Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 97 of 105
Found at i:17364285 original size:41 final size:41
Alignment explanation
Indices: 17364224--17364485 Score: 407
Period size: 41 Copynumber: 6.4 Consensus size: 41
17364214 CAACTTAAAA
* * *
17364224 AAAAATAAATTACTCCTCTAAACAGAGGCACCACGATTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
* * *
17364265 GAAAGTAAATTGCTCATCTAAACAAAGGCACCACGACTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
*
17364306 AAAAGTAAATTGCTCTTCTAAACAGAGGCACCACGACTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
* * * * *
17364347 GAAAGTAAATTACTCCTCTAAGCAGAGGTACCATGACTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
17364388 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
17364429 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTG
1 AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTG
17364471 AAAAGTAAATTGCTC
1 AAAAGTAAATTGCTC
17364486 ATTGACAATC
Statistics
Matches: 200, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
41 181 0.90
42 19 0.09
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG
Found at i:17365499 original size:8 final size:8
Alignment explanation
Indices: 17365487--17365578 Score: 95
Period size: 8 Copynumber: 11.6 Consensus size: 8
17365477 TGAGTCCTCC
*
17365487 TTTTTCAC
1 TTTTTCAT
17365495 TTTTTC-T
1 TTTTTCAT
17365502 TTTTTCAT
1 TTTTTCAT
17365510 TTTTTCCAT
1 TTTTT-CAT
17365519 TTTTTCAT
1 TTTTTCAT
17365527 TTTTTCAT
1 TTTTTCAT
17365535 CATTTTT--T
1 --TTTTTCAT
17365543 TTATTT--T
1 TT-TTTCAT
17365550 TTTTTCAT
1 TTTTTCAT
*
17365558 TTTTTTAT
1 TTTTTCAT
17365566 TTTTTCAT
1 TTTTTCAT
17365574 TTTTT
1 TTTTT
17365579 TAAGCATAGT
Statistics
Matches: 74, Mismatches: 3, Indels: 14
0.81 0.03 0.15
Matches are distributed among these distances:
6 5 0.07
7 12 0.16
8 44 0.59
9 8 0.11
10 5 0.07
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:17365513 original size:9 final size:9
Alignment explanation
Indices: 17365501--17365579 Score: 83
Period size: 9 Copynumber: 8.7 Consensus size: 9
17365491 TCACTTTTTC
17365501 TTTTTTCAT
1 TTTTTTCAT
*
17365510 TTTTTCCA-
1 TTTTTTCAT
17365518 TTTTTTCAT
1 TTTTTTCAT
17365527 TTTTTCATCAT
1 TTTTT--TCAT
*
17365538 TTTTTTTATTT
1 TTTTTTCA--T
17365549 TTTTTTCAT
1 TTTTTTCAT
17365558 TTTTTT-A-
1 TTTTTTCAT
17365565 TTTTTTCAT
1 TTTTTTCAT
17365574 TTTTTT
1 TTTTTT
17365580 AAGCATAGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
7 6 0.10
8 9 0.15
9 27 0.46
11 17 0.29
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:17365579 original size:11 final size:11
Alignment explanation
Indices: 17365518--17365563 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 11
17365508 ATTTTTTCCA
17365518 TTTTTTCATTT
1 TTTTTTCATTT
**
17365529 TTTCATCA-TT
1 TTTTTTCATTT
17365539 TTTTTT-ATTT
1 TTTTTTCATTT
17365549 TTTTTTCATTT
1 TTTTTTCATTT
17365560 TTTT
1 TTTT
17365564 ATTTTTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.03
10 14 0.48
11 14 0.48
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:17368889 original size:8 final size:8
Alignment explanation
Indices: 17368860--17368898 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
17368850 AATTAAACTA
17368860 AATTTATT
1 AATTTATT
*
17368868 AGTTTGATTT
1 AATTT-A-TT
17368878 AATTTATT
1 AATTTATT
17368886 AATTTATT
1 AATTTATT
17368894 AATTT
1 AATTT
17368899 TAAATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 19 0.70
9 2 0.07
10 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (8 bp):
AATTTATT
Found at i:17368936 original size:13 final size:13
Alignment explanation
Indices: 17368920--17368944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17368910 TTTTATACAT
17368920 TATTTTAATATAA
1 TATTTTAATATAA
17368933 TATTTTAATATA
1 TATTTTAATATA
17368945 TTTAAACAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTTAATATAA
Found at i:17387701 original size:31 final size:31
Alignment explanation
Indices: 17387626--17387703 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
17387616 AAGTCAGCTC
* *
17387626 AAATATCTGAAATATCATATTAGATCAAATT
1 AAATATCTGAAATGTCATATTAGATCAAAGT
* * * *
17387657 AAATGTCTGAAATGTCATGTTTGATCAAGGT
1 AAATATCTGAAATGTCATATTAGATCAAAGT
*
17387688 AAATATCTAAAATGTC
1 AAATATCTGAAATGTC
17387704 TCTAATTATC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (31 bp):
AAATATCTGAAATGTCATATTAGATCAAAGT
Found at i:17392052 original size:10 final size:10
Alignment explanation
Indices: 17392037--17392066 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
17392027 ATTGAATTTT
17392037 TATATTTTAA
1 TATATTTTAA
17392047 TATATTTTAA
1 TATATTTTAA
17392057 T-TATTTTAA
1 TATATTTTAA
17392066 T
1 T
17392067 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:17392063 original size:9 final size:9
Alignment explanation
Indices: 17392039--17392068 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
17392029 TGAATTTTTA
17392039 TATTTTAAT
1 TATTTTAAT
17392048 ATATTTTAAT
1 -TATTTTAAT
17392058 TATTTTAAT
1 TATTTTAAT
17392067 TA
1 TA
17392069 ATAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:17392279 original size:25 final size:25
Alignment explanation
Indices: 17392233--17392281 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
17392223 CTAAAATTCA
*
17392233 ATTAAATTTAAATCAAATTTTAAAT
1 ATTAAATTTAAATCAAAGTTTAAAT
*
17392258 ATTAAATTTTAAAT-TAAGTTTAAA
1 ATTAAA-TTTAAATCAAAGTTTAAA
17392282 CTCAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTAAATTTAAATCAAAGTTTAAAT
Found at i:17393705 original size:58 final size:58
Alignment explanation
Indices: 17393643--17393915 Score: 444
Period size: 57 Copynumber: 4.7 Consensus size: 58
17393633 TTTTTTTTAG
* *
17393643 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTTTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
* *
17393701 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
*
17393758 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
* * *
17393816 GAAAAATTGATACTTTCAACTTTTCTCC-AAAAGTA-TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTC-CCTAAAAATATTTTTTTTGAAATTTATTTCTAA
17393873 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
17393916 TGGAACTTTT
Statistics
Matches: 197, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
56 2 0.01
57 103 0.52
58 90 0.46
59 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.45
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
Found at i:17393764 original size:115 final size:115
Alignment explanation
Indices: 17393643--17393915 Score: 510
Period size: 115 Copynumber: 2.4 Consensus size: 115
17393633 TTTTTTTTAG
* *
17393643 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTTTGAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGAGAAAAAT
17393708 TGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
66 TGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
17393758 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGAGAAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGAGAAAAAT
* *
17393823 TGATACTTTCAACTTTTCTCCAAAAGTATTTTTTGGAAATTTATTTCTAA
66 TGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
17393873 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTT
17393916 TGGAACTTTT
Statistics
Matches: 154, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 154 1.00
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.45
Consensus pattern (115 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGAGAAAAAT
TGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:17393983 original size:11 final size:10
Alignment explanation
Indices: 17393953--17394087 Score: 65
Period size: 11 Copynumber: 12.5 Consensus size: 10
17393943 AGAAAAATAG
17393953 AAAAATAAAA
1 AAAAATAAAA
*
17393963 AAAAAAAAAA
1 AAAAATAAAA
17393973 AAAAAGTAAAA
1 AAAAA-TAAAA
*
17393984 CAAAACTAAAA
1 -AAAAATAAAA
17393995 ATAAAATAAAGA
1 A-AAAATAAA-A
* *
17394007 TAAAAAGAATA
1 -AAAAATAAAA
**
17394018 TTAAATAAACCTA
1 AAAAATAAA---A
* *
17394031 ATATAATAAAT
1 A-AAAATAAAA
17394042 AAAAATAATAA
1 AAAAATAA-AA
* *
17394053 ATAAACAAAA
1 AAAAATAAAA
*
17394063 AAAATTCAAAA
1 AAAAAT-AAAA
17394074 AAAAA-AAAA
1 AAAAATAAAA
17394083 AAAAA
1 AAAAA
17394088 CCTGGAGCGG
Statistics
Matches: 92, Mismatches: 22, Indels: 23
0.67 0.16 0.17
Matches are distributed among these distances:
9 9 0.10
10 31 0.34
11 33 0.36
12 11 0.12
13 2 0.02
14 6 0.07
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:17393995 original size:7 final size:6
Alignment explanation
Indices: 17393953--17394084 Score: 50
Period size: 5 Copynumber: 22.8 Consensus size: 6
17393943 AGAAAAATAG
* * *
17393953 AAAAAT AAAAA- AAAAA- AAAAA- AAAAGT -AAAAC AAAACT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * * * ** *
17393997 -AAAAT AAAGAT AAAAA- GAATAT -TAAAT AAACCT -AATAT AATAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT
*
17394042 AAAAAT AATAAAT AAACAAA AAAAATT CAAAAA- AAAAA- AAAAA
1 AAAAAT AA-AAAT AAA-AAT AAAAA-T -AAAAAT AAAAAT AAAAA
17394085 AAACCTGGAG
Statistics
Matches: 95, Mismatches: 20, Indels: 23
0.69 0.14 0.17
Matches are distributed among these distances:
5 41 0.43
6 33 0.35
7 16 0.17
8 5 0.05
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:17394040 original size:18 final size:17
Alignment explanation
Indices: 17394006--17394063 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
17393996 TAAAATAAAG
* *
17394006 ATAAAAAGAAT-ATTAA
1 ATAAAAATAATAAATAA
**
17394022 ATAAACCTAATATAATAA
1 ATAAAAATAATA-AATAA
17394040 ATAAAAATAATAAATAA
1 ATAAAAATAATAAATAA
*
17394057 ACAAAAA
1 ATAAAAA
17394064 AAATTCAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 8 0.24
17 11 0.33
18 14 0.42
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (17 bp):
ATAAAAATAATAAATAA
Found at i:17394447 original size:19 final size:20
Alignment explanation
Indices: 17394403--17394449 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
17394393 GAACACCGGT
* *
17394403 GCCGGATTCTGGAAAAATTC
1 GCCGGAATCTGGAAAAATTA
*
17394423 GCCGGAATCTGG-AAATTTA
1 GCCGGAATCTGGAAAAATTA
17394442 GCCGGAAT
1 GCCGGAAT
17394450 TTCGCCGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (20 bp):
GCCGGAATCTGGAAAAATTA
Found at i:17394494 original size:20 final size:20
