Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009730.1 Corchorus capsularis cultivar CVL-1 contig09751, 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: 59021
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3741 original size:30 final size:29
Alignment explanation
Indices: 3705--3780 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
3695 TTTGACACCG
* *
3705 AGTGCAAACTCACACTCAAATACAATCCCA
1 AGTGCAAACCCACACTCAAAT-CAACCCCA
**
3735 AGTGCAAACCCACACTTGAATCAACCCCA
1 AGTGCAAACCCACACTCAAATCAACCCCA
*
3764 AGTGCACAACCCGCACT
1 AGTGCA-AACCCACACT
3781 TGTAAAAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 13 0.32
30 27 0.68
ACGTcount: A:0.38, C:0.37, G:0.11, T:0.14
Consensus pattern (29 bp):
AGTGCAAACCCACACTCAAATCAACCCCA
Found at i:6182 original size:20 final size:20
Alignment explanation
Indices: 6142--6183 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6132 TCTCACAAGA
* *
6142 TTCTAGCCGTTGGAGCTCTT
1 TTCTAGCCGTTAGAGCACTT
*
6162 TTCTAGCCGTTATAGCACTT
1 TTCTAGCCGTTAGAGCACTT
6182 TT
1 TT
6184 TCAACAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
TTCTAGCCGTTAGAGCACTT
Found at i:7466 original size:2 final size:2
Alignment explanation
Indices: 7459--7491 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7449 TATATCCAAC
7459 TA TA 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 TA TA T
7492 TCATAAGCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7733 original size:21 final size:20
Alignment explanation
Indices: 7703--7747 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
7693 AGAGTCCTAA
*
7703 ATTCAATTC-ATTACTCATAG
1 ATTCAATTCAAATACTCA-AG
7723 ATTCAAATTCAAATACTCAAG
1 ATTC-AATTCAAATACTCAAG
7744 ATTC
1 ATTC
7748 TCCAATAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 11 0.50
22 7 0.32
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (20 bp):
ATTCAATTCAAATACTCAAG
Found at i:11593 original size:20 final size:20
Alignment explanation
Indices: 11553--11594 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
11543 TCTCACAAGA
* *
11553 TTCTAGCCGTTGGAGCTCTT
1 TTCTAGCCGTTAGAGCACTT
*
11573 TTCTAGCCGTTATAGCACTT
1 TTCTAGCCGTTAGAGCACTT
11593 TT
1 TT
11595 TCAACAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
TTCTAGCCGTTAGAGCACTT
Found at i:12397 original size:6 final size:6
Alignment explanation
Indices: 12383--12415 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
12373 AAAGCAAAGC
*
12383 AAATAT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
12416 GCAGAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:13359 original size:10 final size:10
Alignment explanation
Indices: 13344--13369 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13334 GAGGACTCTA
13344 GAATTTTCTG
1 GAATTTTCTG
13354 GAATTTTCTG
1 GAATTTTCTG
13364 GAATTT
1 GAATTT
13370 GGCAGCAACT
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:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:16240 original size:18 final size:19
Alignment explanation
Indices: 16213--16248 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
16203 TAATTGATTG
*
16213 ATTTGGTTGA-TTTTTGTT
1 ATTTGATTGAGTTTTTGTT
16231 ATTTGATTGAGTTTTTGT
1 ATTTGATTGAGTTTTTGT
16249 GCAGCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.14, C:0.00, G:0.22, T:0.64
Consensus pattern (19 bp):
ATTTGATTGAGTTTTTGTT
Found at i:17046 original size:7 final size:7
Alignment explanation
Indices: 17031--17221 Score: 99
Period size: 7 Copynumber: 28.9 Consensus size: 7
17021 TTACTGATTG
17031 CTCTTTA
1 CTCTTTA
*
17038 CTTTTTA
1 CTCTTTA
17045 CTCTTTA
1 CTCTTTA
17052 CTCTTTA
1 CTCTTTA
17059 C-CATTT-
1 CTC-TTTA
*
17065 TTCTTTA
1 CTCTTTA
**
17072 CTGGTTA
1 CTCTTTA
17079 CTCTTT-
1 CTCTTTA
17085 -TCTTTA
1 CTCTTTA
17091 CTCTTTA
1 CTCTTTA
17098 CTCTTTA
1 CTCTTTA
17105 C-CATTT-
1 CTC-TTTA
*
17111 TTCTTTA
1 CTCTTTA
**
17118 CTGATTA
1 CTCTTTA
17125 CTCTTT-
1 CTCTTTA
17131 -TCTTTA
1 CTCTTTA
17137 CTCTTTA
1 CTCTTTA
17144 C-CATTT-
1 CTC-TTTA
17150 -TCTTTA
1 CTCTTTA
**
17156 CTGATTA
1 CTCTTTA
*
17163 CTCTTCA
1 CTCTTTA
*
17170 CTTTTTA
1 CTCTTTA
17177 C-CATTT-
1 CTC-TTTA
*
17183 -TACTTTG
1 CT-CTTTA
**
17190 CTGATTA
1 CTCTTTA
17197 CTCTTTA
1 CTCTTTA
17204 --CTTTA
1 CTCTTTA
17209 CTCTTTA
1 CTCTTTA
17216 CTCTTT
1 CTCTTT
17222 TCCATTTTCT
Statistics
Matches: 136, Mismatches: 27, Indels: 42
0.66 0.13 0.20
