Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000295.1 Hibiscus syriacus cultivar Beakdansim tig00000541_pilon, 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: 2017499
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 2 of 9
Found at i:178826 original size:40 final size:40
Alignment explanation
Indices: 178747--178827 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
178737 ATAGGAGTCA
* * *
178747 AATATTGCATCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCATCGAAGTACTGAGGTCGAGCTTTACTCACCT
*
178787 AATAATGCATCGTAGTACTGAGGTCGAGCTTTAAC-CACCT
1 AATAATGCATCGAAGTACTGAGGTCGAGCTTT-ACTCACCT
178827 A
1 A
178828 GTACACTGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 35 0.97
41 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (40 bp):
AATAATGCATCGAAGTACTGAGGTCGAGCTTTACTCACCT
Found at i:185513 original size:45 final size:45
Alignment explanation
Indices: 185456--185632 Score: 309
Period size: 45 Copynumber: 3.9 Consensus size: 45
185446 AATTTTGTAT
* *
185456 CAATATACTTACCATTTATCCCATAAGCTCGTAGGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
185501 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
185546 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTCATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
**
185591 TGATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
185633 GCATGCTTAC
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 126 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:185587 original size:25 final size:25
Alignment explanation
Indices: 185513--185587 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
185503 ATATACTTAC
185513 CATTTATTCCATAAGCTCGTAAGCT
1 CATTTATTCCATAAGCTCGTAAGCT
* *
185538 TATTT-TACCAATATA-CT--T-A-C-
1 CATTTATTCC-ATA-AGCTCGTAAGCT
185558 CATTTATTCCATAAGCTCGTAAGCT
1 CATTTATTCCATAAGCTCGTAAGCT
185583 CATTT
1 CATTT
185588 TACTGATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
19 1 0.03
20 9 0.24
21 4 0.11
22 2 0.05
23 2 0.05
24 4 0.11
25 14 0.38
26 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (25 bp):
CATTTATTCCATAAGCTCGTAAGCT
Found at i:187480 original size:67 final size:67
Alignment explanation
Indices: 187372--187970 Score: 849
Period size: 67 Copynumber: 8.9 Consensus size: 67
187362 TTACATTAAT
187372 TGTGCATTGACAGAAAGGTG-CTAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
1 TGTGCATTGACAGAAAGGTGTC-AATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
187436 AAC
65 AAC
* * * *
187439 TGTGCATTGACAGAAATGTGACAATTATGCCAGTTAAATGAAAGGCTAAGTGCCTTTAAGGCCTA
1 TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTA
**
187504 GT
66 AC
*
187506 TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAATGCTAAGTGCCTTTGAGGCCT
1 TGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
*
187571 ATC
65 AAC
*
187574 TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGAGGAAAGGCTAAGTGCCTTTGAGGCCTA
1 TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTA
**
187639 GT
66 AC
* * * * *
187641 TGTGCATTTGACAGAATGGTGTCAATTATGCCAGTTAGACGAAAGGCTAAGAGCCTTTAAGGTCT
1 TGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
187706 AAC
65 AAC
* * *
187709 TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTATATGAAAGGGTGAGTGCCTTTGAGGCCTA
1 TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTA
187774 AC
66 AC
* * * ** *
187776 TGTGCATTAACATAAAGGTGTCAATTATGCCAGTTAGATAAAAGTTTAAGTGCCTTTGAGACCTA
1 TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTA
*
187841 GC
66 AC
* * * *
187843 TGTACATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGTTAAGTGCCTTTAAGGCCT
1 TGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
187908 AAC
65 AAC
* * * *
187911 TATGCATTGACAGAAAGGTGTCAATTATGCCAATTATATGAATGGCTAAGTGCCTTTGAG
1 TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
187971 TAAAAGACTA
Statistics
Matches: 471, Mismatches: 57, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
67 293 0.62
68 178 0.38
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (67 bp):
TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTA
AC
Found at i:187620 original size:135 final size:134
Alignment explanation
Indices: 187368--187970 Score: 857
Period size: 135 Copynumber: 4.5 Consensus size: 134
187358 GGTATTACAT
187368 TAATTGTGCATTGACAGAAAGGTG-CTAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 TAATTGTGCATTGACAGAAAGGTGTC-AATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
* * *
187432 GCCTAACTGTGCATTGACAGAAATGTGACAATTATGCCAGTTAAATGAAAGGCTAAGTGCCTTTA
65 GCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTA
187497 AGGCC
130 AGGCC
* *
187502 TAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAATGCTAAGTGCCTTTGAG
1 TAATTGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
* * *
187567 GCCTATCTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGAGGAAAGGCTAAGTGCCTTTG
65 GCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTA
187632 AGGCC
130 AGGCC
* * * * *
187637 TAGTTGTGCATTTGACAGAATGGTGTCAATTATGCCAGTTAGACGAAAGGCTAAGAGCCTTTAAG
1 TAATTGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
* * * * *
187702 GTCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTATATGAAAGGGTGAGTGCCTTTG
65 GCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTA
187767 AGGCC
130 AGGCC
* * * * ** *
187772 TAACTGTGCATTAACATAAAGGTGTCAATTATGCCAGTTAGATAAAAGTTTAAGTGCCTTTGAGA
1 TAATTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGG
* * * *
187837 CCTAGCTGTACATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGTTAAGTGCCTTTA
66 CCTAACTGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTA
187902 AGGCC
130 AGGCC
* * * * *
187907 TAACTATGCATTGACAGAAAGGTGTCAATTATGCCAATTATATGAATGGCTAAGTGCCTTTGAG
1 TAATTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
187971 TAAAAGACTA
Statistics
Matches: 418, Mismatches: 48, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
134 63 0.15
135 354 0.85
136 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (134 bp):
TAATTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGG
CCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTAA
GGCC
Found at i:187721 original size:202 final size:202
Alignment explanation
Indices: 187372--187970 Score: 891
Period size: 202 Copynumber: 3.0 Consensus size: 202
187362 TTACATTAAT
187372 TGTGCATTGACAGAAAGGTG-CTAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
1 TGTGCATTGACAGAAAGGTGTC-AATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCT
* * *
187436 AACTGTGCA-TTGACAGAAAT-GTGACAATTATGCCAGTTAAATGAAAGGCTAAGTGCCTTTAAG
65 AGCTGTGCATTTGACAG-AATGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTAAG
** *
187499 GCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAATGCTAAGTGCCTTT
129 GCCTAACTGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTATATGAAATGCTAAGTGCCTTT
*
187564 GAGGCCTATC
193 GAGGCCTAAC
*
187574 TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGAGGAAAGGCTAAGTGCCTTTGAGGCCTA
1 TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTA
* * * *
187639 GTTGTGCATTTGACAGAATGGTGTCAATTATGCCAGTTAGACGAAAGGCTAAGAGCCTTTAAGGT
66 GCTGTGCATTTGACAGAATGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTAAGGC
* * *
187704 CTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTATATGAAAGGGTGAGTGCCTTTGAG
131 CTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTATATGAAATGCTAAGTGCCTTTGAG
187769 GCCTAAC
196 GCCTAAC
* * * ** *
187776 TGTGCATTAACATAAAGGTGTCAATTATGCCAGTTAGATAAAAGTTTAAGTGCCTTTGAGACCTA
1 TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTA
* * * *
187841 GCTGTACATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGTTAAGTGCCTTTAAGGC
66 GCTGTGCATTTGACAGAATGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTAAGGC
* *
187906 CTAACTATGCATTGACAGAAAGGTGTCAATTATGCCAATTATATG-AATGGCTAAGTGCCTTTGA
131 CTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTATATGAAAT-GCTAAGTGCCTTTGA
187970 G
195 G
187971 TAAAAGACTA
Statistics
Matches: 358, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
201 2 0.01
202 299 0.84
203 57 0.16
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (202 bp):
TGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTA
GCTGTGCATTTGACAGAATGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTAAGGC
CTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTATATGAAATGCTAAGTGCCTTTGAG
GCCTAAC
Found at i:188043 original size:46 final size:46
Alignment explanation
Indices: 187991--188453 Score: 641
Period size: 46 Copynumber: 10.2 Consensus size: 46
187981 GATGTATAGC
* *
187991 AATGCATAATAGCGTATAAAAGGGCATGAAAAGATGCCATAAATGA
1 AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
188037 AATGCATAATAGCATATAAAA-GGCATGAAAGGATGCCATAAATGA
1 AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
* * * *
188082 AATGTATAATAGCGTATAAAAGGGCATGAAAGGATGTCATAATTGA
1 AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
* * *
188128 ACTGTATAATAGCATATAAAAGGCCATGAAAGGATGCCATAAATGA
1 AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
* *
188174 AATGCATAATATCATATAAAA-GGCATGAAATGATGCCATAAATGA
1 AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
* *** *
188219 AATGTATAATAATGTATAAAAGGGCATGAAAGGATGTCATAAATGA
1 AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
* ** *
188265 AATGTATAATA--ACGTAAAAGGGCATGAAAGGATACCATAAATGA
1 AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
*
188309 AATGCATAATAACATATAAAA-GGCATGAAAGGATGCCATAAATGA
1 AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
* * *
188354 AATGTATAATAGCATATAAAAGGACATGAAAGGATGCCATAAATAA
1 AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
* *
188400 AATGCATAATAGCGTATAAAA-GGCATGAAAGGATGCCATAAATAA
1 AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
*
188445 AATTCATAA
1 AATGCATAA
188454 GGGTGCATTA
Statistics
Matches: 373, Mismatches: 39, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
44 38 0.10
45 154 0.41
46 181 0.49
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (46 bp):
AATGCATAATAGCATATAAAAGGGCATGAAAGGATGCCATAAATGA
Found at i:188151 original size:91 final size:91
Alignment explanation
Indices: 187991--188447 Score: 668
Period size: 91 Copynumber: 5.0 Consensus size: 91
187981 GATGTATAGC
* *
187991 AATGCATAATAGCGTATAAAAGGGCATGAAAAGATGCCATAAATGAAATGCATAATAGCATATAA
1 AATGTATAATAGCGTATAAAAGGGCATGAAAGGATGCCATAAATGAAATGCATAATAGCATATAA
188056 AAGGCATGAAAGGATGCCATAAATGA
66 AAGGCATGAAAGGATGCCATAAATGA
* * * *
188082 AATGTATAATAGCGTATAAAAGGGCATGAAAGGATGTCATAATTGAACTGTATAATAGCATATAA
1 AATGTATAATAGCGTATAAAAGGGCATGAAAGGATGCCATAAATGAAATGCATAATAGCATATAA
188147 AAGGCCATGAAAGGATGCCATAAATGA
66 AAGG-CATGAAAGGATGCCATAAATGA
* * * * * ***
188174 AATGCATAATATCATATAAAA-GGCATGAAATGATGCCATAAATGAAATGTATAATAATGTATAA
1 AATGTATAATAGCGTATAAAAGGGCATGAAAGGATGCCATAAATGAAATGCATAATAGCATATAA
*
188238 AAGGGCATGAAAGGATGTCATAAATGA
66 AA-GGCATGAAAGGATGCCATAAATGA
* * *
188265 AATGTATAATAACG--TAAAAGGGCATGAAAGGATACCATAAATGAAATGCATAATAACATATAA
