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 9 of 31
Found at i:2167701 original size:20 final size:19
Alignment explanation
Indices: 2167664--2167703 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2167654 TAATTATTTA
2167664 ATATAATATAATTTAAATT
1 ATATAATATAATTTAAATT
2167683 ATATAATTATTAA-TTAAATT
1 ATATAA-TA-TAATTTAAATT
2167703 A
1 A
2167704 AAATTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 10 0.53
21 3 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATAATATAATTTAAATT
Found at i:2167726 original size:25 final size:26
Alignment explanation
Indices: 2167673--2167726 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
2167663 AATATAATAT
* * **
2167673 AATTTAAATTATATAATTATTAATTA
1 AATTAAAATTATATAACTATTAAAAA
2167699 AATTAAAATT-TATAACTATTAAAAA
1 AATTAAAATTATATAACTATTAAAAA
2167724 AAT
1 AAT
2167727 CTCTTCAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTAAAATTATATAACTATTAAAAA
Found at i:2168512 original size:22 final size:22
Alignment explanation
Indices: 2168487--2168530 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2168477 TTTATTTATT
*
2168487 GTTTAATATATTAAAATTAATA
1 GTTTAATATATTAAAAATAATA
**
2168509 GTTTCTTATATTAAAAATAATA
1 GTTTAATATATTAAAAATAATA
2168531 CTTATTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
GTTTAATATATTAAAAATAATA
Found at i:2168543 original size:22 final size:22
Alignment explanation
Indices: 2168493--2168539 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2168483 TATTGTTTAA
* * *
2168493 TATATTAAAATTAATAGTTTCT
1 TATATTAAAAATAATAGCTTAT
2168515 TATATTAAAAATAATA-CTTAT
1 TATATTAAAAATAATAGCTTAT
2168536 TATA
1 TATA
2168540 ATTACATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
TATATTAAAAATAATAGCTTAT
Found at i:2169693 original size:27 final size:26
Alignment explanation
Indices: 2169659--2169709 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
2169649 TTATATAAAA
* * *
2169659 ATAATAAATATTTTAAAATTTATATT
1 ATAATAAATAATTAAAAAATTATATT
2169685 ATAATTAAATAATTAAAAAATTATA
1 ATAA-TAAATAATTAAAAAATTATA
2169710 AGTAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAATAAATAATTAAAAAATTATATT
Found at i:2169778 original size:21 final size:21
Alignment explanation
Indices: 2169754--2169810 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
2169744 ATTATCAATG
2169754 TAAAATTTATTAATTTAAAAA
1 TAAAATTTATTAATTTAAAAA
2169775 TAAAA-TT-TTAATTT-AAAA
1 TAAAATTTATTAATTTAAAAA
**
2169793 TTTAATTTAATTAATTTA
1 TAAAATTT-ATTAATTTA
2169811 TATAATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 7 0.23
19 9 0.30
20 2 0.07
21 12 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAATTTATTAATTTAAAAA
Found at i:2169798 original size:12 final size:13
Alignment explanation
Indices: 2169775--2169865 Score: 52
Period size: 13 Copynumber: 7.1 Consensus size: 13
2169765 AATTTAAAAA
2169775 TAAAATTTTAATT
1 TAAAATTTTAATT
2169788 TAAAA-TTTAATT
1 TAAAATTTTAATT
2169800 T--AA--TTAATT
1 TAAAATTTTAATT
2169809 TATATAATTATT--TT
1 TA-A-AATT-TTAATT
*
2169823 TAAAATTTAAAATT
1 TAAAATTT-TAATT
**
2169837 TAAAAAATTTTAAAC
1 T--AAAATTTTAATT
2169852 TAAAATTTTAATT
1 TAAAATTTTAATT
2169865 T
1 T
2169866 TTATATTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 24
0.67 0.07 0.27
Matches are distributed among these distances:
9 7 0.12
10 2 0.03
11 1 0.02
12 12 0.20
13 19 0.32
14 7 0.12
15 3 0.05
16 9 0.15
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (13 bp):
TAAAATTTTAATT
Found at i:2171254 original size:2 final size:2
Alignment explanation
Indices: 2171247--2171283 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2171237 CAAATATTTA
2171247 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2171284 GTGCATGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2180126 original size:2 final size:2
Alignment explanation
Indices: 2180119--2180149 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2180109 ATGATGCCAT
2180119 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
2180150 TTGTTGAGAA
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:2180468 original size:12 final size:12
Alignment explanation
Indices: 2180451--2180475 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2180441 AATATGTTAC
2180451 TAATTTAATTTT
1 TAATTTAATTTT
2180463 TAATTTAATTTT
1 TAATTTAATTTT
2180475 T
1 T
2180476 TTATTCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATTTAATTTT
Found at i:2183656 original size:13 final size:13
Alignment explanation
Indices: 2183640--2183664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2183630 AAAATTTCAA
2183640 AAAAATAAAAGAG
1 AAAAATAAAAGAG
2183653 AAAAATAAAAGA
1 AAAAATAAAAGA
2183665 TAATTCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (13 bp):
AAAAATAAAAGAG
Found at i:2187424 original size:22 final size:24
Alignment explanation
Indices: 2187399--2187442 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2187389 AAATAATTAT
*
2187399 AATAAAA-ATT-TAGTTTTAAAAG
1 AATAAAATATTATAATTTTAAAAG
2187421 AATAAAATATTATAATTTTAAA
1 AATAAAATATTATAATTTTAAA
2187443 TTATCGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (24 bp):
AATAAAATATTATAATTTTAAAAG
Found at i:2187474 original size:39 final size:39
Alignment explanation
Indices: 2187430--2187510 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
2187420 GAATAAAATA
*
2187430 TTATAATTTTAAATTATCGATAAAAAAGATTTAAATTTT
1 TTATAATTTTAAATTATAGATAAAAAAGATTTAAATTTT
*
2187469 TTATAATTTTAAATTATAGATAAAAAATATTTAAATTTT
1 TTATAATTTTAAATTATAGATAAAAAAGATTTAAATTTT
2187508 TTA
1 TTA
2187511 AAATAATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (39 bp):
TTATAATTTTAAATTATAGATAAAAAAGATTTAAATTTT
Found at i:2187657 original size:23 final size:22
Alignment explanation
Indices: 2187617--2187668 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
2187607 TATTTCATGA
*
2187617 AATA-AATAAATATATTATTAT
1 AATATAATAAATATATTATAAT
*
2187638 AATATAATAAATAATTTTATAAT
1 AATATAATAAAT-ATATTATAAT
*
2187661 AAAATAAT
1 AATATAAT
2187669 TATATATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
23 15 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATATAATAAATATATTATAAT
Found at i:2187660 original size:15 final size:16
Alignment explanation
Indices: 2187639--2187674 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2187629 TATTATTATA
2187639 ATATAAT-AAATAATT
1 ATATAATAAAATAATT
*
2187654 TTATAATAAAATAATT
1 ATATAATAAAATAATT
2187670 ATATA
1 ATATA
2187675 TGTAAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAATAAAATAATT
Found at i:2188408 original size:24 final size:24
Alignment explanation
Indices: 2188324--2188431 Score: 80
Period size: 24 Copynumber: 4.4 Consensus size: 24
2188314 TTTAAATTTA
2188324 AATTTTAATAA-TA--TTTAATA-
1 AATTTTAATAATTATTTTTAATAT
* *
2188344 AATTTATAAAAATTATATATTAAATAT
1 AATTT-TAATAATTAT-T-TTTAATAT
* *
2188371 AAATAGTTAGTAATTATTTTTAATAT
1 -AAT-TTTAATAATTATTTTTAATAT
* *
2188397 AATTTTAATAATTATTCTTAAAAT
1 AATTTTAATAATTATTTTTAATAT
2188421 AATTTTTAATA
1 AA-TTTTAATA
2188432 GATAAGAGTA
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
20 5 0.07
21 5 0.07
22 2 0.03
24 19 0.28
25 11 0.16
26 13 0.19
27 1 0.01
28 11 0.16
29 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (24 bp):
AATTTTAATAATTATTTTTAATAT
Found at i:2190452 original size:34 final size:34
Alignment explanation
Indices: 2190406--2190590 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
2190396 GTAAAAACCA
*
2190406 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2190440 CCATTTAGTCAACAATGATAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
2190474 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2190508 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2190542 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2190575 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2190591 TCTCCCACTT
