Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002509.1 Hibiscus syriacus cultivar Beakdansim tig00005109_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: 63227
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3197 original size:111 final size:111
Alignment explanation
Indices: 2992--3385 Score: 635
Period size: 111 Copynumber: 3.5 Consensus size: 111
2982 CACCTCTAGG
* *
2992 GTAGGGGATAGTGTTGCTATAAATGTGGATAAAAGTACAACCAAGCTCTCTGTCCCCAATAACTC
1 GTAGGGAATAGTGTTGCTATAAATCTGGATAAAAGTACAACCAAGCTCTCTGTCCCCAATAACTC
3057 TATCCAATTAACAGAAGACCTAAAAGGAGCAGAAACCCAGTCCAGT
66 TATCCAATTAACAGAAGACCTAAAAGGAGCAGAAACCCAGTCCAGT
** * *
3103 GGGGGGAATATTGTTGCTATAAATCTGGATAAAAGTACAACCAAACTCTCTGTCCCCAATAACTC
1 GTAGGGAATAGTGTTGCTATAAATCTGGATAAAAGTACAACCAAGCTCTCTGTCCCCAATAACTC
*
3168 TATCCTATTAACAGAAGACCTAAAAGGAGCAGAAACCCAGTCCAGT
66 TATCCAATTAACAGAAGACCTAAAAGGAGCAGAAACCCAGTCCAGT
* * *
3214 GTAGGGAATAGTGTTACTATAAATCTGGATAAAATTACAACCAAGCTCTCTGTCCCCAATAACTG
1 GTAGGGAATAGTGTTGCTATAAATCTGGATAAAAGTACAACCAAGCTCTCTGTCCCCAATAACTC
* * *
3279 TATCGAATTAACAGAAGACCTCAAAGGAGCAGAAACCCAGTCCAAT
66 TATCCAATTAACAGAAGACCTAAAAGGAGCAGAAACCCAGTCCAGT
* * * *
3325 GTAGGGAATAGTGTTGTTATAAATCTGGATAAAAGTAAAACCAAGCTTTCTGTCTCCAATA
1 GTAGGGAATAGTGTTGCTATAAATCTGGATAAAAGTACAACCAAGCTCTCTGTCCCCAATA
3386 GCTCCAACCA
Statistics
Matches: 259, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 259 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (111 bp):
GTAGGGAATAGTGTTGCTATAAATCTGGATAAAAGTACAACCAAGCTCTCTGTCCCCAATAACTC
TATCCAATTAACAGAAGACCTAAAAGGAGCAGAAACCCAGTCCAGT
Found at i:5520 original size:28 final size:28
Alignment explanation
Indices: 5496--5555 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
5486 ATTATTAGTT
5496 TATTAATATTTTTTTAGAAGTATTAGGA
1 TATTAATATTTTTTTAGAAGTATTAGGA
5524 TATTAATATTTTTTTAGAAGTATTAGGA
1 TATTAATATTTTTTTAGAAGTATTAGGA
5552 TATT
1 TATT
5556 TTTTTATGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (28 bp):
TATTAATATTTTTTTAGAAGTATTAGGA
Found at i:21880 original size:2 final size:2
Alignment explanation
Indices: 21873--21917 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
21863 TATTGTACTT
21873 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
21915 GA G
1 GA G
21918 TATAAGCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23207 original size:18 final size:18
Alignment explanation
Indices: 23154--23208 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 18
23144 AAAATAATTG
*
23154 TTTATTAACGGTGTCTACT
1 TTTATTAACTGTGTCTA-T
* *
23173 TATATTAA-T-TGTTTAT
1 TTTATTAACTGTGTCTAT
23189 TTTATTAACTGTGTCTAT
1 TTTATTAACTGTGTCTAT
23207 TT
1 TT
23209 AAAAAAATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 8 0.28
19 7 0.24
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.56
Consensus pattern (18 bp):
TTTATTAACTGTGTCTAT
Found at i:23218 original size:35 final size:35
Alignment explanation
Indices: 23154--23220 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
23144 AAAATAATTG
* **
23154 TTTATTAACGGTGTCTACTTATATTAATTGTTTAT
1 TTTATTAACGGTGTCTACTTAAAAAAATTGTTTAT
* *
23189 TTTATTAACTGTGTCTATTTAAAAAAATTGTT
1 TTTATTAACGGTGTCTACTTAAAAAAATTGTT
23221 ATTAATATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.52
Consensus pattern (35 bp):
TTTATTAACGGTGTCTACTTAAAAAAATTGTTTAT
Found at i:24054 original size:16 final size:16
Alignment explanation
Indices: 24033--24064 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24023 ACTATTCACA
*
24033 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
