Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001549.1 Hibiscus syriacus cultivar Beakdansim tig00003045_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: 60982
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3766 original size:259 final size:259
Alignment explanation
Indices: 3276--4285 Score: 1276
Period size: 259 Copynumber: 3.9 Consensus size: 259
3266 AAGAGTAATT
* * * * * * *
3276 CCCAATGGTCTTACGGATAGCCCAAAGGACTTAACATCTTGCTTGATAGACTGACATATGACCAT
1 CCCAAAGGTCTTATGGATGGCCCAAAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCT
* * * *
3341 AAGGATCTAAGCATCATGCTCAAAAGGCTGACAGATGACCCAAAGGTTTTACAAATTTGGGAAAT
66 AAGGATTTAAACATCATGCTCAAAAGACTGACAGATGACCCAAAGGATTTACAAATTTGGGAAAT
** * *
3406 AATTTA-CTAGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAATTTCATTTTCTGAACA
131 AATTTACCGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTGAACA
3470 TTAAATGAGAAACA-TTGAAAATTGCTTCCTCATTTTCATGAGAAAATCATGTGTAAACATCCTA
196 TTAAATGAGAAA-ATTTGAAAATTGCTTCCTCATTTTCATGAGAAAATCATGTGTAAACATCCTA
* * * *
3534 CCCAAAGGTCTCATAGATGGCCCTAAGGACTTAACATCTTGCTCGAAAGACTGACATATGACCCT
1 CCCAAAGGTCTTATGGATGGCCCAAAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCT
* * * * *
3599 AAGGATTTAAACATCATGCTCAAAAGACTGACAAATTACCAAAAGGTTTTACAAATTTAGGAAAT
66 AAGGATTTAAACATCATGCTCAAAAGACTGACAGATGACCCAAAGGATTTACAAATTTGGGAAAT
* *
3664 AGTTTACCGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCGTTTTCTGAACA
131 AATTTACCGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTGAACA
*
3729 TTAAATGAGAAAATTTAAAAATTGCTTCCTCATTTTCAT-ATGAAAATCATGTGTAAACATCCTA
196 TTAAATGAGAAAATTTGAAAATTGCTTCCTCATTTTCATGA-GAAAATCATGTGTAAACATCCTA
* * * * * * *
3793 CCCAAAGGTCTTACGGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTAACAGATGGCCCA
1 CCCAAAGGTCTTATGGATGGCCCAAAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCT
* * *
3858 AAGGATTTAAACATCATGCTCGAATGACTGACAGATGACCCAAATGATTTACAAATTTGGGAAAT
66 AAGGATTTAAACATCATGCTCAAAAGACTGACAGATGACCCAAAGGATTTACAAATTTGGGAAAT
* * * *
3923 AATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAATTTTATTTTCTGGACA
131 AATTTACCGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTGAACA
* * * ** * * * *
3988 TTAAATGAGAAACTTCGATAATCACTTTCTCATTTGCATGTGAAAATCATGTGTAAACATCCTG
196 TTAAATGAGAAAATTTGAAAATTGCTTCCTCATTTTCATGAGAAAATCATGTGTAAACATCCTA
** * * * * *
4052 CCTGAAGGTATTATGGATGGCCCAAAGAACTCAACAT-TCAGCTCGAAAGACTGACAGATGGCCC
1 CCCAAAGGTCTTATGGATGGCCCAAAGGACTTAACATCT-TGCTCGAAAGACTGACAGATGACCC
* * *
4116 TAAGGATTTAAGCATCATTG-TCGAAAGACTGACAGATGACCCGAAGGATTTACAAATTTGGGAA
65 TAAGGATTTAAACATCA-TGCTCAAAAGACTGACAGATGACCCAAAGGATTTACAAATTTGGGAA
* * ** * *
4180 ATAGTTTACTGGGTAAGAAACTTTTAAAAT-ATCTTTCTTACTTTTCAACAATTTCATTTTCAGA
129 ATAATTTACCGGGTAAGAAACTTTGGAAATCA-CTTTCTTACTTTTCAAGAATTTCATTTTCTG-
* * * * * *
4244 AAAATTAAATAAGAAACTTTGGAAATTGTTTTCTCATTTTCA
192 AACATTAAATGAGAAAATTTGAAAATTGCTTCCTCATTTTCA
4286 ACTTAGTGGT
Statistics
Matches: 655, Mismatches: 89, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
258 122 0.19
259 499 0.76
260 34 0.05
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (259 bp):
CCCAAAGGTCTTATGGATGGCCCAAAGGACTTAACATCTTGCTCGAAAGACTGACAGATGACCCT
AAGGATTTAAACATCATGCTCAAAAGACTGACAGATGACCCAAAGGATTTACAAATTTGGGAAAT
AATTTACCGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAGAATTTCATTTTCTGAACA
TTAAATGAGAAAATTTGAAAATTGCTTCCTCATTTTCATGAGAAAATCATGTGTAAACATCCTA
Found at i:3893 original size:42 final size:42
Alignment explanation
