Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005775.1 Hibiscus syriacus cultivar Beakdansim tig00013514_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: 75010
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1373 original size:2 final size:2
Alignment explanation
Indices: 1366--1390 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1356 ATTCACCACG
1366 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
1391 TTCGAATCTA
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:2293 original size:13 final size:13
Alignment explanation
Indices: 2275--2300 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2265 AGATAAGCTC
2275 ATTAATGTCTAGT
1 ATTAATGTCTAGT
2288 ATTAATGTCTAGT
1 ATTAATGTCTAGT
2301 GTGAACGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTAATGTCTAGT
Found at i:5888 original size:32 final size:33
Alignment explanation
Indices: 5818--5889 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
5808 CCAAAGGTGA
* *
5818 CCCTTGGGTAGGCTCTGAGGCCCCGAGAAACTT
1 CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACTT
* **
5851 -TCTTGGGTAGGCTCTCAGGCCCCAAGGCA-TT
1 CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACTT
5882 CCCTTGGG
1 CCCTTGGG
5890 GTGGCTCCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.24
Consensus pattern (33 bp):
CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACTT
Found at i:10833 original size:18 final size:18
Alignment explanation
Indices: 10812--10863 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
10802 AATATTATTA
* *
10812 ATATTTTAATTTAAATTT
1 ATATATTAATTTAAATTC
* *
10830 ATATACTAAATTAAATTC
1 ATATATTAATTTAAATTC
*
10848 ATATCTTAATATTAAA
1 ATATATTAAT-TTAAA
10864 AATAAATAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATATTAATTTAAATTC
Found at i:10975 original size:24 final size:24
Alignment explanation
Indices: 10925--10986 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
10915 TTTAAAGCTA
* * **
10925 AAATAAGACTAAAATATACTTTTT
1 AAATAAAAATAAAATATACTTAAT
*
10949 AAATAAAAATAAAATATAGTTAAT
1 AAATAAAAATAAAATATACTTAAT
* *
10973 AAATTAAGATAAAA
1 AAATAAAAATAAAA
10987 ATAAAATATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (24 bp):
AAATAAAAATAAAATATACTTAAT
Found at i:28341 original size:15 final size:14
Alignment explanation
Indices: 28312--28338 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28302 TAATTTGAAG
28312 TTTTTTTTAATTTA
1 TTTTTTTTAATTTA
28326 TTTTTTTTAATTT
1 TTTTTTTTAATTT
28339 TATAAAGGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTTAATTTA
Found at i:29864 original size:12 final size:12
Alignment explanation
Indices: 29847--29882 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
29837 ACCAACTTAT
29847 AAAATTTAAAAA
1 AAAATTTAAAAA
29859 AAAATTATAAAAA
1 AAAATT-TAAAAA
*
29872 AACATTTAAAA
1 AAAATTTAAAA
29883 TATATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAATTTAAAAA
Found at i:45256 original size:22 final size:24
Alignment explanation
Indices: 45220--45265 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
45210 AAAGAAAAAA
45220 TGACACCTCTTTT-AAAAATATTT
1 TGACACCTCTTTTAAAAAATATTT
45243 TGACACC-CTTTTAAAAAATATTT
1 TGACACCTCTTTTAAAAAATATTT
