Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006689.1 Hibiscus syriacus cultivar Beakdansim tig00016617_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: 99778
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:545 original size:20 final size:20
Alignment explanation
Indices: 519--622 Score: 122
Period size: 20 Copynumber: 5.2 Consensus size: 20
509 AAACTTAAAT
519 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
539 TCACAACGCGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
559 TCGCAATGCGAAACTAGAAAA
1 TCGCAACGCGAAAAT-GAAAA
* *
580 TCGCAACGCG-ACATAAAAA
1 TCGCAACGCGAAAATGAAAA
*
599 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
618 TCGCA
1 TCGCA
623 TTGCGATTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
19 23 0.33
20 33 0.47
21 14 0.20
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:599 original size:40 final size:40
Alignment explanation
Indices: 519--622 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 40
509 AAACTTAAAT
* * *
519 TCGCAACGCGAAAATGAAAATCACAACGCGAACATGAAAA
1 TCGCAACGCGAAACTGAAAATCGCAACGCGAACATAAAAA
*
559 TCGCAATGCGAAACTAGAAAATCGCAACGCG-ACATAAAAA
1 TCGCAACGCGAAACT-GAAAATCGCAACGCGAACATAAAAA
599 TCGCAACGCGAAACT-AAAATCGCA
1 TCGCAACGCGAAACTGAAAATCGCA
623 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 9 0.16
40 35 0.60
41 14 0.24
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.12
Consensus pattern (40 bp):
TCGCAACGCGAAACTGAAAATCGCAACGCGAACATAAAAA
Found at i:1030 original size:22 final size:22
Alignment explanation
Indices: 973--1037 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
963 TCTAAGAGAT
*
973 GGAGAT-A-GACGGATTTTGCC
1 GGAGATGAGGACGGATTTCGCC
* * *
993 GGAGATTAGGATGGATTTCGTC
1 GGAGATGAGGACGGATTTCGCC
* *
1015 GGAGATGGGGACGGATGTCGCC
1 GGAGATGAGGACGGATTTCGCC
1037 G
1 G
1038 TAGAGAGTGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 28 0.80
ACGTcount: A:0.22, C:0.14, G:0.42, T:0.23
Consensus pattern (22 bp):
GGAGATGAGGACGGATTTCGCC
Found at i:1253 original size:17 final size:17
Alignment explanation
Indices: 1231--1264 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1221 TCTGTGCGAT
1231 TTCCAAATTCGCGTTGC
1 TTCCAAATTCGCGTTGC
1248 TTCCAAATTCGCGTTGC
1 TTCCAAATTCGCGTTGC
1265 GATTTACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (17 bp):
TTCCAAATTCGCGTTGC
Found at i:11383 original size:17 final size:16
Alignment explanation
Indices: 11359--11390 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11349 AAGGTAAAAC
11359 ATATTAAATAATAAAT
1 ATATTAAATAATAAAT
11375 ATATATAAATAATAAA
1 ATAT-TAAATAATAAA
11391 AAAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATTAAATAATAAAT
Found at i:12810 original size:13 final size:15
Alignment explanation
Indices: 12792--12824 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
12782 TTAAAGTAAA
12792 TTTAAATTT-ATT-T
1 TTTAAATTTAATTGT
12805 TTTAAATTTAATTGT
1 TTTAAATTTAATTGT
12820 TTTAA
1 TTTAA
12825 GCATAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 3 0.17
15 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTAAATTTAATTGT
Found at i:13570 original size:24 final size:23
Alignment explanation
Indices: 13519--13570 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