Matches are distributed among these distances:
5 18 0.13
6 13 0.10
7 104 0.76
8 1 0.01
ACGTcount: A:0.15, C:0.24, G:0.03, T:0.58
Consensus pattern (7 bp):
CTCTTTA
Found at i:17079 original size:27 final size:27
Alignment explanation
Indices: 17049--17130 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
17039 TTTTTACTCT
*
17049 TTACTCTTTACCATTTTTCTTTACTGG
1 TTACTCTTTACCATTTTTCTTTACTGA
**
17076 TTA--C--T--C--TTTTCTTTACTCT
1 TTACTCTTTACCATTTTTCTTTACTGA
17095 TTACTCTTTACCATTTTTCTTTACTGA
1 TTACTCTTTACCATTTTTCTTTACTGA
17122 TTACTCTTT
1 TTACTCTTT
17131 TCTTTACTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
19 14 0.33
21 2 0.05
23 2 0.05
25 2 0.05
27 23 0.53
ACGTcount: A:0.15, C:0.23, G:0.04, T:0.59
Consensus pattern (27 bp):
TTACTCTTTACCATTTTTCTTTACTGA
Found at i:17087 original size:19 final size:19
Alignment explanation
Indices: 17063--17167 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
17053 TCTTTACCAT
*
17063 TTTTCTTTACTGGTTACTC
1 TTTTCTTTACTGATTACTC
**
17082 TTTTCTTTACTCTTTACTC
1 TTTTCTTTACTGATTACTC
17101 TTTACCATTTTTCTTTACTGATTACTC
1 --T-----TTT-CTTTACTGATTACTC
**
17128 TTTTCTTTACTCTTTAC-C
1 TTTTCTTTACTGATTACTC
17146 ATTTTCTTTACTGATTACTC
1 -TTTTCTTTACTGATTACTC
17166 TT
1 TT
17168 CACTTTTTAC
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
18 1 0.01
19 45 0.66
20 4 0.06
21 1 0.01
25 1 0.01
26 3 0.04
27 13 0.19
ACGTcount: A:0.14, C:0.23, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTTCTTTACTGATTACTC
Found at i:17099 original size:46 final size:46
Alignment explanation
Indices: 17020--17144 Score: 205
Period size: 46 Copynumber: 2.7 Consensus size: 46
17010 TGATTACTAT
* *
17020 TTTACTGATTGCTCTTTACTTTTTACTCTTTACTCTTTACCATTTTTC
1 TTTACTGATTACTCTTT--TCTTTACTCTTTACTCTTTACCATTTTTC
*
17068 TTTACTGGTTACTCTTTTCTTTACTCTTTACTCTTTACCATTTTTC
1 TTTACTGATTACTCTTTTCTTTACTCTTTACTCTTTACCATTTTTC
17114 TTTACTGATTACTCTTTTCTTTACTCTTTAC
1 TTTACTGATTACTCTTTTCTTTACTCTTTAC
17145 CATTTTCTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
46 58 0.79
48 15 0.21
ACGTcount: A:0.14, C:0.23, G:0.04, T:0.58
Consensus pattern (46 bp):
TTTACTGATTACTCTTTTCTTTACTCTTTACTCTTTACCATTTTTC
Found at i:17173 original size:19 final size:19
Alignment explanation
Indices: 17109--17167 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
17099 TCTTTACCAT
17109 TTTTCTTTACTGATTACTC
1 TTTTCTTTACTGATTACTC
**
17128 TTTTCTTTACTCTTTAC-C
1 TTTTCTTTACTGATTACTC
17146 ATTTTCTTTACTGATTACTC
1 -TTTTCTTTACTGATTACTC
17166 TT
1 TT
17168 CACTTTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 32 0.94
20 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTCTTTACTGATTACTC
Found at i:17205 original size:19 final size:19
Alignment explanation
Indices: 17181--17221 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
17171 TTTTTACCAT
* *
17181 TTTACTTTGCTGATTACTC
1 TTTACTTTACTCATTACTC
*
17200 TTTACTTTACTCTTTACTC
1 TTTACTTTACTCATTACTC
17219 TTT
1 TTT
17222 TCCATTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.22, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTACTTTACTCATTACTC
Found at i:17281 original size:50 final size:45
Alignment explanation
Indices: 17151--17303 Score: 155
Period size: 46 Copynumber: 3.2 Consensus size: 45
17141 TTACCATTTT
* * * * *
17151 CTTTACTGATTACTCTTCACTTTTTACCATTTTACTTTGCTGATTACT
1 CTTTACT--TTACACTTTACTTTTT-CCATTTTTCTTTACTGATTACC
*
17199 CTTTACTTTACTCTTTACTCTTTTCCA-TTTTCTTTACTGATTACC
1 CTTTACTTTACACTTTACT-TTTTCCATTTTTCTTTACTGATTACC
*
17244 CTTTTACTTAATACACTTTTACTTTTTGGCATTTTTCTTTACTGATTACC
1 C-TTTACTT--TACAC-TTTACTTTTT-CCATTTTTCTTTACTGATTACC
17294 CTTTACTTTA
1 CTTTACTTTA
17304 TTTTTTACTG
Statistics
Matches: 92, Mismatches: 6, Indels: 15
0.81 0.05 0.13
Matches are distributed among these distances:
45 16 0.17
46 21 0.23
47 6 0.07
48 15 0.16
49 15 0.16
50 19 0.21
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.54
Consensus pattern (45 bp):
CTTTACTTTACACTTTACTTTTTCCATTTTTCTTTACTGATTACC
Found at i:17316 original size:26 final size:26
Alignment explanation
Indices: 17279--17338 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
17269 TTGGCATTTT
*
17279 TCTTTACTGATTACCCTTTACTTTAT
1 TCTTTACTGATTACCCTTTACTTTAC
* * *
17305 TTTTTACTGATTACTCTTTTCTTTAC
1 TCTTTACTGATTACCCTTTACTTTAC
17331 TCTTTACT
1 TCTTTACT
17339 CTTTTTTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.58
