Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008339.1 Hibiscus syriacus cultivar Beakdansim tig00111061_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: 1048908
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:466404 original size:19 final size:20
Alignment explanation
Indices: 466373--466415 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
466363 TTTATTAAAA
* *
466373 ATAA-AAAATATTTAGAATT
1 ATAATAAAATATTTACAAGT
466392 ATAATAAAA-ATTTACAAGT
1 ATAATAAAATATTTACAAGT
466411 ATAAT
1 ATAAT
466416 TGTAAACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (20 bp):
ATAATAAAATATTTACAAGT
Found at i:466746 original size:2 final size:2
Alignment explanation
Indices: 466739--466802 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
466729 GATGACAACA
466739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
466781 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
466803 GGAAATTTGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:471689 original size:20 final size:20
Alignment explanation
Indices: 471664--471702 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
471654 ATTAAAATTA
* *
471664 AAATAATACATGATATATTT
1 AAATAATAAATAATATATTT
471684 AAATAATAAATAATATATT
1 AAATAATAAATAATATATT
471703 ATCGATGATT
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:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATAATAAATAATATATTT
Found at i:472751 original size:20 final size:20
Alignment explanation
Indices: 472718--472760 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
472708 AACGTTCAAT
* * *
472718 TTTATGTTTGTTTATGTTCG
1 TTTATATTTATTTATATTCG
472738 TTTATATTTATTTATATTCG
1 TTTATATTTATTTATATTCG
472758 TTT
1 TTT
472761 GTTTATGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.05, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTATATTTATTTATATTCG
Found at i:477123 original size:20 final size:20
Alignment explanation
Indices: 477094--477203 Score: 157
Period size: 20 Copynumber: 5.5 Consensus size: 20
477084 GAAGCCTTTG
* *
477094 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAAAAGGA
***
477114 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCACAA-AAGGA
477135 TGCATCGATGCACAAAAGGA
1 TGCATCGATGCACAAAAGGA
477155 TGCATCGATGCACAAAAGGA
1 TGCATCGATGCACAAAAGGA
*
477175 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAAAAGGA
477195 TGCATCGAT
1 TGCATCGAT
477204 CCACTAATTG
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 64 0.78
21 18 0.22
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAAAAGGA
Found at i:477155 original size:41 final size:40
Alignment explanation
Indices: 477094--477203 Score: 157
Period size: 41 Copynumber: 2.7 Consensus size: 40
477084 GAAGCCTTTG
* * ***
477094 TGCATGGATGCACAACAGGATGCATCGATGCACAACCTTGA
1 TGCATCGATGCACAAAAGGATGCATCGATGCACAA-AAGGA
477135 TGCATCGATGCACAAAAGGATGCATCGATGCACAAAAGGA
1 TGCATCGATGCACAAAAGGATGCATCGATGCACAAAAGGA
*
477175 TGCATCGATGCACAGAAGGATGCATCGAT
1 TGCATCGATGCACAAAAGGATGCATCGAT
477204 CCACTAATTG
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 30 0.48
41 33 0.52
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (40 bp):
TGCATCGATGCACAAAAGGATGCATCGATGCACAAAAGGA
Found at i:477275 original size:22 final size:23
Alignment explanation
Indices: 477242--477284 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
477232 ATGGATGCAC
477242 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
477265 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
477285 GCAGGGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:477297 original size:21 final size:21
Alignment explanation
Indices: 477228--477410 Score: 264
Period size: 21 Copynumber: 8.7 Consensus size: 21
477218 CGGTGTTTGA
*
477228 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
*
477248 GTGCATCGATGCACT--AGTGCAG
1 GTGCATGGATGCACTGCAG-G--G
477270 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
477291 ATGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
477312 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
477333 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
* * *
477354 ATACATGGATACACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
477375 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
477396 GTGCATGGATGCACT
1 GTGCATGGATGCACT
477411 TTGACACCCT
Statistics
Matches: 146, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
18 1 0.01
20 14 0.10
21 113 0.77
22 15 0.10
23 1 0.01
24 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.21
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:477512 original size:29 final size:29
Alignment explanation
Indices: 477491--477548 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
477481 AAACTTTGAA
477491 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
*
477520 TAATTTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
477549 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
30 14 0.54
31 2 0.08
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:481079 original size:73 final size:73
Alignment explanation
Indices: 480959--481096 Score: 222
Period size: 73 Copynumber: 1.9 Consensus size: 73
480949 TTCCCTTTTA
* *
480959 CAAAATAGGATAATTCAAGATTCTTAAGAAAATAAATTCAACTATTTATTTCCTTTTACAAAATA
1 CAAAATAGAATAATTCAAGATTCTTAAGAAAATAAATTCAACAATTTATTTCCTTTTACAAAATA
481024 GAATCATT
66 GAATCATT
* * **
481032 CAAAATAGAATAATTTAGGATTCTTAAGAAAATAAATTCAACAATTTATTTTGTTTTACAAAATA
1 CAAAATAGAATAATTCAAGATTCTTAAGAAAATAAATTCAACAATTTATTTCCTTTTACAAAATA
481097 TAATAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 59 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.36
Consensus pattern (73 bp):
CAAAATAGAATAATTCAAGATTCTTAAGAAAATAAATTCAACAATTTATTTCCTTTTACAAAATA
GAATCATT
Found at i:481122 original size:58 final size:58
Alignment explanation
Indices: 481032--481668 Score: 393
Period size: 58 Copynumber: 10.9 Consensus size: 58
481022 TAGAATCATT
* * * * * *
481032 CAAAATAGAATAATTTAGGATTCTTAAGAAAATAAATTCAACAATTTATTTTGTTTTA
1 CAAAATAGAATCATTCAAGATTCTCAAGAAAATAAATTCAACGATTTATTTTCTTTTA
* * * * *
481090 CAAAATATAATAATTAAAGATTCTTAAGAAAATAAATTTAACGATTTA-TTT-TTTTA
1 CAAAATAGAATCATTCAAGATTCTCAAGAAAATAAATTCAACGATTTATTTTCTTTTA
* * ** * *
481146 GAAAATATAATCATTCAAGATTCTCAAGAAAATAAATTTGATGATTTATTTCCTTTTA
1 CAAAATAGAATCATTCAAGATTCTCAAGAAAATAAATTCAACGATTTATTTTCTTTTA
* * * * * * *
481204 CAAACTAAAAACATAT-AAGATTCGCAGGAAAATAAACTT-AACAAATTA-TTTCATTTTA
1 CAAAATAGAATCAT-TCAAGATTCTCAAGAAAATAAA-TTCAACGATTTATTTTC-TTTTA
* * * * * *
481262 TAAAATAAAAATGATTCAAGATTCCCAAGAAAATAAATTCGACGAGTTT-TTTCCTTTTA
1 CAAAAT-AGAATCATTCAAGATTCTCAAGAAAATAAATTCAACGA-TTTATTTTCTTTTA
** * * * *
481321 CAAGTTAGAATCATAT-AAGATTCACATGAAAATAAATTAAATGATTTATTTTCTTATACAAAAT
1 CAAAATAGAATCAT-TCAAGATTCTCAAGAAAATAAATTCAACGATTTATTTTCTT-T------T
481385 AGA
58 --A
* * * * *
481388 AAAAATAGAATCATTTAAGATT-TATAAGAAAATAAATTAAATGATTTATTTAT-TTTTA
1 CAAAATAGAATCATTCAAGATTCT-CAAGAAAATAAATTCAACGATTTATTT-TCTTTTA
** * * * * * * *
481446 CAAACCAAAATCATGT-AAGATCCACTATAAAATAAATTCAACGA-TTACTTCCTTTTA
1 CAAAATAGAATCAT-TCAAGATTCTCAAGAAAATAAATTCAACGATTTATTTTCTTTTA
** * * ** * *
481503 CACGATAGAATCATTTAAGATTCTCAAGAAAATAAATTAAAAAAATTATTTTATTTTA
1 CAAAATAGAATCATTCAAGATTCTCAAGAAAATAAATTCAACGATTTATTTTCTTTTA
* * ** * *
481561 TAAAATAGAATCATTCAAGATTCTCAAG-AAACAAATTCAATAAGTTA-TCTCTTTTTA
1 CAAAATAGAATCATTCAAGATTCTCAAGAAAATAAATTCAACGATTTATTTTC-TTTTA
* * *
481618 -AAAGATAAAATCATTCGAGATTCTTAAGAAAATAAATTCAACGATTTATTT
1 CAAA-ATAGAATCATTCAAGATTCTCAAGAAAATAAATTCAACGATTTATTT
481669 CCCTTACAAA
Statistics
Matches: 450, Mismatches: 96, Indels: 65
0.74 0.16 0.11
Matches are distributed among these distances:
56 53 0.12
57 92 0.20
58 208 0.46
59 42 0.09
60 6 0.01
65 1 0.00
66 2 0.00
67 45 0.10
68 1 0.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (58 bp):
CAAAATAGAATCATTCAAGATTCTCAAGAAAATAAATTCAACGATTTATTTTCTTTTA
Found at i:481321 original size:117 final size:113
Alignment explanation
Indices: 481057--481360 Score: 308
Period size: 117 Copynumber: 2.6 Consensus size: 113
481047 TAGGATTCTT
* * ** * * ** *
481057 AAGAAAATAAATTCAACAATTTATTTTGTTTTACAAAATATAATA-AT-TAAAGATTCTTAAGAA
1 AAGAAAATAAATTCGACGATTTATTTCCTTTTACAAACTA-AAAACATAT-AAGATTCACAGGAA
* * * *
481120 AATAAATTTAACGATTTATTTTTTTAGAAAATATAATCATTCAAGATTCTC
64 AATAAA-TTAACAAATTATTTTTTTAGAAAATAAAATCATTCAAGATTCCC
* * *
481171 AAGAAAATAAATTTGATGATTTATTTCCTTTTACAAACTAAAAACATATAAGATTCGCAGGAAAA
1 AAGAAAATAAATTCGACGATTTATTTCCTTTTACAAACTAAAAACATATAAGATTCACAGGAAAA
* *
481236 TAAACTTAACAAATTATTTCATTTTATAAAATAAAAATGATTCAAGATTCCC
66 TAAA-TTAACAAATTATTT--TTTTAGAAAAT-AAAATCATTCAAGATTCCC
** * * *
481288 AAGAAAATAAATTCGACGAGTTT-TTTCCTTTTACAAGTTAGAATCATATAAGATTCACATGAAA
1 AAGAAAATAAATTCGACGA-TTTATTTCCTTTTACAAACTAAAAACATATAAGATTCACAGGAAA
481352 ATAAATTAA
65 ATAAATTAA
481361 ATGATTTATT
Statistics
Matches: 158, Mismatches: 26, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
113 3 0.02
114 64 0.41
115 1 0.01
116 14 0.09
117 73 0.46
118 3 0.02
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (113 bp):
AAGAAAATAAATTCGACGATTTATTTCCTTTTACAAACTAAAAACATATAAGATTCACAGGAAAA
TAAATTAACAAATTATTTTTTTAGAAAATAAAATCATTCAAGATTCCC
Found at i:481535 original size:57 final size:56
Alignment explanation
Indices: 481474--481659 Score: 178
Period size: 57 Copynumber: 3.2 Consensus size: 56
481464 GATCCACTAT
* * * * *
481474 AAAATAAATTCAACGATTACTTCCTTTTACACGATAGAATCATTTAAGATTCTCAAG
1 AAAATAAATTCAACAATTA-TTCATTTTAAAAGATAGAATCATTCAAGATTCTCAAG
* * *
481531 AAAATAAATTAAAAAAATTATTTTATTTTATAAA-ATAGAATCATTCAAGATTCTCAAG
1 AAAATAAATT-CAACAATTA-TTCATTTTA-AAAGATAGAATCATTCAAGATTCTCAAG
* * * * * *
481589 -AAACAAATTCAATAAGTTATCTCTTTTTAAAAGATAAAATCATTCGAGATTCTTAAG
