Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 9 of 77
Found at i:1323630 original size:3 final size:3
Alignment explanation
Indices: 1323624--1323659 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1323614 TTGTTGTGAA
1323624 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1323660 TTGTATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1324464 original size:15 final size:15
Alignment explanation
Indices: 1324426--1324457 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1324416 TAGTGATAAC
1324426 ATAA-AATAACAATA
1 ATAATAATAACAATA
1324440 ATAATAATAACAATA
1 ATAATAATAACAATA
1324455 ATA
1 ATA
1324458 TCAATAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (15 bp):
ATAATAATAACAATA
Found at i:1324506 original size:23 final size:21
Alignment explanation
Indices: 1324468--1324525 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
1324458 TCAATAAACT
1324468 AAATAAAT-AAAT--AACATA
1 AAATAAATAAAATCAAACATA
1324486 AAATAATATAAGAATCAAACATA
1 AAATAA-ATAA-AATCAAACATA
1324509 AAATAAATAAAATCAAA
1 AAATAAATAAAATCAAA
1324526 ATCAAAACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.17
19 2 0.06
20 1 0.03
21 10 0.29
22 4 0.11
23 12 0.34
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.21
Consensus pattern (21 bp):
AAATAAATAAAATCAAACATA
Found at i:1324514 original size:28 final size:29
Alignment explanation
Indices: 1324478--1324544 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
1324468 AAATAAATAA
* *
1324478 ATAACATAAAATAATAT-AAGAATC-AAAC
1 ATAAAATAAAATAAAATCAA-AATCAAAAC
1324506 ATAAAAT-AAATAAAATCAAAATCAAAAC
1 ATAAAATAAAATAAAATCAAAATCAAAAC
*
1324534 AAAAAATAAAA
1 ATAAAATAAAA
1324545 AGAAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 12 0.36
28 18 0.55
29 3 0.09
ACGTcount: A:0.72, C:0.09, G:0.01, T:0.18
Consensus pattern (29 bp):
ATAAAATAAAATAAAATCAAAATCAAAAC
Found at i:1324544 original size:5 final size:5
Alignment explanation
Indices: 1324421--1324537 Score: 53
Period size: 6 Copynumber: 22.2 Consensus size: 5
1324411 ATTATTAGTG
* * * *
1324421 ATAAC ATAAA ATAACA ATAATA ATAATA ACAATA ATATCA ATAAA CT-AA
1 ATAAA ATAAA ATAA-A ATAA-A ATAA-A ATAA-A ATA-AA ATAAA ATAAA
* *
1324470 AT-AA AT-AA ATAAC ATAAA ATAAT ATAAGA ATCAAA CATAAA AT-AA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAA-A AT-AAA -ATAAA ATAAA
*
1324515 ATAAA ATCAAA ATCAAA ACAAA A
1 ATAAA AT-AAA AT-AAA ATAAA A
1324538 AATAAAAAGA
Statistics
Matches: 91, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
4 15 0.16
5 33 0.36
6 39 0.43
7 4 0.04
ACGTcount: A:0.68, C:0.09, G:0.01, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:1324550 original size:24 final size:24
Alignment explanation
Indices: 1324513--1324563 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1324503 AACATAAAAT
*
1324513 AAATAAAATC-AAAATCAAAACAAA
1 AAATAAAAACAAAAAT-AAAACAAA
* *
1324537 AAATAAAAAGAAAAATAAAAGAAA
1 AAATAAAAACAAAAATAAAACAAA
1324561 AAA
1 AAA
1324564 CCTGCCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.80, C:0.06, G:0.04, T:0.10
Consensus pattern (24 bp):
AAATAAAAACAAAAATAAAACAAA
Found at i:1325706 original size:40 final size:40
Alignment explanation
Indices: 1325662--1326111 Score: 315
Period size: 40 Copynumber: 11.4 Consensus size: 40
1325652 ACCAGAGGCT
* *
1325662 ATGAAACTTTAAATTCAAAAGGCTCCTCTAACTAGTGGTA
1 ATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGAGGTA
* ** * * *
1325702 ATGAAACTTTAAATTAAAAAATCTCCTCTAACCAGAGGCA
1 ATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGAGGTA
** * * *
1325742 ACAAAAATTTAAATTCAAAAAGCTCATTTAACTAGAGGTA
1 ATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGAGGTA
* *
1325782 ATGAAACTTTAAATTCAAAAGG---AGC--A--A-AGGCA
1 ATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGAGGTA
* * * *
1325814 A-CATAACTTTAAATTCAAAAGGCTCATCTGACCAAAGGCT-
1 ATGA-AACTTTAAATTCAAAAGGCTCATCTAACTAGAGG-TA
* *
1325854 ATGAAACTTTAAATTTAAAAGGCTCATCTAACTAGAGGTT
1 ATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGAGGTA
** * *
1325894 ATGAAACTTTAAATTCAAAAGGCTCCCCTAACCA-ACGGCA
1 ATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGA-GGTA
* * * **
1325934 ATGTAAA-TTTAAATTCAAAAGGCTTATATGACTAGAAACT-
1 ATG-AAACTTTAAATTCAAAAGGCTCATCTAACTAG-AGGTA
* * *
1325974 ATGAAACTTTAAATTTAAAAGGCTCATTTGA-TCAGAGAG-A
1 ATGAAACTTTAAATTCAAAAGGCTCATCTAACT-AGAG-GTA
* * * * *
1326014 ATGAAACTTTAAATTTAAAAAGCTCCTCTAACCAGAGATTA
1 ATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGAG-GTA
* * *
1326055 CT-AAACTTTAAATGCAAAAGGCTCATCTAAGC-AGAAGCT-
1 ATGAAACTTTAAATTCAAAAGGCTCATCTAA-CTAG-AGGTA
1326094 ATGAAACTTTAAATTCAA
1 ATGAAACTTTAAATTCAA
1326112 GTTATGAAAC
Statistics
Matches: 321, Mismatches: 64, Indels: 50
0.74 0.15 0.11
Matches are distributed among these distances:
31 1 0.00
32 23 0.07
33 1 0.00
35 3 0.01
37 2 0.01
39 9 0.03
40 272 0.85
41 9 0.03
42 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.27
Consensus pattern (40 bp):
ATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGAGGTA
Found at i:1325753 original size:80 final size:80
Alignment explanation
Indices: 1325635--1325802 Score: 230
Period size: 80 Copynumber: 2.1 Consensus size: 80
1325625 TTTTGAAAAT
* * ** * * * *
1325635 TTAAAAAGACTCCTCTGACCAGAGGCTATGAAACTTTAAATTCAAAAGGCTCCTCTAACTAGTGG
1 TTAAAAAGACTCCTCTAACCAGAGGCAACAAAAATTTAAATTCAAAAAGCTCATCTAACTAGAGG
1325700 TAATGAAACTTTAAA
66 TAATGAAACTTTAAA
*
1325715 TTAAAAA-ATCTCCTCTAACCAGAGGCAACAAAAATTTAAATTCAAAAAGCTCATTTAACTAGAG
1 TTAAAAAGA-CTCCTCTAACCAGAGGCAACAAAAATTTAAATTCAAAAAGCTCATCTAACTAGAG
1325779 GTAATGAAACTTTAAA
65 GTAATGAAACTTTAAA
*
1325795 TTCAAAAG
1 TTAAAAAG
1325803 GAGCAAAGGC
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
79 1 0.01
80 75 0.99
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.27
Consensus pattern (80 bp):
TTAAAAAGACTCCTCTAACCAGAGGCAACAAAAATTTAAATTCAAAAAGCTCATCTAACTAGAGG
TAATGAAACTTTAAA
Found at i:1325858 original size:72 final size:72
Alignment explanation
Indices: 1325737--1325875 Score: 190
Period size: 72 Copynumber: 1.9 Consensus size: 72
1325727 CTCTAACCAG
* * *
1325737 AGGCAACAAAAATTTAAATTCAAAAAGCTCATTTAACTAGAGGTAATGAAACTTTAAATTCAAAA
1 AGGCAACAAAAATTTAAATTCAAAAAGCTCATCTAACCAAAGGTAATGAAACTTTAAATTCAAAA
1325802 GGAGCAA
66 GGAGCAA
* * * * *
1325809 AGGCAACATAACTTTAAATTCAAAAGGCTCATCTGACCAAAGGCT-ATGAAACTTTAAATTTAAA
1 AGGCAACAAAAATTTAAATTCAAAAAGCTCATCTAACCAAAGG-TAATGAAACTTTAAATTCAAA
1325873 AGG
65 AGG
1325876 CTCATCTAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 57 0.98
73 1 0.02
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (72 bp):
AGGCAACAAAAATTTAAATTCAAAAAGCTCATCTAACCAAAGGTAATGAAACTTTAAATTCAAAA
GGAGCAA
Found at i:1325980 original size:192 final size:192
Alignment explanation
Indices: 1325638--1325995 Score: 495
Period size: 192 Copynumber: 1.9 Consensus size: 192
1325628 TGAAAATTTA
* * * *
1325638 AAAAGACTCCTCTGACCAGAGGCTATGAAACTTTAAATTCAAAAGGCTCCTCTAACTAGTGGTAA
1 AAAAGACTCATCTGACCAAAGGCTATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGAGGTAA
* *
1325703 TGAAACTTTAAATTAAAAAATCTCCTCTAACCAGAGGCAACAAAAATTTAAATTCAAAAAGCTCA
66 TGAAACTTTAAATTAAAAAAGCTCCCCTAACCAGAGGCAACAAAAATTTAAATTCAAAAAGCTCA
* **
1325768 TTTAACTAGAGGTAATGAAACTTTAAATTCAAAAGGAGCAAAGGCAACATAACTTTAAATTC
131 TATAACTAGAACTAATGAAACTTTAAATTCAAAAGGAGCAAAGGCAACATAACTTTAAATTC
* * *
1325830 AAAAGGCTCATCTGACCAAAGGCTATGAAACTTTAAATTTAAAAGGCTCATCTAACTAGAGGTTA
1 AAAAGACTCATCTGACCAAAGGCTATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGAGGTAA
* * *** * *
1325895 TGAAACTTTAAATTCAAAAGGCTCCCCTAACCA-ACGGCAATGTAAATTTAAATTCAAAAGGCTT
66 TGAAACTTTAAATTAAAAAAGCTCCCCTAACCAGA-GGCAACAAAAATTTAAATTCAAAAAGCTC
* *
1325959 ATATGACTAGAAACT-ATGAAACTTTAAATTTAAAAGG
130 ATATAACTAG-AACTAATGAAACTTTAAATTCAAAAGG
1325996 CTCATTTGAT
Statistics
Matches: 143, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
191 1 0.01
192 140 0.98
193 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (192 bp):
AAAAGACTCATCTGACCAAAGGCTATGAAACTTTAAATTCAAAAGGCTCATCTAACTAGAGGTAA
TGAAACTTTAAATTAAAAAAGCTCCCCTAACCAGAGGCAACAAAAATTTAAATTCAAAAAGCTCA
TATAACTAGAACTAATGAAACTTTAAATTCAAAAGGAGCAAAGGCAACATAACTTTAAATTC
Found at i:1326119 original size:21 final size:21
Alignment explanation
Indices: 1326093--1326132 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1326083 AAGCAGAAGC
1326093 TATGAAACTTTAAATTCAAGT
1 TATGAAACTTTAAATTCAAGT
1326114 TATGAAACTTTAAATTCAA
1 TATGAAACTTTAAATTCAA
1326133 AAGGCTTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (21 bp):
TATGAAACTTTAAATTCAAGT
Found at i:1326134 original size:61 final size:61
Alignment explanation
Indices: 1326057--1326172 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
1326047 AGAGATTACT
* *
1326057 AAACTTTAAATGCAAAAGGC-TCATCTAAGCAGAAGCTATGA-AACTTTAAATTCAAGTTATG
1 AAACTTTAAATGCAAAAGGCTTC-TCTAACCAGAAGCAAT-ATAACTTTAAATTCAAGTTATG
* * *
1326118 AAACTTTAAATTCAAAAGGCTTCTCTGACCAGAGGCAATATAACTTTAAATTCAA
1 AAACTTTAAATGCAAAAGGCTTCTCTAACCAGAAGCAATATAACTTTAAATTCAA
1326173 AAGGCTTCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 1 0.02
61 45 0.94
62 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (61 bp):
