Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002605.1 Hibiscus syriacus cultivar Beakdansim tig00005267_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: 53222
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:157 original size:45 final size:46
Alignment explanation
Indices: 57--250 Score: 261
Period size: 46 Copynumber: 4.3 Consensus size: 46
47 GCATATCCAA
* *
57 TATTTTACC-ATATACTTACCA-TTCATTCCATAAGCTCGTAA-CT
1 TATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAGCT
* * * * *
100 TATTTAAACCAATTTACTTATCGTTTAATCCCATAAGCTCGTAAGCT
1 TATTT-TACCAATATACTTACCATTTAATACCATAAGCTCGTAAGCT
147 TA-TTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAGCT
* * *
192 TATTTTATCAATATACTTACCATTAAATACCATAAGCTCGTAAACT
1 TATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAGCT
238 TATTTTACCAATA
1 TATTTTACCAATA
251 AACCATAAAC
Statistics
Matches: 131, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
43 5 0.04
44 3 0.02
45 47 0.36
46 72 0.55
47 4 0.03
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.38
Consensus pattern (46 bp):
TATTTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAGCT
Found at i:225 original size:91 final size:91
Alignment explanation
Indices: 57--250 Score: 259
Period size: 91 Copynumber: 2.1 Consensus size: 91
47 GCATATCCAA
* * * *
57 TATTTTACC-ATATACTTACCATTCATTCCATAAGCTCGTAACTTATTTAAACCAATTTACTTAT
1 TATTTTACCAATATACTTACCATTAATACCATAAGCTCGTAACTTATTTAAACCAATATACTTAC
* * * *
121 CGTTTAATCCCATAAGCTCGTAAGCT
66 CATTAAATACCATAAGCTCGTAAACT
* *
147 TA-TTTACCAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTT-TATCAATATACTT
1 TATTTTACCAATATACTTACCA-TTAATACCATAAGCTCGTAA-CTTATTTAAACCAATATACTT
210 ACCATTAAATACCATAAGCTCGTAAACT
64 ACCATTAAATACCATAAGCTCGTAAACT
238 TATTTTACCAATA
1 TATTTTACCAATA
251 AACCATAAAC
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
89 6 0.07
90 14 0.16
91 53 0.59
92 17 0.19
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.38
Consensus pattern (91 bp):
TATTTTACCAATATACTTACCATTAATACCATAAGCTCGTAACTTATTTAAACCAATATACTTAC
CATTAAATACCATAAGCTCGTAAACT
Found at i:451 original size:59 final size:59
Alignment explanation
Indices: 357--477 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 59
347 CAATCCTGAG
* * **
357 TATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAGTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCGAA
* ** *
416 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCGAA
475 TAT
1 TAT
478 ACAGCCTGCT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCGAA
Found at i:12764 original size:41 final size:39
Alignment explanation
Indices: 12714--12837 Score: 122
Period size: 42 Copynumber: 3.0 Consensus size: 39
12704 ACTTCGACTA
* * *
12714 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCTAAGT
1 TCGCATTGCGATTTACAAATTCG--TTGCGATAATCCAAGT
* *
12755 TCGCGTTGCGATTTTCCAAATTCGTTGCGATAATCCAAGT
1 TCGCATTGCGA-TTTACAAATTCGTTGCGATAATCCAAGT
* * *
12795 TTGCTTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATTTA---CAAATTCGTTGCGATAATCCAAGT
12837 T
1 T
12838 TACAAATTCG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
39 3 0.04
40 23 0.33
41 10 0.14
42 34 0.49
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (39 bp):
TCGCATTGCGATTTACAAATTCGTTGCGATAATCCAAGT
Found at i:12778 original size:21 final size:21
Alignment explanation
Indices: 12714--12827 Score: 58
Period size: 21 Copynumber: 5.6 Consensus size: 21
12704 ACTTCGACTA
* * *
12714 TCGCATTGCGA-TTTACATAT
1 TCGCGTTGCGATTTTCCAAAT
* ** * *
12734 TCGCATTGCGATAGTCTAAGT
1 TCGCGTTGCGATTTTCCAAAT
12755 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
** *
12776 T--CGTTGCGATAATCCAAGT
1 TCGCGTTGCGATTTTCCAAAT
* *
12795 TTGCTTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA-TT-TTCCAAAT
12818 T--CGTTGCGAT
1 TCGCGTTGCGAT
12828 AGTCCAAGTT
Statistics
Matches: 70, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
19 16 0.23
20 12 0.17
21 34 0.49
22 1 0.01
23 7 0.10
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:12782 original size:19 final size:19
Alignment explanation
Indices: 12758--12827 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
12748 TCTAAGTTCG
12758 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** *
12777 CGTTGCGATAATCCAAGTTT
1 CGTTGCGATTTTCCAA-ATT
*
12797 GCTTTGCGATTTATTCCAAATT
1 -CGTTGCGA-TT-TTCCAAATT
12819 CGTTGCGAT
1 CGTTGCGAT
12828 AGTCCAAGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 14 0.36
20 3 0.08
21 14 0.36
22 3 0.08
23 5 0.13
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:12795 original size:40 final size:42
Alignment explanation
Indices: 12739--12837 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
12729 CATATTCGCA
*
12739 TTGCGATAGTCTAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
