Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002080.1 Hibiscus syriacus cultivar Beakdansim tig00004250_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: 123712
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:567 original size:2 final size:2
Alignment explanation
Indices: 562--614 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
552 CTTCACAGCA
562 AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
601 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
615 CTATGTATCC
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9783 original size:69 final size:69
Alignment explanation
Indices: 9703--9838 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 69
9693 TTTCACCTCC
* **
9703 ACAACAATCACCTCCATTGCTATCTACATCCACCACTATTCCTTCTTCATCATATACTTTATCAC
1 ACAACAATCACCTCCATTGCTACCTACATCCACCACTATTCCACCTTCATCATATACTTTATCAC
9768 CTTT
66 CTTT
* *
9772 ACAACAGTCACCTCCATTGCTACCTACATCCACCACTATTCCACCTTCATCATCTACTTTATCAC
1 ACAACAATCACCTCCATTGCTACCTACATCCACCACTATTCCACCTTCATCATATACTTTATCAC
9837 CT
66 CT
9839 CCATTGCTAC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.27, C:0.38, G:0.02, T:0.33
Consensus pattern (69 bp):
ACAACAATCACCTCCATTGCTACCTACATCCACCACTATTCCACCTTCATCATATACTTTATCAC
CTTT
Found at i:11916 original size:162 final size:162
Alignment explanation
Indices: 11738--12052 Score: 603
Period size: 162 Copynumber: 1.9 Consensus size: 162
11728 AATTTAACTT
11738 GATAAATTCGCAAGTAATTCGTTACTTTTTTAATTATTTTTTAGTAATTACCTTAAAAATTGTTT
1 GATAAATTCGCAAGTAATTCGTTACTTTTTTAATTATTTTTTAGTAATTACCTTAAAAATTGTTT
*
11803 CATTAAAAAATCTAATTAATAATTATTAATTTATTACTAGATAATAAAAGTGATACTAGATTACT
66 CATTAAAAAATCTAATTAATAATTATTAATTTATTACTAGATAATAAAAGTGATACTAAATTACT
*
11868 AATTAATAATTACTACTTATTTAACTTGACTC
131 AATTAATAATTACTACTAATTTAACTTGACTC
11900 GATAAATTCGCAAGTAATTCGTTACTTTTTTAATTATTTTTTAGTAATTACCTTAAAAATTGTTT
1 GATAAATTCGCAAGTAATTCGTTACTTTTTTAATTATTTTTTAGTAATTACCTTAAAAATTGTTT
*
11965 CATTAAAAAATCTAATTAATAATTATTAATTTATTACTGGATAATAAAAGTGATACTAAATTACT
66 CATTAAAAAATCTAATTAATAATTATTAATTTATTACTAGATAATAAAAGTGATACTAAATTACT
12030 AATTAATAATTACTACTAATTTA
131 AATTAATAATTACTACTAATTTA
12053 TTATTTTTAA
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
162 150 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (162 bp):
GATAAATTCGCAAGTAATTCGTTACTTTTTTAATTATTTTTTAGTAATTACCTTAAAAATTGTTT
CATTAAAAAATCTAATTAATAATTATTAATTTATTACTAGATAATAAAAGTGATACTAAATTACT
AATTAATAATTACTACTAATTTAACTTGACTC
Found at i:13930 original size:15 final size:15
Alignment explanation
Indices: 13910--13938 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13900 ATAAGATGGT
13910 AAAATAATAATAATA
1 AAAATAATAATAATA
13925 AAAATAATAATAAT
1 AAAATAATAATAAT
13939 TGCATTATAG
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAATAATAATA
Found at i:15687 original size:39 final size:39
Alignment explanation
Indices: 15559--15675 Score: 209
Period size: 39 Copynumber: 3.0 Consensus size: 39
15549 AATGTATGTG
*
15559 TGAGTTATATTAAGATTAGGATTAATTATTAGTATTTTA
1 TGAGTTATATTACGATTAGGATTAATTATTAGTATTTTA
15598 TGAGTTATATTACGATTAGGATTAATTATTAGTATTTTA
1 TGAGTTATATTACGATTAGGATTAATTATTAGTATTTTA
*
15637 TGAGTTATATTACGATCAGGATTAATTATTAGT-TTTTA
1 TGAGTTATATTACGATTAGGATTAATTATTAGTATTTTA
15675 T
1 T
15676 TTTATTTTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
38 6 0.08
39 70 0.92
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (39 bp):
TGAGTTATATTACGATTAGGATTAATTATTAGTATTTTA
Found at i:17771 original size:81 final size:81
Alignment explanation
Indices: 17636--17877 Score: 396
