Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006858.1 Corchorus capsularis cultivar CVL-1 contig06879, 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: 40410
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Found at i:2451 original size:12 final size:12
Alignment explanation
Indices: 2434--2461 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2424 CTTTTAATAC
2434 ATTGTGTTGTCA
1 ATTGTGTTGTCA
2446 ATTGTGTTGTCA
1 ATTGTGTTGTCA
2458 ATTG
1 ATTG
2462 CCTGATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.07, G:0.25, T:0.50
Consensus pattern (12 bp):
ATTGTGTTGTCA
Found at i:5991 original size:2 final size:2
Alignment explanation
Indices: 5984--6014 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5974 TATGGAGTAC
5984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6015 CTAGTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7487 original size:21 final size:20
Alignment explanation
Indices: 7445--7488 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
7435 TCTTGTAATC
*
7445 TAAAATTACTAAAAAAGTTA
1 TAAAATTACTAAAAAAGCTA
* *
7465 TAAAAGTTATTAAAATAGCTA
1 TAAAA-TTACTAAAAAAGCTA
7486 TAA
1 TAA
7489 TTCTTTCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTACTAAAAAAGCTA
Found at i:12544 original size:27 final size:28
Alignment explanation
Indices: 12505--12563 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
12495 TTTATAAATT
*
12505 ATTTAAGAAAATTCAGTTAAGATACGAA
1 ATTTAAGAAAATTCAGTTAAGAAACGAA
*
12533 ATTT-AGAAAATTCAGTTAAGAAATGAA
1 ATTTAAGAAAATTCAGTTAAGAAACGAA
12560 ATTT
1 ATTT
12564 TGTTGTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (28 bp):
ATTTAAGAAAATTCAGTTAAGAAACGAA
Found at i:12850 original size:9 final size:9
Alignment explanation
Indices: 12836--12861 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12826 TAGATTCATG
12836 AACATACAC
1 AACATACAC
12845 AACATACAC
1 AACATACAC
12854 AACATACA
1 AACATACA
12862 TGTATATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.31, G:0.00, T:0.12
Consensus pattern (9 bp):
AACATACAC
Found at i:17204 original size:26 final size:26
Alignment explanation
Indices: 17174--17329 Score: 118
Period size: 26 Copynumber: 5.7 Consensus size: 26
17164 TATTTCTTGA
17174 TTACTAATTACCATTTTTTACTCTTT
1 TTACTAATTACCATTTTTTACTCTTT
* * *
17200 GTACTGATTACCATATTTTACTCTTTT
1 TTACTAATTACCATTTTTTACTC-TTT
* * * * *
17227 TTACTGATGACCCCTTTTTCTTACTGTCT
1 TTACTAATTA--CCATTTT-TTACTCTTT
**
17256 TTACTGAA-TACCACATTTTACTCTTT
1 TTACT-AATTACCATTTTTTACTCTTT
17282 TTACTTAATTACCATTTTTTACTTGCTTTT
1 TTAC-TAATTACCATTTTTTAC-T-C-TTT
17312 TTACTTAA-TACCATTTTT
1 TTAC-TAATTACCATTTTT
17330 GCTCCTTTTT
Statistics
Matches: 102, Mismatches: 18, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
26 33 0.32
27 27 0.26
28 1 0.01
29 24 0.24
30 17 0.17
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (26 bp):
TTACTAATTACCATTTTTTACTCTTT
Found at i:17301 original size:56 final size:52
