Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001312.1 Hibiscus syriacus cultivar Beakdansim tig00002557_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: 45274
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:21171 original size:77 final size:74
Alignment explanation
Indices: 21050--21260 Score: 205
Period size: 77 Copynumber: 2.8 Consensus size: 74
21040 ATTTTTTTTA
* * * * * *
21050 TTTTTCAAGATTTCCAAAATCCATGTTTTCGCTCACATAGCTTTCTTCCCAAAATATTGTTTTTG
1 TTTTTCAAAAATTCCAAAAT-CTTGTTTTC-ATCTCATAGCTTTCTTCCCAAAATATTGTTTTTA
*
21115 CTCCCATACCTT
64 CTCCCATA-CAT
*
21127 TCTTTTCAAAAATTCCAAAATCTTGTTTTCATTCTCATAGCTTTCTTCCCAAAATCTT-TATTTT
1 T-TTTTCAAAAATTCCAAAATCTTGTTTTCA-TCTCATAGCTTTCTTCCCAAAATATTGT-TTTT
* **
21191 ACTTCTGTACAT
63 ACTCCCATACAT
* *
21203 TTTTT-GAAAATTCCAAAATCTTGTTTTCGAT-TCATA-CTTTTCTTTCCAAAATATTGTT
1 TTTTTCAAAAATTCCAAAATCTTGTTTTC-ATCTCATAGC-TTTCTTCCCAAAATATTGTT
21261 CCAAAATCTT
Statistics
Matches: 114, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
72 1 0.01
73 21 0.18
74 24 0.21
75 5 0.04
76 4 0.04
77 42 0.37
78 17 0.15
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.46
Consensus pattern (74 bp):
TTTTTCAAAAATTCCAAAATCTTGTTTTCATCTCATAGCTTTCTTCCCAAAATATTGTTTTTACT
CCCATACAT
Found at i:23300 original size:16 final size:16
Alignment explanation
Indices: 23279--23310 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
23269 TGGATTATTA
*
23279 AATTTAATTTATTTTT
1 AATTTAATATATTTTT
23295 AATTTAATATATTTTT
1 AATTTAATATATTTTT
23311 CTCACCAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATTTAATATATTTTT
Found at i:23629 original size:29 final size:29
Alignment explanation
Indices: 23577--23697 Score: 118
Period size: 29 Copynumber: 4.1 Consensus size: 29
23567 AAATGTTTTT
*
23577 TTATTTTAACCTATCAAATATATTTTATTC
1 TTATTTTAACCTA-AAAATATATTTTATTC
*
23607 TT-TTTGTAACCTAAAAATCTATTTTATTC
1 TTATTT-TAACCTAAAAATATATTTTATTC
** * * *
23636 TTATTTTAATTTAAAAATATATTTGAATG
1 TTATTTTAACCTAAAAATATATTTTATTC
* ** *
23665 TTATCTTAAATTAAAAATATAATTTATTC
1 TTATTTTAACCTAAAAATATATTTTATTC
23694 TTAT
1 TTAT
23698 CTTGACTTAA
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
29 63 0.84
30 12 0.16
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.52
Consensus pattern (29 bp):
TTATTTTAACCTAAAAATATATTTTATTC
Found at i:23814 original size:25 final size:26
Alignment explanation
Indices: 23749--23859 Score: 97
Period size: 24 Copynumber: 4.3 Consensus size: 26
23739 ATTTGGGATA
23749 AAAATAAAATATATTTTATATAAGAT
1 AAAATAAAATATATTTTATATAAGAT
* *
23775 AAAATAAAATATATTTT-TGT-AGTT
1 AAAATAAAATATATTTTATATAAGAT
23799 AAAATAAAA-ATATATTTATAAGCTAAGAT
1 AAAATAAAATATAT-TTTAT-A--TAAGAT
* * *
23828 AAGAATAAAAGATATGTT-T-TAAGTT
1 AA-AATAAAATATATTTTATATAAGAT
23853 AAAATAA
1 AAAATAA
23860 GAATTAATTA
Statistics
Matches: 71, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
23 4 0.06
24 20 0.28
25 10 0.14
26 17 0.24
28 1 0.01
29 6 0.08
30 9 0.13
31 4 0.06
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (26 bp):
AAAATAAAATATATTTTATATAAGAT
Found at i:23835 original size:30 final size:29
Alignment explanation
Indices: 23745--24035 Score: 210
Period size: 30 Copynumber: 10.1 Consensus size: 29
23735 TTAAATTTGG
*
23745 GATAAAAATAAAATATATTT-T-A-TATAA
1 GATAAGAATAAAATATATTTATAAGT-TAA
*
23772 GATAA-AATAAAATATATTT-T-TG-T-A
1 GATAAGAATAAAATATATTTATAAGTTAA
* *
23796 GTTAA-AATAAAAATATATTTATAAGCTAA
1 GATAAGAAT-AAAATATATTTATAAGTTAA
* *
23825 GATAAGAATAAAAGATATGTTTTAAGTTAA
1 GATAAGAATAAAATATAT-TTATAAGTTAA
* * * *
23855 AATAAGAATTAATTATATTTAATAATTTAA
1 GATAAGAATAAAATATATTT-ATAAGTTAA
* * *
23885 GGTAAGAATAGAATATATTTAATAATTTAA
1 GATAAGAATAAAATATATTT-ATAAGTTAA
* * *
23915 GTTAAGAATATAACT-TATGTAATAAGTTAA
1 GATAAGAATA-AAATATAT-TTATAAGTTAA
