Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 17 of 24
Found at i:3394740 original size:41 final size:40
Alignment explanation
Indices: 3394641--3394740 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 40
3394631 ATGTAATTAG
* * * *
3394641 TTAATTGATATAAATTCTTTTGAGAAGATGGTTTTTATAC
1 TTAATTAATATAAATTTTTTTCAGAAAATGGTTTTTATAC
** *
3394681 TTAATTAATA-ATTTTTTTTTTCAGAAAATGATTTTTTATAC
1 TTAATTAATATA-AATTTTTTTCAGAAAATG-GTTTTTATAC
3394722 TTAATTAATATAAATTTTT
1 TTAATTAATATAAATTTTT
3394741 ATTTGCTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
39 1 0.02
40 22 0.46
41 24 0.50
42 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (40 bp):
TTAATTAATATAAATTTTTTTCAGAAAATGGTTTTTATAC
Found at i:3395688 original size:16 final size:17
Alignment explanation
Indices: 3395664--3395701 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
3395654 TTCATATATA
*
3395664 AAATATTTAAATTTTAT
1 AAATATTTAAAGTTTAT
3395681 AAAT-TTTAAAGTTTAT
1 AAATATTTAAAGTTTAT
3395697 AAATA
1 AAATA
3395702 AAATTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AAATATTTAAAGTTTAT
Found at i:3395772 original size:12 final size:12
Alignment explanation
Indices: 3395708--3395781 Score: 50
Period size: 12 Copynumber: 6.6 Consensus size: 12
3395698 AATAAAATTA
* *
3395708 ATATAATAACAT
1 ATATATTAAAAT
*
3395720 ATATCTTAAAAT
1 ATATATTAAAAT
3395732 -T-TA-TAAAA-
1 ATATATTAAAAT
*
3395740 ATAT-TTAAAAA
1 ATATATTAAAAT
* *
3395751 ATAAAATAAAAT
1 ATATATTAAAAT
3395763 ATATATTAAAAT
1 ATATATTAAAAT
*
3395775 TTATATT
1 ATATATT
3395782 TACATTAATA
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
9 6 0.13
10 7 0.15
11 4 0.09
12 30 0.64
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATATTAAAAT
Found at i:3396871 original size:27 final size:27
Alignment explanation
Indices: 3396809--3396912 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 27
3396799 TAAAAATTAG
* *
3396809 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
*
3396833 CCACCATTTTTGACAAAAAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
3396860 CCACCATTTTTGACAAACATAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* *
3396887 CTACCATTTTTGACAAGCACAAAAGG
1 CCACCATTTTTGACAAACA-AAAAGG
3396913 TGGATTTTGT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
24 20 0.29
25 1 0.01
27 42 0.62
28 5 0.07
ACGTcount: A:0.45, C:0.23, G:0.12, T:0.20
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:3401412 original size:27 final size:28
Alignment explanation
Indices: 3401328--3401413 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 28
3401318 AATTTTTACA
3401328 AAAAACAAGCCACCATTTTTAACAAACA-
1 AAAAACAA-CCACCATTTTTAACAAACAC
* * *
3401356 AAAAAGAACTACCATTTTTTACAAACAC
1 AAAAACAACCACCATTTTTAACAAACAC
* * *
3401384 AAAAA-AACCACTATTTTTGACAAATAC
1 AAAAACAACCACCATTTTTAACAAACAC
3401411 AAA
1 AAA
3401414 TGATAGCTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 38 0.76
28 12 0.24
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.22
Consensus pattern (28 bp):
AAAAACAACCACCATTTTTAACAAACAC
Found at i:3401526 original size:11 final size:11
Alignment explanation
Indices: 3401497--3401588 Score: 51
Period size: 11 Copynumber: 9.1 Consensus size: 11
3401487 TAGAAGTAGT
3401497 TATAATATAAA
1 TATAATATAAA
3401508 -A-AATAT--A
1 TATAATATAAA
3401515 TA-AATAT-AA
1 TATAATATAAA
*
3401524 TATAATAATTAA
1 TATAAT-ATAAA
* *
3401536 TGAAAAT-TTAA
1 T-ATAATATAAA
3401547 TATAATATAAA
1 TATAATATAAA
*
3401558 AATAATAT-AA
1 TATAATATAAA
3401568 -AT-ATATAAA
1 TATAATATAAA
*
3401577 TATATTATAAA
1 TATAATATAAA
3401588 T
1 T
3401589 TATTAATAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
7 1 0.02
8 10 0.15
9 12 0.18
10 12 0.18
11 24 0.36
12 3 0.05
13 4 0.06
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (11 bp):
TATAATATAAA
Found at i:3401600 original size:19 final size:20
Alignment explanation
Indices: 3401498--3401603 Score: 73
Period size: 19 Copynumber: 5.5 Consensus size: 20
3401488 AGAAGTAGTT
* *
3401498 ATAATATAAAAAATATATAA
1 ATAATATTATAAATATATAA
* *
3401518 AT-ATAATAT-AATA-ATTA
1 ATAATATTATAAATATATAA
*
3401535 ATGAAAATT-TAATATAATATAA
1 AT-AATATTATAA-AT-ATATAA
*
3401557 A-AATAATATAAATATATAA
1 ATAATATTATAAATATATAA
*
3401576 AT-ATATTATAAAT-TATTA
1 ATAATATTATAAATATATAA
3401594 ATAATATTAT
1 ATAATATTAT
3401604 TTTTTATAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
17 5 0.08
18 11 0.17
19 32 0.48
20 10 0.15
21 4 0.06
22 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (20 bp):
ATAATATTATAAATATATAA
Found at i:3402110 original size:21 final size:20
Alignment explanation
Indices: 3402071--3402115 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
3402061 TAGTTATAAT
* **
3402071 TATTAAAATTTAATTTTTAAA
1 TATTAAAATTAAAAATTT-AA
3402092 TATTAAAATTAAAAATTTAA
1 TATTAAAATTAAAAATTTAA
3402112 TATT
1 TATT
3402116 TTATTAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTAAAATTAAAAATTTAA
Found at i:3402851 original size:36 final size:35
Alignment explanation
Indices: 3402785--3402856 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
3402775 GTTCTCAAAA
*
3402785 TGATTAAAATTAAATTTATAATTTAATATTTGAAAT
1 TGATTAAAATTAAATATATAATTTAATATTT-AAAT
* **
3402821 TGATTTAAATTAAA-ATATTAATTTTTTATTTAAAT
1 TGATTAAAATTAAATATA-TAATTTAATATTTAAAT
3402856 T
1 T
3402857 TAATCATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 7 0.23
36 24 0.77
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (35 bp):
TGATTAAAATTAAATATATAATTTAATATTTAAAT
Found at i:3402887 original size:22 final size:22
Alignment explanation
Indices: 3402851--3402892 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3402841 ATTTTTTATT
3402851 TAAATTTAATCATAAAAATATA
1 TAAATTTAATCATAAAAATATA
3402873 TAAATCTTAAT-ATAAAAATA
1 TAAAT-TTAATCATAAAAATA
3402893 AATTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAATTTAATCATAAAAATATA
Found at i:3403045 original size:10 final size:10
Alignment explanation
Indices: 3403030--3403070 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
3403020 ATTAAAAAAC
3403030 ATATTTAAAT
1 ATATTTAAAT
*
3403040 ATATTTAAAC
1 ATATTTAAAT
3403050 ATATTTAAAAAT
1 ATATTT--AAAT
3403062 ATATTTAAA
1 ATATTTAAA
3403071 ACAAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 18 0.67
12 9 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATTTAAAT
Found at i:3403049 original size:20 final size:21
Alignment explanation
Indices: 3403026--3403070 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
3403016 ATGTATTAAA
3403026 AAACATATTT-AAATATATTT
1 AAACATATTTAAAATATATTT
3403046 AAACATATTTAAAAATATATTT
1 AAACATATTT-AAAATATATTT
3403068 AAA
1 AAA
3403071 ACAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.43
22 13 0.57
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AAACATATTTAAAATATATTT
Found at i:3404108 original size:21 final size:21
Alignment explanation
Indices: 3404060--3404113 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3404050 TTTTTTTATT
* *
3404060 AATTAAAATTATTAAAATTTAA
1 AATTTAAA-TATTAAAATTAAA
**
3404082 TTTTTAAATATTAAAATTAAA
1 AATTTAAATATTAAAATTAAA
3404103 AATTT-AATATT
1 AATTTAAATATT
3404114 TTATTAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 6 0.23
21 15 0.58
22 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTTAAATATTAAAATTAAA
Found at i:3404127 original size:27 final size:27
