Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 19 of 21
Found at i:2165549 original size:37 final size:38
Alignment explanation
Indices: 2165466--2165551 Score: 156
Period size: 38 Copynumber: 2.3 Consensus size: 38
2165456 TAAAAATTTT
*
2165466 AATTTGAAATTAATCGACGGTTGACGATTAGAGAATTC
1 AATTTGAAATTAATCGACGGTTGACGAGTAGAGAATTC
2165504 AATTTGAAATTAATCGACGGTTGACGAGTAGA-AATTC
1 AATTTGAAATTAATCGACGGTTGACGAGTAGAGAATTC
2165541 AATTTGAAATT
1 AATTTGAAATT
2165552 GTCAATTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 16 0.34
38 31 0.66
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (38 bp):
AATTTGAAATTAATCGACGGTTGACGAGTAGAGAATTC
Found at i:2165558 original size:14 final size:14
Alignment explanation
Indices: 2165539--2165566 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2165529 GAGTAGAAAT
2165539 TCAATTTGAAATTG
1 TCAATTTGAAATTG
2165553 TCAATTTGAAATTG
1 TCAATTTGAAATTG
2165567 ACTAGTAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
TCAATTTGAAATTG
Found at i:2169461 original size:2 final size:2
Alignment explanation
Indices: 2169456--2169494 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2169446 AAAAAAGAGA
2169456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2169495 GAGGCGTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2170977 original size:5 final size:5
Alignment explanation
Indices: 2170967--2170999 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
2170957 AACCTGAAAC
2170967 CAGTT CAGTT CAGTT CAGTT CAGTT CAGTT CAG
1 CAGTT CAGTT CAGTT CAGTT CAGTT CAGTT CAG
2171000 GCATGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (5 bp):
CAGTT
Found at i:2172286 original size:22 final size:24
Alignment explanation
Indices: 2172237--2172289 Score: 83
Period size: 22 Copynumber: 2.2 Consensus size: 24
2172227 TTATTATATT
2172237 TAATATTTATATTTATAAATTTAAA
1 TAATA-TTATATTTATAAATTTAAA
2172262 TAATATTA-ATTT-TAAATTTAAA
1 TAATATTATATTTATAAATTTAAA
2172284 TAATAT
1 TAATAT
2172290 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.57
23 4 0.14
24 3 0.11
25 5 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATATTATATTTATAAATTTAAA
Found at i:2172530 original size:27 final size:26
Alignment explanation
Indices: 2172488--2172541 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
2172478 GATAATTTAA
* *
2172488 TGATTTATTATTGTTGTTTAAATAAT
1 TGATTTATGATTGTTGATTAAATAAT
2172514 TGATTTAGTGATTGTTGATTAAATAAT
1 TGATTTA-TGATTGTTGATTAAATAAT
2172541 T
1 T
2172542 AAAAGGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (26 bp):
TGATTTATGATTGTTGATTAAATAAT
Found at i:2177027 original size:34 final size:34
Alignment explanation
Indices: 2176977--2177084 Score: 128
Period size: 34 Copynumber: 3.2 Consensus size: 34
2176967 GGGAGAATTA
* * *
2176977 TTGACTAAATGGGTGATTTGGTGGTTTGCCATTG
1 TTGATTAAATTGGTGATTTGGTGGTTTGACATTG
* *
2177011 CTGATTAAATAT-GTGATTTGGTGGTTTAACATTG
1 TTGATTAAAT-TGGTGATTTGGTGGTTTGACATTG
* * *
2177045 TTGACTAAATTGGTGATTTGGTGATTTGTCATTG
1 TTGATTAAATTGGTGATTTGGTGGTTTGACATTG
2177079 TTGATT
1 TTGATT
2177085 TAACTAAAAG
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
33 1 0.02
34 60 0.98
ACGTcount: A:0.21, C:0.06, G:0.27, T:0.45
Consensus pattern (34 bp):
TTGATTAAATTGGTGATTTGGTGGTTTGACATTG
Found at i:2179082 original size:49 final size:49
Alignment explanation
Indices: 2179023--2179127 Score: 183
Period size: 49 Copynumber: 2.1 Consensus size: 49
2179013 ATTTACATAG
*
2179023 TATTTTATTTAGCCTCTAGTGCTTTTATTTTCAGTACAACATAGATCAA
1 TATTTTATTTAGCCTCTAGTGCTTTTATTTTCAGTAAAACATAGATCAA
*
2179072 TATTTTATTTAGCCTCTAGTGCTTTTATTTTCAGTAAAATATAGATCAA
1 TATTTTATTTAGCCTCTAGTGCTTTTATTTTCAGTAAAACATAGATCAA
*
2179121 TAATTTA
1 TATTTTA
2179128 AAGTTGAAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (49 bp):
TATTTTATTTAGCCTCTAGTGCTTTTATTTTCAGTAAAACATAGATCAA
Found at i:2179721 original size:16 final size:17
Alignment explanation
Indices: 2179697--2179729 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2179687 AATATTTTTC
2179697 TTTTAATTTTTTAATTA
1 TTTTAATTTTTTAATTA
2179714 TTTT-ATTTTTTAATTA
1 TTTTAATTTTTTAATTA
2179730 AGATACTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTAATTTTTTAATTA
Found at i:2182614 original size:23 final size:24
Alignment explanation
Indices: 2182571--2182617 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
2182561 AATTTTTCAC
* *
2182571 TTTTATTTACATTTAATAAATTAT
1 TTTTATTTACATTCAAAAAATTAT
2182595 TTTTATTTA-ATTCAAAAAATTAT
1 TTTTATTTACATTCAAAAAATTAT
2182618 GAATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTATTTACATTCAAAAAATTAT
Found at i:2183173 original size:18 final size:19
Alignment explanation
Indices: 2183145--2183180 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2183135 ATTAAGTATA
2183145 TAAATTAAAAAATTATAAT
1 TAAATTAAAAAATTATAAT
2183164 TAAA-TAAAAAATTATAA
1 TAAATTAAAAAATTATAA
2183181 ATATTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATTAAAAAATTATAAT
Found at i:2192045 original size:13 final size:13
Alignment explanation
Indices: 2192014--2192038 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2192004 TAAAATTTAA
2192014 AATTTATTTTTTT
1 AATTTATTTTTTT
2192027 AATTTATTTTTT
1 AATTTATTTTTT
2192039 ACTTTTAGGC
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
AATTTATTTTTTT
Found at i:2192305 original size:21 final size:19
Alignment explanation
Indices: 2192280--2192337 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
2192270 TCTTTGAAAA
2192280 TAAATGATATTTATATATTTT
1 TAAAT-ATA-TTATATATTTT
* *
2192301 TAAATATAATA-ATTATATT
1 TAAATATATTATA-TATTTT
2192320 TAAA-ATATTATATATTTT
1 TAAATATATTATATATTTT
2192338 ACATAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 11 0.35
19 12 0.39
20 3 0.10
21 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TAAATATATTATATATTTT
Found at i:2192419 original size:8 final size:8
Alignment explanation
Indices: 2192391--2192430 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
2192381 TATATGTATA
2192391 TTTATA-T
1 TTTATATT
*
2192398 TTTATTTAT
1 TTTATAT-T
2192407 TTTATATT
1 TTTATATT
2192415 TTTATATT
1 TTTATATT
2192423 TTTATATT
1 TTTATATT
2192431 ATATACATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 5 0.17
8 17 0.59
9 7 0.24
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTATATT
Found at i:2192591 original size:27 final size:28
Alignment explanation
Indices: 2192560--2192632 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
2192550 GTTGAGCTAA
2192560 AATTTTTAAATATAAATATAAAAA-TAT
1 AATTTTTAAATATAAATATAAAAATTAT
*
2192587 AATTTTTAAA-ATATAT-TAAAAATTAT
1 AATTTTTAAATATAAATATAAAAATTAT
* *
2192613 ATATATTTATAT-TAAATATA
1 A-ATTTTTAAATATAAATATA
2192633 TATTTAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 6 0.16
26 9 0.24
27 21 0.55
28 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATTTTTAAATATAAATATAAAAATTAT
Found at i:2192597 original size:14 final size:14
Alignment explanation
Indices: 2192560--2192601 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2192550 GTTGAGCTAA
2192560 AATTTTT-AAATAT
1 AATTTTTAAAATAT
* * *
2192573 AAATATAAAAATAT
1 AATTTTTAAAATAT
2192587 AATTTTTAAAATAT
1 AATTTTTAAAATAT
2192601 A
1 A
2192602 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTTTTAAAATAT
Found at i:2192863 original size:15 final size:17
Alignment explanation
Indices: 2192834--2192865 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2192824 TCTAAGTACA
2192834 AAAAAGAAAATTTAAAG
1 AAAAAGAAAATTTAAAG
2192851 AAAAA-AAAA-TTAAAG
1 AAAAAGAAAATTTAAAG
2192866 CCTACAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (17 bp):
AAAAAGAAAATTTAAAG
Found at i:2195495 original size:15 final size:15
Alignment explanation
Indices: 2195475--2195503 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2195465 TACAAAACAG
2195475 AAAATAAATAAATAA
1 AAAATAAATAAATAA
2195490 AAAATAAATAAATA
1 AAAATAAATAAATA
2195504 TGCTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAAATAAATAA
Found at i:2195866 original size:20 final size:20
Alignment explanation
Indices: 2195838--2195875 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2195828 AATCAAAATG
*
2195838 ATATTAAATACAATATAATT
