Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002285.1 Hibiscus syriacus cultivar Beakdansim tig00004649_pilon, whole genome shotgun sequence
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: 52828
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Found at i:10896 original size:13 final size:13
Alignment explanation
Indices: 10878--10903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10868 ACACTAACCT
10878 GGGGCTGCGGCTG
1 GGGGCTGCGGCTG
10891 GGGGCTGCGGCTG
1 GGGGCTGCGGCTG
10904 AACATGGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.62, T:0.15
Consensus pattern (13 bp):
GGGGCTGCGGCTG
Found at i:12027 original size:2 final size:2
Alignment explanation
Indices: 11964--12007 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
11954 AGTGTTACCG
*
11964 TA TA CTA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12006 TA
1 TA
12008 ATTTTTTGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:14664 original size:8 final size:8
Alignment explanation
Indices: 14651--14677 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
14641 TAATTACTTT
14651 AAAAATTA
1 AAAAATTA
14659 AAAAATTA
1 AAAAATTA
14667 AAAAATTA
1 AAAAATTA
14675 AAA
1 AAA
14678 CAGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATTA
Found at i:16957 original size:136 final size:136
Alignment explanation
Indices: 16768--17062 Score: 412
Period size: 136 Copynumber: 2.2 Consensus size: 136
16758 GTGAGGTGTC
* * * * *
16768 GCTGATTCGAAGTGTTGTGAGTCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTATTC
1 GCTGATTCAAAGTGTTGTGAATCGAGCAATAAGTCGAACAAGTTATTCGCATTATGAACTTATTC
* *
16833 CCCCTCTGTCGGATGAGTTCTTCTCTTTATGAACTCTCCATCGGAAATATCAATCCCTCAAACGA
66 CCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATATCAATCCCTCAAACGA
*
16898 GTCATT
131 GGCATT
*
16904 GCTGATTCAAAGTGTTGTGAATCGAGCAATAAGTCGAACAAGTTATTCGCATTATGAACTTCTTC
1 GCTGATTCAAAGTGTTGTGAATCGAGCAATAAGTCGAACAAGTTATTCGCATTATGAACTTATTC
* * * * * * *
16969 TCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCATTGGTAATGTCAATCGCTTAAGCGA
66 CCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATATCAATCCCTCAAACGA
17034 GGCATT
131 GGCATT
* *
17040 G-TCGATTTAAAGTATTGTGAATC
1 GCT-GATTCAAAGTGTTGTGAATC
17063 AAATAATATA
Statistics
Matches: 140, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
135 1 0.01
136 139 0.99
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (136 bp):
GCTGATTCAAAGTGTTGTGAATCGAGCAATAAGTCGAACAAGTTATTCGCATTATGAACTTATTC
CCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCATCGGAAATATCAATCCCTCAAACGA
GGCATT
Found at i:18880 original size:37 final size:37
Alignment explanation
Indices: 18827--18931 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
18817 CCTTTTCGTC
*
18827 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * *
18864 TTGCTAGGATTTAAACTTCTAAAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
18901 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
18932 TCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:19569 original size:24 final size:23
Alignment explanation
Indices: 19535--19584 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
19525 TTTATTCTAC
*
19535 TTATTTATATTATATGTATATTTT
1 TTATTTATATTAT-TATATATTTT
* *
19559 TTATTTTTATTATTATATTTTTT
1 TTATTTATATTATTATATATTTT
19582 TTA
1 TTA
19585 CTTTCTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (23 bp):
TTATTTATATTATTATATATTTT
Found at i:19622 original size:12 final size:11
Alignment explanation
Indices: 19600--19640 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
19590 TCTTTCTTTT
19600 TATTATTCTTG
1 TATTATTCTTG
19611 TATTATTACTTG
1 TATTATT-CTTG
* *
19623 TATTATTTTTA
1 TATTATTCTTG
19634 TATTATT
1 TATTATT
19641 TATTTGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:19655 original size:2 final size:2
Alignment explanation
Indices: 19648--19676 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19638 ATTTATTTGT
19648 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 T
