Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold241
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: 220199
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 1 of 2
Found at i:991 original size:20 final size:19
Alignment explanation
Indices: 959--1005 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
949 TAGATGTTTT
*
959 AAGAAAGAGAAAAAGAAGAGAA
1 AAGAAAGA-AAAATGAA-AG-A
981 AAGAAAGAAAAATGAAAGA
1 AAGAAAGAAAAATGAAAGA
1000 AAGAAA
1 AAGAAA
1006 TTCGTTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
20 2 0.08
21 7 0.29
22 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (19 bp):
AAGAAAGAAAAATGAAAGA
Found at i:2030 original size:25 final size:25
Alignment explanation
Indices: 2002--2061 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
1992 TTTTATCATA
*
2002 AAATTATAATAAAAATAAAAATATT
1 AAATTATAATAAAAATAAAAATAAT
* * *
2027 AAATGT-CACTAAAAATAAATATAAT
1 AAAT-TATAATAAAAATAAAAATAAT
*
2052 AAATAATAAT
1 AAATTATAAT
2062 CCTTAACTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (25 bp):
AAATTATAATAAAAATAAAAATAAT
Found at i:3140 original size:30 final size:30
Alignment explanation
Indices: 3106--3171 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
3096 ATTTTTAAAT
3106 TATTTTAATTA-ATATTAAAATTCATTATTA
1 TATTTTAATTATA-ATTAAAATTCATTATTA
* * * *
3136 TATTTTTATTTTAATTAATATTTATTATTA
1 TATTTTAATTATAATTAAAATTCATTATTA
3166 TATTTT
1 TATTTT
3172 TGAGATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TATTTTAATTATAATTAAAATTCATTATTA
Found at i:4092 original size:29 final size:30
Alignment explanation
Indices: 4049--4105 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
4039 TTCAACCAAA
*
4049 AAATAAAAATTTAAT-GATAAATTTTAATT
1 AAATAAAAATATAATCGATAAATTTTAATT
4078 AAATAAAAATATAATCGATAAATTTTAA
1 AAATAAAAATATAATCGATAAATTTTAA
4106 AATTCATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (30 bp):
AAATAAAAATATAATCGATAAATTTTAATT
Found at i:5796 original size:2 final size:2
Alignment explanation
Indices: 5789--5818 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5779 TTTTTAGAAG
5789 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
5819 GAGATATTTA
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:6022 original size:7 final size:7
Alignment explanation
Indices: 6010--6037 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
6000 GCAGTAAAAG
6010 ATTTTAA
1 ATTTTAA
6017 ATTTTAA
1 ATTTTAA
6024 ATTTTAA
1 ATTTTAA
6031 ATTTTAA
1 ATTTTAA
6038 TAATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTTAA
Found at i:6206 original size:2 final size:2
Alignment explanation
Indices: 6199--6235 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6189 AGGTATAATT
6199 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6236 TACCTTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6635 original size:12 final size:12
Alignment explanation
Indices: 6608--6646 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6598 ATTTTTGATT
*
6608 AAAATAAATAGTA
1 AAAATAAA-AGGA
6621 AAAATAAAAGGA
1 AAAATAAAAGGA
*
6633 AAAATAAAATGA
1 AAAATAAAAGGA
6645 AA
1 AA
6647 GTATAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (12 bp):
AAAATAAAAGGA
Found at i:10530 original size:14 final size:14
Alignment explanation
Indices: 10493--10527 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
10483 TTTATTTTTA
10493 TATAATTTTAATAT
1 TATAATTTTAATAT
10507 TAT-ATTTTAA-AT
1 TATAATTTTAATAT
10519 TATAATTTT
1 TATAATTTT
10528 TAATGTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 12 0.60
14 3 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATAATTTTAATAT
Found at i:11036 original size:18 final size:17
Alignment explanation
Indices: 11013--11047 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
11003 TACATTTAAT
11013 TTTTTAAAAAATTTATAA
1 TTTTT-AAAAATTTATAA
11031 TTTTTAAAAATTTATAA
1 TTTTTAAAAATTTATAA
11048 ATAATATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTTAAAAATTTATAA
Found at i:11037 original size:26 final size:27
Alignment explanation
Indices: 10981--11033 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
10971 TTTTATTTAA
10981 TTAATTTATTTAAAAAATATTATACAT
1 TTAATTTATTTAAAAAATATTATACAT
11008 TTAATTT-TTTAAAAAAT-TTATA-AT
1 TTAATTTATTTAAAAAATATTATACAT
11032 TT
1 TT
11034 TTAAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 4 0.15
25 5 0.19
26 10 0.38
27 7 0.27
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAATTTATTTAAAAAATATTATACAT
Found at i:11105 original size:17 final size:17
Alignment explanation
Indices: 11049--11111 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
11039 AATTTATAAA
*
11049 TAATATCATTTCAATTAAA
1 TAATAT-ATTT-AATTAAT
*
11068 GAA-ATATTTAATTAAT
1 TAATATATTTAATTAAT
*
11084 TAATATGATTTAA-TATT
1 TAATAT-ATTTAATTAAT
11101 TAATATATTTA
1 TAATATATTTA
11112 TATAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 13 0.34
17 15 0.39
18 8 0.21
19 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (17 bp):
TAATATATTTAATTAAT
Found at i:12435 original size:20 final size:18
Alignment explanation
Indices: 12410--12524 Score: 70
Period size: 18 Copynumber: 6.7 Consensus size: 18
12400 ATTTAAAAAT
* *
12410 TATTTATGTTATTATTAAGA
1 TATTTATATAATT-TTAA-A
12430 TATTTATATAATTTTAAA
1 TATTTATATAATTTTAAA
12448 TATTTA-ATAA-TTT--A
1 TATTTATATAATTTTAAA
*
12462 TA-TTATATAAATTTAAA
1 TATTTATATAATTTTAAA
* *
12479 TTTTTATAT-A-TTTATAT
1 TATTTATATAATTTTA-AA
*
12496 TATATT-TATAATTTT-TA
1 TAT-TTATATAATTTTAAA
12513 TA-TTATATAATT
1 TATTTATATAATT
12525 ATATTATACA
Statistics
Matches: 78, Mismatches: 7, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
13 3 0.04
14 7 0.09
15 5 0.06
16 14 0.18
17 15 0.19
18 16 0.21
19 7 0.09
20 11 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTTATATAATTTTAAA
Found at i:12459 original size:17 final size:19
Alignment explanation
Indices: 12410--12460 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
12400 ATTTAAAAAT
* *
12410 TATTTATGTTATTATTAAGA
1 TATTTATATAATT-TTAAGA
12430 TATTTATATAATTTTAA-A
1 TATTTATATAATTTTAAGA
12448 TATTTA-ATAATTT
1 TATTTATATAATTT
12461 ATATTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 4 0.14
20 11 0.38
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
TATTTATATAATTTTAAGA
Found at i:12471 original size:31 final size:31
Alignment explanation
Indices: 12433--12500 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
12423 ATTAAGATAT
*
12433 TTATATAATTTTAAATATTTAATA-ATTTATA
1 TTATATAAATTTAAAT-TTTAATATATTTATA
*
12464 TTATATAAATTTAAATTTTTATATATTTATA
1 TTATATAAATTTAAATTTTAATATATTTATA
12495 TTATAT
1 TTATAT
12501 TTATAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 6 0.18
31 28 0.82
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TTATATAAATTTAAATTTTAATATATTTATA
Found at i:12492 original size:8 final size:8
Alignment explanation
Indices: 12429--12528 Score: 55
Period size: 8 Copynumber: 12.2 Consensus size: 8
12419 TATTATTAAG
12429 ATATTTAT
1 ATATTTAT
*
12437 ATAATTTTAA
1 AT-A-TTTAT
12447 ATATTTA-
1 ATATTTAT
12454 ATAATTTAT
1 AT-ATTTAT
*
12463 AT-TATAT
1 ATATTTAT
* *
12470 AAATTTAA
1 ATATTTAT
*
12478 ATTTTTAT
1 ATATTTAT
12486 ATATTTAT
1 ATATTTAT
12494 ATTATATT-T
1 A-TAT-TTAT
*
12503 ATAATTTTT
1 AT-ATTTAT
12512 ATA-TTAT
1 ATATTTAT
*
12519 ATAATTAT
1 ATATTTAT
12527 AT
1 AT
12529 TATACATAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
7 13 0.18
