Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007269.1 Corchorus capsularis cultivar CVL-1 contig07290, 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: 28077
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5854 original size:13 final size:15
Alignment explanation
Indices: 5827--5862 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5817 TTTATGTTAT
5827 ATATATAAGTAAATA
1 ATATATAAGTAAATA
5842 ATATATAA-T-AATA
1 ATATATAAGTAAATA
5855 ATA-ATAAG
1 ATATATAAG
5863 GATTTAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.20
13 7 0.35
14 1 0.05
15 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (15 bp):
ATATATAAGTAAATA
Found at i:6552 original size:16 final size:18
Alignment explanation
Indices: 6513--6552 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
6503 TTGGAACCAT
6513 ATGACCCAAAACCGAAAA
1 ATGACCCAAAACCGAAAA
*
6531 A-CACCC-AAACC-AAAA
1 ATGACCCAAAACCGAAAA
6546 ATGACCC
1 ATGACCC
6553 GACATTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 4 0.21
18 1 0.05
ACGTcount: A:0.53, C:0.35, G:0.07, T:0.05
Consensus pattern (18 bp):
ATGACCCAAAACCGAAAA
Found at i:7062 original size:109 final size:109
Alignment explanation
Indices: 6926--7205 Score: 420
Period size: 109 Copynumber: 2.5 Consensus size: 109
6916 AAAAAAATTA
*
6926 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTATATATTAG
6989 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
*
7034 TATAAAGATATTAGATTGAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTATATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTATATATTAGA
* * *
7099 AAAAGTTTTAGTATATCCAAATTTTTTTGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* * *
7143 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAACTATA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAATTATA
7206 ATAGTTAAGT
Statistics
Matches: 156, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
108 6 0.04
109 114 0.73
110 3 0.02
111 1 0.01
114 32 0.21
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTATATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:10072 original size:22 final size:22
Alignment explanation
Indices: 10047--10104 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
10037 ATCACACTAT
*
10047 AAAATTTCGATAACATTCTTAC
1 AAAATTTTGATAACATTCTTAC
* *
10069 AAAATTTTGATAACTTTCTTAT
1 AAAATTTTGATAACATTCTTAC
10091 AAAATTTTGATAAC
1 AAAATTTTGATAAC
10105 CACAGAACGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (22 bp):
AAAATTTTGATAACATTCTTAC
Found at i:10397 original size:21 final size:22
Alignment explanation
Indices: 10236--10924 Score: 227
Period size: 22 Copynumber: 31.8 Consensus size: 22
10226 CAGTACCACA
* *
10236 CTATAAAATTTTGATAACCTGC
1 CTATGAAATTTTGATAACCTCC
*
10258 ATATGAAATTTTGATAACCTCGC
1 CTATGAAATTTTGATAACCTC-C
*
10281 C-ATGAAATTTCGATAA--TGCC
1 CTATGAAATTTTGATAACCT-CC
* * *
10301 TGTATGAAATTTTGATAACCACAA
1 -CTATGAAATTTTGATAACCTC-C
10325 C-ATGAAATTTTGATAA--TGCC
1 CTATGAAATTTTGATAACCT-CC
* * * * * *
10345 TGTATCAAAATTTGGTAGA-CACA
1 -CTATGAAATTTTGATA-ACCTCC
10368 CTATGAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCTCC
* *
10390 CTAT-AAATTTTCAGA-AACCACA
1 CTATGAAATTTT--GATAACCTCC
* *
10412 CTATGGAATCTTGATTAACCTCC
1 CTATGAAATTTTGA-TAACCTCC
* * *
10435 ATATGAAATTTTGATATCCTCT
1 CTATGAAATTTTGATAACCTCC
* *
10457 CTACGAAATTTTGA-AGGCCTCC
1 CTATGAAATTTTGATA-ACCTCC
* ** *
10479 TTATGAAA-TTTGATTGCCTCT