1 AATGTATAATAGCGTATAAAAGGGCATGAAAGGATGCCATAAATGAAATGCATAATAGCATATAA
188328 AAGGCATGAAAGGATGCCATAAATGA
66 AAGGCATGAAAGGATGCCATAAATGA
* * * *
188354 AATGTATAATAGCATATAAAAGGACATGAAAGGATGCCATAAATAAAATGCATAATAGCGTATAA
1 AATGTATAATAGCGTATAAAAGGGCATGAAAGGATGCCATAAATGAAATGCATAATAGCATATAA
*
188419 AAGGCATGAAAGGATGCCATAAATAA
66 AAGGCATGAAAGGATGCCATAAATGA
188445 AAT
1 AAT
188448 TCATAAGGGT
Statistics
Matches: 327, Mismatches: 34, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
89 40 0.12
90 40 0.12
91 205 0.63
92 42 0.13
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.22
Consensus pattern (91 bp):
AATGTATAATAGCGTATAAAAGGGCATGAAAGGATGCCATAAATGAAATGCATAATAGCATATAA
AAGGCATGAAAGGATGCCATAAATGA
Found at i:193651 original size:13 final size:13
Alignment explanation
Indices: 193635--193665 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
193625 GTCAACGGGT
*
193635 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
193648 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
193661 CGGGT
1 CGGGT
193666 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:193698 original size:10 final size:10
Alignment explanation
Indices: 193678--193732 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
193668 ACGGGTCGTG
193678 ACCGGTC-AA
1 ACCGGTCAAA
193687 ACCGGTCAAA
1 ACCGGTCAAA
193697 ACCGGTTCAAA
1 ACCGG-TCAAA
* *
193708 ACTGGT-TAA
1 ACCGGTCAAA
193717 ACCGGTCAAA
1 ACCGGTCAAA
193727 ACCGGT
1 ACCGGT
193733 TTCCAACGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
9 14 0.36
10 16 0.41
11 9 0.23
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:193718 original size:20 final size:19
Alignment explanation
Indices: 193678--193733 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
193668 ACGGGTCGTG
*
193678 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
*
193697 ACCGGTTCAAAACTGGTTAA
1 ACCGG-TCAAAACCGGTTAA
193717 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
193734 TCCAACGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.50
20 9 0.28
21 7 0.22
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:201492 original size:18 final size:18
Alignment explanation
Indices: 201469--201509 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
201459 CAACGGTCAA
201469 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
201487 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
201505 CGGGT
1 CGGGT
201510 AAACGGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:201509 original size:13 final size:13
Alignment explanation
Indices: 201463--201492 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
201453 ACGGGTCAAC
201463 GGTCAACGGGTCG
1 GGTCAACGGGTCG
201476 GGTCAACGGGTCG
1 GGTCAACGGGTCG
201489 GGTC
1 GGTC
201493 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:201514 original size:13 final size:13
Alignment explanation
Indices: 201487--201517 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
201477 GTCAACGGGT
*
201487 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
201500 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
201513 CGGGT
1 CGGGT
201518 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:201544 original size:9 final size:9
Alignment explanation
Indices: 201530--201578 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
201520 ACGGGTCGTG
201530 ACCGGTCAA
1 ACCGGTCAA
201539 ACCGGTCAAA
1 ACCGGTC-AA
201549 ACCGGTTCAAA
1 ACCGG-TC-AA
*
201560 ACCGGTTAA
1 ACCGGTCAA
*
201569 ACCGATCAA
1 ACCGGTCAA
201578 A
1 A
201579 ATCGGTTTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 17 0.49
10 8 0.23
11 10 0.29
ACGTcount: A:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:201552 original size:19 final size:20
Alignment explanation
Indices: 201530--201584 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
201520 ACGGGTCGTG
201530 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGTCAAA
*
201549 ACCGGTTCAAAACCGGT-TAA
1 ACCGG-TCAAAACCGGTCAAA
* *
201569 ACCGATCAAAATCGGT
1 ACCGGTCAAAACCGGT
201585 TTCCAACGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 15 0.48
20 8 0.26
21 8 0.26
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.16
Consensus pattern (20 bp):
ACCGGTCAAAACCGGTCAAA
Found at i:201560 original size:11 final size:11
Alignment explanation
Indices: 201537--201566 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
201527 GTGACCGGTC
201537 AAACCGG-TCA
1 AAACCGGTTCA
201547 AAACCGGTTCA
1 AAACCGGTTCA
201558 AAACCGGTT
1 AAACCGGTT
201567 AAACCGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.17
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:204826 original size:21 final size:21
Alignment explanation
Indices: 204800--204876 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
204790 AAACCAAAGT
204800 AGTATCGGTACCATAACTAAG
1 AGTATCGGTACCATAACTAAG
* *
204821 AGTATCAGTACTACTACACTAAG
1 AGTATCGGTACCA-TA-ACTAAG
* * *
204844 TAGTATCGATACCGT-A-TATG
1 -AGTATCGGTACCATAACTAAG
204864 -GTATCGGTACCAT
1 AGTATCGGTACCAT
204877 TTTAGCGTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
18 11 0.25
20 3 0.07
21 12 0.27
22 2 0.05
23 7 0.16
24 9 0.20
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (21 bp):
AGTATCGGTACCATAACTAAG
Found at i:209595 original size:25 final size:26
Alignment explanation
Indices: 209551--209601 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
209541 GTCAGGCGAA
* *
209551 CTTGGCTCGGGTTGGTTTGTTGGGTT
1 CTTGGCTCGGGTCGGCTTGTTGGGTT
209577 CTTGGCT-GGGTCGGCTTGTTGGGTT
1 CTTGGCTCGGGTCGGCTTGTTGGGTT
209602 AGGCTTGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.00, C:0.14, G:0.43, T:0.43
Consensus pattern (26 bp):
CTTGGCTCGGGTCGGCTTGTTGGGTT
Found at i:209784 original size:30 final size:32
Alignment explanation
Indices: 209740--209799 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
209730 ATAATACTAG
*
209740 ACTATATAATATATAAATATATTTTTAAAAAA
1 ACTATATAATATATAAATATATTTTCAAAAAA
209772 ACTATATAATATAT--ATATATTTTCAAAA
1 ACTATATAATATATAAATATATTTTCAAAA
209800 TATTTTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 13 0.48
32 14 0.52
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (32 bp):
ACTATATAATATATAAATATATTTTCAAAAAA
Found at i:209803 original size:41 final size:39
Alignment explanation
Indices: 209762--209838 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
209752 ATAAATATAT
209762 TTTTAAAAAAACTATATAATATATATATATTTTCAAAATA
1 TTTT-AAAAAACTATATAATATATATATATTTTCAAAATA
* * * *
209802 TTTTCAAAAACTATATATTATATATATTTTTTTAAAA
1 TTTTAAAAAACTATATAATATATATATATTTTCAAAA
209839 ACTATATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 29 0.88
40 4 0.12
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (39 bp):
TTTTAAAAAACTATATAATATATATATATTTTCAAAATA
Found at i:209816 original size:28 final size:28
Alignment explanation
Indices: 209797--209899 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 28
209787 TATATTTTCA
209797 AAATATTTTCAAAAACTATATATTATAT
1 AAATATTTTCAAAAACTATATATTATAT
* * *
209825 ATATTTTTTTAAAAACTATATTATATATATT
1 AAATATTTTCAAAAACTATA-TAT-TATA-T
* *
209856 CAAAATGTTTTTAAAAACTATATATTATAT
1 --AAATATTTTCAAAAACTATATATTATAT
*
209886 ATATATTTTCAAAA
1 AAATATTTTCAAAA
209900 TGTTTTCAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
28 28 0.45
29 3 0.05
30 5 0.08
31 5 0.08
32 3 0.05
33 18 0.29
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.47
Consensus pattern (28 bp):
AAATATTTTCAAAAACTATATATTATAT
Found at i:209828 original size:26 final size:24
Alignment explanation
Indices: 209799--209855 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
209789 TATTTTCAAA
209799 ATATTTTCAAAAACTATATATTATAT
1 ATATTTTCAAAAAC--TATATTATAT
*
209825 ATATTTTTTTAAAAACTATATTATAT
1 ATA--TTTTCAAAAACTATATTATAT
209851 ATATT
1 ATATT
209856 CAAAATGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 2 0.07
26 16 0.57
28 10 0.36
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATTTTCAAAAACTATATTATAT
Found at i:209850 original size:33 final size:31
Alignment explanation
Indices: 209813--209894 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 31
209803 TTTCAAAAAC
209813 TATATAT-TATATATATTTTTTTAAAAACTA
1 TATATATATATATATATTTTTTTAAAAACTA
* *
209843 TAT-TATATATATTCAAAATGTTTTTAAAAACTA
1 TATATATATATA-T--ATATTTTTTTAAAAACTA
209876 TATAT-TATATATATATTTT
1 TATATATATATATATATTTT
209895 CAAAATGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
29 3 0.07
30 12 0.28
31 1 0.02
32 1 0.02
33 25 0.58
34 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (31 bp):
TATATATATATATATATTTTTTTAAAAACTA
Found at i:209854 original size:37 final size:36
Alignment explanation
Indices: 209813--210039 Score: 189
Period size: 37 Copynumber: 6.2 Consensus size: 36
209803 TTTCAAAAAC
* * *
209813 TATATATTATATATATTTTTTTAAAAACTATA-T-TA
1 TATATATTATA-AAATGTTTTCAAAAACTATATTATA
* *
209848 TATATATT-CAAAATGTTTTTAAAAACTATATATTATA
1 TATATATTATAAAATGTTTTCAAAAAC--TATATTATA
*
209885 TATATATTTTCAAAATGTTTTCAAAAACTATATTATA
1 TATATATTAT-AAAATGTTTTCAAAAACTATATTATA
*
209922 TATAT-TT-TCAAAATATTTTCAAAAACTATATATTATA
1 TATATATTAT-AAAATGTTTTCAAAAAC--TATATTATA
* * *
209959 TGTATGTTTTTAAAATGTTTTCAAAAACTATGTATTATA
1 TATAT-ATTATAAAATGTTTTCAAAAACTA--TATTATA
* * *
209998 TATATATT-CAAAATATTTTTAAAAACTATA-TATTA
1 TATATATTATAAAATGTTTTCAAAAACTATATTA-TA
210033 TATATAT
1 TATATAT
210040 GTTTTCAAAA
Statistics
Matches: 165, Mismatches: 13, Indels: 28
0.80 0.06 0.14
Matches are distributed among these distances:
33 14 0.08
34 3 0.02
35 41 0.25
36 3 0.02
37 56 0.34
38 2 0.01
39 45 0.27
40 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (36 bp):
TATATATTATAAAATGTTTTCAAAAACTATATTATA
Found at i:209900 original size:39 final size:39
Alignment explanation
Indices: 209841--210082 Score: 300
Period size: 39 Copynumber: 6.3 Consensus size: 39
209831 TTTTAAAAAC
* *
209841 TATATTATATATATTCAAAATGTTTTTAAAAACTATATAT
1 TATA-TATATATTTTCAAAATGTTTTCAAAAACTATATAT
209881 TATATATATATTTTCAAAATGTTTTCAAAAAC--TATA-
1 TATATATATATTTTCAAAATGTTTTCAAAAACTATATAT
*
209917 T-TATATATATTTTCAAAATATTTTCAAAAACTATATAT
1 TATATATATATTTTCAAAATGTTTTCAAAAACTATATAT
* * * *
209955 TATATGTATGTTTTTAAAATGTTTTCAAAAACTATGTAT
1 TATATATATATTTTCAAAATGTTTTCAAAAACTATATAT
* *
209994 TATATATATA--TTCAAAATATTTTTAAAAACTATATAT
1 TATATATATATTTTCAAAATGTTTTCAAAAACTATATAT
* *
210031 TATATATATGTTTTCAAAAT-TTTATAAAAAAACTATATAT
1 TATATATATATTTTCAAAATGTTT-T-CAAAAACTATATAT
210071 TATATACTATAT
1 TATATA-TATAT
210083 ATATGTTAAA
Statistics
Matches: 176, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
35 29 0.16
36 1 0.01
37 40 0.23
38 4 0.02
39 75 0.43
40 23 0.13
41 4 0.02
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (39 bp):
TATATATATATTTTCAAAATGTTTTCAAAAACTATATAT
Found at i:209939 original size:11 final size:11
Alignment explanation
Indices: 209888--209945 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
209878 TATTATATAT
209888 ATATTTTCAAA
1 ATATTTTCAAA
*
209899 ATGTTTTCAAAA
1 ATATTTTC-AAA
* *
209911 ACTATATT-ATAT
1 A-TATTTTCA-AA
209923 ATATTTTCAAA
