Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 5 of 25
Found at i:811877 original size:18 final size:18
Alignment explanation
Indices: 811842--811875 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
811832 TTTGTTTTAA
*
811842 TTTATATTTAAGTAAAAT
1 TTTATATTTAAATAAAAT
811860 TTTAT-TTTAAATAAAA
1 TTTATATTTAAATAAAA
811876 ATAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTATATTTAAATAAAAT
Found at i:811926 original size:30 final size:30
Alignment explanation
Indices: 811885--811978 Score: 100
Period size: 30 Copynumber: 3.2 Consensus size: 30
811875 AATAAATTTT
*
811885 ATTAAGAATTTATATAAATATAAATTAAAA
1 ATTAAGAATTTATTTAAATATAAATTAAAA
* *** * *
811915 ATTAAGTATTTATTTATGCATAGATTAATA
1 ATTAAGAATTTATTTAAATATAAATTAAAA
* *
811945 ATTAAAAATTTATTTGAATATAAATT-AAA
1 ATTAAGAATTTATTTAAATATAAATTAAAA
811974 ATTAA
1 ATTAA
811979 AAATCACGGA
Statistics
Matches: 49, Mismatches: 15, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
29 7 0.14
30 42 0.86
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.41
Consensus pattern (30 bp):
ATTAAGAATTTATTTAAATATAAATTAAAA
Found at i:817125 original size:21 final size:21
Alignment explanation
Indices: 817101--817144 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
817091 GATCAGATAA
*
817101 TTTAAAAGTTTAAATTATTAT
1 TTTAAAAGTTTAAATTAATAT
* *
817122 TTTAAAATTTTATATTAATAT
1 TTTAAAAGTTTAAATTAATAT
817143 TT
1 TT
817145 ATATATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAAAAGTTTAAATTAATAT
Found at i:817176 original size:22 final size:22
Alignment explanation
Indices: 817100--817207 Score: 73
Period size: 22 Copynumber: 5.0 Consensus size: 22
817090 CGATCAGATA
* *
817100 ATTTAAAAGTTTA-AATT-ATT
1 ATTTAAAAATTTATAATTAAAT
*
817120 ATTTTAAAATTT-TATATT-AAT
1 ATTTAAAAATTTATA-ATTAAAT
* *
817141 ATTTATATATTTTATAATTAAAT
1 ATTTA-AAAATTTATAATTAAAT
* *
817164 TTTTAAAAATTTATTATTAAAT
1 ATTTAAAAATTTATAATTAAAT
*
817186 ATATAAATTAATTTA-AATTAAA
1 ATTTAAA--AATTTATAATTAAA
817208 AAAATTATGT
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
20 11 0.16
21 9 0.13
22 27 0.40
23 15 0.22
24 6 0.09
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
ATTTAAAAATTTATAATTAAAT
Found at i:817590 original size:2 final size:2
Alignment explanation
Indices: 817583--817607 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
817573 GAAATTGGGA
817583 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
817608 ACATCTACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:819663 original size:18 final size:17
Alignment explanation
Indices: 819642--819684 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
819632 AAATTAATTA
819642 AAATATAATATAAAATAT
1 AAATATAATATAAAA-AT
*
819660 AAATATATTATAAAAAT
1 AAATATAATATAAAAAT
819677 -AATATAAT
1 AAATATAAT
819685 TATGATACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 7 0.30
17 2 0.09
18 14 0.61
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATAATATAAAAAT
Found at i:820187 original size:26 final size:26
Alignment explanation
Indices: 820151--820210 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
820141 AAAATTTATG
820151 ATATATATTTTAGATATTCATATATTT
1 ATATATATTTTAGATATTCAT-TATTT
* *
820178 ATAT-TATTTTATATATTTATTATTT
1 ATATATATTTTAGATATTCATTATTT
*
820203 -TTTATATT
1 ATATATATT
820211 CATATCACGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.07
25 9 0.31
26 14 0.48
27 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
ATATATATTTTAGATATTCATTATTT
Found at i:820190 original size:16 final size:16
Alignment explanation
Indices: 820179--820210 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
820169 CATATATTTA
820179 TATTATTTTATATATT
1 TATTATTTTATATATT
*
820195 TATTATTTTTTATATT
1 TATTATTTTATATATT
820211 CATATCACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTATTTTATATATT
Found at i:820193 original size:18 final size:18
Alignment explanation
Indices: 820170--820209 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
820160 TTAGATATTC
820170 ATATATTTA-TATTATTTT
1 ATATATTTATTATT-TTTT
820188 ATATATTTATTATTTTTT
1 ATATATTTATTATTTTTT
820206 ATAT
1 ATAT
820210 TCATATCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATATATTTATTATTTTTT
Found at i:821798 original size:17 final size:16
Alignment explanation
Indices: 821751--821811 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
821741 CTCAACCTTC
821751 AATTTATATTTAAAT-A
1 AATTT-TATTTAAATAA
*
821767 AATCTTTAATATAAATTAA
1 AAT-TTT-ATTTAAA-TAA
821786 AATTTTATTTAAAATAA
1 AATTTTATTT-AAATAA
*
821803 AAATTTATT
1 AATTTTATT
821812 GTGACAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 4 0.11
17 22 0.59
18 7 0.19
19 4 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTTATTTAAATAA
Found at i:822874 original size:2 final size:2
Alignment explanation
Indices: 822869--822906 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
822859 CAAGTGTGTG
822869 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
822907 TTTATTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:823816 original size:2 final size:2
Alignment explanation
Indices: 823811--823845 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
823801 TTTTGGTTTA
823811 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
823846 ATAGTAGCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:829919 original size:19 final size:20
Alignment explanation
Indices: 829897--829945 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
829887 AATTATATTA
829897 TAAAAATAATAA-TTTAAAT
1 TAAAAATAATAATTTTAAAT
* * *
829916 T-AAATTATTAATTTTTAAT
1 TAAAAATAATAATTTTAAAT
829935 TAAAAATAATA
1 TAAAAATAATA
829946 CGTATTATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
18 8 0.35
19 8 0.35
20 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAAATAATAATTTTAAAT
Found at i:830822 original size:14 final size:14
Alignment explanation
Indices: 830803--830830 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
830793 TTTTTTAGTT
830803 TTAAATATATTTTA
1 TTAAATATATTTTA
830817 TTAAATATATTTTA
1 TTAAATATATTTTA
830831 AATATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:833466 original size:22 final size:21
Alignment explanation
Indices: 833418--833458 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
833408 AATAATCGAT
*
833418 AATTATTTTGTAAATATTAAA
1 AATTATCTTGTAAATATTAAA
833439 ATATTATCTTGTAAA-ATTAA
1 A-ATTATCTTGTAAATATTAA
833459 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (21 bp):
AATTATCTTGTAAATATTAAA
Found at i:836503 original size:88 final size:88
Alignment explanation
Indices: 836354--836526 Score: 319
Period size: 88 Copynumber: 2.0 Consensus size: 88
836344 CTATGTTGCT
* *
836354 TGGACTCTCTATTTCCCTTCAAGTATTTATATTTGACACTTGCGTCTAATACATATTTAAACATG
1 TGGACTCTCTATTTCCCTTCAAGTATTCATATTTGACACTTGCGTCCAATACATATTTAAACATG
*
836419 GGTATAAAGGTATGATCCATGCC
66 GGTATAAAAGTATGATCCATGCC
836442 TGGACTCTCTATTTCCCTTCAAGTATTCATATTTGACACTTGCGTCCAATACATATTTAAACATG
1 TGGACTCTCTATTTCCCTTCAAGTATTCATATTTGACACTTGCGTCCAATACATATTTAAACATG
836507 GGTATAAAAGTATGATCCAT
66 GGTATAAAAGTATGATCCAT
836527 ACTCCAAATA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (88 bp):
