Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011699.1 Corchorus capsularis cultivar CVL-1 contig11720, 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: 105593
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:526 original size:13 final size:14
Alignment explanation
Indices: 508--537 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
498 TCTTGATTGC
508 TTACTTAGTTA-AT
1 TTACTTAGTTAGAT
521 TTACTTAGTTAGAT
1 TTACTTAGTTAGAT
535 TTA
1 TTA
538 ATTTTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (14 bp):
TTACTTAGTTAGAT
Found at i:2683 original size:21 final size:21
Alignment explanation
Indices: 2659--2705 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
2649 GGTTCGAGAG
2659 ATGAGGCAACATAGGAGTGAA
1 ATGAGGCAACATAGGAGTGAA
2680 ATGAGGCAACATAGGAGTGAA
1 ATGAGGCAACATAGGAGTGAA
2701 ATGAG
1 ATGAG
2706 AGCTTACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.34, T:0.15
Consensus pattern (21 bp):
ATGAGGCAACATAGGAGTGAA
Found at i:3750 original size:26 final size:26
Alignment explanation
Indices: 3716--3765 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3706 GTCCCTCTTG
*
3716 AAAAAAAAAAGAGTGTTAGTAACCTC
1 AAAAAAAAAAGAGCGTTAGTAACCTC
* *
3742 AAAAGAAAAAGGGCGTTAGTAACC
1 AAAAAAAAAAGAGCGTTAGTAACC
3766 CCTAAAGCAT
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:0.52, C:0.12, G:0.20, T:0.16
Consensus pattern (26 bp):
AAAAAAAAAAGAGCGTTAGTAACCTC
Found at i:3772 original size:26 final size:26
Alignment explanation
Indices: 3716--3772 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
3706 GTCCCTCTTG
* * *
3716 AAAAAAAAAAGAGTGTTAGTAACCTC
1 AAAAGAAAAAGAGCGTTAGTAACCCC
*
3742 AAAAGAAAAAGGGCGTTAGTAACCCC
1 AAAAGAAAAAGAGCGTTAGTAACCCC
*
3768 TAAAG
1 AAAAG
3773 CATGAACACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (26 bp):
AAAAGAAAAAGAGCGTTAGTAACCCC
Found at i:7464 original size:123 final size:122
Alignment explanation
Indices: 7237--7479 Score: 459
Period size: 123 Copynumber: 2.0 Consensus size: 122
7227 GGAGCAAGGC
*
7237 AAAAGTGCTTGTTAAGTTTTTGAGGTTATTTTATGATGCCACAAGAATACTGTCAGGTTCATTAT
1 AAAAGTGATTGTTAAGTTTTTGAGGTTATTTTATGATGCCACAAGAATACTGTCAGGTTCATTAT
7302 ATGTCTACCTTACACCTTGAGCAAGTATGTCTCTTTCAATCTACTTTTGATGGATTG
66 ATGTCTACCTTACACCTTGAGCAAGTATGTCTCTTTCAATCTACTTTTGATGGATTG
7359 AAAAGTAGATTGTTAAGTTTTTGAGGTTATTTTATGATGCCACAAGAATACTGTCAGGTTCATTA
1 AAAAGT-GATTGTTAAGTTTTTGAGGTTATTTTATGATGCCACAAGAATACTGTCAGGTTCATTA
*
7424 TATGTCTACCTTACACCTTGAGCAAGTTTGTCTCTTTCAATCTACTTTTGATGGAT
65 TATGTCTACCTTACACCTTGAGCAAGTATGTCTCTTTCAATCTACTTTTGATGGAT
7480 GGAGTAATAG
Statistics
Matches: 118, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
122 6 0.05
123 112 0.95
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (122 bp):
AAAAGTGATTGTTAAGTTTTTGAGGTTATTTTATGATGCCACAAGAATACTGTCAGGTTCATTAT
ATGTCTACCTTACACCTTGAGCAAGTATGTCTCTTTCAATCTACTTTTGATGGATTG
Found at i:11291 original size:41 final size:41
Alignment explanation
Indices: 11241--11319 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
11231 AAACATGTAG
* *
11241 TTTTATTTCATTTAGATTAATTAATTATGTAATTATGTATT
1 TTTTATTTCATTTAAATTAATTAATTAGGTAATTATGTATT
11282 TTTTATTTCATTTAAATTAATTAATTAGGTAATTATGT
1 TTTTATTTCATTTAAATTAATTAATTAGGTAATTATGT
11320 TTTATTCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.57
Consensus pattern (41 bp):
TTTTATTTCATTTAAATTAATTAATTAGGTAATTATGTATT
