Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003268.1 Hibiscus syriacus cultivar Beakdansim tig00006868_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: 150736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:128678 original size:33 final size:33
Alignment explanation
Indices: 128630--128700 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
128620 AAAATCGCAA
**
128630 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
128663 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
128696 TGCGA
1 TGCGA
128701 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:128708 original size:33 final size:33
Alignment explanation
Indices: 128641--128722 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
128631 GCGATTTTGG
***
128641 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
128674 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
128707 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
128723 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:128727 original size:20 final size:20
Alignment explanation
Indices: 128653--128741 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
128643 TCGCGTTGCG
128653 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
128673 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
128686 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
128706 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
128726 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
128742 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:128863 original size:33 final size:33
Alignment explanation
Indices: 128821--128891 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
128811 AATACTAACT
*
128821 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
128854 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
128887 TGAAA
1 TGAAA
128892 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:129125 original size:22 final size:22
Alignment explanation
Indices: 129073--129127 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
129063 TGGTTGTGAG
**
129073 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
129095 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
129117 GGATTTCTTCG
1 GGATTTCTTCG
129128 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:129298 original size:20 final size:20
Alignment explanation
Indices: 129273--129445 Score: 179
Period size: 20 Copynumber: 8.6 Consensus size: 20
129263 CTTTAAATAT
129273 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
129293 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
129315 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
129334 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
129354 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
129374 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
129394 CACGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
129414 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
129434 CGCGTTGCGATT
1 CGCGTTGCGATT
129446 ATGGAAAATC
Statistics
Matches: 126, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.02
20 107 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:129526 original size:20 final size:20
Alignment explanation
Indices: 129501--129552 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
129491 AAGAATCGCG
*
129501 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
129521 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
129541 TTGCGATTCTGG
1 TTGCGATTCTGG
129553 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:130600 original size:17 final size:17
Alignment explanation
Indices: 130578--130617 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
130568 AGGGGGTGAT
*
130578 TATTCGATCGATGATTA
1 TATTCGATCGATGAGTA
130595 TATTCGATCGATGAGTA
1 TATTCGATCGATGAGTA
130612 TATTCG
1 TATTCG
130618 TTTTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (17 bp):
TATTCGATCGATGAGTA
Found at i:139083 original size:29 final size:29
Alignment explanation
Indices: 139050--139108 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
139040 CTTCACTGAT
139050 TCCTATCTTTTTCCTGCTTTCAATGCTAC
1 TCCTATCTTTTTCCTGCTTTCAATGCTAC
139079 TCCTATCTTTTTCCTGCTTTCAATGCTAC
1 TCCTATCTTTTTCCTGCTTTCAATGCTAC
139108 T
1 T
139109 ATAATTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.49
Consensus pattern (29 bp):
TCCTATCTTTTTCCTGCTTTCAATGCTAC
Found at i:143678 original size:2 final size:2
Alignment explanation
Indices: 143671--143714 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
143661 CACTTGACCG
143671 AT AT 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 AT AT
143713 AT
1 AT
143715 TATTTTTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.