1 ATATAAAATACAATATAATT
*
2195858 ATATAAAATATAATATAA
1 ATATAAAATACAATATAA
2195876 AAATAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATAAAATACAATATAATT
Found at i:2195893 original size:11 final size:11
Alignment explanation
Indices: 2195842--2195974 Score: 62
Period size: 11 Copynumber: 12.4 Consensus size: 11
2195832 AAAATGATAT
*
2195842 TAAATACAATA
1 TAAATATAATA
*
2195853 TAATTAT-ATA
1 TAAATATAATA
2195863 -AAATATAATA
1 TAAATATAATA
*
2195873 TAAAAATAATA
1 TAAATATAATA
* *
2195884 TAAATTTAATT
1 TAAATATAATA
* * **
2195895 TAAGTGTTTTA
1 TAAATATAATA
2195906 -AAATAT-ATAA
1 TAAATATAAT-A
*
2195916 TAAATTAAAATA
1 TAAA-TATAATA
*
2195928 TAAATATAAAA
1 TAAATATAATA
*
2195939 TATAT-TAAATA
1 TAAATAT-AATA
* *
2195950 TTATTATAATA
1 TAAATATAATA
*
2195961 T-AATAAAATA
1 TAAATATAATA
2195971 TAAA
1 TAAA
2195975 AATTAATATG
Statistics
Matches: 88, Mismatches: 25, Indels: 18
0.67 0.19 0.14
Matches are distributed among these distances:
9 6 0.07
10 20 0.23
11 52 0.59
12 8 0.09
13 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAATATAATA
Found at i:2195939 original size:13 final size:12
Alignment explanation
Indices: 2195915--2195974 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 12
2195905 AAAATATATA
2195915 ATAAATTAAAAT
1 ATAAATTAAAAT
2195927 ATAAATATAAAAT
1 ATAAAT-TAAAAT
2195940 AT--ATT-AAAT
1 ATAAATTAAAAT
* *
2195949 AT-TATTATAAT
1 ATAAATTAAAAT
2195960 AT-AA-TAAAAT
1 ATAAATTAAAAT
2195970 ATAAA
1 ATAAA
2195975 AATTAATATG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 6 0.15
10 11 0.27
11 10 0.24
12 6 0.15
13 8 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAAATTAAAAT
Found at i:2196049 original size:21 final size:21
Alignment explanation
Indices: 2196014--2196075 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
2196004 TTTTTAGTTT
2196014 TAATATATTTATAAATATAAAAA
1 TAATA-ATTT-TAAATATAAAAA
* * **
2196037 TAAT-ATTATTAAAAATTAATT
1 TAATAATT-TTAAATATAAAAA
2196058 TAATAATTTTAAATATAA
1 TAATAATTTTAAATATAA
2196076 TATAAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
21 23 0.74
22 4 0.13
23 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATAATTTTAAATATAAAAA
Found at i:2196081 original size:53 final size:58
Alignment explanation
Indices: 2195956--2196086 Score: 132
Period size: 53 Copynumber: 2.3 Consensus size: 58
2195946 AATATTATTA
* ** *
2195956 TAATATAATA-AAATATAAAAATTAATATGTAATTGTAAAAATTTTACTTTTTTAGTTT
1 TAATATAATATAAATATAAAAATTAATATGTAATTGTAAAAA-TTTAATTTAATAATTT
*
2196014 TAATATATTTATAAATATAAAAA-TAATAT-T-A-T-TAAAAA-TTAATTTAATAATTT
1 TAATATA-ATATAAATATAAAAATTAATATGTAATTGTAAAAATTTAATTTAATAATTT
*
2196067 TAAATATAATATAAAAATAA
1 T-AATATAATATAAATATAA
2196087 TATGCTGATA
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
53 22 0.35
54 6 0.10
55 6 0.10
56 1 0.02
57 1 0.02
58 8 0.13
59 8 0.13
60 11 0.17
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (58 bp):
TAATATAATATAAATATAAAAATTAATATGTAATTGTAAAAATTTAATTTAATAATTT
Found at i:2196843 original size:23 final size:23
Alignment explanation
Indices: 2196817--2196887 Score: 142
Period size: 23 Copynumber: 3.1 Consensus size: 23
2196807 TTCGACTCTT
2196817 CATTTTCTTTAAGTACTCATATC
1 CATTTTCTTTAAGTACTCATATC
2196840 CATTTTCTTTAAGTACTCATATC
1 CATTTTCTTTAAGTACTCATATC
2196863 CATTTTCTTTAAGTACTCATATC
1 CATTTTCTTTAAGTACTCATATC
2196886 CA
1 CA
2196888 ACGCATATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.46
Consensus pattern (23 bp):
CATTTTCTTTAAGTACTCATATC
Found at i:2198773 original size:30 final size:29
Alignment explanation
Indices: 2198722--2198778 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
2198712 TTTATTTTAT
*
2198722 TATTTTTTAAAATTAAATTAAAATAAAAA
1 TATTTTTTAAAAATAAATTAAAATAAAAA
* *
2198751 TATTTTTTAAATAATAATTTAAATTAAA
1 TATTTTTTAAA-AATAAATTAAAATAAA
2198779 TCGATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TATTTTTTAAAAATAAATTAAAATAAAAA
Found at i:2204765 original size:28 final size:29
Alignment explanation
Indices: 2204713--2204783 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
2204703 ATATTTATTT
**
2204713 TTTATTTAAAATATT-TTTATATTATA-A
1 TTTATTTAAAATATTATAAATATTATATA
2204740 TTATATTTAAAATATTATAAAT-TTATATA
1 TT-TATTTAAAATATTATAAATATTATATA
*
2204769 TTT-TTTAATATATTA
1 TTTATTTAAAATATTA
2204784 ATATTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 13 0.34
28 19 0.50
29 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTATTTAAAATATTATAAATATTATATA
Found at i:2204792 original size:20 final size:20
Alignment explanation
Indices: 2204764--2204802 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2204754 TTATAAATTT
* *
2204764 ATATATTTTTTAATATATTA
1 ATATATTTTATAAAATATTA
*
2204784 ATATTTTTTATAAAATATT
1 ATATATTTTATAAAATATT
2204803 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATATTTTATAAAATATTA
Found at i:2204820 original size:6 final size:6
Alignment explanation
Indices: 2204799--2204859 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
2204789 TTTTATAAAA
* * *
2204799 TATTTT T-TTAT T-TTTT TATTTT TATTTT TATTTT TATTAT T-TTTA
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
2204844 TATATTT TATATTT TA
1 TAT-TTT TAT-TTT TA
2204860 ATCATTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
5 11 0.24
6 24 0.52
7 11 0.24
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:2204820 original size:29 final size:30
Alignment explanation
Indices: 2204770--2204854 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 30
2204760 ATTTATATAT
* * *
2204770 TTTTTAATATATTAATATTTTTTATAAAATA
1 TTTTTATTATTTTTATA-TTTTTATAAAATA
* ***
2204801 TTTTT-TTATTTTTTTATTTTTAT-TTTTA
1 TTTTTATTATTTTTATATTTTTATAAAATA
2204829 TTTTTATTATTTTTATATATTTTATA
1 TTTTTATTATTTTTATAT-TTTTATA
2204855 TTTTAATCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
28 7 0.16
29 18 0.42
30 13 0.30
31 5 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTTTATTATTTTTATATTTTTATAAAATA
Found at i:2204841 original size:26 final size:26
Alignment explanation
Indices: 2204803--2204868 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
2204793 ATAAAATATT
*
2204803 TTTTTATT-TTTTTATTTTTATTTT-TA
1 TTTTTATTATTTTTA--TATATTTTATA
2204829 TTTTTATTATTTTTATATATTTTATA
1 TTTTTATTATTTTTATATATTTTATA
* *
2204855 TTTTAATCATTTTT
1 TTTTTATTATTTTT
2204869 TATTATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.20
26 22 0.63
27 6 0.17
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTTATTATTTTTATATATTTTATA
Found at i:2204843 original size:9 final size:9
Alignment explanation
Indices: 2204799--2204874 Score: 63
Period size: 9 Copynumber: 8.7 Consensus size: 9
2204789 TTTTATAAAA
2204799 TATT-TTTT
1 TATTATTTT
2204807 TATT-TTTT
1 TATTATTTT
2204815 TATT-TTTAT
1 TATTATTT-T
*
2204824 TTTTATTTT
1 TATTATTTT
2204833 TATTATTTT
1 TATTATTTT
2204842 TA-TATATTT
1 TATTAT-TTT
2204851 TA-TATTTT
1 TATTATTTT
* *
2204859 AATCATTTTT
1 TATTA-TTTT
2204869 TATTAT
1 TATTAT
2204875 ATAATAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
8 22 0.39
9 25 0.44
10 10 0.18
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (9 bp):
TATTATTTT
Found at i:2204869 original size:18 final size:17
Alignment explanation
Indices: 2204761--2204871 Score: 71
Period size: 15 Copynumber: 6.9 Consensus size: 17
2204751 ATATTATAAA
2204761 TTTATATATTTTTTAATAT
1 TTTA-ATATTTTTT-ATAT
*
2204780 ATTAATATTTTTTATA-
1 TTTAATATTTTTTATAT
*
2204796 --AAATATTTTTT-TAT
1 TTTAATATTTTTTATAT
**
2204810 TTTTTTA-TTTTTAT-T
1 TTTAATATTTTTTATAT
2204825 TTT-AT-TTTTATTAT-T
1 TTTAATATTTT-TTATAT
*
2204840 TTT-ATATATTTTATAT
1 TTTAATATTTTTTATAT
2204856 TTTAATCATTTTTTAT
1 TTTAAT-ATTTTTTAT
2204872 TATATAATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
13 2 0.03
14 14 0.19
15 23 0.31
16 10 0.14
17 5 0.07
18 17 0.23
19 3 0.04
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATATTTTTTATAT
Found at i:2204874 original size:36 final size:29
Alignment explanation
Indices: 2204799--2204859 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
2204789 TTTTATAAAA
2204799 TATTTTT-TTATTTTTTTATTTTTATTTT
1 TATTTTTATTATTTTTTTATTTTTATTTT
*
2204827 TATTTTTATTATTTTTATATATTTTATATTT
1 TATTTTTATTATTTTTTTAT-TTTTAT-TTT
