Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 3 of 19
Found at i:304706 original size:18 final size:18
Alignment explanation
Indices: 304683--304750 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
304673 TGCTAAGTAG
304683 TTTTTAAAAAAATGATAA
1 TTTTTAAAAAAATGATAA
*
304701 TTTTTAAGAAAATGA-AA
1 TTTTTAAAAAAATGATAA
* ** *
304718 ATTTTAAAGTAGTGATAA
1 TTTTTAAAAAAATGATAA
304736 TTCTTTTAAAAAAAT
1 -T-TTTTAAAAAAAT
304751 TATACTTGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
17 12 0.32
18 16 0.43
20 9 0.24
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (18 bp):
TTTTTAAAAAAATGATAA
Found at i:304827 original size:24 final size:23
Alignment explanation
Indices: 304779--304829 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
304769 TACCTTTTCT
* *
304779 AAAAATATATTATATATAAATTA
1 AAAAATATATTACATATAAACTA
304802 AAAAATATTATTACATCA-AAACTA
1 AAAAATA-TATTACAT-ATAAACTA
304826 AAAA
1 AAAA
304830 TTTTATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 16 0.67
25 1 0.04
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAATATATTACATATAAACTA
Found at i:304828 original size:23 final size:23
Alignment explanation
Indices: 304777--304835 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
304767 AGTACCTTTT
*
304777 CTAAAAATA-TATTATATATAAA
1 CTAAAAATATTATTACATATAAA
*
304799 TTAAAAAATATTATTACATCA-AAA
1 CT-AAAAATATTATTACAT-ATAAA
*
304823 CTAAAAATTTTAT
1 CTAAAAATATTAT
304836 ATTAAGAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.03
23 17 0.57
24 11 0.37
25 1 0.03
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAAAATATTATTACATATAAA
Found at i:304883 original size:21 final size:21
Alignment explanation
Indices: 304858--304897 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
304848 AAATAAAAAA
*
304858 TAATTAAAATATAAATTTTTG
1 TAATTAAAATAAAAATTTTTG
304879 TAATTAAAATAAAAATTTT
1 TAATTAAAATAAAAATTTT
304898 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TAATTAAAATAAAAATTTTTG
Found at i:304929 original size:15 final size:15
Alignment explanation
Indices: 304911--304945 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
304901 ATTTTTAATT
304911 AAAAATGTAAAAATA
1 AAAAATGTAAAAATA
* *
304926 AAAAATTTAAAGATA
1 AAAAATGTAAAAATA
304941 AAAAA
1 AAAAA
304946 AAAAGTGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (15 bp):
AAAAATGTAAAAATA
Found at i:307819 original size:16 final size:16
Alignment explanation
Indices: 307798--307849 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
307788 ACTATATTAT
307798 TTTTAATTGATCTTAG
1 TTTTAATTGATCTTAG
* *
307814 TTTTAATAT-AAC-TAA
1 TTTTAAT-TGATCTTAG
307829 TTTTGAATTGATCTTAG
1 TTTT-AATTGATCTTAG
307846 TTTT
1 TTTT
307850 GATATAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 7 0.25
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.56
Consensus pattern (16 bp):
TTTTAATTGATCTTAG
Found at i:307832 original size:32 final size:32
Alignment explanation
Indices: 307796--307857 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
307786 TCACTATATT
*
307796 ATTTTTAATTGATCTTAGTTTTAATATAACTA
1 ATTTTGAATTGATCTTAGTTTTAATATAACTA
*
307828 ATTTTGAATTGATCTTAGTTTTGATATAAC
1 ATTTTGAATTGATCTTAGTTTTAATATAAC
307858 AAAAACTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (32 bp):
ATTTTGAATTGATCTTAGTTTTAATATAACTA
Found at i:307851 original size:17 final size:17
Alignment explanation
Indices: 307797--307851 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
307787 CACTATATTA
*
307797 TTTTTAATTGATCTTAG
1 TTTTGAATTGATCTTAG
* *
307814 TTTT-AATAT-AAC-TAA
1 TTTTGAAT-TGATCTTAG
307829 TTTTGAATTGATCTTAG
1 TTTTGAATTGATCTTAG
307846 TTTTGA
1 TTTTGA
307852 TATAACAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 7 0.23
16 10 0.33
17 13 0.43
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (17 bp):
TTTTGAATTGATCTTAG
Found at i:312095 original size:18 final size:18
Alignment explanation
Indices: 312052--312097 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
312042 ATATTTTTAT
312052 TTTATTTTTTTATTATAA
1 TTTATTTTTTTATTATAA
312070 TTTAATTTTATTTA-TA-AA
1 TTT-ATTTT-TTTATTATAA
312088 TATTATTTTT
1 T-TTATTTTT
312098 AATTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 11 0.44
19 9 0.36
20 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTTTTTATTATAA
Found at i:312115 original size:24 final size:24
Alignment explanation
Indices: 312043--312115 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
312033 TATATATATA
* *
312043 TATTTTT-ATTTTATT-TTTTTAT
1 TATTTTTAATTTAATTATTATTAT
* * * *
312065 TATAATTTAATTTTATTTATAAATAT
1 TAT-TTTTAA-TTTAATTATTATTAT
312091 TATTTTTAATTTAATTATTATTAT
1 TATTTTTAATTTAATTATTATTAT
312115 T
1 T
312116 TTACTCGTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
22 3 0.08
23 3 0.08
24 14 0.38
25 10 0.27
26 7 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TATTTTTAATTTAATTATTATTAT
Found at i:312298 original size:6 final size:6
Alignment explanation
Indices: 312287--312324 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
312277 ATCGATAAGA
* *
312287 TTTTAT TTTTAT TATTAT TTTTA- TTTTAT TTTAAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
312325 AAAAATACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:312313 original size:17 final size:17
Alignment explanation
Indices: 312286--312325 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
312276 TATCGATAAG
312286 ATTTTATTTTTATTATTA
1 ATTTTATTTTTATT-TTA
*
312304 TTTTTA-TTTTATTTTA
1 ATTTTATTTTTATTTTA
312320 ATTTTA
1 ATTTTA
312326 AAAATACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 8 0.40
17 7 0.35
18 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTATTTTTATTTTA
Found at i:312315 original size:11 final size:11
Alignment explanation
Indices: 312286--312325 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
312276 TATCGATAAG
312286 ATTTTATTTTT
1 ATTTTATTTTT
312297 ATTATTATTTTT
1 ATT-TTATTTTT
*
312309 ATTTTATTTTA
1 ATTTTATTTTT
312320 ATTTTA
1 ATTTTA
312326 AAAATACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:313178 original size:24 final size:26
Alignment explanation
Indices: 313154--313204 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
313144 CAATATCTTA
313154 TATATT-T-ATTTAAA-TTTA-ATTT
1 TATATTATAATTTAAATTTTATATTT
313176 TATATTATAATTTAAATTTTATATTT
1 TATATTATAATTTAAATTTTATATTT
313202 TAT
1 TAT
313205 CATAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 1 0.04
24 7 0.28
25 4 0.16
26 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TATATTATAATTTAAATTTTATATTT
Found at i:313195 original size:19 final size:17
Alignment explanation
Indices: 313158--313200 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
313148 ATCTTATATA
313158 TTTAT-TTAAATTTAAT
1 TTTATATTAAATTTAAT
313174 TTTATATTATAATTTAAAT
1 TTTATATTA-AATTT-AAT
313193 TTTATATT
1 TTTATATT
313201 TTATCATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.21
17 3 0.12
18 5 0.21
19 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTATATTAAATTTAAT
Found at i:313209 original size:24 final size:24
Alignment explanation
Indices: 313161--313209 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
313151 TTATATATTT
*
313161 ATTTAAATTTAATTTTATATTATA
1 ATTTAAATTTAATTTTATATCATA
*
313185 ATTTAAATTTTATATTT-TATCATA
1 ATTTAAATTTAAT-TTTATATCATA
313209 A
1 A
313210 ATTTTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTAAATTTAATTTTATATCATA
Found at i:313224 original size:20 final size:19
Alignment explanation
