Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000321.1 Hibiscus syriacus cultivar Beakdansim tig00000603_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: 32100
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:819 original size:15 final size:15
Alignment explanation
Indices: 799--910 Score: 84
Period size: 15 Copynumber: 7.4 Consensus size: 15
789 ACCAGCTGAG
799 CCAGAAATTAATGAA
1 CCAGAAATTAATGAA
* *
814 CCAGAACA--AGTTGAG
1 CCAGAA-ATTA-ATGAA
*
829 CTAGAAATTAATGAA
1 CCAGAAATTAATGAA
* *
844 CCTGGAATTAATGAA
1 CCAGAAATTAATGAA
* ** *
859 CCAGAAACCTGCTGAG
1 CCAGAAA-TTAATGAA
875 CCAGAAATTAATGAA
1 CCAGAAATTAATGAA
* *
890 CCTGAAATTGATGAA
1 CCAGAAATTAATGAA
905 CCAGAA
1 CCAGAA
911 CCTGCTGAGG
Statistics
Matches: 71, Mismatches: 21, Indels: 10
0.70 0.21 0.10
Matches are distributed among these distances:
14 2 0.03
15 56 0.79
16 13 0.18
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.20
Consensus pattern (15 bp):
CCAGAAATTAATGAA
Found at i:835 original size:68 final size:69
Alignment explanation
Indices: 734--862 Score: 179
Period size: 68 Copynumber: 1.9 Consensus size: 69
724 TAATGAACCT
* * * *
734 GAAATTGATGAAGCAGAACCAGTTCAACAAGAAATTACTGAACC-GAAATTAATGAACCAGCTGA
1 GAAATTAATGAACCAGAACAAGTTCAACAAGAAATTAATGAACCTGAAATTAATGAACCAGCTGA
798 GCCA
66 GCCA
* * * *
802 GAAATTAATGAACCAGAACAAGTTGAGCTAGAAATTAATGAACCTGGAATTAATGAACCAG
1 GAAATTAATGAACCAGAACAAGTTCAACAAGAAATTAATGAACCTGAAATTAATGAACCAG
863 AAACCTGCTG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
68 37 0.71
69 15 0.29
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.19
Consensus pattern (69 bp):
GAAATTAATGAACCAGAACAAGTTCAACAAGAAATTAATGAACCTGAAATTAATGAACCAGCTGA
GCCA
Found at i:887 original size:46 final size:45
Alignment explanation
Indices: 802--919 Score: 173
Period size: 46 Copynumber: 2.6 Consensus size: 45
792 AGCTGAGCCA
** * *
802 GAAATTAATGAACCAGAACAAGTTGAGCTAGAAATTAATGAACCT
1 GAAATTAATGAACCAGAACCTGCTGAGCCAGAAATTAATGAACCT
*
847 GGAATTAATGAACCAGAAACCTGCTGAGCCAGAAATTAATGAACCT
1 GAAATTAATGAACCAG-AACCTGCTGAGCCAGAAATTAATGAACCT
*
893 GAAATTGATGAACCAGAACCTGCTGAG
1 GAAATTAATGAACCAGAACCTGCTGAG
920 GTTAGGATAG
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 26 0.40
46 39 0.60
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (45 bp):
GAAATTAATGAACCAGAACCTGCTGAGCCAGAAATTAATGAACCT
Found at i:2833 original size:26 final size:26
Alignment explanation
Indices: 2804--2863 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
2794 CATATTCTTC
2804 ATGCATACTGTTATTACATATTGCTA
1 ATGCATACTGTTATTACATATTGCTA
* * * *
2830 ATGCATAATGTTATTGCATATTGTTC
1 ATGCATACTGTTATTACATATTGCTA
2856 ATGCATAC
1 ATGCATAC
2864 AGTTGTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (26 bp):
ATGCATACTGTTATTACATATTGCTA
Found at i:2836 original size:13 final size:13
Alignment explanation
Indices: 2789--2862 Score: 58
Period size: 13 Copynumber: 5.7 Consensus size: 13
2779 GTTAACTTGG
* *
2789 TAATACATATTCT
1 TAATGCATATTGT
* *
2802 TCATGCATACTGT
1 TAATGCATATTGT
* * *
2815 TATTACATATTGC
1 TAATGCATATTGT
*
2828 TAATGCATAATGT
1 TAATGCATATTGT
*
2841 TATTGCATATTGT
1 TAATGCATATTGT
*
2854 TCATGCATA
1 TAATGCATA
2863 CAGTTGTTGG
Statistics
Matches: 44, Mismatches: 17, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (13 bp):
TAATGCATATTGT
Found at i:4251 original size:26 final size:26
Alignment explanation
Indices: 4215--4264 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
4205 ACATACATTA
4215 CATCTTCAATTCTAACACAAGTCTTG
1 CATCTTCAATTCTAACACAAGTCTTG
*
4241 CATCTTCAATTCTAACACACGTCT
