Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005829.1 Hibiscus syriacus cultivar Beakdansim tig00013667_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: 70862
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:7527 original size:16 final size:16
Alignment explanation
Indices: 7506--7538 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
7496 GCCACAGTAA
7506 AATAATTCTGACCATC
1 AATAATTCTGACCATC
7522 AATAATTCTGACCATC
1 AATAATTCTGACCATC
7538 A
1 A
7539 GCATAGTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.30
Consensus pattern (16 bp):
AATAATTCTGACCATC
Found at i:7669 original size:21 final size:21
Alignment explanation
Indices: 7640--7683 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7630 TTATCATTGC
7640 AAGAATTCATGGCCTCGACAA
1 AAGAATTCATGGCCTCGACAA
* * *
7661 AAGATTTCATGGCGTCTACAA
1 AAGAATTCATGGCCTCGACAA
7682 AA
1 AA
7684 AACCTTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (21 bp):
AAGAATTCATGGCCTCGACAA
Found at i:15991 original size:21 final size:19
Alignment explanation
Indices: 15963--16008 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
15953 TCATTGAATC
15963 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
15983 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
16002 ACTTAGT
1 A-TTAGT
16009 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:20631 original size:20 final size:21
Alignment explanation
Indices: 20585--20645 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
20575 TTCCCCTGTG
*
20585 GGGGGAATTGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
20608 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
20628 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
20646 TGCACCAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:32575 original size:48 final size:47
Alignment explanation
Indices: 32516--32606 Score: 128
Period size: 48 Copynumber: 1.9 Consensus size: 47
32506 TCAACACATA
* * *
32516 ATTTAGATCAGATATCATAACAGAATCCAAGTTAGGAATCAGAACAG
1 ATTTAGATCAGATATCAAAACAGAATCCAAATTAGAAATCAGAACAG
* *
32563 ATTTCAGATCAGATGTCAAAACAGAATTCAAATTAGAAATCAGA
1 ATTT-AGATCAGATATCAAAACAGAATCCAAATTAGAAATCAGA
32607 TAAAATATTC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 4 0.11
48 34 0.89
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.24
Consensus pattern (47 bp):
ATTTAGATCAGATATCAAAACAGAATCCAAATTAGAAATCAGAACAG
Found at i:41656 original size:2 final size:2
Alignment explanation
Indices: 41646--41721 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
41636 AAATACACAC
41646 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41687 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41722 GTGTGTGTGT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48984 original size:25 final size:25
Alignment explanation
Indices: 48955--49004 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
48945 GATTAAAGAC
48955 TAAATCATTAGGATCATAGAATTTG
1 TAAATCATTAGGATCATAGAATTTG
* *
48980 TAAATCCTTAGGATCATTGAATTTG
1 TAAATCATTAGGATCATAGAATTTG
49005 AGTAAGTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (25 bp):
TAAATCATTAGGATCATAGAATTTG
Found at i:57965 original size:16 final size:16
Alignment explanation
Indices: 57944--57980 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
57934 TTATAAGTTC
57944 TGTTGCAATATAGTGA
1 TGTTGCAATATAGTGA
57960 TGTTGCAATATAGTGA
1 TGTTGCAATATAGTGA
57976 TGTTG
1 TGTTG
57981 TGTTCTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (16 bp):
TGTTGCAATATAGTGA
Found at i:67177 original size:20 final size:21
Alignment explanation
Indices: 67149--67188 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
67139 TGAATTAAGG
*
67149 CCTTCTCTTTTTC-TTCATTA
1 CCTTCTCTTCTTCTTTCATTA
*
67169 CCTTTTCTTCTTCTTTCATT
1 CCTTCTCTTCTTCTTTCATT
67189 CTTTTTTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.62
Consensus pattern (21 bp):
CCTTCTCTTCTTCTTTCATTA
Done.