8 37 0.51
9 14 0.19
10 8 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
ATATTTAT
Found at i:12500 original size:13 final size:13
Alignment explanation
Indices: 12482--12532 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 13
12472 ATTTAAATTT
12482 TTATATATTTATA
1 TTATATATTTATA
12495 -T-TATATTTATA
1 TTATATATTTATA
12506 --AT-T-TTTATA
1 TTATATATTTATA
*
12515 TTATATAATTATA
1 TTATATATTTATA
12528 TTATA
1 TTATA
12533 CATAATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
9 6 0.19
10 1 0.03
11 13 0.41
12 2 0.06
13 10 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:12520 original size:31 final size:31
Alignment explanation
Indices: 12429--12532 Score: 89
Period size: 31 Copynumber: 3.5 Consensus size: 31
12419 TATTATTAAG
* *
12429 ATAT-TTATATAAT-TTTAAATATTTAATAATT
1 ATATATTATATTATATTTAAAT-TTTTAT-ATT
*
12460 -TATATTATA-TAAATTTAAA-TTTT-TA-T
1 ATATATTATATTATATTTAAATTTTTATATT
12486 ATAT-TTATATTATATTTATAATTTTTATATT
1 ATATATTATATTATATTTA-AATTTTTATATT
12517 ATATAATTATATTATA
1 ATAT-ATTATATTATA
12533 CATAATTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
26 6 0.10
27 11 0.19
28 3 0.05
29 7 0.12
30 6 0.10
31 16 0.27
33 10 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
ATATATTATATTATATTTAAATTTTTATATT
Found at i:12525 original size:28 final size:27
Alignment explanation
Indices: 12458--12529 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 27
12448 TATTTAATAA
12458 TTTATATTATAT-A--A-ATTTAAATT
1 TTTATATTATATAATTATATTTAAATT
*
12481 TTTATA-TATTTATATTATATTTATAATT
1 TTTATATTATATA-ATTATATTTA-AATT
12509 TTTATATTATATAATTATATT
1 TTTATATTATATAATTATATT
12530 ATACATAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 4 0.10
23 6 0.15
24 1 0.03
26 1 0.03
27 5 0.12
28 18 0.45
29 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTATATTATATAATTATATTTAAATT
Found at i:13241 original size:29 final size:28
Alignment explanation
Indices: 13165--13239 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 28
13155 AGTCATAAAA
*
13165 TTAAAAAT--ATAATTTTATAAAAAGTT
1 TTAAAAATAAATAATTTTTTAAAAAGTT
*** **
13191 TTAAAAATAAATAAAAAATTTAAAATTTT
1 TTAAAAATAAAT-AATTTTTTAAAAAGTT
13220 TTAAAAATAAATAATTTTTT
1 TTAAAAATAAATAATTTTTT
13240 TATTAATGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
26 8 0.22
28 7 0.19
29 22 0.59
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (28 bp):
TTAAAAATAAATAATTTTTTAAAAAGTT
Found at i:13307 original size:12 final size:13
Alignment explanation
Indices: 13270--13311 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
13260 ATTTATGATG
*
13270 TATAAATATTTATA
1 TATAAATA-ATATA
*
13284 TATAATTAATATA
1 TATAAATAATATA
13297 T-TAAATAATATA
1 TATAAATAATATA
13309 TAT
1 TAT
13312 TTTTATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 11 0.46
13 6 0.25
14 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAAATAATATA
Found at i:13685 original size:18 final size:18
Alignment explanation
Indices: 13649--13694 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
13639 TGATCCTTTG
13649 CTTTCATTTTCTTCTTCTT
1 CTTTC-TTTTCTTCTTCTT
13668 CTTT-TTTTCTTCCTTCTT
1 CTTTCTTTTCTT-CTTCTT
13686 CTTTCTTTT
1 CTTTCTTTT
13695 GCTTTGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.28
18 10 0.40
19 8 0.32
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTCTTTTCTTCTTCTT
Found at i:14084 original size:18 final size:18
Alignment explanation
Indices: 14025--14084 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
14015 TAACATGAAT
* *
14025 ATATTTAATA-TACTTATC
1 ATATTTAATATTAATT-TA
14043 ATATTT-ATATTAATTTA
1 ATATTTAATATTAATTTA
*
14060 ATTTTTAATATTATATTT-
1 ATATTTAATATTA-ATTTA
14078 ATATTTA
1 ATATTTA
14085 CACTATTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 9 0.26
18 22 0.63
19 4 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTAATATTAATTTA
Found at i:14116 original size:2 final size:2
Alignment explanation
Indices: 14109--14139 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
14099 TAATAAAGAG
*
14109 AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14140 CTTAATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15447 original size:27 final size:28
Alignment explanation
Indices: 15378--15448 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
15368 ATTAAATTTG
15378 AAAT-AATTTAAATTATAAAAAATTTTAT
1 AAATGAATTTAAA-TATAAAAAATTTTAT
* **
15406 AATTGACATTTAAATATTTAAAA-TTTAT
1 AAATGA-ATTTAAATATAAAAAATTTTAT
15434 AAATGAATTTAAATA
1 AAATGAATTTAAATA
15449 AATAATAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 9 0.24
28 13 0.35
29 8 0.22
30 7 0.19
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (28 bp):
AAATGAATTTAAATATAAAAAATTTTAT
Found at i:15458 original size:28 final size:28
Alignment explanation
Indices: 15392--15459 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
15382 AATTTAAATT
* *
15392 ATAAA-AAATTTTATAATTGACATTTAA
1 ATAAATAAAATTTATAAATGACATTTAA
**
15419 ATATTTAAAATTTATAAATGA-ATTTAA
1 ATAAATAAAATTTATAAATGACATTTAA
15446 ATAAATAATAATTT
1 ATAAATAA-AATTT
15460 TCATTTAGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 15 0.45
28 18 0.55
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
ATAAATAAAATTTATAAATGACATTTAA
Found at i:15729 original size:2 final size:2
Alignment explanation
Indices: 15717--15758 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
15707 AAAACACAGC
*
15717 GA GA GA TA 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
15759 AACCCAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
GA
Found at i:23040 original size:79 final size:79
Alignment explanation
Indices: 22909--23069 Score: 322
Period size: 79 Copynumber: 2.0 Consensus size: 79
22899 TCAAAATACG
22909 GTTGGCTACAATAGCGGACTCATTGTAGGTGTTCTATCTAGAGTTGGTCAAAATTGGGAATAAAA
1 GTTGGCTACAATAGCGGACTCATTGTAGGTGTTCTATCTAGAGTTGGTCAAAATTGGGAATAAAA
22974 CCTTTTTTTTATGC
66 CCTTTTTTTTATGC
22988 GTTGGCTACAATAGCGGACTCATTGTAGGTGTTCTATCTAGAGTTGGTCAAAATTGGGAATAAAA
1 GTTGGCTACAATAGCGGACTCATTGTAGGTGTTCTATCTAGAGTTGGTCAAAATTGGGAATAAAA
23053 CCTTTTTTTTATGC
66 CCTTTTTTTTATGC
23067 GTT
1 GTT
23070 TGATTGAAGC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (79 bp):
GTTGGCTACAATAGCGGACTCATTGTAGGTGTTCTATCTAGAGTTGGTCAAAATTGGGAATAAAA
CCTTTTTTTTATGC
Found at i:26713 original size:23 final size:23
Alignment explanation
Indices: 26686--26730 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
26676 AAACATTATA
*
26686 TTACTCACCATTCTATCTATATG
1 TTACTCAACATTCTATCTATATG
* *
26709 TTACTTAACATTCTATGTATAT
1 TTACTCAACATTCTATCTATAT
26731 ACATGAAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (23 bp):
TTACTCAACATTCTATCTATATG
Found at i:28827 original size:15 final size:15
Alignment explanation
Indices: 28807--28837 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28797 AAATTTTAAC
*
28807 ATATTAATATTTTAT
1 ATATTAATATTATAT
28822 ATATTAATATTATAT
1 ATATTAATATTATAT
28837 A
1 A
28838 ATAATCAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTAATATTATAT
Found at i:29179 original size:2 final size:2
Alignment explanation
Indices: 29172--29207 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29162 TCAAAGTAAA
29172 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
29208 GAACTTGTAA
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:32704 original size:2 final size:2
Alignment explanation