2204858 TA
1 TA
2204860 ATCATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 7 0.24
29 11 0.38
30 6 0.21
31 5 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (29 bp):
TATTTTTATTATTTTTTTATTTTTATTTT
Found at i:2205069 original size:20 final size:21
Alignment explanation
Indices: 2204998--2205073 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 21
2204988 TGAGTGTTGT
2204998 TAAAATATTATTTAAAGT-TAA
1 TAAAATATTATTTAAA-TATAA
*
2205019 GTAATATATTATTTATAATAT--
1 -TAAAATATTATTTA-AATATAA
** *
2205040 TATTATTTTATTTAAATATAA
1 TAAAATATTATTTAAATATAA
2205061 TAAAAT-TTATTTA
1 TAAAATATTATTTA
2205074 TTATTTACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.11
20 19 0.42
21 4 0.09
22 14 0.31
23 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TAAAATATTATTTAAATATAA
Found at i:2205090 original size:27 final size:30
Alignment explanation
Indices: 2205035--2205110 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 30
2205025 TATTATTTAT
*
2205035 AATATTATTATTTTATTTAAATATAAT-AA
1 AATATTATTATATTATTTAAATATAATAAA
*
2205064 AAT-TTATT-TATTATTTACAT-TACATAAA
1 AATATTATTATATTATTTAAATATA-ATAAA
2205092 AATATTATTATATATATTT
1 AATATTATTATAT-TATTT
2205111 TTTAAGTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 2 0.05
27 12 0.30
28 10 0.25
29 8 0.20
30 3 0.08
31 5 0.12
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (30 bp):
AATATTATTATATTATTTAAATATAATAAA
Found at i:2205235 original size:6 final size:6
Alignment explanation
Indices: 2205224--2205281 Score: 100
Period size: 6 Copynumber: 9.7 Consensus size: 6
2205214 AAATATGAAC
2205224 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTATAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT
2205273 TTTT-T TTTT
1 TTTTAT TTTT
2205282 GAAGAAGAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.10
6 40 0.78
7 6 0.12
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:2207741 original size:21 final size:22
Alignment explanation
Indices: 2207717--2207764 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2207707 TTTAAAAGTA
2207717 TTATATTTG-AATTATAA-ATAT
1 TTATA-TTGAAATTATAATATAT
*
2207738 TTATA-TGAAATTTTAATATAT
1 TTATATTGAAATTATAATATAT
2207759 TTATAT
1 TTATAT
2207765 ATTTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.09
20 7 0.30
21 14 0.61
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
TTATATTGAAATTATAATATAT
Found at i:2208219 original size:15 final size:15
Alignment explanation
Indices: 2208134--2208222 Score: 54
Period size: 15 Copynumber: 6.5 Consensus size: 15
2208124 ATTTTATAAC
* *
2208134 TTAAATTAATTTAAG
1 TTAAATTAATTAAAT
2208149 TTAAATT-ATT--AT
1 TTAAATTAATTAAAT
*
2208161 TTAAA-TAATTAAAA
1 TTAAATTAATTAAAT
*
2208175 TT--ATT--TTATAT
1 TTAAATTAATTAAAT
*
2208186 TTAAA--AATAAAATT
1 TTAAATTAATTAAA-T
2208200 TTAAATTAATTAAAT
1 TTAAATTAATTAAAT
2208215 TTAAATTA
1 TTAAATTA
2208223 TAAAATAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 22
0.66 0.08 0.26
Matches are distributed among these distances:
11 7 0.12
12 10 0.18
13 5 0.09
14 12 0.21
15 16 0.29
16 6 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (15 bp):
TTAAATTAATTAAAT
Found at i:2208633 original size:23 final size:22
Alignment explanation
Indices: 2208588--2208665 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
2208578 TTAAAATATA
**
2208588 ATATTTAATAAATT-TTAAATTT
1 ATATTTAA-AAATTATTATTTTT
2208610 ATAATTTAAAAATTATTATTTTT
1 AT-ATTTAAAAATTATTATTTTT
*
2208633 ATTTTTAAATAA-TATT-TTTATT
1 ATATTTAAA-AATTATTATTT-TT
2208655 AT-TTTAAAAAT
1 ATATTTAAAAAT
2208666 ATATATAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
20 2 0.04
21 9 0.19
22 21 0.44
23 16 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTTAAAAATTATTATTTTT
Found at i:2208666 original size:20 final size:21
Alignment explanation
Indices: 2208614--2208667 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
2208604 AAATTTATAA
2208614 TTTAAAAATTATTATTTTTATT
1 TTTAAAAA-TATTATTTTTATT
2208636 TTTAAATAATATT-TTTATTA-T
1 TTTAAA-AATATTATTT-TTATT
2208657 TTTAAAAATAT
1 TTTAAAAATAT
2208668 ATATAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.17
21 10 0.33
22 13 0.43
23 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAAAAATATTATTTTTATT
Found at i:2208714 original size:18 final size:18
Alignment explanation
Indices: 2208643--2208717 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 18
2208633 ATTTTTAAAT
*
2208643 AATATTTTTATTATTTTAAA
1 AATATTTTTAATA-TTT-AA
* * * *
2208663 AATATATATAAAATAT-A
1 AATATTTTTAATATTTAA
*
2208680 AATATTTTTAATTTTTAA
1 AATATTTTTAATATTTAA
2208698 AAT-TTTTTATATATTTAA
1 AATATTTTTA-ATATTTAA
2208716 AA
1 AA
2208718 AATTATATTT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
17 18 0.43
18 13 0.31
19 2 0.05
20 9 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTTTTAATATTTAA
Found at i:2216193 original size:13 final size:14
Alignment explanation
Indices: 2216175--2216209 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2216165 TTATATTAAT
2216175 TATAAATAATA-AA
1 TATAAATAATATAA
2216188 TATAAATAATATAA
1 TATAAATAATATAA
2216202 -ATAAATAA
1 TATAAATAA
2216210 AACCAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.90
14 2 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TATAAATAATATAA
Found at i:2216779 original size:44 final size:42
Alignment explanation
Indices: 2216695--2216776 Score: 103
Period size: 44 Copynumber: 1.9 Consensus size: 42
2216685 AATAATTTAT
* **
2216695 AAATTTATATTATATATTTAATGTATTTTATATATTTTTAAA
1 AAATTTATATTATAAATTTAAAATATTTTATATATTTTTAAA
*
2216737 AAATTTAATATATATAAATTTAAAATATTTTA-ATTTTTTT
1 AAATTT-ATAT-TATAAATTTAAAATATTTTATATATTTTT
2216777 TAATATCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 6 0.18
43 11 0.32
44 17 0.50
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (42 bp):
AAATTTATATTATAAATTTAAAATATTTTATATATTTTTAAA
Found at i:2217130 original size:27 final size:27
Alignment explanation
Indices: 2217095--2217169 Score: 81
Period size: 22 Copynumber: 3.0 Consensus size: 27
2217085 TATATTTTAA
*
2217095 TATATTTATATTATTTTTAAATTATATT
1 TATAATTATATTATTTTTAAATTAT-TT
2217123 T-TAA-T-TA-TA-TTTT-AATTATTT
1 TATAATTATATTATTTTTAAATTATTT
*
2217144 TATAATTATATTATATTTAAATTATT
1 TATAATTATATTATTTTTAAATTATT
2217170 ATATTTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
21 3 0.08
22 9 0.23
23 5 0.13
24 4 0.10
25 4 0.10
26 4 0.10
27 9 0.23
28 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TATAATTATATTATTTTTAAATTATTT
Found at i:2217132 original size:33 final size:32
Alignment explanation
Indices: 2217085--2217155 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
2217075 ATAATTTGCA
2217085 TATATTTTAATATA-TTTATATTATTTT-TAAAT
1 TATATTTTAATATATTTTA-ATTATTTTAT-AAT
2217117 TATATTTTAATTATATTTTAATTATTTTATAAT
1 TATATTTTAA-TATATTTTAATTATTTTATAAT
2217150 TATATT
1 TATATT
2217156 ATATTTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
32 10 0.28
33 21 0.58
34 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
TATATTTTAATATATTTTAATTATTTTATAAT
Found at i:2217158 original size:11 final size:11
Alignment explanation
Indices: 2217085--2217155 Score: 87
Period size: 11 Copynumber: 6.5 Consensus size: 11
2217075 ATAATTTGCA
2217085 TATATTTTAA-
1 TATATTTTAAT
2217095 TATA-TTTATAT
1 TATATTTTA-AT
2217106 TAT-TTTTAAAT
1 TATATTTT-AAT
2217117 TATATTTTAAT
1 TATATTTTAAT
2217128 TATATTTTAAT
1 TATATTTTAAT
2217139 TAT-TTTATAAT
1 TATATTT-TAAT
2217150 TATATT
1 TATATT
2217156 ATATTTAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.07
10 8 0.15
11 35 0.65
12 7 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTTAAT
Found at i:2217180 original size:16 final size:16
Alignment explanation
Indices: 2217137--2217183 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2217127 TTATATTTTA
*
2217137 ATTAT-TTTATAATTAT
1 ATTATATTTATAAAT-T
2217153 ATTATA-TT-TAAATT
1 ATTATATTTATAAATT
2217167 ATTATATTTATAAATT
1 ATTATATTTATAAATT
2217183 A
1 A
2217184 AGTAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 14 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATATTTATAAATT
Found at i:2217183 original size:27 final size:26
Alignment explanation
