Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007108.1 Corchorus capsularis cultivar CVL-1 contig07129, 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: 52368
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7704 original size:21 final size:21
Alignment explanation
Indices: 7678--7726 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
7668 GCATTGGAGG
* * *
7678 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
7699 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
7720 ACATGGG
1 ACATGGG
7727 CCCCCAGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:9317 original size:15 final size:16
Alignment explanation
Indices: 9288--9317 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9278 GTGTGAATTC
9288 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
9304 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
9318 TTAACTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:18739 original size:25 final size:24
Alignment explanation
Indices: 18683--18745 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
18673 CAACAATAGT
*
18683 AAATTA-TAAAATGAAAATGCTGTG
1 AAATTACT-AAATGAAAATGCTATG
18707 AAATTACTAAATGAAAATGCTATG
1 AAATTACTAAATGAAAATGCTATG
*
18731 GAATATACTACAATG
1 AAAT-TACTA-AATG
18746 CTAAAAGTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 24 0.71
25 6 0.18
26 4 0.12
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (24 bp):
AAATTACTAAATGAAAATGCTATG
Found at i:28512 original size:10 final size:10
Alignment explanation
Indices: 28497--28522 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28487 AGTTACTGCC
28497 AAATTCCAGA
1 AAATTCCAGA
28507 AAATTCCAGA
1 AAATTCCAGA
28517 AAATTC
1 AAATTC
28523 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:29814 original size:13 final size:12
Alignment explanation
Indices: 29776--29828 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
29766 AAGATCCAAG
29776 AAACATAAAACAT
1 AAACA-AAAACAT
*
29789 AGAACAAAAATA-
1 A-AACAAAAACAT
*
29801 AAACATAAACAT
1 AAACAAAAACAT
29813 AAACAAATAACAT
1 AAACAAA-AACAT
29826 AAA
1 AAA
29829 TATGCATGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 8 0.24
12 7 0.21
13 14 0.42
14 4 0.12
ACGTcount: A:0.72, C:0.13, G:0.02, T:0.13
Consensus pattern (12 bp):
AAACAAAAACAT
Found at i:30468 original size:305 final size:305
Alignment explanation
Indices: 29917--30529 Score: 1039
Period size: 305 Copynumber: 2.0 Consensus size: 305
29907 GGTATGCACT
*
29917 AGGTTCTCTTGTTGGGAGTCTTAACAAGTCAAGCTAATCGAGCCAAACTTAACCATATTTCTATG
1 AGGTTCTCTTGTTGGGAGTCTTAACAAGTCAAGCTAATCGAGCCAAAATTAACCATATTTCTATG
* *
29982 ATCATTTTCCTATGCTTTTTGGTATTTTTATGTGTGATTTAACCCTATTTTTCAAGTATTTGTGT
66 ATCATTTTCCTATGATTTTTGGTATTTTTATGTGTGATTTAACCCTATTTTACAAGTATTTGTGT
* *
30047 TTTTAGATCTTGAAGAGAAGAAAAGTGGAAAATAGTTGTTTTTCACTATTTTTGGAGCTAATTTG
131 TTTTAGATCTTGAAGAGAAGAAAAGTGGAAAATAGTTGTTTTTCACTATTTTTGAAGCTAATTAG
* * *
30112 ATGACTTTTTGCACAAATATGGGCTTAGCATTTTTGAGTGAAGATTTGAAGATTTGAAGTTCGTG
