Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006315.1 Hibiscus syriacus cultivar Beakdansim tig00015089_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: 37810
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2580 original size:39 final size:38
Alignment explanation
Indices: 2553--2632 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 38
2543 GTTTTTCCCT
*
2553 TATGCACAAAG-AAATTGAGCCTACAGTAAGGACTTACCC
1 TATGCACAAAGCAAA-GGAGCCTACAGTAA-GACTTACCC
*
2592 TATGCACAAAGCAAAGGAGCCTACGGTAAGGACTTACCC
1 TATGCACAAAGCAAAGGAGCCTACAGTAA-GACTTACCC
2631 TA
1 TA
2633 GTCGAAGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 35 0.92
40 3 0.08
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.19
Consensus pattern (38 bp):
TATGCACAAAGCAAAGGAGCCTACAGTAAGACTTACCC
Found at i:13718 original size:15 final size:15
Alignment explanation
Indices: 13698--13745 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
13688 ACATTACCCA
13698 CCCCGCATCCGCCCG
1 CCCCGCATCCGCCCG
13713 CCCCGCATCCGCCCG
1 CCCCGCATCCGCCCG
**
13728 CCCTACATCCGCCCG
1 CCCCGCATCCGCCCG
13743 CCC
1 CCC
13746 AGCTAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.08, C:0.67, G:0.17, T:0.08
Consensus pattern (15 bp):
CCCCGCATCCGCCCG
Found at i:18982 original size:20 final size:20
Alignment explanation
Indices: 18959--19018 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
18949 GAGCATTTCG
18959 AGTTGACTCAGACTGGTTCT
1 AGTTGACTCAGACTGGTTCT
* * *
18979 AGTTGACTCAGTCTGATTCG
1 AGTTGACTCAGACTGGTTCT
**
18999 AGTTGACTTGGACTGGTTCT
1 AGTTGACTCAGACTGGTTCT
19019 GGAATTTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
AGTTGACTCAGACTGGTTCT
Found at i:20772 original size:343 final size:345
Alignment explanation
Indices: 19947--20951 Score: 1367
Period size: 367 Copynumber: 2.8 Consensus size: 345
19937 CTTGAAAAAT
* * *
19947 TCATCTTTTAACCTCCAACCTTTTCATCAAAATTTAATTTAGTCCCCTCAAGAACATTTTAGAAA
1 TCATC-TTGAACCTCCAACGTTTTCATCAAAATTCAATTTAGTCCCCTCAAG-ACATTTTAGAAA
* * * *
20012 ATTTTAACCCTAACTTCA-GGTGTAACACTATCATTGACTATTCTTACTATGATTATTGATCTAA
64 ATTTTAACCCCAACTTCAGGGTGTGACACTATCATTGACTATTCTGACTATGATTATCGATCTAA
* * *
20076 ATATAGTTCTCACAATTCAAATATTATCATTAAAAT-TTATATTTAATATGATTAAATTGGTTAT
129 ATATAGTTCTCACAATTCAAATATTATCATT-AACTCTTATATTTTATATGATTAAATTGGTTAG
* *
20140 ATTTGAATTTGCGAAGAAAATTTGAATTTAATAGAGAATCAAAAATAGGCTATATGGTTTTATTG
193 ATTGGAATTTGTGAAGAAAATTTGAATTTAATAGAGAA-CAAAAATAGGCTATATGGTTTTATTG
20205 AAAGTAACATGAGTGGTGTACATAAGGGTTCTATTATAATTATTGTTTTATGATTTGTGGTTAAA
257 AAAGTAACATGAGTGGTGTACATAAGGGTTCTATTATAATTATTGTTTTATGATTTGTGGTTAAA
*
20270 GGAAAAGGGTAAATTCCCCATAAG
322 GAAAAAGGGTAAATTCCCCATAAG
20294 TCATTGGTCTCTTGAAAAATTCATCTTTTAACCTCCAACGTTTTCATCAAAATTCAATTTAGTCC
1 TCA------TCTTG---------------AACCTCCAACGTTTTCATCAAAATTCAATTTAGTCC
* * * *
20359 CCTAAAGA-AGTTTTAGAAAATTGTAACCCCAACTTCAGGGTATGACACTATCATTGACTATTTT
45 CCTCAAGACA-TTTTAGAAAATTTTAACCCCAACTTCAGGGTGTGACACTATCATTGACTATTCT
* *
20423 GACTATGATCATCGATCTAAATATAGTTCGCACAATTCAAATATTATCATTAACTCTTATATTTT
109 GACTATGATTATCGATCTAAATATAGTTCTCACAATTCAAATATTATCATTAACTCTTATATTTT
*
20488 ATATGATTAAATTTGTTAGATTGGAATTTGTGAAGAAAATTTGAATTTAATAGAGAACAAAAAAT
174 ATATGATTAAATTGGTTAGATTGGAATTTGTGAAGAAAATTTGAATTTAATAGAGAAC-AAAAAT
* *
20553 AGGCTATATAGTTTTATTGGAAGTAACATGAGTGGTGTACATAAGGGTTCTATTATAATTATTGT
