Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 2 of 18
Found at i:183853 original size:17 final size:17
Alignment explanation
Indices: 183831--183869 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
183821 AATAATTGTA
183831 TTTATATTATATCATAT
1 TTTATATTATATCATAT
* *
183848 TTTATATTATTTTATAT
1 TTTATATTATATCATAT
183865 TTTAT
1 TTTAT
183870 TAATCACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTATATCATAT
Found at i:186065 original size:3 final size:3
Alignment explanation
Indices: 186057--186117 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
186047 CCGAAGAATT
*
186057 AGA AGA AGA AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
186105 AGA AGA GGA AGA A
1 AGA AGA AGA AGA A
186118 CATGACGACA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:187546 original size:19 final size:18
Alignment explanation
Indices: 187519--187567 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
187509 TAGATTTGAT
*
187519 TTATGTATTTATATTATGA
1 TTATATATTTATATTAT-A
187538 TTATATATTT-TATTATA
1 TTATATATTTATATTATA
187555 TTAATTATATTTA
1 TT-A-TATATTTA
187568 AAATATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.12
18 7 0.27
19 16 0.62
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (18 bp):
TTATATATTTATATTATA
Found at i:187617 original size:32 final size:31
Alignment explanation
Indices: 187569--187643 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 31
187559 TTATATTTAA
*
187569 AATATTTTATAATTATATAAATTTTAAAATATT
1 AATAATTTAT-ATTATATAAATTTTAAAATA-T
187602 AATAATTTATATTATATAAATTTTAAAATAT
1 AATAATTTATATTATATAAATTTTAAAATAT
187633 -AT-ATTTATATT
1 AATAATTTATATT
187644 TATCATGTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 9 0.22
30 2 0.05
31 1 0.02
32 20 0.49
33 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AATAATTTATATTATATAAATTTTAAAATAT
Found at i:187626 original size:16 final size:17
Alignment explanation
Indices: 187526--187626 Score: 65
Period size: 16 Copynumber: 6.2 Consensus size: 17
187516 GATTTATGTA
*
187526 TTTATATTATGATTATAT
1 TTTATATTAT-ATAATAT
187544 ATTT-TATTATAT--TA-
1 -TTTATATTATATAATAT
* *
187558 ATTATATT-TAAAATAT
1 TTTATATTATATAATAT
187574 TTTATAATTATATAA-AT
1 TTTAT-ATTATATAATAT
* * *
187591 TTTAAAATAT-TAATAA
1 TTTATATTATATAATAT
187607 TTTATATTATATAA-AT
1 TTTATATTATATAATAT
187623 TTTA
1 TTTA
187627 AAATATATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
13 4 0.06
14 4 0.06
15 7 0.11
16 22 0.34
17 14 0.22
18 10 0.16
19 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (17 bp):
TTTATATTATATAATAT
Found at i:187627 original size:24 final size:24
Alignment explanation
Indices: 187583--187642 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
187573 TTTTATAATT
*
187583 ATATAAATTT-TA-AAATATTAATA
1 ATATATATTTATATAAATATTAA-A
* *
187606 ATTTATA-TTATATAAATTTTAAA
1 ATATATATTTATATAAATATTAAA
187629 ATATATATTTATAT
1 ATATATATTTATAT
187643 TTATCATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 2 0.07
23 14 0.47
24 14 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATATATTTATATAAATATTAAA
Found at i:187633 original size:16 final size:16
Alignment explanation
Indices: 187572--187635 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
187562 TATTTAAAAT
*
187572 ATTTTATAATTATATAA
1 ATTTTA-AAATATATAA
187589 ATTTTAAAATAT-TAA
1 ATTTTAAAATATATAA
* * *
187604 TAATTTATATTATATAA
1 -ATTTTAAAATATATAA
187621 ATTTTAAAATATATA
1 ATTTTAAAATATATA
187636 TTTATATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 3 0.08
16 26 0.68
17 9 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAAATATATAA
Found at i:187885 original size:29 final size:29
Alignment explanation
Indices: 187815--187885 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
187805 TTTATATTTA
*
187815 ATATATATTTAA-ATATAAATATAAAAAT
1 ATATTTATTTAATATATAAATATAAAAAT
*
187843 ATAATTT-TTAAATATATAAA-A-AATTAAAT
1 AT-ATTTATTTAATATATAAATATAA--AAAT
187872 ATATTTATTTAATA
1 ATATTTATTTAATA
187886 CATACTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
27 2 0.06
28 11 0.31
29 22 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATATTTATTTAATATATAAATATAAAAAT
Found at i:189063 original size:21 final size:20
Alignment explanation
Indices: 189039--189080 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
189029 ATTTTTTATT
189039 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAA-ATA
189060 TAAAATTTAA-TATAAAAATA
1 T-AAATTTAATTATAAAAATA
189080 T
1 T
189081 TATTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 8 0.40
22 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATTTAATTATAAAAATA
Found at i:189067 original size:22 final size:20
Alignment explanation
Indices: 189040--189080 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
189030 TTTTTTATTT
189040 AAATTTAATTATAAAATATATA
1 AAATTTAA-TATAAAA-ATATA
189062 AAATTTAATATAAAAATAT
1 AAATTTAATATAAAAATAT
189081 TATTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATTTAATATAAAAATATA
Found at i:189325 original size:24 final size:24
Alignment explanation
Indices: 189282--189352 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 24
189272 TTTATTAATA
189282 AATAAAATTTAAATGA--TATATTTT
1 AATAAAA-TTAAAT-ATTTATATTTT
189306 AATAAAATTAAATATTTATAATTTT
1 AATAAAATTAAATATTTAT-ATTTT
*
189331 TATAAAAATT-AATATTTA-ATTT
1 AAT-AAAATTAAATATTTATATTT
189353 ATTGACTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
22 1 0.02
23 10 0.24
24 10 0.24
25 15 0.36
26 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (24 bp):
AATAAAATTAAATATTTATATTTT
Found at i:189335 original size:25 final size:25
Alignment explanation
Indices: 189301--189348 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
189291 TAAATGATAT
189301 ATTTTAAT-AAAATTAAATATTTATA
1 ATTTTAATAAAAATT-AATATTTATA
*
189326 ATTTTTATAAAAATTAATATTTA
1 ATTTTAATAAAAATTAATATTTA
189349 ATTTATTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTTAATAAAAATTAATATTTATA
Found at i:191602 original size:5 final size:5
Alignment explanation
Indices: 191592--191650 Score: 57
Period size: 5 Copynumber: 11.8 Consensus size: 5
191582 TAAATATTTT
** * *
191592 CTTTC CTTTC CTCAAC CT-TC CTTTC TTTTC CTTTC CTTTA CTTTC CTTTC
1 CTTTC CTTTC CT-TTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC
*
191642 TTTTC CTTT
1 CTTTC CTTT
191651 ATTATTGTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
4 3 0.07
5 37 0.86
6 3 0.07
ACGTcount: A:0.05, C:0.36, G:0.00, T:0.59
Consensus pattern (5 bp):
CTTTC
Found at i:191624 original size:25 final size:25
Alignment explanation
Indices: 191589--191650 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
191579 AGATAAATAT
191589 TTTC-TTTCCTTTCCTCAACCTTCC
1 TTTCTTTTCCTTTCCTCAACCTTCC
** *
191613 TTTCTTTTCCTTTCCTTTACTTTCC
1 TTTCTTTTCCTTTCCTCAACCTTCC
191638 TTTCTTTTCCTTT
1 TTTCTTTTCCTTT
191651 ATTATTGTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 4 0.12
25 30 0.88
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTCTTTTCCTTTCCTCAACCTTCC
Found at i:191920 original size:17 final size:17
Alignment explanation
Indices: 191895--191932 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
191885 GATTTGACCC
191895 TTGTCAGCTTT-GTTTG
1 TTGTCAGCTTTAGTTTG
*
191911 ATTGTGAGCTTTAGTTTG
1 -TTGTCAGCTTTAGTTTG
191929 TTGT
1 TTGT
191933 TTAAAAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.11, C:0.08, G:0.26, T:0.55
Consensus pattern (17 bp):
TTGTCAGCTTTAGTTTG
Found at i:197457 original size:18 final size:18
Alignment explanation
