Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003150.1 Hibiscus syriacus cultivar Beakdansim tig00006625_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: 45693
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1305 original size:2 final size:2
Alignment explanation
Indices: 1242--1290 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
1232 ATTATATGAC
* * *
1242 TA TA TA TT TA TT TA TA -A TG TA TA -A 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
1282 TA TA TA TA T
1 TA TA TA TA T
1291 TATTTATGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1372 original size:31 final size:33
Alignment explanation
Indices: 1330--1408 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 33
1320 CATTGTGTAC
* *
1330 TATA-ATTACATA-ATGTAT-ATATTATGTCGT
1 TATATATTACATACATATATAATATTATATCGT
1360 TATATATTACATAGCATATATACATATTATATCGT
1 TATATATTACATA-CATATATA-ATATTATATCGT
*
1395 TACATTATTACATA
1 TATA-TATTACATA
1409 TTATTTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 4 0.10
31 8 0.20
33 5 0.12
35 14 0.35
36 9 0.22
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.44
Consensus pattern (33 bp):
TATATATTACATACATATATAATATTATATCGT
Found at i:1429 original size:23 final size:22
Alignment explanation
Indices: 1377--1433 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
1367 TACATAGCAT
*
1377 ATATACATATTATATCGTTACA
1 ATATACATATTATATCATTACA
* * *
1399 TTATTACATATTATTTTATTACA
1 ATA-TACATATTATATCATTACA
1422 CATATACATATT
1 -ATATACATATT
1434 TATTATTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 2 0.07
23 24 0.86
24 2 0.07
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATACATATTATATCATTACA
Found at i:2592 original size:15 final size:16
Alignment explanation
Indices: 2574--2605 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2564 GTCATGTATG
2574 TTTT-AATTTAATTTT
1 TTTTAAATTTAATTTT
2589 TTTTAAATTTAATTTT
1 TTTTAAATTTAATTTT
2605 T
1 T
2606 AAATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAAATTTAATTTT
Found at i:2604 original size:13 final size:13
Alignment explanation
Indices: 2588--2634 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
2578 AATTTAATTT
2588 TTTTTAAATTTAA
1 TTTTTAAATTTAA
2601 TTTTTAAATTT-A
1 TTTTTAAATTTAA
2613 -TTTT-AATTTAA
1 TTTTTAAATTTAA
*
2624 TTTTTTAATTT
1 TTTTTAAATTT
2635 TATTCATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.16
11 5 0.16
12 5 0.16
13 16 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTAAATTTAA
Found at i:2620 original size:23 final size:24
Alignment explanation
Indices: 2583--2634 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
2573 GTTTTAATTT
*
2583 AATTTTTTTTAAATTTAATTTTTA
1 AATTTATTTTAAATTTAATTTTTA
*
2607 AATTTATTTT-AATTTAATTTTTT
1 AATTTATTTTAAATTTAATTTTTA
2630 AATTT
1 AATTT
2635 TATTCATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
AATTTATTTTAAATTTAATTTTTA
Found at i:2636 original size:24 final size:24
Alignment explanation
