Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 16 of 31
Found at i:3797663 original size:40 final size:40
Alignment explanation
Indices: 3797608--3797689 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
3797598 GACAGAAGGG
3797608 TTACCATTCACATTTACACCCTTCTTTCCATCTATCATCT
1 TTACCATTCACATTTACACCCTTCTTTCCATCTATCATCT
*
3797648 TTACCATTCACATTTACACCCTTCTTTCCATCTGTCATCT
1 TTACCATTCACATTTACACCCTTCTTTCCATCTATCATCT
3797688 TT
1 TT
3797690 GATCCTTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.21, C:0.34, G:0.01, T:0.44
Consensus pattern (40 bp):
TTACCATTCACATTTACACCCTTCTTTCCATCTATCATCT
Found at i:3805526 original size:3 final size:3
Alignment explanation
Indices: 3805518--3805544 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3805508 ATGCTAAACT
3805518 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3805545 AGAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3806255 original size:26 final size:26
Alignment explanation
Indices: 3806226--3806278 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
3806216 ATCTACTTTG
*
3806226 ATTCAATAAATCTCGTAATTTTATTC
1 ATTCAATAAATCTCATAATTTTATTC
*
3806252 ATTCAATAAATCTTATAATTTTATTC
1 ATTCAATAAATCTCATAATTTTATTC
3806278 A
1 A
3806279 CAAAATACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTCAATAAATCTCATAATTTTATTC
Found at i:3806285 original size:26 final size:26
Alignment explanation
Indices: 3806230--3806285 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
3806220 ACTTTGATTC
* ***
3806230 AATAAATCTCGTAATTTTATTCATTC
1 AATAAATCTCATAATTTTATTCACAA
*
3806256 AATAAATCTTATAATTTTATTCACAA
1 AATAAATCTCATAATTTTATTCACAA
3806282 AATA
1 AATA
3806286 CACTGTCGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (26 bp):
AATAAATCTCATAATTTTATTCACAA
Found at i:3810516 original size:27 final size:27
Alignment explanation
Indices: 3810486--3810537 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
3810476 AAATATTAAA
3810486 AAAATAATTTCAT-AAATAAATTTTTAT
1 AAAAT-ATTTCATAAAATAAATTTTTAT
**
3810513 AAAATATTTTTTAAAATAAATTTTT
1 AAAATATTTCATAAAATAAATTTTT
3810538 TATGAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
AAAATATTTCATAAAATAAATTTTTAT
Found at i:3810523 original size:14 final size:15
Alignment explanation
Indices: 3810497--3810545 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 15
3810487 AAATAATTTC
3810497 ATAAATAAA-TTTTT
1 ATAAATAAATTTTTT
*
3810511 ATAAA-ATATTTTTT
1 ATAAATAAATTTTTT
3810525 A-AAATAAATTTTTT
1 ATAAATAAATTTTTT
*
3810539 ATGAATA
1 ATAAATA
3810546 TATTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 5 0.17
14 20 0.69
15 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATAAATAAATTTTTT
Found at i:3810555 original size:27 final size:27
Alignment explanation
Indices: 3810499--3810556 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
3810489 ATAATTTCAT
* **
3810499 AAATAAATTTTTATAAAATATTTTTTA
1 AAATAAATTTTTATAAAATATATTAAA
*
3810526 AAATAAATTTTT-TATGAATATATTAAA
1 AAATAAATTTTTATA-AAATATATTAAA
3810553 AAAT
1 AAAT
3810557 TATCATCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
AAATAAATTTTTATAAAATATATTAAA
Found at i:3810704 original size:28 final size:29
Alignment explanation
Indices: 3810647--3810705 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
3810637 ATTTTAAAAA
**
3810647 TTTAATAAATAATAATATATTATTTTTTT
1 TTTAATAAATAATAATATATTATTAATTT
*
3810676 TTTAATAAA-AATAAT-TTTTAATTAATTT
1 TTTAATAAATAATAATATATT-ATTAATTT
3810704 TT
1 TT
3810706 AAAAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 3 0.12
28 14 0.54
29 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTAATAAATAATAATATATTATTAATTT
Found at i:3810706 original size:64 final size:68
Alignment explanation
Indices: 3810629--3810754 Score: 172
Period size: 68 Copynumber: 1.9 Consensus size: 68
3810619 TTTTTATAAA
* * *
3810629 TTAATTAAATTTT-AAAAATTTA-ATAA-ATAA-TAATATATT-ATTTTTTTTTTAATAAAAATA
1 TTAATTAAATTTTAAAAAATTTACATAATA-AATTAAAATATTAATTATTTTTTAAATAAAAATA
3810689 ATTT
65 ATTT
*
3810693 TTAATTAATTTTTAAAAAATTTACATAATAAATTAAAATATTAATTATTTTTTAAATAAAAA
1 TTAATTAAATTTTAAAAAATTTACATAATAAATTAAAATATTAATTATTTTTTAAATAAAAA
3810755 ATTAAATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
64 12 0.23
65 9 0.17
66 6 0.11
67 9 0.17
68 17 0.32
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (68 bp):
TTAATTAAATTTTAAAAAATTTACATAATAAATTAAAATATTAATTATTTTTTAAATAAAAATAA
TTT
Found at i:3810763 original size:64 final size:60
Alignment explanation
Indices: 3810626--3810765 Score: 140
Period size: 64 Copynumber: 2.2 Consensus size: 60
3810616 ATTTTTTTAT
* * *
3810626 AAATTAATTAAATTTTAAAAATTTAATAAATAATAATATATTATTTTTTTTTTAATAAAA
1 AAATTAATTAAATTTTAAAAATTTAATAAATAATAAAATATTATTATTTTTTAAATAAAA
*
3810686 ATAATTTTTAATTAATTTTTAAAAAATTTACAT-AATAAATTAAAATATTAATTATTTTTTAAAT
1 A-AA---TTAATTAAATTTT-AAAAATTTA-ATAAAT-AA-TAAAATATT-ATTATTTTTTAAAT
3810750 -AAA
57 AAAA
3810753 AAATTAAATTAAA
1 AAATT-AATTAAA
3810766 AAGCATTTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
60 1 0.02
61 2 0.03
63 2 0.03
64 18 0.28
65 12 0.18
66 6 0.09
67 12 0.18
68 12 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (60 bp):
AAATTAATTAAATTTTAAAAATTTAATAAATAATAAAATATTATTATTTTTTAAATAAAA
Found at i:3810874 original size:79 final size:76
Alignment explanation
Indices: 3810772--3810956 Score: 232
Period size: 76 Copynumber: 2.4 Consensus size: 76
3810762 TAAAAAGCAT
* * * *
3810772 TTATTATTATTTTTTAGTAAAATTAAGAATAGTATTTAATTAATTTTAAAAAAATTTATATTAAT
1 TTATTATTATTTTTTAG-AAAATTAAAAATAATATTTAATTAAGTTT--AAAAA-TTAAATTAAT
3810837 AAATTAAAATATTAA
62 AAATTAAAATATTAA
*
3810852 TTATTTTTATTTTTTA-ACAAATTAAAAATAATATTTAATTAAGTTTAAAAATTAAATTAATAAA
1 TTATTATTATTTTTTAGA-AAATTAAAAATAATATTTAATTAAGTTTAAAAATTAAATTAATAAA
3810916 TTAAAATATTAA
65 TTAAAATATTAA
* *
3810928 TTATTATGT-TTTTATA-AAAATAAAAAATA
1 TTATTAT-TATTTTTTAGAAAATTAAAAATA
3810957 TTTATTATTA
Statistics
Matches: 95, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
75 11 0.12
76 37 0.39
77 6 0.06
78 1 0.01
79 25 0.26
80 15 0.16
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (76 bp):
TTATTATTATTTTTTAGAAAATTAAAAATAATATTTAATTAAGTTTAAAAATTAAATTAATAAAT
TAAAATATTAA
Found at i:3810928 original size:38 final size:38
Alignment explanation
Indices: 3810807--3810930 Score: 101
Period size: 38 Copynumber: 3.2 Consensus size: 38
3810797 AGAATAGTAT
*
3810807 TTAATTAATTTTAAAAAAATTTATATTAATAAATTAAAATA
1 TTAATTAATTTT--AAAAA-TTAAATTAATAAATTAAAATA
* **** *
3810848 TTAATTATTTTTATTTTTTAACAAATTAA-AAA-TAATAT-
1 TTAATTAATTTTAAAAATT---AAATTAATAAATTAAAATA
*
3810886 TTAATTAAGTTTAAAAATTAAATTAATAAATTAAAATA
1 TTAATTAATTTTAAAAATTAAATTAATAAATTAAAATA
3810924 TTAATTA
1 TTAATTA
3810931 TTATGTTTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 15
0.68 0.15 0.16
Matches are distributed among these distances:
35 7 0.11
36 3 0.05
37 5 0.08
38 22 0.35
39 6 0.10
40 3 0.05
41 17 0.27
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (38 bp):
TTAATTAATTTTAAAAATTAAATTAATAAATTAAAATA
Found at i:3810996 original size:36 final size:33
Alignment explanation
Indices: 3810918--3810988 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
3810908 TTAATAAATT
*
3810918 AAAATATTAATTATTATGTTTTTATAAAAATAA
1 AAAATATTTATTATTATGTTTTTATAAAAATAA
3810951 AAAATATTTATTATTAT-TTTTT-TAATATAATAA
1 AAAATATTTATTATTATGTTTTTATAA-A-AATAA
3810984 AAAAT
1 AAAAT
3810989 GATATTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
