Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002981.1 Hibiscus syriacus cultivar Beakdansim tig00006165_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: 125403
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8789 original size:2 final size:2
Alignment explanation
Indices: 8782--8807 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8772 AAATAAATAA
8782 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8808 TCGAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9900 original size:11 final size:11
Alignment explanation
Indices: 9884--9912 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
9874 AAGACTGCAC
9884 TTGCTGCAACT
1 TTGCTGCAACT
9895 TTGCTGCAACT
1 TTGCTGCAACT
9906 TTGCTGC
1 TTGCTGC
9913 TACCGCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.38
Consensus pattern (11 bp):
TTGCTGCAACT
Found at i:12525 original size:31 final size:31
Alignment explanation
Indices: 12490--12550 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
12480 TTAAGGATCA
12490 TTTTGTAATACTTCAATAAAATTGAATAACT
1 TTTTGTAATACTTCAATAAAATTGAATAACT
* ** *
12521 TTTTGTAATATTTTGATAAATTTGAATAAC
1 TTTTGTAATACTTCAATAAAATTGAATAAC
12551 CATCTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (31 bp):
TTTTGTAATACTTCAATAAAATTGAATAACT
Found at i:18578 original size:24 final size:22
Alignment explanation
Indices: 18546--18664 Score: 66
Period size: 24 Copynumber: 5.2 Consensus size: 22
18536 CATTTAAATG
* *
18546 ATAAACGAACATAGATGAACGAAC
1 ATAAACGAACAT-G-TAAAAGAAC
18570 ATAAACGAACGGATGTAAAAGAAC
1 ATAAACGAAC--ATGTAAAAGAAC
**
18594 ATAAACGAACAAAATAAAAG-AC
1 ATAAACGAAC-ATGTAAAAGAAC
* *
18616 GTAAAACGAACACAGTAAATA-AAC
1 AT-AAACGAACA-TGTAAA-AGAAC
* *
18640 ATAAAC-AA-ACGTAAATGAAC
1 ATAAACGAACATGTAAAAGAAC
18660 ATAAA
1 ATAAA
18665 TGAAAATATA
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
20 13 0.17
21 1 0.01
22 6 0.08
23 24 0.31
24 31 0.40
25 1 0.01
26 2 0.03
ACGTcount: A:0.60, C:0.14, G:0.13, T:0.13
Consensus pattern (22 bp):
ATAAACGAACATGTAAAAGAAC
Found at i:18645 original size:23 final size:22
Alignment explanation
Indices: 18567--18645 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 22
18557 TAGATGAACG
**
18567 AACATAAACGAACGGATGTAAAA
1 AACATAAACGAACACA-GTAAAA
* *
18590 GAACATAAACGAACAAAATAAAA
1 -AACATAAACGAACACAGTAAAA
* *
18613 GACGTAAAACGAACACAGTAAATA
1 AACAT-AAACGAACACAGTAAA-A
18637 AACATAAAC
1 AACATAAAC
18646 AAACGTAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
22 3 0.07
23 23 0.52
24 18 0.41
ACGTcount: A:0.61, C:0.15, G:0.13, T:0.11
Consensus pattern (22 bp):
AACATAAACGAACACAGTAAAA
Found at i:18741 original size:20 final size:22
Alignment explanation
Indices: 18708--18747 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18698 AGGATTATAT
18708 TTTTATTTAATTGT-TTTAAGA
1 TTTTATTTAATTGTATTTAAGA
*
18729 TTTT-TTTATTTGTATTTAA
1 TTTTATTTAATTGTATTTAA
18748 AATTAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (22 bp):
TTTTATTTAATTGTATTTAAGA
Found at i:30271 original size:18 final size:17
Alignment explanation
Indices: 30235--30267 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30225 GGACCCAAAA
30235 AAAATATACAATTTTAC
1 AAAATATACAATTTTAC
*
30252 AAAATATATAATTTTA
1 AAAATATACAATTTTA
30268 ACAATCCGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATACAATTTTAC
Found at i:30660 original size:22 final size:22
Alignment explanation