196 ATGACTTTTTGCACAAATATGGACTTAGAATTTTTGAGTAAAGATTTGAAGATTTGAAGTTCGTG
** *
30177 ATTGAAGATTTATTGAAGATAATTTCAAGTTGTGAATATCATTGA
261 ATTGAAGATTTATTGAAGATAATTTCAAGTCATGAAGATCATTGA
* * * *
30222 AGGTTCTCTTGTTGGGAGTCTTGA-AAGTCAAGCTGATCGAGCCAAAATTAACCCTATTTTTATG
1 AGGTTCTCTTGTTGGGAGTCTTAACAAGTCAAGCTAATCGAGCCAAAATTAACCATATTTCTATG
* *
30286 ATCGTTTTCCTATGATTTTTGGTATTTTTATGTGTGATTTAACCCTATTTTACAAGTATTTTTGT
66 ATCATTTTCCTATGATTTTTGGTATTTTTATGTGTGATTTAACCCTATTTTACAAGTATTTGTGT
* *
30351 TTTTAGGTCTTGAAGAGAAGAAAAAGTGGAAACTAGTTGTTTTTCACTATTTTTGAAGCTAATTA
131 TTTTAGATCTTGAAGAGAAG-AAAAGTGGAAAATAGTTGTTTTTCACTATTTTTGAAGCTAATTA
30416 GATGACTTTTTGCACAAATATGGACTTAGAATTTTTGAGTAAAGATTTGAAGATTTGAAGTTCGT
195 GATGACTTTTTGCACAAATATGGACTTAGAATTTTTGAGTAAAGATTTGAAGATTTGAAGTTCGT
30481 GATTGAAGATTTATTGAAGATAATTTCAAGTCATGAAGATCATTGA
260 GATTGAAGATTTATTGAAGATAATTTCAAGTCATGAAGATCATTGA
30527 AGG
1 AGG
30530 AAGCTTTCAA
Statistics
Matches: 288, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
304 116 0.40
305 172 0.60
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (305 bp):
AGGTTCTCTTGTTGGGAGTCTTAACAAGTCAAGCTAATCGAGCCAAAATTAACCATATTTCTATG
ATCATTTTCCTATGATTTTTGGTATTTTTATGTGTGATTTAACCCTATTTTACAAGTATTTGTGT
TTTTAGATCTTGAAGAGAAGAAAAGTGGAAAATAGTTGTTTTTCACTATTTTTGAAGCTAATTAG
ATGACTTTTTGCACAAATATGGACTTAGAATTTTTGAGTAAAGATTTGAAGATTTGAAGTTCGTG
ATTGAAGATTTATTGAAGATAATTTCAAGTCATGAAGATCATTGA
Found at i:31113 original size:14 final size:15
Alignment explanation
Indices: 31094--31133 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
31084 CTAGATACAA
31094 TATTTTCTCTACATC
1 TATTTTCTCTACATC
*
31109 T-TTTTCTCTTCATC
1 TATTTTCTCTACATC
*
31123 TATTTTTTCTA
1 TATTTTCTCTA
31134 TTTTTCTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTCTCTACATC
Found at i:42525 original size:21 final size:21
Alignment explanation
Indices: 42484--42525 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
42474 GGTAATCAAG
* *
42484 AGTTTTTAAGATTTAAACAGA
1 AGTTTTCAAGATTCAAACAGA
42505 AGTTTTCAA-ATTCAAATCAGA
1 AGTTTTCAAGATTCAAA-CAGA
42526 CTTAGTCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (21 bp):
AGTTTTCAAGATTCAAACAGA
Found at i:43128 original size:31 final size:30
Alignment explanation
Indices: 43093--43169 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 30
43083 GCAAGTTGCT
*
43093 CAAATTGAGTCTAAACGTTTTTGAGATGCAC
1 CAAATTG-GCCTAAACGTTTTTGAGATGCAC
*
43124 CAAATTCGGCCTAAACGTTTTTTAGATGCAC
1 CAAATT-GGCCTAAACGTTTTTGAGATGCAC
43155 CAAATTGGGCCTAAA
1 CAAATT-GGCCTAAA
43170 AAGAAAAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 41 0.98
32 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (30 bp):
CAAATTGGCCTAAACGTTTTTGAGATGCAC
Found at i:46287 original size:40 final size:40
Alignment explanation
Indices: 46230--46385 Score: 267
Period size: 40 Copynumber: 3.9 Consensus size: 40
46220 GAAAAAAGTA
46230 TACTCTTAATTACCAATTTTCTGATTACTTCTTTTACTTT
1 TACTCTTAATTACCAATTTTCTGATTACTTCTTTTACTTT
*
46270 TACTCTTAATTATCAATTTTCTGATTACTTCTTTTACTTT