Indices: 313188--313239 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
313178 TATTATAATT
*
313188 TAAATTTTATATTTTATCA
1 TAAATTTTATATATTATCA
313207 TAAATTTTAATATATTAT-A
1 TAAATTTT-ATATATTATCA
*
313226 -ATATTTTATATATT
1 TAAATTTTATATATT
313240 TATTTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 7 0.23
18 6 0.20
19 9 0.30
20 8 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TAAATTTTATATATTATCA
Found at i:313236 original size:17 final size:16
Alignment explanation
Indices: 313180--313239 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
313170 TAATTTTATA
313180 TTATA-ATT-TAAATT
1 TTATATATTATAAATT
*
313194 TTATATTTTATCATAAATT
1 TTATA---TATTATAAATT
313213 TTAATATATTATAATATT
1 TT-ATATATTATAA-ATT
313231 TTATATATT
1 TTATATATT
313240 TATTTTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
14 5 0.14
17 14 0.38
18 7 0.19
19 8 0.22
20 3 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATATTATAAATT
Found at i:313633 original size:17 final size:17
Alignment explanation
Indices: 313595--313634 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
313585 ATGATTTTTA
313595 ATAAAAAAATTTAAAAT
1 ATAAAAAAATTTAAAAT
* *
313612 TTAAAAAAATTTAATAT
1 ATAAAAAAATTTAAAAT
313629 ATAAAA
1 ATAAAA
313635 TAATAAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAAAAATTTAAAAT
Found at i:314994 original size:30 final size:31
Alignment explanation
Indices: 314928--314994 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
314918 TGATATTTTT
* * *
314928 ATATTATTTTTTATTTTTTAAAATAATTATT
1 ATATTATCTTTAATTTTTTAAAATAATTATA
*
314959 A-ATTATCTTTAATTTTTTAAAAT-TTTATA
1 ATATTATCTTTAATTTTTTAAAATAATTATA
314988 ATATTAT
1 ATATTAT
314995 TTATGAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 5 0.16
30 25 0.81
31 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (31 bp):
ATATTATCTTTAATTTTTTAAAATAATTATA
Found at i:316050 original size:2 final size:2
Alignment explanation
Indices: 316043--316078 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
316033 AACAAATACC
316043 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
316079 TACTTAATAG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:316512 original size:24 final size:24
Alignment explanation
Indices: 316485--316530 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
316475 AATTTCAGTG
316485 AAATTAAAAATAATAATAATAATA
1 AAATTAAAAATAATAATAATAATA
** *
316509 AAATTAATTATTATAATAATAA
1 AAATTAAAAATAATAATAATAA
316531 GATTCGGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATTAAAAATAATAATAATAATA
Found at i:316516 original size:18 final size:18
Alignment explanation
Indices: 316489--316527 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
316479 TCAGTGAAAT
316489 TAAAAATAATAATAATAA
1 TAAAAATAATAATAATAA
* * *
316507 TAAAATTAATTATTATAA
1 TAAAAATAATAATAATAA
316525 TAA
1 TAA
316528 TAAGATTCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAAATAATAATAATAA
Found at i:316685 original size:17 final size:18
Alignment explanation
Indices: 316663--316701 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
316653 ATTGATAAAT
* *
316663 TATTTATATTTTTATA-A
1 TATTTAAATTTTAATATA
316680 TATTTAAATTTTAATATA
1 TATTTAAATTTTAATATA
316698 TATT
1 TATT
316702 ATTTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTAAATTTTAATATA
Found at i:316783 original size:36 final size:36
Alignment explanation
Indices: 316743--316874 Score: 90
Period size: 36 Copynumber: 3.5 Consensus size: 36
316733 TATATATTTT
316743 TTAATAAAAATACAAATATATATTTTTAAATAAAAA
1 TTAATAAAAATACAAATATATATTTTTAAATAAAAA
*
316779 TTAAT-AAAATA-AAATTATAAAAGCTTTTTAAAATAAATATA
1 TTAATAAAAATACAAA-TAT-ATA--TTTTT-AAATAAA-A-A
* *** *
316820 TTGAA-AAAAATAAAAAATATATATTCAAAAATAATAA
1 TT-AATAAAAAT-ACAAATATATATTTTTAAATAAAAA
* *
316857 TTAAAAAAAAAACAAATA
1 TTAATAAAAATACAAATA
316875 GGGGGAAAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 24
0.70 0.07 0.22
Matches are distributed among these distances:
34 3 0.04
35 9 0.12
36 15 0.20
37 8 0.11
38 6 0.08
39 13 0.17
40 3 0.04
41 3 0.04
42 9 0.12
43 4 0.05
44 3 0.04
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (36 bp):
TTAATAAAAATACAAATATATATTTTTAAATAAAAA
Found at i:316833 original size:23 final size:24
Alignment explanation
Indices: 316807--316856 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
316797 AAAAGCTTTT
*
316807 TAAAATAA-ATATATTGAAAAA-AA
1 TAAAA-AATATATATTCAAAAATAA
316830 TAAAAAATATATATTCAAAAATAA
1 TAAAAAATATATATTCAAAAATAA
316854 TAA
1 TAA
316857 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 2 0.08
23 17 0.71
24 5 0.21
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (24 bp):
TAAAAAATATATATTCAAAAATAA
Found at i:317521 original size:3 final size:3
Alignment explanation
Indices: 317513--317556 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
317503 TTGTAATAAA
317513 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
317557 AAGAGTTTTA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:317718 original size:20 final size:19
Alignment explanation
Indices: 317676--317728 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
317666 AAAGTTGAAT
*
317676 TTTATGTTAAATTTGATATA
1 TTTAT-TTAAATTTGAAATA
*
317696 TTTATTTAAATTTTAAATAA
1 TTTATTTAAATTTGAAAT-A
*
317716 TTT-TTTTAATTTG
1 TTTATTTAAATTTG
317729 GATTAAGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
TTTATTTAAATTTGAAATA
Found at i:318170 original size:2 final size:2
Alignment explanation
Indices: 318159--318195 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
318149 ATGATTAAGG
*
318159 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
318196 TCACAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:318662 original size:6 final size:6
Alignment explanation
Indices: 318644--318692 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
318634 TATTAATAAG
*
318644 TTAAA- TTATAAT TTAAAT TT---T TTAATT TTAAAT TTAAAT TTAAAT
1 TTAAAT TTA-AAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
318689 TTAA
1 TTAA
318693 TTAGATAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
3 3 0.08
5 3 0.08
6 29 0.76
7 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:318776 original size:22 final size:21
Alignment explanation
Indices: 318738--318791 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
318728 TTTATTACAA
*
318738 ATTATTTAAACTT-TAT-TTTT
1 ATTA-TTAAATTTATATATTTT
318758 A-TATTAATATTTATATATTTT
1 ATTATTAA-ATTTATATATTTT
318779 ATTATTAAATTTA
1 ATTATTAAATTTA
318792 AATAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 4 0.14
21 10 0.34
22 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTATTAAATTTATATATTTT
Found at i:320457 original size:17 final size:17
Alignment explanation
Indices: 320432--320466 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
320422 ATAAAAATAA
*
320432 TTAATAAAATTTAAAAT
1 TTAAAAAAATTTAAAAT
*
320449 TTAAAAAAATTTCAAAT
1 TTAAAAAAATTTAAAAT
320466 T
1 T
320467 AATCAGGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAT
Found at i:320468 original size:16 final size:16
Alignment explanation
Indices: 320430--320468 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
320420 ATATAAAAAT
*
320430 AATTAATAAAATTTAA
1 AATTAAAAAAATTTAA
*
320446 AATTTAAAAAAATTTCA
1 AA-TTAAAAAAATTTAA
320463 AATTAA
1 AATTAA
320469 TCAGGTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTAAAAAAATTTAA
Found at i:320535 original size:206 final size:206
Alignment explanation
Indices: 320197--320590 Score: 580