1 AAAATAAATTCAACAA-TTAT-TCATTTTAAAAGATAGAATCATTCAAGATTCTCAAG
481646 AAAATAAATTCAAC
1 AAAATAAATTCAAC
481660 GATTTATTTC
Statistics
Matches: 104, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
56 8 0.08
57 48 0.46
58 47 0.45
59 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (56 bp):
AAAATAAATTCAACAATTATTCATTTTAAAAGATAGAATCATTCAAGATTCTCAAG
Found at i:482252 original size:37 final size:37
Alignment explanation
Indices: 482191--482286 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
482181 ATTTTCGTCC
* *
482191 TACTAAGATTCAAACTCCTAAAAATAGGATAGAATTT-
1 TACTAGGATTAAAACTCCTAAAAATAGGATAG-ATTTA
*
482228 TGCTAGGATTAAAACTCCTAAAAATAGGATAGATTTA
1 TACTAGGATTAAAACTCCTAAAAATAGGATAGATTTA
** *
482265 TACTATTATTTAAACTCCTAAA
1 TACTAGGATTAAAACTCCTAAA
482287 GATATGATTC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 4 0.08
37 47 0.92
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (37 bp):
TACTAGGATTAAAACTCCTAAAAATAGGATAGATTTA
Found at i:482740 original size:23 final size:24
Alignment explanation
Indices: 482712--482759 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
482702 TAAATATATA
482712 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTTATTTCATT
*
482735 TATTTATTATAATTTTTTTTCATT
1 TATTTATTATAATTTTATTTCATT
482759 T
1 T
482760 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTATTATAATTTTATTTCATT
Found at i:483034 original size:19 final size:16
Alignment explanation
Indices: 483010--483050 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
483000 TTACATACAT
483010 TTTTATATTTTTATATATA
1 TTTTATA-TTTTAT-T-TA
483029 TTTTATATTTTATTTA
1 TTTTATATTTTATTTA
483045 TTTTAT
1 TTTTAT
483051 TTATACTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 1 0.05
18 6 0.27
19 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATATTTTATTTA
Found at i:483035 original size:9 final size:9
Alignment explanation
Indices: 483010--483050 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
483000 TTACATACAT
483010 TTTTATAT-
1 TTTTATATA
483018 TTTTATATA
1 TTTTATATA
483027 TATTT-TATA
1 T-TTTATATA
*
483036 TTTTATTTA
1 TTTTATATA
483045 TTTTAT
1 TTTTAT
483051 TTATACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 11 0.38
9 15 0.52
10 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATATA
Found at i:483062 original size:22 final size:20
Alignment explanation
Indices: 483030--483081 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
483020 TTATATATAT
483030 TTTATATTTTATTTATTTTA
1 TTTATATTTTATTTATTTTA
483050 TTTATACTATTTATTTATTTTCA
1 TTTATA-T-TTTATTTATTTT-A
483073 -TTATATTTT
1 TTTATATTTT
483082 TAGTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 9 0.31
21 2 0.07
22 17 0.59
23 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATATTTTATTTATTTTA
Found at i:483182 original size:18 final size:19
Alignment explanation
Indices: 483158--483203 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
483148 TGTATATATA
*
483158 TTTTTTTCTTCA-TTT-AT
1 TTTTTTTATTCAGTTTCAT
483175 TTTATTTTATTCAGTTTCAT
1 TTT-TTTTATTCAGTTTCAT
483195 TTTTTTTAT
1 TTTTTTTAT
483204 ATTTGTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 8 0.32
19 9 0.36
20 5 0.20
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTTATTCAGTTTCAT
Found at i:487766 original size:20 final size:18
Alignment explanation
Indices: 487744--487814 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 18
487734 ACAAAAAGGG
487744 CAAAAAAAAAAGAAAAGAA
1 CAAAAAAAAAAG-AAAGAA
*
487763 GC-AAAAAAGAAG-AA-AA
1 -CAAAAAAAAAAGAAAGAA
487779 CAAAAGAAAAAAGAAAGAA
1 CAAAA-AAAAAAGAAAGAA
487798 CAAAAATCAAAAAGAAA
1 CAAAAA--AAAAAGAAA
487815 AAGGGACAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
15 1 0.02
16 5 0.12
17 8 0.19
18 3 0.07
19 16 0.37
20 10 0.23
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (18 bp):
CAAAAAAAAAAGAAAGAA
Found at i:487795 original size:24 final size:24
Alignment explanation
Indices: 487750--487816 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
487740 AGGGCAAAAA
* *
487750 AAAAAGAAAAGAAGCAAAAAAGAA-
1 AAAAACAAAAGAA-AAAAAAAGAAC
*
487774 GAAAACAAAAGAAAAAAGAAAGAAC
1 AAAAACAAAAGAAAAAA-AAAGAAC
487799 AAAAATCAAAAAGAAAAA
1 AAAAA-C-AAAAGAAAAA
487817 GGGACAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.09
24 17 0.49
25 4 0.11
26 1 0.03
27 10 0.29
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.01
Consensus pattern (24 bp):
AAAAACAAAAGAAAAAAAAAGAAC
Found at i:487815 original size:13 final size:13
Alignment explanation
Indices: 487745--487816 Score: 58
Period size: 13 Copynumber: 5.3 Consensus size: 13
487735 CAAAAAGGGC
487745 AAAAA-AAAAAGA
1 AAAAACAAAAAGA
487757 AAAGAAGCAAAAAAGA
1 AAA-AA-C-AAAAAGA
487773 AGAAAAC-AAAAGA
1 A-AAAACAAAAAGA
* *
487786 AAAAAGAAAGAACA
1 AAAAACAAA-AAGA
*
487800 AAAATCAAAAAGA
1 AAAAACAAAAAGA
487813 AAAA
1 AAAA
487817 GGGACAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
12 7 0.15
13 18 0.38
14 10 0.21
15 1 0.02
16 10 0.21
17 2 0.04
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (13 bp):
AAAAACAAAAAGA
Found at i:489541 original size:106 final size:106
Alignment explanation
Indices: 489414--491321 Score: 2970
Period size: 106 Copynumber: 18.0 Consensus size: 106
489404 ATATCGTGCC
* * * *
489414 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-TGACTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
*
489478 CAAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
489520 ACTCCAGACAACAG-AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAAC-GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
*
489584 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
489626 ACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
489691 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
489732 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
489797 AATTTCAGAGCCAATTTCAACTTCATAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
489838 ACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
489903 AATTTTAGAGCCAATTTCAACTTCACAACTAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
489944 ACTCCAGACAACGCAACTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
490009 AATTTCAGAGCCAATTTCAACATCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
490050 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
490115 AATTTCGGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
490156 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
490221 AATTTC-GAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAG-AGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
490262 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
490327 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGGTATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
490368 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGAGACCGATGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
490433 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
490474 ACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
490539 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
490580 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
490645 AATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
490686 ACTCCAGACAACGCAAGTTCAACTTCATGAAGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
490751 AATTTTAGAGCCAATTTCAACTTCACAACTAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
490792 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
490857 AATTTCAAAGCCAATTTCAACATCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
490898 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
490963 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
491004 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
491069 AATTTC-GAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAG-AGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
491110 ACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * *
491175 AATTTCGGAGTCAATTTTAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * *** * *
491216 ACTTGAGACAACACAAGTTCAACTT--C-AC-AAGGGGTGGCTGGTCGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
491277 AATTCCAGAGCCAATTTCAACTTCAC-GACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
491318 ACTC
1 ACTC
491322 GAAACAATGC
Statistics
Matches: 1671, Mismatches: 123, Indels: 20
0.92 0.07 0.01
Matches are distributed among these distances:
102 65 0.04
103 2 0.00
104 1 0.00
105 3 0.00
106 1597 0.96
107 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:492159 original size:36 final size:36
Alignment explanation
Indices: 492070--492165 Score: 120
Period size: 36 Copynumber: 2.6 Consensus size: 36
492060 CCTTTTCGTC
*
492070 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCT-AAAATAGGATAGAATT
* * *
492107 TTGCTAGGATTCAAACTCCTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
** *
492143 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
492166 GATATGATCC
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 32 0.64
37 18 0.36
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
Found at i:492609 original size:4 final size:4
Alignment explanation
Indices: 492589--492627 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
492579 TAAATATATA
* *
492589 TATT TAAT TATA T-TT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
492628 ATAATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 2 0.07
4 28 0.93
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:492663 original size:5 final size:5
Alignment explanation
Indices: 492653--492701 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
492643 TTTCTTTGCG
* *
492653 TTATA TTATA TTATT TTCCTA TTATA TATATA TATATA TTATA TTATA
1 TTATA TTATA TTATA TT-ATA TTATA T-TATA T-TATA TTATA TTATA
492701 T
