Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 19 of 129
Found at i:3656559 original size:24 final size:24
Alignment explanation
Indices: 3656527--3656597 Score: 115
Period size: 24 Copynumber: 2.9 Consensus size: 24
3656517 CTAATTTTTA
*
3656527 TTTTCGATCACATATTTGCTTATAC
1 TTTT-GATCACGTATTTGCTTATAC
*
3656552 TTTTGATCACGTATTTGCTTATAT
1 TTTTGATCACGTATTTGCTTATAC
3656576 TTTTGATCACGTATTTGCTTAT
1 TTTTGATCACGTATTTGCTTAT
3656598 GCACACAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 40 0.91
25 4 0.09
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.52
Consensus pattern (24 bp):
TTTTGATCACGTATTTGCTTATAC
Found at i:3673812 original size:11 final size:12
Alignment explanation
Indices: 3673796--3673832 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
3673786 AAAATTTTAT
3673796 TAAAAAATTAAA
1 TAAAAAATTAAA
3673808 T-AAAAATTAAAA
1 TAAAAAATT-AAA
3673820 TAAAAAATTAAA
1 TAAAAAATTAAA
3673832 T
1 T
3673833 TTAATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.30
12 9 0.39
13 7 0.30
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAAAATTAAA
Found at i:3673823 original size:24 final size:26
Alignment explanation
Indices: 3673796--3673846 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
3673786 AAAATTTTAT
3673796 TAAAAAATTAAA-TAA-AAATTAAAA
1 TAAAAAATTAAATTAATAAATTAAAA
3673820 TAAAAAATTAAATTTAATAAATTAAAA
1 TAAAAAATTAAA-TTAATAAATTAAAA
3673847 AATTTTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 12 0.50
26 3 0.12
27 9 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (26 bp):
TAAAAAATTAAATTAATAAATTAAAA
Found at i:3673894 original size:9 final size:10
Alignment explanation
Indices: 3673873--3673950 Score: 57
Period size: 10 Copynumber: 7.0 Consensus size: 10
3673863 TTAAGTGTGT
3673873 AAAATTTTAA
1 AAAATTTTAA
3673883 AAAATTTTAA
1 AAAATTTTAA
3673893 AAAATTTTTATA
1 AAAA-TTTTA-A
* *
3673905 TATATTTTAAA
1 AAAATTTT-AA
3673916 TAAATATTTTAACA
1 -AAA-ATTTT-A-A
*
3673930 AAAATATTTAT
1 AAAAT-TTTAA
3673941 AAAATTTTAA
1 AAAATTTTAA
3673951 TTATTGAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
10 18 0.33
11 15 0.27
12 8 0.15
13 13 0.24
14 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:3673924 original size:13 final size:13
Alignment explanation
Indices: 3673886--3673943 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
3673876 ATTTTAAAAA
3673886 ATTTTAAA-AAAT
1 ATTTTAAATAAAT
*
3673898 -TTTT--ATATAT
1 ATTTTAAATAAAT
3673908 ATTTTAAATAAAT
1 ATTTTAAATAAAT
*
3673921 ATTTTAACAAAAAT
1 ATTTTAA-ATAAAT
3673935 ATTTATAAA
1 ATTT-TAAA
3673944 ATTTTAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
9 1 0.03
10 3 0.08
11 8 0.22
13 12 0.32
14 10 0.27
15 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTTAAATAAAT
Found at i:3673936 original size:14 final size:13
Alignment explanation
Indices: 3673906--3673944 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
3673896 ATTTTTATAT
*
3673906 ATATTTTAAATAA
1 ATATTTTAAAAAA
3673919 ATATTTTAACAAAA
1 ATATTTTAA-AAAA
3673933 ATATTTATAAAA
1 ATATTT-TAAAA
3673945 TTTTAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 9 0.39
14 11 0.48
15 3 0.13
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTTTAAAAAA
Found at i:3674019 original size:22 final size:22
Alignment explanation
Indices: 3673988--3674036 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3673978 AATTATAAAT
*
3673988 AATTTTTTCATT-AAATTTTATC
1 AATTTATTCATTAAAATTTT-TC
3674010 AATTTATTCATTAAAATTTTTC
1 AATTTATTCATTAAAATTTTTC
3674032 -ATTTA
1 AATTTA
3674037 AATTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 13 0.52
23 7 0.28
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTATTCATTAAAATTTTTC
Found at i:3674047 original size:12 final size:13
Alignment explanation
Indices: 3674010--3674051 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
3674000 AAATTTTATC
*
3674010 AATTTATTCATTAA
1 AATTT-TTCATTTA
3674024 AATTTTTCATTTA
1 AATTTTTCATTTA
3674037 AATTTTT-ATTTA
1 AATTTTTCATTTA
3674049 AAT
1 AAT
3674052 CATTTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 8 0.30
13 14 0.52
14 5 0.19
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTTTTCATTTA
Found at i:3674059 original size:35 final size:34
Alignment explanation
Indices: 3673991--3674060 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 34
3673981 TATAAATAAT
*
3673991 TTTTTCATTAAATTTTATCAATTTATTCATTAAAA
1 TTTTTCATTAAATTTTAT-AATTTAATCATTAAAA
3674026 TTTTTCATTTAAATTTT-T-ATTTAAATCATTTAAAA
1 TTTTTCA-TTAAATTTTATAATTT-AATCA-TTAAAA
3674061 AAAATTGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
33 4 0.13
34 4 0.13
35 14 0.45
36 9 0.29
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (34 bp):
TTTTTCATTAAATTTTATAATTTAATCATTAAAA
Found at i:3675504 original size:11 final size:11
Alignment explanation
Indices: 3675488--3675529 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
3675478 AATCCCATAA
3675488 GAGATTTGTTT
1 GAGATTTGTTT
* *
3675499 GAGATTTATTA
1 GAGATTTGTTT
3675510 GAGATTTGTTT
1 GAGATTTGTTT
*
3675521 AAGATTTGT
1 GAGATTTGT
3675530 CAGATATTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:3675641 original size:52 final size:52
Alignment explanation
Indices: 3675554--3675659 Score: 135
Period size: 52 Copynumber: 2.0 Consensus size: 52
3675544 TAGACAAGAA
* **
3675554 GACTTGCAAAAGAAGAATTTCAAGAGAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAAAGAAGAATTTAAAGAGAAAGAGGATTCTTAATAGACAAGTTT
* *
3675606 GACTTGTAAGAGAAGAATTCTAAA-AGGAAAG-GGATTCTTAATAGACAAGTTT
1 GACTTGCAAAAGAAGAATT-TAAAGA-GAAAGAGGATTCTTAATAGACAAGTTT
3675658 GA
1 GA
3675660 TTTACAGGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 39 0.83
53 8 0.17
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (52 bp):
GACTTGCAAAAGAAGAATTTAAAGAGAAAGAGGATTCTTAATAGACAAGTTT
Found at i:3677603 original size:16 final size:16
Alignment explanation
Indices: 3677584--3677621 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
3677574 AAGGGTTTGA
3677584 GTTTGTGTTTGTTTAG
1 GTTTGTGTTTGTTTAG
*
3677600 GTTTGTGTTTGTTTGG
1 GTTTGTGTTTGTTTAG
3677616 GTTTGT
1 GTTTGT
3677622 TTGGGTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.03, C:0.00, G:0.34, T:0.63
Consensus pattern (16 bp):
GTTTGTGTTTGTTTAG
Found at i:3678360 original size:52 final size:52
Alignment explanation
Indices: 3678294--3678450 Score: 181
Period size: 52 Copynumber: 3.0 Consensus size: 52
3678284 TGAACAAGAA
* * * * *
3678294 GACTTGTAAAAGAAGAATTCCAAGA-GAAAGAAGATTTTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCCAAAAGGAAAG-AGATTCTTAATAGGCAAGTTT
*
3678346 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCCAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
* * * ** * *
3678398 GACTTACAGGAGAAGAATTCTAGGAGGAGAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCCAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
3678450 G
1 G
3678451 TATGGTTATA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 87 0.95
53 5 0.05
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCCAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:3678617 original size:48 final size:48
Alignment explanation
Indices: 3678560--3678658 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
3678550 GGGGCTTTAC
3678560 GTCTTATGGGTGTGTATGTTTGTGAGTGGACTAGAGGAGATTGAGAGG
1 GTCTTATGGGTGTGTATGTTTGTGAGTGGACTAGAGGAGATTGAGAGG
3678608 GTCTTATGGGTGTGTATGTTTGTGAGTGGACTAGAGGAGATTGAGAGG
1 GTCTTATGGGTGTGTATGTTTGTGAGTGGACTAGAGGAGATTGAGAGG
3678656 GTC
1 GTC
3678659 CACATAGGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.20, C:0.05, G:0.41, T:0.33
Consensus pattern (48 bp):
GTCTTATGGGTGTGTATGTTTGTGAGTGGACTAGAGGAGATTGAGAGG
Found at i:3679821 original size:42 final size:38
Alignment explanation
Indices: 3679774--3679851 Score: 93
Period size: 38 Copynumber: 1.9 Consensus size: 38
3679764 TATTCATAAA
*
