Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold262
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: 1141274
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 8
Found at i:258425 original size:17 final size:17
Alignment explanation
Indices: 258397--258449 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
258387 TTGTAATGAA
258397 TTATATTTTTTTTTTATT
1 TTATA-TTTTTTTTTATT
* *
258415 TTTTATTTTTTTTAATT
1 TTATATTTTTTTTTATT
*
258432 TTATCTTTTTTTTTATT
1 TTATATTTTTTTTTATT
258449 T
1 T
258450 ATAAAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (17 bp):
TTATATTTTTTTTTATT
Found at i:258433 original size:22 final size:22
Alignment explanation
Indices: 258408--258450 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
258398 TATATTTTTT
*
258408 TTTTAT-TTTTTATTTTTTTTAA
1 TTTTATCTTTTT-TTTTATTTAA
258430 TTTTATCTTTTTTTTTATTTA
1 TTTTATCTTTTTTTTTATTTA
258451 TAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTATCTTTTTTTTTATTTAA
Found at i:258450 original size:16 final size:16
Alignment explanation
Indices: 258403--258451 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
258393 TGAATTATAT
*
258403 TTTTTTTTTATTT-TT
1 TTTTTTTTTATTTATC
258418 TATTTTTTTTAATTTTATC
1 T-TTTTTTTT-A-TTTATC
258437 TTTTTTTTTATTTAT
1 TTTTTTTTTATTTAT
258452 AAAAAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 1 0.03
16 13 0.45
17 2 0.07
18 11 0.38
19 2 0.07
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTATTTATC
Found at i:259610 original size:11 final size:11
Alignment explanation
Indices: 259594--259623 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
259584 GAATTCGAAT
*
259594 AATAATATTTA
1 AATAATAATTA
259605 AATAATAATTA
1 AATAATAATTA
259616 AATAATAA
1 AATAATAA
259624 AAAAAATTTA
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATAATAATTA
Found at i:259909 original size:18 final size:18
Alignment explanation
Indices: 259886--259932 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
259876 ATTTTTATAT
259886 TTAAAATAACTCAAAAAA
1 TTAAAATAACTCAAAAAA
259904 TTAAAAATAA-TC-AAAAA
1 TT-AAAATAACTCAAAAAA
*
259921 -TAAATTAACTCA
1 TTAAAATAACTCA
259933 TAATTTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 6 0.24
16 3 0.12
17 5 0.20
18 4 0.16
19 7 0.28
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.26
Consensus pattern (18 bp):
TTAAAATAACTCAAAAAA
Found at i:260466 original size:13 final size:15
Alignment explanation
Indices: 260433--260462 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
260423 ATTTAATAAA
260433 TAATAAAATAAATTT
1 TAATAAAATAAATTT
*
260448 TAATAATATAAATTT
1 TAATAAAATAAATTT
260463 ATAAGTTAAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATAAAATAAATTT
Found at i:260555 original size:21 final size:21
Alignment explanation
Indices: 260531--260590 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 21
260521 TTTTATAAAC
260531 TTAAATATATTATTTATTTTA
1 TTAAATATATTATTTATTTTA
* *
260552 TTAAA-A-AATATTT-TTATA
1 TTAAATATATTATTTATTTTA
*
260570 TT-AATAT-TTATATATTTTA
1 TTAAATATATTATTTATTTTA
260589 TT
1 TT
260591 TTTAAATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
17 2 0.06
18 11 0.35
19 12 0.39
20 1 0.03
21 5 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAATATATTATTTATTTTA
Found at i:260577 original size:14 final size:14
Alignment explanation
Indices: 260558--260600 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
260548 TTTATTAAAA
260558 AATATTTTTATATT
1 AATATTTTTATATT
*
260572 AATATTTATATATT
1 AATATTTTTATATT
* *
260586 -TTATTTTTAAATT
1 AATATTTTTATATT
260599 AA
1 AA
260601 AATAAAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:260621 original size:21 final size:21
Alignment explanation
Indices: 260597--260640 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
260587 TATTTTTAAA
*
260597 TTAAAATAAAAATATATTATT
1 TTAAAATAAAAAAATATTATT
**
260618 TTAATTTAAAAAAATATTATT
1 TTAAAATAAAAAAATATTATT
260639 TT
1 TT
260641 TAATACATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAATAAAAAAATATTATT
Found at i:262301 original size:14 final size:14
Alignment explanation
Indices: 262279--262309 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
262269 TTGATTTTTT
*
262279 TAATTTATTAAATA
1 TAATATATTAAATA
262293 TAATATATTAAATA
1 TAATATATTAAATA
262307 TAA
1 TAA
262310 AAATAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATATATTAAATA
Found at i:263795 original size:18 final size:19
Alignment explanation
Indices: 263761--263796 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
263751 TTAGATATCT
263761 CATATTAATAGTATTTTAA
1 CATATTAATAGTATTTTAA
*
263780 CATATT-ATATTATTTTA
1 CATATTAATAGTATTTTA
263797 TATTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (19 bp):
CATATTAATAGTATTTTAA
Found at i:264395 original size:20 final size:21
Alignment explanation
Indices: 264360--264399 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
264350 TATTTTATAT
*
264360 TTATTAAAATATAAAATTATG
1 TTATTAAAATAAAAAATTATG
264381 TTATT-AAATAAAAAATTAT
1 TTATTAAAATAAAAAATTAT
264400 TTTACTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TTATTAAAATAAAAAATTATG
Found at i:264453 original size:20 final size:22
Alignment explanation
Indices: 264407--264451 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
264397 TATTTTACTA
264407 TTTATTATATTATTAATAATTT
1 TTTATTATATTATTAATAATTT
264429 TTTATTA-A-TATTAATATATTT
1 TTTATTATATTATTAATA-ATTT
264450 TT
1 TT
264452 ATAATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 7 0.32
22 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATTATATTATTAATAATTT
Found at i:264456 original size:19 final size:19
Alignment explanation
Indices: 264405--264456 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
264395 ATTATTTTAC
*
264405 TATTTATTATATTATTAATA
1 TATTT-TTATAATATTAATA
264425 -ATTTTTTATTAATATTAATA
1 TA-TTTTTA-TAATATTAATA
264445 TATTTTTATAAT
1 TATTTTTATAAT
264457 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 8 0.29
20 19 0.68
21 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTATAATATTAATA
Found at i:266671 original size:23 final size:25
Alignment explanation
Indices: 266645--266699 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
266635 ATATAATTAT
*
266645 TAAATTA-AATATTTTAAA-TTTAA
1 TAAATTATAATATATTAAATTTTAA
*
266668 TAAA-AATAATATATTAAATTTTAA
1 TAAATTATAATATATTAAATTTTAA
*
266692 AAAATTAT
1 TAAATTAT
266700 TAAAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 14 0.56
24 8 0.32
25 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAAATTATAATATATTAAATTTTAA
Found at i:266936 original size:32 final size:33
Alignment explanation
Indices: 266869--266949 Score: 110
Period size: 32 Copynumber: 2.4 Consensus size: 33
266859 TTCAATATCT
*
266869 ATTTAAATAATATAAAATATAATAAAATATTAAA
1 ATTTATATAATAT-AAATATAATAAAATATTAAA
* *
266903 ATTTATATAATATAAAT-TATTAATATATTAAA
1 ATTTATATAATATAAATATAATAAAATATTAAA
266935 ATTTATATAAATATA
1 ATTTATAT-AATATA
