Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008573.1 Hibiscus syriacus cultivar Beakdansim tig00111502_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: 313404
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:247774 original size:185 final size:185
Alignment explanation
Indices: 247412--247801 Score: 631
Period size: 185 Copynumber: 2.1 Consensus size: 185
247402 ATAAAATTTT
*
247412 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTCAGCCCAAACCATTTAAAACTCAATTAATAA
* *
247477 TTTAATATACAATAACTTTTAAACCTAAATCGATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATACAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
*
247542 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTAAA
* * *
247597 AAATATTATATATATTATATATAACATATGGACTCAGTCCAAACCATTTAAAACTTAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTCAGCCCAAACCATTTAAAACTCAATTAATAA
** * *
247662 TTTAAGATTTAATAACTTTTAACCCTAAATCAATATTAATTAATT-AAAATTTTATATAAAATTT
66 TTTAAGATACAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
*
247726 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTATA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTG-TTTTTTGAATTAAA
* *
247782 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
247802 AATTATAAAA
Statistics
Matches: 189, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
184 66 0.35
185 123 0.65
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGACTCAGCCCAAACCATTTAAAACTCAATTAATAA
TTTAAGATACAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTAAA
Found at i:251484 original size:25 final size:25
Alignment explanation
Indices: 251450--251503 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
251440 TAATATTTAG
251450 TTTAGGTTTAGGTTTCAATTTTAATA
1 TTTAGGTTTAGGTTTCAATTTT-ATA
*
251476 TTTA-GTTTATGTTTCAATTTTATA
1 TTTAGGTTTAGGTTTCAATTTTATA
251500 TTTA
1 TTTA
251504 TAATTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 7 0.26
25 16 0.59
26 4 0.15
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (25 bp):
TTTAGGTTTAGGTTTCAATTTTATA
Found at i:257126 original size:17 final size:17
Alignment explanation
Indices: 257104--257143 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
257094 TTCCATTAAT
257104 AACATCCCGAAACTATA
1 AACATCCCGAAACTATA
257121 AACATCCCGAAACTATA
1 AACATCCCGAAACTATA
257138 AACATC
1 AACATC
257144 AGCTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.30, G:0.05, T:0.17
Consensus pattern (17 bp):
AACATCCCGAAACTATA
Found at i:271697 original size:29 final size:29
Alignment explanation
Indices: 271664--271722 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
271654 CGCCATAATG
*
271664 CATGTCGCTAGGATGTCCTGGCGACCTAC
1 CATGTCGCTAGGATGCCCTGGCGACCTAC
*
271693 CATGTCGCTTGGATGCCCTGGCGACCTAC
1 CATGTCGCTAGGATGCCCTGGCGACCTAC
271722 C
1 C
271723 CATCGGACGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24
Consensus pattern (29 bp):
CATGTCGCTAGGATGCCCTGGCGACCTAC
Found at i:273606 original size:16 final size:16
Alignment explanation
Indices: 273587--273622 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
