Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009725.1 Corchorus capsularis cultivar CVL-1 contig09746, 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: 84504
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1269 original size:20 final size:20
Alignment explanation
Indices: 1244--1281 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1234 TCCATGCAAT
1244 TAAATTACTACTATTTTGAG
1 TAAATTACTACTATTTTGAG
1264 TAAATTACTACTATTTTG
1 TAAATTACTACTATTTTG
1282 TACCTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (20 bp):
TAAATTACTACTATTTTGAG
Found at i:21343 original size:31 final size:32
Alignment explanation
Indices: 21308--21367 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
21298 ATGTTTTCCG
21308 ATTGTACCCTTATTTTTAAAAT-ATATTTTCA
1 ATTGTACCCTTATTTTTAAAATCATATTTTCA
* *
21339 ATTGTACCTTTTTTTTTAAAATCATATTT
1 ATTGTACCCTTATTTTTAAAATCATATTT
21368 CTAAATTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (32 bp):
ATTGTACCCTTATTTTTAAAATCATATTTTCA
Found at i:21555 original size:38 final size:38
Alignment explanation
Indices: 21491--21586 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 38
21481 AATTTGGTTT
*
21491 TTTGTTTCC-AACGTTCTATTTAATTTTGTCTTTTGTC
1 TTTGTTTCCAAACATTCTATTTAATTTTGTCTTTTGTC
* *
21528 TTTGTTTCCAAACATTGTATTTAATTTTGTTTTTTGTC
1 TTTGTTTCCAAACATTCTATTTAATTTTGTCTTTTGTC
* * *
21566 TTCGTCTCC-AACGTTCTATTT
1 TTTGTTTCCAAACATTCTATTT
21587 GGGCTTAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 19 0.37
38 32 0.63
ACGTcount: A:0.16, C:0.17, G:0.10, T:0.57
Consensus pattern (38 bp):
TTTGTTTCCAAACATTCTATTTAATTTTGTCTTTTGTC
Found at i:21666 original size:22 final size:22
Alignment explanation
Indices: 21638--21712 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
21628 TGGTCCAATT
21638 TCAAAATTTCAAAGCGAGATTA
1 TCAAAATTTCAAAGCGAGATTA
* * *
21660 TCAAAATTACATAA-TGTGATTA
1 TCAAAATTTCA-AAGCGAGATTA
** * * *
21682 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCAAAGCGAGATTA
21704 TCAAAATTT
1 TCAAAATTT
21713 GTAATTATCA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
21 1 0.03
22 36 0.92
23 2 0.05
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (22 bp):
TCAAAATTTCAAAGCGAGATTA
Found at i:21720 original size:38 final size:39
Alignment explanation
Indices: 21678--21751 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
21668 ACATAATGTG
*
21678 ATTATCAAAAAATCATAGGGAGG-TTATCAAAATTTGTA
1 ATTATCAAAAAATCATAAGGAGGTTTATCAAAATTTGTA
* **
21716 ATTATCAAGATTTCATAAGGAGGTTTATCAAAATTT
1 ATTATCAAAAAATCATAAGGAGGTTTATCAAAATTT
21752 TATAGGGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 19 0.61
39 12 0.39
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (39 bp):
ATTATCAAAAAATCATAAGGAGGTTTATCAAAATTTGTA
Found at i:21811 original size:45 final size:44
Alignment explanation
Indices: 21716--21823 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 44
21706 AAAATTTGTA
* * * * *
21716 ATTATCAAGATTTCATAAGGAGGTTTATCAAAATTTTATAGGGAT
1 ATTATCAAAATTTCAT-AGGAGGTTTATCAAAATGTCATAGCGAG
*
21761 ATTATCAAAATTTTATAGGAAGGTTTATCAAAATGTCATAGCGAG
1 ATTATCAAAATTTCATAGG-AGGTTTATCAAAATGTCATAGCGAG
* *
21806 GTTATCACAATTTCATAG
1 ATTATCAAAATTTCATAG
21824 TGTGATTATA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 3 0.06
45 50 0.94