Indices: 197436--197470 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
197426 GAAAACTATG
197436 TAGGGTTAGATCGAATTC
1 TAGGGTTAGATCGAATTC
197454 TAGGGTTAGATCGAATT
1 TAGGGTTAGATCGAATT
197471 TGAGTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.34
Consensus pattern (18 bp):
TAGGGTTAGATCGAATTC
Found at i:201976 original size:15 final size:15
Alignment explanation
Indices: 201924--201979 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
201914 ATATTAATAC
*
201924 ATTTTTAAAATA-AA
1 ATTTTTAAAATATAT
*
201938 ATTTTTACAAAAATAT
1 ATTTTTA-AAATATAT
201954 -TTTCTTAAAATATAT
1 ATTT-TTAAAATATAT
201969 ATTTTTAAAAT
1 ATTTTTAAAAT
201980 TTAAGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
14 7 0.20
15 21 0.60
16 7 0.20
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTTTAAAATATAT
Found at i:203502 original size:16 final size:16
Alignment explanation
Indices: 203483--203535 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
203473 TTTAAAATAT
203483 TTTTATTTTATATAAA
1 TTTTATTTTATATAAA
* *
203499 TTTTAATATAT-TAATA
1 TTTTATTTTATATAA-A
* *
203515 ATTTATATTATATAAA
1 TTTTATTTTATATAAA
203531 TTTTA
1 TTTTA
203536 AAATATTTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
15 3 0.11
16 22 0.79
17 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTATTTTATATAAA
Found at i:203526 original size:32 final size:31
Alignment explanation
Indices: 203484--203581 Score: 105
Period size: 32 Copynumber: 3.2 Consensus size: 31
203474 TTAAAATATT
*
203484 TTTATTTTATATAAATTTTAATATATTAATAA
1 TTTATATTATATAAATTTTAATATATTAAT-A
* *
203516 TTTATATTATATAAATTTTAAAATATTTATA
1 TTTATATTATATAAATTTTAATATATTAATA
*
203547 TTTATATCT-TATTATATTTTAAT-TATT-AT-
1 TTTATAT-TATA-TAAATTTTAATATATTAATA
203576 TTTATA
1 TTTATA
203582 AATTAATTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.10
30 2 0.03
31 14 0.24
32 37 0.63
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTATATTATATAAATTTTAATATATTAATA
Found at i:205141 original size:18 final size:18
Alignment explanation
Indices: 205108--205142 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
205098 GTAATTGAAA
**
205108 ATTTAAATTTTCATTTTC
1 ATTTAAATTTAAATTTTC
205126 ATTTAAATTTAAATTTT
1 ATTTAAATTTAAATTTT
205143 AAAATTTTAG
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:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTAAATTTAAATTTTC
Found at i:208783 original size:2 final size:2
Alignment explanation
Indices: 208776--208810 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
208766 GTTGGCTTCA
208776 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 A
208811 AAGATTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:209454 original size:2 final size:2
Alignment explanation
Indices: 209447--209477 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
209437 AAAAACCAAC
209447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
209478 AAAGAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:211838 original size:15 final size:15
Alignment explanation
Indices: 211814--211845 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
211804 GGCCACCCTC
211814 AAAATCTGAGATTCA
1 AAAATCTGAGATTCA
*
211829 AAAATTTGAGATTCA
1 AAAATCTGAGATTCA
211844 AA
1 AA
211846 TCTCAATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (15 bp):
AAAATCTGAGATTCA
Found at i:214151 original size:2 final size:2
Alignment explanation
Indices: 214137--214170 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
214127 CACCCTTAGT
*
214137 TA TA TA T- TT TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
214171 CCAGATGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:214250 original size:2 final size:2
Alignment explanation
Indices: 214245--214280 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
214235 AGGGGGGTTG
214245 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
214281 CCTTAAGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:218587 original size:24 final size:22
Alignment explanation
Indices: 218560--218614 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
218550 TAATTTAATT
*
218560 TTAATAAAATTTATTATTTATTAA
1 TTAATAAAATTT-TTATAT-TTAA
218584 TTAA-AAATATTTTTATATTTAA
1 TTAATAAA-ATTTTTATATTTAA
218606 TT-ATAAAAT
1 TTAATAAAAT
218615 ATATAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 3 0.11
22 9 0.32
23 8 0.29
24 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATAAAATTTTTATATTTAA
Found at i:218627 original size:22 final size:22
Alignment explanation
Indices: 218578--218659 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 22
218568 ATTTATTATT
* **
218578 TATTAATTA-AAAATATTTTTA
1 TATTAATTATAAAATATATAAA
218599 TATTTAATTATAAAATATATAAA
1 TA-TTAATTATAAAATATATAAA
*
218622 TATTAATT-TAAAAAATA-ATAA
1 TATTAATTATAAAATATATA-AA
218643 TATTAATAATATAAAAT
1 TATTAAT--TATAAAAT
218660 TTTAAATCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.02
21 19 0.38
22 13 0.26
23 12 0.24
24 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTAATTATAAAATATATAAA
Found at i:219857 original size:17 final size:15
Alignment explanation
Indices: 219802--219858 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
219792 TTGACGGATC
* *
219802 AAATTTTAAATAATT
1 AAATTTTAATTTATT
*
219817 AAAATTTTTATTTATT
1 -AAATTTTAATTTATT
*
219833 AAAATTTAATTTGACTT
1 AAATTTTAATTT-A-TT
219850 AAATTTTAA
1 AAATTTTAA
219859 GTGATTTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.30
16 13 0.39
17 10 0.30
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
AAATTTTAATTTATT
Found at i:220342 original size:22 final size:22
Alignment explanation
Indices: 220308--220349 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
220298 TGTTTTGTTT
220308 ATTTAAAATATTTAA-AAATAA
1 ATTTAAAATATTTAACAAATAA
*
220329 ATTTATAAGTATTTAACAAAT
1 ATTTA-AAATATTTAACAAAT
220350 TATTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTTAAAATATTTAACAAATAA
Found at i:220443 original size:19 final size:19
Alignment explanation
Indices: 220417--220464 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
220407 ATTTTAATTC
*
220417 TAAT-AATTTTTAAAAATT
1 TAATAAATTTTTAAAAATA
* * *
220435 TATTAAATTCTTAAATATA
1 TAATAAATTTTTAAAAATA
220454 TAATAAATTTT
1 TAATAAATTTT
220465 ATTATGTATA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATAAATTTTTAAAAATA
Found at i:220590 original size:21 final size:21
Alignment explanation
Indices: 220566--220608 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
220556 AATGTATATC
220566 TCATTATTAATT-TTAATTTTA
1 TCATTA-TAATTATTAATTTTA
220587 TCATTATAATTATTAATTTTA
1 TCATTATAATTATTAATTTTA
220608 T
1 T
220609 TTTTTTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTATAATTATTAATTTTA
Found at i:221084 original size:2 final size:2
Alignment explanation
Indices: 221079--221107 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
221069 TCTCTCACCT
221079 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 A
221108 ATGGCGGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:221288 original size:12 final size:12
Alignment explanation
Indices: 221271--221309 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
221261 TTGCTTTGTT
*
221271 ATCGTCATCGTC
1 ATCGTCATCATC
221283 ATCGTCATCATC
1 ATCGTCATCATC
*
221295 ATCATCATCATC
1 ATCGTCATCATC
221307 ATC
1 ATC
221310 CTAATCCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.26, C:0.33, G:0.08, T:0.33
Consensus pattern (12 bp):
ATCGTCATCATC
Found at i:221295 original size:3 final size:3
Alignment explanation
Indices: 221275--221309 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