Alignment explanation
Indices: 3404052--3404124 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 27
3404042 AAAATTAATT
3404052 TTTTTATTAATTAAAATTATTAAAATTTAA
1 TTTTTATTAA-TAAAATTA--AAAATTTAA
* *
3404082 TTTTTAAATATTAAAATTAAAAATTTAA
1 TTTTT-ATTAATAAAATTAAAAATTTAA
3404110 TATTTTATTAATAAA
1 T-TTTTATTAATAAA
3404125 TTACGTAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
28 17 0.46
29 4 0.11
30 13 0.35
31 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTTTATTAATAAAATTAAAAATTTAA
Found at i:3404864 original size:36 final size:36
Alignment explanation
Indices: 3404804--3404874 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
3404794 AAAATGATTA
* * *
3404804 AAATTAAATTTATAATTTAATATTTGAAGTTAATTT
1 AAATTAAAATAATAATTTAATATTTAAAGTTAATTT
** *
3404840 AAATTAAAATAATAATTTTTTATTTAAATTTAATT
1 AAATTAAAATAATAATTTAATATTTAAAGTTAATT
3404875 ATAACAATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (36 bp):
AAATTAAAATAATAATTTAATATTTAAAGTTAATTT
Found at i:3404897 original size:22 final size:22
Alignment explanation
Indices: 3404864--3404905 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3404854 ATTTTTTATT
*
3404864 TAAATTTAATTATAACAATATA
1 TAAATTTAATTATAAAAATATA
3404886 TAAATATT-ATTATAAAAATA
1 TAAAT-TTAATTATAAAAATA
3404906 AAATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:3412167 original size:2 final size:2
Alignment explanation
Indices: 3412160--3412188 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3412150 TTTTCTATTT
3412160 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
3412189 GTTTTTTATC
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:3412770 original size:16 final size:16
Alignment explanation
Indices: 3412733--3412799 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
3412723 AGGTAATGCT
3412733 AATAGTAAAAAT-ATATT
1 AATA-TAAAAATAATA-T
3412750 AATATAATATAA-AA-AT
1 AATATAA-A-AATAATAT
**
3412766 AATATAAATTTAATAT
1 AATATAAAAATAATAT
*
3412782 AATATAAAGATAATAT
1 AATATAAAAATAATAT
3412798 AA
1 AA
3412800 ATTTAATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
15 3 0.07
16 29 0.71
17 6 0.15
18 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AATATAAAAATAATAT
Found at i:3412810 original size:16 final size:16
Alignment explanation
Indices: 3412764--3412799 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3412754 TAATATAAAA
**
3412764 ATAATATAAATTTAAT
1 ATAATATAAAGATAAT
3412780 ATAATATAAAGATAAT
1 ATAATATAAAGATAAT
3412796 ATAA
1 ATAA
3412800 ATTTAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
ATAATATAAAGATAAT
Found at i:3412821 original size:27 final size:27
Alignment explanation
Indices: 3412748--3412815 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
3412738 TAAAAATATA
*
3412748 TTAATATAATATAAAAATAATATAAAT
1 TTAATATAATATAAAGATAATATAAAT
3412775 TTAATATAATATAAAGATAATATAAAT
1 TTAATATAATATAAAGATAATATAAAT
3412802 TTAATATAAATATA
1 TTAATAT-AATATA
3412816 TTATAAATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 33 0.85
28 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (27 bp):
TTAATATAATATAAAGATAATATAAAT
Found at i:3412823 original size:11 final size:11
Alignment explanation
Indices: 3412732--3412823 Score: 72
Period size: 11 Copynumber: 8.9 Consensus size: 11
3412722 GAGGTAATGC
*
3412732 TAATAGTAAAAA
1 TAATA-TAAATA
*
3412744 T-ATATTAATA
1 TAATATAAATA
*
3412754 TAATATAAAAA
1 TAATATAAATA
3412765 TAATAT-AA-A
1 TAATATAAATA
3412774 T--T-T-AATA
1 TAATATAAATA
*
3412781 TAATATAAAGA
1 TAATATAAATA
*
3412792 TAATATAAATT
1 TAATATAAATA
3412803 TAATATAAATA
1 TAATATAAATA
*
3412814 TATTATAAAT
1 TAATATAAAT
3412824 GATTAATAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
6 3 0.05
7 3 0.05
9 3 0.05
10 8 0.12
11 47 0.72
12 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TAATATAAATA
Found at i:3413107 original size:16 final size:17
Alignment explanation
Indices: 3413075--3413114 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
3413065 ATTGGGCAAT
*
3413075 CAAAACGTGCGTTCAAA
1 CAAAACGTGCCTTCAAA
3413092 CAAAACG-GCCTTCAAA
1 CAAAACGTGCCTTCAAA
3413108 CAAAACG
1 CAAAACG
3413115 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.12
Consensus pattern (17 bp):
CAAAACGTGCCTTCAAA
Found at i:3413194 original size:13 final size:12
Alignment explanation
Indices: 3413171--3413204 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
3413161 TGATAGTTGA
*
3413171 AATTGAAATAAT
1 AATTAAAATAAT
3413183 AATTTAAAATAAT
1 AA-TTAAAATAAT
3413196 AATTAAAAT
1 AATTAAAAT
3413205 TGAAAGAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (12 bp):
AATTAAAATAAT
Found at i:3414275 original size:13 final size:12
Alignment explanation
Indices: 3414249--3414278 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
3414239 TTTTATATTC
3414249 ATATTAAAATAT
1 ATATTAAAATAT
3414261 ATATTAAATATAT
1 ATATTAAA-ATAT
3414274 ATATT
1 ATATT
3414279 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTAAAATAT
Found at i:3414728 original size:14 final size:13
Alignment explanation
Indices: 3414676--3414730 Score: 65
Period size: 13 Copynumber: 4.0 Consensus size: 13
3414666 TAACTCCAGT
3414676 TTTTTTTTCTTTAA
1 TTTTTTTT-TTTAA
*
3414690 TTCTTTTTTTTTCA
1 TT-TTTTTTTTTAA
*
3414704 TTTATTTTTTTAA
1 TTTTTTTTTTTAA
3414717 TTTTTTTATTTTAA
1 TTTTTTT-TTTTAA
3414731 AATTGTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
13 15 0.43
14 14 0.40
15 6 0.17
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTTTTTTAA
Found at i:3414863 original size:22 final size:21
Alignment explanation
Indices: 3414838--3414878 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
3414828 ATTTTTTATT
3414838 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TA-AAAAATATA
3414860 TAAATATTAATAAAAAATA
1 TAAATATTAATAAAAAATA
3414879 AATTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:3416564 original size:15 final size:15
Alignment explanation
Indices: 3416544--3416573 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3416534 ATTTTATCAA
*
3416544 AATTAAATTTTAATT
1 AATTAAATTATAATT
3416559 AATTAAATTATAATT
1 AATTAAATTATAATT
3416574 TAATGCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTAAATTATAATT
Found at i:3420192 original size:18 final size:18
Alignment explanation
Indices: 3420166--3420204 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
3420156 ATAAATAAAT
3420166 TAAATAAAAAT-TCAAAA
1 TAAATAAAAATCTCAAAA
3420183 TAAATAAAAATCTCAAAA
1 TAAATAAAAATCTCAAAA
3420201 TAAA
1 TAAA
3420205 AATTTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAATAAAAATCTCAAAA
Found at i:3420731 original size:38 final size:39
Alignment explanation
Indices: 3420658--3420731 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
3420648 TTAATCAAGC
* *
3420658 AATATAATTTTTTTAATATAAATAAAATCATAATTTACG
1 AATAAAATTTTTTTAATATAAATAAAATCAAAATTTACG
* *
3420697 AATAAAATTTTTTATAA-AT-ATTAAAATTAAAATTT
1 AATAAAATTTTTT-TAATATAAATAAAATCAAAATTT
3420732 TATATTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
38 13 0.43
39 14 0.47
40 3 0.10
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (39 bp):
AATAAAATTTTTTTAATATAAATAAAATCAAAATTTACG
Found at i:3426441 original size:18 final size:20
Alignment explanation
Indices: 3426417--3426460 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
3426407 TAAAATTAAA
*
