Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000745.1 Hibiscus syriacus cultivar Beakdansim tig00001436_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: 71463
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:1163 original size:18 final size:18
Alignment explanation
Indices: 1135--1177 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1125 TCTTCTTATT
*
1135 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
*
1154 TTTATTTAATCGCTTTTA
1 TTTATTTAATCACTTTTA
1172 -TTATTT
1 TTTATTT
1178 TAATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:13921 original size:122 final size:122
Alignment explanation
Indices: 13668--13921 Score: 465
Period size: 122 Copynumber: 2.1 Consensus size: 122
13658 AAATCAAGAT
*
13668 TAAAAATAACAGAATATACAACTTTTAATAATTAAATTATTACTATACTAATTATATATTATTCA
1 TAAAAATAATAGAATATACAACTTTTAATAATTAAATTATTACTATACTAATTATATATTATTCA
13733 TGTGATTCAATTTTAACGATAAAGTATGATGTTTGCAATATATTTAAACTGAACGAC
66 TGTGATTCAATTTTAACGATAAAGTATGATGTTTGCAATATATTTAAACTGAACGAC
*
13790 CAAAAATAATAGAATATACAACTTTTAATAATTAAATTATTACTATACTAATTATATATTATTCA
1 TAAAAATAATAGAATATACAACTTTTAATAATTAAATTATTACTATACTAATTATATATTATTCA
*
13855 TGTGATTCAATTTTAACGATAAAGTATGATGTTTGCAATATA-TTAAACTGAACGGC
66 TGTGATTCAATTTTAACGATAAAGTATGATGTTTGCAATATATTTAAACTGAACGAC
13911 TAAAATATAAT
1 TAAAA-ATAAT
13922 TTCTCAAACT
Statistics
Matches: 127, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
121 17 0.13
122 110 0.87
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.38
Consensus pattern (122 bp):
TAAAAATAATAGAATATACAACTTTTAATAATTAAATTATTACTATACTAATTATATATTATTCA
TGTGATTCAATTTTAACGATAAAGTATGATGTTTGCAATATATTTAAACTGAACGAC
Found at i:16230 original size:2 final size:2
Alignment explanation
Indices: 16213--16248 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
16203 TAGACAAAAT
* *
16213 TA TA AA TA TT 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
16249 GTTTCAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31572 original size:17 final size:18
Alignment explanation
Indices: 31538--31572 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
31528 AACTTGAATC
31538 TCTTCGTTGTCACCGTCG
1 TCTTCGTTGTCACCGTCG
*
31556 TCTTCGTT-TCTCCGTCG
1 TCTTCGTTGTCACCGTCG
31573 AAGTGAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.03, C:0.34, G:0.20, T:0.43
Consensus pattern (18 bp):
TCTTCGTTGTCACCGTCG
Found at i:33303 original size:29 final size:29
Alignment explanation
Indices: 33260--33342 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
33250 CTCACCTAAC
33260 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
33290 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
33319 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
33343 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:36730 original size:15 final size:15
Alignment explanation
Indices: 36710--36739 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36700 CTTTCTCATA
36710 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
36725 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
36740 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:38072 original size:29 final size:29
Alignment explanation
Indices: 38029--38111 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
38019 CTCACCTAAC
38029 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
38059 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
38088 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
38112 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:44016 original size:23 final size:23
Alignment explanation
Indices: 43975--44018 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
43965 CCTGAACTAT
*
43975 TATTATTATTACTACTATTTTAG
1 TATTATTAATACTACTATTTTAG
* *
43998 TATTATTAATATTATTATTTT
1 TATTATTAATACTACTATTTT
44019 TTAATATAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTATTAATACTACTATTTTAG
Found at i:49422 original size:18 final size:18
Alignment explanation
Indices: 49396--49468 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
49386 ACTAAATATT
49396 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * **
49414 TGTCTCGAAAGACCGTTGA
1 TGTCCCGAAGGACCACT-A
* *
49433 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
49452 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
49469 GTTTATCCCT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
18 28 0.68
19 2 0.05
20 11 0.27
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:51378 original size:17 final size:18
Alignment explanation
Indices: 51339--51379 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
51329 TTACTTAACC
* *
51339 CTTTAATTTCCTTTTTCA
1 CTTTACTTTCCTTTATCA
51357 C-TTACTTT-CTTTATCA
1 CTTTACTTTCCTTTATCA
51373 CTTTACT
1 CTTTACT
51380 CCTCCATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 11 0.55
18 1 0.05
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (18 bp):
CTTTACTTTCCTTTATCA
Found at i:53389 original size:4 final size:4
Alignment explanation
Indices: 53374--53592 Score: 429
Period size: 4 Copynumber: 54.5 Consensus size: 4
53364 CATGTAACAA
53374 ATAC ACTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC A-TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53423 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53471 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53519 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53567 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
53593 GTCATTATCA
Statistics
Matches: 214, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
4 210 0.98
5 4 0.02
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:53988 original size:18 final size:18
Alignment explanation
Indices: 53967--54028 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
53957 GTCCCGAAGG
53967 ACCACTATGTCTCAAAGA
1 ACCACTATGTCTCAAAGA
*
53985 ACCACTGATTGT-TCCGAAGA
1 ACCACT-A-TGTCT-CAAAGA
* * *
54005 ACCACTATTTCCCAAAGG
1 ACCACTATGTCTCAAAGA
54023 ACCACT
1 ACCACT
54029 GTTTATCCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 18 0.51
19 3 0.09
20 14 0.40
ACGTcount: A:0.34, C:0.31, G:0.13, T:0.23
Consensus pattern (18 bp):
ACCACTATGTCTCAAAGA
Found at i:54003 original size:38 final size:38
Alignment explanation
Indices: 53955--54029 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
53945 CACTGAATAT
* *
53955 TTGTCCCGAAGGACCACTATGTCTCAAAGAACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCAAAGAACCACTGA
* * *
53993 TTGTTCCGAAGAACCACTATTTCCCAAAGGACCACTG
1 TTGTCCCGAAGAACCACTATGTCCCAAAGAACCACTG
54030 TTTATCCCTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCAAAGAACCACTGA
Found at i:55000 original size:2 final size:2
Alignment explanation
Indices: 54993--55030 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
54983 CATGAATTAG
54993 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
55031 TCATATGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65458 original size:233 final size:230
Alignment explanation
Indices: 65050--65715 Score: 751
Period size: 233 Copynumber: 2.9 Consensus size: 230
65040 TTTATAAGTG
* * * * * *
65050 AAAAAATGATAAAAGTTTCGCATTTAAATCTAAAAATGGAAATTGTTGGAAAGCAAGAAAAGTTT
1 AAAAAATGAAAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
* * * * *
65115 CTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCAGCCAATCAATAAGTTTTTCGAGCAT
66 CTTACCTAGTAAACTATTTTCAAAGTTGGTAAGTCATTCGGCC-ATCAGTAAGTCTTTCGAGCAT
* * * *
65180 GATGCTTAAATCATTTGGGTCATATGTAAGTCTTTCAAGCAAGATGATAAGCCCTTCAAGCCATC
130 GATGCTTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAAGCCATC
* * **
65245 CATAATACCTTTTGGC-ATGATGTTTTCACATGTCTCCT-
195 CATAAGACATTCGGGCGA-GAT-TTTT-ACATGT-TCCTC
* * * *
65283 GAAAAATGAGAAATGTTTCTCATTTAAATCTAAAAATTAAAATTTTTGAAAAGTAAGAAAAGTTT