Alignment explanation
Indices: 17394450--17394497 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
17394440 TAGCCGGAAT
17394450 TTCGCCGGTTTCTGGGATTA
1 TTCGCCGGTTTCTGGGATTA
* *
17394470 GTCGCCGGTTTCTGGGATTC
1 TTCGCCGGTTTCTGGGATTA
17394490 TTCGCCGG
1 TTCGCCGG
17394498 AAACTGGGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.06, C:0.25, G:0.33, T:0.35
Consensus pattern (20 bp):
TTCGCCGGTTTCTGGGATTA
Found at i:17395051 original size:3 final size:3
Alignment explanation
Indices: 17395045--17395078 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
17395035 ATAAAAAAAG
17395045 ATA ATA ATA ATA ATA A-A TATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA A
17395079 ATATATAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 27 0.93
4 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17395066 original size:18 final size:18
Alignment explanation
Indices: 17395045--17395083 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
17395035 ATAAAAAAAG
17395045 ATAATAATAATAATAAAT
1 ATAATAATAATAATAAAT
17395063 ATAATAATAATAATAAAT
1 ATAATAATAATAATAAAT
17395081 ATA
1 ATA
17395084 TAACTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATAATAATAATAAAT
Found at i:17397669 original size:19 final size:20
Alignment explanation
Indices: 17397634--17397671 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
17397624 TAGGGAAATG
17397634 ATGATTGCTGGGAAAGCTGT
1 ATGATTGCTGGGAAAGCTGT
*
17397654 ATGATT-CTGTGAAAGCTG
1 ATGATTGCTGGGAAAGCTG
17397672 GGTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.32
Consensus pattern (20 bp):
ATGATTGCTGGGAAAGCTGT
Found at i:17402816 original size:11 final size:12
Alignment explanation
Indices: 17402789--17402825 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
17402779 GATACGGTTT
17402789 AAAATTATAATA
1 AAAATTATAATA
17402801 AAAATTAT-ATA
1 AAAATTATAATA
*
17402812 TAAATT-TAATA
1 AAAATTATAATA
17402823 AAA
1 AAA
17402826 TAAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 1 0.05
11 13 0.59
12 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAATTATAATA
Found at i:17405291 original size:15 final size:15
Alignment explanation
Indices: 17405271--17405304 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
17405261 ATAATATAGC
*
17405271 ATAAAAATTATATAA
1 ATAAAAATTATAAAA
17405286 ATAAAAATTATAAAA
1 ATAAAAATTATAAAA
17405301 ATAA
1 ATAA
17405305 TATAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAAAAATTATAAAA
Found at i:17405339 original size:24 final size:24
Alignment explanation
Indices: 17405271--17405349 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 24
17405261 ATAATATAGC
*
17405271 ATAAAAATTATATAAATAAAAATT-
1 ATAAAAA-TATATAAATAAAATTTA
*
17405295 ATAAAAATAATATAATTTAAAATTTTA
1 ATAAAAAT-ATATAA-ATAAAA-TTTA
17405322 ATAAAAAT-TATAAAT-AAATTTA
1 ATAAAAATATATAAATAAAATTTA
17405344 ATAAAA
1 ATAAAA
17405350 TTTAAAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.21
23 4 0.08
24 14 0.29
25 10 0.21
26 2 0.04
27 8 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAAAATATATAAATAAAATTTA
Found at i:17406751 original size:24 final size:25
Alignment explanation
Indices: 17406701--17406758 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
17406691 GAATTCGAAC
17406701 TTAAATATAAATAATTAAAATTTTT
1 TTAAATATAAATAATTAAAATTTTT
*
17406726 TTAAATATAAA-AATTAAATTTATTT
1 TTAAATATAAATAATTAAAATT-TTT
*
17406751 TTACATAT
1 TTAAATAT
17406759 TAATCAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TTAAATATAAATAATTAAAATTTTT
Found at i:17408943 original size:31 final size:30
Alignment explanation
Indices: 17408858--17408983 Score: 91
Period size: 30 Copynumber: 4.2 Consensus size: 30
17408848 ACTATTTATC
** *
17408858 AATTAAATTTTTGATA-TT-TTATTATAATT
1 AATTAAATTTTAAATATTTATTTTTA-AATT
* *
17408887 AATTAAGTTTTAAAAATTT-TATTTTAAATT
1 AATTAAATTTTAAATATTTAT-TTTTAAATT
* *
17408917 AATTGAACTTTTAAATATTTATTTTT-ACTT
1 AATT-AAATTTTAAATATTTATTTTTAAATT
* * *
17408947 AATTAAAATTTTATATATCTATTTTT-ATTT
1 AATT-AAATTTTAAATATTTATTTTTAAATT
17408977 AATTAAA
1 AATTAAA
17408984 CTATCGATTA
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
29 15 0.19
30 43 0.54
31 21 0.26
32 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
AATTAAATTTTAAATATTTATTTTTAAATT
Found at i:17408959 original size:30 final size:30
Alignment explanation
Indices: 17408882--17408983 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 30
17408872 TATTTTATTA
* *
17408882 TAATTAATT-AAGTTTTAAAAATTTTATTTT
1 TAATTAATTAAAATTTTAAATA-TTTATTTT
* * *
17408912 AAATTAATTGAACTTTTAAATATTTATTTT
1 TAATTAATTAAAATTTTAAATATTTATTTT
* * *
17408942 TACTTAATTAAAATTTTATATATCTATTTT
1 TAATTAATTAAAATTTTAAATATTTATTTT
*
17408972 TATTTAATTAAA
1 TAATTAATTAAA
17408984 CTATCGATTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
30 51 0.84
31 10 0.16
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (30 bp):
TAATTAATTAAAATTTTAAATATTTATTTT
Found at i:17417722 original size:14 final size:15
Alignment explanation
Indices: 17417703--17417733 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
17417693 TCCTCTTTGG
17417703 AATAAA-ACAAAAAT
1 AATAAATACAAAAAT
17417717 AATAAATACAAAAAT
1 AATAAATACAAAAAT
17417732 AA
1 AA
17417734 CAATTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAATACAAAAAT
Found at i:17423655 original size:30 final size:30
Alignment explanation
Indices: 17423615--17423680 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
17423605 TATTTTTTAT
* *
17423615 ATAATTAA-TTTTAAATGTAATATGTAATAA
1 ATAAATAATTTTTAAATATAATAT-TAATAA
* *
17423645 ATAAATAATTTTTAAATATTATATTAATTA
1 ATAAATAATTTTTAAATATAATATTAATAA
17423675 ATAAAT
1 ATAAAT
17423681 GTATAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
ATAAATAATTTTTAAATATAATATTAATAA
Found at i:17423677 original size:34 final size:32
Alignment explanation
Indices: 17423639--17423702 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
17423629 ATGTAATATG
17423639 TAATAAATAAATAATTTTTAAATATTATATTAAT
1 TAATAAATAAATAA--TTTAAATATTATATTAAT
** *
17423673 TAATAAATGTATAATTTAAATATTTTATTA
1 TAATAAATAAATAATTTAAATATTATATTA
17423703 TATTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 15 0.56
34 12 0.44
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (32 bp):
TAATAAATAAATAATTTAAATATTATATTAAT
Found at i:17425070 original size:2 final size:2
Alignment explanation
Indices: 17425057--17425088 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17425047 ACAGCAGTAC
*
17425057 TA TA TC 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
17425089 ATGTCTGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17429025 original size:14 final size:13
Alignment explanation
Indices: 17428993--17429038 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
17428983 TCTCTGACTC
*
17428993 AATTTATTTTTTA
1 AATTAATTTTTTA
17429006 AGATTAATATTTTTA
1 A-ATTAAT-TTTTTA
17429021 AATTAATTTTTT-
1 AATTAATTTTTTA
17429033 AATTAA
1 AATTAA
17429039 ATCGAGTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 6 0.20
13 6 0.20
14 11 0.37
15 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
AATTAATTTTTTA
Found at i:17429164 original size:19 final size:18
Alignment explanation
Indices: 17429140--17429180 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
17429130 TTTAATAATT
17429140 TATTTAATTATATATATTA
1 TATTTAATTATATAT-TTA
17429159 TATTTAATTATATATTTA
1 TATTTAATTATATATTTA
17429177 TATT
1 TATT
17429181 AAAAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTAATTATATATTTA
Found at i:17431181 original size:62 final size:61
Alignment explanation
Indices: 17431113--17431353 Score: 237
Period size: 60 Copynumber: 4.0 Consensus size: 61
17431103 TATTCAAGAC
* **
17431113 TTTTTTTTACCAAAAA-AGTCTTAAATAATTTCATTGAAAAAAATATTAGAGATTATTTAAGG
1 TTTTTTTTACCAAAAACACT-TTAAATAATTTCATTTTAAAAAA-ATTAGAGATTATTTAAGG
*
17431175 TATTTTTTACTC-AAAACACTTTAAATAA-TTCA-TTTAAAAAAATTAGAGATT-TTTAAGTCG
1 TTTTTTTTAC-CAAAAACACTTTAAATAATTTCATTTTAAAAAAATTAGAGATTATTTAAG--G
* * * *
17431235 TTTTTTTTATCAAAAACACTTTAAATGATATC--TTTCAAAAAATTGAAGAGTATTATTTAAGG
1 TTTTTTTTACCAAAAACACTTTAAATAATTTCATTTTAAAAAAATT--AGAG-ATTATTTAAGG
* * * **
17431297 TTTTTTTTACTAAAAATACCTTAAAT-ATTTTTTTTTAAAAAAATTAGAGATTATTTA
1 TTTTTTTTACCAAAAACACTTTAAATAATTTCATTTTAAAAAAATTAGAGATTATTTA
17431354 TAATAATCCC
Statistics
Matches: 151, Mismatches: 16, Indels: 26
0.78 0.08 0.13
Matches are distributed among these distances:
58 6 0.04
59 11 0.07
60 50 0.33
61 13 0.09
62 48 0.32
63 17 0.11
64 6 0.04
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (61 bp):
TTTTTTTTACCAAAAACACTTTAAATAATTTCATTTTAAAAAAATTAGAGATTATTTAAGG
Found at i:17432363 original size:16 final size:16
Alignment explanation
Indices: 17432344--17432378 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17432334 CATATATTTT
*
17432344 TTATTTTATATTTAGA
1 TTATATTATATTTAGA
*
17432360 TTATATTATATTTCGA
1 TTATATTATATTTAGA
17432376 TTA
1 TTA
17432379 AAATTTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (16 bp):
TTATATTATATTTAGA
Found at i:17434263 original size:11 final size:11
Alignment explanation
Indices: 17434243--17434282 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
17434233 AATTATAATT
*
17434243 TAAAAATTATA
1 TAAAATTTATA
* *
17434254 TGAAATTTATT
1 TAAAATTTATA
17434265 TAAAATTTATA
1 TAAAATTTATA
17434276 TAAAATT
1 TAAAATT
17434283 CACATTTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (11 bp):
TAAAATTTATA
Found at i:17434265 original size:22 final size:22
Alignment explanation
Indices: 17434240--17434282 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17434230 ATTAATTATA
*
17434240 ATTTAAAAATTATATGAAATTT
1 ATTTAAAAATTATATAAAATTT
*
17434262 ATTTAAAATTTATATAAAATT
1 ATTTAAAAATTATATAAAATT
17434283 CACATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTAAAAATTATATAAAATTT
Found at i:17434780 original size:25 final size:24
Alignment explanation
Indices: 17434723--17434834 Score: 91
Period size: 25 Copynumber: 4.4 Consensus size: 24
17434713 GAAATTTAAA
17434723 ATAA-TAATAAAATATTATTATAATT
1 ATAATTAA-AAAAT-TTATTATAATT
*
17434748 ATGATTAAAAAATTTATTATAATT
1 ATAATTAAAAAATTTATTATAATT
* *
