Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015669.1 Corchorus capsularis cultivar CVL-1 contig15690, 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: 61374
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1849 original size:15 final size:15
Alignment explanation
Indices: 1829--1857 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1819 TGTTGTGTAA
1829 TGTAATTATAAGTAT
1 TGTAATTATAAGTAT
1844 TGTAATTATAAGTA
1 TGTAATTATAAGTA
1858 ATTACAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (15 bp):
TGTAATTATAAGTAT
Found at i:1858 original size:25 final size:25
Alignment explanation
Indices: 1830--1882 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1820 GTTGTGTAAT
* *
1830 GTAATTATAAGTATTGTAATTATAA
1 GTAATTACAAGTAATGTAATTATAA
*
1855 GTAATTACAATTAATGTAATTATAA
1 GTAATTACAAGTAATGTAATTATAA
1880 GTA
1 GTA
1883 TTGTTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (25 bp):
GTAATTACAAGTAATGTAATTATAA
Found at i:2768 original size:11 final size:11
Alignment explanation
Indices: 2747--2780 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2737 TTTTCCTTAA
2747 AAAAGGAAAAAG
1 AAAA-GAAAAAG
2759 AAAAGAAAAAG
1 AAAAGAAAAAG
*
2770 AAAAGGAAAAG
1 AAAAGAAAAAG
2781 GGGATAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:2772 original size:17 final size:18
Alignment explanation
Indices: 2746--2780 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2736 TTTTTCCTTA
2746 AAAAAGGAAAAAGAAAAG
1 AAAAAGGAAAAAGAAAAG
*
2764 AAAAA-GAAAAGGAAAAG
1 AAAAAGGAAAAAGAAAAG
2781 GGGATAAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAAAGGAAAAAGAAAAG
Found at i:3124 original size:18 final size:18
Alignment explanation
Indices: 3089--3124 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3079 TCATAGCCTC
* *
3089 ATAATTTTATATTTTATA
1 ATAATTTTATAATATATA
3107 ATAATTTTATAATATATA
1 ATAATTTTATAATATATA
3125 TCTACATAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAATTTTATAATATATA
Found at i:4590 original size:21 final size:21
Alignment explanation
Indices: 4564--4607 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4554 TTCTTCTGGA
4564 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
4585 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
4606 TT
1 TT
4608 TACGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:7103 original size:20 final size:20
Alignment explanation
Indices: 7078--7115 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
7068 CTAACATTAT
7078 GCCACATCAACAATTTTTTG
1 GCCACATCAACAATTTTTTG
*
7098 GCCACATCAGCAATTTTT
1 GCCACATCAACAATTTTT
7116 CACGATCGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (20 bp):
GCCACATCAACAATTTTTTG
Found at i:9758 original size:10 final size:10
Alignment explanation
Indices: 9730--9767 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
9720 TTATTATTTA
9730 CTTTCTCT-T
1 CTTTCTCTCT
9739 CTTCTTCTCTCT
1 C-T-TTCTCTCT
9751 CTTTCTCTCT
1 CTTTCTCTCT
9761 CTTTCTC
1 CTTTCTC
9768 AATTTGTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.04
10 16 0.62
11 7 0.27
12 2 0.08
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (10 bp):
CTTTCTCTCT
Found at i:14007 original size:21 final size:20
Alignment explanation
Indices: 13965--14009 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
