Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold144
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: 3311329
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 3 of 21
Found at i:204440 original size:26 final size:26
Alignment explanation
Indices: 204383--204445 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
204373 TAAAAATAAT
204383 TTTATTTAATAAAATAATATAATTTAA
1 TTTA-TTAATAAAATAATATAATTTAA
*
204410 TTTATTAATAACAT-ATA-AATTTATA
1 TTTATTAATAAAATAATATAATTTA-A
204435 TATTATTAATA
1 T-TTATTAATA
204446 TATAATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 6 0.18
25 5 0.15
26 18 0.55
27 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTATTAATAAAATAATATAATTTAA
Found at i:204448 original size:23 final size:24
Alignment explanation
Indices: 204388--204450 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
204378 ATAATTTTAT
* *
204388 TTAATAAAATAATATAATTTAATTTA
1 TTAATAACAT-ATA-AATTTAATATA
204414 TTAATAACATATAAATTT-ATATA
1 TTAATAACATATAAATTTAATATA
* *
204437 TTATTAATATATAA
1 TTAATAACATATAA
204451 TTAAATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 16 0.48
24 5 0.15
25 3 0.09
26 9 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAATAACATATAAATTTAATATA
Found at i:205304 original size:15 final size:16
Alignment explanation
Indices: 205275--205315 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
205265 AAATTATTAT
205275 TATTATAA-AATTAAA
1 TATTATAATAATTAAA
205290 TATTATAATAA-TAAA
1 TATTATAATAATTAAA
*
205305 TTTTGATAATA
1 TATT-ATAATA
205316 TAATAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TATTATAATAATTAAA
Found at i:205506 original size:18 final size:17
Alignment explanation
Indices: 205470--205509 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
205460 TTTTGAAAAA
205470 AATAAAATAATAATGAT
1 AATAAAATAATAATGAT
* *
205487 AATAAAATTAATTATTAT
1 AATAAAA-TAATAATGAT
205505 AATAA
1 AATAA
205510 TTAAATTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AATAAAATAATAATGAT
Found at i:205523 original size:21 final size:21
Alignment explanation
Indices: 205485--205537 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
205475 AATAATAATG
205485 ATAATAAAATTAATTATTATA
1 ATAATAAAATTAATTATTATA
* *
205506 ATAATTAAATTAGA-TATTTTA
1 ATAATAAAATTA-ATTATTATA
*
205527 TTAATAAAATT
1 ATAATAAAATT
205538 GAAATTAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATAATAAAATTAATTATTATA
Found at i:206302 original size:23 final size:24
Alignment explanation
Indices: 206271--206324 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
206261 TATTTAATTC
* *
206271 GTTTATTTTTTATG-ATTTTATTAA
1 GTTTATTTTTGAAGAATTTT-TTAA
206295 GTTT-TTTTTGAAGAATTTTTTAA
1 GTTTATTTTTGAAGAATTTTTTAA
206318 GTTTATT
1 GTTTATT
206325 AATTTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (24 bp):
GTTTATTTTTGAAGAATTTTTTAA
Found at i:208280 original size:16 final size:16
Alignment explanation
Indices: 208244--208303 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 16
208234 CCCTTACTTT
208244 TTTTTAAAATTTT-TTA
1 TTTTT-AAATTTTATTA
*
208260 ATTTTAAATTTTATT-
1 TTTTTAAATTTTATTA
* * *
208275 TTTTTTATTTTTAATA
1 TTTTTAAATTTTATTA
208291 TTTTTAATATTTT
1 TTTTTAA-ATTTT
208304 TTAATATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 18 0.53
16 12 0.35
17 4 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTAAATTTTATTA
Found at i:208282 original size:9 final size:9
Alignment explanation
Indices: 208268--208315 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
208258 TAATTTTAAA
208268 TTTTAT-TT
1 TTTTATATT
208276 TTTT-TATT
1 TTTTATATT
*
208284 TTTAATATT
1 TTTTATATT
*
208293 TTTAATATT
1 TTTTATATT
208302 TTTTAATATT
1 TTTT-ATATT
208312 TTTT
1 TTTT
208316 TAAATATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 1 0.03
8 9 0.26
9 16 0.46
10 9 0.26
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTATATT
Found at i:208295 original size:10 final size:10
Alignment explanation
Indices: 208282--208329 Score: 62
Period size: 9 Copynumber: 4.6 Consensus size: 10
208272 ATTTTTTTTA
208282 TTTTTAATA-
1 TTTTTAATAT
208291 TTTTTAATAT
1 TTTTTAATAT
208301 TTTTTAATATT
1 TTTTTAATA-T
208312 TTTTTAAATAT
1 TTTTT-AATAT
208323 GTTTTTA
1 -TTTTTA
208330 TTTTTATCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.26
10 9 0.26
11 8 0.23
12 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:208295 original size:19 final size:19
Alignment explanation
Indices: 208271--208315 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
208261 TTTTAAATTT
*
208271 TATTTTTTTTA-TTTTTAA
1 TATTTTTTATATTTTTTAA
*
208289 TATTTTTAATATTTTTTAA
1 TATTTTTTATATTTTTTAA
208308 TATTTTTT
1 TATTTTTT
208316 TAAATATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTTTATATTTTTTAA
Found at i:208321 original size:12 final size:11
Alignment explanation
Indices: 208282--208329 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 11
208272 ATTTTTTTTA
208282 TTTTTAATA--
1 TTTTTAATATT
208291 TTTTTAATA-T
1 TTTTTAATATT
208301 TTTTTAATATT
1 TTTTTAATATT
*
208312 TTTTTAAATATG
1 TTTTT-AATATT
208324 TTTTTA
1 TTTTTA
208330 TTTTTATCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
9 9 0.26
10 9 0.26
11 7 0.20
12 10 0.29
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTTTAATATT
Found at i:209003 original size:17 final size:17
Alignment explanation
Indices: 208942--209007 Score: 53
Period size: 17 Copynumber: 3.7 Consensus size: 17
208932 ATATAAAATT
*
208942 ATTATAGATTAAATAAAA
1 ATTATAAATTAAAT-AAA
* * *
208960 ATGAATGAATTTACATAAA
1 AT-TAT-AAATTAAATAAA
208979 ATTATAAATTAAATAAGA
1 ATTATAAATTAAATAA-A
208997 ATT-TAAATTAA
1 ATTATAAATTAA
209008 TTTTTATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
17 17 0.45
18 8 0.21
19 7 0.18
20 6 0.16
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (17 bp):
ATTATAAATTAAATAAA
Found at i:209137 original size:74 final size:71
Alignment explanation
Indices: 208999--209140 Score: 203
Period size: 74 Copynumber: 2.0 Consensus size: 71
208989 AAATAAGAAT
* * * *
208999 TTAAATTAATTTTTATAAATATGAATGAATTTACGTAAAATTTAAAAATTATAATTGAATTTAAA
1 TTAAATTAATTTTTATAAATATGAATAAATTTACCTAAAATTTAAAAATTATAATAGAACTTAAA
209064 GTGAAC
66 GTGAAC
* *
209070 TTAAATTATTTTTTTATAAATATGAATAAAAATTTACCTAAAATTTAAAAATTATAATAGGACTT
1 TTAAATTA-ATTTTTATAAATATGAAT--AAATTTACCTAAAATTTAAAAATTATAATAGAACTT
209135 AAAGTG
63 AAAGTG
209141 TATATATATA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
71 8 0.13
72 17 0.27
74 37 0.60
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.41
Consensus pattern (71 bp):
TTAAATTAATTTTTATAAATATGAATAAATTTACCTAAAATTTAAAAATTATAATAGAACTTAAA
GTGAAC
Found at i:209835 original size:2 final size:2
Alignment explanation
Indices: 209828--209855 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
209818 GAAAAATCTT
209828 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
209856 CATAAAAACA
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:210081 original size:26 final size:26
Alignment explanation