Statistics
Matches: 133, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
33 18 0.14
34 111 0.83
35 4 0.03
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2195053 original size:34 final size:34
Alignment explanation
Indices: 2195007--2195190 Score: 246
Period size: 34 Copynumber: 5.4 Consensus size: 34
2194997 GTAAAAACCA
*
2195007 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2195041 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
2195075 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2195109 CCATTTAATCAACAATGGTAAGCTACCAAATTTT
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2195143 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2195176 CCATTTAATCAACAA
1 CCATTTAATCAACAA
2195191 AAAGGATTTA
Statistics
Matches: 133, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
33 17 0.13
34 112 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2197735 original size:25 final size:25
Alignment explanation
Indices: 2197694--2197741 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2197684 TTTAAATTTT
*
2197694 ATTACTATTTGTTAAAATTAATAAA
1 ATTACTATTTGTTAAAAATAATAAA
*
2197719 ATTATTATTT-TTAAAAAATAATA
1 ATTACTATTTGTT-AAAAATAATA
2197742 TATTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTACTATTTGTTAAAAATAATAAA
Found at i:2197869 original size:2 final size:2
Alignment explanation
Indices: 2197858--2197894 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2197848 ATTACTTTTA
2197858 AT AT -T 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
2197895 CTTTCAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2206178 original size:16 final size:16
Alignment explanation
Indices: 2206145--2206177 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2206135 TTTTTAAAAG
2206145 TTAATATTGAATAATT
1 TTAATATTGAATAATT
*
2206161 TTAATATT-TATAATT
1 TTAATATTGAATAATT
2206176 TT
1 TT
2206178 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TTAATATTGAATAATT
Found at i:2207693 original size:12 final size:12
Alignment explanation
Indices: 2207678--2207703 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2207668 ACACAAATAA
2207678 AATTGTAATCAT
1 AATTGTAATCAT
2207690 AATTGTAATCAT
1 AATTGTAATCAT
2207702 AA
1 AA
2207704 AATTGTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (12 bp):
AATTGTAATCAT
Found at i:2207707 original size:14 final size:14
Alignment explanation
Indices: 2207674--2207716 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
2207664 GTTAACACAA
2207674 ATAAAATTGTAATC
1 ATAAAATTGTAATC
2207688 AT--AATTGTAATC
1 ATAAAATTGTAATC
*
2207700 ATAAAATTGTAAAC
1 ATAAAATTGTAATC
2207714 ATA
1 ATA
2207717 TTTTATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 12 0.46
14 14 0.54
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (14 bp):
ATAAAATTGTAATC
Found at i:2207937 original size:47 final size:47
Alignment explanation
Indices: 2207881--2207979 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 47
2207871 TTAATTAATA
* *
2207881 ATATA-TTTTTAATTTACTTTCTATCAAATTTATATTATATAATGAT
1 ATATATTTTTTAATTTACTCTCTATCAAATTCATATTATATAATGAT
* * *
2207927 ATATATTTTTTAATTTGCTCTCTTTGAAATTCATATTATATAATGAT
1 ATATATTTTTTAATTTACTCTCTATCAAATTCATATTATATAATGAT
2207974 ATATAT
1 ATATAT
2207980 GATTAGACGT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 5 0.11
47 42 0.89
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (47 bp):
ATATATTTTTTAATTTACTCTCTATCAAATTCATATTATATAATGAT
Found at i:2213443 original size:13 final size:13
Alignment explanation
Indices: 2213425--2213451 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2213415 ATCTAAAGCC
2213425 AACTGACCAATTT
1 AACTGACCAATTT
2213438 AACTGACCAATTT
1 AACTGACCAATTT
2213451 A
1 A
2213452 GCTTAATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
AACTGACCAATTT
Found at i:2221958 original size:16 final size:16
Alignment explanation
Indices: 2221923--2221983 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
2221913 TTTTAAAATT
* *
2221923 TTTAAGTTATTTTTAGA
1 TTTAAATTA-TTTTAAA
2221940 TTTAAATTATTTTAAA
1 TTTAAATTATTTTAAA
* * *
2221956 TTTAGATTTTTTTAAG
1 TTTAAATTATTTTAAA
*
2221972 TTTGAATTATTT
1 TTTAAATTATTT
2221984 CGAGTTCAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 28 0.78
17 8 0.22
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:2222867 original size:16 final size:16
Alignment explanation
Indices: 2222846--2222889 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2222836 ATTATCTAGG
*
2222846 TCATTTCGAGTTCGGA
1 TCATTTCGAGTTCGAA
*
2222862 TCATTT-TAGGTTCGAA
1 TCATTTCGA-GTTCGAA
2222878 TCATTTCGAGTT
1 TCATTTCGAGTT
2222890 TAAGTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.04
16 21 0.91
17 1 0.04
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (16 bp):
TCATTTCGAGTTCGAA
Found at i:2223495 original size:15 final size:16
Alignment explanation
Indices: 2223466--2223496 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2223456 TTTTGAAAAT
2223466 TTTAATATATTTGTTA
1 TTTAATATATTTGTTA
2223482 TTTAATAT-TTTGTTA
1 TTTAATATATTTGTTA
2223497 ATATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTAATATATTTGTTA
Found at i:2223608 original size:13 final size:15
Alignment explanation
Indices: 2223584--2223615 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2223574 TATTATTATA
2223584 AAATTCATAAAAT-T
1 AAATTCATAAAATAT
2223598 AAATT-ATAAAATAT
1 AAATTCATAAAATAT
2223612 AAAT
1 AAAT
2223616 ATTATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTCATAAAATAT
Found at i:2223721 original size:30 final size:30
Alignment explanation
Indices: 2223685--2223748 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
2223675 TGTCAAAACT
2223685 AATTTTTAAATAAACTTAAT-TTTTTACTCA
1 AATTTTT-AATAAACTTAATATTTTTACTCA
** * *
2223715 AATTTTTTTTAAATTTAATATTTTTATTCA
1 AATTTTTAATAAACTTAATATTTTTACTCA
2223745 AATT
1 AATT
2223749 CTCTCAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (30 bp):
AATTTTTAATAAACTTAATATTTTTACTCA
Found at i:2226529 original size:2 final size:2
Alignment explanation
Indices: 2226522--2226556 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2226512 AAGCAGTATG
*
2226522 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2226557 TCAACTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2230706 original size:2 final size:2
Alignment explanation
Indices: 2230694--2230734 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2230684 TCAGGAGATA
2230694 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2230735 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2239976 original size:1 final size:1
Alignment explanation
Indices: 2239972--2240001 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2239962 CCCCCCTTCT
*
2239972 CCCCCCTCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2240002 TCTAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:2240223 original size:32 final size:32
Alignment explanation
Indices: 2240187--2240251 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
2240177 TTTGGTGATA
*
2240187 ATTTATTTTGATTTTAAATT-ATTTTAAATTTG
1 ATTTATTTT-AATTTAAATTCATTTTAAATTTG
* *
2240219 ATTTATTTTAATTTCAATTCATTTTAATTTTG
1 ATTTATTTTAATTTAAATTCATTTTAAATTTG
2240251 A
1 A
2240252 ATCAATCGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 8 0.28
32 21 0.72
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (32 bp):
ATTTATTTTAATTTAAATTCATTTTAAATTTG
Found at i:2240224 original size:16 final size:16
Alignment explanation
Indices: 2240205--2240251 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2240195 TGATTTTAAA
2240205 TTATTTTAAATTTGAT
1 TTATTTTAAATTTGAT
*