Indices: 2580--2638 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
2570 TATGTTTTAA
2580 TTTAATTTT-TTTTAAATTTAATT
1 TTTAATTTTATTTTAAATTTAATT
*
2603 TTTAAATTTATTTT-AATTTAATTT
1 TTTAATTTTATTTTAAATTTAA-TT
2627 TTTAATTTTATT
1 TTTAATTTTATT
2639 CATTTTCCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTAATTTTATTTTAAATTTAATT
Found at i:3734 original size:36 final size:34
Alignment explanation
Indices: 3679--3787 Score: 146
Period size: 36 Copynumber: 3.1 Consensus size: 34
3669 CAAATGGGAT
* *
3679 AATTGTTTTAAGAAAACAATCTTAATTGAGATAA
1 AATTGTTTTAAGAAAACAATCTCAAATGAGATAA
3713 AATTGGTTTTAAGTAAAACAATCTCAAATGAGATAA
1 AATT-GTTTTAAG-AAAACAATCTCAAATGAGATAA
* *
3749 AACTTGTTTTAAGAAAAATAATCTCAAGTGAGATAA
1 AA-TTGTTTTAAG-AAAACAATCTCAAATGAGATAA
3785 AAT
1 AAT
3788 CTTTAAAATG
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
34 4 0.06
35 9 0.13
36 52 0.78
37 2 0.03
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (34 bp):
AATTGTTTTAAGAAAACAATCTCAAATGAGATAA
Found at i:3922 original size:44 final size:44
Alignment explanation
Indices: 3873--4132 Score: 211
Period size: 44 Copynumber: 5.9 Consensus size: 44
3863 GCATCAAACG
* *
3873 AAATATTGTTTTTGATCCAATTCATTATGTGATGAAATCGAGAA
1 AAATATTGATGTTGATCCAATTCATTATGTGATGAAATCGAGAA
* * * * **
3917 AAATATTGATGTTGATCCAACTCCTTATGCGATGAAAACGAGCG
1 AAATATTGATGTTGATCCAATTCATTATGTGATGAAATCGAGAA
* * * * *
3961 AAATATTGATGTTAATCAAAATCCTTATGTGATGGAATCGAGAA
1 AAATATTGATGTTGATCCAATTCATTATGTGATGAAATCGAGAA
* * * **
4005 AAATGTTGATGTTGAT-TAACTT-ATTATGTGATGGAATCGAGCT
1 AAATATTGATGTTGATCCAA-TTCATTATGTGATGAAATCGAGAA
* * * * * * * **
4048 CAATGTTGATGCTGATCCAACTCCTTATATGATGGAATCGAGTG
1 AAATATTGATGTTGATCCAATTCATTATGTGATGAAATCGAGAA
* * *
4092 AAATATTGATGATGATCCAACTCCTTATGTGATTG-AATCGA
1 AAATATTGATGTTGATCCAATTCATTATGTGA-TGAAATCGA
4133 ATGGAAATGT
Statistics
Matches: 177, Mismatches: 35, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
43 35 0.20
44 140 0.79
45 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.34
Consensus pattern (44 bp):
AAATATTGATGTTGATCCAATTCATTATGTGATGAAATCGAGAA
Found at i:4071 original size:131 final size:132
Alignment explanation
Indices: 3896--4158 Score: 332
Period size: 131 Copynumber: 2.0 Consensus size: 132
3886 GATCCAATTC
* *
3896 ATTATGTGATGAAATCGAGAAAAATATTGATGTTGATCCAACTCCTTATGCGATGAAAACGAGCG
1 ATTATGTGATGAAATCGAGAAAAATATTGATGCTGATCCAACTCCTTATACGATGAAAACGAGCG
* *
3961 AAATATTGATGTTAATCAAAATCCTTATGTGATGGAATCG-AGAAAAATGTTGATGTTGAT-TAA
66 AAATATTGATGATAATCAAAATCCTTATGTGATGGAATCGAAG-AAAATGTTGATGATGATCTAA
4024 CTT
130 CTT
* *** * * * * *
4027 ATTATGTGATGGAATCGAGCTCAATGTTGATGCTGATCCAACTCCTTATATGATGGAATCGAGTG
1 ATTATGTGATGAAATCGAGAAAAATATTGATGCTGATCCAACTCCTTATACGATGAAAACGAGCG
* * * * *
4092 AAATATTGATGATGATCCAACTCCTTATGTGATTGAATCGAATGGAAATGTTGATGATGATCTAA
66 AAATATTGATGATAATCAAAATCCTTATGTGATGGAATCGAA-GAAAATGTTGATGATGATCTAA
4157 CT
130 CT
4159 CCTTATATGA
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
131 89 0.80
