Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009159.1 Hibiscus syriacus cultivar Beakdansim tig00112686_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: 192739
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:189696 original size:81 final size:81
Alignment explanation
Indices: 189347--190175 Score: 695
Period size: 81 Copynumber: 10.2 Consensus size: 81
189337 TTAAAGACAA
* * ***
189347 CATTTACGGCATAACTTAAGTCGAGAA-GGTTATCCGCCAACCAAAGACCTTTGAGTTCGATTAC
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-A--AAAGACCCCCGAGTTCGATTAC
*
189411 GCTCAGCTCCAAGGCACAT
63 ACTCAGCTCCAAGGCACAT
* * * *
189430 CGTTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCCCCGAGTTCGATTAC
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-A--AAAGACCCCCGAGTTCGATTAC
* * *
189495 ACTCAGCTTCGAGGGCATAT
63 ACTCAGC-TCCAAGGCACAT
* * * * * **
189515 CATTTACAGCATAGCTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCG-GTTCG-TCTAC
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-CAAAAGACCCCCGAGTTCGAT-TAC
* *
189578 GCTCAGCTCCAAGGTACAT
63 ACTCAGCTCCAAGGCACAT
* *
189597 CATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAGACCCCCGAGTTCGATTACACT
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAGACCCCCGAGTTCGATTACACT
* *
189662 CA-CTTCGAGGGCACAT
66 CAGC-TCCAAGGCACAT
* * *
189678 CATTTACGGTATAACTTAAGTCGAGAAGGGTCATCTGCCAACCAA-A-CCCCGAG-TCGATTACA
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA--AAGACCCCCGAGTTCGATTACA
* * *
189740 CTCAGCTTCGAGGGCATAT
64 CTCAGC-TCCAAGGCACAT
* * * * * ** *
189759 CATTTACAGCATAACTCAAGGT-TATAAGGGTTATATGTCACCAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTTAA-GTCGAGAAGGGTTATCTG-C-CAAAAGACCCCCGAGTTCGATTAC
*
189823 ACTCAGCTCCAAGGTACAT
63 ACTCAGCTCCAAGGCACAT
* * * * *** *
189842 CATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAGACCTTTGAGTTCGATTACG
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-A-AAAGACCCCCGAGTTCGATTACA
*
189907 CTCAGCTCCAAGGCATAT
64 CTCAGCTCCAAGGCACAT
* * ***
189925 CATTT---GTCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAAGACCCTTAAGTTCGATTACAC
1 CATTTACAG-CATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAGACCCCCGAGTTCGATTACAC
* * *
189986 TCAGCTTCAAGGGGATAT
65 TCAGCTCCAA-GGCACAT
* * * * *
190004 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGA--CCTGAGTTCGATTACA
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTG-CCA-AAAGACCCCCGAGTTCGATTACA
190067 CTCAGCTCCAAGG--CAT
64 CTCAGCTCCAAGGCACAT
* *
190083 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCC-AAAGACCCCCGAGTTCGATTACACT
1 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAGACCCCCGAGTTCGATTACACT
* * *
190147 CAACT-CGAGGTCATAT
66 CAGCTCCAAGG-CACAT
*
190163 CATTTACAACATA
1 CATTTACAGCATA
190176 GCTCAAGCAA
Statistics
Matches: 610, Mismatches: 103, Indels: 69
0.78 0.13 0.09
Matches are distributed among these distances:
76 5 0.01
77 4 0.01
78 52 0.09
79 45 0.07
80 38 0.06
81 158 0.26
82 77 0.13
83 123 0.20
84 66 0.11
85 40 0.07
86 1 0.00
87 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (81 bp):
CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAGACCCCCGAGTTCGATTACACT
CAGCTCCAAGGCACAT
Found at i:189961 original size:245 final size:246
Alignment explanation
Indices: 189355--190123 Score: 1053
Period size: 245 Copynumber: 3.1 Consensus size: 246
189345 AACATTTACG
*
189355 GCATAACTTAAGTCGAGAA-GGTTATCCGCCAACCAAAGACCTTTGAGTTCGATTACGCTCAGCT
1 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTTTGAGTTCGATTACGCTCAGCT
* *
189419 CCAAGGCACATCGTTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCCCCG
65 CCAAGGCACATCATTTG--TCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACC-AA-A-CCCCG