3679774 ATTATAAGAAGAATTATATTATTTATATTTAGTTTATTTTTT
1 ATTATAAGAA-AA--ATATTAATTAT-TTTAGTTTATTTTTT
* *
3679816 ATTATAATAAAAATATTAATTATTTTATTTTATTTT
1 ATTATAAGAAAAATATTAATTATTTTAGTTTATTTT
3679852 ATTTTCATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 12 0.36
39 10 0.30
41 2 0.06
42 9 0.27
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (38 bp):
ATTATAAGAAAAATATTAATTATTTTAGTTTATTTTTT
Found at i:3682234 original size:2 final size:2
Alignment explanation
Indices: 3682227--3682264 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3682217 CTATTTCTAC
*
3682227 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3682265 CTTGCTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3687376 original size:2 final size:2
Alignment explanation
Indices: 3687369--3687396 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3687359 GGTCGAGTAA
3687369 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3687397 GATTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3693447 original size:17 final size:17
Alignment explanation
Indices: 3693425--3693458 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3693415 TTAAAAATTT
*
3693425 TAAATATATTTATTAAA
1 TAAATATATTTAATAAA
*
3693442 TAAATATTTTTAATAAA
1 TAAATATATTTAATAAA
3693459 AATATTAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATATATTTAATAAA
Found at i:3693574 original size:27 final size:27
Alignment explanation
Indices: 3693544--3693604 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
3693534 TAAATTATAT
**
3693544 AAATTTATTAAGTTAATTTTTTTAAAA
1 AAATTTATTAAGTTAATTTTAATAAAA
* *
3693571 AAATTTATTTATTTAATTTTAATAAAA
1 AAATTTATTAAGTTAATTTTAATAAAA
3693598 AAATTTA
1 AAATTTA
3693605 ACAAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
AAATTTATTAAGTTAATTTTAATAAAA
Found at i:3694755 original size:5 final size:5
Alignment explanation
Indices: 3694747--3694776 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3694737 CACCGTTAAC
*
3694747 TTTTA TTTTA TTTTA TTTTA TTTCA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
3694777 ATTGTTATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:3700971 original size:25 final size:25
Alignment explanation
Indices: 3700950--3701001 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
3700940 TTTTTATGAA
*
3700950 AAATTTTTTTAATCGTAATTATAAT
1 AAATTTTTTTAATCATAATTATAAT
**
3700975 ATTTTTTTTTAATCATAATTATAAT
1 AAATTTTTTTAATCATAATTATAAT
3701000 AA
1 AA
3701002 TTATTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
AAATTTTTTTAATCATAATTATAAT
Found at i:3701774 original size:18 final size:17
Alignment explanation
Indices: 3701743--3701776 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3701733 ATGTTATTTT
3701743 ATATTTATTAAAATTAG
1 ATATTTATTAAAATTAG
*
3701760 ATATTGTATTTAAATTA
1 ATATT-TATTAAAATTA
3701777 AATACTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
ATATTTATTAAAATTAG
Found at i:3703202 original size:9 final size:9
Alignment explanation
Indices: 3703170--3703195 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3703160 TATTTATGAT
3703170 TTAATTTAA
1 TTAATTTAA
3703179 TTAATTTAA
1 TTAATTTAA
3703188 TTAATTTA
1 TTAATTTA
3703196 TATAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTAATTTAA
Found at i:3705823 original size:28 final size:28
Alignment explanation
Indices: 3705758--3705825 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
3705748 TTCGTATCCG
* * *
3705758 AATAAACTCTTAATTTTAATTTATATCT
1 AATAAGCTTTTAATTTTAATTTATATCA
* *
3705786 AATATG-TTTTAATATTTAATTTGTAT-A
1 AATAAGCTTTTAAT-TTTAATTTATATCA
3705813 AATAAGCTTTTAA
1 AATAAGCTTTTAA
3705826 CATAAATCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (28 bp):
AATAAGCTTTTAATTTTAATTTATATCA
Found at i:3705900 original size:28 final size:27
Alignment explanation
Indices: 3705852--3705904 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
3705842 ATTTGAGATA
3705852 AAAGTTTATTTTGATATTAATCAAAAAT
1 AAAGTTTATTTTGATATTAAT-AAAAAT
3705880 AAAGATTTA-TTTGA-ATATAATAAAA
1 AAAG-TTTATTTTGATAT-TAATAAAA
3705905 TTATAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
27 6 0.26
28 13 0.57
29 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (27 bp):
AAAGTTTATTTTGATATTAATAAAAAT
Found at i:3706830 original size:20 final size:21
Alignment explanation
Indices: 3706788--3706837 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
3706778 ATTTTTAATT
* *
3706788 TTTTAAAAT-TTTAAATATTA
1 TTTTAATATATTTAAATATAA
3706808 TTTTAATATATTTAAATA-AA
1 TTTTAATATATTTAAATATAA
*
3706828 TTTTGATATA
1 TTTTAATATA
3706838 AAATTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTAATATATTTAAATATAA
Found at i:3706886 original size:16 final size:16
Alignment explanation
Indices: 3706865--3706897 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3706855 TTATAAAAAT
*
3706865 TTAAAATATATATAAA
1 TTAAAAAATATATAAA
3706881 TTAAAAAATATATAAA
1 TTAAAAAATATATAAA
3706897 T
1 T
3706898 CGATTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TTAAAAAATATATAAA
Found at i:3707527 original size:24 final size:24
Alignment explanation
Indices: 3707490--3707536 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3707480 ATAAAAAAAA
*
3707490 TTTTTAATCGTAATTATAATAATT
1 TTTTTAATCATAATTATAATAATT
*
3707514 TTTTTAATTATAATTATAATAAT
1 TTTTTAATCATAATTATAATAAT
3707537 AATTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTTTAATCATAATTATAATAATT
Found at i:3707533 original size:12 final size:12
Alignment explanation
Indices: 3707500--3707542 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3707490 TTTTTAATCG
3707500 TAATTATAATAA
1 TAATTATAATAA
** * *
3707512 TTTTTTTAATTA
1 TAATTATAATAA
3707524 TAATTATAATAA
1 TAATTATAATAA
3707536 TAATTAT
1 TAATTAT
3707543 TTTTTTTTTA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TAATTATAATAA
Found at i:3708299 original size:18 final size:17
Alignment explanation
Indices: 3708268--3708301 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3708258 ATGTTATTTT
3708268 ATATTTATTAAAATTAG
1 ATATTTATTAAAATTAG
*
3708285 ATATTGTATTTAAATTA
1 ATATT-TATTAAAATTA
3708302 AATACTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
ATATTTATTAAAATTAG
Found at i:3709259 original size:15 final size:15
Alignment explanation
Indices: 3709239--3709280 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
3709229 ATAAATGATG
3709239 AAATTAATTATAATA
1 AAATTAATTATAATA
*
3709254 AAATTAATAATAATA
1 AAATTAATTATAATA
3709269 AAA-T-ATTATAAT
1 AAATTAATTATAAT
3709281 TATTATTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 7 0.28
14 1 0.04
15 17 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTAATTATAATA
Found at i:3714324 original size:2 final size:2
Alignment explanation
Indices: 3714302--3714344 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
3714292 GAGAAATAAA
* *
3714302 AG AG A- AG AA AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3714343 AG
1 AG
3714345 CTCTTATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.02
Consensus pattern (2 bp):
AG
Found at i:3721261 original size:329 final size:329
Alignment explanation
Indices: 3720577--3721892 Score: 2465
Period size: 329 Copynumber: 4.0 Consensus size: 329
3720567 CTGGGACAAC
* *
3720577 TATGGAGGTTTTTTCTCTGTATATAACTACAGTTCATTTTATGTTTTTCTGTCGTTTTGTCTTCC
1 TATGGAGGTTTTTTCTCTGTATACAACTACAGTTCATTTTATGTTTTTCTGTCGTTTTGTCTTCA
3720642 GAAGACAAATCCCAGAAAGGCATTTTCACTGTATATAACTGAAGACTTGGGAATTGAAGTCAATT
66 GAAGACAAATCCCAGAAAGGCATTTTCACTGTATATAACTGAAGACTTGGGAATTGAAGTCAATT
* *
3720707 CAAGCAGGCAGGAAAGGTTTTTACATTGGGTTAGAGTCGTAGAGAAGAGTGCTGCTGAAAGTTCC
131 CAAGCAGGCAGAAAAGGTTTTTACATTGGGTT-GAGTCGTAGAGAAGAGTGCTGCTGAAAGCTCC
3720772 CTCCTAATGGTTTCTGGAAATAAGAATTTTCAAAAACTTATTCACAATCTATGATGAATTAGTCC
195 CTCCTAATGG-TTCTGGAAATAAGAATTTTCAAAAACTTATTCACAATCTATGATGAATTAGTCC
3720837 ATAAACAGTGATCAAAGCCATGATAAGACAATGATCTACATTTGATTCAACTTCCAAGGTTAATA