1 ATATTTTCAAA
209934 ATATTTTCAAA
1 ATATTTTCAAA
209945 A
1 A
209946 ACTATATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
11 26 0.70
12 7 0.19
13 4 0.11
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (11 bp):
ATATTTTCAAA
Found at i:209947 original size:74 final size:73
Alignment explanation
Indices: 209830--210076 Score: 347
Period size: 74 Copynumber: 3.3 Consensus size: 73
209820 TATATATATT
* * *
209830 TTTTTAAAAACTATATTATATATA-TTCAAAATGTTTTTAAAAACTATATATTATATATATATTT
1 TTTTCAAAAACTATATTATATATATTTCAAAATATTTTTAAAAACTATATATTATATATATGTTT
209894 TCAAAATG
66 TCAAAATG
* *
209902 TTTTCAAAAACTATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATGTATGTT
1 TTTTCAAAAACTATATTATATATA-TTTCAAAATATTTTTAAAAACTATATATTATATATATGTT
*
209967 TTTAAAATG
65 TTCAAAATG
209976 TTTTCAAAAACTATGTATTATATATATATTCAAAATATTTTTAAAAACTATATATTATATATATG
1 TTTTCAAAAACTA--TATTATATATAT-TTCAAAATATTTTTAAAAACTATATATTATATATATG
210041 TTTTCAAAAT-
63 TTTTCAAAATG
*
210051 TTTATAAAAAAACTATA-TATTATATA
1 TTT-T-CAAAAACTATATTA-TATATA
210077 CTATATATAT
Statistics
Matches: 157, Mismatches: 10, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
72 23 0.15
74 58 0.37
75 12 0.08
76 56 0.36
77 8 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (73 bp):
TTTTCAAAAACTATATTATATATATTTCAAAATATTTTTAAAAACTATATATTATATATATGTTT
TCAAAATG
Found at i:216449 original size:54 final size:54
Alignment explanation
Indices: 216366--216858 Score: 634
Period size: 54 Copynumber: 9.1 Consensus size: 54
216356 GTGTATTATT
* *
216366 GACACTAAGTGTGTAACCCATAGAATTCATCATATGTTGATGAACGACCGTATC
1 GACACTAAGTGTGCAAACCATAGAATTCATCATATGTTGATGAACGACCGTATC
* * *
216420 AACACTAAATGTGCAAACCATAGAATTCATTATATGTTGATGAACGACCGTATC
1 GACACTAAGTGTGCAAACCATAGAATTCATCATATGTTGATGAACGACCGTATC
** *
216474 GACACTAAGTGTGCAAACCACGGAATTCATCATATGTTGATTAACGACCGTATC
1 GACACTAAGTGTGCAAACCATAGAATTCATCATATGTTGATGAACGACCGTATC
* ** *
216528 GACACTTAA-TGTGCAAGCCACGGAATTCATCATATGTTGATGAACGACCGTATT
1 GACAC-TAAGTGTGCAAACCATAGAATTCATCATATGTTGATGAACGACCGTATC
*
216582 GACACTAAGTGTGTAAACCATAGAATTCATCATATGTTGATGAACGACCGTATC
1 GACACTAAGTGTGCAAACCATAGAATTCATCATATGTTGATGAACGACCGTATC
* *
216636 GACACTAAGTGTGAAAACCAT-GAAATTCATCATATGTTAATGAACGACCGTATC
1 GACACTAAGTGTGCAAACCATAG-AATTCATCATATGTTGATGAACGACCGTATC
* * *
216690 GACACTAAGTGTGTAAACCATAAAATTCATCATATGTTGATGAACGATCGTATC
1 GACACTAAGTGTGCAAACCATAGAATTCATCATATGTTGATGAACGACCGTATC
* * * * * *
216744 -AGTACTAAGTGTACAAACCA-CGAAATTCATCATATATTGATGAATGATCGTATC
1 GA-CACTAAGTGTGCAAACCATAG-AATTCATCATATGTTGATGAACGACCGTATC
* * * ** * *
216798 GGCACTAAGTGTACAAGCCACGGAATTCATAATATGTTTATGAACGACCGTATC
1 GACACTAAGTGTGCAAACCATAGAATTCATCATATGTTGATGAACGACCGTATC
*
216852 GATACTA
1 GACACTA
216859 CGTATGTATC
Statistics
Matches: 388, Mismatches: 43, Indels: 16
0.87 0.10 0.04
Matches are distributed among these distances:
53 5 0.01
54 379 0.98
55 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (54 bp):
GACACTAAGTGTGCAAACCATAGAATTCATCATATGTTGATGAACGACCGTATC
Found at i:218371 original size:40 final size:43
Alignment explanation
Indices: 218282--218371 Score: 96
Period size: 43 Copynumber: 2.2 Consensus size: 43
218272 AGACAACACG
**
218282 GTTCCTATGTGAAGAGGAAATATGGTTATCTAAGGATGATGTT
1 GTTCCTATGTGAAGAGGAAATATGGTTATCTAAGGATGACATT
* * * * *
218325 GATCCTATGTGATGAGGAGATCTGG-T-T-TATGGATGACATT
1 GTTCCTATGTGAAGAGGAAATATGGTTATCTAAGGATGACATT
218365 GTTCCTA
1 GTTCCTA
218372 CGCAATGAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
40 16 0.41
41 1 0.03
42 1 0.03
43 21 0.54
ACGTcount: A:0.27, C:0.10, G:0.28, T:0.36
Consensus pattern (43 bp):
GTTCCTATGTGAAGAGGAAATATGGTTATCTAAGGATGACATT
Found at i:218522 original size:140 final size:140
Alignment explanation
Indices: 218257--218829 Score: 664
Period size: 140 Copynumber: 4.1 Consensus size: 140
218247 TTTGGTCATT
* * * *
218257 TTTAGGTA-AATTT-GGAGACAACACGGTTCCTATGTGAAGAGGAAATATGGTTATCTAAGGATG
1 TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTATGGTTATCTAAGGATG
*** * * * * *** ** *
218320 ATGTTGATCCTATGTGATGAGGAGATCTGGTTTATGGATGACATTGTTCCTACGCAATGAGGATA
66 ACACTGCTCCTACGTGATAAAGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGATG
*
218385 TCTAGCCATA
131 TCTAGCCATC
* * * *
218395 TTTAGGGATAATTTGGGAGACAACATGGTTCCTACATGATGAGGAAGTCTGGTTATCTGAGGATG
1 TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTATGGTTATCTAAGGATG
* * *
218460 ACACTGCTCCTACGTAAAAAAGAGATCTGGTCGGTGGATGACATTGTTCCTATGTGATGAGGATG
66 ACACTGCTCCTACGTGATAAAGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGATG
218525 TCTAGCCATC
131 TCTAGCCATC
* * * * *
218535 TTTAAGGATAATTTGGGATATAACATGGTTCCTACGTGATGAGGAAGTATAGTTATCTAAGGATG
1 TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTATGGTTATCTAAGGATG
* * * *
218600 ACACTGCTCCTACGTTATAAGGAGATTTGGTTGGTGGATGACATTGTTCCTACGTGATGAGGATG
66 ACACTGCTCCTACGTGATAAAGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGATG
*
218665 TCTATCCATC
131 TCTAGCCATC
* * * * * * * * *
218675 TTTAGGAATAATTTGGTAGACAACACAGTTCTTACGTGATGAGGAAGTCTGGATATATGAGGATA
1 TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTATGGTTATCTAAGGATG
** * * * *
218740 ATGCTGCTCCTACATGATAAAGAGATTTGGTCGGTGGATGACATTGTTCCTATGTGATGAGGACG
66 ACACTGCTCCTACGTGATAAAGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGATG
*
218805 TTTAGCCATC
131 TCTAGCCATC
*
218815 TCTAGGGATAATTTG
1 TTTAGGGATAATTTG
218830 TTTCAAGAAA
Statistics
Matches: 368, Mismatches: 65, Indels: 2
0.85 0.15 0.00
Matches are distributed among these distances:
138 7 0.02
139 5 0.01
140 356 0.97
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.32
Consensus pattern (140 bp):
TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTATGGTTATCTAAGGATG
ACACTGCTCCTACGTGATAAAGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGATG
TCTAGCCATC
Found at i:218782 original size:280 final size:280
Alignment explanation
Indices: 218276--218829 Score: 757
Period size: 280 Copynumber: 2.0 Consensus size: 280
218266 ATTTGGAGAC
* * *** * *
218276 AACACGGTTCCTATGTGAAGAGGAAATATGGTTATCTAAGGATGATGTTGATCCTATGTGATGAG
1 AACACGGTTCCTACGTGAAGAGGAAATATAGTTATCTAAGGATGACACTGATCCTACGTGATAAG
* *
218341 GAGATCTGGTTTATGGATGACATTGTTCCTACGCAATGAGGATATCTAGCCATATTTAGGGATAA
66 GAGATCTGGTTGATGGATGACATTGTTCCTACGCAATGAGGATATCTAGCCATATTTAGGAATAA
** * * *
218406 TTTGGGAGACAACATGGTTCCTACATGATGAGGAAGTCTGGTTATCTGAGGATGACACTGCTCCT
131 TTTGGGAGACAACACAGTTCCTACATGATGAGGAAGTCTGGATATATGAGGATAACACTGCTCCT
* *
218471 ACGTAAAAAAGAGATCTGGTCGGTGGATGACATTGTTCCTATGTGATGAGGATGTCTAGCCATCT
196 ACATAAAAAAGAGATCTGGTCGGTGGATGACATTGTTCCTATGTGATGAGGACGTCTAGCCATCT
*
218536 TTAAGGATAATTTGGGATAT
261 CTAAGGATAATTTGGGATAT
* * * * *
218556 AACATGGTTCCTACGTGATGAGGAAGTATAGTTATCTAAGGATGACACTGCTCCTACGTTATAAG
1 AACACGGTTCCTACGTGAAGAGGAAATATAGTTATCTAAGGATGACACTGATCCTACGTGATAAG
* * ** * * *
218621 GAGATTTGGTTGGTGGATGACATTGTTCCTACGTGATGAGGATGTCTATCCATCTTTAGGAATAA
66 GAGATCTGGTTGATGGATGACATTGTTCCTACGCAATGAGGATATCTAGCCATATTTAGGAATAA
* * * **
218686 TTTGGTAGACAACACAGTTCTTACGTGATGAGGAAGTCTGGATATATGAGGATAATGCTGCTCCT
131 TTTGGGAGACAACACAGTTCCTACATGATGAGGAAGTCTGGATATATGAGGATAACACTGCTCCT
* * * *
218751 ACATGATAAAGAGATTTGGTCGGTGGATGACATTGTTCCTATGTGATGAGGACGTTTAGCCATCT
196 ACATAAAAAAGAGATCTGGTCGGTGGATGACATTGTTCCTATGTGATGAGGACGTCTAGCCATCT
*
218816 CTAGGGATAATTTG
261 CTAAGGATAATTTG
218830 TTTCAAGAAA
Statistics
Matches: 235, Mismatches: 39, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
280 235 1.00
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.32
Consensus pattern (280 bp):
AACACGGTTCCTACGTGAAGAGGAAATATAGTTATCTAAGGATGACACTGATCCTACGTGATAAG
GAGATCTGGTTGATGGATGACATTGTTCCTACGCAATGAGGATATCTAGCCATATTTAGGAATAA
TTTGGGAGACAACACAGTTCCTACATGATGAGGAAGTCTGGATATATGAGGATAACACTGCTCCT
ACATAAAAAAGAGATCTGGTCGGTGGATGACATTGTTCCTATGTGATGAGGACGTCTAGCCATCT
CTAAGGATAATTTGGGATAT
Found at i:218974 original size:103 final size:102
Alignment explanation
Indices: 218827--219158 Score: 387
Period size: 103 Copynumber: 3.2 Consensus size: 102
218817 TAGGGATAAT
* * * * *
218827 TTGTTTCAAGAAAAATTATCTCAAGCGAGA-CAAATTTGTTTCAAGGGAAATAATCCCAATTGTT
1 TTGTTTCAAGAGAAACTATCTCAAACGAGACCAAATTTGTTTCAAGGGAAACAATCTCAATTGTT
*
218891 TATGTTTCAAGATAAACTGTCTCAAGAGAGACAAAAC
66 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
* * * * **
218928 TTCATTTCAAGATAAACTATCTCAAACAAGACCGAATTTGTTTCAAGGGAAACAATCTCAAAAGT
1 TT-GTTTCAAGAGAAACTATCTCAAACGAGACCAAATTTGTTTCAAGGGAAACAATCTCAATTGT
* * * * *
218993 TTATGTTTTAAAAGAAACTGTCACAAGAGAGAGAGAAAT
65 TTATGTTTCAAGAGAAACTGTCTCAAGAGAGACA-AAAC
* * * * * * *
219032 TTGTTTCAAGAGAAAATATATCAAGCGAGACAAAAATTGTTTCAAGGAAAACAATCTCAATTGTC
1 TTGTTTCAAGAGAAACTATCTCAAACGAGACCAAATTTGTTTCAAGGGAAACAATCTCAATTGTT
* *
219097 TGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAC
66 TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
* *
219134 TTGTTTCAAGGGAAACAATCTCAAA
1 TTGTTTCAAGAGAAACTATCTCAAA
219159 GGTTTATCAA
Statistics
Matches: 187, Mismatches: 41, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
101 2 0.01
102 46 0.25
103 134 0.72
104 5 0.03
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTATCTCAAACGAGACCAAATTTGTTTCAAGGGAAACAATCTCAATTGTT
TATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
Found at i:219139 original size:66 final size:66
Alignment explanation
Indices: 219033--219157 Score: 205
Period size: 66 Copynumber: 1.9 Consensus size: 66
219023 GAGAGAAATT
*
219033 TGTTTCAAGAGAAAATATATCAAGCGAGACAAAAATTGTTTCAAGGAAAACAATCTCAATTGTCT
1 TGTTTCAAGAGAAAATATATCAAGAGAGACAAAAATTGTTTCAAGGAAAACAATCTCAATTGTCT
219098 G
66 G
* * * *
219099 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAA
1 TGTTTCAAGAGAAAATATATCAAGAGAGACAAAAATTGTTTCAAGGAAAACAATCTCAA
219158 AGGTTTATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (66 bp):
TGTTTCAAGAGAAAATATATCAAGAGAGACAAAAATTGTTTCAAGGAAAACAATCTCAATTGTCT
G
Found at i:219376 original size:36 final size:36
Alignment explanation
Indices: 219284--219501 Score: 247
Period size: 37 Copynumber: 6.0 Consensus size: 36
219274 TAAGGAAGAT
* **
219284 TGTCTCAAGTGAGATGAAATTTGTTTTTAAGAGAAAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGA-AAAC
* * * *
219321 TGTCTCAAGCAAAATAAAATTTGTTTTTAAGAAATC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAC
*
219357 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAATC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAC
* * * *
219393 TATCTCAAGCGAGACAAAATATATTTTTAGAGAAAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAAC
* * *
219430 TGTCTCAAACGAGACAAAATTTATTTTAAGAGAAAAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAAC
* * *
219467 TGTCTCAAGCTAGACATAATTTGTTTTTAATAAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAA
219502 ATTGTCTATA
Statistics
Matches: 156, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
36 67 0.43
37 89 0.57
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAC
Found at i:219382 original size:73 final size:73
Alignment explanation
