Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 96 of 100
Found at i:19019422 original size:15 final size:15
Alignment explanation
Indices: 19019402--19019441 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
19019392 CCAGATAAAT
19019402 AAAAAAAATCAAA-G
1 AAAAAAAATCAAACG
19019416 AAAAAAAATCAAACG
1 AAAAAAAATCAAACG
*
19019431 AAAATAAATCA
1 AAAAAAAATCA
19019442 GATAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.75, C:0.10, G:0.05, T:0.10
Consensus pattern (15 bp):
AAAAAAAATCAAACG
Found at i:19019636 original size:6 final size:6
Alignment explanation
Indices: 19019548--19019701 Score: 88
Period size: 6 Copynumber: 26.0 Consensus size: 6
19019538 TAAATCTAAG
* * * * * *
19019548 ATAAAA A-AAAA ATAATA ATAATA ATAAAA GA-AAAA ATATAT ATATAC
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA -ATAAAA ATAAAA ATAAAA
* * * *
19019595 ATATATA A-AATA ATAATA ATAAAA ATAAAA AT-AAA ATAAAA ATGTAAA
1 ATA-AAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT-AAAA
* * *
19019643 ATAAAA ATAAAA AT-AAA TTAAAA ATATAAA A-ATAAA ATGAAA AGAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATA-AAA ATA-AAA ATAAAA ATAAAA
*
19019691 AGAAAA A-AAAA
1 ATAAAA ATAAAA
19019702 TACAGACTTA
Statistics
Matches: 122, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
5 23 0.19
6 88 0.72
7 11 0.09
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (6 bp):
ATAAAA
Found at i:19019667 original size:36 final size:36
Alignment explanation
Indices: 19019549--19019703 Score: 110
Period size: 36 Copynumber: 4.4 Consensus size: 36
19019539 AAATCTAAGA
*
19019549 TAAAAA-AAAA-ATAATAATAATAATAAAAGA-AAAAA
1 TAAAAATAAAATATAAAAATAA-AATAAAA-ATAAAAA
* * * *
19019584 TATATATATACATATATAAAAT--AATAATAATAAAAA
1 TAAAAATA-AAATATA-AAAATAAAATAAAAATAAAAA
*
19019620 TAAAAATAAAATA-AAAATGTAAAATAAAAATAAAAA
1 TAAAAATAAAATATAAAA-ATAAAATAAAAATAAAAA
* * *
19019656 T-AAATTAAAAATATAAAAATAAAATGAAAAGAAAAA
1 TAAAAAT-AAAATATAAAAATAAAATAAAAATAAAAA
*
19019692 GAAAAA-AAAATA
1 TAAAAATAAAATA
19019704 CAGACTTACC
Statistics
Matches: 93, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
33 3 0.03
34 2 0.02
35 19 0.20
36 53 0.57
37 9 0.10
38 3 0.03
39 4 0.04
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (36 bp):
TAAAAATAAAATATAAAAATAAAATAAAAATAAAAA
Found at i:19019680 original size:30 final size:31
Alignment explanation
Indices: 19019548--19019679 Score: 119
Period size: 30 Copynumber: 4.2 Consensus size: 31
19019538 TAAATCTAAG
*
19019548 ATAAAAA-AAAAATAATAATAATAATA-AAAGA
1 ATAAAAATAAAAATAA-AATAAAAATATAAA-A
* * * *
19019579 A-AAAATATATATATACATATATAAAATAATAATA
1 ATAAAA-ATAAAAATA-AAATA-AAAAT-ATAAAA
*
19019613 ATAAAAATAAAAATAAAATAAAAATGT-AAA
1 ATAAAAATAAAAATAAAATAAAAATATAAAA
*
19019643 ATAAAAATAAAAATAAATTAAAAATATAAAA
1 ATAAAAATAAAAATAAAATAAAAATATAAAA
19019674 ATAAAA
1 ATAAAA
19019680 TGAAAAGAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
30 31 0.38
31 12 0.15
32 13 0.16
33 9 0.11
34 10 0.12
35 6 0.07
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.23
Consensus pattern (31 bp):
ATAAAAATAAAAATAAAATAAAAATATAAAA
Found at i:19019698 original size:25 final size:24
Alignment explanation
Indices: 19019599--19019699 Score: 71
Period size: 25 Copynumber: 4.0 Consensus size: 24
19019589 ATATACATAT
*
19019599 ATAAAATAATAATAATAAA-AATAAAA
1 ATAAAATAA-AAGAA-AAATAA-AAAA
* *
19019625 ATAAAATAAAAATGTAAAATAAAAAT
1 ATAAAAT-AAAA-GAAAAATAAAAAA
** *
19019651 A-AAAATAAATTAAAAATATAAAA
1 ATAAAATAAAAGAAAAATAAAAAA
*
19019674 ATAAAATGAAAAGAAAAAGAAAAAA
1 ATAAAAT-AAAAGAAAAATAAAAAA
19019699 A
1 A
19019700 AATACAGACT
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
23 10 0.17
24 8 0.14
25 19 0.33
26 16 0.28
27 5 0.09
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (24 bp):
ATAAAATAAAAGAAAAATAAAAAA
Found at i:19019863 original size:9 final size:9
Alignment explanation
Indices: 19019851--19019885 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
19019841 ACCTTTTTAC
19019851 TTTTTTTTG
1 TTTTTTTTG
19019860 TTTTTTTTG
1 TTTTTTTTG
19019869 TTTTTTTT-
1 TTTTTTTTG
*
19019877 TTGTTTTTG
1 TTTTTTTTG
19019886 ATCAAAGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:19019865 original size:11 final size:11
Alignment explanation
Indices: 19019851--19019884 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
19019841 ACCTTTTTAC
19019851 TTTTTTTTG--
1 TTTTTTTTGTT
19019860 TTTTTTTTGTT
1 TTTTTTTTGTT
19019871 TTTTTTTTGTT
1 TTTTTTTTGTT
19019882 TTT
1 TTT
19019885 GATCAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:19020032 original size:81 final size:82
Alignment explanation
Indices: 19019892--19020301 Score: 584
Period size: 81 Copynumber: 5.1 Consensus size: 82
19019882 TTTGATCAAA
* * *
19019892 GCTCCTCTAAACAGAGGC-TCAACGACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCATCA
1 GCTCCTCTAAACAGAGGCACCAA-GACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
19019956 CGACTTTG-AAAGTAAATT
64 CGACTTTGAAAAGTAAATT
* * *
19019974 GCTCCTCTAAATAGATGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
19020039 ACTTTG-AAAGTAAATT
66 ACTTTGAAAAGTAAATT
* * * * * *
19020055 GCTCCTCTAAACAGAGGTACCAAGACTTGGAAAGGTAAATTGCTCTTCTAAACAGAAGCACTACG
1 GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
19020120 ACTTTGAAAAATAAATT
66 ACTTTGAAAAGTAAATT
*
19020137 GGTCCTCTAAACAGAGGCACC-A-ACTTTG-AAAGTAAATTGCTCCTCT-AA-AGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
19020197 ACTTTGAAAAGTAAATT
66 ACTTTGAAAAGTAAATT
* * * *
19020214 GCTCCTCTAAACAGAGGCAACAAAACTTTGGAAAGTAAATTGCTCCTTTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
19020279 ACTTTGAAAAGTAAATT
66 ACTTTGAAAAGTAAATT
19020296 GCTCCT
1 GCTCCT
19020302 TGACAATCAT
Statistics
Matches: 294, Mismatches: 27, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
77 45 0.15
78 3 0.01
79 22 0.07
80 22 0.07
81 114 0.39
82 86 0.29
83 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCAAGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAGTAAATT
Found at i:19020302 original size:41 final size:41
Alignment explanation
Indices: 19019892--19020301 Score: 582
Period size: 41 Copynumber: 10.1 Consensus size: 41
19019882 TTTGATCAAA
* * *
19019892 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
*
19019934 GCTCCTCTAAACAGAGGCATCACGACTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
19019974 GCTCCTCTAAATAGATGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
19020015 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* * * *
19020055 GCTCCTCTAAACAGAGGTACCAAGACTTGGAAAGGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* * * *
19020096 GCTCTTCTAAACAGAAGCACTACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
19020137 GGTCCTCTAAACAGAGGCACCA--ACTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
19020175 GCTCCTCT-AA-AGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* ** *
19020214 GCTCCTCTAAACAGAGGCAACAAAACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
19020255 GCTCCTTTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
19020296 GCTCCT
1 GCTCCT
19020302 TGACAATCAT
Statistics
Matches: 325, Mismatches: 36, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
36 10 0.03
37 2 0.01
38 22 0.07
39 24 0.07
40 75 0.23
41 165 0.51
42 27 0.08
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:19021282 original size:8 final size:8
Alignment explanation
Indices: 19021271--19021339 Score: 65
Period size: 8 Copynumber: 8.8 Consensus size: 8
19021261 TTTTCACCTT
19021271 TTTTTTCA
1 TTTTTTCA
19021279 TTTTTTCCA
1 TTTTTT-CA
19021288 TTTTTTCA
1 TTTTTTCA
19021296 -TTTTT--
1 TTTTTTCA
**
19021301 TTTCATCA
1 TTTTTTCA
19021309 TTTTTTCTCA
1 -TTTTT-TCA
19021319 TTTTTTCA
1 TTTTTTCA
19021327 -TTTTTCA
1 TTTTTTCA
19021334 TTTTTT
1 TTTTTT
19021340 TGAAGCATAG
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
6 3 0.06
7 12 0.24
8 16 0.32
9 16 0.32
10 3 0.06
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:19021313 original size:39 final size:38
Alignment explanation
Indices: 19021260--19021340 Score: 119
Period size: 40 Copynumber: 2.1 Consensus size: 38
19021250 TAAGTCTTCC
*
19021260 TTTTTCACC-TTTTTTTTCATTTTTTCCATTTTTTCATTT
1 TTTTTCACCATTTTTTCTCATTTTTT-CA-TTTTTCATTT
*
19021299 TTTTTCATCATTTTTTCTCATTTTTTCATTTTTCATTT
1 TTTTTCACCATTTTTTCTCATTTTTTCATTTTTCATTT
19021337 TTTT
1 TTTT
19021341 GAAGCATAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
38 14 0.36
39 10 0.26
40 15 0.38
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (38 bp):
TTTTTCACCATTTTTTCTCATTTTTTCATTTTTCATTT
Found at i:19021325 original size:10 final size:10
Alignment explanation
Indices: 19021269--19021325 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
19021259 CTTTTTCACC
*
19021269 TTTTTTTTCA
1 TTTTTTCTCA
19021279 TTTTTTC-CA
1 TTTTTTCTCA
*
19021288 TTTTTTCAT-T
1 TTTTTTC-TCA
19021298 TTTTTTCATCA
1 TTTTTTC-TCA
19021309 TTTTTTCTCA
1 TTTTTTCTCA
19021319 TTTTTTC
1 TTTTTTC
19021326 ATTTTTCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 9 0.22
10 25 0.61
11 7 0.17
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTCTCA
Found at i:19021356 original size:40 final size:40
Alignment explanation
Indices: 19021276--19021356 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 40
19021266 ACCTTTTTTT
** * *
19021276 TCATTTTTTCCATTTTTTCATTTTTTTTCATCATTTTTTC
1 TCATTTTTTCCATTTTTTCATTTTTTTGAAGCATTATTTC
19021316 TCATTTTTT-CA-TTTTTCATTTTTTTGAAGCATAGTATTTC
1 TCATTTTTTCCATTTTTTCATTTTTTTGAAGCAT--TATTTC
19021356 T
1 T
19021357 TCACAACATC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 18 0.51
39 2 0.06
40 15 0.43
ACGTcount: A:0.16, C:0.15, G:0.04, T:0.65
Consensus pattern (40 bp):
TCATTTTTTCCATTTTTTCATTTTTTTGAAGCATTATTTC
Found at i:19028591 original size:15 final size:16
Alignment explanation
Indices: 19028553--19028594 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
19028543 TGTTAAGTGT
*
19028553 AATGAATG-AGAATGC
1 AATGAATGAAAAATGC
19028568 AATGAATGAAAAATGC
1 AATGAATGAAAAATGC
*
19028584 -ATGTATGAAAA
1 AATGAATGAAAA
19028595 GAACATTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (16 bp):
AATGAATGAAAAATGC
Found at i:19031861 original size:58 final size:58
Alignment explanation
Indices: 19031737--19032188 Score: 577
Period size: 58 Copynumber: 7.7 Consensus size: 58
19031727 CTTGTGTAGA
* *
19031737 AAAAATTGATACTTTCAATTTTTCTCCAAAAATA-TTTTTTGAAAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAG
* *
19031794 GAAATTTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAG
* * * * * *
19031852 GAAAATTGATACTTTTAACTTTTTCCCAAAAATATTTTTTAGAAACTTTGATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTT-ATTTTTAAG
* * * ** *
19031911 GAAAATTGATACTTTCAACTTTTTCTCAAAAACCCTTTTTTT-AAATTTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTGAAAATTTATTTTTAAG
* * *
19031969 AAAAATTAATACTTTCAACTTTTCTCCAAAAATATTTTTTTTTAGAAAACTTTGATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTT-GAAAA-TTT-ATTTTTAAG
* * * *
19032032 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAA-ATTTATTTTTAAG
* *
19032091 AAAAATTGATACTTTCAACTTTTTCCAAAAAATA-TTTTTTGAAAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAG
*
19032148 AAAAATTGATACTTTCAACTTTTCCCCAAAGATATTTTTTT
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
19032189 TTATTTTTAT
Statistics
Matches: 344, Mismatches: 40, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
57 72 0.21
58 117 0.34
59 91 0.26
60 13 0.04
61 9 0.03
62 3 0.01
63 39 0.11
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (58 bp):
AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAG
Found at i:19032269 original size:18 final size:17
Alignment explanation
Indices: 19032200--19032297 Score: 53
Period size: 17 Copynumber: 5.6 Consensus size: 17
19032190 TATTTTTATT
19032200 TAAAGAAAATAGAAT-AA
1 TAAAGAAAATA-AATGAA
19032217 TAAAGCAAAATAAAAGTGAAGA
1 TAAAG-AAAAT-AAA-TG-A-A
* *
19032239 GAAAAAAAATAAATGAA
1 TAAAGAAAATAAATGAA
**
19032256 TAAAGAAAAGTAAAACAA
1 TAAAGAAAA-TAAATGAA
*
19032274 -AAATAAAATAAA-G-A
1 TAAAGAAAATAAATGAA
19032288 TAAA-AAAATA
1 TAAAGAAAATA
19032298 TTAAATAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
14 7 0.11
15 3 0.05
16 4 0.06
17 20 0.31
18 14 0.22
19 4 0.06
20 3 0.05
21 6 0.09
22 4 0.06
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.14
Consensus pattern (17 bp):
TAAAGAAAATAAATGAA
Found at i:19032286 original size:21 final size:21
Alignment explanation
Indices: 19032254--19032306 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
19032244 AAAATAAATG
19032254 AATAAAGA-AAAG-TAAAACAAA
1 AATAAA-ATAAAGATAAAA-AAA
19032275 AATAAAATAAAGATAAAAAAA
1 AATAAAATAAAGATAAAAAAA
* *
19032296 TATTAAATAAA
1 AATAAAATAAA
19032307 CCTAATCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 22 0.79
22 5 0.18
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (21 bp):
AATAAAATAAAGATAAAAAAA
Found at i:19032337 original size:4 final size:4
Alignment explanation
Indices: 19032330--19032371 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
19032320 ATAGAAAGAA
19032330 AAAT AAAT AAAT -AA- AAAT AAAT AAAAT AAAT AAAT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT
19032372 TTGATGTGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 7 0.21
4 23 0.68
5 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:19032347 original size:14 final size:13
Alignment explanation
Indices: 19032328--19032370 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
19032318 AAATAGAAAG
19032328 AAAAATAAATAAA
1 AAAAATAAATAAA
19032341 TAAAAATAAATAAA
1 -AAAAATAAATAAA
*
19032355 ATAAATAAATAAA
1 AAAAATAAATAAA
19032368 AAA
1 AAA
19032371 TTTGATGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAATAAATAAA
Found at i:19032349 original size:10 final size:10
Alignment explanation
Indices: 19032315--19032363 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
19032305 AACCTAATCT
*
19032315 AATAAATAGA
1 AATAAATAAA
*
19032325 AAGAAA-AATA
1 AATAAATAA-A
19032335 AATAAATAAA
1 AATAAATAAA
19032345 AATAAAT-AA
1 AATAAATAAA
19032354 AATAAATAAA
1 AATAAATAAA
19032364 TAAAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 10 0.30
10 21 0.64
11 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (10 bp):
AATAAATAAA
Found at i:19033428 original size:47 final size:45
Alignment explanation
Indices: 19033351--19033471 Score: 118
Period size: 47 Copynumber: 2.5 Consensus size: 45
19033341 AATCTAAGAT
* * *
19033351 TAAAATAATAATAATAAAAGA-AAAGAAAAAATATATATATACATATA
1 TAAAATAATAAAAATAAAA-ATAAAGAAAAAATATA-AAATACA-AAA
**
19033398 TAAAATAATAAAAATAAAAATAAATTAAAAATATAAAATACAAAA
1 TAAAATAATAAAAATAAAAATAAAGAAAAAATATAAAATACAAAA
19033443 TAAAAATAAATTAAAAATATAAAAATAAA
1 T-AAAAT-AA-T-AAAA-ATAAAAATAAA
19033472 ATGAAGAGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
45 3 0.05
46 12 0.19
47 32 0.51
48 1 0.02
49 4 0.06
50 11 0.17
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (45 bp):
TAAAATAATAAAAATAAAAATAAAGAAAAAATATAAAATACAAAA
Found at i:19033429 original size:7 final size:6
Alignment explanation
Indices: 19033404--19033472 Score: 70
Period size: 6 Copynumber: 11.2 Consensus size: 6
19033394 TATATAAAAT
*
19033404 AATAAA AATAAA AAT-AA ATTAAA AATATAA AATACAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATA-AA AATA-AA AATAAA AATAAA
*
19033453 TTAA-AAA TATAAA AATAAA A
1 --AATAAA AATAAA AATAAA A
19033473 TGAAGAGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
5 5 0.09
6 31 0.58
7 15 0.28
8 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.22
Consensus pattern (6 bp):
AATAAA
Found at i:19033446 original size:31 final size:30
Alignment explanation
Indices: 19033404--19033472 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 30
19033394 TATATAAAAT
19033404 AATAAAAATAAAAATAAATTAAAAATATAA
1 AATAAAAATAAAAATAAATTAAAAATATAA
19033434 AATACAAAATAAAAATAAATTAAAAATATAAA
1 AATA-AAAATAAAAATAAATTAAAAATAT-AA
19033466 AATAAAA
1 AATAAAA
19033473 TGAAGAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
30 4 0.11
31 27 0.73
32 6 0.16
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.22
Consensus pattern (30 bp):
AATAAAAATAAAAATAAATTAAAAATATAA
Found at i:19037741 original size:25 final size:25
Alignment explanation
Indices: 19037720--19037765 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
19037710 AGCAAAATAG
19037720 ACAACAATA-AAA-TAAAATAAAAA
1 ACAACAATACAAAGTAAAATAAAAA
*
19037743 AGAACAATACAAAGTAAAATAAA
1 ACAACAATACAAAGTAAAATAAA
19037766 TAAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 3 0.15
25 9 0.45
ACGTcount: A:0.74, C:0.09, G:0.04, T:0.13
Consensus pattern (25 bp):
ACAACAATACAAAGTAAAATAAAAA
Found at i:19037824 original size:16 final size:17
Alignment explanation
Indices: 19037803--19037843 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
19037793 ATATGTACAC
19037803 AAATAAAAAAATAA-AA
1 AAATAAAAAAATAATAA
* *
19037819 AAAT-AAATATTAATAA
1 AAATAAAAAAATAATAA
19037835 AAATAAAAA
1 AAATAAAAA
19037844 TAAAAAACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 7 0.35
16 10 0.50
17 3 0.15
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATAAAAAAATAATAA
Found at i:19046820 original size:28 final size:28
Alignment explanation
Indices: 19046789--19046893 Score: 95
Period size: 29 Copynumber: 3.6 Consensus size: 28
19046779 CTATTTTTCT
* *
19046789 TAAATAAATTTTTATTTTTTATTATATC
1 TAAATAAATTTTTATTTTTAATTATATA
* *
19046817 TAAATAAATATTTATATTTTAATTACATA
1 TAAATAAATTTTTAT-TTTTAATTATATA
* * *
19046846 TAAATAAGTTTTT-TTATTTAGATTTGTATT
1 TAAATAAATTTTTATT-TTTA-A-TTATATA
*
19046876 TAAATAAGTTTTTATTTT
1 TAAATAAATTTTTATTTT
19046894 AAATAAAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
27 1 0.02
28 19 0.30
29 22 0.35
30 19 0.30
31 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (28 bp):
TAAATAAATTTTTATTTTTAATTATATA
Found at i:19046952 original size:31 final size:31
Alignment explanation
Indices: 19046917--19046975 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
19046907 TTATATTAAG
*
19046917 ATTTATTT-AATTATAAATTAAAATTTTAAAT
1 ATTTATTTGAA-TATAAATTAAAAATTTAAAT
19046948 ATTTATTTGAATATAAATTAAAAATTTA
1 ATTTATTTGAATATAAATTAAAAATTTA
19046976 TTTAGGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
ATTTATTTGAATATAAATTAAAAATTTAAAT
Found at i:19047006 original size:53 final size:54
Alignment explanation
Indices: 19046917--19047018 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
19046907 TTATATTAAG
* *
19046917 ATTTATTTAATTATAAATTAAAATTTTAAATATTTATTTGAATATAAATTAAAA
1 ATTTATTTAATTATAAATTAAAATTTAAAATATTTATTTAAATATAAATTAAAA
*
19046971 ATTTATTTAGGTT-TAAATTAAAATTTAAAAT-TTTATTTAAATATAAAT
1 ATTTATTTA-ATTATAAATTAAAATTTAAAATATTTATTTAAATATAAAT
19047019 AATCTAACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
53 16 0.36
54 26 0.59
55 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (54 bp):
ATTTATTTAATTATAAATTAAAATTTAAAATATTTATTTAAATATAAATTAAAA
Found at i:19047079 original size:9 final size:9
Alignment explanation
Indices: 19047039--19047070 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
19047029 ATTAAATAAT
19047039 ATTTTTAAA
1 ATTTTTAAA
19047048 ATTTTTAAA
1 ATTTTTAAA
19047057 ATTTTTACAA
1 ATTTTTA-AA
19047067 ATTT
1 ATTT
19047071 ATAATATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:19047079 original size:19 final size:18
Alignment explanation
Indices: 19047034--19047079 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
19047024 AACATATTAA
19047034 ATAATATTTTTAAAATTT
1 ATAATATTTTTAAAATTT
* *
19047052 TTAAAATTTTTACAAATTT
1 ATAATATTTTTA-AAATTT
19047071 ATAATATTT
1 ATAATATTT
19047080 CACATGTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
ATAATATTTTTAAAATTT
Found at i:19047343 original size:29 final size:29
Alignment explanation
Indices: 19047309--19047414 Score: 124
Period size: 30 Copynumber: 3.6 Consensus size: 29
19047299 TTGTTTTTTT
* *
19047309 TTTAAATAAATTTTTATATTTTAATTGTA
1 TTTAAATAAAATTTTATATTTTAATTATA
* *
19047338 TTTAAATAAATATTTT-TATTTTTATTTTTA
1 TTTAAATAAA-ATTTTATA-TTTTAATTATA
* *
19047368 TTCAAATAAAATTTTAAATTTTAATTTATA
1 TTTAAATAAAATTTTATATTTTAA-TTATA
19047398 TTTAAATAAAATTTTAT
1 TTTAAATAAAATTTTAT
19047415 TTTAAATAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
29 22 0.34
30 42 0.66
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (29 bp):
TTTAAATAAAATTTTATATTTTAATTATA
Found at i:19047389 original size:59 final size:58
Alignment explanation
Indices: 19047295--19047417 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 58
19047285 GCCTCTGAAC
* * * * *
19047295 TATTTTGTTTTTTTTTTAAATAAATTTTTATATTTTAA-TTGTATTTAAATAAATATTTT
1 TATTTTGTTTTTTATTCAAATAAAATTTTAAATTTTAATTTATATTTAAATAAA-A-TTT
19047354 TATTTT-TATTTTTATTCAAATAAAATTTTAAATTTTAATTTATATTTAAATAAAATTT
1 TATTTTGT-TTTTTATTCAAATAAAATTTTAAATTTTAATTTATATTTAAATAAAATTT
19047412 TATTTT
1 TATTTT
19047418 AAATAAATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