Indices: 32697--32724 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32687 ATATAAAAAT
32697 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
32725 AATGATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33383 original size:71 final size:72
Alignment explanation
Indices: 33305--33444 Score: 210
Period size: 72 Copynumber: 2.0 Consensus size: 72
33295 CAATCCCATC
* * * *
33305 ACATGATCCCAAATGCACCAGT-TACCAACATTTGACCAATCCATAGCCCAATCTCATTACATGA
1 ACATGATCCCAAATGCACCAATGGACCAACATTTGACCAATCCATAGCCCAATCCCATCACATGA
33369 TCCCGAA
66 TCCCGAA
* * *
33376 ACATGATCCCAAATGCACTAATGGACCAACATTTGACCTATCGATAGCCCAATCCCATCACATGA
1 ACATGATCCCAAATGCACCAATGGACCAACATTTGACCAATCCATAGCCCAATCCCATCACATGA
33441 TCCC
66 TCCC
33445 AAATGCGCCA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
71 20 0.33
72 41 0.67
ACGTcount: A:0.34, C:0.33, G:0.11, T:0.22
Consensus pattern (72 bp):
ACATGATCCCAAATGCACCAATGGACCAACATTTGACCAATCCATAGCCCAATCCCATCACATGA
TCCCGAA
Found at i:33489 original size:58 final size:58
Alignment explanation
Indices: 33376--33520 Score: 204
Period size: 58 Copynumber: 2.5 Consensus size: 58
33366 TGATCCCGAA
* *
33376 ACATGATCCCAAATGCACTAATGGACCAACATTTGACCTATCGATAGCCCAATCCCATC
1 ACATGATCCCAAATGCGCCAAT-GACCAACATTTGACCTATCGATAGCCCAATCCCATC
* *
33435 ACATGATCCCAAATGCGCCAATGACCAACATTTGA-TTAATTC-ATAGTCCAATCCCATC
1 ACATGATCCCAAATGCGCCAATGACCAACATTTGACCT-A-TCGATAGCCCAATCCCATC
*
33493 ACACGATCCCAAATGCGCCAATGACCAA
1 ACATGATCCCAAATGCGCCAATGACCAA
33521 TCTGGGAGAG
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
57 1 0.01
58 56 0.71
59 22 0.28
ACGTcount: A:0.35, C:0.32, G:0.12, T:0.21
Consensus pattern (58 bp):
ACATGATCCCAAATGCGCCAATGACCAACATTTGACCTATCGATAGCCCAATCCCATC
Found at i:35064 original size:6 final size:6
Alignment explanation
Indices: 35053--35082 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35043 TTATGTTTGA
*
35053 AAATTT AAATTT AAATTT AGATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT
35083 TAAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:35486 original size:2 final size:2
Alignment explanation
Indices: 35479--35513 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35469 TACCTAAAAC
35479 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35514 TTATGCTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36229 original size:20 final size:21
Alignment explanation
Indices: 36189--36230 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
36179 AATGATTTAC
* *
36189 TATTTTAGTGATTTTTGTATT
1 TATTTTAGTGAATTTTATATT
36210 TATTTTAG-GAATTTTATATT
1 TATTTTAGTGAATTTTATATT
36230 T
1 T
36231 TTATGTACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (21 bp):
TATTTTAGTGAATTTTATATT
Found at i:36374 original size:28 final size:27
Alignment explanation
Indices: 36320--36390 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
36310 GCCACCCATT
*
36320 TGTTTGTAAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
36347 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
36375 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
36391 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:38235 original size:136 final size:136
Alignment explanation
Indices: 37991--38263 Score: 546
Period size: 136 Copynumber: 2.0 Consensus size: 136
37981 CTTGTATTAC
37991 TACCAGGATAGTACAGTTATTGGAGCAGTAGCAATAGCTTCCGATGGTGACAATTTGGATTCAAC
1 TACCAGGATAGTACAGTTATTGGAGCAGTAGCAATAGCTTCCGATGGTGACAATTTGGATTCAAC
38056 CCAGTTGTGGCATATGCGGTTGGGACACACTGGTGAGAAATCCTTGCAAATTCTGGCAAAGCAAG
66 CCAGTTGTGGCATATGCGGTTGGGACACACTGGTGAGAAATCCTTGCAAATTCTGGCAAAGCAAG
38121 GATTGT
131 GATTGT
38127 TACCAGGATAGTACAGTTATTGGAGCAGTAGCAATAGCTTCCGATGGTGACAATTTGGATTCAAC
1 TACCAGGATAGTACAGTTATTGGAGCAGTAGCAATAGCTTCCGATGGTGACAATTTGGATTCAAC
38192 CCAGTTGTGGCATATGCGGTTGGGACACACTGGTGAGAAATCCTTGCAAATTCTGGCAAAGCAAG
66 CCAGTTGTGGCATATGCGGTTGGGACACACTGGTGAGAAATCCTTGCAAATTCTGGCAAAGCAAG
38257 GATTGT
131 GATTGT
38263 T
1 T
38264 GAAAGGTGCA
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 137 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (136 bp):
TACCAGGATAGTACAGTTATTGGAGCAGTAGCAATAGCTTCCGATGGTGACAATTTGGATTCAAC
CCAGTTGTGGCATATGCGGTTGGGACACACTGGTGAGAAATCCTTGCAAATTCTGGCAAAGCAAG
GATTGT
Found at i:41071 original size:28 final size:27
Alignment explanation
Indices: 41012--41080 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
41002 CACCCATTTG
* * *
41012 TTTGTCAAAAATAGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
41039 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
*
41067 TTTGTCAAATATGG
1 TTTGTCAAAAATGG
41081 AAGCTAGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.50
28 17 0.47
ACGTcount: A:0.26, C:0.07, G:0.20, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:41187 original size:20 final size:20
Alignment explanation
Indices: 41164--41201 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41154 GGCTCCCTCC
41164 TCCCTCTCAAGTATCCCTTA
1 TCCCTCTCAAGTATCCCTTA
**
41184 TCCCTCTCTTGTATCCCT
1 TCCCTCTCAAGTATCCCT
41202 CTTCAAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.42, G:0.05, T:0.39
Consensus pattern (20 bp):
TCCCTCTCAAGTATCCCTTA
Found at i:41573 original size:23 final size:23
Alignment explanation
Indices: 41525--41573 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
41515 AATTAGTTAT
* * *
41525 AAAAAATTGGGATATCAAAATTA
1 AAAAAAATGGGATAACAAAATGA
41548 AAAAAAATGGGATAACAAGAA-GA
1 AAAAAAATGGGATAACAA-AATGA
41571 AAA
1 AAA
41574 TGATTGATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.63, C:0.04, G:0.16, T:0.16
Consensus pattern (23 bp):
AAAAAAATGGGATAACAAAATGA
Found at i:41648 original size:2 final size:2
Alignment explanation
Indices: 41641--41670 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41631 TATCCATTAC
41641 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
41671 ATTCTAGCTG
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:41771 original size:3 final size:3
Alignment explanation
Indices: 41763--41815 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
41753 AGATTTTGTC
41763 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41811 ATAT T
1 -TAT T
41816 TATCATCATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42394 original size:2 final size:2
Alignment explanation
Indices: 42387--42422 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
42377 GAACAAAGAA
*
42387 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42423 TCATTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44321 original size:17 final size:15
Alignment explanation
Indices: 44299--44332 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
44289 ATCTCTTTTT
44299 ATTAATTATTTATTATA
1 ATTAA-TATTTATT-TA
44316 ATTAATATTTATTTA
1 ATTAATATTTATTTA
44331 AT
1 AT
44333 ATAAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTAATATTTATTTA
Found at i:47104 original size:24 final size:25
Alignment explanation
Indices: 47077--47126 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
47067 AATTAGTCAA
47077 TATTTATAAAGTT-TATTTAAT-TAT
1 TATTTATAAA-TTATATTTAATATAT
*
47101 TATTTTTAAATTATATTTAATATAT
1 TATTTATAAATTATATTTAATATAT
47126 T
1 T
47127 TTTTTTACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 17 0.74
25 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTTATAAATTATATTTAATATAT
Found at i:47380 original size:2 final size:2
Alignment explanation
