Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003551.1 Hibiscus syriacus cultivar Beakdansim tig00007496_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: 102512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1148 original size:16 final size:16
Alignment explanation
Indices: 1127--1172 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
1117 GATATACTAA
*
1127 TAATTTTAAATAAAAT
1 TAATTTTTAATAAAAT
*
1143 TAATTTTTTAATATAAT
1 TAA-TTTTTAATAAAAT
1160 T-ATTTTTAATAAA
1 TAATTTTTAATAAA
1173 CTTCGTGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 10 0.38
16 4 0.15
17 12 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTTTTAATAAAAT
Found at i:1816 original size:15 final size:15
Alignment explanation
Indices: 1792--1821 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1782 TTATACATAT
*
1792 TTTAATATTTTTATA
1 TTTAAAATTTTTATA
1807 TTTAAAATTTTTATA
1 TTTAAAATTTTTATA
1822 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAAAATTTTTATA
Found at i:1826 original size:25 final size:24
Alignment explanation
Indices: 1790--1851 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 24
1780 ATTTATACAT
*
1790 ATTTTA-ATATTTTTATATTTAAA
1 ATTTTATAAATTTTTATATTTAAA
*
1813 ATTTTTATAAATTTTTTTTATTTAAA
1 A-TTTTATAAA-TTTTTATATTTAAA
1839 ATTTTATAAATTT
1 ATTTTATAAATTT
1852 ACCCATAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 1 0.03
24 8 0.24
25 11 0.32
26 14 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTTTATAAATTTTTATATTTAAA
Found at i:1828 original size:26 final size:25
Alignment explanation
Indices: 1799--1851 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
1789 TATTTTAATA
1799 TTTTTATATTTAAAATTTTTATAAAT
1 TTTTTATATTTAAAA-TTTTATAAAT
*
1825 TTTTTTTATTTAAAATTTTATAAAT
1 TTTTTATATTTAAAATTTTATAAAT
1850 TT
1 TT
1852 ACCCATAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTTTATATTTAAAATTTTATAAAT
Found at i:7276 original size:23 final size:22
Alignment explanation
Indices: 7250--7294 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
7240 TTAACTCTAA
*
7250 TTTTAAAAAAACTTTAATTTTT
1 TTTTTAAAAAACTTTAATTTTT
**
7272 TTTTTGTAAAACTTTAATTTTT
1 TTTTTAAAAAACTTTAATTTTT
7294 T
1 T
7295 AAAGTTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTAAAAAACTTTAATTTTT
Found at i:8429 original size:2 final size:2
Alignment explanation
Indices: 8424--8470 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
8414 AAAAACACAC
*
8424 CT CT CT C- CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
8465 CT CT CT
1 CT CT CT
8471 ATATATATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:8475 original size:2 final size:2
Alignment explanation
Indices: 8470--8536 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
8460 TCTCTCTCTC
8470 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8512 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
8537 CAAGCGTATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9044 original size:13 final size:13
Alignment explanation
Indices: 9026--9054 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9016 TTGGGATTGC
9026 GATGAAACTCAAA
1 GATGAAACTCAAA
9039 GATGAAACTCAAA
1 GATGAAACTCAAA
9052 GAT
1 GAT
9055 CAATCGAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (13 bp):
GATGAAACTCAAA
Found at i:11561 original size:3 final size:3
Alignment explanation
Indices: 11553--11578 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11543 GACCATCTCT
11553 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
11579 CACCTCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:15297 original size:38 final size:38
