Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011222.1 Corchorus capsularis cultivar CVL-1 contig11243, 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: 10238
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:3958 original size:19 final size:19
Alignment explanation
Indices: 3921--3958 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3911 AGACTAATGG
*
3921 TTAATCATTATTAATGAAC
1 TTAATCATCATTAATGAAC
3940 TTAATTCATCATTAA-GAAC
1 TTAA-TCATCATTAATGAAC
3959 ACATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (19 bp):
TTAATCATCATTAATGAAC
Found at i:5442 original size:18 final size:19
Alignment explanation
Indices: 5404--5443 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
5394 ATTTTCAGGA
*
5404 TTTTCAAAATAAAAGACAT
1 TTTTCAAAATAAAAAACAT
*
5423 TTTTC-AAATAAAAAAGAT
1 TTTTCAAAATAAAAAACAT
5441 TTT
1 TTT
5444 CAAGAAACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTCAAAATAAAAAACAT
Found at i:5475 original size:15 final size:15
Alignment explanation
Indices: 5455--5492 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
5445 AAGAAACTGC
5455 TTTCAAAAGAATGA-T
1 TTTCAAAA-AATGAGT
5470 TTTC-AAAAATGAGT
1 TTTCAAAAAATGAGT
5484 TTTCAAAAA
1 TTTCAAAAA
5493 GGTTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.24
14 8 0.38
15 8 0.38
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (15 bp):
TTTCAAAAAATGAGT
Found at i:5491 original size:13 final size:13
Alignment explanation
Indices: 5432--5492 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 13
5422 TTTTTCAAAT
*
5432 AAAAAAGATTTTC
1 AAAAATGATTTTC
*
5445 AAGAAACTG-CTTTC
1 AA-AAA-TGATTTTC
5459 AAAAGAATGATTTTC
1 -AAA-AATGATTTTC
5474 AAAAATGAGTTTTC
1 AAAAATGA-TTTTC
5488 AAAAA
1 AAAAA
5493 GGTTTTGAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
13 7 0.18
14 23 0.59
15 9 0.23
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (13 bp):
AAAAATGATTTTC
Found at i:6460 original size:87 final size:86
Alignment explanation
Indices: 6308--6475 Score: 239
Period size: 87 Copynumber: 1.9 Consensus size: 86
6298 TGTTTGAAAC
* * * * *
6308 TTTCTTAAGATGAGAAACTGATCCAGAAATATCAATTGAGTTGGGAATATCAATTCGTGATCAAA
1 TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGAGAATATCAATGCATGAACAAA
6373 TTGGAAGAAGATTTGGGAAATA
66 TTGGAAGAAG-TTTGGGAAATA
* * *
6395 TTTCTTAAGAT-AGGAAGCTGATCCAGAACCATCAATTGAGTTGAGAATATCAATGCATTAACAA
1 TTTCTTAAGATGA-GAAACTGATCCAGAAACATCAATTGAGTTGAGAATATCAATGCATGAACAA
6459 ATTGGAAGAAGTTTGGG
65 ATTGGAAGAAGTTTGGG
6476 GCATCAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
86 7 0.10
87 65 0.90
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (86 bp):
TTTCTTAAGATGAGAAACTGATCCAGAAACATCAATTGAGTTGAGAATATCAATGCATGAACAAA
TTGGAAGAAGTTTGGGAAATA
Found at i:7263 original size:37 final size:37
Alignment explanation
Indices: 7204--7799 Score: 368
Period size: 37 Copynumber: 15.7 Consensus size: 37
7194 CAGTCTCATC
*
7204 AAAAT-CTTGTTCAAGATTCCTGTTTAGGTTTCTTAT
1 AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
* * * * *
7240 TAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCAT
1 AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
7277 CAAAAT-CTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
1 -AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
* * * *
7314 AAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCAT
