Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004629.1 Hibiscus syriacus cultivar Beakdansim tig00010361_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: 63448
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:8063 original size:59 final size:59
Alignment explanation
Indices: 7964--8100 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 59
7954 CAGCAGGCTG
** * *
7964 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** * **
8023 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGATGCGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
*
8082 CATACTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
8101 CGGTGCTTAT
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
58 1 0.02
59 61 0.98
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:14551 original size:131 final size:131
Alignment explanation
Indices: 14311--14605 Score: 349
Period size: 131 Copynumber: 2.3 Consensus size: 131
14301 TATCTTCATT
* * * ** ** * *
14311 TCGATTGGAAATAATTAGATATTATCATTCACTCTCGAATTAATATTGATTTTTAAGATGAAATA
1 TCGATTAGAAATAATCAGATATTATCGTTTTCAATCGAATTAATATTGAATTTTAAGACGAAATA
* ** * *
14376 GTGATATCTCTTCATTTCGATTAGAGCAATAAATAATTGTTTTAAGGTATGGGAGGTCATTTATT
66 GTGATATCTCTTCATTTCGATTAGAGCAATAAATAACTACTTTAAGGTATGAGAGGTAATTTATT
14441 C
131 C
* * * * * *
14442 TCGATTGGAAATCATTATATATTATTGTTTTCAATCGAATTGAA-ATTGAATTTTAAGACGGAAT
1 TCGATTAGAAATAATCAGATATTATCGTTTTCAATCGAATT-AATATTGAATTTTAAGACGAAAT
** * * *
14506 AGTGATATCTCTTCATTTTTATTGGAGTAATAAATAACTACTTTAAGGTATGAGATGTAATTTAT
65 AGTGATATCTCTTCATTTCGATTAGAGCAATAAATAACTACTTTAAGGTATGAGAGGTAATTTAT
14571 TC
130 TC
14573 TCGATTAGAAATAATCAGATATTATCGTTTTCA
1 TCGATTAGAAATAATCAGATATTATCGTTTTCA
14606 CTCTTAAATT
Statistics
Matches: 137, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
131 135 0.99
132 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.41
Consensus pattern (131 bp):
TCGATTAGAAATAATCAGATATTATCGTTTTCAATCGAATTAATATTGAATTTTAAGACGAAATA
GTGATATCTCTTCATTTCGATTAGAGCAATAAATAACTACTTTAAGGTATGAGAGGTAATTTATT
C
Found at i:17934 original size:27 final size:26
Alignment explanation
Indices: 17899--17961 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
17889 GACACATAAC
17899 TTTTT-TTTCATTGCACAATCTCT-CT
1 TTTTTATTTCATTGCACAAT-TCTGCT
* *
17924 TTCTTTATTTCCTTTGCACAATTTTGCT
1 TT-TTTATTT-CATTGCACAATTCTGCT
17952 TTTTTATTTC
1 TTTTTATTTC
17962 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
25 2 0.06
26 4 0.12
27 12 0.38
28 14 0.44
ACGTcount: A:0.14, C:0.21, G:0.05, T:0.60
Consensus pattern (26 bp):
TTTTTATTTCATTGCACAATTCTGCT
Found at i:17940 original size:28 final size:27
Alignment explanation
Indices: 17909--17961 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
17899 TTTTTTTTCA
17909 TTGCACAATCTCT-CTTTCTTTATTTCCT
1 TTGCACAAT-TCTGCTTT-TTTATTTCCT
*
17937 TTGCACAATTTTGCTTTTTTATTTC
1 TTGCACAATTCTGCTTTTTTATTTC
17962 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.57
Consensus pattern (27 bp):
TTGCACAATTCTGCTTTTTTATTTCCT
Found at i:18895 original size:25 final size:26
Alignment explanation
