Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016077.1 Corchorus capsularis cultivar CVL-1 contig16098, 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: 30541
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Found at i:1329 original size:32 final size:33
Alignment explanation
Indices: 1268--1332 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1258 AAAGCACAAG
*
1268 TAATGTAAAATAGGAACCCAATCGCACAACCAT
1 TAATGTAAAATAGAAACCCAATCGCACAACCAT
1301 TAATGTAAAATAGAAACCC-ATCGCACAACCAT
1 TAATGTAAAATAGAAACCCAATCGCACAACCAT
1333 ACTATGAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.46, C:0.25, G:0.11, T:0.18
Consensus pattern (33 bp):
TAATGTAAAATAGAAACCCAATCGCACAACCAT
Found at i:4329 original size:27 final size:27
Alignment explanation
Indices: 4299--4369 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
4289 AGGGAACTTA
*
4299 AAATGACCAAAATGCCCCTAAATGTAC
1 AAATGACCAAAATGCCCATAAATGTAC
** *
4326 AAATGACCAAAATGCCCATGCATGTGC
1 AAATGACCAAAATGCCCATAAATGTAC
4353 AAATGACCAAAATGCCC
1 AAATGACCAAAATGCCC
4370 TTGGGTGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCATAAATGTAC
Found at i:4849 original size:12 final size:12
Alignment explanation
Indices: 4832--4856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4822 GATTTGGAAA
4832 TGAAACAAAATT
1 TGAAACAAAATT
4844 TGAAACAAAATT
1 TGAAACAAAATT
4856 T
1 T
4857 AGAATTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (12 bp):
TGAAACAAAATT
Found at i:4851 original size:77 final size:76
Alignment explanation
Indices: 4767--5176 Score: 421
Period size: 64 Copynumber: 6.0 Consensus size: 76
4757 GATTTGAAAA
4767 TGAAACAAAACTTAGAATTGAAACAAGAAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
1 TGAAACAAAACTTAGAATTGAAACAAG-AAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
4832 TGAAACAAAATT
65 TGAAACAAAATT
* *
4844 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTTGATTAGGATTTGGAAAT
1 TGAAACAAAACTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
4909 GAAACAAAA--
66 GAAACAAAATT
* *
4918 T----------TTAGAATTGAAACAAGAAACCCTCTATTAGAGACCTCGATTAAGATTTGGAAAT
1 TGAAACAAAACTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
4973 GAAACAAAA--
66 GAAACAAAATT
4982 T----------TTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
1 TGAAACAAAACTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
5037 GAAACAAAA--
66 GAAACAAAATT
5046 T----------TTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
1 TGAAACAAAACTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
5101 GAAACAAAA--
66 GAAACAAAATT
* *
5110 T----------TTAGAATTGAAGCAAGAAACCCTCGACTAGAGACCTCGATTAGGATTTGGAAAT
1 TGAAACAAAACTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
5165 GAAACAAAATT
66 GAAACAAAATT
5176 T
1 T
5177 AGAATTAAAA
Statistics
Matches: 322, Mismatches: 9, Indels: 15
0.93 0.03 0.04
Matches are distributed among these distances:
64 248 0.77
66 1 0.00
74 1 0.00
76 46 0.14
77 26 0.08
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (76 bp):
TGAAACAAAACTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
GAAACAAAATT
Found at i:4918 original size:64 final size:64
Alignment explanation
Indices: 4844--5462 Score: 1051
Period size: 64 Copynumber: 9.6 Consensus size: 64
4834 AAACAAAATT
*
4844 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTTGATTAGGATTTGGAAA
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
* *
4908 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCTATTAGAGACCTCGATTAAGATTTGGAAA
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
4972 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
