Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 19 of 160
Found at i:5378977 original size:50 final size:50
Alignment explanation
Indices: 5378888--5378985 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
5378878 AACTCAACAT
* *
5378888 TTTTTGGTTTTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGT
1 TTTTTGGTTTTTTTGTTTTTTTTTGTTTTTTTGTATTTTTATTTTTTTGT
*
5378938 TTTTTTGTTTTTTTGTTTTTTGTTT-TTTATTTT-TATTTTTATTTTTTT
1 TTTTTGGTTTTTTTGTTTTTT-TTTGTTT-TTTTGTATTTTTATTTTTTT
5378986 TTACCAAAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
50 36 0.84
51 7 0.16
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (50 bp):
TTTTTGGTTTTTTTGTTTTTTTTTGTTTTTTTGTATTTTTATTTTTTTGT
Found at i:5378985 original size:8 final size:8
Alignment explanation
Indices: 5378887--5378965 Score: 124
Period size: 8 Copynumber: 9.8 Consensus size: 8
5378877 CAACTCAACA
*
5378887 TTTTTTGG
1 TTTTTTTG
5378895 TTTTTTTG
1 TTTTTTTG
5378903 TTTTTTTTTG
1 --TTTTTTTG
5378913 TTTTTTTG
1 TTTTTTTG
5378921 TTTTTTTG
1 TTTTTTTG
5378929 TTTTTTTG
1 TTTTTTTG
5378937 TTTTTTTG
1 TTTTTTTG
5378945 TTTTTTTG
1 TTTTTTTG
5378953 -TTTTTTG
1 TTTTTTTG
5378960 TTTTTT
1 TTTTTT
5378966 ATTTTTATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
7 7 0.10
8 52 0.78
10 8 0.12
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:5378987 original size:24 final size:23
Alignment explanation
Indices: 5378897--5378987 Score: 114
Period size: 24 Copynumber: 4.0 Consensus size: 23
5378887 TTTTTTGGTT
5378897 TTTTTGTTTTTTTTTGTTTTTTTG
1 TTTTT-TTTTTTTTTGTTTTTTTG
5378921 TTTTTTTGTTTTTTTGTTTTTTTG
1 TTTTTTT-TTTTTTTGTTTTTTTG
* *
5378945 TTTTTTTGTTTTTTG-TTTTTTA
1 TTTTTTTTTTTTTTGTTTTTTTG
* *
5378967 TTTTTATTTTTATT-TTTTTTT
1 TTTTTTTTTTTTTTGTTTTTTT
5378988 ACCAAAGCTC
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
22 23 0.38
23 9 0.15
24 28 0.47
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (23 bp):
TTTTTTTTTTTTTTGTTTTTTTG
Found at i:5379157 original size:40 final size:40
Alignment explanation
Indices: 5378994--5379404 Score: 575
Period size: 42 Copynumber: 10.0 Consensus size: 40
5378984 TTTTACCAAA
5378994 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACA-TAAATT
1 GCTCCTCTAAACAGAGG--CAACGACTTTG-GAAA-AGTAAATT
5379037 GCTCCTCTAAACAGAGGCACCACGACTTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGAC-TTTGGAAAAGTAAATT
5379079 GCTCCTCTAAACAGAGGCAACGAAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG--ACTTTGGAAAAGTAAATT
5379120 GCTCCTCTAAACAGAGGCAACGAAC-TTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAATT
5379160 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATT
5379202 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATT
*
5379244 GCTCCTCTAAACAAAGGCAACGAACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAATT
5379284 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATT
5379326 GCTCCTCTAAACAGAGGCAACGAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAATT
* *
5379366 GCTCCTCTAAACAGAGGCAACAAAC-TTGGAAAGGTAAAT
1 GCTCCTCTAAACAGAGGCAAC-GACTTTGGAAAAGTAAAT
5379405 ACTCCTAGAC
Statistics
Matches: 346, Mismatches: 4, Indels: 39
0.89 0.01 0.10
Matches are distributed among these distances:
39 4 0.01
40 117 0.34
41 59 0.17
42 139 0.40
43 23 0.07
44 4 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (40 bp):
GCTCCTCTAAACAGAGGCAACGACTTTGGAAAAGTAAATT
Found at i:5379278 original size:82 final size:82
Alignment explanation
Indices: 5378994--5379384 Score: 614
Period size: 82 Copynumber: 4.7 Consensus size: 82
5378984 TTTTACCAAA
*
5378994 GCTCCTCTAAACAGAGGCTCAACG-ACTTTGAGAAACATAAATTGCTCCTCTAAACAGAGGCACC
1 GCTCCTCTAAACAGAGG--CAACGAACTTTG-GAAA-GTAAATTGCTCCTCTAAACAGAGGCACC
5379058 ACGACTTTTGG-AAAGTAAATT
62 ACGAC-TTTGGAAAAGTAAATT
*
5379079 GCTCCTCTAAACAGAGGCAACGAAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
1 GCTCCTCTAAACAGAGGCAACG-AACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
5379142 AAC-TTGGAAAAGTAAATT
65 -ACTTTGGAAAAGTAAATT
5379160 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCA--ACGAACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCA
5379224 CGACTTTGGAAAAGTAAATT
63 CGACTTTGGAAAAGTAAATT
*
5379244 GCTCCTCTAAACAAAGGCAACGAACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
1 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
5379309 CTTTGGAAAAGTAAATT
66 CTTTGGAAAAGTAAATT
*
5379326 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
1 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCA
5379385 ACAAACTTGG
Statistics
Matches: 289, Mismatches: 6, Indels: 25
0.90 0.02 0.08
Matches are distributed among these distances:
80 4 0.01
81 38 0.13
82 143 0.49
83 42 0.15
84 39 0.13
85 23 0.08
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
CTTTGGAAAAGTAAATT
Found at i:5380649 original size:9 final size:9
Alignment explanation
Indices: 5380629--5380667 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
5380619 TTTGAATCTC
5380629 TTTTTTT-A
1 TTTTTTTCA
5380637 -TTTTTTCA
1 TTTTTTTCA
5380645 -TTTTTTCA
1 TTTTTTTCA
5380653 TTTTTTTCA
1 TTTTTTTCA
5380662 TTTTTT
1 TTTTTT
5380668 CTTCTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 6 0.21
8 9 0.31
9 14 0.48
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:5380665 original size:7 final size:8
Alignment explanation
Indices: 5380629--5380668 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
5380619 TTTGAATCTC
*
5380629 TTTTTTTA
1 TTTTTTCA
5380637 TTTTTTCA
1 TTTTTTCA
5380645 TTTTTTCA
1 TTTTTTCA
5380653 TTTTTTTCA
1 -TTTTTTCA
5380662 TTTTTTC
1 TTTTTTC
5380669 TTCTTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCA
Found at i:5380683 original size:16 final size:15
Alignment explanation
Indices: 5380627--5380699 Score: 62
Period size: 15 Copynumber: 4.7 Consensus size: 15
5380617 AATTTGAATC
5380627 TCTTTTTTTAT-TTTT
1 TCTTTTTTT-TCTTTT
5380642 TCATTTTTTCATT-TTTT
1 TC-TTTTTT--TTCTTTT
*
5380659 TC-ATTTTTTCTTCTT
1 TCTTTTTTTTCTT-TT
5380674 TCTTTCTTTTTCTTTT
1 TCTTT-TTTTTCTTTT
5380690 TCTTTTTTTT
1 TCTTTTTTTT
5380700 TCATCATCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 15 0.31
16 14 0.29
17 15 0.31
18 1 0.02
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (15 bp):
TCTTTTTTTTCTTTT
Found at i:5380698 original size:8 final size:8
Alignment explanation
Indices: 5380627--5380698 Score: 60
Period size: 8 Copynumber: 9.1 Consensus size: 8
5380617 AATTTGAATC
5380627 TCTTTTTT
1 TCTTTTTT
*
5380635 T-ATTTTT
1 TCTTTTTT
*
5380642 TCATTTTT
1 TCTTTTTT
5380650 TCATTTTTT
1 TC-TTTTTT
*
5380659 TCATTTTT
1 TCTTTTTT
*
5380667 TC-TTCTT
1 TCTTTTTT
5380674 TCTTTCTTT
1 TCTTT-TTT
*
5380683 T-TCTTTT
1 TCTTTTTT
5380690 TCTTTTTT
1 TCTTTTTT
5380698 T
1 T
5380699 TTCATCATCT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
7 16 0.31
8 26 0.50
9 10 0.19
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (8 bp):
TCTTTTTT
Found at i:5380700 original size:16 final size:16
Alignment explanation
Indices: 5380662--5380718 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
5380652 ATTTTTTTCA
5380662 TTTTTTCTTCTTTCTTT
1 TTTTTTCTT-TTTCTTT
*
5380679 CTTTTTCTTTTTCTTT
1 TTTTTTCTTTTTCTTT
* **
5380695 TTTTTTCATCATCTTT
1 TTTTTTCTTTTTCTTT
5380711 TTTTTTCT
1 TTTTTTCT
5380719 CATTCTTCAC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
16 26 0.76
17 8 0.24
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTCTTTTTCTTT
Found at i:5380725 original size:16 final size:17
Alignment explanation
Indices: 5380662--5380725 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 17
5380652 ATTTTTTTCA
* *
5380662 TTTTTTCTTCTTTCTTT
1 TTTTTTCATCATTCTTT
* **
5380679 CTTTTTC-TTTTTCTTT
1 TTTTTTCATCATTCTTT
5380695 TTTTTTCATCA-TCTTT
1 TTTTTTCATCATTCTTT
5380711 TTTTTTC-TCATTCTT
1 TTTTTTCATCATTCTT
5380726 CACCTATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.08
16 30 0.75
17 7 0.17
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTCATCATTCTTT
Found at i:5384886 original size:57 final size:57
Alignment explanation
Indices: 5384555--5385060 Score: 795
Period size: 57 Copynumber: 8.7 Consensus size: 57
5384545 TTTTTTGTAG
*
5384555 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAATTT--ATTTCT-AA
