Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008293.1 Hibiscus syriacus cultivar Beakdansim tig00110957_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: 338481
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
File 3 of 3
Found at i:314264 original size:42 final size:42
Alignment explanation
Indices: 314200--314282 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
314190 ATCATCTTCA
*
314200 TCATCATCATCATCGTCATCATCTTCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATCG
* *
314242 TCATCATCATCATCATCGTCATCTTCATCGTCAGCTTCATC
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATC
314283 TCTGCGACGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATCG
Found at i:314271 original size:12 final size:12
Alignment explanation
Indices: 314191--314282 Score: 64
Period size: 12 Copynumber: 7.9 Consensus size: 12
314181 GTTTGGATCA
*
314191 TCATCTTCATCA
1 TCATCTTCATCG
*
314203 TCATCATCATCG
1 TCATCTTCATCG
*
314215 TCA---TCATCT
1 TCATCTTCATCG
** * *
314224 TCATCGCCAGCT
1 TCATCTTCATCG
* *
314236 TCATCGTCATCA
1 TCATCTTCATCG
*
314248 TCATCATCATCG
1 TCATCTTCATCG
314260 TCATCTTCATCG
1 TCATCTTCATCG
*
314272 TCAGCTTCATC
1 TCATCTTCATC
314283 TCTGCGACGC
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
9 8 0.12
12 57 0.88
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:314281 original size:18 final size:18
Alignment explanation
Indices: 314218--314283 Score: 51
Period size: 21 Copynumber: 3.3 Consensus size: 18
314208 ATCATCGTCA
*
314218 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* *
314236 TCATCGTCATCATCATCATCAT
1 TCATC-T--TCATCGTCAGC-T
314258 CGTCATCTTCATCGTCAGCT
1 --TCATCTTCATCGTCAGCT
314278 TCATCT
1 TCATCT
314284 CTGCGACGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
18 11 0.30
19 1 0.03
20 1 0.03
21 17 0.46
22 1 0.03
23 1 0.03
24 5 0.14
ACGTcount: A:0.20, C:0.35, G:0.09, T:0.36
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:316888 original size:199 final size:200
Alignment explanation
Indices: 315731--317288 Score: 2960
Period size: 200 Copynumber: 7.8 Consensus size: 200
315721 TTTAAATTAG
315731 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
315796 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GG-TTCTATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
** *
315859 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTAATTCTGGAAA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
315924 AAAAA
196 AAAAA
315929 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
315994 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
316059 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
316123 AAAAA
196 AAAAA
316128 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
316193 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
316257 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
316321 AAAAA
196 AAAAA
316326 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
316391 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
316456 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
316521 AAAAA
196 AAAAA
316526 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
316591 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
316656 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
316721 AAAAA
196 AAAAA
*
316726 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
316791 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGG-TTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
316855 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
316920 AAAAA
196 AAAAA
316925 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGAC--ATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
316988 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGG-TTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
317051 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
317116 AAAAA
196 AAAAA
317121 TATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
317185 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGG-TTCGATGATTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
317249 TCGACACTTTTTTATATATGGATCGACACTTTATGGGTGC
131 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGC
317289 CCTGTTGGCC
Statistics
Matches: 1346, Mismatches: 6, Indels: 15
0.98 0.00 0.01
Matches are distributed among these distances:
195 6 0.00
196 150 0.11
197 78 0.06
198 361 0.27
199 359 0.27
200 392 0.29
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGATTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
AAAAA
Found at i:317457 original size:19 final size:19
Alignment explanation
Indices: 317411--317459 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
317401 AATTATTCAC
*
317411 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
317430 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
317449 ATACAAAATTA
1 ATACAAAATTA
317460 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:319272 original size:32 final size:32
Alignment explanation
Indices: 319236--319299 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
319226 CATCTTAATA
*
319236 TCACCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCTCAACACCGAAACTTCTTTCACCACT
***
319268 TCACCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCTCAACACCGAAACTTCTTTCACCACT
319300 CCATCTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.44, G:0.02, T:0.30
Consensus pattern (32 bp):
TCACCCTCAACACCGAAACTTCTTTCACCACT
Found at i:322275 original size:228 final size:226
Alignment explanation
Indices: 321874--322320 Score: 754
Period size: 228 Copynumber: 2.0 Consensus size: 226
321864 TTAAAACTGC
321874 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
* *
321939 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTTATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAATATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
322004 TAGCATTTAAATTTAAAAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGCATTTAAATTTAAAAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAAG
* *
322069 TATGTACACTTTTATAAAAATGATATATACTT
195 TATGGACACTTTTATAAAAAGGATATATACTT
*
322101 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
322166 ATTAATTTAATAATTTCATTTACACAAAA-ATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTTAATAATTTAATTTACACAAAATATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
322230 TTTAG-ATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATA
130 -TTAGCA-TTTAAATTTAAAAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATA
322294 AGTATGGACACTTTTATAAAAAGGATA
193 AGTATGGACACTTTTATAAAAAGGATA
322321 GATAATTTAC
Statistics
Matches: 207, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
227 74 0.36
228 133 0.64
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (226 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAATATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TAGCATTTAAATTTAAAAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAGT
ATGGACACTTTTATAAAAAGGATATATACTT
Found at i:335948 original size:31 final size:31
Alignment explanation
Indices: 335911--335972 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
335901 GATCACATCA
335911 TAATTAAATAAAAACGAAAGTGACTATATCT
1 TAATTAAATAAAAACGAAAGTGACTATATCT
335942 TAATTAAATAAAAACGAAAGTGACTATATCT
1 TAATTAAATAAAAACGAAAGTGACTATATCT
335973 ATGTTTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (31 bp):
TAATTAAATAAAAACGAAAGTGACTATATCT
Done.