Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006621.1 Hibiscus syriacus cultivar Beakdansim tig00016262_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: 63684
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:6360 original size:24 final size:21
Alignment explanation
Indices: 6326--6368 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
6316 TCCACAAGAT
*
6326 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
6348 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
6369 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:13816 original size:23 final size:23
Alignment explanation
Indices: 13764--13823 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
13754 CAAGAAAATC
13764 AGAAAGAAAATAAAAGCACTCAAA
1 AGAAAG-AAATAAAAGCACTCAAA
*
13788 AG-AAGAATTAAAAG-ACTCGAAA
1 AGAAAGAAATAAAAGCACTC-AAA
*
13810 AGAAAGAAAAAAAA
1 AGAAAGAAATAAAA
13824 AGAAAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 4 0.13
22 13 0.42
23 12 0.39
24 2 0.06
ACGTcount: A:0.68, C:0.08, G:0.15, T:0.08
Consensus pattern (23 bp):
AGAAAGAAATAAAAGCACTCAAA
Found at i:13824 original size:14 final size:14
Alignment explanation
Indices: 13807--13833 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13797 AAAAGACTCG
13807 AAAAGAAAGAAAAA
1 AAAAGAAAGAAAAA
13821 AAAAGAAAGAAAA
1 AAAAGAAAGAAAA
13834 GTTGGAAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAAAA
Found at i:17678 original size:13 final size:12
Alignment explanation
Indices: 17641--17692 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
17631 TATTTTTTTT
*
17641 AAAATAAAA-AA
1 AAAAAAAAACAA
*
17652 AACAAAAAACAA
1 AAAAAAAAACAA
**
17664 AAAAAAAGGCAA
1 AAAAAAAAACAA
17676 AAAAAAAAACAA
1 AAAAAAAAACAA
17688 AAAAA
1 AAAAA
17693 GCCAAAACAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
11 7 0.21
12 26 0.79
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.02
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:17680 original size:22 final size:22
Alignment explanation
Indices: 17649--17699 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
17639 TTAAAATAAA
*
17649 AAAAACAAAAAACAAAAAAAAAGGC
1 AAAAA-AAAAAACAAA--AAAAGCC
17674 AAAAAAAAAAACAAAAAAAGCC
1 AAAAAAAAAAACAAAAAAAGCC
17696 AAAA
1 AAAA
17700 CAAATCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
24 10 0.40
25 5 0.20
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAACAAAAAAAGCC
Found at i:22807 original size:91 final size:91
Alignment explanation
Indices: 22632--22812 Score: 240
Period size: 91 Copynumber: 2.0 Consensus size: 91
22622 CCTAGAACAC
* *
22632 CCATGTGCCTTGCATATGACCATCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATG
* * *
22697 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAAAGATCTATCCCTATTCGGCCAAG
** * * *
22723 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATATGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATG
22788 AATAAGCATCTAT-CC-ATTCGGCCAA
66 AA-AAG-ATCTATCCCTATTCGGCCAA
22813 TCACTATTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
91 70 0.90
92 4 0.05
93 4 0.05
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATG
AAAAGATCTATCCCTATTCGGCCAAG
Found at i:33964 original size:35 final size:37
Alignment explanation
Indices: 33897--33976 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
33887 ATACTATTTC
*
33897 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
33934 CATCACCATAGTCCGTC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
33969 CATCACCA
1 CATCACCA
33977 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.38, G:0.05, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:41390 original size:35 final size:37
Alignment explanation
Indices: 41325--41400 Score: 120
Period size: 35 Copynumber: 2.1 Consensus size: 37
41315 TATTTCCATA
*
41325 ACCATAATCCATCTTCCATTATCACGCCTATATCATC
1 ACCATAATCCATCTACCATTATCACGCCTATATCATC
*
41362 ACCATAGTCCATC-ACCA-TATCACGCCTATATCATC
1 ACCATAATCCATCTACCATTATCACGCCTATATCATC
41397 ACCA
1 ACCA
41401 AATTCTCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 22 0.59
36 3 0.08
37 12 0.32
ACGTcount: A:0.32, C:0.37, G:0.04, T:0.28
Consensus pattern (37 bp):
ACCATAATCCATCTACCATTATCACGCCTATATCATC
Found at i:41877 original size:14 final size:15
Alignment explanation
Indices: 41843--41889 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
41833 AATTTGTAGT
41843 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
41858 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
41872 TCAAAAGCAATAGAAAA
1 GCAAAAG-AA-AGAAAA
41889 G
1 G
41890 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
16 1 0.04
17 6 0.24
ACGTcount: A:0.70, C:0.06, G:0.19, T:0.04
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:45413 original size:35 final size:37
Alignment explanation
Indices: 45344--45419 Score: 111
Period size: 35 Copynumber: 2.1 Consensus size: 37
45334 TATTTCCATA
*
45344 ACCATAATCCATCTTCCATTATCACGCCTATATCATC
1 ACCATAATCCATCTACCATTATCACGCCTATATCATC
* *
45381 ACCATAGTCCATC-ACCA-TATTACGCCTATATCATC
1 ACCATAATCCATCTACCATTATCACGCCTATATCATC
45416 ACCA
1 ACCA
45420 AATTCTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 21 0.58
36 3 0.08
37 12 0.33
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
ACCATAATCCATCTACCATTATCACGCCTATATCATC
Found at i:49429 original size:35 final size:37
Alignment explanation
Indices: 49356--49435 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
49346 ATACTATTTC
* *
49356 CATCACCATAATCCATCTTCCATTATTACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
49393 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
49428 CATCACCA
1 CATCACCA
49436 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:54455 original size:13 final size:13
Alignment explanation
Indices: 54437--54470 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
54427 GGCGTGAAAA
54437 TGGTGATGGAAGG
1 TGGTGATGGAAGG
54450 TGGTGATGGAAGG
1 TGGTGATGGAAGG
54463 TGGTGATG
1 TGGTGATG
54471 AATAGATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.53, T:0.26
Consensus pattern (13 bp):
TGGTGATGGAAGG
Found at i:58424 original size:12 final size:12
Alignment explanation
Indices: 58394--58418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58384 CAACAAAAGC
58394 AACAAAAAGAAA
1 AACAAAAAGAAA
58406 AACAAAAAGAAA
1 AACAAAAAGAAA
58418 A
1 A
58419 GAAAAAGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AACAAAAAGAAA
Found at i:58642 original size:16 final size:16
Alignment explanation
Indices: 58621--58667 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
58611 GAAAGTTATC
58621 TTCATTTTCTTACTAT
1 TTCATTTTCTTACTAT
* *
58637 TTCA-TTTCTTTATTCT
1 TTCATTTTC-TTACTAT
58653 TTCATTTTTCTTACT
1 TTCA-TTTTCTTACT
58668 TCATTACCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 4 0.16
18 4 0.16
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (16 bp):
TTCATTTTCTTACTAT
Done.