Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006454.1 Hibiscus syriacus cultivar Beakdansim tig00015635_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: 78992
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:2061 original size:31 final size:32
Alignment explanation
Indices: 1988--2080 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 32
1978 CCCGAATGAC
* * *
1988 CTATCCATATATTCC-GAAGAACATAGGTAATC
1 CTATCCATAT-GTCCTGAAGGACATAGGTAATA
*
2020 CTGTCCATATGTCCTGAAGGACATAGGTAA-A
1 CTATCCATATGTCCTGAAGGACATAGGTAATA
*
2051 CTATCCATATGT-CTCGAAAGACATAGGTAA
1 CTATCCATATGTCCT-GAAGGACATAGGTAA
2081 CCCTTGACTC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
30 2 0.04
31 28 0.53
32 23 0.43
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (32 bp):
CTATCCATATGTCCTGAAGGACATAGGTAATA
Found at i:2638 original size:18 final size:18
Alignment explanation
Indices: 2617--2658 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2607 AACATGTCAA
2617 CACATATAATCAT-GCATT
1 CACATA-AATCATAGCATT
* *
2635 CACACAAATCATATCATT
1 CACATAAATCATAGCATT
2653 CACATA
1 CACATA
2659 CTTATAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (18 bp):
CACATAAATCATAGCATT
Found at i:10163 original size:15 final size:15
Alignment explanation
Indices: 10143--10171 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10133 AAATTTTTTG
10143 TTTATAATATTAATA
1 TTTATAATATTAATA
10158 TTTATAATATTAAT
1 TTTATAATATTAAT
10172 CATAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATAATATTAATA
Found at i:10644 original size:30 final size:30
Alignment explanation
Indices: 10602--10667 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
10592 AATGATATTT
* *
10602 TATCTAATGTTTAGGGTTAAAGTAGCATTC
1 TATCTAATGTTTAGAGTCAAAGTAGCATTC
* *
10632 TATCTGAA-GTTTAGAGTCAAATTAGTATTC
1 TATCT-AATGTTTAGAGTCAAAGTAGCATTC
10662 TATCTA
1 TATCTA
10668 CAATTTAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 28 0.90
31 2 0.06
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (30 bp):
TATCTAATGTTTAGAGTCAAAGTAGCATTC
Found at i:10675 original size:30 final size:29
Alignment explanation
Indices: 10628--10699 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
10618 TTAAAGTAGC
*
10628 ATTCTATCTGAAGTTTA-GAGTCAAATTAGT
1 ATTCTATCT-AAATTTAGGA-TCAAATTAGT
*
10658 ATTCTATCTACAATTTAGGATCAAGTTAGT
1 ATTCTATCTA-AATTTAGGATCAAATTAGT
10688 ATTCTATCTAAA
1 ATTCTATCTAAA
10700 GTTCAAGGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 3 0.08
30 33 0.87
31 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (29 bp):
ATTCTATCTAAATTTAGGATCAAATTAGT
Found at i:11090 original size:30 final size:29
Alignment explanation
Indices: 11054--11119 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 29
11044 TAAAGTTTGG
*
11054 AAAAGTTTAAGGACTAAAAGGGTAACTTT
1 AAAAGTTTAAGGACCAAAAGGGTAACTTT
* *
11083 CAAAAGTTTAGGGACCAAAAGTGTAACTTT
1 -AAAAGTTTAAGGACCAAAAGGGTAACTTT
11113 AAAAGTT
1 AAAAGTT
11120 ATGTATTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 7 0.21
30 26 0.79
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (29 bp):
AAAAGTTTAAGGACCAAAAGGGTAACTTT
Found at i:16188 original size:30 final size:30
Alignment explanation
Indices: 16140--16206 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
16130 TAAAGTTTGA
***
16140 AAAAGTTTAAGGTTCAAAAGGGTAATTTTC
1 AAAAGTTTAAGAACCAAAAGGGTAATTTTC
** *
16170 AAAAGTTTAAGAACCAAAAGTTTACTTTTC
