Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 54 of 106
Found at i:9434355 original size:29 final size:29
Alignment explanation
Indices: 9434313--9434370 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
9434303 CAAAAAATCT
9434313 TACCAATATAGTGGAGGATATTTTTAACA
1 TACCAATATAGTGGAGGATATTTTTAACA
9434342 TACCAATATAGTGGAGGATATTTTTAACA
1 TACCAATATAGTGGAGGATATTTTTAACA
9434371 ATAAACCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (29 bp):
TACCAATATAGTGGAGGATATTTTTAACA
Found at i:9437642 original size:109 final size:110
Alignment explanation
Indices: 9437468--9437679 Score: 345
Period size: 109 Copynumber: 1.9 Consensus size: 110
9437458 TAGTAGTAAA
*
9437468 TAAATAATAATAATTTTAAAGGAAAATATATAAAAAAATATGAAAATCTAAATTTTAGGCAAATT
1 TAAATAATAATAATTTTAAAGGAAAATATATAAAAAAATATGAAAATCCAAATTTTAGGCAAATT
*
9437533 ACAAAATACTAACTTGCTCCAAAAGTCTACCTAGATATAATATAT
66 ACAAAATACGAACTTGCTCCAAAAGTCTACCTAGATATAATATAT
* *
9437578 TAAATAATAATAATTTTAAAGGAAAA-ATATATAAAAGTATGAAAATCCAAATTTTAGGCAAATT
1 TAAATAATAATAATTTTAAAGGAAAATATATAAAAAAATATGAAAATCCAAATTTTAGGCAAATT
* * * *
9437642 ATAAAATACGAACTTGTTCCGAAAGTTTACCTAGATAT
66 ACAAAATACGAACTTGCTCCAAAAGTCTACCTAGATAT
9437680 TAAAGATTTT
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
109 68 0.72
110 26 0.28
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (110 bp):
TAAATAATAATAATTTTAAAGGAAAATATATAAAAAAATATGAAAATCCAAATTTTAGGCAAATT
ACAAAATACGAACTTGCTCCAAAAGTCTACCTAGATATAATATAT
Found at i:9437760 original size:14 final size:14
Alignment explanation
Indices: 9437741--9437848 Score: 84
Period size: 14 Copynumber: 8.0 Consensus size: 14
9437731 AACCTTAAAC
9437741 TGAAACTCTAAAAT
1 TGAAACTCTAAAAT
9437755 TGAAAC-CTTAAAA-
1 TGAAACTC-TAAAAT
*
9437768 TCAAAGCTCTAAAAT
1 TGAAA-CTCTAAAAT
* *
9437783 TGAAAC-C-CAAAG
1 TGAAACTCTAAAAT
* *
9437795 TGAAATTTTAAAAT
1 TGAAACTCTAAAAT
* *
9437809 TAAAACCCTAAAAT
1 TGAAACTCTAAAAT
*
9437823 TGAAACCCT-AAA-
1 TGAAACTCTAAAAT
9437835 TGAAACTCTAAAAT
1 TGAAACTCTAAAAT
9437849 AAAAAATTTA
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
12 16 0.22
13 12 0.17
14 39 0.54
15 5 0.07
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.25
Consensus pattern (14 bp):
TGAAACTCTAAAAT
Found at i:9437784 original size:28 final size:27
Alignment explanation
Indices: 9437729--9437789 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 27
9437719 AACCTCAACC
* *
9437729 GAAACCTTAAACTGAAACTCTAAAATT
1 GAAACCTTAAAATCAAACTCTAAAATT
9437756 GAAACCTTAAAATCAAAGCTCTAAAATT
1 GAAACCTTAAAATCAAA-CTCTAAAATT
9437784 GAAACC
1 GAAACC
9437790 CAAAGTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.23
Consensus pattern (27 bp):
GAAACCTTAAAATCAAACTCTAAAATT
Found at i:9437806 original size:40 final size:40
Alignment explanation
Indices: 9437741--9437853 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
9437731 AACCTTAAAC
* * * *
9437741 TGAAACTCTAAAATTGAAACCTTAAAATCAAAGCTCTAAAAT
1 TGAAACCCT-AAA-TGAAACTTTAAAATCAAAACCCTAAAAT
* *
9437783 TGAAACCC-AAAGTGAAATTTTAAAATTAAAACCCTAAAAT
1 TGAAACCCTAAA-TGAAACTTTAAAATCAAAACCCTAAAAT
* *
9437823 TGAAACCCTAAATGAAACTCTAAAATAAAAA
1 TGAAACCCTAAATGAAACTTTAAAATCAAAA
9437854 ATTTAAGTGA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 50 0.83
41 3 0.05
42 7 0.12
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (40 bp):
TGAAACCCTAAATGAAACTTTAAAATCAAAACCCTAAAAT
Found at i:9437840 original size:12 final size:13
Alignment explanation
Indices: 9437729--9437846 Score: 60
Period size: 14 Copynumber: 8.8 Consensus size: 13
9437719 AACCTCAACC
* *
9437729 GAAACCTTAAACT
1 GAAACCCTAAATT
*
9437742 GAAACTCTAAAATT
1 GAAACCCT-AAATT
* *
9437756 GAAACCTTAAAAT
1 GAAACCCTAAATT
* *
9437769 CAAAGCTCTAAAATT
1 GAAA-CCCT-AAATT
*
9437784 GAAACCC-AAAGT
1 GAAACCCTAAATT
***
9437796 GAAATTTTAAAATT
1 GAAACCCT-AAATT
*
9437810 AAAACCCTAAAATT
1 GAAACCCT-AAATT
9437824 GAAACCCTAAA-T
1 GAAACCCTAAATT
*
9437836 GAAACTCTAAA
1 GAAACCCTAAA
9437847 ATAAAAAATT
Statistics
Matches: 77, Mismatches: 23, Indels: 11
0.69 0.21 0.10
Matches are distributed among these distances:
12 19 0.25
13 16 0.21
14 35 0.45
15 7 0.09
ACGTcount: A:0.51, C:0.18, G:0.08, T:0.24
Consensus pattern (13 bp):
GAAACCCTAAATT
Found at i:9444189 original size:15 final size:15
Alignment explanation
Indices: 9444169--9444197 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9444159 TATTTTGTTA
9444169 AATGTAATGAATGAG
1 AATGTAATGAATGAG
9444184 AATGTAATGAATGA
1 AATGTAATGAATGA
9444198 AGATGCATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (15 bp):
AATGTAATGAATGAG
Found at i:9447521 original size:59 final size:61
Alignment explanation
Indices: 9447383--9447538 Score: 199
Period size: 59 Copynumber: 2.6 Consensus size: 61
9447373 TGCTTTTATA
* * * * * *
9447383 CAAGAAAAATTGATACTTTCAACTTTTCTTTAAAAATATCTTTTTTTTTAGAATTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTC-CTCAAAATAGCTTTTTTTTGAAAATTTCATTTT
* * * *
9447445 TAAGGAAAATTGGTACTTCCAACTTTTCCTCAAAAT-GC-TTTTTTTGAAAATTTCATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAATAGCTTTTTTTTGAAAATTTCATTTT
9447504 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAA
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAA
9447539 ATATTTTTTA
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
59 49 0.61
60 1 0.01
61 6 0.08
62 24 0.30
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (61 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAATAGCTTTTTTTTGAAAATTTCATTTT
Found at i:9447561 original size:20 final size:20
Alignment explanation
Indices: 9447536--9447574 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9447526 CTTTTCCTCA
*
9447536 AAAATATTTTTTAGAAATTG
1 AAAATATCTTTTAGAAATTG
9447556 AAAATATCTTTTAGAAATT
1 AAAATATCTTTTAGAAATT
9447575 TTATTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (20 bp):
AAAATATCTTTTAGAAATTG
Found at i:9447758 original size:11 final size:11
Alignment explanation
Indices: 9447736--9447765 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
9447726 ATATTAATAG
9447736 ATAAATAACAAA
1 ATAAA-AACAAA
9447748 ATAAAAACAAA
1 ATAAAAACAAA
9447759 ATAAAAA
1 ATAAAAA
9447766 ATAAAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
ATAAAAACAAA
Found at i:9449862 original size:21 final size:20
Alignment explanation
Indices: 9449829--9449871 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
9449819 AATTATCATG
*
9449829 CAAATATATTATAAATCATAT
1 CAAATATATTAT-AATAATAT
9449850 CAAATATGA-TATAATAATAT
1 CAAATAT-ATTATAATAATAT
9449870 CA
1 CA
9449872 TGCTTAGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 10 0.50
22 1 0.05
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (20 bp):
CAAATATATTATAATAATAT
Found at i:9449935 original size:20 final size:18
Alignment explanation
Indices: 9449916--9449969 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
9449906 GTCATACAAT
9449916 TATATTAATTATCATGCAA
1 TATA-TAATTATCATGCAA
* *
9449935 TA-ATAATAATCATGTAAA
1 TATATAATTATCATG-CAA
9449953 TATATAA-TATCATGCAA
1 TATATAATTATCATGCAA
9449970 CAATATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 12 0.41
18 11 0.38
19 6 0.21
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (18 bp):
TATATAATTATCATGCAA
Found at i:9449946 original size:17 final size:16
Alignment explanation
Indices: 9449925--9449974 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
9449915 TTATATTAAT
9449925 TATCATGCAATAATAA
1 TATCATGCAATAATAA
*
9449941 TAATCATGTAAATATATAA
1 T-ATCATG-CAATA-ATAA
*
9449960 TATCATGCAACAATA
1 TATCATGCAATAATA
9449975 TAAAATACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
18 10 0.36
19 5 0.18
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (16 bp):
TATCATGCAATAATAA
Found at i:9449992 original size:38 final size:35
Alignment explanation
Indices: 9449907--9449998 Score: 85
Period size: 35 Copynumber: 2.5 Consensus size: 35
9449897 TGTAAGAATG
* * *
9449907 TCATACAATTATATTAATTATCATGCAATAATAATAA
1 TCATACAAATATA-TAA-TATCATGCAACAATAAAAA
**
9449944 TCATGTAAATATATAATATCATGCAACAATATAAAA
1 TCATACAAATATATAATATCATGCAACAATA-AAAA
*
9449980 TACCATACAAATACATAAT
1 T--CATACAAATATATAAT
9449999 CATGAAATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
35 14 0.32
36 7 0.16
37 10 0.23
38 13 0.30
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (35 bp):
TCATACAAATATATAATATCATGCAACAATAAAAA
Found at i:9450142 original size:19 final size:18
Alignment explanation
Indices: 9450114--9450173 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
9450104 ATATCATTTA