221265 TTTGTTATCG
* *
221275 TCA TCG TCA TCG TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
221310 CTAATCCTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.26, C:0.34, G:0.06, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:224820 original size:22 final size:20
Alignment explanation
Indices: 224781--224820 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
224771 TTTTTAAAAT
*
224781 TATTTTTTTCAAAAAATTGA
1 TATTTTTTTAAAAAAATTGA
224801 TATTTCTTTTAAAAATAATT
1 TATTT-TTTTAAAAA-AATT
224821 TTGGAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTTTTTAAAAAAATTGA
Found at i:228394 original size:24 final size:24
Alignment explanation
Indices: 228347--228396 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
228337 TAATTAGTGA
*
228347 TATTAAGTATTACTTGATTTTTTT
1 TATTAAGTATTAATTGATTTTTTT
*
228371 TATTAA-TATTAATTGTTTTATTTT
1 TATTAAGTATTAATTGATTT-TTTT
228395 TA
1 TA
228397 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (24 bp):
TATTAAGTATTAATTGATTTTTTT
Found at i:228397 original size:21 final size:24
Alignment explanation
Indices: 228347--228397 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
228337 TAATTAGTGA
* *
228347 TATTAAGTATTACTTGATTTTTTT
1 TATTAAGTATTAATTGATTTTATT
228371 TATTAA-TATTAATTG-TTTTATT
1 TATTAAGTATTAATTGATTTTATT
228393 T-TTAA
1 TATTAA
228398 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 7 0.28
23 8 0.32
24 6 0.24
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (24 bp):
TATTAAGTATTAATTGATTTTATT
Found at i:229439 original size:2 final size:2
Alignment explanation
Indices: 229432--229463 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
229422 CCTCCTCCTT
229432 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
229464 AATAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:229551 original size:21 final size:20
Alignment explanation
Indices: 229527--229577 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
229517 GTGTTATTTT
229527 TAATTATAATAATTTTAAATA
1 TAATTATAATAA-TTTAAATA
*
229548 TAATTTATTAA-AATTTAAATT
1 TAA-TTA-TAATAATTTAAATA
229569 TAATT-TAAT
1 TAATTATAAT
229578 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 3 0.12
20 2 0.08
21 13 0.50
22 5 0.19
23 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTATAATAATTTAAATA
Found at i:229569 original size:6 final size:6
Alignment explanation
Indices: 229558--229603 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
229548 TAATTTATTA
* *
229558 AAATTT AAATTT -AATTT -AATTT AAATTTT AAAATT AATTTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAA-TTT AAATTT AAATTT AAATT
229604 ATTTGAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 10 0.29
6 18 0.53
7 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:229573 original size:11 final size:12
Alignment explanation
Indices: 229536--229603 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
229526 TTAATTATAA
*
229536 TAATTTTAAATA
1 TAATTTTAAATT
229548 TAA-TTT--ATT
1 TAATTTTAAATT
* *
229557 AAAATTTAAATT
1 TAATTTTAAATT
229569 TAA-TTT-AATT
1 TAATTTTAAATT
*
229579 TAAATTTTAAAAT
1 T-AATTTTAAATT
229592 TAATTTTAAATT
1 TAATTTTAAATT
229604 ATTTGAATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
9 4 0.09
10 8 0.18
11 8 0.18
12 21 0.47
13 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TAATTTTAAATT
Found at i:229587 original size:23 final size:21
Alignment explanation
Indices: 229537--229597 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
229527 TAATTATAAT
*
229537 AATTTTAAATATAATTTATTA
1 AATTTTAAATTTAATTTATTA
*
229558 AAATTTAAATTTAATTTAATTTA
1 AATTTTAAATTTAATTT-A-TTA
*
229581 AATTTTAAAATTAATTT
1 AATTTTAAATTTAATTT
229598 TAAATTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 15 0.44
22 1 0.03
23 18 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTTAAATTTAATTTATTA
Found at i:230435 original size:17 final size:19
Alignment explanation
Indices: 230393--230436 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
230383 TAAAGATTTT
230393 TAATTT-TTTTATATTTAA
1 TAATTTATTTTATATTTAA
230411 TACA-TTATTTT-TA-TTAA
1 TA-ATTTATTTTATATTTAA
230428 TAATTTATT
1 TAATTTATT
230437 AATTAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.04
17 11 0.48
18 6 0.26
19 5 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATTTATTTTATATTTAA
Found at i:230460 original size:15 final size:17
Alignment explanation
Indices: 230421--230461 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
230411 TACATTATTT
230421 TTATTAATAATTTATTAA
1 TTATT-ATAATTTATTAA
230439 TTAATTATAATTT-TTAA
1 TT-ATTATAATTTATTAA
230456 -TATTAT
1 TTATTAT
230462 TTTAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.23
16 1 0.05
17 4 0.18
18 9 0.41
19 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTATAATTTATTAA
Found at i:231743 original size:2 final size:2
Alignment explanation
Indices: 231736--231760 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
231726 ATTCATTATT
231736 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
231761 GAATTCAAAG
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:233859 original size:2 final size:2
Alignment explanation
Indices: 233852--233880 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
233842 ACTTAAATAA
233852 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 A
233881 AATTATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:234146 original size:15 final size:16
Alignment explanation
Indices: 234119--234162 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
234109 AATTGAATCG
*
234119 ATTTAATTTAAATTTA
1 ATTTAATTTAAATATA
234135 ATTTAA-TTAAATATA
1 ATTTAATTTAAATATA
234150 ATTT--TTTAAATAT
1 ATTTAATTTAAATAT
234163 TATCCATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 8 0.31
15 12 0.46
16 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTAATTTAAATATA
Found at i:236485 original size:21 final size:23
Alignment explanation
Indices: 236434--236484 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
236424 TTTACAAAAA
236434 TAAAAAATAACAAATAATTATTT
1 TAAAAAATAACAAATAATTATTT
*
236457 TAAAAAAT-A-AAATGATTATTCT
1 TAAAAAATAACAAATAATTATT-T
236479 TAAAAA
1 TAAAAA
236485 TTTTGGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 10 0.38
22 8 0.31
23 8 0.31
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAAAATAACAAATAATTATTT
Found at i:236555 original size:33 final size:33
Alignment explanation
Indices: 236518--236585 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
236508 CTAAAAAATT
* *
236518 TTAAAAATAATTA-TTATCTTTAATATTATTAAA
1 TTAAAAAT-ATTATTTATCTTTAATATAACTAAA
*
236551 TTAAAAATATTATTTATTTTTAATATAACTAAA
1 TTAAAAATATTATTTATCTTTAATATAACTAAA
236584 TT
1 TT
236586 TAATATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 4 0.13
33 27 0.87
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (33 bp):
TTAAAAATATTATTTATCTTTAATATAACTAAA
Found at i:237802 original size:2 final size:2
Alignment explanation
Indices: 237797--237824 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
237787 ATCAAAATTA
237797 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
237825 TGCATTTATT
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:238371 original size:2 final size:2
Alignment explanation
Indices: 238364--238388 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
238354 ACTTACCAAG
238364 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
238389 CCACCTTTTA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:240239 original size:2 final size:2
