Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 15 of 27
Found at i:2405307 original size:4 final size:4
Alignment explanation
Indices: 2405298--2405328 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2405288 TCAAAATACA
2405298 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
2405329 TGGACCTACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2405666 original size:2 final size:2
Alignment explanation
Indices: 2405659--2405683 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2405649 TTCGCCTTCT
2405659 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2405684 TTTTAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2406008 original size:2 final size:2
Alignment explanation
Indices: 2405995--2406028 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2405985 TTGGCTGGCG
*
2405995 CA CA CG CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2406029 TATTAGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2408357 original size:14 final size:15
Alignment explanation
Indices: 2408338--2408366 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2408328 GAAGGTGATA
2408338 ATTGAG-ATTTTATT
1 ATTGAGCATTTTATT
2408352 ATTGAGCATTTTATT
1 ATTGAGCATTTTATT
2408367 TGTACTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.55
Consensus pattern (15 bp):
ATTGAGCATTTTATT
Found at i:2411852 original size:2 final size:2
Alignment explanation
Indices: 2411845--2411880 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2411835 TCAACCTGCA
2411845 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
2411881 CTCAGAGAAT
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:2412848 original size:27 final size:27
Alignment explanation
Indices: 2412810--2412863 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2412800 GACTTGCAGA
2412810 GGGAAAAAGAATACTACTACCAGGACT
1 GGGAAAAAGAATACTACTACCAGGACT
2412837 GGGAAAAAGAATACTACTACCAGGACT
1 GGGAAAAAGAATACTACTACCAGGACT
2412864 ATAACTACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (27 bp):
GGGAAAAAGAATACTACTACCAGGACT
Found at i:2416716 original size:2 final size:2
Alignment explanation
Indices: 2416709--2416740 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2416699 CTGTTTTCTT
2416709 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
2416741 ACTATTATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2416914 original size:18 final size:19
Alignment explanation
Indices: 2416891--2416938 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
2416881 TTATTAAATT
2416891 ATTTATTTAAAT-TTAAAA
1 ATTTATTTAAATATTAAAA
*
2416909 ATTTATCT-AATATTAAAA
1 ATTTATTTAAATATTAAAA
*
2416927 A-TAATTTAAATA
1 ATTTATTTAAATA
2416939 AAGATATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTATTTAAATATTAAAA
Found at i:2416955 original size:17 final size:17
Alignment explanation
Indices: 2416933--2416970 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2416923 AAAAATAATT
2416933 TAAATAAAGA-TATTAAA
1 TAAATAAAGAGTA-TAAA
*
2416950 TAAATAACGAGTATAAA
1 TAAATAAAGAGTATAAA
2416967 TAAA
1 TAAA
2416971 AAAATAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (17 bp):
TAAATAAAGAGTATAAA
Found at i:2417985 original size:2 final size:2
Alignment explanation
Indices: 2417978--2418016 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2417968 ATTTTTCTTT
2417978 TA 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 TA T
2418017 TCGATTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2418180 original size:31 final size:33
Alignment explanation
Indices: 2418111--2418185 Score: 109
Period size: 36 Copynumber: 2.2 Consensus size: 33
2418101 TTAGTACATT
2418111 TTAATTATTAGTTTATTAAAATGCACTTTACACAAA
1 TTAATTATTAGTTTATTAAAATGCACTTT--A-AAA
2418147 TTAATTATTAGTTTATTAAAATGCAC-TT-AAA
1 TTAATTATTAGTTTATTAAAATGCACTTTAAAA
2418178 TTAATTAT
1 TTAATTAT
2418186 AATTAAGAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
31 11 0.28
35 2 0.05
36 26 0.67
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.45
Consensus pattern (33 bp):
TTAATTATTAGTTTATTAAAATGCACTTTAAAA
Found at i:2418440 original size:20 final size:20
Alignment explanation
Indices: 2418415--2418456 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2418405 TTTGTAATTG
2418415 ATTTTAAAATATTATTATAA
1 ATTTTAAAATATTATTATAA
* * *
2418435 ATTTTATATTATTATTTTAA
1 ATTTTAAAATATTATTATAA
2418455 AT
1 AT
2418457 ATAGTCTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTAAAATATTATTATAA
Found at i:2425397 original size:2 final size:2
Alignment explanation
Indices: 2425390--2425429 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2425380 ATCTTCTTCC
2425390 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2425430 GTCGCCATTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2427078 original size:2 final size:2
Alignment explanation
Indices: 2427071--2427112 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2427061 ATATGTGGAC
2427071 AT AT 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 AT AT
2427113 CAACTGTGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2428433 original size:13 final size:13
Alignment explanation
Indices: 2428415--2428441 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2428405 TGTGAATATA
2428415 AATATTTTATTAT
1 AATATTTTATTAT
2428428 AATATTTTATTAT
1 AATATTTTATTAT
2428441 A
1 A
2428442 CAATATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATATTTTATTAT
Found at i:2429079 original size:2 final size:2
Alignment explanation
Indices: 2429072--2429109 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2429062 TTCCTCCCAA
2429072 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2429110 GATGCAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2430584 original size:62 final size:62
Alignment explanation
Indices: 2430483--2430604 Score: 235
Period size: 62 Copynumber: 2.0 Consensus size: 62
2430473 GCTACAATGC
2430483 TACATGCTCTCACAGTTTAAGACACTGTCATTTCAGCAACTGCATGTAAAAAGTGTGATCAA
1 TACATGCTCTCACAGTTTAAGACACTGTCATTTCAGCAACTGCATGTAAAAAGTGTGATCAA
*
2430545 TACATGCTCTCACAGTTTAAGACACTGTCATTTCTGCAACTGCATGTAAAAAGTGTGATC
1 TACATGCTCTCACAGTTTAAGACACTGTCATTTCAGCAACTGCATGTAAAAAGTGTGATC
2430605 CAATCTTTAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (62 bp):
TACATGCTCTCACAGTTTAAGACACTGTCATTTCAGCAACTGCATGTAAAAAGTGTGATCAA
Found at i:2434598 original size:13 final size:14
Alignment explanation
Indices: 2434565--2434598 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2434555 ACTATATAAA
*
2434565 TATATAAATTTTAG
1 TATAAAAATTTTAG
2434579 TATAAAAATTTTAG
1 TATAAAAATTTTAG
2434593 -ATAAAA
1 TATAAAA
2434599 TCAATTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (14 bp):
TATAAAAATTTTAG
Found at i:2436159 original size:18 final size:19