9450114 AATATAATATTAATCATGC
1 AATA-AATATTAATCATGC
9450133 AATAACATA-T-ATCATGC
1 AATAA-ATATTAATCATGC
*
9450150 AATAAATATAAAATCATGC
1 AATAAATAT-TAATCATGC
9450169 AATAA
1 AATAA
9450174 TAAATAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 3 0.08
17 12 0.33
18 2 0.06
19 19 0.53
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (18 bp):
AATAAATATTAATCATGC
Found at i:9450181 original size:4 final size:4
Alignment explanation
Indices: 9450172--9450209 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
9450162 ATCATGCAAT
9450172 AATA AATA AATA AATA AATA AATA AATGCA AATA AATA
1 AATA AATA AATA AATA AATA AATA AAT--A AATA AATA
9450210 TATTAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 28 0.88
6 4 0.12
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:9450182 original size:19 final size:18
Alignment explanation
Indices: 9450125--9450182 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
9450115 ATATAATATT
*
9450125 AATCATGCAAT-AACATA
1 AATCATGCAATAAAAATA
* *
9450142 TATCATGCAATAAATATAA
1 AATCATGCAATAAAAAT-A
9450161 AATCATGCAATAATAAATA
1 AATCATGCAATAA-AAATA
9450180 AAT
1 AAT
9450183 AAATAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.29
18 4 0.12
19 17 0.50
20 3 0.09
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (18 bp):
AATCATGCAATAAAAATA
Found at i:9450316 original size:87 final size:88
Alignment explanation
Indices: 9450254--9450415 Score: 220
Period size: 87 Copynumber: 1.9 Consensus size: 88
9450244 TTAATAATCG
* * * * *
9450254 TGCAAACAGACATGCAATTAAATATATAAACATG-TAATAAATATGCAATTTAATATATAATCAT
1 TGCAAACAAACATACAATTAAATATATAAACATGCAAATAAACATACAATTTAATATATAATCAT
9450318 GCAAATAAA-AATATATAAACAA
66 GCAAATAAATAATATATAAACAA
* * * * *
9450340 TGCAAATAAACATACAATTTAATATATAATCATGCAAATAAACATATAATTAAATATATAATCAT
1 TGCAAACAAACATACAATTAAATATATAAACATGCAAATAAACATACAATTTAATATATAATCAT
9450405 GCAAATAAATA
66 GCAAATAAATA
9450416 TGCAATTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
86 29 0.45
87 34 0.53
88 1 0.02
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (88 bp):
TGCAAACAAACATACAATTAAATATATAAACATGCAAATAAACATACAATTTAATATATAATCAT
GCAAATAAATAATATATAAACAA
Found at i:9450319 original size:20 final size:20
Alignment explanation
Indices: 9450296--9450376 Score: 55
Period size: 20 Copynumber: 4.3 Consensus size: 20
9450286 TGTAATAAAT
9450296 ATGCAATTTAATATATAATC
1 ATGCAATTTAATATATAATC
* * *
9450316 ATGCAAATAAAAATAT-AT-
1 ATGCAATTTAATATATAATC
** **
9450334 AAACAATGCAA-ATA-AA-C
1 ATGCAATTTAATATATAATC
*
9450351 ATACAATTTAATATATAATC
1 ATGCAATTTAATATATAATC
9450371 ATGCAA
1 ATGCAA
9450377 ATAAACATAT
Statistics
Matches: 44, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
17 12 0.27
18 9 0.20
19 4 0.09
20 19 0.43
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (20 bp):
ATGCAATTTAATATATAATC
Found at i:9450333 original size:22 final size:23
Alignment explanation
Indices: 9450305--9450349 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
9450295 TATGCAATTT
*
9450305 AATATATAATC-ATGCAAATAAA
1 AATATATAAACAATGCAAATAAA
9450327 AATATATAAACAATGCAAATAAA
1 AATATATAAACAATGCAAATAAA
9450350 CATACAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.62, C:0.09, G:0.04, T:0.24
Consensus pattern (23 bp):
AATATATAAACAATGCAAATAAA
Found at i:9450379 original size:32 final size:32
Alignment explanation
Indices: 9450326--9450444 Score: 175
Period size: 32 Copynumber: 3.7 Consensus size: 32
9450316 ATGCAAATAA
*
9450326 AAATATATAAACAATGCAAATAAACATACAATT
1 AAATATATAATC-ATGCAAATAAACATACAATT
* *
9450359 TAATATATAATCATGCAAATAAACATATAATT
1 AAATATATAATCATGCAAATAAACATACAATT
* *
9450391 AAATATATAATCATGCAAATAAATATGCAATT
1 AAATATATAATCATGCAAATAAACATACAATT
*
9450423 AAATATATAATCATACAAATAA
1 AAATATATAATCATGCAAATAA
9450445 TAATATATAA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 68 0.87
33 10 0.13
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.29
Consensus pattern (32 bp):
AAATATATAATCATGCAAATAAACATACAATT
Found at i:9450413 original size:20 final size:20
Alignment explanation
Indices: 9450390--9450485 Score: 57
Period size: 20 Copynumber: 5.0 Consensus size: 20
9450380 AACATATAAT
9450390 TAAATATATAATCATGCAAA
1 TAAATATATAATCATGCAAA
**
9450410 TAAATATGCAAT--T--AAA
1 TAAATATATAATCATGCAAA
*
9450426 T--A--TATAATCATACAAA
1 TAAATATATAATCATGCAAA
9450442 TAATAATATATAAATCATGCAAA
1 T-A-AATATAT-AATCATGCAAA
*
9450465 TATAATAT-TAGTCATGCAAA
1 TA-AATATATAATCATGCAAA
9450485 T
1 T
9450486 TCATGCACAA
Statistics
Matches: 59, Mismatches: 6, Indels: 22
0.68 0.07 0.25
Matches are distributed among these distances:
12 4 0.07
14 2 0.03
16 8 0.14
18 1 0.02
20 22 0.37
21 1 0.02
22 10 0.17
23 11 0.19
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAATATATAATCATGCAAA
Found at i:9450449 original size:22 final size:21
Alignment explanation
Indices: 9450415--9450485 Score: 83
Period size: 20 Copynumber: 3.4 Consensus size: 21
9450405 GCAAATAAAT
*
9450415 ATGCAATTA-AATATATAATC
1 ATGCAAATATAATATATAATC
*
9450435 ATACAAATAATAATATATAAATC
1 ATGCAAAT-ATAATATAT-AATC
*
9450458 ATGCAAATATAATAT-TAGTC
1 ATGCAAATATAATATATAATC
9450478 ATGCAAAT
1 ATGCAAAT
9450486 TCATGCACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
20 17 0.39
21 2 0.05
22 14 0.32
23 11 0.25
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (21 bp):
ATGCAAATATAATATATAATC
Found at i:9451140 original size:16 final size:16
Alignment explanation
Indices: 9451119--9451149 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9451109 AAATTAAACT
*
9451119 AAAAAAACTAAAATAC
1 AAAAAAACAAAAATAC
9451135 AAAAAAACAAAAATA
1 AAAAAAACAAAAATA
9451150 AAATTTAGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAAACAAAAATAC
Found at i:9451731 original size:13 final size:13
Alignment explanation
Indices: 9451713--9451737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9451703 TTCCAAATAT
9451713 ATGCAATGAATGC
1 ATGCAATGAATGC
9451726 ATGCAATGAATG
1 ATGCAATGAATG
9451738 AAAAGATTCT
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:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATGCAATGAATGC
Found at i:9453013 original size:9 final size:9
Alignment explanation
Indices: 9453002--9453042 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
9452992 TTCTTTCTCT
*
9453002 TTTTTTTTT
1 TTTTTTTTA
9453011 TTTTTTTTA
1 TTTTTTTTA
9453020 -TTTTTTTA
1 TTTTTTTTA
*
9453028 CTTTTTTTA
1 TTTTTTTTA
9453037 TTTTTT
1 TTTTTT
9453043 GCATATCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.07, C:0.02, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:9453025 original size:17 final size:17
Alignment explanation
Indices: 9453001--9453042 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
9452991 CTTCTTTCTC
9453001 TTTT-TTTTTTT--TTT
1 TTTTATTTTTTTACTTT
9453015 TTTTATTTTTTTACTTT
1 TTTTATTTTTTTACTTT
9453032 TTTTATTTTTT
1 TTTTATTTTTT
9453043 GCATATCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.16
15 7 0.28
17 14 0.56
ACGTcount: A:0.07, C:0.02, G:0.00, T:0.90
Consensus pattern (17 bp):
TTTTATTTTTTTACTTT
Found at i:9459032 original size:20 final size:20
Alignment explanation
Indices: 9458980--9459034 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
9458970 GCAAAAATGT
* * *
9458980 CATGCAAATATATTAATTAT
1 CATGCAAATATATAAAATAC
*
9459000 CATGC-AATAATATAAAATCC
1 CATGCAAAT-ATATAAAATAC
9459020 CATGCAAATATATAA
1 CATGCAAATATATAA
9459035 TCATGAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.10
20 23 0.79
21 3 0.10
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (20 bp):
CATGCAAATATATAAAATAC
Found at i:9459149 original size:17 final size:16
Alignment explanation
Indices: 9459127--9459176 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
9459117 ATACAATCAA
*
9459127 ATATCATTCAATAACAT
1 ATATCATGCAATAA-AT
9459144 ATATCATGCAATAAAT
1 ATATCATGCAATAAAT
9459160 ATAAAATCATGCAATAA
1 AT---ATCATGCAATAA
9459177 TGATAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 4 0.14
17 13 0.45
19 12 0.41
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.30
Consensus pattern (16 bp):
ATATCATGCAATAAAT
Found at i:9459375 original size:32 final size:32
Alignment explanation
Indices: 9459325--9459410 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 32
9459315 AGGCAAATAA
*
9459325 AAATATATAAAACCATGCAAATAAACATACAATT
1 AAATATATAATA--ATGCAAATAAACATACAATT
* * **
9459359 AAATATATAATAATGCAAAAAAATATGTAATT
1 AAATATATAATAATGCAAATAAACATACAATT
*
9459391 AAATATATAATCATGCAAAT
1 AAATATATAATAATGCAAAT