19677 GCGTATGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19878 original size:2 final size:2
Alignment explanation
Indices: 19871--19927 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
19861 TTACTATTAT
19871 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19913 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
19928 TCTACACAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20253 original size:13 final size:13
Alignment explanation
Indices: 20235--20259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20225 GTTATTATTA
20235 TTTTATTTATTTG
1 TTTTATTTATTTG
20248 TTTTATTTATTT
1 TTTTATTTATTT
20260 TCTTTTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTG
Found at i:20257 original size:22 final size:22
Alignment explanation
Indices: 20222--20300 Score: 76
Period size: 22 Copynumber: 3.6 Consensus size: 22
20212 TTATTCGTAC
20222 TTTGTTATTA-TTATTTTATTTA
1 TTTGTT-TTATTTATTTTATTTA
*
20244 TTTGTTTTATTTATTTTCTTT-
1 TTTGTTTTATTTATTTTATTTA
*
20265 TTCTTTTTTATATATATTTTA-TTA
1 TT-TGTTTTAT-T-TATTTTATTTA
20289 TTTGTTTT-TTTA
1 TTTGTTTTATTTA
20301 CTTACTATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 2 0.04
21 6 0.12
22 24 0.50
23 8 0.17
24 8 0.17
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.76
Consensus pattern (22 bp):
TTTGTTTTATTTATTTTATTTA
Found at i:20726 original size:37 final size:37
Alignment explanation
Indices: 20673--20769 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
20663 AATGATCGTC
20673 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
20710 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
20747 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
20770 GATAAGATCA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:21482 original size:12 final size:11
Alignment explanation
Indices: 21460--21500 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
21450 TCTTTCTTTT
21460 TATTATTCTTG
1 TATTATTCTTG
21471 TATTATTACTTG
1 TATTATT-CTTG
* *
21483 TATTATTTTTA
1 TATTATTCTTG
21494 TATTATT
1 TATTATT
21501 TATTTTGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:22020 original size:13 final size:13
Alignment explanation
Indices: 21973--22020 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
21963 TCATTTAATT
*
21973 TATTAATTTATATA
1 TATTTATTT-TATA
* *
21987 TATTTACTTTATT
1 TATTTATTTTATA
22000 TATTTATTTTATA
1 TATTTATTTTATA
*
22013 TATATATT
1 TATTTATT
22021 ATTCGTACTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTTATTTTATA
Found at i:22109 original size:12 final size:11
Alignment explanation
Indices: 22036--22110 Score: 51
Period size: 12 Copynumber: 6.1 Consensus size: 11
22026 TACTTTGTTA
*
22036 TTATTATTTTGT
1 TTATT-TTTTTT
22048 TTATTTGTTTTAT
1 TTATTT-TTTT-T
22061 TTATTTTCTTTT
1 TTATTTT-TTTT
*
22073 TCATTTTCTTTT
1 TTATTTT-TTTT
*
22085 TTATATATATTTTA
1 TTAT-T-T-TTTTT
22099 TTATTTTTTTT
1 TTATTTTTTTT
22110 T
1 T
22111 ACTTACTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
11 6 0.12
12 25 0.48
13 12 0.23
14 8 0.15
15 1 0.02
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.77
Consensus pattern (11 bp):
TTATTTTTTTT
Found at i:22539 original size:37 final size:37
Alignment explanation
Indices: 22482--22586 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
22472 AATGATCGTC
*
22482 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
22519 TTGCTAAGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
22556 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
22587 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:23165 original size:24 final size:23
Alignment explanation
Indices: 23138--23245 Score: 88
Period size: 22 Copynumber: 4.9 Consensus size: 23
23128 CTTTGCATTT
23138 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTA-TA
* *
23162 TTATTTTTACTATTATATTT-TCC
1 TTATTATTACTATTATATTTAT-A
*
23185 TT-TTATT-CTACT-TATTTATA
1 TTATTATTACTATTATATTTATA
23205 TTATATATGTA-TATT-T-TTTATA
1 TTAT-TAT-TACTATTATATTTATA
*
23227 TT-TTATTATTATTATATTT
1 TTATTATTACTATTATATTT
23246 TTTTACTTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