TGGACTCTCTATTTCCCTTCAAGTATTCATATTTGACACTTGCGTCCAATACATATTTAAACATG
GGTATAAAAGTATGATCCATGCC
Found at i:840767 original size:15 final size:16
Alignment explanation
Indices: 840749--840778 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
840739 TTAACAAATA
840749 TTTTAAAAG-TAATTT
1 TTTTAAAAGTTAATTT
840764 TTTTAAAAGTTAATT
1 TTTTAAAAGTTAATT
840779 AATATTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTAAAAGTTAATTT
Found at i:841371 original size:22 final size:21
Alignment explanation
Indices: 841336--841380 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
841326 ATTTATATTT
841336 AATACATATTTAAATATA-AA
1 AATACATATTTAAATATATAA
841356 AATATCATAATTTAAATATATAA
1 AATA-CAT-ATTTAAATATATAA
841379 AA
1 AA
841381 ATAATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 3 0.14
22 11 0.50
23 4 0.18
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (21 bp):
AATACATATTTAAATATATAA
Found at i:844063 original size:30 final size:31
Alignment explanation
Indices: 844009--844066 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
843999 CGACTTTGTG
*
844009 TTTAATTAATAATTAATATTTTTTAATTAAA
1 TTTAATTAATAATAAATATTTTTTAATTAAA
844040 TTTAATT-ATAA-AAATATTTTTTTAATT
1 TTTAATTAATAATAAATA-TTTTTTAATT
844067 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 4 0.16
30 14 0.56
31 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TTTAATTAATAATAAATATTTTTTAATTAAA
Found at i:847208 original size:15 final size:15
Alignment explanation
Indices: 847188--847218 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
847178 TGTCGGTAAT
847188 TAAATTTAAAACATG
1 TAAATTTAAAACATG
*
847203 TAAATTTAAATCATG
1 TAAATTTAAAACATG
847218 T
1 T
847219 CCCCAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
TAAATTTAAAACATG
Found at i:847772 original size:16 final size:16
Alignment explanation
Indices: 847735--847775 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
847725 CATCTACCGG
847735 TAATAT-ATATTTATA
1 TAATATAATATTTATA
847750 T-ATATAATATTTATA
1 TAATATAATATTTATA
847765 TAATATAATAT
1 TAATATAATAT
847776 CATGCTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.17
15 11 0.46
16 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATAATATTTATA
Found at i:848115 original size:13 final size:12
Alignment explanation
Indices: 848088--848120 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
848078 ATATATTTAA
848088 AATATTAT-TAT
1 AATATTATATAT
848099 AATATTATATAAT
1 AATATTATAT-AT
848112 AATATTATA
1 AATATTATA
848121 ACATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 1 0.05
13 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATATTATATAT
Found at i:848308 original size:216 final size:215
Alignment explanation
Indices: 847931--848442 Score: 663
Period size: 216 Copynumber: 2.4 Consensus size: 215
847921 TCTTTTTTTC
* * * * * *
847931 TTCCAAATTTCATAACTAGGTCTTCACATGAGTGCAGCATCTGCCTTTTGCGATTTCATTTTTGG
1 TTCCAAATTTCATAACTAGCTCATCATATGAGTGCAGCATCTGCCTTTTGTGATTTCACTTCTGG
* * *
847996 AAAATTAATTTTATATAGAAAATAGTTATCGCTTATAATCTATATTATTTAAATTCAAGTTTTGA
66 -AAATTAATTTTATATAGAAAATAGTTATCGCTTATAATCTATAGTATCTAAATTCAAGTTCTGA
* *
848061 ATTAATATTAAATATTTATATATTTAAAATATTATTATAATATTATATAATAATATTATAACATA
130 AGTAATATTAAATA-TTATATATTTAAAATATTATTACAATATTATATAATAATATTATAACATA
848126 AATTAAACACTGATATCTATGT
194 AATTAAACACTGATATCTATGT
* *
848148 TTCCAAATTTCATAACTAGCTCACCATATTAGTGCAGCATCTGCCTTTTGTGATTTCACTTCTGG
1 TTCCAAATTTCATAACTAGCTCATCATATGAGTGCAGCATCTGCCTTTTGTGATTTCACTTCTGG
* * * * *
848213 AAATAAATTTTATATAGAAAATATTTATTGGTTATAATCTATAGTATCTAAATTTGAA-TTCTG-
66 AAATTAATTTTATATAGAAAATAGTTATCGCTTATAATCTATAGTATCTAAA-TTCAAGTTCTGA
* * *
848276 AGTAGGTGTTGAGAATA-TATATATTTAAAATATTATTACAATATTATATAATAATATTATAACG
130 AGTA-ATATT-A-AATATTATATATTTAAAATATTATTACAATATTATATAATAATATTATAACA
*
848340 TAAATTAAACATTGATATCTATGT
192 TAAATTAAACACTGATATCTATGT
* * * * * * * *
848364 TTCCAGATTTCATAGCTAGCTCATCATATGACTACAG-ATATACCTTTTGTAATTTCACTCCTGG
1 TTCCAAATTTCATAACTAGCTCATCATATGAGTGCAGCATCTGCCTTTTGTGATTTCACTTCTGG
848428 AAAGTTAATTTTATA
66 AAA-TTAATTTTATA
848443 AAAAATCTGA
Statistics
Matches: 257, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
215 29 0.11
216 162 0.63
217 62 0.24
218 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (215 bp):
TTCCAAATTTCATAACTAGCTCATCATATGAGTGCAGCATCTGCCTTTTGTGATTTCACTTCTGG
AAATTAATTTTATATAGAAAATAGTTATCGCTTATAATCTATAGTATCTAAATTCAAGTTCTGAA
GTAATATTAAATATTATATATTTAAAATATTATTACAATATTATATAATAATATTATAACATAAA
TTAAACACTGATATCTATGT
Found at i:848594 original size:21 final size:22
Alignment explanation
Indices: 848569--848609 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
848559 CCGATATATG
*
848569 TTTAAAATGA-TTATATTTACT
1 TTTAAAATAATTTATATTTACT
*
848590 TTTAAATTAATTTATATTTA
1 TTTAAAATAATTTATATTTA
848610 AAAAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAAATAATTTATATTTACT
Found at i:851275 original size:2 final size:2
Alignment explanation
Indices: 851268--851295 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
851258 ACTATTCCAC
851268 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
851296 TCGGTTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:851391 original size:2 final size:2
Alignment explanation
Indices: 851384--851415 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
851374 AAAACCCTAG
*
851384 CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
851416 TTCCTTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:857279 original size:23 final size:23
Alignment explanation
Indices: 857242--857287 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
857232 CGTTTTCCTT
857242 TTTTAAATTTTTTTAATTT-ATAA
1 TTTTAAATTTTTTT-ATTTGATAA
857265 TTTTATAA-TTTTTTATTTGATAA
1 TTTTA-AATTTTTTTATTTGATAA
857288 ATATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
23 15 0.71
24 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTAAATTTTTTTATTTGATAA
Found at i:857362 original size:18 final size:19
Alignment explanation
Indices: 857322--857363 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
857312 ATTAATCGAT
**
857322 AAATATTTAAAAAAATATT
1 AAATATTTAAAAAAATAGA
*
857341 AAAT-TTTAAAAACATAGA
1 AAATATTTAAAAAAATAGA
857359 AAATA
1 AAATA
857364 AATTTTGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATATTTAAAAAAATAGA
Found at i:857670 original size:21 final size:21
Alignment explanation
Indices: 857646--857687 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
857636 CAAATGCGTT
857646 TTATA-ATTAAAATATCTAAAA
1 TTATAGATT-AAATATCTAAAA
*
857667 TTATAGATTAAATATTTAAAA
1 TTATAGATTAAATATCTAAAA
857688 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TTATAGATTAAATATCTAAAA
Found at i:858022 original size:10 final size:9
Alignment explanation
Indices: 857973--858020 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
857963 TGTAATTTAG
*
857973 ATTTTGAAAA
1 ATTTT-AAAT
857983 ATTTTAAAT
1 ATTTTAAAT
857992 ATTTATCAAAT
1 ATTT-T-AAAT
858003 AATTTTAAAT
1 -ATTTTAAAT
858013 ATTTTAAA
1 ATTTTAAA
858021 ATTAAAATGC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 15 0.44
10 10 0.29
11 5 0.15
12 4 0.12
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:858389 original size:29 final size:27