13955 ATTTACCTTC
* *
13965 AAATACTATTATTTGGGGCT
1 AAATACTATTATTTGAGACT
*
13985 AAATCCTATTGATTTGAGACT
1 AAATACTATT-ATTTGAGACT
14006 AAAT
1 AAAT
14010 TTTAATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (20 bp):
AAATACTATTATTTGAGACT
Found at i:14245 original size:8 final size:8
Alignment explanation
Indices: 14232--14259 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
14222 AATTTAACCC
14232 TTGAAATA
1 TTGAAATA
14240 TTGAAATA
1 TTGAAATA
14248 TTGAAATA
1 TTGAAATA
14256 TTGA
1 TTGA
14260 TAGACTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (8 bp):
TTGAAATA
Found at i:15173 original size:2 final size:2
Alignment explanation
Indices: 15166--15192 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15156 TAATATGTAG
15166 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
15193 TTGTGGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15434 original size:6 final size:6
Alignment explanation
Indices: 15425--15491 Score: 68
Period size: 6 Copynumber: 11.0 Consensus size: 6
15415 ACCCGAAAAT
15425 ACCCGA ACCCGA GACAACCCGA ACCCGA ACCCG- -CCCGA ACCCGA ACCCGA
1 ACCCGA ACCCGA -AC--C-CGA ACCCGA ACCCGA ACCCGA ACCCGA ACCCGA
*
15475 ACCCG- ACCCGA ATCCGA
1 ACCCGA ACCCGA ACCCGA
15492 GATCAAAATA
Statistics
Matches: 53, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
4 4 0.08
5 5 0.09
6 35 0.66
7 3 0.06
9 3 0.06
10 3 0.06
ACGTcount: A:0.31, C:0.49, G:0.18, T:0.01
Consensus pattern (6 bp):
ACCCGA
Found at i:15435 original size:16 final size:16
Alignment explanation
Indices: 15392--15453 Score: 90
Period size: 16 Copynumber: 3.9 Consensus size: 16
15382 AACCCGCCCG
*
15392 TACCCGAACCCAAAAA
1 TACCCGAACCCGAAAA
15408 TACCCGAACCCGAAAA
1 TACCCGAACCCGAAAA
*
15424 TACCCGAACCCGAGACA
1 TACCCGAACCCGA-AAA
15441 -ACCCGAACCCGAA
1 TACCCGAACCCGAA
15454 CCCGCCCGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
15 1 0.02
16 40 0.93
17 2 0.05
ACGTcount: A:0.42, C:0.40, G:0.13, T:0.05
Consensus pattern (16 bp):
TACCCGAACCCGAAAA
Found at i:15450 original size:22 final size:23
Alignment explanation
Indices: 15425--15491 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 23
15415 ACCCGAAAAT
*
15425 ACCCGAACCCGAGAC-AACCCGA
1 ACCCGAACCCGACACGAACCCGA
*
15447 ACCCGAACCCG-CCCGAACCCGA
1 ACCCGAACCCGACACGAACCCGA
* *
15469 ACCCGAACCCGACCCGAATCCGA
1 ACCCGAACCCGACACGAACCCGA
15492 GATCAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 1 0.03
22 29 0.73
23 10 0.25
ACGTcount: A:0.31, C:0.49, G:0.18, T:0.01
Consensus pattern (23 bp):
ACCCGAACCCGACACGAACCCGA
Found at i:15461 original size:16 final size:17
Alignment explanation
Indices: 15441--15491 Score: 70
Period size: 16 Copynumber: 3.1 Consensus size: 17
15431 ACCCGAGACA
15441 ACCCGAACCCGAACCCG
1 ACCCGAACCCGAACCCG
15458 -CCCGAACCCGAACCCG
1 ACCCGAACCCGAACCCG
*
15474 AACCCG-ACCCGAATCCG
1 -ACCCGAACCCGAACCCG
15491 A
1 A
15492 GATCAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 17 0.55
17 10 0.32
18 4 0.13
ACGTcount: A:0.29, C:0.51, G:0.18, T:0.02
Consensus pattern (17 bp):
ACCCGAACCCGAACCCG
Found at i:16265 original size:23 final size:23
Alignment explanation
Indices: 16235--16289 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
16225 TATCGAAAGT
* *
16235 GAACCCGAACCCGAACCGGGTCC
