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 19 of 31
Found at i:4258531 original size:32 final size:32
Alignment explanation
Indices: 4258454--4258538 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 32
4258444 AAAATATTAA
4258454 TAAT-TTATATTATATA--TATTTTAATATATTT
1 TAATATTATATTATATATTTATTTT--TATATTT
* *
4258485 TTATATTATATTATATTTTTATTTTTATATTT
1 TAATATTATATTATATATTTATTTTTATATTT
*
4258517 TAATTATT-TTTTATATATTTAT
1 TAA-TATTATATTATATATTTAT
4258539 ATAATATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 3 0.07
32 32 0.71
33 4 0.09
34 6 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (32 bp):
TAATATTATATTATATATTTATTTTTATATTT
Found at i:4260028 original size:22 final size:23
Alignment explanation
Indices: 4260003--4260045 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4259993 CAACACTATC
*
4260003 TTATTTA-CAAATTATTTAAAAT
1 TTATTTATCAAATCATTTAAAAT
*
4260025 TTATTTATTAAATCATTTAAA
1 TTATTTATCAAATCATTTAAA
4260046 TCTGATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATTTATCAAATCATTTAAAAT
Found at i:4260136 original size:32 final size:32
Alignment explanation
Indices: 4260078--4260144 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
4260068 TTGTATTTTA
* *
4260078 TTTTACTTATTTATAGTATAATAATAT-TTATG
1 TTTTACTTATTTAAAATATAATAATATATT-TG
*
4260110 TTTTATTTATTTAAAAT-TAATAAATATATTTG
1 TTTTACTTATTTAAAATATAAT-AATATATTTG
4260142 TTT
1 TTT
4260145 GTTTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 4 0.13
32 24 0.80
33 2 0.07
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (32 bp):
TTTTACTTATTTAAAATATAATAATATATTTG
Found at i:4262665 original size:13 final size:13
Alignment explanation
Indices: 4262647--4262684 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
4262637 ATCAATGAAA
4262647 TAAATTTTAAAAT
1 TAAATTTTAAAAT
*
4262660 TAAATTTGT-AGAT
1 TAAATTT-TAAAAT
4262673 TAAATTTTAAAA
1 TAAATTTTAAAA
4262685 AAGCAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.05
13 19 0.90
14 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (13 bp):
TAAATTTTAAAAT
Found at i:4266937 original size:19 final size:21
Alignment explanation
Indices: 4266895--4266939 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
4266885 ATTAATTTAG
*
4266895 TTTTATATATTTTTATAATTT
1 TTTTATATATATTTATAATTT
4266916 TTTTATATA-ATTTAT-ATTT
1 TTTTATATATATTTATAATTT
4266935 TTTTA
1 TTTTA
4266940 ATTTAATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 5 0.22
21 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTATATATATTTATAATTT
Found at i:4267283 original size:2 final size:2
Alignment explanation
Indices: 4267265--4267303 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4267255 GTACATAATT
* *
4267265 TA TA TA CA TA TA CA 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 T
4267304 GCTTCAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4267822 original size:20 final size:20
Alignment explanation
Indices: 4267797--4267849 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
4267787 AATTATTAAT
*
4267797 ATATTTAAAATCT-ATATATA
1 ATATTTAAAATATAAT-TATA
*
4267817 ATATTTTAAATATAATTATA
1 ATATTTAAAATATAATTATA
4267837 ATA--TAAAATATAA
1 ATATTTAAAATATAA
4267850 AAATAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 9 0.31
20 18 0.62
21 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTTAAAATATAATTATA
Found at i:4267836 original size:22 final size:23
Alignment explanation
Indices: 4267781--4267836 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 23
4267771 AAATTTATGT
4267781 AATATTAATTAT-TAATATATTTA
1 AATA-TAATTATATAATATATTTA
*
4267804 AA-AT-CTATATATAATAT-TTTA
1 AATATAAT-TATATAATATATTTA
4267825 AATATAATTATA
1 AATATAATTATA
4267837 ATATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
20 1 0.04
21 10 0.37
22 13 0.48
23 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATAATTATATAATATATTTA
Found at i:4267860 original size:9 final size:9
Alignment explanation
Indices: 4267834--4267877 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
4267824 AAATATAATT
4267834 ATAATATAAA
1 ATAATA-AAA
4267844 AT-ATAAAA
1 ATAATAAAA
4267852 ATAATAAAA
1 ATAATAAAA
4267861 AT-ATAAAA
1 ATAATAAAA
4267869 ATAATAAAA
1 ATAATAAAA
4267878 TTACGATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 13 0.41
9 17 0.53
10 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
ATAATAAAA
Found at i:4267861 original size:17 final size:17
Alignment explanation
Indices: 4267824--4267877 Score: 81
Period size: 17 Copynumber: 3.1 Consensus size: 17
4267814 ATAATATTTT
**
4267824 AAATATAATTATAATATA
1 AAATATAAAAATAATA-A
4267842 AAATATAAAAATAATAA
1 AAATATAAAAATAATAA
4267859 AAATATAAAAATAATAA
1 AAATATAAAAATAATAA
4267876 AA
1 AA
4267878 TTACGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 20 0.59
18 14 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATATAAAAATAATAA
Found at i:4268636 original size:2 final size:2
Alignment explanation
Indices: 4268629--4268653 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4268619 AGTTTTTGTG
4268629 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
4268654 TTTTTATTTT
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:4268682 original size:21 final size:20
Alignment explanation
Indices: 4268658--4268699 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
4268648 ATATATTTTT
*
4268658 TATTTTATATTATATTTAAAA
1 TATTTTATATT-TATATAAAA
4268679 TATTTTATATTTATATAAAA
1 TATTTTATATTTATATAAAA
4268699 T
1 T
4268700 TTAATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTATATTTATATAAAA
Found at i:4268684 original size:27 final size:27
Alignment explanation
Indices: 4268654--4268780 Score: 69
Period size: 27 Copynumber: 4.4 Consensus size: 27
4268644 ATATATATAT
*
4268654 TTTTTATTTTATATTATATTTAAAATA
1 TTTTTATTTTATATTAAATTTAAAATA
* *
4268681 -TTTTATATTTATATAAAATTTAATATA
1 TTTTTAT-TTTATATTAAATTTAAAATA
*
4268708 TTAATAATTAATATTATA-TAAATTTTAAAATA
1 TT--T--TT-ATTTTATATTAAA-TTTAAAATA
* * * * *
4268740 TGTTAATATTTATATTATATTTATATTA
1 TTTTTAT-TTTATATTAAATTTAAAATA
4268768 TTTTAATATTTTA
1 TTTT--TATTTTA
4268781 AGTAATAAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
26 6 0.08
27 19 0.26
28 17 0.23
29 7 0.09
30 4 0.05
31 3 0.04
32 16 0.22
33 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTTTATTTTATATTAAATTTAAAATA
Found at i:4268706 original size:18 final size:17
Alignment explanation
Indices: 4268689--4268735 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
4268679 TATTTTATAT
4268689 TTATATAAAATTTAATA
1 TTATATAAAATTTAATA
4268706 -TAT-TAATAA-TTAATA
1 TTATATAA-AATTTAATA
*
4268721 TTATATAAATTTTAA
1 TTATATAAAATTTAA
4268736 AATATGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
15 9 0.36
16 9 0.36
17 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATATAAAATTTAATA
Found at i:4268726 original size:32 final size:32
Alignment explanation
Indices: 4268689--4268759 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
4268679 TATTTTATAT
4268689 TTATATAAAATTT-AATATATTAATAATTAATA
1 TTATATAAAATTTAAATATATTAAT-ATTAATA
* * *
4268721 TTATATAAATTTTAAAATATGTTAATATTTATA
1 TTATATAAAATTT-AAATATATTAATATTAATA
4268754 TTATAT
1 TTATAT
4268760 TTATATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.35
33 12 0.35
34 10 0.29
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (32 bp):
TTATATAAAATTTAAATATATTAATATTAATA
Found at i:4268761 original size:11 final size:11
Alignment explanation