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (44 bp):
ATTATCAAAATTTCATAGGAGGTTTATCAAAATGTCATAGCGAG
Found at i:21821 original size:22 final size:22
Alignment explanation
Indices: 21717--21823 Score: 110
Period size: 22 Copynumber: 4.8 Consensus size: 22
21707 AAATTTGTAA
*
21717 TTATCAAGATTTCATAAGGAGGT
1 TTATCAAAATTTCAT-AGGAGGT
* *
21740 TTATCAAAATTTTATAGG-GAT
1 TTATCAAAATTTCATAGGAGGT
*
21761 ATTATCAAAATTTTATAGGAAGGT
1 -TTATCAAAATTTCATAGG-AGGT
*
21785 TTATCAAAATGTCATAGCGAGG-
1 TTATCAAAATTTCATAG-GAGGT
*
21807 TTATCACAATTTCATAG
1 TTATCAAAATTTCATAG
21824 TGTGATTATA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
21 2 0.03
22 36 0.50
23 31 0.43
24 3 0.04
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAGGT
Found at i:21832 original size:22 final size:21
Alignment explanation
Indices: 21807--21866 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
21797 CATAGCGAGG
*
21807 TTATCACAATTTCATAGTGTGA
1 TTATAACAA-TTCATAGTGTGA
* *
21829 TTATAAAAAATTCAGAGTGTGA
1 TTAT-AACAATTCATAGTGTGA
*
21851 TTACTGACAATTCATA
1 TTA-TAACAATTCATA
21867 TGTTGGTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (21 bp):
TTATAACAATTCATAGTGTGA
Found at i:22006 original size:22 final size:22
Alignment explanation
Indices: 21981--22089 Score: 80
Period size: 22 Copynumber: 5.0 Consensus size: 22
21971 TTACTTAGGG
*
21981 AGGTTAACAAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAAGA
*
22003 AGGTTAAAT-AAAATTT-ATAAAA
1 AGGTT--ATCAAAATTTCATAAGA
* * *
22025 AGGTTCTCGAAATTCCAT-AGTA
1 AGGTTATCAAAATTTCATAAG-A
** ** *
22047 TCGTTATTGAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAAGA
22069 AGGTTATCAAAATTTCATAAG
1 AGGTTATCAAAATTTCATAAG
22090 GACGTCATAA
Statistics
Matches: 64, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
20 1 0.02
21 6 0.09
22 48 0.75
23 8 0.12
24 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAAGA
Found at i:22131 original size:62 final size:62
Alignment explanation
Indices: 22057--22208 Score: 250
Period size: 62 Copynumber: 2.5 Consensus size: 62
22047 TCGTTATTGA
22057 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* *
22119 AATTTCATAGGAATGTTATCAAAATTTCATAAGGACGTTATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
* * * *
22181 AACTTAATAGGAAGATTATCATAATTTC
1 AATTTCATAGGAAGGTTATCAAAATTTC
22209 GTATGAATAT
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 83 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
Found at i:22158 original size:22 final size:22
Alignment explanation
Indices: 22056--22164 Score: 72
Period size: 22 Copynumber: 5.1 Consensus size: 22
22046 ATCGTTATTG
*
22056 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAACGTTATCA
*
22078 AAATTTCATAAGG-ACGTCAT-A
1 AAATTTCAT-AGGAACGTTATCA
*
22099 AAA---AATAGTGTAA--TTATCA
1 AAATTTCATAG-G-AACGTTATCA
* *
22118 TAATTTCATAGGAATGTTATCA
1 AAATTTCATAGGAACGTTATCA
*
22140 AAATTTCATAAGG-ACGTTATAA
1 AAATTTCAT-AGGAACGTTATCA
22162 AAA
1 AAA
22165 ATAGTGTAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 22
0.68 0.09 0.22
Matches are distributed among these distances:
17 2 0.03
18 6 0.09
19 3 0.04
20 3 0.04
21 5 0.07
22 42 0.63
23 6 0.09
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (22 bp):
AAATTTCATAGGAACGTTATCA
Found at i:27155 original size:94 final size:94
Alignment explanation