Indices: 210050--210118 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
210040 TTAATATAAA
* *
210050 TTAATTTATTTTGAGT-TTAAAATTT
1 TTAAATTATTTTGAGTATTAAAAATT
*
210075 TTAAATTATTTTTAGTATTAAAAATT
1 TTAAATTATTTTGAGTATTAAAAATT
* *
210101 TTAAGTTATTAT-AGTATT
1 TTAAATTATTTTGAGTATT
210119 TTGATTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 20 0.53
26 18 0.47
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (26 bp):
TTAAATTATTTTGAGTATTAAAAATT
Found at i:210145 original size:15 final size:16
Alignment explanation
Indices: 210122--210185 Score: 73
Period size: 15 Copynumber: 4.1 Consensus size: 16
210112 TAGTATTTTG
210122 ATTATTTTAATTTTAA
1 ATTATTTTAATTTTAA
*
210138 ATTA-TTTAA-TTAAA
1 ATTATTTTAATTTTAA
210152 ATTATTTTAATTTT-A
1 ATTATTTTAATTTTAA
210167 ATCTATTTTTAA-TTTAA
1 AT-TA-TTTTAATTTTAA
210184 AT
1 AT
210186 CAGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
14 8 0.20
15 13 0.32
16 11 0.27
17 9 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTTTAATTTTAA
Found at i:210261 original size:15 final size:16
Alignment explanation
Indices: 210225--210265 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
210215 TCAGATCTCT
**
210225 TTAAATTTAAATTATT
1 TTAAATTTAAATTAAA
210241 TTAAATTTAAA-TAAA
1 TTAAATTTAAATTAAA
210256 TTAAATTTAA
1 TTAAATTTAA
210266 CACTTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:211397 original size:24 final size:25
Alignment explanation
Indices: 211369--211423 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
211359 CGATTCAAAA
211369 AAATTAAAATTTAAGTTAA-AATTT
1 AAATTAAAATTTAAGTTAATAATTT
** * *
211393 AAATT-TTATTTTATTTAATAATTT
1 AAATTAAAATTTAAGTTAATAATTT
211417 AAATTAA
1 AAATTAA
211424 TTATTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
AAATTAAAATTTAAGTTAATAATTT
Found at i:212175 original size:17 final size:16
Alignment explanation
Indices: 212155--212210 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
212145 GATTTTTTAT
212155 AATTTTATATTTATATA
1 AATTTTATA-TTATATA
212172 AATTTTA-A-TATA-A
1 AATTTTATATTATATA
212185 AATAATTTATATTATATAA
1 AAT--TTTATATTATAT-A
212204 AATTTTA
1 AATTTTA
212211 AAATATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 4 0.12
14 4 0.12
15 4 0.12
16 2 0.06
17 15 0.45
19 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTTATATTATATA
Found at i:212177 original size:26 final size:27
Alignment explanation
Indices: 212148--212223 Score: 75
Period size: 31 Copynumber: 2.7 Consensus size: 27
212138 ATTGCTAGAT
212148 TTTTTATAAT-TTTATATTTATATAAA
1 TTTTTATAATATTTATATTTATATAAA
212174 TTTTAATATAAAATAATTTATA-TTATATAAA
1 TTTT--TAT--AAT-ATTTATATTTATATAAA
* *
212205 ATTTTAAAATATTTATATT
1 TTTTTATAATATTTATATT
212224 ATTTTATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
26 11 0.27
27 4 0.10
28 3 0.07
29 2 0.05
30 3 0.07
31 12 0.29
32 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTTTATAATATTTATATTTATATAAA
Found at i:218131 original size:32 final size:33
Alignment explanation
Indices: 218080--218142 Score: 110
Period size: 32 Copynumber: 1.9 Consensus size: 33
218070 CAAATTGATT
218080 TGAATAAATAAATATATCAAAATTTATATAATG
1 TGAATAAATAAATATATCAAAATTTATATAATG
*
218113 TGAAT-AATTAATATATCAAAATTTATATAA
1 TGAATAAATAAATATATCAAAATTTATATAA
218143 ATATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (33 bp):
TGAATAAATAAATATATCAAAATTTATATAATG
Found at i:218146 original size:18 final size:17
Alignment explanation
Indices: 218093--218151 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
218083 ATAAATAAAT
218093 ATATCAAAATTTATATA
1 ATATCAAAATTTATATA
* *
218110 ATGTGAATAA-TTA-AT-
1 ATATCAA-AATTTATATA
218125 ATATCAAAATTTATATAA
1 ATATCAAAATTTATAT-A
218143 ATAT-AAAAT
1 ATATCAAAAT
218152 ATTTTAGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 2 0.06
15 8 0.24
16 4 0.12
17 13 0.39
18 6 0.18
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
ATATCAAAATTTATATA
Found at i:218193 original size:11 final size:11
Alignment explanation
Indices: 218174--218203 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
218164 ATTATAATCT
*
218174 TAAAAATAATA
1 TAAATATAATA
218185 TAAATATAATA
1 TAAATATAATA
218196 TAAATATA
1 TAAATATA
218204 TAAATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAATA
Found at i:221635 original size:23 final size:22
Alignment explanation
Indices: 221607--221681 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
221597 AATAAAATTA
221607 ATTTAATTATATAATTTATATTT
1 ATTTAATTATATAA-TTATATTT
*
221630 ATTTAATTTTATAATTATATTTT
1 ATTTAATTATATAATTATA-TTT
* *
221653 ATTT-ATTACATAAATCATATTT
1 ATTTAATTATAT-AATTATATTT
221675 A-TTAATT
1 ATTTAATT
221682 TTAAATAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
21 2 0.04
22 17 0.38
23 26 0.58
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTAATTATATAATTATATTT
Found at i:221855 original size:16 final size:16
Alignment explanation
Indices: 221822--221871 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
221812 CATAATTATA
*
221822 TAATTAAATTTAAAAT
1 TAATTATATTTAAAAT
221838 TAATT-TATTTAAATAT
1 TAATTATATTTAAA-AT
*
221854 TAATTATATATAAAAT
1 TAATTATATTTAAAAT
221870 TA
1 TA
221872 TAAAAACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 7 0.23
16 16 0.53
17 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTATATTTAAAAT
Found at i:226803 original size:48 final size:48
Alignment explanation
Indices: 226702--226842 Score: 124
Period size: 48 Copynumber: 2.9 Consensus size: 48
226692 CTCGCAAATG
* * * * * * *
226702 GGGTTCAAGGCTAGGATCTGGATCATTGACGCCAGATGGACTGGGGC-A
1 GGGTTCAAGACTAGGTTCGGGATCATTGACACCAGATGG-TTTGGGCTT
* * * * *
226750 AGGTTCACGACTAGGTTCTGGAT-GTGTGACTCCAGATGGTTTGGGCTT
1 GGGTTCAAGACTAGGTTCGGGATCAT-TGACACCAGATGGTTTGGGCTT
* *
226798 GGGTTCAAGATTGGGTTCGGGATCATTGACACCAGATGGTTTGGG
1 GGGTTCAAGACTAGGTTCGGGATCATTGACACCAGATGGTTTGGG
226843 TCCTGCCTCA
Statistics
Matches: 74, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
47 6 0.08
48 67 0.91
49 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.36, T:0.28
Consensus pattern (48 bp):
GGGTTCAAGACTAGGTTCGGGATCATTGACACCAGATGGTTTGGGCTT
Found at i:228724 original size:16 final size:16
Alignment explanation
Indices: 228700--228737 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
228690 ATATAAAATA
228700 TAAAAATATAACTTTT
1 TAAAAATATAACTTTT
* *
228716 TAAATATATAATTTTT
1 TAAAAATATAACTTTT
228732 TAAAAA
1 TAAAAA
228738 AATTAAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAAATATAACTTTT
Found at i:228901 original size:22 final size:22
Alignment explanation
Indices: 228873--228915 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
228863 GATAAGTTGA
228873 TATTATTTTTAATAGACAAATC
1 TATTATTTTTAATAGACAAATC
228895 TATTATTTTTAATAGACAAAT
1 TATTATTTTTAATAGACAAAT
228916 TTTTAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (22 bp):
TATTATTTTTAATAGACAAATC
Found at i:228930 original size:14 final size:15
Alignment explanation
Indices: 228899--228928 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
