Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004085.1 Hibiscus syriacus cultivar Beakdansim tig00008936_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: 78693
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:4160 original size:13 final size:13
Alignment explanation
Indices: 4133--4176 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
4123 GGTAATACTC
4133 GCCCGATTA-CCG
1 GCCCGATTACCCG
4145 GCCCGATTACCCG
1 GCCCGATTACCCG
*
4158 GCCCTA-TACCCG
1 GCCCGATTACCCG
*
4170 ACCCGAT
1 GCCCGAT
4177 AAATATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 19 0.70
13 8 0.30
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.16
Consensus pattern (13 bp):
GCCCGATTACCCG
Found at i:6369 original size:50 final size:50
Alignment explanation
Indices: 6310--6411 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
6300 CTCGATAGAT
6310 CTGCAGGTGAGTTGTAATTAGAGAAGGACATTAGAGTGATGGGTTTCGAC
1 CTGCAGGTGAGTTGTAATTAGAGAAGGACATTAGAGTGATGGGTTTCGAC
6360 CTGCAGGTGAGTTGTAATTAGAGAAGGACATTAGAGTGATGGGTTTCGAC
1 CTGCAGGTGAGTTGTAATTAGAGAAGGACATTAGAGTGATGGGTTTCGAC
6410 CT
1 CT
6412 AATCTTATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.27, C:0.11, G:0.33, T:0.28
Consensus pattern (50 bp):
CTGCAGGTGAGTTGTAATTAGAGAAGGACATTAGAGTGATGGGTTTCGAC
Found at i:6571 original size:20 final size:21
Alignment explanation
Indices: 6540--6583 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
6530 TCCTTCTATT
6540 TATATATTTTTCAATTAAGTC
1 TATATATTTTTCAATTAAGTC
6561 TATAT-TTTTTCAATTAAGTC
1 TATATATTTTTCAATTAAGTC
6581 TAT
1 TAT
6584 TTTATCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.55
Consensus pattern (21 bp):
TATATATTTTTCAATTAAGTC
Found at i:8196 original size:19 final size:19
Alignment explanation
Indices: 8172--8228 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
8162 AAAAACCCAA
*
8172 ATCTCCTTTCATTTTTCAT
1 ATCTCCGTTCATTTTTCAT
8191 ATCTCCGTTCATTTTTCAT
1 ATCTCCGTTCATTTTTCAT
8210 ATCTCCGTTCATTTTTCAT
1 ATCTCCGTTCATTTTTCAT
8229 GTCCGTGGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.16, C:0.26, G:0.04, T:0.54
Consensus pattern (19 bp):
ATCTCCGTTCATTTTTCAT
Found at i:12411 original size:80 final size:82
Alignment explanation
Indices: 12239--12411 Score: 269
Period size: 80 Copynumber: 2.1 Consensus size: 82
12229 TATCTTAAAT
* * *
12239 TAATTCTTAATTTCTTTAATATTTTAAATTCATCTCTAAATTGCTATCTTTATTTTATATTAGTC
1 TAATT-TT-ATTTCTTGAATATTTTAAATTAATCTCTAAATTACTATCTTTATTTTATATTAGTC
12304 CTCAAAATTGTAGATATTC
64 CTCAAAATTGTAGATATTC
12323 TAATTTTATTTCTTGAATATTTTAAATTAATCTCTAAATTACTATC-TT-TTTTATATTAGTCCT
1 TAATTTTATTTCTTGAATATTTTAAATTAATCTCTAAATTACTATCTTTATTTTATATTAGTCCT
*
12386 CAAAATTTTAGATATTC
66 CAAAATTGTAGATATTC
*
12403 TGATTTTAT
1 TAATTTTAT
12412 CTCCAGTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
80 39 0.46
81 2 0.02
82 36 0.43
83 2 0.02
84 5 0.06
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.53
Consensus pattern (82 bp):
