Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold270
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: 409424
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
File 1 of 4
Found at i:406 original size:28 final size:28
Alignment explanation
Indices: 371--440 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 28
361 ATATTTTTTT
**
371 AATATTAATTATTTTAATTATAAAATTTA
1 AATATTAATTATTTT-ATTATAAAAAATA
* *
400 AAT-TTAA-AATTTTATTTTAAAAAATA
1 AATATTAATTATTTTATTATAAAAAATA
426 AATATTAAATTATTT
1 AATATT-AATTATTT
441 GAGCCAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
26 13 0.39
27 7 0.21
28 6 0.18
29 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
AATATTAATTATTTTATTATAAAAAATA
Found at i:689 original size:18 final size:18
Alignment explanation
Indices: 668--710 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
658 AATAGGATAT
668 AATTTAAAATTA-ATTTAA
1 AATTTAAAATTATATTT-A
**
686 AATTTAATTTTATATTTA
1 AATTTAAAATTATATTTA
704 AATTTAA
1 AATTTAA
711 TTTGTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTAAAATTATATTTA
Found at i:694 original size:12 final size:12
Alignment explanation
Indices: 667--710 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
657 AAATAGGATA
667 TAATTTAAAA-T
1 TAATTTAAAATT
678 TAATTTAAAATT
1 TAATTTAAAATT
* *
690 TAATTTTATATT
1 TAATTTAAAATT
702 TAAATTTAA
1 T-AATTTAA
711 TTTGTTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.36
12 12 0.43
13 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATTTAAAATT
Found at i:786 original size:21 final size:21
Alignment explanation
Indices: 760--802 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
750 AATATAAAAA
760 ATTATTTTGAT-ATTAATATTT
1 ATTATTTTGATAATTAA-ATTT
*
781 ATTATTTTTATAATTAAATTT
1 ATTATTTTGATAATTAAATTT
802 A
1 A
803 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTATTTTGATAATTAAATTT
Found at i:1202 original size:22 final size:22
Alignment explanation
Indices: 1158--1198 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1148 TATTTTTATT
1158 TAAATTTAATTATTAAAATATA
1 TAAATTTAATTATTAAAATATA
1180 TAAATATTAA-TA-TAAAATA
1 TAAAT-TTAATTATTAAAATA
1199 ATATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATTTAATTATTAAAATATA
Found at i:1547 original size:17 final size:17
Alignment explanation
Indices: 1515--1559 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1505 AAATTTAATT
*
1515 ATAAAATA-TATAAATA
1 ATAAAATATTTTAAATA
* *
1531 TTAATATATTTTAAATA
1 ATAAAATATTTTAAATA
1548 ATAAAATATTTT
1 ATAAAATATTTT
1560 TTTAAAACTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATATTTTAAATA
Found at i:2254 original size:30 final size:30
Alignment explanation
Indices: 2220--2285 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
2210 AATAAGTTAT
* *
2220 TAATTTTT-AATTTGTATTCAAGTAAATTTA
1 TAATTTTTAAAATT-TATTCAAATAAATTTA
* *
2250 TAATTTTTAAAATTTATTTAAATAAATTTT
1 TAATTTTTAAAATTTATTCAAATAAATTTA
2280 TAATTT
1 TAATTT
2286 ATACATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (30 bp):
TAATTTTTAAAATTTATTCAAATAAATTTA
Found at i:3393 original size:35 final size:36
Alignment explanation
Indices: 3339--3413 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
3329 AGATTGATTC
** *
3339 AAAATTTTATTTTATTATTTAT-AGT-AATATTAAAT
1 AAAATTTTATACTAATATTTATAAGTAAAT-TTAAAT
*
3374 AAAATTTTATACTAATATTTATAATTAAATTTAAAT
1 AAAATTTTATACTAATATTTATAAGTAAATTTAAAT
3410 AAAA
1 AAAA
3414 ATAATTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 19 0.56
36 12 0.35
37 3 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (36 bp):
AAAATTTTATACTAATATTTATAAGTAAATTTAAAT
Found at i:3995 original size:16 final size:16
Alignment explanation
Indices: 3970--4003 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3960 TTTATTTTTG
3970 TTATGATATTGA-TAT
1 TTATGATATTGATTAT
3985 TTATCGATATTGATTAT
1 TTAT-GATATTGATTAT
4002 TT
1 TT
4004 TAGTGTATCA
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:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (16 bp):
TTATGATATTGATTAT
Found at i:4090 original size:26 final size:25
Alignment explanation
Indices: 4035--4089 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
4025 TTATTATTTT
* *
4035 AAATATTTTTAAATTATATACATGAA
1 AAATATTTTTAAATTAAATAAAT-AA
4061 AAATATTTTTAAATATAAAATAAATAA
1 AAATATTTTTAAAT-T-AAATAAATAA
4088 AA
1 AA
4090 TTAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.56
27 5 0.20
28 6 0.24
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
AAATATTTTTAAATTAAATAAATAA
Found at i:4306 original size:117 final size:118
Alignment explanation
Indices: 4095--4336 Score: 371
Period size: 117 Copynumber: 2.1 Consensus size: 118
4085 TAAAATTAAA
* * *
4095 TAAATTTTATACATCAAATACACATCAATTATAAATAAAGTTTCAAAAAAAAACTTAATCAACTA
1 TAAATTTTATACATAAAAAACACATCAATTATAAATAAAATTTCAAAAAAAAACTTAATCAACTA
* ** *
4160 TAAAAAGATTAATACTATTTTAAGTAATAAGGTTGAAACTTTTTAATAACTAT
66 TAAAAAGATCAATACTATTTTAAAAAATAAGATTGAAACTTTTTAATAACTAT
* *
4213 TAAATTTTATACATAAAAAACACATCAATTATATATAAAATTT-TAAAAAAAACTTAATCAACTA
1 TAAATTTTATACATAAAAAACACATCAATTATAAATAAAATTTCAAAAAAAAACTTAATCAACTA
4277 TAAAAAGATCAATA-TCATTTTAAAAAATAAGATTGAAACTTTTTAATAACTAT
66 TAAAAAGATCAATACT-ATTTTAAAAAATAAGATTGAAACTTTTTAATAACTAT
*
4330 TATATTT
1 TAAATTT
4337 ATAAGTAATT
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
116 1 0.01
117 73 0.65
118 39 0.35
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.36
Consensus pattern (118 bp):
TAAATTTTATACATAAAAAACACATCAATTATAAATAAAATTTCAAAAAAAAACTTAATCAACTA
TAAAAAGATCAATACTATTTTAAAAAATAAGATTGAAACTTTTTAATAACTAT
Found at i:5395 original size:23 final size:23
Alignment explanation
Indices: 5352--5424 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 23
5342 TGATTCGATG
*
5352 TAAATTATTATTT-ATTAATAAATA
1 TAAATT-TTATTTAAAT-ATAAATA
*
5376 TAAATTTTATTTAAATATAATTA
1 TAAATTTTATTTAAATATAAATA
** * *
5399 TAAA-AATATATAAATATTAATA
1 TAAATTTTATTTAAATATAAATA
5421 TAAA
1 TAAA
5425 ATTAATTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 17 0.41
23 16 0.39
24 8 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAATTTTATTTAAATATAAATA
Found at i:6756 original size:18 final size:17
Alignment explanation
Indices: 6723--6758 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
6713 TGGGTAATTT
*
6723 TTTAATTAATAAAAATA
1 TTTAATTAAAAAAAATA
6740 TTTAATTATAAAAAAATA
1 TTTAATTA-AAAAAAATA
6758 T
1 T
6759 AAAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAATTAAAAAAAATA
Found at i:6761 original size:26 final size:25
Alignment explanation
Indices: 6731--6781 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
6721 TTTTTAATTA
6731 ATAAAAATATTTAATTATAAAA-AAAT
1 ATAAAAATA-TTAA-TATAAAATAAAT
6757 ATAAAAATATTAATATAAAATAAAT
1 ATAAAAATATTAATATAAAATAAAT
6782 TTTTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 7 0.29
25 8 0.33