13509 AGTGTCGGAG
*
13519 AAAACTTATAAATTTCAAGAGGA
1 AAAACTCATAAATTTCAAGAGGA
* * *
13542 TAAACTCATAAAATTTTAAGAGTA
1 AAAACTCAT-AAATTTCAAGAGGA
13566 AAAAC
1 AAAAC
13571 ATAATATCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (23 bp):
AAAACTCATAAATTTCAAGAGGA
Found at i:16547 original size:3 final size:3
Alignment explanation
Indices: 16539--16568 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16529 AATGATATAG
16539 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16569 ATAGTTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20063 original size:21 final size:18
Alignment explanation
Indices: 20019--20057 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
20009 TTGATGATAA
20019 TATT-TTTTATTTTTTTT
1 TATTATTTTATTTTTTTT
20036 TATTATTTTA-TTTTTTT
1 TATTATTTTATTTTTTTT
20053 TATTA
1 TATTA
20058 ATTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (18 bp):
TATTATTTTATTTTTTTT
Found at i:20873 original size:51 final size:51
Alignment explanation
Indices: 20808--20926 Score: 195
Period size: 51 Copynumber: 2.3 Consensus size: 51
20798 TTTAGGGTCG
20808 GTTTGTTTGC-CGTAATTAGAATTACAGAATTAGATTTCCTCGAATTCTCGT
1 GTTTGTTT-CACGTAATTAGAATTACAGAATTAGATTTCCTCGAATTCTCGT
* * *
20859 GTTTGTTTCACGTAATTAGAATTACAGAATTGGTTTTCCTCTAATTCTCGT
1 GTTTGTTTCACGTAATTAGAATTACAGAATTAGATTTCCTCGAATTCTCGT
20910 GTTTGTTTCACGTAATT
1 GTTTGTTTCACGTAATT
20927 CGTTTTTCGG
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
50 1 0.02
51 63 0.98
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.45
Consensus pattern (51 bp):
GTTTGTTTCACGTAATTAGAATTACAGAATTAGATTTCCTCGAATTCTCGT
Found at i:20954 original size:42 final size:42
Alignment explanation
Indices: 20907--21010 Score: 163
Period size: 42 Copynumber: 2.5 Consensus size: 42
20897 CTCTAATTCT
*
20907 CGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATATTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
* *
20949 CGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
* *
20991 AGTGTTTATTTCACGTAATT
1 CGTGTTTGTTTCACGTAATT
21011 GGCTTTCCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.48
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
Found at i:21236 original size:17 final size:17
Alignment explanation
Indices: 21216--21251 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21206 ATTAATTTAT
21216 TAATATTTATAATAATA
1 TAATATTTATAATAATA
* *
21233 TAATATTTTTAATATTA
1 TAATATTTATAATAATA
21250 TA
1 TA
21252 TAAAATAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATTTATAATAATA
Found at i:21244 original size:26 final size:26
Alignment explanation
Indices: 21210--21363 Score: 74
Period size: 26 Copynumber: 5.9 Consensus size: 26
21200 TTATTTATTA
21210 ATTTATTAATATTTATAATAATATAAT
1 ATTT-TTAATATTTATAATAATATAAT
21237 ATTTTTAATATTATATAA-AATAATCAATT
1 ATTTTTAATATT-TATAATAAT-AT-AA-T
* * * *
21266 ATATTATAATA-ATATAA-GATATTAT
1 AT-TTTTAATATTTATAATAATATAAT
*
21291 ATTTTT-AT-TTTAATAAT-ATATAAAA
1 ATTTTTAATATTT-ATAATAATAT-AAT
** *
21316 AAATTT-ATATTTAATAATGA-ATAAT
1 ATTTTTAATATTT-ATAATAATATAAT
*
21341 ATTATTATATATTTA-AATAATAT
1 ATTTTTA-ATATTTATAATAATAT
21364 TTTAATTAAG
Statistics
Matches: 98, Mismatches: 15, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