1 CATCTTCAATTCTAACACAAGTCT
4265 ATTAACCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (26 bp):
CATCTTCAATTCTAACACAAGTCTTG
Found at i:11913 original size:35 final size:35
Alignment explanation
Indices: 11874--11946 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
11864 ATCGTCCTCC
* *
11874 GTTCTGGTTTGTGGAATATGGTTTATACTAGCAAG
1 GTTCTGGTTTGTAGAATATGGTATATACTAGCAAG
* *
11909 GTTCTGGTTTGTAGAATATGGTATATGCTAGTAAG
1 GTTCTGGTTTGTAGAATATGGTATATACTAGCAAG
11944 GTT
1 GTT
11947 GCATCCTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.23, C:0.07, G:0.29, T:0.41
Consensus pattern (35 bp):
GTTCTGGTTTGTAGAATATGGTATATACTAGCAAG
Found at i:12452 original size:21 final size:21
Alignment explanation
Indices: 12428--12470 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12418 TTGATGTAAT
12428 ATTAAAATAT-TAAGAATTAAA
1 ATTAAAATATATAA-AATTAAA
*
12449 ATTAAATTATATAAAATTAAA
1 ATTAAAATATATAAAATTAAA
12470 A
1 A
12471 CAAAAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATTAAAATATATAAAATTAAA
Found at i:21673 original size:60 final size:58
Alignment explanation
Indices: 21552--21712 Score: 170
Period size: 60 Copynumber: 2.8 Consensus size: 58
21542 TATAACCTTC
* * *
21552 CTTT-TAAATTGGTCCTTAAACTTTTAAATATTC---TTCATCCCTAAGCTATGACTCT
1 CTTTCTAAATTGGTCCTTAAACTTTT-AATATTCAATTTCATCCCTAAACTAAGACACT
* * *
21607 CATTCTAAATTAGTCCTTAAACTTTTAAGCATTCAAATTTCATCCCTAAACTAAGACACT
1 CTTTCTAAATTGGTCCTTAAACTTTTAA-TATTC-AATTTCATCCCTAAACTAAGACACT
*
21667 CTTTCTAAATTGGT-GTCTAAACTTTTGAATATTCCAATTTCATCCC
1 CTTTCTAAATTGGTCCT-TAAACTTTT-AATATT-CAATTTCATCCC
21713 CAAATTCATT
Statistics
Matches: 87, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
55 5 0.06
56 24 0.28
59 1 0.01
60 54 0.62
61 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (58 bp):
CTTTCTAAATTGGTCCTTAAACTTTTAATATTCAATTTCATCCCTAAACTAAGACACT
Found at i:23670 original size:27 final size:27
Alignment explanation
Indices: 23597--23663 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
23587 GATGAAGAAG
* *
23597 TTATAAGAAATTAAAGAAAACGGGTTT
1 TTATATGAAATTAAAGAAAACGAGTTT
23624 TTATATGAAATTAAAGAAAACGAGTTT
1 TTATATGAAATTAAAGAAAACGAGTTT
23651 TTATATGAAATTA
1 TTATATGAAATTA
23664 TGGAAAAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.34
Consensus pattern (27 bp):
TTATATGAAATTAAAGAAAACGAGTTT
Found at i:26268 original size:2 final size:2
Alignment explanation
Indices: 26261--26285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26251 TATGATAGCT
26261 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 T
26286 TATGAACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27826 original size:104 final size:105
Alignment explanation
Indices: 27708--27915 Score: 373
Period size: 105 Copynumber: 2.0 Consensus size: 105
27698 TTCATATCTC
*
27708 TTTCCGTGTTGTAATGTTATTTAAT-AAATAATATAATTTAAAATTGTAAAATATATTTATAATG
1 TTTCCGTGTTGTAATGTTATTTAATAAAATAATATAATTTAAAATTGTAAAATATATTTATAATA
** *
27772 TTATTTTAAAAAATTATATCTTAGAATTAAGTATTTATAG
66 TTATTTTAAAAAACGATATCTTAGAATAAAGTATTTATAG
27812 TTTCCGTGTTGTAATGTTATTTAATAAAATAATATAATTTAAAATTGTAAAATATATTTATAATA
1 TTTCCGTGTTGTAATGTTATTTAATAAAATAATATAATTTAAAATTGTAAAATATATTTATAATA
27877 TTATTTTAAAAAACGATATCTTAGAATAAAGTATTTATA
66 TTATTTTAAAAAACGATATCTTAGAATAAAGTATTTATA
27916 AGAGCATAAA
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 25 0.25
105 74 0.75
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (105 bp):
TTTCCGTGTTGTAATGTTATTTAATAAAATAATATAATTTAAAATTGTAAAATATATTTATAATA
TTATTTTAAAAAACGATATCTTAGAATAAAGTATTTATAG
Done.