Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 11 of 20
Found at i:1661210 original size:31 final size:31
Alignment explanation
Indices: 1661149--1661210 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1661139 TTTATACAAT
*
1661149 AAATATATAAAATAAATAAAAATATTTTAAA
1 AAATATATAAAATAAATAAAAATATATTAAA
*
1661180 AAATATATAAAATTAATAAATAATA-ATTAAA
1 AAATATATAAAATAAATAAA-AATATATTAAA
1661211 TTTAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (31 bp):
AAATATATAAAATAAATAAAAATATATTAAA
Found at i:1662503 original size:36 final size:42
Alignment explanation
Indices: 1662453--1662538 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 42
1662443 CAATTCAATC
* *
1662453 TAAAATTTTATTT-AAAATT-TA-AATAAAATTAACA-AAAA
1 TAAAATATTATTTAAAAATTATATAATAAAATTAAAATAAAA
*
1662491 -AAAATATT-TTTAAAAATTATATAATAATATTAAAATAAAA
1 TAAAATATTATTTAAAAATTATATAATAAAATTAAAATAAAA
1662531 TAAAATAT
1 TAAAATAT
1662539 AAAATATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
36 3 0.08
37 13 0.32
38 2 0.05
39 11 0.28
40 4 0.10
41 7 0.17
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (42 bp):
TAAAATATTATTTAAAAATTATATAATAAAATTAAAATAAAA
Found at i:1663286 original size:14 final size:15
Alignment explanation
Indices: 1663259--1663287 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1663249 AGGGGGAAAT
1663259 CTCAAGAGGAAAACC
1 CTCAAGAGGAAAACC
1663274 CTCAAGA-GAAAACC
1 CTCAAGAGGAAAACC
1663288 TTGAAAGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (15 bp):
CTCAAGAGGAAAACC
Found at i:1664836 original size:25 final size:25
Alignment explanation
Indices: 1664803--1664850 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1664793 AATTATTAAT
* *
1664803 ATATAAAAATTTAGATAAATATAAA
1 ATATAAAAAATAAGATAAATATAAA
*
1664828 ATATAAAAAATAATATAAATATA
1 ATATAAAAAATAAGATAAATATA
1664851 GTATGAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
ATATAAAAAATAAGATAAATATAAA
Found at i:1665333 original size:14 final size:16
Alignment explanation
Indices: 1665310--1665372 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 16
1665300 TGATCCAAAT
1665310 AAAATAAATT-TAAAA
1 AAAATAAATTATAAAA
1665325 AAAAT-AATTATAAAA
1 AAAATAAATTATAAAA
* *
1665340 ATATATAAA-TATTAATAT
1 A-AAATAAATTA-TAA-AA
1665358 AAAATAATATTATAA
1 AAAATAA-ATTATAA
1665373 CATTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 4 0.11
15 11 0.29
16 5 0.13
17 10 0.26
18 6 0.16
19 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAAATTATAAAA
Found at i:1666090 original size:26 final size:26
Alignment explanation
Indices: 1666050--1666101 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1666040 TCAAGCACAT
*
1666050 TTACATTGTGGCTAAAGAACTTTTCG
1 TTACATTGTGACTAAAGAACTTTTCG
1666076 TTACATTGTGACTAAAGAACTTTTCG
1 TTACATTGTGACTAAAGAACTTTTCG
1666102 AGTGTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (26 bp):
TTACATTGTGACTAAAGAACTTTTCG
Found at i:1666478 original size:20 final size:20
Alignment explanation
Indices: 1666439--1666478 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1666429 TTATTATTTT
*
1666439 GTATTATAATTATATTTAAA
1 GTATTATAATTATATATAAA
1666459 GTATTATATATT-TATATAAA
1 GTATTATA-ATTATATATAAA
1666479 TTTCATCGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
GTATTATAATTATATATAAA
Found at i:1666510 original size:108 final size:105
Alignment explanation
Indices: 1666389--1666587 Score: 265
Period size: 108 Copynumber: 1.9 Consensus size: 105
1666379 ACATTATTCG
* * * *
1666389 AATAATTATTAATTTTGTATCATATTTTATTC-TATTTGTATTATTATTTTGTATTATAATTATA
1 AATAATTATTAATTTTGTATCATATTTCA-TCATA-TTGCATTATT-TTTTATATTATAATCATA
*
1666453 TTTAAAGTATTATATATTTATATAAATTTCATCGTCACTATACA
63 TTTAAAGTATTATAT-TTTATACAAATTTCATCGTCACTATACA
* * *
1666497 AATAATTTTTAATTTTGTGTCATATTTCATCATGATTGCATTATTTTTTATATTATAATCGTATT
1 AATAATTATTAATTTTGTATCATATTTCATCAT-ATTGCATTATTTTTTATATTATAATCATATT
*
1666562 TAACGTATTATATTTTATACAAATTT
65 TAAAGTATTATATTTTATACAAATTT
1666588 GACATATTAA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
106 12 0.15
107 31 0.39
108 36 0.45
109 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.54
Consensus pattern (105 bp):
AATAATTATTAATTTTGTATCATATTTCATCATATTGCATTATTTTTTATATTATAATCATATTT
AAAGTATTATATTTTATACAAATTTCATCGTCACTATACA
Found at i:1671939 original size:11 final size:11
Alignment explanation
Indices: 1671923--1671973 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1671913 TCAATTTTGA
1671923 TATATTTATAT
1 TATATTTATAT
1671934 TATATTT-TAAT
1 TATATTTAT-AT
*
1671945 TATTTTCTCATAT
1 TATATT-T-ATAT
*
1671958 TATATTTGTAT
1 TATATTTATAT
1671969 TATAT
1 TATAT
1671974 CTTAATTCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
10 1 0.03
11 22 0.67
12 2 0.06
13 7 0.21
14 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1672366 original size:11 final size:11
Alignment explanation
Indices: 1672352--1672422 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
1672342 AAATTTGATA
1672352 AAATATATTAT
1 AAATATATTAT
1672363 AAATATATTA-
1 AAATATATTAT
*
1672373 AAATTTA-TAT
1 AAATATATTAT
1672383 -AATATGAATTATT
1 AAATAT--ATTA-T
1672396 AAA-ATATTA-
1 AAATATATTAT
*
1672405 AAATTTA-TAT
1 AAATATATTAT
1672415 AAATATAT
1 AAATATAT
1672423 AAATTTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
9 11 0.23
10 14 0.30
11 15 0.32
12 2 0.04
13 3 0.06
14 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
AAATATATTAT
Found at i:1672382 original size:25 final size:24
Alignment explanation
Indices: 1672354--1672400 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1672344 ATTTGATAAA
*
1672354 ATATATTATAAATATATTAAAATTT
1 ATATAATATAAAT-TATTAAAATTT
*
1672379 ATATAATATGAATTATTAAAAT
1 ATATAATATAAATTATTAAAAT
1672401 ATTAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATATAATATAAATTATTAAAATTT
Found at i:1672403 original size:32 final size:30
Alignment explanation
Indices: 1672341--1672426 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 30
1672331 GTATTAATGA
*
1672341 AAAATTTGATAAAATATATTATAAATATATT
1 AAAATTT-ATATAATATATTATAAATATATT
1672372 AAAATTTATATAATATGAATTATTAAA-ATATT
1 AAAATTTATATAATAT--ATTA-TAAATATATT
1672404 AAAATTTATATAA-ATA-TATAAAT
1 AAAATTTATATAATATATTATAAAT
1672427 TTTAAATTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
27 4 0.08
28 2 0.04
29 1 0.02
30 8 0.16
31 9 0.18
32 22 0.44
33 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
AAAATTTATATAATATATTATAAATATATT
Found at i:1672418 original size:18 final size:18
Alignment explanation
Indices: 1672367--1672430 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
1672357 TATTATAAAT
1672367 ATATTAAAATTTATAT-A
1 ATATTAAAATTTATATAA
*
1672384 ATA-T-GAA-TTAT-TAAA
1 ATATTAAAATTTATAT-AA
1672399 ATATTAAAATTTATATAA
1 ATATTAAAATTTATATAA
*
1672417 ATATATAAATTTTA
1 ATAT-TAAAATTTA
1672431 AATTAAACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 1 0.03
14 4 0.11
15 6 0.16
16 2 0.05
17 5 0.14
18 10 0.27
19 9 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
ATATTAAAATTTATATAA
Found at i:1673643 original size:25 final size:25
Alignment explanation
Indices: 1673611--1673665 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1673601 TTAAAAAATT
1673611 AAAT-ATTAAAATTTGATAA-AATAA
1 AAATAATTAAAA-TTGATAATAATAA
* *
1673635 AAATAATTATAATTGATAATATTAA
1 AAATAATTAAAATTGATAATAATAA
1673660 AAATAA
1 AAATAA
1673666 AAAATGCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