Consensus pattern (26 bp):
TCTTTACTGATTACCCTTTACTTTAC
Found at i:17318 original size:19 final size:18
Alignment explanation
Indices: 17296--17365 Score: 50
Period size: 19 Copynumber: 3.5 Consensus size: 18
17286 TGATTACCCT
17296 TTACTTTATTTTTTACTGA
1 TTACTTT-TTTTTTACTGA
* **
17315 TTACTCTTTTCTTTACTCT
1 TTACT-TTTTTTTTACTGA
17334 TTACTCTTTTTTTCTTTACTGA
1 TTA--C-TTTTTT-TTTACTGA
17356 TTACTCTTTT
1 TTACT-TTTT
17366 ACTTTTTACC
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
19 17 0.44
20 7 0.18
21 5 0.13
22 10 0.26
ACGTcount: A:0.14, C:0.19, G:0.03, T:0.64
Consensus pattern (18 bp):
TTACTTTTTTTTTACTGA
Found at i:17373 original size:22 final size:22
Alignment explanation
Indices: 17300--17729 Score: 307
Period size: 22 Copynumber: 20.1 Consensus size: 22
17290 TACCCTTTAC
*
17300 TTTATTTTTTACTGATTACTCT
1 TTTACTTTTTACTGATTACTCT
**
17322 TTT-C--TTTACTCTTTACTCT
1 TTTACTTTTTACTGATTACTCT
*
17341 TTT-TTTCTTTACTGATTACTCT
1 TTTACTT-TTTACTGATTACTCT
*
17363 TTTACTTTTTACCGATTAC-CAT
1 TTTACTTTTTACTGATTACTC-T
* *
17385 TTTACTCTTTT-CTAATTACTAT
1 TTTACT-TTTTACTGATTACTCT
*
17407 TTTACTTTTTACTAATTAC-CAT
1 TTTACTTTTTACTGATTACTC-T
* *
17429 TTTACTCTTTT-CTAATTACTAT
1 TTTACT-TTTTACTGATTACTCT
17451 TTTAC-TTTTACTGATTAC-CTT
1 TTTACTTTTTACTGATTACTC-T
17472 TTTACTTTTTACTGATTAC-C-
1 TTTACTTTTTACTGATTACTCT
* * *
17492 ATTGCTTCTTACTGATTA-T-T
1 TTTACTTTTTACTGATTACTCT
*
17512 ATTA-TTTTCTACTGATTACTCT
1 TTTACTTTT-TACTGATTACTCT
*
17534 TTTAATTTTTACTGATTAC-CAT
1 TTTACTTTTTACTGATTACTC-T
* * *
17556 TTTAATTTTTACTAATTACTAT
1 TTTACTTTTTACTGATTACTCT
* *
17578 TGTACTTTTTACTAATTAC-CAT
1 TTTACTTTTTACTGATTACTC-T
* * *
17600 TTTACTCTCTT-CTAATTACTAT
1 TTTACT-TTTTACTGATTACTCT
17622 TTTAC-TTTTACTGATTAC-CTT
1 TTTACTTTTTACTGATTACTC-T
17643 TTTACTTTTTACTGATTAC-C-
1 TTTACTTTTTACTGATTACTCT
* * *
17663 ATTGCTTCTTACTGATTA-T-T
1 TTTACTTTTTACTGATTACTCT
* *
17683 ATTA-TTTTCTACTGGTTACTCT
1 TTTACTTTT-TACTGATTACTCT
* *
17705 TTTAATTTTTACTGATTACTAT
1 TTTACTTTTTACTGATTACTCT
17727 TTT
1 TTT
17730 CTGCTCCTTT
Statistics
Matches: 333, Mismatches: 41, Indels: 68
0.75 0.09 0.15
Matches are distributed among these distances:
19 22 0.07
20 60 0.18
21 34 0.10
22 196 0.59
23 21 0.06
ACGTcount: A:0.22, C:0.17, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTACTTTTTACTGATTACTCT
Found at i:17403 original size:44 final size:44
Alignment explanation
Indices: 17348--17729 Score: 348
Period size: 44 Copynumber: 8.9 Consensus size: 44
17338 TCTTTTTTTC
* * *
17348 TTTACTGATTACTCTTTTACTTTTTACCGATTACCATTTTACTCT
1 TTTACTAATTACTATTTTACTTTTTACTGATTACCATTTTACT-T
*
17393 TTT-CTAATTACTATTTTACTTTTTACTAATTACCATTTTACTCT
1 TTTACTAATTACTATTTTACTTTTTACTGATTACCATTTTACT-T
*
17437 TTT-CTAATTACTATTTTAC-TTTTACTGATTACCTTTTTACTT
1 TTTACTAATTACTATTTTACTTTTTACTGATTACCATTTTACTT
* * * *
17479 TTTACTGATTACCA--TTGCTTCTTACTGATT---ATTATTA-TT
1 TTTACTAATTACTATTTTACTTTTTACTGATTACCATT-TTACTT
* * * *
17518 TTCTACTGATTACTCTTTTAATTTTTACTGATTACCATTTTAATT
1 TT-TACTAATTACTATTTTACTTTTTACTGATTACCATTTTACTT
* *
17563 TTTACTAATTACTATTGTACTTTTTACTAATTACCATTTTACTCT
1 TTTACTAATTACTATTTTACTTTTTACTGATTACCATTTTACT-T
* *
17608 CTT-CTAATTACTATTTTAC-TTTTACTGATTACCTTTTTACTT
1 TTTACTAATTACTATTTTACTTTTTACTGATTACCATTTTACTT
* * * *
17650 TTTACTGATTACCA--TTGCTTCTTACTGATT---ATTATTA-TT
1 TTTACTAATTACTATTTTACTTTTTACTGATTACCATT-TTACTT
** * * *
17689 TTCTACTGGTTACTCTTTTAATTTTTACTGATTACTATTTT
1 TT-TACTAATTACTATTTTACTTTTTACTGATTACCATTTT
17730 CTGCTCCTTT
Statistics
Matches: 279, Mismatches: 38, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
39 12 0.04
40 25 0.09
41 6 0.02
42 53 0.19
43 56 0.20
44 111 0.40
45 16 0.06
ACGTcount: A:0.23, C:0.17, G:0.04, T:0.56
Consensus pattern (44 bp):
TTTACTAATTACTATTTTACTTTTTACTGATTACCATTTTACTT
Found at i:17411 original size:8 final size:8
Alignment explanation
Indices: 17378--17456 Score: 53
Period size: 8 Copynumber: 10.6 Consensus size: 8
17368 TTTTTACCGA
*
17378 TTACCATT
1 TTACTATT
*
17386 TTACTCTT
1 TTACTATT
*
17394 TT-CTA-A
1 TTACTATT
17400 TTACTATT
1 TTACTATT
17408 TTACT-TT
1 TTACTATT
*
17415 TTACTA-A
1 TTACTATT
*
17422 TTACCATT
1 TTACTATT
*
17430 TTACTCTT
1 TTACTATT
*
17438 TT-CTA-A
1 TTACTATT
17444 TTACTATT
1 TTACTATT
17452 TTACT
1 TTACT
17457 TTTACTGATT
Statistics
Matches: 52, Mismatches: 13, Indels: 12
0.68 0.17 0.16
