Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006814.1 Hibiscus syriacus cultivar Beakdansim tig00017317_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: 51617
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1319 original size:21 final size:22
Alignment explanation
Indices: 1293--1335 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1283 TGTTCTTATG
1293 AAATAATT-ATGTTTTAA-AATT
1 AAATAATTAAT-TTTTAAGAATT
1314 AAATAATTAATTTTTAAGAATT
1 AAATAATTAATTTTTAAGAATT
1336 TATCGAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
AAATAATTAATTTTTAAGAATT
Found at i:1789 original size:2 final size:2
Alignment explanation
Indices: 1782--1817 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1772 ATTTGATAAT
1782 TA TA TA TA TA 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
1818 GAATAAAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2448 original size:21 final size:20
Alignment explanation
Indices: 2409--2448 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2399 TCAGTTTTGA
*
2409 TTTATTTTATTATATAAATT
1 TTTATTTTATTATAAAAATT
*
2429 TTTATTTTTATTTTAAAAAT
1 TTTA-TTTTATTATAAAAAT
2449 CATACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTATTTTATTATAAAAATT
Found at i:6727 original size:3 final size:3
Alignment explanation
Indices: 6719--6744 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6709 ACCTTCCACC
6719 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
6745 AAAACAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:10713 original size:2 final size:2
Alignment explanation
Indices: 10706--10740 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10696 GAGAAGTAGC
10706 AT AT 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 AT AT A
10741 CACACACGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11279 original size:41 final size:42
Alignment explanation
Indices: 11234--11319 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
11224 CTTGATTCCA
* *
11234 TATCATCTCCAACAACTTTTC-TTTTATGATTCTCGGATGTT
1 TATCATCTCCAACAACTTTGCTTTTTATGATTCTCGAATGTT
11275 TATCATCTCCAACAACTTTGCTTTTTATGATTCTCGAATGTT
1 TATCATCTCCAACAACTTTGCTTTTTATGATTCTCGAATGTT
11317 TAT
1 TAT
11320 ATTTCAGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
41 20 0.48
42 22 0.52
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (42 bp):
TATCATCTCCAACAACTTTGCTTTTTATGATTCTCGAATGTT
Found at i:12689 original size:36 final size:31
Alignment explanation
Indices: 12612--12697 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
12602 TTTAGCTGAC
* *
12612 GAGTTTTCGAGTCCAGTCGAGCTTCATTTCA
1 GAGTTTTCGAGTCAAGTCGAGCTCCATTTCA
12643 GAGTTTTCGAGTCAAGTCGAGCTCCATTTCA
1 GAGTTTTCGAGTCAAGTCGAGCTCCATTTCA
* *
12674 GAGTTTTTGAGTCGAGTCGAGCTC
1 GAGTTTTCGAGTCAAGTCGAGCTC
12698 AGTAATACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.34
Consensus pattern (31 bp):
GAGTTTTCGAGTCAAGTCGAGCTCCATTTCA
Found at i:15001 original size:21 final size:20
Alignment explanation
Indices: 14977--15126 Score: 165
Period size: 20 Copynumber: 7.4 Consensus size: 20
14967 CTCAATTTCC
* *
14977 AAAATCGCAGCGTGAATTGT
1 AAAATCGCAACGTGAATAGT
* *
14997 AAAAATCGTAACGTAAATAGT
1 -AAAATCGCAACGTGAATAGT
**
15018 AAAAATAACAACGTGAATAGT
1 -AAAATCGCAACGTGAATAGT
*
15039 AAAATCACAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
*
15059 AAAATCGCAACGCGAATAGT
1 AAAATCGCAACGTGAATAGT
* *
15079 AAAATCGCAATGCGAATAGT
1 AAAATCGCAACGTGAATAGT
* *
15099 AAAATCGTAACGCGAATAGT
1 AAAATCGCAACGTGAATAGT
*
15119 GAAATCGC
1 AAAATCGC
15127 GTTGCGAATT
Statistics
Matches: 113, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
20 80 0.71
21 33 0.29
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGTGAATAGT
Found at i:15599 original size:20 final size:20
Alignment explanation
Indices: 15471--15642 Score: 147
Period size: 20 Copynumber: 8.6 Consensus size: 20
15461 ATATAGATTT
* *
15471 GTTGCG-ATTTTACTATTCAC
1 GTTGCGAATTTGACTA-TCGC
* *
15491 GTTGCGAAATTGGAGT-TCGC
1 GTTGCG-AATTTGACTATCGC
15511 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* * *
15531 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
* * * *
15551 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
15571 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
15591 GTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GC
*
15611 GTTGCG-ATTT-ACATATTCGA
1 GTTGCGAATTTGAC-TA-TCGC
15631 GTTGCGAATTTG
1 GTTGCGAATTTG
15643 GAAAATCGCA
Statistics
Matches: 127, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.02
19 14 0.11
20 100 0.79
21 6 0.05
22 5 0.04
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:15635 original size:60 final size:60
Alignment explanation
Indices: 15506--15642 Score: 197
