Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003505.1 Hibiscus syriacus cultivar Beakdansim tig00007411_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: 60366
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:9641 original size:18 final size:20
Alignment explanation
Indices: 9608--9658 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
9598 TTTGGTTCAC
9608 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
*
9628 GGAATG-AA-ATTACCGGT-
1 GGAATGTAAGATTACCAGTG
*
9645 GGAA-ATAAGATTAC
1 GGAATGTAAGATTAC
9659 TGGAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 6 0.22
18 13 0.48
19 2 0.07
20 6 0.22
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:9878 original size:37 final size:37
Alignment explanation
Indices: 9804--9878 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
9794 ATTCTACTAT
* *
9804 AATTAATATATTTTCTTTAAAAAATTTAAATTCATAA
1 AATTAATATATTTTCTTTAAAAAATTGAAAATCATAA
* * *
9841 AATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAA
1 AATTAATAT-ATTTTCTTTAAAAAATTGAAAATCATAA
9878 A
1 A
9879 TAGGTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 13 0.41
38 19 0.59
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
AATTAATATATTTTCTTTAAAAAATTGAAAATCATAA
Found at i:10133 original size:25 final size:26
Alignment explanation
Indices: 10086--10140 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 26
10076 AATCCAACAA
10086 TACCTAAAGAAAGGGGGTAATCATAT
1 TACCTAAAGAAAGGGGGTAATCATAT
10112 TACCTAAAGAAA-GGGGTAATCATAT
1 TACCTAAAGAAAGGGGGTAATCATAT
10137 TACC
1 TACC
10141 GGTAATATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (26 bp):
TACCTAAAGAAAGGGGGTAATCATAT
Found at i:11765 original size:315 final size:315
Alignment explanation
Indices: 11137--11835 Score: 922
Period size: 315 Copynumber: 2.2 Consensus size: 315
11127 TTTAGTCCTG
* * * * *
11137 ATTTCATTATTCCTTCAATTCATCTTTTATTTTAAGTCTAT-TTTTTTAACCAAATTTAAACTAT
1 ATTTCCTTATTTCTTCAATTCATCATTTATTTTAAG--TATGTTTTTT-ACCAAATTTAAACCAC
* * *
11201 ATGCTCCTAAACCATCGTAGAATATATATGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCT
63 ATGCTCCTAAACCATCGTAAAATATACATGTACTTTCAATTCCTCTTTTTGATAACAAATTTTCT
*
11266 ATTTTTCAATTTAGTCCTCAATTTTTTATAATTTTCTTATTCCTTCAATTCAACCTTTATTTTAA
128 AATTTTCAATTTAGTCCTCAATTTTTTATAATTTTCTTATTCCTTCAATTCAACCTTTATTTTAA
* *
11331 GTTCGTTTTTACCAAATTTGAACCACATACTCCTAAACCATTATAGAATACATATGTACTTTCAA
193 GTTCGTTTTTACCAAATTTGAACCACATACTCCTAAACCATCATAGAATAAATATGTACTTTCAA
*
11396 TTCCTATTTTTAATAAAAAAAAATCTATTTTTCAATTTAGTCCATTAATTTTTTTATA
258 TTCCTATTTTTAATAAAAAAAAATCTATTTTTCAATTTAGTCCATCAATTTTTTTATA
* * * * *
11454 ATTTCCTTGTTTCTTTAATTCATCCTTTATTTTAAGTATGTTTTTTACTAAATTTAAACCACGTG
1 ATTTCCTTATTTCTTCAATTCATCATTTATTTTAAGTATGTTTTTTACCAAATTTAAACCACATG
* *
11519 CTCTTAAACCATCGTAAAATATACATGTACTTTCAATTCCTCTTTTTGATGACAAATTTTCTAAT
66 CTCCTAAACCATCGTAAAATATACATGTACTTTCAATTCCTCTTTTTGATAACAAATTTTCTAAT
* * * *
11584 TTTCAATTTAGTTCCTC-ATTTTTTATAATTTT-TATATTTCTTCGATTCATCTTTTATTTTAAG