23 3 0.03
24 11 0.11
25 19 0.19
26 26 0.27
27 20 0.20
28 9 0.09
29 3 0.03
30 7 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
ATTTTTAATATTTATAATAATATAAT
Found at i:21386 original size:23 final size:23
Alignment explanation
Indices: 21366--21410 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21356 AATAATATTT
21366 TAATTAAGATAGTTAAAATATAC
1 TAATTAAGATAGTTAAAATATAC
* **
21389 TAATTAATATTTTTAAAATATA
1 TAATTAAGATAGTTAAAATATA
21411 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
TAATTAAGATAGTTAAAATATAC
Found at i:21530 original size:19 final size:19
Alignment explanation
Indices: 21508--21570 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 19
21498 ATAAAAATAC
21508 TATTTAATAATAAATAAAT
1 TATTTAATAATAAATAAAT
*
21527 TATTTTTAATAATAAA-AAAG
1 TA--TTTAATAATAAATAAAT
*
21547 T-TTT-ATGATAAATAATAT
1 TATTTAATAATAAATAA-AT
21565 TATTTA
1 TATTTA
21571 TTGTATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
16 7 0.20
17 5 0.14
18 2 0.06
19 5 0.14
20 4 0.11
21 12 0.34
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTTAATAATAAATAAAT
Found at i:21781 original size:15 final size:15
Alignment explanation
Indices: 21736--21787 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
21726 TTTCAGAAAT
*
21736 GTAATTCTTTTTTCA
1 GTAATTCATTTTTCA
* ** *
21751 G-AATTTAAATTCCA
1 GTAATTCATTTTTCA
21765 GTAATTCATTTTTCA
1 GTAATTCATTTTTCA
21780 GTAATTCA
1 GTAATTCA
21788 AATTTAATTA
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (15 bp):
GTAATTCATTTTTCA
Found at i:21800 original size:30 final size:29
Alignment explanation
Indices: 21736--21803 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
21726 TTTCAGAAAT
* * *
21736 GTAATTCTTTTTTCAGAATTTAAATTCCA
1 GTAATTCATTTTTCAGAATTCAAATTCAA
*
21765 GTAATTCATTTTTCAGTAATTCAAATTTAA
1 GTAATTCATTTTTCAG-AATTCAAATTCAA
*
21795 TTAATTCAT
1 GTAATTCAT
21804 ATTCTAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.49
Consensus pattern (29 bp):
GTAATTCATTTTTCAGAATTCAAATTCAA
Found at i:25736 original size:28 final size:28
Alignment explanation
Indices: 25689--25744 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
25679 AACAAACGCC
* *
25689 GCAAAAGGTCGATATCTATAGCGGCGTT
1 GCAAAAGGTCGAGATATATAGCGGCGTT
*
25717 GCAAAAGGTCTAGATATATAGCGGCGTT
1 GCAAAAGGTCGAGATATATAGCGGCGTT
25745 TTTGGAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (28 bp):
GCAAAAGGTCGAGATATATAGCGGCGTT
Found at i:25780 original size:43 final size:43
Alignment explanation
Indices: 25717--25933 Score: 260
Period size: 43 Copynumber: 5.0 Consensus size: 43
25707 TAGCGGCGTT
* *
25717 GCAAAAGGTCTAGATATATAGCGGCGTTTTTGGAACAAACGCC
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
* * * *
25760 GCAAAATGTCGAGATTTATAGTGGCGTTTTTGGAACAAACGTC
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
** * *
25803 GCAAAAGGTCGAGATCTATAGCGGTATTATTGGACACAAACGTC
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGA-ACAAACGCC
* *
25847 GCAAAAAGTC-AGATCTATAGCGGCGTTTTTGTAACAAACGCC
1 GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
* *
25889 GCAAAAGGT-TAGAT-TAATAGCGGCGCTTTTGGATACAAACGCC
1 GCAAAAGGTCGAGATCT-ATAGCGGCGTTTTTGGA-ACAAACGCC
25932 GC
1 GC
25934 TAATTACCAT
Statistics