58 10 0.18
59 33 0.58
60 14 0.25
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.62
Consensus pattern (58 bp):
TATTTTGTTTTTTATTCAAATAAAATTTTAAATTTTAATTTATATTTAAATAAAATTT
Found at i:19047434 original size:21 final size:19
Alignment explanation
Indices: 19047391--19047438 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 19
19047381 TTAAATTTTA
19047391 ATTTATATTTAAATAAAAT
1 ATTTATATTTAAATAAAAT
19047410 -TTTAT-TTTAAATAAATAAT
1 ATTTATATTTAAAT-AA-AAT
19047429 GATTTATATT
1 -ATTTATATT
19047439 AGAGATTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 3 0.12
21 5 0.21
22 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTATATTTAAATAAAAT
Found at i:19047564 original size:24 final size:25
Alignment explanation
Indices: 19047537--19047590 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
19047527 TTAAACATTT
*
19047537 ATTTAAATAT-AATAAAATTTTAAA
1 ATTTAAATATAAATAAAATTATAAA
* *
19047561 ATTT-TATTTAAATAAAATTATAAA
1 ATTTAAATATAAATAAAATTATAAA
19047585 ATTTAA
1 ATTTAA
19047591 GAACTTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTTAAATATAAATAAAATTATAAA
Found at i:19048666 original size:31 final size:33
Alignment explanation
Indices: 19048616--19048677 Score: 85
Period size: 31 Copynumber: 1.9 Consensus size: 33
19048606 TTAGAAATTA
*
19048616 TTTTTATCAAAATTAATTT-A-TATTTTATAGT
1 TTTTTATCAAAATAAATTTAATTATTTTATAGT
19048647 TTTTTAT-AAAATAACATTTAATTATTTTATA
1 TTTTTATCAAAATAA-ATTTAATTATTTTATA
19048678 AATTACTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 6 0.22
31 11 0.41
32 1 0.04
33 9 0.33
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (33 bp):
TTTTTATCAAAATAAATTTAATTATTTTATAGT
Found at i:19049056 original size:25 final size:25
Alignment explanation
Indices: 19049022--19049070 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
19049012 ACAAGCCATA
19049022 GATGAGACATCTATATATAATTTTG
1 GATGAGACATCTATATATAATTTTG
* *
19049047 GATGAGACATTTATATATTATTTT
1 GATGAGACATCTATATATAATTTT
19049071 AATAGATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (25 bp):
GATGAGACATCTATATATAATTTTG
Found at i:19056488 original size:2 final size:2
Alignment explanation
Indices: 19056481--19056513 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19056471 TATCTTAAGT
19056481 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 T
19056514 TAGAATTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19066807 original size:80 final size:80
Alignment explanation
Indices: 19066708--19066876 Score: 209
Period size: 80 Copynumber: 2.1 Consensus size: 80
19066698 AATGTCATTT
* * * *
19066708 AGCAAACCATTCAATATATGATTTAGCC-CCCTAATATCATACAAA-ACCATTCAG-CAAAATAA
1 AGCAAACCATTCAACATATGATTCAACCTCCC-AATATCATA-AAATACCATT-AGACAAAACAA
*
19066770 TATCAGACAACAAGGTTC
63 TATCAAACAACAAGGTTC
* *
19066788 AGCAAACCATTCAGCATATGATTCAACCTCCCAATATCATAAAATACCATTTGACAAAACAATAT
1 AGCAAACCATTCAACATATGATTCAACCTCCCAATATCATAAAATACCATTAGACAAAACAATAT
* *
19066853 CAAATAACAAGGTTT
66 CAAACAACAAGGTTC
19066868 AGCAAACCA
1 AGCAAACCA
19066877 CAATATTTAA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
79 4 0.05
80 70 0.91
81 3 0.04
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.23
Consensus pattern (80 bp):
AGCAAACCATTCAACATATGATTCAACCTCCCAATATCATAAAATACCATTAGACAAAACAATAT
CAAACAACAAGGTTC
Found at i:19067962 original size:124 final size:123
Alignment explanation
Indices: 19067733--19067995 Score: 277
Period size: 124 Copynumber: 2.1 Consensus size: 123
19067723 GTGTGACGAT
* * *
19067733 TTATTGAAGGTATTTTACAGTAGAAGACGCATTTAATAATCCCAACAAATTTTAGAAGGAAATTA
1 TTATTGAAGGTGTTTTACAGTAAAAGACGCATTTAATAATCCCAACAAATTTTAGAAGAAAATTA
*
19067798 TTGAAGGTGTTTATTATCGAAAAACACCTTCAATATTTATGAAGATAA-TTTAAAAGGAA
66 TTGAAGGTGTTTATTATCGAAAAACACCTTCAATAATTATGAA-ATAAGTTTAAAA-GAA
* * * *
19067857 TTATTGAAGGTGTTTGT-CAGTAAAAGATGCCTTTAATAATTCTAA-AATATTTTAG-AGAAAAA
1 TTATTGAAGGTGTTT-TACAGTAAAAGACGCATTTAATAATCCCAACAA-ATTTTAGAAG-AAAA
* * ** * *
19067919 TTATTGAAGGTGTTTGTTAT-TAACAAATGCCTT-AAGTAATTATGTACTAAGTTTAAAAGAA
63 TTATTGAAGGTGTTTATTATCGAA-AAACACCTTCAA-TAATTATGAAATAAGTTTAAAAGAA
* *
19067980 TTATTAAAGATGTTTT
1 TTATTGAAGGTGTTTT
19067996 TCTGGAATAA
Statistics
Matches: 117, Mismatches: 16, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
122 1 0.01
123 27 0.23
124 88 0.75
125 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.37
Consensus pattern (123 bp):
TTATTGAAGGTGTTTTACAGTAAAAGACGCATTTAATAATCCCAACAAATTTTAGAAGAAAATTA
TTGAAGGTGTTTATTATCGAAAAACACCTTCAATAATTATGAAATAAGTTTAAAAGAA
Found at i:19086119 original size:22 final size:22
Alignment explanation
Indices: 19086077--19086120 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19086067 TTATGGCAAA
* *
19086077 CTGGATGCAAGGTGTAGGCATG
1 CTGGATGCAAGGCGTAAGCATG
19086099 CTGGATGCAAGGCGTAAGCATG
1 CTGGATGCAAGGCGTAAGCATG
19086121 AGTCATGGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.39, T:0.20
Consensus pattern (22 bp):
CTGGATGCAAGGCGTAAGCATG
Found at i:19093082 original size:318 final size:319
Alignment explanation
Indices: 19092501--19093139 Score: 964
Period size: 318 Copynumber: 2.0 Consensus size: 319
19092491 GTAAAATAAT
* *
19092501 TTTTTATGACCCAAATTTAACCTTTAATTTTTTTAAGACTTTAAAAACGTGTATAATAAAATAGA
1 TTTTTATGACCCAAATTTAACCTTTAATTTTTTTAAGACTTAAAAAACGTGTATAACAAAATAGA
* *
19092566 GGTAAGGATTGCTTTTATAATATTTATAGATATATGTTAGTTATAACTTTTTCAATAGAAACATG
66 GGCAAGGATTGCCTTTATAATATTTATAGATATATGTTAGTTATAACTTTTTCAATAGAAACATG
* *
19092631 TAAAATTTCAAAAGAAAAAAAAAAAGAAAAATTTATGGAATAATTCAAATAAATATGTATATATC
131 TAAAATTTCAAAAG-----AAAAAAGAAAAATTTATGGAATAATTCAAATAAACATGCATATATC
* *
19092696 TATTGATTTATTTATTTTCAAGTAAATTACCACTGATGATTGCCATAACATATAAGTTTATAAAT
191 TATTCATTTATTTATTTTCAAGTAAATTACCACTGATGATTGCCATAACATATAAGTTCATAAAT
* *
19092761 ATATAGTTAGAC-TCAATTTTAGGAA-TTCTCA-CTAATCTTTTTTATATAAATAAATAAGTGTA
256 ATATAGTTAGACAT-AACTTTA-GAAGTTATCATC-AATCTTTTTTATATAAATAAATAAGTGTA
19092823 AA
318 AA
** *
19092825 TTTTTATGGTCCAAATTTAACCTTTAATTTTTTTAAGACTTAAAAAACGTGTATAGCAAAATAGA
1 TTTTTATGACCCAAATTTAACCTTTAATTTTTTTAAGACTTAAAAAACGTGTATAACAAAATAGA
* ** *
19092890 GGCAGGAGATTGCCTTTATGGTTTTTATAGATATATGTTAGTTATAACTTTTTCAATAGAAACAT
66 GGCAAG-GATTGCCTTTATAATATTTATAGATATATGTTAGTTATAACTTTTTCAATAGAAACAT
*
19092955 GTAAAATTTCAAAAG-AAAAA-AAAAATTTATGGAATAATTCAAATAAACATGCATATATTTATT
130 GTAAAATTTCAAAAGAAAAAAGAAAAATTTATGGAATAATTCAAATAAACATGCATATATCTATT
* *
19093018 CATTTATTTATTTTCAAGTAAATTATCACTGATGATTGTCATAACATATAAGTTCATAAATATAT
195 CATTTATTTATTTTCAAGTAAATTACCACTGATGATTGCCATAACATATAAGTTCATAAATATAT
* *
19093083 CGTTAGACATAACTTTAGAAGTTATCATCAATCTTTTTTATTTAAATAAATAAGTGT
260 AGTTAGACATAACTTTAGAAGTTATCATCAATCTTTTTTATATAAATAAATAAGTGT
19093140 GATTAGTTAT
Statistics
Matches: 289, Mismatches: 22, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
317 3 0.01
318 146 0.51
319 7 0.02
324 64 0.22
325 69 0.24
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.39
Consensus pattern (319 bp):
TTTTTATGACCCAAATTTAACCTTTAATTTTTTTAAGACTTAAAAAACGTGTATAACAAAATAGA
GGCAAGGATTGCCTTTATAATATTTATAGATATATGTTAGTTATAACTTTTTCAATAGAAACATG
TAAAATTTCAAAAGAAAAAAGAAAAATTTATGGAATAATTCAAATAAACATGCATATATCTATTC
ATTTATTTATTTTCAAGTAAATTACCACTGATGATTGCCATAACATATAAGTTCATAAATATATA
GTTAGACATAACTTTAGAAGTTATCATCAATCTTTTTTATATAAATAAATAAGTGTAAA
Found at i:19094614 original size:21 final size:21
Alignment explanation
Indices: 19094588--19094629 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19094578 AAAACAAAGC
*
19094588 AAAGATAATTAAGATATAAAT
1 AAAGATAATTAAGAAATAAAT
* *
19094609 AAAGATATTTAGGAAATAAAT
1 AAAGATAATTAAGAAATAAAT
19094630 CACTAAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAGATAATTAAGAAATAAAT
Found at i:19095000 original size:22 final size:22
Alignment explanation
Indices: 19094975--19095021 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
19094965 TTCACATACT
19094975 AAAAGTCAAAGATTC-TCAATTG
1 AAAAGTCAAAGATTCAT-AATTG
* *
19094997 AAAATTCAAATATTCATAATTG
1 AAAAGTCAAAGATTCATAATTG
19095019 AAA
1 AAA
19095022 TTAAAGGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAAGTCAAAGATTCATAATTG
Found at i:19095142 original size:20 final size:20
Alignment explanation
Indices: 19095104--19095157 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
19095094 GATTCATAAT
* *
19095104 TAAATTCAAAGGTTTGCAAA
1 TAAATTCAAAGATTCGCAAA
*
19095124 TAAATTCAAATATTCGCAAA
1 TAAATTCAAAGATTCGCAAA
*
19095144 -ATATTCAAAGATTC
1 TAAATTCAAAGATTC
19095158 ACATCAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (20 bp):
TAAATTCAAAGATTCGCAAA
Found at i:19095303 original size:18 final size:18
Alignment explanation
Indices: 19095218--19095305 Score: 72
Period size: 18 Copynumber: 4.9 Consensus size: 18
19095208 TGCAAAAAAC
**
19095218 CAAAGATTCGTAAGAAAT
1 CAAAGATTCACAAGAAAT
*
19095236 CAAAGATTCACAA-ATATT
1 CAAAGATTCACAAGA-AAT
* *
19095254 TAAAGATTCACAA-AAGAC
1 CAAAGATTCACAAGAA-AT
**
19095272 CAAAGATTTGCAAGAAAT
1 CAAAGATTCACAAGAAAT
*
19095290 CAAATATTCACAAGAA
1 CAAAGATTCACAAGAA
19095306 TTTAAAAATT
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
17 2 0.04
18 50 0.93
19 2 0.04
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (18 bp):
CAAAGATTCACAAGAAAT
Found at i:19095384 original size:74 final size:72
Alignment explanation
Indices: 19095247--19095409 Score: 177
Period size: 74 Copynumber: 2.2 Consensus size: 72
19095237 AAAGATTCAC
* * *
19095247 AAAT-ATTTAAAGATTCACAAAAGACCAAAGATTTGCAAGAAATCAAATATTCACAAGAATTTAA
1 AAATAATTTAAAAATTCACAAAAGACCAAAGATTCGCAAGAAATCAAAGATTCACAAGAATTTAA
19095311 AAATTAA
66 AAATTAA
* * * * *
19095318 AAATAATTTAAATATTCACAAAATGGCTTAAAGATTCGTCAA-AAATCAAAGATTCATAAGATTT
1 AAATAATTTAAAAATTCACAAAA-GAC-CAAAGATTCG-CAAGAAATCAAAGATTCACAAGAATT
* *
19095382 TAAAGATTCA
63 TAAAAATTAA
* *
19095392 TAATAATTCAAAAATTCA
1 AAATAATTTAAAAATTCA
19095410 TAAGAATTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
71 4 0.05
72 17 0.22
73 2 0.03
74 50 0.66
75 3 0.04
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.29
Consensus pattern (72 bp):
AAATAATTTAAAAATTCACAAAAGACCAAAGATTCGCAAGAAATCAAAGATTCACAAGAATTTAA
AAATTAA
Found at i:19095386 original size:18 final size:18
Alignment explanation
Indices: 19095363--19095544 Score: 143
Period size: 18 Copynumber: 9.8 Consensus size: 18
19095353 TCGTCAAAAA
*
19095363 TCAAAGATTCATAAGATT
1 TCAAAGATTCATAAGAAT
* *
19095381 TTAAAGATTCATAATAAT
1 TCAAAGATTCATAAGAAT
*
