Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012779.1 Corchorus capsularis cultivar CVL-1 contig12800, 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: 64395
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:4977 original size:14 final size:14
Alignment explanation
Indices: 4958--4988 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4948 TTCAAACTTA
4958 TATATTTGAATTTG
1 TATATTTGAATTTG
4972 TATATTTGAATTTG
1 TATATTTGAATTTG
4986 TAT
1 TAT
4989 GCTGTATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (14 bp):
TATATTTGAATTTG
Found at i:6145 original size:11 final size:11
Alignment explanation
Indices: 6129--6153 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6119 ATTTCCTTAA
6129 TTCTAAAATGC
1 TTCTAAAATGC
6140 TTCTAAAATGC
1 TTCTAAAATGC
6151 TTC
1 TTC
6154 AATTATTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCTAAAATGC
Found at i:6385 original size:25 final size:25
Alignment explanation
Indices: 6333--6386 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
6323 TTAGTTAATT
*
6333 AAATTAGATTGGAACTACATGAATG
1 AAATTAGATTGGAACTACATGAAGG
* * *
6358 AAATTAGATTTGAGCTACATGACGG
1 AAATTAGATTGGAACTACATGAAGG
6383 AAAT
1 AAAT
6387 GCAAACTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (25 bp):
AAATTAGATTGGAACTACATGAAGG
Found at i:6526 original size:26 final size:26
Alignment explanation
Indices: 6477--6526 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
6467 ATCTAGATCA
* *
6477 CTAAAAATGAATTAGCTCATCTAAGC
1 CTAAAAATGAATTAGCTAACCTAAGC
*
6503 CTAAATATGAATTAGCTAACCTAA
1 CTAAAAATGAATTAGCTAACCTAA
6527 ACTAAAAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (26 bp):
CTAAAAATGAATTAGCTAACCTAAGC
Found at i:6872 original size:22 final size:22
Alignment explanation
Indices: 6822--6995 Score: 230
Period size: 22 Copynumber: 8.1 Consensus size: 22
6812 ATTCGAAACC
*
6822 GCCCTGAGACGCTT-AAAGTCC
1 GCCCTGAGACGCTTGAAAGTCT
*
6843 GCCTTGAGACGCTTGAAAGTCT
1 GCCCTGAGACGCTTGAAAGTCT
* * *
6865 ACCCTGAGACACTTCAAAGTCT
1 GCCCTGAGACGCTTGAAAGTCT
* *
6887 GCCCTGAGACACTTGGAAGTCT
1 GCCCTGAGACGCTTGAAAGTCT
*
6909 GCCCTGAGACAC-TGAAAGTCT
1 GCCCTGAGACGCTTGAAAGTCT
6930 GCCCTGAGACGC-TGAAAGTCT
1 GCCCTGAGACGCTTGAAAGTCT
*
6951 ACCCTGAGACGCTTGAAAGTCT
1 GCCCTGAGACGCTTGAAAGTCT
*
6973 GCCCTGAGACGC-TGAAAATCT
1 GCCCTGAGACGCTTGAAAGTCT
6994 GC
1 GC
6996 TAAAATGGTA
Statistics
Matches: 137, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
21 62 0.45
22 75 0.55
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (22 bp):
GCCCTGAGACGCTTGAAAGTCT
Found at i:6968 original size:43 final size:44
Alignment explanation
Indices: 6823--6989 Score: 234
Period size: 43 Copynumber: 3.9 Consensus size: 44
6813 TTCGAAACCG
* * *
6823 CCCTGAGACGCTT-AAAGTCCGCCTTGAGACGCTTGAAAGTCTA
1 CCCTGAGACACTTGAAAGTCTGCCCTGAGACGCTTGAAAGTCTA
* * * *
6866 CCCTGAGACACTTCAAAGTCTGCCCTGAGACACTTGGAAGTCTG
1 CCCTGAGACACTTGAAAGTCTGCCCTGAGACGCTTGAAAGTCTA
6910 CCCTGAGACAC-TGAAAGTCTGCCCTGAGACGC-TGAAAGTCTA
1 CCCTGAGACACTTGAAAGTCTGCCCTGAGACGCTTGAAAGTCTA
*
6952 CCCTGAGACGCTTGAAAGTCTGCCCTGAGACGC-TGAAA
1 CCCTGAGACACTTGAAAGTCTGCCCTGAGACGCTTGAAA
6990 ATCTGCTAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
42 18 0.16
43 57 0.51
44 36 0.32
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (44 bp):