131 TTTCAATTTAG-TCCTCAATTTTTTATAATTTTCT-TATTCCTTCAATTCAACCTTTATTTTAAG
* * * * * * *
11647 TTCGTTTTTATCAAATTTGGATCACATGCTCCTAAATCATCGTATAATAAATATGTACTTTCAAT
194 TTCGTTTTTACCAAATTTGAACCACATACTCCTAAACCATCATAGAATAAATATGTACTTTCAAT
* * * *** * * *
11712 TCCTCTTTTTGAT-AACAATTTTTTATTTTTCAATTTAGTCCCTCATTTTTTTTTATA
259 TCCTATTTTTAATAAAAAAAAATCTATTTTTCAATTTAGTCCATCA-ATTTTTTTATA
* * * *
11769 ATTTCCTTATTTCTTCGATTCATCATTTATTTGAAGTATG-TTTTTACCAAATTTGAACCATATG
1 ATTTCCTTATTTCTTCAATTCATCATTTATTTTAAGTATGTTTTTTACCAAATTTAAACCACATG
11833 CTC
66 CTC
11836 ATAATATCAC
Statistics
Matches: 331, Mismatches: 47, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
314 49 0.15
315 240 0.73
316 11 0.03
317 31 0.09
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49
Consensus pattern (315 bp):
ATTTCCTTATTTCTTCAATTCATCATTTATTTTAAGTATGTTTTTTACCAAATTTAAACCACATG
CTCCTAAACCATCGTAAAATATACATGTACTTTCAATTCCTCTTTTTGATAACAAATTTTCTAAT
TTTCAATTTAGTCCTCAATTTTTTATAATTTTCTTATTCCTTCAATTCAACCTTTATTTTAAGTT
CGTTTTTACCAAATTTGAACCACATACTCCTAAACCATCATAGAATAAATATGTACTTTCAATTC
CTATTTTTAATAAAAAAAAATCTATTTTTCAATTTAGTCCATCAATTTTTTTATA
Found at i:11792 original size:158 final size:156
Alignment explanation
Indices: 11137--11835 Score: 814
Period size: 156 Copynumber: 4.4 Consensus size: 156
11127 TTTAGTCCTG
* * * * * * *
11137 ATTTCATTATTCCTTCAATTCATCTTTTATTTTAAGTCTATTTTTTTAACCAAATTTAAACTATA
1 ATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAG--TATGTTTTT-ACCAAATTTGAACCACA
11202 TGCTCCTAAACCATCGTAGAATATATATGTACTTTCAATTCCTCTTTTTGATAATAAATTTTCTA
63 TGCTCCTAAACCATCGTAGAATATATATGTACTTTCAATTCCTCTTTTTGATAA-AAATTTTCTA
*
11267 TTTTTCAATTTAGT-CCTCAATTTTTTATA
127 TTTTTCAATTTAGTCCCTCATTTTTTTATA
* * * *
11296 ATTTTCTTATTCCTTCAATTCAACCTTTATTTTAAGT-TCGTTTTTACCAAATTTGAACCACATA
1 ATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAGTAT-GTTTTTACCAAATTTGAACCACATG
** * * * ***
11360 CTCCTAAACCATTATAGAATACATATGTACTTTCAATTCCTATTTTTAATAAAAAAAAATCTATT
65 CTCCTAAACCATCGTAGAATATATATGTACTTTCAATTCCTCTTTTTGAT-AAAAATTTTCTATT
* *
11425 TTTCAATTTAGTCCATTAATTTTTTTATA
129 TTTCAATTTAGTCC-CTCATTTTTTTATA
* * * * *
11454 ATTTCCTTGTTTCTTTAATTCATCCTTTATTTTAAGTATGTTTTTTACTAAATTTAAACCACGTG
1 ATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAGTATG-TTTTTACCAAATTTGAACCACATG
* * * * *
11519 CTCTTAAACCATCGTAAAATATACATGTACTTTCAATTCCTCTTTTTGATGACAAATTTTCTAAT
65 CTCCTAAACCATCGTAGAATATATATGTACTTTCAATTCCTCTTTTTGAT-AAAAATTTTCTATT
*
11584 TTTCAATTTAGTTCCTCA-TTTTTTATA
129 TTTCAATTTAGTCCCTCATTTTTTTATA
* * * * * *
11611 ATTT-TTATATTTCTTCGATTCATCTTTTATTTTAAGT-TCGTTTTTATCAAATTTGGATCACAT
1 ATTTCCT-TATTTCTTCAATTCATCCTTTATTTTAAGTAT-GTTTTTACCAAATTTGAACCACAT
* * * * *
11674 GCTCCTAAATCATCGTATAATAAATATGTACTTTCAATTCCTCTTTTTGATAACAATTTTTTATT
64 GCTCCTAAACCATCGTAGAATATATATGTACTTTCAATTCCTCTTTTTGATAAAAATTTTCTATT
11739 TTTCAATTTAGTCCCTCATTTTTTTTTATA
129 TTTCAATTTAGTCCCTCA--TTTTTTTATA
* * * *
11769 ATTTCCTTATTTCTTCGATTCATCATTTATTTGAAGTATGTTTTTACCAAATTTGAACCATATGC
1 ATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAGTATGTTTTTACCAAATTTGAACCACATGC