Indices: 47373--47403 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47363 ATGCTTTAAT
47373 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47404 GCTTTATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48724 original size:11 final size:11
Alignment explanation
Indices: 48693--48732 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
48683 AATTTCCTAA
*
48693 AAAATATTTTG
1 AAAATATTTTT
48704 AAAATATTTTT
1 AAAATATTTTT
*
48715 AAAATTTTTTT
1 AAAATATTTTT
*
48726 AATATAT
1 AAAATAT
48733 AAAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:50300 original size:174 final size:174
Alignment explanation
Indices: 50106--50454 Score: 698
Period size: 174 Copynumber: 2.0 Consensus size: 174
50096 AAAAAAATAA
50106 TTTTATTAAAGTAATAATTTGATAGTAAAAAAGAACATGAATTATAACATTAAAAAAATTAATAT
1 TTTTATTAAAGTAATAATTTGATAGTAAAAAAGAACATGAATTATAACATTAAAAAAATTAATAT
50171 AATTATCTCATTAATGTATAATTATTCATTATTATAAATTGTTTTTCTTTATTTATTTTTAAATT
66 AATTATCTCATTAATGTATAATTATTCATTATTATAAATTGTTTTTCTTTATTTATTTTTAAATT
50236 TTAGAAATAAATTCTCAACGTGCGTCATAAAAACTAGTTTATGT
131 TTAGAAATAAATTCTCAACGTGCGTCATAAAAACTAGTTTATGT
50280 TTTTATTAAAGTAATAATTTGATAGTAAAAAAGAACATGAATTATAACATTAAAAAAATTAATAT
1 TTTTATTAAAGTAATAATTTGATAGTAAAAAAGAACATGAATTATAACATTAAAAAAATTAATAT
50345 AATTATCTCATTAATGTATAATTATTCATTATTATAAATTGTTTTTCTTTATTTATTTTTAAATT
66 AATTATCTCATTAATGTATAATTATTCATTATTATAAATTGTTTTTCTTTATTTATTTTTAAATT
50410 TTAGAAATAAATTCTCAACGTGCGTCATAAAAACTAGTTTATGT
131 TTAGAAATAAATTCTCAACGTGCGTCATAAAAACTAGTTTATGT
50454 T
1 T
50455 ATTGACAATA
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 175 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (174 bp):
TTTTATTAAAGTAATAATTTGATAGTAAAAAAGAACATGAATTATAACATTAAAAAAATTAATAT
AATTATCTCATTAATGTATAATTATTCATTATTATAAATTGTTTTTCTTTATTTATTTTTAAATT
TTAGAAATAAATTCTCAACGTGCGTCATAAAAACTAGTTTATGT
Found at i:59319 original size:22 final size:21
Alignment explanation
Indices: 59293--59353 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
59283 TTATATTAAA
*
59293 ATATAATTTTTAATTAATATT
1 ATATAATTTTTAATTAAAATT
59314 -TATATATTTTTAATTAAAATT
1 ATATA-ATTTTTAATTAAAATT
* *
59335 AAATAAATTTTTTATTAAA
1 ATAT-AATTTTTAATTAAA
59354 TAAATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 4 0.12
21 15 0.44
22 14 0.41
23 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATAATTTTTAATTAAAATT
Found at i:59345 original size:21 final size:21
Alignment explanation
Indices: 59295--59394 Score: 51
Period size: 21 Copynumber: 4.7 Consensus size: 21
59285 ATATTAAAAT
* * *
59295 ATAATTTTTAATTAATATT-T
1 ATAAATTTTAATTAAAATTAA
*
59315 ATATATTTTTAATTAAAATTAA
1 ATA-AATTTTAATTAAAATTAA
* *
59337 ATAAATTTTTTATT-AAATAAATA
1 ATAAA-TTTTAATTAAAAT-TA-A
* *
59360 ATAAATTTTAAATCAAATTAA
1 ATAAATTTTAATTAAAATTAA
* * *
59381 GTCAATTTAAATTA
1 ATAAATTTTAATTA
59395 TAAAAATACT
Statistics
Matches: 61, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
20 3 0.05
21 30 0.49
22 18 0.30
23 10 0.16
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (21 bp):
ATAAATTTTAATTAAAATTAA
Found at i:60172 original size:20 final size:20
Alignment explanation
Indices: 60147--60188 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
60137 TTAGTTTTTA
*
60147 TTTTTAATTTATATTAAAAT
1 TTTTTAATTCATATTAAAAT
*
60167 TTTTTAATTCATATTTAAAT
1 TTTTTAATTCATATTAAAAT
60187 TT
1 TT
60189 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAATTCATATTAAAAT
Found at i:65243 original size:2 final size:2
Alignment explanation
Indices: 65236--65273 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
65226 TTAAAGGAGC
65236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65274 TCATGTATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65429 original size:36 final size:37
Alignment explanation
Indices: 65336--65441 Score: 178
Period size: 38 Copynumber: 2.8 Consensus size: 37
65326 AATAGACAGC
*
65336 TCATTTTCATAAGATATATTTTTTTATTCAGATAAAAA
1 TCATTTTCATAAGA-ACATTTTTTTATTCAGATAAAAA
65374 TCATTTTCATAAGACACATTTTTTTATTCAGATAAAAA
1 TCATTTTCATAAGA-ACATTTTTTTATTCAGATAAAAA
65412 TCATTTTCATAAG-ACATTTTTTTATTCAGA
1 TCATTTTCATAAGAACATTTTTTTATTCAGA
65442 CAATTTTTTA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 17 0.26
38 49 0.74
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (37 bp):
TCATTTTCATAAGAACATTTTTTTATTCAGATAAAAA
Found at i:65530 original size:3 final size:3
Alignment explanation
Indices: 65522--65557 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
65512 ATATTTATCT
* *
65522 TAA TAA TAA CAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
65558 AAAACCTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:71243 original size:21 final size:22
Alignment explanation
Indices: 71205--71250 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
71195 ATCTGCTGAA
* **
71205 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
71226 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
71248 ACT
1 ACT
71251 TGTCTGAACA
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:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:75729 original size:16 final size:16
Alignment explanation
Indices: 75692--75731 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
75682 TTTGAAATAC
75692 ATTTTTTTCAACCCAA
1 ATTTTTTTCAACCCAA
* **
75708 ACTTTTTTCAACTTAA
1 ATTTTTTTCAACCCAA
75724 ATTTTTTT
1 ATTTTTTT
75732 TAAATAACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTTTTCAACCCAA
Found at i:76937 original size:18 final size:18
Alignment explanation
Indices: 76914--76957 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
76904 AACACAAAAC
* *
76914 TTATATAAAATTAGTTTG
1 TTATATAAAATCAATTTG
76932 TTATATAAAATCAATTTG
1 TTATATAAAATCAATTTG
*
76950 TTAAATAA
1 TTATATAA
76958 TTGAATATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (18 bp):
TTATATAAAATCAATTTG
Found at i:79553 original size:26 final size:26
Alignment explanation
Indices: 79519--79573 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
79509 ATTTATTCTT
* *
79519 ATTTATTTATATTTGATTTATGTTTAA
1 ATTTATTTAAATTTGATTTAT-TTAAA
*
79546 ATTT-TTTAAATTTGTTTTATTTAAA
1 ATTTATTTAAATTTGATTTATTTAAA
79571 ATT
1 ATT
79574 AAATATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 14 0.56
27 4 0.16
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (26 bp):
ATTTATTTAAATTTGATTTATTTAAA
Found at i:79687 original size:25 final size:24
Alignment explanation
Indices: 79623--79686 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 24
79613 TGATCATTAA
*
79623 ATAAATATATAATTAAAATATATTC
1 ATAAATA-ATAATAAAAATATATTC
* *
79648 ATAAATAAT--TAAAAATTTATTT
1 ATAAATAATAATAAAAATATATTC
79670 ATAAATAATAATAAAAA
1 ATAAATAATAATAAAAA
79687 AATCTAAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 19 0.56
24 8 0.24
25 7 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAAATAATAATAAAAATATATTC
Found at i:79749 original size:31 final size:32
Alignment explanation
Indices: 79704--79763 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
79694 ACAAAATTTT
79704 TAAAAAAATTAAAAT-TAAATTATTATTAAATA
1 TAAAAAAATTAAAATATAAA-TATTATTAAATA
*
79736 TAAAATAA-TAAAATATAAATATTATTAA
1 TAAAAAAATTAAAATATAAATATTATTAA
79764 TTATGTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAAAAAATTAAAATATAAATATTATTAAATA
Found at i:79782 original size:24 final size:25
Alignment explanation
Indices: 79744--79798 Score: 87
Period size: 24 Copynumber: 2.2 Consensus size: 25
