Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005987.1 Hibiscus syriacus cultivar Beakdansim tig00014077_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: 74046
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4431 original size:18 final size:18
Alignment explanation
Indices: 4404--4443 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4394 CTCTCTTTCC
* *
4404 TGTTCATGTTTATGTTCG
1 TGTTCATGTTCATGATCG
*
4422 TGTTCGTGTTCATGATCG
1 TGTTCATGTTCATGATCG
4440 TGTT
1 TGTT
4444 TGTAACTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.12, G:0.25, T:0.53
Consensus pattern (18 bp):
TGTTCATGTTCATGATCG
Found at i:15314 original size:2 final size:2
Alignment explanation
Indices: 15307--15352 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
15297 AAAAAGAATG
* *
15307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15349 AT AT
1 AT AT
15353 CTAATTGTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16505 original size:4 final size:4
Alignment explanation
Indices: 16498--16523 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
16488 TAAAAAAAAA
16498 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
16524 GACAGTTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:20633 original size:60 final size:60
Alignment explanation
Indices: 20517--20665 Score: 185
Period size: 60 Copynumber: 2.5 Consensus size: 60
20507 GACTAGTATA
* * * *
20517 TATTTATAGTTTGGGATGAAATTGGAATGTTCAAAATGTTTGGGGACCAATTTAGAATGC
1 TATTCATAGTTTGGGATGAAATTGAAATGTTCAAAATGATTGAGGACCAATTTAGAATGC
*
20577 -ACTTCATAGTTTGGGGATGAAATTGAAATGTTCAAAA-GATTGAGGACTAATTTAGAATGC
1 TA-TTCATAGTTT-GGGATGAAATTGAAATGTTCAAAATGATTGAGGACCAATTTAGAATGC
* * *
20637 TATTTATAATTTAGGGATGAAATTAAAAT
1 TATTCATAGTTT-GGGATGAAATTGAAAT
20666 ATTTAAATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
59 1 0.01
60 52 0.68
61 24 0.31
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (60 bp):
TATTCATAGTTTGGGATGAAATTGAAATGTTCAAAATGATTGAGGACCAATTTAGAATGC
Found at i:20679 original size:29 final size:28
Alignment explanation
Indices: 20637--20694 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
20627 TTTAGAATGC
*
20637 TATTTATAATTTAGGGATGAAATTAAAA
1 TATTTAAAATTTAGGGATGAAATTAAAA
* *
20665 TATTTAAATATTTAGGGATTAATTTAAAA
1 TATTTAAA-ATTTAGGGATGAAATTAAAA
20694 T
1 T
20695 GAGGGGCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (28 bp):
TATTTAAAATTTAGGGATGAAATTAAAA
Found at i:26456 original size:12 final size:12
Alignment explanation
Indices: 26441--26467 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
26431 AATTTAAATT
26441 TATCTTATAATC
1 TATCTTATAATC
26453 TATCTTATAATC
1 TATCTTATAATC
26465 TAT
1 TAT
26468 ATTTCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (12 bp):
TATCTTATAATC
Found at i:32649 original size:23 final size:24
Alignment explanation
Indices: 32608--32654 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
32598 TTCAGGACTA
** *
32608 TTATTTTATATTTGTTTTTTATTT
1 TTATTTTATATTTACTTTTAATTT
32632 TTATTTT-TATTTACTTTTAATTT
1 TTATTTTATATTTACTTTTAATTT
32655 ATGTTATACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (24 bp):
TTATTTTATATTTACTTTTAATTT
Found at i:34569 original size:33 final size:34
Alignment explanation
Indices: 34504--34569 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
34494 ATATTCTTAA
* *
34504 ATTATTAAAAATAAAAATTTTAATATATATATAT
1 ATTATTAAAAATAAAAATTTTAATAAAAATATAT
34538 ATTATTAAAAAT-AAAATTTTCAA-AAAAATATA
1 ATTATTAAAAATAAAAATTTT-AATAAAAATATA
34570 AATGTGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (34 bp):
ATTATTAAAAATAAAAATTTTAATAAAAATATAT
Found at i:38889 original size:16 final size:17
Alignment explanation
