Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003677.1 Hibiscus syriacus cultivar Beakdansim tig00007857_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: 52237
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:10636 original size:18 final size:17
Alignment explanation
Indices: 10594--10635 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
10584 ACACAAAATA
10594 TGACTTTTCAAAAATTT
1 TGACTTTTCAAAAATTT
* *
10611 TAACTTTTCGAAAATTT
1 TGACTTTTCAAAAATTT
10628 TGACTTTT
1 TGACTTTT
10636 TGGTCAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (17 bp):
TGACTTTTCAAAAATTT
Found at i:12454 original size:30 final size:30
Alignment explanation
Indices: 12420--12502 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
12410 ACCGAATTTT
* * * **
12420 CAAAAAAATTATCGAAAATATTATTAGGCG
1 CAAAAAAATGATCAAAAATATTACTAAACG
12450 CAAAAAAATGA-CAAAAAATATTACTAAACG
1 CAAAAAAATGATC-AAAAATATTACTAAACG
*
12480 CTAAAAAATGATCAAAAATATTA
1 CAAAAAAATGATCAAAAATATTA
12503 AAAAATAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.02
30 43 0.96
31 1 0.02
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.23
Consensus pattern (30 bp):
CAAAAAAATGATCAAAAATATTACTAAACG
Found at i:15918 original size:226 final size:222
Alignment explanation
Indices: 15421--15886 Score: 613
Period size: 226 Copynumber: 2.1 Consensus size: 222
15411 CTAATTCATA
* * * * * * *
15421 TATTCGGGTTGGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGGTTGGTTTTTTAAGTGTGATAT
1 TATTCGGGTCGAGTCGGGTCAAAGTTTATTTCGGTCGGGTCGGGTCGGTTTTTTAAGTGTGATAT
* * *
15486 TCGGGTTGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCTGACCCGAAAATATATATAATTTTAC
66 TCGGGTCGGGTCGA-----GGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTAC
15551 CTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCCCAATAAAGTCA
126 CTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCCCAATAAAGTCA
15616 CTGTTTTTATTGAATAAAAATATTTTTTTTAT
191 CTGTTTTTATTGAATAAAAATATTTTTTTTAT
** * *
15648 TATTTTGGTCGAGTCGGGTGAAAGTTTATTTCGGTCAGGTCGGGTCGGTTTTTTTAAGTGTGATA
1 TATTCGGGTCGAGTCGGGTCAAAGTTTATTTCGGTCGGGTCGGGTCGG-TTTTTTAAGTGTGATA
*
15713 TTCGGGTCGGGTCGA-GTTTATGGTGAAAAATACCCGACCCGACCCAAAAAATATATAATTTTAC
65 TTCGGGTCGGGTCGAGGTTTAGGGTGAAAAATACCCGACCCG----AAAAAATATATAATTTTAC
* *
15777 CTTATATATTTAGGAATAATTACAATAATA-CCC-CTATATAT-ATTTTGTTT-TCAATTAAGTC
126 CTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTT-TTTCCCAATAAAGTC
15838 ACTGTTTTTATTGAATAAAAATATATTTTTTTA-
190 ACTGTTTTTATTGAATAAAAATAT-TTTTTTTAT
*
15871 T-TTCGGGTCGGGTCGG
1 TATTCGGGTCGAGTCGG
15887 TTTCTAATTC
Statistics
Matches: 214, Mismatches: 18, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
222 36 0.17
223 39 0.18
224 19 0.09
225 3 0.01
226 48 0.22
227 39 0.18
228 30 0.14
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (222 bp):
TATTCGGGTCGAGTCGGGTCAAAGTTTATTTCGGTCGGGTCGGGTCGGTTTTTTAAGTGTGATAT
TCGGGTCGGGTCGAGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTAT
ATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCCCAATAAAGTCACTGTT
TTTATTGAATAAAAATATTTTTTTTAT
Found at i:17121 original size:20 final size:21
Alignment explanation
Indices: 17096--17137 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17086 GAGTCCCATC
* *
17096 TGTTGT-TTTGTATAGTTCTT
1 TGTTGTATCTGTATAGCTCTT
17116 TGTTGTATCTGTATAGCTCTT
1 TGTTGTATCTGTATAGCTCTT
17137 T
1 T
17138 TCGCTTTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.12, C:0.10, G:0.19, T:0.60
Consensus pattern (21 bp):
TGTTGTATCTGTATAGCTCTT
Found at i:22320 original size:21 final size:21
Alignment explanation
Indices: 22288--22365 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
22278 ATCATTCATT
22288 AACCATTAAACCATAGACTATA
1 AACCA-TAAACCATAGACTATA
22310 AACCATAAACCATAGACTATA
1 AACCATAAACCATAGACTATA
* *
22331 AACCACAAACAATAGACTATA
1 AACCATAAACCATAGACTATA
*
22352 AACTATAAACCATA
