Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015720.1 Corchorus capsularis cultivar CVL-1 contig15741, 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: 30581
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Found at i:4785 original size:49 final size:49
Alignment explanation
Indices: 4383--4784 Score: 554
Period size: 49 Copynumber: 8.2 Consensus size: 49
4373 TTACCTACTT
* *
4383 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
* *
4432 TCTCCCAAAGCGCCCTTACCAGACGGAAGCCATTTATTTTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTA-TTTTTACTTGCTA
* *
4482 TTTCCCAAAGCGCCCTTCCAAGACGAAAGCCATTTATTTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
*
4531 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTGCTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
* ** * * *
4580 TTTCCCGAAA-CGCCATTCTTAGACAGAAGCCATTCATCTTTACTTGCTA
1 TTTCCC-AAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
*
4629 TCTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
* * **
4678 TTTCCCAAAGTGCCCTTCCTAGACGGAAGCCATTTATTTTCGCTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
* * * ** * *
4727 TTTCCCAAAACGCCCATCCCGGACGGAAGATATTTATTTTTACCTGCCA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
4776 TTTCCCAAA
1 TTTCCCAAA
4785 ATGCCTTTTC
Statistics
Matches: 309, Mismatches: 41, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
48 3 0.01
49 259 0.84
50 47 0.15
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.32
Consensus pattern (49 bp):
TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
Found at i:6371 original size:25 final size:24
Alignment explanation
Indices: 6315--6371 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
6305 AGTCTTTGAG
6315 GAAGAA-GAAAAAGAAGAAAGTGA
1 GAAGAAGGAAAAAGAAGAAAGTGA
*
6338 GAACG-AGGAAGAAGGAAGAAAG-GAA
1 GAA-GAAGGAA-AAAGAAGAAAGTG-A
6363 GAAGAAGGA
1 GAAGAAGGA
6372 CCTGCTGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
23 4 0.14
24 6 0.21
25 18 0.64
ACGTcount: A:0.60, C:0.02, G:0.37, T:0.02
Consensus pattern (24 bp):
GAAGAAGGAAAAAGAAGAAAGTGA
Found at i:11195 original size:29 final size:29
Alignment explanation
Indices: 11153--11213 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
11143 CTCTATTTCA
11153 TCCCCTTGAAACCATTTTGTGCCTCCTTG
1 TCCCCTTGAAACCATTTTGTGCCTCCTTG
11182 TCCCCTTGAAACCATTTTGTGCCTCCTTG
1 TCCCCTTGAAACCATTTTGTGCCTCCTTG
11211 TCC
1 TCC
11214 AAACCCCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.13, C:0.36, G:0.13, T:0.38
Consensus pattern (29 bp):
TCCCCTTGAAACCATTTTGTGCCTCCTTG
Found at i:12889 original size:2 final size:2
Alignment explanation
Indices: 12882--12914 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12872 CAACAAAATA
*
12882 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12915 CAATATACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14868 original size:29 final size:26
Alignment explanation
Indices: 14808--14874 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 26
14798 TATTTCTTGA
*
14808 TTACTAATTACCATTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
*
14834 GTACTGATTACCATATTTTTACTCTTCTT
1 TTACTGATTACCAT-TTTTTACTC-T-TT
14863 TTACTGATTACC
1 TTACTGATTACC
14875 CCTTTTCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.34
27 9 0.26
28 1 0.03
29 13 0.37
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.52
Consensus pattern (26 bp):
TTACTGATTACCATTTTTTACTCTTT
Found at i:14886 original size:30 final size:30
Alignment explanation
Indices: 14809--14874 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 30