45266 AATAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (24 bp):
TGACACCTCTTTTAAAAAATATTT
Found at i:45442 original size:28 final size:30
Alignment explanation
Indices: 45402--45462 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
45392 AAAACATAAT
45402 ATTTAATCAC-TT-TTTTTATTTAATTAAG
1 ATTTAATCACTTTCTTTTTATTTAATTAAG
* *
45430 ATTTGATCACTTTCGTTTTTATTTTATTAAG
1 ATTTAATCACTTTC-TTTTTATTTAATTAAG
45461 AT
1 AT
45463 GTGGTCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 2 0.07
31 17 0.61
ACGTcount: A:0.28, C:0.08, G:0.07, T:0.57
Consensus pattern (30 bp):
ATTTAATCACTTTCTTTTTATTTAATTAAG
Found at i:48683 original size:75 final size:75
Alignment explanation
Indices: 48530--48685 Score: 172
Period size: 75 Copynumber: 2.1 Consensus size: 75
48520 TGATTCCGGC
* * * *
48530 TTCACATGGTATTGCTTGGGGTTCAAGTTCCAGAAATTTAGAAGACTGATTTCTGAACATGTTGA
1 TTCACATGGTATCGCTTGGGGTCCAAGTTCAAGAAATTTAGAAGACTGATTTCCGAACATGTTGA
*
48595 ATCCAGTAAG
66 ATCCAATAAG
* * ** *
48605 TTCACATGGTATCG-TTCGGGGTCCAGGTTCAAGAAATTTAGATGTTTGTTTTCCGAACATGTT-
1 TTCACATGGTATCGCTT-GGGGTCCAAGTTCAAGAAATTTAGAAGACTGATTTCCGAACATGTTG
**
48668 AAGTCCAATGGG
65 AA-TCCAATAAG
48680 TTCACA
1 TTCACA
48686 AGATATGGCT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
74 4 0.06
75 63 0.94
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (75 bp):
TTCACATGGTATCGCTTGGGGTCCAAGTTCAAGAAATTTAGAAGACTGATTTCCGAACATGTTGA
ATCCAATAAG
Found at i:48938 original size:75 final size:75
Alignment explanation
Indices: 48766--49215 Score: 295
Period size: 75 Copynumber: 6.1 Consensus size: 75
48756 TCAAGTTCAT
* * * * * * **
48766 GAAATTTAGAAGTTTGATTCCCAAAAATG--G-TCCCAGTGGGTTCAGAGGGCATGGCTTGAGGA
1 GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAACTTG-GGA
*
48828 -TCAGGTTCAG
65 TTCAGGTCCAG
* * * * **
48838 GAAATTTTGAAGAC-TGCTTT-TCGAACATGTTCATTTGAGGGGGTTCACAGGGCA-AAGCTTGG
1 GAAATTTAGAAG-CTTG-TTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAA-CTTGG
48900 GATTCAGGTCCAG
63 GATTCAGGTCCAG
* * * * *
48913 GAAATTTAGAAGCTTGTTTCCCGAACATGTTGATTCCTA-GGGGTTCAGAAGGTATAACTTGAGA
1 GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCC-AGGGGGTTCACAGGGCATAACTTGGGA
* *
48977 TT-GGAGTCCTG
65 TTCAG-GTCCAG
* * *
48988 GAAACTTAGAAGTTTGTTTCCCAAACATGTTGATTCCAGTGGGTTCACAGGGCATAACTTGGG-T
1 GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAACTTGGGAT
*
49052 TCCAGGTTCAG
66 T-CAGGTCCAG
* * * * * ** * ** *
49063 AAAATTTAGAAGCCTGTTGCCCAAACATGTTTATTCCAGTGGGTTCACAATGCGTTGCTTGAG-T
1 GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAACTTGGGAT
*
49127 T----T-CTG
66 TCAGGTCCAG
* * * * * ** *
49132 GAAATTTAGAAGCCTGTTTTCCAAACATGTTGATTCCAGAGTGTTCACAAGGCATTGCTTGAGAT
1 GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAACTTGGGAT
49197 TCAGGAT-CAG
66 TCAGG-TCCAG
49207 GAAATTTAG
1 GAAATTTAG
49216 GGTTTTGGTC
Statistics
Matches: 298, Mismatches: 59, Indels: 39
0.75 0.15 0.10
Matches are distributed among these distances:
69 57 0.19
70 3 0.01
72 19 0.06
73 2 0.01
74 11 0.04
75 202 0.68
76 4 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (75 bp):
GAAATTTAGAAGCTTGTTTCCCAAACATGTTGATTCCAGGGGGTTCACAGGGCATAACTTGGGAT
TCAGGTCCAG
Found at i:49212 original size:144 final size:145