Indices: 2217095--2217179 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 26
2217085 TATATTTTAA
*
2217095 TATATTTAT-ATTAT-TTTTAA--AT
1 TATATTTATAATTATATTTAAATTAT
*
2217117 TATATTT-TAATTATATTTTAATTATTT
1 TATATTTATAATTATATTTAAATTA--T
*
2217144 TATAATTAT-ATTATATTTAAATTAT
1 TATATTTATAATTATATTTAAATTAT
2217169 TATATTTATAA
1 TATATTTATAA
2217180 ATTAAGTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
21 1 0.02
22 12 0.23
23 6 0.12
25 10 0.19
26 1 0.02
27 21 0.40
28 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TATATTTATAATTATATTTAAATTAT
Found at i:2217671 original size:15 final size:13
Alignment explanation
Indices: 2217647--2217687 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
2217637 AATAAGTAAA
2217647 AAATTAAATTAAT
1 AAATTAAATTAAT
2217660 AAAGTATAAATTAAT
1 AAA-T-TAAATTAAT
*
2217675 TAATTAAATTAAT
1 AAATTAAATTAAT
2217688 TATTACGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 12 0.48
14 2 0.08
15 11 0.44
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (13 bp):
AAATTAAATTAAT
Found at i:2221069 original size:5 final size:5
Alignment explanation
Indices: 2221058--2221099 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
2221048 TTAAAGAACT
* *
2221058 GAAAA -AAAA AAAAA AAAAA GAAAA GAAAA GAAAA GAAAA GAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAA
2221100 GCATAACATT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:2227670 original size:36 final size:36
Alignment explanation
Indices: 2227630--2227706 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
2227620 GATCCTCTCT
*
2227630 ACTGATCGAATCAAGTAACGACA-TCAGACAATATCG
1 ACTGATCGAATCAAGT-ACGAAATTCAGACAATATCG
* *
2227666 ACTGATCGAATCAAGTATGAAATTCAGACAATATTG
1 ACTGATCGAATCAAGTACGAAATTCAGACAATATCG
2227702 ACTGA
1 ACTGA
2227707 CTTAATCAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 4 0.11
36 33 0.89
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (36 bp):
ACTGATCGAATCAAGTACGAAATTCAGACAATATCG
Found at i:2228404 original size:2 final size:2
Alignment explanation
Indices: 2228397--2228424 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2228387 TGCATATCAC
2228397 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
2228425 GTAAGCACAA
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:2233427 original size:6 final size:6
Alignment explanation
Indices: 2233416--2233441 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2233406 ATGCCGATGT
2233416 AATCGG AATCGG AATCGG AATCGG AA
1 AATCGG AATCGG AATCGG AATCGG AA
2233442 ATCGCCGGTT
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:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (6 bp):
AATCGG
Found at i:2242576 original size:43 final size:44
Alignment explanation
Indices: 2242513--2242601 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 44
2242503 TTAAAAAAAA
* *
2242513 ATTATATTAATATATTTAATTTATATAA-TTAAAA-TTATTTTTT
1 ATTAAATTAAAATATTTAATTT-TATAAGTTAAAATTTATTTTTT
*
2242556 ATTAAATTAAAATCTTTAATTTTATAATGGTTAAAATTTATTTTTT
1 ATTAAATTAAAATATTTAATTTTATAA--GTTAAAATTTATTTTTT
2242602 TTCTTTTGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 5 0.13
43 19 0.49
45 6 0.15
46 9 0.23
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (44 bp):
ATTAAATTAAAATATTTAATTTTATAAGTTAAAATTTATTTTTT
Found at i:2244661 original size:4 final size:4
Alignment explanation
Indices: 2244645--2244685 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
2244635 ATATTTTCAT
* * *
2244645 ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAT ATAT ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
2244686 CACACATAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:2245269 original size:31 final size:31
Alignment explanation
Indices: 2245211--2245286 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
2245201 TTTAAAGTAT
* *
2245211 TTTATATTTATAAAAATTTTAAGTATTAA-TAA
1 TTTATA-TTAT-ATAATTTTAAATATTAATTAA
*
2245243 TTTATATTATATAATTTTAAAATATTAATTTA
1 TTTATATTATATAATTTT-AAATATTAATTAA
*
2245275 TTTATGTTATAT
1 TTTATATTATAT
2245287 CATGCTTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 7 0.18
31 12 0.32
32 19 0.50
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TTTATATTATATAATTTTAAATATTAATTAA
Found at i:2246006 original size:12 final size:12
Alignment explanation
Indices: 2245989--2246025 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2245979 ATAACATAAA
*
2245989 AAATATAAATAT
1 AAATATAAAAAT
2246001 AAATATAAAAAT
1 AAATATAAAAAT
*
2246013 AAATATATAAAT
1 AAATATAAAAAT
2246025 A
1 A
2246026 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATAAAAAT
Found at i:2246026 original size:6 final size:6
Alignment explanation
Indices: 2245989--2246019 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2245979 ATAACATAAA
*
2245989 AAATAT AAATAT AAATAT AAAAAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT AAATAT A
2246020 TAAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATAT
Found at i:2246026 original size:20 final size:20
Alignment explanation
Indices: 2245969--2246026 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2245959 AAAATCTGAT
*
2245969 AAAAT-TAAACATAACATA-A
1 AAAATATAAATATAA-ATATA
2245988 AAAATATAAATATAAATATA
1 AAAATATAAATATAAATATA
2246008 AAAATA-AATATATAAATAT
1 AAAATATAA-ATATAAATAT
2246027 TTTAAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
19 10 0.29
20 25 0.71
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATATAAATATAAATATA
Found at i:2246056 original size:18 final size:18
Alignment explanation
Indices: 2246033--2246088 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 18
2246023 ATATTTTAAA
2246033 ATTAATATAATATAAATT
1 ATTAATATAATATAAATT
* *
2246051 ATTAATTTATTA-AAATT
1 ATTAATATAATATAAATT
*
2246068 -TTAA-AAAATAT-AATT
1 ATTAATATAATATAAATT
2246083 A-TAATA
1 ATTAATA
2246089 AAAATTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
15 10 0.33
16 5 0.17
17 5 0.17
18 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAATATAATATAAATT
Found at i:2246066 original size:32 final size:34
Alignment explanation
Indices: 2246002--2246099 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 34
2245992 TATAAATATA
2246002 AATATAAAAATAAATATATAAATATTTTAAAATT
1 AATATAAAAATAAATATATAAATATTTTAAAATT
* *
2246036 AATAT-AATATAAAT-TATTAAT-TTATTAAAATT
1 AATATAAAAATAAATATATAAATATT-TTAAAATT
* *
2246068 -TTA-AAAAATATAATTATAATAAAAATTTTAAA
1 AATATAAAAATA-AA-TAT-ATAAATATTTTAAA
2246100 TAAATTATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
31 9 0.18
32 16 0.31
33 9 0.18
34 6 0.12
35 9 0.18
36 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AATATAAAAATAAATATATAAATATTTTAAAATT
Found at i:2246109 original size:26 final size:26
Alignment explanation
Indices: 2246044--2246116 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 26
2246034 TTAATATAAT
*
2246044 ATAAATTATTAATTTATTAAAATTTTAA
1 ATAAATTATT-A-TTATAAAAATTTTAA
*
2246072 A-AAATATAATTATAATAAAAATTTTAA
1 ATAAAT-T-ATTATTATAAAAATTTTAA
2246099 ATAAATTATTATTATAAA
1 ATAAATTATTATTATAAA
2246117 TAAATAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 10 0.26
27 19 0.49
28 7 0.18
29 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAAATTATTATTATAAAAATTTTAA
Found at i:2246901 original size:13 final size:15
Alignment explanation
Indices: 2246883--2246914 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2246873 CCACCGGATT
2246883 ATAAATA-A-AAAAA
1 ATAAATACATAAAAA
2246896 ATAAATACATAAAAA
1 ATAAATACATAAAAA
2246911 ATAA
1 ATAA
2246915 TTTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAATACATAAAAA
Found at i:2247115 original size:24 final size:21
Alignment explanation
Indices: 2247064--2247133 Score: 50
Period size: 24 Copynumber: 3.1 Consensus size: 21
2247054 GCAACAATTT
*
2247064 TAAATTTGTATGAATATAAAA
1 TAAATTTGTATAAATATAAAA
**
2247085 TTTATTTGTATTAAATATGTAAAA
1 TAAATTTGTA-TAAATA--TAAAA
* *
2247109 TAAATTTAATATAAATTATTAAA
1 TAAATTT-GTATAAA-TATAAAA
2247132 TA
1 TA
2247134 TGTTAAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
21 8 0.22
22 5 0.14
23 6 0.16
24 14 0.38
25 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (21 bp):
TAAATTTGTATAAATATAAAA