Indices: 18853--18902 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
18843 ATTGTACTCC
18853 GAATAATAAAGAAAAAAATA-AAATA
1 GAATAATAAAGAAAAAAATACAAATA
*
18878 GAATAA-AAAGAACGAAAATACAAAT
1 GAATAATAAAGAA-AAAAATACAAAT
18903 TAAAAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 12 0.55
26 4 0.18
ACGTcount: A:0.72, C:0.04, G:0.10, T:0.14
Consensus pattern (26 bp):
GAATAATAAAGAAAAAAATACAAATA
Found at i:18914 original size:20 final size:18
Alignment explanation
Indices: 18864--18915 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
18854 AATAATAAAG
* *
18864 AAAAAAATAAAATAGAAT
1 AAAAAAAGAAAATAAAAT
18882 AAAAAGAACGAAAATACAAATT
1 AAAAA-AA-GAAAATA-AAA-T
18904 AAAAAAAGAAAA
1 AAAAAAAGAAAA
18916 AGAAAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 5 0.18
19 2 0.07
20 11 0.39
21 4 0.14
22 6 0.21
ACGTcount: A:0.77, C:0.04, G:0.08, T:0.12
Consensus pattern (18 bp):
AAAAAAAGAAAATAAAAT
Found at i:25695 original size:2 final size:2
Alignment explanation
Indices: 25690--25730 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
25680 TACTAATAAG
*
25690 TA TA TA -A TA TA -A TA TA TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25730 T
1 T
25731 GTGTGTGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28463 original size:344 final size:349
Alignment explanation
Indices: 27818--28510 Score: 1342
Period size: 344 Copynumber: 2.0 Consensus size: 349
27808 AAAATATGAC
*
27818 CCTCAAGATTTTTCAAGTGTCATTTGTGACTTGTTATCCCCTTTAATCAAGAGTCAATACCTCAC
1 CCTCAAGATTTTTCAAGTGTCATTTCTGACTTGTTATCCCCTTTAATCAAGAGTCAATACCTCAC
27883 CCCAAGGCCCTTGAGAATGAGGACTAGCTCATCCGCTTATGGCTATGACCCAAATAGTCTTTGTG
66 CCCAAGGCCCTTGAGAATGAGGACTAGCTCATCCGCTTATGGCTATGACCCAAATAGTCTTTGTG
27948 AGTTTCATATGGGGCCATTGGGCCATCGCACTGACAAGTGCATACCATTGATGGAAGAGATAGAA
131 AGTTTCATATGGGGCCATTGGGCCATCGCACTGACAAGTGCATACCATTGATGGAAGAGATAGAA
28013 AAGCTCATTGACAAGGGAGTCCTGACATGAGAAATGATTGAGAGATGGGGATAAAATGAGAATAA
196 AAGCTCATTGACAAGGGAGTCCTGACATGAGAAATGATTGAGAGATGGGGATAAAATGAGAATAA
28078 ATACCCTAATCCAATTAGATACCCAATATTCTAGCATTCTAGATGAACAAGTTGAGGTTGTTATC
261 ATACCCTAATCCAATTAGATACCCAATATTCTAGCATTCTAGATGAACAAGTTGAGGTTGTTATC
28143 CACCACAATTTCACC-TACGTTGA
326 CACCACAATTTCACCTTACGTTGA
28166 CCTCAAGATTTTTC-AGTGTCATTTCTGACTTGTTATCCCCTTTAATCAAGAGTCAATACCTCAC
1 CCTCAAGATTTTTCAAGTGTCATTTCTGACTTGTTATCCCCTTTAATCAAGAGTCAATACCTCAC
28230 CCCAAGGCCCTTGAGAATGAGGACTAGCTCATCCGCTTATGGCTATGACCC-AATAGTCTTTGTG
66 CCCAAGGCCCTTGAGAATGAGGACTAGCTCATCCGCTTATGGCTATGACCCAAATAGTCTTTGTG
28294 AGTTTCATAT-GGGCCATTGGGCCATCGCACTGACAA-TGCATACCATTGATGGAAGAGATAGAA
131 AGTTTCATATGGGGCCATTGGGCCATCGCACTGACAAGTGCATACCATTGATGGAAGAGATAGAA
28357 AAGCTCATTGACAAGGGAGTCCTGACATGAGAAATGATTGAGAGATGGGGATAAAATGAGAATAA
196 AAGCTCATTGACAAGGGAGTCCTGACATGAGAAATGATTGAGAGATGGGGATAAAATGAGAATAA
28422 ATACCCTAATCCAATTAGATACCCAATATTCTAGCATTCTAGATGAACAAGTTGAGGTTGTTATC
261 ATACCCTAATCCAATTAGATACCCAATATTCTAGCATTCTAGATGAACAAGTTGAGGTTGTTATC
28487 CACCACAATTTCACCTTACGTTGA
326 CACCACAATTTCACCTTACGTTGA
28511 AAACATCTTG
Statistics
Matches: 343, Mismatches: 1, Indels: 5