1 GAACCCGAACCCGAACCGAGCCC
*
16258 GAACCCGAACCCGACCCGAGCCC
1 GAACCCGAACCCGAACCGAGCCC
16281 GAACCCGAA
1 GAACCCGAA
16290 AATACCCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.45, G:0.24, T:0.02
Consensus pattern (23 bp):
GAACCCGAACCCGAACCGAGCCC
Found at i:16276 original size:17 final size:17
Alignment explanation
Indices: 16237--16288 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
16227 TCGAAAGTGA
*
16237 ACCCGAACCCGAACCGG
1 ACCCGAACCCGAACCCG
**
16254 GTCCGAACCCGAACCCG
1 ACCCGAACCCGAACCCG
*
16271 ACCCGAGCCCGAACCCG
1 ACCCGAACCCGAACCCG
16288 A
1 A
16289 AAATACCCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.27, C:0.48, G:0.23, T:0.02
Consensus pattern (17 bp):
ACCCGAACCCGAACCCG
Found at i:16299 original size:16 final size:16
Alignment explanation
Indices: 16278--16383 Score: 153
Period size: 16 Copynumber: 6.8 Consensus size: 16
16268 CCGACCCGAG
16278 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
16294 CCCGAACCCG-AAATA
1 CCCGAACCCGAAAATA
*
16309 CCCGAACCCGAAAAAA
1 CCCGAACCCGAAAATA
*
16325 CCCGAACCCGAAATTA
1 CCCGAACCCGAAAATA
*
16341 CCCGAATCCGAAAATA
1 CCCGAACCCGAAAATA
* *
16357 CCTGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
16372 CCCGAACCCGAA
1 CCCGAACCCGAA
16384 CCCGCCAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
15 28 0.35
16 51 0.65
ACGTcount: A:0.41, C:0.38, G:0.14, T:0.08
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:16316 original size:31 final size:31
Alignment explanation
Indices: 16278--16383 Score: 167
Period size: 31 Copynumber: 3.4 Consensus size: 31
16268 CCGACCCGAG
16278 CCCGAACCCGAAAATACCCGAACCCGAAATA
1 CCCGAACCCGAAAATACCCGAACCCGAAATA
*
16309 CCCGAACCCGAAAAAACCCGAACCCGAAATTA
1 CCCGAACCCGAAAATACCCGAACCCGAAA-TA
* * *
16341 CCCGAATCCGAAAATACCTGAACCCGAAGTA
1 CCCGAACCCGAAAATACCCGAACCCGAAATA
16372 CCCGAACCCGAA
1 CCCGAACCCGAA
16384 CCCGCCAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 41 0.60
32 27 0.40
ACGTcount: A:0.41, C:0.38, G:0.14, T:0.08
Consensus pattern (31 bp):
CCCGAACCCGAAAATACCCGAACCCGAAATA
Found at i:16336 original size:6 final size:6
Alignment explanation
Indices: 16235--16289 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
16225 TATCGAAAGT
*** *
16235 GAACCC GAACCC GAA-CC GGGTCC GAACCC GAACCC G-ACCC GAGCCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
16281 GAACCC GAA
1 GAACCC GAA
16290 AATACCCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
5 8 0.20
6 32 0.80
ACGTcount: A:0.29, C:0.45, G:0.24, T:0.02
Consensus pattern (6 bp):
GAACCC
Found at i:16336 original size:47 final size:47
Alignment explanation
Indices: 16278--16383 Score: 151
Period size: 47 Copynumber: 2.3 Consensus size: 47
16268 CCGACCCGAG
16278 CCCGAACCCGAAAATACCCGAACCCG-AAATACCCGAACCCGAAAAAA
1 CCCGAACCCGAAAATACCCGAACCCGAAAATACCCGAACCCG-AAAAA
* * * **
16325 CCCGAACCCGAAATTACCCGAATCCGAAAATACCTGAACCCGAAGTA
1 CCCGAACCCGAAAATACCCGAACCCGAAAATACCCGAACCCGAAAAA
16372 CCCGAACCCGAA
1 CCCGAACCCGAA
16384 CCCGCCAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
47 39 0.74
48 14 0.26
ACGTcount: A:0.41, C:0.38, G:0.14, T:0.08
Consensus pattern (47 bp):
CCCGAACCCGAAAATACCCGAACCCGAAAATACCCGAACCCGAAAAA
Found at i:17564 original size:36 final size:35
