Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004189.1 Hibiscus syriacus cultivar Beakdansim tig00009162_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: 57462
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:5907 original size:24 final size:24
Alignment explanation
Indices: 5880--5926 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5870 TGCTGCAATA
5880 AAAGCAACAAAAAG-AAAAGAAAAG
1 AAAG-AACAAAAAGAAAAAGAAAAG
*
5904 AAAGAATAAAAAGAAAAAGAAAA
1 AAAGAACAAAAAGAAAAAGAAAA
5927 ATAAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAGAACAAAAAGAAAAAGAAAAG
Found at i:5917 original size:18 final size:16
Alignment explanation
Indices: 5888--5937 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 16
5878 TAAAAGCAAC
*
5888 AAAAAGAAAAGAAAAG
1 AAAAATAAAAGAAAAG
5904 AAAGAATAAAAAGAAAAAG
1 AAA-AAT-AAAAG-AAAAG
5923 AAAAATAAAAGAAAA
1 AAAAATAAAAGAAAA
5938 AGACTCTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 8 0.27
19 8 0.27
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (16 bp):
AAAAATAAAAGAAAAG
Found at i:5922 original size:6 final size:6
Alignment explanation
Indices: 5888--5940 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
5878 TAAAAGCAAC
* *
5888 AAAAAG -AAAAG -AAAAG AAAGAAT AAAAAG AAAAAG AAAAA- TAAAAG
1 AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG
5934 AAAAAG A
1 AAAAAG A
5941 CTCTTACATC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 14 0.35
6 21 0.52
7 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:5937 original size:23 final size:24
Alignment explanation
Indices: 5888--5940 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
5878 TAAAAGCAAC
*
5888 AAAAAG-AAAAGAAAAGAAAGAAT
1 AAAAAGAAAAAGAAAAGAAAGAAG
5911 AAAAAGAAAAAGAAAA-ATAA-AAG
1 AAAAAGAAAAAGAAAAGA-AAGAAG
5934 AAAAAGA
1 AAAAAGA
5941 CTCTTACATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (24 bp):
AAAAAGAAAAAGAAAAGAAAGAAG
Found at i:5938 original size:18 final size:19
Alignment explanation
Indices: 5894--5940 Score: 73
Period size: 17 Copynumber: 2.6 Consensus size: 19
5884 CAACAAAAAG
5894 AAAAG-AAAAGAAAGAATA
1 AAAAGAAAAAGAAAGAATA
5912 AAAAGAAAAAGAAA-AAT-
1 AAAAGAAAAAGAAAGAATA
5929 AAAAGAAAAAGA
1 AAAAGAAAAAGA
5941 CTCTTACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 12 0.43
18 8 0.29
19 8 0.29
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (19 bp):
AAAAGAAAAAGAAAGAATA
Found at i:11463 original size:15 final size:15
Alignment explanation
Indices: 11452--11480 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11442 ACTCAAAAAG
11452 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
11467 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
11481 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:19936 original size:14 final size:16
Alignment explanation
Indices: 19919--19956 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
19909 TAGTAATTAA
19919 ATAGAAG-G-ATAAAT
1 ATAGAAGCGAATAAAT
19933 ATAGAAGCGAAATAAAT
1 ATAGAAGCG-AATAAAT
19950 ATAGAAG
1 ATAGAAG
19957 TTGGTGATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 1 0.05
17 13 0.62
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.18
Consensus pattern (16 bp):
ATAGAAGCGAATAAAT
Found at i:23339 original size:28 final size:28
Alignment explanation
Indices: 23304--23362 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
23294 GCTTGCTTTC
* *
23304 TCTTTTTTGAATTTCTTTTTTTTCTTTTTT
1 TCTTTTCTGAA-TT-TTTTTCTTCTTTTTT
23334 TCTTTTCTGAATTTTTTTCTTCTTTTTT
1 TCTTTTCTGAATTTTTTTCTTCTTTTTT
23362 T
