Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold145
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: 2608604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28749 characters in sequence are not A, C, G, or T
File 12 of 15
Found at i:2046629 original size:13 final size:14
Alignment explanation
Indices: 2046606--2046635 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2046596 CTTTTTTTTT
2046606 TTTTAATATTTATA
1 TTTTAATATTTATA
2046620 TTTT-ATATTTATA
1 TTTTAATATTTATA
2046633 TTT
1 TTT
2046636 GATGCATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTAATATTTATA
Found at i:2052797 original size:9 final size:9
Alignment explanation
Indices: 2052783--2052816 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
2052773 TTTATATATA
2052783 TAAATATTT
1 TAAATATTT
*
2052792 TAAATATTA
1 TAAATATTT
2052801 TAAATATTT
1 TAAATATTT
2052810 TAAATAT
1 TAAATAT
2052817 GATTATGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TAAATATTT
Found at i:2052804 original size:18 final size:19
Alignment explanation
Indices: 2052776--2052816 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
2052766 ATCAAAATTT
2052776 ATATATATAAATATTTTAA
1 ATATATATAAATATTTTAA
2052795 ATAT-TATAAATATTTTAA
1 ATATATATAAATATTTTAA
2052813 ATAT
1 ATAT
2052817 GATTATGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATATAAATATTTTAA
Found at i:2054351 original size:135 final size:135
Alignment explanation
Indices: 2054121--2054365 Score: 357
Period size: 135 Copynumber: 1.8 Consensus size: 135
2054111 AATAGTGGGG
*
2054121 ATAGTAGGGAACTATTTGCTCTTTCTTGATTGAAATATTCTAGTCTGAAGAAGCATTGACATGAT
1 ATAGTAGGGAACTATTTGCTCTTTCTGGATTGAAATATTCTAGTC--AAGAAGCATTGACATGAT
** * *
2054186 TGCTGTATTGTTTTTCGGTGTTCATTTTATGACTATGAGTTGTTTTTATGTTGTGGATTTGAATT
64 CACTGTATTGTTGTTCAGTGTTCATTTTATGACTATGAGTTGTTTTTATGTTGTGGATTTGAATT
2054251 GTCATTT
129 GTCATTT
* * * * *
2054258 ATAGTAGGTAACTATTTTGCTGTTTCTGGATTGAAATATTCTGGTC-CGAAGCATTGACCTGATC
1 ATAGTAGGGAACTA-TTTGCTCTTTCTGGATTGAAATATTCTAGTCAAGAAGCATTGACATGATC
*
2054322 ACTGTGTTGTTGTTCAGTGTTCATTTTATGACTATGAGTTGTTT
65 ACTGTATTGTTGTTCAGTGTTCATTTTATGACTATGAGTTGTTT
2054366 ATGTCACTTA
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
135 55 0.57
137 13 0.14
138 28 0.29
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.45
Consensus pattern (135 bp):
ATAGTAGGGAACTATTTGCTCTTTCTGGATTGAAATATTCTAGTCAAGAAGCATTGACATGATCA
CTGTATTGTTGTTCAGTGTTCATTTTATGACTATGAGTTGTTTTTATGTTGTGGATTTGAATTGT
CATTT
Found at i:2056304 original size:19 final size:21
Alignment explanation
Indices: 2056253--2056305 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2056243 TATTTTTATT
2056253 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
2056274 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
*
2056294 -ATATTTTAATAT
1 TAAATTTTAATAT
2056306 TTTTTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 11 0.39
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:2058271 original size:13 final size:13
Alignment explanation
Indices: 2058249--2058280 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2058239 CTGCAGCAGG
2058249 AAGG-AAATGAAA
1 AAGGAAAATGAAA
2058261 AAGGAAAATGAAA
1 AAGGAAAATGAAA
2058274 AA-GAAAA
1 AAGGAAAA
2058281 GATAAGGCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (13 bp):
AAGGAAAATGAAA
Found at i:2058817 original size:21 final size:21
Alignment explanation
Indices: 2058791--2058830 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2058781 ATATTTTTAA
2058791 ATATTTAAATAAATATATTAT
1 ATATTTAAATAAATATATTAT
* *
2058812 ATATTTTATTAAATATATT
1 ATATTTAAATAAATATATT
2058831 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTTAAATAAATATATTAT
Found at i:2061666 original size:4 final size:4
Alignment explanation
Indices: 2061652--2061681 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
2061642 ATATAGATAT
2061652 ATTA TATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA -ATTA ATTA ATTA ATTA ATTA ATTA A
2061682 AGCTGCGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:2062107 original size:16 final size:17
Alignment explanation
Indices: 2062078--2062110 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2062068 TTTAAATAAT
2062078 AAAAAATATTAATTTTTC
1 AAAAAATA-TAATTTTTC
2062096 AAAAAATA-AATTTTT
1 AAAAAATATAATTTTT
2062111 TTTGAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAAAATATAATTTTTC
Found at i:2063584 original size:24 final size:22
Alignment explanation
Indices: 2063557--2063603 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
2063547 AATCAATTTT
2063557 TTTATTAGAAATAAAATGATTTAA
1 TTTATTAGAAATAAAA--ATTTAA
**
2063581 TTTATTATTAATAAAAATTTAA
1 TTTATTAGAAATAAAAATTTAA
2063603 T
1 T
2063604 AATGTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTATTAGAAATAAAAATTTAA
Found at i:2063813 original size:18 final size:18
Alignment explanation
Indices: 2063763--2063828 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
2063753 AATTATTATT
* *
2063763 TAAATAATAATA-AATTT
1 TAAATATTAATATAATTA
*
2063780 TAAAT-TTAAATTTAATTA
1 TAAATATT-AATATAATTA
2063798 TAAATATTAATATAA-TA
1 TAAATATTAATATAATTA
*
2063815 TAAAATTTTAATAT
1 T-AAATATTAATAT
2063829 TATTTTTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
16 1 0.03
17 11 0.28
18 26 0.65
19 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATATTAATATAATTA
Found at i:2063838 original size:30 final size:30
Alignment explanation
Indices: 2063804--2063860 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
2063794 ATTATAAATA
*
2063804 TTAAT-ATAATATAAAATTTTAATATTATTT
1 TTAATAATAAAATAAAATTTTAA-ATTATTT
*
2063834 TTAATAATAAAATAAATTTTTAAATTA
1 TTAATAATAAAATAAAATTTTAAATTA
2063861 ATCTGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAATAATAAAATAAAATTTTAAATTATTT
Found at i:2069089 original size:41 final size:41
Alignment explanation
Indices: 2069033--2069110 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
2069023 TCTTCCATGG
**
2069033 TCCCAATGTCAGATTTTTCGTC-AACAAATGAATTTGATAA
1 TCCCAATGTCAGATTTTTCAACAAACAAATGAATTTGATAA
2069073 TCCCAATTGTCAGATTTTTCAACAAACAAATGAATTTG
1 TCCCAA-TGTCAGATTTTTCAACAAACAAATGAATTTG
2069111 GGTTGCTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 6 0.18
41 14 0.41
42 14 0.41
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (41 bp):
TCCCAATGTCAGATTTTTCAACAAACAAATGAATTTGATAA
Found at i:2075360 original size:2 final size:2
Alignment explanation
Indices: 2075353--2075381 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2075343 CTCAAAATAT
2075353 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2075382 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2075386 original size:2 final size:2
Alignment explanation
Indices: 2075381--2075416 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2075371 TCTCTCTCTC
2075381 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
2075417 AATTTGCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2076701 original size:37 final size:37
Alignment explanation
Indices: 2076651--2076727 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
2076641 TTTGTATGTT
2076651 TCATGCTAGAGTATTAAAACAGGATTCTAGACCTACC
1 TCATGCTAGAGTATTAAAACAGGATTCTAGACCTACC
2076688 TCATGCTAGAGTATTAAAACAGGATTCTAGACCTACC
1 TCATGCTAGAGTATTAAAACAGGATTCTAGACCTACC
2076725 TCA
1 TCA
2076728 ATCAAATTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (37 bp):
TCATGCTAGAGTATTAAAACAGGATTCTAGACCTACC
Found at i:2077788 original size:190 final size:188
Alignment explanation
Indices: 2077249--2077995 Score: 914
