Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002536.1 Hibiscus syriacus cultivar Beakdansim tig00005152_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: 91686
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:3105 original size:237 final size:234
Alignment explanation
Indices: 2693--3166 Score: 704
Period size: 237 Copynumber: 2.0 Consensus size: 234
2683 GGATTTCATT
* * * *
2693 ATTGAATCAAGTGAAAATCCACAACCCTAACCCATATACTATCAGCCGTGGGAAATAAATTAAGG
1 ATTGAATCAACTGAAAATCCACAAACCTAACCCATATACTATCAGCCATGGGAAATAAACTAAGG
* *
2758 GAAAATATGGAACCTCTAATCTTATAAATGATAAAAGATTCTACAAGCTTTAGAATGTTATTTGG
66 GAAAATATGAAACCCCTAATCTTATAAATGATAAAAGATTCTACAAGCTTTAGAATGTTATTTGG
* *
2823 ACCTATTTATAATTTTGTTAAAGTTGGGGACCTATTTAGTAATTAT-AGAAATTATGAGATCAAT
131 ACCTATTTATAATTTTGTTAAAGTTGGGGACCTATTCAATAATTATGA-AAATTATGAGATCAAT
* * *
2887 GTATAATTGATCAATAGTTTATGGACTATACTGAAAATTA
195 GTATAATTGATCAATAATTGATAGACTATACTGAAAATTA
*
2927 ATTGAATCAACTGAAAATCCGCAAAACCTAACCCATATACTATTCAGCCAT-GGAAA-AAACTAA
1 ATTGAATCAACTGAAAATCCAC-AAACCTAACCCATATACTA-TCAGCCATGGGAAATAAACTAA
* *
2990 GGGAAAATAT-AAACCCCTAATCTTATAAATGATATTTGAAAGGTTCTAGAAGCTTTAGAATGTT
64 GGGAAAATATGAAACCCCTAATCTTATAAATGATA----AAAGATTCTACAAGCTTTAGAATGTT
*
3054 ATTTGGACCTATTTGTAATTTTGTTAAAGTTGGGGACCTATTCAATAATTATGTAAAATTATGAG
125 ATTTGGACCTATTTATAATTTTGTTAAAGTTGGGGACCTATTCAATAATTATG-AAAATTATGAG
*
3119 ATCAATGTATAATTGTTCAATAATTGATAGACTATACTGAAAATTA
189 ATCAATGTATAATTGATCAATAATTGATAGACTATACTGAAAATTA
3165 AT
1 AT
3167 GTTAGAGTGT
Statistics
Matches: 216, Mismatches: 16, Indels: 12
0.89 0.07 0.05
Matches are distributed among these distances:
233 22 0.10
234 36 0.17
235 23 0.11
236 7 0.03
237 73 0.34
238 54 0.25
239 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (234 bp):
ATTGAATCAACTGAAAATCCACAAACCTAACCCATATACTATCAGCCATGGGAAATAAACTAAGG
GAAAATATGAAACCCCTAATCTTATAAATGATAAAAGATTCTACAAGCTTTAGAATGTTATTTGG
ACCTATTTATAATTTTGTTAAAGTTGGGGACCTATTCAATAATTATGAAAATTATGAGATCAATG
TATAATTGATCAATAATTGATAGACTATACTGAAAATTA
Found at i:4670 original size:33 final size:33
Alignment explanation
Indices: 4611--4675 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
4601 TCCGGTTTTG
* *
4611 CACTAGAGTGTATACCCAAGATACTTAATGCAA
1 CACTAGAGTGTAAACCCAAGACACTTAATGCAA
* * *
4644 CACTAGAGTTTAAACCCAATACACTTAGTGCA
1 CACTAGAGTGTAAACCCAAGACACTTAATGCA
4676 GATGGTGGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (33 bp):
CACTAGAGTGTAAACCCAAGACACTTAATGCAA
Found at i:4757 original size:70 final size:69
Alignment explanation
Indices: 4644--4839 Score: 266
Period size: 70 Copynumber: 2.8 Consensus size: 69
4634 CTTAATGCAA
* * * *
4644 CACTAGAGTTTAAACCCAATACACTTAGTGCAGATGGTGGGCACGAGCTTATGTGTCATATTCGG
1 CACTAGAGTGTATA-CCAACACACTTAGTGCATATGGTGGGCACGAGCTTATGTGTCATATTCGG
4709 TTTAG
65 TTTAG
4714 CACTAGAGTGTATATCCAACACACTTAGTGCATATGGTGGGCACGAGCTTATGTGTCATATTCGG
1 CACTAGAGTGTATA-CCAACACACTTAGTGCATATGGTGGGCACGAGCTTATGTGTCATATTCGG
4779 TTTAG
65 TTTAG
* * ** * * *
4784 CACTAGAGTGCATACCGAAGACACTTAGTGTGTATGGTAGGCACAACCTTATGTGT
1 CACTAGAGTGTATACC-AACACACTTAGTGCATATGGTGGGCACGAGCTTATGTGT
4840 ATTAGCACTT
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
69 2 0.02
70 111 0.98
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (69 bp):
CACTAGAGTGTATACCAACACACTTAGTGCATATGGTGGGCACGAGCTTATGTGTCATATTCGGT
TTAG
Found at i:6060 original size:35 final size:35
Alignment explanation
Indices: 6014--6093 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
6004 AACATATTAA
6014 TCAATTACATTCTAAACCCCAAAATAC-AAAATACT
1 TCAATTACATTCTAAACCCC-AAATACTAAAATACT
* * *
6049 TTAATTACATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTACATTCTAAACCCCAAATACTAAAATACT
6084 TCAATTACAT
1 TCAATTACAT
6094 GCCCAACCCG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 5 0.12
35 35 0.88
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATACTAAAATACT
Found at i:6108 original size:35 final size:35
Alignment explanation
Indices: 6014--6109 Score: 88
Period size: 35 Copynumber: 2.7 Consensus size: 35
6004 AACATATTAA
* * * *
6014 TCAATTACATTCTAAACCCCAAAATAC-AAAATACT