Alignment explanation
Indices: 17485--17567 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 35
17475 CATTGTTATC
* *
17485 TTTTTGCAA-GCAAGTTTTGAGCAACAGAGTTTTT
1 TTTTTGCAAGGAAAGTTTTCAGCAACAGAGTTTTT
17519 TTTTT-CAAGGAAAG-TTTCAGCAACAGACTGTTTTT
1 TTTTTGCAAGGAAAGTTTTCAGCAACAGA--GTTTTT
17554 TTTTTGCAAGGAAA
1 TTTTTGCAAGGAAA
17568 AACTATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 15 0.35
34 9 0.21
35 11 0.26
36 8 0.19
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (35 bp):
TTTTTGCAAGGAAAGTTTTCAGCAACAGAGTTTTT
Found at i:18504 original size:12 final size:12
Alignment explanation
Indices: 18458--18522 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 12
18448 TAAGGATTTG
**
18458 ATATTATAATCC
1 ATATTATAATAT
*
18470 A-ATTATTATAT
1 ATATTATAATAT
*
18481 ATATCATAATAT
1 ATATTATAATAT
*
18493 -T-TTATAGTAT
1 ATATTATAATAT
18503 ATATTATAATAT
1 ATATTATAATAT
*
18515 ATAATATA
1 ATATTATA
18523 GTTTACTAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
10 7 0.17
11 10 0.24
12 24 0.59
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (12 bp):
ATATTATAATAT
Found at i:20669 original size:15 final size:15
Alignment explanation
Indices: 20645--20679 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20635 CAAACTATGA
20645 AAGAAAAATAAGGAG
1 AAGAAAAATAAGGAG
* *
20660 AAGAAGAATAGGGAG
1 AAGAAAAATAAGGAG
20675 AAGAA
1 AAGAA
20680 TCCAGAGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.31, T:0.06
Consensus pattern (15 bp):
AAGAAAAATAAGGAG
Found at i:26431 original size:12 final size:13
Alignment explanation
Indices: 26391--26431 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
26381 AAAGTTGTCC
*
26391 TTTGCTTTGTTTC
1 TTTGCTTTGTTTT
26404 TTT-CTTTGTTTGT
1 TTTGCTTTGTTT-T
26417 TTTGCTTT-TTTT
1 TTTGCTTTGTTTT
26429 TTT
1 TTT
26432 CTTGTACAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.48
13 9 0.36
14 4 0.16
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (13 bp):
TTTGCTTTGTTTT
Found at i:31493 original size:1 final size:1
Alignment explanation
Indices: 31487--31512 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
31477 AACCCATACC
31487 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
31513 ATAGTGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:37182 original size:14 final size:14
Alignment explanation
Indices: 37163--37214 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
37153 TATCGATTGA
37163 TTCTTCTTCTTTTC
1 TTCTTCTTCTTTTC
*
37177 TTCTTCTTGTTTT-
1 TTCTTCTTCTTTTC
*
37190 TTTTTCCTTCTTTTTC
1 TTCTT-CTTC-TTTTC
*
37206 TTGTTCTTC
1 TTCTTCTTC
37215 ACTTGAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 8 0.26
16 4 0.13
ACGTcount: A:0.00, C:0.23, G:0.04, T:0.73
Consensus pattern (14 bp):
TTCTTCTTCTTTTC
Found at i:39567 original size:2 final size:2
Alignment explanation
Indices: 39560--39585 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39550 GTACTTTTTA
39560 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
39586 GTTAAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40909 original size:65 final size:66
Alignment explanation
Indices: 40793--40927 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 66
40783 GAAATTAATG
* *
40793 ATAGATATTGTTTATCCTCATATATACTATCCCACTTTCAAAAGACACAAAATATATGTTTGTCT
