Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007588.1 Hibiscus syriacus cultivar Beakdansim tig00021847_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: 47352
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Found at i:2982 original size:28 final size:27
Alignment explanation
Indices: 2934--2997 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
2924 GAAAAATCAT
*
2934 TATATATTATTAAAATAAAAG-TATAA
1 TATATATCATTAAAATAAAAGATATAA
*
2960 TATATATCATTATAATATTAAAGAATATAA
1 TATATATCATTA-AA-ATAAAAG-ATATAA
2990 TATCATAT
1 TAT-ATAT
2998 TATAAGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 11 0.35
27 2 0.06
28 6 0.19
30 8 0.26
31 4 0.13
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (27 bp):
TATATATCATTAAAATAAAAGATATAA
Found at i:5935 original size:20 final size:20
Alignment explanation
Indices: 5912--5952 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5902 TTTAATAAAT
5912 TATATAATTTT-TTATTATAA
1 TATAT-ATTTTATTATTATAA
*
5932 TATATATTTTATTATTTTAA
1 TATATATTTTATTATTATAA
5952 T
1 T
5953 TACTATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATATTTTATTATTATAA
Found at i:6135 original size:27 final size:28
Alignment explanation
Indices: 6105--6169 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
6095 ATTGAAAATC
*
6105 ATTATATTATTAAAATAAAAGTATA-AT
1 ATTATATTATTAAAATAAAAGAATATAT
* *
6132 ATTATA-TATTTATAATTAAAGAATATAT
1 ATTATATTA-TTAAAATAAAAGAATATAT
*
6160 ATCATATTAT
1 ATTATATTAT
6170 AAGAATTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
26 2 0.06
27 19 0.61
28 8 0.26
29 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (28 bp):
ATTATATTATTAAAATAAAAGAATATAT
Found at i:9053 original size:20 final size:20
Alignment explanation
Indices: 9030--9070 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
9020 TTTAATAAAT
9030 TATATAATTTT-TTATTATAA
1 TATAT-ATTTTATTATTATAA
*
9050 TATATATTTTATTATTTTAA
1 TATATATTTTATTATTATAA
9070 T
1 T
9071 TACTATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATATTTTATTATTATAA
Found at i:12411 original size:18 final size:19
Alignment explanation
Indices: 12381--12429 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
12371 AGTTTTGTAA
12381 TTTA-TGAATAATACTAT-T
1 TTTATTGAA-AATACTATAT
*
12399 TTTATTGAAAATATTATAT
1 TTTATTGAAAATACTATAT
*
12418 ATTATT-AAAATA
1 TTTATTGAAAATA
12430 AAAGTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TTTATTGAAAATACTATAT
Found at i:12900 original size:2 final size:2
Alignment explanation
Indices: 12893--12920 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12883 TTAATTCTTG
12893 AT 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 AT
12921 TTTTTCTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16120 original size:2 final size:2
Alignment explanation
Indices: 16113--16138 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16103 TTAATTCTTG
16113 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
16139 TTTTTCTGAA
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:27552 original size:4 final size:5
Alignment explanation
Indices: 27528--27585 Score: 59
Period size: 5 Copynumber: 12.2 Consensus size: 5
27518 AACGGTCAAC
* * * *
27528 GGTCG GGTCG GGTCG GGTC- GGTCG GGTAG GTTC- GGT-T GGTCG GGTTG
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
27575 GGTCG GGTCG G
1 GGTCG GGTCG G
27586 ACCGGTTCAG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
4 9 0.21
5 34 0.79
ACGTcount: A:0.02, C:0.16, G:0.57, T:0.26
Consensus pattern (5 bp):
GGTCG
Found at i:27552 original size:9 final size:9
Alignment explanation
Indices: 27527--27585 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
27517 CAACGGTCAA
27527 CGGTCGGGT
1 CGGTCGGGT
27536 CGGGTCGGGT
1 C-GGTCGGGT
27546 CGGTCGGGT
1 CGGTCGGGT
*
27555 AGGTTC-GGT
1 CGG-TCGGGT
*
27564 TGGTCGGGTT
1 CGGTCGGG-T
*
27574 GGGTCGGGT
1 CGGTCGGGT
27583 CGG
1 CGG
27586 ACCGGTTCAG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 2 0.05
9 21 0.50
10 19 0.45
ACGTcount: A:0.02, C:0.17, G:0.56, T:0.25
Consensus pattern (9 bp):
CGGTCGGGT
Found at i:39808 original size:18 final size:19
Alignment explanation
Indices: 39769--39809 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
39759 ATATACATAT
*
39769 ATATTATTTTTTCTGAAAA
1 ATATTATTTTTTATGAAAA
39788 ATATT-TTTTTTAT-AAATA
1 ATATTATTTTTTATGAAA-A
39806 ATAT
1 ATAT
39810 AAAAGTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 12 0.60
19 5 0.25
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
ATATTATTTTTTATGAAAA
Found at i:45487 original size:31 final size:29
Alignment explanation
Indices: 45420--45488 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
45410 AAATCATTAA
* *
45420 ATATTATTAAAATAAAAGTATAATATTAT
1 ATATTATTAAAATAAAAGAATAATAATAT
*
45449 ATATTATTATAATATTAAAGAAT-ATAATAT
1 ATATTATTA-AA-ATAAAAGAATAATAATAT
45479 CATATTATTA
1 -ATATTATTA
45489 GAATTATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.26
30 8 0.24
31 17 0.50
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (29 bp):
ATATTATTAAAATAAAAGAATAATAATAT
Found at i:45910 original size:2 final size:2
Alignment explanation
Indices: 45903--45930 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45893 TTAATTCTTG
45903 AT 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 AT
45931 TATTTTTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45965 original size:18 final size:18
Alignment explanation
Indices: 45927--45966 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
45917 ATATATATAT
*
45927 ATATTATTTTTCTGAAAA
1 ATATTATTTTTATGAAAA
45945 ATATTATTTTTAT-AAATA
1 ATATTATTTTTATGAAA-A
45963 ATAT
1 ATAT
45967 AAAAGTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATATTATTTTTATGAAAA
Done.