Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006157.1 Hibiscus syriacus cultivar Beakdansim tig00014628_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: 86000
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2223 original size:23 final size:23
Alignment explanation
Indices: 2197--2256 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2187 GACACAAACG
* * *
2197 AACGAACATAATAAATTAACATA
1 AACGAACACAAAAAACTAACATA
2220 AACGAACACAAAAAACTAACATA
1 AACGAACACAAAAAACTAACATA
2243 AACGAACAACAAAA
1 AACGAAC-ACAAAA
2257 TACAAAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 27 0.82
24 6 0.18
ACGTcount: A:0.65, C:0.18, G:0.05, T:0.12
Consensus pattern (23 bp):
AACGAACACAAAAAACTAACATA
Found at i:2280 original size:31 final size:30
Alignment explanation
Indices: 2227--2287 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
2217 ATAAACGAAC
*
2227 ACAAAAAACTAACATAAACGAACAACAAAAT
1 ACAAAAAACAAACATAAACGAAC-ACAAAAT
* **
2258 ACAAAAAACAAACTTATTCGAACACAAAAT
1 ACAAAAAACAAACATAAACGAACACAAAAT
2288 GAATGTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.64, C:0.20, G:0.03, T:0.13
Consensus pattern (30 bp):
ACAAAAAACAAACATAAACGAACACAAAAT
Found at i:3823 original size:20 final size:20
Alignment explanation
Indices: 3800--3838 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3790 GCAGAGATGA
3800 CCTTAAGTCTGCAGACGTCG
1 CCTTAAGTCTGCAGACGTCG
*
3820 CCTTATGTCTGCAGACGTC
1 CCTTAAGTCTGCAGACGTC
3839 TTCTAACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.31, G:0.23, T:0.28
Consensus pattern (20 bp):
CCTTAAGTCTGCAGACGTCG
Found at i:3876 original size:12 final size:12
Alignment explanation
Indices: 3859--3908 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
3849 TTCAAAGAGG
3859 TTTTATATTTAA
1 TTTTATATTTAA
3871 TTTTATA-TTATA
1 TTTTATATTTA-A
*
3883 TTTGAT-TTTAA
1 TTTTATATTTAA
*
3894 TTTTA-ATATAA
1 TTTTATATTTAA
3905 TTTT
1 TTTT
3909 TTAAATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 16 0.50
12 16 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:3919 original size:24 final size:24
Alignment explanation
Indices: 3898--3981 Score: 102
Period size: 24 Copynumber: 3.5 Consensus size: 24
3888 TTTTAATTTT
3898 AATA-TAATTTTTTAAATAAATTA
1 AATATTAATTTTTTAAATAAATTA
* *
3921 AATATTAA-TTTTT-ATTATATTATA
1 AATATTAATTTTTTAAATA-AAT-TA
*
3945 AATATTATTTTTTTAAATAAATTA
1 AATATTAATTTTTTAAATAAATTA
3969 AATATTAATTTTT
1 AATATTAATTTTT
3982 AATATTATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
22 3 0.06
23 11 0.22
24 26 0.52
25 7 0.14
26 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATATTAATTTTTTAAATAAATTA
Found at i:3970 original size:48 final size:49
Alignment explanation
Indices: 3897--4000 Score: 160
Period size: 48 Copynumber: 2.1 Consensus size: 49
3887 ATTTTAATTT
*
3897 TAATA-TAATTTTTTAAATAAATTAAATATTAA-TTTT-TATTATATTA
1 TAATATTATTTTTTTAAATAAATTAAATATTAATTTTTATATTATATTA
3943 TAAATATTATTTTTTTAAATAAATTAAATATTAATTTTTAATATTATATTA
1 T-AATATTATTTTTTTAAATAAATTAAATATTAATTTTT-ATATTATATTA
3994 TAATATT
1 TAATATT
4001 TAATTTATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
46 1 0.02
47 4 0.08
48 26 0.50
49 4 0.08
50 6 0.12
51 11 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (49 bp):
TAATATTATTTTTTTAAATAAATTAAATATTAATTTTTATATTATATTA
Found at i:4019 original size:48 final size:47
Alignment explanation
Indices: 3904--4051 Score: 141
Period size: 48 Copynumber: 3.2 Consensus size: 47
3894 TTTTAATATA
*
3904 ATTT-TTTAAATAAATTAAATATTAATTTTTATTATATTATAAATATT
1 ATTTATTTAAATAAATTAAATATTAATTTTTA-TATATTATAAATAAT
* *
3951 ATTTTTTTAAATAAATTAAATATTAATTTTTA-ATATTATATTATAAT
1 ATTTATTTAAATAAATTAAATATTAATTTTTATATATTATA-AATAAT
* * *
3998 ATTTAATTTATAT-CA-TATAA-ATT-A-TTTTATATATTA-AAATTTAT
1 ATTT-ATTTAAATAAATTA-AATATTAATTTTTATATATTATAAA-TAAT
4042 ATTTATTTAA
1 ATTTATTTAA
4052 TTATTTTGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 16
0.78 0.07 0.14
Matches are distributed among these distances:
43 6 0.07
44 13 0.15
45 7 0.08
46 13 0.15
47 15 0.17
48 33 0.38
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (47 bp):
ATTTATTTAAATAAATTAAATATTAATTTTTATATATTATAAATAAT
Found at i:4041 original size:19 final size:20
Alignment explanation
Indices: 3987--4047 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 20
3977 TTTTTAATAT
*
3987 TATATTATAATATTTAATTTA
1 TATATTATAA-ATTTATTTTA
4008 TATCA-TATAAA-TTATTTTA
1 TAT-ATTATAAATTTATTTTA
4027 TATATTA-AAATTTATATTTA
1 TATATTATAAATTTAT-TTTA
4047 T
1 T
4048 TTAATTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
18 4 0.11
19 16 0.46
20 6 0.17
21 8 0.23
22 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATTATAAATTTATTTTA
Found at i:4316 original size:23 final size:23
Alignment explanation
Indices: 4289--4351 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
4279 ATATTTTCTA
4289 AAAATATCATATAATTATAAAAAT
1 AAAATATCATATAATT-TAAAAAT
* *
4313 -AAAT-TGATATATATTTAAAATT
1 AAAATATCATATA-ATTTAAAAAT
*
4335 AAAAGTATTATATAATT
1 AAAA-TATCATATAATT
4352 GCATATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 12 0.38
23 10 0.31
24 4 0.12
25 6 0.19
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (23 bp):