79734 TATAAAATAA
79744 TAAAATATAAATATTATTAATTATGT
1 TAAAATATAAATATTATTAATTAT-T
79770 TAAAAT-T-AATATTATTAATTATT
1 TAAAATATAAATATTATTAATTATT
79793 TAAAAT
1 TAAAAT
79799 CGAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 7 0.24
24 15 0.52
25 1 0.03
26 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TAAAATATAAATATTATTAATTATT
Found at i:79804 original size:24 final size:24
Alignment explanation
Indices: 79753--79804 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
79743 ATAAAATATA
*
79753 AATATTATTAATTATGTTAAAATT
1 AATATTATTAATTATGTTAAAATG
79777 AATATTATTAATTAT-TTAAAATCG
1 AATATTATTAATTATGTTAAAAT-G
79801 AATA
1 AATA
79805 ATAAGCGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AATATTATTAATTATGTTAAAATG
Found at i:83247 original size:50 final size:50
Alignment explanation
Indices: 83182--83476 Score: 455
Period size: 50 Copynumber: 5.9 Consensus size: 50
83172 TTGATTATCA
* * * *
83182 TTCACCAACCTTTGACAATAGAGAGAGGTAGTCGTAATTATTGATGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTC
*
83232 TTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTAATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTC
* **
83282 TTCACCAACTTTTGACAATAGAGAGAGGTGGCTATAATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTC
83332 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTC
* * **
83382 TTCACCAACCTTTGACAATAGAAAGAGGTGGCCATTTTTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTC
* * *
83432 TTCACCAACCTTTGACAATATAGAAAGGTGGCCATAATTGTTGAC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGAC
83477 TCTAAGTATA
Statistics
Matches: 226, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 226 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (50 bp):
TTCACCAACCTTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTC
Found at i:87897 original size:50 final size:50
Alignment explanation
Indices: 87832--88105 Score: 406
Period size: 50 Copynumber: 5.5 Consensus size: 50
87822 TTGACTATCA
87832 TTCACCAACCTTTGACAATAGAGAGAGGTAGCCGTAATTATTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTAGCCGTAATTATTGACGATTC
* * **
87882 TTCACCAACCTTTGACAATAGAGAGAGATGGCCGTAATTATTGATAATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTAGCCGTAATTATTGACGATTC
* * * *
87932 TTCACCAACCTTTGACAATAGAGAGAGATGGCCATAATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTAGCCGTAATTATTGACGATTC
* *
87982 TTCACCAACTTTTGACAATAGAGAGAGGTAGACGTAATTATTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTAGCCGTAATTATTGACGATTC
* * * *
88032 TTCACCAACCTTTGACAATAGAAAGAGGT-GACCATTATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTAG-CCGTAATTATTGACGATTC
88082 TTCACCAACCTTTGACAATAGAGA
1 TTCACCAACCTTTGACAATAGAGA
88106 AATGTGACCA
Statistics
Matches: 202, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
49 1 0.00
50 201 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (50 bp):
TTCACCAACCTTTGACAATAGAGAGAGGTAGCCGTAATTATTGACGATTC
Found at i:88089 original size:150 final size:150
Alignment explanation
Indices: 87818--88126 Score: 471
Period size: 150 Copynumber: 2.1 Consensus size: 150
87808 AGTTATTGCC
* *
87818 ATTGTTGACTATCATTCACCAACCTTTGACAATAGAGAGAGGTAGCCGTAATTATTGACGATTCT
1 ATTGTTGACGATCATTCACCAACCTTTGACAATAGAGAGAGGTAGACGTAATTATTGACGATTCT
* * * *
87883 TCACCAACCTTTGACAATAGAGAGAGATGGCCGTAATTATTGATAATTCTTCACCAACCTTTGAC
66 TCACCAACCTTTGACAATAGAAAGAGATGACCATAATTATTGACAATTCTTCACCAACCTTTGAC
87948 AATAGAGAGAGATG-G-CCATA
131 AATAGAGA-A-ATGTGACCATA
*
87968 ATTGTTGACGATTC-TTCACCAACTTTTGACAATAGAGAGAGGTAGACGTAATTATTGACGATTC
1 ATTGTTGACGA-TCATTCACCAACCTTTGACAATAGAGAGAGGTAGACGTAATTATTGACGATTC
* * * *
88032 TTCACCAACCTTTGACAATAGAAAGAGGTGACCATTATTGTTGACGATTCTTCACCAACCTTTGA
65 TTCACCAACCTTTGACAATAGAAAGAGATGACCATAATTATTGACAATTCTTCACCAACCTTTGA
88097 CAATAGAGAAATGTGACCATA
130 CAATAGAGAAATGTGACCATA
88118 ATTGTTGAC
1 ATTGTTGAC
88127 TCTAAGTATA
Statistics
Matches: 145, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
148 3 0.02
149 2 0.01
150 138 0.95
151 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (150 bp):
ATTGTTGACGATCATTCACCAACCTTTGACAATAGAGAGAGGTAGACGTAATTATTGACGATTCT
TCACCAACCTTTGACAATAGAAAGAGATGACCATAATTATTGACAATTCTTCACCAACCTTTGAC
AATAGAGAAATGTGACCATA
Found at i:88113 original size:50 final size:51
Alignment explanation
Indices: 87818--88126 Score: 384
Period size: 50 Copynumber: 6.2 Consensus size: 51
87808 AGTTATTGCC
* *
87818 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAG-AGAGGT-AGCCGTA
1 ATTGTTGACGATTC-TTCACCAACCTTTGACAATAGAGAAGAGGTGA-CCATA
* * * *
87868 ATTATTGACGATTCTTCACCAACCTTTGACAATAGAG-AGAGATGGCCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAAGAGGTGACCATA
* ** * *
87918 ATTATTGATAATTCTTCACCAACCTTTGACAATAGAG-AGAGATGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAAGAGGTGACCATA
* *
87968 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAG-AGAGGTAGA-CGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAAGAGGT-GACCATA
* *
88018 ATTATTGACGATTCTTCACCAACCTTTGACAATAGA-AAGAGGTGACCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAAGAGGTGACCATA
*
88068 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAA-ATGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAAGAGGTGACCATA
88118 ATTGTTGAC
1 ATTGTTGAC
88127 TCTAAGTATA
Statistics
Matches: 232, Mismatches: 21, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
49 2 0.01
50 225 0.97
51 5 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (51 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAAGAGGTGACCATA
Found at i:91787 original size:2 final size:2
Alignment explanation
Indices: 91780--91808 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
91770 AATTAACATA
91780 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
91809 AATTAAGAGC
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:92720 original size:18 final size:19
Alignment explanation
Indices: 92678--92720 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
92668 TATTATATGT
* *
92678 AATTATTTAATATAATTTA
1 AATTATTTAAAATAATCTA
92697 AA-TATTTAAAAT-ATCTA
1 AATTATTTAAAATAATCTA
92714 AATTATT
1 AATTATT
92721 ATTAATTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTATTTAAAATAATCTA
Found at i:92825 original size:30 final size:32
Alignment explanation
Indices: 92791--92849 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
92781 AATACTAATA
*
92791 TTTGTTA-ACACAAAAATTATAT-AAAATTAT
1 TTTGTTATACAAAAAAATTATATCAAAATTAT
*
92821 TTTGTTATATAAAAAAATTATATCAAAAT
1 TTTGTTATACAAAAAAATTATATCAAAAT
92850 GGAGAAATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 13 0.52
32 5 0.20
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (32 bp):
TTTGTTATACAAAAAAATTATATCAAAATTAT
Found at i:94351 original size:18 final size:17
Alignment explanation
Indices: 94328--94365 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
94318 TGTCTTTTTT
94328 ATTTT-ATTTCTCCATTTA
1 ATTTTAATTT-TCCA-TTA
94346 ATTTTAATTTTCCATTA
1 ATTTTAATTTTCCATTA
94363 ATT
1 ATT
94366 GTTTTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 9 0.47
19 4 0.21
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTAATTTTCCATTA
Found at i:94631 original size:18 final size:18
Alignment explanation
Indices: 94608--94652 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
94598 TAACATCAAA
* *
94608 ATTATATAAAATTAGTTT
1 ATTATATAAAATCAATTT