Alignment explanation
Indices: 858347--858432 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 27
858337 GTTACATCAG
858347 TAAAATAACATTATTTTAATAAATAATTT
1 TAAAAT-A-ATTATTTTAATAAATAATTT
* * *
858376 TAAAATGATATTATTTTGATAATTTATTT
1 TAAAAT-A-ATTATTTTAATAAATAATTT
* * *
858405 CAAAACTAATTACTTTAATTAATAATTT
1 TAAAA-TAATTATTTTAATAAATAATTT
858433 AAATGAGAGA
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
28 15 0.33
29 29 0.64
30 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (27 bp):
TAAAATAATTATTTTAATAAATAATTT
Found at i:858613 original size:2 final size:2
Alignment explanation
Indices: 858608--858632 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
858598 TTTTAAAATT
858608 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
858633 TTTTAAAACC
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:859447 original size:2 final size:2
Alignment explanation
Indices: 859442--859468 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
859432 AAATCCTCTT
859442 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
859469 CTTATTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:859562 original size:23 final size:23
Alignment explanation
Indices: 859532--859583 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
859522 AAGTATATAA
* *
859532 TAAAAAATTAAAAAAAATTAATT
1 TAAAAAATTAAAAAAAAGTAAAT
* *
859555 TAAAAAATTGAAAAATAGTAAAT
1 TAAAAAATTAAAAAAAAGTAAAT
859578 TAAAAA
1 TAAAAA
859584 TTCATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (23 bp):
TAAAAAATTAAAAAAAAGTAAAT
Found at i:860475 original size:14 final size:14
Alignment explanation
Indices: 860439--860477 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
860429 ATTTATTTAT
860439 ATTATTAAA-ATAA
1 ATTATTAAATATAA
860452 A-TA-T-AATATAA
1 ATTATTAAATATAA
860463 ATTATTAAATATAA
1 ATTATTAAATATAA
860477 A
1 A
860478 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
10 2 0.09
11 6 0.27
12 4 0.18
13 2 0.09
14 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTATTAAATATAA
Found at i:860487 original size:24 final size:25
Alignment explanation
Indices: 860433--860503 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 25
860423 TTATTTATTT
*
860433 ATTTATATTATTAAA-ATAAATATA
1 ATTTAAATTATTAAATATAAATATA
*
860457 ATATAAATTATTAAATATAAA-A-A
1 ATTTAAATTATTAAATATAAATATA
860480 ATTTTAAA-TATT-AATATAATATAT
1 A-TTTAAATTATTAAATATAA-ATAT
860504 TAAATATGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 7 0.18
23 7 0.18
24 20 0.51
25 5 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTTAAATTATTAAATATAAATATA
Found at i:860488 original size:16 final size:19
Alignment explanation
Indices: 860449--860510 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
860439 ATTATTAAAA
860449 TAAATATAATATAAATTAT
1 TAAATATAATATAAATTAT
860468 TAAATATAA-A-AAATT-T
1 TAAATATAATATAAATTAT
860484 TAAATATTAATAT-AATATAT
1 TAAATA-TAATATAAAT-TAT
860504 TAAATAT
1 TAAATAT
860511 GTTATGTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
16 7 0.18
17 8 0.21
18 5 0.13
19 11 0.29
20 7 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATATAATATAAATTAT
Found at i:860551 original size:33 final size:35
Alignment explanation
Indices: 860514--860579 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
860504 TAAATATGTT
* *
860514 ATGTTAATTATTTTTTAATA-TT-TTATATTATGA
1 ATGTTAATTATTTATAAATATTTATTATATTATGA
860547 ATGTTAATTATTTATAAATATTTATTATATTAT
1 ATGTTAATTATTTATAAATATTTATTATATTAT
860580 TTTTATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 18 0.62
34 2 0.07
35 9 0.31
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (35 bp):
ATGTTAATTATTTATAAATATTTATTATATTATGA
Found at i:860613 original size:33 final size:35
Alignment explanation
Indices: 860560--860624 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 35
860550 TTAATTATTT
* *
860560 ATAAATATTTATTATATTATTTTTATAATTAATAA
1 ATAAATATTTATTATATTATTATTAAAATTAATAA
860595 ATAAATA-TT-TTATATTATTATTAAAATTAA
1 ATAAATATTTATTATATTATTATTAAAATTAA
860625 CGAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 19 0.68
34 2 0.07
35 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (35 bp):
ATAAATATTTATTATATTATTATTAAAATTAATAA
Found at i:860862 original size:17 final size:16
Alignment explanation
Indices: 860840--860894 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
860830 TATATATTTT
860840 ATTTTATATTAATATAA
1 ATTTTATATT-ATATAA
860857 ATTTTA-ATT-TATTAATA
1 ATTTTATATTATA-T-A-A
860874 ATTTT-TATTATATAA
1 ATTTTATATTATATAA
860889 ATTTTA
1 ATTTTA
860895 AAATATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 13
0.71 0.00 0.29
Matches are distributed among these distances:
14 2 0.06
15 7 0.22
16 5 0.16
17 16 0.50
18 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:861324 original size:2 final size:2
Alignment explanation
Indices: 861317--861345 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
861307 TCCAACTGCC
861317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
861346 TCCCTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:864840 original size:26 final size:26
Alignment explanation
Indices: 864784--864844 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
864774 GAGGTCTCGA
*
864784 TTTAAAAATAAAAATAATTAATAAAT
1 TTTAAAAATAAAAATAAATAATAAAT
* * * * *
864810 ATTAAAATTAAAATTAAATATTATAT
1 TTTAAAAATAAAAATAAATAATAAAT
864836 TTTAAAAAT
1 TTTAAAAAT
864845 TATTACATAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TTTAAAAATAAAAATAAATAATAAAT
Found at i:865125 original size:2 final size:2
Alignment explanation
Indices: 865118--865164 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
865108 CAATTTTGGG
865118 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
865160 GA TA T
1 TA TA T
865165 GGATTAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:865720 original size:2 final size:2
Alignment explanation
Indices: 865715--865751 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
865705 AAACAACAGA
*
865715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
865752 ATGTTTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:869102 original size:3 final size:3
Alignment explanation
Indices: 869094--869124 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
869084 AAAGCAAAAT
869094 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
869125 ACAAAAACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:869665 original size:5 final size:5
Alignment explanation
Indices: 869655--869727 Score: 60
Period size: 5 Copynumber: 14.4 Consensus size: 5
869645 ATATATTTTT
* * *
869655 AATTA AATTA AAATA AA-AA AATTA TAATT- AATTA AATAATA ATTTA
1 AATTA AATTA AATTA AATTA AATTA -AATTA AATTA AAT--TA AATTA
* *
869701 AATTA AATTA AATTA ATTTA AAATA AA
1 AATTA AATTA AATTA AATTA AATTA AA
869728 AATGTGATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
4 7 0.13
5 40 0.73
6 4 0.07
7 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:869721 original size:15 final size:14
Alignment explanation
Indices: 869653--869763 Score: 61
Period size: 15 Copynumber: 7.8 Consensus size: 14
869643 TTATATATTT
869653 TTAATTAAATTAAA
1 TTAATTAAATTAAA
* **
869667 ATAAAAAAATTATAA
1 TTAATTAAATTA-AA
