Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014902.1 Kokia drynarioides strain JFW-HI SEQ_129945, 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: 365448
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:50 original size:2 final size:2
Alignment explanation
Indices: 1--30 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31 GTACATGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12425 original size:2 final size:2
Alignment explanation
Indices: 12418--12442 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12408 TTTAGATTCG
12418 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
12443 TTATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:13006 original size:16 final size:16
Alignment explanation
Indices: 12985--13018 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12975 TTAAATTTAG
12985 TTTTATATATACATTA
1 TTTTATATATACATTA
* *
13001 TTTTATATGTGCATTA
1 TTTTATATATACATTA
13017 TT
1 TT
13019 GTATTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTTATATATACATTA
Found at i:14950 original size:289 final size:289
Alignment explanation
Indices: 14426--14977 Score: 978
Period size: 289 Copynumber: 1.9 Consensus size: 289
14416 AACAAAAAGG
14426 AAACTCCTCAAGCAACTATGGCAGTTAATTCAGAATCCAATAATGCTGGAGATCATGAATCTGGT
1 AAACTCCTCAAGCAACTATGGCAGTTAATTCAGAATCCAATAATGCTGGAGATCATGAATCTGGT
* * *
14491 TCTTTGATTTCGTCTCCTGTCTCGACTGTTCCAGTATTCACATCTGAACAATACCACCAGCTTTT
66 TCTTTGATTTCGTCTCCTATCTCGACTGTTCCAGTATTCACATCTAAACAATACCACCAGATTTT
*
14556 AAGTCTGTTGAACAAGAGTCCATCATCAGATTCTAGTGTGAATCTTGTAGGTACGATAGCTTGCA
131 AAGTCTGTTGAACAAGAGTCCATCATCAGATTCTAGTGTGAATCTTGCAGGTACGATAGCTTGCA
* * *
14621 GTTTACTTGTTGTTAAATTTTTTACTCGTTGGAGTTTGGATACTAGAGCTACTGACCATATCATA
196 GTTTACCTGTTGTTAAATTTTCTACTCATTGGAGTTTGGATACTAGAGCTACTGACCATATCATA
14686 TCTATTTCATATTGGAGATACTGGAGCTT
261 TCTATTTCATATTGGAGATACTGGAGCTT
* *
14715 AAACTCCTCAAGCAGCTATGGCAGTTAATTCAGAATCCAATGATGCTGGAGATCATGAATCTGGT
1 AAACTCCTCAAGCAACTATGGCAGTTAATTCAGAATCCAATAATGCTGGAGATCATGAATCTGGT
14780 TCTTTGATTTCGTCTCCTATCTCGACTGTTCCAGTATTCACATCTAAACAATACCACCAGATTTT
66 TCTTTGATTTCGTCTCCTATCTCGACTGTTCCAGTATTCACATCTAAACAATACCACCAGATTTT
* *
14845 AAGTTTGTTGAACAAGAGTCCATCATCAGATTCTAGTGTGAATCTTGCAGGTACGATAGCTTGTA
131 AAGTCTGTTGAACAAGAGTCCATCATCAGATTCTAGTGTGAATCTTGCAGGTACGATAGCTTGCA
* * *
14910 GTTTACCTGTTGTTAAATTTTCTACTCATTGGATTTTGGATACTGGAGCTATTGACCATATCATA
196 GTTTACCTGTTGTTAAATTTTCTACTCATTGGAGTTTGGATACTAGAGCTACTGACCATATCATA
14975 TCT
261 TCT
14978 GTTTTTGAGA
Statistics
Matches: 249, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
289 249 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (289 bp):
AAACTCCTCAAGCAACTATGGCAGTTAATTCAGAATCCAATAATGCTGGAGATCATGAATCTGGT
TCTTTGATTTCGTCTCCTATCTCGACTGTTCCAGTATTCACATCTAAACAATACCACCAGATTTT
AAGTCTGTTGAACAAGAGTCCATCATCAGATTCTAGTGTGAATCTTGCAGGTACGATAGCTTGCA
GTTTACCTGTTGTTAAATTTTCTACTCATTGGAGTTTGGATACTAGAGCTACTGACCATATCATA
TCTATTTCATATTGGAGATACTGGAGCTT
Found at i:19184 original size:4 final size:4
Alignment explanation
Indices: 19175--19207 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
19165 AACTCATTGG
19175 TAAT TAAT TAAT TAAT TAAT TAAT T--T TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
19208 ACTTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.07
4 25 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:52630 original size:26 final size:26
Alignment explanation
Indices: 52592--52659 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
52582 TAAGAGCGAT
*
52592 ATTGGCTCATAAGAGCGACATACTGA
1 ATTGGCTCGTAAGAGCGACATACTGA
*
52618 ATTGGCTCGTAAGAGCGATATACTGA
1 ATTGGCTCGTAAGAGCGACATACTGA
*
52644 ATTGGCTTGTAAGAGC
1 ATTGGCTCGTAAGAGC
52660 AATGCTCTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (26 bp):
ATTGGCTCGTAAGAGCGACATACTGA
Found at i:56383 original size:15 final size:15
Alignment explanation
Indices: 56363--56394 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
56353 ATGACATTGT
56363 TTCCTCTTTTCTCCC
1 TTCCTCTTTTCTCCC
56378 TTCCTCTTTTCTCCC
1 TTCCTCTTTTCTCCC
56393 TT
1 TT
56395 AATGTCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (15 bp):
TTCCTCTTTTCTCCC
Found at i:59227 original size:37 final size:37
Alignment explanation
Indices: 59172--59345 Score: 152
Period size: 37 Copynumber: 4.7 Consensus size: 37
59162 GTTTGTAAGA
* * *
59172 AATCGAGCTATGTACCTAGCAGGCTTCGTGCCGGTGT
1 AATCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
*** * *
59209 AATTGGGCTGTGTGCCTAGTAGGCTTCGTGCTGGTGT
1 AATCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
** * *
59246 AATCAAGCTATGTGCCTAGTAGGCTTTATACTGGTGT
1 AATCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
** * ** * *
59283 AATCGGGCTATTTGCCTAGTAAACTTTGTGTCGGTG-
1 AATCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
*
59319 AGATCAGGCTATGTGCCTAGTAGGCTT
1 A-ATCAAGCTATGTGCCTAGTAGGCTT
59346 TTGTGTCAAT
Statistics
Matches: 110, Mismatches: 26, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
36 1 0.01
37 109 0.99
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (37 bp):
AATCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
Found at i:59299 original size:74 final size:73
Alignment explanation
Indices: 59172--59346 Score: 190
Period size: 74 Copynumber: 2.4 Consensus size: 73
59162 GTTTGTAAGA
* * * ** * * * **
59172 AATCGAGCTATGTACCTAGCAGGCTTCGTGCCGGTGTAATTGGGCTGTGTGCCTAGTAGGCTTCG
1 AATCAAGCTATGTGCCTAGTAGGCTTTATACCGGTGTAATCGGGCTATGTGCCTAGTAAACTTCG
59237 TG-CTGGTG
66 TGTC-GGTG
* * *
59245 TAATCAAGCTATGTGCCTAGTAGGCTTTATACTGGTGTAATCGGGCTATTTGCCTAGTAAACTTT
1 -AATCAAGCTATGTGCCTAGTAGGCTTTATACCGGTGTAATCGGGCTATGTGCCTAGTAAACTTC
59310 GTGTCGGTG
65 GTGTCGGTG
*
59319 AGATCAGGCTATGTGCCTAGTAGGCTTT
1 A-ATCAAGCTATGTGCCTAGTAGGCTTT
59347 TGTGTCAATT
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
73 1 0.01
74 83 0.98
75 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (73 bp):
AATCAAGCTATGTGCCTAGTAGGCTTTATACCGGTGTAATCGGGCTATGTGCCTAGTAAACTTCG
TGTCGGTG
Found at i:64473 original size:24 final size:23
Alignment explanation
Indices: 64440--64496 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
64430 TTAGTCGAAG
64440 AAAAGAAAAACAAGTAAAAAGAACA
1 AAAAG-AAAACAAGTAAAAA-AACA
* ** *
64465 AAACGAAAATGAGTAAAAATACA
1 AAAAGAAAACAAGTAAAAAAACA
64488 AAAAGAAAA
1 AAAAGAAAA
64497 GGGTAAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 11 0.41
24 12 0.44
25 4 0.15
ACGTcount: A:0.74, C:0.07, G:0.12, T:0.07
Consensus pattern (23 bp):
AAAAGAAAACAAGTAAAAAAACA
Found at i:64488 original size:23 final size:24
Alignment explanation
Indices: 64452--64496 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
64442 AAGAAAAACA
*
64452 AGTAAAAAGAACAAAACGAAAATG
1 AGTAAAAAGAACAAAAAGAAAATG
*
64476 AGTAAAAA-TACAAAAAGAAAA
1 AGTAAAAAGAACAAAAAGAAAA
64497 GGGTAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.71, C:0.07, G:0.13, T:0.09
Consensus pattern (24 bp):
AGTAAAAAGAACAAAAAGAAAATG
Found at i:76187 original size:19 final size:20
Alignment explanation
Indices: 76163--76255 Score: 77
Period size: 20 Copynumber: 4.6 Consensus size: 20
76153 AACTATAAAA
76163 ATAAAA-TTAAATAAAAATT
1 ATAAAATTTAAATAAAAATT
*
76182 ATAAAATTTTAATAAAAAATT
1 ATAAAATTTAAAT-AAAAATT
76203 -TAAAATTTAGAA-AAAAATTT
1 ATAAAATTTA-AATAAAAA-TT
* *
76223 ATAAAAATTTTAA-AAAAATA
1 AT-AAAATTTAAATAAAAATT
*
76243 AAAAAATTGTAAA
1 ATAAAATT-TAAA
76256 CTTTTATAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
19 17 0.28
20 20 0.33
21 17 0.28
22 7 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
ATAAAATTTAAATAAAAATT
Found at i:76197 original size:20 final size:19
Alignment explanation
Indices: 76163--76241 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 19
76153 AACTATAAAA
*
76163 ATAAAATTAAATAAAAATT
1 ATAAAATTTAATAAAAATT
76182 ATAAAATTTTAATAAAAAATT
1 ATAAAA-TTTAAT-AAAAATT
*
76203 -TAAAATTTAGAAAAAAATTT
1 ATAAAATTTA-ATAAAAA-TT
76223 ATAAAAATTTTAA-AAAAAT
1 AT-AAAA-TTTAATAAAAAT
76242 AAAAAAATTG
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
19 15 0.29
20 14 0.27
21 13 0.25
22 5 0.10
23 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (19 bp):
ATAAAATTTAATAAAAATT
Found at i:76241 original size:21 final size:20
Alignment explanation
Indices: 76169--76240 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
76159 AAAAATAAAA
76169 TTAAATAAAAATTATAAAATT
1 TTAAA-AAAAATTATAAAATT
76190 TTAATAAAAAATT-TAAAA-T
1 TTAA-AAAAAATTATAAAATT
76209 TTAGAAAAAAATTTATAAAAATT
1 TTA-AAAAAAA-TTAT-AAAATT
76232 TTAAAAAAA
1 TTAAAAAAA
76241 TAAAAAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
19 10 0.22
20 8 0.18
21 12 0.27
22 11 0.24
23 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (20 bp):
TTAAAAAAAATTATAAAATT
Found at i:76470 original size:9 final size:9
Alignment explanation
Indices: 76456--76558 Score: 73
Period size: 9 Copynumber: 10.9 Consensus size: 9
76446 TTTTTGTACG
76456 ATAATTTTT
1 ATAATTTTT
76465 ATAATTGTTTT
1 ATAA-T-TTTT
*
76476 ATGATTTTT
1 ATAATTTTT
76485 ATAATTTTT
1 ATAATTTTT
* *
76494 CTAATTTTGA
1 ATAATTTT-T
**
76504 ATAAAATTT
1 ATAATTTTT
*
76513 AAATATTTTT
1 ATA-ATTTTT
76523 AT-ATTTTT
1 ATAATTTTT
* *
76531 ATTAAAATTTA
1 A-T-AATTTTT
76542 ATAATTTTT
1 ATAATTTTT
76551 ATAATTTT
1 ATAATTTT
76559 CATTGTTTTT
Statistics
Matches: 71, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
8 7 0.10
9 39 0.55
10 13 0.18
11 12 0.17
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:76528 original size:28 final size:29
Alignment explanation
Indices: 76485--76558 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 29
76475 TATGATTTTT
*
76485 ATAATTTTTCTAATTTTGAATAAAATTTA
1 ATAATTTTTATAATTTTGAATAAAATTTA
* *
76514 A-ATATTTTTAT-ATTTTTATTAAAATTTA
1 ATA-ATTTTTATAATTTTGAATAAAATTTA
76542 ATAATTTTTATAATTTT
1 ATAATTTTTATAATTTT
76559 CATTGTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 25 0.64
29 14 0.36
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (29 bp):