14799 ATTTCTTGAT
*
14809 TACTAATTACCAT-TTTTTA--C-TCTTTG
1 TACTGATTACCATATTTTTACTCTTCTTTG
14835 TACTGATTACCATATTTTTACTCTTCTTT-
1 TACTGATTACCATATTTTTACTCTTCTTTG
14864 TACTGATTACC
1 TACTGATTACC
14875 CCTTTTCTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 12 0.34
27 6 0.17
29 12 0.34
30 5 0.14
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.52
Consensus pattern (30 bp):
TACTGATTACCATATTTTTACTCTTCTTTG
Found at i:14921 original size:27 final size:26
Alignment explanation
Indices: 14876--14995 Score: 100
Period size: 27 Copynumber: 4.4 Consensus size: 26
14866 CTGATTACCC
14876 CTTTTCTTACTGAAT-ACCATATTTTACT
1 CTTTT-TTACTG-ATCACCAT-TTTTACT
14904 CTTTTTTACTGATCACCATTTCTTACT
1 CTTTTTTACTGATCACCATTT-TTACT
* * * * *
14931 CTTTATTAATAATTACTC-TCTTTTACC
1 CTTTTTTACTGATCAC-CAT-TTTTACT
14958 CTTTTTTACTGATCACCATTTTTTACT
1 CTTTTTTACTGATCACCA-TTTTTACT
*
14985 CATTTCTTACT
1 C-TTTTTTACT
14996 CTTTTTACTG
Statistics
Matches: 74, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
26 5 0.07
27 52 0.70
28 17 0.23
ACGTcount: A:0.22, C:0.23, G:0.03, T:0.53
Consensus pattern (26 bp):
CTTTTTTACTGATCACCATTTTTACT
Found at i:14954 original size:74 final size:74
Alignment explanation
Indices: 14808--14946 Score: 176
Period size: 74 Copynumber: 1.9 Consensus size: 74
14798 TATTTCTTGA
* * * * * *
14808 TTACTAATTACCATTTTTTACTCTTTGTACTGATTACCATATTTTTACTCTTCTTTTACTGATTA
1 TTACTAATTACCATATTTTACTCTTTGTACTGATCACCATATTCTTACTCTTCTATTAATAATTA
14873 CCCCTTTTC
66 CCCCTTTTC
*
14882 TTACTGAA-TACCATATTTTACTCTTTTTTACTGATCACCAT-TTCTTACTCTT-TATTAATAAT
1 TTACT-AATTACCATATTTTACTC-TTTGTACTGATCACCATATTCTTACTCTTCTATTAATAAT
14944 TAC
64 TAC
14947 TCTCTTTTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
73 10 0.18
74 29 0.52
75 17 0.30
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.51
Consensus pattern (74 bp):
TTACTAATTACCATATTTTACTCTTTGTACTGATCACCATATTCTTACTCTTCTATTAATAATTA
CCCCTTTTC
Found at i:14989 original size:65 final size:65
Alignment explanation
Indices: 14920--15138 Score: 305
Period size: 65 Copynumber: 3.3 Consensus size: 65
14910 TACTGATCAC
* * * * * *
14920 CATTTCTTACTCTTTATTAATAATTACTCTCTT-TTACCCTTTTTTACTGATCACCATTTTTTAC
1 CATTTCTTACTCTTT-TTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTTTTAC
14984 T
65 T
* *
14985 CATTTCTTACTCTTTTTACTGATTACTATTTTCTTACTCTTTTTTACTGATTACCACTTTTAACT
1 CATTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTTTTACT
15050 CATTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTTTTACT
1 CATTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTTTTACT
* **
15115 CTTCTTCTTTTTCTCTTTTACTGA
1 CAT-TTCTTACTCT-TTTTACTGA
15139 CTACCATTTT
Statistics
Matches: 138, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
64 13 0.09
65 108 0.78
66 8 0.06
67 9 0.07
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.56
Consensus pattern (65 bp):
CATTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTTTTACT
Found at i:15011 original size:27 final size:29
Alignment explanation
Indices: 14980--15038 Score: 97
Period size: 27 Copynumber: 2.1 Consensus size: 29
14970 TCACCATTTT
14980 TTACTCA-TTTCTTACTC-TTTTTACTGA
1 TTACTCATTTTCTTACTCTTTTTTACTGA
15007 TTACT-ATTTTCTTACTCTTTTTTACTGA
1 TTACTCATTTTCTTACTCTTTTTTACTGA
15035 TTAC
1 TTAC
15039 CACTTTTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 1 0.03
27 15 0.50
28 14 0.47
ACGTcount: A:0.19, C:0.20, G:0.03, T:0.58
Consensus pattern (29 bp):
TTACTCATTTTCTTACTCTTTTTTACTGA
Found at i:15032 original size:37 final size:36
Alignment explanation