Alignment explanation
Indices: 240232--240269 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
240222 ATATCTAATC
240232 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
240270 GATCCCATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:241515 original size:38 final size:35
Alignment explanation
Indices: 241467--241557 Score: 92
Period size: 38 Copynumber: 2.4 Consensus size: 35
241457 ATCTAATTCG
*
241467 ATTTAAATTATTATTTTAATAATAAAATATTTTTATTTA
1 ATTT-AATTATTATTTTAATAA-AAAATA-ATTT-TTTA
*
241506 ATTTAATTATATAAATATTAATAAAAAATAATTTTTTA
1 ATTTAATTAT-T--ATTTTAATAAAAAATAATTTTTTA
*
241544 ATTTTATTATTATT
1 ATTTAATTATTATT
241558 CATAAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
35 2 0.04
37 1 0.02
38 19 0.42
39 8 0.18
40 6 0.13
41 9 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
ATTTAATTATTATTTTAATAAAAAATAATTTTTTA
Found at i:241556 original size:41 final size:43
Alignment explanation
Indices: 241482--241565 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 43
241472 AATTATTATT
241482 TTAATAATAAAATATTTTTATTTAATTTAATTA-T-ATAAATA
1 TTAATAATAAAATATTTTTATTTAATTTAATTATTCATAAATA
*
241523 TTAATAA-AAAATA-ATTT-TTTAATTTTATTATTATTCATAAATA
1 TTAATAATAAAATATTTTTATTTAA-TTTA--ATTATTCATAAATA
241566 AATTTTCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
38 5 0.14
39 7 0.19
40 6 0.16
41 11 0.30
42 1 0.03
43 7 0.19
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (43 bp):
TTAATAATAAAATATTTTTATTTAATTTAATTATTCATAAATA
Found at i:243108 original size:25 final size:25
Alignment explanation
Indices: 243059--243108 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
243049 AATTAAATTT
243059 TTTATATGATATAAATAAAATTATA
1 TTTATATGATATAAATAAAATTATA
243084 TTTATAT-A-ATAATATAAAATATATA
1 TTTATATGATATAA-ATAAAAT-TATA
243109 ATATATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.17
24 8 0.35
25 11 0.48
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTATATGATATAAATAAAATTATA
Found at i:243150 original size:23 final size:22
Alignment explanation
Indices: 243067--243156 Score: 74
Period size: 21 Copynumber: 4.4 Consensus size: 22
243057 TTTTTATATG
243067 ATATAA-ATAAAATTATATTTAT
1 ATATAATATAAAATTATA-TTAT
243089 ATAATAATATAAAA-TATA-TA-
1 AT-ATAATATAAAATTATATTAT
243109 ATAT-ATCAT----TTATATTAT
1 ATATAAT-ATAAAATTATATTAT
*
243127 ATATAATATAAAATTAT-TTCT
1 ATATAATATAAAATTATATTAT
243148 ATATAATAT
1 ATATAATAT
243157 TATAAATAGT
Statistics
Matches: 56, Mismatches: 1, Indels: 23
0.70 0.01 0.29
Matches are distributed among these distances:
16 4 0.07
17 2 0.04
18 8 0.14
19 6 0.11
20 2 0.04
21 14 0.25
22 6 0.11
23 8 0.14
24 6 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATAATATAAAATTATATTAT
Found at i:243163 original size:23 final size:23
Alignment explanation
Indices: 243102--243163 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
243092 ATAATATAAA
* *
243102 ATATATAATATATCATTTATATT
1 ATATATAATATATAAATTATATT
243125 ATATATAATATA-AAATTAT-TT
1 ATATATAATATATAAATTATATT
*
243146 CTATATAATATTATAAAT
1 ATATATAATA-TATAAAT
243164 AGTTTTATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.32
22 7 0.21
23 16 0.47
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATAATATATAAATTATATT
Found at i:244159 original size:24 final size:24
Alignment explanation
Indices: 244127--244172 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
244117 AATTTTTAAG
*
244127 ATAATTTTTTATTTTTTAAATATT
1 ATAAATTTTTATTTTTTAAATATT
244151 ATAAATTTTTATTTTTTAAATA
1 ATAAATTTTTATTTTTTAAATA
244173 AATATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATAAATTTTTATTTTTTAAATATT
Found at i:244182 original size:25 final size:24
Alignment explanation
Indices: 244127--244182 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
244117 AATTTTTAAG
* *
244127 ATAATTTTTTATTTTTTAAATATT
1 ATAAATTTTTATTTTTTAAATAAT
244151 ATAAATTTTTATTTTTTAAATAAAT
1 ATAAATTTTTATTTTTTAAAT-AAT
*
244176 ATTAATT
1 ATAAATT
244183 ATCGTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATAAATTTTTATTTTTTAAATAAT
Found at i:244211 original size:5 final size:5
Alignment explanation
Indices: 244187--244257 Score: 59
Period size: 5 Copynumber: 15.8 Consensus size: 5
244177 TTAATTATCG
* *
244187 TTAAT TT-AT TTAAT TT--T TTACT TTAAT TTAAT TTAAT TTGA- -TAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
*
244232 TTAA- TTAAT TT--T TTAAT TTAAA TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
244258 ATAATTTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
3 8 0.15
4 8 0.15
5 38 0.70
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:244224 original size:23 final size:23
Alignment explanation
Indices: 244187--244242 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
244177 TTAATTATCG
** *
244187 TTAATTT-ATTTAATTTTTTACT
1 TTAATTTAATTTAATTTGATAAT
244209 TTAATTTAATTTAATTTGATAAT
1 TTAATTTAATTTAATTTGATAAT
244232 TTAA-TTAATTT
1 TTAATTTAATTT
244243 TTTAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TTAATTTAATTTAATTTGATAAT
Found at i:244241 original size:17 final size:17
Alignment explanation
Indices: 244210--244257 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
244200 TTTTTTACTT
244210 TAATTTAATTTAATTTGA
1 TAATTTAA-TTAATTTGA
**
244228 TAATTTAATTAATTTTT
1 TAATTTAATTAATTTGA
244245 TAATTTAAATTAA
1 TAATTT-AATTAA
244258 ATAATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TAATTTAATTAATTTGA
Found at i:244275 original size:22 final size:22
Alignment explanation
Indices: 244227--244284 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
244217 ATTTAATTTG
* *
244227 ATAATTTAATTAATTTTTTAAT
1 ATAAATTAAATAATTTTTTAAT
*
244249 TTAAATTAAATAATTTTATT-AT
1 ATAAATTAAATAATTTT-TTAAT
244271 ATAAA-T-AATAATTT
1 ATAAATTAAATAATTT
244285 AAATTAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 8 0.26
21 1 0.03
22 20 0.65
23 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAAATTAAATAATTTTTTAAT
Found at i:244689 original size:2 final size:2
Alignment explanation
Indices: 244682--244711 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
244672 TCATTAAGAA
*
244682 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
244712 GTGCGCGCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:245248 original size:22 final size:24
Alignment explanation
Indices: 245220--245265 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
245210 ATTTAAATTA
245220 TTATTTAAA-TAA-TAAAAATATT
1 TTATTTAAATTAATTAAAAATATT
*
245242 TTATTTAAATTAATTATAAATATT
1 TTATTTAAATTAATTAAAAATATT
245266 AATATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 3 0.14
24 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATTTAAATTAATTAAAAATATT
Found at i:245248 original size:34 final size:34
Alignment explanation
Indices: 245200--245306 Score: 96
Period size: 34 Copynumber: 3.1 Consensus size: 34
245190 TTTATAATTT
*
245200 AAATGATTTAATTTAAATTATTATTTAAATAATAA
1 AAAT-ATTTTATTTAAATTATTATTTAAATAATAA
*
245235 AAATATTTTATTTAAATTAATTA-TAAATATTAATATAA
1 AAATATTTTATTTAAATT-ATTATTTAA-A-T-A-ATAA
*
245273 AAATAATTT-TTTAATATTATT-TTT-AATAATAA
1 AAATATTTTATTTAA-ATTATTATTTAAATAATAA
245305 AA
1 AA
245307 TAAATTTTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
32 6 0.10
33 1 0.02
34 17 0.28
35 10 0.16
36 2 0.03
37 10 0.16
38 15 0.25
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (34 bp):
AAATATTTTATTTAAATTATTATTTAAATAATAA
Found at i:245249 original size:39 final size:38
Alignment explanation
Indices: 245205--245287 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