9459411 TCATGCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 34 0.76
34 11 0.24
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.28
Consensus pattern (32 bp):
AAATATATAATAATGCAAATAAACATACAATT
Found at i:9459377 original size:56 final size:52
Alignment explanation
Indices: 9459272--9459381 Score: 139
Period size: 56 Copynumber: 2.0 Consensus size: 52
9459262 ATATGCAATT
* * * *
9459272 AAATATATAAACATGGAATAAACATGCAATTTAATATATAATCAGGCAAATAA
1 AAATATATAAACATGAAATAAACATACAATTAAATATATAATAAGGCAAA-AA
*
9459325 AAATATATAAAACCATGCAAATAAACATACAATTAAATATATAATAATGCAAAAA
1 AAATATAT-AAA-CATG-AAATAAACATACAATTAAATATATAATAAGGCAAAAA
9459380 AA
1 AA
9459382 TATGTAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 8 0.16
54 3 0.06
55 8 0.16
56 30 0.61
ACGTcount: A:0.59, C:0.10, G:0.06, T:0.25
Consensus pattern (52 bp):
AAATATATAAACATGAAATAAACATACAATTAAATATATAATAAGGCAAAAA
Found at i:9460049 original size:22 final size:21
Alignment explanation
Indices: 9460016--9460059 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
9460006 TCTTTTGACT
*
9460016 AAAAAATAAAAATTAAACTAAA
1 AAAAAATAAAAAGTAAA-TAAA
9460038 AAAAAACT-AAAAGTAAATAAA
1 AAAAAA-TAAAAAGTAAATAAA
9460059 A
1 A
9460060 TTTATGGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 14 0.70
23 1 0.05
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (21 bp):
AAAAAATAAAAAGTAAATAAA
Found at i:9477208 original size:2 final size:2
Alignment explanation
Indices: 9477201--9477227 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9477191 ACAAGAAAAT
9477201 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 A
9477228 CAGGAAGGTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9480702 original size:2 final size:2
Alignment explanation
Indices: 9480697--9480729 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9480687 TGGTAACACA
9480697 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
9480730 CTTGGTTGCT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:9481370 original size:70 final size:70
Alignment explanation
Indices: 9481257--9481393 Score: 256
Period size: 70 Copynumber: 2.0 Consensus size: 70
9481247 TGTTAATTTG
*
9481257 AACTATTCTTTAGAAATGGTTGCATTAATCTCTGACATTGAGTAGCATCTAGCATGCACTCCAGA
1 AACTATTCTTTAGAAATGGCTGCATTAATCTCTGACATTGAGTAGCATCTAGCATGCACTCCAGA
9481322 TTTTA
66 TTTTA
*
9481327 AACTATTCTTTAGAAATGGCTGCATTAATCTCTGACATTGAGTAGCATCTAGCATGCATTCCAGA
1 AACTATTCTTTAGAAATGGCTGCATTAATCTCTGACATTGAGTAGCATCTAGCATGCACTCCAGA
9481392 TT
66 TT
9481394 ATGGGAATAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (70 bp):
AACTATTCTTTAGAAATGGCTGCATTAATCTCTGACATTGAGTAGCATCTAGCATGCACTCCAGA
TTTTA
Found at i:9488811 original size:2 final size:2
Alignment explanation
Indices: 9488799--9488848 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
9488789 AAGTGTACTG
*
9488799 CT CT TT CT CT CT CT 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 CT CT CT CT CT CT CT
9488841 CT CT CT CT
1 CT CT CT CT
9488849 GTTATGATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:9489644 original size:22 final size:22
Alignment explanation
Indices: 9489619--9489660 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9489609 TATTTAGAGT
* *
9489619 ATTTCATTTTTTTTAATATTAA
1 ATTTCATATTTTTAAATATTAA
*
9489641 ATTTGATATTTTTAAATATT
1 ATTTCATATTTTTAAATATT
9489661 TTATTTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTTCATATTTTTAAATATTAA
Found at i:9489666 original size:22 final size:22
Alignment explanation
Indices: 9489618--9489666 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
9489608 TTATTTAGAG
* *
9489618 TATTTCATTTTTTTTAATATTA
1 TATTTCATATTTTTAAATATTA
* * *
9489640 AATTTGATATTTTTAAATATTT
1 TATTTCATATTTTTAAATATTA
9489662 TATTT
1 TATTT
9489667 TTTTAAAATC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTTCATATTTTTAAATATTA
Found at i:9489684 original size:17 final size:17
Alignment explanation
Indices: 9489649--9489685 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
9489639 AAATTTGATA
*
9489649 TTTTTAAATATTTTATT
1 TTTTTAAATATCTTATT
9489666 TTTTTAAA-ATCTTATT
1 TTTTTAAATATCTTATT
9489682 TTTT
1 TTTT
9489686 GTTTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTAAATATCTTATT
Found at i:9489805 original size:14 final size:14
Alignment explanation
Indices: 9489786--9489814 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9489776 TTTTCTTAGT
9489786 ATTTTATTTTTTTA
1 ATTTTATTTTTTTA
9489800 ATTTTATTTTTTTA
1 ATTTTATTTTTTTA
9489814 A
1 A
9489815 AAAGTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTTATTTTTTTA
Found at i:9489998 original size:20 final size:21
Alignment explanation
Indices: 9489955--9489999 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
9489945 TTTTTTAATT
*
9489955 TTTTAAAAAAGAGTTTATAAA
1 TTTTAAAAAAGAGTTTACAAA
* *
9489976 TTTTAAAAAA-ATTTTACATA
1 TTTTAAAAAAGAGTTTACAAA
9489996 TTTT
1 TTTT
9490000 TTATGTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTTAAAAAAGAGTTTACAAA
Found at i:9490318 original size:34 final size:35
Alignment explanation
Indices: 9490275--9490354 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 35
9490265 AAAATTTGAA
* *
9490275 AAAAAATAAAA-ACTTTCAAAAATGAATTTT-ATTT
1 AAAAAATAAAATA-TTTAAAAAATAAATTTTAATTT
9490309 AAAAAATAAAATATTTAAAAAATAAATTTTAAATTT
1 AAAAAATAAAATATTTAAAAAATAAATTTT-AATTT
*
9490345 TAAAAATAAA
1 AAAAAATAAA
9490355 GAAAATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
34 26 0.65
35 1 0.03
36 13 0.32
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (35 bp):
AAAAAATAAAATATTTAAAAAATAAATTTTAATTT
Found at i:9490335 original size:15 final size:16
Alignment explanation
Indices: 9490304--9490334 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9490294 AAATGAATTT
9490304 TATTTAAAAAATAAAA
1 TATTTAAAAAATAAAA
9490320 TATTTAAAAAATAAA
1 TATTTAAAAAATAAA
9490335 TTTTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TATTTAAAAAATAAAA
Found at i:9490335 original size:20 final size:19
Alignment explanation
Indices: 9490312--9490368 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
9490302 TTTATTTAAA
9490312 AAATAAAATATTTAAAAAAT
1 AAATAAAAT-TTTAAAAAAT
*
9490332 AAATTTTAAATTTT-AAAAAT
1 AAA--TAAAATTTTAAAAAAT
*
9490352 AAAGAAAATTTTTAAAA
1 AAATAAAA-TTTTAAAA
9490369 TTTCAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 3 0.10
19 4 0.13
20 15 0.50
21 3 0.10
22 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATAAAATTTTAAAAAAT
Found at i:9490520 original size:20 final size:22
Alignment explanation
Indices: 9490480--9490521 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9490470 GAAAAAATTC
*
9490480 TAAAAAATTCAAAATATTGATT
1 TAAAAAAATCAAAATATTGATT
9490502 TAAAAAAAT-AAAATA-TGATT
1 TAAAAAAATCAAAATATTGATT
9490522 GTTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
TAAAAAAATCAAAATATTGATT
Found at i:9495297 original size:19 final size:19
Alignment explanation
Indices: 9495270--9495306 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9495260 CTAGATCTCA
9495270 CATAATTTATAATGATCAT
1 CATAATTTATAATGATCAT
* *
9495289 CATAGTTTATAGTGATCA
1 CATAATTTATAATGATCA
9495307 CTACATCTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (19 bp):
CATAATTTATAATGATCAT
Found at i:9499558 original size:24 final size:24
Alignment explanation
Indices: 9499512--9499572 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
9499502 AACATAATTA
9499512 TCTATTTTGAATAGATAGAAACTG
1 TCTATTTTGAATAGATAGAAACTG
9499536 TCTATTTTTGAATA-ATA-ATAACTG
1 TCTA-TTTTGAATAGATAGA-AACTG
9499560 T-TGA-TTTGAATAG
1 TCT-ATTTTGAATAG
9499573 GTTTGCTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
22 8 0.24
23 2 0.06
24 14 0.42
25 9 0.27
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.43
Consensus pattern (24 bp):
TCTATTTTGAATAGATAGAAACTG
Found at i:9499684 original size:31 final size:31
Alignment explanation
Indices: 9499646--9499706 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
9499636 CTTTAAATTA
9499646 AAATAAAATAATATTTTATTTACTAAACTTT
1 AAATAAAATAATATTTTATTTACTAAACTTT
*
9499677 AAATAAAATAATATTTTATTTACTATACTT
1 AAATAAAATAATATTTTATTTACTAAACTT
9499707 CACTGCACGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (31 bp):
AAATAAAATAATATTTTATTTACTAAACTTT
Found at i:9507461 original size:9 final size:10
Alignment explanation
Indices: 9507447--9507555 Score: 88
Period size: 9 Copynumber: 11.1 Consensus size: 10
9507437 ACATTTTTAT
9507447 TTTATT-TTA
1 TTTATTATTA
9507456 TTTATTATTAGTA
1 TTTATTA-T--TA
*
9507469 TTTTTTATTA