Period size: 206 Copynumber: 1.9 Consensus size: 206
320187 TGTGTGGATG
* *
320197 AGCCCTTTAAATATATCATATAAAAATTATTAGTAAAATTTAAAATTTAAAAAAAATTAAATTAA
1 AGCCCTTTAAATATATCATATAAAAATAATTAATAAAATTTAAAATTTAAAAAAAATTAAATTAA
* * * *
320262 TCAGGTACATATCCTTAATCGTCCTATAAGCTATGTATAGAACAATCTTTTTAAATATATCATTT
66 TCAGGTACAAATCCTTAATCGTCCTATAAGCTATGTATAAAACAATCTTTTTAAACACATCATTT
** **
320327 AAAAATAAAATATAATTATTAAAATACTTAATAAAATAATTTTTTTCCTGGGCGATCACGAGTTA
131 AAAAATAAAATATAACAATTAAAATACTTAATAAAATAATTTTTTTCCTAAGCGATCACGAGTTA
320392 CTATGCAGATA
196 CTATGCAGATA
* *
320403 AGCCTTTTAAATATATCATATAAAAATAATTAATAAAATTTAAAATTTAAAAAAATTTCAAATTA
1 AGCCCTTTAAATATATCATATAAAAATAATTAATAAAATTTAAAATTTAAAAAAAATT-AAATTA
* * *
320468 ATCAGGTACAAAT-CTTAAATCGAT-C-ATGAGCTATGTATAAAATAAT-TATTTTAAACACATT
65 ATCAGGTACAAATCCTT-AATCG-TCCTATAAGCTATGTATAAAACAATCT-TTTTAAACACATC
*
320529 ATTTAAAAATAAAATATAACAATTAAAATATTTAATAAAATAATTTTTTTCCTAAGCGATCA
127 ATTTAAAAATAAAATATAACAATTAAAATACTTAATAAAATAATTTTTTTCCTAAGCGATCA
320591 ATTTGTGAAT
Statistics
Matches: 168, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
205 1 0.01
206 142 0.85
207 24 0.14
208 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.36
Consensus pattern (206 bp):
AGCCCTTTAAATATATCATATAAAAATAATTAATAAAATTTAAAATTTAAAAAAAATTAAATTAA
TCAGGTACAAATCCTTAATCGTCCTATAAGCTATGTATAAAACAATCTTTTTAAACACATCATTT
AAAAATAAAATATAACAATTAAAATACTTAATAAAATAATTTTTTTCCTAAGCGATCACGAGTTA
CTATGCAGATA
Found at i:320804 original size:33 final size:37
Alignment explanation
Indices: 320761--320837 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 37
320751 TGAACGTATC
320761 AAAAAA-TATATATAAAT-A-AATA-ATT-AATATAT
1 AAAAAATTATATATAAATTATAATATATTAAATATAT
*
320793 AAAAAATTATATATAAATTTATAATATTTTAAATATAT
1 AAAAAATTATATATAAA-TTATAATATATTAAATATAT
320831 AAAAAAT
1 AAAAAAT
320838 AATTTAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
32 6 0.16
33 10 0.26
34 1 0.03
35 1 0.03
36 4 0.11
37 2 0.05
38 14 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (37 bp):
AAAAAATTATATATAAATTATAATATATTAAATATAT
Found at i:320843 original size:20 final size:20
Alignment explanation
Indices: 320768--320847 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
320758 ATCAAAAAAT
320768 ATATATAAATAAATAA-TT-A
1 ATATATAAA-AAATAATTTAA
*
320787 ATATATAAAAAATTATATATAA
1 ATATATAAAAAA-TA-ATTTAA
* *
320809 AT-T-T--ATAATATTTTAA
1 ATATATAAAAAATAATTTAA
320825 ATATATAAAAAATAATTTAA
1 ATATATAAAAAATAATTTAA
320845 ATA
1 ATA
320848 CGATATATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
16 6 0.13
17 3 0.06
18 7 0.15
19 11 0.23
20 15 0.32
21 2 0.04
22 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATATAAAAAATAATTTAA
Found at i:321783 original size:25 final size:25
Alignment explanation
Indices: 321754--321802 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
321744 TAGATGTCAC
321754 ATTGCATCCAAATGGCATCAATGTA
1 ATTGCATCCAAATGGCATCAATGTA
*
321779 ATTGCATCCATATGGCATCAATGT
1 ATTGCATCCAAATGGCATCAATGT
321803 GAAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (25 bp):
ATTGCATCCAAATGGCATCAATGTA
Found at i:324137 original size:20 final size:18
Alignment explanation
Indices: 324099--324160 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 18
324089 TATTTTTATT
*
324099 ATTAAAATAA-TAATTTAA
1 ATTAAAA-AATTAATATAA
324117 ATTAAATTAAATTAATATAA
1 ATTAAA--AAATTAATATAA
324137 ATAATAAAAAATTATATATAA
1 AT--TAAAAAATTA-ATATAA
324158 ATT
1 ATT
324161 TAACCTAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
18 6 0.16
19 3 0.08
20 16 0.43
21 8 0.22
22 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTAAAAAATTAATATAA
Found at i:324927 original size:12 final size:12
Alignment explanation
Indices: 324910--324943 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
324900 ACCTTCTTAT
324910 ATACATATATAC
1 ATACATATATAC
*
324922 ATACATATATAT
1 ATACATATATAC
*
324934 ATATATATAT
1 ATACATATAT
324944 CAATTTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (12 bp):
ATACATATATAC
Found at i:325627 original size:21 final size:21
Alignment explanation
Indices: 325603--325642 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
325593 TTTTTTTATT
325603 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
325624 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
325643 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:327123 original size:13 final size:13
Alignment explanation
Indices: 327103--327136 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
327093 TAAAATTATT
*
327103 TTAATTAATTAGA
1 TTAATTAATTAAA
*
327116 TTAGTTAATTAAA
1 TTAATTAATTAAA
327129 TTAATTAA
1 TTAATTAA
327137 ATTTACTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (13 bp):
TTAATTAATTAAA
Found at i:327855 original size:2 final size:2
Alignment explanation
Indices: 327848--327892 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
327838 AAAATGGGAA
* * * *
327848 AT AT AT AT AT AT AT AT AT AT AC AC AC AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
327890 AT A
1 AT A
327893 ATCAATTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:328122 original size:15 final size:16
Alignment explanation
Indices: 328080--328127 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
328070 TATATTTATT
328080 TATTTAATTTATTATAA
1 TATTT-ATTTATTATAA
*
328097 TAATTATTTTATTATAA
1 TATTTA-TTTATTATAA
*
328114 -ATTTATTTAATATA
1 TATTTATTTATTATA
328128 TTATAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTATTTATTATAA
Found at i:328479 original size:16 final size:15
Alignment explanation
Indices: 328458--328488 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
328448 TAATCTAACC
328458 AAATTAATTTAGAATT
1 AAATTAATTTA-AATT
328474 AAATTAATTTAAATT
1 AAATTAATTTAAATT
328489 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
AAATTAATTTAAATT
Found at i:328528 original size:16 final size:16
Alignment explanation
Indices: 328497--328548 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
328487 TTTTTAAAAT
*
328497 TTTAAATTATTTTTGAG
1 TTTAAATCA-TTTTGAG
*
328514 TTTAAATCATTTTGAT
1 TTTAAATCATTTTGAG
* *
328530 TTTAAGTCATTTCGAG
1 TTTAAATCATTTTGAG
328546 TTT
1 TTT
328549 TGAGTTACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 22 0.73
17 8 0.27
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.56
Consensus pattern (16 bp):
TTTAAATCATTTTGAG
Found at i:328834 original size:13 final size:13
Alignment explanation
Indices: 328816--328840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
328806 TTAAAACTAT
328816 TTTTAATTTTTAA
1 TTTTAATTTTTAA
328829 TTTTAATTTTTA
1 TTTTAATTTTTA
328841 TATAATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:330163 original size:23 final size:25
Alignment explanation
Indices: 330133--330185 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
330123 GATATTTAGG
330133 TTTT-TTTATTTATG-AAAA-AA-TA
1 TTTTCTTTATTTA-GCAAAATAATTA
330155 TTTTCTTTATTTAGCAAAATAATTA
1 TTTTCTTTATTTAGCAAAATAATTA
330180 TTTTCT
1 TTTTCT
330186 AACTATCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.19
23 12 0.44
24 2 0.07
25 8 0.30
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTTCTTTATTTAGCAAAATAATTA
Found at i:336389 original size:26 final size:27
Alignment explanation
Indices: 336325--336393 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
336315 ACCTGTTTTT
* *
336325 TTTTTCTTTATTATTATATAATAATTAA
1 TTTTTATTTA-TATTATATAATAACTAA
* **
336353 -TTATAAATATATTATATAAT-ACTAA
1 TTTTTATTTATATTATATAATAACTAA