AAAATATCATATAATTTAAAAAT
Found at i:4895 original size:14 final size:15
Alignment explanation
Indices: 4858--4898 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
4848 TATAAAATAA
* *
4858 ATTTAAATTTAAATT
1 ATTTTAATTTTAATT
4873 ATTTT-ATTTTAA-T
1 ATTTTAATTTTAATT
4886 ATTTTAATTTTAA
1 ATTTTAATTTTAA
4899 ATTCATTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 6 0.26
14 13 0.57
15 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTAATTTTAATT
Found at i:16227 original size:20 final size:20
Alignment explanation
Indices: 16204--16255 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
16194 AACGCGATCC
16204 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
16224 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
16244 CCAAAATCGCAA
1 CCAGAATCGCAA
16256 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:16372 original size:20 final size:20
Alignment explanation
Indices: 16311--16503 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
16301 GATTTTCCAT
* ** *
16311 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
16331 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
16351 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
16371 AATCGTAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
16391 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
16411 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
16431 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
16451 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
16472 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
16492 AATCGCAACGCG
1 AATCGCAACGCG
16504 ATATTTAAAG
Statistics
Matches: 143, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 123 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:16394 original size:60 final size:60
Alignment explanation
Indices: 16311--16503 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
16301 GATTTTCCAT
* ** * *
16311 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * * *** *
16371 AATCGTAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
16431 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
16492 AATCGCAACGCG
1 AATCGCAACGCG
16504 ATATTTAAAG
Statistics
Matches: 109, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 78 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:16917 original size:33 final size:33
Alignment explanation
Indices: 16878--16948 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
16868 TTCACTTAGA
*
16878 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
16911 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
16944 TTTCA
1 TTTCA
16949 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:17088 original size:14 final size:14
Alignment explanation
Indices: 17069--17123 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
17059 AGAATGACTG
17069 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
17083 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
17102 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
17116 TCGCAACG
1 TCGCAACG
17124 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:17136 original size:33 final size:33
Alignment explanation
Indices: 17069--17139 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
17059 AGAATGACTG
***
17069 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
17102 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
17135 TCGCA
1 TCGCA
17140 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:17157 original size:19 final size:19
Alignment explanation
Indices: 17135--17232 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
17125 GAAACCAAAA
*
17135 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
17154 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
17168 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
17187 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
17201 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
17220 TCGCGTTGCGATT
1 TCGCGTTGCGATT
17233 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:17176 original size:14 final size:14
Alignment explanation
Indices: 17157--17246 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
17147 TTTCATTTCG
17157 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
17171 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
17190 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
17204 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
17221 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
17237 CGTTGCGATT
1 CGTTGCGATT
17247 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:17182 original size:33 final size:33
Alignment explanation
Indices: 17140--17254 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
17130 CAAAATCGCA
17140 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
17173 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
17206 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
17239 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
17255 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:19240 original size:182 final size:186
Alignment explanation
Indices: 18933--19309 Score: 717