Alignment explanation
Indices: 17174--17384 Score: 152
Period size: 56 Copynumber: 4.0 Consensus size: 52
17164 TATTTCTTGA
* *
17174 TTACTAATTACCATTTTTTAC-TCTTTGTACTGATTACCATATTTTACTCTTTT
1 TTACTAATTACCATTTTTTACTTCTTTTTACTGAATACCA-ATTTTACTC-TTT
* * **
17227 TTACTGATGACCCCTTTTT-CTTACTGTCTTTACTGAATACCACATTTTACTCTTT
1 TTACTAATTACCATTTTTTACTT-CT-T-TTTACTGAATACCA-ATTTTACTCTTT
* * * *
17282 TTACTTAATTACCATTTTTTACTTGCTTTTTTACTTAATACCATTTTTGCTC--C
1 TTAC-TAATTACCATTTTTTACTT-C-TTTTTACTGAATACCAATTTTACTCTTT
** *
17335 TT--T--TTACCA-TTTTTACCCCTTTTTACTGAATACCACTTTTTACTCTTT
1 TTACTAATTACCATTTTTTACTTCTTTTTACTGAATACCA-ATTTTACTCTTT
17383 TT
1 TT
17385 TACTGATCAG
Statistics
Matches: 127, Mismatches: 21, Indels: 25
0.73 0.12 0.14
Matches are distributed among these distances:
45 15 0.12
46 9 0.07
47 7 0.06
48 8 0.06
50 1 0.01
52 1 0.01
53 18 0.14
54 2 0.02
55 15 0.12
56 45 0.35
57 5 0.04
58 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.53
Consensus pattern (52 bp):
TTACTAATTACCATTTTTTACTTCTTTTTACTGAATACCAATTTTACTCTTT
Found at i:17328 original size:27 final size:24
Alignment explanation
Indices: 17255--17328 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 24
17245 TCTTACTGTC
*
17255 TTTACTGAATACCACATTTTACTCTT
1 TTTACTTAATA-C-CATTTTACTCTT
17281 TTTACTTAATTACCATTTTTTACTTGCTTT
1 TTTACTTAA-TACCA--TTTTAC-T-C-TT
17311 TTTACTTAATACCATTTT
1 TTTACTTAATACCATTTT
17329 TGCTCCTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
25 2 0.05
26 9 0.22
27 12 0.29
28 1 0.02
29 6 0.15
30 11 0.27
ACGTcount: A:0.24, C:0.19, G:0.03, T:0.54
Consensus pattern (24 bp):
TTTACTTAATACCATTTTACTCTT
Found at i:17344 original size:19 final size:19
Alignment explanation
Indices: 17320--17360 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
17310 TTTTACTTAA
* *
17320 TACCATTTTTGCTCCTTTT
1 TACCATTTTTACCCCTTTT
17339 TACCATTTTTACCCCTTTT
1 TACCATTTTTACCCCTTTT
17358 TAC
1 TAC
17361 TGAATACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.29, G:0.02, T:0.54
Consensus pattern (19 bp):
TACCATTTTTACCCCTTTT
Found at i:17374 original size:26 final size:27
Alignment explanation
Indices: 17339--17390 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
17329 TGCTCCTTTT
17339 TACCA-TTTTTACCCCTTTTTACTGAA
1 TACCACTTTTTACCCCTTTTTACTGAA
* *
17365 TACCACTTTTTACTCTTTTTTACTGA
1 TACCACTTTTTACCCCTTTTTACTGA
17391 TCAGCATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.21, C:0.25, G:0.04, T:0.50
Consensus pattern (27 bp):
TACCACTTTTTACCCCTTTTTACTGAA
Found at i:17485 original size:27 final size:27
Alignment explanation
Indices: 17455--17512 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
17445 ATCACCATTT
17455 TTACTCATTTCTTACTATTTTTACTGA
1 TTACTCATTTCTTACTATTTTTACTGA
* *
17482 TTACTCTTTTCTTACTCTTTTTACTGA
1 TTACTCATTTCTTACTATTTTTACTGA
17509 TTAC
1 TTAC
17513 CACTTTTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.03, T:0.57
Consensus pattern (27 bp):