336378 TTTTTATTTATATTAT
1 TTTTTATTTATATTAT
336394 TATTTTTAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
25 4 0.12
26 23 0.72
27 5 0.16
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTTATTTATATTATATAATAACTAA
Found at i:336571 original size:28 final size:29
Alignment explanation
Indices: 336537--336642 Score: 94
Period size: 32 Copynumber: 3.6 Consensus size: 29
336527 ATAATTTAAC
*
336537 ATTAAATA-ATTATTTTATTTATTAATTT
1 ATTAAATATATTATTTTATTAATTAATTT
*
336565 ATTAAAT-T-TTATATTT-TTAAATATATTTT
1 ATTAAATATATTAT-TTTATT-AAT-TAATTT
*
336594 ATTAAATACTTATTATTTTATAAATTATATTT
1 ATTAAATA--TATTATTTTATTAATTA-ATTT
*
336626 ATTAAATATTTTATTTT
1 ATTAAATATATTATTTT
336643 GCGTAAAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
27 6 0.10
28 12 0.19
29 12 0.19
30 8 0.13
31 2 0.03
32 18 0.29
33 5 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTAAATATATTATTTTATTAATTAATTT
Found at i:336591 original size:24 final size:22
Alignment explanation
Indices: 336548--336591 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
336538 TTAAATAATT
*
336548 ATTTTATTTATTAATTTATTAA
1 ATTTTATTTATTAATATATTAA
*
336570 ATTTTATATTTTTAAATATATT
1 ATTTTAT-TTATT-AATATATT
336592 TTATTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 4 0.22
24 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTTATTTATTAATATATTAA
Found at i:336600 original size:14 final size:15
Alignment explanation
Indices: 336561--336634 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 15
336551 TTATTTATTA
*
336561 ATTTATTAAATTTTAT
1 ATTTATTAAA-TATAT
336577 ATTT-TTAAATATAT
1 ATTTATTAAATATAT
336591 -TTTATTAAATACTTATT
1 ATTTATTAAATA--TA-T
336608 ATTT-TATAAAT-TAT
1 ATTTAT-TAAATATAT
336622 ATTTATTAAATAT
1 ATTTATTAAATAT
336635 TTTATTTTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 17
0.73 0.01 0.25
Matches are distributed among these distances:
13 3 0.06
14 21 0.43
15 9 0.18
16 6 0.12
17 2 0.04
18 8 0.16
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTATTAAATATAT
Found at i:336627 original size:32 final size:31
Alignment explanation
Indices: 336537--336642 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 31
336527 ATAATTTAAC
**
336537 ATTAAATA--ATTATTTTATTTATTA-ATTT
1 ATTAAATATTATTATTTTATAAATTATATTT
*
336565 ATTAAATTTTA-TATTTT-TAAA-TATATTTT
1 ATTAAATATTATTATTTTATAAATTATA-TTT
336594 ATTAAATACTTATTATTTTATAAATTATATTT
1 ATTAAATA-TTATTATTTTATAAATTATATTT
336626 ATTAAATATT-TTATTTT
1 ATTAAATATTATTATTTT
336643 GCGTAAAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
27 2 0.03
28 10 0.15
29 16 0.24
30 11 0.17
31 8 0.12
32 15 0.23
33 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (31 bp):
ATTAAATATTATTATTTTATAAATTATATTT
Found at i:336747 original size:16 final size:16
Alignment explanation
Indices: 336726--336775 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
336716 GAAAAAATGT
336726 TATTTTATTTATAAAA
1 TATTTTATTTATAAAA
* *
336742 TATTTTATATCT-AAA
1 TATTTTATTTATAAAA
*
336757 T-TTTATATTTTTAAAA
1 TATTT-TATTTATAAAA
336773 TAT
1 TAT
336776 ATAATAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 3 0.11
15 9 0.33
16 14 0.52
17 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTATTTATAAAA
Found at i:337180 original size:17 final size:18
Alignment explanation
Indices: 337143--337180 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
337133 TATTAGTGTG
*
337143 ATTTATTTATAATATACT
1 ATTTATTTATAATAAACT
*
337161 ATTT-TTTATAATAAATT
1 ATTTATTTATAATAAACT
337178 ATT
1 ATT
337181 AACAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTATTTATAATAAACT
Found at i:338175 original size:11 final size:11
Alignment explanation
Indices: 338159--338188 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
338149 CGGAAAATTC
338159 TTTCTTTTTTT
1 TTTCTTTTTTT
338170 TTTCTTTTTTT
1 TTTCTTTTTTT
338181 TTT-TTTTT
1 TTTCTTTTT
338189 ACTTCGGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:338187 original size:15 final size:15
Alignment explanation
Indices: 338156--338186 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
338146 ACTCGGAAAA
338156 TTCTTTCTTTTTTTT
1 TTCTTTCTTTTTTTT
338171 TTCTTT-TTTTTTTT
1 TTCTTTCTTTTTTTT
338185 TT
1 TT
338187 TTACTTCGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTCTTTCTTTTTTTT
Found at i:338508 original size:2 final size:2
Alignment explanation
Indices: 338501--338526 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
338491 AATTAAGCGC
338501 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
338527 GTTCATTGAT
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:338693 original size:50 final size:51
Alignment explanation
Indices: 338618--338716 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 51
338608 ATATAGACAC
*
338618 ACACTAATTCCTTCACGGTTTTCCAGCC-AAATAAACTTAGGCAAGATTAT
1 ACACTAATTCCTTCACCGTTTTCCAGCCAAAATAAACTTAGGCAAGATTAT
338668 ACACTAATTCCTTCACCGTTTTCCAGCCAAAATAAACTTAGGCAAGATT
1 ACACTAATTCCTTCACCGTTTTCCAGCCAAAATAAACTTAGGCAAGATT
338717 CTGCTGCATA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 27 0.57
51 20 0.43
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.29
Consensus pattern (51 bp):
ACACTAATTCCTTCACCGTTTTCCAGCCAAAATAAACTTAGGCAAGATTAT
Found at i:340528 original size:2 final size:2
Alignment explanation
Indices: 340521--340549 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
340511 CATAAATGAA
340521 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
340550 GCACTTACAG
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:342109 original size:21 final size:22
Alignment explanation
Indices: 342081--342145 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
342071 TGAGTTATTT
342081 AATTTAATTTAAAT-ATTT-TA
1 AATTTAATTTAAATAATTTATA
* * *
342101 ATTTTTAATCTGAATAATTTATA
1 A-ATTTAATTTAAATAATTTATA
*
342124 AATTTAATTTAATTTAATTTAT
1 AATTTAATTTAA-ATAATTTAT
342146 TTTTTTTAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.03
21 10 0.29
22 12 0.35
23 11 0.32
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
AATTTAATTTAAATAATTTATA
Found at i:342153 original size:19 final size:19
Alignment explanation
Indices: 342131--342184 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
342121 ATAAATTTAA
**
342131 TTTAATTTAATTTATTTTT
1 TTTAATTTAATTTAAATTT
*
342150 TTTAA-TTAGTATTAAATTT
1 TTTAATTTAAT-TTAAATTT
342169 TTTAATTTAAATTTAA
1 TTTAATTT-AATTTAA
342185 GTTTGAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 4 0.14
19 16 0.57
20 6 0.21
21 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTAATTTAATTTAAATTT
Found at i:343103 original size:19 final size:21
Alignment explanation
Indices: 343076--343162 Score: 72
Period size: 22 Copynumber: 4.0 Consensus size: 21
343066 AATATTTTTT
343076 ATAATTAAATTTAAATAAA-A
1 ATAATTAAATTTAAATAAATA
343096 AT-ATTAAATTAATAAAT-AATA
1 ATAATTAAATT--TAAATAAATA
* *
343117 ATTAATTTAATTTAATTTAAATA
1 A-TAATTAAATTTAA-ATAAATA
* *
343140 AAAATTAAACTTAAATTAAATA
1 ATAATTAAATTTAAA-TAAATA
343162 A
1 A
343163 ATTATTTAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
19 8 0.15
20 4 0.08
21 10 0.19
22 19 0.36
23 12 0.23
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAATTAAATTTAAATAAATA
Found at i:343173 original size:23 final size:23
Alignment explanation
Indices: 343116--343174 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
343106 AATAAATAAT
* *
343116 AATTAATTTAATTTAATTTAAATA
1 AATT-ATTTAACTTAAATTAAATA
* *
343140 AA-AATTAAACTTAAATTAAATA
1 AATTATTTAACTTAAATTAAATA
343162 AATTATTTAACTT