3426417 AATTTATATTGA-AATTTAT
1 AATTTATATTAATAATTTAT
3426436 -ATTTATATTAATAATTTAT
1 AATTTATATTAATAATTTAT
3426455 AATTTA
1 AATTTA
3426461 ATAATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 7 0.32
20 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AATTTATATTAATAATTTAT
Found at i:3426484 original size:32 final size:31
Alignment explanation
Indices: 3426411--3426484 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
3426401 AAAAAATAAA
* *
3426411 ATTAAAAATTTATATTGAAATTTATATTTAT
1 ATTAAAAATTTATATTAAAATATATATTTAT
*
3426442 ATTAATAATTTATAATTTAATAATAT-TATTT-T
1 ATTAAAAATTTAT-A-TTAA-AATATATATTTAT
3426474 ATTAAAAATTT
1 ATTAAAAATTT
3426485 TTTAAATTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 12 0.33
32 12 0.33
33 8 0.22
34 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (31 bp):
ATTAAAAATTTATATTAAAATATATATTTAT
Found at i:3426754 original size:2 final size:2
Alignment explanation
Indices: 3426747--3426780 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3426737 GTCGGTTTTC
3426747 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
3426781 GGTTTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3427377 original size:26 final size:28
Alignment explanation
Indices: 3427348--3427405 Score: 93
Period size: 26 Copynumber: 2.1 Consensus size: 28
3427338 ATATAATTTA
3427348 AAATTTAATAT-AATATAAAAATA-ATT
1 AAATTTAATATAAATATAAAAATATATT
*
3427374 AAATTTAATATAAATATATAAATATATT
1 AAATTTAATATAAATATAAAAATATATT
3427402 AAAT
1 AAAT
3427406 AACATAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 11 0.38
27 11 0.38
28 7 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AAATTTAATATAAATATAAAAATATATT
Found at i:3427387 original size:11 final size:11
Alignment explanation
Indices: 3427354--3427391 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3427344 TTTAAAATTT
3427354 AATATAATATA
1 AATATAATATA
*
3427365 AAAATAAT-TA
1 AATATAATATA
*
3427375 AATTTAATATA
1 AATATAATATA
3427386 AATATA
1 AATATA
3427392 TAAATATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAATATA
Found at i:3427416 original size:28 final size:27
Alignment explanation
Indices: 3427359--3427417 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
3427349 AATTTAATAT
* *
3427359 AATATAAAAATAATTAAATTTAATATA
1 AATATAAAAATAATTAAATTAAATAAA
*
3427386 AATATATAAATATATTAAA-TAACATAAA
1 AATATAAAAATA-ATTAAATTAA-ATAAA
3427414 AATA
1 AATA
3427418 CGGTATACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
AATATAAAAATAATTAAATTAAATAAA
Found at i:3427737 original size:15 final size:15
Alignment explanation
Indices: 3427702--3427737 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
3427692 GAATCATCTA
3427702 TTAATTTTTTAAATT
1 TTAATTTTTTAAATT
*
3427717 TT-ATTTTTTGAATT
1 TTAATTTTTTAAATT
3427731 TTAATTT
1 TTAATTT
3427738 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTAATTTTTTAAATT
Found at i:3427777 original size:23 final size:19
Alignment explanation
Indices: 3427730--3427779 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 19
3427720 TTTTTTGAAT
3427730 TTTAATTTAAATATTTTTA
1 TTTAATTTAAATATTTTTA
*
3427749 TCTAATTGGTAAATATTATGTTA
1 TTTAATT--TAAATATT-T-TTA
3427772 TTTAATTT
1 TTTAATTT
3427780 TAAGATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 6 0.24
21 9 0.36
22 1 0.04
23 9 0.36
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTAATTTAAATATTTTTA
Found at i:3427863 original size:21 final size:21
Alignment explanation
Indices: 3427823--3427881 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
3427813 ATTTAAATTT
* *
3427823 TTTAAAATTAAAATTATTAAAA
1 TTTAATATTTAAA-TATTAAAA
3427845 TTTAATATTTAAATATTAAAA
1 TTTAATATTTAAATATTAAAA
*
3427866 TTAAATATTT-AATATT
1 TTTAATATTTAAATATT
3427882 CTATCAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 6 0.18
21 17 0.50
22 11 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAATATTTAAATATTAAAA
Found at i:3427950 original size:26 final size:28
Alignment explanation
Indices: 3427913--3427967 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
3427903 ATTTATTATA
3427913 ATATTATATTTAAAAAAT-TA-TATTTT
1 ATATTATATTTAAAAAATATATTATTTT
*
3427939 ATATT-TACTTTAAAATATATATTATTTT
1 ATATTATA-TTTAAAAAATATATTATTTT
3427967 A
1 A
3427968 AAAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 2 0.08
26 14 0.56
27 2 0.08
28 7 0.28
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (28 bp):
ATATTATATTTAAAAAATATATTATTTT
Found at i:3428365 original size:19 final size:20
Alignment explanation
Indices: 3428343--3428385 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
3428333 TTTTTTATAT
*
3428343 TTTAACTCCGGTTTTTTTC-
1 TTTAACTCCGCTTTTTTTCA
* *
3428362 TTTAATTCCTCTTTTTTTCA
1 TTTAACTCCGCTTTTTTTCA
3428382 TTTA
1 TTTA
3428386 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.14, C:0.19, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTAACTCCGCTTTTTTTCA
Found at i:3428534 original size:29 final size:29
Alignment explanation
Indices: 3428482--3428543 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
3428472 GTTTCTAATT
*
3428482 TAATAATTTTATTTTATTTAAATTA-AAA
1 TAATAATTTTATTTAATTTAAATTATAAA
3428510 TAATAATTTTTATTTAAATTT-AATTATAAA
1 TAATAA-TTTTATTT-AATTTAAATTATAAA
3428540 -AATA
1 TAATA
3428544 TATAAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.20
29 17 0.57
30 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATAATTTTATTTAATTTAAATTATAAA
Found at i:3430009 original size:22 final size:22
Alignment explanation
Indices: 3429984--3430025 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3429974 TAATTTTATT
3429984 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
3430006 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
3430026 ATATTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:3430942 original size:33 final size:32
Alignment explanation
Indices: 3430897--3430959 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
3430887 AATATACTTT
3430897 TTATTTTGAATTTAACAAAATTGAAGATGAATA
1 TTATTTTGAATTTAACAAAATTG-AGATGAATA
* *
3430930 TTATCTTT-AATTTAATAATATTGAGATGAA
1 TTAT-TTTGAATTTAACAAAATTGAGATGAA
3430960 AGTCATGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 7 0.26
33 17 0.63
34 3 0.11
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (32 bp):
TTATTTTGAATTTAACAAAATTGAGATGAATA
Found at i:3432038 original size:59 final size:59
Alignment explanation
Indices: 3431966--3432083 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
3431956 ATATTTGAGG
* * *
3431966 TCCGTATCCGACACATATATATGGATATGGATATTAAAAAATTACTCTTCAAGGAGCCC
1 TCCGTATCCGACACATATATATGGACATAGATATTAAAAAAGTACTCTTCAAGGAGCCC
* *
3432025 TCCGTATCCGACACATATATATGGACATAGATATTAAAAAAGTATTCTTCAAGGGGCCC
1 TCCGTATCCGACACATATATATGGACATAGATATTAAAAAAGTACTCTTCAAGGAGCCC
3432084 CGAATATATT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (59 bp):
TCCGTATCCGACACATATATATGGACATAGATATTAAAAAAGTACTCTTCAAGGAGCCC
Found at i:3433992 original size:23 final size:23
Alignment explanation
Indices: 3433966--3434011 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3433956 ATAATTAATG
3433966 TAAAAAAAATTAATAAAAATTTA
1 TAAAAAAAATTAATAAAAATTTA
* *
3433989 TAAATAAAATTAATTAAAATTTA
1 TAAAAAAAATTAATAAAAATTTA
3434012 ATTTTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAAAAAAATTAATAAAAATTTA
Found at i:3435434 original size:20 final size:19
