Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 176 of 240
Found at i:54458620 original size:22 final size:21
Alignment explanation
Indices: 54458595--54458668 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 21
54458585 ATTACTGTAC
54458595 TTATGGCTTGTAGTCATTCTGT
1 TTATGGCTT-TAGTCATTCTGT
* * *
54458617 TTATAGCTTATAGTTATCCTGT
1 TTATGGCTT-TAGTCATTCTGT
* * *
54458639 TTACGGCTCTTAGCCATTCTGG
1 TTATGGCT-TTAGTCATTCTGT
54458661 TTACTGGC
1 TTA-TGGC
54458669 AGCTTTGCTG
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGTCATTCTGT
Found at i:54462039 original size:19 final size:17
Alignment explanation
Indices: 54462017--54462059 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
54462007 AATTTATTTT
54462017 AAAAATAAAAAAATTTTAA
1 AAAAATAAAAAAA--TTAA
*
54462036 AAAAATTAAAAAATTAA
1 AAAAATAAAAAAATTAA
54462053 AAAAATA
1 AAAAATA
54462060 TATATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.45
19 12 0.55
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAATAAAAAAATTAA
Found at i:54462046 original size:17 final size:17
Alignment explanation
Indices: 54462012--54462059 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
54462002 CTAAAAATTT
54462012 ATTTTAAAAATAA-AAAA
1 ATTTTAAAAA-AATAAAA
54462029 ATTTTAAAAAAATTAAAA
1 ATTTTAAAAAAA-TAAAA
*
54462047 A-ATTAAAAAAATA
1 ATTTTAAAAAAATA
54462060 TATATTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.14
17 19 0.68
18 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTTTAAAAAAATAAAA
Found at i:54462405 original size:28 final size:30
Alignment explanation
Indices: 54462348--54462414 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
54462338 TTTTTTATTG
54462348 AAATAATAT-GAAAAACAATTAATTACCT-
1 AAATAATATAGAAAAACAATTAATTACCTA
* *
54462376 AAATAATATAGAATGAA-AATTATTTA-CTA
1 AAATAATATAGAA-AAACAATTAATTACCTA
54462405 AAATAATATA
1 AAATAATATA
54462415 TTTACATAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 11 0.32
29 21 0.62
30 2 0.06
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.31
Consensus pattern (30 bp):
AAATAATATAGAAAAACAATTAATTACCTA
Found at i:54462617 original size:21 final size:22
Alignment explanation
Indices: 54462588--54462635 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
54462578 TCAAGCCTAG
*
54462588 AAAGTATTTGAAGAACTAAGGC
1 AAAGTATTTGAAGAACAAAGGC
54462610 AAAG-ATTTGAAGAACAAAGGC
1 AAAGTATTTGAAGAACAAAGGC
*
54462631 TAAGT
1 AAAGT
54462636 TTTTATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.21
Consensus pattern (22 bp):
AAAGTATTTGAAGAACAAAGGC
Found at i:54465264 original size:20 final size:21
Alignment explanation
Indices: 54465234--54465283 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
54465224 TAAAAATTAA
* *
54465234 AAAAAATATGTATATAGATAT
1 AAAATATATGTATACAGATAT
*
54465255 -AAATATATGTATACAGTTAT
1 AAAATATATGTATACAGATAT
54465275 AAAATATAT
1 AAAATATAT
54465284 AAAATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (21 bp):
AAAATATATGTATACAGATAT
Found at i:54465634 original size:3 final size:3
Alignment explanation
Indices: 54465626--54465651 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54465616 AAACAAAAAT
54465626 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
54465652 AATAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:54465656 original size:3 final size:3
Alignment explanation
Indices: 54465650--54465695 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
54465640 GATGATGATG
54465650 ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
54465696 CATCATCATC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:54467311 original size:85 final size:85
Alignment explanation
Indices: 54467214--54467370 Score: 196
Period size: 85 Copynumber: 1.8 Consensus size: 85
54467204 GTGGTTTTAG
54467214 TCTGCTCCACTGCAAC-GTCA-AGGAGATAAGA-CTTATATTTTTAA-CCTGCTCCACTGCAACT
1 TCTGCTCCACTGCAACTG-CAGA-GAGATAAGATC-TATATTTTTAATCC-GCTCCACTGCAACT
*
54467275 TCAGGGAGATAAGGTTGGATGCGA
62 TCAGAGAGATAAGGTTGGATGCGA
* * * * *
54467299 TCTGCTCTACTGCCACTGCAGAGAGATAAGATCTGTGTTTTTAATCCGCTCCATTGCAACTTCAG
1 TCTGCTCCACTGCAACTGCAGAGAGATAAGATCTATATTTTTAATCCGCTCCACTGCAACTTCAG
54467364 AGAGATA
66 AGAGATA
54467371 GGATTAGTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
85 57 0.92
86 5 0.08
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (85 bp):
TCTGCTCCACTGCAACTGCAGAGAGATAAGATCTATATTTTTAATCCGCTCCACTGCAACTTCAG
AGAGATAAGGTTGGATGCGA
Found at i:54467438 original size:43 final size:43
Alignment explanation
Indices: 54467391--54467632 Score: 238
Period size: 43 Copynumber: 5.6 Consensus size: 43
54467381 CTTCTGTCTG
*
54467391 CTCCACTACTACTTAGGGAGATAAGGCTGGTGCTTTCGATCTA
1 CTCCACTACTGCTTAGGGAGATAAGGCTGGTGCTTTCGATCTA
* * ** *
54467434 CTCCACTACTGCTTAGGGAGATAAGATCT-ATAATCTTCGACCTA
1 CTCCACTACTGCTTAGGGAGATAAG-GCTGGTGCT-TTCGATCTA
* * * * * *
54467478 CTCCGCTGCTGCTCAGGGAGATAAGGTTGGTGCTTTCAATCTG
1 CTCCACTACTGCTTAGGGAGATAAGGCTGGTGCTTTCGATCTA
* * * *
54467521 CTCCACTACTGCTTAGGGAGATAA-GAT-CTACAATCTTCGACCTA
1 CTCCACTACTGCTTAGGGAGATAAGGCTGGTGC--T-TTCGATCTA
* * * *
54467565 CTCCGCTGCTGCTCAGGGAGATAAGGCTGGTGCTTTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGGCTGGTGCTTTCGATCTA
54467608 CTCCACTACTGCTTAGGGAGATAAG
1 CTCCACTACTGCTTAGGGAGATAAG
54467633 ATCTGCAATC
Statistics
Matches: 154, Mismatches: 37, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
41 2 0.01
42 2 0.01
43 84 0.55
44 62 0.40
45 2 0.01
46 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (43 bp):
CTCCACTACTGCTTAGGGAGATAAGGCTGGTGCTTTCGATCTA
Found at i:54467471 original size:87 final size:87
Alignment explanation
Indices: 54467405--54467857 Score: 481
Period size: 87 Copynumber: 5.2 Consensus size: 87
54467395 ACTACTACTT
* *
54467405 AGGGAGATAAGGCTGGTGCTTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCT
1 AGGGAGATAAGGCTGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
54467470 TCGACCTACTCCGCTGCTGCTC
66 TCGACCTACTCCGCTGCTGCTC
* *
54467492 AGGGAGATAAGGTTGGTGCTTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
1 AGGGAGATAAGGCTGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
54467557 TCGACCTACTCCGCTGCTGCTC
66 TCGACCTACTCCGCTGCTGCTC
*
54467579 AGGGAGATAAGGCTGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCT
1 AGGGAGATAAGGCTGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
* *
54467644 TCAACCTATTCCGCTGCTGCTC
66 TCGACCTACTCCGCTGCTGCTC
* ** * ** *
54467666 A-GGAG-TATGGACTGGTGGC-TTAAATTTGCTTCCTACTACT--TTAGAAAGATAAGAT-TCGC
1 AGGGAGATAAGG-CTGGT-GCTTTCGATCTGC-TCC-ACTACTGCTTAGGGAGATAAGATCT-AC
** ** * * * *
54467725 CGTCTTCGGTCTGCTCCACTACTGCTT
61 AATCTTCGACCTACTCCGCTGCTGCTC
* * ** * *
54467752 AGAGAGATAAGATCT--ACCATCTTCGATCCGCTCCGCTACTGCTTAGGGAGATAAGATCTACAA
1 AGGGAGATAAG-GCTGGTGC-T-TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
* * * *
54467815 TCTTCAACCTACTCCACTACTGCTT
63 TCTTCGACCTACTCCGCTGCTGCTC
*
54467840 AGGGAGATAAGGTTGGTG
1 AGGGAGATAAGGCTGGTG
54467858 GCTTAGATTT
Statistics
Matches: 301, Mismatches: 49, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
85 6 0.02
86 54 0.18
87 178 0.59
88 62 0.21
89 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
AGGGAGATAAGGCTGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
TCGACCTACTCCGCTGCTGCTC
Found at i:54467490 original size:44 final size:44
Alignment explanation
Indices: 54467391--54467850 Score: 237
Period size: 44 Copynumber: 10.6 Consensus size: 44
54467381 CTTCTGTCTG
* * ** *
54467391 CTCCACTACTACTTAGGGAGATAAG-GCTGGTGCT-TTCGATCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCGACCTA
*
54467434 CTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCGACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCGACCTA
* * * * ** * * *
54467478 CTCCGCTGCTGCTCAGGGAGATAAGGT-TGGTGCT-TTCAATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCGACCTA
**
54467521 CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCGACCTA
* * * * ** * *
54467565 CTCCGCTGCTGCTCAGGGAGATAAG-GCTGGTGCT-TTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCGACCTA
* *
54467608 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCGACCTA
* * * * * ** ** ** *
54467652 TTCCGCTGCTGCTCA-GGAG-TATGGA-CTGGT-GGCTTAAATTTG
1 CTCCACTACTGCTTAGGGAGATA-AGATCT-GTAATCTTCGACCTA
** *** ** *
54467694 CTTCCTACTACT--TTAGAAAGATAAGAT-TCGCCGTCTTCGGTCTG
1 C-TCC-ACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCGACCTA
* *** *
54467738 CTCCACTACTGCTTAGAGAGATAAGATCTACCATCTTCGATCC-G
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCGA-CCTA
* ** *
54467782 CTCCGCTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCGACCTA
54467826 CTCCACTACTGCTTAGGGAGATAAG
1 CTCCACTACTGCTTAGGGAGATAAG
54467851 GTTGGTGGCT
Statistics
Matches: 312, Mismatches: 84, Indels: 41
0.71 0.19 0.09
Matches are distributed among these distances:
42 18 0.06
43 111 0.36
44 181 0.58
45 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCGACCTA
Found at i:54467600 original size:174 final size:175
Alignment explanation
Indices: 54467408--54468038 Score: 589
Period size: 174 Copynumber: 3.5 Consensus size: 175
54467398 ACTACTTAGG
* * *
54467408 GAGATAAGGCTGGTGCTTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCG
1 GAGATAAGGCTGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
* *
54467473 ACCTACTCCGCTGCTGCTCAGGGAGATAAGG-TTGGTGCTTTCAATCTGCTCCACTACTGCTTAG
66 ACCTACTCCGCTACTGCTCAGGGAGATAAGGATTGGTGCTTTCAATTTGCTCCACTACTGCTTAG
* * *
54467537 GGAGATAAGATCTACAATCTTCGACCTACTCCGCTGCTGCTCAGG
131 GGAGATAAGATCTGCAATCTTCGACCTACTCCACTGCTGCTCAGA
*
54467582 GAGATAAGGCTGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCA
1 GAGATAAGGCTGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
* * * * *
54467647 ACCTATTCCGCTGCTGCTCA-GGAG-TATGGACTGGTGGC-TTAAATTTGCTTCCTACTACT--T
66 ACCTACTCCGCTACTGCTCAGGGAGATAAGGATTGGT-GCTTTCAATTTGC-TCC-ACTACTGCT
** ** ** * * *
54467707 TAGAAAGATAAGAT-TCGCCGTCTTCGGTCTGCTCCACTACTGCTTAGA
128 TAGGGAGATAAGATCT-GCAATCTTCGACCTACTCCACTGCTGCTCAGA
* ** * *
