Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004152.1 Hibiscus syriacus cultivar Beakdansim tig00009081_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: 61269
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2021 original size:4 final size:4
Alignment explanation
Indices: 2006--2048 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
1996 ATTATACATA
* *
2006 TATT TTTT TATT TATT TATTT TATT TATAC TATT TATT TATT T
1 TATT TATT TATT TATT TA-TT TATT TAT-T TATT TATT TATT T
2049 TCATTATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 26 0.79
5 7 0.21
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2029 original size:13 final size:13
Alignment explanation
Indices: 2006--2048 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1996 ATTATACATA
2006 TATTT-TTTTATT
1 TATTTATTTTATT
2018 TATTTATTTTATT
1 TATTTATTTTATT
*
2031 TATACTA-TTTATT
1 TAT-TTATTTTATT
2044 TATTT
1 TATTT
2049 TCATTATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 6 0.22
13 19 0.70
14 2 0.07
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:2157 original size:18 final size:19
Alignment explanation
Indices: 2133--2178 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2123 TGTATATATA
*
2133 TTTTTTTCTTC-ATTT-AT
1 TTTTTTTATTCAATTTCAT
2150 TTTATTTTATTCAATTTCAT
1 TTT-TTTTATTCAATTTCAT
2170 TTTTTTTAT
1 TTTTTTTAT
2179 ATTTGTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 7 0.28
19 10 0.40
20 5 0.20
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTATTCAATTTCAT
Found at i:7736 original size:22 final size:22
Alignment explanation
Indices: 7664--7739 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
7654 CTACCCCATA
*
7664 AAACCGTTGAGCATCAAATGCC
1 AAACCTTTGAGCATCAAATGCC
*
7686 AAACCTATGAGCATCAAATGCC
1 AAACCTTTGAGCATCAAATGCC
*
7708 AAACCTTTGAGCAACAAATGCC
1 AAACCTTTGAGCATCAAATGCC
7730 AAACCTTTGA
1 AAACCTTTGA
7740 CCAAACATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.20
Consensus pattern (22 bp):
AAACCTTTGAGCATCAAATGCC
Found at i:8805 original size:106 final size:106
Alignment explanation
Indices: 8676--9633 Score: 1490
Period size: 106 Copynumber: 9.0 Consensus size: 106
8666 ATATCGTACC
* * * *
8676 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGA-CGACTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
*
8740 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
**
8782 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
8847 AATTTCAGAGCCAATTTCAACTTCAC-GACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
* * * * *
8888 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAATAAATAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
8953 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
8994 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
9059 AATTTCAGAGCCAATTTCAATTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
9100 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
9165 AATTTCAGAGCCAATTTCAACTTTACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
9206 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
9271 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
9312 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
9377 AATTTCAGAGCCAATTTAAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
9418 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
9483 AATTTCGGAGCTAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
9524 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
9589 GATTCCAGATCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
9630 ACTC
1 ACTC
9634 GGAACAATGC
Statistics
Matches: 795, Mismatches: 53, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
105 1 0.00
106 792 1.00