Matches are distributed among these distances:
6 4 0.08
7 22 0.42
8 26 0.50
ACGTcount: A:0.24, C:0.19, G:0.00, T:0.57
Consensus pattern (8 bp):
TTACTATT
Found at i:17534 original size:171 final size:171
Alignment explanation
Indices: 17350--17729 Score: 681
Period size: 171 Copynumber: 2.2 Consensus size: 171
17340 TTTTTTTCTT
* * * *
17350 TACTGATTACTCTTTTACTTTTTACCGATTACCATTTTACTCTTTT-CTAATTACTATTTTACTT
1 TACTGATTACTCTTTTAATTTTTACTGATTACCATTTTAAT-TTTTACTAATTACTATTGTACTT
*
17414 TTTACTAATTACCATTTTACTCTTTTCTAATTACTATTTTACTTTTACTGATTACCTTTTTACTT
65 TTTACTAATTACCATTTTACTCTCTTCTAATTACTATTTTACTTTTACTGATTACCTTTTTACTT
17479 TTTACTGATTACCATTGCTTCTTACTGATTATTATTATTTTC
130 TTTACTGATTACCATTGCTTCTTACTGATTATTATTATTTTC
17521 TACTGATTACTCTTTTAATTTTTACTGATTACCATTTTAATTTTTACTAATTACTATTGTACTTT
1 TACTGATTACTCTTTTAATTTTTACTGATTACCATTTTAATTTTTACTAATTACTATTGTACTTT
17586 TTACTAATTACCATTTTACTCTCTTCTAATTACTATTTTACTTTTACTGATTACCTTTTTACTTT
66 TTACTAATTACCATTTTACTCTCTTCTAATTACTATTTTACTTTTACTGATTACCTTTTTACTTT
17651 TTACTGATTACCATTGCTTCTTACTGATTATTATTATTTTC
131 TTACTGATTACCATTGCTTCTTACTGATTATTATTATTTTC
* *
17692 TACTGGTTACTCTTTTAATTTTTACTGATTACTATTTT
1 TACTGATTACTCTTTTAATTTTTACTGATTACCATTTT
17730 CTGCTCCTTT
Statistics
Matches: 201, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
170 4 0.02
171 197 0.98
ACGTcount: A:0.23, C:0.17, G:0.04, T:0.56
Consensus pattern (171 bp):
TACTGATTACTCTTTTAATTTTTACTGATTACCATTTTAATTTTTACTAATTACTATTGTACTTT
TTACTAATTACCATTTTACTCTCTTCTAATTACTATTTTACTTTTACTGATTACCTTTTTACTTT
TTACTGATTACCATTGCTTCTTACTGATTATTATTATTTTC
Found at i:17696 original size:149 final size:149
Alignment explanation
Indices: 17399--17727 Score: 370
Period size: 149 Copynumber: 2.2 Consensus size: 149
17389 CTCTTTTCTA
* * * * * *
17399 ATTACTATTTTACTTTTTACTAATTACCATTTTACTCTTTTCTAATTACTATTTTACTTTTACTG
1 ATTACCATTTTAATTTTTACTAATTACTATTGTACTCTTTTCTAATTACCATTTTACTTTTACTA
* ** *
17464 ATTACCTTTTTACTTTTTACTGATTACCATTGCTTCTTACTGATTATTATTATTTTCTACTGATT
66 ATTACCTTTTTACTTTTTACTGATTACCATTACTTCTTACTGATTACCATTATTCTCTACTGATT
*
17529 ACTCTTTTAATTTTTACTG
131 ACTCTATTAATTTTTACTG
17548 ATTACCATTTTAATTTTTACTAATTACTATTGTACT-TTTTACTAATTACCATTTTACTCTCTT-
1 ATTACCATTTTAATTTTTACTAATTACTATTGTACTCTTTT-CTAATTACCATTTTACT-T-TTA
* * *
17611 CTAATTA-CTATTTTAC-TTTTACTGATTACCTTTTTACTTTTTACTGATTACCATTGCTTCT-T
63 CTAATTACCT-TTTTACTTTTTACTGATTACC--ATTACTTCTTACTGATTACCATT-ATTCTCT
17673 ACTGATTA-T-TATT-ATTTTCTACTG
124 ACTGATTACTCTATTAATTTT-TACTG
* *
17697 GTTACTC-TTTTAATTTTTACTGATTACTATT
1 ATTAC-CATTTTAATTTTTACTAATTACTATT
17728 TTCTGCTCCT
Statistics
Matches: 155, Mismatches: 16, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
148 9 0.06
149 99 0.64
150 15 0.10
151 29 0.19
152 3 0.02
ACGTcount: A:0.23, C:0.17, G:0.04, T:0.56
Consensus pattern (149 bp):
ATTACCATTTTAATTTTTACTAATTACTATTGTACTCTTTTCTAATTACCATTTTACTTTTACTA
ATTACCTTTTTACTTTTTACTGATTACCATTACTTCTTACTGATTACCATTATTCTCTACTGATT
ACTCTATTAATTTTTACTG
Found at i:17762 original size:26 final size:28
Alignment explanation
Indices: 17710--17764 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
17700 ACTCTTTTAA
* * *
17710 TTTTTACTGATTACTATTTTCTGCTCCT
1 TTTTTACTGATTACCATTTGCTACTCCT
17738 TTTTTACTGATTACCA-TTGC-ACTCCT
1 TTTTTACTGATTACCATTTGCTACTCCT
17764 T
1 T
17765 GAATTGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.25
27 3 0.12
28 15 0.62
ACGTcount: A:0.16, C:0.24, G:0.07, T:0.53
Consensus pattern (28 bp):
TTTTTACTGATTACCATTTGCTACTCCT
Found at i:23451 original size:22 final size:22
Alignment explanation
Indices: 23426--23475 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
23416 GGTTTTTACT
23426 ATGGGCCTTATCTT-GTTCTTTA
1 ATGGGCCTTAT-TTCGTTCTTTA
*
23448 AT-GGCCTTCTTTCGTTCTTTA
1 ATGGGCCTTATTTCGTTCTTTA
23469 ATGGGCC
1 ATGGGCC
23476 ACTATTAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 17 0.68
22 6 0.24
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (22 bp):
ATGGGCCTTATTTCGTTCTTTA
Found at i:24501 original size:24 final size:23
Alignment explanation
Indices: 24474--24519 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
24464 AAGTGGACAG
24474 AATCAAGCAAATT-CAGCAATGCAA
1 AATC-AGCAAATTCCAGC-ATGCAA
*
24498 AATCATCAAATTCCAGCATGCA
1 AATCAGCAAATTCCAGCATGCA
24520 TTCTTACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.20