2240221 TTATTTT-AATTTCAAT
1 TTATTTTAAATTT-GAT
* *
2240237 TCATTTTAATTTTGA
1 TTATTTTAAATTTGA
2240252 ATCAATCGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (16 bp):
TTATTTTAAATTTGAT
Found at i:2242601 original size:21 final size:22
Alignment explanation
Indices: 2242566--2242607 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2242556 TTCTAAGCTT
* *
2242566 CAAATCTTATTGGCTTCTTATA
1 CAAATCATATTGGCTTATTATA
2242588 CAAATCAT-TTGGCTTATTAT
1 CAAATCATATTGGCTTATTAT
2242608 CTTGTATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (22 bp):
CAAATCATATTGGCTTATTATA
Found at i:2244978 original size:29 final size:29
Alignment explanation
Indices: 2244943--2244998 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2244933 AATTAAAAAA
*
2244943 TAATAAGAATTAAATTAATTTAAATTTTT
1 TAATAAGAATTAAATTAAATTAAATTTTT
* *
2244972 TAATAAGTATTAAATTAAATTATATTT
1 TAATAAGAATTAAATTAAATTAAATTT
2244999 AAATTATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (29 bp):
TAATAAGAATTAAATTAAATTAAATTTTT
Found at i:2245002 original size:11 final size:10
Alignment explanation
Indices: 2244986--2245031 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
2244976 AAGTATTAAA
2244986 TTAAATTATAT
1 TTAAATTAT-T
2244997 TTAAATTA--
1 TTAAATTATT
2245005 TTAAA-TATT
1 TTAAATTATT
2245014 TTAAAGTTATT
1 TTAAA-TTATT
2245025 TTAAATT
1 TTAAATT
2245032 TAATTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
7 2 0.06
8 5 0.16
9 5 0.16
10 2 0.06
11 17 0.55
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (10 bp):
TTAAATTATT
Found at i:2245052 original size:34 final size:34
Alignment explanation
Indices: 2245014--2245088 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
2245004 ATTAAATATT
2245014 TTAAAGTTATTTTAAATTTAATTATATATTAATC
1 TTAAAGTTATTTTAAATTTAATTATATATTAATC
* * * *
2245048 TTAAAATTATTTTTAATTTAATTATCTATTAATT
1 TTAAAGTTATTTTAAATTTAATTATATATTAATC
2245082 TTAAAGT
1 TTAAAGT
2245089 AAATTTAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (34 bp):
TTAAAGTTATTTTAAATTTAATTATATATTAATC
Found at i:2245084 original size:17 final size:16
Alignment explanation
Indices: 2245020--2245085 Score: 55
Period size: 15 Copynumber: 4.0 Consensus size: 16
2245010 TATTTTAAAG
*
2245020 TTATT-TTAAATTTAA
1 TTATTATTAATTTTAA
*
2245035 TTATATATTAATCTTAAAA
1 TTAT-TATTAAT-TT-TAA
*
2245054 TTATTTTTAA-TTTAA
1 TTATTATTAATTTTAA
2245069 TTATCTATTAATTTTAA
1 TTAT-TATTAATTTTAA
2245086 AGTAAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 10 0.25
16 8 0.20
17 9 0.22
18 7 0.17
19 6 0.15
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTATTAATTTTAA
Found at i:2248900 original size:10 final size:10
Alignment explanation
Indices: 2248885--2248920 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
2248875 CAATTATTAA
2248885 TTATTTATTT
1 TTATTTATTT
2248895 TTATTTATTT
1 TTATTTATTT
*
2248905 TTGTTTATTT
1 TTATTTATTT
2248915 TTATTT
1 TTATTT
2248921 TTTGACTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (10 bp):
TTATTTATTT
Found at i:2249461 original size:37 final size:37
Alignment explanation
Indices: 2249419--2249528 Score: 93
Period size: 37 Copynumber: 2.9 Consensus size: 37
2249409 TATTTCAAAG
2249419 TTAATATATAATTGAAATAAAAATAATTTTAAAAT-AT
1 TTAATAT-TAATTGAAATAAAAATAATTTTAAAATAAT
* *
2249456 TTAATATGT-ATTTAAATTAAAATATAA-CTTAATAATAAT
1 TTAATAT-TAATTGAAA-TAAAA-ATAATTTTAA-AATAAT
** *
2249495 TTAAT-TTAACAGTAATTAAAAATAATTTTAAAAT
1 TTAATATTAATTG-AAATAAAAATAATTTTAAAAT
2249529 TAACTAAATC
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
36 6 0.10
37 25 0.43
38 18 0.31
39 9 0.16
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (37 bp):
TTAATATTAATTGAAATAAAAATAATTTTAAAATAAT
Found at i:2251578 original size:11 final size:11
Alignment explanation
Indices: 2251533--2251580 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
2251523 GTTAATTCTC
2251533 AATGTATTTAAA
1 AATGT-TTTAAA
* *
2251545 AATCTTTTATAT
1 AATGTTTTA-AA
2251557 AATGATTTTAAA
1 AATG-TTTTAAA
2251569 AATGTTTTAAA
1 AATGTTTTAAA
2251580 A
1 A
2251581 TCATTTCGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
11 12 0.40
12 13 0.43
13 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (11 bp):
AATGTTTTAAA
Found at i:2253856 original size:11 final size:11
Alignment explanation
Indices: 2253840--2253918 Score: 56
Period size: 11 Copynumber: 7.2 Consensus size: 11
2253830 TAAGGTTGAA
2253840 ATTATATTTAT
1 ATTATATTTAT
2253851 ATTATATTTAT
1 ATTATATTTAT
* *
2253862 GTTATTTATTTAA
1 ATTA--TATTTAT
* *
2253875 ATAATAATTAT
1 ATTATATTTAT
*
2253886 ATT-TAATT-T
1 ATTATATTTAT
*
2253895 ATTAGTATTTTT
1 ATTA-TATTTAT
2253907 A-TATATTTAT
1 ATTATATTTAT
2253917 AT
1 AT
2253919 AAGATTTTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
9 4 0.08
10 12 0.23
11 27 0.51
12 2 0.04
13 8 0.15
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:2253916 original size:20 final size:18
Alignment explanation
Indices: 2253891--2253946 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 18
2253881 ATTATATTTA
2253891 ATTTATTAGTATTTTTATAT
1 ATTTATTAG-ATTTTTAT-T
*
2253911 ATTTATATAAGATTTTTGTT
1 ATTTAT-T-AGATTTTTATT
2253931 ATTTATT--ATTTTTATT
1 ATTTATTAGATTTTTATT
2253947 TTATTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 8 0.25
19 1 0.03
20 13 0.41
21 8 0.25
22 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
ATTTATTAGATTTTTATT
Found at i:2257614 original size:2 final size:2
Alignment explanation
Indices: 2257609--2257643 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2257599 AACCTTAAAA
2257609 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2257644 CATGAATACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2262536 original size:16 final size:18
Alignment explanation
Indices: 2262517--2262550 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2262507 TTTTTTATTT
2262517 AAATATA-T-AAATAATA
1 AAATATATTAAAATAATA
2262533 AAATATATTAAAATAATA
1 AAATATATTAAAATAATA
2262551 TTCATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATATTAAAATAATA
Found at i:2262560 original size:29 final size:29
Alignment explanation
Indices: 2262458--2262566 Score: 91
Period size: 29 Copynumber: 3.7 Consensus size: 29
2262448 TAGTATTTAT
2262458 TAATATTAATATAATACATAATATATTATAAA
1 TAATATT-ATATAATA-ATAATATATTA-AAA
* ** * *
2262490 TAAAATTATACTAATAATTTTTTATTTAAA
1 TAATATTATA-TAATAATAATATATTAAAA
*
2262520 T-ATA-TAAATAATAA-AATATATTAAAA
1 TAATATTATATAATAATAATATATTAAAA
2262546 TAATATTCATATAATAA-AATA
1 TAATATT-ATATAATAATAATA
2262567 AATCAGGATA
Statistics
Matches: 61, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
26 9 0.15
27 9 0.15
28 4 0.07
29 14 0.23
30 4 0.07
31 10 0.16
32 11 0.18
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATATTATATAATAATAATATATTAAAA
Found at i:2264891 original size:2 final size:2
Alignment explanation
Indices: 2264884--2264914 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2264874 TTTGATTTGT
2264884 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2264915 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2264919 original size:2 final size:2
Alignment explanation
Indices: 2264914--2264946 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2264904 TCTCTCTCTC
2264914 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2264947 TTCACTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2265866 original size:14 final size:14
Alignment explanation
Indices: 2265847--2265876 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2265837 CTTCTTCTTA
2265847 AACCAAATGGAATG
1 AACCAAATGGAATG
2265861 AACCAAATGGAATG
1 AACCAAATGGAATG
2265875 AA
1 AA
2265877 ACCTCTCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (14 bp):
AACCAAATGGAATG
Found at i:2272282 original size:15 final size:16