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:10473 original size:37 final size:37
Alignment explanation
Indices: 10383--10487 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
10373 CCTTTTCATC
* *
10383 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGACTCAAACTCCTAAAAATAGGATAGAATT
* * *
10420 TTGCTAGGACTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGACTCAAACTCCTAAAAATAGGATAGAATT
** * * *
10457 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGACTCAAACTCCTAAAAATAGGAT
10488 CCACAAGCAT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGACTCAAACTCCTAAAAATAGGATAGAATT
Found at i:10898 original size:2 final size:2
Alignment explanation
Indices: 10885--10924 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
10875 CCTTATTATT
*
10885 TA TA TG 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
10925 ATTATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11005 original size:2 final size:2
Alignment explanation
Indices: 10998--11022 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10988 TTCCTATTAT
10998 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
11023 TTTTTTCTAT
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:11210 original size:20 final size:19
Alignment explanation
Indices: 11185--11232 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
11175 CTATTTAGTA
11185 TTTTATTATATTATACATAT
1 TTTTATTAT-TTATACATAT
* *
11205 TTTTA-TATTTTTATATAT
1 TTTTATTATTTATACATAT
11223 TTTT-TTATTT
1 TTTTATTATTT
11233 TTTATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 17 0.68
19 3 0.12
20 5 0.20
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATTATTTATACATAT
Found at i:11234 original size:27 final size:28
Alignment explanation
Indices: 11204--11261 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
11194 ATTATACATA
*
11204 TTTTTATATT-TTTATA-TATTTTTTTAT
1 TTTTTAT-TTATTTATACTATTTATTTAT
11231 TTTTTATTTATTTATACTATTTATTTAT
1 TTTTTATTTATTTATACTATTTATTTAT
11259 TTT
1 TTT
11262 CATTATGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 2 0.07
27 13 0.46
28 13 0.46
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTTATTTATTTATACTATTTATTTAT
Found at i:11235 original size:20 final size:20
Alignment explanation
Indices: 11185--11235 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
11175 CTATTTAGTA
* *
11185 TTTTATTATATTATACATAT
1 TTTTATTTTTTTATACATAT
* * *
11205 TTTTATATTTTTATATATTT
1 TTTTATTTTTTTATACATAT
11225 TTTTATTTTTT
1 TTTTATTTTTT
11236 ATTTATTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTATTTTTTTATACATAT
Found at i:11242 original size:4 final size:4
Alignment explanation
Indices: 11214--11260 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
11204 TTTTTATATT
* * *
11214 TTTA TATA TTTT TTTA TTT- TTTA TTTA TTTA TACTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTT
11261 TCATTATGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:13206 original size:29 final size:29
Alignment explanation
Indices: 13165--13274 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
13155 AACTAAATTA
13165 ATGTCATTGCTTACATCATTTAAGTAAAT
1 ATGTCATTGCTTACATCATTTAAGTAAAT
*
13194 ATGTCATTACTTACATCATTTAAGTAAAT
1 ATGTCATTGCTTACATCATTTAAGTAAAT
*
13223 ATGTCATTGTTTACATCATTTAAGT-AAT
1 ATGTCATTGCTTACATCATTTAAGTAAAT
13251 GATGTCATTGCTTACATCAATTTA
1 -ATGTCATTGCTTACATC-ATTTA
13275 GTTAGGTGAG
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
28 3 0.04
29 67 0.89
30 5 0.07
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (29 bp):
ATGTCATTGCTTACATCATTTAAGTAAAT
Found at i:15791 original size:392 final size:388
Alignment explanation
Indices: 15173--15958 Score: 1245
Period size: 392 Copynumber: 2.0 Consensus size: 388
15163 TTATATTTAA