31 3 0.09
32 6 0.17
33 26 0.74
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (33 bp):
AAAATATTTATTATTATGTTTTTATAAAAATAA
Found at i:3811493 original size:48 final size:49
Alignment explanation
Indices: 3811406--3811498 Score: 120
Period size: 48 Copynumber: 1.9 Consensus size: 49
3811396 ATTAAATATT
* *
3811406 ATTTTTTATTTTATTAAAAATTATAATAAAAAACTTTTTTTATTTTAAA
1 ATTTTTTATTTTATTAAAAATCATAATAAAAAACTTTTTTAATTTTAAA
*
3811455 ATTTTTTATTTT-TATAAAAA-CATAATAATAAA-TATTTTTAATTT
1 ATTTTTTATTTTAT-TAAAAATCATAATAAAAAACT-TTTTTAATTT
3811499 GTTAATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
47 1 0.03
48 20 0.51
49 18 0.46
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (49 bp):
ATTTTTTATTTTATTAAAAATCATAATAAAAAACTTTTTTAATTTTAAA
Found at i:3811513 original size:21 final size:22
Alignment explanation
Indices: 3811480--3811547 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 22
3811470 AAAAACATAA
*
3811480 TAATA-AATATTTTTAATTT-GT
1 TAATATAAT-TTTTTAATTTAAT
3811501 TAATATAATTTTTTAAATTTAAT
1 TAATATAATTTTTT-AATTTAAT
* *
3811524 TAATATTA-TTTTTAATTTTAT
1 TAATATAATTTTTTAATTTAAT
3811545 TAA
1 TAA
3811548 AAAATAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 20 0.49
22 13 0.32
23 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (22 bp):
TAATATAATTTTTTAATTTAAT
Found at i:3811524 original size:126 final size:116
Alignment explanation
Indices: 3811352--3811654 Score: 349
Period size: 126 Copynumber: 2.5 Consensus size: 116
3811342 TAAAAAACAT
* * * *
3811352 AAAAATCAATATTTTAATTTGTCAATATAAATTTTTTAAACTTAATTAAATATTATTTTTTATTT
1 AAAAATTAATATTTTAATTTGTTAATAT-AATTTTTTAAAATTAATTAAATATTATTTTTAATTT
* ** ***
3811417 TATT-AAAAATTATAATAAAAAACTTTTTTTATTTTAAAATTTTTTATTTTTATAAA
65 TATTAAAAAATAATAATAAAAAACCCTTTTTATTTT---ATTTCAAATTTTT-T-AA
*
3811473 AACATAATAATAAATATTTTTAATTTGTTAATATAATTTTTTAAATTTAATT-AATATTATTTTT
1 AA-A-AAT--T-AATA-TTTTAATTTGTTAATATAATTTTTTAAAATTAATTAAATATTATTTTT
*
3811537 AATTTTATTAAAAAATAATAATAATAAACCCTTTTTATTTTATTTCAAATTTTTTAA
60 AATTTTATTAAAAAATAATAATAAAAAACCCTTTTTATTTTATTTCAAATTTTTTAA
* *
3811594 AAAAATTAATATTTTAATTTGTTAATATATATATTTTAAAATTAATTAAATTTTATTTTTA
1 AAAAATTAATATTTTAATTTGTTAATATA-ATTTTTTAAAATTAATTAAATATTATTTTTA
3811655 TTAAAAATAA
Statistics
Matches: 159, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
115 18 0.11
116 19 0.12
117 13 0.08
119 3 0.02
120 1 0.01
121 6 0.04
122 2 0.01
123 13 0.08
125 20 0.13
126 48 0.30
127 16 0.10
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (116 bp):
AAAAATTAATATTTTAATTTGTTAATATAATTTTTTAAAATTAATTAAATATTATTTTTAATTTT
ATTAAAAAATAATAATAAAAAACCCTTTTTATTTTATTTCAAATTTTTTAA
Found at i:3811537 original size:22 final size:20
Alignment explanation
Indices: 3811487--3811547 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
3811477 TAATAATAAA
*
3811487 TATTTTTAATTTGTTAATAT
1 TATTTTTAATTTATTAATAT
*
3811507 AATTTTTTAAATTTAATTAATAT
1 TA-TTTTT-AATTT-ATTAATAT
3811530 TATTTTTAATTTTATTAA
1 TATTTTTAA-TTTATTAA
3811548 AAAATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 1 0.03
21 12 0.35
22 13 0.38
23 8 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTTTAATTTATTAATAT
Found at i:3812715 original size:92 final size:92
Alignment explanation
Indices: 3812146--3812765 Score: 682
Period size: 87 Copynumber: 6.9 Consensus size: 92
3812136 TAATGTATAA
* * * ** * *
3812146 ATTGTAAATGTCAGA-TCGTAAGAAATAGACTAATGCAT-AGATTCCATCTGAGAGTC-AGTTTC
1 ATTGTAAATGTCAGACT-GCAAGGATTAGACTAATGCATGA-ATTATATCTGAGAATCGA-ATTC
*
3812208 TTTTTTATGAAAAAAAAAGAAAAGTTGATTG
63 TTTTTTAT-AGAAAAAAAGAAAAGTTGATTG
* *
3812239 ATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATTATATCTGAGAATC-AATTCTTT
1 ATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
3812303 TTTATAG---AAAA-AAAAGTTGATTG
66 TTTATAGAAAAAAAGAAAAGTTGATTG
* * * * * * *
3812326 ATTGTAAATATTAGATTGCAAAGATTATACTAATGCATGAATTATATCTGAGAATTGGATTAC-T
1 ATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATT-CTT
*
3812390 TTTTAT-G--GAAAA-AAAA-TTGATTG
65 TTTTATAGAAAAAAAGAAAAGTTGATTG
* ** *
3812413 ATTGTAAATGTTAGACTATAAGGATTAGACTAATGCATGAATGATATCTGAGAATC-AATT-TTT
1 ATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
3812476 TTTATAGAAAAAAAGAAAAGTTGATTG
66 TTTATAGAAAAAAAGAAAAGTTGATTG
* * * * * *
3812503 ATTGTAAATGTCACACTACAAGAATTAGATTAATGCATGAATTATATCTGAAAATCGGATTCTTT
1 ATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
*
3812568 TTTAT-GGAAAAAAGAAAAGTTGATTG
66 TTTATAGAAAAAAAGAAAAGTTGATTG
* * *
3812594 ATTGTAAATGGCAAACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTTTTT
1 ATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
* * *
3812659 TTTATAGAAAAAAAG-AATGACTGATTA
66 TTTATAGAAAAAAAGAAAAG-TTGATTG
* * * * * *
3812686 ATTATAAATGTCAGACTGCAAGGATTAGACTAATGTATAAATTACATATGAAAATCGAATTCTTT
1 ATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
3812751 TTTATAGGAAAAAAA
66 TTTATA-GAAAAAAA
3812766 AGATTGCAAG
Statistics
Matches: 455, Mismatches: 56, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
85 7 0.02
86 4 0.01
87 118 0.26
88 26 0.06
89 5 0.01
90 56 0.12
91 89 0.20
92 94 0.21
93 54 0.12
94 2 0.00
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (92 bp):
ATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCGAATTCTTT
TTTATAGAAAAAAAGAAAAGTTGATTG
Found at i:3816197 original size:16 final size:17
Alignment explanation
Indices: 3816168--3816200 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3816158 TGTTCGAAAA
3816168 AAAGTTATTAAAATTTG
1 AAAGTTATTAAAATTTG
3816185 AAAGTTA-TAAAATTTG
1 AAAGTTATTAAAATTTG
3816201 TAATGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
AAAGTTATTAAAATTTG
Found at i:3816341 original size:38 final size:35
Alignment explanation
Indices: 3816264--3816341 Score: 104
Period size: 37 Copynumber: 2.2 Consensus size: 35
3816254 TTTTTTAAAT
3816264 TTAATTAAATATTATTTTTAATTTTATAAAAATAA
1 TTAATTAAATATTATTTTTAATTTTATAAAAATAA
* *
3816299 -TAATTAATATATTATTTATTAAATTTTTTAAAATTAA
1 TTAATTAA-ATATTATTT-TT-AATTTTATAAAAATAA
3816336 TTAATT
1 TTAATT
3816342 TTATTAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
34 7 0.19
35 9 0.24
36 2 0.05
37 14 0.38
38 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
TTAATTAAATATTATTTTTAATTTTATAAAAATAA
Found at i:3816368 original size:28 final size:28
Alignment explanation
Indices: 3816282--3816368 Score: 67
Period size: 28 Copynumber: 3.1 Consensus size: 28
3816272 ATATTATTTT
3816282 TAATTTTA-TAAA-AATAATAATTAAT-A
1 TAATTTTATTAAATAATAATAA-TAATAA
* * **
3816308 TATTATTTATTAAAT-TTTTTAA-AATTAA
1 TAAT-TTTATTAAATAATAATAATAA-TAA
3816336 TTAATTTTATTAAATAATAATAATAATAA
1 -TAATTTTATTAAATAATAATAATAATAA
3816365 TAAT
1 TAAT
3816369 AAACCCTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
26 5 0.11
27 5 0.11
28 23 0.51
29 10 0.22
30 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TAATTTTATTAAATAATAATAATAATAA
Found at i:3817771 original size:16 final size:15
Alignment explanation
Indices: 3817750--3817779 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3817740 AGAATATAAC
3817750 TTAATAATAACTTAAT
1 TTAATAATAA-TTAAT
3817766 TTAATAATAATTAA
1 TTAATAATAATTAA
3817780 ATATAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAATAATAATTAAT
Found at i:3828090 original size:2 final size:2
Alignment explanation
Indices: 3828083--3828112 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3828073 CCTTCCATCC