0.98 0.00 0.01
Matches are distributed among these distances:
344 172 0.50
345 34 0.10
346 23 0.07
347 100 0.29
348 14 0.04
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (349 bp):
CCTCAAGATTTTTCAAGTGTCATTTCTGACTTGTTATCCCCTTTAATCAAGAGTCAATACCTCAC
CCCAAGGCCCTTGAGAATGAGGACTAGCTCATCCGCTTATGGCTATGACCCAAATAGTCTTTGTG
AGTTTCATATGGGGCCATTGGGCCATCGCACTGACAAGTGCATACCATTGATGGAAGAGATAGAA
AAGCTCATTGACAAGGGAGTCCTGACATGAGAAATGATTGAGAGATGGGGATAAAATGAGAATAA
ATACCCTAATCCAATTAGATACCCAATATTCTAGCATTCTAGATGAACAAGTTGAGGTTGTTATC
CACCACAATTTCACCTTACGTTGA
Found at i:31237 original size:41 final size:42
Alignment explanation
Indices: 31158--31237 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
31148 CATAAGTAAG
* *
31158 TCTTTCGAGCATGATGATTAAATCATTTGGGTCATCTATCAA
1 TCTTTCGAGCATGATGATTAAATCATTAGGGCCATCTATCAA
*
31200 TCTTTCGAGCGA-GATGA-TAAGTCATTAGGGCCATCTAT
1 TCTTTCGAGC-ATGATGATTAAATCATTAGGGCCATCTAT
31238 AAGACCTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 18 0.53
42 15 0.44
43 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (42 bp):
TCTTTCGAGCATGATGATTAAATCATTAGGGCCATCTATCAA
Found at i:38678 original size:16 final size:16
Alignment explanation
Indices: 38657--38703 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
38647 ATATTTGGTT
38657 TAATTGAATGAAGCAA
1 TAATTGAATGAAGCAA
38673 TAATTGAATGAAGCAA
1 TAATTGAATGAAGCAA
38689 TAATTGAAT-AAGCAA
1 TAATTGAATGAAGCAA
38704 GGTCAGGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 6 0.19
16 25 0.81
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (16 bp):
TAATTGAATGAAGCAA
Found at i:39081 original size:2 final size:2
Alignment explanation
Indices: 39074--39117 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
39064 ATTAATCAAG
39074 AT AT AT AT AT AT AT -T 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
39115 AT A
1 AT A
39118 CTATTGTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43575 original size:17 final size:17
Alignment explanation
Indices: 43553--43600 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
43543 GTATAATTAT
43553 TTAAATATTTTAAATAA
1 TTAAATATTTTAAATAA
43570 TTAAAT-TTTATAAA-AA
1 TTAAATATTT-TAAATAA
*
43586 -TATATATTTTAAATA
1 TTAAATATTTTAAATA
43601 TGAAGATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 8 0.30
16 9 0.33
17 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAATATTTTAAATAA
Found at i:43579 original size:15 final size:16
Alignment explanation
Indices: 43559--43600 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
43549 TTATTTAAAT
43559 ATTTTAAATAAT-TAA
1 ATTTTAAATAATATAA
* *
43574 ATTTTATAAAAATATAT
1 ATTTTA-AATAATATAA
43591 ATTTTAAATA
1 ATTTTAAATA
43601 TGAAGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 6 0.27
16 8 0.36
17 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTTAAATAATATAA
Found at i:43598 original size:32 final size:30
Alignment explanation
Indices: 43557--43630 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 30
43547 AATTATTTAA
*
43557 ATATTTTAAATAATTAA-ATTTTATAAAAATAT
