Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002899.1 Hibiscus syriacus cultivar Beakdansim tig00005988_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: 70792
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1537 original size:18 final size:18
Alignment explanation
Indices: 1501--1562 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 18
1491 GCAACGAGAG
1501 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AATGAA
1520 AATCGCAATGCGAATGAA
1 AATCGCAATGCGAATGAA
1538 AATCGCAA--CG-A-GAA
1 AATCGCAATGCGAATGAA
1552 AATCGCAATGC
1 AATCGCAATGC
1563 AATTTTCATT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.27
15 1 0.02
16 3 0.07
18 14 0.34
19 12 0.29
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (18 bp):
AATCGCAATGCGAATGAA
Found at i:1629 original size:19 final size:20
Alignment explanation
Indices: 1583--1637 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1573 TCGCATTGCG
*
1583 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
1603 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
1623 A-TTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
1638 TTTCCCGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1904 original size:41 final size:40
Alignment explanation
Indices: 1806--1922 Score: 162
Period size: 41 Copynumber: 2.9 Consensus size: 40
1796 ATAAGTCAGA
* * ***
1806 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTAAGT
*
1846 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTATATT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTA-AGT
*
1887 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTT
1923 CCAAATTCGC
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 32 0.46
41 37 0.54
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (40 bp):
ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTAAGT
Found at i:1919 original size:20 final size:20
Alignment explanation
Indices: 1798--1918 Score: 134
Period size: 20 Copynumber: 6.0 Consensus size: 20
1788 AAAATCACAT
*
1798 AAGTCAGAATCGCGTTGCGA
1 AAGTCAGTATCGCGTTGCGA
*
1818 AAGTCAGAATCGCGTTGCGA
1 AAGTCAGTATCGCGTTGCGA
*
1838 AAGTAAGTATCGCGTTGCGA
1 AAGTCAGTATCGCGTTGCGA
*
1858 AAGTCAGTATCGCATTGCGA
1 AAGTCAGTATCGCGTTGCGA
*** * *
1878 TTTTATATTATCGCGTTGCGA
1 AAGT-CAGTATCGCGTTGCGA
* *
1899 TAGTCAGTATCGCATTGCGA
1 AAGTCAGTATCGCGTTGCGA
1919 TTTTCCAAAT
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 70 0.82
21 15 0.18
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (20 bp):
AAGTCAGTATCGCGTTGCGA
Found at i:1953 original size:21 final size:20
Alignment explanation
Indices: 1929--2044 Score: 60
Period size: 20 Copynumber: 5.7 Consensus size: 20
1919 TTTTCCAAAT
*
1929 TCGCATTGCGACTTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
1950 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
* * *
1971 TCGTATTGCG-ATAGTAATAA
1 TCGCATTGCGAATTGGAA-AA
* *
1991 TCGCGTTGCGAATCTGGAAAC
1 TCGCATTGCGAAT-TGGAAAA
* *
2012 T-G-ATTTGCGATAATGG-AGA
1 TCGCA-TTGCGA-ATTGGAAAA
2031 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2045 AGCGATCGCA
Statistics
Matches: 69, Mismatches: 18, Indels: 18
0.66 0.17 0.17
Matches are distributed among these distances:
19 9 0.13
20 27 0.39
21 27 0.39
22 6 0.09
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:2427 original size:17 final size:18
Alignment explanation
Indices: 2385--2428 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
2375 TCTTTTGATT
2385 AGTTATTTATTTTATAAA
1 AGTTATTTATTTTATAAA
2403 AGTT-TTTATTTTA-AAA
1 AGTTATTTATTTTATAAA
**
2419 TTTTATTTAT
1 AGTTATTTAT
2429 GTCCATCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 14 0.61
18 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
AGTTATTTATTTTATAAA
Found at i:10600 original size:25 final size:25
Alignment explanation
Indices: 10566--10618 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
10556 TATTAACACG
10566 AACCAAAATATAAATACGATACAAA
1 AACCAAAATATAAATACGATACAAA
10591 AACCAAAATATAAATACGATACAAA
1 AACCAAAATATAAATACGATACAAA
10616 AAC
1 AAC
10619 TAGATGCGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.64, C:0.17, G:0.04, T:0.15
Consensus pattern (25 bp):
AACCAAAATATAAATACGATACAAA
Found at i:19904 original size:13 final size:13
Alignment explanation
Indices: 19886--19915 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19876 ATACTCCTAT
19886 TTTCAGAGGGCTC
1 TTTCAGAGGGCTC
19899 TTTCAGAGGGCTC
1 TTTCAGAGGGCTC
19912 TTTC
1 TTTC
19916 TTCTGATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.27, T:0.37
Consensus pattern (13 bp):
TTTCAGAGGGCTC
Found at i:34138 original size:35 final size:35
Alignment explanation
Indices: 34085--34157 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
34075 GAGCCTCATT
*
34085 AATAATAAAAATAGTCACTAATGTTATCGATTTAA
1 AATAATAAAAATAGTCACTAACGTTATCGATTTAA
*
34120 AATAAT-AAAATTGATCACTAACGTTATCGATTTAA