Indices: 30635--30700 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
30625 TAGTATGGTT
30635 GGCAATGCATACAATTGAGGAC
1 GGCAATGCATACAATTGAGGAC
*
30657 GGCAATGCATTCAATTGAGGAC
1 GGCAATGCATACAATTGAGGAC
30679 GGCAATGCATACAATTGAGGAC
1 GGCAATGCATACAATTGAGGAC
30701 TTTGAGAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (22 bp):
GGCAATGCATACAATTGAGGAC
Found at i:30758 original size:21 final size:21
Alignment explanation
Indices: 30734--30783 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
30724 CCATTTCAAG
30734 TTTTTTACTGCACATTTAATA
1 TTTTTTACTGCACATTTAATA
30755 TTTTTTACTGCACATTTAATA
1 TTTTTTACTGCACATTTAATA
30776 TTTTTTAC
1 TTTTTTAC
30784 CCTCCAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTTTACTGCACATTTAATA
Found at i:35171 original size:20 final size:20
Alignment explanation
Indices: 35142--35181 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35132 TTTGGGAAAA
* *
35142 ATCGGTTTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
35162 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
35182 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:35241 original size:12 final size:12
Alignment explanation
Indices: 35226--35271 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
35216 CGGTTTTTTT
*
35226 ACCGGATAAAAA
1 ACCGGTTAAAAA
35238 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
35253 ACCGGTTAAAAA
1 ACCGGTTAAAAA
35265 ACCGGTT
1 ACCGGTT
35272 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:35253 original size:15 final size:13
Alignment explanation
Indices: 35232--35272 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
35222 TTTTACCGGA
35232 TAAAAAACCGGTT
1 TAAAAAACCGGTT
35245 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
35259 TAAAAAACCGGTT
1 TAAAAAACCGGTT
35272 T
1 T
35273 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:37661 original size:33 final size:33
Alignment explanation
Indices: 37611--37709 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
37601 TTTGTTTCAA
*
37611 TTATTGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
37643 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
37676 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
37709 T
1 T
37710 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 10 0.16
33 52 0.84
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:37738 original size:13 final size:13
Alignment explanation
Indices: 37695--37749 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
37685 TTGGAAGTAT
37695 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
37708 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
37722 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
37735 TTAAGTATTTGAA
1 TTAAGTATTTCAA
37748 TT
1 TT
37750 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:37971 original size:21 final size:21
Alignment explanation
Indices: 37945--38001 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
37935 TGGAGCGTGG
*
37945 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
37966 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
37987 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
38002 AAGTGTAAAA
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:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:38193 original size:15 final size:15
Alignment explanation
Indices: 38168--38222 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