Indices: 4268745--4268777 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4268735 AAATATGTTA
4268745 ATATTTATATT
1 ATATTTATATT
4268756 ATATTTATATT
1 ATATTTATATT
4268767 AT-TTTAATATT
1 ATATTT-ATATT
4268778 TTAAGTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 3 0.14
11 18 0.86
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTTATATT
Found at i:4269917 original size:2 final size:2
Alignment explanation
Indices: 4269875--4269902 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4269865 CCTGCCACGA
4269875 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
4269903 GCATATGCAT
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:4270270 original size:28 final size:27
Alignment explanation
Indices: 4270230--4270292 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
4270220 TGTTAATTTT
4270230 TAATAAAATTAAAAAATTTTATTTAATA
1 TAATAAAATT-AAAAATTTTATTTAATA
* *
4270258 TAATAATAA-TAAAACTTTTATTTTATA
1 TAATAA-AATTAAAAATTTTATTTAATA
4270285 TAA-AAAAT
1 TAATAAAAT
4270293 ATATTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 2 0.06
26 2 0.06
27 18 0.58
28 7 0.23
29 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATAAAATTAAAAATTTTATTTAATA
Found at i:4270757 original size:11 final size:11
Alignment explanation
Indices: 4270722--4270760 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4270712 TATTTTAATA
4270722 ATATTTAAAAT
1 ATATTTAAAAT
*
4270733 ATTATATAAAAT
1 A-TATTTAAAAT
*
4270745 ATATTTTAAAT
1 ATATTTAAAAT
4270756 ATATT
1 ATATT
4270761 ATATAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATATTTAAAAT
Found at i:4270765 original size:25 final size:28
Alignment explanation
Indices: 4270725--4270789 Score: 86
Period size: 25 Copynumber: 2.5 Consensus size: 28
4270715 TTTAATAATA
4270725 TTTAAA-ATATTATATAA-A-AT-ATAT
1 TTTAAATATATTATATAATATATCATAT
4270749 TTTAAATATATTATATAATTATATCATAT
1 TTTAAATATATTATATAA-TATATCATAT
4270778 TTTAAAT-TATTA
1 TTTAAATATATTA
4270790 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
24 6 0.17
25 11 0.31
27 1 0.03
28 7 0.19
29 11 0.31
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTAAATATATTATATAATATATCATAT
Found at i:4271982 original size:6 final size:6
Alignment explanation
Indices: 4271948--4271979 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
4271938 CCTTTTCACT
*
4271948 GCAAAA GCAAAA GCAAAA GCAAAA GCGAAA GC
1 GCAAAA GCAAAA GCAAAA GCAAAA GCAAAA GC
4271980 GAATGAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.59, C:0.19, G:0.22, T:0.00
Consensus pattern (6 bp):
GCAAAA
Found at i:4276671 original size:5 final size:5
Alignment explanation
Indices: 4276661--4276691 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
4276651 TTAAAACCCC
*
4276661 TCTTT TCTTT TCTTT TCTTT TCTAT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
4276692 ATTTGGTGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:4278636 original size:27 final size:27
Alignment explanation
Indices: 4278606--4278658 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
4278596 AAATATTTTA
4278606 ATTTTATAAATAAATTTAAAAATTATT
1 ATTTTATAAATAAATTTAAAAATTATT
* * *
4278633 ATTTTTTAAATATATTTAAAAGTTAT
1 ATTTTATAAATAAATTTAAAAATTAT
4278659 ATGTTACATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
ATTTTATAAATAAATTTAAAAATTATT
Found at i:4278971 original size:6 final size:6
Alignment explanation
Indices: 4278960--4279000 Score: 73
Period size: 6 Copynumber: 6.7 Consensus size: 6
4278950 GCGGCATATG
4278960 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT CTTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT -TTTT
4279001 TGCTCCAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:4279152 original size:14 final size:14
Alignment explanation
Indices: 4279129--4279158 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4279119 AGTTTTATGT
*
4279129 ATTATTTAAATATA
1 ATTATATAAATATA
4279143 ATTATATAAATATA
1 ATTATATAAATATA
4279157 AT
1 AT
4279159 ATAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTATATAAATATA
Found at i:4279242 original size:25 final size:25
Alignment explanation
Indices: 4279183--4279243 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
4279173 TATGTTATAA
* *
4279183 ATAAATA-AATATTTTAAGATTTAT
1 ATAAATATAATATATTAAAATTTAT
*
4279207 A-AATTATTAATATATTAAAATTTAT
1 ATAAATA-TAATATATTAAAATTTAT
4279232 ATAAATATAATA
1 ATAAATATAATA
4279244 AAAATATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 4 0.13
24 1 0.03
25 21 0.70
26 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATAAATATAATATATTAAAATTTAT
Found at i:4282032 original size:3 final size:3
Alignment explanation
Indices: 4282024--4282068 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
4282014 GAAGTTCTTG
4282024 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4282069 CGTGAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4283204 original size:19 final size:19
Alignment explanation
Indices: 4283164--4283201 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4283154 AATATGTTTG
*
4283164 TATAAAAATATTTAATTTT
1 TATAAAAATATTCAATTTT
4283183 TATAAAAATA-TCAATTTT
1 TATAAAAATATTCAATTTT
4283201 T
1 T
4283202 TATTAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TATAAAAATATTCAATTTT
Found at i:4283902 original size:2 final size:2
Alignment explanation
Indices: 4283895--4283947 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
4283885 ACTATCTAAG
* *
4283895 AT AT AT AT AT AT AT AT AT AT -T AA AT AT TT 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
4283936 AT AT AT AT AT AT
1 AT AT AT AT AT AT
4283948 TCAATTTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4284886 original size:2 final size:2
Alignment explanation
Indices: 4284845--4284875 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4284835 AACTTGTATT
4284845 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 T
4284876 TCTCTTATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4285852 original size:27 final size:27
Alignment explanation
Indices: 4285796--4285852 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
4285786 GCCATCAATT
* *
4285796 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
* * *
4285823 TTGAAATTTAATTTGAAACGGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
4285850 TTG
1 TTG
4285853 CATAGTACCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.37
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:4285917 original size:9 final size:9
Alignment explanation
Indices: 4285903--4285935 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4285893 AGAAGGCTCA
4285903 AGCAGAGAC
1 AGCAGAGAC
4285912 AGCAGAGAC
1 AGCAGAGAC
*
4285921 AGCAGAGAT
1 AGCAGAGAC
4285930 AGCAGA
1 AGCAGA
4285936 AAGAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:4290631 original size:27 final size:27
Alignment explanation
Indices: 4290575--4290631 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
4290565 GCCGTCAATT
* *
4290575 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
* *
4290602 TTGAAATTTAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
4290629 TTG
1 TTG
4290632 CATAGTACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:4290696 original size:9 final size:9
Alignment explanation
Indices: 4290682--4290714 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4290672 AGAAGGCTCA
4290682 AGCAGAGAC
1 AGCAGAGAC
4290691 AGCAGAGAC
1 AGCAGAGAC
*
4290700 AGCAGAGAT
1 AGCAGAGAC