26 9 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAAAAATATTAATATAAAATAAAT
Found at i:8979 original size:20 final size:20
Alignment explanation
Indices: 8956--9021 Score: 51
Period size: 20 Copynumber: 3.0 Consensus size: 20
8946 TTTTTTCTGT
8956 TTTAAATATATTTTATTAAATTTA
1 TTTAAATATATTTTATT-AA---A
8980 TTTTAAATATATTTTATTAAA
1 -TTTAAATATATTTTATTAAA
* ** *
9001 TATATTTATATTTCATTAAA
1 TTTAAATATATTTTATTAAA
9021 T
1 T
9022 ATATTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 17 0.46
21 1 0.03
24 2 0.05
25 17 0.46
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAAATATATTTTATTAAA
Found at i:8985 original size:11 final size:11
Alignment explanation
Indices: 8955--9043 Score: 55
Period size: 11 Copynumber: 7.9 Consensus size: 11
8945 GTTTTTTCTG
8955 TTTTAAATATA
1 TTTTAAATATA
*
8966 TTTTATTAAATTTA
1 --TT-TTAAATATA
8980 TTTTAAATATA
1 TTTTAAATATA
8991 TTTTATTAA-ATA
1 TTTTA--AATATA
9003 TATTT--ATAT-
1 T-TTTAAATATA
9012 TTCATTAAATATA
1 TT--TTAAATATA
9025 TTTT-AA-ATA
1 TTTTAAATATA
9034 TTTTAAATAT
1 TTTTAAATAT
9044 TAATTCGATT
Statistics
Matches: 62, Mismatches: 2, Indels: 26
0.69 0.02 0.29
Matches are distributed among these distances:
8 1 0.02
9 9 0.15
10 8 0.13
11 17 0.27
12 10 0.16
13 9 0.15
14 8 0.13
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAATATA
Found at i:8989 original size:25 final size:24
Alignment explanation
Indices: 8955--9034 Score: 96
Period size: 25 Copynumber: 3.4 Consensus size: 24
8945 GTTTTTTCTG
8955 TTTTAAATATATTTTATTAAATTTA
1 TTTTAAATATATTTTATTAAA-TTA
8980 TTTTAAATATATTTTATTAAA-TA
1 TTTTAAATATATTTTATTAAATTA
* *
9003 TATT---TATATTTCATTAAATATA
1 TTTTAAATATATTTTATTAAAT-TA
9025 TTTTAAATAT
1 TTTTAAATAT
9035 TTTAAATATT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 13 0.28
22 5 0.11
23 5 0.11
25 24 0.51
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAAATATATTTTATTAAATTA
Found at i:9022 original size:20 final size:20
Alignment explanation
Indices: 8987--9027 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
8977 TTATTTTAAA
*
8987 TATATTTTATTAAATATATT
1 TATATTTCATTAAATATATT
9007 TATATTTCATTAAATATATT
1 TATATTTCATTAAATATATT
9027 T
1 T
9028 TAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATTTCATTAAATATATT
Found at i:9027 original size:14 final size:14
Alignment explanation
Indices: 8957--9012 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
8947 TTTTTCTGTT
8957 TTAAATATATTTTA
1 TTAAATATATTTTA
*
8971 TTAAAT-T-TATT-
1 TTAAATATATTTTA
8982 TTAAATATATTTTA
1 TTAAATATATTTTA
8996 TTAAATATATTTATA
1 TTAAATATATTT-TA
9011 TT
1 TT
9013 TCATTAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
13 4 0.11
14 18 0.50
15 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:9136 original size:6 final size:6
Alignment explanation
Indices: 9125--9154 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
9115 TATTATAAAT
9125 AAATTA AAATTA AAATTA AAA-TA AAATTA A
1 AAATTA AAATTA AAATTA AAATTA AAATTA A
9155 CCGAACTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:9660 original size:19 final size:19
Alignment explanation
Indices: 9632--9678 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
9622 TTACATATTT
*
9632 TTTTATAAAAAAATTATAA
1 TTTTAAAAAAAAATTATAA
9651 TTTTAAAAAAAAATTATAA
1 TTTTAAAAAAAAATTATAA
*
9670 ATTTAAAAA
1 TTTTAAAAA
9679 TTATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTTAAAAAAAAATTATAA
Found at i:9693 original size:21 final size:21
Alignment explanation
Indices: 9667--9708 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9657 AAAAAAATTA
9667 TAAATTTA-AAAATTATTATTT
1 TAAATTTATAAAA-TATTATTT
*
9688 TAAATTTATTAAATATTATTT
1 TAAATTTATAAAATATTATTT
9709 GTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAATTTATAAAATATTATTT
Found at i:11243 original size:29 final size:30
Alignment explanation
Indices: 11164--11228 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
11154 GTCCTTAACT
* * * * *
11164 TTTAATTTGTATGTGAATAATTTTTTTATC
1 TTTAACTTGTATCTAAATAAATTTTTAATC
11194 TTTAACTTGTATCTAAATAAATTTTTAATC
1 TTTAACTTGTATCTAAATAAATTTTTAATC
11224 TTTAA
1 TTTAA
11229 TTTATACTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (30 bp):
TTTAACTTGTATCTAAATAAATTTTTAATC
Found at i:12803 original size:19 final size:18
Alignment explanation
Indices: 12779--12834 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
12769 TTTGCATAGT
*
12779 TTTTTTGATTTGATTTAAA
1 TTTTTTGATTTGAATT-AA
*
12798 TTTTTTTATTTGAATTAA
1 TTTTTTGATTTGAATTAA
12816 TTTGATTTGATTTGAATTA
1 TTT--TTTGATTTGAATTA
12835 TTATTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.16
19 14 0.44
20 13 0.41
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (18 bp):
TTTTTTGATTTGAATTAA
Found at i:14318 original size:21 final size:19
Alignment explanation
Indices: 14281--14319 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
14271 CAACCATCCT
*
14281 TCTTTTCAAGCATTCTTCA
1 TCTTTTCAAGCAATCTTCA
14300 TCTTTCTCATAGCAATCTTC
1 TCTTT-TCA-AGCAATCTTC
14320 TGATCCCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.21, C:0.28, G:0.05, T:0.46
Consensus pattern (19 bp):
TCTTTTCAAGCAATCTTCA
Found at i:16768 original size:3 final size:3
Alignment explanation
Indices: 16760--16790 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16750 TGATTAAGTT
16760 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16791 GATTTAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16809 original size:22 final size:21
Alignment explanation
Indices: 16777--16839 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
16767 TATTATTATT
**
16777 ATTATTATTATTATGATTTAAG
1 ATTATT-TTATTAAAATTTAAG
*
16799 ATTAATTTTATTTAAAATTTATG
1 ATT-ATTTTA-TTAAAATTTAAG
16822 ATTATTTTATTTAAAATT
1 ATTATTTTA-TTAAAATT
16840 ATGTTTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 21 0.58
23 15 0.42
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTATTTTATTAAAATTTAAG
Found at i:16847 original size:21 final size:22
Alignment explanation
Indices: 16792--16847 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
16782 TATTATTATG
*
16792 ATTTAAGATTAATTTTATTTAAA
1 ATTTATGATT-ATTTTATTTAAA
16815 ATTTATGATTATTTTATTTAAA
1 ATTTATGATTATTTTATTTAAA
*
16837 A-TTATGTTTAT
1 ATTTATGATTAT
16848 ATAGAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 9 0.29
22 13 0.42
23 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
ATTTATGATTATTTTATTTAAA
Found at i:18531 original size:22 final size:22
Alignment explanation
Indices: 18506--18549 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
18496 ATTCAGTAAA
18506 TTTAAAGTTCAAATCTCAATAT
1 TTTAAAGTTCAAATCTCAATAT
18528 TTTAAAGTTCAAATCTCAATAT
1 TTTAAAGTTCAAATCTCAATAT
18550 CTGTAACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
TTTAAAGTTCAAATCTCAATAT
Found at i:19045 original size:17 final size:17
Alignment explanation