19095399 TCAAAAATTCATAAGAAT
1 TCAAAGATTCATAAGAAT
* * *
19095417 TTAAATATTCGTAAGAAT
1 TCAAAGATTCATAAGAAT
* *
19095435 TGAAAAATTCATAAGAAT
1 TCAAAGATTCATAAGAAT
* *
19095453 TCAAAGATTCAAAGATTTGCAAGGC
1 TCAAAGATTCATA-A---G-AA--T
19095478 TCAAAGATTCATAAGAAT
1 TCAAAGATTCATAAGAAT
* *
19095496 TCAAAAATTCGTAAG-AT
1 TCAAAGATTCATAAGAAT
* *
19095513 TCAAAAATTCAAAAGAAT
1 TCAAAGATTCATAAGAAT
19095531 TCACAA-ATTCATAA
1 TCA-AAGATTCATAA
19095545 ATTTAAAAAA
Statistics
Matches: 132, Mismatches: 23, Indels: 18
0.76 0.13 0.10
Matches are distributed among these distances:
17 15 0.11
18 95 0.72
19 3 0.02
20 2 0.02
21 1 0.01
22 1 0.01
23 2 0.02
24 1 0.01
25 12 0.09
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (18 bp):
TCAAAGATTCATAAGAAT
Found at i:19095409 original size:8 final size:8
Alignment explanation
Indices: 19095356--19095574 Score: 64
Period size: 8 Copynumber: 25.1 Consensus size: 8
19095346 TAAAGATTCG
19095356 TCAAAAA-
1 TCAAAAAT
*
19095363 TCAAAGAT
1 TCAAAAAT
*
19095371 TCATAAGATT
1 TCA-AA-AAT
* *
19095381 TTAAAGAT
1 TCAAAAAT
19095389 TCATAATAAT
1 TCA-AA-AAT
19095399 TCAAAAAT
1 TCAAAAAT
19095407 TCATAAGAAT
1 TCA-AA-AAT
* *
19095417 TTAAATAT
1 TCAAAAAT
*
19095425 TCGTAAGAAT
1 TC--AAAAAT
*
19095435 TGAAAAAT
1 TCAAAAAT
19095443 TCATAAGAAT
1 TCA-AA-AAT
*
19095453 TCAAAGAT
1 TCAAAAAT
*
19095461 TCAAAGATT
1 TCAAA-AAT
***
19095470 TGC-AAGGC
1 T-CAAAAAT
*
19095478 TCAAAGAT
1 TCAAAAAT
19095486 TCATAAGAAT
1 TCA-AA-AAT
19095496 TCAAAAAT
1 TCAAAAAT
* *
19095504 TCGTAAGAT
1 TC-AAAAAT
19095513 TCAAAAAT
1 TCAAAAAT
19095521 TCAAAAGAAT
1 TC-AAA-AAT
*
19095531 TCACAAAT
1 TCAAAAAT
*
19095539 TCATAAATT
1 TCA-AAAAT
*
19095548 TAAAAAATT
1 TCAAAAA-T
*
19095557 TGCAAGAAT
1 T-CAAAAAT
19095566 TCAAAAAT
1 TCAAAAAT
19095574 T
1 T
19095575 AGCAAATTTT
Statistics
Matches: 153, Mismatches: 37, Indels: 43
0.66 0.16 0.18
Matches are distributed among these distances:
7 7 0.05
8 63 0.41
9 44 0.29
10 39 0.25
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.30
Consensus pattern (8 bp):
TCAAAAAT
Found at i:19095463 original size:128 final size:128
Alignment explanation
Indices: 19095219--19095463 Score: 280
Period size: 128 Copynumber: 1.9 Consensus size: 128
19095209 GCAAAAAACC
* **
19095219 AAAGATTCGTAAGAAATCAAAGATTCACAAATATTTAAAGATTCACAAAAGACCAAAGATTTGCA
1 AAAGATTCGTAAGAAATCAAAGATTCACAAATATTTAAAGATTCACAAAAGACCAAAAATTCACA
* * * *
19095284 AGAAATCAAATATTCACAAGAATTTAAAAATTAAAAATAATTTAAATATTCACAAAATGGCTT
66 AGAAATCAAATATTCACAAGAATTGAAAAATTAAAAAGAATTCAAAGATTCACAAAATGGCTT
* * **
19095347 AAAGATTCGTCAA-AAATCAAAGATTCATAAGAT-TTTAAAGATTCATAATAA-TTCAAAAATTC
1 AAAGATTCGT-AAGAAATCAAAGATTCACAA-ATATTTAAAGATTCACAA-AAGACCAAAAATTC
* * * ** * *
19095409 ATAAGAATTTAAATATTCGTAAGAATTGAAAAATTCATAAGAATTCAAAGATTCA
63 ACAAGAAATCAAATATTCACAAGAATTGAAAAATTAAAAAGAATTCAAAGATTCA
19095464 AAGATTTGCA
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
128 90 0.94
129 6 0.06
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (128 bp):
AAAGATTCGTAAGAAATCAAAGATTCACAAATATTTAAAGATTCACAAAAGACCAAAAATTCACA
AGAAATCAAATATTCACAAGAATTGAAAAATTAAAAAGAATTCAAAGATTCACAAAATGGCTT
Found at i:19095498 original size:35 final size:34
Alignment explanation
Indices: 19095450--19095540 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 34
19095440 AATTCATAAG
* * *
19095450 AATTCAAAG-ATTCAAAGATTTGCAAGGCTCAAA
1 AATTCAAAGAATTCAAAAATTCGCAAGACTCAAA
* * *
19095483 GATTCATAAGAATTCAAAAATTCGTAAGATTCAAA
1 AATTCA-AAGAATTCAAAAATTCGCAAGACTCAAA
*
19095518 AATTCAAAAGAATTCACAAATTC
1 AATTC-AAAGAATTCAAAAATTC
19095541 ATAAATTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
33 5 0.11
34 3 0.06
35 38 0.81
36 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.26
Consensus pattern (34 bp):
AATTCAAAGAATTCAAAAATTCGCAAGACTCAAA
Found at i:19095531 original size:27 final size:26
Alignment explanation
Indices: 19095481--19095574 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 26
19095471 GCAAGGCTCA
*
19095481 AAGATTCATAAGAATTC-AAAAATTCGT
1 AAGATTCA-AA-AATTCAAAAAATTCGC
*
19095508 AAGATTCAAAAATTCAAAAGAATTCAC
1 AAGATTCAAAAATTCAAAA-AATTCGC
* * *
19095535 AA-ATTCATAAATTTAAAAAATTTGC
1 AAGATTCAAAAATTCAAAAAATTCGC
19095560 AAGAATTCAAAAATT
1 AAG-ATTCAAAAATT
19095575 AGCAAATTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
25 12 0.21
26 19 0.34
27 25 0.45
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (26 bp):
AAGATTCAAAAATTCAAAAAATTCGC
Found at i:19095554 original size:35 final size:35
Alignment explanation
Indices: 19095484--19095574 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
19095474 AGGCTCAAAG
* * *
19095484 ATTCATAAGAATTCAAAAATTCGTAAGATTCAAAA
1 ATTCAAAAGAATTCAAAAATTCATAAGATTAAAAA
*
19095519 ATTCAAAAGAATTCACAAATTCATAA-ATTTAAAAA
1 ATTCAAAAGAATTCAAAAATTCATAAGA-TTAAAAA
***
19095554 ATTTGCAAGAATTCAAAAATT
1 ATTCAAAAGAATTCAAAAATT
19095575 AGCAAATTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 1 0.02
35 46 0.98
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.30
Consensus pattern (35 bp):
ATTCAAAAGAATTCAAAAATTCATAAGATTAAAAA
Found at i:19095573 original size:18 final size:18
Alignment explanation
Indices: 19095490--19095579 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
19095480 AAAGATTCAT
*
19095490 AAGAATTCAAAAATTCGT
1 AAGAATTCAAAAATTCGC
**
19095508 AAG-ATTCAAAAATTCAA
1 AAGAATTCAAAAATTCGC
* **
19095525 AAGAATTCACAAATTCAT
1 AAGAATTCAAAAATTCGC
* * *
19095543 AA-ATTTAAAAAATTTGC
1 AAGAATTCAAAAATTCGC
*
19095560 AAGAATTCAAAAATTAGC
1 AAGAATTCAAAAATTCGC
19095578 AA
1 AA
19095580 ATTTTAAATA
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
17 26 0.46
18 31 0.54
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.27
Consensus pattern (18 bp):
AAGAATTCAAAAATTCGC
Found at i:19095582 original size:35 final size:35
Alignment explanation
Indices: 19095484--19095601 Score: 98
Period size: 35 Copynumber: 3.4 Consensus size: 35
19095474 AGGCTCAAAG
* * *
19095484 ATTCATAAGAATTCAAAAATTCGTAAGA-TTCAAAA
1 ATTCAAAAGAATTCAAAAATTAGTAA-ATTTAAAAA
*
19095519 ATTCAAAAGAATTCACAAATTCA-TAAATTTAAAAA
1 ATTCAAAAGAATTCAAAAATT-AGTAAATTTAAAAA
*** * * *
19095554 ATTTGCAAGAATTCAAAAATTAGCAAATTTTAAAT
1 ATTCAAAAGAATTCAAAAATTAGTAAATTTAAAAA
19095589 ATTCACAAA-AATT
1 ATTCA-AAAGAATT
19095602 TGAGATTCAC
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
34 2 0.03
35 61 0.94
36 2 0.03
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (35 bp):
ATTCAAAAGAATTCAAAAATTAGTAAATTTAAAAA
Found at i:19095856 original size:116 final size:113
Alignment explanation
Indices: 19095723--19095942 Score: 273
Period size: 116 Copynumber: 1.9 Consensus size: 113
19095713 AATTTAAAAC
* * * *
19095723 TTCACATCTAAAATTCAAAAATTTATATTCAAAAAAATTTT-AAGATTTACATTCAAAATTTCAA
1 TTCACACCTAAAATTCAAAAATTCACATT-AAAAAAATTTTGAA-ATTCACATTCAAAATTTCAA
*
19095787 AAATTCATCTTTG-AAAATTGTTAAAGATTCTAATTCGAAAATTTTTAGATT
64 AAATTCATATTTGAAAAATT-TT-AAGATTCTAATTCGAAAATTTTTAGATT
* * *
19095838 TTCACACCTGAAATTTCAAAAATTCACATTGAAAAAATTTTGGAAATTCGCATTCAAAATTTCAA
1 TTCACACCT-AAAATTCAAAAATTCACATTAAAAAAATTTT-GAAATTCACATTCAAAATTTCAA
* * *
19095903 AGATTCATATTTGAAAAATTTTAAGATTTTCATTCGAAAA
64 AAATTCATATTTGAAAAATTTTAAGATTCTAATTCGAAAA
19095943 ATTTAGAAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
115 34 0.38
116 48 0.53
117 8 0.09
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.38
Consensus pattern (113 bp):
TTCACACCTAAAATTCAAAAATTCACATTAAAAAAATTTTGAAATTCACATTCAAAATTTCAAAA
ATTCATATTTGAAAAATTTTAAGATTCTAATTCGAAAATTTTTAGATT
Found at i:19095877 original size:24 final size:24
Alignment explanation
Indices: 19095848--19095920 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 24
19095838 TTCACACCTG
19095848 AAATTTCAAAAATTCACATTGAAA
1 AAATTTCAAAAATTCACATTGAAA
*** * *
19095872 AAATTTTGGAAATTCGCATT--CA
1 AAATTTCAAAAATTCACATTGAAA
* *
19095894 AAATTTCAAAGATTCATATTTGAAA
1 AAATTTCAAAAATTCACA-TTGAAA
19095919 AA
1 AA
19095921 TTTTAAGATT
Statistics
Matches: 34, Mismatches: 12, Indels: 5
0.67 0.24 0.10
Matches are distributed among these distances:
22 13 0.38
23 2 0.06
24 16 0.47
25 3 0.09
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (24 bp):
AAATTTCAAAAATTCACATTGAAA
Found at i:19095959 original size:23 final size:22
Alignment explanation
Indices: 19095856--19096002 Score: 79
Period size: 23 Copynumber: 6.5 Consensus size: 22
19095846 TGAAATTTCA
19095856 AAAATTCACATT-GAAAAAATTTT
1 AAAATTCACATTCG-AAAAA-TTT
* *
19095879 GGAAATTCGCATTC--AAAATTT
1 -AAAATTCACATTCGAAAAATTT
* *
19095900 CAAAGATTCATATTTGAAAAATTTT
1 -AAA-ATTCACATTCGAAAAA-TTT
* **
19095925 AAGATTTTCATTCGAAAAATTT
1 AAAATTCACATTCGAAAAATTT
19095947 AGAAATTCACATTC--AAAATTT
1 A-AAATTCACATTCGAAAAATTT
* * *
19095968 AAATATTCAAATTCGACAATTTT
1 AAA-ATTCACATTCGAAAAATTT
*
19095991 AGAGATTCACAT
1 A-AAATTCACAT
19096003 CTAAACTTCA
Statistics
Matches: 93, Mismatches: 20, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
20 2 0.02
21 22 0.24
22 15 0.16
23 34 0.37
24 17 0.18
25 3 0.03
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (22 bp):
AAAATTCACATTCGAAAAATTT
Found at i:19095964 original size:21 final size:21
Alignment explanation
Indices: 19095883--19096239 Score: 137
Period size: 21 Copynumber: 16.2 Consensus size: 21
19095873 AATTTTGGAA
*
19095883 ATTCGCATTCAAAATTTCAAAG
1 ATTCACATTCAAAATTT-AAAG
* * *
19095905 ATTCATATTTGAAAAATTTTAAG
1 ATTCACA-TT-CAAAATTTAAAG
**
19095928 ATTTTCATTCGAAAAATTTAGAA-
1 ATTCACATTC--AAAATTTA-AAG
*
19095951 ATTCACATTCAAAATTTAAAT
1 ATTCACATTCAAAATTTAAAG
* * *
19095972 ATTCAAATTCGACAATTTTAGAG
1 ATTCACATTC-A-AAATTTAAAG
* *
19095995 ATTCACA-TCTAAACTTCAAAG
1 ATTCACATTC-AAAATTTAAAG
* * *
19096016 A-ACATATTCAAAACTTTAGAG
1 ATTCACATTCAAAA-TTTAAAG
*
19096037 ATTCACATCCAAAATTTAAAG
1 ATTCACATTCAAAATTTAAAG
*
19096058 ATTCACATTAGAAAATTTTAAAG
1 ATTCACATT-CAAAA-TTTAAAG
* ** * *
19096081 GTTCACAACCAAAATTCAAAT
1 ATTCACATTCAAAATTTAAAG
* * *
19096102 ATTCACATTAAAAAATTTTAGAT
1 ATTCACATT-CAAAA-TTTAAAG
** * *
19096125 ATTCTTATCCAAACTTTAAAG
1 ATTCACATTCAAAATTTAAAG
* * *
19096146 ATGCATATTTGAAAATTTTAGAA-
1 ATTCACA-TTCAAAA-TTTA-AAG
* * * *
19096169 ATTTACATCCAAAATTCAAAT
1 ATTCACATTCAAAATTTAAAG
*
19096190 ATTCACATTCGAAAAATTTTAGAG
1 ATTCACATTC--AAAA-TTTAAAG
* * *
19096214 ATTTACATCCAAAATTCTAAAA
1 ATTCACATTCAAAATT-TAAAG
19096236 ATTC
1 ATTC
19096240 GCATCTGAAA
Statistics
Matches: 241, Mismatches: 71, Indels: 46
0.67 0.20 0.13
Matches are distributed among these distances:
20 10 0.04
21 81 0.34
22 54 0.22
23 73 0.30
24 23 0.10
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (21 bp):
ATTCACATTCAAAATTTAAAG
Found at i:19095982 original size:44 final size:44
Alignment explanation
Indices: 19095917--19096239 Score: 249
Period size: 44 Copynumber: 7.3 Consensus size: 44
19095907 TCATATTTGA
* ** *
19095917 AAAATTTTAAGATTTTCATTCGAAAAATTTAGAAATTCACATTC
1 AAAATTTAAAGATTCACATTCGAAAAATTTAGAAATTCACATCC
* * * * * *
19095961 AAAATTTAAATATTCAAATTCGACAATTTTAGAGATTCACATCT
1 AAAATTTAAAGATTCACATTCGAAAAATTTAGAAATTCACATCC
* * * * * *
19096005 AAACTTCAAAGA-ACATATTC-AAAACTTTAGAGATTCACATCC
1 AAAATTTAAAGATTCACATTCGAAAAATTTAGAAATTCACATCC
* * * *
19096047 AAAATTTAAAGATTCACATTAGAAAATTTTA-AAGGTTCACAACC
1 AAAATTTAAAGATTCACATTCGAAAAATTTAGAA-ATTCACATCC
* * * * **
19096091 AAAATTCAAATATTCACATT-AAAAAATTTTAGATATTCTTATCC
1 AAAATTTAAAGATTCACATTCGAAAAA-TTTAGAAATTCACATCC
* * * * * *
19096135 AAACTTTAAAGATGCATATTTGAAAATTTTAGAAATTTACATCC
1 AAAATTTAAAGATTCACATTCGAAAAATTTAGAAATTCACATCC
* * * *
19096179 AAAATTCAAATATTCACATTCGAAAAATTTTAGAGATTTACATCC
1 AAAATTTAAAGATTCACATTCGAAAAA-TTTAGAAATTCACATCC
*
19096224 AAAATTCTAAAAATTC
1 AAAATT-TAAAGATTC
19096240 GCATCTGAAA
Statistics
Matches: 214, Mismatches: 57, Indels: 14
0.75 0.20 0.05
Matches are distributed among these distances:
42 29 0.14
43 16 0.07
44 135 0.63
45 27 0.13
46 7 0.03
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (44 bp):
AAAATTTAAAGATTCACATTCGAAAAATTTAGAAATTCACATCC
Found at i:19096160 original size:88 final size:89
Alignment explanation
Indices: 19095933--19096234 Score: 292
Period size: 88 Copynumber: 3.4 Consensus size: 89
19095923 TTAAGATTTT
* * * * * * * * *
19095933 CATTCGAAAAA-TTTAGAAATTCACATTCAAAATTTAAATATTCAAATTCGACAATTTTAGAGAT
1 CATTCAAAAAATTTTAGAGATTCACATCCAAAATTTAAAGATGCACATTAGAAAATTTTAGAAAT
* * * * *
19095997 TCACATCTAAACTTCAAAGA-ACA
66 TCACAACCAAAATTCAAATATTCA
* * * *
19096020 TATTC--AAAACTTTAGAGATTCACATCCAAAATTTAAAGATTCACATTAGAAAATTTTA-AAGG
1 CATTCAAAAAATTTTAGAGATTCACATCCAAAATTTAAAGATGCACATTAGAAAATTTTAGAA-A
19096082 TTCACAACCAAAATTCAAATATTCA
65 TTCACAACCAAAATTCAAATATTCA
* ** * * *
19096107 CATT-AAAAAATTTTAGATATTCTTATCCAAACTTTAAAGATGCATATTTGAAAATTTTAGAAAT
1 CATTCAAAAAATTTTAGAGATTCACATCCAAAATTTAAAGATGCACATTAGAAAATTTTAGAAAT
* *
19096171 TTACATCCAAAATTCAAATATTCA
66 TCACAACCAAAATTCAAATATTCA
* *
19096195 CATTCGAAAAATTTTAGAGATTTACATCCAAAATTCTAAA
1 CATTCAAAAAATTTTAGAGATTCACATCCAAAATT-TAAA
19096235 AATTCGCATC
Statistics
Matches: 175, Mismatches: 32, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
85 5 0.03
86 59 0.34
87 9 0.05
88 72 0.41
89 26 0.15
90 4 0.02
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (89 bp):
CATTCAAAAAATTTTAGAGATTCACATCCAAAATTTAAAGATGCACATTAGAAAATTTTAGAAAT
TCACAACCAAAATTCAAATATTCA
Found at i:19096182 original size:22 final size:22
Alignment explanation
Indices: 19096157--19096238 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
19096147 TGCATATTTG
19096157 AAAATTTTAGAAATTTACATCC
1 AAAATTTTAGAAATTTACATCC
* * *
19096179 AAAA-TTCA-AATATTCACATTCGA
1 AAAATTTTAGAA-ATTTACA-TC-C
*
19096202 AAAATTTTAGAGATTTACATCC
1 AAAATTTTAGAAATTTACATCC
* *
19096224 AAAATTCTAAAAATT
1 AAAATTTTAGAAATT
19096239 CGCATCTGAA
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
20 2 0.04
21 9 0.20
22 18 0.40
23 6 0.13
24 9 0.20
25 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (22 bp):
AAAATTTTAGAAATTTACATCC
Found at i:19096816 original size:70 final size:70
Alignment explanation
Indices: 19096738--19096905 Score: 194
Period size: 70 Copynumber: 2.4 Consensus size: 70
19096728 TCAAGCAATA
* * * * * *
19096738 ATACAAATGCCATATTCAAAATAATAATTCAAATGTTTGTTAAGTGATACAGATGTATGTCCAAA
1 ATACAAATGCAATATTCAAAATAATAATTCAAATGTTCGCTAAGTGATACAAATGCATCTCCAAA
19096803 TCATG
66 TCATG
* * * * * *
19096808 ATGCAAATGCAAT-TATCAAAACAATTATTGAAATGTTCGCTAAGTGATGCAAATGCATCTTCAA
1 ATACAAATGCAATAT-TCAAAATAATAATTCAAATGTTCGCTAAGTGATACAAATGCATCTCCAA
19096872 ATCATG
65 ATCATG
* *
19096878 ATACAAGTGCAATACTCAAAATAATAAT
1 ATACAAATGCAATATTCAAAATAATAAT
19096906 CCATATACTC
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
69 1 0.01
70 78 0.99
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (70 bp):
ATACAAATGCAATATTCAAAATAATAATTCAAATGTTCGCTAAGTGATACAAATGCATCTCCAAA
TCATG
Found at i:19101557 original size:56 final size:60
Alignment explanation
Indices: 19101492--19101621 Score: 146
Period size: 56 Copynumber: 2.2 Consensus size: 60
19101482 TTCATTGAAG
* * * *
19101492 GAAATATTGATATTTCAATTCTTTC-TT-CA-ATTTTTTTG-AA-ATTATTTTTGTTTTAA
1 GAAAAATTGATATTTCAACT-TTTCTTTAAATATTTTTTTGAAATATTATTTTTATTTTAA
* *
19101548 GAAAAATTGATACTTCAACTTTTCTTTAAAATATTTTTTTGAAATATTTTTTTTATTTTAA
1 GAAAAATTGATATTTCAACTTTTCTTT-AAATATTTTTTTGAAATATTATTTTTATTTTAA
19101609 G-AAAATTGATATT
1 GAAAAATTGATATT
19101622 CCAAAATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
55 4 0.07
56 19 0.31
58 1 0.02
59 9 0.15
60 13 0.21
61 15 0.25
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (60 bp):
GAAAAATTGATATTTCAACTTTTCTTTAAATATTTTTTTGAAATATTATTTTTATTTTAA
Found at i:19101594 original size:13 final size:13
Alignment explanation
Indices: 19101576--19101600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19101566 CTTTTCTTTA
19101576 AAATATTTTTTTG
1 AAATATTTTTTTG
19101589 AAATATTTTTTT
1 AAATATTTTTTT
19101601 TATTTTAAGA
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
AAATATTTTTTTG
Found at i:19104765 original size:5 final size:5
Alignment explanation
Indices: 19104741--19104873 Score: 100
Period size: 5 Copynumber: 27.2 Consensus size: 5
19104731 TTGTTGGTAT
* * * *
19104741 TATTGA TATCA TATCA TATTA TA-T- TATTA TAATA TCTTA TATCT- TATTA
1 TATT-A TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA TATTA
* * * *
19104790 TA-T- TATTA TTATCA TATTA TAGTA TATTA CATCA TATTA TA-T- TATTA
1 TATTA TATTA -TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
*
19104837 TATTA TAGTA TATTA TATTA TTATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA -TATTA TATTA TATTA T
19104874 TGTTGTTGTT
Statistics
Matches: 101, Mismatches: 16, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
3 6 0.06
4 7 0.07
5 75 0.74
6 13 0.13
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (5 bp):
TATTA
Found at i:19104770 original size:3 final size:3
Alignment explanation
Indices: 19104757--19104912 Score: 72
Period size: 3 Copynumber: 56.3 Consensus size: 3
19104747 TATCATATCA
* * *
19104757 TAT TA- TAT TAT TAT AAT ATCT TAT ATCT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* * * *
19104802 CA- TAT TA- TAG TA- TAT TA- CAT CA- TAT TA- TAT TAT TA- TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
19104842 TAG TA- TAT TA- TAT TAT TAT TA- TAT TA- TAT TAT TGT TGT TGT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
19104886 TAT TAT TAT TAT TAT T-T TAT CAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
19104913 TTTCTTCTTT
Statistics
Matches: 122, Mismatches: 14, Indels: 34
0.72 0.08 0.20
Matches are distributed among these distances:
2 27 0.22
3 92 0.75
4 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:19104770 original size:8 final size:8
Alignment explanation
Indices: 19104757--19104874 Score: 80
Period size: 8 Copynumber: 13.5 Consensus size: 8
19104747 TATCATATCA
19104757 TATTATAT
1 TATTATAT
19104765 TATTATAAT
1 TATTAT-AT
*
19104774 ATCTTATATCT
1 -TATTATA--T
19104785 TATTATAT
1 TATTATAT
19104793 TATTATTAT
1 TATTA-TAT
19104802 CATATTATAGT
1 --TATTATA-T
*
19104813 ATATTACAT
1 -TATTATAT
19104822 CATATTATAT
1 --TATTATAT
19104832 TATTATAT
1 TATTATAT
19104840 TA-TAGTA-
1 TATTA-TAT
19104847 TATTATAT
1 TATTATAT
19104855 TATTAT-T
1 TATTATAT
19104862 ATATTATAT
1 -TATTATAT
19104871 TATT
1 TATT
19104875 GTTGTTGTTG
Statistics
Matches: 92, Mismatches: 4, Indels: 28
0.74 0.03 0.23
Matches are distributed among these distances:
7 7 0.08
8 42 0.46
9 8 0.09
10 28 0.30
11 7 0.08
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (8 bp):
TATTATAT
Found at i:19105384 original size:20 final size:21
Alignment explanation
Indices: 19105345--19105386 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
19105335 TTATGGAGTG
*
19105345 TTGGGATTAAGGTTTTAGATTT
1 TTGGGATCAAGG-TTTAGATTT
19105367 TTGGGATCAAGG-TTAGATTT
1 TTGGGATCAAGGTTTAGATTT
19105387 GTGGAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.45
Consensus pattern (21 bp):
TTGGGATCAAGGTTTAGATTT
Found at i:19105750 original size:5 final size:5
Alignment explanation
Indices: 19105740--19105837 Score: 53
Period size: 5 Copynumber: 19.2 Consensus size: 5
19105730 TTGCTTTTTC
* *
19105740 TATTT TATTT T-TATT T-TTT GATTT TATTTT TATTTT TATTT TATCAT
1 TATTT TATTT TAT-TT TATTT TATTT TA-TTT TA-TTT TATTT TAT-TT
* * *
19105787 T-TTA TATTT TAAGTTTT TATTT TCTTT TATTT T-TAT TA-TT TATTT
1 TATTT TATTT T-A--TTT TATTT TATTT TATTT TATTT TATTT TATTT
19105832 TATTT T
1 TATTT T
19105838 GTTGATTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
4 10 0.14
5 44 0.60
6 14 0.19
7 1 0.01
8 4 0.05
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:19105756 original size:19 final size:17
Alignment explanation
Indices: 19105735--19105837 Score: 97
Period size: 18 Copynumber: 5.9 Consensus size: 17
19105725 ATGTTTTGCT
19105735 TTTTCTATTTTATTTTTA
1 TTTT-TATTTTATTTTTA
19105753 TTTTTTGATTTTATTTTTA
1 -TTTTT-ATTTTATTTTTA
*
19105772 TTTTTATTTTA---TCA
1 TTTTTATTTTATTTTTA
19105786 TTTTATATTTTAAGTTTTTA
1 TTTT-TATTTT-A-TTTTTA
*
19105806 -TTTTCTTTTATTTTTA
1 TTTTTATTTTATTTTTA
19105822 TTATTTATTTTATTTT
1 TT-TTTATTTTATTTT
19105838 GTTGATTTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.08
15 6 0.08
16 7 0.10
17 8 0.11
18 23 0.32
19 19 0.27
20 2 0.03
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTATTTTATTTTTA
Found at i:19105758 original size:13 final size:13
Alignment explanation
Indices: 19105742--19105847 Score: 76
Period size: 13 Copynumber: 7.8 Consensus size: 13
19105732 GCTTTTTCTA
19105742 TTTTATTTTTATT
1 TTTTATTTTTATT
19105755 TTTTGA-TTTTA-T
1 TTTT-ATTTTTATT
19105767 TTTTATTTTTATT
1 TTTTATTTTTATT
*
19105780 TTATCA-TTTTATAT
1 TT-TTATTTTTAT-T
*
19105794 TTTAAGTTTTTATTTT
1 TTTTA-TTTTTA--TT
19105810 CTTTTATTTTTATT
1 -TTTTATTTTTATT
*
19105824 ATTTA-TTTTATT
1 TTTTATTTTTATT
19105836 TTGTTGATTTTT
1 TT-TT-ATTTTT
19105848 TATCAAATAT
Statistics
Matches: 75, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