ATAATTTTTATAATTTTGAATAAAATTTA
Found at i:82468 original size:30 final size:30
Alignment explanation
Indices: 82314--82475 Score: 127
Period size: 29 Copynumber: 5.4 Consensus size: 30
82304 AAAGAAAAAT
* *
82314 GGGGTCAAAAATGAAA-TTTTGTAAAGTTT-
1 GGGGTCAAATAT-AAATTTTTGGAAAGTTTA
*
82343 GGGGGCTAAAT-TCAAA-TTTTGGAAAGTTTA
1 GGGGTC-AAATAT-AAATTTTTGGAAAGTTTA
* * ** *
82373 GGGTTAAAATCCAAATTTTTGGGAAGTTT-
1 GGGGTCAAATATAAATTTTTGGAAAGTTTA
* * * *
82402 GAGGTCAAATCTAAATTTTTGGATAGTTAA
1 GGGGTCAAATATAAATTTTTGGAAAGTTTA
* *
82432 GAGGTCAAATATGAATTTTTGGAAAGTTTA
1 GGGGTCAAATATAAATTTTTGGAAAGTTTA
82462 GGGGTCAAAATATA
1 GGGGTC-AAATATA
82476 GTTTTTAAAT
Statistics
Matches: 105, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
29 50 0.48
30 49 0.47
31 6 0.06
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.35
Consensus pattern (30 bp):
GGGGTCAAATATAAATTTTTGGAAAGTTTA
Found at i:82481 original size:30 final size:30
Alignment explanation
Indices: 82359--82475 Score: 123
Period size: 30 Copynumber: 3.9 Consensus size: 30
82349 TAAATTCAAA
*
82359 TTTTGGAAAGTTTAG-GGTTAAA-ATCCAAAT
1 TTTTGGAAAGTTTAGAGGTCAAATAT--AAAT
* *
82389 TTTTGGGAAGTTT-GAGGTCAAATCTAAAT
1 TTTTGGAAAGTTTAGAGGTCAAATATAAAT
* * *
82418 TTTTGGATAGTTAAGAGGTCAAATATGAAT
1 TTTTGGAAAGTTTAGAGGTCAAATATAAAT
*
82448 TTTTGGAAAGTTTAGGGGTCAAAATATA
1 TTTTGGAAAGTTTAGAGGTC-AAATATA
82476 GTTTTTAAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
29 15 0.21
30 49 0.69
31 7 0.10
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTTGGAAAGTTTAGAGGTCAAATATAAAT
Found at i:84175 original size:37 final size:37
Alignment explanation
Indices: 84125--84195 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
84115 CTTCATTGTC
*
84125 TTGATCCACTTCTCTGTATCTCATCAGGAAGATGGAT
1 TTGATCCACTTCTCTATATCTCATCAGGAAGATGGAT
* *
84162 TTGATCTACTTCTCTATATCTCATTAGGAAGATG
1 TTGATCCACTTCTCTATATCTCATCAGGAAGATG
84196 ACCGCTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (37 bp):
TTGATCCACTTCTCTATATCTCATCAGGAAGATGGAT
Found at i:84227 original size:85 final size:85
Alignment explanation
Indices: 84084--84242 Score: 230
Period size: 85 Copynumber: 1.9 Consensus size: 85
84074 CTTTTGGTCC
* * * *
84084 ACTTCTCTGTATCTCATCAGGAAGATGACTACTTCATTGTCTTGATCCACTTCTCTGTATCTCAT
1 ACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTCTCTTGACCCACTTCTCTGTATCTCAT
84149 CAGGAAGATGGATTTGATCT
66 CAGGAAGATGGATTTGATCT
* * * *
84169 ACTTCTCTATATCTCATTAGGAAGATGACCGCTTTATTACT-TTGACCCATTTCTCTGTATCTCA
1 ACTTCTCTATATCTCATCAGGAAGATGACCACTTCATT-CTCTTGACCCACTTCTCTGTATCTCA
84233 TCAGGAAGAT
65 TCAGGAAGAT
84243 AGGGGGCCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
85 64 0.98
86 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (85 bp):
ACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTCTCTTGACCCACTTCTCTGTATCTCAT
CAGGAAGATGGATTTGATCT
Found at i:84430 original size:85 final size:85
Alignment explanation
Indices: 84286--84707 Score: 298
Period size: 85 Copynumber: 4.9 Consensus size: 85
84276 GGCTTCATTG
* * * * * *
84286 ATTTGGTCTACTTCTCTGTATTTCATCAAGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCT
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTAACCCACTTCTCT
84351 GTATCTCATCAGGAAAACGA
66 GTATCTCATCAGGAAAACGA
* * *
84371 ATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCT
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTAACCCACTTCTCT
* * *
84436 GTATCTCATTAGGTAGATGACCGCTTT
66 GTATCTCATCAGG-A-A--AACG---A
* * * * * * * * * *
84463 ATTACTGTGACCCACTTCTCTATATCTTATTAAGAAGATGA-GGGTTTGA-AG-TTTCACTCACA
1 ATT--TG-G-TCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTT-ATTGTTTTAACCCAC-
** *
84525 TTAAGCT-T-TGCT--TC-----ATCG-
60 TT-CTCTGTAT-CTCATCAGGAAAACGA
* * * * * *
84543 ATTTGGTCTACTTCTCTTTATCTCATTAGGAAGATGATCG-TCTCATTGTTTTAATCCACTTCTC
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCT-TTATTGTTTTAACCCACTTCTC
84607 TGTATCTCATCA-GAAAGACGA
65 TGTATCTCATCAGGAAA-ACGA
*
84628 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTCT
1 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTAACCCACTTCTCT
84693 GTATCTCATCAGGAA
66 GTATCTCATCAGGAA
84708 GATGAGGGTT
Statistics
Matches: 258, Mismatches: 48, Indels: 61
0.70 0.13 0.17
Matches are distributed among these distances:
76 30 0.12
77 9 0.03
78 10 0.04
79 2 0.01
80 3 0.01
83 1 0.00
84 5 0.02
85 135 0.52
86 5 0.02
87 1 0.00
89 3 0.01
92 3 0.01
93 1 0.00
94 11 0.04
95 11 0.04
96 28 0.11
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (85 bp):
ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTAACCCACTTCTCT
GTATCTCATCAGGAAAACGA
Found at i:84454 original size:48 final size:48
Alignment explanation
Indices: 84378--84503 Score: 180
Period size: 48 Copynumber: 2.6 Consensus size: 48
84368 CGAATTTGGT
* * * *
84378 CCACTTCTTTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGAC
1 CCACTTCTCTGTATCTCATTAGGAAGATGACCGCTTTATTACTGTGAC
*
84426 CCACTTCTCTGTATCTCATTAGGTAGATGACCGCTTTATTACTGTGAC
1 CCACTTCTCTGTATCTCATTAGGAAGATGACCGCTTTATTACTGTGAC
* * *
84474 CCACTTCTCTATATCTTATTAAGAAGATGA
1 CCACTTCTCTGTATCTCATTAGGAAGATGA
84504 GGGTTTGAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (48 bp):
CCACTTCTCTGTATCTCATTAGGAAGATGACCGCTTTATTACTGTGAC
Found at i:84598 original size:257 final size:259
Alignment explanation
Indices: 84169--84712 Score: 860
Period size: 257 Copynumber: 2.1 Consensus size: 259
84159 GATTTGATCT
* * * *
84169 ACTTCTCTATATCTCATTAGGAAGATGACCGCTTTATTACTTTGACCCATTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATTAGGAAGATGACCGCTTTATTACTGTGACCCACTTCTCTATATCTCAT
* * * *
84234 CAGGAAGATAGGGGGCCTTGAAGTTTCACTCATATTAAGCTTGGCTTCATTGATTTGGTCTACTT
66 CAAGAAGATAGAGGGCCTTGAAGTTTCACTCACATTAAGCTTGGCTTCATCGATTTGGTCTACTT
*
84299 CTCTGTATTTCATCAAGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGTATCTCATCAGG
131 CTCTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGTATCTCATCA-G
*
84364 AAA-ACGAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCC
195 AAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCC
* *
84428 ACTTCTCTGTATCTCATTAGGTAGATGACCGCTTTATTACTGTGACCCACTTCTCTATATCTTAT
1 ACTTCTCTGTATCTCATTAGGAAGATGACCGCTTTATTACTGTGACCCACTTCTCTATATCTCAT
* * *
84493 TAAGAAGAT-GAGGG-TTTGAAGTTTCACTCACATTAAGCTTTGCTTCATCGATTTGGTCTACTT
66 CAAGAAGATAGAGGGCCTTGAAGTTTCACTCACATTAAGCTTGGCTTCATCGATTTGGTCTACTT
* * * * *
84556 CTCTTTATCTCATTAGGAAGATGATCGTCTCATTGTTTTAATCCACTTCTCTGTATCTCATCAGA
131 CTCTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGTATCTCATCAGA
*
84621 AAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCC
196 AAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCC
*
84685 ACTTCTCTGTATCTCATCAGGAAGATGA
1 ACTTCTCTGTATCTCATTAGGAAGATGA
84713 GGGTTTGAAG
Statistics
Matches: 261, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
256 4 0.02
257 187 0.72
258 4 0.02
259 66 0.25
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (259 bp):
ACTTCTCTGTATCTCATTAGGAAGATGACCGCTTTATTACTGTGACCCACTTCTCTATATCTCAT
CAAGAAGATAGAGGGCCTTGAAGTTTCACTCACATTAAGCTTGGCTTCATCGATTTGGTCTACTT
CTCTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGTATCTCATCAGA
AAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCC
Found at i:84711 original size:209 final size:210
Alignment explanation
Indices: 84426--84999 Score: 814
Period size: 209 Copynumber: 2.7 Consensus size: 210
84416 TTGCTTTGAC
* * ** * * *
84426 CCACTTCTCTGTATCTCATTAGGTAGATGACCGCTTTATTACTGTGACCCACTTCTCTATATCTT
1 CCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTCTGTATCTC
* *
84491 ATTAAGAAGATGAGGGTTTGAAGTTTCACTCACATTAAGCTTTGCTTCATCGATTTGGTCTACTT
66 ATCAAGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATCGATTTGGTCTACTT
* * * * *
84556 CTCTTTATCTCATTAGGAAGATGATCGTCTCATTGTTTTAATCCACTTCTCTGTATCTCATCA-G
131 CTCTATATCTCATCAGGAAGATGACCATCTCATTATTTTAATCCACTTCTCTGTATCTCATCAGG
84620 AAAGACGAATTT-GGT
196 AAA-ACGAATTTGGGT
84635 CCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTCTGTATCTC
1 CCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTCTGTATCTC
* * * *
84700 ATCAGGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATTGATTTGGGCTACTT
66 ATCAAGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATCGATTTGGTCTACTT
* * *
84765 CTCTGTATCTCATCAGGAAGATGACCATCTCATTATTTTAATCGACTTCTCTGTATCTCATTAGG
131 CTCTATATCTCATCAGGAAGATGACCATCTCATTATTTTAATCCACTTCTCTGTATCTCATCAGG
84830 AAAACGAATTTGGGT
196 AAAACGAATTTGGGT
* * * * *
84845 -CACTTCTCTATACCTCATCATGAAGATGACCGCTTTGTTGTTTCGACCCACTTCTCTGTATCTC
1 CCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTCTGTATCTC
* * * *
84909 ATCAAGAAGATGGGGGTTTGAAGTTTCACTCTCATTGAG-TTTCGCTTCATCAATTTGGTTTACT
66 ATCAAGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTT-GCTTCATCGATTTGGTCTACT
* *
84973 TCTCTATATCCCATCAAGAAGATGACC
130 TCTCTATATCTCATCAGGAAGATGACC
85000 GCTTCATCAT
Statistics
Matches: 326, Mismatches: 36, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
208 2 0.01
209 317 0.97
210 7 0.02
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (210 bp):
CCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTCTGTATCTC
ATCAAGAAGATGAGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATCGATTTGGTCTACTT
CTCTATATCTCATCAGGAAGATGACCATCTCATTATTTTAATCCACTTCTCTGTATCTCATCAGG
AAAACGAATTTGGGT
Found at i:87340 original size:3 final size:3
Alignment explanation
Indices: 87332--87358 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
87322 GATCATCCCT
87332 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
87359 AATATCGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:97083 original size:30 final size:30
Alignment explanation
Indices: 97049--97193 Score: 163
Period size: 30 Copynumber: 4.9 Consensus size: 30
97039 GCCAAATTTG
*
97049 AATTTTTGGAAAGTTTAAGGGTTAAATCCA
1 AATTTTTGGAAAGTTTAAGGGTCAAATCCA
** *
97079 AATTTTTAGG-AAGTTTGGGGGTCAAATCTA
1 AATTTTT-GGAAAGTTTAAGGGTCAAATCCA
* * *
97109 AATTTTTAGG-AAGTTT-AGAGTCGAATCTA