Found at i:12475 original size:156 final size:156
Alignment explanation
Indices: 12105--12475 Score: 389
Period size: 156 Copynumber: 2.4 Consensus size: 156
12095 TCATCTCAAA
* * * * * **
12105 CAGACTTTGTATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTGGGGTGTCAAACCAAC
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAAACCAAC
* * * * *
12170 TTCTCTATGCTAGAGAATTCGGTTTTACTTAGAATTTTTCCCATAGCTTTATGGGGATAATCTAA
66 TTCACCATGCAAGAGAATTCGGTTTTACTTAGAATTTTTCCCATAGCTTTATGGAGATAATATAA
*
12235 GTCTACTGGTGGAAAATCAGCCTCGTT
131 GTCTACT-GTGGAAAATCAGCCTCATT
* ** * * *
12262 -GGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA-ACTCAGGGAGAGAAACCTA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGA-GGTGAGAAACCAA
* * * *
12325 GTTCACCAT-CAAGGGGAGCTT-GGTTTTACTTAGAATTTTTTCCATAGTCTTT-TGGAGATAAT
65 CTTCACCATGCAA-GAGA-ATTCGGTTTTACTTAGAATTTTTCCCATAG-CTTTATGGAGATAAT
* *
12387 ATAAGTC-CCT-TGGAAAAATTTCAG-TTCATT
127 ATAAGTCTACTGTGG-AAAA--TCAGCCTCATT
12417 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAA
12476 GCTCGGTTTA
Statistics
Matches: 175, Mismatches: 30, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
153 3 0.02
154 4 0.02
155 9 0.05
156 151 0.86
157 8 0.05
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (156 bp):
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGAGAAACCAAC
TTCACCATGCAAGAGAATTCGGTTTTACTTAGAATTTTTCCCATAGCTTTATGGAGATAATATAA
GTCTACTGTGGAAAATCAGCCTCATT
Found at i:12843 original size:17 final size:18
Alignment explanation
Indices: 12821--12858 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
12811 GTTATCCAGC
12821 ACCTCATGCTACCTA-GT
1 ACCTCATGCTACCTAGGT
*
12838 ACCTCATGTTACCTAGGT
1 ACCTCATGCTACCTAGGT
12856 ACC
1 ACC
12859 ATGAGGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.24, C:0.34, G:0.13, T:0.29
Consensus pattern (18 bp):
ACCTCATGCTACCTAGGT
Found at i:17169 original size:2 final size:2
Alignment explanation
Indices: 17159--17187 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17149 TTTTTAACCT
17159 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17188 ACTTAGTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19476 original size:2 final size:2
Alignment explanation
Indices: 19471--19499 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19461 TTAGTGTGTG
19471 TA 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 TA T
19500 TCTCTAACAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22531 original size:15 final size:15
Alignment explanation
Indices: 22513--22542 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22503 TACTTTTGCA
*
22513 ACTTTTATCATTTTT
1 ACTTTTACCATTTTT
22528 ACTTTTACCATTTTT
1 ACTTTTACCATTTTT
22543 CTTACTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (15 bp):
ACTTTTACCATTTTT
Found at i:22629 original size:15 final size:15
Alignment explanation
Indices: 22576--22629 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
22566 TTTGACCCTT
*
22576 TTTTACTTAATATCA
1 TTTTACTTAATACCA
* *
22591 TTTTTACTAAATGCCA
1 -TTTTACTTAATACCA
22607 TTTTACTTAATACCA
1 TTTTACTTAATACCA
22622 TTTTACTT
1 TTTTACTT
22630 TCTATCTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
15 21 0.64
16 12 0.36
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTTACTTAATACCA
Found at i:23074 original size:34 final size:34
Alignment explanation
Indices: 23029--23149 Score: 138