Period size: 81 Copynumber: 3.0 Consensus size: 81
17626 AAACACAACC
* *
17636 ACCTAACACCACTACCGCACCTAACATT-AAAATCATACACCAAACCATTAACCCATTGGACTCT
1 ACCTAACACCACTACCACACCTGACATTGAAAA-CATACACCAAACCATTAACCCATTGGACTCT
* *
17700 TCAAAAACACCAAATCA
65 CCTAAAACACCAAATCA
*
17717 ACCTAACACCACTACCACACCTGACATTGAAAACATACACCAAATCATTAACCCATTGGACTCTC
1 ACCTAACACCACTACCACACCTGACATTGAAAACATACACCAAACCATTAACCCATTGGACTCTC
*
17782 CTAAAACACCAAATCC
66 CTAAAACACCAAATCA
* *
17798 ACCTAACACCACTACCACACCTGACACTGAAAACATACACCAAACCATTAACCCATTGGATTCTC
1 ACCTAACACCACTACCACACCTGACATTGAAAACATACACCAAACCATTAACCCATTGGACTCTC
17863 CTAAAACACCAAATC
66 CTAAAACACCAAATC
17878 CATTTGTGTC
Statistics
Matches: 151, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
81 147 0.97
82 4 0.03
ACGTcount: A:0.42, C:0.36, G:0.05, T:0.18
Consensus pattern (81 bp):
ACCTAACACCACTACCACACCTGACATTGAAAACATACACCAAACCATTAACCCATTGGACTCTC
CTAAAACACCAAATCA
Found at i:41705 original size:16 final size:16
Alignment explanation
Indices: 41684--41715 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41674 TTTATTTTCG
41684 AATTAATCATGTAATT
1 AATTAATCATGTAATT
*
41700 AATTAATTATGTAATT
1 AATTAATCATGTAATT
41716 CCTCTGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
AATTAATCATGTAATT
Found at i:45858 original size:18 final size:18
Alignment explanation
Indices: 45835--45872 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
45825 TCGAGAGAGT
45835 CAGACAACGGTTCTGAGC
1 CAGACAACGGTTCTGAGC
*
45853 CAGACAACGGTTCTGGGC
1 CAGACAACGGTTCTGAGC
45871 CA
1 CA
45873 AGTTCAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (18 bp):
CAGACAACGGTTCTGAGC
Found at i:46429 original size:6 final size:6
Alignment explanation
Indices: 46418--46466 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
46408 TTTGAGATAA
* * *
46418 TACATG TACATG TACATG TACATG TACATG TATATG TATATG TATATG
1 TACATG TACATG TACATG TACATG TACATG TACATG TACATG TACATG
46466 T
1 T
46467 CAACATGTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (6 bp):
TACATG
Found at i:50351 original size:24 final size:23
Alignment explanation
Indices: 50321--50378 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
50311 ATTTAGAAGT
50321 TCAATTGAAGCCTAAAATTTGAGC
1 TCAATTGAAGCCT-AAATTTGAGC
*
50345 TCAATTGAAACCTAAATTTGAGC
1 TCAATTGAAGCCTAAATTTGAGC
50368 TCAATTGAAGC
1 TCAATTGAAGC
50379 GAAAGAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (23 bp):
TCAATTGAAGCCTAAATTTGAGC
Found at i:52266 original size:20 final size:20
Alignment explanation
Indices: 52230--52267 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52220 ATCCTATTCC
**
52230 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
52250 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
52268 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:53861 original size:60 final size:60
Alignment explanation
Indices: 53782--53902 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
53772 TGATCCCCTA
* * * * * * *
53782 ATTATAGGGTACTATTTTGTTGAGTCCTTCTACTATTAAAAATTATGAAATAGTCTCTTG
1 ATTATAGGGTACTACTTTGTTGAGTACTTCAACTATTAAAAAGTATAAAATACTCACTTG
* *
53842 ATTATAGGGTATTGCTTTGTTGAGTACTTCAACTATTAAAAAGTATAAAATACTCACTTG
1 ATTATAGGGTACTACTTTGTTGAGTACTTCAACTATTAAAAAGTATAAAATACTCACTTG
53902 A
1 A
53903 CTATTTATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (60 bp):
ATTATAGGGTACTACTTTGTTGAGTACTTCAACTATTAAAAAGTATAAAATACTCACTTG
Found at i:54584 original size:22 final size:22
Alignment explanation
Indices: 54537--54578 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
54527 ATATAAAATT
*
54537 AAATATTAAAATTTTCATTATA