3828083 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3828113 GTCAGTGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3828377 original size:16 final size:17
Alignment explanation
Indices: 3828356--3828389 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
3828346 TATTACTTTT
3828356 TATTTTT-ATT-TAAAA
1 TATTTTTAATTATAAAA
3828371 TATTTTTAATTATAAAA
1 TATTTTTAATTATAAAA
3828388 TA
1 TA
3828390 ATAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTTAATTATAAAA
Found at i:3828522 original size:14 final size:14
Alignment explanation
Indices: 3828503--3828549 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
3828493 TATATATTAA
3828503 TATTAAAATTAATT
1 TATTAAAATTAATT
3828517 TATTAAAA-TAATTT
1 TATTAAAATTAA-TT
*
3828531 TATTTAAATTAATT
1 TATTAAAATTAATT
*
3828545 AATTA
1 TATTA
3828550 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 3 0.11
14 22 0.79
15 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTAAAATTAATT
Found at i:3828543 original size:15 final size:15
Alignment explanation
Indices: 3828503--3828544 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3828493 TATATATTAA
*
3828503 TATTAAAATTAA-TT
1 TATTTAAATTAATTT
*
3828517 TA-TTAAAATAATTT
1 TATTTAAATTAATTT
3828531 TATTTAAATTAATT
1 TATTTAAATTAATT
3828545 AATTATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 7 0.30
14 6 0.26
15 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAAATTAATTT
Found at i:3829686 original size:14 final size:15
Alignment explanation
Indices: 3829657--3829687 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3829647 TTCTTCTATA
3829657 TTCTCAGTCATCAGT
1 TTCTCAGTCATCAGT
3829672 TTCTCAGTC-TCAGT
1 TTCTCAGTCATCAGT
3829686 TT
1 TT
3829688 TATAATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.16, C:0.26, G:0.13, T:0.45
Consensus pattern (15 bp):
TTCTCAGTCATCAGT
Found at i:3830071 original size:3 final size:3
Alignment explanation
Indices: 3830063--3830100 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3830053 TTAGATCTGT
*
3830063 TTC TTC TTC TTC TTC TTC TTC TTC GTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3830101 TTATTTTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:3831165 original size:2 final size:2
Alignment explanation
Indices: 3831160--3831186 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3831150 GAAAAAATGT
3831160 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
3831187 TATAGTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3833528 original size:56 final size:56
Alignment explanation
Indices: 3833468--3833576 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 56
3833458 TACATATTTT
* *
3833468 TATTATGTGTATTAGGTGATATGTTAGGTAAATATATTAAGTGTGTTAAGTGAGCA
1 TATTAGGTATATTAGGTGATATGTTAGGTAAATATATTAAGTGTGTTAAGTGAGCA
* * * * *
3833524 TATTAGGTATGTTAGGTGGTATGTTAGGTGAGTATATTAAGTGTGTTACGTGA
1 TATTAGGTATATTAGGTGATATGTTAGGTAAATATATTAAGTGTGTTAAGTGA
3833577 TATGTTATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.41
Consensus pattern (56 bp):
TATTAGGTATATTAGGTGATATGTTAGGTAAATATATTAAGTGTGTTAAGTGAGCA
Found at i:3833546 original size:12 final size:12
Alignment explanation
Indices: 3833529--3833558 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
3833519 GAGCATATTA
3833529 GGTATGTTAGGT
1 GGTATGTTAGGT
3833541 GGTATGTTAGGT
1 GGTATGTTAGGT
3833553 GAGTAT
1 G-GTAT
3833559 ATTAAGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (12 bp):
GGTATGTTAGGT
Found at i:3833555 original size:34 final size:34
Alignment explanation
Indices: 3833511--3833591 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
3833501 ATATTAAGTG
* * *
3833511 TGTTAAGTGAGCATATTAGGTATGTTAGGTGGTA
1 TGTTAAGTGAGCATATTAAGTATGTTACGTGATA
* * *
3833545 TGTTAGGTGAGTATATTAAGTGTGTTACGTGATA
1 TGTTAAGTGAGCATATTAAGTATGTTACGTGATA
*
3833579 TGTTATGTGAGCA
1 TGTTAAGTGAGCA
3833592 AGATAATTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.26, C:0.04, G:0.31, T:0.40
Consensus pattern (34 bp):
TGTTAAGTGAGCATATTAAGTATGTTACGTGATA
Found at i:3835553 original size:139 final size:139
Alignment explanation
Indices: 3835303--3835583 Score: 472
Period size: 139 Copynumber: 2.0 Consensus size: 139
3835293 ATTGGTGATA
* *
3835303 CAATGATTGATTCCTATCTGAATCAAAAGTAAGTACAGCTAGAAGATATTTATCGAGTATCTGGG
1 CAATGATTGATTCCTATCTAAATCAAAAGCAAGTACAGCTAGAAGATATTTATCGAGTATCTGGG
* *
3835368 ATGAGAAAGAATCTGTTATCAATCTTATAATTGATTGATACTAGGAAGTTTGTTGTGTTTGGTCC
66 ATGAGAAAGAATCTGTTATCAATCTTACAATTGACTGATACTAGGAAGTTTGTTGTGTTTGGTCC
3835433 TAAAGATGT
131 TAAAGATGT
* * * *
3835442 CAATGATTGATTCCTATCTAAATCAGAAGCAAGTGCAGCTGGAAGATATTTATCGAGTATTTGGG
1 CAATGATTGATTCCTATCTAAATCAAAAGCAAGTACAGCTAGAAGATATTTATCGAGTATCTGGG
*
3835507 ATGAGAAAGAATCTTTTATCAATCTTACAATTGACTGATACTAGGAAGTTTGTTGTGTTTGGTCC
66 ATGAGAAAGAATCTGTTATCAATCTTACAATTGACTGATACTAGGAAGTTTGTTGTGTTTGGTCC
*
3835572 TAGAGATGT
131 TAAAGATGT
3835581 CAA
1 CAA
3835584 GGTTTGTCAA
Statistics
Matches: 132, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
139 132 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (139 bp):
CAATGATTGATTCCTATCTAAATCAAAAGCAAGTACAGCTAGAAGATATTTATCGAGTATCTGGG
ATGAGAAAGAATCTGTTATCAATCTTACAATTGACTGATACTAGGAAGTTTGTTGTGTTTGGTCC
TAAAGATGT
Found at i:3838560 original size:34 final size:34
Alignment explanation
Indices: 3838516--3838627 Score: 188
Period size: 34 Copynumber: 3.3 Consensus size: 34
3838506 GTGTGTTAGG
3838516 TAGGTGAGCATATTAGGTGTGTTAGGTGATGTGT
1 TAGGTGAGCATATTAGGTGTGTTAGGTGATGTGT
* *
3838550 TAGGTAAGCATATTAGGTGTGTTAGGTGATGTAT
1 TAGGTGAGCATATTAGGTGTGTTAGGTGATGTGT
**
3838584 TAGGTGAGCATATTAGGTGTGTTAGGCAATGTGT
1 TAGGTGAGCATATTAGGTGTGTTAGGTGATGTGT
3838618 TAGGTGAGCA
1 TAGGTGAGCA
3838628 AGATAATTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 72 1.00
ACGTcount: A:0.24, C:0.04, G:0.36, T:0.36
Consensus pattern (34 bp):
TAGGTGAGCATATTAGGTGTGTTAGGTGATGTGT
Found at i:3843655 original size:9 final size:9
Alignment explanation
Indices: 3843612--3843683 Score: 53
Period size: 9 Copynumber: 8.0 Consensus size: 9
3843602 TATTTTCAGT
3843612 TTATT-ATA
1 TTATTAATA
3843620 TTTATTATATAA
1 -TTATTA-AT-A
*
3843632 TTATAAATA
1 TTATTAATA
*
3843641 TAATTAATA
1 TTATTAATA
3843650 TTATT-ATA
1 TTATTAATA
3843658 --ATTAATTA
1 TTATTAA-TA
3843666 TTATTAATA
1 TTATTAATA
*
3843675 TTAATAATA
1 TTATTAATA
3843684 AAAAATTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
6 3 0.06
7 1 0.02
8 5 0.10
9 27 0.53
10 7 0.14
11 7 0.14
12 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTATTAATA
Found at i:3843679 original size:16 final size:16
Alignment explanation
Indices: 3843621--3843671 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 16
3843611 TTTATTATAT
3843621 TTATTAT-A-TAATTA
1 TTATTATAATTAATTA
* *
3843635 TAAATATAATTAA-TA
1 TTATTATAATTAATTA
3843650 TTATTATAATTAATTA
1 TTATTATAATTAATTA
3843666 TTATTA
1 TTATTA
3843672 ATATTAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 5 0.17
15 14 0.47
16 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTATAATTAATTA
Found at i:3843682 original size:19 final size:18
Alignment explanation
Indices: 3843640--3843682 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3843630 AATTATAAAT
*
3843640 ATAATTAATATTATTATA
1 ATAATTAATATTAATATA
*
3843658 ATTAATTATTATTAATATTA
1 A-TAATTAATATTAATA-TA
3843678 ATAAT
1 ATAAT
3843683 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 17 0.81
20 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAATTAATATTAATATA
Found at i:3844752 original size:2 final size:2
Alignment explanation
Indices: 3844747--3844791 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3844737 GTGTGTGTGT
3844747 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3844789 GA G
1 GA G
3844792 CAAGTCTACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3844950 original size:2 final size:2
Alignment explanation
Indices: 3844943--3844982 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3844933 GTTCCTGTTC
3844943 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3844983 ATCTTGCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3845919 original size:33 final size:33
Alignment explanation
Indices: 3845882--3845949 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
3845872 AATTAAGAGC
3845882 ATTGATTATATATATTACTCCATCA-AAAGAAAA
1 ATTGATTATATATATTACTCCAT-AGAAAGAAAA
*
3845915 ATTGATTATATATATTACTTCATAGAAAGAAAA
1 ATTGATTATATATATTACTCCATAGAAAGAAAA
3845948 AT
1 AT
3845950 AGAGGATGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (33 bp):
ATTGATTATATATATTACTCCATAGAAAGAAAA
Found at i:3846889 original size:14 final size:14
Alignment explanation
Indices: 3846870--3846913 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3846860 CTTTAGATTC
* *
3846870 AAATTTCGAGTTTT
1 AAATTTCAAATTTT
3846884 AAATTTCAAATTTT
1 AAATTTCAAATTTT
* *
3846898 AAATTTTAAAATTT
1 AAATTTCAAATTTT
3846912 AA
1 AA
3846914 GTAATTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (14 bp):
AAATTTCAAATTTT
Found at i:3846911 original size:8 final size:7
Alignment explanation
Indices: 3846880--3846913 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3846870 AAATTTCGAG
3846880 TTTTAAA
1 TTTTAAA
*
3846887 TTTCAAA
1 TTTTAAA
3846894 TTTTAAA
1 TTTTAAA
3846901 TTTTAAA
1 TTTTAAA
*
3846908 ATTTAA
1 TTTTAA
3846914 GTAATTATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (7 bp):
TTTTAAA
Found at i:3848231 original size:2 final size:2
Alignment explanation
Indices: 3848224--3848258 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3848214 GAACTTCGAT
*
3848224 AC AC AC AC AC AC AC AC AC AC AC AC AC GC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3848259 TATATCATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.49, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3849225 original size:14 final size:15
Alignment explanation
Indices: 3849198--3849243 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3849188 TATCATTAAA
*
3849198 TTTTTTCATATCCTT
1 TTTTTTCATTTCCTT
3849213 TTTTTTC-TTTCCTT
1 TTTTTTCATTTCCTT
*
3849227 CTTCTTTCATTTCCTT
1 -TTTTTTCATTTCCTT
3849243 T
1 T
3849244 CCTCCCTCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 14 0.52
16 7 0.26
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTTCATTTCCTT
Found at i:3850342 original size:32 final size:29
Alignment explanation
Indices: 3850306--3850377 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 29
3850296 TTCATTAATA
*
3850306 TAATAAATAAATTTTATCAATATATAATGAAT
1 TAATAAATAAATTTAAT--ATATA-AATGAAT
* *
3850338 TAATAAATATATTTAATATATAAATTAAT
1 TAATAAATAAATTTAATATATAAATGAAT
3850367 TAA-AAATAAAT
1 TAATAAATAAAT
3850378 AGTTACATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.19
29 9 0.25
30 5 0.14
32 15 0.42
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (29 bp):
TAATAAATAAATTTAATATATAAATGAAT
Found at i:3850437 original size:27 final size:26
Alignment explanation
Indices: 3850396--3850451 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
3850386 AAATAATAAA
**
3850396 AAATTTTAATTTAATAGTTTATAATTT
1 AAATTTTAAAATAATAGTTTA-AATTT
**
3850423 AAATTTTAAAATAATTTTTTAAATTT
1 AAATTTTAAAATAATAGTTTAAATTT
3850449 AAA
1 AAA
3850452 AATTTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
AAATTTTAAAATAATAGTTTAAATTT
Found at i:3851152 original size:2 final size:2
Alignment explanation
Indices: 3851140--3851170 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3851130 AAGGTTGGGT
*
3851140 TA TA AA 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 T
3851171 TAAAACTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3858741 original size:2 final size:2
Alignment explanation
Indices: 3858734--3858783 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
3858724 TATCTAACTT
*
3858734 TA TA TA TA TA TA TA TA TA T- TA TGA T- TA -A TGC TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA TA TA TA
3858775 TA TA TA TA T
1 TA TA TA TA T
3858784 TATTTAAGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
1 3 0.07
2 35 0.85
3 3 0.07
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3859115 original size:2 final size:2
Alignment explanation
Indices: 3859108--3859143 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3859098 ATGTCAAGAG
3859108 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3859144 GAAAAACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3865506 original size:8 final size:8
Alignment explanation
Indices: 3865493--3865517 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3865483 AAATGAGGTG
3865493 TTTAAAGT
1 TTTAAAGT
3865501 TTTAAAGT
1 TTTAAAGT
3865509 TTTAAAGT
1 TTTAAAGT
3865517 T
1 T
3865518 GTGAGATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TTTAAAGT
Found at i:3866138 original size:2 final size:2
Alignment explanation
Indices: 3866131--3866156 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3866121 AGTCTTGTAG
3866131 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
3866157 CCTCCTTGTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3873534 original size:130 final size:130
Alignment explanation
Indices: 3873301--3873560 Score: 502
Period size: 130 Copynumber: 2.0 Consensus size: 130
3873291 TTATCGATGA
* *
3873301 CTTCTCAAGGTATGTGTGGGTGGATTTTATGAAAGAGAAATCAGAAGCTTTGGAGAAATTTAAAA
1 CTTCTCAAGATATGTGTGGGTGGATTTTATGAAAGAGAAATCAAAAGCTTTGGAGAAATTTAAAA
3873366 CCTTCAAAGAAAAGGTTGAAAAAAAAGTTGGCAGGAAAATTCAATGTCTTCGCACAAACAATGGT
66 CCTTCAAAGAAAAGGTTGAAAAAAAAGTTGGCAGGAAAATTCAATGTCTTCGCACAAACAATGGT
3873431 CTTCTCAAGATATGTGTGGGTGGATTTTATGAAAGAGAAATCAAAAGCTTTGGAGAAATTTAAAA
1 CTTCTCAAGATATGTGTGGGTGGATTTTATGAAAGAGAAATCAAAAGCTTTGGAGAAATTTAAAA
3873496 CCTTCAAAGAAAAGGTTGAAAAAAAAGTTGGCAGGAAAATTCAATGTCTTCGCACAAACAATGGT
66 CCTTCAAAGAAAAGGTTGAAAAAAAAGTTGGCAGGAAAATTCAATGTCTTCGCACAAACAATGGT
3873561 GGAGAATATA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 128 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (130 bp):
CTTCTCAAGATATGTGTGGGTGGATTTTATGAAAGAGAAATCAAAAGCTTTGGAGAAATTTAAAA
CCTTCAAAGAAAAGGTTGAAAAAAAAGTTGGCAGGAAAATTCAATGTCTTCGCACAAACAATGGT
Found at i:3876016 original size:21 final size:21
Alignment explanation
Indices: 3875991--3876037 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3875981 TGGTGAGAAT
3875991 TTTTTATTTTATTTTCACTTA
1 TTTTTATTTTATTTTCACTTA
3876012 TTTTTATTTTATTTTCACTTA
1 TTTTTATTTTATTTTCACTTA
3876033 TTTTT
1 TTTTT
3876038 TTGTAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTATTTTATTTTCACTTA
Found at i:3876688 original size:19 final size:20
Alignment explanation
Indices: 3876664--3876705 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
3876654 TTTATAAAAT
*
3876664 AAATAATTAAT-TAAATTAA
1 AAATAATTAATATAAAGTAA
3876683 AAATAATTAATATAAAGTAA
1 AAATAATTAATATAAAGTAA
3876703 AAA
1 AAA
3876706 GATCGATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AAATAATTAATATAAAGTAA
Found at i:3881012 original size:24 final size:24