* **
5384614 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTG-AAATTTATTTCTAA
5384673 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGAAA-TTT-ATTTCT-AA
*
5384733 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATATTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCC-CAAAA-ATAT-TTTTTTGAAATTTATTTCTAA
5384793 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAATTTATTTCTAA
5384849 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAATTTATTTCTAA
*
5384905 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAATTTATTTCTAA
* *
5384962 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAATTTATTTCTAA
*
5385019 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
5385061 TGGAATTTTT
Statistics
Matches: 422, Mismatches: 12, Indels: 28
0.91 0.03 0.06
Matches are distributed among these distances:
56 101 0.24
57 131 0.31
58 7 0.02
59 84 0.20
60 71 0.17
61 15 0.04
62 13 0.03
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAATTTATTTCTAA
Found at i:5384995 original size:27 final size:27
Alignment explanation
Indices: 5384964--5385052 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
5384954 ATTTCTAAGG
5384964 AAAATTGATACTTTCAACTTTTCCCTA
1 AAAATTGATACTTTCAACTTTTCCCTA
** * * **
5384991 AAAA-T-ATTTTTTGGAAATTTATTTCTAA
1 AAAATTGATACTTT-CAACTTT-TCCCT-A
5385019 GGAAAATTGATACTTTCAACTTTTCCCTA
1 --AAAATTGATACTTTCAACTTTTCCCTA
5385048 AAAAT
1 AAAAT
5385053 ATTTTTTTTG
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
25 5 0.12
26 6 0.14
27 12 0.28
28 1 0.02
29 1 0.02
30 7 0.16
31 6 0.14
32 5 0.12
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTCCCTA
Found at i:5386135 original size:16 final size:16
Alignment explanation
Indices: 5386116--5386220 Score: 60
Period size: 16 Copynumber: 6.6 Consensus size: 16
5386106 TATTAGTAAT
5386116 AATACATAAATAATAA
1 AATACATAAATAATAA
*
5386132 AATACACATAAATATTAA
1 AAT--ACATAAATAATAA
* *
5386150 CAAAAAATAAATAA-ATA
1 -AATACATAAATAATA-A
* * *
5386167 AATATATACAT-ATATT
1 AATACATAAATAATA-A
5386183 AATACAT-AATAAT--
1 AATACATAAATAATAA
*
5386196 AATA-ATAAATAATAC
1 AATACATAAATAATAA
5386211 AATACATAAA
1 AATACATAAA
5386221 ATACAAAAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
12 2 0.03
13 10 0.14
15 7 0.10
16 27 0.39
17 9 0.13
18 12 0.17
19 2 0.03
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.28
Consensus pattern (16 bp):
AATACATAAATAATAA
Found at i:5386194 original size:35 final size:34
Alignment explanation
Indices: 5386086--5386211 Score: 100
Period size: 35 Copynumber: 3.6 Consensus size: 34
5386076 AATAAAAAAG
* *
5386086 ATAAA-AAATATATATATACATATTAGTAATAATA
1 ATAAATAAATAAATATATACATA-TATTAATAATA
* * *
5386120 CATAAAT-AATAAA-ATACACATAAATATTAACAAAAA
1 -ATAAATAAATAAATATATACAT--ATATTAA-TAATA
5386156 ATAAATAAATAAATATATACATATATTAATACATA
1 ATAAATAAATAAATATATACATATATTAATA-ATA
5386191 AT-AATAATAATAAATA-ATACA
1 ATAAAT-A-AATAAATATATACA
5386212 ATACATAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
34 11 0.15
35 38 0.51
36 18 0.24
37 7 0.09
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (34 bp):
ATAAATAAATAAATATATACATATATTAATAATA
Found at i:5387129 original size:16 final size:16
Alignment explanation
Indices: 5387110--5387141 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5387100 AATCAAACTG
5387110 AATTCAAAATAATTCA
1 AATTCAAAATAATTCA
*
5387126 AATTTAAAATAATTCA
1 AATTCAAAATAATTCA
5387142 TGTCTGAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTCAAAATAATTCA
Found at i:5387721 original size:12 final size:12
Alignment explanation
Indices: 5387706--5387731 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5387696 GCAAAAATGT
5387706 ATAAAAAATAAA
1 ATAAAAAATAAA
5387718 ATAAAAAATAAA
1 ATAAAAAATAAA
5387730 AT
1 AT
5387732 TACCTAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:5392140 original size:8 final size:8
Alignment explanation
Indices: 5392127--5392155 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
5392117 TTTAATTTTA
5392127 ATTAAAAT
1 ATTAAAAT
5392135 ATTAAAAT
1 ATTAAAAT
5392143 ATTAAAAT
1 ATTAAAAT
5392151 ATTAA
1 ATTAA
5392156 CATTAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATTAAAAT
Found at i:5392994 original size:28 final size:28
Alignment explanation
Indices: 5392962--5393018 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
5392952 ACTGAAAAAC
5392962 ATAGTATTAG-AATTGAATTAGATAATGA
1 ATAGTA-TAGAAATTGAATTAGATAATGA
*
5392990 ATAGTATCGAAATTGAATTAGATAATGA
1 ATAGTATAGAAATTGAATTAGATAATGA
5393018 A
1 A
5393019 CCGTTCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (28 bp):
ATAGTATAGAAATTGAATTAGATAATGA
Found at i:5393446 original size:10 final size:10
Alignment explanation
Indices: 5393420--5393456 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5393410 ATTTATCATT
5393420 TTAA-TAAAA
1 TTAATTAAAA
5393429 TT--TTAAAA
1 TTAATTAAAA
5393437 TTAATTAAAA
1 TTAATTAAAA
5393447 TTAATTAAAA
1 TTAATTAAAA
5393457 AGATAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 2 0.08
10 16 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TTAATTAAAA
Found at i:5395520 original size:14 final size:13
Alignment explanation
Indices: 5395478--5395558 Score: 55
Period size: 12 Copynumber: 6.4 Consensus size: 13
5395468 TCACCAGCCC
*
5395478 TTTTGTTTTTTAT
1 TTTTGTTTTTTCT
*
5395491 TTTT-TTTTTAGC-
1 TTTTGTTTTT-TCT
5395503 TTTTGTTTTTTCGT
1 TTTTGTTTTTTC-T
*
5395517 TTTTGCATTTTTCT
1 TTTTG-TTTTTTCT
*
5395531 ATTTG-TTTTT-T
1 TTTTGTTTTTTCT
*
5395542 TTTTCTTTTTT-T
1 TTTTGTTTTTTCT
5395554 TTTTG
1 TTTTG
5395559 GTATTTTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
11 4 0.07
12 25 0.46
13 9 0.17
14 10 0.19
15 6 0.11
ACGTcount: A:0.05, C:0.06, G:0.09, T:0.80
Consensus pattern (13 bp):
TTTTGTTTTTTCT
Found at i:5395544 original size:17 final size:15
Alignment explanation
Indices: 5395524--5395557 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
5395514 CGTTTTTGCA
5395524 TTTTTCTATTTGTTTTT
1 TTTTTCT-TTT-TTTTT
5395541 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
5395556 TT
1 TT
5395558 GGTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.88
Consensus pattern (15 bp):
TTTTTCTTTTTTTTT
Found at i:5395650 original size:36 final size:36
Alignment explanation
Indices: 5395603--5395674 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
5395593 ATAATAGGCT
5395603 GAGCCTAAAGAACAAAATGAGTTTCGAATCCGATCA
1 GAGCCTAAAGAACAAAATGAGTTTCGAATCCGATCA
5395639 GAGCCTAAAGAACAAAATGAGTTTCGAATCCGATCA
1 GAGCCTAAAGAACAAAATGAGTTTCGAATCCGATCA
5395675 AAATTAGACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (36 bp):
GAGCCTAAAGAACAAAATGAGTTTCGAATCCGATCA
Found at i:5397239 original size:11 final size:11
Alignment explanation
Indices: 5397223--5397248 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5397213 AATTTTCTTT
5397223 TTTTTTAATTC
1 TTTTTTAATTC
5397234 TTTTTTAATTC
1 TTTTTTAATTC
5397245 TTTT
1 TTTT
5397249 AAATAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTAATTC
Found at i:5399812 original size:6 final size:7
Alignment explanation
Indices: 5399795--5399819 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5399785 AAATTTAGAA
5399795 AAAAAAT
1 AAAAAAT
5399802 AAAAAAT
1 AAAAAAT
5399809 AAAAAAT
1 AAAAAAT
5399816 AAAA
1 AAAA
5399820 TTTAGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:5400008 original size:24 final size:23
Alignment explanation
Indices: 5399981--5400025 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
5399971 ATTTTTCAAC
5399981 AAAAAATTATAATAAA-AAAAATCA
1 AAAAAATTA-AA-AAATAAAAATCA
5400005 AAAAAATTAAAAAATAAAAAT
1 AAAAAATTAAAAAATAAAAAT
5400026 TTTGAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAAAATTAAAAAATAAAAATCA
Found at i:5400121 original size:206 final size:199
Alignment explanation
Indices: 5399793--5400192 Score: 433
Period size: 206 Copynumber: 2.0 Consensus size: 199
5399783 TTAAATTTAG
5399793 AAAAAAAATAAAAAATAAAAAATAAAATTTAGGAAAAAATATCAATTATCCAATGATGAAATTTA
1 AAAAAAAATAAAAAATAAAAAATAAAATTTAGGAAAAAATATCAATTATCCAATGATGAAATTTA
* * * * *
5399858 TAGAATTTTTAAATGGTAAATTTTTATAAAATTCCTAGGTGAGAAATTATATCTAAATTTATCCC
66 TAAAAATTTCAAATGGTAAATTTCTATAAAATTCCTAGGTGAAAAATTATATCTAAATTTAT-CC