AAACTTTAAATGCAAAAGGCTTCTCTAACCAGAAGCAATATAACTTTAAATTCAAGTTATG
Found at i:1326174 original size:40 final size:40
Alignment explanation
Indices: 1326115--1326368 Score: 190
Period size: 40 Copynumber: 6.3 Consensus size: 40
1326105 AATTCAAGTT
*
1326115 ATGAAACTTTAAATTCAAAAGGCTTC-TCTGACCAGAGGCA
1 ATGAAACTTTAAATTCAAAAGGC-TCATCTGACCAAAGGCA
* * * **
1326155 AT-ATAACTTTAAATTCAAAAGGCTTC-TTTGACTAGAGGTT
1 ATGA-AACTTTAAATTCAAAAGGC-TCATCTGACCAAAGGCA
** * *
1326195 ATGAAACTTTAAATTTTAAAGGCTCATCTGACTAAAGGGA
1 ATGAAACTTTAAATTCAAAAGGCTCATCTGACCAAAGGCA
* * *
1326235 ATGAAACTTTAAATTTAAAAGGCTCATTTGACCAAAGGCT
1 ATGAAACTTTAAATTCAAAAGGCTCATCTGACCAAAGGCA
* * * * * * * * *
1326275 ATAAAATTTTAAATACAAAAAGCTCTTATAAGCAAAGGCT
1 ATGAAACTTTAAATTCAAAAGGCTCATCTGACCAAAGGCA
* * * * * *
1326315 ATGAAACTTTAAATTTAAAAGGTTCCTCTAACCAAACGCC
1 ATGAAACTTTAAATTCAAAAGGCTCATCTGACCAAAGGCA
* *
1326355 ACGAGACTTTAAAT
1 ATGAAACTTTAAAT
1326369 GGCTCATTTG
Statistics
Matches: 174, Mismatches: 37, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
39 3 0.02
40 170 0.98
41 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (40 bp):
ATGAAACTTTAAATTCAAAAGGCTCATCTGACCAAAGGCA
Found at i:1326239 original size:141 final size:141
Alignment explanation
Indices: 1325973--1326249 Score: 314
Period size: 141 Copynumber: 2.0 Consensus size: 141
1325963 GACTAGAAAC
* * * *
1325973 TATGAAACTTTAAATTTAAAAGGCTCATTTGATCAGAGAGAATGAAACTTTAAATTTAAAAAGCT
1 TATGAAACTTTAAATTCAAAAGGCTCATCTGACCAGAGAGAATGAAACTTTAAATTCAAAAAGCT
*
1326038 CCTCTAACCAGAGATTACTAAACTTTAAATGCAAAAGGCTCATCTAAGCAGAAGCTATGAAACTT
66 CCTCTAACCAGAGATTACTAAACTTTAAATGCAAAAGGCTCATCTAAGCAGAAGCAATGAAACTT
1326103 TAAATTCAAGT
131 TAAATTCAAGT
*
1326114 TATGAAACTTTAAATTCAAAAGGCTTC-TCTGACCAGAG-GCAAT-ATAACTTTAAATTCAAAAG
1 TATGAAACTTTAAATTCAAAAGGC-TCATCTGACCAGAGAG-AATGA-AACTTTAAATTCAAAAA
* * * * * *** * *
1326176 GCTTCTTTGACTAGAGGTTA-TGAAACTTTAAATTTTAAAGGCTCATCTGA-CTA-AAGGGAATG
63 GCTCCTCTAACCAGAGATTACT-AAACTTTAAATGCAAAAGGCTCATCTAAGC-AGAA-GCAATG
1326238 AAACTTTAAATT
125 AAACTTTAAATT
1326250 TAAAAGGCTC
Statistics
Matches: 114, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
140 6 0.05
141 106 0.93
142 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (141 bp):
TATGAAACTTTAAATTCAAAAGGCTCATCTGACCAGAGAGAATGAAACTTTAAATTCAAAAAGCT
CCTCTAACCAGAGATTACTAAACTTTAAATGCAAAAGGCTCATCTAAGCAGAAGCAATGAAACTT
TAAATTCAAGT
Found at i:1326245 original size:80 final size:80
Alignment explanation
Indices: 1326112--1326294 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
1326102 TTAAATTCAA
*
1326112 GTTATGAAACTTTAAATTCAAAAGGCTTCTCTGACCAGAGGCAATATAACTTTAAATTCAAAAGG
1 GTTATGAAACTTTAAATTCAAAAGGCTTCTCTGACCAAAGGCAATATAACTTTAAATTCAAAAGG
1326177 CTTC-TTTGACTAGAG
66 C-TCATTTGACTAGAG
** * * *
1326192 GTTATGAAACTTTAAATTTTAAAGGC-TCATCTGACTAAAGGGAATGA-AACTTTAAATTTAAAA
1 GTTATGAAACTTTAAATTCAAAAGGCTTC-TCTGACCAAAGGCAAT-ATAACTTTAAATTCAAAA
* *
1326255 GGCTCATTTGACCAAAG
64 GGCTCATTTGACTAGAG
* * * *
1326272 GCTATAAAATTTTAAATACAAAA
1 GTTATGAAACTTTAAATTCAAAA
1326295 AGCTCTTATA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
79 4 0.05
80 81 0.94
81 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (80 bp):
GTTATGAAACTTTAAATTCAAAAGGCTTCTCTGACCAAAGGCAATATAACTTTAAATTCAAAAGG
CTCATTTGACTAGAG
Found at i:1326288 original size:221 final size:221
Alignment explanation
Indices: 1325891--1326329 Score: 580
Period size: 221 Copynumber: 2.0 Consensus size: 221
1325881 CTAACTAGAG
*
1325891 GTTATGAAACTTTAAATTCAAAAGGCTCCCCTAACCAACGGCAATGTAAATTTAAATTCAAAAGG
1 GTTATGAAACTTTAAATTCAAAAGGCTCCCCTAACCAACGGCAATATAAATTTAAATTCAAAAGG
* *
1325956 CTTATATGACTAGAAACTATGAAACTTTAAATTTAAAAGGCTCATTTGATCAGAGAGAATGAAAC
66 CTTATATGACTAGAAACTATGAAACTTTAAATTTAAAAGGCTCATCTGATCAAAGAGAATGAAAC
* * * * * *
1326021 TTTAAATTTAAAAAGCTCCTCTAACCAGAGATTACTAAACTTTAAATGCAAAAGGCTCATCTAAG
131 TTTAAATTTAAAAAGCTCATCTAACCAAAGACTACTAAACTTTAAATACAAAAAGCTCATATAAG
1326086 CAGAA-GCTATGAAACTTTAAATTCAA
196 CA-AAGGCTATGAAACTTTAAATTCAA
* * * *
1326112 GTTATGAAACTTTAAATTCAAAAGGCTTCTCTGACCAGA-GGCAATATAACTTTAAATTCAAAAG
1 GTTATGAAACTTTAAATTCAAAAGGCTCCCCTAACCA-ACGGCAATATAAATTTAAATTCAAAAG
* * *** * *
1326176 GCTTCTTTGACTAGAGGTTATGAAACTTTAAATTTTAAAGGCTCATCTGA-CTAAAGGGAATGAA
65 GCTTATATGACTAGAAACTATGAAACTTTAAATTTAAAAGGCTCATCTGATC-AAAGAGAATGAA
* * * * * *
1326240 ACTTTAAATTTAAAAGGCTCATTTGACCAAAGGCTA-TAAAATTTTAAATACAAAAAGCTCTTAT
129 ACTTTAAATTTAAAAAGCTCATCTAACCAAAGACTACT-AAACTTTAAATACAAAAAGCTCATAT
1326304 AAGCAAAGGCTATGAAACTTTAAATT
193 AAGCAAAGGCTATGAAACTTTAAATT
1326330 TAAAAGGTTC
Statistics
Matches: 188, Mismatches: 26, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
220 4 0.02
221 183 0.97
222 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (221 bp):
GTTATGAAACTTTAAATTCAAAAGGCTCCCCTAACCAACGGCAATATAAATTTAAATTCAAAAGG
CTTATATGACTAGAAACTATGAAACTTTAAATTTAAAAGGCTCATCTGATCAAAGAGAATGAAAC
TTTAAATTTAAAAAGCTCATCTAACCAAAGACTACTAAACTTTAAATACAAAAAGCTCATATAAG
CAAAGGCTATGAAACTTTAAATTCAA
Found at i:1326328 original size:120 final size:120
Alignment explanation
Indices: 1326115--1326336 Score: 288
Period size: 120 Copynumber: 1.9 Consensus size: 120
1326105 AATTCAAGTT
* * * *
1326115 ATGAAACTTTAAATTCAAAAGGCTTCTCTGACCAGAGGCAATATAACTTTAAATTCAAAAGGCTT
1 ATGAAACTTTAAATTCAAAAGGCTTCTCTGACCAAAGGCAATAAAACTTTAAATACAAAAAGCTT
* * * *
1326180 CTTTGACTAGAGGTTATGAAACTTTAAATTTTAAAGGCTCATCTGACTAAAGGGA
66 CTTTAACTAAAGGCTATGAAACTTTAAATTTAAAAGGCTCATCTGACTAAAGGGA
* * * *
1326235 ATGAAACTTTAAATTTAAAAGGC-TCATTTGACCAAAGGCTATAAAATTTTAAATACAAAAAGC-
1 ATGAAACTTTAAATTCAAAAGGCTTC-TCTGACCAAAGGCAATAAAACTTTAAATACAAAAAGCT
1326298 TCTTATAAGC-AAAGGCTATGAAACTTTAAATTTAAAAGG
65 TCTT-TAA-CTAAAGGCTATGAAACTTTAAATTTAAAAGG
1326337 TTCCTCTAAC
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
119 6 0.07
120 80 0.92
121 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (120 bp):
ATGAAACTTTAAATTCAAAAGGCTTCTCTGACCAAAGGCAATAAAACTTTAAATACAAAAAGCTT
CTTTAACTAAAGGCTATGAAACTTTAAATTTAAAAGGCTCATCTGACTAAAGGGA
Found at i:1326364 original size:120 final size:120
Alignment explanation
Indices: 1326117--1326368 Score: 267
Period size: 120 Copynumber: 2.1 Consensus size: 120
1326107 TTCAAGTTAT
* * * *
1326117 GAAACTTTAAATTCAAAAGGCTTCTCTGACCAGAGGCAATATAACTTTAAATTCAAAAGGCTTCT
1 GAAACTTTAAATTCAAAAGGCTTCTCTGACCAAAGGCAATAAAACTTTAAATACAAAAAGCTTCT
* * * * * * * * *
1326182 TTGACTAGAGGTTATGAAACTTTAAATTTTAAAGGCTCATCTGACTAAAGGGAAT
66 TTAACTAAAGGCTATGAAACTTTAAATTTAAAAGGCTCATCTAACCAAACGCAAC
* * * *
1326237 GAAACTTTAAATTTAAAAGGC-TCATTTGACCAAAGGCTATAAAATTTTAAATACAAAAAGC-TC
1 GAAACTTTAAATTCAAAAGGCTTC-TCTGACCAAAGGCAATAAAACTTTAAATACAAAAAGCTTC
* * *
1326300 TTATAAGC-AAAGGCTATGAAACTTTAAATTTAAAAGGTTCCTCTAACCAAACGCCAC
65 TT-TAA-CTAAAGGCTATGAAACTTTAAATTTAAAAGGCTCATCTAACCAAACGCAAC
*
1326357 GAGACTTTAAAT
1 GAAACTTTAAAT
1326369 GGCTCATTTG
Statistics
Matches: 108, Mismatches: 21, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
119 6 0.06
120 101 0.94
121 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (120 bp):
GAAACTTTAAATTCAAAAGGCTTCTCTGACCAAAGGCAATAAAACTTTAAATACAAAAAGCTTCT
TTAACTAAAGGCTATGAAACTTTAAATTTAAAAGGCTCATCTAACCAAACGCAAC
Found at i:1326774 original size:204 final size:205
Alignment explanation
Indices: 1326360--1326811 Score: 606
Period size: 204 Copynumber: 2.2 Consensus size: 205
1326350 ACGCCACGAG
* * * *
1326360 ACTTTAAATGGC-TCATTTGACTAAAGACAAAGAAACTTTAAATTAAAAATCTGAAAGTACTTAT
1 ACTTTAAATTGCTTC-TCTGACTAAAGGCAATGAAACTTTAAATTAAAAATCTGAAAGTACTTAT
* *
1326424 AGGTTATGCCCTTGGGTCTTACAAACCATGCTTAATTTTGATGGAATCCTCTTACCAGAGGCTCT
65 AGGTTATGCCCTTGGGTCTTACAAACCATGCTTAATTTTGATGGAATCCTCTAACCAAAGGCTCT
* * * * * *
1326489 TAAAATTAAAAAGCTCCTCTGACCAGAGGCTATAAAACTTTCAATTCAAAAGGCTCATTTGGCTA
130 TAAAATTAAAAAGCTCCTCTGACCAAAGGCTACAAAACTTTCAATTCAAAAGACCCATCTGACTA
1326554 GAAGCTATGAA
195 GAAGCTATGAA
*
1326565 ACTTTAAATTGCTTCTCTGACCAAAGGCAATGAAACTTTAAATTAAAAATCTGAAAAG-ACTTAT
1 ACTTTAAATTGCTTCTCTGACTAAAGGCAATGAAACTTTAAATTAAAAATCTG-AAAGTACTTAT
** * * *
1326629 AGGTTATGCTTTTGGGTCTTAC-AACCATGGTTAATTTTGATGGAGTCCTCTAACCAAATGCTCT
65 AGGTTATGCCCTTGGGTCTTACAAACCATGCTTAATTTTGATGGAATCCTCTAACCAAAGGCTCT
* * * * * *
1326693 TCAAATTAAAAAGCTCCTCTGACTAAAGGCTACAAAACTTTCGATTTAAAATACCCCTCTGACTA
130 TAAAATTAAAAAGCTCCTCTGACCAAAGGCTACAAAACTTTCAATTCAAAAGACCCATCTGACTA
*
1326758 -AAGGTGATGAA
195 GAAGCT-ATGAA
* *
1326769 ACTTTAAATTGCTTCTCTGACTAGAGGCAATAAAACTTTAAAT
1 ACTTTAAATTGCTTCTCTGACTAAAGGCAATGAAACTTTAAAT
1326812 GAGAAAAGGC
Statistics
Matches: 216, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
203 4 0.02
204 135 0.62
205 71 0.33
206 6 0.03
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (205 bp):
ACTTTAAATTGCTTCTCTGACTAAAGGCAATGAAACTTTAAATTAAAAATCTGAAAGTACTTATA
GGTTATGCCCTTGGGTCTTACAAACCATGCTTAATTTTGATGGAATCCTCTAACCAAAGGCTCTT
AAAATTAAAAAGCTCCTCTGACCAAAGGCTACAAAACTTTCAATTCAAAAGACCCATCTGACTAG
AAGCTATGAA
Found at i:1339410 original size:15 final size:15
Alignment explanation
Indices: 1339386--1339429 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1339376 TAGTAATAAC
1339386 ATAA-AATAACAATA
1 ATAATAATAACAATA
1339400 ATAATAATAACAATA
1 ATAATAATAACAATA
