Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006153.1 Hibiscus syriacus cultivar Beakdansim tig00014619_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: 53125
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:89 original size:19 final size:17
Alignment explanation
Indices: 57--91 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
47 GGCAAAAATA
57 TGAAATGAAAATATTAC
1 TGAAATGAAAATATTAC
74 TGAATATGAGAAATATTA
1 TGAA-ATGA-AAATATTA
92 AAATAAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.31
Consensus pattern (17 bp):
TGAAATGAAAATATTAC
Found at i:6558 original size:20 final size:20
Alignment explanation
Indices: 6535--6577 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6525 AATCCACCAC
*
6535 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
6555 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
6575 ATG
1 ATG
6578 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:25758 original size:20 final size:21
Alignment explanation
Indices: 25706--25766 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
25696 TTCCCCTGTG
25706 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
**
25729 GGGGGAATCGGTTCCCTCATT
1 GGGGGAATCGGTTCCCTCAAA
*
25750 GGGGG-ATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
25767 TGCACAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.31
21 8 0.23
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:32674 original size:16 final size:16
Alignment explanation
Indices: 32653--32684 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
32643 CATACTTCTT
32653 CAAGGGGTATCGATAC
1 CAAGGGGTATCGATAC
*
32669 CAAGGGGTATTGATAC
1 CAAGGGGTATCGATAC
32685 TATTCGAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (16 bp):
CAAGGGGTATCGATAC
Found at i:37326 original size:83 final size:83
Alignment explanation
Indices: 37225--37553 Score: 552
Period size: 83 Copynumber: 4.0 Consensus size: 83
37215 GGAAATATAT
* *
37225 GTTTAATA-TTTAAATTTAAAAGGTATTATTATCTTTTTAAATTTAGATATTAAAAGAGTTTTGG
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTTGG
* **
37289 TTTGAGTAAAACTCTCGG
66 TTGGAGTAAAACTCTCAA
*
37307 GTTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTTGG
37372 TTGGAGTAAAACTCTCAA
66 TTGGAGTAAAACTCTCAA
* *
37390 GTTTAATATTTTAAATTTAAAAGATATTTTTATCTGTTTAAATTTAGACATTAAAAGAGTTTTGG
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTTGG
*
37455 TTGGAGTAAAACTCTCAT
66 TTGGAGTAAAACTCTCAA
*
37473 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTTAG
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTTGG
*
37538 TTGTAGTAAAACTCTC
66 TTGGAGTAAAACTCTC
37554 TCGAAATTTC
Statistics
Matches: 233, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
82 8 0.03
83 225 0.97
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (83 bp):
GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAGAGTTTTGG
TTGGAGTAAAACTCTCAA
Found at i:38461 original size:20 final size:20
Alignment explanation
Indices: 38436--38479 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
38426 TACTAATTTG
38436 TTTCTTAGTACCAGAGTTTA
1 TTTCTTAGTACCAGAGTTTA
*
38456 TTTCTTGGTACCAGAGTTTA
1 TTTCTTAGTACCAGAGTTTA
38476 TTTC
1 TTTC
38480 GGGTTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (20 bp):
TTTCTTAGTACCAGAGTTTA
Found at i:47186 original size:81 final size:81
Alignment explanation
Indices: 46941--47513 Score: 828
Period size: 81 Copynumber: 7.1 Consensus size: 81
46931 AAACATTTAG
* * *
46941 TCTTTTAC-CAAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATG
1 TCTTTTACTC-AAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATG
* *
47005 CACACCTAGGCATTTAA
65 CACAGCTAGGCAATTAA
* ** * * * *
47022 TCTTTAACTCAAATCCATTTAGCCTTTCATCTAACT-GCATGATTGACACCTTTCTGCCAACTGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
47086 ACAGCTAGGAAATTAA
66 ACAGCTAGGCAATTAA
*
47102 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGAAACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
47167 ACAGCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
*
47183 TCTTTTACTCAAAGGCATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
47248 ATAGCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* *
47264 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
47329 ACAGCTAGGTAATTAA
66 ACAGCTAGGCAATTAA
** * * * * * *
47345 TCTTTTACTCAAAGATATTTAGCTTTTCATCTAACTGGCATGATTAACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
47410 ACAGCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* * *
47426 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATTATTGACACCTTTCT-TCCAAATG
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGT-CAAATG
*
47490 CACAACTAGGCAATTAA
65 CACAGCTAGGCAATTAA
47507 TCTTTTA
1 TCTTTTA
47514 TTTAAAACAG
Statistics
Matches: 447, Mismatches: 42, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
80 71 0.16
81 375 0.84
82 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCAATTAA
Found at i:50661 original size:83 final size:83
Alignment explanation
Indices: 50517--50714 Score: 328
Period size: 83 Copynumber: 2.4 Consensus size: 83
50507 GGGGTATTGC
*
50517 ATTAAAAGAGTTTTGGTTGGAGTAAAGCTCTCAGGTTTAATATTTTAAATCTTAAAAATATTATT
1 ATTAAAAGAGTTTTGGTTGGAGTAAAACTCTCAGGTTTAATATTTTAAATCTTAAAAATATTATT
* *
50582 ATCTTTTTAAATTTAGAT
66 ATATGTTTAAATTTAGAT
50600 ATTAAAAGAGTTTTGGTTGGAGTAAAACTCTC-GAGTTTAATATTTTAAAT-TTAAAAGATATTA
1 ATTAAAAGAGTTTTGGTTGGAGTAAAACTCTCAG-GTTTAATATTTTAAATCTTAAAA-ATATTA
50663 TTATATGTTTAAATTTAGAT
64 TTATATGTTTAAATTTAGAT
*
50683 ATTAAAAGAGTTTTAGTTGGAGTAAAACTCTC
1 ATTAAAAGAGTTTTGGTTGGAGTAAAACTCTC
50715 TCGAAATTCC
Statistics
Matches: 109, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
82 7 0.06
83 102 0.94
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (83 bp):
ATTAAAAGAGTTTTGGTTGGAGTAAAACTCTCAGGTTTAATATTTTAAATCTTAAAAATATTATT
ATATGTTTAAATTTAGAT
Found at i:50827 original size:22 final size:21
Alignment explanation
Indices: 50777--50827 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
50767 ATTCAAGTAG
*
50777 TTTTCTTCTCTAAAAATATTT
1 TTTTCTTCTCCAAAAATATTT
50798 TCTCTTCTTC-CCAAAAATATGTAT
1 T-T-TTCTTCTCCAAAAATAT-T-T
50822 TTTTCT
1 TTTTCT
50828 CCCTTAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 14 0.56
23 8 0.32
24 2 0.08
ACGTcount: A:0.25, C:0.20, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTCTTCTCCAAAAATATTT
Done.