245195 AATTTAAATG
* *
245205 ATTTAATTTAAATTAT-TAT-TTAAATAATAAAAATATTTT
1 ATTTAATTT-AATTATAAATATT-AAT-ATAAAAATAATTT
*
245244 ATTTAAATTAATTATAAATATTAATATAAAAATAATTT
1 ATTTAATTTAATTATAAATATTAATATAAAAATAATTT
245282 -TTTAAT
1 ATTTAAT
245288 ATTATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
37 5 0.13
38 18 0.47
39 13 0.34
40 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
ATTTAATTTAATTATAAATATTAATATAAAAATAATTT
Found at i:245310 original size:37 final size:38
Alignment explanation
Indices: 245230--245310 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 38
245220 TTATTTAAAT
* *
245230 AATAAAAATATTTTATTTAAATTAATTATAAATATTAA
1 AATAAAAATAATTTATTTAAATTAATTATAAATAATAA
* * *
245268 TATAAAAATAATTT-TTTAATATT-ATTTTTAATAATAA
1 AATAAAAATAATTTATTTAA-ATTAATTATAAATAATAA
245305 AATAAA
1 AATAAA
245311 TTTTTGAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
37 21 0.58
38 15 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (38 bp):
AATAAAAATAATTTATTTAAATTAATTATAAATAATAA
Found at i:245705 original size:8 final size:7
Alignment explanation
Indices: 245692--245736 Score: 51
Period size: 6 Copynumber: 6.7 Consensus size: 7
245682 ATGCAAAAAA
245692 CTTTTTGT
1 CTTTTT-T
245700 CTTTTTT
1 CTTTTTT
245707 C-TTTTT
1 CTTTTTT
*
245713 -TTTTTC
1 CTTTTTT
245719 CTTTTTT
1 CTTTTTT
245726 -TTTTTT
1 CTTTTTT
245732 CTTTT
1 CTTTT
245737 CTGTCAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
6 15 0.47
7 11 0.34
8 6 0.19
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.84
Consensus pattern (7 bp):
CTTTTTT
Found at i:245722 original size:19 final size:19
Alignment explanation
Indices: 245700--245737 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
245690 AACTTTTTGT
245700 CTTTTTTCTTTTTT-TTTTC
1 CTTTTTT-TTTTTTCTTTTC
245719 CTTTTTTTTTTTTCTTTTC
1 CTTTTTTTTTTTTCTTTTC
245738 TGTCAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
CTTTTTTTTTTTTCTTTTC
Found at i:245725 original size:14 final size:13
Alignment explanation
Indices: 245701--245736 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
245691 ACTTTTTGTC
245701 TTTTTTC-TTTTT
1 TTTTTTCTTTTTT
*
245713 TTTTTCCTTTTTT
1 TTTTTTCTTTTTT
245726 TTTTTTCTTTT
1 TTTTTTCTTTT
245737 CTGTCAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:246741 original size:5 final size:5
Alignment explanation
Indices: 246717--246770 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
246707 ATGAATTTTG
* *
246717 ATATT AT-TT ATA-T A-ATT ATATT ATATTT ATATT ATGTTT ATATC ATATT
1 ATATT ATATT ATATT ATATT ATATT ATA-TT ATATT AT-ATT ATATT ATATT
246766 ATATT
1 ATATT
246771 TTAATAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
3 1 0.03
4 8 0.20
5 22 0.55
6 9 0.22
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:246783 original size:27 final size:30
Alignment explanation
Indices: 246734--246799 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 30
246724 TTATATAATT
*
246734 ATATTATA-TTTATATTATGTTTATA-T-C
1 ATATTATATTTTATATAATGTTTATAGTAC
*
246761 ATATTATATTTTA-ATAATTTTTATAGTACC
1 ATATTATATTTTATATAATGTTTATAGTA-C
246791 ATATTATAT
1 ATATTATAT
246800 CTCAAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 18 0.55
28 5 0.15
30 10 0.30
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (30 bp):
ATATTATATTTTATATAATGTTTATAGTAC
Found at i:249633 original size:6 final size:6
Alignment explanation
Indices: 249622--249652 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
249612 AAATTTGATA
*
249622 ATAAAT ATAAAT ATAGAT ATAAAT ATAAAT A
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT A
249653 AATGAGGTGA
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (6 bp):
ATAAAT
Found at i:250210 original size:19 final size:20
Alignment explanation
Indices: 250185--250237 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
250175 AAAATATAAA
*
250185 ATATAATATAATTTGAATAT
1 ATATAATATAATTTAAATAT
*
250205 AT-TAATAT-ATTTAAATTT
1 ATATAATATAATTTAAATAT
250223 ATATAATATGAATTT
1 ATATAATAT-AATTT
250238 TTGCATTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 10 0.36
19 12 0.43
20 2 0.07
21 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
ATATAATATAATTTAAATAT
Found at i:252547 original size:2 final size:2
Alignment explanation
Indices: 252540--252577 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
252530 ATAACGCTTG
252540 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
252578 GTGCGATTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:256007 original size:16 final size:16
Alignment explanation
Indices: 255986--256017 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
255976 TGTGGCATGT
*
255986 AATATATAATATATAA
1 AATATAAAATATATAA
256002 AATATAAAATATATAA
1 AATATAAAATATATAA
256018 TATAATAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATAAAATATATAA
Found at i:256008 original size:14 final size:14
Alignment explanation
Indices: 255989--256024 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
255979 GGCATGTAAT
255989 ATATAATATATAAA
1 ATATAATATATAAA
* *
256003 ATATAAAATATATA
1 ATATAATATATAAA
256017 ATATAATA
1 ATATAATA
256025 GGTGTTATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATAATATATAAA
Found at i:258235 original size:2 final size:2
Alignment explanation
Indices: 258224--258277 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
258214 TGTGTGTATT
* *
258224 TA TA TCA TA TA T- TA CA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
258266 TA TT TA -A TA TA T
1 TA TA TA TA TA TA T
258278 TTTATAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
1 2 0.05
2 39 0.91
3 2 0.05
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:258287 original size:17 final size:17
Alignment explanation
Indices: 258239--258283 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
258229 CATATATTAC
* *
258239 ATATATATATATATAT-
1 ATATATATTTATATTTA
258255 ATATATATTTATATTTA
1 ATATATATTTATATTTA
258272 ATATAT-TTTATA
1 ATATATATTTATA
258284 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATATATTTATATTTA
Found at i:258316 original size:26 final size:28
Alignment explanation
Indices: 258243--258316 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 28
258233 TATTACATAT
* *
258243 ATATATATATATATATATATTTATATTTA
1 ATATAT-TTTATATATATTTTTATATTTA
*
258272 ATATATTTTATA-ATTTTTTTA-ATTTA
1 ATATATTTTATATATATTTTTATATTTA
*
258298 AT-TATTTTATATAAATTTT
1 ATATATTTTATATATATTTT
258317 GAAATATACA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 9 0.23
26 12 0.31
27 7 0.18
28 5 0.13
29 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
ATATATTTTATATATATTTTTATATTTA
Found at i:258735 original size:2 final size:2
Alignment explanation
Indices: 258728--258767 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
258718 AAAAGCACGA
* *
258728 AT AT AT AT AT AT AT AT AT AT AT AC AT AC 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
258768 TCAGCCCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:265099 original size:17 final size:16
Alignment explanation
Indices: 265079--265111 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
265069 TACTAAAATT
265079 TTAAAAAAAATAAAAAA
1 TTAAAAAAAA-AAAAAA
265096 TTAAAAAAAAAAAAAA
1 TTAAAAAAAAAAAAAA
265112 CCCTGATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (16 bp):
TTAAAAAAAAAAAAAA
Found at i:270221 original size:23 final size:24
Alignment explanation
Indices: 270195--270239 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
270185 TGAGGAGGAA
*
270195 ATTT-ATATGAGATTAC-CACCTGG
1 ATTTGATA-GAGATGACTCACCTGG