1 TCAATTACATGCCAAACCTC-AAATTCTAAAATACT
* * *
6049 TTAATTACATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTACATGCCAAACCTCAAATTCTAAAATACT
*
6084 TCAATTACATGCCCAACC-CGAAATTC
1 TCAATTACATGCCAAACCTC-AAATTC
6110 ATAATTCATT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 6 0.12
35 46 0.88
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (35 bp):
TCAATTACATGCCAAACCTCAAATTCTAAAATACT
Found at i:6507 original size:148 final size:147
Alignment explanation
Indices: 6278--6709 Score: 688
Period size: 148 Copynumber: 2.9 Consensus size: 147
6268 CAATTCAGTG
*
6278 TATAAAATAGTTGACTCGAAATTTTTTCGAATTGAGTTTAT-AAATTT-AATCAAGTCGAATTGG
1 TATAAAATAGTTGACTC-AAATTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
6341 ATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTATCACATTACAATATTATTTGA
65 ATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTATCACATTACAATATTATTTGA
6406 TTCTAATTCAGTTCAATT
130 TTCTAATTCAGTTCAATT
*
6424 TATAAAATAGCTGACTCAAATTTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
1 TATAAAATAGTTGACTCAAA-TTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
*
6489 ATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTATCACATGACAATATTATTTGA
65 ATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTATCACATTACAATATTATTTGA
6554 TTCTAATTCAGTTCAATT
130 TTCTAATTCAGTTCAATT
** *
6572 TATAAAATAGTTGACTCAAAAAATTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
1 TATAAAATAGTTGACTC-AAATTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
* * * * * * * * *
6637 AATGAATTTTCGAGTTTCTGTTTAAACTTAATTATAAATATTTATAATACTATAATATTATTTGA
65 ATTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTATCACATTACAATATTATTTGA
6702 TTCTAATT
130 TTCTAATT
6710 TAAATATTTT
Statistics
Matches: 265, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
145 3 0.01
146 36 0.14
147 6 0.02
148 217 0.82
149 3 0.01
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (147 bp):
TATAAAATAGTTGACTCAAATTTTTTCGAATTGAGTTTATAAAATTTAAATCAAGTCGAATTGAA
TTAAATTTTTGAGTTTCTTTTTAAATTTAATTATAAATATTTATCACATTACAATATTATTTGAT
TCTAATTCAGTTCAATT
Found at i:8484 original size:28 final size:28
Alignment explanation
Indices: 8444--8524 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
8434 AGAGTCGAGG
*
8444 GTTCTACGTGGTCCTTCGGAACATATGT
1 GTTCTACGTGGTCCTTCGGGACATATGT
8472 GTTCTACGTGGTCCTTCGGGACATATGT
1 GTTCTACGTGGTCCTTCGGGACATATGT
* * *
8500 GCTCTATGTGGTACTTCGGGACATA
1 GTTCTACGTGGTCCTTCGGGACATA
8525 GTGGTCCCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (28 bp):
GTTCTACGTGGTCCTTCGGGACATATGT
Found at i:9834 original size:35 final size:35
Alignment explanation
Indices: 9795--9874 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
9785 GGGGTTGGGC
* *
9795 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTAGAATTTGAGGTGTAGA
* *
9830 ATGTAATTAAAGTATTTTAGAATTTGGGGTGTAGA
1 ATGTAATTGAAGTATTTTAGAATTTGAGGTGTAGA
9865 ATGTAATTGA
1 ATGTAATTGA
9875 TGGTTGTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTAGAATTTGAGGTGTAGA
Found at i:11369 original size:2 final size:2
Alignment explanation
Indices: 11362--11394 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11352 ATACTAAATA
11362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11395 CGTATAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11451 original size:15 final size:14
Alignment explanation
Indices: 11431--11467 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
11421 ATATGTGACT
11431 ATATATAATAATACA
1 ATATATAAT-ATACA
11446 ATATATAATATACA
1 ATATATAATATACA
11460 ATA-ATAAT
1 ATATATAAT
11468 GCTATAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 8 0.36
15 9 0.41
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATATAATATACA
Found at i:11500 original size:10 final size:11
Alignment explanation
Indices: 11343--11551 Score: 100
Period size: 12 Copynumber: 18.9 Consensus size: 11
11333 TATTATTATG
11343 TATA-ATATAA
1 TATATATATAA
11353 TACTA-A-ATAA
1 TA-TATATATAA
11363 TATATATAT-A
1 TATATATATAA
11373 TATATATATATA
1 TATATATATA-A
*
11385 TATATATATACG
1 TATATATATA-A
*
11397 TATA-AAATAA