TTACTCATTTCTTACTATTTTTACTGA
Found at i:17491 original size:16 final size:16
Alignment explanation
Indices: 17466--17523 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 16
17456 TACTCATTTC
*
17466 TTACTATTTTTACTGA
1 TTACTCTTTTTACTGA
17482 TTACTC-TTTT-C---
1 TTACTCTTTTTACTGA
17493 TTACTCTTTTTACTGA
1 TTACTCTTTTTACTGA
*
17509 TTACCACTTTTTACT
1 TTA-CTCTTTTTACT
17524 CTTCTTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
11 6 0.18
12 4 0.12
13 1 0.03
14 1 0.03
15 4 0.12
16 8 0.24
17 10 0.29
ACGTcount: A:0.19, C:0.21, G:0.03, T:0.57
Consensus pattern (16 bp):
TTACTCTTTTTACTGA
Found at i:17491 original size:54 final size:54
Alignment explanation
Indices: 17374--17497 Score: 128
Period size: 55 Copynumber: 2.3 Consensus size: 54
17364 ATACCACTTT
* * *
17374 TTACTC-TTTTTTACTGATCAGCATTTCTTACTCTTTATTTCTAATTATTCTCT
1 TTACTCTTTTTTTACTGATCACCATTTCTTACTCTTTATTACTAATTATTCTCA
* * * *
17427 TTCACCCTTTTTTTACTGATCACCATTT-TTACTCATTTCTTACT-ATTTTTACTGA
1 TT-ACTCTTTTTTTACTGATCACCATTTCTTACTC-TTTATTACTAATTATT-CTCA
*
17482 TTACTCTTTTCTTACT
1 TTACTCTTTTTTTACT
17498 CTTTTTACTG
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
53 2 0.03
54 26 0.45
55 30 0.52
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.56
Consensus pattern (54 bp):
TTACTCTTTTTTTACTGATCACCATTTCTTACTCTTTATTACTAATTATTCTCA
Found at i:17622 original size:22 final size:21
Alignment explanation
Indices: 17586--17626 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
17576 CTGACTATCA
17586 TTTTACTCTTTATTGATTATT
1 TTTTACTCTTTATTGATTATT
*
17607 TTTTACTTTTTTATTGATTA
1 TTTTAC-TCTTTATTGATTA
17627 CTACTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTACTCTTTATTGATTATT
Found at i:17715 original size:20 final size:19
Alignment explanation
Indices: 17685--17737 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
17675 TTACCCTTTC
*
17685 TACTTTTACTGTTTACTAT
1 TACTTTTACTGATTACTAT
17704 TACTTCTTACTGATTACTAT
1 TACTT-TTACTGATTACTAT
17724 TACTCTTTACTGAT
1 TACT-TTTACTGAT
17738 CATCCCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 5 0.16
20 25 0.81
21 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.53
Consensus pattern (19 bp):
TACTTTTACTGATTACTAT
Found at i:17856 original size:43 final size:43
Alignment explanation
Indices: 17744--17849 Score: 158
Period size: 43 Copynumber: 2.5 Consensus size: 43
17734 TGATCATCCC
*
17744 TTTACTCTTTACTAATTACCATTTTACCCTACACAGATACCTT
1 TTTACTTTTTACTAATTACCATTTTACCCTACACAGATACCTT
* * **
17787 TTTAATTTTTAGTAATTACCATTTTACCCTTTACAGATACCTT
1 TTTACTTTTTACTAATTACCATTTTACCCTACACAGATACCTT
*
17830 TTTACTTTTTACTGATTACC
1 TTTACTTTTTACTAATTACC
17850 TCTTTACTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.26, C:0.23, G:0.04, T:0.47
Consensus pattern (43 bp):
TTTACTTTTTACTAATTACCATTTTACCCTACACAGATACCTT
Found at i:17896 original size:20 final size:20
Alignment explanation
Indices: 17863--17932 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