1 AATAATAAAAATAG-TCACTAACGTTATCGATTTAA
34155 AAT
1 AAT
34158 TTGAGATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 6 0.17
35 29 0.83
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (35 bp):
AATAATAAAAATAGTCACTAACGTTATCGATTTAA
Found at i:37689 original size:24 final size:24
Alignment explanation
Indices: 37662--37716 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
37652 TAATTTATGT
37662 AATTTTCCCTTTTTTCCAACCCAG
1 AATTTTCCCTTTTTTCCAACCCAG
37686 AATTTTCCCTTTTTTCCAACCCAG
1 AATTTTCCCTTTTTTCCAACCCAG
37710 AATTTTC
1 AATTTTC
37717 TTGGATACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.31, G:0.04, T:0.44
Consensus pattern (24 bp):
AATTTTCCCTTTTTTCCAACCCAG
Found at i:37735 original size:15 final size:15
Alignment explanation
Indices: 37717--37754 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
37707 CAGAATTTTC
37717 TTGGATACACCAGTT
1 TTGGATACACCAGTT
37732 TTGGATACACCAGTT
1 TTGGATACACCAGTT
37747 TTGGATAC
1 TTGGATAC
37755 TGTAAGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (15 bp):
TTGGATACACCAGTT
Found at i:43033 original size:25 final size:26
Alignment explanation
Indices: 43005--43061 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
42995 TTAAAAAATT
43005 TTAAATTGAT-TTTATG-AAA-TTCAA
1 TTAAATT-ATATTTATGAAAATTTCAA
43029 GTTAAA-TATATTTATGAAAATTTCAA
1 -TTAAATTATATTTATGAAAATTTCAA
43055 TTAAATT
1 TTAAATT
43062 TTAAATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
23 2 0.07
24 7 0.25
25 13 0.46
26 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (26 bp):
TTAAATTATATTTATGAAAATTTCAA
Found at i:43116 original size:2 final size:2
Alignment explanation
Indices: 43109--43147 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
43099 ACCATTTACG
43109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
43148 TTTTCTCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53052 original size:15 final size:15
Alignment explanation
Indices: 53032--53077 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
53022 TAACCGTCTG
*
53032 ATTGAAAGAAAAAAA
1 ATTGAAATAAAAAAA
*
53047 ATTG-AATTAAAAAA
1 ATTGAAATAAAAAAA
*
53061 ATTGAATTAAAAAAA
1 ATTGAAATAAAAAAA
53076 AT
1 AT
53078 CTCATCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (15 bp):
ATTGAAATAAAAAAA
Found at i:53060 original size:14 final size:14
Alignment explanation
Indices: 53041--53075 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
53031 GATTGAAAGA
53041 AAAAAAATTGAATT
1 AAAAAAATTGAATT
53055 AAAAAAATTGAATT
1 AAAAAAATTGAATT
53069 AAAAAAA
1 AAAAAAA
53076 ATCTCATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (14 bp):
AAAAAAATTGAATT
Found at i:53373 original size:22 final size:23
Alignment explanation
Indices: 53336--53427 Score: 102
Period size: 22 Copynumber: 4.0 Consensus size: 23
53326 TTTAAAAAAT
53336 ATATAGTATATATAGTTTTTGAAA
1 ATATA-TATATATAGTTTTTGAAA
53360 ATATATA-ATATAGTTTTTGAAA
1 ATATATATATATAGTTTTTGAAA
* *
53382 ACATAT-TATATA-ATTTTGAAA
1 ATATATATATATAGTTTTTGAAA
*
53403 ACGTATA-ATATATAGTTTTTTAAA
1 A--TATATATATATAGTTTTTGAAA
53427 A
1 A
53428 ATAATTTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
21 9 0.16
22 25 0.43
23 11 0.19
24 13 0.22
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (23 bp):
ATATATATATATAGTTTTTGAAA
Found at i:53560 original size:10 final size:10
Alignment explanation
Indices: 53523--53608 Score: 70
Period size: 10 Copynumber: 8.5 Consensus size: 10
53513 AATATATACA
* *
53523 TATTATTATA
1 TATTTTTATT
*
53533 TATTATTATT
1 TATTTTTATT
*
53543 AATATTTTATT
1 TAT-TTTTATT
53554 TATTTTT-TCT
1 TATTTTTAT-T
*
53564 TATCTATT-TT
1 TAT-TTTTATT
53574 TATTTTTATT
1 TATTTTTATT
53584 TATTTTTATT
1 TATTTTTATT
53594 TCA-TTTTATT
1 T-ATTTTTATT
53604 TATTT
1 TATTT
53609 CATCTTTGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
9 5 0.08
10 46 0.72
11 13 0.20
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTTATT
Found at i:53587 original size:16 final size:16
Alignment explanation
Indices: 53547--53594 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
53537 ATTATTAATA
53547 TTTTATTTA-TTTT-T
1 TTTTATTTATTTTTAT
* *
53561 TCTTATCTATTTTTAT
1 TTTTATTTATTTTTAT
53577 TTTTATTTATTTTTAT
1 TTTTATTTATTTTTAT
53593 TT
1 TT
53595 CATTTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 7 0.25
15 4 0.14
16 17 0.61
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATTTATTTTTAT
Found at i:53601 original size:16 final size:16
Alignment explanation
Indices: 53546--53604 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
53536 TATTATTAAT
*
53546 ATTTTATTTATTTTTTC
1 ATTTTATTT-TTATTTC
53563 -TTATCTATTTTTATTT-
1 ATT-T-TATTTTTATTTC
*
53579 TTATTTATTTTTATTTC
1 AT-TTTATTTTTATTTC
53596 ATTTTATTT
1 ATTTTATTT
53605 ATTTCATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
16 20 0.57
17 9 0.26
18 6 0.17
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTATTTTTATTTC
Done.