Matches: 150, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
41 1 0.01
42 35 0.23
43 96 0.64
44 18 0.12
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (43 bp):
GCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCC
Found at i:28703 original size:41 final size:41
Alignment explanation
Indices: 28635--29037 Score: 355
Period size: 41 Copynumber: 9.7 Consensus size: 41
28625 TTGTAAACTT
* *
28635 GCGGCGTTTGTAAATACAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGT--ATAAAAACGCCACTAAAGTACAAGTCTATA
** * *
28678 GCGGCGTAAGTATATAAACGACACTAAAGTACAAG-CGTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTC-TATA
* * *
28719 GCGGCATTTGTTTAAAAACGCCACTAAAGTACAAGTGTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * * * *
28760 GCAGCATTTGTAAAAACAAACGCCACAAAATTACAAGTCTATA
1 GCGGCGTTTGT-ATAA-AAACGCCACTAAAGTACAAGTCTATA
* * *
28803 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGCCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * * * * * * *
28844 GCGGCATTTTTATACAAACGCCGCTAAAGTACTACTCTGTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * * *
28885 GTGGTGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * * *
28926 GCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTGTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * * * *
28967 GCGGCGTTTGT-TGAAAAAACGCCGCTATAG-ATGAA-CCTATT
1 GCGGCGTTTGTAT--AAAAACGCCACTAAAGTA-CAAGTCTATA
*
29008 GCGGCGTTTTTATAAAAACGCCACTAAAGT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGT
29038 TACCATTTTG
Statistics
Matches: 291, Mismatches: 60, Indels: 20
0.78 0.16 0.05
Matches are distributed among these distances:
40 16 0.05
41 213 0.73
42 21 0.07
43 41 0.14
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
Found at i:28971 original size:123 final size:123
Alignment explanation
Indices: 28633--29037 Score: 405
Period size: 125 Copynumber: 3.3 Consensus size: 123
28623 AATTGTAAAC
* ** *
28633 TTGCGGCGTTTGTAAATACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTAAGTATATAAACG
1 TTGCGGCGTTTGT--ATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACG
* * * * * *
28698 ACACTAAAGTACAAGC-GTATAGCGGCATTTGTT-TAAAAACGCCACTAAAGTACAAGTGTA
64 CCACTAAAGTAC-ACCTGT-TAGCGGCATTTGTTATAAAAACGCCGCTAAAGTACTACTCTA
* * * * * * *
28758 TAGCAGCATTTGTAAAAACAAACGCCACAAAATTACAAGTCTATAGCGGCGTTTGTATAAAAACG
1 TTGCGGCGTTTGT-ATAA-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACG
* *
28823 CCACTAAAGTACGAGCCT-TTAGCGGCATTT-TTATACAAACGCCGCTAAAGTACTACTCTG
64 CCACTAAAGTAC-A-CCTGTTAGCGGCATTTGTTATAAAAACGCCGCTAAAGTACTACTCTA
* * *
28883 TTGTGGTGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCC
1 TTGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* *
28948 ACTAAAGTACTACTCTGTT-GCGGCGTTTGTTGA-AAAAACGCCGCTATAG-A-TGAAC-CTA
66 ACTAAAGTAC-AC-CTGTTAGCGGCATTTGTT-ATAAAAACGCCGCTAAAGTACT--ACTCTA
*
29006 TTGCGGCGTTTTTATAAAAACGCCACTAAAGT
1 TTGCGGCGTTTGTATAAAAACGCCACTAAAGT
29038 TACCATTTTG
Statistics
Matches: 232, Mismatches: 38, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
122 2 0.01
123 97 0.42
124 28 0.12
125 103 0.44
126 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (123 bp):
TTGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
