Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007189.1 Hibiscus syriacus cultivar Beakdansim tig00018936_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: 67714
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:5894 original size:19 final size:20
Alignment explanation
Indices: 5853--5903 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
5843 TAAACCCCTT
*
5853 TGAAAATACATGATTTATAA
1 TGAAAATACATGACTTATAA
5873 TGAAAATACATGACTT-TAA
1 TGAAAATACATGACTTATAA
5892 TGAAAATACATG
1 TGAAAATACATG
5904 CTATTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (20 bp):
TGAAAATACATGACTTATAA
Found at i:10081 original size:47 final size:45
Alignment explanation
Indices: 10004--10113 Score: 143
Period size: 47 Copynumber: 2.4 Consensus size: 45
9994 TAGTATATGG
*
10004 TTATGGAAT-AAT-GTCAAGTATATTGATAAAATAAGCTTATGAGC
1 TTATGGAATAAATGGT-AAGTATATTGATAAAATAAGCTTACGAGC
* *
10048 TTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCTTACGAGC
1 TTATGGAA--TAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
*
10095 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGGTAAG
10114 AGATTTTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
44 8 0.14
45 11 0.19
46 1 0.02
47 36 0.62
48 2 0.03
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
Found at i:17086 original size:20 final size:20
Alignment explanation
Indices: 17061--17103 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17051 TATATTGGGC
* *
17061 TATTTTCTATTGTTTATGGT
1 TATTTTCTATGGTATATGGT
17081 TATTTTCTATGGTATATGGT
1 TATTTTCTATGGTATATGGT
17101 TAT
1 TAT
17104 GGAATAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.60
Consensus pattern (20 bp):
TATTTTCTATGGTATATGGT
Found at i:18175 original size:24 final size:24
Alignment explanation
Indices: 18148--18197 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
18138 CTTCAAGTGG
*
18148 CATAACTAT-TGGAACGTCAAAGGT
1 CATAACT-TGTGGAACATCAAAGGT
* *
18172 CATATCTTGTGGATCATCAAAGGT
1 CATAACTTGTGGAACATCAAAGGT
18196 CA
1 CA
18198 CAATTATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (24 bp):
CATAACTTGTGGAACATCAAAGGT
Found at i:19443 original size:11 final size:11
Alignment explanation
Indices: 19429--19453 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19419 TTCTTTGTAA
19429 TTTCTTTTCTT
1 TTTCTTTTCTT
19440 TTTCTTTTCTT
1 TTTCTTTTCTT
19451 TTT
1 TTT
19454 TTGAATGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:20158 original size:19 final size:20
Alignment explanation
Indices: 20119--20169 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
20109 GAAACCCCTT
20119 TGAAAATACATGATATTTAA
1 TGAAAATACATGATATTTAA
*
20139 TGAAAATACATGA-CTTTAA
1 TGAAAATACATGATATTTAA
20158 TGAAAATACATG
1 TGAAAATACATG
20170 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (20 bp):
TGAAAATACATGATATTTAA
Found at i:29746 original size:3 final size:3
Alignment explanation
Indices: 29738--29840 Score: 190
Period size: 3 Copynumber: 34.3 Consensus size: 3
29728 TTTTTCAACC
29738 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29785 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29833 ATT CATT A
1 ATT -ATT A
29841 CAAAAATGTG
Statistics
Matches: 98, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.02
3 93 0.95
4 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:40412 original size:20 final size:21
Alignment explanation
Indices: 40358--40420 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
40348 GATTCCCCTG
40358 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
40382 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
40402 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
40421 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:44274 original size:22 final size:21
Alignment explanation
Indices: 44232--44271 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
44222 GAGTTTGTTT
*
44232 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
44253 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
44272 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:46625 original size:14 final size:14
Alignment explanation
Indices: 46606--46636 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
46596 TGTATGTTGG
46606 CATGATATTTATGT
1 CATGATATTTATGT
46620 CATGATATTTATGT
1 CATGATATTTATGT
46634 CAT
1 CAT
46637 TTATCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (14 bp):
CATGATATTTATGT
Found at i:49787 original size:45 final size:46
Alignment explanation
Indices: 49720--49825 Score: 135
Period size: 45 Copynumber: 2.3 Consensus size: 46
49710 TGCACTAAAT
* * *
49720 GTGCATCGATGCATGAAGTGCATTCGA-TATTTCA-AAATAGCCTGA
1 GTGCATCGATGCATCAAATGCATTCGAGTATTTCATAAA-AACCTGA
* *
49765 GTGCATCGATGCATCAAATGCATTCGATGTTTTTTATAAAAACCTGA
1 GTGCATCGATGCATCAAATGCATTCGA-GTATTTCATAAAAACCTGA
49812 GTGCATCGATGCAT
1 GTGCATCGATGCAT
49826 GGTATGTGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
45 25 0.47
47 25 0.47
48 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (46 bp):
GTGCATCGATGCATCAAATGCATTCGAGTATTTCATAAAAACCTGA
Found at i:58551 original size:66 final size:63
Alignment explanation
Indices: 58432--58587 Score: 190
Period size: 66 Copynumber: 2.4 Consensus size: 63
58422 CGGTGCAGTC
* * * *
58432 TCGATGCATGAAGTGCATTCGATGTTTTAAAATAGCCTGAGTGCATCGATGCAT-GTCCTGTGCA
1 TCGATGCAT-AAATGCATTCGATGTTTTAAAATAACCTGAGTGCATCAATGCATGGT-ATGTGCA
*
58496 TCGATGCATCAAATGCATTCGACGTTTTTTATAAA-AACCTGAGTGCATCAATGCATGGTATGTG
1 TCGATGCAT-AAATGCATTCGA--TGTTTTA-AAATAACCTGAGTGCATCAATGCATGGTATGTG
58560 CA
62 CA
58562 TCGATGCATATAATGCATTCGATGTT
1 TCGATGCATA-AATGCATTCGATGTT
58588 CAATTTATTC
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
64 23 0.29
65 1 0.01
66 51 0.64
67 5 0.06
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (63 bp):
TCGATGCATAAATGCATTCGATGTTTTAAAATAACCTGAGTGCATCAATGCATGGTATGTGCA
Found at i:62861 original size:10 final size:10
Alignment explanation
Indices: 62825--62855 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
62815 GTTAAACTTC
62825 ATAAAAATAAA
1 ATAAAAAT-AA
62836 ATAAAAATAA
1 ATAAAAATAA
62846 ATAAAAATAA
1 ATAAAAATAA
62856 CAAAAATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.60
11 8 0.40
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:63388 original size:21 final size:22
Alignment explanation
Indices: 63364--63408 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
63354 TAATTTGGAA
*
63364 TATT-AAAAAGGGATATGAATT
1 TATTCAAAAAAGGATATGAATT
*
63385 TATTCAAAAAATGATATGAATT
1 TATTCAAAAAAGGATATGAATT
63407 TA
1 TA
63409 ATTTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (22 bp):
TATTCAAAAAAGGATATGAATT
Done.