Period size: 182 Copynumber: 4.0 Consensus size: 188
2077239 CTCAACTTGG
* *
2077249 TAATAACTCAACTTCAATATAATCA---T---TGTCAAGTTCAAGTGAAACTCAAGCAGCAATTC
1 TAATAACTCAACTTCAATATAATCATTGTCAATGTCAAGTTCAAGTGACACTCAAACAGCAATTC
* * * * ** *
2077308 AATCCGAGTTCTAGCATTCTAATACCCCACTCAAAATAATTTTCAACAAGTAACACAAACACCCA
66 AATCTGAGTTCTAGCACTCTAATACTCCACTGAAGTTAATTTTCAACAAGTAATACAAACACCCA
* * *
2077373 AGAACGAAAATAGAACAAAAAC-CTAAGACATGAGTTTACATACAGAATAAAACGTGTT
131 AGAAAGAAAATAGAACAAAAACAC-AAGACATGAGTTAACATACAGAATAAAACATGTT
* * * *
2077431 TAATAACTCAACCTCAATATAATCATTGTC-A-G----GTTCAAGTGAGACTCAAGCAGCAATGC
1 TAATAACTCAACTTCAATATAATCATTGTCAATGTCAAGTTCAAGTGACACTCAAACAGCAATTC
* * * * *
2077490 AATCTGAGTTCAAGCATTGTGATACTCCACTGAAGTTAATTTTCAACAAGTAATGCAAACACCCA
66 AATCTGAGTTCTAGCACTCTAATACTCCACTGAAGTTAATTTTCAACAAGTAATACAAACACCCA
* * * *
2077555 AGAAAGAAAAGAGAACAAAAACATAAGGCATGTGCTT-ACATACAGAATAAAACATGTT
131 AGAAAGAAAATAGAACAAAAACACAAGACATGAG-TTAACATACAGAATAAAACATGTT
* * *
2077613 TAATAACTAAACTTTAATATAATCATTGTCGAATGTCAAGTTCAAGTGACACTTAAACAGCAATT
1 TAATAACTCAACTTCAATATAATCATTGTC-AATGTCAAGTTCAAGTGACACTCAAACAGCAATT
* * * * * * *
2077678 CAATCTGATTTTTAGCACTATAATCCTCTCACAGAAGTTAATTTTCAACAAGCAATACAAATACC
65 CAATCTGAGTTCTAGCACTCTAATACTC-CACTGAAGTTAATTTTCAACAAGTAATACAAACACC
2077743 CAA-AGAAGAAAATAGAACAAAAACACAAGACATGAGTTAACATACAGAATAAAACATGTT
129 CAAGA-AAGAAAATAGAACAAAAACACAAGACATGAGTTAACATACAGAATAAAACATGTT
* * *
2077803 TAATAACTCAGCTTCAATATAATCATTGTCAAATGTCAAGTTCAAGTG-CAAGTCAAACAGTAAT
1 TAATAACTCAACTTCAATATAATCATTGTC-AATGTCAAGTTCAAGTGAC-ACTCAAACAGCAAT
*
2077867 TCAATCTGAGTTCTAGCACTCTAATACTCCACTGAAGTTAATTTTCAACAAGTAATGCAAACACC
64 TCAATCTGAGTTCTAGCACTCTAATACTCCACTGAAGTTAATTTTCAACAAGTAATACAAACACC
* * * * *
2077932 CAAGAAAGAAAATAGAACAAAAACATAAGACTTCAGCTAACATACAGAACAAAACATGGTT
129 CAAGAAAGAAAATAGAACAAAAACACAAGACATGAGTTAACATACAGAATAAAACAT-GTT
2077993 TAA
1 TAA
2077996 GCAGAATTCT
Statistics
Matches: 484, Mismatches: 61, Indels: 32
0.84 0.11 0.06
Matches are distributed among these distances:
182 179 0.37
183 2 0.00
184 1 0.00
185 2 0.00
186 1 0.00
189 129 0.27
190 170 0.35
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (188 bp):
TAATAACTCAACTTCAATATAATCATTGTCAATGTCAAGTTCAAGTGACACTCAAACAGCAATTC
AATCTGAGTTCTAGCACTCTAATACTCCACTGAAGTTAATTTTCAACAAGTAATACAAACACCCA
AGAAAGAAAATAGAACAAAAACACAAGACATGAGTTAACATACAGAATAAAACATGTT
Found at i:2079304 original size:33 final size:34
Alignment explanation
Indices: 2079276--2079388 Score: 101
Period size: 33 Copynumber: 3.4 Consensus size: 34
2079266 CAATATGATT
2079276 ATATATATATATATAAATA-ATTAAAATATAATATA
1 ATATA-ATA-ATATAAATATATTAAAATATAATATA
* *
2079311 ATATAATAATATAAATATATTAATATTTATATATA
1 ATATAATAATATAAATATATTAAAATATA-ATATA
* * * *
2079346 ACATAAT--TATTAATATATTATAAT-TTATATA
1 ATATAATAATATAAATATATTAAAATATAATATA
2079377 AT-TATATAATAT
1 ATATA-ATAATAT
2079389 TTTAATTATG
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
30 2 0.03
31 8 0.12
32 1 0.02
33 26 0.40
34 12 0.18
35 16 0.25
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (34 bp):
ATATAATAATATAAATATATTAAAATATAATATA
Found at i:2079342 original size:14 final size:14
Alignment explanation
Indices: 2079267--2079388 Score: 62
Period size: 14 Copynumber: 8.9 Consensus size: 14
2079257 TAATAAATTC
2079267 AATATGATTATATATA
1 AATAT-ATTA-ATATA
* *
2079283 TATATATAAATAATTA
1 AATATATTAAT-A-TA
2079299 AA-ATA-TAATAT-
1 AATATATTAATATA
*
2079310 AATATAATAATATA
1 AATATATTAATATA
*
2079324 AATATATTAATATT
1 AATATATTAATATA
* *
2079338 TATATA-TAACAT-
1 AATATATTAATATA
2079350 AAT-TATTAATAT-
1 AATATATTAATATA
* *
2079362 ATTATAATTTATATA
1 AATAT-ATTAATATA
*
2079377 ATTATA-TAATAT
1 AATATATTAATAT
2079389 TTTAATTATG
Statistics
Matches: 84, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
11 4 0.05
12 13 0.15
13 18 0.21
14 30 0.36
15 12 0.14
16 7 0.08
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (14 bp):
AATATATTAATATA
Found at i:2079346 original size:22 final size:26
Alignment explanation
Indices: 2079276--2079367 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 26
2079266 CAATATGATT
*
2079276 ATATATATATATATAA-ATAATTA-AA
1 ATATAT-TATATATAACATAATTATTA
*
2079301 ATATAATATAATATAATAATATAAATATATTA
1 ATAT-AT-T-ATAT-ATAACAT-AAT-TATTA
2079333 ATAT-TTATATATAACATAATTATTA
1 ATATATTATATATAACATAATTATTA
2079358 ATATATTATA
1 ATATATTATA
2079368 ATTTATATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
25 13 0.23
26 12 0.21
27 10 0.18
28 8 0.14
29 3 0.05
30 4 0.07
31 2 0.04
32 5 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATATTATATATAACATAATTATTA
Found at i:2079918 original size:3 final size:3
Alignment explanation
Indices: 2079910--2079951 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2079900 AACTACTCAA
2079910 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2079952 TATTATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2082117 original size:2 final size:2
Alignment explanation
Indices: 2082110--2082134 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2082100 TTTTGGTTTC
2082110 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2082135 TGTCAAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2082330 original size:5 final size:5
Alignment explanation
Indices: 2082289--2082369 Score: 56
Period size: 5 Copynumber: 17.6 Consensus size: 5
2082279 AAAAATCGAA
*
2082289 TAATT T-ATT TTATT TAA-- TAATT T--TT T-ATT TAAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT T-AATT TAATT TAATT
2082334 TAAATT T--TT T-ATT T-ATT TAAATT TAATT TAATT TAA
1 T-AATT TAATT TAATT TAATT T-AATT TAATT TAATT TAA
2082370 ATTATTATTT
Statistics
Matches: 65, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
3 9 0.14
4 14 0.22
5 29 0.45
6 13 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TAATT
Found at i:2082336 original size:16 final size:16
Alignment explanation
Indices: 2082315--2082372 Score: 82
Period size: 16 Copynumber: 3.6 Consensus size: 16
2082305 ATAATTTTTT
2082315 ATTTAAATTTAATTTA
1 ATTTAAATTTAATTTA
*
2082331 ATTTAAATTTTTTATTT-
1 ATTTAAA--TTTAATTTA
2082348 ATTTAAATTTAATTTA
1 ATTTAAATTTAATTTA
2082364 ATTTAAATT
1 ATTTAAATT
2082373 ATTATTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
15 7 0.19
16 16 0.43
17 7 0.19
18 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTAAATTTAATTTA
Found at i:2082354 original size:33 final size:32
Alignment explanation
Indices: 2082290--2082382 Score: 127
Period size: 33 Copynumber: 2.9 Consensus size: 32
2082280 AAAATCGAAT
* * *
2082290 AATTT-ATTTTATTT-AATAATTTTTTATTTA
1 AATTTAATTTAATTTAAATTATTATTTATTTA
*
2082320 AATTTAATTTAATTTAAATTTTTTATTTATTTA
1 AATTTAATTTAATTTAAA-TTATTATTTATTTA
2082353 AATTTAATTTAATTTAAATTATTATTTATT
1 AATTTAATTTAATTTAAATTATTATTTATT
2082383 AATTAAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
30 5 0.09
31 8 0.15
32 13 0.24
33 29 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
AATTTAATTTAATTTAAATTATTATTTATTTA
Found at i:2082356 original size:28 final size:28
Alignment explanation
Indices: 2082289--2082364 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 28
2082279 AAAAATCGAA
*
2082289 TAATTT-ATTTTATTTAATAATTTTTTATT
1 TAATTTAATTTAATTT-A-AATTTTTTATT
2082318 TAAATTTAATTTAATTTAAATTTTTTATT
1 T-AATTTAATTTAATTTAAATTTTTTATT
2082347 T-ATTTAAATTTAATTTAA
1 TAATTT-AATTTAATTTAA
2082365 TTTAAATTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 4 0.09
28 12 0.28
29 13 0.30
30 6 0.14
31 8 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
TAATTTAATTTAATTTAAATTTTTTATT
Found at i:2082384 original size:20 final size:20