Alignment explanation
Indices: 3435394--3435438 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 19
3435384 ATTTTGCATG
3435394 ATTTTATTTTTTATTAATT
1 ATTTTATTTTTTATTAATT
3435413 ATTTTA-TTTTTA-T-ATT
1 ATTTTATTTTTTATTAATT
3435429 -TTTTATTTTT
1 ATTTTATTTTT
3435439 GAGAGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.20
16 7 0.28
17 1 0.04
18 6 0.24
19 6 0.24
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
ATTTTATTTTTTATTAATT
Found at i:3436409 original size:15 final size:15
Alignment explanation
Indices: 3436385--3436421 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3436375 CAACTCTCAC
3436385 ATTAAATTTAATTAA
1 ATTAAATTTAATTAA
*
3436400 ATTAATTTTAATTAA
1 ATTAAATTTAATTAA
*
3436415 AATAAAT
1 ATTAAAT
3436422 CAAATTAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATTTAATTAA
Found at i:3438893 original size:13 final size:13
Alignment explanation
Indices: 3438875--3438900 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3438865 TACAGCAAGT
3438875 ATGTATCGATACA
1 ATGTATCGATACA
3438888 ATGTATCGATACA
1 ATGTATCGATACA
3438901 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3439874 original size:7 final size:7
Alignment explanation
Indices: 3439857--3439895 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
3439847 TTTTAATAAA
3439857 AATAA-T
1 AATAATT
3439863 AATAATT
1 AATAATT
3439870 AATAATT
1 AATAATT
3439877 AATAATT
1 AATAATT
3439884 AATAATT
1 AATAATT
3439891 AATAA
1 AATAA
3439896 AAAATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATAATT
Found at i:3439901 original size:14 final size:14
Alignment explanation
Indices: 3439849--3439901 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
3439839 ATTTTTATTT
3439849 TTAAT-AAAAATAA
1 TTAATAAAAAATAA
**
3439862 -TAATAATTAATAA
1 TTAATAAAAAATAA
**
3439875 TTAATAATTAATAA
1 TTAATAAAAAATAA
3439889 TTAATAAAAAATA
1 TTAATAAAAAATA
3439902 TATTTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 4 0.12
13 6 0.18
14 24 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAATAAAAAATAA
Found at i:3442871 original size:25 final size:25
Alignment explanation
Indices: 3442843--3442906 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
3442833 TGTTCTTGCA
*
3442843 AAGAGCAAATTTTCAGGCATCAAGG
1 AAGAGCAAATCTTCAGGCATCAAGG
*
3442868 AAGAGCAAAACTTCAGGCATCAAGG
1 AAGAGCAAATCTTCAGGCATCAAGG
3442893 AAGAGCAAATCTTC
1 AAGAGCAAATCTTC
3442907 TTGGTGCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (25 bp):
AAGAGCAAATCTTCAGGCATCAAGG
Found at i:3445811 original size:146 final size:141
Alignment explanation
Indices: 3445525--3445811 Score: 369
Period size: 146 Copynumber: 2.0 Consensus size: 141
3445515 TTGGCCAATC
* *
3445525 AATAGATGTTAATATTTTGGACTTTTTTTGATGGGATGGGATTTTTGTACTTACCATGGAGAAAC
1 AATAGATGCTAATATTTTGGACTTTTTTTGATGGGATGGGATTTTTGTACTTACCACGGAGAAAC
* * *
3445590 TATTTTTTGAGGAAGATAAAGTATCATTAATGTTTTGCTAGTAGAGAGCTATTAATTTTGCATTG
66 TATTTTTTGAGGAAGATAAAGTATCATTAACGTTTTGCTAGTAGAGAGCTATCAATCTTGCATTG
3445655 ATGACGTCTCA
131 ATGACGTCTCA
* * * * *
3445666 AATAGATGCTAGTATTTTGGAATTTTTTTTTGATGGGATGGGGTTTTTTGTATTTTCCACGGAGA
1 AATAGATGCTAATATTTTGG-A-CTTTTTTTGATGGGAT-GGGATTTTTGTACTTACCACGGAGA
* * * *
3445731 AACTATTTTTTCGAGGAAGAT-CAGTTATCATTTAACGTTTTGCTTGTAGAGAGTTGTCAATCTT
63 AACTATTTTTT-GAGGAAGATAAAG-TATCA-TTAACGTTTTGCTAGTAGAGAGCTATCAATCTT
* *
3445795 GCATTGGTGATGTCTCA
125 GCATTGATGACGTCTCA
3445812 GTGGAGGGAG
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
141 18 0.15
142 1 0.01
143 15 0.12
144 34 0.27
145 14 0.11
146 42 0.34
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42
Consensus pattern (141 bp):
AATAGATGCTAATATTTTGGACTTTTTTTGATGGGATGGGATTTTTGTACTTACCACGGAGAAAC
TATTTTTTGAGGAAGATAAAGTATCATTAACGTTTTGCTAGTAGAGAGCTATCAATCTTGCATTG
ATGACGTCTCA
Found at i:3451007 original size:15 final size:16
Alignment explanation
Indices: 3450982--3451014 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3450972 AATGACAAAC
3450982 AAAATTTAATTAAAAT
1 AAAATTTAATTAAAAT
3450998 AAAA-TTAATTAAAAT
1 AAAATTTAATTAAAAT
3451013 AA
1 AA
3451015 TAGATAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTTAATTAAAAT
Found at i:3451986 original size:29 final size:28
Alignment explanation
Indices: 3451923--3451994 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
3451913 TTTCTTCCTA
*
3451923 TGTTTTCTGTTTTTATTTTTTTCATTGTTT
1 TGTTTTCT-CTTTT-TTTTTTTCATTGTTT
*
3451953 T-TTTTCTCTTTTTTTTTTTCATTTTATT
1 TGTTTTCTCTTTTTTTTTTTCATTGT-TT
*
3451981 TGTTTTCTCATTTT
1 TGTTTTCTCTTTTT
3451995 GTGTTTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 12 0.32
28 7 0.19
29 17 0.46
30 1 0.03
ACGTcount: A:0.07, C:0.10, G:0.06, T:0.78
Consensus pattern (28 bp):
TGTTTTCTCTTTTTTTTTTTCATTGTTT
Found at i:3451994 original size:27 final size:27
Alignment explanation
Indices: 3451938--3451994 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
3451928 TCTGTTTTTA
**
3451938 TTTTTTTCATTGTTTTTTTTCTCTTTT
1 TTTTTTTCATTGTTTTTTTTCTCTCAT
3451965 TTTTTTTCATT-TTATTTGTTT-TCTCAT
1 TTTTTTTCATTGTT-TTT-TTTCTCTCAT
3451992 TTT
1 TTT
3451995 GTGTTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 2 0.08
27 21 0.81
28 3 0.12
ACGTcount: A:0.07, C:0.11, G:0.04, T:0.79
Consensus pattern (27 bp):
TTTTTTTCATTGTTTTTTTTCTCTCAT
Found at i:3452017 original size:42 final size:42
Alignment explanation
Indices: 3451934--3452055 Score: 110
Period size: 42 Copynumber: 2.9 Consensus size: 42
3451924 GTTTTCTGTT
* * *
3451934 TTTA-TTTTTTTCATTGTT-TTTTTTCTCTTTTTTTTTTTCA-T-
1 TTTATTTTTTTTCATT-TTATGTTTT-TC-TTATTTTTATCATTC
*
3451975 TTTATTTGTTTTCTCATTTTGTGTTTTGT-TTATTTTTATCATTC
1 TTTATTT-TTTT-TCATTTTATGTTTT-TCTTATTTTTATCATTC
*
3452019 TTTATTTTTTTTCCTTTTATGTTTTTCTTATTTTTAT
1 TTTATTTTTTTTCATTTTATGTTTTTCTTATTTTTAT
3452056 GCTTTTTTGT
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
41 5 0.07
42 34 0.50
43 11 0.16
44 18 0.26
ACGTcount: A:0.10, C:0.09, G:0.05, T:0.76
Consensus pattern (42 bp):
TTTATTTTTTTTCATTTTATGTTTTTCTTATTTTTATCATTC
Found at i:3453469 original size:10 final size:10
Alignment explanation
Indices: 3453454--3453506 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 10
3453444 ATTGTATGCA
3453454 TTCTTTTTTT
1 TTCTTTTTTT
3453464 TTCTTTTTTT
1 TTCTTTTTTT
*
3453474 TTGTATTTTTT
1 TTCT-TTTTTT
3453485 TAT-TTTTATTT
1 T-TCTTTT-TTT
3453496 TTCTTATTTTT
1 TTCTT-TTTTT
3453507 CATGCATGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 17 0.46
11 17 0.46
12 3 0.08
ACGTcount: A:0.08, C:0.06, G:0.02, T:0.85
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:3453502 original size:15 final size:14
Alignment explanation
Indices: 3453467--3453506 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3453457 TTTTTTTTTC
*
3453467 TTTTTT-TTTGTAT
1 TTTTTTATTTTTAT
3453480 TTTTTTATTTTTAT
1 TTTTTTATTTTTAT
3453494 TTTTCTTATTTTT
1 TTTT-TTATTTTT
3453507 CATGCATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 8 0.33
ACGTcount: A:0.10, C:0.03, G:0.03, T:0.85
Consensus pattern (14 bp):
TTTTTTATTTTTAT
Found at i:3454878 original size:9 final size:9
Alignment explanation
Indices: 3454858--3454891 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
3454848 TTAATTAATA
3454858 AAATATTTTT
1 AAATA-TTTT
3454868 AAATATTTT
1 AAATATTTT
3454877 AATATATTTT
1 AA-ATATTTT
3454887 AAATA
1 AAATA
