Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008324.1 Hibiscus syriacus cultivar Beakdansim tig00111028_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: 430640
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 3 of 3
Found at i:407529 original size:26 final size:27
Alignment explanation
Indices: 407500--407562 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
407490 ACGTGAGAAT
407500 AATAAATAAAACAAG-AAAAAATGAA-A
1 AATAAATAAAACAAGTAAAAAAT-AATA
* *
407526 AAT-AACAAAACACGTAAAAAATAATA
1 AATAAATAAAACAAGTAAAAAATAATA
*
407552 AAAAAATAAAA
1 AATAAATAAAA
407563 ATAAACAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
25 11 0.37
26 13 0.43
27 6 0.20
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.13
Consensus pattern (27 bp):
AATAAATAAAACAAGTAAAAAATAATA
Found at i:407645 original size:17 final size:18
Alignment explanation
Indices: 407625--407659 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
407615 TATTAATCGA
407625 GTAAA-AAAATAAAAAAG
1 GTAAAGAAAATAAAAAAG
*
407642 GTAAAGAAATTAAAAAAG
1 GTAAAGAAAATAAAAAAG
407660 AATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
GTAAAGAAAATAAAAAAG
Found at i:407786 original size:5 final size:5
Alignment explanation
Indices: 407778--407812 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
407768 AGAAAAAAAT
*
407778 AATAG AATAA AATAA AATAA AATAAA AATAA AATA
1 AATAA AATAA AATAA AATAA AAT-AA AATAA AATA
407813 TATATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:407796 original size:15 final size:16
Alignment explanation
Indices: 407786--407843 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
407776 ATAATAGAAT
407786 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
*
407802 AAAATAAAATATATATA
1 AAAATAAAATA-AAATA
* *
407819 TATATATAAAT-AAATA
1 AAAATA-AAATAAAATA
*
407835 AAAACAAAA
1 AAAATAAAA
407844 AATAGAATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 3 0.09
16 18 0.55
17 8 0.24
18 4 0.12
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:407903 original size:19 final size:18
Alignment explanation
Indices: 407840--407907 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
407830 AAATAAAAAC
*
407840 AAAAAATAGAATATTAAG
1 AAAAAATATAATATTAAG
**
407858 AAAAAATATATATAAAAACG
1 AAAAAATATA-ATATTAA-G
*
407878 TATAAAATATAATATTAAG
1 -AAAAAATATAATATTAAG
407897 AAAAAAATATA
1 -AAAAAATATA
407908 TATACATAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 9 0.23
19 15 0.38
20 6 0.15
21 9 0.23
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (18 bp):
AAAAAATATAATATTAAG
Found at i:407969 original size:16 final size:16
Alignment explanation
Indices: 407948--407993 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
407938 ATCTATACAT
*
407948 ATATATATAATATAAG
1 ATATATATAATATAAA
407964 ATATATATAATA-AAA
1 ATATATATAATATAAA
407979 ATA-ATATAATATAAA
1 ATATATATAATATAAA
407994 TAAAAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 8 0.29
15 8 0.29
16 12 0.43
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
ATATATATAATATAAA
Found at i:407982 original size:20 final size:20
Alignment explanation
Indices: 407946--407999 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
407936 ACATCTATAC
*
407946 ATATATAT-AT-AATATAAG
1 ATATATATAATAAAAATAAG
*
407964 ATATATATAATAAAAATAAT
1 ATATATATAATAAAAATAAG
407984 ATA-ATATAAATAAAAA
1 ATATATAT-AATAAAAA
408000 ATGAATATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.26
19 6 0.19
20 17 0.55
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATATATATAATAAAAATAAG
Found at i:407994 original size:14 final size:14
Alignment explanation
Indices: 407952--407996 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
407942 ATACATATAT
407952 ATATAATATAAGATA
1 ATATAATATAA-ATA
*
407967 TATATAATAAAAATA
1 -ATATAATATAAATA
407982 ATATAATATAAATA
1 ATATAATATAAATA
407996 A
1 A
407997 AAAATGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 14 0.52
15 3 0.11
16 10 0.37
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
ATATAATATAAATA
Found at i:414614 original size:22 final size:21
Alignment explanation
Indices: 414596--414638 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
414586 TATTGTATCC
*