24049 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
24065 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:30072 original size:24 final size:23
Alignment explanation
Indices: 29994--30081 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
29984 AAATCTTATA
* *
29994 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
30017 TGGCACTTCGGTGCAATTATATG
1 TGGCACTTCGGTGCAATTCTACG
*
30040 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
30064 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
30082 TATACGAGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
22 1 0.02
23 33 0.63
24 17 0.33
25 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:30743 original size:21 final size:21
Alignment explanation
Indices: 30719--30759 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
30709 GAAATTTTAG
*
30719 TGCATCGGTGCACTGTAGCAA
1 TGCATCGATGCACTGTAGCAA
30740 TGCATCGATGCACTGTAGCA
1 TGCATCGATGCACTGTAGCA
30760 CTGTTCACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCACTGTAGCAA
Found at i:30778 original size:12 final size:12
Alignment explanation
Indices: 30759--30790 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
30749 GCACTGTAGC
30759 ACTGTTCACGAT
1 ACTGTTCACGAT
*
30771 ATTGTTCACGAT
1 ACTGTTCACGAT
30783 ACTGTTCA
1 ACTGTTCA
30791 TACCATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (12 bp):
ACTGTTCACGAT
Found at i:41039 original size:25 final size:25
Alignment explanation
Indices: 40991--41041 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
40981 TGGCTAAGAT
* *
40991 GTATGAATGTCGGCTTTATGGATAA
1 GTATGAATGTCGGCTTCATAGATAA
41016 GTATGAATGTCGGCGTTCA-AGATAA
1 GTATGAATGTCGGC-TTCATAGATAA
41041 G
1 G
41042 CATTGACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.31
Consensus pattern (25 bp):
GTATGAATGTCGGCTTCATAGATAA
Found at i:52703 original size:23 final size:21
Alignment explanation
Indices: 52649--52710 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
52639 TTTTGGTGTA
52649 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAATCGATTCCCCCCTT
* *
52669 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCTT
52690 GAAGGGGAATCGATTCCCCCC
1 G-A-GGGAATCGATTCCCCCC
52711 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 15 0.43
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCTT
Found at i:58596 original size:24 final size:24
Alignment explanation
Indices: 58569--58649 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
58559 ACACTTAACA
58569 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
58593 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
58615 -TGCA-CTGATGCA-CTCTTTGAAT
1 GTGCATC-GATGCATCCCTTTGAAT
58637 GTGCATCGATGCA
1 GTGCATCGATGCA
58650 CACGGTCATG
Statistics
Matches: 45, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
20 4 0.09
21 11 0.24
23 13 0.29
24 17 0.38
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:61410 original size:45 final size:44
Alignment explanation
Indices: 61354--61460 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 44
61344 TGCACCAATC
61354 CATGCATCGATGCAC-CATGG-AATT-AATTGAACATCGAATGCATTT
1 CATGCATCGATGCACTCA-GGCAATTCAA---AACATCGAATGCATTT
* *
61399 TATGCATCGATGCACTCAGGCTATTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCAGGC-AATTCAAAACATCGAATGCATTT
61444 CATGCATCGATGCACTC
1 CATGCATCGATGCACTC
61461 TTAGTGCACC
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
45 48 0.87
46 2 0.04
47 3 0.05
48 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (44 bp):
CATGCATCGATGCACTCAGGCAATTCAAAACATCGAATGCATTT
Done.