Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010298.1 Corchorus capsularis cultivar CVL-1 contig10319, 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: 80793
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:11371 original size:24 final size:22
Alignment explanation
Indices: 11328--11371 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
11318 TTAATATATG
11328 TGTACATAATTACTAACATGTA
1 TGTACATAATTACTAACATGTA
* *
11350 TGTATATATATTATTAATCATG
1 TGTACATA-ATTACTAA-CATG
11372 ACTTATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 7 0.39
24 4 0.22
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (22 bp):
TGTACATAATTACTAACATGTA
Found at i:21322 original size:23 final size:23
Alignment explanation
Indices: 21296--21341 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
21286 CAAACAATCT
21296 TGAGCACTCTCGCTCGATCTCTA
1 TGAGCACTCTCGCTCGATCTCTA
*
21319 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGATCTCTA
21342 ACAAACTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.35, G:0.20, T:0.30
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGATCTCTA
Found at i:30929 original size:31 final size:31
Alignment explanation
Indices: 30894--30959 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
30884 AACTTTATGT
* *
30894 TTTCCGATTGTACCATTATTTT-TAAAACATA
1 TTTCCAATTGTACCATT-TTTTAAAAAACATA
*
30925 TTTCCAATTGTACCCTTTTTTAAAAAACATA
1 TTTCCAATTGTACCATTTTTTAAAAAACATA
30956 TTTC
1 TTTC
30960 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (31 bp):
TTTCCAATTGTACCATTTTTTAAAAAACATA
Found at i:31126 original size:37 final size:37
Alignment explanation
Indices: 31056--31152 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 37
31046 AATTTGGTTT
31056 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTATC
1 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTATC
* * * *
31093 TTTGTTTCCAATTGTTCTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCCTTTTATC
*
31131 TTTTTTCTCCAACGTCCTATTT
1 TTTGTT-TCCAACGTCCTATTT
31153 GCTCTTAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 11 0.22
38 35 0.69
39 5 0.10
ACGTcount: A:0.14, C:0.20, G:0.08, T:0.58
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTATC
Found at i:31314 original size:19 final size:20
Alignment explanation
Indices: 31287--31324 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
31277 TACTATTATT
31287 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
31307 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
31325 ACTGTCAATA
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:31515 original size:22 final size:22
Alignment explanation
Indices: 31490--31618 Score: 79
Period size: 22 Copynumber: 5.9 Consensus size: 22
31480 TGTCTCTATG
31490 TGGTTATCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAAAA
* * **
31512 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAAA
* *
31535 -GGTTATCAAAA-TTC-TATAG
1 TGGTTATCAAAATTTCATAAAA
* **
31554 TGTGATTACCAAAATTTCGTATGGAA
1 TG-G-TTATCAAAATTTC--ATAAAA
*
31580 --GTTATCAAAATTTCATAATA
1 TGGTTATCAAAATTTCATAAAA
*
31600 TGGTTACCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
31619 GAATCAAGTT
Statistics
Matches: 79, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
19 1 0.01
20 5 0.06
21 4 0.05
22 61 0.77
23 6 0.08