266950 TAAAATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 21 0.49
33 10 0.23
34 12 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
ATTTATATAATATAAATATAATAAAATATTAAA
Found at i:267420 original size:20 final size:19
Alignment explanation
Indices: 267392--267455 Score: 75
Period size: 17 Copynumber: 3.6 Consensus size: 19
267382 CATTCAGCTC
267392 ATTTCTTATATTTAAATATT
1 ATTT-TTATATTTAAATATT
*
267412 ATTTAT-TA-TTAAA-ATT
1 ATTTTTATATTTAAATATT
267428 -TTTTTATATTTAAATATT
1 ATTTTTATATTTAAATATT
267446 ATTTTT-TATT
1 ATTTTTATATT
267456 ATATTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 4 0.11
16 5 0.13
17 10 0.26
18 9 0.24
19 6 0.16
20 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTATATTTAAATATT
Found at i:267426 original size:18 final size:18
Alignment explanation
Indices: 267400--267456 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
267390 TCATTTCTTA
*
267400 TATTTAAATATTATTTAT
1 TATTAAAATATTATTTAT
*
267418 TATTAAAAT-TTTTTTA-
1 TATTAAAATATTATTTAT
* *
267434 TATTTAAATATTATTTTT
1 TATTAAAATATTATTTAT
267452 TATTA
1 TATTA
267457 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 8 0.26
17 11 0.35
18 12 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTAAAATATTATTTAT
Found at i:267738 original size:6 final size:7
Alignment explanation
Indices: 267718--267749 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
267708 TGTTTATTTT
267718 ATTAAAA
1 ATTAAAA
267725 ATTAAAA
1 ATTAAAA
267732 ATTAAAA
1 ATTAAAA
267739 ATTAAAA
1 ATTAAAA
267746 ATTA
1 ATTA
267750 TTATTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
ATTAAAA
Found at i:268800 original size:23 final size:22
Alignment explanation
Indices: 268773--268817 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
268763 TATTTAATTA
*
268773 AATATTTTAAATTTAATAAAAAT
1 AATATATTAAATTTAA-AAAAAT
*
268796 AATATATTAAATTTTAAAAAAT
1 AATATATTAAATTTAAAAAAAT
268818 TATTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATATATTAAATTTAAAAAAAT
Found at i:268835 original size:30 final size:29
Alignment explanation
Indices: 268745--268846 Score: 84
Period size: 32 Copynumber: 3.4 Consensus size: 29
268735 TTATGATGAT
**
268745 AATTTTAAAAAA-TATAATTATTTAATTA
1 AATTTTAAAAAATTATAAAAATTTAATTA
* * *
268773 AATATTT-TAAATTTAATAAAAATAATATATTA
1 AAT-TTTAAAAAATT-ATAAAAAT-TTA-ATTA
268805 AATTTTAAAAAATTATTAAAAATTTAATT-
1 AATTTTAAAAAATTA-TAAAAATTTAATTA
*
268834 AATATTAAAAAAT
1 AATTTTAAAAAAT
268847 GGCTTAAACT
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
28 6 0.10
29 16 0.28
30 9 0.16
31 8 0.14
32 19 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AATTTTAAAAAATTATAAAAATTTAATTA
Found at i:269019 original size:18 final size:18
Alignment explanation
Indices: 268998--269044 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
268988 AAAATAATAA
*
268998 AAAATATATT-AATATATT
1 AAAATTTATTAAATAT-TT
269016 AAAATTTATATAAATATTT
1 AAAATTTAT-TAAATATTT
269035 AAAATTTATT
1 AAAATTTATT
269045 CATAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 9 0.35
19 12 0.46
20 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATTTATTAAATATTT
Found at i:269036 original size:19 final size:20
Alignment explanation
Indices: 269002--269043 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
268992 TAATAAAAAA
*
269002 TATATTAATATATTAAAATT
1 TATATAAATATATTAAAATT
269022 TATATAAATAT-TTAAAATT
1 TATATAAATATATTAAAATT
269041 TAT
1 TAT
269044 TCATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATAAATATATTAAAATT
Found at i:269871 original size:21 final size:21
Alignment explanation
Indices: 269832--269886 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
269822 CTTATTAAAA
*
269832 AATTAAAATT-TAT-TTTTAT
1 AATTAAATTTATATATTTTAT
269851 AA-TAATATTTATATATTTTAT
1 AATTAA-ATTTATATATTTTAT
269872 AATTAAATTTATATA
1 AATTAAATTTATATA
269887 AAATATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 3 0.10
19 5 0.16
20 3 0.10
21 17 0.55
22 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTAAATTTATATATTTTAT
Found at i:270562 original size:20 final size:21
Alignment explanation
Indices: 270537--270586 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
270527 ATTAAATTTA
270537 AATTTAATTATAGTAATA-TG
1 AATTTAATTATAGTAATACTG
* ** *
270557 AATTTAAATATTTTAATACTT
1 AATTTAATTATAGTAATACTG
270578 AATTTAATT
1 AATTTAATT
270587 TAACCTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (21 bp):
AATTTAATTATAGTAATACTG
Found at i:274756 original size:2 final size:2
Alignment explanation
Indices: 274749--274807 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
274739 GCATGTCTGT
274749 GA GA GA 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 GA GA GA
274791 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
274808 GAATATATGC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:276853 original size:22 final size:22
Alignment explanation
Indices: 276801--276843 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
276791 TTATTTTTGT
*
276801 AAATTA-TTAAAGTTTATTTAA
1 AAATTATTTAAAGTTGATTTAA
276822 AAATTATTTAAAGTTGATTTAA
1 AAATTATTTAAAGTTGATTTAA
276844 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (22 bp):
AAATTATTTAAAGTTGATTTAA
Found at i:276972 original size:6 final size:6
Alignment explanation
Indices: 276963--276995 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
276953 AAAAAAATAT
276963 AATTTA AATTTA AATTTA AATTTA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AAT
276996 AAAAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:277001 original size:18 final size:18
Alignment explanation
Indices: 276963--277001 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
276953 AAAAAAATAT
**
276963 AATTTAAATTTAAATTTA
1 AATTTAAATTTAAATAAA
276981 AATTTAAATTTAAATAAA
1 AATTTAAATTTAAATAAA
276999 AAT
1 AAT
277002 AATAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAAATTTAAATAAA
Found at i:277154 original size:25 final size:25
Alignment explanation
Indices: 277106--277152 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
277096 TTTTTATTTT
* *
277106 AAATTTAGTTTGAATTTTAAAAATA
1 AAATTTAATTTGAATTTAAAAAATA
277131 AAATTTAATTT-AATTTAAAAAA
1 AAATTTAATTTGAATTTAAAAAA
277153 ATTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AAATTTAATTTGAATTTAAAAAATA
Found at i:280804 original size:19 final size:21
Alignment explanation
Indices: 280780--280820 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
280770 TTTGTTTTGG
280780 AATAATAT-T-TTTTAATTAA
1 AATAATATATATTTTAATTAA
*
280799 AATAATATATATTTTATTTAA
1 AATAATATATATTTTAATTAA
280820 A
1 A
280821 TTTAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATAATATATATTTTAATTAA
Found at i:283466 original size:25 final size:25
Alignment explanation
Indices: 283435--283538 Score: 89
Period size: 25 Copynumber: 4.3 Consensus size: 25
283425 TGATTGTAAA
*
283435 TATAATAAATATT-ATTATAATTAAT
1 TATAATAAATATTAATTATAAAT-AT
283460 TATAATAAATATTAATTATAAATAT