Found at i:2247163 original size:42 final size:44
Alignment explanation
Indices: 2247095--2247193 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 44
2247085 TTTATTTGTA
* *
2247095 TTAAATA-TGTAAA-ATAAATTTAATATAAATT-ATTAAAT-AT
1 TTAAATATTTTAAATATAAATATAATATAAATTAATTAAATAAT
* *
2247135 GTTAAA-ATTTTAAATATAAATATAATATATATTAATTATATAAT
1 -TTAAATATTTTAAATATAAATATAATATAAATTAATTAAATAAT
2247179 TTAAATATTTTAAAT
1 TTAAATATTTTAAAT
2247194 TTATCATATC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
40 1 0.02
41 10 0.20
42 16 0.33
43 11 0.22
44 11 0.22
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (44 bp):
TTAAATATTTTAAATATAAATATAATATAAATTAATTAAATAAT
Found at i:2247174 original size:22 final size:22
Alignment explanation
Indices: 2247115--2247202 Score: 64
Period size: 22 Copynumber: 4.3 Consensus size: 22
2247105 AAAATAAATT
*
2247115 TAATATAAAT-TATTAAATATG
1 TAATATAAATATATTAAATATA
2247136 T--TA-AAAT-T-TTAAATATA
1 TAATATAAATATATTAAATATA
*
2247153 -AATATAATATATATTAATTATA
1 TAATATAA-ATATATTAAATATA
* * *
2247175 TAATTTAAATATTTTAAATTTA
1 TAATATAAATATATTAAATATA
*
2247197 TCATAT
1 TAATAT
2247203 CATATTTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
17 8 0.15
18 7 0.13
19 4 0.08
20 2 0.04
21 2 0.04
22 23 0.44
23 6 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
TAATATAAATATATTAAATATA
Found at i:2247714 original size:18 final size:18
Alignment explanation
Indices: 2247691--2247736 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2247681 GAAAATATTT
*
2247691 AATTTTTATTTTAAATTA
1 AATTTTTATTTTAAAATA
*
2247709 AATTTTAATTTTAAAATA
1 AATTTTTATTTTAAAATA
*
2247727 AAATTTTATT
1 AATTTTTATT
2247737 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTTTATTTTAAAATA
Found at i:2247743 original size:22 final size:21
Alignment explanation
Indices: 2247713--2247755 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
2247703 AAATTAAATT
*
2247713 TTAATTTTAAAATAAAATTTTA
1 TTAAATTTAAAAT-AAATTTTA
2247735 TTAAATTTAAAATAAATTTTA
1 TTAAATTTAAAATAAATTTTA
2247756 AATCACAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAATTTAAAATAAATTTTA
Found at i:2247758 original size:18 final size:18
Alignment explanation
Indices: 2247700--2247758 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
2247690 TAATTTTTAT
* *
2247700 TTTAAATTAAATTTTAAT
1 TTTAAAATAAATTTTAAA
2247718 TTTAAAATAAAATTTTATTAAA
1 TTTAAAAT-AAA--TT-TTAAA
2247740 TTTAAAATAAATTTTAAA
1 TTTAAAATAAATTTTAAA
2247758 T
1 T
2247759 CACAGTGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
18 13 0.37
19 5 0.14
21 5 0.14
22 12 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAATAAATTTTAAA
Found at i:2249940 original size:32 final size:33
Alignment explanation
Indices: 2249859--2249952 Score: 113
Period size: 32 Copynumber: 2.9 Consensus size: 33
2249849 TTTTAAATGA
*
2249859 AAATA-ATTAAAATATA-ATAAATATAAATATAT
1 AAATATATTAAAATTTATAT-AATATAAATATAT
* *
2249891 AAATTTATCAAAATTTATATAATATAAAT-TAT
1 AAATATATTAAAATTTATATAATATAAATATAT
* *
2249923 TAATATATTAAAATTTATATAAAATAAATA
1 AAATATATTAAAATTTATATAATATAAATA
2249953 CAAATATATA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 32 0.62
33 18 0.35
34 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
AAATATATTAAAATTTATATAATATAAATATAT
Found at i:2249950 original size:16 final size:16
Alignment explanation
Indices: 2249900--2249950 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2249890 TAAATTTATC
*
2249900 AAAATTTATATAATAT
1 AAAATTTATATAAAAT
* * *
2249916 AAATTATTA-ATATATT
1 AAAAT-TTATATAAAAT
2249932 AAAATTTATATAAAAT
1 AAAATTTATATAAAAT
2249948 AAA
1 AAA
2249951 TACAAATATA
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATTTATATAAAAT
Found at i:2262360 original size:33 final size:35
Alignment explanation
Indices: 2262312--2262422 Score: 97
Period size: 37 Copynumber: 3.2 Consensus size: 35
2262302 ATAGGTGTAG
* *
2262312 ATATAAATTTT-TAAATATTTATATATTTAAA-TT
1 ATATTAATTTTATAAATATTTAAATATTTAAATTT
2262345 ATATT-ATTTTATAAATAAAAATTTAAATATTTAAATTT
1 ATATTAATTTTATAAAT----ATTTAAATATTTAAATTT
* * *
2262383 ATATTAATTGTATAAATAATTTGAAT-TCTAAATTT
1 ATATTAATTTTATAAAT-ATTTAAATATTTAAATTT
2262418 A-ATTA
1 ATATTA
2262423 TCTATTTATA
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
32 5 0.08
33 9 0.14
34 4 0.06
35 9 0.14
36 8 0.12
37 14 0.21
38 7 0.11
39 10 0.15
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (35 bp):
ATATTAATTTTATAAATATTTAAATATTTAAATTT
Found at i:2262377 original size:37 final size:39
Alignment explanation
Indices: 2262323--2262401 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 39
2262313 TATAAATTTT
* * *
2262323 TAAATATTTATATATTTAAA-TTATATT-ATTTTATAAA
1 TAAAAATTTAAATATTTAAATTTATATTAATTGTATAAA
2262360 TAAAAATTTAAATATTTAAATTTATATTAATTGTATAAA
1 TAAAAATTTAAATATTTAAATTTATATTAATTGTATAAA
2262399 TAA
1 TAA
2262402 TTTGAATTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 18 0.49
38 7 0.19
39 12 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (39 bp):
TAAAAATTTAAATATTTAAATTTATATTAATTGTATAAA
Found at i:2262587 original size:11 final size:11
Alignment explanation
Indices: 2262544--2262601 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
2262534 AAATAGTATT
*
2262544 ATTTAATTTAA
1 ATTTAATATAA
2262555 ATTTAA-AT-A
1 ATTTAATATAA
* *
2262564 ATTTTATACAA
1 ATTTAATATAA
2262575 ATTTAATATAA
1 ATTTAATATAA
*
2262586 ATAATAA-ATAA
1 AT-TTAATATAA
2262597 ATTTA
1 ATTTA
2262602 TTATCATCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
9 6 0.16
10 4 0.11
11 24 0.65
12 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
ATTTAATATAA
Found at i:2263982 original size:12 final size:12
Alignment explanation
Indices: 2263937--2263990 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
2263927 TTTTATAATA
2263937 AATTTAATATATTT
1 AATTTAA-A-ATTT
2263951 AATTT-AAATTT
1 AATTTAAAATTT
*
2263962 -A-TAAAAATTT
1 AATTTAAAATTT
*
2263972 TATTTAAAATTT
1 AATTTAAAATTT
2263984 AATTTAA
1 AATTTAA
2263991 TTAAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
9 1 0.03
10 7 0.21
11 5 0.15
12 15 0.44
13 1 0.03
14 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AATTTAAAATTT
Found at i:2264006 original size:14 final size:14
Alignment explanation
Indices: 2263984--2264014 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2263974 TTTAAAATTT
*
2263984 AATTTAATTAAATA
1 AATTAAATTAAATA
2263998 AATTAAATTAAATA
1 AATTAAATTAAATA
2264012 AAT
1 AAT
2264015 AATTCGATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTAAATTAAATA
Found at i:2264116 original size:110 final size:114
Alignment explanation
Indices: 2263997--2264210 Score: 305
Period size: 110 Copynumber: 1.9 Consensus size: 114
2263987 TTAATTAAAT
*
2263997 AAATTAAATTAAATAAATAATTCGATCTTTAATTAAATTTAATAAAA-AACA-AT-TATATTT-A
1 AAATCAAATTAAATAAATAATTCGATCTTTAATTAAATTTAATAAAAGAA-AGATGTAT-TTTAA
2264058 -AAA-ATAATAATTTATATTAAAATAATCATAAAAAGTAATTAAATGAATC
64 TAAAGATAATAATTTATATTAAAATAATCATAAAAAGTAATTAAATGAATC
* * * *
2264107 AAATCAAATTAAATAAATAATTTGATCTTTAATTAAGTTTAGTAAAAGAAAGCTGTATTTTAAAT
1 AAATCAAATTAAATAAATAATTCGATCTTTAATTAAATTTAATAAAAGAAAGATGTATTTT-AAT
*
2264172 AAAGATAATAATTTATATTAGAATAATCATAAAAAGTAA
65 AAAGATAATAATTTATATTAAAATAATCATAAAAAGTAA
2264211 AGTTTTTAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
110 44 0.48
111 6 0.07
112 3 0.03
113 1 0.01
114 3 0.03
115 34 0.37
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (114 bp):
AAATCAAATTAAATAAATAATTCGATCTTTAATTAAATTTAATAAAAGAAAGATGTATTTTAATA
AAGATAATAATTTATATTAAAATAATCATAAAAAGTAATTAAATGAATC
Found at i:2266402 original size:24 final size:24
Alignment explanation
Indices: 2266375--2266425 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2266365 CGTGTAAATA
2266375 TTAAATATATAATATTA-ATTATAT
1 TTAAATATATAATATTATATTAT-T
**
2266399 TTAAATATATTTTATTATATTATT
1 TTAAATATATAATATTATATTATT
2266423 TTA
1 TTA
2266426 TATTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAAATATATAATATTATATTATT
Found at i:2266743 original size:16 final size:14
Alignment explanation
Indices: 2266713--2266763 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2266703 TAAATTGTAA
2266713 TTAATATAATATAT
1 TTAATATAATATAT