Indices: 14943--15155 Score: 126
Period size: 37 Copynumber: 6.2 Consensus size: 36
14933 TTATTAATAA
* *
14943 TTACTCTCTT-TTACCCTTTTTTACTGATCACCATTTT
1 TTACTCT-TTCTTACTC-TTTTTACTGATTACCATTTT
14980 TTACTCATTTCTTACTCTTTTTACTGATTA-C-----
1 TTACTC-TTTCTTACTCTTTTTACTGATTACCATTTT
*
15011 -TA-T-TTTCTTACTCTTTTTTACTGATTACCACTTT
1 TTACTCTTTCTTACTC-TTTTTACTGATTACCATTTT
*
15045 TAACTCATTTCTTACTCTTTTTACTGATTA-C-----
1 TTACTC-TTTCTTACTCTTTTTACTGATTACCATTTT
*
15076 -T-CT-TTTCTTACTCTTTTTTACTGATTACCACTTT
1 TTACTCTTTCTTACTC-TTTTTACTGATTACCATTTT
** *
15110 TTACTCTTCTTCTTTTTCTCTTTTACTGACTACCA--TT
1 TTACTC-T-TTCTTACTCT-TTTTACTGATTACCATTTT
15147 TTACTCTTT
1 TTACTCTTT
15156 GAATTTAATT
Statistics
Matches: 143, Mismatches: 7, Indels: 54
0.70 0.03 0.26
Matches are distributed among these distances:
27 20 0.14
28 26 0.18
29 5 0.03
30 2 0.01
35 4 0.03
36 6 0.04
37 41 0.29
38 18 0.13
39 21 0.15
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.56
Consensus pattern (36 bp):
TTACTCTTTCTTACTCTTTTTACTGATTACCATTTT
Found at i:15050 original size:27 final size:28
Alignment explanation
Indices: 14987--15060 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
14977 TTTTTACTCA
* * *
14987 TTTCTTACTC-TTTTTACTGATTACTAT
1 TTTCTAACTCTTTTTTACTGATTACCAC
*
15014 TTTCTTACTCTTTTTTACTGATTACCAC
1 TTTCTAACTCTTTTTTACTGATTACCAC
*
15042 TTT-TAACTCATTTCTTACT
1 TTTCTAACTC-TTTTTTACT
15061 CTTTTTACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
27 15 0.37
28 26 0.63
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.57
Consensus pattern (28 bp):
TTTCTAACTCTTTTTTACTGATTACCAC
Found at i:15082 original size:27 final size:28
Alignment explanation
Indices: 15047--15117 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 28
15037 ACCACTTTTA
15047 ACTCATTTCTTACTC-TTTTTACTGATT
1 ACTCATTTCTTACTCTTTTTTACTGATT
*
15074 ACTCTTTTCTTACTCTTTTTTACTGATT
1 ACTCATTTCTTACTCTTTTTTACTGATT
15102 AC-CACTTT-TTACTCTT
1 ACTCA-TTTCTTACTCTT
15118 CTTCTTTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.56
Consensus pattern (28 bp):
ACTCATTTCTTACTCTTTTTTACTGATT
Found at i:15134 original size:39 final size:36
Alignment explanation
Indices: 15072--15155 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 36
15062 TTTTTACTGA
* *
15072 TTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTT
1 TTACTCTTTTCTTACTCTCTTTTACTGACTACCA--TT
**
15110 TTACTCTTCTTCTTTTTCTCTTTTACTGACTACCATT
1 TTACTCTT-TTCTTACTCTCTTTTACTGACTACCATT
15147 TTACTCTTT
1 TTACTCTTT
15156 GAATTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.02
37 10 0.24
38 8 0.20
39 22 0.54
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.58
Consensus pattern (36 bp):
TTACTCTTTTCTTACTCTCTTTTACTGACTACCATT
Found at i:15298 original size:22 final size:20
Alignment explanation
Indices: 15271--15490 Score: 119
Period size: 22 Copynumber: 10.4 Consensus size: 20
15261 TGAATCTTGA
15271 TTACTGATTACCCTTTTTACTT
1 TTACTGATTA-CC-TTTTACTT
* *
15293 TTACTGTTTA-CTATTACTT
1 TTACTGATTACCTTTTACTT
* *
15312 CTTACTGATT-TCTATTACTCT
1 -TTACTGATTACCTTTTACT-T
*
15333 TTACCGATTATCAC-TTTACTCT
1 TTACTGATTA-C-CTTTTACT-T
* *
15355 TTACTAATTACCATTTTACCCT
1 TTACTGATTACC-TTTTA-CTT
*
15377 TTACAGA-TACCTTTTTACTTT
1 TTACTGATTACC-TTTTAC-TT
*
15398 TTACTGATTATCTTTTTACTTT
1 TTACTGATTA-CCTTTTAC-TT
* * *
15420 TTACAGTTTA-CTATTACTT
1 TTACTGATTACCTTTTACTT
* *
15439 CTTACTGATT-TCTATTACTAT
1 -TTACTGATTACCTTTTACT-T
15460 TTACTGATTACCATTTTACCTT
1 TTACTGATTACC-TTTTA-CTT
15482 TTACTGATT
1 TTACTGATT
15491 GCATCTTTCT
Statistics
Matches: 157, Mismatches: 23, Indels: 36
0.73 0.11 0.17