CCCTGAGACACTTGAAAGTCTGCCCTGAGACGCTTGAAAGTCTA
Found at i:9773 original size:6 final size:6
Alignment explanation
Indices: 9757--9893 Score: 165
Period size: 6 Copynumber: 23.2 Consensus size: 6
9747 TTATTTTTTC
* * * * * *
9757 TTTCTT CTTCTT GTTCTT TTTCTT GTTCTT GTTCTT GTTCTT GTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
9805 TTTCTT TTTCTT TTTCTT TTTCTT TTTC-T TTT-TT TTTCTTT CTTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT -TTTCTT
*
9853 TTTCTT TCT-TT TTTCTT TTTC-T TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
9894 GCGACTTTTC
Statistics
Matches: 118, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
5 17 0.14
6 93 0.79
7 4 0.03
8 4 0.03
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:11593 original size:19 final size:19
Alignment explanation
Indices: 11557--11596 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11547 CGAATTCATC
* *
11557 CTCTCTCTTCACTCTCTCT
1 CTCTCTCTACACACTCTCT
*
11576 CTCTCTCTACACAGTCTCT
1 CTCTCTCTACACACTCTCT
11595 CT
1 CT
11597 GGAAGATCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.45, G:0.03, T:0.42
Consensus pattern (19 bp):
CTCTCTCTACACACTCTCT
Found at i:13104 original size:45 final size:44
Alignment explanation
Indices: 13050--13157 Score: 162
Period size: 44 Copynumber: 2.4 Consensus size: 44
13040 ACCACTTTGG
* *
13050 AAAACCTTTTGAAAACCATGACTCTTTTTGAAAAAGCATTTTATC
1 AAAACCTTTTGAAAACCATGACTCATTTTG-AAAACCATTTTATC
* * *
13095 AAAATCTTTTAAAAACAATGACTCATTTTGAAAACCATTTTATC
1 AAAACCTTTTGAAAACCATGACTCATTTTGAAAACCATTTTATC
13139 AAAACCTTTTGAAAACCAT
1 AAAACCTTTTGAAAACCAT
13158 CGTTGCTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 29 0.53
45 26 0.47
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (44 bp):
AAAACCTTTTGAAAACCATGACTCATTTTGAAAACCATTTTATC
Found at i:13217 original size:10 final size:9
Alignment explanation
Indices: 13164--13247 Score: 55
Period size: 9 Copynumber: 8.8 Consensus size: 9
13154 CCATCGTTGC
*
13164 TTTTTCTCT
1 TTTTTTTCT
13173 TTTTCTTTCTT
1 TTTT-TTTC-T
13184 TTCTTTTTCT
1 TT-TTTTTCT
* *
13194 TTTTTCATCA
1 TTTTT-TTCT
*
13204 TTTTTATCT
1 TTTTTTTCT
13213 TTTTTCTTCT
1 TTTTT-TTCT
13223 TTTTTTT-T
1 TTTTTTTCT
13231 ATTTTGTTT-T
1 -TTTT-TTTCT
13241 TTTTTTT
1 TTTTTTT
13248 GGAAATTGCA
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
8 4 0.06
9 25 0.40
10 25 0.40
11 7 0.11
12 2 0.03
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:13226 original size:19 final size:18
Alignment explanation
Indices: 13178--13245 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
13168 TCTCTTTTTC
13178 TTTCTT-TTCTTTTTCTTT
1 TTTCTTCTT-TTTTTCTTT
* *
13196 TTTCATCATTTTTATCTTT
1 TTTCTTC-TTTTTTTCTTT
13215 TTTCTTCTTTTTTT-TTAT
1 TTTCTTCTTTTTTTCTT-T
*
13233 TTTGTT-TTTTTTT
1 TTTCTTCTTTTTTT
13246 TTGGAAATTG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
17 9 0.21
18 17 0.40
19 14 0.33
20 2 0.05
ACGTcount: A:0.06, C:0.12, G:0.01, T:0.81
Consensus pattern (18 bp):
TTTCTTCTTTTTTTCTTT
Found at i:16501 original size:12 final size:12
Alignment explanation
Indices: 16484--16514 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16474 TGGACTTGGA
16484 GGTTGAGACATT
1 GGTTGAGACATT
*
16496 GGTTGAGACCTT
1 GGTTGAGACATT
16508 GGTTGAG
1 GGTTGAG
16515 GTTTTGCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.10, G:0.39, T:0.32
