Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002493.1 Hibiscus syriacus cultivar Beakdansim tig00005083_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: 43566
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:4673 original size:28 final size:28
Alignment explanation
Indices: 4614--4675 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
4604 GATAGTTTAC
* *
4614 CTATGTCCTTTGGGACATATGGATAAAC
1 CTATGTCCTTTGGGACATATGGACAAAA
4642 CTATGT-CTTTGGGACATATGGACAAATA
1 CTATGTCCTTTGGGACATATGGACAAA-A
4670 CTATGT
1 CTATGT
4676 TATTCCGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 19 0.61
28 12 0.39
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (28 bp):
CTATGTCCTTTGGGACATATGGACAAAA
Found at i:7225 original size:17 final size:17
Alignment explanation
Indices: 7203--7253 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
7193 GAGGTACCAC
7203 CTGACCGAAAAGTCAAG
1 CTGACCGAAAAGTCAAG
7220 CTGACCGAAAAGTCAAG
1 CTGACCGAAAAGTCAAG
*
7237 CTGACTGAAAAGTCAAG
1 CTGACCGAAAAGTCAAG
7254 TTTAGTATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.14
Consensus pattern (17 bp):
CTGACCGAAAAGTCAAG
Found at i:10668 original size:19 final size:19
Alignment explanation
Indices: 10578--10662 Score: 152
Period size: 19 Copynumber: 4.4 Consensus size: 19
10568 AACTATAAGA
*
10578 AAAGTTTCAAAACTCTTAT
1 AAAGTTTCAAAACTCTTGT
10597 GAAAGTTTCAAAACTCTTGT
1 -AAAGTTTCAAAACTCTTGT
10617 AAAGTTTCAAAACTCTTGT
1 AAAGTTTCAAAACTCTTGT
10636 AAAGTTTCAAAACTCTTGT
1 AAAGTTTCAAAACTCTTGT
10655 AAAGTTTC
1 AAAGTTTC
10663 GTAACTTCAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
19 46 0.72
20 18 0.28
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (19 bp):
AAAGTTTCAAAACTCTTGT
Found at i:10878 original size:2 final size:2
Alignment explanation
Indices: 10871--10933 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
10861 TTATAAAAAC
10871 TA TA TA 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
10913 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
10934 TATGTTAGAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14623 original size:55 final size:55
Alignment explanation
Indices: 14557--15112 Score: 393
Period size: 55 Copynumber: 10.1 Consensus size: 55
14547 AATCTTCGTC
* * * *
14557 AATCGTGTCTGCTCCCCATTTTTCCAGAGAATACAAGACTCAAACGATTCTCGAT
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTCTCAAT
* ** *
14612 AATCGTGTCTGCTCCCTATTTTTTCAGAGAGTATGAGACTCGAACAATTCTCAAT
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTCTCAAT
** * *
14667 AATCGTG-CATGCTCCCTATTTTCTTCAGAGAGA-ATGAGACTCGAACAA-TCTTCAACG
1 AATCGTGTC-TGCTCCCTATTTT-TTCAGAGA-ATACAAGACTCAAACAATTC-TCAA-T
* * ** * *
14724 AA-CGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
* * * ** * *
14778 AATCGTGTCTGCTCTCTATTTCTTCAGAGAGTATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
* * ** * *
14833 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
* * * ** * * *
14888 AAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAAGAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
* * * *
14943 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGAT--GAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGA-ATACAAGACTCAAACAATTC-TCAAT
* * ** * *
14997 AAACGTGTCTGCTCCCTATTTCTTT-AGAGAGTATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTT-TTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
* * ** * *
15052 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA-TCTTCAAC
1 AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTC-TCAAT
15107 AATCGT
1 AATCGT
15113 TGGGAAACCT
Statistics
Matches: 463, Mismatches: 25, Indels: 26
0.90 0.05 0.05
Matches are distributed among these distances:
53 1 0.00
54 50 0.11
55 365 0.79
56 44 0.10
57 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (55 bp):
AATCGTGTCTGCTCCCTATTTTTTCAGAGAATACAAGACTCAAACAATTCTCAAT
