Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 20 of 160
Found at i:5582505 original size:59 final size:58
Alignment explanation
Indices: 5582254--5582787 Score: 639
Period size: 60 Copynumber: 9.0 Consensus size: 58
5582244 TTTCTTTAAA
* * * *
5582254 TAAAAATGACAATTTCCAAAAAAAAATTATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCT
1 TAAAAAT-AAAATTT-CAAAAAAAGA-T-TTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT
* *
5582317 TAAAAAT-AAATTTCAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
5582374 TGAAAATCAAAATTTCCAAAAAAATATTTTT-AGGGAAAAGGTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAAATTT-CAAAAAAAGATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT
* *
5582434 TAAAAAT-AAATTTCAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
1 TAAAAATAAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
5582491 TGAAAATCAAAATTTCCAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAAATTTCAAAAAAAGATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT
*
5582550 TAAAAATAAATTTTCATAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTCCTT
1 TAAAAATAAAATTTC--AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-T
* *
5582610 TGAAAATCAAAATTTCCAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAAATTT-CAAAAAAAGATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT
*
5582670 TAAAAATAAAATTTCAAAAAAAGGGATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCT
1 TAAAAATAAAATTTCAAAAAAA--GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * * * * *
5582730 TGAAAATCAAAATTTCCAAAGAATATTTTTGGGGAAAAGTTGAAAGTATCTATTTTCC
1 TAAAAAT-AAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
5582788 CTACAAAAAA
Statistics
Matches: 413, Mismatches: 38, Indels: 44
0.83 0.08 0.09
Matches are distributed among these distances:
57 76 0.18
58 28 0.07
59 102 0.25
60 168 0.41
61 31 0.08
62 1 0.00
63 7 0.02
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (58 bp):
TAAAAATAAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:5587132 original size:26 final size:28
Alignment explanation
Indices: 5587095--5587160 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 28
5587085 GATGAAGTAG
5587095 AAAAAATG-GAAAAAG-CAAAAAT-AAA
1 AAAAAATGAGAAAAAGTCAAAAATGAAA
* *
5587120 AAAAAATGAG-AAATGTGAAAAATGAAA
1 AAAAAATGAGAAAAAGTCAAAAATGAAA
5587147 AAAAAA-GAGAAAAA
1 AAAAAATGAGAAAAA
5587161 AAAAGAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 12 0.35
26 10 0.29
27 12 0.35
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (28 bp):
AAAAAATGAGAAAAAGTCAAAAATGAAA
Found at i:5588564 original size:34 final size:33
Alignment explanation
Indices: 5588512--5588644 Score: 106
Period size: 34 Copynumber: 3.9 Consensus size: 33
5588502 CAAAATTGAA
* * *
5588512 AATTTTGTGAACCAGAAATTCTTATGAATCTCT
1 AATTTTATGAATCTGAAATTCTTATGAATCTCT
* * *
5588545 AAGTTTAATGAATCTGAAATTCTTGTGAATCTCC
1 AA-TTTTATGAATCTGAAATTCTTATGAATCTCT
* * **
5588579 AATTCTTATGAATCTAAAAATCTTACAAATCT-T
1 AATT-TTATGAATCTGAAATTCTTATGAATCTCT
* * *
5588612 CAATTTTTATGCATTTGAAATTCTTGTGAATCT
1 -AA-TTTTATGAATCTGAAATTCTTATGAATCT
5588645 AAAAATCTTA
Statistics
Matches: 76, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
33 4 0.05
34 70 0.92
35 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (33 bp):
AATTTTATGAATCTGAAATTCTTATGAATCTCT
Found at i:5588573 original size:17 final size:17
Alignment explanation
Indices: 5588526--5588695 Score: 99
Period size: 17 Copynumber: 10.0 Consensus size: 17
5588516 TTGTGAACCA
5588526 GAAATTCTTATGAATCT
1 GAAATTCTTATGAATCT
* * *
5588543 CTAAGTT-TAATGAATCT
1 -GAAATTCTTATGAATCT
*
5588560 GAAATTCTTGTGAATCT
1 GAAATTCTTATGAATCT
**
5588577 CCAATTCTTATGAATCT
1 GAAATTCTTATGAATCT
* * **
5588594 AAAAATCTTACAAATCT
1 GAAATTCTTATGAATCT
** * * *
5588611 TCAATTTTTATGCATTT
1 GAAATTCTTATGAATCT
*
5588628 GAAATTCTTGTGAATCT
1 GAAATTCTTATGAATCT
* * *
5588645 AAAAATCTTACGAATCT
1 GAAATTCTTATGAATCT
** * *
5588662 TCAATTTTTGTGAATCT
1 GAAATTCTTATGAATCT
**
5588679 TCAATTCTTATGAATCT
1 GAAATTCTTATGAATCT
5588696 ATTTTCTTGA
Statistics
Matches: 110, Mismatches: 41, Indels: 3
0.71 0.27 0.02
Matches are distributed among these distances:
16 4 0.04
17 102 0.93
18 4 0.04
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (17 bp):
GAAATTCTTATGAATCT
Found at i:5588610 original size:51 final size:50
Alignment explanation
Indices: 5588461--5588696 Score: 192
Period size: 51 Copynumber: 4.6 Consensus size: 50
5588451 CAAATCTTTG
* *
5588461 AATTTTGTGAATCTTCAATTCTTGTGAA-CTAAAAAATCTTACAAAAT-TGAA
1 AATTTTGTGAATCTGCAATTCTTATGAATCT-AAAAATCTTAC-AAATCTG-A
* * * ** *
5588512 AATTTTGTGAACCAGAAATTCTTATGAATCTCTAAGT-TTA-ATGAATCTGA
1 AATTTTGTGAATCTGCAATTCTTATGAATCTAAAAATCTTACA--AATCTGA
* *
5588562 AATTCTTGTGAATCTCCAATTCTTATGAATCTAAAAATCTTACAAATCTTCA
1 AATT-TTGTGAATCTGCAATTCTTATGAATCTAAAAATCTTACAAATC-TGA
* * * * * * * *
5588614 ATTTTTATGCATTTGAAATTCTTGTGAATCTAAAAATCTTACGAATCTTCA
1 AATTTTGTGAATCTGCAATTCTTATGAATCTAAAAATCTTACAAATC-TGA
* *
5588665 ATTTTTGTGAATCTTCAATTCTTATGAATCTA
1 AATTTTGTGAATCTGCAATTCTTATGAATCTA
5588697 TTTTCTTGAG
Statistics
Matches: 147, Mismatches: 30, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
48 1 0.01
50 11 0.07
51 124 0.84
52 10 0.07
53 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (50 bp):
AATTTTGTGAATCTGCAATTCTTATGAATCTAAAAATCTTACAAATCTGA
Found at i:5588694 original size:34 final size:34
Alignment explanation
Indices: 5588527--5588695 Score: 137
Period size: 34 Copynumber: 5.0 Consensus size: 34
5588517 TGTGAACCAG
* * *
5588527 AAATTCTTATGAATC-TCTAAGTT-TAATGAATCTG
1 AAATTCTTGTGAATCTTC-AA-TTCTTATGAATCTT
* *
5588561 AAATTCTTGTGAATCTCCAATTCTTATGAATCTA
1 AAATTCTTGTGAATCTTCAATTCTTATGAATCTT
* *** * *
5588595 AAAATCTTACAAATCTTCAATTTTTATGCAT-TT
1 AAATTCTTGTGAATCTTCAATTCTTATGAATCTT
** * *
5588628 GAAATTCTTGTGAATCTAAAAATCTTACGAATCTT
1 -AAATTCTTGTGAATCTTCAATTCTTATGAATCTT
* *
5588663 CAATTTTTGTGAATCTTCAATTCTTATGAATCT
1 AAATTCTTGTGAATCTTCAATTCTTATGAATCT
5588696 ATTTTCTTGA
Statistics
Matches: 103, Mismatches: 28, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
33 3 0.03
34 97 0.94
35 3 0.03
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (34 bp):
AAATTCTTGTGAATCTTCAATTCTTATGAATCTT
Found at i:5590952 original size:62 final size:61
Alignment explanation
Indices: 5590876--5591008 Score: 144
Period size: 62 Copynumber: 2.1 Consensus size: 61
5590866 GAATACCAAT
* *
5590876 AAATAAATATTTAAAAAAATGAAA-AAGTTT-TCAGGAAAAGTTAAAAGTGTCAATTTTTTTTAA
1 AAATAAA-A-TTAAAAAAA--AAACAAGTTTATCAGGAAAAGTTAAAAGTATCAATTTTTCTTAA
* * * * *
5590939 AAATTAAAATTAAAAAAAAAACTATTTTATGAGGAAAAGTTGAAAGTATCAATTTTTCTTGA
1 AAA-TAAAATTAAAAAAAAAACAAGTTTATCAGGAAAAGTTAAAAGTATCAATTTTTCTTAA
5591001 AAATAAAA
1 AAATAAAA
5591009 CTTTCAAAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
60 3 0.05
61 9 0.15
62 40 0.67
63 4 0.07
64 4 0.07
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.33
Consensus pattern (61 bp):
AAATAAAATTAAAAAAAAAACAAGTTTATCAGGAAAAGTTAAAAGTATCAATTTTTCTTAA
Found at i:5591052 original size:59 final size:58
Alignment explanation
Indices: 5590910--5591295 Score: 364
Period size: 59 Copynumber: 6.5 Consensus size: 58
5590900 AAGTTTTCAG
* * * *** * *
5590910 GAAAAGTTAAAAGTGTCAATTTTTTTTAAAAATTAAAATTAAAAAAAAAACTATTTTATGAG
1 GAAAAGTTGAAAGTATCAATTTTTCTTAAAAA-TAAAATT-TTCAAAAAA-TATTTT-TTAA
* * *
5590972 GAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAACTTTCAAAAGATATTTTTTGAA
1 GAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAATATTTTTT-AA
* * *** *
5591031 -AAAAGGTTGAGAGTA-CTAATTTTTCTTAAAAATGAAAA-CTTCAAAAAAGGCTCTTTAA
1 GAAAA-GTTGAAAGTATC-AATTTTTCTTAAAAAT-AAAATTTTCAAAAAATATTTTTTAA
* * * * *
5591089 GAAAAAGTTAAAAATATTAATTTTTCTTAAAAATAAAATTTTCAAAAAAAAAATTTTTGGAA
1 G-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTC--AAAAAATATTTTT-TAA
* * * * *
5591151 GAAAAGTTGAAAGTGTCAATTTTTCTTGAAGATAAAATTTTCAAAAGATATTTTTTTA
1 GAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAATATTTTTTAA
* *
5591209 GAAAAAGTTGACAGTATCAATTTTTCTTAAAAATAAAATTTTTAAAAAATATTTTTTAA
1 G-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAATATTTTTTAA
5591268 GGAAAAGTTGAAAGTATCAATTTTTCTT
1 -GAAAAGTTGAAAGTATCAATTTTTCTT
5591296 GAATAAAAGC
Statistics
Matches: 264, Mismatches: 47, Indels: 29
0.78 0.14 0.09
Matches are distributed among these distances:
58 14 0.05
59 155 0.59
60 14 0.05
61 50 0.19
62 31 0.12
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (58 bp):
GAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAATATTTTTTAA
Found at i:5591197 original size:118 final size:116
Alignment explanation
Indices: 5590910--5591298 Score: 347
Period size: 120 Copynumber: 3.2 Consensus size: 116
5590900 AAGTTTTCAG
* * * * * * * *
5590910 GAAAAGTTAAAAGTGTCAATTTTTTTTAAAAATTAAAA-TTAAAAAAAAAACTATTTTATGAGGA
1 GAAAAGTTGAAAGT-TCAATTTTTCTTGAAAATGAAAACTT-CAAAAAGAACT-CTTTA--AGAA
* * *
5590974 AAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAACTTTCAAAAGATATTTTTTGAA
61 AAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAATA-TTTTTGAA
* * * *
5591031 -AAAAGGTTGAGAGTACTAATTTTTCTTAAAAATGAAAACTTCAAAAA-AGGCTCTTTAAGAAAA
1 GAAAA-GTTGAAAGTTC-AATTTTTCTTGAAAATGAAAACTTCAAAAAGA-ACTCTTTAAGAAAA
* * * *
5591094 AGTTAAAAATATTAATTTTTCTTAAAAATAAAATTTTCAAAAAAAAAATTTTTGGAA
63 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTC--AAAAAATATTTTT-GAA
* * * * *
5591151 GAAAAGTTGAAAGTGTCAATTTTTCTTGAAGAT-AAAATTTTC-AAAAGATATTTTTTTAGAAAA
1 GAAAAGTTGAAAGT-TCAATTTTTCTTGAAAATGAAAA-CTTCAAAAAGA-ACTCTTTAAGAAAA
* * *