1 TTTATTATTA
9507479 TTTATTATTA
1 TTTATTATTA
*
9507489 TTAGTATCATTA
1 TT--TATTATTA
9507501 TTTA-T-TTA
1 TTTATTATTA
9507509 TTTATTATTA
1 TTTATTATTA
9507519 -TTATTATTA
1 TTTATTATTA
9507528 -TTATTATTA
1 TTTATTATTA
* *
9507537 -TTATCATTT
1 TTTATTATTA
9507546 TTTATT-TTA
1 TTTATTATTA
9507555 T
1 T
9507556 CTTTTCTTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
8 7 0.08
9 35 0.42
10 22 0.27
11 1 0.01
12 10 0.12
13 8 0.10
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTATTATTA
Found at i:9507465 original size:3 final size:3
Alignment explanation
Indices: 9507443--9507540 Score: 96
Period size: 3 Copynumber: 32.3 Consensus size: 3
9507433 GCTTACATTT
*
9507443 TTA TT- TTA TT- TTA TTTA TTA TTA GTA TT- TT- TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* *
9507486 TTA TTA GTA TCA TTA TTTA TTTA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA
9507534 TTA TTA T
1 TTA TTA T
9507541 CATTTTTTAT
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
2 8 0.10
3 58 0.70
4 17 0.20
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9507475 original size:30 final size:28
Alignment explanation
Indices: 9507440--9507532 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 28
9507430 TGGGCTTACA
9507440 TTTTTATTTTATTTTATTTATTATTAGTAT
1 TTTTTA-TTTA-TTTATTTATTATTAGTAT
9507470 TTTTTA-TTATTTA-TTATTATTAGTA-
1 TTTTTATTTATTTATTTATTATTAGTAT
** *
9507495 TCATTATTTATTTATTTATTATTATTAT
1 TTTTTATTTATTTATTTATTATTAGTAT
9507523 TATTATTATT
1 T-TT-TTATT
9507533 ATTATTATCA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
25 4 0.08
26 19 0.36
27 15 0.28
28 4 0.08
30 11 0.21
ACGTcount: A:0.27, C:0.01, G:0.02, T:0.70
Consensus pattern (28 bp):
TTTTTATTTATTTATTTATTATTAGTAT
Found at i:9507505 original size:45 final size:44
Alignment explanation
Indices: 9507453--9507551 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 44
9507443 TTATTTTATT
9507453 TTATTTATTATTAGTATT-TT-TTATTATTTATTATTATTAGTATCA
1 TTATTTATTATT--TATTATTATTATTA-TTATTATTATTAGTATCA
*
9507498 TTATTTATTTATTTATTATTATTATTATTATTATTATTATTATCA
1 TTATTTA-TTATTTATTATTATTATTATTATTATTATTAGTATCA
*
9507543 TTTTTTATT
1 TTATTTATT
9507552 TTATCTTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
44 6 0.12
45 32 0.65
46 11 0.22
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (44 bp):
TTATTTATTATTTATTATTATTATTATTATTATTATTAGTATCA
Found at i:9508591 original size:59 final size:56
Alignment explanation
Indices: 9508472--9508720 Score: 197
Period size: 59 Copynumber: 4.4 Consensus size: 56
9508462 TTAAAAAAAT
* * * * *
9508472 AAAATAAAAATTTC-AAAAGTATTTTGAGG-GAAAGTTGAAATTATCAATTTCCCTTA
1 AAAAT-AAAATTTCTAAAA-TATTTTGAGGAAAAAGTTAAAAGTATCAATTTTCCTTG
* *
9508528 AAAATAAAAGTGTTCTAAAATATTTTTGAGGAAAAAGTAAAAAATATCAATTTTCCTTG
1 AAAATAAAA-T-TTCTAAAATA-TTTTGAGGAAAAAGTTAAAAGTATCAATTTTCCTTG
* *
9508587 AAAATAAAA-TTCTAAAA-ATTTTGA-GAAAAAATTAAAAGTAT-AAATTTCTCTTG
1 AAAATAAAATTTCTAAAATATTTTGAGGAAAAAGTTAAAAGTATCAATTTTC-CTTG
*** * * * *
9508640 AAAATAGAAAAAGTTAAAAAATATATTTTTAGAAAAAAGTTGAAAGTATCAATTTT-CTTT
1 AAAAT---AAAA-TTTCTAAA-ATATTTTGAGGAAAAAGTTAAAAGTATCAATTTTCCTTG
9508700 AAAAGTAAAATTTCTAAAATA
1 AAAA-TAAAATTTCTAAAATA
9508721 AAAATTCTAA
Statistics
Matches: 155, Mismatches: 22, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
52 6 0.04
53 23 0.15
54 6 0.04
55 5 0.03
56 21 0.14
57 10 0.06
58 20 0.13
59 31 0.20
60 13 0.08
61 15 0.10
62 5 0.03
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (56 bp):
AAAATAAAATTTCTAAAATATTTTGAGGAAAAAGTTAAAAGTATCAATTTTCCTTG
Found at i:9508640 original size:53 final size:57
Alignment explanation
Indices: 9508517--9508720 Score: 143
Period size: 53 Copynumber: 3.5 Consensus size: 57
9508507 TGAAATTATC
* * * *
9508517 AATTTCCCTTAAAAATAAAAGTGTTCTAAAATATTTTTGAGGAAAAAGTAAAAAATATC
1 AATTTCTCTTGAAAATAAAA--GTTCTAAAATATTTTTGAGGAAAAAATAAAAAATATA
* *
9508576 AATTT-TCCTTGAAAATAAAA-TTCTAAAA-A-TTTTGA-GAAAAAATTAAAAGTATA
1 AATTTCT-CTTGAAAATAAAAGTTCTAAAATATTTTTGAGGAAAAAATAAAAAATATA
** * ** * *
9508629 AATTTCTCTTGAAAATAGAAAAAGTTAAAAAATATATTTTTA-GAAAAAAGTTGAAAGTATC
1 AATTTCTCTTGAAAAT---AAAAGTTCTAAAATAT-TTTTGAGGAAAAAA-TAAAAAATATA
* *
9508690 AATTT-TCTTTAAAAGTAAAATTTCTAAAATA
1 AATTTCTCTTGAAAA-TAAAAGTTCTAAAATA
9508721 AAAATTCTAA
Statistics
Matches: 119, Mismatches: 15, Indels: 23
0.76 0.10 0.15
Matches are distributed among these distances:
53 28 0.24
54 7 0.06
55 1 0.01
56 12 0.10
57 6 0.05
58 13 0.11
59 17 0.14
60 20 0.17
61 15 0.13
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (57 bp):
AATTTCTCTTGAAAATAAAAGTTCTAAAATATTTTTGAGGAAAAAATAAAAAATATA
Found at i:9508728 original size:14 final size:15
Alignment explanation
Indices: 9508699--9508733 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
9508689 CAATTTTCTT
*
9508699 TAAAAGTAAAATTTC
1 TAAAAGTAAAAATTC
9508714 TAAAA-TAAAAATTC
1 TAAAAGTAAAAATTC
9508728 TAAAAG
1 TAAAAG
9508734 CATTTTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (15 bp):
TAAAAGTAAAAATTC
Found at i:9512989 original size:9 final size:9
Alignment explanation
Indices: 9512879--9512974 Score: 97
Period size: 9 Copynumber: 10.1 Consensus size: 9
9512869 GGTGAAAGAG
9512879 AAAG-AAAA
1 AAAGAAAAA
9512887 AAAGAAAAA
1 AAAGAAAAA
*
9512896 AAA-AGGAAA
1 AAAGA-AAAA
*
9512905 AAAGAGAAAG
1 AAAGA-AAAA
9512915 AAAGAAAAA
1 AAAGAAAAA
9512924 AGAATGAAAAA
1 A-AA-GAAAAA
9512935 GATAAGAAAAA
1 -A-AAGAAAAA
9512946 AAAGAAAAA
1 AAAGAAAAA
9512955 AAAGAAAAA
1 AAAGAAAAA
9512964 AAAGAGAAAA
1 AAAGA-AAAA
9512974 A
1 A
9512975 TGGAAATAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
8 5 0.07
9 39 0.51
10 17 0.22
11 12 0.16
12 3 0.04
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:9513215 original size:15 final size:16
Alignment explanation
Indices: 9513195--9513224 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9513185 TTTTGAATTG
9513195 TTTGAATAT-TCATTA
1 TTTGAATATCTCATTA
9513210 TTTGAATATCTCATT
1 TTTGAATATCTCATT
9513225 CAGCTCAATG
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:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTGAATATCTCATTA
Found at i:9513765 original size:70 final size:71
Alignment explanation
Indices: 9513607--9513769 Score: 163
Period size: 70 Copynumber: 2.3 Consensus size: 71
9513597 GTTTATTCTA
* ** * *
9513607 AAATGGTTAGTGTTGAGAAGCTTGTGAATGGTGGTGAAAATAGTATGGGTCAATGGATGAAATTT
1 AAATTGTTAGTGTTGAGAAGCCCGTGAATGGTGATGAAAATAGTATGGGTCAATGGATGAAACTT
9513672 ATGCTG
66 ATGCTG
* ** * *
9513678 AAATTATTAGTACTGAGAAGCCCGTGAGTGGTGAT-TAAATGATGTA-GGG-CAATGGATGAAAC
1 AAATTGTTAGTGTTGAGAAGCCCGTGAATGGTGATGAAAAT-A-GTATGGGTCAATGGATGAAAC
* *
9513740 TTGTG-TT
64 TTATGCTG
9513747 AGAATTGTTAGTGTTGAGAAGCC
1 A-AATTGTTAGTGTTGAGAAGCC
9513770 TATGGATGGT
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
69 2 0.03
70 38 0.51
71 31 0.42
72 3 0.04
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.31
Consensus pattern (71 bp):
AAATTGTTAGTGTTGAGAAGCCCGTGAATGGTGATGAAAATAGTATGGGTCAATGGATGAAACTT
ATGCTG
Found at i:9514222 original size:21 final size:21
Alignment explanation
Indices: 9514169--9514324 Score: 105
Period size: 21 Copynumber: 6.9 Consensus size: 21
9514159 AATCCTGATT
*
9514169 TCTTAAATGAGAATCTTTAAAAAG
1 TCTTAAATGAGAATCTTT---GAG
* *
9514193 TCCTCAAATAAGAATCTTTGAG
1 T-CTTAAATGAGAATCTTTGAG
*
9514215 TCTTAAATGATAATCTTTAAGACG
1 TCTTAAATGAGAATCTTT--GA-G
* *
9514239 TTTTCAAATGAGAATCTTTAAG
1 TCTT-AAATGAGAATCTTTGAG
* *
9514261 CCTTAAATAAGAATCTTTAAGATG
1 TCTTAAATGAGAATCTTT--GA-G
* * *
9514285 TTTTCAAATGAGAATTTTTTAG
1 TCTT-AAATGAGAATCTTTGAG
9514307 TCTTAAATGAGAATCTTT
1 TCTTAAATGAGAATCTTT
9514325 AAAATATTTT
Statistics
Matches: 103, Mismatches: 20, Indels: 21
0.72 0.14 0.15
Matches are distributed among these distances:
21 40 0.39
22 10 0.10
23 5 0.05
24 8 0.08
25 40 0.39
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (21 bp):
TCTTAAATGAGAATCTTTGAG
Found at i:9514246 original size:46 final size:46
Alignment explanation
Indices: 9514169--9514352 Score: 233
Period size: 46 Copynumber: 4.0 Consensus size: 46
9514159 AATCCTGATT
* ** *
9514169 TCTTAAATGAGAATCTTTAAAAAGTCCTCAAATAAGAATCTTTGAG
1 TCTTAAATGAGAATCTTTAAAATGTTTTCAAATGAGAATCTTTGAG
* * * *
9514215 TCTTAAATGATAATCTTTAAGACGTTTTCAAATGAGAATCTTTAAG
1 TCTTAAATGAGAATCTTTAAAATGTTTTCAAATGAGAATCTTTGAG
* * * * *
9514261 CCTTAAATAAGAATCTTTAAGATGTTTTCAAATGAGAATTTTTTAG
1 TCTTAAATGAGAATCTTTAAAATGTTTTCAAATGAGAATCTTTGAG
* *
9514307 TCTTAAATGAGAATCTTTAAAATATTTTTAAATGAGAATCTTTGAG
1 TCTTAAATGAGAATCTTTAAAATGTTTTCAAATGAGAATCTTTGAG