869682 TTAATTAAA-T-AA
1 TTAATTAAATTAAA
869694 -TAATTTAAATTAAA
1 TTAA-TTAAATTAAA
*
869708 TTAAATTAATTTAAA
1 TT-AATTAAATTAAA
* *
869723 ATAA--AAATGTGATAT
1 TTAATTAAAT-T-A-AA
869738 TTAATCTAAATTAAA
1 TTAAT-TAAATTAAA
*
869753 TTTATTAAATT
1 TTAATTAAATT
869764 TATAAAATAA
Statistics
Matches: 72, Mismatches: 13, Indels: 24
0.66 0.12 0.22
Matches are distributed among these distances:
11 3 0.04
12 10 0.14
13 2 0.03
14 21 0.29
15 28 0.39
16 3 0.04
17 1 0.01
18 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (14 bp):
TTAATTAAATTAAA
Found at i:869742 original size:56 final size:54
Alignment explanation
Indices: 869655--869763 Score: 130
Period size: 56 Copynumber: 2.0 Consensus size: 54
869645 ATATATTTTT
*
869655 AATTAAATTAAAATAAAAAAATTATAATTAAT-TAAATAATAATTTAAATTAAATTA
1 AATTAAATTAAAATAAAAAAATGATAATTAATCTAAATAA-AATTT--ATTAAATTA
* ** * *
869711 AATTAATTTAAAATAAAAATGTGATATTTAATCTAAATTAAATTTATTAAATT
1 AATTAAATTAAAATAAAAAAATGATAATTAATCTAAATAAAATTTATTAAATT
869764 TATAAAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 8 0.17
56 32 0.70
57 6 0.13
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (54 bp):
AATTAAATTAAAATAAAAAAATGATAATTAATCTAAATAAAATTTATTAAATTA
Found at i:870182 original size:28 final size:27
Alignment explanation
Indices: 870130--870191 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
870120 CATGTGTCCA
870130 AATTA-TTATATATTATATAAAA-TTT
1 AATTATTTATATATTATATAAAATTTT
* *
870155 AATATATTTATATAATTATATCATATTTT
1 AAT-TATTTATAT-ATTATATAAAATTTT
870184 AATTATTT
1 AATTATTT
870192 TTTAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 3 0.10
26 2 0.06
27 6 0.19
28 14 0.45
29 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTATTTATATATTATATAAAATTTT
Found at i:873662 original size:2 final size:2
Alignment explanation
Indices: 873655--873693 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
873645 CAATTCCTGC
873655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
873694 TTGATTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:875174 original size:2 final size:2
Alignment explanation
Indices: 875167--875196 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
875157 TATCAAAGTC
875167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
875197 AAGTTAGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:875626 original size:2 final size:2
Alignment explanation
Indices: 875619--875645 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
875609 CACTCACATA
875619 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
875646 AGTTTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:876018 original size:2 final size:2
Alignment explanation
Indices: 876011--876035 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
876001 TACATACATG
876011 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
876036 GATTATTAAG
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:876478 original size:2 final size:2
Alignment explanation
Indices: 876471--876504 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
876461 GAATATCAAT
876471 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
876505 TATACAGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:876806 original size:2 final size:2
Alignment explanation
Indices: 876799--876823 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
876789 CTGTCATCCC
876799 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
876824 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:880865 original size:20 final size:20
Alignment explanation
Indices: 880831--880868 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
880821 AAAATTAAAA
**
880831 ATTATTATATTTAATATAAT
1 ATTATTATAAATAATATAAT
880851 ATTATTATAAATAATATA
1 ATTATTATAAATAATATA
880869 TTAATTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTATAAATAATATAAT
Found at i:887795 original size:2 final size:2
Alignment explanation
Indices: 887788--887812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
887778 TTCAAAGAAA
887788 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
887813 ATTATATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:888188 original size:20 final size:21
Alignment explanation
Indices: 888154--888202 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
888144 TTAAATTAAA
888154 TTATATTAAATAA-TTAT-TAT
1 TTAT-TTAAATAATTTATATAT
888174 TTATTTAAATAAATTTATATAT
1 TTATTTAAAT-AATTTATATAT
*
888196 TTTTTTA
1 TTATTTA
888203 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 6 0.24
21 4 0.16
22 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTAAATAATTTATATAT
Found at i:888191 original size:18 final size:19
Alignment explanation
Indices: 888154--888197 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
888144 TTAAATTAAA
*
888154 TTATATTAAATAATTATTAT
1 TTAT-TTAAATAAATATTAT
888174 TTATTTAAATAAAT-TTAT
1 TTATTTAAATAAATATTAT
*
888192 ATATTT
1 TTATTT
888198 TTTTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 9 0.41
20 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTTAAATAAATATTAT
Found at i:888192 original size:34 final size:31
Alignment explanation
Indices: 888121--888193 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 31
888111 TATAAATTTT
*
888121 AATTAAATTAAAAATTATATAATTTAAATTA
1 AATTATATTAAAAATTATATAATTTAAATTA
*
888152 AATTATATTAAATAATTATTATTTATTTAAA-TA
1 AATTATATTAAA-AATTA-TA-TAATTTAAATTA
888185 AATTTATAT
1 AA-TTATAT
888194 ATTTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 11 0.31
32 5 0.14
33 6 0.17
34 14 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
AATTATATTAAAAATTATATAATTTAAATTA
Found at i:888653 original size:14 final size:15
Alignment explanation
Indices: 888636--888664 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
888626 ATTAAAACAC
888636 AACACAA-AAAAATA
1 AACACAATAAAAATA
888650 AACACAATAAAAATA
1 AACACAATAAAAATA
888665 TACAAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.14, G:0.00, T:0.10
Consensus pattern (15 bp):
AACACAATAAAAATA
Found at i:889250 original size:11 final size:11
Alignment explanation
Indices: 889234--889289 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
889224 TCTAGACATG
*
889234 ACATAAATACA
1 ACATAAATAAA
889245 ACATAAATAAA
1 ACATAAATAAA
* *
889256 AAATAATTAAA
1 ACATAAATAAA
889267 ACATAATATAAA
1 ACATAA-ATAAA
889279 A-ATAACATAAA
1 ACATAA-ATAAA
889290 CACGATACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 33 0.87
12 5 0.13
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (11 bp):
ACATAAATAAA
Found at i:889261 original size:22 final size:23
Alignment explanation
Indices: 889236--889289 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
889226 TAGACATGAC
*
889236 ATAAATACAACATAA-ATAAAAA
1 ATAAATAAAACATAATATAAAAA
*
889258 ATAATTAAAACATAATAT-AAAA
1 ATAAATAAAACATAATATAAAAA
889280 ATAACATAAA
1 ATAA-ATAAA
889290 CACGATACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (23 bp):
ATAAATAAAACATAATATAAAAA
Found at i:889423 original size:23 final size:23
Alignment explanation
Indices: 889379--889432 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
889369 CTTTAAATAT
*
889379 ATAAAAAATAATACAAATATAAC
1 ATAAAAATTAATACAAATATAAC