94626 ATTATATAAAATCAATTT
1 ATTATATAAAATCAATTT
*
94644 ATTAAATAA
1 ATTATATAA
94653 TTGAATATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTATATAAAATCAATTT
Found at i:95129 original size:23 final size:23
Alignment explanation
Indices: 95055--95129 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 23
95045 AGTTATTTAA
*
95055 TTATAATTGAGTCATTTT-TATT
1 TTATAATTAAGTCATTTTATATT
*
95077 TT-TAGTATTAAATTCTAGTTATTATGATT
1 TTATA--ATT-AAGTC-A-TT-TTAT-ATT
95106 TTATAATTAAGTCATTTTATATT
1 TTATAATTAAGTCATTTTATATT
95129 T
1 T
95130 AAAATATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 17
0.67 0.05 0.28
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 7 0.17
24 7 0.17
25 3 0.07
26 3 0.07
27 6 0.15
28 4 0.10
29 5 0.12
30 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (23 bp):
TTATAATTAAGTCATTTTATATT
Found at i:97062 original size:17 final size:16
Alignment explanation
Indices: 97037--97085 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
97027 TAAAAAAATC
*
97037 AAATTTAAATTATTATT
1 AAATATAAA-TATTATT
* *
97054 AAATATAAA-ATAATA
1 AAATATAAATATTATT
97069 AAATATAAATATTATT
1 AAATATAAATATTATT
97085 A
1 A
97086 TTTATTTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 13 0.50
16 5 0.19
17 8 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATATAAATATTATT
Found at i:97104 original size:24 final size:23
Alignment explanation
Indices: 97067--97121 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
97057 TATAAAATAA
*
97067 TAAAATATAAATATTATTATTTATT
1 TAAAAT-T-AATATTATTAATTATT
97092 TCAAAATTAATATTATTAATTATT
1 T-AAAATTAATATTATTAATTATT
97116 TAAAAT
1 TAAAAT
97122 AGAACAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 5 0.18
24 16 0.57
25 2 0.07
26 5 0.18
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAATTAATATTATTAATTATT
Found at i:101225 original size:27 final size:27
Alignment explanation
Indices: 101179--101251 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
101169 AACCACCCAT
*
101179 TATTTGTCAATAATTA-TGGTTACTTTG
1 TATTTGTCAA-AAATAGTGGTTACTTTG
* * *
101206 TGTTTGTCAAAAATAGTGGTTTCTTTT
1 TATTTGTCAAAAATAGTGGTTACTTTG
101233 TATTTGTCAAAAATAGTGG
1 TATTTGTCAAAAATAGTGG
101252 CATGTTGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.10
27 36 0.90
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (27 bp):
TATTTGTCAAAAATAGTGGTTACTTTG
Found at i:101267 original size:24 final size:25
Alignment explanation
Indices: 101206--101268 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 25
101196 GGTTACTTTG
* *
101206 TGTTTGTCAAAAATAGTGGTTTCTTTT
1 TGTTTGTCAAAAATAGTGG--TCATGT
*
101233 TATTTGTCAAAAATAGTGG-CATGT
1 TGTTTGTCAAAAATAGTGGTCATGT
101257 TGTTTGTCAAAA
1 TGTTTGTCAAAA
101269 TTTGTAGCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 14 0.44
27 18 0.56
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (25 bp):
TGTTTGTCAAAAATAGTGGTCATGT
Found at i:105717 original size:27 final size:27
Alignment explanation
Indices: 105687--105759 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
105677 AACCACCCAT
*
105687 TGTTTGTCAAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* *
105714 TGTTTGTCAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
105741 TATTTGTCAAAAATGGTGG
1 TGTTTGTCAAAAATGGTGG
105760 CATGTTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:105770 original size:24 final size:25
Alignment explanation
Indices: 105686--105776 Score: 94
Period size: 27 Copynumber: 3.5 Consensus size: 25
105676 AAACCACCCA
* *
105686 TTGTTTGTCAAAAATTGTGGTTACTT
1 TTGTTTGTCAAAAATGGTGGTCA-TT
*
105712 TGTGTTTGTCAAAAATGGTGGTTTCTTT
1 T-TGTTTGTCAAAAATGGTGG--TCATT
* *
105740 TTATTTGTCAAAAATGGTGG-CATG
1 TTGTTTGTCAAAAATGGTGGTCATT
105764 TTGTTTGTCAAAA
1 TTGTTTGTCAAAA
105777 TTTGTAGCTA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
24 14 0.25
26 1 0.02
27 36 0.65
28 3 0.05
29 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (25 bp):
TTGTTTGTCAAAAATGGTGGTCATT
Found at i:107606 original size:2 final size:2
Alignment explanation
Indices: 107599--107635 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
107589 TAATGAGTTT
107599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
107636 TTTAAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:108031 original size:14 final size:14
Alignment explanation
Indices: 108012--108064 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
108002 AAAAATAATG
*
108012 TTTTTCTTTTTTTC
1 TTTTTCTTTTTCTC
*
108026 TTTTTCTTTTTGTC
1 TTTTTCTTTTTCTC
*
108040 TTCTTTTCTATTTCTC
1 -T-TTTTCTTTTTCTC
*
108056 TGTTTCTTT
1 TTTTTCTTT
108065 CGACCGACCC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.59
15 2 0.06
16 11 0.34
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (14 bp):
TTTTTCTTTTTCTC
Found at i:108046 original size:22 final size:21
Alignment explanation
Indices: 108012--108063 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
108002 AAAAATAATG
* *
108012 TTTTTCTTTTTTTCTTTTTCT
1 TTTTTCTTCTTTTCTATTTCT
108033 TTTTGTCTTCTTTTCTATTTCT
1 TTTT-TCTTCTTTTCTATTTCT
*
108055 CTGTTTCTT
1 -TTTTTCTT
108064 TCGACCGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 19 0.73
23 3 0.12
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (21 bp):
TTTTTCTTCTTTTCTATTTCT
Found at i:108325 original size:18 final size:17
Alignment explanation
Indices: 108302--108342 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
108292 GTAACCTTTA
**
108302 TTTTTTTCTCTTTTCAT
1 TTTTTTTCTCACTTCAT
108319 CTTTTTTTCTCACTTCAT
1 -TTTTTTTCTCACTTCAT
108337 TTTTTT
1 TTTTTT
108343 AATTTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTTCTCACTTCAT
Found at i:108520 original size:29 final size:30
Alignment explanation
Indices: 108488--108545 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
108478 TATTAAAATA
108488 TAAATAAATTATCAAAATAC-ATTATTTTT
1 TAAATAAATTATCAAAATACTATTATTTTT
* * * *
108517 TAAATTATTTTTCAAATTACTATTATTTT
1 TAAATAAATTATCAAAATACTATTATTTT
108546 GACTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (30 bp):
TAAATAAATTATCAAAATACTATTATTTTT
Found at i:108805 original size:32 final size:32
Alignment explanation
Indices: 108764--108833 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
108754 AACTAGATAA
*
108764 GCTGAGTGGCCCAGCGCATTCACGTTGGATGC
1 GCTGAGTGGCCCAGCACATTCACGTTGGATGC
108796 GCTGAGTGGCCCAGCACATTCACGTTGGATGC
1 GCTGAGTGGCCCAGCACATTCACGTTGGATGC
108828 GCTGAG
1 GCTGAG
108834 CCCTTTAGCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.17, C:0.27, G:0.34, T:0.21
Consensus pattern (32 bp):
GCTGAGTGGCCCAGCACATTCACGTTGGATGC
Found at i:109318 original size:27 final size:27
Alignment explanation
Indices: 109280--109337 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
109270 CTGGGTCGTG
*
109280 GTAGGATATGATGGGTATAGAGGTTGA
1 GTAGGATATGATAGGTATAGAGGTTGA
109307 GTAGGATATGATAGGTATAGAGGTTGA
1 GTAGGATATGATAGGTATAGAGGTTGA
109334 GTAG
1 GTAG
109338 AAAAATATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.40, T:0.29
Consensus pattern (27 bp):
GTAGGATATGATAGGTATAGAGGTTGA
Found at i:116768 original size:16 final size:17
Alignment explanation
Indices: 116738--116772 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
116728 TCACTTTTTC
*
116738 ATTTGAAATAGAAATTT
1 ATTTGAAATACAAATTT
116755 ATTT-AAATACAAATTT
1 ATTTGAAATACAAATTT
116771 AT
1 AT
116773 GAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (17 bp):