Found at i:14854 original size:110 final size:110
Alignment explanation
Indices: 14518--15112 Score: 884
Period size: 110 Copynumber: 5.4 Consensus size: 110
14508 TGGTTTTATC
* * * ** *
14518 CCCTATTGCTTCAGGGAGTA--AAACTCGAA-AATCTTCGTCAATCGTGTCTGCTCCCCATTT-T
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCT
* ** * * * *
14579 TCCAGAGAATACAAGACTCAAACGAT-TCTCGATAATCGTGTCTGCT
66 T-CAGAGAGTATGAGACTCGAACAATCT-TCAACAATCGTGTCTGCT
* *
14625 CCCTATTTTTTCAGAGAGTATGAGACTCGAACAAT-TCTCAATAATCGTG-CATGCTCCCTATTT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCT-TCAACAATCGTGTC-TGCTCCCTA-TT
*
14688 TCTTCAGAGAGAATGAGACTCGAACAATCTTCAACGAA-CGTGTCTGCT
63 TCTTCAGAGAGTATGAGACTCGAACAATCTTCAAC-AATCGTGTCTGCT
*
14736 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCTCTATTTCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCT
14801 TCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
66 TCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
14846 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCT
*
14911 TCAGAGAGTATGAGACTCGAAGAATCTTCAACAATCGTGTCTGCT
66 TCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
14956 CCCTATTTCTTCAGAGAG-ATGAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCT
*
15020 TTAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
66 TCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
15065 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
15113 TGGGAAACCT
Statistics
Matches: 449, Mismatches: 26, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
107 17 0.04
109 119 0.27
110 219 0.49
111 87 0.19
112 7 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (110 bp):
CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCT
TCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
Found at i:15058 original size:274 final size:276
Alignment explanation
Indices: 14518--15112 Score: 911
Period size: 274 Copynumber: 2.2 Consensus size: 276
14508 TGGTTTTATC
* * * **
14518 CCCTATTGCTTCAGGGAGTA--AAACTCGAA-AATCTTCGTCAATCGTGTCTGCTCCCCATTTTT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCCATTTTT
* * * * *
14580 CCAGAGAATACAAGACTCAAACGATTCTCGATAATCGTGTCTGCTCCCTATTTTTTCAGAGAGTA
66 CCAGAGAATACAAGACTCAAACAATTCTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTA
*
14645 TGAGACTCGAACAATTCTCAATAATCGTGCATGCTCCCTATTTTCTTCAGAGAGAATGAGACTCG
131 TGAGACTCGAACAATTCTCAACAATCGTGCATGCTCCCTATTTTCTTCAGAGAGAATGAGACTCG
*
14710 AACAATCTTCAACGAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTC
196 AACAATCTTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTC
14775 AACAATCGTGTCTGCT
261 AACAATCGTGTCTGCT
* *
14791 CTCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCCATTT-T
* ** *
14856 T-CAGAGAGTATGAGACTCGAACAA-TCTTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAG
65 TCCAGAGAATACAAGACTCAAACAATTC-TCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAG
*
14919 TATGAGACTCGAAGAA-TCTTCAACAATCGTGTC-TGCTCCCTA-TTTCTTCAGAGAG-ATGAGA
129 TATGAGACTCGAACAATTC-TCAACAATCGTG-CATGCTCCCTATTTTCTTCAGAGAGAATGAGA
*
14980 CTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTTCTTTAGAGAGTATGAGACTCGAACAAT
192 CTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAAT
15045 CTTCAACAATCGTGTCTGCT
257 CTTCAACAATCGTGTCTGCT
15065 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
15113 TGGGAAACCT
Statistics
Matches: 294, Mismatches: 21, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
273 17 0.06
274 136 0.46
275 25 0.09
276 113 0.38
277 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (276 bp):
CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCCATTTTT
CCAGAGAATACAAGACTCAAACAATTCTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTA
TGAGACTCGAACAATTCTCAACAATCGTGCATGCTCCCTATTTTCTTCAGAGAGAATGAGACTCG
AACAATCTTCAACAAACGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTC
AACAATCGTGTCTGCT