17434772 ATAATTTAAAAAATTTAATAAAAATT
1 ATAA-TTAAAAAATTT-ATTATAATT
* *
17434798 TTATATTAAATAAATTTTATTAAAATT
1 ATA-ATTAAA-AAA-TTTATTATAATT
*
17434825 AATATTTAAA
1 -ATAATTAAA
17434835 TTTAATTGAT
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
24 14 0.19
25 19 0.26
26 17 0.24
27 17 0.24
28 5 0.07
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (24 bp):
ATAATTAAAAAATTTATTATAATT
Found at i:17434807 original size:14 final size:14
Alignment explanation
Indices: 17434777--17434822 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
17434767 TAATTATAAT
17434777 TTAAAAAATTTA-A
1 TTAAAAAATTTATA
*
17434790 -TAAAAATTTTATA
1 TTAAAAAATTTATA
17434803 TTAAATAAATTT-TA
1 TTAAA-AAATTTATA
17434817 TTAAAA
1 TTAAAA
17434823 TTAATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 10 0.36
13 2 0.07
14 11 0.39
15 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAAATTTATA
Found at i:17434822 original size:27 final size:26
Alignment explanation
Indices: 17434746--17434824 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
17434736 ATTATTATAA
*
17434746 TTATGATTAAAAAA-TTTATTATAATT
1 TTAT-ATTAAAAAATTTTATTAAAATT
* * *
17434772 ATA-ATTTAAAAAATTTAATAAAAATT
1 TTATA-TTAAAAAATTTTATTAAAATT
17434798 TTATATTAAATAAATTTTATTAAAATT
1 TTATATTAAA-AAATTTTATTAAAATT
17434825 AATATTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
24 1 0.02
25 8 0.19
26 18 0.43
27 15 0.36
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
TTATATTAAAAAATTTTATTAAAATT
Found at i:17437070 original size:30 final size:30
Alignment explanation
Indices: 17437034--17437095 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
17437024 ATTAAGATTA
17437034 ATTATGATAA-AATTAAAAATAATTATTATT
1 ATTATGATAATAATTAAAAA-AATTATTATT
17437064 ATTATGATAATTGTAATTAAAAAAATTATTAT
1 ATTATGATAA---TAATTAAAAAAATTATTAT
17437096 AATTGAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 10 0.36
33 9 0.32
34 9 0.32
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (30 bp):
ATTATGATAATAATTAAAAAAATTATTATT
Found at i:17437091 original size:24 final size:25
Alignment explanation
Indices: 17437064--17437116 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
17437054 AATTATTATT
* *
17437064 ATTATGATAATTGTAAT-TAAAAAA
1 ATTATGATAATTGAAATCGAAAAAA
*
17437088 ATTATTATAATTGAAATCGAAAAAA
1 ATTATGATAATTGAAATCGAAAAAA
17437113 ATTA
1 ATTA
17437117 ATAAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.36
Consensus pattern (25 bp):
ATTATGATAATTGAAATCGAAAAAA
Found at i:17448914 original size:54 final size:54
Alignment explanation
Indices: 17448855--17448958 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
17448845 TATATTTAAA
* *
17448855 TGATGATTTAAAAAGTATTTAGAAATAAGGAACACAAGATAATGGAGATGTAAC
1 TGATGATTTAAAAAGCATTTAGAAATAAGGAACACAAAATAATGGAGATGTAAC
* * ***
17448909 TGATGATTTAAAATGCATTTGGAAATGTTGAACACAAAATAATGGAGATG
1 TGATGATTTAAAAAGCATTTAGAAATAAGGAACACAAAATAATGGAGATG
17448959 AACCCAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (54 bp):
TGATGATTTAAAAAGCATTTAGAAATAAGGAACACAAAATAATGGAGATGTAAC
Found at i:17451062 original size:17 final size:16
Alignment explanation
Indices: 17451040--17451085 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
17451030 GTTTATGTGC
17451040 AAAGAAAAAAAATAGAA
1 AAAGAAAAAAAA-AGAA
*
17451057 AAAGAAAAAGAAAATAA
1 AAAGAAAAA-AAAAGAA
17451074 AAAGCAAAAAAA
1 AAAG-AAAAAAA
17451086 GGAATTCTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.83, C:0.02, G:0.11, T:0.04
Consensus pattern (16 bp):
AAAGAAAAAAAAAGAA
Found at i:17470140 original size:13 final size:15
Alignment explanation
Indices: 17470120--17470161 Score: 61
Period size: 13 Copynumber: 2.9 Consensus size: 15
17470110 TGTTTATTTT
17470120 ATATTTTAATAAA-A
1 ATATTTTAATAAAGA
17470134 A-ATTTTAATAAATGA
1 ATATTTTAATAAA-GA
17470149 ATATTTTAATAAA
1 ATATTTTAATAAA
17470162 TTAAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.44
14 1 0.04
15 2 0.08
16 11 0.44
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATATTTTAATAAAGA
Found at i:17470156 original size:16 final size:15
Alignment explanation
Indices: 17470120--17470162 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
17470110 TGTTTATTTT
17470120 ATATTTTAATAAA-A
1 ATATTTTAATAAATA
17470134 A-ATTTTAATAAATGA
1 ATATTTTAATAAAT-A
17470149 ATATTTTAATAAAT
1 ATATTTTAATAAAT
17470163 TAAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
15 2 0.08
16 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATTTTAATAAATA
Found at i:17470253 original size:26 final size:27
Alignment explanation
Indices: 17470208--17470259 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
17470198 TTAAACTTAA
** *
17470208 ATAAATATTTAAATTGATTTGAATATT
1 ATAAATATTTAAATAAATTTAAATATT
17470235 ATAAATA-TTAAATAAATTTAAATAT
1 ATAAATATTTAAATAAATTTAAATAT
17470260 GAATATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (27 bp):
ATAAATATTTAAATAAATTTAAATATT
Found at i:17471022 original size:20 final size:22
Alignment explanation
Indices: 17470980--17471023 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
17470970 TTTTTTTAAT
*
17470980 TAAATATTTAAAAAGTATATTA
1 TAAATATTTAAAAAGAATATTA
*
17471002 TAAATTTTTAAAAA-AAT-TTA
1 TAAATATTTAAAAAGAATATTA
17471022 TA
1 TA
17471024 TCTTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATATTTAAAAAGAATATTA
Found at i:17475035 original size:19 final size:20
Alignment explanation
Indices: 17475011--17475049 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
17475001 ACTCATTGTG
*
17475011 TAATGTAATGTTTG-ACTTT
1 TAATGTAATATTTGTACTTT
*
17475030 TAATGTGATATTTGTACTTT
1 TAATGTAATATTTGTACTTT
17475050 AAAAATATTT
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:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (20 bp):
TAATGTAATATTTGTACTTT
Found at i:17475785 original size:17 final size:16
Alignment explanation
Indices: 17475759--17475800 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
17475749 AATTTAATTA
*
17475759 TTTTACTTTATTCTATT
1 TTTTATTTTATTCT-TT
17475776 TTTTATTTTATTCTTT
1 TTTTATTTTATTCTTT
17475792 TTCTTATTT
1 TT-TTATTT
17475801 CTTATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATTTTATTCTTT
Found at i:17476354 original size:33 final size:34
Alignment explanation
Indices: 17476311--17476382 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
17476301 TATTGATGAA
* *
17476311 TTAAATAATAATAATTAATTATTAAA-ATAAATT
1 TTAAAAAATAATAATTAATTAATAAATATAAATT
* * *
17476344 TTAAAAAATAATATTTTATTAATAAATATATATT
1 TTAAAAAATAATAATTAATTAATAAATATAAATT
17476378 TTAAA
1 TTAAA
17476383 CTTTTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
TTAAAAAATAATAATTAATTAATAAATATAAATT
Found at i:17476361 original size:15 final size:15
Alignment explanation
Indices: 17476334--17476382 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 15
17476324 ATTAATTATT
17476334 AAAATAA-ATTTTAA
1 AAAATAATATTTTAA
17476348 AAAATAATATTTTATTA
1 AAAATAATATTTTA--A
17476365 ATAAATATATATTTTAA
1 A-AAATA-ATATTTTAA
17476382 A
1 A
17476383 CTTTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.23
15 6 0.20
17 4 0.13
18 5 0.17
19 8 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATAATATTTTAA
Found at i:17476370 original size:18 final size:19
Alignment explanation
Indices: 17476344--17476380 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
17476334 AAAATAAATT
17476344 TTAAAAAATA-ATATTTTA
1 TTAAAAAATATATATTTTA
*
17476362 TTAATAAATATATATTTTA
1 TTAAAAAATATATATTTTA
17476381 AACTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAAAATATATATTTTA
Found at i:17476492 original size:21 final size:24
Alignment explanation
Indices: 17476452--17476506 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
17476442 CATTTGATTC
*
17476452 AATAATATATAAAATTTATACAC-T
1 AATAATATATAAAA-TTATAAACTT
17476476 AATAATATAT-AAA-TATAAACTT
1 AATAATATATAAAATTATAAACTT
17476498 ATATAATAT
1 A-ATAATAT
17476507 TTTTTTCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.21
22 2 0.07
23 10 0.36
24 10 0.36
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (24 bp):
AATAATATATAAAATTATAAACTT
Found at i:17476836 original size:25 final size:25
Alignment explanation
Indices: 17476777--17476838 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
17476767 TTTAATTTAA
17476777 TTTTATATTT-ATAATATTTAAATT
1 TTTTATATTTAATAATATTTAAATT
* * * **
17476801 TGATTAGATTTAATAATTTTTTTATT
1 T-TTTATATTTAATAATATTTAAATT
17476827 TTTTATATTTAA
1 TTTTATATTTAA
17476839 ATGTAATTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
24 1 0.03
25 16 0.55
26 12 0.41
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (25 bp):
TTTTATATTTAATAATATTTAAATT
Found at i:17477525 original size:30 final size:30
Alignment explanation
Indices: 17477454--17477510 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
17477444 TTAATTTAAT
17477454 CTTAATTAAATAAAAATAAATATTTGAACA
1 CTTAATTAAATAAAAATAAATATTTGAACA
* *
17477484 CTTAATCAAATAAAAATAAATGTTTGA
1 CTTAATTAAATAAAAATAAATATTTGA
17477511 GTTTTCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.33
Consensus pattern (30 bp):
CTTAATTAAATAAAAATAAATATTTGAACA
Found at i:17480237 original size:17 final size:17
Alignment explanation
Indices: 17480215--17480250 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
17480205 AAACAATTTC
17480215 GGTACTGTT-ACCGCGTT
1 GGTACTGTTCACC-CGTT
17480232 GGTACTGTTCACCCGTT
1 GGTACTGTTCACCCGTT
17480249 GG
1 GG
17480251 GCTACAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.11, C:0.25, G:0.31, T:0.33
Consensus pattern (17 bp):
GGTACTGTTCACCCGTT
Found at i:17494369 original size:13 final size:14
Alignment explanation
Indices: 17494343--17494371 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17494333 ATATAATATA
17494343 ATTTTCATAAATTT
1 ATTTTCATAAATTT
17494357 ATTTTCA-AAATTT
1 ATTTTCATAAATTT
17494370 AT
1 AT
17494372 ATTATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTCATAAATTT
Found at i:17494444 original size:22 final size:22
Alignment explanation
Indices: 17494419--17494462 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
17494409 ATATTCTCGA
17494419 AAATTTATT-TTTGAAA-ATATAT
1 AAATTT-TTGTTT-AAATATATAT
17494441 AAATTTTTGTTTAAATATATAT