1 TATAATAAATATTAATTATAAATAT
283485 TGATAATAAA-A--AATTA-AAATTAT
1 T-ATAATAAATATTAATTATAAA-TAT
*
283508 TA-AATAAAAATCATAA-TAT-AATAT
1 TATAATAAATAT--TAATTATAAATAT
283532 TATAATA
1 TATAATA
283539 CTATTTAAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 20
0.76 0.01 0.22
Matches are distributed among these distances:
21 6 0.09
22 5 0.07
23 9 0.13
24 5 0.07
25 25 0.37
26 18 0.26
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (25 bp):
TATAATAAATATTAATTATAAATAT
Found at i:283493 original size:13 final size:12
Alignment explanation
Indices: 283435--283538 Score: 79
Period size: 13 Copynumber: 8.6 Consensus size: 12
283425 TGATTGTAAA
283435 TATAATAAATAT
1 TATAATAAATAT
* *
283447 TATTATAATTAAT
1 TATAATAAAT-AT
283460 TATAATAAATAT
1 TATAATAAATAT
*
283472 TAATTATAAATAT
1 T-ATAATAAATAT
* *
283485 TGATAATAAAAAA
1 T-ATAATAAATAT
*
283498 T-TAA-AATTAT
1 TATAATAAATAT
*
283508 TA-AATAAAAAT
1 TATAATAAATAT
*
283519 CATAATATAATAT
1 TATAATA-AATAT
283532 TATAATA
1 TATAATA
283539 CTATTTAAAT
Statistics
Matches: 69, Mismatches: 17, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
10 6 0.09
11 8 0.12
12 15 0.22
13 40 0.58
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (12 bp):
TATAATAAATAT
Found at i:283828 original size:13 final size:13
Alignment explanation
Indices: 283810--283859 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
283800 ATTTATTTTT
*
283810 TAAAATAATTAAA
1 TAAAATATTTAAA
283823 TAAAATATTTAAA
1 TAAAATATTTAAA
*
283836 TTAAAT-TTTAAA
1 TAAAATATTTAAA
283848 TAAAA-ATTTAAA
1 TAAAATATTTAAA
283860 AGAGAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
12 16 0.48
13 17 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATTTAAA
Found at i:283847 original size:12 final size:12
Alignment explanation
Indices: 283818--283859 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
283808 TTTAAAATAA
283818 TTAAATAAAATAT
1 TTAAATAAAAT-T
*
283831 TTAAATTAAATT
1 TTAAATAAAATT
*
283843 TTAAATAAAAAT
1 TTAAATAAAATT
283855 TTAAA
1 TTAAA
283860 AGAGAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TTAAATAAAATT
Found at i:283867 original size:25 final size:25
Alignment explanation
Indices: 283818--283867 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
283808 TTTAAAATAA
**
283818 TTAAATAAAATATTTAAATTAAATT
1 TTAAATAAAATATTTAAAAGAAATT
283843 TTAAATAAAA-ATTTAAAAGAGAATT
1 TTAAATAAAATATTTAAAAGA-AATT
283868 AAAATGTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TTAAATAAAATATTTAAAAGAAATT
Found at i:283953 original size:30 final size:30
Alignment explanation
Indices: 283917--283974 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
283907 TTTATTATTA
283917 ATATTAATAATTA-ATATGTTATAATTAATC
1 ATATTAATAATTATATAT-TTATAATTAATC
*
283947 ATATTAATATTTATTATATTTATAATTA
1 ATATTAATAATTA-TATATTTATAATTA
283975 TAATATACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 12 0.48
31 9 0.36
32 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
ATATTAATAATTATATATTTATAATTAATC
Found at i:285817 original size:24 final size:24
Alignment explanation
Indices: 285781--285826 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
285771 ATGGTTATTT
*
285781 TTGTATGTAAAAAATGGTGGCTTG
1 TTGTATGTAAAAAATGATGGCTTG
* * *
285805 TTGTTTGTCAAAATTGATGGCT
1 TTGTATGTAAAAAATGATGGCT
285827 AATTTTTATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (24 bp):
TTGTATGTAAAAAATGATGGCTTG
Found at i:288220 original size:21 final size:22
Alignment explanation
Indices: 288191--288236 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
288181 TGTTCAGACA
** *
288191 AGTAGTACTCCGTAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
288213 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
288234 AGT
1 AGT
288237 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:290172 original size:28 final size:29
Alignment explanation
Indices: 290140--290203 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 29
290130 AAATGCCACC
290140 CTTTGTATTTGTCAAATATGGTGATT-TT
1 CTTTGTATTTGTCAAATATGGTGATTATT
* *
290168 CTTTGTATTTGTTAAATATGGTGGTTATT
1 CTTTGTATTTGTCAAATATGGTGATTATT
290197 -TTTGTAT
1 CTTTGTAT
290204 GTAAAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.20, C:0.05, G:0.19, T:0.56
Consensus pattern (29 bp):
CTTTGTATTTGTCAAATATGGTGATTATT
Found at i:290234 original size:24 final size:26
Alignment explanation
Indices: 290175--290241 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 26
290165 TTTCTTTGTA
* * *
290175 TTTGTTAAATATGGTGGTTATTTTTG
1 TTTGTAAAAAATGGTGGTTATTGTTG
*
290201 TATGTAAAAAATGGTGG-T-TTGTTG
1 TTTGTAAAAAATGGTGGTTATTGTTG
* *
290225 TTTGTCAAAATTGGTGG
1 TTTGTAAAAAATGGTGG
290242 CTAATTTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 19 0.56
25 1 0.03
26 14 0.41
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.48
Consensus pattern (26 bp):
TTTGTAAAAAATGGTGGTTATTGTTG
Found at i:292178 original size:6 final size:6
Alignment explanation
Indices: 292169--292201 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
292159 AATGCCATCG
292169 CCACCT CCACCT CCACCT CCACCT CCACCT CCA
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCA
292202 ACCTTCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.67, G:0.00, T:0.15
Consensus pattern (6 bp):
CCACCT
Found at i:292448 original size:22 final size:22
Alignment explanation
Indices: 292397--292457 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
292387 TTACTTTTTG
* *
292397 TAATATAATTATATTCTAAATAT
1 TAATATATTTATA-TATAAATAT
* *
292420 TATTATATATT-TATATAAATTT
1 TAATATAT-TTATATATAAATAT
292442 TAATATATTTATATAT
1 TAATATATTTATATAT
292458 TTATATTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.06
22 19 0.61
23 8 0.26
24 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATATTTATATATAAATAT
Found at i:292478 original size:28 final size:26
Alignment explanation
Indices: 292417--292479 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 26
292407 ATATTCTAAA
292417 TATTA-TTATATATTTATATAAATTT
1 TATTATTTATATATTTATATAAATTT
*
292442 TAATATATTTATATATTTATATTATATTT
1 T-AT-TATTTATATATTTATA-TAAATTT
292471 GTATTATTT
1 -TATTATTT
292480 TTTGTATCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 1 0.03
26 2 0.06
27 2 0.06
28 18 0.56
29 8 0.25
30 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTATTTATATATTTATATAAATTT
Found at i:294918 original size:10 final size:11
Alignment explanation
Indices: 294870--294960 Score: 53
Period size: 11 Copynumber: 7.9 Consensus size: 11
294860 AAGACACCTC
294870 ATAAACAAT-AT
1 ATAAA-AATAAT
* *
294881 ATGAAACTAAT
1 ATAAAAATAAT
*
294892 -TAAAAATAAC
1 ATAAAAATAAT
294902 ATAAAAATAAT
1 ATAAAAATAAT
294913 ATAAAAA-AAT
1 ATAAAAATAAT
*
294923 ACAAATATATGAAT
1 ATAAA-A-AT-AAT
*
294937 ATATCAAAATTTAT
1 ATA--AAAA-TAAT
294951 ATAAAAATAA
1 ATAAAAATAA
294961 CTATTAATGT
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
10 16 0.26
11 25 0.41
12 5 0.08
14 11 0.18
