Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000322.1 Hibiscus syriacus cultivar Beakdansim tig00000604_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: 48312
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:832 original size:22 final size:22
Alignment explanation
Indices: 804--854 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
794 ATTTGAGGTT
804 TGTTGCATGCACATCTAACGGC
1 TGTTGCATGCACATCTAACGGC
826 TGTTGCATGCACATCTAACGGC
1 TGTTGCATGCACATCTAACGGC
848 TGTTGCA
1 TGTTGCA
855 CTTTGAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (22 bp):
TGTTGCATGCACATCTAACGGC
Found at i:4011 original size:45 final size:45
Alignment explanation
Indices: 3947--4128 Score: 328
Period size: 45 Copynumber: 4.0 Consensus size: 45
3937 GGTAAACATG
*
3947 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
3992 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
*
4037 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTCGT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
* *
4082 AAAATAAGCTTACGAGCTTATGGGATAAATGGAAAATATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
4127 AA
1 AA
4129 GAAATTTTAT
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 132 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
Found at i:4066 original size:25 final size:25
Alignment explanation
Indices: 3993--4066 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
3983 TATATTGGTA
3993 AAATAAGCTTACGAGCTTATGGGAT
1 AAATAAGCTTACGAGCTTATGGGAT
* *
4018 AAAT--G-GTA--AG-TATATTGG-T
1 AAATAAGCTTACGAGCT-TATGGGAT
4037 AAAATAAGCTTACGAGCTTATGGGAT
1 -AAATAAGCTTACGAGCTTATGGGAT
4063 AAAT
1 AAAT
4067 GGTAAGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
22 3 0.08
23 3 0.08
25 15 0.42
26 2 0.06
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (25 bp):
AAATAAGCTTACGAGCTTATGGGAT
Found at i:6842 original size:9 final size:9
Alignment explanation
Indices: 6814--6932 Score: 73
Period size: 10 Copynumber: 12.4 Consensus size: 9
6804 CATAAGAACT
6814 AAAAAAATAG
1 AAAAAAA-AG
6824 AAAAAGAAAAG
1 -AAAA-AAAAG
6835 AAAAAAAAG
1 AAAAAAAAG
*
6844 AAGAAAAAG
1 AAAAAAAAG
6853 AAAAAAGAAG
1 AAAAAA-AAG
* *
6863 AAAAAATAT
1 AAAAAAAAG
6872 AAAGAAGAAA-
1 AAA-AA-AAAG
* *
6882 AAGACAAAG
1 AAAAAAAAG
6891 AAAAAAAAAG
1 -AAAAAAAAG
6901 AAACAAAAA-
1 AAA-AAAAAG
6910 AATGAAAAAAG
1 AA--AAAAAAG
*
6921 -TAAAAAAG
1 AAAAAAAAG
6929 AAAA
1 AAAA
6933 TAAATGAGAG
Statistics
Matches: 86, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
8 10 0.12
9 30 0.35
10 34 0.40
11 9 0.10
12 3 0.03
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:6858 original size:16 final size:15
Alignment explanation
Indices: 6814--6932 Score: 93
Period size: 16 Copynumber: 7.8 Consensus size: 15
6804 CATAAGAACT
*
6814 AAAAAAATAGAAAAAG
1 AAAAAAAGA-AAAAAG
*
6830 AAAAGAA-AAAAAAG
1 AAAAAAAGAAAAAAG
6844 AAGAAAAAGAAAAAAG
1 AA-AAAAAGAAAAAAG
*
6860 AAGAAAAA-ATATAAAG
1 AA-AAAAAGA-AAAAAG
*
6876 AAGAAAAAG-ACAAAG
1 AA-AAAAAGAAAAAAG
* *
6891 AAAAAAA-AAGAAAC
1 AAAAAAAGAAAAAAG
6905 AAAAAAATGAAAAAAG
1 AAAAAAA-GAAAAAAG
*
6921 TAAAAAAGAAAA
1 AAAAAAAGAAAA
6933 TAAATGAGAG
Statistics
Matches: 87, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
14 24 0.28
15 18 0.21
16 45 0.52
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:6929 original size:38 final size:38
Alignment explanation
Indices: 6837--6932 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 38
6827 AAGAAAAGAA
*
6837 AAAAAAGAAGAAAAAGAAAAAAGAAGAAAAAATATAAAG
