Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000908.1 Hibiscus syriacus cultivar Beakdansim tig00001802_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: 480356
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 3
Found at i:445134 original size:3 final size:3
Alignment explanation
Indices: 445126--445198 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
445116 ATTTTTATCC
*
445126 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
445174 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
445199 AATATATTAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:445645 original size:25 final size:25
Alignment explanation
Indices: 445598--445646 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
445588 CCCCAACCTG
*
445598 AAAAAAAAGAGACAGAAAGGGAGAC
1 AAAAAAAAGAGACAGAAACGGAGAC
* *
445623 AAAAAACAGAGACAGAACCGGAGA
1 AAAAAAAAGAGACAGAAACGGAGA
445647 GAAAGGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.61, C:0.12, G:0.27, T:0.00
Consensus pattern (25 bp):
AAAAAAAAGAGACAGAAACGGAGAC
Found at i:445672 original size:15 final size:16
Alignment explanation
Indices: 445644--445673 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
445634 ACAGAACCGG
445644 AGAGAAAGGAAAAAAC
1 AGAGAAAGGAAAAAAC
445660 AGAGAAA-GAAAAAA
1 AGAGAAAGGAAAAAA
445674 AACAACAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.03, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAGAAAGGAAAAAAC
Found at i:445677 original size:17 final size:16
Alignment explanation
Indices: 445644--445674 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
445634 ACAGAACCGG
*
445644 AGAGAAAGGAAAAAAC
1 AGAGAAAGAAAAAAAC
445660 AGAGAAAGAAAAAAA
1 AGAGAAAGAAAAAAA
445675 ACAACAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAAAAAAAC
Found at i:446602 original size:20 final size:21
Alignment explanation
Indices: 446565--446605 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
446555 GATATTTTTA
**
446565 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
446586 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
446606 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:462861 original size:2 final size:2
Alignment explanation
Indices: 462854--462881 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
462844 TAAAATTACT
462854 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
462882 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:464014 original size:26 final size:27
Alignment explanation
Indices: 463931--464019 Score: 94
Period size: 26 Copynumber: 3.4 Consensus size: 27
463921 TATTTCAATT
* *
463931 ATTTTGGAGCTT-GGGATGTTTTGGTC
1 ATTTTGGAGTTTAGGGATATTTTGGTC
*
463957 ATTTTAGAGTTTAGGGATATTTTGGT-
1 ATTTTGGAGTTTAGGGATATTTTGGTC
* * *
463983 AATTTGGATTTTAGGGGTA-TTTGGTC
1 ATTTTGGAGTTTAGGGATATTTTGGTC
*
464009 ATTTTGAAGTT
1 ATTTTGGAGTT
464020 CATGGGTACT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
25 6 0.12
26 33 0.65
27 12 0.24
ACGTcount: A:0.19, C:0.03, G:0.29, T:0.48
Consensus pattern (27 bp):
ATTTTGGAGTTTAGGGATATTTTGGTC
Found at i:465502 original size:2 final size:2
Alignment explanation
Indices: 465495--465532 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
465485 ACATGGTTTG
465495 AT 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 AT
465533 TTCACTGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:478314 original size:21 final size:21
Alignment explanation
Indices: 478290--478329 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
478280 TTTTATTTTA
*
478290 TTTATTTATTTGATAATTATG
1 TTTATTTATTTGACAATTATG
478311 TTTATTTATTTGACAATTA
1 TTTATTTATTTGACAATTA
478330 CAACTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTATTTATTTGACAATTATG
Done.