Indices: 3808--3908 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
3798 AGGTCTTACG
* * * *
3808 GATGGCCCTAAGGACTT-ATCATCTTGCTCAAAAGACTAACA
1 GATGGCCCAAAGGATTTAAACATCATGCTCAAAAGACTAACA
* * *
3849 GATGGCCCAAAGGATTTAAACATCATGCTCGAATGACTGACA
1 GATGGCCCAAAGGATTTAAACATCATGCTCAAAAGACTAACA
* *
3891 GATGACCCAAATGATTTA
1 GATGGCCCAAAGGATTTA
3909 CAAATTTGGG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 15 0.30
42 35 0.70
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (42 bp):
GATGGCCCAAAGGATTTAAACATCATGCTCAAAAGACTAACA
Found at i:27006 original size:15 final size:15
Alignment explanation
Indices: 26986--27017 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
26976 TATATATAGT
26986 TTATAGTTTATAAAC
1 TTATAGTTTATAAAC
*
27001 TTATAGTTTATATAC
1 TTATAGTTTATAAAC
27016 TT
1 TT
27018 TTTTTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (15 bp):
TTATAGTTTATAAAC
Found at i:27663 original size:8 final size:8
Alignment explanation
Indices: 27629--27653 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
27619 TCAGTCTAAT
27629 TTAATATA
1 TTAATATA
27637 TTAATATA
1 TTAATATA
27645 TTAATATA
1 TTAATATA
27653 T
1 T
27654 ATATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTAATATA
Found at i:28805 original size:4 final size:4
Alignment explanation
Indices: 28796--28833 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
28786 AATACTATAC
*
28796 TTTA TTTA TTTA TTTA TTTA TGTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
28834 TCATTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:28891 original size:15 final size:16
Alignment explanation
Indices: 28873--28913 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
28863 GTCTCTATTT
28873 TTTTATTATTATAT-A
1 TTTTATTATTATATCA
*
28888 TTTTATT-TTATTTCA
1 TTTTATTATTATATCA
28903 TTTT-TTATTAT
1 TTTTATTATTAT
28914 TTTCCCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATTATTATATCA
Found at i:29179 original size:2 final size:2
Alignment explanation
Indices: 29172--29214 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
29162 AACACTACAT
29172 TA TA TA TA TA TA TA TA TA TA 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
29214 T
1 T
29215 TCTTTTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29353 original size:27 final size:27
Alignment explanation
Indices: 29318--29370 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
29308 GTTGTTTTGT
29318 TTTATTTTTATTTAGTTTACCATTTTA
1 TTTATTTTTATTTAGTTTACCATTTTA
* *
29345 TTTATTTTTATTTATTTTATCATTTT
1 TTTATTTTTATTTAGTTTACCATTTT
29371 TCCTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTATTTTTATTTAGTTTACCATTTTA
Found at i:37878 original size:21 final size:21
Alignment explanation
Indices: 37854--37899 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
37844 AGAATCTAAC
*
37854 AAAGCTCTTCCAGAGATTAAG
1 AAAGCTCTTCCAGAAATTAAG
37875 AAAGCTCTTCCAGAAATTAAG
1 AAAGCTCTTCCAGAAATTAAG
37896 AAAG
1 AAAG
37900 TTCCAGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAGCTCTTCCAGAAATTAAG
Found at i:37905 original size:18 final size:19
Alignment explanation
Indices: 37860--37905 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
37850 TAACAAAGCT
*
37860 CTTCCAGAGATTAAGAAAG
1 CTTCCAGAAATTAAGAAAG
37879 CTCTTCCAGAAATTAAGAAAG
1 --CTTCCAGAAATTAAGAAAG
37900 -TTCCAG
1 CTTCCAG
37906 TTGAGGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
21 18 0.75
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (19 bp):
CTTCCAGAAATTAAGAAAG
Found at i:40535 original size:11 final size:10