AAATAATTAAAATTGATAATAATAA
Found at i:1677753 original size:9 final size:9
Alignment explanation
Indices: 1677739--1677780 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
1677729 ATTCGTCGAC
1677739 TAATTTATT
1 TAATTTATT
*
1677748 TAATTTAAT
1 TAATTTATT
*
1677757 AAATTTATT
1 TAATTTATT
1677766 TAATTTAATT
1 TAATTT-ATT
1677776 TAATT
1 TAATT
1677781 ATAATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TAATTTATT
Found at i:1677755 original size:5 final size:5
Alignment explanation
Indices: 1677739--1677817 Score: 67
Period size: 5 Copynumber: 16.0 Consensus size: 5
1677729 ATTCGTCGAC
*
1677739 TAATT T-ATT TAATT TAA-T AAATT T-ATT TAATT TAATT TAATT ATAATT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT -TAATT
* * *
1677787 TAA-A TAATAA TAATT ATTATT TAATT TAATT
1 TAATT TAAT-T TAATT -TAATT TAATT TAATT
1677818 ATAAATATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
4 14 0.23
5 33 0.54
6 14 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TAATT
Found at i:1677763 original size:18 final size:18
Alignment explanation
Indices: 1677740--1677816 Score: 73
Period size: 18 Copynumber: 3.9 Consensus size: 18
1677730 TTCGTCGACT
1677740 AATTTATTTAATTTAATA
1 AATTTATTTAATTTAATA
*
1677758 AATTTATTTAATTTAATTT
1 AATTTATTTAATTTAA-TA
*
1677777 AATTATAATTTAAATAATAATA
1 AATT-T-ATTT-AAT-TTAATA
*
1677799 ATTATTATTTAATTTAAT
1 AAT-TTATTTAATTTAAT
1677817 TATAAATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
18 16 0.33
19 9 0.19
20 4 0.08
21 8 0.17
22 7 0.15
23 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTTATTTAATTTAATA
Found at i:1678573 original size:22 final size:23
Alignment explanation
Indices: 1678531--1678601 Score: 76
Period size: 22 Copynumber: 3.1 Consensus size: 23
1678521 TTATTTAAAA
1678531 TATAATAAAATATTAAA-AATAAT
1 TATAATAAAA-ATTAAATAATAAT
* *
1678554 T-TATTAAAAATTATATAAT-AT
1 TATAATAAAAATTAAATAATAAT
*
1678575 TATAATAAAATTTAAATAATATAT
1 TATAATAAAAATTAAATAATA-AT
1678599 TAT
1 TAT
1678602 TTTAATTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 8 0.21
22 25 0.64
23 1 0.03
24 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TATAATAAAAATTAAATAATAAT
Found at i:1681514 original size:2 final size:2
Alignment explanation
Indices: 1681507--1681535 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1681497 TGAATGCATG
1681507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1681536 TTATGTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1690246 original size:19 final size:19
Alignment explanation
Indices: 1690224--1690261 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1690214 TCAGGTTAAC
1690224 TTTTTTT-TTT-TTTACAT
1 TTTTTTTCTTTGTTTACAT
*
1690241 TTTTTTTCTTTGTTTATAT
1 TTTTTTTCTTTGTTTACAT
1690260 TT
1 TT
1690262 GAATGTGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.11, C:0.05, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTTTTCTTTGTTTACAT
Found at i:1690565 original size:37 final size:37
Alignment explanation
Indices: 1690524--1690596 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
1690514 TTTTCCAGCA
1690524 TTTCTCTACTCGTCCACATTTATTACATAATTATCAG
1 TTTCTCTACTCGTCCACATTTATTACATAATTATCAG
* * * *
1690561 TTTCTCTATTTGTCCAGATTTATTATATAATTATCA
1 TTTCTCTACTCGTCCACATTTATTACATAATTATCA
1690597 CAGTTCCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.48
Consensus pattern (37 bp):
TTTCTCTACTCGTCCACATTTATTACATAATTATCAG
Found at i:1691496 original size:2 final size:2
Alignment explanation
Indices: 1691489--1691515 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1691479 CTTCTGTGAA
1691489 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1691516 CCATTCCACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1693458 original size:13 final size:13
Alignment explanation
Indices: 1693415--1693458 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1693405 TCTTCATATT
1693415 AATATTT-AAATA
1 AATATTTAAAATA
* *
1693427 TATATCTAAAATA
1 AATATTTAAAATA
1693440 AATATTTAAAATA
1 AATATTTAAAATA
*
1693453 ACTATT
1 AATATT
1693459 ATTTTTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATTTAAAATA
Found at i:1695062 original size:2 final size:2
Alignment explanation
Indices: 1695057--1695090 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1695047 TAACGTTTTG
*
1695057 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1695091 GGGGCAGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1695793 original size:36 final size:35
Alignment explanation
Indices: 1695753--1695851 Score: 96
Period size: 36 Copynumber: 2.8 Consensus size: 35
1695743 TTAGATAAAG
*
1695753 TTTAAAATATATTTTTAATAATATAAATAGATTTCA
1 TTTAAATTATATTTTTAATAATATAAATA-ATTTCA
* *
1695789 TTTAAATTATTATTTATTTAATAA-A-AAATATTTTTA
1 TTTAAATTA-TA-TT-TTTAATAATATAAATAATTTCA
*
1695825 TTTAAATTAAATTTTATAAT-ATATAAA
1 TTTAAATTATATTTT-TAATAATATAAA
1695852 CTTTTTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
33 3 0.06
34 7 0.13
35 4 0.08
36 21 0.40
37 7 0.13
38 3 0.06
39 8 0.15
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (35 bp):
TTTAAATTATATTTTTAATAATATAAATAATTTCA
Found at i:1696460 original size:15 final size:15
Alignment explanation
Indices: 1696413--1696460 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
1696403 ATTACAGTTT
1696413 ATTTT-ATTAAAATA
1 ATTTTAATTAAAATA
*
1696427 ATTTGTAA-AAAATATA
1 ATTT-TAATTAAA-ATA
1696443 ATTTTAATTAAAATA
1 ATTTTAATTAAAATA
1696458 ATT
1 ATT
1696461 AAGAGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 4 0.14
15 13 0.46
16 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTTTAATTAAAATA
Found at i:1696470 original size:31 final size:30
Alignment explanation
Indices: 1696413--1696479 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
1696403 ATTACAGTTT
*
1696413 ATTTTATTAAAATAATTTGTAAAAAATATA
1 ATTTTATTAAAATAATTAGTAAAAAATATA
*
1696443 ATTTTAATTAAAATAATTAAGAGAAAATAATATA
1 ATTTT-ATTAAAATAATT-AG-TAAAA-AATATA
1696477 ATT
1 ATT
1696480 GCGTTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 5 0.16
31 12 0.39
32 1 0.03
33 4 0.13
34 9 0.29
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (30 bp):
ATTTTATTAAAATAATTAGTAAAAAATATA
Found at i:1698136 original size:16 final size:16
Alignment explanation
Indices: 1698115--1698151 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1698105 CATATATAAG
1698115 GAAGTTATTGCTTTTT
1 GAAGTTATTGCTTTTT
1698131 GAAGTTATTGCTTTTT
1 GAAGTTATTGCTTTTT
1698147 GAAGT
1 GAAGT
1698152 CCTAGAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (16 bp):
GAAGTTATTGCTTTTT
Found at i:1698631 original size:130 final size:130
Alignment explanation
Indices: 1698398--1698657 Score: 423
Period size: 130 Copynumber: 2.0 Consensus size: 130
1698388 CCAAATGTTG
* * *
1698398 TGGCAGGTTAAGAAAATAGAAAGTGGGGAGTGGAGAGAATATGAAGTAGGAACTGGAGAGTAAAG
1 TGGCAGGTTAAGAAAATAGAAAGTAGGGAGTGGAGAGAATATGAAATAGGAACTGGAGAGAAAAG
* *
1698463 AATAGGTGGTATGGAATTAAGAACTGTAATTGGCAGTATATGCTTGAAGT-GGATGAGTGAGACA
66 AACAGGTGGCATGGAATTAAGAACTGTAATTGGCAGTATATGCTTGAAGTAGG-TGAGTGAGACA
1698527 A
130 A
* * *
1698528 TGGCAGGTTAAGAAAATCGAAAGTAGGGATTGGAGAGAATATGAAATAGGAACTGGATAGAAAAG
1 TGGCAGGTTAAGAAAATAGAAAGTAGGGAGTGGAGAGAATATGAAATAGGAACTGGAGAGAAAAG
*
1698593 AACAGGTGGCATGGAATTAAGAACTTTAATTGGCAGTATATGCTTGAAGTAGGTGAGTGAGACAA
66 AACAGGTGGCATGGAATTAAGAACTGTAATTGGCAGTATATGCTTGAAGTAGGTGAGTGAGACAA
1698658 GAGCTTTATG