38158 ATCTGGAATA
*
38168 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
38183 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
38198 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
38215 TTAAAACC
1 TTAAAACC
38223 AAAACCGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 20 0.61
17 13 0.39
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.44
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:38232 original size:21 final size:18
Alignment explanation
Indices: 38187--38220 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38177 GTTTTTTTAT
38187 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
38204 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
38221 CCAAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:38340 original size:15 final size:17
Alignment explanation
Indices: 38314--38345 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
38304 TTCTATAGGA
38314 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
38330 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
38346 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:42367 original size:31 final size:31
Alignment explanation
Indices: 42329--42398 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
42319 CTTTTAAAAC
42329 TTGCAATACAATCCCCCAACATTTA-TTCTAT
1 TTGCAATACAATCCCCCAACATTTAGTT-TAT
** * *
42360 TTGCAATATGATTCCCCAACATTTAGTTTGT
1 TTGCAATACAATCCCCCAACATTTAGTTTAT
42391 TTGCAATA
1 TTGCAATA
42399 TGATATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (31 bp):
TTGCAATACAATCCCCCAACATTTAGTTTAT
Found at i:42399 original size:31 final size:31
Alignment explanation
Indices: 42342--42402 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
42332 CAATACAATC
42342 CCCCAACATTTATTCTATTTGCAATATGATT
1 CCCCAACATTTATTCTATTTGCAATATGATT
*
42373 CCCCAACATTTAGTT-TGTTTGCAATATGAT
1 CCCCAACATTTA-TTCTATTTGCAATATGAT
42403 ATTTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (31 bp):
CCCCAACATTTATTCTATTTGCAATATGATT
Found at i:47415 original size:30 final size:30
Alignment explanation
Indices: 47379--47439 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
47369 TCTACGTCCA
47379 CTACCTTAGCTATCCACACTAAGAATTTTC
1 CTACCTTAGCTATCCACACTAAGAATTTTC
47409 CTACCTTAGCTATCCACACTAAGAATTTTC
1 CTACCTTAGCTATCCACACTAAGAATTTTC
47439 C
1 C
47440 ACAAAGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.33
Consensus pattern (30 bp):
CTACCTTAGCTATCCACACTAAGAATTTTC
Found at i:47614 original size:538 final size:538
Alignment explanation
Indices: 46911--47953 Score: 1944
Period size: 538 Copynumber: 1.9 Consensus size: 538
46901 AAATTATACA
*
46911 TTCAAATGCCAAATAAAGAATTTTAATTGTTTTATTTAAATGTTTATATTCACATCTGAATTTTT
1 TTCAAATGCCAAATAAAGAATTTTAATTGTTTTATTTAAATGTTTATATTCACAGCTGAATTTTT
46976 CATCTAGATAATAATTAAAACAAAATATAATAAAGATTGTATATCTCTTTATTTTACTGAAATGA
66 CATCTAGATAATAATTAAAACAAAATATAATAAAGATTGTATATCTCTTTATTTTACTGAAATGA
*
47041 TTTTAAATTTTATATCAAATTTAGGGTCACTTTCTTTTTCTCTAATCTAAGTTTTATCTCAATAT
131 TTTTAAATTTTATATCAAATTTAGGGTCACTTTCTTTTTCTCTAACCTAAGTTTTATCTCAATAT
47106 TTTTGTGTTATATTTTTCTTTTTCTTTAATTTTTTTAACTGATAGCGACACCAATTTTAATATTG
196 TTTTGTGTTATA-TTTTCTTTTTCTTTAATTTTTTTAACTGATAGCGACACCAATTTTAATATTG
47171 ATTTATGATCATCGGTGATCATAATTGTGGTTATAATTTTATAAG-TTTATATTTTATATTTTAT
260 ATTTATGATCATCGGTGATCATAATTGTGGTTATAATTTTATAAGTTTTATATTTTATATTTTAT
*