1 AACCATAAACCATA
22366 AACCATAGCC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 46 0.90
22 5 0.10
ACGTcount: A:0.54, C:0.23, G:0.04, T:0.19
Consensus pattern (21 bp):
AACCATAAACCATAGACTATA
Found at i:22323 original size:7 final size:7
Alignment explanation
Indices: 22288--22372 Score: 80
Period size: 7 Copynumber: 12.0 Consensus size: 7
22278 ATCATTCATT
22288 AACCATTA
1 AACCA-TA
22296 AACCATA
1 AACCATA
* *
22303 GACTATA
1 AACCATA
22310 AACCATA
1 AACCATA
22317 AACCATA
1 AACCATA
* *
22324 GACTATA
1 AACCATA
*
22331 AACCACA
1 AACCATA
*
22338 AACAATA
1 AACCATA
* *
22345 GACTATA
1 AACCATA
*
22352 AACTATA
1 AACCATA
22359 AACCATA
1 AACCATA
22366 AACCATA
1 AACCATA
22373 GCCCAATATA
Statistics
Matches: 62, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
7 57 0.92
8 5 0.08
ACGTcount: A:0.54, C:0.24, G:0.04, T:0.19
Consensus pattern (7 bp):
AACCATA
Found at i:22915 original size:24 final size:24
Alignment explanation
Indices: 22883--22928 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
22873 AGTCTTCCTG
22883 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
22907 ATGATGTATAAAACATTTATGT
1 ATGATGTATAAAACATCTATGT
22929 TCAATGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:23504 original size:31 final size:30
Alignment explanation
Indices: 23468--23525 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
23458 CAACCATTCA
* *
23468 CAACTTTTCTAAAATTATCAAATTGGTCCCC
1 CAACTTTTCAAAAATTA-CAAAATGGTCCCC
23499 CAACTTTTCAAAAATTACAAAATGGTC
1 CAACTTTTCAAAAATTACAAAATGGTC
23526 TCTAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (30 bp):
CAACTTTTCAAAAATTACAAAATGGTCCCC
Found at i:26162 original size:8 final size:8
Alignment explanation
Indices: 26146--26208 Score: 75
Period size: 8 Copynumber: 8.6 Consensus size: 8
26136 TCTCTCATCT
26146 TTTTTTTC
1 TTTTTTTC
*
26154 TTCTTTTC
1 TTTTTTTC
26162 --TTTTTC
1 TTTTTTTC
26168 --TTTTTC
1 TTTTTTTC
26174 TTTTTTTC
1 TTTTTTTC
26182 TTTTTTTC
1 TTTTTTTC
26190 -TTTTTTC
1 TTTTTTTC
26197 -TTTTTTC
1 TTTTTTTC
26204 TTTTT
1 TTTTT
26209 CTTGTTTTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
6 11 0.22
7 14 0.28
8 25 0.50
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTTC
Found at i:26167 original size:14 final size:13
Alignment explanation
Indices: 26148--26216 Score: 84
Period size: 14 Copynumber: 4.9 Consensus size: 13
26138 TCTCATCTTT
26148 TTTTTCTTCTTTTC
1 TTTTTCTT-TTTTC
*
26162 TTTTTCTTTTTCTT
1 TTTTTCTTTTT-TC
26176 TTTTTCTTTTTTTC
1 TTTTTC-TTTTTTC
26190 TTTTTTCTTTTTTC
1 -TTTTTCTTTTTTC
26204 TTTTTCTTGTTTT
1 TTTTTCTT-TTTT
26217 TAGCTTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.22
14 27 0.55
15 11 0.22
ACGTcount: A:0.00, C:0.14, G:0.01, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:26178 original size:7 final size:7
Alignment explanation
Indices: 26147--26208 Score: 83
Period size: 7 Copynumber: 8.7 Consensus size: 7
26137 CTCTCATCTT
26147 TTTTTTC
1 TTTTTTC
26154 TTCTTTTC
1 TT-TTTTC
26162 -TTTTTC
1 TTTTTTC
26168 -TTTTTC
1 TTTTTTC
26174 TTTTTTTC
1 -TTTTTTC
26182 TTTTTTTC
1 -TTTTTTC
26190 TTTTTTC
1 TTTTTTC
26197 TTTTTTC
1 TTTTTTC
26204 TTTTT
1 TTTTT
26209 CTTGTTTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
6 11 0.21
7 22 0.42
8 19 0.37
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:26186 original size:36 final size:38
Alignment explanation
Indices: 26146--26226 Score: 123
Period size: 36 Copynumber: 2.2 Consensus size: 38
26136 TCTCTCATCT
26146 TTTTTTTCTTCTTTTC-TTTTTCTTTTTCTT-TTTTT-C
1 TTTTTTTCTT-TTTTCTTTTTTCTTTTTCTTGTTTTTAC
26182 TTTTTTTCTTTTTTCTTTTTTCTTTTTCTTGTTTTTAGC
1 TTTTTTTCTTTTTTCTTTTTTCTTTTTCTTGTTTTTA-C
26221 TTTTTT
1 TTTTTT
26227 AGCTCTTATG
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
35 5 0.12
36 24 0.59
37 5 0.12
39 7 0.17
ACGTcount: A:0.01, C:0.14, G:0.02, T:0.83
Consensus pattern (38 bp):