1 AAAAGTTTAAGAACCAAAAGGGTAATTTTC
16200 AAAAGTT
1 AAAAGTT
16207 ATGTATTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (30 bp):
AAAAGTTTAAGAACCAAAAGGGTAATTTTC
Found at i:17340 original size:19 final size:19
Alignment explanation
Indices: 17312--17409 Score: 101
Period size: 19 Copynumber: 5.2 Consensus size: 19
17302 GATATAAACG
17312 TGAAAGTAAGCTATGAATT
1 TGAAAGTAAGCTATGAATT
* * *
17331 TGAAATTAAGCTATAAATC
1 TGAAAGTAAGCTATGAATT
*
17350 CGAAA-TAAAGCTATGAATT
1 TGAAAGT-AAGCTATGAATT
* *
17369 TGAAAGTAAGTTATGAA-C
1 TGAAAGTAAGCTATGAATT
*
17387 TGAGAAGTAAGTTATGAATT
1 TGA-AAGTAAGCTATGAATT
17407 TGA
1 TGA
17410 GAACGAATTC
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.06
19 57 0.88
20 4 0.06
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (19 bp):
TGAAAGTAAGCTATGAATT
Found at i:17403 original size:38 final size:38
Alignment explanation
Indices: 17313--17409 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 38
17303 ATATAAACGT
*
17313 GAAAGTAAGCTATGAATTTGAAATTAAGCTATAAATCC
1 GAAAGTAAGCTATGAATTTGAAAGTAAGCTATAAATCC
* * *
17351 GAAA-TAAAGCTATGAATTTGAAAGTAAGTTATGAA-CT
1 GAAAGT-AAGCTATGAATTTGAAAGTAAGCTATAAATCC
*
17388 GAGAAGTAAGTTATGAATTTGA
1 GA-AAGTAAGCTATGAATTTGA
17410 GAACGAATTC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
37 4 0.08
38 46 0.90
39 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (38 bp):
GAAAGTAAGCTATGAATTTGAAAGTAAGCTATAAATCC
Found at i:19409 original size:129 final size:129
Alignment explanation
Indices: 19253--19549 Score: 504
Period size: 129 Copynumber: 2.3 Consensus size: 129
19243 CTAACTTAAT
* * *
19253 ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAACTTTTAAATGGCGATCAATTTATCATA
1 ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAACTATTAAATGGCGATAAATTTAACATA
* *
19318 AATATCTATTTGAGTAGAACTTTATCAAATCATTTACCTAACTCAGTGATTTAACGTTTGATTA
66 AATATCTATTTGAGTAGAACTTTATCAAATCATTTACCTAACTCAGTGATCTAACGTTTAATTA
* *
19382 ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAACTATTAAATGGGGGTAAATTTAACATA
1 ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAACTATTAAATGGCGATAAATTTAACATA
* *
19447 AATATCTATTTGAGTATAACTTTATCAAATCATTTACCTAACTCAGTGATCTAACTTTTAATTA
66 AATATCTATTTGAGTAGAACTTTATCAAATCATTTACCTAACTCAGTGATCTAACGTTTAATTA
*
19511 ATATATTATTGAGAGCTATAGAGGAAGTAAAAGTATAAC
1 ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAAC
19550 CTGCGGAAGC
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 158 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (129 bp):
ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAACTATTAAATGGCGATAAATTTAACATA
AATATCTATTTGAGTAGAACTTTATCAAATCATTTACCTAACTCAGTGATCTAACGTTTAATTA
Found at i:20784 original size:21 final size:21
Alignment explanation
Indices: 20758--20816 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
20748 ATTATCCAAT
*
20758 AAACTTGACATCCATAACAAA
1 AAACTTGAAATCCATAACAAA
*
20779 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAA
20800 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
20817 TAATAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAA
Found at i:32579 original size:28 final size:28
Alignment explanation
Indices: 32548--32610 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
32538 ACAAAAATTT
* *
32548 ATAAATATTAAAA-AATACAATTAATATG
1 ATAAACATAAAAATAATACAA-TAATATG
* *
32576 ATAAACATAAAAATAATATAATAATATT
1 ATAAACATAAAAATAATACAATAATATG
32604 ATAAACA
