Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003939.1 Hibiscus syriacus cultivar Beakdansim tig00008512_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: 32473
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7459 original size:7 final size:7
Alignment explanation
Indices: 7447--7473 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
7437 TTACTTTAAG
7447 CATGTGT
1 CATGTGT
7454 CATGTGT
1 CATGTGT
7461 CATGTGT
1 CATGTGT
7468 CATGTG
1 CATGTG
7474 ACATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.41
Consensus pattern (7 bp):
CATGTGT
Found at i:8475 original size:44 final size:44
Alignment explanation
Indices: 8425--8569 Score: 152
Period size: 43 Copynumber: 3.3 Consensus size: 44
8415 CTTTAGGCGG
* *
8425 CGTTTTTTGTATAAGTGTCACAATATGTTATGATATTTAGCAG-
1 CGTTTTTTGTATAAATGTCACAAAATGTTATGATATTTAGCAGA
* * * * * *
8468 TGTTTTTTTGCATAAACGCCACAACATGTTATGATATTTAG-TGA
1 CG-TTTTTTGTATAAATGTCACAAAATGTTATGATATTTAGCAGA
* *
8512 CGTTTTTTGTATAAATGTCACAAAAGGTTATGATATTTAGC-GG
1 CGTTTTTTGTATAAATGTCACAAAATGTTATGATATTTAGCAGA
* *
8555 CATTTTTTATATAAA
1 CGTTTTTTGTATAAA
8570 CGCCTCAAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
43 49 0.59
44 34 0.41
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (44 bp):
CGTTTTTTGTATAAATGTCACAAAATGTTATGATATTTAGCAGA
Found at i:8836 original size:26 final size:27
Alignment explanation
Indices: 8777--8838 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
8767 CAAGTAATGG
8777 AGTTCAACATTAAGTCAAATGTAATAT
1 AGTTCAACATTAAGTCAAATGTAATAT
* *
8804 AGTTCAACATTAAGTGAATTGT-ATAT
1 AGTTCAACATTAAGTCAAATGTAATAT
8830 AGTTCAACA
1 AGTTCAACA
8839 GTATAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
26 13 0.39
27 20 0.61
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (27 bp):
AGTTCAACATTAAGTCAAATGTAATAT
Found at i:9013 original size:21 final size:21
Alignment explanation
Indices: 8967--9013 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
8957 CTGATATGTT
*
8967 GCTTCTCTCTCTACTTCTTTC
1 GCTTCTCTCTCTACTTCTATC
* *
8988 ACTTCTCGT-TCTGCTTCTATC
1 GCTTCTC-TCTCTACTTCTATC
9009 GCTTC
1 GCTTC
9014 AGCTTCGTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.06, C:0.36, G:0.09, T:0.49
Consensus pattern (21 bp):
GCTTCTCTCTCTACTTCTATC
Found at i:13405 original size:26 final size:26
Alignment explanation
Indices: 13376--13425 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
13366 TGCACAGATT
13376 ACTTCAGCCTCATTATAAGGTTTGAC
1 ACTTCAGCCTCATTATAAGGTTTGAC
*
13402 ACTTCAGCCTCATTATATGGTTTG
1 ACTTCAGCCTCATTATAAGGTTTG
13426 GCCAAGGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (26 bp):
ACTTCAGCCTCATTATAAGGTTTGAC
Found at i:17975 original size:77 final size:77
Alignment explanation
Indices: 17775--17983 Score: 264
Period size: 76 Copynumber: 2.8 Consensus size: 77
17765 GACCGTTGAA
* * *
17775 CAGGGGGGAATCGGTACC-CCT-TGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCAG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAG
**
17838 AACAAAAATGTT
66 AACAAAAACATT
* *
17850 TAGGGGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCG
1 CA-GGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCA
* * *
17913 GAGCCAAACCATT
65 GAACAAAAACATT
* * *
17926 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCAGTTCCCTCTGAGCAATCTGGAA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
17984 TTTTTGGCTT
Statistics
Matches: 115, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
75 23 0.20
76 59 0.51
77 32 0.28
78 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.22
Consensus pattern (77 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAG
AACAAAAACATT
Found at i:20601 original size:20 final size:20
Alignment explanation
Indices: 20576--20614 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20566 CAGAACCCCA
*
20576 TGGGGGTATCGATTCCCCTG
1 TGGGGGAATCGATTCCCCTG
*
20596 TGGGGGAATCGGTTCCCCT
1 TGGGGGAATCGATTCCCCT
20615 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.26, G:0.36, T:0.28
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCTG
Found at i:20643 original size:19 final size:20
Alignment explanation
Indices: 20597--20656 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
20587 ATTCCCCTGT
20597 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
20620 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
20639 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
20657 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:26511 original size:55 final size:55
Alignment explanation
Indices: 26398--26523 Score: 173
Period size: 55 Copynumber: 2.3 Consensus size: 55
26388 GGTACCCCTT
* ** *
26398 GGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAATGTTTA
1 GGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCA
* * * *
26453 GGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCAAACCATTCA
1 GGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCA
26508 -GGGGGGAATCGGTTCC
1 GGGGGGGAATCGGTTCC
26524 TCCTATGGGG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 16 0.25
55 47 0.75
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.21
Consensus pattern (55 bp):
GGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAAAAACATTCA
Done.