Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002552.1 Hibiscus syriacus cultivar Beakdansim tig00005179_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: 180643
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:178323 original size:66 final size:66
Alignment explanation
Indices: 178219--178364 Score: 188
Period size: 66 Copynumber: 2.2 Consensus size: 66
178209 TTTCGTCTAT
**
178219 CTTGAGACAGTTTCCCTTGAAACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTTATCTC
1 CTTGAGACAGTTTCCCTTGAAACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATCTC
178283 C
66 C
* * * * *
178284 CTTGAGACAG-TTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATC
178348 TCC
64 TCC
*
178351 CTTGAGACCGTTTC
1 CTTGAGACAGTTTC
178365 TCAAAACAGC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 7 0.10
65 12 0.17
66 28 0.41
67 19 0.28
68 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (66 bp):
CTTGAGACAGTTTCCCTTGAAACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTATCTC
C
Found at i:179516 original size:103 final size:105
Alignment explanation
Indices: 179003--179930 Score: 1319
Period size: 104 Copynumber: 9.0 Consensus size: 105
178993 GCACTCGAGG
* * * * * *
179003 CAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAATTTCTCAATTTC--
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
179066 AGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
179107 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTACCTATC-ACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
179171 GCCAATTTCAACTTCACAATGAAGGATAATGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
179211 CAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGCCTATCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
179276 GCCAATTTCAACTTTACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
179316 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
179381 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
179421 TAACGCAAGTTC-ACTTCACGACGAAGGGACCGCTGCTTTTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
179485 GCCAA-TTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
179524 CAA-GCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTC-CTAATCTCAT
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTC-AATTTCAG
179587 AGCC-ATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
179627 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAATAACTTC-CAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
179691 GCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
179730 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * * *
179790 TTCAATTTCAACTTCATAACAAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * * ** *
179830 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAAAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
179895 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
179931 TGGAACAATG
Statistics
Matches: 753, Mismatches: 55, Indels: 30
0.90 0.07 0.04
Matches are distributed among these distances:
99 19 0.03
100 62 0.08
101 5 0.01
102 30 0.04
103 203 0.27
104 230 0.31
105 170 0.23
106 34 0.05
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:180514 original size:33 final size:35
Alignment explanation
Indices: 180471--180568 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 35
180461 TTTCGTCATA
* *
180471 CTAGGATTCAAACTCCTAAAAATATGATATAA-TT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
180505 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAA-TTT
180540 GCTAGGATTCAAACTCCT-AAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
180569 GAGTTATACT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
33 29 0.50
35 2 0.03
36 11 0.19
37 16 0.28
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
Done.