ACTAAAGTACACCTGTTAGCGGCATTTGTTATAAAAACGCCGCTAAAGTACTACTCTA
Found at i:30353 original size:16 final size:16
Alignment explanation
Indices: 30334--30367 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30324 ATGTTATGAA
* *
30334 TTAATTTTATATTTAT
1 TTAATTATATAATTAT
30350 TTAATTATATAATTAT
1 TTAATTATATAATTAT
30366 TT
1 TT
30368 TTTTAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATTATATAATTAT
Found at i:31631 original size:15 final size:15
Alignment explanation
Indices: 31611--31650 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
31601 GTAAAAGTAA
*
31611 AAAATATATCAAACT
1 AAAATATATAAAACT
* *
31626 AAAATATAAAAAATT
1 AAAATATATAAAACT
31641 AAAATATATA
1 AAAATATATA
31651 TTAGTTTGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATATATAAAACT
Found at i:43437 original size:60 final size:60
Alignment explanation
Indices: 43339--43548 Score: 305
Period size: 60 Copynumber: 3.5 Consensus size: 60
43329 AGATTCGGCG
* * *
43339 GTGGATCTCGTTTTCAACCCAATTCCAGCCGTGTATATCTGGTTCAAGCCAATTCCATCA
1 GTGGACCTCGTTTTCAACCCAATTCCAGCCGTGCATATCTGGTTCAACCCAATTCCATCA
*
43399 GTGGACCTCGTTTTCAACCCAATTCCAGTCGTGCATATCTGGTTCAACCCAATTCCATCA
1 GTGGACCTCGTTTTCAACCCAATTCCAGCCGTGCATATCTGGTTCAACCCAATTCCATCA
* * * * *
43459 ATGGACCTCGTTTTCAACCCAATTCCAGCCGTGCATA-CGAGGATCAACCCAATTCCAGCG
1 GTGGACCTCGTTTTCAACCCAATTCCAGCCGTGCATATC-TGGTTCAACCCAATTCCATCA
* *
43519 GTGGACCTCGTTTTCAATCCAATTACAGCC
1 GTGGACCTCGTTTTCAACCCAATTCCAGCC
43549 ACTCATACGA
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
59 1 0.01
60 135 0.99
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (60 bp):
GTGGACCTCGTTTTCAACCCAATTCCAGCCGTGCATATCTGGTTCAACCCAATTCCATCA
Found at i:43541 original size:30 final size:30
Alignment explanation
Indices: 43339--43547 Score: 140
Period size: 30 Copynumber: 7.0 Consensus size: 30
43329 AGATTCGGCG
* *
43339 GTGGATCTCGTTTTCAACCCAATTCCAGCC
1 GTGGACCTCGTTTTCAACCCAATTCCAGCA
* ** * * *
43369 GTGTATATC-TGGTTCAAGCCAATTCCATCA
1 GTGGACCTCGT-TTTCAACCCAATTCCAGCA
43399 GTGGACCTCGTTTTCAACCCAATTCCAGTC-
1 GTGGACCTCGTTTTCAACCCAATTCCAG-CA
* ** * *
43429 GTGCATATC-TGGTTCAACCCAATTCCATCA
1 GTGGACCTCGT-TTTCAACCCAATTCCAGCA
* *
43459 ATGGACCTCGTTTTCAACCCAATTCCAGCC
1 GTGGACCTCGTTTTCAACCCAATTCCAGCA
* *** *
43489 GT-G-CATACGAGGATCAACCCAATTCCAGCG
1 GTGGACCT-CG-TTTTCAACCCAATTCCAGCA
* *
43519 GTGGACCTCGTTTTCAATCCAATTACAGC
1 GTGGACCTCGTTTTCAACCCAATTCCAGC
43548 CACTCATACG
Statistics
Matches: 133, Mismatches: 36, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
28 2 0.02
29 6 0.05
30 117 0.88
31 6 0.05
32 2 0.02
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (30 bp):
GTGGACCTCGTTTTCAACCCAATTCCAGCA
Found at i:43556 original size:60 final size:60
Alignment explanation
Indices: 43339--43577 Score: 295
Period size: 60 Copynumber: 4.0 Consensus size: 60
43329 AGATTCGGCG
* * * * *
43339 GTGGATCTCGTTTTCAACCCAATTCCAGCCGTGTATATC-TGGTTCAAGCCAATTCCATCA
1 GTGGACCTCGTTTTCAACCCAATTCCAGCCGTGCATA-CGAGGTTCAACCCAATTCCAGCA
* * *
43399 GTGGACCTCGTTTTCAACCCAATTCCAGTCGTGCATATC-TGGTTCAACCCAATTCCATCA
1 GTGGACCTCGTTTTCAACCCAATTCCAGCCGTGCATA-CGAGGTTCAACCCAATTCCAGCA
* * *
43459 ATGGACCTCGTTTTCAACCCAATTCCAGCCGTGCATACGAGGATCAACCCAATTCCAGCG
1 GTGGACCTCGTTTTCAACCCAATTCCAGCCGTGCATACGAGGTTCAACCCAATTCCAGCA