1 TACTCTTAATTACCAATTTTCTGATTACTTCTTTTACTTT
* * *
46310 TACTCTTAATTACCAATTTACTGCTTACTCCTTTTACTTT
1 TACTCTTAATTACCAATTTTCTGATTACTTCTTTTACTTT
*
46350 TACTCGTAATTACCAATTTTCTGATTACTTCTTTTA
1 TACTCTTAATTACCAATTTTCTGATTACTTCTTTTA
46386 TTACCAATTT
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 107 1.00
ACGTcount: A:0.23, C:0.21, G:0.03, T:0.53
Consensus pattern (40 bp):
TACTCTTAATTACCAATTTTCTGATTACTTCTTTTACTTT
Found at i:46393 original size:27 final size:27
Alignment explanation
Indices: 46358--46412 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
46348 TTTACTCGTA
*
46358 ATTACCAATTTTCTGATTACTT-CTTTT
1 ATTACCAATTTACTGATTA-TTCCTTTT
*
46385 ATTACCAATTTACTGCTTATTCCTTTT
1 ATTACCAATTTACTGATTATTCCTTTT
46412 A
1 A
46413 CTTTTACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.53
Consensus pattern (27 bp):
ATTACCAATTTACTGATTATTCCTTTT
Found at i:46400 original size:67 final size:67
Alignment explanation
Indices: 46318--46673 Score: 272
Period size: 67 Copynumber: 5.0 Consensus size: 67
46308 TTTACTCTTA
*
46318 ATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCGTAATTACCAATTTTCTGATTACTTCTT
1 ATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCTT
46383 TT
66 TT
*
46385 ATTACCAATTTACTGCTTATTCCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCTT
1 ATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTA---C--
46450 TTACTTTACTCTT
61 TT-C--T--T-TT
* * * *
46463 AATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCTTAATTAGCAATTTACTTATTACTCCT
1 -ATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCT
46528 TTT
65 TTT
*** ** * * *
46531 ACTTTTACTCTTAA-TTACCAATTTACTGATTACTT-CTTTTACT-TTTACT-CC-ATTTTATTG
1 A---TTAC-C--AATTTA-CTGCTTACTCCTT--TTACTTTTACTCTTAATTACCAATTTT-CTG
46591 ATTACTTCTTTT
56 ATTACTTCTTTT
* * * *
46603 ACTTTTACTCCACTTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATTAC
1 A---TTA--CCAATTTACTGCTTACTCCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTAC
46668 TTCTTT
61 TTCTTT
46674 CACTTTTACT
Statistics
Matches: 231, Mismatches: 29, Indels: 53
0.74 0.09 0.17
Matches are distributed among these distances:
67 58 0.25
68 2 0.01
69 3 0.01
70 13 0.06
71 19 0.08
72 43 0.19
73 21 0.09
74 10 0.04
75 3 0.01
76 1 0.00
77 1 0.00
78 2 0.01
79 55 0.24
ACGTcount: A:0.23, C:0.22, G:0.03, T:0.53
Consensus pattern (67 bp):
ATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCTT
TT
Found at i:46415 original size:107 final size:106
Alignment explanation
Indices: 46278--46708 Score: 403
Period size: 104 Copynumber: 3.9 Consensus size: 106
46268 TTTACTCTTA
* * *
46278 ATTATCAATTTTCTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACTGCTTACTCCTT
1 ATTACCAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATTACTCCTT
* *
46343 TTACTTTTACTCGTAATTACCAATTTTCTGATTACTTCTTTT
66 TTAC-TTTACTCGTAATTACCAATTTACTGATTACTCCTTTT
* * *
46385 ATTACCAATTTACTGCTTA-TTCCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCT
1 ATTACCAATTTACTGATTACTT-CTTTTACTTTTACTCTTAATTACCAATTTACTGATTACTCCT