Period size: 34 Copynumber: 3.5 Consensus size: 34
23019 TTAGTTATCA
*
23029 ATTTACCGATTACTATCTTTTTACCTGATTACTG
1 ATTTACTGATTACTATCTTTTTACCTGATTACTG
** * *
23063 ATTTACTGATTACTAT-TATCTGGACTCTTAATTA-TCA
1 ATTTACTGATTACTATCT-T-TTTAC-C-TGATTACT-G
23100 ATTTACTGATTACTATCTTTTTACCTGATTACTG
1 ATTTACTGATTACTATCTTTTTACCTGATTACTG
23134 ATTTACTGATTACTAT
1 ATTTACTGATTACTAT
23150 TACCTTGACT
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
33 1 0.01
34 37 0.52
35 5 0.07
36 5 0.07
37 22 0.31
38 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.48
Consensus pattern (34 bp):
ATTTACTGATTACTATCTTTTTACCTGATTACTG
Found at i:23099 original size:71 final size:71
Alignment explanation
Indices: 22992--23161 Score: 268
Period size: 71 Copynumber: 2.4 Consensus size: 71
22982 GGCTCTTTAA
* * *
22992 TTACTGATTAATCTCTTACCTTGACTCTTAGTTATCAATTTACCGATTACTATCTTTTTACCTGA
1 TTACTGATT-A-CTATTACCTGGACTCTTAATTATCAATTTACCGATTACTATCTTTTTACCTGA
23057 TTACTGAT
64 TTACTGAT
* *
23065 TTACTGATTACTATTATCTGGACTCTTAATTATCAATTTACTGATTACTATCTTTTTACCTGATT
1 TTACTGATTACTATTACCTGGACTCTTAATTATCAATTTACCGATTACTATCTTTTTACCTGATT
23130 ACTGAT
66 ACTGAT
*
23136 TTACTGATTACTATTACCTTGACTCT
1 TTACTGATTACTATTACCTGGACTCT
23162 GATTAATCTC
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
71 80 0.89
72 1 0.01
73 9 0.10
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.47
Consensus pattern (71 bp):
TTACTGATTACTATTACCTGGACTCTTAATTATCAATTTACCGATTACTATCTTTTTACCTGATT
ACTGAT
Found at i:23164 original size:55 final size:55
Alignment explanation
Indices: 23105--23501 Score: 632
Period size: 55 Copynumber: 7.2 Consensus size: 55
23095 TATCAATTTA
* * * *
23105 CTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
*
23160 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACCATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
* *
23215 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACCATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
*
23270 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
* * * *
23325 CTGATTAATTTCTTTTCACTTAATTACTGATTTACTGCTTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
*
23380 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
* *
23435 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTATTATTGACTTTGACT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATT-ACCTTGACT
*
23491 CTTAATTAATC
1 C-TGATTAATC
23502 AATTTACTGA
Statistics
Matches: 323, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
55 307 0.95
56 8 0.02
57 8 0.02
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
Found at i:23194 original size:71 final size:68
Alignment explanation
Indices: 22943--23161 Score: 197
Period size: 71 Copynumber: 3.1 Consensus size: 68
22933 GATCACTTTA
* * * ** * * *
22943 ACTCTTAATTATCGATTTATTGATTACTATTTTTACCTAGGCT-CTTTAATTACTGATTAATCTC
1 ACTCTTAATTATCAATTTACTAATTACTA-TTTTACCT-GATTAC-TGATTTACTGATT-A-CTA
*
23007 TTACCTTG
61 TTACCTGG
* **
23015 ACTCTTAGTTATCAATTTACCGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATT
1 ACTCTTAATTATCAATTTACTAATTACTA---TTTTACCTGATTACTGATTTACTGATTACTATT
*
23080 ATCTGG
63 ACCTGG
*
23086 ACTCTTAATTATCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATT
1 ACTCTTAATTATCAATTTACTAATTACTA---TTTTACCTGATTACTGATTTACTGATTACTATT
*
23151 ACCTTG
63 ACCTGG
23157 ACTCT
1 ACTCT
23162 GATTAATCTC
Statistics