1 T
492702 ATTATTTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 24 0.63
6 14 0.37
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:492765 original size:2 final size:2
Alignment explanation
Indices: 492758--492782 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
492748 TTCCTAACGT
492758 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
492783 TCTTACTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:492936 original size:27 final size:31
Alignment explanation
Indices: 492906--492968 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
492896 TTATACATAC
492906 ATTTT-TATATTTT-TATATA-TATTT-TTT
1 ATTTTATATATTTTATATATACTATTTATTT
* *
492933 ATTTTATTTATTTTATTTATACTATTTATTT
1 ATTTTATATATTTTATATATACTATTTATTT
492964 ATTTT
1 ATTTT
492969 CATTATGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 7 0.23
29 5 0.17
30 5 0.17
31 8 0.27
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (31 bp):
ATTTTATATATTTTATATATACTATTTATTT
Found at i:492939 original size:18 final size:18
Alignment explanation
Indices: 492906--492952 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
492896 TTATACATAC
492906 ATTTTTATATTTTTATATAT
1 ATTTTT-TA-TTTTATATAT
*
492926 ATTTTTTATTTTATTTAT
1 ATTTTTTATTTTATATAT
492944 -TTTATTTAT
1 ATTT-TTTAT
492953 ACTATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 14 0.56
19 2 0.08
20 6 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTTATTTTATATAT
Found at i:492944 original size:9 final size:9
Alignment explanation
Indices: 492916--492967 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
492906 ATTTTTATAT
*
492916 TTTTATATA
1 TTTTATTTA
492925 TATTT-TTTA
1 T-TTTATTTA
492934 TTTTATTTA
1 TTTTATTTA
492943 TTTTATTTA
1 TTTTATTTA
**
492952 TACTATTTA
1 TTTTATTTA
492961 -TTTATTT
1 TTTTATTT
492968 TCATTATGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
8 8 0.22
9 25 0.69
10 3 0.08
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATTTA
Found at i:493081 original size:18 final size:19
Alignment explanation
Indices: 493057--493102 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
493047 TGTATATATA
*
493057 TTTTTTTCTTC-ATTT-AT
1 TTTTTTTATTCAATTTCAT
493074 TTTATTTTATTCAATTTCAT
1 TTT-TTTTATTCAATTTCAT
493094 TTTTTTTAT
1 TTTTTTTAT
493103 ATTTGTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 7 0.28
19 10 0.40
20 5 0.20
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTATTCAATTTCAT
Found at i:498494 original size:45 final size:45
Alignment explanation
Indices: 498318--498575 Score: 204
Period size: 45 Copynumber: 5.6 Consensus size: 45
498308 GAATTAATCA
* * * * *
498318 TTTAATTTTAGCAACTCAATAATAAAAAAAAAGAACTAA-CCTTTTGAA
1 TTTAATTTTGGCAACCCAATAAT---CAAAAGGAACTAATCC-TTTGAT
* * * *
498366 TTTAATTTTTGCATCCCAATAATCAAAAAGAACTAATCATATTTGAT
1 TTTAATTTTGGCAACCCAATAATCAAAAGGAACTAATC--CTTTGAT
* * *
498413 TTTAATTTCT-GTAA--CAAGTAATCGAAAGGAATTAATCCTTTGAT
1 TTTAATTT-TGGCAACCCAA-TAATCAAAAGGAACTAATCCTTTGAT
* *
498457 TTTAATTTTGGCAACCCAATAATCAAAAGGGACTAATCCTTTAAT
1 TTTAATTTTGGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
* * * *
498502 TTTACTTTTGGC-ACCACAATAATCAAAATGAACTAATCTTTTTAT
1 TTTAATTTTGGCAACC-CAATAATCAAAAGGAACTAATCCTTTGAT
* *
498547 TTTACTTTTAGG-AATCCAATAATCAAAAG
1 TTTAATTTT-GGCAACCCAATAATCAAAAG
498576 CCTTGGATTA
Statistics
Matches: 175, Mismatches: 24, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 20 0.11
45 94 0.54
46 24 0.14
47 15 0.09
48 21 0.12
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (45 bp):
TTTAATTTTGGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
Found at i:498747 original size:14 final size:15
Alignment explanation
Indices: 498721--498751 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
498711 AAAGATATTC
498721 TTTAATCATGTCATA
1 TTTAATCATGTCATA
498736 TTTAAT-ATGTCATA
1 TTTAATCATGTCATA
498750 TT
1 TT
498752 AAAAGACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (15 bp):
TTTAATCATGTCATA
Found at i:500069 original size:2 final size:2
Alignment explanation
Indices: 500062--500101 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
500052 CTTGTTGAAA
500062 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
500102 CATAAGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:500619 original size:21 final size:20
Alignment explanation
Indices: 500582--500620 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
500572 CATGATTAAA
*
500582 AATTTAATAATTTTTTTTTT
1 AATTTAATAATTATTTTTTT
*
500602 AATTTGAATACTTATTTTT
1 AATTT-AATAATTATTTTT
500621 ACATGAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
AATTTAATAATTATTTTTTT
Found at i:500953 original size:19 final size:21
Alignment explanation
Indices: 500931--500973 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
500921 TTTTATTACT
*
500931 ATTTTTATTT-TAA-ATTAAA
1 ATTTTCATTTCTAATATTAAA
*
500950 ATTTTCATTTCTAATTTTAAA
1 ATTTTCATTTCTAATATTAAA
500971 ATT
1 ATT
500974 ATTTTACCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 3 0.15
21 8 0.40
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTTCATTTCTAATATTAAA
Found at i:501215 original size:18 final size:18
Alignment explanation
Indices: 501188--501228 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
501178 TGGATTTTTG
*
501188 TAAA-AAAATAATATAAA
1 TAAATAAAATAAAATAAA
*
501205 TTAATAAAATAAAATAAA
1 TAAATAAAATAAAATAAA
501223 TAAATA
1 TAAATA
501229 TTAATCAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAATAAAATAAAATAAA
Found at i:503893 original size:33 final size:33
Alignment explanation
Indices: 503851--503915 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
503841 TCGGGTCGGG
503851 TTTTTAAGTGTGATATTCGGGTCGAGTCGGGTT
1 TTTTTAAGTGTGATATTCGGGTCGAGTCGGGTT
*
503884 TTTTTAAGTGTGATATTCGGGTCGGGTCGGGT
1 TTTTTAAGTGTGATATTCGGGTCGAGTCGGGT
503916 CGGGTTTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.14, C:0.09, G:0.35, T:0.42
Consensus pattern (33 bp):
TTTTTAAGTGTGATATTCGGGTCGAGTCGGGTT
Found at i:504482 original size:18 final size:17
Alignment explanation
Indices: 504438--504484 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
504428 TATGGAATTG
*
504438 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
504455 GATTCTAATTCCTTCACA
1 GATTCCAATTCC-TCACA
*
504473 GTTTCCAATTCC
1 GATTCCAATTCC
504485 CTCAGAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:504735 original size:19 final size:20
Alignment explanation
Indices: 504696--504745 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
504686 GAAACCCCTT
*
504696 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATCTTTAA
504716 TGAAAATACATGA-CTTTAA
1 TGAAAATACATGATCTTTAA
*
504735 TGAAAACACAT
1 TGAAAATACAT
504746 ACTCTTGGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (20 bp):
TGAAAATACATGATCTTTAA
Found at i:505017 original size:15 final size:15
Alignment explanation
Indices: 504999--505030 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
504989 CCATGCATTG
*
504999 TGCATCGATGCACCC
1 TGCATCCATGCACCC
505014 TGCATCCATGCACCC
1 TGCATCCATGCACCC
505029 TG
1 TG
505031 GCTGCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.41, G:0.19, T:0.22
Consensus pattern (15 bp):
TGCATCCATGCACCC
Found at i:508155 original size:18 final size:17
Alignment explanation
Indices: 508132--508185 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
508122 TATATTTTCC
508132 AACAATTAGTATCTTTTT
1 AACAATT-GTATCTTTTT
*
508150 AACAATTGAAATCCTTTTTT
1 AACAATTG-TAT-C-TTTTT
508170 AACAATTGGTATCTTT
1 AACAATT-GTATCTTT
508186 ATCATTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 1 0.03
18 12 0.40
19 2 0.07
20 14 0.47
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.46
Consensus pattern (17 bp):
AACAATTGTATCTTTTT
Found at i:510591 original size:16 final size:16
Alignment explanation
Indices: 510570--510601 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
510560 GATTTAAATG
510570 ACCATGTCCTTTCACC
1 ACCATGTCCTTTCACC
510586 ACCATGTCCTTTCACC
1 ACCATGTCCTTTCACC
510602 TTTGTGCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (16 bp):
ACCATGTCCTTTCACC
Found at i:517831 original size:2 final size:2
Alignment explanation
Indices: 517824--517854 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
517814 CATATTTTAG
*
517824 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
517855 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:519874 original size:59 final size:58
Alignment explanation
Indices: 519752--519906 Score: 145
Period size: 58 Copynumber: 2.7 Consensus size: 58
519742 TCGAGTGACT
* * * * * * * *
519752 ATTTTGTAACTTTCAAGAGTCAAGAGATTCAACAAAACAACATATTATAGTCGGAGATT
1 ATTTTGTAACTTTTAATAGTCGA-AGACTCAACAAAACAACATATTATAATCGAAAATA
*
519811 ATTTTGTAACTTTTAATTGTCGAAGACTCAACAAAACAACAT-TCTATAATCAGAAAATA
1 ATTTTGTAACTTTTAATAGTCGAAGACTCAACAAAACAACATAT-TATAATC-GAAAATA
* **
519870 ATTTTATAAC--TTACATAGTCGGGGACTCAACAAAACA
1 ATTTTGTAACTTTTA-ATAGTCGAAGACTCAACAAAACA
519907 TCACATCGAG
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
57 4 0.05
58 44 0.55
59 32 0.40
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (58 bp):
ATTTTGTAACTTTTAATAGTCGAAGACTCAACAAAACAACATATTATAATCGAAAATA
Found at i:521273 original size:23 final size:21
Alignment explanation
Indices: 521238--521280 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
521228 GTATTGAATT
*
521238 TCCTCTCATTTTGCACCGAAAAC
1 TCCTCTCACTTTG-ACC-AAAAC
*
521261 TCCTCTCCCTTTGACCAAAA
1 TCCTCTCACTTTGACCAAAA
521281 TCCCCACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.26, C:0.37, G:0.07, T:0.30
Consensus pattern (21 bp):
TCCTCTCACTTTGACCAAAAC
Found at i:528139 original size:21 final size:21
Alignment explanation
Indices: 528115--528185 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
528105 TTATTTGAGA