Indices: 19006--19038 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
18996 AAAAAATAAA
19006 AAATATATATTTATATC
1 AAATATATATTTATATC
19023 AAATATATATTTATAT
1 AAATATATATTTATAT
19039 TTAATATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATATATATTTATATC
Found at i:19802 original size:2 final size:2
Alignment explanation
Indices: 19795--19826 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19785 TATGGAAGCA
19795 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
19827 TTTTTTTACT
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:21220 original size:18 final size:17
Alignment explanation
Indices: 21199--21246 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
21189 AATTAGTGAT
*
21199 ATTATTTTTTATATTATA
1 ATTATATTTTA-ATTATA
*
21217 ATTATATTTTAATTATT
1 ATTATATTTTAATTATA
*
21234 ATATATATATTAA
1 AT-TATATTTTAA
21247 AATTTATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTATATTTTAATTATA
Found at i:21442 original size:18 final size:18
Alignment explanation
Indices: 21421--21476 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
21411 ATTTTTAAAA
21421 ATTAATTTATATGATTAT
1 ATTAATTTATATGATTAT
**
21439 ATTATATGAATATGATATAT
1 ATTA-ATTTATATGAT-TAT
*
21459 TTTAA-TTAT-TGATTAT
1 ATTAATTTATATGATTAT
21475 AT
1 AT
21477 ACTTATATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 6 0.20
19 10 0.33
20 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (18 bp):
ATTAATTTATATGATTAT
Found at i:21756 original size:19 final size:19
Alignment explanation
Indices: 21721--21757 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21711 CGTAATTTTA
21721 TTTATTTTTAAATAATAAT
1 TTTATTTTTAAATAATAAT
21740 TTTATATTTTAAA-AATAA
1 TTTAT-TTTTAAATAATAA
21758 ATAAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATTTTTAAATAATAAT
Found at i:23289 original size:2 final size:2
Alignment explanation
Indices: 23282--23317 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
23272 AAATGAAATA
23282 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
23318 GTATGTATGA
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:23522 original size:4 final size:4
Alignment explanation
Indices: 23513--23539 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
23503 GCCAAAGAAT
23513 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
23540 TGATTTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:23894 original size:24 final size:25
Alignment explanation
Indices: 23867--23917 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
23857 TAATTTTTTT
* *
23867 TATTTTTTTTATATATAAAAAT-TA
1 TATTTTATATATATATAAAAATGTA
*
23891 TATTTTATATATATTTAAAAATGTA
1 TATTTTATATATATATAAAAATGTA
23916 TA
1 TA
23918 AAATGTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TATTTTATATATATATAAAAATGTA
Found at i:25464 original size:1 final size:1
Alignment explanation
Indices: 25458--25482 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
25448 ATCCTACAGC
25458 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
25483 GAATGTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25968 original size:14 final size:11
Alignment explanation
Indices: 25937--25966 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
25927 TATAATTCTC
25937 TTAATAATTCA
1 TTAATAATTCA
25948 TTAATAATTCA
1 TTAATAATTCA
25959 TTAATAAT
1 TTAATAAT
25967 AACAGCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAATAATTCA
Found at i:27711 original size:17 final size:17
Alignment explanation
Indices: 27691--27743 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
27681 CACAAGTAGG
*
27691 TTAATTTTTTTATATAT
1 TTAATTTTTATATATAT
* *
27708 TTAA-TATGAT-TATAT
1 TTAATTTTTATATATAT
*
27723 TTAATTTTTATATAAAT
1 TTAATTTTTATATATAT
27740 TTAA
1 TTAA
27744 ATGATCATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 9 0.32
16 7 0.25
17 12 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTAATTTTTATATATAT
Found at i:27748 original size:31 final size:32
Alignment explanation
Indices: 27691--27756 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
27681 CACAAGTAGG
* * *
27691 TTAATTTTTTTATATATTTAATATGATTATAT
1 TTAATTTTTATATAAATTTAATATGATCATAT
27723 TTAATTTTTATATAAATTTAA-ATGATCATAT
1 TTAATTTTTATATAAATTTAATATGATCATAT
27754 TTA
1 TTA
27757 TATATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (32 bp):
TTAATTTTTATATAAATTTAATATGATCATAT
Found at i:29614 original size:11 final size:11
Alignment explanation
Indices: 29568--29668 Score: 63
Period size: 11 Copynumber: 9.7 Consensus size: 11
29558 ATGACACGAA
29568 AAATATA-TAT
1 AAATATATTAT
* *
29578 AAATTTAATAT
1 AAATATATTAT
*
29589 AAAAATATTAT
1 AAATATATTAT
*
29600 AAATATGTTAT
1 AAATATATTAT
29611 AAATA-A--AT
1 AAATATATTAT
*
29619 TAATATATTA-
1 AAATATATTAT
*
29629 AAATTTA-TAT
1 AAATATATTAT
*
29639 AATATAAATTAT
1 AA-ATATATTAT
* *
29651 TAATTTATTA-
1 AAATATATTAT
29661 AAATATAT
1 AAATATAT
29669 AATACATTAA
Statistics
Matches: 67, Mismatches: 17, Indels: 14
0.68 0.17 0.14
Matches are distributed among these distances:
8 6 0.09
9 3 0.04
10 19 0.28
11 35 0.52
12 4 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
AAATATATTAT
Found at i:29637 original size:37 final size:38
Alignment explanation
Indices: 29571--29643 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 38
29561 ACACGAAAAA
*
29571 TATATATAAATTTAATATAAAAATATTATA-AATATGT
1 TATAAATAAATTTAATATAAAAATATTATATAATATGT
29608 TATAAATAAA-TTAATATATTAAAAT-TTATATAATAT
1 TATAAATAAATTTAATATA--AAAATATTATATAATAT
29644 AAATTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 8 0.25
37 14 0.44
38 10 0.31
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (38 bp):
TATAAATAAATTTAATATAAAAATATTATATAATATGT
Found at i:29660 original size:32 final size:31
Alignment explanation
Indices: 29608--29672 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
29598 ATAAATATGT
29608 TATAAATAAATTAATATATTAAAATTTATATAA
1 TATAAATAAATTAATATATTAAAA--TATATAA
* *
29641 TATAAAT-TATTAATTTATTAAAATATATAA
1 TATAAATAAATTAATATATTAAAATATATAA
29671 TA
1 TA
29673 CATTAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 9 0.30
32 14 0.47
33 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TATAAATAAATTAATATATTAAAATATATAA
Found at i:29677 original size:17 final size:17
Alignment explanation
Indices: 29585--29680 Score: 63
Period size: 16 Copynumber: 5.5 Consensus size: 17
29575 TATAAATTTA
*
29585 ATATAAAAATATTATAAAT
1 ATATTAAAATA-TAT-AAT
* *
29604 ATGTTATAAATAAATTAAT
1 ATATTA-AAATATA-TAAT
*
29623 ATATTAAAATTTAT-AT
1 ATATTAAAATATATAAT
*
29639 A-ATATAAATTAT-TAAT
1 ATAT-TAAAATATATAAT
*
29655 TTATTAAAATATATAAT
1 ATATTAAAATATATAAT
*
29672 ACATTAAAA
1 ATATTAAAA
29681 ATAAAAGAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
15 3 0.05
16 18 0.31
17 14 0.24
18 5 0.08
19 13 0.22
20 6 0.10
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
ATATTAAAATATATAAT
Found at i:30976 original size:22 final size:22