Alignment explanation
Indices: 3880965--3881008 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
3880955 TTGAGATGTT
3880965 TTTACTTTATATTATTTTTTTAAA
1 TTTACTTTATATTATTTTTTTAAA
*
3880989 TTTA-TTTA-ATTATTTATTTA
1 TTTACTTTATATTATTTTTTTA
3881009 TAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 4 0.21
24 4 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTACTTTATATTATTTTTTTAAA
Found at i:3882780 original size:49 final size:49
Alignment explanation
Indices: 3882708--3882806 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
3882698 ATGGTATGGT
*
3882708 TTTCCTTGTCTTTTAGATCTGTTTGATGATCTGTGTGTGTGTGTGTGTG
1 TTTCCTTGTCTTTTAGATCTGTTTGATGATCTGAGTGTGTGTGTGTGTG
3882757 TTTCCTTGTCTTTTAGATCTGTTTGATGATCTGAGTGTGTGTGTGTGTG
1 TTTCCTTGTCTTTTAGATCTGTTTGATGATCTGAGTGTGTGTGTGTGTG
3882806 T
1 T
3882807 GTGTGTGTGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.09, C:0.10, G:0.28, T:0.53
Consensus pattern (49 bp):
TTTCCTTGTCTTTTAGATCTGTTTGATGATCTGAGTGTGTGTGTGTGTG
Found at i:3882798 original size:2 final size:2
Alignment explanation
Indices: 3882791--3882819 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3882781 GATGATCTGA
3882791 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
3882820 AGTGATATCT
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:3887374 original size:47 final size:47
Alignment explanation
Indices: 3887319--3887413 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
3887309 AGAATTCTAG
3887319 ACTTCAGTTCACGACTCAAAACAAGAGTTCCCGATCAATTACGTAAA
1 ACTTCAGTTCACGACTCAAAACAAGAGTTCCCGATCAATTACGTAAA
3887366 ACTTCAGTTCACGACTCAAAACAAGAGTTCCCGATCAATTACGTAAA
1 ACTTCAGTTCACGACTCAAAACAAGAGTTCCCGATCAATTACGTAAA
3887413 A
1 A
3887414 TTACAAGCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (47 bp):
ACTTCAGTTCACGACTCAAAACAAGAGTTCCCGATCAATTACGTAAA
Found at i:3890221 original size:3 final size:3
Alignment explanation
Indices: 3890213--3890245 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3890203 AAATAAAATT
3890213 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3890246 CGTTTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3893468 original size:2 final size:2
Alignment explanation
Indices: 3893455--3893493 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3893445 TGTTTAGATA
*
3893455 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3893494 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3893498 original size:2 final size:2
Alignment explanation
Indices: 3893493--3893527 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3893483 ATATATATAT
3893493 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3893528 AATCGCAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3893711 original size:2 final size:2
Alignment explanation
Indices: 3893704--3893735 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3893694 TCTTTTGGGG
3893704 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3893736 CGGCGGAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3894191 original size:3 final size:3
Alignment explanation
Indices: 3894177--3894206 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3894167 TACTCCTCTG
*
3894177 CAA CAG CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
3894207 AAAAGAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.33, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:3896459 original size:32 final size:29
Alignment explanation
Indices: 3896409--3896467 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
3896399 ACTTATTTTA
* *
3896409 ATAACAAAAAGTTAAAATATATCTTTAATT
1 ATAACAAAAAATTAAAATAAAT-TTTAATT
3896439 ATAACATAAAAATTATAAATAAATTTTAA
1 ATAACA-AAAAATTA-AAATAAATTTTAA
3896468 CTGAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.24
31 12 0.48
32 7 0.28
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (29 bp):
ATAACAAAAAATTAAAATAAATTTTAATT
Found at i:3896595 original size:18 final size:17
Alignment explanation
Indices: 3896574--3896626 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
3896564 ACTTAATTTC
3896574 AAATTTAAATTTAAATCT
1 AAATTTAAATTTAAAT-T
* *
3896592 AAATTTTATTTTAAATT
1 AAATTTAAATTTAAATT
*
3896609 AAGTTTTAAATTTCAAAT
1 AA-ATTTAAATTT-AAAT
3896627 ATGTGATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 3 0.11
18 21 0.75
19 4 0.14
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATTTAAATTTAAATT
Found at i:3896615 original size:17 final size:18
Alignment explanation
Indices: 3896583--3896616 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3896573 CAAATTTAAA
3896583 TTTAAATCTAAATTTTAT
1 TTTAAATCTAAATTTTAT
*
3896601 TTTAAAT-TAAGTTTTA
1 TTTAAATCTAAATTTTA
3896617 AATTTCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAAATCTAAATTTTAT
Found at i:3896697 original size:3 final size:3
Alignment explanation
Indices: 3896689--3896729 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3896679 ACAAAAAAGG
3896689 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3896730 CCACAATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3897645 original size:5 final size:5
Alignment explanation
Indices: 3897630--3897689 Score: 66
Period size: 5 Copynumber: 11.2 Consensus size: 5
3897620 GCTTTTATAA
* *
3897630 AATATT AATAT AATAT AACTTT AGTAT ATATAT ATATAT AATAT AATAT
1 AATA-T AATAT AATAT AA-TAT AATAT A-ATAT A-ATAT AATAT AATAT
3897679 AATAT AATAT A
1 AATAT AATAT A
3897690 CTAGATAGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
5 31 0.65
6 17 0.35
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (5 bp):
AATAT
Found at i:3897688 original size:28 final size:28
Alignment explanation
Indices: 3897630--3897689 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
3897620 GCTTTTATAA
* *
3897630 AATAT-TAATATAATATAACTTTAGTAT
1 AATATATAATATAATATAACTATAATAT
3897657 -ATATATATATATAATATAA-TATAATAT
1 AATATATA-ATATAATATAACTATAATAT
3897684 AATATA
1 AATATA
3897690 CTAGATAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.14
27 8 0.29
28 16 0.57
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
AATATATAATATAATATAACTATAATAT
Found at i:3898273 original size:20 final size:21
Alignment explanation
Indices: 3898248--3898296 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
3898238 TAATTAAATT
* *
3898248 AATTTATAAA-ATTATTTTTA
1 AATTTATAAATATAAATTTTA
3898268 AATTTA-AAATATAAATTTTA
1 AATTTATAAATATAAATTTTA
3898288 ATATTTATA
1 A-ATTTATA
3898297 TCCTTTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 15 0.62
21 5 0.21
22 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTATAAATATAAATTTTA
Found at i:3899915 original size:2 final size:2
Alignment explanation
Indices: 3899910--3899946 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3899900 AAAGTGTGTG
3899910 TA 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 TA T
3899947 GTATGAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3901309 original size:24 final size:23
Alignment explanation
Indices: 3901282--3901327 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
3901272 TTTATTTAAA
* *
3901282 ATTTTGAATGAAATCATAAATAAT
1 ATTTTAAATAAAAT-ATAAATAAT
*
3901306 ATTTTAAATAAAATATATATAA
1 ATTTTAAATAAAATATAAATAA
3901328 ATGTAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (23 bp):
ATTTTAAATAAAATATAAATAAT
Found at i:3907477 original size:42 final size:42
Alignment explanation
Indices: 3907430--3907513 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