1 AATTATTTAACTT
343175 TTAAATAACC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 18 0.64
23 8 0.29
24 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTATTTAACTTAAATTAAATA
Found at i:343511 original size:16 final size:16
Alignment explanation
Indices: 343490--343637 Score: 67
Period size: 16 Copynumber: 8.9 Consensus size: 16
343480 GAGAAATTAA
343490 ATTTAATAATTTATAT
1 ATTTAATAATTTATAT
343506 ATTTAATTATATTTATAT
1 ATTTAA-TA-ATTTATAT
* *
343524 -TTTTATATGTTATAATTAT
1 ATTTAATA-ATT-T-A-TAT
343543 ATTTAA-AATATTATAT
1 ATTTAATAAT-TTATAT
*
343559 ATTTATAAAATTT-TAAT
1 ATTTA-ATAATTTAT-AT
*
343576 AAATTAATAATTTATAT
1 -ATTTAATAATTTATAT
* *
343593 -TAT-ATATTTTAATAT
1 ATTTAATAATTT-ATAT
343608 ATTT-ATATATTTATAT
1 ATTTAATA-ATTTATAT
*
343624 -TTTATTAATATTAT
1 ATTTAATAAT-TTAT
343638 TTTTATATAT
Statistics
Matches: 103, Mismatches: 12, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
14 6 0.06
15 10 0.10
16 35 0.34
17 24 0.23
18 19 0.18
19 5 0.05
20 4 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (16 bp):
ATTTAATAATTTATAT
Found at i:343513 original size:21 final size:20
Alignment explanation
Indices: 343489--343625 Score: 57
Period size: 22 Copynumber: 6.2 Consensus size: 20
343479 TGAGAAATTA
343489 AATTTAATAATTTATATATTT
1 AATTT-ATAATTTATATATTT
*
343510 AA-TTAT-ATTTATATTTTT
1 AATTTATAATTTATATATTT
*
343528 ATATGTTATAA-TTATAT-TTAA
1 A-AT-TTATAATTTATATATT-T
*
343549 AATATTATATATTTATAAAATTTT
1 AAT-TTATA-ATTTAT-ATA-TTT
*
343573 AATAAATTAATAATTTATATTATAT
1 AAT---TT-ATAATTTATA-TATTT
*
343598 ATTTTAATATATTTATATATTT
1 AATTT-ATA-ATTTATATATTT
343620 ATATTT
1 A-ATTT
343626 TATTAATATT
Statistics
Matches: 90, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
18 12 0.13
19 3 0.03
20 11 0.12
21 14 0.16
22 16 0.18
23 11 0.12
24 3 0.03
25 7 0.08
26 10 0.11
27 3 0.03
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (20 bp):
AATTTATAATTTATATATTT
Found at i:343556 original size:27 final size:25
Alignment explanation
Indices: 343484--343563 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 25
343474 AAATTTGAGA
*
343484 AATTAAATTTAATAATTTATATATTT
1 AATTATATTTAA-AATTTATATATTT
** *
343510 AATTATATTTATATTTTTATATGTTAT
1 AATTATATTTA-AAATTTATATATT-T
343537 AATTATATTTAAAATATTATATATTT
1 AATTATATTTAAAAT-TTATATATTT
343563 A
1 A
343564 TAAAATTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
26 23 0.52
27 21 0.48
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (25 bp):
AATTATATTTAAAATTTATATATTT
Found at i:343615 original size:8 final size:8
Alignment explanation
Indices: 343498--343658 Score: 80
Period size: 7 Copynumber: 21.0 Consensus size: 8
343488 AAATTTAATA
343498 ATTTATAT
1 ATTTATAT
343506 ATTTAATTAT
1 ATTT-A-TAT
343516 ATTTATAT
1 ATTTATAT
343524 -TTT-TAT
1 ATTTATAT
343530 ATGTTATA-
1 AT-TTATAT
343538 A-TTATAT
1 ATTTATAT
* *
343545 -TTAAAAT
1 ATTTATAT
343552 A-TTATAT
1 ATTTATAT
*
343559 ATTTATAAA
1 ATTTAT-AT
*
343568 ATTTTAATAA
1 A-TTT-ATAT
*
343578 ATTAATA-
1 ATTTATAT
343585 ATTTATAT
1 ATTTATAT
*
343593 -TATATAT
1 ATTTATAT
343600 -TTTAATAT
1 ATTT-ATAT
343608 ATTTATAT
1 ATTTATAT
343616 ATTTATAT
1 ATTTATAT
343624 -TTTAT-T
1 ATTTATAT
*
343630 A-ATAT-T
1 ATTTATAT
*
343636 ATTTTTAT
1 ATTTATAT
*
343644 ATAT-TAT
1 ATTTATAT
343651 ATTTATAT
1 ATTTATAT
343659 TGAGTAATTA
Statistics
Matches: 120, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
6 14 0.12
7 40 0.33
8 40 0.33
9 11 0.09
10 13 0.11
11 2 0.02
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (8 bp):
ATTTATAT
Found at i:344706 original size:15 final size:15
Alignment explanation
Indices: 344688--344751 Score: 83
Period size: 15 Copynumber: 4.3 Consensus size: 15
344678 TCAACACCAG
*
344688 CAACGACGACGACAA
1 CAACAACGACGACAA
**
344703 CAACAACGATAACAA
1 CAACAACGACGACAA
*
344718 CAACAACGACGTCAA
1 CAACAACGACGACAA
*
344733 CAACAACGACGTCAA
1 CAACAACGACGACAA
344748 CAAC
1 CAAC
344752 GCTGCAGTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.50, C:0.33, G:0.12, T:0.05
Consensus pattern (15 bp):
CAACAACGACGACAA
Found at i:344751 original size:18 final size:18
Alignment explanation
Indices: 344678--344751 Score: 70
Period size: 15 Copynumber: 4.4 Consensus size: 18
344668 GCTAACAACA
* *
344678 TCAACACCAGCAACGACG
1 TCAACAACAACAACGACG
* *
344696 ACGACAACAACAACGA--
1 TCAACAACAACAACGACG
344712 T-AACAACAACAACGACG
1 TCAACAACAACAACGACG
344729 T---CAACAACAACGACG
1 TCAACAACAACAACGACG
344744 TCAACAAC
1 TCAACAAC
344752 GCTGCAGTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
15 28 0.62
17 1 0.02
18 16 0.36
ACGTcount: A:0.49, C:0.34, G:0.12, T:0.05
Consensus pattern (18 bp):
TCAACAACAACAACGACG
Found at i:348775 original size:3 final size:3
Alignment explanation
Indices: 348767--348792 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
348757 GGGGTTGAGT
348767 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
348793 GCAGTTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:350512 original size:8 final size:8
Alignment explanation
Indices: 350501--350535 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
350491 GGGGGGGGGG
350501 GGGGGAGA
1 GGGGGAGA
350509 GGGGGAGA
1 GGGGGAGA
350517 GGGGGAGA
1 GGGGGAGA
350525 GGGGGAG-
1 GGGGGAGA
350532 GGGG
1 GGGG
350536 TTTATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.15
8 23 0.85
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (8 bp):
GGGGGAGA
Found at i:350520 original size:16 final size:15
Alignment explanation
Indices: 350494--350535 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
350484 GGTGGGGGGG
*
350494 GGGGGGGGGGGGAGA
1 GGGGGAGGGGGGAGA
350509 GGGGGAGAGGGGGAGA
1 GGGGGAG-GGGGGAGA
350525 GGGGGAGGGGG
1 GGGGGAGGGGG
350536 TTTATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (15 bp):
GGGGGAGGGGGGAGA
Found at i:351619 original size:67 final size:67
Alignment explanation
Indices: 351541--351677 Score: 265
Period size: 67 Copynumber: 2.0 Consensus size: 67
351531 AGTACAAAAG
351541 ATAGATTGAAGGAACAATCTTATAAACTACGCATAATTCCATTGAAGTCCTAAAAGGAAACAGTT
1 ATAGATTGAAGGAACAATCTTATAAACTACGCATAATTCCATTGAAGTCCTAAAAGGAAACAGTT
351606 AA
66 AA
*
351608 ATAGATTGAAGGAACCATCTTATAAACTACGCATAATTCCATTGAAGTCCTAAAAGGAAACAGTT
1 ATAGATTGAAGGAACAATCTTATAAACTACGCATAATTCCATTGAAGTCCTAAAAGGAAACAGTT
351673 AA
66 AA
351675 ATA
1 ATA
351678 ACAAATAAGC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.26
Consensus pattern (67 bp):
ATAGATTGAAGGAACAATCTTATAAACTACGCATAATTCCATTGAAGTCCTAAAAGGAAACAGTT
AA
Found at i:352810 original size:9 final size:9
Alignment explanation
Indices: 352796--352833 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
352786 CTCCTGCTCG
352796 TCTTGTTCA
1 TCTTGTTCA
*
352805 TCTTGTTCC
1 TCTTGTTCA
352814 TCTTGTTCA
1 TCTTGTTCA
352823 TCTTGTTCA
1 TCTTGTTCA
352832 TC
1 TC
352834 CTGCTCCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.08, C:0.26, G:0.11, T:0.55
Consensus pattern (9 bp):
TCTTGTTCA
Found at i:352811 original size:27 final size:27
Alignment explanation
Indices: 352774--352842 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
352764 GAAATCCCTC
* *
352774 TTCATGCTGTTCCTCCTGCTCGTCTTG
1 TTCATCCTGTTCCTCCTGCTCATCTTG
* * *
352801 TTCATCTTGTTCCTCTTGTTCATCTTG
1 TTCATCCTGTTCCTCCTGCTCATCTTG
*
352828 TTCATCCTGCTCCTC
1 TTCATCCTGTTCCTC
352843 TCCCTTTCCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.06, C:0.33, G:0.13, T:0.48
Consensus pattern (27 bp):
TTCATCCTGTTCCTCCTGCTCATCTTG
Found at i:354504 original size:20 final size:20