Alignment explanation
Indices: 15255--15364 Score: 90
Period size: 38 Copynumber: 3.0 Consensus size: 38
15245 TAAATTATGA
15255 AAAAAAAAATACATTAATACGTTTGATTCACTAAATAT
1 AAAAAAAAATACATTAATACGTTTGATTCACTAAATAT
* * * *
15293 AAAAAAACGAAT--A-TAATGCCATTTCA-TCA--AATTAT
1 AAAAAAA--AATACATTAAT-ACGTTTGATTCACTAAATAT
* *
15328 -ATAAAAAATACATTAATACGTTTGATTAACTAAATAT
1 AAAAAAAAATACATTAATACGTTTGATTCACTAAATAT
15365 TTAAAAAACG
Statistics
Matches: 53, Mismatches: 10, Indels: 19
0.65 0.12 0.23
Matches are distributed among these distances:
32 3 0.06
34 11 0.21
35 11 0.21
37 12 0.23
38 13 0.25
40 3 0.06
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (38 bp):
AAAAAAAAATACATTAATACGTTTGATTCACTAAATAT
Found at i:15342 original size:72 final size:73
Alignment explanation
Indices: 15258--15434 Score: 248
Period size: 73 Copynumber: 2.4 Consensus size: 73
15248 ATTATGAAAA
*
15258 AAAAAATACATTAATACGTTTGATTCACTAAATA-TAAAAAAACGAATATAATGCCATTTCATCA
1 AAAAAATACATTAATACGTTTGATTCACTAAATATTAAAAAAACGAATATAATGCCATTACATCA
*
15322 AATTATAT
66 AATTACAT
* * *** * *
15330 AAAAAATACATTAATACGTTTGATTAACTAAATATTTAAAAAACGAATATAATTTTATTACTTGA
1 AAAAAATACATTAATACGTTTGATTCACTAAATATTAAAAAAACGAATATAATGCCATTACATCA
15395 AATTACAT
66 AATTACAT
* *
15403 AAAAAATTCATTACTACGTTTGATTCACTAAA
1 AAAAAATACATTAATACGTTTGATTCACTAAA
15435 CTTTATCGGC
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 33 0.36
73 59 0.64
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (73 bp):
AAAAAATACATTAATACGTTTGATTCACTAAATATTAAAAAAACGAATATAATGCCATTACATCA
AATTACAT
Found at i:15370 original size:37 final size:35
Alignment explanation
Indices: 15258--15372 Score: 87
Period size: 37 Copynumber: 3.2 Consensus size: 35
15248 ATTATGAAAA
15258 AAAAAATACATTAATACGTTTGATTCACTAAATA-T
1 AAAAAATACATTAATACGTTTGATT-ACTAAATATT
* * *
15293 AAAAAA-ACGAATATAATGCCATTTCA-T-C-AAATTATAT
1 AAAAAATAC--AT-TAAT-ACGTTTGATTACTAAA-TAT-T
15330 AAAAAATACATTAATACGTTTGATTAACTAAATATTT
1 AAAAAATACATTAATACGTTTGATT-ACTAAATA-TT
15367 AAAAAA
1 AAAAAA
15373 CGAATATAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
34 10 0.16
35 14 0.23
36 4 0.07
37 22 0.36
38 11 0.18
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.32
Consensus pattern (35 bp):
AAAAAATACATTAATACGTTTGATTACTAAATATT
Found at i:24458 original size:32 final size:34
Alignment explanation
Indices: 24395--24461 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 34
24385 TATGCATCAC
*
24395 ATTTGATTTTATATAATTATGTAATTTAAATTTT
1 ATTTGATTTTATATAATTATATAATTTAAATTTT
*
24429 ATTT-ATTTT-TATAATTATAT-GTTTGAAATTTT
1 ATTTGATTTTATATAATTATATAATTT-AAATTTT
24461 A
1 A
24462 ATTTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 3 0.10
32 18 0.60
33 5 0.17
34 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (34 bp):
ATTTGATTTTATATAATTATATAATTTAAATTTT
Found at i:24775 original size:69 final size:69
Alignment explanation
Indices: 24664--24808 Score: 263
Period size: 69 Copynumber: 2.1 Consensus size: 69
24654 GAACAAATTT
*
24664 TCATGAAACTTGTAAGGAATGTTAGAAACACTTTTACTGTTTTACCGCAACATATTGAGTTAATA
1 TCATGTAACTTGTAAGGAATGTTAGAAACACTTTTACTGTTTTACCGCAACATATTGAGTTAATA
24729 TGTA
66 TGTA
* *
24733 TCATGTAACTTGTAAGGAATGTTAGAAATACTTTTACTGTTTTACTGCAACATATTGAGTTAATA
1 TCATGTAACTTGTAAGGAATGTTAGAAACACTTTTACTGTTTTACCGCAACATATTGAGTTAATA
24798 TGTA
66 TGTA
24802 TCATGTA
1 TCATGTA
24809 GCTGGTGTAT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (69 bp):
TCATGTAACTTGTAAGGAATGTTAGAAACACTTTTACTGTTTTACCGCAACATATTGAGTTAATA
TGTA