1 T
23363 GTCATTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 15 0.56
29 2 0.07
30 10 0.37
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (28 bp):
TCTTTTCTGAATTTTTTTCTTCTTTTTT
Found at i:35180 original size:24 final size:24
Alignment explanation
Indices: 35135--35180 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
35125 AACTAAAGCA
* * *
35135 TGTGACTTTTCAAGAGCCAAGAGG
1 TGTGACTATTCAAAAGCAAAGAGG
*
35159 TGTGACTATTGAAAAGCAAAGA
1 TGTGACTATTCAAAAGCAAAGA
35181 ATGGTAATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (24 bp):
TGTGACTATTCAAAAGCAAAGAGG
Found at i:39566 original size:23 final size:23
Alignment explanation
Indices: 39539--39595 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
39529 GATTACCGCT
39539 TGATGTAAGGCTCTGATACCAC-
1 TGATGTAAGGCTCTGATACCACA
39561 TAGATGTAAGGCTCTGATACCACA
1 T-GATGTAAGGCTCTGATACCACA
39585 TGATGTAAGGC
1 TGATGTAAGGC
39596 ACTTGTCCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (23 bp):
TGATGTAAGGCTCTGATACCACA
Found at i:45309 original size:26 final size:25
Alignment explanation
Indices: 45280--45328 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
45270 CATTCACATG
*
45280 TTAGTT-ATTATGTTACTATCATATGC
1 TTAGTTGATCATGTTA-TA-CATATGC
45306 TTAGTTGATCATGTTATACATAT
1 TTAGTTGATCATGTTATACATAT
45329 CATTGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 8 0.38
27 8 0.38
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (25 bp):
TTAGTTGATCATGTTATACATATGC
Found at i:49426 original size:6 final size:5
Alignment explanation
Indices: 49393--49440 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
49383 AAAATTAGAA
*
49393 TCTTT TCTTT TCTTT T-TTT T-TTT T-TTT TGCTTT TCTTT CCTTT T-TTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T-CTTT TCTTT TCTTT TCTTT
49440 T
1 T
49441 TTAATTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
4 16 0.41
5 19 0.49
6 4 0.10
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:49426 original size:23 final size:22
Alignment explanation
Indices: 49395--49442 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
49385 AATTAGAATC
**
49395 TTTTCTTTTCTTTTTTTTTTTT
1 TTTTCTTTTCTTTCCTTTTTTT
49417 TTTTGCTTTTCTTTCCTTTTTTT
1 TTTT-CTTTTCTTTCCTTTTTTT
49440 TTT
1 TTT
49443 AATTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (22 bp):
TTTTCTTTTCTTTCCTTTTTTT
Found at i:49448 original size:28 final size:28
Alignment explanation
Indices: 49394--49448 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
49384 AAATTAGAAT
* **
49394 CTTTTCTTTTCTTTTTTTTTTTTTTTTG
1 CTTTTCTTTCCTTTTTTTTTTAATTTTG
49422 CTTTTCTTTCCTTTTTTTTTTAATTTT
1 CTTTTCTTTCCTTTTTTTTTTAATTTT
49449 TAATTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.82
Consensus pattern (28 bp):
CTTTTCTTTCCTTTTTTTTTTAATTTTG
Found at i:49449 original size:23 final size:23
Alignment explanation
Indices: 49399--49449 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
49389 AGAATCTTTT
** **
49399 CTTTTCTTTTTTTTTTTTTTTTG
1 CTTTTCTTTCCTTTTTTTTTTAA
49422 CTTTTCTTTCCTTTTTTTTTTAA
1 CTTTTCTTTCCTTTTTTTTTTAA
*
49445 TTTTT
1 CTTTT
49450 AATTTTTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (23 bp):
CTTTTCTTTCCTTTTTTTTTTAA
Found at i:49456 original size:8 final size:8
Alignment explanation
Indices: 49437--49465 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
49427 CTTTCCTTTT
49437 TTTTTTAA
1 TTTTTTAA
49445 -TTTTTAA
1 TTTTTTAA
49452 TTTTTTAA
1 TTTTTTAA
49460 TTTTTT
1 TTTTTT
49466 TAAAATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTAA
Done.