Consensus pattern (12 bp):
GGTTGAGACATT
Found at i:18575 original size:23 final size:22
Alignment explanation
Indices: 18549--18601 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
18539 AATGCTGTGA
*
18549 TAAAAACTTTTTATTTTTGTTTT
1 TAAAAACTTTTTATTTTT-TCTT
**
18572 TAAAGTC-TTTTATTTTTTCTT
1 TAAAAACTTTTTATTTTTTCTT
*
18593 TGAAAACTT
1 TAAAAACTT
18602 CCATTTTAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
21 7 0.30
22 11 0.48
23 5 0.22
ACGTcount: A:0.26, C:0.08, G:0.06, T:0.60
Consensus pattern (22 bp):
TAAAAACTTTTTATTTTTTCTT
Found at i:20091 original size:16 final size:16
Alignment explanation
Indices: 20067--20097 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20057 CAAAGTAAAG
20067 AAGAAAAAAGGAAAAA
1 AAGAAAAAAGGAAAAA
*
20083 AAGAGAAAAGGAAAA
1 AAGAAAAAAGGAAAA
20098 CCTTGGCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGGAAAAA
Found at i:20686 original size:6 final size:6
Alignment explanation
Indices: 20675--20740 Score: 82
Period size: 6 Copynumber: 10.8 Consensus size: 6
20665 GTAAAAATTG
*
20675 AAAGAA AAAG-A AAAGAA AAA-AGA AAAGAAA AAAGAA AAAGAA AAAGCA
1 AAAGAA AAAGAA AAAGAA AAAGA-A AAAG-AA AAAGAA AAAGAA AAAGAA
20723 AAAGAAA AAAGAA AAAGA
1 AAAG-AA AAAGAA AAAGA
20741 GAATGAAGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
5 6 0.11
6 36 0.68
7 10 0.19
8 1 0.02
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:20694 original size:12 final size:12
Alignment explanation
Indices: 20675--20737 Score: 94
Period size: 12 Copynumber: 5.2 Consensus size: 12
20665 GTAAAAATTG
20675 AAAG-AAAAAGA
1 AAAGAAAAAAGA
20686 AAAGAAAAAAGA
1 AAAGAAAAAAGA
20698 AAAGAAAAAAGA
1 AAAGAAAAAAGA
20710 AAA-AGAAAAAGCA
1 AAAGA-AAAAAG-A
20723 AAAGAAAAAAGA
1 AAAGAAAAAAGA
20735 AAA
1 AAA
20738 AGAGAATGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.10
12 32 0.67
13 10 0.21
14 1 0.02
ACGTcount: A:0.83, C:0.02, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAGA
Found at i:20725 original size:25 final size:24
Alignment explanation
Indices: 20675--20740 Score: 100
Period size: 25 Copynumber: 2.8 Consensus size: 24
20665 GTAAAAATTG
20675 AAAG-AAAAAG-AAAAGAAAAAAGA
1 AAAGAAAAAAGAAAAAG-AAAAAGA
20698 AAAGAAAAAAGAAAAAGAAAAAGCA
1 AAAGAAAAAAGAAAAAGAAAAAG-A
20723 AAAGAAAAAAGAAAAAGA
1 AAAGAAAAAAGAAAAAGA
20741 GAATGAAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.10
24 12 0.30
25 24 0.60
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (24 bp):
AAAGAAAAAAGAAAAAGAAAAAGA
Found at i:20752 original size:19 final size:19
Alignment explanation
Indices: 20675--20740 Score: 93
Period size: 19 Copynumber: 3.6 Consensus size: 19
20665 GTAAAAATTG
20675 AAAGAAAAAG-AAAAGAAA
1 AAAGAAAAAGAAAAAGAAA
20693 AAAG-AAAAGAAAAA-AGAA
1 AAAGAAAAAGAAAAAGA-AA
*
20711 AAAGAAAAAGCAAAAGAAA
1 AAAGAAAAAGAAAAAGAAA
20730 AAAGAAAAAGA
1 AAAGAAAAAGA
20741 GAATGAAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.14
18 14 0.33
19 21 0.50
20 1 0.02
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAGAAAAAGAAA
Found at i:22100 original size:16 final size:16
Alignment explanation
Indices: 22079--22117 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
22069 CACATGCGCG
22079 CGCGTCAGACAGCCAC
1 CGCGTCAGACAGCCAC
22095 CGCGTCAGACAGCCAC
1 CGCGTCAGACAGCCAC
22111 CGCGTCA