Alignment explanation
Indices: 354479--354525 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
354469 ATGATCTTTA
*
354479 TTAATTATTTATTTTAT-TTT
1 TTAATTATTT-TTATATATTT
354499 TTAATT-TTTTTATATATTT
1 TTAATTATTTTTATATATTT
354518 TTAATTAT
1 TTAATTAT
354526 AAAATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.21
19 12 0.50
20 7 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTAATTATTTTTATATATTT
Found at i:354736 original size:18 final size:19
Alignment explanation
Indices: 354715--354751 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
354705 GTACAAAAAT
354715 ATTTAAATT-TAT-TTTTAA
1 ATTT-AATTATATATTTTAA
354733 ATTTAATTATATATTTTAA
1 ATTTAATTATATATTTTAA
354752 CTTTGATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTAATTATATATTTTAA
Found at i:357557 original size:13 final size:13
Alignment explanation
Indices: 357514--357563 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
357504 TATAAAATAA
*
357514 AAAAATTAAATTT
1 AAAAATTAAAATT
* *
357527 ATAAAATTATAATA
1 A-AAAATTAAAATT
357541 AAAAATTAAAATT
1 AAAAATTAAAATT
*
357554 AAAATTTAAA
1 AAAAATTAAA
357564 GATAATATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:359664 original size:13 final size:13
Alignment explanation
Indices: 359646--359671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
359636 TATGCATATC
359646 AATTTTATTAAAA
1 AATTTTATTAAAA
359659 AATTTTATTAAAA
1 AATTTTATTAAAA
359672 TTTAAGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTTATTAAAA
Found at i:360855 original size:23 final size:22
Alignment explanation
Indices: 360824--360871 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
360814 ATATATGTTT
360824 ATATATTATTATAATTAAATTAA
1 ATATATTATTATAATTAAA-TAA
* *
360847 ATATTTTATTATTATTAAATAA
1 ATATATTATTATAATTAAATAA
360869 ATA
1 ATA
360872 ATAATTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATATTATTATAATTAAATAA
Found at i:363299 original size:3 final size:3
Alignment explanation
Indices: 363293--363319 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
363283 AATAATAATA
363293 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
363320 TCATTAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:363972 original size:20 final size:19
Alignment explanation
Indices: 363921--363973 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
363911 AGTTACTGTA
363921 TTAATAAATAAAAAAATAAT
1 TTAA-AAATAAAAAAATAAT
* * *
363941 TTAAATATTAAAATTAATATT
1 TTAAA-AATAAAA-AAATAAT
363962 TTAAAAATAAAA
1 TTAAAAATAAAA
363974 GAATCGCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 16 0.59
21 10 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAAATAAAAAAATAAT
Found at i:364160 original size:30 final size:28
Alignment explanation
Indices: 364079--364170 Score: 112
Period size: 29 Copynumber: 3.1 Consensus size: 28
364069 AAAACTTTAA
* *
364079 ATTTTATTATTTTATTTAAATAAATTTTT
1 ATTTT-TTATTTTATCTAAATAAGTTTTT
* *
364108 ATATTTTTATTATATGTAAATAAGTTTTT
1 AT-TTTTTATTTTATCTAAATAAGTTTTT
364137 ATTTTTTAATTTTTATCTAAATAAGTTTTT
1 ATTTTTT-A-TTTTATCTAAATAAGTTTTT
364167 ATTT
1 ATTT
364171 CAAAAGAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
28 5 0.09
29 25 0.45
30 25 0.45
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (28 bp):
ATTTTTTATTTTATCTAAATAAGTTTTT
Found at i:364533 original size:29 final size:29
Alignment explanation
Indices: 364457--364533 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 29
364447 TATTAATTGG
* *
364457 TTATTTAAGTTTAAATTAAAAATTATAAGT
1 TTATTTAA-TATAAATTAAAAATTACAAGT
* * * *
364487 TT-TTTTATATAATTTAAAAGTTACGAGT
1 TTATTTAATATAAATTAAAAATTACAAGT
364515 TTATTTAATATAAATTAAA
1 TTATTTAATATAAATTAAA
364534 CATTGAAAGC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 18 0.47
29 18 0.47
30 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.48
Consensus pattern (29 bp):
TTATTTAATATAAATTAAAAATTACAAGT
Found at i:364618 original size:3 final size:3
Alignment explanation
Indices: 364610--364636 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
364600 TTTTAACCAC
364610 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
364637 TTATATCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:365858 original size:19 final size:20
Alignment explanation
Indices: 365827--365864 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
365817 AGTTCAACCC
365827 AAAATATTATTTAATTAATA
1 AAAATATTATTTAATTAATA
*
365847 AAAATATT-TTTATTTAAT
1 AAAATATTATTTAATTAAT
365865 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATATTATTTAATTAATA
Found at i:372453 original size:26 final size:26
Alignment explanation
Indices: 372424--372473 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
372414 AATTTTAATT
372424 ACAT-TTTAAAATACCTTAATTTTTAA
1 ACATCTTT-AAATACCTTAATTTTTAA
**
372450 ACATCTTTAAATATTTTAATTTTT
1 ACATCTTTAAATACCTTAATTTTT
372474 CAATTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (26 bp):
ACATCTTTAAATACCTTAATTTTTAA
Found at i:374042 original size:15 final size:15
Alignment explanation
Indices: 374019--374048 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
374009 CAACTGTTGA
374019 GCCCACTAGACCTAT
1 GCCCACTAGACCTAT
*
374034 GCCCGCTAGACCTAT
1 GCCCACTAGACCTAT
374049 ATCCAACATT
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:0.23, C:0.40, G:0.17, T:0.20
Consensus pattern (15 bp):
GCCCACTAGACCTAT
Found at i:376804 original size:50 final size:50
Alignment explanation
Indices: 376729--376826 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
376719 ATTAAGAAAG
* *
376729 AAATATAAAAGACAATCCGTTTAATTGAGCAACCACCTTTTCAAGTCTAC
1 AAATATAAAAGACAATCCGTTTAATTAAGCAACAACCTTTTCAAGTCTAC
*
376779 AAATATAAAAGACAATCTC-TTTAATTAAGCAAGAACCTTTTCAAGTCT
1 AAATATAAAAGACAATC-CGTTTAATTAAGCAACAACCTTTTCAAGTCT
376827 TGCAACCTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 43 0.98
51 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (50 bp):
AAATATAAAAGACAATCCGTTTAATTAAGCAACAACCTTTTCAAGTCTAC
Found at i:393529 original size:400 final size:409
Alignment explanation
Indices: 392731--393561 Score: 940
Period size: 400 Copynumber: 2.0 Consensus size: 409
392721 TAAAGATTTA
** **
392731 ACTTTTATATATTTATAATGTAAGATTTTTATATTTTTAATTATAGAATTTATTTTCGATCATTA
1 ACTTTTATATATTTATAATAAAAGATTTTTATATTTTTAATTATAGAAACTATTTTCGATCATTA
* * * * **
392796 TTTACTATTTGAACTTGATTTATTTTTAAAATTAAATTTAAATGGTTTTAAATTATCATTTATAA
66 TTTACTATTTGAACTTGATTTATTTTCAAAATTAAATTTAAATGGCTTCAAATTACCACGTATAA
* * *
392861 AAAAACACTCCTATTTATAGTATTCTCTTAAATAAATTTAATTTAATATTTTTGTGAGATTTAAA
131 AAAAACACTCCTATTTATAGTAATCTATTAAATAAATTTAATTTAATATTTTTGTGAGATATAAA
* * **
392926 AATAAAATAAAACTTTATTTGTGTACATATATATAAGATAAGTCACTTTAAAATATAAAAAGAAA
196 AAGAAAATAAAACTTTATTTGTG---ATATATATAAGA-AAGTCAATAGAAAATATAAAAAGAAA
* * * * *
392991 TAAATATAATTAATTATATGAAATATTTTAGTTTTAAATTAAATAAAGTTAAAATAATTAAATGT
257 TAAATATAAGTAATTATATAAAATATTTTAATATTAAATTAAATAAA--TAAAATAATTAAATAT
* * * * * *
393056 AGGACATAAGATAACTTTTTATGATCATTCACATGTGAATAATATAAGCTATCTACGTTAAATAA
320 AGGACACAAGATAACTTTTTATAACCATCCACATGTGAATAAAATAAGCTATCTACATTAAATAA
393121 TTACCTTTTT-TGTAAAAAATTTTG
385 TTACCTTTTTATGTAAAAAATTTTG
* * * * *
393145 GCTTTTATATATTTATCATATAAAAGTTTTTTATATTTTTTAATTATTA-AAACTATTTTTGGTT
1 ACTTTTATATATTTAT-A-ATAAAAGATTTTTATA-TTTTTAATTA-TAGAAACTATTTTCGATC
* * *
393209 ATT-TTTATTATTTGAACTTGATTTATTTTCAAAATTAAATTTAAATGGCTTCCAATTGCCACGT
62 ATTATTTACTATTTGAACTTGATTTATTTTCAAAATTAAATTTAAATGGCTTCAAATTACCACGT
* * * *
