Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001123.1 Hibiscus syriacus cultivar Beakdansim tig00002221_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: 102309
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4885 original size:16 final size:15
Alignment explanation
Indices: 4862--4900 Score: 69
Period size: 16 Copynumber: 2.5 Consensus size: 15
4852 AGAGTCTCTG
4862 AATCATTCAGCACTT
1 AATCATTCAGCACTT
4877 AATTCATTCAGCACTT
1 AA-TCATTCAGCACTT
4893 AATCATTC
1 AATCATTC
4901 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (15 bp):
AATCATTCAGCACTT
Found at i:5342 original size:23 final size:23
Alignment explanation
Indices: 5307--5365 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
5297 GAACAAGTGT
*
5307 AAACGATTATAAACGAACACAAA
1 AAACGAATATAAACGAACACAAA
* *
5330 AAACGAATGTAAACGAACACAAT
1 AAACGAATATAAACGAACACAAA
*
5353 AAATGAA-ATAAAC
1 AAACGAATATAAAC
5366 AAATATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.61, C:0.15, G:0.10, T:0.14
Consensus pattern (23 bp):
AAACGAATATAAACGAACACAAA
Found at i:5434 original size:23 final size:23
Alignment explanation
Indices: 5314--5435 Score: 92
Period size: 23 Copynumber: 5.5 Consensus size: 23
5304 TGTAAACGAT
* *
5314 TATAAACGAACACAAAAAACGAA
1 TATAAACGAACACAATAAATGAA
*
5337 TGTAAACGAACACAATAAATGAA
1 TATAAACGAACACAATAAATGAA
*
5360 -ATAAAC-AA-A-TATAAATGAA
1 TATAAACGAACACAATAAATGAA
** * * *
5379 -ATTGCACAAACATAACAAATGAA
1 TA-TAAACGAACACAATAAATGAA
* *
5402 CATAATCGAACACAATAAATGAA
1 TATAAACGAACACAATAAATGAA
*
5425 TGTAAACGAAC
1 TATAAACGAAC
5436 GTAAGAAACA
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
19 10 0.13
20 4 0.05
21 4 0.05
22 6 0.08
23 51 0.67
24 1 0.01
ACGTcount: A:0.59, C:0.15, G:0.10, T:0.16
Consensus pattern (23 bp):
TATAAACGAACACAATAAATGAA
Found at i:5685 original size:23 final size:23
Alignment explanation
Indices: 5645--5691 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5635 ACGAACATAA
***
5645 ACGAACATACATGGACATAAATG
1 ACGAACATACACAAACATAAATG
5668 ACGAACATACACAAACATAAATG
1 ACGAACATACACAAACATAAATG
5691 A
1 A
5692 ATGAACGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.15
Consensus pattern (23 bp):
ACGAACATACACAAACATAAATG
Found at i:10127 original size:20 final size:20
Alignment explanation
Indices: 10083--10337 Score: 183
Period size: 20 Copynumber: 12.6 Consensus size: 20
10073 AATGACCAAT
* *
10083 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
10102 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
10122 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
10142 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
10162 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
10183 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
10206 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* *
10226 AGAATCGCAACGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* *
10246 AGAATCGCAACGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
10266 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
10286 AGAGTCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
10306 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
10326 AAAATCGCAACG
1 AAAATCGCAACG
10338 GTCAAAAGAA
Statistics
Matches: 192, Mismatches: 35, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.09
20 147 0.77
21 14 0.07
23 14 0.07
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:10268 original size:40 final size:40
Alignment explanation
Indices: 10187--10337 Score: 203
Period size: 40 Copynumber: 3.7 Consensus size: 40
10177 GCTTCCAAGT
*
10187 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAACGCGATTGATAGAA
* *
10230 TCGCAACGCGATTTATAGAATCGCAACGCGATTTATAGAA
1 TCGCAACGCGATTTAGAGAATCGCAACGCGATTGATAGAA
* * * *
10270 TCGCAATGCGATTGAGAGAGTCGCAACGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAGAATCGCAACGCGATTGATAGAA
*
10310 TCGCAACGCGATTTAGAAAATCGCAACG
1 TCGCAACGCGATTTAGAGAATCGCAACG
10338 GTCAAAAGAA
Statistics
Matches: 95, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
40 78 0.82
42 2 0.02
43 15 0.16
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAGAATCGCAACGCGATTGATAGAA
Found at i:10282 original size:60 final size:60
Alignment explanation
Indices: 10187--10335 Score: 210