9514353 GTGTAAAATC
Statistics
Matches: 118, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 118 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (46 bp):
TCTTAAATGAGAATCTTTAAAATGTTTTCAAATGAGAATCTTTGAG
Found at i:9514247 original size:25 final size:25
Alignment explanation
Indices: 9514173--9514349 Score: 117
Period size: 25 Copynumber: 7.6 Consensus size: 25
9514163 CTGATTTCTT
* * **
9514173 AAATGAGAATCTTTAAAAAGTCCTC
1 AAATGAGAATCTTTAAGACGTTTTC
* *
9514198 AAATAAGAATCTTT--GA-GTCTT-
1 AAATGAGAATCTTTAAGACGTTTTC
*
9514219 AAATGATAATCTTTAAGACGTTTTC
1 AAATGAGAATCTTTAAGACGTTTTC
*
9514244 AAATGAGAATCTTTAAG-C--CTT-
1 AAATGAGAATCTTTAAGACGTTTTC
* *
9514265 AAATAAGAATCTTTAAGATGTTTTC
1 AAATGAGAATCTTTAAGACGTTTTC
** *
9514290 AAATGAGAAT-TTT-TTA-GTCTT-
1 AAATGAGAATCTTTAAGACGTTTTC
* ** *
9514311 AAATGAGAATCTTTAAAATATTTTT
1 AAATGAGAATCTTTAAGACGTTTTC
9514336 AAATGAGAATCTTT
1 AAATGAGAATCTTT
9514350 GAGGTGTAAA
Statistics
Matches: 121, Mismatches: 19, Indels: 24
0.74 0.12 0.15
Matches are distributed among these distances:
21 38 0.31
22 13 0.11
23 5 0.04
24 13 0.11
25 52 0.43
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (25 bp):
AAATGAGAATCTTTAAGACGTTTTC
Found at i:9514641 original size:3 final size:3
Alignment explanation
Indices: 9514607--9514726 Score: 111
Period size: 3 Copynumber: 38.3 Consensus size: 3
9514597 CCATATTTTT
*
9514607 TTA TT- TTA TT- TTA TTTA TTTA TTTA TTTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA TTA
* *
9514654 TTA TTTA TTTA TTA TTTA TTA TTA TTA TTA GTA TCA TTA TTTA TT- TTA
1 TTA -TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
9514702 TTA TTA TTA TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
9514727 CATTTTTTTT
Statistics
Matches: 102, Mismatches: 8, Indels: 14
0.82 0.06 0.11
Matches are distributed among these distances:
2 6 0.06
3 68 0.67
4 28 0.27
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9514649 original size:33 final size:34
Alignment explanation
Indices: 9514612--9514726 Score: 128
Period size: 33 Copynumber: 3.3 Consensus size: 34
9514602 TTTTTTTATT
*
9514612 TTATT-TTATTTATTTATTTATTTATTATTAGTA
1 TTATTATTATTTATTTATTTATTTATTATTACTA
*
9514645 TTATTATTA-TTATTTATTTA-TTATTTATTATTA
1 TTATTATTATTTATTTATTTATTTA-TTATTACTA
*
9514678 TTATTAGTATCATTATTTATTTTATTATTATTATTACTA
1 TTATTATTAT--TTATTTA-TTTA-T-TTATTATTACTA
9514717 TTATTATTAT
1 TTATTATTAT
9514727 CATTTTTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
32 3 0.04
33 32 0.46
34 3 0.04
36 7 0.10
37 4 0.06
39 17 0.25
40 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (34 bp):
TTATTATTATTTATTTATTTATTTATTATTACTA
Found at i:9514669 original size:36 final size:36
Alignment explanation
Indices: 9514608--9514731 Score: 164
Period size: 36 Copynumber: 3.5 Consensus size: 36
9514598 CATATTTTTT
*
9514608 TATT-TTATT-TTATTTATTTATTTATTTATTATTAG
1 TATTATTATTATTATTTATTTA-TTATTTATTATTAC
*
9514643 TATTATTATTATTATTTATTTATTATTTATTATTAT
1 TATTATTATTATTATTTATTTATTATTTATTATTAC
* *
9514679 TATTAGTATCATTATTTATTTTATTA-TTATTATTAC
1 TATTATTATTATTATTTA-TTTATTATTTATTATTAC
*
9514715 TATTATTATTATCATTT
1 TATTATTATTATTATTT
9514732 TTTTTGGATT
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
35 4 0.05
36 57 0.72
37 18 0.23
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (36 bp):
TATTATTATTATTATTTATTTATTATTTATTATTAC
Found at i:9514699 original size:4 final size:4
Alignment explanation
Indices: 9514600--9514673 Score: 61
Period size: 4 Copynumber: 19.0 Consensus size: 4
9514590 GATGGGCCCA
*
9514600 TATT TTTT TATTT TATTT TATT TATT TATT TATT TA-T TA-T TAGTAT
1 TATT TATT TA-TT TA-TT TATT TATT TATT TATT TATT TATT TA-T-T
9514646 TA-T TA-T TA-T TATT TATT TA-T TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
9514674 ATTATTATTA
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
3 18 0.29
4 32 0.52
5 9 0.15
6 3 0.05
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:9515834 original size:59 final size:57
Alignment explanation
Indices: 9515632--9515927 Score: 161
Period size: 59 Copynumber: 4.9 Consensus size: 57
9515622 AAAGAATTAA
* * * * * *
9515632 AAAAAAAACATTTTAAGGAAAAATTGAAATTATCAATTTTTCTTAAAAAATAAA-AT-
1 AAAAAAAACATTTTGAGGAAAAGTTGAAAGTATTAATTTTTCTT-GAAAATAAATGTG
* *
9515688 AAAATTTTCAAAAGCATTTTGA-GAGAAAGTTGAAAGTATTAATTTTTTTTGAAAATAAAAGTG
1 AAAA-----AAAA-CATTTTGAGGA-AAAGTTGAAAGTATTAATTTTTCTTGAAAATAAATGTG
**** * * *
9515751 TTCTAAAATATTTTGGAGGAAAAAGTTGAAAGTATTAATTTTTCTTGAAATTAAATTTCAG
1 AAAAAAAACATTTT-GAGG-AAAAGTTGAAAGTATTAATTTTTCTTGAAAATAAATGT--G
* * * * *
9515812 AAAAAAAACATTTTGAGGAAAAGTTGGAAA-TACTAATTTTCCTTAAAAATAAATAAAAATT
1 AAAAAAAACATTTTGAGGAAAAGTT-GAAAGTATTAATTTTTCTTGAAAATAAAT----GTG
* * * *
9515873 ATCAAGAAAAACATTTTAAGGAAATGTTGAAAGTATCAATTTTCCTT-AAAATAAA
1 A--AA-AAAAACATTTTGAGGAAAAGTTGAAAGTATTAATTTTTCTTGAAAATAAA
9515928 AAGCTTTCAA
Statistics
Matches: 186, Mismatches: 31, Indels: 39
0.73 0.12 0.15
Matches are distributed among these distances:
56 4 0.02
57 5 0.03
58 6 0.03
59 61 0.33
60 9 0.05
61 25 0.13
62 29 0.16
63 15 0.08
64 32 0.17
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (57 bp):
AAAAAAAACATTTTGAGGAAAAGTTGAAAGTATTAATTTTTCTTGAAAATAAATGTG
Found at i:9518153 original size:2 final size:2
Alignment explanation
Indices: 9518146--9518172 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9518136 ATCAGTTACA
9518146 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
9518173 AAGTATAACA
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:9527785 original size:19 final size:19
Alignment explanation
Indices: 9527761--9527804 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
9527751 TTGATATATG
* *
9527761 AAAAATCATTCTAATTATA
1 AAAAATCAGTCTAATAATA
*
9527780 AAAAATGAGTCTAATAATA
1 AAAAATCAGTCTAATAATA
9527799 AAAAAT
1 AAAAAT
9527805 TCACTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAATCAGTCTAATAATA
Found at i:9528392 original size:20 final size:20
Alignment explanation
Indices: 9528367--9528408 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
9528357 ATGAATTGGG
9528367 TATTTTAAGCTTATAGAATA
1 TATTTTAAGCTTATAGAATA
9528387 TATTTTAAGCTTATAGAATA
1 TATTTTAAGCTTATAGAATA
9528407 TA
1 TA
9528409 GATTTCTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (20 bp):
TATTTTAAGCTTATAGAATA
Found at i:9528534 original size:3 final size:3
Alignment explanation
Indices: 9528526--9528556 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
9528516 CATTAGTCTT
9528526 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
9528557 GTATGCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:9529584 original size:20 final size:20
Alignment explanation
Indices: 9529530--9529584 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
9529520 CAATTTATTA
9529530 TTTTTTTATGTGTTA-CTAC
1 TTTTTTTATGTGTTATCTAC
*
9529549 TTTTTTTATGTATTATC-AC
1 TTTTTTTATGTGTTATCTAC
*
9529568 TTTTTTTTTTGTGTTAT
1 -TTTTTTTATGTGTTAT
9529585 TAGTCTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.15, C:0.07, G:0.09, T:0.69
Consensus pattern (20 bp):
TTTTTTTATGTGTTATCTAC
Found at i:9529593 original size:20 final size:20
Alignment explanation
Indices: 9529530--9529593 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
9529520 CAATTTATTA
*
9529530 TTTTTTTATGTGTTACTA-C
1 TTTTTTTATGTGTTATTATC
* *
9529549 TTTTTTTATGTATTATCA-C
1 TTTTTTTATGTGTTATTATC
*
9529568 TTTTTTTTTTGTGTTATTAGTC
1 -TTTTTTTATGTGTTATTA-TC
9529590 TTTT
1 TTTT
9529594 GTAGACATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 16 0.44
20 15 0.42
21 4 0.11
22 1 0.03
ACGTcount: A:0.14, C:0.08, G:0.09, T:0.69
Consensus pattern (20 bp):
TTTTTTTATGTGTTATTATC
Found at i:9530014 original size:16 final size:16
Alignment explanation
Indices: 9529994--9530059 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
9529984 GATCTAAACC
9529994 TGAAATAATTTAAAAT
1 TGAAATAATTTAAAAT
* * *
9530010 CGAAATAATTTGAATT
1 TGAAATAATTTAAAAT
* **
9530026 TAAAATAATCAAAAAT
1 TGAAATAATTTAAAAT
9530042 TGAAATAATTTGAAAAT
1 TGAAATAATTT-AAAAT
9530059 T
1 T
9530060 TAATCCAAAA
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
16 31 0.84
17 6 0.16
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.35
Consensus pattern (16 bp):
TGAAATAATTTAAAAT
Found at i:9530530 original size:15 final size:15
Alignment explanation
Indices: 9530512--9530540 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9530502 TTAAAATCCA
9530512 AAATAATAAACTACT
1 AAATAATAAACTACT
9530527 AAATAATAAACTAC
1 AAATAATAAACTAC
