Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004940.1 Hibiscus syriacus cultivar Beakdansim tig00011110_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: 30304
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:248 original size:12 final size:12
Alignment explanation
Indices: 226--258 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
216 TCTATTAAAT
226 TCATT-TAATTA
1 TCATTATAATTA
237 TCATTATAATTA
1 TCATTATAATTA
249 TCA-TATAATT
1 TCATTATAATT
259 GATTTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATTATAATTA
Found at i:9284 original size:22 final size:24
Alignment explanation
Indices: 9236--9286 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
9226 TGTTGTGTTT
*
9236 TTATATAAAATGATAGCATATTTA
1 TTATATAAAATGATAGCATATTAA
9260 TTATATAAAATGATAG-AT-TTAA
1 TTATATAAAATGATAGCATATTAA
9282 TTATA
1 TTATA
9287 AATGCAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 8 0.31
23 2 0.08
24 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (24 bp):
TTATATAAAATGATAGCATATTAA
Found at i:9546 original size:9 final size:9
Alignment explanation
Indices: 9532--9560 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
9522 AGAGGCAGAG
9532 GAGAAGGAA
1 GAGAAGGAA
9541 GAGAAGGAA
1 GAGAAGGAA
9550 GAGAAGGAA
1 GAGAAGGAA
9559 GA
1 GA
9561 AGAGAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (9 bp):
GAGAAGGAA
Found at i:15029 original size:200 final size:200
Alignment explanation
Indices: 14725--15744 Score: 1316
Period size: 200 Copynumber: 5.1 Consensus size: 200
14715 TAAACACAAA
** * * * *
14725 GTATCGATACTAATTGTCAAGTATGCTTTCCAAACTAGATCCACGCAGAAAGTATCGATAAACGT
1 GTATCGATACTTTTTGTCCAGTATGCTTTCCAAACTAGATGCACACAGAAAGTATCGATACACGT
*
14790 ATGAGAAGTATCGATTCTTAAAACTGT-GAAACTGATTAGTATAAAGTAATAGGTAAATTTACAA
66 ATGAGAAGTATCGATTCTTAAAACT-TCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAA
* ** * * *
14854 TGTAAGCGATAAAAATATATTGGTTTAATGATAAAATATGTAAACACAAAGTATCAATACTTTTC
130 TGTAAGCGGTAAAAATATACCGGTTTAATGACAAAATATGTAAACACAAAGTATCGATACTTTTT
*
14919 GTATTT
195 GTATAT
* **
14925 GTATCGTTACTAATTGTCCAGTATGCTTTCCAAACTAGATGCACACAGAAAGTATCGATACACGT
1 GTATCGATACTTTTTGTCCAGTATGCTTTCCAAACTAGATGCACACAGAAAGTATCGATACACGT
*
14990 ATGAGAAGTATCGATTCTTAAAACTTCTAAACCGATTAGTATAAAGTAATAGGTAAATTTACAAT
66 ATGAGAAGTATCGATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAAT
* * * * *
15055 GTTAGCGGTAACAATATACCGGTTTAATGACAAGATATGTAAACATAAAGTATTGATACTTTTTG
131 GTAAGCGGTAAAAATATACCGGTTTAATGACAAAATATGTAAACACAAAGTATCGATACTTTTTG
*
15120 TATGT
196 TATAT
* * * * * * * * *
15125 GTACCGATACTTTTTGTCCAGTATGCATTGCAAACGAGATACACGCATAACGTATCGATACACTT
1 GTATCGATACTTTTTGTCCAGTATGCTTTCCAAACTAGATGCACACAGAAAGTATCGATACACGT
* * * *
15190 ATGTA-AATTATCGATTCTTAAAACTTCGAAACCGATTAATTTAAGGTAATAGGTAAATTTACAA
66 ATG-AGAAGTATCGATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAA
* * * * * * *
15254 GGTTAGAGGTAAAAATATACCGATTTAATGACAAAATACGTAAATATAAAGTATCGATACTTTTT
130 TGTAAGCGGTAAAAATATACCGGTTTAATGACAAAATATGTAAACACAAAGTATCGATACTTTTT
* *
15319 ATATTT
195 GTATAT
* * * * *
15325 GTATCGATACTTTTTGTCCAATATGCTTTCCAAACTAGACGCACACAGAAAATATCGATATATGT