Period size: 60 Copynumber: 2.4 Consensus size: 60
10177 GCTTCCAAGT
* * *
10187 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAACGCGATTTATAGAA
1 TCGCAACGCGATTTA-AAG--AATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAGAA
* *
10250 TCGCAACGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTGAGAGAA
1 TCGCAACGCGATTTAAAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAGAA
10310 TCGCAACGCGATTTAGAA-AATCGCAA
1 TCGCAACGCGATTTA-AAGAATCGCAA
10336 CGGTCAAAAG
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
60 61 0.77
61 1 0.01
62 2 0.03
63 15 0.19
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (60 bp):
TCGCAACGCGATTTAAAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAGAA
Found at i:10436 original size:6 final size:6
Alignment explanation
Indices: 10425--10481 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
10415 GACACGTATT
10425 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
10473 ACCACG ACC
1 ACCACG ACC
10482 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:11178 original size:6 final size:6
Alignment explanation
Indices: 11167--11253 Score: 174
Period size: 6 Copynumber: 14.5 Consensus size: 6
11157 TCTCGTCTCG
11167 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
11215 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
11254 AATACGTGTC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:11386 original size:20 final size:20
Alignment explanation
Indices: 11363--11573 Score: 307
Period size: 20 Copynumber: 10.4 Consensus size: 20
11353 ATTTTCAACG
*
11363 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTATCAATCGCA
* *
11383 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATCAATCGCA
*
11403 TTGCGATTTTCT-TCTAAATCGCG
1 TTGCGA--TTCTATC--AATCGCA
* *
11426 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTATCAATCGCA
* *
11446 TTGCGATTATATAAATCGCA
1 TTGCGATTCTATCAATCGCA
11466 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
11486 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
11506 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
11526 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
11546 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
11566 TTGCGATT
1 TTGCGATT
11574 TTCTTCTAAA
Statistics
Matches: 173, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
20 151 0.87
21 5 0.03
22 6 0.03
23 11 0.06
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTATCAATCGCA
Found at i:11633 original size:20 final size:20
Alignment explanation
Indices: 11608--11661 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
11598 TGGAAGCTCG
*
11608 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
11628 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
11648 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
11662 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:11688 original size:19 final size:20
Alignment explanation
Indices: 11648--11698 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
11638 TTCTTTTTAA
*
11648 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
11668 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
11687 CGTTGCGATTTT
1 CGTTGCGATTTT
11699 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:15414 original size:12 final size:13
Alignment explanation
Indices: 15392--15424 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
15382 AAAATTTTAA
15392 AATAAATATAATT
1 AATAAATATAATT
15405 AATAAA-ATAATT
1 AATAAATATAATT
*
15417 AATTAATA
1 AATAAATA
15425 CAAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATAAATATAATT
Found at i:21353 original size:81 final size:81
Alignment explanation
Indices: 21218--21381 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
21208 AGACACATTG
21218 AAACCATGAGAAAGAGAAAAATATTCATTATACTAAACTAGTATCTAAAAGTAGTACTCGTGCAC
1 AAACCATGAGAAAGAGAAAAATATTCATTATACTAAACTAGTATCTAAAAGTAGTACTCGTGCAC
21283 CAGAAAAGTTGATGTT
66 CAGAAAAGTTGATGTT
21299 AAACCATGAGAAAGAGAAAAATATTCATTATACTAAACTAGTATCTAAAAGTAGTACTCGTGCAC
1 AAACCATGAGAAAGAGAAAAATATTCATTATACTAAACTAGTATCTAAAAGTAGTACTCGTGCAC
21364 CAGAAAAGTTGATGTT
66 CAGAAAAGTTGATGTT
21380 AA
1 AA
21382 CCTTCAAGGT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (81 bp):
AAACCATGAGAAAGAGAAAAATATTCATTATACTAAACTAGTATCTAAAAGTAGTACTCGTGCAC
CAGAAAAGTTGATGTT