4290709 AGCAGA
1 AGCAGA
4290715 AAGAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:4292963 original size:20 final size:20
Alignment explanation
Indices: 4292940--4292980 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4292930 ATATTTTTTA
*
4292940 TATAATAAATATATTTAAAT
1 TATAATAAATATATATAAAT
* *
4292960 TATAATATATTTATATAAAT
1 TATAATAAATATATATAAAT
4292980 T
1 T
4292981 TTGATACGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAATAAATATATATAAAT
Found at i:4293872 original size:2 final size:2
Alignment explanation
Indices: 4293865--4293911 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4293855 GAAACCAGTG
4293865 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
4293907 TA TA T
1 TA TA T
4293912 CAATGGTGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4294147 original size:2 final size:2
Alignment explanation
Indices: 4294140--4294180 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4294130 TTTTAATACC
*
4294140 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4294181 AGCCTAACCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4295114 original size:5 final size:5
Alignment explanation
Indices: 4295104--4295129 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4295094 ATAATAGAAA
4295104 GGGAG GGGAG GGGAG GGGAG GGGAG G
1 GGGAG GGGAG GGGAG GGGAG GGGAG G
4295130 TGGGGGGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:4295439 original size:18 final size:17
Alignment explanation
Indices: 4295413--4295446 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4295403 ATTGTAAATA
*
4295413 TAAAGTTAAAATGTTAAT
1 TAAAATTAAAAT-TTAAT
4295431 TAAAATTAAAATTTAA
1 TAAAATTAAAATTTAA
4295447 CGAGTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
TAAAATTAAAATTTAAT
Found at i:4306560 original size:2 final size:2
Alignment explanation
Indices: 4306553--4306592 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4306543 TTTTCCATGA
4306553 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
4306593 GTTTGAATAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4306989 original size:24 final size:24
Alignment explanation
Indices: 4306961--4307020 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
4306951 TTTTTATTTA
4306961 AATTTAATTATAAA-AATATATAAAT
1 AATTT-ATTATAAATAATATAT-AAT
* * *
4306986 ATTTTATTAAAAATAATTTATAAT
1 AATTTATTATAAATAATATATAAT
4307010 AATTTATTATA
1 AATTTATTATA
4307021 TTTTAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 19 0.66
25 10 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTTATTATAAATAATATATAAT
Found at i:4307007 original size:35 final size:32
Alignment explanation
Indices: 4306968--4307037 Score: 77
Period size: 35 Copynumber: 2.1 Consensus size: 32
4306958 TTAAATTTAA
4306968 TTATAAAAATATATAAATATTTTATTAAAAATAAT
1 TTATAAAAATATAT-AATATTTTA--AAAAATAAT
* * * *
4307003 TTATAATAATTTATTATATTTTAAATAATAAT
1 TTATAAAAATATATAATATTTTAAAAAATAAT
4307035 TTA
1 TTA
4307038 AGTCATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 11 0.35
34 8 0.26
35 12 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TTATAAAAATATATAATATTTTAAAAAATAAT
Found at i:4307734 original size:3 final size:3
Alignment explanation
Indices: 4307726--4307754 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4307716 ATTACTATAC
4307726 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4307755 CTATGAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:4308468 original size:20 final size:21
Alignment explanation
Indices: 4308445--4308484 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4308435 TTTTATTGAT
4308445 ATTAA-AATTTTATTTAAAAG
1 ATTAATAATTTTATTTAAAAG
*
4308465 ATTAATATTTTTATTTAAAA
1 ATTAATAATTTTATTTAAAA
4308485 TAAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
ATTAATAATTTTATTTAAAAG
Found at i:4310465 original size:24 final size:24
Alignment explanation
Indices: 4310417--4310538 Score: 98
Period size: 24 Copynumber: 5.2 Consensus size: 24
4310407 TTTTGTATAA
** *
4310417 ATTATAATTATA-TTTAAAATGTT
1 ATTATAATTATATTTTAATTTATT
4310440 ATTATACATTA-ATTTTAATTTATT
1 ATTATA-ATTATATTTTAATTTATT
*
4310464 ATTA-AATTATATATTTATTTTATT
1 ATTATAATTATAT-TTTAATTTATT
*
4310488 TTTATAA-TATATTTTAA-TTATT
1 ATTATAATTATATTTTAATTTATT
*
4310510 TTTAT-ATTA-A-TTTAATTTATAT
1 ATTATAATTATATTTTAATTTAT-T
4310532 AATTATA
1 -ATTATA
4310539 TTTAAAATTT
Statistics
Matches: 82, Mismatches: 7, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
20 5 0.06
21 6 0.07
22 17 0.21
23 18 0.22
24 34 0.41
25 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (24 bp):
ATTATAATTATATTTTAATTTATT
Found at i:4310491 original size:11 final size:11
Alignment explanation
Indices: 4310477--4310518 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
4310467 AAATTATATA
*
4310477 TTTATTTTATT
1 TTTATATTATT
*
4310488 TTTATAATATAT
1 TTTATATTAT-T
4310500 TTTA-ATTATT
1 TTTATATTATT
4310510 TTTATATTA
1 TTTATATTA
4310519 ATTTAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 5 0.19
11 16 0.62
12 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATATTATT
Found at i:4310500 original size:22 final size:22
Alignment explanation
Indices: 4310472--4310529 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
4310462 TTATTAAATT
4310472 ATATATTTATTTTATTTTTATA
1 ATATATTTATTTTATTTTTATA
*
4310494 ATATATTT-TAATTATTTTTATA
1 ATATATTTAT-TTTATTTTTATA
* *
4310516 TTA-ATTTAATTTAT
1 ATATATTTATTTTAT
4310530 ATAATTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATATATTTATTTTATTTTTATA
Found at i:4310521 original size:15 final size:15
Alignment explanation
Indices: 4310501--4310542 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4310491 ATAATATATT
*
4310501 TTAATTATTTTTATA
1 TTAATTATATTTATA
4310516 TTAATT-TAATTTATA
1 TTAATTAT-ATTTATA
4310531 -TAATTATATTTA
1 TTAATTATATTTA
4310543 AAATTTTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATTATATTTATA
Found at i:4310776 original size:16 final size:17
Alignment explanation
Indices: 4310755--4310799 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
4310745 ATCATGTTCG
*
4310755 TATTTAATATATTTT-A
1 TATTTAATAAATTTTAA
4310771 TATTTATATAAATTTTAA
1 TATTTA-ATAAATTTTAA
4310789 TATATTAATAA
1 TAT-TTAATAA
4310800 TATATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
18 8 0.32
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTAATAAATTTTAA
Found at i:4310794 original size:20 final size:21
Alignment explanation
Indices: 4310769--4310808 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4310759 TAATATATTT
*
4310769 TATATTTAT-ATAAATTTTAA
1 TATATTAATAATAAATTTTAA
*
4310789 TATATTAATAATATATTTTA
1 TATATTAATAATAAATTTTA
4310809 TGTAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTAATAATAAATTTTAA
Found at i:4313551 original size:17 final size:17
Alignment explanation
Indices: 4313510--4313554 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
4313500 TATGTTTTTC
*
4313510 ATGGGTTGGGTAGGATA
1 ATGGGTTGGGTAGAATA
* *
4313527 ATTGGGTTGGGTATAATG
1 A-TGGGTTGGGTAGAATA
4313545 ATGGGTTGGG
1 ATGGGTTGGG
4313555 ATTGGTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (17 bp):
ATGGGTTGGGTAGAATA
Found at i:4314149 original size:303 final size:305
Alignment explanation
Indices: 4313564--4314150 Score: 860
Period size: 303 Copynumber: 1.9 Consensus size: 305
4313554 GATTGGTTGA
* * * * *
4313564 TATAATCCTCTGGACTTCATGGAGAATGAAACTCCTTATTCAGGAGATATAGAGGTCTACATGCA
