Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000674.1 Hibiscus syriacus cultivar Beakdansim tig00001308_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: 47892
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:68 original size:24 final size:25
Alignment explanation
Indices: 21--69 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
11 TTTAATAATT
*
21 AATATTTTGATTAAAATGATATTAA
1 AATATTTTGATTAAAATGAAATTAA
* *
46 AATATTTT-ATTAATATTAAATTAA
1 AATATTTTGATTAAAATGAAATTAA
70 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
AATATTTTGATTAAAATGAAATTAA
Found at i:284 original size:42 final size:42
Alignment explanation
Indices: 224--317 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
214 TCCTCCAACC
* * *
224 AAACACTGGAAAACATTTTCCGGAAAATGAATTACGTGAAAA
1 AAACACGGGAAAACATTTTCCGAAAAACGAATTACGTGAAAA
* *
266 AAACACGGGAAAATATTTTCCGAAAAACGAATTACGTGAAAT
1 AAACACGGGAAAACATTTTCCGAAAAACGAATTACGTGAAAA
308 AAACACGGGA
1 AAACACGGGA
318 TTTCCGATTC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (42 bp):
AAACACGGGAAAACATTTTCCGAAAAACGAATTACGTGAAAA
Found at i:3097 original size:6 final size:6
Alignment explanation
Indices: 3063--3094 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3053 CTCGTCTCGA
*
3063 GTCGTG GTCGTG GTCGTG GTCGTG GTAGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
3095 AGTACGTGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.12, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:3244 original size:21 final size:21
Alignment explanation
Indices: 3220--3266 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3210 AAATCACAAC
*
3220 GCGAACTTCGACTGTCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
3241 GCGAACTTGGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
3262 GCGAA
1 GCGAA
3267 TATGTAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:11990 original size:26 final size:26
Alignment explanation
Indices: 11954--12006 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
11944 ACTATCTACG
11954 TCATATTGTTTAATATAAAACAGAAA
1 TCATATTGTTTAATATAAAACAGAAA
11980 TCATATTGTTTAATATAAAACAGAAA
1 TCATATTGTTTAATATAAAACAGAAA
12006 T
1 T
12007 AAGTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (26 bp):
TCATATTGTTTAATATAAAACAGAAA
Found at i:15974 original size:99 final size:99
Alignment explanation
Indices: 15803--16000 Score: 351
Period size: 99 Copynumber: 2.0 Consensus size: 99
15793 AGATACTTTT
* *
15803 TCATTTCTCAAATCCAACTCAGAAGTGTCCTCTCCAGGTTGAGTACTCATCTTTTGATCAGGTGG
1 TCATTTCTCAAATCCAACTCAGAAGTATCCTCTCCAGGTTGAGAACTCATCTTTTGATCAGGTGG
15868 AAGGCATGCTGCATTGTTTAACATGGAACCATCC
66 AAGGCATGCTGCATTGTTTAACATGGAACCATCC
* *
15902 TCATTTCTCATATCCAATTCAGAAGTATCCTCTCCAGGTTGAGAACTCATCTTTTGATCAGGTGG
1 TCATTTCTCAAATCCAACTCAGAAGTATCCTCTCCAGGTTGAGAACTCATCTTTTGATCAGGTGG
*
15967 AAGGCATGCTTCATTGTTTAACATGGAACCATCC
66 AAGGCATGCTGCATTGTTTAACATGGAACCATCC
16001 ATGATGTTGG
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (99 bp):
TCATTTCTCAAATCCAACTCAGAAGTATCCTCTCCAGGTTGAGAACTCATCTTTTGATCAGGTGG
AAGGCATGCTGCATTGTTTAACATGGAACCATCC
Found at i:35635 original size:38 final size:38
Alignment explanation
Indices: 35584--35662 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
35574 ATTTTATGTA
35584 TTTAAACTCATTGTTATTTTAATTTTAATAATGGGTTC
1 TTTAAACTCATTGTTATTTTAATTTTAATAATGGGTTC
35622 TTTAAACTCATTGTTATTTTAATTTTAATAATGGGTTC
1 TTTAAACTCATTGTTATTTTAATTTTAATAATGGGTTC
35660 TTT
1 TTT
35663 TCATTTCATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (38 bp):
TTTAAACTCATTGTTATTTTAATTTTAATAATGGGTTC
Done.