Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009721.1 Corchorus capsularis cultivar CVL-1 contig09742, 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: 64931
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:261 original size:29 final size:29
Alignment explanation
Indices: 224--294 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
214 CTTGGCAACA
****
224 GGGCTTATTTGACTTTTTTAAGAGTTCAG
1 GGGCTTATTTGACTGAAATAAGAGTTCAG
* *
253 GGGCTTATTTGGCTGAAATAATAGTTCAG
1 GGGCTTATTTGACTGAAATAAGAGTTCAG
282 GGGCTTATTTGAC
1 GGGCTTATTTGAC
295 GGTTCGATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (29 bp):
GGGCTTATTTGACTGAAATAAGAGTTCAG
Found at i:994 original size:23 final size:24
Alignment explanation
Indices: 968--1018 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
958 TTGGTGAGTT
968 TTGAAG-CCTTCACAAGTGATCTC
1 TTGAAGCCCTTCACAAGTGATCTC
991 TTGAAGCCCTTCACAAGTGATCTC
1 TTGAAGCCCTTCACAAGTGATCTC
1015 TTGA
1 TTGA
1019 CTTATGCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (24 bp):
TTGAAGCCCTTCACAAGTGATCTC
Found at i:31140 original size:38 final size:41
Alignment explanation
Indices: 31097--31178 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 41
31087 TGGATAGATT
31097 TTACTTTGCTTGCAAGTAAAG-AA-T-ATTAGCATTAAATG
1 TTACTTTGCTTGCAAGTAAAGAAAGTAATTAGCATTAAATG
*
31135 TTACTTTGCTTGCAAGTCAAGTAAAGTAGATTAGCATTAAATG
1 TTACTTTGCTTGCAAGTAAAG-AAAGTA-ATTAGCATTAAATG
31178 T
1 T
31179 AAATGGGATC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
38 20 0.53
40 2 0.05
41 1 0.03
43 15 0.39
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (41 bp):
TTACTTTGCTTGCAAGTAAAGAAAGTAATTAGCATTAAATG
Found at i:31495 original size:40 final size:40
Alignment explanation
Indices: 31451--31531 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
31441 TTTCAATTTA
31451 ATTGGCACCAGAAGTTGCCATATGAAATTATTATCTTGAC
1 ATTGGCACCAGAAGTTGCCATATGAAATTATTATCTTGAC
*
31491 ATTGGCACCTGAAGTTGCCATATGAAATTATTATCTTGAC
1 ATTGGCACCAGAAGTTGCCATATGAAATTATTATCTTGAC
31531 A
1 A
31532 CCAGAAGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (40 bp):
ATTGGCACCAGAAGTTGCCATATGAAATTATTATCTTGAC
Found at i:31539 original size:34 final size:34
Alignment explanation
Indices: 31456--31708 Score: 215
Period size: 34 Copynumber: 7.5 Consensus size: 34
31446 ATTTAATTGG
*
31456 CACCAGAAGTTGCCATATGAAATTATTATCTTGACA
1 CACCAGAAGTTGTCATATGAAATTATTATCTTG--A
* *
31492 TTGGCACCTGAAGTTGCCATATGAAATTATTATCTTGA
1 ----CACCAGAAGTTGTCATATGAAATTATTATCTTGA
*
31530 CACCAGAAGTTGTCATATTGAAA--ATGA--TTGA
1 CACCAGAAGTTGTCATA-TGAAATTATTATCTTGA
* *
31561 CACCAGAAGTTGTTATATCAAATTATTATCTTGA
1 CACCAGAAGTTGTCATATGAAATTATTATCTTGA
* *
31595 CACCAGAAGTTGTCATGTTGAAA--ATGA--TTGA
1 CACCAGAAGTTGTCAT-ATGAAATTATTATCTTGA
*
31626 CACCAGAAGTTGTCATATCAAATTATTATCTTGA
1 CACCAGAAGTTGTCATATGAAATTATTATCTTGA
** *
31660 CACTGGAAGTTGTCATGCTGAGGAA--ATTA--TTGA
1 CACCAGAAGTTGTCAT-ATGA--AATTATTATCTTGA
31693 CACCAGAAGTTGTCAT
1 CACCAGAAGTTGTCAT
31709 CCTAAGATTG
Statistics