5591214 AGTTGACAGTATCAATTTTTCTTAAAAATAAAATTTTTAAAAAATATTTTTTAA
63 AGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAATATTTTTGAA
5591268 GGAAAAGTTGAAAGTATCAATTTTTCTTGAA
1 -GAAAAGTTGAAAGT-TCAATTTTTCTTGAA
5591299 TAAAAGCATT
Statistics
Matches: 222, Mismatches: 34, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
117 2 0.01
118 79 0.36
119 13 0.06
120 88 0.40
121 38 0.17
122 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.37
Consensus pattern (116 bp):
GAAAAGTTGAAAGTTCAATTTTTCTTGAAAATGAAAACTTCAAAAAGAACTCTTTAAGAAAAAGT
TGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAATATTTTTGAA
Found at i:5591233 original size:179 final size:179
Alignment explanation
Indices: 5590911--5591295 Score: 485
Period size: 179 Copynumber: 2.1 Consensus size: 179
5590901 AGTTTTCAGG
* * * * *
5590911 AAAAGTTAAAAGTGTCAATTTTTTTTAAAAATTAAAATTAAAAAAAAAACTATTTTATGAGGAAA
1 AAAAGTTAAAAATATCAATTTTTCTTAAAAATTAAAATTAAAAAAAAAACTATTTTAGGAAGAAA
5590976 AGTTGAAAGTATCAATTTTTCTTGAAAATAAAACTTTCAAAAGATATTTTTTGAAAAAAGGTTGA
66 AGTTGAAAGTATCAATTTTTCTTGAAAATAAAACTTTCAAAAGATATTTTTTGAAAAAAGGTTGA
*
5591041 GAGTACTAATTTTTCTTAAAAATGAAAACTTCAAAAAAGGCTCTTTAAGA
131 CAGTACTAATTTTTCTTAAAAAT-AAAACTTCAAAAAAGGCTCTTTAAGA
*
5591091 AAAAGTTAAAAATATTAATTTTTCTTAAAAA-TAAAATTTTCAAAAAAAAAA-T-TTTT-GGAAG
1 AAAAGTTAAAAATATCAATTTTTCTTAAAAATTAAAA--TT-AAAAAAAAAACTATTTTAGGAAG
* * * *
5591152 AAAAGTTGAAAGTGTCAATTTTTCTTGAAGATAAAATTTTCAAAAGATATTTTTTTAGAAAAA-G
63 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAACTTTCAAAAGATATTTTTTGA-AAAAAGG
* * *** * *
5591216 TTGACAGTA-TCAATTTTTCTTAAAAATAAAATTTTTAAAAAATATTTTTTAAGG
127 TTGACAGTACT-AATTTTTCTTAAAAATAAAA-CTTCAAAAAAGGCTCTTTAAGA
* *
5591270 AAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAGTTAAAAATATCAATTTTTCTT
5591296 GAATAAAAGC
Statistics
Matches: 178, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
178 5 0.03
179 124 0.70
180 36 0.20
181 3 0.02
182 10 0.06
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (179 bp):
AAAAGTTAAAAATATCAATTTTTCTTAAAAATTAAAATTAAAAAAAAAACTATTTTAGGAAGAAA
AGTTGAAAGTATCAATTTTTCTTGAAAATAAAACTTTCAAAAGATATTTTTTGAAAAAAGGTTGA
CAGTACTAATTTTTCTTAAAAATAAAACTTCAAAAAAGGCTCTTTAAGA
Found at i:5605291 original size:27 final size:28
Alignment explanation
Indices: 5605260--5605317 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 28
5605250 ACGAAAATTT
5605260 AAATGGATCCTTACTC-TCTTATTTCTG
1 AAATGGATCCTTACTCATCTTATTTCTG
5605287 AAATGGATCCTTACTCTATCTTATTTCTG
1 AAATGGATCCTTACTC-ATCTTATTTCTG
5605316 AA
1 AA
5605318 CCAACCCAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 16 0.55
29 13 0.45
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (28 bp):
AAATGGATCCTTACTCATCTTATTTCTG
Found at i:5607139 original size:21 final size:20
Alignment explanation
Indices: 5607103--5607161 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
5607093 CGTGAAAAAT
5607103 AATATCATGCAA-TAATATA
1 AATATCATGCAATTAATATA
*
5607122 ATATATCATACAATTAATATA
1 A-ATATCATGCAATTAATATA
5607143 AACTATCATGCAATTAATA
1 AA-TATCATGCAATTAATA
5607162 ATCATGCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 23 0.66
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (20 bp):
AATATCATGCAATTAATATA
Found at i:5607288 original size:20 final size:20
Alignment explanation
Indices: 5607264--5607312 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
5607254 AACTATATGT
*
5607264 AAAAAAATGAAAAAATAAAAC
1 AAAAAAAAG-AAAAATAAAAC
5607285 AAAAAAAAGAAAAATAAAA-
1 AAAAAAAAGAAAAATAAAAC
5607304 AAGAAAAAA
1 AA-AAAAAA
5607313 AAGTGACACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 16 0.62
21 8 0.31
ACGTcount: A:0.86, C:0.02, G:0.06, T:0.06
Consensus pattern (20 bp):
AAAAAAAAGAAAAATAAAAC
Found at i:5607292 original size:22 final size:22
Alignment explanation
Indices: 5607264--5607315 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
5607254 AACTATATGT
* *
5607264 AAAAAAATGAAAAA-ATAAAAC
1 AAAAAAAAGAAAAATAAAAAAC
*
5607285 AAAAAAAAGAAAAATAAAAAAG
1 AAAAAAAAGAAAAATAAAAAAC
5607307 AAAAAAAAG
1 AAAAAAAAG
5607316 TGACACCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.85, C:0.02, G:0.08, T:0.06
Consensus pattern (22 bp):
AAAAAAAAGAAAAATAAAAAAC
Found at i:5607303 original size:13 final size:13
Alignment explanation
Indices: 5607266--5607311 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
5607256 CTATATGTAA
*
5607266 AAAAATGAAAAAAT
1 AAAAAT-AAAAAAG
*
5607280 AAAACAAAAAAAAG
1 AAAA-ATAAAAAAG
5607294 AAAAATAAAAAAG
1 AAAAATAAAAAAG
5607307 AAAAA
1 AAAAA
5607312 AAAGTGACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 13 0.46
14 14 0.50
15 1 0.04
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAAATAAAAAAG
Found at i:5608172 original size:20 final size:19
Alignment explanation
Indices: 5608147--5608216 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
5608137 ATAATCCCCG
5608147 TTTTTTATTTTTCCTTTTCC
1 TTTTTT-TTTTTCCTTTTCC
** **
5608167 TTTTTTTTTGGCCTTTGAC
1 TTTTTTTTTTTCCTTTTCC
*
5608186 TTTTTTTTTTTACTTTTGACC
1 TTTTTTTTTTTCCTTTT--CC
5608207 TTTTTTTTTT
1 TTTTTTTTTT
5608217 ACTAGAAATA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
19 22 0.56
20 6 0.15
21 11 0.28
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (19 bp):
TTTTTTTTTTTCCTTTTCC
Found at i:5608217 original size:20 final size:20
Alignment explanation
Indices: 5608148--5608219 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
5608138 TAATCCCCGT
*
5608148 TTTTTATTTTTCCTTTT--CC
1 TTTTT-TTTTTACTTTTGACC
** * *
5608167 TTTTTTTTTGGCCTTTGACT
1 TTTTTTTTTTACTTTTGACC
5608187 TTTTTTTTTTACTTTTGACC
1 TTTTTTTTTTACTTTTGACC
5608207 TTTTTTTTTTACT
1 TTTTTTTTTTACT
5608220 AGAAATAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
18 8 0.19
19 5 0.12
20 30 0.70
ACGTcount: A:0.07, C:0.15, G:0.06, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTTACTTTTGACC
Found at i:5609620 original size:2 final size:2
Alignment explanation
Indices: 5609613--5609638 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5609603 ATATGATGTG
5609613 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
5609639 CTAAACCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5611759 original size:45 final size:45
Alignment explanation
Indices: 5611708--5611794 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
5611698 TAATGTTACG
**
5611708 GGTTATAACAGTGATCGTAACTAACAATAAATTAATGATAATTAT
1 GGTTATAACAACGATCGTAACTAACAATAAATTAATGATAATTAT
5611753 GGTTATAACAACGATCGTAACTAACAATAAATTAATGATAAT
1 GGTTATAACAACGATCGTAACTAACAATAAATTAATGATAAT
5611795 GATGATTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (45 bp):
GGTTATAACAACGATCGTAACTAACAATAAATTAATGATAATTAT
Found at i:5613317 original size:22 final size:25
Alignment explanation
Indices: 5613273--5613317 Score: 69
Period size: 22 Copynumber: 1.9 Consensus size: 25
5613263 GTAATTGAAT
5613273 TTATTATATTATTAATTAAATTTAA
1 TTATTATATTATTAATTAAATTTAA
5613298 TTATTA-ATT-TTAA-TAAATTT
1 TTATTATATTATTAATTAAATTT
5613318 TATTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 3 0.15
25 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTATTATATTATTAATTAAATTTAA
Found at i:5613337 original size:14 final size:13
Alignment explanation
Indices: 5613305--5613349 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
5613295 TAATTATTAA
*
5613305 TTTTAATAAATTT
1 TTTTAATAAAATT
5613318 TATTTAATATAAATT
1 T-TTTAATA-AAATT
*
5613333 TTTTATTAAAATT
1 TTTTAATAAAATT
5613346 TTTT
1 TTTT
5613350 TCAATCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 10 0.36
14 13 0.46
15 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAATAAAATT
Found at i:5613590 original size:23 final size:23
Alignment explanation
Indices: 5613546--5613604 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
5613536 ATTTTGATGA
* *
5613546 AATTAAAATTAATA-ATTATTAT
1 AATTATAATTAAAATATTATTAT
* *
5613568 TATTATTATTAAAATATTATTAT
1 AATTATAATTAAAATATTATTAT
5613591 AATTATAATTAAAA
1 AATTATAATTAAAA
5613605 AATTTTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTATAATTAAAATATTATTAT
Found at i:5613636 original size:15 final size:15
Alignment explanation
Indices: 5613605--5613655 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
5613595 ATAATTAAAA
*
5613605 AATTTTAATAAAA--
1 AATTTTATTAAAATT
5613618 AATTTATATT-AAATT
1 AATTT-TATTAAAATT
5613633 AATTTTATTAAAATT
1 AATTTTATTAAAATT
5613648 AATATTTA
1 AAT-TTTA
5613656 AATTTAATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 8 0.25
14 7 0.22
15 13 0.41
16 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTTTATTAAAATT
Found at i:5614253 original size:25 final size:26
Alignment explanation
Indices: 5614192--5614264 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
5614182 GCACTGAACT
* *
5614192 TTTATATAAAT-TTAATAATTTAAAA
1 TTTATATAAATAATAATAATATAAAA
*
5614217 TATGATAT-AATAAT-ATAATATAAAA
1 T-TTATATAAATAATAATAATATAAAA
*
5614242 TTTATATAAATAAAAAATAATAT
1 TTTATATAAAT-AATAATAATAT
5614265 GATTCAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
24 5 0.13
25 18 0.47
26 8 0.21
27 7 0.18
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
TTTATATAAATAATAATAATATAAAA
Found at i:5614290 original size:10 final size:10
Alignment explanation
Indices: 5614270--5614316 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
5614260 AATATGATTC
5614270 AAAAATT-TA
1 AAAAATTATA
5614279 AAAAATTATA
1 AAAAATTATA
*
5614289 AAAAATTTTA
1 AAAAATTATA
*
5614299 ATAAA--ATA
1 AAAAATTATA
5614307 AAAAATTATA
1 AAAAATTATA
5614317 TTTTATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
8 6 0.19
9 7 0.23