Alignment explanation
Indices: 2082360--2082407 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2082350 TTAAATTTAA
*
2082360 TTTAATTTAAATTATT-ATT
1 TTTAATTTAAAATATTAATT
2082379 TATTAA-TTAAAATATTAATT
1 T-TTAATTTAAAATATTAATT
2082399 TTT-ATTTAA
1 TTTAATTTAA
2082408 TTTTAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 16 0.64
20 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATTTAAAATATTAATT
Found at i:2082397 original size:32 final size:33
Alignment explanation
Indices: 2082312--2082399 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 33
2082302 TTAATAATTT
* *
2082312 TTTATTTAAATTTAATTTAATTTAAATTTTTTA
1 TTTATTTAAATTAAATTTAATTTAAATTTATTA
*
2082345 TTTATTTAAATTTAATTTAATTTAAA-TTATTA
1 TTTATTTAAATTAAATTTAATTTAAATTTATTA
2082377 TTTA-TT-AATTAAAATATTAATTT
1 TTTATTTAAATT-AAAT-TTAATTT
2082400 TTATTTAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
30 4 0.08
31 5 0.10
32 16 0.31
33 26 0.51
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TTTATTTAAATTAAATTTAATTTAAATTTATTA
Found at i:2084213 original size:18 final size:18
Alignment explanation
Indices: 2084190--2084225 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2084180 ATTAGGATGC
2084190 CCTTCCTTCCCCCGTTCT
1 CCTTCCTTCCCCCGTTCT
* *
2084208 CCTTCCTTTCCCCTTTCT
1 CCTTCCTTCCCCCGTTCT
2084226 TTCATTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.53, G:0.03, T:0.44
Consensus pattern (18 bp):
CCTTCCTTCCCCCGTTCT
Found at i:2091181 original size:19 final size:19
Alignment explanation
Indices: 2091146--2091182 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2091136 TTTATAATTA
* *
2091146 TTTATTATATTTTTATTTT
1 TTTATTATAATTATATTTT
2091165 TTTATTATAATTATATTT
1 TTTATTATAATTATATTT
2091183 AAAATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTATAATTATATTTT
Found at i:2094934 original size:19 final size:20
Alignment explanation
Indices: 2094902--2094940 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2094892 AAAAAATTAA
2094902 ATATTAAAAATTAT-TATTT
1 ATATTAAAAATTATATATTT
* *
2094921 ATATTAATATTTATATATTT
1 ATATTAAAAATTATATATTT
2094941 TTATAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTAAAAATTATATATTT
Found at i:2096134 original size:12 final size:12
Alignment explanation
Indices: 2096117--2096155 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2096107 GCTTACTAAT
2096117 ATTACCAATAAA
1 ATTACCAATAAA
*
2096129 ATTACCAACAAA
1 ATTACCAATAAA
*
2096141 ATTAGCAATAAA
1 ATTACCAATAAA
2096153 ATT
1 ATT
2096156 TATTTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (12 bp):
ATTACCAATAAA
Found at i:2097780 original size:13 final size:13
Alignment explanation
Indices: 2097762--2097786 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2097752 TTTTTAATGT
2097762 TATTATATATTTA
1 TATTATATATTTA
2097775 TATTATATATTT
1 TATTATATATTT
2097787 TGTAATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATATATTTA
Found at i:2098019 original size:17 final size:17
Alignment explanation
Indices: 2097985--2098023 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2097975 AAATTTTTTC
* * *
2097985 ATTTTTAAATATATTTT
1 ATTTTTAAAAAAAATTT
2098002 ATTTTTAAAAAAAATTT
1 ATTTTTAAAAAAAATTT
2098019 ATTTT
1 ATTTT
2098024 AATATTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTTAAAAAAAATTT
Found at i:2099144 original size:18 final size:19
Alignment explanation
Indices: 2099103--2099144 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2099093 CCAGTCTCAC
* *
2099103 GACCACGACCTCCTCCTCT
1 GACCACGACCACCTCCTAT
2099122 G-CCACGACCACCTCC-AT
1 GACCACGACCACCTCCTAT
2099139 GACCAC
1 GACCAC
2099145 CTGCACTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 17 0.85
19 1 0.05
ACGTcount: A:0.21, C:0.52, G:0.12, T:0.14
Consensus pattern (19 bp):
GACCACGACCACCTCCTAT
Found at i:2099895 original size:27 final size:26
Alignment explanation
Indices: 2099847--2099909 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
2099837 ATATTTTTAT
* *
2099847 TATATT-TATAATTTTTTAAAATAAA
1 TATATTATATAAATTTTAAAAATAAA
*
2099872 TATATTATATAAATTTTAATAAATTAA
1 TATATTATATAAATTTTAA-AAATAAA
*
2099899 TAAATTATATA
1 TATATTATATA
2099910 TTTAAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 6 0.19
26 10 0.31
27 16 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATATTATATAAATTTTAAAAATAAA
Found at i:2100744 original size:17 final size:18
Alignment explanation
Indices: 2100704--2100744 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2100694 TAATTTTTTA
2100704 AATATAATATTATTAATT
1 AATATAATATTATTAATT
2100722 ATATATAA-ATT-TTAATTT
1 A-ATATAATATTATTAA-TT
2100740 AATAT
1 AATAT
2100745 TTTTAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.38
18 7 0.33
19 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATAATATTATTAATT
Found at i:2100744 original size:19 final size:21
Alignment explanation
Indices: 2100700--2100744 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
2100690 GTTTTAATTT
2100700 TTTAA-ATATAATATTATTAA
1 TTTAATATATAATATTATTAA
2100720 -TT-ATATATAA-ATT-TTAA
1 TTTAATATATAATATTATTAA
2100737 TTTAATAT
1 TTTAATAT
2100745 TTTTAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
19 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATATATAATATTATTAA
Found at i:2100750 original size:14 final size:14
Alignment explanation
Indices: 2100692--2100751 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
2100682 ATGATTTCGT
2100692 TTTAAT-TTTTTAAA
1 TTTAATATTTTT-AA
* *
2100706 TATAATATTATTAA
1 TTTAATATTTTTAA
*
2100720 TTATATATAAATTTTAA
1 TT-TA-AT-ATTTTTAA
2100737 TTTAATATTTTTAA
1 TTTAATATTTTTAA
2100751 T
1 T
2100752 AATTAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
14 16 0.44
15 8 0.22
16 4 0.11
17 8 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAATATTTTTAA
Found at i:2102958 original size:2 final size:2
Alignment explanation
Indices: 2102946--2102976 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2102936 ATGATTGTTT
*
2102946 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2102977 GCTCTCAAAT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2103063 original size:29 final size:29
Alignment explanation
Indices: 2103020--2103075 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
2103010 ATTTTGAGAT
2103020 AAAAATTAAAGATT-AAAGATTTGATTTGA
1 AAAAATTAAAGATTAAAAGATTT-ATTTGA
2103049 AAAAATTATAA-ATTAAAAGATTTATTT
1 AAAAATTA-AAGATTAAAAGATTTATTT
2103076 AAATATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.38
Consensus pattern (29 bp):
AAAAATTAAAGATTAAAAGATTTATTTGA
Found at i:2103186 original size:24 final size:22
Alignment explanation
Indices: 2103138--2103186 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 22
2103128 AAATGGTTGA
*
2103138 AAATTTAAATAAATTATTATTT
1 AAATTTAAATAAATTATTATAT
2103160 AAATTTAATTATAAA-TATTAATAT
1 AAATTTAA--ATAAATTATT-ATAT
2103184 AAA
1 AAA
2103187 AATTAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 8 0.35
23 4 0.17
24 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATTTAAATAAATTATTATAT
Found at i:2107369 original size:15 final size:16
Alignment explanation
Indices: 2107329--2107377 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2107319 ATTATAATTC
2107329 AATCTAAAA-AGATTTA
1 AATCTAAAATA-ATTTA
2107345 AATCTAAAATAATTTA
1 AATCTAAAATAATTTA
* *
2107361 AAT-TTAAATTATTTA
1 AATCTAAAATAATTTA
2107376 AA
1 AA
2107378 AAATTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 12 0.40
16 17 0.57
17 1 0.03
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (16 bp):
AATCTAAAATAATTTA