Alignment explanation
Indices: 30949--30991 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30939 AAAAAAATTA
30949 TTTTAT-ATTAATATTCATATAT
1 TTTTATAATTAA-ATTCATATAT
*
30971 TTTTATAATTAAATTTATATA
1 TTTTATAATTAAATTCATATA
30992 AAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATAATTAAATTCATATAT
Found at i:35927 original size:19 final size:19
Alignment explanation
Indices: 35890--35927 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
35880 TATGATACTT
*
35890 TTATTTATTTTAATATCTA
1 TTATTTATATTAATATCTA
35909 TTATTTATAATTAAT-TCTA
1 TTATTTAT-ATTAATATCTA
35928 AAATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTTATATTAATATCTA
Found at i:50381 original size:23 final size:22
Alignment explanation
Indices: 50330--50382 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
50320 AATTATTTTT
* *
50330 ATAAT-ATTTATATATTTTATA
1 ATAATAATTTAAATATATTATA
*
50351 ATTA-AATTTAAATATATTATAA
1 ATAATAATTTAAATATATTAT-A
50373 ATAATAATTT
1 ATAATAATTT
50383 TACATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 16 0.64
22 4 0.16
23 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATAATTTAAATATATTATA
Found at i:50430 original size:16 final size:16
Alignment explanation
Indices: 50406--50450 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
50396 ATTAAAAGAT
* *
50406 TTTACTTCAAATTTAA
1 TTTAATTCAAATTAAA
50422 TTTAATTCAAATTAAA
1 TTTAATTCAAATTAAA
50438 TTTGAA-TCAAATT
1 TTT-AATTCAAATT
50451 GATTGAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 24 0.92
17 2 0.08
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTAATTCAAATTAAA
Found at i:50458 original size:14 final size:14
Alignment explanation
Indices: 50439--50472 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
50429 CAAATTAAAT
50439 TTGAATCAAATTGA
1 TTGAATCAAATTGA
*
50453 TTGAATGAAATTGA
1 TTGAATCAAATTGA
50467 TTGAAT
1 TTGAAT
50473 TAGAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (14 bp):
TTGAATCAAATTGA
Found at i:50730 original size:16 final size:17
Alignment explanation
Indices: 50687--50733 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
50677 AGATTATTTC
*
50687 GAGTTCGGATCA-TTTA
1 GAGTTCGGGTCATTTTA
**
50703 GAGTTCAAGTCATTTTA
1 GAGTTCGGGTCATTTTA
50720 -AGTTCGGGTCATTT
1 GAGTTCGGGTCATTT
50734 CGAATTCAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (17 bp):
GAGTTCGGGTCATTTTA
Found at i:51409 original size:16 final size:16
Alignment explanation
Indices: 51388--51431 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
51378 ATTAATTATC
51388 CGAATCATTTCAGATT
1 CGAATCATTTCAGATT
*
51404 CGAATCATTTCAGGTT
1 CGAATCATTTCAGATT
*
51420 CGGATCATTTCA
1 CGAATCATTTCA
51432 AGTTCAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (16 bp):
CGAATCATTTCAGATT
Found at i:51436 original size:16 final size:16
Alignment explanation
Indices: 51388--51436 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
51378 ATTAATTATC
51388 CGAATCATTTC-AGATT
1 CGAATCATTTCAAG-TT
*
51404 CGAATCATTTCAGGTT
1 CGAATCATTTCAAGTT
*
51420 CGGATCATTTCAAGTT
1 CGAATCATTTCAAGTT
51436 C
1 C
51437 AAGATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 28 0.97
17 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (16 bp):
CGAATCATTTCAAGTT
Found at i:51451 original size:16 final size:16
Alignment explanation
Indices: 51432--51478 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
51422 GATCATTTCA
51432 AGTTCAAGA-TATTTTG
1 AGTTCAA-ATTATTTTG
*
51448 AGTTTAAATTATTTTG
1 AGTTCAAATTATTTTG
* *
51464 AATTTAAATTATTTT
1 AGTTCAAATTATTTT
51479 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 1 0.04
16 27 0.96
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (16 bp):
AGTTCAAATTATTTTG
Found at i:51483 original size:16 final size:17
Alignment explanation
Indices: 51450--51489 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
51440 ATATTTTGAG
*
51450 TTTAAATTATTTTGAA-
1 TTTAAATTATTTTAAAT
51466 TTTAAATTATTTTAAAT
1 TTTAAATTATTTTAAAT
51483 TTTAAAT
1 TTTAAAT
51490 CAATCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTATTTTAAAT
Found at i:56572 original size:22 final size:23
Alignment explanation
Indices: 56529--56573 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
56519 ATTTAATTTA
*
56529 AAATAAATTAAATTAAATTATAT
1 AAATAAATTAAATAAAATTATAT
56552 AAAT-AATT-AATAAAATATATAT
1 AAATAAATTAAATAAAAT-TATAT
56574 TTTTAGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 9 0.45
23 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATAAATTAAATAAAATTATAT
Found at i:56812 original size:44 final size:42
Alignment explanation
Indices: 56730--56816 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
56720 CTCATTTTAA
* * * *
56730 ATTATTTATATTTATTATTTATAATTAATAATATATTTAAAT
1 ATTATTTATATATAATATTTAAAATTAATAATAAATTTAAAT
* *
56772 ATTATTTTTATATAATATTTAAATATTTATAATTAAATTTAAAT
1 ATTATTTATATATAATATTTAAA-ATTAATAA-TAAATTTAAAT
56816 A
1 A
56817 AAAATATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
42 19 0.51
43 7 0.19
44 11 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (42 bp):
ATTATTTATATATAATATTTAAAATTAATAATAAATTTAAAT
Found at i:58037 original size:22 final size:23
Alignment explanation
Indices: 58009--58079 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 23
57999 AACTCAATTC
58009 AAATTATT-A-TTTAATTAATAAA
1 AAATTATTAATTTTAATT-ATAAA
58031 AAATTATTCAATTTTAATTATAAA
1 AAATTATT-AATTTTAATTATAAA
* * *
58055 ATA-TATAAATATTAA-TATAAA
1 AAATTATTAATTTTAATTATAAA
58076 AAAT
1 AAAT
58080 ATATAAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 8 0.20
22 15 0.37
23 3 0.07
24 8 0.20
25 7 0.17
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTATTAATTTTAATTATAAA
Found at i:58082 original size:23 final size:23
Alignment explanation
Indices: 58022--58089 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
58012 TTATTATTTA
* *
58022 ATTAATA-AAAAATTAT-TCAAT
1 ATTAATATAAAAAATATATAAAT
* *
58043 TTTAAT-TATAAAATATATAAAT
1 ATTAATATAAAAAATATATAAAT
58065 ATTAATATAAAAAATATATAAAT
1 ATTAATATAAAAAATATATAAAT
58088 AT
1 AT
58090 ATTAAACAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
21 12 0.32
22 9 0.24
23 17 0.45
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTAATATAAAAAATATATAAAT
Found at i:58927 original size:16 final size:16
Alignment explanation
Indices: 58906--58959 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
58896 CACCATTAAG
58906 AATATAAAATTTATAT
1 AATATAAAATTTATAT
**
58922 AATATAACTTATTA-AT
1 AATATAAAAT-TTATAT
58938 AATATCAAAATTTATAT
1 AATAT-AAAATTTATAT
58955 GAATA
1 -AATA
58960 AATAATACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 18 0.60
17 8 0.27
18 4 0.13
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (16 bp):
AATATAAAATTTATAT
Found at i:59016 original size:13 final size:11
Alignment explanation
Indices: 58989--59026 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
