Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004521.1 Hibiscus syriacus cultivar Beakdansim tig00009969_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: 45019
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:611 original size:16 final size:15
Alignment explanation
Indices: 575--610 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
565 AAATTTTGGC
*
575 TTTTTTGGCTTTTTT
1 TTTTTTGCCTTTTTT
590 TTTTTTGCCTTTTTT
1 TTTTTTGCCTTTTTT
605 TTTTTT
1 TTTTTT
611 TTTTTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (15 bp):
TTTTTTGCCTTTTTT
Found at i:2232 original size:18 final size:18
Alignment explanation
Indices: 2180--2235 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
2170 AGAAGGTAAA
2180 ATTTCATAATTTGAGC-T
1 ATTTCATAATTTGAGCTT
**
2197 ACTTTCCATGTTTTTGAGCTT
1 A-TTT-CAT-AATTTGAGCTT
2218 ATTTCATAATTTGAGCTT
1 ATTTCATAATTTGAGCTT
2236 CTTTTTAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 1 0.03
18 12 0.39
19 6 0.19
20 10 0.32
21 2 0.06
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.50
Consensus pattern (18 bp):
ATTTCATAATTTGAGCTT
Found at i:3687 original size:21 final size:18
Alignment explanation
Indices: 3655--3696 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
3645 TAAGTCTAAT
3655 AGCTAAAATGAATGCATATA
1 AGCTAAAATGAATG-AT-TA
3675 AGCTAACAATGAATGATTA
1 AGCTAA-AATGAATGATTA
3694 AGC
1 AGC
3697 ATGCTACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.24
Consensus pattern (18 bp):
AGCTAAAATGAATGATTA
Found at i:5282 original size:22 final size:22
Alignment explanation
Indices: 5250--5299 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
5240 CTCTTATGCA
* *
5250 AGGCATGTGGGTGTGTCCGAAT
1 AGGCATATGGGTGTGGCCGAAT
5272 AGGCATATGGGTGTGGCCGAAT
1 AGGCATATGGGTGTGGCCGAAT
5294 AGGCAT
1 AGGCAT
5300 GGAGTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.14, G:0.40, T:0.24
Consensus pattern (22 bp):
AGGCATATGGGTGTGGCCGAAT
Found at i:8285 original size:22 final size:22
Alignment explanation
Indices: 8237--8288 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
8227 TTTCCTTGGC
*
8237 TTTTTC-TTTTCTTTTTGAAAT
1 TTTTTCTTTTTCTTTTTCAAAT
**
8258 TCTTTTCTTTTTCTTTTTCTGAT
1 T-TTTTCTTTTTCTTTTTCAAAT
8281 TTTTTCTT
1 TTTTTCTT
8289 CTTTTTGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 12 0.46
23 13 0.50
ACGTcount: A:0.08, C:0.13, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTTTCTTTTTCTTTTTCAAAT
Found at i:14828 original size:17 final size:17
Alignment explanation
Indices: 14806--14852 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
14796 GTATGCCTAC
14806 AATAAATAAAGA-AATAA
1 AATAAA-AAAGATAATAA
*
14823 AATAAAAAGGATAATAA
1 AATAAAAAAGATAATAA
*
14840 AAGAAAAAA-ATAA
1 AATAAAAAAGATAA
14853 CTTAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.15
Consensus pattern (17 bp):
AATAAAAAAGATAATAA
Found at i:18709 original size:42 final size:40
Alignment explanation
Indices: 18621--18710 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 40
18611 TGACTTCGAT
* *
18621 TTTCCTTTCCTCATAGCCTCAACACTTTGTTTCATCTTCGA
1 TTTCCTTTCCTCATAGCCTCAACACTTTGTATAATCTTC-A
18662 TTTTCCTTTCCTCATAGCCTCAACACTTAGATGTATAATCTTC-
1 -TTTCCTTTCCTCATAGCCTCAACACTT---TGTATAATCTTCA
18705 TTTCCT
1 TTTCCT
18711 CCATGGTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
42 33 0.77
45 10 0.23
ACGTcount: A:0.19, C:0.30, G:0.07, T:0.44
Consensus pattern (40 bp):
TTTCCTTTCCTCATAGCCTCAACACTTTGTATAATCTTCA
Found at i:33558 original size:25 final size:25
Alignment explanation
Indices: 33524--33583 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
33514 ACAACTTTGA
33524 AGTTCTTCCAAGATAATTCTAAGGG
1 AGTTCTTCCAAGATAATTCTAAGGG
* *
33549 AGTTTTTCCAAGATGATTCTAAGGG
1 AGTTCTTCCAAGATAATTCTAAGGG
33574 AGTTCTTCCA
1 AGTTCTTCCA
33584 TATTTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (25 bp):
AGTTCTTCCAAGATAATTCTAAGGG
Found at i:40788 original size:1 final size:1
Alignment explanation
Indices: 40784--40823 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
40774 CTTTTTTGGC
*
40784 TTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40824 GAAAAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Done.