393273 CT-AGAATAC-C-CTTATTTATAGTAATCTATTAAATAAATTTAATTTAATATTTTTGTGAGATA
127 ATAAAAAAACACTCCTATTTATAGTAATCTATTAAATAAATTTAATTTAATATTTTTGTGAGATA
* * *
393335 TGAAAAGAAAATTAAAATTTTA-TT-TG-T-TA-A-CAG-AAGTCAATAGAAAATATAAAAAGAA
192 TAAAAAGAAAA-TAAAACTTTATTTGTGATATATATAAGAAAGTCAATAGAAAATATAAAAAGAA
393393 ATAAATATAAGTAATTATATAAAATATTTTAATATTAAATTAAA-ATAA-AAAATAATTAAATAT
256 ATAAATATAAGTAATTATATAAAATATTTTAATATTAAATTAAATA-AATAAAATAATTAAATAT
** ** * * *
393456 TTGACACATTATGGA-TTTTTATAACCATCCACATGTGAATAAAATAGGCTAGT-TACATTGAAT
320 AGGACACAAGAT-AACTTTTTATAACCATCCACATGTGAATAAAATAAGCTA-TCTACATTAAAT
**
393519 AATTACCTTTTTATGTAAAATGTTTTG
383 AATTACCTTTTTATGTAAAAAATTTTG
*
393546 ACTTTTAAATATTTAT
1 ACTTTTATATATTTAT
393562 TTATTTACTT
Statistics
Matches: 354, Mismatches: 54, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
400 72 0.20
401 28 0.08
402 1 0.00
403 64 0.18
405 2 0.01
406 1 0.00
407 2 0.01
408 1 0.00
412 2 0.01
413 59 0.17
414 25 0.07
415 6 0.02
416 66 0.19
417 23 0.06
418 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.44
Consensus pattern (409 bp):
ACTTTTATATATTTATAATAAAAGATTTTTATATTTTTAATTATAGAAACTATTTTCGATCATTA
TTTACTATTTGAACTTGATTTATTTTCAAAATTAAATTTAAATGGCTTCAAATTACCACGTATAA
AAAAACACTCCTATTTATAGTAATCTATTAAATAAATTTAATTTAATATTTTTGTGAGATATAAA
AAGAAAATAAAACTTTATTTGTGATATATATAAGAAAGTCAATAGAAAATATAAAAAGAAATAAA
TATAAGTAATTATATAAAATATTTTAATATTAAATTAAATAAATAAAATAATTAAATATAGGACA
CAAGATAACTTTTTATAACCATCCACATGTGAATAAAATAAGCTATCTACATTAAATAATTACCT
TTTTATGTAAAAAATTTTG
Found at i:393578 original size:2 final size:2
Alignment explanation
Indices: 393571--393600 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
393561 TTTATTTACT
393571 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
393601 AGGTAAGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:395255 original size:3 final size:3
Alignment explanation
Indices: 395247--395272 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
395237 AAATATTTTC
395247 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
395273 CCTATATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:395510 original size:13 final size:13
Alignment explanation
Indices: 395472--395513 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
395462 ATTTTTTAAA
395472 ATTTAAATATTAT
1 ATTTAAATATTAT
* *
395485 A--TATATTTTAT
1 ATTTAAATATTAT
395496 ATTTAAATATTAT
1 ATTTAAATATTAT
395509 ATTTA
1 ATTTA
395514 TTATTCCTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 9 0.39
13 14 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTAAATATTAT
Found at i:396276 original size:18 final size:18
Alignment explanation
Indices: 396250--396296 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
396240 TATTTAATTT
396250 TTATATTAAAATATAAAA
1 TTATATTAAAATATAAAA
* *
396268 TTATTTTAATATAT-AAA
1 TTATATTAAAATATAAAA
396285 TATATATTAAAA
1 T-TATATTAAAA
396297 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTATATTAAAATATAAAA
Found at i:396298 original size:37 final size:36
Alignment explanation
Indices: 396251--396320 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
396241 ATTTAATTTT
* *
396251 TATATTAAAA-TATAAAATTATTTTAATATATAAATA
1 TATATTAAAATTATAAAA-TATTTAAATAAATAAATA
*
396287 TATATTAAAAATTTTAAAATATTTAAATAAATAA
1 TATATT-AAAATTATAAAATATTTAAATAAATAA
396321 TTATTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 6 0.21
37 17 0.59
38 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (36 bp):
TATATTAAAATTATAAAATATTTAAATAAATAAATA
Found at i:396326 original size:33 final size:33
Alignment explanation
Indices: 396280--396345 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
396270 ATTTTAATAT
*
396280 ATAAATATATATTAAAAATT-TTAAAATATTTAA
1 ATAAATATATATT-AAAATTATTAAAAAATTTAA
*
396313 ATAAATA-ATTATTAAATTTATTAAAAAATTTAA
1 ATAAATATA-TATTAAAATTATTAAAAAATTTAA
396346 TTCTCCAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 6 0.21
33 23 0.79
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
ATAAATATATATTAAAATTATTAAAAAATTTAA
Found at i:397406 original size:23 final size:24
Alignment explanation
Indices: 397380--397424 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
397370 TAAAAAAATT
*
397380 AATATGATATTTAT-AAATTTATA
1 AATATGATAATTATAAAATTTATA
*
397403 AATATTATAATTATAAAATTTA
1 AATATGATAATTATAAAATTTA
397425 ATAAGCATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
AATATGATAATTATAAAATTTATA
Found at i:397890 original size:5 final size:5
Alignment explanation
Indices: 397880--397914 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
397870 TAATATTTTT
397880 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA -TAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
397915 AAAAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:399205 original size:2 final size:2
Alignment explanation
Indices: 399200--399250 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
399190 TCTCTCTCTC
399200 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
399242 TA TA TA TA T
1 TA TA TA TA T
399251 GAAAGCATGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:400474 original size:2 final size:2
Alignment explanation
Indices: 400467--400496 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
400457 TCCTTTTTGA
400467 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
400497 GGATTTTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:403695 original size:33 final size:33
Alignment explanation
Indices: 403616--403698 Score: 105
Period size: 32 Copynumber: 2.5 Consensus size: 33
403606 CATAATTGTG
* *
403616 TTTATATTATTTTATATTTATATAAATTTTAAAATA
1 TTTATA-TA-TTTATA-TTAGATAAATTATAAAATA
*
403652 TTAATA-ATTTATATTAGATAAATTATAAAATA
1 TTTATATATTTATATTAGATAAATTATAAAATA
403684 TTTATATATTTATAT
1 TTTATATATTTATAT
403699 AATATTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 22 0.52
33 14 0.33
34 1 0.02
36 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (33 bp):
TTTATATATTTATATTAGATAAATTATAAAATA
Found at i:404471 original size:117 final size:116
Alignment explanation
Indices: 404233--404547 Score: 311
Period size: 117 Copynumber: 2.7 Consensus size: 116
404223 CCAATTTGAT
* * *
404233 TTTGATTTAGACATAAAATAAAAATTAAAAATATTATT-TTTATATTTAATTATAAAATATATGA
1 TTTGATTTAGA-ATAAAATAAAAATT-AAAATATTTTTATTTAAATTTAATTAT-AAATATATAA
* * ** *
404297 ATATTTTTAATATTATTTAAATAAAAAGTAAAATTTTAAATCGATTGGGGTTCAA
63 ATA-TTTTAATATTATTGAAATAAAAAATAAAATAATAAATCGATTGGAGTTCAA
*
404352 TTTGATTTAGATATAAAATAAAAATTTAAAATATTTTTATTTAAACTTAATTAT-AATATATAAA
1 TTTGATTTAGA-ATAAAATAAAAA-TTAAAATATTTTTATTTAAATTTAATTATAAATATATAAA
* * * * *
404416 TATTTTAATATTATTGAAATAAAAAAT-ATATCAATGAGTCGATTTGAGTTTAA
64 TATTTTAATATTATTGAAATAAAAAATAAAAT-AATAAATCGATTGGAGTTCAA
* * **
404469 TTTGATTCT-GAACAAAA-ATAAA--AAAATATTTTTATAAAAATTTAATTATAAAAAATATATA
1 TTTGATT-TAGAATAAAATAAAAATTAAAATATTTTTATTTAAATTTAATTAT---AAATATATA
404530 AATATTTATAATATTATT
62 AATATTT-TAATATTATT
404548 TATAAATAAT
Statistics
Matches: 167, Mismatches: 20, Indels: 20
0.81 0.10 0.10
Matches are distributed among these distances:
112 24 0.14
115 4 0.02
116 23 0.14
117 56 0.34
118 12 0.07
119 33 0.20
120 15 0.09
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (116 bp):
TTTGATTTAGAATAAAATAAAAATTAAAATATTTTTATTTAAATTTAATTATAAATATATAAATA
TTTTAATATTATTGAAATAAAAAATAAAATAATAAATCGATTGGAGTTCAA
Found at i:406566 original size:2 final size:2
Alignment explanation
Indices: 406559--406583 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
406549 AAATTTTAAT