132 16 0.14
133 6 0.05
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (132 bp):
ATTATGTGATGAAATCGAGAAAAATATTGATGCTGATCCAACTCCTTATACGATGAAAACGAGCG
AAATATTGATGATAATCAAAATCCTTATGTGATGGAATCGAAGAAAATGTTGATGATGATCTAAC
TT
Found at i:6625 original size:23 final size:23
Alignment explanation
Indices: 6599--6656 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 23
6589 GGAGAAGGCC
6599 ATCTTGATC-CTTACAAGGGTTCA
1 ATCTTG-TCACTTACAAGGGTTCA
6622 ATCTTGTCACTTACAAGGGTTCA
1 ATCTTGTCACTTACAAGGGTTCA
6645 ATCTTGTCACTT
1 ATCTTGTCACTT
6657 TTCTAAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 2 0.06
23 32 0.94
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (23 bp):
ATCTTGTCACTTACAAGGGTTCA
Found at i:8475 original size:12 final size:12
Alignment explanation
Indices: 8338--8484 Score: 123
Period size: 12 Copynumber: 12.2 Consensus size: 12
8328 GAGTGATGCA
* *
8338 CATTCATTCATT
1 CATTCGTTCGTT
8350 CATTCGTTCGTT
1 CATTCGTTCGTT
*
8362 CGTTCGTTCGTT
1 CATTCGTTCGTT
*
8374 CGTTCGTTCGTT
1 CATTCGTTCGTT
* *
8386 CGTTCGTTCATT
1 CATTCGTTCGTT
* * * *
8398 CATCCATCCATT
1 CATTCGTTCGTT
* * *
8410 CATCCATCCGTT
1 CATTCGTTCGTT
8422 CATTCGTTCGTT
1 CATTCGTTCGTT
*
8434 CGTTCGTTCGTT
1 CATTCGTTCGTT
*
8446 CGTTCGTTCGTT
1 CATTCGTTCGTT
* *
8458 CGTTCATTCGTT
1 CATTCGTTCGTT
* *
8470 CATTCATTCATT
1 CATTCGTTCGTT
8482 CAT
1 CAT
8485 CCTAGGTACA
Statistics
Matches: 119, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 119 1.00
ACGTcount: A:0.11, C:0.28, G:0.14, T:0.47
Consensus pattern (12 bp):
CATTCGTTCGTT
Found at i:8484 original size:4 final size:4
Alignment explanation
Indices: 8352--8470 Score: 130
Period size: 4 Copynumber: 29.8 Consensus size: 4
8342 CATTCATTCA
* *
8352 TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCA TTCA
1 TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG
* * * * * * * * *
8400 TCCA TCCA TTCA TCCA TCCG TTCA TTCG TTCG TTCG TTCG TTCG TTCG
1 TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG TTCG
*
8448 TTCG TTCG TTCG TTCA TTCG TTC
1 TTCG TTCG TTCG TTCG TTCG TTC
8471 ATTCATTCAT
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 105 1.00
ACGTcount: A:0.07, C:0.29, G:0.18, T:0.47
Consensus pattern (4 bp):
TTCG
Found at i:8484 original size:8 final size:8
Alignment explanation
Indices: 8340--8482 Score: 124
Period size: 8 Copynumber: 17.9 Consensus size: 8
8330 GTGATGCACA
*
8340 TTCATTCA
1 TTCATTCG
8348 TTCATTCG
1 TTCATTCG
*
8356 TTCGTTCG
1 TTCATTCG
*
8364 TTCGTTCG
1 TTCATTCG
*
8372 TTCGTTCG
1 TTCATTCG
*
8380 TTCGTTCG
1 TTCATTCG
* *
8388 TTCGTTCA
1 TTCATTCG
* *
8396 TTCATCCA
1 TTCATTCG
* *
8404 TCCATTCA
1 TTCATTCG
* *
8412 TCCATCCG
1 TTCATTCG
8420 TTCATTCG
1 TTCATTCG
*
8428 TTCGTTCG
1 TTCATTCG
*
8436 TTCGTTCG
1 TTCATTCG
*
8444 TTCGTTCG
1 TTCATTCG
*
8452 TTCGTTCG
1 TTCATTCG
8460 TTCATTCG
1 TTCATTCG
*
8468 TTCATTCA
1 TTCATTCG
8476 TTCATTC
1 TTCATTC
8483 ATCCTAGGTA
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 121 1.00