Matches are distributed among these distances:
19 9 0.06
20 56 0.36
21 20 0.13
22 67 0.43
23 5 0.03
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTT
Found at i:15318 original size:20 final size:19
Alignment explanation
Indices: 15287--15468 Score: 82
Period size: 20 Copynumber: 8.8 Consensus size: 19
15277 ATTACCCTTT
15287 TTACTTTTACTG-TTTACTA
1 TTACTTTTACTGATTT-CTA
15306 TTACTTCTTACTGATTTCTA
1 TTACTT-TTACTGATTTCTA
*
15326 TTACTCTTTACCGATTATC-A
1 TTACT-TTTACTGATT-TCTA
* * *
15346 CTTTACTCTTTACTAATTACCATT
1 --TTACT-TTTACTGATT-TC-TA
* * ** *
15370 TTACCCTTTACAGATACCTTT
1 TTA-CTTTTACTGATTTC-TA
*
15391 TTACTTTTTACTGATTATCTTT
1 TTAC-TTTTACTGATT-TC-TA
*
15413 TTACTTTTTACAG-TTTACTA
1 TTAC-TTTTACTGATTT-CTA
15433 TTACTTCTTACTGATTTCTA
1 TTACTT-TTACTGATTTCTA
15453 TTACTATTTACTGATT
1 TTACT-TTTACTGATT
15469 ACCATTTTAC
Statistics
Matches: 131, Mismatches: 17, Indels: 29
0.74 0.10 0.16
Matches are distributed among these distances:
19 8 0.06
20 52 0.40
21 28 0.21
22 42 0.32
23 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.04, T:0.53
Consensus pattern (19 bp):
TTACTTTTACTGATTTCTA
Found at i:15419 original size:29 final size:27
Alignment explanation
Indices: 15387--15444 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
15377 TTACAGATAC
** *
15387 CTTTTTACTTTTTACTGATTATCTTTTTA
1 CTTTTTACAGTTTACT-ATTA-CTTCTTA
15416 CTTTTTACAGTTTACTATTACTTCTTA
1 CTTTTTACAGTTTACTATTACTTCTTA
15443 CT
1 CT
15445 GATTTCTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.31
28 4 0.15
29 14 0.54
ACGTcount: A:0.19, C:0.17, G:0.03, T:0.60
Consensus pattern (27 bp):
CTTTTTACAGTTTACTATTACTTCTTA
Found at i:16616 original size:51 final size:51
Alignment explanation
Indices: 16561--16698 Score: 224
Period size: 51 Copynumber: 2.7 Consensus size: 51
16551 GAATTACAAA
*
16561 AACTCAACCCTTATTACATAAAGATTTAATTTTTATGATTAAAATCACTAG
1 AACTCAACCCTTACTACATAAAGATTTAATTTTTATGATTAAAATCACTAG
* *
16612 AACTCAACCCTTACTACATAAAGATTCAATTTTTATGGTTAAAATCACTAG
1 AACTCAACCCTTACTACATAAAGATTTAATTTTTATGATTAAAATCACTAG
*
16663 AACTCAACCCTTACTATATAAAGATTCT-ATTTTTAT
1 AACTCAACCCTTACTACATAAAGATT-TAATTTTTAT
16699 TTGCCAAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (51 bp):
AACTCAACCCTTACTACATAAAGATTTAATTTTTATGATTAAAATCACTAG
Found at i:17475 original size:19 final size:20
Alignment explanation
Indices: 17439--17480 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
17429 ATCGACCCAA
17439 AAAAACCTCTGTTCTTTC-C
1 AAAAACCTCTGTTCTTTCTC
* * *
17458 AAAACCCTCTTTTTTTTCTC
1 AAAAACCTCTGTTCTTTCTC
17478 AAA
1 AAA
17481 TATCCCGCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAAACCTCTGTTCTTTCTC
Found at i:17941 original size:16 final size:16
Alignment explanation
Indices: 17916--17948 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17906 TTCTTTTTTC
*
17916 CTTTTTTCTGCTTGTT
1 CTTTTGTCTGCTTGTT
17932 CTTTTGTCTGCTTGTT
1 CTTTTGTCTGCTTGTT
17948 C
1 C
17949 ATGTAGGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.21, G:0.15, T:0.64
Consensus pattern (16 bp):
CTTTTGTCTGCTTGTT
Found at i:18752 original size:50 final size:50
Alignment explanation
Indices: 18688--18899 Score: 271
Period size: 50 Copynumber: 4.2 Consensus size: 50
18678 GAATCAACTT
* * * *
18688 CTTCGAATTGTCTTCCAATTCAATCTTAAAAGGACCATCTTTCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATATTAAAAGGACCGTCTTCCGCTTATC
* * * *
18738 CTTCGAACTGTCTTCCAATTTAATATTAAAACGATCGTCTTCCGCCTATC
1 CTTCGAACTGTCTTCCAATTCAATATTAAAAGGACCGTCTTCCGCTTATC
* * *
18788 CTTTGAACTATCTTCCAATTCACATATTAAAAGGACCGTCTTCTGCTTATC
