Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008599.1 Hibiscus syriacus cultivar Beakdansim tig00111550_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: 235039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:222751 original size:29 final size:29
Alignment explanation
Indices: 222671--222760 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
222661 AAACATAATG
222671 AATAGTCGAGTGG-TCATTTTGTAACTTCT
1 AATAGTCGAG-GGATCATTTTGTAACTTCT
* * **
222700 AATAGTTG-GGAACTCA-AATGTAACTCTCT
1 AATAGTCGAGGGA-TCATTTTGTAACT-TCT
*
222729 -ATAGTCGAGGGATCATTTTGTAACTTTT
1 AATAGTCGAGGGATCATTTTGTAACTTCT
222757 AATA
1 AATA
222761 ATCAGTTGAT
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
27 1 0.02
28 19 0.41
29 26 0.57
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (29 bp):
AATAGTCGAGGGATCATTTTGTAACTTCT
Found at i:223109 original size:15 final size:16
Alignment explanation
Indices: 223086--223118 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
223076 TTACATTTTC
223086 CCAAAAAAATTAGGGT
1 CCAAAAAAATTAGGGT
223102 CCAAAAAAATTAGGGT
1 CCAAAAAAATTAGGGT
223118 C
1 C
223119 TAACTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
CCAAAAAAATTAGGGT
Found at i:224821 original size:92 final size:92
Alignment explanation
Indices: 224546--224821 Score: 480
Period size: 92 Copynumber: 3.0 Consensus size: 92
224536 CCATCCAAAA
*
224546 TCCAAGAAATCCAAGCTTGAGAAACTAGAGAGTTAGAGAGCCTCTTTGAGAGAGAAGAGAGATAG
1 TCCAAGAAATCCAAGCTTGAGATACTAGAGAGTTAGAGAGCCTCTTTGAGAGAGAAGAGAGATAG
* * *
224611 TTTGGGAAGGCTTTATCCTCAAGTTTA
66 CTTGGGAAGGCTTTATCCTCAAGCTTG
* * *
224638 TCCAAGAAATTCAAGCTTGAGATACTAGAGAGTTAGAGAGTCTCTTTGAGAGAGAATAGAGATAG
1 TCCAAGAAATCCAAGCTTGAGATACTAGAGAGTTAGAGAGCCTCTTTGAGAGAGAAGAGAGATAG
224703 CTTGGGAAGGCTTTATCCTCAAGCTTG
66 CTTGGGAAGGCTTTATCCTCAAGCTTG
224730 TCCAAGAAATCCAAGCTTGAGATACTAGAGAGTTAGAGAGCCTCTTTGAGAGAGAAGAGAGATAG
1 TCCAAGAAATCCAAGCTTGAGATACTAGAGAGTTAGAGAGCCTCTTTGAGAGAGAAGAGAGATAG
*
224795 CTTGGGAAGCCTTTATCCTCAAGCTTG
66 CTTGGGAAGGCTTTATCCTCAAGCTTG
224822 AGTGAGCCAC
Statistics
Matches: 173, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 173 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (92 bp):
TCCAAGAAATCCAAGCTTGAGATACTAGAGAGTTAGAGAGCCTCTTTGAGAGAGAAGAGAGATAG
CTTGGGAAGGCTTTATCCTCAAGCTTG
Found at i:229235 original size:2 final size:2
Alignment explanation
Indices: 229228--229290 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
229218 AACATATTCA
229228 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
229270 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
229291 ACATTTGGTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:230115 original size:100 final size:97
Alignment explanation
Indices: 230000--230293 Score: 324
Period size: 100 Copynumber: 3.0 Consensus size: 97
229990 TTTTATATAT
* * * * * * * *
230000 TTACACCGTTATAAGTATGTGTTAAGTATTATATTTTATTTTATTTTATTCGCTTACATTAATAT
1 TTACACTGGTATAAGTATGTGTTAAGTGTTATA-TTT-GTTTATTTTATTCACTTACATCAGTGT
230065 AGTATGTGTTAAGTGATATACATTTTTTTATTCAC