TAATTTTATTTCTTGAATATTTTAAATTAATCTCTAAATTACTATCTTTATTTTATATTAGTCCT
CAAAATTGTAGATATTC
Found at i:12488 original size:13 final size:13
Alignment explanation
Indices: 12470--12499 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12460 TTTAAGGATT
12470 AATTTAAAATAAA
1 AATTTAAAATAAA
*
12483 AATTTAAAATAAG
1 AATTTAAAATAAA
12496 AATT
1 AATT
12500 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AATTTAAAATAAA
Found at i:12627 original size:20 final size:17
Alignment explanation
Indices: 12589--12624 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
12579 TTTAAAACTT
12589 TAAAAATAAATTTAAAA
1 TAAAAATAAATTTAAAA
12606 TAAAAATTATAATTTAAAA
1 TAAAAA-TA-AATTTAAAA
12625 ATATGTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAATAAATTTAAAA
Found at i:15829 original size:249 final size:248
Alignment explanation
Indices: 15401--16017 Score: 743
Period size: 249 Copynumber: 2.5 Consensus size: 248
15391 AATCTGTTTT
* * *
15401 GTGAAGTTGAGCTTTGGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATGTAAGT-TGTGT
1 GTGAAGTTGAGCCTT-GAATTGGATATCATTCGTCATGAAGTTGAAATCCAATGT-TGTAT-TG-
* *
15465 TTTTTCGATGCCAATATCCTTCGCCGTGAAATTGAAATTGACTCTGAAACTGGAAAGTTTATTGA
62 -TTTT-GAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAACTGGAAAGTTTATTGA
** * * * * *
15530 CTACTCTCATTCTTTAAGTTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGGTG
125 AGACTCTCATTCTCTAAGTTGAATATCCTTCGCCGTGAAGTTAAAATCCAATATAGAGATGGATG
* * * *
15595 CTGTTTGTGTGCACGATTCCCTTCGTCGTGAAGTTGAAACCGCGGGTGGCCCCTAATTC
190 CTGCTTGTGTGCACGATTCCCTTCATCGTGAAGTTGAAACCGCGGATGGCCCCTAAGTC
* * ** *
15654 GTGAAGTTGAGCCTTGACTTGAATATCATTCGTTGTGAAGTTGAAATCCAATCTTGTATTGTTTT
1 GTGAAGTTGAGCCTTGAATTGGATATCATTCGTCATGAAGTTGAAATCCAATGTTGTATTGTTTT
** * * * *
15719 GAGGCCAATATCCTTCGATGTGAAGTTGAAGTTGACTTTGAAACTGGATAGTTTGTTGAAAGACT
66 GAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAACTGGAAAGTTTATTG-AAGACT
* * * *
15784 CTCCTTCTCTGAGTTGGATATCC-TCTGCCGTGAAGTTAAAATCCAATATGGAGATGGATGCTGC
130 CTCATTCTCTAAGTTGAATATCCTTC-GCCGTGAAGTTAAAATCCAATATAGAGATGGATGCTGC
* * **
15848 TTGTGTGCATGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCCCTCCGTC
194 TTGTGTGCACGATTCCCTTCATCGTGAAGTTGAAACCGCGGATGGCCCCTAAGTC
* * *
15903 GTGAAGTTGAGCCTTGAATTGGATATCATTCATCACGAAGTTAAAATCCAAGTAAGTTGTATTGT
1 GTGAAGTTGAGCCTTGAATTGGATATCATTCGTCATGAAGTTGAAATCCAA-T--GTTGTATTGT
* * * *
15968 TTCGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGAAACTGG
63 TTTGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAACTGG
16018 GAAGCCCCTT
Statistics
Matches: 307, Mismatches: 51, Indels: 13
0.83 0.14 0.04
Matches are distributed among these distances:
248 52 0.17
249 151 0.49
250 1 0.00
251 4 0.01
252 85 0.28
253 14 0.05
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (248 bp):
GTGAAGTTGAGCCTTGAATTGGATATCATTCGTCATGAAGTTGAAATCCAATGTTGTATTGTTTT
GAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAACTGGAAAGTTTATTGAAGACTC
TCATTCTCTAAGTTGAATATCCTTCGCCGTGAAGTTAAAATCCAATATAGAGATGGATGCTGCTT
