Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006385.1 Hibiscus syriacus cultivar Beakdansim tig00015374_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: 216924
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 2 of 2
Found at i:209728 original size:32 final size:33
Alignment explanation
Indices: 209662--209774 Score: 185
Period size: 32 Copynumber: 3.5 Consensus size: 33
209652 TCTTTTGGTT
209662 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
209695 GAGATGACAATCACAACGAGAGAA-CGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
209727 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
209760 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
209775 TGCGATTTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
32 38 0.52
33 35 0.48
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:209810 original size:14 final size:14
Alignment explanation
Indices: 209791--209843 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
209781 TTTGGTTTCG
209791 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
209805 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
209822 CGCGTGCGATTCTCT
1 CG-TTGCGATTCTCT
209837 CGTTGCG
1 CGTTGCG
209844 CTTTTCATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 12 0.39
15 4 0.13
16 6 0.19
17 4 0.13
18 5 0.16
ACGTcount: A:0.08, C:0.26, G:0.25, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:209835 original size:32 final size:33
Alignment explanation
Indices: 209775--209854 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 33
209765 GAAATCGCAA
**
209775 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
209808 TGCGATTTTCATTTCGCG-TGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
209840 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
209855 TCTCGTTGCG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 28 0.64
33 16 0.36
ACGTcount: A:0.07, C:0.24, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:209890 original size:41 final size:41
Alignment explanation
Indices: 209830--209907 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
209820 TTCGCGTGCG
* *
209830 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
209871 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
209908 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:209906 original size:21 final size:21
Alignment explanation
Indices: 209831--209906 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
209821 TCGCGTGCGA
*
209831 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
209852 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
209872 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
209893 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
209907 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:210033 original size:33 final size:33
Alignment explanation
Indices: 209986--210056 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
209976 AATACTAACT
* *
209986 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
210019 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
210052 TGAAA
1 TGAAA
210057 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:210461 original size:20 final size:20
Alignment explanation
Indices: 210436--210628 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
210426 CTTTAAATAT
210436 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
210456 CGCGTTGCGATTTATGTATTA
1 CGCGTTGCGATTTACGGA-TA
*
210477 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
210496 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
210516 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
210536 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
210556 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
210576 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
210596 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
210616 CGCGTTGCGATTT
1 CGCGTTGCGATTT
210629 TCATATTCGC
Statistics
Matches: 147, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 142 0.97
21 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:210512 original size:60 final size:60
Alignment explanation
Indices: 210436--210646 Score: 253
Period size: 60 Copynumber: 3.5 Consensus size: 60
210426 CTTTAAATAT
*
210436 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
* * ***
210496 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCA-TACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTA-GCGTTGCGATTTACGGATA
* * * * ** *
210556 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
* ** *
210616 CGCGTTGCGATTTTCATATTCGCGTTGCGAT
1 CGCGTTGCGATTTACGGATACGCGTTGCGAT
210647 GGAAAATCGC
Statistics
Matches: 126, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
59 2 0.02
60 123 0.98
61 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
Found at i:210629 original size:20 final size:20
Alignment explanation
Indices: 210576--210646 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
210566 TTTACGGATA
* *
210576 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
210596 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
210616 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
210636 CGCGTTGCGAT
1 CGCGTTGCGAT
210647 GGAAAATCGC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 1 0.02
20 47 0.98
ACGTcount: A:0.13, C:0.20, G:0.25, T:0.42
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:214544 original size:14 final size:14
Alignment explanation
Indices: 214527--214563 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
214517 TAAATACGAA
214527 TAATTAATTTAATT
1 TAATTAATTTAATT
*
214541 TAATTAATTTGATT
1 TAATTAATTTAATT
*
214555 TAATCAATT
1 TAATTAATT
214564 ATTTAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (14 bp):
TAATTAATTTAATT
Done.