1339415 AT-ATCAATAA-AATA
1 ATAAT-AATAACAATA
1339429 A
1 A
1339430 ATAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (15 bp):
ATAATAATAACAATA
Found at i:1339448 original size:15 final size:15
Alignment explanation
Indices: 1339380--1339448 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
1339370 TATTATTAGT
*
1339380 AATAACATAAAATAAC
1 AATAACAT-AAATAAA
* *
1339396 AATAATA-ATAATAAC
1 AATAACATA-AATAAA
* *
1339411 AATAATATCAAT-AA
1 AATAACATAAATAAA
1339425 AATAA-ATAAATAAA
1 AATAACATAAATAAA
1339439 AATAACATAA
1 AATAACATAA
1339449 GAATCAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
13 5 0.11
14 14 0.31
15 20 0.44
16 6 0.13
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAACATAAATAAA
Found at i:1339465 original size:26 final size:25
Alignment explanation
Indices: 1339420--1339495 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 25
1339410 CAATAATATC
1339420 AATAAAAT-AAATA-AATAAAAATAA
1 AATAAAATCAAATACAA-AAAAATAA
*
1339444 CATAAGAATCAAATACAAAAAAATAA
1 AATAA-AATCAAATACAAAAAAATAA
*
1339470 AATAAAAATCAAA-AC-AGAAAATAA
1 AAT-AAAATCAAATACAAAAAAATAA
1339494 AA
1 AA
1339496 AGAAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
24 14 0.31
25 5 0.11
26 22 0.49
27 4 0.09
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.16
Consensus pattern (25 bp):
AATAAAATCAAATACAAAAAAATAA
Found at i:1339483 original size:6 final size:5
Alignment explanation
Indices: 1339380--1339476 Score: 56
Period size: 6 Copynumber: 18.4 Consensus size: 5
1339370 TATTATTAGT
* * *
1339380 AATAA CATAA AATAA CAATAA TAATAA TAACAA TAATATC AATAA AAT-A
1 AATAA AATAA AATAA -AATAA -AATAA -AATAA -AATA-A AATAA AATAA
* *
1339429 AAT-A AATAAA AATAA CATAA GAATCA AATACA AA-AA AATAA AATAA
1 AATAA AAT-AA AATAA AATAA -AATAA AATA-A AATAA AATAA AATAA
1339475 AA
1 AA
1339477 ATCAAAACAG
Statistics
Matches: 74, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
4 11 0.15
5 30 0.41
6 33 0.45
ACGTcount: A:0.71, C:0.07, G:0.01, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:1339490 original size:13 final size:11
Alignment explanation
Indices: 1339454--1339513 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
1339444 CATAAGAATC
*
1339454 AAATACAAA-A
1 AAATAAAAAGA
1339464 AAATAAAATA-A
1 AAATAAAA-AGA
1339475 AAATCAAAACAGA
1 AAAT-AAAA-AGA
1339488 AAATAAAAAGA
1 AAATAAAAAGA
*
1339499 AAAAAAAAAGGA
1 AAATAAAAA-GA
1339511 AAA
1 AAA
1339514 ACTTATCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
10 7 0.16
11 17 0.40
12 14 0.33
13 5 0.12
ACGTcount: A:0.80, C:0.05, G:0.07, T:0.08
Consensus pattern (11 bp):
AAATAAAAAGA
Found at i:1339835 original size:20 final size:20
Alignment explanation
Indices: 1339810--1339859 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1339800 TCATATTCCA
* *
1339810 GTGGCCAAAAAATTCATCTT
1 GTGGCCAAAAAATTCAACTG
*
1339830 GTGGCCAGAAAATTCAACTG
1 GTGGCCAAAAAATTCAACTG
1339850 GT-GCCAAAAA
1 GTGGCCAAAAA
1339860 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
GTGGCCAAAAAATTCAACTG
Found at i:1340041 original size:27 final size:26
Alignment explanation
Indices: 1340002--1340055 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1339992 ATGGTTTCCA
**
1340002 GTTTCTAGTAAAAGAAATTTTTTTTTT
1 GTTTCTACCAAAA-AAATTTTTTTTTT
*
1340029 GTTTCTACCAAAAAACTTTTTTTTTT
1 GTTTCTACCAAAAAAATTTTTTTTTT
1340055 G
1 G
1340056 CCAGTGGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (26 bp):
GTTTCTACCAAAAAAATTTTTTTTTT
Found at i:1343104 original size:17 final size:17
Alignment explanation
Indices: 1343078--1343110 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1343068 TTTACATTAG
*
1343078 TCAATTTTTCAAGATTT
1 TCAATCTTTCAAGATTT
1343095 TCAATCTTTCAAGATT
1 TCAATCTTTCAAGATT
1343111 AATGGACGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.48
Consensus pattern (17 bp):
TCAATCTTTCAAGATTT
Found at i:1344147 original size:19 final size:20
Alignment explanation
Indices: 1344123--1344161 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1344113 TTTTTAGTAT
1344123 ATCTA-TAAAAAAAATTTTG
1 ATCTAGTAAAAAAAATTTTG
1344142 ATCTATGTAAAAAAAATTTT
1 ATCTA-GTAAAAAAAATTTT
1344162 CAAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
ATCTAGTAAAAAAAATTTTG
Found at i:1344892 original size:23 final size:25
Alignment explanation
Indices: 1344848--1344898 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
1344838 CGGTCCGATC
*
1344848 ATTTCATATTATTTCGAGTTT-AAT
1 ATTTCATATTATTTCAAGTTTAAAT
1344872 ATTTCA-ATTATTT-AAGTTTTAAAT
1 ATTTCATATTATTTCAAG-TTTAAAT
1344896 ATT
1 ATT
1344899 AAGAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 2 0.08
23 10 0.42
24 12 0.50
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (25 bp):
ATTTCATATTATTTCAAGTTTAAAT
Found at i:1344906 original size:22 final size:23
Alignment explanation
Indices: 1344881--1344923 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1344871 TATTTCAATT
1344881 ATTTAAGTT-TTAAATATTAAGA
1 ATTTAAGTTATTAAATATTAAGA
*
1344903 ATTTAAGTTATTAAATTTTAA
1 ATTTAAGTTATTAAATATTAA
1344924 AATCAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (23 bp):
ATTTAAGTTATTAAATATTAAGA
Found at i:1347570 original size:5 final size:6
Alignment explanation
Indices: 1347561--1347590 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1347551 CCCTTTTTCT
1347561 TTTTTG TTTTTG TTTTTG TTTTTGG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTT-G TTTTT
1347591 TCCTTCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:1349575 original size:23 final size:22
Alignment explanation
Indices: 1349537--1349581 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1349527 AGCCCATCCG
1349537 ATAATTATTTTATTATAAAATA
1 ATAATTATTTTATTATAAAATA
*
1349559 ATAATATATTATT-TTATATAATA
1 ATAAT-TATT-TTATTATAAAATA
1349582 TTCTAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 13 0.65
24 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATTATTTTATTATAAAATA
Found at i:1350332 original size:27 final size:27
Alignment explanation
Indices: 1350302--1350375 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 27
1350292 ATTAAATATC
*
1350302 ATATTA-ATTAACATATTTATAATTCAA
1 ATATTATATTAA-ATATTTAAAATTCAA
* * *
1350329 ATATTATATAAAAAAATTTTAAAATTTAA
1 ATATTATAT-TAAATA-TTTAAAATTCAA
1350358 ATATTATATTAAATATTT
1 ATATTATATTAAATATTT
1350376 TATTTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 9 0.24
28 8 0.21
29 21 0.55
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATTATATTAAATATTTAAAATTCAA
Found at i:1351096 original size:35 final size:35
Alignment explanation
Indices: 1351051--1351121 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1351041 GTTTTGCTGG
*
1351051 GTTTGTTTTTGCCTTTGCTTAGTGAATAATTGCAT
1 GTTTGCTTTTGCCTTTGCTTAGTGAATAATTGCAT
*
1351086 GTTTGCTTTTGCTTTTGCTTAGTGAATAATTGCAT
1 GTTTGCTTTTGCCTTTGCTTAGTGAATAATTGCAT
1351121 G
1 G
1351122 CTTACATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.11, G:0.21, T:0.51
Consensus pattern (35 bp):
GTTTGCTTTTGCCTTTGCTTAGTGAATAATTGCAT
Found at i:1351442 original size:29 final size:30
Alignment explanation
Indices: 1351397--1351473 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 30
1351387 CTAAAATTAA
* *
1351397 ATAA-TAATTGAAGTTTTTATTAT-TTTATT
1 ATAATTAATT-AAATTTTTATGATATTTATT
*
1351426 ATAATTAATTAAA-TTTTAAGATATTTATT
1 ATAATTAATTAAATTTTTATGATATTTATT
* *
1351455 -TCATTAATTAATTTTTTAT
1 ATAATTAATTAAATTTTTAT
1351474 AAAATAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 17 0.44
29 17 0.44
30 5 0.13
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (30 bp):
ATAATTAATTAAATTTTTATGATATTTATT
Found at i:1352094 original size:23 final size:22
Alignment explanation
Indices: 1352059--1352106 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
1352049 TATTTAACAC
1352059 TTAAAACTTTTTTTATATATATT
1 TTAAAACTTTTTTTATATAT-TT
1352082 TTAAAA-TTATTTTTATATATTT
1 TTAAAACTT-TTTTTATATATTT
1352104 TTA
1 TTA
1352107 TTTTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTAAAACTTTTTTTATATATTT
Found at i:1352100 original size:21 final size:23
Alignment explanation
Indices: 1352059--1352104 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
1352049 TATTTAACAC
*
1352059 TTAAAACTTTTTTTATATATATT
1 TTAAAACTTATTTTATATATATT
1352082 TTAAAA-TTATTTT-TATATATT
1 TTAAAACTTATTTTATATATATT
1352103 TT
1 TT
1352105 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 6 0.27
23 6 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TTAAAACTTATTTTATATATATT
Found at i:1352104 original size:10 final size:10
Alignment explanation
Indices: 1352068--1352117 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
1352058 CTTAAAACTT
1352068 TTTTTATATA
1 TTTTTATATA
*
1352078 TATTTTAAAATTA
1 T-TTTT-ATA-TA
1352091 TTTTTATATA
1 TTTTTATATA
1352101 TTTTTAT-T-
1 TTTTTATATA
1352109 TTTTTATAT
1 TTTTTATAT
1352118 TAAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 7 0.21
9 2 0.06
10 10 0.29
11 6 0.18
12 6 0.18
13 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTATATA
Found at i:1352109 original size:16 final size:16
Alignment explanation
Indices: 1352088--1352118 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1352078 TATTTTAAAA