Found at i:26403 original size:12 final size:12
Alignment explanation
Indices: 26386--26412 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
26376 GAATCGAGTA
26386 AACGAGTTTATG
1 AACGAGTTTATG
26398 AACGAGTTTATG
1 AACGAGTTTATG
26410 AAC
1 AAC
26413 AAATCAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (12 bp):
AACGAGTTTATG
Found at i:28578 original size:15 final size:15
Alignment explanation
Indices: 28558--28587 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28548 TATCACAATC
28558 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
*
28573 GCGCAGGATTTCGGG
1 GCGCAGGATTCCGGG
28588 AGCACCGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:45483 original size:22 final size:22
Alignment explanation
Indices: 45462--45505 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
45452 ATTTTAAATA
45462 ATTT-TTTATTTAATC-ATTAAT
1 ATTTATTTA-TTAATCAATTAAT
45483 ATTTAATTTATTAATCAATTAAT
1 ATTT-ATTTATTAATCAATTAAT
45506 TTGAATGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
22 6 0.30
23 10 0.50
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTATTTATTAATCAATTAAT
Found at i:50146 original size:39 final size:39
Alignment explanation
Indices: 50087--50162 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
50077 ATGTGAAACG
50087 TTCAGTTTGGTGCATGCCAATAGATGCATTGGCAATGTT
1 TTCAGTTTGGTGCATGCCAATAGATGCATTGGCAATGTT
* *
50126 TTCATTTTGGTGGATGCCAATAGATGCATTGGCAATG
1 TTCAGTTTGGTGCATGCCAATAGATGCATTGGCAATG
50163 ATTCATATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (39 bp):
TTCAGTTTGGTGCATGCCAATAGATGCATTGGCAATGTT
Found at i:51384 original size:26 final size:25
Alignment explanation
Indices: 51362--51420 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
51352 TTTAATTACT
*
51362 TAACTTTCAAATTACTTATAATTTAA
1 TAACTTTCAAATTACTCATAA-TTAA
*
51388 TCACTTTCAAATTACTCATAATTTAA
1 TAACTTTCAAATTACTCATAA-TTAA
*
51414 TCACTTT
1 TAACTTT
51421 AACTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (25 bp):
TAACTTTCAAATTACTCATAATTAA
Found at i:55068 original size:11 final size:11
Alignment explanation
Indices: 55037--55062 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55027 ATATTAGTTT
55037 TAAAACTTTTA
1 TAAAACTTTTA
55048 TAAAACTTTTA
1 TAAAACTTTTA
55059 TAAA
1 TAAA
55063 TATTTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAAACTTTTA
Found at i:57690 original size:15 final size:15
Alignment explanation
Indices: 57662--57700 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
57652 AATTTAAATT
* *
57662 TTAAAATAATATTAA
1 TTAATATAAAATTAA
*
57677 TTATTATAAAATTAA
1 TTAATATAAAATTAA
57692 TTAATATAA
1 TTAATATAA
57701 CTATATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAATATAAAATTAA
Found at i:58426 original size:59 final size:59
Alignment explanation
Indices: 58269--58447 Score: 236
Period size: 59 Copynumber: 3.0 Consensus size: 59
58259 AATAGTCAAT
* * * * * * *
58269 GGATCATTTTATAACTTCTAATAGTC-AGAGGA-TTCAACAAAGAAACACCCTATCGTCGG
1 GGATCATTTTGTAACTTTTAATAGTCGAGA-GACTT-AAGAAAGCATCACCTTATAGTCGG
* *
58328 GGATCATTTTGTAACTTTTAATAGTCGAGAAACTCAAGAAAGCATCACCTTATAGTCGG
1 GGATCATTTTGTAACTTTTAATAGTCGAGAGACTTAAGAAAGCATCACCTTATAGTCGG
*
58387 GGATCATTTTGTAACTTTTAATAGTCGAGAGACTTAAGAAAGCATCAGCTTATAGTCGG
1 GGATCATTTTGTAACTTTTAATAGTCGAGAGACTTAAGAAAGCATCACCTTATAGTCGG
58446 GG
1 GG
58448 GACCATATGT
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
59 102 0.96
60 4 0.04
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (59 bp):
GGATCATTTTGTAACTTTTAATAGTCGAGAGACTTAAGAAAGCATCACCTTATAGTCGG
Found at i:60501 original size:20 final size:20
Alignment explanation
Indices: 60476--60516 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
60466 GGAAAATATT
60476 TATAT-ATTTTCTTTAAAAAA
1 TATATAATTTT-TTTAAAAAA
*
60496 TATATAATTTTTTTACAAAA
1 TATATAATTTTTTTAAAAAA
60516 T
1 T
60517 TGAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATAATTTTTTTAAAAAA
Found at i:61589 original size:19 final size:18
Alignment explanation
Indices: 61526--61592 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 18
61516 TTGTTCACAT
* *
61526 TTTTAAATTATGATTTTA
1 TTTTAAATTATAATTTCA
* *
61544 TTTTAAATTTTTAACTTCA
1 TTTTAAA-TTATAATTTCA
61563 TCTTTAAATTATAAGTTTCA
1 T-TTTAAATTATAA-TTTCA
61583 TTTTAAATTA
1 TTTTAAATTA