1 ATAAACA
32611 AAATTTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (28 bp):
ATAAACATAAAAATAATACAATAATATG
Found at i:33430 original size:30 final size:30
Alignment explanation
Indices: 33394--33460 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
33384 TAAAGTTTGG
*
33394 AAAAGTTTAAGGACCAAAAGAGTAACTTTC
1 AAAAGTTTAAGGACCAAAAGAGTAACTTTA
* *
33424 AAAAGTTTAGGGACCAAAAGTGTAACTTTA
1 AAAAGTTTAAGGACCAAAAGAGTAACTTTA
33454 AAAAGTT
1 AAAAGTT
33461 ATGTATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (30 bp):
AAAAGTTTAAGGACCAAAAGAGTAACTTTA
Found at i:38197 original size:30 final size:30
Alignment explanation
Indices: 38163--38229 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
38153 TAAAGTTTGA
***
38163 AAAAGTTTAAGTTTCAAAAGGGTAATTTTC
1 AAAAGTTTAAGAACCAAAAGGGTAATTTTC
**
38193 AAAAGTTTAAGAACCAAAAGTTTAATTTTC
1 AAAAGTTTAAGAACCAAAAGGGTAATTTTC
38223 AAAAGTT
1 AAAAGTT
38230 ATGTATTCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.34
Consensus pattern (30 bp):
AAAAGTTTAAGAACCAAAAGGGTAATTTTC
Found at i:38225 original size:15 final size:15
Alignment explanation
Indices: 38163--38229 Score: 71
Period size: 15 Copynumber: 4.5 Consensus size: 15
38153 TAAAGTTTGA
38163 AAAAGTTTAAGTTTC
1 AAAAGTTTAAGTTTC
** *
38178 AAAAGGGTAATTTTC
1 AAAAGTTTAAGTTTC
***
38193 AAAAGTTTAAGAACC
1 AAAAGTTTAAGTTTC
*
38208 AAAAGTTTAATTTTC
1 AAAAGTTTAAGTTTC
38223 AAAAGTT
1 AAAAGTT
38230 ATGTATTCGT
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.34
Consensus pattern (15 bp):
AAAAGTTTAAGTTTC
Found at i:39165 original size:31 final size:32
Alignment explanation
Indices: 39092--39184 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 32
39082 CCCGAATGAC
* * *
39092 CTATCCATATATTCC-GAAGAACATAGGTAATC
1 CTATCCATAT-GTCCTGAAGGACATAGGTAATA
*
39124 CTGTCCATATGTCCTGAAGGACATAGGTAA-A
1 CTATCCATATGTCCTGAAGGACATAGGTAATA
*
39155 CTATCCATATGT-CTCGAAAGACATAGGTAA
1 CTATCCATATGTCCT-GAAGGACATAGGTAA
39185 CCCTTGACTC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
30 2 0.04
31 28 0.53
32 23 0.43
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (32 bp):
CTATCCATATGTCCTGAAGGACATAGGTAATA
Found at i:39744 original size:18 final size:18
Alignment explanation
Indices: 39723--39764 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
39713 AACATGTCAA
39723 CACATATAATCAT-GCATT
1 CACATA-AATCATAGCATT
* *
39741 CACACAAATCATATCATT
1 CACATAAATCATAGCATT
39759 CACATA
1 CACATA
39765 CTTATAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (18 bp):
CACATAAATCATAGCATT
Found at i:47284 original size:15 final size:15
Alignment explanation
Indices: 47264--47292 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47254 AAATTTTTTG
47264 TTTATAATATTAATA
1 TTTATAATATTAATA
47279 TTTATAATATTAAT
1 TTTATAATATTAAT
47293 CATAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATAATATTAATA
Found at i:47762 original size:30 final size:30
Alignment explanation
Indices: 47720--47785 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
47710 AATGATATTT
* *
47720 TATCTAATGTTTAGGGTTAAAGTAGCATTC
1 TATCTAATGTTTAGAGTCAAAGTAGCATTC
* *
47750 TATCTGAA-GTTTAGAGTCAAATTAGTATTC
1 TATCT-AATGTTTAGAGTCAAAGTAGCATTC
47780 TATCTA
1 TATCTA
47786 CAATTTAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 28 0.90
31 2 0.06
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (30 bp):
TATCTAATGTTTAGAGTCAAAGTAGCATTC