Found at i:33118 original size:35 final size:35
Alignment explanation
Indices: 33079--33149 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
33069 CTTTAACCAC
*
33079 TGAAATAATTTGATTCGTACTGATTCAATAACCTT
1 TGAAATAACTTGATTCGTACTGATTCAATAACCTT
*
33114 TGAAATAGCTTGATTCGTACTGATTCAATAACCTT
1 TGAAATAACTTGATTCGTACTGATTCAATAACCTT
33149 T
1 T
33150 TACTTGTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (35 bp):
TGAAATAACTTGATTCGTACTGATTCAATAACCTT
Found at i:39269 original size:35 final size:35
Alignment explanation
Indices: 39223--39302 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
39213 AACACAACCA
*
39223 TCAATTACATTCTAAACC-CAAAAATCTAAAATACT
1 TCAATTACATTCTAAACCTC-AAAATCCAAAATACT
*
39258 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCTCAAAATCCAAAATACT
*
39293 TTAATTACAT
1 TCAATTACAT
39303 GCCCAACCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 40 0.98
36 1 0.02
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAAATCCAAAATACT
Found at i:39316 original size:35 final size:35
Alignment explanation
Indices: 39223--39318 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 35
39213 AACACAACCA
* * * * *
39223 TCAATTACATTCTAAACCCAAAAATCTAAAATACT
1 TCAATTACATGCCAAACCCCAAATTCCAAAATACT
* * *
39258 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATGCCAAACCCCAAATTCCAAAATACT
* *
39293 TTAATTACATGCCCAACCCCAAATTC
1 TCAATTACATGCCAAACCCCAAATTC
39319 ATAATCCATT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.29
Consensus pattern (35 bp):
TCAATTACATGCCAAACCCCAAATTCCAAAATACT
Found at i:39659 original size:143 final size:144
Alignment explanation
Indices: 39482--39759 Score: 450
Period size: 148 Copynumber: 1.9 Consensus size: 144
39472 ATCCAGTTTA
*
39482 TAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC-GAATTGAA
1 TAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCAGAATTGAA
* * *
39546 TTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATCATATTATAATATTATTTTATTATAA
66 TTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTATAA
39611 TCCAGGTTAATTTG
131 TCCAGGTTAATTTG
*
39625 TAAAATAATTGACTTGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGAAT
1 TAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC--A--GAAT
*
39690 TGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATT
62 TGAATTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATT
*
39755 CTAAT
127 ATAAT
39760 TTAAATAGTT
Statistics
Matches: 123, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
143 54 0.44
148 69 0.56
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (144 bp):
TAAAATAATTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCAGAATTGAA
TTTTCGAGTTTATGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTATAA
TCCAGGTTAATTTG
Found at i:43454 original size:15 final size:16
Alignment explanation
Indices: 43434--43463 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43424 CAAAATACAA
43434 TATTCCC-AGTAATCC
1 TATTCCCTAGTAATCC
43449 TATTCCCTAGTAATC
1 TATTCCCTAGTAATC
43464 TTTTATTCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.30, G:0.07, T:0.37
Consensus pattern (16 bp):
TATTCCCTAGTAATCC
Found at i:46416 original size:33 final size:33
Alignment explanation
Indices: 46379--46448 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
46369 TGCTTAAACA
*
46379 ATATTAGAATATAAAGCATTACCATATATGTTT
1 ATATTAGAATATAAAGCATTACCATATATATTT
46412 ATATTAGAATATAAAGCATTACCATATATATTT
1 ATATTAGAATATAAAGCATTACCATATATATTT
46445 ATAT
1 ATAT
46449 CTACAGTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (33 bp):
ATATTAGAATATAAAGCATTACCATATATATTT