1 TATATATATAA
*
11407 AATACTA-ATAA
1 TATA-TATATAA
* *
11418 TATATATGTGAC
1 TATATATAT-AA
11430 TATATATAATAA
1 TATATAT-ATAA
*
11442 TACA-ATAT-A
1 TATATATATAA
*
11451 TA-ATATACAA
1 TATATATATAA
**
11461 TA-ATA-ATGC
1 TATATATATAA
11470 TATAGTATATAA
1 TATA-TATATAA
*
11482 CACTATATATAA
1 TA-TATATATAA
11494 TAT-TATATAA
1 TATATATATAA
*
11504 TACTAGATATAAA
1 TA-TATATAT-AA
*
11517 TATCGTATAATAA
1 TAT-ATAT-ATAA
11530 TATACTATATAA
1 TATA-TATATAA
*
11542 TTTATATATA
1 TATATATATA
11552 TGTAATAATA
Statistics
Matches: 153, Mismatches: 24, Indels: 43
0.70 0.11 0.20
Matches are distributed among these distances:
8 1 0.01
9 11 0.07
10 42 0.27
11 29 0.19
12 51 0.33
13 17 0.11
14 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (11 bp):
TATATATATAA
Found at i:11501 original size:22 final size:22
Alignment explanation
Indices: 11475--11549 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 22
11465 AATGCTATAG
*
11475 TATATAACACTATATATAATAT
1 TATATAATACTATATATAATAT
*
11497 TATATAATACTAGATATAAATAT
1 TATATAATACTATATAT-AATAT
11520 CGTATAATAATA-TACTATATAAT-T
1 --TAT-ATAATACTA-TATATAATAT
11544 TATATA
1 TATATA
11550 TATGTAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
21 3 0.07
22 18 0.40
23 5 0.11
24 1 0.02
25 8 0.18
26 10 0.22
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (22 bp):
TATATAATACTATATATAATAT
Found at i:12233 original size:27 final size:25
Alignment explanation
Indices: 12203--12260 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
12193 CATAAAATAT
*
12203 ATATTTTTAAATTAAGTTACTA-ATAAA
1 ATATTTTT-AA-TAAGTTAATATA-AAA
*
12230 ATATATTTAATAAGTTAATATAAAA
1 ATATTTTTAATAAGTTAATATAAAA
12255 ATATTT
1 ATATTT
12261 AAGTTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 17 0.63
26 3 0.11
27 7 0.26
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (25 bp):
ATATTTTTAATAAGTTAATATAAAA
Found at i:12262 original size:23 final size:25
Alignment explanation
Indices: 12215--12262 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
12205 ATTTTTAAAT
*
12215 TAAGTTACTAATAAAATATATTTAA
1 TAAGTTAATAATAAAATATATTTAA
12240 TAAGTTAAT-ATAAAA-ATATTTAA
1 TAAGTTAATAATAAAATATATTTAA
12263 GTTAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.36
24 6 0.27
25 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
TAAGTTAATAATAAAATATATTTAA
Found at i:12274 original size:2 final size:2
Alignment explanation
Indices: 12267--12301 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12257 ATTTAAGTTA
12267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12302 ATTTAAGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12278 original size:20 final size:20
Alignment explanation
Indices: 12230--12307 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
12220 TACTAATAAA
*
12230 ATATATTTA-ATAAGTTAAT
1 ATATATATATATAAGTTAAT
* * *
12249 ATAAAAATATTTAAGTTAAT
1 ATATATATATATAAGTTAAT
12269 ATATATATATAT-A-TATATAT
1 ATATATATATATAAGT-TA-AT
*
12289 ATATATATATATAATTTAA
1 ATATATATATATAAGTTAA
12308 GTATTTATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.02
19 9 0.19
20 33 0.70
21 3 0.06
22 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
ATATATATATATAAGTTAAT
Found at i:18114 original size:2 final size:2
Alignment explanation
Indices: 18107--18187 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
18097 ATGAAACATG
18107 TA TA TA TA 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 TA TA TA TA
18149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18188 TCATGGGACT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18301 original size:14 final size:14
Alignment explanation
Indices: 18284--18319 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
18274 TAAAAACATA
18284 AAATTAAAGTAAAG
1 AAATTAAAGTAAAG
* *
18298 AAATTAGAGTAATG
1 AAATTAAAGTAAAG
18312 AAATTAAA
1 AAATTAAA
18320 CAAATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (14 bp):
AAATTAAAGTAAAG
Found at i:19847 original size:39 final size:40
Alignment explanation
Indices: 19790--19880 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 40
19780 CTACAAGTTC
* *