Found at i:2107388 original size:25 final size:26
Alignment explanation
Indices: 2107349--2107402 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
2107339 GATTTAAATC
*
2107349 TAAAATAATTTAAATTT-AAATTATT
1 TAAAATAATTTAAATTTAAAATAATT
2107374 TAAAA-AATTTAAAATTTAAAATAATT
1 TAAAATAATTT-AAATTTAAAATAATT
2107400 TAA
1 TAA
2107403 CTTAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 11 0.42
26 10 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAAATAATTTAAATTTAAAATAATT
Found at i:2107401 original size:17 final size:17
Alignment explanation
Indices: 2107360--2107402 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2107350 AAAATAATTT
2107360 AAATTTAAATTATTTAAA
1 AAATTTAAA-TATTTAAA
2107378 AAATTTAAA-ATTTAAA
1 AAATTTAAATATTTAAA
2107394 ATAATTTAA
1 A-AATTTAA
2107403 CTTAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.33
17 7 0.29
18 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTAAATATTTAAA
Found at i:2107408 original size:40 final size:41
Alignment explanation
Indices: 2107333--2107411 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
2107323 TAATTCAATC
*
2107333 TAAAAAGATTTAAATCTAAAATAATTTAAATTTAAATTATT
1 TAAAAAGATTTAAATCTAAAATAATTTAAACTTAAATTATT
*
2107374 TAAAAA-ATTTAAAATTTAAAATAATTT-AACTTAAATTA
1 TAAAAAGATTT-AAATCTAAAATAATTTAAACTTAAATTA
2107412 AACTGATACG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 14 0.40
41 21 0.60
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (41 bp):
TAAAAAGATTTAAATCTAAAATAATTTAAACTTAAATTATT
Found at i:2112771 original size:9 final size:9
Alignment explanation
Indices: 2112757--2112795 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2112747 TATGTTTGCT
2112757 AAAAATAAA
1 AAAAATAAA
2112766 AAAAATAAGA
1 AAAAATAA-A
*
2112776 AAAAAAAAA
1 AAAAATAAA
*
2112785 AAAAACAAA
1 AAAAATAAA
2112794 AA
1 AA
2112796 TTGGAACCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.90, C:0.03, G:0.03, T:0.05
Consensus pattern (9 bp):
AAAAATAAA
Found at i:2113357 original size:30 final size:30
Alignment explanation
Indices: 2113297--2113353 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
2113287 TTTGAGTTTG
* * *
2113297 ATTTAACATAATTTAAAATTTTAGTTTATT
1 ATTTAAAATAATTAAAAATTTAAGTTTATT
2113327 ATTTAAAAT-ATTAAAAATTTAA-TTTAT
1 ATTTAAAATAATTAAAAATTTAAGTTTAT
2113354 ATTAGTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 11 0.46
30 8 0.33
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (30 bp):
ATTTAAAATAATTAAAAATTTAAGTTTATT
Found at i:2114110 original size:4 final size:4
Alignment explanation
Indices: 2114101--2114129 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2114091 TTAACAAACC
2114101 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
2114130 TTTTGTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:2115391 original size:2 final size:2
Alignment explanation
Indices: 2115384--2115415 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2115374 AAAAGATTGA
2115384 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
2115416 GAGAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2115656 original size:30 final size:30
Alignment explanation
Indices: 2115630--2115685 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
2115620 ATAATTTTGG
2115630 AAAAT-AATAAAAAAATA-ATTAAAA-TTT
1 AAAATGAATAAAAAAATATATTAAAATTTT
* *
2115657 AATATGAATATAAAAATATATTAAAATTT
1 AAAATGAATAAAAAAATATATTAAAATTT
2115686 ATATAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.17
28 11 0.46
29 7 0.29
30 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAATGAATAAAAAAATATATTAAAATTTT
Found at i:2115897 original size:12 final size:12
Alignment explanation
Indices: 2115882--2115932 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
2115872 AAGCTTATTT
2115882 TATTATTTATAA
1 TATTATTTATAA
*
2115894 TATTA-TTAAAA
1 TATTATTTATAA
*
2115905 TATTATTTTATAT
1 TATTA-TTTATAA
*
2115918 TAATATTTAT-A
1 TATTATTTATAA
2115929 TATT
1 TATT
2115933 TTATAATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
11 13 0.42
12 10 0.32
13 8 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTTATAA
Found at i:2115932 original size:21 final size:21
Alignment explanation
Indices: 2115908--2115951 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2115898 ATTAAAATAT
2115908 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
2115929 TATTTTATAATTAAATTTATA
1 TATTTTATAATTAAATTTATA
2115950 TA
1 TA
2115952 AAAATTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:2116372 original size:61 final size:60
Alignment explanation
Indices: 2116275--2116396 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 60
2116265 TGGAAGTTTC
2116275 CACCAATCCTAAAAAACAAACACAGATTTTTTCCAATTCCACTCGGCAAAGCCTCCCTCA
1 CACCAATCCTAAAAAACAAACACAGATTTTTTCCAATTCCACTCGGCAAAGCCTCCCTCA
*
2116335 CACCAATCCTAAAAAGACAAACACTA-ATTTTTTCCAATTCCACTCGGCAAAGCCTCTCTCA
1 CACCAATCCTAAAAA-ACAAACAC-AGATTTTTTCCAATTCCACTCGGCAAAGCCTCCCTCA
2116396 C
1 C
2116397 CTCTCTTTTC
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
60 15 0.25
61 43 0.73
62 1 0.02
ACGTcount: A:0.36, C:0.34, G:0.07, T:0.23
Consensus pattern (60 bp):
CACCAATCCTAAAAAACAAACACAGATTTTTTCCAATTCCACTCGGCAAAGCCTCCCTCA
Found at i:2122903 original size:24 final size:24
Alignment explanation
Indices: 2122876--2122924 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2122866 TTTAACTAAG
* *
2122876 TTTCGTTAAACCTGGGTAAGTTAA
1 TTTCGTTAAACCAGGGCAAGTTAA
*
2122900 TTTCGTTAATCCAGGGCAAGTTAA
1 TTTCGTTAAACCAGGGCAAGTTAA
2122924 T
1 T
2122925 GAAGATTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (24 bp):
TTTCGTTAAACCAGGGCAAGTTAA
Found at i:2123244 original size:21 final size:19
Alignment explanation
Indices: 2123219--2123268 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2123209 TGTATTTAAA
2123219 ATTAAAATAAATAAAAAATTT
1 ATTAAAATAAAT--AAAATTT
*
2123240 ATTAATATTAAATAAAATTT
1 ATTAA-AATAAATAAAATTT
*
2123260 ATTTAAATA
1 ATTAAAATA
2123269 TTGATTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 11 0.44
21 5 0.20
22 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAAATAAATAAAATTT
Found at i:2123639 original size:10 final size:10
Alignment explanation
Indices: 2123613--2123656 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
2123603 TTTTTTAAAT
2123613 TTAAATTT-A
1 TTAAATTTAA
2123622 TTAAATTTAA
1 TTAAATTTAA
*
2123632 TTAGATTTATTA
1 TTAAATTTA--A
2123644 TTAAATTTAA
1 TTAAATTTAA
2123654 TTA
1 TTA
2123657 TAAAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 8 0.27
10 13 0.43
12 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
TTAAATTTAA
Found at i:2123735 original size:22 final size:23
Alignment explanation
Indices: 2123683--2123748 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
2123673 TTAATATAAA
2123683 AAATTTAATAATTTATTAA-TTTAT
1 AAATTTAATAATTTA--AACTTTAT
2123707 AAA--TAATAATTTAAACTTT-T
1 AAATTTAATAATTTAAACTTTAT
2123727 AAATTTAATTTAATTTAAACTT
1 AAATTTAA--TAATTTAAACTT
2123749 AAATAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.16
21 3 0.08
22 13 0.35
24 15 0.41
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATTTAATAATTTAAACTTTAT
Found at i:2131805 original size:32 final size:31
Alignment explanation
Indices: 2131756--2131818 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
2131746 ATAAAATTTA
*
2131756 TTATTATATTATGATTTTAATATTGAATTTTG
1 TTATTATATTATAATTTT-ATATTGAATTTTG
* * *
2131788 TTATTATATTTTAATTTTTTATTGATTTTTG
1 TTATTATATTATAATTTTATATTGAATTTTG
2131819 AAATAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (31 bp):
TTATTATATTATAATTTTATATTGAATTTTG