1 AAATATTAAAATATTCATTATA
*
54559 AAATATTATAATATTC-TTAT
1 AAATATTAAAATATTCATTAT
54579 TGAAATCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATATTAAAATATTCATTATA
Found at i:54664 original size:26 final size:25
Alignment explanation
Indices: 54617--54666 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
54607 AGACAGAGAA
*
54617 AAATTATATATTTATTATTAATTTT
1 AAATTATATATATATTATTAATTTT
54642 AAATTAATATACTATATTA-TAATTT
1 AAATT-ATATA-TATATTATTAATTT
54667 GATAAGCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 11 0.50
27 6 0.27
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
AAATTATATATATATTATTAATTTT
Found at i:54771 original size:2 final size:2
Alignment explanation
Indices: 54764--54807 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
54754 AACTCAATTA
54764 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
54806 AT
1 AT
54808 TATTAACCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57205 original size:43 final size:42
Alignment explanation
Indices: 57135--57446 Score: 190
Period size: 43 Copynumber: 7.2 Consensus size: 42
57125 GCTAAAGTTC
* *
57135 GCGGCGTTTGTTAACGAAAAACGCCGCAATAGGTGATGATATATA
1 GCGGCGTTTGTT-A--AAAAACGCCGCAATAGGTGATGTTATTTA
57180 GCGGCGTTTGTTGAAAAAACGCCGCAATAGGT-ATTGTTATTTA
1 GCGGCGTTTGTT-AAAAAACGCCGCAATAGGTGA-TGTTATTTA
* * * * *
57223 GCAGCGTTTGTCTTAAAAATGCCGCAATAGGTGTTGTTGTTTA
1 GCGGCGTTTGT-TAAAAAACGCCGCAATAGGTGATGTTATTTA
* * *
57266 GCGGCGTTT-TCCCT-ATAAACGCCGCAGTAGGT-ATTGCTATTTA
1 GCGGCGTTTGT---TAAAAAACGCCGCAATAGGTGA-TGTTATTTA
* *
57309 GCGGCGTTTGGCTT-ACAAACGCCGCAATAGGTG-TCGTTGTTTA
1 GCGGCGTTT-G-TTAAAAAACGCCGCAATAGGTGAT-GTTATTTA
* * * * *
57352 GCGGCATTT-TTCCCACAAACGCCGCAATAGGTGTTGTTGTTTA
1 GCGGCGTTTGTT--AAAAAACGCCGCAATAGGTGATGTTATTTA
* * * * * * **
57395 GCAGTGTTT-TTCAAACAAGCGCCGCAATAAGCGTTGAGATTTA
1 GCGGCGTTTGTT-AAA-AAACGCCGCAATAGGTGATGTTATTTA
57438 GCGGCGTTT
1 GCGGCGTTT
57447 TTATCGAAAG
Statistics
Matches: 218, Mismatches: 33, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
40 2 0.01
42 5 0.02
43 193 0.89
44 4 0.02
45 13 0.06
46 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (42 bp):
GCGGCGTTTGTTAAAAAACGCCGCAATAGGTGATGTTATTTA
Found at i:57297 original size:86 final size:86
Alignment explanation
Indices: 57196--57403 Score: 292
Period size: 86 Copynumber: 2.4 Consensus size: 86
57186 TTTGTTGAAA
* * *
57196 AAACGCCGCAATAGGTATTGTTATTTAGCAGCGTTTGTCTTAAAAATGCCGCAATAGGTGTTGTT
1 AAACGCCGCAATAGGTATTGTTATTTAGCAGCGTTTGGCTTAAAAACGCCGCAATAGGTGTCGTT
*
57261 GTTTAGCGGC-GTTTTCCCTAT
66 GTTTAGCGGCAGTTTTCCC-AC
* * * *
57282 AAACGCCGCAGTAGGTATTGCTATTTAGCGGCGTTTGGCTTACAAACGCCGCAATAGGTGTCGTT
1 AAACGCCGCAATAGGTATTGTTATTTAGCAGCGTTTGGCTTAAAAACGCCGCAATAGGTGTCGTT
*
57347 GTTTAGCGGCATTTTTCCCAC
66 GTTTAGCGGCAGTTTTCCCAC
* * *
57368 AAACGCCGCAATAGGTGTTGTTGTTTAGCAGTGTTT
1 AAACGCCGCAATAGGTATTGTTATTTAGCAGCGTTT
57404 TTCAAACAAG
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 99 0.93
87 7 0.07
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (86 bp):
AAACGCCGCAATAGGTATTGTTATTTAGCAGCGTTTGGCTTAAAAACGCCGCAATAGGTGTCGTT
GTTTAGCGGCAGTTTTCCCAC
Found at i:57297 original size:129 final size:129
Alignment explanation
Indices: 57153--57396 Score: 314
Period size: 129 Copynumber: 1.9 Consensus size: 129
57143 TGTTAACGAA
*
57153 AAACGCCGCAATAGGTGA-TGATATATAGCGGCGTTT-G-TTGAAAAAACGCCGCAATAGGTATT
1 AAACGCCGCAATAGGT-ATTGATATATAGCGGCGTTTGGCTT--AAAAACGCCGCAATAGGTATC
* ** *
57215 GTTATTTAGCAGCGTTTGTCTTAAAAATGCCGCAATAGGTGTTGTTGTTTAGCGGCGTTTTCCCT
63 GTTATTTAGCAGCATTTGTCCCAAAAACGCCGCAATAGGTGTTGTTGTTTAGCGGCGTTTTCCCT