17853 TTACTTTTTT
17863 TTACT-ATTTACTATTACTTC
1 TTACTGATTTACTATTAC-TC
17883 TTACTGATTT-CTATTACTC
1 TTACTGATTTACTATTACTC
17902 TTACTGATTATCACT-TTACTC
1 TTACTGATT-T-ACTATTACTC
17923 TTTACTGATT
1 -TTACTGATT
17933 ACCATTTTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.24
20 13 0.29
21 10 0.22
22 11 0.24
ACGTcount: A:0.23, C:0.20, G:0.04, T:0.53
Consensus pattern (20 bp):
TTACTGATTTACTATTACTC
Found at i:17948 original size:22 final size:22
Alignment explanation
Indices: 17751--17955 Score: 72
Period size: 22 Copynumber: 9.5 Consensus size: 22
17741 CCCTTTACTC
* *
17751 TTTACTAATTACCATTTTACCC
1 TTTACTGATTACCATTTTACCT
** * * **
17773 TACACAGA-TACCTTTTTAATT
1 TTTACTGATTACCATTTTACCT
* * *
17794 TTTAGTAATTACCATTTTACCC
1 TTTACTGATTACCATTTTACCT
* * *
17816 TTTACAGA-TACCTTTTTACTT
1 TTTACTGATTACCATTTTACCT
*
17837 TTTACTGATTACC-TCTTTACTTTTT
1 TTTACTGATTACCAT-TTTAC---CT
*
17862 TTTACT-ATTTA-C-TATTA-CT
1 TTTACTGA-TTACCATTTTACCT
* *
17881 TCTTACTGATT-TC-TATTA-CT
1 T-TTACTGATTACCATTTTACCT
* * *
17901 CTTACTGATTATCACTTTA-CT
1 TTTACTGATTACCATTTTACCT
17922 CTTTACTGATTACCATTTTACCT
1 -TTTACTGATTACCATTTTACCT
*
17945 TTTACCGATTA
1 TTTACTGATTA
17956 TTTTTTGCTA
Statistics
Matches: 136, Mismatches: 33, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
19 11 0.08
20 17 0.12
21 36 0.26
22 53 0.39
23 5 0.04
24 3 0.02
25 11 0.08
ACGTcount: A:0.24, C:0.21, G:0.04, T:0.50
Consensus pattern (22 bp):
TTTACTGATTACCATTTTACCT
Found at i:18015 original size:20 final size:20
Alignment explanation
Indices: 17992--18056 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
17982 TACTTTATCT
*
17992 TCTTACTAATTACCTCTTAC
1 TCTTACTAATTACCTTTTAC
*
18012 TCTTACTGATTACCTTTTAC
1 TCTTACTAATTACCTTTTAC
* *
18032 TCTTACTAATCATCTTTTAC
1 TCTTACTAATTACCTTTTAC
18052 TCTTA
1 TCTTA
18057 ATGTTTATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.23, C:0.26, G:0.02, T:0.49
Consensus pattern (20 bp):
TCTTACTAATTACCTTTTAC
Found at i:18032 original size:34 final size:33
Alignment explanation
Indices: 17958--18032 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
17948 ACCGATTATT
* * * *
17958 TTTTGCTAATTACCCTTTTGCTCTTACTTTATC
1 TTTTACTAATTACCCTCTTACTCTTACTTTACC
17991 TTCTTACTAATTA-CCTCTTACTCTTACTGATTACC
1 TT-TTACTAATTACCCTCTTACTCTTACT--TTACC
18026 TTTTACT
1 TTTTACT
18033 CTTACTAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 15 0.43
34 14 0.40
35 6 0.17
ACGTcount: A:0.19, C:0.25, G:0.04, T:0.52
Consensus pattern (33 bp):
TTTTACTAATTACCCTCTTACTCTTACTTTACC
Found at i:21187 original size:50 final size:50
Alignment explanation
Indices: 21109--21217 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
21099 GTTAATTCTT
* * *
21109 TATCAAAATCAGAGGCTTTCAATCTAAAGGTTAAG-CTTTTATTATCAATC
1 TATCAAAATCAGAGGCTTTCAATCTAAAGATT-AGTCTTTTATCACCAATC
* * * *
21159 TATCAAAATGAGAGTCTTTTAGA-CTAAAGATTAGTCTTTTATCACCAATT
1 TATCAAAATCAGAGGCTTTCA-ATCTAAAGATTAGTCTTTTATCACCAATC