1 AAAAAAG-AGAAAAAGAAAAAAAAAGAAAAAATATAAAG
*
6876 AAGAAAA-AGACAAAGAAAAAAAAAGAAACAAA-A-AAATG
1 AA-AAAAGAGAAAAAGAAAAAAAAAGAAA-AAATATAAA-G
6914 AAAAAAGTA-AAAAAGAAAA
1 AAAAAAG-AGAAAAAGAAAA
6933 TAAATGAGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
37 7 0.14
38 32 0.65
39 6 0.12
40 4 0.08
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (38 bp):
AAAAAAGAGAAAAAGAAAAAAAAAGAAAAAATATAAAG
Found at i:6939 original size:25 final size:24
Alignment explanation
Indices: 6815--6932 Score: 93
Period size: 23 Copynumber: 4.8 Consensus size: 24
6805 ATAAGAACTA
6815 AAAAAATAGAAAAAGAAAAGAAAA-
1 AAAAAATAGAAAAAGAAAA-AAAAG
*
6839 AAAAGA-AGAAAAAGAAAAAAGAAG
1 AAAAAATAGAAAAAGAAAAAA-AAG
*
6863 AAAAAATATAAAGAAGAAAAAGACAAAG
1 AAAAAATAGAAA-AAG-AAAA-A-AAAG
* *
6891 AAAAAA-A-AAGAAACAAAAAAATG
1 AAAAAATAGAA-AAAGAAAAAAAAG
6914 AAAAAAGTA-AAAAAGAAAA
1 AAAAAA-TAGAAAAAGAAAA
6933 TAAATGAGAG
Statistics
Matches: 78, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
22 2 0.03
23 23 0.29
24 18 0.23
25 11 0.14
26 7 0.09
27 6 0.08
28 10 0.13
29 1 0.01
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.04
Consensus pattern (24 bp):
AAAAAATAGAAAAAGAAAAAAAAG
Found at i:10085 original size:23 final size:24
Alignment explanation
Indices: 10042--10090 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 24
10032 AAATTAAATT
10042 AATATGTTTTTTATAATATAGAATA
1 AATATGTTTTTTAT-ATATAGAATA
10067 AATAT-TTTTTTAT-TCATAGAATA
1 AATATGTTTTTTATAT-ATAGAATA
10090 A
1 A
10091 TAAATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 1 0.04
23 9 0.39
24 8 0.35
25 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
AATATGTTTTTTATATATAGAATA
Found at i:19781 original size:12 final size:12
Alignment explanation
Indices: 19764--19810 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
19754 AAGTCCGCCC
19764 CCGCCTCCACCT
1 CCGCCTCCACCT
*
19776 CCGCCTCCCCCACCC
1 CCGCCT---CCACCT
19791 CCGCCTCCACCT
1 CCGCCTCCACCT
19803 CCGCCTCC
1 CCGCCTCC
19811 CCCACCCCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 19 0.63
15 11 0.37
ACGTcount: A:0.06, C:0.72, G:0.09, T:0.13
Consensus pattern (12 bp):
CCGCCTCCACCT
Found at i:19794 original size:15 final size:15
Alignment explanation
Indices: 19770--19822 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
19760 GCCCCCGCCT
*
19770 CCACCTCCGCCTCCC
1 CCACCCCCGCCTCCC
19785 CCACCCCCGCCT---
1 CCACCCCCGCCTCCC
*
19797 CCACCTCCGCCTCCC
1 CCACCCCCGCCTCCC
19812 CCACCCCCGCC
1 CCACCCCCGCC
19823 ATCGCCCCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 11 0.34
15 21 0.66
ACGTcount: A:0.08, C:0.75, G:0.08, T:0.09
Consensus pattern (15 bp):
CCACCCCCGCCTCCC
Found at i:19799 original size:27 final size:27
Alignment explanation
Indices: 19761--19822 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
19751 TATAAGTCCG
19761 CCCCCGCCTCCACCTCCGCCTCCCCCA
1 CCCCCGCCTCCACCTCCGCCTCCCCCA
19788 CCCCCGCCTCCACCTCCGCCTCCCCCA
1 CCCCCGCCTCCACCTCCGCCTCCCCCA
19815 CCCCCGCC
1 CCCCCGCC
19823 ATCGCCCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.06, C:0.76, G:0.08, T:0.10
Consensus pattern (27 bp):
CCCCCGCCTCCACCTCCGCCTCCCCCA
Found at i:24873 original size:284 final size:284
Alignment explanation
Indices: 24361--24932 Score: 1054
Period size: 284 Copynumber: 2.0 Consensus size: 284
24351 GGAAGGGAAC
* * *
24361 CATAAAGCTACAGCTATTTGCTCATTCAAATATGGTAATTGATTAATTAATAATATGCACATGCT
1 CATAAAGCTAAAGCTATTTGCTCATTCAAATATGGTAATTGACTAATTAATAATATGCACATCCT