15 2 0.03
16 2 0.03
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.27
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:295679 original size:20 final size:20
Alignment explanation
Indices: 295650--295689 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
295640 AATTAAAAAA
*
295650 ATTATAAATATTTTATTATT
1 ATTATAAATATTTTAATATT
*
295670 ATTATTAATATTTTAATATT
1 ATTATAAATATTTTAATATT
295690 CTTTTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATAAATATTTTAATATT
Found at i:297669 original size:21 final size:19
Alignment explanation
Indices: 297643--297695 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
297633 TGTATATATA
297643 TATATATATGGAAAAAATGTG
1 TATATATAT--AAAAAATGTG
* *
297664 TATATATATATAGAATGTG
1 TATATATATAAAAAATGTG
297683 TATATATATAAAA
1 TATATATATAAAA
297696 GAAAGTGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 19 0.68
21 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (19 bp):
TATATATATAAAAAATGTG
Found at i:298443 original size:16 final size:17
Alignment explanation
Indices: 298411--298444 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
298401 TTATTTTTAA
*
298411 TTTAATAATATTAATTT
1 TTTAAGAATATTAATTT
298428 TTTAAGAATA-TAATTT
1 TTTAAGAATATTAATTT
298444 T
1 T
298445 AAAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAGAATATTAATTT
Found at i:299230 original size:15 final size:15
Alignment explanation
Indices: 299203--299250 Score: 73
Period size: 14 Copynumber: 3.3 Consensus size: 15
299193 TAACGTGGTT
299203 TTTTAAAAT-TATTA
1 TTTTAAAATATATTA
299217 TTTTAAAATATATTA
1 TTTTAAAATATATTA
299232 -TTTAAAATATAATTA
1 TTTTAAAATAT-ATTA
299247 TTTT
1 TTTT
299251 TATTATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 19 0.61
15 9 0.29
16 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTAAAATATATTA
Found at i:300708 original size:25 final size:25
Alignment explanation
Indices: 300672--300728 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
300662 AAATTTAGGG
300672 TTTTA-ATCTTAATATATACAA-TTAT
1 TTTTATATCTTAA-AT-TACAACTTAT
*
300697 TTTTATAT-TTAAATTACAACTTTT
1 TTTTATATCTTAAATTACAACTTAT
300721 TTTTATAT
1 TTTTATAT
300729 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.17
24 13 0.45
25 9 0.31
26 2 0.07
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTTATATCTTAAATTACAACTTAT
Found at i:302326 original size:20 final size:20
Alignment explanation
Indices: 302269--302332 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
302259 CAAACTTTTA
*
302269 ATATTATTTTCATATGTATT
1 ATATTATTTTCATATTTATT
* *
302289 AAATATATAATATCATATTTATT
1 --ATAT-TATTTTCATATTTATT
302312 ATATTATTTTCATATTTATT
1 ATATTATTTTCATATTTATT
302332 A
1 A
302333 CACGTATCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 15 0.42
21 4 0.11
22 4 0.11
23 13 0.36
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
ATATTATTTTCATATTTATT
Found at i:304346 original size:2 final size:2
Alignment explanation
Indices: 304339--304367 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
304329 AAGAAAATGA
304339 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
304368 GAATTGTCTA
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:304681 original size:12 final size:13
Alignment explanation
Indices: 304649--304679 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
304639 TAAGTTATGT
304649 TTTATTTATTATA
1 TTTATTTATTATA
304662 -TTATTTATTATA
1 TTTATTTATTATA
304674 TTTATT
1 TTTATT
304680 ATATATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTATTATA
Found at i:307707 original size:2 final size:2
Alignment explanation
Indices: 307700--307738 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
307690 TTGTACCAAT
* * *
307700 TA TA TA TA TA CA TA TA TA TA TA TG TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
307739 GTATGTATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:307736 original size:20 final size:20
Alignment explanation
Indices: 307711--307748 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
307701 ATATATATAC
307711 ATATATATATATGTATGTAT
1 ATATATATATATGTATGTAT
*
307731 ATATATATGTATGTATGT
1 ATATATATATATGTATGT
307749 GAAGGTAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (20 bp):
ATATATATATATGTATGTAT
Found at i:307739 original size:16 final size:16
Alignment explanation
Indices: 307712--307746 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
307702 TATATATACA
307712 TATATATATATGTATG
1 TATATATATATGTATG
307728 TATATATATATGTATG
1 TATATATATATGTATG
307744 TAT
1 TAT
307747 GTGAAGGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (16 bp):
TATATATATATGTATG
Found at i:310960 original size:3 final size:3
Alignment explanation
Indices: 310952--310997 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
310942 AGCAACTAGG
310952 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
310998 TTTTTTGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:313018 original size:36 final size:37
Alignment explanation
Indices: 312945--313021 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
312935 ATTATTATTT
*
312945 AATATTTTTTAAATTTTAATTTAATTATAATATATAA
1 AATATTTTTTAAATTTTAATTCAATTATAATATATAA
* *
312982 AATATTTTTTATATTTTAATATCACTTA-AATA-ATAA
1 AATATTTTTTAAATTTTAAT-TCAATTATAATATATAA
313018 AATA
1 AATA
313022 AAATATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 8 0.22
37 23 0.64
38 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (37 bp):
AATATTTTTTAAATTTTAATTCAATTATAATATATAA
Found at i:313357 original size:21 final size:21
Alignment explanation
Indices: 313333--313377 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
313323 AAACATTAAG
**
313333 ATTTAATTTAATTTTTTTATA
1 ATTTAATTTAATAATTTTATA
* *
313354 ATTTTATTTACTAATTTTATA
1 ATTTAATTTAATAATTTTATA
313375 ATT
1 ATT
313378 AATATTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTAATTTAATAATTTTATA
Found at i:313370 original size:13 final size:12
Alignment explanation
Indices: 313341--313373 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
313331 AGATTTAATT
313341 TAATTTT-TTTA
1 TAATTTTATTTA
313352 TAATTTTATTTA
1 TAATTTTATTTA
313364 CTAATTTTAT
1 -TAATTTTAT
313374 AATTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 4 0.20
13 9 0.45
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
TAATTTTATTTA
Found at i:313404 original size:3 final size:3
Alignment explanation
Indices: 313388--313474 Score: 65
Period size: 3 Copynumber: 29.3 Consensus size: 3
313378 AATATTTATT
* * * * *
313388 ATA ATTA ATC ATA ATA ATA TTA ATT AT- ATCA ATA ATT TTA ATA A-A
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
*
313433 TATA AT- ATA AT- ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
313475 AAGCTTATGA
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
2 6 0.09
3 54 0.82
4 6 0.09
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:316581 original size:23 final size:23
Alignment explanation
