Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011503.1 Corchorus capsularis cultivar CVL-1 contig11524, 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: 87585
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2580 original size:30 final size:30
Alignment explanation
Indices: 2522--2617 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
2512 TTGGTTAGGT
* * *
2522 GATTTAGCCACGG-GATTTGGCACAGTTTTA
1 GATTTTGCCACGGTG-TTTGCCACGGTTTTA
*
2552 GATTTTGCTACGGTGTTTGCCACGGTTTTA
1 GATTTTGCCACGGTGTTTGCCACGGTTTTA
* *
2582 GAGTTTGCCACGGTTTTTGCCACGAG-TTTA
1 GATTTTGCCACGGTGTTTGCCACG-GTTTTA
2612 GATTTT
1 GATTTT
2618 TCTTTTTTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 54 0.96
31 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.40
Consensus pattern (30 bp):
GATTTTGCCACGGTGTTTGCCACGGTTTTA
Found at i:2686 original size:30 final size:30
Alignment explanation
Indices: 2650--2722 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
2640 GCGGGCTTTG
* *
2650 CCACGGTTTT-GGGTTTTGCCACGGTGTTTA
1 CCACGGTTTTAGAG-TTTACCACGGTGTTTA
*
2680 CCACGGTTTTAGAGTTTACCACGGTGTTTG
1 CCACGGTTTTAGAGTTTACCACGGTGTTTA
*
2710 CCACGGGTTTAGA
1 CCACGGTTTTAGA
2723 TTTTTCTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 36 0.95
31 2 0.05
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.36
Consensus pattern (30 bp):
CCACGGTTTTAGAGTTTACCACGGTGTTTA
Found at i:5287 original size:34 final size:34
Alignment explanation
Indices: 5231--5314 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
5221 TTGTTTGGTG
* *
5231 GACTGTTTTTTTT-TTAATATTATCTTATATGCA
1 GACTGTTTTTTTTGTTTAGATTATCTTATATGCA
5264 GACTGTTTTTTTTGTTTAGATTATCTTATATGCA
1 GACTGTTTTTTTTGTTTAGATTATCTTATATGCA
5298 GACTGTTTTTTTTGTTT
1 GACTGTTTTTTTTGTTT
5315 GGCTTCGTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 13 0.27
34 35 0.73
ACGTcount: A:0.19, C:0.08, G:0.13, T:0.60
Consensus pattern (34 bp):
GACTGTTTTTTTTGTTTAGATTATCTTATATGCA
Found at i:5421 original size:290 final size:296
Alignment explanation
Indices: 4889--5481 Score: 952
Period size: 290 Copynumber: 2.0 Consensus size: 296
4879 TGTTGTTTGT
** *
4889 TGGATTTGATTCTAGTAACATGTTCCCTTCTTGTTTGGTGGACTGTTTTTTTTTTAAATATTATC
1 TGGATTTGATTCTAGTAACATGAACCATTCTTGTTTGGTGGACTGTTTTTTTTTTAAATATTATC
*
4954 TTATATGTAGACTGTTTTTTTTTTGTTTAGATTATCTTATATTCTTGTATGCAGACTGTTTTTTT
66 TTATATGCAGACTG-TTTTTTTTTGTTTAGATTATCTTATA----T-TATGCAGACTGTTTTTTT
*
5019 TTTTTTCGGCTTCGTCTTTGTTTCTTGAGTTTGGTTTAGTTGATTTTGATGGACACTGTTTTCGT
125 TTGTTTCGGCTTCGTCTTTGTTTCTTGAGTTTGGTTTAGTTGATTTTGATGGACACTGTTTTCGT
*
5084 TTAGTGTTATATATTTGAACTTATGTTTTGTCTTTGAGTGAAAGACTTTTTATGGGCAGTTGATG
190 TTAGTGTTATATATTTGAACTTATGTTCTGTCTTTGAGTGAAAGACTTTTTAT-GGCAGTTGATG
5149 TTTATTGTTGTTACA-TTGCTTGGTGGTGCTCTTTTTTTTACA
254 TTTATTGTTGTTACATTTGCTTGGTGGTGCTCTTTTTTTTACA
*
5191 TGGATTTGATTCTAGTAAGAT-AACACATTCTTGTTTGGTGGACTGTTTTTTTTTT-AATATTAT
1 TGGATTTGATTCTAGTAACATGAAC-CATTCTTGTTTGGTGGACTGTTTTTTTTTTAAATATTAT
5254 CTTATATGCAGACTG-TTTTTTTTGTTTAGATTATC-T-TA-TATGCAGACTG-TTTTTTTTGTT
65 CTTATATGCAGACTGTTTTTTTTTGTTTAGATTATCTTATATTATGCAGACTGTTTTTTTTTGTT
*
5314 T-GGCTTCGTCCTTTGTTTCTTGAGTTTGGTTTAGTTGATTTTGATGGACACTGTTTTCTTTTAG
130 TCGGCTTCGT-CTTTGTTTCTTGAGTTTGGTTTAGTTGATTTTGATGGACACTGTTTTCGTTTAG
5378 TGTTATATATTTGAACTTATGTTCTGTCTTTGAGTGAAAGACTTTTTATGGCAGTTGATGTTTAT
194 TGTTATATATTTGAACTTATGTTCTGTCTTTGAGTGAAAGACTTTTTATGGCAGTTGATGTTTAT