3907420 CAGTATTTTT
* *
3907430 CTTTACCAGATTACCAGATCAATTATAACCAATAATACAAGC
1 CTTTACCAGATGACCAGATCAATCATAACCAATAATACAAGC
*
3907472 CTTTACCAGATGACCAGATCAATCATAATCAATAATACAAGC
1 CTTTACCAGATGACCAGATCAATCATAACCAATAATACAAGC
3907514 ACGTCCACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (42 bp):
CTTTACCAGATGACCAGATCAATCATAACCAATAATACAAGC
Found at i:3910517 original size:2 final size:2
Alignment explanation
Indices: 3910510--3910552 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3910500 TGAATTATTA
3910510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3910552 A
1 A
3910553 AAAGACATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3910900 original size:18 final size:17
Alignment explanation
Indices: 3910865--3910917 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
3910855 TTTATGATAT
3910865 AAAATATAATATAATAA
1 AAAATATAATATAATAA
*
3910882 AAAATATAA-ATACATTA
1 AAAATATAATATA-ATAA
*
3910899 AAAAT-TTATATAATAA
1 AAAATATAATATAATAA
3910915 AAA
1 AAA
3910918 TTATTGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 11 0.35
17 20 0.65
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATATAATATAATAA
Found at i:3910917 original size:15 final size:15
Alignment explanation
Indices: 3910850--3910919 Score: 54
Period size: 17 Copynumber: 4.5 Consensus size: 15
3910840 TAAAAATGTA
3910850 AAAAATTTATGAT-AT
1 AAAAATTTAT-ATAAT
*
3910865 -AAAATATAATATAAT
1 AAAAAT-TTATATAAT
* *
3910880 AAAAAATATAAATACATT
1 -AAAAATTTATATA-A-T
3910898 AAAAATTTATATAAT
1 AAAAATTTATATAAT
3910913 AAAAATT
1 AAAAATT
3910920 ATTGTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
14 7 0.16
15 13 0.30
16 5 0.12
17 17 0.40
18 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (15 bp):
AAAAATTTATATAAT
Found at i:3911765 original size:3 final size:3
Alignment explanation
Indices: 3911753--3911790 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
3911743 ATTACTAAAC
*
3911753 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3911791 GTTACTAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3912411 original size:3 final size:3
Alignment explanation
Indices: 3912405--3912456 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
3912395 TACTTTCCTT
*
3912405 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3912453 TTA T
1 TTA T
3912457 AAGATGAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3915617 original size:20 final size:21
Alignment explanation
Indices: 3915592--3915632 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
3915582 TCACTTATAA
3915592 AAAAATTATTTA-TATTTAAT
1 AAAAATTATTTATTATTTAAT
3915612 AAAAATTATTTATTATTTAAT
1 AAAAATTATTTATTATTTAAT
3915633 GAGCGTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAAATTATTTATTATTTAAT
Found at i:3916399 original size:2 final size:2
Alignment explanation
Indices: 3916392--3916424 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3916382 TGAAGTGTTA
3916392 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3916425 AATTTTGCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3919657 original size:29 final size:28
Alignment explanation
Indices: 3919621--3919685 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 28
3919611 ATATTCATTC
3919621 ATTTATATTATAATTAGTTTTT-TATTTT
1 ATTTATATTATAATTA-TTTTTATATTTT
*
3919649 ATATTATATTTTAATTATTTTTATATTTT
1 AT-TTATATTATAATTATTTTTATATTTT
3919678 ATTTATAT
1 ATTTATAT
3919686 GAAATATTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (28 bp):
ATTTATATTATAATTATTTTTATATTTT
Found at i:3919660 original size:17 final size:17
Alignment explanation
Indices: 3919640--3919685 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
3919630 ATAATTAGTT
3919640 TTTTATTTTATATTATA
1 TTTTATTTTATATTATA
3919657 TTTTAATTATT-T-TTATA
1 TTTT-ATT-TTATATTATA
3919674 TTTTA-TTTATAT
1 TTTTATTTTATAT
3919686 GAAATATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
14 2 0.08
15 2 0.08
16 2 0.08
17 13 0.52
18 4 0.16
19 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATTTTATATTATA
Found at i:3919886 original size:1 final size:1
Alignment explanation
Indices: 3919880--3919905 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3919870 CTTCGAGCAC
3919880 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
3919906 CAAAAGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3920557 original size:2 final size:2
Alignment explanation
Indices: 3920550--3920599 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
3920540 TTCTTCATTC
3920550 TA TA TA 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 TA TA TA TA
*
3920591 TA TC TA TA T
1 TA TA TA TA T
3920600 TGAGAGAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3924542 original size:27 final size:27
Alignment explanation
Indices: 3924489--3924542 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3924479 AACACTTAAG
* *
3924489 TCGTATAATTACTGCAATTTTAGTATT
1 TCGTATAATTACTGCAATTTCAATATT
*
3924516 TCGTATAATTATTGCAATTTCAATATT
1 TCGTATAATTACTGCAATTTCAATATT
3924543 CTTATAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (27 bp):
TCGTATAATTACTGCAATTTCAATATT
Found at i:3925091 original size:23 final size:24
Alignment explanation
Indices: 3925065--3925115 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3925055 CCATATGTTC
3925065 ATTTC-TTAACTCAATTATCA-GAA
1 ATTTCTTTAACTCAATTAT-AGGAA
*
3925088 ATTTCTTTATCTCAATTATAGGAA
1 ATTTCTTTAACTCAATTATAGGAA
3925112 ATTT
1 ATTT
3925116 AATGATTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (24 bp):
ATTTCTTTAACTCAATTATAGGAA
Found at i:3925497 original size:6 final size:6
Alignment explanation
Indices: 3925486--3925514 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3925476 AATATAACAT
3925486 AAAATA AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAAT
3925515 TATTTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:3926198 original size:24 final size:26
Alignment explanation
Indices: 3926166--3926218 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
3926156 TTAAATATCG
*
3926166 ATTTAATTTTATAT-TAAAATAAAAA
1 ATTTAATTTGATATATAAAATAAAAA
* *
3926191 ATTT-ATTTGATATATATATTAAAAA
1 ATTTAATTTGATATATAAAATAAAAA
3926216 ATT
1 ATT
3926219 CAAAATACGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTTAATTTGATATATAAAATAAAAA
Found at i:3928156 original size:2 final size:2
Alignment explanation
Indices: 3928151--3928180 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3928141 AATATAAAAG
3928151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3928181 GATTTGAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3930792 original size:2 final size:2
Alignment explanation
Indices: 3930785--3930810 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3930775 TGCTGCAATA
3930785 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
3930811 GGAGGTTGGA
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:3931960 original size:17 final size:17
Alignment explanation
Indices: 3931934--3931967 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3931924 TGTTAAGAGA
*
3931934 TGCTCCTTAATGTGGGG
1 TGCTCATTAATGTGGGG
3931951 TGCTCATTAATGTGGGG
1 TGCTCATTAATGTGGGG
3931968 CTCCAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (17 bp):
TGCTCATTAATGTGGGG
Found at i:3932018 original size:2 final size:2
Alignment explanation
Indices: 3932011--3932036 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3932001 TTTTGACTAC