528115 GTGCATCGGTACACATTGAAT
1 GTGCATCGGTACACATTGAAT
*
528136 GTGCATCAGTACACATTGAAT
1 GTGCATCGGTACACATTGAAT
528157 GTGCATCGGTACACATTGAAT
1 GTGCATCGGTACACATTGAAT
528178 GTGCATCG
1 GTGCATCG
528186 ATGCACACAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (21 bp):
GTGCATCGGTACACATTGAAT
Found at i:535803 original size:25 final size:26
Alignment explanation
Indices: 535774--535831 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
535764 GTTTTACTAT
535774 TTTTTTTCGAAATCTCCTTTTT-TCTA
1 TTTTTTTCGAAATCT-CTTTTTCTCTA
* *
535800 TTTTTTTCGAACTCTCTTTTTCTCTG
1 TTTTTTTCGAAATCTCTTTTTCTCTA
535826 TTTTTT
1 TTTTTT
535832 CTCTTCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.10, C:0.19, G:0.05, T:0.66
Consensus pattern (26 bp):
TTTTTTTCGAAATCTCTTTTTCTCTA
Found at i:535803 original size:26 final size:25
Alignment explanation
Indices: 535765--535831 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
535755 TCTTTTTTCG
*
535765 TTTTACTATTTTTTTTCGAAATCTCCT
1 TTTTTCTA-TTTTTTTCGAAATCT-CT
*
535792 TTTTTCTATTTTTTTCGAACTCTCT
1 TTTTTCTATTTTTTTCGAAATCTCT
*
535817 TTTTCTCTGTTTTTT
1 TTTT-TCTATTTTTT
535832 CTCTTCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.17
26 23 0.64
27 7 0.19
ACGTcount: A:0.12, C:0.18, G:0.04, T:0.66
Consensus pattern (25 bp):
TTTTTCTATTTTTTTCGAAATCTCT
Found at i:536736 original size:41 final size:42
Alignment explanation
Indices: 536690--536769 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
536680 CCAATGGTCT
*
536690 ATAGATGACCCGAAAGACTT-ATCATCTTACTCAAAAGATTG
1 ATAGATGACCCGAAAGACTTAATCATCATACTCAAAAGATTG
* * * *
536731 ATAGATGACCTGAAGGATTTAATCATCATGCTCAAAAGA
1 ATAGATGACCCGAAAGACTTAATCATCATACTCAAAAGA
536770 CTTACTGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 17 0.52
42 16 0.48
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.26
Consensus pattern (42 bp):
ATAGATGACCCGAAAGACTTAATCATCATACTCAAAAGATTG
Found at i:536765 original size:42 final size:42
Alignment explanation
Indices: 536689--536793 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 42
536679 CCCAATGGTC
* * * *
536689 TATAGATGACCCGAAAGACTT-ATCATCTTACTCAAAAGA-T
1 TATAGATGACCTGAAGGATTTAATCATCATACTCAAAAGACT
*
536729 TGATAGATGACCTGAAGGATTTAATCATCATGCTCAAAAGACT
1 T-ATAGATGACCTGAAGGATTTAATCATCATACTCAAAAGACT
536772 TACT-GATTG-CCTGAAGGATTTA
1 TA-TAGA-TGACCTGAAGGATTTA
536794 CCAATTTTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
40 1 0.02
41 17 0.31
42 32 0.58
43 5 0.09
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (42 bp):
TATAGATGACCTGAAGGATTTAATCATCATACTCAAAAGACT
Found at i:536997 original size:260 final size:254
Alignment explanation
Indices: 536478--537386 Score: 1022
Period size: 260 Copynumber: 3.6 Consensus size: 254
536468 AGACTACTAA
*
536478 ATGACCCGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATT
1 ATGACCCGAAGGATTTAGTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATT
* * * *
536543 TTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGTTTTCTTGCTTTTCAAAAAATTCATTT
66 TTGGAAATATTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTT
* * * * * * *
536608 TCTGAACATACTAAA-GAGAAACTTTGAAAATCGTTTTCTCA-TTTTTCAAGTTATCCTATGAAA
131 TCAGAAAATACTAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTTGAA--AATCATGTGAAA
* * * *
536671 GCATCTTGCCCAATGGTCTATAGATGACCCGAAAGACTTATCATCTTACTCAAAA-GATTGATAG
194 ACATCATGCCCAA--GTCTAT-GATGACCCGAATGACTTATCATCTTACTCAAAAGGCTT-ATAG
* * * * * *
536735 ATGACCTGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATTGCCTGAAGGATTTACCAATT
1 ATGACCCGAAGGATTTAGTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATT
* * * * *
536800 TTGGAAATATTTTTCCACGTAAGAAACTTTGGAAAAT-GCTTTCTTACTTTTTAAAATTTTCAAT
66 TTGGAAATATTTTACTAGGTAAGAAACTTTGG-AAATCGCTTTCTTACTTTTCAAAAATTTC-AT
* * *
536864 TTTCAAAAAATATTTAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTTGAAAATCGTGTGAA
129 TTTCAGAAAATA-CTAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTTGAAAATCATGTGAA
536929 AACATCATGCCCGAAAGTCTTATGGATGACCCGAATGACTTATCATCTTACTCAAAAGGCTTATA
193 AACATCATGCCC--AAGTC-TAT-GATGACCCGAATGACTTATCATCTTACTCAAAAGGCTTATA
536994 G
254 G
*
536995 ATGACCCGAAGGATTTAGGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATT
1 ATGACCCGAAGGATTTAGTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATT
*** * * * *
537060 GAAGAAATAATTTACTATGTAAGAAACTTTGGAAATTGCTTCCTTA---TT--AAAATTTCAATT
66 TTGGAAATATTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTC-ATT
* * * * * *
537120 TTCATAAAAGATTTAAATGAGAAACTTTGGAAATCATTTTCTCATTTTTCGAAAATCACGTGAAA
130 TTCAGAAAATA-CTAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTTGAAAATCATGTGAAA
* * * * *
537185 ACATCATG--C----C-----T-----GAATGACTTATCATCTTGCTCGAAAGACTGACAG
194 ACATCATGCCCAAGTCTATGATGACCCGAATGACTTATCATCTTACTCAAAAGGCTTATAG
* *
537230 ATGACCCGAAGGATTTAGTCATCATGCTCGAAAGACATACTGATGGCCCGAAAGACTTACCAATT
1 ATGACCCGAAGGATTTAGTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATT
* *
537295 TTGGAAAAATTTTACTAGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCATTT
66 TTGGAAATATTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTT
*
537360 TCTGAAAATACTAAATGAGAAACTTTG
131 TCAGAAAATACTAAATGAGAAACTTTG
537387 AAAACCACTT
Statistics
Matches: 565, Mismatches: 72, Indels: 49
0.82 0.10 0.07
Matches are distributed among these distances:
235 128 0.23
238 18 0.03
239 11 0.02
240 9 0.02
247 1 0.00
253 1 0.00
255 78 0.14
257 108 0.19
258 15 0.03
259 29 0.05
260 155 0.27
261 12 0.02
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (254 bp):
ATGACCCGAAGGATTTAGTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATT
TTGGAAATATTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTT
TCAGAAAATACTAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTTGAAAATCATGTGAAAAC
ATCATGCCCAAGTCTATGATGACCCGAATGACTTATCATCTTACTCAAAAGGCTTATAG
Found at i:539480 original size:17 final size:17
Alignment explanation
Indices: 539458--539494 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
539448 AGTAAAAAAA
539458 GTATATTTTCATGCACT
1 GTATATTTTCATGCACT
539475 GTATATTTTCATGCACT
1 GTATATTTTCATGCACT
539492 GTA
1 GTA
539495 AACTTTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (17 bp):
GTATATTTTCATGCACT
Found at i:542487 original size:17 final size:19
Alignment explanation
Indices: 542449--542487 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
542439 GTACTATTTT
*
542449 AAAAAATACATTGCAACCA
1 AAAAAATACATTGCAACAA
542468 AAAAAATACA-TG-AACAA
1 AAAAAATACATTGCAACAA
542485 AAA
1 AAA
542488 TGTAATCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.67, C:0.15, G:0.05, T:0.13
Consensus pattern (19 bp):
AAAAAATACATTGCAACAA
Found at i:544231 original size:59 final size:59
Alignment explanation
Indices: 544131--544244 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
544121 TGGTTTAAGC
* *
544131 CATATTATCGAGTTTTCCTTTTCATTGCGACTAAGAGGGTTCGATAGGACACTTAGTGT
1 CATATTATCGAGTTTGCCTTTTCATTGCGACTAAGAAGGTTCGATAGGACACTTAGTGT
* *
544190 CATATTATCGAGTTTGCCTTTTCATTGTGACTAGGAAGGTTCGATAGGACACTTA
1 CATATTATCGAGTTTGCCTTTTCATTGCGACTAAGAAGGTTCGATAGGACACTTA
544245 TCCATCCTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.37
Consensus pattern (59 bp):
CATATTATCGAGTTTGCCTTTTCATTGCGACTAAGAAGGTTCGATAGGACACTTAGTGT
Found at i:550095 original size:19 final size:19
Alignment explanation
Indices: 550071--550109 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
550061 GTTGAAAATG
*
550071 ATTTGATTTTGAAAGTCAA
1 ATTTGATTTTGAAAATCAA
550090 ATTTGATTTTGAAAATCAA
1 ATTTGATTTTGAAAATCAA
550109 A
1 A
550110 ATGAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (19 bp):
ATTTGATTTTGAAAATCAA
Found at i:556570 original size:20 final size:21
Alignment explanation
Indices: 556538--556580 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
556528 TTTATTTCTA
*
556538 AATAATTTATTTTAATTATTT
1 AATAATTTATTTTAATTACTT
*
556559 AATAATTT-TTTTCATTACTT
1 AATAATTTATTTTAATTACTT
556579 AA
1 AA
556581 AATAAATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (21 bp):
AATAATTTATTTTAATTACTT
Found at i:557049 original size:22 final size:21
Alignment explanation
Indices: 557024--557074 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
557014 AAAATATTAT
*
557024 TAATATTAATAAGTATATATCA
1 TAATATTAATAAGTATAAAT-A
557046 TAATATTAATAAGTATAAATA
1 TAATATTAATAAGTATAAATA
557067 TAAT-TTAA
1 TAATATTAA
557075 ATTTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 4 0.14
21 5 0.18
22 19 0.68
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (21 bp):
TAATATTAATAAGTATAAATA
Found at i:557195 original size:3 final size:3
Alignment explanation
Indices: 557187--557263 Score: 111
Period size: 3 Copynumber: 25.3 Consensus size: 3
557177 CATATAATTT
* *
557187 TTA TTA TTAA ATA TTA TTA TTA TTA TAAA TTA TTA TTA TTA -TA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
557233 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
557264 AAAATATTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 2 0.03
3 61 0.91
4 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:557295 original size:51 final size:52
Alignment explanation
Indices: 557188--557301 Score: 126
Period size: 51 Copynumber: 2.2 Consensus size: 52
557178 ATATAATTTT
* * * * *
557188 TATTATTAAATATTATTATTATTATAAATTATTATTATTATATTATTATTAT
1 TATTATTAAATATTATTATTATTATAAAATATTATTAATATAATATCATTAA
*
557240 TATTATT-ATTATTATTATTATTATAAAATATTAATTTAATA-AATA-CATTAA
1 TATTATTAAATATTATTATTATTATAAAATATT-A-TTAATATAATATCATTAA
*
557291 TATTATAAAAT
1 TATTATTAAAT
557302 TACAATCCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
51 33 0.65
52 13 0.25
53 5 0.10
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (52 bp):
TATTATTAAATATTATTATTATTATAAAATATTATTAATATAATATCATTAA
