Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000053.1 Hibiscus syriacus cultivar Beakdansim tig00000080_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: 66648
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:15540 original size:24 final size:24
Alignment explanation
Indices: 15507--15552 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
15497 TCAAATAACA
*
15507 GTTTAGTGGTTTAATATAGTCCTT
1 GTTTAATGGTTTAATATAGTCCTT
15531 GTTTAATGGTTTAATATAGTCC
1 GTTTAATGGTTTAATATAGTCC
15553 ATTAGTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.48
Consensus pattern (24 bp):
GTTTAATGGTTTAATATAGTCCTT
Found at i:28743 original size:20 final size:21
Alignment explanation
Indices: 28718--28768 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
28708 ATTTGTAATA
*
28718 ATATTTTTAATAAAATA-TTT
1 ATATTTTAAATAAAATATTTT
28738 ATATTTTAAATAAAATATTTT
1 ATATTTTAAATAAAATATTTT
28759 ATATTTTAAA
1 ATATTTTAAA
28769 AAATGACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTTTAAATAAAATATTTT
Found at i:30109 original size:17 final size:18
Alignment explanation
Indices: 30075--30121 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
30065 AATTAAATTC
30075 ATATTTTTATTGAATAAAA
1 ATATTTTT-TTGAATAAAA
*
30094 ATATTTTTTT-AATAAAT
1 ATATTTTTTTGAATAAAA
*
30111 ATATTATTTTG
1 ATATTTTTTTG
30122 GGTCGGATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 15 0.60
18 2 0.08
19 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
ATATTTTTTTGAATAAAA
Found at i:30868 original size:18 final size:18
Alignment explanation
Indices: 30845--30882 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
30835 CCCAACATTG
30845 TCGACCTTTTCTTCAACC
1 TCGACCTTTTCTTCAACC
30863 TCGACCTTTTCTTCAACC
1 TCGACCTTTTCTTCAACC
30881 TC
1 TC
30883 ACCGCCGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.39, G:0.05, T:0.39
Consensus pattern (18 bp):
TCGACCTTTTCTTCAACC
Found at i:38717 original size:117 final size:117
Alignment explanation
Indices: 38511--38747 Score: 413
Period size: 117 Copynumber: 2.0 Consensus size: 117
38501 CAATGGCCAA
* *
38511 GCCCAAAAAAGAAGCTTCAAAATTTGGGTACGTGATGGTAACATTAATGAAAGTAGGACACCAAG
1 GCCCAAAAAAGAAGCTTCAAAATATGGGTACGTGATGGTAACATTAATGAAAGTAGCACACCAAG
38576 AAAAATAAACGGGTCACATTAACATATGTC-AGCCACGTTAAAATAATAAAAG
66 AAAAATAAACGGGTCACATTAACATATGTCGA-CCACGTTAAAATAATAAAAG
*
38628 GCCCAAAAAAGAATCTTCAAAATATGGGTACGTGATGGTAACATTAATGAAAGTAGCACACCAAG
1 GCCCAAAAAAGAAGCTTCAAAATATGGGTACGTGATGGTAACATTAATGAAAGTAGCACACCAAG
* *
38693 AAAAATAAATGGGTCCCATTAACATATGTCGACCACGTTAAAATAATAAAAG
66 AAAAATAAACGGGTCACATTAACATATGTCGACCACGTTAAAATAATAAAAG
38745 GCC
1 GCC
38748 TAATTAACTT
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
117 113 0.99
118 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (117 bp):
GCCCAAAAAAGAAGCTTCAAAATATGGGTACGTGATGGTAACATTAATGAAAGTAGCACACCAAG
AAAAATAAACGGGTCACATTAACATATGTCGACCACGTTAAAATAATAAAAG
Found at i:40259 original size:27 final size:27
Alignment explanation
Indices: 40211--40294 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
40201 CCATGTCAGT
* * * * *
40211 TAAAACTAACGGGAGGTGACAATATGC
1 TAAAACTAACGTGAGATAACAACATAC
* *
40238 TAAAACTAACATGAGATAACAACATAT
1 TAAAACTAACGTGAGATAACAACATAC
*
40265 TAAAACTAACGTGGGATAACAACATA-
1 TAAAACTAACGTGAGATAACAACATAC
40291 TAAA
1 TAAA
40295 CGAATTAACT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
26 4 0.08
27 44 0.92
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.20
Consensus pattern (27 bp):
TAAAACTAACGTGAGATAACAACATAC
Found at i:41279 original size:23 final size:23
Alignment explanation
Indices: 41253--41299 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
41243 TTGAGTGAGA
41253 GGGACGAGTTTGTTTATAGGGAT
1 GGGACGAGTTTGTTTATAGGGAT
41276 GGGACGAGTTTGTTTATAGGGAT
1 GGGACGAGTTTGTTTATAGGGAT
41299 G
1 G
41300 TTCAAACGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.40, T:0.34
Consensus pattern (23 bp):
GGGACGAGTTTGTTTATAGGGAT
Found at i:41511 original size:2 final size:2