Alignment explanation
Indices: 2436128--2436186 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 19
2436118 ATTTAAGATG
2436128 ATATATTTATATAAATTT-TA
1 ATATA-TTA-ATAAATTTATA
2436148 ATATATTAAT-AATTTATA
1 ATATATTAATAAATTTATA
*
2436166 TTATATTAATATATATTTATA
1 ATATATTAATA-A-ATTTATA
2436187 TTTATATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 5 0.15
18 13 0.38
19 3 0.09
20 6 0.18
21 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATATTAATAAATTTATA
Found at i:2436175 original size:15 final size:14
Alignment explanation
Indices: 2436149--2436196 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 14
2436139 TAAATTTTAA
2436149 TATATTA-ATAATT
1 TATATTATATAATT
*
2436162 TATATTATATTAATA
1 TATATTATA-TAATT
2436177 TATATT-TAT-ATT
1 TATATTATATAATT
2436189 TATATTAT
1 TATATTAT
2436197 TTTTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 8 0.27
13 9 0.30
14 3 0.10
15 10 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATTATATAATT
Found at i:2436186 original size:6 final size:6
Alignment explanation
Indices: 2436149--2436208 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
2436139 TAAATTTTAA
* *
2436149 TATATT AATAATT TATA-T TATA-T TA-ATA TATATT TATATT TATA-T
1 TATATT TAT-ATT TATATT TATATT TATATT TATATT TATATT TATATT
*
2436194 TATTTT TATATT TAT
1 TATATT TATATT TAT
2436209 CATGTTTAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 1 0.02
5 14 0.32
6 24 0.55
7 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:2436203 original size:17 final size:16
Alignment explanation
Indices: 2436129--2436208 Score: 61
Period size: 17 Copynumber: 4.6 Consensus size: 16
2436119 TTTAAGATGA
*
2436129 TATATTTATATAAATTT
1 TATATTTATATATA-TT
*
2436146 TAATATATTAATAATTTATAT
1 T-ATAT-TT-AT-ATATAT-T
*
2436167 TATATTAATATATATT
1 TATATTTATATATATT
*
2436183 TATATTTATATTATTTT
1 TATATTTATA-TATATT
2436200 TATATTTAT
1 TATATTTAT
2436209 CATGTTTAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
16 10 0.20
17 20 0.39
18 6 0.12
19 3 0.06
20 7 0.14
21 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATTTATATATATT
Found at i:2436204 original size:27 final size:27
Alignment explanation
Indices: 2436129--2436204 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
2436119 TTTAAGATGA
* *
2436129 TATATTTATATAAATTTTA-ATATATT
1 TATATTTATATTATTTTTATATATATT
* * *
2436155 AATAATTTATATTATATTAATATATATT
1 TAT-ATTTATATTATTTTTATATATATT
2436183 TATATTTATATTATTTTTATAT
1 TATATTTATATTATTTTTATAT
2436205 TTATCATGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.05
27 29 0.73
28 9 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TATATTTATATTATTTTTATATATATT
Found at i:2437039 original size:14 final size:15
Alignment explanation
Indices: 2437013--2437042 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2437003 AAAGTTATAA
2437013 AAAAATATATTAATT
1 AAAAATATATTAATT
2437028 AAAAATAT-TTAATT
1 AAAAATATATTAATT
2437042 A
1 A
2437043 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAATATATTAATT
Found at i:2437061 original size:17 final size:17
Alignment explanation
Indices: 2437010--2437061 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 17
2437000 TTTAAAGTTA
*
2437010 TAAAAAAATATATTAAT
1 TAAAAAATTATATTAAT
*
2437027 TAAAAATATTTAATTATTATT
1 TAAAAA-A-TT-A-TATTAAT
2437048 TAAAAAATTATATT
1 TAAAAAATTATATT
2437062 TAATATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.34
18 2 0.07
19 3 0.10
20 2 0.07
21 12 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAAAATTATATTAAT
Found at i:2437068 original size:21 final size:21
Alignment explanation
Indices: 2437026--2437069 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2437016 AATATATTAA
*
2437026 TTAAAAATATTTAATTATTAT
1 TTAAAAATATTTAATTAATAT
*
2437047 TTAAAAA-ATTATATTTAATAT
1 TTAAAAATATT-TAATTAATAT
2437068 TT
1 TT
2437070 TATTAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAAAAATATTTAATTAATAT
Found at i:2437075 original size:25 final size:25
Alignment explanation
Indices: 2437034--2437127 Score: 95
Period size: 25 Copynumber: 3.8 Consensus size: 25
2437024 AATTAAAAAT
* *
2437034 ATTTAAT-TATTATTTAAAAAATTAT
1 ATTTAATATATTA-TTAATAAATTAA
* *
2437059 ATTTAATATTTTATTAATATA-TAA
1 ATTTAATATATTATTAATAAATTAA
2437083 ATTT-ATATATTATTAATAAATTAAA
1 ATTTAATATATTATTAATAAATT-AA
* *
2437108 ATTTATTATTTTATTAATAA
1 ATTTAATATATTATTAATAA
2437128 TAAAATTATT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
23 14 0.25
24 7 0.12
25 19 0.33
26 17 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTAATATATTATTAATAAATTAA
Found at i:2437095 original size:23 final size:22
Alignment explanation
Indices: 2437059--2437143 Score: 91
Period size: 23 Copynumber: 3.6 Consensus size: 22
2437049 AAAAAATTAT
2437059 ATTTAATATTTTATTAATATATAA
1 ATTT-ATATTTTATTAATA-ATAA
*
2437083 ATTTATATATTATTAATAAATTAAA
1 ATTTATATTTTATTAAT-AA-T-AA
2437108 ATTTATTATTTTATTAATAATAA
1 ATTTA-TATTTTATTAATAATAA
*
2437131 AATTAT-TTTTATT
1 ATTTATATTTTATT
2437144 TATTTTTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
21 7 0.13
22 1 0.02
23 19 0.35
24 7 0.13
25 9 0.17
26 11 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTATATTTTATTAATAATAA
Found at i:2437096 original size:49 final size:48
Alignment explanation
Indices: 2437039--2437145 Score: 137
Period size: 49 Copynumber: 2.2 Consensus size: 48
2437029 AAAATATTTA
* *
2437039 ATTATTATTTAAAAAATT-ATATTTAATATTTTATTAATATATAAATTT
1 ATTATTATTTAAAAAATTAAAATTTAATATTTTATTAATA-ATAAAATT
* *
2437087 ATATATTA-TTAATAAATTAAAATTTATTATTTTATTAATAATAAAATT
1 AT-TATTATTTAAAAAATTAAAATTTAATATTTTATTAATAATAAAATT
*
2437135 ATTTTTATTTA
1 ATTATTATTTA
2437146 TTTTTTAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
47 4 0.08
48 23 0.45
49 24 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (48 bp):
ATTATTATTTAAAAAATTAAAATTTAATATTTTATTAATAATAAAATT
Found at i:2437142 original size:26 final size:25
Alignment explanation
Indices: 2437065--2437144 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
2437055 TTATATTTAA
* *
2437065 TATTTTATTAAT-ATATAA-ATTTA
1 TATTTTATTAATAATAAAATATTTT
* *
2437088 TATATTATTAATAAATTAAAAT-TTAT
1 TATTTTATTAAT-AA-TAAAATATTTT
2437114 TATTTTATTAATAATAAAATTATTTT
1 TATTTTATTAATAATAAAA-TATTTT
2437140 TATTT
1 TATTT
2437145 ATTTTTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 11 0.24
24 5 0.11
25 4 0.09
26 25 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTTATTAATAATAAAATATTTT
Found at i:2442149 original size:3 final size:3
Alignment explanation
Indices: 2442141--2442166 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2442131 AAAATTACTA
2442141 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2442167 ATAAAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2444428 original size:19 final size:19