61593 GTTCTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 7 0.17
19 22 0.55
20 11 0.28
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTAAATTATAATTTCA
Found at i:66827 original size:22 final size:22
Alignment explanation
Indices: 66802--66866 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
66792 TATTTTAATT
66802 TTTATATTATTAAAATATATTA
1 TTTATATTATTAAAATATATTA
*
66824 TTTATATTTATTAAAA-ATATAAA
1 TTTATA-TTATTAAAATATAT-TA
66847 TTT-TATTA-TAAAATATATTA
1 TTTATATTATTAAAATATATTA
66867 ATCTAACAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 6 0.16
21 7 0.18
22 12 0.32
23 13 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTATATTATTAAAATATATTA
Found at i:69904 original size:2 final size:2
Alignment explanation
Indices: 69899--69950 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
69889 ATTTCTAATT
* *
69899 TA TA TA TA TA TT TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69941 TA TA TA TA TA
1 TA TA TA TA TA
69951 ATAAAATTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:70561 original size:65 final size:64
Alignment explanation
Indices: 70343--70599 Score: 451
Period size: 64 Copynumber: 4.0 Consensus size: 64
70333 AGTATTTGAT
*
70343 CACCTTAAATAATTTCAGTTTAGATATATAATTATTACTTTTTCTTTTATAAATTTGAAGTAAA
1 CACCTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTATAAATTTGAAGTAAA
*
70407 CAACTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTATAAATTTGAAGTAAA
1 CACCTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTATAAATTTGAAGTAAA
*
70471 TACCTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTATAAAATTTGAAGTAAA
1 CACCTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTAT-AAATTTGAAGTAAA
* * *
70536 CACCTTAAATAATTTAAGTTTAGATATATAATTATCACTTTTTCTTCTATAAATTTAAAGTAAA
1 CACCTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTATAAATTTGAAGTAAA
70600 TATAAGAGAG
Statistics
Matches: 184, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
64 123 0.67
65 61 0.33
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (64 bp):
CACCTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTATAAATTTGAAGTAAA
Found at i:70576 original size:129 final size:128
Alignment explanation
Indices: 70344--70601 Score: 462
Period size: 129 Copynumber: 2.0 Consensus size: 128
70334 GTATTTGATC
*
70344 ACCTTAAATAATTTCAGTTTAGATATATAATTATTACTTTTTCTTTTATAAATTTGAAGTAAACA
1 ACCTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTATAAATTTGAAGTAAACA
* * *
70409 ACTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTATAAATTTGAAGTAAAT
66 ACTTAAATAATTTAAGTTTAGATATATAATTATCACTTTTTCTTCTATAAATTTAAAGTAAAT
70472 ACCTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTATAAAATTTGAAGTAAAC
1 ACCTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTAT-AAATTTGAAGTAAAC
*
70537 ACCTTAAATAATTTAAGTTTAGATATATAATTATCACTTTTTCTTCTATAAATTTAAAGTAAAT
65 AACTTAAATAATTTAAGTTTAGATATATAATTATCACTTTTTCTTCTATAAATTTAAAGTAAAT
70601 A
1 A
70602 TAAGAGAGTA
Statistics
Matches: 124, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
128 48 0.39
129 76 0.61
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (128 bp):
ACCTTAAATAATTTAAGTTTAGATATATAATTATTACTTTTTCTTTTATAAATTTGAAGTAAACA
ACTTAAATAATTTAAGTTTAGATATATAATTATCACTTTTTCTTCTATAAATTTAAAGTAAAT
Found at i:71001 original size:23 final size:23
Alignment explanation
Indices: 70975--71038 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
70965 TATTTTGATG
70975 TTGAATCATTCAGCATTGTTTTA
1 TTGAATCATTCAGCATTGTTTTA
* ** *
70998 TTGAATCATTCAACACCGTTTTG
1 TTGAATCATTCAGCATTGTTTTA
*
71021 TTGAATCAGTCAGCATTG
1 TTGAATCATTCAGCATTG
71039 AATCATTCAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (23 bp):
TTGAATCATTCAGCATTGTTTTA
Found at i:75836 original size:35 final size:32
Alignment explanation
Indices: 75797--75881 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 32
75787 GTATTTCAGT
75797 TAATTTTGTTTATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTTATTACCATTTAATA-C--TTATTG
* *
75832 TAATTTGGTAATCATTTACCATTTAATACTTATTG
1 TAATTTTGT--TTA-TTACCATTTAATACTTATTG
*
75867 TAAGTTTGTTGTATT
1 TAATTTTGTT-TATT
75882 TAAAATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
33 3 0.07
34 1 0.02
35 21 0.51
37 3 0.07
38 13 0.32
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (32 bp):