11 1 0.01
12 18 0.24
13 26 0.35
14 9 0.12
15 9 0.12
16 7 0.09
17 5 0.07
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:19105770 original size:25 final size:25
Alignment explanation
Indices: 19105742--19105846 Score: 104
Period size: 25 Copynumber: 3.9 Consensus size: 25
19105732 GCTTTTTCTA
19105742 TTTTATTTTTATTTTTTGATTTTAT
1 TTTTATTTTTATTTTTTGATTTTAT
* *
19105767 TTTTATTTTTATTTTATCATTTTAT
1 TTTTATTTTTATTTTTTGATTTTAT
*
19105792 ATTTTAAGTTTTTATTTTCTTTTATTTTTAT
1 -TTTT-A-TTTTTA-TTT-TTTGA-TTTTAT
19105823 TATTTA-TTTTATTTTGTTGATTTT
1 T-TTTATTTTTATTTT-TTGATTTT
19105847 TTATCAAATA
Statistics
Matches: 67, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
25 23 0.34
26 9 0.13
27 7 0.10
28 11 0.16
29 3 0.04
30 5 0.07
31 9 0.13
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (25 bp):
TTTTATTTTTATTTTTTGATTTTAT
Found at i:19105830 original size:7 final size:6
Alignment explanation
Indices: 19105742--19105837 Score: 83
Period size: 6 Copynumber: 15.5 Consensus size: 6
19105732 GCTTTTTCTA
19105742 TTTTAT TTTTAT TTTT-T GATTTTAT TTTTAT TTTTAT TTTATCAT TTTATAT
1 TTTTAT TTTTAT TTTTAT --TTTTAT TTTTAT TTTTAT TTT-T-AT TTT-TAT
* *
19105794 TTTAAGT TTTTA- TTTT-C TTTTAT TTTTAT TATTTA- TTTTAT TTT
1 TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT TTT
19105838 GTTGATTTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 20
0.77 0.03 0.20
Matches are distributed among these distances:
5 13 0.17
6 37 0.48
7 19 0.25
8 8 0.10
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:19105845 original size:18 final size:18
Alignment explanation
Indices: 19105740--19105837 Score: 57
Period size: 19 Copynumber: 5.6 Consensus size: 18
19105730 TTGCTTTTTC
**
19105740 TATTTTATTTTTATTTTT
1 TATTTTATTTTTATGATT
*
19105758 TGATTTTATTTTTAT-TTT
1 T-ATTTTATTTTTATGATT
19105776 TATTTTATCATTTTAT-A--
1 TATTTTAT--TTTTATGATT
*
19105793 T-TTTAAGTTTTTAT--TT
1 TATTTTA-TTTTTATGATT
* *
19105809 TCTTTTATTTTTATTATT
1 TATTTTATTTTTATGATT
19105827 TATTTTATTTT
1 TATTTTATTTT
19105838 GTTGATTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
15 6 0.09
16 12 0.18
17 13 0.19
18 17 0.25
19 19 0.28
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
TATTTTATTTTTATGATT
Found at i:19117848 original size:3 final size:3
Alignment explanation
Indices: 19117840--19118026 Score: 116
Period size: 3 Copynumber: 66.3 Consensus size: 3
19117830 AAGTCGATTT
* * * * *
19117840 TTA TTA TTA CTA TTA CTA TTA TTA TT- TTG TTA TTA ATA TTA TTA TTTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * * *
19117888 TTA TTG TTG GTA TTA TTGA -TA TCA -TA TTA -TG TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
19117929 TTA -TA TTA -TA TTA TTA -TA TTA -TA TTA -TA TTA TTA -TA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
19117971 TATA TTA -CA TCA -TA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19118015 TTA TTA TT- TTA T
1 TTA TTA TTA TTA T
19118027 CTTTATTTTT
Statistics
Matches: 143, Mismatches: 23, Indels: 36
0.71 0.11 0.18
Matches are distributed among these distances:
2 25 0.17
3 113 0.79
4 5 0.03
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:19117879 original size:20 final size:19
Alignment explanation
Indices: 19117850--19117892 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
19117840 TTATTATTAC
*
19117850 TATTACTATTATTATTTTGT
1 TATTAATATTATTA-TTTGT
19117870 TATTAATATTATTATTTGT
1 TATTAATATTATTATTTGT
19117889 TATT
1 TATT
19117893 GTTGGTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (19 bp):
TATTAATATTATTATTTGT
Found at i:19117922 original size:5 final size:5
Alignment explanation
Indices: 19117901--19118018 Score: 109
Period size: 5 Copynumber: 23.2 Consensus size: 5
19117891 TTGTTGGTAT
* *
19117901 TATTGA TATCA TATTA TGTTA TATTA TATTA TATTA TA-T- TATTA TATTA
1 TATT-A TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* * *
19117950 TATTA TA-T- TATTA TATTA TAATA TATTA CATCA TATTA TCATTA TTATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA T-ATTA -TATTA
19118000 TTATTA TTATTA TTATTA T
1 -TATTA -TATTA -TATTA T
19118019 TATTTTATCT
Statistics
Matches: 96, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
3 4 0.04
4 4 0.04
5 58 0.60
6 29 0.30
7 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:19118873 original size:5 final size:5
Alignment explanation
Indices: 19118863--19118941 Score: 51
Period size: 5 Copynumber: 16.2 Consensus size: 5
19118853 GTTTTTTTTC
* ** *
19118863 TATTT TATTTT TATTTT TATTT TA--T CATTT TATATT TAGAT T-TTA
1 TATTT TA-TTT TA-TTT TATTT TATTT TATTT TAT-TT TATTT TATTT
*
19118908 TATTT TATTT TATTT T-TAT T-TTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT T
19118942 GCTGATTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
3 2 0.03
4 7 0.12
5 34 0.59
6 15 0.26
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:19118876 original size:6 final size:6
Alignment explanation
Indices: 19118865--19118941 Score: 70
Period size: 6 Copynumber: 12.5 Consensus size: 6
19118855 TTTTTTTCTA
* *
19118865 TTTTAT TTTTAT TTTTA- TTTTAT CATTTTAT ATTTAGA TTTTAT ATTTTA-
1 TTTTAT TTTTAT TTTTAT TTTTAT --TTTTAT TTTTA-T TTTTAT -TTTTAT
19118915 TTTTAT TTTTAT TTTT-T ATTTTAT TTT
1 TTTTAT TTTTAT TTTTAT -TTTTAT TTT
19118942 GCTGATTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
5 11 0.19
6 32 0.54
7 10 0.17
8 6 0.10
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:19125711 original size:131 final size:128
Alignment explanation
Indices: 19125519--19125821 Score: 337
Period size: 131 Copynumber: 2.4 Consensus size: 128
19125509 CTATGTGTCC
* * * * *
19125519 TAAAAAGAGCAAAAATTACCC-AAAAAAATGAAATGAA-GTACATAATAAAATGTTTACATGGAT
1 TAAAGAGAGCAAAAATTGCCCTAGACAAATAAAAT-AATGTACATAATAAAATGTTTACATGGAT
* * *
19125582 GAAAAAATGTATGTACAATTTA-AAGTATGCCAAACAATGGTTCAATATTTCCAATTATGTATGA
65 GAAAAAATGCATGTACAA-TTACAAGTATGCCAAACAATGGTT---TATTTACAATTATGTA-CA
19125646 AA-G
125 AAGG
* * *
19125649 TAAAGAGAGCAAAGATTGCCCTAGACAAATAAAATTATGTACAT-ATAAAAATGTTTATATGGAT
1 TAAAGAGAGCAAAAATTGCCCTAGACAAATAAAATAATGTACATAAT-AAAATGTTTACATGGAT
* * * * * *
19125713 GAAAAGATGCATGTACAATTACATGTATGCCAAACAATTGTTTGTTTATAATTGTGTACAAAGG
65 GAAAAAATGCATGTACAATTACAAGTATGCCAAACAATGGTTTATTTACAATTATGTACAAAGG
* *
19125777 TAAAGAGAGCAAAAATTGTCCTAGACAAATAAAATAATATACATA
1 TAAAGAGAGCAAAAATTGCCCTAGACAAATAAAATAATGTACATA
19125822 CAAAGATGCT
Statistics
Matches: 146, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
127 3 0.02
128 53 0.36
130 24 0.16
131 66 0.45
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (128 bp):
TAAAGAGAGCAAAAATTGCCCTAGACAAATAAAATAATGTACATAATAAAATGTTTACATGGATG
AAAAAATGCATGTACAATTACAAGTATGCCAAACAATGGTTTATTTACAATTATGTACAAAGG
Found at i:19127284 original size:25 final size:26
Alignment explanation
Indices: 19127234--19127291 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
19127224 TTCTCATATA
19127234 GAAATTTCTCAAAAATTTAATCATTT
1 GAAATTTCTCAAAAATTTAATCATTT
*
19127260 GAAATTTCT-AAAAATCTT-ATTATTT
1 GAAATTTCTCAAAAAT-TTAATCATTT
19127285 GACAATT
1 GA-AATT
19127292 GTTATTCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.43
Consensus pattern (26 bp):
GAAATTTCTCAAAAATTTAATCATTT
Found at i:19128250 original size:17 final size:17
Alignment explanation
Indices: 19128200--19128257 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
19128190 TATTTTTGTT
19128200 TAAAAAAATATAAAAGAAA
1 TAAAAAAATAT--AAGAAA
*
19128219 GTAAAGATAAT-TAAGAAA
1 -TAAA-AAAATATAAGAAA
19128237 TAAAAAAATATAAGAAA
1 TAAAAAAATATAAGAAA
19128254 TAAA
1 TAAA
19128258 TCATTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 4 0.12
17 15 0.44
18 6 0.18
20 5 0.15
21 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (17 bp):
TAAAAAAATATAAGAAA
Found at i:19135719 original size:15 final size:15
Alignment explanation
Indices: 19135699--19135729 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19135689 GACAAAAAAG
*
19135699 TATATATTTAAATTA
1 TATATATGTAAATTA
19135714 TATATATGTAAATTA
1 TATATATGTAAATTA
19135729 T
1 T
19135730 TAGAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
TATATATGTAAATTA
Found at i:19135825 original size:14 final size:15
Alignment explanation
Indices: 19135795--19135830 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
19135785 TTTTAAAAGA
*
19135795 TAAATTATATATATT
1 TAAATTAAATATATT
19135810 TAAATTAAAT-TATT
1 TAAATTAAATATATT
19135824 TAAATTA
1 TAAATTA
19135831 TTAGAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATTAAATATATT
Found at i:19135864 original size:101 final size:105
Alignment explanation
Indices: 19135677--19135884 Score: 282
Period size: 103 Copynumber: 2.0 Consensus size: 105
19135667 TTTTAAAATC
*
19135677 TTAATTTTAAAAGACAAAAAAGTATATATTTAAATTATATATATGTAAATTATTAGAAAATTAAT
1 TTAATTTTAAAAGACAAAAAAGTATATATTTAAATTAAATATATGTAAATTATTAGAAAATTAAT
* * *
19135742 TGTGGATAGCTAATCATTTTTAAATA-TTTAGTTATTTGA
66 TGTGAATAGCAAATCATTTTTAAATACTTTAATTATTTGA
* ** * *
19135781 TTAATTTTAAAAGATAAATTA-TATATATTTAAATTAAAT-TATTTAAATTATTAGAAAATTAGT
1 TTAATTTTAAAAGACAAAAAAGTATATATTTAAATTAAATATATGTAAATTATTAGAAAATTAAT
19135844 T-TGAATAAG-AAATCATTTTTAAATACGTTTAATTATTTGA
66 TGTGAAT-AGCAAATCATTTTTAAATAC-TTTAATTATTTGA
19135884 T
1 T
19135885 AAATACAATA
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
101 19 0.21
102 25 0.27
103 30 0.33
104 18 0.20
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (105 bp):
TTAATTTTAAAAGACAAAAAAGTATATATTTAAATTAAATATATGTAAATTATTAGAAAATTAAT
TGTGAATAGCAAATCATTTTTAAATACTTTAATTATTTGA
Found at i:19136444 original size:29 final size:29
Alignment explanation
Indices: 19136412--19136467 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
19136402 TTCTATTTTT
*
19136412 AGGAATTTAATCCCTCTAGTATTATTTAA
1 AGGAATTTAATCACTCTAGTATTATTTAA
* * *
19136441 AGGAATTTAGTCATTGTAGTATTATTT
1 AGGAATTTAATCACTCTAGTATTATTT
19136468 TCTAAGAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (29 bp):
AGGAATTTAATCACTCTAGTATTATTTAA
Found at i:19136541 original size:32 final size:32
Alignment explanation
Indices: 19136500--19136582 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 32
19136490 TTAACAATGC
*
19136500 ACAAGGACTAAATTCTTTAAAAAAATAATACT
1 ACAATGACTAAATTCTTTAAAAAAATAATACT
* * *
19136532 ATAATGACTAAATT-TTT--TAAAATAATATT
1 ACAATGACTAAATTCTTTAAAAAAATAATACT
19136561 ACAATGACTAAATTCCTTTAAA
1 ACAATGACTAAATT-CTTTAAA
19136583 TAATATTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