Alignment explanation
Indices: 2272246--2272283 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2272236 TCTAAATTAA
2272246 AAAATAATACATAAGAT
1 AAAA-AATACATAAGAT
*
2272263 AAAAAATATATAAG-T
1 AAAAAATACATAAGAT
2272278 AAAAAA
1 AAAAAA
2272284 ATAAAAACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 9 0.45
17 4 0.20
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (16 bp):
AAAAAATACATAAGAT
Found at i:2275944 original size:211 final size:211
Alignment explanation
Indices: 2275359--2275989 Score: 983
Period size: 212 Copynumber: 3.0 Consensus size: 211
2275349 TGGTCAGTTA
** * * * * *
2275359 TCATGGCTGATATATAGAAACGTGACCGAACACCGTTGTTGGTTAATTTATAATTTCATGATGCA
1 TCATGGCTGATATATAGAAACGTTTCCAAACGCTGTTTTTGGTTAATTTATAGTTTCATGATGCA
*
2275424 ATAGTTGAAAAACGAGATTAAAGCATTGTTGAAAACGATCTCATACTTCTGCATCAAGTTTAGTG
66 ATAGTTGAAAAACGAGATTAAAGCATTGTTGAAAACGATCTCGTACTTCTGCATCAAGTTTAGTG
* *
2275489 GTTATTTGCATTTTCTATGACTATTTATGTTCTTAATAGACTTTCTTCGCAGGTTACAAAAGTCT
131 GTTATTTGCATTTTCTATGACTATTTATTTTCTTAGTAGACTTTCTTCGCAGGTTACAAAAGTCT
2275554 ATTTTTGTGCATTTGT
196 ATTTTTGTGCATTTGT
* * *
2275570 TCATGGCTGATATATCGAAACGTTTCCAAACGCTGTTTTTTGTTTAATTTATAGTTTCATAATGC
1 TCATGGCTGATATATAGAAACGTTTCCAAACGCTG-TTTTTGGTTAATTTATAGTTTCATGATGC
* * * *
2275635 AATAATTGAAAAACGAGATTAAAGCATTGCTGAAAACGATCTCGCACTTCTGCATCAAGTTCAGT
65 AATAGTTGAAAAACGAGATTAAAGCATTGTTGAAAACGATCTCGTACTTCTGCATCAAGTTTAGT
2275700 GGTTATTTGCATTTTCTATGACTATTTATTTTCTTAGTAGACTTTCTTCGCAGGTTACAAAAGTC
130 GGTTATTTGCATTTTCTATGACTATTTATTTTCTTAGTAGACTTTCTTCGCAGGTTACAAAAGTC
*
2275765 TACTTTTGTGCATTTGT
195 TATTTTTGTGCATTTGT
* * *
2275782 TCATGGCTGATATATAGAAACGTTTCCTAACGTTGTTTTTGGTTAATTTCTAGTTTCATGATGCA
1 TCATGGCTGATATATAGAAACGTTTCCAAACGCTGTTTTTGGTTAATTTATAGTTTCATGATGCA
* * *
2275847 ATAGTTGAAAAACGACAGTAGAGCATTGTTGAAAACGATCTCGTACTTCTGCATCAAGTTTAGTG
66 ATAGTTGAAAAACGAGATTAAAGCATTGTTGAAAACGATCTCGTACTTCTGCATCAAGTTTAGTG
* * * * * *
2275912 GTTATTTGCATTTTCTACGGCTACTAATTTTCTTGGTAGACTTTCTTCGCAGGCTACAAAAGTCT
131 GTTATTTGCATTTTCTATGACTATTTATTTTCTTAGTAGACTTTCTTCGCAGGTTACAAAAGTCT
2275977 ATTTTTGTGCATT
196 ATTTTTGTGCATT
2275990 GCTTTAATCT
Statistics
Matches: 381, Mismatches: 38, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
211 185 0.49
212 196 0.51
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (211 bp):
TCATGGCTGATATATAGAAACGTTTCCAAACGCTGTTTTTGGTTAATTTATAGTTTCATGATGCA
ATAGTTGAAAAACGAGATTAAAGCATTGTTGAAAACGATCTCGTACTTCTGCATCAAGTTTAGTG
GTTATTTGCATTTTCTATGACTATTTATTTTCTTAGTAGACTTTCTTCGCAGGTTACAAAAGTCT
ATTTTTGTGCATTTGT
Found at i:2282079 original size:2 final size:2
Alignment explanation
Indices: 2282074--2282101 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2282064 ACACACATAC
2282074 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
2282102 CATGGCAGGC
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:2286100 original size:40 final size:41
Alignment explanation
Indices: 2286024--2286105 Score: 130
Period size: 40 Copynumber: 2.0 Consensus size: 41
2286014 TGTTAAACCT
2286024 TAACCGATTCATGTTAGAAAAAAAAAAAGGAATGAATGAGAG
1 TAACCGATTCATGTTA-AAAAAAAAAAAGGAATGAATGAGAG
* *
2286066 TAACCGATTCATGTT-TAACAAAAAAAGGAATGAATGAGAG
1 TAACCGATTCATGTTAAAAAAAAAAAAGGAATGAATGAGAG
2286106 ATAGAAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 23 0.61
42 15 0.39
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.21
Consensus pattern (41 bp):
TAACCGATTCATGTTAAAAAAAAAAAAGGAATGAATGAGAG
Found at i:2287053 original size:12 final size:13
Alignment explanation
Indices: 2287007--2287060 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
2286997 ATTAAAAATT
*
2287007 ATTTTTATATTAA
1 ATTTTTAAATTAA
*
2287020 TATTTATATAATTAA
1 -ATTTTTA-AATTAA
2287035 A--TTTAAA-TAA
1 ATTTTTAAATTAA
2287045 ATTTTTAAATTAA
1 ATTTTTAAATTAA
2287058 ATT
1 ATT
2287061 CAATTAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.12
11 2 0.06
12 9 0.27
13 6 0.18
14 7 0.21
15 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTTAAATTAA
Found at i:2288091 original size:22 final size:22
Alignment explanation
Indices: 2288012--2288081 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 22
2288002 AAATGCAAAC
2288012 ATTATAATCATAATTAAA-TATTATA
1 ATTA-AAT-ATAA-TAAATTATTA-A
*
2288037 TTTAAATA-AA-AAATTATTAA
1 ATTAAATATAATAAATTATTAA
2288057 ATTAAATATAATAAATTAATTAA
1 ATTAAATATAATAAATT-ATTAA
2288080 AT
1 AT
2288082 AATTTTAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 11 0.28
21 7 0.18
22 7 0.18
23 8 0.21
24 3 0.08
25 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAAATATAATAAATTATTAA
Found at i:2288273 original size:2 final size:2
Alignment explanation
Indices: 2288266--2288290 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2288256 AGGGATATTT
2288266 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
2288291 GACATGATAT
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:2288326 original size:11 final size:12
Alignment explanation
Indices: 2288269--2288330 Score: 58
Period size: 12 Copynumber: 5.1 Consensus size: 12
2288259 GATATTTTAT
2288269 ATATAT-ATATA
1 ATATATGATATA
2288280 TATATAT-ATATGA
1 -ATATATGATAT-A
*
2288293 CATGATATGATTTA
1 -AT-ATATGATATA
2288307 ATATATGATATA
1 ATATATGATATA
2288319 AT-TATGATATA
1 ATATATGATATA
2288330 A
1 A
2288331 ACAATAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
11 10 0.23
12 21 0.48
13 5 0.11
14 5 0.11
15 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (12 bp):
ATATATGATATA
Found at i:2288357 original size:16 final size:16
Alignment explanation
Indices: 2288338--2288418 Score: 68
Period size: 15 Copynumber: 5.4 Consensus size: 16
2288328 TAAACAATAA
2288338 TAAATATATAATATTT
1 TAAATATATAATATTT
* *
2288354 TAAATTTAT-ATAATT
1 TAAATATATAATATTT
*
2288369 TAAA-ATTTTAATATTT
1 TAAATA-TATAATATTT
*
2288385 TAAATAT-T--TA-TA
1 TAAATATATAATATTT
2288397 TAAATATA-AATATTT
1 TAAATATATAATATTT
2288412 TAAATAT
1 TAAATAT
2288419 TATTATAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
12 8 0.16
13 2 0.04
14 2 0.04
15 20 0.39
16 18 0.35
17 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAATATATAATATTT
Found at i:2290945 original size:2 final size:2
Alignment explanation
Indices: 2290938--2290975 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2290928 CAACATCACT
2290938 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
2290976 CACCAGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2291428 original size:20 final size:21
Alignment explanation
Indices: 2291400--2291438 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2291390 GTAAATAAAT
*
2291400 TTTATTTTAATAAT-GTATGA
1 TTTAATTTAATAATAGTATGA
*
2291420 TTTAATTTATTAATAGTAT
1 TTTAATTTAATAATAGTAT
2291439 ATAAATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (21 bp):
TTTAATTTAATAATAGTATGA
Found at i:2293197 original size:52 final size:52
Alignment explanation
Indices: 2293119--2293221 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
2293109 AAAACCTGTG
2293119 TTACTTGTACATGTTTTTCGGCATGTCTGA-CTAGAGAAATATACAATCTATA
1 TTACTTGTACATGTTTTTCGGCATGTCTGACCT-GAGAAATATACAATCTATA
*
2293171 TTACTTGTACGTGTTTTTCAGG-ATGTCTGACCTGAGAAATATACAATCTAT
1 TTACTTGTACATGTTTTTC-GGCATGTCTGACCTGAGAAATATACAATCTAT
2293222 GTACTTAGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
52 44 0.92
53 4 0.08
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (52 bp):
TTACTTGTACATGTTTTTCGGCATGTCTGACCTGAGAAATATACAATCTATA
Found at i:2294599 original size:18 final size:16
Alignment explanation
Indices: 2294563--2294605 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
2294553 ATATTTCTCT
*
2294563 ATTTTTATTATTTAGA
1 ATTTTTATTATTTAAA
2294579 ATTTTTATTACATTTAAA
1 ATTTTTATT--ATTTAAA
*
2294597 ATTATTATT
1 ATTTTTATT