1 CTTCGAACTGTCTTCCAATTCA-ATATTAAAAGGACCGTCTTCCGCTTATC
* * * *
18839 CTTTGAAATGTCTTCCAATTTAATATTAAAAGGACCGTGTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATATTAAAAGGACCGTCTTCCGCTTATC
*
18889 TTTCGAACTGT
1 CTTCGAACTGT
18900 TTCTGATGCG
Statistics
Matches: 138, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
50 95 0.69
51 43 0.31
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (50 bp):
CTTCGAACTGTCTTCCAATTCAATATTAAAAGGACCGTCTTCCGCTTATC
Found at i:18836 original size:101 final size:100
Alignment explanation
Indices: 18689--18897 Score: 287
Period size: 101 Copynumber: 2.1 Consensus size: 100
18679 AATCAACTTC
* * * *
18689 TTCGAATTGTCTTCCAATTCAATCTTAAAAGGACCATCTTTCGCTTATCCTTCGAACTGTCTTCC
1 TTCGAACTATCTTCCAATTCAATATTAAAAGGACCATCTTTCGCTTATCCTTCGAAATGTCTTCC
*
18754 AATTTAATATTAAAACGATCGTCTTCCGCCTATCCT
66 AATTTAATATTAAAACGACCGTCTTCCGCCTAT-CT
* *
18790 TT-GAACTATCTTCCAATTCACATATTAAAAGGACCGTC-TTCTGCTTATCCTTTGAAATGTCTT
1 TTCGAACTATCTTCCAATTCA-ATATTAAAAGGACCATCTTTC-GCTTATCCTTCGAAATGTCTT
* * *
18853 CCAATTTAATATTAAAAGGACCGTGTTCCGCTTATCT
64 CCAATTTAATATTAAAACGACCGTCTTCCGCCTATCT
18890 TTCGAACT
1 TTCGAACT
18898 GTTTCTGATG
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
100 23 0.24
101 72 0.76
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (100 bp):
TTCGAACTATCTTCCAATTCAATATTAAAAGGACCATCTTTCGCTTATCCTTCGAAATGTCTTCC
AATTTAATATTAAAACGACCGTCTTCCGCCTATCT
Found at i:25540 original size:38 final size:38
Alignment explanation
Indices: 25491--25680 Score: 137
Period size: 38 Copynumber: 4.8 Consensus size: 38
25481 AGAATACAGT
*
25491 CCACCAACTGTTGAATAATACCATAAACTCTGAAAACA
1 CCACCCACTGTTGAATAATACCATAAACTCTGAAAACA
* *
25529 CCACCCACTGTTGAATAATACCATAAACTCCGAATACAA
1 CCACCCACTGTTGAATAATACCATAAACTCTGAAAAC-A
** ** * * * * * * **
25568 GTACTGAATAATGATATCAATAATTAAACACATAGTCTGAAAATT
1 CCAC---CCACTG-T-TGAATAA-T-ACCATAAACTCTGAAAACA
* * * *
25613 CCATCCACTGCTGAATAATACCATAAACTTTGAAAATA
1 CCACCCACTGTTGAATAATACCATAAACTCTGAAAACA
25651 CCACCCACTGTTGAATAATACCATAAACTC
1 CCACCCACTGTTGAATAATACCATAAACTC
25681 CGAATACAAG
Statistics
Matches: 110, Mismatches: 34, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
38 74 0.67
39 4 0.04
40 6 0.05
42 6 0.05
43 1 0.01
44 6 0.05
45 2 0.02
46 11 0.10
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (38 bp):
CCACCCACTGTTGAATAATACCATAAACTCTGAAAACA
Found at i:25652 original size:18 final size:20
Alignment explanation
Indices: 25619--25679 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
25609 AATTCCATCC
*
25619 ACTGCTGAATAATACCATAA
1 ACTGTTGAATAATACCATAA
***
25639 ACT-TTGAA-AATACCACCC
1 ACTGTTGAATAATACCATAA
25657 ACTGTTGAATAATACCATAA
1 ACTGTTGAATAATACCATAA
25677 ACT
1 ACT
25680 CCGAATACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
18 10 0.31
19 9 0.28
20 13 0.41
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (20 bp):
ACTGTTGAATAATACCATAA
Found at i:25672 original size:20 final size:20
Alignment explanation
Indices: 25617--25673 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 20
25607 AAAATTCCAT
* *
25617 CCACTGCTGAATAATACCAT
1 CCACTGTTGAATAATACCAC
**
25637 AAACT-TTGAA-AATACCAC
1 CCACTGTTGAATAATACCAC
25655 CCACTGTTGAATAATACCA
1 CCACTGTTGAATAATACCA
25674 TAAACTCCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
18 10 0.34
19 9 0.31
20 10 0.34
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.25
Consensus pattern (20 bp):
CCACTGTTGAATAATACCAC
Found at i:29384 original size:29 final size:26
Alignment explanation
Indices: 29324--29390 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 26