47235 ATGTTGAGTTAATCGATTGACGGAATCGACCAAGAGGTGGGTGAATTGGCAATAAAAATTTTGGT
325 ATGTTGAGTTAATCGATTGACGGAATCGACCAAAAGGTGGGTGAATTGGCAATAAAAATTTTGGT
*
47300 GGAAGCTTTTGCAGAAAATTGAAAGAAATTGCACAGCGATTTAGAGTGGTTCGACTTTCTCAACC
390 GGAAGCTTTTGCAGAAAATTGAAAGAAATTGCACAACGATTTAGAGTGGTTCGACTTTCTCAACC
47365 AAAGTCTACGTCCACTACCTTAGCTATCCACACTAAGAATTTTCCTACCTTAGCTATCCACACTA
455 AAAGTCTACGTCCACTACCTTAGCTATCCACACTAAGAATTTTCCTACCTTAGCTATCCACACTA
47430 AGAATTTTCCACAAAGTAT
520 AGAATTTTCCACAAAGTAT
47449 TTCAAATGCCAAATAAAGAATTTTAATTGTTTTATTTAAATGTTTATATTCACAGCTGAATTTTT
1 TTCAAATGCCAAATAAAGAATTTTAATTGTTTTATTTAAATGTTTATATTCACAGCTGAATTTTT
47514 CATCTAGATAATAATTAAAACAAAATATAATAAAGATTGTATATCTCTTTATTTTACTGAAATGA
66 CATCTAGATAATAATTAAAACAAAATATAATAAAGATTGTATATCTCTTTATTTTACTGAAATGA
*
47579 TTTTAAATTTTATATCAAATTTAGGGTTACTTTCTTTTTCTCTAACCTAAGTTTTATCTCAATAT
131 TTTTAAATTTTATATCAAATTTAGGGTCACTTTCTTTTTCTCTAACCTAAGTTTTATCTCAATAT
47644 TTTTGTGTTATATTTTCTTTTTCTTTAATTTTTTTAACTGATAGCGACACCAATTTTAATATTGA
196 TTTTGTGTTATATTTTCTTTTTCTTTAATTTTTTTAACTGATAGCGACACCAATTTTAATATTGA
47709 TTTATGATCATCGGTGATCATAATTGTGGTTATAATTTTATAAGTTTATATTTTATATTTTATAT
261 TTTATGATCATCGGTGATCATAATTGTGGTTATAATTTTATAAG------TTTTATATTTTATAT
* *
47774 TTTATATGTTGAGTTAATCGATTGACGGAATCGGCCAAAAGGTGGGTGAATTGGCAATAAAATTT
320 TTTATATGTTGAGTTAATCGATTGACGGAATCGACCAAAAGGTGGGTGAATTGGCAATAAAAATT
47839 TTGGTGGAAGCTTTTGCAGAAAATTGAAAGAAATTGCACAACGATTTAGAGTGGTTCGACTTTCT
385 TTGGTGGAAGCTTTTGCAGAAAATTGAAAGAAATTGCACAACGATTTAGAGTGGTTCGACTTTCT
*
47904 CAACCAAAGTCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCC
450 CAACCAAAGTCTACGTCCACTACCTTAGCTATCCACACTAAGAATTTTCC
47954 ACAAATTCAC
Statistics
Matches: 490, Mismatches: 8, Indels: 8
0.97 0.02 0.02
Matches are distributed among these distances:
537 97 0.20
538 204 0.42
544 189 0.39
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (538 bp):
TTCAAATGCCAAATAAAGAATTTTAATTGTTTTATTTAAATGTTTATATTCACAGCTGAATTTTT
CATCTAGATAATAATTAAAACAAAATATAATAAAGATTGTATATCTCTTTATTTTACTGAAATGA
TTTTAAATTTTATATCAAATTTAGGGTCACTTTCTTTTTCTCTAACCTAAGTTTTATCTCAATAT
TTTTGTGTTATATTTTCTTTTTCTTTAATTTTTTTAACTGATAGCGACACCAATTTTAATATTGA
TTTATGATCATCGGTGATCATAATTGTGGTTATAATTTTATAAGTTTTATATTTTATATTTTATA
TGTTGAGTTAATCGATTGACGGAATCGACCAAAAGGTGGGTGAATTGGCAATAAAAATTTTGGTG
GAAGCTTTTGCAGAAAATTGAAAGAAATTGCACAACGATTTAGAGTGGTTCGACTTTCTCAACCA
AAGTCTACGTCCACTACCTTAGCTATCCACACTAAGAATTTTCCTACCTTAGCTATCCACACTAA
GAATTTTCCACAAAGTAT
Found at i:47765 original size:7 final size:7
Alignment explanation
Indices: 47738--47780 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
47728 ATAATTGTGG
47738 TTATAATT
1 TTAT-ATT
*
47746 TTATAAGT
1 TTAT-ATT
47754 TTATATT
1 TTATATT
47761 TTATATT
1 TTATATT
47768 TTATATT
1 TTATATT
47775 TTATAT
1 TTATAT
47781 GTTGAGTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
7 22 0.67
8 11 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (7 bp):
TTATATT
Found at i:51235 original size:21 final size:21
Alignment explanation
Indices: 51209--51248 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51199 CAGAACCCCA
*
51209 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
51230 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
51249 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:57275 original size:47 final size:47
Alignment explanation
Indices: 57205--57352 Score: 233
Period size: 47 Copynumber: 3.1 Consensus size: 47