*
189484 AGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAGCTCAAGGCTAGAAGGGTTAT
125 AGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
* * *
189549 CTGTCACCAAAGACCTTCG-GTTCGTCTACGCTCAGCTCCAAGGTACATCATTTACA
190 CTGTCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGTACATCATTTGCA
* * *** *
189605 GCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A-AAAGACCCCCGAGTTCGATTACACTCA-CTT
1 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGATTACGCTCAGC-T
* * *
189667 CGAGGGCACATCATTTACGGT-ATAACTTAAGTCGAGAAGGG-TCATCTGCCAACCAAACCCCGA
65 CCAAGGCACATCATTT---GTCATAGCTTAAGTCGAGAAGGGCT-ATCTGCCAACCAAACCCCGA
* * *
189730 G-TCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGTTATAAGGGTTATA
126 GTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC
189794 TGTCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGTACATCATTTGCA
191 TGTCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGTACATCATTTGCA
* * *
189850 GCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAGACCTTTGAGTTCGATTACGCTCAGCTC
1 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGATTACGCTCAGCTC
* * **
189915 CAAGGCATATCATTTGTCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA--AGACCCTTAAGTTC
66 CAAGGCACATCATTTGTCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAACCC-CGAGTTC
* *
189978 GATTACACTCAGCTTCAAGGGGATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC
130 GATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC
* *
190043 AACAAAGACC-T-GAGTTCGATTACACTCAGCTCCAAGG--CATCATTTGCA
195 ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGTACATCATTTGCA
*
190091 GCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA
1 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
190124 AGACCCCCGA
Statistics
Matches: 459, Mismatches: 46, Indels: 37
0.85 0.08 0.07
Matches are distributed among these distances:
241 40 0.09
243 30 0.07
244 82 0.18
245 166 0.36
246 3 0.01
247 41 0.09
248 68 0.15
250 19 0.04
251 10 0.02
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (246 bp):
GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGATTACGCTCAGCTC
CAAGGCACATCATTTGTCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAACCCCGAGTTCG
ATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGTACATCATTTGCA
Found at i:192035 original size:31 final size:33
Alignment explanation
Indices: 192000--192060 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
191990 GTTTCTAGTT
192000 TTGTT-TTTTATTATATA-TTTTATT-TTTTCCC
1 TTGTTCTTTT-TTATATATTTTTATTATTTTCCC
*
192031 TTGTTCTTTTTTTTATATTTTTATTATTTT
1 TTGTTCTTTTTTATATATTTTTATTATTTT
192061 TTCCTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 11 0.42
32 11 0.42
33 4 0.15
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (33 bp):
TTGTTCTTTTTTATATATTTTTATTATTTTCCC
Found at i:192070 original size:15 final size:16
Alignment explanation
Indices: 192050--192081 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
192040 TTTTTATATT
192050 TTTATTAT-TTTTTCC
1 TTTATTATATTTTTCC
192065 TTTATTATATTTTTCC
1 TTTATTATATTTTTCC
192081 T
1 T
192082 ATTTAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTATTATATTTTTCC
Found at i:192085 original size:35 final size:35
Alignment explanation
Indices: 192019--192085 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
192009 ATTATATATT
* * * *
192019 TTATTTTTTCCCTTGTTCTTTTTTTTATATTTTTA
1 TTATTTTTTCCCTTATTATATTTTTCATATTTTTA
* *
192054 TTATTTTTTCCTTTATTATATTTTTCCTATTT
1 TTATTTTTTCCCTTATTATATTTTTCATATTT
192086 AACTTTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.13, C:0.12, G:0.01, T:0.73
Consensus pattern (35 bp):
TTATTTTTTCCCTTATTATATTTTTCATATTTTTA
Done.