Matches: 129, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
71 80 0.62
72 26 0.20
73 13 0.10
74 10 0.08
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (68 bp):
ACTCTTAATTATCAATTTACTAATTACTATTTTACCTGATTACTGATTTACTGATTACTATTACC
TGG
Found at i:23509 original size:47 final size:47
Alignment explanation
Indices: 23458--23560 Score: 206
Period size: 47 Copynumber: 2.2 Consensus size: 47
23448 TTTTACTTAA
23458 TTACTGATTTACTGATTATTATTGACTTTGACTCTTAATTAATCAAT
1 TTACTGATTTACTGATTATTATTGACTTTGACTCTTAATTAATCAAT
23505 TTACTGATTTACTGATTATTATTGACTTTGACTCTTAATTAATCAAT
1 TTACTGATTTACTGATTATTATTGACTTTGACTCTTAATTAATCAAT
23552 TTACTGATT
1 TTACTGATT
23561 ACCGTCTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.50
Consensus pattern (47 bp):
TTACTGATTTACTGATTATTATTGACTTTGACTCTTAATTAATCAAT
Found at i:23600 original size:25 final size:26
Alignment explanation
Indices: 23552--23600 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
23542 ATTAATCAAT
*
23552 TTACTGATTACCGTCTTTTTACTTAA
1 TTACTGATTACCGCCTTTTTACTTAA
*
23578 TTACTGATTGCC-CCTTTTTACTT
1 TTACTGATTACCGCCTTTTTACTT
23601 TTCTGACTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.18, C:0.22, G:0.08, T:0.51
Consensus pattern (26 bp):
TTACTGATTACCGCCTTTTTACTTAA
Found at i:24454 original size:50 final size:50
Alignment explanation
Indices: 24390--24633 Score: 330
Period size: 53 Copynumber: 4.8 Consensus size: 50
24380 TAATTACTTT
*
24390 TTAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTATTTACTAATTAC
1 TTAAAAATTCAATCTTTTATTCAAAGGTGACATCTTTATTTACTAATTAC
* **
24440 TTAAAAATTTAATCTTTTGCTCAAAGGTGACATTTCTATTATTTACTAATTAC
1 TTAAAAATTCAATCTTTTATTCAAAGGTGACA--TCT-TTATTTACTAATTAC
24493 TTAAAAAATTCAATCTTTTATTCAAAGGTGACAT-TTTATTTACT-ATCTAC
1 TT-AAAAATTCAATCTTTTATTCAAAGGTGACATCTTTATTTACTAAT-TAC
** *
24543 TTAAAAATTCAATCTTTTACCCAAAGGTGACATTTTTATTATTTACTAATTAC
1 TTAAAAATTCAATCTTTTATTCAAAGGTGACA--TCT-TTATTTACTAATTAC
*
24596 TTAAAAATTCAATCTTTTATTCAAAGGTGACATTTTTA
1 TTAAAAATTCAATCTTTTATTCAAAGGTGACATCTTTA
24634 CTTCAAAGAT
Statistics
Matches: 173, Mismatches: 11, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
49 30 0.17
50 45 0.26
51 5 0.03
52 5 0.03
53 59 0.34
54 29 0.17
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.45
Consensus pattern (50 bp):
TTAAAAATTCAATCTTTTATTCAAAGGTGACATCTTTATTTACTAATTAC
Found at i:24547 original size:103 final size:102
Alignment explanation
Indices: 24390--24631 Score: 405
Period size: 103 Copynumber: 2.4 Consensus size: 102
24380 TAATTACTTT
* *
24390 TTAAAAATTCAATCTTTTATTCAAAGGTTACATCTTTATTTACTAATTACTTAAAAATTTAATCT
1 TTAAAAATTCAATCTTTTATTCAAAGGTGACAT-TTTATTTACTAATTACTTAAAAATTCAATCT
* *
24455 TTTGCTCAAAGGTGACATTTCTATTATTTACTAATTAC
65 TTTACCCAAAGGTGACATTTCTATTATTTACTAATTAC
24493 TTAAAAAATTCAATCTTTTATTCAAAGGTGACATTTTATTTACT-ATCTACTTAAAAATTCAATC
1 TT-AAAAATTCAATCTTTTATTCAAAGGTGACATTTTATTTACTAAT-TACTTAAAAATTCAATC
*
24557 TTTTACCCAAAGGTGACATTTTTATTATTTACTAATTAC
64 TTTTACCCAAAGGTGACATTTCTATTATTTACTAATTAC
24596 TTAAAAATTCAATCTTTTATTCAAAGGTGACATTTT
1 TTAAAAATTCAATCTTTTATTCAAAGGTGACATTTT
24632 TACTTCAAAG
Statistics
Matches: 132, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
102 36 0.27
103 66 0.50
104 30 0.23
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.45
Consensus pattern (102 bp):
TTAAAAATTCAATCTTTTATTCAAAGGTGACATTTTATTTACTAATTACTTAAAAATTCAATCTT