64 AGTATGTGTTAAGTG-TATACATTTTTTTATTCAC
* * * * *
230100 TTACACTGGTATAAGTATGTATTAAGTGTTACACTTGTTTATTTTA-TCACTTACACCGGTGTAT
1 TTACACTGGTATAAGTATGTGTTAAGTGTTATATTTGTTTATTTTATTCACTTACATCAGTGTA-
* *
230164 GTATGTATTAAGTGCTACACTTATTTATTTTA-TCAC
65 GTATGTGTTAAGTG-TATAC--ATTT-TTTTATTCAC
* *
230200 TTACACTGGTGTAAGTATGTGTTAAGTGTTATATTTGTTTATTTTATTCACTTATATCAGTGTAA
1 TTACACTGGTATAAGTATGTGTTAAGTGTTATATTTGTTTATTTTATTCACTTACATCAGTGT-A
230265 GTATGTGTTAAGTGT-TACATTCTTTTTAT
65 GTATGTGTTAAGTGTATACATT-TTTTTAT
230294 AGTATGAATT
Statistics
Matches: 161, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
97 19 0.12
98 27 0.17
99 4 0.02
100 79 0.49
101 31 0.19
102 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (97 bp):
TTACACTGGTATAAGTATGTGTTAAGTGTTATATTTGTTTATTTTATTCACTTACATCAGTGTAG
TATGTGTTAAGTGTATACATTTTTTTATTCAC
Found at i:230168 original size:50 final size:51
Alignment explanation
Indices: 230090--230283 Score: 257
Period size: 50 Copynumber: 3.8 Consensus size: 51
230080 ATATACATTT
* *
230090 TTTTATTCACTTACACTGGTATAAGTATGTATTAAGTGTTACACTTGTTTA
1 TTTTATTCACTTACACCGGTGTAAGTATGTATTAAGTGTTACACTTGTTTA
* * *
230141 TTTTA-TCACTTACACCGGTGTATGTATGTATTAAGTGCTACACTTATTTA
1 TTTTATTCACTTACACCGGTGTAAGTATGTATTAAGTGTTACACTTGTTTA
* * * *
230191 TTTTA-TCACTTACACTGGTGTAAGTATGTGTTAAGTGTTATATTTGTTTA
1 TTTTATTCACTTACACCGGTGTAAGTATGTATTAAGTGTTACACTTGTTTA
* * * *
230241 TTTTATTCACTTATATCAGTGTAAGTATGTGTTAAGTGTTACA
1 TTTTATTCACTTACACCGGTGTAAGTATGTATTAAGTGTTACA
230284 TTCTTTTTAT
Statistics
Matches: 125, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
50 88 0.70
51 37 0.30
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.47
Consensus pattern (51 bp):
TTTTATTCACTTACACCGGTGTAAGTATGTATTAAGTGTTACACTTGTTTA
Found at i:230269 original size:51 final size:50
Alignment explanation
Indices: 229968--230281 Score: 250
Period size: 50 Copynumber: 6.2 Consensus size: 50
229958 AATAAATATA
* * * * *
229968 TGTTAAATGCTATACTTT-TTTATTTTATAT-ATTTACACCGTTATAAGTATG
1 TGTTAAGTGTTATA-TTTATTTATTTTAT-TCACTTACA-CGGTGTAAGTATG
* * * *
230019 TGTTAAGTATTATATTTTATTTTATTTTATTCGCTTACA--TTAATATAGTATG
1 TGTTAAGTGTTATA-TTTA-TTTATTTTATTCACTTACACGGT-GTA-AGTATG
** *
230071 TGTTAAGTG--ATATACATTT-TTTTATTCACTTACACTGGTATAAGTATG
1 TGTTAAGTGTTATATTTATTTATTTTATTCACTTACAC-GGTGTAAGTATG
* * * * *
230119 TATTAAGTGTTACACTTGTTTATTTTA-TCACTTACACCGGTGTATGTATG
1 TGTTAAGTGTTATATTTATTTATTTTATTCACTTACA-CGGTGTAAGTATG
* * * *
230169 TATTAAGTGCTACACTTATTTATTTTA-TCACTTACACTGGTGTAAGTATG
1 TGTTAAGTGTTATATTTATTTATTTTATTCACTTACAC-GGTGTAAGTATG
* * *
230219 TGTTAAGTGTTATATTTGTTTATTTTATTCACTTATATCAGTGTAAGTATG
1 TGTTAAGTGTTATATTTATTTATTTTATTCACTTACA-CGGTGTAAGTATG
230270 TGTTAAGTGTTA
1 TGTTAAGTGTTA
230282 CATTCTTTTT
Statistics
Matches: 219, Mismatches: 29, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
47 14 0.06
48 17 0.08
49 6 0.03
50 97 0.44
51 54 0.25
52 16 0.07
53 15 0.07
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (50 bp):
TGTTAAGTGTTATATTTATTTATTTTATTCACTTACACGGTGTAAGTATG
Done.