Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003449.1 Hibiscus syriacus cultivar Beakdansim tig00007285_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: 51328
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1430 original size:22 final size:22
Alignment explanation
Indices: 1405--1452 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1395 TTCACCCAAC
1405 GCCTGAACATTTATTCAACAAG
1 GCCTGAACATTTATTCAACAAG
1427 GCCTGAACATTTATTCAACAAG
1 GCCTGAACATTTATTCAACAAG
1449 GCCT
1 GCCT
1453 AAAGAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (22 bp):
GCCTGAACATTTATTCAACAAG
Found at i:18222 original size:37 final size:36
Alignment explanation
Indices: 18174--18248 Score: 114
Period size: 37 Copynumber: 2.1 Consensus size: 36
18164 AAAGTTTACA
*
18174 AAATATGACAACACATCTAAATTTATAAAAAGATGAC
1 AAATATGACAACACATCCAAATTTAT-AAAAGATGAC
* *
18211 AAATATGACAACATATCCAAATTTATACAAGATGAC
1 AAATATGACAACACATCCAAATTTATAAAAGATGAC
18247 AA
1 AA
18249 TATTTTCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 11 0.31
37 24 0.69
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.24
Consensus pattern (36 bp):
AAATATGACAACACATCCAAATTTATAAAAGATGAC
Found at i:18591 original size:7 final size:7
Alignment explanation
Indices: 18579--18604 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18569 CACGGAAAAT
18579 CCCCCTC
1 CCCCCTC
18586 CCCCCTC
1 CCCCCTC
18593 CCCCCTC
1 CCCCCTC
18600 CCCCC
1 CCCCC
18605 AACAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.88, G:0.00, T:0.12
Consensus pattern (7 bp):
CCCCCTC
Found at i:20963 original size:16 final size:16
Alignment explanation
Indices: 20942--20974 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20932 TAATAAATAA
20942 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
20958 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
20974 A
1 A
20975 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:21066 original size:16 final size:16
Alignment explanation
Indices: 21045--21105 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
21035 TAATAAATAA
*
21045 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
21061 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
21077 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
21093 ACGAACATAAACG
1 ACGAACATAAACG
21106 TTGGAGACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:22295 original size:14 final size:14
Alignment explanation
Indices: 22278--22328 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
22268 TATTGGGTTA
*
22278 AACATAAATGAACG
1 AACATAAACGAACG
22292 AACAT--A--AACG
1 AACATAAACGAACG
*
22302 AACATAACCGAACG
1 AACATAAACGAACG
22316 AACATAAACGAAC
1 AACATAAACGAAC
22329 ATAACCGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 9 0.29
12 1 0.03
14 21 0.68
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:22303 original size:10 final size:10
Alignment explanation
Indices: 22288--22338 Score: 57
Period size: 10 Copynumber: 4.7 Consensus size: 10
22278 AACATAAATG
22288 AACGAACATA
1 AACGAACATA
22298 AACGAACATAA
1 AACGAACAT-A
22309 CCGAACGAACATA
1 ---AACGAACATA
22322 AACGAACATA
1 AACGAACATA
*
22332 ACCGAAC
1 AACGAAC
22339 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 25 0.69
11 1 0.03
13 1 0.03
14 9 0.25
ACGTcount: A:0.55, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
AACGAACATA
Found at i:22314 original size:24 final size:24
Alignment explanation
Indices: 22278--22339 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
22268 TATTGGGTTA
**
22278 AACATAAATGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
22302 AACATAACCGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
22326 AACATAACCGAACG
1 AACATAACCGAACG
22340 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (24 bp):
AACATAACCGAACGAACATAAACG
Found at i:22339 original size:14 final size:14
Alignment explanation
Indices: 22298--22339 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
22288 AACGAACATA
22298 AACGAACATAACCG
1 AACGAACATAACCG
22312 AACGAACAT-A---
1 AACGAACATAACCG
22322 AACGAACATAACCG