3454892 ATAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AAATATTTT
Found at i:3454899 original size:19 final size:18
Alignment explanation
Indices: 3454842--3454899 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
3454832 TTTATCAAAT
*
3454842 TATTATTTAATTAATAAAA
1 TATT-TTTAAATAATAAAA
* **
3454861 TATTTTTAAATATTTTAA
1 TATTTTTAAATAATAAAA
3454879 TATATTTTAAATAATAAAA
1 TAT-TTTTAAATAATAAAA
3454898 TA
1 TA
3454900 AACTTTTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTTTAAATAATAAAA
Found at i:3455256 original size:21 final size:20
Alignment explanation
Indices: 3455232--3455279 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3455222 TATAATTATG
*
3455232 AAATAATTAATTA-ACTAATTA
1 AAATAATTAAATAGA-TAA-TA
*
3455253 AAATATTTAAATAGATAATA
1 AAATAATTAAATAGATAATA
3455273 AAATAAT
1 AAATAAT
3455280 ATGTATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 8 0.35
21 14 0.61
22 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATAATTAAATAGATAATA
Found at i:3455315 original size:18 final size:19
Alignment explanation
Indices: 3455277--3455315 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3455267 ATAATAAAAT
* *
3455277 AATATGTATTAAAATTTTA
1 AATATGTATTAAAAATATA
3455296 AATAT-TATTAAAAATATA
1 AATATGTATTAAAAATATA
3455314 AA
1 AA
3455316 AATAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AATATGTATTAAAAATATA
Found at i:3455873 original size:9 final size:9
Alignment explanation
Indices: 3455859--3455891 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3455849 TCAATTATAA
3455859 AAAAAATAT
1 AAAAAATAT
3455868 AAAAAATA-
1 AAAAAATAT
3455876 AAAAAATGAT
1 AAAAAAT-AT
3455886 AAAAAA
1 AAAAAA
3455892 ATTATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.32
9 9 0.41
10 6 0.27
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (9 bp):
AAAAAATAT
Found at i:3455878 original size:18 final size:18
Alignment explanation
Indices: 3455858--3455891 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3455848 TTCAATTATA
3455858 AAAAAAAT-ATAAAAAAT
1 AAAAAAATGATAAAAAAT
3455875 AAAAAAATGATAAAAAA
1 AAAAAAATGATAAAAAA
3455892 ATTATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAAAAATGATAAAAAAT
Found at i:3455949 original size:22 final size:22
Alignment explanation
Indices: 3455918--3455970 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3455908 TATATTAATT
3455918 TTTAATATAATAAATAT-TATAAA
1 TTTAA-ATAA-AAATATATATAAA
*
3455941 TTTAAATAAAAATATATATATA
1 TTTAAATAAAAATATATATAAA
*
3455963 TTTTAATA
1 TTTAAATA
3455971 TATTCGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 6 0.22
22 16 0.59
23 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAATAAAAATATATATAAA
Found at i:3456489 original size:20 final size:19
Alignment explanation
Indices: 3456453--3456502 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
3456443 ATAAAAATAT
3456453 ATTTAATTAATATATTTTA
1 ATTTAATTAATATATTTTA
*
3456472 ATTTAAATTACATA-ATTTTTT
1 ATTT-AATTA-ATATA-TTTTA
3456493 ATTTAATTAA
1 ATTTAATTAA
3456503 AATTCATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.19
20 11 0.41
21 11 0.41
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAATTAATATATTTTA
Found at i:3464480 original size:13 final size:13
Alignment explanation
Indices: 3464464--3464499 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3464454 CTCTTAATTT
*
3464464 TATTTATTTTTTA
1 TATTTATTTTTAA
3464477 TATTTATTTTTAA
1 TATTTATTTTTAA
*
3464490 TATATATTTT
1 TATTTATTTT
3464500 ATATTTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTATTTTTAA
Found at i:3464572 original size:29 final size:29
Alignment explanation
Indices: 3464533--3464664 Score: 99
Period size: 29 Copynumber: 4.4 Consensus size: 29
3464523 ACAATTTTAA
*
3464533 TAATTTTATATTATTTATTATATATATTT
1 TAATTTAATATTATTTATTATATATATTT
* * * *
3464562 TAATTTAATATCT-TTAATAATACATTTTTT
1 TAATTTAATAT-TATTTATTATATA-TATTT
* * *
3464592 TAATATAAT-TCATCTCATTATCATCATCAATTT
1 TAATTTAATATTAT-TTATTAT-AT-AT--ATTT
3464625 TAATTTTAA-ATTATTTATTATATATATTT
1 TAA-TTTAATATTATTTATTATATATATTT
3464654 TAATTTAATAT
1 TAATTTAATAT
3464665 CTTTAATAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 22
0.68 0.12 0.19
Matches are distributed among these distances:
28 5 0.06
29 29 0.37
30 18 0.23
31 4 0.05
32 3 0.04
33 12 0.15
34 7 0.09
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (29 bp):
TAATTTAATATTATTTATTATATATATTT
Found at i:3464638 original size:92 final size:91
Alignment explanation
Indices: 3464533--3464752 Score: 370
Period size: 92 Copynumber: 2.4 Consensus size: 91
3464523 ACAATTTTAA
*
3464533 TAATTTTATATTATTTATTATATATATTTTAATTTAATATCTTTAATAATACATTTTTTTAATAT
1 TAATTTTAAATTATTTATTATATATATTTTAATTTAATATCTTTAATAATACA-TTTTTTAATAT
3464598 AATTCATCTCATTATCATCATCAATTT
65 AATTCATCTCATTATCATCATCAATTT
3464625 TAATTTTAAATTATTTATTATATATATTTTAATTTAATATCTTTAATAATACATTTTTTAATATA
1 TAATTTTAAATTATTTATTATATATATTTTAATTTAATATCTTTAATAATACATTTTTTAATATA
3464690 ATTCATCTCATTATCATCATCAATTT
66 ATTCATCTCATTATCATCATCAATTT
* *
3464716 TAATTTTAAATATATATCTTATCAT-TAATTTTAATTT
1 TAATTTTAAAT-TATTTATTAT-ATAT-ATTTTAATTT
3464753 TTTTATTTTA
Statistics
Matches: 122, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
91 49 0.40
92 61 0.50
93 12 0.10
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (91 bp):
TAATTTTAAATTATTTATTATATATATTTTAATTTAATATCTTTAATAATACATTTTTTAATATA
ATTCATCTCATTATCATCATCAATTT
Found at i:3464683 original size:29 final size:30
Alignment explanation
Indices: 3464533--3464691 Score: 98
Period size: 29 Copynumber: 5.3 Consensus size: 30
3464523 ACAATTTTAA
* * * *
3464533 TAATTTTATAT-TATTTATTATATATATTT
1 TAATTTAATATCTATTAATAATACATATTT
*
3464562 TAATTTAATATCT-TTAATAATACATTTTTT
1 TAATTTAATATCTATTAATAATACA-TATTT
* *
3464592 TAATATAATTCATCTCATT-ATCAT-CATCAATTT
1 TAATTTAA-T-ATCT-ATTAATAATACAT--ATTT
* * *
3464625 TAATTTTAA-AT-TATTTATTATATATATTT
1 TAA-TTTAATATCTATTAATAATACATATTT
*
3464654 TAATTTAATATCT-TTAATAATACATTTTT
1 TAATTTAATATCTATTAATAATACATATTT
*
3464683 TAATATAAT
1 TAATTTAAT
3464692 TCATCTCATT
Statistics
Matches: 101, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
28 5 0.05
29 50 0.50
30 18 0.18
31 6 0.06
32 6 0.06
33 10 0.10
34 6 0.06
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (30 bp):
TAATTTAATATCTATTAATAATACATATTT
Found at i:3468676 original size:7 final size:7
Alignment explanation
Indices: 3468664--3468693 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3468654 AAGCTCATCG
3468664 AAAATAA
1 AAAATAA
3468671 AAAATAA
1 AAAATAA
3468678 AAAATAA
1 AAAATAA
3468685 AAAA-AA
1 AAAATAA
3468691 AAA
1 AAA
3468694 CAAATATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAATAA
Found at i:3469490 original size:33 final size:33
Alignment explanation
Indices: 3469452--3469518 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
3469442 TTAGTATAAA
3469452 ATTTTAATTTTTTATATATTTTTA-AATT-TATTT
1 ATTTTAATTTTTTA-AT-TTTTTATAATTATATTT
*
3469485 ATTTTATTTTTTTAATTTTTTATAATTATATTT
1 ATTTTAATTTTTTAATTTTTTATAATTATATTT
3469518 A
1 A
3469519 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 6 0.19
32 6 0.19
33 19 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (33 bp):
ATTTTAATTTTTTAATTTTTTATAATTATATTT
Found at i:3470059 original size:6 final size:6
Alignment explanation
Indices: 3470048--3470076 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3470038 GAAGTCCCCT
