Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002511.1 Hibiscus syriacus cultivar Beakdansim tig00005111_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: 64455
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:17542 original size:23 final size:23
Alignment explanation
Indices: 17516--17567 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
17506 TGTCCCGAAT
*
17516 GACCACTCATATATGCCCCTAAG
1 GACCACTCATAAATGCCCCTAAG
*
17539 GACCA--CATAAATGTCCCTAAG
1 GACCACTCATAAATGCCCCTAAG
17560 GACCACTC
1 GACCACTC
17568 CTTAAGGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 19 0.76
23 6 0.24
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.19
Consensus pattern (23 bp):
GACCACTCATAAATGCCCCTAAG
Found at i:19181 original size:29 final size:27
Alignment explanation
Indices: 19148--19215 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
19138 TCCTACACAA
**
19148 AATTTTCTATATAAGTCCTTAAACTTTTC
1 AATTTTCTATAT-AGTCAGTAAA-TTTTC
*
19177 AATTTATCTACTATAGTCAGTAAATTTTG
1 AATTT-TCTA-TATAGTCAGTAAATTTTC
19206 AATTTT-TATA
1 AATTTTCTATA
19216 ATTTGGTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
28 1 0.03
29 14 0.41
30 12 0.35
31 3 0.09
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.49
Consensus pattern (27 bp):
AATTTTCTATATAGTCAGTAAATTTTC
Found at i:24620 original size:23 final size:23
Alignment explanation
Indices: 24594--24645 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
24584 TATCCTGAAT
** *
24594 GACCACTCATATTTGTCCCTAAG
1 GACCACTCATAAATGTCCCAAAG
24617 GACCA--CATAAATGTCCCAAAG
1 GACCACTCATAAATGTCCCAAAG
24638 GACCACTC
1 GACCACTC
24646 CTTAAGGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 18 0.75
23 6 0.25
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.21
Consensus pattern (23 bp):
GACCACTCATAAATGTCCCAAAG
Found at i:25388 original size:19 final size:19
Alignment explanation
Indices: 25366--25414 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
25356 CCCTAGCTGT
25366 GGTATCGATACTGAGCTTG
1 GGTATCGATACTGAGCTTG
*
25385 GGTATCGATATTGAGCTTG
1 GGTATCGATACTGAGCTTG
25404 GGTATCGATAC
1 GGTATCGATAC
25415 CCAATTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (19 bp):
GGTATCGATACTGAGCTTG
Found at i:34838 original size:14 final size:14
Alignment explanation
Indices: 34806--34839 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
34796 GATTTGGCTA
*
34806 AACATAAATGACCG
1 AACATAAATGAACG
*
34820 CACATAAATGAACG
1 AACATAAATGAACG
34834 AACATA
1 AACATA
34840 TTATCGAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.21, G:0.12, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:42026 original size:23 final size:24
Alignment explanation
Indices: 41973--42027 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
41963 CCACTAGGGG
* *
41973 CATATA-AAATTGTCCCTAATGAC
1 CATATAGAAATTGTCCCAAAGGAC
**
41996 CACGTAGAAA-TGTCCCAAAGGAC
1 CATATAGAAATTGTCCCAAAGGAC
42019 CATATAGAA
1 CATATAGAA
42028 CCCTCGACTC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (24 bp):
CATATAGAAATTGTCCCAAAGGAC
Found at i:46426 original size:46 final size:46
Alignment explanation
Indices: 46376--46469 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
46366 AGAAAAAGAT
46376 TTATCTTTTTCATTGAAAAATATAGCAAATTAATCATCATAGCCAC
1 TTATCTTTTTCATTGAAAAATATAGCAAATTAATCATCATAGCCAC
46422 TTATCTTTTTCATTGAAAAATATAGCAAATTAATCATCATAGCCAC
1 TTATCTTTTTCATTGAAAAATATAGCAAATTAATCATCATAGCCAC
46468 TT
1 TT
46470 GATAAATTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (46 bp):
TTATCTTTTTCATTGAAAAATATAGCAAATTAATCATCATAGCCAC
Found at i:48436 original size:33 final size:33
Alignment explanation
Indices: 48394--48459 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
48384 ACCCAGCAAG
48394 AAGCTCAAATTGAGGTAACTGTTAACTTTCTCT
1 AAGCTCAAATTGAGGTAACTGTTAACTTTCTCT
48427 AAGCTCAAATTGAGGTAACTGTTAACTTTCTCT
1 AAGCTCAAATTGAGGTAACTGTTAACTTTCTCT
48460 GAACAAGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (33 bp):
AAGCTCAAATTGAGGTAACTGTTAACTTTCTCT
Found at i:53342 original size:21 final size:21
Alignment explanation
Indices: 53316--53360 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
53306 GATTTCTGGG
* *
53316 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
53337 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
53358 CAA
1 CAA
53361 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:54197 original size:31 final size:31
Alignment explanation
Indices: 54159--54283 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
54149 AGGGTCGAGG
54159 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
54190 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
54221 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
54252 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
54283 G
1 G
54284 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:59721 original size:21 final size:21
Alignment explanation
Indices: 59695--59736 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
59685 TGTTATAGGG
59695 GTATCGATACCCTACTACAGT
1 GTATCGATACCCTACTACAGT
* *
59716 GTATCGATACCTTGCTACAGT
1 GTATCGATACCCTACTACAGT
59737 AATTTCGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (21 bp):
GTATCGATACCCTACTACAGT
Found at i:63002 original size:18 final size:18
Alignment explanation
Indices: 62976--63023 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
62966 TTCCCTTCAG
*
62976 GGTATCGATA-CTCCTCAA
1 GGTAACGATACCT-CTCAA
62994 GGTAACGATACCTCTCAA
1 GGTAACGATACCTCTCAA
63012 GGTAACGATACC
1 GGTAACGATACC
63024 ATTCCGAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 26 0.93
19 2 0.07
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (18 bp):
GGTAACGATACCTCTCAA
Done.