1 CGCGTCA
22118 TTTCTTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.44, G:0.26, T:0.08
Consensus pattern (16 bp):
CGCGTCAGACAGCCAC
Found at i:23726 original size:70 final size:69
Alignment explanation
Indices: 23639--23904 Score: 299
Period size: 69 Copynumber: 3.8 Consensus size: 69
23629 AATGCTTCGA
* * *
23639 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGGT-AGATCAAGCCTTGGTTCCATCCAAGCATT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGA-GTCAG-TTAAGCCTTGGTTCCATCCAAGCATT
23703 CAAGGG
64 CAAGGG
* * * ** *
23709 CTTTTCCACAAGCCAAACTCGTTTTCACACGAGTCAGTTTAGCCTTGGTTCTGTCCAAGCA-ACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCATTCA
23773 TA-GG
66 -AGGG
* * * **
23777 CTTTTCCACAAGCCGAACTCGTTTCCATACGAGGT-ACCTTAAGCTTTGGTTCCATCCAAATATT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGA-GTCA-GTTAAGCCTTGGTTCCATCCAAGCATT
23841 C-AGGCG
64 CAAGG-G
* *
23847 CTTTTCCACAAGCCAATCTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAA
23905 AATTATGCAT
Statistics
Matches: 163, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
68 35 0.21
69 65 0.40
70 63 0.39
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCATTCA
AGGG
Found at i:23887 original size:138 final size:138
Alignment explanation
Indices: 23639--23897 Score: 394
Period size: 138 Copynumber: 1.9 Consensus size: 138
23629 AATGCTTCGA
* * * *
23639 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGGTAGATCAAGCCTTGGTTCCATCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGGTACATCAAGCCTTGGTTCCATCCAAACATTC
*
23704 AAGGGCTTTTCCACAAGCCAAACTCGTTTTCACACGAGTCAGTTTAGCCTTGGTTCTGTCCAAGC
66 AAGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTTTAGCCTTGGTTCTGTCCAAGC
23769 AACATAGG
131 AACATAGG
* * * * *
23777 CTTTTCCACAAGCCGAACTCGTTTCCATACGAGGTACCTTAAGCTTTGGTTCCATCCAAATATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGGTACATCAAGCCTTGGTTCCATCCAAACATTC
* *
23842 -AGGCGCTTTTCCACAAGCCAATCTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTC
66 AAGG-GCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTTTAGCCTTGGTTC
23898 CATCCAAAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
137 3 0.03
138 105 0.97
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (138 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGGTACATCAAGCCTTGGTTCCATCCAAACATTC
AAGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTTTAGCCTTGGTTCTGTCCAAGC
AACATAGG
Found at i:26332 original size:19 final size:19
Alignment explanation
Indices: 26296--26335 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
26286 CGGATTCATC
* *
26296 CTCTCTCTTCACTCTCTCT
1 CTCTCTCTACACACTCTCT
*
26315 CTCTCTCTACACAGTCTCT
1 CTCTCTCTACACACTCTCT
26334 CT
1 CT
26336 AGAAGATCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.45, G:0.03, T:0.42
Consensus pattern (19 bp):
CTCTCTCTACACACTCTCT
Found at i:27579 original size:30 final size:31
Alignment explanation
Indices: 27511--27588 Score: 104
Period size: 30 Copynumber: 2.5 Consensus size: 31
27501 ACGGTGTTCG
*
27511 ACGTGGCATACCACGTGGATCAAAAAGTAAC
1 ACGTGGCACACCACGTGGATCAAAAAGTAAC
* * *
27542 ACATGGCACACCACGTGGAT-TAAAAGTGAC
1 ACGTGGCACACCACGTGGATCAAAAAGTAAC
*
27572 ACGTGGCACACCGCGTG
1 ACGTGGCACACCACGTG
27589 TGCCAAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 23 0.56