54467755 GAGATAAGATCT--ACCATCTTCGATCCGCTCCGCTACTGCTTAGGGAGATAAGATCTACAATCT
1 GAGATAAG-GCTGGTGC-T-TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCT
* * * *
54467818 TCAACCTACTCCACTACTGCTTAGGGAGATAAGGTTGGTGGCTTAGATTTGCTGTCTTCGATTTG
63 TCAACCTACTCCGCTACTGCTCAGGGAGATAAGGAT--T-G----G---TGC--T-TTCAATTTG
*
54467883 CTCCGCTACTGCTTAGGGAGATAAGATCTGCAATCTTCGACCTACTCCACTGCTGCTCAGA
115 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCGACCTACTCCACTGCTGCTCAGA
* ** * * * ** *
54467944 GAGAT-AGGATTCATGGTTTTGATATGCTCTGCTACTGCTTAGGGAGATAAGATCTACCATCTTC
1 GAGATAAGG-CTGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
* * * *
54468008 GATCTGCTCCGCTACTGCTTAGGGAGATAAG
65 AACCTACTCCGCTACTGCTCAGGGAGATAAG
54468039 ATCTACAATC
Statistics
Matches: 367, Mismatches: 60, Indels: 46
0.78 0.13 0.10
Matches are distributed among these distances:
172 6 0.02
173 60 0.16
174 148 0.40
175 10 0.03
176 4 0.01
178 1 0.00
179 1 0.00
183 1 0.00
185 2 0.01
186 1 0.00
187 5 0.01
188 75 0.20
189 52 0.14
190 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (175 bp):
GAGATAAGGCTGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
ACCTACTCCGCTACTGCTCAGGGAGATAAGGATTGGTGCTTTCAATTTGCTCCACTACTGCTTAG
GGAGATAAGATCTGCAATCTTCGACCTACTCCACTGCTGCTCAGA
Found at i:54467939 original size:44 final size:44
Alignment explanation
Indices: 54467883--54468082 Score: 190
Period size: 44 Copynumber: 4.6 Consensus size: 44
54467873 CTTCGATTTG
* *
54467883 CTCCGCTACTGCTTAGGGAGATAAGATCTGCAATCTTCGACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTA
* * * * * * ** *
54467927 CTCCACTGCTGCTCAGAGAGATAGGAT-T-C-ATGGTTTTGATATG
1 CTCCACTACTGCTTAGGGAGATAAGATCTACAAT--CTTCGACCTA
** * * *
54467970 CTCTGCTACTGCTTAGGGAGATAAGATCTACCATCTTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTA
* *
54468014 CTCCGCTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTA
*
54468058 CTCTACTACTGCTTAGGGAGATAAG
1 CTCCACTACTGCTTAGGGAGATAAG
54468083 GCTGGTGGCT
Statistics
Matches: 125, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 27 0.22
44 92 0.74
45 1 0.01
46 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTA
Found at i:54468149 original size:232 final size:233
Alignment explanation
Indices: 54467743--54468184 Score: 753
Period size: 232 Copynumber: 1.9 Consensus size: 233
54467733 GTCTGCTCCA
54467743 CTACTGCTTAGAGAGATAAGATCTACCATCTTCGATCCGCTCCGCTACTGCTTAGGGAGATAAGA
1 CTACTGCTTAGAGAGATAAGATCTACCATCTTCGATCCGCTCCGCTACTGCTTAGGGAGATAAGA
*
54467808 TCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAAGGTTGGTGGCTTAGATTTGCTGT
66 TCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAAGGCTGGTGGCTTAGATTTGCTGT
* * * *
54467873 CTTCGATTTGCTCCGCTACTGCTTAGGGAGATAAGATCTGCAATCTTCGACCTACTCCACTGCTG
131 CTTCGATCTGCTCCGCTACTGCTTAGGAAGATAAGATCTGCAATCTTCAACATACTCCACTGCTG
54467938 C-TCAGAGAG-ATAGGATTCATGGTTTTGATATGCTCTG
196 CTTCAG-GAGTATAGGATTCATGGTTTTGATATGCTCTG
* *
54467975 CTACTGCTTAGGGAGATAAGATCTACCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGA
1 CTACTGCTTAGAGAGATAAGATCTACCATCTTCGATCCGCTCCGCTACTGCTTAGGGAGATAAGA
* *
54468040 TCTACAATCTTCAACCTACTCTACTACTGCTTAGGGAGATAAGGCTGGTGGCTTCGATTTGCTGT
66 TCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAAGGCTGGTGGCTTAGATTTGCTGT
* * *
54468105 CTTCGATCTGTTCCGCTACTGCTTAGGAAGATAAGATCTGCAATCTTCAACATATTCCACTTCTG
131 CTTCGATCTGCTCCGCTACTGCTTAGGAAGATAAGATCTGCAATCTTCAACATACTCCACTGCTG
54468170 CTTCAGGAGTATAGG
196 CTTCAGGAGTATAGG
54468185 TAACTTCATT
Statistics
Matches: 196, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
232 187 0.95
233 9 0.05
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (233 bp):
CTACTGCTTAGAGAGATAAGATCTACCATCTTCGATCCGCTCCGCTACTGCTTAGGGAGATAAGA
TCTACAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAAGGCTGGTGGCTTAGATTTGCTGT
CTTCGATCTGCTCCGCTACTGCTTAGGAAGATAAGATCTGCAATCTTCAACATACTCCACTGCTG
CTTCAGGAGTATAGGATTCATGGTTTTGATATGCTCTG
Found at i:54468502 original size:24 final size:24
Alignment explanation
Indices: 54468466--54468545 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
54468456 AGATTGCCCC
*
54468466 CCACTGTAATCTTCAAAGTTCAAT
1 CCACTGTACTCTTCAAAGTTCAAT
** *
54468490 CTGCTGTACTCTTCAAGGTTCAAT
1 CCACTGTACTCTTCAAAGTTCAAT
* * *
54468514 CCACTGTACTCTTCAAGGTTTAGT
1 CCACTGTACTCTTCAAAGTTCAAT
54468538 CCACTGTA
1 CCACTGTA
54468546 ATAAAATTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (24 bp):
CCACTGTACTCTTCAAAGTTCAAT
Found at i:54469405 original size:13 final size:13
Alignment explanation
Indices: 54469387--54469438 Score: 70
Period size: 13 Copynumber: 3.8 Consensus size: 13
54469377 TCCTTTTTAT
54469387 TTTTCTTCTTTTC
1 TTTTCTTCTTTTC
54469400 TTTTCTTCTTTTC
1 TTTTCTTCTTTTC
54469413 TTCTT-TTCTTTTTTC
1 TT-TTCTTC--TTTTC
54469428 TTTTCTTCTTT
1 TTTTCTTCTTT
54469439 ATTGTTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 21 0.60
14 4 0.11
15 10 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTCTTTTC
Found at i:54469438 original size:8 final size:8
Alignment explanation
Indices: 54469397--54469429 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
54469387 TTTTCTTCTT
54469397 TTCTTTTC
1 TTCTTTTC
54469405 TTCTTTTC
1 TTCTTTTC
54469413 TTCTTTTC
1 TTCTTTTC
54469421 TT-TTTTC
1 TTCTTTTC
54469428 TT
1 TT
54469430 TTCTTCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTCTTTTC
Found at i:54474358 original size:20 final size:21
Alignment explanation
Indices: 54474328--54474377 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
54474318 AAAATTAAAA
* *
54474328 AAAAAATATGTATATAGATAT
1 AAAATATATGTATACAGATAT
*
54474349 -AAATATATGTATACAGTTAT
1 AAAATATATGTATACAGATAT
54474369 AAAATATAT
1 AAAATATAT
54474378 AAAATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (21 bp):
AAAATATATGTATACAGATAT
Found at i:54474784 original size:3 final size:3
Alignment explanation
Indices: 54474778--54474827 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
54474768 AAATATGATG
* *
54474778 ATA ATA ACA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54474826 AT
1 AT
54474828 CATCAATAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:54484603 original size:21 final size:21
Alignment explanation
Indices: 54484577--54484618 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
54484567 ATCCAACATG
54484577 GCTAGTTAATTGGCCACGTCA
1 GCTAGTTAATTGGCCACGTCA
54484598 GCTAGTTAATTGGCCACGTCA
1 GCTAGTTAATTGGCCACGTCA
54484619 CCTGTCCCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
GCTAGTTAATTGGCCACGTCA
Found at i:54485783 original size:30 final size:31
Alignment explanation
Indices: 54485744--54485803 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
54485734 GGAGGTGGGA
*
54485744 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
54485775 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
54485804 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:54486031 original size:9 final size:9
Alignment explanation
Indices: 54486017--54486053 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54486007 TATAGTTTGA
54486017 TATTCGAAT
1 TATTCGAAT
54486026 TATTCGAAT
1 TATTCGAAT
*
54486035 TATTCGAGT
1 TATTCGAAT
54486044 TATTCGAAT
1 TATTCGAAT
54486053 T
1 T
54486054 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54486394 original size:3 final size:3
Alignment explanation
Indices: 54486386--54486411 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54486376 TCACAAAAAT
54486386 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
54486412 TATTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54486422 original size:12 final size:13
Alignment explanation
Indices: 54486384--54486424 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 13
54486374 ACTCACAAAA
54486384 ATTTATTATTATT
1 ATTTATTATTATT
54486397 A-TTATTATTATT
1 ATTTATTATTATT
*
54486409 ATTTATT-TTTTT
1 ATTTATTATTATT
54486421 ATTT
1 ATTT
54486425 TTTAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTTATTATTATT
Found at i:54488332 original size:19 final size:20
Alignment explanation
Indices: 54488298--54488338 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54488288 GATTAAAATT
*
54488298 AAAAAATAAATATTTTTTTA
1 AAAAAATAAATATTTTATTA
*
54488318 AAAAAATTAAT-TTTTATTA
1 AAAAAATAAATATTTTATTA
54488337 AA
1 AA
54488339 TGGAAGCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAAATAAATATTTTATTA
Found at i:54506920 original size:6 final size:6
Alignment explanation
Indices: 54506909--54506937 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54506899 GACAAAATAA
54506909 ATATTT ATATTT ATATTT ATATTT ATATT
1 ATATTT ATATTT ATATTT ATATTT ATATT
54506938 AGATTATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:54515448 original size:50 final size:50
Alignment explanation
Indices: 54515373--54515503 Score: 190
Period size: 50 Copynumber: 2.6 Consensus size: 50
54515363 GAGTAAACTT
* * *
54515373 AGTTCGGCAGCCTTTCAGATCTATTTTGACTGATGTGTTCAAATCTGTTC
1 AGTTCAGCAGCCTTTCAGATCTATTTTGACTGATGTGCTCAAATCTGCTC
** *
54515423 AGTTCAGCAGCCTTTTGGATCTATTTTGACTGATGTGCTCAACTCTGCTC
1 AGTTCAGCAGCCTTTCAGATCTATTTTGACTGATGTGCTCAAATCTGCTC
* *
54515473 AGTTCAGCAGTCTTTCAGATCTATTCTGACT
1 AGTTCAGCAGCCTTTCAGATCTATTTTGACT
54515504 AGAGCGCTCC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (50 bp):
AGTTCAGCAGCCTTTCAGATCTATTTTGACTGATGTGCTCAAATCTGCTC
Found at i:54515708 original size:21 final size:23
Alignment explanation
Indices: 54515661--54515709 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
54515651 GAGAAAACTA
*
54515661 AAGTGAGTGAGAGAGGAATGTTG
1 AAGTGAGTGAGAGAGGAATGTAG
*
54515684 -AGTGA-TGAGAGATGAATG-AG
1 AAGTGAGTGAGAGAGGAATGTAG
54515704 AAGTGA
1 AAGTGA
54515710 AAGATGGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (23 bp):
AAGTGAGTGAGAGAGGAATGTAG
Found at i:54516262 original size:21 final size:20
Alignment explanation
Indices: 54516207--54516262 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
54516197 ATATATACAT
*
54516207 TAATA-AATTAA-CATGAAT
1 TAATATAATTAAGCATGAAA