3470048 TTCACC TTCACC TTCACC TTCACC TTCAC
1 TTCACC TTCACC TTCACC TTCACC TTCAC
3470077 ACCTTGTTGG
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:0.17, C:0.48, G:0.00, T:0.34
Consensus pattern (6 bp):
TTCACC
Found at i:3470670 original size:16 final size:16
Alignment explanation
Indices: 3470649--3470703 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
3470639 TAAAGTATTA
3470649 TTATATATTTTAAAAT
1 TTATATATTTTAAAAT
* * *
3470665 TTATATAATATAAATT
1 TTATATATTTTAAAAT
*
3470681 ATTA-ATATATTAAAAT
1 -TTATATATTTTAAAAT
3470697 TTATATA
1 TTATATA
3470704 AATATAAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 3 0.10
16 24 0.80
17 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATATATTTTAAAAT
Found at i:3470699 original size:32 final size:34
Alignment explanation
Indices: 3470645--3470716 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 34
3470635 TAATTAAAGT
*
3470645 ATTATTATATATTTTAAAATTTATAT-AATATAA
1 ATTATTATATATATTAAAATTTATATAAATATAA
3470678 ATTATTA-ATATATTAAAATTTATATAAATATAA
1 ATTATTATATATATTAAAATTTATATAAATATAA
*
3470711 AATATT
1 ATTATT
3470717 TTAAATATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 17 0.47
33 19 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
ATTATTATATATATTAAAATTTATATAAATATAA
Found at i:3470707 original size:20 final size:20
Alignment explanation
Indices: 3470684--3470766 Score: 54
Period size: 20 Copynumber: 4.3 Consensus size: 20
3470674 ATAAATTATT
3470684 AATATATTAAAATTTATAT-
1 AATATATTAAAATTTATATA
3470703 AA-ATA-TAAAATATT-T-TA
1 AATATATTAAAAT-TTATATA
* *
3470720 AATATGATTATAATATA-ATA
1 AATAT-ATTAAAATTTATATA
* *
3470740 AA-ATATATAAAAATAATATA
1 AATATAT-TAAAATTTATATA
3470760 AATATAT
1 AATATAT
3470767 AAATTATCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
16 1 0.02
17 9 0.19
18 9 0.19
19 11 0.23
20 14 0.29
21 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
AATATATTAAAATTTATATA
Found at i:3470711 original size:17 final size:17
Alignment explanation
Indices: 3470659--3470713 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
3470649 TTATATATTT
3470659 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
3470675 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
3470690 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
3470708 TAAAAT
1 TAAAAT
3470714 ATTTTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
16 2 0.06
17 9 0.27
18 7 0.21
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:3470746 original size:10 final size:9
Alignment explanation
Indices: 3470672--3470769 Score: 60
Period size: 9 Copynumber: 10.8 Consensus size: 9
3470662 AATTTATATA
*
3470672 ATATAAATT
1 ATATAAAAT
*
3470681 AT-TAATAT
1 ATATAAAAT
3470689 AT-TAAAAT
1 ATATAAAAT
* *
3470697 TTATATAA-
1 ATATAAAAT
3470705 ATATAAAAT
1 ATATAAAAT
* *
3470714 ATTTTAAAT
1 ATATAAAAT
*
3470723 ATGATTATAAT
1 AT-A-TAAAAT
3470734 ATAATAAAAT
1 AT-ATAAAAT
3470744 ATATAAAA-
1 ATATAAAAT
3470752 ATAATATAAAT
1 AT-ATA-AAAT
3470763 ATATAAA
1 ATATAAA
3470770 TTATCAAGTA
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
8 20 0.29
9 26 0.38
10 13 0.19
11 9 0.13
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (9 bp):
ATATAAAAT
Found at i:3470764 original size:19 final size:18
Alignment explanation
Indices: 3470734--3470769 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
3470724 TGATTATAAT
3470734 ATAATAAAATATATAAAA
1 ATAATAAAATATATAAAA
3470752 ATAATATAAATATATAAA
1 ATAATA-AAATATATAAA
3470770 TTATCAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATAAAATATATAAAA
Found at i:3470830 original size:16 final size:17
Alignment explanation
Indices: 3470803--3470835 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3470793 TAATTTTATA
3470803 TTAAAAAGATATAAATT
1 TTAAAAAGATATAAATT
*
3470820 TTAAAAA-ATATCAATT
1 TTAAAAAGATATAAATT
3470836 CTTTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
TTAAAAAGATATAAATT
Found at i:3471022 original size:3 final size:3
Alignment explanation
Indices: 3471014--3471039 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3471004 AAATTTCATT
3471014 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3471040 GTCTGTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3471610 original size:17 final size:18
Alignment explanation
Indices: 3471573--3471613 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3471563 TTTAATTTCA
*
3471573 AAATTTTATATAATTATT
1 AAATTTTATATAATAATT
*
3471591 AAATTTTAT-TTATAATT
1 AAATTTTATATAATAATT
3471608 AAATTT
1 AAATTT
3471614 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTTTATATAATAATT
Found at i:3471632 original size:26 final size:26
Alignment explanation
Indices: 3471597--3471668 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
3471587 TATTAAATTT
*
3471597 TATTTATAATTAAATTTAAATAAAAA
1 TATTTTTAATTAAATTTAAATAAAAA
* *
3471623 TATTTTTAATT--ATATAAATAATAA
1 TATTTTTAATTAAATTTAAATAAAAA
*
3471647 TTTTAATTTAATTAAA-TTAAAT
1 TATT--TTTAATTAAATTTAAAT
3471669 TACTAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 14 0.38
26 17 0.46
27 5 0.14
28 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTTTTAATTAAATTTAAATAAAAA
Found at i:3471645 original size:21 final size:20
Alignment explanation
Indices: 3471616--3471654 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3471606 TTAAATTTAA
*
3471616 ATAAAAATATTTTTAATTAT
1 ATAAAAATAATTTTAATTAT
3471636 ATAAATAATAATTTTAATT
1 ATAAA-AATAATTTTAATT
3471655 TAATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAAAATAATTTTAATTAT
Found at i:3471665 original size:31 final size:30
Alignment explanation
Indices: 3471630--3471687 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3471620 AAATATTTTT
*
3471630 AATTATATAAATAATAATTTTAATTTAATTA
1 AATTAAATAAATAA-AATTTTAATTTAATTA
* * *
3471661 AATTAAATTACTAAAATTTTTATTTAA
1 AATTAAATAAATAAAATTTTAATTTAA
3471688 ACTCCGCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 12 0.52
31 11 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
AATTAAATAAATAAAATTTTAATTTAATTA
Found at i:3471755 original size:16 final size:16
Alignment explanation
Indices: 3471734--3471772 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
3471724 TAAATTGATT
3471734 AATATAATTATTT-TTA
1 AATATAATT-TTTATTA
3471750 AATATAATTTTTATTA
1 AATATAATTTTTATTA
3471766 AATATAA
1 AATATAA
3471773 AATTTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATATAATTTTTATTA
Found at i:3472663 original size:16 final size:16
Alignment explanation
Indices: 3472632--3472679 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
3472622 TAAGTTTGAT
* *
3472632 TAATTCAAATTTAAAA
1 TAATTCAAAATCAAAA
*
3472648 TAATTTAAAATCAAAA
1 TAATTCAAAATCAAAA
*
3472664 TAATTCAAAATTAAAA
1 TAATTCAAAATCAAAA
3472680 AATCAATTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATTCAAAATCAAAA
Found at i:3475154 original size:11 final size:11
Alignment explanation
Indices: 3475138--3475166 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
3475128 ATATGTTTTA
3475138 TTTTTTAACTT
1 TTTTTTAACTT
3475149 TTTTTT-ACTT
1 TTTTTTAACTT
3475159 TTTTTTAA
1 TTTTTTAA
3475167 AAAATTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTAACTT
Found at i:3481360 original size:9 final size:9
Alignment explanation
Indices: 3481334--3481367 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3481324 GACTTCTAAT