273577 TTTATTTCAA
* *
273587 AAATAATTTAAACTCG
1 AAATAACTTAAACCCG
273603 AAATAACTTAAACCCG
1 AAATAACTTAAACCCG
273619 AAAT
1 AAAT
273623 CCGGAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (16 bp):
AAATAACTTAAACCCG
Found at i:280160 original size:8 final size:8
Alignment explanation
Indices: 280147--280172 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
280137 CTCCAGTTCT
280147 CTCTCTCC
1 CTCTCTCC
280155 CTCTCTCC
1 CTCTCTCC
280163 CTCTCTCC
1 CTCTCTCC
280171 CT
1 CT
280173 TTAGGGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (8 bp):
CTCTCTCC
Found at i:288240 original size:29 final size:28
Alignment explanation
Indices: 288186--288243 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
288176 TGCAAATATA
288186 ATAATTTTTCAAATTAAATCGAAAAAAG
1 ATAATTTTTCAAATTAAATCGAAAAAAG
* *
288214 ATAATTTTTCAAGTTAAATCGTAAAAAG
1 ATAATTTTTCAAATTAAATCGAAAAAAG
288242 AT
1 AT
288244 TCCACCAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (28 bp):
ATAATTTTTCAAATTAAATCGAAAAAAG
Found at i:292476 original size:84 final size:83
Alignment explanation
Indices: 292339--292656 Score: 349
Period size: 84 Copynumber: 3.8 Consensus size: 83
292329 CCCCTGAATC
* * *
292339 CCTTGAATTCTGGTGTGGCAGCGTTGCAAAATACCCTGAATCCTGCTACACATTTACAGACTGGG
1 CCTTGAATCCTGGTGTGACAGCGTTGCAAAATCCCCTGAATCCTGCTACACATTTACAGACTGGG
* * *
292404 CAGTTGCAGTTGCAAAAT
66 AAATTGCAGCTGCAAAAT
* *
292422 CCCTTGAATCCTAGTGTGACAGCGTTGCAAAATCCCGTGAATCCTGCTACACATTTACAGACTGG
1 -CCTTGAATCCTGGTGTGACAGCGTTGCAAAATCCCCTGAATCCTGCTACACATTTACAGACTGG
*
292487 GTAACA-T-CAACTGCAACAAT
65 G-AA-ATTGCAGCTGCAA-AAT
*
292507 --TTGATCAGCCTCCTGGTGTCGA-AGCGTTGCAAAATCCCCTGAATCCTGCTACACATTTATAG
1 CCTTGA--A---TCCTGGTGT-GACAGCGTTGCAAAATCCCCTGAATCCTGCTACACATTTACAG
* * * *
292569 ATTGCGTAATTGCAGGTGCAAAAT
60 ACTGGGAAATTGCAGCTGCAAAAT
* * *
292593 CCTCTGAATCTTGGTGTGACAGCGTTGCAAAATCCCCTGATTCCTACTACACATTTACAGACTG
1 CCT-TGAATCCTGGTGTGACAGCGTTGCAAAATCCCCTGAATCCTGCTACACATTTACAGACTG
292657 AGCAACAGCA
Statistics
Matches: 197, Mismatches: 22, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
82 4 0.02
83 2 0.01
84 116 0.59
85 6 0.03
86 5 0.03
87 58 0.29
88 3 0.02
89 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (83 bp):
CCTTGAATCCTGGTGTGACAGCGTTGCAAAATCCCCTGAATCCTGCTACACATTTACAGACTGGG
AAATTGCAGCTGCAAAAT
Found at i:292564 original size:171 final size:171
Alignment explanation
Indices: 292348--292680 Score: 497
Period size: 171 Copynumber: 1.9 Consensus size: 171
292338 CCCTTGAATT
* * * *
292348 CTGGTGTGGCAGCGTTGCAAAATACCCTGAATCCTGCTACACATTTACAGACTGGGCAGTTGCAG
1 CTGGTGTCGAAGCGTTGCAAAATACCCTGAATCCTGCTACACATTTACAGACTGCGCAATTGCAG
* * *
292413 TTGCAAAATCC-CTTGAATCCTAGTGTGACAGCGTTGCAAAATCCCGTGAATCCTGCTACACATT
66 GTGCAAAATCCTC-TGAATCCTAGTGTGACAGCGTTGCAAAATCCCCTGAATCCTACTACACATT
* * *
292477 TACAGACTGGGTAACATCAACTGCAACAATTTGATCAGCCTC
130 TACAGACTGAGCAACAGCAACTGCAACAATTTGATCAGCCTC
* * * *
292519 CTGGTGTCGAAGCGTTGCAAAATCCCCTGAATCCTGCTACACATTTATAGATTGCGTAATTGCAG
1 CTGGTGTCGAAGCGTTGCAAAATACCCTGAATCCTGCTACACATTTACAGACTGCGCAATTGCAG
* * *