2266727 TTAATATACATTATAT
1 TTAATATA-A-TATAT
*
2266743 TTATATTTAA-A-AT
1 TTA-ATATAATATAT
2266756 TTAATATA
1 TTAATATA
2266764 TTTAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 4 0.12
13 5 0.16
14 9 0.28
15 1 0.03
16 9 0.28
17 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAATATAATATAT
Found at i:2267129 original size:53 final size:52
Alignment explanation
Indices: 2267070--2267189 Score: 126
Period size: 52 Copynumber: 2.3 Consensus size: 52
2267060 TTGAATTGAT
2267070 ATTTAATAATTAAAAAAT-AA-TTTTTATTTAA-ATTTAATTATAAAATATATAA
1 ATTTAATAATTAAAAAATAAATTTTTTATTTAATA-TTAATTAT-AAATA-ATAA
**
2267122 ATATTAAT-A-T-AAAAATAAATTTTTTATTTTTTATTAATTATAAATAATAA
1 AT-TTAATAATTAAAAAATAAATTTTTTATTTAATATTAATTATAAATAATAA
2267172 ATTTATATAATATAAAAA
1 ATTTA-ATAAT-TAAAAA
2267190 CTCATATTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
49 3 0.05
50 14 0.25
51 9 0.16
52 20 0.35
53 7 0.12
54 4 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (52 bp):
ATTTAATAATTAAAAAATAAATTTTTTATTTAATATTAATTATAAATAATAA
Found at i:2267271 original size:8 final size:8
Alignment explanation
Indices: 2267246--2267310 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
2267236 ATAATTTAAT
2267246 TAATAAAA
1 TAATAAAA
2267254 TAATTAAAAA
1 TAA-T-AAAA
2267264 TAATAAAA
1 TAATAAAA
2267272 T-ATAAAA
1 TAATAAAA
*
2267279 TATTAAAA
1 TAATAAAA
*
2267287 -AATAATA
1 TAATAAAA
2267294 T-ATAAATA
1 TAATAAA-A
*
2267302 TATTAAAA
1 TAATAAAA
2267310 T
1 T
2267311 GTATATATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 16 0.35
8 17 0.37
9 6 0.13
10 7 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
TAATAAAA
Found at i:2267278 original size:15 final size:16
Alignment explanation
Indices: 2267246--2267310 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 16
2267236 ATAATTTAAT
2267246 TAATAAAATAATTAAAAA
1 TAATAAAAT-ATT-AAAA
2267264 TAATAAAATA-TAAAA
1 TAATAAAATATTAAAA
* * *
2267279 TATTAAAA-AATAATA
1 TAATAAAATATTAAAA
2267294 T-ATAAATATATTAAAA
1 TAATAAA-ATATTAAAA
2267310 T
1 T
2267311 GTATATATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.13
15 17 0.44
16 7 0.18
17 1 0.03
18 9 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATAAAATATTAAAA
Found at i:2267287 original size:25 final size:22
Alignment explanation
Indices: 2267248--2267309 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 22
2267238 AATTTAATTA
*
2267248 ATAAAATAATTAAAAATAATAAAAT
1 ATAAAAT-ATT-AAAA-AATAATAT
2267273 ATAAAATATTAAAAAATAATAT
1 ATAAAATATTAAAAAATAATAT
2267295 ATAAATATATTAAAA
1 ATAAA-ATATTAAAA
2267310 TGTATATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
22 12 0.34
23 13 0.37
24 3 0.09
25 7 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAAATATTAAAAAATAATAT
Found at i:2270772 original size:45 final size:47
Alignment explanation
Indices: 2270684--2270772 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
2270674 CGTGGTAAGC
*
2270684 TAATTGTCTTTGGAATTGTTTTTACGTCAGAGATTAATAAACTTAGA
1 TAATTGTCTTCGGAATTGTTTTTACGTCAGAGATTAATAAACTTAGA
2270731 TAATTGTCTTCGGAATTG-TTTT-CGTCAGAGATTAATAAACTT
1 TAATTGTCTTCGGAATTGTTTTTACGTCAGAGATTAATAAACTT
2270773 GAGGTACCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 20 0.49
46 4 0.10
47 17 0.41
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (47 bp):
TAATTGTCTTCGGAATTGTTTTTACGTCAGAGATTAATAAACTTAGA
Found at i:2272867 original size:18 final size:19
Alignment explanation
Indices: 2272841--2272876 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2272831 AAAAAAATAT
2272841 AAATATATAAAT-ATATTA
1 AAATATATAAATAATATTA
*
2272859 AAATTTATAAATAATATT
1 AAATATATAAATAATATT
2272877 TTAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATATATAAATAATATTA
Found at i:2273136 original size:2 final size:2
Alignment explanation
Indices: 2273129--2273168 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2273119 GACAACGCCC
2273129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2273169 CCAGAAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2276508 original size:2 final size:2
Alignment explanation
Indices: 2276496--2276529 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2276486 AAAGCGATAA
2276496 AG AG A- 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
2276530 ATTCAAGTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2276733 original size:27 final size:26
Alignment explanation
Indices: 2276693--2276770 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 26
2276683 ATATAGGAGA
*
2276693 TATAATATAAAATATGTTATATCA-AAT
1 TATAATAT-AAATATTTTATAT-ATAAT
* *
2276720 TATAAAATATAATATTTTAAATATAAT
1 TATAATATA-AATATTTTATATATAAT
*
2276747 TATAATATAAATATTTTATTTATA
1 TATAATATAAATATTTTATATATA
2276771 TACATAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 15 0.35
27 28 0.65
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
TATAATATAAATATTTTATATATAAT
Found at i:2276741 original size:22 final size:21
Alignment explanation
Indices: 2276696--2276755 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 21
2276686 TAGGAGATAT
**
2276696 AATATAAAATATGTTATATCA
1 AATATAAAATATAATATATCA
* *
2276717 AATTATAAAATATAATATTTTA
1 AA-TATAAAATATAATATATCA
*
2276739 AATAT-AATTATAATATA
1 AATATAAAATATAATATA
2276756 AATATTTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 10 0.31
21 5 0.16
22 17 0.53
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AATATAAAATATAATATATCA
Found at i:2277406 original size:2 final size:2
Alignment explanation
Indices: 2277401--2277425 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2277391 GACCAATGTG
2277401 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
2277426 TATTTTCAAG
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:2283631 original size:2 final size:2
Alignment explanation
Indices: 2283624--2283654 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2283614 ACGAATAAAA
2283624 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
2283655 CCTGCACATG
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:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:2290506 original size:18 final size:18
Alignment explanation
Indices: 2290471--2290506 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2290461 TTGGGCGTCA
*
2290471 TTTTTTTTTATTACTTTT
1 TTTTTTTTTATTAATTTT
*
2290489 TTTTTTTTTTTTAATTTT
1 TTTTTTTTTATTAATTTT
2290507 GCGAAATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTATTAATTTT
Found at i:2290943 original size:28 final size:28
Alignment explanation
Indices: 2290912--2290993 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 28
2290902 TGATAGATAC
2290912 TATTTAAATTAATATTTAATTAATAAAA
1 TATTTAAATTAATATTTAATTAATAAAA
* *
2290940 TATTTTTATTTAA-ATTTAATT-AT-AAA
1 TA-TTTAAATTAATATTTAATTAATAAAA
*
2290966 TA-TTAATATT-AT-TTTAAATAATAAAA
1 TATTTAA-ATTAATATTTAATTAATAAAA
2290992 TA
1 TA
2290994 AATTTCAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
24 10 0.23
25 4 0.09
26 10 0.23
27 2 0.05
28 10 0.23
29 8 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TATTTAAATTAATATTTAATTAATAAAA
Found at i:2296595 original size:16 final size:18
Alignment explanation
Indices: 2296572--2296619 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
2296562 ATAAAATGAT
2296572 TAATATAATTTTATTA-A
1 TAATATAATTTTATTATA
2296589 T-ATATAATTTTAATTATA
1 TAATATAATTTT-ATTATA
*
2296607 TAATTTAATTTTA
1 TAATATAATTTTA
2296620 AATTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 10 0.37
17 5 0.19
18 3 0.11
19 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATATAATTTTATTATA
Found at i:2296626 original size:16 final size:16
Alignment explanation
Indices: 2296570--2296628 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
2296560 AAATAAAATG
*
2296570 ATTAATATAATTTT--
1 ATTAATTTAATTTTAA
2296584 ATTAATATATAATTTTAA
1 ATTAAT-T-TAATTTTAA
2296602 TTATATAATTTAATTTTAA
1 --AT-TAATTTAATTTTAA
2296621 ATTAATTT
1 ATTAATTT
2296629 TTTAATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
14 6 0.16
16 13 0.35
17 2 0.05
19 9 0.24
20 3 0.08
21 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTAATTTAATTTTAA
Found at i:2299762 original size:18 final size:18
Alignment explanation