1 AAATTTTTGTTTAAATATATAT
17494463 TTAATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
AAATTTTTGTTTAAATATATAT
Found at i:17494520 original size:19 final size:19
Alignment explanation
Indices: 17494496--17494532 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
17494486 TTTAATTTTA
17494496 ATTTAA-TTAAAATAAATAC
1 ATTTAATTTAAAA-AAATAC
17494515 ATTTAATTTAAAAAAATA
1 ATTTAATTTAAAAAAATA
17494533 ATACTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTAATTTAAAAAAATAC
Found at i:17498621 original size:19 final size:19
Alignment explanation
Indices: 17498585--17498623 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17498575 TTTCCTTGCT
*
17498585 TCTTCCCTTTGTTCTTTTC
1 TCTTCCCTTTCTTCTTTTC
17498604 TCTTCCCTTATCTT-TTTTC
1 TCTTCCCTT-TCTTCTTTTC
17498623 T
1 T
17498624 GTTTCTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.03, C:0.31, G:0.03, T:0.64
Consensus pattern (19 bp):
TCTTCCCTTTCTTCTTTTC
Found at i:17502395 original size:22 final size:22
Alignment explanation
Indices: 17502326--17502396 Score: 58
Period size: 24 Copynumber: 3.2 Consensus size: 22
17502316 ATACAAATAC
*
17502326 AAAAATGATATA-AAAATT-AA
1 AAAAATTATATATAAAATTAAA
* * *
17502346 AATAA-TATAATTTAAAATTTTAAT
1 AAAAATTAT-ATATAAAA--TTAAA
17502370 AAAAATTATATATAAAATTAAA
1 AAAAATTATATATAAAATTAAA
17502392 AAAAA
1 AAAAA
17502397 ATTAAAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
19 2 0.05
20 6 0.16
21 4 0.11
22 9 0.24
23 2 0.05
24 12 0.32
25 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (22 bp):
AAAAATTATATATAAAATTAAA
Found at i:17502824 original size:3 final size:3
Alignment explanation
Indices: 17502816--17502843 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17502806 AATATAACTA
17502816 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17502844 TTTAGTTTTA
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:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17507829 original size:16 final size:17
Alignment explanation
Indices: 17507810--17507844 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
17507800 ATGATATTTT
*
17507810 TTTATAATTGA-AATAA
1 TTTAAAATTGATAATAA
17507826 TTTAAAATTGATAATAA
1 TTTAAAATTGATAATAA
17507843 TT
1 TT
17507845 AATTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
TTTAAAATTGATAATAA
Found at i:17508216 original size:25 final size:26
Alignment explanation
Indices: 17508157--17508217 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
17508147 ATATGTCACT
* *
17508157 AATATATTA-TAAAATTATTATCTTTA
1 AATA-ATTATTAAAATCATTATATTTA
*
17508183 AACAA-TATTAAAATCATTA-ATTTA
1 AATAATTATTAAAATCATTATATTTA
17508207 AATAATTATTA
1 AATAATTATTA
17508218 CAATAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
24 10 0.34
25 16 0.55
26 3 0.10
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAATTATTAAAATCATTATATTTA
Found at i:17508805 original size:27 final size:28
Alignment explanation
Indices: 17508771--17508835 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
17508761 TTAATTTTAA
** *
17508771 TTAA-TTAATTTTTTAAATTAAAA-AAT
1 TTAATTTAATTTAATAAAATAAAATAAT
*
17508797 TTAATTTAA-CTAATAAAATAAAATAAT
1 TTAATTTAATTTAATAAAATAAAATAAT
17508824 TTAATTTAATTT
1 TTAATTTAATTT
17508836 GAAAGTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
26 14 0.45
27 16 0.52
28 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
TTAATTTAATTTAATAAAATAAAATAAT
Found at i:17509665 original size:24 final size:24
Alignment explanation
Indices: 17509619--17509665 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
17509609 TTTTAAAATT
* *
17509619 ATAATTATAATAATTTTTTTTATC
1 ATAATTATAATAATTATTATTATC
*
17509643 ATAATTATGATAATTATTATTAT
1 ATAATTATAATAATTATTATTAT
17509666 TATTTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
ATAATTATAATAATTATTATTATC
Found at i:17513928 original size:16 final size:16
Alignment explanation
Indices: 17513909--17513941 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17513899 AATTTATTGA
*
17513909 TTTATATTTTTAATTT
1 TTTATATTATTAATTT
17513925 TTTATATTATTAATTT
1 TTTATATTATTAATTT
17513941 T
1 T
17513942 AATAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATATTATTAATTT
Found at i:17522859 original size:16 final size:16
Alignment explanation
Indices: 17522833--17522866 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
17522823 AAAATGATAC
17522833 AAATAAATAATATATAA
1 AAATAAATAATA-ATAA
17522850 AAAT-AATAATAATAA
1 AAATAAATAATAATAA
17522865 AA
1 AA
17522867 TTTTGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 7 0.41
17 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAAATAATAATAA
Found at i:17524316 original size:38 final size:38
Alignment explanation
Indices: 17524272--17524389 Score: 140
Period size: 38 Copynumber: 3.2 Consensus size: 38
17524262 AAAAGCGACT
17524272 AGGATTAAATCACAAGTCAGGAAACTATAGAAATGATA
1 AGGATTAAATCACAAGTCAGGAAACTATAGAAATGATA
** * *
17524310 AGGATTAAA--A-AAGTCA--AAAAAATAAAAACGACT-
1 AGGATTAAATCACAAGTCAGGAAACTATAGAAATGA-TA
*
17524343 GGGATTAAATCACAAGTCAGGAAACTATAGAAATGATA
1 AGGATTAAATCACAAGTCAGGAAACTATAGAAATGATA
17524381 AGGATTAAA
1 AGGATTAAA
17524390 CCATGAATTG
Statistics
Matches: 63, Mismatches: 10, Indels: 14
0.72 0.11 0.16
Matches are distributed among these distances:
33 19 0.30
34 1 0.02
35 7 0.11
36 7 0.11
37 1 0.02
38 28 0.44
ACGTcount: A:0.53, C:0.09, G:0.18, T:0.19
Consensus pattern (38 bp):
AGGATTAAATCACAAGTCAGGAAACTATAGAAATGATA
Found at i:17524324 original size:71 final size:71
Alignment explanation
Indices: 17524249--17524389 Score: 255
Period size: 71 Copynumber: 2.0 Consensus size: 71
17524239 ACTGAACCAT
* *
17524249 AAGTCAGAAAAATAAAAGCGACTAGGATTAAATCACAAGTCAGGAAACTATAGAAATGATAAGGA
1 AAGTCAAAAAAATAAAAACGACTAGGATTAAATCACAAGTCAGGAAACTATAGAAATGATAAGGA
17524314 TTAAAA
66 TTAAAA
*
17524320 AAGTCAAAAAAATAAAAACGACTGGGATTAAATCACAAGTCAGGAAACTATAGAAATGATAAGGA
1 AAGTCAAAAAAATAAAAACGACTAGGATTAAATCACAAGTCAGGAAACTATAGAAATGATAAGGA
17524385 TTAAA
66 TTAAA
17524390 CCATGAATTG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.54, C:0.10, G:0.18, T:0.18
Consensus pattern (71 bp):
AAGTCAAAAAAATAAAAACGACTAGGATTAAATCACAAGTCAGGAAACTATAGAAATGATAAGGA
TTAAAA
Found at i:17524370 original size:180 final size:180
Alignment explanation
Indices: 17524140--17524486 Score: 457
Period size: 180 Copynumber: 1.9 Consensus size: 180
17524130 ACTGAATCAC
* * * *
17524140 AAGTCAAAAAAATAAAAGCGACTGAGATTAAACCATAATTCAAAAAACTATAGAAATGAC-CGAG
1 AAGTCAAAAAAATAAAAACGACTGAGATTAAACCACAAGTCAAAAAACTATAGAAATGACAAG-G
* *
17524204 ATTAAACCACT-AGTCCAAGATTAATGACGATTGGGACTGAACCATAAGTCAGAAAAATAAAAGC
65 ATTAAACCA-TGAATCCAAGATTAATGACGACTGGGACTGAACCATAAGTCAGAAAAATAAAAGC
* *
17524268 GACTA-GGATTAAATCACAAGTCAGGAAACTATAGAAATGATAAGGATTAAAA
129 GAC-AGGGATTAAACCACAAGTCAGAAAACTATAGAAATGATAAGGATTAAAA
* * ** *
17524320 AAGTCAAAAAAATAAAAACGACTGGGATTAAATCACAAGTCAGGAAACTATAGAAATGATAAGGA
1 AAGTCAAAAAAATAAAAACGACTGAGATTAAACCACAAGTCAAAAAACTATAGAAATGACAAGGA
*** * * *
17524385 TTAAACCATGAATTGGAGATTAATGATGACTGGGATTGAACCATAAGTCAGAAAAATAAAAGTGA
66 TTAAACCATGAATCCAAGATTAATGACGACTGGGACTGAACCATAAGTCAGAAAAATAAAAGCGA
* *
17524450 CAGGGATTAAACCGCAAGTTAGAAAACTATAGAAATG
131 CAGGGATTAAACCACAAGTCAGAAAACTATAGAAATG
17524487 GCCAAGATTA
Statistics
Matches: 143, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
179 2 0.01
180 140 0.98
181 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.20
Consensus pattern (180 bp):
AAGTCAAAAAAATAAAAACGACTGAGATTAAACCACAAGTCAAAAAACTATAGAAATGACAAGGA
TTAAACCATGAATCCAAGATTAATGACGACTGGGACTGAACCATAAGTCAGAAAAATAAAAGCGA
CAGGGATTAAACCACAAGTCAGAAAACTATAGAAATGATAAGGATTAAAA
Found at i:17524856 original size:218 final size:218
Alignment explanation
Indices: 17524320--17526162 Score: 1839
Period size: 218 Copynumber: 8.5 Consensus size: 218
17524310 AGGATTAAAA
* * * ** *
17524320 AAGTCAAAAAAATAAAAACGACTGGGATTAA-ATCACAAGTCAGGAAACTA-TAGAAATGATAAG
1 AAGTCAAAAAAATAAAAAGGACTGGGATTAACCT-AAAAGTCAGGAAACTATTA-AAATGACCAT
* * * * * *
17524383 GATTAAACCATGAATTGGAGATTAATGATGACTGGGATTGAACCATAAGTCAGAAAAATAAAAGT
64 GATTAAACCATGAGTTAGAGATTAACGATGACTGGGACTGAACCACAAGTCAGAAAAATAAAAGC
* * * ** ** * *
17524448 GACAGGGATTAAACCGCAAGTT-AGAAAACTATAGAAATGGCCAAGATTAAACCACGAGTCAAAG
129 GACTGGGATTAAATCGTAAGTTAAG-AAACTATAGAAATGATCGGGATTAAACCAAGAGTTAAAG
* * * *
17524512 ATTAATAATGA-TTGGACTAAATCGC
193 ATTAATGACGACTGGGACTAAACCGC
* * * * * ** * * *
17524537 AAGTTAAAAAAATAAAAACGACTAGGATTAA-ATCACAAGTCAAAAAATTA-TAGTAATGATCAT
1 AAGTCAAAAAAATAAAAAGGACTGGGATTAACCT-AAAAGTCAGGAAACTATTA-AAATGACCAT
* * * * * * * **
17524600 GATTAAATCACGAGTCAAAGATTAATGATGATTGGGACTGAACCACAAGTCAAAAAAATAAAATT
64 GATTAAACCATGAGTTAGAGATTAACGATGACTGGGACTGAACCACAAGTCAGAAAAATAAAAGC
* * *
17524665 GACTGAGATTAAATCGCAAGTTAAGAAATTATAGAAATGATCGGGATTAAACCAAGAGTTAAAGA
129 GACTGGGATTAAATCGTAAGTTAAGAAACTATAGAAATGATCGGGATTAAACCAAGAGTTAAAGA
*
17524730 TTAATGACGATTGGGACTAAACCGC
194 TTAATGACGACTGGGACTAAACCGC
* * *
17524755 AAGTCAAAAAAATAAAAAGGATTGGGATTAACCTAAAAGTCAAGAAATTATTAAAATGACCATGA
1 AAGTCAAAAAAATAAAAAGGACTGGGATTAACCTAAAAGTCAGGAAACTATTAAAATGACCATGA
* * *
17524820 TTAAACCATGAGTTAGAGATTAACGACGACTGGGACTAAACCACAAGTCAGAACAATAAAAGCGA
66 TTAAACCATGAGTTAGAGATTAACGATGACTGGGACTGAACCACAAGTCAGAAAAATAAAAGCGA
* * * *
17524885 TTGGGATTAAATCGTAAGTAAAAAAACTATAGAAATGTTCGGGATTAAACCAAGAGTTAAAGATT
131 CTGGGATTAAATCGTAAGTTAAGAAACTATAGAAATGATCGGGATTAAACCAAGAGTTAAAGATT
*
17524950 AATGACGACTGGGACTAAATCGC
196 AATGACGACTGGGACTAAACCGC
* * * * *
17524973 AAGTCCAAAAAAT--AAA--A-TGGGATTAACCTAAAAGTTAGGAAACTATTGAAATGATCGTGA
1 AAGTCAAAAAAATAAAAAGGACTGGGATTAACCTAAAAGTCAGGAAACTATTAAAATGACCATGA
* * * * *
17525033 TTAAACCATGAGTTAAAGATTAACGATGACTGAGATTGAACCACAAGTCAGAATAACAAAAGCGA
66 TTAAACCATGAGTTAGAGATTAACGATGACTGGGACTGAACCACAAGTCAGAAAAATAAAAGCGA
* * * * *
17525098 TTGGGATTAAATCGTAAG-TCAGAAAATTATAGAAATGTTCGGGATTAAACCAAAAGTTAAAGAT
131 CTGGGATTAAATCGTAAGTTAAG-AAACTATAGAAATGATCGGGATTAAACCAAGAGTTAAAGAT
*
17525162 TAATGACGACTGGGACTTAACCGC
195 TAATGACGACTGGGACTAAACCGC
* * **
17525186 AAGTCAAAAAAATAAAACGGATTGGGATTAACCTAAAAGTCAGGAAACTATTAAAATGACTGTGA
1 AAGTCAAAAAAATAAAAAGGACTGGGATTAACCTAAAAGTCAGGAAACTATTAAAATGACCATGA
* * * *