26 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAAA
Found at i:31570 original size:44 final size:44
Alignment explanation
Indices: 31492--31618 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 44
31482 TCTCTATGTG
* * ** * *
31492 GTTATCAAAATTTCATAAAATGGTTATTATAATTTCATGA-GGAG
1 GTTATCAAAATTTCATAATATGATTACCAAAATTTCAT-ATGGAA
* * *
31536 GTTATCAAAA-TTCTATAGTGTGATTACCAAAATTTCGTATGGAA
1 GTTATCAAAATTTC-ATAATATGATTACCAAAATTTCATATGGAA
*
31580 GTTATCAAAATTTCATAATATGGTTACCAAAATTTCATA
1 GTTATCAAAATTTCATAATATGATTACCAAAATTTCATA
31619 GAATCAAGTT
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
43 4 0.06
44 60 0.90
45 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (44 bp):
GTTATCAAAATTTCATAATATGATTACCAAAATTTCATATGGAA
Found at i:31651 original size:46 final size:46
Alignment explanation
Indices: 31492--31639 Score: 119
Period size: 44 Copynumber: 3.3 Consensus size: 46
31482 TCTCTATGTG
* ** * ** *
31492 GTTATCAAAATTTCATAAAATGGTTATTATAATTTCAT-G-AGGAG
1 GTTATCAAAATTTCATAATATGGTTACCAAAATTTCATAGAATCAA
* * * * *
31536 GTTATCAAAA-TTCTATAGTGTGATTACCAAAATTTC---GTATGGAA
1 GTTATCAAAATTTC-ATAATATGGTTACCAAAATTTCATAGAAT-CAA
31580 GTTATCAAAATTTCATAATATGGTTACCAAAATTTCATAGAATCAA
1 GTTATCAAAATTTCATAATATGGTTACCAAAATTTCATAGAATCAA
*
31626 GTTATTAAAATTTC
1 GTTATCAAAATTTC
31640 TTAGGTTGGT
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 56 0.68
45 3 0.04
46 15 0.18
47 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (46 bp):
GTTATCAAAATTTCATAATATGGTTACCAAAATTTCATAGAATCAA
Found at i:31658 original size:22 final size:22
Alignment explanation
Indices: 31489--31673 Score: 77
Period size: 22 Copynumber: 8.3 Consensus size: 22
31479 TTGTCTCTAT
* **
31489 GTGGTTATCAAAATTTCATAAA
1 GTGGTTATTAAAATTTCATAGG
* *
31511 ATGGTTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * *
31533 GAGGTTATCAAAA-TTCTATAGT
1 GTGGTTATTAAAATTTC-ATAGG
* ** * *
31555 GTGATTACCAAAATTTCGTATG
1 GTGGTTATTAAAATTTCATAGG
** * **
31577 GAAGTTATCAAAATTTCATAAT
1 GTGGTTATTAAAATTTCATAGG
* ** *
31599 ATGGTTACCAAAATTTCATAGA
1 GTGGTTATTAAAATTTCATAGG
* * *
31621 ATCAAGTTATTAAAATTTCTTAGG
1 GT--GGTTATTAAAATTTCATAGG
* *
31645 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
31667 GTGGTTA
1 GTGGTTA
31674 ATTATCACAA
Statistics
Matches: 118, Mismatches: 39, Indels: 12
0.70 0.23 0.07
Matches are distributed among these distances:
21 3 0.03
22 95 0.81
23 4 0.03
24 16 0.14
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:31776 original size:22 final size:21
Alignment explanation
Indices: 31751--31826 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 21
31741 TTCGTAGTGT
31751 GGTTAATAAAATTTCATTAGAA
1 GGTT-ATAAAATTTCATTAGAA
* ** *
31773 GGTTACTAATATTTCATGGGGA
1 GGTTA-TAAAATTTCATTAGAA
31795 GGTTATCAAAATTTCA-TATGAA
1 GGTTAT-AAAATTTCATTA-GAA
31817 GGTTATAAAA
1 GGTTATAAAA
31827 GTCTCAATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
21 6 0.14
22 37 0.86
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (21 bp):
GGTTATAAAATTTCATTAGAA
Found at i:31776 original size:44 final size:43
Alignment explanation
Indices: 31709--31826 Score: 107
Period size: 44 Copynumber: 2.7 Consensus size: 43
31699 ATCAAAGAGA
* * * * *
31709 TTATCAAAATGTCATA-GCGAGGTTATAAGAATTTCGTAGTGTGG
1 TTATCAAAATTTCATATG-AAGGTTATAA-AATTTCATAGGGAGG