ACGTcount: A:0.10, C:0.28, G:0.15, T:0.48
Consensus pattern (8 bp):
TTCATTCG
Found at i:16315 original size:14 final size:11
Alignment explanation
Indices: 16283--16308 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16273 TAATGTTGAT
16283 ATAATATTTTA
1 ATAATATTTTA
16294 ATAATATTTTA
1 ATAATATTTTA
16305 ATAA
1 ATAA
16309 AAATATTAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATAATATTTTA
Found at i:16370 original size:11 final size:11
Alignment explanation
Indices: 16283--16393 Score: 51
Period size: 11 Copynumber: 10.6 Consensus size: 11
16273 TAATGTTGAT
*
16283 ATAATATTTTA
1 ATAATATTATA
*
16294 ATAATATTTTA
1 ATAATATTATA
*
16305 ATAA-A-AATA
1 ATAATATTATA
* *
16314 TTAATGATTAAA
1 ATAAT-ATTATA
*
16326 AT-AT-TTAAA
1 ATAATATTATA
16335 AT-ATATTA-A
1 ATAATATTATA
*
16344 TTAATATT-T-
1 ATAATATTATA
*
16353 TTAATATTATA
1 ATAATATTATA
16364 ATAATA-TACTCA
1 ATAATATTA-T-A
*
16376 ATTATATTATA
1 ATAATATTATA
16387 ATAATAT
1 ATAATAT
16394 ATGATATTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
9 24 0.30
10 12 0.15
11 31 0.39
12 10 0.13
13 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (11 bp):
ATAATATTATA
Found at i:31980 original size:32 final size:31
Alignment explanation
Indices: 31937--32004 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
31927 GGCTTTAGAG
*
31937 AAGTTAAGAGTG-AATGTTATCCCCTATATGTA
1 AAGTTAAGAGTGAAAT-CTAT-CCCTATATGTA
*
31969 AAGTTAGGAGTGAAATCTATCCCTATATGTA
1 AAGTTAAGAGTGAAATCTATCCCTATATGTA
32000 AAGTT
1 AAGTT
32005 TTATTTGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 16 0.48
32 14 0.42
33 3 0.09
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (31 bp):
AAGTTAAGAGTGAAATCTATCCCTATATGTA
Found at i:34484 original size:71 final size:71
Alignment explanation
Indices: 34368--34507 Score: 244
Period size: 71 Copynumber: 2.0 Consensus size: 71
34358 ACAATAAAGC
*
34368 TTGAGTTATCCCCTAAAGCAATTGGTTAATAGCCCTGGCTTTATGGATAATATTCAGCTAGCCTG
1 TTGAGTTACCCCCTAAAGCAATTGGTTAATAGCCCTGGCTTTATGGATAATATTCAGCTAGCCTG
34433 TTATGA
66 TTATGA
* * *
34439 TTGAGTTGCCCCCTAAAGCAATTGGTTAATCGCCCTGGCTTTATGGATAATATTCAGCTAGCTTG
1 TTGAGTTACCCCCTAAAGCAATTGGTTAATAGCCCTGGCTTTATGGATAATATTCAGCTAGCCTG
34504 TTAT
66 TTAT
34508 ACTATTATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (71 bp):
TTGAGTTACCCCCTAAAGCAATTGGTTAATAGCCCTGGCTTTATGGATAATATTCAGCTAGCCTG
TTATGA
Found at i:45059 original size:22 final size:22
Alignment explanation
Indices: 45010--45109 Score: 159
Period size: 22 Copynumber: 4.6 Consensus size: 22
45000 CTATCTATAT
*
45010 TCTTCAAAGATGATA-ATT-TAT
1 TCTTCAAAGATGATAGATTCT-C
45031 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
45053 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
45075 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
45097 TTTTCAAAGATGA
1 TCTTCAAAGATGA
45110 AAGCTCTATT
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
21 15 0.20
22 59 0.79
23 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Done.