17525251 TTAAACCATGAGTTAGAGATTAACGACGACTGAGACTGAACCACAAGTCAGAACAATAAAAGTGA
66 TTAAACCATGAGTTAGAGATTAACGATGACTGGGACTGAACCACAAGTCAGAAAAATAAAAGCGA
* * * * *
17525316 TTGGAATTAAATCGTAAGTCAGGAAACTATAGAAATGATCGAGATTAAACCAAGAGTTAAAGATT
131 CTGGGATTAAATCGTAAGTTAAGAAACTATAGAAATGATCGGGATTAAACCAAGAGTTAAAGATT
* *
17525381 AATGACGACTGGAACTAAACTGC
196 AATGACGACTGGGACTAAACCGC
* * * *
17525404 AAGTCAAAAAAATAAAAGGGATTGGGATTAACCTAAAAGTCAGGAAACTATTGAAATGACCGTGA
1 AAGTCAAAAAAATAAAAAGGACTGGGATTAACCTAAAAGTCAGGAAACTATTAAAATGACCATGA
* * * * *
17525469 TTAAATCATGAGTTAAAGATTAACGACGACTGGGACTGAACCACAAGTCAGAACAATAAAAACGA
66 TTAAACCATGAGTTAGAGATTAACGATGACTGGGACTGAACCACAAGTCAGAAAAATAAAAGCGA
* * * * *
17525534 TTGGGATTAAATCGTAAG-TCAGAAAACTATAGAAATTATCGGGATTAAACCACA-AATTAAAAA
131 CTGGGATTAAATCGTAAGTTAAG-AAACTATAGAAATGATCGGGATTAAACCA-AGAGTTAAAGA
* * * * *
17525597 TTAACGACGATTGAGACTGAACCGT
194 TTAATGACGACTGGGACTAAACCGC
* * * *
17525622 AAGTCAAAAAAAT-AAAAGCGACTGGGATTAAATCGT--AAGTCAGAAAACTATAAAAATGACCG
1 AAGTCAAAAAAATAAAAAG-GACTGGGATT-AA-CCTAAAAGTCAGGAAACTATTAAAATGACCA
* * * * * * *
17525684 GGATTAAACCATAAGTCATG-GATTAATGATGACTGGGACTGAA-TAGTAAGTCAAAAAAATAAA
63 TGATTAAACCATGAGTTA-GAGATTAACGATGACTGGGACTGAACCA-CAAGTCAGAAAAATAAA
* * * * * * *
17525747 AGTGACTGGAATTAAACCGTAAGTCAGGAAACTATAGAAATGA-CTGGGATT-AATCACGAGTTA
126 AGCGACTGGGATTAAATCGTAAGTTAAGAAACTATAGAAATGATC-GGGATTAAACCAAGAGTTA
* * *
17525810 AAGATTAACGACGACTGGGACTGAATCGC
190 AAGATTAATGACGACTGGGACTAAACCGC
* * * * * * *
17525839 AAGTCAAAAAAATAAAAACGATTAGGATTAAACCGT--AAGTTAGGAAACTATAAAAATGATCAA
1 AAGTCAAAAAAATAAAAAGGACTGGGATT-AACC-TAAAAGTCAGGAAACTATTAAAATGACCAT
* * *
17525902 GATTAAACCATGAGTCAGAGATTAACGATGACTGGGACTGAACCACAAGTTAAAAAAATAAAAGC
64 GATTAAACCATGAGTTAGAGATTAACGATGACTGGGACTGAACCACAAGTCAGAAAAATAAAAGC
* * * * * *** * *
17525967 GACTAGGATTAAACCGCAAGTCAAAAAACTATAGAAATGATCAAAATTAAATCACGAGTTAAAGA
129 GACTGGGATTAAATCGTAAGTTAAGAAACTATAGAAATGATCGGGATTAAACCAAGAGTTAAAGA
* *** **
17526032 TTAATGATGACTAACACTAAATTGC
194 TTAATGACGACTGGGACTAAACCGC
* * * * *
17526057 AAGTAAAAAAAATAAAAATGACTGGGATTAAACC-ATAAGTCAGAAAACTA-TAGAAATGATCGA
1 AAGTCAAAAAAATAAAAAGGACTGGGATT-AACCTAAAAGTCAGGAAACTATTA-AAATGA-CCA
* * * * *
17526120 -GATTAAACTATGAGTCAGAGATTAATGATGACTGAGATTGAAC
63 TGATTAAACCATGAGTTAGAGATTAACGATGACTGGGACTGAAC
17526163 TGCAAGTTAA
Statistics
Matches: 1388, Mismatches: 207, Indels: 61
0.84 0.12 0.04
Matches are distributed among these distances:
212 1 0.00
213 186 0.13
214 1 0.00
215 2 0.00
216 5 0.00
217 350 0.25
218 832 0.60
219 9 0.01
220 2 0.00
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (218 bp):
AAGTCAAAAAAATAAAAAGGACTGGGATTAACCTAAAAGTCAGGAAACTATTAAAATGACCATGA
TTAAACCATGAGTTAGAGATTAACGATGACTGGGACTGAACCACAAGTCAGAAAAATAAAAGCGA
CTGGGATTAAATCGTAAGTTAAGAAACTATAGAAATGATCGGGATTAAACCAAGAGTTAAAGATT
AATGACGACTGGGACTAAACCGC
Found at i:17525659 original size:36 final size:36
Alignment explanation
Indices: 17525616--17525799 Score: 131
Period size: 38 Copynumber: 5.0 Consensus size: 36
17525606 ATTGAGACTG
*
17525616 AACCGTAAGTCAAAAAAATAAAAGCGACTGGGATTA
1 AACCGTAAGTCAAAAAAATAAAAGTGACTGGGATTA
* * * *
17525652 AATCGTAAGTCAGAAAACTATAAAAATGACCGGGATTA
1 AACCGTAAGTCA-AAAA-AATAAAAGTGACTGGGATTA
* *** * * * *
17525690 AACCATAAGTC--ATGGATTAATGATGACTGGGACTG
1 AACCGTAAGTCAAAAAAATAAAAG-TGACTGGGATTA
** *
17525725 AATAGTAAGTCAAAAAAATAAAAGTGACTGGAATTA
1 AACCGTAAGTCAAAAAAATAAAAGTGACTGGGATTA
**
17525761 AACCGTAAGTCAGGAAACTATAGAAA-TGACTGGGATTA
1 AACCGTAAGTCA--AAAAAATA-AAAGTGACTGGGATTA
17525799 A
1 A
17525800 TCACGAGTTA
Statistics
Matches: 108, Mismatches: 32, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
34 4 0.04
35 18 0.17
36 30 0.28
37 10 0.09
38 43 0.40
39 3 0.03
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (36 bp):
AACCGTAAGTCAAAAAAATAAAAGTGACTGGGATTA
Found at i:17525687 original size:38 final size:37
Alignment explanation
Indices: 17525513--17526006 Score: 151
Period size: 36 Copynumber: 13.6 Consensus size: 37
17525503 ACTGAACCAC
* * * *
17525513 AAGTCAGAACA-ATAAAAACGATTGGGATTAAATCGT
1 AAGTCAGAAAATATAAAAATGACTGGGATTAAACCGT
* * **
17525549 AAGTCAGAAAACTATAGAAATTA-TCGGGATTAAACCAC
1 AAGTCAGAAAA-TATAAAAATGACT-GGGATTAAACCGT
* * ** * * * * *
17525587 AAATTA-AAAAT-TAACGACGATTGAGACTGAACCGT
1 AAGTCAGAAAATATAAAAATGACTGGGATTAAACCGT
* ** *
17525622 AAGTCA-AAAAAATAAAAGCGACTGGGATTAAATCGT
1 AAGTCAGAAAATATAAAAATGACTGGGATTAAACCGT
* *
17525658 AAGTCAGAAAACTATAAAAATGACCGGGATTAAACCAT
1 AAGTCAGAAAA-TATAAAAATGACTGGGATTAAACCGT
* ** * * **
17525696 AAGTCATG--GAT-TAATGATGACTGGGACTGAATAGT
1 AAGTCA-GAAAATATAAAAATGACTGGGATTAAACCGT
* * *
17525731 AAGTCA-AAAAAATAAAAGTGACTGGAATTAAACCGT
1 AAGTCAGAAAATATAAAAATGACTGGGATTAAACCGT
* * *
17525767 AAGTCAGGAAACTATAGAAATGACTGGGATTAATCACG-
1 AAGTCA-GAAAATATAAAAATGACTGGGATTAAAC-CGT
* * ** * * * * *
17525805 -AGTTA-AAGAT-TAACGACGACTGGGACTGAATCGC
1 AAGTCAGAAAATATAAAAATGACTGGGATTAAACCGT
* * * *
17525839 AAGTCA-AAAAAATAAAAACGATTAGGATTAAACCGT
1 AAGTCAGAAAATATAAAAATGACTGGGATTAAACCGT
* * ** *
17525875 AAGTTAGGAAACTATAAAAATGA-TCAAGATTAAACCAT
1 AAGTCA-GAAAATATAAAAATGACT-GGGATTAAACCGT
* * ** * * **
17525913 GAGTCAG-AGAT-TAACGATGACTGGGACTGAACCAC
1 AAGTCAGAAAATATAAAAATGACTGGGATTAAACCGT
* * ** * *
17525948 AAGTTA-AAAAAATAAAAGCGACTAGGATTAAACCGC
1 AAGTCAGAAAATATAAAAATGACTGGGATTAAACCGT
* *
17525984 AAGTCAAAAAACTATAGAAATGA
1 AAGTCAGAAAA-TATAAAAATGA
17526007 TCAAAATTAA
Statistics
Matches: 316, Mismatches: 117, Indels: 48
0.66 0.24 0.10
Matches are distributed among these distances:
33 2 0.01
34 13 0.04
35 74 0.23
36 102 0.32
37 20 0.06
38 102 0.32
39 3 0.01
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (37 bp):
AAGTCAGAAAATATAAAAATGACTGGGATTAAACCGT
Found at i:17526167 original size:109 final size:109
Alignment explanation
Indices: 17524320--17526179 Score: 1612
Period size: 109 Copynumber: 17.1 Consensus size: 109
17524310 AGGATTAAAA
* * ** * *
17524320 AAGTCAAAAAAATAAAAACGACTGGGATTAAATCACAAGTCAGGAAACTATAGAAATGAT-AAGG
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGA-G
* ** * * **
17524384 ATTAAACCATGAATTGGAGATTAATGATGACTGGGATTGAACCAT
65 ATTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * * * ** *
17524429 AAGTCAGAAAAATAAAAGTGACAGGGATTAAACCGCAAGTTAGAAAACTATAGAAATGGCCAAGA
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGAGA
* * * * * * *
17524494 TTAAACCACGAGTCAAAGATTAATAATGA-TTGGACTAAATCGC
66 TTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * * ** * * *
17524537 AAGTTAAAAAAATAAAAACGACTAGGATTAAATCACAAGTCAAAAAATTATAGTAATGATC-ATG
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGA-G
* * * * * *
17524601 ATTAAATCACGAGTCAAAGATTAATGATGATTGGGACTGAACCAC
65 ATTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
** * * * * * *
17524646 AAGTCAAAAAAATAAAATTGACTGAGATTAAATCGCAAGTTA-AGAAATTATAGAAATGATCGGG
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGA-AAACTATAGAAATGATCGAG
* * *
17524710 ATTAAACCAAGAGTTAAAGATTAATGACGATTGGGACTAAACCGC
65 ATTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* *
17524755 AAGTCAAAAAAATAAAAAG-GATTGGGATT-AACC-TAAAAGTCA-AGAAATTATTA-AAATGA-
1 AAGTCAAAAAAAT-AAAAGCGACTGGGATTAAACCGT--AAGTCAGA-AAACTA-TAGAAATGAT
* * * * *
17524814 CCATGATTAAACCATGAGTTAGAGATTAACGACGACTGGGACTAAACCAC
61 CGA-GATTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * * * * * *
17524864 AAGTCAGAACAATAAAAGCGATTGGGATTAAATCGTAAGTAAAAAAACTATAGAAATGTTCGGGA
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGAGA
* * *
17524929 TTAAACCAAGAGTTAAAGATTAATGACGACTGGGACTAAATCGC
66 TTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * * *
17524973 AAGTCCAAAAAAT-AAA---A-TGGGATT-AACC-TAAAAGTTAGGAAACTATTGAAATGATCGT
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGT--AAGTCAGAAAACTATAGAAATGATCGA
* * * * *
17525031 GATTAAACCATGAGTTAAAGATTAACGATGACTGAGATTGAACCAC
64 GATTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * * * * * *
17525077 AAGTCAGAATAACAAAAGCGATTGGGATTAAATCGTAAGTCAGAAAATTATAGAAATGTTCGGGA
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGAGA
** *
17525142 TTAAACCAAAAGTTAAAGATTAATGACGACTGGGACTTAACCGC
66 TTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* *
17525186 AAGTCAAAAAAATAAAA-CGGATTGGGATT-AACC-TAAAAGTCAGGAAACTATTA-AAATGA-C
1 AAGTCAAAAAAATAAAAGC-GACTGGGATTAAACCGT--AAGTCAGAAAACTA-TAGAAATGATC
* * * * *
17525246 TGTGATTAAACCATGAGTTAGAGATTAACGACGACTGAGACTGAACCAC
62 -GAGATTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * * * * *
17525295 AAGTCAGAACAATAAAAGTGATTGGAATTAAATCGTAAGTCAGGAAACTATAGAAATGATCGAGA
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGAGA
* * * *
17525360 TTAAACCAAGAGTTAAAGATTAATGACGACTGGAACTAAACTGC
66 TTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * * * *
17525404 AAGTCAAAAAAATAAAAGGGATTGGGATT-AACC-TAAAAGTCAGGAAACTATTGAAATGACCGT
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGT--AAGTCAGAAAACTATAGAAATGATCGA
* * *
17525467 GATTAAATCATGAGTTAAAGATTAACGACGACTGGGACTGAACCAC
64 GATTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * * * * *
17525513 AAGTCAGAACAATAAAAACGATTGGGATTAAATCGTAAGTCAGAAAACTATAGAAATTATCGGGA
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGAGA
** * * * * * *
17525578 TTAAACCACAAATTAAAAATTAACGACGATTGAGACTGAACCGT
66 TTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * *
17525622 AAGTCAAAAAAATAAAAGCGACTGGGATTAAATCGTAAGTCAGAAAACTATAAAAATGACCGGGA
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGAGA
* * ** * ** *
17525687 TTAAACCATAAGTCATGGATTAATGATGACTGGGACTGAATAGT
66 TTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * *
17525731 AAGTCAAAAAAATAAAAGTGACTGGAATTAAACCGTAAGTCAGGAAACTATAGAAATGA-CTGGG
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATC-GAG
* * * *
17525795 ATT-AATCACGAGTTAAAGATTAACGACGACTGGGACTGAATCGC
65 ATTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * * * * *
17525839 AAGTCAAAAAAATAAAAACGATTAGGATTAAACCGTAAGTTAGGAAACTATAAAAATGATCAAGA
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGAGA
* * * * *
17525904 TTAAACCATGAGTCAGAGATTAACGATGACTGGGACTGAACCAC
66 TTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* * * * * *