ATTTGAAATACAAATTT
Found at i:116960 original size:2 final size:2
Alignment explanation
Indices: 116953--116988 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
116943 TAATATGGGC
116953 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
116989 GTCTTTTCAA
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:119322 original size:2 final size:2
Alignment explanation
Indices: 119315--119345 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
119305 GGGAGCATGC
119315 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
119346 GAAAATATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:120026 original size:14 final size:15
Alignment explanation
Indices: 119992--120024 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
119982 TGAACATAAT
*
119992 TTTTTC-AATCTAAA
1 TTTTTCTAATCCAAA
120006 TTTTTCTAATCCAAA
1 TTTTTCTAATCCAAA
120021 TTTT
1 TTTT
120025 CTTTTTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTCTAATCCAAA
Found at i:120198 original size:28 final size:27
Alignment explanation
Indices: 120132--120205 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
120122 AAAAGTCACT
*
120132 CTTTGTGTTTGTCAAAAATGGTGGTTA
1 CTTTGTGTTTGTCAAAAATGGTGATTA
* *
120159 CTTTGTATTTGTCAAAAATGGTGATTT
1 CTTTGTGTTTGTCAAAAATGGTGATTA
*
120186 CTTTTTTGTTTGTCAAAAAT
1 C-TTTGTGTTTGTCAAAAAT
120206 TATAGCTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.24, C:0.08, G:0.19, T:0.49
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGGTGATTA
Found at i:122801 original size:21 final size:22
Alignment explanation
Indices: 122772--122817 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
122762 TGTTCAGACA
* *
122772 AGTAGTACTCCACAGTAGGTGG
1 AGTAGTACTCCAAAATAGGTGG
122794 AGTA-TACTCCAAAATAGGTGG
1 AGTAGTACTCCAAAATAGGTGG
122815 AGT
1 AGT
122818 TTCAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (22 bp):
AGTAGTACTCCAAAATAGGTGG
Found at i:124763 original size:28 final size:28
Alignment explanation
Indices: 124695--124770 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 28
124685 ACAAAAGCCA
124695 CCTTTTGTGTTTGTCAAAAATGGTTGTT
1 CCTTTTGTGTTTGTCAAAAATGGTTGTT
* *
124723 AC-TTTGTATTTGTCAAAAATGG-TGATT
1 CCTTTTGTGTTTGTCAAAAATGGTTG-TT
* *
124750 CCTTTTTTGTTTGTTAAAAAT
1 CCTTTTGTGTTTGTCAAAAAT
124771 TATGGCTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.05
27 22 0.55
28 16 0.40
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (28 bp):
CCTTTTGTGTTTGTCAAAAATGGTTGTT
Found at i:125554 original size:6 final size:6
Alignment explanation
Indices: 125528--125561 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
125518 TAATTTTAAA
125528 TATATT TAATATT TATA-T TATATT TATATT TATA
1 TATATT T-ATATT TATATT TATATT TATATT TATA
125562 AATTTGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 15 0.58
7 6 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:125556 original size:17 final size:18
Alignment explanation
Indices: 125528--125561 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
125518 TAATTTTAAA
125528 TATATTTAATATTTATAT
1 TATATTTAATATTTATAT
125546 TATATTT-ATATTTATA
1 TATATTTAATATTTATA
125562 AATTTGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTAATATTTATAT
Found at i:125559 original size:43 final size:44
Alignment explanation
Indices: 125512--125610 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 44
125502 TTGAATGTAA
125512 ATTTAATAATTTTAAATATATTTAAT-A-TTTATATTATATTTAT
1 ATTTAATAATTTTAAA-ATATTTAATCATTTTATATTATATTTAT
* * * * *
125555 ATTT-ATAAATTTGAAATATTTAATCATTTTTTGTTGTATTTAT
1 ATTTAATAATTTTAAAATATTTAATCATTTTATATTATATTTAT
125598 ATTTAAATAATTT
1 ATTT-AATAATTT
125611 ATATAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
41 9 0.20
42 10 0.22
43 21 0.46
45 6 0.13
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (44 bp):
ATTTAATAATTTTAAAATATTTAATCATTTTATATTATATTTAT
Found at i:128010 original size:12 final size:12
Alignment explanation
Indices: 127993--128017 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
127983 TTTTATTATT
127993 TTAATACAACGA
1 TTAATACAACGA
128005 TTAATACAACGA
1 TTAATACAACGA
128017 T
1 T
128018 ATTATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (12 bp):
TTAATACAACGA
Found at i:130930 original size:24 final size:24
Alignment explanation
Indices: 130902--130947 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
130892 AATAAAAATT
*
130902 AGCCACTAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* *
130926 AGCCACCATTTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
130948 AAATAACCAC
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:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:130975 original size:28 final size:27
Alignment explanation
Indices: 130928--131005 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 27
130918 AAACAACAAG
* *
130928 CCACCATTTTTTAC-AA-ACAAAAATAA
1 CCACCATATTTGACAAATACAAAAA-AA
*
130954 CCACCATATTTGACAAATACAAAGGAAA
1 CCACCATATTTGACAAATACAAA-AAAA
130982 CCACCATATTTGACAAATACAAAA
1 CCACCATATTTGACAAATACAAAA
131006 TATGGTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
26 12 0.27
27 2 0.04
28 30 0.67
29 1 0.02
ACGTcount: A:0.50, C:0.23, G:0.05, T:0.22
Consensus pattern (27 bp):
CCACCATATTTGACAAATACAAAAAAA
Found at i:131405 original size:15 final size:17
Alignment explanation
Indices: 131387--131419 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
131377 TTTTTTAATG
131387 AAATATA-TTTTT-TTA
1 AAATATAGTTTTTATTA
131402 AAATATAGTTTTTATTA
1 AAATATAGTTTTTATTA
131419 A
1 A
131420 TTTAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AAATATAGTTTTTATTA
Found at i:134312 original size:34 final size:33
Alignment explanation
Indices: 134264--134382 Score: 159
Period size: 34 Copynumber: 3.5 Consensus size: 33
134254 TGGTAAAAAC
*
134264 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
134297 CTACCATTTAGTCAACAATGATAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
134331 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
134365 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
134383 TCTCCCACTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.24
34 54 0.73
35 2 0.03
ACGTcount: A:0.43, C:0.27, G:0.06, T:0.24
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:138836 original size:34 final size:33
Alignment explanation
Indices: 138788--138904 Score: 164
Period size: 34 Copynumber: 3.5 Consensus size: 33
138778 TGGTAAAAAC
*
138788 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
138821 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
138855 CACCTATTTAATCAATAATGGTAAACTACCAAAT
1 CACC-ATTTAATCAACAATGGTAACCTACCAAAT
138889 CACCATTTAATCAACA
1 CACCATTTAATCAACA
138905 GAAAATATAT
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
33 16 0.22
34 56 0.76
35 2 0.03
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:138982 original size:7 final size:7
Alignment explanation
Indices: 138970--139001 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
138960 TAGTGGAATT
138970 TTTTATA
1 TTTTATA
138977 TTTTATA
1 TTTTATA
138984 TTTTATA
1 TTTTATA
138991 TTTTATA
1 TTTTATA
138998 TTTT
1 TTTT
139002 TCAATACTTA
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:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTATA
Found at i:139594 original size:17 final size:15
Alignment explanation