Indices: 316537--316606 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
316527 ATTTAAAAAG
* * *
316537 TAAATTTAATATTAAATAAATAT
1 TAAATTTAATTTTTAATTAATAT
*
316560 TAAATTTAATTTTTAATTAATAA
1 TAAATTTAATTTTTAATTAATAT
* * *
316583 AAAATAT-ATTTTT-ATTAAAAT
1 TAAATTTAATTTTTAATTAATAT
316604 TAA
1 TAA
316607 TAACTTATAA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 8 0.21
22 6 0.16
23 24 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATTTAATTTTTAATTAATAT
Found at i:320687 original size:33 final size:34
Alignment explanation
Indices: 320647--320712 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
320637 TTTTGAGATG
* * *
320647 ATATTTATTTTTAATATTATTAAATTAA-ATAAT
1 ATATTTATCTGTAATACTATTAAATTAAGATAAT
*
320680 ATATTTATCTGTAATACTATTAATTTAAGATAA
1 ATATTTATCTGTAATACTATTAAATTAAGATAA
320713 AAAGAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (34 bp):
ATATTTATCTGTAATACTATTAAATTAAGATAAT
Found at i:321595 original size:3 final size:3
Alignment explanation
Indices: 321581--321618 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
321571 CTTCATATTT
* *
321581 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
321619 TAATCTCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:321910 original size:21 final size:19
Alignment explanation
Indices: 321871--321914 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
321861 TTCTTAAATT
*
321871 ATTTATTTAA-ATTTAAAA
1 ATTTATATAATATTTAAAA
321889 ATTTATATAATATTTATTAAA
1 ATTTATATAATATTTA--AAA
321910 ATTTA
1 ATTTA
321915 AAAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 5 0.23
21 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTATATAATATTTAAAA
Found at i:321929 original size:16 final size:17
Alignment explanation
Indices: 321903--321934 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
321893 ATATAATATT
321903 TATTAAAATTTAAAAAA
1 TATTAAAATTTAAAAAA
321920 TATT-AAATTTAAAAA
1 TATTAAAATTTAAAAA
321935 TAAATCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATTAAAATTTAAAAAA
Found at i:325509 original size:2 final size:2
Alignment explanation
Indices: 325502--325527 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
325492 TTAGCTTGCA
325502 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
325528 GGTTTTTTTC
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:326421 original size:2 final size:2
Alignment explanation
Indices: 326410--326451 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
326400 TAGAAATTAC
326410 TA TA -A TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
326449 TA T
1 TA T
326452 TTTGGCCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:328697 original size:32 final size:33
Alignment explanation
Indices: 328644--328729 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 33
328634 GATTATATTT
* * *
328644 TATATGTAT-TATATATTTTATATAAATTTTAA
1 TATATCTATATATTTATATTATATAAATTTTAA
* *
328676 TATAT-TA-ATAATTTTTATTATATAAATTTTGA
1 TATATCTATAT-ATTTATATTATATAAATTTTAA
328708 TATATCTATATATTTATATTAT
1 TATATCTATATATTTATATTAT
328730 GTTTGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 3 0.07
32 28 0.62
33 12 0.27
34 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (33 bp):
TATATCTATATATTTATATTATATAAATTTTAA
Found at i:328717 original size:18 final size:16
Alignment explanation
Indices: 328664--328726 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 16
328654 ATATATTTTA
328664 TATAAATTTTAATATAT
1 TATAAATTTT-ATATAT
*
328681 TAATAATTTTTAT-TA-
1 T-ATAAATTTTATATAT
328696 TATAAATTTTGATATAT
1 TATAAATTTT-ATATAT
*
328713 CTATATA-TTTATAT
1 -TATAAATTTTATAT
328727 TATGTTTGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 8 0.21
15 3 0.08
16 8 0.21
17 6 0.16
18 13 0.34
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
TATAAATTTTATATAT
Found at i:329582 original size:18 final size:18
Alignment explanation
Indices: 329559--329594 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
329549 ATTCAAGAGT
329559 TTTATATTTGTCCATGGA
1 TTTATATTTGTCCATGGA
329577 TTTATATTTGTCCATGGA
1 TTTATATTTGTCCATGGA
329595 CCGGACTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (18 bp):
TTTATATTTGTCCATGGA
Found at i:329762 original size:15 final size:15
Alignment explanation
Indices: 329711--329777 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 15
329701 ATAATATTTT
329711 TATTTAAA-T-TTAA
1 TATTTAAATTATTAA
*
329724 TTATATAAA-TATTAA
1 -TATTTAAATTATTAA
**
329739 TATAAAAATTATTAA
1 TATTTAAATTATTAA
329754 TATTTAAATTA-T-A
1 TATTTAAATTATTAA
329767 -ATTTAAATTAT
1 TATTTAAATTAT
329778 CGAGTCAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
12 10 0.22
13 1 0.02
14 16 0.35
15 19 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTTAAATTATTAA
Found at i:329769 original size:21 final size:22
Alignment explanation
Indices: 329711--329769 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
329701 ATAATATTTT
329711 TATTTAAATT-TAATTATATAA
1 TATTTAAATTATAATTATATAA
* *
329732 -ATATTAATATAAAAATTAT-TAA
1 TAT-TTAA-ATTATAATTATATAA
329754 TATTTAAATTATAATT
1 TATTTAAATTATAATT
329770 TAAATTATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
20 2 0.07
21 11 0.37
22 9 0.30
23 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTAAATTATAATTATATAA
Found at i:332258 original size:88 final size:87
Alignment explanation
Indices: 332105--332283 Score: 288
Period size: 88 Copynumber: 2.0 Consensus size: 87
332095 TGGACTAATG
* *
332105 TCCAAAGCTATGTCACTCGAACTCGGGAGAGAGTATCGAACACAGATATGTGTCTAACATAGATA
1 TCCAAAGCTATGTCACTCGAACTCGGGAGAGAGTATCGAACACAGATAAGTGTCCAACATAGATA
*
332170 TGTTCAATTTTTTTCTAAGTTTT
66 TGTTCAA-TTTTTTCCAAGTTTT
* *
332193 TCCAAAGCTATGTCACTCGAACTCGGGAGAGAGTATC-AGACACAGGTAAGTGTCCAACATGGAT
1 TCCAAAGCTATGTCACTCGAACTCGGGAGAGAGTATCGA-ACACAGATAAGTGTCCAACATAGAT
332257 ATGTTCAATTTTTTCCAAGTTTT
65 ATGTTCAATTTTTTCCAAGTTTT
332280 TCCA
1 TCCA
332284 TGTATTTAGA
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
87 19 0.22
88 66 0.78
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (87 bp):
TCCAAAGCTATGTCACTCGAACTCGGGAGAGAGTATCGAACACAGATAAGTGTCCAACATAGATA
TGTTCAATTTTTTCCAAGTTTT
Found at i:332692 original size:17 final size:17
Alignment explanation
Indices: 332670--332704 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
332660 ATGCAATTGC
332670 AATTTAAAGATCACAGA
1 AATTTAAAGATCACAGA
332687 AATTTAAAGATCACAGA
1 AATTTAAAGATCACAGA
332704 A
1 A
332705 CATATACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (17 bp):
AATTTAAAGATCACAGA
Found at i:335407 original size:14 final size:15
Alignment explanation
Indices: 335388--335416 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
335378 GCCCATTGGT
335388 CGGTGAC-GCAGCGG
1 CGGTGACAGCAGCGG
335402 CGGTGACAGCAGCGG
1 CGGTGACAGCAGCGG
335417 AGCTGTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.17, C:0.28, G:0.48, T:0.07
Consensus pattern (15 bp):
CGGTGACAGCAGCGG
Found at i:335894 original size:23 final size:23
Alignment explanation