Found at i:2132185 original size:17 final size:17
Alignment explanation
Indices: 2132163--2132211 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
2132153 TATTATTATT
2132163 TAAATATTTTATAATTA
1 TAAATATTTTATAATTA
* *
2132180 TAAATAATTTATTATTA
1 TAAATATTTTATAATTA
2132197 TAATAATATTTTATA
1 T-A-AATATTTTATA
2132212 TTTAATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 16 0.62
18 1 0.04
19 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATATTTTATAATTA
Found at i:2132210 original size:16 final size:17
Alignment explanation
Indices: 2132155--2132203 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
2132145 TAATTTGATA
*
2132155 TTATTATT-TAAATATT
1 TTATTATTATAAATAAT
*
2132171 TTATAATTATAAATAAT
1 TTATTATTATAAATAAT
2132188 TTATTATTAT-AATAAT
1 TTATTATTATAAATAAT
2132204 ATTTTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTATTATAAATAAT
Found at i:2132214 original size:25 final size:27
Alignment explanation
Indices: 2132173--2132237 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 27
2132163 TAAATATTTT
* * * *
2132173 ATAATTATAAATA-ATTTATTATTATA
1 ATAATTATTATTATATTTAATATAATA
2132199 ATAA-TATT-TTATATTTAATATAATA
1 ATAATTATTATTATATTTAATATAATA
2132224 ATAATTATTATTAT
1 ATAATTATTATTAT
2132238 TTTGATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
24 2 0.06
25 18 0.56
26 8 0.25
27 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATAATTATTATTATATTTAATATAATA
Found at i:2132217 original size:17 final size:17
Alignment explanation
Indices: 2132165--2132218 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
2132155 TTATTATTTA
*
2132165 AATATTTTATAATT-AT
1 AATATTTTATATTTAAT
*
2132181 AAATAATTTATTATTATAAT
1 -AATATTTTA-TATT-TAAT
2132201 AATATTTTATATTTAAT
1 AATATTTTATATTTAAT
2132218 A
1 A
2132219 TAATAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 13 0.42
18 7 0.23
19 9 0.29
20 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATTTTATATTTAAT
Found at i:2132221 original size:19 final size:18
Alignment explanation
Indices: 2132165--2132223 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
2132155 TTATTATTTA
*
2132165 AATATTTTATAATTATA-
1 AATATTTTATATTTATAT
*
2132182 AATAATTTAT-TATTATAAT
1 AATATTTTATAT-TTAT-AT
2132201 AATATTTTATATTTAATAT
1 AATATTTTATATTT-ATAT
2132220 AATA
1 AATA
2132224 ATAATTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 13 0.38
18 1 0.03
19 17 0.50
20 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTTTATATTTATAT
Found at i:2132238 original size:25 final size:25
Alignment explanation
Indices: 2132153--2132239 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
2132143 ATTAATTTGA
* *
2132153 TATTATTATTTAA-ATATTTTATAAT
1 TATTATTATTTAATATA-ATAATAAT
* * * *
2132178 TATAAATAATTTATTATTATAATAAT
1 TAT-TATTATTTAATATAATAATAAT
*
2132204 ATTTTA-TATTTAATATAATAATAAT
1 -TATTATTATTTAATATAATAATAAT
2132229 TATTATTATTT
1 TATTATTATTT
2132240 TGATAAATTT
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
24 4 0.09
25 24 0.52
26 14 0.30
27 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATTATTTAATATAATAATAAT
Found at i:2135542 original size:20 final size:20
Alignment explanation
Indices: 2135517--2135559 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2135507 GAAAAATTCG
* *
2135517 GAAACATTATAAAGATTTAT
1 GAAACATTATAAAAACTTAT
*
2135537 GAAACATTTTAAAAACTTAT
1 GAAACATTATAAAAACTTAT
2135557 GAA
1 GAA
2135560 GAATTTTTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (20 bp):
GAAACATTATAAAAACTTAT
Found at i:2140928 original size:2 final size:2
Alignment explanation
Indices: 2140921--2140951 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2140911 TTGCATTAGG
2140921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2140952 CTTTTGAGCG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2141744 original size:2 final size:2
Alignment explanation
Indices: 2141737--2141766 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2141727 TTTAATTTTA
2141737 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
2141767 TAGGAGCTTT
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:2145937 original size:40 final size:37
Alignment explanation
Indices: 2145868--2145952 Score: 91
Period size: 40 Copynumber: 2.2 Consensus size: 37
2145858 AATATTAATT
*
2145868 AAAATTTTTATATTAATATGTATAATTAAATTTAAATA
1 AAAATTTTTATATTAATATGAATAATTAAA-TTAAATA
*
2145906 AAAATATTTTATTATTTATAT-AATAATTTAAATTAAATTA
1 AAAAT-TTTTA-TATTAATATGAATAA-TTAAATTAAA-TA
*
2145946 TAAATTT
1 AAAATTT
2145953 ATTTTAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
38 5 0.12
39 16 0.40
40 19 0.47
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (37 bp):
AAAATTTTTATATTAATATGAATAATTAAATTAAATA
Found at i:2145960 original size:28 final size:27
Alignment explanation
Indices: 2145929--2146009 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 27
2145919 ATTTATATAA
*
2145929 TAATTTAAATTAAATTATAAATTTATTT
1 TAATTTAAATTAAATTATAAATTTA-AT
* * *
2145957 TAATATAAATTAAAATAAACAATTTAAT
1 TAATTTAAATTAAATTATA-AATTTAAT
*
2145985 TAATTTATAAATAAATT-T-AATTTAA
1 TAATTTA-AATTAAATTATAAATTTAA
2146010 CTTACAACAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
26 7 0.16
28 23 0.53
29 13 0.30
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TAATTTAAATTAAATTATAAATTTAAT
Found at i:2145965 original size:23 final size:21
Alignment explanation
Indices: 2145931--2145972 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2145921 TTATATAATA
2145931 ATTTAAATTAAATTATAAATTT
1 ATTTAAATTAAATTA-AAATTT
*
2145953 ATTTTAATATAAATTAAAAT
1 ATTTAAAT-TAAATTAAAAT
2145973 AAACAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTAAATTAAATTAAAATTT
Found at i:2146001 original size:34 final size:34
Alignment explanation
Indices: 2145849--2146001 Score: 91
Period size: 34 Copynumber: 4.4 Consensus size: 34
2145839 AAATTATTTT
* **
2145849 ATTTA-AAATAATATT-AATTAAAATTTTTATATTA
1 ATTTATAAATAA-ATTAAAATAAAAAATTTA-ATTA
* * *
2145883 ATATGTATAATTAAATTTAAATAAAAATATTTTATT-
1 AT-T-TATAAATAAATTAAAATAAAAA-ATTTAATTA
* * ** * *
2145919 ATTTATATAATAATTTAAATTAAATTA-TAAATTT
1 ATTTATA-AATAAATTAAAATAAAAAATTTAATTA
*
2145953 ATTT-TAATATAAATTAAAATAAACAATTTAATTA
1 ATTTATAA-ATAAATTAAAATAAAAAATTTAATTA
2145987 ATTTATAAATAAATT
1 ATTTATAAATAAATT
2146002 TAATTTAACT
Statistics
Matches: 90, Mismatches: 19, Indels: 20
0.70 0.15 0.16
Matches are distributed among these distances:
32 1 0.01
33 20 0.22
34 27 0.30
35 17 0.19
36 7 0.08
37 15 0.17
38 3 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (34 bp):
ATTTATAAATAAATTAAAATAAAAAATTTAATTA
Found at i:2146599 original size:2 final size:2
Alignment explanation
Indices: 2146592--2146619 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2146582 TTTTGGAGTT
2146592 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
2146620 GTAATGAATG
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):
TA
Found at i:2183674 original size:27 final size:26
Alignment explanation
Indices: 2183644--2183698 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2183634 TTAAAAATTA
2183644 TTTTAT-TTAAAATAATATTAATTAAAT
1 TTTTATATTAAAAT-ATA-TAATTAAAT
* *
2183671 TTTTATATTAATATGTATAATTAAAT
1 TTTTATATTAAAATATATAATTAAAT
2183697 TT
1 TT
2183699 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.44
27 8 0.32
28 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTTATATTAAAATATATAATTAAAT
Found at i:2183758 original size:28 final size:27
Alignment explanation
Indices: 2183727--2183807 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 27
2183717 ATTTATATAA
*