*
5399923 AAATTG-TAGAATAATTTAAAT-AAAGTTTCAATAACAA-TAATTAATATTATTTTTCAACAAAA
130 AAAATGATAGAATAATTTAAATGAAA-TTTCAA-AACAAGTAATT-ATATTATTTTTCAA-AAAA
5399985 AATTATAAT
191 AATTATAAT
*
5399994 AAAAAAAATCAAAAAAATTAAAAAATAAAAATTT-TGAAATTAAATA-CAAATTA-CTCAATGAT
1 AAAAAAAAT--AAAAAA-TAAAAAAT-AAAATTTAGGAAA--AAATATC-AATTATC-CAATGAT
* * *
5400056 GAGATTTTTAAAAATTTCAAATGGT-AATTTCCTA-AGAAA-TCTCTAGGTGAAAAA-TATTCTC
58 GAAATTTATAAAAATTTCAAATGGTAAATTT-CTATA-AAATTC-CTAGGTGAAAAATTA-TATC
* * * * *
5400117 TAAATTTGTCCAAAATGATAGAATAATTTAGATGAAATTTCAACACAAGTAATTGTATTCTTTTT
119 TAAATTTATCCAAAATGATAGAATAATTTAAATGAAATTTCAAAACAAGTAATTATATTATTTTT
*
5400182 CAAATAAAATT
184 CAAAAAAAATT
5400193 TTGGTTGAAA
Statistics
Matches: 168, Mismatches: 16, Indels: 27
0.80 0.08 0.13
Matches are distributed among these distances:
201 9 0.05
203 6 0.04
204 19 0.11
205 42 0.25
206 89 0.53
207 3 0.02
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (199 bp):
AAAAAAAATAAAAAATAAAAAATAAAATTTAGGAAAAAATATCAATTATCCAATGATGAAATTTA
TAAAAATTTCAAATGGTAAATTTCTATAAAATTCCTAGGTGAAAAATTATATCTAAATTTATCCA
AAATGATAGAATAATTTAAATGAAATTTCAAAACAAGTAATTATATTATTTTTCAAAAAAAATTA
TAAT
Found at i:5401238 original size:13 final size:13
Alignment explanation
Indices: 5401214--5401267 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
5401204 AAATTCACAC
5401214 AAAAATAT-AATA
1 AAAAATATAAATA
5401226 AAAAATATAAATA
1 AAAAATATAAATA
*
5401239 ATAGAA-ATAAATA
1 A-AAAATATAAATA
5401252 ATAAAATATAAA-A
1 A-AAAATATAAATA
5401265 AAA
1 AAA
5401268 TGAGCAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
12 10 0.27
13 19 0.51
14 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (13 bp):
AAAAATATAAATA
Found at i:5401256 original size:29 final size:28
Alignment explanation
Indices: 5401214--5401306 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 28
5401204 AAATTCACAC
*
5401214 AAAAATATAATAAAAAATATAAATAAT-AG
1 AAAAA-ATAATAAAAAATA-AAAAAATGAG
*
5401243 AAATAAATAATAAAATATAAAAAAATGAG
1 AAA-AAATAATAAAAAATAAAAAAATGAG
* *
5401272 CAAAAA-AATAAAAAAT-AAAAAATTATG
1 AAAAAATAATAAAAAATAAAAAAATGA-G
5401299 AAAAAATA
1 AAAAAATA
5401307 TTGAAAATGC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
26 8 0.15
27 15 0.28
28 10 0.19
29 19 0.35
30 2 0.04
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.20
Consensus pattern (28 bp):
AAAAAATAATAAAAAATAAAAAAATGAG
Found at i:5401303 original size:27 final size:27
Alignment explanation
Indices: 5401214--5401306 Score: 93
Period size: 27 Copynumber: 3.3 Consensus size: 27
5401204 AAATTCACAC
5401214 AAAAATATAATAAAAAATATAAATAATA-G
1 AAAAA-ATAATAAAAAATA-AAA-AATATG
*
5401243 AAATAAATAATAAAATATAAAAAA-ATG
1 AAA-AAATAATAAAAAATAAAAAATATG
5401270 AGCAAAAA-AATAAAAAATAAAAAATTATG
1 A--AAAAATAATAAAAAATAAAAAA-TATG
5401299 AAAAAATA
1 AAAAAATA
5401307 TTGAAAATGC
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
26 1 0.02
27 24 0.44
28 7 0.13
29 21 0.38
30 2 0.04
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.20
Consensus pattern (27 bp):
AAAAAATAATAAAAAATAAAAAATATG
Found at i:5406244 original size:25 final size:23
Alignment explanation
Indices: 5406186--5406246 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
5406176 AACCGAGCCG
5406186 TTTTGATTTTTTTTTTTGCATTT
1 TTTTGATTTTTTTTTTTGCATTT
* *
5406209 TCTTTGGTTTTTTCTTTTTGGTATTT
1 T-TTTGATTTTTT-TTTTT-GCATTT
*
5406235 TTTTTATTTTTT
1 TTTTGATTTTTT
5406247 ATTTATGCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 10 0.32
25 14 0.45
26 6 0.19
ACGTcount: A:0.07, C:0.05, G:0.10, T:0.79
Consensus pattern (23 bp):
TTTTGATTTTTTTTTTTGCATTT
Found at i:5406351 original size:15 final size:15
Alignment explanation
Indices: 5406331--5406359 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5406321 ATAAAATAAA
5406331 ATTTTTAAGAAAAAT
1 ATTTTTAAGAAAAAT
5406346 ATTTTTAAGAAAAA
1 ATTTTTAAGAAAAA
5406360 GTTGAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
ATTTTTAAGAAAAAT
Found at i:5406506 original size:59 final size:60
Alignment explanation
Indices: 5406323--5406570 Score: 218
Period size: 60 Copynumber: 4.0 Consensus size: 60
5406313 TAAAAAATAT
* * * *
5406323 AAAATAAAATTTTTAAGAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAATAAAATTATCAAGAAAAAAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
** ** *
5406383 AAAATAAAA--AAAAATCTCAAAAAGTATTTTGAGGAAAAGTTGAAAGTTTGAAAGTATCAATTT
1 AAAATAAAATTATCAA--GAAAAAAAT-TTTTGA-G--AA----AAAG-TTGAAAGTATCAATTT
5406446 TTCTTG
55 TTCTTG
* * *
5406452 AAATTAAAATT-TCAA-AAAAAAATATTTTGAGAAAAAGTTGGAAGTA-CAAATTTTTCTTA
1 AAAATAAAATTATCAAGAAAAAAAT-TTTTGAGAAAAAGTTGAAAGTATC-AATTTTTCTTG
* *
5406511 AAAATAAAATTATCAAGAAAAACATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAATAAAATTATCAAGAAAAAAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
5406571 TATAAAAGCA
Statistics
Matches: 151, Mismatches: 20, Indels: 34
0.74 0.10 0.17
Matches are distributed among these distances:
58 3 0.02
59 28 0.19
60 52 0.34
61 13 0.09
62 1 0.01
64 4 0.03
66 1 0.01
67 13 0.09
68 4 0.03
69 30 0.20
70 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.34
Consensus pattern (60 bp):
AAAATAAAATTATCAAGAAAAAAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:5408010 original size:21 final size:22
Alignment explanation
Indices: 5407986--5408030 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5407976 ATAAGTATAA
5407986 TTAC-CTTTAAAATAATATTTT
1 TTACACTTTAAAATAATATTTT
* *
5408007 TTACACTTTAAAGTTATATTTT
1 TTACACTTTAAAATAATATTTT
5408029 TT
1 TT
5408031 TCTTTCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (22 bp):
TTACACTTTAAAATAATATTTT
Found at i:5408486 original size:30 final size:30
Alignment explanation
Indices: 5408418--5408490 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
5408408 ATTTTTATTG
*
5408418 TATTTAAATAAATTTTTAACTTTTAATTTGA
1 TATTCAAAT-AATTTTTAACTTTTAATTTGA
**
5408449 -ACCCAAATAATTCTTTAACTTTTAATTT-A
1 TATTCAAATAATT-TTTAACTTTTAATTTGA
5408478 TATTCAAATAATT
1 TATTCAAATAATT
5408491 GATCACTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (30 bp):
TATTCAAATAATTTTTAACTTTTAATTTGA
Found at i:5414018 original size:11 final size:11
Alignment explanation
Indices: 5413994--5414031 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5413984 TTTTAAACTG
5413994 TATTATTTATA
1 TATTATTTATA
5414005 TATT-TTTATCA
1 TATTATTTAT-A
*
5414016 TATCATTTATA
1 TATTATTTATA
5414027 TATTA
1 TATTA
5414032 CATCATCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 5 0.22
11 13 0.57
12 5 0.22
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTATTTATA
Found at i:5418638 original size:3 final size:3
Alignment explanation
Indices: 5418630--5418655 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5418620 GTCCTATATA
5418630 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
5418656 ATGGCTACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:5423527 original size:14 final size:13
Alignment explanation
Indices: 5423510--5423541 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
5423500 TCATTTTATG
5423510 TTTTATGTTTTTTT
1 TTTTA-GTTTTTTT
5423524 TTTTAGTTTTTTT
1 TTTTAGTTTTTTT
5423537 TTTTA
1 TTTTA
5423542 ATTATAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.84
Consensus pattern (13 bp):
TTTTAGTTTTTTT
Found at i:5423887 original size:21 final size:21
Alignment explanation
Indices: 5423865--5423906 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5423855 TGTTTTTAAA
5423865 TTAAAATAAAATAAAATAAAAT
1 TTAAAA-AAAATAAAATAAAAT
* *
5423887 TTTAAAAATATAAAATAAAA
1 TTAAAAAAAATAAAATAAAA
5423907 AAACATACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
TTAAAAAAAATAAAATAAAAT
Found at i:5426636 original size:19 final size:20
Alignment explanation
Indices: 5426600--5426642 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
5426590 TGTTATCTCA
**
5426600 TTTAATTTTTTATCATTTT-
1 TTTAATTTTTTAAAATTTTG
*
5426619 TTTATTTTTTTAAAATTTTG
1 TTTAATTTTTTAAAATTTTG
5426639 TTTA
1 TTTA
5426643 CAATAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTAATTTTTTAAAATTTTG
Found at i:5427089 original size:21 final size:22
Alignment explanation