238 AGGCTATATGGTTTTATTGAAAGTAACATGAGTGGTGTACATAAGGGTTCTATTATAATTATTGT
*
20618 TTTATGATTTGTGGTTAAAGAAAAAGGGTAAATTCCCTATAAG
303 TTTATGATTTGTGGTTAAAGAAAAAGGGTAAATTCCCCATAAG
** * *
20661 TCA-C-TG-ACCTCCATTGTTTTCATCAAAATTCAATTTAGT-CACTCAAGTACTTTTTAGAAAA
1 TCATCTTGAACCTCCAACGTTTTCATCAAAATTCAATTTAGTCCCCTCAAG-ACATTTTAGAAAA
*
20722 TTTTAACCCCAACTTCAGGGTGTGACACTATCATTGACTATTCTGACTATGATTATCGGTCTAAA
65 TTTTAACCCCAACTTCAGGGTGTGACACTATCATTGACTATTCTGACTATGATTATCGATCTAAA
* * * * *
20787 TATAGTTATCACATTTCAAATATTATCATTAACACTTATATTTTAGATGCTTAAATTGGTTAGAT
130 TATAGTTCTCACAATTCAAATATTATCATTAACTCTTATATTTTATATGATTAAATTGGTTAGAT
* *
20852 TGGAATTTTTGAAGAAAATTTGAATTTAATACAGAACCAAAAATAGGCTATATGGTTTTATTGAA
195 TGGAATTTGTGAAGAAAATTTGAATTTAATAGAGAA-CAAAAATAGGCTATATGGTTTTATTGAA
* *
20917 AGTTACATGAGTCGTGTACATAAGGGTTCTATTAT
259 AGTAACATGAGTGGTGTACATAAGGGTTCTATTAT
20952 TGTTGGGCCT
Statistics
Matches: 584, Mismatches: 46, Indels: 60
0.85 0.07 0.09
Matches are distributed among these distances:
342 6 0.01
343 252 0.43
344 1 0.00
347 3 0.01
352 2 0.00
353 2 0.00
359 2 0.00
360 1 0.00
365 1 0.00
366 30 0.05
367 284 0.49
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (345 bp):
TCATCTTGAACCTCCAACGTTTTCATCAAAATTCAATTTAGTCCCCTCAAGACATTTTAGAAAAT
TTTAACCCCAACTTCAGGGTGTGACACTATCATTGACTATTCTGACTATGATTATCGATCTAAAT
ATAGTTCTCACAATTCAAATATTATCATTAACTCTTATATTTTATATGATTAAATTGGTTAGATT
GGAATTTGTGAAGAAAATTTGAATTTAATAGAGAACAAAAATAGGCTATATGGTTTTATTGAAAG
TAACATGAGTGGTGTACATAAGGGTTCTATTATAATTATTGTTTTATGATTTGTGGTTAAAGAAA
AAGGGTAAATTCCCCATAAG
Found at i:22858 original size:16 final size:16
Alignment explanation
Indices: 22834--22866 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22824 AGAGAAGATT
22834 GAAGAGGAAGCAATTG
1 GAAGAGGAAGCAATTG
*
22850 GAAGTGGAAGCAATTG
1 GAAGAGGAAGCAATTG
22866 G
1 G
22867 TAGGAGCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.39, T:0.15
Consensus pattern (16 bp):
GAAGAGGAAGCAATTG
Found at i:27087 original size:26 final size:26
Alignment explanation
Indices: 27016--27088 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
27006 AGTGTATATA
*
27016 GTGGGCACGACCTTATGTGCATTACG
1 GTGGGCACGACCTTATGTGTATTACG
* *
27042 ATGGCCACGACCTTATGTGTATTACG
1 GTGGGCACGACCTTATGTGTATTACG
27068 GTGGGCACGACCTTATGTGTA
1 GTGGGCACGACCTTATGTGTA
27089 AGCCCTACGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.29
Consensus pattern (26 bp):
GTGGGCACGACCTTATGTGTATTACG
Found at i:30389 original size:16 final size:17
Alignment explanation
Indices: 30368--30406 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
30358 GCAATGGGGG
*
30368 AAAATTTTGAA-GGGAA
1 AAAATTTTGAATGAGAA
30384 AAAATTTTTGAATGAGAA
1 AAAA-TTTTGAATGAGAA
30402 AAAAT
1 AAAAT
30407 AATGCATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 8 0.40
18 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.28
Consensus pattern (17 bp):
AAAATTTTGAATGAGAA
Found at i:30394 original size:17 final size:18
Alignment explanation
Indices: 30368--30406 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
30358 GCAATGGGGG
*
30368 AAAA-TTTTGAA-GGGAA
1 AAAATTTTTGAATGAGAA
30384 AAAATTTTTGAATGAGAA
1 AAAATTTTTGAATGAGAA
30402 AAAAT
1 AAAAT
30407 AATGCATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.28
Consensus pattern (18 bp):
AAAATTTTTGAATGAGAA
Done.