2183727 TAATTTAAATTAAATTATAAATTTATTT
1 TAATTTAAATTAAATTATAAATTTA-AT
* * *
2183755 TAATATAAATTAAAATAAACAATTTAAT
1 TAATTTAAATTAAATTATA-AATTTAAT
*
2183783 TAATTTATAAATAAATT-T-AATTTAA
1 TAATTTA-AATTAAATTATAAATTTAA
2183808 CTTACAACAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
26 7 0.16
28 23 0.53
29 13 0.30
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TAATTTAAATTAAATTATAAATTTAAT
Found at i:2183763 original size:23 final size:21
Alignment explanation
Indices: 2183729--2183770 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2183719 TTATATAATA
2183729 ATTTAAATTAAATTATAAATTT
1 ATTTAAATTAAATTA-AAATTT
*
2183751 ATTTTAATATAAATTAAAAT
1 ATTTAAAT-TAAATTAAAAT
2183771 AAACAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTAAATTAAATTAAAATTT
Found at i:2183799 original size:34 final size:34
Alignment explanation
Indices: 2183672--2183799 Score: 91
Period size: 34 Copynumber: 3.7 Consensus size: 34
2183662 TAATTAAATT
* *
2183672 TTTATATTAATATGTATAATTAAATTTAAATAAAAATA
1 TTTA-ATTAAT-T-TATAAATAAATTAAAATAAAAA-A
* * * **
2183710 TTTTATT-ATTTATATAATAATTTAAATTAAATTA
1 TTTAATTAATTTATA-AATAAATTAAAATAAAAAA
* * *
2183744 -TAAATTTATTT-TAATATAAATTAAAATAAACAA
1 TTTAATTAATTTATAA-ATAAATTAAAATAAAAAA
2183777 TTTAATTAATTTATAAATAAATT
1 TTTAATTAATTTATAAATAAATT
2183800 TAATTTAACT
Statistics
Matches: 70, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
32 1 0.01
33 20 0.29
34 25 0.36
35 16 0.23
36 2 0.03
37 3 0.04
38 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (34 bp):
TTTAATTAATTTATAAATAAATTAAAATAAAAAA
Found at i:2186353 original size:2 final size:2
Alignment explanation
Indices: 2186346--2186376 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2186336 GGAAATTGAA
2186346 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2186377 GCAAAGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2186367 original size:13 final size:13
Alignment explanation
Indices: 2186349--2186374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2186339 AATTGAAATA
2186349 TATATATATATAT
1 TATATATATATAT
2186362 TATATATATATAT
1 TATATATATATAT
2186375 ATGCAAAGCA
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:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:2186367 original size:15 final size:15
Alignment explanation
Indices: 2186347--2186376 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2186337 GAAATTGAAA
2186347 TATATATATATATAT
1 TATATATATATATAT
2186362 TATATATATATATAT
1 TATATATATATATAT
2186377 GCAAAGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:2189392 original size:42 final size:40
Alignment explanation
Indices: 2189314--2189419 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 40
2189304 ATTATTATTT
* * *
2189314 AATAATAAAATAATATTTTTATTTAAATTTAATAATATAATA
1 AATAATAAAATAAAATTTTAAATT-AATTTAATAATAT-ATA
* *
2189356 AATAATAAAATAAAATTTTAAATTAATTTGATTAATATTTA
1 AATAATAAAATAAAATTTTAAATTAATTT-AATAATATATA
* *
2189397 AAT-TTTAAA-AAAATTTTAAATTA
1 AATAATAAAATAAAATTTTAAATTA
2189420 TAATTCGATT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
39 14 0.25
40 4 0.07
41 10 0.18
42 28 0.50
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (40 bp):
AATAATAAAATAAAATTTTAAATTAATTTAATAATATATA
Found at i:2190391 original size:18 final size:18
Alignment explanation
Indices: 2190361--2190400 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
2190351 ATGCAGAATC
2190361 AAATTAAATTTAATATTA
1 AAATTAAATTTAATATTA
2190379 AAATTGAAA-TTAATATTA
1 AAATT-AAATTTAATATTA
2190397 AAAT
1 AAAT
2190401 ATATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAATTAAATTTAATATTA
Found at i:2190910 original size:21 final size:19
Alignment explanation
Indices: 2190886--2190963 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 19
2190876 TCGAGATATG
*
2190886 TATTTTTATATATTATAATTA
1 TATTTATATATATT-T-ATTA
* *
2190907 TATTTATATAAATTTTTTA
1 TATTTATATATATTTATTA
2190926 TATTTATATTATATTTTATTA
1 TATTTATA-TATA-TTTATTA
2190947 TATTT-TA-ATTATTTATT
1 TATTTATATA-TATTTATT
2190964 TAGATGATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
18 7 0.14
19 13 0.27
20 6 0.12
21 23 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTATATATATTTATTA
Found at i:2190914 original size:19 final size:19
Alignment explanation
Indices: 2190890--2190958 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 19
2190880 GATATGTATT
2190890 TTTATATATTATAATTATA
1 TTTATATATTATAATTATA
2190909 -TT-TATA-TA-AATT-T-
1 TTTATATATTATAATTATA
2190922 TTTATAT-TTAT-ATTATA
1 TTTATATATTATAATTATA
*
2190939 TTTTATTATATTTTAATTAT
1 -TTTA-TATATTATAATTAT
2190959 TTATTTAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 18
0.67 0.02 0.31
Matches are distributed among these distances:
14 3 0.08
15 12 0.31
16 3 0.08
17 4 0.10
18 6 0.15
19 3 0.08
20 3 0.08
21 5 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATATATTATAATTATA
Found at i:2190962 original size:36 final size:36
Alignment explanation
Indices: 2190894--2190962 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
2190884 TGTATTTTTA
*
2190894 TATATTATAATTATATTTATATAAATTTTTTATATT
1 TATATTATAATTATATTTATATAAATTATTTATATT
* * *
2190930 TATATTAT-ATTTTATTATATTTTAATTATTTAT
1 TATATTATAATTATATT-TATATAAATTATTTAT
2190963 TTAGATGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 7 0.25
36 21 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (36 bp):
TATATTATAATTATATTTATATAAATTATTTATATT
Found at i:2192130 original size:24 final size:22
Alignment explanation
Indices: 2192084--2192150 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 22
2192074 TTAAAAAAAT
*
2192084 AATTTAATAATTAATAA-TATTTA
1 AATTTAAT-ATT-ATAATTTTTTA
2192107 AATTTTAATAGTTATAATTTTTTA
1 AA-TTTAATA-TTATAATTTTTTA
*
2192131 TATTTAA-ATTATAATTTTTT
1 AATTTAATATTATAATTTTTT
2192151 TCATTAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 12 0.31
22 1 0.03
23 12 0.31
24 14 0.36
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (22 bp):
AATTTAATATTATAATTTTTTA
Found at i:2192285 original size:2 final size:2
Alignment explanation
Indices: 2192278--2192384 Score: 135
Period size: 2 Copynumber: 53.0 Consensus size: 2
2192268 GAGATGAGAC
*
2192278 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
2192320 TA TT TG T- TCA TA GA GA CCA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
2192363 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
2192385 CCCACACGCA
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.01
2 92 0.97
3 2 0.02
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2192835 original size:18 final size:18
Alignment explanation
Indices: 2192812--2192850 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2192802 TAACATCATA
2192812 AAAAAATATTATA-AAAAT
1 AAAAAAT-TTATATAAAAT
2192830 AAAAAATTTATATAAAAT
1 AAAAAATTTATATAAAAT
2192848 AAA
1 AAA
2192851 TTATTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATTTATATAAAAT
Found at i:2193422 original size:40 final size:41
Alignment explanation
Indices: 2193378--2193458 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
2193368 TTTTATTATA
*
2193378 TATTTATAAAA-TAAAAAA-TAAATGAATAATTTTTTAATTT
1 TATTTATAAAATTAAAAAACTAAAT-AATAATTTATTAATTT
* *
2193418 TATTTATAAAATTAAAAAACTCAATAATTATTTATTAATTT
1 TATTTATAAAATTAAAAAACTAAATAATAATTTATTAATTT
2193459 AATTAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 11 0.31
41 21 0.58
42 4 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (41 bp):
TATTTATAAAATTAAAAAACTAAATAATAATTTATTAATTT
Found at i:2194115 original size:3 final size:3
Alignment explanation