19 2 0.03
20 14 0.20
21 8 0.12
22 19 0.28
23 7 0.10
24 19 0.28
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATTATTACTATTATATTTATA
Found at i:23249 original size:27 final size:28
Alignment explanation
Indices: 23197--23248 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
23187 TTATTCTACT
23197 TATTTATATTATATATGTATATTTTTTA
1 TATTTATATTATATATGTATATTTTTTA
23225 TATTT-TATTAT-TAT-TATATTTTTT
1 TATTTATATTATATATGTATATTTTTT
23249 TACTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TATTTATATTATATATGTATATTTTTTA
Found at i:23288 original size:12 final size:11
Alignment explanation
Indices: 23266--23306 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
23256 TCTTTCTTTT
23266 TATTATTCTTG
1 TATTATTCTTG
23277 TATTATTACTTG
1 TATTATT-CTTG
* *
23289 TATTATTTTTA
1 TATTATTCTTG
23300 TATTATT
1 TATTATT
23307 TATTTTGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:24336 original size:37 final size:37
Alignment explanation
Indices: 24283--24379 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
24273 AATGATCGTC
24283 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
24320 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
24357 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
24380 GATAAGATCC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:24963 original size:24 final size:23
Alignment explanation
Indices: 24936--25043 Score: 88
Period size: 22 Copynumber: 4.9 Consensus size: 23
24926 CTTTGCATTT
24936 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTA-TA
* *
24960 TTATTTTTACTATTATATTT-TCC
1 TTATTATTACTATTATATTTAT-A
*
24983 TT-TTATT-CTACT-TATTTATA
1 TTATTATTACTATTATATTTATA
25003 TTATATATGTA-TATT-T-TTTATA
1 TTAT-TAT-TACTATTATATTTATA
*
25025 TT-TTATTATTATTATATTT
1 TTATTATTACTATTATATTT
25044 TTTTACTTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
19 2 0.03
20 14 0.20
21 8 0.12
22 19 0.28
23 7 0.10
24 19 0.28
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATTATTACTATTATATTTATA
Found at i:25047 original size:27 final size:28
Alignment explanation
Indices: 24995--25046 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
24985 TTATTCTACT
24995 TATTTATATTATATATGTATATTTTTTA
1 TATTTATATTATATATGTATATTTTTTA
25023 TATTT-TATTAT-TAT-TATATTTTTT
1 TATTTATATTATATATGTATATTTTTT
25047 TACTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TATTTATATTATATATGTATATTTTTTA
Found at i:25086 original size:12 final size:11
Alignment explanation
Indices: 25064--25093 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
25054 TCTTTCTTTT
25064 TATTATTCTTG
1 TATTATTCTTG
25075 TATTATTACTTG
1 TATTATT-CTTG
25087 TATTATT
1 TATTATT
25094 TTTATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:25323 original size:2 final size:2
Alignment explanation
Indices: 25318--25352 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25308 ATTTTACTAT
25318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25353 TCTACACAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26146 original size:37 final size:37
Alignment explanation
Indices: 26093--26197 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
26083 AATGATCGTC
26093 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
26130 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
26167 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
26198 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:26902 original size:12 final size:11
Alignment explanation
Indices: 26880--26909 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
26870 TCTTTCTTTT
26880 TATTATTCTTG
1 TATTATTCTTG
26891 TATTATTACTTG
1 TATTATT-CTTG
26903 TATTATT
1 TATTATT
26910 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:26917 original size:2 final size:2
Alignment explanation
Indices: 26910--26994 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
26900 TTGTATTATT
26910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26994 T
1 T
26995 GCGTATGTTC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27310 original size:170 final size:171