1352088 TTATTTTTATATATTT
1 TTATTTTTATATATTT
*
1352104 TTATTTTTTTATATT
1 TTATTTTTATATATT
1352119 AAAAATTATC
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTTATATATTT
Found at i:1352156 original size:24 final size:26
Alignment explanation
Indices: 1352110--1352161 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 26
1352100 ATTTTTATTT
1352110 TTTTATATTAAAAATTATCAAATTTAA
1 TTTTATA-TAAAAATTATCAAATTTAA
*
1352137 TTTTATA-AAAAATT-TTAAATTTAA
1 TTTTATATAAAAATTATCAAATTTAA
1352161 T
1 T
1352162 ATTAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 10 0.42
25 7 0.29
27 7 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTATATAAAAATTATCAAATTTAA
Found at i:1353047 original size:18 final size:18
Alignment explanation
Indices: 1353019--1353061 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1353009 TTTAGAATTA
1353019 AAATT-AAATATTAT-TT
1 AAATTCAAATATTATCTT
*
1353035 AATATTCAAATATTTTCTT
1 AA-ATTCAAATATTATCTT
1353054 AAATTCAA
1 AAATTCAA
1353062 TTCATGGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 3 0.13
18 14 0.61
19 4 0.17
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTCAAATATTATCTT
Found at i:1356075 original size:12 final size:12
Alignment explanation
Indices: 1356060--1356085 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1356050 CTTTATTGTT
1356060 TTTATTATTTTA
1 TTTATTATTTTA
1356072 TTTATTATTTTA
1 TTTATTATTTTA
1356084 TT
1 TT
1356086 CTTTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:1356160 original size:13 final size:13
Alignment explanation
Indices: 1356123--1356163 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1356113 TTCATTAAAA
1356123 TTTTTATTTTCATT
1 TTTTTATTTT-ATT
* *
1356137 ATTTCATTTTATT
1 TTTTTATTTTATT
1356150 TTTTTATTTTATT
1 TTTTTATTTTATT
1356163 T
1 T
1356164 AAGAGAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:1356374 original size:18 final size:19
Alignment explanation
Indices: 1356339--1356374 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1356329 AAATATATAT
1356339 ATAAAAAATTGAGCAAAAA
1 ATAAAAAATTGAGCAAAAA
1356358 ATAAAAAA-TGA-CAAAAA
1 ATAAAAAATTGAGCAAAAA
1356375 TACCTACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (19 bp):
ATAAAAAATTGAGCAAAAA
Found at i:1358180 original size:57 final size:58
Alignment explanation
Indices: 1358117--1358242 Score: 139
Period size: 58 Copynumber: 2.2 Consensus size: 58
1358107 ATAACCTTCA
* * **
1358117 AAAAAATACAAATGA-CTTCAGATATTACCATCAAA-AGAAACTTGAATATCACCATAG
1 AAAAAATACAAATAAGCTTCA-ATATCACCATCAAAGAGAAACTCAAATATCACCATAG
* * * * * *
1358174 AGAAAATGCAAATAAGCTTGAATATCGCCATCAAAGAGAAACTCAAATATCACTATCG
1 AAAAAATACAAATAAGCTTCAATATCACCATCAAAGAGAAACTCAAATATCACCATAG
1358232 AAAAAATACAA
1 AAAAAATACAA
1358243 TTGTAGAGAA
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
57 24 0.44
58 31 0.56
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (58 bp):
AAAAAATACAAATAAGCTTCAATATCACCATCAAAGAGAAACTCAAATATCACCATAG
Found at i:1358345 original size:119 final size:120
Alignment explanation
Indices: 1358210--1358428 Score: 300
Period size: 121 Copynumber: 1.8 Consensus size: 120
1358200 GCCATCAAAG
* * * *
1358210 AGAAACTCAAATATCACTATCGAAAAAATACAATTGTAGAG-AAAAATGCAAATTCAAACTTTAA
1 AGAAACTCAAATATCACCATCGAAAAAATACAAATATAGAGAAAAAATACAAATTCAAACTTTAA
1358274 ACTCGA-ATATCACCA-CCATGTGATTTTGAAAATGTCTCGCATATTACCACCAAGA
66 ACT-GAGATATCACCATCCA-GTGATTTTGAAAATGTCTCGCATATTACCACCAAGA
* * *
1358329 AGAAACTCGAATATCACCATCGAGAAAATAGAAATATAGAGAAAAAAATACAAATTCAAACTTTA
1 AGAAACTCAAATATCACCATCGAAAAAATACAAATATAGAG-AAAAAATACAAATTCAAACTTTA
* **
1358394 AACTTAGATATCACCATTGAGTGATTTTGAAAATG
65 AACTGAGATATCACCATCCAGTGATTTTGAAAATG
1358429 GACTCGAATA
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
119 35 0.41
120 1 0.01
121 49 0.57
122 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (120 bp):
AGAAACTCAAATATCACCATCGAAAAAATACAAATATAGAGAAAAAATACAAATTCAAACTTTAA
ACTGAGATATCACCATCCAGTGATTTTGAAAATGTCTCGCATATTACCACCAAGA
Found at i:1359977 original size:12 final size:12
Alignment explanation
Indices: 1359956--1359997 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1359946 GTTTGAAGGT
* *
1359956 GATCAAACCAAA
1 GATCATACCAAG
1359968 GATCATACCAAG
1 GATCATACCAAG
*
1359980 GTTCATACCAAG
1 GATCATACCAAG
1359992 GATCAT
1 GATCAT
1359998 TTCATATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (12 bp):
GATCATACCAAG
Found at i:1365607 original size:5 final size:5
Alignment explanation
Indices: 1365597--1365639 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
1365587 TTCAGCCCCT
*
1365597 CCGAG CCGAG CCGAG CCGAG CCGAG CCGCA- CCAAG CCGAG CCG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCG-AG CCGAG CCGAG CCG
1365640 CGATCCGAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 1 0.03
5 32 0.94
6 1 0.03
ACGTcount: A:0.21, C:0.44, G:0.35, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:1365608 original size:15 final size:15
Alignment explanation
Indices: 1365597--1365651 Score: 67
Period size: 15 Copynumber: 3.5 Consensus size: 15
1365587 TTCAGCCCCT
1365597 CCGAGCCGAGCCG-A
1 CCGAGCCGAGCCGCA
1365611 GCCGAGCCGAGCCGCA
1 -CCGAGCCGAGCCGCA
*
1365627 CCAAGCCGAGCCGCGA
1 CCGAGCCGAGCCGC-A
1365643 TCCGAGCCG
1 -CCGAGCCG
1365652 CTCCAGGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 26 0.74
16 2 0.06
17 7 0.20
ACGTcount: A:0.20, C:0.44, G:0.35, T:0.02
Consensus pattern (15 bp):
CCGAGCCGAGCCGCA
Found at i:1366331 original size:156 final size:156
Alignment explanation
Indices: 1365716--1366313 Score: 999
Period size: 156 Copynumber: 3.8 Consensus size: 156
1365706 TTTTTCCTTA
* *
1365716 TTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAG-TTTTCTTGCATACTCCT
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATACTCCT
*
1365780 GAGGTGAGGGAA-TTTCTCAATTTTCTGCTAAAA-TATTAGAGTCAATTGAGAATAATTTCCGAT
65 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
* *
1365843 AATTAATTACTTGGCTGATTTTGATTTTTTT
130 AATTAATTAATTGGTTGATTTTGA----TTT
1365874 TTCTTTAATTAATCCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCAATACTCC
1 TTCTTTAATTAAT-CCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGC-ATACTCC
*
1365939 TGAGGTGAGGGAATTTTTCTCAATTTTTTGCT-AAAGTATTAGAGTCAATTGAGAATAATTTTCG
64 TGAGGTGAGGGAA-TTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCG
*
1366003 ATAATTAATTAATTGGTTGATCTTGA-TT
128 ATAATTAATTAATTGGTTGATTTTGATTT
1366031 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTTCTTGCATACTCCT
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAG-TTTTTCTTGCATACTCCT
1366096 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
65 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
1366161 AATTAATTAATTGGTTGATTTTGATTT
130 AATTAATTAATTGGTTGATTTTGATTT
* *
1366188 TTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCTTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1366253 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
1366314 AACAACTAAC
Statistics
Matches: 420, Mismatches: 11, Indels: 20
0.93 0.02 0.04
Matches are distributed among these distances:
155 17 0.04
156 189 0.45
157 72 0.17
158 22 0.05
159 31 0.07
160 20 0.05
161 3 0.01
162 66 0.16
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (156 bp):
TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
ATTAATTAATTGGTTGATTTTGATTT
Found at i:1369551 original size:1 final size:1
Alignment explanation
Indices: 1369547--1369574 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1369537 GTAATTTTTG
1369547 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1369575 CCACAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1369996 original size:16 final size:17
Alignment explanation
Indices: 1369975--1370040 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 17
1369965 AAAAAAGATG
1369975 ATGAAAAAA-AAAAAAA
1 ATGAAAAAAGAAAAAAA
*
1369991 AAGAAAGAAAGAAAAAAA
1 ATGAAA-AAAGAAAAAAA
*
1370009 ATGAGAAAATG--AAAAA
1 ATGA-AAAAAGAAAAAAA
*
1370025 ATGAAAAAATAAAAAA
1 ATGAAAAAAGAAAAAA
1370041 GAGATCCGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 4 0.10
16 14 0.35
17 7 0.17
18 13 0.32
19 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (17 bp):
ATGAAAAAAGAAAAAAA
Found at i:1370015 original size:20 final size:20
Alignment explanation
Indices: 1369957--1370016 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
1369947 ATAATAGGTG
*
1369957 AAGAATGAAAAAAAGATGATGA
1 AAGAAAGAAAAAAA-ATGA-GA
1369979 AA-AAA-AAAAAAAA--AGA
1 AAGAAAGAAAAAAAATGAGA
1369995 AAGAAAGAAAAAAAATGAGA
1 AAGAAAGAAAAAAAATGAGA
1370015 AA
1 AA
1370017 ATGAAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 4 0.12
17 4 0.12
18 8 0.24
19 1 0.03
20 12 0.36
21 2 0.06
22 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (20 bp):
AAGAAAGAAAAAAAATGAGA
Found at i:1370017 original size:8 final size:8
Alignment explanation
Indices: 1370004--1370040 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
1369994 AAAGAAAGAA
1370004 AAAAAATG
1 AAAAAATG
*
1370012 AGAAAATG
1 AAAAAATG
1370020 AAAAAATG
1 AAAAAATG
1370028 AAAAAAT-
1 AAAAAATG
1370035 AAAAAA
1 AAAAAA
1370041 GAGATCCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:1371284 original size:42 final size:42