1 AATTTTT-GGAAAGTTTAAGGGTCAAATCCA
97138 AATTTTTGGAAAG-TTAAGGGGTCAAATCCA
1 AATTTTTGGAAAGTTTAA-GGGTCAAATCCA
*
97168 AATTTTTGGAAAGTTTAGGGGTCAAA
1 AATTTTTGGAAAGTTTAAGGGTCAAA
97194 ATATAGTTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
28 4 0.04
29 21 0.21
30 69 0.70
31 5 0.05
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTAAGGGTCAAATCCA
Found at i:97160 original size:59 final size:59
Alignment explanation
Indices: 97049--97185 Score: 170
Period size: 59 Copynumber: 2.3 Consensus size: 59
97039 GCCAAATTTG
* ** ** *
97049 AATTTTTGGAAAGTTTAAGGGTTAAATCCAAATTTTTAGGAAGTTTGGGGGTCAAATCTA
1 AATTTTTGGAAAGTTT-AGAGTCGAATCCAAATTTTTAGGAAGTTAAGGGGTCAAATCCA
*
97109 AATTTTTAGG-AAGTTTAGAGTCGAATCTAAATTTTT-GGAAAGTTAAGGGGTCAAATCCA
1 AATTTTT-GGAAAGTTTAGAGTCGAATCCAAATTTTTAGG-AAGTTAAGGGGTCAAATCCA
97168 AATTTTTGGAAAGTTTAG
1 AATTTTTGGAAAGTTTAG
97186 GGGTCAAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
58 4 0.06
59 48 0.72
60 13 0.19
61 2 0.03
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (59 bp):
AATTTTTGGAAAGTTTAGAGTCGAATCCAAATTTTTAGGAAGTTAAGGGGTCAAATCCA
Found at i:97840 original size:13 final size:13
Alignment explanation
Indices: 97809--97839 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
97799 GGTTTAACCC
97809 TTTTTTGTTTTAT
1 TTTTTTGTTTTAT
97822 TTTTTTG-TTTAT
1 TTTTTTGTTTTAT
97834 TTTTTT
1 TTTTTT
97840 TCACATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.87
Consensus pattern (13 bp):
TTTTTTGTTTTAT
Found at i:98431 original size:18 final size:18
Alignment explanation
Indices: 98419--98457 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
98409 TATAGCTGCT
98419 AAGAAAGTCATAGCCGCC
1 AAGAAAGTCATAGCCGCC
98437 AAGAAAGTCATAGCCGCC
1 AAGAAAGTCATAGCCGCC
98455 AAG
1 AAG
98458 TCTTCCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.26, G:0.23, T:0.10
Consensus pattern (18 bp):
AAGAAAGTCATAGCCGCC
Found at i:99745 original size:16 final size:15
Alignment explanation
Indices: 99720--99749 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
99710 CTCGTACCCA
99720 ATTTTTATATATATT
1 ATTTTTATATATATT
99735 ATTTTTAATATATAT
1 ATTTTT-ATATATAT
99750 ATTCTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTATATATATT
Found at i:100018 original size:21 final size:21
Alignment explanation
Indices: 99993--100032 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
99983 AACGAAGGCA
99993 AAATTTTATTTATTTACATTC
1 AAATTTTATTTATTTACATTC
100014 AAATTTTATTTATTTACAT
1 AAATTTTATTTATTTACAT
100033 AGTTTGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATTTTATTTATTTACATTC
Found at i:103605 original size:24 final size:24
Alignment explanation
Indices: 103570--103617 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
103560 ATTCTTTGCC
*
103570 TAAGGACTGCTTTTACGCTGTGGT
1 TAAGGACCGCTTTTACGCTGTGGT
103594 TAAGGACCGCTTTTACGCTGTGGT
1 TAAGGACCGCTTTTACGCTGTGGT
103618 CACCTATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (24 bp):
TAAGGACCGCTTTTACGCTGTGGT
Found at i:117608 original size:13 final size:13
Alignment explanation
Indices: 117590--117614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
117580 TAAGCAAAAA
117590 TGAGCATTTGAAT
1 TGAGCATTTGAAT
117603 TGAGCATTTGAA
1 TGAGCATTTGAA
117615 ACATAACCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (13 bp):
TGAGCATTTGAAT
Found at i:122761 original size:15 final size:16
Alignment explanation
Indices: 122741--122770 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
122731 ACTCCATACT
122741 TTAAAT-TTTATTTAC
1 TTAAATGTTTATTTAC
122756 TTAAATGTTTATTTA
1 TTAAATGTTTATTTA
122771 TTATTGCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TTAAATGTTTATTTAC
Found at i:126821 original size:80 final size:80
Alignment explanation
Indices: 126681--126836 Score: 224
Period size: 80 Copynumber: 1.9 Consensus size: 80
126671 GGCGCAAATC
* * *
126681 GTTGGTTAATCCAACTAGAACTGGTGTTACTTATCGCGGCTTATCCGCTAAGCACAGGGTGCCAT
1 GTTGGTTAATCCAACTAGAACTGGTCTCACTTATCGCGGCTTAACCGCTAAGCACAGGGTGCCAT
126746 GAATTGACAGACTTT
66 GAATTGACAGACTTT
* * * **
126761 GTTGGTTAATCCAACTAGAGCTAGG-CTCACTTATCGCGGTTTAACCGCTAGGCATTGGGTGCCA
1 GTTGGTTAATCCAACTAGAACT-GGTCTCACTTATCGCGGCTTAACCGCTAAGCACAGGGTGCCA
126825 TGAATTGACAGA
65 TGAATTGACAGA
126837 AATTATGAGC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 65 0.97
81 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (80 bp):
GTTGGTTAATCCAACTAGAACTGGTCTCACTTATCGCGGCTTAACCGCTAAGCACAGGGTGCCAT
GAATTGACAGACTTT
Found at i:126902 original size:2 final size:2
Alignment explanation
Indices: 126897--126930 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
126887 ACACACACAC
* *
126897 AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
126931 GGAGTAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:127369 original size:14 final size:14
Alignment explanation
Indices: 127350--127378 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
127340 GATTATAATT
127350 AAACGAACCAAGGC
1 AAACGAACCAAGGC
127364 AAACGAACCAAGGC
1 AAACGAACCAAGGC
127378 A
1 A
127379 CCACGTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.28, G:0.21, T:0.00
Consensus pattern (14 bp):
AAACGAACCAAGGC
Found at i:129377 original size:108 final size:109
Alignment explanation
Indices: 129211--129426 Score: 330
Period size: 108 Copynumber: 2.0 Consensus size: 109
129201 AATCAAGACA
*
129211 ATGTTCTTTTATTTAGAGAATTCGAGAAATTGTGCTCAAATGTATTTGGTATG-GTTTTTTCTTT
1 ATGTTCTTTTATTTAGAGAATTCGAGAAATTGTGCTCAAACGTA-TTGGTATGTGTTTTTTCTTT
129275 GAACCT-AATAATCAAATATCCTATTTAAAATCAATAAATGTTTG
65 GAACCTAAATAATCAAATATCCTATTTAAAATCAATAAATGTTTG
* *
129319 ATGTTCTTTTATTTAGGGAATTCGAGAAATTGTGCTCAAACGTA-TGGTATGATTTTTTTTTCTT
1 ATGTTCTTTTATTTAGAGAATTCGAGAAATTGTGCTCAAACGTATTGGTATG--TGTTTTTTCTT
* * *
129383 TGAACCTAAATAATCGAGTATCCTATTTTAAATCAATAAATGTT
64 TGAACCTAAATAATCAAATATCCTATTTAAAATCAATAAATGTT
129427 CTTTAGTTTC
Statistics
Matches: 98, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
106 7 0.07
108 42 0.43
109 16 0.16
110 33 0.34
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (109 bp):
ATGTTCTTTTATTTAGAGAATTCGAGAAATTGTGCTCAAACGTATTGGTATGTGTTTTTTCTTTG
AACCTAAATAATCAAATATCCTATTTAAAATCAATAAATGTTTG
Found at i:131144 original size:22 final size:22
Alignment explanation
Indices: 131119--131163 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
131109 TTTTTTAAAA
*
131119 ATGAAATGAAACAACTAAACCT
1 ATGAAAAGAAACAACTAAACCT
*
131141 ATGAAAAGAAATAACTAAACCT
1 ATGAAAAGAAACAACTAAACCT
131163 A
1 A
131164 AATTACAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.58, C:0.16, G:0.09, T:0.18
Consensus pattern (22 bp):
ATGAAAAGAAACAACTAAACCT
Found at i:134405 original size:2 final size:2
Alignment explanation
Indices: 134398--134422 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
134388 CATGTATTCC
134398 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
134423 CTTTTACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:135102 original size:30 final size:30
Alignment explanation
Indices: 135046--135185 Score: 144
Period size: 30 Copynumber: 4.7 Consensus size: 30
135036 TTTAAAAAAA
* *
135046 AATTTGACCCCT-AACTTTCTAAAAATTTG
1 AATTTGACCCCTAAATTTTCCAAAAATTTG
**
135075 AATTTGACCCCTAAATTTTCCAAAAATTCA
1 AATTTGACCCCTAAATTTTCCAAAAATTTG
* *
135105 AATTTGACCCCCAAATTTTACAAAAATTTTG
1 AATTTGACCCCTAAATTTTCCAAAAA-TTTG
* * *
135136 -ATTTAATCCCC-AAACTTTCCAAAAAATT-
1 AATTTGA-CCCCTAAATTTTCCAAAAATTTG
135164 AATTTGACCCCTAAAGTTTTCC
1 AATTTGACCCCTAAA-TTTTCC
135186 CTTGTCTCGG
Statistics
Matches: 91, Mismatches: 14, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
28 4 0.04
29 22 0.24
30 59 0.65
31 6 0.07
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (30 bp):
AATTTGACCCCTAAATTTTCCAAAAATTTG
Found at i:135115 original size:59 final size:59
Alignment explanation
Indices: 135045--135183 Score: 153
Period size: 59 Copynumber: 2.3 Consensus size: 59
135035 ATTTAAAAAA
* * *
135045 AAATTTGACCCCTAACTTTCT-AAAAA-TTTGAATTTGA-CCCCTAAATTTTCC-AAAAATT
1 AAATTTGACCCCTAAATTT-TAAAAAATTTTG-ATTTAATCCCC-AAACTTTCCAAAAAATT
*
135103 CAAATTTGACCCCCAAATTTTACAAAAATTTTGATTTAATCCCCAAACTTTCCAAAAAATT
1 -AAATTTGACCCCTAAATTTTA-AAAAATTTTGATTTAATCCCCAAACTTTCCAAAAAATT
135164 -AATTTGACCCCTAAAGTTTT
1 AAATTTGACCCCTAAA-TTTT
135184 CCCTTGTCTC
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
58 1 0.01
59 31 0.45
60 22 0.32
61 15 0.22
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (59 bp):
AAATTTGACCCCTAAATTTTAAAAAATTTTGATTTAATCCCCAAACTTTCCAAAAAATT
Found at i:146521 original size:50 final size:50
Alignment explanation
Indices: 146419--146538 Score: 118
Period size: 50 Copynumber: 2.4 Consensus size: 50
146409 CGCAATGGCA
* * * *
146419 AATCTTATACACCTAAAGCTATAAAGAGGCAGATTGAAGCCTCAACGGTG
1 AATCTCATACACCTAAAGCTATAAAGAGGCAGATTAAAGCCTCAAAGATG
* * *
146469 AATCTCATTCACCTAAAGCTATAAAG-GAGCGGATTAAAGTCGT-AAAGATG
1 AATCTCATACACCTAAAGCTATAAAGAG-GCAGATTAAAG-CCTCAAAGATG
* * *
146519 AATCTTATACTCCTGAAGCT
1 AATCTCATACACCTAAAGCT
146539 GAGGTGGAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
49 1 0.02
50 54 0.95
51 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (50 bp):
AATCTCATACACCTAAAGCTATAAAGAGGCAGATTAAAGCCTCAAAGATG
Found at i:146733 original size:80 final size:79
Alignment explanation
Indices: 146564--146855 Score: 298
Period size: 80 Copynumber: 3.7 Consensus size: 79
146554 TACAACCCCG
* * * *
146564 AATCTTTTACCCCAATCATGAGACAGATTGAAGAAATCCAATCGTTTACCCTAA-CTAGAGGGCA
1 AATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAATC-AGAGGGCA
* *
146628 AATTGGAGACCATCC
65 GATTGAAGACCATCC
* * * * * * *
146643 GATCTCTTACCCCGATCATGGGGGCGGATTGAAGGAATTCAATCTTTTACCCTAATCAAAGGGGA
1 AATCTTTTACCCCGATCAT-GGGGCAGATTGAAGAAATCCAATCTTTTACCCTAATCAGAGGGCA
* *
146708 GATTGAAGATCATTC
65 GATTGAAGACCATCC
* * *
146723 AATCTTTTACCCCGATCATAGGGTAGATTGAAGAAATCCAATCTTTTTACCCTAATCAGAGGGTA
1 AATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATC-TTTTACCCTAATCAGAGGGCA
