Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004833.1 Hibiscus syriacus cultivar Beakdansim tig00010887_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: 78485
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7275 original size:13 final size:13
Alignment explanation
Indices: 7259--7305 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
7249 AAATTGATAT
7259 TAAATTAATAATA
1 TAAATTAATAATA
*
7272 TAAAATAATAAATTA
1 TAAATTAAT-AA-TA
7287 TCAAATTAATAATA
1 T-AAATTAATAATA
7301 -AAATT
1 TAAATT
7306 TTAAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 5 0.17
13 8 0.28
14 4 0.14
15 5 0.17
16 7 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAATTAATAATA
Found at i:7321 original size:29 final size:30
Alignment explanation
Indices: 7244--7324 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
7234 ATTCCTCAAT
*
7244 ATTTAAAATTGATATTAAATTAATAATATAAA
1 ATTTTAAATT-AT-TTAAATTAATAATATAAA
** *
7276 ATAATAAATTA-TCAAATTAAT-A-ATAAA
1 ATTTTAAATTATTTAAATTAATAATATAAA
7303 ATTTTAAATTATTTTAAATTAA
1 ATTTTAAATTA-TTTAAATTAA
7325 AATGAAGACC
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
27 14 0.35
28 1 0.03
29 17 0.43
31 1 0.03
32 7 0.17
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (30 bp):
ATTTTAAATTATTTAAATTAATAATATAAA
Found at i:10367 original size:11 final size:11
Alignment explanation
Indices: 10351--10378 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
10341 CAAGATATTT
10351 AGTTGCAATTA
1 AGTTGCAATTA
10362 AGTTGCAATTA
1 AGTTGCAATTA
10373 AGTTGC
1 AGTTGC
10379 TGTCACTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (11 bp):
AGTTGCAATTA
Found at i:14686 original size:35 final size:35
Alignment explanation
Indices: 14568--14707 Score: 172
Period size: 36 Copynumber: 3.9 Consensus size: 35
14558 TGAATAAGAA
14568 GAACGAAAGGAAGCATCAACACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCAACACTTTCGATTC-AAGT
* * * * *
14604 GGACGGAAGGAAGCATCGACACTTTAGATTCAAGAA
1 GAACGAAAGGAAGCATCAACACTTTCGATTCAAG-T
**
14640 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCAACACTTTCGATTCAAGT
* * *
14675 GAACGGAAGGAAGCGTCAGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCAACACTTTCGATTCAA
14708 TTGTTCATCT
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
35 33 0.37
36 57 0.63
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCAACACTTTCGATTCAAGT
Found at i:14756 original size:3 final size:3
Alignment explanation
Indices: 14743--14788 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
14733 GCTAAGATGT
14743 AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
14789 TAGAGGGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:15397 original size:19 final size:19
Alignment explanation
Indices: 15373--15409 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
15363 TAGTTAGCAG
15373 AGGTTGTTAAAGTCAGTTT
1 AGGTTGTTAAAGTCAGTTT
15392 AGGTTGTTAAAGTCAGTT
1 AGGTTGTTAAAGTCAGTT
15410 AAGGATAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (19 bp):
AGGTTGTTAAAGTCAGTTT
Found at i:15849 original size:23 final size:24
Alignment explanation
Indices: 15812--15857 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
15802 CTCGAATGTT
*
15812 TTTTTTAAATTATATTTTTATTTTA
1 TTTTTTAAA-TATATTTTAATTTTA
15837 TTTTTTAAA-ATATTTTAATTT
1 TTTTTTAAATATATTTTAATTT
15858 CAACATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
25 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTTAAATATATTTTAATTTTA
Found at i:20090 original size:21 final size:21
Alignment explanation
Indices: 20064--20105 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20054 TTATCACAAA
20064 TTTGAGCCCATCATTCATGTT
1 TTTGAGCCCATCATTCATGTT
*
20085 TTTGAGCCCATCATTCGTGTT
1 TTTGAGCCCATCATTCATGTT
20106 CTTGCAGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (21 bp):
TTTGAGCCCATCATTCATGTT
Found at i:22131 original size:123 final size:118
Alignment explanation
Indices: 21912--22155 Score: 346
Period size: 123 Copynumber: 2.0 Consensus size: 118
21902 ACAATGCAAG
* * *
21912 TCCTGATCCGTCTCAAGAATCGCCTGATGATCAGATTAAGTCTTCGGGAAGTGAAGCAGTTGAAG
1 TCCTGATCCCTCTCAAGAATCGACTGATAATCAGATTAAGTCTTCGGGAAGTGAAGCAGTTGAAG
*
21977 AAAAAGAAAATCAATCTGAGGATACCAAGGAAGAAGTGCAGATAGAGACACCATTTTC
66 --AAAGAAAATCAATCTGAGGATACCAAGGAAG-A-T-CAGATAGAGACACCAGTTTC
*
22035 TCCTGATCCCTCTCAAGAATCGACTGATAATCAGATTAAGTCTTCTGGAAGTGAAGCAGTTGAAG
1 TCCTGATCCCTCTCAAGAATCGACTGATAATCAGATTAAGTCTTCGGGAAGTGAAGCAGTTGAAG
* *
22100 -AAGAGAATCCATCTGAGGATACCAAGGAGGAAGATCAGATAGAGACACCAGTTTC
66 AAAGAAAATCAATCTGAGGATACC-A--AGGAAGATCAGATAGAGACACCAGTTTC
22155 T
1 T