Indices: 2299739--2299781 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2299729 ATTTAACTTA
* *
2299739 TAATAAAAATTATATAAT
1 TAATAAAAAATATAAAAT
*
2299757 TTATAAAAAATATAAAAT
1 TAATAAAAAATATAAAAT
2299775 TAATAAA
1 TAATAAA
2299782 TAGATCTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATAAAAAATATAAAAT
Found at i:2303162 original size:53 final size:53
Alignment explanation
Indices: 2303082--2303185 Score: 181
Period size: 53 Copynumber: 2.0 Consensus size: 53
2303072 TGGGAACTGT
* **
2303082 GTGTTTCATTGCATTGTGAAAACAATATATTCAAGTGATCATCCATGCAATAA
1 GTGTTTCATGGCACGGTGAAAACAATATATTCAAGTGATCATCCATGCAATAA
2303135 GTGTTTCATGGCACGGTGAAAACAATATATTCAAGTGATCATCCATGCAAT
1 GTGTTTCATGGCACGGTGAAAACAATATATTCAAGTGATCATCCATGCAAT
2303186 GAAATTAACA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (53 bp):
GTGTTTCATGGCACGGTGAAAACAATATATTCAAGTGATCATCCATGCAATAA
Found at i:2306039 original size:30 final size:30
Alignment explanation
Indices: 2305998--2306066 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
2305988 ACACATATTC
2305998 AAATAT-TAACATAAGATATAAGATTCTCA
1 AAATATATAACATAAGATATAAGATTCTCA
2306027 AAATATATAACATAAGATATAAGATTCTCA
1 AAATATATAACATAAGATATAAGATTCTCA
2306057 AAATATATAA
1 AAATATATAA
2306067 AAAAATTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
29 6 0.15
30 33 0.85
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (30 bp):
AAATATATAACATAAGATATAAGATTCTCA
Found at i:2309571 original size:15 final size:15
Alignment explanation
Indices: 2309533--2309571 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2309523 TATGATTGAA
*
2309533 ATATATTTTTTTTTT
1 ATATATTTTTTATTT
* *
2309548 ATGTTTTTTTTATTT
1 ATATATTTTTTATTT
2309563 ATATATTTT
1 ATATATTTT
2309572 GAATATTAAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATATATTTTTTATTT
Found at i:2310161 original size:20 final size:20
Alignment explanation
Indices: 2310125--2310162 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2310115 TAATTTTTTT
* *
2310125 TAAAAATTTTTATAAATATA
1 TAAAAATTTTAAAAAATATA
2310145 TAAAAATTTTAAAAAATA
1 TAAAAATTTTAAAAAATA
2310163 AATATATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAAATTTTAAAAAATATA
Found at i:2311443 original size:10 final size:10
Alignment explanation
Indices: 2311424--2311454 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2311414 TTATGTTATT
*
2311424 AAATTTAAAA
1 AAATTAAAAA
2311434 AAATTAAAAA
1 AAATTAAAAA
2311444 AAATTAAAAA
1 AAATTAAAAA
2311454 A
1 A
2311455 TTATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAATTAAAAA
Found at i:2311482 original size:29 final size:30
Alignment explanation
Indices: 2311445--2311503 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
2311435 AATTAAAAAA
* *
2311445 AATTAAAAAATTATTTATATATTAATATTT
1 AATTAAAAAAGTATTAATATATTAATATTT
* *
2311475 AATT-AAAAAGTATTAATTTATTTATATTT
1 AATTAAAAAAGTATTAATATATTAATATTT
2311504 TTATTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
AATTAAAAAAGTATTAATATATTAATATTT
Found at i:2324621 original size:6 final size:6
Alignment explanation
Indices: 2324610--2324634 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2324600 AAATTTTTTT
2324610 AATTTA AATTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA A
2324635 GCAAAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:2324796 original size:12 final size:11
Alignment explanation
Indices: 2324772--2324810 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
2324762 AAAACTCAAA
*
2324772 TAAATTTACAT
1 TAAATTTAAAT
2324783 TAAATTTTAAAT
1 TAAA-TTTAAAT
2324795 TAAATTTAAACT
1 TAAATTTAAA-T
2324807 TAAA
1 TAAA
2324811 CTTACTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:2334292 original size:2 final size:2
Alignment explanation
Indices: 2334285--2334320 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2334275 AATTAGTAAA
*
2334285 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2334321 CAGCTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2334741 original size:20 final size:19
Alignment explanation
Indices: 2334702--2334745 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2334692 CATGTTCATC
* *
2334702 TCTTTTTTTCTTTTTCTTTT
1 TCTTTTTTTCTTATT-ATTT
*
2334722 TCTTTTTTTGTTATTATTT
1 TCTTTTTTTCTTATTATTT
2334741 TCTTT
1 TCTTT
2334746 CACCCTTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.05, C:0.11, G:0.02, T:0.82
Consensus pattern (19 bp):
TCTTTTTTTCTTATTATTT
Found at i:2336964 original size:19 final size:19
Alignment explanation
Indices: 2336940--2336978 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2336930 AAAGTTAAAA
2336940 GATGGAAATATATGTATAT
1 GATGGAAATATATGTATAT
*
2336959 GATGGAAATATGTGTATAT
1 GATGGAAATATATGTATAT
2336978 G
1 G
2336979 TGTGTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (19 bp):
GATGGAAATATATGTATAT
Found at i:2337983 original size:24 final size:24
Alignment explanation
Indices: 2337933--2337984 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2337923 ATAATAAAAA
*
2337933 TATAATATTAATATATAAATTTTT
1 TATAATATTAATATATAAATTTAT
2337957 TATAAT-TTATATATTATAAA-TTAT
1 TATAATATTA-ATA-TATAAATTTAT
2337981 TATA
1 TATA
2337985 TATCAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 3 0.12
24 16 0.64
25 6 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATAATATTAATATATAAATTTAT
Found at i:2337985 original size:17 final size:15
Alignment explanation
Indices: 2337956--2338008 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 15
2337946 TATAAATTTT
2337956 TTAT-AATTTATATA
1 TTATAAATTTATATA
2337970 TTATAAATTATTATATA
1 TTATAAA-T-TTATATA
*
2337987 TCA-AAATTTATATAA
1 TTATAAATTTATAT-A
2338002 TTATAAA
1 TTATAAA
2338009 AATAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 10 0.31
15 6 0.19
16 7 0.22
17 9 0.28
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATAAATTTATATA
Found at i:2338009 original size:17 final size:16
Alignment explanation
Indices: 2337960--2338009 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
2337950 AATTTTTTAT
2337960 AATTTATATATTAT-A
1 AATTTATATATTATAA
2337975 AA-TTAT-TATATATCAA
1 AATTTATATAT-TAT-AA
2337991 AATTTATATAATTATAA
1 AATTTATAT-ATTATAA
2338008 AA
1 AA
2338010 ATAAAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.10
14 7 0.24
15 2 0.07
16 3 0.10
17 8 0.28
18 4 0.14
19 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTTATATATTATAA
Found at i:2338017 original size:39 final size:39
Alignment explanation
Indices: 2337926--2338027 Score: 102
Period size: 40 Copynumber: 2.6 Consensus size: 39
2337916 TATAAAAATA
* * *
2337926 ATAAAAATATAA-TATTAATATATAAATTTTTTATAATT
1 ATAAAAATAAAATTATTAATATATAAAATTTATATAATT
* *
2337964 -TATATATTATAAATTATT-ATATATCAAAATTTATATAATT
1 ATA-AAAATA-AAATTATTAATATAT-AAAATTTATATAATT
*
2338004 ATAAAAATAAAATTATAAATATAT
1 ATAAAAATAAAATTATTAATATAT
2338028 TTACAATTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
37 2 0.04
38 4 0.08
39 15 0.30
40 27 0.54
41 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (39 bp):
ATAAAAATAAAATTATTAATATATAAAATTTATATAATT
Found at i:2347939 original size:18 final size:17
Alignment explanation
Indices: 2347916--2347957 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2347906 TTTATACGTA
2347916 AAATATAAAAT-TTTATAT
1 AAATATAAAATATTT-T-T
*
2347934 AAATATATAATATTTTT
1 AAATATAAAATATTTTT
2347951 AAATATA
1 AAATATA
2347958 TTATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 11 0.50
19 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATAAAATATTTTT
Found at i:2348618 original size:18 final size:17
Alignment explanation
Indices: 2348582--2348623 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2348572 TTTACCCTTT
*
2348582 TTTTTTTTTAATTATTA
1 TTTTTTTTAAATTATTA
2348599 TTATTTTTTAAAGTTA-TA
1 TT-TTTTTTAAA-TTATTA
2348617 TTTTTTT
1 TTTTTTT
2348624 CATTCTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 3 0.14
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTTTTTAAATTATTA
Found at i:2348725 original size:5 final size:5
Alignment explanation
Indices: 2348715--2348762 Score: 55
Period size: 5 Copynumber: 10.0 Consensus size: 5
2348705 AAAATGTTAT
* * *