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
130 118 0.98
131 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.22
Consensus pattern (130 bp):
TGGCAGGTTAAGAAAATAGAAAGTAGGGAGTGGAGAGAATATGAAATAGGAACTGGAGAGAAAAG
AACAGGTGGCATGGAATTAAGAACTGTAATTGGCAGTATATGCTTGAAGTAGGTGAGTGAGACAA
Found at i:1699166 original size:235 final size:235
Alignment explanation
Indices: 1698755--1699225 Score: 789
Period size: 235 Copynumber: 2.0 Consensus size: 235
1698745 TAGATAATAC
* *
1698755 CTGCAAAACATGATAATTCACATGGTTAAATTTATAATGTCATGATTAGCCAACAAACAAGCATC
1 CTGCAAAACATGATAAGTCACATGGTTAAATTTATAATGTCATGATTAGCCAAAAAACAAGCATC
* *
1698820 TAGATGGTGTAAGATAAATGATTATCACAGAATTTAATGATTTTTATCTTGATCCTTGGAAGTCC
66 TAGATGGTGTAAGATAAATGATTATCACAGAATTTAATGATTTTGATCTTGATCCTTGAAAGTCC
* * *
1698885 ACAATCCTTGTACTAGACTATCTTGCTTCTCCTAGTGGTATATGCTGGTAGTTACATCCTTAGTT
131 ACAATCCTTGTACTAGACTATCTTGCTCCTCCTAGTGGTATATGCTGGTAGTCACATCCTTAATT
1698950 TCTTTGTCTTCCAATGATTTCCAAGTTACCTAAGCTTGTG
196 TCTTTGTCTTCCAATGATTTCCAAGTTACCTAAGCTTGTG
* * *
1698990 CTGCAAAACATGATAAGTCACATGGTTAAATTTATAATGTCTTGATTAGCCAAAAAACAAGCGTT
1 CTGCAAAACATGATAAGTCACATGGTTAAATTTATAATGTCATGATTAGCCAAAAAACAAGCATC
* *
1699055 TAGATGGTGTAATATAAATGATTATCACAGAATTTAATGATTTTGATCTTGATCCTTGAAAGTTC
66 TAGATGGTGTAAGATAAATGATTATCACAGAATTTAATGATTTTGATCTTGATCCTTGAAAGTCC
* *
1699120 ACAATCGTTGTACTAGATTATCTTGCTCCTCCTAGTGGTATATGCTGGTAGTCACATCCTTAATT
131 ACAATCCTTGTACTAGACTATCTTGCTCCTCCTAGTGGTATATGCTGGTAGTCACATCCTTAATT
* * *
1699185 TCTTTGTCTTCCTATGGTTTCCAAGTTTCCTAAGCTTGTG
196 TCTTTGTCTTCCAATGATTTCCAAGTTACCTAAGCTTGTG
1699225 C
1 C
1699226 GTTACTATGA
Statistics
Matches: 219, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
235 219 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (235 bp):
CTGCAAAACATGATAAGTCACATGGTTAAATTTATAATGTCATGATTAGCCAAAAAACAAGCATC
TAGATGGTGTAAGATAAATGATTATCACAGAATTTAATGATTTTGATCTTGATCCTTGAAAGTCC
ACAATCCTTGTACTAGACTATCTTGCTCCTCCTAGTGGTATATGCTGGTAGTCACATCCTTAATT
TCTTTGTCTTCCAATGATTTCCAAGTTACCTAAGCTTGTG
Found at i:1701529 original size:3 final size:3
Alignment explanation
Indices: 1701521--1701568 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1701511 GGGTGATTGA
1701521 AAT AAT 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 AAT AAT
1701569 CTTCAATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1701661 original size:29 final size:28
Alignment explanation
Indices: 1701628--1701707 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
1701618 GTAAGGATTC
* * *
1701628 TTAATTTATATCTGAATATATTTGAATTT
1 TTAATTTATAT-TAAAAAAATTTGAATTT
* *
1701657 TTAATTTGTATTAAAAAAATTTTAATTT
1 TTAATTTATATTAAAAAAATTTGAATTT
*
1701685 TTAATTTATATTTAAATAAATTT
1 TTAATTTATA-TTAAAAAAATTT
1701708 TAAATATAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 22 0.51
29 21 0.49
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (28 bp):
TTAATTTATATTAAAAAAATTTGAATTT
Found at i:1701708 original size:29 final size:29
Alignment explanation
Indices: 1701628--1701710 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 29
1701618 GTAAGGATTC
* * * *
1701628 TTAATTTATATCTGAATATATTTGAATTT
1 TTAATTTATATTTAAATAAATTTTAATTT
* *
1701657 TTAATTTGTA-TTAAAAAAATTTTAATTT
1 TTAATTTATATTTAAATAAATTTTAATTT
1701685 TTAATTTATATTTAAATAAATTTTAA
1 TTAATTTATATTTAAATAAATTTTAA
1701711 ATATAAATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
28 22 0.49
29 23 0.51
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (29 bp):
TTAATTTATATTTAAATAAATTTTAATTT
Found at i:1701719 original size:29 final size:29
Alignment explanation
Indices: 1701659--1701753 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 29
1701649 TTGAATTTTT
* * * * *
1701659 AATTTGTA-TTAAAAAAATTTTAATTTTT
1 AATTTATATTTAAATAAATTTTAAATATA
1701687 AATTTATATTTAAATAAATTTTAAATATA
1 AATTTATATTTAAATAAATTTTAAATATA
*
1701716 AA-TTATTATTT-TATAAACTTTT-AATA-A
1 AATTTA-TATTTAAATAAA-TTTTAAATATA
*
1701743 AATTAATATTT
1 AATTTATATTT
1701754 TATTTAAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
27 8 0.14
28 21 0.38
29 27 0.48
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (29 bp):
AATTTATATTTAAATAAATTTTAAATATA
Found at i:1701732 original size:28 final size:27
Alignment explanation
Indices: 1701700--1701756 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1701690 TTATATTTAA
*
1701700 ATAAA-TTTTAAATATAAATTATTATTTT
1 ATAAACTTTT-AATA-AAATTAATATTTT
1701728 ATAAACTTTTAATAAAATTAATATTTT
1 ATAAACTTTTAATAAAATTAATATTTT
1701755 AT
1 AT
1701757 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 14 0.52
28 9 0.33
29 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
ATAAACTTTTAATAAAATTAATATTTT
Found at i:1701753 original size:27 final size:28
Alignment explanation
Indices: 1701673--1701756 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 28
1701663 TGTATTAAAA
* * * * *
1701673 AAATTTTAATTTTTAATTTATATTTAAAT
1 AAATTTTAAATATAAATTAATATTT-TAT
*
1701702 AAATTTTAAATATAAATTATTATTTTAT
1 AAATTTTAAATATAAATTAATATTTTAT
1701730 AAACTTTT-AATA-AAATTAATATTTTAT
1 AAA-TTTTAAATATAAATTAATATTTTAT
1701757 TTAAAATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
27 14 0.30
28 9 0.19
29 24 0.51
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (28 bp):
AAATTTTAAATATAAATTAATATTTTAT
Found at i:1701801 original size:16 final size:16
Alignment explanation
Indices: 1701753--1701801 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1701743 AATTAATATT
*
1701753 TTATTTAAAATAAATA
1 TTATTTAAAATAAAAA
**
1701769 CAATTTAAAAGATAAAAA
1 TTATTT-AAA-ATAAAAA
1701787 TTATTTAAAATAAAA
1 TTATTTAAAATAAAA
1701802 TAAAAGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 10 0.38
17 6 0.23
18 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
TTATTTAAAATAAAAA
Found at i:1702026 original size:73 final size:73
Alignment explanation
Indices: 1701896--1702033 Score: 177
Period size: 73 Copynumber: 1.9 Consensus size: 73
1701886 TGCGGTACTA
* * * * *
1701896 AATCAATCTCCCAAATTGACGAGAAGCTTGCTTAATATTAATGGTACCAACAGTATTGGAAGTTG
1 AATCAATCTCCCAAATTGACGAGAAGCTTCCATAACATTAATGGCACCAACAATATTGGAAGTTG
1701961 TGTTACCC
66 TGTTACCC
** ** * *
1701969 AATCAATCTCCCAAATTGACGAGAAGCTTCCATGCCATTAATGGCGTCGACAATATTGGAGGTTG
1 AATCAATCTCCCAAATTGACGAGAAGCTTCCATAACATTAATGGCACCAACAATATTGGAAGTTG
1702034 CAATGCATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
73 54 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (73 bp):
AATCAATCTCCCAAATTGACGAGAAGCTTCCATAACATTAATGGCACCAACAATATTGGAAGTTG
TGTTACCC
Found at i:1704569 original size:21 final size:22
Alignment explanation
Indices: 1704545--1704585 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1704535 ATATATATAT
*
1704545 ATATAAATTA-TTAATAAAATC
1 ATATAAATAATTTAATAAAATC
*
1704566 ATATTAATAATTTAATAAAA
1 ATATAAATAATTTAATAAAA
1704586 AAGTAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATAAATAATTTAATAAAATC
Found at i:1704711 original size:33 final size:35
Alignment explanation
Indices: 1704643--1704724 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 35
1704633 TGTAGTTATT
*
1704643 TTATAT-ATATATATTTTTTAACATTTTAATATAA
1 TTATATAATTTATATTTTTTAACATTTTAATATAA
* *
1704677 TTATATAATTTAT-TTTTTTAACA-TTTATTTTAA
1 TTATATAATTTATATTTTTTAACATTTTAATATAA
1704710 TTAT-TAATTTTATAT
1 TTATATAA-TTTATAT
1704725 ATATATTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 3 0.07
33 17 0.40
34 17 0.40
35 5 0.12