* * * *
43519 GTGGACCTCGTTTTCAATCCAATTACAGCCACT-CATACGAGGTTCAACCCGATTCCAGC
1 GTGGACCTCGTTTTCAACCCAATTCCAGCC-GTGCATACGAGGTTCAACCCAATTCCAGC
43578 GTTGCAGACG
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
59 1 0.01
60 159 0.99
61 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (60 bp):
GTGGACCTCGTTTTCAACCCAATTCCAGCCGTGCATACGAGGTTCAACCCAATTCCAGCA
Found at i:43663 original size:30 final size:30
Alignment explanation
Indices: 43626--43699 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
43616 CGTGGATCAT
* * *
43626 CCAAATTCCAATGGTGCAAATGGGGTTCAA
1 CCAAATTCCAACGGCGCAAATGGGGTGCAA
*
43656 CCCAATTCCAACGGCGCAAATGGGGTGCAA
1 CCAAATTCCAACGGCGCAAATGGGGTGCAA
43686 CCAAATTCCAACGG
1 CCAAATTCCAACGG
43700 TTCACGTTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (30 bp):
CCAAATTCCAACGGCGCAAATGGGGTGCAA
Found at i:62617 original size:23 final size:24
Alignment explanation
Indices: 62590--62653 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 24
62580 AAGAATAATT
62590 ATATTAATTATTTTTAAT-AAAAA
1 ATATTAATTATTTTTAATGAAAAA
*
62613 ATATTAATTGAAGTTTTTATTGAAAAA
1 ATATTAATT--A-TTTTTAATGAAAAA
*
62640 ATATTTATCTATTT
1 ATATTAAT-TATTT
62654 ATTTATCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 9 0.26
25 4 0.12
26 8 0.24
27 12 0.35
28 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (24 bp):
ATATTAATTATTTTTAATGAAAAA
Found at i:63069 original size:19 final size:19
Alignment explanation
Indices: 63041--63098 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
63031 AGATAATTAT
*
63041 AAAATAATATATGTTTTAAA
1 AAAAT-ATATATTTTTTAAA
*
63061 AAAATATATATATTTTTTAA
1 AAAATATATAT-TTTTTAAA
*
63081 AGAAT-TATATTTTTTAAA
1 AAAATATATATTTTTTAAA
63099 GAATTATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.21
19 11 0.33
20 15 0.45
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AAAATATATATTTTTTAAA
Found at i:63073 original size:21 final size:21
Alignment explanation
Indices: 63041--63090 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
63031 AGATAATTAT
63041 AAAATA-ATATATGTTTTAAA
1 AAAATATATATATGTTTTAAA
*
63061 AAAATATATATATTTTTTAAA
1 AAAATATATATATGTTTTAAA
* *
63082 GAATTATAT
1 AAAATATAT
63091 TTTTTAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
AAAATATATATATGTTTTAAA
Found at i:63091 original size:17 final size:17
Alignment explanation
Indices: 63069--63106 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
63059 AAAAAATATA
63069 TATATTTTTTAAAGAAT
1 TATATTTTTTAAAGAAT
63086 TATATTTTTTAAAGAAT
1 TATATTTTTTAAAGAAT
63103 TATA
1 TATA
63107 ATACAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TATATTTTTTAAAGAAT
Found at i:68144 original size:2 final size:2
Alignment explanation
Indices: 68132--68163 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
68122 TAACACGATA
68132 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
68164 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:78620 original size:57 final size:57
Alignment explanation
Indices: 78530--78644 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
78520 CATGATTTCT
*
78530 TTTTAAATTCATTATTTGAGTCTTTAGACATAATTTATAATCATAATTCGAAGATTA
1 TTTTAAATTCATTATTTGAGTCTTTAAACATAATTTATAATCATAATTCGAAGATTA
*