1 ATAGATATTGTTTATCCGCA-ATATACCATCCCACTTTCAAAAGACACAAAATATATGTTTGTCT
40858 TC
65 TC
*
40860 ATAGATATTGTTTATCCGC-ATATACCATCCCACTTTCAAAAGACGCAAAATATATGTTTGTCTT
1 ATAGATATTGTTTATCCGCAATATACCATCCCACTTTCAAAAGACACAAAATATATGTTTGTCTT
40924 C
66 C
40925 ATA
1 ATA
40928 TCACTATCCA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
65 47 0.72
67 18 0.28
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (66 bp):
ATAGATATTGTTTATCCGCAATATACCATCCCACTTTCAAAAGACACAAAATATATGTTTGTCTT
C
Found at i:41294 original size:24 final size:24
Alignment explanation
Indices: 41262--41319 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
41252 ACGATAGCCT
**
41262 AGAGAAGTCAACATATTAGGCAGC
1 AGAGAAGTCAACATAGCAGGCAGC
* * *
41286 AGAGAAGTCATCATAGCAGGGAGT
1 AGAGAAGTCAACATAGCAGGCAGC
41310 AGAGAAGTCA
1 AGAGAAGTCA
41320 GTATACTAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.29, T:0.16
Consensus pattern (24 bp):
AGAGAAGTCAACATAGCAGGCAGC
Found at i:41330 original size:24 final size:23
Alignment explanation
Indices: 41261--41333 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
41251 GACGATAGCC
* * *
41261 TAGAGAAGTCAACATATTAGGCAG
1 TAGAGAAGTC-ATATACTAGGGAG
*
41285 CAGAGAAGTCATCATAGC-AGGGAG
1 TAGAGAAGTCAT-ATA-CTAGGGAG
41309 TAGAGAAGTCAGTATACTAGGGAG
1 TAGAGAAGTCA-TATACTAGGGAG
41333 T
1 T
41334 TCTCCTGTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
23 2 0.05
24 37 0.93
25 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.19
Consensus pattern (23 bp):
TAGAGAAGTCATATACTAGGGAG
Found at i:41996 original size:3 final size:3
Alignment explanation
Indices: 41983--42015 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
41973 AAAACCCCTC
41983 TCT TC- TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
42016 TTCACTTCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:52930 original size:55 final size:55
Alignment explanation
Indices: 52846--52954 Score: 218
Period size: 55 Copynumber: 2.0 Consensus size: 55
52836 AAAAGTTACT
52846 CAAATTGAGGATCTTGGTTGATATTCTACAACAGACTGGGGCATGGCAATTTCCC
1 CAAATTGAGGATCTTGGTTGATATTCTACAACAGACTGGGGCATGGCAATTTCCC
52901 CAAATTGAGGATCTTGGTTGATATTCTACAACAGACTGGGGCATGGCAATTTCC
1 CAAATTGAGGATCTTGGTTGATATTCTACAACAGACTGGGGCATGGCAATTTCC
52955 AGGGGGAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (55 bp):
CAAATTGAGGATCTTGGTTGATATTCTACAACAGACTGGGGCATGGCAATTTCCC
Found at i:56379 original size:19 final size:19
Alignment explanation
Indices: 56357--56414 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
56347 ATGTTAATAA
56357 AAAAAGCATTTAGTATTGT
1 AAAAAGCATTTAGTATTGT
* **
56376 AAAAGAGAATGTTA--A-TAA
1 AAAA-AGCAT-TTAGTATTGT
56394 AAAAAGCATTTAGTATTGT
1 AAAAAGCATTTAGTATTGT
56413 AA
1 AA
56415 TTTGTTAGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 10
0.64 0.14 0.23
Matches are distributed among these distances:
16 3 0.11
17 4 0.14
18 6 0.21
19 8 0.29
20 4 0.14
21 3 0.11
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.31
Consensus pattern (19 bp):
AAAAAGCATTTAGTATTGT
Found at i:56379 original size:37 final size:37
Alignment explanation
Indices: 56338--56414 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
56328 AAATTAATTA
56338 TAAAAGAGAATGTTAATAAAAAAAGCATTTAGTATTG
1 TAAAAGAGAATGTTAATAAAAAAAGCATTTAGTATTG