Found at i:47245 original size:4 final size:4
Alignment explanation
Indices: 47236--47467 Score: 464
Period size: 4 Copynumber: 58.0 Consensus size: 4
47226 ATATAACATT
47236 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47284 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47332 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47380 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47428 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47468 AACCTGAATA
Statistics
Matches: 228, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 228 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:49077 original size:2 final size:2
Alignment explanation
Indices: 49070--49114 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
49060 AGCAGGCATT
49070 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
49112 GA G
1 GA G
49115 GAGTGTCTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52017 original size:35 final size:35
Alignment explanation
Indices: 51971--52046 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
51961 AAAATAGTCC
*
51971 TCAATTTCATTCTAAACCCCAATTTCC-AAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAAG-AAT
*
52006 TCAATTTCATTCTAAACCCTAAATTCCAAAAGAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAAGAAT
52041 TCAATT
1 TCAATT
52047 AAATTCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 34 0.89
36 4 0.11
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAAGAAT
Found at i:52586 original size:129 final size:130
Alignment explanation
Indices: 52443--52689 Score: 388
Period size: 129 Copynumber: 1.9 Consensus size: 130
52433 TATTTATATA
* * *
52443 ATCAATTTGATCCTAAATTAAATAGAATTTAATAAATTAATTATTTAAATAGGATCTAACATGTG
1 ATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAACAGGATCTAACATGTG
* * *
52508 TTAGCACATGATCATGACACGTG-TCATTGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTTAATGGTGACACATGTCACCACCTAATTATTTATATATGCT
* * *
52572 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAACAGGATCTAACATGTG
* *
52637 TTAACACATGATCATGATATGTGTTAATGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACGTGTTAATGGTGACACATGTCACCACCTAATTA
52690 GAAGAAAATT
Statistics
Matches: 106, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
129 79 0.75
130 27 0.25
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGATCCTAAATTAAATAAAATTTAATAAATTAATCATTTAAACAGGATCTAACATGTG
TTAACACATGATCATGACACGTGTTAATGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:52659 original size:23 final size:21
Alignment explanation
Indices: 52616--52663 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
52606 AATTAATCAT
52616 TTAACCAGGATCTGACATGTG
1 TTAACCAGGATCTGACATGTG
* *
52637 TTAACACATGATCATGATATGTG
1 TTAAC-CAGGATC-TGACATGTG
52660 TTAA
1 TTAA
52664 TGGTGACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 6 0.26
23 12 0.52
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (21 bp):
TTAACCAGGATCTGACATGTG
Found at i:53174 original size:16 final size:18
Alignment explanation
Indices: 53153--53185 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
53143 ATTTCTTATT
53153 AAAATA-AAAT-ATTCAA
1 AAAATATAAATGATTCAA
53169 AAAATATAAATGATTCA
1 AAAATATAAATGATTCA
53186 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAATATAAATGATTCAA
Found at i:53701 original size:2 final size:2
Alignment explanation
Indices: 53694--53746 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
53684 TTGCGATCCC
53694 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53736 TA TA TA TA TA T