3932011 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
3932037 GTTTTGTACA
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:3939311 original size:2 final size:2
Alignment explanation
Indices: 3939304--3939330 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3939294 TGATTGAGAA
3939304 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3939331 ATAAGTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3939686 original size:2 final size:2
Alignment explanation
Indices: 3939679--3939707 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3939669 CAAATGACAT
3939679 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
3939708 TTGCAATTAT
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:3940020 original size:21 final size:24
Alignment explanation
Indices: 3939977--3940025 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 24
3939967 GTATTTAATA
3939977 TATTAATAACATATAAATATATAT
1 TATTAATAACATATAAATATATAT
*
3940001 TATTAATAA-AT-TTAAT-TATAT
1 TATTAATAACATATAAATATATAT
3940022 TATT
1 TATT
3940026 TTATTAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 4 0.17
23 2 0.08
24 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTAATAACATATAAATATATAT
Found at i:3940929 original size:2 final size:2
Alignment explanation
Indices: 3940922--3940951 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3940912 TAAGCAATGA
3940922 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3940952 TGTTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3941346 original size:29 final size:29
Alignment explanation
Indices: 3941313--3941368 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
3941303 TATAGGTTAT
3941313 AAATATAAAAGAAAACAAATACTATATGA
1 AAATATAAAAGAAAACAAATACTATATGA
3941342 AAATATAAAAGAAAACAAATACTATAT
1 AAATATAAAAGAAAACAAATACTATAT
3941369 AAATCTACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.21
Consensus pattern (29 bp):
AAATATAAAAGAAAACAAATACTATATGA
Found at i:3947672 original size:2 final size:2
Alignment explanation
Indices: 3947665--3947701 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3947655 AGGATAAAAG
3947665 TA 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 TA T
3947702 TACTAGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3948200 original size:34 final size:34
Alignment explanation
Indices: 3948132--3948348 Score: 285
Period size: 34 Copynumber: 6.4 Consensus size: 34
3948122 CAAGTTCCTC
* **
3948132 TTGTTGATTAAAT-GGTGATTTAGTAATTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
3948165 TTGTTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
*
3948199 TTGTTGACTAAATGGG-GATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* **
3948232 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
3948266 TTATTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
3948300 TTGTTGATTAAATGGGTGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
*
3948334 TTATTGATTAAATGG
1 TTGTTGATTAAATGG
3948349 TGGTTTTTAC
Statistics
Matches: 161, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 41 0.25
34 120 0.75
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:3948312 original size:68 final size:68
Alignment explanation
Indices: 3948135--3948348 Score: 297
Period size: 67 Copynumber: 3.2 Consensus size: 68
3948125 GTTCCTCTTG
* ** * *
3948135 TTGATTAAAT-GGTGATTTAGTAATTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGCTTGCCA
*
3948199 TTG
66 TTA
* * ** *
3948202 TTGACTAAATGGG-GATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTTACCA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGCTTGCCA
3948266 TTA
66 TTA
* *
3948269 TTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGGTTGCCA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGCTTGCCA
3948334 TTA
66 TTA
3948337 TTGATTAAATGG
1 TTGATTAAATGG
3948349 TGGTTTTTAC
Statistics
Matches: 127, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
67 65 0.51
68 62 0.49
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (68 bp):
TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGCTTGCCA
TTA
Found at i:3948674 original size:20 final size:19
Alignment explanation
Indices: 3948649--3948706 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 19
3948639 TTGGTTGTCG
*
3948649 AGGTACTATTCACGTATATT
1 AGGTACTATTCACGTATA-C
3948669 AGGTACTATTCACGTATAC
1 AGGTACTATTCACGTATAC
* *
3948688 GGGTACTATTCAAGTATAC
1 AGGTACTATTCACGTATAC
3948707 GGTTACTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (19 bp):
AGGTACTATTCACGTATAC
Found at i:3948694 original size:19 final size:19
Alignment explanation
Indices: 3948650--3948713 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
3948640 TGGTTGTCGA
**
3948650 GGTACTATTCACGTATATTA
1 GGTACTATTCACGTATA-CG
3948670 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
3948689 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
3948708 GTTACT
1 GGTACT
3948714 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:3952848 original size:34 final size:34
Alignment explanation
Indices: 3952779--3952996 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
3952769 AAGTGGGAGA
* *
3952779 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
3952812 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
*
3952846 ATTGTTGACTAAATGGG-GATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
3952879 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
3952913 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
3952947 ATTGTTGATTAAATGGGTGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
*
3952981 ATTATTGATTAAATGG
1 ATTGTTGATTAAATGG
3952997 TGGTTTTTAC
Statistics
Matches: 163, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
33 42 0.26
34 121 0.74
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:3952960 original size:68 final size:68
Alignment explanation
Indices: 3952783--3952996 Score: 306
Period size: 67 Copynumber: 3.2 Consensus size: 68
3952773 GGGAGAATTG
* * * *
3952783 TTGATTAAAT-GGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGCTTGCCA
*
3952847 TTG
66 TTA
* * ** *
3952850 TTGACTAAATGGG-GATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTTACCA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGCTTGCCA
3952914 TTA
66 TTA
* *
3952917 TTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGGTTGCCA
1 TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGCTTGCCA
3952982 TTA
66 TTA
3952985 TTGATTAAATGG
1 TTGATTAAATGG
3952997 TGGTTTTTAC
Statistics
Matches: 128, Mismatches: 17, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
67 66 0.52
68 62 0.48
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (68 bp):
TTGATTAAATGGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTAGCTTGCCA
TTA
Found at i:3953610 original size:5 final size:6
Alignment explanation
Indices: 3953588--3953619 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
3953578 TTTAAATGAA
3953588 AAAAAGT AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAA-T AAAAAT AAAAAT AAAAAT AAAAAT A
3953620 TTTAATAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:3954975 original size:179 final size:174
Alignment explanation
Indices: 3954672--3955202 Score: 617
Period size: 179 Copynumber: 3.0 Consensus size: 174
3954662 AAAATCTTGT
* * * *
3954672 CTAAATAAATCCAGTTTGAATTAGATTTACTTATTGTTTAGAA-ATCTGAAAAATGCAATGAACT
1 CTAAATAAATCCAGTTTGAATTAGATTTATTTATTG--TAGAAGAACTAAAAAATACAATGAACT
* * *