Period size: 182 Copynumber: 2.0 Consensus size: 186
18923 TAGATTGCTT
18933 AGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
18998 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
19063 GTGTATTCTTTAACACTGTG-AA-A-TATTTGTCTTT-TTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
19115 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19180 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
19245 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
19301 AGTAAATTT
1 AGTAAATTT
19310 ATCCATTCAA
Statistics
Matches: 190, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
182 149 0.78
183 2 0.01
184 1 0.01
185 11 0.06
186 27 0.14
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:19256 original size:93 final size:93
Alignment explanation
Indices: 18933--19309 Score: 717
Period size: 93 Copynumber: 4.1 Consensus size: 93
18923 TAGATTGCTT
*
18933 AGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
18998 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19026 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19088 TTTGTCTTT-TTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19115 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19180 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19208 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19273 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19301 AGTAAATTT
1 AGTAAATTT
19310 ATCCATTCAA
Statistics
Matches: 279, Mismatches: 1, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
89 75 0.27
90 13 0.05
91 2 0.01
92 13 0.05
93 176 0.63
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:19389 original size:19 final size:19
Alignment explanation
Indices: 19349--19475 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
19339 TAGTTTACTT
* *
19349 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
19369 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
19388 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
19407 TCGCAA--CG-----AGAA
1 TCGCAACGCGAAACCAAAA
19419 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
19438 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
19452 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
19471 TCGCA
1 TCGCA
19476 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 25
0.73 0.07 0.21
Matches are distributed among these distances:
12 9 0.10
14 12 0.14
15 1 0.01
16 2 0.02
17 4 0.05
18 1 0.01
19 45 0.52
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:19424 original size:31 final size:32
Alignment explanation
Indices: 19385--19475 Score: 139
Period size: 31 Copynumber: 2.8 Consensus size: 32
19375 CGCGAAACCA
**
19385 AAATCGCAACGCGAAATGAAAATCGCAACGA-
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
19416 GAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
19448 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
19476 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 28 0.52
32 1 0.02
33 25 0.46
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:19493 original size:19 final size:19
Alignment explanation
Indices: 19471--19605 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
19461 GAAACCAAAA
*
19471 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19490 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
19506 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
19523 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
19539 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
19556 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
19575 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
19595 TCGTGTTGCGA
1 TCGCGTTGCGA
19606 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:19512 original size:14 final size:14
Alignment explanation
Indices: 19493--19549 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
19483 TTTCATTTCG
19493 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
19507 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
19524 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
19540 CGTTGCGATT
1 CGTTGCGATT
19550 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:19518 original size:33 final size:33
Alignment explanation
Indices: 19476--19568 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
19466 CAAAATCGCA
*
19476 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
19509 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
19542 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
19569 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:21460 original size:38 final size:38
Alignment explanation
Indices: 21417--21489 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
21407 AATTGATTGT
*
21417 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
21455 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
21490 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:21476 original size:19 final size:19
Alignment explanation
Indices: 21412--21476 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
21402 AGTTTAATTG
*
21412 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
21431 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