* *
146788 GATTGGAGACCACCC
65 GATTGAAGACCATCC
* * ** * * * *
146803 ATTCTCTTACCCTAACCATGGGGCAGAGTGAAGCAATCCAATATTTTACCCTA
1 AATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTA
146856 TTGAAGACCA
Statistics
Matches: 172, Mismatches: 38, Indels: 6
0.80 0.18 0.03
Matches are distributed among these distances:
79 45 0.26
80 126 0.73
81 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (79 bp):
AATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAATCAGAGGGCAG
ATTGAAGACCATCC
Found at i:146786 original size:40 final size:39
Alignment explanation
Indices: 146564--146855 Score: 203
Period size: 40 Copynumber: 7.4 Consensus size: 39
146554 TACAACCCCG
* *
146564 AATCTTTTACCCCAATCATGA-GACAGATTGAAGAAATCC
1 AATCTTTTACCCTAATCA-GAGGGCAGATTGAAGAAATCC
* * * *
146603 AATCGTTTACCCTAA-CTAGAGGGCAAATTGGAGACCATCC
1 AATCTTTTACCCTAATC-AGAGGGCAGATTGAAGA-AATCC
* * ** * * * *
146643 GATCTCTTACCCCGATCATGGGGGCGGATTGAAGGAATTC
1 AATCTTTTACCCTAATCA-GAGGGCAGATTGAAGAAATCC
* * * *
146683 AATCTTTTACCCTAATCAAAGGGGAGATTGAAGATCATTC
1 AATCTTTTACCCTAATCAGAGGGCAGATTGAAGA-AATCC
** * *
146723 AATCTTTTACCCCGATCATAGGGTAGATTGAAGAAATCC
1 AATCTTTTACCCTAATCAGAGGGCAGATTGAAGAAATCC
* * * *
146762 AATCTTTTTACCCTAATCAGAGGGTAGATTGGAGACCACCC
1 AATC-TTTTACCCTAATCAGAGGGCAGATTGAAGA-AATCC
* * * * *
146803 ATTCTCTTACCCTAACCATG-GGGCAGAGTGAAGCAATCC
1 AATCTTTTACCCTAATCA-GAGGGCAGATTGAAGAAATCC
*
146842 AATATTTTACCCTA
1 AATCTTTTACCCTA
146856 TTGAAGACCA
Statistics
Matches: 192, Mismatches: 52, Indels: 18
0.73 0.20 0.07
Matches are distributed among these distances:
38 3 0.02
39 56 0.29
40 114 0.59
41 19 0.10
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (39 bp):
AATCTTTTACCCTAATCAGAGGGCAGATTGAAGAAATCC
Found at i:146853 original size:159 final size:159
Alignment explanation
Indices: 146564--146855 Score: 385
Period size: 159 Copynumber: 1.8 Consensus size: 159
146554 TACAACCCCG
146564 AATCTTTTACCCCAATCATGAGACAGATTGAAGAAATCCAATCGTTTACCCTAACTAGAGGGCAA
1 AATCTTTTACCCCAATCATGAGACAGATTGAAGAAATCCAATCGTTTACCCTAACTAGAGGGCAA
* * * * * * * *
146629 ATTGGAGACCATCCGATCTCTTACCCCGATCATGGGGGCGGATTGAAGGAATTCAATCTTTTACC
66 ATTGGAGACCATCCCATCTCTTACCCCAACCATGGGGGCAGAGTGAAGCAATCCAATATTTTACC
146694 CTAATCAAAGGGGAGATTGAAGATCATTC
131 CTAATCAAAGGGGAGATTGAAGATCATTC
* ** *
146723 AATCTTTTACCCCGATCAT-AGGGTAGATTGAAGAAATCCAATCTTTTTACCCTAA-TCAGAGGG
1 AATCTTTTACCCCAATCATGA-GACAGATTGAAGAAATCCAATC-GTTTACCCTAACT-AGAGGG
* * *
146786 TAGATTGGAGACCA-CCCATTCTCTTACCCTAACCAT-GGGGCAGAGTGAAGCAATCCAATATTT
63 CAAATTGGAGACCATCCCA-TCTCTTACCCCAACCATGGGGGCAGAGTGAAGCAATCCAATATTT
146849 TACCCTA
127 TACCCTA
146856 TTGAAGACCA
Statistics
Matches: 114, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
158 1 0.01
159 71 0.62
160 42 0.37
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (159 bp):
AATCTTTTACCCCAATCATGAGACAGATTGAAGAAATCCAATCGTTTACCCTAACTAGAGGGCAA
ATTGGAGACCATCCCATCTCTTACCCCAACCATGGGGGCAGAGTGAAGCAATCCAATATTTTACC
CTAATCAAAGGGGAGATTGAAGATCATTC
Found at i:148709 original size:59 final size:58
Alignment explanation
Indices: 148646--148842 Score: 225
Period size: 59 Copynumber: 3.3 Consensus size: 58
148636 TTAACTCGAG
* * *
148646 TTTTCTAAAAATTCAAAATTGAACCTTAAATTTTCTAAAAAATCAAATTTGACCCTAAA
1 TTTTCCAAAAATTC-AAATTGAACCTTAAATTTTCTAAAAATTCCAATTTGACCCTAAA
* * * * *
148705 TTTTCCAAAAATTCAAATTTAACCACTAAATTTTCCAAAAATTCCAATTTAACCCCAAA
1 TTTTCCAAAAATTCAAATTGAACC-TTAAATTTTCTAAAAATTCCAATTTGACCCTAAA
* * * * *
148764 CTTTCCAAAAATTCTAATTTAACCCTCAAACTTTCTAAAAATTCCAATTTGACCCTTAAA
1 TTTTCCAAAAATTCAAATTGAA-CCTTAAATTTTCTAAAAATTCCAATTTGACCC-TAAA
148824 GTTTT-CAAAAATTCAAATT
1 -TTTTCCAAAAATTCAAATT
148843 TGACCTAGTT
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
58 9 0.08
59 86 0.74
60 18 0.16
61 3 0.03
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (58 bp):
TTTTCCAAAAATTCAAATTGAACCTTAAATTTTCTAAAAATTCCAATTTGACCCTAAA
Found at i:148843 original size:30 final size:28
Alignment explanation
Indices: 148646--148847 Score: 197
Period size: 30 Copynumber: 6.8 Consensus size: 28
148636 TTAACTCGAG
* *
148646 TTTTCTAAAAATTCAAAATTGAACCTTAAA
1 TTTTC-AAAAATTCAAATTTG-ACCCTAAA
*
148676 TTTTCTAAAAAATCAAATTTGACCCTAAA
1 TTTTC-AAAAATTCAAATTTGACCCTAAA
*
148705 TTTTCCAAAAATTCAAATTTAACCACTAAA
1 TTTT-CAAAAATTCAAATTTGACC-CTAAA
* * *
148735 TTTTCCAAAAATTCCAATTTAACCCCAAA
1 TTTT-CAAAAATTCAAATTTGACCCTAAA
* * *
148764 CTTTCCAAAAATTCTAATTTAACCCTCAAA
1 -TTTTCAAAAATTCAAATTTGACCCT-AAA
* *
148794 CTTTCTAAAAATTCCAATTTGACCCTTAAA
1 TTTTC-AAAAATTCAAATTTGACCC-TAAA
148824 GTTTTCAAAAATTCAAATTTGACC
1 -TTTTCAAAAATTCAAATTTGACC
148848 TAGTTTTAAT
Statistics
Matches: 149, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
29 53 0.36
30 91 0.61
31 5 0.03
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (28 bp):
TTTTCAAAAATTCAAATTTGACCCTAAA
Found at i:154268 original size:10 final size:11
Alignment explanation
Indices: 154243--154268 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
154233 TGAGATAATA
154243 AAAAAAGAATG
1 AAAAAAGAATG
154254 AAAAAAGAATG
1 AAAAAAGAATG
154265 AAAA
1 AAAA
154269 TTTTGAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAAAAGAATG
Found at i:154584 original size:30 final size:30
Alignment explanation
Indices: 154550--154625 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
154540 CCTAAACTTC
* *
154550 CCAAAAATTTGAATTCAAAC-CCCAAGTTTT
1 CCAAAAATTTAAATT-AAACACCCAAATTTT
**
154580 CCAAAAATTTAAATTTGACACCCAAATTTT
1 CCAAAAATTTAAATTAAACACCCAAATTTT
*
154610 CCAAAAATTCAAATTA
1 CCAAAAATTTAAATTA
154626 GACCCATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 2 0.05
30 37 0.95
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (30 bp):
CCAAAAATTTAAATTAAACACCCAAATTTT
Found at i:154640 original size:60 final size:59
Alignment explanation
Indices: 154576--154748 Score: 163
Period size: 60 Copynumber: 2.9 Consensus size: 59
154566 AAACCCCAAG
* *
154576 TTTTCCAAAAATTTAAATTTGACACCCAAATTTTCCAAAAATTCAAATTAGACCCAT-AAA-
1 TTTT-CAAAAATTTAAATTTGAC-CCCAAACTTTCCAAAAATTCAAATTTGACCC-TCAAAC
** * * ***
154636 TTTTCTGAAATTTCCAATTTGTCCACCAAACTTTCCAAAAATTTTGATTTGACCCTCAAAC
1 TTTTCAAAAATTT-AAATTTGACC-CCAAACTTTCCAAAAATTCAAATTTGACCCTCAAAC
** *
154697 TTTTCAAAAATTTTGATTTGACCCCTAAAGTTT-CAAAAATTCAAATTTGACC
1 TTTTCAAAAATTTAAATTTGACCCC-AAACTTTCCAAAAATTCAAATTTGACC
154749 TGGTTTTAAT
Statistics
Matches: 90, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
59 27 0.30
60 52 0.58
61 11 0.12
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (59 bp):
TTTTCAAAAATTTAAATTTGACCCCAAACTTTCCAAAAATTCAAATTTGACCCTCAAAC
Found at i:154696 original size:30 final size:28
Alignment explanation
Indices: 154652--154737 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 28
154642 GAAATTTCCA
*
154652 ATTTGTCCACCAAACTTTCCAAAAATTTTG
1 ATTTGACC-CCAAACTTT-CAAAAATTTTG
154682 ATTTGACCCTCAAACTTTTCAAAAATTTTG
1 ATTTGACCC-CAAAC-TTTCAAAAATTTTG
*
154712 ATTTGACCCCTAAAGTTTCAAAAATT
1 ATTTGACCCC-AAACTTTCAAAAATT
154738 CAAATTTGAC
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
29 13 0.25
30 35 0.69
31 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (28 bp):
ATTTGACCCCAAACTTTCAAAAATTTTG
Found at i:154737 original size:90 final size:89
Alignment explanation
Indices: 154577--154745 Score: 198
Period size: 90 Copynumber: 1.9 Consensus size: 89
154567 AACCCCAAGT
*
154577 TTTCCAAAAATTTAAATTTGACACCCAAATTTTCCAAAAATTCAAATTAGACCCATAAATTTTCT
1 TTTCCAAAAATTTAAATTTGACACCCAAATTTTCCAAAAATTCAAATTAGACCCATAAAGTTTC-
* * *
154642 GAAATTTCCAATTTGTCCACCAAAC
65 AAAAATTCAAATTTGTCCACCAAAC
** *** * *
154667 TTTCCAAAAATTTTGATTTGAC-CCTCAAACTTTT-CAAAAATTTTGATTTGACCCCTAAAGTTT
1 TTTCCAAAAATTTAAATTTGACACC-CAAA-TTTTCCAAAAATTCAAATTAGACCCATAAAGTTT
154730 CAAAAATTCAAATTTG
64 CAAAAATTCAAATTTG
154746 ACCTGGTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
89 14 0.21
90 48 0.73
91 4 0.06
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (89 bp):
TTTCCAAAAATTTAAATTTGACACCCAAATTTTCCAAAAATTCAAATTAGACCCATAAAGTTTCA
AAAATTCAAATTTGTCCACCAAAC
Found at i:154835 original size:18 final size:18
Alignment explanation
Indices: 154792--154854 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
154782 TGTATATGCA
154792 TATGTATAT-TATTTTATTG
1 TATGTAT-TGTATTTTA-TG
154811 TATTGTATTGTATTTTATG
1 TA-TGTATTGTATTTTATG
*
154830 TATGTATTGTTTTTTTAT-
1 TATGTATTG-TATTTTATG
154848 TATGTAT
1 TATGTAT
154855 ACTTGTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 14 0.35
19 14 0.35
20 12 0.30
ACGTcount: A:0.22, C:0.00, G:0.13, T:0.65
Consensus pattern (18 bp):
TATGTATTGTATTTTATG
Found at i:161095 original size:52 final size:52
Alignment explanation
Indices: 161004--161297 Score: 453
Period size: 52 Copynumber: 5.7 Consensus size: 52
160994 GTAAATAAAG
* * *
161004 AAAAGGTCTGATAACTATGTGTTATCGTGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
* *
161056 AAATGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
*
161108 AAAAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
* *
161160 AAAAGGTCCGATGACTATGTGTCATCGTGAGAATATGATTCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
** * * * *
161212 AAAAGGTTTGATGACTATGTGTCATCATGAGTATATGATTCCTTCACGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
*
161264 AAGAGGTCCGATGACTATGTGTCATCGTGAGTAT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTAT
161298 TAAATAAAAT
Statistics
Matches: 221, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 221 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.36
Consensus pattern (52 bp):
AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
Found at i:166860 original size:3 final size:3
Alignment explanation
Indices: 166846--166908 Score: 92
Period size: 3 Copynumber: 21.3 Consensus size: 3
166836 AATAACAATC
* *
166846 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
166894 TAA TAA -AA TAT TAA T
1 TAA TAA TAA TAA TAA T