*
5443 TGTTGTTATATTTTGCTTGGTGGTGCTCTTTTTTTTACA
259 TGTTGTTACA-TTTGCTTGGTGGTGCTCTTTTTTTTACA
5482 GGAAAAATTT
Statistics
Matches: 278, Mismatches: 9, Indels: 19
0.91 0.03 0.06
Matches are distributed among these distances:
289 33 0.12
290 112 0.40
291 38 0.14
297 2 0.01
298 1 0.00
299 20 0.07
301 23 0.08
302 49 0.18
ACGTcount: A:0.17, C:0.10, G:0.19, T:0.54
Consensus pattern (296 bp):
TGGATTTGATTCTAGTAACATGAACCATTCTTGTTTGGTGGACTGTTTTTTTTTTAAATATTATC
TTATATGCAGACTGTTTTTTTTTGTTTAGATTATCTTATATTATGCAGACTGTTTTTTTTTGTTT
CGGCTTCGTCTTTGTTTCTTGAGTTTGGTTTAGTTGATTTTGATGGACACTGTTTTCGTTTAGTG
TTATATATTTGAACTTATGTTCTGTCTTTGAGTGAAAGACTTTTTATGGCAGTTGATGTTTATTG
TTGTTACATTTGCTTGGTGGTGCTCTTTTTTTTACA
Found at i:9391 original size:7 final size:7
Alignment explanation
Indices: 9376--9481 Score: 61
Period size: 6 Copynumber: 15.9 Consensus size: 7
9366 TCACCTATGT
9376 TAATATA
1 TAATATA
*
9383 TAATTTA
1 TAATATA
9390 TAA-ATCA
1 TAATAT-A
9397 T-ATAT-
1 TAATATA
9402 TAA-ATA
1 TAATATA
9408 -AATATAA
1 TAATAT-A
*
9415 TAAATAAA
1 T-AATATA
9423 TAA-ATA
1 TAATATA
9429 TAA-ATA
1 TAATATA
9435 TAA-ATA
1 TAATATA
9441 TAATCATA
1 TAAT-ATA
*
9449 TATTATA
1 TAATATA
9456 -AATCATA
1 TAAT-ATA
*
9463 TAATAAA
1 TAATATA
9470 TAA-ATA
1 TAATATA
9476 TAATAT
1 TAATAT
9482 TGTTAAAGCT
Statistics
Matches: 78, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
5 5 0.06
6 29 0.37
7 29 0.37
8 11 0.14
9 4 0.05
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (7 bp):
TAATATA
Found at i:9414 original size:29 final size:29
Alignment explanation
Indices: 9380--9479 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 29
9370 CTATGTTAAT
9380 ATATAATTTATAAATCATATATTAAATAA
1 ATATAATTTATAAATCATATATTAAATAA
** *
9409 ATATAATAAATAAATAAATATAAATATAAATATA
1 ATATAATTTATAAAT-CATAT--AT-TAAATA-A
*
9443 ATCAT-ATATTATAAATCATATAATAAATAA
1 AT-ATAAT-TTATAAATCATATATTAAATAA
9473 ATATAAT
1 ATATAAT
9480 ATTGTTAAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
29 15 0.27
30 9 0.16
31 6 0.11
32 3 0.05
33 6 0.11
34 9 0.16
35 8 0.14
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (29 bp):
ATATAATTTATAAATCATATATTAAATAA
Found at i:9418 original size:13 final size:13
Alignment explanation
Indices: 9396--9480 Score: 79
Period size: 13 Copynumber: 6.6 Consensus size: 13
9386 TTTATAAATC
*
9396 ATATATTAAATAA
1 ATATAATAAATAA
9409 ATATAATAAATAA
1 ATATAATAAATAA
9422 ATA-AAT--ATAA
1 ATATAATAAATAA
*
9432 ATATAAATATAATCAT
1 ATAT-AATA-AAT-AA
* *
9448 ATATTATAAAT-C
1 ATATAATAAATAA
9460 ATATAATAAATAA
1 ATATAATAAATAA
9473 ATATAATA
1 ATATAATA
9481 TTGTTAAAGC
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
10 7 0.12
12 16 0.27
13 23 0.39
14 3 0.05
15 5 0.08
16 5 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAATAAATAA
Found at i:11946 original size:15 final size:15
Alignment explanation
Indices: 11926--11957 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
11916 AATTTCTGTC
11926 TTCTCTCTCTCTTTT
1 TTCTCTCTCTCTTTT
11941 TTCTCTCTCTCTTTT
1 TTCTCTCTCTCTTTT
11956 TT
1 TT
11958 TTTTCTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCTCTCTCTCTTTT
Found at i:11959 original size:17 final size:17
Alignment explanation
Indices: 11926--11963 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
11916 AATTTCTGTC
11926 TTCTCTCTCTCTTTTTT
1 TTCTCTCTCTCTTTTTT
* *
11943 CTCTCTCTCTTTTTTTT
1 TTCTCTCTCTCTTTTTT