57280 AT
128 AT
* * * * *
57282 AAACGCCGCAGTAGGTATTGCTATTTAGCGGCGTTTGGCTTACAAACGCCGCAATAGGTGTCGTT
1 AAACGCCGCAATAGGTATTGATATATAGCGGCGTTTGGCTTAAAAACGCCGCAATAGGTATCGTT
* * * *
57347 GTTTAGCGGCATTTTTCCCACAAACGCCGCAATAGGTGTTGTTGTTTAGC
66 ATTTAGCAGCATTTGTCCCAAAAACGCCGCAATAGGTGTTGTTGTTTAGC
57397 AGTGTTTTTC
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
128 1 0.01
129 94 0.96
130 1 0.01
131 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (129 bp):
AAACGCCGCAATAGGTATTGATATATAGCGGCGTTTGGCTTAAAAACGCCGCAATAGGTATCGTT
ATTTAGCAGCATTTGTCCCAAAAACGCCGCAATAGGTGTTGTTGTTTAGCGGCGTTTTCCCTAT
Found at i:57437 original size:129 final size:129
Alignment explanation
Indices: 57196--57446 Score: 295
Period size: 129 Copynumber: 1.9 Consensus size: 129
57186 TTTGTTGAAA
* * ** *
57196 AAACGCCGCAATAGGTATTGTTATTTAGCAGCGTTTGTCTTAAAAATGCCGCAATAGGTGTTGTT
1 AAACGCCGCAATAGGTATCGTTATTTAGCAGCATTTGTCCCAAAAACGCCGCAATAGGTGTTGTT
* ** * * * * **
57261 GTTTAGCGGCGTTTTCCCTATAAACGCCGCAGTAGGTATTGCTATTTAGCGGCGTTTGGCTTAC
66 GTTTAGCAGCGTTTTCCAAACAAACGCCGCAATAAGCATTGAGATTTAGCGGCGTTTGGCTTAC
* * * * *
57325 AAACGCCGCAATAGGTGTCGTTGTTTAGCGGCATTTTTCCCACAAACGCCGCAATAGGTGTTGTT
1 AAACGCCGCAATAGGTATCGTTATTTAGCAGCATTTGTCCCAAAAACGCCGCAATAGGTGTTGTT
* * * *
57390 GTTTAGCAGTGTTTTTCAAACAAGCGCCGCAATAAGCGTTGAGATTTAGCGGCGTTT
66 GTTTAGCAGCGTTTTCCAAACAAACGCCGCAATAAGCATTGAGATTTAGCGGCGTTT
57447 TTATCGAAAG
Statistics
Matches: 99, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
129 99 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (129 bp):
AAACGCCGCAATAGGTATCGTTATTTAGCAGCATTTGTCCCAAAAACGCCGCAATAGGTGTTGTT
GTTTAGCAGCGTTTTCCAAACAAACGCCGCAATAAGCATTGAGATTTAGCGGCGTTTGGCTTAC
Found at i:60738 original size:39 final size:38
Alignment explanation
Indices: 60657--60733 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
60647 AAAATTTACC
* *
60657 ATTTTATATTTTTAATTTTGTAAAAAAAAATTATATAA
1 ATTTTATAATTTAAATTTTGTAAAAAAAAATTATATAA
* *
60695 ATTTTATGAATTTAAATTTT-TTAAAGAAAA-TATATAA
1 ATTTTAT-AATTTAAATTTTGTAAAAAAAAATTATATAA
60732 AT
1 AT
60734 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 9 0.26
38 15 0.44
39 10 0.29
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (38 bp):
ATTTTATAATTTAAATTTTGTAAAAAAAAATTATATAA
Found at i:63254 original size:22 final size:22
Alignment explanation
Indices: 63207--63248 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
63197 ATATAAAATT
*
63207 AAATATTAAAATTTTCATTATA
1 AAATATTAAAATATTCATTATA
*
63229 AAATATTATAATATTC-TTAT
1 AAATATTAAAATATTCATTAT
63249 TGAAATCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATATTAAAATATTCATTATA
Found at i:65212 original size:16 final size:18
Alignment explanation
Indices: 65187--65229 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
65177 ATACTTGCAA
65187 TATCGATACCCT-A-GAG
1 TATCGATACCCTGATGAG
*
65203 TATTGATACCCTGATGAG
1 TATCGATACCCTGATGAG
65221 TATCGATAC
1 TATCGATAC
65230 AAAAAATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
17 1 0.04
18 11 0.48
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (18 bp):
TATCGATACCCTGATGAG
Found at i:71837 original size:39 final size:38
Alignment explanation
Indices: 71751--71872 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 38
71741 TGGTTAGTGA
**
71751 ATGCTTAAACC-AAAATGAATAACATATGTTGTAATAT
1 ATGCTTAAACCAAAAATGAATAATGTATGTTGTAATAT
71788 ATGCTTAAACCAAAAATGAATAATGTATGCTTGTAATAT
1 ATGCTTAAACCAAAAATGAATAATGTATG-TTGTAATAT
*
71827 ATGCTCAAACCAAAAATGAATAATGTATGTTCGT-ATAT
1 ATGCTTAAACCAAAAATGAATAATGTATGTT-GTAATAT
*
71865 ATGATTAA
1 ATGCTTAA
71873 TGGTGTGGCA