3481334 GGTTTTAAG
1 GGTTTTAAG
*
3481343 GGCTTTTAAA
1 GG-TTTTAAG
3481353 GGTTTTAAG
1 GGTTTTAAG
3481362 GGTTTT
1 GGTTTT
3481368 GAAACTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.21, C:0.03, G:0.29, T:0.47
Consensus pattern (9 bp):
GGTTTTAAG
Found at i:3481377 original size:19 final size:19
Alignment explanation
Indices: 3481335--3481376 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3481325 ACTTCTAATG
*
3481335 GTTTTAAGGGCTTTTAAAG
1 GTTTTAAGGGCTTTTAAAC
3481354 GTTTTAAGGG-TTTTGAAAC
1 GTTTTAAGGGCTTTT-AAAC
3481373 -TTTT
1 GTTTT
3481377 TCGTGCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.48
Consensus pattern (19 bp):
GTTTTAAGGGCTTTTAAAC
Found at i:3489903 original size:2 final size:2
Alignment explanation
Indices: 3489891--3489924 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3489881 TTTAAAGATA
*
3489891 AT AT AT TT 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
3489925 TTACTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3491431 original size:19 final size:18
Alignment explanation
Indices: 3491405--3491447 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3491395 AAAGAGATGA
3491405 TTAA-AATATATT-TAATG
1 TTAATAATAT-TTATAATG
3491422 TGTAATAATATTTATAATG
1 T-TAATAATATTTATAATG
3491441 TTAATAA
1 TTAATAA
3491448 ATTCAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 11 0.48
19 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (18 bp):
TTAATAATATTTATAATG
Found at i:3491456 original size:18 final size:19
Alignment explanation
Indices: 3491417--3491457 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
3491407 AAAATATATT
*
3491417 TAATGTGTAATAATATTTA
1 TAATGTGTAATAATATTAA
3491436 TAATGT-TAATAA-ATTCAA
1 TAATGTGTAATAATATT-AA
3491454 TAAT
1 TAAT
3491458 ATAATCGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 11 0.55
19 6 0.30
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (19 bp):
TAATGTGTAATAATATTAA
Found at i:3491528 original size:23 final size:22
Alignment explanation
Indices: 3491473--3491535 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
3491463 CGATCAAAAA
* * *
3491473 TTTTAAAAAATAAATAATTTTAT
1 TTTTAATAAAT-AATTATTTAAT
* *
3491496 TTTTACTAAATTATTATTTAAT
1 TTTTAATAAATAATTATTTAAT
3491518 TTATTAATAAATAATTAT
1 TT-TTAATAAATAATTAT
3491536 ATATTATTAG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAATAAATAATTATTTAAT
Found at i:3494924 original size:6 final size:6
Alignment explanation
Indices: 3494908--3494945 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
3494898 ACATATTTTT
* *
3494908 TAAATA AAAATA TAAATA TAAAAA TAAATA TAAATA TA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TA
3494946 TAATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
TAAATA
Found at i:3494958 original size:21 final size:20
Alignment explanation
Indices: 3494932--3494984 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
3494922 AATATAAAAA
3494932 TAAATATAAATATATAATTTT
1 TAAATATAAATATAT-ATTTT
*
3494953 TAAATATATAA-AAATATTTT
1 TAAATATA-AATATATATTTT
*
3494973 T-AATTTAAATAT
1 TAAATATAAATAT
3494985 TTATATGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.07
19 6 0.22
20 6 0.22
21 11 0.41
22 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATATAAATATATATTTT
Found at i:3500190 original size:22 final size:22
Alignment explanation
Indices: 3500146--3500190 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3500136 TTGTCTAACC
* * * *
3500146 AAAAAATTAATTTAATATTTTA
1 AAAAAATTAAATAAAAATATTA
3500168 AAAAAATTAAATAAAAATATTA
1 AAAAAATTAAATAAAAATATTA
3500190 A
1 A
3500191 GTTTAAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAAATTAAATAAAAATATTA
Found at i:3500208 original size:13 final size:13
Alignment explanation
Indices: 3500169--3500210 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3500159 AATATTTTAA
*
3500169 AAAAATTAAA-TA
1 AAAAATTAAATTT
*
3500181 AAAATATTAAGTTT
1 AAAA-ATTAAATTT
3500195 AAAAATTAAATTT
1 AAAAATTAAATTT
3500208 AAA
1 AAA
3500211 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 4 0.16
13 16 0.64
14 5 0.20
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
AAAAATTAAATTT
Found at i:3502444 original size:2 final size:2
Alignment explanation
Indices: 3502422--3502469 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
3502412 TTTGATTCTG
* *
3502422 AT AT -T AT AA AT AT AT AG 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
3502463 AT AT AT A
1 AT AT AT A
3502470 AAGTGACAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3503879 original size:23 final size:20
Alignment explanation
Indices: 3503841--3503888 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
3503831 TTATTTATTA
*
3503841 TATTATTAAAATATTATTTT
1 TATTATTAAAATATTAATTT
3503861 TATTATTTAATAATGATTAATTT
1 TATTA-TTAA-AAT-ATTAATTT
*
3503884 AATTA
1 TATTA
3503889 AAATTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
22 3 0.13
23 11 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTATTAAAATATTAATTT
Found at i:3503880 original size:31 final size:31
Alignment explanation
Indices: 3503818--3503880 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
3503808 AAAAAGGACG
* * *
3503818 AAATTTTATTTTATTATTTATTATATTATTA
1 AAATATTATTTTATTATTTAATATATGATTA
3503849 AAATATTATTTTTATTATTTAATA-ATGATTA
1 AAATATTA-TTTTATTATTTAATATATGATTA
3503880 A
1 A
3503881 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (31 bp):
AAATATTATTTTATTATTTAATATATGATTA
Found at i:3505200 original size:21 final size:22
Alignment explanation
Indices: 3505154--3505200 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
3505144 ATATTATAAT
*
3505154 ATATATAAAAAATTATATATTT
1 ATATATAAAAAATTATATATTA
*
3505176 ATAT-TAAAATATTA-ATAATTA
1 ATATATAAAAAATTATAT-ATTA
3505197 ATAT
1 ATAT
3505201 CATATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 16 0.73
22 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATATAAAAAATTATATATTA
Found at i:3507214 original size:3 final size:3
Alignment explanation
Indices: 3507206--3507236 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3507196 TTAGCAGGTA
3507206 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3507237 AGGGAATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3515622 original size:2 final size:2
Alignment explanation
Indices: 3515615--3515640 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3515605 CATTAAAATA
3515615 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
3515641 GGGAACAAAA
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:3516902 original size:22 final size:21
Alignment explanation
Indices: 3516870--3516932 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
3516860 GTTTTTTAAA
*
3516870 AAATAAATTTATTAAATATTT
1 AAATTAATTTATTAAATATTT
* *
3516891 AAAATTATTTTA-TAAATTAATT
1 -AAATTAATTTATTAAA-TATTT
*
3516913 AAATTAAGTTATTAAA-ATTT
1 AAATTAATTTATTAAATATTT
3516933 TGGCTGTCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
20 3 0.09
21 13 0.39
22 17 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATTAATTTATTAAATATTT
Found at i:3517607 original size:16 final size:16
Alignment explanation
Indices: 3517588--3517655 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
3517578 ATAAATATCT
3517588 TAAAATATATAAAATA
1 TAAAATATATAAAATA
* *