1 TATAATCCGCTGGACTTCAAGGAGAATAAAACTCCTTATTCAGGAGATATAGACGTATACATGCA
*
4313629 TTGTCTTAATACATTTAATATTATAAAACTTTCTGATAGTTGATTTAGTATCCATGGATATTCTT
66 TTCTCTTAATACATTTAATATTATAAAACTTTCTGATAGTTGATTTAGTATCCATGGATATTCTT
* * * * *
4313694 TGATCACCAAGCCGGCCAAACTTTACGTAAGCAACTAAAACAACTGAACCGAAATTTAATCAATT
131 AGATCACCAAGCCAGACAAACTTTACGTAAGCAACCAAAACAACCGAACCGAAATTTAATCAATT
* * *
4313759 CAGTTTGGTCGGTTATGTTGTTCATGGGTTGGATAGGATAATTGGATTGAATATGAGTAGTATAA
196 CAGTTCGGTCGGTTATATTGTTCATGGGTTGGATAGGACAATTGGATTGAATATGAGTAGTATAA
*
4313824 TGATGGGTTGGAATTGGTTAATATTAAAATGTGTAGTGAAAAGGT
261 TGATGGGTTGGAATTCGTTAATATTAAAATGTGTAGTGAAAAGGT
4313869 TATAATCCGCTGGGACTTCAAGGAGAATAAAACTCCTTATTCAGGAGATATAGACGTATACATGC
1 TATAATCCGCT-GGACTTCAAGGAGAATAAAACTCCTTATTCAGGAGATATAGACGTATACATGC
* * *
4313934 ATTCTCTT-ATATATTTAATATTATAAAACTTTCTGATAGTTGATTTAGTGTCCATGGATCTTCT
65 ATTCTCTTAATACATTTAATATTATAAAACTTTCTGATAGTTGATTTAGTATCCATGGATATTCT
* **
4313998 TAGATCA-CAAGCCAGACAAACTTTATGTAAGCAACCAAAACAACCGAATTGAAA-TTAATCAAT
130 TAGATCACCAAGCCAGACAAACTTTACGTAAGCAACCAAAACAACCGAACCGAAATTTAATCAAT
* * * *
4314061 TCAGTTCGGTCGGTTATATCTG-TCATGGGTTGGGTAGGACAATTGGGTTGAGTATGGGTAGTAT
195 TCAGTTCGGTCGGTTATAT-TGTTCATGGGTTGGATAGGACAATTGGATTGAATATGAGTAGTAT
* * *
4314125 AGTTATGGGTTGG-GTATCGTTAATAT
259 AATGATGGGTTGGAAT-TCGTTAATAT
4314151 AAATAAAATT
Statistics
Matches: 251, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
302 1 0.00
303 83 0.33
304 42 0.17
305 69 0.27
306 56 0.22
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.34
Consensus pattern (305 bp):
TATAATCCGCTGGACTTCAAGGAGAATAAAACTCCTTATTCAGGAGATATAGACGTATACATGCA
TTCTCTTAATACATTTAATATTATAAAACTTTCTGATAGTTGATTTAGTATCCATGGATATTCTT
AGATCACCAAGCCAGACAAACTTTACGTAAGCAACCAAAACAACCGAACCGAAATTTAATCAATT
CAGTTCGGTCGGTTATATTGTTCATGGGTTGGATAGGACAATTGGATTGAATATGAGTAGTATAA
TGATGGGTTGGAATTCGTTAATATTAAAATGTGTAGTGAAAAGGT
Found at i:4327948 original size:24 final size:23
Alignment explanation
Indices: 4327921--4327968 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
4327911 ACGCAACAAA
*
4327921 AGCAACAG-CAGCAAGAGCACGAAG
1 AGCAACAGACA-CAACAGCA-GAAG
4327945 AGCAACAGACACAACAGCAGAAG
1 AGCAACAGACACAACAGCAGAAG
4327968 A
1 A
4327969 AGATGAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 15 0.68
25 2 0.09
ACGTcount: A:0.50, C:0.25, G:0.25, T:0.00
Consensus pattern (23 bp):
AGCAACAGACACAACAGCAGAAG
Found at i:4328777 original size:11 final size:12
Alignment explanation
Indices: 4328761--4328789 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4328751 GTCCTTAAAG
4328761 TCCAAAA-CATC
1 TCCAAAATCATC
4328772 TCCAAAATCATC
1 TCCAAAATCATC
4328784 TCCAAA
1 TCCAAA
4328790 TTCGAAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (12 bp):
TCCAAAATCATC
Found at i:4334111 original size:37 final size:37
Alignment explanation
Indices: 4334068--4334217 Score: 300
Period size: 37 Copynumber: 4.1 Consensus size: 37
4334058 ATGCATGTTA
4334068 AGGATTTAATCAAAGGAGAGAGCAGGCTAAGATGAGT
1 AGGATTTAATCAAAGGAGAGAGCAGGCTAAGATGAGT
4334105 AGGATTTAATCAAAGGAGAGAGCAGGCTAAGATGAGT
1 AGGATTTAATCAAAGGAGAGAGCAGGCTAAGATGAGT
4334142 AGGATTTAATCAAAGGAGAGAGCAGGCTAAGATGAGT
1 AGGATTTAATCAAAGGAGAGAGCAGGCTAAGATGAGT
4334179 AGGATTTAATCAAAGGAGAGAGCAGGCTAAGATGAGT
1 AGGATTTAATCAAAGGAGAGAGCAGGCTAAGATGAGT
4334216 AG
1 AG
4334218 AACTAGAACT
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 113 1.00
ACGTcount: A:0.41, C:0.08, G:0.33, T:0.19
Consensus pattern (37 bp):
AGGATTTAATCAAAGGAGAGAGCAGGCTAAGATGAGT
Found at i:4339283 original size:19 final size:19
Alignment explanation
Indices: 4339243--4339285 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4339233 GATAATCAGC
* *
4339243 ATAAATTAAAATAATATTT
1 ATAAATAAAAATAATATAT
4339262 ATAAATAAAAATATATAATAT
1 ATAAATAAAAATA-AT-ATAT
4339283 ATA
1 ATA
4339286 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAAATAAAAATAATATAT
Found at i:4340247 original size:17 final size:17
Alignment explanation
Indices: 4340227--4340293 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 17
4340217 ATATCACTCA
4340227 ATTAAATATATATTTTT
1 ATTAAATATATATTTTT
* *
4340244 ATTAAATATTTA-TTAT
1 ATTAAATATATATTTTT
* *
4340260 ATTTAATAT-TTTTTTACT
1 ATTAAATATATATTTT--T
4340278 ATTAAATTATATATTT
1 ATTAAA-TATATATTT
4340294 AATATTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
15 1 0.03
16 13 0.34
17 11 0.29
18 6 0.16
19 3 0.08
20 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTAAATATATATTTTT
Found at i:4340661 original size:14 final size:14
Alignment explanation
Indices: 4340642--4340668 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4340632 AGGCATCTTA
4340642 AAATTTAATTTAAC
1 AAATTTAATTTAAC
4340656 AAATTTAATTTAA
1 AAATTTAATTTAA
4340669 ATTTAAGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTAATTTAAC
Found at i:4341034 original size:20 final size:22
Alignment explanation
Indices: 4341009--4341049 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
4340999 ATATTAGTAT
4341009 TTATTTTT-TAAA-AAAAAATA
1 TTATTTTTATAAAGAAAAAATA
4341029 TTATTTTTATAAAGAAAAAAT
1 TTATTTTTATAAAGAAAAAAT
4341050 TCTTCATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTATTTTTATAAAGAAAAAATA
Found at i:4341260 original size:19 final size:18
Alignment explanation
Indices: 4341210--4341272 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
4341200 AAATTAAGCG
*
4341210 ATATAAATTTAATTAAAAA
1 ATATATATTT-ATTAAAAA
*
4341229 AT-TATA--TAATAAATAA
1 ATATATATTTATTAAA-AA
*
4341245 ATATATATTTATTAAAAT
1 ATATATATTTATTAAAAA
*
4341263 ATTTATATTT
1 ATATATATTT
4341273 TTTATTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
15 5 0.14
16 5 0.14
17 4 0.11
18 13 0.37
19 8 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATATATTTATTAAAAA
Found at i:4341587 original size:17 final size:17
Alignment explanation
Indices: 4341554--4341585 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4341544 AGTTATTAAT
4341554 TTTATTTTTATTATTTA
1 TTTATTTTTATTATTTA
4341571 TTTATTTTTA-TATTT
1 TTTATTTTTATTATTT
4341586 TAATAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTTATTATTTA
Found at i:4341796 original size:14 final size:15
Alignment explanation
Indices: 4341767--4341807 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
4341757 AATCTTATGA
*
4341767 ATTAAATGATATAAAT
1 ATTAAATGA-AAAAAT
4341783 -TTAAATGAAAAAAT
1 ATTAAATGAAAAAAT
4341797 ATTAAAT-AAAA
1 ATTAAATGAAAA
4341808 TATTAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
ATTAAATGAAAAAAT
Found at i:4346724 original size:6 final size:7
Alignment explanation
Indices: 4346702--4346727 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4346692 TTTTAAGTAT
4346702 AAATTAA
1 AAATTAA
4346709 AAATTAA
1 AAATTAA
4346716 AAATTAA
1 AAATTAA
4346723 AAATT
1 AAATT
4346728 TATTTAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATTAA
Found at i:4346768 original size:29 final size:29
Alignment explanation
Indices: 4346709--4346785 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
4346699 TATAAATTAA
*
4346709 AAATTAAAAATTAAAAATTTATTTAAACAT
1 AAATTAAAAATT-AAACTTTATTTAAACAT
* * *
4346739 AAATTCAAACTTAAACTTTATTTAAGCAT
1 AAATTAAAAATTAAACTTTATTTAAACAT
4346768 AAATTAAAAATTAAACTT
1 AAATTAAAAATTAAACTT
4346786 GAATAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 31 0.76
30 10 0.24
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.36
Consensus pattern (29 bp):
AAATTAAAAATTAAACTTTATTTAAACAT
Found at i:4354969 original size:31 final size:31