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (35 bp):
TTATATAATTTATATTTTTTAACATTTTAATATAA
Found at i:1707444 original size:2 final size:2
Alignment explanation
Indices: 1707431--1707484 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
1707421 CATTCCCCTT
*
1707431 TA TA TA -A T- TA TA TA T- TA TA TA T- TA TA GA TA TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1707467 TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1707485 GAAGTGATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
1 7 0.16
2 36 0.84
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1707468 original size:19 final size:22
Alignment explanation
Indices: 1707431--1707484 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
1707421 CATTCCCCTT
1707431 TATATA-ATTATATATTATA-TA
1 TATATAGA-TATATATTATATTA
1707452 T-TATAGATATA-ATTATATTA
1 TATATAGATATATATTATATTA
*
1707472 TATATATATATAT
1 TATATAGATATAT
1707485 GAAGTGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 6 0.21
20 11 0.39
21 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATATAGATATATATTATATTA
Found at i:1707940 original size:15 final size:15
Alignment explanation
Indices: 1707906--1707944 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1707896 ATTTATATTA
* *
1707906 TATTTAT-ATATTTT
1 TATTTATAATAATTG
1707920 TATTTATAATAATTG
1 TATTTATAATAATTG
1707935 TATTTATAAT
1 TATTTATAAT
1707945 GTATTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTTATAATAATTG
Found at i:1708038 original size:10 final size:10
Alignment explanation
Indices: 1708023--1708056 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1708013 GAATTTATTT
1708023 TTTTATTATA
1 TTTTATTATA
1708033 TTTTATTATA
1 TTTTATTATA
*
1708043 TTTTAAT-TA
1 TTTTATTATA
1708052 TTTTA
1 TTTTA
1708057 ATATTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTATTATA
Found at i:1708670 original size:30 final size:28
Alignment explanation
Indices: 1708639--1708702 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
1708629 TTAATTTTAT
* *
1708639 TTTTTAAAAAATTTATATTAAATTAATTA
1 TTTTTAAAAAATTTA-ATAAAAATAATTA
**
1708668 TTTTTATGAAATTTAATAAAAATAATTAA
1 TTTTTAAAAAATTTAATAAAAATAATT-A
1708697 TTTTTA
1 TTTTTA
1708703 TCATTTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
TTTTTAAAAAATTTAATAAAAATAATTA
Found at i:1708694 original size:28 final size:30
Alignment explanation
Indices: 1708647--1708703 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1708637 ATTTTTTAAA
* *
1708647 AAATTTATATTAAATTAATT-ATTTTTATG
1 AAATTTATATAAAAATAATTAATTTTTATG
1708676 AAATTTA-ATAAAAATAATTAATTTTTAT
1 AAATTTATATAAAAATAATTAATTTTTAT
1708704 CATTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
AAATTTATATAAAAATAATTAATTTTTATG
Found at i:1709455 original size:27 final size:28
Alignment explanation
Indices: 1709424--1709508 Score: 90
Period size: 27 Copynumber: 3.2 Consensus size: 28
1709414 TTCAATTTTA
1709424 AAATTTTAAAAATTAATTAAATTAAAT-
1 AAATTTTAAAAATTAATTAAATTAAATC
* * *
1709451 AAATTTAAAAAATTAATCACATT-AATC
1 AAATTTTAAAAATTAATTAAATTAAATC
*
1709478 GAATTTTATAAAA--AATTAAATT-AATC
1 AAATTTTA-AAAATTAATTAAATTAAATC
1709504 AAATT
1 AAATT
1709509 AAAATTAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
26 18 0.38
27 26 0.54
28 4 0.08
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (28 bp):
AAATTTTAAAAATTAATTAAATTAAATC
Found at i:1709626 original size:2 final size:2
Alignment explanation
Indices: 1709619--1709658 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
1709609 AGTATGATTA
1709619 AT AT AT AT AT AT AT AT AT AT -T AT GAT -T A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
1709659 GTAATTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.09
2 29 0.85
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1711322 original size:13 final size:12
Alignment explanation
Indices: 1711275--1711322 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
1711265 ATTACTTTAA
1711275 TAATATTATATT
1 TAATATTATATT
*
1711287 TATATAATCATATT
1 TA-AT-ATTATATT
1711301 TAATATTATATAT
1 TAATATTATAT-T
*
1711314 TAATGTTAT
1 TAATATTAT
1711323 TATCAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 8 0.27
13 13 0.43
14 9 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (12 bp):
TAATATTATATT
Found at i:1712710 original size:22 final size:22
Alignment explanation
Indices: 1712663--1712704 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1712653 AACATGATTT
1712663 ATATAAAAATTTAATTATAAAA
1 ATATAAAAATTTAATTATAAAA
1712685 ATATAAAAA-TTAA-TATAAAA
1 ATATAAAAATTTAATTATAAAA
1712705 TAATATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 4 0.20
22 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATAAAAATTTAATTATAAAA
Found at i:1714515 original size:14 final size:13
Alignment explanation
Indices: 1714492--1714525 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
1714482 ACTTTGTCCG
1714492 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
1714505 AAAAAAGAAAAAGA
1 AAAAAA-AAAAAGA
1714519 AAAAAAA
1 AAAAAAA
1714526 TCCAATGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:1730309 original size:16 final size:16
Alignment explanation
Indices: 1730288--1730318 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1730278 AATTTAAGAT
*
1730288 TTAAATTTTATATTTA
1 TTAAATATTATATTTA
1730304 TTAAATATTATATTT
1 TTAAATATTATATTT
1730319 TAAAAAAAAT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAAATATTATATTTA
Found at i:1731540 original size:23 final size:23
Alignment explanation
Indices: 1731513--1731567 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1731503 CGGAGAAAAA
1731513 GATGGCTGAACTGATGCAAAAGG
1 GATGGCTGAACTGATGCAAAAGG
1731536 GATGGCTGAACTGATGCAAAAGG
1 GATGGCTGAACTGATGCAAAAGG
*
1731559 AATGGCTGA
1 GATGGCTGA
1731568 CTCCCTTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.35, T:0.18
Consensus pattern (23 bp):
GATGGCTGAACTGATGCAAAAGG
Found at i:1733061 original size:2 final size:2
Alignment explanation
Indices: 1733054--1733082 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1733044 CTTTTTATTT
1733054 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1733083 TTCTTATCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1733262 original size:10 final size:10
Alignment explanation
Indices: 1733247--1733287 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1733237 ATTAGTATTT
1733247 TTTTATAATA
1 TTTTATAATA
1733257 TTTTAT-ATA
1 TTTTATAATA
1733266 TTTATATAA-A
1 TTT-TATAATA
*
1733276 TTTTATTATA
1 TTTTATAATA
1733286 TT
1 TT
1733288 AATAATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 10 0.37
10 16 0.59
11 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTATAATA
Found at i:1733269 original size:18 final size:18
Alignment explanation
Indices: 1733248--1733321 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 18
1733238 TTAGTATTTT
1733248 TTTATAATATTTTATATA
1 TTTATAATATTTTATATA
*
1733266 TTTATATAAATTTTAT-TA
1 TTTATA-ATATTTTATATA
* *
1733284 TAT-TAATAATTTATAT-
1 TTTATAATATTTTATATA
*
1733300 TATATAA-ATTTTAATATA
1 TTTATAATATTTT-ATATA
1733318 TTTA
1 TTTA
1733322 AAAATTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
16 14 0.31
17 10 0.22
18 13 0.29
19 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTATAATATTTTATATA
Found at i:1733286 original size:14 final size:14
Alignment explanation
Indices: 1733267--1733318 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