TTTTTTTCTTTTTTCTTTTTTCTTTTTCTTGTTTTTAC
Found at i:26188 original size:28 final size:28
Alignment explanation
Indices: 26145--26226 Score: 103
Period size: 28 Copynumber: 2.8 Consensus size: 28
26135 ATCTCTCATC
*
26145 TTTTTTTTCTTCTTTTC-TTTTTCTTTT
1 TTTTTTTTCTTTTTTTCTTTTTTCTTTT
26172 TCTTTTTTTCTTTTTTTCTTTTTTCTTTT
1 T-TTTTTTTCTTTTTTTCTTTTTTCTTTT
*
26201 TTCTTTTTCTTGTTTTTAGCTTTTTT
1 TTTTTTTTCTT-TTTTT--CTTTTTT
26227 AGCTCTTATG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.02
28 24 0.50
29 16 0.33
31 7 0.15
ACGTcount: A:0.01, C:0.13, G:0.02, T:0.83
Consensus pattern (28 bp):
TTTTTTTTCTTTTTTTCTTTTTTCTTTT
Found at i:34756 original size:115 final size:115
Alignment explanation
Indices: 34554--34868 Score: 569
Period size: 115 Copynumber: 2.7 Consensus size: 115
34544 GAATGTGCTC
34554 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
*
34619 TCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTCA
66 TCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
34669 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
34734 TCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
66 TCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
* * * *
34784 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTCGGTA-GGAACCCCAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
*
34848 TCATTGGAATTGAAAGATGAA
66 TCATTGGATTTGAAAGATGAA
34869 CTGCATGATC
Statistics
Matches: 194, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
114 34 0.18
115 160 0.82
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (115 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
TCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
Found at i:38228 original size:76 final size:76
Alignment explanation
Indices: 38102--38833 Score: 1266
Period size: 76 Copynumber: 9.6 Consensus size: 76
38092 CTATTTCCCA
38102 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
38167 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
38178 CATCTATAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
38243 AGCCTTAGGGT
66 AGCCTTAGGGT
38254 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
38319 AGCCTCAGGGT
66 AGCCTTAGGGT
* *
38330 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCCTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
38395 AGCCTTAGGGT
66 AGCCTTAGGGT
*
38406 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
38471 AGCCTCAGGGT
66 AGCCTTAGGGT
*
38482 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
38547 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
38558 CACCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
38623 AAGCCTTAGGGT
65 AAGCCTTAGGGT
* * * *
38635 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTATGTTCTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
38700 AGCCTCAGGGT
66 AGCCTTAGGGT
* * *
38711 CGTCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
38776 AGCCTCAGGGT
66 AGCCTTAGGGT
* *
38787 TATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGA
38834 TTTTTTTTTG
Statistics
Matches: 623, Mismatches: 32, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
76 552 0.89
77 71 0.11
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:39033 original size:3 final size:3
Alignment explanation
Indices: 39025--39083 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
39015 TTTCACTTAA
** * *
39025 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT A-T ATT AAT AAT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
39073 ATT ATTT ATT A
1 ATT A-TT ATT A
39084 AATATTACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:39605 original size:13 final size:13
Alignment explanation
Indices: 39570--39605 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
39560 GAAGAGATAC
39570 ACAGAGACGAGCA
1 ACAGAGACGAGCA
* *
39583 ATAGAAACGAGCA
1 ACAGAGACGAGCA
39596 ACAGAGACGA
1 ACAGAGACGA