228889 CAAATCTATT
228899 ATTTTTAATAGACAA
1 ATTTTTAATAGACAA
228914 ATTTTTAATAGACAA
1 ATTTTTAATAGACAA
228929 TTCATTAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTTTTAATAGACAA
Found at i:230302 original size:53 final size:53
Alignment explanation
Indices: 230241--230341 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
230231 AAGATTAGGG
* * **
230241 TATTTAAATTTATTATCTGC-ATATATAATATTGATTTGAATAATAAATTTAAA
1 TATTTAAATTTATTATCT-CTATAAATAACATAAATTTGAATAATAAATTTAAA
230294 TATTTAAATTTATTATCTCTATAAATAACATAAATTTGAATAATAAAT
1 TATTTAAATTTATTATCTCTATAAATAACATAAATTTGAATAATAAAT
230342 ATTTAAAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.02
53 42 0.98
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (53 bp):
TATTTAAATTTATTATCTCTATAAATAACATAAATTTGAATAATAAATTTAAA
Found at i:230775 original size:14 final size:16
Alignment explanation
Indices: 230741--230781 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
230731 ACATAAATAT
230741 TATATATTTATATCAA
1 TATATATTTATATCAA
* *
230757 TATATTTTTATATAAA
1 TATATATTTATATCAA
*
230773 TATAAATTT
1 TATATATTT
230782 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATATTTATATCAA
Found at i:231034 original size:10 final size:10
Alignment explanation
Indices: 231019--231090 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
231009 TATTGATGTG
231019 TATAAATTAA
1 TATAAATTAA
*
231029 TATAAATTGA
1 TATAAATTAA
*
231039 TATAATTTATA
1 TATAAATTA-A
* *
231050 TAAAAATTGA
1 TATAAATTAA
*
231060 TA-AAA-AAA
1 TATAAATTAA
*
231068 T-TAAAATAA
1 TATAAATTAA
231077 TATAATATTAA
1 TATAA-ATTAA
231088 TAT
1 TAT
231091 TATTTTTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
8 5 0.11
9 6 0.13
10 22 0.47
11 14 0.30
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
TATAAATTAA
Found at i:231058 original size:21 final size:20
Alignment explanation
Indices: 231019--231061 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
231009 TATTGATGTG
*
231019 TATAAATTAATATAAATTGA
1 TATAAATTAATAAAAATTGA
*
231039 TATAATTTATATAAAAATTGA
1 TATAAATTA-ATAAAAATTGA
231060 TA
1 TA
231062 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
TATAAATTAATAAAAATTGA
Found at i:247394 original size:58 final size:58
Alignment explanation
Indices: 247300--247410 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 58
247290 TAAAGCTTCA
** * *
247300 AGCCCAATTCGTATGTCCAAGAAGAGTGAAGCCCAATTTGCATGTATTCATGGCTTGG
1 AGCCCAATTCACACGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATGGCTTGG
* * *
247358 AGCCCAATTCACACGTCCAAGAAGAGTGGAGTCCAATTTGCATATATTTATGG
1 AGCCCAATTCACACGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATGG
247411 GCCTATTGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (58 bp):
AGCCCAATTCACACGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATGGCTTGG
Found at i:260863 original size:20 final size:20
Alignment explanation
Indices: 260838--260880 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
260828 GATCTAAAAT
*
260838 GAGATCATAATTTGGAGCAG
1 GAGATCATAATCTGGAGCAG
260858 GAGATCATAATCTGGAGCAG
1 GAGATCATAATCTGGAGCAG
260878 GAG
1 GAG
260881 CTTACCTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.21
Consensus pattern (20 bp):
GAGATCATAATCTGGAGCAG
Found at i:263618 original size:4 final size:4
Alignment explanation
Indices: 263609--263639 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
263599 AACGCGAAGC
263609 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
263640 CAAAAAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:264151 original size:35 final size:35
Alignment explanation
Indices: 264084--264181 Score: 85
Period size: 39 Copynumber: 2.7 Consensus size: 35
264074 ATATTATTTT
**
264084 TAATTAAATTTGATATATAAAATTAAATATAATCA
1 TAATTAAATTAAATATATAAAATTAAATATAATCA
* *
264119 TAATTAAATTAAATAT-TAAATTTATATAATAATTTATCA
1 TAATTAAATTAAATATATAAA-AT-TA-AAT-A-TAATCA
*
264158 AAATTAAATTAAATA-A-AAAATTAA
1 TAATTAAATTAAATATATAAAATTAA
264182 TAACAAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
34 4 0.08
35 16 0.31
36 4 0.08
37 4 0.08
38 4 0.08
39 19 0.37
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (35 bp):
TAATTAAATTAAATATATAAAATTAAATATAATCA
Found at i:264192 original size:39 final size:39
Alignment explanation
Indices: 264115--264194 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
264105 ATTAAATATA
* ** * *
264115 ATCATAATTAAATTAAATATTAAATTTATATAATAATTT
1 ATCAAAATTAAATTAAATAAAAAATTAATATAAAAATTT
264154 ATCAAAATTAAATTAAATAAAAAATTAATA-ACAAAATTT
1 ATCAAAATTAAATTAAATAAAAAATTAATATA-AAAATTT
264193 AT
1 AT
264195 AATTTAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (39 bp):
ATCAAAATTAAATTAAATAAAAAATTAATATAAAAATTT
Found at i:264227 original size:29 final size:28
Alignment explanation
Indices: 264119--264229 Score: 77
Period size: 29 Copynumber: 3.8 Consensus size: 28
264109 AATATAATCA
*
264119 TAATTAAATTAAATATTAAATTTATATAATAAT
1 TAATAAAATT-AA-ATTAAATTTA-A-AA-AAT
*
264152 TTATCAAAATTAAATTAAA--TAAAAAAT
1 TAAT-AAAATTAAATTAAATTTAAAAAAT
* *
264179 TAATAACAA--AATTTATAATTTAAAAATTT
1 TAATAA-AATTAAATTA-AATTTAAAAA-AT
264208 TAATAAAATTAAATTAAATTTA
1 TAATAAAATTAAATTAAATTTA
264230 TATCAATTAG
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
25 5 0.08
26 4 0.06
27 8 0.12
28 10 0.16
29 14 0.22
30 7 0.11
32 6 0.09
33 5 0.08
34 5 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TAATAAAATTAAATTAAATTTAAAAAAT
Found at i:265212 original size:2 final size:2
Alignment explanation
Indices: 265205--265235 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
265195 TCAATGACTT
265205 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
265236 TATGTTTTCA
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:272674 original size:20 final size:19
Alignment explanation
Indices: 272624--272701 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
272614 GGTAAAAAGA
272624 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* *
272643 GCAGAATATATCGATACATT
1 -CATAATGTATCGATACATT
*
272663 CATACATGTATCGATATATT
1 CATA-ATGTATCGATACATT
* *
272683 AAAAATTGTATCGATACAT
1 CATAA-TGTATCGATACAT
272702 CAGGATAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.08
20 44 0.92
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:277697 original size:16 final size:16
Alignment explanation
Indices: 277656--277712 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
277646 ATATTAAAAA
* *
277656 AAATA-TTATTTAACT
1 AAATATTTATTTTATT
*
277671 AAATATATATTTTATT
1 AAATATTTATTTTATT
*
277687 AAATATTTATTATATT
1 AAATATTTATTTTATT
*
277703 TAATATTTAT
1 AAATATTTAT
277713 ATTTTTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
15 5 0.14
16 30 0.86
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATTTATTTTATT
Found at i:277785 original size:13 final size:13
Alignment explanation
Indices: 277767--277800 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
277757 CTCAAAGCTC
*
277767 TCAATTTACGCTA
1 TCAATTGACGCTA
*
277780 TCAATTGACGTTA
1 TCAATTGACGCTA
