Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001836.1 Hibiscus syriacus cultivar Beakdansim tig00003715_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: 2428596
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2399953 original size:19 final size:19
Alignment explanation
Indices: 2399929--2399979 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
2399919 TTTAATGGGG
*
2399929 ATGCATCGATGCACTCTTT
1 ATGCATCGATGCACTCCTT
2399948 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
2399967 ATGCATCGATGCA
1 ATGCATCGATGCA
2399980 TAAATCCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:2400016 original size:83 final size:83
Alignment explanation
Indices: 2399863--2400044 Score: 237
Period size: 83 Copynumber: 2.2 Consensus size: 83
2399853 TTAATGGAGG
*
2399863 TATGCATCGATGCACTACACTATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGG
1 TATGCATCGATGCACTACACTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GG
* *
2399928 GATGCATCGATGCACT-CTT
65 AATGCATCGATGCACTGC-A
*
2399947 TATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT
1 TATGCATCGATGCACTACAC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AAT
*
2400010 -TAATGCATCGATGCACTGCA
63 GGAATGCATCGATGCACTGCA
*
2400030 TGTGCATCGATGCAC
1 TATGCATCGATGCAC
2400045 CTTAAACAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
82 1 0.01
83 60 0.68
84 24 0.27
85 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (83 bp):
TATGCATCGATGCACTACACTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
ATGCATCGATGCACTGCA
Found at i:2412354 original size:22 final size:21
Alignment explanation
Indices: 2412311--2412354 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2412301 ATAGTACTAT
**
2412311 ACAGTATGAACAATACTGTGA
1 ACAGTATGAACAATACCATGA
2412332 ACAGTAATGAACAATACCATGA
1 ACAGT-ATGAACAATACCATGA
2412354 A
1 A
2412355 TAGTGGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (21 bp):
ACAGTATGAACAATACCATGA
Found at i:2413139 original size:20 final size:20
Alignment explanation
Indices: 2413110--2413167 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2413100 ATATGAAATT
* *
2413110 TGTCCTGAATGGCCTATGTA
1 TGTCCCGAATGACCTATGTA
*
2413130 TGTCCCGAATGACCTCTGTA
1 TGTCCCGAATGACCTATGTA
* *
2413150 TATCCCGAAAGACCTATG
1 TGTCCCGAATGACCTATG
2413168 AACCCTCGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (20 bp):
TGTCCCGAATGACCTATGTA
Found at i:2415646 original size:30 final size:30
Alignment explanation
Indices: 2415590--2415648 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2415580 GATTTATTTA
* *
2415590 GTGACCAAATTATAAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAAATTTGGAAAAGTTTG
*
2415620 GTGATCAAAGTATAAACTTT-GAAAAGTTT
1 GTGACCAAAGTATAAA-TTTGGAAAAGTTT
2415649 AGGGATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (30 bp):
GTGACCAAAGTATAAATTTGGAAAAGTTTG
Found at i:2417563 original size:2 final size:2
Alignment explanation
Indices: 2417556--2417584 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2417546 TTTTATGAGT
2417556 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 T
2417585 TGTTGAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2421881 original size:33 final size:33
Alignment explanation
Indices: 2421844--2421906 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2421834 AAATGAAAAT
*
2421844 GGATTTTGAA-AATCAAAATGAAATCTTGAAGAA
1 GGATTTAGAACAATCAAAATGAAAT-TTGAAGAA
**
2421877 GGATTTAGAACTCTCAAAATGAAATTTGAA
1 GGATTTAGAACAATCAAAATGAAATTTGAA
2421907 AGTATTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 14 0.54
34 12 0.46
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (33 bp):
GGATTTAGAACAATCAAAATGAAATTTGAAGAA
Found at i:2425753 original size:20 final size:22
Alignment explanation
Indices: 2425730--2425811 Score: 89
Period size: 21 Copynumber: 3.8 Consensus size: 22
2425720 TTGGTGCAGA
2425730 GGGAATCGA-TCCCCCCTTGA-
1 GGGAATCGATTCCCCCCTTGAG
* *
2425750 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCCCTTG-AG
**
2425773 GGGAATCGATTCCCCCC-ACAG
1 GGGAATCGATTCCCCCCTTGAG
*
2425794 GGGAATCGATACCCCCCT
1 GGGAATCGATTCCCCCCT
2425812 GGGGTTCTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.16
21 27 0.53
22 1 0.02
23 15 0.29
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAATCGATTCCCCCCTTGAG
Done.