19790 TTCTC-ATTATGAATTTATTCTCCTTTTTTGAATGAGCTA
1 TTCTCAATTATGAACTTATTCTCCTTCTTTGAATGAGCTA
* * *
19829 TTCTCAATT-TGAACTTATTCTCCTTCTTTGGATGAGTTT
1 TTCTCAATTATGAACTTATTCTCCTTCTTTGAATGAGCTA
19868 TTCTC-ATTATGAA
1 TTCTCAATTATGAA
19881 TCCTTCCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 3 0.07
39 39 0.87
40 3 0.07
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (40 bp):
TTCTCAATTATGAACTTATTCTCCTTCTTTGAATGAGCTA
Found at i:20133 original size:129 final size:129
Alignment explanation
Indices: 19894--20177 Score: 351
Period size: 129 Copynumber: 2.2 Consensus size: 129
19884 TTCCATTAGA
* * ** *
19894 AATACTGATCCATCTCCTAGTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCTTTCTG
1 AATATTGATCCACCTCCTTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCTTTATG
* * * *
19959 AACTTATTATTCCTTTGATTATACTGGTCCACCTCCTTCTATGATGAACTCTAGA-AA-GACTGA
66 AACATATTATTCCTTTGATTATACTGATCCACCTCCTTCTATGATGAAATATA-ACAAGGA-TGA
20022 C
129 C
* * *
20023 AATGTTGATCCACCTTCTTCTGTGATGGATTTGAGTAAAAGGTCGAAGAAGTTCTTCT-TATTAT
1 AATATTGATCCACCTCCTTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCT-TTAT
* * * *
20087 GAACATCTTCTTCCTTTGATTATGA-TGATCCACCTCTTTCTGTGATGAAATATAACAAGGATGA
65 GAACATATTATTCCTTTGATTAT-ACTGATCCACCTCCTTCTATGATGAAATATAACAAGGATGA
20151 C
129 C
*
20152 AATATTGATCGACCTCCTTCTGTGAT
1 AATATTGATCCACCTCCTTCTGTGAT
20178 TGAATCAAAC
Statistics
Matches: 132, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
128 2 0.02
129 127 0.96
130 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (129 bp):
AATATTGATCCACCTCCTTCTGTGATGGATTTGAGTAAAAGGTCGAACAAGTTCTTCTCTTTATG
AACATATTATTCCTTTGATTATACTGATCCACCTCCTTCTATGATGAAATATAACAAGGATGAC
Found at i:20192 original size:129 final size:128
Alignment explanation
Indices: 19930--20217 Score: 314
Period size: 129 Copynumber: 2.2 Consensus size: 128
19920 GGATTTGAGT
* * *
19930 AAAAGGTCGAACAAGTTCTTCTCTTTCTGAACTTATTATTCCTTTGATTATACTGGTCCACCTCC
1 AAAAGGTCGAACAAGTTCTTCT-TTTATGAACATATTATTCCTTTGATTATACTGATCCACCTCC
* * * * * ** **
19995 TTCTATGATGAACTCTAGAAAGACTGACAATGTTGATCCACCTTCTTCTGTGATGGATTTGAGT
65 TTCTATGATGAAATATAGAAAGACTGACAATATTGATCCACCTCCTTCTGTGATGGAATCAAAC
* * *
20059 AAAAGGTCGAAGAAGTTCTTCTTATTATGAACATCTTCTTCCTTTGATTATGA-TGATCCACCTC
1 AAAAGGTCGAACAAGTTCTTCTT-TTATGAACATATTATTCCTTTGATTAT-ACTGATCCACCTC
* * * *
20123 TTTCTGTGATGAAATATA-ACAAGGA-TGACAATATTGATCGACCTCCTTCTGTGATTGAATCAA
64 CTTCTATGATGAAATATAGA-AA-GACTGACAATATTGATCCACCTCCTTCTGTGATGGAATCAA
20186 AC
127 AC
* *
20188 AAAAGGTTGAACAAGCTCTTC-TTTATGAAC
1 AAAAGGTCGAACAAGTTCTTCTTTTATGAAC
20218 TCATTCTCAC
Statistics
Matches: 133, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
127 8 0.06
128 3 0.02
129 119 0.89
130 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (128 bp):
AAAAGGTCGAACAAGTTCTTCTTTTATGAACATATTATTCCTTTGATTATACTGATCCACCTCCT
TCTATGATGAAATATAGAAAGACTGACAATATTGATCCACCTCCTTCTGTGATGGAATCAAAC
Found at i:20405 original size:160 final size:160
Alignment explanation
Indices: 20221--20536 Score: 485
Period size: 160 Copynumber: 2.0 Consensus size: 160
20211 TATGAACTCA
* *
20221 TTCTCACTCTTCAGACGAGTTCTTCTCATTATTAACCATTCCATTGGAAATGATGATCCACCTCA
1 TTCTCACTCTTCAGACGAGTTCTTCTCATTATGAACCATTCCATTGGAAATGACGATCCACCTC-
* * *
20286 T-TCTGTGATGGATTCGATCAAAATGATGATGCTGATCTATCTCCTTATGTGATAG-AGTCGAG-
65 TGTCTATGATGGATTCGATCAAAATGATGATGCTGATATATCTCCTTATGTAATAGAAGTC-AGT
20348 AAAATGGGTGAACAAGTTCTTCTCATTATAAAC
129 AAAA-GGGTGAACAAGTTCTTCTCATTATAAAC
*
20381 TTCTCACTCTTCAGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGACGATCCACCTCT
1 TTCTCACTCTTCAGACGAGTTCTTCTCATTATGAACCATTCCATTGGAAATGACGATCCACCTCT
* * * * *
20446 GTCTATGATGGATTCGATCAAAATGCTGATGTTGATATATCTTCTTCTGTAATAGAATTCAGTAA
66 GTCTATGATGGATTCGATCAAAATGATGATGCTGATATATCTCCTTATGTAATAGAAGTCAGTAA
20511 AAGGGTGAACAAGTTCTTCTCATTAT
131 AAGGGTGAACAAGTTCTTCTCATTAT
20537 GAACCTCTTC
Statistics
Matches: 142, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
159 1 0.01
160 134 0.94
161 7 0.05
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (160 bp):
TTCTCACTCTTCAGACGAGTTCTTCTCATTATGAACCATTCCATTGGAAATGACGATCCACCTCT