10 18 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:5614291 original size:18 final size:18
Alignment explanation
Indices: 5614270--5614311 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
5614260 AATATGATTC
5614270 AAAAATTTAA-AAAATTATA
1 AAAAATTTAATAAAA-TA-A
5614289 AAAAATTTTAATAAAATAA
1 AAAAA-TTTAATAAAATAA
5614308 AAAA
1 AAAA
5614312 TTATATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATTTAATAAAATAA
Found at i:5621754 original size:20 final size:20
Alignment explanation
Indices: 5621729--5621811 Score: 66
Period size: 20 Copynumber: 4.1 Consensus size: 20
5621719 ATTACAATAT
5621729 ATATTAATTTAAAAATATAA
1 ATATTAATTTAAAAATATAA
*
5621749 ATATTATACTATTAAATAATA-AC
1 ATATTA-A-T-TTAAA-AATATAA
5621772 A-ATTAATTTAAAAA-ATAAA
1 ATATTAATTTAAAAATAT-AA
* *
5621791 ATTTTAATTTACAAAT-TAA
1 ATATTAATTTAAAAATATAA
5621810 AT
1 AT
5621812 CGATAAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
17 1 0.02
18 2 0.04
19 11 0.22
20 19 0.37
21 2 0.04
22 5 0.10
23 7 0.14
24 4 0.08
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATTAATTTAAAAATATAA
Found at i:5623116 original size:38 final size:38
Alignment explanation
Indices: 5623065--5623140 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
5623055 CGAATTATTA
5623065 ATTTTATACTTACTATGTTGTATCCCTTTATTTGATAT
1 ATTTTATACTTACTATGTTGTATCCCTTTATTTGATAT
*
5623103 ATTTTATACTTACTATGTTGTATCTCTTTATTTGATAT
1 ATTTTATACTTACTATGTTGTATCCCTTTATTTGATAT
5623141 GCCATGTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.57
Consensus pattern (38 bp):
ATTTTATACTTACTATGTTGTATCCCTTTATTTGATAT
Found at i:5623414 original size:30 final size:30
Alignment explanation
Indices: 5623380--5623474 Score: 122
Period size: 30 Copynumber: 3.2 Consensus size: 30
5623370 TGTTAAACAC
*
5623380 TTATTAAGATACAAATTAAAAATTTATAAT
1 TTATTAAGATACAAATTAAAAATTTAAAAT
**
5623410 TTATTTGGATACAAATTAAAAA-TTAAAATT
1 TTATTAAGATACAAATTAAAAATTTAAAA-T
*
5623440 TTAATTAAG-TACAAATTAAAAATTAAAAAT
1 TT-ATTAAGATACAAATTAAAAATTTAAAAT
5623470 TTATT
1 TTATT
5623475 TAAATATAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
29 8 0.14
30 39 0.70
31 9 0.16
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (30 bp):
TTATTAAGATACAAATTAAAAATTTAAAAT
Found at i:5625747 original size:13 final size:13
Alignment explanation
Indices: 5625729--5625754 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5625719 CTAACTCACT
5625729 AGATATGTATACA
1 AGATATGTATACA
5625742 AGATATGTATACA
1 AGATATGTATACA
5625755 GACAAAATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AGATATGTATACA
Found at i:5633852 original size:16 final size:16
Alignment explanation
Indices: 5633831--5633861 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5633821 AAGTTCAGAG
5633831 TGACTTAAAAGCACAA
1 TGACTTAAAAGCACAA
5633847 TGACTTAAAAGCACA
1 TGACTTAAAAGCACA
5633862 TCTTCTTTCA
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:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
TGACTTAAAAGCACAA
Found at i:5637325 original size:35 final size:37
Alignment explanation
Indices: 5637285--5637356 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
5637275 GCTTCAAATA
*
5637285 TATAAACT-A-AAACATCTAAGATTTACAAATTGTAT
1 TATAAACTGATAAACAACTAAGATTTACAAATTGTAT
5637320 TATAAACTGGAATAAACAACTAAGATTTACAAATTGT
1 TATAAACT-G-ATAAACAACTAAGATTTACAAATTGT
5637357 GTTCATGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 8 0.25
38 1 0.03
39 23 0.72
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (37 bp):
TATAAACTGATAAACAACTAAGATTTACAAATTGTAT
Found at i:5638132 original size:56 final size:56
Alignment explanation
Indices: 5638069--5638183 Score: 185
Period size: 56 Copynumber: 2.1 Consensus size: 56
5638059 CACAATATAA
*
5638069 TTTAATTTGCAGCCGTTTGCTTCATTCACAAAACTGTGTAGCCATCAGGTTTCACT
1 TTTAATTTACAGCCGTTTGCTTCATTCACAAAACTGTGTAGCCATCAGGTTTCACT
* * * *
5638125 TTTAATTTACAGCTGTTTGCTTCATTCACACAACTGTGTAGCCATCATGTTTTACT
1 TTTAATTTACAGCCGTTTGCTTCATTCACAAAACTGTGTAGCCATCAGGTTTCACT
5638181 TTT
1 TTT
5638184 TAGTAGCCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.42
Consensus pattern (56 bp):
TTTAATTTACAGCCGTTTGCTTCATTCACAAAACTGTGTAGCCATCAGGTTTCACT
Found at i:5638908 original size:22 final size:22
Alignment explanation
Indices: 5638883--5638931 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
5638873 CGCTGCTGCC
5638883 TTTTGCAGGTCCAACGAAATTT
1 TTTTGCAGGTCCAACGAAATTT
* *
5638905 TTTTGCAGGTTCAATGAAATTT
1 TTTTGCAGGTCCAACGAAATTT
*
5638927 CTTTG
1 TTTTG
5638932 TATTTTCAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.43
Consensus pattern (22 bp):
TTTTGCAGGTCCAACGAAATTT
Found at i:5639367 original size:18 final size:18
Alignment explanation
Indices: 5639330--5639363 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5639320 TTTGTCACAA
*
5639330 TTTACATATATAAATAAT
1 TTTACAAATATAAATAAT
5639348 TTTACAAAT-TAAATAA
1 TTTACAAATATAAATAA
5639364 ATTTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTACAAATATAAATAAT
Found at i:5643725 original size:17 final size:17
Alignment explanation
Indices: 5643705--5643777 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
5643695 ATAAATATTT
5643705 AAAAAGAAAAAAGAAAA
1 AAAAAGAAAAAAGAAAA
* *
5643722 AAAAAGTAAATAGAAAA
1 AAAAAGAAAAAAGAAAA
* * *
5643739 ATGATA-AAGAAAGAAAA
1 A-AAAAGAAAAAAGAAAA
*
5643756 AAAAAGATTAAAAGAAAGA
1 AAAAAGA-AAAAAGAAA-A
5643775 AAA
1 AAA
5643778 TAACTTGACA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
16 2 0.05
17 26 0.63
18 9 0.22
19 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (17 bp):
AAAAAGAAAAAAGAAAA
Found at i:5643731 original size:24 final size:24
Alignment explanation
Indices: 5643704--5643760 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
5643694 TATAAATATT
5643704 TAAAAAGAAAAAAGAAAAAAAAAG
1 TAAAAAGAAAAAAGAAAAAAAAAG
* * * *
5643728 TAAATAGAAAAATGATAAAGAAAG
1 TAAAAAGAAAAAAGAAAAAAAAAG
5643752 -AAAAA-AAAA
1 TAAAAAGAAAA
5643761 GATTAAAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 4 0.14
23 4 0.14
24 20 0.71
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (24 bp):
TAAAAAGAAAAAAGAAAAAAAAAG
Found at i:5643767 original size:21 final size:21
Alignment explanation
Indices: 5643711--5643777 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 21
5643701 ATTTAAAAAG
*
5643711 AAAAAAGA-AAAAAAAAGTAAA
1 AAAAAAGATAAAAGAAAG-AAA
5643732 TAGAAAAATGAT-AAAGAAAGAAA
1 -A-AAAAA-GATAAAAGAAAGAAA
5643755 AAAAAAGATTAAAAGAAAGAAA
1 AAAAAAGA-TAAAAGAAAGAAA
5643777 A
1 A
5643778 TAACTTGACA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
20 2 0.05
21 6 0.15
22 14 0.36
23 8 0.21
24 9 0.23
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (21 bp):
AAAAAAGATAAAAGAAAGAAA
Found at i:5644558 original size:52 final size:52
Alignment explanation
Indices: 5644468--5644587 Score: 136
Period size: 52 Copynumber: 2.3 Consensus size: 52
5644458 TATAACTATA
* *
5644468 CAAACTTG-CTCATTAAGAATCCCTCTCATCTTAGAATTCTTTTCCT-GTAAGT
1 CAAACTTGCCT-ATTAAGAATCCCTCTCATCTTAAAATTCTTCTCCTAG-AAGT
* * * *
5644520 CAAACTTGCCTATTAAGAATCCCTTTCTTTTTAAAATTCTTCTCTTAGAAGT
1 CAAACTTGCCTATTAAGAATCCCTCTCATCTTAAAATTCTTCTCCTAGAAGT
* *
5644572 CAAACGTACCTATTAA
1 CAAACTTGCCTATTAA
5644588 AAATTATCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
52 55 0.95
53 3 0.05
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTCTCATCTTAAAATTCTTCTCCTAGAAGT
Found at i:5644970 original size:24 final size:25
Alignment explanation
Indices: 5644923--5645022 Score: 87
Period size: 25 Copynumber: 4.0 Consensus size: 25
5644913 ACTATGCACT
5644923 TCTCAAACCTTTAGCTCTTCTCACA
1 TCTCAAACCTTTAGCTCTTCTCACA
* *
5644948 TCTCAAACTTTTAGCTCTT-TCACG
1 TCTCAAACCTTTAGCTCTTCTCACA
* * *
5644972 TCTCGAACC-TTCGACTCTTTTCACA
1 TCTCAAACCTTTAG-CTCTTCTCACA
** * * *
5644997 TCTTGAATCTTCAACTCTTCTCACA
1 TCTCAAACCTTTAGCTCTTCTCACA
5645022 T
1 T
5645023 TTTGAATCTT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
23 3 0.05
24 16 0.27
25 40 0.67
26 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.39
Consensus pattern (25 bp):
TCTCAAACCTTTAGCTCTTCTCACA
Found at i:5645008 original size:25 final size:25
Alignment explanation
Indices: 5644965--5645039 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
5644955 CTTTTAGCTC
* * * *
5644965 TTTCACGTCTCGAACCTTCGACTCT
1 TTTCACATCTTGAATCTTCAACTCT
5644990 TTTCACATCTTGAATCTTCAACTCT
1 TTTCACATCTTGAATCTTCAACTCT
* * *
5645015 TCTCACATTTTGAATCTTCAGCTCT
1 TTTCACATCTTGAATCTTCAACTCT
5645040 GATACCACTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.20, C:0.31, G:0.08, T:0.41
Consensus pattern (25 bp):
TTTCACATCTTGAATCTTCAACTCT
Found at i:5645663 original size:52 final size:52
Alignment explanation
Indices: 5645573--5645729 Score: 185
Period size: 52 Copynumber: 3.0 Consensus size: 52
5645563 TATAATCATA
* *
5645573 CAAACTTG-CTCATTAAGAATCTCTCTCTTCTTAAAATTCTTCTCTTGTAAGT
1 CAAACTTGCCT-ATTAAGAATCCCTCTCTTCTTAAAATTCTTCTCTTGCAAGT
* *
5645625 CAAACTTGCCTATTAAGAATCCCTTTTCTT-TTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCC-TCTCTTCTTAAAATTCTTCTCTTGCAAGT
* * * * *
5645677 CAAACTTACCTATTAAGAATTCTCTCTCTT-TTAAAATTTTTCTTTTACAAGT
1 CAAACTTGCCTATTAAGAA-TCCCTCTCTTCTTAAAATTCTTCTCTTGCAAGT
5645729 C
1 C
5645730 TTCTTGTCCA
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
52 81 0.89
53 10 0.11
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.43
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTCTCTTCTTAAAATTCTTCTCTTGCAAGT
Found at i:5648221 original size:35 final size:35
Alignment explanation
Indices: 5648181--5648247 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
