Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001856.1 Hibiscus syriacus cultivar Beakdansim tig00003757_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: 42595
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:1600 original size:22 final size:24
Alignment explanation
Indices: 1564--1609 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1554 TCTCCATCAC
*
1564 CTTCATTCTATTTCCATTACCATA
1 CTTCATTCTATTTCCATTAACATA
*
1588 CTTCA-TC-ATTTCCTTTAACATA
1 CTTCATTCTATTTCCATTAACATA
1610 TTACCAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 2 0.10
24 5 0.25
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (24 bp):
CTTCATTCTATTTCCATTAACATA
Found at i:6272 original size:26 final size:28
Alignment explanation
Indices: 6234--6285 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
6224 GAAATATGAA
6234 ATAAGAAATGGAAAGATGG-AATGAAATG
1 ATAAGAAATGGAAA-ATGGAAATGAAATG
6262 ATAAG-AA-GGAAAATGGAAATGAAA
1 ATAAGAAATGGAAAATGGAAATGAAA
6286 GAAATGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.17
26 12 0.52
27 2 0.09
28 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (28 bp):
ATAAGAAATGGAAAATGGAAATGAAATG
Found at i:6480 original size:13 final size:13
Alignment explanation
Indices: 6462--6486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6452 ATAGGTGTGA
6462 ATAGTGATGGAAT
1 ATAGTGATGGAAT
6475 ATAGTGATGGAA
1 ATAGTGATGGAA
6487 AGATATTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (13 bp):
ATAGTGATGGAAT
Found at i:22103 original size:12 final size:11
Alignment explanation
Indices: 22085--22115 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
22075 AAAAAAAAAG
22085 AAGAAAAGCAA
1 AAGAAAAGCAA
22096 AAGCAAAAGCAA
1 AAG-AAAAGCAA
22108 AAGAAAAG
1 AAGAAAAG
22116 TGAAGCAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.71, C:0.10, G:0.19, T:0.00
Consensus pattern (11 bp):
AAGAAAAGCAA
Found at i:28999 original size:15 final size:15
Alignment explanation
Indices: 28963--28992 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28953 GTGCTTCAAC
28963 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
28977 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
28992 T
1 T
28993 CTTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:29015 original size:27 final size:28
Alignment explanation
Indices: 28985--29046 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
28975 CTTTTCTTTG
* *
28985 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTTGGAATGCTTCAATTT
*
29012 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGCTTCAATTT
29040 CTTTTCT
1 CTTTTCT
29047 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 8 0.28
29 4 0.14
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAATGCTTCAATTT
Found at i:38137 original size:17 final size:16
Alignment explanation
Indices: 38096--38167 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 16
38086 ATTCATGCAT
38096 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
*
38113 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
*
38131 CTAGTTCATTTATCAAA
1 CTAGTTCATTAAT-AAA
*
38148 CTAGTTGATTTAATAAA
1 CTAGTTCA-TTAATAAA
38165 CTA
1 CTA
38168 ACCCTTAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.02
17 28 0.61
18 17 0.37
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:40196 original size:17 final size:16
Alignment explanation
Indices: 40127--40198 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 16
40117 ATTCATGCAT
40127 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
*
40144 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
* *
40162 GTAGTTCATTCATCAAA
1 CTAGTTCATTAAT-AAA
40179 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
40196 CTA
1 CTA
40199 ACTCTTAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.02
17 28 0.61
18 17 0.37
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:41726 original size:17 final size:18
Alignment explanation
Indices: 41701--41734 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41691 GGTTAGTAAG
41701 AAAGAAAAAAA-GAAAAA
1 AAAGAAAAAAAGGAAAAA
*
41718 AAAGGAAAAAAGGAAAA
1 AAAGAAAAAAAGGAAAA
41735 TTTAAAGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAGGAAAAA
Done.