292584 GTGCAAAATCCTCTGAATCTTGGTGTGACAGCGTTGCAAAATCCCCTGATTCCTACTACACATTT
66 GTGCAAAATCCTCTGAATCCTAGTGTGACAGCGTTGCAAAATCCCCTGAATCCTACTACACATTT
292649 ACAGACTGAGCAACAGCAACTGCAACAATTTG
131 ACAGACTGAGCAACAGCAACTGCAACAATTTG
292681 GTCAACCCTA
Statistics
Matches: 144, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
171 143 0.99
172 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (171 bp):
CTGGTGTCGAAGCGTTGCAAAATACCCTGAATCCTGCTACACATTTACAGACTGCGCAATTGCAG
GTGCAAAATCCTCTGAATCCTAGTGTGACAGCGTTGCAAAATCCCCTGAATCCTACTACACATTT
ACAGACTGAGCAACAGCAACTGCAACAATTTGATCAGCCTC
Found at i:302060 original size:98 final size:100
Alignment explanation
Indices: 301890--302088 Score: 316
Period size: 98 Copynumber: 2.0 Consensus size: 100
301880 TCCCCATATT
*
301890 TGGAAAGCTGCTCATTTTCCCTGTATTCAATACAGAAAAAATACAATTACACAACTAGGAAGATT
1 TGGAAAGCTGCTCATTTTCCCTGTATTCAATACAGAAAAAATACAATTACACAACTAGGAAGATA
* * *
301955 TCAGGCATTCATCAGGGTTTGG-TTTACGTTAAAA
66 TCAGGCATTCATCAGGATTCGGTTTTACATTAAAA
301989 TGGAAAGCTGCTCATTTTCCCTGTCA-TCAGA-ACAG-AAAAATACAATTACACAACTAGGAAGA
1 TGGAAAGCTGCTCATTTTCCCTGT-ATTCA-ATACAGAAAAAATACAATTACACAACTAGGAAGA
302051 TATCAGGCATTCATCAGGATTCGGTTTTACATTAAAA
64 TATCAGGCATTCATCAGGATTCGGTTTTACATTAAAA
302088 T
1 T
302089 TAAAGTTTTC
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
98 48 0.52
99 43 0.46
100 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (100 bp):
TGGAAAGCTGCTCATTTTCCCTGTATTCAATACAGAAAAAATACAATTACACAACTAGGAAGATA
TCAGGCATTCATCAGGATTCGGTTTTACATTAAAA
Found at i:309405 original size:11 final size:11
Alignment explanation
Indices: 309367--309406 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
309357 ATTTTTTTTT
309367 CAAAAAAAAATG
1 CAAAAAAAAA-G
*
309379 CAAAAAAAAGG
1 CAAAAAAAAAG
309390 CAAAAAAAAA-
1 CAAAAAAAAAG
309400 CAAAAAA
1 CAAAAAA
309407 GCCAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 7 0.27
11 10 0.38
12 9 0.35
ACGTcount: A:0.80, C:0.10, G:0.07, T:0.03
Consensus pattern (11 bp):
CAAAAAAAAAG
Found at i:309414 original size:10 final size:10
Alignment explanation
Indices: 309370--309423 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
309360 TTTTTTTCAA
*
309370 AAAAAAATGCA
1 AAAAAAA-GCC
*
309381 AAAAAAAGGC
1 AAAAAAAGCC
**
309391 AAAAAAAAAC
1 AAAAAAAGCC
309401 -AAAAAAGCC
1 AAAAAAAGCC
309410 AAAAAAAGCC
1 AAAAAAAGCC
309420 AAAA
1 AAAA
309424 TTTCAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.19
10 22 0.61
11 7 0.19
ACGTcount: A:0.76, C:0.13, G:0.09, T:0.02
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:309415 original size:11 final size:10
Alignment explanation
Indices: 309369--309423 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 10
309359 TTTTTTTTCA
309369 AAAAAAAATGC
1 AAAAAAAA-GC
309380 AAAAAAAAGGC
1 AAAAAAAA-GC
309391 AAAAAAAA--
1 AAAAAAAAGC
*
309399 ACAAAAAAGC
1 AAAAAAAAGC
*
309409 CAAAAAAAGCC
1 AAAAAAAAG-C
309420 AAAA
1 AAAA
309424 TTTCAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
8 7 0.19
10 7 0.19
11 22 0.61
ACGTcount: A:0.76, C:0.13, G:0.09, T:0.02
Consensus pattern (10 bp):
AAAAAAAAGC
Done.