21449 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
21469 ATTGATTT
1 ATTGATTT
21477 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:21490 original size:14 final size:14
Alignment explanation
Indices: 21471--21506 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
21461 ATTGTTTAAT
21471 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
21485 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
21499 TGATTTGT
1 TGATTTGT
21507 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:21629 original size:19 final size:19
Alignment explanation
Indices: 21613--21714 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
21603 AAAAATGACT
21613 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
21632 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
21651 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
21665 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
21684 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
21704 ATCGCAATGCG
1 ATCGCAATGCG
21715 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:21763 original size:33 final size:33
Alignment explanation
Indices: 21721--22050 Score: 212
Period size: 33 Copynumber: 9.5 Consensus size: 33
21711 TGCGTTTATA
21721 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
21754 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCT-CG--TTGCGATTTTC
*
21791 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
21826 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
21864 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
21897 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
21937 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
21968 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
22001 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
22035 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
22051 GTATTTTCCG
Statistics
Matches: 251, Mismatches: 20, Indels: 52
0.78 0.06 0.16
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 82 0.33
34 46 0.18
35 15 0.06
36 20 0.08
37 9 0.04
38 47 0.19
39 9 0.04
40 9 0.04
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:21767 original size:19 final size:19
Alignment explanation
Indices: 21743--22050 Score: 351
Period size: 19 Copynumber: 17.4 Consensus size: 19
21733 GATTATCTCG
21743 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
21762 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
21782 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
21796 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
21815 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
21834 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
21853 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
21872 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
21887 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
21905 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
21924 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
21938 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
21957 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
21976 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
21990 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
22010 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
22024 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
22043 TTGCGATT
1 TTGCGATT
22051 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 13, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 28 0.11
17 28 0.11
18 8 0.03
19 129 0.52
20 22 0.09
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:21920 original size:52 final size:52
Alignment explanation
Indices: 21743--22022 Score: 338
Period size: 52 Copynumber: 5.2 Consensus size: 52
21733 GATTATCTCG
*
21743 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TT-ATCT-CG--TTGCGATTTTCATTTCGCA
* *
21796 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCA
* *
21853 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTC-GTTGCGATTTTCATTTCGCA
*
21905 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCA
*
21957 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCA
22010 TTGCGATTTTCAT
1 TTGCGATTTTCAT
22023 GTTGGGATTT
Statistics
Matches: 213, Mismatches: 6, Indels: 16
0.91 0.03 0.07
Matches are distributed among these distances:
51 3 0.01
52 118 0.55
53 53 0.25
54 7 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCA
Found at i:24553 original size:23 final size:23
Alignment explanation
Indices: 24521--24565 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
24511 CTGAAACATC
24521 ATCAAATCCGTG-TATTGACCAAT
1 ATCAAATCCG-GATATTGACCAAT
*
24544 ATCAAGTCCGGATATTGACCAA
1 ATCAAATCCGGATATTGACCAA
24566 GACCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (23 bp):
ATCAAATCCGGATATTGACCAAT
Found at i:25265 original size:20 final size:20
Alignment explanation
Indices: 25237--25605 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
25227 AAATTTCAGT
* * * *
25237 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
25257 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
25277 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