1733257 TTTTATATAT
1733267 TTATATAAATTTTA
1 TTATATAAATTTTA
1733281 TTATATTAATAATTTATA
1 TTATA-T-A-AATTT-TA
1733299 TTATATAAATTTTA
1 TTATATAAATTTTA
*
1733313 ATATAT
1 TTATAT
1733319 TTAAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 12 0.36
15 6 0.18
16 2 0.06
17 6 0.18
18 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:1733328 original size:18 final size:17
Alignment explanation
Indices: 1733256--1733328 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 17
1733246 TTTTTATAAT
1733256 ATTTTATATATTTATATAA
1 ATTTTATATATTTA-A-AA
*
1733275 ATTTTAT-TATATTAATA
1 ATTTTATATAT-TTAAAA
* *
1733292 A-TTTATAT-TATATAA
1 ATTTTATATATTTAAAA
1733307 ATTTTAATATATTTAAAA
1 ATTTT-ATATATTTAAAA
1733325 ATTT
1 ATTT
1733329 ATTATTTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
15 4 0.09
16 9 0.21
17 7 0.16
18 13 0.30
19 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATATTTAAAA
Found at i:1733328 original size:33 final size:33
Alignment explanation
Indices: 1733262--1733335 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 33
1733252 TAATATTTTA
* *
1733262 TATATTTATATAAATTTTATTATATTAATAATT
1 TATATTTATATAAATTTTAATATATTAAAAATT
1733295 TATA-TTATATAAATTTTAATATATTTAAAAATT
1 TATATTTATATAAATTTTAATATA-TTAAAAATT
1733328 TATTATTT
1 TA-TATTT
1733336 TTATTATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 18 0.50
33 14 0.39
34 2 0.06
35 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TATATTTATATAAATTTTAATATATTAAAAATT
Found at i:1733576 original size:24 final size:25
Alignment explanation
Indices: 1733549--1733602 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
1733539 ATATATTTTG
*
1733549 ATTTATT-AT-TTTAAATTTATTAAT
1 ATTTATTAATATTT-AATTTATAAAT
*
1733573 ATTT-TTAATATTTTATTTATAAAT
1 ATTTATTAATATTTAATTTATAAAT
1733597 ATTTAT
1 ATTTAT
1733603 ATAAATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 2 0.08
24 19 0.76
25 4 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTATTAATATTTAATTTATAAAT
Found at i:1733675 original size:17 final size:18
Alignment explanation
Indices: 1733641--1733678 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1733631 AAAATTATAT
*
1733641 ATTTAAATA-AATAGAAA
1 ATTTAAATATTATAGAAA
*
1733658 ATTTAAATATTATAAAAA
1 ATTTAAATATTATAGAAA
1733676 ATT
1 ATT
1733679 AATATTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
ATTTAAATATTATAGAAA
Found at i:1733677 original size:25 final size:24
Alignment explanation
Indices: 1733631--1733677 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1733621 TTTATTAGAT
*
1733631 AAAATTATATATTTAAATAAATAG
1 AAAATTAAATATTTAAATAAATAG
1733655 AAAATTTAAATATTATAAA-AAAT
1 AAAA-TTAAATATT-TAAATAAAT
1733678 TAATATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 12 0.60
26 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAATTAAATATTTAAATAAATAG
Found at i:1734908 original size:2 final size:2
Alignment explanation
Indices: 1734901--1734928 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1734891 TGATACATAC
1734901 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
1734929 TTATGCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1736295 original size:15 final size:15
Alignment explanation
Indices: 1736275--1736304 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1736265 TTCATATAAT
1736275 TATTTTAAAAAATTA
1 TATTTTAAAAAATTA
*
1736290 TATTTTATAAAATTA
1 TATTTTAAAAAATTA
1736305 AAATTTTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAAAAATTA
Found at i:1736471 original size:3 final size:3
Alignment explanation
Indices: 1736463--1736514 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1736453 TAAATTAGAC
1736463 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1736511 ATT A
1 ATT A
1736515 CTCAGAATAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1738249 original size:22 final size:21
Alignment explanation
Indices: 1738222--1738274 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
1738212 ATATAATATG
* *
1738222 AAATATAATTATAAAATTAAA
1 AAATATAAATAAAAAATTAAA
1738243 TAAATATAAATAAAAAATTAAA
1 -AAATATAAATAAAAAATTAAA
1738265 AATATATAAA
1 AA-ATATAAA
1738275 ATTAAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATATAAATAAAAAATTAAA
Found at i:1739452 original size:19 final size:17
Alignment explanation
Indices: 1739424--1739476 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
1739414 TAAATATTAT
*
1739424 TATAATAAATTATGATAAA
1 TATAA-AAAATAT-ATAAA
1739443 TATAAAAAATATATAAA
1 TATAAAAAATATATAAA
*
1739460 AAT-AAAAATATA-AAA
1 TATAAAAAATATATAAA
1739475 TA
1 TA
1739477 ATAATCATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 4 0.13
16 9 0.29
17 7 0.23
18 6 0.19
19 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
TATAAAAAATATATAAA
Found at i:1739464 original size:23 final size:22
Alignment explanation
Indices: 1739438--1739480 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1739428 ATAAATTATG
*
1739438 ATAAATATAAAAAATATATAAAA
1 ATAAAAATAAAAAATA-ATAAAA
*
1739461 ATAAAAATATAAAATAATAA
1 ATAAAAATAAAAAATAATAA
1739481 TCATAAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAAAAATAAAAAATAATAAAA
Found at i:1739466 original size:16 final size:16
Alignment explanation
Indices: 1739447--1739480 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1739437 GATAAATATA
1739447 AAAAATATATAAA-AAT
1 AAAAATATA-AAATAAT
1739463 AAAAATATAAAATAAT
1 AAAAATATAAAATAAT
1739479 AA
1 AA
1739481 TCATAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATATAAAATAAT
Found at i:1740403 original size:28 final size:29
Alignment explanation
Indices: 1740372--1740428 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
1740362 ATTAAAATTT
* *
1740372 ATATTTTTATAATTACAT-ATAAATAAAA
1 ATATTTTTAAAATTAAATAATAAATAAAA
*
1740400 ATATTTTTAAAATTAAATAATAATTAAAA
1 ATATTTTTAAAATTAAATAATAAATAAAA
1740429 TCTTGTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATTTTTAAAATTAAATAATAAATAAAA
Found at i:1740820 original size:2 final size:2
Alignment explanation
Indices: 1740813--1740854 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1740803 GCCTCGAAGG
*
1740813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1740855 GAAGGATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1742850 original size:10 final size:10
Alignment explanation
Indices: 1742827--1742867 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
1742817 TCATATTTTT
1742827 AAATTTAA-A
1 AAATTTAATA
1742836 AAATTTAATA
1 AAATTTAATA
*
1742846 AAA-TTATTA
1 AAATTTAATA
1742855 AAATTTAATA
1 AAATTTAATA
1742865 AAA
1 AAA
1742868 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 16 0.57
10 12 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATTTAATA
Found at i:1742857 original size:19 final size:19
Alignment explanation
Indices: 1742835--1742872 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1742825 TTAAATTTAA
*
1742835 AAAATTTAATAAAATTATT
1 AAAATTTAATAAAAATATT
1742854 AAAATTTAATAAAAATATT
1 AAAATTTAATAAAAATATT
1742873 TTTAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTTAATAAAAATATT
Found at i:1743615 original size:12 final size:11
Alignment explanation
Indices: 1743602--1743648 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
1743592 AAAATATTTA
1743602 AAATATAATAT
1 AAATATAATAT
1743613 AAA-AT-A-A-
1 AAATATAATAT
1743620 AAA-ATAATATT
1 AAATATAATA-T
1743631 AAATATAATAT
1 AAATATAATAT
1743642 AAATATA
1 AAATATA