9530541 AATTATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAATAAACTACT
Found at i:9539755 original size:115 final size:114
Alignment explanation
Indices: 9539550--9539776 Score: 346
Period size: 115 Copynumber: 2.0 Consensus size: 114
9539540 ACTGGGCCCA
*
9539550 ACCATGTGCCGCACCTCGATCATCAATGCTTTTGCTTGGCCTAACTGGGTGCTCGCGCATCTCGC
1 ACCATGCGCCGCACCTCGATCATCAATGCTTTTGCTTGGCCTAACTGGGTGCTCGCGCATCTCGC
* * * *
9539615 ACCAGCACCCACCCCAGGGCTTGACTCAATCCTGCGGAACCTAAACATT
66 ACCAACACCCACCCCAAGGCCTGACTCAATCCTACGGAACCTAAACATT
* * * *
9539664 ACCATGCGTCGCACCTTGATCATTAATGCTTTTGCTTGGGCCTAACTGGGTGCTCGTGCATCTCG
1 ACCATGCGCCGCACCTCGATCATCAATGCTTTTGCTT-GGCCTAACTGGGTGCTCGCGCATCTCG
* *
9539729 CACCAACGCCCACCCCAAGGCCTGACTCAATCTTACGGAACCTAAACA
65 CACCAACACCCACCCCAAGGCCTGACTCAATCCTACGGAACCTAAACA
9539777 CCTTCCTTAA
Statistics
Matches: 101, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
114 33 0.33
115 68 0.67
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (114 bp):
ACCATGCGCCGCACCTCGATCATCAATGCTTTTGCTTGGCCTAACTGGGTGCTCGCGCATCTCGC
ACCAACACCCACCCCAAGGCCTGACTCAATCCTACGGAACCTAAACATT
Found at i:9540131 original size:17 final size:17
Alignment explanation
Indices: 9540109--9540150 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
9540099 TTGTTATAAG
*
9540109 AAAAAAACTCAAA-AAA
1 AAAAAAAATCAAAGAAA
*
9540125 AAAAAAAATGAAAGGAAA
1 AAAAAAAATCAAA-GAAA
9540143 AAAAAAAA
1 AAAAAAAA
9540151 GAATTTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 11 0.50
18 11 0.50
ACGTcount: A:0.83, C:0.05, G:0.07, T:0.05
Consensus pattern (17 bp):
AAAAAAAATCAAAGAAA
Found at i:9542307 original size:13 final size:13
Alignment explanation
Indices: 9542291--9542329 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
9542281 TTTATTTTTA
*
9542291 ATTTTTATATATT
1 ATTTTAATATATT
**
9542304 ATTTTAATATAAA
1 ATTTTAATATATT
9542317 ATTTTAATATATT
1 ATTTTAATATATT
9542330 TAAGTGGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:9542401 original size:20 final size:18
Alignment explanation
Indices: 9542365--9542411 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
9542355 ATTTTTATTT
9542365 TATA-AAAATTTAAAATA
1 TATATAAAATTTAAAATA
*
9542382 TATATAAAATTTAAAAAA
1 TATATAAAATTTAAAATA
*
9542400 TATATATAATTT
1 TATATAAAATTT
9542412 CGTTCAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATATAAAATTTAAAATA
Found at i:9542857 original size:11 final size:12
Alignment explanation
Indices: 9542838--9542885 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
9542828 ATTTAAATCA
9542838 AATATAAATTTT
1 AATATAAATTTT
9542850 AATA-AAATTTATTT
1 AATATAAA--T-TTT
9542864 AATATAAATTTT
1 AATATAAATTTT
9542876 AATA-AAATTT
1 AATATAAATTT
9542886 ATTTAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 9 0.28
12 11 0.34
13 2 0.06
14 7 0.22
15 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATATAAATTTT
Found at i:9542866 original size:14 final size:14
Alignment explanation
Indices: 9542847--9542920 Score: 82
Period size: 14 Copynumber: 5.4 Consensus size: 14
9542837 AAATATAAAT
9542847 TTTAATAAAATTTA
1 TTTAATAAAATTTA
9542861 TTTAATATAAA--T-
1 TTTAATA-AAATTTA
9542873 TTTAATAAAATTTA
1 TTTAATAAAATTTA
* *
9542887 TTTAATATAATTTT
1 TTTAATAAAATTTA
* *
9542901 TTTTATAAAATTTT
1 TTTAATAAAATTTA
9542915 TTTAAT
1 TTTAAT
9542921 CATAAATACA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
11 3 0.06
12 7 0.14
13 2 0.04
14 36 0.71
15 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAAAATTTA
Found at i:9542868 original size:26 final size:26
Alignment explanation
Indices: 9542838--9542927 Score: 126
Period size: 26 Copynumber: 3.3 Consensus size: 26
9542828 ATTTAAATCA
9542838 AATATAAATTTTAATAAAATTTATTT
1 AATATAAATTTTAATAAAATTTATTT
9542864 AATATAAATTTTAATAAAATTTATTT
1 AATATAAATTTTAATAAAATTTATTT
* * *
9542890 AATATAATTTTTTTTATAAAATTTTTTT
1 AATATAA--ATTTTAATAAAATTTATTT
9542918 AATCATAAAT
1 AAT-ATAAAT
9542928 ACAAAAACTT
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
26 33 0.58
27 1 0.02
28 19 0.33
29 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (26 bp):
AATATAAATTTTAATAAAATTTATTT
Found at i:9546099 original size:27 final size:25
Alignment explanation
Indices: 9546069--9546134 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
9546059 ATACCTAAAT
*
9546069 TTTAAATATTTTAAATATTATATATTA
1 TTTAAATATTTTAAATA--ATATATAA
* *
9546096 TTTATGAATGTTTTAACTAATATATAA
1 TTTA--AATATTTTAAATAATATATAA
9546123 TTTAAA-ATTTTA
1 TTTAAATATTTTA
9546135 TTTATCTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
24 5 0.15
25 2 0.06
27 15 0.45
29 11 0.33
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (25 bp):
TTTAAATATTTTAAATAATATATAA
Found at i:9546251 original size:12 final size:12
Alignment explanation
Indices: 9546236--9546265 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
9546226 AATTTTTAAA
9546236 ATTAAATATTTC
1 ATTAAATATTTC
9546248 ATTAAATATTTC
1 ATTAAATATTTC
9546260 ATTAAA
1 ATTAAA
9546266 GTCATTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTAAATATTTC
Found at i:9550337 original size:3 final size:3
Alignment explanation
Indices: 9550329--9550393 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
9550319 CAGATTTTAC
*
9550329 TAT TAT TAT TAT TAT TAT TCT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9550377 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
9550394 GATTTTTGAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:9552722 original size:39 final size:39
Alignment explanation
Indices: 9552592--9552727 Score: 143
Period size: 39 Copynumber: 3.5 Consensus size: 39
9552582 GGTATTATCG
* *
9552592 TTATTTTTAAAGTTGTGTGC-TTCTATTGAT-AAAGAACTC
1 TTATTTTTAAAGTTGTGTGCATT-TATTGATGAGA-AACCC
* * *
9552631 TTA-TTTTAAAGTTGTGTGCACCTCTATTGATGAGGAGCCC
1 TTATTTTTAAAGTTGTGTGCA--TTTATTGATGAGAAACCC
* * *
9552671 TTATGTTTAAAGTTGTGTGCATTTATTTATGTGAAACCC
1 TTATTTTTAAAGTTGTGTGCATTTATTGATGAGAAACCC
9552710 TTATTTTTAAAGTTGTGT
1 TTATTTTTAAAGTTGTGT
9552728 ACCTCTATTT
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
38 16 0.20
39 33 0.41
40 13 0.16
41 18 0.22
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (39 bp):
TTATTTTTAAAGTTGTGTGCATTTATTGATGAGAAACCC
Found at i:9554852 original size:54 final size:53
Alignment explanation
Indices: 9554784--9554892 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 53
9554774 GATTCCAAGA
* *
9554784 AAGATATTTCTAAATTTA-ACTCAAATTG-TGAAAATTTCATAAATGAAACTTGT
1 AAGATATTTCTAAA-TTAGACTCAAA-TGATGAAAATTTCAAAAATAAAACTTGT
** *
9554837 AAGATATTTTCTAAATTAGGTTCAAATGATGAAAATTTTAAAAATAAAACTTGT
1 AAGATA-TTTCTAAATTAGACTCAAATGATGAAAATTTCAAAAATAAAACTTGT
9554891 AA
1 AA
9554893 AATACAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
53 11 0.23
54 37 0.77
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (53 bp):
AAGATATTTCTAAATTAGACTCAAATGATGAAAATTTCAAAAATAAAACTTGT
Found at i:9566320 original size:164 final size:164
Alignment explanation
Indices: 9566038--9566366 Score: 577
Period size: 164 Copynumber: 2.0 Consensus size: 164
9566028 AAGTACATTG
*
9566038 ATCATGATACTAAGAAATCATAAGAGCATTACCATAAGCTATTGCTGAAGCAATATTGAGCTTTG
1 ATCATGATACTAAGAAATCATAAGAGCATTACCAGAAGCTATTGCTGAAGCAATATTGAGCTTTG
* * *
9566103 ACTCATCAGAGAGGCCTTCTGAAGAGACAAGGACGACAGCCACGCTCCTGGCTTGAGCAGTCTTT
66 ACTCATCAGAAAGGCCTTCTGAAGAGACAAGGACGACAGCCACACTACTGGCTTGAGCAGTCTTT
9566168 GCGGTTGCAGAAACAGCCTCACCAAGCCCACGAA
131 GCGGTTGCAGAAACAGCCTCACCAAGCCCACGAA
* * *
9566202 ATCATGGTACTAAGAAATTATAAGAGCATTACCAGAAGCTATTGCTGAAGCAGTATTGAGCTTTG
1 ATCATGATACTAAGAAATCATAAGAGCATTACCAGAAGCTATTGCTGAAGCAATATTGAGCTTTG
*
9566267 ACTCATCAGAAAGGCCTTCTGAAGAGGCAAGGACGACAGCCACACTACTGGCTTGAGCAGTCTTT
66 ACTCATCAGAAAGGCCTTCTGAAGAGACAAGGACGACAGCCACACTACTGGCTTGAGCAGTCTTT
*
9566332 GCGGTTGCAGCAACAGCCTCACCAAGCCCACGAA
131 GCGGTTGCAGAAACAGCCTCACCAAGCCCACGAA
9566366 A
1 A
9566367 AGCAGCTGGA
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
164 156 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.21
Consensus pattern (164 bp):
ATCATGATACTAAGAAATCATAAGAGCATTACCAGAAGCTATTGCTGAAGCAATATTGAGCTTTG
ACTCATCAGAAAGGCCTTCTGAAGAGACAAGGACGACAGCCACACTACTGGCTTGAGCAGTCTTT
GCGGTTGCAGAAACAGCCTCACCAAGCCCACGAA
Found at i:9568121 original size:20 final size:20
Alignment explanation
Indices: 9568096--9568135 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9568086 CTTAGTTTTC
9568096 TATATTCTTTTGTTGTATAA
1 TATATTCTTTTGTTGTATAA
9568116 TATATTCTTTTGTTGTATAA
1 TATATTCTTTTGTTGTATAA
9568136 AGTGTTCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (20 bp):
