Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006408.1 Hibiscus syriacus cultivar Beakdansim tig00015453_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: 49620
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2016 original size:21 final size:21
Alignment explanation
Indices: 1992--2035 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1982 CCGTTGATGA
* *
1992 AACTAAAACTTTTAATTAAGC
1 AACTAAAACATGTAATTAAGC
*
2013 AACTAAAACATGTCATTAAGC
1 AACTAAAACATGTAATTAAGC
2034 AA
1 AA
2036 ATAGCAAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (21 bp):
AACTAAAACATGTAATTAAGC
Found at i:4213 original size:15 final size:15
Alignment explanation
Indices: 4189--4226 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
4179 TAATATCATT
4189 AGTG-AAAAGAGCTC
1 AGTGAAAAAGAGCTC
4203 AGTGAAAAAGAGCTC
1 AGTGAAAAAGAGCTC
4218 AGTGAAAAA
1 AGTGAAAAA
4227 AAACTCAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.50, C:0.11, G:0.26, T:0.13
Consensus pattern (15 bp):
AGTGAAAAAGAGCTC
Found at i:4233 original size:15 final size:15
Alignment explanation
Indices: 4200--4233 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4190 GTGAAAAGAG
* *
4200 CTCAGTGAAAAAGAG
1 CTCAGTGAAAAAAAA
4215 CTCAGTGAAAAAAAA
1 CTCAGTGAAAAAAAA
4230 CTCA
1 CTCA
4234 ATGTATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.18, T:0.15
Consensus pattern (15 bp):
CTCAGTGAAAAAAAA
Found at i:9969 original size:16 final size:14
Alignment explanation
Indices: 9934--9967 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
9924 TATGACATTT
9934 TATAT-TTTGTTAA
1 TATATATTTGTTAA
9947 TATATATTTGTTAA
1 TATATATTTGTTAA
9961 TATATAT
1 TATATAT
9968 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (14 bp):
TATATATTTGTTAA
Found at i:11624 original size:13 final size:13
Alignment explanation
Indices: 11606--11630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11596 TTCTCCAGAA
11606 CTTCTTCTTCCTT
1 CTTCTTCTTCCTT
11619 CTTCTTCTTCCT
1 CTTCTTCTTCCT
11631 CTCCTCCCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
CTTCTTCTTCCTT
Found at i:13791 original size:18 final size:18
Alignment explanation
Indices: 13768--13840 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
13758 GTTCTTAAAG
13768 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
13786 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
13805 CAGTGGTCTTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
13824 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
13841 AATATTCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 4 0.09
20 13 0.28
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:13819 original size:38 final size:38
Alignment explanation
Indices: 13768--13841 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
13758 GTTCTTAAAG
*
13768 AGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACAATC
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATC
* *
13806 AGTGGTCTTTCGGGACATAGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAA
13842 ATATTCAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATC
Found at i:19277 original size:2 final size:2
Alignment explanation
Indices: 19270--19321 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
19260 AAACTTTTGC
19270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
19312 TT AT CT AT AT
1 AT AT AT AT AT
19322 TTAAAATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:19782 original size:30 final size:30
Alignment explanation
Indices: 19726--19782 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
19716 GACGTGGCTT
*
19726 AATTGTTTTTTTTATTGAGTTCAAGGGTCA
1 AATTGTTTTTTTTATTAAGTTCAAGGGTCA
* *
19756 AATTAGTTTTTTTT-TTAATTTTAAGGG
1 AATT-GTTTTTTTTATTAAGTTCAAGGG
19783 CTTAATTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 14 0.61
31 9 0.39
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.54
Consensus pattern (30 bp):
AATTGTTTTTTTTATTAAGTTCAAGGGTCA
Found at i:27371 original size:41 final size:41
Alignment explanation
Indices: 27326--27578 Score: 310
Period size: 41 Copynumber: 6.0 Consensus size: 41
27316 ATTCACGTTG
* * *
27326 CATTTCGCATTGCGATAGTTGAAAATCGCGTTACGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * * *
27367 CATTTCGCGTTGCGATAGTTGAAATCGTAACGCGATCT-CCACTATC
1 CATTTCGCGTTGCGATAGTTGAAA----ATCGCG-T-TGCGATTTTC
* *
27413 GCAAATTCGCGTTACGATAGTTGAAAATCGCGTTGCGATTTTC
1 -C-ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
27456 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
27497 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
27538 CATTTCGCGTTGCGATAGTTGAAATTCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
27579 TGCAGTTGTC
Statistics
Matches: 187, Mismatches: 16, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
41 141 0.75
42 2 0.01
43 6 0.03
44 5 0.03
45 5 0.03
46 5 0.03
47 2 0.01
48 21 0.11
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:27443 original size:21 final size:21
Alignment explanation
Indices: 27415--27574 Score: 164
Period size: 21 Copynumber: 7.8 Consensus size: 21
27405 CCACTATCGC
*
27415 AAATTCGCGTTACGATAGTTG
1 AAATTCGCGTTGCGATAGTTG
* * *
27436 AAAATCGCGTTGCGAT-TTTC
1 AAATTCGCGTTGCGATAGTTG
* *
27456 CATTTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATAGTTG
* *
27477 AAATTCGCGTTGCGAT-TTTC
1 AAATTCGCGTTGCGATAGTTG
* *
27497 CATTTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATAGTTG
* *
27518 AAATTCGCGTTGCGAT-TTTC
1 AAATTCGCGTTGCGATAGTTG
* *
27538 CATTTCGCGTTGCGATAGTTG
1 AAATTCGCGTTGCGATAGTTG
*
27559 AAATTCGCATTGCGAT
1 AAATTCGCGTTGCGAT
27575 TTTCTGCAGT
Statistics
Matches: 108, Mismatches: 28, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
20 47 0.44
21 61 0.56
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (21 bp):
AAATTCGCGTTGCGATAGTTG
Found at i:27465 original size:20 final size:20
Alignment explanation
Indices: 27440--27608 Score: 142
