Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007868.1 Hibiscus syriacus cultivar Beakdansim tig00110241_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: 250609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:233420 original size:19 final size:19
Alignment explanation
Indices: 233396--233434 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
233386 TGTTTGTTCT
233396 TTCTTTTTACTTTTCAATC
1 TTCTTTTTACTTTTCAATC
* *
233415 TTCTTTTTCCTTTTGAATC
1 TTCTTTTTACTTTTCAATC
233434 T
1 T
233435 CAACATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.21, G:0.03, T:0.64
Consensus pattern (19 bp):
TTCTTTTTACTTTTCAATC
Found at i:235162 original size:39 final size:39
Alignment explanation
Indices: 235108--235224 Score: 198
Period size: 39 Copynumber: 3.0 Consensus size: 39
235098 CTTGGCAACC
* *
235108 AATTTCAAAAAAGGATGCACCAACAAGTTTGACCAACAA
1 AATTTCAACAAAGGATGCACCTACAAGTTTGACCAACAA
235147 AATTTCAACAAAGGATGCACCTACAAGTTTGACCAACAA
1 AATTTCAACAAAGGATGCACCTACAAGTTTGACCAACAA
* *
235186 AATTTCAACAAATGATGCACCTGCAAGTTTGACCAACAA
1 AATTTCAACAAAGGATGCACCTACAAGTTTGACCAACAA
235225 TCTCCCACTT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.21
Consensus pattern (39 bp):
AATTTCAACAAAGGATGCACCTACAAGTTTGACCAACAA
Found at i:239767 original size:39 final size:39
Alignment explanation
Indices: 239703--239817 Score: 151
Period size: 39 Copynumber: 2.9 Consensus size: 39
239693 TGGCAACCAA
* * *
239703 TTTCAACAAAGGATGCACCAACAAGTTTAACCAACAAAT
1 TTTCAACAAAGGATGCACCTACAAGTTTGACCAACAAAG
* * *
239742 TTTCAACAAATGATGTACCTGCAAGTTTGACCAACAAAAG
1 TTTCAACAAAGGATGCACCTACAAGTTTGACCAAC-AAAG
*
239782 TTT-AACAAAGGATGCACCTACAAGTTTGACTAACAA
1 TTTCAACAAAGGATGCACCTACAAGTTTGACCAACAA
239818 GGCATTATGA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
38 2 0.03
39 57 0.88
40 6 0.09
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (39 bp):
TTTCAACAAAGGATGCACCTACAAGTTTGACCAACAAAG
Found at i:246112 original size:276 final size:276
Alignment explanation
Indices: 245620--246432 Score: 1371
Period size: 276 Copynumber: 2.9 Consensus size: 276
245610 TTGGACCTCA
245620 GACTATTTTGTTCTCTTCGCTCGACTATGATTTACAGTTTGTCGGCAGTCTTTCAATAATTTTAT
1 GACTATTTTGTTCTCTTCGCTCGACTATGATTTACAGTTTGTCGGCAGTCTTTCAATAATTTTAT
245685 CCTTTTTTTAGTTCGTTCGCTAATTCATTCAAATCTG-TTGTATCTATATTTTGTTCAAATTCTT
66 CCTTTTTTTAGTTCGTTCGCTAATTCATTCAAATCTGTTTGTATCTATATTTTGTTCAAATTCTT
245749 TTATTAGGTTTTTAATCTTTTCTTATATGATCCTAAGTAACTATTTTTTTTGTTAATAATTATAG
131 TTATTAGGTTTTTAATCTTTTCTTATATGATCCTAAGTAACTATTTTTTTTGTTAATAATTATAG
245814 GAAAATGTCTTAATTATATGATTACTTTACATTTATGATCGTAAACATTCATTATAATTTTAGAT
196 GAAAATGTCTTAATTATATGATTACTTTACATTTATGATCGTAAACATTCATTATAATTTTAGAT
245879 ACGTCATTGCGTTCGT
261 ACGTCATTGCGTTCGT
*
245895 GACTATTTTGTTCTCTTCGCTCGACTATGATTTACAGTTTATCGGCAGTCTTTCAATAATTTTAT
1 GACTATTTTGTTCTCTTCGCTCGACTATGATTTACAGTTTGTCGGCAGTCTTTCAATAATTTTAT
245960 CCTTTTTTTAGTTCGTTCGCTAATTCATTCAAATCTGTTTGTATCTATATTTTGTTCAAATTCTT
66 CCTTTTTTTAGTTCGTTCGCTAATTCATTCAAATCTGTTTGTATCTATATTTTGTTCAAATTCTT
246025 TTATTAGGTTTTTAATCTTTTCTTATATGATCCTAAGTAACTATTTTTTTTGTTAATAATTATAG
131 TTATTAGGTTTTTAATCTTTTCTTATATGATCCTAAGTAACTATTTTTTTTGTTAATAATTATAG
246090 GAAAATGTCTTAATTATATGATTACTTTACATTTATGATCGTAAACATTCATTATAATTTTAGAT
196 GAAAATGTCTTAATTATATGATTACTTTACATTTATGATCGTAAACATTCATTATAATTTTAGAT
246155 ACGTCATTGCGTTCGT
261 ACGTCATTGCGTTCGT
* ** ** *
246171 GACTATTTTGTTCTCTTCGCTCGATTATGATTTGTAGTTTGTCGATAGTATTTCAATAATTTTAT
1 GACTATTTTGTTCTCTTCGCTCGACTATGATTTACAGTTTGTCGGCAGTCTTTCAATAATTTTAT
*** * * * **
246236 CCTTTTTTGTAGTTCGTTTATTGATTCATCCAAACCTGTTTGTATCTATATTTTGTT-TGATTGC
66 CCTTTTTT-TAGTTCGTTCGCTAATTCATTCAAATCTGTTTGTATCTATATTTTGTTCAAATT-C
* * * * *
246300 TTTGATTAGGTCTTTAAT-TTTTCCTTATATGATCCTAAGTGACTAATTTTTGTTGTTGATAATT
129 TTTTATTAGGTTTTTAATCTTTT-CTTATATGATCCTAAGTAACT-ATTTTTTTTGTTAATAATT
* *
246364 ATAGGAAAGTGTCTTAATTATATGATTACTTTACATTTATGATCGAAAACATTCATTATAATTTT
192 ATAGGAAAATGTCTTAATTATATGATTACTTTACATTTATGATCGTAAACATTCATTATAATTTT
246429 AGAT
257 AGAT
246433 TTTTTCAATA
Statistics
Matches: 510, Mismatches: 23, Indels: 7
0.94 0.04 0.01
Matches are distributed among these distances:
275 101 0.20
276 246 0.48
277 79 0.15
278 84 0.16
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.49
Consensus pattern (276 bp):
GACTATTTTGTTCTCTTCGCTCGACTATGATTTACAGTTTGTCGGCAGTCTTTCAATAATTTTAT
CCTTTTTTTAGTTCGTTCGCTAATTCATTCAAATCTGTTTGTATCTATATTTTGTTCAAATTCTT
TTATTAGGTTTTTAATCTTTTCTTATATGATCCTAAGTAACTATTTTTTTTGTTAATAATTATAG
GAAAATGTCTTAATTATATGATTACTTTACATTTATGATCGTAAACATTCATTATAATTTTAGAT
ACGTCATTGCGTTCGT
Done.