Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004175.1 Hibiscus syriacus cultivar Beakdansim tig00009130_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: 47930
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:157 original size:18 final size:17
Alignment explanation
Indices: 108--161 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
98 TATTTATGTA
*
108 TATTATATTATT-ATTAT
1 TATTATTTTATTCATT-T
*
125 TATTATCTTTCTTCATTT
1 TATTAT-TTTATTCATTT
143 TATTTATTTTATTCATTT
1 TA-TTATTTTATTCATTT
161 T
1 T
162 TACCTTTACC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 6 0.19
18 18 0.58
19 7 0.23
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATTTTATTCATTT
Found at i:207 original size:24 final size:24
Alignment explanation
Indices: 141--226 Score: 59
Period size: 24 Copynumber: 3.5 Consensus size: 24
131 CTTTCTTCAT
**
141 TTTATTTATTTTATTCA-TTTTTACC
1 TTTATTTATTTT-TT-ATTTTTTTTC
*
166 TTTACCTTTA-TTTGTATTTTTTTTC
1 TTTA--TTTATTTTTTATTTTTTTTC
**
191 TTTATTTATTTTTTATTTACTTTC
1 TTTATTTATTTTTTATTTTTTTTC
*
215 TTCATTTCATTT
1 TTTATTT-ATTT
227 GTTTGTGTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
23 4 0.08
24 19 0.39
25 19 0.39
26 3 0.06
27 4 0.08
ACGTcount: A:0.16, C:0.12, G:0.01, T:0.71
Consensus pattern (24 bp):
TTTATTTATTTTTTATTTTTTTTC
Found at i:2762 original size:23 final size:22
Alignment explanation
Indices: 2719--2763 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2709 GAAGCTCACA
*
2719 GCCTGATAAAAAAGTTTGAGGG
1 GCCTGATAAAAAAGTTGGAGGG
* *
2741 GCCTGATGAAAATGCTTGGAGGG
1 GCCTGATAAAAAAG-TTGGAGGG
2764 AACAGCTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.31, C:0.11, G:0.36, T:0.22
Consensus pattern (22 bp):
GCCTGATAAAAAAGTTGGAGGG
Found at i:10445 original size:7 final size:7
Alignment explanation
Indices: 10429--10472 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
10419 CCCTAAATTG
10429 AAAA-AA
1 AAAAGAA
10435 AAAAGAA
1 AAAAGAA
10442 AAAAGAA
1 AAAAGAA
10449 CAAAAG-A
1 -AAAAGAA
*
10456 AAAAGAG
1 AAAAGAA
10463 AAAAGAA
1 AAAAGAA
10470 AAA
1 AAA
10473 TAAGGTGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
6 9 0.27
7 19 0.58
8 5 0.15
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:10458 original size:21 final size:21
Alignment explanation
Indices: 10429--10469 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10419 CCCTAAATTG
10429 AAAAAAAAAAGAAAAAAGAAC
1 AAAAAAAAAAGAAAAAAGAAC
* *
10450 AAAAGAAAAAGAGAAAAGAA
1 AAAAAAAAAAGAAAAAAGAA
10470 AAATAAGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAGAAAAAAGAAC
Found at i:13458 original size:21 final size:21
Alignment explanation
Indices: 13434--13475 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13424 TATGAGAAAT
*
13434 TATTTTAAAATAT-AAAAATGA
1 TATTTCAAAAT-TGAAAAATGA
13455 TATTTCAAAATTGAAAAATGA
1 TATTTCAAAATTGAAAAATGA
13476 AAACAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (21 bp):
TATTTCAAAATTGAAAAATGA
Found at i:21101 original size:9 final size:9
Alignment explanation
Indices: 21087--21111 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21077 TCCCCTTTAA
21087 AACATTTTT
1 AACATTTTT
21096 AACATTTTT
1 AACATTTTT
21105 AACATTT
1 AACATTT
21112 CTCCCCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (9 bp):
AACATTTTT
Found at i:23383 original size:23 final size:23
Alignment explanation
Indices: 23329--23389 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
23319 TCCCTACATA
* *
23329 GGGGAATCAGTTCCCTTTCAAAG
1 GGGGAATCGGTTCCCATTCAAAG
*
23352 GGGGAATCGGTTCCCATTCAAGG
1 GGGGAATCGGTTCCCATTCAAAG
* *
23375 GGGGTATCGATTCCC
1 GGGGAATCGGTTCCC
23390 TCTACACTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (23 bp):
GGGGAATCGGTTCCCATTCAAAG
Found at i:38388 original size:3 final size:3
Alignment explanation
Indices: 38380--38404 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38370 GAATTGGGTT
38380 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
38405 ATAAATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:40921 original size:10 final size:10
Alignment explanation
Indices: 40906--40934 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
40896 TTAACCTAAA
40906 AGTAAACCTT
1 AGTAAACCTT
40916 AGTAAACCTT
1 AGTAAACCTT
40926 AGTAAACCT
1 AGTAAACCT
40935 ACGAATAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (10 bp):
AGTAAACCTT
Found at i:42909 original size:19 final size:17
Alignment explanation
Indices: 42865--42909 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
42855 TTATTTATTA
42865 TTTTTTC-TTT-TTCTT
1 TTTTTTCTTTTCTTCTT
42880 TTTTTTCTTTTCTTCTAT
1 TTTTTTCTTTTCTTCT-T
42898 TTTTTTCATTTT
1 TTTTTTC-TTTT
42910 TTGTCTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.27
16 3 0.12
17 4 0.15
18 8 0.31
19 4 0.15
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCTTTTCTTCTT
Found at i:43019 original size:44 final size:44
Alignment explanation
Indices: 42940--43374 Score: 494
Period size: 44 Copynumber: 9.9 Consensus size: 44
42930 AAGGTTATCA
* * * * *
42940 ATGTTGTTTCAACTCTTTATGTGATGAAAACGAGCAAAATGTTG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
* * * *
42984 ATGCTGGTCCAGCTCCTTATGTGATGAAATCGAGCAAAATG-TG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
* * * * *
43027 ATGTTAATCTAACTCCTTATGTGATGGAATCAAACGAAATGTTG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
43071 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
*
43115 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGATG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
* * ** *
43159 ATGTTGATCCAACTCCTCATGTGATGGAATTGAGTGAAATGGTG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
* * * **
43203 ATGTTGATCTAACTCCTCATGTGATGGAATTGAGTGAAATGTTG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
* * *
43247 ATGCTGATCTAACTCATTATGTGATGGAATCGAGCAAAATGTTG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
* * * * * *
43291 GTGCTAATCCAACTCTTTATGTGATAGAATCGAGCGAAATGTTG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
*** * * * *
43335 ATGCCAATCCAACTCTTTATGTGATAGAATCAAGCGAAAT
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAAT
43375 TAAATTCTGT
Statistics
Matches: 347, Mismatches: 43, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
43 34 0.10
44 313 0.90
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (44 bp):
ATGTTGATCCAACTCCTTATGTGATGGAATCGAGCAAAATGTTG
Done.