259 ATAAACAGTGATCAAAGCCATGATAAGACAATGATCTACATTTGATTCAACTTCCAAGGTTAATA
3720902 CATCAG
324 CATCAG
3720908 TATGGAGGTTTTTTCTCTGTATACAACTACAGTTCATTTTATGTTTTTCTGTCGTTTTGTCTTCA
1 TATGGAGGTTTTTTCTCTGTATACAACTACAGTTCATTTTATGTTTTTCTGTCGTTTTGTCTTCA
* *
3720973 GAAGACAAATCCCAGAAAGGCTTTTTCACTGTATATTACTGAAGACTTGGGAATTGAAGTCAATT
66 GAAGACAAATCCCAGAAAGGCATTTTCACTGTATATAACTGAAGACTTGGGAATTGAAGTCAATT
3721038 CAAGCAGGCAGAAAAGGTTTTTACAATT-GGTTGAGTCGTAGAGAAGAGTGCTGCTGAAAGCTCC
131 CAAGCAGGCAGAAAAGGTTTTTAC-ATTGGGTTGAGTCGTAGAGAAGAGTGCTGCTGAAAGCTCC
3721102 CTCCTAATGGTTCTGGAAATAAGAATTTTCAAAAACTTATTCACAATCTATGATGAATTAGTCCA
195 CTCCTAATGGTTCTGGAAATAAGAATTTTCAAAAACTTATTCACAATCTATGATGAATTAGTCCA
3721167 TAAACAGTGATCAAAGCCATGATAAGACAATGATCTACATTTGATTCAACTTCCAAGGTTAATAC
260 TAAACAGTGATCAAAGCCATGATAAGACAATGATCTACATTTGATTCAACTTCCAAGGTTAATAC
3721232 ATCAG
325 ATCAG
*
3721237 TATGGAGGTTTTTTCTCTGTATACAACTACAGTTCATTTTATGTTTTTCTGTCGTTTTGTCTTCC
1 TATGGAGGTTTTTTCTCTGTATACAACTACAGTTCATTTTATGTTTTTCTGTCGTTTTGTCTTCA
3721302 GAAGACAAATCCCAGAAAGGCATTTTCACTGTATATAACTGAAGACTTGGGAATTGAAGTCAATT
66 GAAGACAAATCCCAGAAAGGCATTTTCACTGTATATAACTGAAGACTTGGGAATTGAAGTCAATT
* *
3721367 CAAGCAGGCAGGAAAGGTTTTTACATTGGGTAGAGTCGTAGAGAAGAGTGCTGCTGAAAGCTCCC
131 CAAGCAGGCAGAAAAGGTTTTTACATTGGGTTGAGTCGTAGAGAAGAGTGCTGCTGAAAGCTCCC
3721432 TCCTAATGGTTCTGGAAATAAGAATTTTCAAAAACTTATTCACAATCTATGATGAATTAGTCCAT
196 TCCTAATGGTTCTGGAAATAAGAATTTTCAAAAACTTATTCACAATCTATGATGAATTAGTCCAT
3721497 AAACAGTGATCAAAGCCATGATAAGACAATGATCTACATTTGATTCAACTTCCAAGGTTAATACA
261 AAACAGTGATCAAAGCCATGATAAGACAATGATCTACATTTGATTCAACTTCCAAGGTTAATACA
3721562 TCAG
326 TCAG
*
3721566 TATGGAGGTTTTTTCTCTGTATACAACTACAGTTCATTTTATGTTTTTCCGTCGTTTTGTCTTCA
1 TATGGAGGTTTTTTCTCTGTATACAACTACAGTTCATTTTATGTTTTTCTGTCGTTTTGTCTTCA
* * *
3721631 GAAGACAAATCCCAGAAAGGCTTTTTCACTGTATATTACTGAAGACTTGGGAATAGAAGTCAATT
66 GAAGACAAATCCCAGAAAGGCATTTTCACTGTATATAACTGAAGACTTGGGAATTGAAGTCAATT
3721696 CAAGCAGGCAGAAAAGGTTTTTACAATT-GGTTGAGTCGTAGAGAAGAGTGCTGCTGAAAGCTCC
131 CAAGCAGGCAGAAAAGGTTTTTAC-ATTGGGTTGAGTCGTAGAGAAGAGTGCTGCTGAAAGCTCC
3721760 CTCCTAATGGTTCTGGAAATAAGAATTTTCAAAAACTTATTCACAATCTATGATGAATTAGTCCA
195 CTCCTAATGGTTCTGGAAATAAGAATTTTCAAAAACTTATTCACAATCTATGATGAATTAGTCCA
3721825 TAAACAGTGATCAAAGCCATGATAAGACAATGATCTACATTTGATTCAACTTCCAAGGTTAATAC
260 TAAACAGTGATCAAAGCCATGATAAGACAATGATCTACATTTGATTCAACTTCCAAGGTTAATAC
3721890 ATC
325 ATC
3721893 TTCTCCTAAC
Statistics
Matches: 964, Mismatches: 18, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
328 3 0.00
329 761 0.79
330 44 0.05
331 153 0.16
332 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (329 bp):
TATGGAGGTTTTTTCTCTGTATACAACTACAGTTCATTTTATGTTTTTCTGTCGTTTTGTCTTCA
GAAGACAAATCCCAGAAAGGCATTTTCACTGTATATAACTGAAGACTTGGGAATTGAAGTCAATT
CAAGCAGGCAGAAAAGGTTTTTACATTGGGTTGAGTCGTAGAGAAGAGTGCTGCTGAAAGCTCCC
TCCTAATGGTTCTGGAAATAAGAATTTTCAAAAACTTATTCACAATCTATGATGAATTAGTCCAT
AAACAGTGATCAAAGCCATGATAAGACAATGATCTACATTTGATTCAACTTCCAAGGTTAATACA
TCAG
Found at i:3723402 original size:20 final size:22
Alignment explanation
Indices: 3723368--3723425 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 22
3723358 CAACTCATAA
3723368 AAAAAATTTATAAAT-TTT-TT
1 AAAAAATTTATAAATATTTATT
3723388 AAAAAATTTCA-AAATATTTATT
1 AAAAAATTT-ATAAATATTTATT
*
3723410 AATAAAAGATTATAAA
1 AA-AAAA-TTTATAAA
3723426 ATTCAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 13 0.42
21 4 0.13
22 4 0.13
23 5 0.16
24 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAAATTTATAAATATTTATT
Found at i:3724884 original size:2 final size:2
Alignment explanation
Indices: 3724877--3724902 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3724867 TGAATCCTTC
3724877 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3724903 CCATTATAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3736077 original size:2 final size:2
Alignment explanation
Indices: 3736070--3736100 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3736060 TGTAAGCATA
3736070 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3736101 ATATACAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3743825 original size:22 final size:25
Alignment explanation
Indices: 3743782--3743832 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 25
3743772 TTAAATAAAA
*
3743782 AAATTATTTTTTATATAATTATTAGT
1 AAATTATTTTTTATAT-ATTATAAGT
3743808 AAATT-TTTTTTAT-T-TTATAAGT
1 AAATTATTTTTTATATATTATAAGT
3743830 AAA
1 AAA
3743833 ATTAAGAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 10 0.42
24 1 0.04
25 8 0.33
26 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
AAATTATTTTTTATATATTATAAGT
Found at i:3743834 original size:23 final size:26
Alignment explanation
Indices: 3743781--3743836 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
3743771 ATTAAATAAA
*
3743781 AAAATTATTTTTTATATAATTATTAGT
1 AAAATTATTTTTTATAT-ATTATAAGT
3743808 -AAATT-TTTTTTAT-T-TTATAAGT
1 AAAATTATTTTTTATATATTATAAGT
3743830 AAAATTA
1 AAAATTA
3743837 AGAGATTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 7 0.27
23 5 0.19
24 1 0.04
25 8 0.31
26 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
AAAATTATTTTTTATATATTATAAGT
Found at i:3751241 original size:31 final size:31
Alignment explanation
Indices: 3751203--3751261 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3751193 CATTTTGATC
* *
3751203 TTTTATTATGTAATAAATTAATGAATAAATT
1 TTTTATTATATAATAAATTAATAAATAAATT
3751234 TTTTATTATATAATAAATTAATAAATAA
1 TTTTATTATATAATAAATTAATAAATAA
3751262 TTAACTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTTATTATATAATAAATTAATAAATAAATT
Found at i:3751452 original size:3 final size:3
Alignment explanation
Indices: 3751436--3751495 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
3751426 TTACGTTAAA
* * * *
3751436 ATT A-T ATT -TT ATT ATT ATT -TT ATT TTT ATT ATT ATA ATA ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
3751481 ATT ATT TTT ATT ATT
1 ATT ATT ATT ATT ATT
3751496 TTTTTTAATC
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 6 0.13
3 40 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3751464 original size:17 final size:18
Alignment explanation
Indices: 3751437--3751470 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3751427 TACGTTAAAA
3751437 TTATATTTTATTATTATT
1 TTATATTTTATTATTATT
3751455 TTAT-TTTTATTATTAT
1 TTATATTTTATTATTAT
3751471 AATAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATATTTTATTATTATT
Found at i:3751466 original size:27 final size:27
Alignment explanation
Indices: 3751436--3751498 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3751426 TTACGTTAAA
* *
3751436 ATTATATTTTATTATT-ATTTTATTTTT
1 ATTAT-TTTTATAATTAATATTATTTTT
* *
3751463 ATTATTATAATAATTAATATTATTTTT
1 ATTATTTTTATAATTAATATTATTTTT
3751490 ATTATTTTT
1 ATTATTTTT
3751499 TTTAATCTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (27 bp):
ATTATTTTTATAATTAATATTATTTTT
Found at i:3752611 original size:11 final size:11
Alignment explanation
Indices: 3752597--3752652 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
3752587 AATATAACTT
3752597 AAAATTTTATA
1 AAAATTTTATA
*
3752608 AAAATTATATA
1 AAAATTTTATA
* *
3752619 AATATTTAAT-
1 AAAATTTTATA
*
3752629 AAAATTTTAAA
1 AAAATTTTATA
3752640 AATATATTTTATA
1 AA-A-ATTTTATA
3752653 TTTTTATATC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.56
12 1 0.03
13 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAAATTTTATA
Found at i:3753602 original size:17 final size:18
Alignment explanation
Indices: 3753570--3753603 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3753560 ATATTTTATT
3753570 AATTAAAATAATAAAAAA
1 AATTAAAATAATAAAAAA
*
3753588 AATTTAAAT-ATAAAAA
1 AATTAAAATAATAAAAA
3753604 CTCGATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATTAAAATAATAAAAAA
Found at i:3761037 original size:12 final size:12
Alignment explanation
