Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007777.1 Hibiscus syriacus cultivar Beakdansim tig00110059_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: 1720799
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1712267 original size:2 final size:2
Alignment explanation
Indices: 1712214--1712248 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1712204 CTGGGTTTTG
1712214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1712249 TGAATTTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1714758 original size:20 final size:20
Alignment explanation
Indices: 1714744--1714781 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1714734 TATACCAGTG
*
1714744 TTTTGGTATGGATACCAATA
1 TTTTGGTATCGATACCAATA
1714764 TTTTGGTATCGATACCAA
1 TTTTGGTATCGATACCAA
1714782 AACATCTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (20 bp):
TTTTGGTATCGATACCAATA
Found at i:1715032 original size:40 final size:40
Alignment explanation
Indices: 1714956--1715032 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
1714946 GCAAAGCAAG
* **
1714956 TACTGATAATGTTCTTACAGTATCGATACCGTATAAACAA
1 TACTAATAATGTTCTTACAGTATCGATACCAAATAAACAA
* * *
1714996 TACTAATATTGTTCTTGCAGTATTGATACCAAATAAA
1 TACTAATAATGTTCTTACAGTATCGATACCAAATAAA
1715033 AGTACACGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (40 bp):
TACTAATAATGTTCTTACAGTATCGATACCAAATAAACAA
Found at i:1718373 original size:66 final size:65
Alignment explanation
Indices: 1718302--1718504 Score: 166
Period size: 66 Copynumber: 3.1 Consensus size: 65
1718292 TATTTTTTAT
* *
1718302 AATTTTTTTACTGTGACTAAATAATTTTGTAACAATTTGTTATTGTGAAAGAATATTAATTGTCA
1 AATTTTTTTAATGTGAC-AAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTAATTGTCA
1718367 C
65 C
* * * * * * * *
1718368 AATTTTTTATAATGAGA-AATTAATATTTGTTATAAATTATTATTTTGATTA-AATA--AATTTA
1 AATTTTTT-TAATGTGACAAATAAT-TTTGTTACAATTTGTTATTGTGA-AAGAATATTAA-TTG
1718429 TCAC
62 TCAC
* * * * *
1718433 TA-TTTTTTAATTTGACAAA-ATATTGTGTTGCAATTTGTTATTGTGAAAGAATATTACTTGTCA
1 AATTTTTTTAATGTGACAAATA-ATTTTGTTACAATTTGTTATTGTGAAAGAATATTAATTGTCA
*
1718496 T
65 C
1718497 AATTTTTT
1 AATTTTTT
1718505 ATGATTAGAA
Statistics
Matches: 102, Mismatches: 25, Indels: 21
0.69 0.17 0.14
Matches are distributed among these distances:
62 1 0.01
63 28 0.27
64 17 0.17
65 19 0.19
66 30 0.29
67 7 0.07
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.49
Consensus pattern (65 bp):
AATTTTTTTAATGTGACAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTAATTGTCAC
Found at i:1718470 original size:129 final size:129
Alignment explanation
Indices: 1718334--1718582 Score: 401
Period size: 129 Copynumber: 1.9 Consensus size: 129
1718324 AATTTTGTAA
1718334 CAATTTGTTATTGTGAAAGAATATTAATTGTCACAATTTTTTATAATGAGAAATTAATATTTGTT
1 CAATTTGTTATTGTGAAAGAATATTAATTGTCACAATTTTTTATAATGAGAAATTAATATTTGTT
* *
1718399 ATAAATTATTATTTTGATTAAATAAATTTATCACT-ATTTTTTAATTTGACAAAATATTGTGTTG
66 ATAAATTATTATTTTGATTAAATAAATTTAT-AATAAATTTTTAATTTGACAAAATATTGTGTTG
* * * * *
1718463 CAATTTGTTATTGTGAAAGAATATTACTTGTCATAATTTTTTATGATTAGAAATTAATATTTTTT
1 CAATTTGTTATTGTGAAAGAATATTAATTGTCACAATTTTTTATAATGAGAAATTAATATTTGTT
* *
1718528 ATAAATTATTATTTTGATTAAATAAATTTGTAATAAATTTTTATTTTGACAAAAT
66 ATAAATTATTATTTTGATTAAATAAATTTATAATAAATTTTTAATTTGACAAAAT
1718583 TTTTGTAAAT
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
128 2 0.02
129 108 0.98
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (129 bp):
CAATTTGTTATTGTGAAAGAATATTAATTGTCACAATTTTTTATAATGAGAAATTAATATTTGTT
ATAAATTATTATTTTGATTAAATAAATTTATAATAAATTTTTAATTTGACAAAATATTGTGTTG
Found at i:1718567 original size:66 final size:64
Alignment explanation
Indices: 1718368--1718571 Score: 175
Period size: 65 Copynumber: 3.2 Consensus size: 64
1718358 TAATTGTCAC
* * *
1718368 AATTTTTTATAATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTATCAC
1 AATTTTTTAT-ATTAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGT-AA
1718433 T
64 T
* ** * * * * * *
1718434 -ATTTTTTA-ATTTGACAA--AATATTGTGTTGCAATTTGTTATTGTGA-AAGAATATTACTTGT
1 AATTTTTTATATTAGA-AATTAATATT-TGTTATAAATTATTATTTTGATTA-AATA-AATTTGT
*
1718494 CAT
62 AAT
*
1718497 AATTTTTTATGATTAGAAATTAATATTTTTTATAAATTATTATTTTGATTAAATAAATTTGTAAT
1 AATTTTTTAT-ATTAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTAAT
*
1718562 AAATTTTTAT
1 AATTTTTTAT
1718572 TTTGACAAAA
Statistics
Matches: 103, Mismatches: 25, Indels: 21
0.69 0.17 0.14
Matches are distributed among these distances:
62 7 0.07
63 25 0.24
64 14 0.14
65 26 0.25
66 24 0.23
67 7 0.07
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (64 bp):
AATTTTTTATATTAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTAAT
Done.