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
37 11 0.14
38 27 0.35
39 39 0.51
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (38 bp):
ATGCTTAAACCAAAAATGAATAATGTATGTTGTAATAT
Found at i:80967 original size:30 final size:30
Alignment explanation
Indices: 80931--80999 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
80921 CAAAGGGTGA
* *
80931 TGGATATCCCTGAGGAGGGTAGCCTTGTGG
1 TGGATATCCCTGAGGAAGGTAACCTTGTGG
*
80961 TGGATATCCCTGAGTAAGGTAACCTTGTGG
1 TGGATATCCCTGAGGAAGGTAACCTTGTGG
80991 TGGATATCC
1 TGGATATCC
81000 GTGCGAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.29
Consensus pattern (30 bp):
TGGATATCCCTGAGGAAGGTAACCTTGTGG
Found at i:82572 original size:29 final size:28
Alignment explanation
Indices: 82522--82599 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
82512 TTGATAAATT
* * *
82522 TAATTGATTTTTTTATTAAGTTCAAGGGCC
1 TAATTGA-TTTTTTA-AAAGTTCAAGGACA
*
82552 TAATTGATTTTTTAGAAAGTTTAAGGACA
1 TAATTGATTTTTTA-AAAGTTCAAGGACA
* *
82581 TATTTAATTTTTTAAAAGT
1 TAATTGATTTTTTAAAAGT
82600 ATTAAGATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 5 0.12
29 29 0.71
30 7 0.17
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.47
Consensus pattern (28 bp):
TAATTGATTTTTTAAAAGTTCAAGGACA
Found at i:83052 original size:16 final size:16
Alignment explanation
Indices: 83033--83066 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
83023 CAATATACGA
83033 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
83049 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
83065 AT
1 AT
83067 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:83141 original size:17 final size:18
Alignment explanation
Indices: 83106--83141 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
83096 TATATTAATG
83106 TTTGAATCATTTATATTT
1 TTTGAATCATTTATATTT
83124 TTTGAAT-ATTT-TATTT
1 TTTGAATCATTTATATTT
83140 TT
1 TT
83142 AATAAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 4 0.22
18 7 0.39
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.67
Consensus pattern (18 bp):
TTTGAATCATTTATATTT
Found at i:83665 original size:23 final size:21
Alignment explanation
Indices: 83639--83685 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
83629 GTGTCACCAA
*
83639 TAACATATATCATGATCATGTGT
1 TAACACATATCA-GATCATG-GT
*
83662 TAACACATATCAGATCCTGGT
1 TAACACATATCAGATCATGGT
83683 TAA
1 TAA
83686 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (21 bp):
TAACACATATCAGATCATGGT
Found at i:83816 original size:130 final size:130
Alignment explanation
Indices: 83612--83856 Score: 400
Period size: 130 Copynumber: 1.9 Consensus size: 130
83602 AATTTTCTTC
* *
83612 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATATCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATATCAGAT
** *
83677 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
83742 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATATCAGAT
*
83807 TCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATT
83857 TGATTATATA
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 105 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATATCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:84307 original size:35 final size:35
Alignment explanation
Indices: 84257--84332 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
84247 AATTGAATTT
* *
84257 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
84292 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
84327 AATTGA
1 AATTGA
84333 GGATTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:91007 original size:65 final size:65