GTCTATGATGGATTCGATCAAAATGATGATGCTGATATATCTCCTTATGTAATAGAAGTCAGTAA
AAGGGTGAACAAGTTCTTCTCATTATAAAC
Found at i:21001 original size:101 final size:100
Alignment explanation
Indices: 20829--21078 Score: 234
Period size: 101 Copynumber: 2.5 Consensus size: 100
20819 ATGTAAACGA
* * * * * * * *
20829 ATAAGAAATTTGTTTTCAAGAGAAGCTATCTCAGGTGAGATAAAATTTTGTTTCGAGTGAACAAT
1 ATAAGAAATTGGTTTT-AAGAAAAACAATCTCAAGTGAGAT-AAATCTTATTTCAAGTGAACAAT
* * * * * *
20894 TTCAAAATTTGTGTTTCAAA-GGAAACTGTCTCAA-GCG
64 TCCAAAACTCGTGCTT-AAATGGAAAATGACT-AATGCG
* *
20931 ATAAGAAATTGGTTTTAAGAAAAACAATCTCAAATGAGATAAATCTTATTTCAAGTGAAGTAATT
1 ATAAGAAATTGGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTATTTCAAGTGAA-CAATT
*
20996 CCAAAACTCGTGCTTAAATGGAAAATGACTAATGTG
65 CCAAAACTCGTGCTTAAATGGAAAATGACTAATGCG
* * * ** *
21032 AGACGAAATTGATTTTAAGGTAAACAATATCAAGTGAGATAAATCTT
1 ATAAGAAATTGGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTT
21079 GTCATATCAA
Statistics
Matches: 121, Mismatches: 24, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
100 21 0.17
101 85 0.70
102 15 0.12
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (100 bp):
ATAAGAAATTGGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTATTTCAAGTGAACAATTC
CAAAACTCGTGCTTAAATGGAAAATGACTAATGCG
Found at i:23193 original size:35 final size:35
Alignment explanation
Indices: 23134--23269 Score: 108
Period size: 34 Copynumber: 4.0 Consensus size: 35
23124 CTCCTTTCAG
* * *
23134 TTTTCTTTT-TTCTCTTTTTCTTTATTTTTTCTTC
1 TTTTATTTTCTTCTCTCTTTATTTATTTTTTCTTC
23168 TTTT-TATTTCTTCTCTCTTTATTTA-TTTTTCTT-
1 TTTTAT-TTTCTTCTCTCTTTATTTATTTTTTCTTC
* *
23201 TTTTCTTTTCTT-TCTTTTTTATTT-TTATTTTC-TC
1 TTTTATTTTCTTCTC-TCTTTATTTATT-TTTTCTTC
* * *
23235 TTTTATTTTTCTTCT-TCTTTTTTTCTCTTTTCTTC
1 TTTTA-TTTTCTTCTCTCTTTATTTATTTTTTCTTC
23270 AGGTGTAATT
Statistics
Matches: 84, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
32 2 0.02
33 21 0.25
34 37 0.44
35 23 0.27
36 1 0.01
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (35 bp):
TTTTATTTTCTTCTCTCTTTATTTATTTTTTCTTC
Found at i:23219 original size:67 final size:68
Alignment explanation
Indices: 23134--23268 Score: 163
Period size: 67 Copynumber: 2.0 Consensus size: 68
23124 CTCCTTTCAG
23134 TTTTCTTTTTTCTCTTTTTCT-TTATT-TTTTCTTCTTTT-TATTTCTTCTCTCTTTATTTAT-T
1 TTTTCTTTTTTCTCTTTTT-TATTATTATTTTC-TCTTTTATATTTCTTCT-TCTTTATTTATCT
23195 TTTCTT
63 TTTCTT
* * * *
23201 TTTTCTTTTCTT-TCTTTTTTATTTTTATTTTCTCTTTTATTTTTCTTCTTCTTTTTTTCTCTTT
1 TTTTCTTTT-TTCTCTTTTTTATTATTATTTTCTCTTTTATATTTCTTCTTCTTTATTTATCTTT
23265 TCTT
65 TCTT
23269 CAGGTGTAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
66 1 0.02
67 35 0.59
68 23 0.39
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (68 bp):
TTTTCTTTTTTCTCTTTTTTATTATTATTTTCTCTTTTATATTTCTTCTTCTTTATTTATCTTTT
CTT
Found at i:23240 original size:47 final size:48
Alignment explanation
Indices: 23148--23265 Score: 124
Period size: 45 Copynumber: 2.6 Consensus size: 48
23138 CTTTTTTCTC
*
23148 TTTTTCTTTATT-TTTTC-TTC-TTTTTATTTCTTCTCTCTTTATTTA
1 TTTTTCTTTATTCTTTTCTTTCTTTTTTATTTCTTCTCTCTCTATTTA
* * *
23193 TTTTTCTTTTTTCTTTTCTTTCTTTTTTATTT-TTATTTTCTCT-TTTA
1 TTTTTCTTTATTCTTTTCTTTCTTTTTTATTTCTT-CTCTCTCTATTTA
* *
23240 TTTTTC-TTCTTCTTTT-TTTCTCTTTT
1 TTTTTCTTTATTCTTTTCTTTCTTTTTT
23266 CTTCAGGTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
45 20 0.32
46 14 0.22
47 15 0.24
48 14 0.22
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (48 bp):
TTTTTCTTTATTCTTTTCTTTCTTTTTTATTTCTTCTCTCTCTATTTA
Found at i:29753 original size:37 final size:38
Alignment explanation
Indices: 29692--29770 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
29682 GCGTCACATC
* * * *
29692 AAAATTAAAATAAATAAAATGTAAAAAGTG-AACAAAT
1 AAAATGAAAATAAATAAAAGGTAAAAAATGAAACAAAA
**
29729 AAAATGAAAATAAATAATGGGTAAAAAATGAAACAAAA
1 AAAATGAAAATAAATAAAAGGTAAAAAATGAAACAAAA
29767 AAAA
1 AAAA
29771 GATAAAATGG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 25 0.71
38 10 0.29
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.18
Consensus pattern (38 bp):
AAAATGAAAATAAATAAAAGGTAAAAAATGAAACAAAA