Indices: 3761019--3761048 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3761009 AAGTTTCTGA
3761019 GAAAAGTAAAAG
1 GAAAAGTAAAAG
*
3761031 TAAAAGTAAAAG
1 GAAAAGTAAAAG
3761043 GAAAAG
1 GAAAAG
3761049 AAATGAGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (12 bp):
GAAAAGTAAAAG
Found at i:3764669 original size:7 final size:7
Alignment explanation
Indices: 3764657--3764689 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
3764647 TCGAATAAAA
3764657 AAAATTT
1 AAAATTT
3764664 AAAATTT
1 AAAATTT
3764671 AAAATTT
1 AAAATTT
3764678 AAAATTT
1 AAAATTT
3764685 AAAAT
1 AAAAT
3764690 GATTTGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:3765101 original size:14 final size:15
Alignment explanation
Indices: 3765082--3765110 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3765072 AGTTGTCAAA
3765082 ATTAAAA-TTAAAAT
1 ATTAAAATTTAAAAT
3765096 ATTAAAATTTAAAAT
1 ATTAAAATTTAAAAT
3765111 CTAATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAATTTAAAAT
Found at i:3765335 original size:16 final size:16
Alignment explanation
Indices: 3765314--3765356 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
3765304 ATTATTTTTT
*
3765314 AAATATAAATATTTAA
1 AAATATAAATATATAA
* *
3765330 AAATATTATTATATAA
1 AAATATAAATATATAA
*
3765346 ATATATAAATA
1 AAATATAAATA
3765357 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATAAATATATAA
Found at i:3765474 original size:17 final size:19
Alignment explanation
Indices: 3765454--3765490 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3765444 ACTAAATTTG
3765454 AAAT-CTAAATTTTA-AAA
1 AAATACTAAATTTTATAAA
*
3765471 AAATACTTAATTTTATAAA
1 AAATACTAAATTTTATAAA
3765490 A
1 A
3765491 TCAAATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATACTAAATTTTATAAA
Found at i:3768609 original size:2 final size:2
Alignment explanation
Indices: 3768602--3768626 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3768592 CATGTTAATC
3768602 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3768627 TTGAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3783465 original size:40 final size:40
Alignment explanation
Indices: 3783421--3783513 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
3783411 TGAAGATTAA
*
3783421 TCACACGTATACCGGACACTATAAAATAGCATTTAAATTG
1 TCACACGTATACCGGACACTACAAAATAGCATTTAAATTG
3783461 TCACACGTATACCGGACACTACAAAATAGCATTTAAATTG
1 TCACACGTATACCGGACACTACAAAATAGCATTTAAATTG
**
3783501 TCACTTGTATACC
1 TCACACGTATACC
3783514 TTACACAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (40 bp):
TCACACGTATACCGGACACTACAAAATAGCATTTAAATTG
Found at i:3795367 original size:18 final size:17
Alignment explanation
Indices: 3795340--3795374 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3795330 AACCCAATCC
*
3795340 CTTTTTTTTTTGCTTTT
1 CTTTTTTTTTTCCTTTT
3795357 CTTTTTCTTTTTCCTTTT
1 CTTTTT-TTTTTCCTTTT
3795375 TGTGTACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (17 bp):
CTTTTTTTTTTCCTTTT
Found at i:3796281 original size:20 final size:22
Alignment explanation
Indices: 3796256--3796309 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
3796246 GATATTTTTA
3796256 AATATTTATATTT-AAAA-AAT
1 AATATTTATATTTAAAAATAAT
3796276 AATATTTATATTTAAAAATAAT
1 AATATTTATATTTAAAAATAAT
*
3796298 AATATTTTTATT
1 AATATTTATATT
3796310 AATTTTGGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 13 0.42
21 4 0.13
22 14 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTATATTTAAAAATAAT
Found at i:3796302 original size:16 final size:18
Alignment explanation
Indices: 3796262--3796304 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3796252 TTTAAATATT
3796262 TATATTTAAAAAATAATA
1 TATATTTAAAAAATAATA
3796280 TTTATATTT-AAAAATAATA
1 --TATATTTAAAAAATAATA
3796299 -ATATTT
1 TATATTT
3796305 TTATTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.26
19 10 0.43
20 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATTTAAAAAATAATA
Found at i:3797786 original size:19 final size:19
Alignment explanation
Indices: 3797762--3797823 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
3797752 TTCTTGGACA
*
3797762 TTTAAATTATTAATTGGAT
1 TTTAAATTATAAATTGGAT
3797781 TTTAAATTGATAAATTAGG-T
1 TTTAAATT-ATAAATT-GGAT
*
3797801 TTT-AATT-TCAATTTGGAT
1 TTTAAATTAT-AAATTGGAT
3797819 TTTAA
1 TTTAA
3797824 GTCTAATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 3 0.08
18 8 0.22
19 13 0.36
20 10 0.28
21 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTAAATTATAAATTGGAT
Found at i:3797796 original size:20 final size:19
Alignment explanation
Indices: 3797762--3797805 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3797752 TTCTTGGACA
*
3797762 TTTAAATTATTAATT-GGAT
1 TTTAAATTATAAATTAGG-T
3797781 TTTAAATTGATAAATTAGGT
1 TTTAAATT-ATAAATTAGGT
3797801 TTTAA
1 TTTAA
3797806 TTTCAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 12 0.55
21 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTAAATTATAAATTAGGT
Found at i:3797925 original size:7 final size:8
Alignment explanation
Indices: 3797903--3797947 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
3797893 TTCAATATTT
3797903 TAAAAATA
1 TAAAAATA
*
3797911 TGAAAATA
1 TAAAAATA
3797919 T-AAAATA
1 TAAAAATA
3797926 TAAAAATA
1 TAAAAATA
3797934 TAAAAGAT-
1 TAAAA-ATA
3797942 TAAAAA
1 TAAAAA
3797948 AAAAAACTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
7 8 0.24
8 24 0.71
9 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (8 bp):
TAAAAATA
Found at i:3797925 original size:15 final size:15
Alignment explanation
Indices: 3797905--3797938 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3797895 CAATATTTTA
*
3797905 AAAATATGAAAATAT
1 AAAATATAAAAATAT
3797920 AAAATATAAAAATAT
1 AAAATATAAAAATAT
3797935 AAAA
1 AAAA
3797939 GATTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAATATAAAAATAT
Found at i:3797945 original size:23 final size:23
Alignment explanation
Indices: 3797903--3797946 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3797893 TTCAATATTT
*
3797903 TAAAAATATGAAAATATAAAATA
1 TAAAAATATAAAAATATAAAATA
3797926 TAAAAATATAAAAGAT-TAAAA
1 TAAAAATATAAAA-ATATAAAA
3797947 AAAAAAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (23 bp):
TAAAAATATAAAAATATAAAATA
Found at i:3797946 original size:15 final size:15
Alignment explanation
Indices: 3797913--3797947 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3797903 TAAAAATATG
*
3797913 AAAATATAAAATATA
1 AAAATATAAAAGATA
3797928 AAAATATAAAAGATTA
1 AAAATATAAAAGA-TA
3797944 AAAA
1 AAAA
3797948 AAAAAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAATATAAAAGATA
Found at i:3799195 original size:10 final size:10
Alignment explanation
Indices: 3799180--3799208 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3799170 TATGATCTAA
3799180 AAAATTAAAT
1 AAAATTAAAT
3799190 AAAATTAAAT
1 AAAATTAAAT
3799200 AAAA-TAAAT
1 AAAATTAAAT
3799209 GATGAGTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATTAAAT
Found at i:3799844 original size:12 final size:12
Alignment explanation
Indices: 3799829--3799894 Score: 55
Period size: 12 Copynumber: 5.3 Consensus size: 12
3799819 ATTTTTAATA
3799829 TAAATATAAAAT
1 TAAATATAAAAT
3799841 TAAATATATATAA-
1 TAAATATA-A-AAT
* *
3799854 AAATATATAAAAA
1 TAA-ATATAAAAT
*
3799867 TAAGTATAAAAT
1 TAAATATAAAAT
3799879 TAAATA-AATAAT
1 TAAATATAA-AAT
3799891 TAAA
1 TAAA
3799895 AAATTTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 2 0.05
12 29 0.66
13 6 0.14
14 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:3799864 original size:20 final size:20
Alignment explanation
Indices: 3799826--3799896 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 20
3799816 ATTATTTTTA
*
3799826 ATATAAATATAAAATTAAATAT
1 ATATAAAAAT-AAA-TAAATAT
* *
3799848 ATATAAAAATATATAAAAAT
1 ATATAAAAATAAATAAATAT
*
3799868 AAGTATAAAATTAAATAAATA-
1 -A-TATAAAAATAAATAAATAT
3799889 AT-TAAAAA