1 AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
*
7351 CAAAAT-CTTGTTTAAGATTCCTGCTTAGGTTTCTTAT
1 -AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
* * * * *
7388 AAAATCTTTGTTTAAGGTCCCTGTTTAGGTATCTCAT
1 AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
*
7425 CAAAAT-CTTGTTTAAGATTCCTGTTTAAGTTTCTTAT
1 -AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
* * * * * *
7462 AAAATCCTTGTTTCATCAAAATCTTGTTTAAGATTCCTGTTT
1 AAAATCCTTGTTT-A--AGATTCCTGTTT-AGGTTTCT-TAT
*** * * ** * * *
7504 AGGTTTCTTATCAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCAT
1 AAAATCCTTGTTTAA-----G----A-TT-CCTGTTTAGGTTTCTTAT
* **
7552 CAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
1 AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
* * * * *
7589 TAAATCCTTGTTTATGGTCCCTGTTTAGGTGTC--AT
1 AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
* * *
7624 CAAAAT-CTTGTTCAAGATTCCTATTTAGCTTTCTTAT
1 -AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
* * * * *
7661 AAAAATCCTTGTTTAAGGTACCTGTTTAGGTGTGTCAT
1 -AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
* * *
7699 CAAAA-CCTTGTTCAAGATGCATGTTTAGGTTTCTTAT
1 -AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
* * * * *
7736 CAAATCCTTATTTAA-AGTCCCTGTTTAGGTGTCTCAT
1 AAAATCCTTGTTTAAGA-TTCCTGTTTAGGTTTCTTAT
*
7773 CAAAAT-CTTGTTTATG-TTCCCTGTTTA
1 -AAAATCCTTGTTTAAGATT-CCTGTTTA
7800 AGTGTTCAAA
Statistics
Matches: 420, Mismatches: 108, Indels: 63
0.71 0.18 0.11
Matches are distributed among these distances:
35 22 0.05
36 28 0.07
37 276 0.66
38 47 0.11
39 2 0.00
40 9 0.02
41 6 0.01
42 8 0.02
43 1 0.00
48 9 0.02
49 6 0.01
50 6 0.01
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.45
Consensus pattern (37 bp):
AAAATCCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT
Found at i:7288 original size:74 final size:74
Alignment explanation
Indices: 7196--7474 Score: 504
Period size: 74 Copynumber: 3.8 Consensus size: 74
7186 AAAAAATTCA
* *
7196 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCC
7261 TGTTTAGGT
66 TGTTTAGGT
7270 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCC
7335 TGTTTAGGT
66 TGTTTAGGT
* *
7344 GTCTCATCAAAATCTTGTTTAAGATTCCTGCTTAGGTTTCTTATAAAATCTTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCC
7409 TGTTTAGGT
66 TGTTTAGGT
* *
7418 ATCTCATCAAAATCTTGTTTAAGATTCCTGTTTAAGTTTCTTATAAAATCCTTGTTT
1 GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATAAAATCCTTGTTT
7475 CATCAAAATC
Statistics
Matches: 197, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 197 1.00
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (74 bp):
GTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCC
TGTTTAGGT
Found at i:7481 original size:53 final size:53
Alignment explanation
Indices: 7421--7527 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
7411 TTTAGGTATC
7421 TCATCAAAATCTTGTTTAAGATTCCTGTTTAAGTTTCTTATAAAATCCTTGTT
1 TCATCAAAATCTTGTTTAAGATTCCTGTTTAAGTTTCTTATAAAATCCTTGTT
* *
7474 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTT
1 TCATCAAAATCTTGTTTAAGATTCCTGTTTAAGTTTCTTATAAAATCCTTGTT
7527 T
1 T
7528 AAGGTCCCTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (53 bp):
TCATCAAAATCTTGTTTAAGATTCCTGTTTAAGTTTCTTATAAAATCCTTGTT
Found at i:7509 original size:127 final size:127
Alignment explanation