29314 TATTTCTTGA
*
29324 TTACTAATTACCATTTTTTACTCTTT
1 TTACTGATTACCATTTTTTACTCTTT
*
29350 GTACTGATTACCATATTTTTACTCTTCTT
1 TTACTGATTACCAT-TTTTTACTC-T-TT
29379 TTACTGATTACC
1 TTACTGATTACC
29391 CCTTTTCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.34
27 9 0.26
28 1 0.03
29 13 0.37
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.52
Consensus pattern (26 bp):
TTACTGATTACCATTTTTTACTCTTT
Found at i:29402 original size:30 final size:30
Alignment explanation
Indices: 29325--29390 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 30
29315 ATTTCTTGAT
*
29325 TACTAATTACCAT-TTTTTA--C-TCTTTG
1 TACTGATTACCATATTTTTACTCTTCTTTG
29351 TACTGATTACCATATTTTTACTCTTCTTT-
1 TACTGATTACCATATTTTTACTCTTCTTTG
29380 TACTGATTACC
1 TACTGATTACC
29391 CCTTTTCTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 12 0.34
27 6 0.17
29 12 0.34
30 5 0.14
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.52
Consensus pattern (30 bp):
TACTGATTACCATATTTTTACTCTTCTTTG
Found at i:29410 original size:74 final size:73
Alignment explanation
Indices: 29324--29462 Score: 174
Period size: 74 Copynumber: 1.9 Consensus size: 73
29314 TATTTCTTGA
** * * * *
29324 TTACTAATTACCATTTTTTACTC-TTTGTACTGATTACCATATTTTTACTCTTCTTTTACTGATT
1 TTACTAATTACCACATTTTACTCTTTTGTACTGATCACCAT-TTCTTACTCTT-TATTACTAATT
29388 ACCCCTTTTC
64 ACCCCTTTTC
*
29398 TTACTGAA-TACCACATTTTACTCTTTTTTACTGATCACCATTTCTTACTCTTTATTACTAATTA
1 TTACT-AATTACCACATTTTACTCTTTTGTACTGATCACCATTTCTTACTCTTTATTACTAATTA
29462 C
65 C
29463 TCTCTTTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
73 11 0.20
74 28 0.50
75 17 0.30
ACGTcount: A:0.23, C:0.23, G:0.04, T:0.50
Consensus pattern (73 bp):
TTACTAATTACCACATTTTACTCTTTTGTACTGATCACCATTTCTTACTCTTTATTACTAATTAC
CCCTTTTC
Found at i:29437 original size:27 final size:27
Alignment explanation
Indices: 29392--29511 Score: 111
Period size: 27 Copynumber: 4.4 Consensus size: 27
29382 CTGATTACCC
*
29392 CTTTTCTTACTGAAT-ACCACATTTTACT
1 CTTTT-TTACTG-ATCACCACTTTTTACT
29420 CTTTTTTACTGATCACCA-TTTCTTACT
1 CTTTTTTACTGATCACCACTTT-TTACT
* * * * *
29447 CTTTATTACTAATTACTCTCTTTTAAC-
1 CTTTTTTACTGATCAC-CACTTTTTACT
*
29474 CTTTTTTACTGATCACCATTTTTTACT
1 CTTTTTTACTGATCACCACTTTTTACT
29501 CTTTTCTTACT
1 CTTTT-TTACT
29512 CTTTTTACTG
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
26 11 0.15
27 46 0.62
28 14 0.19
29 3 0.04
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (27 bp):
CTTTTTTACTGATCACCACTTTTTACT
Found at i:29507 original size:65 final size:65
Alignment explanation
Indices: 29438--29654 Score: 303
Period size: 65 Copynumber: 3.3 Consensus size: 65
29428 CTGATCACCA
* * * *
29438 TTTCTTACTCTTTATTACTAATTACTCTCTTT-TAAC-CTTTTTTACTGATCACCATTTTTTACT
1 TTTCTTACTCTTT-TTACTGATTACTCT-TTTCTTACTCTTTTTTACTGATTACCACTTTTTACT
29501 CT
64 CT
* * *
29503 TTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTCTTTTACTGATTACCACTTTTAACTCA
1 TTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTTTTACTCT
29568 TTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTTTTACTCT
1 TTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTTTTACTCT
**
29633 TCTTCTTTTTCTCTTTTACTGA
1 T-TTCTTACTCT-TTTTACTGA
29655 CTACCATTTT
Statistics
Matches: 136, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
63 3 0.02
64 16 0.12
65 100 0.74
66 8 0.06
67 9 0.07
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.57
Consensus pattern (65 bp):
TTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTTTTACTCT
Found at i:29544 original size:13 final size:13
Alignment explanation