Indices: 335844--335916 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
335834 ATTTAATCAT
* *
335844 TATTTTTATTTAAATAATATTAAAA
1 TATTTTTA-TT-ATTAATATTTAAA
*
335869 TATATTTTA-TATTAATATTTATA
1 TAT-TTTTATTATTAATATTTAAA
*
335892 TATTTTTATTATTAAAATTTAAA
1 TATTTTTATTATTAATATTTAAA
335915 TA
1 TA
335917 AAAAATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 5 0.12
23 27 0.66
24 1 0.02
25 3 0.07
26 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTTTATTATTAATATTTAAA
Found at i:335946 original size:34 final size:32
Alignment explanation
Indices: 335892--335956 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
335882 AATATTTATA
*
335892 TATTTTTATTATTAAAATTTAAA-TAAAAAAT
1 TATTTTTATTAATAAAATTTAAATTAAAAAAT
335923 TATTTATTATTAAATAATAATTTAAATTAAAAAA
1 TATTT-TTATT-AATAA-AATTTAAATTAAAAAA
335957 ATCAAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 5 0.17
32 5 0.17
33 4 0.14
34 8 0.28
35 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
TATTTTTATTAATAAAATTTAAATTAAAAAAT
Found at i:339771 original size:14 final size:14
Alignment explanation
Indices: 339752--339779 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
339742 AATTCATATT
339752 TAAAATATATTTAA
1 TAAAATATATTTAA
339766 TAAAATATATTTAA
1 TAAAATATATTTAA
339780 AATCGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATATATTTAA
Found at i:340176 original size:30 final size:29
Alignment explanation
Indices: 340142--340228 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 29
340132 TGGTTTAATA
340142 TTATTATTATTTAATAATAAAAAATATTTT
1 TTATT-TTATTTAATAATAAAAAATATTTT
340172 TTATTTTAATTTAATAAT-AAAAATAATTTT
1 TTATTTT-ATTTAATAATAAAAAAT-ATTTT
* *
340202 TAATTTT-TTTACT-ATAAAAATATATTT
1 TTATTTTATTTAATAATAAAAA-ATATTT
340229 ATATATAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
27 2 0.04
28 13 0.25
29 10 0.20
30 26 0.51
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (29 bp):
TTATTTTATTTAATAATAAAAAATATTTT
Found at i:340186 original size:27 final size:28
Alignment explanation
Indices: 340142--340242 Score: 82
Period size: 30 Copynumber: 3.5 Consensus size: 28
340132 TGGTTTAATA
340142 TTATTATT-ATTTAATAATAAAAAATATTTT
1 TTATT-TTAATTTAAT-AT-AAAAATATTTT
340172 TTATTTTAATTTAATAATAAAAATAATTTT
1 TTATTTTAATTTAAT-ATAAAAAT-ATTTT
* *
340202 TAATTTT--TTTACTATAAAAATATATTT
1 TTATTTTAATTTAATATAAAAATAT-TTT
* * *
340229 ATATATAAATTTAA
1 TTATTTTAATTTAA
340243 GTTAAATTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
26 2 0.03
27 14 0.24
28 5 0.08
29 12 0.20
30 26 0.44
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (28 bp):
TTATTTTAATTTAATATAAAAATATTTT
Found at i:342274 original size:24 final size:26
Alignment explanation
Indices: 342220--342275 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
342210 ATATGATAAA
* *
342220 AAATATAATATTAAATATAATATATT
1 AAATATAATATAAAATATAATATACT
*
342246 TAATA-AATATAAAAT-TAATATACT
1 AAATATAATATAAAATATAATATACT
342270 AAATAT
1 AAATAT
342276 GATACAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 12 0.48
25 9 0.36
26 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATATAATATAAAATATAATATACT
Found at i:344263 original size:20 final size:20
Alignment explanation
Indices: 344238--344278 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
344228 AAATCTAACA
344238 CGAATAGGTATTGAGATTGT
1 CGAATAGGTATTGAGATTGT
344258 CGAATAGGTATTGAGATTGT
1 CGAATAGGTATTGAGATTGT
344278 C
1 C
344279 AAATGTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.34
Consensus pattern (20 bp):
CGAATAGGTATTGAGATTGT
Found at i:346337 original size:32 final size:32
Alignment explanation
Indices: 346296--346359 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
346286 CAATATCTGA
346296 GCAAGTTAGTAACCTTTTCTAAGAGTACAACC
1 GCAAGTTAGTAACCTTTTCTAAGAGTACAACC
346328 GCAAGTTAGTAACCTTTTCTAAGAGTACAACC
1 GCAAGTTAGTAACCTTTTCTAAGAGTACAACC
346360 ACAAATATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (32 bp):
GCAAGTTAGTAACCTTTTCTAAGAGTACAACC
Found at i:350698 original size:10 final size:10
Alignment explanation
Indices: 350666--350698 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
350656 TTTGAAATAA
350666 TAATTTAAAT
1 TAATTTAAAT
*
350676 TAATTTAATT
1 TAATTTAAAT
350686 TAATTTAAAT
1 TAATTTAAAT
350696 TAA
1 TAA
350699 AAATTTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:351921 original size:18 final size:18
Alignment explanation
Indices: 351894--351952 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
351884 TTATTATAAT
*
351894 TATTTTTAAAATATTATA
1 TATTTATAAAATATTATA
351912 TATTTAT-AAATATTTATA
1 TATTTATAAAATA-TTATA
* *
351930 TATTAATAATTTATATTATA
1 TATTTATAA--AATATTATA
351950 TAT
1 TAT
351953 AAATTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.15
18 17 0.50
19 1 0.03
20 8 0.24
21 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTATAAAATATTATA
Found at i:351960 original size:18 final size:16
Alignment explanation
Indices: 351902--351967 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 16
351892 ATTATTTTTA
*
351902 AAATATTATATATTTAT
1 AAATTTTATATA-TTAT
351919 AAATATTTATATATTA-
1 AAAT-TTTATATATTAT
351935 ATAA-TTTATATTATATAT
1 A-AATTTTATA-TAT-TAT
351953 AAATTTTAATATATT
1 AAATTTT-ATATATT
351968 TTTATATTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
15 6 0.15
16 4 0.10
17 14 0.34
18 14 0.34
19 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTTTATATATTAT
Found at i:351987 original size:29 final size:28
Alignment explanation
Indices: 351939--352004 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
351929 ATATTAATAA
351939 TTTATATTATATATAAATTT-TAATATATT
1 TTTATATTATATATAAATTTAT-AT-TATT
*
351968 TTTATATTCATAT-TATATTTATATTATT
1 TTTATATT-ATATATAAATTTATATTATT
351996 TTTA-ATTAT
1 TTTATATTAT
352005 TTTTTAACGT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 2 0.06
27 3 0.09
28 8 0.24
29 16 0.47
30 5 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTATATTATATATAAATTTATATTATT
Found at i:352728 original size:25 final size:26
Alignment explanation
Indices: 352700--352759 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
352690 ATATACTTAC
*
352700 ATTTTAAAAAAT-TAAATAAAA-ATT
1 ATTTTAAAAAATAAAAATAAAATATT
352724 AATTTTAAAAAATAAAAATAAAATATT
1 -ATTTTAAAAAATAAAAATAAAATATT
352751 A-TTTAAAAA
1 ATTTTAAAAA
352760 TATTTTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 20 0.62
26 9 0.28
27 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
ATTTTAAAAAATAAAAATAAAATATT
Found at i:352791 original size:25 final size:26
Alignment explanation
Indices: 352758--352807 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
352748 ATTATTTAAA
*
352758 AATATTTTTTAACA-TAAAA-TAAAAT
1 AATAATTTTTAA-ATTAAAATTAAAAT
352783 AATAATTTTTAAATTAAAATTAAAA
1 AATAATTTTTAAATTAAAATTAAAA
352808 ATTTCAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 16 0.73
26 5 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AATAATTTTTAAATTAAAATTAAAAT