Found at i:31241 original size:163 final size:163
Alignment explanation
Indices: 30953--31340 Score: 496
Period size: 163 Copynumber: 2.4 Consensus size: 163
30943 AAGCTCTTCT
* * * * *
30953 TTAT-AAACTCCTTATCACTCTTCATACGAGTTCTTCTCATTATGAACCATTCCATTAGAAATGA
1 TTATGAAACT-CTTCTCACTCTTCAGATGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGA
* * * ** * *
31017 CGATCCACCTTATTCTATGATGGATTTAATCAAAATGTTGATGCTGATCTATATTCTTCTGCAAT
65 CAATCCACCTCATTATATGATGGATCCAATAAAAATGTTGATGCTGATCTATATCCTTCTGCAAT
*
31082 AGAATCGAGAAAAAGGG-TGAATAAGTTATTCTCA
130 AGAATCGAG-AAAAGGGTTGAACAAGTTATTCTCA
* *
31116 TTATGAAATTCTTCTCACTCTTCAGATGAGTTCTTCTCATTTTGAACCCTTCCATTGGAAATGAC
1 TTATGAAACTCTTCTCACTCTTCAGATGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGAC
* * *
31181 AATCCACCTCCTTATATGATGGATCCAATAAAAATGTTGATGCTGATCTATCTCCTTCTGCGATA
66 AATCCACCTCATTATATGATGGATCCAATAAAAATGTTGATGCTGATCTATATCCTTCTGCAATA
* *
31246 GAATCTAGCAAAGGGTTGAACAAGTTATTCTCA
131 GAATCGAGAAAAGGGTTGAACAAGTTATTCTCA
* * * * *
31279 TTATGAACCTCTTCTCCCTC-TCAGGATGAGTTCCTCTCATTATGAACTC-TCTATTGGAAATG
1 TTATGAAACTCTTCTCACTCTTCA-GATGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATG
31341 TTGATCCATT
Statistics
Matches: 195, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
162 21 0.11
163 170 0.87
164 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (163 bp):
TTATGAAACTCTTCTCACTCTTCAGATGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGAC
AATCCACCTCATTATATGATGGATCCAATAAAAATGTTGATGCTGATCTATATCCTTCTGCAATA
GAATCGAGAAAAGGGTTGAACAAGTTATTCTCA
Found at i:33387 original size:24 final size:23
Alignment explanation
Indices: 33349--33393 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
33339 AGGGAACAAT
* *
33349 AATATTTTCTAAGAAGGATATAA
1 AATATTTTCAAAGAAGAATATAA
33372 AATATTTTCAAGAGAAGAATAT
1 AATATTTTCAA-AGAAGAATAT
33394 TTCTTGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (23 bp):
AATATTTTCAAAGAAGAATATAA
Found at i:33596 original size:83 final size:82
Alignment explanation
Indices: 33457--33618 Score: 256
Period size: 83 Copynumber: 2.0 Consensus size: 82
33447 GGAATTTTGA
*
33457 GAGAGTTTTACTCACTCTAAAACTCCTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAA
1 GAGAGTTTTACTCACACTAAAACTCCTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAA
33522 ATTTAAAATATTAAACCT
66 ATTT-AAATATTAAACCT
* *
33540 GAGAGTTTTACTC-CAACT-AAACATCTTTTAATATCTAAATTTAAACAACTAATAATATCTTTT
1 GAGAGTTTTACTCAC-ACTAAAAC-TCCTTTAATATCTAAATTTAAACAAATAATAATATCTTTT
33603 AAATTTAAATATTAAA
64 AAATTTAAATATTAAA
33619 TAGATATACA
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
82 15 0.20
83 59 0.80
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.39
Consensus pattern (82 bp):
GAGAGTTTTACTCACACTAAAACTCCTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAA
ATTTAAATATTAAACCT
Found at i:35462 original size:30 final size:31
Alignment explanation
Indices: 35406--35469 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
35396 TAAAGTTTGA
*
35406 AAAAGTTTAAGGGACTAAAAGAGTAATTTTC
1 AAAAGTTTAAGGGACCAAAAGAGTAATTTTC
*
35437 AAAAGTTTAA-GGACCAAAAGTGTAATTTTC
1 AAAAGTTTAAGGGACCAAAAGAGTAATTTTC
35467 AAA
1 AAA
35470 TTTTTTGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (31 bp):
AAAAGTTTAAGGGACCAAAAGAGTAATTTTC
Found at i:59071 original size:28 final size:27
Alignment explanation
Indices: 59035--59097 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
59025 GAATAATGAT
* *
59035 AAAAGAGAAAAATAAAGAGAAAGAAAAG
1 AAAAAAGAAAAATAAAAAGAAA-AAAAG
* *
59063 AAAAAAGAAAATTAAAAAGAAAAAAAT
1 AAAAAAGAAAAATAAAAAGAAAAAAAG
59090 AATAAAAG
1 AA-AAAAG
59098 GGGGCTAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (27 bp):
AAAAAAGAAAAATAAAAAGAAAAAAAG
Found at i:60357 original size:37 final size:37
Alignment explanation
Indices: 60302--60417 Score: 166
Period size: 37 Copynumber: 3.2 Consensus size: 37
60292 AGGTTCCTTC
*
60302 GAAGTAAGTCAATCTTAAGCCTTCAC-GAAGGAGTAGT
1 GAAGCAAGTCAATCTTAAGCCTTCACGGAA-GAGTAGT
*
60339 GAAGCAAGTCAATATTAAGCCTTCACGGAAGAGTAGT
1 GAAGCAAGTCAATCTTAAGCCTTCACGGAAGAGTAGT
* *