1743649 GAACATATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
7 5 0.16
8 2 0.06
9 2 0.06
10 2 0.06
11 14 0.45
12 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1743643 original size:17 final size:17
Alignment explanation
Indices: 1743600--1743648 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1743590 GAAAAATATT
1743600 TAAAATATAATATAAAA
1 TAAAATATAATATAAAA
* *
1743617 TAAAAAATAATATTAAA
1 TAAAATATAATATAAAA
*
1743634 TATAATATAAATATA
1 TAAAATAT-AATATA
1743649 GAACATATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATATAATATAAAA
Found at i:1745742 original size:15 final size:14
Alignment explanation
Indices: 1745719--1745748 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1745709 AAATTTTTAA
1745719 TATTAAATAAATAT
1 TATTAAATAAATAT
1745733 TATTATAATAAATAT
1 TATTA-AATAAATAT
1745748 T
1 T
1745749 TAATAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTAAATAAATAT
Found at i:1746719 original size:3 final size:3
Alignment explanation
Indices: 1746711--1746743 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1746701 GATCTCATTT
1746711 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1746744 TGTCTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1747012 original size:2 final size:2
Alignment explanation
Indices: 1747007--1747042 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1746997 TGTGAATTTA
1747007 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
1747043 CATGATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1748720 original size:21 final size:21
Alignment explanation
Indices: 1748683--1748722 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1748673 AGTTTTTATT
*
1748683 TAAATTTAATTATAAAATATA
1 TAAATTTAATTAAAAAATATA
1748704 TAAATATTAA-TAAAAAATA
1 TAAAT-TTAATTAAAAAATA
1748723 ATTTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAATTAAAAAATATA
Found at i:1756398 original size:92 final size:92
Alignment explanation
Indices: 1756241--1756425 Score: 361
Period size: 92 Copynumber: 2.0 Consensus size: 92
1756231 CTTGAGGACC
1756241 TGTATACACAAGAAATAACCAATACAAAATTAGGAACAAAACATCTCAACTTCCGCATACAACAT
1 TGTATACACAAGAAATAACCAATACAAAATTAGGAACAAAACATCTCAACTTCCGCATACAACAT
1756306 ACTAAAAATGCAATGAGTAATAAACAA
66 ACTAAAAATGCAATGAGTAATAAACAA
*
1756333 TGTATACACAAGAAATAACCAATACAAAATTAGGAACAAAACATCTCAACTTCCTCATACAACAT
1 TGTATACACAAGAAATAACCAATACAAAATTAGGAACAAAACATCTCAACTTCCGCATACAACAT
1756398 ACTAAAAATGCAATGAGTAATAAACAA
66 ACTAAAAATGCAATGAGTAATAAACAA
1756425 T
1 T
1756426 CTTAAGAACA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (92 bp):
TGTATACACAAGAAATAACCAATACAAAATTAGGAACAAAACATCTCAACTTCCGCATACAACAT
ACTAAAAATGCAATGAGTAATAAACAA
Found at i:1757927 original size:24 final size:27
Alignment explanation
Indices: 1757871--1757927 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 27
1757861 ATAGATATAA
1757871 TATTATTAATTTTTTAATTAATTAATTT
1 TATTA-TAATTTTTTAATTAATTAATTT
*
1757899 T-TTATAA-TTTTTAA-TAATT-TTTT
1 TATTATAATTTTTTAATTAATTAATTT
1757922 TATTAT
1 TATTAT
1757928 TTAAATTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 4 0.15
24 9 0.33
25 7 0.26
26 3 0.11
27 3 0.11
28 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TATTATAATTTTTTAATTAATTAATTT
Found at i:1758195 original size:37 final size:38
Alignment explanation
Indices: 1758149--1758246 Score: 98
Period size: 37 Copynumber: 2.7 Consensus size: 38
1758139 CACATTTTAT
*
1758149 TTTATTATTTA-AAATAATATTAAAATATAAA-AATTA
1 TTTATTATTTAGAAATAATATTAAAATAAAAATAATTA
* * *
1758185 TCTTAATATTTAGAATTAA-ATTTAAATAAAAATAATT-
1 T-TTATTATTTAGAAATAATATTAAAATAAAAATAATTA
*
1758222 TTTATTATTTATACAATAAT-TTAAA
1 TTTATTATTTAGA-AATAATATTAAA
1758247 TCAAAAAGAC
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
36 11 0.22
37 29 0.59
38 9 0.18
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (38 bp):
TTTATTATTTAGAAATAATATTAAAATAAAAATAATTA
Found at i:1758243 original size:36 final size:33
Alignment explanation
Indices: 1758148--1758253 Score: 95
Period size: 36 Copynumber: 2.9 Consensus size: 33
1758138 TCACATTTTA
*
1758148 TTTTATTATTTAAAATAATATTAAAATATAAAAAT
1 TTTTATTATTTAAAATAAT-TT-AAATAAAAAAAT
* *
1758183 TATCTTAATATTTAGAATTAAATTTAAATAAAAATAAT
1 T-T-TTATTATTTA-AAAT-AATTTAAATAAAAA-AAT
*
1758221 TTTTATTATTTATACAATAATTTAAATCAAAAA
1 TTTTATTATTTA-A-AATAATTTAAATAAAAAA
1758254 GACTCAAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
35 2 0.03
36 24 0.41
37 20 0.34
38 9 0.16
39 3 0.05
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (33 bp):
TTTTATTATTTAAAATAATTTAAATAAAAAAAT
Found at i:1760164 original size:15 final size:16
Alignment explanation
Indices: 1760139--1760172 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1760129 TTGAATATAA
1760139 ATATCATGTTTAATAT
1 ATATCATGTTTAATAT
*
1760155 ATAT-ATGTTTAATTT
1 ATATCATGTTTAATAT
1760170 ATA
1 ATA
1760173 AAAAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
ATATCATGTTTAATAT
Found at i:1761777 original size:28 final size:27
Alignment explanation
Indices: 1761727--1761779 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
1761717 TTATATTAGA
*
1761727 GTTAAAATTATATAAATTAAATTATGT
1 GTTAAAATTATATAAAATAAATTATGT
1761754 GTTAAATATTATATAAAA-ATAATTAT
1 GTTAAA-ATTATATAAAATA-AATTAT
1761780 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (27 bp):
GTTAAAATTATATAAAATAAATTATGT
Found at i:1762564 original size:16 final size:17
Alignment explanation
Indices: 1762545--1762578 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1762535 TTAAAAAATT
*
1762545 AATTATTTATT-ATAAA
1 AATTATTAATTAATAAA
1762561 AATTATTAATTAATAAA
1 AATTATTAATTAATAAA
1762578 A
1 A
1762579 TAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTATTAATTAATAAA
Found at i:1763183 original size:18 final size:19
Alignment explanation
Indices: 1763160--1763209 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1763150 GCCTTACATG
1763160 TTAAATTATAT-ATTTTAA
1 TTAAATTATATAATTTTAA
1763178 TTAAATT-TAATAATTTTAA
1 TTAAATTAT-ATAATTTTAA
*
1763197 ATAAA--ATATAATT
1 TTAAATTATATAATT
1763210 AATTACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.25
18 10 0.36
19 11 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATTATATAATTTTAA
Found at i:1763208 original size:20 final size:20
Alignment explanation
Indices: 1763171--1763213 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1763161 TAAATTATAT
* *
1763171 ATTTTAATTAAATTTAA-TA
1 ATTTTAATAAAATATAATTA
1763190 ATTTTAAATAAAATATAATTA
1 ATTTT-AATAAAATATAATTA
1763211 ATT
1 ATT
1763214 ACAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 10 0.50
21 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTAATAAAATATAATTA
Found at i:1763241 original size:11 final size:11
Alignment explanation
Indices: 1763221--1763310 Score: 63
Period size: 11 Copynumber: 8.7 Consensus size: 11
1763211 ATTACAAAAA
1763221 AAAT-TAATAT
1 AAATATAATAT
1763231 AAATATAATAT
1 AAATATAATAT
1763242 -AA-ATAATAT
1 AAATATAATAT
1763251 ATAATA-AAT-T
1 A-AATATAATAT
1763261 ATAATATAATAT
1 A-AATATAATAT
*
1763273 AAAT-TTATAAT
1 AAATATAAT-AT
*
1763284 AAATATATTA-
1 AAATATAATAT
*
1763294 AAAT-TTATAT
1 AAATATAATAT
1763304 -AATATAA
1 AAATATAA
1763311 ATTATTAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
9 13 0.20
10 22 0.34
11 24 0.38
12 5 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1763245 original size:21 final size:21
Alignment explanation