TATATTCTTTTGTTGTATAA
Found at i:9568855 original size:45 final size:45
Alignment explanation
Indices: 9568805--9568890 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
9568795 AGAATTAATG
* * *
9568805 AGGATAT-GGTTAGGCATGAATTTTATGATGGTTTAGGTGTTGATA
1 AGGATATGGGTAAGG-ATGAATTTAATGATGGTTTAGATGTTGATA
*
9568850 AGGATATGGGTAATGATGAATTTAATGATGGTTTAGATGTT
1 AGGATATGGGTAAGGATGAATTTAATGATGGTTTAGATGTT
9568891 ATTGGCGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 31 0.86
46 5 0.14
ACGTcount: A:0.29, C:0.01, G:0.30, T:0.40
Consensus pattern (45 bp):
AGGATATGGGTAAGGATGAATTTAATGATGGTTTAGATGTTGATA
Found at i:9572892 original size:2 final size:2
Alignment explanation
Indices: 9572885--9572909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9572875 GGTTAGTATT
9572885 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
9572910 TTCTCTAAAA
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:9574234 original size:20 final size:20
Alignment explanation
Indices: 9574209--9574248 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9574199 CTTAGTTTTC
9574209 TATATTCTTTTGTTGTATAA
1 TATATTCTTTTGTTGTATAA
9574229 TATATTCTTTTGTTGTATAA
1 TATATTCTTTTGTTGTATAA
9574249 AGTGTTCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (20 bp):
TATATTCTTTTGTTGTATAA
Found at i:9574968 original size:45 final size:45
Alignment explanation
Indices: 9574918--9575003 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
9574908 AGAATTAATG
* * *
9574918 AGGATAT-GGTTAGGCATGAATTTTATGATGGTTTAGGTGTTGATA
1 AGGATATGGGTAAGG-ATGAATTTAATGATGGTTTAGATGTTGATA
*
9574963 AGGATATGGGTAATGATGAATTTAATGATGGTTTAGATGTT
1 AGGATATGGGTAAGGATGAATTTAATGATGGTTTAGATGTT
9575004 ATTGGCGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 31 0.86
46 5 0.14
ACGTcount: A:0.29, C:0.01, G:0.30, T:0.40
Consensus pattern (45 bp):
AGGATATGGGTAAGGATGAATTTAATGATGGTTTAGATGTTGATA
Found at i:9577972 original size:13 final size:14
Alignment explanation
Indices: 9577949--9577977 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9577939 GATTGTTGAA
9577949 CTTTGTTTTTTTTT
1 CTTTGTTTTTTTTT
9577963 CTTT-TTTTTTTTT
1 CTTTGTTTTTTTTT
9577976 CT
1 CT
9577978 ATTAGTACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.86
Consensus pattern (14 bp):
CTTTGTTTTTTTTT
Found at i:9580348 original size:20 final size:20
Alignment explanation
Indices: 9580323--9580362 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9580313 CTTAGTTTTC
9580323 TATATTCTTTTGTTGTATAA
1 TATATTCTTTTGTTGTATAA
9580343 TATATTCTTTTGTTGTATAA
1 TATATTCTTTTGTTGTATAA
9580363 AGTGTTCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (20 bp):
TATATTCTTTTGTTGTATAA
Found at i:9581082 original size:45 final size:45
Alignment explanation
Indices: 9581032--9581117 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
9581022 AGAATTAATG
* * *
9581032 AGGATAT-GGTTAGGCATGAATTTTATGATGGTTTAGGTGTTGATA
1 AGGATATGGGTAAGG-ATGAATTTAATGATGGTTTAGATGTTGATA
*
9581077 AGGATATGGGTAATGATGAATTTAATGATGGTTTAGATGTT
1 AGGATATGGGTAAGGATGAATTTAATGATGGTTTAGATGTT
9581118 ATTGGCGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 31 0.86
46 5 0.14
ACGTcount: A:0.29, C:0.01, G:0.30, T:0.40
Consensus pattern (45 bp):
AGGATATGGGTAAGGATGAATTTAATGATGGTTTAGATGTTGATA
Found at i:9584090 original size:13 final size:14
Alignment explanation
Indices: 9584067--9584095 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9584057 GATTGTTGAA
9584067 CTTTGTTTTTTTTT
1 CTTTGTTTTTTTTT
9584081 CTTT-TTTTTTTTT
1 CTTTGTTTTTTTTT
9584094 CT
1 CT
9584096 ATTAGTACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.86
Consensus pattern (14 bp):
CTTTGTTTTTTTTT
Found at i:9586464 original size:19 final size:20
Alignment explanation
Indices: 9586440--9586478 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9586430 CTTAGTTTTC
9586440 TATATTC-TTTGTTGTATAA
1 TATATTCTTTTGTTGTATAA
9586459 TATATTCTTTTGTTGTATAA
1 TATATTCTTTTGTTGTATAA
9586479 AGTGTTCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (20 bp):
TATATTCTTTTGTTGTATAA
Found at i:9587209 original size:45 final size:45
Alignment explanation
Indices: 9587159--9587244 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
9587149 AGAATTAATG
* * *
9587159 AGGATAT-GGTTAGGCATGAATTTTATGATGGTTTAGGTGTTGATA
1 AGGATATGGGTAAGG-ATGAATTTAATGATGGTTTAGATGTTGATA
*
9587204 AGGATATGGGTAATGATGAATTTAATGATGGTTTAGATGTT
1 AGGATATGGGTAAGGATGAATTTAATGATGGTTTAGATGTT
9587245 ATTGGCGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 31 0.86
46 5 0.14
ACGTcount: A:0.29, C:0.01, G:0.30, T:0.40
Consensus pattern (45 bp):
AGGATATGGGTAAGGATGAATTTAATGATGGTTTAGATGTTGATA
Found at i:9590215 original size:13 final size:14
Alignment explanation
Indices: 9590192--9590220 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9590182 GATTGTTGAA
9590192 CTTTGTTTTTTTTT
1 CTTTGTTTTTTTTT
9590206 CTTT-TTTTTTTTT
1 CTTTGTTTTTTTTT
9590219 CT
1 CT
9590221 ATTAGTACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.86
Consensus pattern (14 bp):
CTTTGTTTTTTTTT
Found at i:9597681 original size:77 final size:77
Alignment explanation
Indices: 9597554--9597704 Score: 205
Period size: 77 Copynumber: 2.0 Consensus size: 77
9597544 TATCCCTATA
* * * * * *
9597554 TTATTGATGAGTCATCTTATAAAGGATAAATTCATAATGCTTTTATGACCATAAAATGCTCTAAT
1 TTATTGATGAGTCACCTTATAAAGGATAAATCCATAATGCTGTTATGACCAAAAAATACCCTAAT
9597619 CATATGTTCTTC
66 CATATGTTCTTC
* *
9597631 TTATTTATGAGTCACCTTATGAAA-GATAAATCCATAATTCTGTTATGACCAAAAAATACCCTAA
1 TTATTGATGAGTCACCTTAT-AAAGGATAAATCCATAATGCTGTTATGACCAAAAAATACCCTAA
*
9597695 TCGTATGTTC
65 TCATATGTTC
9597705 CTTTATCAAG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
77 61 0.95
78 3 0.05
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (77 bp):
TTATTGATGAGTCACCTTATAAAGGATAAATCCATAATGCTGTTATGACCAAAAAATACCCTAAT
CATATGTTCTTC
Found at i:9597907 original size:43 final size:43
Alignment explanation
Indices: 9597859--9597940 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
9597849 GTGATCCTTA
* * *
9597859 TAGAGCCAAGCTTATATTTATGATGGTCCTAACATGATTTTTG
1 TAGAGCCAAGCCTATATTTAGGATAGTCCTAACATGATTTTTG
* *
9597902 TAGAGCCAAGCCTATCTTTAGGATAGTCCTAACGTGATT
1 TAGAGCCAAGCCTATATTTAGGATAGTCCTAACATGATT
9597941 CTTATAAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (43 bp):
TAGAGCCAAGCCTATATTTAGGATAGTCCTAACATGATTTTTG
Found at i:9612613 original size:74 final size:74
Alignment explanation
Indices: 9612523--9612691 Score: 297
Period size: 74 Copynumber: 2.3 Consensus size: 74
9612513 ATAAAAAAAA
*
9612523 ATTATTTAA-ATTGTTTTCTATAAAAATAAAATGTCCATAATTTAAATGAACCATAATATAATTT
1 ATTATTTAAGA-TGTTTTCTATAAAAATAAAATGTCCATAATTTAAATGAACCATAACATAATTT
9612587 TTATTAAAGG
65 TTATTAAAGG
9612597 ATTATTTAAGATGTTTTCTATAAAAATAAAATGTCCATAATTTAAATGAACCATAACATAATTTT
1 ATTATTTAAGATGTTTTCTATAAAAATAAAATGTCCATAATTTAAATGAACCATAACATAATTTT
*
9612662 TGTTAAAGG
66 TATTAAAGG
9612671 ATTATTTAAGATGTTTT-TATA
1 ATTATTTAAGATGTTTTCTATA
9612692 TATAACATAT
Statistics
Matches: 92, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
73 4 0.04
74 87 0.95
75 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (74 bp):
ATTATTTAAGATGTTTTCTATAAAAATAAAATGTCCATAATTTAAATGAACCATAACATAATTTT
TATTAAAGG
Found at i:9613478 original size:1 final size:1
Alignment explanation
Indices: 9613472--9613496 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
9613462 AAAGAGCTGG
9613472 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
9613497 ACAGGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9620988 original size:2 final size:2
Alignment explanation
Indices: 9620981--9621013 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9620971 TTCCGGCAAA
9620981 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 A
9621014 ATTGAACATG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9625385 original size:18 final size:19
Alignment explanation
Indices: 9625364--9625405 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
9625354 TTATATAATA
* *
9625364 TTTAT-AAAAATTTTAAAT
1 TTTATAAAAAAATTAAAAT
9625382 TTTATAAAAAAATTAAAAT
1 TTTATAAAAAAATTAAAAT
9625401 TTTAT
1 TTTAT
9625406 TATATATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTATAAAAAAATTAAAAT
Found at i:9625444 original size:22 final size:22
Alignment explanation
Indices: 9625393--9625443 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
9625383 TTATAAAAAA
*
9625393 ATTAAAATTTTATTATATATGT
1 ATTAAAATTTTATTATATATGC
* *
9625415 ATTAAAATTTTAATTTTTTATGC