1 AACGAACATAACCG
22336 AACG
1 AACG
22340 TTCACGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.52, C:0.26, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:22348 original size:34 final size:34
Alignment explanation
Indices: 22282--22362 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
22272 GGGTTAAACA
*
22282 TAAATGAACGAACATAAACGAACATAACCGAACG
1 TAAATAAACGAACATAAACGAACATAACCGAACG
* * *
22316 -AACATAAACGAACATAACCGAACGT-TCACGAACG
1 TAA-ATAAACGAACATAAACGAACATAAC-CGAACG
*
22350 TAAATGAACGAAC
1 TAAATAAACGAAC
22363 GAGACCTATG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 3 0.08
34 34 0.87
35 2 0.05
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.12
Consensus pattern (34 bp):
TAAATAAACGAACATAAACGAACATAACCGAACG
Found at i:24219 original size:39 final size:38
Alignment explanation
Indices: 24176--24265 Score: 89
Period size: 38 Copynumber: 2.4 Consensus size: 38
24166 AACAAATTAG
* *
24176 AAAATATTTATAT-ATTT-TCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATAATTTGT-TTTAAAAAATTGAAAAT-AT
*
24215 -AAAATTTATATAATTTGTTTTATAAAATTGAAAATAT
1 AAAAATTTATATAATTTGTTTTAAAAAATTGAAAATAT
24252 AAAAAATTTA-ATAA
1 -AAAAATTTATATAA
24266 AAGGGTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
37 10 0.23
38 25 0.57
39 9 0.20
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATAATTTGTTTTAAAAAATTGAAAATAT
Found at i:24254 original size:37 final size:37
Alignment explanation
Indices: 24181--24255 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
24171 ATTAGAAAAT
* *
24181 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
24218 ATTTATATAATTTGT-TTTATAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTT-TCTTTAAAAAATTGAAAATCATAAA
24255 A
1 A
24256 AATTTAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 18 0.55
39 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:35584 original size:84 final size:83
Alignment explanation
Indices: 35290--36265 Score: 912
Period size: 84 Copynumber: 11.7 Consensus size: 83
35280 CTGAATGAAA
* *
35290 TCGAACTCGAAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TCGAACTC-AAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* *
35355 TGCCTTAGAGCTGGGCGCGTAG
64 TGCCTTGGAGCT--GAGCGTAG
* * * * * *
35377 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTT-TC-ATCCTTGAGTTATGCTGTAAATGATA
1 TCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTCGA--CTTAAGTTATGCTGCAAATGATG
* * * * *
35440 TGCACTCGAAGTTGAGTGTAA
64 TGC-CTTGGAGCTGAGCGTAG
* * * * * * *
35461 TCAAACTCGAGGGTC--T-TTAGCAGATAACCCTTCTTGACTTAAGCTATGCTACAAATGATGTG
1 TCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
35523 CCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * * *
35541 TCGAACTCAAAAGTATTTGGTTGGCAGATAACCATTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCAAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
35606 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * * ** * *
35625 TCGAACTCCAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGGTGT
1 TCGAACTCAAAGGTC-TTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
35690 GCTCTCGAAGCTGAGTGTAA
65 GC-CTTGGAGCTGAGCGTAG
* * * *
35710 TCGAACTCGAGGGTC--T-TTGGCAGATATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
*
35772 TCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * * ** *
35790 TTGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTCAAGTTATATTGCAAATGATATG
1 TCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
*
35855 CCTTGTAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* ** * * * * * * * ** *
35873 TTGAACTTGAAGGTATTTGGTGACAGATAACCCTTATAGCCTTGAGTTATATTGTAAATGATGTG
1 TCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* * * *
35938 CCCTCGAAGCTGAGTGTAA
66 -CCTTGGAGCTGAGCGTAG
* * * * * *
35957 TCGAACTCGAGGGTC--T-TTGGCAGATAGCCCTTATTGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
36019 CCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * * *
36037 TCAAACTCGAAAAGTCTTTAGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATA
1 TCGAACTC-AAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