* *
54516225 TAATATAAAATATGCATGAAAA
1 TAATAT-AATTAAGCATG-AAA
54516247 TAATATAATTAAGCAT
1 TAATATAATTAAGCAT
54516263 AATTTCACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.17
20 4 0.14
21 12 0.41
22 8 0.28
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAATATAATTAAGCATGAAA
Found at i:54518882 original size:22 final size:22
Alignment explanation
Indices: 54518852--54518893 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54518842 ACACCAAAAC
* *
54518852 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGACGCTTTTTT
54518874 AGGCCTTTAGCGACGCTTTT
1 AGGCCTTTAGCGACGCTTTT
54518894 CAAAGCGCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.40
Consensus pattern (22 bp):
AGGCCTTTAGCGACGCTTTTTT
Found at i:54519196 original size:86 final size:87
Alignment explanation
Indices: 54519106--54519307 Score: 280
Period size: 86 Copynumber: 2.3 Consensus size: 87
54519096 TAGATCAGGG
*** * * * *
54519106 TCTTTAGCGGCGTTTTTTTCTCAAATGCCACAATAGACCCTGATCTATAGCGGCGCTTTGACCAC
1 TCTTTAGCGGCGTTTTCCCCTAAAACGCCACAATAGACCCTGATCTATAACGGCGCTTCGACCAC
*
54519171 -AAACACCACTAAAGAACTTAA
66 AAAACACCACTAAAGAACCTAA
* *
54519192 TCTTTAGCAGCGTTTTCCCCTAAAACGCCGCAATAGACCCTGATCTATAACGGCGCTTCGACCAC
1 TCTTTAGCGGCGTTTTCCCCTAAAACGCCACAATAGACCCTGATCTATAACGGCGCTTCGACCAC
*
54519257 AAAACGCCACTAAAGAACCTAA
66 AAAACACCACTAAAGAACCTAA
* *
54519279 TCTTTAGCGGCGCTTTCCCCAAAAACGCC
1 TCTTTAGCGGCGTTTTCCCCTAAAACGCC
54519308 GCTAAAGACC
Statistics
Matches: 101, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 56 0.55
87 45 0.45
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (87 bp):
TCTTTAGCGGCGTTTTCCCCTAAAACGCCACAATAGACCCTGATCTATAACGGCGCTTCGACCAC
AAAACACCACTAAAGAACCTAA
Found at i:54519313 original size:43 final size:43
Alignment explanation
Indices: 54519148--54519400 Score: 226
Period size: 43 Copynumber: 5.9 Consensus size: 43
54519138 ATAGACCCTG
* * * * *
54519148 ATCTATAGCGGCGCTTTGACCACAAACACCACTAAAGAACTTA
1 ATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGAACCTA
* * * * * * *
54519191 ATCTTTAGCAGCGTTTTCCCCTAAAACGCCGC-AATAGACCCTG
1 ATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAA-AGAACCTA
* *
54519234 ATCTATAACGGCGC-TTCGACCACAAAACGCCACTAAAGAACCTA
1 ATCTTTAGCGGCGCTTTC-ACCA-AAAACGCCACTAAAGAACCTA
* *
54519278 ATCTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAG-ACCATA
1 ATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGAACC-TA
* ** * * *
54519321 ATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAA-AACCCTT
1 ATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGAA-CCTA
*
54519364 ATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAG
1 ATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAG
54519401 GCCAACACCT
Statistics
Matches: 166, Mismatches: 35, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
42 8 0.05
43 121 0.73
44 32 0.19
45 5 0.03
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (43 bp):
ATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGAACCTA
Found at i:54519323 original size:130 final size:129
Alignment explanation
Indices: 54519148--54519400 Score: 305
Period size: 130 Copynumber: 2.0 Consensus size: 129
54519138 ATAGACCCTG
* * *
54519148 ATCTATAGCGGCGCTTTGACCACAAACACCACTAAAGAACTTAATCTTTAGCAGCG-TTTTCCC-
1 ATCTATAGCGGCGCTTTCACCAAAAACACCACTAAAGAACATAATCTTTAGCAGCGCTTTTCCCA
*
54519211 CTAAAACGCCGC-AATAGACCCTGATCTATAACGGCGCTTCGACCACAAAACGCCACTAAAGAAC
66 C--AAACGCCGCTAA-AAACCCTGATCTATAACGGCGCTTCGACCA-AAAACGCCACTAAAGAAC
54519275 CTA
127 CTA
* * * * * ** *
54519278 ATCTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGACCATAATCTTTAGTGGCGCTTTTTCCA
1 ATCTATAGCGGCGCTTTCACCAAAAACACCACTAAAGAACATAATCTTTAGCAGCGCTTTTCCCA
* * * *
54519343 CAAACGCCGCTAAAAACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAG
66 CAAACGCCGCTAAAAACCCTGATCTATAACGGCGCTTCGACCAAAAACGCCACTAAAG
54519401 GCCAACACCT
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
129 15 0.14
130 80 0.77
131 8 0.08
132 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (129 bp):
ATCTATAGCGGCGCTTTCACCAAAAACACCACTAAAGAACATAATCTTTAGCAGCGCTTTTCCCA
CAAACGCCGCTAAAAACCCTGATCTATAACGGCGCTTCGACCAAAAACGCCACTAAAGAACCTA
Found at i:54519387 original size:86 final size:87
Alignment explanation
Indices: 54519253--54519444 Score: 237
Period size: 86 Copynumber: 2.2 Consensus size: 87
54519243 GGCGCTTCGA
* *
54519253 CCACAAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGACC
1 CCACAAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGACC
*
54519318 ATA-ATCTTTAGTGGCGCTTTTT
66 A-ACACCTTTAGTGGCGCTTTTT
* * * *
54519340 CCAC-AAACGCCGCTAAA-AACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGGC
1 CCACAAAACGCCACTAAAGAA-CCTAATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGAC
*
54519403 CAACACCTTTAGTGGCGTTTTTT
65 CAACACCTTTAGTGGCGCTTTTT
** *
54519426 AAAAAAAAACGCCACTAAA
1 -CCACAAAACGCCACTAAA
54519445 TTTGGCAGAT
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
85 3 0.03
86 69 0.78
87 5 0.06
88 12 0.13
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (87 bp):
CCACAAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCACCAAAAACGCCACTAAAGACC
AACACCTTTAGTGGCGCTTTTT
Found at i:54519772 original size:21 final size:21
Alignment explanation
Indices: 54519746--54519879 Score: 128
Period size: 21 Copynumber: 6.4 Consensus size: 21
54519736 TTTGACGCTG
*
54519746 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
**
54519767 CTCTGCTT-TCCTCGCTTTAGC
1 CTCTGCTTCT-CTCGCTGCAGC
54519788 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
* * * * *
54519809 TTGTACTTCTCTAGCTGCCGC
1 CTCTGCTTCTCTCGCTGCAGC
*
54519830 CTCTGCTTCTCTTGCTGCCA-C
1 CTCTGCTTCTCTCGCTG-CAGC
* *
54519851 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCTCTCGCTGCAGC
*
54519872 ATCTGCTT
1 CTCTGCTT
54519880 TAAGCTGCTG
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
20 1 0.01
21 89 0.97
22 2 0.02
ACGTcount: A:0.05, C:0.40, G:0.17, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCTCTCGCTGCAGC
Found at i:54519925 original size:66 final size:66
Alignment explanation
Indices: 54519849--54519996 Score: 201
Period size: 66 Copynumber: 2.2 Consensus size: 66
54519839 TCTTGCTGCC
* *
54519849 ACCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCAT
1 ACCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-AT
54519912 TGA
64 TGA
* * * *
54519915 ACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTG
1 ACCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTATTG
54519980 A
66 A
*
54519981 ACATCAGCTTCTCTCG
1 ACCTCAGCTTCTCTCG
54519997 ATGTTGCCTC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 68 0.93
67 4 0.05
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.40
Consensus pattern (66 bp):
ACCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTATTG
A
Found at i:54520012 original size:66 final size:66
Alignment explanation
Indices: 54519855--54520019 Score: 190
Period size: 66 Copynumber: 2.5 Consensus size: 66
54519845 TGCCACCTCT
* * * * * *
54519855 GCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATACTTTCATTGAACCT
1 GCTTCTCTCGATGCTGCATCCGCTTTAAGTTG-TAGCTGGAGTTCTTCATACTTTCATTGAACAT
54519919 CA
65 CA
* * * *
54519921 GCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTGAACAT
1 GCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTAGCTGGAGTTCTTCATA-CTTTCATTGAACAT
54519985 CA
65 CA
* *
54519987 GCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGT
1 GCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
54520020 GTAATTTGCT
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 1 0.01
66 81 0.94
67 4 0.05
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.41
Consensus pattern (66 bp):
GCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTAGCTGGAGTTCTTCATACTTTCATTGAACATC
A
Found at i:54525458 original size:9 final size:9
Alignment explanation
Indices: 54525441--54525642 Score: 96
Period size: 9 Copynumber: 24.2 Consensus size: 9
54525431 TAAGTATAAT
*
54525441 TAAGCTATG
1 TAAGTTATG
54525450 TAAGTTATG
1 TAAGTTATG
54525459 T-A-TTATG
1 TAAGTTATG
54525466 TAAGTTAT-
1 TAAGTTATG
*
54525474 TTA-TTATG
1 TAAGTTATG
* **
54525482 AAAACTATG
1 TAAGTTATG
*
54525491 TAAGTTGTG
1 TAAGTTATG
54525500 T-A-TTATG
1 TAAGTTATG
*
54525507 -AA--AAT-
1 TAAGTTATG
* *
54525512 TATGCTATG
1 TAAGTTATG
*
54525521 TAAGTTATA
1 TAAGTTATG
* *
54525530 TAAGTCATA
1 TAAGTTATG
54525539 TAAGTTATG
1 TAAGTTATG
54525548 T-A-TTATG
1 TAAGTTATG
54525555 TAAGTTATG
1 TAAGTTATG
54525564 TAAGTTAT-
1 TAAGTTATG
*
54525572 TTA-TTATG
1 TAAGTTATG
* * *
54525580 CAAATTAAG
1 TAAGTTATG
54525589 TAAGTTATG
1 TAAGTTATG
54525598 TAAGTTATG
1 TAAGTTATG
*
54525607 TATA-ATAT-
1 TA-AGTTATG
**
54525615 TAA-TTAAC
1 TAAGTTATG
54525623 TAAGTTATG
1 TAAGTTATG
*
54525632 TAATTTATG
1 TAAGTTATG
54525641 TA
1 TA
54525643 TAATATTTAT
Statistics
Matches: 145, Mismatches: 32, Indels: 32
0.69 0.15 0.15
Matches are distributed among these distances:
6 3 0.02
7 28 0.19
8 18 0.12
9 95 0.66
10 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:54525467 original size:16 final size:16
Alignment explanation
Indices: 54525446--54525565 Score: 78
Period size: 16 Copynumber: 7.9 Consensus size: 16
54525436 ATAATTAAGC
54525446 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
54525462 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
*
54525478 TATG-AA---A---AC
1 TATGTAAGTTATGTAT
*
54525487 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
54525503 TATGAAAATTATG--C
1 TATGTAAGTTATGTAT
*
54525517 TATGTAAGTTATATAAGT
1 TATGTAAGTTATGT-A-T
* *
54525535 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
54525551 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
54525566 AGTTATTTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
12 1 0.01
14 10 0.13
15 2 0.03
16 44 0.58
17 1 0.01
18 11 0.14
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.45
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:54525490 original size:25 final size:25