Period size: 21 Copynumber: 8.2 Consensus size: 20
27430 TAGTTGAAAA
*
27440 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
* **
27460 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCAAT
*
27481 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
* **
27501 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCAAT
*
27522 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
* **
27542 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCAAT
* *
27563 TCGCATTGCGATTTTCTGCAGT
1 TCGCGTTGCGATTTTC--CAAT
27585 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AAT
27606 TCG
1 TCG
27609 TTGCGATAGT
Statistics
Matches: 114, Mismatches: 27, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
20 47 0.41
21 51 0.45
22 16 0.14
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAAT
Found at i:27555 original size:82 final size:83
Alignment explanation
Indices: 27325--27596 Score: 343
Period size: 82 Copynumber: 3.2 Consensus size: 83
27315 AATTCACGTT
* * *
27325 GCATTTCGCATTGCGATAGTTGAAAATCGCGTTACGTTTTTCCATTTCGCGTTGCGATAGTTGAA
1 GCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAA
* * *
27390 ATCGTAACGCGATCT-CCACTATC
66 AT--T--CGCG-T-TGCGATTTTC
* *
27413 GCAAATTCGCGTTACGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGA
1 GC-ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGA
27478 AATTCGCGTTGCGATTTTC
65 AATTCGCGTTGCGATTTTC
*
27497 -CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAA
1 GCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAA
*
27561 ATTCGCATTGCGATTTTC
66 ATTCGCGTTGCGATTTTC
*
27579 TGCAGTT-GTCGTTGCGAT
1 -GCATTTCG-CGTTGCGAT
27597 TTTCCAAATT
Statistics
Matches: 166, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
82 77 0.46
83 3 0.02
84 19 0.11
85 4 0.02
87 1 0.01
88 2 0.01
89 60 0.36
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (83 bp):
GCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAA
ATTCGCGTTGCGATTTTC
Found at i:27596 original size:22 final size:21
Alignment explanation
Indices: 27568--27641 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 21
27558 GAAATTCGCA
27568 TTGCGATTTTCTGCAGTTGTCG
1 TTGCGATTTTCT-CAGTTGTCG
**
27590 TTGCGATTTTC-CAAAT-TCG
1 TTGCGATTTTCTCAGTTGTCG
**
27609 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATTTTCT-CAGTTGTCG
27631 TTGCGATTTTC
1 TTGCGATTTTC
27642 CAAATTCGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
19 12 0.29
20 3 0.07
21 3 0.07
22 23 0.56
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (21 bp):
TTGCGATTTTCTCAGTTGTCG
Found at i:27611 original size:19 final size:19
Alignment explanation
Indices: 27587--27652 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
27577 TCTGCAGTTG
27587 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
27606 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
27627 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
27647 TCGTTG
1 TCGTTG
27653 AAAAAAAAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:27995 original size:6 final size:6
Alignment explanation
Indices: 27974--28016 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
27964 TCTCGTCTCG
*
27974 GGTCG- GGTCG- GGTCGT GGTCGT TGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
28017 AATACGTGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:28163 original size:20 final size:20
Alignment explanation
Indices: 28138--28292 Score: 130
Period size: 20 Copynumber: 7.6 Consensus size: 20
28128 ACTTTAGACT
*
28138 ATCGCAACGCGAAACGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** *
28158 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
28179 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
28199 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
28220 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
28240 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
28261 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
28281 ATCGCAACGCGA
1 ATCGCAACGCGA
28293 TTTTCAACTA
Statistics
Matches: 101, Mismatches: 31, Indels: 6
0.73 0.22 0.04
Matches are distributed among these distances:
20 56 0.55
21 45 0.45
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:28184 original size:21 final size:21
Alignment explanation
Indices: 28158--28314 Score: 140
Period size: 21 Copynumber: 7.6 Consensus size: 21
28148 GAAACGGAAA
28158 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAATTTCAACT
* ** *
28179 ATCGCAACGCGAAATAGAA-A
1 ATCGCAACGCGAATTTCAACT
* *
28199 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGAATTTCAACT
* ** *
28220 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAATTTCAACT
*
28240 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATTTCAACT
* ** *
28261 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAATTTCAACT
*
28281 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATTTCAACT
*
28302 ATCTCAACGCGAA
1 ATCGCAACGCGAA
28315 ATGCAACGCG
Statistics
Matches: 100, Mismatches: 33, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
20 44 0.44
21 56 0.56
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAATTTCAACT
Found at i:28334 original size:41 final size:41
Alignment explanation
Indices: 28110--28317 Score: 328
Period size: 41 Copynumber: 5.0 Consensus size: 41
28100 ACAACGAATT
* *
28110 TGGAAAATCGCAACGACAACTTT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAA
* *
28152 CGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
* *
28193 TAGAAAATCGCAATGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
28234 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
*
28275 TGGAAAATCGCAACGCGATTTTCAACTATCTCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
28316 TG
1 TG
28318 CAACGCGAAT
Statistics
Matches: 155, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
41 140 0.90
42 15 0.10
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
Done.