414596 ATGTGT-CTGTGTTTGTGTAT
1 ATGTGTACTGTGTGTGTGTAT
414616 ATGTGTAACTGTGTGTGTGTAT
1 ATGTGT-ACTGTGTGTGTGTAT
414638 A
1 A
414639 CTTTCTCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.16, C:0.05, G:0.30, T:0.49
Consensus pattern (21 bp):
ATGTGTACTGTGTGTGTGTAT
Found at i:418624 original size:218 final size:218
Alignment explanation
Indices: 418204--418629 Score: 685
Period size: 217 Copynumber: 2.0 Consensus size: 218
418194 ATATTTAGTT
* * * * *
418204 CACGACTTTTTTCTTTTTCAAAATCATATCTATTGTTATGTTTTCGTTTCATTTTGATCACATGC
1 CACGACTTCTTTCTTCTTCAAAATCATATCTAATGTTATATTTTCGTTTCATTTTCATCACATGC
* *
418269 TGTAAAAAAACAGTGATATTGATGTGTCACCATAAGATAATATCATATAATCATTGAAAAAAATT
66 TGTAAAAAAACAGTGATAATGATGTATCACCATAAGATAATATCATATAATCATTGAAAAAAATT
*
418334 ACGATGTCACAGTTATGTTAATCTTTAATAGCGGGAGGCCAAAAAGAAAGCAAAATATAACGTTA
131 ACGATGTCACAGTTATATTAATCTTTAATAGCGGGAGGCCAAAAAGAAAGCAAAATATAACGTTA
418399 GATATAATTTTGAATTTTGGTCA
196 GATATAATTTTGAATTTTGGTCA
* *
418422 CACGACTTCTTT-TTCTTCAAAATCATATCTAATG-TATATTTTGGTTTTATTTTCATCACATGC
1 CACGACTTCTTTCTTCTTCAAAATCATATCTAATGTTATATTTTCGTTTCATTTTCATCACATGC
* *
418485 TGTTAAAAAAACAGTGATAATGATGTATCACCATAAGATAATGTCATATAATCATTGAAAAAACT
66 TG-TAAAAAAACAGTGATAATGATGTATCACCATAAGATAATATCATATAATCATTGAAAAAAAT
* *
418550 TACGATGTCATCAGTTATATTAATCTTTAATAGCGGGTGGCCAAAAAGAAAGCAAAATATAGCGT
130 TACGATGTCA-CAGTTATATTAATCTTTAATAGCGGGAGGCCAAAAAGAAAGCAAAATATAACGT
*
418615 TGGATATAATTTTGA
194 TAGATATAATTTTGA
418630 GAGAAAAAAA
Statistics
Matches: 191, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
216 27 0.14
217 88 0.46
218 76 0.40
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (218 bp):
CACGACTTCTTTCTTCTTCAAAATCATATCTAATGTTATATTTTCGTTTCATTTTCATCACATGC
TGTAAAAAAACAGTGATAATGATGTATCACCATAAGATAATATCATATAATCATTGAAAAAAATT
ACGATGTCACAGTTATATTAATCTTTAATAGCGGGAGGCCAAAAAGAAAGCAAAATATAACGTTA
GATATAATTTTGAATTTTGGTCA
Found at i:419108 original size:42 final size:42
Alignment explanation
Indices: 419039--419380 Score: 443
Period size: 42 Copynumber: 8.1 Consensus size: 42
419029 AACAGATACT
* * * * *
419039 GCAGAATCCAAACAATCAGTA-CAGAAGCTTTCCACGGAAATC
1 GCAGAATCCAAACAATCGGTAGC-GAAGCCTTCGACGGGAACC
*
419081 GCAGAATCCAAACAATCGGTGGCGAAGCCTTCGACGGGAACC
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
** * *
419123 GTTGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGAAATC
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
*
419165 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACG
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
419207 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
* *
419249 GCAGAATCCAAACAATCGGTGGAGAAGCCTTCGACGGGAACC
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
* * * * *
419291 GCGGAATCCAAACAATCGGTGGAGAAGCCTTTGACGGAAACC
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
* * * * * * *
419333 GCGGAATCTAAACAATCGGTTGAGAAGCCTTCGTCGGAAACA
1 GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
419375 GCAGAA
1 GCAGAA
419381 CCAGAGTCGA
Statistics
Matches: 271, Mismatches: 28, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 270 1.00
43 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.14
Consensus pattern (42 bp):
GCAGAATCCAAACAATCGGTAGCGAAGCCTTCGACGGGAACC
Found at i:422522 original size:14 final size:14
Alignment explanation
Indices: 422503--422532 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
422493 TTTTTAACCC
422503 CTTTTCTCCTTCTT
1 CTTTTCTCCTTCTT
422517 CTTTTCTCCTTCTT
1 CTTTTCTCCTTCTT
422531 CT
1 CT
422533 CCTCTTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
CTTTTCTCCTTCTT
Found at i:427306 original size:34 final size:32
Alignment explanation
Indices: 427232--427308 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 32
427222 TAAAATAAAC
*
427232 GACCATTTTATCATAATTTAATAAATTTTAAT
1 GACCATTTTATCATAATTTAATAAACTTTAAT
** *
427264 GATTATTTTATTATAATTATTTAA-AAACTTTAAT
1 GACCATTTTATCAT-A--ATTTAATAAACTTTAAT
427298 GACCATTTTAT
1 GACCATTTTAT
427309 AATTTAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
32 11 0.31
33 1 0.03
34 18 0.50
35 6 0.17
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (32 bp):
GACCATTTTATCATAATTTAATAAACTTTAAT
Done.