5036 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
* *
5100 TGAAACAAAATTTAGAATTGAAGCAAGAAACCCTCGACTAGAGACCTCGATTAGGATTTGGAAA
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
* * * *
5164 TGAAACAAAATTTAGAATTAAAACATGAAACCCTCAATTAGAGACCTCGATTAGGATTTCGAAA
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
* *
5228 TGAAACAAAATTTGGAATTGAAACAAGAAACCCTCGATTAGAGACCTCAATTAGGATTTGGAAA
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
* *
5292 TGAAAGAAAATTTAGAATT-AAAGCAAGAAACCCTCGACTAGAGACCTCGATTAGGATTTGGAAA
1 TGAAACAAAATTTAGAATTGAAA-CAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
* * *
5356 TGAAACAAAATTTAGAATTGAAACATGAAATCCTCAATTAGAGACCTCGATTAGGATTTGGAAA
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
*
5420 TGTAACAAAATTTTAGAATTTGAAACAAGAAACCCTCGATTAG
1 TGAAACAAAA-TTTAGAA-TTGAAACAAGAAACCCTCGATTAG
5463 GATTTGGAAA
Statistics
Matches: 519, Mismatches: 32, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
63 3 0.01
64 485 0.93
65 10 0.02
66 21 0.04
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (64 bp):
TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
Found at i:4995 original size:128 final size:128
Alignment explanation
Indices: 4844--5722 Score: 1326
Period size: 128 Copynumber: 7.0 Consensus size: 128
4834 AAACAAAATT
*
4844 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTTGATTAGGATTTGGAAAT
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
* *
4909 GAAACAAAATTTAGAATTGAAACAAGAAACCCTCTATTAGAGACCTCGATTAAGATTTGGAAA
66 GAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
4972 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
5037 GAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
66 GAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
* *
5100 TGAAACAAAATTTAGAATTGAAGCAAGAAACCCTCGACTAGAGACCTCGATTAGGATTTGGAAAT
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
* * * *
5165 GAAACAAAATTTAGAATTAAAACATGAAACCCTCAATTAGAGACCTCGATTAGGATTTCGAAA
66 GAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
* *
5228 TGAAACAAAATTTGGAATTGAAACAAGAAACCCTCGATTAGAGACCTCAATTAGGATTTGGAAAT
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
* *
5293 GAAAGAAAATTTAGAATT-AAAGCAAGAAACCCTCGACTAGAGACCTCGATTAGGATTTGGAAA
66 GAAACAAAATTTAGAATTGAAA-CAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
* * *
5356 TGAAACAAAATTTAGAATTGAAACATGAAATCCTCAATTAGAGACCTCGATTAGGATTTGGAAAT
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
*
5421 GTAACAAAATTTTAGAATTTGAAACAAGAAA----C---------CCTCGATTAGGATTTGGAAA
66 GAAACAAAA-TTTAGAA-TTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
5473 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTC--------A-----ATTAGGATTTGGAAAT
1 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
5525 GAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
66 GAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
*
5588 TGAAACAAAATTTTAGAATTGAAACAAGAAACCCTTGATTAGAGACCTCGATTAGGATTTGGAAA
1 TGAAACAAAA-TTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
* ** * *
5653 TGAAACAAAATTTAGAATTGAAGCAAGAAATTCTCGACTAGAGACCTCGATTAGGATTTGGAAT
65 TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
5717 TGAAAC
1 TGAAAC
5723 TAGTCTTTGG
Statistics
Matches: 686, Mismatches: 34, Indels: 61
0.88 0.04 0.08
Matches are distributed among these distances:
102 13 0.02
103 7 0.01
104 24 0.03
106 1 0.00
109 1 0.00
115 30 0.04
116 24 0.03
117 53 0.08
124 1 0.00
126 1 0.00
127 3 0.00
128 429 0.63
129 87 0.13
130 9 0.01
131 3 0.00
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (128 bp):
TGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAAT
GAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAA
Found at i:5010 original size:51 final size:57
Alignment explanation
Indices: 4969--5697 Score: 602
Period size: 64 Copynumber: 11.8 Consensus size: 57
4959 TAAGATTTGG
4969 AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTT
1 AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA-CT--ATTAGGA--T
5031 GGAAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTT
1 --AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA-CT--ATTAGGA--T
* *
5095 GGAAATGAAACAAAATTTAGAATTGAAGCAAGAAACCCTCGACTAGAGACCTCGATTAGGATTT
1 --AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA-CT--ATTAGGA--T
* * *
5159 GGAAATGAAACAAAATTTAGAATTAAAACATGAAACCCTCAATTAGAGACCTCGATTAGGATTT
1 --AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA-CT--ATTAGGA--T
*
5223 CGAAATGAAACAAAATTTGGAATTGAAACAAGAAACCCTCGATTAGAGACCTCAATTAGGATTT
1 --AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA-CT--ATTAGGA--T
* *
5287 GGAAATGAAAGAAAATTTAGAATT-AAAGCAAGAAACCCTCGACTAGAGACCTCGATTAGGATTT
1 --AAATGAAACAAAATTTAGAATTGAAA-CAAGAAACCCTCGATTAGAGA-CT--ATTAGGA--T
* * *
5351 GGAAATGAAACAAAATTTAGAATTGAAACATGAAATCCTCAATTAGAGACCTCGATTAGGATTT
1 --AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA-CT--ATTAGGA--T
*
5415 GGAAATGTAACAAAATTTTAGAATTTGAAACAAGAAACCCTCGATTAG-GA-T-TT-GG--
1 --AAATGAAACAAAA-TTTAGAA-TTGAAACAAGAAACCCTCGATTAGAGACTATTAGGAT
*
5470 AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCAATTAG-GA-T-TT-GG--
1 AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACTATTAGGAT
5521 AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTT
1 AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA-CT--ATTAGGA--T
*
5583 GGAAATGAAACAAAATTTTAGAATTGAAACAAGAAACCCTTGATTAGAGACCTCGATTAGGATTT
1 --AAATGAAACAAAA-TTTAGAATTGAAACAAGAAACCCTCGATTAGAGA-CT--ATTAGGA--T
* ** *
5648 GGAAATGAAACAAAATTTAGAATTGAAGCAAGAAATTCTCGACTAGAGAC
1 --AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGAC
5698 CTCGATTAGG
Statistics
Matches: 611, Mismatches: 36, Indels: 37
0.89 0.05 0.05
Matches are distributed among these distances:
51 73 0.12
52 9 0.01
53 12 0.02
54 1 0.00
57 2 0.00
58 2 0.00
59 2 0.00
60 2 0.00
63 5 0.01
64 407 0.67
65 75 0.12
66 21 0.03
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (57 bp):
AAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACTATTAGGAT
Found at i:5055 original size:192 final size:192
Alignment explanation
Indices: 4733--5722 Score: 1431
Period size: 192 Copynumber: 5.2 Consensus size: 192
4723 TGATTTGAAG
* *
4733 CCCTCGACTAGAGACCTCGATTAGGATTTGAAAATGAAACAAAACTTAGAATTGAAACAAGAAAA
1 CCCTCGACTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAG-AAA
4798 CCCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTGAAACAAAATTTAGAATT
65 CCCTCGATTAGAGACCTCGATTAGGATTT-G----G-----AAA--TGAAACAAAATTTAGAATT
*
4863 GAAACAAGAAACCCTCGATTAGAGACCTTGATTAGGATTTGGAAATGAAACAAAATTTAGAATTG
118 GAAACAAGAAACCCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTG
4928 AAACAAGAAA
183 AAACAAGAAA
* * *
4938 CCCTCTATTAGAGACCTCGATTAAGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
1 CCCTCGACTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
5003 CCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACC
66 CCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACC
*
5068 CTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAGCAAGAAA
131 CTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAA
* *
5130 CCCTCGACTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTAAAACATGAAAC
1 CCCTCGACTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
* * *
5195 CCTCAATTAGAGACCTCGATTAGGATTTCGAAATGAAACAAAATTTGGAATTGAAACAAGAAACC
66 CCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACC
* *
5260 CTCGATTAGAGACCTCAATTAGGATTTGGAAATGAAAGAAAATTTAGAATT-AAAGCAAGAAA
131 CTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAA-CAAGAAA
* *
5322 CCCTCGACTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACATGAAAT
1 CCCTCGACTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
* *
5387 CCTCAATTAGAGACCTCGATTAGGATTTGGAAATGTAACAAAATTTTAGAATTTGAAACAAGAAA
66 CCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAA-TTTAGAA-TTGAAACAAGAAA
5452 ----C---------CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAA
129 CCCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAA
5503 CCCT---C-----A-----ATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
1 CCCTCGACTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
5555 CCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTTAGAATTGAAACAAGAAAC
66 CCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAA-TTTAGAATTGAAACAAGAAAC
* *
5620 CCTTGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAGCAAGAAA
130 CCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAA
** *
5683 TTCTCGACTAGAGACCTCGATTAGGATTTGGAATTGAAAC
1 CCCTCGACTAGAGACCTCGATTAGGATTTGGAAATGAAAC
5723 TAGTCTTTGG
Statistics
Matches: 721, Mismatches: 34, Indels: 72
0.87 0.04 0.09
Matches are distributed among these distances:
167 13 0.02
168 93 0.13
173 1 0.00
178 1 0.00
180 51 0.07
181 48 0.07
182 3 0.00
183 1 0.00
188 1 0.00
190 1 0.00
191 2 0.00
192 374 0.52
193 26 0.04
194 16 0.02
199 1 0.00
203 1 0.00
204 32 0.04
205 56 0.08
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (192 bp):
CCCTCGACTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
CCTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACC
CTCGATTAGAGACCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAA
Found at i:5467 original size:27 final size:27
Alignment explanation
Indices: 5432--5519 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 27
5422 TAACAAAATT
* *
5432 TTAGAATTTGAAACAAGAAACCCTCGA
1 TTAGGATTTGAAACAAGAAACCCTCAA
* * **
5459 TTAGGATTTGGAA-ATGAAA--CAAAA
1 TTAGGATTTGAAACAAGAAACCCTCAA
*
5483 TTTA-GAATTGAAACAAGAAACCCTCAA
1 -TTAGGATTTGAAACAAGAAACCCTCAA
5510 TTAGGATTTG
1 TTAGGATTTG
5520 GAAATGAAAC
Statistics
Matches: 44, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
24 9 0.20
25 8 0.18
26 8 0.18
27 19 0.43
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (27 bp):
TTAGGATTTGAAACAAGAAACCCTCAA
Found at i:5480 original size:53 final size:51
Alignment explanation
Indices: 5400--5564 Score: 294
Period size: 51 Copynumber: 3.2 Consensus size: 51
5390 CAATTAGAGA
*
5400 CCTCGATTAGGATTTGGAAATGTAACAAAATTTTAGAATTTGAAACAAGAAAC
1 CCTCGATTAGGATTTGGAAATGAAACAAAA-TTTAGAA-TTGAAACAAGAAAC
5453 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
*
5504 CCTCAATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
5555 CCTCGATTAG
1 CCTCGATTAG
5565 AGACCTCGAT
Statistics
Matches: 109, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
51 73 0.67
52 7 0.06
53 29 0.27
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (51 bp):
CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAAC
Found at i:5502 original size:25 final size:25
Alignment explanation
Indices: 5474--5554 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
5464 ATTTGGAAAT
5474 GAAACAAAATTTAGAATTGAAACAA
1 GAAACAAAATTTAGAATTGAAACAA
** * * *
5499 GAAACCCTCAA-TTAGGATTTGGAA-AT