Indices: 5427065--5427106 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5427055 TATTTTAATT
5427065 TAATAAAATTAT-ATTTATATA
1 TAATAAAATTATAATTTATATA
* *
5427086 TAATTAAGTTATAATTTATAT
1 TAATAAAATTATAATTTATAT
5427107 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TAATAAAATTATAATTTATATA
Found at i:5428770 original size:24 final size:24
Alignment explanation
Indices: 5428743--5428794 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5428733 TTTGATATTG
*
5428743 TTTTATG-TTATGCAGTGCAAGTTC
1 TTTTATGCTT-TGCAGTCCAAGTTC
*
5428767 TTTTATGCTTTGCATTCCAAGTTC
1 TTTTATGCTTTGCAGTCCAAGTTC
5428791 TTTT
1 TTTT
5428795 TAGTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.52
Consensus pattern (24 bp):
TTTTATGCTTTGCAGTCCAAGTTC
Found at i:5437649 original size:14 final size:14
Alignment explanation
Indices: 5437616--5437649 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5437606 TATATGATTT
*
5437616 TAATTTATATTTTA
1 TAATTTATATTTAA
5437630 TAATTTATATTTAA
1 TAATTTATATTTAA
*
5437644 TTATTT
1 TAATTT
5437650 TCATTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TAATTTATATTTAA
Found at i:5438167 original size:15 final size:16
Alignment explanation
Indices: 5438137--5438167 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5438127 GGTTAAACCT
*
5438137 TTAAATTTGAAAAAAA
1 TTAAATTCGAAAAAAA
5438153 TTAAATTCGAAAAAA
1 TTAAATTCGAAAAAA
5438168 CAAAAACCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.29
Consensus pattern (16 bp):
TTAAATTCGAAAAAAA
Found at i:5439979 original size:4 final size:4
Alignment explanation
Indices: 5439970--5439994 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5439960 CAAGGAAGCA
5439970 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
5439995 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:5444087 original size:30 final size:32
Alignment explanation
Indices: 5444034--5444092 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
5444024 TTTCCATAAC
*
5444034 TTTTTTTGTCATTAAAATCAAATCAAGTTTTT
1 TTTTTTTGCCATTAAAATCAAATCAAGTTTTT
*
5444066 TTTTTTTGCCA-T-AAATTAAATCAAGTT
1 TTTTTTTGCCATTAAAATCAAATCAAGTT
5444093 GAAACCTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.56
31 1 0.04
32 10 0.40
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (32 bp):
TTTTTTTGCCATTAAAATCAAATCAAGTTTTT
Found at i:5447724 original size:14 final size:13
Alignment explanation
Indices: 5447698--5447731 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5447688 TAAAAAAATC
5447698 AATTTTATTAAAA
1 AATTTTATTAAAA
*
5447711 AATTTTATTTAAA
1 AATTTTATTAAAA
*
5447724 AATATTAT
1 AATTTTAT
5447732 AGAAACTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTTATTAAAA
Found at i:5448621 original size:21 final size:20
Alignment explanation
Indices: 5448592--5448753 Score: 107
Period size: 20 Copynumber: 8.1 Consensus size: 20
5448582 GGTTAAGAGG
*
5448592 TTGACTTTGGGTTTTAAGGT
1 TTGACTTTGGGGTTTAAGGT
* * *
5448612 TTGACTTTTGAGTTTAGGGT
1 TTGACTTTGGGGTTTAAGGT
* **
5448632 TTGTCTTTAAGGTTT-AGGAT
1 TTGACTTTGGGGTTTAAGG-T
* * *
5448652 TTAACATTGGGGTTTAGGGT
1 TTGACTTTGGGGTTTAAGGT
*
5448672 TTGAATTTTGGGGTTTAAGGT
1 TTG-ACTTTGGGGTTTAAGGT
*
5448693 TTGACTTTGGGGGTTT-AGGAG
1 TTGACTTT-GGGGTTTAAGG-T
* * *
5448714 TTGACTTT-AGATTTTAGTGT
1 TTGACTTTGGGGTTTAAG-GT
*
5448734 TTGACTTT-GGGTTTAGGGT
1 TTGACTTTGGGGTTTAAGGT
5448753 T
1 T
5448754 AAGTTTTGAG
Statistics
Matches: 107, Mismatches: 28, Indels: 15
0.71 0.19 0.10
Matches are distributed among these distances:
19 9 0.08
20 63 0.59
21 35 0.33
ACGTcount: A:0.17, C:0.04, G:0.31, T:0.48
Consensus pattern (20 bp):
TTGACTTTGGGGTTTAAGGT
Found at i:5450419 original size:10 final size:10
Alignment explanation
Indices: 5450385--5450419 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
5450375 CTATTTGTTT
*
5450385 ACCATGTTTG
1 ACCATATTTG
*
5450395 ACCACATTTG
1 ACCATATTTG
5450405 ACCATATTTG
1 ACCATATTTG
5450415 ACCAT
1 ACCAT
5450420 GGGATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (10 bp):
ACCATATTTG
Found at i:5452123 original size:45 final size:46
Alignment explanation
Indices: 5452072--5452162 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
5452062 CTTTATATCT
*
5452072 AAACACATAATTTGTTTTATTTTAGAAGAAAAAAAT-AAATAATAA
1 AAACACATAATTTGTCTTATTTTAGAAGAAAAAAATAAAATAATAA
* *
5452117 AAACACATAATTTGTCTTCTTTTAGAAGAAAAAGATAAAATAATAA
1 AAACACATAATTTGTCTTATTTTAGAAGAAAAAAATAAAATAATAA
5452163 TACTAAGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 33 0.79
46 9 0.21
ACGTcount: A:0.54, C:0.07, G:0.08, T:0.32
Consensus pattern (46 bp):
AAACACATAATTTGTCTTATTTTAGAAGAAAAAAATAAAATAATAA
Found at i:5453715 original size:30 final size:30
Alignment explanation
Indices: 5453681--5453775 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
5453671 TTATTATAAT
5453681 CAATTAAATTTTTAAATATTTATTTTCATC
1 CAATTAAATTTTTAAATATTTATTTTCATC
* *
5453711 CAATTAAACTATTT-AATATTTATTTT-AAC
1 CAATTAAA-TTTTTAAATATTTATTTTCATC
* * * *
5453740 CAAATTGAATTCTTAAACATATATTTTCATC
1 C-AATTAAATTTTTAAATATTTATTTTCATC
*
5453771 TAATT
1 CAATT
5453776 GAATCCATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
29 6 0.12
30 40 0.77
31 6 0.12
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (30 bp):
CAATTAAATTTTTAAATATTTATTTTCATC
Found at i:5453790 original size:60 final size:60
Alignment explanation
Indices: 5453682--5453796 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
5453672 TATTATAATC
* * * * *
5453682 AATTAAATTTTTAAATATTTATTTTCATCCAATTAAACTATTTAATATTTATTTTAACCA
1 AATTAAATTCTTAAACATATATTTTCATCCAATTAAACCATATAATATTTATTTTAACCA
* * *
5453742 AATTGAATTCTTAAACATATATTTTCATCTAATTGAATCCATAT-ATATTTATTTT
1 AATTAAATTCTTAAACATATATTTTCATCCAATT-AAACCATATAATATTTATTTT
5453797 TATCCTAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 40 0.87
61 6 0.13
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (60 bp):
AATTAAATTCTTAAACATATATTTTCATCCAATTAAACCATATAATATTTATTTTAACCA
Found at i:5453795 original size:30 final size:30
Alignment explanation
Indices: 5453696--5453808 Score: 84
Period size: 30 Copynumber: 3.7 Consensus size: 30
5453686 AAATTTTTAA
* * * *
5453696 ATATTTATTTTCATCCAATT-AAACTATTT
1 ATATTTATTTTCATCTAATTGAATCCATAT
* * * * * *
5453725 AATATTTATTTTAACCAAATTGAATTCTTAA
1 -ATATTTATTTTCATCTAATTGAATCCATAT
* *
5453756 ACATATATTTTCATCTAATTGAATCCATAT
1 ATATTTATTTTCATCTAATTGAATCCATAT
*
5453786 ATATTTATTTTTATCCTAATTGA
1 ATATTTATTTTCAT-CTAATTGA
5453809 GCCATCGATT
Statistics
Matches: 61, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
30 50 0.82
31 11 0.18
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.49
Consensus pattern (30 bp):
ATATTTATTTTCATCTAATTGAATCCATAT
Found at i:5456320 original size:12 final size:12
Alignment explanation
Indices: 5456303--5456327 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5456293 TTCTGTTCAG
5456303 GAGGTGGAGGTA
1 GAGGTGGAGGTA
5456315 GAGGTGGAGGTA
1 GAGGTGGAGGTA
5456327 G
1 G
5456328 GTGCTTCTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.60, T:0.16
Consensus pattern (12 bp):
GAGGTGGAGGTA
Found at i:5462956 original size:2 final size:2
Alignment explanation
Indices: 5462949--5462976 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5462939 TTATCTTTTC
5462949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5462977 AAAGAAGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5464721 original size:2 final size:2
Alignment explanation
Indices: 5464714--5464748 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5464704 ATCTCATTCC
5464714 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5464749 ATTCTTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:5465123 original size:23 final size:24
Alignment explanation
Indices: 5465096--5465140 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5465086 TGAGTTGTAT
* *
5465096 CTTATCTGTTTTTGA-GGTTTTCA
1 CTTATCTGGTGTTGACGGTTTTCA
5465119 CTTATCTGGTGTTGACGGTTTT
1 CTTATCTGGTGTTGACGGTTTT
5465141 GAAACCTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.11, C:0.13, G:0.22, T:0.53
Consensus pattern (24 bp):
CTTATCTGGTGTTGACGGTTTTCA
Found at i:5465262 original size:17 final size:18
Alignment explanation
