Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001372.1 Hibiscus syriacus cultivar Beakdansim tig00002684_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: 540953
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:537182 original size:22 final size:19
Alignment explanation
Indices: 537131--537183 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
537121 GGATTATGGC
537131 AGTATCGATACCTTAGGATG
1 AGTATCGATA-CTTAGGATG
* *
537151 AGTATTGATACTATAGTGTTG
1 AGTATCGATACT-TAG-GATG
537172 AGGTATCGATAC
1 A-GTATCGATAC
537184 CATATGATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.07
20 12 0.44
21 4 0.15
22 9 0.33
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (19 bp):
AGTATCGATACTTAGGATG
Found at i:537303 original size:41 final size:41
Alignment explanation
Indices: 537234--537311 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
537224 TTGAAAAATA
*
537234 CCCTAGTATCGATACCCCTATGGGGAGTATCGATACTCCTG
1 CCCTAGTATCGATACCCCTATGGGGAGTATCAATACTCCTG
* * *
537275 CCCTAGTATCGATA-CTCTGTGAGTGAGTATCAATACT
1 CCCTAGTATCGATACCCCTATG-GGGAGTATCAATACT
537312 ACCCTTCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 5 0.16
41 27 0.84
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (41 bp):
CCCTAGTATCGATACCCCTATGGGGAGTATCAATACTCCTG
Found at i:539315 original size:10 final size:10
Alignment explanation
Indices: 539286--539351 Score: 66
Period size: 10 Copynumber: 6.8 Consensus size: 10
539276 GCTGCTGGAA
539286 AACCGGTTTG
1 AACCGGTTTG
*
539296 -ACCAGTTTTG
1 AACC-GGTTTG
539306 AACCGGTTTG
1 AACCGGTTTG
*
539316 -ACCGGTCTG
1 AACCGGTTTG
539325 AACCGGTTTG
1 AACCGGTTTG
*
539335 -ACCGGTCTG
1 AACCGGTTTG
*
539344 AACGGGTT
1 AACCGGTT
539352 GACCCGACCC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
9 19 0.42
10 23 0.51
11 3 0.07
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:539319 original size:9 final size:9
Alignment explanation
Indices: 539287--539355 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
539277 CTGCTGGAAA
539287 ACCGGTTTG
1 ACCGGTTTG
*
539296 ACCAGTTTTG
1 ACC-GGTTTG
539306 AACCGGTTTG
1 -ACCGGTTTG
*
539316 ACCGGTCTG
1 ACCGGTTTG
539325 AACCGGTTTG
1 -ACCGGTTTG
*
539335 ACCGGTCTG
1 ACCGGTTTG
* *
539344 AACGGGTTG
1 ACCGGTTTG
539353 ACC
1 ACC
539356 CGACCCGACT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 27 0.56
10 18 0.38
11 3 0.06
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:539328 original size:19 final size:19
Alignment explanation
Indices: 539286--539355 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
539276 GCTGCTGGAA
* *
539286 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
539306 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
539325 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
539344 AA-CGGGTTGACC
1 AACCGGTTTGACC
539356 CGACCCGACT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 9 0.19
19 25 0.53
20 13 0.28
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:539380 original size:15 final size:15
Alignment explanation
Indices: 539349--539403 Score: 74
Period size: 15 Copynumber: 3.5 Consensus size: 15
539339 GTCTGAACGG
539349 GTTGACCCGACCCGACT
1 GTTGA-CCGA-CCGACT
539366 GTTGACCGACCGACT
1 GTTGACCGACCGACT
* *
539381 GTTGACCGACTGACC
1 GTTGACCGACCGACT
539396 GTTGACCG
1 GTTGACCG
539404 TTGACCGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 27 0.75
16 4 0.11
17 5 0.14
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (15 bp):
GTTGACCGACCGACT
Found at i:539403 original size:7 final size:7
Alignment explanation
Indices: 539381--539455 Score: 118
Period size: 7 Copynumber: 10.9 Consensus size: 7
539371 CCGACCGACT
539381 GTTGACC
1 GTTGACC
*
539388 GACTGACC
1 G-TTGACC
539396 GTTGACC
1 GTTGACC
539403 GTTGACC
1 GTTGACC
539410 GTTGACC
1 GTTGACC
539417 GTTGACC
1 GTTGACC
539424 GTTGA-C
1 GTTGACC
539430 GTTGACC
1 GTTGACC
539437 G-TGACC
1 GTTGACC
539443 GTTGACC
1 GTTGACC
539450 GTTGAC
1 GTTGAC
539456 TTTCTTTGAC
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
6 12 0.19
7 45 0.71
8 6 0.10
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.27
Consensus pattern (7 bp):
GTTGACC
Done.