270218 ATTTGATAGAGATGACTCACCT
1 ATTTGATAGAGATGACTCACCT
270240 AACTCAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (24 bp):
ATTTGATAGAGATGACTCACCTGG
Found at i:276854 original size:54 final size:54
Alignment explanation
Indices: 276790--276967 Score: 329
Period size: 54 Copynumber: 3.3 Consensus size: 54
276780 ATGACTTAGC
276790 CTGGTTTTGAGACTCAGAATGTGGCAGATTTTGGTTTTCATTATGTACTTGGGA
1 CTGGTTTTGAGACTCAGAATGTGGCAGATTTTGGTTTTCATTATGTACTTGGGA
276844 CTGGTTTTGAGACTCAGAATGTGGCAGATTTTGGTTTTCATTATGTACTTGGGA
1 CTGGTTTTGAGACTCAGAATGTGGCAGATTTTGGTTTTCATTATGTACTTGGGA
**
276898 CTGGTTTTGAGACTCAGAATGTGGCAGATTTTGGTTTTTGTTATGTACTTGGGA
1 CTGGTTTTGAGACTCAGAATGTGGCAGATTTTGGTTTTCATTATGTACTTGGGA
*
276952 CTGATTTTGAGACTCA
1 CTGGTTTTGAGACTCA
276968 AACTGTAGTA
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 121 1.00
ACGTcount: A:0.20, C:0.11, G:0.28, T:0.41
Consensus pattern (54 bp):
CTGGTTTTGAGACTCAGAATGTGGCAGATTTTGGTTTTCATTATGTACTTGGGA
Found at i:283703 original size:33 final size:33
Alignment explanation
Indices: 283661--283727 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
283651 TGGAAGATAG
283661 AGTAAATCACAAGAAAGGACTGATTATATGCAA
1 AGTAAATCACAAGAAAGGACTGATTATATGCAA
*
283694 AGTAAATCACATGAAAGGACTGATTATATGCAA
1 AGTAAATCACAAGAAAGGACTGATTATATGCAA
283727 A
1 A
283728 ATATTCCATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (33 bp):
AGTAAATCACAAGAAAGGACTGATTATATGCAA
Found at i:288626 original size:37 final size:34
Alignment explanation
Indices: 288565--288693 Score: 109
Period size: 37 Copynumber: 3.5 Consensus size: 34
288555 AAAATTTTAT
*
288565 ATAAATAAATTTAAAATTAAAATTAAATTATTATAATAA
1 ATAAA-AAATATAAAA-T-AAATTAAA-TATTAT-ATAA
*
288604 ATTAAAAAATATAAAATAAATTAAGATATGATATAA
1 A-TAAAAAATATAAAATAAATTAA-ATATTATATAA
* *
288640 ATATAATATA-AAAAT-AATTAAATATTATATAATA
1 ATAAAAAATATAAAATAAATTAAATATTATAT-A-A
288674 ATAAAATAATATAAATATAA
1 ATAAAA-AATATAAA-ATAA
288694 TATAATATGA
Statistics
Matches: 75, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
32 8 0.11
33 7 0.09
34 11 0.15
35 10 0.13
36 8 0.11
37 14 0.19
38 3 0.04
39 10 0.13
40 4 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (34 bp):
ATAAAAAATATAAAATAAATTAAATATTATATAA
Found at i:288643 original size:11 final size:11
Alignment explanation
Indices: 288611--288698 Score: 68
Period size: 11 Copynumber: 8.6 Consensus size: 11
288601 TAAATTAAAA
288611 AATATAAA-AT
1 AATATAAATAT
288621 AA-ATTAAGATAT
1 AATA-TAA-ATAT
*
288633 GATATAAATAT
1 AATATAAATAT
*
288644 AATATAAAAAT
1 AATATAAATAT
288655 AAT-TAAATAT
1 AATATAAATAT
*
288665 --TATATA-AT
1 AATATAAATAT
288673 -A-ATAAA-AT
1 AATATAAATAT
288681 AATATAAATAT
1 AATATAAATAT
288692 AATATAA
1 AATATAA
288699 TATGAATGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
8 9 0.14
9 5 0.08
10 16 0.25
11 26 0.41
12 6 0.10
13 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AATATAAATAT
Found at i:288647 original size:5 final size:5
Alignment explanation
Indices: 288629--288701 Score: 58
Period size: 5 Copynumber: 13.8 Consensus size: 5
288619 ATAAATTAAG
* * *
288629 ATATG ATATAA ATATA ATATAA AAATA AT-TAA ATATT ATATA ATAATA
1 ATATA ATAT-A ATATA ATAT-A ATATA ATAT-A ATATA ATATA AT-ATA
*
288677 AAATA ATATAA ATATA ATATA ATAT
1 ATATA ATAT-A ATATA ATATA ATAT
288702 GAATGTATGA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
4 1 0.02
5 36 0.65
6 18 0.33
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:288661 original size:21 final size:22
Alignment explanation
Indices: 288634--288698 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 22
288624 TTAAGATATG
288634 ATATAAATATAATATAAAAATA
1 ATATAAATATAATATAAAAATA
288656 AT-TAAATATTATATAATAATAAAATA
1 ATATAAATA-TA-AT-AT-A-AAAATA
288682 ATATAAATATAATATAA
1 ATATAAATATAATATAA
288699 TATGAATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
21 6 0.16
22 5 0.14
23 3 0.08
24 4 0.11
25 3 0.08
26 10 0.27
27 6 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATAAATATAATATAAAAATA
Found at i:288694 original size:37 final size:35
Alignment explanation
Indices: 288585--288694 Score: 111
Period size: 37 Copynumber: 3.1 Consensus size: 35
288575 TTAAAATTAA
*
288585 AATTAAATTATTATAATAAATTAAAA-AATATAAAAT
1 AATTAAA-TATTAT-ATAAAATAAAATAATATAAAAT
* *
288621 AAATTAAGATATGATAT-AAATATAAT-ATA-AAAAT
1 -AATTAA-ATATTATATAAAATAAAATAATATAAAAT
288655 AATTAAATATTATATAATAATAAAATAATATAAATAT
1 AATTAAATATTATATAA-AATAAAATAATATAAA-AT
288692 AAT
1 AAT
288695 ATAATATGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
32 8 0.13
33 7 0.11
34 12 0.20
35 12 0.20
36 5 0.08
37 16 0.26
38 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (35 bp):
AATTAAATATTATATAAAATAAAATAATATAAAAT
Found at i:288951 original size:9 final size:9
Alignment explanation
Indices: 288933--289047 Score: 68
Period size: 9 Copynumber: 13.3 Consensus size: 9
288923 AATCATGATA
*
288933 ATAAATTAT
1 ATAAAATAT
288942 AT-AAA-AT
1 ATAAAATAT
*
288949 ATAAAATAA
1 ATAAAATAT
*
288958 AT-TAATAT
1 ATAAAATAT
* *
288966 ATAATATAA
1 ATAAAATAT
288975 ATAAAATAT
1 ATAAAATAT
288984 AATTAAAATA-
1 -A-TAAAATAT
288994 ATTAAAATAT
1 A-TAAAATAT
*
289004 -T-ATAT-T
1 ATAAAATAT
*
289010 AAAAAATA-
1 ATAAAATAT
289018 ATATAAATAT
1 ATA-AAATAT
289028 ATAAAATAT
1 ATAAAATAT
289037 -TAAAATAT
1 ATAAAATAT
289045 ATA
1 ATA
289048 TGACATTAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
6 1 0.01
7 7 0.09
8 25 0.31
9 37 0.46
10 4 0.05
11 7 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATAAAATAT
Found at i:288997 original size:36 final size:39
Alignment explanation
Indices: 288950--289045 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 39
288940 ATATAAAATA
* *
288950 TAAAATAAATTAATATATAATA-TAAATAA-AATATAAT
1 TAAAATAAATTAAAATATAATATTAAAAAATAATATAAT
*
288987 TAAAAT-AATTAAAATATTATATTAAAAAATAATATAAAT
1 TAAAATAAATTAAAATATAATATTAAAAAATAATAT-AAT
*
289026 ATATAAA-ATATTAAAATATA
1 -TA-AAATAAATTAAAATATA
289046 TATGACATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 13 0.27
37 12 0.25
38 5 0.10
39 3 0.06
40 2 0.04
41 13 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (39 bp):
TAAAATAAATTAAAATATAATATTAAAAAATAATATAAT
Found at i:289012 original size:13 final size:13
Alignment explanation
Indices: 288994--289045 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
288984 AATTAAAATA
*
288994 ATTAAAATATTAT
1 ATTAAAATATAAT
*
289007 ATTAAAAAATAAT
1 ATTAAAATATAAT
289020 A-TAAATATATAAAAT
1 ATTAAA-ATAT--AAT
289035 ATTAAAATATA
1 ATTAAAATATA
289046 TATGACATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 4 0.12
13 16 0.50
15 8 0.25
16 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTAAAATATAAT
Found at i:289013 original size:33 final size:32
Alignment explanation
Indices: 288937--289038 Score: 102
Period size: 33 Copynumber: 3.1 Consensus size: 32
288927 ATGATAATAA
* *
288937 ATTATATAAAATATAAAATAAATTAATATATAAT
1 ATTATATAAAATAT--AATAAAATAATATAAAAT
*
288971 A-TAAATAAAATATAATTAAAATAAT-TAAAAT
1 ATTATATAAAATATAA-TAAAATAATATAAAAT
*
289002 ATTATATTAAAAAATAATATAAAT-ATATAAAAT
1 ATTATA-TAAAATATAATA-AAATAATATAAAAT
289035 ATTA
1 ATTA
289039 AAATATATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
31 8 0.14
32 15 0.26
33 34 0.59
34 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (32 bp):
ATTATATAAAATATAATAAAATAATATAAAAT
Found at i:289046 original size:17 final size:17
Alignment explanation
Indices: 288934--289047 Score: 67
Period size: 17 Copynumber: 6.6 Consensus size: 17
288924 ATCATGATAA
*
288934 TAAATTATATAAAATA-