24426 ATGATATGAAAAATTAATTAAATACGCCATCACAAAGTCTTTCATTCTTGTAGACACTAGATTGC
66 ATGATATGAAAAATTAATTAAATACGCCATCACAAAGTCTTTCATTCTTGTAGACACTAGATTGC
24491 TAATTGAATATACCAAAATTTTCAATGCCAGACAAAACAATCCTAACAGTAAAATCATTTTGGTT
131 TAATTGAATATACCAAAATTTTCAATGCCAGACAAAACAATCCTAACAGTAAAATCATTTTGGTT
*
24556 AGCATAAACACGAGTAGCGCATTACATATCGAAGATTCGAATTTCTTACCCCTAAAACTAAATCA
196 AGCATAAACACGAGTAGCGCATTACACATCGAAGATTCGAATTTCTTACCCCTAAAACTAAATCA
24621 GCAACTCCGGCACCAAATGTCCTA
261 GCAACTCCGGCACCAAATGTCCTA
24645 CATAAAGCTAAAGCTATTTGCTCATTCAAATATGGTAATTGACTAATTAATAATATGCACATCCT
1 CATAAAGCTAAAGCTATTTGCTCATTCAAATATGGTAATTGACTAATTAATAATATGCACATCCT
* *
24710 ATGATATGAAAAATTAATTAAATATGCCATCACAAAGTCTTTCATTCTTGTAGACATTAGATTGC
66 ATGATATGAAAAATTAATTAAATACGCCATCACAAAGTCTTTCATTCTTGTAGACACTAGATTGC
* *
24775 TAATTGAATATACCAAAATTTTCAATGCCAGACAAAACAATCGTAACAGTAGAATCATTTTGGTT
131 TAATTGAATATACCAAAATTTTCAATGCCAGACAAAACAATCCTAACAGTAAAATCATTTTGGTT
24840 AGCATAAACACGAGTAGCGCATTACACATCGAAGATTCGAATTTCTTACCCCTAAAACTAAATCA
196 AGCATAAACACGAGTAGCGCATTACACATCGAAGATTCGAATTTCTTACCCCTAAAACTAAATCA
* *
24905 GCAACTCCGGCATCGAATGTCCTA
261 GCAACTCCGGCACCAAATGTCCTA
24929 CATA
1 CATA
24933 TATAATCATA
Statistics
Matches: 278, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
284 278 1.00
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (284 bp):
CATAAAGCTAAAGCTATTTGCTCATTCAAATATGGTAATTGACTAATTAATAATATGCACATCCT
ATGATATGAAAAATTAATTAAATACGCCATCACAAAGTCTTTCATTCTTGTAGACACTAGATTGC
TAATTGAATATACCAAAATTTTCAATGCCAGACAAAACAATCCTAACAGTAAAATCATTTTGGTT
AGCATAAACACGAGTAGCGCATTACACATCGAAGATTCGAATTTCTTACCCCTAAAACTAAATCA
GCAACTCCGGCACCAAATGTCCTA
Found at i:27043 original size:13 final size:13
Alignment explanation
Indices: 27023--27058 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
27013 CTTGATCGAG
*
27023 TCGATCTCTAGAA
1 TCGATCTCGAGAA
*
27036 TTGATCTCGAGAA
1 TCGATCTCGAGAA
27049 TCGATCTCGA
1 TCGATCTCGA
27059 ATGACTCACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (13 bp):
TCGATCTCGAGAA
Found at i:34364 original size:38 final size:38
Alignment explanation
Indices: 34313--34389 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
34303 GTTCAGCTTA
*
34313 TCTCAGTTCTACTTGTATTAATCTTGATTTCATAATAG
1 TCTCAGTTCTACTTATATTAATCTTGATTTCATAATAG
*
34351 TCTCAGTTCTACTTATATTAGTCTTGATTTCATAATAG
1 TCTCAGTTCTACTTATATTAATCTTGATTTCATAATAG
34389 T
1 T
34390 TGATGAACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (38 bp):
TCTCAGTTCTACTTATATTAATCTTGATTTCATAATAG
Found at i:40791 original size:6 final size:6
Alignment explanation
Indices: 40782--40874 Score: 57
Period size: 6 Copynumber: 15.5 Consensus size: 6
40772 TGTATATGTG
* * * *
40782 TACACA TACACA TACACA TACACACA TACATA TATAGA TACAGA T--ACA
1 TACACA TACACA TACACA T--ACACA TACACA TACACA TACACA TACACA
* * * * *
40830 TAC-CA TACCATA TACGCA TACACA TACGCA TACGCA TACGCA TAC
1 TACACA TA-CACA TACACA TACACA TACACA TACACA TACACA TAC
40875 GCAACCCTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
4 3 0.04
5 4 0.06
6 55 0.77
7 3 0.04
8 6 0.08
ACGTcount: A:0.44, C:0.29, G:0.06, T:0.20
Consensus pattern (6 bp):
TACACA
Found at i:40875 original size:6 final size:6
Alignment explanation
Indices: 40841--40877 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
40831 ACCATACCAT
*
40841 ATACGC ATACAC ATACGC ATACGC ATACGC ATACGC A
1 ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC A
40878 ACCCTTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (6 bp):
ATACGC
Done.