29 23 0.56
31 6 0.15
32 12 0.29
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (32 bp):
ACAATGACTAAATTCTTTAAAAAAATAATACT
Found at i:19136566 original size:29 final size:30
Alignment explanation
Indices: 19136521--19136590 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
19136511 ATTCTTTAAA
* * *
19136521 AAAATAATACTATAATGACTAAATT-TTTT
1 AAAATAATATTACAATGACTAAATTCCTTT
19136550 AAAATAATATTACAATGACTAAATTCCTTT
1 AAAATAATATTACAATGACTAAATTCCTTT
19136580 -AAATAATATTA
1 AAAATAATATTA
19136591 TAGGGATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 34 0.92
30 3 0.08
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATAATATTACAATGACTAAATTCCTTT
Found at i:19138068 original size:14 final size:14
Alignment explanation
Indices: 19138003--19138068 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
19137993 TGAAATTGAA
*
19138003 AAAATAAATTTAATT
1 AAAATAAA-CTAATT
*
19138018 AAAAAAAACTAATT
1 AAAATAAACTAATT
*
19138032 AAAATAAATTGAATT
1 AAAATAAACT-AATT
* *
19138047 CAATTAAACTAATT
1 AAAATAAACTAATT
*
19138061 AATATAAA
1 AAAATAAA
19138069 TACATATAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
14 22 0.55
15 18 0.45
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (14 bp):
AAAATAAACTAATT
Found at i:19138126 original size:29 final size:29
Alignment explanation
Indices: 19138003--19138129 Score: 98
Period size: 29 Copynumber: 4.3 Consensus size: 29
19137993 TGAAATTGAA
* **
19138003 AAAATAAATTTAATTAAAAAAAACTAATT
1 AAAATAAATTTAATTTAATTAAACTAATT
* *
19138032 AAAATAAATTGAATTCAATTAAACTAATT
1 AAAATAAATTTAATTTAATTAAACTAATT
* * ** *
19138061 AATATAAA--TACATATAATTTGA-TAGTT
1 AAAATAAATTTA-ATTTAATTAAACTAATT
*
19138088 AGCTAAATAAATTTAATTTAGTTAAACTAATT
1 A---AAATAAATTTAATTTAATTAAACTAATT
19138120 AAAATAAATT
1 AAAATAAATT
19138130 AAAAAATACA
Statistics
Matches: 74, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
27 6 0.08
28 7 0.09
29 41 0.55
30 6 0.08
31 7 0.09
32 7 0.09
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATAAATTTAATTTAATTAAACTAATT
Found at i:19140948 original size:41 final size:41
Alignment explanation
Indices: 19140903--19140988 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
19140893 AAGTGACATC
*
19140903 TATTATGATAATAAACCA-CGTTTACTTTCTCAAACATCATT
1 TATTATGATAATAAA-CAGCGATTACTTTCTCAAACATCATT
* *
19140944 TATTATGATTATAAACAGCGATTACTTTCTCAAACATTATT
1 TATTATGATAATAAACAGCGATTACTTTCTCAAACATCATT
19140985 TATT
1 TATT
19140989 TTCTAACTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 2 0.05
41 39 0.95
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (41 bp):
TATTATGATAATAAACAGCGATTACTTTCTCAAACATCATT
Found at i:19142779 original size:9 final size:9
Alignment explanation
Indices: 19142765--19142794 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
19142755 GGTGAATTAT
19142765 TAATTAAAA
1 TAATTAAAA
19142774 TAATTAAAA
1 TAATTAAAA
19142783 TATATTAAAA
1 TA-ATTAAAA
19142793 TA
1 TA
19142795 TAAAAATTTG
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:19142791 original size:10 final size:10
Alignment explanation
Indices: 19142767--19142796 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
19142757 TGAATTATTA
19142767 ATTAAAATA-
1 ATTAAAATAT
19142776 ATTAAAATAT
1 ATTAAAATAT
19142786 ATTAAAATAT
1 ATTAAAATAT
19142796 A
1 A
19142797 AAAATTTGAT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:19143494 original size:16 final size:16
Alignment explanation
Indices: 19143473--19143535 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 16
19143463 AAAATATTAA
19143473 ATAATAATTTATATAT
1 ATAATAATTTATATAT
*
19143489 ATAAT-ATATATA-AT
1 ATAATAATTTATATAT
* *
19143503 ATAA-AA-TTAGATAA
1 ATAATAATTTATATAT
* *
19143517 ATAATAAATTATATCT
1 ATAATAATTTATATAT
19143533 ATA
1 ATA
19143536 TATATATCCG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
13 3 0.08
14 12 0.33
15 8 0.22
16 13 0.36
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
ATAATAATTTATATAT
Found at i:19143497 original size:28 final size:27
Alignment explanation
Indices: 19143457--19143527 Score: 63
Period size: 28 Copynumber: 2.5 Consensus size: 27
19143447 GTACACTTAT
* *
19143457 TAAATTAAAATATTAA-ATAATAATTTATA
1 TAAA-TAATATATTAATATAA-AA-TTAGA
*
19143486 TATATAATATATATAATATAAAATTAGA
1 TAAATAATATAT-TAATATAAAATTAGA
*
19143514 TAAATAATAAATTA
1 TAAATAATATATTA
19143528 TATCTATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
27 2 0.06
28 21 0.60
29 8 0.23
30 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (27 bp):
TAAATAATATATTAATATAAAATTAGA
Found at i:19143652 original size:34 final size:35
Alignment explanation
Indices: 19143595--19143685 Score: 116
Period size: 34 Copynumber: 2.6 Consensus size: 35
19143585 AATGGGTTTA
19143595 AAAAAATTAAAATATAAAA-ATATTTATTAAATA-TG
1 AAAAAA-T-AAATATAAAATATATTTATTAAATATTG
*
19143630 AAAAAATAAATATAAAATATATTTATTAAATATTTT
1 AAAAAATAAATATAAAATATATTTATTAAATA-TTG
*
19143666 AAAAAGTAAATA-AAAATATA
1 AAAAAATAAATATAAAATATA
19143686 AAAATAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
33 10 0.20
34 15 0.29
35 14 0.27
36 12 0.24
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (35 bp):
AAAAAATAAATATAAAATATATTTATTAAATATTG
Found at i:19143804 original size:20 final size:19
Alignment explanation
Indices: 19143783--19143847 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 19
19143773 TAAAAAATTA
19143783 AAATATAAAAATATTTATT
1 AAATATAAAAATATTTATT
* *
19143802 AAATATCAAAA-A---AGT
1 AAATATAAAAATATTTATT
19143817 AAATATAAAATATATTTATT
1 AAATATAAAA-ATATTTATT
19143837 AAATATAAAAA
1 AAATATAAAAA
19143848 AAGGCAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
15 11 0.30
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.30
20 12 0.32
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATATAAAAATATTTATT
Found at i:19143813 original size:35 final size:35
Alignment explanation
Indices: 19143774--19143850 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
19143764 CAAATGGGTT
* *
19143774 AAAAAATTAAAATATAAAA-ATATTTATTAAATATC
1 AAAAAAGT-AAATATAAAATATATTTATTAAATATA
19143809 AAAAAAGTAAATATAAAATATATTTATTAAATATA
1 AAAAAAGTAAATATAAAATATATTTATTAAATATA
19143844 AAAAAAG
1 AAAAAAG
19143851 GCAAAAGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
34 10 0.26
35 29 0.74
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (35 bp):
AAAAAAGTAAATATAAAATATATTTATTAAATATA
Found at i:19143863 original size:35 final size:34
Alignment explanation
Indices: 19143783--19143863 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 34
19143773 TAAAAAATTA
* * *
19143783 AAATATAAAAATATTTATTAAATATCAAAAAAGT
1 AAATATAAATATATTTATTAAATATAAAAAAAGC
19143817 AAATATAAAATATATTTATTAAATATAAAAAAAGGC
1 AAATAT-AAATATATTTATTAAATATAAAAAAA-GC
19143853 AAA-AGTAAATA
1 AAATA-TAAATA
19143864 AAAACATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 6 0.15
35 30 0.73
36 5 0.12
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (34 bp):
AAATATAAATATATTTATTAAATATAAAAAAAGC
Found at i:19144229 original size:12 final size:12
Alignment explanation
Indices: 19144212--19144237 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19144202 TCCTTTGCTT
19144212 CGATCTCCTCTC
1 CGATCTCCTCTC
19144224 CGATCTCCTCTC
1 CGATCTCCTCTC
19144236 CG
1 CG
19144238 CCCTCGACGA
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:0.08, C:0.50, G:0.12, T:0.31
Consensus pattern (12 bp):
CGATCTCCTCTC
Found at i:19145211 original size:2 final size:2
Alignment explanation
Indices: 19145206--19145240 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19145196 ATTGAGTGTG
19145206 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
19145241 GATCATAACT
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:19148889 original size:198 final size:199
Alignment explanation
Indices: 19148551--19148952 Score: 788
Period size: 198 Copynumber: 2.0 Consensus size: 199
19148541 TATTGCATCT
19148551 ATATCATAAAATTTGAATACTAATGAAGACTTACCCACTGACTCATTAATTTTTGTGTGTGTAAT
1 ATATCATAAAATTTGAATACTAATGAAGACTTACCCACTGACTCATTAATTTTTGTGTGTGTAAT
19148616 ATATATATCTTAGTTTGTGTTTCTGCTTCTGATGTTGCTCCTTTGATTGTAAGATAATGCTCATA
66 ATATATATCTTAGTTTGTGTTTCTGCTTCTGATGTTGCTCCTTTGATTGTAAGATAATGCTCATA
*
19148681 ATCAATAACTTTGCCCCCCTTTTTTTGGGGT-AGTGTTGGTGGATTTTCTCATTAAAAGTCTGCT
131 ATCAATAACTTTGCCCCCCTTTTTTTGGGGTGAGTGGTGGTGGATTTTCTCATTAAAAGTCTGCT
19148745 TCTC
196 TCTC
19148749 ATATCATAAAATTTGAATACTAATGAAGACTTACCCACTGACTCATTAATTTTTGTGTGTGTAAT
1 ATATCATAAAATTTGAATACTAATGAAGACTTACCCACTGACTCATTAATTTTTGTGTGTGTAAT
19148814 ATATATATCTTAGTTTGTGTTTCTGCTTCTGATGTTGCTCCTTTGATTGTAAGATAATGCTCATA
66 ATATATATCTTAGTTTGTGTTTCTGCTTCTGATGTTGCTCCTTTGATTGTAAGATAATGCTCATA
19148879 ATCAATAACTTTGCCCCCCTTTTTTTGGGGTGAGTGGTGGTGGATTTTCTCATTAAAAGTCTGCT
131 ATCAATAACTTTGCCCCCCTTTTTTTGGGGTGAGTGGTGGTGGATTTTCTCATTAAAAGTCTGCT
19148944 TCTC
196 TCTC
19148948 ATATC
1 ATATC
19148953 CTCAAGAGTT
Statistics
Matches: 202, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
198 161 0.80
199 41 0.20
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (199 bp):
ATATCATAAAATTTGAATACTAATGAAGACTTACCCACTGACTCATTAATTTTTGTGTGTGTAAT
ATATATATCTTAGTTTGTGTTTCTGCTTCTGATGTTGCTCCTTTGATTGTAAGATAATGCTCATA
ATCAATAACTTTGCCCCCCTTTTTTTGGGGTGAGTGGTGGTGGATTTTCTCATTAAAAGTCTGCT
TCTC
Found at i:19149760 original size:42 final size:42
Alignment explanation
Indices: 19149675--19149760 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
19149665 TAGAGTTAGG
*
19149675 TAATTATATATCTTACGCTTATTTTATATATATACGTTAACA
1 TAATTATATATCTTACGCTTATTTTATATATATACGATAACA
* * * *
19149717 TAATTATTTATCTTAGGCTTGTTTTATGTATATAC-ATACACA
1 TAATTATATATCTTACGCTTATTTTATATATATACGATA-ACA
19149759 TA
1 TA
19149761 CATATTGGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 2 0.05
42 36 0.95
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.48
Consensus pattern (42 bp):
TAATTATATATCTTACGCTTATTTTATATATATACGATAACA
Found at i:19153600 original size:22 final size:22
Alignment explanation
Indices: 19153574--19153617 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19153564 TGTATATTTA
* *
19153574 TATTTGTATCTCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
19153596 TATTTATATCCCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
19153618 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTATATCCCTAGAATTAAG
Found at i:19171442 original size:28 final size:28
Alignment explanation