GTGTGCACGATTCCCTTCATCGTGAAGTTGAAACCGCGGATGGCCCCTAAGTC
Found at i:16346 original size:111 final size:110
Alignment explanation
Indices: 16210--16524 Score: 442
Period size: 111 Copynumber: 2.9 Consensus size: 110
16200 TATTGTTTCA
* *
16210 AGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTTGTTG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG-TTTGTTG
* *
16275 ACATACAGTCGCCCCTTCGGTGTGAAGTTGAGCTTGTGTTGTCTTG
65 ACATACAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
* * *
16321 AGTCTAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAACGAAACTGAAAAAGTTGTTTGTTG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG-AAAAGTTGTTTGTTG
*
16386 ACAGT-CAGTCGCCCCTTCGCTGTGAAGTTAAGCTTGTGTTGTCTCG
65 ACA-TACAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
* * * * *
16432 AGTCCATTATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAATTGTTTATTG-
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
*
16496 ---ACAGTCGCCCCTTCGTTGTGAAGTTGAGC
66 CATACAGTCGCCCCTTCGCTGTGAAGTTGAGC
16525 AACCACCATC
Statistics
Matches: 183, Mismatches: 18, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
106 26 0.14
110 13 0.07
111 135 0.74
112 9 0.05
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (110 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
CATACAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
Found at i:21850 original size:36 final size:36
Alignment explanation
Indices: 21808--21883 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
21798 TTATAGCTAA
*
21808 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
21844 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
21880 AAAA
1 AAAA
21884 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:26845 original size:36 final size:36
Alignment explanation
Indices: 26803--26878 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
26793 TTATAGCTAA
*
26803 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
26839 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
26875 AAAA
1 AAAA
26879 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:33643 original size:156 final size:155
Alignment explanation
Indices: 33461--33950 Score: 592
Period size: 156 Copynumber: 3.1 Consensus size: 155
33451 GCTCGAATTT
* *
33461 TCTCTGGCAGTGTTGTTGGCATTGTGGCTGTTGTTTTTGTCCTTGTTGTCGGCACTGTTGTTGGC
1 TCTCTAGCACTGTTGTTGGCATTGTGGCTGTTGTTTTTGTCCTTGTTGTCGGCACTGTTGTTGGC
** * * *
33526 ATTCCTCGAACCTCCTCCGGGGATCTTCTGGCTTCGAATCGTGGAGGCGACGACCTCTCTCTTCT
66 ATTCCTCGAACCTCCTATGGGGATCTTCAGGC-TCGAATCATGGCGGCGACGACCTCTCTCTTCT
*
33591 TGTTGCTCTCTCTGATCCTTGAATTC
130 TGTTGCTCTCTCTGATCCTTGAAATC
* * ** * *
33617 TCTTTAGCACTGTTGGTGGCATTGTGGCTACTGTTTTTGTCCTTGTT-CCTGGCACCGTTGTTGG
1 TCTCTAGCACTGTTGTTGGCATTGTGGCTGTTGTTTTTGTCCTTGTTGTC-GGCACTGTTGTTGG
* * * *
33681 CATTCCTCAAACCTCCTTTGGGGATCTTCGGGACTCGAATCATGGCGGC-AGCGGCCTCTCTCTT
65 CATTCCTCGAACCTCCTATGGGGATCTTCAGG-CTCGAATCATGGCGGCGA-CGACCTCTCTCTT
* *
33745 CTTATTGCTCTTTCTGATCCTTGAAATC