17525948 AAGTTAAAAAAATAAAAGCGACTAGGATTAAACCGCAAGTCAAAAAACTATAGAAATGATCAAAA
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGAGA
* * * *** * **
17526013 TTAAATCACGAGTTAAAGATTAATGATGACTAACACTAAATTGC
66 TTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
* ** *
17526057 AAGTAAAAAAAATAAAAATGACTGGGATTAAACCATAAGTCAGAAAACTATAGAAATGATCGAGA
1 AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGAGA
* * * * * * *
17526122 TTAAACTATGAGTCAGAGATTAATGATGACTGAGATTGAACTGC
66 TTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
*
17526166 AAGTTAAGAAAAAT
1 AAGTCAA-AAAAAT
17526180 GACGATTGGG
Statistics
Matches: 1434, Mismatches: 274, Indels: 85
0.80 0.15 0.05
Matches are distributed among these distances:
102 1 0.00
103 3 0.00
104 75 0.05
105 4 0.00
107 3 0.00
108 198 0.14
109 1115 0.78
110 31 0.02
111 4 0.00
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (109 bp):
AAGTCAAAAAAATAAAAGCGACTGGGATTAAACCGTAAGTCAGAAAACTATAGAAATGATCGAGA
TTAAACCATGAGTTAAAGATTAATGACGACTGGGACTGAACCGC
Found at i:17537022 original size:4 final size:4
Alignment explanation
Indices: 17536995--17537042 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
17536985 TAAACAAGTC
* * *
17536995 AATA ATATA AATA AAAA AATTA AATA AATG AGTA AATA AATA AATA AA
1 AATA A-ATA AATA AATA AA-TA AATA AATA AATA AATA AATA AATA AA
17537043 CAAGTATAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
4 29 0.81
5 7 0.19
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:17539200 original size:26 final size:23
Alignment explanation
Indices: 17539166--17539232 Score: 66
Period size: 26 Copynumber: 2.8 Consensus size: 23
17539156 AAGCATGCGT
*
17539166 AAAT-AACAATAATAATGATGTTAA
1 AAATGAACAATAATAAT-AT-ATAA
17539190 AAATGATACAAATAAATAATATATAA
1 AAATGA-AC-AAT-AATAATATATAA
17539216 AAATGAA-AATAATAATA
1 AAATGAACAATAATAATA
17539233 AAATTTTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
22 7 0.18
23 3 0.08
24 4 0.11
25 2 0.05
26 11 0.29
27 5 0.13
28 6 0.16
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (23 bp):
AAATGAACAATAATAATATATAA
Found at i:17545782 original size:2 final size:2
Alignment explanation
Indices: 17545775--17545804 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17545765 TAGTTTACTA
*
17545775 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
17545805 GTAAAATTGG
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:17552588 original size:3 final size:3
Alignment explanation
Indices: 17552580--17552637 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
17552570 CATGTCGTCT
17552580 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCT- TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
17552624 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
17552638 TTGATAAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 3 0.06
3 49 0.92
4 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17552995 original size:30 final size:30
Alignment explanation
Indices: 17552954--17553010 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
17552944 ATTTTTTATT
* * *
17552954 ATATATATATTTATATAATGATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
17552984 ATATTTATATTTAAAAAATAATATTTT
1 ATATATATATTTAAAAAATAATATTTT
17553011 ATATTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:17553013 original size:21 final size:22
Alignment explanation
Indices: 17552983--17553034 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
17552973 GATATTTTTA
17552983 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
17553003 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
17553025 AATATTTTAT
1 AATATTTTAT
17553035 TAATTTCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:17556557 original size:37 final size:36
Alignment explanation
Indices: 17556485--17556557 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 36
17556475 ATTGATATTT
*
17556485 AAATTTTAAATTTATCAAATATTAATGTTTAAAAATA
1 AAATTTTAAATTTA-CAAATATTAATGTATAAAAATA
* *
17556522 AAATTTTATATTTA-ATATATTATATGTATATAAAAT
1 AAATTTTAAATTTACAAATATTA-ATGTATA-AAAAT
17556558 TTATTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 7 0.23
36 6 0.19
37 18 0.58
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (36 bp):
AAATTTTAAATTTACAAATATTAATGTATAAAAATA
Found at i:17560406 original size:38 final size:38
Alignment explanation
Indices: 17560355--17560429 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
17560345 GAGGCTAAGG
*
17560355 ACACTCTGCCAATTTAGACTTGAGAGATGGGAACTAAA
1 ACACTCTGCCAATTTAGACTCGAGAGATGGGAACTAAA
*
17560393 ACACTGTGCCAATTTAGACTCGAGAGATGGGAACTAA
1 ACACTCTGCCAATTTAGACTCGAGAGATGGGAACTAA
17560430 GTATAGACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (38 bp):
ACACTCTGCCAATTTAGACTCGAGAGATGGGAACTAAA
Found at i:17567771 original size:19 final size:19
Alignment explanation
Indices: 17567743--17567781 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
17567733 CTTGATTTTT
* * *
17567743 TTTTCTTTGATTTTTCATG
1 TTTTCCTTGAGTTTTAATG
17567762 TTTTCCTTGAGTTTTAATG
1 TTTTCCTTGAGTTTTAATG
17567781 T
1 T
17567782 AATTAAATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.64
Consensus pattern (19 bp):
TTTTCCTTGAGTTTTAATG
Found at i:17569221 original size:14 final size:14
Alignment explanation
Indices: 17569199--17569240 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
17569189 GTCATTTAAT
17569199 AGAAAAAAAACAAA
1 AGAAAAAAAACAAA
*
17569213 A-ACAAAAAACAAA
1 AGAAAAAAAACAAA
*
17569226 AGAAAGAAAACAAA
1 AGAAAAAAAACAAA
17569240 A
1 A
17569241 CAATGTGGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAACAAA
Found at i:17572238 original size:2 final size:2
Alignment explanation
Indices: 17572231--17572256 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17572221 AGATGTGTAC
17572231 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
17572257 TGATAAAAAA
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:17580531 original size:15 final size:15
Alignment explanation
Indices: 17580507--17580539 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17580497 ATTTCAATTA
*
17580507 TAATTGAAAAATAAT
1 TAATTAAAAAATAAT
17580522 TAATTAAAAAATAAT
1 TAATTAAAAAATAAT
17580537 TAA
1 TAA
17580540 AATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
TAATTAAAAAATAAT
Found at i:17580547 original size:14 final size:14
Alignment explanation
Indices: 17580514--17580565 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
17580504 TTATAATTGA
17580514 AAAATAATTAATTAA-
1 AAAATAATTAA--AAT
17580529 AAAATAATTAAAATT
1 AAAATAATTAAAA-T
*
17580544 AAATTAA-TAAAAT
1 AAAATAATTAAAAT
17580557 AAAATAATT
1 AAAATAATT
17580566 TATACATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 9 0.28
14 6 0.19
15 17 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAATTAAAAT
Found at i:17580550 original size:26 final size:28
Alignment explanation
Indices: 17580506--17580565 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
17580496 GATTTCAATT
*
17580506 ATAATTGAAAAATAATTAAT-TAA-AAA
1 ATAATTGAAAAATAATTAATAAAATAAA
*
17580532 ATAATT-AAAATTAAATTAATAAAATAAA
1 ATAATTGAAAAAT-AATTAATAAAATAAA
17580560 ATAATT
1 ATAATT
17580566 TATACATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 13 0.45
27 2 0.07
28 9 0.31
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (28 bp):
ATAATTGAAAAATAATTAATAAAATAAA
Found at i:17582531 original size:51 final size:52
Alignment explanation
Indices: 17582408--17582549 Score: 153
Period size: 51 Copynumber: 2.8 Consensus size: 52
17582398 AAACTTATTC
* * ** * *
17582408 ATTAAGAATCCT-TCTCCTTTTAGAATTCTTCTCTTGTAAGTTAAATTTACCT
1 ATTAAGAAT-CTATTTCCTTTTAGAATTTTTCTCTTACAAGTCAAACTTACCT
17582460 ATTAAGAATCTATTTCCTTTT-GAATTTTTCTCTTACAAGTCAAACTTACCT
1 ATTAAGAATCTATTTCCTTTTAGAATTTTTCTCTTACAAGTCAAACTTACCT
* * * * * *
17582511 ATTAAGAATTTTTTTTCTTTTAAAATTTTTTTTTTACAA
1 ATTAAGAATCTATTTCCTTTTAGAATTTTTCTCTTACAA
17582550 ATATTCTTGT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
51 45 0.59
52 31 0.41
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (52 bp):
ATTAAGAATCTATTTCCTTTTAGAATTTTTCTCTTACAAGTCAAACTTACCT
Found at i:17582921 original size:27 final size:27
Alignment explanation
Indices: 17582864--17582921 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
17582854 AATTAAAAAT
* * * * *
17582864 AATAATAAAAATGATATTAATTATTAT
1 AATAATAAAAATAAAATTAATAATAAA
*
17582891 AATAATAAAATTAAAATTAATAATAAA
1 AATAATAAAAATAAAATTAATAATAAA
17582918 AATA
1 AATA
17582922 TATGTTTGAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
AATAATAAAAATAAAATTAATAATAAA
Found at i:17583167 original size:21 final size:21
Alignment explanation
Indices: 17583123--17583168 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17583113 ATAACAATAA
* *
17583123 TATATTAAATAGTATTTTTAT
1 TATATTAAATAGAATTATTAT
17583144 TATATTAAATTAGAATTATT-T
1 TATATTAAA-TAGAATTATTAT
17583165 TATA
1 TATA
17583169 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TATATTAAATAGAATTATTAT
Found at i:17585495 original size:125 final size:124
Alignment explanation
Indices: 17585348--17585594 Score: 352
Period size: 125 Copynumber: 2.0 Consensus size: 124
17585338 AAATATAAAA
* * * *
17585348 ACAATTTCAAGAAAGCTTTTATTATTGGTAGTTCTTAATTATATAATTTTTTCAATATCCCTCTA
1 ACAATTTCAAGAAAACCTTTATTATTAGTAGTTCTTAATTATATAATTTTTTCAATATCCCACTA
* * *
17585413 AACTAAACGTATTTTT-TCTTACTATTAATTTAGTATCTTTTTGTATTAGTCTATTCTTGC
66 AACTAAACATATTTTTCT-TTACTATTAATTTAATATCTTTTT-TATTAATCTATTCTTGC
* * *
17585473 ACAATTTCAAGAAAACCTTTATTATTAGTAGTTTTTAATTATATTATTTTTTCAATATTCCACTA
1 ACAATTTCAAGAAAACCTTTATTATTAGTAGTTCTTAATTATATAATTTTTTCAATATCCCACTA
* * *
17585538 AATTAAGCATATTTTTCTTTACTATTAATTTAATCTCTTTTTTATTAATCTATTCTT
66 AACTAAACATATTTTTCTTTACTATTAATTTAATATCTTTTTTATTAATCTATTCTT
17585595 ACTATAAAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
124 14 0.13
125 93 0.86
126 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (124 bp):
ACAATTTCAAGAAAACCTTTATTATTAGTAGTTCTTAATTATATAATTTTTTCAATATCCCACTA
AACTAAACATATTTTTCTTTACTATTAATTTAATATCTTTTTTATTAATCTATTCTTGC
Found at i:17585701 original size:21 final size:20
Alignment explanation
Indices: 17585629--17585704 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