2294606 TAACTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTTTATTATTTAAA
Found at i:2300389 original size:16 final size:14
Alignment explanation
Indices: 2300347--2300394 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
2300337 AAATAATAAA
2300347 AATATATTAAAATT
1 AATATATTAAAATT
*
2300361 TATATAATATAAATTATT
1 AATAT-AT-TAAA--ATT
2300379 AATATATTAAAATT
1 AATATATTAAAATT
2300393 AA
1 AA
2300395 AATAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 2 0.07
16 8 0.29
17 2 0.07
18 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATATTAAAATT
Found at i:2300393 original size:17 final size:17
Alignment explanation
Indices: 2300347--2300393 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
2300337 AAATAATAAA
2300347 AATATATTAAAA-T-TT
1 AATATATTAAAATTATT
*
2300362 -ATATAATATAAATTATT
1 AATATATTA-AAATTATT
2300379 AATATATTAAAATTA
1 AATATATTAAAATTA
2300394 AAATAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 7 0.27
15 3 0.12
16 1 0.04
17 8 0.31
18 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATATTAAAATTATT
Found at i:2300394 original size:38 final size:40
Alignment explanation
Indices: 2300352--2300428 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
2300342 ATAAAAATAT
*
2300352 ATTAAAAT-TTATATAATA-TAAATTATTAA-TATATTAAA
1 ATTAAAATAATATATAATATTAAATTA-TAATTATATTAAA
*
2300390 ATTAAAATAAATATATAATATTTAATTATAATTATATTA
1 ATTAAAAT-AATATATAATATTAAATTATAATTATATTA
2300429 TATAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
38 8 0.24
40 12 0.36
41 13 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (40 bp):
ATTAAAATAATATATAATATTAAATTATAATTATATTAAA
Found at i:2300415 original size:7 final size:7
Alignment explanation
Indices: 2300361--2300433 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 7
2300351 TATTAAAATT
2300361 TATATAA
1 TATATAA
2300368 TATA-AA
1 TATATAA
2300374 T-TATTAA
1 TATA-TAA
2300381 TATATTAA
1 TATA-TAA
*
2300389 AAT-TAA
1 TATATAA
*
2300395 AATA-AA
1 TATATAA
2300401 TATATAA
1 TATATAA
*
2300408 TATTTAA
1 TATATAA
2300415 T-TATAA
1 TATATAA
*
2300421 T-TATAT
1 TATATAA
2300427 TATATAA
1 TATATAA
2300434 AAATATCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
5 2 0.04
6 24 0.44
7 20 0.37
8 8 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TATATAA
Found at i:2300437 original size:40 final size:40
Alignment explanation
Indices: 2300361--2300438 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
2300351 TATTAAAATT
*
2300361 TATATAATATAAATTATTAATATATTAAAATTAAAATAAA
1 TATATAATATAAATTATTAATATATTAAAATAAAAATAAA
* *
2300401 TATATAATATTTAATTA-TAATTATATT-ATATAAAAATA
1 TATATAATA-TAAATTATTAA-TATATTAAAATAAAAATA
2300439 TCTAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 21 0.64
41 12 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (40 bp):
TATATAATATAAATTATTAATATATTAAAATAAAAATAAA
Found at i:2307974 original size:21 final size:23
Alignment explanation
Indices: 2307950--2307995 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2307940 TTTTATTATT
2307950 TAATAT-A-ATTATCTTAAATAA
1 TAATATAACATTATCTTAAATAA
*
2307971 TAATGTAACTATTATCTTAAATAA
1 TAATATAAC-ATTATCTTAAATAA
2307995 T
1 T
2307996 GTTCAGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 1 0.05
24 15 0.71
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (23 bp):
TAATATAACATTATCTTAAATAA
Found at i:2308036 original size:18 final size:21
Alignment explanation
Indices: 2308013--2308052 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2308003 TTTATTAGAT
2308013 ATAA-TTTAT-ATTAAA-AAA
1 ATAATTTTATAATTAAATAAA
2308031 ATAATTTTATAATTAAATAAA
1 ATAATTTTATAATTAAATAAA
2308052 A
1 A
2308053 GGCTGTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 5 0.26
20 6 0.32
21 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATTTTATAATTAAATAAA
Found at i:2308406 original size:17 final size:17
Alignment explanation
Indices: 2308386--2308441 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
2308376 AATTTGATAA
2308386 TATTTTAAATTTATTTT
1 TATTTTAAATTTATTTT
**
2308403 TATTTTAAAAATATTTT
1 TATTTTAAATTTATTTT
*
2308420 TATATT-AATTT-TTTT
1 TATTTTAAATTTATTTT
2308435 ATATTTT
1 -TATTTT
2308442 TATAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 20 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTAAATTTATTTT
Found at i:2309049 original size:2 final size:2
Alignment explanation
Indices: 2309042--2309078 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2309032 CCTTGAAATA
*
2309042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2309079 CTATTAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2309587 original size:11 final size:11
Alignment explanation
Indices: 2309494--2309608 Score: 62
Period size: 11 Copynumber: 10.5 Consensus size: 11
2309484 AGTATTATAA
*
2309494 ATTTATATAAT
1 ATTTATATTAT
2309505 ATTTATAAATTAT
1 ATTTAT--ATTAT
*
2309518 -TTTTTA-TAT
1 ATTTATATTAT
*
2309527 TTTTATATT-T
1 ATTTATATTAT
* *
2309537 CTATTATATTAA
1 AT-TTATATTAT
*
2309549 ATTTTTATTAT
1 ATTTATATTAT
2309560 ATTT-TAATTAAT
1 ATTTAT-ATT-AT
*
2309572 TTTTATATTAT
1 ATTTATATTAT
*
2309583 ATTTATGTTAT
1 ATTTATATTAT
2309594 -TTTCATA-TAT
1 ATTT-ATATTAT
2309604 ATTTA
1 ATTTA
2309609 AAGTATTAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
9 3 0.04
10 16 0.20
11 44 0.54
12 13 0.16
13 5 0.06
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:2309733 original size:11 final size:12
Alignment explanation
Indices: 2309693--2309733 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
2309683 TGTCATGTTA
*
2309693 ATATTATTTTTT
1 ATATTATATTTT
*
2309705 ATGTTATATTTT
1 ATATTATATTTT
2309717 -TATTATATTTT
1 ATATTATATTTT
2309728 AT-TTAT
1 ATATTAT
2309734 GTTATATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:2309948 original size:36 final size:37
Alignment explanation
Indices: 2309908--2309993 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 37
2309898 TTAATAATAT
* * *
2309908 ATTTATATTATTTTTTATAT-TCAAAATATTAG-ATAA
1 ATTTATATAATTTTTTAGATAGCAAAA-ATTAGTATAA
* *
2309944 ATTTACATAATTTTTTAGATAGCAATAATTAGTATAA
1 ATTTATATAATTTTTTAGATAGCAAAAATTAGTATAA
2309981 ATTTATA-AATTTT
1 ATTTATATAATTTT
2309994 ATGTATTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
36 28 0.67
37 14 0.33
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (37 bp):
ATTTATATAATTTTTTAGATAGCAAAAATTAGTATAA
Found at i:2310208 original size:16 final size:15
Alignment explanation
Indices: 2310187--2310227 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 15
2310177 ATAATAATAT
2310187 AATTTTAATTATATAA
1 AATTTTAATTATA-AA
2310203 AATTTTAAATTATAAA
1 AATTTT-AATTATAAA
2310219 AATATTTAA
1 AAT-TTTAA
2310228 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTTTAATTATAAA
Found at i:2310215 original size:17 final size:16
Alignment explanation
Indices: 2310187--2310234 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
2310177 ATAATAATAT
2310187 AATTTT-AATTATATAA
1 AATTTTAAATTATA-AA
2310203 AATTTTAAATTATAAA
1 AATTTTAAATTATAAA
*
2310219 AATATTTAAATAATAA
1 AAT-TTTAAATTATAA
2310235 TAAGTAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 11 0.38
17 18 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTTAAATTATAAA
Found at i:2310290 original size:26 final size:27
Alignment explanation
Indices: 2310250--2310303 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
2310240 AGTTGATAGT
*
2310250 ATTTAATTTAAATTTATATAATTATTA
1 ATTTAATTTAAATTTATATAAATATTA
*
2310277 ATTTAA-TTAAATTTTTATAAATATTA
1 ATTTAATTTAAATTTATATAAATATTA
2310303 A
1 A
2310304 AATTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTAATTTAAATTTATATAAATATTA
Found at i:2320766 original size:17 final size:17
Alignment explanation
