Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006308.1 Hibiscus syriacus cultivar Beakdansim tig00015072_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: 56335
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1896 original size:19 final size:19
Alignment explanation
Indices: 1872--1920 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1862 ATTTTAAAAT
1872 TTATAAAATAATCATTAAC
1 TTATAAAATAATCATTAAC
1891 TTATAAAATAATCATTAAC
1 TTATAAAATAATCATTAAC
1910 TTATAAAATAA
1 TTATAAAATAA
1921 ATTTATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
TTATAAAATAATCATTAAC
Found at i:13330 original size:15 final size:15
Alignment explanation
Indices: 13307--13337 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13297 CGGCCTTCCA
*
13307 GGCGGCTTCACGCTC
1 GGCGACTTCACGCTC
13322 GGCGACTTCACGCTC
1 GGCGACTTCACGCTC
13337 G
1 G
13338 CGTTCCTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.39, G:0.32, T:0.19
Consensus pattern (15 bp):
GGCGACTTCACGCTC
Found at i:17253 original size:28 final size:30
Alignment explanation
Indices: 17221--17283 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
17211 TAAAAAATAG
*
17221 TGATACGAC-AT-TAACGTGTTGAAAGAGA
1 TGATACGACAATATAACATGTTGAAAGAGA
*
17249 TGATATGACATATATAACATGTTGAAAGAGA
1 TGATACGACA-ATATAACATGTTGAAAGAGA
17280 TGAT
1 TGAT
17284 GGGTCAGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 8 0.27
30 2 0.07
31 20 0.67
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (30 bp):
TGATACGACAATATAACATGTTGAAAGAGA
Found at i:29356 original size:6 final size:7
Alignment explanation
Indices: 29325--29353 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
29315 CAACGACCAT
29325 GGAAAGG
1 GGAAAGG
29332 GGAAAGG
1 GGAAAGG
29339 GGAAAGG
1 GGAAAGG
29346 GGAAAGG
1 GGAAAGG
29353 G
1 G
29354 AAAAAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (7 bp):
GGAAAGG
Found at i:32319 original size:21 final size:21
Alignment explanation
Indices: 32293--32345 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
32283 GTTTCCAGAT
32293 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
32314 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
*
32335 TCGCAATGCGA
1 TCGCAACGCGA
32346 TTTACATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTGGACTA
Found at i:32379 original size:21 final size:21
Alignment explanation
Indices: 32353--32647 Score: 148
Period size: 21 Copynumber: 14.3 Consensus size: 21
32343 CGATTTACAT
*
32353 ATTCGCATTGCGATAGTTCAA
1 ATTCGCGTTGCGATAGTTCAA
32374 ATTCGCGTTGCGATAG-TCGAA
1 ATTCGCGTTGCGATAGTTC-AA
* *
32395 GTTCGCGTTGCGAT-TTTCCAA
1 ATTCGCGTTGCGATAGTT-CAA
32416 ATT--CGTTGCGATAG-TCGAA
1 ATTCGCGTTGCGATAGTTC-AA
*
32435 GTTCGCGTTGCGATTTA-TTCCAA
1 ATTCGCGTTGCGA--TAGTT-CAA
32458 ATT--CGTTGCGATAG-TCGAA
1 ATTCGCGTTGCGATAGTTC-AA
* * **
32477 GTTTGCGTTGCGATTTTTCAA
1 ATTCGCGTTGCGATAGTTCAA
32498 ATT--CGTTGCGATAG-TCGAA
1 ATTCGCGTTGCGATAGTTC-AA
*
32517 GTTCGCGTTGCGATTTA-TTCCAA
1 ATTCGCGTTGCGA--TAGTT-CAA
32540 ATT--CGTTGCGATAG-TCGAA
1 ATTCGCGTTGCGATAGTTC-AA
* *
32559 GTTCGCGTTGCGTTTA-TTCCAA
1 ATTCGCGTTGCG-ATAGTT-CAA
*
32581 ATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTTCAA
*
32600 GTTCGCGTTGCGATTTA-TTCCAA
1 ATTCGCGTTGCGA--TAGTT-CAA
*
32623 ATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTTCAA
*
32642 AATCGC
1 ATTCGC
32648 AACGACTGGT
Statistics
Matches: 210, Mismatches: 25, Indels: 78
0.67 0.08 0.25
Matches are distributed among these distances:
18 5 0.02
19 55 0.26
20 11 0.05
21 104 0.50
22 11 0.05
23 22 0.10
24 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
ATTCGCGTTGCGATAGTTCAA
Found at i:32491 original size:82 final size:82
Alignment explanation
Indices: 32379--32638 Score: 475
Period size: 82 Copynumber: 3.2 Consensus size: 82
32369 TTCAAATTCG
32379 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
32444 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
* *
32461 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTTTCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
32526 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
* *
32543 CGTTGCGATAGTCGAAGTTCGCGTTGCGTTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
32608 TGCGATTTATTCCAAATT
65 TGCGATTTATTCCAAATT
32626 CGTTGCGATAGTC
1 CGTTGCGATAGTC
32639 CAAAATCGCA
Statistics