31 18 0.44
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (31 bp):
ACGTGGCACACCACGTGGATCAAAAAGTAAC
Found at i:27633 original size:31 final size:31
Alignment explanation
Indices: 27598--27671 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
27588 GTGCCAAAAA
* * *
27598 GTGGCACGTCACATGTACCAAAAAGTGATAT
1 GTGGCACGCCACATGTACCAAAAAGTGACAC
* **
27629 GTGGCACGCCACGTGTACTGAAAAGTGACAC
1 GTGGCACGCCACATGTACCAAAAAGTGACAC
*
27660 GTGGCATGCCAC
1 GTGGCACGCCAC
27672 GTGCACTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (31 bp):
GTGGCACGCCACATGTACCAAAAAGTGACAC
Found at i:28588 original size:17 final size:17
Alignment explanation
Indices: 28565--28619 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
28555 GGTTAAGATT
28565 TGAAGAAAAAGCAAAAAA
1 TGAAGAAAAAG-AAAAAA
28583 -GAAGAAGGAAAAGAAAAAA
1 TGAAG-A--AAAAGAAAAAA
28602 TGAA-AAAAAGGAAAAAA
1 TGAAGAAAAA-GAAAAAA
28619 T
1 T
28620 CAGAAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 4 0.12
17 12 0.38
18 2 0.06
19 6 0.19
20 8 0.25
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (17 bp):
TGAAGAAAAAGAAAAAA
Found at i:28911 original size:23 final size:22
Alignment explanation
Indices: 28861--28911 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28851 TAAAATGGAA
* *
28861 GTTTTCAAAGCAAAAATAAAAG
1 GTTTTAAAAACAAAAATAAAAG
**
28883 ACTTTAAAAACAAAAATAAAAAG
1 GTTTTAAAAACAAAAAT-AAAAG
28906 GTTTTA
1 GTTTTA
28912 TCACAGCATT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (22 bp):
GTTTTAAAAACAAAAATAAAAG
Found at i:30607 original size:36 final size:36
Alignment explanation
Indices: 30539--30721 Score: 224
Period size: 36 Copynumber: 4.9 Consensus size: 36
30529 GATTAAGTTC
30539 TTTATTGACTCCACTTAATTA-CCTGAATTAAGCCT
1 TTTATTGACTCCACTTAATTACCCTGAATTAAGCCT
*
30574 TTTATTGACTCCACTTAATTACCCTGAGTTAAGCCTAAGT
1 TTTATTGACTCCACTTAATTACCCTGAATTAAGCC----T
* * *
30614 ACTTTATTGAGTCAACTTAATTACCCTGAATTAAGTCT
1 --TTTATTGACTCCACTTAATTACCCTGAATTAAGCCT
* *
30652 TTTATTGACGCTACTTAATTACCCTGAATTAAGTCCT
1 TTTATTGACTCCACTTAATTACCCTGAATTAAG-CCT
* *
30689 TTTATTGACGCTACTTAATTACCCTGAATTAAG
1 TTTATTGACTCCACTTAATTACCCTGAATTAAG
30722 TCCCTGACTT
Statistics
Matches: 131, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
35 21 0.16
36 42 0.32
37 35 0.27
38 1 0.01
40 1 0.01
42 31 0.24
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTATTGACTCCACTTAATTACCCTGAATTAAGCCT
Found at i:30668 original size:78 final size:78
Alignment explanation
Indices: 30532--30723 Score: 238
Period size: 78 Copynumber: 2.5 Consensus size: 78
30522 CTTTTTAGAT
* * * *
30532 TAAGTTCTTTATTGACTCCACTTAATTA-CCTGAATTAAGCCTTTTATTGACTCCACTTAATTAC
1 TAAG-TCTTTATTGAGTCAACTTAATTACCCTGAATTAAGTCTTTTATTGACGCCACTTAATTAC
*
30596 CCTGAGTTAAG-CC
65 CCTGAATTAAGTCC
*
30609 TAAGTACTTTATTGAGTCAACTTAATTACCCTGAATTAAGTCTTTTATTGACGCTACTTAATTAC
1 TAAGT-CTTTATTGAGTCAACTTAATTACCCTGAATTAAGTCTTTTATTGACGCCACTTAATTAC
30674 CCTGAATTAAGTCC
65 CCTGAATTAAGTCC
*
30688 ----T-TTTATTGACG-CTACTTAATTACCCTGAATTAAGTC
1 TAAGTCTTTATTGA-GTCAACTTAATTACCCTGAATTAAGTC
30724 CCTGACTTGA
Statistics
Matches: 104, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
73 32 0.31
74 1 0.01
75 1 0.01
76 1 0.01
77 24 0.23
78 43 0.41
79 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.40
Consensus pattern (78 bp):