1 CTATGAAATTTTGATAACCTCC
* * *
10500 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCTCC
* * *
10522 CTAT-AAAGTTTCAGTAACATCC
1 CTATGAAATTTTGA-TAACCTCC
* * *
10544 TTATGAAA-TTTAATTAA--TCT
1 CTATGAAATTTTGA-TAACCTCC
* * * *
10564 CTATGAAATTTTAAT-ATCACA
1 CTATGAAATTTTGATAACCTCC
* * *
10585 ATATAAAAATTTTGGA-AACCTCT
1 CTAT-GAAATTTT-GATAACCTCC
* *
10608 CTATGAAACTTTGGTAA--T--
1 CTATGAAATTTTGATAACCTCC
* * * * *
10626 CT-T-CACTTTTGATAAGCACA
1 CTATGAAATTTTGATAACCTCC
* *
10646 TTATGAAATTTTGATAACCTTC
1 CTATGAAATTTTGATAACCTCC
* * * *
10668 TTAGGAAACTTTGATAACCTTC
1 CTATGAAATTTTGATAACCTCC
* * ** *
10690 TTATGAAATTCTGATAACAACA
1 CTATGAAATTTTGATAACCTCC
*
10712 C--TGAAATTTTAATAACCT-C
1 CTATGAAATTTTGATAACCTCC
*
10731 CTCATG-AATTTT-AGTAA-CTACA
1 CT-ATGAAATTTTGA-TAACCT-CC
10753 CTATGAAATTTTGATAA-CTACC
1 CTATGAAATTTTGATAACCT-CC
* * *
10775 CTATGAAATTTTGATAGCCACA
1 CTATGAAATTTTGATAACCTCC
* * * **
10797 CTGTGCAAA-TGTGATAACTTTG
1 CTATG-AAATTTTGATAACCTCC
* * *
10819 TTATGAAATTTTGATAACATCA
1 CTATGAAATTTTGATAACCTCC
*
10841 CTATGAAATTTTGATAA-CTACA
1 CTATGAAATTTTGATAACCT-CC
* * ** *
10863 TTACGAAATTTTGATAACAACA
1 CTATGAAATTTTGATAACCTCC
* *
10885 CTATGAAATTTCGATAACCTCA
1 CTATGAAATTTTGATAACCTCC
*
10907 TTATGAAATTTTGATAAC
1 CTATGAAATTTTGATAAC
10925 TACATAGAGA
Statistics
Matches: 490, Mismatches: 128, Indels: 98
0.68 0.18 0.14
Matches are distributed among these distances:
16 8 0.02
17 1 0.00
18 2 0.00
19 2 0.00
20 30 0.06
21 65 0.13
22 340 0.69
23 42 0.09
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTCC
Found at i:10508 original size:43 final size:44
Alignment explanation
Indices: 10430--10513 Score: 118
Period size: 43 Copynumber: 1.9 Consensus size: 44
10420 TCTTGATTAA
10430 CCTCCATATGAAATTTTGATATCCTCTCTACGAAATTTTGAAGG
1 CCTCCATATGAAATTTTGATATCCTCTCTACGAAATTTTGAAGG
* * *
10474 CCTCCTTATGAAA-TTTGAT-TGCCTCTTTATGAAATTTTGA
1 CCTCCATATGAAATTTTGATAT-CCTCTCTACGAAATTTTGA
10514 TAACCACACT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 1 0.03
43 23 0.64
44 12 0.33
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (44 bp):
CCTCCATATGAAATTTTGATATCCTCTCTACGAAATTTTGAAGG
Found at i:10923 original size:44 final size:44
Alignment explanation
Indices: 10233--10924 Score: 295
Period size: 44 Copynumber: 16.0 Consensus size: 44
10223 CCACAGTACC
* *
10233 ACACTATAAAATTTTGATAACCTGCA-TATGAAATTTTGATAACC
1 ACACTATGAAATTTTGATAACCT-CATTATGAAATTTTGATAACA
* * * * * *
10277 TCGCCATGAAATTTCGATAATGCCT--GTATGAAATTTTGATAACC
1 ACACTATGAAATTTTGATAA--CCTCATTATGAAATTTTGATAACA
* * * *
10321 ACAAC-ATGAAATTTTGATAATGCCT--GTATCAAAATTTGGTAGAC-
1 AC-ACTATGAAATTTTGATAA--CCTCATTATGAAATTTTGATA-ACA
** *
10365 ACACTATGAAATTTTGATAACCTCCCTAT-AAATTTTCAGA-AACC
1 ACACTATGAAATTTTGATAACCTCATTATGAAATTTT--GATAACA
* * * *
10409 ACACTATGGAATCTTGATTAACCTCCA-TATGAAATTTTGATATCC
1 ACACTATGAAATTTTGA-TAACCT-CATTATGAAATTTTGATAACA
* * * * * ** *
10454 TCTCTACGAAATTTTGA-AGGCCTCCTTATGAAA-TTTGATTGCC
1 ACACTATGAAATTTTGATA-ACCTCATTATGAAATTTTGATAACA
* ** * * * *
10497 TCTTTATGAAATTTTGATAACCACACTAT-AAAGTTTCAGTAACA
1 ACACTATGAAATTTTGATAACCTCATTATGAAATTTTGA-TAACA
* * * * *
10541 TC-CTTATGAAA-TTTAATTAATCTC--TATGAAATTTTAATATC-
1 ACAC-TATGAAATTTTGA-TAACCTCATTATGAAATTTTGATAACA
* * * *
10582 ACAATATAAAAATTTTGGA-AACCTC-TCTATGAAACTTTGGT---A
1 ACACTAT-GAAATTTT-GATAACCTCAT-TATGAAATTTTGATAACA
* * * * *
10624 A-TCT-T-CACTTTTGATAAGCACATTATGAAATTTTGATAAC-