Found at i:47793 original size:30 final size:29
Alignment explanation
Indices: 47746--47817 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
47736 TTAAAGTAGC
*
47746 ATTCTATCTGAAGTTTA-GAGTCAAATTAGT
1 ATTCTATCT-AAATTTAGGA-TCAAATTAGT
*
47776 ATTCTATCTACAATTTAGGATCAAGTTAGT
1 ATTCTATCTA-AATTTAGGATCAAATTAGT
47806 ATTCTATCTAAA
1 ATTCTATCTAAA
47818 GTTCAAGGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 3 0.08
30 33 0.87
31 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (29 bp):
ATTCTATCTAAATTTAGGATCAAATTAGT
Found at i:48208 original size:30 final size:30
Alignment explanation
Indices: 48172--48238 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
48162 TAAAGTTTGG
*
48172 AAAAGTTTAAGGACTAAAAGGGTAACTTTC
1 AAAAGTTTAAGGACCAAAAGGGTAACTTTC
* *
48202 AAAAGTTTAGGGACCAAAAGTGTAACTTTC
1 AAAAGTTTAAGGACCAAAAGGGTAACTTTC
48232 AAAAGTT
1 AAAAGTT
48239 ATGTATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.27
Consensus pattern (30 bp):
AAAAGTTTAAGGACCAAAAGGGTAACTTTC
Found at i:53308 original size:30 final size:30
Alignment explanation
Indices: 53260--53326 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
53250 TAAAGTTTGA
***
53260 AAAAGTTTAAGGTTCAAAAGGGTAATTTTC
1 AAAAGTTTAAGAACCAAAAGGGTAATTTTC
** *
53290 AAAAGTTTAAGAACCAAAAGTTTACTTTTC
1 AAAAGTTTAAGAACCAAAAGGGTAATTTTC
53320 AAAAGTT
1 AAAAGTT
53327 ATGTATTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (30 bp):
AAAAGTTTAAGAACCAAAAGGGTAATTTTC
Found at i:54460 original size:19 final size:19
Alignment explanation
Indices: 54432--54529 Score: 101
Period size: 19 Copynumber: 5.2 Consensus size: 19
54422 GATATAAACG
54432 TGAAAGTAAGCTATGAATT
1 TGAAAGTAAGCTATGAATT
* * *
54451 TGAAATTAAGCTATAAATC
1 TGAAAGTAAGCTATGAATT
*
54470 CGAAA-TAAAGCTATGAATT
1 TGAAAGT-AAGCTATGAATT
* *
54489 TGAAAGTAAGTTATGAA-C
1 TGAAAGTAAGCTATGAATT
*
54507 TGAGAAGTAAGTTATGAATT
1 TGA-AAGTAAGCTATGAATT
54527 TGA
1 TGA
54530 GAACGAATTC
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.06
19 57 0.88
20 4 0.06
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (19 bp):
TGAAAGTAAGCTATGAATT
Found at i:54523 original size:38 final size:38
Alignment explanation
Indices: 54433--54529 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 38
54423 ATATAAACGT
*
54433 GAAAGTAAGCTATGAATTTGAAATTAAGCTATAAATCC
1 GAAAGTAAGCTATGAATTTGAAAGTAAGCTATAAATCC
* * *
54471 GAAA-TAAAGCTATGAATTTGAAAGTAAGTTATGAA-CT
1 GAAAGT-AAGCTATGAATTTGAAAGTAAGCTATAAATCC
*
54508 GAGAAGTAAGTTATGAATTTGA
1 GA-AAGTAAGCTATGAATTTGA
54530 GAACGAATTC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
37 4 0.08
38 46 0.90
39 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (38 bp):
GAAAGTAAGCTATGAATTTGAAAGTAAGCTATAAATCC
Found at i:56604 original size:129 final size:129
Alignment explanation
Indices: 56374--56670 Score: 504
Period size: 129 Copynumber: 2.3 Consensus size: 129
56364 CTAACTTAAT
* * *
56374 ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAACTTTTAAATGGCGATCAATTTATCATA
1 ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAACTATTAAATGGCGATAAATTTAACATA
* *
56439 AATATCTATTTGAGTAGAACTTTATCAAATCATTTACCTAACTCAGTGATTTAACGTTTGATTA
66 AATATCTATTTGAGTAGAACTTTATCAAATCATTTACCTAACTCAGTGATCTAACGTTTAATTA
* *
56503 ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAACTATTAAATGGGGGTAAATTTAACATA
1 ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAACTATTAAATGGCGATAAATTTAACATA
* *