17585619 TTATAATAGA
*
17585629 TATTATTTTATGAAATATAC
1 TATTATTTTATTAAATATAC
* * *
17585649 TATTTATTTTATCAAATAAAAA
1 TA-TTATTTTATTAAAT-ATAC
17585671 TATTATTTTATTAAATATAC
1 TATTATTTTATTAAATATAC
*
17585691 TATTCACTTTATTA
1 TATT-ATTTTATTA
17585705 TGTAAAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.17
21 34 0.74
22 4 0.09
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (20 bp):
TATTATTTTATTAAATATAC
Found at i:17586102 original size:17 final size:17
Alignment explanation
Indices: 17586076--17586110 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
17586066 TATAATATTA
17586076 TAAAATTTTAAATTTAAT
1 TAAAATTTTAAA-TTAAT
17586094 TAAAA-TTTAAATTAAT
1 TAAAATTTTAAATTAAT
17586110 T
1 T
17586111 TTTTAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 6 0.35
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATTTTAAATTAAT
Found at i:17586251 original size:36 final size:36
Alignment explanation
Indices: 17586210--17586279 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
17586200 TTATTTTAAT
*
17586210 ATAATTTTTTTATATTTA-AATAAATTT-AAATATAAA
1 ATAATTATTTTA-ATTTATAA-AAATTTAAAATATAAA
*
17586246 ATAATTATTTTAGTTTATAAAAATTTAAAATATA
1 ATAATTATTTTAATTTATAAAAATTTAAAATATA
17586280 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 10 0.33
36 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (36 bp):
ATAATTATTTTAATTTATAAAAATTTAAAATATAAA
Found at i:17586841 original size:33 final size:33
Alignment explanation
Indices: 17586799--17586861 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
17586789 TCTTCTGGTG
17586799 CTGCAGTATAATGGAAGCCCAAGCAGAAACTCC
1 CTGCAGTATAATGGAAGCCCAAGCAGAAACTCC
*
17586832 CTGCAGTATAGTGGAAGCCCAAGCAGAAAC
1 CTGCAGTATAATGGAAGCCCAAGCAGAAAC
17586862 CAGGGAGTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.24, T:0.14
Consensus pattern (33 bp):
CTGCAGTATAATGGAAGCCCAAGCAGAAACTCC
Found at i:17588854 original size:13 final size:14
Alignment explanation
Indices: 17588822--17588854 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
17588812 TTTAAAAAAA
17588822 TTAAATAAAATTAT
1 TTAAATAAAATTAT
17588836 TT-AATAAAA-TAT
1 TTAAATAAAATTAT
17588848 TTAAATA
1 TTAAATA
17588855 TTATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 11 0.61
14 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAATAAAATTAT
Found at i:17597796 original size:160 final size:160
Alignment explanation
Indices: 17597532--17597853 Score: 635
Period size: 160 Copynumber: 2.0 Consensus size: 160
17597522 AGAATCAACC
17597532 TTTCGGAGGTAATTAAGTGCAATATATGAATCATGGTAGTGCCTTTTTACTATTTGCACTTTATT
1 TTTCGGAGGTAATTAAGTGCAATATATGAATCATGGTAGTGCCTTTTTACTATTTGCACTTTATT
17597597 CTTTGAACTTGATTTGTCAACTCTACTCAATAAACCACTTTTTTGTTGGTTTGAGCTGACTAATC
66 CTTTGAACTTGATTTGTCAACTCTACTCAATAAACCACTTTTTTGTTGGTTTGAGCTGACTAATC
17597662 ATGTTCAAAGGGTAATGAACAAATAATGAG
131 ATGTTCAAAGGGTAATGAACAAATAATGAG
*
17597692 TTTCGGAGGTAATTAAGTGCAATATATGAATCATGGTAGTGCTTTTTTACTATTTGCACTTTATT
1 TTTCGGAGGTAATTAAGTGCAATATATGAATCATGGTAGTGCCTTTTTACTATTTGCACTTTATT
17597757 CTTTGAACTTGATTTGTCAACTCTACTCAATAAACCACTTTTTTGTTGGTTTGAGCTGACTAATC
66 CTTTGAACTTGATTTGTCAACTCTACTCAATAAACCACTTTTTTGTTGGTTTGAGCTGACTAATC
17597822 ATGTTCAAAGGGTAATGAACAAATAATGAG
131 ATGTTCAAAGGGTAATGAACAAATAATGAG
17597852 TT
1 TT
17597854 GATTTGTCAG
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 161 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (160 bp):
TTTCGGAGGTAATTAAGTGCAATATATGAATCATGGTAGTGCCTTTTTACTATTTGCACTTTATT
CTTTGAACTTGATTTGTCAACTCTACTCAATAAACCACTTTTTTGTTGGTTTGAGCTGACTAATC
ATGTTCAAAGGGTAATGAACAAATAATGAG
Found at i:17599500 original size:31 final size:29
Alignment explanation
Indices: 17599425--17599501 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
17599415 TTTAGGATTC
*
17599425 AATTATGATTTACTGCAATGGCAAAAAAA
1 AATTATGATTTACTGCAAGGGCAAAAAAA
** * *
17599454 AATTATGATCCACTGCAAGGGCCAAAATGAG
1 AATTATGATTTACTGCAAGGG-CAAAA-AAA
*
17599485 CATTATGATTTACTGCA
1 AATTATGATTTACTGCA
17599502 TTGAATCGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 18 0.47
30 5 0.13
31 15 0.39
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (29 bp):
AATTATGATTTACTGCAAGGGCAAAAAAA
Found at i:17604246 original size:38 final size:37
Alignment explanation
Indices: 17604175--17604250 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
17604165 ATAAAAAAAT
* * *
17604175 TATTTATTTAATTATTTAATTATATATGTATATTTTA
1 TATTTATTTAATTATTTAATTAAAAATGAATATTTTA
17604212 TATTTATTTAATTTATTTATATTAAAAAT-AATATTTTA
1 TATTTATTTAA-TTATTTA-ATTAAAAATGAATATTTTA
17604250 T
1 T
17604251 TAATTTTAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 11 0.32
38 16 0.47
39 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (37 bp):
TATTTATTTAATTATTTAATTAAAAATGAATATTTTA
Found at i:17612523 original size:25 final size:23
Alignment explanation
Indices: 17612478--17612524 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
17612468 TAGTATTTCA
17612478 TTTACAATTTTTATTATAATAAT
1 TTTACAATTTTTATTATAATAAT
*
17612501 TTTATAATTATTTAATTATAATAA
1 TTTACAATT-TTT-ATTATAATAA
17612525 AAAATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 3 0.14
25 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTACAATTTTTATTATAATAAT
Found at i:17630139 original size:18 final size:18
Alignment explanation
Indices: 17630116--17630163 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
17630106 ACCAGTCCAC
17630116 TTAGCTTAGCCAAGACAT
1 TTAGCTTAGCCAAGACAT
* *
17630134 TTAGCTAACCCAAGACAT
1 TTAGCTTAGCCAAGACAT
17630152 TTAGCTTAGCCA
1 TTAGCTTAGCCA
17630164 CAAAAAAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (18 bp):
TTAGCTTAGCCAAGACAT
Found at i:17639545 original size:6 final size:6
Alignment explanation
Indices: 17639534--17639577 Score: 70
Period size: 6 Copynumber: 7.0 Consensus size: 6
17639524 TTACAAGCAC
17639534 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGAGAGA GAGGGA
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAG-G-GA GAGGGA
17639578 CGGGAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 29 0.81
7 2 0.06
8 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:17639975 original size:30 final size:28
Alignment explanation
Indices: 17639939--17640034 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 28
17639929 ATAAAATAAT
*
17639939 AATTTTTTATTTTATCATTTTATTTAAATA
1 AATTTTTTATTTT-T-ATTATATTTAAATA
* *
17639969 AATTTTTATAATTTTATTATATTCAAATA
1 AATTTTT-TATTTTTATTATATTTAAATA
*
17639998 AATTTTTAATTTTTAATTCATATTTAAATA
1 AATTTTTTATTTTT-ATT-ATATTTAAATA
17640028 AATTTTT
1 AATTTTT
17640035 AACATAAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 5 0.09
29 22 0.39
30 25 0.44
31 5 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
AATTTTTTATTTTTATTATATTTAAATA
Found at i:17640035 original size:30 final size:28
Alignment explanation
Indices: 17639959--17640036 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 28
17639949 TTTATCATTT
17639959 TATTTAAATAAATTTTTATAATTTTATTA
1 TATTTAAATAAATTTTTA-AATTTTATTA
* *
17639988 TATTCAAATAAATTTTTAATTTTTAATTCA
1 TATTTAAATAAATTTTTAAATTTT-ATT-A
17640018 TATTTAAATAAATTTTTAA
1 TATTTAAATAAATTTTTAA
17640037 CATAAAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 5 0.11
29 20 0.45
30 19 0.43
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (28 bp):
TATTTAAATAAATTTTTAAATTTTATTA
Found at i:17640046 original size:18 final size:18
Alignment explanation
Indices: 17640023--17640062 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17640013 ATTCATATTT
*
17640023 AAATAAATTTTTAACATA
1 AAATAAATTTTTAAAATA
*
17640041 AAATAATTTTTTAAAATA
1 AAATAAATTTTTAAAATA
17640059 AAAT
1 AAAT
17640063 TTTATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATAAATTTTTAAAATA
Found at i:17640095 original size:29 final size:29
Alignment explanation
Indices: 17640056--17640130 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
17640046 ATTTTTTAAA
*
17640056 ATAAAATTTTATTTAAATATAAATTAAAATT
1 ATAAAA-TTTATTTAAATAT-AATAAAAATT
* *
17640087 -TAAAATTTATTTCATTATAATAAAAATT
1 ATAAAATTTATTTAAATATAATAAAAATT
* *
17640115 AAAAAATATATTTAAA
1 ATAAAATTTATTTAAA
17640131 AAACAAAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
28 9 0.25
29 22 0.61
30 5 0.14
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
ATAAAATTTATTTAAATATAATAAAAATT
Found at i:17642065 original size:2 final size:2
Alignment explanation
Indices: 17642058--17642092 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
17642048 CGTTGGCAAT
17642058 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17642093 AGTGGATACC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17643765 original size:14 final size:14
Alignment explanation
Indices: 17643746--17643786 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
17643736 CAAAGATTGG
17643746 TGTTCTTTGTATTT
1 TGTTCTTTGTATTT
17643760 TGTTCTTTGTATTT
1 TGTTCTTTGTATTT
*
17643774 GGTT-TTTGT-TTT
1 TGTTCTTTGTATTT
17643786 T
1 T
17643787 TATTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 3 0.12
13 5 0.20
14 17 0.68
ACGTcount: A:0.05, C:0.05, G:0.17, T:0.73
Consensus pattern (14 bp):
TGTTCTTTGTATTT
Found at i:17649305 original size:13 final size:13
Alignment explanation
Indices: 17649287--17649311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17649277 TGTACGAACC
17649287 TTTTTTCCTTTTT
1 TTTTTTCCTTTTT
17649300 TTTTTTCCTTTT
1 TTTTTTCCTTTT
17649312 CGTCTTGTTT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCCTTTTT
Found at i:17651160 original size:93 final size:93
Alignment explanation
Indices: 17651044--17651232 Score: 263
Period size: 93 Copynumber: 2.0 Consensus size: 93
17651034 AGAGATTTTG
* * * *
17651044 GACGTTTTCTCTTTGTACACTTAAAGACCGTTGTATCAG-CTTCTGGATCATCTATTTTTCTTTT
1 GACGTTTCCTCTTTGCACACTTAAAGACCATTGTATC-GTCTTCTGGATCATCCATTTTTCTTTT
* *
17651108 CGGAAATTCAGTTATAATGCAAATATCCT
65 CAGAAATTCAGTTATAATGCAAACATCCT
* * * *
17651137 GACGTTTCCTCTTTGCACTCTTAAAGACCATTGTATCGTTTTCTGGGTCATCCATTTTTTTTTTC
1 GACGTTTCCTCTTTGCACACTTAAAGACCATTGTATCGTCTTCTGGATCATCCATTTTTCTTTTC
*
17651202 AGAAATTCAGTTATAATGCATACATCCT
66 AGAAATTCAGTTATAATGCAAACATCCT
17651230 GAC
1 GAC