1 GAAA--CAAAATTTA-GAATTGAAACAA
5525 GAAACAAAATTTAGAATTGAAACAA
1 GAAACAAAATTTAGAATTGAAACAA
5550 GAAAC
1 GAAAC
5555 CCTCGATTAG
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
24 10 0.24
25 13 0.32
26 8 0.20
27 10 0.24
ACGTcount: A:0.53, C:0.11, G:0.15, T:0.21
Consensus pattern (25 bp):
GAAACAAAATTTAGAATTGAAACAA
Found at i:5528 original size:26 final size:26
Alignment explanation
Indices: 5448--5529 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
5438 TTTGAAACAA
*
5448 GAAACCCTCGATTAGGATTTGGAAAT
1 GAAACCCTCAATTAGGATTTGGAAAT
** * * *
5474 GAAA--CAAAATTTA-GAATTGAAACAA
1 GAAACCCTCAA-TTAGGATTTGGAA-AT
5499 GAAACCCTCAATTAGGATTTGGAAAT
1 GAAACCCTCAATTAGGATTTGGAAAT
5525 GAAAC
1 GAAAC
5530 AAAATTTAGA
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
24 9 0.22
25 8 0.20
26 13 0.32
27 10 0.25
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.23
Consensus pattern (26 bp):
GAAACCCTCAATTAGGATTTGGAAAT
Found at i:5628 original size:65 final size:64
Alignment explanation
Indices: 5504--5722 Score: 366
Period size: 64 Copynumber: 3.4 Consensus size: 64
5494 AACAAGAAAC
*
5504 CCTCAATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
*
5568 CCTCGATTAGGATTTGGAAATGAAACAAAATTTTAGAATTGAAACAAGAAACCCTTGATTAGAGA
1 CCTCGATTAGGATTTGGAAATGAAACAAAA-TTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
* ** *
5633 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAGCAAGAAATTCTCGACTAGAGA
1 CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
*
5697 CCTCGATTAGGATTTGGAATTGAAAC
1 CCTCGATTAGGATTTGGAAATGAAAC
5723 TAGTCTTTGG
Statistics
Matches: 146, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
64 83 0.57
65 63 0.43
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (64 bp):
CCTCGATTAGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGA
Found at i:5787 original size:129 final size:125
Alignment explanation
Indices: 5512--5782 Score: 298
Period size: 129 Copynumber: 2.2 Consensus size: 125
5502 ACCCTCAATT
* * *
5512 AGGATTTGGAAATGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGATTAGAGACCTCGATTA
1 AGGATTTGAAAAAGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGACTAGAGACCTCGATTA
* * * **
5577 GGATTTGGAAATGAAACAAAATTTTAGAATTGAAACAAGAAACCCTTGATTAGAGACCTCGATT
66 GGATTTGGAAATGAAACAAAATTTTAGAATTG----AAGAAACCCTCGACTAGAGACCTCAAGC
* * * **
5641 AGGATTTGGAAATGAAACAAAATTTAGAATTGAAGCAAGAAATTCTCGACTAGAGACCTCGATTA
1 AGGATTTGAAAAAGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGACTAGAGACCTCGATTA
* * * * *
5706 GGATTTGGAATTGAAAC-TAGTCTTTGGAATTG-A-AAACTCTCGACTAGAGACCTCAAGC
66 GGATTTGGAAATGAAACAAAAT-TTTAGAATTGAAGAAACCCTCGACTAGAGACCTCAAGC
*
5764 AGGATTT-AAAATGAAACAA
1 AGGATTTGAAAAAGAAACAA
5783 GAAACTCTCG
Statistics
Matches: 126, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
122 11 0.09
123 26 0.21
124 1 0.01
128 2 0.02
129 86 0.68
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (125 bp):
AGGATTTGAAAAAGAAACAAAATTTAGAATTGAAACAAGAAACCCTCGACTAGAGACCTCGATTA
GGATTTGGAAATGAAACAAAATTTTAGAATTGAAGAAACCCTCGACTAGAGACCTCAAGC
Found at i:5884 original size:63 final size:63
Alignment explanation
Indices: 5772--5893 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
5762 GCAGGATTTA
** * ** **
5772 AAATGAAACAAGAAACTCTCGATTAGAGACCTCGATTAGAATTTGAAAAGAACAAGATTCTGG
1 AAATGAAACAAGAAACTCTCGACCAGAGACCTCAAGCAGAATTCAAAAAGAACAAGATTCTGG
*
5835 AAATGAAACAAGAAACTCTCGACCAGAGACCTCAAGCAGGATTCAAAAAGAACAAGATT
1 AAATGAAACAAGAAACTCTCGACCAGAGACCTCAAGCAGAATTCAAAAAGAACAAGATT
5894 TAGAATTGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.18