Indices: 2320744--2320778 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2320734 CTATGTCCAA
2320744 TGCAGTTACATTGGAGC
1 TGCAGTTACATTGGAGC
2320761 TGCAGTTACATTGGAGC
1 TGCAGTTACATTGGAGC
2320778 T
1 T
2320779 AGGAATCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (17 bp):
TGCAGTTACATTGGAGC
Found at i:2323356 original size:10 final size:11
Alignment explanation
Indices: 2323340--2323390 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 11
2323330 TAATTTTTTA
2323340 ATTAAATATTT
1 ATTAAATATTT
2323351 -TTAAATATTT
1 ATTAAATATTT
*
2323361 ATTAAA-ATTA
1 ATTAAATATTT
2323371 ATT-AATATATT
1 ATTAAATAT-TT
2323382 ATTATAATA
1 ATTA-AATA
2323391 ATATTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 2 0.06
10 18 0.55
11 9 0.27
13 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTAAATATTT
Found at i:2323408 original size:14 final size:14
Alignment explanation
Indices: 2323373--2323401 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2323363 TAAAATTAAT
2323373 TAAT-ATATTATTA
1 TAATAATATTATTA
2323386 TAATAATATTATTA
1 TAATAATATTATTA
2323400 TA
1 TA
2323402 TAAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATAATATTATTA
Found at i:2323460 original size:20 final size:20
Alignment explanation
Indices: 2323432--2323469 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2323422 TCATTTATTT
*
2323432 TTAATAAAATTATAATAATC
1 TTAAAAAAATTATAATAATC
2323452 TTAAAAAAATTATAATAA
1 TTAAAAAAATTATAATAA
2323470 ATAAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAAAAATTATAATAATC
Found at i:2326389 original size:144 final size:144
Alignment explanation
Indices: 2326124--2326408 Score: 381
Period size: 144 Copynumber: 2.0 Consensus size: 144
2326114 TTAATAGACA
* ** * *
2326124 GTTAAGATTAATACTTATTTACAAAATCTAAAATTCAAAATAAGTTTAAATTCTATCGCTCTATC
1 GTTAAGATTAATACTTATCTACAAAATCTAAAACCCAAAATAAGTTTAAACTCTATCACTCTATC
* * *
2326189 TCTATAGAGTTCTAATTAAGTTGAAGTAATTATAGTTTAGTAATTTTTTAAGCTTTTAAAAACTT
66 TCTATAGAGTTCTAATTAAGCTGAAGTAATTATAGTTGAGTAACTTTTTAAGCTTTTAAAAACTT
2326254 TAAACAAACTGACC
131 TAAACAAACTGACC
* **
2326268 GTTAGGATTAATACTTATCTACAAAATCTAAAACCCCTAATAAGTTTAAACTCTATCACTCTATC
1 GTTAAGATTAATACTTATCTACAAAATCTAAAACCCAAAATAAGTTTAAACTCTATCACTCTATC
* * * * * * * * *
2326333 TTTATAGAGTTTTAATTAAGCTGAAGTAGTTGTGGTTGATTGACTTTTTAATCTTTTAGAAACTT
66 TCTATAGAGTTCTAATTAAGCTGAAGTAATTATAGTTGAGTAACTTTTTAAGCTTTTAAAAACTT
*
2326398 TAAATAAACTG
131 TAAACAAACTG
2326409 GGTCTTTTAA
Statistics
Matches: 120, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
144 120 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (144 bp):
GTTAAGATTAATACTTATCTACAAAATCTAAAACCCAAAATAAGTTTAAACTCTATCACTCTATC
TCTATAGAGTTCTAATTAAGCTGAAGTAATTATAGTTGAGTAACTTTTTAAGCTTTTAAAAACTT
TAAACAAACTGACC
Found at i:2329331 original size:21 final size:21
Alignment explanation
Indices: 2329305--2329345 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2329295 TCATTCATCG
2329305 TTTAATATAATAAATTTAAAA
1 TTTAATATAATAAATTTAAAA
* *
2329326 TTTAATTTAATTAATTTAAA
1 TTTAATATAATAAATTTAAA
2329346 TAATTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAATATAATAAATTTAAAA
Found at i:2336052 original size:18 final size:17
Alignment explanation
Indices: 2336031--2336067 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
2336021 TATTTATGTA
2336031 TTTTTATTATATATAATT
1 TTTTTATTATAT-TAATT
2336049 TTTTTATTATATTAATT
1 TTTTTATTATATTAATT
2336066 TT
1 TT
2336068 AATATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTATTATATTAATT
Found at i:2336067 original size:14 final size:14
Alignment explanation
Indices: 2336050--2336132 Score: 53
Period size: 14 Copynumber: 5.6 Consensus size: 14
2336040 TATATAATTT
2336050 TTTTATTATATTAA
1 TTTTATTATATTAA
*
2336064 TTTTAATATATTAA
1 TTTTATTATATTAA
*
2336078 TAATTTATTTATATCAA
1 T--TTTA-TTATATTAA
*
2336095 TATTATT-TATATATA
1 TTTTATTATAT-TA-A
*
2336110 TAATT-TTATATTAA
1 T-TTTATTATATTAA
*
2336124 TTTAATTAT
1 TTTTATTAT
2336133 TTTTATGTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
13 4 0.07
14 23 0.43
15 9 0.17
16 10 0.19
17 8 0.15
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTATTATATTAA
Found at i:2336090 original size:17 final size:15
Alignment explanation
Indices: 2336051--2336124 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 15
2336041 ATATAATTTT
2336051 TTTATTATATTAAT-
1 TTTATTATATTAATA
*
2336065 TTTAATATATTAATAA
1 TTTATTATATTAAT-A
*
2336081 TTTATTTATATCAATA
1 TTTA-TTATATTAATA
2336097 -TTATT-TATATATATA
1 TTTATTATAT-TA-ATA
*
2336112 ATT-TTATATTAAT
1 TTTATTATATTAAT
2336125 TTAATTATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
13 3 0.06
14 18 0.37
15 10 0.20
16 10 0.20
17 8 0.16
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATTATATTAATA
Found at i:2336138 original size:34 final size:32
Alignment explanation
Indices: 2336021--2336138 Score: 93
Period size: 34 Copynumber: 3.5 Consensus size: 32
2336011 TTTCTTTAGA
2336021 TATTT-ATGTATTTTTATTATATATAATTTT-TT
1 TATTTAAT-TATTTTTA-TATATATAATTTTATT
*
2336053 TA-TTATATTAATTTTA-ATATATTAATAATTTATT
1 TATTTA-ATTATTTTTATATATA-TAAT--TTTATT
*
2336087 TATATCAA-TATTATTTATATATATAATTTTATAT
1 TAT-TTAATTATT-TTTATATATATAATTTTAT-T
2336121 TAATTTAATTATTTTTAT
1 T-ATTTAATTATTTTTAT
2336139 GTTATTGAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
30 5 0.07
31 6 0.09
32 9 0.13
33 10 0.14
34 17 0.25
35 15 0.22
36 7 0.10
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (32 bp):
TATTTAATTATTTTTATATATATAATTTTATT
Found at i:2342355 original size:2 final size:2
Alignment explanation
Indices: 2342348--2342375 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2342338 TATTAAATCT
2342348 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
2342376 AAAGCTAAAA
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):
TA
Found at i:2344911 original size:11 final size:11
Alignment explanation
Indices: 2344864--2344941 Score: 65
Period size: 11 Copynumber: 7.1 Consensus size: 11
2344854 TAAATTTTTA
*
2344864 TATATTAATAAT
1 TATATT-ATATT
2344876 TATATTATATT
1 TATATTATATT
*
2344887 AATATTATTTATT
1 TATATTA--TATT
2344900 TATATTATATT
1 TATATTATATT
*
2344911 T-TAATTATTTT
1 TAT-ATTATATT
2344922 TATATTAT-TT
1 TATATTATATT
2344932 T-T-TTATATT
1 TATATTATATT
2344941 T
1 T
2344942 TGTTAGGTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 4 0.07
11 28 0.49
12 7 0.12
13 10 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATTATATT
Found at i:2344917 original size:24 final size:23
Alignment explanation
Indices: 2344875--2344940 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
2344865 ATATTAATAA
*
2344875 TTATATTATA-TTAATATTATTTAT
1 TTATATTATATTTTATATTA-TT-T
2344899 TTATATTATATTTTA-ATTATTT
1 TTATATTATATTTTATATTATTT
*
2344921 TTATATTATTTTTTTATATT
1 TTATATTA-TATTTTATATT
2344941 TTGTTAGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
22 9 0.24
23 8 0.22
24 17 0.46
25 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TTATATTATATTTTATATTATTT
Found at i:2351743 original size:80 final size:79
Alignment explanation
Indices: 2351637--2351794 Score: 271
Period size: 80 Copynumber: 2.0 Consensus size: 79
2351627 AAAAAAAAGA
2351637 AACTTTAGAATTCTGTACAGGATGTGAACATCGAGTCATAAGTCATCTAGCCTAATAAAAATGAA
1 AACTTTAGAATTCTGTACAGGATGTGAACATCGAGTCATAAGTCATCTAGCCTAAT-AAAATGAA
*
2351702 CACAGAAGTAATCAT
65 CACAAAAGTAATCAT
* * *
2351717 AACTTTAGAATTCTGTGCAGGGTGTGAACATCGAGTCATAGGTCATCTAGCCTAATAAAATGAAC
1 AACTTTAGAATTCTGTACAGGATGTGAACATCGAGTCATAAGTCATCTAGCCTAATAAAATGAAC
2351782 ACAAAAGTAATCA
66 ACAAAAGTAATCA
2351795 AAAGGTTCAT
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
79 21 0.28
80 53 0.72
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (79 bp):
AACTTTAGAATTCTGTACAGGATGTGAACATCGAGTCATAAGTCATCTAGCCTAATAAAATGAAC