25297 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
25317 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
25337 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
25357 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
25377 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
25397 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
25417 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
25437 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
25457 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
25477 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
25497 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
25517 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
25537 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
25557 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
25577 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
25597 GTTGCGATT
1 GTTGCGATT
25606 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:29034 original size:6 final size:6
Alignment explanation
Indices: 29013--29074 Score: 78
Period size: 6 Copynumber: 11.0 Consensus size: 6
29003 ATCGAATAGA
* *
29013 CTCGA- CTCGAG ATCGAG CTCGAG CTCGA- CTCGA- CTCGAG ATCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG
29058 CTCGAG CTCGA- CTCGAG
1 CTCGAG CTCGAG CTCGAG
29075 TTCTTAAGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
5 20 0.40
6 30 0.60
ACGTcount: A:0.21, C:0.32, G:0.29, T:0.18
Consensus pattern (6 bp):
CTCGAG
Found at i:29045 original size:28 final size:28
Alignment explanation
Indices: 29011--29073 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
29001 AGATCGAATA
29011 GACTCGACTCGAGATCGAGCTCGAGCTC
1 GACTCGACTCGAGATCGAGCTCGAGCTC
29039 GACTCGACTCGAGATCGAGCTCGAGCTC
1 GACTCGACTCGAGATCGAGCTCGAGCTC
29067 GACTCGA
1 GACTCGA
29074 GTTCTTAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.22, C:0.32, G:0.29, T:0.17
Consensus pattern (28 bp):
GACTCGACTCGAGATCGAGCTCGAGCTC
Found at i:32598 original size:21 final size:21
Alignment explanation
Indices: 32574--32661 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 21
32564 TCAAAATGAT
* *
32574 ACATAATTATCCCAAATGACC
1 ACATATTTGTCCCAAATGACC
*
32595 ACATAGGTTTG-CACCGAA-GTACC
1 ACATA--TTTGTC-CCAAATG-ACC
**
32618 ACATATTTGTCCCAAAAAACC
1 ACATATTTGTCCCAAATGACC
32639 ACATATTTGTCCCAAATGACC
1 ACATATTTGTCCCAAATGACC
32660 AC
1 AC
32662 GTAAGACCCT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
21 37 0.69
22 3 0.06
23 14 0.26
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (21 bp):
ACATATTTGTCCCAAATGACC
Found at i:34481 original size:25 final size:25
Alignment explanation
Indices: 34447--34529 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 25
34437 TCAATGGACT
34447 TGTTTTTATTTATTTTGTTTCTTAA
1 TGTTTTTATTTATTTTGTTTCTTAA
* *
34472 TGTTTTTATTTAATTATG------GA
1 TGTTTTTATTT-ATTTTGTTTCTTAA
*
34492 -CTTTTTATTTATTTTGTTTCTTAA
1 TGTTTTTATTTATTTTGTTTCTTAA
34516 TGTTTTTA-TTATTT
1 TGTTTTTATTTATTT
34530 AATTGTTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 17
0.66 0.09 0.25
Matches are distributed among these distances:
18 5 0.11
19 9 0.20
20 1 0.02
24 7 0.16
25 17 0.39
26 5 0.11
ACGTcount: A:0.18, C:0.04, G:0.08, T:0.70
Consensus pattern (25 bp):
TGTTTTTATTTATTTTGTTTCTTAA
Found at i:53570 original size:323 final size:323
Alignment explanation
Indices: 52980--53621 Score: 1088
Period size: 323 Copynumber: 2.0 Consensus size: 323
52970 GTTGAGTGAT
* *
52980 TTGATTGATAAAATTTAAAAAATGATGGTCAAAATGAAAAGAGACAATAGTTAGGTGGTCATTGG
1 TTGATTGATAAAATTTAAAAAATGATGGTCAAAATGAAAAGAGACAATAGTTAGGTAGTCACTGG
53045 TATAATTTACCCTTTATTTTAAATAATTTACTTTTAAATATTTTTAACTAATTTATAATTTTATA
66 TATAATTTACCCTTTATTTTAAATAATTTACTTTTAAATATTTTTAACTAATTTATAATTTTATA
* *
53110 TGTTGGGCTCTTTAAAATTTAAATTTTTATAAATTGGTGTTCATCGTTAATAGTATTGGTCGAGT
131 TGTTGGGCTCTTTAAAATTTAAATTTTTATAAATTGGTATTCATCGTTAATAGTATTCGTCGAGT
*
53175 ACCATAGAATTTTCCTAAAGAAAATCATAATAAGATCTAAATATTACTAAAATTCCATATTAGCC
196 ACCATAGAATTTTCCTAAAGAAAATCACAATAAGATCTAAATATTACTAAAATTCCATATTAGCC
*
53240 GACCAACTATAGTAAAAAAAGTATTCGTTATCCAAATGTAAAAGAAATCATTACAGAATTGAC
261 AACCAACTATAGTAAAAAAAGTATTCGTTATCCAAATGTAAAAGAAATCATTACAGAATTGAC
* * * * *
53303 TTGATTGATAAAATTTCAAAATTTATTGTCAAAATGAAAAGAGATAATAGTTAGGTAGTCACTGG
1 TTGATTGATAAAATTTAAAAAATGATGGTCAAAATGAAAAGAGACAATAGTTAGGTAGTCACTGG
*
53368 TATAGTTTACCCTTTATTTTAAATAATTTACTTTTTAAAT-TTTTTAACTAATTTATAATTTTAT
66 TATAATTTACCCTTTATTTTAAATAATTTAC-TTTTAAATATTTTTAACTAATTTATAATTTTAT
* *
53432 ATGTTGGGCTCTTTAAAATTTAAATTTTTATAAATTGGTATTCATCGTTAATGGTGTTCGTCGAG
130 ATGTTGGGCTCTTTAAAATTTAAATTTTTATAAATTGGTATTCATCGTTAATAGTATTCGTCGAG
* * * *
53497 TATCGTAGAATTTTCCTAAAGAAAATCACAGTAAGATCTTAATATTACTAAAATTCCATATTAGC
195 TACCATAGAATTTTCCTAAAGAAAATCACAATAAGATCTAAATATTACTAAAATTCCATATTAGC
* *
53562 CAACCAACTGTAGTAAAAAAAGTATTCGTTATCCAAATGTAAAAGAAATCATTATAGAAT
260 CAACCAACTATAGTAAAAAAAGTATTCGTTATCCAAATGTAAAAGAAATCATTACAGAAT
53622 AAAAGATATC
Statistics
Matches: 298, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
323 290 0.97
324 8 0.03
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (323 bp):