21209 TATCAAAAT
1 TATCAAAAT
21218 TTCGTTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 2 0.04
50 47 0.94
51 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (50 bp):
TATCAAAATCAGAGGCTTTCAATCTAAAGATTAGTCTTTTATCACCAATC
Found at i:31771 original size:63 final size:63
Alignment explanation
Indices: 31699--31817 Score: 229
Period size: 63 Copynumber: 1.9 Consensus size: 63
31689 TAATTACATC
31699 CATAATTAAACACATAGTCTGAAAATACCATCCACTGCTGAATAATACCATAAACTTTGAGTA
1 CATAATTAAACACATAGTCTGAAAATACCATCCACTGCTGAATAATACCATAAACTTTGAGTA
*
31762 CATAATTAAACACATAGTCTGAAAATACCATCCACTGCTGAATAATACTATAAACT
1 CATAATTAAACACATAGTCTGAAAATACCATCCACTGCTGAATAATACCATAAACT
31818 CTAAAAATAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (63 bp):
CATAATTAAACACATAGTCTGAAAATACCATCCACTGCTGAATAATACCATAAACTTTGAGTA
Found at i:31825 original size:38 final size:38
Alignment explanation
Indices: 31783--31856 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 38
31773 ACATAGTCTG
*
31783 AAAATACCA-TCCACTGCTGAATAATACTATAAACTCTA
1 AAAATACCACT-CACTGCTGAATAATACCATAAACTCTA
31821 AAAATACCACTCACTGCTGAATAATACCATAAACTC
1 AAAATACCACTCACTGCTGAATAATACCATAAACTC
31857 CAAATACAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (38 bp):
AAAATACCACTCACTGCTGAATAATACCATAAACTCTA
Found at i:31848 original size:20 final size:20
Alignment explanation
Indices: 31717--31851 Score: 75
Period size: 20 Copynumber: 6.8 Consensus size: 20
31707 AACACATAGT
*
31717 CTGAA-AATACCATCCACTG
1 CTGAATAATACCATACACTG
*
31736 CTGAATAATACCATAAACT-
1 CTGAATAATACCATACACTG
* * ** *
31755 TTGAGTACATAATTAAACACATAG
1 CTGAATA-AT-ACCATACAC-T-G
*
31779 TCTGAA-AATACCATCCACTG
1 -CTGAATAATACCATACACTG
* *
31799 CTGAATAATACTATAAACT-
1 CTGAATAATACCATACACTG
*
31818 CT-AAAAATACCACT-CACTG
1 CTGAATAATACCA-TACACTG
31837 CTGAATAATACCATA
1 CTGAATAATACCATA
31852 AACTCCAAAT
Statistics
Matches: 83, Mismatches: 21, Indels: 23
0.65 0.17 0.18
Matches are distributed among these distances:
18 11 0.13
19 21 0.25
20 33 0.40
21 6 0.07
22 6 0.07
23 2 0.02
24 1 0.01
25 3 0.04
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (20 bp):
CTGAATAATACCATACACTG
Found at i:35466 original size:26 final size:26
Alignment explanation
Indices: 35436--35664 Score: 169
Period size: 27 Copynumber: 8.4 Consensus size: 26
35426 TATTTCTTGA
35436 TTACTAATTACCATTTTTTACTCTTT
1 TTACTAATTACCATTTTTTACTCTTT
* * *
35462 GTACTGATTACCATATTTTACTCTTTT
1 TTACTAATTACCATTTTTTACTC-TTT
* * * * *
35489 TTACTGATGACCCCTTTTCTTACTATCT
1 TTACTAATTA-CCATTTT-TTACTCTTT
*
35517 TTACTGAA-TACCACTTTTTACTCTTT
1 TTACT-AATTACCATTTTTTACTCTTT
35543 TTACTTAATTACCATTTTTTACTCTCCTTTT
1 TTAC-TAATTACCATTTTTTA--CT-C-TTT
*
35574 TTACTTAA-TACCA-TTTTTACCCCTTT
1 TTAC-TAATTACCATTTTTTA-CTCTTT
*
35600 TTACTGAA-TACCACTTTTTACTCTTTT
1 TTACT-AATTACCATTTTTTACTC-TTT
* * *
35627 TTACTGATCACCATTTCTTACTCTTT
1 TTACTAATTACCATTTTTTACTCTTT
*
35653 ATTTCTAATTAC
1 -TTACTAATTAC
