Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008649.1 Hibiscus syriacus cultivar Beakdansim tig00111639_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: 25997
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Found at i:78 original size:23 final size:22
Alignment explanation
Indices: 19--85 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
9 TATGGACATC
*
19 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
41 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
63 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
86 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:3213 original size:21 final size:21
Alignment explanation
Indices: 3187--3231 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3177 GATTTCTGGG
* *
3187 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3208 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3229 CAA
1 CAA
3232 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4961 original size:23 final size:22
Alignment explanation
Indices: 4902--4968 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
4892 TATGGACATC
*
4902 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
4924 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
4946 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
4969 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:10319 original size:18 final size:18
Alignment explanation
Indices: 10296--10365 Score: 88
Period size: 18 Copynumber: 3.8 Consensus size: 18
10286 ATTTTGATTA
10296 TTTTCCTTTGCTTTTAAT
1 TTTTCCTTTGCTTTTAAT
* *
10314 TTTTCCTTTGATTTTGATT
1 TTTTCCTTTGCTTTT-AAT
*
10333 CTTTTCCTTTGCTTTCAAT
1 -TTTTCCTTTGCTTTTAAT
10352 TTTTCCTTTG-TTTT
1 TTTTCCTTTGCTTTT
10366 TGATTCTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
17 3 0.07
18 24 0.55
19 4 0.09
20 13 0.30
ACGTcount: A:0.09, C:0.17, G:0.07, T:0.67
Consensus pattern (18 bp):
TTTTCCTTTGCTTTTAAT
Found at i:10338 original size:38 final size:38
Alignment explanation
Indices: 10282--10376 Score: 163
Period size: 38 Copynumber: 2.5 Consensus size: 38
10272 TTACTTTACT
* *
10282 TTTGATTTTGATTATTTTCCTTTGCTTTTAATTTTTCC
1 TTTGATTTTGATTCTTTTCCTTTGCTTTCAATTTTTCC
10320 TTTGATTTTGATTCTTTTCCTTTGCTTTCAATTTTTCC
1 TTTGATTTTGATTCTTTTCCTTTGCTTTCAATTTTTCC
*
10358 TTTGTTTTTGATTCTTTTC
1 TTTGATTTTGATTCTTTTC
10377 TAATAGTCTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.11, C:0.15, G:0.08, T:0.66
Consensus pattern (38 bp):
TTTGATTTTGATTCTTTTCCTTTGCTTTCAATTTTTCC
Found at i:13708 original size:18 final size:18
Alignment explanation
Indices: 13673--13708 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13663 AAAATGGGTA
* *
13673 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
13691 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
13709 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:16504 original size:2 final size:2
Alignment explanation
Indices: 16497--16557 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
16487 TAGGTCATTA
*
16497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
*
16539 CT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
16558 AAAAGAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18564 original size:21 final size:19
Alignment explanation
Indices: 18526--18567 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
18516 TATAATATAA
*
18526 CATATGATTACGTTTATGT
1 CATATGATTACATTTATGT
18545 CATATGTATTATCATTTATGT
1 CATATG-ATTA-CATTTATGT
18566 CA
1 CA
18568 ATATCAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 4 0.20
21 10 0.50
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (19 bp):
CATATGATTACATTTATGT
Found at i:20223 original size:15 final size:15
Alignment explanation
Indices: 20203--20233 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20193 CAAAAAATAA
20203 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
20218 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
20233 A
1 A
20234 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:20425 original size:19 final size:18
Alignment explanation
Indices: 20383--20425 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
20373 CAGTAATCCT
**
20383 ATTCCCTGGTAATCTTTT
1 ATTCCCTGGTAATCTTAC
20401 ATTTCCACTGGTAATCTTAC
1 A-TTCC-CTGGTAATCTTAC
20421 ATTCC
1 ATTCC
20426 GTGAATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 8 0.38
20 12 0.57
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
ATTCCCTGGTAATCTTAC
Found at i:22399 original size:18 final size:18
Alignment explanation
Indices: 22378--22419 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
22368 CCGACCTGTT
22378 GACCCGAACCGTTGACTC
1 GACCCGAACCGTTGACTC
*
22396 GACCCGAATCGTTGACTC
1 GACCCGAACCGTTGACTC
22414 GACCCG
1 GACCCG
22420 TTGACCCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (18 bp):
GACCCGAACCGTTGACTC
Found at i:24905 original size:23 final size:23
Alignment explanation
Indices: 24852--24921 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
24842 ATACGTTACC
*
24852 TGAATTCTGTTATGATTCTGATC
1 TGAATTCTGTTATGATTCTGATA
* *
24875 TGGA-TCTGTTCTGATATCTGATA
1 TGAATTCTGTTATGAT-TCTGATA
*
24898 T-AATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGA-TTCTGATA
24921 T
1 T
24922 CTCCGTTTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 11 0.28
23 27 0.69
24 1 0.03
ACGTcount: A:0.21, C:0.11, G:0.17, T:0.50
Consensus pattern (23 bp):
TGAATTCTGTTATGATTCTGATA
Done.