Alignment explanation
Indices: 26982--27315 Score: 568
Period size: 171 Copynumber: 2.0 Consensus size: 171
26972 TATATATATA
26982 TATATATATATATGCGTATGTTCTTTTTAAATATTTTAGTTTTTATACCTATTATTAATAAATAT
1 TATATATATATATGCGTATGTTCTTTTTAAATATTTTAGTTTTTATACCTATTATTAATAAATAT
*
27047 TTGATTTTTTTATTTTAAGTGCTATATTTTATAATATTATACATATATTTTTCTATTAATTTTCT
66 TTGATTTTTTTATTTTAAGTGCTATATTTTATAATATTATACATATATTTTTATATTAATTTTCT
* *
27112 AGTATTATTACTTGTATTATTTTTATA-TTATTTATTTTGC
131 AGTATTATTACTTATATTATTATTATATTTATTTATTTTGC
27152 TATATATATATATGCGTATGTTCTTTTTAAATATTTTAGTTTTTATACCTATTATTAATAAATAT
1 TATATATATATATGCGTATGTTCTTTTTAAATATTTTAGTTTTTATACCTATTATTAATAAATAT
*
27217 TTCGTTTTTTTTATTTTAAGTGCTATATTTTATAATATTATACATATATTTTTATATTAATTTTC
66 TT-GATTTTTTTATTTTAAGTGCTATATTTTATAATATTATACATATATTTTTATATTAATTTTC
*
27282 TA-TAATTTTTA-TTATCATTA-TATTATATTTATTT
130 TAGT-ATTATTACTTAT-ATTATTATTATATTTATTT
27316 TCTTTTTTTA
Statistics
Matches: 155, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
170 77 0.50
171 78 0.50
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (171 bp):
TATATATATATATGCGTATGTTCTTTTTAAATATTTTAGTTTTTATACCTATTATTAATAAATAT
TTGATTTTTTTATTTTAAGTGCTATATTTTATAATATTATACATATATTTTTATATTAATTTTCT
AGTATTATTACTTATATTATTATTATATTTATTTATTTTGC
Found at i:27366 original size:2 final size:2
Alignment explanation
Indices: 27361--27395 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27351 ATTTTACTAT
27361 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27396 TCTATACAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28189 original size:37 final size:37
Alignment explanation
Indices: 28136--28232 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
28126 AATGATCGTC
28136 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
28173 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
28210 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
28233 GATAAGATCT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:28907 original size:27 final size:28
Alignment explanation
Indices: 28855--28906 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
28845 TTATTCTACT
28855 TATTTATATTATATATGTATATTTTTTA
1 TATTTATATTATATATGTATATTTTTTA
28883 TATTT-TATTAT-TAT-TATATTTTTT
1 TATTTATATTATATATGTATATTTTTT
28907 TACTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TATTTATATTATATATGTATATTTTTTA
Found at i:28946 original size:12 final size:11
Alignment explanation
Indices: 28924--28964 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
28914 TCTTTCTTTT
28924 TATTATTCTTG
1 TATTATTCTTG
28935 TATTATTACTTG
1 TATTATT-CTTG
* *
28947 TATTATTTTTA
1 TATTATTCTTG
28958 TATTATT
1 TATTATT
28965 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:29631 original size:40 final size:38
Alignment explanation
Indices: 29570--29644 Score: 89
Period size: 40 Copynumber: 1.9 Consensus size: 38
29560 TTATTTGTTT
*
29570 TTTTACTTACTATTTTATCTTTGCTTTCTTCATTTTATCA
1 TTTTACTTAATATTTTATCTTTGC-TT-TTCATTTTATCA
* *
29610 TTTTACTTAAT-TTGTTTTCTTTTCTTTTCATTTTA
1 TTTTACTTAATATT-TTATCTTTGCTTTTCATTTTA
29645 ATTTAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
38 9 0.29
39 4 0.13
40 18 0.58
ACGTcount: A:0.16, C:0.15, G:0.03, T:0.67
Consensus pattern (38 bp):
TTTTACTTAATATTTTATCTTTGCTTTTCATTTTATCA
Found at i:34177 original size:16 final size:15
Alignment explanation
Indices: 34158--34209 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
34148 GAACAAAAAT
34158 AAAAAAGAAAAGAAGC
1 AAAAAAGAAAAGAA-C
34174 AAAAAAGAAGAA-AAC
1 AAAAAAGAA-AAGAAC
*
34189 AAAAAAAAGAAAGAAC
1 AAAAAAGA-AAAGAAC
34205 AAAAA
1 AAAAA
34210 TCAAAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.31
16 20 0.62
17 2 0.06
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAGAAC
Found at i:34903 original size:22 final size:22
Alignment explanation
Indices: 34829--34905 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
34819 GCTACCCCAT
*
34829 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