TAATTTTGTTTATTACCATTTAATACTTATTG
Found at i:79860 original size:19 final size:18
Alignment explanation
Indices: 79833--79868 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
79823 GGTTTGTTTG
*
79833 TTAAGATAATTTATAATTA
1 TTAAAATAATTTA-AATTA
79852 TTAAAATAATTTAAATT
1 TTAAAATAATTTAAATT
79869 TCAAAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTAAAATAATTTAAATTA
Found at i:81003 original size:19 final size:19
Alignment explanation
Indices: 80981--81034 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
80971 AACAGATTCC
80981 CCCCTGGGGGGTATCGATT
1 CCCCTGGGGGGTATCGATT
*
81000 CCCC----GGG-AACAGATT
1 CCCCTGGGGGGTATC-GATT
81015 CCCCTGGGGGGTATCGATT
1 CCCCTGGGGGGTATCGATT
81034 C
1 C
81035 TCCCCTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
19 12 0.44
20 2 0.07
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (19 bp):
CCCCTGGGGGGTATCGATT
Found at i:81039 original size:36 final size:35
Alignment explanation
Indices: 80968--81034 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
80958 TATGTGCAGG
80968 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATT-CCCCCTGGGGGGTATCGATTCCCC
81004 GGGAACAGATT-CCCCTGGGGGGTATCGATTC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTC
81035 TCCCCTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 20 0.65
36 11 0.35
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
Found at i:87861 original size:36 final size:36
Alignment explanation
Indices: 87814--87883 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
87804 TGTGCAGGGG
*
87814 GAACAGATTCCCCCCT-AGGGGGTATCGATTCCCCGT
1 GAACAAATT-CCCCCTGAGGGGGTATCGATTCCCCGT
*
87850 GAACAAATTCCCCCTGGGGGGGTATCGATTCCCC
1 GAACAAATTCCCCCTGAGGGGGTATCGATTCCCC
87884 CTAAATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.21
Consensus pattern (36 bp):
GAACAAATTCCCCCTGAGGGGGTATCGATTCCCCGT
Found at i:88508 original size:15 final size:15
Alignment explanation
Indices: 88490--88524 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
88480 CGAGGGTATT
88490 GTAGTCCTTCGGAAC
1 GTAGTCCTTCGGAAC
*
88505 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGAAC
88520 GTAGT
1 GTAGT
88525 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGAAC
Found at i:91471 original size:20 final size:21
Alignment explanation
Indices: 91434--91472 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
91424 TCAACATTTA
91434 ATTTTTTTAATATCTAAATCT
1 ATTTTTTTAATATCTAAATCT
*
91455 ATTTTTTTAA-ATTTAAAT
1 ATTTTTTTAATATCTAAAT
91473 TAATATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTTTTAATATCTAAATCT
Found at i:91838 original size:15 final size:16
Alignment explanation
Indices: 91820--91857 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
91810 TTAAAGCATC
*
91820 ATAAA-TGTCAAGAAT
1 ATAAACTGTCAAAAAT
91835 ATAAACGTGTCAAAAAT
1 ATAAAC-TGTCAAAAAT
91852 ATAAAC
1 ATAAAC
91858 GTTCAATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
17 15 0.75
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.24
Consensus pattern (16 bp):
ATAAACTGTCAAAAAT
Found at i:91847 original size:17 final size:17
Alignment explanation
Indices: 91825--91863 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
91815 GCATCATAAA
*
91825 TGTCAAGAATATAAACG
1 TGTCAAAAATATAAACG
91842 TGTCAAAAATATAAACG
1 TGTCAAAAATATAAACG
91859 T-TCAA
1 TGTCAA
91864 TATCGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (17 bp):
TGTCAAAAATATAAACG
Found at i:97739 original size:15 final size:15
Alignment explanation
Indices: 97719--97749 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
97709 GATGCTTTCC
97719 GCTGTCTGAACGGAG
1 GCTGTCTGAACGGAG
97734 GCTGTCTGAACGGAG
1 GCTGTCTGAACGGAG
97749 G
1 G
97750 TTCTCTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.19
Consensus pattern (15 bp):
GCTGTCTGAACGGAG
Found at i:101136 original size:28 final size:28
Alignment explanation
Indices: 101104--101170 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
101094 AGCACAACAG
101104 CAAGAAACCTCATTATGACCCAGATATA
1 CAAGAAACCTCATTATGACCCAGATATA
101132 CAAGAAACCTCATTATGACCCAGATATA
1 CAAGAAACCTCATTATGACCCAGATATA
101160 CAAG-AACCTCA
1 CAAGAAACCTCA
101171 ATAACTAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.19
Consensus pattern (28 bp):
CAAGAAACCTCATTATGACCCAGATATA
Done.