Indices: 29499--29545 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
29489 CCATTTTTTA
29499 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
29512 CT-TTTTACTGATT
1 CTCTTTT-CTTACT
29525 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
29539 CTCTTTT
1 CTCTTTT
29546 ACTGATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.11, C:0.26, G:0.02, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:29548 original size:37 final size:37
Alignment explanation
Indices: 29459--29548 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 37
29449 TTATTACTAA
29459 TTACTCTCTTTTAAC-CTTTTTTACTGATCACCATTTT
1 TTACTCTCTTTT-ACTCTTTTTTACTGATCACCATTTT
* *
29496 TTACTCTTTTCTTACTC-TTTTTACTGATTACTC-TTTT
1 TTACTCTCTT-TTACTCTTTTTTACTGATCAC-CATTTT
29533 CTTACTCTCTTTTACT
1 -TTACTCTCTTTTACT
29549 GATTACCACT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
37 33 0.72
38 13 0.28
ACGTcount: A:0.16, C:0.24, G:0.02, T:0.58
Consensus pattern (37 bp):
TTACTCTCTTTTACTCTTTTTTACTGATCACCATTTT
Found at i:29554 original size:28 final size:27
Alignment explanation
Indices: 29496--29619 Score: 140
Period size: 27 Copynumber: 4.1 Consensus size: 27
29486 TCACCATTTT
29496 TTACTCTTTTCTTACTCTTTTTACTGA
1 TTACTCTTTTCTTACTCTTTTTACTGA
29523 TTACTCTTTTCTTACTCTCTTTTACTGA
1 TTACTCTTTTCTTACTCT-TTTTACTGA
29551 TTACCACTTTTAACTCATTTCTTACTCTTTTTACTGA
1 TT---AC---T--CT--TTTCTTACTCTTTTTACTGA
29588 TTACTCTTTTCTTACTCTTTTTTACTGA
1 TTACTCTTTTCTTACTC-TTTTTACTGA
29616 TTAC
1 TTAC
29620 CACTTTTTAC
Statistics
Matches: 85, Mismatches: 0, Indels: 23
0.79 0.00 0.21
Matches are distributed among these distances:
27 28 0.33
28 25 0.29
29 2 0.02
31 3 0.04
34 3 0.04
36 2 0.02
37 11 0.13
38 11 0.13
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.56
Consensus pattern (27 bp):
TTACTCTTTTCTTACTCTTTTTACTGA
Found at i:29613 original size:37 final size:37
Alignment explanation
Indices: 29523--29671 Score: 115
Period size: 37 Copynumber: 4.2 Consensus size: 37
29513 TTTTTACTGA
29523 TTACTCTTTTCTTACTCTCTTTTACTGATTACCACTTT
1 TTACTCTTTT-TTACTCTCTTTTACTGATTACCACTTT
* *
29561 TAACTCATTTCTTACTCT-TTTTACTGATT---AC---
1 TTACTC-TTTTTTACTCTCTTTTACTGATTACCACTTT
* *
29592 -T-CT-TTTCTTACTCTTTTTTACTGATTACCACTTT
1 TTACTCTTTTTTACTCTCTTTTACTGATTACCACTTT
** *
29626 TTACTCTTCTTCTTTTTCTCTTTTACTGACTACCA--TT
1 TTACTCTT-TT-TTACTCTCTTTTACTGATTACCACTTT
29663 TTACTCTTT
1 TTACTCTTT
29672 GAATTTAATT
Statistics
Matches: 90, Mismatches: 8, Indels: 28
0.71 0.06 0.22
Matches are distributed among these distances:
27 11 0.12
28 11 0.12
29 2 0.02
31 2 0.02
34 2 0.02
35 1 0.01
36 3 0.03
37 23 0.26
38 13 0.14
39 22 0.24
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (37 bp):
TTACTCTTTTTTACTCTCTTTTACTGATTACCACTTT
Found at i:29629 original size:27 final size:28
Alignment explanation
Indices: 29563--29633 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
29553 ACCACTTTTA
*
29563 ACTCATTTCTTACTC-TTTTTACTGATT
1 ACTCCTTTCTTACTCTTTTTTACTGATT
*
29590 ACTCTTTTCTTACTCTTTTTTACTGATT
1 ACTCCTTTCTTACTCTTTTTTACTGATT
29618 AC-CACTTT-TTACTCTT
1 ACTC-CTTTCTTACTCTT
29634 CTTCTTTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.56
Consensus pattern (28 bp):
ACTCCTTTCTTACTCTTTTTTACTGATT
Found at i:29650 original size:39 final size:36
Alignment explanation
Indices: 29588--29671 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 36
29578 TTTTTACTGA
* *
29588 TTACTCTTTTCTTACTCTTTTTTACTGATTACCACTTT
1 TTACTCTTTTCTTACTCTCTTTTACTGACTACCA--TT
**
29626 TTACTCTTCTTCTTTTTCTCTTTTACTGACTACCATT
1 TTACTCTT-TTCTTACTCTCTTTTACTGACTACCATT