34851 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
34873 CAAACCTTTAAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
34895 CAAACCTTTGA
1 CAAACCTTTGA
34906 CCAAACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:35814 original size:106 final size:106
Alignment explanation
Indices: 35629--36607 Score: 1384
Period size: 106 Copynumber: 9.3 Consensus size: 106
35619 TCGAGAGTAG
* *
35629 ATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
35694 ACCACTGGTTGTCAATAAATAACTTCCCAATTTCATAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
35735 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
35800 ACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* **
35841 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTGCGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
35906 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTTAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* * *
35947 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACAAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
36012 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTTAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* *
36053 ATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGC-AGTTCAACTTAACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * *
36117 ACTGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGTCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* *
36158 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
36223 ACCGCTGGTTGTCAATAAACAATTTCCCATTTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* * * * *
36264 ATTTCAACTTCACAGCGTAGGATATTGGACTCAAGATAATGCATGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
36329 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* * * *
36370 ATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGG
* * * * * * *
36434 GGCGGTTGATTGTCAA-CAA-AA-TT-TC-A-TTCAGAGTCA
65 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* * *
36470 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
36535 A-CGACTGGTTGTCAACAAATAATTTCCCGGTTCCAGAGCCA
66 ACCG-CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
*
36576 ATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 ATTTCAACTTCACAG-CGAAGGATATTGGACTC
36608 AGAACAATGC
Statistics
Matches: 781, Mismatches: 81, Indels: 22
0.88 0.09 0.02
Matches are distributed among these distances:
99 1 0.00
100 76 0.10
101 4 0.01
102 3 0.00
103 4 0.01
104 3 0.00
105 100 0.13
106 590 0.76
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (106 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
Found at i:37389 original size:37 final size:37
Alignment explanation
Indices: 37338--37434 Score: 158
Period size: 37 Copynumber: 2.6 Consensus size: 37
37328 CCTTTTCGTC
*
37338 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATATGATAGAATT
* *
37375 TTACTATGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATATGATAGAATT
*
37412 CTACTATGATTTAAACTCCTAAA
1 CTACTATGATTCAAACTCCTAAA
37435 GATAGGATCC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.33
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATATGATAGAATT
Found at i:38106 original size:15 final size:15
Alignment explanation
Indices: 38000--38108 Score: 52
Period size: 15 Copynumber: 7.3 Consensus size: 15
37990 TTCTTTGCAT
38000 TTTTATTATTACTATTA
1 TTTTATTATTA-TA-TA
*
38017 TTATTATTATTTTATA
1 TT-TTATTATTATATA
* *
38033 TTATACTATTATAT-
1 TTTTATTATTATATA
*
38047 TTCCTT-TTATTCTACT-
1 TT--TTATTATTATA-TA
38063 TATTTA-TATTA-ATA
1 T-TTTATTATTATATA
* *
38077 -TGTATT-TTTTATA
1 TTTTATTATTATATA
38090 TTTTATTATTATATA
1 TTTTATTATTATATA
38105 TTTT
1 TTTT
38109 TTTTACTTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
12 5 0.07
13 5 0.07
14 8 0.12
15 31 0.45
16 7 0.10
17 5 0.07
18 8 0.12
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (15 bp):
TTTTATTATTATATA
Found at i:38106 original size:24 final size:25
Alignment explanation
Indices: 38063--38110 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