166909 TAATGATGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:167027 original size:4 final size:4
Alignment explanation
Indices: 167018--167115 Score: 57
Period size: 4 Copynumber: 25.5 Consensus size: 4
167008 AAAAAGACAT
* *
167018 AATA AATA AATA AA-A AATA AATG AATA AA-A ACA-A AATA AA-A AATG
1 AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA AATA AATA
* * * * *
167063 AATA TATA AAAA AAT- GATA AA-A TATGA ATTA AATA CAA-A AATA AATA
1 AATA AATA AATA AATA AATA AATA AAT-A AATA AATA -AATA AATA AATA
167110 AATA AA
1 AATA AA
167116 CAATAAACAA
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
3 15 0.21
4 52 0.73
5 4 0.06
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:167054 original size:26 final size:26
Alignment explanation
Indices: 167025--167115 Score: 75
Period size: 26 Copynumber: 3.5 Consensus size: 26
167015 CATAATAAAT
167025 AAATAAAAAATAAATGAATAAAAACA
1 AAATAAAAAATAAATGAATAAAAACA
* *
167051 AAATAAAAAATGAAT--ATATAAA-A
1 AAATAAAAAATAAATGAATAAAAACA
* *
167074 AAATGATAAAAT--ATGAATTAAATACAA
1 AAAT-AAAAAATAAATGAA-TAAAAAC-A
167101 AAATAAATAAATAAA
1 AAATAAA-AAATAAA
167116 CAATAAACAA
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
22 2 0.04
23 5 0.10
24 13 0.26
25 4 0.08
26 16 0.32
27 9 0.18
29 1 0.02
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (26 bp):
AAATAAAAAATAAATGAATAAAAACA
Found at i:167265 original size:25 final size:26
Alignment explanation
Indices: 167226--167279 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
167216 ATTAAAAACT
*
167226 AAAAAACAAATTAAA-GGTTAAAATA
1 AAAAAACAAATTAAATGATTAAAATA
*
167251 AAAAAACAGAA-TAAATGATTAAATTA
1 AAAAAACA-AATTAAATGATTAAAATA
167277 AAA
1 AAA
167280 CAATATACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (26 bp):
AAAAAACAAATTAAATGATTAAAATA
Found at i:169023 original size:101 final size:101
Alignment explanation
Indices: 168853--169282 Score: 367
Period size: 101 Copynumber: 4.3 Consensus size: 101
168843 CAATCTGACT
* * * * * *
168853 CACTACAACTTTAGGGGTATAGGATTTGATATG-GTAGCTTCATCTTGCTCTACTGTAACTTCAG
1 CACTGCAACTTCAGGGATATAGGATTTG-TATGTGTAGCCTCATCTTGCTCTACTATAACTTTAG
168917 AGAGATAAAAATTTGCTATTGTAA-TTTTAATTTGATC
65 AGAGATAAAAATTTGCT-TTGTAACTTTTAATTTGATC
* * * * *
168954 C-TTGCAACTTCAGGGATATAGGATTCGTATGTCGCAGCCTCATCTTGATCCACTATAACTTTAG
1 CACTGCAACTTCAGGGATATAGGATTTGTATGT-GTAGCCTCATCTTGCTCTACTATAACTTTAG
* * * * *
169018 GGAGATAAATATTTTCTTTTGTAATTTTTAATTTGACC
65 AGAGATAAAAATTTGC-TTTGTAACTTTTAATTTGATC
* * * *
169056 CACTGTAACTTTAGGGGTATAGGATTTG-ATGTTGTAGCCTCATCTTGCTCTACTACAACTTTAG
1 CACTGCAACTTCAGGGATATAGGATTTGTATG-TGTAGCCTCATCTTGCTCTACTATAACTTTAG
* * ***
169120 AGAGAT-AAGATTTGCTTTCGTAACTTTTGATCCAATC
65 AGAGATAAAAATTTGCTTT-GTAACTTTTAATTTGATC
* * * * * *
169157 CACTACAACTTCAGGGATATAGG-TCTTG-ATGT-T-GTCTGATCTTGCTCCACTGTAACTTTAA
1 CACTGCAACTTCAGGGATATAGGAT-TTGTATGTGTAGCCTCATCTTGCTCTACTATAACTTTAG
* * * * **
169218 AGAGATCAAGATTTGCTTCTGT-AGTTTCAATCCGATC
65 AGAGATAAAAATTTGCTT-TGTAACTTTTAATTTGATC
* *
169255 CATTGCAACTTCAGGGGTATAGGATTTG
1 CACTGCAACTTCAGGGATATAGGATTTG
169283 GAGTTATAAC
Statistics
Matches: 268, Mismatches: 50, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
98 62 0.23
99 19 0.07
100 27 0.10
101 89 0.33
102 49 0.18
103 22 0.08
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (101 bp):
CACTGCAACTTCAGGGATATAGGATTTGTATGTGTAGCCTCATCTTGCTCTACTATAACTTTAGA
GAGATAAAAATTTGCTTTGTAACTTTTAATTTGATC
Found at i:169398 original size:102 final size:102
Alignment explanation
Indices: 169271--169500 Score: 257
Period size: 102 Copynumber: 2.3 Consensus size: 102
169261 AACTTCAGGG
* * * * *
169271 GTATAGGATTTGGAGTTATAACTTCACTCCATTCCACTGCAACTTCT-GGGAGATTAAGATTTGC
1 GTATAGGATTTGGTGTTGTAGCTTCACTCCATTCCACTACAACTT-TAGGGAGATTAAGATCTGC
* * ** *
169335 TATTGTTAGTTTTAATTTGATCCACTACAA-TTTTAGA
65 TACTATTAGTTTTAATCCGACCCACTACAACTTTTAGA
* * * * * *
169372 GATATAGGATTTGGTTTTGTGGCTTCACTCTATTCCATTACAACTTTAGGGAGATTGAGATCTGT
1 G-TATAGGATTTGGTGTTGTAGCTTCACTCCATTCCACTACAACTTTAGGGAGATTAAGATCTGC
* **
169437 TACTATTGGTTTTAATCCGACCCACTGTAACTTTTAGA
65 TACTATTAGTTTTAATCCGACCCACTACAACTTTTAGA
169475 GTATAGGATTTGGTGTTGTAGCTTCA
1 GTATAGGATTTGGTGTTGTAGCTTCA
169501 TCCTACTCTA
Statistics
Matches: 105, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
101 2 0.02
102 95 0.90
103 8 0.08
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (102 bp):
GTATAGGATTTGGTGTTGTAGCTTCACTCCATTCCACTACAACTTTAGGGAGATTAAGATCTGCT
ACTATTAGTTTTAATCCGACCCACTACAACTTTTAGA
Found at i:170465 original size:7 final size:7
Alignment explanation
Indices: 170451--170511 Score: 63
Period size: 7 Copynumber: 8.9 Consensus size: 7
170441 TCTCGACCTC
170451 TCTTTTT
1 TCTTTTT
*
170458 TGTTTTT
1 TCTTTTT
170465 TCTTTTT
1 TCTTTTT
*
170472 T-TCCTTT
1 TCT-TTTT
*
170479 TCTCTTT
1 TCTTTTT
170486 TCTTTTT
1 TCTTTTT
170493 TCTTTTT
1 TCTTTTT
*
170500 TC-CTTT
1 TCTTTTT
170506 TCTTTT
1 TCTTTT
170512 CTTTCCTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
6 6 0.13
7 38 0.84
8 1 0.02
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (7 bp):
TCTTTTT
Found at i:170470 original size:5 final size:5
Alignment explanation
Indices: 170462--170530 Score: 56
Period size: 5 Copynumber: 13.8 Consensus size: 5
170452 CTTTTTTGTT
*
170462 TTTTC TTTT- TTTCC TTTTCTC TTTTC TTTT- TTCTT- TTTTCC TTTTC
1 TTTTC TTTTC TTTTC -TTT-TC TTTTC TTTTC TT-TTC TTTT-C TTTTC
*
170508 TTTTC TTTCC TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTT
170531 AGGTGAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
4 11 0.20
5 32 0.59
6 10 0.19
7 1 0.02
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:170470 original size:14 final size:13
Alignment explanation
Indices: 170451--170530 Score: 70
Period size: 14 Copynumber: 5.8 Consensus size: 13
170441 TCTCGACCTC
170451 TCTTTTTTGTTTTT
1 TCTTTTTT-TTTTT
*
170465 TCTTTTTTTCCTTT
1 TCTTTTTTT-TTTT
*
170479 TCTCTTTTCTTTTT
1 TCT-TTTTTTTTTT
**
170493 TCTTTTTTCCTTT
1 TCTTTTTTTTTTT
*
170506 TCTTTTCTTTCCTTT
1 TCTTTT-TTT-TTTT
170521 TCTTTTTTTT
1 TCTTTTTTTT
170531 AGGTGAAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
13 14 0.26
14 25 0.46
15 15 0.28
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:170490 original size:35 final size:35
Alignment explanation
Indices: 170451--170528 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 35
170441 TCTCGACCTC
*
170451 TCTTTTTTGTTTTTT-CTTTT-TTTCCTTTTCTCTTT
1 TCTTTTTTCTTTTTTCCTTTTCTTTCC-TTTC-CTTT
*
170486 TCTTTTTTCTTTTTTCCTTTTCTTTTCTTTCCTTT
1 TCTTTTTTCTTTTTTCCTTTTCTTTCCTTTCCTTT
170521 TCTTTTTT
1 TCTTTTTT
170529 TTAGGTGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 26 0.67
36 9 0.23
37 4 0.10
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.79
Consensus pattern (35 bp):
TCTTTTTTCTTTTTTCCTTTTCTTTCCTTTCCTTT
Found at i:170493 original size:20 final size:21
Alignment explanation
Indices: 170462--170528 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 21
170452 CTTTTTTGTT
170462 TTTTCTTTTTTTCCTTTTCTC
1 TTTTCTTTTTTTCCTTTTCTC
*
170483 TTTTC-TTTTTT-CTTTTTTCC
1 TTTTCTTTTTTTCCTTTTCT-C
*
170503 TTTTCTTTTCTTTCCTTTTCTT
1 TTTTCTTTT-TTTCCTTTTCTC
170525 TTTT
1 TTTT
170529 TTAGGTGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 6 0.15
20 12 0.31
21 8 0.21
22 7 0.18
23 6 0.15
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTCTTTTTTTCCTTTTCTC
Found at i:170493 original size:28 final size:26
Alignment explanation
Indices: 170455--170529 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 26
170445 GACCTCTCTT
*
170455 TTTTGTTTTTTCTTTTTTTCCTTTTCTC
1 TTTTCTTTTTTCTTTTTTTCC-TTT-TC
170483 TTTTCTTTTTTC-TTTTTTCCTTTTC
1 TTTTCTTTTTTCTTTTTTTCCTTTTC
170508 TTTTCTTTCCTTTTCTTTTTTT
1 TTTTC-TT--TTTTCTTTTTTT
170530 TAGGTGAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 7 0.17
26 5 0.12
27 8 0.19
28 16 0.38
29 6 0.14
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (26 bp):
TTTTCTTTTTTCTTTTTTTCCTTTTC
Found at i:176419 original size:19 final size:20
Alignment explanation
Indices: 176395--176439 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
176385 TGTAAATTAT
* *
176395 TTTATTCATTTGTTC-TTTA
1 TTTATTCATTTATTCGGTTA
176414 TTTATTCATTTATTCGGTTA
1 TTTATTCATTTATTCGGTTA
176434 TTTATT
1 TTTATT
176440 TACTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.18, C:0.09, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTATTCATTTATTCGGTTA
Found at i:176494 original size:18 final size:18
Alignment explanation
Indices: 176447--176500 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
176437 ATTTACTTTA
176447 TTTATTATCT-TATTGTAT
1 TTTATTAT-TATATTGTAT
176465 TTTATGTA-TATATTGT-T
1 TTTAT-TATTATATTGTAT
176482 TTTATTATTTATACTTGTA
1 TTTATTA-TTATA-TTGTA
176501 AATCATGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 2 0.07
17 7 0.23
18 15 0.50
19 6 0.20
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTATTATTATATTGTAT
Found at i:198223 original size:39 final size:39
Alignment explanation
Indices: 198166--198261 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 39
198156 GAAGTCACCA
** *
198166 CATCCAATCTCTTT-CCCTGGTCATGGGGCA-ATTGAAGAC
1 CATCCAATCT-TTTACCCTGACCATGGGGCAGATTAAAG-C
198205 CATCCAATCTTTTACCCTGACCATGGGGCAGATTAAAGC
1 CATCCAATCTTTTACCCTGACCATGGGGCAGATTAAAGC
*
198244 AATCCAATCTTTTACCCT
1 CATCCAATCTTTTACCCT
198262 AATCAGAGGG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 3 0.06
39 42 0.82
40 6 0.12
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (39 bp):
CATCCAATCTTTTACCCTGACCATGGGGCAGATTAAAGC
Found at i:199709 original size:28 final size:29
Alignment explanation
Indices: 199667--199759 Score: 98
Period size: 36 Copynumber: 3.0 Consensus size: 29
199657 CGATATTCGA
* *
199667 TTTACTTCCTGTTGACCCAAAGGTCATGC
1 TTTACTCCCTATTGACCCAAAGGTCATGC
199696 -TTACTCCCTATTGACCCAAAGGTCATGATGCTC
1 TTTACTCCCTATTGACCCAAAGGTC---ATG--C
199729 ATTTTACTCCCTATTGACCCAAAGGTCATGC
1 --TTTACTCCCTATTGACCCAAAGGTCATGC
199760 CTGTTACCAG