11834 TC
66 TC
11836 ATAATATCAC
Statistics
Matches: 453, Mismatches: 74, Indels: 27
0.82 0.13 0.05
Matches are distributed among these distances:
155 27 0.06
156 147 0.32
157 49 0.11
158 111 0.25
159 119 0.26
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49
Consensus pattern (156 bp):
ATTTCCTTATTTCTTCAATTCATCCTTTATTTTAAGTATGTTTTTACCAAATTTGAACCACATGC
TCCTAAACCATCGTAGAATATATATGTACTTTCAATTCCTCTTTTTGATAAAAATTTTCTATTTT
TCAATTTAGTCCCTCATTTTTTTATA
Found at i:15952 original size:41 final size:41
Alignment explanation
Indices: 15904--16432 Score: 424
Period size: 41 Copynumber: 13.0 Consensus size: 41
15894 TTTTTTGAAC
* **
15904 AAACGCCGGTAAATACTTGTGTTTTAGTGGCGTTTTTATAT
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTATAT
** **
15945 AAACGCCGCTACCTAC-TGTACTTTAGTGGCGTTTTCGTAT
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTATAT
* ** * * *
15985 AAACGCCGCTAAATA-ATGTACAATAGTGGCGTTTTAAGCAC
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTA-TAT
* * *
16026 AAACGCCGCTAAATGCTCGTACTTTAGTGGCGTTTCTATAT
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTATAT
* * * * * * *
16067 AAACGCCGCTAAATA-ATATACTATAGTGACGTTTTAAGCAC
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTA-TAT
* * *
16108 AAACGCCGCTAAATGCTCGTACTTTAGTGGCGTTTTTGTAT
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTATAT
* * * * *
16149 AAACGCCGCTAAATAC-TATACTTTAGTGGCATTTTAAGCAC
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTA-TAT
* * *
16190 AAACGCCGCTAAATTCTCGTACTTTAGTGGCG--TTTCTAT
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTATAT
* * *
16229 AAACGACGCTATAA-ACTCGTACTTTAGTAGCGTTTTTATAT
1 AAACGCCGCTA-AATACTTGTACTTTAGTGGCGTTTTTATAT
* * * *
16270 AAACGACGCTATAGACTTGTACTTTAGTGGCGTTTTTATAA
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTATAT
** * * * * *
16311 AAACTTCGCTAAAGACTCGTACTTTAGAGGCGTTTATATAC
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTATAT
* * * * * *
16352 AAGCGCCGCTATACACTTGTACTTTCGTGGCATTTTTATAC
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTATAT
* * * * * * *
16393 AAACGCCGTTATACAATTATACTTTAGTGGTGTTTATATA
1 AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTATA
16433 CAAATGTCGA
Statistics
Matches: 384, Mismatches: 93, Indels: 22
0.77 0.19 0.04
Matches are distributed among these distances:
39 27 0.07
40 86 0.22
41 228 0.59
42 43 0.11
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
AAACGCCGCTAAATACTTGTACTTTAGTGGCGTTTTTATAT
Found at i:16262 original size:121 final size:121
Alignment explanation
Indices: 16123--16422 Score: 325
Period size: 121 Copynumber: 2.4 Consensus size: 121
16113 CCGCTAAATG
*
16123 CTCGTACTTTAGTGGCGTTTTTGTATAAACGCCGCTAAATACTATACTTTAGTGGCATTTTAAGC
1 CTCGTACTTTAGTGGCGTTTTTATATAAACGCCGCTAAA-ACTATACTTTAGTGGCATTTTAA-C
* ** * *
16188 ACAAACGCCGCTAAATTCTCGTACTTTAGTGGCGTTTCTATA-AA-CGACGCTATAAA
64 AAAAACGCCGCTAAAGACTCGTACTTTAGAGGCGTTTATATACAAGCGACGCTATAAA
* * * * * * *
16244 CTCGTACTTTAGTAGCGTTTTTATATAAACGACGCTATAGACTTGTACTTTAGTGGCGTTTTTAT
