Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008346.1 Hibiscus syriacus cultivar Beakdansim tig00111074_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: 71456
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7768 original size:2 final size:2
Alignment explanation
Indices: 7761--7793 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7751 TGATAATAAT
7761 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 T
7794 TTCTTCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20023 original size:219 final size:215
Alignment explanation
Indices: 19648--20080 Score: 794
Period size: 219 Copynumber: 2.0 Consensus size: 215
19638 GACTTAAGCT
19648 CTCAACTAAATCTTCAGCACCGTAGAGTACAACAATAACAATGCTGTTTCCATACACATATAAGA
1 CTCAACTAAATCTTCAGCACCGTAGAGTACAACAATAACAATGCTGTTTCCATACACATATAAGA
19713 CATTCTATGAGTTACTAAGATCAGGAATGGCGGAACATCATGGTTCCAGGAAAGTTAAATTAGTT
66 CATTCTATGAGTTACTAAGATCAGGAATGGCGGAACATCATGGTTCCAGGAAAGTTAAATTAGTT
19778 TCTTTTGTAGTCGAGAGGCCTGCAATATCCAAAGCCAGGAGCAGGATACAGGCCTTTGAAGGGAA
131 TCTTTTGTAGTCGAGAGGCCTGCAATATCCAAAGCCAGGAGCAGGATACAGGCCTTTGAAGGGAA
19843 TAGAAAGCATAAAAACTAAA
196 TAGAAAGCATAAAAACTAAA
19863 CTCAACTAAATCTTCAGCACCGTAGAGTACAACAATAACAATGCTGTTTCCATACACATGCGTAT
1 CTCAACTAAATCTTCAGCACCGTAGAGTACAACAATAACAATGCTGTTTCCATACACA----TAT
* *
19928 GAGACATTCTATGAGTTACTAAGATTAGGAATGGCGGAACATCATGGTTCCAGGAAAGTTAAATT
62 AAGACATTCTATGAGTTACTAAGATCAGGAATGGCGGAACATCATGGTTCCAGGAAAGTTAAATT
*
19993 AGTTTCTTTTGTAGTCGAGTGGCCTGCAATATCCAAAGCCAGGAGCAGGATACAGGCCTTTGAAG
127 AGTTTCTTTTGTAGTCGAGAGGCCTGCAATATCCAAAGCCAGGAGCAGGATACAGGCCTTTGAAG
*
20058 GGAATAGAAAGCATAAAAGCTAA
192 GGAATAGAAAGCATAAAAACTAA
20081 GATCCTATGA
Statistics
Matches: 210, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
215 58 0.28
219 152 0.72
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (215 bp):
CTCAACTAAATCTTCAGCACCGTAGAGTACAACAATAACAATGCTGTTTCCATACACATATAAGA
CATTCTATGAGTTACTAAGATCAGGAATGGCGGAACATCATGGTTCCAGGAAAGTTAAATTAGTT
TCTTTTGTAGTCGAGAGGCCTGCAATATCCAAAGCCAGGAGCAGGATACAGGCCTTTGAAGGGAA
TAGAAAGCATAAAAACTAAA
Found at i:21704 original size:3 final size:3
Alignment explanation
Indices: 21696--21737 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
21686 TTATCATAAA
* *
21696 TAT TAT TAT TTT TAT TAT TTT TAT TAT TAT TAT ATAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
21738 CGATTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:21712 original size:9 final size:9
Alignment explanation
Indices: 21698--21735 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
21688 ATCATAAATA
21698 TTATTATTT
1 TTATTATTT
21707 TTATTATTT
1 TTATTATTT
*
21716 TTATTATTA
1 TTATTATTT
21725 TTATATATTT
1 TTAT-TATTT
21735 T
1 T
21736 ATCGATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 21 0.81
10 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTATTT
Found at i:21847 original size:21 final size:21
Alignment explanation
Indices: 21821--21865 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
21811 TTGTAAATAT
*
21821 TAAAAATATTAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
*
21842 TAAAAATAATAATTTTTTAAA
1 TAAAAATAATAATATTTTAAA
21863 TAA
1 TAA
21866 TTTTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:22572 original size:2 final size:2
Alignment explanation
Indices: 22565--22640 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
22555 TATACATTGG
22565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22641 TGAAATTAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24075 original size:18 final size:18
Alignment explanation
Indices: 24040--24077 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
24030 TGTTGTCCCG
*
24040 AAATTAGTTTTGATTTAA
1 AAATTAGTTTTAATTTAA
24058 AAATTAG-TTTAATATTAA
1 AAATTAGTTTTAAT-TTAA
24076 AA
1 AA
24078 TAAGTGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (18 bp):
AAATTAGTTTTAATTTAA
Found at i:26660 original size:2 final size:2
Alignment explanation
Indices: 26653--26722 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
26643 GGCTAAGGAA
*
26653 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
26695 AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26723 GATAATCCAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26808 original size:22 final size:22
Alignment explanation
Indices: 26781--26826 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
26771 CGTACACATT
*
26781 AAGTTAAATTATAATGGACTAA
1 AAGTTAAACTATAATGGACTAA
*
26803 AAGTTAAACTATGATGGACTAA
1 AAGTTAAACTATAATGGACTAA
26825 AA
1 AA
26827 CATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (22 bp):
AAGTTAAACTATAATGGACTAA
Found at i:28364 original size:3 final size:3
Alignment explanation
Indices: 28346--28395 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
28336 GCAAATGTAA
* *
28346 AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AAT AAC AAT -AT AATT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