*
889402 ATTAAAAATTAATTA-AAA-ATAAT
1 A-TAAAAATTAA-TACAAATATAAC
889425 ATAAAAAT
1 ATAAAAAT
889433 ATAACATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 7 0.26
23 6 0.22
24 12 0.44
25 2 0.07
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
ATAAAAATTAATACAAATATAAC
Found at i:889433 original size:11 final size:11
Alignment explanation
Indices: 889373--889433 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
889363 TTAATACTTT
889373 AAAT-ATATAAA
1 AAATAATAT-AA
*
889384 AAATAATACAA
1 AAATAATATAA
* *
889395 ATATAACATTAA
1 AAATAATA-TAA
889407 AAATTAAT-TAA
1 AAA-TAATATAA
889418 AAATAATATAA
1 AAATAATATAA
889429 AAATA
1 AAATA
889434 TAACATGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 4 0.10
11 26 0.65
12 7 0.17
13 3 0.08
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATAATATAA
Found at i:889623 original size:18 final size:18
Alignment explanation
Indices: 889600--889648 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
889590 AAATTAATTA
889600 AAATATAATATAAA-AAAT
1 AAATATAA-ATAAATAAAT
*
889618 AAATATAACATAAATATAT
1 AAATATAA-ATAAATAAAT
889637 AAATATAAATAA
1 AAATATAAATAA
889649 TATTTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATAAATAAATAAAT
Found at i:889630 original size:23 final size:22
Alignment explanation
Indices: 889565--889648 Score: 62
Period size: 23 Copynumber: 3.6 Consensus size: 22
889555 TTAAATATAC
*
889565 AAAAAATACATAAATC-TAATATT
1 AAAAAATAAATAAA-CATAATA-T
* * *
889588 AAAAATTAATTAAAATATAATAT
1 AAAAAATAAAT-AAACATAATAT
889611 AAAAAATAAATATAACATAAATAT
1 AAAAAATAAATA-AACAT-AATAT
*
889635 ATAAATATAAATAA
1 A-AAAAATAAATAA
889649 TATTTATTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
22 1 0.02
23 22 0.46
24 15 0.31
25 10 0.21
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAAATAAATAAACATAATAT
Found at i:889660 original size:19 final size:18
Alignment explanation
Indices: 889619--889679 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
889609 ATAAAAAATA
* *
889619 AATATAACATAAATATATA
1 AATATAA-ATAAATTTATT
889638 AATATAAATAATATTTATT
1 AATATAAATAA-ATTTATT
*
889657 AATATTATATAAATTTA-T
1 AATA-TAAATAAATTTATT
889675 AATAT
1 AATAT
889680 TTTAAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.03
18 9 0.24
19 21 0.57
20 6 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATAAATAAATTTATT
Found at i:895386 original size:17 final size:18
Alignment explanation
Indices: 895357--895390 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
895347 ATTAAATATT
895357 AATAAATAATATAATTAA
1 AATAAATAATATAATTAA
895375 AATAAA-AATATAATTA
1 AATAAATAATATAATTA
895391 CATCTCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATAATATAATTAA
Found at i:896576 original size:14 final size:14
Alignment explanation
Indices: 896557--896584 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
896547 TAAATTTAAA
896557 AATATTAAAATATT
1 AATATTAAAATATT
896571 AATATTAAAATATT
1 AATATTAAAATATT
896585 TTAATATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATTAAAATATT
Found at i:896748 original size:20 final size:18
Alignment explanation
Indices: 896733--896828 Score: 60
Period size: 18 Copynumber: 5.4 Consensus size: 18
896723 TAATATAAAT
*
896733 ATATTAAAATTTATATTA
1 ATATTAAAATTTATATAA
896751 ATA-T-AAA--TAT-TAA
1 ATATTAAAATTTATATAA
*
896764 TATTTTAAAATTTATATAA
1 -ATATTAAAATTTATATAA
* *
896783 ATATTATAATATATATATAT
1 ATATTA-AA-ATTTATATAA
* *
896803 ATACTAAAA-ATATATAAA
1 ATATTAAAATTTATAT-AA
896821 ATATTAAA
1 ATATTAAA
896829 TTTTTTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
13 2 0.03
14 5 0.08
15 1 0.02
16 6 0.10
17 7 0.11
18 20 0.33
19 7 0.11
20 13 0.21
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTAAAATTTATATAA
Found at i:896760 original size:32 final size:31
Alignment explanation
Indices: 896673--896802 Score: 102
Period size: 32 Copynumber: 4.0 Consensus size: 31
896663 TAATATAAGA
*
896673 TAAAATTATATTAATATGACAAAAATAAA-ATAT
1 TAAAATTATATTAATAT---AAATATAAATATAT
* * *
896706 TTAAATTATAATAGAT-TTAATATAAATATAT
1 TAAAATTATATTA-ATATAAATATAAATATAT
* *
896737 TAAAATTTATATTAATATAAATATTAATATTT
1 TAAAA-TTATATTAATATAAATATAAATATAT
* *
896769 TAAAATTTATATAAATATTATAATATATATATAT
1 TAAAA-TTATATTAATA-TA-AATATAAATATAT
896803 ATACTAAAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
30 7 0.09
31 10 0.13
32 35 0.45
33 14 0.18
34 12 0.15
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (31 bp):
TAAAATTATATTAATATAAATATAAATATAT
Found at i:896805 original size:26 final size:26
Alignment explanation
Indices: 896710--896824 Score: 69
Period size: 25 Copynumber: 4.5 Consensus size: 26
896700 AAATATTTAA
* *
896710 ATTATAATAGATTTA-ATATA-AATAT
1 ATTATAATATATATATATATATAA-AT
* *
896735 ATTAAAATTTATAT-TA-ATATAAAT
1 ATTATAATATATATATATATATAAAT
* * * *
896759 ATTAATATTTTA-AAATTTATATAAAT
1 ATT-ATAATATATATATATATATAAAT
*
896785 ATTATAATATATATATATATACTAAAA
1 ATTATAATATATATATATATA-TAAAT
*
896812 ATATATAAAATAT
1 AT-TATAATATAT
896825 TAAATTTTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
24 9 0.13
25 26 0.38
26 18 0.26
27 6 0.09
28 9 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
ATTATAATATATATATATATATAAAT
Found at i:900597 original size:49 final size:49
Alignment explanation
Indices: 900524--900618 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 49
900514 TAGATACAGG
* * *
900524 TCAAATAAAAATATTCCACGTAAGATAAAGT-AAGAGACTTCCGAAAGCA
1 TCAAATAAAAACATTCCACATAAGATAAAGTGAA-AGAATTCCGAAAGCA
* *
900573 TCAAATAAAGACATTCCACATAAGATAACGTGAAAGAATTCCGAAA
1 TCAAATAAAAACATTCCACATAAGATAAAGTGAAAGAATTCCGAAA
900619 AATATTCCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 38 0.95
50 2 0.05
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (49 bp):
TCAAATAAAAACATTCCACATAAGATAAAGTGAAAGAATTCCGAAAGCA
Found at i:902028 original size:15 final size:16
Alignment explanation
Indices: 901999--902031 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
901989 AACATCAAAT
901999 CACTCATATTATTGAC
1 CACTCATATTATTGAC
902015 CACTCATA-TATTGAC
1 CACTCATATTATTGAC
902030 CA
1 CA
902032 ATAATTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CACTCATATTATTGAC
Found at i:903599 original size:17 final size:17
Alignment explanation
Indices: 903561--903646 Score: 52
Period size: 16 Copynumber: 5.0 Consensus size: 17
903551 AAATTCAGTA
*
903561 AAAATATTTAAATAT-AT
1 AAAAT-TTTATATATAAT
*
903578 TAAATTTTATAT-TAAAT
1 AAAATTTTATATAT-AAT
*
903595 AAAATATTA-ATATAAT
1 AAAATTTTATATATAAT
* *
903611 AAAATTATATAAAATATAT
1 AAAATTTTAT-ATATA-AT
* *
903630 AATATTTTAAATATAAT
1 AAAATTTTATATATAAT
903647 TATAATAAAA
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
15 1 0.02
16 18 0.35
17 16 0.31
18 8 0.15
19 9 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTTTATATATAAT
Found at i:903641 original size:26 final size:26
Alignment explanation
Indices: 903570--903641 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
903560 AAAAATATTT
*
903570 AAATATATTAA-ATTTTATATTAAATA
1 AAATATA-TAATATTTTAAATTAAATA
* * *
903596 AAATAT-TAATATAATAAAATTATATA
1 AAATATATAATAT-TTTAAATTAAATA
903622 AAATATATAATATTTTAAAT
1 AAATATATAATATTTTAAAT
903642 ATAATTATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 3 0.08