1 ATATAAAAA
3799897 ATTTATTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
18 5 0.12
19 1 0.03
20 7 0.17
21 3 0.08
22 24 0.60
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (20 bp):
ATATAAAAATAAATAAATAT
Found at i:3799897 original size:20 final size:19
Alignment explanation
Indices: 3799831--3799899 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
3799821 TTTTAATATA
* *
3799831 AATATAAAATTAAATATAT
1 AATAAAAAATTAAATAAAT
3799850 -AT-AAAAATATATAA-AAAT
1 AATAAAAAAT-TA-AATAAAT
*
3799868 AAGTATAAAATTAAATAAAT
1 AA-TAAAAAATTAAATAAAT
3799888 AATTAAAAAATT
1 AA-TAAAAAATT
3799900 TATTTTTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
17 5 0.13
18 7 0.18
19 5 0.13
20 17 0.44
21 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (19 bp):
AATAAAAAATTAAATAAAT
Found at i:3811120 original size:19 final size:19
Alignment explanation
Indices: 3811096--3811151 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
3811086 CGCTTACAAT
3811096 AATTATAATACAATTAATC
1 AATTATAATACAATTAATC
3811115 AATTATAAT----TTAA--
1 AATTATAATACAATTAATC
3811128 AATTATAATACAATTAATC
1 AATTATAATACAATTAATC
3811147 AATTA
1 AATTA
3811152 CAAGTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 9 0.29
15 4 0.13
17 4 0.13
19 14 0.45
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTATAATACAATTAATC
Found at i:3811135 original size:32 final size:32
Alignment explanation
Indices: 3811096--3811164 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
3811086 CGCTTACAAT
* *
3811096 AATTATAATACAATTAATCAATTATAATTTAA
1 AATTATAATACAATTAATCAATTACAAGTTAA
3811128 AATTATAATACAATTAATCAATTACAAGTTAA
1 AATTATAATACAATTAATCAATTACAAGTTAA
3811160 AATTA
1 AATTA
3811165 CGTGAAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (32 bp):
AATTATAATACAATTAATCAATTACAAGTTAA
Found at i:3811393 original size:37 final size:37
Alignment explanation
Indices: 3811343--3811416 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
3811333 TTAAAAAGAT
*
3811343 AAACTTTGAATTCGAACAAATCTTTAGTTATTTACCC
1 AAACTTTGAATTCGAACAAATATTTAGTTATTTACCC
3811380 AAACTTTGAATTCGAACAAATATTTAGTTATTTACCC
1 AAACTTTGAATTCGAACAAATATTTAGTTATTTACCC
3811417 TCACCTCCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (37 bp):
AAACTTTGAATTCGAACAAATATTTAGTTATTTACCC
Found at i:3817775 original size:22 final size:21
Alignment explanation
Indices: 3817735--3817786 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
3817725 CATATACTAA
* * *
3817735 TATTATTATAAAATTATTTTT
1 TATTATTAAAAAATAATTTAT
3817756 TATTATTAAATAAATAATTTAT
1 TATTATTAAA-AAATAATTTAT
*
3817778 TATAATTAA
1 TATTATTAA
3817787 TATTTATCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATTAAAAAATAATTTAT
Found at i:3818163 original size:28 final size:26
Alignment explanation
Indices: 3818129--3818181 Score: 88
Period size: 28 Copynumber: 2.0 Consensus size: 26
3818119 ATTTTATTAA
3818129 TTTTAATTTTAATTTTTATATATATATT
1 TTTTAATTTTAATTTTT-TA-ATATATT
3818157 TTTTAATTTTAATTTTTTAATATAT
1 TTTTAATTTTAATTTTTTAATATAT
3818182 GTGAATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 6 0.24
27 2 0.08
28 17 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTAATTTTAATTTTTTAATATATT
Found at i:3818171 original size:14 final size:14
Alignment explanation
Indices: 3818129--3818177 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
3818119 ATTTTATTAA
3818129 TTTTAATTTTAA-T
1 TTTTAATTTTAATT
*
3818142 TTTT-ATATATATATT
1 TTTTAAT-TTTA-ATT
3818157 TTTTAATTTTAATT
1 TTTTAATTTTAATT
3818171 TTTTAAT
1 TTTTAAT
3818178 ATATGTGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 2 0.07
13 7 0.23
14 11 0.37
15 8 0.27
16 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTAATTTTAATT
Found at i:3818940 original size:15 final size:14
Alignment explanation
Indices: 3818913--3818942 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3818903 GTATATTATG
3818913 TATAATTATTATAA
1 TATAATTATTATAA
3818927 TATAATTAATTATAA
1 TATAATT-ATTATAA
3818942 T
1 T
3818943 TTAAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAATTATTATAA
Found at i:3820711 original size:147 final size:147
Alignment explanation
Indices: 3820442--3820720 Score: 355
Period size: 147 Copynumber: 1.9 Consensus size: 147
3820432 AAAAACACAC
* * * *
3820442 TAGAGATGTGAGGTTATCTGACCTAAATAAGGTGTTAATAGGACTTATTCGCTTGAAGTGTAAGC
1 TAGAGATGTGAAGTTATCTGACCCAAATAAGGTGTTAATAGAACTTACTCGCTTGAAGTGTAAGC
* * *
3820507 TAAGCTTGAGGAAGCACTGAGACAACATAGGTGACAAGATAGAATGCTATGGCCTGACCTAAAAA
66 TAAACTTGAGGAAGCACCGAGACAACATAAGTGACAAGATAGAATGCTATGGCCTGACCTAAAAA
3820572 GTACGCTAAGAGCGCAT
131 GTACGCTAAGAGCGCAT
* * * * *
3820589 TAGAGATGTGAAGTTGTCTGACCCAAATGAGGTGTTGATAGAATTTACTCGTTTGAAGTGTAAG-
1 TAGAGATGTGAAGTTATCTGACCCAAATAAGGTGTTAATAGAACTTACTCGCTTGAAGTGTAAGC
* * ** * * *
3820653 TCAAACTTGAAGG-AGTACCGAGACAACTTAAGTGGTAAGATAGAGTGCTGTGGTCTGACCTAAA
66 T-AAACTTG-AGGAAGCACCGAGACAACATAAGTGACAAGATAGAATGCTATGGCCTGACCTAAA
3820717 AAGT
129 AAGT
3820721 GCACTAAAGA
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
146 1 0.01
147 107 0.96
148 3 0.03
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.26
Consensus pattern (147 bp):
TAGAGATGTGAAGTTATCTGACCCAAATAAGGTGTTAATAGAACTTACTCGCTTGAAGTGTAAGC
TAAACTTGAGGAAGCACCGAGACAACATAAGTGACAAGATAGAATGCTATGGCCTGACCTAAAAA
GTACGCTAAGAGCGCAT
Found at i:3824112 original size:3 final size:3
Alignment explanation
Indices: 3824104--3824166 Score: 54
Period size: 3 Copynumber: 20.7 Consensus size: 3
3824094 AGAGGGAATT
* * * * * * *
3824104 GAA GAA GAA GAA GAT GAA GAA GAA GCGA GAC GAG GAT GAT GAG GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA
3824150 GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GA
3824167 GGAGGGAGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 48 0.96
4 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.38, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:3830631 original size:27 final size:28
Alignment explanation
Indices: 3830601--3830661 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
3830591 ATTTATTAAT
*
3830601 ATAATTATTAAGTTATAAA-ATAAAA-AA
1 ATAATTA-TAAATTATAAACATAAAATAA
* *
3830628 ATAATTATAAATTTTAAACATAAAATTA
1 ATAATTATAAATTATAAACATAAAATAA
3830656 ATAATT
1 ATAATT
3830662 TTTTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 9 0.31
27 13 0.45
28 7 0.24
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (28 bp):
ATAATTATAAATTATAAACATAAAATAA
Found at i:3830884 original size:5 final size:5
Alignment explanation
Indices: 3830870--3830899 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3830860 TCTATAGCAC
*
3830870 AGGCA AGGCA CGGCA AGGCA AGGCA AGGCA
1 AGGCA AGGCA AGGCA AGGCA AGGCA AGGCA
3830900 TGCTTTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.40, T:0.00
Consensus pattern (5 bp):
AGGCA
Found at i:3830886 original size:10 final size:10
Alignment explanation
Indices: 3830866--3830899 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3830856 ACAATCTATA
3830866 GCACAGGCAAG
1 GCAC-GGCAAG
3830877 GCACGGCAAG
1 GCACGGCAAG
*
3830887 GCAAGGCAAG
1 GCACGGCAAG
3830897 GCA
1 GCA
3830900 TGCTTTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.35, C:0.26, G:0.38, T:0.00
Consensus pattern (10 bp):
GCACGGCAAG
Found at i:3836783 original size:16 final size:16
Alignment explanation
Indices: 3836762--3836794 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3836752 GTCCATGTAG
3836762 TGTGTGTATATATATA
1 TGTGTGTATATATATA
3836778 TGTGTGTATATATATA
1 TGTGTGTATATATATA
3836794 T
1 T
3836795 ACAAAGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (16 bp):
TGTGTGTATATATATA
Found at i:3838512 original size:21 final size:21
Alignment explanation
Indices: 3838461--3838503 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3838451 TTAAGCAACT
*
3838461 TATCAGATATTGCAATGATTC
1 TATCAGTTATTGCAATGATTC
3838482 TATCAGTTATTGCAATGATTC