Found at i:557298 original size:17 final size:16
Alignment explanation
Indices: 557253--557300 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
557243 TATTATTATT
* *
557253 ATTATTATTATAAAAT
1 ATTAATATTATAAAAC
557269 ATTAAT-TTAATAAATAC
1 ATTAATATT-ATAAA-AC
557286 ATTAATATTATAAAA
1 ATTAATATTATAAAA
557301 TTACAATCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 2 0.07
16 11 0.41
17 12 0.44
18 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAATATTATAAAAC
Found at i:557403 original size:15 final size:16
Alignment explanation
Indices: 557383--557424 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
557373 CCTAATCCCT
557383 AGCCGCCTCT-AATCC
1 AGCCGCCTCTGAATCC
**
557398 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGAATCC
557414 AGCCGCCTCTG
1 AGCCGCCTCTG
557425 CCTCCATCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.50, G:0.19, T:0.19
Consensus pattern (16 bp):
AGCCGCCTCTGAATCC
Found at i:557416 original size:16 final size:16
Alignment explanation
Indices: 557395--557430 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
557385 CCGCCTCTAA
557395 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
557411 TCCAGCCGCCTCTGCC
1 TCCAGCCGCCTCTGCC
557427 TCCA
1 TCCA
557431 TCGCTGCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.56, G:0.17, T:0.19
Consensus pattern (16 bp):
TCCAGCCGCCTCTGCC
Found at i:557644 original size:19 final size:17
Alignment explanation
Indices: 557620--557658 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
557610 GACAGAGACA
557620 AGAAAGACAGAAAATACAC
1 AGAAAGA-AGAAAA-ACAC
*
557639 AGAAAGAAGAGAAACAC
1 AGAAAGAAGAAAAACAC
557656 AGA
1 AGA
557659 GAATCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.64, C:0.13, G:0.21, T:0.03
Consensus pattern (17 bp):
AGAAAGAAGAAAAACAC
Found at i:557661 original size:19 final size:19
Alignment explanation
Indices: 557620--557661 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
557610 GACAGAGACA
*
557620 AGAAAGACAGAAAATACAC
1 AGAAAGACAGAAAACACAC
*
557639 AGAAAGA-AGAGAAACACAG
1 AGAAAGACAGA-AAACACAC
557658 AGAA
1 AGAA
557662 TCAAATACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.64, C:0.12, G:0.21, T:0.02
Consensus pattern (19 bp):
AGAAAGACAGAAAACACAC
Found at i:558318 original size:25 final size:26
Alignment explanation
Indices: 558249--558327 Score: 90
Period size: 25 Copynumber: 3.1 Consensus size: 26
558239 TTATAGGGGG
* * *
558249 TTTAGGTTAAAGTGGTTTAGAGTTGAT
1 TTTAAGTTAAAGTGGTTTAGGGTT-TT
* *
558276 TTTATGTTAAA-TGATTTAGGGTTTT
1 TTTAAGTTAAAGTGGTTTAGGGTTTT
558301 TTTAAG-TAAAGTGGTTTAGGGTTTT
1 TTTAAGTTAAAGTGGTTTAGGGTTTT
558326 TT
1 TT
558328 GTTTAAATGG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.09
25 21 0.47
26 10 0.22
27 10 0.22
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (26 bp):
TTTAAGTTAAAGTGGTTTAGGGTTTT
Found at i:559244 original size:13 final size:13
Alignment explanation
Indices: 559226--559251 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
559216 GAGTCAACTA
559226 GTTGACTTTGACC
1 GTTGACTTTGACC
559239 GTTGACTTTGACC
1 GTTGACTTTGACC
559252 AAAAAGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
GTTGACTTTGACC
Found at i:561019 original size:35 final size:35
Alignment explanation
Indices: 560970--561095 Score: 166
Period size: 35 Copynumber: 3.6 Consensus size: 35
560960 GTTCAACTTA
*
560970 ATCAAA-TGATAATTCCTTATATAGGTTCAAACCG
1 ATCAAACTGGTAATTCCTTATATAGGTTCAAACCG
* * *
561004 ATCGAACTGGTAATTCCTTACGACAGGTTC-AACTCG
1 ATCAAACTGGTAATTCCTTA-TATAGGTTCAAAC-CG
* *
561040 ATCAAACTAGTAATTCCTTATATAGGTTCAGACCG
1 ATCAAACTGGTAATTCCTTATATAGGTTCAAACCG
561075 ATCAAACTGGTAATTCCTTAT
1 ATCAAACTGGTAATTCCTTAT
561096 GGATATAATG
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
34 5 0.06
35 44 0.56
36 29 0.37
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (35 bp):
ATCAAACTGGTAATTCCTTATATAGGTTCAAACCG
Found at i:563795 original size:18 final size:18
Alignment explanation
Indices: 563772--563806 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
563762 CTATCGGTTC
*
563772 ACTGGTTCAACCGGTCGT
1 ACTGGTCCAACCGGTCGT
*
563790 ACTGGTCCGACCGGTCG
1 ACTGGTCCAACCGGTCG
563807 GAAGATCCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.23
Consensus pattern (18 bp):
ACTGGTCCAACCGGTCGT
Found at i:567092 original size:21 final size:22
Alignment explanation
Indices: 567067--567118 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
567057 AAGTTCCCCG
567067 GGTATCGATA-CCCTCCCCATA-
1 GGTATCGATACCCCT-CCCATAT
*
567088 GGTATCGATACCCCTTCCATAT
1 GGTATCGATACCCCTCCCATAT
567110 GGTATCGAT
1 GGTATCGAT
567119 CTTGTTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (22 bp):
GGTATCGATACCCCTCCCATAT
Found at i:567997 original size:30 final size:31
Alignment explanation
Indices: 567952--568031 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
567942 TGACCATCAC
* *
567952 TTATGTAATTGTATTTTCTAATA-TTTAAAT
1 TTATGTGATTTTATTTTCTAATACTTTAAAT
** *
567982 TTATGTGATTTTATTTTCTTGTACTTTCAAT
1 TTATGTGATTTTATTTTCTAATACTTTAAAT
* *
568013 TAACGTGATTTTATTTTCT
1 TTATGTGATTTTATTTTCT
568032 TTTATTTTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 19 0.45
31 23 0.55
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.59
Consensus pattern (31 bp):
TTATGTGATTTTATTTTCTAATACTTTAAAT
Found at i:568177 original size:24 final size:25
Alignment explanation
Indices: 568150--568200 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
568140 ATTCTAATCT
*
568150 AACTCTAAACCATTTGAACA-AAAA
1 AACTCTAAACCATTTCAACATAAAA
568174 AACTCTAAACCATTTCAACATAAAA
1 AACTCTAAACCATTTCAACATAAAA
568199 AA
1 AA
568201 TCATAACCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.55, C:0.22, G:0.02, T:0.22
Consensus pattern (25 bp):
AACTCTAAACCATTTCAACATAAAA
Found at i:568236 original size:32 final size:31
Alignment explanation
Indices: 568179--568238 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
568169 AAAAAAACTC
568179 TAAACCATTTCAACATAAAAAATCATAACCT
1 TAAACCATTTCAACATAAAAAATCATAACCT
*
568210 TAAACCATTTTAACCCA-AAAAAATCATAA
1 TAAACCATTTCAA--CATAAAAAATCATAA
568239 ACCATTGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 12 0.46
32 12 0.46
33 2 0.08
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (31 bp):
TAAACCATTTCAACATAAAAAATCATAACCT
Found at i:568689 original size:29 final size:31
Alignment explanation
Indices: 568646--568703 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
568636 TATTTATTTT
** *
568646 TATGAATAAACTAAATTATTATTACCAAATG
1 TATGAATAAACTAAAAAATTATTAACAAATG
568677 TATGAAT-AA-TAAAAAATTATTAACAAA
1 TATGAATAAACTAAAAAATTATTAACAAA
568704 ATTAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.62
30 2 0.08
31 7 0.29
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (31 bp):
TATGAATAAACTAAAAAATTATTAACAAATG
Found at i:572729 original size:16 final size:18
Alignment explanation
Indices: 572708--572743 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
572698 TGATAATATA
572708 ATTTTTTTA-AT-AAAAT
1 ATTTTTTTATATAAAAAT
572724 A-TTTTTTATATAAAAAT
1 ATTTTTTTATATAAAAAT
572741 ATT
1 ATT
572744 ATATTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 6 0.35
18 1 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTTTATATAAAAAT
Found at i:572729 original size:17 final size:17
Alignment explanation
Indices: 572710--572743 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
572700 ATAATATAAT
572710 TTTTTTA-AT-AAAATA
1 TTTTTTATATAAAAATA
572725 TTTTTTATATAAAAATA
1 TTTTTTATATAAAAATA
572742 TT
1 TT
572744 ATATTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 2 0.12
17 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTTATATAAAAATA
Found at i:572899 original size:36 final size:37
Alignment explanation
Indices: 572842--572911 Score: 117
Period size: 36 Copynumber: 1.9 Consensus size: 37
572832 TTTCGTCCTA
572842 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
572879 CTAGGATTC-AACTC-CTAAAAATAGGATAGAATT
1 CTAGGATTCAAACTCTC-AAAAATAGGATAGAATT
572912 TTTCTATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
35 1 0.03
36 22 0.69
37 9 0.28
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:574972 original size:21 final size:21
Alignment explanation
Indices: 574928--574972 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
574918 TGCATTCTTG
* **
574928 CATTTTTTGCATCTTCATCTA
1 CATTTTTAGCATCTTCATAAA
*
574949 CATTTTTAGCATTTTCATAAA
1 CATTTTTAGCATCTTCATAAA
574970 CAT
1 CAT
574973 GAAATTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (21 bp):
CATTTTTAGCATCTTCATAAA
Found at i:576071 original size:211 final size:210
Alignment explanation
Indices: 575668--576094 Score: 766
Period size: 211 Copynumber: 2.0 Consensus size: 210
575658 GATACAGTTT
575668 GGGGCATCTCGCCAGGAGCCTGAACATTGAGACATGTTGGGAGCAAGGAGAAGAAAAATAATTCA
1 GGGGCATCTCGCCAGGAGCCTGAACATTGAGACATGTTGGGAGCAAGGAGAAGAAAAATAATTCA
575733 TTCGAAATAATTCTCATGCATTAATTGCACTGTTTTCATGTGAATAGAATTAATCTGAAAATCTA
66 TTCGAAATAATTCTCATGCATTAATTGCACTGTTTTCATGTGAATAGAATTAATCTGAAAATCTA
*
575798 TCCCCCTGGGGATACCTCTCTGTGAAGACTTACATATATGAAATGATGAACGCTTTCTTTCTTTA
131 TCCCCCTGGGGATACCTCTCTGTGAAGACTTACATATATGAAATGATGAACG-TGTCTTTCTTTA
575863 TCCCTTCACAACAGGA
195 TCCCTTCACAACAGGA
575879 GGGGCATCTCGCCAGGAGCCTGAACATTGAGACATGTTGGGAGCAAGGAGAAGAAAAATAATTCA
1 GGGGCATCTCGCCAGGAGCCTGAACATTGAGACATGTTGGGAGCAAGGAGAAGAAAAATAATTCA
575944 TTCGAAATAATTCTATCATGCATTAATTGCACTGTTTTCATGTGAATAGAATTAATCCTGAAAAT
66 TTCGAAATAATTC--TCATGCATTAATTGCACTGTTTTCATGTGAATAGAATTAAT-CTGAAAAT
*
576009 CTATCCCCCTGGGGATACCTCTTCTGTGAAGACTTACATATATG-AATGATGAACGGCTTTCTTT
128 CTATCCCCCTGGGGATACCTC-TCTGTGAAGACTTACATATATGAAATGATGAAC-G-TGTCTTT
576073 CTTTATCCCTTCACAACAGGA
190 CTTTATCCCTTCACAACAGGA
576094 G
1 G
576095 AAAATATATA
Statistics