277793 TCAATTGA
1 TCAATTGA
277801 TAAGATTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (13 bp):
TCAATTGACGCTA
Found at i:293308 original size:17 final size:16
Alignment explanation
Indices: 293286--293340 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
293276 TATAATAAAC
293286 TAAATATATATTTTTAT
1 TAAATAT-TATTTTTAT
* *
293303 TAAATATTAATTATAT
1 TAAATATTATTTTTAT
*
293319 TTAATATTTATTTTATAT
1 TAAATA-TTATTTT-TAT
293337 TAAA
1 TAAA
293341 CCTAATGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 12 0.40
17 12 0.40
18 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATATTATTTTTAT
Found at i:295069 original size:15 final size:15
Alignment explanation
Indices: 295046--295114 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 15
295036 CATACATATT
*
295046 TATATTTTAATAATA
1 TATAATTTAATAATA
*
295061 TATAATTTAATATTA
1 TATAATTTAATAATA
*
295076 T-TTATTTAATAATA
1 TATAATTTAATAATA
* *
295090 -ATTAATATAATATTAA
1 TA-TAATTTAATAAT-A
295106 TATAATTTA
1 TATAATTTA
295115 TTATTTTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
14 11 0.26
15 23 0.55
16 7 0.17
17 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATAATTTAATAATA
Found at i:295511 original size:18 final size:18
Alignment explanation
Indices: 295467--295513 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
295457 TATATTAATG
295467 TAAATAATATTTTAAAAA
1 TAAATAATATTTTAAAAA
*
295485 TAACGATAATATTTTAAATA
1 TAA--ATAATATTTTAAAAA
*
295505 TTAATAATA
1 TAAATAATA
295514 AATAGGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAATAATATTTTAAAAA
Found at i:295741 original size:12 final size:13
Alignment explanation
Indices: 295718--295746 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
295708 AATTTGTTAT
295718 TTTTAGTTTGAGG
1 TTTTAGTTTGAGG
295731 TTTTA-TTTGAGG
1 TTTTAGTTTGAGG
295743 TTTT
1 TTTT
295747 TTTATTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.24, T:0.62
Consensus pattern (13 bp):
TTTTAGTTTGAGG
Found at i:296201 original size:21 final size:22
Alignment explanation
Indices: 296168--296208 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
296158 TAAAGAAAAT
* *
296168 CAAAATAATAAAATTTAAAAGG
1 CAAAATAAAAAAATGTAAAAGG
296190 CAAAA-AAAAAAATGTAAAA
1 CAAAATAAAAAAATGTAAAA
296209 CATGAGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.71, C:0.05, G:0.07, T:0.17
Consensus pattern (22 bp):
CAAAATAAAAAAATGTAAAAGG
Found at i:296386 original size:16 final size:16
Alignment explanation
Indices: 296362--296403 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
296352 AAATAAATCA
**
296362 AAATC-AAAATAATTT
1 AAATCTAAAATAACCT
296377 AAATCTAAAATAACCT
1 AAATCTAAAATAACCT
*
296393 GAATCTAAAAT
1 AAATCTAAAAT
296404 TTATTTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (16 bp):
AAATCTAAAATAACCT
Found at i:302821 original size:16 final size:16
Alignment explanation
Indices: 302800--302841 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
302790 ACTTTATTTT
*
302800 TTTTTCCAGCCTAAGC
1 TTTTTCCAACCTAAGC
*
302816 TTTTTCTAACCTAAGC
1 TTTTTCCAACCTAAGC
302832 TTTTTTCCAA
1 -TTTTTCCAA
302842 TAGTAATGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.21, C:0.26, G:0.07, T:0.45
Consensus pattern (16 bp):
TTTTTCCAACCTAAGC
Found at i:303715 original size:17 final size:18
Alignment explanation
Indices: 303674--303729 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
303664 AAAAAATTAT
**
303674 AAGAAATTATTTTTAATG
1 AAGAAATTATTTTTAAAA
*
303692 AATAAATT-TTTTTAAAA
1 AAGAAATTATTTTTAAAA
303709 AAGAAATTTATTTTTAAAA
1 AAGAAA-TTATTTTTAAAA
303728 AA
1 AA
303730 TATACTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 12 0.38
18 9 0.28
19 11 0.34
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (18 bp):
AAGAAATTATTTTTAAAA
Found at i:304071 original size:13 final size:13
Alignment explanation
Indices: 304053--304077 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
304043 CATAAAGTGT
304053 TGTATCGATACAA
1 TGTATCGATACAA
304066 TGTATCGATACA
1 TGTATCGATACA
304078 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:304088 original size:32 final size:33
Alignment explanation
Indices: 304033--304098 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
304023 TTCAACGATT
304033 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
304066 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
304098 T
1 T
304099 ATAAGCTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 20 0.61
33 13 0.39
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:304273 original size:52 final size:52
Alignment explanation
Indices: 304159--304275 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
304149 CACTGATCTT
* *
304159 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATATATGCAGGCAAATTTGCCCAGATGTATAGATACACTATAAAA
* *
304211 TGTATCGATATATGCAGGCAAATTTGTCCAGATGTATAGATATACTATAAAA
1 TGTATCGATATATGCAGGCAAATTTGCCCAGATGTATAGATACACTATAAAA
304263 TGTATCGATATAT
1 TGTATCGATATAT
304276 CGATATACTA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (52 bp):
TGTATCGATATATGCAGGCAAATTTGCCCAGATGTATAGATACACTATAAAA
Found at i:304326 original size:80 final size:80
Alignment explanation
Indices: 304193--304352 Score: 275
Period size: 80 Copynumber: 2.0 Consensus size: 80
304183 TGCCCAGATG
* * *
304193 TATCGATACACTATAAAATGTATCGATATATGCAGGCAAATTTGTCCAGATGTATAGATATACTA
1 TATCGATACACTATAAAATGTATCGATACATGCACGCAAATTTGTCCAGATGTATAGATACACTA
304258 TAAAATGTATCGATA
66 TAAAATGTATCGATA
* *
304273 TATCGATATACTATAAAATGTATCGATACATGCACGCAAATTTGTCCAGATGTATCGATACACTA
1 TATCGATACACTATAAAATGTATCGATACATGCACGCAAATTTGTCCAGATGTATAGATACACTA
304338 TAAAATGTATCGATA
66 TAAAATGTATCGATA
304353 CATGCACGCA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (80 bp):
TATCGATACACTATAAAATGTATCGATACATGCACGCAAATTTGTCCAGATGTATAGATACACTA
TAAAATGTATCGATA
Found at i:312481 original size:15 final size:15
Alignment explanation
Indices: 312463--312496 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
312453 AATAGAAATT
*
312463 ATTTGAATAATTTTG
1 ATTTGAATAAATTTG
*
312478 ATTTGCATAAATTTG
1 ATTTGAATAAATTTG
312493 ATTT
1 ATTT
312497 ATTCATTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTTGAATAAATTTG
Found at i:312793 original size:15 final size:15
Alignment explanation
Indices: 312768--312806 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
312758 AGTATTGGTA
*
312768 TAAATTTTTTTAATT
1 TAAATTATTTTAATT
* *
312783 TTAATTATTTTGATT
1 TAAATTATTTTAATT
312798 TAAATTATT
1 TAAATTATT
312807 ATTCAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TAAATTATTTTAATT
Found at i:317137 original size:25 final size:26
Alignment explanation
Indices: 317089--317143 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
317079 ATTACTCTTT
*
317089 AAATTTAATAATAAAAAAATTATAAC
1 AAATTTAATAATAAAAAAATTATAAA
*
317115 AAATTTTA-AATAAATAAAA-TATAAA
1 AAATTTAATAATAAA-AAAATTATAAA
317140 AAAT
1 AAAT
317144 AAATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATTTAATAATAAAAAAATTATAAA
Found at i:318401 original size:30 final size:30
Alignment explanation
Indices: 318324--318407 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
318314 AGTTAATAAT
* * *
318324 TAATTAAAATTTATTAAATATATTTAAATA
1 TAATTAATATTTATTAATTATATTTAAAAA
* *
318354 TAAAATAATATAT-TTAATTATATTTAAAAA
1 T-AATTAATATTTATTAATTATATTTAAAAA
*
318384 TAATTAATATTTATTAATTTTATT
1 TAATTAATATTTATTAATTATATT
318408 ATTTTATAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 9 0.20
30 27 0.61
31 8 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TAATTAATATTTATTAATTATATTTAAAAA
Found at i:318403 original size:25 final size:25
Alignment explanation
Indices: 318355--318403 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
318345 ATTTAAATAT
318355 AAAATAATATATTTAATTATATTTA
1 AAAATAATATATTTAATTATATTTA
318380 AAAATAATTAATATTT-ATTA-ATTT
1 AAAATAA-T-ATATTTAATTATATTT
318404 TATTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 11 0.50
26 5 0.23
27 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATAATATATTTAATTATATTTA
Found at i:318924 original size:18 final size:18
Alignment explanation
Indices: 318897--318968 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
318887 TGAGTGAAAT
*
318897 TAAAAATAATGATAATAA
1 TAAAATTAATGATAATAA
* *
318915 TAAAATTAATTATTATAA
1 TAAAATTAATGATAATAA
318933 TAAAAAATTAATGAT-AT--
1 T--AAAATTAATGATAATAA
*
318950 TAAAATTAATAATAA-AA
1 TAAAATTAATGATAATAA
318967 TA
1 TA
318969 TGTATTAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
15 11 0.25
16 1 0.02
17 3 0.07
18 16 0.36
19 2 0.05
20 11 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TAAAATTAATGATAATAA
Found at i:320212 original size:16 final size:16
Alignment explanation
Indices: 320191--320221 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
320181 ATTTTTATAT
*
320191 AAATTTTAATATATTA
1 AAATTTTAAAATATTA
320207 AAATTTTAAAATATT
1 AAATTTTAAAATATT
320222 TATAAATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTTAAAATATTA
Found at i:323116 original size:21 final size:21
Alignment explanation
Indices: 323092--323133 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
323082 TGAAATGATG
*
323092 CATTGATTGGATGAAAGAATA
1 CATTGATTGGATGAAAAAATA
**
323113 CATTTTTTGGATGAAAAAATA
1 CATTGATTGGATGAAAAAATA
323134 TAACCTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (21 bp):
CATTGATTGGATGAAAAAATA
Found at i:328170 original size:21 final size:21
Alignment explanation
Indices: 328127--328170 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
328117 GATGCATTGG
* **
328127 TTGGATGAAATAATATATTTT
1 TTGGATGAAAAAATATAACTT
*
328148 TTGGATGAAAAAATGTAACTT
1 TTGGATGAAAAAATATAACTT
328169 TT
1 TT
328171 ATGACCAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (21 bp):
TTGGATGAAAAAATATAACTT
Found at i:329586 original size:28 final size:28
Alignment explanation
Indices: 329546--329603 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
329536 TGGACTTATG
329546 GTTATCTGCTTGTATATCTATGTCTATA
1 GTTATCTGCTTGTATATCTATGTCTATA
329574 GTTATCTGCTTGTATATCTATGTCTATA
1 GTTATCTGCTTGTATATCTATGTCTATA
329602 GT
1 GT
329604 GATTTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.50
Consensus pattern (28 bp):
GTTATCTGCTTGTATATCTATGTCTATA
Found at i:335392 original size:17 final size:17
Alignment explanation
Indices: 335372--335450 Score: 54
Period size: 17 Copynumber: 4.7 Consensus size: 17
335362 AATTTCATAA
*
335372 TTCATAATGCATAAATG
1 TTCATAATACATAAATG
* ** *
335389 TTCATAGTTTATAAATT
1 TTCATAATACATAAATG
*
335406 TTCATAATACATGAATG
1 TTCATAATACATAAATG
* * *
335423 -TC-TATATTCATGAATC
1 TTCATA-ATACATAAATG
335439 TTCATAATACAT
1 TTCATAATACAT
335451 GAGACTTACG
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
15 2 0.04
16 11 0.23
17 32 0.68
18 2 0.04
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (17 bp):
TTCATAATACATAAATG
Found at i:336998 original size:16 final size:16
Alignment explanation
Indices: 336977--337023 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
336967 TTTAGATATT
336977 TTCAAGTTTGAGTCAC
1 TTCAAGTTTGAGTCAC
*
336993 TTCAAGTTTG-GATCAT
1 TTCAAGTTTGAG-TCAC
*
337009 TTCAAGTTTAAGTCA
1 TTCAAGTTTGAGTCA
337024 TTTTGAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (16 bp):
TTCAAGTTTGAGTCAC
Found at i:337178 original size:21 final size:22
Alignment explanation
Indices: 337138--337178 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
337128 GTTAAATCAG
* *
337138 GTTTAAATCATTTTAAGTTTAA
1 GTTTAAATCATATCAAGTTTAA
337160 GTTTAAATCA-ATCAAGTTT
1 GTTTAAATCATATCAAGTTT
337179 GATAGTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (22 bp):
GTTTAAATCATATCAAGTTTAA
Found at i:340312 original size:2 final size:2
Alignment explanation
Indices: 340305--340337 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
340295 AAAAGTTTTC
340305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
340338 AGCTTTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:342676 original size:2 final size:2
Alignment explanation
Indices: 342669--342693 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
342659 AAAAGTTTTC
342669 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
342694 AGCTTTTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:343120 original size:5 final size:6
Alignment explanation
Indices: 343103--343130 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
343093 TGGATCAATG
343103 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
343131 TGATGGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:345057 original size:34 final size:34
Alignment explanation
Indices: 344993--345209 Score: 301
Period size: 34 Copynumber: 6.4 Consensus size: 34
344983 AAGCAGAAAA
*
344993 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
345026 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
*
345060 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
345094 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
345128 TGTTGACTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
345162 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
345196 TGTTGATTAAATGG
1 TGTTGATTAAATGG
345210 TGGTTTTTAC
Statistics
Matches: 166, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 11 0.07
34 155 0.93
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
Found at i:345181 original size:102 final size:102
Alignment explanation
Indices: 344995--345209 Score: 342
Period size: 102 Copynumber: 2.1 Consensus size: 102
344985 GCAGAAAATG
344995 TTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
*
345059 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTA
66 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTA
* ** * *
345096 TTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGTGATTTGGTGGTTTACCA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
* * *
345161 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCATTG
66 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTA
345198 TTGATTAAATGG
1 TTGATTAAATGG