1 CTCGTACTTTAGTGGCGTTTTTATATAAACGCCGCTA-AAAC-TATACTTTAGTGGCATTTTAAC
** * *
16309 AAAAACTTCGCTAAAGACTCGTACTTTAGAGGCGTTTATATACAAGCGCCGCTATACA
64 AAAAACGCCGCTAAAGACTCGTACTTTAGAGGCGTTTATATACAAGCGACGCTATAAA
* * * * * *
16367 CTTGTACTTTCGTGGCATTTTTATACAAACGCCGTTATACAATTATACTTTAGTGG
1 CTCGTACTTTAGTGGCGTTTTTATATAAACGCCGCTA-A-AACTATACTTTAGTGG
16423 TGTTTATATA
Statistics
Matches: 147, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
121 71 0.48
122 21 0.14
123 54 0.37
124 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (121 bp):
CTCGTACTTTAGTGGCGTTTTTATATAAACGCCGCTAAAACTATACTTTAGTGGCATTTTAACAA
AAACGCCGCTAAAGACTCGTACTTTAGAGGCGTTTATATACAAGCGACGCTATAAA
Found at i:16418 original size:203 final size:203
Alignment explanation
Indices: 16041--16432 Score: 434
Period size: 203 Copynumber: 1.9 Consensus size: 203
16031 CCGCTAAATG
* * *
16041 CTCGTACTTTAGTGGCGTTTCTATATAAACGCCGCTAAATAATATACTATAGTGACGTTTTAAGC
1 CTCGTACTTTAGTAGCGTTTCTATATAAACGACGCTAAAGAATATACTATAGTGACGTTTTAAGC
* * * * * *
16106 ACAAACGCCGCTAAATGCTCGTACTTTAGTGGCGTTTTTGTATAAACGCCGCTAAATACTATACT
66 AAAAACGCCGCTAAATGCTCGTACTTTAGAGGCGTTTATATACAAACGCCGCTAAACACTATACT
* * *
16171 TTAGTGGCATTTTAAGCACAAACGCCGCTAAATTCTCGTACTTTAGTGGCGTTTCTATAAACGAC
131 TTAGTGGCATTTTAAGCACAAACGCCGCTAAAATCTCATACTTTAGTGGCGTTTATATAAACGAC
16236 GCTATAAA
196 GCTATAAA
* * * * * * *
16244 CTCGTACTTTAGTAGCGTTTTTATATAAACGACGCTATAGACTTGTACTTTAGTGGCGTTTTTA-
1 CTCGTACTTTAGTAGCGTTTCTATATAAACGACGCTAAAGA-ATATACTATAGTGACGTTTTAAG
* ** * * *
16308 TAAAAACTTCGCTAAA-GACTCGTACTTTAGAGGCGTTTATATACAAGCGCCGCTATACACTTGT
65 CAAAAACGCCGCTAAATG-CTCGTACTTTAGAGGCGTTTATATACAAACGCCGCTAAACAC-TAT
* * * * *
16372 ACTTTCGTGGCATTTTTA-TACAAACGCCGTTATACAAT-T-ATACTTTAGTGGTGTTTATATA
128 ACTTTAGTGGCATTTTAAGCACAAACGCCGCTA-A-AATCTCATACTTTAGTGGCGTTTATATA
16433 CAAATGTCGA
Statistics
Matches: 154, Mismatches: 30, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
202 1 0.01
203 114 0.74
204 37 0.24
205 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (203 bp):
CTCGTACTTTAGTAGCGTTTCTATATAAACGACGCTAAAGAATATACTATAGTGACGTTTTAAGC
AAAAACGCCGCTAAATGCTCGTACTTTAGAGGCGTTTATATACAAACGCCGCTAAACACTATACT
TTAGTGGCATTTTAAGCACAAACGCCGCTAAAATCTCATACTTTAGTGGCGTTTATATAAACGAC
GCTATAAA
Found at i:19260 original size:43 final size:42
Alignment explanation
Indices: 19212--19753 Score: 672
Period size: 43 Copynumber: 12.6 Consensus size: 42
19202 GAATGGTAAT
* *
19212 TATAGATCTGACTTTTTGCGGCGTTTGTGTCCAAAAACGTCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
19255 TATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
19298 TATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
*
19341 TATAGATCTGTA-CTTTTGCAGCGTTTGTATCCAAAAACGCCGC
1 TATAGATCTG-ACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * * *
19384 TAAATATCTAACCTTTTGCGGCGTTTGTTTCCAAAAACGCCAC
1 TATAGATCTGACCTTTTGCGGCGTTTG-TTCCAAAAACGCCGC
* * *
19427 TATAGATCTGTCCTTTTGCAGCATTTGTATCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * * * *
19470 TAAATATCTAACCTTTTGCGACGTTTGTTACAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
*
19512 TATAGATCTCGACCTTTTGCGGCATTTGTATCCAAAAACGCCGC
1 TATAGATCT-GACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * * * *
19556 TAAATATCTAACCTTTTGCGACGTTTGTTACAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* *
19598 TATAGATCTCGACCTTTTGCGGCATTTGTTCCATAAACGCCGC
1 TATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* *
19641 TAGAGATCTTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGC
1 TATAGATC-TGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* * * *
19684 TATATATATCGATCTTTTGCGACGTTTGTTCCAAAAACGCCGC
1 TATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* * *
19727 TATAGATCTTGAACTATAGCGGCGTTT
1 TATAGATC-TGACCTTTTGCGGCGTTT
19754 TTGGTTCTCA
Statistics
Matches: 430, Mismatches: 59, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
42 43 0.10
43 363 0.84
44 24 0.06
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (42 bp):
TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
Found at i:20132 original size:12 final size:12
Alignment explanation
Indices: 20115--20155 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
20105 TAAATAATTT
20115 ATAAATGAGTCA
1 ATAAATGAGTCA
*
20127 ATAAATGAG-CTT
1 ATAAATGAGTC-A
20139 ATAAATGAGTCA
1 ATAAATGAGTCA
20151 ATAAA
1 ATAAA
20156 CGAGCTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (12 bp):
ATAAATGAGTCA
Found at i:20141 original size:24 final size:24
Alignment explanation
Indices: 20113--20161 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
20103 AGTAAATAAT
*
20113 TTATAAATGAGTCAATAAATGAGC
1 TTATAAATGAGTCAATAAACGAGC
20137 TTATAAATGAGTCAATAAACGAGC
1 TTATAAATGAGTCAATAAACGAGC
20161 T
1 T
20162 AACAAAGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (24 bp):
TTATAAATGAGTCAATAAACGAGC
Found at i:20828 original size:25 final size:25
Alignment explanation
Indices: 20799--20847 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
20789 ACCAAGTTGT
*
20799 ATAATTTACATCCTAGAAACAAGTA
1 ATAATTTACATCCGAGAAACAAGTA
20824 ATAATTTACATCCGAGAAACAAGT
1 ATAATTTACATCCGAGAAACAAGT
20848 GAGCATTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (25 bp):
ATAATTTACATCCGAGAAACAAGTA
Found at i:21598 original size:17 final size:17
Alignment explanation
Indices: 21566--21597 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21556 GTTAAGGTTG
21566 GAGATTTGAGATTTTTA
1 GAGATTTGAGATTTTTA
21583 GAGATTTGAG-TTTTT
1 GAGATTTGAGATTTTT
21598 TTTTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (17 bp):
GAGATTTGAGATTTTTA
Found at i:24012 original size:15 final size:14
Alignment explanation
Indices: 23992--24026 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
23982 GAAAATCAAG
*
23992 AATAAAGATTAAGA
1 AATAAAGACTAAGA
24006 CAATAAAGACTAAGA
1 -AATAAAGACTAAGA
24021 AATAAA
1 AATAAA
24027 AATAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (14 bp):
AATAAAGACTAAGA
Found at i:24148 original size:16 final size:16
Alignment explanation
Indices: 24127--24158 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