TTGATTGATAAAATTTAAAAAATGATGGTCAAAATGAAAAGAGACAATAGTTAGGTAGTCACTGG
TATAATTTACCCTTTATTTTAAATAATTTACTTTTAAATATTTTTAACTAATTTATAATTTTATA
TGTTGGGCTCTTTAAAATTTAAATTTTTATAAATTGGTATTCATCGTTAATAGTATTCGTCGAGT
ACCATAGAATTTTCCTAAAGAAAATCACAATAAGATCTAAATATTACTAAAATTCCATATTAGCC
AACCAACTATAGTAAAAAAAGTATTCGTTATCCAAATGTAAAAGAAATCATTACAGAATTGAC
Found at i:59507 original size:198 final size:200
Alignment explanation
Indices: 59111--59616 Score: 669
Period size: 198 Copynumber: 2.5 Consensus size: 200
59101 TGGAGATAAT
* *
59111 TTGATGTTAAAGACGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTT-AGGTGAATTGTT
1 TTGATGTTGAAGATGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTTCAGGTGAATTGTT
* * * *
59175 TGTTGAAGATGGCGATGTTCCTTCGCGTTGAGGAAAGCGGGTCTATCTGGAGATAATTTGGAGGC
66 TGTTGAAGATGACGTTGTTCCTTCGCGTTGAGGAAAGCAGGTCAATCTGGAG--AA-TT----G-
* *
59240 AATACAGTTCATTCGTGTTGAGAAAGTCTGATTGTCTTAGGATGACGCTGCACCTTCGTGTTGAG
123 AATACAGTTCATTCGTGTTGAGAAAGTCTGATTGTCTTAGGATGACGATGCACCTTCGTGTTAAG
* *
59305 GAGATCGGGTCAA
188 GAGATCAGGTAAA
*
59318 TTGATGTTGAAGATGACGCTGCTCATCCGTGTTGAAGAGATCTTGTCATTTTCAGGTGAATTGTT
1 TTGATGTTGAAGATGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTTCAGGTGAATTGTT
* * * *
59383 TGTTGAAGATGACGTTGTTCCTTTGCGTTTGGGGAAATCAGGTCAATCTGGAG-A-T-AATACGG
66 TGTTGAAGATGACGTTGTTCCTTCGCG-TTGAGGAAAGCAGGTCAATCTGGAGAATTGAATACAG
* * * *
59445 TTCCTTCGTGTTGAGGAAGTCTGGTTGTCTTAGGATGACGATGCTCCTTCGTGTTAAGGAGATCA
130 TTCATTCGTGTTGAGAAAGTCTGATTGTCTTAGGATGACGATGCACCTTCGTGTTAAGGAGATCA
59510 GGTAAA
195 GGTAAA
* * * *
59516 TTGATTTTGAAGATGACGATGCTCATTCGTGTTGAAGAGATCTGGTCATTTTCAGGTAAATTGTT
1 TTGATGTTGAAGATGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTTCAGGTGAATTGTT
* * *
59581 TGTTGAAGATGACATTATTCCTCCGCGTTGAGGAAA
66 TGTTGAAGATGACGTTGTTCCTTCGCGTTGAGGAAA
59617 TCGAGTCCAT
Statistics
Matches: 268, Mismatches: 29, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
197 8 0.03
198 152 0.57
204 1 0.00
206 1 0.00
207 49 0.18
208 36 0.13
209 21 0.08
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.34
Consensus pattern (200 bp):
TTGATGTTGAAGATGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTTCAGGTGAATTGTT
TGTTGAAGATGACGTTGTTCCTTCGCGTTGAGGAAAGCAGGTCAATCTGGAGAATTGAATACAGT
TCATTCGTGTTGAGAAAGTCTGATTGTCTTAGGATGACGATGCACCTTCGTGTTAAGGAGATCAG
GTAAA
Found at i:59903 original size:406 final size:398
Alignment explanation
Indices: 59111--59979 Score: 943
Period size: 406 Copynumber: 2.1 Consensus size: 398
59101 TGGAGATAAT
* * *
59111 TTGATGTTAAAGACGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTTAGGTGAATTGTTT
1 TTGATGTTGAAGACGACGATGCTCATCCGTGTTGAAGAGATCTGGTCATTTTAGGTAAATTGTTT
* * * * * * *
59176 GTTGAAGATGGCGATGTTCCTTCGCGTTGAGGAAAGCGGGTCTATCTGGAGATAATTTGGAGGCA
66 GTTGAAGATGACGATATTCCTCCGCGTTGAGGAAAGCGAGTCCATCAGAAGATAATTTGGAGGCA
* * *
59241 ATACAGTTCATTCGTGTTGAGAAAGTCTGATTGTCTTAGGATGACGCTGCACCTTCGTGTTGAGG
131 ATACAGTTCATTCGTATTGAGAAAGTCTGATTGTCTTAGGATGACACTGCACCTTCGCGTTGAGG
*** * * * * *
59306 AGATCGGGTCAATTGATGTTGAAGATGACGCTGCTCATCCGTGTTGAAGAGATCTTGTCATTTTC
196 AGATCCAATCAATTGATGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATATAGTCATTTT-
*** * * * *
59371 AGGTGAATTGTTTGTTGAAGATGACGTTGTTCCTTTGCGTTTGGGGAAATCAGGTCAATCTGGAG
260 --GTGAA-T-TAAATT--A-ATGACGTTGCTCCTTCGCGTTTGAGGAAATCAGGTCAATCAGGAG
* * * * *
59436 ATAATACGGTTCCTTCGTGTTGAGGAAGTCTGGTTGTCTTAGGATGACGATGCTCCTTCGTGTTA
318 ATAATACGGTTCCTTCGTGATGAGGAAATCTGATTGTCTGAAGATGACGATGCTCCTTCGTGTTA
59501 AGGAGATCAGGT-AAA
383 AGGAGATCAGGTCAAA
* * *
59516 TTGATTTTGAAGATGACGATGCTCATTCGTGTTGAAGAGATCTGGTCATTTTCAGGTAAATTGTT
1 TTGATGTTGAAGACGACGATGCTCATCCGTGTTGAAGAGATCTGGTCATTTT-AGGTAAATTGTT
*
59581 TGTTGAAGATGAC-ATTATTCCTCCGCGTTGAGGAAATCGAGTCCATCAGAAGATAATTTGGAGG
65 TGTTGAAGATGACGA-TATTCCTCCGCGTTGAGGAAAGCGAGTCCATCAGAAGATAATTTGGAGG
* * *
59645 CAATAC-GATTCTTTCGTATTGA-AGAAGTCTGATTGT-TTGAGGTTGACAACTGCTCCTTCGCG
129 CAATACAG-TTCATTCGTATTGAGA-AAGTCTGATTGTCTT-AGGATGAC-ACTGCACCTTCGCG
59707 TTGAGGAGATCCAATCAATTTGATGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATATAGT
190 TTGAGGAGATCCAATCAA-TTGATGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATATAGT
* *
59772 CGTTTT-T-AA-TAAATT-ATGACGTTGCTCCTTCGCG-TTGAGGAAATCGGGTCAATCAGGAGA
254 CATTTTGTGAATTAAATTAATGACGTTGCTCCTTCGCGTTTGAGGAAATCAGGTCAATCAGGAG-
*
59832 TATTTTAGGGACAATACGGTTCCTTCGTGATGAGGAAATTTGATTGTCTGAAGATGAC-ACTGCT
318 -A---T------AATACGGTTCCTTCGTGATGAGGAAATCTGATTGTCTGAAGATGACGA-TGCT
* * * *
59896 TCTTCGTGTTGAGGAGATCGGGTCAAT
372 CCTTCGTGTTAAGGAGATCAGGTCAAA
* *
59923 TTGATGTTGAAGACGA-TACTGCTCATCCGTGTTGAAGAGATCTTGGACATCTTTAGG
1 TTGATGTTGAAGACGACGA-TGCTCATCCGTGTTGAAGAGATC-TGGTCAT-TTTAGG
59980 AAGGGTGATA
Statistics
Matches: 389, Mismatches: 52, Indels: 43
0.80 0.11 0.09
Matches are distributed among these distances:
395 22 0.06
396 17 0.04
397 1 0.00
400 4 0.01
403 2 0.01
404 1 0.00
405 53 0.14
406 167 0.43
407 64 0.16
408 55 0.14
409 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (398 bp):
TTGATGTTGAAGACGACGATGCTCATCCGTGTTGAAGAGATCTGGTCATTTTAGGTAAATTGTTT
GTTGAAGATGACGATATTCCTCCGCGTTGAGGAAAGCGAGTCCATCAGAAGATAATTTGGAGGCA
ATACAGTTCATTCGTATTGAGAAAGTCTGATTGTCTTAGGATGACACTGCACCTTCGCGTTGAGG
AGATCCAATCAATTGATGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATATAGTCATTTTG
TGAATTAAATTAATGACGTTGCTCCTTCGCGTTTGAGGAAATCAGGTCAATCAGGAGATAATACG
GTTCCTTCGTGATGAGGAAATCTGATTGTCTGAAGATGACGATGCTCCTTCGTGTTAAGGAGATC
AGGTCAAA
Found at i:59945 original size:50 final size:52
Alignment explanation
Indices: 59868--59964 Score: 128
Period size: 50 Copynumber: 1.9 Consensus size: 52
59858 GTGATGAGGA
* * *
59868 AATTTGATTGTCTGAAGATGACACTGCTTC-TTCGTGTTGAGGAGATCGGGTC
1 AATTTGATTGTCTGAAGACGACACTGC-TCATCCGTGTTGAAGAGATCGGGTC
*
59920 AATTTGA-TGT-TGAAGACGATACTGCTCATCCGTGTTGAAGAGATC
1 AATTTGATTGTCTGAAGACGACACTGCTCATCCGTGTTGAAGAGATC
59965 TTGGACATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 2 0.05
50 28 0.70
51 3 0.08
52 7 0.17
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (52 bp):
AATTTGATTGTCTGAAGACGACACTGCTCATCCGTGTTGAAGAGATCGGGTC
Found at i:59946 original size:197 final size:198
Alignment explanation
Indices: 59599--59963 Score: 502
Period size: 198 Copynumber: 1.8 Consensus size: 198
59589 ATGACATTAT
* * *
59599 TCCTCCGCGTTGAGGAAATCGAGTCCATCAGAAGATAATTTGGAGGCAATACGATTCTTTCGTAT
1 TCCTCCGCGTTGAGGAAATCGAGTCAATCAGAAGATAATTTGGAGACAATACGATTCCTTCGTAT
* * * *
59664 TGAAGAAGTCTGATTGTTTGAGGTTGACAACTGCTCCTTCGCGTTGAGGAGATCCAATCAATTTG
66 TGAAGAAATCTGATTGTCTGAAGATGACAACTGCTCCTTCGCGTTGAGGAGATCCAATCAATTTG
59729 ATGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATATAGTCGTTTTTAATAAATTATGACGT
131 ATGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATATAGTCGTTTTTAATAAATTATGACGT
59794 TGC
196 TGC
* * * * *
59797 TCCTTCGCGTTGAGGAAATCGGGTCAATCAGGAGATATTTTAGG-GACAATACGGTTCCTTCGTG
1 TCCTCCGCGTTGAGGAAATCGAGTCAATCAGAAGATAATTT-GGAGACAATACGATTCCTTCGT-
* * * * ***
59861 A-TGAGGAAATTTGATTGTCTGAAGATGAC-ACTGCTTCTTCGTGTTGAGGAGATCGGGTCAATT
64 ATTGAAGAAATCTGATTGTCTGAAGATGACAACTGCTCCTTCGCGTTGAGGAGATCCAATCAATT
* *
59924 TGATGTTGAAGACGATACTGCTCATCCGTGTTGAAGAGAT
129 TGATGTTGAAGACGACACTGCTCATCCATGTTGAAGAGAT
59964 CTTGGACATC
Statistics
Matches: 144, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
197 67 0.47
198 74 0.51
199 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (198 bp):
TCCTCCGCGTTGAGGAAATCGAGTCAATCAGAAGATAATTTGGAGACAATACGATTCCTTCGTAT
TGAAGAAATCTGATTGTCTGAAGATGACAACTGCTCCTTCGCGTTGAGGAGATCCAATCAATTTG
ATGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATATAGTCGTTTTTAATAAATTATGACGT
TGC
Found at i:60870 original size:82 final size:83
Alignment explanation
Indices: 60769--60960 Score: 228
Period size: 82 Copynumber: 2.3 Consensus size: 83
60759 TTGTTAACAG
* * *
60769 ATAACCCTTATCGCATTGAGTTATGATGTAAATTTGACATGTCC-TTGAGTTGAATGTA-TCAAA
1 ATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGACATG-CCTTTGAGCTGAATGTAGTCAAA
60832 CTCGAAGGA-TGGTTGACAA
65 CTCGAA-GATTGGTTGACAA
* * * * *
60851 ATAACCCTTCTCACCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAGTGTAGTCGAAC
1 ATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGACATGCCTTTGAGCTGAATGTAGTCAAAC
*
60916 TCGAAGATCTTGGTTGACAG
66 TCGAAGA--TTGGTTGACAA
* *
60936 ATAGCCCTTCTCGCCTTGAGCTATG
1 ATAACCCTTCTCGCCTTGAGTTATG
60961 CTGTGAATAG
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
81 2 0.02
82 50 0.54
83 10 0.11
85 31 0.33
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (83 bp):
ATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGACATGCCTTTGAGCTGAATGTAGTCAAAC
TCGAAGATTGGTTGACAA
Found at i:61545 original size:32 final size:32
Alignment explanation
Indices: 61480--61550 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
61470 ATCAGGATGG
* * *
61480 TGAATCCCCAAAGATGCCCCAATATTCATTGT
1 TGAATCTCCAAAGATGCCCCAACATTCACTGT
* **
61512 TGAATCTCCAAATATGCCCCAACATTTGCTGT
1 TGAATCTCCAAAGATGCCCCAACATTCACTGT
61544 TGAATCT
1 TGAATCT
61551 TTAAAGATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.31
Consensus pattern (32 bp):
TGAATCTCCAAAGATGCCCCAACATTCACTGT
Found at i:62668 original size:19 final size:18
Alignment explanation
Indices: 62640--62681 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
62630 TTGATTTTTC
62640 TTTTTTTTTTCTAATATT
1 TTTTTTTTTTCTAATATT
*
62658 TTTTCTTTTTTCTGATATT
1 TTTT-TTTTTTCTAATATT
62677 TTTTT
1 TTTTT
62682 GTTATTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTTCTAATATT
Found at i:64917 original size:63 final size:63
Alignment explanation
Indices: 64814--64937 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
64804 TATGATGATC
* *
64814 ATGCAGAATGCGAATATGCAAATGCAGATGCAAAAGTGATGATCCTCTGACATGCAATGCATT
1 ATGCAGAATGCGAAGATGCAAATGCAGATGCAAAAGTGATGATCCTCTGAAATGCAATGCATT
* * *
64877 ATGCATAATGCGAAGATGCAAATGCAGATGCAAAATTGATGATCCTCTTAAATGCAATGCA
1 ATGCAGAATGCGAAGATGCAAATGCAGATGCAAAAGTGATGATCCTCTGAAATGCAATGCA
64938 ACAAGGGACG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (63 bp):
ATGCAGAATGCGAAGATGCAAATGCAGATGCAAAAGTGATGATCCTCTGAAATGCAATGCATT
Found at i:66974 original size:33 final size:32
Alignment explanation
Indices: 66937--67023 Score: 84
Period size: 36 Copynumber: 2.6 Consensus size: 32
66927 TTAATTTGTG
*
66937 CAATAAAATAAAATGTTAGTAAATTAGTAAGAA
1 CAATAAAATAAAA-GTTAGGAAATTAGTAAGAA
* ** *
66970 CAATAAAAATAAAAAAAGTCAGGATGTTAGTATGAA
1 CAAT-AAAAT---AAAAGTTAGGAAATTAGTAAGAA
