Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000422.1 Hibiscus syriacus cultivar Beakdansim tig00000773_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: 2457469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2423492 original size:389 final size:389
Alignment explanation
Indices: 2422775--2423558 Score: 1559
Period size: 389 Copynumber: 2.0 Consensus size: 389
2422765 ACTTTCTGGC
2422775 ACATAGTTTACCAAGACTTGCTTCAATGCTACCTTCTCAGGAACAAAGTGAACATCGAGTTCAAC
1 ACATAGTTTACCAAGACTTGCTTCAATGCTACCTTCTCAGGAACAAAGTGAACATCGAGTTCAAC
2422840 ATGTTTACTATTCTCATGATAAATTGGTTTTGCTATCATGGCTACAGCACTGCTGTTATCACACC
66 ATGTTTACTATTCTCATGATAAATTGGTTTTGCTATCATGGCTACAGCACTGCTGTTATCACACC
*
2422905 AAGATATAGGAATTTTCTACCTTGTAACGCCCAAATCATTTAGAAGACTATCCACCCACGTTGTT
131 AAGATATAGGAATTTTCTACCTTGTAACACCCAAATCATTTAGAAGACTATCCACCCACGTTGTT
2422970 TCAGCAGTAACATCTGCTACACTTCTGTACTCAGCTTTCATAGTCGACCTGGAAACTGATTTTTG
196 TCAGCAGTAACATCTGCTACACTTCTGTACTCAGCTTTCATAGTCGACCTGGAAACTGATTTTTG
2423035 TTTCTTAGAGTTCCACATCATGAGATTGTCACCAACAAACACACAGTAACCTGGGACAGACTTGC
261 TTTCTTAGAGTTCCACATCATGAGATTGTCACCAACAAACACACAGTAACCTGGGACAGACTTGC
2423100 AATCATCAGCACTTGCAGCCCAGTCAGCATCAAAATTAGGATAAACTACATAAATGACCACCCA
326 AATCATCAGCACTTGCAGCCCAGTCAGCATCAAAATTAGGATAAACTACATAAATGACCACCCA
2423164 ACATAGTTTACCAAGACTTGCTTCAATGCTACCTTCTCAGGAACAAAGTGAACATCGAGTTCAAC
1 ACATAGTTTACCAAGACTTGCTTCAATGCTACCTTCTCAGGAACAAAGTGAACATCGAGTTCAAC
2423229 ATGTTTACTATTCTCATGATAAATTGGTTTTGCTATCATGGCTACAGCACTGCTGTTATCACACC
66 ATGTTTACTATTCTCATGATAAATTGGTTTTGCTATCATGGCTACAGCACTGCTGTTATCACACC
2423294 AAGATATAGGAATTTTCTACCTTGTAACACCCAAATCATTTAGAAGACTATCCACCCACGTTGTT
131 AAGATATAGGAATTTTCTACCTTGTAACACCCAAATCATTTAGAAGACTATCCACCCACGTTGTT
2423359 TCAGCAGTAACATCTGCTACACTTCTGTACTCAGCTTTCATAGTCGACCTGGAAACTGATTTTTG
196 TCAGCAGTAACATCTGCTACACTTCTGTACTCAGCTTTCATAGTCGACCTGGAAACTGATTTTTG
2423424 TTTCTTAGAGTTCCACATCATGAGATTGTCACCAACAAACACACAGTAACCTGGGACAGACTTGC
261 TTTCTTAGAGTTCCACATCATGAGATTGTCACCAACAAACACACAGTAACCTGGGACAGACTTGC
2423489 AATCATCAGCACTTGCAGCCCAGTCAGCATCAAAATTAGGATAAACTACATAAATGACCACCCA
326 AATCATCAGCACTTGCAGCCCAGTCAGCATCAAAATTAGGATAAACTACATAAATGACCACCCA
2423553 ACATAG
1 ACATAG
2423559 GGCTTGGTCT
Statistics
Matches: 394, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
389 394 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (389 bp):
ACATAGTTTACCAAGACTTGCTTCAATGCTACCTTCTCAGGAACAAAGTGAACATCGAGTTCAAC
ATGTTTACTATTCTCATGATAAATTGGTTTTGCTATCATGGCTACAGCACTGCTGTTATCACACC
AAGATATAGGAATTTTCTACCTTGTAACACCCAAATCATTTAGAAGACTATCCACCCACGTTGTT
TCAGCAGTAACATCTGCTACACTTCTGTACTCAGCTTTCATAGTCGACCTGGAAACTGATTTTTG
TTTCTTAGAGTTCCACATCATGAGATTGTCACCAACAAACACACAGTAACCTGGGACAGACTTGC
AATCATCAGCACTTGCAGCCCAGTCAGCATCAAAATTAGGATAAACTACATAAATGACCACCCA
Found at i:2427380 original size:20 final size:20
Alignment explanation
Indices: 2427355--2427438 Score: 96
Period size: 20 Copynumber: 4.2 Consensus size: 20
2427345 TGAATGACTG
*
2427355 ACAAATGACCCAAAGGATTT
1 ACAAATGACCCAAAGGCTTT
* ** *
2427375 ACAAATTATGCAAAGGTTTT
1 ACAAATGACCCAAAGGCTTT
* *
2427395 ACAAATAACCTAAAGGCTTT
1 ACAAATGACCCAAAGGCTTT
*
2427415 ACAAATGACCCGAAGGCTTT
1 ACAAATGACCCAAAGGCTTT
2427435 ACAA
1 ACAA
2427439 TAATTTCATT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (20 bp):
ACAAATGACCCAAAGGCTTT
Found at i:2435787 original size:13 final size:13
Alignment explanation
Indices: 2435765--2435797 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2435755 GGGCCTTATA
2435765 AATA-ATAATATT
1 AATATATAATATT
2435777 AATATATAATATT
1 AATATATAATATT
*
2435790 ATTATATA
1 AATATATA
2435798 TATAACAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATATATAATATT
Found at i:2449420 original size:18 final size:18
Alignment explanation
Indices: 2449397--2449431 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2449387 TAAGCTGAAT
2449397 ATGTTCTATTTTAACCAA
1 ATGTTCTATTTTAACCAA
2449415 ATGTTCTATTTTAACCA
1 ATGTTCTATTTTAACCA
2449432 TACACGCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGTTCTATTTTAACCAA
Found at i:2457072 original size:19 final size:20
Alignment explanation
Indices: 2457029--2457072 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2457019 TACTAAGCTG
*
2457029 GAAATTAATGTTAGAGTGTT
1 GAAATTAATGTTAGAATGTT
* *
2457049 GAAATTGATTTTAGAATG-T
1 GAAATTAATGTTAGAATGTT
2457068 GAAAT
1 GAAAT
2457073 CGGGTAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Done.