Indices: 5465235--5465269 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5465225 TTGACTAATT
5465235 AATATTCTTAAATACAAG
1 AATATTCTTAAATACAAG
5465253 AATA-TCTTAAATACAAG
1 AATATTCTTAAATACAAG
5465270 TATGTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (18 bp):
AATATTCTTAAATACAAG
Found at i:5466001 original size:25 final size:23
Alignment explanation
Indices: 5465973--5466018 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
5465963 GTATAGTGAT
*
5465973 AAATAAATTGATTAAAACAAAAAAA
1 AAATAAAATGA-TAAAA-AAAAAAA
5465998 AAATAAAATGATAAAAAAAAA
1 AAATAAAATGATAAAAAAAAA
5466019 GGGAAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 5 0.25
25 10 0.50
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.17
Consensus pattern (23 bp):
AAATAAAATGATAAAAAAAAAAA
Found at i:5470116 original size:2 final size:2
Alignment explanation
Indices: 5470109--5470140 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5470099 GACTCAAACC
*
5470109 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5470141 TTAAGATATT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5470187 original size:24 final size:21
Alignment explanation
Indices: 5470154--5470210 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 21
5470144 AGATATTAAT
5470154 TTAATAAAAATATTATATTTATA
1 TTAAT-AAAATATTA-ATTTATA
5470177 TATAATTAAAATA-TAATTTATA
1 T-TAA-TAAAATATTAATTTATA
5470199 TTAA-AAAATATT
1 TTAATAAAATATT
5470211 TTATAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
19 6 0.19
20 1 0.03
21 3 0.10
22 8 0.26
23 3 0.10
24 9 0.29
25 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAATAAAATATTAATTTATA
Found at i:5470203 original size:17 final size:17
Alignment explanation
Indices: 5470181--5470215 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5470171 TTTATATATA
*
5470181 ATTAAAATATAATTTAT
1 ATTAAAAAATAATTTAT
*
5470198 ATTAAAAAATATTTTAT
1 ATTAAAAAATAATTTAT
5470215 A
1 A
5470216 AATATTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTAAAAAATAATTTAT
Found at i:5470206 original size:43 final size:41
Alignment explanation
Indices: 5470121--5470226 Score: 115
Period size: 41 Copynumber: 2.5 Consensus size: 41
5470111 ATATATACAT
* *
5470121 ATATATATATATATATATATTTAAGATATTAATTTAATAAAA
1 ATAT-TATATATATATATAATTAAAATATTAATTTAATAAAA
*
5470163 ATATTATATTTATATATAATTAAAATA-TAATTTATATTAAAAA
1 ATATTATATATATATATAATTAAAATATTAATTTA-A-T-AAAA
* *
5470206 ATATTTTATAAATATTATAAT
1 ATATTATATATATA-TATAAT
5470227 AAATTAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
40 7 0.13
41 21 0.39
42 5 0.09
43 15 0.28
44 6 0.11
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (41 bp):
ATATTATATATATATATAATTAAAATATTAATTTAATAAAA
Found at i:5472775 original size:22 final size:22
Alignment explanation
Indices: 5472749--5472791 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5472739 TGTATATTTA
* *
5472749 TATTTGTATCTCTAGAATTAAC
1 TATTTGCATCCCTAGAATTAAC
5472771 TATTTGCATCCCTAGAATTAA
1 TATTTGCATCCCTAGAATTAA
5472792 GGGCACAAAA
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:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (22 bp):
TATTTGCATCCCTAGAATTAAC
Found at i:5472974 original size:24 final size:24
Alignment explanation
Indices: 5472924--5472975 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5472914 AATATACATT
*
5472924 CAGTTTTACTCTTAGTTTTTCATA
1 CAGTTTTACTCTTAGTTTTTCACA
*
5472948 CAGTTTTATTTCTTAGTTTTTC-CA
1 CAGTTTTA-CTCTTAGTTTTTCACA
5472972 CAGT
1 CAGT
5472976 AAACTAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (24 bp):
CAGTTTTACTCTTAGTTTTTCACA
Found at i:5479920 original size:19 final size:18
Alignment explanation
Indices: 5479883--5479921 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5479873 TTCCCGTTTT
*
5479883 ATTCGTTTGAATTTAAAA
1 ATTCGTTTAAATTTAAAA
5479901 ATTCGTTTAAAATTTTAAAA
1 ATTCGTTT-AAA-TTTAAAA
5479921 A
1 A
5479922 ATTTGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 2 0.11
20 8 0.44
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (18 bp):
ATTCGTTTAAATTTAAAA
Found at i:5482205 original size:5 final size:5
Alignment explanation
Indices: 5482195--5482228 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
5482185 ACATACTTTT
5482195 TAAAA TAAAA TAAAA TAAAA TTAAAA TTAAAA TA
1 TAAAA TAAAA TAAAA TAAAA -TAAAA -TAAAA TA
5482229 CTTGATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
TAAAA
Found at i:5485117 original size:15 final size:16
Alignment explanation
Indices: 5485097--5485126 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5485087 TATATCTTTT
5485097 TTTTATTT-TTTTTAA
1 TTTTATTTATTTTTAA
5485112 TTTTATTTATTTTTA
1 TTTTATTTATTTTTA
5485127 TAAAATAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATTTATTTTTAA
Found at i:5487876 original size:84 final size:85
Alignment explanation
Indices: 5487735--5487910 Score: 327
Period size: 84 Copynumber: 2.1 Consensus size: 85
5487725 TTCCACTGAA
* *
5487735 AAAAATAGGTTTCAAATAAATTTAACAAAAAAGAAAGAAAGTAAGGAAATAGCAAAACAAATTTG
1 AAAAATAGGTTTCAAATAAATTTAACAAAAAAGAAAGAAAGTAAGGAAATAGAAAAACAAACTTG
5487800 AAAAGG-AAAATGGCTACTT
66 AAAAGGAAAAATGGCTACTT
5487819 AAAAATAGGTTTCAAATAAATTTAACAAAAAAGAAAGAAAGTAAGGAAATAGAAAAACAAACTTG
1 AAAAATAGGTTTCAAATAAATTTAACAAAAAAGAAAGAAAGTAAGGAAATAGAAAAACAAACTTG
5487884 AAAAGGAAAAATGGCTACTT
66 AAAAGGAAAAATGGCTACTT
5487904 AAAAATA
1 AAAAATA
5487911 ACAGAGAATA
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 69 0.78
85 20 0.22
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.19
Consensus pattern (85 bp):
AAAAATAGGTTTCAAATAAATTTAACAAAAAAGAAAGAAAGTAAGGAAATAGAAAAACAAACTTG
AAAAGGAAAAATGGCTACTT
Found at i:5501473 original size:13 final size:13
Alignment explanation
Indices: 5501455--5501483 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5501445 ATGTAACAGG
5501455 AAACAAACAAAAA
1 AAACAAACAAAAA
5501468 AAACAAACAAAAA
1 AAACAAACAAAAA
5501481 AAA
1 AAA
5501484 ATTTTCACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACAAACAAAAA
Found at i:5521290 original size:12 final size:12
Alignment explanation
Indices: 5521273--5521307 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
5521263 CTTCTTCTTC
5521273 TCTCTCTCTCAT
1 TCTCTCTCTCAT
5521285 TCTCTCTCTCAT
1 TCTCTCTCTCAT
5521297 TCTCTCTCTCA
1 TCTCTCTCTCA
5521308 CATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.09, C:0.43, G:0.00, T:0.49
Consensus pattern (12 bp):
TCTCTCTCTCAT
Found at i:5525349 original size:23 final size:23
Alignment explanation
Indices: 5525323--5525369 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5525313 GAGCATTCTT
5525323 ATACTCAGCTCAAGTAGCTCGCG
1 ATACTCAGCTCAAGTAGCTCGCG
5525346 ATACTCAGCTCAAGTAGCTCGCG
1 ATACTCAGCTCAAGTAGCTCGCG
5525369 A
1 A
5525370 GCCTAATCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (23 bp):
ATACTCAGCTCAAGTAGCTCGCG
Found at i:5525400 original size:10 final size:10
Alignment explanation
Indices: 5525385--5525414 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5525375 ATCGATCTTT
5525385 TATATTTTAA
1 TATATTTTAA
5525395 TATATTTTAA
1 TATATTTTAA
5525405 T-TATTTTAA
1 TATATTTTAA
5525414 T
1 T
5525415 TAATAAACTA
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:5525411 original size:9 final size:9
Alignment explanation
Indices: 5525387--5525416 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5525377 CGATCTTTTA
5525387 TATTTTAAT
1 TATTTTAAT
5525396 ATATTTTAAT
1 -TATTTTAAT
5525406 TATTTTAAT
1 TATTTTAAT
5525415 TA
1 TA
5525417 ATAAACTATC
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:5527087 original size:39 final size:39
Alignment explanation
Indices: 5527042--5527117 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
5527032 GACTTTGGGC
* * *
5527042 TTGGAGGATCTGGTTGGATGTTTTGGACTTGAAAGGGTG
1 TTGGAGGATCTGGTTGGATATTTTGAACGTGAAAGGGTG
5527081 TTGGAGGATCTGGTTGGATATTTTGAACGTGAAAGGG
1 TTGGAGGATCTGGTTGGATATTTTGAACGTGAAAGGG
5527118 AGTTTGAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.21, C:0.05, G:0.39, T:0.34
Consensus pattern (39 bp):
TTGGAGGATCTGGTTGGATATTTTGAACGTGAAAGGGTG
Found at i:5531475 original size:3 final size:3
Alignment explanation
Indices: 5531467--5531494 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5531457 TTTGAAGATT