Alignment explanation
Indices: 4354934--4354992 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
4354924 TGATAATAGA
* *
4354934 TAATCAATTGAAAGGTATTTGTGGTAAAATT
1 TAATCAATTGAAAGGTAATTGTAGTAAAATT
* *
4354965 TAATCAGTTGAAGGGTAATTGTAGTAAA
1 TAATCAATTGAAAGGTAATTGTAGTAAA
4354993 TGTCAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (31 bp):
TAATCAATTGAAAGGTAATTGTAGTAAAATT
Found at i:4356005 original size:17 final size:15
Alignment explanation
Indices: 4355975--4356034 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 15
4355965 ATATTTTAAA
4355975 ATTAATATATAAATT
1 ATTAATATATAAATT
4355990 ATTAATATATTAAAATTT
1 ATTAATATA-T-AAA-TT
4356008 ATATAA-ATATAAATAT
1 AT-TAATATATAAAT-T
*
4356024 TTTAA-ATATAA
1 ATTAATATATAA
4356035 TATACAATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 19 0.49
16 6 0.15
17 4 0.10
18 7 0.18
19 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAATATATAAATT
Found at i:4356396 original size:17 final size:17
Alignment explanation
Indices: 4356374--4356406 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4356364 TTAGATTAGG
4356374 TTATTAT-TATTATTTTA
1 TTATTATATA-TATTTTA
4356391 TTATTATATATATTTT
1 TTATTATATATATTTT
4356407 TTGCAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTATATATATTTTA
Found at i:4356636 original size:2 final size:2
Alignment explanation
Indices: 4356631--4356655 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4356621 GCTCTTCAGA
4356631 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 A
4356656 AAAGAGCTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4357046 original size:25 final size:26
Alignment explanation
Indices: 4357004--4357057 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
4356994 AAATTTTAAA
*
4357004 AATAAATATAAATAATTTTATTT-TT
1 AATAAATATAAATAATTTAATTTATT
*
4357029 AATAAA-ATAACATTATTTAATTTATT
1 AATAAATATAA-ATAATTTAATTTATT
4357055 AAT
1 AAT
4357058 TTATTGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 16 0.64
26 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATAAATATAAATAATTTAATTTATT
Found at i:4359058 original size:37 final size:33
Alignment explanation
Indices: 4358991--4359059 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 33
4358981 TTTGATGAAT
4358991 TTCCATATAAAAATAAAAAAAATGGGATCTTTC
1 TTCCATATAAAAATAAAAAAAATGGGATCTTTC
4359024 TTCCATATACGAATAATAAACAAAAATGGGATCTTT
1 TTCCATATA--AA-AATAAA-AAAAATGGGATCTTT
4359060 TTTCAACCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 9 0.28
35 2 0.06
36 6 0.19
37 15 0.47
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.30
Consensus pattern (33 bp):
TTCCATATAAAAATAAAAAAAATGGGATCTTTC
Found at i:4360828 original size:2 final size:2
Alignment explanation
Indices: 4360823--4360862 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
4360813 AAATTTTTTA
* * *
4360823 AT AT AT AT AT TT AA AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4360863 GAGAAAATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4362479 original size:14 final size:13
Alignment explanation
Indices: 4362446--4362527 Score: 55
Period size: 14 Copynumber: 6.4 Consensus size: 13
4362436 TGATAATTTA
**
4362446 TTATATATAAATT
1 TTATATATTTATT
4362459 TTAATATATTTATAT
1 TT-ATATATTTAT-T
4362474 TTATATATTTATT
1 TTATATATTTATT
* *
4362487 TTATGT-TAATATT
1 TTATATAT-TTATT
**
4362500 TT-TATA-TTAAA
1 TTATATATTTATT
4362511 TTATAT-TTTATT
1 TTATATATTTATT
4362523 TTATA
1 TTATA
4362528 ATATAATTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
11 4 0.08
12 14 0.26
13 14 0.26
14 18 0.34
15 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (13 bp):
TTATATATTTATT
Found at i:4362497 original size:33 final size:36
Alignment explanation
Indices: 4362459--4362526 Score: 97
Period size: 33 Copynumber: 2.0 Consensus size: 36
4362449 TATATAAATT
*
4362459 TTAATATATTTATATT-TA-TATA-TTTATTTTATG
1 TTAATATATTTATATTAAATTATATTTTATTTTATG
*
4362492 TTAATATTTTTATATTAAATTATATTTTATTTTAT
1 TTAATATATTTATATTAAATTATATTTTATTTTAT
4362527 AATATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 15 0.50
34 1 0.03
35 4 0.13
36 10 0.33
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (36 bp):
TTAATATATTTATATTAAATTATATTTTATTTTATG
Found at i:4362498 original size:19 final size:17
Alignment explanation
Indices: 4362467--4362532 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 17
4362457 TTTTAATATA
4362467 TTTATATTTATATATTTAT
1 TTTATA-TTATAT-TTTAT
*
4362486 TTTATGTTAATATTTTTAT
1 TTTATATT-ATA-TTTTAT
* *
4362505 ATTAAATTATATTTTAT
1 TTTATATTATATTTTAT
*
4362522 TTTATAATATA
1 TTTATATTATA
4362533 ATTAATTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
17 14 0.37
18 5 0.13
19 18 0.47
20 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTATATTATATTTTAT
Found at i:4363398 original size:18 final size:20
Alignment explanation
Indices: 4363377--4363419 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
4363367 TTTATAGATG
4363377 TTTATTAATTTT-A-TTTTT
1 TTTATTAATTTTCACTTTTT
4363395 TTTATTAATTTTCACTTTTT
1 TTTATTAATTTTCACTTTTT
4363415 TTTAT
1 TTTAT
4363420 ATGATCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 12 0.52
19 1 0.04
20 10 0.43
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTAATTTTCACTTTTT
Found at i:4364102 original size:15 final size:15
Alignment explanation
Indices: 4364076--4364113 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4364066 TTAAATTTAT
4364076 TAAATAAATAAAAATAA
1 TAAAT-AAT-AAAATAA
4364093 -AAATAATAAAATAA
1 TAAATAATAAAATAA
4364107 TAAATAA
1 TAAATAA
4364114 GATAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.35
15 9 0.45
16 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAATAATAAAATAA
Found at i:4364375 original size:21 final size:21
Alignment explanation
Indices: 4364354--4364403 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
4364344 ATATATTTTT
4364354 ATTTAAAATATAAATTAATTTA
1 ATTTAAAATATAAATT-ATTTA
* *
4364376 ATATAAAATATATATTATTTA
1 ATTTAAAATATAAATTATTTA
4364397 ATTTAAA
1 ATTTAAA
4364404 TCTACACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTTAAAATATAAATTATTTA
Found at i:4365579 original size:28 final size:27
Alignment explanation
Indices: 4365540--4365613 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 27
4365530 TTGAAATATT
* *
4365540 TAATTTTTATTTTAATATATAAATATA
1 TAATTATTATTTTAATATATAAATAAA
*
4365567 T-ATTAAATTATTTTAAATATTTAAATAAA
1 TAATT--ATTATTTT-AATATATAAATAAA
4365596 TAATTATTA-TTTAATATA
1 TAATTATTATTTTAATATA
4365614 ATTGAAGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
26 8 0.21
27 4 0.10
28 11 0.28
29 13 0.33
30 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TAATTATTATTTTAATATATAAATAAA
Found at i:4365910 original size:17 final size:17
Alignment explanation
Indices: 4365878--4365951 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 17
4365868 TTAATTTTTT
4365878 ATATATAAATATTAATTTA
1 ATAT-TAAATA-TAATTTA
4365897 ATATTAAATATAATTAATA
1 ATATTAAATATAATT--TA
*
4365916 ATTAATAAATATATATTTA
1 A-TATTAAATATA-ATTTA
4365935 AT-TTAATGATATAATTT
1 ATATTAA--ATATAATTT
4365952 TTAATATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
17 8 0.17
18 11 0.23
19 15 0.32
20 10 0.21
21 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (17 bp):
ATATTAAATATAATTTA
Found at i:4365931 original size:24 final size:24
Alignment explanation
Indices: 4365877--4365931 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