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
28 22 0.41
31 4 0.07
33 4 0.07
36 24 0.44
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (29 bp):
TTTACTCCCTATTGACCCAAAGGTCATGC
Found at i:201399 original size:40 final size:39
Alignment explanation
Indices: 201291--201421 Score: 165
Period size: 39 Copynumber: 3.3 Consensus size: 39
201281 GTAGACCATT
* *
201291 CAATCTTTTACCCCGACCATGGGGCAAATTGAAGCAATC
1 CAATCTTTTACCCTGACCATGGGGCAGATTGAAGCAATC
* * * *
201330 CAATCTTTTACCCTAACCA-GAGGGTAGATTGAGGACCATC
1 CAATCTTTTACCCTGACCATG-GGGCAGATTGAAG-CAATC
* *
201370 CAATCTCTTACCCTGATCATGGGGCAGATTGAAGCAATC
1 CAATCTTTTACCCTGACCATGGGGCAGATTGAAGCAATC
201409 CAATCTTTTACCC
1 CAATCTTTTACCC
201422 CTAAAGCTAT
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 1 0.01
39 43 0.57
40 31 0.41
41 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (39 bp):
CAATCTTTTACCCTGACCATGGGGCAGATTGAAGCAATC
Found at i:201488 original size:50 final size:51
Alignment explanation
Indices: 201410--201512 Score: 127
Period size: 50 Copynumber: 2.0 Consensus size: 51
201400 GAAGCAATCC
* *
201410 AATCTTTTACCCCTAAAGCTATAGAGGGGTAAATTAAAGCT-ACAGAAGTA
1 AATCTTATACCCCTAAAGCTATAGAGGGGTAAATTAAAACTCACAGAAGTA
* * * ** *
201460 AATCTTATACCCCTAAAGTTGTATAGGGGTGGATTAAAACTCACAGTAGTA
1 AATCTTATACCCCTAAAGCTATAGAGGGGTAAATTAAAACTCACAGAAGTA
201511 AA
1 AA
201513 CTTTGATCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 34 0.77
51 10 0.23
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (51 bp):
AATCTTATACCCCTAAAGCTATAGAGGGGTAAATTAAAACTCACAGAAGTA
Found at i:208641 original size:37 final size:37
Alignment explanation
Indices: 208591--208665 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
208581 GGGTACCGTG
208591 GAGCTATGACTACAGCGTAACGATACTAAATGATGAA
1 GAGCTATGACTACAGCGTAACGATACTAAATGATGAA
208628 GAGCTATGACTACAGCGTAACGATACTAAATGATGAA
1 GAGCTATGACTACAGCGTAACGATACTAAATGATGAA
208665 G
1 G
208666 GATCGAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (37 bp):
GAGCTATGACTACAGCGTAACGATACTAAATGATGAA
Found at i:215609 original size:24 final size:23
Alignment explanation
Indices: 215582--215651 Score: 58
Period size: 24 Copynumber: 3.2 Consensus size: 23
215572 TTTTTACTGA
*
215582 TTTGGTGTTACTTTTGCTGTTAGT
1 TTTGGTGCTACTTTTGCTGTT-GT
* * *
215606 TTTGTTGCTATTTTTGTTGTTGT
1 TTTGGTGCTACTTTTGCTGTTGT
*
215629 TTT-GT--TA-TTTTGTTGTTGT
1 TTTGGTGCTACTTTTGCTGTTGT
215648 TTTG
1 TTTG
215652 ATTGTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 15 0.38
20 2 0.05
22 1 0.03
23 5 0.12
24 17 0.43
ACGTcount: A:0.06, C:0.04, G:0.23, T:0.67
Consensus pattern (23 bp):
TTTGGTGCTACTTTTGCTGTTGT
Found at i:215630 original size:23 final size:22
Alignment explanation
Indices: 215593--215668 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 22
215583 TTGGTGTTAC
*
215593 TTTTGCTGTTAGTTTTGTTGCTAT
1 TTTTGTTGTT-GTTTTGTTG-TAT
215617 TTTTGTTGTTGTTTTG-T-TA-
1 TTTTGTTGTTGTTTTGTTGTAT
*
215636 TTTTGTTGTTGTTTTGATTGTTT
1 TTTTGTTGTTGTTTTG-TTGTAT
215659 TTTTGTTGTT
1 TTTTGTTGTT
215669 TGGATGTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
19 16 0.35
20 2 0.04
21 1 0.02
22 2 0.04
23 16 0.35
24 9 0.20
ACGTcount: A:0.05, C:0.03, G:0.21, T:0.71
Consensus pattern (22 bp):
TTTTGTTGTTGTTTTGTTGTAT
Found at i:215640 original size:31 final size:32
Alignment explanation
Indices: 215599--215669 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
215589 TTACTTTTGC
215599 TGTTAGTTTTGTTGCTAT-TTTTG-TTGTTGTTT
1 TGTTAGTTTTGTTG-T-TGTTTTGATTGTTGTTT
*
215631 TGTTA-TTTTGTTGTTGTTTTGATTGTTTTTT
1 TGTTAGTTTTGTTGTTGTTTTGATTGTTGTTT
215662 TGTT-GTTT
1 TGTTAGTTT
215670 GGATGTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
29 1 0.03
30 6 0.17
31 23 0.66
32 5 0.14
ACGTcount: A:0.06, C:0.01, G:0.21, T:0.72
Consensus pattern (32 bp):
TGTTAGTTTTGTTGTTGTTTTGATTGTTGTTT
Found at i:215669 original size:11 final size:11
Alignment explanation
Indices: 215605--215669 Score: 55
Period size: 12 Copynumber: 6.0 Consensus size: 11
215595 TTGCTGTTAG
*
215605 TTTTGTTGCTAT
1 TTTTGTTG-TTT
215617 TTTTGTTG--T
1 TTTTGTTGTTT
* *
215626 TGTT-TTGTTA
1 TTTTGTTGTTT
*
215636 TTTTGTTGTTG
1 TTTTGTTGTTT
215647 TTTTGATTGTTT
1 TTTTG-TTGTTT
215659 TTTTGTTGTTT
1 TTTTGTTGTTT
215670 GGATGTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
8 3 0.07
9 4 0.09
10 3 0.07
11 16 0.36
12 18 0.41
ACGTcount: A:0.05, C:0.02, G:0.20, T:0.74
Consensus pattern (11 bp):
TTTTGTTGTTT
Found at i:215670 original size:19 final size:19
Alignment explanation
Indices: 215529--215683 Score: 78
Period size: 20 Copynumber: 7.4 Consensus size: 19
215519 ATTATATTGC
215529 TATTTTTTTGTTGTTTTGGT
1 TATTTTTTTGTTGTTTT-GT
** * *
215549 GCTGTTTTTTGCTGTTTTGG
1 TAT-TTTTTTGTTGTTTTGT
**
215569 T-TTTTTTTACTGATTTGGTGT
1 TATTTTTTTGTTG-TTT--TGT
**
215590 TACTTTTGCTGTTAGTTTTGTT
1 TA-TTTTTTTGTT-GTTTTG-T
215612 GCTATTTTTGTTGTTGTTTTGT
1 --TATTTTT-TTGTTGTTTTGT
*
215634 TATTTTGTTGTTGTTTTGAT
1 TATTTTTTTGTTGTTTTG-T
*
215654 TGTTTTTTTGTTGTTTGGATGT
1 TATTTTTTTGTTGTTT---TGT
215676 TATTTTTT
1 TATTTTTT
215684 ATGCATTTTT
Statistics
Matches: 103, Mismatches: 17, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
18 9 0.09
19 15 0.15
20 23 0.22
21 18 0.17
22 10 0.10
23 21 0.20
24 7 0.07
ACGTcount: A:0.06, C:0.04, G:0.21, T:0.68
Consensus pattern (19 bp):
TATTTTTTTGTTGTTTTGT
Found at i:215677 original size:42 final size:41
Alignment explanation
Indices: 215531--215681 Score: 121
Period size: 42 Copynumber: 3.6 Consensus size: 41
215521 TATATTGCTA
* * * * *
215531 TTTTTTTGTTGTTTTGGTGCTGTTTT-TTGCTGTTTTGGT-
1 TTTTTTTGTTGATTTGGTGTTATTTTGTTGTTGTTTTGTTG
** *
215570 TTTTTTTACTGATTTGGTGTTACTTTTGCTGTTAGTTTTGTTG
1 TTTTTTTGTTGATTTGGTGTTA-TTTTGTTGTT-GTTTTGTTG
* **
215613 CTATTTTTGTTG-TTGTTTTGTTATTTTGTTGTTGTTTTGATTG
1 -TTTTTTTGTTGATT-TGGTGTTATTTTGTTGTTGTTTTG-TTG
215656 TTTTTTTGTTG-TTTGGATGTTATTTT
1 TTTTTTTGTTGATTTGG-TGTTATTTT
215682 TTATGCATTT
Statistics
Matches: 87, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
39 17 0.20
40 4 0.05
41 4 0.05
42 34 0.39
43 14 0.16
44 14 0.16
ACGTcount: A:0.06, C:0.04, G:0.22, T:0.68
Consensus pattern (41 bp):
TTTTTTTGTTGATTTGGTGTTATTTTGTTGTTGTTTTGTTG
Found at i:215828 original size:20 final size:19
Alignment explanation
Indices: 215788--215830 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
215778 CATCTTAATA
215788 TAAATTTTTTTAATGTATTT
1 TAAATTTTTTTAA-GTATTT
215808 TAAATTTATTTTAA-TACTTT
1 TAAATTT-TTTTAAGTA-TTT
215828 TAA
1 TAA
215831 GTGTATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.10
20 13 0.62
21 6 0.29
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TAAATTTTTTTAAGTATTT
Found at i:220575 original size:20 final size:20
Alignment explanation
Indices: 220550--220590 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
220540 TGCTTGCTCC
220550 TCTTCTCTTTACAAAGGAAA
1 TCTTCTCTTTACAAAGGAAA
220570 TCTTCTCTTTACAAAGGAAA
1 TCTTCTCTTTACAAAGGAAA
220590 T
1 T
220591 AAATATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCTTCTCTTTACAAAGGAAA
Found at i:225296 original size:20 final size:18
Alignment explanation
Indices: 225249--225355 Score: 69
Period size: 19 Copynumber: 5.8 Consensus size: 18
225239 ACAAGATAAC
225249 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
225266 ATTAAGA-TAATTACTTTAAT
1 ATTAA-ATTAA-TA-TTTAAT
***
225286 ATTAAATTAATAAAAAACT
1 ATTAAATTAATATTTAA-T
*
225305 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
*
225322 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
225342 ATTAAAATAATATT
1 ATTAAATTAATATT
225356 ATTTTTCGAA
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
17 16 0.23
18 9 0.13
19 23 0.33
20 22 0.31
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:225341 original size:37 final size:36
Alignment explanation
Indices: 225281--225356 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 36
225271 GATAATTACT
225281 TTAATATTAAATTAATAAAAAACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAAAACTATTAAAATAA-TA
**
225318 TTAA-ATTAAATTTAATATTAAACTATTAAAATAATA
1 TTAATATTAAA-TTAATAAAAAACTATTAAAATAATA
225354 TTA
1 TTA
225357 TTTTTCGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 11 0.31
37 25 0.69
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAAAACTATTAAAATAATA
Found at i:232561 original size:16 final size:16
Alignment explanation
Indices: 232550--232610 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
232540 TTAATTACTT
232550 TAATATTAAATTAATA
1 TAATATTAAATTAATA
* * *
232566 TAATATT-TATCAAGA
1 TAATATTAAATTAATA
* *
232581 TAAATATTAGATTAAATT
1 T-AATATTAAATT-AATA
232599 TAATATTAAATT
1 TAATATTAAATT
232611 TTATTAAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
15 6 0.18
16 13 0.38
17 12 0.35
18 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (16 bp):
TAATATTAAATTAATA
Found at i:232624 original size:59 final size:60
Alignment explanation
Indices: 232553--232669 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 60
232543 ATTACTTTAA
* * * * *
232553 TATTAAATTAATATAATATTTATC-AAGATAAATATTAGATTAAATTTAATATTAAATTT
1 TATTAAAATAATAAAATATTTATCTAAGAAAAACATTAAATTAAATTTAATATTAAATTT
*
232612 TATTAAAATAATAAAATATTTATCTTGTAGAAAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAAAATATTTATC-T-AAGAAAAACATTAAATTAAATTTAATATTAA
232670 GAAAATCACT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 22 0.45
62 27 0.55
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (60 bp):
TATTAAAATAATAAAATATTTATCTAAGAAAAACATTAAATTAAATTTAATATTAAATTT
Found at i:232699 original size:25 final size:26
Alignment explanation
Indices: 232660--232708 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
232650 TAAATTAAAT
232660 TTAATATTAAGAAAATCACT-TTAATA
1 TTAATATTAAGAAAAT-ACTATTAATA
*
232686 TTAA-ATTAATAAAATACTATTAA
1 TTAATATTAAGAAAATACTATTAA
232709 AATAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (26 bp):
TTAATATTAAGAAAATACTATTAATA
Found at i:232742 original size:37 final size:37