1 TATCAGTTATTGCAATGATTC
3838503 T
1 T
3838504 TGTGGTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (21 bp):
TATCAGTTATTGCAATGATTC
Found at i:3838553 original size:27 final size:27
Alignment explanation
Indices: 3838513--3838565 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3838503 TTGTGGTTAT
*
3838513 CAATTCTGCTAGCAACATTTAATTTTG
1 CAATTCTGCCAGCAACATTTAATTTTG
*
3838540 CAATTCTGCCAGCAGCATTTAATTTT
1 CAATTCTGCCAGCAACATTTAATTTT
3838566 TAAGTCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (27 bp):
CAATTCTGCCAGCAACATTTAATTTTG
Found at i:3841811 original size:39 final size:39
Alignment explanation
Indices: 3841757--3841836 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
3841747 AATCCAAACA
*
3841757 AACAAAACTAACAGCAAGAATAACCTACATTACCTAAGT
1 AACAAAACTAACAGCAAGAATAACCCACATTACCTAAGT
3841796 AACAAAACTAACAGCAAGAATAACCCACATTACCTAAGT
1 AACAAAACTAACAGCAAGAATAACCCACATTACCTAAGT
3841835 AA
1 AA
3841837 TTAAGTTCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.53, C:0.24, G:0.07, T:0.16
Consensus pattern (39 bp):
AACAAAACTAACAGCAAGAATAACCCACATTACCTAAGT
Found at i:3844521 original size:34 final size:34
Alignment explanation
Indices: 3844474--3844540 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
3844464 CACAAGCTAA
*
3844474 GATCAATGTGTAGGAAAAATGCTTTCAGTTTCAT
1 GATCAATGAGTAGGAAAAATGCTTTCAGTTTCAT
* *
3844508 GATCAATGAGTAGGAAAATTGTTTTCAGTTTCA
1 GATCAATGAGTAGGAAAAATGCTTTCAGTTTCA
3844541 ACCAACCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (34 bp):
GATCAATGAGTAGGAAAAATGCTTTCAGTTTCAT
Found at i:3846331 original size:27 final size:27
Alignment explanation
Indices: 3846293--3846346 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
3846283 AAAATTTAAA
*
3846293 AAAATTATTATAATTATGATTAAAAAT
1 AAAATTATTATAAATATGATTAAAAAT
3846320 AAAATTATTATAAATATGATTAAAAAT
1 AAAATTATTATAAATATGATTAAAAAT
3846347 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (27 bp):
AAAATTATTATAAATATGATTAAAAAT
Found at i:3846363 original size:22 final size:22
Alignment explanation
Indices: 3846292--3846375 Score: 62
Period size: 27 Copynumber: 3.5 Consensus size: 22
3846282 TAAAATTTAA
* *
3846292 AAAAATTATTATAATTATGATT
1 AAAAATTTTTATAAATATGATT
3846314 AAAAATAAAATTATTATAAATATGATT
1 AAAAAT----TT-TTATAAATATGATT
*
3846341 AAAAATTTTTA-AAATATATATT
1 AAAAATTTTTATAAATAT-GATT
*
3846363 AAATAAATTTTAT
1 AAA-AATTTTTAT
3846376 TAAAATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
21 6 0.12
22 15 0.30
23 9 0.18
26 1 0.02
27 19 0.38
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAAATTTTTATAAATATGATT
Found at i:3847061 original size:25 final size:25
Alignment explanation
Indices: 3847033--3847080 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3847023 TAATAAAAGT
*
3847033 TATT-TAGCTATAATTGAAAAAAAAC
1 TATTGTAGCTACAATT-AAAAAAAAC
*
3847058 TATTGTAGTTACAATTAAAAAAA
1 TATTGTAGCTACAATTAAAAAAA
3847081 TTTTAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (25 bp):
TATTGTAGCTACAATTAAAAAAAAC
Found at i:3849927 original size:15 final size:14
Alignment explanation
Indices: 3849896--3849930 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3849886 AATCTATAAC
*
3849896 CAAACAAATTTAAA
1 CAAATAAATTTAAA
3849910 CAAATAAATTTCAAA
1 CAAATAAATTT-AAA
3849925 CAAATA
1 CAAATA
3849931 TAAACAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (14 bp):
CAAATAAATTTAAA
Found at i:3849970 original size:21 final size:21
Alignment explanation
Indices: 3849920--3849960 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3849910 CAAATAAATT
*
3849920 TCAAAC-AAATATAAACAAAC
1 TCAAACAAAACATAAACAAAC
3849940 TCAAACAAAACATAAACAAAC
1 TCAAACAAAACATAAACAAAC
3849961 CTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.66, C:0.22, G:0.00, T:0.12
Consensus pattern (21 bp):
TCAAACAAAACATAAACAAAC
Found at i:3852470 original size:24 final size:23
Alignment explanation
Indices: 3852407--3852467 Score: 86
Period size: 24 Copynumber: 2.6 Consensus size: 23
3852397 AATATGACTG
* *
3852407 TTTATTTTGAATAATAAAAATTA
1 TTTATTTTAAATAATTAAAATTA
*
3852430 TTTGTTTTTAAATAATTAAAATTA
1 TTT-ATTTTAAATAATTAAAATTA
3852454 TTTATTTTAAATAA
1 TTTATTTTAAATAA
3852468 ATTTATCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 13 0.39
24 20 0.61
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (23 bp):
TTTATTTTAAATAATTAAAATTA
Found at i:3854882 original size:24 final size:24
Alignment explanation
Indices: 3854855--3854903 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3854845 TAAACATGAT
3854855 AGCTCACTGCTTTAAGCTTTGAAG
1 AGCTCACTGCTTTAAGCTTTGAAG
3854879 AGCTCACTGCTTTAAGCTTTGAAG
1 AGCTCACTGCTTTAAGCTTTGAAG
3854903 A
1 A
3854904 TTTGGAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (24 bp):
AGCTCACTGCTTTAAGCTTTGAAG
Found at i:3855414 original size:23 final size:23
Alignment explanation
Indices: 3855388--3855529 Score: 94
Period size: 23 Copynumber: 6.1 Consensus size: 23
3855378 TATATTAGTA
3855388 AATAATATAATAATAAATATAAT
1 AATAATATAATAATAAATATAAT
* *
3855411 AATAATATATTAATAAATAATATT
1 AATAATATAATAATAAAT-ATAAT
* *
3855435 ATTAATA-AATAATATACTATTAAT
1 AATAATATAATAATA-AATA-TAAT
* * *
3855459 -ATAATATATTGATAAATATTATT
1 AATAATATAATAATAAATA-TAAT
* * * *
3855482 AACAAAATAATATTATAATATATT
1 AATAATATAATAATA-AATATAAT
*
3855506 AATAA-ATAAT-ATAAAGAATAAT
1 AATAATATAATAATAAA-TATAAT
3855528 AA
1 AA
3855530 ATAGTTTTAT
Statistics
Matches: 92, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
21 2 0.02
22 8 0.09
23 41 0.45
24 37 0.40
25 4 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (23 bp):
AATAATATAATAATAAATATAAT
Found at i:3855423 original size:57 final size:59
Alignment explanation
Indices: 3855326--3855498 Score: 196
Period size: 57 Copynumber: 2.9 Consensus size: 59
3855316 AATTTTACTT
* * *
3855326 ATAAATAATATTATATTAATAAAAAT-ATTATAATATATTAATAAAATTATATTATATTA
1 ATAAATAATA-TATATTAATAAATATAATAATAATATATTAATAAAATAATATTATATTA
*
3855385 GTAAATAATATA-A-TAATAAATATAATAATAATATATTAAT-AAATAATA-T-TATTA
1 ATAAATAATATATATTAATAAATATAATAATAATATATTAATAAAATAATATTATATTA
* * *
3855439 ATAAATAATATACTATTAATATAATATATTGATAAATATTATTAACAAAATAATATTATA
1 ATAAATAATATA-TATTAATA-AATATAATAAT-AATA-TATTAATAAAATAATATTATA
3855499 ATATATTAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
54 16 0.17
55 1 0.01
56 17 0.18
57 21 0.22
58 11 0.11
59 13 0.14
60 6 0.06
61 8 0.08
62 1 0.01
63 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (59 bp):
ATAAATAATATATATTAATAAATATAATAATAATATATTAATAAAATAATATTATATTA
Found at i:3855429 original size:38 final size:38
Alignment explanation
Indices: 3855328--3855519 Score: 143
Period size: 39 Copynumber: 4.8 Consensus size: 38
3855318 TTTTACTTAT
* *
3855328 AAATAATATTATATTAATAAAAATATTATAATATATTAATA
1 AAATAATATTATATTAAT--AAATAATATAATA-ATAAATA
* *
3855369 AAATTATATTATATTAGTAAATAATATAATAATAAATA
1 AAATAATATTATATTAATAAATAATATAATAATAAATA
* * *
3855407 TAATAATAATATATTAATAAATAATATTATTAATAAATA
1 AAATAATATTATATTAATAAATAATA-TAATAATAAATA
* * * *
3855446 ATATACTATTA-ATATAATATATTGATAAATATTATTAACAAAATA
1 AAATAATATTATAT-TAATA-A---AT-AATA-TAATAA-TAAATA
* * *
3855491 ATATTATAATATATTAATAAATAATATAA
1 AAATAATATTATATTAATAAATAATATAA
3855520 AGAATAATAA
Statistics
Matches: 124, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
38 30 0.24
39 37 0.30
40 5 0.04
41 18 0.15
43 2 0.02
44 12 0.10
45 18 0.15
46 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (38 bp):
AAATAATATTATATTAATAAATAATATAATAATAAATA
Found at i:3855446 original size:34 final size:33
Alignment explanation
Indices: 3855355--3855516 Score: 123
Period size: 34 Copynumber: 4.6 Consensus size: 33
3855345 TAAAAATATT
* * *
3855355 ATAATATATTAATAAAATTATATTATATTAGTAA
1 ATAATATATTAAT-AAATAATAATATATTAATAA
3855389 ATAATATAATAATAAATATAATAATAATATATTAATAA
1 ATAATAT-AT--T-AATA-AATAATAATATATTAATAA
3855427 ATAATATTATTAATAAATAAT-ATACTATTAAT--