Found at i:16132 original size:20 final size:20
Alignment explanation
Indices: 16109--16165 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
16099 TTGAACCCTC
16109 ATTTTTTCATTTTTTTCATT
1 ATTTTTTCATTTTTTTCATT
*
16129 ATTTTTTTA-TTTTTTCATT
1 ATTTTTTCATTTTTTTCATT
*
16148 -TTTTCACTCATTTTTTTC
1 ATTTT--TTCATTTTTTTC
16166 TTCTTCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 4 0.13
19 10 0.32
20 10 0.32
21 7 0.23
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTTTCATTTTTTTCATT
Found at i:16141 original size:27 final size:29
Alignment explanation
Indices: 16109--16164 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
16099 TTGAACCCTC
*
16109 ATTTTTTCATTTTTTTCA-TTATTTTTTT
1 ATTTTTTCATTTTTTTCACTCATTTTTTT
16137 ATTTTTTCA-TTTTTTCACTCATTTTTTT
1 ATTTTTTCATTTTTTTCACTCATTTTTTT
16165 CTTCTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (29 bp):
ATTTTTTCATTTTTTTCACTCATTTTTTT
Found at i:16176 original size:27 final size:27
Alignment explanation
Indices: 16118--16177 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
16108 CATTTTTTCA
* * *
16118 TTTTTTTCATTATTTTTTTATTTTTTC
1 TTTTTTTCATCATTTTTTTACTTCTTC
*
16145 ATTTTTTCACTCATTTTTTT-CTTCTTC
1 TTTTTTTCA-TCATTTTTTTACTTCTTC
16172 TTTTTT
1 TTTTTT
16178 CTTCAAGCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTTTTTCATCATTTTTTTACTTCTTC
Found at i:31935 original size:19 final size:19
Alignment explanation
Indices: 31911--31948 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31901 TTTATTTTCT
31911 ATCCAATCAAGAGGTGATA
1 ATCCAATCAAGAGGTGATA
* *
31930 ATCCAATCATGTGGTGATA
1 ATCCAATCAAGAGGTGATA
31949 TTAGCACCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (19 bp):
ATCCAATCAAGAGGTGATA
Found at i:36000 original size:20 final size:20
Alignment explanation
Indices: 35975--36013 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35965 AGAATGTCCA
*
35975 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCAATTCCCCCTG
35995 GGGGGTATCAATTCCCCCT
1 GGGGGTATCAATTCCCCCT
36014 AAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.31, G:0.31, T:0.26
Consensus pattern (20 bp):
GGGGGTATCAATTCCCCCTG
Found at i:36375 original size:14 final size:15
Alignment explanation
Indices: 36358--36386 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36348 TATATGATAT
36358 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
36372 GCATAAAACATAAGA
1 GCATAAAACATAAGA
36387 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:36680 original size:15 final size:15
Alignment explanation
Indices: 36662--36696 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
36652 CGAGGGTATT
36662 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
36677 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
36692 GTAGT
1 GTAGT
36697 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:42080 original size:21 final size:20
Alignment explanation
Indices: 42041--42078 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42031 AGAATGTCCA
42041 GGGGGTATCAATTCCCCCTG
1 GGGGGTATCAATTCCCCCTG
*
42061 GGGGGTATCGATTCCCCC
1 GGGGGTATCAATTCCCCC
42079 CTAAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.32, G:0.32, T:0.24
Consensus pattern (20 bp):
GGGGGTATCAATTCCCCCTG
Found at i:42434 original size:14 final size:15
Alignment explanation
Indices: 42417--42445 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42407 TATATGATAT
42417 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
42431 GCATAAAACATAAGA
1 GCATAAAACATAAGA
42446 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:42737 original size:15 final size:15
Alignment explanation
Indices: 42719--42753 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
42709 CGAGGGTATT
42719 GTAGTCATTCGGGAC
1 GTAGTCATTCGGGAC
*
42734 GTAGTCCTTCGGGAC
1 GTAGTCATTCGGGAC
42749 GTAGT
1 GTAGT
42754 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCATTCGGGAC
Done.