22156 GAGGGCGAAA
Statistics
Matches: 111, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
120 41 0.37
121 2 0.02
122 1 0.01
123 67 0.60
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (118 bp):
TCCTGATCCCTCTCAAGAATCGACTGATAATCAGATTAAGTCTTCGGGAAGTGAAGCAGTTGAAG
AAAGAAAATCAATCTGAGGATACCAAGGAAGATCAGATAGAGACACCAGTTTC
Found at i:29497 original size:23 final size:23
Alignment explanation
Indices: 29471--29525 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
29461 CTGAGGCTAT
* *
29471 CCGAGCGAGCTATGCGAGGTCAG
1 CCGAGCAAGCTATGCGAGGGCAG
*
29494 CCGAGCAAGCTATGCGAGGGCAT
1 CCGAGCAAGCTATGCGAGGGCAG
29517 CCGAGCAAG
1 CCGAGCAAG
29526 GGTAGGTCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.36, T:0.11
Consensus pattern (23 bp):
CCGAGCAAGCTATGCGAGGGCAG
Found at i:31362 original size:20 final size:20
Alignment explanation
Indices: 31305--31368 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
31295 TATTCTCTGG
*
31305 TAATCTTTTATTCTCAATGA
1 TAATCTTTTATTCTCACTGA
*
31325 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCTCACTGA
*
31345 TAATCTTTTATTCTCACTAA
1 TAATCTTTTATTCTCACTGA
31365 TAAT
1 TAAT
31369 TTTACATTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.30, C:0.19, G:0.03, T:0.48
Consensus pattern (20 bp):
TAATCTTTTATTCTCACTGA
Found at i:45004 original size:32 final size:30
Alignment explanation
Indices: 44928--45004 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 30
44918 TAACAATCTT
* * *
44928 TCAAA-TATTATAAAATAGTTATTAAAATT
1 TCAAATTATTATAAAATAATCATTAAAATA
* *
44957 TTAAATAATTATAAAATAATCATTAAAAGATA
1 TCAAATTATTATAAAATAATCATT-AAA-ATA
44989 TCAAATTATTATAAAA
1 TCAAATTATTATAAAA
45005 CATTTTCTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 4 0.11
30 15 0.39
31 3 0.08
32 16 0.42
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (30 bp):
TCAAATTATTATAAAATAATCATTAAAATA
Found at i:46091 original size:12 final size:12
Alignment explanation
Indices: 46074--46109 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
46064 ATAACTAATA
*
46074 ATATTAATTATT
1 ATATTAAATATT
*
46086 ATATTAAATAAT
1 ATATTAAATATT
46098 ATATTAAATATT
1 ATATTAAATATT
46110 TATGTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATTAAATATT
Found at i:49116 original size:8 final size:8
Alignment explanation
Indices: 49103--49143 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
49093 CTCATTTTCA
49103 GAGAATTT
1 GAGAATTT
49111 GAGAATTT
1 GAGAATTT
*
49119 -AGAGTTT
1 GAGAATTT
*
49126 GGGAATTT
1 GAGAATTT
49134 GAGAATTT
1 GAGAATTT
49142 GA
1 GA
49144 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:49603 original size:128 final size:128
Alignment explanation
Indices: 49216--50097 Score: 1588
Period size: 128 Copynumber: 6.9 Consensus size: 128
49206 ATCGGAGTAT
49216 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
49281 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
49344 TATTCACATGAAGGCGCGTTCCC-AGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
49408 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
49471 TATTCACATGAAGGCGCGTTCCCGGGGGGGCACCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
49536 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
49599 TATTCACATAAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
49664 TTGCCCTAGTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
49727 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
49792 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
49855 TATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
49920 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * * * * * *
49983 -AGGGGACATGAAGGCGCGTTCCCGGGGGCGCACTTTTCATTATTTTGTCATAGAATATATTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
50047 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
50098 AATCAGGTAA
Statistics
Matches: 728, Mismatches: 24, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
127 127 0.17
128 601 0.83
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:50558 original size:33 final size:34
Alignment explanation
Indices: 50497--50596 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
50487 AAATTTAATG
*
50497 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
50531 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
50564 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
50597 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:51146 original size:21 final size:20
Alignment explanation
Indices: 51119--51188 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
51109 GGTATAAAAC
*
51119 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