Indices: 27020--27209 Score: 380
Period size: 94 Copynumber: 2.0 Consensus size: 94
27010 TGATTCCATT
27020 CACTAGTGTTCACCCAGCTTGTCTTTGAGGATGTTTAGATGCACAGCAAACTAACAAAGTGAGAA
1 CACTAGTGTTCACCCAGCTTGTCTTTGAGGATGTTTAGATGCACAGCAAACTAACAAAGTGAGAA
27085 TTTAAAATTCTAAATTTAATGTCTGATGG
66 TTTAAAATTCTAAATTTAATGTCTGATGG
27114 CACTAGTGTTCACCCAGCTTGTCTTTGAGGATGTTTAGATGCACAGCAAACTAACAAAGTGAGAA
1 CACTAGTGTTCACCCAGCTTGTCTTTGAGGATGTTTAGATGCACAGCAAACTAACAAAGTGAGAA
27179 TTTAAAATTCTAAATTTAATGTCTGATGG
66 TTTAAAATTCTAAATTTAATGTCTGATGG
27208 CA
1 CA
27210 ACTCATATAG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (94 bp):
CACTAGTGTTCACCCAGCTTGTCTTTGAGGATGTTTAGATGCACAGCAAACTAACAAAGTGAGAA
TTTAAAATTCTAAATTTAATGTCTGATGG
Found at i:29378 original size:12 final size:12
Alignment explanation
Indices: 29353--29469 Score: 127
Period size: 12 Copynumber: 10.0 Consensus size: 12
29343 AAGATATTCC
* *
29353 CGTTCCTTATGT
1 CGTTCCTGAAGT
*
29365 CGTTCTTGAAGT
1 CGTTCCTGAAGT
29377 CGTTCCTGAAAGT
1 CGTTCCTG-AAGT
29390 CGTTCCTGAAGT
1 CGTTCCTGAAGT
*
29402 TGTTCC-----T
1 CGTTCCTGAAGT
*
29409 CGTTCCTGATGT
1 CGTTCCTGAAGT
29421 CGTTCCTGAAGT
1 CGTTCCTGAAGT
29433 CGTTCCTGAAAGT
1 CGTTCCTG-AAGT
*
29446 CATTCCTGAAGT
1 CGTTCCTGAAGT
29458 CGTTCCTGAAGT
1 CGTTCCTGAAGT
29470 AAAAAAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 14
0.79 0.08 0.12
Matches are distributed among these distances:
7 6 0.07
12 60 0.67
13 23 0.26
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (12 bp):
CGTTCCTGAAGT
Found at i:29394 original size:25 final size:24
Alignment explanation
Indices: 29353--29469 Score: 127
Period size: 25 Copynumber: 5.0 Consensus size: 24
29343 AAGATATTCC
* * *
29353 CGTTCCTTATGTCGTTCTTGAAGT
1 CGTTCCTGAAGTCGTTCCTGAAGT
29377 CGTTCCTGAAAGTCGTTCCTGAAGT
1 CGTTCCTG-AAGTCGTTCCTGAAGT
* *
29402 TGTTCC-----TCGTTCCTGATGT
1 CGTTCCTGAAGTCGTTCCTGAAGT
29421 CGTTCCTGAAGTCGTTCCTGAAAGT
1 CGTTCCTGAAGTCGTTCCTG-AAGT
*
29446 CATTCCTGAAGTCGTTCCTGAAGT
1 CGTTCCTGAAGTCGTTCCTGAAGT
29470 AAAAAAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
19 17 0.22
24 20 0.26
25 41 0.53
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (24 bp):
CGTTCCTGAAGTCGTTCCTGAAGT
Found at i:29413 original size:19 final size:19
Alignment explanation
Indices: 29389--29427 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29379 TTCCTGAAAG
*
29389 TCGTTCCTGAAGTTGTTCC
1 TCGTTCCTGAAGTCGTTCC
*
29408 TCGTTCCTGATGTCGTTCC
1 TCGTTCCTGAAGTCGTTCC
29427 T
1 T
29428 GAAGTCGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.28, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGTTCCTGAAGTCGTTCC
Found at i:29421 original size:56 final size:56
Alignment explanation
Indices: 29349--29464 Score: 189
Period size: 56 Copynumber: 2.1 Consensus size: 56
29339 ACAAAAGATA
* * * *
29349 TTCC-CGTTCCTTATGTCGTTCTTGAAGTCGTTCCTGAAAGTCGTTCCTGAAGTTG
1 TTCCTCGTTCCTGATGTCGTTCCTGAAGTCGTTCCTGAAAGTCATTCCTGAAGTCG
29404 TTCCTCGTTCCTGATGTCGTTCCTGAAGTCGTTCCTGAAAGTCATTCCTGAAGTCG
1 TTCCTCGTTCCTGATGTCGTTCCTGAAGTCGTTCCTGAAAGTCATTCCTGAAGTCG
29460 TTCCT
1 TTCCT
29465 GAAGTAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
55 4 0.07
56 52 0.93
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.39
Consensus pattern (56 bp):
TTCCTCGTTCCTGATGTCGTTCCTGAAGTCGTTCCTGAAAGTCATTCCTGAAGTCG