Indices: 2194109--2194133 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2194099 ATTCAAACCC
2194109 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
2194134 TTCTTCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:2194228 original size:3 final size:3
Alignment explanation
Indices: 2194220--2194254 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2194210 CTTAATTCTC
* *
2194220 TTA TTA TTA TTA TTA GTA TTA TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2194255 TTACTACTGC
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:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2194770 original size:2 final size:2
Alignment explanation
Indices: 2194765--2194802 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2194755 CCAAGAAAAC
2194765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2194803 GACTTTCAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2203992 original size:15 final size:16
Alignment explanation
Indices: 2203960--2204000 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2203950 TTTATTTAAT
2203960 AATAAATTAAATATAA
1 AATAAATTAAATATAA
* *
2203976 AATAATTTAAATAAAA
1 AATAAATTAAATATAA
2203992 AATTAAATT
1 AA-TAAATT
2204001 TTGTGCTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAAATTAAATATAA
Found at i:2204572 original size:18 final size:19
Alignment explanation
Indices: 2204541--2204592 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
2204531 ATATAATATA
2204541 ATATT-AAATATTAT-TTTT
1 ATATTAAAAT-TTATATTTT
2204559 ATATTAAAATTTATATATTTT
1 ATATTAAAA-TT-TATATTTT
*
2204580 ATAATAAAATTTA
1 ATATTAAAATTTA
2204593 AAATAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.17
19 6 0.21
20 6 0.21
21 12 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTAAAATTTATATTTT
Found at i:2204573 original size:12 final size:12
Alignment explanation
Indices: 2204556--2204612 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
2204546 AAATATTATT
*
2204556 TTTATATTAAAA
1 TTTATAATAAAA
*
2204568 TTTAT-AT--AT
1 TTTATAATAAAA
2204577 TTTATAATAAAA
1 TTTATAATAAAA
*
2204589 TTTAAAATAAAA
1 TTTATAATAAAA
*
2204601 TTT-TATTAAAA
1 TTTATAATAAAA
2204612 T
1 T
2204613 AATAATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 8 0.22
12 20 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTATAATAAAA
Found at i:2204636 original size:28 final size:28
Alignment explanation
Indices: 2204582--2204637 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2204572 TATATTTTAT
**
2204582 AATAAAATTTAAAATAAAATTTTATTAA
1 AATAAAATTTAAAATAAAATTAAATTAA
*
2204610 AATAATAATTT-AAATTAAATTAAATTAA
1 AATAA-AATTTAAAATAAAATTAAATTAA
2204638 TTTTATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
AATAAAATTTAAAATAAAATTAAATTAA
Found at i:2207713 original size:16 final size:16
Alignment explanation
Indices: 2207694--2207724 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2207684 AATCAAAATT
*
2207694 AAATTAAATTTAATAA
1 AAATTAAATTAAATAA
2207710 AAATTAAATTAAATA
1 AAATTAAATTAAATA
2207725 TTATAATTCA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTAAATTAAATAA
Found at i:2210253 original size:6 final size:6
Alignment explanation
Indices: 2210191--2210250 Score: 102
Period size: 6 Copynumber: 10.0 Consensus size: 6
2210181 TAAGGAAACC
2210191 TGAGAA TGAGAA TGAGAA TGAGAA TGAGAA TGAGAA TGAGAA TGAGAA
1 TGAGAA TGAGAA TGAGAA TGAGAA TGAGAA TGAGAA TGAGAA TGAGAA
* *
2210239 AGAGAA AGAGAA
1 TGAGAA TGAGAA
2210251 AGATGTATTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (6 bp):
TGAGAA
Found at i:2215825 original size:17 final size:19
Alignment explanation
Indices: 2215803--2215845 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2215793 TCGATTTGAT
2215803 TTAAAATAAT-T-TTTTAA
1 TTAAAATAATATATTTTAA
*
2215820 TTAAAATAATATATTTTTA
1 TTAAAATAATATATTTTAA
2215839 TTAAAAT
1 TTAAAAT
2215846 TTAATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.43
18 1 0.04
19 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATAATATATTTTAA
Found at i:2220412 original size:17 final size:17
Alignment explanation
Indices: 2220390--2220437 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2220380 CATATAGTGA
2220390 TAAATTTATTAAAAAAT
1 TAAATTTATTAAAAAAT
*
2220407 TAAATTTA-TAATATAAT
1 TAAATTTATTAA-AAAAT
*
2220424 CAAACTTTATTAAA
1 TAAA-TTTATTAAA
2220438 TTATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.12
17 15 0.58
18 5 0.19
19 3 0.12
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTATTAAAAAAT
Found at i:2221723 original size:19 final size:19
Alignment explanation
Indices: 2221699--2221738 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2221689 TCGAAAATGA
*
2221699 ATCTTATTAGATAATTTTT
1 ATCTTATAAGATAATTTTT
*
2221718 ATCTTATAATATAATTTTT
1 ATCTTATAAGATAATTTTT
2221737 AT
1 AT
2221739 TATTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (19 bp):
ATCTTATAAGATAATTTTT
Found at i:2222462 original size:2 final size:2
Alignment explanation
Indices: 2222457--2222482 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2222447 AAAAATTTAC
2222457 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
2222483 TTTTGTGCAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:2224764 original size:2 final size:2
Alignment explanation
Indices: 2224759--2224787 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2224749 CTCTCTCTCT
2224759 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
2224788 TCGTGCGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2225736 original size:23 final size:23
Alignment explanation
Indices: 2225706--2225777 Score: 126
Period size: 23 Copynumber: 3.1 Consensus size: 23
2225696 TTTTCACTTT
2225706 TAGGTTATTGTGTGTGTTTAGTG
1 TAGGTTATTGTGTGTGTTTAGTG
2225729 TAGGTTATTGTGTGTGTTTAGTG
1 TAGGTTATTGTGTGTGTTTAGTG
*
2225752 TAGGTTATTGTGTGTATTTTAGTG
1 TAGGTTATTGTGTGT-GTTTAGTG
2225776 TA
1 TA
2225778 ACTAAAGATT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 38 0.81
24 9 0.19
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.53
Consensus pattern (23 bp):
TAGGTTATTGTGTGTGTTTAGTG
Found at i:2226676 original size:23 final size:23
Alignment explanation
Indices: 2226650--2226697 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2226640 ATCTTAAGGC
2226650 AATAATTATCTATACACATTTGA
1 AATAATTATCTATACACATTTGA
2226673 AATAATTATCTATACACATTTGA
1 AATAATTATCTATACACATTTGA
2226696 AA
1 AA
2226698 ATTGGATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (23 bp):
AATAATTATCTATACACATTTGA
Found at i:2228003 original size:14 final size:14
Alignment explanation
Indices: 2227967--2227993 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2227957 TTTAATTTTT
2227967 TAAAATTATATATA
1 TAAAATTATATATA
2227981 TAAAATTATATAT
1 TAAAATTATATAT
2227994 TTATATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAATTATATATA
Found at i:2228561 original size:17 final size:17
Alignment explanation
Indices: 2228541--2228598 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 17
2228531 GATTGGGTGA
2228541 ATAAAAAAATTGAAAAG
1 ATAAAAAAATTGAAAAG
*
2228558 AT-AAAAAATT-TAAAG
1 ATAAAAAAATTGAAAAG
* *
2228573 A-AAATAAATGTGAGAAG
1 ATAAAAAAAT-TGAAAAG
2228590 ATAAAAAAA
1 ATAAAAAAA
2228599 AATATTTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 11 0.34
16 9 0.28
17 6 0.19
18 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (17 bp):
ATAAAAAAATTGAAAAG
Found at i:2229958 original size:34 final size:34
Alignment explanation
Indices: 2229909--2230085 Score: 187
Period size: 34 Copynumber: 5.2 Consensus size: 34
2229899 TTCCATGTTA
* *
2229909 ATTAAATG-GTGATTTGGTAGTTTATCATTATTG