1 ACACTATGAAATTTTGATAACCTCATTATGAAATTTTGATAACA
* * * *
10664 -CTTCTTAGGAAACTTTGATAACCTTC-TTATGAAATTCTGATAACA
1 AC-AC-TATGAAATTTTGATAACC-TCATTATGAAATTTTGATAACA
* * * *
10709 ACAC--TGAAATTTTAATAACCTCCTCATG-AATTTT-AGTAACT
1 ACACTATGAAATTTTGATAACCTCATTATGAAATTTTGA-TAACA
** * *
10750 ACACTATGAAATTTTGATAA-CTACCCTATGAAATTTTGATAGCC
1 ACACTATGAAATTTTGATAACCT-CATTATGAAATTTTGATAACA
* * * **
10794 ACACTGTGCAAA-TGTGATAACTTTGTTATGAAATTTTGATAACA
1 ACACTATG-AAATTTTGATAACCTCATTATGAAATTTTGATAACA
* *
10838 TCACTATGAAATTTTGATAA-CTACATTACGAAATTTTGATAACA
1 ACACTATGAAATTTTGATAACCT-CATTATGAAATTTTGATAACA
*
10882 ACACTATGAAATTTCGATAACCTCATTATGAAATTTTGATAAC
1 ACACTATGAAATTTTGATAACCTCATTATGAAATTTTGATAAC
10925 TACATAGAGA
Statistics
Matches: 496, Mismatches: 97, Indels: 110
0.71 0.14 0.16
Matches are distributed among these distances:
37 2 0.00
38 21 0.04
39 1 0.00
40 2 0.00
41 22 0.04
42 41 0.08
43 81 0.16
44 277 0.56
45 37 0.07
46 12 0.02
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (44 bp):
ACACTATGAAATTTTGATAACCTCATTATGAAATTTTGATAACA
Found at i:12406 original size:16 final size:17
Alignment explanation
Indices: 12385--12424 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
12375 ATCACCCCCC
12385 AGATCACTAGTGAT-TA
1 AGATCACTAGTGATGTA
*
12401 AGATCATTAGTGATGTA
1 AGATCACTAGTGATGTA
12418 AGATCAC
1 AGATCAC
12425 CGGTGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (17 bp):
AGATCACTAGTGATGTA
Found at i:12648 original size:53 final size:52
Alignment explanation
Indices: 12580--12680 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 52
12570 AAAATTGTGT
*
12580 AACCAAACGGGGTGATCTGAGATCACCACCCAAGATCACCAATAGGTGAACCC
1 AACCAAACAGGGTGATCTGAGATCACCACCCAAGATCA-CAATAGGTGAACCC
* * *
12633 AACCAAACAGTGTGATCTGAGATCACCACCTAAGATCACTATAGGTGA
1 AACCAAACAGGGTGATCTGAGATCACCACCCAAGATCACAATAGGTGA
12681 TCAAACGCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 9 0.20
53 35 0.80
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.17
Consensus pattern (52 bp):
AACCAAACAGGGTGATCTGAGATCACCACCCAAGATCACAATAGGTGAACCC
Found at i:15175 original size:27 final size:30
Alignment explanation
Indices: 15137--15229 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 30
15127 GTGCCCAATG
*
15137 ATTTGAGCCAA-TTG-ACT-TTAGGGACTA
1 ATTTGAGCCAATTTGCAATGTTAGGGACTA
15164 ATTTGAGCCAATTTTGCAATGTTAGGGACTA
1 ATTTGAGCCAA-TTTGCAATGTTAGGGACTA
* * * *
15195 ACTTGAGCCGATTTAGCAACGTTAGAGACTTA
1 ATTTGAGCCAATTT-GCAATGTTAGGGAC-TA
15227 ATT
1 ATT
15230 AGCCAAGTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
27 11 0.20
29 3 0.06
30 5 0.09
31 31 0.57
32 4 0.07
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (30 bp):
ATTTGAGCCAATTTGCAATGTTAGGGACTA
Found at i:15192 original size:31 final size:31
Alignment explanation
Indices: 15154--15229 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
15144 CCAATTGACT
* *
15154 TTAGGGACTAATTTGAGCCAATTTTGCAATG
1 TTAGGGACTAATTTGAGCCAATTTAGCAACG
* *
15185 TTAGGGACTAACTTGAGCCGATTTAGCAACG
1 TTAGGGACTAATTTGAGCCAATTTAGCAACG
*
15216 TTAGAGACTTAATT
1 TTAGGGAC-TAATT
15230 AGCCAAGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (31 bp):
TTAGGGACTAATTTGAGCCAATTTAGCAACG
Found at i:18416 original size:13 final size:13
Alignment explanation
Indices: 18398--18432 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
18388 CGTGGGTTGA
18398 TTTAAAAAATATT