56375 TAAAAGAGAATGTTAATAAAAAAAGCATTTAGTATTG
1 TAAAAGAGAATGTTAATAAAAAAAGCATTTAGTATTG
56412 TAA
1 TAA
56415 TTTGTTAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.30
Consensus pattern (37 bp):
TAAAAGAGAATGTTAATAAAAAAAGCATTTAGTATTG
Found at i:56397 original size:18 final size:18
Alignment explanation
Indices: 56339--56397 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
56329 AATTAATTAT
56339 AAAAGAGAATGTTAATAA
1 AAAAGAGAATGTTAATAA
* **
56357 AAAA-AGCAT-TTAGTATTGT
1 AAAAGAGAATGTTA--A-TAA
56376 AAAAGAGAATGTTAATAA
1 AAAAGAGAATGTTAATAA
56394 AAAA
1 AAAA
56398 AGCATTTAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 10 0.33
19 6 0.20
20 4 0.13
21 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.15, T:0.25
Consensus pattern (18 bp):
AAAAGAGAATGTTAATAA
Found at i:57846 original size:33 final size:33
Alignment explanation
Indices: 57809--57882 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
57799 TTTCTTCTTC
57809 CTTTTCTTCTCCGTTTTCTGCTTTTATCAATTT
1 CTTTTCTTCTCCGTTTTCTGCTTTTATCAATTT
57842 CTTTTCTTCTCCGTTTTCTGCTTTTATCAATTT
1 CTTTTCTTCTCCGTTTTCTGCTTTTATCAATTT
57875 CTTTTCTT
1 CTTTTCTT
57883 AAATTTTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.08, C:0.24, G:0.05, T:0.62
Consensus pattern (33 bp):
CTTTTCTTCTCCGTTTTCTGCTTTTATCAATTT
Found at i:57998 original size:25 final size:24
Alignment explanation
Indices: 57975--58020 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
57965 CTTAATTTCA
57975 CCTTTT-TTTTCTTAATTTTTTTT
1 CCTTTTCTTTTCTTAATTTTTTTT
*
57998 CTTTTTCCTTTTCTTAATTTTTT
1 CCTTTT-CTTTTCTTAATTTTTT
58021 CTTAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
25 15 0.75
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (24 bp):
CCTTTTCTTTTCTTAATTTTTTTT
Found at i:58029 original size:12 final size:11
Alignment explanation
Indices: 57910--58025 Score: 67
Period size: 11 Copynumber: 9.7 Consensus size: 11
57900 TCTTCCTCAA
57910 TTTCTTAATTT
1 TTTCTTAATTT
57921 TTTCTTAAGTTT
1 TTTCTTAA-TTT
57933 TTATACGTTATATACTT
1 TT-T-C-TTA-AT--TT
57950 TTTCTTAAATTT
1 TTTCTT-AATTT
57962 TTTCTTAATTT
1 TTTCTTAATTT
***
57973 CACCTT--TTT
1 TTTCTTAATTT
57982 TTTCTTAATTTTT
1 TTTCTTAA--TTT
*
57995 TTTCTT-TTTCCT
1 TTTCTTAATT--T
58007 TTTCTTAATTT
1 TTTCTTAATTT
58018 TTTCTTAA
1 TTTCTTAA
58026 ATTTATTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 30
0.68 0.07 0.25
Matches are distributed among these distances:
9 6 0.07
10 2 0.02
11 25 0.30
12 20 0.24
13 12 0.15
14 5 0.06
15 6 0.07
16 2 0.02
17 4 0.05
ACGTcount: A:0.18, C:0.13, G:0.02, T:0.67
Consensus pattern (11 bp):
TTTCTTAATTT
Found at i:58411 original size:24 final size:23
Alignment explanation
Indices: 58367--58411 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
58357 TCTAAAGAAT
* * *
58367 TTGGGGATGGTGCATAAGATTAA
1 TTGGGGATGATGAAAAAGATTAA
58390 TTGGGGATGATGAAAAATGATT
1 TTGGGGATGATGAAAAA-GATT
58412 TGGGTATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.31
Consensus pattern (23 bp):
TTGGGGATGATGAAAAAGATTAA
Found at i:58423 original size:220 final size:220
Alignment explanation
Indices: 58040--58562 Score: 823
Period size: 220 Copynumber: 2.4 Consensus size: 220
58030 ATTTTCCACC
* * *
58040 ATCATATAGACGTGATTTATTCAATTAATTATATCCCTAAAATATGGATTAAACCACTTTTTAAA