TAAGTCTTTATTGAGTCAACTTAATTACCCTGAATTAAGTCTTTTATTGACGCCACTTAATTACC
CTGAATTAAGTCC
Found at i:30756 original size:37 final size:35
Alignment explanation
Indices: 30715--30868 Score: 134
Period size: 37 Copynumber: 4.3 Consensus size: 35
30705 AATTACCCTG
**
30715 AATTAAGTCCCTGACTTGAGTTAATTTCCTTCCTTGA
1 AATTAAGTCCCT-ACTT-ACCTAATTTCCTTCCTTGA
* * *
30752 AATTAAGTCCTTAACTCTACCTAATTCCCTTCCTTGG
1 AATTAAGTCCCT-ACT-TACCTAATTTCCTTCCTTGA
* *
30789 AATCAAGT-CCT-C-TACTTAATTTCCTTCCTTGA
1 AATTAAGTCCCTACTTACCTAATTTCCTTCCTTGA
* *
30821 AATTAAGTCAGTCTTTCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTC---CCTAC-TTACCTAATTTCCTTCCTTGA
30860 AATTAAGTC
1 AATTAAGTC
30869 AATCTTCTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
32 24 0.25
34 1 0.01
36 4 0.04
37 37 0.39
38 1 0.01
39 28 0.29
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.41
Consensus pattern (35 bp):
AATTAAGTCCCTACTTACCTAATTTCCTTCCTTGA
Found at i:30809 original size:32 final size:32
Alignment explanation
Indices: 30766--30829 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
30756 AAGTCCTTAA
*
30766 CTCTACCTAATTCCCTTCCTTGGAATCAAGTC
1 CTCTACCTAATTCCCTTCCTTGAAATCAAGTC
* * *
30798 CTCTACTTAATTTCCTTCCTTGAAATTAAGTC
1 CTCTACCTAATTCCCTTCCTTGAAATCAAGTC
30830 AGTCTTTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.30, G:0.08, T:0.39
Consensus pattern (32 bp):
CTCTACCTAATTCCCTTCCTTGAAATCAAGTC
Found at i:30898 original size:35 final size:35
Alignment explanation
Indices: 30813--31019 Score: 290
Period size: 35 Copynumber: 5.8 Consensus size: 35
30803 CTTAATTTCC
30813 TTCCTTGAAATTAAGTCAGTCTT-TCTTTACCTAATTT
1 TTCCTTGAAATTAAGTCAGTCTTCT-TTTACCTAA--T
*
30850 CCTTCCTTGAAATTAAGTCAATCTTCTTTTACCTAAT
1 --TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
*
30887 TTCCTTGAAATTAAGACAGTCTTCTTTTACCTAAT
1 TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
*
30922 TTCCTTGAAATTTAGTCAGTCTTCTTTTACCTAAT
1 TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
* *
30957 TTCCTTGAAATTTAGTCAGTCTTATTTTACCTAAT
1 TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
* * *
30992 TTCCTTGAAATTAAATCAGACATCTTTT
1 TTCCTTGAAATTAAGTCAGTCTTCTTTT
31020 TTTTATTTTT
Statistics
Matches: 156, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
35 123 0.79
37 1 0.01
39 31 0.20
40 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.46
Consensus pattern (35 bp):
TTCCTTGAAATTAAGTCAGTCTTCTTTTACCTAAT
Found at i:37331 original size:281 final size:281
Alignment explanation
Indices: 36828--37394 Score: 1116
Period size: 281 Copynumber: 2.0 Consensus size: 281
36818 CGCACTAGGA
36828 TCTAGTGGTGATGGAGATGATGAAAGGGGTATGTCGCATGATGATGAGGATGATGATGGTAACAC
1 TCTAGTGGTGATGGAGATGATGAAAGGGGTATGTCGCATGATGATGAGGATGATGATGGTAACAC
36893 ACCGGCACTCTTGAACTTAGTTGCAAGAAGAACTTTAAGTGCCTATGTTAAAGGAGATGTGCACA
66 ACCGGCACTCTTGAACTTAGTTGCAAGAAGAACTTTAAGTGCCTATGTTAAAGGAGATGTGCACA
36958 ATCAAAGGGAGAATTTGTTTCATACTAGGATGTATGCGAATGGAAAGCCTAGTAATGTGATCATT
131 ATCAAAGGGAGAATTTGTTTCATACTAGGATGTATGCGAATGGAAAGCCTAGTAATGTGATCATT
37023 GAGGGAGGGAGTTGTACAAACATAGCTAGTGTGTACTTAGTAAAGGAGTTAGCGTTACCTACCAC
196 GAGGGAGGGAGTTGTACAAACATAGCTAGTGTGTACTTAGTAAAGGAGTTAGCGTTACCTACCAC
37088 TAAACACCCTAAACCCTATAG
261 TAAACACCCTAAACCCTATAG
*
37109 TCTAGTGGTGATGGAGATGATGAAAGGGGTATGTCGCATGATGATGAGGATGATGATGGTAACAT