25 2 0.05
26 26 0.70
27 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATATATAATATTTTAAATTAAATA
Found at i:904223 original size:6 final size:6
Alignment explanation
Indices: 904212--904244 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
904202 TAATTTATAA
*
904212 AAATTT AAATTT AAATTT -AATTT AAGTTT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
904245 AATTTAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:904249 original size:32 final size:31
Alignment explanation
Indices: 904199--904300 Score: 87
Period size: 33 Copynumber: 3.1 Consensus size: 31
904189 CGATGTTGTT
*
904199 ATTTAATTTATAAAAATTTAAATTTAAATTTA
1 ATTTAATTTA-AATAATTTAAATTTAAATTTA
* * *
904231 ATTTAAGTTTAAATAATTTAAGTTATAAAATAA
1 ATTTAA-TTTAAATAATTTAAATT-TAAATTTA
* * * *
904264 ATTTACTTTTAAGTATTTTAAATATTTAATTTA
1 ATTTA-ATTTAAATAATTTAAAT-TTAAATTTA
904297 ATTT
1 ATTT
904301 TTAATATTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
32 17 0.31
33 37 0.67
34 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTTAATTTAAATAATTTAAATTTAAATTTA
Found at i:904275 original size:33 final size:32
Alignment explanation
Indices: 904199--904286 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
904189 CGATGTTGTT
* *
904199 ATTTAATTTATAAA-AATTTAAATTTAAATTTA
1 ATTTAATTT-TAAATAATTTAAATTTAAAATAA
* *
904231 ATTTAAGTTTAAATAATTTAAGTTATAAAATAA
1 ATTTAATTTTAAATAATTTAAATT-TAAAATAA
* * *
904264 ATTTACTTTTAAGTATTTTAAAT
1 ATTTAATTTTAAATAATTTAAAT
904287 ATTTAATTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 4 0.09
32 17 0.38
33 24 0.53
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (32 bp):
ATTTAATTTTAAATAATTTAAATTTAAAATAA
Found at i:909605 original size:13 final size:14
Alignment explanation
Indices: 909575--909610 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
909565 ATCTCATAAC
909575 AAAATTATAAATATT
1 AAAATT-TAAATATT
909590 AAAATTTAAA-ATT
1 AAAATTTAAATATT
909603 AAAATTTA
1 AAAATTTA
909611 TTTAAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.52
14 4 0.19
15 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATTTAAATATT
Found at i:909888 original size:2 final size:2
Alignment explanation
Indices: 909881--909909 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
909871 TTCATCACCG
909881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
909910 GATGTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:915611 original size:2 final size:2
Alignment explanation
Indices: 915604--915639 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
915594 TCATTCCTTC
915604 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
915640 TGGCCAGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:931243 original size:2 final size:2
Alignment explanation
Indices: 931236--931279 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
931226 GTTAATGCGA
* *
931236 AT AT AT AT AT AT AT AT AT AA AT AT AA 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
931278 AT
1 AT
931280 TTTACTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:933672 original size:51 final size:52
Alignment explanation
Indices: 933602--934022 Score: 403
Period size: 51 Copynumber: 8.1 Consensus size: 52
933592 ATGGCCATCA
* * * *
933602 TGCTCCTGCTCTGATTGTAGCTGGGCGTGT-TGCAATTGCAAATGGCCAAGC
1 TGCTGCTGTTCTGATTGTAGCTGGGCGTTTCTGCAATTGTAAATGGCCAAGC
** * * **
933653 TGCTGCTGTTCTGGCTGTAGCTGGCCG-TTCTGCAACTGTACGTGGCCAAGC
1 TGCTGCTGTTCTGATTGTAGCTGGGCGTTTCTGCAATTGTAAATGGCCAAGC
933704 TGCTGCTGTTCTGATTGTAGCTGGGC-TTTCTGCAATTGTAAATGGCCAAGC
1 TGCTGCTGTTCTGATTGTAGCTGGGCGTTTCTGCAATTGTAAATGGCCAAGC
* * * * *
933755 TGCGGCTGTTCTGATTGTAGTTGGGCGTTT-TGCAAGTGTAAACGGCCAACC
1 TGCTGCTGTTCTGATTGTAGCTGGGCGTTTCTGCAATTGTAAATGGCCAAGC
* *
933806 TGCTGCTGCTT-TGATTGTAGCTGGGC-TTTCTGCAATTGTAAATGACCCAGC
1 TGCTGCTG-TTCTGATTGTAGCTGGGCGTTTCTGCAATTGTAAATGGCCAAGC
* * * *
933857 TG-TGGCTGTTCTGATTGTAGTTGGGC-ATTCTGCAAGTGTAAACGGCCAAGC
1 TGCT-GCTGTTCTGATTGTAGCTGGGCGTTTCTGCAATTGTAAATGGCCAAGC
* * * *
933908 TGCTGCTGCTGTCTTGATTGTGGCTGGGCG-TCCTGCAACTGTAAATGACCAAGCTGC
1 TGCTGCTG-T-TC-TGATTGTAGCTGGGCGTTTCTGCAATTGTAAATGGCCAA---GC
* * * * *
933965 TGCGGCTGCTGTTTTGATTGTAGCTGGGCG-TCCTGCAACTGTACATGGCCACGC
1 T---GCTGCTGTTCTGATTGTAGCTGGGCGTTTCTGCAATTGTAAATGGCCAAGC
934019 TGCT
1 TGCT
934023 CGTTTTGCTG
Statistics
Matches: 307, Mismatches: 45, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
50 7 0.02
51 211 0.69
52 7 0.02
53 2 0.01
54 34 0.11
57 37 0.12
58 1 0.00
59 1 0.00
60 7 0.02
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.32
Consensus pattern (52 bp):
TGCTGCTGTTCTGATTGTAGCTGGGCGTTTCTGCAATTGTAAATGGCCAAGC
Found at i:933719 original size:102 final size:103
Alignment explanation
Indices: 933602--933967 Score: 463
Period size: 102 Copynumber: 3.6 Consensus size: 103
933592 ATGGCCATCA
* * * *
933602 TGCTCCTGC-TCTGATTGTAGCTGGGCGTGT-TGCAATTGCAAATGGCCAAGCTGCTGCTGTTCT
1 TGCTGCTGCTTCTGATTGTAGCTGGGC-TTTCTGCAATTGTAAATGACCAAGCTGCTGCTGTTCT
** * * * ***
933665 GGCTGTAGCTGGCCGTTCTGCAACTGTACGTGGCCAAGC
65 GATTGTAGTTGGGCGTTCTGCAAGTGTAAACGGCCAAGC
* *
933704 TGCTGCTG-TTCTGATTGTAGCTGGGCTTTCTGCAATTGTAAATGGCCAAGCTGCGGCTGTTCTG
1 TGCTGCTGCTTCTGATTGTAGCTGGGCTTTCTGCAATTGTAAATGACCAAGCTGCTGCTGTTCTG
* *
933768 ATTGTAGTTGGGCGTTTTGCAAGTGTAAACGGCCAACC
66 ATTGTAGTTGGGCGTTCTGCAAGTGTAAACGGCCAAGC
*
933806 TGCTGCTGCTT-TGATTGTAGCTGGGCTTTCTGCAATTGTAAATGACCCAGCTG-TGGCTGTTCT
1 TGCTGCTGCTTCTGATTGTAGCTGGGCTTTCTGCAATTGTAAATGACCAAGCTGCT-GCTGTTCT
*
933869 GATTGTAGTTGGGCATTCTGCAAGTGTAAACGGCCAAGC
65 GATTGTAGTTGGGCGTTCTGCAAGTGTAAACGGCCAAGC
* * * *
933908 TGCTGCTGCTGTCTTGATTGTGGCTGGGCGTCCTGCAACTGTAAATGACCAAGCTGCTGC
1 TGCTGCTGCT-TC-TGATTGTAGCTGGGCTTTCTGCAATTGTAAATGACCAAGCTGCTGC
933968 GGCTGCTGTT
Statistics
Matches: 231, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
101 2 0.01
102 186 0.81
103 3 0.01
105 39 0.17
106 1 0.00
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.32
Consensus pattern (103 bp):
TGCTGCTGCTTCTGATTGTAGCTGGGCTTTCTGCAATTGTAAATGACCAAGCTGCTGCTGTTCTG
ATTGTAGTTGGGCGTTCTGCAAGTGTAAACGGCCAAGC
Found at i:935046 original size:13 final size:13
Alignment explanation
Indices: 935028--935052 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
935018 TATTGGACAT
935028 ATGCTCATACCTA
1 ATGCTCATACCTA
935041 ATGCTCATACCT
1 ATGCTCATACCT
935053 GAATTCGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (13 bp):
ATGCTCATACCTA
Found at i:935975 original size:17 final size:17
Alignment explanation
Indices: 935947--935989 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
935937 ACCTCTTACC
*
935947 TTATATTTATATTATTTT
1 TTATA-TTATATTATATT
935965 TTATATTATATTATATT
1 TTATATTATATTATATT
935982 TTA-ATTAT
1 TTATATTAT
935990 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 14 0.58
18 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTATATTATATT
Found at i:936003 original size:28 final size:29
Alignment explanation
Indices: 935947--936008 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
935937 ACCTCTTACC
* **
935947 TTATA-TTTATATTATTTTTTATATTATA
1 TTATATTTTATATTATTTTTTAAAAAATA
935975 TTATATTTTA-ATTATTTTTTAAAAAATA
1 TTATATTTTATATTATTTTTTAAAAAATA
936003 TT-TATT