Alignment explanation
Indices: 2444399--2444436 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2444389 ATTTAATTAC
2444399 AATAATATTATATTATTTCT
1 AATAATATTATATT-TTTCT
2444419 AATAAT-TTATATTTTTCT
1 AATAATATTATATTTTTCT
2444437 CTTTTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (19 bp):
AATAATATTATATTTTTCT
Found at i:2445126 original size:2 final size:2
Alignment explanation
Indices: 2445119--2445145 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2445109 AAAATTAGGC
2445119 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 A
2445146 CACAGTCGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2451389 original size:34 final size:34
Alignment explanation
Indices: 2451346--2451416 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
2451336 TTCAATGCAT
2451346 AACAAATTGTCAGTTACATTATGCTTGAATATAA
1 AACAAATTGTCAGTTACATTATGCTTGAATATAA
* * *
2451380 AACAAATTGTTATTTACGTTATGCTTGAATATAA
1 AACAAATTGTCAGTTACATTATGCTTGAATATAA
2451414 AAC
1 AAC
2451417 TCCGTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (34 bp):
AACAAATTGTCAGTTACATTATGCTTGAATATAA
Found at i:2454981 original size:3 final size:3
Alignment explanation
Indices: 2454973--2455008 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2454963 AATTACCCAT
2454973 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2455009 AACCTTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2456555 original size:23 final size:23
Alignment explanation
Indices: 2456505--2456548 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2456495 TTATATGCAT
**
2456505 ATAAAAAAAATCATAGTATAAAG
1 ATAAAAAAAAGAATAGTATAAAG
2456528 ATAAAAAAAAGAATA-TATAAA
1 ATAAAAAAAAGAATAGTATAAA
2456549 TATTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (23 bp):
ATAAAAAAAAGAATAGTATAAAG
Found at i:2461769 original size:2 final size:2
Alignment explanation
Indices: 2461762--2461792 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2461752 CTACAACAAT
2461762 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2461793 AACTCTTCAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2465272 original size:4 final size:4
Alignment explanation
Indices: 2465263--2465296 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2465253 TGGTGAATAA
2465263 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
2465297 TGGGTTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:2465495 original size:17 final size:17
Alignment explanation
Indices: 2465452--2465495 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2465442 TTTATAATTA
*
2465452 AATTTAAATAAAAAAAT
1 AATTTAAATTAAAAAAT
*
2465469 TATATT-AATTAAAAAAT
1 AAT-TTAAATTAAAAAAT
2465486 AATTTAAATT
1 AATTTAAATT
2465496 GATTTGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTTAAATTAAAAAAT
Found at i:2466863 original size:2 final size:2
Alignment explanation
Indices: 2466858--2466889 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2466848 AAAAGAAAAA
2466858 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2466890 TTAATTAAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2467296 original size:22 final size:21
Alignment explanation
Indices: 2467270--2467340 Score: 56
Period size: 22 Copynumber: 3.4 Consensus size: 21
2467260 TATTAAAATT
2467270 TAATTAAATTAGATATTTAATA
1 TAATTAAATTA-ATATTTAATA
* * * *
2467292 TAATTAATTTATATAATTATTT
1 TAATTAAATTA-ATATTTAATA
*
2467314 TAA-TAAATT-ATATTAAATA
1 TAATTAAATTAATATTTAATA
*
2467333 TATTTAAA
1 TAATTAAA
2467341 ATTTAAATCT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
19 8 0.22
20 4 0.11
21 5 0.14
22 20 0.54
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TAATTAAATTAATATTTAATA
Found at i:2467322 original size:13 final size:14
Alignment explanation
Indices: 2467285--2467334 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
2467275 AAATTAGATA
*
2467285 TTTAATATAATTAA
1 TTTAATATAATTAT
2467299 TTT-ATATAATTAT
1 TTTAATATAATTAT
2467312 TTTAATA-AATTAT
1 TTTAATATAATTAT
*
2467325 ATTAAATATA
1 -TTTAATATA
2467335 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 18 0.58
14 12 0.39
15 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATATAATTAT
Found at i:2468210 original size:29 final size:29
Alignment explanation
Indices: 2468177--2468235 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2468167 AATTAATATG
*
2468177 ATATAAATATAAAATAAATTTAAAATTTT
1 ATATAAATATAAAATAAATTCAAAATTTT
* **
2468206 ATATAAATATCAAATCGATTCAAAATTTT
1 ATATAAATATAAAATAAATTCAAAATTTT
2468235 A
1 A
2468236 ATTACTAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (29 bp):
ATATAAATATAAAATAAATTCAAAATTTT
Found at i:2469160 original size:13 final size:12
Alignment explanation
Indices: 2469130--2469183 Score: 56
Period size: 13 Copynumber: 4.4 Consensus size: 12
2469120 ATTTTAAACG
2469130 TAATAAATATTA
1 TAATAAATATTA
* *
2469142 TTATAATTAATTA
1 TAATAAAT-ATTA
2469155 TAATAAATATTAA
1 TAATAAATATT-A
*
2469168 TAATAAA-ATAA
1 TAATAAATATTA
2469179 TAATA
1 TAATA
2469184 TTATTATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 6 0.17
12 11 0.31
13 18 0.51
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAAATATTA
Found at i:2471041 original size:22 final size:21
Alignment explanation
Indices: 2470975--2471041 Score: 50
Period size: 22 Copynumber: 3.1 Consensus size: 21
2470965 GCTTATAATT
* *
2470975 AAATATTTATTATC-ATAAATC
1 AAATAATTATTA-CAATAAATA
2470996 AAATATATTATT--AATAAATATA
1 AAATA-ATTATTACAAT-AA-ATA
2471018 AAATAATTATTACAATAAACTA
1 AAATAATTATTACAATAAA-TA
2471040 AA
1 AA
2471042 CATGTTAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
20 2 0.05
21 14 0.38
22 18 0.49
23 3 0.08
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATAATTATTACAATAAATA
Found at i:2473415 original size:16 final size:17
Alignment explanation
Indices: 2473380--2473416 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
2473370 TAAAAAAAAA
2473380 TATAATATTTTTATATT
1 TATAATATTTTTATATT
2473397 TATAA-ATTATTTA-ATT
1 TATAATATT-TTTATATT
2473413 TATA
1 TATA
2473417 TCATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATAATATTTTTATATT
Found at i:2473655 original size:26 final size:27
Alignment explanation
Indices: 2473582--2473655 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 27
2473572 ATTTACAAAT
* *
2473582 AAAAATAAATTTAACATTTAAACTTTTA
1 AAAAATAAATATAATA-TTAAACTTTTA
* *
2473610 AATCAAA-AACTA-AATTTTAAA-TTTTA
1 AA--AAATAAATATAATATTAAACTTTTA
2473636 AAAAATAAATATAATATTAA
1 AAAAATAAATATAATATTAA
2473656 TATTATATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
24 3 0.08
25 4 0.11
26 14 0.39
27 5 0.14
28 4 0.11
29 3 0.08
30 3 0.08
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (27 bp):
AAAAATAAATATAATATTAAACTTTTA
Found at i:2475371 original size:19 final size:19