57195 TTTCTAATTG
57205 GTTTGTCGGTAGTTACGCATTGTCAGATCCCTCTTTGGTAAAATGTT
1 GTTTGTCGGTAGTTACGCATTGTCAGATCCCTCTTTGGTAAAATGTT
* * * * *
57252 TTTTGTCGGTAATTACGCATTGTCAGAGCTCTCTTTGGTAAAATATT
1 GTTTGTCGGTAGTTACGCATTGTCAGATCCCTCTTTGGTAAAATGTT
* *
57299 GTTTGTCAGTAGTTACGCATTGTCATATCCCTCTTTGGTAAAATGTT
1 GTTTGTCGGTAGTTACGCATTGTCAGATCCCTCTTTGGTAAAATGTT
57346 GTTTGTC
1 GTTTGTC
57353 AATATAATCA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 89 1.00
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (47 bp):
GTTTGTCGGTAGTTACGCATTGTCAGATCCCTCTTTGGTAAAATGTT
Found at i:68738 original size:18 final size:19
Alignment explanation
Indices: 68692--68747 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 19
68682 CAGCCTTCAC
*
68692 AAATCATTGAATGAG-AAGT
1 AAATCATCGAA-GAGTAAGT
68711 AAATTCATCGAAGAGTAAG-
1 AAA-TCATCGAAGAGTAAGT
68730 AAATCATCGAAGAGTAAG
1 AAATCATCGAAGAGTAAG
68748 GGCTGATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 15 0.44
19 9 0.26
20 10 0.29
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.21
Consensus pattern (19 bp):
AAATCATCGAAGAGTAAGT
Found at i:74344 original size:20 final size:20
Alignment explanation
Indices: 74319--74366 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
74309 AACCGTTCAT
74319 CATTCAGCGTTGAATGGCTC
1 CATTCAGCGTTGAATGGCTC
*
74339 CATTCAGCGTTGAATGGTTC
1 CATTCAGCGTTGAATGGCTC
74359 CATTCAGC
1 CATTCAGC
74367 AGTAAACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (20 bp):
CATTCAGCGTTGAATGGCTC
Found at i:76849 original size:19 final size:19
Alignment explanation
Indices: 76827--76885 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
76817 TACATATAGG
76827 ATACATGCATTAATAAATT
1 ATACATGCATTAATAAATT
* ** *
76846 ATACAT--A--CATGCATG
1 ATACATGCATTAATAAATT
76861 ATACATGCATTAATAAATT
1 ATACATGCATTAATAAATT
76880 ATACAT
1 ATACAT
76886 ACATATACAT
Statistics
Matches: 28, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
15 10 0.36
17 2 0.07
19 16 0.57
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (19 bp):
ATACATGCATTAATAAATT
Found at i:76855 original size:34 final size:33
Alignment explanation
Indices: 76812--76952 Score: 148
Period size: 34 Copynumber: 4.2 Consensus size: 33
76802 GCATTTATAC
76812 ATACATACATATAGGATACATGCATTAATAAATT
1 ATACATACATATA-GATACATGCATTAATAAATT
76846 ATACATACATGCAT-GATACATGCATTAATAAATT
1 ATACATACAT--ATAGATACATGCATTAATAAATT
76880 ATACATAC--AT--ATACATGCATTAATAAATT
1 ATACATACATATAGATACATGCATTAATAAATT
* *
76909 ATACATATATAAATATATACATACATGCATTAATAAATT
1 ATAC----AT--ACATATAGATACATGCATTAATAAATT
76948 ATACA
1 ATACA
76953 GGCATAAATG
Statistics
Matches: 94, Mismatches: 1, Indels: 23
0.80 0.01 0.19
Matches are distributed among these distances:
29 23 0.24
30 2 0.02
33 2 0.02
34 38 0.40
35 2 0.02
36 2 0.02
37 2 0.02
39 23 0.24
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (33 bp):
ATACATACATATAGATACATGCATTAATAAATT
Found at i:76929 original size:16 final size:15
Alignment explanation
Indices: 76902--76931 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
76892 ACATGCATTA
76902 ATAAATTATACATAT
1 ATAAATTATACATAT
76917 ATAAATATATACATA
1 ATAAAT-TATACATA
76932 CATGCATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAATTATACATAT
Found at i:77750 original size:31 final size:31
Alignment explanation
Indices: 77686--77750 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