1 TTATATT
936009 ACAGAAAGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 22 0.73
29 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATATTTTATATTATTTTTTAAAAAATA
Found at i:936243 original size:36 final size:36
Alignment explanation
Indices: 936193--936271 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
936183 ATAATTTATT
*
936193 ATATTATAATTATATTTAA-AATATTTAATATTTATAAA
1 ATATTTTAA-TATA-TTAATAATATTTAATATTT-TAAA
* *
936231 A-ATTTTAATATATTAATAATTTTTATTATTTTAAA
1 ATATTTTAATATATTAATAATATTTAATATTTTAAA
936266 ATATTT
1 ATATTT
936272 ATTTTTTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
35 9 0.25
36 20 0.56
37 6 0.17
38 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
ATATTTTAATATATTAATAATATTTAATATTTTAAA
Found at i:936261 original size:26 final size:23
Alignment explanation
Indices: 936177--936301 Score: 69
Period size: 26 Copynumber: 5.1 Consensus size: 23
936167 AACCTCATGT
* *
936177 ATTTTTATAATTTATTATATTATA
1 ATTTTTATATTTTAATATATT-TA
*
936201 A---TTATA-TTTAAAATATTTA
1 ATTTTTATATTTTAATATATTTA
*
936220 ATATTTATAAAAATTTTAATATATTAATA
1 AT-TTT-T--ATATTTTAATATATT--TA
*
936249 ATTTTTATTATTTTAAAATATTTA
1 ATTTTTA-TATTTTAATATATTTA
*
936273 TTTTTTATATTTTATATTATATTTTA
1 ATTTTTATATTTTA-A-TATA-TTTA
936299 ATT
1 ATT
936302 ATATTTAATA
Statistics
Matches: 78, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
19 3 0.04
20 9 0.12
21 5 0.06
23 8 0.10
24 11 0.14
25 4 0.05
26 20 0.26
27 11 0.14
28 3 0.04
29 4 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTTATATTTTAATATATTTA
Found at i:936272 original size:17 final size:17
Alignment explanation
Indices: 936201--936279 Score: 72
Period size: 18 Copynumber: 4.5 Consensus size: 17
936191 TTATATTATA
936201 ATTATATTTAAAATATTT
1 ATTAT-TTTAAAATATTT
*
936219 AATATTTATAAAA-ATTTT
1 ATTATTT-TAAAATA-TTT
* * *
936237 AATATATTAATAATTTTT
1 ATTATTTTAA-AATATTT
936255 ATTATTTTAAAATATTT
1 ATTATTTTAAAATATTT
936272 ATT-TTTTA
1 ATTATTTTA
936280 TATTTTATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
16 5 0.10
17 15 0.29
18 31 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATTTTAAAATATTT
Found at i:936283 original size:23 final size:25
Alignment explanation
Indices: 936201--936309 Score: 70
Period size: 26 Copynumber: 4.4 Consensus size: 25
936191 TTATATTATA
936201 ATTATATTTAAAATATT-TAATATTTAT
1 ATTAT-TTTAAAATATTATAAT-TTT-T
** *
936228 AAAAATTTTAATATATTAATAATTTTT
1 -ATTATTTTAAAATATT-ATAATTTTT
*
936255 ATTATTTTAAAATATT-TATTTTTT
1 ATTATTTTAAAATATTATAATTTTT
*
936279 A-TATTTT---ATATTAT-ATTTTA
1 ATTATTTTAAAATATTATAATTTTT
936299 ATTATATTTAA
1 ATTAT-TTTAA
936310 TATTATCATG
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
20 10 0.15
21 4 0.06
22 3 0.05
23 6 0.09
24 8 0.12
26 13 0.20
27 11 0.17
28 6 0.09
29 4 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTTAAAATATTATAATTTTT
Found at i:936304 original size:11 final size:12
Alignment explanation
Indices: 936277--936315 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
936267 TATTTATTTT
936277 TTATATTTTATA
1 TTATATTTTATA
936289 TTATATTTTA-A
1 TTATATTTTATA
*
936300 TTATATTTAATA
1 TTATATTTTATA
936312 TTAT
1 TTAT
936316 CATGCTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:936312 original size:23 final size:21
Alignment explanation
Indices: 936265--936315 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
936255 ATTATTTTAA
936265 AATATT-TATTTTTTATATTT
1 AATATTATATTTTTTATATTT
*
936285 TATATTATATTTTAATTATATTT
1 AATATTATATTTT--TTATATTT
936308 AATATTAT
1 AATATTAT
936316 CATGCTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 6 0.23
23 15 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
AATATTATATTTTTTATATTT
Found at i:941905 original size:11 final size:12
Alignment explanation
Indices: 941889--941921 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
941879 CATATATATA
941889 ATTAAATATT-T
1 ATTAAATATTAT
941900 ATTAAATATTAAT
1 ATTAAATATT-AT
941913 ATTAAATAT
1 ATTAAATAT
941922 ATTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAAATATTAT
Found at i:946249 original size:28 final size:27
Alignment explanation
Indices: 946179--946250 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 27
946169 TTAGGTTCAG
*
946179 TTTT-TAAATATTTTTTACATTTTATA
1 TTTTATAAATATATTTTACATTTTATA
*
946205 TTTTATAAATTAAATTTTA-ATTTTAT-
1 TTTTATAAA-TATATTTTACATTTTATA
946231 TTTTGGATAAATCATATTTT
1 TTTT--ATAAAT-ATATTTT
946251 CCTTTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 8 0.21
27 12 0.32
28 18 0.47
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (27 bp):
TTTTATAAATATATTTTACATTTTATA
Found at i:946593 original size:20 final size:20
Alignment explanation
Indices: 946555--946593 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
946545 ATCTTAAATT
* *
946555 AAATTTAAATTTTTCTATAA
1 AAATTTAAATTATTATATAA
*
946575 AAATTTATATTATTATATA
1 AAATTTAAATTATTATATA
946594 TATATATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATTTAAATTATTATATAA
Found at i:952625 original size:28 final size:28
Alignment explanation
Indices: 952593--952649 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
952583 TGCAAAATCC
952593 ATTTGTTCTTATAGCTTAAATGTTGGAA
1 ATTTGTTCTTATAGCTTAAATGTTGGAA
952621 ATTTGTTCTTATAGCTTAAATGTTGGAA
1 ATTTGTTCTTATAGCTTAAATGTTGGAA
952649 A
1 A
952650 ATCCTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.46
Consensus pattern (28 bp):
ATTTGTTCTTATAGCTTAAATGTTGGAA
Found at i:955320 original size:2 final size:2
Alignment explanation
Indices: 955313--955345 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
955303 TGCAAAAGAA
955313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
955346 CTTCTATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:957791 original size:2 final size:2
Alignment explanation
Indices: 957784--957814 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
957774 ACTTCCCTAA
957784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
957815 GCTAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:959178 original size:12 final size:12
Alignment explanation
Indices: 959161--959195 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
959151 TGTGTTGAAC
*
959161 AATGTAGTTTAA
1 AATGTACTTTAA
959173 AATGTACTTTAA
1 AATGTACTTTAA
*
959185 TATGTACTTTA
1 AATGTACTTTA
959196 GTGGTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (12 bp):
AATGTACTTTAA
Found at i:959481 original size:6 final size:6
Alignment explanation
Indices: 959470--959508 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
959460 TGTCTCCAAA
*
959470 CCTGCT CCTGCT CCTGCT CCTGCT CCTGCT GCTGCT CCT
1 CCTGCT CCTGCT CCTGCT CCTGCT CCTGCT CCTGCT CCT
959509 CAACCAGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.18, T:0.33
Consensus pattern (6 bp):
CCTGCT
Found at i:960670 original size:2 final size:2
Alignment explanation
Indices: 960663--960694 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
960653 TTATGCCTTA
960663 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
960695 CTTTGATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:960889 original size:11 final size:10
Alignment explanation
Indices: 960861--960890 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