* *
31753 TTAAT-AAAATTTCAT-TAGAAGGTTACTAATATTTCATGGGGAGG
1 TT-ATCAAAATTTCATAT-GAAGGTTA-TAAAATTTCATAGGGAGG
31797 TTATCAAAATTTCATATGAAGGTTATAAAA
1 TTATCAAAATTTCATATGAAGGTTATAAAA
31827 GTCTCAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
43 6 0.10
44 47 0.78
45 7 0.12
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (43 bp):
TTATCAAAATTTCATATGAAGGTTATAAAATTTCATAGGGAGG
Found at i:31936 original size:21 final size:22
Alignment explanation
Indices: 31904--31948 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
31894 TATTCCATAG
31904 AGAACAGATATCAAAATTT-AT
1 AGAACAGATATCAAAATTTCAT
31925 AGAA-AGATTATCAAAATTTCAT
1 AGAACAGA-TATCAAAATTTCAT
31947 AG
1 AG
31949 TTTTGTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 15 0.68
22 4 0.18
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (22 bp):
AGAACAGATATCAAAATTTCAT
Found at i:32050 original size:22 final size:22
Alignment explanation
Indices: 31912--32070 Score: 112
Period size: 22 Copynumber: 7.3 Consensus size: 22
31902 AGAGAACAGA
*
31912 TATCAAAATTT-ATAGAA-AGAT
1 TATCAAAATTTCATA-AAGAGGT
*****
31933 TATCAAAATTTCATAGTTTTGT
1 TATCAAAATTTCATAAAGAGGT
* *
31955 TATCAAAATTTCA-AAGCGAGTT
1 TATCAAAATTTCATAA-AGAGGT
* * * *
31977 TATCAAAATTACATAATGTGAT
1 TATCAAAATTTCATAAAGAGGT
31999 TATCAGAAA-TTCATAGAAG-GGT
1 TATCA-AAATTTCATA-AAGAGGT
* * *
32021 CAACAAAATTTTATAAAGAGGT
1 TATCAAAATTTCATAAAGAGGT
32043 TATCAAAATTTCATAAAGAGGT
1 TATCAAAATTTCATAAAGAGGT
32065 TATCAA
1 TATCAA
32071 GTTTTCAAAA
Statistics
Matches: 106, Mismatches: 24, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
21 18 0.17
22 81 0.76
23 7 0.07
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (22 bp):
TATCAAAATTTCATAAAGAGGT
Found at i:32076 original size:22 final size:22
Alignment explanation
Indices: 32026--32077 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
32016 AGGGTCAACA
32026 AAATTTT-ATAAAGAGGTTATC
1 AAATTTTCATAAAGAGGTTATC
*
32047 AAAATTTCATAAAGAGGTTATC
1 AAATTTTCATAAAGAGGTTATC
*
32069 AAGTTTTCA
1 AAATTTTCA
32078 AAATGTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (22 bp):
AAATTTTCATAAAGAGGTTATC
Found at i:32208 original size:20 final size:20
Alignment explanation
Indices: 32183--32234 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
32173 TTATGGAGTA
32183 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
32203 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
32223 ATCACAATTTCA
1 ATCAAAATTTCA
32235 TAGTTTAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:32374 original size:103 final size:106
Alignment explanation
Indices: 32255--32460 Score: 240
Period size: 103 Copynumber: 2.0 Consensus size: 106
32245 TTCATAAGAA
* *
32255 AGTTATCAAAATTTCAT-AGTATGTAGATCAAAATTTCATAAGGA-GATTAACAAAATTTCATAA
1 AGTTATCAAAATTTCATAAGAAAGT-GATCAAAATTTCATAAGGAGGATTAACAAAATTTCATAA
*
32318 TAAG-GTTATCAAAAAATCATAG-GAGGTTATCAAAATTCGT
65 GAAGAGTTATCAAAAAATCATAGCGAGGTTATCAAAATTCGT
* * * * * * * *
32358 AGTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGG
1 AGTTATCAAAATTTCATAAGAAAGTGATCAAAATTTCATAAGGAGGATTAACAAAATTTCATAAG
* ** *
32423 AAGATTTATCAAAACTTCATAGCGAGGTTATCACAATT
66 AAGAGTTATCAAAAAATCATAGCGAGGTTATCAAAATT
32461 TCATAGTACT
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
103 32 0.38
104 23 0.27