67006 CAATAAAATAAAAGTTAG
1 CAATAAAATAAAAGTTAG
67024 AATGTTAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
32 8 0.18
33 4 0.09
34 5 0.11
35 5 0.11
36 18 0.41
37 4 0.09
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGGAAATTAGTAAGAA
Found at i:67029 original size:32 final size:32
Alignment explanation
Indices: 66937--67035 Score: 101
Period size: 32 Copynumber: 2.9 Consensus size: 32
66927 TTAATTTGTG
*
66937 CAATAAAATAAAATGTTAGTAA-ATTAGTAAGAA
1 CAATAAAATAAAA-GTTAG-AATGTTAGTAAGAA
* * *
66970 CAATAAAAATAAAAAAAGTCAGGATGTTAGTATGAA
1 CAAT-AAAAT---AAAAGTTAGAATGTTAGTAAGAA
67006 CAATAAAATAAAAGTTAGAATGTTAGTAAG
1 CAATAAAATAAAAGTTAGAATGTTAGTAAG
67036 TTAGAAAAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
32 18 0.33
33 4 0.07
34 5 0.09
35 6 0.11
36 17 0.31
37 4 0.07
ACGTcount: A:0.56, C:0.04, G:0.15, T:0.25
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGAATGTTAGTAAGAA
Found at i:68880 original size:19 final size:19
Alignment explanation
Indices: 68856--68898 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
68846 ATTTTTTGAA
68856 TTTTATAAATTTAATAAT-T
1 TTTTATAAATTT-ATAATAT
**
68875 TTTTATTTATTTATAATAT
1 TTTTATAAATTTATAATAT
68894 TTTTA
1 TTTTA
68899 AATAATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATAAATTTATAATAT
Found at i:70195 original size:24 final size:22
Alignment explanation
Indices: 70155--70202 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
70145 ACCTCGATTT
70155 AATTTTTTTTTAAATTTATAAA
1 AATTTTTTTTTAAATTTATAAA
*
70177 AATTTTATTTATTAAATTTTTAAA
1 AATTTT-TTT-TTAAATTTATAAA
70201 AA
1 AA
70203 ATAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.26
23 3 0.13
24 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTTTTTTTAAATTTATAAA
Found at i:76053 original size:9 final size:9
Alignment explanation
Indices: 76041--76077 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
76031 CTCTTCTTCT
76041 TTCTCTTTC
1 TTCTCTTTC
*
76050 TTCTTTTTC
1 TTCTCTTTC
*
76059 TTCTCCTTC
1 TTCTCTTTC
76068 TTCTCTTTC
1 TTCTCTTTC
76077 T
1 T
76078 CCTTTGCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (9 bp):
TTCTCTTTC
Found at i:81930 original size:22 final size:21
Alignment explanation
Indices: 81898--81939 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
81888 GTACAATAAC
*
81898 ATATTAAGTAGCTCTTATATA
1 ATATTAAGTAGCGCTTATATA
81919 ATATATAAGTAGCGCTTATAT
1 ATAT-TAAGTAGCGCTTATAT
81940 TGACCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
ATATTAAGTAGCGCTTATATA
Found at i:83952 original size:20 final size:20
Alignment explanation
Indices: 83914--83955 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
83904 TTTACGGTTT
**
83914 TCATTTTGATACCGGTTTTA
1 TCATTTTGATACCAATTTTA
83934 TCATTTTGATACCAATTTTA
1 TCATTTTGATACCAATTTTA
83954 TC
1 TC
83956 GTTGTGGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.50
Consensus pattern (20 bp):
TCATTTTGATACCAATTTTA
Found at i:84932 original size:20 final size:20
Alignment explanation
Indices: 84887--85094 Score: 224
Period size: 20 Copynumber: 10.5 Consensus size: 20
84877 CGAATATGAA
*
84887 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
84907 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
84927 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
84947 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
84967 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
84987 AAATCGCAACG-TAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
85006 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
85026 AAATCGCAACGATAAT-CGT
1 AAATCGCAACGCGAATCCGT
*
85045 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
85065 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
85085 AAATCACAAC
1 AAATCGCAAC
85095 ACTGAAATTT
Statistics
Matches: 166, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
19 34 0.20
20 131 0.79
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:85033 original size:59 final size:58
Alignment explanation
Indices: 84906--85094 Score: 229
Period size: 59 Copynumber: 3.2 Consensus size: 58
84896 CGCGAACACA
* * * * *
84906 TAAATCGCAACGTGTATCCGTATATCGCAACGCGT-ATCCGTAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCGTAAATCGCAA--CGTAATCCGTAAATCGCAACGAGAATCTG
*
84966 TATATCGCAACGCGTATCCGTAAATCGCAACGTAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCGTAAATCGCAACGTAATCCGTAAATCGCAACGAGAATCTG
* *
85025 TAAATCGCAACGATAAT-CGTAAATCGCAACGAGAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGGT-ATCCGTAAATCGCAACG-TAATCCGTAAATCGCAACGAGAATCTG
*
85084 TAAATCACAAC
1 TAAATCGCAAC
85095 ACTGAAATTT
Statistics
Matches: 115, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
58 18 0.16
59 70 0.61
60 27 0.23
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (58 bp):
TAAATCGCAACGGTATCCGTAAATCGCAACGTAATCCGTAAATCGCAACGAGAATCTG
Found at i:85793 original size:24 final size:24
Alignment explanation
Indices: 85766--85812 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
85756 CAAATTGGTC
85766 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
85790 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
85813 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Done.