Alignment explanation
Indices: 40518--40548 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
40508 GCCCTAAATT
40518 GAAAAAAAAA
1 GAAAAAAAAA
40528 GAAAAAAAAA
1 GAAAAAAAAA
40538 GAAAAAAAAA
1 GAAAAAAAAA
40548 G
1 G
40549 GTGAGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:43264 original size:57 final size:56
Alignment explanation
Indices: 43202--43326 Score: 155
Period size: 57 Copynumber: 2.2 Consensus size: 56
43192 TCTTTAATAC
*
43202 TATATTTTATTTATGTATGTATTTATTTATTATT-TTGATTATATATATATATATATA
1 TATATTTTATTTATGTATCTATTT-TTTATTATTATT-ATTATATATATATATATATA
* * * *
43259 TATATTTTCTTTTTTGTCTCTGTTTTTTATTATTATTATTATATATATATATATATA
1 TATATTTT-ATTTATGTATCTATTTTTTATTATTATTATTATATATATATATATATA
43316 T-TATTATTATT
1 TATATT-TTATT
43327 ATTATTACTA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
56 6 0.10
57 40 0.68
58 13 0.22
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (56 bp):
TATATTTTATTTATGTATCTATTTTTTATTATTATTATTATATATATATATATATA
Found at i:43293 original size:3 final size:3
Alignment explanation
Indices: 43285--43341 Score: 69
Period size: 3 Copynumber: 17.7 Consensus size: 3
43275 TCTCTGTTTT
43285 TTA TTA TTA TTA TTA TATA TATA TATA TATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA
*
43334 CTA TTA TT
1 TTA TTA TT
43342 GTTTTTTCTC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 36 0.71
4 15 0.29
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:43375 original size:14 final size:14
Alignment explanation
Indices: 43340--43377 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
43330 ATTACTATTA
43340 TTGTTTT-TTCTCAT
1 TTGTTTTATT-TCAT
43354 TT-TTTTATTTCAT
1 TTGTTTTATTTCAT
43367 TTGTTTTATTT
1 TTGTTTTATTT
43378 AGTTCTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (14 bp):
TTGTTTTATTTCAT
Found at i:43400 original size:20 final size:18
Alignment explanation
Indices: 43353--43413 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
43343 TTTTTTCTCA
* *
43353 TTTT-TTTATTTCATTTG
1 TTTTATTTAGTTCTTTTG
43370 TTTTATTTAGTTCTTTTG
1 TTTTATTTAGTTCTTTTG
43388 TTTTAGCTTTAGTT-TTTAT-
1 TTTTA--TTTAGTTCTTT-TG
43407 TTTTATT
1 TTTTATT
43414 ATCATTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 6 0.16
18 16 0.42
19 8 0.21
20 8 0.21
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (18 bp):
TTTTATTTAGTTCTTTTG
Found at i:43746 original size:17 final size:17
Alignment explanation
Indices: 43721--43758 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
43711 TTTGTTTTAT
*
43721 TTTTGTTTATTTTACCA
1 TTTTATTTATTTTACCA
*
43738 TTTTATTTATTTTATCA
1 TTTTATTTATTTTACCA
43755 TTTT
1 TTTT
43759 TCCTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTATTTATTTTACCA
Found at i:44459 original size:22 final size:22
Alignment explanation
Indices: 44415--44459 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
44405 AACTAAAATT
* *
44415 AATTTGACCTAAACTCGAACTG
1 AATTTGACCCAAACCCGAACTG
* *
44437 AATTTGACCCAGACCCGACCTG
1 AATTTGACCCAAACCCGAACTG
44459 A
1 A
44460 TACGAGTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (22 bp):
AATTTGACCCAAACCCGAACTG
Found at i:58446 original size:21 final size:19
Alignment explanation
Indices: 58413--58453 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
58403 TGCATCAAGG
58413 TCTTTGTTGAAGCCATGAAA
1 TCTTTGTTGAAGCCAT-AAA
*
58433 TCTTTTTTCGAAGCCATAAA
1 TCTTTGTT-GAAGCCATAAA
58453 T
1 T
58454 TCCTGCAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (19 bp):
TCTTTGTTGAAGCCATAAA
Done.