*
36102 TGCCTTGGAGTTGAGCGTAG
64 TGCCTTGGAGCTGAGCGTAG
* * * * * * *
36122 TCGAACTCAAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCAAAGGTC-TTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
36187 GCCTTGGAGCTGAGTGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * *
36206 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATG
1 TCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
36266 TTGTCTTTTA
Statistics
Matches: 718, Mismatches: 150, Indels: 46
0.79 0.16 0.05
Matches are distributed among these distances:
80 69 0.10
81 109 0.15
82 6 0.01
83 154 0.21
84 226 0.31
85 132 0.18
86 14 0.02
87 8 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (83 bp):
TCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAG
Found at i:35751 original size:249 final size:249
Alignment explanation
Indices: 35290--36265 Score: 1334
Period size: 249 Copynumber: 3.9 Consensus size: 249
35280 CTGAATGAAA
* * * *
35290 TCGAACTCGAAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TCGAACTCGAAAAGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATA
* * *
35355 TGCCTTAGAGCTGGGCGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTT-TCATCC
66 TGCCTTGGAGCT--GAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCT-AGCC
** * * * *
35418 TTGAGTTATGCTGTAAATGATATGCACTCGAAGTTGAGTGTAATCAAACTCGAGGGTCTTTAGCA
128 TTGAGTTATATTGTAAATGATGTGC-CTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCA
*
35483 GATAACCCTTCTTGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAG
192 GATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* *
35541 TCGAACTC-AAAAGTATTTGGTTGGCAGATAACCATTCTCGACTTAAGTTATGCTGCAAATGATA
1 TCGAACTCGAAAAGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATA
*
35605 TGCCTTGGAGCTGAGCGTAGTCGAACTCCAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTG
66 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTG
*
35670 AGTTATATTGTAAATGGTGTGCTCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
131 AGTTATATTGTAAATGATGTGC-CTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
* * *
35735 ATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCTTGGAGCTGAGCGTAG
195 AACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * **
35790 TTGAACTCG-AAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTCAAGTTATATTGCAAATGATA
1 TCGAACTCGAAAAGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATA
* * * * *
35853 TGCCTTGTAGCTGAGCGTAGTTGAACTTGAAGGT-ATTTGGTGACAGATAACCCTTATAGCCTTG
66 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTG
35917 AGTTATATTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
131 AGTTATATTGTAAATGATGTG-CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
* *
35982 AGCCCTTATTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
195 AACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * *
36037 TCAAACTCGAAAAGTCTTTAGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATA
1 TCGAACTCGAAAAGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATA
* * * * * * *
36102 TGCCTTGGAGTTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTG
66 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTG
* * * * * * *
36167 AGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGTTGGCAG
131 AGTTATATTGTAAATGATGTGCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T-TTGGCAG
* * * * *
36232 ATAACCCTTCTAGCCTTGAGTTATGTTGCAAATG
193 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATG
36266 TTGTCTTTTA
Statistics
Matches: 642, Mismatches: 73, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
247 148 0.23
248 101 0.16
249 247 0.38
250 103 0.16
251 9 0.01
252 34 0.05
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (249 bp):
TCGAACTCGAAAAGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATA
TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTG
AGTTATATTGTAAATGATGTGCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATA
ACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
Found at i:41552 original size:20 final size:19
Alignment explanation