5648171 TCATGTAAAG
5648181 ATTAATAGTATATGATCAAAATTTAAGCTATGCCA
1 ATTAATAGTATATGATCAAAATTTAAGCTATGCCA
5648216 ATTAATAGTATATGATCAAAATTTAAGCTATG
1 ATTAATAGTATATGATCAAAATTTAAGCTATG
5648248 TCACACTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (35 bp):
ATTAATAGTATATGATCAAAATTTAAGCTATGCCA
Found at i:5648307 original size:15 final size:15
Alignment explanation
Indices: 5648280--5648321 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
5648270 TGTCAATTAT
5648280 TTTTATATTTTATACA
1 TTTTAT-TTTTATACA
*
5648296 TATTT-TTTTTATAGA
1 T-TTTATTTTTATACA
5648311 TTTTATTTTTA
1 TTTTATTTTTA
5648322 AAAAGTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 3 0.13
15 15 0.65
16 2 0.09
17 3 0.13
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTTATTTTTATACA
Found at i:5649270 original size:9 final size:9
Alignment explanation
Indices: 5649258--5649286 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5649248 ATTTTTCTCC
5649258 TTTTTA-TT
1 TTTTTATTT
5649266 TTTTTATTT
1 TTTTTATTT
5649275 TTTTTATTT
1 TTTTTATTT
5649284 TTT
1 TTT
5649287 AAAAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:5649494 original size:2 final size:2
Alignment explanation
Indices: 5649489--5649537 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5649479 TGTGTGTGTC
5649489 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5649531 TA TA TA T
1 TA TA TA T
5649538 GAATTTTGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5650234 original size:243 final size:244
Alignment explanation
Indices: 5649777--5650239 Score: 770
Period size: 243 Copynumber: 1.9 Consensus size: 244
5649767 TAATCACCTT
* *
5649777 ATTTTTTCTCACAATTTTATTTTTCTTTATTTACTCTTCTATTTTCTCTAAAAATAAATGTAATT
1 ATTTTTTCTCACAATCTTATTTTACTTTATTTACTCTTCTATTTTCTCTAAAAATAAATGTAATT
* *
5649842 TAGAATAACATAAAATTTTATCCATCTATATATTTTAGATTATTTAATCTTCATTTTATTATGTA
66 AAAAATAACATAAAATTTTATCCATCTATATATTTTAGATTATTTAATCTTCATTTTATTATGTA
5649907 TTTTTAAATTCTTTGTAGTTTCTTGCTGGCGGGAGATTTTGATTTTCAAAGGAAATGGACATGTA
131 TTTTTAAATTCTTTGTAGTTTCTTGCTGGCGGGAGATTTTGATTTTCAAAGGAAATGGACATGTA
5649972 TATAATAATAAAGAAATGAAAGAGAAAAAGATGAAATAAAAAAATTTAA
196 TATAATAATAAAGAAATGAAAGAGAAAAAGATGAAATAAAAAAATTTAA
*
5650021 ATTTTTTCTCACAACTCTTATTTTACTTTATTTACTCTTCTATTTTCTCTAAAAATAAATTTAAT
1 ATTTTTTCTCACAA-TCTTATTTTACTTTATTTACTCTTCTATTTTCTCTAAAAATAAATGTAAT
* *
5650086 TAAAAATAACATAAAATTTTATCCATCTATATA-TTTAGATTATTTTA-CTTCCTTTTATTATGT
65 TAAAAATAACATAAAATTTTATCCATCTATATATTTTAGATTATTTAATCTTCATTTTATTATGT
* * * *
5650149 ATTTTTAAATTCTTTTTAGTTTCTTGGTGGTGGGAGATTTTGATTTTCAAATGAAATGGACATGT
130 ATTTTTAAATTCTTTGTAGTTTCTTGCTGGCGGGAGATTTTGATTTTCAAAGGAAATGGACATGT
* *
5650214 TTATAGTAATATAA-AAATGAAAGAGA
195 ATATAATAATA-AAGAAATGAAAGAGA
5650240 TAACTTAAAA
Statistics
Matches: 204, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
243 97 0.48
244 29 0.14
245 78 0.38
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (244 bp):
ATTTTTTCTCACAATCTTATTTTACTTTATTTACTCTTCTATTTTCTCTAAAAATAAATGTAATT
AAAAATAACATAAAATTTTATCCATCTATATATTTTAGATTATTTAATCTTCATTTTATTATGTA
TTTTTAAATTCTTTGTAGTTTCTTGCTGGCGGGAGATTTTGATTTTCAAAGGAAATGGACATGTA
TATAATAATAAAGAAATGAAAGAGAAAAAGATGAAATAAAAAAATTTAA
Found at i:5650468 original size:22 final size:21
Alignment explanation
Indices: 5650432--5650490 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
5650422 GTTATATTAA
* *
5650432 AAAATTTTAATAAAAAAATTCG
1 AAAATTTCAAAAAAAAAATT-G
*
5650454 GAAATTTCAAAAAAAAAATTG
1 AAAATTTCAAAAAAAAAATTG
*
5650475 AAAGATTCCAAAAAAA
1 AAA-ATTTCAAAAAAA
5650491 TTAAAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAATTTCAAAAAAAAAATTG
Found at i:5650591 original size:19 final size:19
Alignment explanation
Indices: 5650542--5650598 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
5650532 AATTTTGTTG
*
5650542 AAAAA-TCT-AAAACTTTTA
1 AAAAATTCTGAAAA-TTTTT
*
5650560 AAAAATACATGAAAATTTTT
1 AAAAATTC-TGAAAATTTTT
*
5650580 AAAAATTCTGAAAGTTTTT
1 AAAAATTCTGAAAATTTTT
5650599 CAATTTTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 12 0.38
21 4 0.12
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (19 bp):
AAAAATTCTGAAAATTTTT
Found at i:5650643 original size:32 final size:30
Alignment explanation
Indices: 5650601--5650659 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
5650591 AAGTTTTTCA
5650601 ATTTTGTAATTTTAAAATTTGCATTTTTATAT
1 ATTTTGTAATTTTAAAATTT-C-TTTTTATAT
* *
5650633 ATTTTTTAATTTTTAAATTTCTTTTTA
1 ATTTTGTAATTTTAAAATTTCTTTTTA
5650660 AATTTCGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 1 0.04
32 18 0.72
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (30 bp):
ATTTTGTAATTTTAAAATTTCTTTTTATAT
Found at i:5650950 original size:17 final size:16
Alignment explanation
Indices: 5650928--5650985 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 16
5650918 TCCATATATC
5650928 TTTTAATTTTTGTAATT
1 TTTTAATTTTT-TAATT
*
5650945 TTTTAAATATTTTATATT
1 TTTT-AATTTTTTA-ATT
5650963 TTTTAATTTTTATAATT
1 TTTTAATTTTT-TAATT
5650980 TTTTAA
1 TTTTAA
5650986 AAAATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 21 0.58
18 15 0.42
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTAATTTTTTAATT
Found at i:5650965 original size:18 final size:18
Alignment explanation
Indices: 5650905--5650986 Score: 80
Period size: 18 Copynumber: 4.6 Consensus size: 18
5650895 ATTTTTTTGA
* **
5650905 AATTTTTAAAATTTCCAT
1 AATTTTTTAAATTTTTAT
* *
5650923 ATATCTTTT-AATTTTTGT
1 A-ATTTTTTAAATTTTTAT
5650941 AATTTTTTAAATATTTTAT
1 AATTTTTTAAAT-TTTTAT
5650960 -ATTTTTT-AATTTTTAT
1 AATTTTTTAAATTTTTAT
5650976 AATTTTTTAAA
1 AATTTTTTAAA
5650987 AAATATTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
16 6 0.12
17 16 0.31
18 20 0.38
19 10 0.19
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (18 bp):
AATTTTTTAAATTTTTAT
Found at i:5650972 original size:7 final size:8
Alignment explanation
Indices: 5650928--5650985 Score: 71
Period size: 9 Copynumber: 6.8 Consensus size: 8
5650918 TCCATATATC
5650928 TTTTAATT
1 TTTTAATT
5650936 TTTGTAATT
1 TTT-TAATT
*
5650945 TTTTAAATA
1 TTTT-AATT
5650954 TTTTATATT
1 TTTTA-ATT
5650963 TTTTAATT
1 TTTTAATT
5650971 TTTATAATT
1 TTT-TAATT
5650980 TTTTAA
1 TTTTAA
5650986 AAAATATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 14 0.32
9 30 0.68
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (8 bp):
TTTTAATT
Found at i:5651764 original size:114 final size:113
Alignment explanation
Indices: 5651559--5651772 Score: 276
Period size: 114 Copynumber: 1.9 Consensus size: 113
5651549 TATGTTTTTG
* * *
5651559 TCTTAAAAATATCGTTTTATTAAATTCTAAAAAATATATTTTTTATGTTTTCAATAAAAATTACA
1 TCTTAAAAACATCGTATTATTAAATTCTAAAAAATATATTTTTTATGTTTTCAACAAAAATTACA
5651624 TTTTTTATCTTAGAAAAATCATTTTTTT-AACAAAAGCTACATTGTTA
66 TTTTTTATCTTAGAAAAATCATTTTTTTCAACAAAAGCTACATTGTTA
* **
5651671 TCTTAAAAACATCGTCATTA-TAGAATTTTAAAAAATATATTTTTTTATGTTTTCAACAAATGCT
1 TCTTAAAAACATCGT-ATTATTA-AATTCTAAAAAATATA-TTTTTTATGTTTTCAACAAA-AAT
*
5651735 ATA-ATTTTTTATCTTA-AAAATGTCA-TTTTTTCAACAAA
62 -TACATTTTTTATCTTAGAAAA-ATCATTTTTTTCAACAAA
5651773 GATCGAGTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
112 16 0.18
113 18 0.20
114 29 0.33
115 23 0.26
116 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (113 bp):
TCTTAAAAACATCGTATTATTAAATTCTAAAAAATATATTTTTTATGTTTTCAACAAAAATTACA
TTTTTTATCTTAGAAAAATCATTTTTTTCAACAAAAGCTACATTGTTA
Found at i:5651771 original size:115 final size:112
Alignment explanation
Indices: 5651559--5651772 Score: 281
Period size: 115 Copynumber: 1.9 Consensus size: 112
5651549 TATGTTTTTG
* * *
5651559 TCTTAAAAATATCGTTTTATTAAATTCTAAAAAATATATTTTTTATGTTTTCAATAAAAATTACA
1 TCTTAAAAACATCGTATTATTAAATTCTAAAAAATATATTTTTTATGTTTTCAACAAAAATTACA
*
5651624 TTTTTTATCTTAGAAAAATCATTTTTTTAACAAAAGCTACATTGTTA
66 TTTTTTATCTTAGAAAAATCATTTTTTCAACAAAAGCTACATTGTTA
* **
5651671 TCTTAAAAACATCGTCATTA-TAGAATTTTAAAAAATATATTTTTTTATGTTTTCAACAAATGCT
1 TCTTAAAAACATCGT-ATTATTA-AATTCTAAAAAATATA-TTTTTTATGTTTTCAACAAA-AAT
*
5651735 ATA-ATTTTTTATCTTA-AAAATGTCATTTTTTCAACAAA
62 -TACATTTTTTATCTTAGAAAA-ATCATTTTTTCAACAAA
5651773 GATCGAGTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
112 16 0.18
113 18 0.20
114 23 0.26
115 29 0.33
116 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (112 bp):
TCTTAAAAACATCGTATTATTAAATTCTAAAAAATATATTTTTTATGTTTTCAACAAAAATTACA
TTTTTTATCTTAGAAAAATCATTTTTTCAACAAAAGCTACATTGTTA
Found at i:5651816 original size:115 final size:111
Alignment explanation
Indices: 5651578--5651822 Score: 251
Period size: 115 Copynumber: 2.1 Consensus size: 111
5651568 TATCGTTTTA
*
5651578 TTAAATTCTAAAAAATATATTTTTTATGTTTTCAATAAAAATTACATTTTTTATCTTAGAAAAAT
1 TTAAATT-TAAAAAATATATTTTTTATGTTTTCAACAAAAATTACATTTTTTATCTTAGAAAAAT
* * *
5651643 CATTTTTTTAACAAAAGCTACATTGTTATCTTAAAAACATCGTCATT
65 CATTTTTTCAACAAAAGCGACATTGTTATCTTAAAAACATCATCATT
* **
5651690 ATAGAATTTTAAAAAATATATTTTTTTATGTTTTCAACAAATGCTATA-ATTTTTTATCTTA-AA
1 TTA-AA-TTTAAAAAATATA-TTTTTTATGTTTTCAACAAA-AAT-TACATTTTTTATCTTAGAA
* * ** * * * * *
5651753 AATGTCATTTTTTCAACAAAGATCGAGTTTTTTATCTTAAGAATATTATCTTT
61 AA-ATCATTTTTTCAACAAA-AGCGACATTGTTATCTTAAAAACATCATCATT
5651806 GTTAAATTTAAAAAATA
1 -TTAAATTTAAAAAATA
5651823 AAATTTCATA
Statistics
Matches: 108, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
112 2 0.02
113 13 0.12
114 25 0.23
115 40 0.37
116 26 0.24
117 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (111 bp):
TTAAATTTAAAAAATATATTTTTTATGTTTTCAACAAAAATTACATTTTTTATCTTAGAAAAATC
ATTTTTTCAACAAAAGCGACATTGTTATCTTAAAAACATCATCATT
Found at i:5653832 original size:9 final size:9