Alignment explanation
Indices: 232680--232750 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
232670 GAAAATCACT
232680 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
*
232717 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAA
232751 TTTTATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 6 0.19
37 23 0.74
38 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (37 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
Found at i:236445 original size:12 final size:12
Alignment explanation
Indices: 236428--236460 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
236418 TAAGTTAAAA
236428 ATGCTAAAATGC
1 ATGCTAAAATGC
236440 ATGCTAAAATGC
1 ATGCTAAAATGC
236452 ATGCTAAAA
1 ATGCTAAAA
236461 AATGATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (12 bp):
ATGCTAAAATGC
Found at i:249012 original size:28 final size:28
Alignment explanation
Indices: 248955--249013 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
248945 ATTCTCCGAA
* * *
248955 AAAGTGAGCCTTTGTGGTTGATTTTCTT
1 AAAGTGAGCCTTTGTGATTGATTCTATT
*
248983 AAAGTGAGTCTTTGTGATTGATTCTATT
1 AAAGTGAGCCTTTGTGATTGATTCTATT
249011 AAA
1 AAA
249014 TGGAGAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.44
Consensus pattern (28 bp):
AAAGTGAGCCTTTGTGATTGATTCTATT
Found at i:249080 original size:28 final size:28
Alignment explanation
Indices: 249049--249152 Score: 104
Period size: 28 Copynumber: 3.7 Consensus size: 28
249039 AAAGTGACAT
* *
249049 TTTGTAGCTAATTCTGATAAATGAAGTC
1 TTTGTGGCTAATTCTGATAAATGAAGCC
* *
249077 TTTGTGGTTAATT-TTATTAAAGTG-AGCC
1 TTTGTGGCTAATTCTGA-TAAA-TGAAGCC
* *
249105 TTTGTGGCTAATTATGTTAAATGAAGCC
1 TTTGTGGCTAATTCTGATAAATGAAGCC
* *
249133 TTTGCGGCTAATTCTAATAA
1 TTTGTGGCTAATTCTGATAA
249153 TAGAGCTTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
27 4 0.07
28 54 0.89
29 3 0.05
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (28 bp):
TTTGTGGCTAATTCTGATAAATGAAGCC
Found at i:249081 original size:56 final size:55
Alignment explanation
Indices: 249021--249146 Score: 137
Period size: 56 Copynumber: 2.3 Consensus size: 55
249011 AAATGGAGAA
* * * *
249021 TTTGTGACTAATTCAGTTAAAGTGA-CATTTTGTAGCTAATTCTGATAAATGAAGTC
1 TTTGTGGCTAATTCA-TTAAAGTGAGC-CTTTGTAGCTAATTATGATAAATGAAGCC
* * * *
249077 TTTGTGGTTAATTTTATTAAAGTGAGCCTTTGTGGCTAATTATGTTAAATGAAGCC
1 TTTGTGGCTAA-TTCATTAAAGTGAGCCTTTGTAGCTAATTATGATAAATGAAGCC
*
249133 TTTGCGGCTAATTC
1 TTTGTGGCTAATTC
249147 TAATAATAGA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
55 2 0.04
56 51 0.89
57 4 0.07
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (55 bp):
TTTGTGGCTAATTCATTAAAGTGAGCCTTTGTAGCTAATTATGATAAATGAAGCC
Found at i:258468 original size:167 final size:166
Alignment explanation
Indices: 258169--258497 Score: 534
Period size: 167 Copynumber: 2.0 Consensus size: 166
258159 TGAACTCTGA
* *
258169 GACCTTGAACTTGGGAGGAGTACCAAATCTAGGACCAGACTTATCTCTTTAGCGTCTATCTCATA
1 GACCTTGAACTTGGGAGGAGTACCAAATCTAGGACCAGACTTAACTCATTAGCGTCTATCTCATA
* * *
258234 GGAGTTTTTAGTTCCTTGCATCGCCTCAATCTTTTCCTTTAATCGCTTATATTTTTCGTCCATCT
66 GGAGTTTTCAGTTCCTTGCATCGCCTCAATCTTTTCCTCTAATCACTTATATTTTTCGTCCATCT
258299 GTCTAGGAAGATCTGCTCTCATCATCTCATCGTTGG
131 GTCTAGGAAGATCTGCTCTCATCATCTCATCGTTGG
* * *
258335 GACCTTTAACTTGGGAGGGAGTATCAAATCTAGGAGCAGACTTAACTCATTAGCGTCTATC-CTA
1 GACCTTGAACTTGGGA-GGAGTACCAAATCTAGGACCAGACTTAACTCATTAGCGTCTATCTC-A
* *
258399 TAGGAGTTTTCAGTTCCTTGCATCGCCTCAATCTTTTCCTCTAATCACTTATATTTTTCTTTCAT
64 TAGGAGTTTTCAGTTCCTTGCATCGCCTCAATCTTTTCCTCTAATCACTTATATTTTTCGTCCAT
*
258464 CTGTCTAGGAAGATCTGCTCTGATCATCTCATCG
129 CTGTCTAGGAAGATCTGCTCTCATCATCTCATCG
258498 AAGTCCGAGA
Statistics
Matches: 150, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
166 16 0.11
167 134 0.89
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (166 bp):
GACCTTGAACTTGGGAGGAGTACCAAATCTAGGACCAGACTTAACTCATTAGCGTCTATCTCATA
GGAGTTTTCAGTTCCTTGCATCGCCTCAATCTTTTCCTCTAATCACTTATATTTTTCGTCCATCT
GTCTAGGAAGATCTGCTCTCATCATCTCATCGTTGG
Found at i:262500 original size:30 final size:30
Alignment explanation
Indices: 262464--262771 Score: 304
Period size: 30 Copynumber: 10.4 Consensus size: 30
262454 GTTAAAATGT
*
262464 AATGTAATTTTAGAAAAAGTTT-GGGGTAAA
1 AATGTAATTTTAG-AAAAGTTTAGGGGTTAA
*
262494 AATGTAATTTTAGGAAAGTTT-GGTGGTTAA
1 AATGTAATTTTAGAAAAGTTTAGG-GGTTAA
* * * *
262524 AATGTTATTTTAGAGAAGTTTAGAGGTCAA
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAA
* * * *
262554 AATGTAAATTTATAATAGTTTAAGGGTTAA
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAA
* **
262584 AATGTGATTTTA-AAGAAGTTTAGGAATTAA
1 AATGTAATTTTAGAA-AAGTTTAGGGGTTAA
* * * * *
262614 AATGCAATTTT-GGAAATTTTAAGGGTTAG
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAA
* *
262643 AATGCAATTTTAGAAAATTTTAGGGGTTAA
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAA
* *
262673 AATGTAATTTTAGAAAAGTTT-GAGGTTAG
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAA
*
262702 AATGTAATTTTGGAAAAGTTTAGGGGTTAA
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAA
* * *
262732 AATGTAATTTTAGAAACGTTTA-TGGTCAA
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAA
*
262761 AATGTGATTTT
1 AATGTAATTTT
262772 CAAAGAAAAT
Statistics
Matches: 228, Mismatches: 44, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
29 73 0.32
30 154 0.68
31 1 0.00
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (30 bp):
AATGTAATTTTAGAAAAGTTTAGGGGTTAA
Found at i:262765 original size:59 final size:59
Alignment explanation
Indices: 262464--262771 Score: 311
Period size: 59 Copynumber: 5.2 Consensus size: 59
262454 GTTAAAATGT
* *
262464 AATGTAATTTTAGAAAAAGTTT-GGGGTAAAAATGTAATTTTAGGAAAGTTT-GGTGGTTAA
1 AATGTAATTTTAG-AAAAGTTTAGGGGTTAAAATGTAATTTTA-GAAAGTTTAAG-GGTTAA
* * * * * *
262524 AATGTTATTTTAGAGAAGTTTAGAGGTCAAAATGTAAATTTATAATAGTTTAAGGGTTAA
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAA-AGTTTAAGGGTTAA
* ** * * * *
262584 AATGTGATTTTA-AAGAAGTTTAGGAATTAAAATGCAATTTTGGAAATTTTAAGGGTTAG
1 AATGTAATTTTAGAA-AAGTTTAGGGGTTAAAATGTAATTTTAGAAAGTTTAAGGGTTAA
* * * *
262643 AATGCAATTTTAGAAAATTTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTGA-GGTTAG
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAG-AAAGTTTAAGGGTTAA
* * *
262702 AATGTAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAACGTTT-ATGGTCAA
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAA-GTTTAAGGGTTAA
*
262761 AATGTGATTTT
1 AATGTAATTTT
262772 CAAAGAAAAT
Statistics
Matches: 206, Mismatches: 34, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
58 4 0.02
59 119 0.58
60 82 0.40
61 1 0.00
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (59 bp):
AATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAGTTTAAGGGTTAA
Found at i:263979 original size:11 final size:11
Alignment explanation
Indices: 263963--263997 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
263953 GTCTGAAAGC
263963 TTTGAATCTGA
1 TTTGAATCTGA
263974 TTTGAATCTGA
1 TTTGAATCTGA
263985 TTTGAATCT-A
1 TTTGAATCTGA
263995 TTT
1 TTT
263998 TTTTTTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (11 bp):
TTTGAATCTGA
Found at i:275789 original size:2 final size:2
Alignment explanation
Indices: 275784--275820 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
275774 AGGATAAAAA
275784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
275821 ACAAATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:277066 original size:24 final size:25
Alignment explanation
Indices: 277037--277086 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
277027 GGTTTTCTTA
* *
277037 ATGGGTGTTTAGG-TTTTGGGCTTG
1 ATGGGTCTTTAGGATATTGGGCTTG
*
277061 ATGGGTCTTTTGGATATTGGGCTTG
1 ATGGGTCTTTAGGATATTGGGCTTG
277086 A
1 A
277087 GTTTGGGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.12, C:0.06, G:0.38, T:0.44
Consensus pattern (25 bp):
ATGGGTCTTTAGGATATTGGGCTTG
Found at i:277468 original size:8 final size:8
Alignment explanation
Indices: 277451--277479 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
277441 TGTATTGATC
277451 TTTTTT-T
1 TTTTTTCT
277458 TTTTTTCT
1 TTTTTTCT
277466 TTTTTTCT
1 TTTTTTCT
277474 TTTTTT
1 TTTTTT
277480 ATAAAGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (8 bp):
TTTTTTCT
Found at i:277468 original size:14 final size:15
Alignment explanation
Indices: 277449--277478 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
277439 GATGTATTGA
277449 TCTTTTTTT-TTTTT
1 TCTTTTTTTCTTTTT
277463 TCTTTTTTTCTTTTT
1 TCTTTTTTTCTTTTT
277478 T
1 T
277479 TATAAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TCTTTTTTTCTTTTT
Found at i:277807 original size:15 final size:15
Alignment explanation
Indices: 277787--277838 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
277777 TGTTTGATAA
277787 ATTAAAATTTTAAAT
1 ATTAAAATTTTAAAT
*
277802 ATTAAAAATTTAAACT
1 ATTAAAATTTTAAA-T
*
277818 ATTAAAATTTTGAAT
1 ATTAAAATTTTAAAT
*
277833 ACTAAA
1 ATTAAA
277839 TTTAAGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTAAAATTTTAAAT
Found at i:277811 original size:16 final size:16
Alignment explanation
Indices: 277790--277838 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
277780 TTGATAAATT
277790 AAAATTTTAAATATTA
1 AAAATTTTAAATATTA
277806 AAAA-TTTAAACTATT-
1 AAAATTTTAAA-TATTA
* *
277821 AAAATTTTGAATACTA
1 AAAATTTTAAATATTA
277837 AA
1 AA
277839 TTTAAGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTTTAAATATTA
Found at i:277874 original size:23 final size:22
Alignment explanation
Indices: 277848--277907 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
277838 ATTTAAGTTA
*
277848 TAAAATATATTTGATATATTACT
1 TAAAATATATTTGATATA-TAAT
*
277871 TAAAACTA-ATTATGAAATATAAT
1 TAAAA-TATATT-TGATATATAAT
277894 T-AAAT-TATTTGATA
1 TAAAATATATTTGATA
277908 AATATAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
20 4 0.13
21 4 0.13
22 3 0.10
23 12 0.39
24 8 0.26
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (22 bp):
TAAAATATATTTGATATATAAT