Indices: 219284--219508 Score: 256
Period size: 73 Copynumber: 3.1 Consensus size: 73
219274 TAAGGAAGAT
* ** * *
219284 TGTCTCAAGTGAGATGAAATTTGTTTTTAAGAGAAACTGTCTCAAGCAAAATAAAATTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAGAAACTGTCTCAAGCAAGACAAAATTTGTTTTT
**
219349 AAGAAATC
66 AAGAAAAA
* * * * *
219357 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGA-AATCTATCTCAAGCGAGACAAAATATATTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAGAAACTGTCTCAAGCAAGACAAAATTTGTTTTT
219421 AGAGAAAAA
66 A-AGAAAAA
* * * *
219430 TGTCTCAAACGAGACAAAATTT-ATTTTAAGAGAAAACTGTCTCAAGCTAGACATAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAG-AAACTGTCTCAAGCAAGACAAAATTTGTTTT
*
219494 TAATAAAAA
65 TAAGAAAAA
219503 TTGTCT
1 -TGTCT
219509 ATAGCGAATC
Statistics
Matches: 127, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
72 34 0.27
73 61 0.48
74 32 0.25
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.34
Consensus pattern (73 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAGAAACTGTCTCAAGCAAGACAAAATTTGTTTTT
AAGAAAAA
Found at i:221438 original size:21 final size:21
Alignment explanation
Indices: 221414--221464 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
221404 GGCATGTTGG
*
221414 TTTTGAGGTTAGCTACCTACA
1 TTTTGAGGTTAGCCACCTACA
* *
221435 TTTTTAGGTTAGCCACCTATA
1 TTTTGAGGTTAGCCACCTACA
221456 TTTTGAGGT
1 TTTTGAGGT
221465 CTATTTCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (21 bp):
TTTTGAGGTTAGCCACCTACA
Found at i:224188 original size:21 final size:21
Alignment explanation
Indices: 224130--224188 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
224120 TTATTTAATA
*
224130 TTATGGATTTCAAGTTGGTTG
1 TTATGGATTTCAAGTTTGTTG
*
224151 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTGTTG
*
224172 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
224189 ATTGGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.03, G:0.25, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTGTTG
Found at i:226794 original size:16 final size:16
Alignment explanation
Indices: 226764--226804 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
226754 TAAATTACTT
*
226764 ATTAACATTATTTTAAA
1 ATTAA-ATTAATTTAAA
226781 ATTAAATTAATTTAAA
1 ATTAAATTAATTTAAA
*
226797 TTTAAATT
1 ATTAAATT
226805 GAAATTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAATTAATTTAAA
Found at i:227402 original size:19 final size:20
Alignment explanation
Indices: 227358--227402 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
227348 ATTTGTTTTT
*
227358 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
227378 ATTAAATTTTTATTTA-CAA
1 AATAAATTTTTATCTATCAA
227397 AATAAA
1 AATAAA
227403 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:228239 original size:24 final size:24
Alignment explanation
Indices: 228210--228266 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
228200 TATCTAGTAT
*
228210 ATAATATAAAGAAT-AAATAAAGAA
1 ATAATATAAA-AATAAAATAAAAAA
*
228234 ATAATATCATAAATAAAATAAAAAA
1 ATAATAT-AAAAATAAAATAAAAAA
*
228259 AGAATATA
1 ATAATATA
228267 TTCCTTGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (24 bp):
ATAATATAAAAATAAAATAAAAAA
Found at i:228400 original size:20 final size:20
Alignment explanation
Indices: 228375--228413 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
228365 ACCAATGCAA
* *
228375 ATAAATAAATAAATAATATT
1 ATAAATAAAAAAAGAATATT
228395 ATAAATAAAAAAAGAATAT
1 ATAAATAAAAAAAGAATAT
228414 ATTCCTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
ATAAATAAAAAAAGAATATT
Found at i:229242 original size:20 final size:20
Alignment explanation
Indices: 229203--229247 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
229193 TTGTTTTTAA
*
229203 TAAATTTTTATCTATGAAAT
1 TAAATTTTTATCTATAAAAT
* *
229223 TAAATTTTTATTTTTAAAAT
1 TAAATTTTTATCTATAAAAT
*
229243 AAAAT
1 TAAAT
229248 ATTAAAAGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TAAATTTTTATCTATAAAAT
Found at i:233483 original size:21 final size:21
Alignment explanation
Indices: 233424--233520 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
233414 AACAATTTTC
* * *
233424 TTCATGAAAAGATTAAATCCT
1 TTCATCAAAAGGTTAAGTCCT
* *
233445 TTCATGAAAAGTTTAAGTCCT
1 TTCATCAAAAGGTTAAGTCCT
** *
233466 TTCATCAAAAGGAGAAGTCTT
1 TTCATCAAAAGGTTAAGTCCT
*
233487 TTAATCAAAAGGTTAAGTCCT
1 TTCATCAAAAGGTTAAGTCCT
*
233508 TTCATCGAAAGGT
1 TTCATCAAAAGGT
233521 CTTAACTTCT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (21 bp):
TTCATCAAAAGGTTAAGTCCT
Found at i:243969 original size:23 final size:23
Alignment explanation
Indices: 243936--244009 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
243926 AATAACATAT
*
243936 TAGGTACCGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATGTAA
*
243959 TATGTAACGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATGTAA
* * **
243982 TAGGTAGCACTTATATAATAAAA
1 TAGGTAACGCTTATATAATGTAA
244005 TAGGT
1 TAGGT
244010 TAATTACTAG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATGTAA
Found at i:244040 original size:110 final size:110
Alignment explanation
Indices: 243872--244085 Score: 331
Period size: 110 Copynumber: 1.9 Consensus size: 110
243862 AATAACATAT
* * *
243872 TAGGTACCGCTTATATAATAAAATAGGTTAATTAGTAGAAATATTATTAAGCACAATAACATATT
1 TAGGTACCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATTAAGCACAATAACATATT
* *
243937 AGGTACCGCTTATATAA-TGTAATATGTAACGCTTATATAATGTAA
66 AGGCACCGCTTATATAACT-TAATATATAACGCTTATATAATGTAA
*
243982 TAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATTAAGCACAATAACATATT
1 TAGGTACCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATTAAGCACAATAACATATT
* * *
244047 AGGCAGCGCTTATATAACTTAATATATAGCGTTTATATA
66 AGGCACCGCTTATATAACTTAATATATAACGCTTATATA
244086 TTTGTTGAGT
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
110 93 0.99
111 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (110 bp):
TAGGTACCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATTAAGCACAATAACATATT
AGGCACCGCTTATATAACTTAATATATAACGCTTATATAATGTAA
Found at i:247490 original size:21 final size:21
Alignment explanation
Indices: 247464--247503 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
247454 CAGAACCCCA
*
247464 GGGGGGTATCGATTCCCCTGC
1 GGGGGGAATCGATTCCCCTGC
*
247485 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
247504 TCAAAGGGGG
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:0.10, C:0.28, G:0.40, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGC
Found at i:247538 original size:20 final size:21
Alignment explanation
Indices: 247485--247546 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
247475 ATTCCCCTGC
247485 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGGTT-CCC-TCAAA
* *
247509 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
247529 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
247547 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:254202 original size:112 final size:111
Alignment explanation
Indices: 254051--254534 Score: 702
Period size: 111 Copynumber: 4.3 Consensus size: 111
254041 TAGCGCCTAT
* * * *
254051 AAAGTATCGATAC-TTTATAAAAATGTATCGATATTTTACAATATAACAAGTAAAAATATGACAA
1 AAAGTATCGATCCTTTTATAAAAA-GGATCGATACTTTACAATATAACAGGTAAAAATATGACAA
* * * *
254115 AATCAATTTCATTATGACAAAACCGGTAAAATTTACCTGATATGTTG
65 AACCAGTTTCATTATGACAAAAACGGTAAAATTTATCTGATATGTTG
254162 AAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAA
1 AAAGTATCGATCC-TTTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAA
*
254227 AACCAGTTTCATTACGACAAAAACGGTAAAATTTATCTGATATGTTG
65 AACCAGTTTCATTATGACAAAAACGGTAAAATTTATCTGATATGTTG
*
254274 AAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* * *
254339 ACCAGTTTCATTATGACAAAAACGATAAAATTTAGCTAATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTATCTGATATGTTG
* * * * *
254385 AACGTATCGATCCTTTTATAAAAATGATAGATATTTTACAATATAACAGGTAAAAATATGATAAA
1 AAAGTATCGATCCTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
254450 ACCAGTTTCATTATGAC-AAAACAGGTAAAATTTATCTGATATGTTG
66 ACCAGTTTCATTATGACAAAAAC-GGTAAAATTTATCTGATATGTTG
** ** *
254496 AAAGTATAAATATTTTTTTATAAAAAAGATCGATACTTT
1 AAAGTAT--CGATCCTTTTATAAAAAGGATCGATACTTT
254535 TTTGAAAGTT
Statistics
Matches: 339, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
110 5 0.01
111 209 0.62
112 92 0.27
113 33 0.10
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.32
Consensus pattern (111 bp):
AAAGTATCGATCCTTTTATAAAAAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGACAAAAACGGTAAAATTTATCTGATATGTTG
Found at i:255202 original size:108 final size:108
Alignment explanation
Indices: 254996--255204 Score: 328
Period size: 108 Copynumber: 1.9 Consensus size: 108
254986 AAAATGTATC
* *
254996 GATATTTTACAATATAACAGGTAAAAATATGACAAAACCAATTTCATTATGACAAAAACGGTGAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAATTTCATTATGACAAAAACGGTAAA
* *
255061 ATTTACCTGATATGTTAAAAGTATCGATCCTTTTTAAAGGATT
66 ATTTACCTGATATGTTAAAAGTATAGATACTTTTTAAAGGATT
* * *
255104 GATACTTTACAATATAACATGTATAAATATGACAAAACCAATTTCATTATGACAAAACCGGTAAA
1 GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAATTTCATTATGACAAAAACGGTAAA
* * *
255169 ATTTATCTGATATGTTGAACGTATAGATACTTTTTA
66 ATTTACCTGATATGTTAAAAGTATAGATACTTTTTA
255205 TAAAAAGGAT
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 91 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (108 bp):
GATACTTTACAATATAACAGGTAAAAATATGACAAAACCAATTTCATTATGACAAAAACGGTAAA
ATTTACCTGATATGTTAAAAGTATAGATACTTTTTAAAGGATT
Found at i:255222 original size:22 final size:22
Alignment explanation
Indices: 255194--255252 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
255184 TGAACGTATA
255194 GATACTTTTTATAAAAAGGATC
1 GATACTTTTTATAAAAAGGATC
*
255216 GATACTTTTTATAAAAATGATC
1 GATACTTTTTATAAAAAGGATC
*
255238 GATACTTTTTTTAAA
1 GATACTTTTTATAAA
255253 GTTATATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (22 bp):
GATACTTTTTATAAAAAGGATC
Found at i:258320 original size:13 final size:13
Alignment explanation
Indices: 258302--258343 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
258292 ACCGGTCAAC
*
258302 GGTCAACGGGTCT
1 GGTCAACGGGTCG
258315 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
258327 GGTAAACGGGTCG
1 GGTCAACGGGTCG
258340 GGTC
1 GGTC
258344 GGGTAAACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.17, C:0.21, G:0.43, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:258345 original size:18 final size:18
Alignment explanation
Indices: 258322--258375 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
258312 TCTGGTCAAC
258322 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
258340 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
258358 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
258376 TGACCGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:259325 original size:112 final size:111
Alignment explanation
Indices: 259173--259513 Score: 504
Period size: 111 Copynumber: 3.1 Consensus size: 111
259163 TAGCGCCTAT
* *