1 ATATTTTAAAT-ATGAAGATTTT-TAAAAAT-T
43589 ATATTTTAAATATGAAGATTTTTAAAAATT
1 ATATTTTAAATATGAAGATTTTTAAAAATT
*
43619 AT-TTTTACATAT
1 ATATTTTAAATAT
43631 TTTTATCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 9 0.23
30 3 0.08
31 11 0.28
32 16 0.41
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (30 bp):
ATATTTTAAATATGAAGATTTTTAAAAATT
Found at i:62579 original size:28 final size:26
Alignment explanation
Indices: 62420--62596 Score: 170
Period size: 25 Copynumber: 6.8 Consensus size: 26
62410 GCATAAAAAA
* *
62420 AAAAAG-AAAAGGAAAAGGAATAAAG
1 AAAAAGAAAAAGAAAAAGAAATAAAG
* *
62445 AAAAAGAAAAAGAAAAAGGAA-AAGG
1 AAAAAGAAAAAGAAAAAGAAATAAAG
* *
62470 AAAAGGAAAAGGAATAAAG-AA-AAAG
1 AAAAAGAAAAAGAA-AAAGAAATAAAG
62495 AAAAAGAAAAAGAAAAAG-AATAAAG
1 AAAAAGAAAAAGAAAAAGAAATAAAG
62520 AATAAAGAATAAAGAAAAAGAAA-AAGAGG
1 AA-AAAGAA-AAAGAAAAAGAAATAA-A-G
*
62549 AAAAATGAAAAAGGAAAAGAAATAAATG
1 AAAAA-GAAAAAGAAAAAGAAATAAA-G
*
62577 AAAAAGAAAGA-AAAAAGAAA
1 AAAAAGAAAAAGAAAAAGAAA
62597 AAGAATAATG
Statistics
Matches: 131, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
24 6 0.05
25 44 0.34
26 31 0.24
27 17 0.13
28 25 0.19
29 8 0.06
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (26 bp):
AAAAAGAAAAAGAAAAAGAAATAAAG
Found at i:62597 original size:38 final size:36
Alignment explanation
Indices: 62414--62610 Score: 184
Period size: 38 Copynumber: 5.3 Consensus size: 36
62404 TGTTATGCAT
* * *
62414 AAAAAAAAAAAGAAAAGGAAAAGGAATAAAGAAAAAG
1 AAAAAGAAAAAGAAAAAGAAAA-GAAAAAAGAAAAAG
* * *
62451 AAAAAGAAAAAGGAAAAGGAAAAGGAAAAGGAATAAAG
1 AAAAAGAAAAA-GAAAAAGAAAAGAAAAAAGAA-AAAG
*
62489 AAAAAGAAAAAGAAAAAGAAAAAGAATAAAGAATAAAG
1 AAAAAGAAAAAGAAAAAG-AAAAGAAAAAAGAA-AAAG
* *
62527 AATAAAGAAAAAGAAAAAG--AGGAAAAATGAAAAAG
1 AA-AAAGAAAAAGAAAAAGAAAAGAAAAAAGAAAAAG
*
62562 GAAAAGAAATAAATGAAAAAG-AAAGAAAAAAGAAAAAG
1 AAAAAG-AA-AAA-GAAAAAGAAAAGAAAAAAGAAAAAG
*
62600 AATAATGAAAA
1 AA-AAAGAAAA
62611 TAAAAAGGAG
Statistics
Matches: 135, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
34 4 0.03
35 7 0.05
36 12 0.09
37 32 0.24
38 61 0.45
39 19 0.14
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (36 bp):
AAAAAGAAAAAGAAAAAGAAAAGAAAAAAGAAAAAG
Found at i:62616 original size:6 final size:6
Alignment explanation
Indices: 62414--62601 Score: 180
Period size: 6 Copynumber: 29.3 Consensus size: 6
62404 TGTTATGCAT
* * *
62414 AAAAAA AAAAAG AAAAGG AAAAGG AATAAAG AAAAAG AAAAAG AAAAAGG
1 AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG AAAAA-G
* * *
62464 AAAAGG AAAAGG AAAAGG AATAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG
62513 AATAAAG AATAAAG AATAAAG AAAAAG AAAAAGAGG AAAAATG AAAAAG
1 AA-AAAG AA-AAAG AA-AAAG AAAAAG -AAAA-A-G AAAAA-G AAAAAG
* *
62562 GAAAAG AAATAAATG AAAAAG AAAGA- AAAAAG AAAAAG AA
1 AAAAAG -AA-AAA-G AAAAAG AAAAAG AAAAAG AAAAAG AA
62602 TAATGAAAAT
Statistics
Matches: 161, Mismatches: 10, Indels: 22
0.83 0.05 0.11
Matches are distributed among these distances:
5 4 0.02
6 95 0.59
7 50 0.31
8 10 0.06
9 2 0.01
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (6 bp):
AAAAAG
Done.