5531467 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5531495 AGGTCATCAT
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):
TTA
Found at i:5533305 original size:30 final size:30
Alignment explanation
Indices: 5533271--5533357 Score: 165
Period size: 30 Copynumber: 2.9 Consensus size: 30
5533261 CTAATCTCAG
*
5533271 TTTGTTTTGATAGCATTTGGTTTGTCTCGT
1 TTTGTTTTGTTAGCATTTGGTTTGTCTCGT
5533301 TTTGTTTTGTTAGCATTTGGTTTGTCTCGT
1 TTTGTTTTGTTAGCATTTGGTTTGTCTCGT
5533331 TTTGTTTTGTTAGCATTTGGTTTGTCT
1 TTTGTTTTGTTAGCATTTGGTTTGTCT
5533358 TGTATAAATC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.08, C:0.09, G:0.23, T:0.60
Consensus pattern (30 bp):
TTTGTTTTGTTAGCATTTGGTTTGTCTCGT
Found at i:5533349 original size:15 final size:15
Alignment explanation
Indices: 5533271--5533355 Score: 66
Period size: 15 Copynumber: 5.7 Consensus size: 15
5533261 CTAATCTCAG
* *
5533271 TTTGTTTTGATAGCA
1 TTTGGTTTGTTAGCA
* *
5533286 TTTGGTTTGTCTCG-T
1 TTTGGTTTGT-TAGCA
*
5533301 TTTGTTTTGTTAGCA
1 TTTGGTTTGTTAGCA
* *
5533316 TTTGGTTTGTCTCG-T
1 TTTGGTTTGT-TAGCA
*
5533331 TTTGTTTTGTTAGCA
1 TTTGGTTTGTTAGCA
5533346 TTTGGTTTGT
1 TTTGGTTTGT
5533356 CTTGTATAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
14 4 0.08
15 44 0.85
16 4 0.08
ACGTcount: A:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (15 bp):
TTTGGTTTGTTAGCA
Found at i:5533724 original size:1 final size:1
Alignment explanation
Indices: 5533718--5533743 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
5533708 CAAGCGTGAG
5533718 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
5533744 AACGATACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5534021 original size:15 final size:15
Alignment explanation
Indices: 5533998--5534030 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5533988 GCGCCAAGCT
*
5533998 TTGGTAGCATTGAAA
1 TTGGCAGCATTGAAA
5534013 TTGGCAGCATTGAAA
1 TTGGCAGCATTGAAA
5534028 TTG
1 TTG
5534031 CTTAGTGGTT
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:0.30, C:0.09, G:0.27, T:0.33
Consensus pattern (15 bp):
TTGGCAGCATTGAAA
Found at i:5548690 original size:10 final size:10
Alignment explanation
Indices: 5548675--5548704 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5548665 ATCGATCTTT
5548675 TATATTTTAA
1 TATATTTTAA
5548685 TATATTTTAA
1 TATATTTTAA
5548695 T-TATTTTAA
1 TATATTTTAA
5548704 T
1 T
5548705 TAATAAACTA
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:5548701 original size:9 final size:9
Alignment explanation
Indices: 5548677--5548706 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5548667 CGATCTTTTA
5548677 TATTTTAAT
1 TATTTTAAT
5548686 ATATTTTAAT
1 -TATTTTAAT
5548696 TATTTTAAT
1 TATTTTAAT
5548705 TA
1 TA
5548707 ATAAACTATC
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:5550380 original size:39 final size:39
Alignment explanation
Indices: 5550335--5550414 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
5550325 GACTTTGGGC
* * *
5550335 TTGGAGGATCTGGTTGGATGTTTTGGACTTGAAAGGGAG
1 TTGGAGGATCTGGTTGGATATTTTGAACGTGAAAGGGAG
5550374 TTGGAGGATCTGGTTGGATATTTTGAACGTGAAAGGGAG
1 TTGGAGGATCTGGTTGGATATTTTGAACGTGAAAGGGAG
5550413 TT
1 TT
5550415 TGAGAAGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.23, C:0.05, G:0.39, T:0.34
Consensus pattern (39 bp):
TTGGAGGATCTGGTTGGATATTTTGAACGTGAAAGGGAG
Found at i:5556518 original size:30 final size:30
Alignment explanation
Indices: 5556478--5556540 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
5556468 GTTCACCTAA
5556478 TCTCGATTTGTTTTGATAGCATTTGGTTTG
1 TCTCGATTTGTTTTGATAGCATTTGGTTTG
* *
5556508 TCTCGTTTTGTTTTGTTAGCATTTGGTTTG
1 TCTCGATTTGTTTTGATAGCATTTGGTTTG
5556538 TCT
1 TCT
5556541 TGTATAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.10, C:0.11, G:0.22, T:0.57
Consensus pattern (30 bp):
TCTCGATTTGTTTTGATAGCATTTGGTTTG
Found at i:5556532 original size:15 final size:15
Alignment explanation
Indices: 5556483--5556538 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
5556473 CCTAATCTCG
* *
5556483 ATTTGTTTTGATAGC
1 ATTTGGTTTGTTAGC
*
5556498 ATTTGGTTTGTCTCG-
1 ATTTGGTTTGT-TAGC
* *
5556513 TTTTGTTTTGTTAGC
1 ATTTGGTTTGTTAGC
5556528 ATTTGGTTTGT
1 ATTTGGTTTGT
5556539 CTTGTATAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.11, C:0.07, G:0.23, T:0.59
Consensus pattern (15 bp):
ATTTGGTTTGTTAGC
Found at i:5557194 original size:15 final size:15
Alignment explanation
Indices: 5557171--5557203 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5557161 GCGCCAAGCT
*
5557171 TTGGTAGCATTGAAA
1 TTGGCAGCATTGAAA
5557186 TTGGCAGCATTGAAA
1 TTGGCAGCATTGAAA
5557201 TTG
1 TTG
5557204 CTTAGTGGTT
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:0.30, C:0.09, G:0.27, T:0.33
Consensus pattern (15 bp):
TTGGCAGCATTGAAA
Found at i:5557342 original size:77 final size:77
Alignment explanation
Indices: 5557245--5557401 Score: 233
Period size: 77 Copynumber: 2.0 Consensus size: 77
5557235 TTGTGTTATA
* * * * * *
5557245 ATAATTAATTATAATTTAAAATTTTATTTCATAACAATTGTGAACGATGGATTCTTGCATTAACA
1 ATAAATAATCATAATTTAAAATTTAATGTCATAACAATTGTGAACGATGAATTCTTGCATAAACA
*
5557310 ATTGATGATATG
66 ATTGATGATACG
* *
5557322 ATAAATAATCATAATTTAAAATTTAATGTCATAATAATTGTGAACGGTGAATTCTTGCATAAACA
1 ATAAATAATCATAATTTAAAATTTAATGTCATAACAATTGTGAACGATGAATTCTTGCATAAACA
5557387 ATTGATGATACG
66 ATTGATGATACG
5557399 ATA
1 ATA
5557402 GATTGAGTGA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.38
Consensus pattern (77 bp):
ATAAATAATCATAATTTAAAATTTAATGTCATAACAATTGTGAACGATGAATTCTTGCATAAACA
ATTGATGATACG
Found at i:5570076 original size:2 final size:2
Alignment explanation
Indices: 5570065--5570094 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5570055 TAAAAATGGT
5570065 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5570095 TTATCAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5570325 original size:21 final size:21
Alignment explanation
Indices: 5570294--5570370 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 21
5570284 AAAATTTTTT
*
5570294 TAAAAAAAA-TTAGAAAATTC
1 TAAAAAAAATTTAAAAAATTC
5570314 TAAAAAAGAATTTAAAAAATT-
1 TAAAAAA-AATTTAAAAAATTC
* * *
5570335 T-GAAATATTTTAAAAAA---
1 TAAAAAAAATTTAAAAAATTC
*
5570352 TATAAAAAATTTAAAAAAT
1 TAAAAAAAATTTAAAAAAT
5570371 ATGAAATGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
17 1 0.02
18 13 0.28
19 10 0.22
20 10 0.22
21 3 0.07
22 9 0.20
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (21 bp):
TAAAAAAAATTTAAAAAATTC
Found at i:5570332 original size:22 final size:20
Alignment explanation
Indices: 5570294--5570334 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
5570284 AAAATTTTTT
*
5570294 TAAAAAAAATTAGAAAATTC
1 TAAAAAAAATTAAAAAATTC
5570314 TAAAAAAGAATTTAAAAAATT
1 TAAAAAA-AA-TTAAAAAATT
5570335 TGAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAAAAAAATTAAAAAATTC
Found at i:5570334 original size:9 final size:9
Alignment explanation
Indices: 5570317--5570370 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
5570307 AAAATTCTAA
5570317 AAAAGAATTT
1 AAAA-AATTT
5570327 AAAAAATTT
1 AAAAAATTT
* *
5570336 GAAATATTTT
1 -AAAAAATTT
*
5570346 AAAAAATAT
1 AAAAAATTT
5570355 AAAAAATTT
1 AAAAAATTT
5570364 AAAAAAT
1 AAAAAAT
5570371 ATGAAATGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
9 26 0.70
10 11 0.30
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAAAATTT
Found at i:5570348 original size:19 final size:19
Alignment explanation
Indices: 5570324--5570387 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 19
5570314 TAAAAAAGAA
*
5570324 TTTAAAAAATTTGAAATAT
1 TTTAAAAAATATGAAATAT
* *
5570343 TTTAAAAAATAT-AAAAAA
1 TTTAAAAAATATGAAATAT
*
5570361 TTTAAAAAATATGAAATGTT
1 TTTAAAAAATATGAAAT-AT
5570381 TTTAAAA
1 TTTAAAA
5570388 TTAAGAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 16 0.43
19 14 0.38
20 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTAAAAAATATGAAATAT
Found at i:5570371 original size:18 final size:19
Alignment explanation
Indices: 5570317--5570376 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
5570307 AAAATTCTAA
*
5570317 AAAAGAATTTAAAAAATTTG
1 AAAA-AATTTAAAAAATATG
* *
5570337 AAATATTTTAAAAAATAT-