Alignment explanation
Indices: 2475343--2475380 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2475333 CAATACAAAA
2475343 CTAGTCGAATTTCAGTATT
1 CTAGTCGAATTTCAGTATT
*
2475362 CTAGTTGAATTTCAGTATT
1 CTAGTCGAATTTCAGTATT
2475381 ATGTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (19 bp):
CTAGTCGAATTTCAGTATT
Found at i:2477335 original size:59 final size:59
Alignment explanation
Indices: 2477243--2477360 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
2477233 GCTCTCTGCA
*
2477243 GATATTAAAAATTTTTCACACCTAATTACTATATTAAAGTGTATCAAATGGGGAAGAGC
1 GATATTAAAAATTTTTCACACCTAATTACTATATTAAAGTATATCAAATGGGGAAGAGC
*
2477302 GATATTAAAATTTTTTCACACCTAATTACTATATTAAAGTATATCAAATGGGGAAGAGC
1 GATATTAAAAATTTTTCACACCTAATTACTATATTAAAGTATATCAAATGGGGAAGAGC
2477361 ATTTAATTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (59 bp):
GATATTAAAAATTTTTCACACCTAATTACTATATTAAAGTATATCAAATGGGGAAGAGC
Found at i:2480892 original size:16 final size:15
Alignment explanation
Indices: 2480871--2480900 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
2480861 GGCTTCCTAT
2480871 CAAAACAAAAACAAAG
1 CAAAAC-AAAACAAAG
2480887 CAAAACAAAACAAA
1 CAAAACAAAACAAA
2480901 ACCAAAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.77, C:0.20, G:0.03, T:0.00
Consensus pattern (15 bp):
CAAAACAAAACAAAG
Found at i:2482102 original size:32 final size:32
Alignment explanation
Indices: 2482066--2482152 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
2482056 TATTTTAAGG
* *
2482066 TAATTTATATTTTAAATTAT-TAAATTTAATAT
1 TAATTTATA-TATAAATTATAAAAATTTAATAT
*
2482098 TAATTTTTATATAAATTATAAAAATTTAAT-T
1 TAATTTATATATAAATTATAAAAATTTAATAT
* * *
2482129 TTA-TTA-AAATATATTATAAAAATT
1 TAATTTATATATAAATTATAAAAATT
2482153 AGGTTATTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 16 0.34
30 2 0.04
31 12 0.26
32 17 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TAATTTATATATAAATTATAAAAATTTAATAT
Found at i:2482346 original size:22 final size:22
Alignment explanation
Indices: 2482311--2482382 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
2482301 AATTTATTAA
2482311 TAATAAAATTTTAATGATATAATT
1 TAATAAAA--TTAATGATATAATT
**
2482335 TAATAAAATTAAAAATATAATT
1 TAATAAAATTAATGATATAATT
* *
2482357 TATATAAAATTGATGATA-AATA
1 TA-ATAAAATTAATGATATAATT
2482379 TAAT
1 TAAT
2482383 GTGTCTTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
21 2 0.05
22 19 0.46
23 12 0.29
24 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
TAATAAAATTAATGATATAATT
Found at i:2482348 original size:30 final size:30
Alignment explanation
Indices: 2482274--2482348 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 30
2482264 TTTTTTAATT
*
2482274 ATTTAATAAAATT--AATGTGAATAATTTA
1 ATTTAATAAAATTAAAATGTGAATAATATA
* * * *
2482302 ATTTATTAATAA-TAAAATTTTAATGATATA
1 ATTTAATAA-AATTAAAATGTGAATAATATA
2482332 ATTTAATAAAATTAAAA
1 ATTTAATAAAATTAAAA
2482349 ATATAATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 9 0.24
29 4 0.11
30 24 0.65
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (30 bp):
ATTTAATAAAATTAAAATGTGAATAATATA
Found at i:2485875 original size:16 final size:16
Alignment explanation
Indices: 2485856--2485917 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 16
2485846 ATGAAATTAA
2485856 AAAAATATAAATATTT
1 AAAAATATAAATATTT
*
2485872 AAAAATATTAAATTTTAT
1 AAAAATA-TAAATATT-T
2485890 AAAAAAATATATAATATTT
1 --AAAAATATA-AATATTT
*
2485909 -TAAATATAA
1 AAAAATATAA
2485918 TTAAAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
15 1 0.03
16 14 0.37
17 7 0.18
18 1 0.03
19 3 0.08
20 12 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAAATATAAATATTT
Found at i:2485875 original size:17 final size:18
Alignment explanation
Indices: 2485852--2485908 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
2485842 CAACATGAAA
2485852 TTAAAAAAATATAAATAT
1 TTAAAAAAATATAAATAT
* *
2485870 TTAAAAATAT-TAAATTT
1 TTAAAAAAATATAAATAT
2485887 TATAAAAAAATATATAATAT
1 T-TAAAAAAATATA-AATAT
2485907 TT
1 TT
2485909 TAAATATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 7 0.22
18 17 0.53
19 3 0.09
20 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAAAAATATAAATAT
Found at i:2485911 original size:38 final size:37
Alignment explanation
Indices: 2485853--2485930 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 37
2485843 AACATGAAAT
*
2485853 TAAAAAAATATAAATATTTAAAAAT-ATTAAATTTTA
1 TAAAAAAATATAAATATTTAAAAATAATTAAAATTTA
*
2485889 TAAAAAAATATATAATATTTTAAATATAATTAAAATTTA
1 TAAAAAAATATA-AATA-TTTAAAAATAATTAAAATTTA
2485928 TAA
1 TAA
2485931 TATTAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 12 0.32
37 4 0.11
38 8 0.22
39 13 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (37 bp):
TAAAAAAATATAAATATTTAAAAATAATTAAAATTTA
Found at i:2485942 original size:25 final size:26
Alignment explanation
Indices: 2485893--2485952 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
2485883 ATTTTATAAA
*
2485893 AAAATATATAATATTTTAAATATAATT
1 AAAATATATAATA-TTTAAAAATAATT
*
2485920 AAAATTTATAATA-TTAAAAATAA-T
1 AAAATATATAATATTTAAAAATAATT
2485944 ACAAATATA
1 A-AAATATA
2485953 ATAAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.07
25 15 0.52
27 12 0.41
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATATATAATATTTAAAAATAATT
Found at i:2490276 original size:11 final size:11
Alignment explanation
Indices: 2490260--2490296 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
2490250 TTTATGAAAA
2490260 AAATTATTTAT
1 AAATTATTTAT
*
2490271 AAATTAATTATT
1 AAATTATTTA-T
2490283 AAATTATTTAT
1 AAATTATTTAT
2490294 AAA
1 AAA
2490297 AATATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AAATTATTTAT
Found at i:2490285 original size:12 final size:12
Alignment explanation
Indices: 2490260--2490304 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
2490250 TTTATGAAAA
2490260 AAATTATTTA-T
1 AAATTATTTATT
*
2490271 AAATTAATTATT
1 AAATTATTTATT
*
2490283 AAATTATTTATA
1 AAATTATTTATT
*
2490295 AAAATATTTA
1 AAATTATTTA
2490305 AAAATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AAATTATTTATT
Found at i:2490309 original size:23 final size:23
Alignment explanation
Indices: 2490258--2490324 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
2490248 TATTTATGAA
*
2490258 AAAAATTATTTAT-AAATTAATT
1 AAAAATTATTTATAAAAATAATT
* *
2490280 ATTAAATTATTTATAAAAATATTT
1 A-AAAATTATTTATAAAAATAATT
2490304 AAAAA-TATATTA-AAAAATAAT
1 AAAAATTAT-TTATAAAAATAAT
2490325 GTATTATCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 12 0.32
23 17 0.46
24 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAAATTATTTATAAAAATAATT
Found at i:2492350 original size:17 final size:16
Alignment explanation
Indices: 2492291--2492355 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