Consensus pattern (23 bp):
AATCAGCAAATTCCAGCATGCAA
Found at i:26553 original size:52 final size:52
Alignment explanation
Indices: 26492--26594 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
26482 TTTTTTCATC
* *
26492 AAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCCCATT
1 AAGTTTTCAAAGTACTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCATT
*
26544 AAGTTTTCAAAGTGCTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCAT
1 AAGTTTTCAAAGTACTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCAT
26595 CGAGTCTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (52 bp):
AAGTTTTCAAAGTACTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCATT
Found at i:33396 original size:33 final size:33
Alignment explanation
Indices: 33354--33420 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
33344 ACACTCAATG
33354 AGAGTTTTGTACATAAAATTAATAGTAGGTTTA
1 AGAGTTTTGTACATAAAATTAATAGTAGGTTTA
33387 AGAGTTTTGTACATAAAATTAATAGTAGGTTTA
1 AGAGTTTTGTACATAAAATTAATAGTAGGTTTA
33420 A
1 A
33421 TATGGACGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (33 bp):
AGAGTTTTGTACATAAAATTAATAGTAGGTTTA
Found at i:33816 original size:29 final size:29
Alignment explanation
Indices: 33766--33823 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
33756 TAACTATCCA
* *** *
33766 TTTTGGGATAAATTGGTTCCTTAAGTTTT
1 TTTTGGGACAAATTGCCCCCTTAACTTTT
33795 TTTTGGGACAAATTGCCCCCTTAACTTTT
1 TTTTGGGACAAATTGCCCCCTTAACTTTT
33824 AAAAACGAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (29 bp):
TTTTGGGACAAATTGCCCCCTTAACTTTT
Found at i:36581 original size:2 final size:2
Alignment explanation
Indices: 36574--36604 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
36564 CAAAAATACC
*
36574 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36605 TTACATATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:36605 original size:8 final size:8
Alignment explanation
Indices: 36574--36613 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
36564 CAAAAATACC
*
36574 TATATATA
1 TATATATT
*
36582 TATATATA
1 TATATATT
36590 TATATATT
1 TATATATT
36598 TATATATT
1 TATATATT
*
36606 TACATATT
1 TATATATT
36614 GATGCTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (8 bp):
TATATATT
Found at i:39731 original size:22 final size:22
Alignment explanation
Indices: 39706--39813 Score: 85
Period size: 22 Copynumber: 4.9 Consensus size: 22
39696 TATGATGCCA
39706 TTATGAAATTTTGATAACCTTC
1 TTATGAAATTTTGATAACCTTC
* ** *
39728 TTATGAAATTTTAATAATGATAC
1 TTATGAAATTTTGATAA-CCTTC
* * * *
39751 -TATGGAATTTCGAGAACCTTT
1 TTATGAAATTTTGATAACCTTC
**
39772 TTAT-AAATTTTTTTTAACCTTC
1 TTATGAAA-TTTTGATAACCTTC
*
39794 TTATGAAATTTTGTTAACCT
1 TTATGAAATTTTGATAACCT
39814 CCCTCAAGGA
Statistics
Matches: 63, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
21 3 0.05
22 55 0.87
23 5 0.08
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.47
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCTTC
Found at i:39953 original size:23 final size:23
Alignment explanation
Indices: 39927--39976 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
39917 TGATAACCAC
* *
39927 ATAAATCTTCCTATAAAATTTTG
1 ATAAAACTCCCTATAAAATTTTG
39950 ATAAAACTCCCTATAAAATTTTG
1 ATAAAACTCCCTATAAAATTTTG
39973 ATAA
1 ATAA
39977 TTTTCTTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.38
Consensus pattern (23 bp):
ATAAAACTCCCTATAAAATTTTG
Found at i:40053 original size:22 final size:22
Alignment explanation
Indices: 40003--40142 Score: 101
Period size: 22 Copynumber: 6.5 Consensus size: 22
39993 TGATAACTAC
* *
40003 AAATTTTGATAACCTCCCTA-C
1 AAATTTTGATAACCTCACTATG
* *
40024 AATTTTTTGATAACCTCATTATG
1 AA-ATTTTGATAACCTCACTATG
* *
40047 AAATTTTGTTAACCTCCCTATG
1 AAATTTTGATAACCTCACTATG
**
40069 AAATTTTGATAA-CTCTTTTATG
1 AAATTTTGATAACCTC-ACTATG
* * *
40091 AAAATTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CACTATG
* *
40113 AAATTTTGATATCCTC-C-CTG
1 AAATTTTGATAACCTCACTATG
40133 AAATTTTGAT
1 AAATTTTGAT
40143 TACTCCATAA
Statistics
Matches: 93, Mismatches: 20, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
20 12 0.13
21 8 0.09
22 68 0.73
23 5 0.05
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATG
Found at i:40076 original size:44 final size:44
Alignment explanation
Indices: 40003--40099 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
39993 TGATAACTAC
*
