Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 65 of 65
Found at i:12880452 original size:32 final size:32
Alignment explanation
Indices: 12880411--12880507 Score: 194
Period size: 32 Copynumber: 3.0 Consensus size: 32
12880401 CAAGAGAAAA
12880411 AACATTACATTCAACGAATTGTAACTTGTCAT
1 AACATTACATTCAACGAATTGTAACTTGTCAT
12880443 AACATTACATTCAACGAATTGTAACTTGTCAT
1 AACATTACATTCAACGAATTGTAACTTGTCAT
12880475 AACATTACATTCAACGAATTGTAACTTGTCAT
1 AACATTACATTCAACGAATTGTAACTTGTCAT
12880507 A
1 A
12880508 CTGCATAAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (32 bp):
AACATTACATTCAACGAATTGTAACTTGTCAT
Found at i:12882729 original size:26 final size:27
Alignment explanation
Indices: 12882699--12882752 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
12882689 TGATAATGAT
12882699 AAAGATATAAATAATGAG-AA-AAATAA
1 AAAGATATAAATAAT-AGTAATAAATAA
*
12882725 AAAGATATATATAATAGTAATAAATAA
1 AAAGATATAAATAATAGTAATAAATAA
12882752 A
1 A
12882753 TAAAAACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 16 0.64
27 7 0.28
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (27 bp):
AAAGATATAAATAATAGTAATAAATAA
Found at i:12883085 original size:2 final size:2
Alignment explanation
Indices: 12883078--12883108 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12883068 TATACATAAA
12883078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12883109 AAGGAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12885018 original size:105 final size:105
Alignment explanation
Indices: 12884894--12885563 Score: 1277
Period size: 105 Copynumber: 6.4 Consensus size: 105
12884884 GTATTGTTCA
*
12884894 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
12884959 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
12884999 GAGTCGAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
12885064 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
12885104 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
12885169 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
12885209 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
12885274 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
12885314 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
12885379 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
12885419 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
12885484 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
12885524 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
12885564 GGTGAAACCT
Statistics
Matches: 557, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 557 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:12895807 original size:20 final size:20
Alignment explanation
Indices: 12895769--12895812 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
12895759 ATGGTTAGTA
*
12895769 AAATAAAAATAAATGGAAAT
1 AAATAAAAATAAATAGAAAT
12895789 AAATAAAAATAACA-AGAAAT
1 AAATAAAAATAA-ATAGAAAT
12895809 AAAT
1 AAAT
12895813 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAATAGAAAT
Found at i:12897417 original size:11 final size:10
Alignment explanation
Indices: 12897388--12897458 Score: 65
Period size: 11 Copynumber: 6.8 Consensus size: 10
12897378 TATATATATG
12897388 TATAATAAAA
1 TATAATAAAA
12897398 TA-AATAAAA
1 TATAATAAAA
12897407 TATACATAAAA
1 TATA-ATAAAA
*
12897418 TATATATATATA
1 TATA-ATA-AAA
12897430 TATAATAATAA
1 TATAATAA-AA
*
12897441 -AGGAATAAAA
1 TA-TAATAAAA
12897451 TATAATAA
1 TATAATAA
12897459 TAATGAAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
9 9 0.18
10 12 0.24
11 23 0.46
12 6 0.12
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (10 bp):
TATAATAAAA
Found at i:12897425 original size:44 final size:43
Alignment explanation
Indices: 12897376--12897482 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 43
12897366 TGATTATATG
* *
12897376 TATATATATATGTATAAT-A-AAATAAATAAAATATACATAAAA
1 TATATATATATATATAATAATAAAGAAATAAAATATA-ATAAAA
*
12897418 TATATATATATATATAATAATAAAGGAATAAAATATAATAATAA
1 TATATATATATATATAATAATAAAGAAATAAAATATAATAA-AA
12897462 TGA-A-A-ATAGTATATAATAATA
1 T-ATATATATA-TATATAATAATA
12897483 GTAGGGACTA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
42 20 0.35
43 18 0.32
44 18 0.32
45 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.34
Consensus pattern (43 bp):
TATATATATATATATAATAATAAAGAAATAAAATATAATAAAA
Found at i:12897475 original size:22 final size:21
Alignment explanation