Alignment explanation
Indices: 54525460--54525596 Score: 118
Period size: 25 Copynumber: 5.6 Consensus size: 25
54525450 TAAGTTATGT
54525460 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* * *
54525485 ACTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* * *
54525510 ATTATGCTATGTAAGTTA-TAT--AA
1 ATTATG-TAAGTTATTTATTATGAAA
* * * * *
54525533 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
54525558 GTTATGTAAGTTATTTATTATGCAA
1 ATTATGTAAGTTATTTATTATGAAA
*
54525583 ATTAAGTAAGTTAT
1 ATTATGTAAGTTAT
54525597 GTAAGTTATG
Statistics
Matches: 86, Mismatches: 22, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
22 7 0.08
23 8 0.09
25 65 0.76
26 6 0.07
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:54525640 original size:43 final size:42
Alignment explanation
Indices: 54525539--54525677 Score: 110
Period size: 43 Copynumber: 3.3 Consensus size: 42
54525529 ATAAGTCATA
* * *
54525539 TAAGTTATGT-ATTATGTAAGTTATGTA-AGTTATTTATTATGC
1 TAAGTTATGTAATTATGTAAGTTATGTATA-ATATTAATTA-AC
* *
54525581 -AAATTAAGTAAGTTATGTAAGTTATGTATAATATTAATTAAC
1 TAAGTTATGTAA-TTATGTAAGTTATGTATAATATTAATTAAC
*
54525623 TAAGTTATGTAATTTATGTATAATATTTATGTATAATATTAA-T-A-
1 TAAGTTATGTAA-TTATG--T-A-AGTTATGTATAATATTAATTAAC
54525667 TAAGTTATGTA
1 TAAGTTATGTA
54525678 TAATATTAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
41 7 0.09
42 2 0.03
43 38 0.47
44 12 0.15
45 2 0.03
46 2 0.03
47 17 0.21
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (42 bp):
TAAGTTATGTAATTATGTAAGTTATGTATAATATTAATTAAC
Found at i:54525652 original size:13 final size:13
Alignment explanation
Indices: 54525634--54525662 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54525624 AAGTTATGTA
54525634 ATTTATGTATAAT
1 ATTTATGTATAAT
54525647 ATTTATGTATAAT
1 ATTTATGTATAAT
54525660 ATT
1 ATT
54525663 AATATAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTATGTATAAT
Found at i:54525692 original size:56 final size:56
Alignment explanation
Indices: 54525647--54525773 Score: 245
Period size: 56 Copynumber: 2.3 Consensus size: 56
54525637 TATGTATAAT
54525647 ATTTATGTATAATATTAATATAAGTTATGTATAATATTAATTAATTAAGTTATGTA
1 ATTTATGTATAATATTAATATAAGTTATGTATAATATTAATTAATTAAGTTATGTA
*
54525703 ATTTATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTA
1 ATTTATGTATAATATTAATATAAGTTATGTATAATATTAATTAATTAAGTTATGTA
54525759 ATTTATGTATAATAT
1 ATTTATGTATAATAT
54525774 CACATCATCC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 70 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (56 bp):
ATTTATGTATAATATTAATATAAGTTATGTATAATATTAATTAATTAAGTTATGTA
Found at i:54525717 original size:34 final size:33
Alignment explanation
Indices: 54525555--54525773 Score: 192
Period size: 34 Copynumber: 6.8 Consensus size: 33
54525545 ATGTATTATG
* * ***
54525555 TAAGTTATGTAAGTTATTTATTATGCAAATTAA
1 TAAGTTATGTAAGTTATGTATAATATTAATTAA
54525588 GTAAGTTATGTAAGTTATGTATAATATTAATTAA
1 -TAAGTTATGTAAGTTATGTATAATATTAATTAA
* *
54525622 CTAAGTTATGTAATTTATGTATAATATTTATGT-A
1 -TAAGTTATGTAAGTTATGTATAATATTAAT-TAA
* *
54525656 TAATATTAATATAAGTTATGTATAATATTAATTAA
1 TAA-GTT-ATGTAAGTTATGTATAATATTAATTAA
*
54525691 TTAAGTTATGTAATTTATGTAT-A-A-T-A-T--
1 -TAAGTTATGTAAGTTATGTATAATATTAATTAA
54525718 T-A---ATGTAAGTTATGTATAATATTAATTAA
1 TAAGTTATGTAAGTTATGTATAATATTAATTAA
*
54525747 TTAAGTTATGTAATTTATGTATAATAT
1 -TAAGTTATGTAAGTTATGTATAATAT
54525774 CACATCATCC
Statistics
Matches: 151, Mismatches: 17, Indels: 34
0.75 0.08 0.17
Matches are distributed among these distances:
22 14 0.09
23 1 0.01
24 1 0.01
25 2 0.01
26 2 0.01
27 1 0.01
29 1 0.01
30 2 0.01
31 2 0.01
32 1 0.01
33 4 0.03
34 92 0.61
35 25 0.17
36 3 0.02
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (33 bp):
TAAGTTATGTAAGTTATGTATAATATTAATTAA
Found at i:54525723 original size:22 final size:22
Alignment explanation
Indices: 54525698--54525748 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
54525688 TAATTAAGTT
54525698 ATGTAATTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
*
54525720 ATGTAAGTTATGTATAATATTA
1 ATGTAATTTATGTATAATATTA
54525742 AT-TAATT
1 ATGTAATT
54525749 AAGTTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (22 bp):
ATGTAATTTATGTATAATATTA
Found at i:54525856 original size:13 final size:13
Alignment explanation
Indices: 54525838--54525874 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
54525828 ATATAAGTTT
54525838 ATGTAAGTTATGA
1 ATGTAAGTTATGA
*
54525851 ATGTAAGTTATGT
1 ATGTAAGTTATGA
54525864 ATGTAAGTTAT
1 ATGTAAGTTAT
54525875 TTAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (13 bp):
ATGTAAGTTATGA
Found at i:54537992 original size:16 final size:17
Alignment explanation
Indices: 54537971--54538004 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
54537961 TAATTAAAAA
54537971 TTTTAAAAAAAT-CAAT
1 TTTTAAAAAAATACAAT
*
54537987 TTTTAAAATAATACAAT
1 TTTTAAAAAAATACAAT
54538004 T
1 T
54538005 GTGTTACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTTAAAAAAATACAAT
Found at i:54538506 original size:3 final size:3
Alignment explanation
Indices: 54538500--54538545 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
54538490 CTACTACTAC
54538500 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54538546 GACCCACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:54556886 original size:23 final size:23
Alignment explanation
Indices: 54556821--54556933 Score: 97
Period size: 23 Copynumber: 5.0 Consensus size: 23
54556811 ATACCAGATA
54556821 CGCCACAAAGGTTA-ACAGAATG
1 CGCCACAAAGGTTATACAGAATG
* * * * * *
54556843 -TCAAGAAA-GCTACACAAAATG
1 CGCCACAAAGGTTATACAGAATG
* *
54556864 TGCCACAAAGGCTATACAGAATG
1 CGCCACAAAGGTTATACAGAATG
* *
54556887 CGCCATAAAGGTTATACAGAGTG
1 CGCCACAAAGGTTATACAGAATG
* *
54556910 CACCACAAAAGTTATACAGAATG
1 CGCCACAAAGGTTATACAGAATG
54556933 C
1 C
54556934 TACAAAAGCA
Statistics
Matches: 70, Mismatches: 18, Indels: 5
0.75 0.19 0.05
Matches are distributed among these distances:
20 3 0.04
21 12 0.17
22 5 0.07
23 50 0.71
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.17
Consensus pattern (23 bp):
CGCCACAAAGGTTATACAGAATG
Found at i:54556940 original size:21 final size:21
Alignment explanation
Indices: 54556864--54556941 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 21
54556854 ACACAAAATG
* *
54556864 TGCCACAAAGGCTATACAGAA
1 TGCCACAAAAGTTATACAGAA
*
54556885 TGCGC-CATAAAGGTTATACAGAG
1 TGC-CACA-AAA-GTTATACAGAA
54556908 TGCACCACAAAAGTTATACAGAA
1 TG--CCACAAAAGTTATACAGAA
*
54556931 TGCTACAAAAG
1 TGCCACAAAAG
54556942 CACCCCAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 13 0.28
22 3 0.07
23 23 0.50
24 4 0.09
25 3 0.07
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (21 bp):
TGCCACAAAAGTTATACAGAA
Found at i:54558234 original size:21 final size:19
Alignment explanation
Indices: 54558206--54558248 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
54558196 GAATAGGAGG
*
54558206 TCTTCTAACCTTATCTTCAC
1 TCTTCTAAACTTATCTTC-C
*
54558226 TCTTACTAAAGTTATCTTCC
1 TCTT-CTAAACTTATCTTCC
54558246 TCT
1 TCT
54558249 CCTCCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.21, C:0.30, G:0.02, T:0.47
Consensus pattern (19 bp):
TCTTCTAAACTTATCTTCC
Found at i:54567699 original size:25 final size:25
Alignment explanation
Indices: 54567671--54567728 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
54567661 CACATAAATG
*
54567671 GGAAGCTCTTCTGAGCCATATAACA
1 GGAAGCTCTTCCGAGCCATATAACA
*
54567696 GGAAGCTCTTCCGAGCCATATAACG
1 GGAAGCTCTTCCGAGCCATATAACA
54567721 GGAAGCTC
1 GGAAGCTC
54567729 ATGAGAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (25 bp):
GGAAGCTCTTCCGAGCCATATAACA
Found at i:54567736 original size:25 final size:25
Alignment explanation
Indices: 54567683--54567813 Score: 110
Period size: 25 Copynumber: 5.3 Consensus size: 25
54567673 AAGCTCTTCT
* **
54567683 GAGCCATATAACAGGAAGCTCTTCC
1 GAGCCATATAACAGGAAGCTCATGA
*
54567708 GAGCCATATAACGGGAAGCTCATGA
1 GAGCCATATAACAGGAAGCTCATGA
* *
54567733 GAG-C-TATAATCTGGAAGCTCATGC
1 GAGCCATATAA-CAGGAAGCTCATGA
**
54567757 GAGCCA-ATATTAGGAAGCTC-TGGA
1 GAGCCATATAACAGGAAGCTCAT-GA
* *
54567781 GAGCCATA-AATTAGGAAGCTCATAA
1 GAGCCATATAA-CAGGAAGCTCATGA
54567806 GAGCCATA
1 GAGCCATA
54567814 AACGAGACTT
Statistics
Matches: 87, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
23 6 0.07
24 32 0.37
25 48 0.55
26 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATGA
Found at i:54567760 original size:49 final size:50
Alignment explanation
Indices: 54567650--54567817 Score: 127
Period size: 49 Copynumber: 3.4 Consensus size: 50
54567640 ATTTGGGTAT
* * *** *
54567650 GCTCATACAAGCACATA-AATGGGAAGCTCTTCTGAGCCATATAA-CAGGAA
1 GCTCATACGAGC-CATATAACGGGAAGCTCTGGAGAGCCATA-AATTAGGAA
* * *
54567700 GCTCTTCCGAGCCATATAACGGGAAGCTCAT-GAGAGCTAT-AATCT-GGAA
1 GCTCATACGAGCCATATAACGGGAAGCTC-TGGAGAGCCATAAAT-TAGGAA
* *
54567749 GCTCATGCGAGCCAATATTA--GGAAGCTCTGGAGAGCCATAAATTAGGAA
1 GCTCATACGAGCC-ATATAACGGGAAGCTCTGGAGAGCCATAAATTAGGAA
*
54567798 GCTCATAAGAGCCATA-AACG
1 GCTCATACGAGCCATATAACG
54567818 AGACTTAATA
Statistics
Matches: 93, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
47 2 0.02
48 22 0.24
49 37 0.40
50 31 0.33
51 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.20
Consensus pattern (50 bp):
GCTCATACGAGCCATATAACGGGAAGCTCTGGAGAGCCATAAATTAGGAA
Found at i:54567814 original size:25 final size:25
Alignment explanation
Indices: 54567721--54567815 Score: 108
Period size: 24 Copynumber: 3.9 Consensus size: 25
54567711 CCATATAACG
*
54567721 GGAAGCTCATGAGAGCTAT-AATCT-
1 GGAAGCTCATGAGAGCCATAAAT-TA
* *
54567745 GGAAGCTCATGCGAGCCA-ATATTA
1 GGAAGCTCATGAGAGCCATAAATTA
54567769 GGAAGCTC-TGGAGAGCCATAAATTA
1 GGAAGCTCAT-GAGAGCCATAAATTA
*
54567794 GGAAGCTCATAAGAGCCATAAA
1 GGAAGCTCATGAGAGCCATAAA
54567816 CGAGACTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
23 2 0.03
24 33 0.55
25 24 0.40
26 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (25 bp):
GGAAGCTCATGAGAGCCATAAATTA
