Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005674.1 Hibiscus syriacus cultivar Beakdansim tig00013268_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: 52064
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12962 original size:23 final size:24
Alignment explanation
Indices: 12913--12965 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
12903 TTCTTTGCTT
* *
12913 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
12936 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
12959 TTTCTTT
1 TTTCTTT
12966 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:14494 original size:18 final size:18
Alignment explanation
Indices: 14471--14514 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
14461 GTCTCCTTCA
14471 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
*
14489 AGCTAGCTTGAGTTTTGG
1 AGCTAGCTTGAGTTGTGG
14507 AGCTAGCT
1 AGCTAGCT
14515 AGAAAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.34
Consensus pattern (18 bp):
AGCTAGCTTGAGTTGTGG
Found at i:15627 original size:13 final size:12
Alignment explanation
Indices: 15593--15634 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
15583 TTGCAATTCC
*
15593 TTTATCTT-TTC
1 TTTATCTTATTT
15604 TTTATCTT-TTT
1 TTTATCTTATTT
*
15615 TTAATCTTATTT
1 TTTATCTTATTT
15627 TTTATCTT
1 TTTATCTT
15635 GTTTCGAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATCTTATTT
Found at i:21444 original size:15 final size:15
Alignment explanation
Indices: 21407--21447 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
21397 ATTTAAAAAC
21407 AAAAC-AAAAACAAA
1 AAAACAAAAAACAAA
*
21421 AAAGGCAAAAAACAAA
1 AAA-ACAAAAAACAAA
21437 AAAACAAAAAA
1 AAAACAAAAAA
21448 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 3 0.13
15 8 0.35
16 12 0.52
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAACAAA
Found at i:21444 original size:24 final size:25
Alignment explanation
Indices: 21412--21476 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
21402 AAAACAAAAC
21412 AAAAACAAAAAAGGCAAAA-AACAA
1 AAAAACAAAAAAGGCAAAATAACAA
* **
21436 AAAAACAAAAAAGCCAAAATTTCAA
1 AAAAACAAAAAAGGCAAAATAACAA
21461 AAAAA-AAAAAA-GCAAA
1 AAAAACAAAAAAGGCAAA
21477 CGAAAGTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 4 0.11
24 24 0.67
25 8 0.22
ACGTcount: A:0.77, C:0.12, G:0.06, T:0.05
Consensus pattern (25 bp):
AAAAACAAAAAAGGCAAAATAACAA
Found at i:24189 original size:43 final size:43
Alignment explanation
Indices: 24128--24213 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
24118 TTAAGCATGC
*
24128 TACTATTCCATGAATTGAACATATAAAAAATGTATATCACGAT
1 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
24171 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
1 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
24214 AACTCGGATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.31
Consensus pattern (43 bp):
TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
Found at i:26105 original size:10 final size:10
Alignment explanation
Indices: 26072--26096 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
26062 AGCTATTTTT
26072 AAAAAAACAA
1 AAAAAAACAA
26082 AAAAAAACAA
1 AAAAAAACAA
26092 AAAAA
1 AAAAA
26097 GGCAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:26113 original size:16 final size:17
Alignment explanation
Indices: 26083--26133 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
26073 AAAAAACAAA
*
26083 AAAAAACAAAAAAAGGC
1 AAAAAACAAAAAAAGCC
26100 AAAAAAC-AAAAAAGCC
1 AAAAAACAAAAAAAGCC
*
26116 AAAATTAAAAAAAAAAGC
1 AAAA--AACAAAAAAAGC
26134 AAACGAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 12 0.41
17 7 0.24
18 2 0.07
19 8 0.28
ACGTcount: A:0.76, C:0.12, G:0.08, T:0.04
Consensus pattern (17 bp):
AAAAAACAAAAAAAGCC
Found at i:28796 original size:43 final size:43
Alignment explanation
Indices: 28735--28820 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
28725 TTAAGCATGC
28735 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
1 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
28778 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
1 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
28821 AACTCGGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (43 bp):
TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
Found at i:30636 original size:11 final size:11
Alignment explanation
Indices: 30610--30648 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
30600 TGCTGGAAAC
30610 AAGATTAAAAA
1 AAGATTAAAAA
30621 TAAGATTAAAAA
1 -AAGATTAAAAA
30633 AAGA-TAAAGAA
1 AAGATTAAA-AA
30644 AAGAT
1 AAGAT
30649 AAAGGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.16
11 10 0.40
12 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (11 bp):
AAGATTAAAAA
Found at i:38355 original size:11 final size:11
Alignment explanation
Indices: 38329--38367 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
38319 TGCTCGAAAC
38329 AAGATTAAAAA
1 AAGATTAAAAA
38340 TAAGATTAAAAA
1 -AAGATTAAAAA
38352 AAGA-TAAAGAA
1 AAGATTAAA-AA
38363 AAGAT
1 AAGAT
38368 AAAGGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.16
11 10 0.40
12 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (11 bp):
AAGATTAAAAA
Found at i:44292 original size:18 final size:19
Alignment explanation
Indices: 44269--44317 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
44259 AATTTGAATG
44269 CAAAAAGAAAA-AAAAAGA
1 CAAAAAGAAAAGAAAAAGA
**
44287 CAAAAAGAAAAGAAAAATT
1 CAAAAAGAAAAGAAAAAGA
44306 CAAAAGAGAAAA
1 CAAAA-AGAAAA
44318 CAAGCCAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 11 0.41
19 10 0.37
20 6 0.22
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.04
Consensus pattern (19 bp):
CAAAAAGAAAAGAAAAAGA
Found at i:47179 original size:11 final size:11
Alignment explanation
Indices: 47163--47189 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
47153 GATACTATTT
47163 CCATCCATATC
1 CCATCCATATC
47174 CCATCCATATC
1 CCATCCATATC
47185 CCATC
1 CCATC
47190 ACCTTCACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (11 bp):
CCATCCATATC
Found at i:47707 original size:33 final size:32
Alignment explanation
Indices: 47662--47724 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
47652 GCACAAAATT
* *
47662 AGAGAAAGAAATGAATAA-AATGGAATATGGAAG
1 AGAGAAACAAATG-ATAAGAAAGGAA-ATGGAAG
47695 AGAGAAACAAATGATAAGAAAGGAAATGGA
1 AGAGAAACAAATGATAAGAAAGGAAATGGA
47725 TTAAATGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.59, C:0.02, G:0.27, T:0.13
Consensus pattern (32 bp):
AGAGAAACAAATGATAAGAAAGGAAATGGAAG
Done.