105 15 0.18
106 14 0.17
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (106 bp):
AGTTATCAAAATTTCATAAGAAAGTGATCAAAATTTCATAAGGAGGATTAACAAAATTTCATAAG
AAGAGTTATCAAAAAATCATAGCGAGGTTATCAAAATTCGT
Found at i:32410 original size:23 final size:23
Alignment explanation
Indices: 32360--32466 Score: 101
Period size: 23 Copynumber: 4.7 Consensus size: 23
32350 AAATTCGTAG
* * * *
32360 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTCATAGGGAGGT
*
32382 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
32405 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
* *
32428 TTATCAAAACTTCATAGCGAGG-
1 TTATCAAAATTTCATAGGGAGGT
*
32450 TTATCACAATTTCATAG
1 TTATCAAAATTTCATAG
32467 TACTATTATC
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
22 32 0.46
23 38 0.54
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:32454 original size:45 final size:44
Alignment explanation
Indices: 32244--32466 Score: 140
Period size: 45 Copynumber: 5.2 Consensus size: 44
32234 ATAGTTTAGT
* * * * *
32244 TTTCATAAGAAAGTTATCAAAATTTCATAG-TATGTAGATCAAAA
1 TTTCATAGGAAAGTTATCAAAACTTCATAGCGAGGT-TATCAAAA
* * * ***
32288 TTTCATAAGGAGA-TTAACAAAATTTCATAATAAGGTTATCAAAA
1 TTTCAT-AGGAAAGTTATCAAAACTTCATAGCGAGGTTATCAAAA
** * * *
32332 AATCATAGG-AGGTTATCAAAA-TTC---G-TA-GTTATCAAGA
1 TTTCATAGGAAAGTTATCAAAACTTCATAGCGAGGTTATCAAAA
* * * *
32369 TTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAAA
1 TTTCATAGGAAAGTTATCAAAACTTCATAGCGAGG-TTATCAAAA
* * *
32414 TTTTATAGGAAGATTTATCAAAACTTCATAGCGAGGTTATCACAA
1 TTTCATAGGAA-AGTTATCAAAACTTCATAGCGAGGTTATCAAAA
32459 TTTCATAG
1 TTTCATAG
32467 TACTATTATC
Statistics
Matches: 137, Mismatches: 30, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
37 15 0.11
38 12 0.09
39 2 0.01
42 4 0.03
43 12 0.09
44 33 0.24
45 39 0.28
46 20 0.15
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (44 bp):
TTTCATAGGAAAGTTATCAAAACTTCATAGCGAGGTTATCAAAA
Found at i:32466 original size:22 final size:21
Alignment explanation
Indices: 32256--32681 Score: 177
Period size: 22 Copynumber: 19.6 Consensus size: 21
32246 TCATAAGAAA
* *
32256 GTTATCAAAATTTCATAGTAT
1 GTTATCAAAATTTCATAGGAG
*
32277 GTAGATCAAAATTTCATAAGGAG
1 GT-TATCAAAATTTCAT-AGGAG
* * **
32300 ATTAACAAAATTTCATAATAAG
1 GTTATCAAAATTTCAT-AGGAG
**
32322 GTTATCAAAAAATCATAGGAG
1 GTTATCAAAATTTCATAGGAG
*
32343 GTTATCAAAA-TTC---GTA-
1 GTTATCAAAATTTCATAGGAG
* * *
32359 GTTATCAAGATTTCATAAGAAA
1 GTTATCAAAATTTCAT-AGGAG
*
32381 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATA-GGAG
*
32403 GTTTATCAAAATTTTATAGGAAG
1 G-TTATCAAAATTTCATAGG-AG
* *
32426 ATTTATCAAAACTTCATAGCGAG
1 -GTTATCAAAATTTCATAG-GAG
* * *
32449 GTTATCACAATTTCATAGTACT
1 GTTATCAAAATTTCATAGGA-G
* * *
32471 ATTATCAAAATTTCAGAGTGTG
1 GTTATCAAAATTTCATAG-GAG
*
32493 ATTA-CTAACAA-TTCATATGGAG
1 GTTATC-AA-AATTTCATA-GGAG
* * * * * *
32515 GTTTTTAAATTTTCGTAACGTG
1 GTTATCAAAATTTCAT-AGGAG
* *
32537 GTTA-CAATATATCATATGGAG
1 GTTATCAAAATTTCATA-GGAG
* * *
32558 GTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATAG-G-AG
* *
32581 GTTATCAAAATTTCAATGGGAA
1 GTTATCAAAATTTC-ATAGGAG
*
32603 GTTATCAAAATTTCATATTGAG
1 GTTATCAAAATTTCATA-GGAG
* *
32625 GTCT-TCAAAATTCCTTATGGAG
1 GT-TATCAAAATTTCATA-GGAG
* * *
32647 GTTAACAGAATTTCATAAGAAG
1 GTTATCAAAATTTCAT-AGGAG
**
32669 GTTAAAAAAATTT
1 GTTATCAAAATTT