*
23945 GATAAGAATAAAATATATTT-TTAGTTTAA
1 GATAAGAATAAAATATATTTATAAG-TTAA
**
23974 GCCAAGAATAAAATATATTTA-AAGTTAA
1 GATAAGAATAAAATATATTTATAAGTTAA
* * *
24002 TATAACAATAAAATATTATTTTTAATGTTAA
1 GATAAGAATAAAATA-TATTTATAA-GTTAA
24033 GAT
1 GAT
24036 GAAAAATTAA
Statistics
Matches: 211, Mismatches: 36, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
24 8 0.04
25 12 0.06
26 16 0.08
27 6 0.03
28 19 0.09
29 48 0.23
30 92 0.44
31 10 0.05
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (29 bp):
GATAAGAATAAAATATATTTATAAGTTAA
Found at i:23856 original size:54 final size:51
Alignment explanation
Indices: 23749--23859 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 51
23739 ATTTGGGATA
* *
23749 AAAAT-AAAATATATTTTATATAAGATAAAATAAAATATATTTTTGTAGTT
1 AAAATAAAAATATATTTTATATAAGATAAAATAAAAGATATTTTTGAAGTT
23799 AAAATAAAAATATA-TTTATAAGCTAAGATAAGAATAAAAGATATGTTTT-AAGTT
1 AAAATAAAAATATATTTTAT-A--TAAGATAA-AATAAAAGATAT-TTTTGAAGTT
23853 AAAATAA
1 AAAATAA
23860 GAATTAATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
50 10 0.19
51 9 0.17
53 8 0.15
54 22 0.42
55 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (51 bp):
AAAATAAAAATATATTTTATATAAGATAAAATAAAAGATATTTTTGAAGTT
Found at i:26349 original size:2 final size:2
Alignment explanation
Indices: 26337--26379 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
26327 GTCCACCAAT
*
26337 TA TA AA 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
26379 T
1 T
26380 CATTCAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28121 original size:32 final size:32
Alignment explanation
Indices: 28083--28169 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
28073 TCTGTTATAA
28083 TCAATATCGGATCGATT-GACTTTTGGGTCGGG
1 TCAATATCGGATCGATTAGA-TTTTGGGTCGGG
*
28115 TTAATATCGGATCGATTAGATTTTGGGTCGGG
1 TCAATATCGGATCGATTAGATTTTGGGTCGGG
* *
28147 TCAATGTCGGATCGGTTA-ATTTT
1 TCAATATCGGATCGATTAGATTTT
28170 TGAATTGAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 5 0.10
32 43 0.86
33 2 0.04
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.38
Consensus pattern (32 bp):
TCAATATCGGATCGATTAGATTTTGGGTCGGG
Found at i:33816 original size:22 final size:22
Alignment explanation
Indices: 33788--33834 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
33778 GATGCCTAAA
33788 GTAGGAAGTCGATATCAGAATT
1 GTAGGAAGTCGATATCAGAATT
33810 GTAGGAAGTCGATATCAGAATT
1 GTAGGAAGTCGATATCAGAATT
33832 GTA
1 GTA
33835 AGCCCTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (22 bp):
GTAGGAAGTCGATATCAGAATT
Found at i:37888 original size:16 final size:16
Alignment explanation
Indices: 37869--37899 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37859 ATTTTGGATA
*
37869 GGGTATTGTTTGGGTC
1 GGGTATGGTTTGGGTC
37885 GGGTATGGTTTGGGT
1 GGGTATGGTTTGGGT
37900 TCAGATCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.03, G:0.48, T:0.42
Consensus pattern (16 bp):
GGGTATGGTTTGGGTC
Found at i:42399 original size:54 final size:54
Alignment explanation
Indices: 42314--42496 Score: 294
Period size: 54 Copynumber: 3.4 Consensus size: 54
42304 AATGCGAAAA
* * * * * *
42314 TAAGTTGCACACGTAGTACCAATACGGAAATTCAGAGACTCATTATGAATTTAT
1 TAAGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCT
*
42368 TAAGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCT
1 TAAGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCT
42422 TAAGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCT
1 TAAGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCT
*
42476 TAAGTAGCACACATAGTGCCA
1 TAAGTTGCACACATAGTGCCA
42497 TTTGGTAATC
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 120 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (54 bp):
TAAGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCT
Done.