Indices: 38868--38902 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
38858 AATAAAATTT
*
38868 TATCAAATT-TATTAAA
1 TATCAAATTAAATTAAA
38884 TATCAAATTAAATTAAA
1 TATCAAATTAAATTAAA
38901 TA
1 TA
38903 AAGATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
TATCAAATTAAATTAAA
Found at i:42050 original size:219 final size:219
Alignment explanation
Indices: 41632--42130 Score: 583
Period size: 219 Copynumber: 2.2 Consensus size: 219
41622 TGAACCGATC
* *
41632 CGAGGACAGTAAAGTATTTTTTTATATAAATTTATGGATAATTCTTATAATATCCTGTGTCTCTA
1 CGAGGACAGTAAAGTA--TTTTTATATAAA-TTATGGATAATTCTTATAATA-CCTATCTCTCTA
* * ** *
41697 TAGTATTTTTTTTAATTAGGTCCTTAATTTGTGCCGGATCCAATCAGGTTAGGTTTTTAGTCTAA
62 TAG---TTTTTTTAATTAGGTCCTTAATTTGTGCAGGATACAATCAGGTTAGGTTCATAGTCAAA
** * *
41762 AAAATCGAATTAGATTAAGTTCGGGTGGATGACATATATTTTTTAGGTCGGATTGGATTTCAGTG
124 AAAATCGAATTAGATTAAGTTCAAGTGGAGGACATATATTTTTCAGGTCGGATTGGATTTCAGTG
*
41827 GAGGGTG-AGAACCTCCGACCCAACCCAACT
189 GAGGGTGAAAAACCTCCGACCCAACCCAACT
**
41857 CGAGGGTAGTAAAGTATTTTTATATAAATTAATGGATAATTCTTATAATACCTCATCTCTCTATA
1 CGAGGACAGTAAAGTATTTTTATATAAATT-ATGGATAATTCTTATAATACCT-ATCTCTCTATA
* * * **
41922 G-TTTTTTAATTAGGTCTTTAATTTGTGTATGATATGATCAGGTT-GAGTTCATAGTCAAAAAAA
64 GTTTTTTTAATTAGGTCCTTAATTTGTGCAGGATACAATCAGGTTAG-GTTCATAGTCAAAAAAA
* * * * *
41985 TCGGATTAGATTAAGTTCAAGTGGAGGACATATATTTTTCGGGTTGGGTTGGGTTTC-GATGGAG
128 TCGAATTAGATTAAGTTCAAGTGGAGGACATATATTTTTCAGGTCGGATTGGATTTCAG-TGGAG
** *
42049 GGTGAAAAACCTTTGACCCAACCCGACT
192 GGTGAAAAACCTCCGACCCAACCCAACT
* *
42077 CGAGGACAGTAGAGTGATTTTTCATATAAACTTATAGATAATTCTTATAATACC
1 CGAGGACAGTAAAGT-ATTTTT-ATATAAA-TTATGGATAATTCTTATAATACC
42131 CCTCTCTGCC
Statistics
Matches: 235, Mismatches: 31, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
218 2 0.01
219 107 0.46
220 31 0.13
221 6 0.03
222 32 0.14
223 43 0.18
225 14 0.06
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (219 bp):
CGAGGACAGTAAAGTATTTTTATATAAATTATGGATAATTCTTATAATACCTATCTCTCTATAGT
TTTTTTAATTAGGTCCTTAATTTGTGCAGGATACAATCAGGTTAGGTTCATAGTCAAAAAAATCG
AATTAGATTAAGTTCAAGTGGAGGACATATATTTTTCAGGTCGGATTGGATTTCAGTGGAGGGTG
AAAAACCTCCGACCCAACCCAACT
Found at i:42184 original size:220 final size:217
Alignment explanation
Indices: 41632--42205 Score: 568
Period size: 219 Copynumber: 2.6 Consensus size: 217
41622 TGAACCGATC
* * ***
41632 CGAGGACAGTAAAGTATTTTTTTATATAAATTTATGGATAATTCTTATAATATCCTGTGTCTCTA
1 CGAGGACAGTAAAGTA--TTTTTATATAAATTAATAGATAATTCTTATAATA-CCTCACTCTCTA
* ** * * *
41697 TAGTATTTTTTTTAATTAGGTCCTTAATTTGTGCCGGATCCA-ATCAGGTT-AGGTTTTTAGTCT
63 CAG----GCTTTTAATTAGGTCCTTAATTTGTGTC-GAT-AAGATCAGGTTGA-GTTTATAGTCT
** * *
41760 AAAAAATCGAATTAGATTAAGTTCGGGTGGATGACATATATTTTTTAGGTCGGATTGGATTTCAG
121 AAAAAATCGAATTAGATTAAGTTCAAGTGGAGGACATATATTTTTCAGGTCGGATTGGATTTCAG
*
41825 TGGAGGGTGAGAACCTCCGACCCAACCCAACT
186 TGGAGGGTGAAAACCTCCGACCCAACCCAACT
** * *
41857 CGAGGGTAGTAAAGTATTTTTATATAAATTAATGGATAATTCTTATAATACCTCATCTCTCTATA
1 CGAGGACAGTAAAGTATTTTTATATAAATTAATAGATAATTCTTATAATACCTCA-CTCTCTACA
** * * * * *
41922 GTTTTTTAATTAGGTCTTTAATTTGTGTATGATATGATCAGGTTGAGTTCATAGTCAAAAAAATC
65 GGCTTTTAATTAGGTCCTTAATTTGTGT-CGATAAGATCAGGTTGAGTTTATAGTCTAAAAAATC
* * * * *
41987 GGATTAGATTAAGTTCAAGTGGAGGACATATATTTTTCGGGTTGGGTTGGGTTTC-GATGGAGGG
129 GAATTAGATTAAGTTCAAGTGGAGGACATATATTTTTCAGGTCGGATTGGATTTCAG-TGGAGGG
** *
42051 TGAAAAACCTTTGACCCAACCCGACT
193 TG-AAAACCTCCGACCCAACCCAACT
* *
42077 CGAGGACAGTAGAGTGATTTTTCATATAAACTT-ATAGATAATTCTTATAATACC-C-CTCTCTG
1 CGAGGACAGTAAAGT-ATTTTT-ATATAAA-TTAATAGATAATTCTTATAATACCTCACTCTCTA
* *
42139 CCGCGCTTTTAATTAGGTCCTTAATTTATGTCGAATAAGATCAGGTTG-GATTTATAGTCTAAAA
63 CAG-GCTTTTAATTAGGTCCTTAATTTGTGTCG-ATAAGATCAGGTTGAG-TTTATAGTCTAAAA
