Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006028.1 Hibiscus syriacus cultivar Beakdansim tig00014231_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: 182679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:178339 original size:17 final size:17
Alignment explanation
Indices: 178317--178355 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
178307 TGAATCAAAT
178317 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
178334 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
178351 -AATTA
1 TAATTA
178356 ATTATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:180591 original size:139 final size:140
Alignment explanation
Indices: 180340--180608 Score: 513
Period size: 139 Copynumber: 1.9 Consensus size: 140
180330 AAACGTTGTA
180340 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
180405 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
180470 TATGTGTATT
131 TATGTGTATT
*
180480 TTATGTGTAAACTTTTAACATTTTTAGTTAGGCATGTATTAGTAACTTGAG-TTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
180544 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
180609 CGCAACTCAA
Statistics
Matches: 127, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
139 77 0.61
140 50 0.39
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:180604 original size:20 final size:20
Alignment explanation
Indices: 180579--180837 Score: 194
Period size: 20 Copynumber: 13.8 Consensus size: 20
180569 TTACACATTC
*
180579 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
180599 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
180618 A----A-AATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
** *
180633 ATTTGACTATCATAACACGA
1 ATTTGACTATCGCAACGCGA
* *
180653 ATATGACTATCGCAACAC-A
1 ATTTGACTATCGCAACGCGA
*
180672 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
180687 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
**
180707 ATTTTTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
180727 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
*
180747 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
180767 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
180781 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
180801 ATTTGATTATCGCAATGGGT
1 ATTTGACTATCGCAACGCGA
*
180821 ATTTTACTATCGCAACG
1 ATTTGACTATCGCAACG
180838 AGAAAATCGC
Statistics
Matches: 190, Mismatches: 31, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
14 30 0.16
15 6 0.03
16 1 0.01
18 1 0.01
19 5 0.03
20 147 0.77
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:180708 original size:54 final size:54
Alignment explanation
Indices: 180579--180722 Score: 198
Period size: 54 Copynumber: 2.7 Consensus size: 54
180569 TTACACATTC
* *
180579 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTCAAAAATCGCAACACGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACAAAAATCGCAACACGA
** * * *
180633 ATTTGACTATCATAACACGAATATGACTATCGCAACACAAAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACAAAAATCGCAACACGA
* **
180687 ATTTGTCTATCGCAACGCGAATTTTTCTATCGCAAC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAC
180723 GCGAATTTGA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (54 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACACAAAAATCGCAACACGA
Found at i:180773 original size:74 final size:74
Alignment explanation
Indices: 180695--180874 Score: 292
Period size: 74 Copynumber: 2.5 Consensus size: 74
180685 GAATTTGTCT
**
180695 ATCGCAACGCGAATTTTTCTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGC
180760 AACGAGAAA
66 AACGAGAAA
* *
180769 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAATGGGTATTTTACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGC
180834 AACGAGAAA
66 AACGAGAAA
* *
180843 ATCGCAAAGCG--TTAGACTATCGCAACGCGAAT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAAT
180875 GACTTTCGCG
Statistics
Matches: 100, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
72 20 0.20
74 80 0.80
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGC
AACGAGAAA
Found at i:180785 original size:34 final size:34
Alignment explanation
Indices: 180735--180869 Score: 130
Period size: 34 Copynumber: 3.9 Consensus size: 34
180725 GAATTTGATT
*
180735 ATCGCAACGGGTATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCGTATTTGACTATCGCAACGAGAAA
* *
180769 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGA
1 ATCGCAACGCGTATTTGACTATCGCAACGAGAA----A
* * *
180807 TTATCGCAATGGGTATTTTACTATCGCAACGAGAAA
1 --ATCGCAACGCGTATTTGACTATCGCAACGAGAAA
* *
180843 ATCGCAAAGCG--TTAGACTATCGCAACG
1 ATCGCAACGCGTATTTGACTATCGCAACG
180870 CGAATGACTT
Statistics
Matches: 83, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
32 14 0.17
34 39 0.47
36 1 0.01
38 1 0.01
40 28 0.34
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (34 bp):
ATCGCAACGCGTATTTGACTATCGCAACGAGAAA
Found at i:180832 original size:94 final size:94
Alignment explanation
Indices: 180587--180837 Score: 275
Period size: 94 Copynumber: 2.7 Consensus size: 94
180577 TCATTTGAAT
* * * **
180587 ATCGCAACGCGAATTTGACTATCGCAACTC-AA---A--AATCGCAACACGAATTTGACTATCAT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTATCTATCGCAACGCGAATTTGACTATCGC
** * *
180646 AACACGAATATGACTATCGCAACACAAAA
66 AACGGGTATTTGACTATCGCAACACAAAA
* * *
180675 ATCGCAACGCGAATTTGTCTATCGCAACGCGAATTTTTCTATCGCAACGCGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTATCTATCGCAACGCGAATTTGACTATCGC
*
180740 AACGGGTATTTGACTATCGCAACGA-GAAA
66 AACGGGTATTTGACTATCGCAAC-ACAAAA
* * * *
180769 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGAT-TATCGCAATGGGTATTTTACTATCG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTT-ATCTATCGCAACGCGAATTTGACTATCG
180833 CAACG
65 CAACG
180838 AGAAAATCGC
Statistics
Matches: 135, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
88 28 0.21
89 2 0.01
94 103 0.76
95 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTATCTATCGCAACGCGAATTTGACTATCGC
AACGGGTATTTGACTATCGCAACACAAAA
Found at i:180899 original size:20 final size:20
Alignment explanation
Indices: 180874--180913 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
180864 GCAACGCGAA
*
180874 TGACTTTCGCGTTGCGATTT
1 TGACTTTCGCATTGCGATTT
180894 TGACTTTCGCATTGCGATTT
1 TGACTTTCGCATTGCGATTT
180914 GAGTTTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (20 bp):
TGACTTTCGCATTGCGATTT
Found at i:180927 original size:19 final size:20
Alignment explanation
Indices: 180874--180929 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
180864 GCAACGCGAA
* *
180874 TGACTTTCGCGTTGCGATTT
1 TGACTTTAGCATTGCGATTT
*
180894 TGACTTTCGCATTGCGA-TT
1 TGACTTTAGCATTGCGATTT
* *
180913 TGAGTTTAGCTTTGCGA
1 TGACTTTAGCATTGCGA
180930 AAGTGTACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.14, C:0.18, G:0.25, T:0.43
Consensus pattern (20 bp):
TGACTTTAGCATTGCGATTT
Found at i:182529 original size:18 final size:19
Alignment explanation
Indices: 182506--182545 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
182496 CTCTTGAGGG
182506 ATGATA-GAGGCCTCTTGA
1 ATGATAGGAGGCCTCTTGA
182524 ATGATAGGGGAGGCCTCTTGA
1 ATGATA--GGAGGCCTCTTGA
182545 A
1 A
182546 CGATGACAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.25
Consensus pattern (19 bp):
ATGATAGGAGGCCTCTTGA
Done.