Found at i:29426 original size:31 final size:32
Alignment explanation
Indices: 29376--29439 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
29366 GTTCTTGAAG
*
29376 TCGTTCCTGAAAGTCGTTCCTGAAGTTGTTCC
1 TCGTTCCTGAAAGTCGTTCCTGAAGTCGTTCC
*
29408 TCGTTCCTG-ATGTCGTTCCTGAAGTCGTTCC
1 TCGTTCCTGAAAGTCGTTCCTGAAGTCGTTCC
29439 T
1 T
29440 GAAAGTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (32 bp):
TCGTTCCTGAAAGTCGTTCCTGAAGTCGTTCC
Found at i:30830 original size:20 final size:21
Alignment explanation
Indices: 30805--30843 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30795 TGAATCATCA
*
30805 GTTAATCAA-TTTAGCATTTT
1 GTTAATAAATTTTAGCATTTT
30825 GTTAATAAATTTTAGCATT
1 GTTAATAAATTTTAGCATT
30844 AGTTCCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (21 bp):
GTTAATAAATTTTAGCATTTT
Found at i:34582 original size:3 final size:3
Alignment explanation
Indices: 34574--34604 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
34564 TATGGTATAG
34574 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
34605 AGGCGACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:37647 original size:9 final size:9
Alignment explanation
Indices: 37633--37662 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
37623 CATATTTGGG
37633 TAAAAGTAA
1 TAAAAGTAA
37642 TAAAAGTAA
1 TAAAAGTAA
*
37651 TAATAGTAA
1 TAAAAGTAA
37660 TAA
1 TAA
37663 TTGCACATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (9 bp):
TAAAAGTAA
Found at i:41804 original size:3 final size:3
Alignment explanation
Indices: 41796--41822 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
41786 GAAAGATTTC
41796 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
41823 CAGAGGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:46988 original size:67 final size:66
Alignment explanation
Indices: 46876--47009 Score: 232
Period size: 67 Copynumber: 2.0 Consensus size: 66
46866 TACGAACCTC
*
46876 TAGTATTTAGTAATCATTTAAGTCCCGATTAATCTAGAGTTAGTCCTATATTTTCATGATGAACT
1 TAGTATTTAGTAATCATTTAAGTCCCGATTAATCTAGAGTCAGTCCTATATTTTCATGATGAACT
46941 T
66 T
* *
46942 TAGTATTTAGTAATCACTTTAAGTCCCGATTAATCTGGAGTCAGTCCTATATTTTCATGGTGAAC
1 TAGTATTTAGTAATCA-TTTAAGTCCCGATTAATCTAGAGTCAGTCCTATATTTTCATGATGAAC
47007 TT
65 TT
47009 T
1 T
47010 TTTAGGTAAG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
66 16 0.25
67 48 0.75
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (66 bp):
TAGTATTTAGTAATCATTTAAGTCCCGATTAATCTAGAGTCAGTCCTATATTTTCATGATGAACT
T
Found at i:60229 original size:6 final size:7
Alignment explanation
Indices: 60208--60238 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
60198 TATATTGGAC
60208 TTCTATTT
1 TTCT-TTT
60216 TTCTTTT
1 TTCTTTT
60223 TTCTTTT
1 TTCTTTT
60230 TTCTTTT
1 TTCTTTT
60237 TT
1 TT
60239 GGACAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (7 bp):
TTCTTTT
Found at i:69668 original size:32 final size:33
Alignment explanation
Indices: 69627--69695 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
69617 ATCTCTATCA
*
69627 CTCAGTCTTGGGCA-TTTTTTGTAGGTTGATTT
1 CTCAATCTTGGGCATTTTTTTGTAGGTTGATTT
69659 CTCAATCTTGGGCATTTTTTTGTAGGTTGATTT
1 CTCAATCTTGGGCATTTTTTTGTAGGTTGATTT
69692 CTCA
1 CTCA
69696 TCAGATTCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 13 0.37
33 22 0.63
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.49