28392 AAT A
1 AAT A
28396 TTTATAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:28703 original size:51 final size:51
Alignment explanation
Indices: 28646--28928 Score: 325
Period size: 51 Copynumber: 5.4 Consensus size: 51
28636 AGTTCGTTCT
28646 CTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAATGTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAATGTGTCCGCTCC
* * *
28697 CCATTCCTTCAGAGAGTATAGGACTCAATCTTCAATCAAACGTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTAAATCTTCAA-CAAATGTGTCCGCTCC
* * * * *
28749 CTATTTCTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGTGTCCTCTCC
1 CTATTCCTTCAGAGAGTATAGGAC-T--A-AATCTTCAACAAATGTGTCCGCTCC
* * *
28804 CTATTCCTTCAGAAAGTATAGGACTCAATCTTCAACAAATGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAATGTGTCCGCTCC
* * * *
28855 CTATTCCTTCAGAGAGTATAAGACTCGAATAATTTTCAAC-ATTCGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAGGACT---A-AATCTTCAACAAAT-GTGTCCGCTCC
*
28910 CTATTTCTTCAGAGAGTAT
1 CTATTCCTTCAGAGAGTAT
28929 TAGACTCGAA
Statistics
Matches: 199, Mismatches: 23, Indels: 16
0.84 0.10 0.07
Matches are distributed among these distances:
51 77 0.39
52 36 0.18
53 1 0.01
54 3 0.02
55 74 0.37
56 8 0.04
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31
Consensus pattern (51 bp):
CTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAATGTGTCCGCTCC
Found at i:28804 original size:55 final size:55
Alignment explanation
Indices: 28646--29057 Score: 422
Period size: 55 Copynumber: 7.7 Consensus size: 55
28636 AGTTCGTTCT
* *
28646 CTATTCCTTCAGAGAGTATAGGAC-T--A-AATCTTCAACAAATGTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
* *
28697 CCATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAATCAAACGTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAA-CAAACGTGTCTGCTCC
* * *
28749 CTATTTCTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGTGTCCT-CTCC
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGTGT-CTGCTCC
* *
28804 CTATTCCTTCAGAAAGTATAGGAC-T---CAATCTTCAACAAATGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
* * * * **
28855 CTATTCCTTCAGAGAGTATAAGACTCGAATAATTTTCAACATTCGTGTCTGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
* * * * ** *
28910 CTATTTCTTCAGAGAGTATTA-GACTCGAACAATTTTCAATATTCATGTCTGCTCC
1 CTATTCCTTCAGAGAGTA-TAGGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
* * * *
28965 CTATTGCTTAAGAGAGTAT-GAGACTTGAACAATCTTCAACAATCGTGTCTGCTCT
1 CTATTCCTTCAGAGAGTATAG-GACTTGAACAATCTTCAACAAACGTGTCTGCTCC
** *
29020 CTATTTGTTCAGAGAGTATAAGACTTGAACAATCTTCA
1 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCA
29058 TTTGCTTCAC
Statistics
Matches: 309, Mismatches: 36, Indels: 28
0.83 0.10 0.08
Matches are distributed among these distances:
50 2 0.01
51 76 0.25
52 36 0.12
53 1 0.00
54 2 0.01
55 180 0.58
56 12 0.04
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (55 bp):
CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
Found at i:41621 original size:2 final size:2
Alignment explanation
Indices: 41614--41657 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
41604 GGCTAAGGAA
* *
41614 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41656 AT
1 AT
41658 GATAATCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41741 original size:22 final size:22
Alignment explanation
Indices: 41714--41759 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
41704 CGTACACATT
*
41714 AAGTTAAATTATAATGGACTAA
1 AAGTTAAACTATAATGGACTAA
*
41736 AAGTTAAACTATGATGGACTAA
1 AAGTTAAACTATAATGGACTAA
41758 AA
1 AA
41760 CATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (22 bp):
AAGTTAAACTATAATGGACTAA
Found at i:43298 original size:3 final size:3
Alignment explanation
Indices: 43280--43329 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
43270 GCAAATGTAA
* *
43280 AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AAT AAC AAT -AT AATT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
43326 AAT A
1 AAT A
43330 TTTATAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:43574 original size:21 final size:23
Alignment explanation
Indices: 43539--43584 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
43529 TATTATTTTA
*
43539 AATATATTTATATTATAT-AATT
1 AATATATTTAAATTATATAAATT
*
43561 AATA-ATTTAAATTATCTAAATT
1 AATATATTTAAATTATATAAATT
43583 AA
1 AA
43585 AGTTCAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATATTTAAATTATATAAATT
Found at i:47785 original size:29 final size:30
Alignment explanation
Indices: 47753--47810 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
47743 AAACTACGTA
*
47753 TTTATTAGTTAAACTATT-ATTTTTTTAAT
1 TTTAGTAGTTAAACTATTAATTTTTTTAAT
* *
47782 TTTAGTATTTAAACTTTTAATTTTTTTAA
1 TTTAGTAGTTAAACTATTAATTTTTTTAA
47811 AATCATACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTAGTAGTTAAACTATTAATTTTTTTAAT
Done.