Matches: 180, Mismatches: 20, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.04
31 40 0.22
32 6 0.03
33 24 0.13
34 52 0.29
35 15 0.08
37 2 0.01
38 1 0.01
40 32 0.18
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (34 bp):
CACCAGAAGTTGTCATATGAAATTATTATCTTGA
Found at i:31605 original size:65 final size:65
Alignment explanation
Indices: 31491--31708 Score: 328
Period size: 65 Copynumber: 3.3 Consensus size: 65
31481 TTATCTTGAC
* * * * *
31491 ATTGGCACCTGAAGTTGCCATATGAAATTATTATCTTGACACCAGAAGTTGTCATATTGAAAATG
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGTTGAAAATG
*
31556 ATTGACACCAGAAGTTGTTATATCAAATTATTATCTTGACACCAGAAGTTGTCATGTTGAAAATG
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGTTGAAAATG
** *
31621 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACTGGAAGTTGTCATGCTGAGGAAA
1 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGTTGA--AAA
*
31686 TT
64 TG
31688 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
31709 CCTAAGATTG
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
65 115 0.82
67 25 0.18
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (65 bp):
ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGTTGAAAATG
Found at i:36724 original size:43 final size:43
Alignment explanation
Indices: 36663--36751 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
36653 TTATGCCTTG
36663 GTCTAGAGCTTGAGCACAAAGAACATGGAATATTTGTCCATCA
1 GTCTAGAGCTTGAGCACAAAGAACATGGAATATTTGTCCATCA
36706 GTCTAGAGCTTGAGCACAAAGAACATGGAATATTTGTCCATCA
1 GTCTAGAGCTTGAGCACAAAGAACATGGAATATTTGTCCATCA
36749 GTC
1 GTC
36752 AGCGTACACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (43 bp):
GTCTAGAGCTTGAGCACAAAGAACATGGAATATTTGTCCATCA
Found at i:38076 original size:38 final size:41
Alignment explanation
Indices: 38034--38115 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 41
38024 TGGATAGATT
*
38034 TTACTTTGCTTGCAAGT-A-AAGC-AGATTAGCATTAAATG
1 TTACTTTGCTTGCAAGTAAGAAACTAGATTAGCATTAAATG
38072 TTACTTTGCTTGCAAGTCAAGTAAACTAGATTAGCATTAAATG
1 TTACTTTGCTTGCAAGT-AAG-AAACTAGATTAGCATTAAATG
38115 T
1 T
38116 AAAGGGGATC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
38 17 0.45
40 1 0.03
42 3 0.08
43 17 0.45
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (41 bp):
TTACTTTGCTTGCAAGTAAGAAACTAGATTAGCATTAAATG
Found at i:39493 original size:16 final size:16
Alignment explanation
Indices: 39472--39505 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39462 GAACCTGCCC
*
39472 GATCCGAGACCCGAAT
1 GATCCGAAACCCGAAT
39488 GATCCGAAACCCGAAT
1 GATCCGAAACCCGAAT
39504 GA
1 GA
39506 CTCGTATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.24, T:0.12
Consensus pattern (16 bp):
GATCCGAAACCCGAAT
Found at i:39557 original size:9 final size:9
Alignment explanation
Indices: 39479--39535 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
39469 CCCGATCCGA
39479 GACCCGAAT
1 GACCCGAAT
*
39488 GATCCGAA-
1 GACCCGAAT
39496 -ACCCGAAT
1 GACCCGAAT
* *
39504 GACTCGTAT
1 GACCCGAAT
39513 GACCCGAA-
1 GACCCGAAT
39521 -ACCCGAAT
1 GACCCGAAT
*
39529 AACCCGA
1 GACCCGA