2492281 AAATTTTTTG
*
2492291 ATTATTTTCGAGTTCGG
1 ATTA-TTTCGAGTTCGA
* *
2492308 ATCATTTCG-GATTTGA
1 ATTATTTCGAG-TTCGA
*
2492324 GTTATTTCGAGTTCGA
1 ATTATTTCGAGTTCGA
2492340 ATTATTTTCGAGTTCG
1 ATTA-TTTCGAGTTCG
2492356 GGTCATTTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
15 1 0.03
16 22 0.58
17 15 0.39
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.46
Consensus pattern (16 bp):
ATTATTTCGAGTTCGA
Found at i:2493229 original size:16 final size:16
Alignment explanation
Indices: 2493217--2493257 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
2493207 TGGGTTCAAG
2493217 TCATTTCAAGTTCGAA
1 TCATTTCAAGTTCGAA
**
2493233 TCATTTTGAGTTCGAA
1 TCATTTCAAGTTCGAA
2493249 TCATTTCAA
1 TCATTTCAA
2493258 ATTCAAGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (16 bp):
TCATTTCAAGTTCGAA
Found at i:2495014 original size:3 final size:3
Alignment explanation
Indices: 2495006--2495030 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2494996 CTTTTGAATA
2495006 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2495031 TCTACATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2495571 original size:18 final size:17
Alignment explanation
Indices: 2495548--2495584 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2495538 ATATTTACTG
2495548 TATTTAATATTTATTTAA
1 TATTTAAT-TTTATTTAA
*
2495566 TATTTAATTTTTTTTAA
1 TATTTAATTTTATTTAA
2495583 TA
1 TA
2495585 CAACAGTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTAATTTTATTTAA
Found at i:2499441 original size:2 final size:2
Alignment explanation
Indices: 2499434--2499471 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2499424 ACAAACTGAT
2499434 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2499472 AAGGATCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2500875 original size:27 final size:27
Alignment explanation
Indices: 2500837--2500889 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
2500827 GATAAGGGGT
*
2500837 TTTTTTATTATTATT-TTTTTCTTTTAA
1 TTTTTAATTATT-TTCTTTTTCTTTTAA
2500864 TTTTTAATTATTTTCCTTTTTCTTTT
1 TTTTTAATTATTTT-CTTTTTCTTTT
2500890 TTAATGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.09
27 11 0.48
28 10 0.43
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTTTAATTATTTTCTTTTTCTTTTAA
Found at i:2502802 original size:12 final size:12
Alignment explanation
Indices: 2502785--2502820 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2502775 ATTATAAATA
2502785 TTAAAATTTAAT
1 TTAAAATTTAAT
2502797 TTAAAATTT-AT
1 TTAAAATTTAAT
*
2502808 TTAATATTTAAT
1 TTAAAATTTAAT
2502820 T
1 T
2502821 GCATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTAAAATTTAAT
Found at i:2503733 original size:14 final size:14
Alignment explanation
Indices: 2503695--2503743 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
2503685 AATTATATAA
* *
2503695 ATTTAATATGTTTT
1 ATTTTATATTTTTT
*
2503709 A-TTCATA-TTTTT
1 ATTTTATATTTTTT
2503721 -TTTTATATTTTTT
1 ATTTTATATTTTTT
2503734 ATTTTATATT
1 ATTTTATATT
2503744 ATATTTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 9 0.31
13 10 0.34
14 10 0.34
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (14 bp):
ATTTTATATTTTTT
Found at i:2506067 original size:30 final size:30
Alignment explanation
Indices: 2506031--2506157 Score: 110
Period size: 30 Copynumber: 4.2 Consensus size: 30
2506021 CCACCTGCCT
* **
2506031 CTCCTCCCCCGGCAACTCCACCTCCCGCTA
1 CTCCTCCACCGGCTTCTCCACCTCCCGCTA
* * * *
2506061 CTCCTCCACCGTCTTCCCCACCTCCTGCCA
1 CTCCTCCACCGGCTTCTCCACCTCCCGCTA
* * *
2506091 CTCCACCACCGGCTTCTCCCCCTCCGGCTA
1 CTCCTCCACCGGCTTCTCCACCTCCCGCTA
* * * * * *
2506121 CTCCTCCACCTGCATCTCCCCCACCAGCAA
1 CTCCTCCACCGGCTTCTCCACCTCCCGCTA
2506151 CTCCTCC
1 CTCCTCC
2506158 TCCAGCTACC
Statistics
Matches: 78, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.13, C:0.59, G:0.09, T:0.20
Consensus pattern (30 bp):
CTCCTCCACCGGCTTCTCCACCTCCCGCTA
Found at i:2506109 original size:15 final size:15
Alignment explanation
Indices: 2506091--2506145 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
2506081 CCTCCTGCCA
*
2506091 CTCCACCACCGGCTT
1 CTCCCCCACCGGCTT
* *
2506106 CTCCCCCTCCGGCTA
1 CTCCCCCACCGGCTT
* * *
2506121 CTCCTCCACCTGCAT
1 CTCCCCCACCGGCTT
2506136 CTCCCCCACC
1 CTCCCCCACC
2506146 AGCAACTCCT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.11, C:0.60, G:0.09, T:0.20
Consensus pattern (15 bp):
CTCCCCCACCGGCTT
Found at i:2507641 original size:14 final size:14
Alignment explanation
Indices: 2507606--2507648 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
2507596 ATTTAATTAA
2507606 TTTAAATAA-TTATT
1 TTTAAA-AATTTATT
*
2507620 TATAAAAAATTTATT
1 T-TTAAAAATTTATT
2507635 TTTAAAAATTTATT
1 TTTAAAAATTTATT
2507649 ATTTTGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAAAAATTTATT
Found at i:2508936 original size:3 final size:3
Alignment explanation
Indices: 2508930--2508964 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2508920 TTTAAAGCCT
2508930 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2508965 TTCTTAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2515666 original size:10 final size:10
Alignment explanation
Indices: 2515632--2515659 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2515622 TTATTATATT
2515632 TATTTTTAAA
1 TATTTTTAAA
2515642 TATTTTTAAA
1 TATTTTTAAA
2515652 TATTTTTA
1 TATTTTTA
2515660 TTTATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:2515846 original size:14 final size:13
Alignment explanation
Indices: 2515816--2515852 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
2515806 ATATTTATTA
2515816 TTTAA-AATAATT
1 TTTAATAATAATT
2515828 TTTAATAATAATAT
1 TTTAATAATAAT-T
2515842 TTTAATAATAA
1 TTTAATAATAA
2515853 ATAATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.22
13 6 0.26
14 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTAATAATAATT
Found at i:2516526 original size:16 final size:18
Alignment explanation
Indices: 2516501--2516546 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
2516491 TTATAATTAT
* *
2516501 ATTTAAAATAT-TTTATA
1 ATTTATAATATATTAATA
2516518 ATTT-TAATATATTAATA
1 ATTTATAATATATTAATA
2516535 ATTTATAATATA
1 ATTTATAATATA
2516547 AAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.20
17 13 0.52
18 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTATAATATATTAATA
Found at i:2516529 original size:48 final size:46
Alignment explanation
Indices: 2516476--2516580 Score: 108
Period size: 48 Copynumber: 2.3 Consensus size: 46
2516466 TATTATATTT
* *
2516476 ATATATTTTATTATATTATAAT-T-ATATTTAAAATATTTTATAATTTTA
1 ATATATTTTATTAT-TTATAATATAAAATTTAAAATA---TAAAATTTTA
* *
2516524 ATATA-TTAATAATTTATAATATAAAATTTAAAATATAAAATTTTA
1 ATATATTTTATTATTTATAATATAAAATTTAAAATATAAAATTTTA