Found at i:54569148 original size:20 final size:20
Alignment explanation
Indices: 54569123--54569166 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
54569113 ATCTTGTTTT
*
54569123 ATTTGATTCCAATCAATTTG
1 ATTTGATTCCAATCAAATTG
**
54569143 ATTTGATTTTAATCAAATTG
1 ATTTGATTCCAATCAAATTG
54569163 ATTT
1 ATTT
54569167 AATGGATCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
ATTTGATTCCAATCAAATTG
Found at i:54573594 original size:20 final size:20
Alignment explanation
Indices: 54573569--54573612 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
54573559 ATCTTGTTTT
*
54573569 ATTTGATTCTAATCCAATTG
1 ATTTGATTCTAATCAAATTG
*
54573589 ATTTGATTTTAATCAAATTG
1 ATTTGATTCTAATCAAATTG
54573609 ATTT
1 ATTT
54573613 AATGGCAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
ATTTGATTCTAATCAAATTG
Found at i:54574065 original size:19 final size:18
Alignment explanation
Indices: 54574021--54574070 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
54574011 AATTTATTCA
*
54574021 ATTTATATTTTATTTTAT
1 ATTTATATTTTTTTTTAT
**
54574039 ATAAATATTTTTTATTTAT
1 ATTTATATTTTTT-TTTAT
54574058 ATTTATATATTTT
1 ATTTATAT-TTTT
54574071 GTCCGCTAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 10 0.40
19 11 0.44
20 4 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTATATTTTTTTTTAT
Found at i:54574069 original size:21 final size:20
Alignment explanation
Indices: 54574028--54574070 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
54574018 TCAATTTATA
54574028 TTTTATTTTATATAAATATT
1 TTTTATTTTATATAAATATT
* *
54574048 TTTTATTTATATTTATATATT
1 TTTTATTT-TATATAAATATT
54574069 TT
1 TT
54574071 GTCCGCTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATTTTATATAAATATT
Found at i:54582443 original size:25 final size:25
Alignment explanation
Indices: 54582415--54582462 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
54582405 GCAATTAAGG
* *
54582415 TGTCTGAACTAAGTCCAATTTAATT
1 TGTCTAAACTAAGACCAATTTAATT
54582440 TGTCTAAACTAAGACCAATTTAA
1 TGTCTAAACTAAGACCAATTTAA
54582463 ATCACATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (25 bp):
TGTCTAAACTAAGACCAATTTAATT
Found at i:54583679 original size:20 final size:21
Alignment explanation
Indices: 54583646--54583695 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
54583636 CCACTTTTAT
54583646 TTTCTTTTTCTTTTTCAATCC
1 TTTCTTTTTCTTTTTCAATCC
54583667 TTTCTTTTT-TTTTTCAATCC
1 TTTCTTTTTCTTTTTCAATCC
*
54583687 TTTCCTTTT
1 TTTCTTTTT
54583696 GATTTTCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTTTTTCTTTTTCAATCC
Found at i:54583701 original size:21 final size:20
Alignment explanation
Indices: 54583657--54583702 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
54583647 TTCTTTTTCT
**
54583657 TTTTCAATCCTTTCTTTTTT
1 TTTTCAATCCTTTCTTTTGA
54583677 TTTTCAATCCTTTCCTTTTGA
1 TTTTCAATCCTTT-CTTTTGA
54583698 TTTTC
1 TTTTC
54583703 TCTCAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTCAATCCTTTCTTTTGA
Found at i:54585474 original size:17 final size:17
Alignment explanation
Indices: 54585452--54585485 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54585442 ATCCACTAAT
*
54585452 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
54585469 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
54585486 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:54590113 original size:17 final size:17
Alignment explanation
Indices: 54590091--54590124 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54590081 ATCCACTAAT
*
54590091 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
54590108 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
54590125 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:54590909 original size:14 final size:14
Alignment explanation
Indices: 54590890--54590916 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54590880 TTAGACTTTA
54590890 CAATTTTTTTAATT
1 CAATTTTTTTAATT
54590904 CAATTTTTTTAAT
1 CAATTTTTTTAAT
54590917 CTATCCTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
CAATTTTTTTAATT
Found at i:54592128 original size:25 final size:25
Alignment explanation
Indices: 54592092--54592153 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
54592082 TCTAGACGAT
54592092 AGACACAA-TTAAGGTGTCTGAACTA
1 AGAC-CAATTTAAGGTGTCTGAACTA
** *
54592117 AGACCAATTTAATTTGTCTTAACTA
1 AGACCAATTTAAGGTGTCTGAACTA
54592142 AGACCAATTTAA
1 AGACCAATTTAA
54592154 ATCACATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 3 0.09
25 30 0.91
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (25 bp):
AGACCAATTTAAGGTGTCTGAACTA
Found at i:54597222 original size:24 final size:24
Alignment explanation
Indices: 54597172--54597223 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54597162 TTTCTAGAAA
* * *
54597172 ATTTAGCATTTATTAGTATCATAT
1 ATTTAGCACTTATTAGCATAATAT
*
54597196 ATTTAGCACTTATTAGCATAATTT
1 ATTTAGCACTTATTAGCATAATAT
54597220 ATTT
1 ATTT
54597224 GACTTACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCACTTATTAGCATAATAT
Found at i:54598351 original size:21 final size:21
Alignment explanation
Indices: 54598318--54598370 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
54598308 AGACTACTAC
* *
54598318 TTTTCCTTGTTGTT-TTTTACT
1 TTTTACTTTTTGTTATTTT-CT
54598339 TTTTACTTTTTGTTATTTTCT
1 TTTTACTTTTTGTTATTTTCT
*
54598360 TTCTACTTTTT
1 TTTTACTTTTT
54598371 CACTATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.08, C:0.13, G:0.06, T:0.74
Consensus pattern (21 bp):
TTTTACTTTTTGTTATTTTCT
Found at i:54603579 original size:3 final size:3
Alignment explanation
Indices: 54603571--54603610 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
54603561 AATCTAATAC
* *
54603571 TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TGT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54603611 CACTCATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54614201 original size:24 final size:25
Alignment explanation
Indices: 54614138--54614189 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
54614128 GCTATTAATG
* *
54614138 GGAAGCTCATGAGAGCTATATATCA
1 GGAAACTCATGAGAGCCATATATCA
*
54614163 GGAAACTCAAGAGAGCCA-ATATCA
1 GGAAACTCATGAGAGCCATATATCA
54614187 GGA
1 GGA
54614190 TGCTTATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (25 bp):
GGAAACTCATGAGAGCCATATATCA
Found at i:54614553 original size:5 final size:5
Alignment explanation
Indices: 54614543--54614567 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54614533 ATCATTTTAT
54614543 ATTCA ATTCA ATTCA ATTCA ATTCA
1 ATTCA ATTCA ATTCA ATTCA ATTCA
54614568 CATCTTTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCA
Found at i:54620338 original size:12 final size:12
Alignment explanation
Indices: 54620321--54620354 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54620311 TTCATCACAC
54620321 GGCCGTGTGGTA
1 GGCCGTGTGGTA
*
54620333 GGCCGTATGGTA
1 GGCCGTGTGGTA
*
54620345 GACCGTGTGG
1 GGCCGTGTGG
54620355 CTGGTCGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.18, G:0.47, T:0.24
Consensus pattern (12 bp):
GGCCGTGTGGTA
Found at i:54620439 original size:50 final size:50
Alignment explanation
Indices: 54620362--54620456 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
54620352 TGGCTGGTCG
54620362 TGTGGGGCCACATGGGTATGTGAGATTACACGGGTAAATCAGGTAAACCA
1 TGTGGGGCCACATGGGTATGTGAGATTACACGGGTAAATCAGGTAAACCA
** * *
54620412 TGTGGGGGGACAT-GGTCATGTGCGATTACACGGGTAATTCAGGTA
1 TGTGGGGCCACATGGGT-ATGTGAGATTACACGGGTAAATCAGGTA
54620457 GGCCATATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 3 0.08
50 37 0.93
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (50 bp):
TGTGGGGCCACATGGGTATGTGAGATTACACGGGTAAATCAGGTAAACCA
Found at i:54635141 original size:25 final size:25
Alignment explanation
Indices: 54635079--54635141 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
54635069 ATTTTAATAA
**
54635079 CTTGTGTGAGCATTCTGATTCACAG
1 CTTGTGTGAGCATTCCAATTCACAG
* *
54635104 CTCGCGTGAGCATTCCAATTCACAG
1 CTTGTGTGAGCATTCCAATTCACAG
*
54635129 CTTGTGTGGGCAT
1 CTTGTGTGAGCAT
54635142 ACATGTACAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (25 bp):
CTTGTGTGAGCATTCCAATTCACAG
Found at i:54636298 original size:15 final size:16
Alignment explanation
Indices: 54636278--54636307 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54636268 TGGTGCCTTA
54636278 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
54636293 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
54636308 AGTATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:54637247 original size:67 final size:67
Alignment explanation
Indices: 54637155--54637290 Score: 211
Period size: 67 Copynumber: 2.0 Consensus size: 67
54637145 CACGGCCATG
**
54637155 TGTCCCTTGTAAATTTTTATAGGTTACATTTCGAGTGTTACA-AGGCCTGGCACACGGGCATGTG
1 TGTCCCTTGTAAATTTTTATAGGTTACATTTCGAAAGTTACACA-GCCTGGCACACGGGCATGTG
54637219 GCT
65 GCT
* * *
54637222 TGTCCCTTGTAAGTTTTTATAGGTTACATTTTGAAAGTTACACAGCCTGGCACACGGGCGTGTGG
1 TGTCCCTTGTAAATTTTTATAGGTTACATTTCGAAAGTTACACAGCCTGGCACACGGGCATGTGG
54637287 CT
66 CT
54637289 TG
1 TG
54637291 CTGTGTGAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 62 0.98
68 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (67 bp):
TGTCCCTTGTAAATTTTTATAGGTTACATTTCGAAAGTTACACAGCCTGGCACACGGGCATGTGG
CT
Found at i:54642117 original size:23 final size:23
Alignment explanation
Indices: 54642063--54642132 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 23
54642053 ACTAATCTTC
* *
54642063 ATTTAATTAGTACAAATATATATT
1 ATTTAATTA-TAAAAAAATATATT
*
54642087 -TTGAAATTATAAAAAAATATATT
1 ATT-TAATTATAAAAAAATATATT
* *
54642110 ATTTAATTAATTAAAAATTATAT
1 ATTTAATT-ATAAAAAAATATAT
54642133 AAAATCGTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (23 bp):
ATTTAATTATAAAAAAATATATT
Found at i:54644930 original size:19 final size:19
Alignment explanation
Indices: 54644877--54644948 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
54644867 TTTTTTTCAT
* *
54644877 TTTATTTAATATTTTTATAAT