1 ATCATATAGACGTGGTTTATTCAATTAATTAGAT-CCTAAAATATGGATTAAAACACTTTTTAAA
* * *
58105 GTCAAATTTGTGTATATGAGAAAATATCAATTTCTAAAGAATTTGGAAATGGTGCATATGATTAT
65 GTCAAATTTGTGTATATGAGAAAATATCAATCTCTAAAGAATTTGGAAATGGTGCATAAGATTAA
* * *
58170 TTGGGGATGGTGAGAAATGATTTGAGTATAAAGTATATCAGTTTGGGGATATTGAATTTCACATT
130 TTGGGGATGATGAAAAATGATTTGAGTATAAAGTATATCAGTTTGGGGATACTGAATTTCACATT
*
58235 TTTTTTAATTATGAGATGGCGCTAAA
195 TTGTTTAATTATGAGATGGCGCTAAA
**
58261 ATCATATAGACGTGGTTTATTCAATTAATTAGAAT-GAAAAATATGGATTAAAACACTTTTTAAA
1 ATCATATAGACGTGGTTTATTCAATTAATTAG-ATCCTAAAATATGGATTAAAACACTTTTTAAA
* * **
58325 GTCCAATTTGTGTATATGAGAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATAAGATTAA
65 GTCAAATTTGTGTATATGAGAAAATATCAATCTCTAAAGAATTTGGAAATGGTGCATAAGATTAA
* * **
58390 TTGGGGATGATGAAAAATGATTTGGGTATAAAGTATATCATTTTGGGGATACTGAATTTTGCATT
130 TTGGGGATGATGAAAAATGATTTGAGTATAAAGTATATCAGTTTGGGGATACTGAATTTCACATT
58455 TTGTTTAATTATGAGATGGCGCTAAA
195 TTGTTTAATTATGAGATGGCGCTAAA
*
58481 ATCATATAGACGTGGTTTATTCAATTAATTAGATCCCTAAAATATGGATTAAAGCACTTTTTAAA
1 ATCATATAGACGTGGTTTATTCAATTAATTAGAT-CCTAAAATATGGATTAAAACACTTTTTAAA
58546 GTCAAATTTGTGTATAT
65 GTCAAATTTGTGTATAT
58563 ACATATGCAC
Statistics
Matches: 275, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
219 2 0.01
220 199 0.72
221 72 0.26
222 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (220 bp):
ATCATATAGACGTGGTTTATTCAATTAATTAGATCCTAAAATATGGATTAAAACACTTTTTAAAG
TCAAATTTGTGTATATGAGAAAATATCAATCTCTAAAGAATTTGGAAATGGTGCATAAGATTAAT
TGGGGATGATGAAAAATGATTTGAGTATAAAGTATATCAGTTTGGGGATACTGAATTTCACATTT
TGTTTAATTATGAGATGGCGCTAAA
Found at i:58955 original size:220 final size:220
Alignment explanation
Indices: 58642--59135 Score: 735
Period size: 220 Copynumber: 2.2 Consensus size: 220
58632 AAATTTGACT
* * *
58642 TTTAATCCATATTTTAGGGATCTAATTAATTGAATAAACCACGTCTATATGATTTTAGCGCCGTC
1 TTTAAACCATATTTTA-GCATCTAATTAATTGAATAAACCACGTCTATATGATTTTAGCGCCATC
58707 TCATAATTAAACAAAATGTAAAATTCAGTATCCCCAAAATGATATACTTTATACCCAAATCATTT
65 TCATAATTAAACAAAATGTAAAATTCAGTATCCCCAAAATGATATACTTTATACCCAAATCATTT
* * * * * *
58772 TTCATCATCCCCAATTAATCTTATGCACCA-TCCTCAAATTCTTTAGAGATTGAC-ATTTTCTCA
130 CTCACCATCCCCAAATAATCATATCCACCATTCC-CAAATTCTTTAGAAATTG-CTATTTTCTCA
* *
58835 TATACACAAATTGGACTTTAAAAGGTGT
193 TATACACAAATTGGACTTTAAAAAGTGC
* *
58863 TTTAAACCATATTTT-TCATTCTAATTAATTGAATAAACCACATCTATATGATTTTAGC-CTCAT
1 TTTAAACCATATTTTAGCA-TCTAATTAATTGAATAAACCACGTCTATATGATTTTAGCGC-CAT
* * *
58926 CTCATAATTAAACAAAATGTGAAATTCAGTATTCCCAAACTGATATACTTTATACCCAAATCATT
64 CTCATAATTAAACAAAATGTAAAATTCAGTATCCCCAAAATGATATACTTTATACCCAAATCATT
58991 TCTCACCATCCCCAAATAATCATATCCACCATTCCCAAATTCTTTAGAAATTGCTATTTTCTCAT
129 TCTCACCATCCCCAAATAATCATATCCACCATTCCCAAATTCTTTAGAAATTGCTATTTTCTCAT
*
59056 ATACACAAATTTGACTTTAAAAAGTGC
194 ATACACAAATTGGACTTTAAAAAGTGC
* *
59083 TTTAATCCATATTTTAGGGATCTAATTAATTGAATAAACCACGTCTATATGAT
1 TTTAAACCATATTTTA-GCATCTAATTAATTGAATAAACCACGTCTATATGAT
59136 GGTGGAAAAT
Statistics
Matches: 246, Mismatches: 21, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
219 3 0.01
220 193 0.78
221 49 0.20
222 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (220 bp):
TTTAAACCATATTTTAGCATCTAATTAATTGAATAAACCACGTCTATATGATTTTAGCGCCATCT