1 ATAATA-TATTAATAAATAATAATA-TATTAATAA
* * * * *
3855459 ATAATATATTGATAAATATTATTAACAAAATAATATT
1 ATAATATATTAATAAATA--A-TAATATATTAATA-A
3855496 ATAATATATTAATAAATAATA
1 ATAATATATTAATAAATAATA
3855517 TAAAGAATAA
Statistics
Matches: 106, Mismatches: 8, Indels: 28
0.75 0.06 0.20
Matches are distributed among these distances:
31 11 0.10
32 6 0.06
33 4 0.04
34 28 0.26
35 9 0.08
36 1 0.01
37 19 0.18
38 27 0.25
39 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (33 bp):
ATAATATATTAATAAATAATAATATATTAATAA
Found at i:3855467 original size:18 final size:17
Alignment explanation
Indices: 3855326--3855467 Score: 119
Period size: 18 Copynumber: 7.8 Consensus size: 17
3855316 AATTTTACTT
3855326 ATAAATAATATTATATTA
1 ATAAATAATA-TATATTA
3855344 ATAAAAATATTATAATATATTA
1 AT--AAATA--AT-ATATATTA
*
3855366 ATAAAATTATATTATATTA
1 AT-AAATAATA-TATATTA
* *
3855385 GTAAATAATATAATAATAA
1 ATAAATAATAT-AT-ATTA
3855404 ATATAATAATAATATATTA
1 ATA-AATAAT-ATATATTA
3855423 ATAAATAATAT-TATTA
1 ATAAATAATATATATTA
3855439 ATAAATAATATACTATTA
1 ATAAATAATATA-TATTA
3855457 AT--ATAATATAT
1 ATAAATAATATAT
3855468 TGATAAATAT
Statistics
Matches: 106, Mismatches: 6, Indels: 27
0.76 0.04 0.19
Matches are distributed among these distances:
15 1 0.01
16 24 0.23
17 3 0.03
18 25 0.24
19 21 0.20
20 13 0.12
21 7 0.07
22 11 0.10
23 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
ATAAATAATATATATTA
Found at i:3855576 original size:19 final size:18
Alignment explanation
Indices: 3855549--3855636 Score: 60
Period size: 19 Copynumber: 4.9 Consensus size: 18
3855539 TTTTAGGTGT
*
3855549 TTTTTATATTAACATAATA
1 TTTTAATATTAA-ATAATA
*
3855568 TTTTAATATTAAATATTA
1 TTTTAATATTAAATAATA
*
3855586 TTATTAA-A--ATATAATTA
1 TT-TTAATATTAAATAA-TA
*
3855603 TTTT-TTATT-AATAATAA
1 TTTTAATATTAAATAAT-A
*
3855620 TTTTAATAATAAATAAT
1 TTTTAATATTAAATAAT
3855637 TTCAATATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
16 8 0.15
17 13 0.25
18 11 0.21
19 21 0.40
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:3855634 original size:16 final size:15
Alignment explanation
Indices: 3855605--3855670 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
3855595 TATAATTATT
*
3855605 TTTTATTAATAATAA
1 TTTTAATAATAATAA
3855620 TTTTAATAATAAATAA
1 TTTTAATAAT-AATAA
*
3855636 -TTT--CAAT-AT-A
1 TTTTAATAATAATAA
3855646 TTTTAATAATAAATAA
1 TTTTAATAAT-AATAA
3855662 TTTTTAATA
1 -TTTTAATA
3855671 TTTTAATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
10 1 0.03
11 5 0.12
13 6 0.15
15 14 0.35
16 6 0.15
17 8 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTAATAATAATAA
Found at i:3855648 original size:26 final size:26
Alignment explanation
Indices: 3855615--3855678 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
3855605 TTTTATTAAT
3855615 AATA-ATTTTAATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
*
3855640 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
3855666 TA-ATATTTTAATA
1 AATATATTTTAATA
3855679 GTTATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:3855670 original size:10 final size:9
Alignment explanation
Indices: 3855614--3855678 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
3855604 TTTTTATTAA
3855614 TAATAATTT
1 TAATAATTT
3855623 TAATAA--T
1 TAATAATTT
*
3855630 AAATAATTT
1 TAATAATTT
*
3855639 CAATATATTT
1 TAATA-ATTT
3855649 TAATAA--T
1 TAATAATTT
*
3855656 AAATAATTTT
1 TAATAA-TTT
3855666 TAAT-ATTT
1 TAATAATTT
3855674 TAATA
1 TAATA
3855679 GTTATATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
7 12 0.27
8 7 0.16
9 13 0.30
10 12 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (9 bp):
TAATAATTT
Found at i:3855946 original size:25 final size:25
Alignment explanation
Indices: 3855881--3855932 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
3855871 TATTAAAAAA
* *
3855881 TTTTAAATTATAATTATAATAATTT
1 TTTTCAATTATAATTACAATAATTT
3855906 TTTTCAATTATAATTACAATAATTT
1 TTTTCAATTATAATTACAATAATTT
3855931 TT
1 TT
3855933 ATTATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTCAATTATAATTACAATAATTT
Found at i:3860851 original size:13 final size:14
Alignment explanation
Indices: 3860803--3860853 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
3860793 TAAACAACTC
3860803 AAATTATTGGTTTAA
1 AAATTATTGG-TTAA
3860818 AAATTGAATTGGTATATA
1 AAATT--ATTGGT-TA-A
3860836 AAATTATT-GTTAA
1 AAATTATTGGTTAA
3860849 AAATT
1 AAATT
3860854 GAATTGGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 6 0.19
14 2 0.06
15 7 0.22
16 4 0.12
17 7 0.22
18 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (14 bp):
AAATTATTGGTTAA
Found at i:3860880 original size:31 final size:31
Alignment explanation
Indices: 3860814--3860882 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
3860804 AATTATTGGT
**
3860814 TTAAAAATTGAATTGGTATATAAAATTATTG
1 TTAAAAATTGAATTGGTATATAAAATTATAA
* *
3860845 TTAAAAATTGAATTGG-ATTTCACAATTATAA
1 TTAAAAATTGAATTGGTATAT-AAAATTATAA
3860876 TTAAAAA
1 TTAAAAA
3860883 AATGATATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 3 0.09
31 30 0.91
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (31 bp):
TTAAAAATTGAATTGGTATATAAAATTATAA
Found at i:3872699 original size:11 final size:11
Alignment explanation
Indices: 3872683--3872743 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 11
3872673 TTTTTTATTT
3872683 AATTTAAATTA
1 AATTTAAATTA
3872694 AATTTAAATATTA
1 AATTT-AA-ATTA
*
3872707 AATATATATATTA
1 AAT-T-TAAATTA
*
3872720 AATTTAAATCGA
1 AATTTAAAT-TA
*
3872732 ATTTTAAATTA
1 AATTTAAATTA
3872743 A
1 A
3872744 GATGTAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
11 11 0.28
12 12 0.30
13 14 0.35
14 2 0.05
15 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:3872700 original size:6 final size:6
Alignment explanation
Indices: 3872679--3872728 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
3872669 TGAATTTTTT
* *
3872679 ATTT-A ATTTAA A-TTAA ATTTAA ATATTAA ATATAT ATATTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA AT-TTAA ATTTAA
3872727 AT
1 AT
3872729 CGAATTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
5 9 0.24
6 18 0.49
7 10 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:3872708 original size:13 final size:13
Alignment explanation
Indices: 3872678--3872728 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
3872668 TTGAATTTTT
*
3872678 TATTTAATTT-AA
1 TATTAAATTTAAA
3872690 -ATTAAATTTAAA
1 TATTAAATTTAAA
* *
3872702 TATTAAATATATA
1 TATTAAATTTAAA
3872715 TATTAAATTTAAA
1 TATTAAATTTAAA
3872728 T
1 T
3872729 CGAATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 8 0.25
12 2 0.06
13 22 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATTAAATTTAAA
Found at i:3873727 original size:16 final size:17
Alignment explanation
Indices: 3873703--3873741 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
3873693 ATTATTTTTT
3873703 TATTCTTATATTTTTA-A
1 TATT-TTATATTTTTAGA
*
3873720 TATTTTATTTTTTTAGA
1 TATTTTATATTTTTAGA
3873737 TATTT
1 TATTT
3873742 CAATTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TATTTTATATTTTTAGA
Found at i:3880387 original size:33 final size:30
Alignment explanation
Indices: 3880343--3880403 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 30
3880333 AAGAAAATTA
* *
3880343 CATAATTTTTTAGAAATTAATTTTTGAAAGT
1 CATAATTTTTTAAAAATGAA-TTTTGAAAGT
3880374 CATAATTCATTTTAAAAATGAATTTTGAAA
1 CATAATT--TTTTAAAAATGAATTTTGAAA
3880404 AATTATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 7 0.27
32 8 0.31
33 11 0.42
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (30 bp):
CATAATTTTTTAAAAATGAATTTTGAAAGT
Found at i:3881722 original size:26 final size:26
Alignment explanation
Indices: 3881666--3881723 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
3881656 CTTTCATGGC
* * *
3881666 TCATATAGGATTTCCTGATCTTTATT
1 TCATTTAGAATTTCCTGATCTTTATG
3881692 TCATTTAGAATTTCCTGATCTTTATG