Alignment explanation
Indices: 5653793--5653968 Score: 59
Period size: 9 Copynumber: 19.7 Consensus size: 9
5653783 ACGTTAGAAG
*
5653793 AAAATTCAA
1 AAAATTTAA
*
5653802 AATATTTAA
1 AAAATTTAA
* *
5653811 AATATCTAAA
1 AAAAT-TTAA
*
5653821 AAAATTTTA
1 AAAATTTAA
5653830 AAAA--TAA
1 AAAATTTAA
*
5653837 AAAATTCAA
1 AAAATTTAA
*
5653846 AAATATTTTAG
1 AAA-A-TTTAA
5653857 AAAATTTAA
1 AAAATTTAA
*
5653866 AAAA-TT-C
1 AAAATTTAA
*
5653873 AAAATCT-A
1 AAAATTTAA
*
5653881 AAAA-TTAG
1 AAAATTTAA
5653889 AAAATCATT--
1 AAAAT--TTAA
* *
5653898 AAATTTTCCA
1 AAAATTT-AA
5653908 AAAA--TAA
1 AAAATTTAA
5653915 AAAATTATAA
1 AAAATT-TAA
*
5653925 AAATTTTCTAA
1 AAA-ATT-TAA
5653936 AAAATTTAA
1 AAAATTTAA
5653945 AAAA-TTACA
1 AAAATTTA-A
*
5653954 AAATTTTAA
1 AAAATTTAA
5653963 AAAATT
1 AAAATT
5653969 CCAAATAATT
Statistics
Matches: 124, Mismatches: 24, Indels: 38
0.67 0.13 0.20
Matches are distributed among these distances:
7 18 0.15
8 15 0.12
9 52 0.42
10 23 0.19
11 16 0.13
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAATTTAA
Found at i:5653839 original size:27 final size:27
Alignment explanation
Indices: 5653809--5653876 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 27
5653799 CAAAATATTT
5653809 AAAATATCTAAAAAAATTTTA-AAAATAA
1 AAAAT-TC-AAAAAAATTTTAGAAAATAA
*
5653837 AAAATTCAAAAATATTTTAGAAAATTTAA
1 AAAATTCAAAAAAATTTTAGAAAA--TAA
5653866 AAAATTCAAAA
1 AAAATTCAAAA
5653877 TCTAAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
26 11 0.31
27 6 0.17
28 5 0.14
29 14 0.39
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (27 bp):
AAAATTCAAAAAAATTTTAGAAAATAA
Found at i:5653877 original size:36 final size:36
Alignment explanation
Indices: 5653793--5653885 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 36
5653783 ACGTTAGAAG
** *
5653793 AAAATTCAAAATATTTAAAATATCTAAAAAAATTTTA
1 AAAATTCAAAAT-TCAAAAATATCTAAAAAAATTTAA
** * * *
5653830 AAAATAAAAAATTCAAAAATATTTTAGAAAATTTAA
1 AAAATTCAAAATTCAAAAATATCTAAAAAAATTTAA
5653866 AAAATTCAAAA-TCTAAAAAT
1 AAAATTCAAAATTC-AAAAAT
5653886 TAGAAAATCA
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 2 0.04
36 33 0.73
37 10 0.22
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.31
Consensus pattern (36 bp):
AAAATTCAAAATTCAAAAATATCTAAAAAAATTTAA
Found at i:5653892 original size:16 final size:17
Alignment explanation
Indices: 5653853--5653894 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
5653843 CAAAAATATT
*
5653853 TTAGAAAATTTAAAAAA
1 TTAGAAAATCTAAAAAA
*
5653870 TT-CAAAATCT-AAAAA
1 TTAGAAAATCTAAAAAA
5653885 TTAGAAAATC
1 TTAGAAAATC
5653895 ATTAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.33
16 12 0.57
17 2 0.10
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.29
Consensus pattern (17 bp):
TTAGAAAATCTAAAAAA
Found at i:5653918 original size:26 final size:28
Alignment explanation
Indices: 5653880--5653949 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
5653870 TTCAAAATCT
* *
5653880 AAAAATTAGAAAATCAT-TAAATTTTCC
1 AAAAATTAAAAAATCATAAAAATTTTCC
* *
5653907 AAAAA-TAAAAAATTATAAAAATTTTCTA
1 AAAAATTAAAAAATCATAAAAATTTTC-C
5653935 AAAAATTTAAAAAAT
1 AAAAA-TTAAAAAAT
5653950 TACAAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 9 0.26
27 13 0.37
28 5 0.14
30 8 0.23
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.31
Consensus pattern (28 bp):
AAAAATTAAAAAATCATAAAAATTTTCC
Found at i:5653961 original size:18 final size:18
Alignment explanation
Indices: 5653935--5653985 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
5653925 AAATTTTCTA
5653935 AAAAATTTAAAAAATTAC
1 AAAAATTTAAAAAATTAC
* *
5653953 AAAATTTTAAAAAATTCC
1 AAAAATTTAAAAAATTAC
*
5653971 AAATAATTGAAAAAA
1 AAA-AATTTAAAAAA
5653986 GGTAAAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 19 0.68
19 9 0.32
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAATTTAAAAAATTAC
Found at i:5654608 original size:27 final size:25
Alignment explanation
Indices: 5654575--5654649 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 25
5654565 TTTTTTGTTT
5654575 TATTTTTTACTATTTTTAAATATTTCA
1 TATTTTTTA-TATTTTTAAAT-TTTCA
* * *
5654602 TATTTTTTAAAATTTTAAAATTTTTA
1 TATTTTTT-ATATTTTTAAATTTTCA
*
5654628 TA-TTTTTATATTTTTTAATTTT
1 TATTTTTTATATTTTTAAATTTT
5654650 TTGAAATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
24 12 0.29
25 5 0.12
26 6 0.15
27 17 0.41
28 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTTTTTATATTTTTAAATTTTCA
Found at i:5654641 original size:7 final size:8
Alignment explanation
Indices: 5654572--5654642 Score: 54
Period size: 8 Copynumber: 8.5 Consensus size: 8
5654562 TAATTTTTTG
5654572 TTTTAT-T
1 TTTTATAT
5654579 TTTTACTAT
1 TTTTA-TAT
*
5654588 TTTTAAAT
1 TTTTATAT
*
5654596 ATTTCATATT
1 -TTTTATA-T
*
5654606 TTTTAAAAT
1 TTTT-ATAT
* *
5654615 TTTAAAAT
1 TTTTATAT
5654623 TTTTATAT
1 TTTTATAT
5654631 TTTTATAT
1 TTTTATAT
5654639 TTTT
1 TTTT
5654643 TAATTTTTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
7 5 0.10
8 25 0.49
9 18 0.35
10 3 0.06
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTATAT
Found at i:5654645 original size:26 final size:26
Alignment explanation
Indices: 5654572--5654642 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
5654562 TAATTTTTTG
5654572 TTTTAT-TTTTTACTATTTTT-AAATA
1 TTTTATATTTTTA-TATTTTTAAAATA
* * *
5654597 TTTCATATTTTTTAAAATTTTAAAAT-
1 TTTTATA-TTTTTATATTTTTAAAATA
5654623 TTTTATATTTTTATATTTTT
1 TTTTATATTTTTATATTTTT
5654643 TAATTTTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 16 0.43
26 11 0.30
27 10 0.27
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTATATTTTTATATTTTTAAAATA
Found at i:5654650 original size:17 final size:17
Alignment explanation
Indices: 5654572--5654651 Score: 65
Period size: 17 Copynumber: 4.7 Consensus size: 17
5654562 TAATTTTTTG
5654572 TTTT-ATTTTTTACTATT
1 TTTTAATTTTTTA-TATT
* * *
5654589 TTTAAATATTTCATATT
1 TTTTAATTTTTTATATT
** * *
5654606 TTTTAAAATTTTAAAAT
1 TTTTAATTTTTTATATT
5654623 TTTT-ATATTTTTATATT
1 TTTTAAT-TTTTTATATT
5654640 TTTTAATTTTTT
1 TTTTAATTTTTT
5654652 GAAATTTATA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
16 1 0.02
17 39 0.81
18 8 0.17
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAATTTTTTATATT
Found at i:5656488 original size:2 final size:2
Alignment explanation
Indices: 5656481--5656514 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5656471 TTATTGAATG
5656481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5656515 CATTGAGCCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5663534 original size:149 final size:148
Alignment explanation
Indices: 5663263--5663536 Score: 361
Period size: 149 Copynumber: 1.8 Consensus size: 148
5663253 GACCTTTTAC
* *
5663263 AATATTTTTTACTCTTTCCAAATAAAAAAGCTTATTGACATCAAAATATTAGAAAAGTTATTTTG
1 AATATTCTTTACTCTTTCCAAATAAAAAAGCTTATTGACATCAAAATATTAAAAAAGTTATTTTG
* * * * * * * *
5663328 AATGATGGTAATAAGAATGAAGCAACAATTTAAAATCTATCGTCTTTTCATTTAGTAGAAGAAAT
66 AATGATGATAATAAGAATAAAGCAAAAATTAAAAATATACCATCTTTTCATTCAGTAGAAGAAAT
5663393 TTTTTATGAAAAATACGA
131 TTTTTATGAAAAATACGA
* * * ** *
5663411 AATATTCTTTATTCTTTCCAAATGAAGAAG-TTGATTGGTATCAAAATATTAAAAAATTTTATTT
1 AATATTCTTTACTCTTTCCAAATAAAAAAGCTT-ATTGACATCAAAATATTAAAAAA-GTTATTT
* *
5663475 TGAATGATGATAATAAGAATAAAGCAAAAATTAAAAATATACCATGTTTTCGTTCAGTAGAA
64 TGAATGATGATAATAAGAATAAAGCAAAAATTAAAAATATACCATCTTTTCATTCAGTAGAA
5663537 AAAAAATTTT
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
147 2 0.02
148 46 0.43
149 58 0.55
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (148 bp):
AATATTCTTTACTCTTTCCAAATAAAAAAGCTTATTGACATCAAAATATTAAAAAAGTTATTTTG
AATGATGATAATAAGAATAAAGCAAAAATTAAAAATATACCATCTTTTCATTCAGTAGAAGAAAT
TTTTTATGAAAAATACGA
Found at i:5664247 original size:22 final size:22
Alignment explanation
Indices: 5664215--5664295 Score: 99
Period size: 22 Copynumber: 3.7 Consensus size: 22
5664205 ATATGATACT
*
5664215 AATAATTGATAATTTAGTAGTA
1 AATAAATGATAATTTAGTAGTA
* * *
5664237 AATTAGTGATAATTTAATAGTA
1 AATAAATGATAATTTAGTAGTA
* *
5664259 AATAAATGATAATTTGGTAATA
1 AATAAATGATAATTTAGTAGTA
*
5664281 AATAATTGATAATTT
1 AATAAATGATAATTT
5664296 TTAATAAATC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (22 bp):
AATAAATGATAATTTAGTAGTA
Found at i:5664474 original size:22 final size:22
Alignment explanation
Indices: 5664449--5664497 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5664439 ATGATAAAAA
5664449 TAAATCAATAATAACTTT-ATAG
1 TAAATCAATAATAA-TTTGATAG
* *
5664471 TAAATTAGTAATAATTTGATAG
1 TAAATCAATAATAATTTGATAG
5664493 TAAAT
1 TAAAT
5664498 TAATTTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (22 bp):
TAAATCAATAATAATTTGATAG
Found at i:5664498 original size:22 final size:22
Alignment explanation
Indices: 5664457--5664499 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5664447 AATAAATCAA
5664457 TAATAACTTTATAGTAAATTAG
1 TAATAACTTTATAGTAAATTAG
5664479 TAATAA-TTTGATAGTAAATTA
1 TAATAACTTT-ATAGTAAATTA
5664500 ATTTCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (22 bp):
TAATAACTTTATAGTAAATTAG
Found at i:5664521 original size:21 final size:22
Alignment explanation
Indices: 5664483--5664523 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5664473 AATTAGTAAT
*
5664483 AATTTGATAGTAAATTAATTTC
1 AATTTAATAGTAAATTAATTTC
5664505 AATTTAATAGT-AATTAATT
1 AATTTAATAGTAAATTAATT
5664524 GATAGTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (22 bp):
AATTTAATAGTAAATTAATTTC
Found at i:5664544 original size:25 final size:26
Alignment explanation
Indices: 5664516--5664571 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