Indices: 7347--7601 Score: 456
Period size: 127 Copynumber: 2.0 Consensus size: 127
7337 TTTAGGTGTC
*
7347 TCATCAAAATCTTGTTTAAGATTCCTGCTTAGGTTTCTTATAAAATCTTTGTTTAAGGTCCCTGT
1 TCATCAAAATCTTGTTTAAGATTCCTGCTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCCTGT
7412 TTAGGTATCTCATCAAAATCTTGTTTAAGATTCCTGTTTAAGTTTCTTATAAAATCCTTGTT
66 TTAGGTATCTCATCAAAATCTTGTTTAAGATTCCTGTTTAAGTTTCTTATAAAATCCTTGTT
* *
7474 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCCTGT
1 TCATCAAAATCTTGTTTAAGATTCCTGCTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCCTGT
* * *
7539 TTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTT
66 TTAGGTATCTCATCAAAATCTTGTTTAAGATTCCTGTTTAAGTTTCTTATAAAATCCTTGTT
7601 T
1 T
7602 ATGGTCCCTG
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 122 1.00
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.46
Consensus pattern (127 bp):
TCATCAAAATCTTGTTTAAGATTCCTGCTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCCTGT
TTAGGTATCTCATCAAAATCTTGTTTAAGATTCCTGTTTAAGTTTCTTATAAAATCCTTGTT
Found at i:7517 original size:90 final size:91
Alignment explanation
Indices: 7388--7564 Score: 234
Period size: 90 Copynumber: 2.0 Consensus size: 91
7378 GGTTTCTTAT
* *
7388 AAAATCTTTGTTTAAGGTCCCTGTTTAGGTATCTCATCAAAAT-CTTGTTTAAGATTCCTGTTTA
1 AAAATCTTTGTTTAAGATCCCTGTTTAGGTATCTCATC-AAATCCTTGTTTAAGATCCCTGTTTA
* *
7452 AGTTTCTTAT-AAAATCCTTGTTTCATC
65 AGTGTCTCATCAAAAT-CTTGTTTCATC
* * * * *
7479 AAAATC-TTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCCTGTTTAG
1 AAAATCTTTGTTTAAGATCCCTGTTTAGGTATCTCATCAAATCCTTGTTTAAGATCCCTGTTTAA
7543 GTGTCTCATCAAAATCTTGTTT
66 GTGTCTCATCAAAATCTTGTTT
7565 AAGATTCCTG
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
89 4 0.05
90 60 0.80
91 11 0.15
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (91 bp):
AAAATCTTTGTTTAAGATCCCTGTTTAGGTATCTCATCAAATCCTTGTTTAAGATCCCTGTTTAA
GTGTCTCATCAAAATCTTGTTTCATC
Found at i:7561 original size:74 final size:74
Alignment explanation
Indices: 7474--7799 Score: 478
Period size: 74 Copynumber: 4.4 Consensus size: 74
7464 AATCCTTGTT
7474 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCCTGT
1 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCCTGT
7539 TTAGGTGTC
66 TTAGGTGTC
* *
7548 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTATGGTCCCTGT
1 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCCTGT
7613 TTAGGTG--
66 TTAGGTGTC
* * * * *
7620 TCATCAAAATCTTGTTCAAGATTCCTATTTAGCTTTCTTATAAAAATCCTTGTTTAAGGTACCTG
1 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT-CAAATCCTTGTTTAAGGTCCCTG
*
7685 TTTAGGTGTG
65 TTTAGGTGTC
* * * * * *
7695 TCATCAAAACCTTGTTCAAGATGCATGTTTAGGTTTCTTATCAAATCCTTATTTAAAGTCCCTGT
1 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCCTGT
7760 TTAGGTGTC
66 TTAGGTGTC
*
7769 TCATCAAAATCTTGTTTATG-TTCCCTGTTTA
1 TCATCAAAATCTTGTTTAAGATT-CCTGTTTA
7800 AGTGTTCAAA
Statistics
Matches: 225, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
72 38 0.17
73 29 0.13
74 122 0.54
75 36 0.16
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (74 bp):
TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCCTGT
TTAGGTGTC
Found at i:7618 original size:201 final size:200
Alignment explanation
Indices: 7273--7674 Score: 691
Period size: 201 Copynumber: 2.0 Consensus size: 200
7263 TTTAGGTGTC