259173 AAAGTATCGATAC-TTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATATAATAA
1 AAAGTATCGATACTTTTATAAAAATG-ATCGATACTTTACAATATAACAGGTAAAAATATGATAA
* *
259237 AACTAGTTTCATTATGACAAAAAAGGGTAAAATTTACCTGATATGTTG
65 AACCAGTTTCATTATGAC-AAAAACGGTAAAATTTACCTGATATGTTG
* * *
259285 AAAGTATCGATTCTTTTATAAAAACGATCGATACTTTACAATATAACATGTAAAAATATGATAAA
1 AAAGTATCGATACTTTTATAAAAATGATCGATACTTTACAATATAACAGGTAAAAATATGATAAA
* * *
259350 ACCAGTTTCATTATGACAAAAACGATAAAATTTACTTGATATATTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
* * * * *
259396 AAAGTATCAATCCTTTTATAAAAATGATCGATACTTTACAATATAATAGGTATAAATATGACAAA
1 AAAGTATCGATACTTTTATAAAAATGATCGATACTTTACAATATAACAGGTAAAAATATGATAAA
* *
259461 ACCAGTTTCATTATGACAAAATCGGTAAAATTTACCTTATATGTTG
66 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
259507 AAAGTAT
1 AAAGTAT
259514 AAATATTTTT
Statistics
Matches: 206, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
111 131 0.64
112 64 0.31
113 11 0.05
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (111 bp):
AAAGTATCGATACTTTTATAAAAATGATCGATACTTTACAATATAACAGGTAAAAATATGATAAA
ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
Found at i:259887 original size:3 final size:3
Alignment explanation
Indices: 259879--259939 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
259869 AATGAATAAT
259879 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
259927 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
259940 CATCATCTGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:261611 original size:18 final size:18
Alignment explanation
Indices: 261584--261636 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
261574 ACTGAATATT
* *
261584 TGTCCAGAAGAACCATTA
1 TGTCCCGAAGGACCATTA
*
261602 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCATTA
261620 TGTCCCGAAGGACCATT
1 TGTCCCGAAGGACCATT
261637 CCTTAAGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCATTA
Found at i:262901 original size:30 final size:30
Alignment explanation
Indices: 262865--262937 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
262855 CATATTCTAA
262865 TCTTTCATTTCTTAAACTAAAAGAAAGGCT
1 TCTTTCATTTCTTAAACTAAAAGAAAGGCT
262895 TCTTTCATTTCTTAAACTAAAAGAAAGGCT
1 TCTTTCATTTCTTAAACTAAAAGAAAGGCT
262925 TCTTTCATTTCTT
1 TCTTTCATTTCTT
262938 TTTTAAGGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (30 bp):
TCTTTCATTTCTTAAACTAAAAGAAAGGCT
Found at i:268435 original size:20 final size:19
Alignment explanation
Indices: 268396--268445 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
268386 ACATATTTTT
* *
268396 TATGAATAATATTGTACTG
1 TATGAATAGTATCGTACTG
268415 TATGAATAGTATCGATACTG
1 TATGAATAGTATCG-TACTG
* *
268435 TGTGAACAGTA
1 TATGAATAGTA
268446 ATGAAGAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (19 bp):
TATGAATAGTATCGTACTG
Found at i:276118 original size:20 final size:20
Alignment explanation
Indices: 276093--276131 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
276083 GTATTGTATG
276093 AATAGTA-TCGATACTGTGTC
1 AATAGTACT-GATACTGTGTC
276113 AATAGTACTGATACTGTGT
1 AATAGTACTGATACTGTGT
276132 GAACAGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (20 bp):
AATAGTACTGATACTGTGTC
Found at i:276139 original size:20 final size:20
Alignment explanation
Indices: 276102--276139 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
276092 GAATAGTATC
*
276102 GATACTGTGTCAATAGTACT
1 GATACTGTGTCAACAGTACT
*
276122 GATACTGTGTGAACAGTA
1 GATACTGTGTCAACAGTA
276140 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (20 bp):
GATACTGTGTCAACAGTACT
Found at i:277268 original size:19 final size:19
Alignment explanation
Indices: 277241--277283 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
277231 TAAAGTTTGA
277241 TATGCTATTTTAACCATGC
1 TATGCTATTTTAACCATGC
*
277260 TATGTTATTTTAACCATGC
1 TATGCTATTTTAACCATGC
277279 TATGC
1 TATGC
277284 ATATGCACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (19 bp):
TATGCTATTTTAACCATGC
Found at i:278813 original size:21 final size:21
Alignment explanation
Indices: 278789--278842 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
278779 TTGATGTTTA
278789 AAGCTTATATAAGCTTTCCTT
1 AAGCTTATATAAGCTTTCCTT
278810 AAGCTTATATAAGCTTTCCTT
1 AAGCTTATATAAGCTTTCCTT
278831 AAGCTTATATAA
1 AAGCTTATATAA
278843 CATCCAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
AAGCTTATATAAGCTTTCCTT
Found at i:282579 original size:64 final size:64
Alignment explanation
Indices: 282478--282605 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
282468 AGGAGTGGCT
282478 TGAGGTTCGACGTTCTCCAAGCCAAAACTTCTTAAGCATGCCATTTATGTATTTAGCTTGATTG
1 TGAGGTTCGACGTTCTCCAAGCCAAAACTTCTTAAGCATGCCATTTATGTATTTAGCTTGATTG
282542 TGAGGTTCGACGTTCTCCAAGCCAAAACTTCTTAAGCATGCCATTTATGTATTTAGCTTGATTG
1 TGAGGTTCGACGTTCTCCAAGCCAAAACTTCTTAAGCATGCCATTTATGTATTTAGCTTGATTG
282606 ATGAAGATGC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (64 bp):
TGAGGTTCGACGTTCTCCAAGCCAAAACTTCTTAAGCATGCCATTTATGTATTTAGCTTGATTG
Found at i:283203 original size:19 final size:19
Alignment explanation
Indices: 283134--283205 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
283124 TTGCAACCCA
* *
283134 AAGTTTCGAAACTTTAGGGG
1 AAGTTTCAAAACTTTA-TGG
283154 AAGTTTCAAAACTTT-TGAG
1 AAGTTTCAAAACTTTATG-G
283173 ATAGTTTCAAAACTTTATGG
1 A-AGTTTCAAAACTTTATGG
*
283193 AAGTATCAAAACT
1 AAGTTTCAAAACT
283206 CTGAAGTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 1 0.02
19 13 0.28
20 30 0.65
21 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (19 bp):
AAGTTTCAAAACTTTATGG
Found at i:292086 original size:3 final size:3
Alignment explanation
Indices: 292074--292112 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
292064 GCCTACTATC
* *
292074 ATT A-T ATT ATT ATT ATT ATT ATT AAT ATC ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
292113 ATACAATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:292121 original size:15 final size:15
Alignment explanation
Indices: 292070--292115 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
292060 TTCGGCCTAC
*
292070 TATCATTA-TATTAT
1 TATCATTATTATTAA
*
292084 TATTATTATTATTAA
1 TATCATTATTATTAA
292099 TATCATTATTATTAA
1 TATCATTATTATTAA
292114 TA
1 TA
292116 CAATTACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 7 0.25
15 21 0.75
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (15 bp):
TATCATTATTATTAA
Found at i:292493 original size:19 final size:21
Alignment explanation
Indices: 292466--292505 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
292456 GTATTTTAAA
292466 TTAAATAGG-TTT-TAATATT
1 TTAAATAGGATTTATAATATT
*
292485 TTAATTAGGATTTATAATATT
1 TTAAATAGGATTTATAATATT
292506 ATATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (21 bp):
TTAAATAGGATTTATAATATT
Found at i:292517 original size:64 final size:63
Alignment explanation
Indices: 292432--292562 Score: 194
Period size: 64 Copynumber: 2.1 Consensus size: 63
292422 TGATATTATT
*
292432 TTTATATTTTATATTTGTTTTTAGGTATTTTAAATTAAATAGGTTTTAA-TATTTTAATTAGGA
1 TTTATATATTATATTTGTTTTTAGGTATTTTAAATTAAATA-GTTTTAAGTATTTTAATTAGGA
**
292495 TTTATAATATTATATTAT-TTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGA
1 TTTAT-ATATTATATT-TGTTTTTAGGTATTTTAAATTAAATAGTTTTAAGTATTTTAATTAGGA
292559 TTTA
1 TTTA
292563 AGATGTTTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
63 12 0.19
64 49 0.79
65 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (63 bp):
TTTATATATTATATTTGTTTTTAGGTATTTTAAATTAAATAGTTTTAAGTATTTTAATTAGGA
Found at i:293195 original size:4 final size:4
Alignment explanation
Indices: 293145--293177 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
293135 CTCAATCTCT
293145 TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
293178 ATTGTTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:296452 original size:3 final size:3
Alignment explanation
Indices: 296446--296481 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
296436 CTTGATAATA
*
296446 ATT ATT ATT ATT ATT A-T ATT ATT ATT AAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
296482 ATACTGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:296468 original size:17 final size:17
Alignment explanation
Indices: 296446--296479 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
296436 CTTGATAATA
*
296446 ATTATTATTATTATTAT
1 ATTATTATTAATATTAT
296463 ATTATTATTAATATTAT
1 ATTATTATTAATATTAT
296480 TAATACTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATTATTAATATTAT
Found at i:296482 original size:9 final size:9
Alignment explanation
Indices: 296441--296484 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
296431 AATGTCTTGA
296441 TAATAATTAT
1 TAAT-ATTAT
*
296451 TATTATTAT
1 TAATATTAT
296460 TATATTATTAT
1 TA-A-TATTAT
296471 TAATATTAT
1 TAATATTAT
296480 TAATA
1 TAATA
296485 CTGTTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 18 0.60
10 4 0.13
11 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TAATATTAT
Found at i:297940 original size:20 final size:20
Alignment explanation
Indices: 297917--298002 Score: 163
Period size: 20 Copynumber: 4.3 Consensus size: 20
297907 AATTTGTAAA
297917 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
297937 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
297957 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
297977 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
297997 TCGCAA
1 TCGCAA
298003 AGCGCGTTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.45, C:0.26, G:0.14, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:298625 original size:21 final size:22
Alignment explanation
Indices: 298584--298626 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
298574 GCGATATTTG
**
298584 CGTTGCGATTTTTTATTTTTCA
1 CGTTGCGATTTTTTAAGTTTCA
298606 CGTTGCGA-TTTTTAAGTTTCA
1 CGTTGCGATTTTTTAAGTTTCA
298627 GAAACTACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.53
Consensus pattern (22 bp):
CGTTGCGATTTTTTAAGTTTCA
Found at i:302232 original size:40 final size:40
Alignment explanation
Indices: 302177--302378 Score: 386
Period size: 40 Copynumber: 5.0 Consensus size: 40
302167 TGTAGGTTTA
302177 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
302217 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
302257 TAATACACTTCGGTGTACATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
302297 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
302337 TAATACACTTCGGTGTATATGGTGGGCACGACCTTGTGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
302377 TA
1 TA
302379 GCACTACGGT
Statistics
Matches: 159, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 159 1.00
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:304113 original size:21 final size:21
Alignment explanation
Indices: 304095--304170 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
304085 TGCGCCTCCT
304095 ATCATTCAAGAGGCCCCTCTC
1 ATCATTCAAGAGGCCCCTCTC
*
304116 ATCATTGAAGAGGCCCCTCTC
1 ATCATTCAAGAGGCCCCTCTC
* * *
304137 ACCGTTCAAGAGGCCCCTATC
1 ATCATTCAAGAGGCCCCTCTC
*
304158 ATCGTTCAAGAGG