345210 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 10 0.10
102 94 0.90
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (102 bp):
TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTA
Found at i:345567 original size:19 final size:19
Alignment explanation
Indices: 345514--345576 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
345504 TGGTTGTCGA
**
345514 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
345533 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
* *
345552 GGTACTATTTAAGTATACG
1 GGTACTATTCACGTATACG
*
345571 GTTACT
1 GGTACT
345577 GTACACGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:349701 original size:34 final size:34
Alignment explanation
Indices: 349635--349853 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
349625 AAGTGGGAGA
*
349635 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * * *
349668 ATTGTTGACTAAATGGGAAATTTGATAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
*
349702 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
349736 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
349770 ATTGTTGACTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
349804 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
349838 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
349854 TGGTTTTTAC
Statistics
Matches: 166, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.08
34 153 0.92
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
Found at i:349825 original size:102 final size:102
Alignment explanation
Indices: 349639--349853 Score: 333
Period size: 102 Copynumber: 2.1 Consensus size: 102
349629 GGGAGAATTG
349639 TTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGATAGCTTACCA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGATAGCTTACCA
*
349703 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTA
66 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTA
* ** * * *
349740 TTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGTGATTTGGTGGTTTACCA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGATAGCTTACCA
* * *
349805 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCATTG
66 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTA
349842 TTGATTAAATGG
1 TTGATTAAATGG
349854 TGGTTTTTAC
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 10 0.10
102 93 0.90
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (102 bp):
TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGATAGCTTACCA
TTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTA
Found at i:350472 original size:22 final size:22
Alignment explanation
Indices: 350446--350488 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
350436 TACATGAAAG
350446 CTAACATTATAATAAAAATTTA
1 CTAACATTATAATAAAAATTTA
350468 CTAACATTATAATAAAAATTT
1 CTAACATTATAATAAAAATTT
350489 GTCATTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
CTAACATTATAATAAAAATTTA
Found at i:350793 original size:15 final size:15
Alignment explanation
Indices: 350773--350802 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
350763 GTGTTTTTTA
*
350773 ATTTTTTTAAAAAAT
1 ATTTTTTAAAAAAAT
350788 ATTTTTTAAAAAAAT
1 ATTTTTTAAAAAAAT
350803 TTATAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTTAAAAAAAT
Found at i:350804 original size:13 final size:14
Alignment explanation
Indices: 350775--350804 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
350765 GTTTTTTAAT
350775 TTTTTTAAAAAATA
1 TTTTTTAAAAAATA
350789 TTTTTTAAAAAA-A
1 TTTTTTAAAAAATA
350802 TTT
1 TTT
350805 ATAATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTTTAAAAAATA
Found at i:352723 original size:19 final size:18
Alignment explanation
Indices: 352699--352734 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
352689 ACTATGCGAA
352699 TAAAAAATATATATATTTT
1 TAAAAAATAT-TATATTTT
*
352718 TAAAAATTATTATATTT
1 TAAAAAATATTATATTT
352735 AAAAATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAAAAATATTATATTTT
Found at i:352737 original size:16 final size:18
Alignment explanation
Indices: 352701--352740 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
352691 TATGCGAATA
*
352701 AAAAATATATATATTTTT
1 AAAAATATATATATATTT
352719 AAAAAT-TAT-TATATTT
1 AAAAATATATATATATTT
352735 AAAAAT
1 AAAAAT
352741 GTTAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
17 3 0.14
18 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAAATATATATATATTT
Found at i:354384 original size:21 final size:22
Alignment explanation
Indices: 354360--354400 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
354350 TAATTTATTT
354360 TATTATA-AT-TAATATTTAAAA
1 TATTATATATATAA-ATTTAAAA
354381 TATTATATATATAAATTTAA
1 TATTATATATATAAATTTAA
354401 TTTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 8 0.44
23 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTATATATATAAATTTAAAA
Found at i:354502 original size:15 final size:16
Alignment explanation
Indices: 354467--354502 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
354457 TATATTTTAA
354467 TTAAT-TTATACATAT
1 TTAATATTATACATAT
354482 TT-ATATTAT-CATAT
1 TTAATATTATACATAT
354496 TTAATAT
1 TTAATAT
354503 AATATATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATATTATACATAT
Found at i:360907 original size:8 final size:8
Alignment explanation
Indices: 360894--360919 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
360884 CAAACCACTA
360894 TGCTGATT
1 TGCTGATT
360902 TGCTGATT
1 TGCTGATT
360910 TGCTGATT
1 TGCTGATT
360918 TG
1 TG
360920 GAGTGGCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.27, T:0.50
Consensus pattern (8 bp):
TGCTGATT
Found at i:361610 original size:52 final size:52
Alignment explanation
Indices: 361525--361649 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
361515 ATATGAAAAG
* *
361525 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
361577 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
361629 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
361650 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:361662 original size:52 final size:51
Alignment explanation
Indices: 361525--361669 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
361515 ATATGAAAAG
*
361525 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
361577 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
361629 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
361670 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:361676 original size:13 final size:13
Alignment explanation
Indices: 361658--361682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
361648 CAAAGATCAG
361658 TGTATCGATACAA
1 TGTATCGATACAA
361671 TGTATCGATACA
1 TGTATCGATACA
361683 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:361764 original size:13 final size:13
Alignment explanation
Indices: 361746--361770 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
361736 CAAAAAAATA
361746 TGTATCGATACAT
1 TGTATCGATACAT
361759 TGTATCGATACA
1 TGTATCGATACA