58979 TTATTATCAT
58989 TATAATATATAA
1 TATAATATA-AA
59001 TAATAA-ATAAA
1 T-ATAATATAAA
59012 TATAATATAAA
1 TATAATATAAA
59023 TATA
1 TATA
59027 CGAATTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.17
11 12 0.50
12 4 0.17
13 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAATATAAA
Found at i:59546 original size:3 final size:3
Alignment explanation
Indices: 59533--59580 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
59523 TAAATTTAAA
59533 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
59579 AT
1 AT
59581 ATGATGAACA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:59895 original size:14 final size:14
Alignment explanation
Indices: 59876--59909 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
59866 AAGATTTTGA
59876 TATATTTAATAATT
1 TATATTTAATAATT
59890 TATATTTAATAATT
1 TATATTTAATAATT
59904 TATATT
1 TATATT
59910 ATATTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATATTTAATAATT
Found at i:59921 original size:17 final size:19
Alignment explanation
Indices: 59889--59923 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
59879 ATTTAATAAT
59889 TTATATTTAATAATTTATA
1 TTATATTTAATAATTTATA
59908 TTATA-TTAAT-ATTTAT
1 TTATATTTAATAATTTAT
59924 TAGACTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATTTAATAATTTATA
Found at i:60112 original size:11 final size:11
Alignment explanation
Indices: 60019--60113 Score: 50
Period size: 11 Copynumber: 8.1 Consensus size: 11
60009 AAGCTTTTTT
60019 TATTATTCATTA
1 TATTATT-ATTA
**
60031 TATTATTAAAA
1 TATTATTATTA
*
60042 TATTATTTTTA
1 TATTATTATTA
*
60053 TATTAATATTTA
1 TATTATTA-TTA
*
60065 TATCTTATAATTA
1 TA--TTATTATTA
*
60078 AATT-TTATTAAAAA
1 TATTATTATT----A
60092 TATT-TTATTA
1 TATTATTATTA
60102 TATTATTATTA
1 TATTATTATTA
60113 T
1 T
60114 TATCTAATCG
Statistics
Matches: 63, Mismatches: 12, Indels: 17
0.68 0.13 0.18
Matches are distributed among these distances:
10 9 0.14
11 25 0.40
12 12 0.19
13 4 0.06
14 13 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTATTATTA
Found at i:62466 original size:20 final size:20
Alignment explanation
Indices: 62428--62482 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
62418 ATAAAAAATT
*
62428 AAAA-AAATATAGT-TATAA
1 AAAATAAATATAATATATAA
*
62446 AATATAAATATAATATATAA
1 AAAATAAATATAATATATAA
* *
62466 AAAATAATTAAAATATA
1 AAAATAAATATAATATA
62483 ATTTAATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 3 0.10
19 8 0.27
20 19 0.63
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATAAATATAATATATAA
Found at i:62469 original size:22 final size:21
Alignment explanation
Indices: 62415--62471 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
62405 CTTTAATTAT
62415 TATATAAAAAAT-TAAAAAAA
1 TATATAAAAAATATAAAAAAA
* *
62435 TATAGTTATAAAATATAAATATAA
1 TATA--TAAAAAATATAAA-AAAA
62459 TATATAAAAAATA
1 TATATAAAAAATA
62472 ATTAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.13
22 15 0.50
23 4 0.13
24 7 0.23
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TATATAAAAAATATAAAAAAA
Found at i:62743 original size:12 final size:12
Alignment explanation
Indices: 62726--62750 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62716 AAAATTCACT
62726 TTAAAGCTTTTA
1 TTAAAGCTTTTA
62738 TTAAAGCTTTTA
1 TTAAAGCTTTTA
62750 T
1 T
62751 GATAAAATTA
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TTAAAGCTTTTA
Found at i:63927 original size:26 final size:25
Alignment explanation
Indices: 63893--63952 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
63883 AACAAATTTA
63893 ATTTA-TAATTT-ATTAAAAATTATT
1 ATTTATTAATTTAATT-AAAATTATT
* *
63917 TTTTAATTAATTTAATTTAAATTATT
1 ATTT-ATTAATTTAATTAAAATTATT
63943 ATTTATTAAT
1 ATTTATTAAT
63953 AATATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 3 0.10
25 7 0.23
26 17 0.57
27 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTATTAATTTAATTAAAATTATT
Found at i:63936 original size:43 final size:44
Alignment explanation
Indices: 63887--63987 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 44
63877 TTATTTAACA
* *
63887 AATTTAATTTATAATTTATTAAAAAT-TATTTTTTAATT-AATTT
1 AATTTAAATTATAATTTATTAAAAATATA-TATTTAATTAAATTT
* * *
63930 AATTTAAATTATTATTTATTAATAATATATATTTATTTAAATTT
1 AATTTAAATTATAATTTATTAAAAATATATATTTAATTAAATTT
*
63974 AATTATAAAATATA
1 AATT-TAAATTATA
63988 GATTAATATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
43 30 0.62
44 11 0.23
45 7 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (44 bp):
AATTTAAATTATAATTTATTAAAAATATATATTTAATTAAATTT
Found at i:63946 original size:17 final size:17
Alignment explanation
Indices: 63888--63972 Score: 55
Period size: 15 Copynumber: 5.5 Consensus size: 17
63878 TATTTAACAA
*
63888 ATTTAATTTATA-ATTT
1 ATTTAAATTATATATTT
*
63904 A-TTAAA-AAT-TATTT
1 ATTTAAATTATATATTT
*
63918 -TTT-AATTA-AT-TTA
1 ATTTAAATTATATATTT
63931 ATTTAAATTAT-TATTT
1 ATTTAAATTATATATTT
*
63947 A-TTAATAATATATATTT
1 ATTTAA-ATTATATATTT
63964 ATTTAAATT
1 ATTTAAATT
63973 TAATTATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 21
0.65 0.09 0.27
Matches are distributed among these distances:
13 4 0.08
14 13 0.25
15 14 0.27
16 8 0.16
17 8 0.16
18 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAAATTATATATTT
Found at i:68207 original size:56 final size:56
Alignment explanation
Indices: 68133--68244 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
68123 TGCTTGATTT
*
68133 CCAAAAATCACATAAACAACCAATTCACACAATATCAAACATATTTTGCATTGTGG
1 CCAAAAATCACATAAACAACCAATTCACACAATATCAAACATATTTTGCACTGTGG
68189 CCAAAAATCACATAAACAACCAATTCACACAATATCAAACATATTTTGCACTGTGG
1 CCAAAAATCACATAAACAACCAATTCACACAATATCAAACATATTTTGCACTGTGG
68245 GTTCTAATAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.45, C:0.24, G:0.07, T:0.24
Consensus pattern (56 bp):
CCAAAAATCACATAAACAACCAATTCACACAATATCAAACATATTTTGCACTGTGG
Found at i:69268 original size:14 final size:14
Alignment explanation
Indices: 69249--69299 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
69239 ATTTTAATAT
69249 ATATTATTATATAA
1 ATATTATTATATAA
*
69263 ATATTAAATATAATAA
1 ATATT-ATTAT-ATAA
69279 ATATT-TTATA-AA
1 ATATTATTATATAA
69291 ATATATATT
1 ATAT-TATT
69300 TATTTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 6 0.19
13 2 0.06
14 10 0.32
15 4 0.13
16 9 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATTATTATATAA
Found at i:69293 original size:16 final size:16
Alignment explanation
Indices: 69259--69301 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
69249 ATATTATTAT
* *
69259 ATAAATATTAAATATA
1 ATAAATATTTAATAAA
*
69275 ATAAATATTTTATAAA
1 ATAAATATTTAATAAA
*
69291 ATATATATTTA
1 ATAAATATTTA
69302 TTTTAATAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAATATTTAATAAA
Found at i:69809 original size:2 final size:2
Alignment explanation
Indices: 69802--69881 Score: 124