Alignment explanation
Indices: 90873--91033 Score: 256
Period size: 65 Copynumber: 2.5 Consensus size: 65
90863 GTGCACCAAG
*
90873 TGTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGCT
* *
90937 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGG-
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGATGCATGGC
91000 T
65 T
91001 ATGTGCATCGATGCATAAAATGCATTCGATGTT
1 -TGTGCATCGATGCATAAAATGCATTCGATGTT
91034 CAATTTATTT
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
64 29 0.33
65 57 0.64
66 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (65 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGCT
Found at i:91073 original size:65 final size:64
Alignment explanation
Indices: 90873--91081 Score: 246
Period size: 65 Copynumber: 3.2 Consensus size: 64
90863 GTGCACCAAG
*
90873 TGTGCATCGATGCATAAAATGCATTCGATGTTTCAA-AATAGCCTGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTCAATAATACCCTGAGTGCATCGATGCATGG-T
* * *
90937 GGTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACCCTGAGTGCATCGATGCATGGT
1 TGTGCATCGATGCATAAAATGCATTCGATG-TTTCAATAATACCCTGAGTGCATCGATGCATGGT
* ** * *
91001 ATGTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATTTCATG-GTGTATCGATGCATGG
1 -TGTGCATCGATGCATAAAATGCATTCGATGTTTCAA-TAATACCCTGAGTGCATCGATGCATGG
91064 AT
64 -T
*
91066 TGTTGCATCGGTGCAT
1 TG-TGCATCGATGCAT
91082 CACTTTGAAA
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 3 0.02
64 48 0.38
65 74 0.59
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (64 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTCAATAATACCCTGAGTGCATCGATGCATGGT
Found at i:93780 original size:20 final size:20
Alignment explanation
Indices: 93755--93806 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
93745 ACCCGACAGA
* *
93755 TGCATCGATGTATGGCCTTG
1 TGCATCGATGCATGACCTTG
*
93775 TGCATCGATGCATGACCTTT
1 TGCATCGATGCATGACCTTG
*
93795 TGCATCGGTGCA
1 TGCATCGATGCA
93807 CATTCAAGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (20 bp):
TGCATCGATGCATGACCTTG
Found at i:99747 original size:19 final size:19
Alignment explanation
Indices: 99723--99786 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
99713 AATAGCCTGA
99723 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
99742 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
*
99761 GTGCATCGATGCACGGCTG
1 GTGCATCGATGCATGGCTG
*
99780 ATGCATC
1 GTGCATC
99787 AAATGCATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.25
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:100619 original size:2 final size:2
Alignment explanation
Indices: 100612--100648 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
100602 TTATCAAGGA
100612 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
100649 TGTATGTACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:100667 original size:16 final size:16
Alignment explanation
Indices: 100648--100678 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
100638 ACACACACAC
100648 ATGTATGTACGTACAT
1 ATGTATGTACGTACAT
100664 ATGTATGTACGTACA
1 ATGTATGTACGTACA
100679 CACACATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (16 bp):
ATGTATGTACGTACAT
Found at i:102324 original size:49 final size:49
Alignment explanation
Indices: 102234--102327 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
102224 AATAAGAATA
* ** *
102234 AAAATGATTATTTAGTCAAATGTTAGAACTAAAATATTTTAAAAAAACC
1 AAAATGATTATTTAATCAAACATTAGAACGAAAATATTTTAAAAAAACC
102283 AAAATGATTATTTAATCAAACATTGAGATACGAAAA-A-TTTAAAAA
1 AAAATGATTATTTAATCAAACATT-AGA-ACGAAAATATTTTAAAAA