38053 TTATTCTACT
*
38063 TATTTATATTAATATGTATTTTTTA
1 TATTTATATTAATATATATTTTTTA
*
38088 TATTT-TATTATTATATATTTTTT
1 TATTTATATTAATATATATTTTTT
38111 TTACTTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TATTTATATTAATATATATTTTTTA
Found at i:38151 original size:12 final size:11
Alignment explanation
Indices: 38129--38169 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
38119 TCTTTCTTTT
38129 TATTATTCTTG
1 TATTATTCTTG
38140 TATTATTACTTG
1 TATTATT-CTTG
* *
38152 TATTATTTTTA
1 TATTATTCTTG
38163 TATTATT
1 TATTATT
38170 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:38694 original size:29 final size:27
Alignment explanation
Indices: 38619--38768 Score: 73
Period size: 27 Copynumber: 5.5 Consensus size: 27
38609 TCGTCATTTA
* * *
38619 ATTATTAATTTATATATTTACTTTTTT
1 ATTATTATTTTATTTATTTACTTTGTT
38646 ATT-TATATTATATATATTATTCGTACTTTGTT
1 ATTAT-TATT-T-TAT-TTATT--TACTTTGTT
** *
38678 ATTATTATTTTATTTATTTGGTTT-AT
1 ATTATTATTTTATTTATTTACTTTGTT
*
38704 -TTATT-TTTT-TTTCATTTTC-TT-TT
1 ATTATTATTTTATTT-ATTTACTTTGTT
* *
38727 ATATATATATTTTA-TTATTTATTTTTTT
1 AT-TAT-TATTTTATTTATTTACTTTGTT
38755 ACTTATTATTTTAT
1 A-TTATTATTTTAT
38769 CTTTGCTTTC
Statistics
Matches: 95, Mismatches: 11, Indels: 33
0.68 0.08 0.24
Matches are distributed among these distances:
23 6 0.06
24 9 0.09
25 8 0.08
26 7 0.07
27 25 0.26
28 7 0.07
29 9 0.09
30 7 0.07
31 1 0.01
32 15 0.16
33 1 0.01
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.69
Consensus pattern (27 bp):
ATTATTATTTTATTTATTTACTTTGTT
Found at i:38707 original size:25 final size:25
Alignment explanation
Indices: 38679--38746 Score: 61
Period size: 25 Copynumber: 2.7 Consensus size: 25
38669 TACTTTGTTA
*
38679 TTATTATTTTATTTATTTGGTTTAT
1 TTATTATTTTATTTATTTCGTTTAT
*
38704 TTATT-TTTT-TTTCATTTTCTTTTAT
1 TTATTATTTTATTT-A-TTTCGTTTAT
*
38729 ATATATATTTTA-TTATTT
1 TTAT-TATTTTATTTATTT
38747 ATTTTTTTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
23 3 0.09
24 5 0.14
25 19 0.54
26 2 0.06
27 6 0.17
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (25 bp):
TTATTATTTTATTTATTTCGTTTAT
Found at i:38751 original size:12 final size:12
Alignment explanation
Indices: 38676--38761 Score: 52
Period size: 12 Copynumber: 7.0 Consensus size: 12
38666 TCGTACTTTG
38676 TTATTA-TTATT
1 TTATTATTTATT
**
38687 TTATTTATTTGGT
1 TTA-TTATTTATT
38700 TTATTTATTT-TT
1 TTA-TTATTTATT
*
38712 TT-TTCATTTTCTT
1 TTATT-A-TTTATT
*
38725 TTATATATATATT
1 TTAT-TATTTATT
38738 TTATTATTTATT
1 TTATTATTTATT
* *
38750 TTTTTACTTATT
1 TTATTATTTATT
38762 ATTTTATCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
10 2 0.03
11 4 0.07
12 26 0.43
13 25 0.42
14 2 0.03
15 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.73
Consensus pattern (12 bp):
TTATTATTTATT
Found at i:38840 original size:29 final size:30
Alignment explanation
Indices: 38792--38849 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
38782 ATTTTATCAT
* * **
38792 TTTACTTAATTTATTTTCTTTTCATTTTAA
1 TTTAATTAATTTAATTTCTTACCATTTTAA
38822 TTTAATTAA-TTAATTTCTTACCATTTTA
1 TTTAATTAATTTAATTTCTTACCATTTTA
38850 TCTAACATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTAATTAATTTAATTTCTTACCATTTTAA
Found at i:42092 original size:122 final size:122
Alignment explanation
Indices: 41875--42158 Score: 514
Period size: 122 Copynumber: 2.3 Consensus size: 122
41865 AGAGATTTCT
41875 TTGTTGAACTCTGGGATGTGTCGGGACATGAGAGATACAAAGATTGCAGGTCTCTATTTTATTCA
1 TTGTTGAACTCTGGGATGTGTCGGGACATGAGAGATACAAAGATTGCAGGTCTCTATTTTATTCA
*
41940 CAAATTAATGGTGAGTAGTTAATCTCTTTACTTGAGAATATGTTAAGTTCTTGATAA
66 CAAATTAATGGTGAGTAGTTAATCTCTTTACTTGAGAATATGTTAAGGTCTTGATAA
* * *
41997 TTGTTGAACTCTGGAATGTGTCGGGACATGAGAGATACCAAGATTGTAGGTCTCTATTTTATTCA
1 TTGTTGAACTCTGGGATGTGTCGGGACATGAGAGATACAAAGATTGCAGGTCTCTATTTTATTCA
42062 CAAATTAATGGTGAGTAGTTAATCTCTTTACTTGAGAATATGTTAAGGTCTTGATAA
66 CAAATTAATGGTGAGTAGTTAATCTCTTTACTTGAGAATATGTTAAGGTCTTGATAA
* *
42119 TTGTTGAACTCTGGGACGTGTCGGGAGATGAGAGATACAA
1 TTGTTGAACTCTGGGATGTGTCGGGACATGAGAGATACAA
42159 TAATTGTCTA
Statistics