Alignment explanation
Indices: 41504--41534 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41494 AAACTAAATA
41504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41535 ATAGTTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41596 original size:20 final size:20
Alignment explanation
Indices: 41554--41596 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41544 GTTAATTAAA
**
41554 TGAACCGAATTAACCGATTT
1 TGAACCGAATTAACCGAAAT
*
41574 TGAACCGAATTAATCGAAAT
1 TGAACCGAATTAACCGAAAT
41594 TGA
1 TGA
41597 CATTTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (20 bp):
TGAACCGAATTAACCGAAAT
Found at i:45570 original size:162 final size:160
Alignment explanation
Indices: 45248--45539 Score: 444
Period size: 162 Copynumber: 1.8 Consensus size: 160
45238 ATTAAAATTT
*
45248 AAATATTAAATATATTATATATAACATATGAACTTAACCCAAACTATTTAAAACCTAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAACTTAACCCAAACCATTTAAAACCTAATTAATAA
* **
45313 TTTAAGATTAAATAACTTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATATTATTT
66 TTTAAGATCAAATAACTTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTT
45378 AAATTAATTGTAAACTATTTTTTTAAATTAAA
131 --ATTAATTGTAAACTATTTTTTTAAATTAAA
* ** *
45410 AAATATTATATATATTATATATAACATAT-AGGTTAAACCTAAACCATTTAAAACCTAATTAATA
1 AAATATTAAATATATTATATATAACATATGAACTT-AACCCAAACCATTTAAAACCTAATTAATA
* *
45474 ATTTAAGATCCAATAAC-TTTTAAACTTAAATCAATATTAATTAATTAAAAAAATTATATAAAAT
65 ATTTAAGATCAAATAACTTTTTAAACCTAAATCAATATTAATTAATT-AAAAAATTATATAAAAT
45538 TT
129 TT
45540 TTATTTTATA
Statistics
Matches: 118, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
161 31 0.26
162 87 0.74
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (160 bp):
AAATATTAAATATATTATATATAACATATGAACTTAACCCAAACCATTTAAAACCTAATTAATAA
TTTAAGATCAAATAACTTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTT
ATTAATTGTAAACTATTTTTTTAAATTAAA
Found at i:50668 original size:12 final size:12
Alignment explanation
Indices: 50651--50736 Score: 100
Period size: 12 Copynumber: 7.2 Consensus size: 12
50641 CGGACCTGCT
50651 AAGGAAGAAAAG
1 AAGGAAGAAAAG
50663 AAGGAAGAAAAG
1 AAGGAAGAAAAG
* * *
50675 AAAGAGGAGAAG
1 AAGGAAGAAAAG
*
50687 AAGGAAGAGAAG
1 AAGGAAGAAAAG
* *
50699 AAAGAGGAAAAG
1 AAGGAAGAAAAG
* *
50711 AAAGAAGAGAAG
1 AAGGAAGAAAAG
50723 AAGGAAGAAAAG
1 AAGGAAGAAAAG
50735 AA
1 AA
50737 ATGAATTTTG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 62 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (12 bp):
AAGGAAGAAAAG
Found at i:50692 original size:24 final size:24
Alignment explanation
Indices: 50657--50736 Score: 115
Period size: 24 Copynumber: 3.3 Consensus size: 24
50647 TGCTAAGGAA
*
50657 GAAAAGAAGGAAGAAAAGAAAGAG
1 GAAAAGAAGGAAGAGAAGAAAGAG
*
50681 GAGAAGAAGGAAGAGAAGAAAGAG
1 GAAAAGAAGGAAGAGAAGAAAGAG
* * *
50705 GAAAAGAAAGAAGAGAAGAAGGAA
1 GAAAAGAAGGAAGAGAAGAAAGAG
50729 GAAAAGAA
1 GAAAAGAA
50737 ATGAATTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (24 bp):
GAAAAGAAGGAAGAGAAGAAAGAG
Found at i:50700 original size:36 final size:36
Alignment explanation
Indices: 50651--50737 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
50641 CGGACCTGCT
* *
50651 AAGGAAGAAAAGAAGGAAGAAAAGAAAGAGGAGAAG
1 AAGGAAGAAAAGAAAGAAGAAAAGAAAGAAGAGAAG
* *
50687 AAGGAAGAGAAGAAAGAGGAAAAGAAAGAAGAGAAG
1 AAGGAAGAAAAGAAAGAAGAAAAGAAAGAAGAGAAG
50723 AAGGAAGAAAAGAAA
1 AAGGAAGAAAAGAAA
50738 TGAATTTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (36 bp):
AAGGAAGAAAAGAAAGAAGAAAAGAAAGAAGAGAAG
Found at i:59674 original size:34 final size:34
Alignment explanation
Indices: 59631--59711 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
59621 CTTCTATGAT
59631 TGTTTCATGAAACTAACATATCACTGTCTAGTTG
1 TGTTTCATGAAACTAACATATCACTGTCTAGTTG
59665 TGTTTCATGAAACTAACATATCACTGTCTAGTTG
1 TGTTTCATGAAACTAACATATCACTGTCTAGTTG
59699 TGTTTCATGAAAC
1 TGTTTCATGAAAC
59712 GATATTATTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (34 bp):
TGTTTCATGAAACTAACATATCACTGTCTAGTTG
Done.