1 GTATCGATACTTTTTGTCCAGTATGCTTTCCAAACTAGATGCACACAGAAAGTATCGATACACGT
* * * **
15390 ACGAGATGTATCGATTCTTAAAACTTTGAAACAAATTAGTATAAAGTAATAGGTAAATTTACAAT
66 ATGAGAAGTATCGATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAAT
* * * *
15455 GAAAGCGGTAAAAATATACTGGTTTAGTGACAATATATGTAAACACAAAGTATCGATACTTTTTG
131 GTAAGCGGTAAAAATATACCGGTTTAATGACAAAATATGTAAACACAAAGTATCGATACTTTTTG
15520 TATAT
196 TATAT
* *
15525 GTATCGATACTTTTTGTCCAGTAAGCTTTCCAAACTAGATGCACACATAAAGTATCGATACACGT
1 GTATCGATACTTTTTGTCCAGTATGCTTTCCAAACTAGATGCACACAGAAAGTATCGATACACGT
* * *
15590 ACGAG-A--A--GATTCTTAAAACTTCAAAACCGATTAGTATAAAGTAATAGATAAATTTACAAT
66 ATGAGAAGTATCGATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAAT
** * * * *
15650 GTAATTGGTTAAAATATACCAGTTAAATGACAAAATAAGTAAACACAAAGTATCGATACTTTTTG
131 GTAAGCGGTAAAAATATACCGGTTTAATGACAAAATATGTAAACACAAAGTATCGATACTTTTTG
15715 TATAT
196 TATAT
* *
15720 GTATTGATACTTTTTATCCAGTATG
1 GTATCGATACTTTTTGTCCAGTATG
15745 AAAGCACTGA
Statistics
Matches: 709, Mismatches: 108, Indels: 11
0.86 0.13 0.01
Matches are distributed among these distances:
195 130 0.18
197 1 0.00
199 2 0.00
200 575 0.81
201 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (200 bp):
GTATCGATACTTTTTGTCCAGTATGCTTTCCAAACTAGATGCACACAGAAAGTATCGATACACGT
ATGAGAAGTATCGATTCTTAAAACTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAAT
GTAAGCGGTAAAAATATACCGGTTTAATGACAAAATATGTAAACACAAAGTATCGATACTTTTTG
TATAT
Found at i:15322 original size:22 final size:21
Alignment explanation
Indices: 15297--15339 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
15287 AAATACGTAA
15297 ATATAAAGTATCGATACTTTTT
1 ATAT-AAGTATCGATACTTTTT
**
15319 ATATTTGTATCGATACTTTTT
1 ATATAAGTATCGATACTTTTT
15340 GTCCAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (21 bp):
ATATAAGTATCGATACTTTTT
Found at i:16206 original size:18 final size:18
Alignment explanation
Indices: 16164--16207 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
16154 GAGGCGTGAG
16164 TCTTCTCAACCAAAACCT
1 TCTTCTCAACCAAAACCT
16182 T-TATCTCAACC-AAACTCT
1 TCT-TCTCAACCAAAAC-CT
16200 TCTTCTCA
1 TCTTCTCA
16208 CGTAATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 5 0.22
18 17 0.74
19 1 0.04
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.34
Consensus pattern (18 bp):
TCTTCTCAACCAAAACCT
Found at i:16532 original size:2 final size:2
Alignment explanation
Indices: 16525--16568 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
16515 ATGGGGAAGG
16525 AT AT 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 AT AT
16567 AT
1 AT
16569 CTCCGGATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18567 original size:15 final size:15
Alignment explanation
Indices: 18547--18576 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18537 AAAAGAAGAA
18547 AACATTGTTATGTAT
1 AACATTGTTATGTAT
*
18562 AACATTGTTTTGTAT
1 AACATTGTTATGTAT
18577 GTATGTTTGG
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:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (15 bp):
AACATTGTTATGTAT
Found at i:18840 original size:6 final size:6
Alignment explanation
Indices: 18829--18946 Score: 112
Period size: 6 Copynumber: 19.7 Consensus size: 6