1 TA TA TA TA TA T
53747 TGTTATATGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56577 original size:15 final size:15
Alignment explanation
Indices: 56559--56588 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56549 GATATTTAGT
*
56559 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
56574 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
56589 ATGTAAGGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.67, T:0.10
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:57923 original size:18 final size:18
Alignment explanation
Indices: 57896--57944 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
57886 AAAATTCAAT
57896 GCAT-GGGCGGCTAATTA
1 GCATGGGGCGGCTAATTA
57913 GCATGGGGCGGCTAATTA
1 GCATGGGGCGGCTAATTA
57931 GCATGGGGCGGCTA
1 GCATGGGGCGGCTA
57945 TTTTAGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 4 0.13
18 27 0.87
ACGTcount: A:0.20, C:0.18, G:0.41, T:0.20
Consensus pattern (18 bp):
GCATGGGGCGGCTAATTA
Found at i:60667 original size:21 final size:21
Alignment explanation
Indices: 60638--60685 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
60628 TTATCTTTGT
* *
60638 AGAATATAAACTACAAATAAA
1 AGAAGATAAACTACAAAGAAA
60659 AGAAGATAAACTACAAAGAAA
1 AGAAGATAAACTACAAAGAAA
60680 AGAAGA
1 AGAAGA
60686 AGATGGTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.67, C:0.08, G:0.12, T:0.12
Consensus pattern (21 bp):
AGAAGATAAACTACAAAGAAA
Found at i:65840 original size:20 final size:21
Alignment explanation
Indices: 65815--65856 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
65805 TTTTTACAAA
65815 TTATAATA-TTTTCTTTAAAT
1 TTATAATATTTTTCTTTAAAT
65835 TTATAATATTTTTCTTTAAAT
1 TTATAATATTTTTCTTTAAAT
65856 T
1 T
65857 ATTAACATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATAATATTTTTCTTTAAAT
Found at i:65858 original size:20 final size:19
Alignment explanation
Indices: 65812--65858 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
65802 TTGTTTTTAC
65812 AAATTATAATATTTTCTTT
1 AAATTATAATATTTTCTTT
65831 AAATTTATAATATTTTTCTTT
1 AAA-TTATAATA-TTTTCTTT
65852 AAATTAT
1 AAATTAT
65859 TAACATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 11 0.42
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATTATAATATTTTCTTT
Found at i:77689 original size:90 final size:91
Alignment explanation
Indices: 77535--77707 Score: 244
Period size: 90 Copynumber: 1.9 Consensus size: 91
77525 TTTTTCAAAG
* *
77535 TGATGCACCGATGCACCAATCCATGCATCAATGCACCATGGATTAAATTAAACATCGAATGCATT
1 TGATGCACCGATGCACCAAACCATGCATCAATGCACCATGGACTAAATTAAACATCGAATGCATT
77600 TTATGCATCGATGCACTCAGTGCGTT
66 TTATGCATCGATGCACTCAGTGCGTT
* * **
77626 TGATGCATCGATGCA-CAAACCATGCATCGATGCACTC-TGG-CTATTTTGAAACATCGAATGCA
1 TGATGCACCGATGCACCAAACCATGCATCAATGCAC-CATGGACTAAATT-AAACATCGAATGCA
*
77688 TTTTATGCATCGTTGCACTC
64 TTTTATGCATCGATGCACTC
77708 TTAGTGCATC
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
89 4 0.05
90 54 0.74
91 15 0.21
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (91 bp):
TGATGCACCGATGCACCAAACCATGCATCAATGCACCATGGACTAAATTAAACATCGAATGCATT
TTATGCATCGATGCACTCAGTGCGTT
Found at i:77696 original size:45 final size:44
Alignment explanation
Indices: 77584--77708 Score: 119
Period size: 45 Copynumber: 2.8 Consensus size: 44
77574 GGATTAAATT
*
77584 AAACATCGAATGCATTTTATGCATCGATGCACTCAGTGCGTTTG
1 AAACATCGAATGCATTTTATGCATCGATGCACTCTGTGCGTTTG
** **** *
77628 ATGCATCG-ATGCACAAACCATGCATCGATGCACTCTG-GCTATTTTG
1 AAACATCGAATG--CATTTTATGCATCGATGCACTCTGTGC--GTTTG
*
77674 AAACATCGAATGCATTTTATGCATCGTTGCACTCT
1 AAACATCGAATGCATTTTATGCATCGATGCACTCT