11960 TTCT
1 TTCT
11964 AGTAATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTCTCTCTCTTTTTT
Found at i:13555 original size:53 final size:53
Alignment explanation
Indices: 13495--13597 Score: 197
Period size: 53 Copynumber: 1.9 Consensus size: 53
13485 CGGCTTTTTT
*
13495 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGCGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGCGA
13548 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTG
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTG
13598 TGAAATGATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.42
Consensus pattern (53 bp):
ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGCGA
Found at i:15002 original size:18 final size:17
Alignment explanation
Indices: 14962--15005 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
14952 GATTAAGGTA
14962 ATAATAATTTTACTACT
1 ATAATAATTTTACTACT
* *
14979 ACTAATAATTATTATTATT
1 A-TAATAATT-TTACTACT
14998 ATAATAAT
1 ATAATAAT
15006 AAGAAGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 15 0.65
19 7 0.30
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAATAATTTTACTACT
Found at i:15024 original size:24 final size:24
Alignment explanation
Indices: 14995--15040 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
14985 AATTATTATT
14995 ATTATAATAATAAGAAGTTTAATA
1 ATTATAATAATAAGAAGTTTAATA
* *
15019 ATTATAATGATAAGATGTTTAA
1 ATTATAATAATAAGAAGTTTAA
15041 CGTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (24 bp):
ATTATAATAATAAGAAGTTTAATA
Found at i:16679 original size:2 final size:2
Alignment explanation
Indices: 16672--16700 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16662 ATACCAAGTA
16672 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 A
16701 AGTTAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19131 original size:11 final size:11
Alignment explanation
Indices: 19115--19142 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
19105 GATGGATATA
19115 AATTGAATGAG
1 AATTGAATGAG
19126 AATTGAATGAG
1 AATTGAATGAG
19137 AATTGA
1 AATTGA
19143 GAACAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (11 bp):
AATTGAATGAG
Found at i:19297 original size:22 final size:21
Alignment explanation
Indices: 19267--19317 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
19257 CTTTATCAAG
19267 GAAAGAATTAAAAAATATTAATT
1 GAAA-AATTAAAAAATA-TAATT
* *
19290 GAAAAATTAAATATTATAATT
1 GAAAAATTAAAAAATATAATT
*
19311 AAAAAAT
1 GAAAAAT
19318 ATTATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.44
22 10 0.40
23 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (21 bp):
GAAAAATTAAAAAATATAATT
Found at i:19476 original size:6 final size:6
Alignment explanation
Indices: 19465--19491 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19455 AATAAATAAG
19465 ATAGAT ATAGAT ATAGAT ATAGAT ATA
1 ATAGAT ATAGAT ATAGAT ATAGAT ATA
19492 TACTATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
ATAGAT
Found at i:28530 original size:16 final size:16
Alignment explanation
Indices: 28511--28542 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28501 TTTTTTCCTC
28511 AAATTTTTTTGTCTGG
1 AAATTTTTTTGTCTGG
28527 AAATTTTTTTGTCTGG
1 AAATTTTTTTGTCTGG
28543 TTCAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (16 bp):
AAATTTTTTTGTCTGG
Found at i:32613 original size:21 final size:21
Alignment explanation