40003 AAATTTTGATAACCTCCCTACAATTTTTTGATAAC-CTCATTATG
1 AAATTTTGATAACCTCCCTACAATATTTTGATAACTCT-ATTATG
* * *
40047 AAATTTTGTTAACCTCCCTATGAA-ATTTTGATAACTCTTTTATG
1 AAATTTTGATAACCTCCCTA-CAATATTTTGATAACTCTATTATG
*
40091 AAAATTTGA
1 AAATTTTGA
40100 AAACTAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 41 0.91
45 4 0.09
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.42
Consensus pattern (44 bp):
AAATTTTGATAACCTCCCTACAATATTTTGATAACTCTATTATG
Found at i:40364 original size:21 final size:22
Alignment explanation
Indices: 40333--40433 Score: 84
Period size: 21 Copynumber: 4.6 Consensus size: 22
40323 GATAACAGAA
*
40333 CTATGAAATTTTTATAATCTTC
1 CTATGAAATTTTGATAATCTTC
40355 CTAT-AAATTTTGATAATCTGATC
1 CTATGAAATTTTGATAATCT--TC
* *
40378 TCTATGAAATTTCGATAATC-AC
1 -CTATGAAATTTTGATAATCTTC
* *
40400 TCTATGAGA-TTTGATAACCTT-
1 -CTATGAAATTTTGATAATCTTC
*
40421 CTATCAAATTTTG
1 CTATGAAATTTTG
40434 GTACTCCTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
20 6 0.09
21 26 0.41
22 13 0.20
23 2 0.03
24 4 0.06
25 13 0.20
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.44
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTTC
Found at i:40405 original size:22 final size:22
Alignment explanation
Indices: 40223--40450 Score: 88
Period size: 22 Copynumber: 10.5 Consensus size: 22
40213 ATAAATACCA
40223 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* *
40246 -TTTGAAAATTTGATAA-C-CT
1 CTATGAAATTTTGATAATCACT
* * * * *
40265 CTTCATAAAATTTTGCTGACCCCT
1 C-T-ATGAAATTTTGATAATCACT
* *
40289 CTATAAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
**
40312 -TAT-ATAATTTTGATAA-CAGAA
1 CTATGA-AATTTTGATAATCA-CT
* *
40333 CTATGAAATTTTTATAATC-TT
1 CTATGAAATTTTGATAATCACT
40354 CCTAT-AAATTTTGATAATCTGATCT
1 -CTATGAAATTTTGATAATC--A-CT
*
40379 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
40401 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
* * *
40421 CTATCAAATTTTGGTACTC-CT
1 CTATGAAATTTTGATAATCACT
40442 -TATGAAATT
1 CTATGAAATT
40451 GAGACTTTTA
Statistics
Matches: 156, Mismatches: 28, Indels: 45
0.68 0.12 0.20
Matches are distributed among these distances:
19 2 0.01
20 17 0.11
21 36 0.23
22 74 0.47
23 6 0.04
24 7 0.04
25 14 0.09
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:40496 original size:22 final size:22
Alignment explanation
Indices: 40456--40573 Score: 89
Period size: 22 Copynumber: 5.4 Consensus size: 22
40446 AAATTGAGAC
* * *
40456 TTTTATAACATTCATATGAAAT
1 TTTTATAACCTCCCTATGAAAT
*
40478 TTTTATAACCTCCCCATGAAA-
1 TTTTATAACCTCCCTATGAAAT
* *
40499 TATTAGTAACCT-TCTAATGAAAT
1 TTTTA-TAACCTCCCT-ATGAAAT
* *
40522 TTTGT-TAACCACACTATGAAAT
1 TTT-TATAACCTCCCTATGAAAT
* *
40544 TCTTATAACCTCGCTATGAAAT
1 TTTTATAACCTCCCTATGAAAT
*
40566 TTTGATAA
1 TTTTATAA
40574 TCTCTTTGAT
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
21 6 0.08
22 64 0.85
23 4 0.05
24 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (22 bp):
TTTTATAACCTCCCTATGAAAT
Found at i:40541 original size:44 final size:45
Alignment explanation
Indices: 40470--40573 Score: 110
Period size: 44 Copynumber: 2.4 Consensus size: 45
40460 ATAACATTCA
* * *
40470 TATGAAATTTT-TATAACCTCCCCATGAAA-TATTAGTAACCT-TC
1 TATGAAATTTTGTATAACCACACCATGAAATTATTA-TAACCTCGC
* *
40513 TAATGAAATTTTGT-TAACCACACTATGAAATTCTTATAACCTCGC
1 T-ATGAAATTTTGTATAACCACACCATGAAATTATTATAACCTCGC
40558 TATGAAATTTTG-ATAA
1 TATGAAATTTTGTATAA
40574 TCTCTTTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
43 1 0.02
44 43 0.84
45 7 0.14
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (45 bp):
TATGAAATTTTGTATAACCACACCATGAAATTATTATAACCTCGC
Found at i:40635 original size:22 final size:22
Alignment explanation
Indices: 40607--40792 Score: 144
Period size: 22 Copynumber: 8.4 Consensus size: 22
40597 AATTGTGATA
*
40607 AATAACCACCCTATGAAATTTC
1 AATAACCACCCTATGAAATTTT
* *
40629 AATAACCAACCTAAGAAATTTT
1 AATAACCACCCTATGAAATTTT
* *
40651 AATAACATGATCCTATGAAATTTT
1 AATAAC--CACCCTATGAAATTTT
** *
40675 GGTAACCACACTATGAAATTTT
1 AATAACCACCCTATGAAATTTT
** *
40697 AATAACTTCCATATGAAATTTT
1 AATAACCACCCTATGAAATTTT
** *
40719 GGTAACCACACTATGGAAA-TTT
1 AATAACCACCCTAT-GAAATTTT
* *
40741 -ATAACC-TCCTCATGAAATTAT
1 AATAACCACCCT-ATGAAATTTT
* *
40762 AATAACCATCTTATGAAATTTT
1 AATAACCACCCTATGAAATTTT
*
40784 GATAACCAC
1 AATAACCAC
40793 ATAGAGACAA
Statistics