4365867 ATTAATTTTT
* *
4365877 TATATATAAATATTAATTTAATAT
1 TATATATAAATAATAATTTAATAA
* *
4365901 TAAATATAATTAATAA-TTAATAAA
1 TATATATAAATAATAATTTAAT-AA
4365925 TATATAT
1 TATATAT
4365932 TTAATTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATATATAAATAATAATTTAATAA
Found at i:4365941 original size:24 final size:23
Alignment explanation
Indices: 4365880--4365941 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 23
4365870 AATTTTTTAT
*
4365880 ATATAAATATTAATTTAA-TATTAA
1 ATAT-AAT-TTAATTTAATTAATAA
4365904 ATATAATT-AA--TAATTAATAA
1 ATATAATTTAATTTAATTAATAA
4365924 ATATATATTTAATTTAAT
1 ATATA-ATTTAATTTAAT
4365942 GATATAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
19 3 0.09
20 10 0.31
21 5 0.16
22 3 0.09
23 3 0.09
24 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAATTTAATTTAATTAATAA
Found at i:4365977 original size:21 final size:21
Alignment explanation
Indices: 4365947--4365993 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4365937 TTAATGATAT
*
4365947 AATTT-TTAA-TATAAAATTAA
1 AATTTATTAATTAT-AAATAAA
4365967 AATTTATTAATTATAAATAAA
1 AATTTATTAATTATAAATAAA
4365988 AATTTA
1 AATTTA
4365994 GAAATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 16 0.67
22 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTATTAATTATAAATAAA
Found at i:4366003 original size:22 final size:22
Alignment explanation
Indices: 4365954--4366003 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
4365944 TATAATTTTT
* **
4365954 AATATA-AAATTAAAATTTATT
1 AATATATAAATAAAAATTTAGA
4365975 AAT-TATAAATAAAAATTTAGA
1 AATATATAAATAAAAATTTAGA
4365996 AATATATA
1 AATATATA
4366004 TAATTGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AATATATAAATAAAAATTTAGA
Found at i:4366922 original size:32 final size:35
Alignment explanation
Indices: 4366884--4366963 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 35
4366874 TATTATATTT
4366884 ATATATTTTATTATATTA-TAATTTTAAT-TA-AA
1 ATATATTTTATTATATTATTAATTTTAATATATAA
*
4366916 ATATA-TTTATT-TA-TATTAATTTTAATATATTA
1 ATATATTTTATTATATTATTAATTTTAATATATAA
4366948 ATA-ATTTATATTATAT
1 ATATATTT-TATTATAT
4366964 AAAATTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
29 2 0.05
30 12 0.30
31 9 0.22
32 11 0.28
33 4 0.10
34 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (35 bp):
ATATATTTTATTATATTATTAATTTTAATATATAA
Found at i:4366964 original size:20 final size:19
Alignment explanation
Indices: 4366861--4366963 Score: 68
Period size: 19 Copynumber: 5.1 Consensus size: 19
4366851 AAATTTAATA
4366861 ATTTAATAATTTATATTAT
1 ATTTAATAATTTATATTAT
*
4366880 ATTTATATATTTTATTATATTAT
1 ATTTA-ATA--AT-TTATATTAT
**
4366903 AATTTTAATTAAAATATATT-T
1 -A-TTTAA-TAATTTATATTAT
*
4366924 ATTTATATTAATTT-TAATAT
1 ATTTA-A-TAATTTATATTAT
4366944 A-TTAATAATTTATATTAT
1 ATTTAATAATTTATATTAT
4366962 AT
1 AT
4366964 AAAATTAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
17 6 0.09
18 7 0.11
19 15 0.23
20 12 0.18
21 1 0.02
22 7 0.11
23 9 0.14
24 2 0.03
25 6 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTAATAATTTATATTAT
Found at i:4366964 original size:44 final size:44
Alignment explanation
Indices: 4366855--4366964 Score: 122
Period size: 44 Copynumber: 2.5 Consensus size: 44
4366845 AAAAATAAAT
*
4366855 TTAATAATTTAATAATT-TATATTATATTTATATATTTTATTATA
1 TTAATAATTT-ATAATTATATATTATATTTATATATTTTAATATA
4366899 TT-ATAATTT-TAATTAAAATATATT-TATTTATATTAATTTTAATATA
1 TTAATAATTTATAATT---ATATATTATATTTATA-T-ATTTTAATATA
4366945 TTAATAATTTAT-ATTATATA
1 TTAATAATTTATAATTATATA
4366965 AAATTAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
41 5 0.09
43 7 0.12
44 15 0.26
45 7 0.12
46 12 0.21
47 10 0.18
48 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (44 bp):
TTAATAATTTATAATTATATATTATATTTATATATTTTAATATA
Found at i:4367002 original size:20 final size:18
Alignment explanation
Indices: 4366980--4367051 Score: 61
Period size: 15 Copynumber: 4.4 Consensus size: 18
4366970 AAAAAAATAT
4366980 TTTTATCATATATTAATTA
1 TTTTAT-ATATATTAATTA
4366999 TTTTATATATATT-A-TA
1 TTTTATATATATTAATTA
4367015 -TTTATATA-ATT-A-TA
1 TTTTATATATATTAATTA
* *
4367029 TTTAATAT-TATTAAAT-
1 TTTTATATATATTAATTA
4367045 TTTTATA
1 TTTTATA
4367052 GGGTGTGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
14 6 0.13
15 17 0.36
16 9 0.19
17 2 0.04
18 7 0.15
19 6 0.13
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATATATATTAATTA
Found at i:4367005 original size:14 final size:14
Alignment explanation
Indices: 4366988--4367051 Score: 67
Period size: 14 Copynumber: 4.4 Consensus size: 14
4366978 ATTTTTATCA
4366988 TATATTAATTAT-TT
1 TATA-TAATTATATT
4367002 TATATATATTATATT
1 TATATA-ATTATATT
4367017 TATATAATTATATT
1 TATATAATTATATT
* *
4367031 TAATATTATTAAATT
1 T-ATATAATTATATT
*
4367046 TTTATA
1 TATATA
4367052 GGGTGTGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
13 2 0.05
14 21 0.49
15 20 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATATAATTATATT
Found at i:4367620 original size:231 final size:221
Alignment explanation
Indices: 4367363--4367788 Score: 479
Period size: 231 Copynumber: 1.9 Consensus size: 221
4367353 CCATATTGTG
* * *
4367363 TATTTTTCTAAAATTCGATGTTGAATGTGAAAAAGGAATTTTA-T-AT-AATTGTATTTTCAAAT
1 TATTTTTCTAAAATTCCATATTGAATGTGAAAAAGGAATTTTAGTGATAAATTCTATTTTCAAAT
*
4367425 TTTA-TCTCCAAAGGTGAAATTTATGAAATTTTTTATTTGTTTACTAAGATATCGAC-ATTTTAC
66 TTCATTC-CCAAAGGTGAAATTTATG-AA---TTT-TTT-TTTACT--G--A--GACTA-TTT--
* * * *
4367488 TATTTTTAACGCAATTATTA-TTTTTTAATTTTAA-TTAAAAATTTATTTTAAATATTTTTTTAA
115 T-TTATTAACGCAATTATTATTTTTTTAATTTTAACTAAAAAATTAATTTTAAATATTCTTTTAA
4367551 TGTTATTATAAATACCTATACATTTTTAAAAACTTAATGACAT
179 TGTTATTATAAATACCTATACATTTTTAAAAACTTAATGACAT
* *** * *
4367594 TATTTTTCTTAAATTCCATATTGAATGTGAGTGATGAATTTTATGTGGCTCAAATTCTATTTTCA
1 TATTTTTCTAAAATTCCATATTGAATGTGAAAAAGGAATTTTA-GT-GAT-AAATTCTATTTTCA
* *
4367659 AATTTCATTCCCAAAGTTGAAATTTATGAATTTTTTTTTACTGAGACTATTTTTTATTAATGCAA
63 AATTTCATTCCCAAAGGTGAAATTTATGAATTTTTTTTTACTGAGACTATTTTTTATTAACGCAA
4367724 TTATTATTTTTTTAATTTTAACTAAAAAATTAATTTTAAATATTCTTTTAATGTTATTATAAATA
128 TTATTATTTTTTTAATTTTAACTAAAAAATTAATTTTAAATATTCTTTTAATGTTATTATAAATA
4367789 TATATATATA
Statistics
Matches: 169, Mismatches: 16, Indels: 27
0.80 0.08 0.13
Matches are distributed among these distances:
222 16 0.09
223 15 0.09
224 40 0.24
225 6 0.04
226 1 0.01
227 1 0.01
229 1 0.01
231 42 0.25
232 3 0.02
233 4 0.02
235 1 0.01
236 2 0.01
237 35 0.21
238 2 0.01
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (221 bp):
TATTTTTCTAAAATTCCATATTGAATGTGAAAAAGGAATTTTAGTGATAAATTCTATTTTCAAAT
TTCATTCCCAAAGGTGAAATTTATGAATTTTTTTTTACTGAGACTATTTTTTATTAACGCAATTA
TTATTTTTTTAATTTTAACTAAAAAATTAATTTTAAATATTCTTTTAATGTTATTATAAATACCT
ATACATTTTTAAAAACTTAATGACAT
Found at i:4369674 original size:2 final size:2
Alignment explanation
Indices: 4369667--4369705 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4369657 ATTTAAACAT
4369667 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 T
4369706 CCAATTCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4372883 original size:26 final size:28
Alignment explanation
Indices: 4372854--4372906 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
4372844 TTAAAGTTAA
4372854 TTTAATTTTACATTT-TTTAAT-AATTT
1 TTTAATTTTACATTTATTTAATCAATTT
**
4372880 TTTAATTTTTTATTTATTTAATCAATT
1 TTTAATTTTACATTTATTTAATCAATT
4372907 AGATCTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