1 ATCATTCAAGAGG
304171 TCCCGCCCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCATTCAAGAGGCCCCTCTC
Found at i:304146 original size:42 final size:42
Alignment explanation
Indices: 304099--304190 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
304089 CCTCCTATCA
* * * *
304099 TTCAAGAGGCCCCTCTCATCATTGAAGAGGCCCCTCTCACCG
1 TTCAAGAGGCCCCTATCATCATTCAAGAGGCCCCGCCCACCG
* * *
304141 TTCAAGAGGCCCCTATCATCGTTCAAGAGGTCCCGCCCGCCG
1 TTCAAGAGGCCCCTATCATCATTCAAGAGGCCCCGCCCACCG
304183 TTCAAGAG
1 TTCAAGAG
304191 CTCGATTCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.21
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCATTCAAGAGGCCCCGCCCACCG
Found at i:305623 original size:14 final size:14
Alignment explanation
Indices: 305604--305641 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
305594 TTTTTTGCTT
305604 GTTGATTTGTAAAA
1 GTTGATTTGTAAAA
305618 GTTGATTTGTAAAA
1 GTTGATTTGTAAAA
*
305632 GATGATTTGT
1 GTTGATTTGT
305642 TTAATTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.45
Consensus pattern (14 bp):
GTTGATTTGTAAAA
Found at i:305784 original size:20 final size:20
Alignment explanation
Indices: 305759--305800 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
305749 AAGGTACACT
305759 TTTGCAACGCGAAAGTCAAA
1 TTTGCAACGCGAAAGTCAAA
*
305779 TTTGCAATGCGAAAGTCAAA
1 TTTGCAACGCGAAAGTCAAA
305799 TT
1 TT
305801 CGCGTTGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (20 bp):
TTTGCAACGCGAAAGTCAAA
Found at i:305854 original size:54 final size:54
Alignment explanation
Indices: 305767--305869 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
305757 CTTTTGCAAC
*
305767 GCGAAAGTCAAATTTGCAATGCGAAAGTCAAATTCGCGTTGCA-ATTTTCTCATT
1 GCGAAAGTCAAATTTGCAACGCGAAAGTCAAATTCGCGTTG-AGATTTTCTCATT
* *
305821 GCGATAGTCAAATTTGCAACGCGAAAGTCAAATTTGCGTTGAGATTTTC
1 GCGAAAGTCAAATTTGCAACGCGAAAGTCAAATTCGCGTTGAGATTTTC
305870 AGTTTACGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
53 1 0.02
54 44 0.98
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (54 bp):
GCGAAAGTCAAATTTGCAACGCGAAAGTCAAATTCGCGTTGAGATTTTCTCATT
Found at i:305903 original size:20 final size:20
Alignment explanation
Indices: 305880--305929 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
305870 AGTTTACGAT
*
305880 TTTGATTTTCGCGTTGCGAA
1 TTTGACTTTCGCGTTGCGAA
*
305900 TTTGACTTTCGTGTTGCGAA
1 TTTGACTTTCGCGTTGCGAA
*
305920 TTTTACTTTC
1 TTTGACTTTC
305930 ACAACAATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTGACTTTCGCGTTGCGAA
Found at i:308450 original size:24 final size:24
Alignment explanation
Indices: 308416--308471 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
308406 CTGAAACATC
*
308416 ATCAAAATCCAAGTATTGACCAAG
1 ATCAAATTCCAAGTATTGACCAAG
*
308440 ATCAAATTCCAGGTATTGACCAAG
1 ATCAAATTCCAAGTATTGACCAAG
308464 ATCAAATT
1 ATCAAATT
308472 TCGAATACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCAAATTCCAAGTATTGACCAAG
Found at i:309449 original size:20 final size:20
Alignment explanation
Indices: 309401--309533 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
309391 AACTAAAACC
*
309401 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
* *
309420 TGTTGTGAATTTGAAAATCG
1 TGTTGCGAATTTGAAATTCG
*
309440 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTC-G
*
309461 TGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTC-G
* ** *
309481 TGATGCGAATTTGACTTTTG
1 TGTTGCGAATTTGAAATTCG
*
309501 TGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTC-G
309521 TGTTGCGAATTTG
1 TGTTGCGAATTTG
309534 CCTTCTATGT
Statistics
Matches: 93, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.13
20 66 0.71
21 15 0.16
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:309538 original size:20 final size:20
Alignment explanation
Indices: 309441--309548 Score: 153
Period size: 20 Copynumber: 5.3 Consensus size: 20
309431 TGAAAATCGA
* *
309441 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTCTGT
309462 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
* *
309482 GATGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
309502 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
* *
309522 GTTGCGAATTTGCCTTCTAT
1 GTTGCGAATTTGACTTCTGT
309542 GTTGCGA
1 GTTGCGA
309549 TTTACAAATT
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
20 67 0.85
21 12 0.15
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:309565 original size:20 final size:20
Alignment explanation
Indices: 309542--309585 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
309532 TGCCTTCTAT
309542 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
309562 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
309582 GTTG
1 GTTG
309586 GGAATTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:309566 original size:60 final size:61
Alignment explanation
Indices: 309426--309568 Score: 148
Period size: 60 Copynumber: 2.4 Consensus size: 61
309416 TTCGTGTTGT
* * * *
309426 GAATTTGAAAATCGAGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTCTGTGATGC
1 GAATTTGACATTCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTCTATGATGC
* * * * * * *
309487 GAATTTGACTTTTGTGTTGCGAATTTG-ACTTCTGTGTTGCGAATTTGCCTTCTATGTTGC
1 GAATTTGACATTCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTCTATGATGC
309547 G-ATTT-ACAAATTCGCGTTGCGA
1 GAATTTGAC--ATTCGCGTTGCGA
309569 TTTACATATT
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
58 2 0.03
59 4 0.06
60 39 0.58
61 22 0.33
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (61 bp):
GAATTTGACATTCGCGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTCTATGATGC
Found at i:310735 original size:17 final size:18
Alignment explanation
Indices: 310703--310738 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
310693 AAACCTCAAT
310703 TTATTGTTTTAATTAAAA
1 TTATTGTTTTAATTAAAA
*
310721 TTATT-TTTTATTTAAAA
1 TTATTGTTTTAATTAAAA
310738 T
1 T
310739 GACAACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TTATTGTTTTAATTAAAA
Found at i:311780 original size:11 final size:11
Alignment explanation
Indices: 311766--311806 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
311756 GTTATATTTT
311766 TTTTATTTTCA
1 TTTTATTTTCA
*
311777 TTTTA-TTTCG
1 TTTTATTTTCA
*
311787 TTTTATTTTTA
1 TTTTATTTTCA
311798 TTTTATTTT
1 TTTTATTTT
311807 TAGCGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:311784 original size:5 final size:5
Alignment explanation
Indices: 311760--311856 Score: 65
Period size: 5 Copynumber: 19.2 Consensus size: 5
311750 CATTTCGTTA
**
311760 TATTT T-TTT TATTT TCATTT TATTT CGTTT TATTTT TATTT TATTTT
1 TATTT TATTT TATTT T-ATTT TATTT TATTT TA-TTT TATTT TA-TTT
*** * * *
311807 TAGCG AATTT TATTC TA-TT TATTT TATTT TGA-TT AATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT T-ATTT TATTT TATTT TATTT
311856 T
1 T
311857 TTCTAAACAG
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
4 8 0.12
5 45 0.65
6 16 0.23
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:311792 original size:21 final size:21
Alignment explanation
Indices: 311766--311805 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
311756 GTTATATTTT
311766 TTTTATTTTCATTTTATTTCG
1 TTTTATTTTCATTTTATTTCG
*
311787 TTTTATTTTTATTTTATTT
1 TTTTATTTTCATTTTATTT
311806 TTAGCGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTATTTTCATTTTATTTCG
Found at i:311807 original size:11 final size:11
Alignment explanation
Indices: 311757--311808 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
311747 ACCCATTTCG
311757 TTATATTTT-TT
1 TTAT-TTTTATT
*
311768 TTATTTTCATT
1 TTATTTTTATT
**
311779 TTA-TTTCGTT
1 TTATTTTTATT
311789 TTATTTTTATT
1 TTATTTTTATT
311800 TTATTTTTA
1 TTATTTTTA
311809 GCGAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
10 12 0.34
11 23 0.66
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:311846 original size:29 final size:30
Alignment explanation
Indices: 311794--311855 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
311784 TCGTTTTATT
*
311794 TTTATTTTATTTTTAGCGAATTTTATTCTA
1 TTTATTTTATTTTGAGCGAATTTTATTCTA
** *
311824 TTTATTTTATTTTGA-TTAATTTTATTTTA
1 TTTATTTTATTTTGAGCGAATTTTATTCTA
311853 TTT
1 TTT
311856 TTTCTAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (30 bp):
TTTATTTTATTTTGAGCGAATTTTATTCTA
Found at i:311979 original size:53 final size:52
Alignment explanation
Indices: 311896--312077 Score: 177
Period size: 64 Copynumber: 3.3 Consensus size: 52
311886 ATTTAACGGA
* *
311896 AACAAACAGGGCAG-AAAAACTGACTTGGTTCGAACTGTGCAGAAAAATTCG
1 AACAAACAGTGCAGAAAAAACTGATTTGGTTCGAACTGTGCAGAAAAATTCG
*
311947 AACAGAACAGTGCAGAAAAAACTGATTTGGTTCGAACAGTGCAGAAAAATACACAGCAGATTCG
1 AACA-AACAGTGCAGAAAAAACTGATTTGGTTCGAACTGTGCAG------A-A-A--A-ATTCG
* * *
312011 AACAATATAGTGCAGAAAAAACAGATTTGGTTCGAACTGTGCAGAAAAGTTCG
1 AACAA-ACAGTGCAGAAAAAACTGATTTGGTTCGAACTGTGCAGAAAAATTCG
*
312064 AACAAAAAGTGCAG
1 AACAAACAGTGCAG
312078 TATTGTACAT
Statistics
Matches: 109, Mismatches: 8, Indels: 27
0.76 0.06 0.19
Matches are distributed among these distances:
51 4 0.04
52 17 0.16
53 35 0.32
54 1 0.01
56 1 0.01
57 1 0.01
58 1 0.01
59 1 0.01
60 1 0.01
61 1 0.01
63 2 0.02
64 44 0.40
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (52 bp):
AACAAACAGTGCAGAAAAAACTGATTTGGTTCGAACTGTGCAGAAAAATTCG
Found at i:311984 original size:29 final size:29
Alignment explanation
Indices: 311951--312058 Score: 99
Period size: 29 Copynumber: 3.5 Consensus size: 29
311941 AATTCGAACA
*
311951 GAACAGTGCAGAAAAAACTGATTTGGTTC
1 GAACAGTGCAGAAAAAACAGATTTGGTTC
* *** *
311980 GAACAGTGCAGAAAAATACACAGCAGATTC
1 GAACAGTGCAGAAAAA-ACAGATTTGGTTC
312010 GAACAATATAGTGCAGAAAAAACAGATTTGGTTC
1 GAAC-----AGTGCAGAAAAAACAGATTTGGTTC
*
312044 GAACTGTGCAGAAAA
1 GAACAGTGCAGAAAA
312059 GTTCGAACAA
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
29 26 0.43
30 11 0.18
34 12 0.20
35 12 0.20
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (29 bp):
GAACAGTGCAGAAAAAACAGATTTGGTTC
Found at i:315692 original size:16 final size:16
Alignment explanation
Indices: 315673--315707 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
315663 AATTAAAATG
* *
315673 AAAATAGAAAAAATAA
1 AAAAAAGAAAAAAGAA
315689 AAAAAAGAAAAAAGAA
1 AAAAAAGAAAAAAGAA
315705 AAA
1 AAA
315708 GGTTGGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.06
Consensus pattern (16 bp):
AAAAAAGAAAAAAGAA
Found at i:317581 original size:129 final size:129
Alignment explanation
Indices: 317417--317650 Score: 351
Period size: 129 Copynumber: 1.8 Consensus size: 129
317407 TTTTAGACGG
* * * * * *
317417 AATATTAATATCTCTTTATTTCAATTGGGGTAATAAATGACTGTTTTAATGCACTAAATGTCGTT
1 AATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATAACTGTTTTAATGCACGAAAGGTCATT
* * *
317482 TATTCTCAATTGAAAATCATTAGATGTTATTATTTTCACTTGAATCGATATTAAATTAAGATGA
66 TATTCTCAATTGAAAATAATTAGATATTATCATTTTCACTTGAATCGATATTAAATTAAGATGA
* *
317546 AATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATAATTGTTTTAATGCACGAAAGGTCATT
1 AATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATAACTGTTTTAATGCACGAAAGGTCATT