Matches: 126, Mismatches: 31, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
20 6 0.05
21 9 0.07
22 87 0.69
23 7 0.06
24 17 0.13
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (22 bp):
AATAACCACCCTATGAAATTTT
Found at i:40672 original size:46 final size:43
Alignment explanation
Indices: 40616--40769 Score: 127
Period size: 46 Copynumber: 3.5 Consensus size: 43
40606 AAATAACCAC
40616 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACATGAT
1 CCTATGAAATTTCAATAACCACA-CTAAGAAATTTTAATAAC-T--T
*** *
40662 CCTATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTT
1 CCTATGAAATTTCAATAACCACACTAAGAAATTTTAATAACTT
*** * *
40705 CCATATGAAATTTTGGTAACCACACTATGGAAA-TTT-ATAACCT
1 CC-TATGAAATTTCAATAACCACACTA-AGAAATTTTAATAACTT
40748 CCTCATGAAATTAT-AATAACCA
1 CCT-ATGAAATT-TCAATAACCA
40770 TCTTATGAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
42 1 0.01
43 25 0.26
44 28 0.29
45 5 0.05
46 35 0.37
47 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.32
Consensus pattern (43 bp):
CCTATGAAATTTCAATAACCACACTAAGAAATTTTAATAACTT
Found at i:40891 original size:6 final size:6
Alignment explanation
Indices: 40880--40910 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
40870 CGAATAGTAT
*
40880 TGTTAG TGTTAG TGTTAG TTTTAG TGTTAG T
1 TGTTAG TGTTAG TGTTAG TGTTAG TGTTAG T
40911 TTAATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (6 bp):
TGTTAG
Found at i:42388 original size:30 final size:32
Alignment explanation
Indices: 42354--42421 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 32
42344 GGCAATTTAG
*
42354 AAATATGCTTTAAAAA-AAGGGTACAAT-TGA
1 AAATATGCTTTAAAAATAAGGGTACAATCAGA
*
42384 AAATATGTTTTAAAAATAAGGGTACAATCAGA
1 AAATATGCTTTAAAAATAAGGGTACAATCAGA
42416 AAATAT
1 AAATAT
42422 AAAGTTTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 15 0.44
31 11 0.32
32 8 0.24
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (32 bp):
AAATATGCTTTAAAAATAAGGGTACAATCAGA
Found at i:42482 original size:161 final size:161
Alignment explanation
Indices: 42287--42588 Score: 509
Period size: 161 Copynumber: 1.9 Consensus size: 161
42277 ATACTTAAAT
* *
42287 AATGGAATAACTTATGATTAAAAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTT
1 AATGAAATAACTTATGATTAAAAAAATAATGGAATAATTAAAATATTATTTAGTAATGACAATTT
*
42352 AGAAATATGCTTT-AAAAAAAGGGTACAATTGAAAATATGTTTTAAAAATAAGGGTACAATCAGA
66 AGAAATATG-TTTAAAAAAAAGGATACAATTGAAAATATGTTTTAAAAATAA-GGTACAATCAGA
42416 AAATATAAAGTTTTCCTAATAATTAATAATGGA
129 AAATATAAAGTTTTCCTAATAATTAATAATGGA
*
42449 AATGAAATAATTTATGATT-AAAAAATAATGGAATAATTAAAATATTATTTAGTAATGACAATTT
1 AATGAAATAACTTATGATTAAAAAAATAATGGAATAATTAAAATATTATTTAGTAATGACAATTT
* * *
42513 AGAAATATGTTTAAAAAAAATGATACAATTGGAAATATGTTTTAAAAATAAGGTACAATCGGAAA
66 AGAAATATGTTTAAAAAAAAGGATACAATTGAAAATATGTTTTAAAAATAAGGTACAATCAGAAA
42578 ATATAAAGTTT
131 ATATAAAGTTT
42589 CCCCTTATTC
Statistics
Matches: 132, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
160 27 0.20
161 88 0.67
162 17 0.13
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.33
Consensus pattern (161 bp):
AATGAAATAACTTATGATTAAAAAAATAATGGAATAATTAAAATATTATTTAGTAATGACAATTT
AGAAATATGTTTAAAAAAAAGGATACAATTGAAAATATGTTTTAAAAATAAGGTACAATCAGAAA
ATATAAAGTTTTCCTAATAATTAATAATGGA
Found at i:42581 original size:31 final size:30
Alignment explanation
Indices: 42514--42577 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
42504 TGACAATTTA
*
42514 GAAATATGTTTAAAAAAAATGATACAATTG
1 GAAATATGTTTAAAAAAAATGATACAATCG
* *
42544 GAAATATGTTTTAAAAATAA-GGTACAATCG
1 GAAATATG-TTTAAAAAAAATGATACAATCG
42574 GAAA
1 GAAA
42578 ATATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.28
Consensus pattern (30 bp):
GAAATATGTTTAAAAAAAATGATACAATCG
Found at i:42846 original size:21 final size:21
Alignment explanation
Indices: 42820--42863 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42810 TATTTGGGGG
*
42820 TTGCTAAAT-ACCGCCCTATTT
1 TTGCT-AATCACCGCCCCATTT
*
42841 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
42862 TT
1 TT
42864 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:42999 original size:32 final size:32
Alignment explanation
Indices: 42928--43036 Score: 182
Period size: 32 Copynumber: 3.4 Consensus size: 32
42918 GGAGCCTCCT
* *
42928 CACTAGGACGGCTCTGCCACGGCGGAGCCTCCC
1 CACTAGGACGGCTCTGCCACGGC-TAGCCGCCC
42961 CACTAGGACGGCTCTGCCACGGCTAGCCGCCC
