Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000148.1 Hibiscus syriacus cultivar Beakdansim tig00000263_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: 28454
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:3290 original size:23 final size:22
Alignment explanation
Indices: 3264--3306 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3254 ATGTCATTAT
* *
3264 TGTGTATATATGTATATATATGA
1 TGTGAATATATATATA-ATATGA
3287 TGTGAATATATATATAATAT
1 TGTGAATATATATATAATAT
3307 TGTTAGTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (22 bp):
TGTGAATATATATATAATATGA
Found at i:4826 original size:18 final size:18
Alignment explanation
Indices: 4803--4855 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
4793 ACTGAATATT
4803 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
4821 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
4839 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
4856 GAAAATCCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5104 original size:2 final size:2
Alignment explanation
Indices: 5097--5140 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5087 CATAACATTA
5097 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
5139 AT
1 AT
5141 GCATGAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12030 original size:14 final size:14
Alignment explanation
Indices: 12011--12037 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12001 ATCTTAAGGG
12011 GTGTATCGATACAT
1 GTGTATCGATACAT
12025 GTGTATCGATACA
1 GTGTATCGATACA
12038 CTTATTGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (14 bp):
GTGTATCGATACAT
Found at i:14312 original size:16 final size:16
Alignment explanation
Indices: 14291--14322 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14281 ATAAATTAAA
14291 TTAGTGATACTCATCG
1 TTAGTGATACTCATCG
*
14307 TTAGTGATGCTCATCG
1 TTAGTGATACTCATCG
14323 GTACTTGTCG
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:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (16 bp):
TTAGTGATACTCATCG
Found at i:15296 original size:3 final size:3
Alignment explanation
Indices: 15288--15314 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
15278 AAGATTTGAG
15288 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
15315 ATGATCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:15452 original size:31 final size:31
Alignment explanation
Indices: 15397--15459 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
15387 GAAGAATAAG
***
15397 AAGAAGAAGAAATGGTCATCACACACGACAT
1 AAGAAGAAGAAACAATCATCACACACGACAT
* *
15428 AAGAAGAAGAAACAATCATTACACACGGCAT
1 AAGAAGAAGAAACAATCATCACACACGACAT
15459 A
1 A
15460 TACTCCGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (31 bp):
AAGAAGAAGAAACAATCATCACACACGACAT
Found at i:15730 original size:19 final size:18
Alignment explanation
Indices: 15694--15731 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
15684 GATGATTCCA
15694 TTAAAATAATTTAGAAAT
1 TTAAAATAATTTAGAAAT
15712 TTAAAGATAACTTTA-AAAT
1 TTAAA-ATAA-TTTAGAAAT
15731 T
1 T
15732 ATATATCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (18 bp):
TTAAAATAATTTAGAAAT
Found at i:16105 original size:19 final size:19
Alignment explanation
Indices: 16055--16112 Score: 89
Period size: 21 Copynumber: 2.9 Consensus size: 19
16045 AAACATTGAT
16055 ATATGTAATTTATATAAAA
1 ATATGTAATTTATATAAAA
*
16074 ATATGATCTATTTATATAAAA
1 ATATG-T-AATTTATATAAAA
16095 ATATGTAATTTATATAAA
1 ATATGTAATTTATATAAA
16113 GATTGCAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.46
20 2 0.06
21 17 0.49
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (19 bp):
ATATGTAATTTATATAAAA
Found at i:18234 original size:22 final size:22
Alignment explanation
Indices: 18169--18234 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
18159 ATCGAATATA
* * * *
18169 TAAACGAACGATAAACAAACAC
1 TAAAAGAACGCTAAACGAACAT
*
18191 TAAAACAACGCTAAACGAACAT
1 TAAAAGAACGCTAAACGAACAT
*
18213 TAAATGAACGCTAAACGAACAT
1 TAAAAGAACGCTAAACGAACAT
18235 GTTCGTGAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.55, C:0.21, G:0.11, T:0.14
Consensus pattern (22 bp):
TAAAAGAACGCTAAACGAACAT
Found at i:20238 original size:2 final size:2
Alignment explanation
Indices: 20233--20263 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20223 AGACACACAC
20233 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
20264 ATCTCATTAT
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:21473 original size:64 final size:65
Alignment explanation
Indices: 21386--21518 Score: 207
Period size: 65 Copynumber: 2.1 Consensus size: 65
21376 TCCTAATTCA
* * *
21386 AATGCATTTTGTGTACCAATGCACAG-CCATGCATCGATGCACTCCTGA-TTTTATTGAAACATC
1 AATGCATTTTATGAACCAATGCACAGACCATGCATCGATGCACTCCTGACTCTT-TTGAAACATC
21449 G
65 G
*
21450 AATGCATTTTATGAACCGATGCACAGACCATGCATCGATGCACTCCTGACTCTTTTGAAACATCG
1 AATGCATTTTATGAACCAATGCACAGACCATGCATCGATGCACTCCTGACTCTTTTGAAACATCG
21515 AATG
1 AATG
21519 TAATTAGTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
64 23 0.37
65 37 0.59
66 3 0.05
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (65 bp):
AATGCATTTTATGAACCAATGCACAGACCATGCATCGATGCACTCCTGACTCTTTTGAAACATCG
Found at i:27336 original size:23 final size:22
Alignment explanation
Indices: 27310--27380 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
27300 GAAAGTGTAC
27310 CGATGCATTCCTTGAATATGCAT
1 CGATGCA-TCCTTGAATATGCAT
* *
27333 CGATGCA--CTATGAAGATGCAC
1 CGATGCATCCT-TGAATATGCAT
* *
27354 CGATGTATGCCTTGAATGTGCAT
1 CGATGCAT-CCTTGAATATGCAT
27377 CGAT
1 CGAT
27381 ACACTCGTCG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.05
21 15 0.39
23 19 0.50
24 2 0.05
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (22 bp):
CGATGCATCCTTGAATATGCAT
Found at i:27356 original size:44 final size:44
Alignment explanation
Indices: 27284--27385 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
27274 TTGTGCACTG
* * *
27284 TGCATTGATACACTATGAAAGTGTACCGATGCATTCCTTGAATA
1 TGCATCGATACACTATGAAAGTGCACCGATGCATGCCTTGAATA
* * *
27328 TGCATCGATGCACTATG-AAGATGCACCGATGTATGCCTTGAATG
1 TGCATCGATACACTATGAAAG-TGCACCGATGCATGCCTTGAATA
27372 TGCATCGATACACT
1 TGCATCGATACACT
27386 CGTCGGGTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 3 0.06
44 47 0.94
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGCACCGATGCATGCCTTGAATA
Found at i:27869 original size:13 final size:13
Alignment explanation
Indices: 27846--27884 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
27836 AAAACTTCAT
27846 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAC
27860 ATTGTTTTCAAAC
1 ATTGTTTTCAAAC
*
27873 ATAGTTTTCAAA
1 ATTGTTTTCAAA
27885 ATTACCCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Done.