Matches: 211, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
211 78 0.37
213 41 0.19
214 39 0.18
215 53 0.25
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (210 bp):
GGGGCATCTCGCCAGGAGCCTGAACATTGAGACATGTTGGGAGCAAGGAGAAGAAAAATAATTCA
TTCGAAATAATTCTCATGCATTAATTGCACTGTTTTCATGTGAATAGAATTAATCTGAAAATCTA
TCCCCCTGGGGATACCTCTCTGTGAAGACTTACATATATGAAATGATGAACGTGTCTTTCTTTAT
CCCTTCACAACAGGA
Found at i:576154 original size:16 final size:17
Alignment explanation
Indices: 576118--576155 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
576108 CTTGCGTCCC
576118 TTTTGAGCCTATAGTAT
1 TTTTGAGCCTATAGTAT
576135 TTTTGAGCCTATAGTAT
1 TTTTGAGCCTATAGTAT
576152 TTTT
1 TTTT
576156 TTCTTCTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.53
Consensus pattern (17 bp):
TTTTGAGCCTATAGTAT
Found at i:576339 original size:22 final size:21
Alignment explanation
Indices: 576307--576357 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
576297 CAAAAAGGGC
*
576307 AAAAAGAAAAATGA-AAGAAGCA
1 AAAAAGAAAAA-AACAAGAA-CA
*
576329 AAAAAGGAAAAAACAAGAACA
1 AAAAAGAAAAAAACAAGAACA
576350 AAAAAGAA
1 AAAAAGAA
576358 GAACAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.76, C:0.06, G:0.16, T:0.02
Consensus pattern (21 bp):
AAAAAGAAAAAAACAAGAACA
Found at i:576354 original size:13 final size:13
Alignment explanation
Indices: 576336--576366 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
576326 GCAAAAAAGG
576336 AAAAAACAAGAAC
1 AAAAAACAAGAAC
*
576349 AAAAAAGAAGAAC
1 AAAAAACAAGAAC
576362 AAAAA
1 AAAAA
576367 TAAAAAGGGA
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:0.81, C:0.10, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAACAAGAAC
Found at i:577850 original size:37 final size:37
Alignment explanation
Indices: 577757--577865 Score: 159
Period size: 35 Copynumber: 3.0 Consensus size: 37
577747 GTGCTCACCA
577757 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
577793 TTGTCT-TCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
577829 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
577866 ATTGAAAACA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 24 0.37
36 15 0.23
37 23 0.35
38 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:577916 original size:84 final size:84
Alignment explanation
Indices: 577820--577987 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
577810 TTTCCCTTGA
577820 AACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTTCCTTG
1 AACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTTCCTTG
577885 AAATGAGTTTTATCTCTCT
66 AAATGAGTTTTATCTCTCT
577904 AACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTTCCTTG
1 AACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTTCCTTG
577969 AAATGAGTTTTATCTCTCT
66 AAATGAGTTTTATCTCTCT
577988 TGAGATAGTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (84 bp):
AACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTTCCTTG
AAATGAGTTTTATCTCTCT
Found at i:578044 original size:36 final size:37
Alignment explanation
Indices: 577976--578045 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 37
577966 TTGAAATGAG
* *
577976 TTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
*
578013 TTTT-TCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
578046 TAAACATTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.41
Consensus pattern (37 bp):
TTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:578128 original size:37 final size:37
Alignment explanation
Indices: 578061--578147 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
578051 ATTGGAAACA
** *
578061 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
578097 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
578134 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
578148 TAAACATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 12 0.26
37 32 0.70
38 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
Found at i:578168 original size:102 final size:102
Alignment explanation
Indices: 577904--578248 Score: 595
Period size: 101 Copynumber: 3.4 Consensus size: 102
577894 TTATCTCTCT
* *
577904 AACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTTCCTTG
1 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
* *
577969 AAATGAGTTTTATCTCTCTTGAGATAGTTTCCCTTGA
66 AAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
*
578006 AACAAAATTTT-TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGGAAACATTTCCCTTG
1 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
578070 AAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
66 AAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
* *
578107 AACAAAATTTTGTCTCCCTTGAGATAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTG
1 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
* *
578172 AAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGA
66 AAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
578209 AAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
578249 CAAAACCTTT
Statistics
Matches: 231, Mismatches: 11, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
101 132 0.57
102 99 0.43
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
AAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
Found at i:578209 original size:36 final size:36
Alignment explanation
Indices: 578162--578248 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
578152 CATTGAAAAC
** * *
578162 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
*
578198 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
578234 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
578249 CAAAACCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:578339 original size:67 final size:67
Alignment explanation
Indices: 578190--578348 Score: 232
Period size: 67 Copynumber: 2.4 Consensus size: 67
578180 TTCGTCTCTC
** *
578190 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
578255 CT
66 CT
* *
578257 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
578322 CT
66 CT
*
578324 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
578349 ATTTCGTTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 78 0.94
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
CT
Found at i:579119 original size:109 final size:109
Alignment explanation
Indices: 578927--579398 Score: 542
Period size: 109 Copynumber: 4.4 Consensus size: 109
578917 TAGCTAGAGT
* * * * *
578927 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAA-TAATAATTTCCCAATTTCGGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
*
578991 ATTTCAACTCCATGACGGAGGATATCGTGCTACCCGAGACAACA
66 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* *
579035 CAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
*
579100 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGAAAACA
66 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* * ** * **
579144 CAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAACTTTTCAGTTTCA-TCCGC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAAC-C
* * *
579208 GATTTCAACTCCACGATGGAGGATATCGTGCCACTCGAGACAACA
65 GATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* ** * ** * * * *
579253 CAAGTTCAACTTCACAATGAAGGGACAACTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
* * * * *
579318 ATTTCAATTTCAC-AGCGAAGGATAT--TG-GACTCGAGACAACA
66 ATTTCAACTCCACGA-CGGAGGATATCGTGCTACCCGAGACAACA
* * * *
579359 CAAGTTCAACTCCACAATGAAGTGACGGCTGATTGTCAAC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
579399 AAGATTTCGT
Statistics
Matches: 314, Mismatches: 46, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
106 48 0.15
107 2 0.01
108 39 0.12
109 224 0.71
110 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (109 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
Found at i:579324 original size:218 final size:213
Alignment explanation
Indices: 578927--579555 Score: 553
Period size: 218 Copynumber: 2.9 Consensus size: 213
578917 TAGCTAGAGT
* *
578927 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAATAATAATTTCCCAATTTCGGAACCGA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAACAATTTCCCAATTTC-GAACCGA
* *
578992 TTTCAACTCCATGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGAAG
65 TTTCAACTCCACGACGGAGGATATCGTGCCACCCGAGACAACACAAGTTCAACTTCACAACGAAG
*** * * * *
579057 GGACGGTTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCGATTTCAACTCCAC-GACGGAGG
130 GGACAACTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTCCACAG-CGAAGG
*
579121 ATATCGTGCTACCCGAGAAAACA
194 ATAT--TG-GACCCGAGAAAACA
* * * *
579144 CAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAACTTT-TCAGTTTC-ATCCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAT-AACAA-TTTCCCAATTTCGA-AC-
* * *
579207 CGATTTCAACTCCACGATGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAATG
62 CGATTTCAACTCCACGACGGAGGATATCGTGCCACCCGAGACAACACAAGTTCAACTTCACAACG
** * * * * *
579272 AAGGGACAACTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTTCAATTTCACAGCGAA
127 AAGGGACAACTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTCCACAGCGAA
* *
579337 GGATATTGGACTCGAGACAACA
192 GGATATTGGACCCGAGAAAACA
* * * * * * * * ** *
579359 CAAGTTCAACTCCACAATGAAGTGACGGCTGATTGTCAACAA-GATTT--C-GTTTAGAGTCAAT
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAACAATTTCCCAATTTCGAACCGAT
* * * * * *
579420 TTCAACTTCAC-AGCGAAGGATAT--TAG--ACTCGAGACAGCACAAGCTCAACTTCACAGCGAA
66 TTCAACTCCACGA-CGGAGGATATCGT-GCCACCCGAGACAACACAAGTTCAACTTCACAACGAA
* ** ** * *** * *
579480 GGGGCGGCTGACTGTCAACAAACAATTTCCCCGGTTCCAGAACCAAATTTCAACTTCACAGCGGA
129 GGGACAACTGGTTGTCAACAAACAACTT-CCAAATTCCAGAACC-AATTTCAACTCCACAGCGAA
579545 GGATATTGGAC
192 GGATATTGGAC
579556 TCGGAACAAT
Statistics
Matches: 342, Mismatches: 60, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