Indices: 139568--139601 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
139558 CTAATAGAAT
139568 TTTTTATTTTAATATA
1 TTTTTATTTTAAT-TA
139584 TTTTTATTTTTAATTA
1 TTTTTA-TTTTAATTA
139600 TT
1 TT
139602 ATTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTTTAATTA
Found at i:141372 original size:2 final size:2
Alignment explanation
Indices: 141356--141388 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
141346 AATTATAATT
*
141356 TA TA T- TA TT 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
141389 AGTATAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:141688 original size:9 final size:9
Alignment explanation
Indices: 141674--141712 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
141664 TTATCTTTTG
141674 TATATATAA
1 TATATATAA
141683 TATATATAA
1 TATATATAA
141692 TAATAATGATAA
1 T-AT-AT-ATAA
141704 TATATATAA
1 TATATATAA
141713 AAATACGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 14 0.52
10 4 0.15
11 4 0.15
12 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (9 bp):
TATATATAA
Found at i:148341 original size:30 final size:30
Alignment explanation
Indices: 148294--148364 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
148284 TAATTAAATG
*
148294 TTAA-TTTTTATTAAATTTTGCTACTTAAC-
1 TTAAGTTTTGATTAAATTTTGC-ACTTAACT
* *
148323 TTAAGTTTTGATTGAATTTTGCATTTAACT
1 TTAAGTTTTGATTAAATTTTGCACTTAACT
*
148353 TTGAGTTTTGAT
1 TTAAGTTTTGAT
148365 GATTTAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (30 bp):
TTAAGTTTTGATTAAATTTTGCACTTAACT
Found at i:149988 original size:63 final size:66
Alignment explanation
Indices: 149865--149988 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
149855 TAATTAATTC
* * *
149865 TTTTAATCATTTTGTAGGTTGCTTTTTCCCAACTTTGGAGAAAAATCACAATCTCCCATTTAACT
1 TTTTAATAATTATGCAGGTTGCTTTTTCCCAACTTTGGAGAAAAATCACAATCTCCCATTTAACT
149930 T
66 T
* *
149931 TTTTAATAATTATGCAGGTTGC-TTTTCCCAAC-TTGGAG-AAAATCAGAATCTCTCATTT
1 TTTTAATAATTATGCAGGTTGCTTTTTCCCAACTTTGGAGAAAAATCACAATCTCCCATTT
149989 GGGAAATGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 18 0.34
64 6 0.11
65 10 0.19
66 19 0.36
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (66 bp):
TTTTAATAATTATGCAGGTTGCTTTTTCCCAACTTTGGAGAAAAATCACAATCTCCCATTTAACT
T
Found at i:151843 original size:22 final size:22
Alignment explanation
Indices: 151818--151901 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 22
151808 ATTTTTTATA
*
151818 TTTATTAAAAATAATAATTTTTT
1 TTTATCAAAAATAATAA-TTTTT
151841 TTATATTTATCAAAAATAATAATTTTT
1 TT-TA----TCAAAAATAATAATTTTT
*
151868 TTTATCAAAAATAGTAATTTATT
1 TTTATCAAAAATAATAATTT-TT
151891 GTTTATCAAAA
1 -TTTATCAAAA
151902 TTGACAATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
22 15 0.29
23 4 0.08
24 12 0.23
26 2 0.04
27 7 0.13
28 12 0.23
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTATCAAAAATAATAATTTTT
Found at i:151849 original size:28 final size:28
Alignment explanation
Indices: 151798--151872 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 28
151788 GTGATTAGTC
* *
151798 AATAAAAATTATTTTTTATATTTATTAAA
1 AATAATAATT-TTTTTTATATTTATCAAA
151827 AATAATAATTTTTTTTATATTTATCAAA
1 AATAATAATTTTTTTTATATTTATCAAA
151855 AATAATAATTTTTTTTAT
1 AATAATAATTTTTTTTAT
151873 CAAAAATAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 35 0.80
29 9 0.20
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (28 bp):
AATAATAATTTTTTTTATATTTATCAAA
Found at i:154475 original size:21 final size:22
Alignment explanation
Indices: 154432--154477 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
154422 TATTCAGACA
* *
154432 AGTAGTACTCCATAGCAGATGG
1 AGTAGTACTCCAAAACAGATGG
*
154454 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGATGG
154475 AGT
1 AGT
154478 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:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGATGG
Found at i:160550 original size:21 final size:20
Alignment explanation
Indices: 160514--160553 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
160504 AAGGTTAGTT
*
160514 TTTATTTTATATTTATTTTA
1 TTTATTTTACATTTATTTTA
160534 TTTATTTATACATTTATTTT
1 TTTATTT-TACATTTATTTT
160554 TCCTTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTTTACATTTATTTTA
Found at i:160598 original size:2 final size:2
Alignment explanation
Indices: 160591--160630 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
160581 GTCTAACTTC
160591 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
160631 CATGCACACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:162895 original size:47 final size:47
Alignment explanation
Indices: 162826--162919 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
162816 AAGAAAAGAG
*
162826 AAAACTAAAAATTATCAAATCTTAGTCTTCCAAACATTTTCAAATCC
1 AAAACTAAAAATTATCAAATCTTAATCTTCCAAACATTTTCAAATCC
162873 AAAACTAAAAATTATCAAATCTTAATCTTCCAAACATTTTCAAATCC
1 AAAACTAAAAATTATCAAATCTTAATCTTCCAAACATTTTCAAATCC
162920 GATCTTTTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (47 bp):
AAAACTAAAAATTATCAAATCTTAATCTTCCAAACATTTTCAAATCC
Found at i:162915 original size:25 final size:25
Alignment explanation
Indices: 162840--162918 Score: 83
Period size: 25 Copynumber: 3.3 Consensus size: 25
162830 CTAAAAATTA
*
162840 TCAAATCTTAGTCTTCCAAACATTT
1 TCAAATCTTAATCTTCCAAACATTT
** * * *
162865 TCAAATCCAAAAC-T--AAAAATTA
1 TCAAATCTTAATCTTCCAAACATTT
162887 TCAAATCTTAATCTTCCAAACATTT
1 TCAAATCTTAATCTTCCAAACATTT
162912 TCAAATC
1 TCAAATC
162919 CGATCTTTTT
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
22 16 0.40
23 1 0.03
24 1 0.03
25 22 0.55
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (25 bp):
TCAAATCTTAATCTTCCAAACATTT
Found at i:167896 original size:27 final size:27
Alignment explanation
Indices: 167858--167919 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
167848 ATAAAAATTA
167858 TTTTTTATATTTATCAAAAATAATAAT
1 TTTTTTATATTTATCAAAAATAATAAT
* *
167885 TTTTTTATATTTATTAAAAATGATAAT
1 TTTTTTATATTTATCAAAAATAATAAT
167912 TTTTTTAT
1 TTTTTTAT
167920 CAAAAATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTTATATTTATCAAAAATAATAAT
Found at i:167918 original size:21 final size:21
Alignment explanation
Indices: 167894--167948 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
167884 TTTTTTTATA
*
167894 TTTATTAAAAAT-GATAATTTT
1 TTTATCAAAAATAG-TAATTTT
167915 TTTATCAAAAATAGTAATTTATT
1 TTTATCAAAAATAGTAA-TT-TT
167938 GTTTATCAAAA
1 -TTTATCAAAA
167949 TTGACAGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 14 0.48
22 3 0.10
23 2 0.07
24 10 0.34
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (21 bp):
TTTATCAAAAATAGTAATTTT
Found at i:170508 original size:21 final size:22
Alignment explanation
Indices: 170479--170524 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
170469 TATTCAGACA
* *
170479 AGTAGTACTCCACAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
170501 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
170522 AGT
1 AGT
170525 TTCAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:172023 original size:24 final size:24
Alignment explanation
Indices: 171995--172040 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
171985 GGTTCCTTTT
171995 TTGTTTGCCAAAAA-TGGTGGCTTG
1 TTGTTTG-CAAAAATTGGTGGCTTG
*
172019 TTGTTTGTAAAAATTGGTGGCT
1 TTGTTTGCAAAAATTGGTGGCT
172041 AATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (24 bp):
TTGTTTGCAAAAATTGGTGGCTTG
Done.