1 ATTAAAATTTT-ATTATATATGC
9625438 ATTAAA
1 ATTAAA
9625444 TAAAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTAAAATTTTATTATATATGC
Found at i:9629083 original size:35 final size:35
Alignment explanation
Indices: 9629037--9629105 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
9629027 TTTTATCATG
*
9629037 TTTAACGAAACATGATATATCTCAACGATCTTAAC
1 TTTAACGAAACATGATATATCTCAAAGATCTTAAC
*
9629072 TTTAAGGAAACATGATATATCTCAAAGATCTTAA
1 TTTAACGAAACATGATATATCTCAAAGATCTTAA
9629106 ATTGATGCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (35 bp):
TTTAACGAAACATGATATATCTCAAAGATCTTAAC
Found at i:9630874 original size:57 final size:57
Alignment explanation
Indices: 9630805--9630917 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
9630795 CTTTTCTCAT
*
9630805 TCTAAAAGTCTCACAATTGTAAAGATTTATTTGATAGTGGATTAGGTTTGGAGTAGG
1 TCTAAAAGTCTCACAATTGTAAAGATTTATTTGATAATGGATTAGGTTTGGAGTAGG
9630862 TCTAAAAGTCTCACAATTGTAAAGATTTATTTGATAATGGATTAGGTTTGGAGTAG
1 TCTAAAAGTCTCACAATTGTAAAGATTTATTTGATAATGGATTAGGTTTGGAGTAG
9630918 ACCATTTTGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (57 bp):
TCTAAAAGTCTCACAATTGTAAAGATTTATTTGATAATGGATTAGGTTTGGAGTAGG
Found at i:9633598 original size:13 final size:13
Alignment explanation
Indices: 9633580--9633611 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
9633570 ATTCGCATCC
9633580 AACTCCACAAAGT
1 AACTCCACAAAGT
9633593 AACTCCACAAAGT
1 AACTCCACAAAGT
9633606 AACTCC
1 AACTCC
9633612 TATCATTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.34, G:0.06, T:0.16
Consensus pattern (13 bp):
AACTCCACAAAGT
Found at i:9637683 original size:15 final size:16
Alignment explanation
Indices: 9637645--9637697 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
9637635 TTGAAGTATC
* *
9637645 AATTTTCTTTAAAGAA
1 AATTTTATTTTAAGAA
**
9637661 AAAATTATTTTAA-AA
1 AATTTTATTTTAAGAA
9637676 AATTTTATTTTAAGAA
1 AATTTTATTTTAAGAA
9637692 AATTTT
1 AATTTT
9637698 CAAATATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTTTATTTTAAGAA
Found at i:9637735 original size:16 final size:16
Alignment explanation
Indices: 9637690--9637738 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
9637680 TTATTTTAAG
* *
9637690 AAAATTTTCAAATATA
1 AAAATTTTTAAAAATA
**
9637706 AATTTTTCTTAAAAATA
1 AAAATTT-TTAAAAATA
9637723 AAAATTTTTAAAAATA
1 AAAATTTTTAAAAATA
9637739 TTTTGAGGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATTTTTAAAAATA
Found at i:9637954 original size:57 final size:55
Alignment explanation
Indices: 9637602--9638023 Score: 211
Period size: 58 Copynumber: 7.3 Consensus size: 55
9637592 AAAATATTTC
* * * *
9637602 AAAAATATTTTAAAAAATTTTTTGAGAAAAAAATTGAAGT-ATCAATTTTCTTTAAAGAA
1 AAAAATATTTTAAAAAA-ATTTTAAG-AAAAAGTTGAAGTAAT-AATTTT-TCTAAA-AA
* ** * *
9637661 AAAATTATTTTAAAAAATTTTATTTTAAGAAAATTTTCAAAT-ATAAATTTTTCTTAAAAA
1 AAAAATATTTTAAAAAA----ATTTTAAGAAAAAGTTGAAGTAAT-AATTTTTC-TAAAAA
* * * *
9637721 TAAAAAT-TTTTAAAAATATTTTGAGGAAAAGTTGAAGT-ATCAACTTTT-T--AAA
1 -AAAAATATTTTAAAAAAATTTTAAGAAAAAGTTGAAGTAAT-AATTTTTCTAAAAA
** * *
9637773 AAAAATA-TAGAAAAAAATGGCATTTTAGGAAAAGTTGAAG-AATTAATTTTTCCTAAAATA
1 AAAAATATTTTAAAAAAAT----TTTAAGAAAAAGTTGAAGTAA-TAATTTTT-CTAAAA-A
* * * *
9637833 AAAGTAATGTTTTAGAAAAATGTTTTAAAGAAAAA-TTGAAGTATTAATTTTCCTAAAATAA
1 AAA--AATATTTTA-AAAAA-ATTTT-AAGAAAAAGTTGAAGTAATAATTTTTCT-AAA-AA
9637894 AAAAATATTTTAAAAAAATTGTTAAGAAAAAGTTGAAGTAATAATTTTTCTAAAATAA
1 AAAAATATTTTAAAAAAATT-TTAAGAAAAAGTTGAAGTAATAATTTTTCT-AAA-AA
* * * * *
9637952 AAAAATATTTCAAAAAATATTTAAAG-AAAGGTTGAAG-AACCAATTTTTCTTAAAAC
1 AAAAATATTTTAAAAAA-ATTTTAAGAAAAAGTTGAAGTAA-TAATTTTTC-TAAAAA
* *
9638008 AAAAATAATTTCAAAA
1 AAAAATATTTTAAAAA
9638024 GGATTTGAGG
Statistics
Matches: 288, Mismatches: 44, Indels: 65
0.73 0.11 0.16
Matches are distributed among these distances:
51 14 0.05
52 3 0.01
54 1 0.00
55 24 0.08
56 40 0.14
57 32 0.11
58 52 0.18
59 29 0.10
60 18 0.06
61 49 0.17
62 18 0.06
63 2 0.01
64 5 0.02
65 1 0.00
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (55 bp):
AAAAATATTTTAAAAAAATTTTAAGAAAAAGTTGAAGTAATAATTTTTCTAAAAA
Found at i:9638006 original size:58 final size:58
Alignment explanation
Indices: 9637801--9638023 Score: 231
Period size: 58 Copynumber: 3.8 Consensus size: 58
9637791 GGCATTTTAG
* * * *
9637801 GAAAAGTTGAAGAATTAATTTTTCCTAAAATAAAAGTAATGTTTTAGAAAAATGTTTTAAA
1 GAAAAGTTGAAGAATTAATTTTTCCTAAAATAAAA-AAATATTTCA-AAAAAT-ATTTAAA
* * * *
9637862 GAAAAATTGAAGTATTAA-TTTTCCTAAAATAAAAAAATATTTTAAAAAA-ATTGTTAA
1 GAAAAGTTGAAGAATTAATTTTTCCTAAAATAAAAAAATATTTCAAAAAATATT-TAAA
9637919 GAAAAAGTTGAAGTAA-TAATTTTT-CTAAAATAAAAAAATATTTCAAAAAATATTTAAA
1 G-AAAAGTTGAAG-AATTAATTTTTCCTAAAATAAAAAAATATTTCAAAAAATATTTAAA
* ** * * *
9637977 GAAAGGTTGAAGAACCAATTTTTCTTAAAACAAAAATA-ATTTCAAAA
1 GAAAAGTTGAAGAATTAATTTTTCCTAAAATAAAAAAATATTTCAAAA
9638024 GGATTTGAGG
Statistics
Matches: 140, Mismatches: 15, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
56 4 0.03
57 30 0.21
58 58 0.41
59 16 0.11
60 16 0.11
61 16 0.11
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.33
Consensus pattern (58 bp):
GAAAAGTTGAAGAATTAATTTTTCCTAAAATAAAAAAATATTTCAAAAAATATTTAAA
Found at i:9642094 original size:7 final size:7
Alignment explanation
Indices: 9642082--9642136 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 7
9642072 TTAAACTCAT
9642082 AAGAAAA
1 AAGAAAA
9642089 AAGAAAA
1 AAGAAAA
*
9642096 AAG-GAA
1 AAGAAAA
9642102 AAGAAAA
1 AAGAAAA
*
9642109 AA-ATGAA
1 AAGA-AAA
9642116 AA-AAAA
1 AAGAAAA
9642122 AAGAAAA
1 AAGAAAA
9642129 AAGAAAA
1 AAGAAAA
9642136 A
1 A
9642137 TAAGGAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 10 0.24
7 31 0.76
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAGAAAA
Found at i:9642117 original size:27 final size:28
Alignment explanation
Indices: 9642087--9642146 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
9642077 CTCATAAGAA
* *
9642087 AAAAGAAAAAAG-GAAAAGAAAAA-AATG
1 AAAA-AAAAAAGAAAAAAGAAAAATAAGG
9642114 AAAAAAAAAAGAAAAAAGAAAAATAAGG
1 AAAAAAAAAAGAAAAAAGAAAAATAAGG
9642142 AAAAA
1 AAAAA
9642147 GATGAAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.24
27 14 0.48
28 8 0.28
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (28 bp):
AAAAAAAAAAGAAAAAAGAAAAATAAGG
Found at i:9642120 original size:12 final size:11
Alignment explanation
Indices: 9642085--9642135 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
9642075 AACTCATAAG
9642085 AAAAAAGAAAA
1 AAAAAAGAAAA
9642096 AAGGAAAAG--AA
1 AA--AAAAGAAAA
*
9642107 AAAAATGAAAA
1 AAAAAAGAAAA
9642118 AAAAAAGAAAA
1 AAAAAAGAAAA
9642129 AAGAAAA
1 AA-AAAA
9642136 ATAAGGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
9 4 0.12
11 20 0.61
12 4 0.12
13 5 0.15
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:9642190 original size:16 final size:17
Alignment explanation
Indices: 9642169--9642200 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
9642159 GTTTGAAGGA
9642169 AAGAAAAATG-TCCTTT
1 AAGAAAAATGATCCTTT
9642185 AAGAAAAATGATCCTT
1 AAGAAAAATGATCCTT
9642201 GGTTCAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
AAGAAAAATGATCCTTT
Found at i:9642410 original size:17 final size:17
Alignment explanation
Indices: 9642378--9642412 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9642368 TACTAAATGT
* *
9642378 TAAAATCATTTTAATAA
1 TAAAATCATCTCAATAA
9642395 TAAAATCATCTCAATAA
1 TAAAATCATCTCAATAA
9642412 T
1 T
9642413 TATATTACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAATCATCTCAATAA
Found at i:9646917 original size:14 final size:14
Alignment explanation
Indices: 9646898--9646926 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9646888 ACAATCTAAA
9646898 ACTCTACAAACCTT
1 ACTCTACAAACCTT
9646912 ACTCTACAAACCTT
1 ACTCTACAAACCTT
9646926 A
1 A
9646927 ATTATAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (14 bp):
ACTCTACAAACCTT
Found at i:9648727 original size:46 final size:46
Alignment explanation
Indices: 9648666--9648760 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 46
9648656 CAACAAAACG
* *
9648666 TTTTAAGGAAAAGTTAAAGTATCAATTTTCTTCA-AATAAAAAAATA
1 TTTTAAAGAAAAGTTAAACTATCAATTTT-TTCAGAATAAAAAAATA
* * *
9648712 TTTTAAAGAACAGTTAAACTATTAATTTTTTTAGAATAAAAAAATA
1 TTTTAAAGAAAAGTTAAACTATCAATTTTTTCAGAATAAAAAAATA
9648758 TTT
1 TTT
9648761 CAAAAAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 3 0.07
46 40 0.93
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.39
Consensus pattern (46 bp):
TTTTAAAGAAAAGTTAAACTATCAATTTTTTCAGAATAAAAAAATA
Done.