1 AAAAAATGAAAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
* **
65348 CTTACCTAATAAACTATTTTCAAAGTCAGTAAGTCATTCGGTCCATCAGTAAGTCTTTCGAGCAT
66 CTTACCTAGTAAACTATTTTCAAAGTTGGTAAGTCATTCGG-CCATCAGTAAGTCTTTCGAGCAT
* * * * * * **
65413 AATGCTTAAACCCTTCGGGTCATCTGTAAGTTTTTCGAGCAAGATGATAAATTCTTCTGGCCATC
130 GATGCTTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAAGCCATC
**
65478 CATAAGACATTCGGGCGAGATTTTTACATGTTTTTC
195 CATAAGACATTCGGGCGAGATTTTTACATGTTCCTC
** * * ** *
65514 AAAAACAAAAAAAAAGTTTCTCAGTTAAATCTGAAAATTGATTTTTTTAAAAAGTAAGAAAAGTT
1 AAAAA-ATGAAAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTT
* * * *
65579 TCTTACCTAGTAAACTATTCTCAAATTTGGTAAGTCTTTCGACCCATCAGTAAGTCTTTCGAGCA
65 TCTTACCTAGTAAACTATTTTCAAAGTTGGTAAGTCATTCG-GCCATCAGTAAGTCTTTCGAGCA
* * * * * ** *
65644 TGATGTTTAAATCATTCGGATCATCTATAAGACTCTCGAGCAAGATGATAAGTCCTTCGGGTCAT
129 TGATGCTTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAAGCCAT
65709 CCATAAG
194 CCATAAG
65716 TTCTTCGGGC
Statistics
Matches: 362, Mismatches: 66, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
230 2 0.01
231 10 0.03
232 169 0.47
233 178 0.49
234 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (230 bp):
AAAAAATGAAAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTT
CTTACCTAGTAAACTATTTTCAAAGTTGGTAAGTCATTCGGCCATCAGTAAGTCTTTCGAGCATG
ATGCTTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAAGCCATCC
ATAAGACATTCGGGCGAGATTTTTACATGTTCCTC
Found at i:65628 original size:232 final size:232
Alignment explanation
Indices: 65060--65741 Score: 728
Period size: 232 Copynumber: 2.9 Consensus size: 232
65050 AAAAAATGAT
* * ** * ** *
65060 AAAAGTTTCGCATTTAAATCTAAAAATGGAAATTGTTGGAAAGCAAGAAAAGTTTCTTACCTAGT
1 AAAAGTTTCTCAGTTAAATCTAAAAATTAAAATTTTTAAAAAGTAAGAAAAGTTTCTTACCTAGT
* * * *
65125 AAACTATTTCCAAAGTTGGTAAGTCCTTC-AGCCAATCAATAAGTTTTTCGAGCATGATGCTTAA
66 AAACTATTT-CAAAGTTGGTAAGTCATTCGA-CCCATCAGTAAGTCTTTCGAGCATGATGCTTAA
* * * * * * *
65189 ATCATTTGGGTCATATGTAAGTCTTTCAAGCAAGATGATAAGCCCTTCAAGCCATCCATAATACC
129 ATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACA
** * ** *
65254 TTTTGGCATGATGTTTTCACATGTCTCCTGAAAAATGAG
194 TTCGGGCATGATGTTTTCACATGTCTCCTAAAAAAAAAA
* * * *
65293 AAATGTTTCTCATTTAAATCTAAAAATTAAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAAT
1 AAAAGTTTCTCAGTTAAATCTAAAAATTAAAATTTTTAAAAAGTAAGAAAAGTTTCTTACCTAGT
** ** *
65358 AAACTATTTTCAAAGTCAGTAAGTCATTCGGTCCATCAGTAAGTCTTTCGAGCATAATGCTTAAA
66 AAACTA-TTTCAAAGTTGGTAAGTCATTCGACCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
* * * * * *
65423 CCCTTCGGGTCATCTGTAAGTTTTTCGAGCAAGATGATAAATTCTTCTGGCCATCCATAAGACAT
130 TCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACAT
**
65488 TCGGGCGA-GAT-TTTT-ACATGT-TTTTCAAAAACAAAAA
195 TCGGGC-ATGATGTTTTCACATGTCTCCT-AAAAA-AAAAA
* * **
65525 AAAAGTTTCTCAGTTAAATCTGAAAATTGATTTTTTTAAAAAGTAAGAAAAGTTTCTTACCTAGT
1 AAAAGTTTCTCAGTTAAATCTAAAAATTAAAATTTTTAAAAAGTAAGAAAAGTTTCTTACCTAGT
* * *
65590 AAACTATTCTCAAATTTGGTAAGTCTTTCGACCCATCAGTAAGTCTTTCGAGCATGATGTTTAAA
66 AAACTATT-TCAAAGTTGGTAAGTCATTCGACCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
* * * * * * *
65655 TCATTCGGATCATCTATAAGACTCTCGAGCAAGATGATAAGTCCTTCGGGTCATCCATAAGTTC-
130 TCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAG-ACA
* *
65719 TTCGGGCATGATGCTTTCGCATG
194 TTCGGGCATGATGTTTTCACATG
65742 ATTTTCCGAA
Statistics
Matches: 371, Mismatches: 68, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
230 2 0.01
231 13 0.04
232 177 0.48
233 171 0.46
234 8 0.02
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (232 bp):
AAAAGTTTCTCAGTTAAATCTAAAAATTAAAATTTTTAAAAAGTAAGAAAAGTTTCTTACCTAGT
AAACTATTTCAAAGTTGGTAAGTCATTCGACCCATCAGTAAGTCTTTCGAGCATGATGCTTAAAT
CATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACATT
CGGGCATGATGTTTTCACATGTCTCCTAAAAAAAAAA
Done.