206 52 0.15
207 10 0.03
208 31 0.09
209 21 0.06
210 4 0.01
211 2 0.01
212 3 0.01
213 1 0.00
214 2 0.01
215 45 0.13
216 3 0.01
217 39 0.11
218 125 0.37
219 4 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (213 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAACAATTTCCCAATTTCGAACCGAT
TTCAACTCCACGACGGAGGATATCGTGCCACCCGAGACAACACAAGTTCAACTTCACAACGAAGG
GACAACTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTCCACAGCGAAGGAT
ATTGGACCCGAGAAAACA
Found at i:579395 original size:106 final size:104
Alignment explanation
Indices: 579025--579558 Score: 400
Period size: 109 Copynumber: 5.0 Consensus size: 104
579015 TCGTGCTACC
* * * * * ** *
579025 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACGAACAACTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAAAC-ATTTTTC-GT
* * * * * * *
579090 TCCAGAACCGATTTCAACTCCAC-GACGGAGGATATCGTGCTACC
64 TTCAGAGCCAATTTCAACTTCACAG-CGAAGGATAT--TG-GACT
* * * * ** *
579134 CGAGAAAACACAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAACTTTTCAGT
1 CGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAAAC-ATTTTTC-GT
** * * *
579199 TTCA-TCCGCGATTTCAACTCCACGATG-G-AGGATATCGTGCCACT
64 TTCAGAGC-CAATTTCAACTTCAC-A-GCGAAGGATAT--TG-GACT
** * *
579243 CGAGACAACACAAGTTCAACTTCACAATGAAGGGACAACTGGTTGTCAACAAACATTTTTCAAAT
1 CGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAAACATTTTTC--GT
*
579308 TTCAGAGCCAATTTCAATTTCACAGCGAAGGATATTGGACT
64 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * *
579349 CGAGACAACACAAGTTCAACTCCACAATGAAGTGACGGCTGATTGTCAAC-AAGA--TTTCGTTT
1 CGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAAACATTTTTCGTTT
* *
579411 -AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACT
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * ** * * **
579449 CGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCCGG
1 CGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAAAC-ATTT-TTC-G
* * *
579514 TTCCAGAACCAAATTTCAACTTCACAGCGGAGGATATTGGACT
63 TTTCAGAGCC-AATTTCAACTTCACAGCGAAGGATATTGGACT
579557 CG
1 CG
579559 GAACAATATT
Statistics
Matches: 356, Mismatches: 53, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
100 77 0.22
101 5 0.01
102 1 0.00
103 4 0.01
104 1 0.00
105 4 0.01
106 51 0.14
107 7 0.02
108 41 0.12
109 162 0.46
110 2 0.01
112 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (104 bp):
CGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAAACATTTTTCGTTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
Found at i:579462 original size:100 final size:103
Alignment explanation
Indices: 578927--579558 Score: 379
Period size: 109 Copynumber: 5.9 Consensus size: 103
578917 TAGCTAGAGT
* * * * * * * * *
578927 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAATAATAATTTCCCAATTTCGGAACCGA
1 CAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAA-CATTT-TCAATTTCAGAGCCAA
* *
578992 TTTCAAC-TC-CATGACGGAGGATATCGT-GCTACCCGAGACAACA
64 TTTCAACTTCACA-G-CGAAGGATAT--TAG--ACTCGAGACAACA
* * * ** * * *
579035 CAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCG
1 CAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAAC-AAC-A-TTTTCAATTTCAGAGCCA
* * * *
579100 ATTTCAACTCCAC-GACGGAGGATATCGT-GCTACCCGAGAAAACA
63 ATTTCAACTTCACAG-CGAAGGATAT--TAG--ACTCGAGACAACA
* * * * * **
579144 CAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAACTTTTCAGTTTCA-TCCGC
1 CAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAA-CAAC-A-TTTTCAATTTCAGAGC-C
* *
579208 GATTTCAACTCCACGATG-G-AGGATATCGT-GCCACTCGAGACAACA
62 AATTTCAACTTCAC-A-GCGAAGGATAT--TAG--ACTCGAGACAACA
** *
579253 CAAGTTCAACTTCACAATGAAGGGACAACTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAAC-AACA-TTTTC-AATTTCAGAGCCA
* *
579318 ATTTCAATTTCACAGCGAAGGATATTGGACTCGAGACAACA
63 ATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACA
* * * * *
579359 CAAGTTCAACTCCACAATGAAGTGACGGCTGATTGTCAACAAGA-TTTC-GTTT-AGAGTCAATT
1 CAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAACATTTTCAATTTCAGAGCCAATT
*
579421 TCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCA
66 TCAACTTCACAGCGAAGGATATTAGACTCGAGACAACA
* ** * * * ** * *
579459 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCCGGTTCCAGAACC
1 CAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAAC-AAC-ATTT--TCAATTTCAGAGCC
* *
579524 AAATTTCAACTTCACAGCGGAGGATATTGGACTCG
62 -AATTTCAACTTCACAGCGAAGGATATTAGACTCG
579559 GAACAATATT
Statistics
Matches: 442, Mismatches: 58, Indels: 48
0.81 0.11 0.09
Matches are distributed among these distances:
100 77 0.17
101 5 0.01
102 1 0.00
103 6 0.01
105 4 0.01
106 51 0.12
107 6 0.01
108 79 0.18
109 206 0.47
110 5 0.01
111 1 0.00
112 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (103 bp):
CAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAACAACATTTTCAATTTCAGAGCCAATT
TCAACTTCACAGCGAAGGATATTAGACTCGAGACAACA
Found at i:580076 original size:36 final size:37
Alignment explanation
Indices: 580019--580088 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 37
580009 TTTCGTCCTA
580019 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
*
580056 CTAGGATTC-AACTC-CTAAAAATAGGATATAATT
1 CTAGGATTCAAACTCTC-AAAAATAGGATAGAATT
580089 TTTCTATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 1 0.03
36 21 0.68
37 9 0.29
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:581363 original size:28 final size:28
Alignment explanation
Indices: 581290--581356 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
581280 TTGAATTATT
581290 TATAAAAAGTTTAAAATTTAAAATTAAA
1 TATAAAAAGTTTAAAATTTAAAATTAAA
581318 TATAAAAAGTTTAAAATTTAAAATTAAA
1 TATAAAAAGTTTAAAATTTAAAATTAAA
581346 TATAAAAAGTT
1 TATAAAAAGTT
581357 GAGAATTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (28 bp):
TATAAAAAGTTTAAAATTTAAAATTAAA
Found at i:593967 original size:18 final size:18
Alignment explanation
Indices: 593944--593981 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
593934 ATTCTCTTAT
*
593944 TTTATTAAATTACTTTTA
1 TTTATTAAATCACTTTTA
*
593962 TTTATTTAATCACTTTTA
1 TTTATTAAATCACTTTTA
593980 TT
1 TT
593982 ACTTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATTAAATCACTTTTA
Found at i:596530 original size:8 final size:8
Alignment explanation
Indices: 596514--596564 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
596504 ATTCCGTATA
596514 TTTTATTT
1 TTTTATTT
596522 TTTT-TTT
1 TTTTATTT
*
596529 TTTCATTT
1 TTTTATTT
596537 TTTTA-TT
1 TTTTATTT
*
596544 TTTCATTT
1 TTTTATTT
596552 TCATTTATTT
1 T--TTTATTT
596562 TTT
1 TTT
596565 CGATCAGGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 12 0.34
8 16 0.46
10 7 0.20
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTATTT
Found at i:596538 original size:15 final size:15
Alignment explanation
Indices: 596514--596563 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
596504 ATTCCGTATA
*
596514 TTTT-ATTTTTTTTT
1 TTTTCATTTTTTTAT
596528 TTTTCATTTTTTTAT
1 TTTTCATTTTTTTAT
596543 TTTTCATTTTCATTTAT
1 TTTTCATTTT--TTTAT
596560 TTTT
1 TTTT
596564 TCGATCAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 4 0.12
15 19 0.59
17 9 0.28
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCATTTTTTTAT
Found at i:596545 original size:21 final size:20
Alignment explanation
Indices: 596513--596564 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
596503 AATTCCGTAT
*
596513 ATTTTATTTTTTTT-TTTTTC
1 ATTTT-TTTTTTTTCATTTTC
596533 ATTTTTTTATTTTTCATTTTC
1 ATTTTTTT-TTTTTCATTTTC
596554 ATTTATTTTTT
1 ATTT-TTTTTT
596565 CGATCAGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.11
20 10 0.36
21 11 0.39
22 4 0.14
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (20 bp):
ATTTTTTTTTTTTCATTTTC
Found at i:597336 original size:159 final size:159
Alignment explanation
Indices: 597014--597336 Score: 621
Period size: 159 Copynumber: 2.0 Consensus size: 159
597004 TTCATCTTCT
597014 CCAACTTAATCGCCATCCCCAAACAAACGCAAAATCATCACCCCTTCTTCTCCTCACCGCCGACG
1 CCAACTTAATCGCCATCCCCAAACAAACGCAAAATCATCACCCCTTCTTCTCCTCACCGCCGACG
597079 GCATAATCGAAAAACTTACTCGCTAATGAGTTTCCACGCTATCCGCTCCTCTCTACTCCATGATG
66 GCATAATCGAAAAACTTACTCGCTAATGAGTTTCCACGCTATCCGCTCCTCTCTACTCCATGATG
*
597144 GTGCACACGCAAAACCAACCCGACAACCT
131 GTGCACACGCAAAACCAACCCGACAACCG
597173 CCAACTTAATCGCCATCCCCAAACAAACGCAAAATCATCACCCCTTCTTCTCCTCACCGCCGACG
1 CCAACTTAATCGCCATCCCCAAACAAACGCAAAATCATCACCCCTTCTTCTCCTCACCGCCGACG
597238 GCATAATCGAAAAACTCTACTCGCTAATGAGTTTCCACGCTATCCGCTCCTCTCTACTCCATGAT
66 GCATAATCGAAAAACT-TACTCGCTAATGAGTTTCCACGCTATCCGCTCCTCTCTACTCCATGAT
597303 GGTGCACACGCAAAACCAACCCGACAA-CG
130 GGTGCACACGCAAAACCAACCCGACAACCG
597332 CCAAC
1 CCAAC
597337 GCTTCTCCGC
Statistics
Matches: 162, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
159 87 0.54
160 75 0.46
ACGTcount: A:0.30, C:0.39, G:0.11, T:0.20
Consensus pattern (159 bp):
CCAACTTAATCGCCATCCCCAAACAAACGCAAAATCATCACCCCTTCTTCTCCTCACCGCCGACG
GCATAATCGAAAAACTTACTCGCTAATGAGTTTCCACGCTATCCGCTCCTCTCTACTCCATGATG
GTGCACACGCAAAACCAACCCGACAACCG
Found at i:601268 original size:18 final size:18
Alignment explanation
Indices: 601245--601281 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
601235 AAGTATTGAT
601245 ACTCTATAAGTAATATCG
1 ACTCTATAAGTAATATCG
601263 ACTCTATAAGTAATATCG
1 ACTCTATAAGTAATATCG
601281 A
1 A
601282 TACTACCGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (18 bp):
ACTCTATAAGTAATATCG
Found at i:605421 original size:15 final size:15
Alignment explanation
Indices: 605389--605428 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
605379 GGGCAAATCC
*
605389 GGTACCCGGATTTTCG
1 GGTACCC-GATTTCCG
605405 GGTACCCGATTTCCG
1 GGTACCCGATTTCCG
605420 GGTACCCGA
1 GGTACCCGA
605429 AACTTCCGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (15 bp):
GGTACCCGATTTCCG