1 TCATTTAGAATTTCCTGATCTTTATG
3881718 TCATTT
1 TCATTT
3881724 TTTTTTCTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (26 bp):
TCATTTAGAATTTCCTGATCTTTATG
Found at i:3891539 original size:29 final size:31
Alignment explanation
Indices: 3891507--3891568 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
3891497 AAAATATCTT
*
3891507 ATTTTTTATT-ATGTGTAA-ATAAATTTATA
1 ATTTTTTATTAATCTGTAATATAAATTTATA
3891536 ATTTTTTATTAATCTGTAATTATAAATTTATA
1 ATTTTTTATTAATCTGTAA-TATAAATTTATA
3891568 A
1 A
3891569 CCATACATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.34
30 7 0.24
32 12 0.41
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (31 bp):
ATTTTTTATTAATCTGTAATATAAATTTATA
Found at i:3897589 original size:19 final size:19
Alignment explanation
Indices: 3897557--3897601 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3897547 GATAAAATAT
3897557 TACTA-AAATTTTTAT-AA
1 TACTATAAATTTTTATAAA
3897574 TACTATAAATTGTTTATAAA
1 TACTATAAATT-TTTATAAA
3897594 TA-TATAAA
1 TACTATAAA
3897602 ATTAAAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.20
18 5 0.20
19 11 0.44
20 4 0.16
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (19 bp):
TACTATAAATTTTTATAAA
Found at i:3897980 original size:27 final size:27
Alignment explanation
Indices: 3897940--3898010 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 27
3897930 GAAATTTTCC
* *
3897940 TAAAATAACTTAATTTATAAA-ATAAT-
1 TAAAAAAATTTAATTTATAAATA-AATA
*
3897966 TAAAAAAATTATAA-TTATAATTAAATA
1 TAAAAAAATT-TAATTTATAAATAAATA
*
3897993 TAAAAAAATTTATTTTAT
1 TAAAAAAATTTAATTTAT
3898011 TTACATGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
26 19 0.51
27 18 0.49
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAAAAAATTTAATTTATAAATAAATA
Found at i:3905313 original size:91 final size:91
Alignment explanation
Indices: 3905158--3905333 Score: 307
Period size: 91 Copynumber: 1.9 Consensus size: 91
3905148 CACATTGGGC
*
3905158 ATGCAGCATTCTCCATTAGAAAGGAATTAAAATACTAGGATGGTCATACAGAAGATAAAGGTACT
1 ATGCAGCATTCTCCATTAGAAAGGAATTAAAATACTAGGATGGTCATACAGAAGAGAAAGGTACT
3905223 TTGCTGTATTAGCGATGACACTGGAA
66 TTGCTGTATTAGCGATGACACTGGAA
* * *
3905249 ATGCAGCATTCTCCATTAGAAAGGAATTTAATTACTAGGATGGTCATACAGAAGGGAAAGGTACT
1 ATGCAGCATTCTCCATTAGAAAGGAATTAAAATACTAGGATGGTCATACAGAAGAGAAAGGTACT
*
3905314 TTGCTGTATTAGTGATGACA
66 TTGCTGTATTAGCGATGACA
3905334 TTTATTTTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (91 bp):
ATGCAGCATTCTCCATTAGAAAGGAATTAAAATACTAGGATGGTCATACAGAAGAGAAAGGTACT
TTGCTGTATTAGCGATGACACTGGAA
Found at i:3912253 original size:26 final size:25
Alignment explanation
Indices: 3912207--3912269 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
3912197 ATTAATTAAA
*
3912207 ATTAATATAT-TTTATTCAAAATATAT
1 ATTAATATATATTTATT-AAAA-AAAT
3912233 ATTAATATATATTTA-TAAAAAAAT
1 ATTAATATATATTTATTAAAAAAAT
3912257 ACTTAAATATATA
1 A-TT-AATATATA
3912270 AGATAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.12
25 6 0.18
26 19 0.58
27 4 0.12
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTAATATATATTTATTAAAAAAAT
Found at i:3920490 original size:23 final size:22
Alignment explanation
Indices: 3920456--3920502 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
3920446 ATATTAAAAT
* *
3920456 ATATTTTTATAAATATATGTTA
1 ATATTTTTATAAAAATATATTA
3920478 ATATTTTTAATAAAAATATATTA
1 ATATTTTT-ATAAAAATATATTA
3920501 AT
1 AT
3920503 TGTAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATTTTTATAAAAATATATTA
Found at i:3921748 original size:134 final size:134
Alignment explanation
Indices: 3921509--3921751 Score: 301
Period size: 134 Copynumber: 1.8 Consensus size: 134
3921499 GCTTCACTCA
** *
3921509 ACTTGTAATCCAAACCCCTTTATTTACTCATACTTCTCTATGAAGAGACTTTTCATTTTGACTAT
1 ACTTGTAATCCAAACCCCTTTATGGACTCATACTTCTCTATGAAGAGACTTTTCAGTTTGACTAT
** * * *
3921574 GGATGCATGACCATCACGATCCACGCACACATCCATATATATATATATTCTCTTTATTTACTTCA
66 AAATGCATGAACATCACGATCCACACACACATACATATATATATATATTCTCTTTATTTACTTCA
3921639 TTGT
131 TTGT
* * * * * * * *
3921643 ACTTGTAATCCAAACCCCTTTCTGGACTCATATTTTTTTATGTAGGGATTTTTC-GTTTGACTTT
1 ACTTGTAATCCAAACCCCTTTATGGACTCATACTTCTCTATGAAGAGACTTTTCAGTTTGACTAT
* * *
3921707 AAATGCATGAACATCACGAT-CACACATATATACATACATATATAT
66 AAATGCATGAACATCACGATCCACACACACATACATATATATATAT
3921752 TAATATGAAA
Statistics
Matches: 90, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
132 20 0.22
133 25 0.28
134 45 0.50
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39
Consensus pattern (134 bp):
ACTTGTAATCCAAACCCCTTTATGGACTCATACTTCTCTATGAAGAGACTTTTCAGTTTGACTAT
AAATGCATGAACATCACGATCCACACACACATACATATATATATATATTCTCTTTATTTACTTCA
TTGT
Found at i:3932177 original size:22 final size:22
Alignment explanation
Indices: 3932152--3932213 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
3932142 TTTTAAAAAA
*
3932152 TAAAAATTATATATATTTATCT
1 TAAAAATTATATATATTTATAT
* *
3932174 TAAAAATTAATAAAAATTTATAT
1 TAAAAATT-ATATATATTTATAT
* *
3932197 TCAAAATAATAT-TATTT
1 TAAAAATTATATATATTT
3932214 GATTCTCATC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 4 0.12
22 11 0.34
23 17 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAAATTATATATATTTATAT
Found at i:3939237 original size:16 final size:16
Alignment explanation
Indices: 3939186--3939253 Score: 84
Period size: 16 Copynumber: 4.2 Consensus size: 16
3939176 AATATTAGTC
*
3939186 CATAATTAATTAAATT
1 CATAAATAATTAAATT
3939202 CATAAAT-ATTATATATT
1 CATAAATAATTA-A-ATT
*
3939219 CATGAATAATTAAATT
1 CATAAATAATTAAATT
*
3939235 CATAAATAATTAGATT
1 CATAAATAATTAAATT
3939251 CAT
1 CAT
3939254 GTAATTTAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.09
16 27 0.60
17 10 0.22
18 4 0.09
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (16 bp):
CATAAATAATTAAATT
Found at i:3940072 original size:12 final size:12
Alignment explanation
Indices: 3940039--3940074 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3940029 TACATTTATT
*
3940039 TATATATATATA
1 TATATATATGTA
3940051 TATATATATGTA
1 TATATATATGTA
*
3940063 TGTATATATGTA
1 TATATATATGTA
3940075 GTCACCGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATATATATGTA
Found at i:3940322 original size:45 final size:42
Alignment explanation
Indices: 3940271--3940354 Score: 114
Period size: 45 Copynumber: 1.9 Consensus size: 42
3940261 TTTTATGTGA
3940271 ATATGAATTATAATATATTATTTTCATATAAAATATAATACAAAT
1 ATATGAATTAT-ATATATTATTTT-ATATAAAATA-AATACAAAT
* * *
3940316 ATATGAATTATTTTTATTATTTTATATAATATAAATACA
1 ATATGAATTATATATATTATTTTATATAAAATAAATACA
3940355 TAAATTATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 6 0.17
43 9 0.25
44 10 0.28
45 11 0.31
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (42 bp):
ATATGAATTATATATATTATTTTATATAAAATAAATACAAAT
Found at i:3941181 original size:2 final size:2
Alignment explanation
Indices: 3941176--3941207 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
3941166 CAAAAAAGTG
3941176 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
3941208 CCGTCATTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3944608 original size:30 final size:29
Alignment explanation
Indices: 3944567--3944623 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
3944557 TATAAAATAT
*
3944567 AATTTTTAATTTTATTT-ATAATTTTTATTA
1 AATTTTAAATTTT-TTTAAT-ATTTTTATTA
3944597 AATTTTAAATTTTTTTAATATTTTTAT
1 AATTTTAAATTTTTTTAATATTTTTAT
3944624 ATCATATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
AATTTTAAATTTTTTTAATATTTTTATTA
Found at i:3944620 original size:18 final size:19
Alignment explanation
Indices: 3944581--3944620 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3944571 TTTAATTTTA
3944581 TTTATAATTTTTATTAAAT
1 TTTATAATTTTTATTAAAT
3944600 TTTA-AATTTTT-TTAATAT
1 TTTATAATTTTTATTAA-AT
3944618 TTT
1 TTT
3944621 TATATCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATAATTTTTATTAAAT
Done.