1 TCTAGTGGTGATGGAGATGATGAAAGGGGTATGTCGCATGATGATGAGGATGATGATGGTAACAC
37174 ACCGGCACTCTTGAACTTAGTTGCAAGAAGAACTTTAAGTGCCTATGTTAAAGGAGATGTGCACA
66 ACCGGCACTCTTGAACTTAGTTGCAAGAAGAACTTTAAGTGCCTATGTTAAAGGAGATGTGCACA
*
37239 ATCAAAGGGAGAATTTGTTTCATACTAGGATGTATGCGAATGGAAAGCCTAGTAGTGTGATCATT
131 ATCAAAGGGAGAATTTGTTTCATACTAGGATGTATGCGAATGGAAAGCCTAGTAATGTGATCATT
37304 GAGGGAGGGAGTTGTACAAACATAGCTAGTGTGTACTTAGTAAAGGAGTTAGCGTTACCTACCAC
196 GAGGGAGGGAGTTGTACAAACATAGCTAGTGTGTACTTAGTAAAGGAGTTAGCGTTACCTACCAC
37369 TAAACACCCTAAACCCTATAG
261 TAAACACCCTAAACCCTATAG
37390 TCTAG
1 TCTAG
37395 GATGGTTCAA
Statistics
Matches: 284, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
281 284 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (281 bp):
TCTAGTGGTGATGGAGATGATGAAAGGGGTATGTCGCATGATGATGAGGATGATGATGGTAACAC
ACCGGCACTCTTGAACTTAGTTGCAAGAAGAACTTTAAGTGCCTATGTTAAAGGAGATGTGCACA
ATCAAAGGGAGAATTTGTTTCATACTAGGATGTATGCGAATGGAAAGCCTAGTAATGTGATCATT
GAGGGAGGGAGTTGTACAAACATAGCTAGTGTGTACTTAGTAAAGGAGTTAGCGTTACCTACCAC
TAAACACCCTAAACCCTATAG
Found at i:42031 original size:25 final size:25
Alignment explanation
Indices: 42003--42056 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
41993 TTAGTTAATT
42003 AAATTAGATTGGAACTACATGAATG
1 AAATTAGATTGGAACTACATGAATG
* * *
42028 AAATTAGATTTGAGCTACATGACTG
1 AAATTAGATTGGAACTACATGAATG
42053 AAAT
1 AAAT
42057 GCAAACTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (25 bp):
AAATTAGATTGGAACTACATGAATG
Found at i:42196 original size:26 final size:26
Alignment explanation
Indices: 42147--42196 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
42137 ATCTAGATGA
** *
42147 CTAAAAATGAATTAGCTCATCTAAGC
1 CTAAAAATGAATTAGCGAACCTAAGC
*
42173 CTAAATATGAATTAGCGAACCTAA
1 CTAAAAATGAATTAGCGAACCTAA
42197 ACTAAAAGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (26 bp):
CTAAAAATGAATTAGCGAACCTAAGC
Found at i:45125 original size:41 final size:41
Alignment explanation
Indices: 45079--45229 Score: 142
Period size: 41 Copynumber: 3.6 Consensus size: 41
45069 ACCCAATATC
*
45079 CAAAGTCCCCAAACACAATCCTAACACAGGGGCAACT-CTTT
1 CAAAGTCCCCAAACACAATCATAACACAGGGGCAA-TACTTT
* * ** * * *
45120 CAAAGTCCTCAAACACATTCATAACACAAAGGCATTAATAT
1 CAAAGTCCCCAAACACAATCATAACACAGGGGCAATACTTT
* * *
45161 CAAAGTCCCCAAACACAATTATAACATAGGGGCAATCCTTTCT
1 CAAAGTCCCCAAACACAATCATAACACAGGGGCAATAC-TT-T
* * *
45204 CAAAGTCCTCAAACACATTCTTAACA
1 CAAAGTCCCCAAACACAATCATAACA
45230 GAGACAGCTA
Statistics
Matches: 85, Mismatches: 22, Indels: 4
0.77 0.20 0.04
Matches are distributed among these distances:
40 1 0.01
41 60 0.71
42 1 0.01
43 23 0.27
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.21
Consensus pattern (41 bp):
CAAAGTCCCCAAACACAATCATAACACAGGGGCAATACTTT
Found at i:45170 original size:82 final size:85
Alignment explanation
Indices: 45073--45229 Score: 241
Period size: 82 Copynumber: 1.9 Consensus size: 85
45063 TCTCTTACCC
*
45073 AATATCCAAAGTCCCCAAACACAATCCTAACACAGGGGCAA--CTCTT-TCAAAGTCCTCAAACA
1 AATATCCAAAGTCCCCAAACACAATCATAACACAGGGGCAATCCT-TTCTCAAAGTCCTCAAACA
45135 CATTCATAACACAAAGGCATT
65 CATTCATAACACAAAGGCATT
* *
45156 AATAT-CAAAGTCCCCAAACACAATTATAACATAGGGGCAATCCTTTCTCAAAGTCCTCAAACAC
1 AATATCCAAAGTCCCCAAACACAATCATAACACAGGGGCAATCCTTTCTCAAAGTCCTCAAACAC
*