Indices: 19171410--19171471 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
19171400 CTTACATGAC
19171410 GATGATATTAGATGACCAAGATTGTTTA
1 GATGATATTAGATGACCAAGATTGTTTA
*
19171438 GATGATCTTAGATGACCAAGATTGTTTA
1 GATGATATTAGATGACCAAGATTGTTTA
19171466 GATGAT
1 GATGAT
19171472 TGCCTTGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (28 bp):
GATGATATTAGATGACCAAGATTGTTTA
Found at i:19187049 original size:2 final size:2
Alignment explanation
Indices: 19187042--19187070 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19187032 ATCTTCTTTC
19187042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19187071 TATTCGAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19188843 original size:23 final size:23
Alignment explanation
Indices: 19188817--19188860 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
19188807 TCATACGTTA
19188817 TCTCTAAAACC-AAATCAATTCTC
1 TCTCT-AAACCTAAATCAATTCTC
*
19188840 TCTCTAAACCTAGATCAATTC
1 TCTCTAAACCTAAATCAATTC
19188861 ATAAACAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTCTAAACCTAAATCAATTCTC
Found at i:19189747 original size:21 final size:20
Alignment explanation
Indices: 19189697--19189754 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
19189687 TAGTTTTAGG
19189697 GAAAGAAA-ATAAATTTTTA
1 GAAAGAAATATAAATTTTTA
*
19189716 GAGAGAAAATATAAATTTTTA
1 GAAAG-AAATATAAATTTTTA
*
19189737 GAAAGAGAATATGAATTT
1 GAAAGA-AATATAAATTT
19189755 AGATGAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 25 0.76
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (20 bp):
GAAAGAAATATAAATTTTTA
Found at i:19196796 original size:3 final size:3
Alignment explanation
Indices: 19196788--19196813 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19196778 ATAAAAACTA
19196788 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
19196814 ATAAAAATTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19199826 original size:7 final size:7
Alignment explanation
Indices: 19199813--19199851 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
19199803 AAAATGACAA
19199813 AAAAGAAT
1 AAAA-AAT
*
19199821 AAAGAAT
1 AAAAAAT
19199828 AAAAAAT
1 AAAAAAT
19199835 AAAAAAT
1 AAAAAAT
19199842 AAAAAAT
1 AAAAAAT
19199849 AAA
1 AAA
19199852 GTGTCATGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 26 0.90
8 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:19204460 original size:13 final size:12
Alignment explanation
Indices: 19204432--19204468 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
19204422 TTTTTTTTAA
19204432 TTTTAGATTTTT
1 TTTTAGATTTTT
19204444 TTTTCAGATTTTT
1 TTTT-AGATTTTT
19204457 TTTTA-ATTTTT
1 TTTTAGATTTTT
19204468 T
1 T
19204469 AAAAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 7 0.29
12 5 0.21
13 12 0.50
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (12 bp):
TTTTAGATTTTT
Found at i:19205237 original size:22 final size:22
Alignment explanation
Indices: 19205197--19205247 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
19205187 ATTATCTCTA
* *
19205197 TTTTCTCTTTTTTTTTTTTTCCC
1 TTTTCTCTTTGTTTCTTTTT-CC
19205220 TTTT-TCTTTGTTTCTTTTTCC
1 TTTTCTCTTTGTTTCTTTTTCC
19205241 TTTTCTC
1 TTTTCTC
19205248 ACTTTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.24
22 15 0.60
23 4 0.16
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTCTCTTTGTTTCTTTTTCC
Found at i:19205264 original size:30 final size:29
Alignment explanation
Indices: 19205195--19205265 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 29
19205185 CAATTATCTC
* ** * *
19205195 TATTTTCTCTTTTTTTTTTTTTCCCTTTT
1 TATTTTTTCTTTTTCCTTTTCTCACTTTT
*
19205224 TCTTTGTTTCTTTTTCCTTTTCTCACTTTAT
1 TATTT-TTTCTTTTTCCTTTTCTCACTTT-T
19205255 TATTTTTTCTT
1 TATTTTTTCTT
19205266 CATTTTTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 4 0.12
30 24 0.73
31 5 0.15
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (29 bp):
TATTTTTTCTTTTTCCTTTTCTCACTTTT
Found at i:19210820 original size:3 final size:3
Alignment explanation
Indices: 19210814--19210848 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19210804 TTTTTTCATC
19210814 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19210849 AGCTTTTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19211704 original size:29 final size:28
Alignment explanation
Indices: 19211660--19211718 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
19211650 AAATTAAATA
** *
19211660 TTATATTTTGATTTTGTTATTTATTAAT
1 TTATATTTTGATTTTGAAATTTAATAAT
19211688 TTATAATTTT-ATATTTGAAATTTAATAAT
1 TTAT-ATTTTGAT-TTTGAAATTTAATAAT
19211717 TT
1 TT
19211719 TTTTGTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (28 bp):
TTATATTTTGATTTTGAAATTTAATAAT
Found at i:19214022 original size:208 final size:208
Alignment explanation
Indices: 19213608--19213979 Score: 478
Period size: 208 Copynumber: 1.8 Consensus size: 208
19213598 GAATTAATTA
* * *
19213608 TATTGAAGATTTTCTATAAATATTATAATACACTAGTAATATTTTACAAAAAATCTTTTCACCTA
1 TATTGAAAATTTTCTATAAATATCATAATACACTAGTAATATTTTAAAAAAAATCTTTTCACCTA
** *
19213673 GGGATTTCTTAAAGCATCTCTACTCGAAATACTTTTAGAATCCCATCATTGGATAAAATTTCCTT
66 AAGATTTCTTAAAGCATCACTACTCGAAATACTTTTAGAATCCCATCATTGGATAAAATTTCCTT
* * * *
19213738 TCTTCTCATTTTTATTACTTATATTTTTAATTTATTAATCAATTTTTATTTATTGTTAACAAAAA
131 TCTTCTCATTTTTATTACTAATATTATTAATTTATAAATCAATTTTTATTCATTGTTAACAAAAA
19213803 AAAAATTTTATTG
196 AAAAATTTTATTG
* *
19213816 TATTGAAAAATTTT-TATAAATACTCA-AATACACTGGTAGTA-TTTAAAAAAAATTCTTTTCAC
1 TATTG-AAAATTTTCTATAAATA-TCATAATACACTAGTAATATTTTAAAAAAAA-TCTTTTCAC
19213878 CTAAAGA-TT-TTATAAGCATCACTACTCGAAATA-TCTTTA-AATCCCATCATTGGATAAAATT
63 CTAAAGATTTCTTA-AAGCATCACTACTCGAAATACT-TTTAGAATCCCATCATTGGATAAAATT
* *
19213939 TCC-TT-TTCTTATTTTT-TTA-TCAATATTATTATTATTATAAA
126 TCCTTTCTTCTCATTTTTATTACT-AATATTATTAAT-TTATAAA
19213980 GTTTCATTAT
Statistics
Matches: 144, Mismatches: 13, Indels: 18
0.82 0.07 0.10
Matches are distributed among these distances:
202 1 0.01
203 12 0.08
204 16 0.11
205 2 0.01
206 29 0.20
207 35 0.24
208 40 0.28
209 9 0.06
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (208 bp):
TATTGAAAATTTTCTATAAATATCATAATACACTAGTAATATTTTAAAAAAAATCTTTTCACCTA
AAGATTTCTTAAAGCATCACTACTCGAAATACTTTTAGAATCCCATCATTGGATAAAATTTCCTT
TCTTCTCATTTTTATTACTAATATTATTAATTTATAAATCAATTTTTATTCATTGTTAACAAAAA
AAAAATTTTATTG
Found at i:19215137 original size:11 final size:10
Alignment explanation
Indices: 19215117--19215162 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
19215107 GATAAGGAAG
*
19215117 AAAAAGAAGA
1 AAAAAGAAAA
19215127 AAAAAGAAAGA
1 AAAAAGAAA-A
*
19215138 AAAAAGAGAA
1 AAAAAGAAAA
*
19215148 AAAAATAAAA
1 AAAAAGAAAA
19215158 AAAAA
1 AAAAA
19215163 TTAAATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:19215152 original size:10 final size:10
Alignment explanation
Indices: 19215113--19215151 Score: 55
Period size: 9 Copynumber: 4.0 Consensus size: 10
19215103 ACCGGATAAG
19215113 GAAG-AAAAA
1 GAAGAAAAAA
19215122 GAAGAAAAAA
1 GAAGAAAAAA
19215132 GAAAGAAAAAA
1 G-AAGAAAAAA
19215143 G-AGAAAAAA
1 GAAGAAAAAA
19215152 ATAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 12 0.43
10 6 0.21
11 10 0.36
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
GAAGAAAAAA
Found at i:19215543 original size:100 final size:99
Alignment explanation
Indices: 19215363--19215772 Score: 326
Period size: 100 Copynumber: 4.0 Consensus size: 99
19215353 TTGAAAATTT
* * * * *
19215363 AAAAGGCTCCTCTTAGCAGAGACTCAATAATTTTAAAATT-TT-TATCTGAAAAAGCTCCTCTCA
1 AAAA-GCTCATCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATAT-TGAAAAAGCTCCTCTCA
* ** *
19215426 GTAGAAGCTCAGTAACTTTAAGAATCTTTCATCTTGG
64 ATAG-AGCTCAACAACTTTAAAAATCTTTCATCTTGG
* * *
19215463 AAAAGCTCTTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATATTGTAAAAGCTCCTCTCAAC
1 AAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATATTGAAAAAGCTCCTCTCAAT
* *
19215528 AGAGCCTCAACAACTTTAAAAATCTTTCATTTTGA
66 AGAG-CTCAACAACTTTAAAAATCTTTCATCTTGG
* * * * * * *
19215563 AAAAGCTCATCTCAGCAGAAGCTCAACAACTTTAACTTTACAAATCTGATCTTGGAAAAGTTTCT
1 AAAAGCTCATCTCAGCAGAGGCTCAACAACTTT-A----A-AATTCTTATATTGAAAAAGCTCCT
19215628 CTCAATAGAGGCTCAACAACTTTAAAAATCTCTT-ATCTTGG
60 CTCAATAGA-GCTCAACAACTTTAAAAATCT-TTCATCTTGG
* * ** * *
19215669 AGAAGCTCATATCAATAGAGGCTCAATAACTTTAACTTTAAAAATT-TGATTTTTGAAAAAGCTC
1 AAAAGCTCATCTCAGCAGAGGCTC---AAC---AACTTT-AAAATTCTTA-TATTGAAAAAGCTC
**
19215733 CTCTCAGCAGAGGCTCAACAACTTTAAAAAAT-TTTCATCT
58 CTCTCAATAGA-GCTCAACAACTTT-AAAAATCTTTCATCT
19215773 GTTTTCAAAT
Statistics
Matches: 254, Mismatches: 36, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
99 32 0.13
100 80 0.31
101 4 0.02
105 1 0.00
106 75 0.30
107 44 0.17
108 7 0.03
109 3 0.01
112 8 0.03
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (99 bp):
AAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATATTGAAAAAGCTCCTCTCAAT
AGAGCTCAACAACTTTAAAAATCTTTCATCTTGG
Found at i:19215657 original size:106 final size:105
Alignment explanation
Indices: 19215409--19215772 Score: 391
Period size: 106 Copynumber: 3.5 Consensus size: 105
19215399 AATTTTTATC
** * ** * *
19215409 TGAAAAAGCTCCTCTCAGTAGAAGCTCAGTAACTTTAAGAATCTTTCATCTTGGAAAAGCTCTTC
1 TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATCTTTCATCTTGGAAAAGCTCATC
* *
19215474 TCAGCAGAGGCTCAACAACTTT-A----AAATTCTTATAT
66 TCAGCAGAGGCTCAACAACTTTAACTTTAAAATCTGATAT
* * * *
19215509 TGTAAAAGCTCCTCTCAACAGAGCCTCAACAACTTTAAAAATCTTTCATTTTGAAAAAGCTCATC
1 TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATCTTTCATCTTGGAAAAGCTCATC
* *
19215574 TCAGCAGAAGCTCAACAACTTTAACTTTACAAATCTGATCT
66 TCAGCAGAGGCTCAACAACTTTAACTTTA-AAATCTGATAT
* * * * *
19215615 TGGAAAAGTTTCTCTCAATAGAGGCTCAACAACTTTAAAAATCTCTT-ATCTTGGAGAAGCTCAT
1 TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATCT-TTCATCTTGGAAAAGCTCAT
* ** * * *
19215679 ATCAATAGAGGCTCAATAACTTTAACTTTAAAAATTTGATTTT
65 CTCAGCAGAGGCTCAACAACTTTAACTTT-AAAATCTGA-TAT
*
19215722 TGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAAT-TTTCATCT
1 TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTT-AAAAATCTTTCATCT
19215773 GTTTTCAAAT
Statistics
Matches: 218, Mismatches: 35, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
100 75 0.34
101 1 0.00
105 1 0.00
106 94 0.43
107 41 0.19
108 6 0.03
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (105 bp):
TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATCTTTCATCTTGGAAAAGCTCATC
TCAGCAGAGGCTCAACAACTTTAACTTTAAAATCTGATAT
Done.