Matches: 154, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
122 154 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (122 bp):
TTGTTGAACTCTGGGATGTGTCGGGACATGAGAGATACAAAGATTGCAGGTCTCTATTTTATTCA
CAAATTAATGGTGAGTAGTTAATCTCTTTACTTGAGAATATGTTAAGGTCTTGATAA
Found at i:43743 original size:19 final size:20
Alignment explanation
Indices: 43713--43756 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
43703 AGCTCGAGCT
43713 CGAGTCGAGTCCATTCGATC
1 CGAGTCGAGTCCATTCGATC
43733 CGAGT-GAGTCCATTCGATC
1 CGAGTCGAGTCCATTCGATC
43752 CGAGT
1 CGAGT
43757 ATTTATCGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (20 bp):
CGAGTCGAGTCCATTCGATC
Found at i:52143 original size:21 final size:20
Alignment explanation
Indices: 52119--52161 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
52109 ATTATTTCTA
52119 TTAAT-TTAGATATTTTATATT
1 TTAATCTTAGA-ATTTTA-ATT
*
52140 TTAATCTTATAATTTTAATT
1 TTAATCTTAGAATTTTAATT
52160 TT
1 TT
52162 CTTTATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTAATCTTAGAATTTTAATT
Found at i:52204 original size:26 final size:27
Alignment explanation
Indices: 52146--52204 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
52136 TATTTTAATC
* * *
52146 TTATAATTTTAATTTTCTTTATTTTGG
1 TTATTATTTTAATTTTATTTATTTTGA
* *
52173 TCATTATTTT-ATTTTATTTATTTTTA
1 TTATTATTTTAATTTTATTTATTTTGA
52199 TTATTA
1 TTATTA
52205 CCCCTTTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (27 bp):
TTATTATTTTAATTTTATTTATTTTGA
Found at i:52710 original size:11 final size:11
Alignment explanation
Indices: 52695--52757 Score: 76
Period size: 11 Copynumber: 5.6 Consensus size: 11
52685 GTCTTTTTAT
*
52695 TTATTATATTT
1 TTATTATATTA
52706 TTATTATATTA
1 TTATTATATTA
52717 TTA-T-TATTA
1 TTATTATATTA
52726 TTATTATATTA
1 TTATTATATTA
52737 TTATTAATAGATTA
1 TTATT-AT--ATTA
52751 TTATTAT
1 TTATTAT
52758 TAATTTTGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
9 8 0.17
10 2 0.04
11 23 0.50
12 2 0.04
13 2 0.04
14 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATTATATTA
Found at i:52712 original size:3 final size:3
Alignment explanation
Indices: 52695--52759 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
52685 GTCTTTTTAT
*
52695 TTA TTA -TA TTT TTA TTA -TA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
52740 TTA ATA -GA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
52760 ATTTTGTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 7 0.13
3 46 0.87
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:52712 original size:14 final size:14
Alignment explanation
Indices: 52695--52759 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
52685 GTCTTTTTAT
*
52695 TTATTATATTTTTA
1 TTATTATATTATTA
52709 TTATATTATTATTATTA
1 -T-TATTA-TATTATTA
52726 TTATTATATTATTA
1 TTATTATATTATTA
* *
52740 TTAATAGATTATTA
1 TTATTATATTATTA
52754 TTATTA
1 TTATTA
52760 ATTTTGTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
14 25 0.57
15 6 0.14
16 6 0.14
17 7 0.16
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TTATTATATTATTA
Found at i:52724 original size:20 final size:20
Alignment explanation
Indices: 52691--52742 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
52681 GTTTGTCTTT
*
52691 TTAT-TTATTA-TATTTTTA
1 TTATATTATTATTATTATTA
52709 TTATATTATTATTATTATTA
1 TTATATTATTATTATTATTA
52729 TTATATTATTATTA
1 TTATATTATTATTA
52743 ATAGATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 4 0.13
19 6 0.19
20 21 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTATTATTATTA
Found at i:52760 original size:17 final size:16
Alignment explanation
Indices: 52701--52761 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
52691 TTATTTATTA
*
52701 TATTTTTATT-AT-AT
1 TATTATTATTAATAAT
* *
52715 TATTATTATTATTATT
1 TATTATTATTAATAAT
52731 ATATTATTATTAATAGAT
1 -TATTATTATTAATA-AT
52749 TATTATTATTAAT
1 TATTATTATTAAT
52762 TTTGTTTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.24
15 1 0.03
16 1 0.03
17 26 0.68
18 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATTATTATTAATAAT
Done.