39606 ACCCACAACC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.19, G:0.28, T:0.03
Consensus pattern (13 bp):
ACAGAGACGAGCA
Found at i:40424 original size:22 final size:21
Alignment explanation
Indices: 40394--40447 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
40384 TATTTTATTG
40394 TTATATATTTAAATTAATAATAA
1 TTAT-TATTTAAA-TAATAATAA
* *
40417 TTATTATTTTAATAATATTAA
1 TTATTATTTAAATAATAATAA
40438 TATATTATTT
1 T-TATTATTT
40448 GATTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 9 0.32
22 15 0.54
23 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTATTTAAATAATAATAA
Found at i:40454 original size:22 final size:21
Alignment explanation
Indices: 40406--40454 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
40396 ATATATTTAA
*
40406 ATTAATAATAATTATTATTTT
1 ATTAATAATAATTATTATTTG
* *
40427 AATAATATTAATATATTATTTG
1 ATTAATAATAAT-TATTATTTG
40449 ATTAAT
1 ATTAAT
40455 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTAATAATAATTATTATTTG
Found at i:43249 original size:21 final size:21
Alignment explanation
Indices: 43217--43295 Score: 131
Period size: 21 Copynumber: 3.7 Consensus size: 21
43207 ATCATTCATT
43217 AACCATTAAACCATAGACTATA
1 AACCA-TAAACCATAGACTATA
43239 AACCATAAACCATAGACTATA
1 AACCATAAACCATAGACTATA
* *
43260 AACCATAAACTATAAACTATA
1 AACCATAAACCATAGACTATA
43281 AACCATAAACCATAG
1 AACCATAAACCATAG
43296 CCCAATATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 48 0.91
22 5 0.09
ACGTcount: A:0.53, C:0.23, G:0.04, T:0.20
Consensus pattern (21 bp):
AACCATAAACCATAGACTATA
Found at i:43294 original size:7 final size:7
Alignment explanation
Indices: 43217--43294 Score: 93
Period size: 7 Copynumber: 11.0 Consensus size: 7
43207 ATCATTCATT
43217 AACCATTA
1 AACCA-TA
43225 AACCATA
1 AACCATA
* *
43232 GACTATA
1 AACCATA
43239 AACCATA
1 AACCATA
43246 AACCATA
1 AACCATA
* *
43253 GACTATA
1 AACCATA
43260 AACCATA
1 AACCATA
*
43267 AACTATA
1 AACCATA
*
43274 AACTATA
1 AACCATA
43281 AACCATA
1 AACCATA
43288 AACCATA
1 AACCATA
43295 GCCCAATATA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
7 55 0.92
8 5 0.08
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.21
Consensus pattern (7 bp):
AACCATA
Found at i:43851 original size:24 final size:25
Alignment explanation
Indices: 43806--43855 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
43796 AGTCTTCCTG
43806 ATGATGTATAAAAACATATATGTAC
1 ATGATGTATAAAAACATATATGTAC
*
43831 ATGATGTAT-AAAACATCTATGTAC
1 ATGATGTATAAAAACATATATGTAC
43855 A
1 A
43856 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (25 bp):
ATGATGTATAAAAACATATATGTAC
Found at i:46768 original size:16 final size:16
Alignment explanation
Indices: 46747--46778 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46737 CACTTACACT
46747 TCTCCCCTTTAAAACA
1 TCTCCCCTTTAAAACA
46763 TCTCCCCTTTAAAACA
1 TCTCCCCTTTAAAACA
46779 CTTTAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (16 bp):
TCTCCCCTTTAAAACA
Found at i:49035 original size:23 final size:22
Alignment explanation
Indices: 48989--49059 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
48979 CCATGAGGGT
* * *
48989 ATCGATTCCCCTACAGGGGGGA
1 ATCGGTTCCCCTTCAAGGGGGA
49011 ATCGGTTCCCCTTCAAAGGGGGA
1 ATCGGTTCCCCTTC-AAGGGGGA
* * *
49034 ATTGGTTCCTCTTCAAGGGGGT
1 ATCGGTTCCCCTTCAAGGGGGA
49056 ATCG
1 ATCG
49060 ATTCTCTCTG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 22 0.54
23 19 0.46
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (22 bp):
ATCGGTTCCCCTTCAAGGGGGA
Found at i:51990 original size:19 final size:20
Alignment explanation
Indices: 51956--51997 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
51946 TACTAGCATG
51956 ACCTAGTCTCTTGTGCCATA
1 ACCTAGTCTCTTGTGCCATA
51976 ACCTAGTCT-TTGTGCCATA
1 ACCTAGTCTCTTGTGCCATA
51995 ACC
1 ACC
51998 ACTATCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (20 bp):
ACCTAGTCTCTTGTGCCATA
Done.