18819 TTTATGCAAT
* * *
18829 TTTCAA TTTCAA TTTCAA TTTCAGA -CTGAA TTTCAT TTTCAA TTTCAA
1 TTTCAA TTTCAA TTTCAA TTTCA-A TTTCAA TTTCAA TTTCAA TTTCAA
* * * * * * * *
18877 TTTTAA TTTGAG TTTCAA TTTCAA TATCAA TTTTAA TTTTAA TTTGAG
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*
18925 TTTGAA TTTCAA TTTCAA TTTC
1 TTTCAA TTTCAA TTTCAA TTTC
18947 GGCTCCATTA
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
5 1 0.01
6 90 0.98
7 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.52
Consensus pattern (6 bp):
TTTCAA
Found at i:18874 original size:36 final size:36
Alignment explanation
Indices: 18829--18946 Score: 164
Period size: 36 Copynumber: 3.3 Consensus size: 36
18819 TTTATGCAAT
* * ** *
18829 TTTCAATTTCAATTTCAATTTCAGACTGAATTTCAT
1 TTTCAATTTCAATTTTAATTTGAGTTTGAATTTCAA
*
18865 TTTCAATTTCAATTTTAATTTGAGTTTCAATTTCAA
1 TTTCAATTTCAATTTTAATTTGAGTTTGAATTTCAA
* *
18901 TATCAATTTTAATTTTAATTTGAGTTTGAATTTCAA
1 TTTCAATTTCAATTTTAATTTGAGTTTGAATTTCAA
18937 TTTCAATTTC
1 TTTCAATTTC
18947 GGCTCCATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.52
Consensus pattern (36 bp):
TTTCAATTTCAATTTTAATTTGAGTTTGAATTTCAA
Found at i:18945 original size:30 final size:30
Alignment explanation
Indices: 18829--18945 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
18819 TTTATGCAAT
*
18829 TTTCAATTTCAATTTCAATTTCAGA-CTGAA
1 TTTCAATTTCAATTTCAATTTCA-ATTTGAA
* * *
18859 TTTCATTTTCAATTTCAATTTTAATTTGAG
1 TTTCAATTTCAATTTCAATTTCAATTTGAA
* * *
18889 TTTCAATTTCAATATCAATTTTAATTTTAA
1 TTTCAATTTCAATTTCAATTTCAATTTGAA
* * *
18919 TTTGAGTTTGAATTTCAATTTCAATTT
1 TTTCAATTTCAATTTCAATTTCAATTT
18946 CGGCTCCATT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
29 1 0.01
30 72 0.99
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (30 bp):
TTTCAATTTCAATTTCAATTTCAATTTGAA
Found at i:20817 original size:20 final size:20
Alignment explanation
Indices: 20772--20810 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
20762 GTTAACATAA
20772 AGTATCGATACTTTTTGTAT
1 AGTATCGATACTTTTTGTAT
20792 ATGTATCGATACTTTTTGT
1 A-GTATCGATACTTTTTGT
20811 TCAGTATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.51
Consensus pattern (20 bp):
AGTATCGATACTTTTTGTAT
Found at i:21229 original size:446 final size:445
Alignment explanation
Indices: 20396--21462 Score: 1570
Period size: 446 Copynumber: 2.4 Consensus size: 445
20386 TTGCTCCTAC
* * * * * *
20396 AAAGTATCGGTACCTAAGAAACATGTATCGATACATGACAATATAACAAGTTGAAAATTTAGAAA
1 AAAGTATCGATACATAATACACATGTATCGATACATGACAATATAACAAGTTG-AAATTGATAAA
** * * * * *
20461 ATTGGTTTCAATATGCCAATACCAGTAAAGAGATACCGGTTTACAAAAAAACGAAATGTCTCGAA
65 ACCGGTTTCAATATGACAA-AACAGTAAAAAGATACCGGTTTACAAAAAAATGAAACGTCTCGAA
* ** * * * *
20526 AATATTAATACCTTATAAAAAAGTATCGATACTTAGGT-AAGAGTAATGGTATCGATTAAATATA
129 AGTATCGATACCATACAAAAAAGTATCGATACTTAAGTAAAGAGTAATGCTATCGATTAAATATA
* * *
20590 AATAACTTAACAGGTTCAAAATGACAAAATCGGTTTCCATAATTGCATCTATAAAGTATCAATAC
194 AATAACTTAACACGTTCAAAATAACAAAATCGGTTTCCATAATTGCACCTATAAAGTATCAATAC
*
20655 ACGTACGAGAAGTATCAATTCTTAAAACTTCAAAACGGATTACTTTAAAGTAATAGGTAAATTTA
259 ACGTACGAAAAGTATCAATTCTTAAAACTTCAAAACGGATTACTTTAAAGTAATAGGTAAATTTA