51139 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
51160 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
51181 CCCTGCGG
1 -CCTGCGG
51189 ATATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:51218 original size:21 final size:21
Alignment explanation
Indices: 51192--51239 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
51182 CCTGCGGATA
*
51192 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
51213 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
51234 GGGCAT
1 TGGCAT
51240 GTATCCCTGC
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:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:53000 original size:17 final size:19
Alignment explanation
Indices: 52978--53021 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
52968 ATAATTATAT
52978 AAATATTAT-TTTA-ATAA
1 AAATATTATATTTACATAA
*
52995 AAATATAATATTTACATAA
1 AAATATTATATTTACATAA
*
53014 ATATATTA
1 AAATATTA
53022 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTATATTTACATAA
Found at i:53013 original size:19 final size:18
Alignment explanation
Indices: 52965--53052 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 18
52955 ATCTAAATAA
* *
52965 ATAATAATT-ATATAAAT
1 ATAATATTTAATAAAAAT
*
52982 ATTAT-TTTAATAAAAAT
1 ATAATATTTAATAAAAAT
*
52999 ATAATATTTACATAAATAT
1 ATAATATTTA-ATAAAAAT
53018 ATTAATA--T-A-AAAAAT
1 A-TAATATTTAATAAAAAT
53033 AATAACTATTTAA-AAAAAT
1 -ATAA-TATTTAATAAAAAT
53052 A
1 A
53053 CTAACATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
15 8 0.14
16 6 0.11
17 15 0.27
18 7 0.12
19 15 0.27
20 5 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATATTTAATAAAAAT
Found at i:53062 original size:34 final size:34
Alignment explanation
Indices: 52993--53064 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
52983 TTATTTTAAT
* * *
52993 AAAAATATAATATTTACATAAATATATTAATATA
1 AAAAATATAATATTTACATAAAAATACTAACATA
53027 AAAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAAAT-ATAA-TATTTACATAAAAATACTAACATA
53061 AAAA
1 AAAA
53065 TAAATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 22 0.67
35 5 0.15
36 6 0.18
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (34 bp):
AAAAATATAATATTTACATAAAAATACTAACATA
Found at i:60317 original size:16 final size:16
Alignment explanation
Indices: 60296--60334 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
60286 TTATCGTTTA
60296 ATATTATTTCTAAAAT
1 ATATTATTTCTAAAAT
60312 ATATTA--TCTAAAAT
1 ATATTATTTCTAAAAT
*
60326 GTATTATTT
1 ATATTATTT
60335 TCATGGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 13 0.65
16 7 0.35
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (16 bp):
ATATTATTTCTAAAAT
Found at i:60830 original size:14 final size:15
Alignment explanation
Indices: 60811--60844 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
60801 TTTTTGATGC
60811 AATTTATA-ATAATA
1 AATTTATATATAATA
*
60825 AATTTATATATAATT
1 AATTTATATATAATA
60840 AATTT
1 AATTT
60845 GATTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTATATATAATA
Found at i:63038 original size:22 final size:20
Alignment explanation
Indices: 63013--63052 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
63003 CTTTTTTTTC
63013 AATTATTCATTTATTGTGTATG
1 AATTA-TCATTT-TTGTGTATG
*
63035 AATTATGATTTTTGTGTA
1 AATTATCATTTTTGTGTA
63053 AATACAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 5 0.29
22 5 0.29
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.55
Consensus pattern (20 bp):
AATTATCATTTTTGTGTATG
Found at i:73825 original size:36 final size:34
Alignment explanation
Indices: 73779--73848 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
73769 AACTTTGAAA
*
73779 AATTTTCAAAGTTTAGTAAATGTTTCTTTGAAAAAT
1 AATTTTCAAAG-TTAGTAAATGTTT-GTTGAAAAAT
* *
73815 AATTTTCAAAGTTGGTAGATGTTTGTTGAAAAAT
1 AATTTTCAAAGTTAGTAAATGTTTGTTGAAAAAT
73849 GATAATGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 9 0.29
35 11 0.35
36 11 0.35
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (34 bp):
AATTTTCAAAGTTAGTAAATGTTTGTTGAAAAAT
Found at i:74736 original size:30 final size:30
Alignment explanation
Indices: 74695--74769 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
74685 GCAAGTGGTA
*
74695 GTTTAGATGCAGATGCACAACCTGTCCGTAT
1 GTTT-GATGCAGATGCACAACCTGTCCGCAT
74726 GTTTGATGCAGATGCACAACCTGTCCGCAT
1 GTTTGATGCAGATGCACAACCTGTCCGCAT
74756 GTTTGATGCAGATG
1 GTTTGATGCAGATG
74770 GTGGGGAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 39 0.91
31 4 0.09
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (30 bp):
GTTTGATGCAGATGCACAACCTGTCCGCAT
Done.