Alignment explanation
Indices: 1371232--1371499 Score: 338
Period size: 42 Copynumber: 6.5 Consensus size: 42
1371222 GTCTAGGAGT
*
1371232 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
*
1371274 ATTTACTTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
* *
1371315 ATTTATTTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
*
1371357 ATTTAC-TTTCCAAAGTTCGT--TGCCTCTGTTTAGAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTACCTCTG-TT-GAGAGGAGCA
* *
1371399 ATTTAC-TTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCCAAAG-TCGTGGTACCTCTGTTGAGAGGAGCA
* *
1371439 ATTTA-TCTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACT-TTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
*
1371481 ATTTA-TTTTTCAAAGTCGT
1 ATTTACTTTTCCAAAGTCGT
1371500 AGAGCCTCTG
Statistics
Matches: 209, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
40 25 0.12
41 72 0.34
42 112 0.54
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (42 bp):
ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
Found at i:1371337 original size:83 final size:82
Alignment explanation
Indices: 1371232--1371499 Score: 382
Period size: 83 Copynumber: 3.2 Consensus size: 82
1371222 GTCTAGGAGT
* *
1371232 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTA
1 ATTTA-TTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTCGTGGTG
1371297 CCTCTGTTTAGAGGAGCA
65 CCTCTGTTTAGAGGAGCA
*
1371315 ATTTATTTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTTCGT--T
1 ATTTA-TTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAG-TCGTGGT
1371378 GCCTCTGTTTAGAGAGGAGCA
64 GCCTCTGTTT--AGAGGAGCA
* * *
1371399 ATTTACTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTATCTTTCCAAAGTCGTGGT
1 ATTTATTTTCCAAAG-TCGTGGTACCTCTGTTGAGAGGAGCAATTTA-CTTTCCAAAGTCGTGGT
1371462 GCCTCTGTTTAGAGGAGCA
64 GCCTCTGTTTAGAGGAGCA
*
1371481 ATTTATTTTTCAAAGTCGT
1 ATTTATTTTCCAAAGTCGT
1371500 AGAGCCTCTG
Statistics
Matches: 169, Mismatches: 9, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
81 4 0.02
82 59 0.35
83 73 0.43
84 33 0.20
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (82 bp):
ATTTATTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGC
CTCTGTTTAGAGGAGCA
Found at i:1371429 original size:124 final size:123
Alignment explanation
Indices: 1371239--1371496 Score: 369
Period size: 124 Copynumber: 2.1 Consensus size: 123
1371229 AGTATTTATT
*
1371239 TTTCCAAAG-TCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTG
1 TTTCCAAAGTTCGT-GTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTCGT-GTACCTCTG
* *
1371303 TTTAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTAC
64 TTTAGAGGAGCAATTTATCTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTAC
* *
1371363 TTTCCAAAGTTCGT-TGCCTCTGTTTAGAGAGGAGCAATTTACTTTCCAAAGTTCGT-TGCCTCT
1 TTTCCAAAGTTCGTGTACCTCTG-TT-GAGAGGAGCAATTTACTTTCCAAAG-TCGTGTACCTCT
* * *
1371426 GTTTAGAGGAGCAATTTATCTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAT
63 GTTTAGAGGAGCAATTTATCTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTAC
*
1371487 TTTTCAAAGT
1 TTTCCAAAGT
1371497 CGTAGAGCCT
Statistics
Matches: 121, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
123 7 0.06
124 82 0.68
125 28 0.23
126 4 0.03
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (123 bp):
TTTCCAAAGTTCGTGTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTCGTGTACCTCTGTT
TAGAGGAGCAATTTATCTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTAC
Found at i:1371528 original size:1 final size:1
Alignment explanation
Indices: 1371522--1371548 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1371512 AAGAGGAGCT
1371522 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1371549 GGTCGAGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1371676 original size:20 final size:20
Alignment explanation
Indices: 1371651--1371709 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
1371641 CAGGTCCGGG
1371651 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
1371671 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
* *
1371691 CCCAGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
1371710 GCCCAAATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.22
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:1372033 original size:12 final size:12
Alignment explanation
Indices: 1372006--1372038 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1371996 AATTATCTAG
1372006 ATTTTT-TTTTA
1 ATTTTTATTTTA
1372017 A-TTTTATTTTA
1 ATTTTTATTTTA
1372028 ATTTTTATTTT
1 ATTTTTATTTT
1372039 GGAGGGCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.20
11 7 0.35
12 9 0.45
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:1372424 original size:31 final size:31
Alignment explanation
Indices: 1372353--1372425 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
1372343 AATTTCCAGA
* *
1372353 TTCCGGCGAAAATTCCGGCGACTTTTGAATT
1 TTCCGGCGACAATTCCGGCGACTTTTGAAGT
1372384 TTCCGGCGACAATTCCGGCGAAC-TTTGAAGT
1 TTCCGGCGACAATTCCGGCG-ACTTTTGAAGT
1372415 TTCCGGCGACA
1 TTCCGGCGACA
1372426 GACCCAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 37 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (31 bp):
TTCCGGCGACAATTCCGGCGACTTTTGAAGT
Found at i:1372511 original size:19 final size:19
Alignment explanation
Indices: 1372487--1372531 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1372477 TTCGGCCAAT
1372487 TTCCGGCGAAATTCCCAGA
1 TTCCGGCGAAATTCCCAGA
*
1372506 TTCCGGCGAAATTTCCAGA
1 TTCCGGCGAAATTCCCAGA
*
1372525 ATCCGGC
1 TTCCGGC
1372532 ACCGGCGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (19 bp):
TTCCGGCGAAATTCCCAGA
Found at i:1372761 original size:5 final size:5
Alignment explanation
Indices: 1372751--1372793 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
1372741 TTCAGCCCCT
*
1372751 CCGAG CCGAG CCGAG CCGAG CCGAG CCGCA- CCAAG CCGAG CCG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCG-AG CCGAG CCGAG CCG
1372794 CGATCCGAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 1 0.03
5 32 0.94
6 1 0.03
ACGTcount: A:0.21, C:0.44, G:0.35, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:1372762 original size:15 final size:15
Alignment explanation
Indices: 1372751--1372805 Score: 67
Period size: 15 Copynumber: 3.5 Consensus size: 15
1372741 TTCAGCCCCT
1372751 CCGAGCCGAGCCG-A
1 CCGAGCCGAGCCGCA
1372765 GCCGAGCCGAGCCGCA
1 -CCGAGCCGAGCCGCA
*
1372781 CCAAGCCGAGCCGCGA
1 CCGAGCCGAGCCGC-A
1372797 TCCGAGCCG
1 -CCGAGCCG
1372806 CTCCAGGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 26 0.74
16 2 0.06
17 7 0.20
ACGTcount: A:0.20, C:0.44, G:0.35, T:0.02
Consensus pattern (15 bp):
CCGAGCCGAGCCGCA
Found at i:1372819 original size:1 final size:1
Alignment explanation
Indices: 1372813--1372838 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1372803 CCGCTCCAGG
1372813 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1372839 GACTTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1373295 original size:157 final size:156
Alignment explanation
Indices: 1372874--1373474 Score: 1058
Period size: 157 Copynumber: 3.8 Consensus size: 156
1372864 TTTTTCCTTA
* *
1372874 TTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACTCCT
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATACTCCT
*
1372939 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTCCGAT
65 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
* * *
1373004 AATTAATTACTTGGCTGATTTTGATTTTTTTT
130 AATTAATTAATTGGTTGATCTTGA-----TTT
1373036 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1373101 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
1373166 ATTAATTAATTGGTTGATCTTGATTT
131 ATTAATTAATTGGTTGATCTTGATTT
1373192 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTTCTTGCATACTCCT
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAG-TTTTTCTTGCATACTCCT
1373257 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
65 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
1373322 AATTAATTAATTGGTTGATCTTGATTT
130 AATTAATTAATTGGTTGATCTTGATTT
* * *
1373349 TTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTTAAACAGTAGTTTTTCTTGCATACTCTTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1373414 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
1373475 AACAACTAAC
Statistics
Matches: 429, Mismatches: 9, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
156 128 0.30
157 154 0.36
161 112 0.26
162 35 0.08
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (156 bp):
TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
ATTAATTAATTGGTTGATCTTGATTT
Found at i:1379199 original size:35 final size:35
Alignment explanation
Indices: 1379154--1379221 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1379144 TAATTAATAT
* *
1379154 ATTTATAATTTAGATATTATATAAAAAATTTTAAA
1 ATTTAAAATTTAAATATTATATAAAAAATTTTAAA
* *
1379189 ATTTAAAATTTAAATATTATATTAAATATTTTA
1 ATTTAAAATTTAAATATTATATAAAAAATTTTA
1379222 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (35 bp):
ATTTAAAATTTAAATATTATATAAAAAATTTTAAA
Found at i:1381188 original size:22 final size:20
Alignment explanation