Period size: 2 Copynumber: 40.0 Consensus size: 2
69792 AAAGATGAAG
* *
69802 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
69844 AT AT AT AT AT AT AA AT AT AA 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
69882 TAATTTCTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:69892 original size:20 final size:20
Alignment explanation
Indices: 69802--69881 Score: 142
Period size: 20 Copynumber: 3.9 Consensus size: 20
69792 AAAGATGAAG
69802 ATATATATATATATATATAA
1 ATATATATATATATATATAA
69822 ATATATATATATATATATAA
1 ATATATATATATATATATAA
69842 ATATATATATATATAAATATAA
1 ATATATATATATAT--ATATAA
69864 ATATATATATATATATAT
1 ATATATATATATATATAT
69882 TAATTTCTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
20 38 0.66
22 20 0.34
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATATATATATATATAA
Found at i:70814 original size:18 final size:19
Alignment explanation
Indices: 70777--70815 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
70767 TTATAATTTT
* *
70777 TTATTATTTTTTTTGTTAG
1 TTATTATTTTTTATGATAG
70796 TTATTA-TTTTTATGATAG
1 TTATTATTTTTTATGATAG
70814 TT
1 TT
70816 GCAAGCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (19 bp):
TTATTATTTTTTATGATAG
Found at i:73037 original size:2 final size:2
Alignment explanation
Indices: 73030--73063 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
73020 AATCATATGC
*
73030 TA TA TA TA TA TA TA TA TA TG TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
73064 TACCTTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:73840 original size:4 final size:4
Alignment explanation
Indices: 73833--73864 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
73823 CAACAAACAA
*
73833 TAAT TAAT TAAC TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
73865 CAAGCTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
TAAT
Found at i:74552 original size:3 final size:3
Alignment explanation
Indices: 74544--74581 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
74534 AATTTGACAT
74544 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
74582 TCTTTTCCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:74891 original size:26 final size:26
Alignment explanation
Indices: 74839--74906 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
74829 TCATTTGTAA
74839 ATAAA-AAATCAATAAATTAAATTAT
1 ATAAATAAATCAATAAATTAAATTAT
*
74864 ATAAATAAATCAAT-AATTATATTA-
1 ATAAATAAATCAATAAATTAAATTAT
* * *
74888 ATATATAATTAAATAAATT
1 ATAAATAAATCAATAAATT
74907 TAACGTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 11 0.30
25 18 0.49
26 8 0.22
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAAATAAATCAATAAATTAAATTAT
Found at i:75100 original size:15 final size:14
Alignment explanation
Indices: 75082--75118 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
75072 ATATTTTTAC
75082 TATATAATAAATAAA
1 TATATAATAAA-AAA
75097 TATATAAT--AAAA
1 TATATAATAAAAAA
75109 TATATAATAA
1 TATATAATAA
75119 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 11 0.55
13 1 0.05
15 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATATAATAAAAAA
Found at i:75710 original size:18 final size:19
Alignment explanation
Indices: 75681--75721 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
75671 AGTTTATATA
*
75681 TATTTATATTTATATTTTT
1 TATTTATATTTATATATTT
75700 TATTT-TATTTATATATTT
1 TATTTATATTTATATATTT
75718 TATT
1 TATT
75722 GCTAGGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTTATATTTATATATTT
Found at i:75716 original size:13 final size:13
Alignment explanation
Indices: 75681--75721 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
75671 AGTTTATATA
*
75681 TATTTATAT-TTA
1 TATTTATATATTT
*
75693 TATTT-TTTATTT
1 TATTTATATATTT
75705 TATTTATATATTT
1 TATTTATATATTT
75718 TATT
1 TATT
75722 GCTAGGAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 2 0.08
12 12 0.50
13 10 0.42
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTTATATATTT
Found at i:76019 original size:20 final size:20
Alignment explanation
Indices: 75981--76021 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
75971 TGGGGTCAAT
*
75981 TAATTTATATATTTATATAA
1 TAATTTATATATCTATATAA
76001 TAATTTATATACTACTATATA
1 TAATTTATATA-T-CTATATA
76022 TTATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 1 0.06
22 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTTATATATCTATATAA
Found at i:76132 original size:12 final size:12
Alignment explanation
Indices: 76107--76139 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
76097 TATATTTATT
*
76107 TTAT-TTTTATA
1 TTATATTTTACA
76118 TTATATTTTACA
1 TTATATTTTACA
76130 TTATATTTTA
1 TTATATTTTA
76140 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTTTACA
Found at i:76133 original size:17 final size:17
Alignment explanation
Indices: 76054--76148 Score: 74
Period size: 17 Copynumber: 5.8 Consensus size: 17
76044 ATATTTTTGA
*
76054 TATATTTTAAATTAT-T
1 TATATTTTATATTATAT
*
76070 AATA-TTTATATTATAT
1 TATATTTTATATTATAT
*
76086 ATAAATTTTA-A-TATAT
1 -TATATTTTATATTATAT
*
76102 T-TATTTTATTTTTATAT
1 TATATTTTA-TATTATAT
*
76119 TATATTTTACATTATAT
1 TATATTTTATATTATAT
* *
76136 TTTATTTTTTATT
1 TATATTTTATATT
76149 TTTAATCCAA
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
14 6 0.10
15 10 0.16
16 9 0.15
17 25 0.41
18 11 0.18
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATTTTATATTATAT
Found at i:78145 original size:30 final size:31
Alignment explanation
Indices: 78110--78200 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
78100 AAGATTTTAT
**
78110 TTTTAA-GAGTTTATTTGGGTAAAAATT-AAA
1 TTTTAATGA-TTTATTTGAATAAAAATTAAAA
* *
78140 TTTTAATGACTTATTTGAATATAAATTAAAA
1 TTTTAATGATTTATTTGAATAAAAATTAAAA
**
78171 TTTTAATGATTTATTTGAATGTAAATTAAA
1 TTTTAATGATTTATTTGAATAAAAATTAAA
78201 GATTAAAGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 20 0.38
31 33 0.62
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.46
Consensus pattern (31 bp):
TTTTAATGATTTATTTGAATAAAAATTAAAA
Found at i:78172 original size:31 final size:31
Alignment explanation
Indices: 78132--78200 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
78122 ATTTGGGTAA
78132 AAATT-AAATTTTAATGACTTATTTGAATAT
1 AAATTAAAATTTTAATGACTTATTTGAATAT
* *
78162 AAATTAAAATTTTAATGATTTATTTGAATGT
1 AAATTAAAATTTTAATGACTTATTTGAATAT
78193 AAATTAAA
1 AAATTAAA
78201 GATTAAAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 5 0.14
31 31 0.86
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (31 bp):
AAATTAAAATTTTAATGACTTATTTGAATAT
Found at i:78889 original size:17 final size:17
Alignment explanation
Indices: 78850--78892 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
78840 TTTTTTACCG
78850 TTTATATAAAAATATCA
1 TTTATATAAAAATATCA
* * * *
78867 TATATATATATATATCT
1 TTTATATAAAAATATCA
78884 TTTATATAA
1 TTTATATAA
78893 TACAAACTAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTATATAAAAATATCA
Found at i:79830 original size:8 final size:8
Alignment explanation
Indices: 79817--79856 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
79807 TGATGAATTT
79817 AAATTAAA
1 AAATTAAA
79825 AAATTAAA
1 AAATTAAA
79833 AAATTAATA
1 AAATTAA-A
*
79842 AAATT-AT
1 AAATTAAA
79849 AAATTAAA
1 AAATTAAA
79857 TTTAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 5 0.18
8 17 0.61
9 6 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AAATTAAA
Found at i:80828 original size:4 final size:4
Alignment explanation
Indices: 80819--80844 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
80809 TGAGTAATTA
80819 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
80845 TTCAGGTGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:84820 original size:14 final size:16
Alignment explanation
Indices: 84786--84818 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
84776 TTTAAAATAT
84786 TTTATATTTATATAAA
1 TTTATATTTATATAAA
84802 TTTAT-TTTATATAAA
1 TTTATATTTATATAAA
84817 TT
1 TT
84819 ATAAGATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATATTTATATAAA
Found at i:84859 original size:16 final size:19
Alignment explanation
Indices: 84824--84860 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
84814 AAATTATAAG
84824 ATATTCATATATTTATATT
1 ATATTCATATATTTATATT
84843 ATATT-ATAT-TTTA-ATT
1 ATATTCATATATTTATATT
84859 AT
1 AT
84861 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 4 0.22
18 4 0.22
19 5 0.28
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTCATATATTTATATT
Found at i:86885 original size:14 final size:14
Alignment explanation
Indices: 86849--86889 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
86839 ATTCAAGCTC
86849 AGCTAGTTTA-TTA
1 AGCTAGTTTATTTA
86862 A--TATGTTTATTTA
1 AGCTA-GTTTATTTA
86875 AGCTAGTTTATTTA
1 AGCTAGTTTATTTA
86889 A
1 A
86890 ATTAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
11 2 0.08
12 5 0.21
13 5 0.21
14 10 0.42
15 2 0.08
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (14 bp):
AGCTAGTTTATTTA
Found at i:87289 original size:16 final size:17
Alignment explanation
Indices: 87224--87291 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
87214 TACTATTTAA
* *
87224 TAATTTAAAAATAATTT
1 TAATATAAATATAATTT
* * *
87241 TTATTTAAATATAATTA
1 TAATATAAATATAATTT
87258 TAA-A-AATATATAAATTT
1 TAATATAA-ATAT-AATTT
87275 TAATATAAA-ATAATTT
1 TAATATAAATATAATTT
87291 T
1 T
87292 TTAAAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
15 2 0.05
16 10 0.24
17 25 0.61
18 2 0.05
19 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAAATATAATTT
Found at i:87607 original size:4 final size:4
Alignment explanation
Indices: 87600--87640 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
87590 ATGGCAAATA
87600 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
87641 GATAGAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TAAT
Found at i:88018 original size:6 final size:7
Alignment explanation
Indices: 87999--88023 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
87989 ATTTAAATAA
87999 TATTTTT
1 TATTTTT
88006 TATTTTT
1 TATTTTT
88013 TATTTTT
1 TATTTTT
88020 TATT
1 TATT
88024 AATTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TATTTTT
Found at i:88043 original size:26 final size:29
Alignment explanation
Indices: 88013--88066 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
88003 TTTTATTTTT
88013 TATTT-TTTATTAATTT-T-AAAATAAAG
1 TATTTATTTATTAATTTATAAAAATAAAG
* *
88039 TATTTATTTTTTATTTTATAAAAATAAA
1 TATTTATTTATTAATTTATAAAAATAAA
88067 ATTTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 9 0.39
28 1 0.04
29 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (29 bp):
TATTTATTTATTAATTTATAAAAATAAAG
Found at i:88172 original size:11 final size:11
Alignment explanation
Indices: 88156--88198 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
88146 TTTATTACTA
88156 AAATTAAAATT
1 AAATTAAAATT
88167 AAATTAACAA-T
1 AAATTAA-AATT
*
88178 -AATAAAAATT
1 AAATTAAAATT
88188 AAATTAAAATT
1 AAATTAAAATT
88199 GAATCGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 2 0.07
10 6 0.22
11 17 0.63
12 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:89062 original size:16 final size:16
Alignment explanation
Indices: 89037--89078 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
89027 TTTATCGTAT
89037 AATATTTATAT-TTAA
1 AATATTTATATATTAA
89052 AATATTTTATATATTAA
1 AATA-TTTATATATTAA
*
89069 TA-ATTTATAT
1 AATATTTATAT
89079 TATATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 11 0.46
16 8 0.33
17 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATATTTATATATTAA
Found at i:89869 original size:17 final size:17
Alignment explanation
Indices: 89847--89880 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
89837 ATATTATAAC
89847 TTTTTATAAATTTAATT
1 TTTTTATAAATTTAATT
89864 TTTTTATAAATTTAATT
1 TTTTTATAAATTTAATT
89881 AAATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTATAAATTTAATT
Found at i:90674 original size:18 final size:18
Alignment explanation
Indices: 90620--90675 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
90610 GATGATTCAT
*
90620 TTAAATAAATTTTTAAATA
1 TTAAATAAA-TATTAAATA
** *
90639 TTGGATAAAAAATT-AATA
1 TTAAAT-AAATATTAAATA
90657 TTAAATAAATATTAAATA
1 TTAAATAAATATTAAATA
90675 T
1 T
90676 ACTAAATTAC
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
17 6 0.21
18 13 0.46
19 6 0.21
20 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (18 bp):
TTAAATAAATATTAAATA
Found at i:91921 original size:36 final size:36
Alignment explanation
Indices: 91851--91924 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
91841 ACCCCACCTG
* * *
91851 TCATAATCATATGAAATACTTGACTGCCAGTTATCA
1 TCATAATCATATGAAATACTTAACTACCAATTATCA
* * *
91887 TCATCATCATCTGAAATACTTAACTATCAATTATCA
1 TCATAATCATATGAAATACTTAACTACCAATTATCA
91923 TC
1 TC
91925 TTCAGTTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (36 bp):
TCATAATCATATGAAATACTTAACTACCAATTATCA
Found at i:94193 original size:25 final size:25
Alignment explanation
Indices: 94164--94215 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
94154 ATATCTTTTT
*
94164 AATTTTT-TTAAATTTTTAAAATTTA
1 AATTTTTATT-AATTTTTAAAATATA
*
94189 AATTTTTATTTATTTTTAAAATATA
1 AATTTTTATTAATTTTTAAAATATA
94214 AA
1 AA
94216 ATATGAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AATTTTTATTAATTTTTAAAATATA
Found at i:94287 original size:16 final size:16
Alignment explanation
Indices: 94266--94296 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
94256 AATATTTATG
94266 TATATATGATATAAAT
1 TATATATGATATAAAT
*
94282 TATATATTATATAAA
1 TATATATGATATAAA
94297 AATAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TATATATGATATAAAT
Found at i:94418 original size:13 final size:14
Alignment explanation
Indices: 94400--94429 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