32682 ATAAAAGGGT
Statistics
Matches: 301, Mismatches: 74, Indels: 59
0.69 0.17 0.14
Matches are distributed among these distances:
16 9 0.03
17 5 0.02
20 3 0.01
21 37 0.12
22 184 0.61
23 59 0.20
24 4 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGAG
Found at i:32692 original size:21 final size:22
Alignment explanation
Indices: 32645--32689 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
32635 TTCCTTATGG
* *
32645 AGGTTAACAGAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAGA
32667 AGGTTAAAAAAATTT-ATAA-A
1 AGGTTAAAAAAATTTCATAAGA
32687 AGG
1 AGG
32690 GTTCTCGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 4 0.19
22 13 0.62
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAGA
Found at i:46236 original size:15 final size:15
Alignment explanation
Indices: 46212--46241 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46202 TATGGTCCCT
*
46212 AGCTCGAAATCTTCA
1 AGCTCCAAATCTTCA
46227 AGCTCCAAATCTTCA
1 AGCTCCAAATCTTCA
46242 TTCTGGTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.27
Consensus pattern (15 bp):
AGCTCCAAATCTTCA
Found at i:58669 original size:8 final size:8
Alignment explanation
Indices: 58658--58692 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
58648 GAAATCAATT
58658 AATCATCA
1 AATCATCA
*
58666 AATCATAA
1 AATCATCA
*
58674 AATCGTCA
1 AATCATCA
58682 AATCATCA
1 AATCATCA
58690 AAT
1 AAT
58693 AATACCCATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (8 bp):
AATCATCA
Found at i:58851 original size:34 final size:34
Alignment explanation
Indices: 58808--59041 Score: 343
Period size: 34 Copynumber: 7.0 Consensus size: 34
58798 TAGTAGGGCC
*
58808 GTCTTCCAGTTATTATCACAACCCACTGGACAGG
1 GTCTTCCAGTTATTATCACAACCCACTGGGCAGG
* *
58842 GTCTTCCAGTTATTATCACCACCCACTGGGCAGT
1 GTCTTCCAGTTATTATCACAACCCACTGGGCAGG
* *
58876 GTC-TCCAGTTATTATCTCAACCCACTGGGTAGG
1 GTCTTCCAGTTATTATCACAACCCACTGGGCAGG
* *
58909 GTC-TCCAGTTATTATCTCAACCCACTGAGCAGG
1 GTCTTCCAGTTATTATCACAACCCACTGGGCAGG
*
58942 GTCTTCCAGTTATTATCACAACCCACTGGGCATG
1 GTCTTCCAGTTATTATCACAACCCACTGGGCAGG
*
58976 GTCTTCCAGTTATTATCTCAACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCACAACCCACTGGGCAGG
*
59010 GTCTTCCAATTATTAT---AACCCACTGGGCAGG
1 GTCTTCCAGTTATTATCACAACCCACTGGGCAGG
59041 G
1 G
59042 CCGATAAAAC
Statistics
Matches: 184, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
31 16 0.09
33 60 0.33
34 108 0.59
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (34 bp):
GTCTTCCAGTTATTATCACAACCCACTGGGCAGG
Found at i:71523 original size:18 final size:20
Alignment explanation
Indices: 71482--71525 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
71472 AACATGTCTG
71482 TATATGAAATTACTATGTTA
1 TATATGAAATTACTATGTTA
71502 TATATGAAATTACTATGTTA
1 TATATGAAATTACTATGTTA
71522 TATA
1 TATA
71526 GAACAACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (20 bp):
TATATGAAATTACTATGTTA
Found at i:73513 original size:26 final size:26
Alignment explanation
Indices: 73477--73528 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
73467 GCAATTTCTT
73477 GCATTCTCTAGGCAATCTGATACATC
1 GCATTCTCTAGGCAATCTGATACATC
73503 GCATTCTCTAGGCAATCTGATACATC
1 GCATTCTCTAGGCAATCTGATACATC
73529 CTGACCAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (26 bp):
GCATTCTCTAGGCAATCTGATACATC
Done.