Alignment explanation
Indices: 48878--49215 Score: 364
Period size: 150 Copynumber: 2.3 Consensus size: 145
48868 TCATTTGAGG
* * * *
48878 GGGTTCACAGGGCAAAGCTTGGGATTCAGGTCCAGGAAATTTAGAAGCTTGTTTCCCGAACATGT
1 GGGTTCACAGGGCATAGCTT-GGATTCAGGT-CAGGAAATTTAGAAGCCTGTTGCCCAAACATGT
* **
48943 TGATTCCTAGGGGTTCAGAAGGTATAACTTGAGATTGGAGTCCTGGAAACTTAGAAGTTTGTTTC
64 TGATTCCTAGGGGTTCACAAGGTATAACTTGAGATT---GTCCTGGAAACTTAGAAGCCTGTTTC
*
49008 CCAAACATGTTGATTCCAGT
126 CCAAACATGTTGATTCCAGA
* * *
49028 GGGTTCACAGGGCATAACTTGGGTTCCAGGTTCAGAAAATTTAGAAGCCTGTTGCCCAAACATGT
1 GGGTTCACAGGGCATAGCTTGGATT-CAGG-TCAGGAAATTTAGAAGCCTGTTGCCCAAACATGT
* * * *
49093 TTATTCC-AGTGGGTTCACAATGCGT-T-GCTTGAG-TT-T-CTGGAAATTTAGAAGCCTGTTTT
64 TGATTCCTAG-GGGTTCACAA-G-GTATAACTTGAGATTGTCCTGGAAACTTAGAAGCCTGTTTC
49152 CCAAACATGTTGATTCCAGA
126 CCAAACATGTTGATTCCAGA
* * *
49172 GTGTTCACAAGGCATTGCTTGAGATTCAGGATCAGGAAATTTAG
1 GGGTTCACAGGGCATAGCTTG-GATTCAGG-TCAGGAAATTTAG
49216 GGTTTTGGTC
Statistics
Matches: 160, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
144 71 0.44
145 4 0.03
149 8 0.05
150 72 0.45
151 3 0.02
152 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (145 bp):
GGGTTCACAGGGCATAGCTTGGATTCAGGTCAGGAAATTTAGAAGCCTGTTGCCCAAACATGTTG
ATTCCTAGGGGTTCACAAGGTATAACTTGAGATTGTCCTGGAAACTTAGAAGCCTGTTTCCCAAA
CATGTTGATTCCAGA
Found at i:51971 original size:23 final size:22
Alignment explanation
Indices: 51944--51994 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
51934 AATATTTATG
* *
51944 GTTCTAGATTTTAAGGATTCAGA
1 GTTCTAAAATTTAA-GATTCAGA
*
51967 GTTCTAAAATTTAAGATTTAGA
1 GTTCTAAAATTTAAGATTCAGA
51989 G-TCTAA
1 GTTCTAA
51995 GGCTTTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.20
22 8 0.32
23 12 0.48
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (22 bp):
GTTCTAAAATTTAAGATTCAGA
Found at i:65907 original size:18 final size:18
Alignment explanation
Indices: 65872--65942 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 18
65862 ACAAACCAAA
** *
65872 CAAAATAATACAACATTC
1 CAAAATAATATTATATTC
65890 CAAAATAATATTATATT-
1 CAAAATAATATTATATTC
* *
65907 C-TAATAAT-TT-TAATC
1 CAAAATAATATTATATTC
*
65922 CAAAAATAATCTTATATTC
1 C-AAAATAATATTATATTC
65941 CA
1 CA
65943 TGAATAAAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
14 3 0.07
15 3 0.07
16 6 0.15
17 7 0.17
18 17 0.41
19 5 0.12
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.35
Consensus pattern (18 bp):
CAAAATAATATTATATTC
Found at i:68619 original size:10 final size:10
Alignment explanation
Indices: 68604--68642 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
68594 TCATCACACC
*
68604 AAATTCTCTA
1 AAATTCTCTT
68614 AAATTCTCTT
1 AAATTCTCTT
68624 AAATTCTCTT
1 AAATTCTCTT
*
68634 AAATACTCT
1 AAATTCTCT
68643 CTCGTTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (10 bp):
AAATTCTCTT
Found at i:68721 original size:17 final size:18
Alignment explanation
Indices: 68684--68724 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
68674 ATATTATGTA
*
68684 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
68702 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
68719 TTTACT
1 TTTACT
68725 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Done.