ACAAAAGTAATCAT
Found at i:2354790 original size:10 final size:10
Alignment explanation
Indices: 2354761--2354863 Score: 52
Period size: 10 Copynumber: 10.0 Consensus size: 10
2354751 ACAATTTTGG
*
2354761 TAACTTTTGA
1 TAACTTTTAA
2354771 TAACATTTTAA
1 TAAC-TTTTAA
2354782 TAACTTTTAA
1 TAACTTTTAA
* *
2354792 TATA-ATTTAC
1 TA-ACTTTTAA
* *
2354802 TAAGCCTATAACA
1 TAA--CTTTTA-A
2354815 TAA-TTTTAA
1 TAACTTTTAA
*
2354824 TAATTTTTATA
1 TAACTTTTA-A
*
2354835 TAA-TTTGAA
1 TAACTTTTAA
2354844 TAA-TATTTAA
1 TAACT-TTTAA
2354854 TAACTTTTAA
1 TAACTTTTAA
2354864 CATAATTTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
9 10 0.14
10 42 0.58
11 15 0.21
12 2 0.03
13 3 0.04
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.48
Consensus pattern (10 bp):
TAACTTTTAA
Found at i:2354799 original size:21 final size:21
Alignment explanation
Indices: 2354723--2354863 Score: 76
Period size: 21 Copynumber: 6.8 Consensus size: 21
2354713 TTTTATAATC
* * *
2354723 TTTAATATAATTGTGATAATTT
1 TTTAATATAATTTTAATAA-CT
* * **
2354745 TTTTATACAATTTTGGTAACT
1 TTTAATATAATTTTAATAACT
*
2354766 TTTGATA-ACATTTTAATAACT
1 TTTAATATA-ATTTTAATAACT
* *
2354787 TTTAATATAA-TTTACTAAGCC
1 TTTAATATAATTTTAATAA-CT
* *
2354808 TATAACATAATTTTAATAA-T
1 TTTAATATAATTTTAATAACT
* *
2354828 TTTTATATAATTTGAATAA-T
1 TTTAATATAATTTTAATAACT
*
2354848 ATTTAATA-ACTTTTAA
1 -TTTAATATAATTTTAA
2354864 CATAATTTTA
Statistics
Matches: 92, Mismatches: 22, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
20 30 0.33
21 39 0.42
22 23 0.25
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTAATATAATTTTAATAACT
Found at i:2354828 original size:9 final size:9
Alignment explanation
Indices: 2354814--2354881 Score: 64
Period size: 10 Copynumber: 6.9 Consensus size: 9
2354804 AGCCTATAAC
2354814 ATAATTTTA
1 ATAATTTTA
2354823 ATAATTTTTA
1 ATAA-TTTTA
*
2354833 TATAATTTGA
1 -ATAATTTTA
2354843 ATAATATTTA
1 ATAAT-TTTA
2354853 ATAACTTTTAA
1 ATAA-TTTT-A
2354864 CATAATTTTA
1 -ATAATTTTA
*
2354874 AAAATTTT
1 ATAATTTT
2354882 TGTTAAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
9 16 0.32
10 20 0.40
11 10 0.20
12 4 0.08
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (9 bp):
ATAATTTTA
Found at i:2355300 original size:2 final size:2
Alignment explanation
Indices: 2355293--2355331 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
2355283 TTCATACGTG
* *
2355293 TA TA TA TA CA TA CTA TA CA 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
2355332 CACGAATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2355825 original size:54 final size:54
Alignment explanation
Indices: 2355738--2355848 Score: 186
Period size: 54 Copynumber: 2.1 Consensus size: 54
2355728 GCAAAGGAGA
* *
2355738 TGGTGGCGGTTTTGGCAGAGGGGGAGGTGTAGGCAATGGCGGTTCCGGTGGCTT
1 TGGTGGCGGTTTTGGCAGAGGGGGAGGTATAGGCAATGGCGGTACCGGTGGCTT
**
2355792 TGGTGGCGGTTTTGGCAGAGGGGGAGGTATAGGCAATGGCGGTAGTGGTGGCTT
1 TGGTGGCGGTTTTGGCAGAGGGGGAGGTATAGGCAATGGCGGTACCGGTGGCTT
2355846 TGG
1 TGG
2355849 CAGTGGGGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.13, C:0.11, G:0.50, T:0.26
Consensus pattern (54 bp):
TGGTGGCGGTTTTGGCAGAGGGGGAGGTATAGGCAATGGCGGTACCGGTGGCTT
Found at i:2355882 original size:42 final size:42
Alignment explanation
Indices: 2355792--2355884 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
2355782 CCGGTGGCTT
* *
2355792 TGGTGGCGGTTTTGGCAGAGGGGGAGGTATAGGCAATGGCGG
1 TGGTGGTGGCTTTGGCAGAGGGGGAGGTATAGGCAATGGCGG
* * * * **
2355834 TAGTGGTGGCTTTGGCAGTGGGGGAGGTGTGGGCAATGTTGG
1 TGGTGGTGGCTTTGGCAGAGGGGGAGGTATAGGCAATGGCGG
2355876 TGGTGGTGG
1 TGGTGGTGG
2355885 TTCTGGGTCT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.13, C:0.08, G:0.54, T:0.26
Consensus pattern (42 bp):
TGGTGGTGGCTTTGGCAGAGGGGGAGGTATAGGCAATGGCGG
Found at i:2355994 original size:5 final size:6
Alignment explanation
Indices: 2355979--2356004 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2355969 CTATGGTTCA
2355979 GGGGGT GGGGGT GGGGGT GGGGGT GG
1 GGGGGT GGGGGT GGGGGT GGGGGT GG
2356005 AGGCGGAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.85, T:0.15
Consensus pattern (6 bp):
GGGGGT
Found at i:2355995 original size:60 final size:60
Alignment explanation
Indices: 2355931--2356058 Score: 220
Period size: 60 Copynumber: 2.1 Consensus size: 60
2355921 CTATGGCTCA
*
2355931 GGGGGTGGGGGGGGAGGCGGAGCGAATGGTGGAGGAGGCTATGGTTCAGGGGGTGGGGGT
1 GGGGGTGGGGGGGGAGGCGGAGCGAATGGTGGAGGAGGCTATGGCTCAGGGGGTGGGGGT
* *
2355991 GGGGGTGGGGGTGGAGGCGGAGGGAATGGTGGAGGAGGCTATGGCTCAGGGGGTGGGGGT
1 GGGGGTGGGGGGGGAGGCGGAGCGAATGGTGGAGGAGGCTATGGCTCAGGGGGTGGGGGT
*
2356051 GGAGGTGG
1 GGGGGTGG
2356059 AGGGAACGGT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.13, C:0.06, G:0.66, T:0.15
Consensus pattern (60 bp):
GGGGGTGGGGGGGGAGGCGGAGCGAATGGTGGAGGAGGCTATGGCTCAGGGGGTGGGGGT
Found at i:2356042 original size:108 final size:108
Alignment explanation
Indices: 2355919--2356126 Score: 303
Period size: 108 Copynumber: 1.9 Consensus size: 108
2355909 GCAGGGTGGT
*
2355919 GGCTATGGCTCAGGGGGTGGGGGGGGAGGCGGAGCGAATGGTGGAGGAGGCTATGG-TTCAGGGG
1 GGCTATGGCTCAGGGGGTGGGGGGGGAGGCGGAGCGAACGGTGGAGGAGGCTATGGCTT-AGGGG
* * *
2355983 GTGGGGGT-GGGGGTGGGGGTGGAGGCGGAGGGAATGGTGGAGGA
65 GT-GGGGTCGGAGGTGGAGGTGGAGGCAGAGGGAATGGTGGAGGA
* * * *
2356027 GGCTATGGCTCAGGGGGTGGGGGTGGAGGTGGAGGGAACGGTGGAGTAGGCTATGGCTTAGGGGG
1 GGCTATGGCTCAGGGGGTGGGGGGGGAGGCGGAGCGAACGGTGGAGGAGGCTATGGCTTAGGGGG
*
2356092 TGGGTTCGGAGGTGGAGGTGGAGGCAGAGGGAATG
66 TGGGGTCGGAGGTGGAGGTGGAGGCAGAGGGAATG
2356127 ATGGCGGCAG
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 4 0.04
108 83 0.93
109 2 0.02
ACGTcount: A:0.16, C:0.08, G:0.60, T:0.16
Consensus pattern (108 bp):
GGCTATGGCTCAGGGGGTGGGGGGGGAGGCGGAGCGAACGGTGGAGGAGGCTATGGCTTAGGGGG
TGGGGTCGGAGGTGGAGGTGGAGGCAGAGGGAATGGTGGAGGA
Found at i:2356103 original size:48 final size:48
Alignment explanation
Indices: 2355991--2356109 Score: 177
Period size: 48 Copynumber: 2.5 Consensus size: 48
2355981 GGGTGGGGGT
* *
2355991 GGGGGTGGGGGTGGAGGCGGAGGGAATGGTGGAGGAGGCTATGGCTCA
1 GGGGGTGGGGGTGGAGGTGGAGGGAACGGTGGAGGAGGCTATGGCTCA
* *
2356039 GGGGGTGGGGGTGGAGGTGGAGGGAACGGTGGAGTAGGCTATGGCTTA
1 GGGGGTGGGGGTGGAGGTGGAGGGAACGGTGGAGGAGGCTATGGCTCA
*
2356087 GGGGGT-GGGTTCGGAGGTGGAGG
1 GGGGGTGGGGGT-GGAGGTGGAGG
2356110 TGGAGGCAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 4 0.06
48 61 0.94
ACGTcount: A:0.15, C:0.07, G:0.61, T:0.17
Consensus pattern (48 bp):
GGGGGTGGGGGTGGAGGTGGAGGGAACGGTGGAGGAGGCTATGGCTCA
Found at i:2356160 original size:108 final size:108
Alignment explanation
Indices: 2355919--2356166 Score: 232
Period size: 108 Copynumber: 2.3 Consensus size: 108
2355909 GCAGGGTGGT
*** * * * *
2355919 GGCTATGGCTCAGGGGGTGGGGGGGGAGGCGGAGCGAATGGTGGAGGAGGCTATGGTTCAGGGGG
1 GGCTATGGCTCAGGCAATGGAGGTGGAGGTGGAGCGAACGGTGGAGGAGGCTATGGTTCAGGGGG
* * * *
2355984 TGGGGGTGGGGGTGGGGGTGGAGGCGGAGGGAATGGTGGAGGA
66 TGGGGGTGGAGGTGGAGGTGGAGGCAGAGGGAATGATGGAGGA
*** * * *
2356027 GGCTATGGCTCAGGGGGTGGGGGTGGAGGTGGAGGGAACGGTGGAGTAGGCTATGGCTT-AGGGG
1 GGCTATGGCTCAGGCAATGGAGGTGGAGGTGGAGCGAACGGTGGAGGAGGCTATGG-TTCAGGGG
* *
2356091 GT-GGGTTCGGAGGTGGAGGTGGAGGCAGAGGGAATGATGGCGGCA
65 GTGGGGGT-GGAGGTGGAGGTGGAGGCAGAGGGAATGATGGAGG-A
* ** * *
2356136 -GCTATGGTTTTGGCAATGTAGGTGGTGGTGG
1 GGCTATGGCTCAGGCAATGGAGGTGGAGGTGG
2356167 TGGTGGTTTT
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
107 4 0.03
108 110 0.94
109 3 0.03
ACGTcount: A:0.16, C:0.08, G:0.58, T:0.19
Consensus pattern (108 bp):
GGCTATGGCTCAGGCAATGGAGGTGGAGGTGGAGCGAACGGTGGAGGAGGCTATGGTTCAGGGGG
TGGGGGTGGAGGTGGAGGTGGAGGCAGAGGGAATGATGGAGGA
Found at i:2360094 original size:12 final size:12
Alignment explanation
Indices: 2360077--2360121 Score: 81