17651233 ATGTAAACAT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 1 0.01
93 83 0.99
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.42
Consensus pattern (93 bp):
GACGTTTCCTCTTTGCACACTTAAAGACCATTGTATCGTCTTCTGGATCATCCATTTTTCTTTTC
AGAAATTCAGTTATAATGCAAACATCCT
Found at i:17652984 original size:97 final size:95
Alignment explanation
Indices: 17652801--17652994 Score: 354
Period size: 97 Copynumber: 2.0 Consensus size: 95
17652791 AAGGTTTATG
17652801 CAGCTGCTAATGAAAGAAATTGACTAATAATATCAGAGTAACATAGAGCTGAACAAATCCTCAGG
1 CAGCTGCTAATGAAAGAAATTGACTAATAATATCAGAGTAACATAGAGCTGAACAAATCCTCAGG
17652866 TAGTTTTGACAAGGTGAATTCTAATACTAA
66 TAGTTTTGACAAGGTGAATTCTAATACTAA
17652896 CAGCTGCTAATGAAAGAAATTGACAATTAATAATATCAGAGTAACATAGAGCTGAAC-AATCCTC
1 CAGCTGCTAATGAAAGAAATTGAC---TAATAATATCAGAGTAACATAGAGCTGAACAAATCCTC
17652960 AGGTAGTTTTGACAAGGTGAATTCTAATACTAA
63 AGGTAGTTTTGACAAGGTGAATTCTAATACTAA
17652993 CA
1 CA
17652995 TCTAGTTATA
Statistics
Matches: 96, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
95 24 0.25
97 42 0.44
98 30 0.31
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (95 bp):
CAGCTGCTAATGAAAGAAATTGACTAATAATATCAGAGTAACATAGAGCTGAACAAATCCTCAGG
TAGTTTTGACAAGGTGAATTCTAATACTAA
Found at i:17655379 original size:2 final size:2
Alignment explanation
Indices: 17655372--17655402 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17655362 ACAGAAAGTA
*
17655372 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17655403 CCGAGGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17656228 original size:74 final size:74
Alignment explanation
Indices: 17656103--17656246 Score: 236
Period size: 74 Copynumber: 1.9 Consensus size: 74
17656093 TTTAATATAA
*
17656103 GATATAACATTTTTGAATTCATTCAAATAAGGCCATCTATTATAGTTATGGTTTACATACATAAA
1 GATATAACATTTTTGAATTCATTCAAATAAGGCCATCTATTATAGTGATGGTTTACATACATAAA
17656168 AAATAACAG
66 AAATAACAG
* * *
17656177 GATATAACATTTTTTAATTCATTCAAATAAGGTCC-TCTGTTATAGTGATGGTTTACATACGTAA
1 GATATAACATTTTTGAATTCATTCAAATAAGG-CCATCTATTATAGTGATGGTTTACATACATAA
17656241 AAAATA
65 AAAATA
17656247 GCGTAAATTA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
74 63 0.97
75 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (74 bp):
GATATAACATTTTTGAATTCATTCAAATAAGGCCATCTATTATAGTGATGGTTTACATACATAAA
AAATAACAG
Found at i:17657179 original size:35 final size:36
Alignment explanation
Indices: 17657096--17657183 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 36
17657086 TTTCTTGAAA
*
17657096 AAAAATTGAAATACTTATAAACTTAGGTTTAAAAAAAT
1 AAAAATT-AAA-ACTTATAAAATTAGGTTTAAAAAAAT
* * *
17657134 -AAACTATAAAA-TTATAAAATTTGGTTTGAAAAAAT
1 AAAAAT-TAAAACTTATAAAATTAGGTTTAAAAAAAT
17657169 AAAAATTAAAACTTA
1 AAAAATTAAAACTTA
17657184 ACTTTTAAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
35 26 0.62
36 8 0.19
37 7 0.17
38 1 0.02
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (36 bp):
AAAAATTAAAACTTATAAAATTAGGTTTAAAAAAAT
Found at i:17661921 original size:858 final size:859
Alignment explanation
Indices: 17660363--17662083 Score: 3345
Period size: 858 Copynumber: 2.0 Consensus size: 859
17660353 TTGATATAAC
17660363 ATACAATTATATTCAATTAATGGAAGCACCAACCTAAGATTATCTTAAGTAAAAAAATGAGATGA
1 ATACAATTATATTCAATTAATGGAAGCACCAACCTAAGATTATCTTAAGTAAAAAAATGAGATGA
17660428 AAGATTGATTGGTTATGCATAACTTTATTTTCTCCATATGACAAAGAAAGTTAGTACAATATAAG
66 AAGATTGATTGGTTATGCATAACTTTATTTTCTCCATATGACAAAGAAAGTTAGTACAATATAAG
17660493 GTTTCAATGAAAAATATACTAATATATTGATTTCAAATTTCTTTAAGATTAATATGAAACACTTT
131 GTTTCAATGAAAAATATACTAATATATTGATTTCAAATTTCTTTAAGATTAATATGAAACACTTT
17660558 TATTTAGAAAATCATTACGTGATATCAAAAATTTTAAGATTGTCATATTAGGTAATATTTTTTTA
196 TATTTAGAAAATCATTACGTGATATCAAAAATTTTAAGATTGTCATATTAGGTAATA-TTTTTTA
17660623 AATGAAATGAAATTTATCAAATTAATTATCACATTATATTTAATATAAAAATATTATTATAAATT
260 AATGAAATGAAATTTATCAAATTAATTATCACATTATATTTAATATAAAAATATTATTATAAATT
*
17660688 AAAATTTAACTAAACATAAAAGTGATATAAGATCATTTATTAGTAAAATTCATTTGATAAATCTT
325 AAAATTTAACTAAACATAAAAGTGATATAAGAGCATTTATTAGTAAAATTCATTTGATAAATCTT
17660753 TATTTAATTATATATTTAGTATTTCAATCATTTTGAATTATGACTTTTTATACTTTCAAGTTGGA
390 TATTTAATTATATATTTAGTATTTCAATCATTTTGAATTATGACTTTTTATACTTTCAAGTTGGA
17660818 TTCTAGACATAGGATCAGTGATCAATTGAGTTAAGTCAAGTTTTATTGTATACTTTTATTCATAG
455 TTCTAGACATAGGATCAGTGATCAATTGAGTTAAGTCAAGTTTTATTGTATACTTTTATTCATAG
* *
17660883 AGTACTCAATTATTTACTTATGCAATTGTGCAAAATTAACTTAATAATTTGTGTGTACTTATTTT
520 AGTACTCAATTATTTACTTATGCAATTGTGCAAAATTAACTTAATAATTTATGTATACTTATTTT
* *
17660948 TTATTAAAAAACTAGATTCAAATCGTCTTAAATCCAAATAGAAAAGAAATAACTCAATTACTTAT
585 TTATTAAAAAACTAGATTCAAATCATCTTAAATCCAAATAAAAAAGAAATAACTCAATTACTTAT
17661013 AATTGCAATTTCATTTTAGAAATACTCTTAAAATTAACTAACCAATTCAATCACAAAGACAATAA
650 AATTGCAATTTCATTTTAGAAATACTCTTAAAATTAACTAACCAATTCAATCACAAAGACAATAA
*
17661078 AAATAAGACATTAAAGATGAATGGAAAAAAAACTTAAATAAGAAACTTTTAAATTGTTACAAAAG
715 AAATAAGACATTAAAGATGAATGGAAAAAAAACTTAAATAAGAAACTGTTAAATTGTTACAAAAG
17661143 ATGAATAAGAAATATTAGATTTTTATTGGGTTAGTATTTCAATTTGGATTATGATTATACTAAAT
780 ATGAATAAGAAATATTAGATTTTTATTGGGTTAGTATTTCAATTTGGATTATGATTATACTAAAT
17661208 CATTTCAGGTTTTAA
845 CATTTCAGGTTTTAA
*
17661223 ATACAATTATATTCAATTAATGGAAGCACCAACCTAAGATTATCTTAAGTAGAAAAATGAGATGA
1 ATACAATTATATTCAATTAATGGAAGCACCAACCTAAGATTATCTTAAGTAAAAAAATGAGATGA
*
17661288 AAGATTGATTGGTTATGCATAACTTTATTTTCTCCATATGACAAAGAAAGTTAGTACAATATGAG
66 AAGATTGATTGGTTATGCATAACTTTATTTTCTCCATATGACAAAGAAAGTTAGTACAATATAAG
17661353 GTTTCAATGAAAAATATACTAATATATTGATTTCAAATTTCTTTAAGATTAATATGAAACACTTT
131 GTTTCAATGAAAAATATACTAATATATTGATTTCAAATTTCTTTAAGATTAATATGAAACACTTT
17661418 TATTTAGAAAATCATTACGTGATATCAAAAATTTTAAGATTGTCATATTAGGTAATA-TTTTTAA
196 TATTTAGAAAATCATTACGTGATATCAAAAATTTTAAGATTGTCATATTAGGTAATATTTTTTAA
17661482 ATGAAATGAAATTTATCAAATTAATTATCACATTATATTTAATATAAAAATATTATTATAAATTA
261 ATGAAATGAAATTTATCAAATTAATTATCACATTATATTTAATATAAAAATATTATTATAAATTA
17661547 AAATTTAACTAAACATAAAAGTGATATAAGAGCATTTATTAGTAAAATTCATTTGATAAATCTTT
326 AAATTTAACTAAACATAAAAGTGATATAAGAGCATTTATTAGTAAAATTCATTTGATAAATCTTT
17661612 ATTTAATTATATATTTAGTATTTCAATCATTTTGAATTATGACTTTTTATACTTTCAAGTTGGAT
391 ATTTAATTATATATTTAGTATTTCAATCATTTTGAATTATGACTTTTTATACTTTCAAGTTGGAT
17661677 TCTAGACATAGGATCAGTGATCAATTGAGTTAAGTCAAGTTTTATTGTATACTTTTATTCATAGA
456 TCTAGACATAGGATCAGTGATCAATTGAGTTAAGTCAAGTTTTATTGTATACTTTTATTCATAGA
*
17661742 GTACTCAATTATTTACTTATGCAATTGTGCAAATTTAACTTAATAATTTATGTATACTTATTTTT
521 GTACTCAATTATTTACTTATGCAATTGTGCAAAATTAACTTAATAATTTATGTATACTTATTTTT
17661807 TATTAAAAAACTAGATTCAAATCATCTTAAATCCAAATAAAAAAGAAATAACTCAATTACTTATA
586 TATTAAAAAACTAGATTCAAATCATCTTAAATCCAAATAAAAAAGAAATAACTCAATTACTTATA
17661872 ATTGCAATTTCATTTTAGAAATACTCTTAAAATTAACTAACCAATTCAATCACAAAGACAATAAA
651 ATTGCAATTTCATTTTAGAAATACTCTTAAAATTAACTAACCAATTCAATCACAAAGACAATAAA
17661937 AATAAGACATTAAAGATGAATGGAAAAAAAACTTAAATAAGAAACTGTTAAATTGTTACAAAAGA
716 AATAAGACATTAAAGATGAATGGAAAAAAAACTTAAATAAGAAACTGTTAAATTGTTACAAAAGA
17662002 TGAATAAGAAATATTAGATTTTTATTGGGTTAGTATTTCAATTTGGATTATGATTATACTAAATC
781 TGAATAAGAAATATTAGATTTTTATTGGGTTAGTATTTCAATTTGGATTATGATTATACTAAATC
17662067 ATTTCAGGTTTTAA
846 ATTTCAGGTTTTAA
17662081 ATA
1 ATA
17662084 ACTATTAAGT
Statistics
Matches: 852, Mismatches: 9, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
858 602 0.71
860 250 0.29
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.38
Consensus pattern (859 bp):
ATACAATTATATTCAATTAATGGAAGCACCAACCTAAGATTATCTTAAGTAAAAAAATGAGATGA
AAGATTGATTGGTTATGCATAACTTTATTTTCTCCATATGACAAAGAAAGTTAGTACAATATAAG
GTTTCAATGAAAAATATACTAATATATTGATTTCAAATTTCTTTAAGATTAATATGAAACACTTT
TATTTAGAAAATCATTACGTGATATCAAAAATTTTAAGATTGTCATATTAGGTAATATTTTTTAA
ATGAAATGAAATTTATCAAATTAATTATCACATTATATTTAATATAAAAATATTATTATAAATTA
AAATTTAACTAAACATAAAAGTGATATAAGAGCATTTATTAGTAAAATTCATTTGATAAATCTTT
ATTTAATTATATATTTAGTATTTCAATCATTTTGAATTATGACTTTTTATACTTTCAAGTTGGAT
TCTAGACATAGGATCAGTGATCAATTGAGTTAAGTCAAGTTTTATTGTATACTTTTATTCATAGA
GTACTCAATTATTTACTTATGCAATTGTGCAAAATTAACTTAATAATTTATGTATACTTATTTTT
TATTAAAAAACTAGATTCAAATCATCTTAAATCCAAATAAAAAAGAAATAACTCAATTACTTATA
ATTGCAATTTCATTTTAGAAATACTCTTAAAATTAACTAACCAATTCAATCACAAAGACAATAAA
AATAAGACATTAAAGATGAATGGAAAAAAAACTTAAATAAGAAACTGTTAAATTGTTACAAAAGA
TGAATAAGAAATATTAGATTTTTATTGGGTTAGTATTTCAATTTGGATTATGATTATACTAAATC
ATTTCAGGTTTTAA
Found at i:17663425 original size:22 final size:22
Alignment explanation
Indices: 17663400--17663469 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
17663390 ATAATTATCC
*
17663400 ATAATTTAGCAGTACATTAATG
1 ATAATTTAGTAGTACATTAATG
* * *
17663422 ATAACTT-GATAGTAAATGAATG
1 ATAATTTAG-TAGTACATTAATG
*
17663444 ATAATTTAGTAGT-CAATAATTG
1 ATAATTTAGTAGTACATTAA-TG
17663466 ATAA
1 ATAA
17663470 CTTTTTAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
21 4 0.11
22 32 0.86
23 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (22 bp):
ATAATTTAGTAGTACATTAATG
Found at i:17663492 original size:44 final size:44
Alignment explanation
Indices: 17663400--17663492 Score: 98
Period size: 44 Copynumber: 2.1 Consensus size: 44
17663390 ATAATTATCC
* * * *
17663400 ATAATTTAGCAGTACATTAATGATAACTTGATAGTAAATGAATG
1 ATAATTTAGCAGTACAATAATGATAACTTGATAATAAATCAATA
* ** *
17663444 ATAATTTAGTAGT-CAATAATTGATAACTTTTTAATAAATCATTA
1 ATAATTTAGCAGTACAATAA-TGATAACTTGATAATAAATCAATA
17663488 ATAAT
1 ATAAT
17663493 ATAATAATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
43 5 0.12
44 35 0.88
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (44 bp):
ATAATTTAGCAGTACAATAATGATAACTTGATAATAAATCAATA
Found at i:17665606 original size:43 final size:44
Alignment explanation
Indices: 17665503--17665610 Score: 125
Period size: 43 Copynumber: 2.5 Consensus size: 44
17665493 TATAAACAAA
* *
17665503 TTAGTAGTAAATCAATT-ATAAATTAAAAGTAAATAATTGATAAT
1 TTAGTAGTAAATC-ATTGATAAATTAAAAGAAAATAATTGATAAC
* *
17665547 TTAGTAGTTAACCATTGA-AAACTTAAAAGAAAATCAA-T-ATAAC
1 TTAGTAGTAAATCATTGATAAA-TTAAAAGAAAAT-AATTGATAAC
17665590 TTAGTAGTAAATCATTGATAA
1 TTAGTAGTAAATCATTGATAA
17665611 CATAATAGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
43 26 0.48
44 26 0.48
45 2 0.04
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.33
Consensus pattern (44 bp):
TTAGTAGTAAATCATTGATAAATTAAAAGAAAATAATTGATAAC
Done.