2348715 TTTAA TTTAA TTTAA -TAAA ATTAA TTTAA ATTAA TTT-A TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
2348763 AATATTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
4 7 0.19
5 29 0.81
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTTAA
Found at i:2348757 original size:19 final size:19
Alignment explanation
Indices: 2348715--2348776 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
2348705 AAAATGTTAT
* **
2348715 TTTAATTTAATTTAATAAA
1 TTTAATTTAAATTAATTTA
*
2348734 ATTAATTTAAATTAATTTA
1 TTTAATTTAAATTAATTTA
*
2348753 TTTAATTTAAAAT-A-TTA
1 TTTAATTTAAATTAATTTA
2348770 TTTAATT
1 TTTAATT
2348777 AATAGAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
17 10 0.27
18 1 0.03
19 26 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAATTTAAATTAATTTA
Found at i:2349554 original size:8 final size:8
Alignment explanation
Indices: 2349531--2349564 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
2349521 TTTTAATTTA
2349531 ATTTATAAT
1 ATTTAT-AT
2349540 AATTTATAT
1 -ATTTATAT
2349549 ATTTATAT
1 ATTTATAT
2349557 ATTTATAT
1 ATTTATAT
2349565 TATATTCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 2 0.08
10 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTTATAT
Found at i:2349737 original size:268 final size:266
Alignment explanation
Indices: 2349260--2350078 Score: 1534
Period size: 268 Copynumber: 3.1 Consensus size: 266
2349250 ATAATTTATA
*
2349260 TTAATTTAAAATTAGATTTGATA-ATTTATATATTTATATTATATTCGTATATTATGTAGTATTA
1 TTAATTTATAA-TA-ATTT-ATATATTTATATATTTATATTATATTCGTATATTATGTAGTATTA
2349324 TAATTATGTTAAAAGTATTATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGA
63 TAATTATGTTAAAAGTATTATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGA
2349389 TTTTTAGATATGTGTTTGTGTCCCATTGTATTTTTATTGCTTTATACATATTAATTCGTATAATT
128 TTTTTAGATATGTGTTTGTGTCCCATTGTATTTTTATTGCTTTATACATATTAATTCGTATAATT
2349454 ATGTTTAAAATTACGAAATTTATTTAGAGCAACTTATATTATATATCTTTTTAATATTTTTCTAA
193 ATGTTTAAAATTACGAAATTTATTTAGAGCAACTTATATTATATATCTTTTTAATATTTTTCTAA
2349519 TTTTTTAAT
258 TTTTTTAAT
*
2349528 TTAATTTATAATAATTTATATATTTATATATTTATATTATATTCGTATATTATGTAATATTATAA
1 TTAATTTATAATAATTTATATATTTATATATTTATATTATATTCGTATATTATGTAGTATTATAA
2349593 TTATGTTAAAAGTATTATATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGAT
66 TTATGTTAAAAGTA-T-TATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGAT
2349658 TTTTAGATATGTGTTTGTGTCCCATTGTATTTTTATTGCTTTATACATATTAATTCGTATAATTA
129 TTTTAGATATGTGTTTGTGTCCCATTGTATTTTTATTGCTTTATACATATTAATTCGTATAATTA
2349723 TGTTTAAAATTACGAAATTTATTTAGAGCAACTTATATTATATATCTTTTTAATATTTTTCTAAT
194 TGTTTAAAATTACGAAATTTATTTAGAGCAACTTATATTATATATCTTTTTAATATTTTTCTAAT
2349788 TTTTTAAT
259 TTTTTAAT
2349796 TTAATTTATAATAATTTATATATTTATATATTTATATTATATTCGTATATTATGTAGTATTATAA
1 TTAATTTATAATAATTTATATATTTATATATTTATATTATATTCGTATATTATGTAGTATTATAA
2349861 TTATGTTAAAAGTATTATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGATTT
66 TTATGTTAAAAGTATTATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGATTT
*
2349926 TTAGATATGTGTTTGTGTCCCATTGTATTTTTATTACTTTATACATATTAATTCGTATAATTATG
131 TTAGATATGTGTTTGTGTCCCATTGTATTTTTATTGCTTTATACATATTAATTCGTATAATTATG
* *
2349991 TTTAAAATTATGAAATTTATTTAGAGCAACCTATATTATATATCTTTTTAATA-TTTTCTAATTT
196 TTTAAAATTACGAAATTTATTTAGAGCAACTTATATTATATATCTTTTTAATATTTTTCTAATTT
2350055 TTTAAT
261 TTTAAT
2350061 TTAATTTATAATAATTTA
1 TTAATTTATAATAATTTA
2350079 ATCATTTTTA
Statistics
Matches: 542, Mismatches: 6, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
265 38 0.07
266 226 0.42
267 4 0.01
268 274 0.51
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (266 bp):
TTAATTTATAATAATTTATATATTTATATATTTATATTATATTCGTATATTATGTAGTATTATAA
TTATGTTAAAAGTATTATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGATTT
TTAGATATGTGTTTGTGTCCCATTGTATTTTTATTGCTTTATACATATTAATTCGTATAATTATG
TTTAAAATTACGAAATTTATTTAGAGCAACTTATATTATATATCTTTTTAATATTTTTCTAATTT
TTTAAT
Found at i:2349822 original size:8 final size:8
Alignment explanation
Indices: 2349799--2349832 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
2349789 TTTTAATTTA
2349799 ATTTATAAT
1 ATTTAT-AT
2349808 AATTTATAT
1 -ATTTATAT
2349817 ATTTATAT
1 ATTTATAT
2349825 ATTTATAT
1 ATTTATAT
2349833 TATATTCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 2 0.08
10 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTTATAT
Found at i:2350187 original size:9 final size:9
Alignment explanation
Indices: 2350175--2350199 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2350165 TTATACAATA
2350175 TATATAAAT
1 TATATAAAT
2350184 TATATAAAT
1 TATATAAAT
2350193 TATATAA
1 TATATAA
2350200 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TATATAAAT
Found at i:2350309 original size:534 final size:533
Alignment explanation
Indices: 2349260--2350240 Score: 1298
Period size: 534 Copynumber: 1.8 Consensus size: 533
2349250 ATAATTTATA
2349260 TTAATTTAAAATTAGATTTGATAATTTATATATTTATATTATATTCGTATATTATGTAGTATTAT
1 TTAATTTAAAATTAGATTTGATAATTTATATATTTATATTATATTCGTATATTATGTAGTATTAT
2349325 AATTATGTTAAAAGTATTATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGAT
66 AATTATGTTAAAAGTATTATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGAT
*
2349390 TTTTAGATATGTGTTTGTGTCCCATTGTATTTTTATTGCTTTATACATATTAATTCGTATAATTA
131 TTTTAGATATGTGTTTGTGTCCCATTGTATTTTTATTACTTTATACATATTAATTCGTATAATTA
*
2349455 TGTTTAAAATTACGAAATTTATTTAGAGCAACTTATATTATATATCTTTTTAATATTTTTCTAAT
196 TGTTTAAAATTACGAAATTTATTTAGAGCAACCTATATTATATATCTTTTTAATATTTTTCTAAT
* * * **
2349520 TTTTTAATTTAATTTATAATAATTTATATATTTATATATTTATATTATATTCGTATATTATGTAA
261 TTTTTAATTTAATTTATAATAATTTATATATTTATAAATTTAAATTAGAAACGTATATTATGTAA
* * * * * * *
2349585 TATTATAATTATGTTAAAAGTATTATATATATATATATAAATTTTAATAATTTAATAACTCATAT
326 TATTATAATCATGATAAAAGTATTATATATATAGATATAAATTATAACAATATAATAAAT-ATAT
* **** *** ** * * * * *
2349650 TATAAGATTTTTAGATATGTGTTTGTGTCCCATTGTATTTTTATTGCTTTATACATATTAATTCG
390 TATAAGATTTATAGATAAAAATAAATGTCAAATTGAAATTTAAAT-CTTTATACATATTAATTAG
* *
2349715 TATAATTATGTTTAAAATTACGAAATTTATTTAGAGCAACTTATATTATATATCTTTTTAATATT
454 TATAATTATGTTTAAAA-TACGAAATTAATTTAGAGCAACTTATATTATAAATCTTTTTAATATT
2349780 TTTCTAATTTTTTAAT
518 TTTCTAATTTTTTAAT
*
2349796 TTAATTTATAA-TA-ATTT-ATATATTTATATATTTATATTATATTCGTATATTATGTAGTATTA
1 TTAATTTAAAATTAGATTTGATA-ATTTATATATTTATATTATATTCGTATATTATGTAGTATTA
2349858 TAATTATGTTAAAAGTATTATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGA
65 TAATTATGTTAAAAGTATTATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGA
2349923 TTTTTAGATATGTGTTTGTGTCCCATTGTATTTTTATTACTTTATACATATTAATTCGTATAATT
130 TTTTTAGATATGTGTTTGTGTCCCATTGTATTTTTATTACTTTATACATATTAATTCGTATAATT
*
2349988 ATGTTTAAAATTATGAAATTTATTTAGAGCAACCTATATTATATATCTTTTTAATA-TTTTCTAA
195 ATGTTTAAAATTACGAAATTTATTTAGAGCAACCTATATTATATATCTTTTTAATATTTTTCTAA
* *
2350052 TTTTTTAATTTAATTTATAATAATTTAATCATTTTTATTAAACTTTTAAATATAGACAACTTA-A
260 TTTTTTAATTTAATTTATAATAATTT-AT-ATATTTA-TAAA--TTTAAAT-TAGA-AACGTATA
* ** * * *
2350116 TTTATTTTAATATTTATAA-CATGATATTA-TATTTTTTATA-AGATATCAATTAT-ACAATATA
318 -TTA-TGTAATA-TTATAATCATGATAAAAGTATTATATATATAGATATAAATTATAACAATATA
2350177 TATAAAT-TA-TATAA-ATTATATA-ATTAAAAAATAAAT-T-AAATT-AAATTTAAAT-TTTA-
380 -ATAAATATATTATAAGATT-TATAGA-T-AAAAATAAATGTCAAATTGAAATTTAAATCTTTAT
2350233 A-ATATTAA
441 ACATATTAA
2350241 AATTAAGATA
Statistics
Matches: 392, Mismatches: 38, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
530 7 0.02
531 1 0.00
532 4 0.01
533 37 0.09
534 236 0.60
535 15 0.04
536 23 0.06
537 5 0.01
538 12 0.03
539 19 0.05
540 15 0.04
541 12 0.03
542 6 0.02
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (533 bp):
TTAATTTAAAATTAGATTTGATAATTTATATATTTATATTATATTCGTATATTATGTAGTATTAT
AATTATGTTAAAAGTATTATATATATATATAAATTTTAATAATTTAATAACTCATATTATAAGAT
TTTTAGATATGTGTTTGTGTCCCATTGTATTTTTATTACTTTATACATATTAATTCGTATAATTA
TGTTTAAAATTACGAAATTTATTTAGAGCAACCTATATTATATATCTTTTTAATATTTTTCTAAT
TTTTTAATTTAATTTATAATAATTTATATATTTATAAATTTAAATTAGAAACGTATATTATGTAA
TATTATAATCATGATAAAAGTATTATATATATAGATATAAATTATAACAATATAATAAATATATT
ATAAGATTTATAGATAAAAATAAATGTCAAATTGAAATTTAAATCTTTATACATATTAATTAGTA
TAATTATGTTTAAAATACGAAATTAATTTAGAGCAACTTATATTATAAATCTTTTTAATATTTTT
CTAATTTTTTAAT
Done.