1 AAAAAATTTAAAAAATATG
5570355 AAAAAATTTAAAAAATATG
1 AAAAAATTTAAAAAATATG
5570374 AAA
1 AAA
5570377 TGTTTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 16 0.47
19 15 0.44
20 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAAATTTAAAAAATATG
Found at i:5570430 original size:20 final size:20
Alignment explanation
Indices: 5570409--5570445 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
5570399 TGAAATTTTA
5570409 AAATTTTAA-AAAAATCTTT
1 AAATTTTAATAAAAATCTTT
5570428 AAATTTTAATAAAAATCT
1 AAATTTTAATAAAAATCT
5570446 AAAAAATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTTTAATAAAAATCTTT
Found at i:5570463 original size:11 final size:10
Alignment explanation
Indices: 5570428--5570472 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
5570418 AAAAATCTTT
*
5570428 AAATTTTAATA
1 AAATTCTAA-A
*
5570439 AAAATCTAAA
1 AAATTCTAAA
5570449 AAATTCTAGAA
1 AAATTCTA-AA
5570460 AAATTCTAAA
1 AAATTCTAAA
5570470 AAA
1 AAA
5570473 ACGAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 13 0.43
11 17 0.57
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (10 bp):
AAATTCTAAA
Found at i:5570514 original size:16 final size:17
Alignment explanation
Indices: 5570477--5570520 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
5570467 AAAAAAACGA
*
5570477 AAAAATGAAATTTTCAT
1 AAAAATAAAATTTTCAT
5570494 AAAAATAAAATTTT-ATT
1 AAAAATAAAATTTTCA-T
*
5570511 AAAATTAAAA
1 AAAAATAAAA
5570521 AAATCACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAAATAAAATTTTCAT
Found at i:5570554 original size:15 final size:16
Alignment explanation
Indices: 5570518--5570556 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5570508 ATTAAAATTA
5570518 AAAAAATCACAAAACT
1 AAAAAATCACAAAACT
* *
5570534 TAAAAA-CAGAAAACT
1 AAAAAATCACAAAACT
5570549 AAAAAATC
1 AAAAAATC
5570557 TAAAATTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.69, C:0.15, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAATCACAAAACT
Found at i:5570574 original size:11 final size:10
Alignment explanation
Indices: 5570558--5570634 Score: 68
Period size: 10 Copynumber: 7.6 Consensus size: 10
5570548 TAAAAAATCT
5570558 AAAATTGTTGA
1 AAAATT-TTGA
5570569 AAAATTTTTGA
1 AAAA-TTTTGA
5570580 AAAATTATT-A
1 AAAATT-TTGA
*
5570590 AAAATTTTAA
1 AAAATTTTGA
**
5570600 AAAATTCAGA
1 AAAATTTTGA
*
5570610 AAAATTTTTA
1 AAAATTTTGA
*
5570620 AAAA-TATGA
1 AAAATTTTGA
5570629 AAAATT
1 AAAATT
5570635 AAAAATTTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
9 9 0.17
10 29 0.54
11 14 0.26
12 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.36
Consensus pattern (10 bp):
AAAATTTTGA
Found at i:5570582 original size:10 final size:11
Alignment explanation
Indices: 5570558--5570624 Score: 61
Period size: 11 Copynumber: 6.5 Consensus size: 11
5570548 TAAAAAATCT
*
5570558 AAAATTGTTGA
1 AAAATTTTTGA
5570569 AAAATTTTTGA
1 AAAATTTTTGA
*
5570580 AAAATTATT-A
1 AAAATTTTTGA
5570590 AAAA-TTTT-A
1 AAAATTTTTGA
* **
5570599 AAAAATTCAGA
1 AAAATTTTTGA
5570610 AAAATTTTT-A
1 AAAATTTTTGA
5570620 AAAAT
1 AAAAT
5570625 ATGAAAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
9 8 0.17
10 13 0.28
11 25 0.54
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.37
Consensus pattern (11 bp):
AAAATTTTTGA
Found at i:5570677 original size:10 final size:10
Alignment explanation
Indices: 5570558--5570723 Score: 60
Period size: 10 Copynumber: 17.5 Consensus size: 10
5570548 TAAAAAATCT
*
5570558 AAAATTGTTGA
1 AAAATTATT-A
*
5570569 AAAATTTTTGA
1 AAAATTATT-A
5570580 AAAATTATTA
1 AAAATTATTA
5570590 AAAATT-TTAA
1 AAAATTATT-A
*
5570600 AAAATTCA-GA
1 AAAATT-ATTA
*
5570610 AAAATTTTTA
1 AAAATTATTA
*
5570620 AAAA-TA-TG
1 AAAATTATTA
5570628 AAAA--ATTA
1 AAAATTATTA
*
5570636 AAAA-T-TTC
1 AAAATTATTA
*
5570644 AAAA-TCTTA
1 AAAATTATTA
*
5570653 AACATT-TTAA
1 AAAATTATT-A
5570663 AAAATTATTA
1 AAAATTATTA
5570673 AAAA-T-TTA
1 AAAATTATTA
5570681 AAAAGTT-TCTA
1 AAAA-TTAT-TA
5570692 AAAA--A-TA
1 AAAATTATTA
*
5570699 AAAATTTTTA
1 AAAATTATTA
5570709 AAAA-TATATA
1 AAAATTAT-TA
5570719 AAAAT
1 AAAAT
5570724 GTAAGATAAG
Statistics
Matches: 122, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
7 7 0.06
8 24 0.20
9 13 0.11
10 52 0.43
11 26 0.21
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (10 bp):
AAAATTATTA
Found at i:5570683 original size:8 final size:8
Alignment explanation
Indices: 5570616--5570684 Score: 50
Period size: 8 Copynumber: 8.0 Consensus size: 8
5570606 CAGAAAAATT
5570616 TTTAAAAA
1 TTTAAAAA
*
5570624 TATGAAAAA
1 T-TTAAAAA
5570633 -TTAAAAA
1 TTTAAAAA
*
5570640 TTTCAAAA
1 TTTAAAAA
*
5570648 TCTTAAACAT
1 T-TTAAA-AA
5570658 TTTAAAAAA
1 TTT-AAAAA
5570667 TTATTAAAAA
1 -T-TTAAAAA
5570677 TTTAAAAA
1 TTTAAAAA
5570685 GTTTCTAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
7 6 0.12
8 15 0.31
9 14 0.29
10 11 0.23
11 2 0.04
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (8 bp):
TTTAAAAA
Found at i:5570723 original size:20 final size:19
Alignment explanation
Indices: 5570568--5570723 Score: 114
Period size: 20 Copynumber: 8.3 Consensus size: 19
5570558 AAAATTGTTG
5570568 AAAAATTTTTGAAAAATTATT
1 AAAAATTTTT-AAAAATTA-T
* *
5570589 AAAAATTTTAAAAAATTCAG
1 AAAAATTTTTAAAAATT-AT
5570609 AAAAATTTTTAAAAA-TAT
1 AAAAATTTTTAAAAATTAT
5570627 GAAAAA---TTAAAAATT-T
1 -AAAAATTTTTAAAAATTAT
* * * *
5570643 CAAAA-TCTTAAACATTTT
1 AAAAATTTTTAAAAATTAT
*
5570661 AAAAAATTATTAAAAATT-T
1 -AAAAATTTTTAAAAATTAT
*
5570680 AAAAAGTTTCTAAAAA--AT
1 AAAAA-TTTTTAAAAATTAT
5570698 AAAAATTTTTAAAAATATAT
1 AAAAATTTTTAAAAAT-TAT
5570718 AAAAAT
1 AAAAAT
5570724 GTAAGATAAG
Statistics
Matches: 110, Mismatches: 12, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
15 4 0.04
16 8 0.07
17 18 0.16
18 13 0.12
19 19 0.17
20 38 0.35
21 10 0.09
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
AAAAATTTTTAAAAATTAT
Found at i:5570799 original size:19 final size:19
Alignment explanation
Indices: 5570760--5570822 Score: 90
Period size: 19 Copynumber: 3.2 Consensus size: 19
5570750 AGAAAATTAA
5570760 AAAAAAACTTTTACTATTTTTT
1 AAAAAAA-TTTTA-TA-TTTTT
5570782 AAAAAAATTTTATATTTTT
1 AAAAAAATTTTATATTTTT
*
5570801 AAAAAAAATTTATATTTTT
1 AAAAAAATTTTATATTTTT
5570820 AAA
1 AAA
5570823 TTTTTTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
19 26 0.65
20 2 0.05
21 5 0.12
22 7 0.17
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAAAAATTTTATATTTTT
Found at i:5570831 original size:38 final size:38
Alignment explanation
Indices: 5570789--5570864 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
5570779 TTTAAAAAAA
5570789 TTTTATATTTTTAAAAAA-AATTTA-TATTTTTAAATTTT
1 TTTTATA-TTTTAAAAAATAATTTAGT-TTTTTAAATTTT
*
5570827 TTTTATATTTTAAAAAATAATTTAGTTTTTTTAATTTT
1 TTTTATATTTTAAAAAATAATTTAGTTTTTTAAATTTT
5570865 CAAAATTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
37 10 0.29
38 24 0.69
39 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (38 bp):
TTTTATATTTTAAAAAATAATTTAGTTTTTTAAATTTT
Found at i:5570850 original size:19 final size:18
Alignment explanation
Indices: 5570778--5570850 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 18
5570768 TTTTACTATT
*
5570778 TTTTAAAAAAATTTTATA
1 TTTTAAAAAAAATTTATA
5570796 TTTTTAAAAAAAATTTATA
1 -TTTTAAAAAAAATTTATA
*****
5570815 TTTTTAAATTTTTTTTATA
1 -TTTTAAAAAAAATTTATA
5570834 TTTTAAAAAATAATTTA
1 TTTTAAAAAA-AATTTA
5570851 GTTTTTTTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 7 0.17
19 35 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAAAAAAAATTTATA
Found at i:5571075 original size:35 final size:36
Alignment explanation
Indices: 5570996--5571075 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 36
5570986 TTTATGTTTT
* *
5570996 TATA-ATTTTTTAATTTTTAAAAACACTTCACTTTT
1 TATATATTTTTTAATTTTTAAAAACACTTCACTATA
* * * *
5571031 TA-ATTTTTTTTAATTTTTAAAAATATTTTA-TATA
1 TATATATTTTTTAATTTTTAAAAACACTTCACTATA
5571065 TATATATTTTT
1 TATATATTTTT
5571076 GAAATTTTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
34 5 0.14
35 31 0.86
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (36 bp):
TATATATTTTTTAATTTTTAAAAACACTTCACTATA
Found at i:5574069 original size:2 final size:2
Alignment explanation