1 TTTA-TTAAT-TTTTTAAAAA
* *
54644898 TTTAATAATGTTTTAAAAA
1 TTTATTAATTTTTTAAAAA
54644917 TTTATTAATTTTTTTCAAAAA
1 TTTATTAA-TTTTTT-AAAAA
*
54644938 ATTA-TAATTTT
1 TTTATTAATTTT
54644949 AGATAAATCT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 18 0.43
20 12 0.29
21 12 0.29
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (19 bp):
TTTATTAATTTTTTAAAAA
Found at i:54644931 original size:20 final size:20
Alignment explanation
Indices: 54644877--54644948 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
54644867 TTTTTTTCAT
* * *
54644877 TTTATTTAATATTTTTATAAT
1 TTTA-TTAATTTTTTTAAAAA
* *
54644898 TTTAATAA-TGTTTTAAAAA
1 TTTATTAATTTTTTTAAAAA
54644917 TTTATTAATTTTTTTCAAAAA
1 TTTATTAATTTTTTT-AAAAA
*
54644938 ATTA-TAATTTT
1 TTTATTAATTTT
54644949 AGATAAATCT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 14 0.34
20 15 0.37
21 12 0.29
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
TTTATTAATTTTTTTAAAAA
Found at i:54648187 original size:20 final size:19
Alignment explanation
Indices: 54648150--54648200 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
54648140 AAGAAAAAAA
*
54648150 ATAAAAATTTATAGAAAATC
1 ATAAAAA-TTATAAAAAATC
*
54648170 ATAAAAATTATACAAAAATT
1 ATAAAAATTATA-AAAAATC
54648190 ATTAAAAATTA
1 A-TAAAAATTA
54648201 CAATATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 13 0.48
21 9 0.33
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAATTATAAAAAATC
Found at i:54648836 original size:25 final size:24
Alignment explanation
Indices: 54648789--54648836 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
54648779 TAAAAAGATA
54648789 GAAAATTACAAAAATCATATAAAT
1 GAAAATTACAAAAATCATATAAAT
* *
54648813 GAAAATTTATAAAAATCATTTAAA
1 GAAAA-TTACAAAAATCATATAAA
54648837 AAGTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.29
Consensus pattern (24 bp):
GAAAATTACAAAAATCATATAAAT
Found at i:54648880 original size:22 final size:22
Alignment explanation
Indices: 54648853--54648900 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
54648843 AAATAAAAAT
*
54648853 AAAAATAAT-ATAATTATGAAGA
1 AAAAATAATAAAAATTATGAA-A
*
54648875 AAAAATTATAAAAATTATGAAA
1 AAAAATAATAAAAATTATGAAA
54648897 AAAA
1 AAAA
54648901 TTAAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (22 bp):
AAAAATAATAAAAATTATGAAA
Found at i:54648905 original size:19 final size:20
Alignment explanation
Indices: 54648873--54648910 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
54648863 TAATTATGAA
*
54648873 GAAAAAATTATAAAAATTAT
1 GAAAAAAATATAAAAATTAT
*
54648893 GAAAAAAAT-TAAATATTA
1 GAAAAAAATATAAAAATTA
54648911 AAAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
GAAAAAAATATAAAAATTAT
Found at i:54649595 original size:18 final size:19
Alignment explanation
Indices: 54649574--54649614 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
54649564 ATTTTTTCAT
*
54649574 TTTTCTATATTT-TTATTA
1 TTTTCTATATTTCTAATTA
54649592 TTTTCTATATTTCTAATTA
1 TTTTCTATATTTCTAATTA
54649611 TTTT
1 TTTT
54649615 AAATGTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCTATATTTCTAATTA
Found at i:54651474 original size:23 final size:23
Alignment explanation
Indices: 54651438--54651499 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
54651428 TGTTGGGTCG
*
54651438 TGTAGA-CCTATTTTGGTCTAAT
1 TGTAGAGCCCATTTTGGTCTAAT
* *
54651460 TGTAGTGCCCATTTTGGTCTGAT
1 TGTAGAGCCCATTTTGGTCTAAT
54651483 TGTAGAGCCCATTTTGG
1 TGTAGAGCCCATTTTGG
54651500 GCTGGGAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 5 0.14
23 30 0.86
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (23 bp):
TGTAGAGCCCATTTTGGTCTAAT
Found at i:54654029 original size:243 final size:243
Alignment explanation
Indices: 54653566--54654036 Score: 782
Period size: 242 Copynumber: 1.9 Consensus size: 243
54653556 TACACGATGT
* * * *
54653566 TGGTCACACGAGCTATGGAGAATCCTCAACAAATGTAGGACTTCAGCCATCGGTAGGAAATTCAA
1 TGGTCACACGAGCTATGGAGAATCCTCAAAAAATGTAGGACCTCAGCCATCGATAGCAAATTCAA
* *
54653631 GACCAGCACCTGAAACATGAAATCCCTAATGACATGTCATTTGTATCTTAAGAATTCTTAAGGTT
66 GACCAGCACCCGAAACATGAAATCCCTAATGACATGTCATTTGTATCCTAAGAATTCTTAAGGTT
* *
54653696 CAACCGGGACTTGATATCTGTCAATTCATCACAATGTGGATACATTTTCATATATATGATTCATT
131 CAACCGGGACTTGATATCCGTCAATTCATCACAATGTGGATACATTCTCATATATATGATTCATT
54653761 TACATTAAAAACAACATAGTAAACATTTAATTTGGTAAGTTCGTATGC
196 TACATTAAAAACAACATAGTAAACATTTAATTTGGTAAGTTCGTATGC
* * *
54653809 TGGTCATACGAGCTGTGGAGAATCCTCAAAAAATGTAGGACCTCAGCCATC-ATAGCACATTCAA
1 TGGTCACACGAGCTATGGAGAATCCTCAAAAAATGTAGGACCTCAGCCATCGATAGCAAATTCAA
*
54653873 GACCAGCACCCGAAACATGAAATCCTTAATGACATGTCATTTGTATCCTAAGAATTCTTAAGGTT
66 GACCAGCACCCGAAACATGAAATCCCTAATGACATGTCATTTGTATCCTAAGAATTCTTAAGGTT
* *
54653938 CAACCGGGACTTGATATCCGTCGATTCGTCACAATGTGGATACATTCTCATATATATTGATTCAT
131 CAACCGGGACTTGATATCCGTCAATTCATCACAATGTGGATACATTCTCATATATA-TGATTCAT
**
54654003 TTACATTAAAAACAATGTAGTAAACATTTAATTT
195 TTACATTAAAAACAACATAGTAAACATTTAATTT
54654037 AAATAATATT
Statistics
Matches: 211, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
242 124 0.59
243 87 0.41
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (243 bp):
TGGTCACACGAGCTATGGAGAATCCTCAAAAAATGTAGGACCTCAGCCATCGATAGCAAATTCAA
GACCAGCACCCGAAACATGAAATCCCTAATGACATGTCATTTGTATCCTAAGAATTCTTAAGGTT
CAACCGGGACTTGATATCCGTCAATTCATCACAATGTGGATACATTCTCATATATATGATTCATT
TACATTAAAAACAACATAGTAAACATTTAATTTGGTAAGTTCGTATGC
Found at i:54656176 original size:45 final size:44
Alignment explanation
Indices: 54656123--54656221 Score: 146
Period size: 44 Copynumber: 2.2 Consensus size: 44
54656113 TTTGGTTCGC
54656123 TGTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAA
* *
54656168 TGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAA
*
54656212 TGGAATGGAA
1 TGTAATGGAA
54656222 GTGTAATAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
43 1 0.02
44 25 0.50
45 24 0.48
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAA
Found at i:54656496 original size:120 final size:120
Alignment explanation
Indices: 54656359--54656796 Score: 759
Period size: 120 Copynumber: 3.6 Consensus size: 120
54656349 ATATTTTAAC
*
54656359 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTGATAAAATTCTTAGTATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
* *
54656424 TCTTATATGAATTTACTAAAATCATAATATATGACACTATAAAATGTAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
54656479 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
54656544 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * *
54656599 ATAATAATTATTAAATATATTTTAATTAAAATTTATAATTTAATAAAACTCTTAGTATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
* *
54656664 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * **
54656719 ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAACATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
*
54656784 TCTTATATAAATT
66 TCTTATATGAATT
54656797 CTTAACATTA
Statistics
Matches: 302, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 302 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:54656514 original size:18 final size:17
Alignment explanation
Indices: 54656493--54656527 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54656483 TTATTATTAA
*
54656493 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54656511 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54656528 TCTTAGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54656515 original size:61 final size:59
Alignment explanation
Indices: 54656359--54656755 Score: 144
Period size: 59 Copynumber: 6.6 Consensus size: 59
54656349 ATATTTTAAC
** * * *
54656359 ATAATTATTATTAAATATATTTTAATTAAAATATATA--ATTTGATAAAATT-CTTAGTA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATATGAACT-ATAAAATTAATTTGAA
* * * * * *
54656416 TTAAATATTCTT--ATATGAATTTACTAAAATCATAATATATGACACTATAAAATGTAATTTGAA
1 ATAATTATTATTAAATAT-ATTTTAATTAAA--AT-ATATATGA-ACTATAAAAT-TAATTTGAA
** * * *
54656479 ATAATTATTATTAAATATATTTTAATTAAAATATATA--ATTTAATAAAATT-CTTAGTA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATATGAACT-ATAAAATTAATTTGAA
* * * * * *
54656536 TTAAATATTCTT--ATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
1 ATAATTATTATTAAATAT-ATTTTAATTAAA--AT-ATATATGA-ACTATAAAAT-TAATTTGAA
* * *
54656599 ATAATAATTATTAAATATATTTTAATTAAAAT-T-TAT-AATTTAATAAAACTCTTAGTATT-AA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATATGAA-CT-ATAAAA---TTAAT-TTGAA
* * * * ** * * *
54656660 AT-ATTCTTATATGAATTTACTAAAATCATAATATATA--ATACTATAAAATATAATTTAAA
1 ATAATTATTAT-TAAATATATTTTAATTAAAATATATATGA-ACTATAAAAT-TAATTTGAA
* *
54656719 ATAATTATTATTAAATATAATTTAATAAAAATATATA
1 ATAATTATTATTAAATATATTTTAATTAAAATATATA
54656756 ATTTAATAAA
Statistics
Matches: 243, Mismatches: 61, Indels: 70
0.65 0.16 0.19
Matches are distributed among these distances:
55 8 0.03
56 18 0.07
57 23 0.09
58 11 0.05
59 53 0.22
60 14 0.06
61 48 0.20
62 14 0.06
63 28 0.12
64 18 0.07
65 8 0.03
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (59 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATATGAACTATAAAATTAATTTGAA
Found at i:54656787 original size:16 final size:15
Alignment explanation
Indices: 54656762--54656808 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
54656752 TATAATTTAA
54656762 TAAAATTCTTAACAT
1 TAAAATTCTTAACAT
*
54656777 TAAATATTCTT-ATA-
1 TAAA-ATTCTTAACAT
54656791 T-AAATTCTTAACAT
1 TAAAATTCTTAACAT
54656805 TAAA
1 TAAA
54656809 TATAATTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 2 0.08
15 8 0.31
16 6 0.23
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATTCTTAACAT
Found at i:54656808 original size:14 final size:14
Alignment explanation
Indices: 54656764--54656809 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 14
54656754 TAATTTAATA
54656764 AAATTCTTAACATT
1 AAATTCTTAACATT
*
54656778 AAATATTCTT-ATA-T
1 -AA-ATTCTTAACATT
54656792 AAATTCTTAACATT
1 AAATTCTTAACATT
54656806 AAAT
1 AAAT
54656810 ATAATTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 6 0.23
15 4 0.15
16 6 0.23