Indices: 41524--41577 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
41514 TTGTATTAAG
41524 AAAAAAATAAAAATAA-AGT
1 AAAAAAATAAAAATAATA-T
41543 AAAGAAAATAAAAATAATAT
1 AAA-AAAATAAAAATAATAT
*
41563 AAAAATATAAAAATA
1 AAAAAAATAAAAATA
41578 CGTGTATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 14 0.44
20 17 0.53
21 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.19
Consensus pattern (19 bp):
AAAAAAATAAAAATAATAT
Found at i:41564 original size:11 final size:10
Alignment explanation
Indices: 41524--41577 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 10
41514 TTGTATTAAG
41524 AAAA-AAATA
1 AAAATAAATA
41533 AAAATAAAGTA
1 AAAATAAA-TA
*
41544 AAGA-AAATA
1 AAAATAAATA
41553 AAAATAATATA
1 AAAATAA-ATA
41564 AAAAT--ATA
1 AAAATAAATA
41572 AAAATA
1 AAAATA
41578 CGTGTATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.21
9 9 0.24
10 8 0.21
11 13 0.34
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.19
Consensus pattern (10 bp):
AAAATAAATA
Found at i:44688 original size:2 final size:2
Alignment explanation
Indices: 44683--44707 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44673 CATTTTTTTA
44683 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 A
44708 CTTTTAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44824 original size:8 final size:9
Alignment explanation
Indices: 44806--44841 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44796 AATACATATA
44806 TTTTTATTT
1 TTTTTATTT
44815 TTTTTATTT
1 TTTTTATTT
44824 TTTTTA-TT
1 TTTTTATTT
44832 TTTTTATTT
1 TTTTTATTT
44841 T
1 T
44842 CATTTTGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTATTT
Found at i:44833 original size:17 final size:18
Alignment explanation
Indices: 44806--44841 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
44796 AATACATATA
44806 TTTTTATTTTTTTTATTT
1 TTTTTATTTTTTTTATTT
44824 TTTTTA-TTTTTTTATTT
1 TTTTTATTTTTTTTATTT
44841 T
1 T
44842 CATTTTGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTATTTTTTTTATTT
Found at i:46530 original size:16 final size:15
Alignment explanation
Indices: 46509--46539 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
46499 TATATAATAA
46509 TTTTTGAAAAACATAT
1 TTTTTG-AAAACATAT
46525 TTTTTGAAAACATAT
1 TTTTTGAAAACATAT
46540 ATATATATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (15 bp):
TTTTTGAAAACATAT
Found at i:46566 original size:38 final size:38
Alignment explanation
Indices: 46471--46585 Score: 132
Period size: 38 Copynumber: 3.1 Consensus size: 38
46461 TGAAAACATA
*
46471 ATATTTTAAAAAATGG-TTTTTGAAAACATATATA-AT
1 ATATTTTTAAAAATGGTTTTTTGAAAACATATATATAT
*
46507 A-ATTTTTGAAAAACAT-ATTTTTTGAAAACATATATATAT
1 ATATTTTT--AAAA-ATGGTTTTTTGAAAACATATATATAT
*
46546 ATAGTTTTT-AAAATGGTTTTTTGAAAACGTATATATAT
1 ATA-TTTTTAAAAATGGTTTTTTGAAAACATATATATAT
46584 AT
1 AT
46586 GTAATCTTTG
Statistics
Matches: 67, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
35 5 0.07
36 1 0.01
37 6 0.09
38 46 0.69
39 3 0.04
40 1 0.01
41 5 0.07
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.44
Consensus pattern (38 bp):
ATATTTTTAAAAATGGTTTTTTGAAAACATATATATAT
Found at i:49047 original size:20 final size:20
Alignment explanation
Indices: 49024--49112 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
49014 AATCTGTAAA
49024 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
49044 TCGCAAC-GTGATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
49064 TCACAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * * *
49084 TCGTAACAC-GAATTTAATT
1 TCGCAACACAGAAGTCAAAT
49103 TCGCAACACA
1 TCGCAACACA
49113 AATGTTTTGG
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
19 16 0.30
20 36 0.68
21 1 0.02
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:49845 original size:12 final size:12
Alignment explanation
Indices: 49824--49857 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
49814 ACCACATTTC
*
49824 CAATACCAAACA
1 CAATATCAAACA
49836 CAATATCAAACA
1 CAATATCAAACA
*
49848 CAATCTCAAA
1 CAATATCAAA
49858 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Done.