128 CTTGTTGCTCTCTCTGATCCTTGAAATC
* * * *
33773 TCTCTGGCACTGTTGTTGGCATTGTGGTTGTTGTTTCTGTCCTTGTTGTCAGCA-TCGTTGTTGG
1 TCTCTAGCACTGTTGTTGGCATTGTGGCTGTTGTTTTTGTCCTTGTTGTCGGCACT-GTTGTTGG
*
33837 CATTCCTTGAACCTCCTATGGGGATCTTCAAGGCTCGAATCATGGCGGCGTA-GACCTCTCTCTT
65 CATTCCTCGAACCTCCTATGGGGATCTTC-AGGCTCGAATCATGGCGGCG-ACGACCTCTCTCTT
* * * **
33901 CTTGTTTCTCTCTCTGATGCTCGAGTTC
128 CTTGTTGCTCTCTCTGATCCTTGAAATC
* * *
33929 TCTCTGGCACTGCTGTTCGCAT
1 TCTCTAGCACTGTTGTTGGCAT
33951 CGCAGCTACG
Statistics
Matches: 284, Mismatches: 42, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
155 2 0.01
156 277 0.98
157 4 0.01
158 1 0.00
ACGTcount: A:0.11, C:0.26, G:0.24, T:0.39
Consensus pattern (155 bp):
TCTCTAGCACTGTTGTTGGCATTGTGGCTGTTGTTTTTGTCCTTGTTGTCGGCACTGTTGTTGGC
ATTCCTCGAACCTCCTATGGGGATCTTCAGGCTCGAATCATGGCGGCGACGACCTCTCTCTTCTT
GTTGCTCTCTCTGATCCTTGAAATC
Found at i:34036 original size:312 final size:312
Alignment explanation
Indices: 33461--34039 Score: 711
Period size: 312 Copynumber: 1.9 Consensus size: 312
33451 GCTCGAATTT
* * *
33461 TCTCTGGCAGTGTTGTTGGCATTGTGGCTGTTGTTTTTGTCCTTGTTGTCGGCACTGTTGTTGGC
1 TCTCTGGCACTGTTGTTGGCATTGTGGCTGTTGTTTCTGTCCTTGTTGTCAGCACTGTTGTTGGC
* * *
33526 ATTCCTCGAACCTCCTCCGGGGATCTTCTGGCTTCGAATCGTGGAGGCGACGACCTCTCTCTTCT
66 ATTCCTCGAACCTCCTACGGGGATCTTCAGGCTTCGAATCATGGAGGCGACGACCTCTCTCTTCT
* * * * * ** * ****
33591 TGTTGCTCTCTCTGATCCTTGAATTCTCTTTAGCACTGTTGGTGGCATTGTGGCTACTGTTTTTG
131 TGTTGCTCTCTCTGATCCTCGAATTCTCTCTAGCACTGCTGGTCGCATCGCAGCTACGGCCCCTG
** * * * * *
33656 TCCTTGTTCCTGGCACCGTTGTTGGCATTCCTCAAACCTCCTTTGGGGATCTTCGGGACTCGAAT
196 TCCTTCATACTGGCACCGTTGCTGACACTCCTCAAACCTCCTTTGGGGATCTTCGGGACTCAAAT
33721 CATGGCGGCAGCGGCCTCTCTCTTCTTATTGCTCTTTCTGATCCTTGAAATC
261 CATGGCGGCAGCGGCCTCTCTCTTCTTATTGCTCTTTCTGATCCTTGAAATC
*
33773 TCTCTGGCACTGTTGTTGGCATTGTGGTTGTTGTTTCTGTCCTTGTTGTCAGCA-TCGTTGTTGG
1 TCTCTGGCACTGTTGTTGGCATTGTGGCTGTTGTTTCTGTCCTTGTTGTCAGCACT-GTTGTTGG
* * *
33837 CATTCCTTGAACCTCCTATGGGGATCTTCAAGGC-TCGAATCATGGCGGCGTA-GACCTCTCTCT
65 CATTCCTCGAACCTCCTACGGGGATCTTC-AGGCTTCGAATCATGGAGGCG-ACGACCTCTCTCT
* * * * *
33900 TCTTGTTTCTCTCTCTGATGCTCGAGTTCTCTCTGGCACTGCTGTTCGCATCGCAGCTACGGCCC
128 TCTTGTTGCTCTCTCTGATCCTCGAATTCTCTCTAGCACTGCTGGTCGCATCGCAGCTACGGCCC
* * * **
33965 CTG-CTCTTCATATTGGCATC-TTCGCTGACACTCCTCGAACCT-CTTCTGGGGATCTTCGGGGT
193 CTGTC-CTTCATACTGGCACCGTT-GCTGACACTCCTCAAACCTCCTT-TGGGGATCTTCGGGAC
34027 TCAAATCATGGCG
255 TCAAATCATGGCG
34040 ACGACTACCT
Statistics
Matches: 222, Mismatches: 39, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
311 7 0.03
312 211 0.95
313 4 0.02
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.37
Consensus pattern (312 bp):
TCTCTGGCACTGTTGTTGGCATTGTGGCTGTTGTTTCTGTCCTTGTTGTCAGCACTGTTGTTGGC
ATTCCTCGAACCTCCTACGGGGATCTTCAGGCTTCGAATCATGGAGGCGACGACCTCTCTCTTCT
TGTTGCTCTCTCTGATCCTCGAATTCTCTCTAGCACTGCTGGTCGCATCGCAGCTACGGCCCCTG
TCCTTCATACTGGCACCGTTGCTGACACTCCTCAAACCTCCTTTGGGGATCTTCGGGACTCAAAT