1 ATTAAATGAGTGATTTGGTAGCTTACCATTATTG
* **
2229942 ATTAAATGAGTGATTTGGTAGTTTGTCATTATTG
1 ATTAAATGAGTGATTTGGTAGCTTACCATTATTG
* * ** *
2229976 ACTAAATGAGAGATTTAATAGCTTACCATTGTTG
1 ATTAAATGAGTGATTTGGTAGCTTACCATTATTG
* **
2230010 ATTAAATAAGAAATTTGGTAGCTTACCATTATTG
1 ATTAAATGAGTGATTTGGTAGCTTACCATTATTG
* *
2230044 ATTAAATG-GATGATTTGGTGGCTTACCATTGTTG
1 ATTAAATGAG-TGATTTGGTAGCTTACCATTATTG
*
2230078 ACTAAATG
1 ATTAAATG
2230086 GTAGGATTGG
Statistics
Matches: 121, Mismatches: 21, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
33 9 0.07
34 112 0.93
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (34 bp):
ATTAAATGAGTGATTTGGTAGCTTACCATTATTG
Found at i:2230086 original size:34 final size:34
Alignment explanation
Indices: 2229909--2230118 Score: 178
Period size: 34 Copynumber: 6.2 Consensus size: 34
2229899 TTCCATGTTA
* *
2229909 ATTAAATGG-TGATTTGGTAGTTTATCATTATTG
1 ATTAAATGGATGATTTGGTAGCTTACCATTATTG
* **
2229942 ATTAAAT-GAGTGATTTGGTAGTTTGTCATTATTG
1 ATTAAATGGA-TGATTTGGTAGCTTACCATTATTG
* ** *
2229976 ACTAAATGAGA-GATTTAATAGCTTACCATTGTTG
1 ATTAAATG-GATGATTTGGTAGCTTACCATTATTG
* *
2230010 ATTAAATAAGA-AATTTGGTAGCTTACCATTATTG
1 ATTAAAT-GGATGATTTGGTAGCTTACCATTATTG
* *
2230044 ATTAAATGGATGATTTGGTGGCTTACCATTGTTG
1 ATTAAATGGATGATTTGGTAGCTTACCATTATTG
* * * ** *
2230078 ACTAAATGGTAGGA-TTGGTAGGTTGTCATTGTTG
1 ATTAAATGG-ATGATTTGGTAGCTTACCATTATTG
2230112 ATTAAAT
1 ATTAAAT
2230119 AGTGGTTTTT
Statistics
Matches: 145, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
32 1 0.01
33 9 0.06
34 130 0.90
35 3 0.02
36 2 0.01
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (34 bp):
ATTAAATGGATGATTTGGTAGCTTACCATTATTG
Found at i:2230096 original size:68 final size:68
Alignment explanation
Indices: 2229909--2230118 Score: 221
Period size: 68 Copynumber: 3.1 Consensus size: 68
2229899 TTCCATGTTA
* * * * *
2229909 ATTAAATGG-TGATTTGGTAGTTTATCATTATTGATTAAATGAGTGATTTGGTAGTTTGTCATTA
1 ATTAAATGGATGATTTGGTAGCTTACCATTGTTGATTAAATGAGAGATTTGGTAGCTTGTCATTA
2229973 TTG
66 TTG
* ** * * **
2229976 ACTAAATGAGA-GATTTAATAGCTTACCATTGTTGATTAAATAAGAAATTTGGTAGCTTACCATT
1 ATTAAATG-GATGATTTGGTAGCTTACCATTGTTGATTAAATGAGAGATTTGGTAGCTTGTCATT
2230040 ATTG
65 ATTG
* * *
2230044 ATTAAATGGATGATTTGGTGGCTTACCATTGTTGACTAAATG-GTAGGA-TTGGTAGGTTGTCAT
1 ATTAAATGGATGATTTGGTAGCTTACCATTGTTGATTAAATGAG-A-GATTTGGTAGCTTGTCAT
*
2230107 TGTTG
64 TATTG
2230112 ATTAAAT
1 ATTAAAT
2230119 AGTGGTTTTT
Statistics
Matches: 115, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
67 10 0.09
68 104 0.90
69 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (68 bp):
ATTAAATGGATGATTTGGTAGCTTACCATTGTTGATTAAATGAGAGATTTGGTAGCTTGTCATTA
TTG
Found at i:2234591 original size:34 final size:34
Alignment explanation
Indices: 2234534--2234752 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
2234524 AAGTGGGAGA
*
2234534 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2234567 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2234601 ATTGTTGACTAAATGAGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
2234635 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2234669 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2234703 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
2234737 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2234753 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
33 17 0.10
34 144 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2234677 original size:102 final size:101
Alignment explanation
Indices: 2234534--2234752 Score: 341
Period size: 102 Copynumber: 2.2 Consensus size: 101
2234524 AAGTGGGAGA
** * * * *
2234534 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
2234599 CCATTGTTGACTAAATGAG-AGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATG-GTAGATTTGGTAGCTTACC
2234635 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* *
2234700 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGTAGATTTGGTAGCTTACC
2234737 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2234753 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
101 17 0.16
102 91 0.84
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGTAGATTTGGTAGCTTACC
Found at i:2237072 original size:3 final size:3
Alignment explanation
Indices: 2237064--2237091 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2237054 AAACAAAACC
2237064 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
2237092 GCTGTCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:2238848 original size:14 final size:13
Alignment explanation
Indices: 2238825--2238854 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
2238815 TCATCTACAT
2238825 AAAAAAAATTATA
1 AAAAAAAATTATA
2238838 AAAATAAAATTATA
1 AAAA-AAAATTATA
2238852 AAA
1 AAA
2238855 TAATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAAAATTATA
Found at i:2238854 original size:13 final size:13
Alignment explanation
Indices: 2238823--2238857 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2238813 GATCATCTAC
2238823 ATAAAA-AAAATT
1 ATAAAATAAAATT
2238835 ATAAAAATAAAATT
1 AT-AAAATAAAATT
2238849 ATAAAATAA
1 ATAAAATAA
2238858 TTTTAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.10
13 11 0.52
14 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAAATAAAATT
Found at i:2239339 original size:24 final size:24
Alignment explanation
Indices: 2239288--2239349 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
2239278 GAGCCTTGTT
2239288 TTTAAGGATATAAAAAATGAAGAA
1 TTTAAGGATATAAAAAATGAAGAA
2239312 -TTAAGGATATAAAAAATGAAGAA
1 TTTAAGGATATAAAAAATGAAGAA
**
2239335 TTTAAGTTTATAAAA
1 TTTAAGGATATAAAA
2239350 TTAAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.66
24 12 0.34
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (24 bp):
TTTAAGGATATAAAAAATGAAGAA
Found at i:2241800 original size:2 final size:2
Alignment explanation
Indices: 2241795--2241826 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2241785 TATCTGTGAA
2241795 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
2241827 CCATATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2242271 original size:19 final size:20
Alignment explanation
Indices: 2242235--2242287 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
2242225 TTATTGATTT
*
2242235 TATTTTATAT-TT-TTATTA
1 TATTTTATATATTATAATTA
2242253 T-TTTTATATATTATAATTA
1 TATTTTATATATTATAATTA
* *
2242272 TATTTAAAATATTATA
1 TATTTTATATATTATA
2242288 CGTTCATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 8 0.28
18 3 0.10
19 6 0.21
20 12 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTATATATTATAATTA
Found at i:2242275 original size:24 final size:22
Alignment explanation
Indices: 2242232--2242275 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
2242222 CTTTTATTGA
* *
2242232 TTTTATTTTATATTTTTATTAT
1 TTTTATTTTATAATTATATTAT
2242254 TTTTATATATTATAATTATATT
1 TTTTAT-T-TTATAATTATATT
2242276 TAAAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 1 0.06
24 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATTTTATAATTATATTAT
Found at i:2244254 original size:33 final size:33
Alignment explanation
Indices: 2244217--2244287 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
2244207 TTTTCCCCAA
* * *
2244217 TACTTAAGCAGCTTTTAGGG-GAATCATCCCTGC
1 TACTTAACCAGCTTAT-GGGTGAATCATCACTGC
* *
2244250 TACTTAACCTGCTTATGGGTGCATCATCACTGC
1 TACTTAACCAGCTTATGGGTGAATCATCACTGC
2244283 TACTT
1 TACTT
2244288 GGCCCACTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (33 bp):
TACTTAACCAGCTTATGGGTGAATCATCACTGC
Done.