Period size: 60 Copynumber: 2.3 Consensus size: 60
15496 GAAATTGGAG
* * *
15506 TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGTGAATTTGACT
1 TTCGAGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACT
* *
15566 TTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAT
1 TTCGAGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-T
15625 ATTCGAGTTGCGAATTTG
1 -TTCGAGTTGCGAATTTG
15643 GAAAATCGCA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
58 2 0.03
59 5 0.07
60 62 0.90
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.43
Consensus pattern (60 bp):
TTCGAGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACT
Found at i:15677 original size:20 final size:20
Alignment explanation
Indices: 15611--15678 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
15601 TGACTTCTGT
*
15611 GTTGCGATTTACATATTCGA
1 GTTGCGATTTACATATTCGC
** * *
15631 GTTGCGAATTTGGAAAATCGC
1 GTTGCG-ATTTACATATTCGC
** *
15652 AATGCGATTTATATATTCGC
1 GTTGCGATTTACATATTCGC
15672 GTTGCGA
1 GTTGCGA
15679 AATTGGAGTT
Statistics
Matches: 34, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 21 0.62
21 13 0.38
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:19150 original size:2 final size:2
Alignment explanation
Indices: 19143--19173 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19133 TTTCAAAATG
19143 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19174 TATTTTACCG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26185 original size:31 final size:31
Alignment explanation
Indices: 26125--26192 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
26115 TTACAATACA
* *
26125 GTCCTCCAACATTTAATCTGTTAGCAATATG
1 GTCCCCCAACATTTAATCCGTTAGCAATATG
* * *
26156 GTCCCCCAACATTTAGTCCGTTTGTAATATG
1 GTCCCCCAACATTTAATCCGTTAGCAATATG
26187 GTCCCC
1 GTCCCC
26193 AATGTAACTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.34
Consensus pattern (31 bp):
GTCCCCCAACATTTAATCCGTTAGCAATATG
Found at i:28265 original size:31 final size:31
Alignment explanation
Indices: 28205--28272 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
28195 ATGGCTTTTT
* *
28205 TATTAATATTTTTCTATGACTTGACATATTC
1 TATTAATATTTTTCTATGACATAACATATTC
* *
28236 TATTAATATTTTAT-TATGACATAATATATTT
1 TATTAATATTTT-TCTATGACATAACATATTC
28267 TATTAA
1 TATTAA
28273 CATGACCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.53
Consensus pattern (31 bp):
TATTAATATTTTTCTATGACATAACATATTC
Found at i:29400 original size:7 final size:7
Alignment explanation
Indices: 29388--29431 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
29378 GACCCGACCC
29388 GACCGTT
1 GACCGTT
29395 GACCGTT
1 GACCGTT
*
29402 GACTGTT
1 GACCGTT
29409 GACCG-T
1 GACCGTT
*
29415 GACCATT
1 GACCGTT
29422 GACCGTT
1 GACCGTT
29429 GAC
1 GAC
29432 TTCCTTTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:29423 original size:20 final size:21
Alignment explanation
Indices: 29388--29431 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
29378 GACCCGACCC
* *
29388 GACCGTTGACCGTTGACTGTT
1 GACCGTTGACCATTGACCGTT
29409 GACCG-TGACCATTGACCGTT
1 GACCGTTGACCATTGACCGTT
29429 GAC
1 GAC
29432 TTCCTTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (21 bp):
GACCGTTGACCATTGACCGTT
Found at i:41154 original size:2 final size:2
Alignment explanation
Indices: 41100--41135 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41090 TAGTTGTACA
41100 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
41136 TGATAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42430 original size:39 final size:39
Alignment explanation
Indices: 42376--42454 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
42366 GAGTTTCTCT
42376 TCAACTTTACTTAAATTTTGCTGTTGCATTCACTTATCA
1 TCAACTTTACTTAAATTTTGCTGTTGCATTCACTTATCA
42415 TCAACTTTACTTAAATTTTGCTGTTGCATTCACTTATCA
1 TCAACTTTACTTAAATTTTGCTGTTGCATTCACTTATCA
42454 T
1 T
42455 GTCCCTGCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (39 bp):
TCAACTTTACTTAAATTTTGCTGTTGCATTCACTTATCA
Found at i:46056 original size:21 final size:21
Alignment explanation
Indices: 46032--46071 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46022 CGCGATTGCT
* *
46032 GCCATAGCGGGCGCTATTGTG
1 GCCATAGCAGGCACTATTGTG
46053 GCCATAGCAGGCACTATTG
1 GCCATAGCAGGCACTATTG
46072 CTCTATAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.23
Consensus pattern (21 bp):
GCCATAGCAGGCACTATTGTG
Found at i:49270 original size:15 final size:16
Alignment explanation
Indices: 49250--49281 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
49240 AATTTTTCTC
49250 AATAATTTTA-ATTTG
1 AATAATTTTAGATTTG
49265 AATAATTTTAGATTTG
1 AATAATTTTAGATTTG
49281 A
1 A
49282 GTTAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
AATAATTTTAGATTTG
Done.