1 CACTAGGACGGCTCTGCCACGGCTAGCCGCCC
42993 CACTAGGACGGCTCTGCCACGGCTAGCCGCCC
1 CACTAGGACGGCTCTGCCACGGCTAGCCGCCC
*
43025 CACTAGGGCGGC
1 CACTAGGACGGC
43037 AATGTTTTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 50 0.68
33 23 0.32
ACGTcount: A:0.16, C:0.42, G:0.30, T:0.12
Consensus pattern (32 bp):
CACTAGGACGGCTCTGCCACGGCTAGCCGCCC
Found at i:43121 original size:33 final size:33
Alignment explanation
Indices: 43079--43255 Score: 225
Period size: 33 Copynumber: 5.4 Consensus size: 33
43069 TAGTACCGGT
* * **
43079 GCCGCCCCAGGGGGGCGGTCTATCCATGGTAGG
1 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGG
*
43112 GCCGCCCCAGGGAGGCGGCCTGGCCATGATAGG
1 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGG
*
43145 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGG
*
43178 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGG
* *
43211 GCCGCCTCA-GGAGGGCGGCTTGGCCATGGCTCA--
1 GCCGCCCCAGGGA-GGCGGCCTGGCCATGG-T-AGG
43244 GCCGCCCCAGGG
1 GCCGCCCCAGGG
43256 GGACGGCACC
Statistics
Matches: 130, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
32 3 0.02
33 123 0.95
34 3 0.02
35 1 0.01
ACGTcount: A:0.12, C:0.34, G:0.42, T:0.12
Consensus pattern (33 bp):
GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGG
Found at i:43375 original size:32 final size:33
Alignment explanation
Indices: 43334--43406 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
43324 AAATTAGCCG
43334 AGCCGCCCCACCGGGACGGCCTGCCC-TGGCT-A
1 AGCCGCCCCACCGGGACGGCCTGCCCATGG-TGA
** *
43366 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCACCGGGACGGCCTGCCCATGGTGA
43399 AGCCGCCC
1 AGCCGCCC
43407 TCTTGGGACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 24 0.67
33 12 0.33
ACGTcount: A:0.12, C:0.44, G:0.34, T:0.10
Consensus pattern (33 bp):
AGCCGCCCCACCGGGACGGCCTGCCCATGGTGA
Found at i:44494 original size:1 final size:1
Alignment explanation
Indices: 44490--44524 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
44480 GGTAAAAATG
44490 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
44525 GCGAAATCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44811 original size:2 final size:2
Alignment explanation
Indices: 44804--44831 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44794 AATTTAAATT
44804 TA TA 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
44832 ATAAAATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55806 original size:5 final size:5
Alignment explanation
Indices: 55792--55823 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
55782 AGAAATTTAT
55792 AAAT- AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
55824 AACCACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:56759 original size:25 final size:26
Alignment explanation
Indices: 56725--56778 Score: 92
Period size: 25 Copynumber: 2.1 Consensus size: 26
56715 CCTTTTAGAT
56725 TTTAGTTTTATGGCAGACTCTATG-C
1 TTTAGTTTTATGGCAGACTCTATGAC
*
56750 TTTAGTTTTATGGTAGACTCTATGAC
1 TTTAGTTTTATGGCAGACTCTATGAC
56776 TTT
1 TTT
56779 TAAAATTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (26 bp):
TTTAGTTTTATGGCAGACTCTATGAC
Found at i:58888 original size:111 final size:112
Alignment explanation
Indices: 58693--59002 Score: 498
Period size: 111 Copynumber: 2.8 Consensus size: 112
58683 AAACAATAAT
* * *
58693 AAAAAACTATTTTAAACAAAGAAAATTATAAACCCCTGCAGG-GGTGGCTTAGTGGCAGGAAACC
1 AAAAAACTATTTTAAACAAAGAAAATTATAAGCCCCTG-TGGAGGTGGCTTAGTGGCAGGAAGCC
*
58757 GAGTGTACGGTTCCTGCAGGTGTGAGCTCACATAAAATCTTGCTTT-A
65 GAGTGTAAGGTTCCTGCAGGTGTGAGCTCACATAAAATCTTGCTTTAA
*
58804 AAAAAACAATTTTAAACAAAGAAAATTATAAGCCCCTGTGGAGGTGGCTTAGTGGCAGGAAGCCG
1 AAAAAACTATTTTAAACAAAGAAAATTATAAGCCCCTGTGGAGGTGGCTTAGTGGCAGGAAGCCG
* * *
58869 AGTGTAAGGTTCCTACAGGTGTGAGCTCACATGAACTCTTGCTTTAAA
66 AGTGTAAGGTTCCTGCAGGTGTGAGCTCACATAAAATCTTGCTTT-AA
*
58917 AAAAAACTATTTTAAACAAAGAAAATTATAAGCCCTTGTGGAGGTGGCTTAGTGGCAGGAAGCCG
1 AAAAAACTATTTTAAACAAAGAAAATTATAAGCCCCTGTGGAGGTGGCTTAGTGGCAGGAAGCCG
*
58982 AGCGTAAGGTTCCTGCAGGTG
66 AGTGTAAGGTTCCTGCAGGTG
59003 CGGTCATGGG
Statistics
Matches: 184, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
110 2 0.01
111 99 0.54
113 83 0.45
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (112 bp):
AAAAAACTATTTTAAACAAAGAAAATTATAAGCCCCTGTGGAGGTGGCTTAGTGGCAGGAAGCCG
AGTGTAAGGTTCCTGCAGGTGTGAGCTCACATAAAATCTTGCTTTAA
Done.