Found at i:355264 original size:27 final size:27
Alignment explanation
Indices: 355234--355292 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
355224 GGTTAAAAAA
355234 TAATTGAA-TTAAATTAATTAATTTAAT
1 TAATTGAATTTAAATTAA-TAATTTAAT
*
355261 TAATTGAATTTAAATTAATAATTTATT
1 TAATTGAATTTAAATTAATAATTTAAT
355288 TAATT
1 TAATT
355293 TAATACATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (27 bp):
TAATTGAATTTAAATTAATAATTTAAT
Found at i:355284 original size:13 final size:14
Alignment explanation
Indices: 355242--355285 Score: 65
Period size: 13 Copynumber: 3.2 Consensus size: 14
355232 AATAATTGAA
355242 TTAAATTAATTAAT
1 TTAAATTAATTAAT
355256 TT-AATTAATTGAAT
1 TTAAATTAATT-AAT
355270 TTAAATTAA-TAAT
1 TTAAATTAATTAAT
355283 TTA
1 TTA
355286 TTTAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 14 0.50
14 8 0.29
15 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTAAATTAATTAAT
Found at i:355304 original size:27 final size:28
Alignment explanation
Indices: 355234--355304 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 28
355224 GGTTAAAAAA
*
355234 TAATTGAAT-TAAATTAATTAATTTAAT
1 TAATTGAATACAAATTAATTAATTTAAT
** *
355261 TAATTGAATTTAAATTAA-TAATTTATT
1 TAATTGAATACAAATTAATTAATTTAAT
* *
355288 TAATTTAATACATATTA
1 TAATTGAATACAAATTA
355305 TAAAATCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 30 0.79
28 8 0.21
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (28 bp):
TAATTGAATACAAATTAATTAATTTAAT
Found at i:358237 original size:2 final size:2
Alignment explanation
Indices: 358230--358256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
358220 AGCGAATAAC
358230 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
358257 CTGTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:358329 original size:40 final size:40
Alignment explanation
Indices: 358285--358365 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
358275 TTGTTCAACA
358285 TTTCCTTTTAGAACTGTATCTTTTTTATGGATAAATATGG
1 TTTCCTTTTAGAACTGTATCTTTTTTATGGATAAATATGG
358325 TTTCCTTTTAGAACTGTATCTTTTTTATGGATAAATATGG
1 TTTCCTTTTAGAACTGTATCTTTTTTATGGATAAATATGG
358365 T
1 T
358366 AAGTACTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.51
Consensus pattern (40 bp):
TTTCCTTTTAGAACTGTATCTTTTTTATGGATAAATATGG
Found at i:366123 original size:14 final size:14
Alignment explanation
Indices: 366103--366142 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
366093 GATAAAATAT
366103 TATTTTTAATAATTA
1 TATTTTTAA-AATTA
366118 -ATTTTTAAAATTA
1 TATTTTTAAAATTA
366131 TATTTTTTAAAA
1 TA-TTTTTAAAA
366143 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.22
14 9 0.39
15 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTTTTAAAATTA
Found at i:366143 original size:16 final size:14
Alignment explanation
Indices: 366095--366144 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
366085 ATTTTAGTGA
366095 TAAAATATT-ATTTT
1 TAAAA-ATTAATTTT
*
366109 TAATAATTAATTTT
1 TAAAAATTAATTTT
366123 T-AAAATTATATTTTT
1 TAAAAATTA-A-TTTT
366138 TAAAAAT
1 TAAAAAT
366145 ATTAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 9 0.30
14 11 0.37
15 5 0.17
16 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAAAAATTAATTTT
Found at i:366175 original size:28 final size:28
Alignment explanation
Indices: 366135--366209 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 28
366125 AAATTATATT
* * *
366135 TTTTAAAAATATTAAAAATAATATTTAC
1 TTTTAATATTATTAAAAAAAATATTTAC
*
366163 TTTTAATATTATTAAATTAAAAAATATTTAT
1 TTTTAATATTATT-AA--AAAAAATATTTAC
366194 TTTTAATATTATTAAA
1 TTTTAATATTATTAAA
366210 TTAAATATCG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 12 0.30
29 2 0.05
30 2 0.05
31 24 0.60
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTTAATATTATTAAAAAAAATATTTAC
Found at i:366192 original size:31 final size:32
Alignment explanation
Indices: 366149--366214 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
366139 AAAAATATTA
366149 AAAATAATATTTACTTTTAATATTATTAAATT
1 AAAATAATATTTACTTTTAATATTATTAAATT
*
366181 AAAA-AATATTTATTTTTAATATTATTAAATT
1 AAAATAATATTTACTTTTAATATTATTAAATT
366212 AAA
1 AAA
366215 TATCGATGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
AAAATAATATTTACTTTTAATATTATTAAATT
Found at i:366800 original size:16 final size:18
Alignment explanation
Indices: 366772--366807 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
366762 TATATAACAT
366772 AAAATTTTAT-AAAATAA
1 AAAATTTTATAAAAATAA
366789 AAAATTTT-TAAAAATAA
1 AAAATTTTATAAAAATAA
366806 AA
1 AA
366808 TAAGGGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTTTATAAAAATAA
Found at i:366901 original size:27 final size:26
Alignment explanation
Indices: 366870--366921 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
366860 AATATTGTAT
*
366870 AAAAAATATTTTTAAAATATAATTTTAG
1 AAAAAA-ATTATTAAAA-ATAATTTTAG
*
366898 AAAAAAATTATTAAAAATATTTTT
1 AAAAAAATTATTAAAAATAATTTT
366922 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 9 0.41
28 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
AAAAAAATTATTAAAAATAATTTTAG
Found at i:368470 original size:36 final size:36
Alignment explanation
Indices: 368347--368456 Score: 193
Period size: 36 Copynumber: 3.1 Consensus size: 36
368337 ACTATCAACA
*
368347 ATCAAGTTTCCCATGAAACAAAAGTAGAAAGAAAAT
1 ATCAAGTTTCCCATGGAACAAAAGTAGAAAGAAAAT
* *
368383 ATCAAGTTTCCCAAGGAACAAAAGCAGAAAGAAAAT
1 ATCAAGTTTCCCATGGAACAAAAGTAGAAAGAAAAT
368419 ATCAAGTTTCCCATGGAACAAAAGTAGAAAGAAAAT
1 ATCAAGTTTCCCATGGAACAAAAGTAGAAAGAAAAT
368455 AT
1 AT
368457 ATATAATACC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (36 bp):
ATCAAGTTTCCCATGGAACAAAAGTAGAAAGAAAAT
Found at i:369576 original size:28 final size:28
Alignment explanation
Indices: 369535--369606 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
369525 GATAGAATGT
369535 TGAGATT-AGAATTTTAAATTATAAATA-
1 TGAGATTCA-AATTTTAAATTATAAATAG
* * *
369562 TCGAGATTCAAATTTCAAGTTGTAAATAG
1 T-GAGATTCAAATTTTAAATTATAAATAG
*
369591 TAAGATTCAAATTTTA
1 TGAGATTCAAATTTTA
369607 CATTTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 34 0.92
29 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (28 bp):
TGAGATTCAAATTTTAAATTATAAATAG
Found at i:370975 original size:50 final size:50
Alignment explanation
Indices: 370915--371074 Score: 250
Period size: 50 Copynumber: 3.2 Consensus size: 50
370905 ATATACTTAG
370915 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
* * *
370965 CGTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGGAT
1 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
* * *
371015 GGTTAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA-AGAT
1 AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGA-AT
371065 AGTCAACAAT
1 AGTCAACAAT
371075 GGCAACAACT
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
50 99 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:375540 original size:50 final size:50
Alignment explanation