78587 TTTTAAATTCATTATTTGAGTCTTTAAATATAATTTATAATCATAATTCGAAGATTA
1 TTTTAAATTCATTATTTGAGTCTTTAAACATAATTTATAATCATAATTCGAAGATTA
78644 T
1 T
78645 AAATATAAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (57 bp):
TTTTAAATTCATTATTTGAGTCTTTAAACATAATTTATAATCATAATTCGAAGATTA
Found at i:85959 original size:30 final size:30
Alignment explanation
Indices: 85910--85972 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
85900 TATCGAGTTC
* * *
85910 GAGTTCTTATATATACAGAAAATCTCTGTT
1 GAGTCCTTATATATACAGAAAATCCCTATT
* *
85940 GAGTCCTTATGTATGCAGAAAATCCCTATT
1 GAGTCCTTATATATACAGAAAATCCCTATT
85970 GAG
1 GAG
85973 AGACTCGCCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (30 bp):
GAGTCCTTATATATACAGAAAATCCCTATT
Found at i:92326 original size:25 final size:24
Alignment explanation
Indices: 92270--92326 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
92260 TCCAGGTATG
*
92270 CATACTTCATAAACCAGTAAATTT
1 CATATTTCATAAACCAGTAAATTT
*
92294 CATGATTTCATAAATCATGTACAA-TT
1 CAT-ATTTCATAAACCA-GTA-AATTT
92320 CATATTT
1 CATATTT
92327 TTCGATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.11
25 15 0.54
26 8 0.29
27 2 0.07
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.39
Consensus pattern (24 bp):
CATATTTCATAAACCAGTAAATTT
Found at i:94882 original size:17 final size:18
Alignment explanation
Indices: 94846--94891 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 18
94836 GGTCAAAGTT
94846 CTGGTCAACAATGGTCAACG
1 CTGGTCAACAA--GTCAACG
94866 CTGGTCAACAA-TCAACG
1 CTGGTCAACAAGTCAACG
94883 -TAGGTCAAC
1 CT-GGTCAAC
94892 GGTCAACAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.04
17 13 0.52
20 11 0.44
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.20
Consensus pattern (18 bp):
CTGGTCAACAAGTCAACG
Found at i:96429 original size:4 final size:5
Alignment explanation
Indices: 96377--96426 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
96367 TGAACTATTT
** *
96377 TTTTA TTTTTA TGTTTA TTTGG TTTTG TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA -TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
96427 ATTAATTAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
5 29 0.74
6 10 0.26
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:96684 original size:21 final size:21
Alignment explanation
Indices: 96648--96726 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
96638 CTCTACTAAC
*
96648 ATTTCT-ATCACTAACCGCTA
1 ATTTCTAACCACTAACCGCTA
** *
96668 ATTTCTAACTGCTAACCACTA
1 ATTTCTAACCACTAACCGCTA
96689 ATTTCTAACCACTAACCGCTA
1 ATTTCTAACCACTAACCGCTA
*
96710 ACTTTCTAACAACTAAC
1 A-TTTCTAACCACTAAC
96727 TTTTCTAACC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 6 0.12
21 29 0.59
22 14 0.29
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (21 bp):
ATTTCTAACCACTAACCGCTA
Found at i:96689 original size:14 final size:14
Alignment explanation
Indices: 96672--96711 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
96662 CCGCTAATTT
96672 CTAACTGCTAACCA
1 CTAACTGCTAACCA
* *
96686 CTAATTTCTAACCA
1 CTAACTGCTAACCA
*
96700 CTAACCGCTAAC
1 CTAACTGCTAAC
96712 TTTCTAACAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.35, C:0.35, G:0.05, T:0.25
Consensus pattern (14 bp):
CTAACTGCTAACCA
Done.