*
2516569 ATATATTATATT
1 ATATATTTTATT
2516581 TTAATTATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
45 14 0.30
46 10 0.21
47 7 0.15
48 16 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (46 bp):
ATATATTTTATTATTTATAATATAAAATTTAAAATATAAAATTTTA
Found at i:2516551 original size:14 final size:14
Alignment explanation
Indices: 2516534--2516573 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
2516524 ATATATTAAT
2516534 AATTTATAATATAA
1 AATTTATAATATAA
*
2516548 AATTTAAAATATAA
1 AATTTATAATATAA
2516562 AATTT-TAATATA
1 AATTTATAATATA
2516574 TTATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTTATAATATAA
Found at i:2516594 original size:14 final size:15
Alignment explanation
Indices: 2516465--2516595 Score: 76
Period size: 15 Copynumber: 8.7 Consensus size: 15
2516455 AGCTAATCAC
2516465 ATATTATA-TTT-AT
1 ATATTATATTTTAAT
* * *
2516478 ATATTTTATTATATT
1 ATATTATATTTTAAT
*
2516493 ATAATTATATTTAAAAT
1 AT-ATTATATTT-TAAT
*
2516510 ATTTTATAATTTTAAT
1 ATATTAT-ATTTTAAT
2516526 ATATTAATAATTTATAAT
1 ATATT-AT-ATTT-TAAT
* *
2516544 ATA--A-AATTTAAA
1 ATATTATATTTTAAT
* *
2516556 ATATAAAATTTTAAT
1 ATATTATATTTTAAT
2516571 ATATTATATTTTAAT
1 ATATTATATTTTAAT
*
2516586 -TATTTTATTT
1 ATATTATATTT
2516596 ATATATAATC
Statistics
Matches: 91, Mismatches: 17, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
12 6 0.07
13 10 0.11
14 12 0.13
15 23 0.25
16 18 0.20
17 15 0.16
18 7 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTATATTTTAAT
Found at i:2519241 original size:19 final size:21
Alignment explanation
Indices: 2519188--2519241 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 21
2519178 ATAAAAATCA
2519188 TATTATTTAATTAATTGATATT
1 TATTATTT-ATTAATTGATATT
2519210 T-TTATTAAATATT-ATT-ATATT
1 TATTATT---TATTAATTGATATT
2519231 TATTATTTATT
1 TATTATTTATT
2519242 TAATATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
19 4 0.14
21 11 0.39
22 9 0.32
23 3 0.11
24 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTATTTATTAATTGATATT
Found at i:2519669 original size:23 final size:23
Alignment explanation
Indices: 2519604--2519671 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 23
2519594 TTATTATCAC
2519604 TTTTATTATTAATGTATTAAAATAT
1 TTTTATTATTAA--TATTAAAATAT
* * *
2519629 TATAATTTATT-ATTTTAAAAT-T
1 TTTTA-TTATTAATATTAAAATAT
2519651 TTTTATTAATTAATATTAAAA
1 TTTTATT-ATTAATATTAAAA
2519672 AAATTTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
21 2 0.06
22 7 0.21
23 16 0.47
25 4 0.12
26 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (23 bp):
TTTTATTATTAATATTAAAATAT
Found at i:2519686 original size:25 final size:25
Alignment explanation
Indices: 2519645--2519694 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
2519635 TTATTATTTT
2519645 AAAATTTTTTATTAA-TTAATATTAAA
1 AAAATTTTTTA-TAATTTAAT-TTAAA
2519671 AAAATTTATTTA-AATTTAATTTAA
1 AAAATTT-TTTATAATTTAATTTAA
2519695 TATAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
25 6 0.27
26 12 0.55
27 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AAAATTTTTTATAATTTAATTTAAA
Found at i:2520248 original size:15 final size:15
Alignment explanation
Indices: 2520228--2520257 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2520218 AATAATTTAA
*
2520228 TTTAAATATAAAATT
1 TTTAAAAATAAAATT
2520243 TTTAAAAATAAAATT
1 TTTAAAAATAAAATT
2520258 AACTTAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTAAAAATAAAATT
Found at i:2534022 original size:3 final size:3
Alignment explanation
Indices: 2534007--2534044 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
2533997 ACTAATGCAT
*
2534007 TTA TTA TTT TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2534045 ATAATTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:2534028 original size:17 final size:17
Alignment explanation
Indices: 2534006--2534040 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2533996 AACTAATGCA
*
2534006 TTTATTATTTTTATTAT
1 TTTATTATTATTATTAT
2534023 TTTATTATTATTATTAT
1 TTTATTATTATTATTAT
2534040 T
1 T
2534041 ATTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTATTATTATTAT
Found at i:2535588 original size:20 final size:20
Alignment explanation
Indices: 2535550--2535588 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2535540 TATTTTTATT
*
2535550 TATTATAATTATATTTAAAA
1 TATTATAATTATATATAAAA
2535570 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
2535589 TTTGTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAA
Found at i:2535658 original size:19 final size:19
Alignment explanation
Indices: 2535630--2535673 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2535620 AAATTGATAC
2535630 ATTT-TATATTTTTATTAT
1 ATTTATATATTTTTATTAT
2535648 ATTTATATATTTTTATTAT
1 ATTTATATATTTTTATTAT
2535667 A-TTATAT
1 ATTTATAT
2535674 TTTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTATATATTTTTATTAT
Found at i:2535681 original size:11 final size:12
Alignment explanation
Indices: 2535633--2535689 Score: 59
Period size: 11 Copynumber: 4.9 Consensus size: 12
2535623 TTGATACATT
2535633 TTATATTTT-TA
1 TTATATTTTATA
2535644 TTATATTTATATA
1 TTATATTT-TATA
2535657 TT-T-TTATTATA
1 TTATATT-TTATA
2535668 TTATATTTTA-A
1 TTATATTTTATA
*
2535679 TTATTTTTTAT
1 TTATATTTTAT
2535690 CATATTCAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
11 26 0.67
12 7 0.18
13 6 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:2535682 original size:19 final size:17
Alignment explanation
Indices: 2535632--2535689 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
2535622 ATTGATACAT
2535632 TTTATATTTTTATTA-TA
1 TTTATA-TTTTATTATTA
2535649 TTTATATATTT-TTATTA
1 TTTATAT-TTTATTATTA
*
2535666 TATTATATTTTAATTATTT
1 T-TTATATTTT-ATTATTA
2535685 TTTAT
1 TTTAT
2535690 CATATTCAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 4 0.11
17 15 0.43
18 10 0.29
19 6 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATATTTTATTATTA
Found at i:2535685 original size:24 final size:23
Alignment explanation
Indices: 2535638--2535695 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
2535628 ACATTTTATA
2535638 TTTT-TATTATATTTATATATTT
1 TTTTATATTATATTTATATATTT
2535660 TTATTATATTATATTT-TA-ATTAT
1 TT-TTATATTATATTTATATATT-T
*
2535683 TTTT-TATCATATT
1 TTTTATATTATATT
2535696 CAACGTAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 8 0.25
22 7 0.22
23 7 0.22
24 10 0.31
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTATATTATATTTATATATTT
Found at i:2535694 original size:26 final size:24
Alignment explanation
Indices: 2535642--2535695 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
2535632 TTTATATTTT
*
2535642 TATTATATTTATATATTTTTATTA
1 TATTATATTTATATATTTTTATCA
2535666 TATTATATTT-TAATTATTTTTTATCA
1 TATTATATTTAT-A-TA-TTTTTATCA
2535692 TATT