60376 AAAGCAAATC-ATCTT-AGCCTTCACGGAAGAGTAGT
1 GAAGCAAGTCAATCTTAAGCCTTCACGGAAGAGTAGT
60411 GAAGCAA
1 GAAGCAA
60418 ATCAGTCTCG
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 26 0.36
36 4 0.06
37 39 0.54
38 3 0.04
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (37 bp):
GAAGCAAGTCAATCTTAAGCCTTCACGGAAGAGTAGT
Found at i:60402 original size:35 final size:36
Alignment explanation
Indices: 60313--60421 Score: 159
Period size: 35 Copynumber: 3.0 Consensus size: 36
60303 AAGTAAGTCA
*
60313 ATCTTAAGCCTTCAC-GAAGGAGTAGTGAAGCAAGTC
1 ATCTTAAGCCTTCACGGAA-GAGTAGTGAAGCAAATC
* *
60349 AATATTAAGCCTTCACGGAAGAGTAGTAAAGCAAATC
1 -ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
60386 ATCTT-AGCCTTCACGGAAGAGTAGTGAAGCAAATC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
60421 A
1 A
60422 GTCTCGAGTC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 30 0.45
36 4 0.06
37 29 0.44
38 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
Found at i:60583 original size:55 final size:55
Alignment explanation
Indices: 60425--60627 Score: 162
Period size: 55 Copynumber: 3.7 Consensus size: 55
60415 CAAATCAGTC
* * * ** *
60425 TCGAGTCTGAT-CTCCCTGAAAGAAGAGGAAGCATACCCA-TTTTCAGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGACTCATTTTTC-GAAGATTGT
* * * * * * **
60479 TAGAGTTTTGTACTCCCTGAAATAATAGGGAGTGAAC-C-TGGTTACCGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGACTCAT--TTTTCGAAGATTGT
60534 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGACTCATTTTTCGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGACTCATTTTTCGAAGATTGT
* ** * * * *
60589 TTGAGTCCAATACTCCTTGAAAGAAAAAGGAGTGGACTC
1 TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGACTC
60628 GTCCTTTAAA
Statistics
Matches: 116, Mismatches: 27, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
54 8 0.07
55 103 0.89
56 4 0.03
57 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (55 bp):
TCGAGTCTTATACTCCCTGAAAGAATAGGGAGCGGACTCATTTTTCGAAGATTGT
Found at i:61047 original size:11 final size:11
Alignment explanation
Indices: 61031--61055 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
61021 TTGGCAGAAG
61031 TAAATGAGGAA
1 TAAATGAGGAA
61042 TAAATGAGGAA
1 TAAATGAGGAA
61053 TAA
1 TAA
61056 TATATCAGCA
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:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (11 bp):
TAAATGAGGAA
Found at i:63232 original size:30 final size:30
Alignment explanation
Indices: 63168--63234 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
63158 TAAAGTTTAA
* * *
63168 AAAAGTTTAGTGACTAAAAGGGTATTTTTT
1 AAAAGTTTAGGGACTAAAAGGGTAATTTTC
* **
63198 AAAAGTTTAGGGACTATAAGTTTAATTTTC
1 AAAAGTTTAGGGACTAAAAGGGTAATTTTC
63228 AAAAGTT
1 AAAAGTT
63235 ATGTATTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (30 bp):
AAAAGTTTAGGGACTAAAAGGGTAATTTTC
Found at i:63337 original size:17 final size:17
Alignment explanation
Indices: 63315--63356 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
63305 TCCAGAATTT
63315 GTGTTAAAAGCGAGAAA
1 GTGTTAAAAGCGAGAAA
63332 GTGTTAAAAGCGAGAAA
1 GTGTTAAAAGCGAGAAA
*
63349 ATGTTAAA
1 GTGTTAAA
63357 TTCCGGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.05, G:0.26, T:0.21
Consensus pattern (17 bp):
GTGTTAAAAGCGAGAAA
Found at i:64241 original size:20 final size:21
Alignment explanation
Indices: 64213--64251 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
64203 TGATGTACTA
64213 TGCTGGAAATTAATGTTAGAG
1 TGCTGGAAATTAATGTTAGAG
*
64234 TGCT-GAAATTGATGTTAG
1 TGCTGGAAATTAATGTTAG
64252 GATGTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (21 bp):
TGCTGGAAATTAATGTTAGAG
Found at i:64261 original size:19 final size:20
Alignment explanation
Indices: 64213--64263 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
64203 TGATGTACTA
*
64213 TGCTGGAAATTAATGTTAGAG
1 TGCT-GAAATTGATGTTAGAG
64234 TGCTGAAATTGATGTTAG-G
1 TGCTGAAATTGATGTTAGAG
64253 ATG-TGAAATTG
1 -TGCTGAAATTG
64264 GGTCATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 9 0.32
20 15 0.54
21 4 0.14
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.35