Indices: 1381147--1381189 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
1381137 AAGTTTTATG
*
1381147 ATTTTAATTTTTTTTCTTTA
1 ATTTTAATTTTTTTTATTTA
1381167 ATTTTAATGTTTTTTATATTTA
1 ATTTTAAT-TTTTTT-TATTTA
1381189 A
1 A
1381190 AAAATTATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTTAATTTTTTTTATTTA
Found at i:1381767 original size:21 final size:20
Alignment explanation
Indices: 1381743--1381792 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1381733 CTTGTTTAAT
1381743 TTAAATTTAT-TATTAAAAATA
1 TTAAATTTATATATT--AAATA
1381764 TT-AATTTATATATTAAATA
1 TTAAATTTATATATTAAATA
1381783 TTAATATTTA
1 TTAA-ATTTA
1381793 GAAATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.27
20 8 0.31
21 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAAATTTATATATTAAATA
Found at i:1381783 original size:19 final size:19
Alignment explanation
Indices: 1381746--1381787 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1381736 GTTTAATTTA
1381746 AATTTATTATTAAAAATATT
1 AATTTATTATT-AAAATATT
1381766 AATTTATATATT-AAATATT
1 AATTTAT-TATTAAAATATT
1381785 AAT
1 AAT
1381788 ATTTAGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTTATTATTAAAATATT
Found at i:1384047 original size:22 final size:22
Alignment explanation
Indices: 1383989--1384061 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 22
1383979 TTTTTAGAAA
1383989 ATTTAAATATATTATTTAATTT
1 ATTTAAATATATTATTTAATTT
*
1384011 TTTGAAATAAATATATTATTTAATTT
1 ATT----TAAATATATTATTTAATTT
*
1384037 ATTTAAGTATATATT-TTTATTTT
1 ATTTAA--ATATATTATTTAATTT
1384060 AT
1 AT
1384062 CATAAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
22 5 0.12
23 9 0.21
24 7 0.17
26 21 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (22 bp):
ATTTAAATATATTATTTAATTT
Found at i:1385856 original size:16 final size:16
Alignment explanation
Indices: 1385835--1385873 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1385825 AAGTTTATAC
*
1385835 AAAAATAAAATAAAAT
1 AAAAATAAAACAAAAT
**
1385851 AAAAATACTACAAAAT
1 AAAAATAAAACAAAAT
1385867 AAAAATA
1 AAAAATA
1385874 TATAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAATAAAACAAAAT
Found at i:1385880 original size:15 final size:16
Alignment explanation
Indices: 1385844--1385880 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1385834 CAAAAATAAA
1385844 ATAAAATAAAAATACT
1 ATAAAATAAAAATACT
*
1385860 ACAAAATAAAAATA-T
1 ATAAAATAAAAATACT
1385875 ATAAAA
1 ATAAAA
1385881 AATTGAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAAATAAAAATACT
Found at i:1387217 original size:3 final size:3
Alignment explanation
Indices: 1387143--1387199 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
1387133 TTAATAAATG
1387143 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1387191 ATA ATA ATA
1 ATA ATA ATA
1387200 GAACCCAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1387906 original size:119 final size:119
Alignment explanation
Indices: 1387771--1388009 Score: 290
Period size: 121 Copynumber: 2.0 Consensus size: 119
1387761 ATCTCCATCG
** * **
1387771 AAGAAAAACTCGAATATCACTATTGAGAAAA-AGTAGTTGTAGAG-AAAAAT-CTAAATTCAAAC
1 AAGAAAAACTCGAATATCACTATCAAGAAAATA-CAAATGTAGAGAAAAAATAC-AAATTCAAAC
* *
1387833 TTTAAACTCGAATATCACCACCGTGTGA-TTTTGAAAAT-GTCTCTGATATCACCACT
64 TTTAAACTCGAATATCACCACCGAGT-ATTTTTGAAAATAG-CTCGGATATCACCACT
*
1387889 AAGAAGAAACTTGAATATCACTATCAAGAAAATACAAATGTAGAGAAAAAAATACAAATTCAAAC
1 AAGAA-AAACTCGAATATCACTATCAAGAAAATACAAATGTAGAG-AAAAAATACAAATTCAAAC
* *
1387954 TTTAAACTTGGATATCACCACCGAGTATTTTTGAAAATAAGCTCGGATATCACCAC
64 TTTAAACTCGAATATCACCACCGAGTATTTTTGAAAAT-AGCTCGGATATCACCAC
1388010 CGAAGAGAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
118 5 0.05
119 31 0.30
120 2 0.02
121 49 0.48
122 15 0.15
123 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (119 bp):
AAGAAAAACTCGAATATCACTATCAAGAAAATACAAATGTAGAGAAAAAATACAAATTCAAACTT
TAAACTCGAATATCACCACCGAGTATTTTTGAAAATAGCTCGGATATCACCACT
Found at i:1389629 original size:26 final size:27
Alignment explanation
Indices: 1389574--1389631 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
1389564 TGCCCCCCTT
** *
1389574 CTTTTTCTTTTTCTTTTTATCGTTCCA
1 CTTTTTCTTTTTCTTTACATCGTTCAA
1389601 CTTTTTCTTTTTC-TTACAT-GTTTCAA
1 CTTTTTCTTTTTCTTTACATCG-TTCAA
1389627 CTTTT
1 CTTTT
1389632 GCTAGAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 13 0.48
27 13 0.48
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.66
Consensus pattern (27 bp):
CTTTTTCTTTTTCTTTACATCGTTCAA
Found at i:1395494 original size:6 final size:6
Alignment explanation
Indices: 1395485--1395554 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
1395475 GATAAAGATA
* * *
1395485 AAAAAT AAAAAG AGAAAGT AAAAAT AAAAAT -AAAA- ACAAAT AAAAAT
1 AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * *
1395532 AAACA- AAAAGT GAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT
1395555 CAAATTAATG
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
5 10 0.21
6 34 0.71
7 4 0.08
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:1395527 original size:16 final size:16
Alignment explanation
Indices: 1395506--1395559 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
1395496 GAGAAAGTAA
1395506 AAATAAAAATAAAAAC
1 AAATAAAAATAAAAAC
1395522 AAATAAAAATAAACAA-
1 AAATAAAAATAAA-AAC
*
1395538 AAAGTGAAAATAAAAATC
1 AAA-TAAAAATAAAAA-C
1395556 AAAT
1 AAAT
1395560 TAATGTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
16 18 0.55
17 12 0.36
18 3 0.09
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.15
Consensus pattern (16 bp):
AAATAAAAATAAAAAC
Found at i:1399369 original size:3 final size:3
Alignment explanation
Indices: 1399361--1399400 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1399351 TTGGATCATT
1399361 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1399401 CATATTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1408588 original size:10 final size:10
Alignment explanation
Indices: 1408570--1408603 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1408560 GTTTTTTCTC
*
1408570 AAATAAAAAA
1 AAATGAAAAA
1408580 AAATGAAAAA
1 AAATGAAAAA
*
1408590 AAAGGAAAAA
1 AAATGAAAAA
1408600 AAAT
1 AAAT
1408604 AGAGAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (10 bp):
AAATGAAAAA
Found at i:1409154 original size:35 final size:34
Alignment explanation
Indices: 1409114--1409335 Score: 106
Period size: 35 Copynumber: 6.4 Consensus size: 34
1409104 ATCCAATCTT
1409114 GATCATTTTTATTTGTCAACTTGCAACTCAATCCC
1 GATCATTTTTATTT-TCAACTTGCAACTCAATCCC
* * * ** ** *
1409149 AATCATCTTTGTTCTTTGACTTGTTA-TCCAATCCT
1 GATCATTTTTATT-TTCAACTTGCAACT-CAATCCC
* * * * * *
1409184 AATTATTTTT-TTTTCAATTTACAGCTCAGTCCC
1 GATCATTTTTATTTTCAACTTGCAACTCAATCCC
* * * * * ***
1409217 GATCATCTTTATTTTTCGACTTACTATTCAATGTT
1 GATCATTTTTA-TTTTCAACTTGCAACTCAATCCC
* * * * *
1409252 GATCATTTTTATTTCTCAACTTTCAGCTTAGTCCT
1 GATCATTTTTATTT-TCAACTTGCAACTCAATCCC
* *
1409287 GATCATTTTTATTCTTCAACTTGCTATTCAATCCC
1 GATCATTTTTATT-TTCAACTTGCAACTCAATCCC
*
1409322 TATCATTTTTATTT
1 GATCATTTTTATTT
1409336 CTTGACTCAT
Statistics
Matches: 131, Mismatches: 49, Indels: 15
0.67 0.25 0.08
Matches are distributed among these distances:
33 17 0.13
34 8 0.06
35 104 0.79
36 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.49
Consensus pattern (34 bp):
GATCATTTTTATTTTCAACTTGCAACTCAATCCC
Found at i:1409298 original size:70 final size:70
Alignment explanation
Indices: 1409115--1409337 Score: 195
Period size: 70 Copynumber: 3.2 Consensus size: 70
1409105 TCCAATCTTG
* * * * * * * ** ** *
1409115 ATCATTTTTATTTGTCAACTTGCAACTCAATCCCAATCATCTTTGTTCTTTGACTTGTTATCCAA
1 ATCATTTTTATTTCTCAATTTACAGCTCAGTCCCGATCATCTTTATTCTTCAACTTACTATTCAA
1409180 T-CCT
66 TCCCT
* * *
1409184 AATTATTTTT-TTT-TCAATTTACAGCTCAGTCCCGATCATCTTTATTTTTCGACTTACTATTCA
1 -ATCATTTTTATTTCTCAATTTACAGCTCAGTCCCGATCATCTTTATTCTTCAACTTACTATTCA
**
1409247 AT-GTT
65 ATCCCT
* * * *
1409252 GATCATTTTTATTTCTCAACTTT-CAGCTTAGTCCTGATCATTTTTATTCTTCAACTTGCTATTC
1 -ATCATTTTTATTTCTCAA-TTTACAGCTCAGTCCCGATCATCTTTATTCTTCAACTTACTATTC
1409316 AATCCCT
64 AATCCCT
1409323 ATCATTTTTATTTCT
1 ATCATTTTTATTTCT
1409338 TGACTCATGA
Statistics
Matches: 125, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
68 50 0.40
69 6 0.05
70 65 0.52
71 4 0.03
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (70 bp):
ATCATTTTTATTTCTCAATTTACAGCTCAGTCCCGATCATCTTTATTCTTCAACTTACTATTCAA
TCCCT
Found at i:1409758 original size:19 final size:18
Alignment explanation
Indices: 1409734--1409819 Score: 57
Period size: 19 Copynumber: 4.7 Consensus size: 18
1409724 CTTTAATAAT
*
1409734 AATAAAATAATAACCAAAA
1 AATAAAA-AAAAACCAAAA
1409753 AATAAAAAAAAACCTAAAA
1 AATAAAAAAAAACC-AAAA
* ** ** *
1409772 ATTTCAAAAAAATGAAGA
1 AATAAAAAAAAACCAAAA
*
1409790 AATAGAAAAAAAA-GAAAA
1 AATA-AAAAAAAACCAAAA
*
1409808 AAGAAAAAAAAA
1 AATAAAAAAAAA
1409820 TTTAGAAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
17 8 0.15
18 18 0.34
19 27 0.51
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.12
Consensus pattern (18 bp):
AATAAAAAAAAACCAAAA
Found at i:1409771 original size:18 final size:19
Alignment explanation
Indices: 1409734--1409773 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1409724 CTTTAATAAT