77709 TAGTGCATCG
Statistics
Matches: 61, Mismatches: 15, Indels: 9
0.72 0.18 0.11
Matches are distributed among these distances:
43 3 0.05
44 8 0.13
45 37 0.61
46 10 0.16
47 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
AAACATCGAATGCATTTTATGCATCGATGCACTCTGTGCGTTTG
Found at i:83584 original size:21 final size:22
Alignment explanation
Indices: 83538--83585 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
83528 GCACCTAACC
* * *
83538 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATACATCCATGAAG
83560 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATACATCCATGAAG
83581 GTGCA
1 GTGCA
83586 CTGATGCACG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATACATCCATGAAG
Found at i:83607 original size:23 final size:23
Alignment explanation
Indices: 83538--83618 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
83528 GCACCTAACC
*
83538 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
83560 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
*
83581 GTGCA-CTGATGCACGCCTTGAAT
1 GTGCATC-GATGCACACCTTGAAT
83604 GTGCATCGATGCACA
1 GTGCATCGATGCACA
83619 AGGTCATGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 2 0.04
21 14 0.30
22 10 0.21
23 20 0.43
24 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:83635 original size:43 final size:42
Alignment explanation
Indices: 83538--83636 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 42
83528 GCACCTAACC
* * *
83538 GTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGAA
1 GTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGAA
* *
83580 GGTGCA-CTGATGCACGCCTTGAATGTGCATCGATGCACAAGGTCA
1 -GTGCATC-GATGCA-GCCTTGAATGTGCATCGATACACAAGG-AA
83625 -TGCATCGATGCA
1 GTGCATCGATGCA
83637 TCCGTCGGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
42 1 0.02
43 21 0.45
44 24 0.51
45 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.24
Consensus pattern (42 bp):
GTGCATCGATGCAGCCTTGAATGTGCATCGATACACAAGGAA
Found at i:86241 original size:19 final size:19
Alignment explanation
Indices: 86217--86268 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
86207 AATGTATTTT
*
86217 ATGCATCGATGCACATACC
1 ATGCATCGATGCACAAACC
86236 ATGCATCGATGCACAAACC
1 ATGCATCGATGCACAAACC
86255 ATGCATCGATGCAC
1 ATGCATCGATGCAC
86269 TTTGGCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACAAACC
Found at i:86292 original size:83 final size:84
Alignment explanation
Indices: 86152--86313 Score: 220
Period size: 83 Copynumber: 1.9 Consensus size: 84
86142 TTTCAAAGTG
* * *
86152 ATGCACCGATGCACCAATCCATGCATCGATGCACCATGGATTAAATTGAACATCGAATGTATTTT
1 ATGCACCGATGCACCAAACCATGCATCGATGCACCATGGACTAAATTGAACATCGAATGCATTTT
86217 ATGCATCGATGCACATACC
66 ATGCATCGATGCACATACC
* ** **
86236 ATGCATCGATGCA-CAAACCATGCATCGATGCACTTTGG-CTATTTTGAAACATCGAATGCATTT
1 ATGCACCGATGCACCAAACCATGCATCGATGCACCATGGACTAAATTG-AACATCGAATGCATTT
*
86299 TATGCATCGTTGCAC
65 TATGCATCGATGCAC
86314 TCTTAGTGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
82 5 0.07
83 51 0.75
84 12 0.18
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (84 bp):
ATGCACCGATGCACCAAACCATGCATCGATGCACCATGGACTAAATTGAACATCGAATGCATTTT
ATGCATCGATGCACATACC
Found at i:101033 original size:14 final size:14
Alignment explanation
Indices: 101014--101040 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
101004 CCAGCATTAT
101014 CCTGTCCACTATAC
1 CCTGTCCACTATAC
101028 CCTGTCCACTATA
1 CCTGTCCACTATA
101041 TAGTACATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.41, G:0.07, T:0.30
Consensus pattern (14 bp):
CCTGTCCACTATAC
Done.