TTACCCAAAGGTGACATTTCTATTATTTACTAATTAC
Found at i:28287 original size:32 final size:31
Alignment explanation
Indices: 28244--28375 Score: 104
Period size: 32 Copynumber: 4.1 Consensus size: 31
28234 CTAATTTGGG
*
28244 GCGTCTCTAGAAGAAAACGCCTTAAAATAGGA
1 GCGTCTATAGAAGAAAACGCCTT-AAATAGGA
* * * * *
28276 GCGTCTATAGAAGAAAAAGCCCCTAATTTGGG
1 GCGTCTATAGAAGAAAACG-CCTTAAATAGGA
* **
28308 GCGTCTATAAAAGAAAACGCCTGTATTTAGCG-
1 GCGTCTATAGAAGAAAACGCCT-TAAATAG-GA
* * *
28340 GCGTCTATTGAAGGAAACGCCTTAAAATAAGA
1 GCGTCTATAGAAGAAAACGCCTT-AAATAGGA
28372 GCGT
1 GCGT
28376 TTAAACGCCC
Statistics
Matches: 78, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
31 4 0.05
32 70 0.90
33 4 0.05
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.22
Consensus pattern (31 bp):
GCGTCTATAGAAGAAAACGCCTTAAATAGGA
Found at i:28680 original size:89 final size:89
Alignment explanation
Indices: 28515--28680 Score: 210
Period size: 89 Copynumber: 1.9 Consensus size: 89
28505 CCGCTGTATT
* * * *
28515 CAATTTAAGAAACTTAGTATTTTCGAAAAGAAAAATGTATGGAGGCGTTTAAACGCCTCTAAATG
1 CAATTTAAAAAACTTAGTATTTTCGAAAAAAAAAATGTATCGAGGCATTTAAACGCCTCTAAATG
* *
28580 ACGGTGTTTAAACACAGTTATATG
66 ACGGCGCTTAAACACAGTTATATG
* * * *
28604 CAATTTAAAAAACTTAGTATTTTTGAAAAAAAAAAAT-TA-CGACGTCATTTAAATGCCTCTACA
1 CAATTTAAAAAACTTAGTATTTTCG-AAAAAAAAAATGTATCGA-GGCATTTAAACGCCTCTAAA
28667 TGACGGCGCTTAAA
64 TGACGGCGCTTAAA
28681 TGCCGATATG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
88 2 0.03
89 53 0.82
90 10 0.15
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (89 bp):
CAATTTAAAAAACTTAGTATTTTCGAAAAAAAAAATGTATCGAGGCATTTAAACGCCTCTAAATG
ACGGCGCTTAAACACAGTTATATG
Found at i:40604 original size:21 final size:21
Alignment explanation
Indices: 40579--40621 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40569 CAAATTACGC
40579 TGAGTAGTTAGTGGATAAGTT
1 TGAGTAGTTAGTGGATAAGTT
40600 TGAGTAGTTAGTGGATAAGTT
1 TGAGTAGTTAGTGGATAAGTT
40621 T
1 T
40622 AATGGTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.40
Consensus pattern (21 bp):
TGAGTAGTTAGTGGATAAGTT
Found at i:40692 original size:16 final size:16
Alignment explanation
Indices: 40671--40715 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
40661 GTCTAATGAG
40671 TTGTAAATATTTTATA
1 TTGTAAATATTTTATA
*
40687 TTGTAAATATATTATA
1 TTGTAAATATTTTATA
40703 TTGTTAAATATTT
1 TTG-TAAATATTT
40716 ATTTGTTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 18 0.69
17 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (16 bp):
TTGTAAATATTTTATA
Found at i:40717 original size:16 final size:16
Alignment explanation
Indices: 40674--40722 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
40664 TAATGAGTTG
40674 TAAATATTTTATATTG-
1 TAAATA-TTTATATTGT
40690 TAAATATATTATATTGT
1 TAAATAT-TTATATTGT
40707 TAAATATTTAT-TTGT
1 TAAATATTTATATTGT
40722 T
1 T
40723 CGTGAGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.19
16 18 0.58
17 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
TAAATATTTATATTGT
Found at i:44094 original size:186 final size:186
Alignment explanation
Indices: 43775--44145 Score: 661
Period size: 186 Copynumber: 2.0 Consensus size: 186
43765 GGGGGGGGGG
* * *
43775 GGGGGGATGGCCCTTGCCTGCCCCCCATAAATCCGCCTCTGGTGAAGAATATATGCAACAAAGAA
1 GGGGCGATGGCCCCTGCCTGCCCCCCATAAATCCGCCTATGGTGAAGAATATATGCAACAAAGAA
* *
