Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004455.1 Hibiscus syriacus cultivar Beakdansim tig00009798_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: 53339
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:4492 original size:17 final size:18
Alignment explanation
Indices: 4457--4511 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
4447 GAAAGTTTCA
*
4457 TGGGTATTAGACTCATTT
1 TGGGTATTAGACTCGTTT
*
4475 TGGGTATT-CACTCGTTT
1 TGGGTATTAGACTCGTTT
4492 TGGGTATTAGACTCGTTT
1 TGGGTATTAGACTCGTTT
4510 TG
1 TG
4512 TGTAGCAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 15 0.45
18 18 0.55
ACGTcount: A:0.16, C:0.13, G:0.25, T:0.45
Consensus pattern (18 bp):
TGGGTATTAGACTCGTTT
Found at i:15808 original size:10 final size:10
Alignment explanation
Indices: 15793--15817 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15783 AAAGGGAAAA
15793 AACAACAACC
1 AACAACAACC
15803 AACAACAACC
1 AACAACAACC
15813 AACAA
1 AACAA
15818 TCACTAAAAA
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:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (10 bp):
AACAACAACC
Found at i:24518 original size:257 final size:257
Alignment explanation
Indices: 24016--25090 Score: 1421
Period size: 257 Copynumber: 4.2 Consensus size: 257
24006 AGTTGTTTTG
* * *
24016 AAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAATGTTTT-A-AAAATGATATTTTTGAAAAG
1 AAAAT-AGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCAGAAAATGAAATTTTTGAAAAG
* * * * * *
24079 TAAGAAAGTGATTTCCAAATTTTCTTACCCAATAAACTATTTCCTAAATTAGTAAGTTCTTCGAG
65 TAAGAAAGCGATTACCAAAGTTTCTTACCCAATAAATTATTTCCCAAATTAGTAAGTCCTTCG-G
* * * *
24144 AC-ATCAGTAAATCTTTCGAGCATGATGACTAAATCCTTTGGGTTATATGTAAGTCTTTCGAGCA
129 GCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATGTAAGTCTTTCGAGCA
* *
24208 AGATGATAAGTCTTTCGGGCCATCCATAAGACCTTCGGGTAGGATGATTTCACATGAATT-TGAA
194 AGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTATG-A
*** **
24272 AAAATAGAAAGATTTTTCCAAAGTTTCTCATTTAAAGTTTTCAGAAAATGAAATTTTTGAAAAGT
1 AAAATAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCAGAAAATGAAATTTTTGAAAAGT
* *
24337 AAGAAAGCGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCCAAATTAGTAAGTTCTTCGGGC
66 AAGAAAGCGATTACCAAAGTTTCTTACCCAATAAATTATTTCCCAAATTAGTAAGTCCTTCGGGC
* * * *
24402 TATCAGTAAGTCTTTCGAGCAAGATGATTAAATCCTTTAGGTTATATGTCAGTCTTTCGAGCAAG
131 TATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATGTAAGTCTTTCGAGCAAG
* * * *
24467 ATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCAGGTAGAATGTTTTCACAAGAATT-TGA
196 ATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTATGA
*
24528 AAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTTTTGAAAAG
1 AAAAT-AGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCAGAAAATGAAATTTTTGAAAAG
* * * *
24593 TAAGAAAACGATTACCAAAGTTTCTTACCTAATACATTATTTCCCAAAATTTGTAAGTCCTTCGG
65 TAAGAAAGCGATTACCAAAGTTTCTTACCCAATAAATTATTTCCC-AAATTAGTAAGTCCTTCGG
* * * * * *
24658 GCTATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGCCATCTGTAAGTCTTTCAAACA
129 GCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATGTAAGTCTTTCGAGCA
* ** * * * *
24723 AGATGATAAGTCCTTTGGGAAATCCGT-AGACCTTCGGGTAGGATGCTTTCACATTAATTGTG-
194 AGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTATGA
* * * *
24785 AAAATGTGAAAGTGATTTCCAAAGTTTCTCATTTAATCTCTTCTGAAAATGAAATTTTTGAAAAG
1 AAAAT-AGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCAGAAAATGAAATTTTTGAAAAG
* * * * *
24850 TAAGAAAGTGATTACCAAAGTTTCTTA-CCAAGTAAATTATTTTCCAAAATTGGAAAGTCCTTCA
65 TAAGAAAGCGATTACCAAAGTTTCTTACCCAA-TAAATTA-TTTCCCAAATTAGTAAGTCCTTCG
* * * *
24914 GGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGC
128 GGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATGTAAGTCTTTCGAGC
* *
24979 AAGATGATAAGTCCTTCGGGCCATCCACAAGACATT-GGGTAGGATGTTTTCACATGAATTATGA
193 AAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTATGA
* * *
25043 AAAAGAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTCTTCTGAAAA
1 AAAATAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCAGAAAA
25091 GTCCTATCGG
Statistics
Matches: 729, Mismatches: 80, Indels: 19
0.88 0.10 0.02
Matches are distributed among these distances:
255 32 0.04
256 17 0.02
257 567 0.78
258 113 0.16
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (257 bp):
AAAATAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCAGAAAATGAAATTTTTGAAAAGT
AAGAAAGCGATTACCAAAGTTTCTTACCCAATAAATTATTTCCCAAATTAGTAAGTCCTTCGGGC
TATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATGTAAGTCTTTCGAGCAAG
ATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTATGA
Found at i:24728 original size:42 final size:41
Alignment explanation
Indices: 24650--24737 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 41
24640 AATTTGTAAG
* ** * *
24650 TCCTTCGGGCTATCAGTAAGTCTTTTGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAACAAGATGA-TAAA
* *
24692 TCCTTCGGGCCATCTGTAAGTCTTTCAAACAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAACAAGATGATAAA
24733 TCCTT
1 TCCTT
24738 TGGGAAATCC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 8 0.21
42 31 0.79
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCAAACAAGATGATAAA
Found at i:24970 original size:42 final size:41
Alignment explanation
Indices: 24907--25003 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 41
24897 AATTGGAAAG
* * *
24907 TCCTTCAGGCCATC-AGTAAGTCTTTTGAGCATGATGATTAAA
1 TCCTTCGGGCCATCTA-TAAGTCTTTCGAGCAAGATGA-TAAA
* * *
24949 TCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGCCATCTATAAGTCTTTCGAGCAAGATGATAAA
24990 TCCTTCGGGCCATC
1 TCCTTCGGGCCATC
25004 CACAAGACAT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 15 0.33
42 30 0.65
43 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (41 bp):
TCCTTCGGGCCATCTATAAGTCTTTCGAGCAAGATGATAAA
Found at i:31813 original size:29 final size:29
Alignment explanation
Indices: 31775--31841 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 29
31765 AAAAAAATTA
31775 ATTAAATAAAATATTAAAAAAT-TTAAAT
1 ATTAAATAAAATATTAAAAAATATTAAAT
31803 ACTTAAAT--AA-ATTAAAAAATATTAAAT
1 A-TTAAATAAAATATTAAAAAATATTAAAT
31830 A-T-AATAAAATAT
1 ATTAAATAAAATAT
31842 ACCTTAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
24 3 0.09
25 1 0.03
26 12 0.35
27 11 0.32
28 1 0.03
29 6 0.18
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
ATTAAATAAAATATTAAAAAATATTAAAT
Found at i:31835 original size:24 final size:24
Alignment explanation
Indices: 31766--31837 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 24
31756 TTATATGCAA
*
31766 AAAAAATTAATTAAATA-AA-ATATT
1 AAAAAA-T-ATTAAATATAATAAATT
31790 AAAAAAT-TTAAATACTTAAATAAATT
1 AAAAAATATTAAATA--T-AATAAATT
31816 AAAAAATATTAAATATAATAAA
1 AAAAAATATTAAATATAATAAA
31838 ATATACCTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
21 7 0.17
23 1 0.02
24 12 0.29
25 3 0.07
26 11 0.27
27 7 0.17
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAAATATTAAATATAATAAATT
Found at i:31837 original size:19 final size:20
Alignment explanation
Indices: 31799--31858 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
31789 TAAAAAATTT
31799 AAATACTTAAATAAATTAAA
1 AAATACTTAAATAAATTAAA
31819 AAATA-TTAAATATAA-TAAA
1 AAATACTTAAATA-AATTAAA
* *
31838 ATATACCTTAAA-CAATTAAA
1 AAATA-CTTAAATAAATTAAA
31858 A
1 A
31859 TAGAATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 17 0.50
20 12 0.35
21 5 0.15
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATACTTAAATAAATTAAA
Found at i:33684 original size:24 final size:24
Alignment explanation
Indices: 33655--33700 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
33645 GTCATGTTTA
33655 AAAATATTTTATTTTAAAAAACTT
1 AAAATATTTTATTTTAAAAAACTT
*
33679 AAAATATTTTATTTTCAAAAAC
1 AAAATATTTTATTTTAAAAAAC
33701 CCTAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATATTTTATTTTAAAAAACTT
Found at i:34346 original size:5 final size:5
Alignment explanation
Indices: 34329--34358 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
34319 TAATGTTAAA
34329 AAAAT ACAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAA
34359 GATCAAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Done.