Period size: 12 Copynumber: 3.8 Consensus size: 12
2360067 ATAGATTTAT
2360077 TTATAAATTAAA
1 TTATAAATTAAA
2360089 TTATAAATTAAA
1 TTATAAATTAAA
2360101 TTATAAATTAAA
1 TTATAAATTAAA
*
2360113 TTTTAAATT
1 TTATAAATT
2360122 TTTTTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTATAAATTAAA
Found at i:2360128 original size:24 final size:24
Alignment explanation
Indices: 2360071--2360128 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
2360061 ATATAAATAG
2360071 ATTTATTTATAAATTAAATTATAA
1 ATTTATTTATAAATTAAATTATAA
* * *
2360095 ATTAAATTATAAATTAAATTTTAA
1 ATTTATTTATAAATTAAATTATAA
*
2360119 ATTTTTTTAT
1 ATTTATTTAT
2360129 TAATATATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTATTTATAAATTAAATTATAA
Found at i:2360257 original size:20 final size:21
Alignment explanation
Indices: 2360234--2360276 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2360224 AATTAATAAT
2360234 AATTCA-AAAAAATTAATTTA
1 AATTCATAAAAAATTAATTTA
* *
2360254 AATTTATAAAAACTTAATTTA
1 AATTCATAAAAAATTAATTTA
2360275 AA
1 AA
2360277 ATCTAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTCATAAAAAATTAATTTA
Found at i:2360781 original size:2 final size:2
Alignment explanation
Indices: 2360774--2360800 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2360764 TTAGCAGTGG
2360774 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 T
2360801 TAATTCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2363761 original size:21 final size:21
Alignment explanation
Indices: 2363727--2363788 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
2363717 TTTCACAACT
*
2363727 TATTATTT-TATTAAAATATTAG
1 TATT-TTTATATT-AAATATTAA
2363749 T-TTTTTATATT-AATATTAA
1 TATTTTTATATTAAATATTAA
2363768 TATTTTTATATTTAAAT-TTAA
1 TATTTTTATA-TTAAATATTAA
2363789 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 8 0.23
20 11 0.31
21 12 0.34
22 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTTTATATTAAATATTAA
Found at i:2363763 original size:19 final size:20
Alignment explanation
Indices: 2363741--2363779 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2363731 ATTTTATTAA
*
2363741 AATATTAGT-TTTTTATATT
1 AATATTAATATTTTTATATT
2363760 AATATTAATATTTTTATATT
1 AATATTAATATTTTTATATT
2363780 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
AATATTAATATTTTTATATT
Found at i:2369844 original size:16 final size:16
Alignment explanation
Indices: 2369817--2369856 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2369807 TATGAATAAT
2369817 AATTTTTA-ATATATA
1 AATTTTTATATATATA
*
2369832 AATTTTTATATATTTA
1 AATTTTTATATATATA
*
2369848 TATTTTTAT
1 AATTTTTAT
2369857 TAATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTTTATATATATA
Found at i:2369857 original size:12 final size:12
Alignment explanation
Indices: 2369842--2369888 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
2369832 AATTTTTATA
2369842 TATTTATATTTT
1 TATTTATATTTT
*
2369854 TATTAATA-TTT
1 TATTTATATTTT
2369865 TATTATATATTTT
1 TATT-TATATTTT
2369878 TATTTTATATT
1 TA-TTTATATT
2369889 ATACATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 7 0.23
12 10 0.33
13 11 0.37
14 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:2369867 original size:11 final size:12
Alignment explanation
Indices: 2369845--2369888 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
2369835 TTTTATATAT
2369845 TTATAT-TTTTA
1 TTATATATTTTA
2369856 TTA-ATATTTTA
1 TTATATATTTTA
2369867 TTATATATTTTTA
1 TTATATA-TTTTA
*
2369880 TTTTATATT
1 TTATATATT
2369889 ATACATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 2 0.07
11 11 0.38
12 5 0.17
13 11 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATATATTTTA
Found at i:2369875 original size:18 final size:17
Alignment explanation
Indices: 2369841--2369906 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 17
2369831 AAATTTTTAT
*
2369841 ATATTTATATTTTTATTA
1 ATATTT-TATTTATATTA
*
2369859 ATATTTTATTATATATTT
1 ATATTTTATT-TATATTA
* *
2369877 TTATTTTATATTATACATA
1 ATATTTTAT-TTATA-TTA
*
2369896 ATATTATATTT
1 ATATTTTATTT
2369907 TAATTATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
17 4 0.11
18 25 0.66
19 9 0.24
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTTTATTTATATTA
Found at i:2378349 original size:30 final size:31
Alignment explanation
Indices: 2378315--2378415 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 31
2378305 AATTTTTTAT
2378315 AATTTTTAATTATTAATAAAAATA-ATATAA
1 AATTTTTAATTATTAATAAAAATAGATATAA
* *
2378345 AA--TTTAATTTGATTAAGTAATAATTATATATTTAA
1 AATTTTTAA-TT-ATTAA-TAA-AA--ATAGATATAA
2378380 AATTTTT-ATT-TTAAATAAAAATAAGATATAA
1 AATTTTTAATTATT-AATAAAAAT-AGATATAA
2378411 AATTT
1 AATTT
2378416 AAATTAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 21
0.70 0.04 0.26
Matches are distributed among these distances:
28 5 0.09
29 2 0.04
30 9 0.16
31 14 0.25
32 4 0.07
33 5 0.09
34 5 0.09
35 9 0.16
36 1 0.02
37 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
AATTTTTAATTATTAATAAAAATAGATATAA
Found at i:2379432 original size:13 final size:14
Alignment explanation
Indices: 2379407--2379436 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2379397 AATTATTTAA
2379407 AAAATTAAAATAAT
1 AAAATTAAAATAAT
2379421 AAAATT-AAATAAT
1 AAAATTAAAATAAT
2379434 AAA
1 AAA
2379437 TTTTTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTAAAATAAT
Found at i:2389849 original size:25 final size:26
Alignment explanation
Indices: 2389815--2389864 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
2389805 TTATTTCGGA
* * *
2389815 TAATTTTTATGTATT-TATTTATATT
1 TAATTATTATGAATTATATTAATATT
2389840 TAATTATTATGAATTATATTAATAT
1 TAATTATTATGAATTATATTAATAT
2389865 AAATTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (26 bp):
TAATTATTATGAATTATATTAATATT
Found at i:2390796 original size:3 final size:3
Alignment explanation
Indices: 2390788--2390824 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2390778 ACCTAGCTTG
2390788 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2390825 ATCAATTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2393623 original size:8 final size:8
Alignment explanation
Indices: 2393612--2393711 Score: 53
Period size: 8 Copynumber: 11.9 Consensus size: 8
2393602 TTTAAATATA
2393612 ATATAATT
1 ATATAATT
2393620 ATATAA-T
1 ATATAATT
*
2393627 ATATAATA
1 ATATAATT
*
2393635 ATATAATA
1 ATATAATT
2393643 AT-TAATAT
1 ATATAAT-T
*
2393651 AAATATATT
1 ATATA-ATT
2393660 A-ATATATT
1 ATATA-ATT
*
2393668 AATATAAAT
1 -ATATAATT
2393677 ATATTAATAT
1 ATA-TAAT-T
*
2393687 ATTAAAATTT
1 A-TATAA-TT
*
2393697 ATATAAAT
1 ATATAATT
2393705 ATATAAT
1 ATATAAT
2393712 ATTTTAAATA
Statistics
Matches: 73, Mismatches: 9, Indels: 20
0.72 0.09 0.20
Matches are distributed among these distances:
7 11 0.15
8 34 0.47
9 14 0.19
10 11 0.15
11 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
ATATAATT
Found at i:2393632 original size:20 final size:20
Alignment explanation
Indices: 2393596--2393734 Score: 79
Period size: 22 Copynumber: 7.2 Consensus size: 20
2393586 GATTTTTTTT
2393596 TATAATT-T-TAA-ATATAA
1 TATAATTATATAATATATAA
2393613 TATAATTATATAATATAT-A
1 TATAATTATATAATATATAA
2393632 -AT-A--ATATAATA-ATTAA
1 TATAATTATATAATATA-TAA
*
2393648 TATAAATATATTAATATATTAA
1 TATAATTATA-TAATATA-TAA
*
2393670 TATAAATATATTAATATATTAA
1 TATAATTATA-TAATATA-TAA
*
2393692 -A-ATTTATATAAATATATAA
1 TATAATTATAT-AATATATAA
*
2393711 TAT-TTTAAATATAAT-TATAA
1 TATAATT--ATATAATATATAA
2393731 TATA
1 TATA
2393735 TAAAAATATG
Statistics
Matches: 103, Mismatches: 2, Indels: 30
0.76 0.01 0.22
Matches are distributed among these distances:
14 1 0.01
15 9 0.09
16 1 0.01
17 10 0.10
18 4 0.04
19 8 0.08
20 30 0.29
21 9 0.09
22 31 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAATTATATAATATATAA
Done.