361771 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:361766 original size:33 final size:33
Alignment explanation
Indices: 361724--361790 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
361714 AGTAGCTTAA
361724 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
361757 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
361790 A
1 A
361791 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:363372 original size:16 final size:17
Alignment explanation
Indices: 363351--363386 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
363341 AATTTTAAAT
*
363351 TTTTTATTTTGATTT-A
1 TTTTTAATTTGATTTGA
363367 TTTTTAATTTGATTTGA
1 TTTTTAATTTGATTTGA
363384 TTT
1 TTT
363387 ATTCATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.72
Consensus pattern (17 bp):
TTTTTAATTTGATTTGA
Found at i:364243 original size:18 final size:18
Alignment explanation
Indices: 364216--364250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
364206 TTAGCAGAAT
*
364216 GTTTTTGTTTATACTAAC
1 GTTTTGGTTTATACTAAC
*
364234 GTTTTGGTTTGTACTAA
1 GTTTTGGTTTATACTAA
364251 TTTATGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (18 bp):
GTTTTGGTTTATACTAAC
Found at i:365864 original size:16 final size:16
Alignment explanation
Indices: 365845--365877 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
365835 CACGAATACT
365845 ATATAA-ATAAAACATA
1 ATATAACATAAAA-ATA
365861 ATATAACATAAAAATA
1 ATATAACATAAAAATA
365877 A
1 A
365878 CAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (16 bp):
ATATAACATAAAAATA
Found at i:366731 original size:16 final size:16
Alignment explanation
Indices: 366676--366778 Score: 64
Period size: 16 Copynumber: 5.9 Consensus size: 16
366666 AATATTATAA
*
366676 TATTTTATTA-AATTA
1 TATTTTATTATAATTT
*
366691 AATTATTATTATAACTATT
1 TATT-TTATTATAA-T-TT
*
366710 CAATTTTATTATAATTT
1 -TATTTTATTATAATTT
*
366727 TATTTTATTTTTATAAAATAAT
1 TATTTTA---TTAT--AAT-TT
366749 TATTTTATTATAATTT
1 TATTTTATTATAATTT
*
366765 TATTTTATTTTAAT
1 TATTTTATTATAAT
366779 AAATTAAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 21
0.72 0.06 0.21
Matches are distributed among these distances:
15 3 0.04
16 26 0.37
17 7 0.10
18 2 0.03
19 18 0.25
20 4 0.06
21 3 0.04
22 8 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTATTATAATTT
Found at i:368060 original size:21 final size:20
Alignment explanation
Indices: 368031--368069 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
368021 TATTTTTATT
*
368031 TAATTTTAATTATAAAATATA
1 TAATATTAA-TATAAAATATA
368052 TAATATTAATATAAAATA
1 TAATATTAATATAAAATA
368070 ATTTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATTAATATAAAATATA
Found at i:368471 original size:14 final size:14
Alignment explanation
Indices: 368452--368484 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
368442 CTAAAAAATT
368452 ATATTATTTA-ATAA
1 ATATTATTTACAT-A
368466 ATATTATTTACATA
1 ATATTATTTACATA
368480 ATATT
1 ATATT
368485 TAAATCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTATTTACATA
Found at i:369125 original size:15 final size:15
Alignment explanation
Indices: 369092--369131 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
369082 TTATTATTAT
369092 TAATATTTA-T-AAA
1 TAATATTTATTAAAA
369105 TAATATTTATTAAAA
1 TAATATTTATTAAAA
*
369120 TTATATTTATTA
1 TAATATTTATTA
369132 TATTCATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 9 0.38
14 1 0.04
15 14 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATATTTATTAAAA
Found at i:369535 original size:19 final size:19
Alignment explanation
Indices: 369513--369551 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
369503 TATATATATT
369513 TAAATAT-ATAAATCCAATA
1 TAAATATCATAAAT-CAATA
*
369532 TAAATATCATATATCAATA
1 TAAATATCATAAATCAATA
369551 T
1 T
369552 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATCATAAATCAATA
Found at i:370539 original size:20 final size:20
Alignment explanation
Indices: 370514--370562 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
370504 TATATTTTTT
370514 ATAATTTAATTTATATAAA-A
1 ATAATTTAATTTAT-TAAATA
**
370534 ATAATTTTTTTTATTAAATA
1 ATAATTTAATTTATTAAATA
370554 ATAATTTAA
1 ATAATTTAA
370563 ATAAAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATTTAATTTATTAAATA
Found at i:371069 original size:14 final size:15
Alignment explanation
Indices: 371029--371070 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
371019 ATCATAAATT
*
371029 TAAATTTATATTTGA
1 TAAATTTATATATGA
371044 TAAA-TTATTATAT-A
1 TAAATTTA-TATATGA
371058 TAAATTTATATAT
1 TAAATTTATATAT
371071 TATTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
TAAATTTATATATGA
Found at i:376760 original size:2 final size:2
Alignment explanation
Indices: 376753--376792 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
376743 TACATTTTGA
376753 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
376793 TAAAATTTGC
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:377314 original size:13 final size:13
Alignment explanation
Indices: 377295--377327 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
377285 TGGGTCATGA
377295 AAATTTTAAAATT
1 AAATTTTAAAATT
*
377308 TAATTTTAAAATT
1 AAATTTTAAAATT
377321 AAATTTT
1 AAATTTT
377328 TTTGTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATTTTAAAATT
Found at i:379005 original size:5 final size:5
Alignment explanation
Indices: 378995--379028 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
378985 TAAAGCTTTA
378995 TGAAC TGAAC TGAAC TGAAC TGAAC TGAAC TGAA
1 TGAAC TGAAC TGAAC TGAAC TGAAC TGAAC TGAA
379029 TCAATGTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (5 bp):
TGAAC
Found at i:379433 original size:22 final size:23
Alignment explanation
Indices: 379397--379441 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
379387 AAATTATCAT
*
379397 TTTATTTTTTATTATTAA-TAAAA
1 TTTATTTTATATTA-TAAGTAAAA
379420 TTTATTTTAT-TTATAAGTAAAA
1 TTTATTTTATATTATAAGTAAAA
379442 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 8 0.40
23 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTATTTTATATTATAAGTAAAA
Found at i:380911 original size:16 final size:15
Alignment explanation
Indices: 380888--380917 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
380878 AAATAATTAA
380888 TGAAAAATTAAATTT
1 TGAAAAATTAAATTT
380903 TGAAGAAATTAAATT
1 TGAA-AAATTAAATT
380918 GTTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (15 bp):
TGAAAAATTAAATTT
Found at i:381832 original size:8 final size:8
Alignment explanation
Indices: 381819--381861 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
381809 TAATATATAT
381819 TAAAAGAA
1 TAAAAGAA
*
381827 TAAAAGAG
1 TAAAAGAA
381835 T-AAAGAA
1 TAAAAGAA
381842 T-AAAGAA
1 TAAAAGAA
*
381849 TAAAATAA
1 TAAAAGAA
381857 TAAAA
1 TAAAA
381862 ATATAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (8 bp):
TAAAAGAA
Found at i:381860 original size:22 final size:21
Alignment explanation
Indices: 381821--381864 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
381811 ATATATATTA
*
