACC
1 CCAAAGTTTGATAGTCAATCC
35270 CCAAAGTTTGATAGTCAATCC
1 CCAAAGTTTGATAGTCAATCC
*
35291 CCAAAGTTTGATAGTCAAACC
1 CCAAAGTTTGATAGTCAATCC
35312 CC-AAGTTTGATAGTCAATCC
1 CCAAAGTTTGATAGTCAATCC
35332 CCAAAGTTTGATAGTCAATCC
1 CCAAAGTTTGATAGTCAATCC
35353 CCAAA-TTTGATAG-----CC
1 CCAAAGTTTGATAGTCAATCC
* *
35368 CTAAAGTTTGATTGTCAATCC
1 CCAAAGTTTGATAGTCAATCC
* * *
35389 CC-AAGTTTTATAGTTAAACC
1 CCAAAGTTTGATAGTCAATCC
35409 CCAAAGTTTGATAGTC-AT--
1 CCAAAGTTTGATAGTCAATCC
*
35427 TCAAAGTTTGATAGTCAATCC
1 CCAAAGTTTGATAGTCAATCC
*
35448 CC-AAGTTTGATAGTCAAACC
1 CCAAAGTTTGATAGTCAATCC
*
35468 CCAAA-TTTGATAGTCAAACC
1 CCAAAGTTTGATAGTCAATCC
* * * *
35488 CCAAAATTTGATTGTTAAACC
1 CCAAAGTTTGATAGTCAATCC
*
35509 CCAAAGTTTAATAGTC
1 CCAAAGTTTGATAGTC
35525 CACATGTTAA
Statistics
Matches: 514, Mismatches: 81, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
15 6 0.01
16 7 0.01
18 15 0.03
19 2 0.00
20 103 0.20
21 378 0.74
22 3 0.01
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (21 bp):
CCAAAGTTTGATAGTCAATCC
Found at i:36047 original size:3 final size:3
Alignment explanation
Indices: 36039--36094 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
36029 ATCTCCCATG
* * * * *
36039 ATA ATA ATA ATA ATA GTA ATA ATA ATA ATT TTCC ATA ATA AT- TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
36084 ATA ATA ATA AT
1 ATA ATA ATA AT
36095 CATTAATTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
2 1 0.02
3 40 0.95
4 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (3 bp):
ATA
Done.