7273 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCCTGT
1 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCCTGT
*
7338 TTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGCTTAGGTTTCTTATAAAATCTTTGTTTAA
66 TTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGCTTAGGTTTCTTATAAAATCCTTGTTTAA
* *
7403 GGTCCCTGTTTAGGTATCTCATCAAAATCTTGTTTAAGATTCCTGTTTAAG-TTTCTTAT-AAAA
131 GGTCCCTGTTTAGG--TCTCATCAAAATCTTGTTCAAGATTCCTATTT-AGCTTTCTTATAAAAA
7466 TCCTTGTT
193 TCCTTGTT
*
7474 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCCTGT
1 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCCTGT
* * *
7539 TTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAT
66 TTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGCTTAGGTTTCTTATAAAATCCTTGTTTAA
*
7604 GGTCCCTGTTTAGGTGTCATCAAAATCTTGTTCAAGATTCCTATTTAGCTTTCTTATAAAAATCC
131 GGTCCCTGTTTAGGTCTCATCAAAATCTTGTTCAAGATTCCTATTTAGCTTTCTTATAAAAATCC
7669 TTGTT
196 TTGTT
7674 T
1 T
7675 AAGGTACCTG
Statistics
Matches: 191, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
198 2 0.01
199 37 0.19
200 13 0.07
201 139 0.73
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (200 bp):
TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATAAAATCCTTGTTTAAGGTCCCTGT
TTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGCTTAGGTTTCTTATAAAATCCTTGTTTAA
GGTCCCTGTTTAGGTCTCATCAAAATCTTGTTCAAGATTCCTATTTAGCTTTCTTATAAAAATCC
TTGTT
Found at i:7741 original size:147 final size:147
Alignment explanation
Indices: 7474--7784 Score: 471
Period size: 147 Copynumber: 2.1 Consensus size: 147
7464 AATCCTTGTT
* * * * *
7474 TCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTGTTTAAGGTCCCTGT
1 TCATCAAAATCTTGTTCAAGATTCCTATTTAGCTTTCTTATAAAATCCTTGTTTAAGGTACCTGT
* * * * * * *
7539 TTAGGTGTCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAT
66 TTAGGTGTCTCATCAAAACCTTGTTCAAGATGCATGTTTAGGTTTCTTATCAAATCCTTATTTAA
*
7604 GGTCCCTGTTTAGGTG-
131 AGTCCCTGTTTAGGTGC
7620 TCATCAAAATCTTGTTCAAGATTCCTATTTAGCTTTCTTATAAAAATCCTTGTTTAAGGTACCTG
1 TCATCAAAATCTTGTTCAAGATTCCTATTTAGCTTTCTTAT-AAAATCCTTGTTTAAGGTACCTG
*
7685 TTTAGGTGTGTCATCAAAACCTTGTTCAAGATGCATGTTTAGGTTTCTTATCAAATCCTTATTTA
65 TTTAGGTGTCTCATCAAAACCTTGTTCAAGATGCATGTTTAGGTTTCTTATCAAATCCTTATTTA
7750 AAGTCCCTGTTTAGGTGTC
130 AAGTCCCTGTTTAGGTG-C
7769 TCATCAAAATCTTGTT
1 TCATCAAAATCTTGTT
7785 TATGTTCCCT
Statistics
Matches: 148, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
146 38 0.26
147 94 0.64
149 16 0.11
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (147 bp):
TCATCAAAATCTTGTTCAAGATTCCTATTTAGCTTTCTTATAAAATCCTTGTTTAAGGTACCTGT
TTAGGTGTCTCATCAAAACCTTGTTCAAGATGCATGTTTAGGTTTCTTATCAAATCCTTATTTAA
AGTCCCTGTTTAGGTGC
Found at i:8011 original size:42 final size:43
Alignment explanation
Indices: 7952--8067 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 43
7942 ATTTCTTGGC
* * *
7952 TCAAAAATCAAATTTCAAAACCTGCA-TTC-A-TTGTTTATTCT
1 TCAAAAATCAAAATTCAAAACATGCATTTCAACAT-TTTATTCT
7993 TCAAAAAATCAAAATTCAAAACATGCATTTCAACATTTTATTCT
1 TC-AAAAATCAAAATTCAAAACATGCATTTCAACATTTTATTCT
* * **
8037 TCGAAAATCAAAGTTCAAAATTTGCATTTCA
1 TCAAAAATCAAAATTCAAAACATGCATTTCA
8068 TTATTCAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
41 2 0.03
42 22 0.34
43 28 0.44
44 11 0.17
45 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.35
Consensus pattern (43 bp):