* *
317611 TATTCTCGATTGAAAATAATTAGATATTATCGTTTTCACT
66 TATTCTCAATTGAAAATAATTAGATATTATCATTTTCACT
317651 CTTAAAATTA
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
129 92 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (129 bp):
AATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATAACTGTTTTAATGCACGAAAGGTCATT
TATTCTCAATTGAAAATAATTAGATATTATCATTTTCACTTGAATCGATATTAAATTAAGATGA
Found at i:319256 original size:60 final size:60
Alignment explanation
Indices: 319182--319301 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
319172 CTTCGATGAC
*
319182 CATTTTGTAACTTTTAATAGTTG-GGAGACAAAACAAAGA-AACACCCTATAGTCGAAGGAT
1 CATTTTATAACTTTTAATAGTTGAGG-GACAAAACAAA-ACAACACCCTATAGTCGAAGGAT
* ** * *
319242 CATTTTATAACTTTTATTAGTTGAGGGACTCAACAAAACATCACCCTATAGTCGAGGGAT
1 CATTTTATAACTTTTAATAGTTGAGGGACAAAACAAAACAACACCCTATAGTCGAAGGAT
319302 TTGTGTACTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 1 0.02
60 49 0.94
61 2 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAGTTGAGGGACAAAACAAAACAACACCCTATAGTCGAAGGAT
Found at i:319579 original size:28 final size:28
Alignment explanation
Indices: 319546--319627 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 28
319536 CAATTAGTTC
319546 AATTTGGTCCTTAATTGTTTGATTAATA
1 AATTTGGTCCTTAATTGTTTGATTAATA
* * * * *
319574 AATTTGG-CCTTTATT-TCTAATTACCTC
1 AATTTGGTCCTTAATTGTTTGATTA-ATA
* *
319601 AATTTGGTCCTTAATTGATTGCTTAAT
1 AATTTGGTCCTTAATTGTTTGATTAAT
319628 TTCTAATTAC
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
26 6 0.15
27 15 0.38
28 15 0.38
29 4 0.10
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.49
Consensus pattern (28 bp):
AATTTGGTCCTTAATTGTTTGATTAATA
Found at i:323149 original size:22 final size:22
Alignment explanation
Indices: 323123--323165 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
323113 TAATAAATTA
323123 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
323145 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
323166 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:323174 original size:22 final size:22
Alignment explanation
Indices: 323125--323173 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
323115 ATAAATTATT
**
323125 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
323147 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
323170 TAAA
1 TAAA
323174 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:323212 original size:26 final size:26
Alignment explanation
Indices: 323182--323383 Score: 109
Period size: 26 Copynumber: 7.6 Consensus size: 26
323172 AATTATTTAA
323182 AATAAATCAATCCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
* **
323208 AATAAATCAATCCAT---ATTTTAA-
1 AATAAATCAATCCATACAACTACAAT
*
323230 AATAAATCAATCCATACTAA-TAAATTATTT
1 AATAAATCAATCCATAC-AACTACA--A--T
*
323260 AAAATAAATCAATCCATACAACTACAAC
1 --AATAAATCAATCCATACAACTACAAT
* * **
323288 GATAAATCAATCCAT---ATTTTAA-
1 AATAAATCAATCCATACAACTACAAT
* *
323310 AATAAATCAATCCAGACTAA-TAAATTATTT
1 AATAAATCAATCCATAC-AACTACA--A--T
323340 AAAATAAATCAATCCATACAACTACAAT
1 --AATAAATCAATCCATACAACTACAAT
323368 AATAAATCAATCCATA
1 AATAAATCAATCCATA
323384 TTTTAAAATA
Statistics
Matches: 135, Mismatches: 17, Indels: 48
0.68 0.09 0.24
Matches are distributed among these distances:
22 28 0.21
23 8 0.06
25 4 0.03
26 47 0.35
27 2 0.01
28 1 0.01
30 2 0.01
31 4 0.03
32 39 0.29
ACGTcount: A:0.52, C:0.18, G:0.01, T:0.29
Consensus pattern (26 bp):
AATAAATCAATCCATACAACTACAAT
Found at i:323218 original size:80 final size:80
Alignment explanation
Indices: 323128--323437 Score: 584
Period size: 80 Copynumber: 3.9 Consensus size: 80
323118 AATTATTTAA
323128 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
323193 CCATACAACTACAAT
66 CCATACAACTACAAT
323208 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
323273 CCATACAACTACAAC
66 CCATACAACTACAAT
* *
323288 GATAAATCAATCCATATTTTAAAATAAATCAATCCAGACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
323353 CCATACAACTACAAT
66 CCATACAACTACAAT
*
323368 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAAAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
323433 CCATA
66 CCATA
323438 TTTTAAAATA
Statistics
Matches: 223, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 223 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.31
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:323254 original size:22 final size:23
Alignment explanation
Indices: 323179--323253 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
323169 ATAAATTATT
323179 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
323201 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
323227 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
323250 TAAA
1 TAAA
323254 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:323413 original size:22 final size:22
Alignment explanation
Indices: 323340--323414 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 22
323330 TAAATTATTT
323340 AAAATAAATCAATCCATACAACTACA
1 AAAATAAATCAATCCAT---ACTA-A
* * **
323366 ATAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATACTAA
323388 AAAATAAATCAATCCATACTAA
1 AAAATAAATCAATCCATACTAA
323410 AAAAT
1 AAAAT
323415 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 23 0.56
23 2 0.05
26 16 0.39
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATAAATCAATCCATACTAA
Found at i:323435 original size:54 final size:54
Alignment explanation
Indices: 323208--323588 Score: 344
Period size: 54 Copynumber: 7.1 Consensus size: 54
323198 CAACTACAAT
*
323208 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAAAAATTATTTAA
*** * ** * * *
323262 AATAAATCAATCCATACAACTACAACGATAAATCAATCCATATTTTAAAATAAATCAA
1 AATAAATCAATCCATA-TTTTA-AA--ATAAATCAATCCATACTAAAAAATTATTTAA
*** * ** * *
323320 TCCAGA-CTAATAAAT-TATTTAAAATAAATCAATCCATAC-----AACTA--CAA
1 AATAAATC-AATCCATAT-TTTAAAATAAATCAATCCATACTAAAAAATTATTTAA
323367 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAAAAATTATTTAA
1 -AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAAAAATTATTTAA
* *
323422 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAAAAATTATTTAA
*
323476 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAAAAATTATTTAA
*
323530 AAT--A--AAT---TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATA--CTA-AA-AAATTA-TTTAA
323582 AATAAAT
1 AATAAAT
323589 TATTTTATAA
Statistics
Matches: 268, Mismatches: 35, Indels: 47
0.77 0.10 0.13
Matches are distributed among these distances:
47 27 0.10
48 29 0.11
49 7 0.03
50 4 0.01
51 6 0.02
52 9 0.03
53 4 0.01
54 140 0.52
55 4 0.01
56 4 0.01
57 3 0.01
58 31 0.12
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAAAAATTATTTAA
Found at i:323468 original size:22 final size:22
Alignment explanation
Indices: 323419--323467 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
323409 AAAAATTATT
**
323419 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
323441 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
323464 TAAA
1 TAAA
323468 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:323497 original size:22 final size:22
Alignment explanation
Indices: 323471--323573 Score: 98
Period size: 22 Copynumber: 4.5 Consensus size: 22
323461 TAATAAATTA
323471 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
323493 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
323516 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
323540 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
323562 TTTATAATAAAT
1 TTTAAAATAAAT
323574 TATTTTAAAA
Statistics
Matches: 61, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
22 35 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:323545 original size:15 final size:15
Alignment explanation
Indices: 323516--323633 Score: 130
Period size: 15 Copynumber: 7.5 Consensus size: 15
323506 AATCCATACT
323516 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
323530 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
323545 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
323567 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
323582 AATAAATTATTTTAT
1 AATAAATTATTTTAA
323597 AATAAATTATTTTAA
1 AATAAATTATTTTAA
**
323612 AATAAATTATTTCGA
1 AATAAATTATTTTAA
323627 AATAAAT
1 AATAAAT
323634 AACCTTATTA
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
14 9 0.10
15 63 0.70
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:323551 original size:69 final size:67
Alignment explanation
Indices: 323462--323618 Score: 219
Period size: 69 Copynumber: 2.3 Consensus size: 67
323452 AATCTATACT
*
323462 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAAT-AAT-CATA-AAATAAATTAT
323525 TTTAA
63 TTTAA
* * **
323530 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATCATAAAATAAATTATTTT
*
323595 AT
66 AA
323597 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
323619 TATTTCGAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
66 9 0.11
67 28 0.35
68 11 0.14
69 33 0.41
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATCATAAAATAAATTATTTT
AA
Found at i:327619 original size:137 final size:136
Alignment explanation
Indices: 327252--327997 Score: 970
Period size: 135 Copynumber: 5.5 Consensus size: 136
327242 TACTATTCAC
* * * *
327252 GTGAAAGTGTGTTTCAGGGGGCGTGCCTTCCCTTTTTTTGTCAAAGAATAGGTTATAATTGCCCT
1 GTGAAAGCGCGTTTCAGGGGGCGCGCCTTCCC-TTTTTTGTCAGAGAATAGGTTATAATTGCCCT
* *
327317 ATTATGTGTGATGTCCCCTGGAGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCA
65 ATTATGTGTGATGTCCCCCGG-GGGAACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCA
327382 ACAAAGTG
129 ACAAAGTG
* * * * * *
327390 GTTAAAGTGCGTTTCA-GGGG-GCGTCTTCCTTTTTTTGTCAGATAATAGGTTATAATTACCCTA
1 GTGAAAGCGCGTTTCAGGGGGCGCGCCTTCCCTTTTTTGTCAGAGAATAGGTTATAATTGCCCTA
* ** * * * * *
327453 TTATGTGTGATGTCCCTCAAGGGAACTATTCATTTCAGTACCTATAATTTTTGAGGGGATGCATC
66 TTATGTGTGATGTCCCCCGGGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAAC
327518 AAAGTG
131 AAAGTG
* * * *
327524 GTGAAAGCGTGTTTCAGGGGGCGCGTCTTCCCTTTTTTTGTTAGAGAATATGTTATAATTGCCCT
1 GTGAAAGCGCGTTTCAGGGGGCGCGCCTTCCC-TTTTTTGTCAGAGAATAGGTTATAATTGCCCT
* *
327589 ATTATGTGTGATGTCCCCCGGGGGAACTATTCATATAAGTACCTATCATGTTTGAGGGGACGCAA
65 ATTATGTGTGATGTCCCCCGGGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAA
327654 CAAAGTG
130 CAAAGTG
* * * * *
327661 GTGAAAGCGCGTTTCAGGGGGTGAGCCTTCCCTTTTTTGTCAGAGAATATGTTATAATTACCTTA
1 GTGAAAGCGCGTTTCAGGGGGCGCGCCTTCCCTTTTTTGTCAGAGAATAGGTTATAATTGCCCTA
* * * *
327726 TTATGTGTGATGT-CCCCTGGGGTACTATTCATGTCAGTACCTATCATGTTTCAGGGGACACAAC
66 TTATGTGTGATGTCCCCCGGGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAAC
327790 AAAGTG
131 AAAGTG
* * * *
327796 GTGAAAGCGTGTTTCA-GGGG-G-GCCTTCCCTTTTTTGTCTGAGAATATGTTTTAAGTT-CCCT
1 GTGAAAGCGCGTTTCAGGGGGCGCGCCTTCCCTTTTTTGTCAGAGAATAGGTTATAA-TTGCCCT
* * *
327857 TTTATGTGTGATG-CCCCCAGGGGGCACTATTCATGTCAGTACCTATCATGTCTGAGGGGACGCA
65 ATTATGTGTGATGTCCCCC-GGGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCA
327921 ACAAAGTG
129 ACAAAGTG
* * * *
327929 GTGAAAGGGCATTTCA-GGGGCGTGCCTTCCCTTTTTTGTCAGATAATAGGTTATAATTGCCCTA
1 GTGAAAGCGCGTTTCAGGGGGCGCGCCTTCCCTTTTTTGTCAGAGAATAGGTTATAATTGCCCTA
327993 TTATG
66 TTATG
327998 CTTGAAATTT
Statistics
Matches: 533, Mismatches: 66, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
132 50 0.09
133 68 0.13
134 65 0.12
135 154 0.29
136 59 0.11
137 123 0.23
138 14 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (136 bp):
GTGAAAGCGCGTTTCAGGGGGCGCGCCTTCCCTTTTTTGTCAGAGAATAGGTTATAATTGCCCTA
TTATGTGTGATGTCCCCCGGGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAAC
AAAGTG
Found at i:327755 original size:272 final size:271
Alignment explanation
Indices: 327252--327997 Score: 1060
Period size: 272 Copynumber: 2.8 Consensus size: 271
327242 TACTATTCAC
* * * * *
327252 GTGAAAGTGTGTTTCAGGGGGCGTGCCTTCCCTTTTTTTGTCAAAGAATAGGTTATAATTGCCCT
1 GTGAAAGCGTGTTTCAGGGGGCGCG-CTTCCCTTTTTTTGTTAGAGAATATGTTATAATTGCCCT
*
327317 ATTATGTGTGATGTCCCCTGGAGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCA
65 ATTATGTGTGATGTCCCCCGG-GGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCA
* * * * *
327382 ACAAAGTGGTTAAAGTGCGTTTCAGGGGG-CGTCTTCCTTTTTTTGTCAGATAATAGGTTATAAT
129 ACAAAGTGGTGAAAGCGCGTTTCAGGGGGTGGCCTTCCCTTTTTTGTCAGATAATAGGTTATAAT
* * *
327446 TACCCTATTATGTGTGATGTCCCTCAAGGGAACTATTCATTTCAGTACCTATAATTTTTGAGGGG
194 TACCCTATTATGTGTGATGTCCCTCAAGGGAACTATTCATGTCAGTACCTATAATGTTTCAGGGG
** *
327511 ATGCATCAAAGTG
259 ACACAACAAAGTG
327524 GTGAAAGCGTGTTTCAGGGGGCGCGTCTTCCCTTTTTTTGTTAGAGAATATGTTATAATTGCCCT
1 GTGAAAGCGTGTTTCAGGGGGCGCG-CTTCCCTTTTTTTGTTAGAGAATATGTTATAATTGCCCT
* * *
327589 ATTATGTGTGATGTCCCCCGGGGGAACTATTCATATAAGTACCTATCATGTTTGAGGGGACGCAA
65 ATTATGTGTGATGTCCCCCGGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAA
* *
327654 CAAAGTGGTGAAAGCGCGTTTCAGGGGGTGAGCCTTCCCTTTTTTGTCAGAGAATATGTTATAAT
130 CAAAGTGGTGAAAGCGCGTTTCAGGGGGTG-GCCTTCCCTTTTTTGTCAGATAATAGGTTATAAT
* ** * *
327719 TACCTTATTATGTGTGATGTCCC-CTGGGGTACTATTCATGTCAGTACCTATCATGTTTCAGGGG
194 TACCCTATTATGTGTGATGTCCCTCAAGGGAACTATTCATGTCAGTACCTATAATGTTTCAGGGG
327783 ACACAACAAAGTG
259 ACACAACAAAGTG
*
327796 GTGAAAGCGTGTTTCAGGGGG-GC-CTTCCC-TTTTTTGTCT-GAGAATATGTTTTAAGTT-CCC
1 GTGAAAGCGTGTTTCAGGGGGCGCGCTTCCCTTTTTTTGT-TAGAGAATATGTTATAA-TTGCCC
* *
327856 TTTTATGTGTGATG-CCCCCAGGGGGCACTATTCATGTCAGTACCTATCATGTCTGAGGGGACGC
64 TATTATGTGTGATGTCCCCC-GGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGC
* *
327920 AACAAAGTGGTGAAAGGGCATTTCAGGGGCGT-GCCTTCCCTTTTTTGTCAGATAATAGGTTATA
128 AACAAAGTGGTGAAAGCGCGTTTCAGGGG-GTGGCCTTCCCTTTTTTGTCAGATAATAGGTTATA
*
327984 ATTGCCCTATTATG
192 ATTACCCTATTATG
327998 CTTGAAATTT
Statistics
Matches: 428, Mismatches: 40, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
267 47 0.11
268 105 0.25
269 11 0.03
271 69 0.16
272 144 0.34
273 52 0.12
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (271 bp):
GTGAAAGCGTGTTTCAGGGGGCGCGCTTCCCTTTTTTTGTTAGAGAATATGTTATAATTGCCCTA
TTATGTGTGATGTCCCCCGGGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAAC
AAAGTGGTGAAAGCGCGTTTCAGGGGGTGGCCTTCCCTTTTTTGTCAGATAATAGGTTATAATTA
CCCTATTATGTGTGATGTCCCTCAAGGGAACTATTCATGTCAGTACCTATAATGTTTCAGGGGAC
ACAACAAAGTG
Found at i:328015 original size:13 final size:13
Alignment explanation
Indices: 327993--328025 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
327983 AATTGCCCTA
*
327993 TTATGCTTGAAAT
1 TTATGTTTGAAAT
328006 TTATGTTTGAAAT
1 TTATGTTTGAAAT
328019 TTATGTT
1 TTATGTT
328026 AGAGTGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (13 bp):
TTATGTTTGAAAT
Found at i:328058 original size:20 final size:20
Alignment explanation
Indices: 328012--328058 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
328002 AAATTTATGT
*
328012 TTGAAATTTATGTTAGAGTG
1 TTGAAATTTATGTTAGAATG
328032 TTG-AATTTGATGTTAGAATG
1 TTGAAATTT-ATGTTAGAATG
328052 -TGAAATT
1 TTGAAATT
328059 AGGTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (20 bp):
TTGAAATTTATGTTAGAATG
Found at i:329151 original size:42 final size:41
Alignment explanation
Indices: 329079--329165 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 41
329069 TAGGAATGTA
329079 ACCCTGCGAAGATGGCATATAAACTAGTGGGCTT-GGCATAT
1 ACCCTGCGAAGATGGCATATAAACTAGTGGG-TTGGGCATAT
* * * * *
329120 ACCCTTGCGGAGATGGCATCTGAACTGGTGGGTTGGGCATGT
1 ACCC-TGCGAAGATGGCATATAAACTAGTGGGTTGGGCATAT
329162 ACCC
1 ACCC
329166 CTGTGGCATC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 6 0.15
42 33 0.85
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.24
Consensus pattern (41 bp):
ACCCTGCGAAGATGGCATATAAACTAGTGGGTTGGGCATAT
Found at i:329744 original size:17 final size:17
Alignment explanation
Indices: 329722--329757 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
329712 AAACTGAAAC
329722 ATAAATAT-ATAATTCTA
1 ATAAATATAAT-ATTCTA
329739 ATAAATATAATATTCTA
1 ATAAATATAATATTCTA
329756 AT
1 AT
329758 TATATCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATAATATTCTA
Found at i:337197 original size:3 final size:3
Alignment explanation
Indices: 337189--337237 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
337179 AAAAATATTA
*
337189 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
337237 A
1 A
337238 GTAAATAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:338253 original size:124 final size:124
Alignment explanation
Indices: 337975--338532 Score: 739
Period size: 124 Copynumber: 4.5 Consensus size: 124
337965 GTAAAAATTT
*
337975 TGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATC
1 TGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
** * * * * * * * * *
338040 C-A---AGGGTTGCATTGCTGCTTGTGGGCACAATAT-CCTTCGTCGTGAATTTGATATCG
66 CAATCTAAAGATG-AATGTTGCTGGTGAGCACGAT-TCCCTTCGTCGTGAAGTTGAAACCG
** *
338096 TGGATGGCTTCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGATGTTGAAATC
1 TGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
* * *
338161 CAATCTAAAGATGAATATTGTTGGTGGGCACGATTCCCTTCGTCGTGAAGTTGAAACCG
66 CAATCTAAAGATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCG
* * * *
338220 TGGATGACCCCTTCGTTATGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTAAAGTTGAAATC
1 TGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
* * *
338285 AAATCTAAAGATGAATGTTGCTGGTGAGCAAGATTCTCTTCGTCGTGAAGTTGAAACCG
66 CAATCTAAAGATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCG
* * *
338344 TGGATGGCCCCTTCGTTGTGAAGTGGAGCCTTGAATTGGATATCCTTTGTCGTGAAGTTTAAATC
1 TGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
* * * * *
338409 CAATCTAAATATGAATGTTGCTGGTGAGTACGATTTCCTTCATCGTGAATTTGAAACCG
66 CAATCTAAAGATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCG
* * *
338468 TGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCTTTGTCGTGAAGTTGAAATC
1 TGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
338533 TAAGCTTGTA
Statistics
Matches: 384, Mismatches: 48, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
121 62 0.16
122 1 0.00
123 1 0.00
124 316 0.82
125 4 0.01
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (124 bp):
TGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
CAATCTAAAGATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCG
Found at i:338734 original size:240 final size:239
Alignment explanation
Indices: 338438--339015 Score: 904
Period size: 240 Copynumber: 2.4 Consensus size: 239
338428 GCTGGTGAGT
* * *
338438 ACGATTTCCTTCATCGTGAATTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAC
1 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGG-CCCTTCGTTGTGAAGTTGAGCCTTGAC
* ** * *
338503 TTGAATATCCTTTGTCGTGAAGTTGAAATCTAAGCTTGTATTTTTTCGAGTCCAATATCCTTCGC
65 TTAAATATCCTTCATCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCGC
338568 CGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCCATGAAGTTGAACTTTGAA
130 CGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCCATGAAGTTGAACTTTGAA
* * * * *
338633 TTGGATATCTTTCGTCGTGAAGTTGAAATCTAATCTAGAGTTGGC
195 TTAGATATCCTTCGTCGTGAAGTTAAAATCCAATATAGAGTTGGC
* * * *
338678 ACGATATCATTCATCCTGAAGTTGAAATCGTGGATGGTCCCTTTGTTGTGAAGTTGAGCCTTAAC
1 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGG-CCCTTCGTTGTGAAGTTGAGCCTTGAC
* *
338743 TTTAATATCCTTCATCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCGT
65 TTAAATATCCTTCATCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCGC
* * *
338808 CGTGAAGTTGAAATTGGCTCTGAATGAAATTGGGAAGCCCCTTCGCCTTGAAGTTGAGCTTTGAA
130 CGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCCATGAAGTTGAACTTTGAA
338873 TTAGATATCCTTCGTCGTGAAGTTAAAATCCAATATAGAGTTGGC
195 TTAGATATCCTTCGTCGTGAAGTTAAAATCCAATATAGAGTTGGC
*
338918 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCATTCATTGTGAAGTTGAGCCTTGAC
1 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCC-TTCGTTGTGAAGTTGAGCCTTGAC
* *
338983 TTAAATATGCTTCATCTTGAAGTTGAAATCCAA
65 TTAAATATCCTTCATCGTGAAGTTGAAATCCAA
339016 TTATTGTATG
Statistics
Matches: 307, Mismatches: 30, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
239 3 0.01
240 304 0.99
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (239 bp):
ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCTTCGTTGTGAAGTTGAGCCTTGACT
TAAATATCCTTCATCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCGCC
GTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCCATGAAGTTGAACTTTGAAT
TAGATATCCTTCGTCGTGAAGTTAAAATCCAATATAGAGTTGGC
Found at i:346504 original size:25 final size:25
Alignment explanation
Indices: 346476--346527 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
346466 TGCACCATGT
346476 ATAAGTTCCCTATTCTATGACCAAC
1 ATAAGTTCCCTATTCTATGACCAAC
346501 ATAAGTTCCCTATTCTATGACCAAC
1 ATAAGTTCCCTATTCTATGACCAAC
346526 AT
1 AT
346528 GCATAATCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.33
Consensus pattern (25 bp):
ATAAGTTCCCTATTCTATGACCAAC
Found at i:352705 original size:138 final size:139
Alignment explanation
Indices: 352553--352829 Score: 466
Period size: 139 Copynumber: 2.0 Consensus size: 139
352543 ATATCATCAA
*
352553 AGATATTGATTGATAACTCAGTAAAAAGACTGTATTTTA-GTTTTTTTACTTAAGTTATTAATTG
1 AGATATTGATTGATAACTCAGTAAAAAGACTATATTTTAGGTTTTTTTACTTAAGTTATTAATTG
* * * *
352617 TTTAGAAGCCATTGACATAGCATTTTAGTTGCATATATTTGCATTTAGGACATTTTTTCATGTGG
66 TTTAAAAGCCATTGACATAGCATTTTAGCTGCATATAGTTGCATTTAGGACATTTTTGCATGTGG
*
352682 TGGATAAGT
131 TAGATAAGT
* * *
352691 AGATATTGATTGATAACTCCGTAAAAATACTATATTTTAGGTTTTTTTACTTAAGTTATTGATTG
1 AGATATTGATTGATAACTCAGTAAAAAGACTATATTTTAGGTTTTTTTACTTAAGTTATTAATTG
352756 TTTAAAAGCCATTGACATAGCATTTTAGCTGCATATAGTTGCATTTAGGACATTTTTGCATGTGG
66 TTTAAAAGCCATTGACATAGCATTTTAGCTGCATATAGTTGCATTTAGGACATTTTTGCATGTGG
352821 TAGATAAGT
131 TAGATAAGT
352830 TTTGCCGCGA
Statistics
Matches: 129, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
138 36 0.28
139 93 0.72
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (139 bp):
AGATATTGATTGATAACTCAGTAAAAAGACTATATTTTAGGTTTTTTTACTTAAGTTATTAATTG
TTTAAAAGCCATTGACATAGCATTTTAGCTGCATATAGTTGCATTTAGGACATTTTTGCATGTGG
TAGATAAGT
Done.