56568 AATATCTATTTGAGTATAACTTTATCAAATCATTTACCTAACTCAGTGATCTAACTTTTAATTA
66 AATATCTATTTGAGTAGAACTTTATCAAATCATTTACCTAACTCAGTGATCTAACGTTTAATTA
*
56632 ATATATTATTGAGAGCTATAGAGGAAGTAAAAGTATAAC
1 ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAAC
56671 CTGCGGAAGC
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 158 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (129 bp):
ATATATTATTGAGAGCTATAGAGGAAGCAAAAGTATAACTATTAAATGGCGATAAATTTAACATA
AATATCTATTTGAGTAGAACTTTATCAAATCATTTACCTAACTCAGTGATCTAACGTTTAATTA
Found at i:56918 original size:20 final size:21
Alignment explanation
Indices: 56878--56919 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
56868 TATTTTGATA
* *
56878 AAAACAATAATATATATAATT
1 AAAACAATAAAATACATAATT
56899 AAAACAA-AAAATACATAATT
1 AAAACAATAAAATACATAATT
56919 A
1 A
56920 GGGAGCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAACAATAAAATACATAATT
Found at i:57906 original size:21 final size:21
Alignment explanation
Indices: 57880--57938 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
57870 ATTATCCAAT
*
57880 AAACTTGACATCCATAACAAA
1 AAACTTGAAATCCATAACAAA
*
57901 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAA
57922 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
57939 TAATAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAA
Found at i:69699 original size:28 final size:28
Alignment explanation
Indices: 69668--69730 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
69658 ACAAAAATTT
* *
69668 ATAAATATTAAAA-AATACAATTAATATG
1 ATAAACATAAAAATAATACAA-TAATATG
* *
69696 ATAAACATAAAAATAATATAATAATATT
1 ATAAACATAAAAATAATACAATAATATG
69724 ATAAACA
1 ATAAACA
69731 AAATTTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (28 bp):
ATAAACATAAAAATAATACAATAATATG
Found at i:70550 original size:30 final size:30
Alignment explanation
Indices: 70514--70580 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
70504 TAAAGTTTGG
*
70514 AAAAGTTTAAGGACCAAAAGAGTAACTTTC
1 AAAAGTTTAAGGACCAAAAGAGTAACTTTA
* *
70544 AAAAGTTTAGGGACCAAAAGTGTAACTTTA
1 AAAAGTTTAAGGACCAAAAGAGTAACTTTA
70574 AAAAGTT
1 AAAAGTT
70581 ATGTATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (30 bp):
AAAAGTTTAAGGACCAAAAGAGTAACTTTA
Found at i:75330 original size:15 final size:15
Alignment explanation
Indices: 75269--75333 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 15
75259 TAAAGTTTGA
75269 AAAAG-TTAAGTTTC
1 AAAAGTTTAAGTTTC
** *
75283 AAAAGGGTAATTTTC
1 AAAAGTTTAAGTTTC
***
75298 AAAAGTTTAAGAACC
1 AAAAGTTTAAGTTTC
*
75313 AAAAGTTTAATTTTC
1 AAAAGTTTAAGTTTC
75328 AAAAGT
1 AAAAGT
75334 ATGTATTCGT
Statistics
Matches: 38, Mismatches: 12, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
14 5 0.13
15 33 0.87
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (15 bp):
AAAAGTTTAAGTTTC
Found at i:76259 original size:31 final size:32
Alignment explanation
Indices: 76186--76278 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 32
76176 CCCGAATGAC
* * *
76186 CTATCCATATATTCC-GAAGAACATAGGTAATC
1 CTATCCATAT-GTCCTGAAGGACATAGGTAATA
*
76218 CTGTCCATATGTCCTGAAGGACATAGGTAA-A
1 CTATCCATATGTCCTGAAGGACATAGGTAATA
*
76249 CTATCCATATGT-CTCGAAAGACATAGGTAA
1 CTATCCATATGTCCT-GAAGGACATAGGTAA
76279 CCCTTGACTC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
30 2 0.04
31 28 0.53
32 23 0.43
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (32 bp):
CTATCCATATGTCCTGAAGGACATAGGTAATA
Done.