Consensus pattern (33 bp):
CTCAATCTTGGGCATTTTTTTGTAGGTTGATTT
Found at i:71707 original size:14 final size:14
Alignment explanation
Indices: 71688--71715 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
71678 TTCCCCTCAG
71688 TGAAAGAAATTGAA
1 TGAAAGAAATTGAA
71702 TGAAAGAAATTGAA
1 TGAAAGAAATTGAA
71716 GATATGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (14 bp):
TGAAAGAAATTGAA
Found at i:72345 original size:41 final size:42
Alignment explanation
Indices: 72227--72345 Score: 204
Period size: 42 Copynumber: 2.8 Consensus size: 42
72217 CACTTATAAA
*
72227 AATATAGAAAAAACTATAAAAAAAACATTAATAACAATCCTAAT
1 AATATAG-AAAAACTAT-AAAAAAACATTAATAAAAATCCTAAT
72271 AATATAGAAAAACTATAAAAAAACATTAATAAAAATCCTAAT
1 AATATAGAAAAACTATAAAAAAACATTAATAAAAATCCTAAT
72313 AATATAGAAAAACTAT-AAAAAACATTAATAAAA
1 AATATAGAAAAACTATAAAAAAACATTAATAAAA
72346 TAAAATTTCT
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
41 17 0.23
42 41 0.55
43 9 0.12
44 7 0.09
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.23
Consensus pattern (42 bp):
AATATAGAAAAACTATAAAAAAACATTAATAAAAATCCTAAT
Found at i:72533 original size:42 final size:43
Alignment explanation
Indices: 72445--72535 Score: 121
Period size: 48 Copynumber: 2.0 Consensus size: 43
72435 CTATGATAGG
*
72445 AAAATCATCATCAAATCACTTTTACTTACAGCATCAACACTTGGTTCA
1 AAAATCATCATCAAATCACTTTTACCTACAGCAT----A-TTGGTTCA
72493 AAAATCATCATCAAATCACTTTTACCTACAGCAT-TTGGTTCA
1 AAAATCATCATCAAATCACTTTTACCTACAGCATATTGGTTCA
72535 A
1 A
72536 CAGCAACAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
42 9 0.21
48 33 0.79
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (43 bp):
AAAATCATCATCAAATCACTTTTACCTACAGCATATTGGTTCA
Found at i:72797 original size:56 final size:56
Alignment explanation
Indices: 72711--72822 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
72701 CCTATCGTTA
72711 AATTAGCATCTACAGAATAAGAAAACTTGTGAACTCGTTTGAATATGGCTGCCGAT
1 AATTAGCATCTACAGAATAAGAAAACTTGTGAACTCGTTTGAATATGGCTGCCGAT
72767 AATTAGCATCTACAGAATAAGAAAACTTGTGAACTCGTTTGAATATGGCTGCCGAT
1 AATTAGCATCTACAGAATAAGAAAACTTGTGAACTCGTTTGAATATGGCTGCCGAT
72823 GTCACCATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (56 bp):
AATTAGCATCTACAGAATAAGAAAACTTGTGAACTCGTTTGAATATGGCTGCCGAT
Found at i:73101 original size:25 final size:25
Alignment explanation
Indices: 73067--73116 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
73057 TACTCTGTTC
73067 TAGATTGGGTCGAGAAAGAATTCCT
1 TAGATTGGGTCGAGAAAGAATTCCT
* *
73092 TAGATTGGGTTGAGAAAGGATTCCT
1 TAGATTGGGTCGAGAAAGAATTCCT
73117 AAATAGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (25 bp):
TAGATTGGGTCGAGAAAGAATTCCT
Found at i:81442 original size:41 final size:41
Alignment explanation
Indices: 81355--81451 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
81345 TTTCTCTTTT
*
81355 TATCTCACTTAGGGTTTAATGTATTTTTTGAGGGTTTCTTC
1 TATCTCACTTAGGGTTTAATGTATTTGTTGAGGGTTTCTTC
*
81396 TATCTCACTTAGGGTTTATAT-TGTTTGTT-AGGGTTTGGCTTC
1 TATCTCACTTAGGGTTTA-ATGTATTTGTTGAGGGTTT--CTTC
81438 -ATCTCAC--AGGGTTT
1 TATCTCACTTAGGGTTT
81452 GTCATGTCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
39 7 0.14
40 7 0.14
41 31 0.61
42 6 0.12
ACGTcount: A:0.16, C:0.13, G:0.22, T:0.48
Consensus pattern (41 bp):
TATCTCACTTAGGGTTTAATGTATTTGTTGAGGGTTTCTTC
Done.