CATGGCGGCAGCGGCCTCTCTCTTCTTATTGCTCTTTCTGATCCTTGAAATC
Found at i:36050 original size:18 final size:17
Alignment explanation
Indices: 36029--36071 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
36019 TTATTAATAA
36029 TAATTAAATTTATTTATT
1 TAATT-AATTTATTTATT
*
36047 TAATTAATTTTTTTA-T
1 TAATTAATTTATTTATT
*
36063 AAATTAATT
1 TAATTAATT
36072 GATTAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 9 0.39
18 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATTAATTTATTTATT
Found at i:36127 original size:19 final size:20
Alignment explanation
Indices: 36105--36145 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
36095 TTTTATTAAG
36105 TTAA-ATTAA-AAAAACTGTT
1 TTAACATTAAGAAAAA-TGTT
*
36124 TTAACTTTAAGAAAAATGTT
1 TTAACATTAAGAAAAATGTT
36144 TT
1 TT
36146 TATTCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (20 bp):
TTAACATTAAGAAAAATGTT
Found at i:37647 original size:3 final size:3
Alignment explanation
Indices: 37641--37678 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
37631 TTGTTGTTGC
37641 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CTCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT T
37679 ACAGCTCGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:41569 original size:18 final size:18
Alignment explanation
Indices: 41546--41595 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
41536 AACCCATTCT
*
41546 GGAGTAATCACTAGGTCG
1 GGAGTAATCACTAGGCCG
* *
41564 GGAGTAGTCGCTAGGCCG
1 GGAGTAATCACTAGGCCG
*
41582 GGAGAAATCACTAG
1 GGAGTAATCACTAG
41596 ACCTATTACC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.18, G:0.36, T:0.18
Consensus pattern (18 bp):
GGAGTAATCACTAGGCCG
Found at i:49068 original size:4 final size:5
Alignment explanation
Indices: 49040--49068 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
49030 GCCATGCCGA
49040 GACGG GACGG GACGG GACGG GAC-G GACGG
1 GACGG GACGG GACGG GACGG GACGG GACGG
49069 CGGCGGCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.21, G:0.59, T:0.00
Consensus pattern (5 bp):
GACGG
Found at i:52223 original size:33 final size:33
Alignment explanation
Indices: 52180--52246 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
52170 GATTTGTAAT
52180 TAGTTAGCTGTATTTGGTTTCAAATATTAATCA
1 TAGTTAGCTGTATTTGGTTTCAAATATTAATCA
*
52213 TAGTTGGCTGTATTTGGTTTCAAATATTAATCA
1 TAGTTAGCTGTATTTGGTTTCAAATATTAATCA
52246 T
1 T
52247 GTGGCATATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.46
Consensus pattern (33 bp):
TAGTTAGCTGTATTTGGTTTCAAATATTAATCA
Found at i:63936 original size:17 final size:17
Alignment explanation
Indices: 63914--63971 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
63904 ATGAATCCTC
63914 AACCCGAGATCCGATCT
1 AACCCGAGATCCGATCT
*
63931 AACCCGATATCCGATCT
1 AACCCGAGATCCGATCT
63948 AACCCGAGATCCGATCT
1 AACCCGAGATCCGATCT
63965 AACCCGA
1 AACCCGA
63972 CCAAAACAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.31, C:0.36, G:0.16, T:0.17
Consensus pattern (17 bp):
AACCCGAGATCCGATCT
Done.