Found at i:606371 original size:83 final size:83
Alignment explanation
Indices: 606149--606377 Score: 221
Period size: 83 Copynumber: 2.8 Consensus size: 83
606139 AAAATGCCGT
* * * * * ** *
606149 AATAGAGTAGTAATTTAGCGACGTTT-TTATACAAATGCCACAACAGGGTTGTTTATAGTGGCGT
1 AATAGAGAAGTAATTTAGCGGCGTTTATCAAACAAACGCCGTAATAGGGTTGTTTATAGTGGCGT
606213 TTGTCCAACAAACGACGC
66 TTGTCCAACAAACGACGC
* * *
606231 TATAGAGAAGTAATTTAGCGGCGTTTATCAAACAAACGCCGTAATAGGGATGCTTATAGTGGCGT
1 AATAGAGAAGTAATTTAGCGGCGTTTATCAAACAAACGCCGTAATAGGGTTGTTTATAGTGGCGT
* * *
606296 TTGTGCAA-AAATTGCCGC
66 TTGTCCAACAAA-CGACGC
* * ** * * * *
606314 AATAGAGTAA-TAATTTAGCGGTGTTTGTCGTACGATCGCCGTAATATGTTTGTTTATAGTGGCG
1 AATAGAG-AAGTAATTTAGCGGCGTTTATCAAACAAACGCCGTAATAGGGTTGTTTATAGTGGCG
606378 ATTTTATAAA
Statistics
Matches: 119, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
82 26 0.22
83 91 0.76
84 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (83 bp):
AATAGAGAAGTAATTTAGCGGCGTTTATCAAACAAACGCCGTAATAGGGTTGTTTATAGTGGCGT
TTGTCCAACAAACGACGC
Found at i:606832 original size:21 final size:20
Alignment explanation
Indices: 606808--606846 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
606798 TCTGCTTTCG
606808 ATAGAAAAATAATAGCTTTGA
1 ATAGAAAAAT-ATAGCTTTGA
* *
606829 ATAGGAAAGTATAGCTTT
1 ATAGAAAAATATAGCTTT
606847 TGAAAACCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (20 bp):
ATAGAAAAATATAGCTTTGA
Found at i:609014 original size:3 final size:3
Alignment explanation
Indices: 609006--609064 Score: 91
Period size: 3 Copynumber: 19.0 Consensus size: 3
608996 CAGTTTGCTT
*
609006 TTA TTA TTA TTA TTA TTA TTA TTA TACA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA
609053 TTA TTA TTA TTA
1 TTA TTA TTA TTA
609065 AATAAATATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 47 0.90
4 5 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:609038 original size:19 final size:19
Alignment explanation
Indices: 609014--609064 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
609004 TTTTATTATT
609014 ATTATTATTATTATTATAC
1 ATTATTATTATTATTATAC
**
609033 ATTATTATTATTATTATTT
1 ATTATTATTATTATTATAC
609052 ATTATTATTATTA
1 ATTATTATTATTA
609065 AATAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTATTATTATTATTATAC
Found at i:609557 original size:50 final size:47
Alignment explanation
Indices: 609477--609587 Score: 168
Period size: 50 Copynumber: 2.3 Consensus size: 47
609467 GGGAGCAACC
*
609477 AACAGCAAACCCAAAATAGATGAGCAACAGGAGCGACAGACAACAACGAGG
1 AACA-CAAA-CCAAAATAGAAGAGCAACAGGAGCGACAGACAAC-ACGA-G
609528 AACACAAACCAAAATAGAGAGAGCAACAGGAGCGACAGACAACACGAG
1 AACACAAACCAAAATAGA-AGAGCAACAGGAGCGACAGACAACACGAG
609576 AACACAAACCAA
1 AACACAAACCAA
609588 CAACGACAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
48 13 0.22
49 14 0.24
50 27 0.47
51 4 0.07
ACGTcount: A:0.52, C:0.24, G:0.21, T:0.03
Consensus pattern (47 bp):
AACACAAACCAAAATAGAAGAGCAACAGGAGCGACAGACAACACGAG
Found at i:609599 original size:50 final size:50
Alignment explanation
Indices: 609498--609602 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 50
609488 CAAAATAGAT
* *
609498 GAGCAACAGGAGCGACAGACAACAACGAGGAACACAAACCAAAATAGAGA
1 GAGCAACAGGAGCGACAGACAACAACGAGGAACACAAACCAAAAGACAGA
609548 GAGCAACAGGAGCGACAGACAAC-ACGA-GAACACAAACCAACAACGACAGA
1 GAGCAACAGGAGCGACAGACAACAACGAGGAACACAAACCAA-AA-GACAGA
609598 GAGCA
1 GAGCA
609603 GAGTGAACCC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
48 13 0.25
49 6 0.12
50 32 0.63
ACGTcount: A:0.50, C:0.25, G:0.24, T:0.01
Consensus pattern (50 bp):
GAGCAACAGGAGCGACAGACAACAACGAGGAACACAAACCAAAAGACAGA
Found at i:610051 original size:12 final size:11
Alignment explanation
Indices: 610031--610093 Score: 78
Period size: 11 Copynumber: 5.8 Consensus size: 11
610021 TTATTTACAA
610031 TATTATTTTAT
1 TATTATTTTAT
610042 TATTACTTTTA-
1 TATTA-TTTTAT
*
610053 TA-T-TTTAAT
1 TATTATTTTAT
610062 TATTATTTTAAT
1 TATTATTTT-AT
610074 TATTATTTTAT
1 TATTATTTTAT
610085 TATTATTTT
1 TATTATTTT
610094 TATCTTAGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
8 4 0.09
9 2 0.04
10 2 0.04
11 21 0.47
12 16 0.36
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:610063 original size:20 final size:18
Alignment explanation
Indices: 610034--610096 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
610024 TTTACAATAT
610034 TATTTTATTATTACTTTTA
1 TATTTTATTATTA-TTTTA
610053 TATTTTAATTATTATTTTA
1 TATTTT-ATTATTATTTTA
610072 -ATTATTATT-TTATTATTA
1 TATT-TTATTATTATT-TTA
610090 T-TTTTAT
1 TATTTTAT
610097 CTTAGTCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 9 0.22
18 11 0.28
19 13 0.32
20 7 0.17
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTTTATTATTATTTTA
Found at i:610076 original size:23 final size:23
Alignment explanation
Indices: 610031--610093 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
610021 TTATTTACAA
610031 TATTATTTTATTATTACTTTT-A-
1 TATTATTTTATTATTA-TTTTAAT
*
610053 TA-T-TTTAATTATTATTTTAAT
1 TATTATTTTATTATTATTTTAAT
610074 TATTATTTTATTATTATTTT
1 TATTATTTTATTATTATTTT
610094 TATCTTAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 4 0.11
20 11 0.31
21 3 0.09
22 3 0.09
23 14 0.40
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTATTTTATTATTATTTTAAT
Found at i:610096 original size:12 final size:12
Alignment explanation
Indices: 610053--610093 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
610043 ATTACTTTTA
610053 TATTTTAATTAT
1 TATTTTAATTAT
610065 TATTTTAATTAT
1 TATTTTAATTAT
610077 TATTTT-ATTAT
1 TATTTTAATTAT
610088 TATTTT
1 TATTTT
610094 TATCTTAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:610314 original size:22 final size:22
Alignment explanation
Indices: 610272--610345 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 22
610262 CATTTTCTGA
610272 TATTTTTAAATAAATAAATATTT
1 TATTTTT-AATAAATAAATATTT
610295 TATTTTT-ATAAATTATATATATTT
1 TATTTTTAATAAA-TA-A-ATATTT
* *
610319 TAATTGTTT-TTAGATAAATATTT
1 T-ATT-TTTAATAAATAAATATTT
610342 TATT
1 TATT
610346 AATATTTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
21 5 0.11
22 5 0.11
23 15 0.34
24 8 0.18
25 5 0.11
26 6 0.14
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (22 bp):
TATTTTTAATAAATAAATATTT
Found at i:610756 original size:24 final size:24
Alignment explanation
Indices: 610724--610799 Score: 152
Period size: 24 Copynumber: 3.2 Consensus size: 24
610714 GATTTTTTTC
610724 TTTTAATTGGTACTAACCAATTTA
1 TTTTAATTGGTACTAACCAATTTA
610748 TTTTAATTGGTACTAACCAATTTA
1 TTTTAATTGGTACTAACCAATTTA
610772 TTTTAATTGGTACTAACCAATTTA
1 TTTTAATTGGTACTAACCAATTTA
610796 TTTT
1 TTTT
610800 TTCCTTTCTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.49
Consensus pattern (24 bp):
TTTTAATTGGTACTAACCAATTTA
Found at i:611808 original size:34 final size:34
Alignment explanation
Indices: 611770--611844 Score: 150
Period size: 34 Copynumber: 2.2 Consensus size: 34
611760 CAATTTGCAT
611770 TTTTTTTGTTACATTCACATATTTACATTTTGTA
1 TTTTTTTGTTACATTCACATATTTACATTTTGTA
611804 TTTTTTTGTTACATTCACATATTTACATTTTGTA
1 TTTTTTTGTTACATTCACATATTTACATTTTGTA
611838 TTTTTTT
1 TTTTTTT
611845 TATTTTTACG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63
Consensus pattern (34 bp):
TTTTTTTGTTACATTCACATATTTACATTTTGTA
Found at i:615105 original size:32 final size:32
Alignment explanation
Indices: 615064--615125 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
615054 TCTGGAAATA
615064 AGAAGTATCTCTACAAGATGAGCATAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
615096 AGAAGTATCTCTACAAGATGAGCATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
615126 TCATTTCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:619367 original size:22 final size:23
Alignment explanation
Indices: 619339--619396 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 23
619329 CATATCTACA
*
619339 TTCTTCAAAAATGATAAATTAT-
1 TTCTTCAAAGATGATAAATTATC
*
619361 TTCTTCAAAGATGATAGATTATC
1 TTCTTCAAAGATGATAAATTATC
619384 TT-TTCAAAGATGA
1 TTCTTCAAAGATGA
619397 AAGTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (23 bp):
TTCTTCAAAGATGATAAATTATC
Found at i:620114 original size:45 final size:45
Alignment explanation
Indices: 620050--620211 Score: 254
Period size: 45 Copynumber: 3.6 Consensus size: 45
620040 CTATTTCCCA
620050 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
620095 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
620140 CATCTGTAAGCCCTTCAGTGCA-GAATGTTTTCTAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATG-ATGTTTTCAAAACCTTCGGGT
* * *
620185 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGCCCTTCAGTGCATGATG
620212 ATAAGACCTC
Statistics
Matches: 109, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
44 1 0.01
45 107 0.98
46 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:620393 original size:3 final size:3
Alignment explanation
Indices: 620385--620454 Score: 115
Period size: 3 Copynumber: 23.3 Consensus size: 3
620375 TAGTTTGCTT
*
620385 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TACA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
620430 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
620455 AATATTATAA
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 59 0.94
4 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:620557 original size:3 final size:3
Alignment explanation
Indices: 620549--620616 Score: 104
Period size: 3 Copynumber: 23.0 Consensus size: 3
620539 TAGTTTGCTT
*
620549 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TACA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
620594 TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
620617 AATAAATATT
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.07
3 54 0.90
4 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Done.