39536 GAAGTTAACC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
7 13 0.34
9 25 0.66
ACGTcount: A:0.35, C:0.33, G:0.19, T:0.12
Consensus pattern (9 bp):
GACCCGAAT
Found at i:40375 original size:7 final size:7
Alignment explanation
Indices: 40365--40455 Score: 83
Period size: 7 Copynumber: 11.9 Consensus size: 7
40355 AACCCGCCCA
40365 ACCCGAG
1 ACCCGAG
40372 ACCCGGTAG
1 ACCC-G-AG
40381 ACCCGAG
1 ACCCGAG
40388 ACCCGAG
1 ACCCGAG
40395 ACCCGAG
1 ACCCGAG
40402 ACCCGAATG
1 ACCCG-A-G
*
40411 ACCCGAA
1 ACCCGAG
40418 ACCCGTATG
1 ACCCG-A-G
*
40427 ACCTGAG
1 ACCCGAG
40434 ACCCGAATG
1 ACCCG-A-G
*
40443 ACCCGAA
1 ACCCGAG
40450 ACCCGA
1 ACCCGA
40456 ATCCAGATGA
Statistics
Matches: 71, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
7 41 0.58
8 8 0.11
9 22 0.31
ACGTcount: A:0.31, C:0.38, G:0.24, T:0.07
Consensus pattern (7 bp):
ACCCGAG
Found at i:40392 original size:23 final size:22
Alignment explanation
Indices: 40365--40439 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 22
40355 AACCCGCCCA
40365 ACCCGAGACCCGGTAGACCCGAG
1 ACCCGAGACCC-GTAGACCCGAG
40388 ACCCGAGACCCG-AGACCCGAATG
1 ACCCGAGACCCGTAGACCCG-A-G
* *
40411 ACCCGAAACCCGTATGACCTGAG
1 ACCCGAGACCCGTA-GACCCGAG
40434 ACCCGA
1 ACCCGA
40440 ATGACCCGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.15
22 2 0.04
23 30 0.65
24 2 0.04
25 5 0.11
ACGTcount: A:0.29, C:0.39, G:0.25, T:0.07
Consensus pattern (22 bp):
ACCCGAGACCCGTAGACCCGAG
Found at i:40415 original size:9 final size:9
Alignment explanation
Indices: 40401--40457 Score: 54
Period size: 9 Copynumber: 7.0 Consensus size: 9
40391 CGAGACCCGA
40401 GACCCGAAT
1 GACCCGAAT
40410 GACCCGAA-
1 GACCCGAAT
*
40418 -ACCCGTAT
1 GACCCGAAT
*
40426 GACCTG-A-
1 GACCCGAAT
40433 GACCCGAAT
1 GACCCGAAT
40442 GACCCGAA-
1 GACCCGAAT
40450 -ACCCGAAT
1 GACCCGAAT
40458 CCAGATGACC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
7 18 0.45
8 2 0.05
9 20 0.50
ACGTcount: A:0.33, C:0.35, G:0.21, T:0.11
Consensus pattern (9 bp):
GACCCGAAT
Found at i:40455 original size:16 final size:16
Alignment explanation
Indices: 40365--40457 Score: 111
Period size: 16 Copynumber: 5.9 Consensus size: 16
40355 AACCCGCCCA
*
40365 ACCCGAGACCCG-GTAG
1 ACCCGAGACCCGAAT-G
40381 ACCCGAGACCCG-A-G
1 ACCCGAGACCCGAATG
40395 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
* *
40411 ACCCGAAACCCGTATG
1 ACCCGAGACCCGAATG
*
40427 ACCTGAGACCCGAATG
1 ACCCGAGACCCGAATG
*
40443 ACCCGAAACCCGAAT
1 ACCCGAGACCCGAAT
40458 CCAGATGACC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
14 13 0.19
15 1 0.01
16 53 0.79
ACGTcount: A:0.31, C:0.38, G:0.24, T:0.08
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:41885 original size:86 final size:86
Alignment explanation
Indices: 41772--41947 Score: 316
Period size: 86 Copynumber: 2.0 Consensus size: 86
41762 TGTCATTATT
*
41772 AAAATTTAGCATAATCTTACTCCCTCTGTTCCCATTTATTTGTCATCACTCTGGTCAAATGACTT
1 AAAATTTAGCATAATCTTACTCCCTCTGTTCCCATTTATTTGTCATCACTCTGGTCAAATAACTT
41837 CAACTTTAACCATTAGTTAAA
66 CAACTTTAACCATTAGTTAAA
* *