Indices: 5574062--5574096 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5574052 TAAACAAAGT
5574062 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5574097 TGAGATGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5574159 original size:20 final size:21
Alignment explanation
Indices: 5574134--5574177 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
5574124 GTGATAGATT
*
5574134 ATTAAATTTTAT-TTTTAATA
1 ATTAAAATTTATATTTTAATA
*
5574154 ATTAAAATTTATATTTTGATA
1 ATTAAAATTTATATTTTAATA
5574175 ATT
1 ATT
5574178 TTTTTTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTAAAATTTATATTTTAATA
Found at i:5578705 original size:17 final size:17
Alignment explanation
Indices: 5578670--5578710 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5578660 CATTACTCTG
*
5578670 AAAATAAATAAAACGAT
1 AAAATAAATAAAACAAT
5578687 AAAATAAATTAAAA-AAT
1 AAAATAAA-TAAAACAAT
5578704 -AAATAAA
1 AAAATAAA
5578711 ACAAGTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 10 0.45
18 5 0.23
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAATAAATAAAACAAT
Found at i:5580737 original size:59 final size:59
Alignment explanation
Indices: 5580574--5580840 Score: 252
Period size: 60 Copynumber: 4.5 Consensus size: 59
5580564 TACGAAAGGG
*
5580574 TTTGAAGGAAAAGTTGAAAATATTAATTTTTTTTAAAAATAAAAATTTTAAAAAAATATTT
1 TTTG-AGGAAAAGTTGAAAGTATTAATTTTTTTTAAAAAT-AAAATTTTAAAAAAATATTT
* * *
5580635 TTTGAGGAAAAGTTGAAAGTATTAATTTTTTTTTGAAAATAAAATTTTCAAAAGATATTT
1 TTTGAGGAAAAGTTGAAAGTATTAA-TTTTTTTTAAAAATAAAATTTTAAAAAAATATTT
* * *** * ** *
5580695 TTTGAGGAAATGTT-AAGAGTATTAATTTTTCTTAAAAATAAAAACATCAAAAAATGCTC
1 TTTGAGGAAAAGTTGAA-AGTATTAATTTTTTTTAAAAATAAAATTTTAAAAAAATATTT
* * * * * * * * *
5580754 TTTAAAGAAAAGTTAAAAATATCAATTTTCTTT-AAAATAAAA-ATTAAAAAAAAAATT
1 TTTGAGGAAAAGTTGAAAGTATTAATTTTTTTTAAAAATAAAATTTTAAAAAAATATTT
* * *
5580811 TTGGAGGAAAAGTTAAAAGTATCAATTTTT
1 TTTGAGGAAAAGTTGAAAGTATTAATTTTT
5580841 CTTGAATAAA
Statistics
Matches: 170, Mismatches: 33, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
57 33 0.19
58 9 0.05
59 50 0.29
60 61 0.36
61 17 0.10
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (59 bp):
TTTGAGGAAAAGTTGAAAGTATTAATTTTTTTTAAAAATAAAATTTTAAAAAAATATTT
Found at i:5581161 original size:17 final size:17
Alignment explanation
Indices: 5581139--5581174 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
5581129 ATTTATATAC
5581139 TTATA-TATGTATTATTA
1 TTATATTAT-TATTATTA
5581156 TTATATTATTATTATTA
1 TTATATTATTATTATTA
5581173 TT
1 TT
5581175 TTTTATAATA
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:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATATTATTATTATTA
Found at i:5581165 original size:14 final size:15
Alignment explanation
Indices: 5581142--5581173 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
5581132 TATATACTTA
5581142 TATATGTATTATTAT
1 TATATGTATTATTAT
5581157 TATAT-TATTATTAT
1 TATATGTATTATTAT
5581171 TAT
1 TAT
5581174 TTTTTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TATATGTATTATTAT
Found at i:5581234 original size:35 final size:37
Alignment explanation
Indices: 5581164--5581236 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 37
5581154 TATTATATTA
* *
5581164 TTATTATTATTTTTTATAATATATTTTTAGGTTTATC
1 TTATTATTATTTTTTATAATATATTGTTAAGTTTATC
*
5581201 TTATT-TTATTTTTTA-AAT-TATCTGTTAATTTTATC
1 TTATTATTATTTTTTATAATATAT-TGTTAAGTTTATC
5581236 T
1 T
5581237 GATCTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 3 0.09
35 14 0.44
36 10 0.31
37 5 0.16
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (37 bp):
TTATTATTATTTTTTATAATATATTGTTAAGTTTATC
Found at i:5581267 original size:15 final size:16
Alignment explanation
Indices: 5581229--5581269 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
5581219 TATCTGTTAA
5581229 TTTTATCTGATCTTTT
1 TTTTATCTGATCTTTT
5581245 TTGATTATCTGAT-TTTT
1 TT--TTATCTGATCTTTT
5581262 TTTTATCT
1 TTTTATCT
5581270 TTTCTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.26
16 2 0.09
17 6 0.26
18 9 0.39
ACGTcount: A:0.15, C:0.10, G:0.07, T:0.68
Consensus pattern (16 bp):
TTTTATCTGATCTTTT
Found at i:5581269 original size:28 final size:27
Alignment explanation
Indices: 5581238--5581290 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
5581228 ATTTTATCTG
* * *
5581238 ATCTTTTTTGATTATCTGATTTTTTTTT
1 ATCTTTTCTAATTATCT-ATCTTTTTTT
5581266 ATCTTTTCTAATTATCTATCTTTTT
1 ATCTTTTCTAATTATCTATCTTTTT
5581291 ATTTTATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.68
Consensus pattern (27 bp):
ATCTTTTCTAATTATCTATCTTTTTTT
Found at i:5581587 original size:25 final size:25
Alignment explanation
Indices: 5581558--5581611 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
5581548 TTCTGGGAGT
*
5581558 GAAAAAATTTT-TAGAAATTTTTGG
1 GAAAAAATTTTCTAGAAATTTCTGG
* *
5581582 CGAAAAATTTTTCTGGAAATTTCTGG
1 -GAAAAAATTTTCTAGAAATTTCTGG
5581608 GAAA
1 GAAA
5581612 TTTCCAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.37
Consensus pattern (25 bp):
GAAAAAATTTTCTAGAAATTTCTGG
Found at i:5582126 original size:9 final size:9
Alignment explanation
Indices: 5582112--5582136 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5582102 GCTCCAGGTT
5582112 TTTATTTTA
1 TTTATTTTA
5582121 TTTATTTTA
1 TTTATTTTA
5582130 TTTATTT
1 TTTATTT
5582137 ATTAGATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTTA
Found at i:5582183 original size:6 final size:6
Alignment explanation
Indices: 5582162--5582246 Score: 50
Period size: 6 Copynumber: 13.7 Consensus size: 6
5582152 TCTAATATTC
* * *
5582162 TTTTTA TCTTTA -TTTTA TTTTTTA TTTCT- GTTTTA CTTTTCT- TTATTTA
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA -TTTT-TA TT-TTTA
* *
5582211 TTTTTA TTTTTA TTTATC TTTTTA TTATTCTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT-TT-TA TTTT
5582247 CTTTAAATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
5 7 0.12
6 32 0.53
7 16 0.27
8 5 0.08
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:5582226 original size:16 final size:15
Alignment explanation
Indices: 5582198--5582246 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
5582188 TCTGTTTTAC
*
5582198 TTTTCTTTATTTATT
1 TTTTTTTTATTTATT
*
5582213 TTTATTTTTATTTATC
1 TTT-TTTTTATTTATT
*
5582229 TTTTTATTATTCTATT
1 TTTTTTTTATT-TATT
5582245 TT
1 TT
5582247 CTTTAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTTTATTTATT
Found at i:5582395 original size:120 final size:118
Alignment explanation
Indices: 5582264--5582787 Score: 851
Period size: 117 Copynumber: 4.4 Consensus size: 118
5582254 TAAAAATGAC
*
5582264 AATTTCCAAAAAAAAATTATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAATAAATT
1 AATTTCC--AAAAAAA-TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATT
*
5582329 TC-AAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAA
63 TCAAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAA
*
5582384 AATTTCCAAAAAAATATTTTTAGGGAAAAGGTGAAAGTATCAATTTTCCTTAAAAATAAATTTC-
1 AATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCA
*
5582448 AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAA
66 AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAA
5582501 AATTTCC-AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC
*
5582565 ATAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTCCTTTGAAAATCAA
65 A-AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-TTGAAAATCAA
5582620 AATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
1 AATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTC
* *
5582685 AAAAAAAGGGATTTTTGAGGAAAAATTGAAAGTATCAATTTTCCTTGAAAATCAA
65 AAAAAAAAGG-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAA
* * *
5582740 AATTTCC-AAAGAATATTTTTGGGGAAAAGTTGAAAGTATCTATTTTCC
1 AATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
5582788 CTACAAAAAA
Statistics
Matches: 383, Mismatches: 13, Indels: 17
0.93 0.03 0.04
Matches are distributed among these distances:
116 51 0.13
117 110 0.29
118 11 0.03
119 98 0.26
120 105 0.27
121 8 0.02
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (118 bp):
AATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCA
AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAA
Done.