Indices: 1763221--1763339 Score: 70
Period size: 21 Copynumber: 5.5 Consensus size: 21
1763211 ATTACAAAAA
1763221 AAATTAATATAAATATAATAT
1 AAATTAATATAAATATAATAT
1763242 AAA-TAATATATAATA-AAT-T
1 AAATTAATATA-AATATAATAT
1763261 ATAATATAATATAAATTTATAATAAAT
1 A-AAT-TAATATAAA--TATAAT--AT
* * **
1763288 ATATTAAAATTTATATAATAT
1 AAATTAATATAAATATAATAT
1763309 AAATT-AT-TAATATATTAATAT
1 AAATTAATATAA-ATA-TAATAT
1763330 ATAA-TAATAT
1 A-AATTAATAT
1763340 TTAATAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
19 3 0.04
20 16 0.21
21 23 0.31
22 11 0.15
23 9 0.12
24 3 0.04
25 6 0.08
26 2 0.03
27 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTAATATAAATATAATAT
Found at i:1763271 original size:42 final size:40
Alignment explanation
Indices: 1763225--1763345 Score: 135
Period size: 42 Copynumber: 3.0 Consensus size: 40
1763215 CAAAAAAAAT
1763225 TAATATAAATATAATATAAATAATATATAATAAATTATAATA
1 TAATATAAATATAATAT-AATAATATATAATAAATT-TAATA
*
1763267 TAATATAAAT-T--TATAATAA-ATATATTAAAATTT-ATA
1 TAATATAAATATAATATAATAATATATAAT-AAATTTAATA
*
1763303 TAATATAAATTATTAATATATTAATATATAATAATATTTAATA
1 TAATATAAA-TA-TAATATAATAATATATAATAA-ATTTAATA
1763346 AATTTATTAA
Statistics
Matches: 67, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
36 12 0.18
37 8 0.12
38 10 0.15
39 4 0.06
41 10 0.15
42 20 0.30
43 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (40 bp):
TAATATAAATATAATATAATAATATATAATAAATTTAATA
Found at i:1763294 original size:67 final size:61
Alignment explanation
Indices: 1763223--1763356 Score: 144
Period size: 67 Copynumber: 2.1 Consensus size: 61
1763213 TACAAAAAAA
1763223 ATTAATATAAATATAATATAAATAATATATAATAAATT-ATAATATAATATAAATTTATAATAAA
1 ATTAATATAAATATAATATAAAT--TAT-TAATAAATTAAT-ATATAATA-AAA-TT-TAATAAA
1763287 TAT
59 TAT
* ** * * *
1763290 ATTAAAATTTATATAATATAAATTATTAATATATTAATATATAATAATATTTAATAAATTT
1 ATTAATATAAATATAATATAAATTATTAATAAATTAATATATAATAAAATTTAATAAATAT
1763351 ATTAAT
1 ATTAAT
1763357 CTTCATACTA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
61 14 0.24
62 2 0.03
63 2 0.03
64 16 0.27
65 5 0.08
67 20 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (61 bp):
ATTAATATAAATATAATATAAATTATTAATAAATTAATATATAATAAAATTTAATAAATAT
Found at i:1763334 original size:51 final size:55
Alignment explanation
Indices: 1763229--1763356 Score: 141
Period size: 53 Copynumber: 2.5 Consensus size: 55
1763219 AAAAATTAAT
* * *
1763229 ATAAATATAATATAAA-TAATAT-ATAATAAATTATAATATAATATAAATTTATA
1 ATAAATATATTATAAATTTATATAATAATAAATTATAATATAATATAAATATATA
1763282 ATAAATATATTA-AAATTTATATAAT-ATAAATTATTAATAT-AT-T-AATATATA
1 ATAAATATATTATAAATTTATATAATAATAAATTA-TAATATAATATAAATATATA
1763333 AT-AATAT-TTAATAAATTTAT-TAAT
1 ATAAATATATT-ATAAATTTATATAAT
1763357 CTTCATACTA
Statistics
Matches: 67, Mismatches: 3, Indels: 13
0.81 0.04 0.16
Matches are distributed among these distances:
49 2 0.03
50 10 0.15
51 17 0.25
52 4 0.06
53 26 0.39
54 8 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (55 bp):
ATAAATATATTATAAATTTATATAATAATAAATTATAATATAATATAAATATATA
Found at i:1769265 original size:13 final size:14
Alignment explanation
Indices: 1769244--1769276 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1769234 TAAATAGACA
1769244 TATATAATATATAT
1 TATATAATATATAT
1769258 TATA-AATATATAT
1 TATATAATATATAT
*
1769271 CATATA
1 TATATA
1769277 CAAGCATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAATATATAT
Found at i:1769490 original size:3 final size:3
Alignment explanation
Indices: 1769482--1769507 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1769472 GCATTCAAGG
1769482 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1769508 GGAAATTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1770597 original size:2 final size:2
Alignment explanation
Indices: 1770586--1770630 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1770576 TCCTTTCATT
*
1770586 TA TA -A TA TA TA TA TA T- TA TA TA TA TA TA TT 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
1770626 TA TA T
1 TA TA T
1770631 TGATTTAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1772569 original size:27 final size:31
Alignment explanation
Indices: 1772517--1772578 Score: 96
Period size: 28 Copynumber: 2.1 Consensus size: 31
1772507 TACTATAAAA
1772517 TTTTAAAAAATTAAAAAAATTAATAATT-AT
1 TTTTAAAAAATTAAAAAAATTAATAATTAAT
1772547 TTTTAAAAAA-T-AAAAAA-TAATAATTAAT
1 TTTTAAAAAATTAAAAAAATTAATAATTAAT
1772575 TTTT
1 TTTT
1772579 GTAATTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 8 0.26
28 12 0.39
29 1 0.03
30 10 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTAAAAAATTAAAAAAATTAATAATTAAT
Found at i:1772575 original size:31 final size:30
Alignment explanation
Indices: 1772517--1772578 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 30
1772507 TACTATAAAA
*
1772517 TTTTAAAAAATTAAAAAAATTAATAATTAT
1 TTTTAAAAAATTAAAAAAAATAATAATTAT
1772547 TTTTAAAAAA-T--AAAAAATAATAATTAAT
1 TTTTAAAAAATTAAAAAAAATAATAATT-AT
1772575 TTTT
1 TTTT
1772579 GTAATTATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 13 0.43
28 6 0.20
29 1 0.03
30 10 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TTTTAAAAAATTAAAAAAAATAATAATTAT
Found at i:1774760 original size:13 final size:13
Alignment explanation
Indices: 1774742--1774768 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1774732 AGAATTATAT
1774742 TTAATTTTTTTAA
1 TTAATTTTTTTAA
1774755 TTAATTTTTTTAA
1 TTAATTTTTTTAA
1774768 T
1 T
1774769 ATTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTAATTTTTTTAA
Found at i:1774976 original size:19 final size:19
Alignment explanation
Indices: 1774926--1774978 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1774916 ACTGCTGAGA
* *
1774926 TTTTATTGTATGTTTTATT
1 TTTTATTATATTTTTTATT
**
1774945 TTTTAAAATTATTTTTTATT
1 TTTTATTA-TATTTTTTATT
1774965 TTTTATTATATTTT
1 TTTTATTATATTTT
1774979 GAGAATAAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTATTATATTTTTTATT
Found at i:1775375 original size:2 final size:2
Alignment explanation
Indices: 1775368--1775397 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1775358 CTTGACCTAG
*
1775368 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1775398 GTTAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1775644 original size:14 final size:16
Alignment explanation
Indices: 1775614--1775646 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1775604 TTAATTCAAT
1775614 AAATTAATACATATAA
1 AAATTAATACATATAA
1775630 AAATTAAT-CAT-TAA
1 AAATTAATACATATAA
1775644 AAA
1 AAA
1775647 AAAGTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 3 0.18
16 8 0.47
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTAATACATATAA
Found at i:1775719 original size:2 final size:2
Alignment explanation
Indices: 1775712--1775746 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1775702 TGGCCAATAA
1775712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1775747 GTCAAAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1775909 original size:11 final size:11
Alignment explanation
Indices: 1775893--1775921 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1775883 ATTAAATAAA
1775893 TATATTTTTAT
1 TATATTTTTAT
1775904 TATATTTTTAT
1 TATATTTTTAT
1775915 TATATTT
1 TATATTT
1775922 AAAATTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:1776778 original size:16 final size:16
Alignment explanation