12779 TTGCGATAATCCAAGTTTGCTTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
12821 TTGCGATAGTCCAAGTT
1 TTGCGATAGTCCAAGTT
12838 TACAAATTCG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 23 0.44
41 2 0.04
42 27 0.52
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:12870 original size:21 final size:21
Alignment explanation
Indices: 12840--12900 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
12830 TCCAAGTTTA
12840 CAAATTCGTTGCGATAGTCTC
1 CAAATTCGTTGCGATAGTCTC
* *
12861 CAAGTTCGTTGCAATAGTCTC
1 CAAATTCGTTGCGATAGTCTC
12882 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
12901 CAAAATCGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (21 bp):
CAAATTCGTTGCGATAGTCTC
Found at i:14059 original size:21 final size:21
Alignment explanation
Indices: 14033--14077 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
14023 AATTTGGAAT
*
14033 ACGCAAACTTGGACTATCGCA
1 ACGCAAACTTAGACTATCGCA
14054 ACGCAAACTTAGACTATCGCA
1 ACGCAAACTTAGACTATCGCA
14075 ACG
1 ACG
14078 AATTTGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.18
Consensus pattern (21 bp):
ACGCAAACTTAGACTATCGCA
Found at i:15020 original size:17 final size:16
Alignment explanation
Indices: 14961--15053 Score: 53
Period size: 17 Copynumber: 5.4 Consensus size: 16
14951 AATTTATTTT
*
14961 TATTAGTATTTTTTAAA
1 TATTA-TATTTATTAAA
* *
14978 TAGTTATTATTTTTTATAT
1 TA-TTA-TATTTATTA-AA
*
14997 TAATATATTTATGTAAA
1 TATTATATTTAT-TAAA
15014 TATTATATTTTTATTAAA
1 TATTATA--TTTATTAAA
* *
15032 -ATAATATTTATATAAT
1 TATTATATTTAT-TAAA
15048 TATTAT
1 TATTAT
15054 TTATTTAGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
15 5 0.08
16 3 0.05
17 24 0.40
18 20 0.33
19 8 0.13
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TATTATATTTATTAAA
Found at i:15026 original size:19 final size:18
Alignment explanation
Indices: 14993--15053 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
14983 ATTATTTTTT
*
14993 ATATTAATATATTTATGTAA
1 ATATT-ATATTTTTAT-TAA
15013 ATATTATATTTTTATTAA
1 ATATTATATTTTTATTAA
* *
15031 A-ATAATATTTATA-TAA
1 ATATTATATTTTTATTAA
*
15047 TTATTAT
1 ATATTAT
15054 TTATTTAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 3 0.09
17 14 0.40
18 4 0.11
19 9 0.26
20 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATATTATATTTTTATTAA
Found at i:15059 original size:36 final size:33
Alignment explanation
Indices: 14952--15060 Score: 89
Period size: 34 Copynumber: 3.3 Consensus size: 33
14942 GTGGTAAGAA
* * * * *
14952 ATTTATTTTTATTAGTATTTTTTAAATAGTTATT
1 ATTTATTTATATTAATA-TATTTATATAATTATT
* *
14986 ATTT-TTTATATTAATATATTTATGTAAATATT
1 ATTTATTTATATTAATATATTTATATAATTATT
*
15018 ATATT-TTTAT-TAAAATAATATTTATATAATTATT
1 AT-TTATTTATAT-TAAT-ATATTTATATAATTATT
15052 ATTTATTTA
1 ATTTATTTA
15061 GAATTATTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
32 14 0.23
33 22 0.36
34 25 0.41
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (33 bp):
ATTTATTTATATTAATATATTTATATAATTATT
Found at i:15220 original size:17 final size:17
Alignment explanation
Indices: 15198--15251 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
15188 AATGTTAATA
15198 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
15215 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
15232 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
15249 TTT
1 TTT
15252 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:16804 original size:21 final size:21
Alignment explanation
Indices: 16774--16821 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
16764 GCAGGGGTAC
* *
16774 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
16795 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
16816 ATGCCA
1 ATGCCA
16822 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:16851 original size:21 final size:21
Alignment explanation
Indices: 16825--16897 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
16815 TATGCCATCT
16825 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
16846 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
* *
16867 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
16888 CCGCAGGGTT
1 CCGCAGGGTT
16898 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.29, T:0.19
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:17478 original size:33 final size:34
Alignment explanation
Indices: 17419--17515 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
17409 AAATGTTTTT
*
17419 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
17453 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
17486 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
17516 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:17522 original size:34 final size:33
Alignment explanation