Indices: 375463--375601 Score: 226
Period size: 50 Copynumber: 2.8 Consensus size: 50
375453 TATACTTAGA
* * *
375463 GTCAACAATTATGGCCACCTCCCTCTATGGTTAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
375513 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
*
375563 GTCAACAATTATGGCCATCT-CTCTCTATTGTCAAAGGTT
1 GTCAACAATTATGGCCACCTCCT-TCTATTGTCAAAGGTT
375602 AATGAAAGAT
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
49 2 0.02
50 82 0.98
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:375617 original size:50 final size:49
Alignment explanation
Indices: 375462--375621 Score: 214
Period size: 50 Copynumber: 3.2 Consensus size: 49
375452 ATATACTTAG
* *
375462 AGTCAACAATTATGGCCACCTCCCTCTATGGTTAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCT-CCTCTATTGTCAAAGGTTGGTGAAGAAT
*
375512 CGTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGCCACCTCC-TCTATTGTCAAAGGTTGGTGAAGAAT
* * **
375562 CGTCAACAATTATGGCCATCTCTCTCTATTGTCAAAGGTTAATGAA-AGAT
1 AGTCAACAATTATGGCCACCTC-CTCTATTGTCAAAGGTTGGTGAAGA-AT
375612 AGTCAACAAT
1 AGTCAACAAT
375622 GACAACAACT
Statistics
Matches: 100, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
49 3 0.03
50 96 0.96
51 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (49 bp):
AGTCAACAATTATGGCCACCTCCTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:378202 original size:2 final size:2
Alignment explanation
Indices: 378195--378219 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
378185 AAGCATACAT
378195 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
378220 TGGTTGGACC
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:378909 original size:27 final size:27
Alignment explanation
Indices: 378878--378957 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
378868 AAGTAACAAG
*
378878 CCATCATTTTCGACAAACAAAAAGGAA
1 CCATCATTTTTGACAAACAAAAAGGAA
* *
378905 CCATCATTTTTGACAAACACAAATGAA
1 CCATCATTTTTGACAAACAAAAAGGAA
* *
378932 CCACCATTTTTGACAAAAACAAAAGG
1 CCATCATTTTTGACAAACA-AAAAGG
378958 TAGTTTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 41 0.91
28 4 0.09
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (27 bp):
CCATCATTTTTGACAAACAAAAAGGAA
Found at i:385489 original size:22 final size:22
Alignment explanation
Indices: 385464--385506 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
385454 TTATAAAAAT
385464 TAAAAA-TTAATTAAAATTTAAA
1 TAAAAATTTAATT-AAATTTAAA
*
385486 TAAAAATTTAATTTAATTTAA
1 TAAAAATTTAATTAAATTTAA
385507 TTCAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAATTTAATTAAATTTAAA
Found at i:386057 original size:10 final size:10
Alignment explanation
Indices: 386036--386067 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
386026 AGGCTCAAGC
386036 AGACAG-CAG
1 AGACAGACAG
386045 AGACAGACAG
1 AGACAGACAG
386055 AGACAGACAG
1 AGACAGACAG
386065 AGA
1 AGA
386068 AGAGAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.50, C:0.19, G:0.31, T:0.00
Consensus pattern (10 bp):
AGACAGACAG
Found at i:390667 original size:12 final size:12
Alignment explanation
Indices: 390650--390675 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
390640 GAAAACAAAG
390650 GCTGCCAACTGT
1 GCTGCCAACTGT
390662 GCTGCCAACTGT
1 GCTGCCAACTGT
390674 GC
1 GC
390676 CGTCAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.27, T:0.23
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:390700 original size:12 final size:12
Alignment explanation
Indices: 390678--390728 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
390668 AACTGTGCCG
390678 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
390691 TCAATTTGAAAT
1 TCAATTTGAAAT
*
390703 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
390718 TCAATTTGAAA
1 TCAATTTGAAA
390729 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:390740 original size:27 final size:27
Alignment explanation
Indices: 390684--390740 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
390674 GCCGTCAATT
* *
390684 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
390711 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
390738 TTG
1 TTG
390741 CATAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:390881 original size:14 final size:14
Alignment explanation
Indices: 390862--390897 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
390852 ATAGTGTGAA
390862 ACACTGGGGTTATC
1 ACACTGGGGTTATC
390876 ACACTGGGGTTATC
1 ACACTGGGGTTATC
390890 ACACTGGG
1 ACACTGGG
390898 AAAAATAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (14 bp):
ACACTGGGGTTATC
Found at i:392552 original size:15 final size:16
Alignment explanation
Indices: 392524--392553 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
392514 TTCATCTTAA
392524 AATTTTACAAAGATAT
1 AATTTTACAAAGATAT
392540 AATTTTA-AAAGATA
1 AATTTTACAAAGATA
392554 ATTATTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (16 bp):
AATTTTACAAAGATAT
Found at i:392620 original size:20 final size:21
Alignment explanation
Indices: 392586--392626 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
392576 TTTTTAAAAC
*
392586 TTTTAGAGATGAATTTTTAAT
1 TTTTAGAGATGAATTATTAAT
*
392607 TTTTGGAGAT-AATTATTAAT
1 TTTTAGAGATGAATTATTAAT
392627 CATCTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (21 bp):
TTTTAGAGATGAATTATTAAT
Found at i:393246 original size:31 final size:30
Alignment explanation
Indices: 393189--393246 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
393179 ATTTAATAGT
* * **
393189 AAAAAATATTTTTATTAAAATTTAATTATA
1 AAAAAATATTATTAATAAAAAATAATTATA
393219 AAAAAATAATTATTAATAAAAAATAATT
1 AAAAAAT-ATTATTAATAAAAAATAATT
393247 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 7 0.30
31 16 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAAAATATTATTAATAAAAAATAATTATA
Found at i:394704 original size:27 final size:27
Alignment explanation
Indices: 394639--394704 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
394629 TTTTATATTG
*
394639 TAAAAAATTA-AAAATTAATTAAAATT
1 TAAATAATTATAAAATTAATTAAAATT
**
394665 TAAATAAAAATAAAATTCAATT-AAATT
1 TAAATAATTATAAAATT-AATTAAAATT
*
394692 TGAATAATTATAA
1 TAAATAATTATAA
394705 TTTTTTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 7 0.22
27 21 0.66
28 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (27 bp):
TAAATAATTATAAAATTAATTAAAATT
Found at i:394968 original size:15 final size:16
Alignment explanation
Indices: 394943--394972 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
394933 GGTATTTAAA
394943 AAAAAATTAATATATT
1 AAAAAATTAATATATT
394959 AAAAAA-TAATATAT
1 AAAAAATTAATATAT
394973 ATTTACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAATTAATATATT
Found at i:395421 original size:3 final size:3
Alignment explanation
Indices: 395413--395456 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
395403 AATGCTAGAA
395413 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
395457 AAGTTTCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.