35665 TCTCTTTCAC
Statistics
Matches: 162, Mismatches: 26, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
25 1 0.01
26 53 0.33
27 63 0.39
28 14 0.09
29 14 0.09
30 6 0.04
31 11 0.07
ACGTcount: A:0.22, C:0.23, G:0.03, T:0.52
Consensus pattern (26 bp):
TTACTAATTACCATTTTTTACTCTTT
Found at i:35586 original size:57 final size:56
Alignment explanation
Indices: 35516--35647 Score: 157
Period size: 57 Copynumber: 2.4 Consensus size: 56
35506 TCTTACTATC
* * *
35516 TTTACTGAATACCACTTTTTA-CTCTTTTTACTTAATTACCATTTTTTACTCTCCTTT
1 TTTACTGAATACCA-TTTTTACCCCTTTTTACTGAA-TACCACTTTTTACTCTCCTTT
*
35573 TTTACTTAATACCATTTTTACCCCTTTTTACTGAATACCACTTTTTA--CT-CTTT
1 TTTACTGAATACCATTTTTACCCCTTTTTACTGAATACCACTTTTTACTCTCCTTT
35626 TTTACTG-ATCACCATTTCTTAC
1 TTTACTGAAT-ACCATTT-TTAC
35648 TCTTTATTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
52 2 0.03
53 17 0.25
54 6 0.09
56 17 0.25
57 25 0.37
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.52
Consensus pattern (56 bp):
TTTACTGAATACCATTTTTACCCCTTTTTACTGAATACCACTTTTTACTCTCCTTT
Found at i:35592 original size:16 final size:16
Alignment explanation
Indices: 35540--35593 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
35530 CTTTTTACTC
35540 TTTTTACTTAATTACCA
1 TTTTTACTTAA-TACCA
* *
35557 TTTTTTAC-T-CT-CCT
1 -TTTTTACTTAATACCA
35571 TTTTTACTTAATACCA
1 TTTTTACTTAATACCA
35587 TTTTTAC
1 TTTTTAC
35594 CCCTTTTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 7 0.24
14 3 0.10
15 2 0.07
16 9 0.31
17 1 0.03
18 7 0.24
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTTACTTAATACCA
Found at i:35728 original size:27 final size:27
Alignment explanation
Indices: 35698--35769 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
35688 ATCACCATTT
35698 TTACTCATTTCTTACTCTTTTTACTGA
1 TTACTCATTTCTTACTCTTTTTACTGA
*
35725 TTACTCTTTTCTTACTCTTTTTACTGA
1 TTACTCATTTCTTACTCTTTTTACTGA
35752 TTAC-CACTTT-TTACTCTT
1 TTACTCA-TTTCTTACTCTT
35770 CCTCTTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
26 9 0.21
27 33 0.79
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.57
Consensus pattern (27 bp):
TTACTCATTTCTTACTCTTTTTACTGA
Found at i:35730 original size:16 final size:16
Alignment explanation
Indices: 35709--35766 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 16
35699 TACTCATTTC
35709 TTACTCTTTTTACTGA
1 TTACTCTTTTTACTGA
35725 TTACTC-TTTT-C---
1 TTACTCTTTTTACTGA
35736 TTACTCTTTTTACTGA
1 TTACTCTTTTTACTGA
*
35752 TTACCACTTTTTACT
1 TTA-CTCTTTTTACT
35767 CTTCCTCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
13 1 0.03
14 1 0.03
15 4 0.11
16 9 0.26
17 10 0.29
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.57
Consensus pattern (16 bp):
TTACTCTTTTTACTGA
Found at i:35766 original size:64 final size:65
Alignment explanation
Indices: 35638--35767 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 65
35628 TACTGATCAC
* * *
35638 CATTTCTTACTCTTTATTTCTAATTACTCTCTTTCACCCTTTTTTTACTGATCACCATTTTTACT