3517604 TAAATTAT-TAATATAA
1 TAAAATATATAAAAT-A
* *
3517620 TAAATTTTATATAAATA
1 TAAAATATATA-AAATA
* *
3517637 TAAAATATTTTAAATA
1 TAAAATATATAAAATA
3517653 TAA
1 TAA
3517656 TTATGATATA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
15 5 0.12
16 23 0.56
17 10 0.24
18 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATATATAAAATA
Found at i:3517614 original size:24 final size:25
Alignment explanation
Indices: 3517568--3517623 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
3517558 AAATAACATC
*
3517568 ATATA-AAAAAATAAATATCTTAAA
1 ATATATAAAAAATAAATATATTAAA
* *
3517592 ATATATAAAATATAAAT-TATTAAT
1 ATATATAAAAAATAAATATATTAAA
3517616 ATA-ATAAA
1 ATATATAAA
3517624 TTTTATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 5 0.18
24 13 0.46
25 10 0.36
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
ATATATAAAAAATAAATATATTAAA
Found at i:3517665 original size:33 final size:33
Alignment explanation
Indices: 3517594--3517666 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 33
3517584 ATCTTAAAAT
* *
3517594 ATATAAAATATAAATTATTAATATAATAAATTTT
1 ATAT-AAATATAAAATATTAATATAATAAATTTG
*
3517628 ATATAAATATAAAATATT-TTA-AATATAATTATG
1 ATATAAATATAAAATATTAATATAATA-AATT-TG
3517661 ATATAA
1 ATATAA
3517667 TAAATATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 4 0.12
32 6 0.18
33 20 0.59
34 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (33 bp):
ATATAAATATAAAATATTAATATAATAAATTTG
Found at i:3519791 original size:3 final size:3
Alignment explanation
Indices: 3519783--3519829 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3519773 ATCCTAAGTT
3519783 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3519830 TAGTTCTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3530582 original size:25 final size:25
Alignment explanation
Indices: 3530549--3530597 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3530539 TTTTATATAA
*
3530549 TCATGATTTTA-AATATAAAATTAAT
1 TCATAATTTTATAAT-TAAAATTAAT
*
3530574 TCATAATTTTATAATTAAATTTAA
1 TCATAATTTTATAATTAAAATTAA
3530598 ATATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (25 bp):
TCATAATTTTATAATTAAAATTAAT
Found at i:3537360 original size:21 final size:21
Alignment explanation
Indices: 3537322--3537394 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
3537312 TAGACTCAAT
*
3537322 AATATTAAATGTAATTATATA
1 AATATTAAATATAATTATATA
* * *
3537343 AATATTATATATATTTATGTAA
1 AATATTAAATATAATTATAT-A
*
3537365 AATAATTAAAATATAACCTAATATA
1 AAT-ATT-AAATATAA--TTATATA
3537390 AATAT
1 AATAT
3537395 ATATTTTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
21 16 0.41
22 4 0.10
23 3 0.08
24 8 0.21
25 4 0.10
26 4 0.10
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (21 bp):
AATATTAAATATAATTATATA
Found at i:3537436 original size:32 final size:29
Alignment explanation
Indices: 3537383--3537489 Score: 83
Period size: 32 Copynumber: 3.5 Consensus size: 29
3537373 AAATATAACC
* *
3537383 TAATATAAATATATATTTTAAAATTTATA
1 TAATATAAATATATATATTAAAATTGATA
3537412 TAATATAAATTATTTATATATTAAAATTGATA
1 TAATATAAA-TA--TATATATTAAAATTGATA
* * *
3537444 TAAATGTAAA-ATATTATAAATATAATTATGATA
1 T-AATATAAATATA-TAT-ATTA-AAAT-TGATA
3537477 TAATA-AAATATAT
1 TAATATAAATATAT
3537490 TAATATGATA
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
29 11 0.17
30 5 0.08
31 8 0.13
32 26 0.41
33 13 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (29 bp):
TAATATAAATATATATATTAAAATTGATA
Found at i:3537514 original size:23 final size:23
Alignment explanation
Indices: 3537453--3537514 Score: 54
Period size: 23 Copynumber: 2.6 Consensus size: 23
3537443 ATAAATGTAA
*
3537453 AATATTATAAATATAATTATGATAT
1 AATA-TATAAAT-TAATTATGATAG
* *
3537478 AATAAAATATATTAA-TATGATACG
1 AAT-ATATAAATTAATTATGATA-G
3537502 AATATATAAATTA
1 AATATATAAATTA
3537515 TTAAATTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
23 15 0.50
24 6 0.20
25 8 0.27
26 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
AATATATAAATTAATTATGATAG
Found at i:3547722 original size:18 final size:18
Alignment explanation
Indices: 3547677--3547724 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
3547667 TTATTTTTTT
3547677 ATTTTAA-AT-AAA-TAA
1 ATTTTAATATAAAATTAA
*
3547692 ATTTGAAGT-TAAAATTAA
1 ATTTTAA-TATAAAATTAA
3547710 ATTTTAATATAAAAT
1 ATTTTAATATAAAAT
3547725 ATTGAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 6 0.23
16 1 0.04
17 4 0.15
18 15 0.58
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
ATTTTAATATAAAATTAA
Found at i:3548127 original size:24 final size:24
Alignment explanation
Indices: 3548075--3548127 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
3548065 AACTTGTCTT
* * **
3548075 AAATATAATATAAAAAAATAATTA
1 AAATACAATACAAAAAAATAAACA
3548099 AAATACAATACAAAAAAATAAACA
1 AAATACAATACAAAAAAATAAACA
*
3548123 CAATA
1 AAATA
3548128 AAAAACACAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (24 bp):
AAATACAATACAAAAAAATAAACA
Found at i:3548231 original size:8 final size:8
Alignment explanation
Indices: 3548220--3548264 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
3548210 AAATACATAA
3548220 TTTTTTTC
1 TTTTTTTC
**
3548228 TTTTTCAC
1 TTTTTTTC
3548236 TTTTTTTC
1 TTTTTTTC
3548244 TTTTTTT-
1 TTTTTTTC
3548251 TCTTTTTTC
1 T-TTTTTTC
3548260 TTTTT
1 TTTTT
3548265 ATATTTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 1 0.03
8 29 0.94
9 1 0.03
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTC
Found at i:3548272 original size:16 final size:16
Alignment explanation
Indices: 3548219--3548272 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
3548209 TAAATACATA
3548219 ATTTTTTTCTTTTTCA-
1 ATTTTTTTCTTTTT-AT
*
3548235 CTTTTTTTCTTTTT-T
1 ATTTTTTTCTTTTTAT
*
3548250 TTCTTTTTTCTTTTTAT
1 AT-TTTTTTCTTTTTAT
3548267 ATTTTT
1 ATTTTT
3548273 CTCTATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 1 0.03
16 29 0.91
17 2 0.06
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (16 bp):
ATTTTTTTCTTTTTAT
Found at i:3548740 original size:22 final size:22
Alignment explanation
Indices: 3548715--3548760 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3548705 GAGACACTAT
*
3548715 ATAAATACAACATAAATA-AAAA
1 ATAAATAAAACAT-AATACAAAA
*
3548737 ATAATTAAAACATAATACAAAA
1 ATAAATAAAACATAATACAAAA
3548759 AT
1 AT
3548761 GACATGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.22
Consensus pattern (22 bp):
ATAAATAAAACATAATACAAAA
Found at i:3549023 original size:14 final size:15
Alignment explanation
Indices: 3549006--3549046 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
3548996 AATACTTAAA
3549006 TTTTTTTCTCTCTT-
1 TTTTTTTCTCTCTTC
*
3549020 TTTTTTTCT-TATTC
1 TTTTTTTCTCTCTTC
*
3549034 TTTTTTTCCCTCT
1 TTTTTTTCTCTCT
3549047 CTCTCTGCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 3 0.14
14 17 0.77
15 2 0.09
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTCTCTCTTC
Found at i:3553209 original size:20 final size:20
Alignment explanation
Indices: 3553152--3553207 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
3553142 AGTGTTTTAC
* *
3553152 ATTATGATTTAAGGTTTAGA
1 ATTAAGATTTAAGATTTAGA
*
3553172 AGTAAGATTTAAGATTTAGA
1 ATTAAGATTTAAGATTTAGA
*
3553192 ATTAAGGTTT-AGATTT
1 ATTAAGATTTAAGATTT
3553208 TAAATTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.43
Consensus pattern (20 bp):
ATTAAGATTTAAGATTTAGA
Done.