102328 TATATAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
49 29 0.74
50 4 0.10
51 6 0.15
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (49 bp):
AAAATGATTATTTAATCAAACATTAGAACGAAAATATTTTAAAAAAACC
Found at i:102892 original size:27 final size:27
Alignment explanation
Indices: 102862--102913 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
102852 TATATATCAT
102862 GTCATTTAAAATAATGATGTGACATGC
1 GTCATTTAAAATAATGATGTGACATGC
*
102889 GTCATTTAAAATGATGATGTGACAT
1 GTCATTTAAAATAATGATGTGACAT
102914 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (27 bp):
GTCATTTAAAATAATGATGTGACATGC
Found at i:106090 original size:13 final size:11
Alignment explanation
Indices: 106063--106087 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
106053 ATGATATATG
106063 TATGAAAAAAA
1 TATGAAAAAAA
106074 TATGAAAAAAA
1 TATGAAAAAAA
106085 TAT
1 TAT
106088 ATGTACATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (11 bp):
TATGAAAAAAA
Found at i:108026 original size:6 final size:6
Alignment explanation
Indices: 108015--108045 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
108005 TATCTCGGTT
108015 ATATAA ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA ATATAA A
108046 ATTTATTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:119940 original size:15 final size:15
Alignment explanation
Indices: 119900--119941 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
119890 TCATTTTCTT
*
119900 TTTTTTC-TTCTTCA
1 TTTTTTCATTTTTCA
119914 -TTTTTCACTTTTTCA
1 TTTTTTCA-TTTTTCA
119929 TTTTTTCATTTTT
1 TTTTTTCATTTTT
119942 TTTTAAACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 6 0.25
15 11 0.46
16 7 0.29
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTCATTTTTCA
Found at i:119943 original size:9 final size:8
Alignment explanation
Indices: 119910--119942 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
119900 TTTTTTCTTC
119910 TTCA-TTT
1 TTCATTTT
*
119917 TTCACTTT
1 TTCATTTT
119925 TTCATTTT
1 TTCATTTT
119933 TTCATTTT
1 TTCATTTT
119941 TT
1 TT
119943 TTTAAACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (8 bp):
TTCATTTT
Found at i:120080 original size:41 final size:42
Alignment explanation
Indices: 120012--120136 Score: 135
Period size: 42 Copynumber: 3.0 Consensus size: 42
120002 TAAAACAACC
* * * *
120012 TGCTCGAAGGTCTTACAAATGGCCCGAAGGACTT-ATCATCT
1 TGCTCGAAAGACTTACAGATGGCCCGAAGGACTTAATCATCA
* * * * *
120053 TGCTTGAAAGACTTACAGATGACCCGAAGTATTTCATCATCA
1 TGCTCGAAAGACTTACAGATGGCCCGAAGGACTTAATCATCA
** *
120095 TGCTCGAAAGACTTATTGATGGCCCAAAGGACTTAATCATCA
1 TGCTCGAAAGACTTACAGATGGCCCGAAGGACTTAATCATCA
120137 AGAAACCTTT
Statistics
Matches: 67, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 27 0.40
42 40 0.60
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (42 bp):
TGCTCGAAAGACTTACAGATGGCCCGAAGGACTTAATCATCA
Found at i:120253 original size:75 final size:75
Alignment explanation
Indices: 120128--120268 Score: 237
Period size: 75 Copynumber: 1.9 Consensus size: 75
120118 CCAAAGGACT
* *
120128 TAATCATCAAGAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAATTTCATTTGAAAACATCATA
1 TAATCATCAAGAAACCATTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
120193 TCGGTCAGGG
66 TCGGTCAGGG
* * *
120203 TAATCGTCAATAAACCATTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAATATCATA
1 TAATCATCAAGAAACCATTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
120268 T
66 T
120269 GGTTGGGTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (75 bp):
TAATCATCAAGAAACCATTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
TCGGTCAGGG
Done.