3954736 AAGTATCATATCCGTGCGTTACACAGGTTCGTAATATATCTTATGTTTTAAATCACATTATTATC
64 -AGTATCATAT-C-TG-GTTACACAGATTTGTAATGTATCTTATGTTTTAAATCACATTATTATC
* *
3954801 GTCAATAATAAAATCATATTATGAAGATTAATTAAATAAAATTCATATTA
125 GTCAATAATAAAATCATATTATGAAGATTAGTTAAATAAAATTCATATCA
* * *
3954851 CTAAATAAATCTAGTTTGAATTGGATTTATTTATTGTAGAAGAACTTAAAAAATACAATGACCTA
1 CTAAATAAATCCAGTTTGAATTAGATTTATTTATTGTAGAAGAAC-TAAAAAATACAATGAACTA
* * * *
3954916 GGTATCATACTCATGTATTACACAGATTTGTAATGCATCTTATGTTTTAAATTACATTATTATGG
65 -GTATCATA-TC-TG-GTTACACAGATTTGTAATGTATCTTATGTTTTAAATCACATTATTATCG
*
3954981 TCAATAATAAAATCATATTATGAAGATTAGTTAAATAAAATGCATATCA
126 TCAATAATAAAATCATATTATGAAGATTAGTTAAATAAAATTCATATCA
* * * * * *
3955030 CCAAATAAATCCAATTTGAATCAAATTTATTTATTGTATAAGAACCTAAAAAATACAATAAACTA
1 CTAAATAAATCCAGTTTGAATTAGATTTATTTATTGTAGAAGAA-CTAAAAAATACAATGAACTA
* * * * * *
3955095 --A--GTAT-TGGTTA-ACATGAGTTTATAATGTATCATATATTTTAAATCGCATTATTATCATC
65 GTATCATATCTGGTTACACA-GA-TTTGTAATGTATCTTATGTTTTAAATCACATTATTATCGTC
*
3955154 AATAATAAAATCATATTATGAATATTAGTTAAATAAAATTCATATCA
128 AATAATAAAATCATATTATGAAGATTAGTTAAATAAAATTCATATCA
3955201 CT
1 CT
3955203 TTAAATGTAT
Statistics
Matches: 304, Mismatches: 41, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
169 3 0.01
170 5 0.02
171 81 0.27
173 1 0.00
174 2 0.01
176 1 0.00
177 5 0.02
178 3 0.01
179 201 0.66
180 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (174 bp):
CTAAATAAATCCAGTTTGAATTAGATTTATTTATTGTAGAAGAACTAAAAAATACAATGAACTAG
TATCATATCTGGTTACACAGATTTGTAATGTATCTTATGTTTTAAATCACATTATTATCGTCAAT
AATAAAATCATATTATGAAGATTAGTTAAATAAAATTCATATCA
Found at i:3956509 original size:22 final size:20
Alignment explanation
Indices: 3956484--3956534 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
3956474 ATATTTGTAA
*
3956484 ATATTTAATTAAATTAATAATT
1 ATATTAAATTAAATT-AT-ATT
*
3956506 ATATAAAATTAAATTATATT
1 ATATTAAATTAAATTATATT
3956526 ATATTAAAT
1 ATATTAAAT
3956535 AATTATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 11 0.42
21 2 0.08
22 13 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTAAATTAAATTATATT
Found at i:3956589 original size:15 final size:17
Alignment explanation
Indices: 3956532--3956585 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
3956522 TATTATATTA
* *
3956532 AATAATTATTATTTATATA
1 AATAATT-TTATGTA-ATT
*
3956551 AAT-ATTTTTTGTAATT
1 AATAATTTTATGTAATT
3956567 AATAATTTTATGTAATT
1 AATAATTTTATGTAATT
3956584 AA
1 AA
3956586 ATTTGAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 5 0.17
17 19 0.63
18 3 0.10
19 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATAATTTTATGTAATT
Found at i:3957353 original size:23 final size:21
Alignment explanation
Indices: 3957311--3957358 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
3957301 CACTAATGTA
*
3957311 AATAAAAAATAATTTAAATAC
1 AATAAAAAATAATATAAATAC
* *
3957332 AATACAAAACATAATATGAATAT
1 AATA-AAAA-ATAATATAAATAC
3957355 AATA
1 AATA
3957359 TGAATATACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 4 0.18
23 14 0.64
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (21 bp):
AATAAAAAATAATATAAATAC
Found at i:3957358 original size:11 final size:11
Alignment explanation
Indices: 3957342--3957366 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3957332 AATACAAAAC
3957342 ATAATATGAAT
1 ATAATATGAAT
3957353 ATAATATGAAT
1 ATAATATGAAT
3957364 ATA
1 ATA
3957367 CGAATGTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
ATAATATGAAT
Found at i:3957524 original size:8 final size:8
Alignment explanation
Indices: 3957511--3957535 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3957501 TATGATATGG
3957511 ATATAAAA
1 ATATAAAA
3957519 ATATAAAA
1 ATATAAAA
3957527 ATATAAAA
1 ATATAAAA
3957535 A
1 A
3957536 ATATTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATATAAAA
Found at i:3962830 original size:2 final size:2
Alignment explanation
Indices: 3962825--3962855 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3962815 CTCTTTACTA
3962825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3962856 AACAAAACTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3963008 original size:3 final size:3
Alignment explanation
Indices: 3963000--3963034 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3962990 TAATCATATC
3963000 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3963035 TTTATTAATA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3966067 original size:16 final size:16
Alignment explanation
Indices: 3966042--3966080 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3966032 TTTTCATTTG
* *
3966042 AAAAACGAAAATAACA
1 AAAAAGGAAAAAAACA
3966058 AAAAAGGAAAAAAACA
1 AAAAAGGAAAAAAACA
3966074 AAGAAAG
1 AA-AAAG
3966081 AATTTTGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.03
Consensus pattern (16 bp):
AAAAAGGAAAAAAACA
Found at i:3967800 original size:2 final size:2
Alignment explanation
Indices: 3967793--3967836 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3967783 AATGGCCTTT
3967793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3967835 TA
1 TA
3967837 AAACTAGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3968287 original size:13 final size:13
Alignment explanation
Indices: 3968269--3968293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3968259 AACTCAAAAC
3968269 TTAATTTAATTAA
1 TTAATTTAATTAA
3968282 TTAATTTAATTA
1 TTAATTTAATTA
3968294 TTTTTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:3971440 original size:2 final size:2
Alignment explanation
Indices: 3971429--3971469 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
3971419 AAATACCCCT
*
3971429 TA TA -A TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3971470 AGCCAATCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3973651 original size:59 final size:62
Alignment explanation
Indices: 3973564--3973685 Score: 169
Period size: 59 Copynumber: 2.0 Consensus size: 62
3973554 TGGATAATGC
** * *
3973564 ATGAAGAATATGCTACATAAAACAAAAATGATGATAGAAATATAAAATTATGTGAAAATTAT
1 ATGAAGAATATGCTACATAAAACAAAAATGACAAAAGAAATAGAAAATTATGTGAAAATTAT
* *
3973626 ATGAA-AATATGCTACAT-TAA-AAAAATGACAAAAGAAATAGAAAATTATGTGAAGATTAT
1 ATGAAGAATATGCTACATAAAACAAAAATGACAAAAGAAATAGAAAATTATGTGAAAATTAT
3973685 A
1 A
3973686 AAACGACACA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
59 35 0.65
60 2 0.04
61 12 0.22
62 5 0.09
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (62 bp):
ATGAAGAATATGCTACATAAAACAAAAATGACAAAAGAAATAGAAAATTATGTGAAAATTAT
Found at i:3978087 original size:28 final size:29
Alignment explanation
Indices: 3978056--3978117 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
3978046 TTATAAAAAA
*
3978056 TTTTAAAAATATATTT-TATT-TTTATATT
1 TTTTAAAAAT-TATTTAAATTATTTATATT
*
3978084 TTTT-ATAATTATTTAAATTATTTATATT
1 TTTTAAAAATTATTTAAATTATTTATATT
3978112 TTTTAA
1 TTTTAA
3978118 TATATTGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 7 0.24
28 16 0.55
29 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTAAAAATTATTTAAATTATTTATATT
Found at i:3978088 original size:9 final size:9
Alignment explanation
Indices: 3978074--3978116 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3978064 ATATATTTTA
3978074 TTTTTATAT
1 TTTTTATAT
3978083 TTTTTATAAT
1 TTTTTAT-AT
* *
3978093 TATTTAAAT
1 TTTTTATAT
*
3978102 TATTTATAT
1 TTTTTATAT
3978111 TTTTTA
1 TTTTTA
3978117 ATATATTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTATAT
Done.