CATAATTAAACAAAATGTAAAATTCAGTATCCCCAAAATGATATACTTTATACCCAAATCATTTC
TCACCATCCCCAAATAATCATATCCACCATTCCCAAATTCTTTAGAAATTGCTATTTTCTCATAT
ACACAAATTGGACTTTAAAAAGTGC
Found at i:59027 original size:23 final size:24
Alignment explanation
Indices: 58984--59030 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
58974 TTTATACCCA
*
58984 AATCATTTCTCACCATCCCCAAAT
1 AATCATATCTCACCATCCCCAAAT
*
59008 AATCATATC-CACCATTCCCAAAT
1 AATCATATCTCACCATCCCCAAAT
59031 TCTTTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (24 bp):
AATCATATCTCACCATCCCCAAAT
Found at i:59194 original size:11 final size:11
Alignment explanation
Indices: 59180--59256 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
59170 GGAAAAAGAA
59180 AAGAAAAAATT
1 AAGAAAAAATT
59191 AAGAAAAAA--
1 AAGAAAAAATT
***
59200 AAGGTGAAATT
1 AAGAAAAAATT
59211 AAGAAAAAATAT
1 AAGAAAAAAT-T
59223 ACAACGTATAAAAATTT
1 --AA-G-A-AAAAA-TT
59240 AAGAAAAAATT
1 AAGAAAAAATT
59251 AAGAAA
1 AAGAAA
59257 TTGGGGAAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
9 6 0.12
11 24 0.47
12 6 0.12
13 1 0.02
14 3 0.06
15 3 0.06
16 1 0.02
17 6 0.12
18 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.18
Consensus pattern (11 bp):
AAGAAAAAATT
Found at i:59311 original size:21 final size:21
Alignment explanation
Indices: 59285--59356 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
59275 AAAAAATTTA
59285 AGAAAAGAAATTGATAAAAGC
1 AGAAAAGAAATTGATAAAAGC
* *
59306 AGAAAACGGAGAA--GAAAAGGAAGA
1 AGAAAA--GA-AATTGATAA--AAGC
59330 AGAAAAGAAATTGATAAAAGC
1 AGAAAAGAAATTGATAAAAGC
59351 AGAAAA
1 AGAAAA
59357 CGGAGAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
21 17 0.43
22 6 0.15
23 6 0.15
24 11 0.28
ACGTcount: A:0.64, C:0.04, G:0.24, T:0.08
Consensus pattern (21 bp):
AGAAAAGAAATTGATAAAAGC
Found at i:59323 original size:12 final size:12
Alignment explanation
Indices: 59306--59381 Score: 56
Period size: 12 Copynumber: 6.6 Consensus size: 12
59296 TGATAAAAGC
59306 AGAAAACGG-AGA
1 AGAAAA-GGAAGA
59318 AGAAAAGGAAGA
1 AGAAAAGGAAGA
59330 AGAAAA-GAA-A
1 AGAAAAGGAAGA
* * *
59340 TTGATAA--AAGC
1 -AGAAAAGGAAGA
59351 AGAAAACGG-AGA
1 AGAAAA-GGAAGA
59363 AGAAAAGGAAGA
1 AGAAAAGGAAGA
59375 AGAAAAG
1 AGAAAAG
59382 AAATTGGGGA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
10 7 0.14
11 11 0.22
12 33 0.65
ACGTcount: A:0.63, C:0.04, G:0.29, T:0.04
Consensus pattern (12 bp):
AGAAAAGGAAGA
Found at i:59334 original size:45 final size:45
Alignment explanation
Indices: 59284--59387 Score: 208
Period size: 45 Copynumber: 2.3 Consensus size: 45
59274 GAAAAAATTT
59284 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
59329 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
1 AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
59374 AAGAAAAGAAATTG
1 AAGAAAAGAAATTG
59388 GGGAAAATAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.62, C:0.04, G:0.26, T:0.08
Consensus pattern (45 bp):
AAGAAAAGAAATTGATAAAAGCAGAAAACGGAGAAGAAAAGGAAG
Found at i:60232 original size:2 final size:2
Alignment explanation
Indices: 60225--60249 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60215 AAGCATCCAC
60225 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 A
60250 CTAGCTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.