5664506 ATTTAATAGT
*
5664516 AATTAATT-GATAGT-AGTAAATCATA
1 AATTAATTAG-TAGTAAATAAATCATA
* *
5664541 AATTACTTAGTAGTAAATAAATGATA
1 AATTAATTAGTAGTAAATAAATCATA
5664567 AATTA
1 AATTA
5664572 GTATTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.36
Consensus pattern (26 bp):
AATTAATTAGTAGTAAATAAATCATA
Found at i:5664623 original size:21 final size:21
Alignment explanation
Indices: 5664598--5664697 Score: 71
Period size: 22 Copynumber: 4.8 Consensus size: 21
5664588 AATTTAAAAG
*
5664598 TAAATCAGTATAACTTAGTAA
1 TAAATCAGTATAACTTAATAA
* *
5664619 TAAATC--TATAACATAATTA
1 TAAATCAGTATAACTTAATAA
* * * *
5664638 TTAGTCAATAATAACTTTATAA
1 TAAATCAGT-ATAACTTAATAA
*
5664660 TAAATCATGTATAATTTAAT-A
1 TAAATCA-GTATAACTTAATAA
*
5664681 TAAATTAGTAATAACTT
1 TAAATCAGT-ATAACTT
5664698 GATTGTGAAT
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
19 14 0.24
20 2 0.03
21 20 0.34
22 22 0.37
23 1 0.02
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (21 bp):
TAAATCAGTATAACTTAATAA
Found at i:5664740 original size:94 final size:94
Alignment explanation
Indices: 5664616--5664805 Score: 344
Period size: 94 Copynumber: 2.0 Consensus size: 94
5664606 TATAACTTAG
* * *
5664616 TAATAAATCTATAACATAATTATTAGTCAATAATAACTTTATAATAAATCATGTATAATTTAATA
1 TAATAAATCTATAACATAATAATTAATCAATAATAACTTTATAATAAATCATATATAATTTAATA
5664681 TAAATTAGTAATAACTTGATTGTGAATCA
66 TAAATTAGTAATAACTTGATTGTGAATCA
*
5664710 TAATAAATCTATAACATAATAATTAATCAATAATAACTTTATAATAAATTATATATAATTTAATA
1 TAATAAATCTATAACATAATAATTAATCAATAATAACTTTATAATAAATCATATATAATTTAATA
5664775 TAAATTAGTAATAACTTGATTGTGAATCA
66 TAAATTAGTAATAACTTGATTGTGAATCA
5664804 TA
1 TA
5664806 GATAGTTTAA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (94 bp):
TAATAAATCTATAACATAATAATTAATCAATAATAACTTTATAATAAATCATATATAATTTAATA
TAAATTAGTAATAACTTGATTGTGAATCA
Found at i:5664840 original size:22 final size:22
Alignment explanation
Indices: 5664738--5665022 Score: 194
Period size: 22 Copynumber: 13.1 Consensus size: 22
5664728 ATAATTAATC
*
5664738 AATAATAACTTT-ATAATAAATT
1 AATAATAA-TTTAATAGTAAATT
5664760 -ATATATAATTTAATA-TAAATT
1 AATA-ATAATTTAATAGTAAATT
* * * * *
5664781 AGTAATAACTTGATTGTGAA-T
1 AATAATAATTTAATAGTAAATT
* *
5664802 CATAGATAGTTTAATAGTAAATT
1 AATA-ATAATTTAATAGTAAATT
*
5664825 AATAATAATTTTATAGTAAA-T
1 AATAATAATTTAATAGTAAATT
* * *
5664846 AATCATAAATTAAGTAGTAAATC
1 AATAATAATTTAA-TAGTAAATT
**
5664869 AATAATAAACTAATAGTAAA-T
1 AATAATAATTTAATAGTAAATT
* * *
5664890 ATATAAAAATATAATAGTAAATC
1 A-ATAATAATTTAATAGTAAATT
* * *
5664913 ATTGATAATTTAATAATAAA-T
1 AATAATAATTTAATAGTAAATT
*
5664934 --TAATAATTTAATAGTAAATC
1 AATAATAATTTAATAGTAAATT
* **
5664954 ACTAATAATACAATAGTAAATT
1 AATAATAATTTAATAGTAAATT
* * *
5664976 ACTAATAAATTAAGT-GTAAATC
1 AATAATAATTTAA-TAGTAAATT
*
5664998 AATAATAATTTAATAGTATATT
1 AATAATAATTTAATAGTAAATT
5665020 AAT
1 AAT
5665023 TATTAATAAT
Statistics
Matches: 202, Mismatches: 46, Indels: 30
0.73 0.17 0.11
Matches are distributed among these distances:
19 16 0.08
21 36 0.18
22 133 0.66
23 17 0.08
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (22 bp):
AATAATAATTTAATAGTAAATT
Found at i:5664959 original size:19 final size:19
Alignment explanation
Indices: 5664917--5664959 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5664907 TAAATCATTG
*
5664917 ATAATTTAATAATAAATTA
1 ATAATTTAATAATAAATCA
*
5664936 ATAATTTAATAGTAAATCA
1 ATAATTTAATAATAAATCA
*
5664955 CTAAT
1 ATAAT
5664960 AATACAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAATTTAATAATAAATCA
Found at i:5665167 original size:22 final size:22
Alignment explanation
Indices: 5665101--5665183 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 22
5665091 TCAACAAATC
* * * *
5665101 ATAACTTAATAGTAAATCACTC
1 ATAACTTAGTAATAAATCATTG
* **
5665123 ATAAATTAAAAATAAATCATTG
1 ATAACTTAGTAATAAATCATTG
* * *
5665145 ATAATTTAGTAGTAAATCTTTG
1 ATAACTTAGTAATAAATCATTG
5665167 ATAACTTAGTAATAAAT
1 ATAACTTAGTAATAAAT
5665184 AACTAATAAC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.36
Consensus pattern (22 bp):
ATAACTTAGTAATAAATCATTG
Found at i:5665541 original size:44 final size:44
Alignment explanation
Indices: 5665513--5665640 Score: 116
Period size: 44 Copynumber: 2.9 Consensus size: 44
5665503 TTAATTTTTT
*
5665513 ATAACTTAATAATAAATCAATGATAATTTAATAGTAAATTAGTG
1 ATAACTTAATAATAAATCAATGATAATTTAGTAGTAAATTAGTG
** ** * *
5665557 ATAACTTAATGGTAAATCAATTTTAATTTAGTAAT-AATTAATTG
1 ATAACTTAATAATAAATCAATGATAATTTAGTAGTAAATT-AGTG
* * * *
5665601 ATAAACTTAATATTAAAT-TATAGATATTTTAATAGTAAAT
1 AT-AACTTAATAATAAATCAAT-GATAATTTAGTAGTAAAT
5665641 CAATAATAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
43 4 0.06
44 36 0.55
45 22 0.34
46 3 0.05
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.41
Consensus pattern (44 bp):
ATAACTTAATAATAAATCAATGATAATTTAGTAGTAAATTAGTG
Found at i:5665543 original size:22 final size:22
Alignment explanation
Indices: 5665513--5665658 Score: 98
Period size: 22 Copynumber: 6.6 Consensus size: 22
5665503 TTAATTTTTT
* *
5665513 ATAACTTAATAATAAATCAATG
1 ATAATTTAATAGTAAATCAATG
* *
5665535 ATAATTTAATAGTAAATTAGTG
1 ATAATTTAATAGTAAATCAATG
* * *
5665557 ATAACTTAATGGTAAATCAATT
1 ATAATTTAATAGTAAATCAATG
* * * *
5665579 TTAATTTAGTAAT-AATTAATTG
1 ATAATTTAATAGTAAATCAA-TG
* * *
5665601 ATAAACTTAATATTAAAT-TATAG
1 AT-AATTTAATAGTAAATCAAT-G
* *
5665624 ATATTTTAATAGTAAATCAATA
1 ATAATTTAATAGTAAATCAATG
*
5665646 ATAATTTAGTAGT
1 ATAATTTAATAGT
5665659 TAATTGTTGA
Statistics
Matches: 91, Mismatches: 28, Indels: 10
0.71 0.22 0.08
Matches are distributed among these distances:
21 5 0.05
22 69 0.76
23 14 0.15
24 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.40
Consensus pattern (22 bp):
ATAATTTAATAGTAAATCAATG
Found at i:5665737 original size:16 final size:15
Alignment explanation
Indices: 5665712--5665745 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5665702 ATTAGTCATC
*
5665712 AATAATTTAATAATTA
1 AATAACTTAATAA-TA
5665728 AATAACTTAATAATA
1 AATAACTTAATAATA
5665743 AAT
1 AAT
5665746 TATAGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAACTTAATAATA
Found at i:5665774 original size:21 final size:22
Alignment explanation
Indices: 5665729--5665784 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
5665719 TAATAATTAA
5665729 ATAACTTAATAATAAATTATAG
1 ATAACTTAATAATAAATTATAG
*
5665751 ATAATTTAAT-ATAAATTACT-G
1 ATAACTTAATAATAAATTA-TAG
*
5665772 ATAACTTGATAAT
1 ATAACTTAATAAT
5665785 GAATCATGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (22 bp):
ATAACTTAATAATAAATTATAG
Found at i:5665853 original size:22 final size:21
Alignment explanation
Indices: 5665828--5665877 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
5665818 TATTTTGTAG
5665828 TAAATAATCAAAAAATAAATAA
1 TAAATAATCAAAAAAT-AATAA
* * *
5665850 TAAATCAATGATAACATAATAA
1 TAAAT-AATCAAAAAATAATAA
5665872 TAAATA
1 TAAATA
5665878 CATAATAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAATAATCAAAAAATAATAA
Found at i:5665854 original size:11 final size:11
Alignment explanation
Indices: 5665840--5665890 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
5665830 AATAATCAAA
5665840 AAATAAATAAT
1 AAATAAATAAT
* *
5665851 AAATCAATGAT
1 AAATAAATAAT
5665862 AACAT-AATAAT
1 AA-ATAAATAAT
*
5665873 AAATACATAAT
1 AAATAAATAAT
5665884 AACATAA
1 AA-ATAA
5665891 TAGTAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.06
11 25 0.78
12 5 0.16
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:5665885 original size:22 final size:22
Alignment explanation
Indices: 5665845--5665929 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 22
5665835 TCAAAAAATA
*
5665845 AATAATAAATCAATGATAACAT
1 AATAATAAATCAATAATAACAT
5665867 AATAATAAAT-ACATAATAACAT
1 AATAATAAATCA-ATAATAACAT
* * * **
5665889 AATAGTAAATTATTAATAATTT
1 AATAATAAATCAATAATAACAT
* *
5665911 CATAGTAAATCAATAATAA
1 AATAATAAATCAATAATAA
5665930 TTTAGTAGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.02
22 51 0.96
23 1 0.02
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.32
Consensus pattern (22 bp):
AATAATAAATCAATAATAACAT
Found at i:5665930 original size:22 final size:21
Alignment explanation
Indices: 5665890--5665942 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
5665880 TAATAACATA
* *
5665890 ATAGTAAATTATTAATAATTT
1 ATAGTAAATCAATAATAATTT
5665911 CATAGTAAATCAATAATAATTT
1 -ATAGTAAATCAATAATAATTT
5665933 AGTAGTAAAT
1 A-TAGTAAAT
5665943 TAGTTAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.40
Consensus pattern (21 bp):
ATAGTAAATCAATAATAATTT
Found at i:5666083 original size:141 final size:140
Alignment explanation
Indices: 5665814--5666083 Score: 310
Period size: 141 Copynumber: 1.9 Consensus size: 140
5665804 AATAAATTTA
*
5665814 TGATTATTTTGTAGTAAATAATCAAAAAATAAATAATAAATCAATGATAACATAATAATAAATAC
1 TGATTATTTTGTAGTAAATAACCAAAAAATAAATAATAAATCAATGATAACATAATAATAAATAC
* * * * * * *
5665879 ATAATAACATAATAGTAAATTATTAATAATTTCATAGTAAATCAATAATAATTTAGTAGTAAATT
66 ATAATAACATAATAATAAATCATTAACAATTTAATAGTAAATCAATAATAACTTAATAATAAATT
5665944 AGTTAATTAT
131 AGTTAATTAT
* * * * * * *
5665954 TGATTAGTTTTGTAGTAAATCACCAATAAATTAATAGTAAATCAATTATAACTTTATAATAAAT-
1 TGATTA-TTTTGTAGTAAATAACCAAAAAATAAATAATAAATCAATGATAACATAATAATAAATA
* * * * * *
5666018 TATCAATAACTTAGTAATAAATCATTAACAATTTAATAGTAAAT-TATGCATAGCTTAATAATAA
65 CAT-AATAACATAATAATAAATCATTAACAATTTAATAGTAAATCAAT-AATAACTTAATAATAA
5666082 AT
128 AT
5666084 CATTCATAAA
Statistics
Matches: 106, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
140 10 0.09
141 96 0.91
