Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000089.1 Hibiscus syriacus cultivar Beakdansim tig00000164_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: 62952
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:4601 original size:29 final size:28
Alignment explanation
Indices: 4564--4629 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
4554 ACTAAACATT
4564 TTATGAAATTATACAAAA-TAGAGACCCTAA
1 TTAT-AAATTA-A-AAAATTAGAGACCCTAA
*
4594 TTATAAATTAAAAAATTGGAGACCCTAA
1 TTATAAATTAAAAAATTAGAGACCCTAA
*
4622 CTATAAAT
1 TTATAAAT
4630 ACAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 4 0.12
28 19 0.58
29 6 0.18
30 4 0.12
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (28 bp):
TTATAAATTAAAAAATTAGAGACCCTAA
Found at i:6512 original size:19 final size:18
Alignment explanation
Indices: 6487--6529 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
6477 GATTTAAAAA
6487 AATAATAAATAACTTATTTT
1 AATAATAAATAA--TATTTT
*
6507 -ATAATATATAATATTTT
1 AATAATAAATAATATTTT
6524 AATAAT
1 AATAAT
6530 TTAAAACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 5 0.24
19 10 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAATAAATAATATTTT
Found at i:7028 original size:31 final size:30
Alignment explanation
Indices: 6991--7092 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 30
6981 CGAATGATTC
6991 GATATTGATCCGACCTGAAATCAACCGATCT
1 GATATTGA-CCGACCTGAAATCAACCGATCT
* * * ** *
7022 GGTATTGACCCAGCCCGAAAATCAATTGATAT
1 GATATTGACCGA-CCTG-AAATCAACCGATCT
* *
7054 GATTTTGACCTGACCTGAAATCAACCTATCT
1 GATATTGACC-GACCTGAAATCAACCGATCT
*
7085 GATTTTGA
1 GATATTGA
7093 TCCGGCCCAA
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
30 3 0.06
31 28 0.52
32 22 0.41
33 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (30 bp):
GATATTGACCGACCTGAAATCAACCGATCT
Found at i:7769 original size:14 final size:14
Alignment explanation
Indices: 7750--7782 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
7740 TAATGCTTCA
7750 AGCATTGGCTCGAT
1 AGCATTGGCTCGAT
7764 AGCATTGGCTCGAT
1 AGCATTGGCTCGAT
7778 AGCAT
1 AGCAT
7783 AATATAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (14 bp):
AGCATTGGCTCGAT
Found at i:11222 original size:13 final size:14
Alignment explanation
Indices: 11204--11236 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
11194 ATGGAACAGC
11204 GATTTTATA-AAAT
1 GATTTTATATAAAT
11217 GATTTTATATAAAT
1 GATTTTATATAAAT
*
11231 TATTTT
1 GATTTT
11237 TGTTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
GATTTTATATAAAT
Found at i:14817 original size:2 final size:2
Alignment explanation
Indices: 14810--14835 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14800 AATACTATTC
14810 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
14836 TATTTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20616 original size:16 final size:16
Alignment explanation
Indices: 20595--20628 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
20585 ATAATATTGT
20595 ATAAAACAT-TAATAAA
1 ATAAAACATGT-ATAAA
20611 ATAAAACATGTATAAA
1 ATAAAACATGTATAAA
20627 AT
1 AT
20629 TAGTTGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
ATAAAACATGTATAAA
Found at i:21348 original size:23 final size:22
Alignment explanation
Indices: 21301--21353 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
21291 TTCATACCCA
*
21301 AAATAATATAAAAACTATTTGT
1 AAATAATATAAAAACTATTTAT
*
21323 AAATCAATATAAAGA-TATTTCAT
1 AAAT-AATATAAAAACTATTT-AT
21346 AAAATAAT
1 -AAATAAT
21354 TCAAATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 9 0.35
23 13 0.50
24 4 0.15
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.34
Consensus pattern (22 bp):
AAATAATATAAAAACTATTTAT
Found at i:53566 original size:253 final size:253
Alignment explanation
Indices: 53056--53566 Score: 891
Period size: 254 Copynumber: 2.0 Consensus size: 253
53046 TAAAGTTTTC
* *
53056 TGAACTGAGAAAGGTATTTGAAAACTGGGAATTGAAAGAATTTTTGTAAAAGAGAATAGAAATAA
1 TGAACTGAGAAAGGTATTTGAAAACTGGGAATTGAAAGAATTTCTGTAAAAGAGAACAGAAATAA
*
53121 ATTCACTTTTATGTTTCTTTGAAAAATTCTAGGCCTACTATATACAAGAAACTAATCTATTCTAA
66 ATTCACTTTTATGTTTCTTTGAAAAATTCTAGGCCTACAATATACAAGAAACTAATCTATTCTAA
* *
53186 TGCTTACAATCTGCGAAGTACTAGAGATTAGATAGCAACAAATCAGGTATTGATATTGAGAAAAA
131 TACTTACAATCTGCGAAGTACTAGAGATTAGATAGCAACAAATCAGGTATTGATACTGAGAAAAA
*
53251 TAAAAGTAAAATAATATTCCTAAACTAGCTCCTAGAAATATGGAAATTAATAAATTGA
196 TAAAAGTAAAATAATATTCCTAAACTAACTCCTAGAAATATGGAAATTAATAAATTGA
53309 TGAACTGAGAAAGGTATTTGAAAAACTGGGAATTGAAAGAATTTCTGTAAAAGAGAACAGAAATA
1 TGAACTGAGAAAGGTATTTG-AAAACTGGGAATTGAAAGAATTTCTGTAAAAGAGAACAGAAATA
*
53374 AATTTACTTTTATGTTTCTTTGAAAAATTCTAGGCCTACAATATACAAGAAACT-ATCCTATTCT
65 AATTCACTTTTATGTTTCTTTGAAAAATTCTAGGCCTACAATATACAAGAAACTAAT-CTATTCT
* * * *
53438 AATACTTAGAATCTGTGAAGTACTAGAGATTAGATAGTAACAAGTCAGGTATTGATACTGAGAAA
129 AATACTTACAATCTGCGAAGTACTAGAGATTAGATAGCAACAAATCAGGTATTGATACTGAGAAA
53503 AATAAAAGT-AAATAATATTCCTAAACTAACTCCTAGAAATATGGAAATTAATAAATTGA
194 AATAAAAGTAAAATAATATTCCTAAACTAACTCCTAGAAATATGGAAATTAATAAATTGA
53562 TGAAC
1 TGAAC
53567 GGTCAATGCT
Statistics
Matches: 245, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
253 76 0.31
254 169 0.69
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (253 bp):
TGAACTGAGAAAGGTATTTGAAAACTGGGAATTGAAAGAATTTCTGTAAAAGAGAACAGAAATAA
ATTCACTTTTATGTTTCTTTGAAAAATTCTAGGCCTACAATATACAAGAAACTAATCTATTCTAA
TACTTACAATCTGCGAAGTACTAGAGATTAGATAGCAACAAATCAGGTATTGATACTGAGAAAAA
TAAAAGTAAAATAATATTCCTAAACTAACTCCTAGAAATATGGAAATTAATAAATTGA
Done.