43840 GATTCAGTACCGTTACACACTGAACAAACATCATCTACTGGAATCCCTCGCCGTTGCAAGTTCAA
66 GATTCAGTACCATTACACACTGAACAAACATCATCTACTGGAATCCCTCGCCATTGCAAGTTCAA
* *
43905 TTTTGTTGGCAAAATATTATGCCATAATCGCCACAAGAAGAATTTAACCTTCGGCA
131 TTTTGTTGGCAAAATATTATGCCATAATCGCCAAAAGAAGAACTTAACCTTCGGCA
*
43961 GGGGCGATGGCCCCTGCCTGCCCCCCATAAATCCGTCTATGGTGAAGAATATATGCAACAAAGAA
1 GGGGCGATGGCCCCTGCCTGCCCCCCATAAATCCGCCTATGGTGAAGAATATATGCAACAAAGAA
*
44026 GATTCAGTGCCATTACACACTGAACAAACATCATCTACTGGAATCCCTCGCCATTGCAAGTTCAA
66 GATTCAGTACCATTACACACTGAACAAACATCATCTACTGGAATCCCTCGCCATTGCAAGTTCAA
44091 TTTTGTTGGCAAAATATTATGCCATAATCGCCAAAAGAAGAACTTAACCTTCGGC
131 TTTTGTTGGCAAAATATTATGCCATAATCGCCAAAAGAAGAACTTAACCTTCGGC
44146 TGAAAAGATG
Statistics
Matches: 176, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
186 176 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (186 bp):
GGGGCGATGGCCCCTGCCTGCCCCCCATAAATCCGCCTATGGTGAAGAATATATGCAACAAAGAA
GATTCAGTACCATTACACACTGAACAAACATCATCTACTGGAATCCCTCGCCATTGCAAGTTCAA
TTTTGTTGGCAAAATATTATGCCATAATCGCCAAAAGAAGAACTTAACCTTCGGCA
Found at i:48076 original size:17 final size:17
Alignment explanation
Indices: 48054--48089 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
48044 GGACAAAAAA
48054 ATTATTTTATAGAGATT
1 ATTATTTTATAGAGATT
*
48071 ATTATTTTATAGAGGTT
1 ATTATTTTATAGAGATT
48088 AT
1 AT
48090 ACTGTACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (17 bp):
ATTATTTTATAGAGATT
Found at i:49170 original size:19 final size:21
Alignment explanation
Indices: 49146--49197 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 21
49136 TATATCTTTT
49146 ATATATATAA-T-TAACCTAC
1 ATATATATAATTATAACCTAC
49165 ATATATATAATTCTATAACCTAC
1 ATATATATAA-T-TATAACCTAC
49188 ATATATATAA
1 ATATATATAA
49198 CCTATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.34
22 1 0.03
23 18 0.62
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATATAATTATAACCTAC
Found at i:49198 original size:15 final size:15
Alignment explanation
Indices: 49178--49211 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
49168 TATATAATTC
49178 TATAACCTACATATA
1 TATAACCTACATATA
*
49193 TATAACCTATATATA
1 TATAACCTACATATA
49208 TATA
1 TATA
49212 TATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (15 bp):
TATAACCTACATATA
Found at i:49429 original size:65 final size:65
Alignment explanation
Indices: 49344--49469 Score: 225
Period size: 65 Copynumber: 1.9 Consensus size: 65
49334 ACCTTTGTTA
*
49344 TTCTATAATCGAGCTTCATCTCTTATTTTTCTTGATTTTTCTTTGGAACTCCCATTGGGTTCTTC
1 TTCTATAATCGAGCTCCATCTCTTATTTTTCTTGATTTTTCTTTGGAACTCCCATTGGGTTCTTC
* *
49409 TTCTATAATCGGGCTCCATCTCTTATTTTTCTTGATTTTTCTTTGGAACTCCCTTTGGGTT
1 TTCTATAATCGAGCTCCATCTCTTATTTTTCTTGATTTTTCTTTGGAACTCCCATTGGGTT
49470 GGTGGAGACA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.14, C:0.21, G:0.13, T:0.51
Consensus pattern (65 bp):
TTCTATAATCGAGCTCCATCTCTTATTTTTCTTGATTTTTCTTTGGAACTCCCATTGGGTTCTTC
Found at i:50682 original size:30 final size:30
Alignment explanation
Indices: 50646--50707 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
50636 TCGAATGCGA
50646 CATCGCATGGAGCAACCG-GCCACAACCGGC
1 CATCGCATGGAGCAACCGCG-CACAACCGGC
* *
50676 CATCGCATGGGGCATCCGCGCACAACCGGC
1 CATCGCATGGAGCAACCGCGCACAACCGGC
50706 CA
1 CA
50708 ATGGATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.24, C:0.40, G:0.27, T:0.08
Consensus pattern (30 bp):
CATCGCATGGAGCAACCGCGCACAACCGGC