Found at i:279158 original size:21 final size:21
Alignment explanation
Indices: 279134--279177 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
279124 TTATAAAAGA
279134 AGAAGAAAA-AAACAGAAAAAT
1 AGAA-AAAATAAACAGAAAAAT
* *
279155 AGAAAAAATAAAGAGAAGAAT
1 AGAAAAAATAAACAGAAAAAT
279176 AG
1 AG
279178 TTTAGATACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (21 bp):
AGAAAAAATAAACAGAAAAAT
Found at i:283239 original size:13 final size:14
Alignment explanation
Indices: 283210--283259 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
283200 TTAAAACTTA
283210 TTTTC-TTTTCACT
1 TTTTCATTTTCACT
*
283223 TTTTCATTTTCTC-
1 TTTTCATTTTCACT
283236 TTTTCATCTCTTCACT
1 TTTTCAT-T-TTCACT
283252 TTTTCATT
1 TTTTCATT
283260 CAACCAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 12 0.39
14 7 0.23
15 5 0.16
16 7 0.23
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTCATTTTCACT
Found at i:293507 original size:53 final size:53
Alignment explanation
Indices: 293445--293553 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
293435 ACAAGTCGTA
293445 ACATACACACAAAATAAATTATTTTAATCTCATCATATCATACCTTAAACATG
1 ACATACACACAAAATAAATTATTTTAATCTCATCATATCATACCTTAAACATG
293498 ACATACACACAAAATAAATTATTTTAATCTCATCATATCATACCTTAAACATG
1 ACATACACACAAAATAAATTATTTTAATCTCATCATATCATACCTTAAACATG
293551 ACA
1 ACA
293554 ATTACCATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (53 bp):
ACATACACACAAAATAAATTATTTTAATCTCATCATATCATACCTTAAACATG
Found at i:299187 original size:31 final size:32
Alignment explanation
Indices: 299124--299188 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
299114 TTAACCCTGT
299124 ACTTTGGGTTATCCTATTTATTCTAAAAAAAA
1 ACTTTGGGTTATCCTATTTATTCTAAAAAAAA
299156 ACTTTGGGTTATCCTATTTATTCTAAAAAAAA
1 ACTTTGGGTTATCCTATTTATTCTAAAAAAAA
299188 A
1 A
299189 AAGAATCTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (32 bp):
ACTTTGGGTTATCCTATTTATTCTAAAAAAAA
Found at i:308173 original size:31 final size:31
Alignment explanation
Indices: 308135--308214 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
308125 TAGTTTTATT
308135 AAAGTGATAATATCGAATACTATTAAAAAAA
1 AAAGTGATAATATCGAATACTATTAAAAAAA
308166 AAAGTGATAATATCGAATACTATTAAAAAAA
1 AAAGTGATAATATCGAATACTATTAAAAAAA
*
308197 AAAGTGATAATCTCGAAT
1 AAAGTGATAATATCGAAT
308215 GTTTGGATCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.26
Consensus pattern (31 bp):
AAAGTGATAATATCGAATACTATTAAAAAAA
Found at i:308324 original size:31 final size:31
Alignment explanation
Indices: 308286--308369 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
308276 AATTTTAAAA
* *
308286 TTATATATTAATTTTAGTTTAATGTGTAATT
1 TTATATATAAATTTTAGTTTAATGTATAATT
* **
308317 TTATATATGACCTTTAGTTT--TGTATAATT
1 TTATATATAAATTTTAGTTTAATGTATAATT
*
308346 TTATATATAAAATTTTAATTTAAT
1 TTATATAT-AAATTTTAGTTTAAT
308370 CTAACTCTCA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
29 16 0.38
30 8 0.19
31 17 0.40
32 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (31 bp):
TTATATATAAATTTTAGTTTAATGTATAATT
Found at i:308905 original size:17 final size:17
Alignment explanation
Indices: 308865--308906 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
308855 TTTATTTCAT
*
308865 TTATC-TTTTAATTAAT
1 TTATCATTTTAATTAAA
308881 TTCA-CATTTTAATTAAA
1 TT-ATCATTTTAATTAAA
308898 TTATCATTT
1 TTATCATTT
308907 ATTTTAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATCATTTTAATTAAA
Found at i:310916 original size:21 final size:21
Alignment explanation
Indices: 310890--310929 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
310880 CTCGAAAAAA
*
310890 GTCAACGATTAACAGTCAATG
1 GTCAACGATCAACAGTCAATG
*
310911 GTCAACGATCAACGGTCAA
1 GTCAACGATCAACAGTCAA
310930 CGGTTTCGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (21 bp):
GTCAACGATCAACAGTCAATG
Found at i:316823 original size:14 final size:15
Alignment explanation
Indices: 316804--316832 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
316794 ATCATCTTCA
316804 CATCACAAT-ACAAT
1 CATCACAATAACAAT
316818 CATCACAATAACAAT
1 CATCACAATAACAAT
316833 ATACCTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
CATCACAATAACAAT
Found at i:317399 original size:26 final size:26
Alignment explanation
Indices: 317369--317452 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
317359 AATGGTTAAT
* * *
317369 GGGTTTAGGTTGTCGGGTTGATCAAC
1 GGGTTCAGGTTGTCGAGTCGATCAAC
*
317395 GGGTTCAGGTTGTCGAGTCGATTAAC
1 GGGTTCAGGTTGTCGAGTCGATCAAC
* * * * *
317421 GGGTTCAAGTCGTCGGGTCAATCAAT
1 GGGTTCAGGTTGTCGAGTCGATCAAC
317447 GGGTTC
1 GGGTTC
317453 GGGTCATTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.18, C:0.15, G:0.36, T:0.31
Consensus pattern (26 bp):
GGGTTCAGGTTGTCGAGTCGATCAAC
Found at i:325163 original size:42 final size:42
Alignment explanation
Indices: 325116--325201 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
325106 GTCATAAGTG
* * *
325116 TTCCTTTAATCATAATCTCACTCTCATCTTGAGACATGACTC
1 TTCCTTTAATCATAATATCACTCTAATCTCGAGACATGACTC
* *
325158 TTCCTTTAATCATAATATCATTCTAATCTCGAGACATGAGTC
1 TTCCTTTAATCATAATATCACTCTAATCTCGAGACATGACTC
325200 TT
1 TT
325202 TCATTTATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (42 bp):
TTCCTTTAATCATAATATCACTCTAATCTCGAGACATGACTC
Found at i:332121 original size:42 final size:42
Alignment explanation
Indices: 332048--332236 Score: 231
Period size: 42 Copynumber: 4.5 Consensus size: 42
332038 TATGCTCTAA
* * *
332048 CGAGTCATAAGTCATCCTTTAATCATATTCTCATTCTCAACCT
1 CGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTC-ACCT
* *
332091 -GAGACATGAGTCTTCCTTCAATCATATTCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCACCT
* *
332132 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCACCT
* * *
332174 CGAGACATGAGTATTCCATTT-ATACAAATTCTCATGCTCAACC-
1 CGAGACATGAGTCTTCC-TTTAAT-CATATTCTCATTCTC-ACCT
332217 CGAGACATGAGTCTTCCTTT
1 CGAGACATGAGTCTTCCTTT
332237 TTATATATCA
Statistics
Matches: 129, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
41 3 0.02
42 93 0.72
43 31 0.24
44 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.36
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCACCT
Found at i:334526 original size:102 final size:102
Alignment explanation
Indices: 334335--334539 Score: 347
Period size: 102 Copynumber: 2.0 Consensus size: 102
334325 ATTTTCTTCT
334335 GCTCTTGCATTATTCATCATTGTTGAGTATGCTAGTGAAATATTAGATGAAATTGGGGGGACTTC
1 GCTCTTGCATTATTCATCATTGTTGAGTATGCTAGTGAAATATTAGATGAAATTGGGGGGACTTC
* * *
334400 CATCCTGTCTAGCAAAGATTGATTGAGCTATATTTGA
66 CATCCTATCTACCAAAGATAGATTGAGCTATATTTGA
* *
334437 GCTCTTGCATTATTCGTCATTGTTGAGTATGCTGGTGAAATATTAGATGAAATTGGGGGGACTTC
1 GCTCTTGCATTATTCATCATTGTTGAGTATGCTAGTGAAATATTAGATGAAATTGGGGGGACTTC
* *
334502 CATCCTATCTACCATAGATAGATTGGGCTATATTTGA
66 CATCCTATCTACCAAAGATAGATTGAGCTATATTTGA
334539 G
1 G
334540 GAATTATCTA
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (102 bp):
GCTCTTGCATTATTCATCATTGTTGAGTATGCTAGTGAAATATTAGATGAAATTGGGGGGACTTC
CATCCTATCTACCAAAGATAGATTGAGCTATATTTGA
Found at i:338071 original size:3 final size:3
Alignment explanation
Indices: 338063--338089 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
338053 TAGTAAGGGC
338063 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
338090 ATAGGCTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:341470 original size:58 final size:57
Alignment explanation
Indices: 341408--341636 Score: 232
Period size: 58 Copynumber: 3.9 Consensus size: 57
341398 TTAGTCATGT
*
341408 CATAGCCGAAACC-ACCTTTATCAGATAAAATAAATCA-TTTTTTTGGTGTCGCCCAAAA
1 CATAGCCGACACCTA-CTTTATCAGATAAAA-AAAT-ATTTTTTTTGGTGTCGCCCAAAA
* * *
341466 CATAGCTGACACCTATTTTATCAGAT-AAAAAATAATTTTTTTTGGTGTAGCCCAAAA
1 CATAGCCGACACCTACTTTATCAGATAAAAAAAT-ATTTTTTTTGGTGTCGCCCAAAA
* * * ** ***
341523 CATGGCCGACACCTAATTTATCAGATAAAAAAATATTTTTTTCTGATGTCATCCATGC
1 CATAGCCGACACCTACTTTATCAGATAAAAAAATATTTTTTT-TGGTGTCGCCCAAAA
* *
341581 CATGGCCGACACC-ACCTTTATCTGATAAAAAAATATTTTTTTCTTGGTGTCGCCCA
1 CATAGCCGACACCTA-CTTTATCAGATAAAAAAATA-TTTTTT-TTGGTGTCGCCCA
341637 TGCCATGGTC
Statistics
Matches: 144, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
56 5 0.03
57 55 0.38
58 67 0.47
59 16 0.11
60 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (57 bp):
CATAGCCGACACCTACTTTATCAGATAAAAAAATATTTTTTTTGGTGTCGCCCAAAA
Found at i:341534 original size:57 final size:56
Alignment explanation
Indices: 341424--341636 Score: 205
Period size: 57 Copynumber: 3.7 Consensus size: 56
341414 CGAAACCACC
* * * * *
341424 TTTATCAGATAAAATAAATCATTTTTTTGGTGTCGCCCAAAACATAGCTGACACCTAT
1 TTTATCAGATAAAAAAAAT--TTTTTTTGGTGTAGCCCAAAACATGGCCGACACCTAA
341482 TTTATCAGATAAAAAATAATTTTTTTTGGTGTAGCCCAAAACATGGCCGACACCTAA
1 TTTATCAGATAAAAAA-AATTTTTTTTGGTGTAGCCCAAAACATGGCCGACACCTAA
* * *** *
341539 TTTATCAGATAAAAAAATATTTTTTTCTGATGTCA-TCCATGCCATGGCCGACACC-ACC
1 TTTATCAGATAAAAAAA-ATTTTTTT-TGGTGT-AGCCCAAAACATGGCCGACACCTA-A
* *
341597 TTTATCTGATAAAAAAATATTTTTTTCTTGGTGTCGCCCA
1 TTTATCAGATAAAAAAA-A-TTTTTT-TTGGTGTAGCCCA
341637 TGCCATGGTC
Statistics
Matches: 132, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
56 1 0.01
57 58 0.44
58 54 0.41
59 18 0.14
60 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (56 bp):
TTTATCAGATAAAAAAAATTTTTTTTGGTGTAGCCCAAAACATGGCCGACACCTAA
Found at i:343248 original size:30 final size:30
Alignment explanation
Indices: 343213--343329 Score: 144
Period size: 30 Copynumber: 3.8 Consensus size: 30
343203 AAAAAATAAT
* * *
343213 AATTAGAAATGAAATTTAAAATAAAAATGA
1 AATTACAAATTAAATTTAAAATAAAAACGA
* * *
343243 AATTAGAAATTAAATTGAAAATATAAACGA
1 AATTACAAATTAAATTTAAAATAAAAACGA
* *
343273 AATTACAAATTAAATTTAATATATAAACGA
1 AATTACAAATTAAATTTAAAATAAAAACGA
343303 AATTACAAATTAAATTTCGAAAATAAA
1 AATTACAAATTAAATTT--AAAATAAA
343330 CGAAAAAATC
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
30 70 0.92
32 6 0.08
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (30 bp):
AATTACAAATTAAATTTAAAATAAAAACGA
Done.