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTCTTAACATT
Found at i:54668429 original size:26 final size:25
Alignment explanation
Indices: 54668400--54668767 Score: 205
Period size: 26 Copynumber: 14.2 Consensus size: 25
54668390 AAACGAAACA
* *
54668400 AAATAATATATAGAACAATTTGAAGT
1 AAATAATATATA-AACAATTTAAAAT
* *
54668426 AAATAGTATA-AAACAATTTAAAGT
1 AAATAATATATAAACAATTTAAAAT
* * *
54668450 AAATAATGTGTAAAACAAATTAAAAT
1 AAATAATATAT-AAACAATTTAAAAT
* *
54668476 AAATAATATACAAAGAAATTTAAAAT
1 AAATAATATATAAA-CAATTTAAAAT
*
54668502 AAATAACATATAAGACAATTTAAAAT
1 AAATAATATATAA-ACAATTTAAAAT
*
54668528 -AAT-ATATA-AAA-AGTTTAAAAT
1 AAATAATATATAAACAATTTAAAAT
* *
54668549 AAATAATATACAAAACAATTAAAAAAAT
1 AAATAATATA-TAAACAATT--TAAAAT
*
54668577 AAATGATATATATAAAAAACAATTCAAAAT
1 AAAT-A-ATATAT--A-AACAATTTAAAAT
* ** *
54668607 AAAGAATATATGTGACAGTTTAAAAAT
1 AAATAATATAT-AAACAATTT-AAAAT
*
54668634 AAATAATATATAAAAAATTTAAAAT
1 AAATAATATATAAACAATTTAAAAT
** * * *
54668659 GGATAATAGTTTGAAATAGTTTAAAAT
1 AAATAATA-TAT-AAACAATTTAAAAT
* ** * * *
54668686 ACATTGTATGTGGAA-AACTTAAAAT
1 AAATAATATAT-AAACAATTTAAAAT
54668711 AAAT-A-ATA-AAACAATTTAAAAT
1 AAATAATATATAAACAATTTAAAAT
*
54668733 AAATAATATATGAGAAAAATGTTTAAAAT
1 AAATAATATAT-A-AACAA--TTTAAAAT
54668762 AAATAA
1 AAATAA
54668768 ATAAATAACA
Statistics
Matches: 264, Mismatches: 51, Indels: 51
0.72 0.14 0.14
Matches are distributed among these distances:
21 11 0.04
22 17 0.06
23 10 0.04
24 26 0.10
25 32 0.12
26 80 0.30
27 36 0.14
28 15 0.06
29 16 0.06
30 13 0.05
31 1 0.00
32 7 0.03
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (25 bp):
AAATAATATATAAACAATTTAAAAT
Found at i:54668527 original size:22 final size:21
Alignment explanation
Indices: 54668502--54668550 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
54668492 AATTTAAAAT
54668502 AAATAACATATAAGACAA-TTTA
1 AAATAACATATAA-A-AAGTTTA
*
54668524 AAATAATATATAAAAAGTTTA
1 AAATAACATATAAAAAGTTTA
54668545 AAATAA
1 AAATAA
54668551 ATAATATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 11 0.44
22 12 0.48
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (21 bp):
AAATAACATATAAAAAGTTTA
Found at i:54668551 original size:47 final size:47
Alignment explanation
Indices: 54668476--54668577 Score: 134
Period size: 47 Copynumber: 2.2 Consensus size: 47
54668466 AAATTAAAAT
* *
54668476 AAATAATATACAAAGAAATTTAAAATAAATAACATATAAGACAATTTA
1 AAATAATATACAAAGAAATTTAAAATAAATAACATACAAAACAA-TTA
* * *
54668524 AAATAATATATAAA-AAGTTTAAAATAAATAATATACAAAACAATTA
1 AAATAATATACAAAGAAATTTAAAATAAATAACATACAAAACAATTA
*
54668570 AAAAAATA
1 AAATAATA
54668578 AATGATATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 10 0.21
47 25 0.52
48 13 0.27
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (47 bp):
AAATAATATACAAAGAAATTTAAAATAAATAACATACAAAACAATTA
Found at i:54668606 original size:30 final size:29
Alignment explanation
Indices: 54668554--54668617 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 29
54668544 AAAATAAATA
*
54668554 ATATACAAAACAATTAAAAAAATAAATGATAT
1 ATATAAAAAACAATT-AAAAAATAAA-GA-AT
*
54668586 ATATAAAAAACAATT-CAAAATAAAGAAT
1 ATATAAAAAACAATTAAAAAATAAAGAAT
54668614 ATAT
1 ATAT
54668618 GTGACAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 6 0.20
29 2 0.07
30 8 0.27
32 14 0.47
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (29 bp):
ATATAAAAAACAATTAAAAAATAAAGAAT
Found at i:54668740 original size:29 final size:30
Alignment explanation
Indices: 54668707--54668775 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
54668697 GGAAAACTTA
*
54668707 AAATAAATAATAAAACA-ATTTAAAATAAAT
1 AAATAAATAAGAAAA-ATATTTAAAATAAAT
* * *
54668737 -AATATATGAGAAAAATGTTTAAAATAAAT
1 AAATAAATAAGAAAAATATTTAAAATAAAT
54668766 AAATAAATAA
1 AAATAAATAA
54668776 CAAATTTGCG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
28 1 0.03
29 23 0.74
30 7 0.23
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (30 bp):
AAATAAATAAGAAAAATATTTAAAATAAAT
Found at i:54670300 original size:50 final size:50
Alignment explanation
Indices: 54670179--54670273 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
54670169 ATTAAATACA
* * * *
54670179 AAATTTAAACAAATAAT-ATAAACAAATATTTATATTTATGTAAAAACACC
1 AAATCTAAACAAAAAATAAT-AATAAATACTTATATTTATGTAAAAACACC
*
54670229 AAATCTAAACAAAAAATAATAATAAATACTTATATTTATTTAAAA
1 AAATCTAAACAAAAAATAATAATAAATACTTATATTTATGTAAAA
54670274 CATCAGATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 37 0.95
51 2 0.05
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (50 bp):
AAATCTAAACAAAAAATAATAATAAATACTTATATTTATGTAAAAACACC
Found at i:54671714 original size:24 final size:24
Alignment explanation
Indices: 54671687--54671763 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
54671677 AACTATTTTG
*
54671687 AAATAAAGTTTTGATTTTTAAGAA
1 AAATAAAGTTTTGATTTTTAAAAA
** *
54671711 AAATAGTGATTTT-TTTTTTAAAAA
1 AAATAAAG-TTTTGATTTTTAAAAA
* *
54671735 AAGAGAAAGTTTAGATTTTTAAAATA
1 AA-ATAAAGTTTTGATTTTTAAAA-A
54671761 AAA
1 AAA
54671764 ATTTGTTTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
24 20 0.50
25 17 0.43
26 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (24 bp):
AAATAAAGTTTTGATTTTTAAAAA
Found at i:54671833 original size:152 final size:149
Alignment explanation
Indices: 54671575--54671864 Score: 422
Period size: 152 Copynumber: 1.9 Consensus size: 149
54671565 AAGTTTTGAA
*
54671575 TTTTTTAAAAAAAAATAAAGTTTAGATTTTTAAAATAAATTTTTTTCGTAGTCATATTAAAAGAA
1 TTTTTTAAAAAAAAAGAAAGTTTAGATTTTTAAAATAAATTTTTTTCGTAGTCATATTAAAAGAA
*
54671640 AAGTTTAAATTCTTAAAATAAAATTTTGATCTTTTTTAACTATTTTGAAATAAAGTTTTGATTTT
66 AAGTTTAAATTCTTAAAATAAAATTTTGATCTTTTTTAACTATTTTGAAATAAAGTTTTAATTTT
54671705 TAAGAAAAATAGTGATTTT
131 TAAGAAAAATAGTGATTTT
* ** * *
54671724 TTTTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAATAAAAATTTGTTTTTTTAGTCATTTTAAAG
1 TTTTTTAAAAAAAAAGAAAGTTTAGATTTTTAAAAT--AAATTT-TTTTCGTAGTCATATTAAAA
* ** *
54671789 GAAAAGTTTAAATTTTTTTCAA-AAAGTTTTGAT-TTTTTTCAACTATTTTGAAATAAAGTTTTA
63 GAAAAGTTTAAA-TTCTTAAAATAAAATTTTGATCTTTTTT-AACTATTTTGAAATAAAGTTTTA
54671852 ATTTTTAAGAAAA
126 ATTTTTAAGAAAA
54671865 GTAATGACTT
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
149 34 0.27
151 12 0.10
152 73 0.58
153 6 0.05
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.46
Consensus pattern (149 bp):
TTTTTTAAAAAAAAAGAAAGTTTAGATTTTTAAAATAAATTTTTTTCGTAGTCATATTAAAAGAA
AAGTTTAAATTCTTAAAATAAAATTTTGATCTTTTTTAACTATTTTGAAATAAAGTTTTAATTTT
TAAGAAAAATAGTGATTTT
Found at i:54671839 original size:19 final size:20
Alignment explanation
Indices: 54671790--54671830 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54671780 ATTTTAAAGG
**
54671790 AAAAGTTTAAATTTTTTTCA
1 AAAAGTTTTGATTTTTTTCA
54671810 AAAAGTTTTGATTTTTTTCA
1 AAAAGTTTTGATTTTTTTCA
54671830 A
1 A
54671831 CTATTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (20 bp):
AAAAGTTTTGATTTTTTTCA
Found at i:54683015 original size:143 final size:143
Alignment explanation
Indices: 54682746--54683015 Score: 326
Period size: 143 Copynumber: 1.9 Consensus size: 143
54682736 ATTTTAAGAA
* * * **
54682746 TCTTTACAGTTTGCTGATTTACAATCGCAACTGATATTATTAAAGCTTCTTGATTTACGATCATG
1 TCTTAACAGTTTGCTGATTTACAATCGCAACTGATATCATTAAAGCTTCTTGATTTACAATCACA
** ** * * **
54682811 TTTTAACTTCATTGATATATGATCATGAACAATTCATCTAAAGTTCATTGGTTTATGATCACGAC
66 ACTTAACTTCATTGATATACAATCATGAACAATTCATCTAAAGCTCATTGATTTACAATCACGAC
54682876 TCCTCTTGACTCC
131 TCCTCTTGACTCC
** * *
54682889 TCTTAACAGTTTGCTGATTTATGATCGCAACTGGTATCATTAAAGC-TCGTTGATTTACAATCGC
1 TCTTAACAGTTTGCTGATTTACAATCGCAACTGATATCATTAAAGCTTC-TTGATTTACAATCAC
* * * * *
54682953 AACTTAAGTTCATTGATTTACAATCATGAATAATTCATCTAGAGCTCGTTGATTTACAATCAC
65 AACTTAACTTCATTGATATACAATCATGAACAATTCATCTAAAGCTCATTGATTTACAATCAC
54683016 AACTTGTAAT
Statistics
Matches: 104, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
142 2 0.02
143 102 0.98
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (143 bp):
TCTTAACAGTTTGCTGATTTACAATCGCAACTGATATCATTAAAGCTTCTTGATTTACAATCACA
ACTTAACTTCATTGATATACAATCATGAACAATTCATCTAAAGCTCATTGATTTACAATCACGAC
TCCTCTTGACTCC
Found at i:54687215 original size:42 final size:43
Alignment explanation
Indices: 54687061--54687226 Score: 194
Period size: 43 Copynumber: 3.9 Consensus size: 43
54687051 GTACAGTAAT
* * *
54687061 AATGCC-ATATCCCAGATATGGTCTTACATGTAATCTCGTATC
1 AATGCCAATATCCCAGACATGGTCTTACACGTAATCTCATATC
* * * ** *
54687103 AATGCCAATAGCTCAGCCATGGTCTTACACAAAATCACATATC
1 AATGCCAATATCCCAGACATGGTCTTACACGTAATCTCATATC
* *
54687146 GATGCCAATGTCCCAGACATGGTCTTACACG-AACTCTCATATC
1 AATGCCAATATCCCAGACATGGTCTTACACGTAA-TCTCATATC
*
54687189 AATG-CAATATCCCAGATATGGTCTTACACGTAATCTCA
1 AATGCCAATATCCCAGACATGGTCTTACACGTAATCTCA
54687227 GTAACCCTAA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 37 0.36
43 65 0.64
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.28
Consensus pattern (43 bp):
AATGCCAATATCCCAGACATGGTCTTACACGTAATCTCATATC
Found at i:54692248 original size:17 final size:18
Alignment explanation
Indices: 54692221--54692256 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
54692211 ATGCAGCAAT
54692221 AGAAGAAAAACATGGAGA
1 AGAAGAAAAACATGGAGA
*
54692239 AGAA-AAAAACATTGAGA
1 AGAAGAAAAACATGGAGA
54692256 A
1 A
54692257 AATGAGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.64, C:0.06, G:0.22, T:0.08
Consensus pattern (18 bp):
AGAAGAAAAACATGGAGA
Found at i:54693944 original size:205 final size:200
Alignment explanation
Indices: 54693587--54694192 Score: 708
Period size: 205 Copynumber: 3.0 Consensus size: 200
54693577 AATTAGAAAA
* * * *
54693587 TTGAATGCCTTAATAAGGATGCATGGTATGGTG-TTTCTATCTTGTAATGCTTGAAAAATGTGTA
1 TTGAATGCCTTAATATGGATGCATGATATAGTGTTTTC-ATCTTGTAATGCTTG-AAAA-CTGTA
* * *
54693651 TAAACCAAAATGGATGAAAGTATAATTGCATCTTGTG--TTT-T-AAAATTAGTAATATTTCTGT
63 TAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTTGTCAAAATTAGCAATATTTCTGT
* * * *
54693712 CATTAACTGTTGATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTAGATGATTTTACCATAT
128 CATTAACTGCTGATTT-CATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTATACCATAT
54693777 ATAATGTAAG
192 A-AATGTAAG
* *
54693787 TTGACTGCCTTAATATGGATTCATGATATAGTGTTTTCATCTTGTAATGCTTGAAAACTGTATAA
1 TTGAATGCCTTAATATGGATGCATGATATAGTGTTTTCATCTTGTAATGCTTGAAAACTGTATAA
* * * *
54693852 ACCAGAGTGGATTG-AAGTATTATTGGATCTTGTGTTTTGTGTACCAAAATTAGCAATATATCTA
66 ACCAGAGTGGA-TGAAAGTATAATTGCATCTTGTGTTTT-TGT--CAAAATTAGCAATATTTCTG
** *
54693916 TCATTAACTGCAAAGTTTCATGTTCTGCTGCTCTCCCTTGTTTTCATTTGGATAATTATACCATA
127 TCATTAACTGCTGA-TTTCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTATACCATA
54693981 TAAGATGTAAG
191 TAA-ATGTAAG
*
54693992 TTGAATTG-CTTAATATGGATGCATGATATAGTGTTTTCATCTTATAATGCTTGAAAACTGTATA
1 TTGAA-TGCCTTAATATGGATGCATGATATAGTGTTTTCATCTTGTAATGCTTGAAAACTG--TA
*
54694056 TAAACCTGAGTGGATGAAAGTATAATTGCAT-TTGTGTTTTATGTTTCAAAACTTA-CTAATATT
63 TAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTT-TG--TCAAAA-TTAGC-AATATT
* ** * * *
54694119 TCTGTCATTGAACTGCTGATTTTATTGTTCCACTGCTCTGCCTTGATTTCTTTTGGATAATTGTA
123 TCTGTCATT-AACTGCTGATTTCA-TGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTATA
54694184 CCATATAAA
186 CCATATAAA
54694193 ATGCAAGAGA
Statistics
Matches: 347, Mismatches: 38, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
198 34 0.10
199 6 0.02
200 45 0.13
201 5 0.01
202 1 0.00
204 1 0.00
205 133 0.38
206 24 0.07
207 48 0.14
208 50 0.14
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (200 bp):
TTGAATGCCTTAATATGGATGCATGATATAGTGTTTTCATCTTGTAATGCTTGAAAACTGTATAA
ACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTTGTCAAAATTAGCAATATTTCTGTCAT
TAACTGCTGATTTCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTATACCATATAAAT
GTAAG
Found at i:54694317 original size:39 final size:40
Alignment explanation
Indices: 54694274--54694355 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 40
54694264 GAGGAAACAA
54694274 AAGAAATATATAGAGAACATC-AAAAGGAATCAACAGAGT
1 AAGAAATATATAGAGAACATCGAAAAGGAATCAACAGAGT
* *
54694313 AAGAAATATATAGAGAATATCGAAAAGGAATCAACATAGT
1 AAGAAATATATAGAGAACATCGAAAAGGAATCAACAGAGT
54694353 AAG
1 AAG
54694356 GAATCAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 20 0.50
40 20 0.50
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.17
Consensus pattern (40 bp):
AAGAAATATATAGAGAACATCGAAAAGGAATCAACAGAGT
Found at i:54696580 original size:32 final size:32
Alignment explanation
Indices: 54696541--54696633 Score: 150
Period size: 32 Copynumber: 2.9 Consensus size: 32
54696531 TTAGATATTG
* *
54696541 ATTATGTTTTAAGCTTGTTAGATATTTAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
*
54696573 ATTATGTTTTAAGCTTGTTGGTTATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
*
54696605 ATTATGTTTTAAGCTTGTTGGATACTGAA
1 ATTATGTTTTAAGCTTGTTGGATATTGAA
54696634 ATGATTGACA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.53
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTGGATATTGAATTT
Found at i:54698509 original size:18 final size:19
Alignment explanation
Indices: 54698474--54698512 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54698464 AGTTCAAAAA
54698474 TATTAAAAAAAAACATTTT
1 TATTAAAAAAAAACATTTT
* *
54698493 TATTCAAAAATAA-ATTTT
1 TATTAAAAAAAAACATTTT
54698511 TA
1 TA
54698513 AAGTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TATTAAAAAAAAACATTTT
Found at i:54698670 original size:56 final size:57
Alignment explanation
Indices: 54698527--54698680 Score: 159
Period size: 59 Copynumber: 2.7 Consensus size: 57
54698517 TTTTTTTAAC
* * **
54698527 TTTTAAAATTAGAATTAAATTGATAAGTTTTGTAAATGTTCAGAGCTAAATTTATTGAA
1 TTTTTAAATTAGAATTAAATTGATAAATTTTGTAAACATTCAGAGCTAAA--TATTGAA
* * * * *
54698586 TTTTTAGAATTAGAATTAGA-TGACAAATTTTGTAAACATTGAGGGCTAAA-ATTGAG
1 TTTTTA-AATTAGAATTAAATTGATAAATTTTGTAAACATTCAGAGCTAAATATTGAA
* * *
54698642 TTTTTAAATTAGGATCAAATTGATAAATTGTGTAAACAT
1 TTTTTAAATTAGAATTAAATTGATAAATTTTGTAAACAT
54698681 GGAATGACTA
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
55 10 0.13
56 28 0.35
59 29 0.37
60 12 0.15
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (57 bp):
TTTTTAAATTAGAATTAAATTGATAAATTTTGTAAACATTCAGAGCTAAATATTGAA
Found at i:54698942 original size:21 final size:21
Alignment explanation
Indices: 54698918--54698957 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54698908 ATTTAATTTA
*
54698918 ATAAATTAATATATAATTATG
1 ATAAATCAATATATAATTATG
*
54698939 ATAAATCAATGTATAATTA
1 ATAAATCAATATATAATTA
54698958 CAGTTTGAAT
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:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (21 bp):
ATAAATCAATATATAATTATG
Found at i:54703359 original size:22 final size:21
Alignment explanation
Indices: 54703312--54703359 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
54703302 TTTAATTTGG
* *
54703312 AATTTAATTTTAGGATTTTAG
1 AATTTAAGTTTAGGATTTTAA
* *
54703333 TATTTAAGGTTTAGGGTTTTAA
1 AATTTAA-GTTTAGGATTTTAA
54703355 AATTT
1 AATTT
54703360 TATAAGAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (21 bp):
AATTTAAGTTTAGGATTTTAA
Found at i:54703934 original size:89 final size:91
Alignment explanation
Indices: 54703773--54703992 Score: 261
Period size: 89 Copynumber: 2.4 Consensus size: 91
54703763 TTAAGGAAGC
* * * *
54703773 AAAAAGCCTTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCAGCTCTCTTTATTTGCACTCATTT
1 AAAAAGCC-TCAAACCTTTTC-AAAAAAGCAATTAAACCCCAGCTCTCTTTATTTGCACTCAATT
*
54703838 GGGTACTTAAACTTTTAAAATGCATAAAA
64 GGGTACTTAAACTTTCAAAATGCAT-AAA
* * *
54703867 AAAAAGCCTGAAACCTTTTCAAAACAAGTAATTAACCCCCA-CT-T-TTT-TTTGCACTCAATTG
1 AAAAAGCCTCAAACCTTTTCAAAA-AAGCAATTAAACCCCAGCTCTCTTTATTTGCACTCAATTG
* *
54703928 GGTACTTGAACTTTCAAAATGCATCAA
65 GGTACTTAAACTTTCAAAATGCATAAA
* *
54703955 AAAGACCCTCAAA-CTTTTCAAAAAAGCAATTAAACCCC
1 AAAAAGCCTCAAACCTTTTCAAAAAAGCAATTAAACCCC
54703993 TGCTTTTATT
Statistics
Matches: 111, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
86 13 0.12
87 10 0.09
88 12 0.11
89 35 0.32
90 3 0.03
91 1 0.01
92 6 0.05
93 23 0.21
94 8 0.07
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (91 bp):
AAAAAGCCTCAAACCTTTTCAAAAAAGCAATTAAACCCCAGCTCTCTTTATTTGCACTCAATTGG
GTACTTAAACTTTCAAAATGCATAAA
Found at i:54704077 original size:14 final size:13
Alignment explanation
Indices: 54704054--54704097 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
54704044 AAATTTTATT
54704054 AAAATTTAATAAA
1 AAAATTTAATAAA
*
54704067 AAAATTTTAATATTA
1 AAAA-TTTAATA-AA
*
54704082 AAAATTTATTAAA
1 AAAATTTAATAAA
54704095 AAA
1 AAA
54704098 TAGAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 8 0.31
14 13 0.50
15 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTTAATAAA
Found at i:54704133 original size:28 final size:27
Alignment explanation
Indices: 54704092--54704161 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
54704082 AAAATTTATT
* *
54704092 AAAAAATAGAAAAAAATATA-AGAATCGTA
1 AAAAAATA-TAAAAAATATAGA-AAT-ATA
*
54704121 AAAAAATATAAAATATATAGAAATATA
1 AAAAAATATAAAAAATATAGAAATATA
54704148 AAAAAATTATAAAA
1 AAAAAA-TATAAAA
54704162 TTTTATAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.22
28 19 0.53
29 9 0.25
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (27 bp):
AAAAAATATAAAAAATATAGAAATATA
Found at i:54704427 original size:29 final size:29
Alignment explanation
Indices: 54704369--54704431 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
54704359 GTCATTAAAT
* **
54704369 TTTTTTATGATTTTTATAAAATTTTATAA
1 TTTTTTACGATTTTTATAAAAAATTATAA
* *
54704398 TTTTTTACGTTTTTTATAAAAAATTCTAA
1 TTTTTTACGATTTTTATAAAAAATTATAA
54704427 TTTTT
1 TTTTT
54704432 AATAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTTTTACGATTTTTATAAAAAATTATAA
Found at i:54704487 original size:28 final size:27
Alignment explanation
Indices: 54704421--54704487 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
54704411 TTATAAAAAA
*
54704421 TTCTAATTTTTAATAAATTTTAATTTTT
1 TTCT-ATTTTTAATAAAATTTAATTTTT
** *
54704449 TTAAATCTTTTCATAAAATTTAATATTTT
1 TTCTAT-TTTTAATAAAATTTAAT-TTTT
54704478 TTCTATTTTT
1 TTCTATTTTT
54704488 TTTATTTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
27 2 0.06
28 21 0.68
29 8 0.26
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (27 bp):
TTCTATTTTTAATAAAATTTAATTTTT
Found at i:54704521 original size:19 final size:20
Alignment explanation
Indices: 54704483--54704522 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
54704473 ATTTTTTCTA
*
54704483 TTTTTTTTATTTTTCATAATT
1 TTTTTTTTACTTTT-ATAATT
54704504 TTTTTTTTACTTTT-TAATT
1 TTTTTTTTACTTTTATAATT
54704523 GGAGCAGCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTTTACTTTTATAATT
Found at i:54704695 original size:85 final size:84
Alignment explanation
Indices: 54704534--54704688 Score: 195
Period size: 85 Copynumber: 1.8 Consensus size: 84
54704524 GAGCAGCGGA
* * * * *
54704534 TTAATTGCTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAACTCAAGTACCCAAT
1 TTAATTGCTTTTTTGAAAAAGTTTGAGAGCCCTTTTGATGCATTTTGAAAACTCAAGTACCCAAC
54704599 TGAGTGAAAAAAAAGTTGT
66 TGAGTGAAAAAAAAGTTGT
* * * * *
54704618 TTAATTGCTTTTTTTGAAGAAGTTTGAGAGCCCTTTTGATGTATTTT-AAAAGTTCAAGTGCTCA
1 TTAATTGC-TTTTTTGAAAAAGTTTGAGAGCCCTTTTGATGCATTTTGAAAA-CTCAAGTACCCA
54704682 ACTGAGT
64 ACTGAGT
54704689 ACAAAAAGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
84 12 0.20
85 47 0.80
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (84 bp):
TTAATTGCTTTTTTGAAAAAGTTTGAGAGCCCTTTTGATGCATTTTGAAAACTCAAGTACCCAAC
TGAGTGAAAAAAAAGTTGT
Found at i:54705403 original size:19 final size:17
Alignment explanation
Indices: 54705341--54705395 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 17
54705331 TTTCATGAGT
*
54705341 TAAATAAATAATCATAAAA
1 TAAATAAAT-ATTA-AAAA
*
54705360 TAATTAATGATATTAAAAA
1 TAAATAA--ATATTAAAAA
54705379 TAAATAAATATTAAAAA
1 TAAATAAATATTAAAAA
54705396 ATGTAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 10 0.32
19 16 0.52
20 3 0.10
21 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAATAAATATTAAAAA
Done.