41858 AAAATTTAGCATAATTTTACTCCCTCTGTTCCTATTTATTTGTCATCACTCTGGTCAAATAACTT
1 AAAATTTAGCATAATCTTACTCCCTCTGTTCCCATTTATTTGTCATCACTCTGGTCAAATAACTT
*
41923 CAACTTTGACCATTAGTTAAA
66 CAACTTTAACCATTAGTTAAA
41944 AAAA
1 AAAA
41948 AATATGTAGA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.39
Consensus pattern (86 bp):
AAAATTTAGCATAATCTTACTCCCTCTGTTCCCATTTATTTGTCATCACTCTGGTCAAATAACTT
CAACTTTAACCATTAGTTAAA
Found at i:42302 original size:22 final size:22
Alignment explanation
Indices: 42277--42324 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
42267 ATGTGATTAT
*
42277 CAAAATTTCATAGAGGGGTTAA
1 CAAAATTTCATAGAGAGGTTAA
* *
42299 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAA
42321 CAAA
1 CAAA
42325 TTGTCAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTTAA
Found at i:42580 original size:22 final size:22
Alignment explanation
Indices: 42488--42825 Score: 132
Period size: 22 Copynumber: 15.5 Consensus size: 22
42478 AGTTTAGTTT
42488 TCAAAATTTCATAA-GAGGGTTA
1 TCAAAATTTCATAATGA-GGTTA
*
42510 TCAAAATTTC-TTATGTA-G--A
1 TCAAAATTTCATAATG-AGGTTA
** *
42529 TCAAAATTTCATAGCTATGAAATCA
1 TCAAAATTTCATA---ATGAGGTTA
*
42554 ACAAAATTTCATAATGAGGTTA
1 TCAAAATTTCATAATGAGGTTA
** **
42576 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAATGAGGTTA
*
42598 TCAAAA-TT--T-GT-A-GTTA
1 TCAAAATTTCATAATGAGGTTA
* *
42614 TCAAGATTTCATAAGGAGGTTA
1 TCAAAATTTCATAATGAGGTTA
* * *
42636 TCAAAATTTTATAGGA-AAGTTTA
1 TCAAAATTTCATA--ATGAGGTTA
**
42659 TCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATAATGAGGTTA
* * * *
42681 TCACAATTTCATAGTGTGATTA
1 TCAAAATTTCATAATGAGGTTA
* * * * *
42703 TTAAAATTTCAGAGTGTGATTA
1 TCAAAATTTCATAATGAGGTTA
*
42725 -CTAACAA-TTCAT-ATGAAGGTTT
1 TC-AA-AATTTCATAATG-AGGTTA
* * * *
42747 TTAAATTTTCATAACGTGGTTA
1 TCAAAATTTCATAATGAGGTTA
* *
42769 TCAATATATCAT-ATGGAGGTTA
1 TCAAAATTTCATAAT-GAGGTTA
* * *
42791 TCAACATTTCATAGTGTTGGTTA
1 TCAAAATTTCATAATG-AGGTTA
42814 TCAAAATTTCAT
1 TCAAAATTTCAT
42826 TGGGAAATAA
Statistics
Matches: 235, Mismatches: 54, Indels: 53
0.69 0.16 0.15
Matches are distributed among these distances:
16 9 0.04
17 3 0.01
18 1 0.00
19 13 0.06
20 1 0.00
21 9 0.04
22 143 0.61
23 42 0.18
24 1 0.00
25 13 0.06
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAATGAGGTTA
Found at i:42985 original size:22 final size:22
Alignment explanation
Indices: 42555--42985 Score: 146
Period size: 22 Copynumber: 19.9 Consensus size: 22
42545 ATGAAATCAA
*
42555 CAAAATTTCATAATGAGGTTAT
1 CAAAATTTCATAAGGAGGTTAT
** *
42577 CAAAAAATCATAGGGAGGTTAT
1 CAAAATTTCATAAGGAGGTTAT
*
42599 CAAAA-TT--T--GTA-GTTAT
1 CAAAATTTCATAAGGAGGTTAT
*
42615 CAAGATTTCATAAGGAGGTTAT
1 CAAAATTTCATAAGGAGGTTAT
* *
42637 CAAAATTTTAT-AGGAAAGTTTAT
1 CAAAATTTCATAAGG--AGGTTAT
42660 CAAAATTTCAT-AGCGAGGTTAT
1 CAAAATTTCATAAG-GAGGTTAT
* * *
42682 CACAATTTCAT-AGTGTGATTAT
1 CAAAATTTCATAAG-GAGGTTAT
* * * *
42704 TAAAATTTCA-GAGTGTGATTA-
1 CAAAATTTCATAAG-GAGGTTAT
* * *
42725 CTAACAA-TTCATATGAAGGTTTT
1 C-AA-AATTTCATAAGGAGGTTAT
* * * *
42748 TAAATTTTCATAACGTGGTTAT
1 CAAAATTTCATAAGGAGGTTAT