24117 AGATGGTGGC
24127 GTGGATGATATTGATA
1 GTGGATGATATTGATA
24143 GTGGATGATATTGATA
1 GTGGATGATATTGATA
24159 ATGAAGATAA
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:0.00, G:0.31, T:0.38
Consensus pattern (16 bp):
GTGGATGATATTGATA
Found at i:24906 original size:26 final size:27
Alignment explanation
Indices: 24877--24928 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
24867 GTCTATAGAC
*
24877 AAATTTTTAATTT-AATTAATTTTTAA
1 AAATTATTAATTTAAATTAATTTTTAA
24903 AAATTATTAATTTAAAATTAATTTTT
1 AAATTATTAATTT-AAATTAATTTTT
24929 GGTTTCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 12 0.52
28 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATTATTAATTTAAATTAATTTTTAA
Found at i:28693 original size:36 final size:36
Alignment explanation
Indices: 28646--28733 Score: 176
Period size: 36 Copynumber: 2.4 Consensus size: 36
28636 TTTGGATATG
28646 CTTCAGTAGGGTATGAAGTATGAACCATGATACATA
1 CTTCAGTAGGGTATGAAGTATGAACCATGATACATA
28682 CTTCAGTAGGGTATGAAGTATGAACCATGATACATA
1 CTTCAGTAGGGTATGAAGTATGAACCATGATACATA
28718 CTTCAGTAGGGTATGA
1 CTTCAGTAGGGTATGA
28734 TATATATATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (36 bp):
CTTCAGTAGGGTATGAAGTATGAACCATGATACATA
Found at i:28740 original size:2 final size:2
Alignment explanation
Indices: 28733--28769 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28723 GTAGGGTATG
28733 AT 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 AT A
28770 GAGAGAGAGA
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:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28774 original size:2 final size:2
Alignment explanation
Indices: 28769--28802 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28759 ATATATATAT
*
28769 AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28803 GACGGTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35774 original size:19 final size:19
Alignment explanation
Indices: 35752--35791 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
35742 TTAAAGAGGA
35752 TAAGGGAAGTTGAAGAACT
1 TAAGGGAAGTTGAAGAACT
35771 TAAGGGAAGTTGAAGAACT
1 TAAGGGAAGTTGAAGAACT
35790 TA
1 TA
35792 TTCAACAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.30, T:0.23
Consensus pattern (19 bp):
TAAGGGAAGTTGAAGAACT
Found at i:40301 original size:20 final size:20
Alignment explanation
Indices: 40276--40317 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
40266 GCGCCTGTGG
40276 GGGAAACCTTTGAGGTGTTT
1 GGGAAACCTTTGAGGTGTTT
*
40296 GGGAAACTTTTGAGGTGTTT
1 GGGAAACCTTTGAGGTGTTT
40316 GG
1 GG
40318 TAGGAACGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.07, G:0.38, T:0.36
Consensus pattern (20 bp):
GGGAAACCTTTGAGGTGTTT
Found at i:40722 original size:153 final size:155
Alignment explanation
Indices: 40509--40816 Score: 570
Period size: 153 Copynumber: 2.0 Consensus size: 155
40499 ATAATAAGCT
40509 TATGGATCAGAAGATGGACCTTGTGAGGTCGTGCAGAAGATCAATGATAATGCTTACAGGTTGCG
1 TATGGATCAGAAGATGGACCTTGTGAGGTCGTGCAGAAGATCAATGATAATGCTTACAGGTTGCG