960851 CATTGAAAAG
960861 TTTTATAATT
1 TTTTATAATT
960871 TTTTATAATT
1 TTTTATAATT
960881 TTTTAATAAT
1 TTTT-ATAAT
960891 AAATAAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:961848 original size:17 final size:16
Alignment explanation
Indices: 961821--961897 Score: 61
Period size: 17 Copynumber: 4.8 Consensus size: 16
961811 AAATAAATTT
961821 TTATTTAAAATAAAAAA
1 TTATTT-AAATAAAAAA
*
961838 TTGATTTAAATTAAAAAT
1 TT-ATTTAAA-TAAAAAA
* *
961856 TTATTTAAGT-ATAAA
1 TTATTTAAATAAAAAA
*
961871 TTA--AAAATAAAAAA
1 TTATTTAAATAAAAAA
961885 TTAATTTAAATAA
1 TT-ATTTAAATAA
961898 TTAAATATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
13 3 0.07
14 6 0.13
15 7 0.15
16 1 0.02
17 17 0.37
18 12 0.26
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTATTTAAATAAAAAA
Found at i:961886 original size:30 final size:27
Alignment explanation
Indices: 961845--961908 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 27
961835 AAATTGATTT
* *
961845 AAATTAAAAATTTATTTAAGTATAAATTAA
1 AAATAAAAAATTAATTTAA--AT-AATTAA
961875 AAATAAAAAATTAATTTAAATAATTAA
1 AAATAAAAAATTAATTTAAATAATTAA
*
961902 ATATAAA
1 AAATAAA
961909 TTAAAAGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 12 0.39
28 2 0.06
30 17 0.55
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
AAATAAAAAATTAATTTAAATAATTAA
Found at i:961912 original size:19 final size:18
Alignment explanation
Indices: 961860--961920 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
961850 AAAAATTTAT
*
961860 TTAAGTATAAATTAAAAA
1 TTAAATATAAATTAAAAA
* * *
961878 TAAAAAATTAATTTAAATAA
1 TTAAATA-TAAATTAAA-AA
*
961898 TTAAATATAAATTAAAAG
1 TTAAATATAAATTAAAAA
961916 TTAAA
1 TTAAA
961921 CATTTATTTC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 10 0.30
19 16 0.48
20 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TTAAATATAAATTAAAAA
Found at i:965850 original size:15 final size:15
Alignment explanation
Indices: 965832--965881 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
965822 ATGAATTGAT
*
965832 TTAATTTAAATTTAA
1 TTAATTAAAATTTAA
*
965847 TTAATTAAAAATTAA
1 TTAATTAAAATTTAA
965862 TT-ATTAAAATTTAA
1 TTAATTAAAATTTAA
*
965876 TAAATT
1 TTAATT
965882 TTTAAATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAATTAAAATTTAA
Found at i:967002 original size:24 final size:25
Alignment explanation
Indices: 966958--967010 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
966948 ATATTATTCC
* *
966958 ATTTAAAACATATTTTGTATT-CAT
1 ATTTAAAACATATTATATATTACAT
966982 ATTTAAAA-ATAATTATATATTACAT
1 ATTTAAAACAT-ATTATATATTACAT
967007 -TTTA
1 ATTTA
967011 TGTAATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 2 0.08
24 20 0.80
25 3 0.12
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTTAAAACATATTATATATTACAT
Found at i:967159 original size:40 final size:40
Alignment explanation
Indices: 967115--967198 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
967105 TCTTGTCTCA
*
967115 ATCTTCATATCCTTATATATGATTGTACAAAAGATATAGC
1 ATCTTCATATCCTTAAATATGATTGTACAAAAGATATAGC
967155 ATCTTCATATCCTTAAATATGATTGTACAAAAGATATAGC
1 ATCTTCATATCCTTAAATATGATTGTACAAAAGATATAGC
967195 ATCT
1 ATCT
967199 CTTTCTTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (40 bp):
ATCTTCATATCCTTAAATATGATTGTACAAAAGATATAGC
Found at i:968004 original size:2 final size:2
Alignment explanation
Indices: 967999--968041 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
967989 TCAACAGAAT
* * *
967999 TA TA TA CA TA TA GA TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
968041 T
1 T
968042 TTGTAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:969025 original size:2 final size:2
Alignment explanation
Indices: 969020--969065 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
969010 AAAATGAACT
* * *
969020 TA TA TA TA TA CA GA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
969062 TA TA
1 TA TA
969066 GAATATTTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:969935 original size:2 final size:2
Alignment explanation
Indices: 969928--969967 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
969918 AAGGTCATAC
* *
969928 AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT GT 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
969968 TCTTCCAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:979800 original size:18 final size:17
Alignment explanation
Indices: 979766--979815 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
979756 TGTTTATTAT
979766 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
979783 ATTTTCATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
979800 A-TTTATATTTTATATA
1 ATTTTATA-TTTATATA
979816 TTTCAAGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 6 0.21
16 6 0.21
17 7 0.25
18 6 0.21
19 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:981366 original size:7 final size:6
Alignment explanation
Indices: 981347--981380 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
981337 CTTCTTCCTC
* *
981347 TTCTTT TTCTTT TTCATT TTCTTT TTCTTC TTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT
981381 CCCTCTCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (6 bp):
TTCTTT
Found at i:985008 original size:7 final size:7
Alignment explanation
Indices: 984996--985047 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
984986 TTATGAAAAA
984996 ATTTAAT
1 ATTTAAT
985003 ATTTAAT
1 ATTTAAT
*
985010 AATTAA-
1 ATTTAAT
985016 ATTTAAT
1 ATTTAAT
985023 ATTTAAT
1 ATTTAAT
*
985030 AATTAA-
1 ATTTAAT
985036 ATTTAATT
1 ATTTAA-T
985044 ATTT
1 ATTT
985048 TAAATATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 10 0.26
7 24 0.63
8 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
ATTTAAT
Found at i:985019 original size:20 final size:20
Alignment explanation
Indices: 984994--985047 Score: 99
Period size: 20 Copynumber: 2.6 Consensus size: 20
984984 GTTTATGAAA
984994 AAATTTAATATTTAATAATT
1 AAATTTAATATTTAATAATT
985014 AAATTTAATATTTAATAATT
1 AAATTTAATATTTAATAATT
985034 AAATTTAATTATTT
1 AAATTTAA-TATTT
985048 TAAATATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 28 0.85
21 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATTTAATATTTAATAATT
Found at i:985021 original size:13 final size:14
Alignment explanation
Indices: 984996--985047 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
984986 TTATGAAAAA
984996 ATTTAATATTTAAT
1 ATTTAATATTTAAT
*
985010 AATTAA-ATTTAAT
1 ATTTAATATTTAAT
*
985023 ATTTAATAATTAA-
1 ATTTAATATTTAAT
985036 ATTTAATTATTT
1 ATTTAA-TATTT
985048 TAAATATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 18 0.56
14 14 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTAATATTTAAT
Found at i:985080 original size:14 final size:14
Alignment explanation
Indices: 985051--985097 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
985041 ATTATTTTAA
985051 ATATAATATAAA-T
1 ATATAATATAAATT
985064 ATATAA-ATAAAATT
1 ATATAATAT-AAATT
985078 ATATAATATAAATT
1 ATATAATATAAATT
985092 AT-TAAT
1 ATATAAT
985098 TTTTACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.06
13 13 0.42
14 14 0.45
15 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAATATAAATT
Done.