1 TATT
2535696 CAACGTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 1 0.04
24 11 0.42
25 2 0.08
26 12 0.46
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTATATTTATATATTTTTATCA
Found at i:2536632 original size:2 final size:2
Alignment explanation
Indices: 2536625--2536656 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2536615 TTGTACGGAC
2536625 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
2536657 CTGCAAGTGC
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:2537371 original size:16 final size:17
Alignment explanation
Indices: 2537350--2537392 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
2537340 GCAGTACATT
2537350 GAGAAA-AATCGAAGAG
1 GAGAAATAATCGAAGAG
2537366 GAGAAATATAATCGAAGAG
1 GAG-AA-ATAATCGAAGAG
2537385 GAGAAATA
1 GAGAAATA
2537393 TCCCCGGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.12
17 5 0.21
18 3 0.12
19 13 0.54
ACGTcount: A:0.56, C:0.05, G:0.28, T:0.12
Consensus pattern (17 bp):
GAGAAATAATCGAAGAG
Found at i:2537380 original size:19 final size:19
Alignment explanation
Indices: 2537356--2537393 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2537346 CATTGAGAAA
2537356 AATCGAAGAGGAGAAATAT
1 AATCGAAGAGGAGAAATAT
2537375 AATCGAAGAGGAGAAATAT
1 AATCGAAGAGGAGAAATAT
2537394 CCCCGGCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.26, T:0.16
Consensus pattern (19 bp):
AATCGAAGAGGAGAAATAT
Found at i:2544688 original size:20 final size:20
Alignment explanation
Indices: 2544660--2544700 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2544650 CAATAAATAA
2544660 AATAATTTTAATTA-ATTTTT
1 AATAATTTT-ATTATATTTTT
*
2544680 AATATTTTTATTATATTTTT
1 AATAATTTTATTATATTTTT
2544700 A
1 A
2544701 TAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
AATAATTTTATTATATTTTT
Found at i:2545384 original size:37 final size:37
Alignment explanation
Indices: 2545334--2545404 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
2545324 GCATTGATTG
2545334 TCCATATATGCTGTTTTTACGTAAAACAGGGGATTTT
1 TCCATATATGCTGTTTTTACGTAAAACAGGGGATTTT
* *
2545371 TCCATGTATGCTGTTTTTACGTAGAACAGGGGAT
1 TCCATATATGCTGTTTTTACGTAAAACAGGGGAT
2545405 GTTTAAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (37 bp):
TCCATATATGCTGTTTTTACGTAAAACAGGGGATTTT
Found at i:2546498 original size:13 final size:14
Alignment explanation
Indices: 2546474--2546509 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2546464 CATGTTCAAA
2546474 TAAATA-AAATA-T
1 TAAATATAAATATT
2546486 TAAATATAAATATT
1 TAAATATAAATATT
2546500 TAAATATAAA
1 TAAATATAAA
2546510 GTCGAGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.27
13 5 0.23
14 11 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATATAAATATT
Found at i:2549303 original size:2 final size:2
Alignment explanation
Indices: 2549296--2549336 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2549286 GAGGAAAAAG
2549296 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2549337 TTTTGTTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2549547 original size:25 final size:23
Alignment explanation
Indices: 2549517--2549583 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 23
2549507 ATTTAATTTG
2549517 ATTTAATATTATTAATAAAAATAAT
1 ATTTAA-A-TATTAATAAAAATAAT
* *
2549542 ATTTAAAT-TTAATTATAA-AAT
1 ATTTAAATATTAATAAAAATAAT
*
2549563 ATATAAATATTAATAAAAATA
1 ATTTAAATATTAATAAAAATA
2549584 TTTAATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 10 0.29
22 16 0.46
23 2 0.06
24 1 0.03
25 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTAAATATTAATAAAAATAAT
Found at i:2549617 original size:35 final size:35
Alignment explanation
Indices: 2549548--2549616 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
2549538 TAATATTTAA
*
2549548 ATTTAATTATAAAATATATAAATATTAATAAAAAT
1 ATTTAATTATAAAATACATAAATATTAATAAAAAT
* *
2549583 ATTTAATTAATATAATCACATAAAT-TTTATAAAA
1 ATTTAATT-ATAAAAT-ACATAAATATTAATAAAA
2549617 TTTGTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 8 0.28
36 14 0.48
37 7 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (35 bp):
ATTTAATTATAAAATACATAAATATTAATAAAAAT
Found at i:2550119 original size:3 final size:3
Alignment explanation
Indices: 2550109--2550138 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2550099 TATTAAATTT
2550109 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2550139 GAGTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2550347 original size:21 final size:19
Alignment explanation
Indices: 2550328--2550365 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2550318 TTATAATTAA
2550328 ATTTAAATAAAAATATATT
1 ATTTAAATAAAAATATATT
* *
2550347 ATTTTAATTAAAATATATT
1 ATTTAAATAAAAATATATT
2550366 GTTTTGAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATAAAAATATATT
Found at i:2550358 original size:20 final size:19
Alignment explanation
Indices: 2550329--2550370 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2550319 TATAATTAAA
2550329 TTTAAATAAAAATATATTAT
1 TTTAAAT-AAAATATATTAT
* *
2550349 TTTAATTAAAATATATTGT
1 TTTAAATAAAATATATTAT
2550368 TTT
1 TTT
2550371 GAGTTAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAAATAAAATATATTAT
Found at i:2553060 original size:29 final size:29
Alignment explanation
Indices: 2552977--2553066 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
2552967 AAGCTTAAGT
*
2552977 TAAAATTTTATTTTTATTT-TTAAATATTA
1 TAAAATTTAATTTTTATTTATTAAAT-TTA
* * * *
2553006 AAAAACTTATTTTTTA-TAATTAAATTTA
1 TAAAATTTAATTTTTATTTATTAAATTTA
*
2553034 GTAAAATTTAATTTTTATTTATT-AATTAA
1 -TAAAATTTAATTTTTATTTATTAAATTTA
2553063 TAAA
1 TAAA
2553067 TTCAATAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
28 8 0.17
29 36 0.75
30 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (29 bp):
TAAAATTTAATTTTTATTTATTAAATTTA
Found at i:2553251 original size:28 final size:27
Alignment explanation
Indices: 2553186--2553254 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
2553176 ATATTTTAAA
2553186 ATATAA-A-ATAATTAAAAAATTATTT
1 ATATAATATATAATTAAAAAATTATTT
* *
2553211 ATATATTTTATAATTAAATTAAATTATTT
1 ATATAATATATAATTAAA--AAATTATTT
2553240 -TATAATATATAATTA
1 ATATAATATATAATTA
2553255 GTAATTTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 5 0.14
27 9 0.25
28 13 0.36
29 9 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATAATATATAATTAAAAAATTATTT
Found at i:2553604 original size:18 final size:18
Alignment explanation
Indices: 2553563--2553610 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
2553553 TAAAAATGTG
2553563 TTTAATAAATATAATAAA
1 TTTAATAAATATAATAAA
* * * *
2553581 TATAATTAATATGATATA
1 TTTAATAAATATAATAAA
*
2553599 TTTAATATATAT
1 TTTAATAAATAT
2553611 TATATTTATA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TTTAATAAATATAATAAA