40574 CCTTCCTAGCCACTTG-AGACTTCTGATGTCTTAATGTGAAGCACCTGAGCCATG-TTTGTGGAT
66 CCTTCCTAGCCAC-TGAAGACTTCTGATGTCTTAATGTGAAGCACCTGAGCCATGTTTTGTGGAT
40637 CTGATGACACTACTATGAA-TCGAGG
130 CTGATGACACTACTATGAACTCGAGG
40662 TATGGATCAGAAGATTGGACCTTGTGAGGT-GTGCAGAAGATCAATGATAATGCTTACAGGTTGC
1 TATGGATCAGAAGA-TGGACCTTGTGAGGTCGTGCAGAAGATCAATGATAATGCTTACAGGTTGC
40726 GCCTTCCTAGCCACTGAAGACTTCTGATGTCTTAATGTGAAGCACCTGAGCCATGTTTTGTGGAT
65 GCCTTCCTAGCCACTGAAGACTTCTGATGTCTTAATGTGAAGCACCTGAGCCATGTTTTGTGGAT
40791 CTGATGACACTACTATGAACTCGAGG
130 CTGATGACACTACTATGAACTCGAGG
40817 ACGACACTAC
Statistics
Matches: 151, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
152 2 0.01
153 100 0.66
154 43 0.28
155 6 0.04
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (155 bp):
TATGGATCAGAAGATGGACCTTGTGAGGTCGTGCAGAAGATCAATGATAATGCTTACAGGTTGCG
CCTTCCTAGCCACTGAAGACTTCTGATGTCTTAATGTGAAGCACCTGAGCCATGTTTTGTGGATC
TGATGACACTACTATGAACTCGAGG
Found at i:40826 original size:23 final size:23
Alignment explanation
Indices: 40796--40843 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
40786 TGGATCTGAT
40796 GACACTACTATGAACTCGAGGAC
1 GACACTACTATGAACTCGAGGAC
40819 GACACTACTATGAACTCGAGGAC
1 GACACTACTATGAACTCGAGGAC
40842 GA
1 GA
40844 GTTCTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (23 bp):
GACACTACTATGAACTCGAGGAC
Found at i:47871 original size:21 final size:20
Alignment explanation
Indices: 47847--47885 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
47837 TATAAAAACA
*
47847 ATAAAAAATTCTTGATAATTT
1 ATAAAAAATTATT-ATAATTT
*
47868 ATAAATAATTATTATAAT
1 ATAAAAAATTATTATAAT
47886 CCTAAACCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
ATAAAAAATTATTATAATTT
Found at i:50929 original size:39 final size:39
Alignment explanation
Indices: 50886--50993 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 39
50876 ATAGTTATTT
* * *
50886 AATTATTTCACCATAACATTTTAAATTCTTAATTTCA-GA
1 AATTATTTCACCATAACATTGTAAATTATTAATAT-ATGA
* * *
50925 AATTATTTTACTATAACATTGTAAATTATTAATATATTA
1 AATTATTTCACCATAACATTGTAAATTATTAATATATGA
* *
50964 AATTATTTCACCATAACATTCTAAGTTATT
1 AATTATTTCACCATAACATTGTAAATTATT
50994 TCTCTTAACT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 1 0.02
39 57 0.98
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (39 bp):
AATTATTTCACCATAACATTGTAAATTATTAATATATGA
Found at i:51097 original size:24 final size:24
Alignment explanation
Indices: 51067--51114 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
51057 TATCTTTTGA
* *
51067 TTATGTAATT-TAAATTTTTAAATT
1 TTATGT-ATTATAAAATTTCAAATT
51091 TTATGTATTATAAAATTTCAAATT
1 TTATGTATTATAAAATTTCAAATT
51115 CTATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
TTATGTATTATAAAATTTCAAATT
Found at i:59970 original size:2 final size:2
Alignment explanation
Indices: 59965--59989 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59955 AGGTGAAATA
59965 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 A
59990 AAGATATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.