Indices: 12897427--12897482 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
12897417 ATATATATAT
*
12897427 ATATATAATAATAAAGGAATA
1 ATATATAATAATAAAGAAATA
* *
12897448 AAATATAATAATAATGAAAATA
1 ATATATAATAATAAAG-AAATA
*
12897470 GTATATAATAATA
1 ATATATAATAATA
12897483 GTAGGGACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
ATATATAATAATAAAGAAATA
Found at i:12897479 original size:19 final size:17
Alignment explanation
Indices: 12897447--12897481 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
12897437 ATAAAGGAAT
12897447 AAAATATAATAATAATG
1 AAAATATAATAATAATG
12897464 AAAATAGTATATAATAAT
1 AAAATA-TA-ATAATAAT
12897482 AGTAGGGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAATATAATAATAATG
Found at i:12904448 original size:28 final size:30
Alignment explanation
Indices: 12904417--12904477 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
12904407 GACTAGAAAC
* *
12904417 ATTATTATG-TGTTAAAA-TGATCGAAAAT
1 ATTATTATGCTCTAAAAATTGATCGAAAAT
12904445 ATTATTATGCTCTAAAAATTGATCGAAAAT
1 ATTATTATGCTCTAAAAATTGATCGAAAAT
12904475 ATT
1 ATT
12904478 TTAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.31
29 6 0.21
30 14 0.48
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (30 bp):
ATTATTATGCTCTAAAAATTGATCGAAAAT
Found at i:12905641 original size:39 final size:39
Alignment explanation
Indices: 12905537--12905642 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 39
12905527 CATAATTCTC
* ** * *
12905537 AAATTATTTCACTATAACATTCTAAAATCCTAATTTTTT
1 AAATTATTTCACAATAATGTTCTAAATTCCTAATTTATT
* * *
12905576 AAATT-TTGACACCATAATGTTCTAAATTCTTAATTTATT
1 AAATTATT-TCACAATAATGTTCTAAATTCCTAATTTATT
12905615 AAATTATTTCACAATAATGTTCTAAATT
1 AAATTATTTCACAATAATGTTCTAAATT
12905643 GTTTTTTAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.04
39 52 0.93
40 2 0.04
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (39 bp):
AAATTATTTCACAATAATGTTCTAAATTCCTAATTTATT
Found at i:12905963 original size:26 final size:23
Alignment explanation
Indices: 12905886--12905967 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 23
12905876 TATATATATA
*
12905886 ATTTTATATATATTAAATTAAAAAT
1 ATTTTAT-TAAATT-AATTAAAAAT
*
12905911 ATTTATATTAAATT-ATTAAATAT
1 ATTT-TATTAAATTAATTAAAAAT
*
12905934 ATTTTATTATGAACTTAATTAAAAAC
1 ATTTTATTA--AA-TTAATTAAAAAT
12905960 ATTTTATT
1 ATTTTATT
12905968 TTTATTTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
22 5 0.10
23 12 0.25
24 2 0.04
25 11 0.23
26 18 0.38
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTTTATTAAATTAATTAAAAAT
Found at i:12906149 original size:31 final size:31
Alignment explanation
Indices: 12906106--12906181 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
12906096 GTTAACTCGG
* *
12906106 GTGATCAAATCTTACTTAAATAAAAATGAAA
1 GTGATCATATCTTAATTAAATAAAAATGAAA
*
12906137 TTGATCATATCTTAATTAAATAAAAATGAAA
1 GTGATCATATCTTAATTAAATAAAAATGAAA
12906168 GTGA-CAATATCTTA
1 GTGATC-ATATCTTA
12906182 TATTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.03
31 39 0.98
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (31 bp):
GTGATCATATCTTAATTAAATAAAAATGAAA
Found at i:12909524 original size:12 final size:12
Alignment explanation
Indices: 12909509--12909551 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
12909499 AGGTGATGAC
*
12909509 AATGGTGGTGAT
1 AATGATGGTGAT
12909521 AATGATGGTGAT
1 AATGATGGTGAT
**
12909533 GGTGATGGTGAT
1 AATGATGGTGAT
12909545 AATGATG
1 AATGATG
12909552 AAAAAGATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.40, T:0.33
Consensus pattern (12 bp):
AATGATGGTGAT
Found at i:12909676 original size:20 final size:20
Alignment explanation
Indices: 12909648--12909687 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
12909638 TTTTAATCCG
*
12909648 AAAAATTA-TGTAATGTTTT
1 AAAAATTATTGTAATATTTT
12909667 AAAAATTTATTGTAATATTTT
1 AAAAA-TTATTGTAATATTTT
12909688 TTTGAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
AAAAATTATTGTAATATTTT
Found at i:12915828 original size:32 final size:31
Alignment explanation
Indices: 12915779--12915847 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
12915769 AAATATAATT
*
12915779 TTTTATTAAATTAATATCATTTAGTTTATTA
1 TTTTATTAAATTAATATCAATTAGTTTATTA
* * *
12915810 TTTTGTTAATATTGATATCAATTAGTTTA-TC
1 TTTTATTAA-ATTAATATCAATTAGTTTATTA
12915841 TTTTATT
1 TTTTATT
12915848 TAAAACTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.59
Consensus pattern (31 bp):
TTTTATTAAATTAATATCAATTAGTTTATTA
Done.