Found at i:53368 original size:33 final size:34
Alignment explanation
Indices: 53331--53410 Score: 110
Period size: 33 Copynumber: 2.4 Consensus size: 34
53321 TTAAAATAAT
53331 TCTGTTTTGGTTGATCATAGCATGGAAAACA-AA
1 TCTGTTTTGGTTGATCATAGCATGGAAAACAGAA
* * * *
53364 TCTGTTTTGGTTTATCATAGCATTGAAAATAGGA
1 TCTGTTTTGGTTGATCATAGCATGGAAAACAGAA
53398 -CTGTTTTGGTTGA
1 TCTGTTTTGGTTGA
53411 AAAGATAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
33 40 0.98
34 1 0.02
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.40
Consensus pattern (34 bp):
TCTGTTTTGGTTGATCATAGCATGGAAAACAGAA
Found at i:56440 original size:13 final size:13
Alignment explanation
Indices: 56422--56447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56412 TGATAATAAT
56422 AATATAATACAAA
1 AATATAATACAAA
56435 AATATAATACAAA
1 AATATAATACAAA
56448 CATAATTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
AATATAATACAAA
Found at i:58196 original size:58 final size:58
Alignment explanation
Indices: 58125--58238 Score: 174
Period size: 58 Copynumber: 2.0 Consensus size: 58
58115 ATTATTTTTC
* *
58125 ATTATTCATTTATTCTTTGAGAATTTTTAAAATAATAAAACCATCTAATTTAGAACAA
1 ATTATTCAATTATTCTTTAAGAATTTTTAAAATAATAAAACCATCTAATTTAGAACAA
* * * *
58183 ATTATTCAATTATTCTTTAAGAATTTTTATAATTATGAAATCATCTAATTTAGAAC
1 ATTATTCAATTATTCTTTAAGAATTTTTAAAATAATAAAACCATCTAATTTAGAAC
58239 TATTAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (58 bp):
ATTATTCAATTATTCTTTAAGAATTTTTAAAATAATAAAACCATCTAATTTAGAACAA
Found at i:64564 original size:30 final size:32
Alignment explanation
Indices: 64505--64574 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 32
64495 TTCATTTAGT
64505 TTTAAAATTTATAATAATTAAATATAAATAAA
1 TTTAAAATTTATAATAATTAAATATAAATAAA
64537 CTTTAAAATTTAT-A-AA-TATAA-ATAAATAAA
1 -TTTAAAATTTATAATAATTA-AATATAAATAAA
64567 TATTAAAA
1 T-TTAAAA
64575 AAGATGAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
29 1 0.03
30 17 0.49
31 4 0.11
32 1 0.03
33 12 0.34
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
TTTAAAATTTATAATAATTAAATATAAATAAA
Found at i:69141 original size:15 final size:15
Alignment explanation
Indices: 69121--69153 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
69111 ACTGTGTACA
69121 ATATATTTATAATTT
1 ATATATTTATAATTT
*
69136 ATATATTTATAGTTT
1 ATATATTTATAATTT
69151 ATA
1 ATA
69154 CACATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATATATTTATAATTT
Found at i:69305 original size:35 final size:35
Alignment explanation
Indices: 69259--69328 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
69249 CAAAGAACGG
69259 CTCGAATAAGGTTAATTTGTAAATATACTAAAAAA
1 CTCGAATAAGGTTAATTTGTAAATATACTAAAAAA
69294 CTCGAATAAGGTTAATTTGTAAATATACTAAAAAA
1 CTCGAATAAGGTTAATTTGTAAATATACTAAAAAA
69329 ATAATAATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (35 bp):
CTCGAATAAGGTTAATTTGTAAATATACTAAAAAA
Found at i:76267 original size:16 final size:16
Alignment explanation
Indices: 76246--76279 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
76236 ACAATTCAGA
76246 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
76262 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
76278 AA
1 AA
76280 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:79579 original size:32 final size:31
Alignment explanation
Indices: 79543--79644 Score: 105
Period size: 32 Copynumber: 3.2 Consensus size: 31