1 TTTAAAAAATATT
*
18411 TTTAAAAAATTTT
1 TTTAAAAAATATT
18424 TTTAAAAAA
1 TTTAAAAAA
18433 AGAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAAAAATATT
Found at i:18664 original size:24 final size:25
Alignment explanation
Indices: 18625--18684 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
18615 AAAATTAAGG
*
18625 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
18648 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
18673 GAAATGAAGTTT
1 AAAATGAAGTTT
18685 AGGGTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:19370 original size:30 final size:32
Alignment explanation
Indices: 19316--19381 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
19306 AACTTTATGT
* *
19316 TTTCCAATTGTACCCTTATTTTT-AAAATATA
1 TTTCCAATTATACCATTATTTTTAAAAATATA
*
19347 TTTCCAATTATACCATT-TTTTTAAAAATGTA
1 TTTCCAATTATACCATTATTTTTAAAAATATA
19378 TTTC
1 TTTC
19382 TAAATTGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (32 bp):
TTTCCAATTATACCATTATTTTTAAAAATATA
Found at i:25309 original size:22 final size:22
Alignment explanation
Indices: 25152--25313 Score: 119
Period size: 22 Copynumber: 7.3 Consensus size: 22
25142 TCTCTATGTA
* * *
25152 GTTATCAAAATTTCATAAGATG
1 GTTATTAAAATTTCATAGGGTG
* *
25174 GTTATTATAATTTCAT-GAGGAG
1 GTTATTAAAATTTCATAG-GGTG
* * **
25196 GTTATCAAAATTCCATACTGTG
1 GTTATTAAAATTTCATAGGGTG
** *
25218 GTTACCAAAATTTCATAGTGTG
1 GTTATTAAAATTTCATAGGGTG
* ** *
25240 GTAACCAAAATTTCATAGGATCAG
1 GTTATTAAAATTTCATAGGGT--G
* *
25264 GTTATTAAAATTTCTTAGGTTG
1 GTTATTAAAATTTCATAGGGTG
*
25286 GTTATTGAAATTTCATAGGGTG
1 GTTATTAAAATTTCATAGGGTG
25308 GTTATT
1 GTTATT
25314 TATCACAATT
Statistics
Matches: 111, Mismatches: 25, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
22 94 0.85
24 17 0.15
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (22 bp):
GTTATTAAAATTTCATAGGGTG
Found at i:25372 original size:22 final size:22
Alignment explanation
Indices: 25347--25765 Score: 185
Period size: 22 Copynumber: 18.9 Consensus size: 22
25337 ATCAAAGAGA
* *
25347 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
25369 TTAT-AAGAATTTTATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
25391 TTAACAAAATTTCATTAG-GAGC
1 TTATCAAAATTTCA-TAGTGAGG
* * *
25413 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
25435 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
25457 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
25479 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
25504 AGTACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
25526 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
25547 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
*
25571 ATTATCAAAATTT-ATA-TGAAGA
1 -TTATCAAAATTTCATAGTG-AGG
* **
25593 TTATCAAAATTTAATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* * *
25615 TTATCAAAATTTCAAAGCGACG
1 TTATCAAAATTTCATAGTGAGG
* * * *
25637 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
25659 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* ** **
25681 TTAACAAAATTTTGTAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
25703 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
25725 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
25747 TTA-CAATAATTTCATAGTG
1 TTATCAA-AATTTCATAGTG
25766 GTATTTCTGG
Statistics
Matches: 298, Mismatches: 75, Indels: 48
0.71 0.18 0.11
Matches are distributed among these distances:
20 9 0.03
21 35 0.12
22 212 0.71
23 11 0.04
24 5 0.02
25 16 0.05
26 6 0.02
27 4 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:25869 original size:20 final size:20
Alignment explanation
Indices: 25844--25894 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
25834 TTATGGAGTA
*
25844 ATCAAAATTTCAGGGAGGGT
1 ATCAAAATTTCAGGGAGGAT
25864 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
25883 ATCAAAATTTCA
1 ATCAAAATTTCA
25895 TATGAAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAGGGAGGAT
Found at i:26101 original size:23 final size:23
Alignment explanation
Indices: 26073--26176 Score: 113
Period size: 23 Copynumber: 4.6 Consensus size: 23
26063 CATAAGAAAG
*
26073 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
26096 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
*
26119 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * * *
26141 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGT
26163 TTATCAAAATTTCA
1 TTATCAAAATTTCA
26177 GATTGTGATT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 1 0.01
22 30 0.43
23 39 0.56
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:26157 original size:22 final size:21
Alignment explanation
Indices: 25844--26415 Score: 231
Period size: 22 Copynumber: 26.7 Consensus size: 21
25834 TTATGGAGTA
* *
25844 ATCAAAATTTCA-GGGAGGGT
1 ATCAAAATTTCATAGGAGGTT
* *
25864 ATCAAAA-TTCA-GGGAGGAT
1 ATCAAAATTTCATAGGAGGTT
*
25883 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATA-GGAGGTT
*
25905 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG--GAGGTT
* *
25927 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATAGGA-GGTT
* * *
25949 ATCAAAATTTCATAGTATGTAG
1 ATCAAAATTTCATAGGAGGT-T
*
25971 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATA-GGAGGTT
* *
25993 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
** *
26015 ATCAAAAAATCATAGGGAGCTT
1 ATCAAAATTTCATA-GGAGGTT
* *
26037 ATCAAAA-TT--T-GCA-GCT
1 ATCAAAATTTCATAGGAGGTT
* * *
26053 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCAT-AGGAGGTT
*
26075 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA-GGAGG-TT
* *
26098 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGG-AG-GTT
26121 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAG-GAGGTT
* * *
26143 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAG-GAGGTT
* *
26165 ATCAAAATTTC--A-GATTGTG
1 ATCAAAATTTCATAGGA-GGTT
**
26184 AT-TTAA-TTCATATGGAGGTT
1 ATCAAAATTTCATA-GGAGGTT
* * * * *
26204 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* * *
26226 ATCAATATATCATATGGCGGTT
1 ATCAAAATTTCATA-GGAGGTT
* * *
26248 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-G-AGGTT
*
26271 ATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATA-GGAGGT-T
* *
26294 -TCAAAATTCCTTAGAGAGGTT
1 ATCAAAATTTCATAG-GAGGTT
* *
26315 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
** ** *
26337 AAAAAAATTT-ATAAAAAGATT
1 ATCAAAATTTCAT-AGGAGGTT
* * * * *
26358 CTCGAAATTCCATAGTATCGTT
1 ATCAAAATTTCATAGGA-GGTT
* * *
26380 ATTAAAATTTCATAGAAATGTT
1 ATCAAAATTTCATAG-GAGGTT
26402 ATCAAAATTTCATA
1 ATCAAAATTTCATA
26416 ATGGAATCAT
Statistics
Matches: 413, Mismatches: 98, Indels: 80
0.70 0.17 0.14
Matches are distributed among these distances:
16 7 0.02
17 7 0.02
18 3 0.01
19 24 0.06
20 16 0.04
21 30 0.07
22 262 0.63
23 63 0.15
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Done.