27 6 0.26
28 4 0.17
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTAATTTTACATTTATTTAATCAATTT
Found at i:4377525 original size:20 final size:20
Alignment explanation
Indices: 4377497--4377553 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
4377487 TTTACATTTT
*
4377497 TTTAAATTTTTATAATACGA
1 TTTATATTTTTATAATACGA
*
4377517 TTTATATTTATT-TAATTCGA
1 TTTATATTT-TTATAATACGA
4377537 -TTATTATATTTTATAAT
1 TTTA-TAT-TTTTATAAT
4377554 TTACGTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 3 0.10
20 20 0.65
21 8 0.26
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTATATTTTTATAATACGA
Found at i:4379902 original size:14 final size:14
Alignment explanation
Indices: 4379883--4379952 Score: 59
Period size: 14 Copynumber: 4.6 Consensus size: 14
4379873 ATTTATATAC
4379883 TTTAATAATCATAA
1 TTTAATAATCATAA
*
4379897 TTTAATAATCAATGA
1 TTTAATAATC-ATAA
** *
4379912 TGAAATATATTTATATA
1 TTTAATA-A-TCATA-A
4379929 TTTTAATAATCATAA
1 -TTTAATAATCATAA
4379944 TTTAATAAT
1 TTTAATAAT
4379953 TAATGCCACG
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
14 19 0.44
15 9 0.21
16 7 0.16
17 3 0.07
18 5 0.12
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (14 bp):
TTTAATAATCATAA
Found at i:4379924 original size:47 final size:47
Alignment explanation
Indices: 4379868--4379957 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
4379858 TATTTTATGG
4379868 AATATATTTATATACTTTAATAATCATAATTTAATAATCAATGATGA
1 AATATATTTATATACTTTAATAATCATAATTTAATAATCAATGATGA
* *
4379915 AATATATTTATATATTTTAATAATCATAATTTAATAATTAATG
1 AATATATTTATATACTTTAATAATCATAATTTAATAATCAATG
4379958 CCACGACTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (47 bp):
AATATATTTATATACTTTAATAATCATAATTTAATAATCAATGATGA
Found at i:4380656 original size:2 final size:2
Alignment explanation
Indices: 4380649--4380679 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4380639 GACAAAAATA
4380649 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
4380680 AAGTTTTTCG
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:4383054 original size:2 final size:2
Alignment explanation
Indices: 4383047--4383085 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4383037 GCAAGGCACG
4383047 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 T
4383086 TTCCGGTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4384491 original size:15 final size:17
Alignment explanation
Indices: 4384473--4384505 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4384463 TATGAATGAA
4384473 TTAAT-TTAA-ATATAT
1 TTAATATTAATATATAT
4384488 TTAATATTAATATATAT
1 TTAATATTAATATATAT
4384505 T
1 T
4384506 AAAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 4 0.25
17 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAATATTAATATATAT
Found at i:4385772 original size:16 final size:17
Alignment explanation
Indices: 4385751--4385793 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
4385741 AAAATTTCAT
4385751 ATAAAATATTT-TCTTA
1 ATAAAATATTTATCTTA
4385767 ATAAAATTATTTACTCTTA
1 ATAAAA-TATTTA-TCTTA
4385786 A-AAAATAT
1 ATAAAATAT
4385794 CATTGCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.25
17 8 0.33
18 4 0.17
19 6 0.25
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATATTTATCTTA
Found at i:4385994 original size:19 final size:19
Alignment explanation
Indices: 4385964--4386000 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
4385954 TTTATTTAAT
4385964 ATAATAATATTA-TTAAAA
1 ATAATAATATTACTTAAAA
4385982 ATAATATATATTACTTAAA
1 ATAATA-ATATTACTTAAA
4386001 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 6 0.35
20 5 0.29
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAATAATATTACTTAAAA
Found at i:4386228 original size:10 final size:11
Alignment explanation
Indices: 4386202--4386293 Score: 67
Period size: 10 Copynumber: 9.0 Consensus size: 11
4386192 AAAAAAAAAA
*
4386202 AAAAGGAGAAGG
1 AAAA-GAGAAAG
4386214 AAAAGA-AAAG
1 AAAAGAGAAAG
**
4386224 AAAAGAGACTG
1 AAAAGAGAAAG
*
4386235 -AGAGAGAAAG
1 AAAAGAGAAAG
4386245 -AAAGAGAAAG
1 AAAAGAGAAAG
4386255 AGAAAGAGAAAG
1 A-AAAGAGAAAG
4386267 AAAA-A-AAA-
1 AAAAGAGAAAG
4386275 AAAA-A-AAAG
1 AAAAGAGAAAG
4386284 AAAAGA-AAAG
1 AAAAGAGAAAG
4386294 GGGGGAGGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
8 8 0.12
9 7 0.10
10 31 0.46
11 7 0.10
12 15 0.22
ACGTcount: A:0.72, C:0.01, G:0.26, T:0.01
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:4386252 original size:6 final size:6
Alignment explanation
Indices: 4386243--4386267 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4386233 TGAGAGAGAA
4386243 AGAAAG AGAAAG AGAAAG AGAAAG A
1 AGAAAG AGAAAG AGAAAG AGAAAG A
4386268 AAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:4386263 original size:26 final size:26
Alignment explanation
Indices: 4386215--4386291 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
4386205 AGGAGAAGGA
** *
4386215 AAAGAAAAGAAAAGAGACTGAGAGAG
1 AAAGAAAAGAAAAGAGAAAGAGAAAG
4386241 AAAG-AAAGAGAAAGAGAAAGAGAAAG
1 AAAGAAAAGA-AAAGAGAAAGAGAAAG
*
4386267 AAA-AAAA-AAAA-AAAAAGA-AAAG
1 AAAGAAAAGAAAAGAGAAAGAGAAAG
4386289 AAA
1 AAA
4386292 AGGGGGGAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 7 0.16
23 6 0.13
24 3 0.07
25 6 0.13
26 23 0.51
ACGTcount: A:0.74, C:0.01, G:0.23, T:0.01
Consensus pattern (26 bp):
AAAGAAAAGAAAAGAGAAAGAGAAAG
Found at i:4393763 original size:2 final size:2
Alignment explanation
Indices: 4393758--4393796 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4393748 TATATATATA
*
4393758 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG AG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4393797 CTGTATAGAT
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:0.03, C:0.00, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:4402152 original size:33 final size:35
Alignment explanation
Indices: 4402115--4402179 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
4402105 ATATAATATA
4402115 AATATATA-AATTATATTT-TATATATTAAAAAAT
1 AATATATATAATTATATTTATATATATTAAAAAAT
* *
4402148 AATATTTATATTTATATTTATATATATTAAAA
1 AATATATATAATTATATTTATATATATTAAAA
4402180 TTTAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 7 0.25
34 9 0.32
35 12 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
AATATATATAATTATATTTATATATATTAAAAAAT
Found at i:4402211 original size:35 final size:33
Alignment explanation
Indices: 4402172--4402251 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 33
4402162 TATTTATATA
*
4402172 TATTAAAATTTAATTTTAAAAATATAAAATTAATT
1 TATTAAAATTTAATTATAAAAAT-TAAAATTAA-T
* * *
4402207 TATTAAATATTTTATTATAAATATTAAAATTGAT
1 TATTAAA-ATTTAATTATAAAAATTAAAATTAAT
*
4402241 AATTAAAATTT
1 TATTAAAATTT
4402252 TTATTTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.18
35 15 0.38
36 13 0.33
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
TATTAAAATTTAATTATAAAAATTAAAATTAAT
Found at i:4402254 original size:34 final size:34
Alignment explanation
Indices: 4402173--4402256 Score: 84
Period size: 34 Copynumber: 2.4 Consensus size: 34
4402163 ATTTATATAT
*
4402173 ATTAAAATTTAATT-TTAAAAATATAAAATTAATTT
1 ATTAAAATTT--TTATTAAAAATATAAAATTAATTA
* *
4402208 ATT-AAATATTTTATTATAAATATTAAAATTGA-TA
1 ATTAAAAT-TTTTATTAAAAATA-TAAAATTAATTA
4402242 ATTAAAATTTTTATT
1 ATTAAAATTTTTATT
4402257 TTTATAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
33 2 0.05
34 23 0.55
35 17 0.40
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