Found at i:2553676 original size:17 final size:17
Alignment explanation
Indices: 2553633--2553676 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
2553623 TTTTAATTTT
2553633 ATTTAATAATTTATATTA
1 ATTTAAT-ATTTATATTA
*
2553651 ATTTTATATTTATATATA
1 ATTTAATATTTATAT-TA
2553669 A-TTAATAT
1 ATTTAATAT
2553677 AAAAAATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTAATATTTATATTA
Found at i:2554064 original size:21 final size:23
Alignment explanation
Indices: 2554035--2554079 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
2554025 ATACAAAAAT
2554035 AATTACATA-TATTAAA-ATTAA
1 AATTACATATTATTAAATATTAA
*
2554056 AATTTCATATTTATTAAATATTAA
1 AATTACATA-TTATTAAATATTAA
2554080 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTACATATTATTAAATATTAA
Found at i:2554411 original size:30 final size:30
Alignment explanation
Indices: 2554376--2554461 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 30
2554366 TTGTTTAGAT
* * * *
2554376 ATAAATAAAAAATTAAAGACTTATTTCAAC
1 ATAAATTAAAAATTAAAAAATTATTTAAAC
* * *
2554406 ATAAATTAAAGATTAAATAATTATTTAAAT
1 ATAAATTAAAAATTAAAAAATTATTTAAAC
* *
2554436 ATTAATTAAAAATTAAAAATTTATTT
1 ATAAATTAAAAATTAAAAAATTATTT
2554462 TGATATAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.38
Consensus pattern (30 bp):
ATAAATTAAAAATTAAAAAATTATTTAAAC
Found at i:2556128 original size:13 final size:12
Alignment explanation
Indices: 2556112--2556179 Score: 50
Period size: 13 Copynumber: 5.4 Consensus size: 12
2556102 TAAAATTTAT
2556112 AAATAAAATAATA
1 AAATAAAA-AATA
2556125 AAAT-AAAAAT-
1 AAATAAAAAATA
* *
2556135 ATATATTAAAATA
1 AAATA-AAAAATA
*
2556148 ATATTAAAAAATAA
1 A-AATAAAAAAT-A
2556162 AAATAAAAATATA
1 AAATAAAAA-ATA
2556175 AAATA
1 AAATA
2556180 TAAGACCATT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
10 3 0.07
11 3 0.07
12 8 0.19
13 23 0.53
14 6 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:2556632 original size:16 final size:19
Alignment explanation
Indices: 2556592--2556637 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 19
2556582 TTATAATAGA
2556592 AAAAT-TTTAATATTAATT
1 AAAATATTTAATATTAATT
2556610 AAAATATTTAATA-TAA-T
1 AAAATATTTAATATTAATT
2556627 -AAATATTTAAT
1 AAAATATTTAAT
2556638 TAAATAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.41
17 1 0.04
18 8 0.30
19 7 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATATTTAATATTAATT
Found at i:2557185 original size:19 final size:19
Alignment explanation
Indices: 2557161--2557198 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2557151 ATATTTGATG
2557161 TATTAATTA-TATATAAATT
1 TATTAATTATTA-ATAAATT
2557180 TATTAATTATTAATAAATT
1 TATTAATTATTAATAAATT
2557199 AAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTAATTATTAATAAATT
Found at i:2558584 original size:4 final size:4
Alignment explanation
Indices: 2558577--2558605 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2558567 TAATTATATT
2558577 TTAA TTAA TTAA TTAA TTAA -TAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
2558606 TAAAGAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:2558608 original size:12 final size:12
Alignment explanation
Indices: 2558577--2558605 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2558567 TAATTATATT
2558577 TTAATTAATTAA
1 TTAATTAATTAA
2558589 TTAATTAA-TAA
1 TTAATTAATTAA
2558600 TTAATT
1 TTAATT
2558606 TAAAGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTAATTAA
Found at i:2571369 original size:27 final size:28
Alignment explanation
Indices: 2571339--2571398 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
2571329 TGAATACAAT
* * *
2571339 TATATGATTAAAAAAATATTAATGT-AA
1 TATATAATTAAAAAAATATAAATATGAA
*
2571366 TATATAATTAAAATAATATAAATATGAA
1 TATATAATTAAAAAAATATAAATATGAA
2571394 TATAT
1 TATAT
2571399 TAAATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (28 bp):
TATATAATTAAAAAAATATAAATATGAA
Found at i:2575317 original size:33 final size:32
Alignment explanation
Indices: 2575240--2575318 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 32
2575230 ATCTTATTTT
* *
2575240 TTAA-AATATTTAAAATATTTTATATATTAAA
1 TTAAGAATAATTAAAATATTTAATATATTAAA
* *
2575271 AT-AGAAGTAAATTATAATATTTAATAATATTAAA
1 TTAAGAA-T-AATTAAAATATTTAAT-ATATTAAA
2575305 TTAAGAATAATTAA
1 TTAAGAATAATTAA
2575319 TAAAACATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
30 1 0.03
31 3 0.08
32 1 0.03
33 18 0.49
34 10 0.27
35 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (32 bp):
TTAAGAATAATTAAAATATTTAATATATTAAA
Found at i:2576607 original size:25 final size:26
Alignment explanation
Indices: 2576566--2576622 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
2576556 TATGTTATAA
2576566 TTATATAATTATAATATAATAA-A-T
1 TTATATAATTATAATATAATAATACT
* *
2576590 TTATATAAATTTTGATATAATAATACT
1 TTATAT-AATTATAATATAATAATACT
2576617 TTATAT
1 TTATAT
2576623 CATATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 14 0.50
26 1 0.04
27 7 0.25
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TTATATAATTATAATATAATAATACT
Found at i:2579226 original size:2 final size:2
Alignment explanation
Indices: 2579219--2579270 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
2579209 AGATCCTAAT
* * * *
2579219 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TG TA TG CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2579261 TA TA TA TA TA
1 TA TA TA TA TA
2579271 GCGTGTTTGG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2579543 original size:20 final size:20
Alignment explanation
Indices: 2579520--2579558 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2579510 TTATAATTAA
2579520 AATTAAATAAA-AATAATTTT
1 AATT-AATAAATAATAATTTT
*
2579540 AATTATTAAATAATAATTT
1 AATTAATAAATAATAATTT
2579559 AGATTTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTAATAAATAATAATTTT
Found at i:2581071 original size:21 final size:20
Alignment explanation
Indices: 2581039--2581077 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2581029 GTCTAATTGC
* *
2581039 AAAACAATTCTTTGTTCTGT
1 AAAACAAATCTTCGTTCTGT
2581059 AAAAGCAAATCTTCGTTCT
1 AAAA-CAAATCTTCGTTCT
2581078 TTCTTCCCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
AAAACAAATCTTCGTTCTGT
Found at i:2582644 original size:28 final size:26
Alignment explanation
Indices: 2582593--2582656 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 26
2582583 AAATTTTTTT
2582593 TAAACAAATCAAATTGAAAGTCTTCA
1 TAAACAAATCAAATTGAAAGTCTTCA
* *
2582619 TAAACAAAATGCAAATTGGAATTCTTCA
1 TAAAC-AAAT-CAAATTGAAAGTCTTCA
2582647 -AAA-AAATCAA
1 TAAACAAATCAA
2582657 TAAATGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 3 0.09
25 4 0.12
26 5 0.15
27 7 0.21
28 15 0.44
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.25
Consensus pattern (26 bp):
TAAACAAATCAAATTGAAAGTCTTCA
Done.