*
15173 TTTAGTCATTTTAGGGTAACTTGTGTGACATTTAAAAAAATTCACAACCACGATACCCGCAATAA
1 TTTAGTCATTTTAGGGTAACTTGTGTGACATTTAAAAAAATTCACAACCACAATACCCGCAATAA
** * * * * * *
15238 CTGCAATGACATTCGTTATGTCCGCAACTGTGATAATCGCGACGCGGCCGAAAATGTGACTGCGA
66 CCACAATGACATCCATTACGTCCGCAACTGTGATAAACGCGACGCGACCGAAAATGT-ACCGCGA
*
15303 ACGCTATTTAAAACCCTAGCCACACATGCAAGTTCTGCAACTTGATCTCAGTCATTGCCCAGAAA
130 ACGCTATTTAAAACCCTAGCCACACATGCAAGTTCTGCAACTTGATCTCAGCCATTGCCCAGAAA
* *
15368 AAACCAAGTACATCAGGGAAATTTTAGGAAGATGATGGATTGATGTTGGTTATTTTGTTCTTGGG
195 AAACCAAGTACATAAGGGAAATTTTAGGAAGATGATGGATTGATGTTGGTTATTTTGCTCTTGGG
* *
15433 GATTCATCTCGACTTATTCCTTCCCATCAGGAGGT-TTCCCTCGCTCACCGCTTTAATTATTATA
260 GATTCATCTCGACTTATTCCTTCCCATCAAGAGGTGTTCCAT-GCTCACCGCTTTAATTATTATA
*
15497 AGTAACATTTGGTTTATGGAGACTATA-GCAATTTTTTATTTGGGTGGAGAACTGCAATCGATGA
324 AGTAACATTTGGTTTATGGAGACTATAGGCAA-TTTTTATTTGGGTGGAGAACTGCAATCAATGA
15561 T
388 T
* *
15562 TTTAGTCATTTTAGGGTAACTTGTGTGACATTTAAAAAAATTCACGACCACAATACCCGCAATGA
1 TTTAGTCATTTTAGGGTAACTTGTGTGACATTTAAAAAAATTCACAACCACAATACCCGCAATAA
*
15627 CCACAATGACATCCATTACGTCCGCAACTGTGATAAACGCGATGCGACACGACCGAAATCGT-CC
66 CCACAATGACATCCATTACGTCCGCAACTGTGATAAACGCGACGCGAC-CGA---AAAT-GTACC
* * * *
15691 GCGAACGCTATTTAAAACCCTGGCCACACATGCAAGTTCTGTAGCTTGATCTCAGCCATTGGCCA
126 GCGAACGCTATTTAAAACCCTAGCCACACATGCAAGTTCTGCAACTTGATCTCAGCCATTGCCCA
15756 GAAAAAACCAAGTACATAAGGGAAATTTTAGGAAGATGATGGATTGATGTTGGTTATTTTGCTCT
191 GAAAAAACCAAGTACATAAGGGAAATTTTAGGAAGATGATGGATTGATGTTGGTTATTTTGCTCT
15821 TGGGGATTCATCTCGACTTATTCCTTCCCATCAAGAGGTGTTCCATGCTCACCGCTTTAATTATT
256 TGGGGATTCATCTCGACTTATTCCTTCCCATCAAGAGGTGTTCCATGCTCACCGCTTTAATTATT
* ** *
15886 ATAAGTAACATTTGGTTTATTGAGACTATAGGTGATTTTTATTTGGGTGGAGAGCTGCAATCAAT
321 ATAAGTAACATTTGGTTTATGGAGACTATAGGCAATTTTTATTTGGGTGGAGAACTGCAATCAAT
15951 GAT
386 GAT
15954 TTTAG
1 TTTAG
15959 AAGGAGAAAT
Statistics
Matches: 364, Mismatches: 26, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
389 102 0.28
390 3 0.01
392 246 0.68
393 11 0.03
394 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (388 bp):
TTTAGTCATTTTAGGGTAACTTGTGTGACATTTAAAAAAATTCACAACCACAATACCCGCAATAA
CCACAATGACATCCATTACGTCCGCAACTGTGATAAACGCGACGCGACCGAAAATGTACCGCGAA
CGCTATTTAAAACCCTAGCCACACATGCAAGTTCTGCAACTTGATCTCAGCCATTGCCCAGAAAA
AACCAAGTACATAAGGGAAATTTTAGGAAGATGATGGATTGATGTTGGTTATTTTGCTCTTGGGG
ATTCATCTCGACTTATTCCTTCCCATCAAGAGGTGTTCCATGCTCACCGCTTTAATTATTATAAG
TAACATTTGGTTTATGGAGACTATAGGCAATTTTTATTTGGGTGGAGAACTGCAATCAATGAT
Found at i:38081 original size:22 final size:22
Alignment explanation
Indices: 38053--38104 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
38043 CTAGAGACTT
*
38053 TTTTCTCTAGTTTTTGGGTGAA
1 TTTTCTCTAGTTTTTGGGCGAA
*
38075 TTTTCTCTGGTTTTTGGGCGAA
1 TTTTCTCTAGTTTTTGGGCGAA
38097 TTTTCTCT
1 TTTTCTCT
38105 TGTGAATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.10, C:0.13, G:0.21, T:0.56
Consensus pattern (22 bp):
TTTTCTCTAGTTTTTGGGCGAA
Found at i:49355 original size:14 final size:14
Alignment explanation
Indices: 49317--49355 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
49307 GTATTACTCT
49317 ATAATCTCTAAACC
1 ATAATCTCTAAACC
* *
49331 ATAAGCCCTAAACC
1 ATAATCTCTAAACC
*
49345 TTAATCTCTAA
1 ATAATCTCTAA
49356 CTTAAAATCC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (14 bp):
ATAATCTCTAAACC
Found at i:57042 original size:15 final size:15
Alignment explanation
Indices: 57022--57065 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
57012 CATTTGCAAT
57022 TTTTTATTTTTTTTA
1 TTTTTATTTTTTTTA
*
57037 TTTTTATTTTGTTTTG
1 TTTTTATTTT-TTTTA
*
57053 TTTTTGTTTTTTT
1 TTTTTATTTTTTT
57066 ATGAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (15 bp):
TTTTTATTTTTTTTA
Done.