1 TAAAATATATAAAATAT
* *
288950 TAAAATAAAT-TAATAT
1 TAAAATATATAAAATAT
* *
288966 ATAATATAAATAAAATATAAT
1 -TAAAATATAT-AAA-AT-AT
288987 TAAAATA-ATTAAAATAT
1 TAAAATATA-TAAAATAT
* * *
289004 T-ATAT-TAAAAAATAA
1 TAAAATATATAAAATAT
289019 TATAAATATATAAAATAT
1 TA-AAATATATAAAATAT
289037 TAAAATATATA
1 TAAAATATATA
289048 TGACATTAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 21
0.69 0.11 0.19
Matches are distributed among these distances:
15 11 0.15
16 12 0.16
17 24 0.32
18 12 0.16
19 5 0.07
20 9 0.12
21 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATATATAAAATAT
Found at i:289329 original size:31 final size:32
Alignment explanation
Indices: 289285--289366 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
289275 TTAAAATATT
* *
289285 ATTTAT-TTATATAATTTTAATATATT-AATA
1 ATTTATATTATATAATTTTAATAAATTCAAGA
* *
289315 ATTTATATTATATAAATTTTGATAAATTCAAGC
1 ATTTATATTATAT-AATTTTAATAAATTCAAGA
* *
289348 ATTCATATTATATTATTTT
1 ATTTATATTATATAATTTT
289367 TTCGTGTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
30 6 0.14
31 6 0.14
32 17 0.40
33 14 0.33
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (32 bp):
ATTTATATTATATAATTTTAATAAATTCAAGA
Found at i:294221 original size:29 final size:27
Alignment explanation
Indices: 294182--294268 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 27
294172 CGATCCAATG
294182 AAATTATCAAAAATTTAATTTTTATAATTA
1 AAATT-TC-AAAA-TTAATTTTTATAATTA
* ***
294212 AAATTTCAAAATAAAAAATTATAATTTA
1 AAATTTCAAAATTAATTTTTATAA-TTA
*
294240 ATAATTTTAAAATTAATTTTTATAATTA
1 A-AATTTCAAAATTAATTTTTATAATTA
294268 A
1 A
294269 TTAAAAATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
27 9 0.20
28 12 0.26
29 20 0.43
30 5 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATTTCAAAATTAATTTTTATAATTA
Found at i:294870 original size:16 final size:16
Alignment explanation
Indices: 294851--294892 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
294841 TCTCTTTTTG
294851 TTTTTTTCTATATCCT
1 TTTTTTTCTATATCCT
* *
294867 TTTTTTTTTATTTCCT
1 TTTTTTTCTATATCCT
294883 TTTTTATTCT
1 TTTTT-TTCT
294893 CTCCTTCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTTCTATATCCT
Found at i:297836 original size:2 final size:2
Alignment explanation
Indices: 297829--297861 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
297819 ACTTTTTGGC
297829 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
297862 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:303303 original size:16 final size:15
Alignment explanation
Indices: 303263--303305 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
303253 TTTTATATTT
*
303263 ATATT-AATATTTAA
1 ATATTAAATAATTAA
*
303277 ATATTATATAATTAA
1 ATATTAAATAATTAA
303292 ATTATTAAATAATT
1 A-TATTAAATAATT
303306 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.21
15 8 0.33
16 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTAAATAATTAA
Found at i:304404 original size:21 final size:21
Alignment explanation
Indices: 304347--304468 Score: 90
Period size: 24 Copynumber: 5.6 Consensus size: 21
304337 TTGTGGAGGC
* *
304347 AAAGGAGTTGCAGGCGGTGGTAA
1 AAAGG-GTTGCTGGCGGTGG-CA
304370 TAAAGGGATTGCTGGCGGTGGCA
1 -AAAGGG-TTGCTGGCGGTGGCA
*
304393 AAAGGGTTGCT---GGAGGC-
1 AAAGGGTTGCTGGCGGTGGCA
* * *
304410 GAAGGAGTTGCAGGCGGTGGTAA
1 AAAGG-GTTGCTGGCGGTGG-CA
304433 TAAAGGGATTGCTGGCGGTGGCA
1 -AAAGGG-TTGCTGGCGGTGGCA
304456 AAAGGGTTGCTGG
1 AAAGGGTTGCTGG
304469 AGGCGAAGGA
Statistics
Matches: 79, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
17 4 0.05
18 10 0.13
21 16 0.20
22 12 0.15
23 4 0.05
24 33 0.42
ACGTcount: A:0.25, C:0.11, G:0.45, T:0.20
Consensus pattern (21 bp):
AAAGGGTTGCTGGCGGTGGCA
Found at i:304439 original size:63 final size:63
Alignment explanation
Indices: 304340--304670 Score: 493
Period size: 63 Copynumber: 5.3 Consensus size: 63
304330 TCGTGCCTTG
* *
304340 TGGAGGCAAAGGAGTTGCAGGCGGTGGTAATAAAGGGATTGCTGGCGGTGGCAAAAGGGTTGC
1 TGGAGGCGAAGGAGTTTCAGGCGGTGGTAATAAAGGGATTGCTGGCGGTGGCAAAAGGGTTGC
*
304403 TGGAGGCGAAGGAGTTGCAGGCGGTGGTAATAAAGGGATTGCTGGCGGTGGCAAAAGGGTTGC
1 TGGAGGCGAAGGAGTTTCAGGCGGTGGTAATAAAGGGATTGCTGGCGGTGGCAAAAGGGTTGC
*** * * *
304466 TGGAGGCGAAGGAGTTTCAGGAAATGGTAATAAAGGGGTTGCTGGCGGGGGCAAAAGAGTTGC
1 TGGAGGCGAAGGAGTTTCAGGCGGTGGTAATAAAGGGATTGCTGGCGGTGGCAAAAGGGTTGC
* * * * * *
304529 TGGAGGCGAGGGAGTTTCAGGTGGCGGTAATAAGGGGGTTGCTGGCGGTGGCAAAACGGTTGC
1 TGGAGGCGAAGGAGTTTCAGGCGGTGGTAATAAAGGGATTGCTGGCGGTGGCAAAAGGGTTGC
* * *
304592 TGGAGGCGAGGGAGTTTCAGGTGGTGGTAATAAAGGGATTGCAGGCGGTGGCAAAAGGGTTGC
1 TGGAGGCGAAGGAGTTTCAGGCGGTGGTAATAAAGGGATTGCTGGCGGTGGCAAAAGGGTTGC
304655 TGGAGGCGAAGG-GTTT
1 TGGAGGCGAAGGAGTTT
304671 ATAATTGGGG
Statistics
Matches: 245, Mismatches: 23, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
62 4 0.02
63 241 0.98
ACGTcount: A:0.24, C:0.11, G:0.46, T:0.20
Consensus pattern (63 bp):
TGGAGGCGAAGGAGTTTCAGGCGGTGGTAATAAAGGGATTGCTGGCGGTGGCAAAAGGGTTGC
Found at i:304754 original size:30 final size:30
Alignment explanation
Indices: 304720--304809 Score: 180
Period size: 30 Copynumber: 3.0 Consensus size: 30
304710 GGAGGGATGT
304720 CGGGTATCGAAGGAGTAGCTGGATCAAAAG
1 CGGGTATCGAAGGAGTAGCTGGATCAAAAG
304750 CGGGTATCGAAGGAGTAGCTGGATCAAAAG
1 CGGGTATCGAAGGAGTAGCTGGATCAAAAG
304780 CGGGTATCGAAGGAGTAGCTGGATCAAAAG
1 CGGGTATCGAAGGAGTAGCTGGATCAAAAG
304810 GTGATGGATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.33, C:0.13, G:0.37, T:0.17
Consensus pattern (30 bp):
CGGGTATCGAAGGAGTAGCTGGATCAAAAG
Found at i:306876 original size:25 final size:25
Alignment explanation
Indices: 306843--306907 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
306833 TCTTATATAT
306843 GATATTAAATTATATTTTGCTTATC
1 GATATTAAATTATATTTTGCTTATC
306868 GATATTAAATTATATTTTGCTTATC
1 GATATTAAATTATATTTTGCTTATC
*
306893 AATATTAAATTATAT
1 GATATTAAATTATAT
306908 GAAAAAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (25 bp):
GATATTAAATTATATTTTGCTTATC
Found at i:308995 original size:2 final size:2
Alignment explanation
Indices: 308988--309013 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
308978 CTGGTATAAC
308988 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
309014 GCACTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:313647 original size:22 final size:23
Alignment explanation
Indices: 313612--313711 Score: 89
Period size: 23 Copynumber: 4.3 Consensus size: 23
313602 TGTTTACAAT
*
313612 TATTTATTTATTATTCATGAATA
1 TATTTATTAATTATTCATGAATA
313635 TATTT-TTAATTATTCATGAATA
1 TATTTATTAATTATTCATGAATA
* * *
313657 TGTTTGATT-ATATGTTCATAAATA
1 TATTT-ATTAAT-TATTCATGAATA
* *
313681 TGTTTATTTATTATTCGA-GAATA
1 TATTTATTAATTATTC-ATGAATA
*
313704 AATTTATT
1 TATTTATT
313712 TGATTTAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
22 20 0.31
23 24 0.38
24 20 0.31
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (23 bp):
TATTTATTAATTATTCATGAATA
Found at i:313691 original size:24 final size:23
Alignment explanation
Indices: 313614--313696 Score: 98
Period size: 22 Copynumber: 3.6 Consensus size: 23
313604 TTTACAATTA
*
313614 TTTATTTATTATTCATGAATATA
1 TTTATTTATTATTCATGAATATG
*
313637 TTT-TTAATTATTCATGAATATG
1 TTTATTTATTATTCATGAATATG
* *
313659 TTTGA-TTATATGTTCATAAATATG
1 TTT-ATTTAT-TATTCATGAATATG
313683 TTTATTTATTATTC
1 TTTATTTATTATTC
313697 GAGAATAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
22 20 0.40
23 11 0.22
24 19 0.38
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (23 bp):
TTTATTTATTATTCATGAATATG
Found at i:313912 original size:2 final size:2