Matches: 171, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
82 109 0.64
83 62 0.36
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (82 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATT
Found at i:32641 original size:42 final size:42
Alignment explanation
Indices: 32379--32638 Score: 467
Period size: 42 Copynumber: 6.3 Consensus size: 42
32369 TTCAAATTCG
32379 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
32419 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
32461 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTT-TT-CAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
32501 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
32543 CGTTGCGATAGTCGAAGTTCGCGTTGCG-TTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
32584 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
32626 CGTTGCGATAGTC
1 CGTTGCGATAGTC
32639 CAAAATCGCA
Statistics
Matches: 212, Mismatches: 3, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
40 66 0.31
41 46 0.22
42 100 0.47
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:32745 original size:21 final size:21
Alignment explanation
Indices: 32719--32761 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
32709 GGACGTGTCG
*
32719 AAGACACGTATTACCACGACC
1 AAGACACATATTACCACGACC
32740 AAGACACATATTACCACGACC
1 AAGACACATATTACCACGACC
32761 A
1 A
32762 CGACCCGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.33, G:0.12, T:0.14
Consensus pattern (21 bp):
AAGACACATATTACCACGACC
Found at i:33428 original size:21 final size:20
Alignment explanation
Indices: 33382--33437 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
33372 GATTTTAGAC
*
33382 TATCGCAA-CGAATTTGGAA
1 TATCGCAAGCGAACTTGGAA
33401 TAAATCGCAACGCGAACTTGGAA
1 T--ATCGCAA-GCGAACTTGGAA
33424 TATCGCAATGCGAA
1 TATCGCAA-GCGAA
33438 TATGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 1 0.03
21 19 0.61
23 11 0.35
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
TATCGCAAGCGAACTTGGAA
Found at i:33450 original size:20 final size:20
Alignment explanation
Indices: 33401--33456 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
33391 GAATTTGGAA
*
33401 TAAATCGCAACGCGAACTTG
1 TAAATCGCAATGCGAACTTG
*
33421 GAATATCGCAATGCGAA-TATG
1 TAA-ATCGCAATGCGAACT-TG
33442 TAAATCGCAATGCGA
1 TAAATCGCAATGCGA
33457 TAGTCGAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
TAAATCGCAATGCGAACTTG
Found at i:36901 original size:37 final size:36
Alignment explanation
Indices: 36826--36901 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
36816 TTTTTATATT
*
36826 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
36862 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
36899 TTT
1 TTT
36902 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:37083 original size:20 final size:20
Alignment explanation
Indices: 37047--37084 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37037 ATCCTATTCC
**
37047 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
37067 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
37085 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:42890 original size:18 final size:17
Alignment explanation
Indices: 42864--42905 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
42854 TAATATAATA
*
42864 TATAAAAAATATCTAAAT
1 TATATAAAA-ATCTAAAT
*
42882 TATATAAAAATTTAAAT
1 TATATAAAAATCTAAAT
42899 T-TATAAA
1 TATATAAA
42906 GATACGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 6 0.27
17 8 0.36
18 8 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TATATAAAAATCTAAAT
Found at i:52922 original size:51 final size:51
Alignment explanation
Indices: 52840--52997 Score: 208
Period size: 51 Copynumber: 3.1 Consensus size: 51
52830 GCCTGGCTTG
* * * * * *
52840 GCTCCAAGCTTCTCCCGGCTATTCCAGCTTCTTTACTTGACTCAGCAACCT
1 GCTCCAAACTTCTCCCAGATATTCCAACTTCTTTACTTGATTCAGCAGCCT
* * *
52891 GTTCCAAACTTCTCCCAGATATTCCAACTTCTTTTCTTGATTCAGCGGCCT
1 GCTCCAAACTTCTCCCAGATATTCCAACTTCTTTACTTGATTCAGCAGCCT
* * *
52942 GCTCCAAACTTCTCCCAGATGTTCCAACTTCCTTCCTTGATTCAGCAGCCT
1 GCTCCAAACTTCTCCCAGATATTCCAACTTCTTTACTTGATTCAGCAGCCT
52993 GCTCC
1 GCTCC
52998 GACCTCGGAT
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 93 1.00
ACGTcount: A:0.18, C:0.36, G:0.13, T:0.33
Consensus pattern (51 bp):
GCTCCAAACTTCTCCCAGATATTCCAACTTCTTTACTTGATTCAGCAGCCT
Done.