* *
46449 TTTACTTTACTCTTAATTACCAATTTACTGCTTACTCCTTTT
65 TTTACTTTACTCGTAATTACCAATTTACTGATTACTCCTTTT
* *
46491 ACTTTTACTCTTAATTAGCAATTTACTTATTACTCCTTTTACTTTTACTCTTAATTACCAATTTA
1 A---TTA--C--------CAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTA
* * * * *
46556 CTGATTACTTCTTTTAC-TT--T--T-ACT-CCATTTTATTGATTACTTCTTTT
53 CTGATTACTCCTTTTACTTTACTCGTAATTACCAATTTACTGATTACTCCTTTT
*
46603 ACTTTTACTCCACTTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATTAC
1 A---TTA--CCAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATTAC
* * * *
46668 TTCTTTCACTTTTACTC-TGAATTACCAATTTATTAATTACT
61 TCCTTTTAC-TTTACTCGT-AATTACCAATTTACTGATTACT
46709 TCTTCTTCTT
Statistics
Matches: 275, Mismatches: 26, Indels: 41
0.80 0.08 0.12
Matches are distributed among these distances:
104 60 0.22
106 38 0.14
107 60 0.22
108 1 0.00
109 4 0.01
111 3 0.01
112 44 0.16
113 2 0.01
114 1 0.00
116 1 0.00
118 2 0.01
119 58 0.21
120 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.03, T:0.52
Consensus pattern (106 bp):
ATTACCAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTACTGATTACTCCTT
TTACTTTACTCGTAATTACCAATTTACTGATTACTCCTTTT
Found at i:46430 original size:40 final size:40
Alignment explanation
Indices: 46385--46726 Score: 327
Period size: 40 Copynumber: 9.0 Consensus size: 40
46375 TACTTCTTTT
*
46385 ATTACCAATTTACTGCTTATTCCTTTTACTTTTACTCTTA
1 ATTACCAATTTACTGATTATTCCTTTTACTTTTACTCTTA
*
46425 ATTACCAATTTTCTGATTACTT-CTTTTAC-TTTACTCTTA
1 ATTACCAATTTACTGATTA-TTCCTTTTACTTTTACTCTTA
* *
46464 ATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCTTA
1 ATTACCAATTTACTGATTATTCCTTTTACTTTTACTCTTA
* * *
46504 ATTAGCAATTTACTTATTACTCCTTTTACTTTTACTCTTA
1 ATTACCAATTTACTGATTATTCCTTTTACTTTTACTCTTA
46544 ATTACCAATTTACTGATTACTT-CTTTTACTTTTA--C---
1 ATTACCAATTTACTGATTA-TTCCTTTTACTTTTACTCTTA
* *
46579 --T-CCATTTTATTGATTACTT-CTTTTACTTTTA--C---
1 ATTACCAATTTACTGATTA-TTCCTTTTACTTTTACTCTTA
*
46611 --T-CCACTTTACTGATTACTT-CTTTTACTTTTACTCTTA
1 ATTACCAATTTACTGATTA-TTCCTTTTACTTTTACTCTTA
* *
46648 ATTACCAATTTACTGATTACTT-CTTTCACTTTTACTCTGA
1 ATTACCAATTTACTGATTA-TTCCTTTTACTTTTACTCTTA
* *
46688 ATTACCAATTTATTAATTACTT-CTTCTT-CTTTTACTCTT
1 ATTACCAATTTACTGATTA-TTCCTT-TTACTTTTACTCTT
46727 TTTAGCTTAA
Statistics
Matches: 267, Mismatches: 22, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
32 58 0.22
33 1 0.00
34 1 0.00
38 2 0.01
39 35 0.13
40 166 0.62
41 4 0.01
ACGTcount: A:0.23, C:0.22, G:0.03, T:0.53
Consensus pattern (40 bp):
ATTACCAATTTACTGATTATTCCTTTTACTTTTACTCTTA
Found at i:46523 original size:146 final size:147
Alignment explanation
Indices: 46238--46531 Score: 493
Period size: 146 Copynumber: 2.0 Consensus size: 147
46228 TATACTCTTA
* *
46238 ATTACCAATTTTCTGATTACTTCTTTTACTTTTACTCTTAATTATCAATTTTCTGATTACTTCTT
1 ATTACCAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCTT
46303 TTACTTTTACTCTTAATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCGTAATTACCAATT
66 TTACTTTTACTCTTAATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCGTAATTACCAATT
* *
46368 TTCTGATTACTTCTTTT
131 TACTGATTACTCCTTTT
*
46385 ATTACCAATTTACTGCTTA-TTCCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCT
1 ATTACCAATTTACTGATTACTT-CTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCT
* *
46449 TTTAC-TTTACTCTTAATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCTTAATTAGCAAT
65 TTTACTTTTACTCTTAATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCGTAATTACCAAT
*
46513 TTACTTATTACTCCTTTT
130 TTACTGATTACTCCTTTT
46531 A
1 A
46532 CTTTTACTCT
Statistics
Matches: 138, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
146 75 0.54
147 63 0.46
ACGTcount: A:0.23, C:0.21, G:0.03, T:0.53
Consensus pattern (147 bp):
ATTACCAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCAATTTTCTGATTACTTCTT
TTACTTTTACTCTTAATTACCAATTTACTGCTTACTCCTTTTACTTTTACTCGTAATTACCAATT
TACTGATTACTCCTTTT
Found at i:46578 original size:15 final size:15
Alignment explanation
Indices: 46560--46643 Score: 80
Period size: 16 Copynumber: 5.3 Consensus size: 15
46550 AATTTACTGA
46560 TTACTTCTTTTACTT
1 TTACTTCTTTTACTT
*
46575 TTACTCCATTTTA-TT
1 TTACTTC-TTTTACTT
46590 GATTACTTCTTTTACTT
1 --TTACTTCTTTTACTT
* * *
46607 TTACTCCACTTTACTGA
1 TTACTTC-TTTTACT-T
46624 TTACTTCTTTTACTT
1 TTACTTCTTTTACTT
46639 TTACT
1 TTACT
46644 CTTAATTACC
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 19 0.35
16 22 0.40
17 14 0.25
ACGTcount: A:0.18, C:0.21, G:0.02, T:0.58
Consensus pattern (15 bp):
TTACTTCTTTTACTT
Found at i:46594 original size:32 final size:32
Alignment explanation
Indices: 46552--46644 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
46542 TAATTACCAA
*
46552 TTTACTGATTACTTCTTTTACTTTTACTCCAT
1 TTTACTGATTACTTCTTTTACTTTTACTCCAC
*
46584 TTTATTGATTACTTCTTTTACTTTTACTCCAC
1 TTTACTGATTACTTCTTTTACTTTTACTCCAC
46616 TTTACTGATTACTTCTTTTACTTTTACTC
1 TTTACTGATTACTTCTTTTACTTTTACTC
46645 TTAATTACCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.18, C:0.22, G:0.03, T:0.57
Consensus pattern (32 bp):
TTTACTGATTACTTCTTTTACTTTTACTCCAC
Found at i:48697 original size:10 final size:10
Alignment explanation
Indices: 48682--48706 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
48672 GTTGCTACAC
48682 AATTCCAGAA
1 AATTCCAGAA
48692 AATTCCAGAA
1 AATTCCAGAA
48702 AATTC
1 AATTC
48707 TAGAGTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:50134 original size:42 final size:37
Alignment explanation
Indices: 50060--50139 Score: 88
Period size: 42 Copynumber: 2.0 Consensus size: 37
50050 GGGTTTCCGA
*
50060 TTTTTCTTTTAAAAAAAATTAATTCTTCTTTTCCGTT
1 TTTTTCTTTTAAAAAAAATTAATTCTTATTTTCCGTT
* *
50097 TTTTTCCTTTTAAATAAAAAATATATATTTTTATTTTCTGTT
1 TTTTT-CTTTT-AA-AAAAAAT-TA-ATTCTTATTTTCCGTT
50139 T
1 T
50140 CTGCTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
37 5 0.14
38 5 0.14
39 2 0.06
40 7 0.20
41 2 0.06
42 14 0.40
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.59
Consensus pattern (37 bp):
TTTTTCTTTTAAAAAAAATTAATTCTTATTTTCCGTT
Done.