42203 AAT
125 AAT
42206 TAGGTTATAT
Statistics
Matches: 295, Mismatches: 42, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
218 1 0.00
219 116 0.39
220 83 0.28
221 7 0.02
222 30 0.10
223 44 0.15
225 14 0.05
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (217 bp):
CGAGGACAGTAAAGTATTTTTATATAAATTAATAGATAATTCTTATAATACCTCACTCTCTACAG
GCTTTTAATTAGGTCCTTAATTTGTGTCGATAAGATCAGGTTGAGTTTATAGTCTAAAAAATCGA
ATTAGATTAAGTTCAAGTGGAGGACATATATTTTTCAGGTCGGATTGGATTTCAGTGGAGGGTGA
AAACCTCCGACCCAACCCAACT
Found at i:49434 original size:25 final size:27
Alignment explanation
Indices: 49406--49457 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
49396 TTGCCCCGTC
*
49406 CCCGAACCC-AA-CCCAAAATATTATA
1 CCCGAACCCAAATCCAAAAATATTATA
49431 CCCGAACCCAAATCCAAAAATATTATA
1 CCCGAACCCAAATCCAAAAATATTATA
49458 TATATGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.38
26 2 0.08
27 13 0.54
ACGTcount: A:0.46, C:0.33, G:0.04, T:0.17
Consensus pattern (27 bp):
CCCGAACCCAAATCCAAAAATATTATA
Found at i:49487 original size:25 final size:25
Alignment explanation
Indices: 49459--49509 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
49449 AATATTATAT
49459 ATATGAT-TAATATAAAAAATATAAA
1 ATATGATAT-ATATAAAAAATATAAA
* **
49484 ATATTATATATATAATTAATATAAA
1 ATATGATATATATAAAAAATATAAA
49509 A
1 A
49510 AATATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
ATATGATATATATAAAAAATATAAA
Found at i:49490 original size:34 final size:34
Alignment explanation
Indices: 49447--49531 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
49437 CCCAAATCCA
*
49447 AAAATATTATATATATGATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
49481 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
49515 AAAATATTATATATATA
1 AAAATATTATATATATA
49532 TAATCGGGGC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:52191 original size:6 final size:6
Alignment explanation
Indices: 52181--52276 Score: 95
Period size: 6 Copynumber: 16.0 Consensus size: 6
52171 ATGTACAACG
* * *
52181 ACACAT GCACAT ACACAT ACACAT ACACAT ACACAT ATACAT ACACAA
1 ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT
* * * * * *
52229 ACACAT ACACACG A-ACAT ATATAT ACACAT ACAAAT ATACAT ATACAT
1 ACACAT ACACA-T ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT
52277 GTTTGTTAAC
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
5 1 0.01
6 72 0.97
7 1 0.01
ACGTcount: A:0.51, C:0.27, G:0.02, T:0.20
Consensus pattern (6 bp):
ACACAT
Found at i:53197 original size:19 final size:18
Alignment explanation
Indices: 53161--53217 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
53151 AGGTTTATTT
*
53161 TTTATAAAAATAATAATA
1 TTTATAAAAATAAAAATA
53179 TTTATAAAAATTAAAAATAAA
1 TTTATAAAAA-TAAAAAT--A
* *
53200 TTTTTAAAAATATAAATA
1 TTTATAAAAATAAAAATA
53218 CGACATACGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 6 0.18
21 10 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTATAAAAATAAAAATA
Found at i:53207 original size:21 final size:23
Alignment explanation
Indices: 53172--53215 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
53162 TTATAAAAAT
53172 AATAATATTTATAAAAAT-TAAA
1 AATAATATTTATAAAAATATAAA
*
53194 AATAA-ATTTTTAAAAATATAAA
1 AATAATATTTATAAAAATATAAA
53216 TACGACATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATAATATTTATAAAAATATAAA
Found at i:60912 original size:11 final size:11
Alignment explanation
Indices: 60896--60921 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
60886 ATTTTTATAG
60896 TTTATTTTAAT
1 TTTATTTTAAT
60907 TTTATTTTAAT
1 TTTATTTTAAT
60918 TTTA
1 TTTA
60922 AAAATTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATTTTAAT
Done.