381821 AAAGAATAAAAGAGTAAAGAAT
1 AAAGAATAAAAGAATAAA-AAT
*
381843 AAAGAATAAAATAATAAAAAT
1 AAAGAATAAAAGAATAAAAAT
381864 A
1 A
381865 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (21 bp):
AAAGAATAAAAGAATAAAAAT
Found at i:383336 original size:18 final size:17
Alignment explanation
Indices: 383270--383337 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 17
383260 ACAACTTAAT
383270 ATATATTATATTTATTTA
1 ATATATTATATTTA-TTA
383288 AT-TAATTATATTTTAATATA
1 ATAT-ATTATA-TTT-AT-TA
* *
383308 TTATTTTATATTTATTA
1 ATATATTATATTTATTA
383325 CATATATTATATT
1 -ATATATTATATT
383338 AATATCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 3 0.08
18 20 0.50
19 7 0.17
20 9 0.22
21 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATATTATATTTATTA
Found at i:383399 original size:15 final size:15
Alignment explanation
Indices: 383369--383399 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
383359 ATTTAAAATT
*
383369 ATTTAAATATAAAAA
1 ATTTAAATAAAAAAA
383384 ATTTAAATAAAAAAA
1 ATTTAAATAAAAAAA
383399 A
1 A
383400 AGTCTTAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTTAAATAAAAAAA
Found at i:384789 original size:28 final size:29
Alignment explanation
Indices: 384730--384794 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
384720 TTTTTACATG
*
384730 TTAAAATAAAAATATTTTGATAATTTATT
1 TTAAAATAAAAATATTTTAATAATTTATT
* *
384759 TTAAATTAAAATTATTTTAATAATTTATT
1 TTAAAATAAAAATATTTTAATAATTTATT
*
384788 TAAAAAT
1 TTAAAAT
384795 TAAGTAAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TTAAAATAAAAATATTTTAATAATTTATT
Found at i:388044 original size:10 final size:10
Alignment explanation
Indices: 388029--388063 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
388019 TAGATTTTAA
388029 TATATTATTT
1 TATATTATTT
*
388039 TATATT-TAT
1 TATATTATTT
388048 TATATTATTT
1 TATATTATTT
388058 TATATT
1 TATATT
388064 TATTAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATATTATTT
Found at i:388066 original size:19 final size:19
Alignment explanation
Indices: 388000--388068 Score: 86
Period size: 19 Copynumber: 3.6 Consensus size: 19
387990 TTAATATATA
* *
388000 TTATATTTATCATATTA-A
1 TTATATTTATTATATTATT
* *
388018 TTAGATTTTAATATATTATT
1 TTATA-TTTATTATATTATT
388038 TTATATTTATTATATTATT
1 TTATATTTATTATATTATT
388057 TTATATTTATTA
1 TTATATTTATTA
388069 AATAGATTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 4 0.09
19 35 0.81
20 4 0.09
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (19 bp):
TTATATTTATTATATTATT
Found at i:388121 original size:35 final size:36
Alignment explanation
Indices: 388054--388129 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 36
388044 TTATTATATT
*
388054 ATTTTATATTTATTAAATAGATTATATTAATATCAAA
1 ATTTTATATATATTAAATAGATTATATTAATAT-AAA
*
388091 ATTTTATATATATTTAA-A-ATTAT-TTAAATATAAA
1 ATTTTATATATATTAAATAGATTATATT-AATATAAA
*
388125 TTTTT
1 ATTTT
388130 TAAAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 9 0.26
35 10 0.29
36 1 0.03
37 15 0.43
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (36 bp):
ATTTTATATATATTAAATAGATTATATTAATATAAA
Found at i:388771 original size:18 final size:18
Alignment explanation
Indices: 388728--388779 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
388718 ATTTTTTAAC
* *
388728 ATTAATAAAAATTATATT
1 ATTAATAAAAATAATATA
388746 ATTAATAAAAGATAATATA
1 ATTAATAAAA-ATAATATA
*
388765 ATT-ATAAATATAATA
1 ATTAATAAAAATAATA
388780 ACAATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 6 0.20
18 15 0.50
19 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
ATTAATAAAAATAATATA
Found at i:393244 original size:25 final size:26
Alignment explanation
Indices: 393205--393254 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
393195 ATTTTATTAT
393205 TTAAAATAATATTA-TAAAAATAAAA
1 TTAAAATAATATTATTAAAAATAAAA
* * *
393230 TTAAAATATTTTTATTAAATATAAA
1 TTAAAATAATATTATTAAAAATAAA
393255 TTTTGATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TTAAAATAATATTATTAAAAATAAAA
Found at i:396408 original size:18 final size:18
Alignment explanation
Indices: 396387--396431 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
396377 TAAACACGAG
*
396387 ATAAATATATTATAAAAA
1 ATAAATATAATATAAAAA
* *
396405 ATAATTAAAATATAAAAA
1 ATAAATATAATATAAAAA
396423 AT-AATATAA
1 ATAAATATAA
396432 AAATAATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAATATAATATAAAAA
Found at i:396413 original size:11 final size:10
Alignment explanation
Indices: 396398--396443 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
396388 TAAATATATT
396398 ATAAAAAATA
1 ATAAAAAATA
*
396408 AT-TAAAAT-
1 ATAAAAAATA
396416 ATAAAAAATA
1 ATAAAAAATA
396426 ATATAAAAATA
1 ATA-AAAAATA
396437 ATTAAAA
1 A-TAAAA
396444 TATTATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 2 0.07
9 10 0.33
10 5 0.17
11 11 0.37
12 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:396416 original size:9 final size:10
Alignment explanation
Indices: 396402--396450 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
396392 TATATTATAA
396402 AAAATAAT-T
1 AAAATAATAT
*
396411 AAAAT-ATAA
1 AAAATAATAT
396420 AAAATAATAT
1 AAAATAATAT
396430 AAAAATAAT-T
1 -AAAATAATAT
*
396440 AAAATATTAT
1 AAAATAATAT
396450 A
1 A
396451 TAATTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
8 2 0.06
9 17 0.52
10 6 0.18
11 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATAATAT
Found at i:396419 original size:29 final size:29
Alignment explanation
Indices: 396387--396478 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
396377 TAAACACGAG
396387 ATAAATATATTATAAAAAATAATTAAAAT
1 ATAAATATATTATAAAAAATAATTAAAAT
* *
396416 ATAAA-AAATAATATAAAAATAATTAAAAT
1 ATAAATATATTATA-AAAAATAATTAAAAT
*
396445 AT-TATATAATT-T-AAAAATAA--AAAGAT
1 ATAAATAT-ATTATAAAAAATAATTAAA-AT
396471 ATAAATAT
1 ATAAATAT
396479 TTTAAATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 12 0.23
28 7 0.13
29 24 0.46
30 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (29 bp):
ATAAATATATTATAAAAAATAATTAAAAT
Found at i:396430 original size:12 final size:12
Alignment explanation
Indices: 396413--396453 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
396403 AAATAATTAA
396413 AATATAAAAAAT
1 AATATAAAAAAT
396425 AATAT-AAAAAT
1 AATATAAAAAAT
*
396436 AAT-TAAAATAT
1 AATATAAAAAAT
*
396447 TATATAA
1 AATATAA
396454 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 1 0.04
11 16 0.64
12 8 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATAAAAAAT
Found at i:396443 original size:20 final size:19
Alignment explanation
Indices: 396397--396461 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 19
396387 ATAAATATAT
396397 TATAAAAAATAAT-TAAAA
1 TATAAAAAATAATATAAAA
396415 TATAAAAAATAATATAAAA
1 TATAAAAAATAATATAAAA
* *
396434 -ATAATTAAAATATTATATAA
1 TATAA--AAAATAATATAAAA
*
396454 TTTAAAAA
1 TATAAAAA
396462 TAAAAAGATA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 17 0.43
19 8 0.20
20 12 0.30
21 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TATAAAAAATAATATAAAA
Done.