* * *
42770 CAATATATCATATGGAGGTTAT
1 CAAAATTTCATAAGGAGGTTAT
* *
42792 CAACATTTCAT-AGTGTTGGTTAT
1 CAAAATTTCATAAG-G-AGGTTAT
** ** * *
42815 CAAAATTTCATTGGGAAATAAA
1 CAAAATTTCATAAGGAGGTTAT
42837 CAAAACTTT-AT-AGTGAGGTCT-T
1 CAAAA-TTTCATAAG-GAGGT-TAT
* * * * *
42859 CAAAATTGCTTAGGGAGATTAA
1 CAAAATTTCATAAGGAGGTTAT
* *
42881 CAAAATTCCATAAGAAGGTTA-
1 CAAAATTTCATAAGGAGGTTAT
* ** *
42902 AAAAATTT-ATAAAAAGGTTCT
1 CAAAATTTCATAAGGAGGTTAT
* * * * *
42923 CGAAATTCCGT-AGTATCGTTAT
1 CAAAATTTCATAAGGA-GGTTAT
*
42945 TAAAATTTCAT-AGGAAGGTTAT
1 CAAAATTTCATAAGG-AGGTTAT
42967 CAAAATTTCATAAGGAGGT
1 CAAAATTTCATAAGGAGGT
42986 CATAAAAAAT
Statistics
Matches: 295, Mismatches: 85, Indels: 58
0.67 0.19 0.13
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
20 10 0.03
21 25 0.08
22 197 0.67
23 46 0.16
24 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAAGGAGGTTAT
Found at i:42995 original size:23 final size:22
Alignment explanation
Indices: 42946--42993 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
42936 TATCGTTATT
* *
42946 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAGGAAGGTCATA
42968 AAAATTTCATAAGG-AGGTCATA
1 AAAATTTCAT-AGGAAGGTCATA
42990 AAAA
1 AAAA
42994 ATAGTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATA
Found at i:48271 original size:24 final size:23
Alignment explanation
Indices: 48231--48281 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
48221 CTAATAATAA
48231 TTAAAATAATAATAATAAGAAGT
1 TTAAAATAATAATAATAAGAAGT
* *
48254 TTAATAATTATAATAATAAGAGGT
1 TTAA-AATAATAATAATAAGAAGT
48278 TTAA
1 TTAA
48282 CGTAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (23 bp):
TTAAAATAATAATAATAAGAAGT
Found at i:48367 original size:110 final size:107
Alignment explanation
Indices: 48238--48435 Score: 299
Period size: 110 Copynumber: 1.8 Consensus size: 107
48228 TAATTAAAAT
48238 AATAATAATAAGAAGTTTAATAATTATAATAATAAGAGGTTTAACGTAAAAAAAATTGTTACTAT
1 AATAATAATAAGAAGTTTAATAATTATAATAATAAGAGGTTTAACGTAAAAAAAATTG-T--TAT
48303 TATTTTAGA-TTTTGTAATATGGAAAGAAAAACGTTATGATATAG
63 TATTTTAGACTTTTGTAATATGGAAAGAAAAACGTTATGATATAG
* * ** *
48347 AATAACTAATAATAATTTTAATAATTATAATAATAAGTTGTTTAACGTAAAAATAATTGTTATTA
1 AATAA-TAATAAGAAGTTTAATAATTATAATAATAAGAGGTTTAACGTAAAAAAAATTGTTATTA
*
48412 TTTTAGACTTTTTTAATATGGAAA
65 TTTTAGACTTTTGTAATATGGAAA
48436 TATTTTAAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
107 12 0.15
108 15 0.19
109 6 0.07
110 48 0.59
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.39
Consensus pattern (107 bp):
AATAATAATAAGAAGTTTAATAATTATAATAATAAGAGGTTTAACGTAAAAAAAATTGTTATTAT
TTTAGACTTTTGTAATATGGAAAGAAAAACGTTATGATATAG
Found at i:54145 original size:17 final size:17
Alignment explanation
Indices: 54125--54159 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
54115 GTGAGCGTAT
54125 TGGGAGGGTGATCAAAA
1 TGGGAGGGTGATCAAAA
54142 TGGGAGGGTGATCAAAA
1 TGGGAGGGTGATCAAAA
54159 T
1 T
54160 TGATTCAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.40, T:0.20
Consensus pattern (17 bp):
TGGGAGGGTGATCAAAA
Done.