*
20720 CAATGTAAGCGGTAAAAATATACCAGTTTAATGACAAAATATGTTAACATAAAGTATCGATACTT
324 CAATGTAAGAGGTAAAAATATACCAGTTTAATGACAAAATATGTTAACATAAAGTATCGATACTT
* *
20785 TTTGTATATGTATCGATACTTTTTGTTCAGTATGCTTCCCAAACTAGATACACGCAG
389 TTTGTATATGTATCGATACTTTTTGTCCAGTATACTTCCCAAACTAGATACACGCAG
* * *
20842 AAAGTATTGATAC-TAAATACACATGTATCGAGACATGACAATATAACAGGTTGAAATTGATAAA
1 AAAGTATCGATACAT-AATACACATGTATCGATACATGACAATATAACAAGTTGAAATTGATAAA
* *
20906 ACCGGTTTCAATATG-CAAAACATGTAAAAAGATACTGGTTTACAAAAAAATAAAACGTCTCGAA
65 ACCGGTTTCAATATGACAAAACA-GTAAAAAGATACCGGTTTACAAAAAAATGAAACGTCTCGAA
*
20970 AGTATCGATACCATACAAAAAAAGTATTGATACTTAAGTAAAG-GTAATGCTATCGATTAAATAT
129 AGTATCGATACCATAC-AAAAAAGTATCGATACTTAAGTAAAGAGTAATGCTATCGATTAAATAT
21034 AAATAACTTAACACGTTCAAAATTAACAAAA-CGGATTTCCATAATTGCACCTATAAAGTATCAA
193 AAATAACTTAACACGTTCAAAA-TAACAAAATCGG-TTTCCATAATTGCACCTATAAAGTATCAA
** * *
21098 TACACGTACGAAAAGTATCAATTCTTAAAACTTTGAAATGGATTACTTTAAAGTAATATGTAAAT
256 TACACGTACGAAAAGTATCAATTCTTAAAACTTCAAAACGGATTACTTTAAAGTAATAGGTAAAT
21163 TTACAATGTAAGAGGTAAAAATATACCAGTTTAATGACAAAATATGTTAACATAAAGTATCGATA
321 TTACAATGTAAGAGGTAAAAATATACCAGTTTAATGACAAAATATGTTAACATAAAGTATCGATA
* * *
21228 CTTTTTGTATATGTATCGATACTTTTTGTCCAGTATACTTCCCAAACTATATGCACGTAG
386 CTTTTTGTATATGTATCGATACTTTTTGTCCAGTATACTTCCCAAACTAGATACACGCAG
* * *
21288 AAAGTATCGATACATAATACACATGTATCGATACATGACAATATAATATGTTAAAATTTGATAAA
1 AAAGTATCGATACATAATACACATGTATCGATACATGACAATATAACAAGTTGAAA-TTGATAAA
* ** * *
21353 ACCTGTTTCAATATGACAAAACAGGTAAAAAGATACCATTTTACACAAAAATGAAACGACTCGAA
65 ACCGGTTTCAATATGACAAAACA-GTAAAAAGATACCGGTTTACAAAAAAATGAAACGTCTCGAA
*
21418 AGTATCGATACCATACAAAAAAGTATCGATACTTCAGT-AAGAGTA
129 AGTATCGATACCATACAAAAAAGTATCGATACTTAAGTAAAGAGTA
21463 TTCAATTTAA
Statistics
Matches: 558, Mismatches: 53, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
443 3 0.01
444 50 0.09
445 87 0.16
446 314 0.56
447 46 0.08
448 58 0.10
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (445 bp):
AAAGTATCGATACATAATACACATGTATCGATACATGACAATATAACAAGTTGAAATTGATAAAA
CCGGTTTCAATATGACAAAACAGTAAAAAGATACCGGTTTACAAAAAAATGAAACGTCTCGAAAG
TATCGATACCATACAAAAAAGTATCGATACTTAAGTAAAGAGTAATGCTATCGATTAAATATAAA
TAACTTAACACGTTCAAAATAACAAAATCGGTTTCCATAATTGCACCTATAAAGTATCAATACAC
GTACGAAAAGTATCAATTCTTAAAACTTCAAAACGGATTACTTTAAAGTAATAGGTAAATTTACA
ATGTAAGAGGTAAAAATATACCAGTTTAATGACAAAATATGTTAACATAAAGTATCGATACTTTT
TGTATATGTATCGATACTTTTTGTCCAGTATACTTCCCAAACTAGATACACGCAG
Found at i:21263 original size:20 final size:20
Alignment explanation
Indices: 21218--21263 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
21208 GTTAACATAA
*
21218 AGTATCGATACTTTTTGTAT
1 AGTATCGATACTTTTTGTAC
*
21238 ATGTATCGATACTTTTTGTCC
1 A-GTATCGATACTTTTTGTAC
21259 AGTAT
1 AGTAT
21264 ACTTCCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (20 bp):
AGTATCGATACTTTTTGTAC
Found at i:23323 original size:2 final size:2
Alignment explanation
Indices: 23316--23357 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
23306 AAATGTATCG
23316 AT AT 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 AT AT
23358 CATACTTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.