Indices: 1776731--1776802 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 16
1776721 TAATATCTTG
*
1776731 TTAATATTAAAAAAATAA
1 TTAA-ATTAATAAAAT-A
*
1776749 TATAATTTAA-AAAATA
1 T-TAAATTAATAAAATA
*
1776765 TTAAATTATTAAAATAA
1 TTAAATTAATAAAAT-A
*
1776782 TT-TATTAATAAAATA
1 TTAAATTAATAAAATA
1776797 -TAAATT
1 TTAAATT
1776803 TAAATAATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
14 1 0.02
15 10 0.23
16 17 0.39
17 8 0.18
18 5 0.11
19 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATTAATAAAATA
Found at i:1778742 original size:25 final size:26
Alignment explanation
Indices: 1778714--1778775 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
1778704 TATGATGTAT
1778714 ATTTAAATATAA-ATATAAAAATATA
1 ATTTAAATATAATATATAAAAATATA
*** *
1778739 ATTTTTTTA-AATATATAAAAATATT
1 ATTTAAATATAATATATAAAAATATA
1778764 ATATTAAATATA
1 AT-TTAAATATA
1778776 TATTCATATT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
24 2 0.07
25 20 0.74
26 4 0.15
27 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTAAATATAATATATAAAAATATA
Found at i:1778773 original size:22 final size:24
Alignment explanation
Indices: 1778723--1778777 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
1778713 TATTTAAATA
* *
1778723 TAAATATA-AAAATATAATTTTTT
1 TAAATATATAAAATATAATTATAT
1778746 TAAATATATAAAA-AT-ATTATAT
1 TAAATATATAAAATATAATTATAT
1778768 TAAATATATA
1 TAAATATATA
1778778 TTCATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 15 0.52
23 10 0.34
24 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAATATATAAAATATAATTATAT
Found at i:1779183 original size:21 final size:22
Alignment explanation
Indices: 1779143--1779194 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1779133 TCTTATATAA
*
1779143 TTATATTTAAAAAATTAATTAT
1 TTATATTTAAAAAATAAATTAT
*
1779165 TTATA-TTAAATAATAAATTAT
1 TTATATTTAAAAAATAAATTAT
*
1779186 TTATTTTTA
1 TTATATTTA
1779195 TTAATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATATTTAAAAAATAAATTAT
Found at i:1779212 original size:25 final size:25
Alignment explanation
Indices: 1779161--1779213 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1779151 AAAAAATTAA
*
1779161 TTATTTATATTAAATAATAAATTAT
1 TTATTTATATTAAATAATAAATGAT
* * * *
1779186 TTATTTTTATTAATTTATTAATGAT
1 TTATTTATATTAAATAATAAATGAT
1779211 TTA
1 TTA
1779214 ATAATAGATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTATTTATATTAAATAATAAATGAT
Found at i:1780236 original size:19 final size:19
Alignment explanation
Indices: 1780212--1780251 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1780202 TAATTCAATT
1780212 AAAATA-ATTTTAAGTATTA
1 AAAATATATTTTAA-TATTA
*
1780231 AAAATATTTTTTAATATTA
1 AAAATATATTTTAATATTA
1780250 AA
1 AA
1780252 TAAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
AAAATATATTTTAATATTA
Found at i:1780648 original size:2 final size:2
Alignment explanation
Indices: 1780641--1780668 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1780631 TATTTATAGA
1780641 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
1780669 GTATGAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1781533 original size:2 final size:2
Alignment explanation
Indices: 1781528--1781553 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1781518 ACATAGATAC
1781528 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
1781554 CCATACTATT
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:1782205 original size:2 final size:2
Alignment explanation
Indices: 1782198--1782222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1782188 AGGCAGCAAC
1782198 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1782223 CACTATGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1783647 original size:16 final size:16
Alignment explanation
Indices: 1783626--1783667 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1783616 TTTCGCTATA
1783626 TTCTCTACTCTG-ACTC
1 TTCTCT-CTCTGTACTC
*
1783642 TTCTCTCTGTGTACTC
1 TTCTCTCTCTGTACTC
1783658 TTCTCTCTCT
1 TTCTCTCTCT
1783668 CATCGATCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.07, C:0.36, G:0.07, T:0.50
Consensus pattern (16 bp):
TTCTCTCTCTGTACTC
Found at i:1788431 original size:13 final size:13
Alignment explanation
Indices: 1788413--1788437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1788403 ATGGACTTAT
1788413 AAAAATATTTTTA
1 AAAAATATTTTTA
1788426 AAAAATATTTTT
1 AAAAATATTTTT
1788438 TTTTATTTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAAATATTTTTA
Found at i:1789808 original size:29 final size:30
Alignment explanation
Indices: 1789750--1789808 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1789740 TAAAATATAC
* * *
1789750 ATAAATTTTTATATATTAATAATATGTATT
1 ATAAATTTTGACATATTAATAATATCTATT
*
1789780 ATAAATTTTGACATATTCAT-ATATCTATT
1 ATAAATTTTGACATATTAATAATATCTATT
1789809 TTATTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (30 bp):
ATAAATTTTGACATATTAATAATATCTATT
Found at i:1789840 original size:40 final size:40
Alignment explanation
Indices: 1789796--1789872 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
1789786 TTTGACATAT
* * * *
1789796 TCATATATCT-ATTTTATTTTTTTATTATTTTTATATCGTA
1 TCATAT-TCTAATTATATTTTTATATCATATTTATATCGTA
*
1789836 TCATATTTTAATTATATTTTTATATCATATTTATATC
1 TCATATTCTAATTATATTTTTATATCATATTTATATC
1789873 ATAGAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.06
40 29 0.94
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.62
Consensus pattern (40 bp):
TCATATTCTAATTATATTTTTATATCATATTTATATCGTA
Found at i:1789867 original size:13 final size:12
Alignment explanation
Indices: 1789834--1789875 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
1789824 TTTTATATCG
1789834 TATCATATTTTA
1 TATCATATTTTA
*
1789846 -ATTATATTTTTA
1 TATCATA-TTTTA
1789858 TATCATA-TTTA
1 TATCATATTTTA
1789869 TATCATA
1 TATCATA
1789876 GAATTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 16 0.62
12 5 0.19
13 5 0.19
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
TATCATATTTTA
Found at i:1793887 original size:18 final size:18
Alignment explanation
Indices: 1793861--1793905 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1793851 GCTGAAGCAC
*
1793861 CCAAGTCTTATTGGTTCT
1 CCAACTCTTATTGGTTCT
1793879 CCAACTCTTATTGGTTCT
1 CCAACTCTTATTGGTTCT
1793897 CCAACTCTT
1 CCAACTCTT
1793906 CTGATCAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (18 bp):
CCAACTCTTATTGGTTCT
Found at i:1796778 original size:105 final size:109
Alignment explanation
Indices: 1796574--1796771 Score: 302
Period size: 105 Copynumber: 1.9 Consensus size: 109
1796564 TATAATGATA
* *
1796574 TTTATTTCTTTTAATTATTTTATATAATATATATTTTAAAAAATCTTTTCACTCATTTAAAAAAA
1 TTTATTTCTTTTAATTATTTTATATAATATATATTTAAAAAAATCTTATCACTCATTT-AAAAAA
* *
1796639 AATTACCCTTTTTCTACCTAGTAACATTTAAAAAACCCTACCACT
65 AATTACCCTTTTTCTACCTACTAACATTAAAAAAACCCTACCACT
1796684 TTTATTTC-TTTAATTA-TTT-TAT-ATA-ATATTTAAAAAAATCTTATCACTCATTT-AAAAAA
1 TTTATTTCTTTTAATTATTTTATATAATATATATTTAAAAAAATCTTATCACTCATTTAAAAAAA
1796743 ATTACCCTTTTT-TACCTACTAACATTAAA
66 ATTACCCTTTTTCTACCTACTAACATTAAA
1796772 GGAAAAAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
102 15 0.18
103 18 0.21
105 26 0.31
106 3 0.04
107 3 0.04
108 3 0.04
109 8 0.10
110 8 0.10
ACGTcount: A:0.39, C:0.15, G:0.01, T:0.45
Consensus pattern (109 bp):
TTTATTTCTTTTAATTATTTTATATAATATATATTTAAAAAAATCTTATCACTCATTTAAAAAAA
ATTACCCTTTTTCTACCTACTAACATTAAAAAAACCCTACCACT
Done.