1 CATTTCTTACTCTTTATTACTAATTACTCTCTTTCACACTCTTTTTACTGATCACCATTTTTACT
* ** *
35703 CATTTCTTACTCTTT-TTACTGATTACTCT-TTTCTTACTCTTTTTACTGATTACCACTTTTTAC
1 CATTTCTTACTCTTTATTACTAATTACTCTCTTTCACACTCTTTTTACTGATCACCA-TTTTTAC
35766 T
65 T
35767 C
1 C
35768 TTCCTCTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
63 21 0.37
64 21 0.37
65 15 0.26
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.55
Consensus pattern (65 bp):
CATTTCTTACTCTTTATTACTAATTACTCTCTTTCACACTCTTTTTACTGATCACCATTTTTACT
Found at i:35767 original size:37 final size:36
Alignment explanation
Indices: 35725--35807 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 36
35715 TTTTTACTGA
*
35725 TTACTCTTTTCTTACTCT-TTTTACTGATTACCACTTT
1 TTACTCTTTTCTTACTCTCTTTTACTGACTACCA--TT
* **
35762 TTACTCTTCCTCTTTTTCTCTTTTACTGACTACCATT
1 TTACTCTT-TTCTTACTCTCTTTTACTGACTACCATT
35799 TTACTCTTT
1 TTACTCTTT
35808 GAATTTAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
37 18 0.46
38 7 0.18
39 14 0.36
ACGTcount: A:0.14, C:0.27, G:0.02, T:0.57
Consensus pattern (36 bp):
TTACTCTTTTCTTACTCTCTTTTACTGACTACCATT
Found at i:35803 original size:63 final size:63
Alignment explanation
Indices: 35679--35807 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 63
35669 TTTCACCCTT
* *
35679 TTTTTACTGATCACCATTTTTACTCATTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTC
1 TTTTTACTGATCACCATTTTTACTCATTTCTTACTCTTTTTACTGACTACTCTATTCTTACTC
* **
35742 TTTTTACTGATTACCACTTTTTACTC-TTCCTCTTTTTCTCTTTTACTGACTAC-C-ATT-TTAC
1 TTTTTACTGATCACCA-TTTTTACTCATT--TCTTACTCT-TTTTACTGACTACTCTATTCTTAC
35803 TC
62 TC
35805 TTT
1 TTT
35808 GAATTTAATC
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
63 26 0.46
64 11 0.19
65 8 0.14
66 12 0.21
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (63 bp):
TTTTTACTGATCACCATTTTTACTCATTTCTTACTCTTTTTACTGACTACTCTATTCTTACTC
Found at i:35902 original size:43 final size:45
Alignment explanation
Indices: 35828--35915 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
35818 ACTGACTATC
*** *
35828 ATTTTACTCTTTACTGATTATTTTTTATTTTTTTA-TTGATTACT
1 ATTTTACTCTTTACTGATTATCCATTATTTTTTAACTTGATTACT
35872 ATTTTACTC-TTACTGATTA-CCATTACTTTTTTAACTTGATTACT
1 ATTTTACTCTTTACTGATTATCCATTA-TTTTTTAACTTGATTACT
35916 GATTACCCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 3 0.08
43 17 0.45
44 18 0.47
ACGTcount: A:0.23, C:0.14, G:0.05, T:0.59
Consensus pattern (45 bp):
ATTTTACTCTTTACTGATTATCCATTATTTTTTAACTTGATTACT
Found at i:35958 original size:20 final size:19
Alignment explanation
Indices: 35928--35980 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
35918 TTACCCTTTC
*
35928 TACTTTTACTGTTTACTAT
1 TACTTTTACTGATTACTAT
35947 TACTTCTTACTGATTACTAT
1 TACTT-TTACTGATTACTAT
35967 TACTCTTTACTGAT
1 TACT-TTTACTGAT
35981 CATCCCTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 5 0.16
20 25 0.81
21 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.53