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (140 bp):
TGATTATTTTGTAGTAAATAACCAAAAAATAAATAATAAATCAATGATAACATAATAATAAATAC
ATAATAACATAATAATAAATCATTAACAATTTAATAGTAAATCAATAATAACTTAATAATAAATT
AGTTAATTAT
Found at i:5666091 original size:22 final size:22
Alignment explanation
Indices: 5665979--5666171 Score: 120
Period size: 22 Copynumber: 8.8 Consensus size: 22
5665969 TAAATCACCA
* *
5665979 ATAAATTAATAGTAAATCAATT-
1 ATAACTTAATAATAAATC-ATTC
* *
5666001 ATAACTTTATAATAAATTA-TC
1 ATAACTTAATAATAAATCATTC
* *
5666022 AATAACTTAGTAATAAATCATTA
1 -ATAACTTAATAATAAATCATTC
* * * * *
5666045 ACAATTTAATAGTAAATTATGC
1 ATAACTTAATAATAAATCATTC
*
5666067 ATAGCTTAATAATAAATCATTC
1 ATAACTTAATAATAAATCATTC
* * * * *
5666089 ATAAATTACTAATAAATTAATG
1 ATAACTTAATAATAAATCATTC
* * *
5666111 TTAATTTAATAATAAATCATTG
1 ATAACTTAATAATAAATCATTC
* * * *
5666133 ATGATTTAATAATATATCATTT
1 ATAACTTAATAATAAATCATTC
* *
5666155 ATAGCTTAGTAATAAAT
1 ATAACTTAATAATAAAT
5666172 TACTGGATAA
Statistics
Matches: 127, Mismatches: 41, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 124 0.98
23 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (22 bp):
ATAACTTAATAATAAATCATTC
Found at i:5666105 original size:44 final size:42
Alignment explanation
Indices: 5665979--5666146 Score: 142
Period size: 44 Copynumber: 3.8 Consensus size: 42
5665969 TAAATCACCA
* *
5665979 ATAAATTAATAGTAAATCAATTATAACTTTATAATAAATTAT-C
1 ATAACTTAATAATAAATC-ATTATAA-TTTATAATAAATTATGC
* * *
5666022 AATAACTTAGTAATAAATCATTAACAATTTAATAGTAAATTATGC
1 -ATAACTTAATAATAAATCATT-ATAATTT-ATAATAAATTATGC
* *
5666067 ATAGCTTAATAATAAATCATTCATAAATTACTAATAAATTAATG-
1 ATAACTTAATAATAAATCATT-ATAATTTA-TAATAAATT-ATGC
* * *
5666111 TTAATTTAATAATAAATCATTGATGATTTAATAATA
1 ATAACTTAATAATAAATCATT-ATAATTT-ATAATA
5666147 TATCATTTAT
Statistics
Matches: 101, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
43 7 0.07
44 89 0.88
45 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (42 bp):
ATAACTTAATAATAAATCATTATAATTTATAATAAATTATGC
Found at i:5666208 original size:66 final size:66
Alignment explanation
Indices: 5665985--5666208 Score: 157
Period size: 66 Copynumber: 3.4 Consensus size: 66
5665975 ACCAATAAAT
* * * * * * * * * *
5665985 TAATAGTAAATCAATTATAACTTTATAATAAATTA-TCAATAACTTAGTAATAAATCATTAACAA
1 TAATAATAAATCAATAATAACTTAATAATAAATCATTC-ATAAATTACTAATAAATTAATGATAA
*
5666049 TT
65 TA
* * * * *
5666051 TAATAGTAAAT-TATGCATAGCTTAATAATAAATCATTCATAAATTACTAATAAATTAATGTTAA
1 TAATAATAAATCAAT-AATAACTTAATAATAAATCATTCATAAATTACTAATAAATTAATGATAA
*
5666115 TT
65 TA
* * * * * * ** * *
5666117 TAATAATAAATCATTGATGATTTAATAATATATCATTTATAGCTTAGTAATAAATTACTGGATAA
1 TAATAATAAATCAATAATAACTTAATAATAAATCATTCATAAATTACTAATAAATTAAT-GATAA
5666182 TA
65 TA
5666184 TAATAAT-AATCAATAATAACTTAAT
1 TAATAATAAATCAATAATAACTTAAT
5666209 TATCAATTAT
Statistics
Matches: 123, Mismatches: 31, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
65 2 0.02
66 106 0.86
67 15 0.12
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (66 bp):
TAATAATAAATCAATAATAACTTAATAATAAATCATTCATAAATTACTAATAAATTAATGATAAT
A
Found at i:5666577 original size:21 final size:21
Alignment explanation
Indices: 5666522--5666600 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
5666512 AATTATATTA
* *
5666522 AAAAGTTATCAAAGTTTTATC
1 AAAAGTTATCAAAATTGTATC
*
5666543 -AATGATTATCAAAATTGTATC
1 AAAAG-TTATCAAAATTGTATC
* *
5666564 AAAAGTTA-CTAAAATTTTATT
1 AAAAGTTATC-AAAATTGTATC
5666585 AAAAGTTATCAAAATT
1 AAAAGTTATCAAAATT
5666601 AAAATTGTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 4 0.08
21 40 0.83
22 4 0.08
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (21 bp):
AAAAGTTATCAAAATTGTATC
Found at i:5666627 original size:26 final size:27
Alignment explanation
Indices: 5666573--5666624 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5666563 CAAAAGTTAC
* *
5666573 TAAAATTTTATTAAAAGTTATCAAAAT
1 TAAAATTGTATAAAAAGTTATCAAAAT
5666600 TAAAATTGTATAAAAAGTTATCAAA
1 TAAAATTGTATAAAAAGTTATCAAA
5666625 TTATACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (27 bp):
TAAAATTGTATAAAAAGTTATCAAAAT
Found at i:5666640 original size:27 final size:28
Alignment explanation
Indices: 5666573--5666640 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
5666563 CAAAAGTTAC
*
5666573 TAAAATTTTATT-AAAAGTTATCAAAAT
1 TAAAATTATATTAAAAAGTTATCAAAAT
*
5666600 TAAAATTGTA-TAAAAAGTTATC-AAAT
1 TAAAATTATATTAAAAAGTTATCAAAAT
* *
5666626 TATACTTATATTAAA
1 TAAAATTATATTAAA
5666641 CCAAAATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (28 bp):
TAAAATTATATTAAAAAGTTATCAAAAT
Found at i:5666695 original size:48 final size:48
Alignment explanation
Indices: 5666594--5666703 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
5666584 TAAAAGTTAT
* * *
5666594 CAAAATTAAAATTGTATAAAAAGTTATCAAATTATACTTATATTAAAC
1 CAAAATCAAAATTATATAAAAAGTTATCAAATTATACATATATTAAAC
* *
5666642 CAAAATCAAAATTATATCAAAAGTTATCAAAATT-TACATATTATTATA-
1 CAAAATCAAAATTATATAAAAAGTTATC-AAATTATACATA-TATTAAAC
*
5666690 TAAAATCAAAATTA
1 CAAAATCAAAATTA
5666704 AATTATTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
48 43 0.80
49 11 0.20
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.35
Consensus pattern (48 bp):
CAAAATCAAAATTATATAAAAAGTTATCAAATTATACATATATTAAAC
Found at i:5668388 original size:22 final size:22
Alignment explanation
Indices: 5668360--5668403 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5668350 TGAACTTAAG
5668360 GCTGTGAAGAAAAAGAATAGCA
1 GCTGTGAAGAAAAAGAATAGCA
*
5668382 GCTGTGAAGAAATAGAATAGCA
1 GCTGTGAAGAAAAAGAATAGCA
5668404 AGCAAGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.27, T:0.16
Consensus pattern (22 bp):
GCTGTGAAGAAAAAGAATAGCA
Found at i:5670757 original size:3 final size:3
Alignment explanation
Indices: 5670736--5670770 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5670726 AAACATCGCT
* *
5670736 TTG TTG ATG TTG ATG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
5670771 TCCATTATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.06, C:0.00, G:0.31, T:0.63
Consensus pattern (3 bp):
TTG
Found at i:5685472 original size:19 final size:19
Alignment explanation
Indices: 5685448--5685518 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
5685438 TTACAACTGG
5685448 TTGTAATCTGTATAGCTGA
1 TTGTAATCTGTATAGCTGA
*
5685467 TTGTAATCTGTGTAGCTGA
1 TTGTAATCTGTATAGCTGA
*
5685486 TTGTAATCTGTGTAGCTGA
1 TTGTAATCTGTATAGCTGA
*
5685505 TTGTAATCTATATA
1 TTGTAATCTGTATA
5685519 TATTTGAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (19 bp):
TTGTAATCTGTATAGCTGA
Found at i:5685800 original size:25 final size:25
Alignment explanation
Indices: 5685768--5685855 Score: 113
Period size: 25 Copynumber: 3.5 Consensus size: 25
5685758 TGACTTCTAT
*
5685768 TTTAGGCCTTCATTGCCGAACCCTG
1 TTTAGGCCTTCATTGCCGAACCCTA
5685793 TTTAGGCCTTCATTGCCGAACCCTA
1 TTTAGGCCTTCATTGCCGAACCCTA
* * * *
5685818 TTAAGGCCTTTATTGTCGAACGCTA
1 TTTAGGCCTTCATTGCCGAACCCTA
* *
5685843 TTAAGACCTTCAT
1 TTTAGGCCTTCAT
5685856 AGCCATTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (25 bp):
TTTAGGCCTTCATTGCCGAACCCTA
Found at i:5692060 original size:317 final size:317
Alignment explanation
Indices: 5691632--5692258 Score: 892
Period size: 317 Copynumber: 2.0 Consensus size: 317
5691622 CATTTTCCCC
* * *
5691632 TTTTTAGGCCAATTTTCTACTACCTACAAAACCATTAGATACTTCACTGTCCATCCCAATAGTCT
1 TTTTTAGGCCAAATTTCTACTACCTACAAAACCATTAGATACTTCACCGTACATCCCAATAGTCT
* * *
5691697 ATGCAAGAAGAAAGTGTCGGAGTTCCTTAAGAAATTAATATGTAGATTTT-ATCTTTAGCACCAA
66 ATGCAAGAAGAAAGGGTCGGAGTTCCTTAAGAAATAAATATGTAGATTTTGA-ATTTAGCACC-A
*
5691761 AATTTTGAGGGAAAAAGGGATTAAAAAAGAG-AAAAAAAAAAGGTCACTCACACCTAAAGAACCT
129 AATTTTGAGGAAAAAAGGGA-TAAAAAAGAGAAAAAAAAAAAGGTCACTCACACCTAAAGAACCT
* *
5691825 TCACATTATTTTTAACAAATAATCTGAAGA-TGGAAACACCA-TTATGACATTCCCATTTCTTAA
193 TCACATTATTTTTAACAAATAATCTGAAGATTGG-AACACCATTTATGAAATTCCCATTTCCTAA
5691888 ACTAAAGCTTTCACACAATCCTCCCCA-TCCACCCATGCTTGTCTGCAGTCGCTCCCCACCT
257 ACTAAAGCTTTCACACAATCCTCCCCACT-CACCCATGCTTGTCTGCAGTCGCTCCCCACCT
* * *
5691949 TTTTTAGGCCAAATTTCTACT-CTCTAGAGAACCATTAGGTACTTCACCGTACATCCCAATAGTC
1 TTTTTAGGCCAAATTTCTACTAC-CTACAAAACCATTAGATACTTCACCGTACATCCCAATAGTC
* *
5692013 TATGCATA-AAGAAAGGGTCTGAGTTCCTTAAGAAACTAAAT-TGTAGATTTTGAATTTAGCAGC
65 TATGCA-AGAAGAAAGGGTCGGAGTTCCTTAAGAAA-TAAATATGTAGATTTTGAATTTAGCACC
* *
5692076 AAATTTTGTGGAAAAAAGGGATAAAAAAGAGAAAAAAAAAAAAAAAGGTCACTCGCACCTAAAGA
128 AAATTTTGAGGAAAAAAGGGATAAAAAAGAG----AAAAAAAAAAAGGTCACTCACACCTAAAGA
* * * *
5692141 ACCTTCACATTATTTTTAACAAATATTTTGAAGATTGGAATACCATTTTTGAAATTCCCATTTCC
189 ACCTTCACATTATTTTTAACAAATAATCTGAAGATTGGAACACCATTTATGAAATTCCCATTTCC
* *
5692206 TAAACTAAAGCTTTCAGACAATCCTCCCCACTCACCCATGCTTGTCTGTAGTC
254 TAAACTAAAGCTTTCACACAATCCTCCCCACTCACCCATGCTTGTCTGCAGTC
5692259 AAAGGAGGAG
Statistics
Matches: 276, Mismatches: 22, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
315 10 0.04
316 20 0.07
317 105 0.38
318 6 0.02
320 66 0.24
321 68 0.25
322 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (317 bp):
TTTTTAGGCCAAATTTCTACTACCTACAAAACCATTAGATACTTCACCGTACATCCCAATAGTCT
ATGCAAGAAGAAAGGGTCGGAGTTCCTTAAGAAATAAATATGTAGATTTTGAATTTAGCACCAAA
TTTTGAGGAAAAAAGGGATAAAAAAGAGAAAAAAAAAAAGGTCACTCACACCTAAAGAACCTTCA
CATTATTTTTAACAAATAATCTGAAGATTGGAACACCATTTATGAAATTCCCATTTCCTAAACTA
AAGCTTTCACACAATCCTCCCCACTCACCCATGCTTGTCTGCAGTCGCTCCCCACCT
Found at i:5693024 original size:4 final size:4
Alignment explanation
Indices: 5693017--5693042 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5693007 TATATATATA
5693017 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