Consensus pattern (63 bp):
AAATGAAACAAGAAACTCTCGACCAGAGACCTCAAGCAGAATTCAAAAAGAACAAGATTCTGG
Found at i:6937 original size:12 final size:12
Alignment explanation
Indices: 6916--6949 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6906 GGCCAAGTTG
*
6916 TTTTTGTTTTGT
1 TTTTTGTTTTCT
*
6928 TTTTTCTTTTCT
1 TTTTTGTTTTCT
6940 TTTTTGTTTT
1 TTTTTGTTTT
6950 TTTCTTCCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (12 bp):
TTTTTGTTTTCT
Found at i:16069 original size:69 final size:70
Alignment explanation
Indices: 15951--16105 Score: 222
Period size: 69 Copynumber: 2.2 Consensus size: 70
15941 ATTTGTATCA
* * *
15951 CTTTTCTACAAGCCAAACTCGTTTCCATATGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCA-AT
1 CTTTTCTACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCATAT
16015 AGGGG
66 AGGGG
* ** *
16020 CTTTTCTACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTGTATCCAAGCATTT
1 CTTTTCTACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCATAT
16085 AGGGG
66 AGGGG
* *
16090 CTTTTCCATAAGTCAA
1 CTTTTCTACAAGTCAA
16106 GTTCAATGAG
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
69 56 0.74
70 20 0.26
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (70 bp):
CTTTTCTACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCATAT
AGGGG
Found at i:19615 original size:6 final size:6
Alignment explanation
Indices: 19599--19629 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
19589 CTAAGCAAAG
19599 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
19630 TGGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:22133 original size:27 final size:28
Alignment explanation
Indices: 22101--22154 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
22091 GTTTTGCCCC
22101 CTGAACTTCAATCTT-GGACATTTTGCA
1 CTGAACTTCAATCTTGGGACATTTTGCA
* * *
22128 CTGAACTTTAATTTTGGGACGTTTTGC
1 CTGAACTTCAATCTTGGGACATTTTGC
22155 CTCCTCAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (28 bp):
CTGAACTTCAATCTTGGGACATTTTGCA
Found at i:22409 original size:29 final size:30
Alignment explanation
Indices: 22350--22456 Score: 119
Period size: 29 Copynumber: 3.6 Consensus size: 30
22340 TGGAGCCGTT
* * *
22350 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCTCAAGATTG
*
22380 AAGTTCAGGGGGCAAAATGT-TCAAGATTG
1 AAGTTCAGGGGGCAAAACGTCTCAAGATTG
* * *
22409 AAGTTCGGGGGGCAAAACGTCTAAACG-TTAC
1 AAGTTCAGGGGGCAAAACGTCTCAA-GATT-G
22440 AAGTTCAGGGGGCAAAA
1 AAGTTCAGGGGGCAAAA
22457 TGGTTGTTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
29 25 0.38
30 23 0.35
31 17 0.26
ACGTcount: A:0.36, C:0.15, G:0.31, T:0.19
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCTCAAGATTG
Found at i:24403 original size:15 final size:15
Alignment explanation
Indices: 24383--24425 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
24373 TGTCTAAGTT
*
24383 GCTCATCTTCTTGTG
1 GCTCATCTTCTGGTG
24398 GCTCATCTTCTGGTG
1 GCTCATCTTCTGGTG
24413 GCTCATCTTCTGG
1 GCTCATCTTCTGG
24426 CTTAGCAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.07, C:0.28, G:0.23, T:0.42
Consensus pattern (15 bp):
GCTCATCTTCTGGTG
Found at i:25556 original size:19 final size:18
Alignment explanation
Indices: 25519--25567 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
25509 CTCTAACCCT
*
25519 AAATTTATTTTTTTTACGC
1 AAATTT-TTTTTTTGACGC
25538 AAATTTTTTTTTTCGACGC
1 AAATTTTTTTTTT-GACGC
25557 --ATTTTTTTTTT
1 AAATTTTTTTTTT
25568 AGAAAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 11 0.39
18 7 0.25
19 10 0.36
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.63
Consensus pattern (18 bp):
AAATTTTTTTTTTGACGC
Done.