*
1409734 AATAAAATAATAACCAAAA
1 AATAAAATAAAAACCAAAA
*
1409753 AATAAAA-AAAAACCTAAA
1 AATAAAATAAAAACCAAAA
1409771 AAT
1 AAT
1409774 TTCAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (19 bp):
AATAAAATAAAAACCAAAA
Found at i:1409804 original size:15 final size:16
Alignment explanation
Indices: 1409777--1409818 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
1409767 TAAAAATTTC
*
1409777 AAAAAAATGAAGAAATAG
1 AAAAAAAAGAA-AAA-AG
1409795 AAAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
1409811 AAAAAAAA
1 AAAAAAAA
1409819 ATTTAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.43
17 3 0.13
18 10 0.43
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:1411220 original size:6 final size:6
Alignment explanation
Indices: 1411209--1411263 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 6
1411199 AGAAAGGCAA
*
1411209 AAAAAG AAAAAG -AAAAG AAAAA- AAAAGAG AAAAAG -GAAA- AAAAA-
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG
1411253 AAAAAG AAAAA
1 AAAAAG AAAAA
1411264 AAAGATAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
5 20 0.48
6 18 0.43
7 4 0.10
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1411231 original size:21 final size:22
Alignment explanation
Indices: 1411207--1411263 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
1411197 TGAGAAAGGC
1411207 AAAAAAAGAAAAA-GAAAAGAAA
1 AAAAAAAGAAAAAGGAAAA-AAA
1411229 AAAAAAGAGAAAAAGG-AAAAAA
1 AAAAAA-AGAAAAAGGAAAAAAA
1411251 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
1411264 AAAGATAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.21
22 15 0.45
23 10 0.30
24 1 0.03
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAAAAAGGAAAAAAA
Found at i:1411239 original size:23 final size:23
Alignment explanation
Indices: 1411207--1411265 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
1411197 TGAGAAAGGC
1411207 AAAAAA-AGAAAAA-GAAAAGAAA
1 AAAAAAGAGAAAAAGGAAAA-AAA
1411229 AAAAAAGAGAAAAAGGAAAAAAA
1 AAAAAAGAGAAAAAGGAAAAAAA
*
1411252 AAAAAAGAAAAAAA
1 AAAAAAGAGAAAAA
1411266 AGATAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 6 0.18
23 23 0.68
24 5 0.15
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (23 bp):
AAAAAAGAGAAAAAGGAAAAAAA
Found at i:1411248 original size:30 final size:30
Alignment explanation
Indices: 1411208--1411273 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1411198 GAGAAAGGCA
* * *
1411208 AAAAAAGAAAAAGAAAAGAAA-AAAAAAGAG
1 AAAAAGGAAAAA-AAAAAAAAGAAAAAAAAG
1411238 AAAAAGGAAAAAAAAAAAAAGAAAAAAAAG
1 AAAAAGGAAAAAAAAAAAAAGAAAAAAAAG
*
1411268 ATAAAG
1 AAAAAG
1411274 TTTTGAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (30 bp):
AAAAAGGAAAAAAAAAAAAAGAAAAAAAAG
Found at i:1411273 original size:15 final size:14
Alignment explanation
Indices: 1411207--1411266 Score: 68
Period size: 14 Copynumber: 4.1 Consensus size: 14
1411197 TGAGAAAGGC
1411207 AAAAAAAGAAAAAGA
1 AAAAAAAGAAAAA-A
1411222 AAAGAAAA-AAAAAGA
1 AAA-AAAAGAAAAA-A
* *
1411237 GAAAAAGGAAAAAA
1 AAAAAAAGAAAAAA
1411251 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
1411265 AA
1 AA
1411267 GATAAAGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
14 18 0.46
15 17 0.44
16 4 0.10
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAA
Found at i:1411334 original size:22 final size:22
Alignment explanation
Indices: 1411304--1411370 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
1411294 AAAAGGTAGC
*
1411304 TTTGAAAAACAAAATAAAAAAAT
1 TTTGAAAAGCAAAA-AAAAAAAT
**
1411327 TTTGAAAAGCAAAAAAAAAGGT
1 TTTGAAAAGCAAAAAAAAAAAT
* *
1411349 TTTGAAATGTAAAAAAAAAAAT
1 TTTGAAAAGCAAAAAAAAAAAT
1411371 AAAAAAAAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 24 0.65
23 13 0.35
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.22
Consensus pattern (22 bp):
TTTGAAAAGCAAAAAAAAAAAT
Found at i:1412263 original size:8 final size:8
Alignment explanation
Indices: 1412252--1412506 Score: 123
Period size: 8 Copynumber: 33.2 Consensus size: 8
1412242 TAAAACTTCG
1412252 AAACCCTA
1 AAACCCTA
1412260 AAA--CTA
1 AAACCCTA
*
1412266 AAACTC-A
1 AAACCCTA
* *
1412273 AAACCTTG
1 AAACCCTA
1412281 AAACCCT-
1 AAACCCTA
1412288 AAA-CCTCA
1 AAACCCT-A
*
1412296 AAACCTTA
1 AAACCCTA
*
1412304 AAA-CCTT
1 AAACCCTA
*
1412311 AAACCATA
1 AAACCCTA
1412319 AAA-CCTCA
1 AAACCCT-A
1412327 AAACCCTA
1 AAACCCTA
*
1412335 AAACCTTA
1 AAACCCTA
**
1412343 AAACTTTA
1 AAACCCTA
*
1412351 AAA-TCTCA
1 AAACCCT-A
1412359 AAACCCTA
1 AAACCCTA
**
1412367 AGGCCCTA
1 AAACCCTA
1412375 AAACCCTA
1 AAACCCTA
1412383 AAACCCTA
1 AAACCCTA
1412391 AAA-CCTCA
1 AAACCCT-A
1412399 AAACCCTA
1 AAACCCTA
* *
1412407 GAA-CTTCA
1 AAACCCT-A
1412415 AAACCCTA
1 AAACCCTA
* *
1412423 AAA-CATG
1 AAACCCTA
* *
1412430 AAACTCAA
1 AAACCCTA
*
1412438 AAAACCT-
1 AAACCCTA
1412445 AAACCCTA
1 AAACCCTA
*
1412453 AAACTC-A
1 AAACCCTA
**
1412460 AAACTTTA
1 AAACCCTA
1412468 AAACCC-A
1 AAACCCTA
1412475 AAA--CTA
1 AAACCCTA
1412481 TAAACCCTA
1 -AAACCCTA
1412490 AAA-CCTCA
1 AAACCCT-A
1412498 AAA-CCTA
1 AAACCCTA
1412505 AA
1 AA
1412507 TGCTCAAAAC
Statistics
Matches: 188, Mismatches: 36, Indels: 47
0.69 0.13 0.17
Matches are distributed among these distances:
5 1 0.01
6 10 0.05
7 52 0.28
8 110 0.59
9 15 0.08
ACGTcount: A:0.51, C:0.30, G:0.02, T:0.17
Consensus pattern (8 bp):
AAACCCTA
Found at i:1412310 original size:31 final size:31
Alignment explanation
Indices: 1412242--1412346 Score: 119
Period size: 31 Copynumber: 3.5 Consensus size: 31
1412232 TTTGAAACAC
*
1412242 TAAAA-CTTCGAAACCCTAAAACT-AAAA-CT
1 TAAAACCTT-GAAACCCTAAACCTCAAAACCT
*
1412271 CAAAACCTTGAAACCCTAAACCTCAAAACCT
1 TAAAACCTTGAAACCCTAAACCTCAAAACCT
* *
1412302 TAAAACCTT-AAACCATAAAACCTCAAAACCC
1 TAAAACCTTGAAACCCT-AAACCTCAAAACCT
*
1412333 TAAAACCTTAAAAC
1 TAAAACCTTGAAAC
1412347 TTTAAAATCT
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
29 17 0.26
30 13 0.20
31 32 0.48
32 4 0.06
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.18
Consensus pattern (31 bp):
TAAAACCTTGAAACCCTAAACCTCAAAACCT
Found at i:1412479 original size:15 final size:15
Alignment explanation
Indices: 1412451--1412493 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1412441 ACCTAAACCC
* *
1412451 TAAAACTCAAAACTT
1 TAAAACCCAAAACTA
1412466 TAAAACCCAAAACTA
1 TAAAACCCAAAACTA
1412481 T-AAACCCTAAAAC
1 TAAAACCC-AAAAC
1412494 CTCAAAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAAACCCAAAACTA
Found at i:1412485 original size:22 final size:22
Alignment explanation
Indices: 1412243--1412501 Score: 114
Period size: 23 Copynumber: 11.2 Consensus size: 22
1412233 TTGAAACACT
* *
1412243 AAAACTTCGAAACCCTAAAA-CT
1 AAAAC-TCAAAACCCTAAAACCC
* *
1412265 AAAACTCAAAACCTTGAAACCC
1 AAAACTCAAAACCCTAAAACCC
* * *
1412287 TAAACCTCAAAACCTTAAAACCT
1 -AAAACTCAAAACCCTAAAACCC
* *
1412310 TAAAC-CATAAAACCTCAAAACCC
1 AAAACTCA-AAACCCT-AAAACCC
* ** *
1412333 TAAAACCTTAAAACTTTAAAATCTC
1 -AAAA-CTCAAAACCCTAAAA-CCC
* **
1412358 AAAACCCTAAGGCCCTAAAACCC
1 AAAACTC-AAAACCCTAAAACCC
*
1412381 TAAAACCCTAAAA-CCTCAAAACCC
1 -AAAACTC-AAAACCCT-AAAACCC
* **
1412405 TAGAACTTCAAAACCCTAAAACAT
1 -AAAAC-TCAAAACCCTAAAACCC
* *
1412429 GAAACTCAAAAAACCT-AAACCC
1 AAAACTC-AAAACCCTAAAACCC
**
1412451 TAAAACTCAAAACTTTAAAACCC
1 -AAAACTCAAAACCCTAAAACCC
1412474 AAAACT-ATAAACCCTAAAACCTC
1 AAAACTCA-AAACCCTAAAACC-C
1412497 AAAAC
1 AAAAC
1412502 CTAAATGCTC
Statistics
Matches: 177, Mismatches: 42, Indels: 35
0.70 0.17 0.14
Matches are distributed among these distances:
21 14 0.08
22 42 0.24
23 59 0.33
24 50 0.28
25 11 0.06
26 1 0.01
ACGTcount: A:0.51, C:0.30, G:0.02, T:0.17
Consensus pattern (22 bp):
AAAACTCAAAACCCTAAAACCC
Found at i:1412556 original size:15 final size:15
Alignment explanation
Indices: 1412537--1412581 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
1412527 ACTTCCAAAC
1412537 CCTAAAACA-TGAAA
1 CCTAAAACATTGAAA
1412551 CTCTAAAACATTGAAA
1 C-CTAAAACATTGAAA
*
1412567 CCTAAAACCTTGAAA
1 CCTAAAACATTGAAA
1412582 TCTTAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 1 0.04
15 21 0.75
16 6 0.21
ACGTcount: A:0.51, C:0.22, G:0.07, T:0.20
Consensus pattern (15 bp):
CCTAAAACATTGAAA
Found at i:1412591 original size:24 final size:23
Alignment explanation
Indices: 1412570--1412653 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 23
1412560 ATTGAAACCT
*
1412570 AAAACCTTGAAATCTTAAAAACTC
1 AAAACCTTAAAATC-TAAAAACTC
*
1412594 GAAACCTTAAAATCTAAAATA-TC
1 AAAACCTTAAAATCTAAAA-ACTC
* * * * *
1412617 AAAACCCTAAAACTTTGAAACCCC
1 AAAACCTTAAAA-TCTAAAAACTC
1412641 AAAACCTTAAAAT
1 AAAACCTTAAAAT
1412654 AAGGACCCTA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
23 18 0.38
24 30 0.62
ACGTcount: A:0.51, C:0.23, G:0.04, T:0.23
Consensus pattern (23 bp):
AAAACCTTAAAATCTAAAAACTC
Found at i:1421009 original size:2 final size:2
Alignment explanation
Indices: 1421002--1421029 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1420992 TATCAACTTA
1421002 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
1421030 CAACTACCGG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1423804 original size:35 final size:35
Alignment explanation