TCAAAAATCAAAATTCAAAACATGCATTTCAACATTTTATTCT
Found at i:8065 original size:35 final size:35
Alignment explanation
Indices: 8026--8240 Score: 101
Period size: 35 Copynumber: 5.9 Consensus size: 35
8016 TGCATTTCAA
* * * **
8026 CATTTTATTCTTCGAAAATCAAAGTTCAAAATTTG
1 CATTTCATTATTCAAAAATCAAAAATCAAAATTTG
**
8061 CATTTCATTATTCAAAAATCAAAAATCAAAATCAG
1 CATTTCATTATTCAAAAATCAAAAATCAAAATTTG
* ** * * *** *
8096 CATCTCATGGTTCAAAATTC-AAAACCTGCA-TTA
1 CATTTCATTATTCAAAAATCAAAAATCAAAATTTG
* * * *
8129 CACGGTTCATTATTCAAAAGTCAAAATTCAAAACTTG
1 CA--TTTCATTATTCAAAAATCAAAAATCAAAATTTG
* **
8166 CATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTG
1 CATTT---CA-T-TA---TTCAAAAATCAAAAATCAAAATTTG
**
8209 CATTTCATTATTCAAAAATCAAAGTTCAAAAT
1 CATTTCATTATTCAAAAATCAAAAATCAAAAT
8241 CAGAATCTCA
Statistics
Matches: 133, Mismatches: 35, Indels: 24
0.69 0.18 0.12
Matches are distributed among these distances:
33 2 0.02
34 6 0.05
35 80 0.60
36 5 0.04
37 4 0.03
38 4 0.03
39 2 0.02
40 4 0.03
43 26 0.20
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.33
Consensus pattern (35 bp):
CATTTCATTATTCAAAAATCAAAAATCAAAATTTG
Found at i:8117 original size:148 final size:147
Alignment explanation
Indices: 7959--8409 Score: 626
Period size: 148 Copynumber: 3.1 Consensus size: 147
7949 GGCTCAAAAA
* ** * * *
7959 TCAAATTTCAAAACCTGCATTCATTGTTTATTCTTCAAAAAATCAAAATTCAAAACATGCATTTC
1 TCAAAATTCAAAACCTGCATTCACGGTTCATTCTTC-AAAAGTCAAAATTCAAAACTTGCATTTC
**
8024 AACATTTTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATCAAAAATCA
65 AACATTTTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATCAAAGTTCA
8089 AAATCAGCATCTCATGGT
130 AAATCAGCATCTCATGGT
*
8107 TCAAAATTCAAAACCTGCATTACACGGTTCATTATTCAAAAGTCAAAATTCAAAACTTGCATTTC
1 TCAAAATTCAAAACCTGCATT-CACGGTTCATTCTTCAAAAGTCAAAATTCAAAACTTGCATTTC
* *
8172 AGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATCAAAGTTCA
65 AACATTTTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATCAAAGTTCA
*
8237 AAATCAGAATCTCATGGT
130 AAATCAGCATCTCATGGT
8255 TCAAAATTCAAAACCTGCATTTCACGGTTCATTCTTCAAAAGTCAAAATTCAAAACTTGCATTTC
1 TCAAAATTCAAAACCTGCA-TTCACGGTTCATTCTTCAAAAGTCAAAATTCAAAACTTGCATTTC
* * ** * * * * *
8320 -A-GTATTCCT-TTCGAAAATTAAAATTCAAAATTTGCATTTCA-T-TTCAAAATTCAATGTTGA
65 AACATTTTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATCAAAGTTCA
*
8380 AAATCTGCATCTCAT-GT
130 AAATCAGCATCTCATGGT
*
8397 TCAAAACTCAAAA
1 TCAAAATTCAAAA
8410 TCCAGCATCA
Statistics
Matches: 274, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
142 14 0.05
143 28 0.10
144 1 0.00
145 30 0.11
146 3 0.01
148 185 0.68
149 13 0.05
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (147 bp):
TCAAAATTCAAAACCTGCATTCACGGTTCATTCTTCAAAAGTCAAAATTCAAAACTTGCATTTCA
ACATTTTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTTCATTATTCAAAAATCAAAGTTCAA
AATCAGCATCTCATGGT
Found at i:8258 original size:35 final size:35
Alignment explanation
Indices: 8188--8266 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 35
8178 CTATTCTTCG
** * * *
8188 AAAATCAAAGTTCAAAATTTGCATTTCATTATTCA
1 AAAATCAAAGTTCAAAATCAGAATCTCATGATTCA
*
8223 AAAATCAAAGTTCAAAATCAGAATCTCATGGTTCA
1 AAAATCAAAGTTCAAAATCAGAATCTCATGATTCA
*
8258 AAATTCAAA
1 AAAATCAAA
8267 ACCTGCATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (35 bp):
AAAATCAAAGTTCAAAATCAGAATCTCATGATTCA
Done.