77676 TGAGTGACCG
* *
77686 ATTTATTATAAATCAATAACATTAATGATCA
1 ATTTATTATAAATCAATAACATTAATAACCA
* * * *
77717 ATTTGTTATAAATCTATAATATTAGTAACCA
1 ATTTATTATAAATCAATAACATTAATAACCA
77748 ATT
1 ATT
77751 CATCATTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTTATTATAAATCAATAACATTAATAACCA
Found at i:78176 original size:15 final size:16
Alignment explanation
Indices: 78156--78193 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
78146 ATTTGAATAT
*
78156 ATTTATAGA-ATAAAA
1 ATTTATAAATATAAAA
78171 ATTTATAAATATAAAA
1 ATTTATAAATATAAAA
*
78187 ATATATA
1 ATTTATA
78194 TTAATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTTATAAATATAAAA
Found at i:89378 original size:2 final size:2
Alignment explanation
Indices: 89371--89404 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
89361 TATGAGTCGC
89371 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
89405 GTTCACATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:94269 original size:40 final size:41
Alignment explanation
Indices: 94190--94271 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
94180 CATAAATGAT
* * * *
94190 TGTATAAGCTTTGGGTTGTTCATCAGCAAAGAAATCAAAAC
1 TGTATAAGCTTTAGATTGTTCAACAGCAAAGAAACCAAAAC
*
94231 TGTATAGGCTTTAGATTGTT-AACAGCAAAGAAACCAAAAC
1 TGTATAAGCTTTAGATTGTTCAACAGCAAAGAAACCAAAAC
94271 T
1 T
94272 ATCTATCACT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 19 0.53
41 17 0.47
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (41 bp):
TGTATAAGCTTTAGATTGTTCAACAGCAAAGAAACCAAAAC
Found at i:103445 original size:25 final size:25
Alignment explanation
Indices: 103417--103475 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
103407 AATATTATAA
*
103417 AAATAAATTATAAAAGGGCTCTCTT
1 AAATAAATTATAAAAGGACTCTCTT
103442 AAATAAATTATAAAAGGACTCTCTT
1 AAATAAATTATAAAAGGACTCTCTT
103467 AAATAAATT
1 AAATAAATT
103476 TGATTTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.32
Consensus pattern (25 bp):
AAATAAATTATAAAAGGACTCTCTT
Found at i:105141 original size:26 final size:26
Alignment explanation
Indices: 105107--105159 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
105097 AGGTCTCTGT
105107 TAATAATACTTCATTGTTCAAATCAA
1 TAATAATACTTCATTGTTCAAATCAA
105133 TAATAATACTTCATTGTTCAAATCAA
1 TAATAATACTTCATTGTTCAAATCAA
105159 T
1 T
105160 CTTAGATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.40
Consensus pattern (26 bp):
TAATAATACTTCATTGTTCAAATCAA
Found at i:107173 original size:21 final size:20
Alignment explanation
Indices: 107149--107192 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
107139 CGATAAAAAA
* *
107149 TTATTGATAATATTATTATTT
1 TTATTGAAAATATTAAT-TTT
*
107170 TTATTTAAAATATTAATTTT
1 TTATTGAAAATATTAATTTT
107190 TTA
1 TTA
107193 ATATTTTCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATTGAAAATATTAATTTT
Found at i:107267 original size:30 final size:29
Alignment explanation
Indices: 107191--107271 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
107181 ATTAATTTTT
** *
107191 TAATATTTTCGATCATTTTTTAGTGCCTAT
1 TAATATTTT-GATCATTTTTTAACGCCTAA
* * *
107221 TAATGTTTTTGGTCATTTTTTAACGTCTAA
1 TAAT-ATTTTGATCATTTTTTAACGCCTAA
107251 TAATATTTCTGATCATTTTTT
1 TAATATTT-TGATCATTTTTT
107272 TGAAAATCCG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 3 0.07
30 34 0.83
31 4 0.10
ACGTcount: A:0.23, C:0.11, G:0.10, T:0.56
Consensus pattern (29 bp):
TAATATTTTGATCATTTTTTAACGCCTAA
Done.