79533 CCAATCCGAG
** *
79543 CCCGAATCCGAATTAATTTGACCCAAAATTGA
1 CCCGAA-CCGAATTAACCTGACCCAAAATTAA
* *
79575 CCCGAACCCGAATCAACCTGACCCAAATTTAA
1 CCCGAA-CCGAATTAACCTGACCCAAAATTAA
* **
79607 CCCGAACCTGAATTAACCCGACCCAATTTTAA
1 CCCGAACC-GAATTAACCTGACCCAAAATTAA
79639 CCCGAA
1 CCCGAA
79645 TCCAACTTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
31 2 0.03
32 58 0.97
ACGTcount: A:0.36, C:0.33, G:0.11, T:0.20
Consensus pattern (31 bp):
CCCGAACCGAATTAACCTGACCCAAAATTAA
Found at i:89352 original size:54 final size:53
Alignment explanation
Indices: 89243--89345 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 53
89233 GGTAAATCAT
**
89243 TTTTTGCATTAGTTAATCCGTTTGTATATGATTTAGGATCGTTGGTAAAAGGTA
1 TTTTTGCATTAGTTAATCCGTCGGTATATGATTTAGGA-CGTTGGTAAAAGGTA
89297 TTTTTGCATTAGTTAATCCGTCGGTATATGATTTACAGG-CGTTGGTAAA
1 TTTTTGCATTAGTTAATCCGTCGGTATATGATTT--AGGACGTTGGTAAA
89346 GAGTATTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
54 42 0.93
56 3 0.07
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.43
Consensus pattern (53 bp):
TTTTTGCATTAGTTAATCCGTCGGTATATGATTTAGGACGTTGGTAAAAGGTA
Found at i:90039 original size:21 final size:21
Alignment explanation
Indices: 90014--90085 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
90004 CCTCAAATTC
90014 ATAATCTAACACAACCAAACA
1 ATAATCTAACACAACCAAACA
* **
90035 ATAAT-TAA-AAAAAAAAATGCA
1 ATAATCTAACACAACCAAA--CA
90056 A-AATCTAACACAACCAAACA
1 ATAATCTAACACAACCAAACA
90076 ATAATC-AACA
1 ATAATCTAACA
90086 GAAAAAATGG
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
19 6 0.15
20 13 0.32
21 15 0.38
22 6 0.15
ACGTcount: A:0.62, C:0.21, G:0.01, T:0.15
Consensus pattern (21 bp):
ATAATCTAACACAACCAAACA
Found at i:90073 original size:41 final size:41
Alignment explanation
Indices: 90016--90094 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
90006 TCAAATTCAT
*
90016 AATCTAACACAACCAAACAATAATTAAAAAAAAAAATGCAA
1 AATCTAACACAACCAAACAATAATCAAAAAAAAAAATGCAA
* *
90057 AATCTAACACAACCAAACAATAATCAACAGAAAAAATG
1 AATCTAACACAACCAAACAATAATCAAAAAAAAAAATG
90095 GTTTATGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.63, C:0.19, G:0.04, T:0.14
Consensus pattern (41 bp):
AATCTAACACAACCAAACAATAATCAAAAAAAAAAATGCAA
Found at i:94238 original size:24 final size:24
Alignment explanation
Indices: 94193--94239 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
94183 AATCATTCTT
*
94193 AAAAATTCAAAGCAATCATCAATC
1 AAAAATTCAAAGCAATAATCAATC
*
94217 AAAAA-TCAAATCAATAACTCAAT
1 AAAAATTCAAAGCAATAA-TCAAT
94240 ACATATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAAATTCAAAGCAATAATCAATC
Found at i:98616 original size:12 final size:12
Alignment explanation
Indices: 98581--98694 Score: 86
Period size: 12 Copynumber: 9.5 Consensus size: 12
98571 TCTACAGCCA
*
98581 CAGATTGTTGTC
1 CAGATTGCTGTC
*
98593 CTGATCT-CTGTC
1 CAGAT-TGCTGTC
* *
98605 TAGATTGTTGTC
1 CAGATTGCTGTC
*
98617 CAGATTACTGTC
1 CAGATTGCTGTC
* * *
98629 TAGAGTGTTGTC
1 CAGATTGCTGTC
*
98641 CAGATGGCTGTC
1 CAGATTGCTGTC
* *
98653 CAGATTGCTCTT
1 CAGATTGCTGTC
98665 CAGATTGCTGTC
1 CAGATTGCTGTC
* * *
98677 GAGATGGCTGTT
1 CAGATTGCTGTC
98689 CAGATT
1 CAGATT
98695 CAGAAGCAGA
Statistics
Matches: 74, Mismatches: 26, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
11 1 0.01
12 72 0.97
13 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (12 bp):
CAGATTGCTGTC
Done.