5693043 CATATTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:5696031 original size:185 final size:185
Alignment explanation
Indices: 5695709--5696075 Score: 610
Period size: 185 Copynumber: 2.0 Consensus size: 185
5695699 CTATCAAACA
*
5695709 TTAAAAGCATACGCAAAGGAAGTGTTGATGACGAGAAAAGATTTGGACCTGAAACACGTGACAGG
1 TTAAAAGCATACGCAAAGGAAGTGTTGATGACGAGAAAAGATTTGGACCTGAAACACATGACAGG
* * *
5695774 GTATATGACAATCATAGTGAACAATGCCTGGAGTTAACGTCAGGCTCCCCTAATCTTAACATGCC
66 GTATATAACAATCATAGTGAACAATGCCTGGAGTCAACGTCAGGCTCCCCTAATCTTAAAATGCC
5695839 AGAATATATTGTATACTTCCCTGATGTTATTCAAATCATATCTAGCCTGCATAGT
131 AGAATATATTGTATACTTCCCTGATGTTATTCAAATCATATCTAGCCTGCATAGT
* * * **
5695894 TTAAAAGCATATGCAAAGGAAGTGTTGATGATGAGAAAAGATTTGGAGCTGAAACACATGATGGG
1 TTAAAAGCATACGCAAAGGAAGTGTTGATGACGAGAAAAGATTTGGACCTGAAACACATGACAGG
5695959 GTATATAACAATCCA-AGTGAACAATGCCTGGAGTCAACGTCAGGCTCCCCTAATCTTAAAATGC
66 GTATATAACAAT-CATAGTGAACAATGCCTGGAGTCAACGTCAGGCTCCCCTAATCTTAAAATGC
* * *
5696023 CTGAATATATTGTATACTTTCCTGATGTTATTCAAATCATATCTAGCTTGCAT
130 CAGAATATATTGTATACTTCCCTGATGTTATTCAAATCATATCTAGCCTGCAT
5696076 GGTTGTTCAA
Statistics
Matches: 169, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
185 167 0.99
186 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (185 bp):
TTAAAAGCATACGCAAAGGAAGTGTTGATGACGAGAAAAGATTTGGACCTGAAACACATGACAGG
GTATATAACAATCATAGTGAACAATGCCTGGAGTCAACGTCAGGCTCCCCTAATCTTAAAATGCC
AGAATATATTGTATACTTCCCTGATGTTATTCAAATCATATCTAGCCTGCATAGT
Found at i:5699307 original size:46 final size:46
Alignment explanation
Indices: 5699240--5699334 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
5699230 TGGCTAAAAG
5699240 AATGTCAATTAGCAGAACCACAAGGGTTAAACAAGTACTTCTTAGT
1 AATGTCAATTAGCAGAACCACAAGGGTTAAACAAGTACTTCTTAGT
*
5699286 AATGTCAATTAGCGGAACCACAAGGGTTAAACAAGTACTTCTTAGT
1 AATGTCAATTAGCAGAACCACAAGGGTTAAACAAGTACTTCTTAGT
5699332 AAT
1 AAT
5699335 AGGATGTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (46 bp):
AATGTCAATTAGCAGAACCACAAGGGTTAAACAAGTACTTCTTAGT
Found at i:5702366 original size:8 final size:8
Alignment explanation
Indices: 5702353--5702378 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5702343 AAAGAACCTG
5702353 CTGTTTGC
1 CTGTTTGC
5702361 CTGTTTGC
1 CTGTTTGC
5702369 CTGTTTGC
1 CTGTTTGC
5702377 CT
1 CT
5702379 TTGCGTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.27, G:0.23, T:0.50
Consensus pattern (8 bp):
CTGTTTGC
Found at i:5707703 original size:6 final size:6
Alignment explanation
Indices: 5707692--5707716 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5707682 CAGTGGCAGA
5707692 GGAAAT GGAAAT GGAAAT GGAAAT G
1 GGAAAT GGAAAT GGAAAT GGAAAT G
5707717 CTTCCCGCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GGAAAT
Found at i:5708993 original size:20 final size:20
Alignment explanation
Indices: 5708968--5709005 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5708958 AATAAAATTC
* *
5708968 AAAAAAAGAAAGAAAGGAAA
1 AAAAAAAAAAAAAAAGGAAA
5708988 AAAAAAAAAAAAAAAGGA
1 AAAAAAAAAAAAAAAGGA
5709006 GCAAATGCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAGGAAA
Found at i:5712418 original size:42 final size:42
Alignment explanation
Indices: 5712372--5712458 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
5712362 TTAATTCCCC
* *
5712372 AAGCTTTCCTTTTTCTTTTCGCTTGAAGTAATAAATAGTAAA
1 AAGCTTTCCTTTTTCCTTTCGCTAGAAGTAATAAATAGTAAA
5712414 AAGCTTTCCTTTTTCCTTTCGCTAGAAGTAATAAATAGTAAA
1 AAGCTTTCCTTTTTCCTTTCGCTAGAAGTAATAAATAGTAAA
5712456 AAG
1 AAG
5712459 GACGAGGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (42 bp):
AAGCTTTCCTTTTTCCTTTCGCTAGAAGTAATAAATAGTAAA
Found at i:5712612 original size:4 final size:4
Alignment explanation
Indices: 5712588--5712628 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
5712578 TTGACTATTA
* *
5712588 AAAG AAAAG AAAA AAAA AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
5712629 CCTAATATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:5713013 original size:20 final size:21
Alignment explanation
Indices: 5712981--5713040 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
5712971 TTATTGCAAT
* *
5712981 ATATTTGTAAAATTATTTTTTG
1 ATATTT-TAAAATTAGTTTTTA
5713003 A-ATTTTAAAA-TAGTTTTTA
1 ATATTTTAAAATTAGTTTTTA
*
5713022 ATTATTTTAAAATTCGTTT
1 A-TATTTTAAAATTAGTTT
5713041 AAAAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 8 0.25
20 5 0.16
21 13 0.41
22 6 0.19
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
ATATTTTAAAATTAGTTTTTA
Found at i:5719897 original size:22 final size:22
Alignment explanation
Indices: 5719869--5719915 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
5719859 TCGCTTTGAT
5719869 TTAGGTTTGATAATTTATATTA
1 TTAGGTTTGATAATTTATATTA
*
5719891 TTAGGTTTGATCATTTATATTA
1 TTAGGTTTGATAATTTATATTA
5719913 TTA
1 TTA
5719916 TATCATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (22 bp):
TTAGGTTTGATAATTTATATTA
Found at i:5720022 original size:21 final size:21
Alignment explanation
Indices: 5719993--5720037 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5719983 TGAAAATATA
* *
5719993 AAATATATTTTTTATTTTATT
1 AAATATATTTATAATTTTATT
* *
5720014 AAATTTATTTATAATTTTTTT
1 AAATATATTTATAATTTTATT
5720035 AAA
1 AAA
5720038 AATTTTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AAATATATTTATAATTTTATT
Found at i:5722515 original size:26 final size:25
Alignment explanation
Indices: 5722463--5722524 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
5722453 GATAGATATC
5722463 AATTTCAATTTAAATAATTATCCAAA
1 AATTT-AATTTAAATAATTATCCAAA
*
5722489 ATATTTAATTTAAATAATTTAT-TAAA
1 A-ATTTAATTTAAATAA-TTATCCAAA
*
5722515 AATTTTATTT
1 AATTTAATTT
5722525 GATAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 8 0.25
26 16 0.50
27 8 0.25
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (25 bp):
AATTTAATTTAAATAATTATCCAAA
Found at i:5723738 original size:14 final size:14
Alignment explanation
Indices: 5723719--5723747 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5723709 AATGACAGTT
5723719 ATTACAAACTCTTA
1 ATTACAAACTCTTA
5723733 ATTACAAACTCTTA
1 ATTACAAACTCTTA
5723747 A
1 A
5723748 ATGTTGGATT
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:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTACAAACTCTTA
Found at i:5726289 original size:12 final size:12
Alignment explanation
Indices: 5726261--5726295 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5726251 TATATAAAAG
*
5726261 TTATTTTATAT-
1 TTATATTATATA
5726272 TTATATTATATA
1 TTATATTATATA
5726284 TTATATTATATA
1 TTATATTATATA
5726296 AAATAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATATTATATA
Found at i:5730577 original size:21 final size:21
Alignment explanation
Indices: 5730552--5730592 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5730542 TATTTTTGTC
5730552 AAATTATAAATGATATTATTA
1 AAATTATAAATGATATTATTA
* *
5730573 AAATTTTAAATTATATTATT
1 AAATTATAAATGATATTATT
5730593 TTCGTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATTATAAATGATATTATTA
Found at i:5749830 original size:2 final size:2
Alignment explanation
Indices: 5749823--5749859 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5749813 ATTAGTAACC
*
5749823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5749860 CATGTGTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5757416 original size:12 final size:13
Alignment explanation
Indices: 5757394--5757424 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
5757384 TTAGAAATTG
5757394 ACAATATTATTTT
1 ACAATATTATTTT
5757407 ACAA-ATTATTTT
1 ACAATATTATTTT
5757419 ACAATA
1 ACAATA
5757425 ACAAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (13 bp):
ACAATATTATTTT
Found at i:5757670 original size:28 final size:28
Alignment explanation
Indices: 5757638--5757693 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
5757628 CTTAATTTAC
5757638 TTATTCCTATCTTATTGCTTACTCCCAA
1 TTATTCCTATCTTATTGCTTACTCCCAA
*
5757666 TTATTCCTATCTTATTGCTTACTTCCAA
1 TTATTCCTATCTTATTGCTTACTCCCAA
5757694 CGCCGTGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.27, G:0.04, T:0.48
Consensus pattern (28 bp):
TTATTCCTATCTTATTGCTTACTCCCAA
Found at i:5762222 original size:62 final size:62
Alignment explanation
Indices: 5762146--5762270 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 62
5762136 CTGGGGTACT
* *
5762146 AACGATGTGTGACCGAAGACGGTGAGTATCCGTT-GAAGTGGAGGAGGATATCATGGTCAGGA
1 AACGATGTGTGACCGAAGACGGTGAGGATCCGTTAG-AGTGGAGGAAGATATCATGGTCAGGA
*
5762208 AACGATGTGTGACCGAAGACGGTGAGGATCCGTTAGAGTGGAGGAAGATGTCATGGTCAGGA
1 AACGATGTGTGACCGAAGACGGTGAGGATCCGTTAGAGTGGAGGAAGATATCATGGTCAGGA
5762270 A
1 A
5762271 TTTCATATCG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 58 0.98
63 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.38, T:0.20
Consensus pattern (62 bp):
AACGATGTGTGACCGAAGACGGTGAGGATCCGTTAGAGTGGAGGAAGATATCATGGTCAGGA
Found at i:5764923 original size:14 final size:14
Alignment explanation
Indices: 5764904--5764934 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5764894 AGTTCCGTTG
5764904 TAATTTATAGAAAC
1 TAATTTATAGAAAC
5764918 TAATTTATAGAAAC
1 TAATTTATAGAAAC
5764932 TAA
1 TAA
5764935 CTCAGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (14 bp):
TAATTTATAGAAAC
Found at i:5766883 original size:2 final size:2
Alignment explanation
Indices: 5766878--5766908 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5766868 AAAAAAAAAA
5766878 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5766909 AACAAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.