Indices: 32587--32632 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
32577 AAACCAAAAT
32587 AAATAAATCAACATTGGATTG
1 AAATAAATCAACATTGGATTG
32608 AAATAAATCAACATTGGATTG
1 AAATAAATCAACATTGGATTG
32629 AAAT
1 AAAT
32633 GGTAAATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (21 bp):
AAATAAATCAACATTGGATTG
Found at i:39005 original size:19 final size:19
Alignment explanation
Indices: 38981--39019 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
38971 ACCATGCCGG
38981 TTGTGGATGCGTAATAGGA
1 TTGTGGATGCGTAATAGGA
39000 TTGTGGATGCGTAATAGGA
1 TTGTGGATGCGTAATAGGA
39019 T
1 T
39020 GCTGATATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.33
Consensus pattern (19 bp):
TTGTGGATGCGTAATAGGA
Found at i:42313 original size:87 final size:87
Alignment explanation
Indices: 42099--42402 Score: 477
Period size: 87 Copynumber: 3.5 Consensus size: 87
42089 TTCCTTTTTT
* *
42099 ATATCTTCTAAAGCTCCCACAATTTGGCAAGATTTAGAAAATATTTTCATTATTATTAAATCTTT
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
*
42164 ATAATTTATTTGTTTT-TTAAA
66 ATAATTTATTTATTTTCTTAAA
* * * * * *
42185 ATA-CTCCTAAACCTTCCACAACTTGACAAGATTTAGAAAATATTATCATCATTATTATATCTTT
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
42249 ATAATTTATTTATTTTCTTAAA
66 ATAATTTATTTATTTTCTTAAA
*
42271 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTC
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
42336 ATAATTTATTTATTTTCTTAAA
66 ATAATTTATTTATTTTCTTAAA
* * *
42358 ATATCTTCTAAATCTCCCACAATTTGCCAAGATTTAGAAAATATT
1 ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATT
42403 CTCTTTACAA
Statistics
Matches: 197, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
85 68 0.35
86 11 0.06
87 118 0.60
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (87 bp):
ATATCTTCTAAAGCTCCCACAACTTGGCAAGATTTAGAAAATATTATCATTATTATTAAATCTTT
ATAATTTATTTATTTTCTTAAA
Found at i:53381 original size:31 final size:30
Alignment explanation
Indices: 53284--53388 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 30
53274 AGCCTAATGT
53284 CCAAATTGGGCCTAAACCTTTTCAAACTTGC-
1 CCAAATTGGGCCTAAACC-TTTCAAA-TTGCA
* * *
53315 TCAATTTGAGCCTAAACCTTTCAACA-TG-A
1 CCAAATTGGGCCTAAACCTTTCAA-ATTGCA
* *
53344 CCAAATTGGGCCTAAACGTTAGCAAATTGCA
1 CCAAATTGGGCCTAAACCTT-TCAAATTGCA
53375 CCAAATTGGGCCTA
1 CCAAATTGGGCCTA
53389 TTTTGGACGG
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
29 19 0.31
30 11 0.18
31 31 0.51
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (30 bp):
CCAAATTGGGCCTAAACCTTTCAAATTGCA
Found at i:58991 original size:13 final size:14
Alignment explanation
Indices: 58973--59003 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
58963 CTTTTTTAAA
58973 ATTTAAATTAA-TT
1 ATTTAAATTAAGTT
58986 ATTTAAATTAAGTT
1 ATTTAAATTAAGTT
59000 ATTT
1 ATTT
59004 TTCAACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
ATTTAAATTAAGTT
Found at i:59705 original size:24 final size:24
Alignment explanation
Indices: 59678--59753 Score: 91
Period size: 23 Copynumber: 3.2 Consensus size: 24
59668 TTCTCTCTCT
59678 CTTTCTTTCTTTTAACTTTTCCTA
1 CTTTCTTTCTTTTAACTTTTCCTA
** *
59702 CTTTCTTTCTTTTAA-TTTTTTTT
1 CTTTCTTTCTTTTAACTTTTCCTA
* *
59725 CTCTCTCTCTTTTAACTTTTTCCTA
1 CTTTCTTTCTTTTAAC-TTTTCCTA
59750 CTTT
1 CTTT
59754 TGTTGTAGTA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 18 0.44
24 15 0.37
25 8 0.20
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.66
