Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004805.1 Hibiscus syriacus cultivar Beakdansim tig00010823_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: 66883
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:5582 original size:17 final size:17
Alignment explanation
Indices: 5556--5588 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5546 TATCAATTTT
5556 AATTTAATATAATATATA
1 AATTTAATATAA-ATATA
5574 AATTT-ATATAAATAT
1 AATTTAATATAAATAT
5589 TCCAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTAATATAAATATA
Found at i:18759 original size:32 final size:31
Alignment explanation
Indices: 18700--18761 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
18690 ATCTTTTAAA
* * * *
18700 TATTATAAATTAGTCCTTAAATTTATCAAAT
1 TATTATAAAATAATCCGTAAACTTATCAAAT
18731 TATTATGAAAATAATCCGTAAACTTATCAAA
1 TATTAT-AAAATAATCCGTAAACTTATCAAA
18762 ATGTATTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (31 bp):
TATTATAAAATAATCCGTAAACTTATCAAAT
Found at i:37216 original size:9 final size:8
Alignment explanation
Indices: 37183--37356 Score: 101
Period size: 8 Copynumber: 21.4 Consensus size: 8
37173 TCGCTTGAAG
37183 AAGAAATAA
1 AAGAAA-AA
37192 AAGGAAAAA
1 AA-GAAAAA
*
37201 ACG-AAAA
1 AAGAAAAA
*
37208 ACGAAAAA
1 AAGAAAAA
*
37216 AATAATAAA
1 AAGAA-AAA
*
37225 AATGAGAAA
1 AA-GAAAAA
37234 AAG--AAA
1 AAGAAAAA
*
37240 AAGAAGAA
1 AAGAAAAA
37248 AAGAAAAA
1 AAGAAAAA
37256 AAGAAAAA
1 AAGAAAAA
37264 AAGAAAAA
1 AAGAAAAA
*
37272 ATGAGAAAA
1 AAGA-AAAA
*
37281 AA-TAAAA
1 AAGAAAAA
*
37288 ATGAGAAAA
1 AAGA-AAAA
*
37297 AA-TAAAA
1 AAGAAAAA
*
37304 ATG-AAAA
1 AAGAAAAA
37311 AAGAAAGAA
1 AAGAAA-AA
*
37320 AA-ATAAA
1 AAGAAAAA
37327 AAGAGAAAA
1 AAGA-AAAA
*
37336 ATGAAAAA
1 AAGAAAAA
37344 AGAGAAATAA
1 A-AGAAA-AA
37354 AAG
1 AAG
37357 GAGGGTTCAA
Statistics
Matches: 129, Mismatches: 20, Indels: 32
0.71 0.11 0.18
Matches are distributed among these distances:
6 6 0.05
7 27 0.21
8 47 0.36
9 41 0.32
10 8 0.06
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.07
Consensus pattern (8 bp):
AAGAAAAA
Found at i:37281 original size:55 final size:54
Alignment explanation
Indices: 37180--37355 Score: 145
Period size: 55 Copynumber: 3.3 Consensus size: 54
37170 ATTTCGCTTG
* * * * *
37180 AAGAAGAAAT-AAAAGGAAAAAACG-AAAAACGAAAAAAATAATAAAAATGAGAAA
1 AAGAAAAAATAAAAAGGAAAAAAAGAAAAAAAG-AAAAAATGAGAAAAATGA-AAA
37234 AAGAAAAAGA-AGAAAA-GAAAAAAAGAAAAAAAGAAAAAATGAGAAAAAAT-AAAA
1 AAGAAAAA-ATA-AAAAGGAAAAAAAGAAAAAAAGAAAAAATGAG-AAAAATGAAAA
*
37288 ATGAGAAAAAATAAAAATG-AAAAAAGAAAGAAAA-ATAAAAA-GAGAAAAATGAAAA
1 A--AGAAAAAATAAAAAGGAAAAAAAGAAA-AAAAGA-AAAAATGAGAAAAATGAAAA
*
37343 AAG-AGAAATAAAA
1 AAGAAAAAATAAAA
37356 GGAGGGTTCA
Statistics
Matches: 104, Mismatches: 6, Indels: 26
0.76 0.04 0.19
Matches are distributed among these distances:
52 9 0.09
53 2 0.02
54 17 0.16
55 42 0.40
56 34 0.33
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.07
Consensus pattern (54 bp):
AAGAAAAAATAAAAAGGAAAAAAAGAAAAAAAGAAAAAATGAGAAAAATGAAAA
Found at i:37336 original size:32 final size:34
Alignment explanation
Indices: 37183--37355 Score: 131
Period size: 32 Copynumber: 5.3 Consensus size: 34
37173 TCGCTTGAAG
* *
37183 AAGAAAT-AAAA-G-GAAAAAACGAAAAACGAAAA
1 AAGAAATAAAAATGAGAAAAGA-GAAAAATGAAAA
37215 AA-ATAATAAAAATGAGAAAA-AGAAAAA-GAAGAA
1 AAGA-AATAAAAATGAGAAAAGAGAAAAATGAA-AA
* *
37248 AAG-AA-AAAAA-GA-AAAAAAGAAAAAATG-AGA
1 AAGAAATAAAAATGAGAAAAGAG-AAAAATGAAAA
* *
37278 AA-AAATAAAAATGAGAAAAAATAAAAATGAAAA
1 AAGAAATAAAAATGAGAAAAGAGAAAAATGAAAA
*
37311 AAGAAAGAAAAAT-A-AAAAGAGAAAAATGAAAAA
1 AAGAAATAAAAATGAGAAAAGAGAAAAATG-AAAA
37344 AGAGAAATAAAA
1 A-AGAAATAAAA
37356 GGAGGGTTCA
Statistics
Matches: 117, Mismatches: 7, Indels: 32
0.75 0.04 0.21
Matches are distributed among these distances:
29 4 0.03
30 9 0.08
31 17 0.15
32 32 0.27
33 30 0.26
34 20 0.17
35 5 0.04
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.07
Consensus pattern (34 bp):
AAGAAATAAAAATGAGAAAAGAGAAAAATGAAAA
Found at i:37351 original size:14 final size:13
Alignment explanation
Indices: 37231--37355 Score: 80
Period size: 14 Copynumber: 9.2 Consensus size: 13
37221 TAAAAATGAG
*
37231 AAAAAGAAAAAGA
1 AAAAAGAAAAATA
37244 AGAAAAGAAAAA-A
1 A-AAAAGAAAAATA
37257 AGAAAA-AAAGAA-A
1 A-AAAAGAAA-AATA
*
37270 AAATGAGAAAAAATA
1 AAA-AAG-AAAAATA
37285 AAAATGAGAAAAAATA
1 AAAA--AG-AAAAATA
*
37301 AAAATG-AAAA-A
1 AAAAAGAAAAATA
*
37312 AGAAAGAAAAATA
1 AAAAAGAAAAATA
37325 AAAAGAGAAAAATGA
1 AAAA-AGAAAAAT-A
*
37340 AAAAAGAGAAATA
1 AAAAAGAAAAATA
37353 AAA
1 AAA
37356 GGAGGGTTCA
Statistics