45220 ATTCTTAACA
66 ATTCATAACA
45230 GAGACAGCTA
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
82 32 0.48
83 7 0.10
84 28 0.42
ACGTcount: A:0.41, C:0.29, G:0.09, T:0.22
Consensus pattern (85 bp):
AATATCCAAAGTCCCCAAACACAATCATAACACAGGGGCAATCCTTTCTCAAAGTCCTCAAACAC
ATTCATAACACAAAGGCATT
Found at i:48036 original size:21 final size:24
Alignment explanation
Indices: 48007--48057 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
47997 TTTTGAACTC
48007 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
48030 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
48053 ATTAT
1 ATTAT
48058 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:48052 original size:25 final size:25
Alignment explanation
Indices: 48007--48055 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
47997 TTTTGAACTC
*
48007 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
48032 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
48056 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:48373 original size:11 final size:11
Alignment explanation
Indices: 48329--48367 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
48319 TTTCCTATAT
*
48329 TAAATAAATTA
1 TAAATTAATTA
48340 TCAAA-TAATTA
1 T-AAATTAATTA
48351 TAAATTAATTA
1 TAAATTAATTA
48362 TAAATT
1 TAAATT
48368 TGTTATGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 3 0.12
11 19 0.76
12 3 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATTAATTA
Found at i:51757 original size:2 final size:2
Alignment explanation
Indices: 51715--51746 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
51705 AAGAAGTGTC
51715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51747 TACTGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55227 original size:30 final size:30
Alignment explanation
Indices: 55193--55254 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
55183 CACCAAACCA
55193 TTTCATTACAGCCTAAAACTCATGAAGATT
1 TTTCATTACAGCCTAAAACTCATGAAGATT
55223 TTTCATTACAGCCTAAAACTCATGAAGATT
1 TTTCATTACAGCCTAAAACTCATGAAGATT
55253 TT
1 TT
55255 AGGTGCCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (30 bp):
TTTCATTACAGCCTAAAACTCATGAAGATT
Found at i:63721 original size:23 final size:23
Alignment explanation
Indices: 63691--63736 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
63681 CCTGACTCTA
63691 ATTTTTTTTCAA-AAAAAAAATAT
1 ATTTTTTTT-AATAAAAAAAATAT
63714 ATTTTTTTTAATAAAAAAAATAT
1 ATTTTTTTTAATAAAAAAAATAT
63737 GACGTGGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTTTTTTAATAAAAAAAATAT
Found at i:64327 original size:32 final size:32
Alignment explanation
Indices: 64254--64395 Score: 171
Period size: 32 Copynumber: 4.4 Consensus size: 32
64244 ACTAGGACGG
* *
64254 TTCAGCCACGGCAGAGCCTCCC-CAGTGGGGAGGC
1 TTCA-CCACGGCA-AGCCGCCCTCA-TGGGGCGGC
64288 -TCAACCACGGCAAGCCGCCCTCATGGGGCGGC
1 TTC-ACCACGGCAAGCCGCCCTCATGGGGCGGC
* *
64320 TTCACCACGGTAGGCCGCCCTCATGGGGCGGC
1 TTCACCACGGCAAGCCGCCCTCATGGGGCGGC
* *
64352 TTCACCACGGTAGGCCGCCCTCATGGGGCGGC
1 TTCACCACGGCAAGCCGCCCTCATGGGGCGGC
*
64384 TTCGCCACGGCA
1 TTCACCACGGCA
Statistics
Matches: 99, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
32 84 0.85
33 14 0.14
34 1 0.01
ACGTcount: A:0.15, C:0.38, G:0.33, T:0.13
Consensus pattern (32 bp):
TTCACCACGGCAAGCCGCCCTCATGGGGCGGC
Done.