29663 TTACTCTTT
1 TTACTCTTT
29672 GAATTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.02
37 10 0.24
38 8 0.20
39 22 0.54
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.58
Consensus pattern (36 bp):
TTACTCTTTTCTTACTCTCTTTTACTGACTACCATT
Found at i:29812 original size:22 final size:20
Alignment explanation
Indices: 29785--30026 Score: 156
Period size: 22 Copynumber: 11.4 Consensus size: 20
29775 TGAATCTTGA
29785 TTACTGATTACCCTTTTTACTT
1 TTACTGATTA-CC-TTTTACTT
* *
29807 TTACTGTTTA-CTATTACTT
1 TTACTGATTACCTTTTACTT
* *
29826 CTTACTGATT-TCTATTACTCT
1 -TTACTGATTACCTTTTACT-T
29847 TTACTGATTATCAC-TTTACTCT
1 TTACTGATTA-C-CTTTTACT-T
* *
29869 TTACTAATTACCATTTTACCCT
1 TTACTGATTACC-TTTTA-CTT
*
29891 TTACAGA-TACCTTTTTACTTT
1 TTACTGATTACC-TTTTAC-TT
29912 TTACTGATTACCTTTTTACTTT
1 TTACTGATTACC-TTTTAC-TT
* *
29934 TTACTGTTTA-CTATTACTT
1 TTACTGATTACCTTTTACTT
* *
29953 CTTACTGATT-TCTATTACTCT
1 -TTACTGATTACCTTTTACT-T
29974 TTACTGATTATCAC-TTTACTCT
1 TTACTGATTA-C-CTTTTACT-T
29996 TTACTGATTACCATTTTACCTT
1 TTACTGATTACC-TTTTA-CTT
30018 TTACTGATT
1 TTACTGATT
30027 GCATCTTTCT
Statistics
Matches: 183, Mismatches: 17, Indels: 40
0.76 0.07 0.17
Matches are distributed among these distances:
19 9 0.05
20 59 0.32
21 21 0.11
22 89 0.49
23 5 0.03
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTT
Found at i:29911 original size:7 final size:7
Alignment explanation
Indices: 29901--29958 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
29891 TTACAGATAC
29901 CTTTTTA
1 CTTTTTA
29908 CTTTTTA
1 CTTTTTA
**
29915 CTGATTA
1 CTTTTTA
29922 CCTTTTTA
1 -CTTTTTA
29930 CTTTTTA
1 CTTTTTA
*
29937 CTGTTTA
1 CTTTTTA
*
29944 C-TATTA
1 CTTTTTA
*
29950 CTTCTTA
1 CTTTTTA
29957 CT
1 CT
29959 GATTTCTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 4 0.10
7 32 0.78
8 5 0.12
ACGTcount: A:0.17, C:0.19, G:0.03, T:0.60
Consensus pattern (7 bp):
CTTTTTA
Found at i:29934 original size:29 final size:27
Alignment explanation
Indices: 29901--29958 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
29891 TTACAGATAC
* *
29901 CTTTTTACTTTTTACTGATTACCTTTTTA
1 CTTTTTACTGTTTACT-ATTA-CTTCTTA
29930 CTTTTTACTGTTTACTATTACTTCTTA
1 CTTTTTACTGTTTACTATTACTTCTTA
29957 CT
1 CT
29959 GATTTCTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 8 0.30
28 4 0.15
29 15 0.56
ACGTcount: A:0.17, C:0.19, G:0.03, T:0.60
Consensus pattern (27 bp):
CTTTTTACTGTTTACTATTACTTCTTA
Found at i:29936 original size:127 final size:127
Alignment explanation
Indices: 29785--30021 Score: 440
Period size: 127 Copynumber: 1.9 Consensus size: 127
29775 TGAATCTTGA
29785 TTACTGATTACCCTTTTTACTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTA
1 TTACTGATTACCCTTTTTACTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTA
29850 CTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCTTTTTACTTT
66 CTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCTTTTTACTTT
29912 TTACTGATTA-CCTTTTTACTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTT
1 TTACTGATTACCCTTTTTAC-TTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTT
* *
29976 ACTGATTATCACTTTACTCTTTACTGATTACCATTTTACCTTTTAC
65 ACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTAC
30022 TGATTGCATC
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
126 9 0.08
127 98 0.92
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.53
Consensus pattern (127 bp):
TTACTGATTACCCTTTTTACTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTTA
CTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTTTACAGATACCTTTTTACTTT
Done.