Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002247.1 Hibiscus syriacus cultivar Beakdansim tig00004566_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: 46071
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:8008 original size:286 final size:286
Alignment explanation
Indices: 7496--8071 Score: 1071
Period size: 286 Copynumber: 2.0 Consensus size: 286
7486 TCAACTTCTT
*
7496 GCAACAAGAGTATCTATCTAATAAGCCTAGGCTTGACATTCTTTTTATTCACTATGTATTTAATG
1 GCAACAAGAGTATCTATCTAATAAGCCTAGGCTTGACATTCTTTTTATTCACTATATATTTAATG
7561 GCTGAGTGACCACTGTGTACAATGACCTTAGTGCATATAAGGTATGCCCTAAACTTATCAAAAGT
66 GCTGAGTGACCACTGTGTACAATGACCTTAGTGCATATAAGGTATGCCCTAAACTTATCAAAAGT
*
7626 GAATACCACAGCAAGCAATTTTTTTTCAGTGGTGGTATATTTAAGTTATGCATCATACAACTAGC
131 GAATACCACAACAAGCAATTTTTTTTCAGTGGTGGTATATTTAAGTTATGCATCATACAACTAGC
* *
7691 ATAATAAATGACATGAAAGATTTTACCTTTTCTTTGTCCTAGCATCATCCCTACTATGTAGTCAT
196 ATAATAAATGACATGAAAGATTTTACCTTTTCTTTATCCTAGCATCATCCCTACTATGTAGTCAC
7756 TTGCATCGTACATCAGCTCGAATAGA
261 TTGCATCGTACATCAGCTCGAATAGA
*
7782 GCAACAAGAGTATCTATCTAATAAGCCTAGGCTTGGCATTCTTTTTATTCACTATATATTTAATG
1 GCAACAAGAGTATCTATCTAATAAGCCTAGGCTTGACATTCTTTTTATTCACTATATATTTAATG
*
7847 GCTGAGTGACCAGTGTGTACAATGACCTTAGTGCATATAAGGTATGCCCTAAACTTATCAAAAGT
66 GCTGAGTGACCACTGTGTACAATGACCTTAGTGCATATAAGGTATGCCCTAAACTTATCAAAAGT
7912 GAATACCACAACAAGCAATTTTTTTTCAGTGGTGGTATATTTAAGTTATGCATCATACAACTAGC
131 GAATACCACAACAAGCAATTTTTTTTCAGTGGTGGTATATTTAAGTTATGCATCATACAACTAGC
* *
7977 ATAATAAATGACATGAAATATTTTACCTTTTCTTTATCCTAGCATCGTCCCTACTATGTAGTCAC
196 ATAATAAATGACATGAAAGATTTTACCTTTTCTTTATCCTAGCATCATCCCTACTATGTAGTCAC
*
8042 TTGCATCGTACATCAGCTCGAATAGG
261 TTGCATCGTACATCAGCTCGAATAGA
8068 GCAA
1 GCAA
8072 GTTTTGTATT
Statistics
Matches: 281, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
286 281 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (286 bp):
GCAACAAGAGTATCTATCTAATAAGCCTAGGCTTGACATTCTTTTTATTCACTATATATTTAATG
GCTGAGTGACCACTGTGTACAATGACCTTAGTGCATATAAGGTATGCCCTAAACTTATCAAAAGT
GAATACCACAACAAGCAATTTTTTTTCAGTGGTGGTATATTTAAGTTATGCATCATACAACTAGC
ATAATAAATGACATGAAAGATTTTACCTTTTCTTTATCCTAGCATCATCCCTACTATGTAGTCAC
TTGCATCGTACATCAGCTCGAATAGA
Found at i:16487 original size:21 final size:20
Alignment explanation
Indices: 16463--16501 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
16453 CAGTAGAGCC
16463 TTTGTTGAAGCCATGAAATAT
1 TTTGTTGAAGCCAT-AAATAT
*
16484 TTTGTTGAGGCCATAAAT
1 TTTGTTGAAGCCATAAAT
16502 TCTTATAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (20 bp):
TTTGTTGAAGCCATAAATAT
Found at i:26308 original size:34 final size:34
Alignment explanation
Indices: 26249--26315 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
26239 TTCTTGAGAG
*
26249 TTGTTTTCTCCTTTTTAACAAGAGAGAA-TTGTCA
1 TTGTTTTCTCCTTATTAAC-AGAGAGAAGTTGTCA
26283 TTGTTTTCTCCTTATTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTTATTA-A-CAGAGAGAAGTTGT
26316 AATTCGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 5 0.17
36 1 0.03
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (34 bp):
TTGTTTTCTCCTTATTAACAGAGAGAAGTTGTCA
Found at i:27221 original size:15 final size:16
Alignment explanation
Indices: 27179--27220 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
27169 CTGCTATTCT
*
27179 ACAAGAAAAAATCGAC
1 ACAAGAAAAAATCAAC
27195 ACAAGAAAAAATCAAC
1 ACAAGAAAAAATCAAC
*
27211 GCAAGAAAAA
1 ACAAGAAAAA
27221 TTTAGACAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.67, C:0.17, G:0.12, T:0.05
Consensus pattern (16 bp):
ACAAGAAAAAATCAAC
Found at i:39132 original size:35 final size:34
Alignment explanation
Indices: 39086--39186 Score: 132
Period size: 35 Copynumber: 2.9 Consensus size: 34
39076 AACACGATTA
39086 TCAATTACATTCTAAACCCAGAATTCCAAAATACT
1 TCAATTACATTCTAAACCCA-AATTCCAAAATACT
* *
39121 TCAATTACATTCTAAACCTCAAATTCTAAAATATT
1 TCAATTACATTCTAAACC-CAAATTCCAAAATACT
* *
39156 TCAATTACATGCTCAACCCCAAATT-CAAAAT
1 TCAATTACATTCT-AAACCCAAATTCCAAAAT
39187 GCATTATCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
34 5 0.08
35 48 0.81
36 6 0.10
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.31
Consensus pattern (34 bp):
TCAATTACATTCTAAACCCAAATTCCAAAATACT
Found at i:41505 original size:29 final size:29
Alignment explanation
Indices: 41463--41533 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
41453 TTGTTAATCT
41463 TGTAATAATGCATGCATACTTTTGCTGAA
1 TGTAATAATGCATGCATACTTTTGCTGAA
41492 TGTAATAATGCATGCATACTTTTGCTGAA
1 TGTAATAATGCATGCATACTTTTGCTGAA
41521 TGTAATAATGCAT
1 TGTAATAATGCAT
41534 TATCAACATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (29 bp):
TGTAATAATGCATGCATACTTTTGCTGAA
Found at i:45163 original size:16 final size:16
Alignment explanation
Indices: 45111--45164 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
45101 TTCAGAAAAG
*
45111 AAAAATAATAAAATATA
1 AAAAATAATAAAACA-A
** * *
45128 AAAAATGTTAAAAGAG
1 AAAAATAATAAAACAA
45144 AAAAATAATAAAACAA
1 AAAAATAATAAAACAA
45160 AAAAA
1 AAAAA
45165 AAAAGAAGTG
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (16 bp):
AAAAATAATAAAACAA
Done.