Indices: 17417--17522 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
17407 ATAAATGTTT
*
17417 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
17451 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
17483 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
17518 TTAAA
1 TTAAA
17523 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:19985 original size:2 final size:2
Alignment explanation
Indices: 19978--20002 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19968 TTGCAGGAAA
19978 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
20003 TGGCTTTGAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28390 original size:25 final size:25
Alignment explanation
Indices: 28361--28415 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
28351 TCTATATTTT
28361 TCTTTCCATTAACAATTTTGTATTC
1 TCTTTCCATTAACAATTTTGTATTC
*
28386 TCTTTCCATTTACAATTTTGTATTC
1 TCTTTCCATTAACAATTTTGTATTC
28411 TCTTT
1 TCTTT
28416 TGTGAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.56
Consensus pattern (25 bp):
TCTTTCCATTAACAATTTTGTATTC
Found at i:32415 original size:18 final size:19
Alignment explanation
Indices: 32374--32421 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
32364 GTTTCCTACT
32374 GTCTGTTTTC-TACTATACA
1 GTCTGTTTTCTTACTATA-A
*
32393 GTCTGTTTTCTTTCTAT-A
1 GTCTGTTTTCTTACTATAA
*
32411 GTCTGATTTCT
1 GTCTGTTTTCT
32422 ACATTATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 10 0.38
20 5 0.19
ACGTcount: A:0.15, C:0.19, G:0.12, T:0.54
Consensus pattern (19 bp):
GTCTGTTTTCTTACTATAA
Found at i:39411 original size:58 final size:58
Alignment explanation
Indices: 39321--39436 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
39311 CCGACCTGCA
39321 CCACATGAGGATTCGCACGTTTTTGCCCCTAAAATGGGAAAATCCTATTTCAGCCCCC
1 CCACATGAGGATTCGCACGTTTTTGCCCCTAAAATGGGAAAATCCTATTTCAGCCCCC
* * *
39379 CCACATGAGGATTCGCACGTTTTTGCCCCTAAAATGGGAAAATCTTGTTTTAGCCCCC
1 CCACATGAGGATTCGCACGTTTTTGCCCCTAAAATGGGAAAATCCTATTTCAGCCCCC
39437 TCGTTTTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (58 bp):
CCACATGAGGATTCGCACGTTTTTGCCCCTAAAATGGGAAAATCCTATTTCAGCCCCC
Found at i:39741 original size:23 final size:24
Alignment explanation
Indices: 39715--39766 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
39705 TTTATTACTA
39715 TTATTATTATATATATTT-CAT-TT
1 TTATTATTATATAT-TTTACATGTT
39738 TTATTATTATATATTTTACATGTT
1 TTATTATTATATATTTTACATGTT
39762 TTATT
1 TTATT
39767 TTGTTTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
24 7 0.26
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (24 bp):
TTATTATTATATATTTTACATGTT
Found at i:39967 original size:22 final size:23
Alignment explanation
Indices: 39913--39968 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
39903 CATCTATATA
*
39913 TTGTC-ATTATTATTATTATTAT
1 TTGTCTATTTTTATTATTATTAT
* *
39935 TTATCTTTTTTTATTATT-TTAT
1 TTGTCTATTTTTATTATTATTAT
39957 TTGTCTATTTTT
1 TTGTCTATTTTT
39969 TACTTTATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (23 bp):
TTGTCTATTTTTATTATTATTAT
Found at i:39976 original size:25 final size:23
Alignment explanation
Indices: 39922--39970 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
39912 ATTGTCATTA
39922 TTATTATTATTATTTATCTTTTT
1 TTATTATTATTATTTATCTTTTT
*
39945 TTATTATT-TTATTTGTCTATTTT
1 TTATTATTATTATTTATCT-TTTT
39968 TTA
1 TTA
39971 CTTTATGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (23 bp):
TTATTATTATTATTTATCTTTTT
Found at i:41475 original size:25 final size:27
Alignment explanation
Indices: 41447--41511 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
41437 ACTTACAAAC
41447 AAAATAATAAAAAA-TAC-TTAATAAT
1 AAAATAATAAAAAATTACTTTAATAAT
*
41472 AAAAAAATAAAAAAATTACTTTAATAAT
1 AAAATAAT-AAAAAATTACTTTAATAAT
*
41500 ATTAATAATAAA
1 A-AAATAATAAA
41512 TAAAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 7 0.21
26 6 0.18
27 3 0.09
28 12 0.36
29 5 0.15
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAATAATAAAAAATTACTTTAATAAT
Found at i:41495 original size:28 final size:28
Alignment explanation
Indices: 41447--41500 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
41437 ACTTACAAAC
41447 AAAATAATAAAAAATACTTAATAATAAA
1 AAAATAATAAAAAATACTTAATAATAAA
*
41475 AAAATAA-AAAAATTACTTTAATAATA
1 AAAATAATAAAAAATAC-TTAATAATA
41501 TTAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAATAATAAAAAATACTTAATAATAAA
Found at i:42379 original size:21 final size:21
Alignment explanation
Indices: 42325--42381 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
42315 TTGGGCCAAT
*
42325 AGTATCGATACTCTATGAGTG
1 AGTATCGATACTTTATGAGTG
*
42346 AGTATCGATACTTTGTGAGTG
1 AGTATCGATACTTTATGAGTG
42367 AGTATCGATACTTTA
1 AGTATCGATACTTTA
42382 CTCTCAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (21 bp):
AGTATCGATACTTTATGAGTG
Done.