Consensus pattern (24 bp):
CTTTCTTTCTTTTAACTTTTCCTA
Found at i:59818 original size:32 final size:32
Alignment explanation
Indices: 59779--59842 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
59769 TATTTAAATT
* * *
59779 AATTTCATTTATTAAT-TATAAATAATATAATA
1 AATTTCATGTAATAATAAATAAATAA-ATAATA
59811 AATTTCATGTAATAATAAATAAATAAATAATA
1 AATTTCATGTAATAATAAATAAATAAATAATA
59843 TTGTAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (32 bp):
AATTTCATGTAATAATAAATAAATAAATAATA
Found at i:59878 original size:17 final size:19
Alignment explanation
Indices: 59858--59905 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 19
59848 ATTAATTATA
59858 AATTTAATAT-TAT-TAAT
1 AATTTAATATATATATAAT
*
59875 AA-TT-ATATATATATACT
1 AATTTAATATATATATAAT
*
59892 AATTTAATAAATAT
1 AATTTAATATATAT
59906 TATATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.16
16 5 0.20
17 7 0.28
18 2 0.08
19 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AATTTAATATATATATAAT
Found at i:77062 original size:18 final size:17
Alignment explanation
Indices: 77007--77142 Score: 85
Period size: 18 Copynumber: 7.6 Consensus size: 17
76997 CCTGATTTTC
*
77007 CTCCAAGTTTATGTTCTG
1 CTCCAAGTTTA-ATTCTG
* *
77025 CTCCACA-TCTATGTTCTG
1 CTCCA-AGTTTA-ATTCTG
*
77043 CTCCAAGTTTATATTGTG
1 CTCCAAGTTTA-ATTCTG
*
77061 CTCTAAGTTTAAGTTCTG
1 CTCCAAGTTTAA-TTCTG
* * *
77079 TTCCAAGTTCAAGTCATG
1 CTCCAAGTTTAATTC-TG
* *
77097 TTCCAAGTTTGGATTCTG
1 CTCCAAGTTT-AATTCTG
* *
77115 CTCCAAGTCTAAGTTGTG
1 CTCCAAGTTTAA-TTCTG
77133 CTCCAAGTTT
1 CTCCAAGTTT
77143 TCAGTTTCTT
Statistics
Matches: 94, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
17 5 0.05
18 85 0.90
19 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (17 bp):
CTCCAAGTTTAATTCTG
Found at i:77138 original size:36 final size:35
Alignment explanation
Indices: 77037--77142 Score: 99
Period size: 36 Copynumber: 2.9 Consensus size: 35
77027 CCACATCTAT
*
77037 GTTCTGCTCCAAGTTTATA-TTGTGCTCTAAGTTTAA
1 GTTCTGCTCCAAG-TTA-AGTTGTGCTCCAAGTTTAA
* ** * *
77073 GTTCTGTTCCAAGTTCAAGTCATGTTCCAAGTTT-G
1 GTTCTGCTCCAAGTT-AAGTTGTGCTCCAAGTTTAA
77108 GATTCTGCTCCAAGTCTAAGTTGTGCTCCAAGTTT
1 G-TTCTGCTCCAAGT-TAAGTTGTGCTCCAAGTTT
77143 TCAGTTTCTT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
35 4 0.07
36 51 0.91
37 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.41
Consensus pattern (35 bp):
GTTCTGCTCCAAGTTAAGTTGTGCTCCAAGTTTAA
Found at i:77196 original size:27 final size:27
Alignment explanation
Indices: 77158--77240 Score: 150
Period size: 27 Copynumber: 3.1 Consensus size: 27
77148 TTCTTGTAAC
77158 TGTTCCTCCCCC-GATTCAACATAGCCT
1 TGTTCCTCCCCCTG-TTCAACATAGCCT
77185 TGTTCCTCCCCCTGTTCAACATAGCCT
1 TGTTCCTCCCCCTGTTCAACATAGCCT
77212 TGTTCCTCCCCCTGTTCAACATAGCCT
1 TGTTCCTCCCCCTGTTCAACATAGCCT
77239 TG
1 TG
77241 ATCAACTTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 54 0.98
28 1 0.02
ACGTcount: A:0.16, C:0.40, G:0.12, T:0.33
Consensus pattern (27 bp):
TGTTCCTCCCCCTGTTCAACATAGCCT
Found at i:85816 original size:20 final size:20
Alignment explanation
Indices: 85771--85816 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
85761 CTATATAATT
*
85771 AAAAAATTACCCATTTAAAA
1 AAAAAATTACACATTTAAAA
* *
85791 AGAAAATTACATATTTAAAA
1 AAAAAATTACACATTTAAAA
85811 AAAAAA
1 AAAAAA
85817 CTATCTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAAATTACACATTTAAAA
Done.