Indices: 1423753--1423829 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
1423743 TGCAACATGT
* * *
1423753 CATGCAACCATGCACTTAATCACGATACAAAGAGC
1 CATGCAACCATCCACTTAATCACAATACAAAAAGC
* * *
1423788 CATGCAACCATCCACTTAGTCACAATGCAAAAAGT
1 CATGCAACCATCCACTTAATCACAATACAAAAAGC
1423823 CATGCAA
1 CATGCAA
1423830 ATCAAGTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.18
Consensus pattern (35 bp):
CATGCAACCATCCACTTAATCACAATACAAAAAGC
Found at i:1427265 original size:2 final size:2
Alignment explanation
Indices: 1427258--1427295 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1427248 TCGACATTAC
1427258 CT 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
1427296 TTGCTAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1428701 original size:12 final size:13
Alignment explanation
Indices: 1428672--1428698 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1428662 GAAATTTATA
1428672 TTATTATTGATTT
1 TTATTATTGATTT
1428685 TTATTATTGATTT
1 TTATTATTGATTT
1428698 T
1 T
1428699 ATTTTTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
TTATTATTGATTT
Found at i:1430724 original size:2 final size:2
Alignment explanation
Indices: 1430717--1430746 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1430707 TAAGTATTGA
1430717 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
1430747 TAGATTTGAA
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):
AT
Found at i:1431603 original size:22 final size:23
Alignment explanation
Indices: 1431570--1431613 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1431560 TAAAATATTT
*
1431570 AATTTAATATATTA-ATTTAAAA
1 AATTTAATATATAATATTTAAAA
1431592 AATTT-ATAATATAATATTTAAA
1 AATTTAAT-ATATAATATTTAAA
1431614 TTATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.11
22 10 0.53
23 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTAATATATAATATTTAAAA
Found at i:1431608 original size:27 final size:26
Alignment explanation
Indices: 1431578--1431635 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
1431568 TTAATTTAAT
*
1431578 ATATTAATTTAAAAAATTT-ATAATATA
1 ATATTAAATT-AAAAATTTGATAAT-TA
*
1431605 ATATTTAAATTATAAATTTGATAATTA
1 ATA-TTAAATTAAAAATTTGATAATTA
1431632 ATAT
1 ATAT
1431636 GATATTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 1 0.04
27 15 0.56
28 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
ATATTAAATTAAAAATTTGATAATTA
Found at i:1431867 original size:23 final size:25
Alignment explanation
Indices: 1431841--1431886 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
1431831 TGTTGCACCT
*
1431841 GAAGCAATA-ATCACAA-CAATACA
1 GAAGCAATAGATAACAATCAATACA
1431864 GAAGCAATAGATAACAATCAATA
1 GAAGCAATAGATAACAATCAATA
1431887 ATCAAAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.57, C:0.17, G:0.11, T:0.15
Consensus pattern (25 bp):
GAAGCAATAGATAACAATCAATACA
Found at i:1440763 original size:18 final size:19
Alignment explanation
Indices: 1440723--1440765 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1440713 ATACGATATT
* *
1440723 ATTTTATTAATAAAAATAT
1 ATTTTTTTAATAAAAATAA
*
1440742 ATTTTTTTAA-AAAATTAA
1 ATTTTTTTAATAAAAATAA
1440760 ATTTTT
1 ATTTTT
1440766 ATGTATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTTTTAATAAAAATAA
Found at i:1441657 original size:18 final size:17
Alignment explanation
Indices: 1441619--1441653 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1441609 TATTGACAGA
1441619 TAGATAAGTTGAAACTT
1 TAGATAAGTTGAAACTT
1441636 TAGATAAGTTGAAACTT
1 TAGATAAGTTGAAACTT
1441653 T
1 T
1441654 TAGAAGGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (17 bp):
TAGATAAGTTGAAACTT
Found at i:1444056 original size:13 final size:11
Alignment explanation
Indices: 1444026--1444055 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1444016 ATACGGTAAT
*
1444026 ATAACATAAAA
1 ATAATATAAAA
1444037 ATAATATAAAA
1 ATAATATAAAA
1444048 ATAATATA
1 ATAATATA
1444056 TTTTATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:1444154 original size:18 final size:18
Alignment explanation
Indices: 1444127--1444172 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1444117 TTTATATTAA
1444127 TATAATATAATATATAAAT
1 TATAA-ATAATATATAAAT
* * *
1444146 TATTAATAATTTATATAT
1 TATAAATAATATATAAAT
1444164 TATAAATAA
1 TATAAATAA
1444173 AAAAATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATAAATAATATATAAAT
Found at i:1444162 original size:32 final size:33
Alignment explanation
Indices: 1444126--1444221 Score: 85
Period size: 30 Copynumber: 2.9 Consensus size: 33
1444116 TTTTATATTA
1444126 ATATAATATAATATATAAATTATTAATAATTT-
1 ATATAATATAATATATAAATTATTAATAATTTG
* ** *
1444158 ATATATTATAA-ATA-AAAAAATTTAT-ATTTG
1 ATATAATATAATATATAAATTATTAATAATTTG
1444188 ATATATATATTAAATATATAAATT-TTATATAATT
1 ATATA-ATA-T-AATATATAAATTATTA-ATAATT
1444222 ATCAATTGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
29 4 0.08
30 13 0.27
31 5 0.10
32 11 0.23
33 2 0.04
34 5 0.10
35 5 0.10
36 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
ATATAATATAATATATAAATTATTAATAATTTG
Found at i:1444252 original size:24 final size:23
Alignment explanation
Indices: 1444235--1444278 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1444225 AATTGAATCC
1444235 AAATAATAATAATTAATTAATAA
1 AAATAATAATAATTAATTAATAA
1444258 AAATAA-AATATATTAA-TAATA
1 AAATAATAATA-ATTAATTAATA
1444279 CTTTATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATAATAATAATTAATTAATAA
Found at i:1444357 original size:21 final size:21
Alignment explanation
Indices: 1444311--1444371 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1444301 TAATTATTTT
*
1444311 AATTTATATATATTTATTTTAAA
1 AATTAATAT-TATTTA-TTTAAA
1444334 AATTAATATTATTTA-TTAATA
1 AATTAATATTATTTATTTAA-A
*
1444355 AATTATTATTA-TTATTT
1 AATTAATATTATTTATTT
1444372 TATTTATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 7 0.21
21 13 0.38
22 6 0.18
23 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTAATATTATTTATTTAAA
Found at i:1453695 original size:2 final size:2
Alignment explanation
Indices: 1453688--1453718 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1453678 GTTTTTCAGC
*
1453688 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1453719 GCGAGAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1453726 original size:2 final size:2
Alignment explanation
Indices: 1453721--1453754 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1453711 TATATATAGC
1453721 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
1453755 CATACACACA
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:1456801 original size:71 final size:71
Alignment explanation
Indices: 1456685--1456829 Score: 272
Period size: 71 Copynumber: 2.0 Consensus size: 71
1456675 TGATAGTGAA
*
1456685 TTGGCTGTAACATGTAGCCACCTCTCCTTACAAATATTGGTGTGTTTTAGACACACAAGGATGTT
1 TTGGCTGTAACATGTAGCCACATCTCCTTACAAATATTGGTGTGTTTTAGACACACAAGGATGTT
1456750 ACAATC
66 ACAATC
*
1456756 TTGGCTGTAACATGTGGCCACATCTCCTTACAAATATTGGTGTGTTTTAGACACACAAGGATGTT
1 TTGGCTGTAACATGTAGCCACATCTCCTTACAAATATTGGTGTGTTTTAGACACACAAGGATGTT
1456821 ACAATC
66 ACAATC
1456827 TTG
1 TTG
1456830 TCCAACATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (71 bp):
TTGGCTGTAACATGTAGCCACATCTCCTTACAAATATTGGTGTGTTTTAGACACACAAGGATGTT
ACAATC
Found at i:1456936 original size:2 final size:2
Alignment explanation
Indices: 1456931--1456963 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1456921 TTCTTGTGTG
*
1456931 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1456964 GCAAATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 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):
TA
Found at i:1461564 original size:2 final size:2
Alignment explanation
Indices: 1461559--1461594 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1461549 TGTGTGTATG
1461559 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1461595 GCTATATATA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1461602 original size:2 final size:2
Alignment explanation
Indices: 1461597--1461627 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1461587 TCTCTCTCGC
*
1461597 TA TA TA TA TT 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 TA T
1461628 GCTGAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1470019 original size:16 final size:15
Alignment explanation
Indices: 1469998--1470029 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1469988 AAGTCCTCAC
1469998 TTCTTGTTCTTTCTTT
1 TTCTTGTTC-TTCTTT
1470014 TTCTTGTTCTTCTTT
1 TTCTTGTTCTTCTTT
1470029 T
1 T
1470030 CTTCTACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.75
Consensus pattern (15 bp):
TTCTTGTTCTTCTTT
Found at i:1470923 original size:22 final size:22
Alignment explanation
Indices: 1470898--1470964 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
1470888 GTCTTACATT
1470898 ATTTATAAATAAAATAATAATA
1 ATTTATAAATAAAATAATAATA
* *
1470920 ATTTATTAAT-AAATAAATATTA
1 ATTTATAAATAAAAT-AATAATA
*
1470942 ATTTTTAAAATAAATATATATAA
1 ATTTAT-AAATAAA-ATA-ATAA
1470965 ATTAAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
21 4 0.11
22 20 0.57
23 3 0.09
24 3 0.09
25 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTATAAATAAAATAATAATA
Done.