Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005115.1 Hibiscus syriacus cultivar Beakdansim tig00011502_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: 62827
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3086 original size:198 final size:196
Alignment explanation
Indices: 2713--3106 Score: 761
Period size: 198 Copynumber: 2.0 Consensus size: 196
2703 TTTGACTCCA
2713 TTATTCCTGGATGTTGGGGTTTATAGTCTCCTGTCCCTTTTTTTTGTAGAGCATCTGTTGAATCT
1 TTATTCCTGGATGTTGGGGTTTATAGTCTCCTGTCCCTTTTTTTTGTAGAGCATCTGTTGAATCT
*
2778 TTTTATGCATCTATGAAGGTTTTTAATCATTCTAATCATTCACAGATTTATCGAATTCTCTTTAG
66 TTTTATGCATCTATGAAGGTTTTTAATCATTCTAATCATTCACAAATTTATCGAATTCTCTTTAG
2843 CATTTGGGCATTGAAGACAGTACACACACACACGTGTATATAATGTGTGTACCAAAGTTGGGGTG
131 CATTTGGGCATTGAAGACAGTACACACACACACGTGTATATAATGTGTGTACCAAAGTTGGGGTG
2908 G
196 G
2909 TTATTCCTGGATGTTGGGGTTTATAGTCTCCTGTCCCTTTTTTTTGTTAGAGCATCTGTTGAATC
1 TTATTCCTGGATGTTGGGGTTTATAGTCTCCTGTCCCTTTTTTTTG-TAGAGCATCTGTTGAATC
2974 TTTTTATGCATCTATGAAGGTTTTTAATCATTCTAATCATTTCACAAATTTATCGAATTCTCTTT
65 TTTTTATGCATCTATGAAGGTTTTTAATCATTCTAATCA-TTCACAAATTTATCGAATTCTCTTT
3039 AGCATTTGGGCATTGAAGACAGTACACACACACACGTGTATATAATGTGTGTACCAAAGTTGGGG
129 AGCATTTGGGCATTGAAGACAGTACACACACACACGTGTATATAATGTGTGTACCAAAGTTGGGG
3104 TGG
194 TGG
3107 CCGCAGATAA
Statistics
Matches: 195, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
196 46 0.24
197 57 0.29
198 92 0.47
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (196 bp):
TTATTCCTGGATGTTGGGGTTTATAGTCTCCTGTCCCTTTTTTTTGTAGAGCATCTGTTGAATCT
TTTTATGCATCTATGAAGGTTTTTAATCATTCTAATCATTCACAAATTTATCGAATTCTCTTTAG
CATTTGGGCATTGAAGACAGTACACACACACACGTGTATATAATGTGTGTACCAAAGTTGGGGTG
G
Found at i:10562 original size:24 final size:24
Alignment explanation
Indices: 10530--10575 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
10520 CAATTGCTCC
10530 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCTCTCTTCTTCGA
*
10554 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCGTCTCTCTTCTTC
10576 TTCTACATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCGTCTCTCTTCTTCGA
Found at i:20415 original size:15 final size:16
Alignment explanation
Indices: 20391--20431 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
20381 CTTTCGATAA
20391 CCTC-TTCTTCCTCTT
1 CCTCGTTCTTCCTCTT
*
20406 -CTCGTTCTTCTTCTT
1 CCTCGTTCTTCCTCTT
*
20421 CCTTGTTCTTC
1 CCTCGTTCTTC
20432 TTCTCTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.00, C:0.39, G:0.05, T:0.56
Consensus pattern (16 bp):
CCTCGTTCTTCCTCTT
Found at i:20430 original size:16 final size:15
Alignment explanation
Indices: 20395--20435 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
20385 CGATAACCTC
*
20395 TTCTTCCTCTTCTCG
1 TTCTTCTTCTTCTCG
*
20410 TTCTTCTTCTTCCTTG
1 TTCTTCTTCTT-CTCG
20426 TTCTTCTTCT
1 TTCTTCTTCT
20436 CTCCAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.00, C:0.34, G:0.05, T:0.61
Consensus pattern (15 bp):
TTCTTCTTCTTCTCG
Found at i:21388 original size:2 final size:2
Alignment explanation
Indices: 21383--21408 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21373 TTTTTATCTA
21383 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
21409 CGAGTCGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34645 original size:2 final size:2
Alignment explanation
Indices: 34640--34676 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34630 ACACACACAC
34640 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34677 AAAGACTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38296 original size:15 final size:16
Alignment explanation
Indices: 38264--38296 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
38254 AAAATCTTTC
38264 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
38280 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
38295 TT
1 TT
38297 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:39071 original size:16 final size:17
Alignment explanation
Indices: 39046--39077 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39036 TCGCCGACCG
39046 AATTTCACTATTCACGA
1 AATTTCACTATTCACGA
39063 AATTT-ACTATTCACG
1 AATTTCACTATTCACG
39078 TGAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (17 bp):
AATTTCACTATTCACGA
Found at i:51427 original size:17 final size:17
Alignment explanation
Indices: 51386--51430 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
51376 CTCTACTTGA
51386 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
51403 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
51420 TTAAATATTTA
1 TTAAATATTTA
51431 TTTTTACATA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:56038 original size:32 final size:32
Alignment explanation
Indices: 55977--56038 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
55967 GGTACCCATA
* *
55977 TATTTTTAAAAATATATATATTTATTTTATTT
1 TATTTTTAAAAATATATATATTAAATTTATTT
* * *
56009 TATTTTTAAATATTTTTATATTAAATTTAT
1 TATTTTTAAAAATATATATATTAAATTTAT
56039 AAAATAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
TATTTTTAAAAATATATATATTAAATTTATTT
Done.