Consensus pattern (20 bp):
TGCTGAAATTGATGTTAGAG
Found at i:65517 original size:22 final size:22
Alignment explanation
Indices: 65490--65534 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
65480 CACTAGTTAT
65490 TATATATGATGTTTATCATGAA
1 TATATATGATGTTTATCATGAA
*
65512 TATATATGATGTTTATTATGAA
1 TATATATGATGTTTATCATGAA
65534 T
1 T
65535 GTTATTTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (22 bp):
TATATATGATGTTTATCATGAA
Found at i:69330 original size:21 final size:21
Alignment explanation
Indices: 69305--69344 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
69295 AAGACTTTAT
69305 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
69326 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
69345 AAATAGTCTT
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:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:72886 original size:47 final size:45
Alignment explanation
Indices: 72819--72945 Score: 175
Period size: 47 Copynumber: 2.8 Consensus size: 45
72809 TATAAAATCC
72819 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* * *
72864 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* *
72911 CTTGCCA-TTATTCCAAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTT
72946 ATATGCTTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
44 5 0.07
45 29 0.39
46 2 0.03
47 38 0.51
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
Found at i:73158 original size:59 final size:59
Alignment explanation
Indices: 73054--73182 Score: 170
Period size: 59 Copynumber: 2.2 Consensus size: 59
73044 CGTAGTGCTA
* * **
73054 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTAATAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAG
* ** *
73113 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACA-AGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACA-ATAGGTATCCTTAAGTACAG
73172 TCCCGAATATG
1 TCCCGAATATG
73183 CAGCCTGCTG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 60 0.98
60 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAG
Found at i:77012 original size:17 final size:17
Alignment explanation
Indices: 76990--77049 Score: 102
Period size: 17 Copynumber: 3.5 Consensus size: 17
76980 TAATTTAATA
76990 AATGAACTAGTTTGATG
1 AATGAACTAGTTTGATG
77007 AATGAACTAGTTTGATG
1 AATGAACTAGTTTGATG
* *
77024 AATGAACTAGTTTAATT
1 AATGAACTAGTTTGATG
77041 AATGAACTA
1 AATGAACTA
77050 CTTCCCTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (17 bp):
AATGAACTAGTTTGATG
Found at i:77062 original size:34 final size:34
Alignment explanation
Indices: 76987--77067 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
76977 AGTTAATTTA
* * **
76987 ATAAATGAACTAGTTTGATGAATGAACTAGTTTG
1 ATAAATGAACTAGTTTAATGAATGAACTACTTCC
* *
77021 ATGAATGAACTAGTTTAATTAATGAACTACTTCC
1 ATAAATGAACTAGTTTAATGAATGAACTACTTCC
*
77055 CTAAATGAACTAG
1 ATAAATGAACTAG
77068 ATGATTTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (34 bp):
ATAAATGAACTAGTTTAATGAATGAACTACTTCC
Found at i:84745 original size:50 final size:50
Alignment explanation
Indices: 84660--84758 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
84650 GCACATGAAG
* *
84660 ACTTTGGCACTAAGATGAACCAATACATCATCATTCGGCCAAGGAAGATA
1 ACTTTGGCACCAAGATGAACCAATACATCACCATTCGGCCAAGGAAGATA
* *
84710 ACTTTGGCACCAAGATGAA-CAA-GCATGTCACCATTCGGCCAAGGGAGAT
1 ACTTTGGCACCAAGATGAACCAATACA--TCACCATTCGGCCAAGGAAGAT
84759 GTATCTTCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 2 0.05
49 3 0.07
50 38 0.88
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.20
Consensus pattern (50 bp):
ACTTTGGCACCAAGATGAACCAATACATCACCATTCGGCCAAGGAAGATA
Found at i:89407 original size:19 final size:20
Alignment explanation
Indices: 89383--89432 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
89373 CTTTTCTATC
89383 CTTATTCCATTAATTA-TTA
1 CTTATTCCATTAATTATTTA
*
89402 CTTATTCAATTAATTATTTTA
1 CTTATTCCATTAATTA-TTTA
89423 CTTA-TCCATT
1 CTTATTCCATT
89433 TCTTATACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 15 0.56
20 5 0.19
21 7 0.26
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (20 bp):
CTTATTCCATTAATTATTTA
Done.