ATTAAAATTTTTATTAAAAATATAAAATTAATTA
Found at i:4404568 original size:15 final size:14
Alignment explanation
Indices: 4404550--4404593 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
4404540 GGAAAGGAGG
4404550 GAAAAAGAAAGAAAA
1 GAAAAAGAAA-AAAA
*
4404565 GAAAGAGAAAAAAAA
1 GAAAAAG-AAAAAAA
*
4404580 GACAAAGAAAAAAA
1 GAAAAAGAAAAAAA
4404594 TTTGTATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 7 0.28
15 15 0.60
16 3 0.12
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAAAAA
Found at i:4404576 original size:21 final size:21
Alignment explanation
Indices: 4404550--4404589 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4404540 GGAAAGGAGG
4404550 GAAAAAGAAAGA-AAAGAAAGA
1 GAAAAA-AAAGACAAAGAAAGA
4404571 GAAAAAAAAGACAAAGAAA
1 GAAAAAAAAGACAAAGAAA
4404590 AAAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (21 bp):
GAAAAAAAAGACAAAGAAAGA
Found at i:4405736 original size:16 final size:15
Alignment explanation
Indices: 4405680--4405741 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 15
4405670 AAATTTAACT
4405680 TTAAAT-TTATTT-A
1 TTAAATATTATTTAA
4405693 TTAAATATT-TTTAA
1 TTAAATATTATTTAA
*
4405707 ATAAA-ATT-TATTAA
1 TTAAATATTAT-TTAA
4405721 TTATAATATTATTTAA
1 TTA-AATATTATTTAA
4405737 TTAAA
1 TTAAA
4405742 AATTTTATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 13 0.32
14 13 0.32
15 4 0.10
16 10 0.24
17 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAAATATTATTTAA
Found at i:4406030 original size:3 final size:3
Alignment explanation
Indices: 4406015--4406046 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
4406005 GGTGAGTTAC
4406015 TTA TTA CTTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T
4406047 ATTGGCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4406776 original size:30 final size:31
Alignment explanation
Indices: 4406742--4406807 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
4406732 AAAAATCTTG
*
4406742 TTTTAAAAGCTT-AATTAGATAAAAATAGTA
1 TTTTAAAAGATTAAATTAGATAAAAATAGTA
* *
4406772 TTTT-AAAGATTAAATTAGCTAAAAGTAGTA
1 TTTTAAAAGATTAAATTAGATAAAAATAGTA
4406802 TTTTAA
1 TTTTAA
4406808 GGATTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 6 0.19
30 24 0.77
31 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (31 bp):
TTTTAAAAGATTAAATTAGATAAAAATAGTA
Found at i:4406784 original size:29 final size:29
Alignment explanation
Indices: 4406742--4406822 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
4406732 AAAAATCTTG
*
4406742 TTTTAAAAGCTTAATTAGATAAAAATAGTA
1 TTTT-AAAGATTAATTAGATAAAAATAGTA
* *
4406772 TTTTAAAGATTAAATTAGCTAAAAGTAGTA
1 TTTTAAAGATT-AATTAGATAAAAATAGTA
* *
4406802 TTTTAAGGATTTATTAAGATA
1 TTTTAAAGATTAATT-AGATA
4406823 CAATAAAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.21
30 34 0.79
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (29 bp):
TTTTAAAGATTAATTAGATAAAAATAGTA
Found at i:4407845 original size:18 final size:17
Alignment explanation
Indices: 4407813--4407851 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
4407803 TTGTTTTATA
4407813 ATTT-GATATTAATTTT
1 ATTTAGATATTAATTTT
4407829 ATTTAGATATATAATTTT
1 ATTTAGATAT-TAATTTT
*
4407847 TTTTA
1 ATTTA
4407852 AAAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 5 0.25
18 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
ATTTAGATATTAATTTT
Found at i:4409972 original size:40 final size:42
Alignment explanation
Indices: 4409893--4409972 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
4409883 AAAATAAATA
*
4409893 AAGAAGATTAAAAGTAAAGGAAATGATAAATATGCAAGACGG
1 AAGAAGACTAAAAGTAAAGGAAATGATAAATATGCAAGACGG
* * *
4409935 AAGAAGACTAAAAGTGAA-GTAAT-ATAAATATTCAAGAC
1 AAGAAGACTAAAAGTAAAGGAAATGATAAATATGCAAGAC
4409973 CCAAAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 14 0.41
41 4 0.12
42 16 0.47
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.19
Consensus pattern (42 bp):
AAGAAGACTAAAAGTAAAGGAAATGATAAATATGCAAGACGG
Found at i:4410180 original size:28 final size:29
Alignment explanation
Indices: 4410115--4410183 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
4410105 ATTTTAAATT
4410115 TTAAATAAAT-T-AA-AAATATTTAACTA
1 TTAAATAAATATAAATAAATATTTAACTA
* *
4410141 TTTATTAAATATAAATAAAT-TTTAACTA
1 TTAAATAAATATAAATAAATATTTAACTA
*
4410169 TTAAATATATATAAA
1 TTAAATAAATATAAA
4410184 ATTAATAGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 8 0.23
27 1 0.03
28 22 0.63
29 4 0.11
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (29 bp):
TTAAATAAATATAAATAAATATTTAACTA
Found at i:4414610 original size:35 final size:35
Alignment explanation
Indices: 4414566--4414637 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
4414556 GATATTTTTT
* *
4414566 AAGGTATATTTAAAAATTAAAAGAATAATT-TAAA
1 AAGGTATATTTAAAAACTAAAAAAATAATTATAAA
4414600 AAGGATATATTTAAAAACTAAAAAAATAATTATAAA
1 AAGG-TATATTTAAAAACTAAAAAAATAATTATAAA
4414636 AA
1 AA
4414638 ATATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 4 0.12
35 24 0.71
36 6 0.18
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.29
Consensus pattern (35 bp):
AAGGTATATTTAAAAACTAAAAAAATAATTATAAA
Found at i:4414644 original size:36 final size:35
Alignment explanation
Indices: 4414570--4414645 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
4414560 TTTTTTAAGG
* * *
4414570 TATATTTAAAAATTAAAAGAATAATTTAAAAAGGA
1 TATATTTAAAAACTAAAAAAATAATTTAAAAAAGA
*
4414605 TATATTTAAAAACTAAAAAAATAATTATAAAAAATA
1 TATATTTAAAAACTAAAAAAATAATT-TAAAAAAGA
4414641 TATAT
1 TATAT
4414646 ATGATAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 24 0.67
36 12 0.33
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (35 bp):
TATATTTAAAAACTAAAAAAATAATTTAAAAAAGA
Found at i:4414944 original size:109 final size:111
Alignment explanation
Indices: 4414709--4414945 Score: 284
Period size: 109 Copynumber: 2.1 Consensus size: 111
4414699 TGGATAATCA
* * * *
4414709 AATTTGGTGATAGAAATTTAAGACTTAAGATTAATTTGACGATTTTAGTTTATGACTATAAATCT
1 AATTTGGTGATATAAATCTAAGACATAAGATTAATTTCACGATTTTAGTTTATGACTATAAATCT
* * * *
4414774 TTTACTCTTTACATTATTAAGAAAAAAAAAACACCTTTTATGCACAT
66 TTTAC-CTATACATAAGTAAGAAAAAAAAAACACCTTTTATGCAAAT
* * *
4414821 AATTTGGTGATATAAATCT-AGAACATAAGATTAA-TTCATGATTTTAGTTTATGATTGTAATAT
1 AATTTGGTGATATAAATCTAAG-ACATAAGATTAATTTCACGATTTTAGTTTATGACTATAA-AT
* * * *
4414884 CTTTTA-CTATATATAAGTAAG-ACAAAAATACACTTTTTATGCAAAT
64 CTTTTACCTATACATAAGTAAGAAAAAAAAAACACCTTTTATGCAAAT
4414930 AATTTGGTGATATAAA
1 AATTTGGTGATATAAA
4414946 ATATAAATCT
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
109 37 0.34
110 11 0.10
111 24 0.22
112 36 0.33
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (111 bp):
AATTTGGTGATATAAATCTAAGACATAAGATTAATTTCACGATTTTAGTTTATGACTATAAATCT
TTTACCTATACATAAGTAAGAAAAAAAAAACACCTTTTATGCAAAT
Found at i:4415004 original size:2 final size:2
Alignment explanation
Indices: 4414993--4415022 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4414983 GACATTCATA
4414993 AT AT -T 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
4415023 AAAGTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4415565 original size:8 final size:7
Alignment explanation
Indices: 4415539--4415573 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
4415529 GATCTTAAAT
4415539 AATTTTA
1 AATTTTA
4415546 AATTTTA
1 AATTTTA
4415553 AATTTTA
1 AATTTTA
*
4415560 AAATTTA
1 AATTTTA
4415567 TAATTTT
1 -AATTTT
4415574 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTTTA
Done.