94390 ATTTATTAAA
94400 TTAAATTTAT-TTT
1 TTAAATTTATATTT
94413 TTAAATTTATATTT
1 TTAAATTTATATTT
94427 TTA
1 TTA
94430 TTTAAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTAAATTTATATTT
Found at i:94691 original size:4 final size:4
Alignment explanation
Indices: 94682--94707 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
94672 TTTGACTTGG
94682 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
94708 GTGACAGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:95319 original size:13 final size:15
Alignment explanation
Indices: 95293--95329 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
95283 TTTTAAAAAA
95293 TTAATATATCTATAT
1 TTAATATATCTATAT
95308 TTAATAT-T-TATAT
1 TTAATATATCTATAT
*
95321 TTAAAATAT
1 TTAATATAT
95330 TCATTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 11 0.55
14 2 0.10
15 7 0.35
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAATATATCTATAT
Found at i:98125 original size:44 final size:44
Alignment explanation
Indices: 98062--98181 Score: 197
Period size: 44 Copynumber: 2.8 Consensus size: 44
98052 TTAGAATTTT
*
98062 GGTGGCTATGCCAATCCACGGAAAAATAAATAAATATGCAATTG
1 GGTGGCTATGCCAATCCACGGAAAAATAAATAAATATGCAATTA
* *
98106 GGTGGCTATGCTAATCCACGAAAAAATAAATAAATATGCAATTA
1 GGTGGCTATGCCAATCCACGGAAAAATAAATAAATATGCAATTA
*
98150 GGTAGCTATGCCAATCCAC-GAAAAATAAATAA
1 GGTGGCTATGCCAATCCACGGAAAAATAAATAA
98182 TAAAAACACC
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
43 12 0.17
44 58 0.83
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (44 bp):
GGTGGCTATGCCAATCCACGGAAAAATAAATAAATATGCAATTA
Found at i:98579 original size:15 final size:14
Alignment explanation
Indices: 98545--98613 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
98535 CAACCTTCAC
98545 TGTTTCAAATTGA-
1 TGTTTCAAATTGAT
*
98558 -ATTTCAAAATTGAT
1 TGTTTC-AAATTGAT
98572 TGTTTCAAATTGA-
1 TGTTTCAAATTGAT
* **
98585 -ATTTCAAAATTGGC
1 TGTTTC-AAATTGAT
98599 TGTTTCAAATTGAT
1 TGTTTCAAATTGAT
98613 T
1 T
98614 TTCCTGTCAG
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
12 8 0.19
13 13 0.30
14 14 0.33
15 8 0.19
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (14 bp):
TGTTTCAAATTGAT
Found at i:98583 original size:14 final size:13
Alignment explanation
Indices: 98545--98616 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
98535 CAACCTTCAC
98545 TGTTTCAAATTGA
1 TGTTTCAAATTGA
*
98558 -ATTTCAAAATTGA
1 TGTTTC-AAATTGA
98571 TTGTTTCAAATTGA
1 -TGTTTCAAATTGA
* *
98585 -ATTTCAAAATTGGC
1 TGTTTC-AAATT-GA
98599 TGTTTCAAATTGA
1 TGTTTCAAATTGA
98612 T-TTTC
1 TGTTTC
98617 CTGTCAGCTA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
12 12 0.26
13 14 0.30
14 13 0.28
15 8 0.17
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (13 bp):
TGTTTCAAATTGA
Found at i:98583 original size:27 final size:27
Alignment explanation
Indices: 98543--98616 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
98533 TGCAACCTTC
98543 ACTGTTTCAAATTGAATTTCAAAATTG
1 ACTGTTTCAAATTGAATTTCAAAATTG
*
98570 ATTGTTTCAAATTGAATTTCAAAATTG
1 ACTGTTTCAAATTGAATTTCAAAATTG
* *
98597 GCTGTTTCAAATTGATTTTC
1 ACTGTTTCAAATTGAATTTC
98617 CTGTCAGCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (27 bp):
ACTGTTTCAAATTGAATTTCAAAATTG
Found at i:98596 original size:13 final size:12
Alignment explanation
Indices: 98547--98592 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
98537 ACCTTCACTG
98547 TTTCAAATTGAA
1 TTTCAAATTGAA
*
98559 TTTCAAAATTGATTG
1 TTTC-AAATTGA--A
98574 TTTCAAATTGAA
1 TTTCAAATTGAA
98586 TTTCAAA
1 TTTCAAA
98593 ATTGGCTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 7 0.24
15 4 0.14
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:98962 original size:44 final size:44
Alignment explanation
Indices: 98880--98999 Score: 197
Period size: 44 Copynumber: 2.8 Consensus size: 44
98870 GGTGTTTTTA
* *
98880 TTATTTATTTTT-TGTGAATTGGCATAGCCACCCAATTGCATAT
1 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
* *
98923 TTATTTATTTTTCCGTGGATTGACATAACCACCCAATTGCATAT
1 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
98967 TTATTTATTTTTCCGTGGATTGGCATAGCCACC
1 TTATTTATTTTTCCGTGGATTGGCATAGCCACC
99000 AAAATTCTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
43 12 0.17
44 58 0.83
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.42
Consensus pattern (44 bp):
TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
Found at i:103282 original size:15 final size:15
Alignment explanation
Indices: 103262--103310 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
103252 GGAAAATCAA
103262 TTTGAAACAGCCAAT
1 TTTGAAACAGCCAAT
**
103277 TTTG-AA-ATTC-AT
1 TTTGAAACAGCCAAT
103289 TTTGAAACAGCCAAT
1 TTTGAAACAGCCAAT
103304 TTTGAAA
1 TTTGAAA
103311 TTCAATTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 6 0.22
13 4 0.15
14 4 0.15
15 13 0.48
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (15 bp):
TTTGAAACAGCCAAT
Found at i:103292 original size:27 final size:27
Alignment explanation
Indices: 103253--103325 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
103243 CAGTTGGCAG
*
103253 GAAAATCAATTTGAAACAGCCAATTTT
1 GAAATTCAATTTGAAACAGCCAATTTT
*
103280 GAAATTCATTTTGAAACAGCCAATTTT
1 GAAATTCAATTTGAAACAGCCAATTTT
103307 GAAATTCAATTTGAAACAG
1 GAAATTCAATTTGAAACAG
103326 TGAAAGCTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (27 bp):
GAAATTCAATTTGAAACAGCCAATTTT
Found at i:103318 original size:13 final size:13
Alignment explanation
Indices: 103273--103322 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
103263 TTGAAACAGC
103273 CAATTTTGAAATT
1 CAATTTTGAAATT
**
103286 C-ATTTTGAAACAGC
1 CAATTTTG-AA-ATT
103300 CAATTTTGAAATT
1 CAATTTTGAAATT
103313 CAA-TTTGAAA
1 CAATTTTGAAA
103323 CAGTGAAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
12 13 0.43
13 7 0.23
14 4 0.13
15 6 0.20
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (13 bp):
CAATTTTGAAATT
Found at i:105121 original size:2 final size:2
Alignment explanation
Indices: 105114--105150 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
105104 ACAAGGACAA
105114 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
105151 AACATGCACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:106749 original size:28 final size:27
Alignment explanation
Indices: 106662--106751 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 27
106652 TTTTAATTAA
106662 ATAAAATTATAATTAAT--AAAATTTAT
1 ATAAAATT-TAATTAATAAAAAATTTAT
* * * *
106688 TTAAAA-ATATTTAATAAATAAATTTAA
1 ATAAAATTTAATTAATAAA-AAATTTAT
106715 AGTTAAAATTTAATTATATAAAAAATTTAT
1 A--TAAAATTTAATTA-ATAAAAAATTTAT
106745 ATAAAAT
1 ATAAAAT
106752 ATAAGATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 7 0.14
26 6 0.12
27 7 0.14
28 6 0.12
29 5 0.10
30 13 0.27
31 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATAAAATTTAATTAATAAAAAATTTAT
Done.