Alignment explanation
Indices: 313905--313943 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
313895 TTTTGGACCC
313905 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
313944 AAAGTATATT
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:317234 original size:318 final size:312
Alignment explanation
Indices: 316683--317282 Score: 668
Period size: 318 Copynumber: 1.9 Consensus size: 312
316673 TTGTAATTCT
* *
316683 TAGGTGAATAATTAAGAATTATTTTTTAAAATAAATTTAATTTAAATAAATTAAATTGTCAATAT
1 TAGGTGAATAATTAAGAATTATTTCTTAAAATAAATTTAATTTAAATAAATCAAATTGTCAATAT
* *
316748 AATTATAAATCTTTAAATTAAAAAAATTAATAATGAATCAGACTAAATTCATTTGTTTCATGATT
66 AATTACAAATCTTTAAATTAAAAAAATTAATAATCAAT---ACTAAATTCATTTGTTTCATGATT
* ** * * *
316813 GATTTTTTTCTAAATATATTGTTTTTTTTTAATATGAAATCAAATCAAATATATTTATTAGTGGA
128 GATTTTTTTCTAAATAAATAATTTTTTTTTAATATAAAATCAAATCAAATAAATTTATTAGTAGA
* * * * * *
316878 CTCATGTTGTCTTATCTATGAATTTAATTGAGAGTGA-TTTAAGATAAA-T-ATTA-ATAAGAAT
193 CACATGTTATCTTATATATAAATTTAATTGAAAGTGATTTTAA-A-AAACTAATTATAAAAGAAT
316939 AGATGTAATTAATTGATTTTTAAAGCTATAGTTATCTTTTTTTTTAAAAATTTAATTTG
256 --ATGTAATTAATTGATTTTTAAAGCTATAGTTATCTTTTTTTTTAAAAATTTAATTTG
* * *
316998 TAGGTGAATAATTGAGAATTGTTTCTTAAAATAAATTT-ATTTAAATAAGTCAAATTGTCAA-AG
1 TAGGTGAATAATTAAGAATTATTTCTTAAAATAAATTTAATTTAAATAAATCAAATTGTCAATA-
* * * * *
317061 TAATTGCATATCTTTAGATTTAAGACAATTAATAATCAAT-C-AAA-TCTATTTGTTTCATGATT
65 TAATTACAAATCTTTA-AATTAAAAAAATTAATAATCAATACTAAATTC-ATTTGTTTCATGATT
*
317123 GATTTTTCTT-TGAATAAATCAATTTTTTAAATTTAAAAAGTATAAAATCAAATCAAATAAATTT
128 GATTTTT-TTCTAAATAAAT-AATTTTTT---TTT---AA-TATAAAATCAAATCAAATAAATTT
317187 ATTAAG-AGACACATGTTAAT-TTATATATAAATTTAATT-ATAAGTGATTTTAAAAAACTAATT
184 ATT-AGTAGACACATGTT-ATCTTATATATAAATTTAATTGA-AAGTGATTTTAAAAAACTAATT
* *
317249 ATAAAAGAATATTTAATTAATTGATTTTTGAAGC
246 ATAAAAGAATATGTAATTAATTGATTTTTAAAGC
317283 ATAAGTCAAA
Statistics
Matches: 239, Mismatches: 27, Indels: 35
0.79 0.09 0.12
Matches are distributed among these distances:
309 2 0.01
310 32 0.13
311 9 0.04
313 1 0.00
314 37 0.15
315 54 0.23
317 6 0.03
318 79 0.33
319 12 0.05
320 7 0.03
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (312 bp):
TAGGTGAATAATTAAGAATTATTTCTTAAAATAAATTTAATTTAAATAAATCAAATTGTCAATAT
AATTACAAATCTTTAAATTAAAAAAATTAATAATCAATACTAAATTCATTTGTTTCATGATTGAT
TTTTTTCTAAATAAATAATTTTTTTTTAATATAAAATCAAATCAAATAAATTTATTAGTAGACAC
ATGTTATCTTATATATAAATTTAATTGAAAGTGATTTTAAAAAACTAATTATAAAAGAATATGTA
ATTAATTGATTTTTAAAGCTATAGTTATCTTTTTTTTTAAAAATTTAATTTG
Found at i:317686 original size:17 final size:18
Alignment explanation
Indices: 317661--317715 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
317651 AAAAATTTTA
317661 AAATA-TTAA-AAATAAT
1 AAATATTTAATAAATAAT
317677 AAATATTTAATAAA-AAT
1 AAATATTTAATAAATAAT
317694 ATATATATTTAATTAAATAAT
1 A-A-ATATTTAA-TAAATAAT
317715 A
1 A
317716 TGATTTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
16 5 0.15
17 8 0.24
18 4 0.12
19 8 0.24
20 4 0.12
21 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTTAATAAATAAT
Found at i:317691 original size:19 final size:19
Alignment explanation
Indices: 317669--317715 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
317659 TAAAATATTA
317669 AAAATAATAAATATTTAAT
1 AAAATAATAAATATTTAAT
*
317688 AAAA-ATATATATATTTAAT
1 AAAATA-ATAAATATTTAAT
*
317707 TAAATAATA
1 AAAATAATA
317716 TGATTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.04
19 22 0.92
20 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATAATAAATATTTAAT
Found at i:317716 original size:17 final size:18
Alignment explanation
Indices: 317667--317721 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
317657 TTTAAAATAT
317667 TAAAAATAATAAATATTTAA
1 TAAAAATAAT--ATATTTAA
317687 TAAAAATATATATATTTAA
1 TAAAAATA-ATATATTTAA
*
317706 T-TAAATAATATGATTT
1 TAAAAATAATAT-ATTT
317722 TTTGATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 4 0.12
18 9 0.28
19 9 0.28
20 8 0.25
21 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
TAAAAATAATATATTTAA
Found at i:320424 original size:52 final size:52
Alignment explanation
Indices: 320325--320424 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
320315 TATAAACAAA
*
320325 ATGATTAAATAAACTAACTGCAAAATGGGTAATCCCATGGATGCTTATGCTT
1 ATGATTAAATAAACTAACTGCAAAATGGGTAATCCCATGGATACTTATGCTT
* *
320377 ATGATTAAATAAACTAACTGCAAAATGGGTAATCCTATGGGTACTTAT
1 ATGATTAAATAAACTAACTGCAAAATGGGTAATCCCATGGATACTTAT
320425 ATGGCACGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (52 bp):
ATGATTAAATAAACTAACTGCAAAATGGGTAATCCCATGGATACTTATGCTT
Found at i:335831 original size:32 final size:33
Alignment explanation
Indices: 335790--335851 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
335780 GAATATGTTT
* *
335790 AAATTTATATAATATTAATTATTAA-AATATTA
1 AAATTTATATAAAAATAATTATTAATAATATTA
*
335822 AAATTTATATAAAAATAATTTTTAATAATA
1 AAATTTATATAAAAATAATTATTAATAATA
335852 ATTATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AAATTTATATAAAAATAATTATTAATAATATTA
Found at i:335895 original size:28 final size:30
Alignment explanation
Indices: 335828--335895 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 30
335818 ATTAAAATTT
* * * *
335828 ATATAAAAATAATTTTTAATAATAATTATA
1 ATATAAAAATAATTATAAATAACAATAATA
335858 ATATAAAAATAA-TATAAAT-ACAATAATA
1 ATATAAAAATAATTATAAATAACAATAATA
335886 ATATAAAAAT
1 ATATAAAAAT
335896 TACAAGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 17 0.50
29 5 0.15
30 12 0.35
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (30 bp):
ATATAAAAATAATTATAAATAACAATAATA
Found at i:335900 original size:20 final size:17
Alignment explanation
Indices: 335845--335892 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
335835 AATAATTTTT
335845 AATAATAATTATAATATA-
1 AATAATAA-TATAA-ATAC
335863 AA-AATAATATAAATAC
1 AATAATAATATAAATAC
335879 AATAATAATATAAA
1 AATAATAATATAAA
335893 AATTACAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.11
16 7 0.25
17 16 0.57
18 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAATAATATAAATAC
Found at i:337239 original size:2 final size:2
Alignment explanation
Indices: 337232--337256 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
337222 AACTTTATGA
337232 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
337257 ATGTTGAATT
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:337925 original size:24 final size:24
Alignment explanation
Indices: 337879--337929 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
337869 AAGCATGTAA
337879 TTTTTTACAAAATAAGTAGATTTT
1 TTTTTTACAAAATAAGTAGATTTT
* *
337903 TTTTTTGATAAAATAGGTA-ATTTT
1 TTTTTT-ACAAAATAAGTAGATTTT
337927 TTT
1 TTT
337930 AAAGAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTTTTACAAAATAAGTAGATTTT
Found at i:338440 original size:30 final size:29
Alignment explanation
Indices: 338406--338543 Score: 172
Period size: 30 Copynumber: 4.7 Consensus size: 29
338396 TTACTTTTAG
*
338406 AATTTATTTGAATACAAATTAAAGATTAA
1 AATTTATTTAAATACAAATTAAAGATTAA
*
338435 CAATTTATTTAAATACAAATTAAAAATTAA
1 -AATTTATTTAAATACAAATTAAAGATTAA
*
338465 AATTTATTTAAATATAAATTAAAGATTAA
1 AATTTATTTAAATACAAATTAAAGATTAA
* *
338494 TAATGTATTTAAATATAATAATTAAA-ATATAA
1 -AATTTATTTAAATA-CA-AATTAAAGAT-TAA
338526 AATTTATTTAAATA-AAAT
1 AATTTATTTAAATACAAAT
338544 GATAAGGTTC
Statistics
Matches: 97, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
28 3 0.03
29 28 0.29
30 40 0.41
31 16 0.16
32 10 0.10
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (29 bp):
AATTTATTTAAATACAAATTAAAGATTAA
Done.