Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007084.1 Hibiscus syriacus cultivar Beakdansim tig00018483_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: 192361
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:168854 original size:23 final size:22
Alignment explanation
Indices: 168790--168868 Score: 97
Period size: 23 Copynumber: 3.6 Consensus size: 22
168780 ACACCTAACA
168790 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
* * * *
168812 GTGTATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
*
168833 GTGCACCGATGCATGCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
168856 GTGCATCGATGCA
1 GTGCATCGATGCA
168869 CAAGGCCATG
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 16 0.36
22 11 0.24
23 18 0.40
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:171427 original size:12 final size:12
Alignment explanation
Indices: 171407--171441 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
171397 TTTTATACTT
* *
171407 AAACTATTTTTG
1 AAACAATTTTCG
171419 AAACAATTTTCG
1 AAACAATTTTCG
171431 AAACAATTTTC
1 AAACAATTTTC
171442 ATAAAGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (12 bp):
AAACAATTTTCG
Found at i:175094 original size:20 final size:22
Alignment explanation
Indices: 175069--175109 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
175059 AAAAAATTAC
175069 TTAAAATATT-AT-TTTTTTAT
1 TTAAAATATTAATATTTTTTAT
175089 TTAAAATATTAATATTTTTTA
1 TTAAAATATTAATATTTTTTA
175110 ACATTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAAAATATTAATATTTTTTAT
Found at i:175193 original size:18 final size:18
Alignment explanation
Indices: 175170--175209 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
175160 AATAAAATCG
*
175170 ATAAAAT-ACTAAATAATA
1 ATAAAATCAATAAA-AATA
175188 ATAAAATCAATAAAAATA
1 ATAAAATCAATAAAAATA
175206 ATAA
1 ATAA
175210 TATTTATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAAAATCAATAAAAATA
Found at i:175803 original size:28 final size:29
Alignment explanation
Indices: 175757--175857 Score: 114
Period size: 31 Copynumber: 3.4 Consensus size: 29
175747 GAAAAAGTTT
* * *
175757 AAATACTTTAGGTATCTATTTTTA-CATA
1 AAATACTTTAGGTACCTATTTTGACCAAA
* *
175785 AAATACTTTAGGTGCCTATGTTGACCAAA
1 AAATACTTTAGGTACCTATTTTGACCAAA
* *
175814 AAGATAACTTTGGGTACTTATTTTGACCAAA
1 AA-AT-ACTTTAGGTACCTATTTTGACCAAA
175845 AAATACTTTAGGT
1 AAATACTTTAGGT
175858 GTTTAAATGA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
28 20 0.33
29 13 0.22
30 4 0.07
31 23 0.38
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Consensus pattern (29 bp):
AAATACTTTAGGTACCTATTTTGACCAAA
Found at i:176595 original size:32 final size:33
Alignment explanation
Indices: 176526--176595 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
176516 ATTTGGTATC
* * * *
176526 GATACCGCATGTACAATATTGATAGTAGATATT
1 GATACCACATATACAATATTGATACTAAATATT
176559 GATACCACATATACAATATT-ATACTAAATATT
1 GATACCACATATACAATATTGATACTAAATATT
176591 GATAC
1 GATAC
176596 TAGATATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 15 0.45
33 18 0.55
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (33 bp):
GATACCACATATACAATATTGATACTAAATATT
Found at i:178264 original size:188 final size:188
Alignment explanation
Indices: 177942--178301 Score: 522