Matches: 93, Mismatches: 7, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
11 5 0.05
12 13 0.14
13 21 0.23
14 28 0.30
15 12 0.13
16 14 0.15
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.06
Consensus pattern (13 bp):
AAAAAGAAAAATA
Found at i:38707 original size:36 final size:36
Alignment explanation
Indices: 38621--38758 Score: 222
Period size: 36 Copynumber: 3.8 Consensus size: 36
38611 AAACAGGTCA
* * * *
38621 ATCTTAAGCCTTCATGAAAGAGCAGTGAAGCAATTC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
*
38657 AAACTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
1 -ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
38694 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
38730 ATCTTAAGCCTTCACGGAAGAGTAGTGAA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAA
38759 ATAAACTCGT
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 64 0.67
37 31 0.33
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
Found at i:38826 original size:51 final size:51
Alignment explanation
Indices: 38771--39382 Score: 807
Period size: 51 Copynumber: 11.8 Consensus size: 51
38761 AAACTCGTTT
*
38771 GTTGAAGATTGAATCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
38822 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
38873 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
38924 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
38975 GTTGAAGATTGAGTCATATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
39026 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
39077 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* ** *
39128 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTC
* * * * **
39180 GTTGAAGATTGTTCGAGTTCTGTACTCTCTGATA-GATTAGAGAGCGGACCCGTTC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGA-AGGAATAGGGAGCGGACAAGTTC
* * *
39235 GTTGAAGATTGTTTGAGTCC--TGCTCTCTGAAGGAATAGGGAGCGGACATGTTT
1 GTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * * * * * * *
39288 ATTGAAGATCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
39339 GTTGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAG
1 GTTGAAGA----TTGAGTCCTATACTCTCTGAAGGAATAGGGAG
39383 AAGACATGTT
Statistics
Matches: 514, Mismatches: 33, Indels: 24
0.90 0.06 0.04
Matches are distributed among these distances:
49 6 0.01
51 381 0.74
52 11 0.02
53 32 0.06
55 47 0.09
56 36 0.07
57 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:45789 original size:2 final size:2
Alignment explanation
Indices: 45776--45810 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
45766 CAAGAATCTG
*
45776 AT AT AA 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 A
45811 GTTAAGCACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:47651 original size:2 final size:2
Alignment explanation
Indices: 47638--47680 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
47628 CAAGAATCTG
*
47638 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47680 A
1 A
47681 GTTAAGCACC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51234 original size:18 final size:19
Alignment explanation
Indices: 51195--51242 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
51185 GCTCAGGACA
* *
51195 ACGACGATGACGAACGATG
1 ACGATGATGACGAACGACG
*
51214 ACGATGGTGACG-ACGACG
1 ACGATGATGACGAACGACG
51232 ACGATGATGAC
1 ACGATGATGAC
51243 AGCGAGGAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.33, C:0.21, G:0.33, T:0.12
Consensus pattern (19 bp):
ACGATGATGACGAACGACG
Found at i:53127 original size:2 final size:2
Alignment explanation
Indices: 53120--53167 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
53110 GATAGATGGA
53120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
53162 GT AT AT
1 AT AT AT
53168 GTTATGATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55920 original size:28 final size:28
Alignment explanation
Indices: 55884--55938 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
55874 CTGTTGTTGC
*
55884 TTTCAAACACT-GACTTAACGACATAATG
1 TTTCAAACACTAG-CTTAAAGACATAATG
* *
55912 TTTCTAACAGTAGCTTAAAGACATAAT
1 TTTCAAACACTAGCTTAAAGACATAAT
55939 ATAAACGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (28 bp):
TTTCAAACACTAGCTTAAAGACATAATG
Found at i:57093 original size:29 final size:29
Alignment explanation
Indices: 57051--57109 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
57041 ATTTTCACCT
57051 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
57080 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
57109 A
1 A
57110 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Done.