406559 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
406584 CAAATTTTAA
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:406947 original size:18 final size:18
Alignment explanation
Indices: 406909--406947 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
406899 TTATTAGTTT
*
406909 AATTAATTAAATTTATTA
1 AATTAATTAAATTTATAA
406927 AATTAATT-AATTATATAA
1 AATTAATTAAATT-TATAA
406945 AAT
1 AAT
406948 CATTGTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTAATTAAATTTATAA
Found at i:407124 original size:16 final size:15
Alignment explanation
Indices: 407078--407166 Score: 53
Period size: 16 Copynumber: 5.9 Consensus size: 15
407068 ATAATTTTAA
407078 AATATTAAATAT-AT
1 AATATTAAATATAAT
*
407092 AATTTTGATAATA-AAT
1 AATATT-A-AATATAAT
407108 AAGTATTAAATATAAT
1 AA-TATTAAATATAAT
*
407124 AAATATTTAATA-AA-
1 -AATATTAAATATAAT
*
407138 AATATGAAAT-TAACT
1 AATATTAAATATAA-T
*
407153 AAATATTTAATATA
1 -AATATTAAATATA
407167 TTTTTAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
13 10 0.18
14 5 0.09
15 7 0.12
16 28 0.49
17 7 0.12
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (15 bp):
AATATTAAATATAAT
Found at i:407147 original size:29 final size:31
Alignment explanation
Indices: 407100--407164 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
407090 ATAATTTTGA
*
407100 TAATAAATAAGTATTAAATATAA-TAAATATT
1 TAATAAATAAGTATGAAAT-TAACTAAATATT
407131 TAATAAA-AA-TATGAAATTAACTAAATATT
1 TAATAAATAAGTATGAAATTAACTAAATATT
407160 TAATA
1 TAATA
407165 TATTTTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 3 0.09
29 20 0.62
30 2 0.06
31 7 0.22
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (31 bp):
TAATAAATAAGTATGAAATTAACTAAATATT
Found at i:407695 original size:2 final size:2
Alignment explanation
Indices: 407688--407721 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
407678 ATTTAATTTT
407688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
407722 ATCCAAGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:408545 original size:19 final size:19
Alignment explanation
Indices: 408523--408561 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
408513 TTATAATTTT
* *
408523 AATATTTTTTATTATAATA
1 AATATTTATTATCATAATA
408542 AATATTTATTATCATAATA
1 AATATTTATTATCATAATA
408561 A
1 A
408562 TATGATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
AATATTTATTATCATAATA
Found at i:410299 original size:16 final size:17
Alignment explanation
Indices: 410266--410302 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
410256 TAATTTTGAA
410266 TTAAATTTATTTATAAT
1 TTAAATTTATTTATAAT
410283 TTAAA-TTATTT-TAAAT
1 TTAAATTTATTTAT-AAT
410299 TTAA
1 TTAA
410303 TTTTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.05
16 13 0.68
17 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTATTTATAAT
Found at i:410310 original size:16 final size:17
Alignment explanation
Indices: 410266--410302 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
410256 TAATTTTGAA
410266 TTAAATT-TATTTATAAT
1 TTAAATTAT-TTTATAAT
410283 TTAAATTATTTTA-AAT
1 TTAAATTATTTTATAAT
410299 TTAA
1 TTAA
410303 TTTTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 11 0.58
18 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTATTTTATAAT
Found at i:410492 original size:16 final size:16
Alignment explanation
Indices: 410467--410497 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
410457 TAATTAATTT
410467 TTAAAATTAAATAAAA
1 TTAAAATTAAATAAAA
*
410483 TTAAATTTAAATAAA
1 TTAAAATTAAATAAA
410498 TTATTTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAAATTAAATAAAA
Found at i:410780 original size:5 final size:6
Alignment explanation
Indices: 410766--410795 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
410756 ACTTTTTTTC
410766 AAAATA AAAATA AAAATA AAAATA ATAAAT
1 AAAATA AAAATA AAAATA AAAATA A-AAAT
410796 TAATTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:410944 original size:18 final size:19
Alignment explanation
Indices: 410921--410966 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
410911 TTAATGTAAG
*
410921 AATATATAATT-TTTTTAT
1 AATATATAATTCTTATTAT
410939 AATATATAATTCTTATTAT
1 AATATATAATTCTTATTAT
410958 AATAATATA
1 AAT-ATATA
410967 TTTGTGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 11 0.44
19 9 0.36
20 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATATAATTCTTATTAT
Found at i:412249 original size:24 final size:24
Alignment explanation
Indices: 412222--412271 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
412212 GCGATAGCGA
*
412222 TCCCTATCCCTATCTCTATCTCTG
1 TCCCTATCCCTATCCCTATCTCTG
* *
412246 TCCCTCTCTCTATCCCTATCTCTG
1 TCCCTATCCCTATCCCTATCTCTG
412270 TC
1 TC
412272 ACGGCCACGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.44, G:0.04, T:0.42
Consensus pattern (24 bp):
TCCCTATCCCTATCCCTATCTCTG
Found at i:412255 original size:12 final size:12
Alignment explanation
Indices: 412222--412271 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
412212 GCGATAGCGA
* *
412222 TCCCTATCCCTA
1 TCCCTATCTCTG
*
412234 TCTCTATCTCTG
1 TCCCTATCTCTG
* *
412246 TCCCTCTCTCTA
1 TCCCTATCTCTG
412258 TCCCTATCTCTG
1 TCCCTATCTCTG
412270 TC
1 TC
412272 ACGGCCACGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.10, C:0.44, G:0.04, T:0.42
Consensus pattern (12 bp):
TCCCTATCTCTG
Found at i:416271 original size:2 final size:2
Alignment explanation
Indices: 416264--416295 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
416254 ATTCATAACA
416264 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
416296 TACTATTTTA
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):
AT
Found at i:439465 original size:33 final size:33
Alignment explanation
Indices: 439423--439495 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
439413 TGAGGAACAG
439423 TCCCAACCTGAAATACAGCCCATTCAACCTCAA
1 TCCCAACCTGAAATACAGCCCATTCAACCTCAA
439456 TCCCAACCTGAAATACAGCCCATTCAACCTCAA
1 TCCCAACCTGAAATACAGCCCATTCAACCTCAA
439489 TCCCAAC
1 TCCCAAC
439496 TTGTTGCTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.36, C:0.41, G:0.05, T:0.18
Consensus pattern (33 bp):
TCCCAACCTGAAATACAGCCCATTCAACCTCAA
Found at i:447794 original size:2 final size:2
Alignment explanation
Indices: 447787--447816 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
447777 ACATACATAC
447787 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
447817 CTTCATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:452528 original size:41 final size:40
Alignment explanation
Indices: 452483--452580 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 40
452473 TTAATTAAAA
* * *
452483 TAAAATTTTATCATTAAGAAAATTTTTAAATATAAACTTTT
1 TAAAATTTTATCATTAAGAAAATTTGTAAATACAAAC-TCT
*
452524 TAAAACTTTATCATTAAGAAAATTTGTAAATACAAACTCT
1 TAAAATTTTATCATTAAGAAAATTTGTAAATACAAACTCT
* *
452564 TAAACTTTTATAATTAA
1 TAAAATTTTATCATTAA
452581 ATATATTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 16 0.32
41 34 0.68
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (40 bp):
TAAAATTTTATCATTAAGAAAATTTGTAAATACAAACTCT
Found at i:453736 original size:19 final size:19
Alignment explanation
Indices: 453693--453736 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
453683 CCTTTGTTCA
* *
453693 AATTTTTTGTTAATTACCT
1 AATTATTTGTTAATTACAT
* *
453712 ATTTATTTGTTTATTACAT
1 AATTATTTGTTAATTACAT
453731 AATTAT
1 AATTAT
453737 ATAAATTATC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.59
Consensus pattern (19 bp):
AATTATTTGTTAATTACAT
Done.