Period size: 188 Copynumber: 1.9 Consensus size: 188
177932 CTTCTTTTTC
** * *
177942 TATTATTGTTATGTTTATAGAGGTATTTGATCCGCTTTTGTTTATTTGAACTTGTTAAAAACATG
1 TATTATTGTTATGTTTATAGAAATACTTGATCCGCTTTTGTTTATGTGAACTTGTTAAAAACATG
* * * *
178007 TCTAAGTTCTTGTTTGTGTTTCTATTTTGGTTCTCATTACAGATTTAATAATATTGATTTGTGGT
66 GCGAAGTGCTTGTTTGTGTTTCTATTTTAGTTCTCATTACAGATTTAATAATATTGATTTGTGGT
* *
178072 TCATGCTTCATGATGTTATTTTAAAAGTTTTTCTGTGAATTTACATTAGTTCTCAATA
131 TCATGCCTCATGATGTTATTTTAAAAGATTTTCTGTGAATTTACATTAGTTCTCAATA
* ** * * *
178130 TATTTTTGTTATGTTTATAGAAATACTTGATTTGCTTTTGTTTGTGTGAACTTGTTAAAATCTTG
1 TATTATTGTTATGTTTATAGAAATACTTGATCCGCTTTTGTTTATGTGAACTTGTTAAAAACATG
*
178195 GCGAAGTGCTTGTTTGTGTTTCTATTTTAGTTCTCATTACAGATTTAGTAATATTGATTTGTGGT
66 GCGAAGTGCTTGTTTGTGTTTCTATTTTAGTTCTCATTACAGATTTAATAATATTGATTTGTGGT
* * * **
178260 TCATGCCTCGTGCTGTTGTTTTACTAGATTTTCTGTGAATTT
131 TCATGCCTCATGATGTTATTTTAAAAGATTTTCTGTGAATTT
178302 GTGTTAGTTT
Statistics
Matches: 150, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
188 150 1.00
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (188 bp):
TATTATTGTTATGTTTATAGAAATACTTGATCCGCTTTTGTTTATGTGAACTTGTTAAAAACATG
GCGAAGTGCTTGTTTGTGTTTCTATTTTAGTTCTCATTACAGATTTAATAATATTGATTTGTGGT
TCATGCCTCATGATGTTATTTTAAAAGATTTTCTGTGAATTTACATTAGTTCTCAATA
Found at i:183790 original size:25 final size:27
Alignment explanation
Indices: 183739--183790 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
183729 AATTAAAGTC
**
183739 CTTAAATTATGTTTTTTTACTTTAAATT
1 CTTAAATTA-GTTTTTTTACTCAAAATT
183767 CTTAAATTA-TTTTTTTAC-CAAAAT
1 CTTAAATTAGTTTTTTTACTCAAAAT
183791 AAATCCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 9 0.41
28 9 0.41
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.56
Consensus pattern (27 bp):
CTTAAATTAGTTTTTTTACTCAAAATT
Found at i:186613 original size:33 final size:33
Alignment explanation
Indices: 186569--186634 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
186559 TTAAAGTCTG
*
186569 ATTTTCGATTTACTAAAGTAAGCCTGATTGTTT
1 ATTTTCAATTTACTAAAGTAAGCCTGATTGTTT
*
186602 ATTTTCAATTTACTAAAGTAAGTCTGATTGTTT
1 ATTTTCAATTTACTAAAGTAAGCCTGATTGTTT
186635 GATTCCTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.47
Consensus pattern (33 bp):
ATTTTCAATTTACTAAAGTAAGCCTGATTGTTT
Found at i:190028 original size:18 final size:18
Alignment explanation
Indices: 190004--190084 Score: 90
Period size: 18 Copynumber: 4.3 Consensus size: 18
189994 TTTGTCCCAG
*
190004 AGGACCACTATGTCCTGA
1 AGGACCACTATGTCCCGA
*
190022 AGAACCACTAAATATGTCCCGA
1 AGGACCAC----TATGTCCCGA
*
190044 AGGACCACTATGTTCCGA
1 AGGACCACTATGTCCCGA
*
190062 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
190080 AGGAC
1 AGGAC
190085 AGCGTAGACC
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
18 37 0.70
22 16 0.30
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:190040 original size:22 final size:22
Alignment explanation
Indices: 190012--190053 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
190002 AGAGGACCAC
*
190012 TATGTCCTGAAGAACCACTAAA
1 TATGTCCCGAAGAACCACTAAA
*
190034 TATGTCCCGAAGGACCACTA
1 TATGTCCCGAAGAACCACTA
190054 TGTTCCGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (22 bp):
TATGTCCCGAAGAACCACTAAA
Done.