Consensus pattern (19 bp):
TACTTTTACTGATTACTAT
Found at i:36012 original size:22 final size:22
Alignment explanation
Indices: 35911--36197 Score: 147
Period size: 22 Copynumber: 13.5 Consensus size: 22
35901 TTTAACTTGA
*
35911 TTACTGATTACCCTTTCTACT-T
1 TTACTGATTACCATTT-TACTCT
* *
35933 TTACTGTTTA-C-TATTACT-T
1 TTACTGATTACCATTTTACTCT
*
35952 CTTACTGATTA-C-TATTACTCT
1 -TTACTGATTACCATTTTACTCT
* *
35973 TTACTGATCATCC-CTTTACTCT
1 TTACTGATTA-CCATTTTACTCT
* *
35995 TTACTAATTACCATTTTACCCT
1 TTACTGATTACCATTTTACTCT
* * *
36017 TTACAGA-TACCTTTTTACTTT
1 TTACTGATTACCATTTTACTCT
** * *
36038 TTGGTAATTACCATTTTACCCT
1 TTACTGATTACCATTTTACTCT
* ** *
36060 TTACAGA-TACTTTTTTACTTT
1 TTACTGATTACCATTTTACTCT
* *
36081 TTACTGATTACCTTTTTACTTTTT
1 TTACTGATTACCATTTTAC--TCT
* *
36105 TTACTGTTTA-C-TATTACT-T
1 TTACTGATTACCATTTTACTCT
* *
36124 CTTACTGATT-TC-TATTACTC-
1 -TTACTGATTACCATTTTACTCT
* *
36144 TTACTGATTATCACTTTACTCT
1 TTACTGATTACCATTTTACTCT
36166 TTACTGATTACCATTTTAC-CTT
1 TTACTGATTACCATTTTACTC-T
*
36188 TTACCGATTA
1 TTACTGATTA
36198 TTTTTTGCTA
Statistics
Matches: 209, Mismatches: 40, Indels: 32
0.74 0.14 0.11
Matches are distributed among these distances:
19 15 0.07
20 47 0.22
21 41 0.20
22 93 0.44
23 1 0.00
24 12 0.06
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (22 bp):
TTACTGATTACCATTTTACTCT
Found at i:36091 original size:43 final size:43
Alignment explanation
Indices: 35987--36099 Score: 172
Period size: 43 Copynumber: 2.6 Consensus size: 43
35977 TGATCATCCC
*
35987 TTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCTT
1 TTTACTTTTTACTAATTACCATTTTACCCTTTACAGATACCTT
** *
36030 TTTACTTTTTGGTAATTACCATTTTACCCTTTACAGATACTTT
1 TTTACTTTTTACTAATTACCATTTTACCCTTTACAGATACCTT
* *
36073 TTTACTTTTTACTGATTACCTTTTTAC
1 TTTACTTTTTACTAATTACCATTTTAC
36100 TTTTTTTACT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.23, C:0.21, G:0.04, T:0.51
Consensus pattern (43 bp):
TTTACTTTTTACTAATTACCATTTTACCCTTTACAGATACCTT
Found at i:36130 original size:20 final size:19
Alignment explanation
Indices: 36105--36174 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 19
36095 TTTACTTTTT
36105 TTACTG-TTTACTATTACTTC
1 TTACTGATTT-CTATTAC-TC
36125 TTACTGATTTCTATTACTC
1 TTACTGATTTCTATTACTC
36144 TTACTGATTATC-ACTTTACTC
1 TTACTGATT-TCTA--TTACTC
36165 TTTACTGATT
1 -TTACTGATT
36175 ACCATTTTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.27
20 15 0.33
21 9 0.20
22 9 0.20
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (19 bp):
TTACTGATTTCTATTACTC
Found at i:36260 original size:20 final size:20
Alignment explanation
Indices: 36237--36280 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
36227 TTTATCTTCT
36237 TACTGATTACCTCTTACTCA
1 TACTGATTACCTCTTACTCA
* *
36257 TACTGATTACCTTTTACTCT
1 TACTGATTACCTCTTACTCA
36277 TACT
1 TACT
36281 AATCATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.05, T:0.45
Consensus pattern (20 bp):
TACTGATTACCTCTTACTCA
Done.