Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009011.1 Hibiscus syriacus cultivar Beakdansim tig00112399_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: 579188
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 4 of 4
Found at i:566929 original size:20 final size:19
Alignment explanation
Indices: 566875--566920 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
566865 TCCGGTATCA
566875 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
566894 TGTTACCGGTTTTATCATAT
1 TTTTACCGGTTTTATCAT-T
566914 TTTTACC
1 TTTTACC
566921 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:567067 original size:20 final size:20
Alignment explanation
Indices: 567041--567086 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
567031 CACTTTTAAA
567041 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
567060 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
567081 TTTACC
1 TTTACC
567087 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:568437 original size:20 final size:20
Alignment explanation
Indices: 568412--568452 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
568402 ATAAGAAATA
568412 AGGTCAGACCAGACTTTAAT
1 AGGTCAGACCAGACTTTAAT
* * *
568432 AGGTCAGGCCGGGCTTTAAT
1 AGGTCAGACCAGACTTTAAT
568452 A
1 A
568453 ATTTTTATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
AGGTCAGACCAGACTTTAAT
Found at i:568521 original size:17 final size:17
Alignment explanation
Indices: 568495--568532 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
568485 TTAGGTCTAA
568495 TTTGGCATGTTTAAAAG
1 TTTGGCATGTTTAAAAG
*
568512 TTTGGTATGTTTAAAAG
1 TTTGGCATGTTTAAAAG
568529 TTTG
1 TTTG
568533 TTAACAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTGGCATGTTTAAAAG
Found at i:569506 original size:2 final size:2
Alignment explanation
Indices: 569452--569490 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
569442 TATTTTTTTA
569452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
569491 GGATGGATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:575304 original size:31 final size:31
Alignment explanation
Indices: 575231--575305 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
575221 TCAAAAAACA
* *
575231 TAAGATATGGTAACTTTCGTTTTTATTTAAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
575262 TAAGATATGGTCACTTTCATTTTTATTTAAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
*
575293 TAAGATGTGGTCA
1 TAAGATATGGTCA
575306 TCACGGGTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCATTTTTATTTAAT
Found at i:575492 original size:27 final size:26
Alignment explanation
Indices: 575461--575552 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 26
575451 GAAAAATAAA
575461 AATAAAATATTTTTAAATTAAGTTAATT
1 AATAAAATATTTTT--ATTAAGTTAATT
* *
575489 -ATAAAATATATTTAGTAAGTTAATAT
1 AATAAAATATTTTTATTAAGTTAAT-T
*
575515 AAAAAAATATTTTT-TTAAGTTAATTT
1 AATAAAATATTTTTATTAAGTTAA-TT
575541 ATATAAAATATT
1 A-ATAAAATATT
575553 ATGAATTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 10 0.19
26 11 0.20
27 33 0.61
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
AATAAAATATTTTTATTAAGTTAATT
Found at i:575519 original size:25 final size:25
Alignment explanation
Indices: 575479--575552 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
575469 ATTTTTAAAT
*
575479 TAAGTTAATTATAAAATATATTTAG
1 TAAGTTAATTATAAAAAATATTTAG
**
575504 TAAGTTAA-TATAAAAAAATATTTTTT
1 TAAGTTAATTAT-AAAAAATA-TTTAG
*
575530 TAAGTTAATTTATATAAAATATT
1 TAAGTTAA-TTATAAAAAATATT
575553 ATGAATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 3 0.07
25 15 0.37
26 13 0.32
27 7 0.17
28 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (25 bp):
TAAGTTAATTATAAAAAATATTTAG
Done.