Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001729.1 Hibiscus syriacus cultivar Beakdansim tig00003494_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: 62664
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5372 original size:20 final size:21
Alignment explanation
Indices: 5318--5372 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
5308 ATATTACATT
5318 TATAACATAATAATATTTTATAA
1 TATAA-ATAAT-ATATTTTATAA
*
5341 TATAAATTATATATTTT-TACA
1 TATAAATAATATATTTTATA-A
5362 T-TAAATAATAT
1 TATAAATAATAT
5373 CAATATCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 11 0.38
21 9 0.31
22 4 0.14
23 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAAATAATATATTTTATAA
Found at i:5528 original size:13 final size:13
Alignment explanation
Indices: 5510--5553 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
5500 GGATGAAATT
5510 AATTTAATAATAA
1 AATTTAATAATAA
*
5523 AATTTAATAATATT
1 AATTTAATAATA-A
5537 AATTTAATAAATAA
1 AATTTAAT-AATAA
5551 AAT
1 AAT
5554 ATTTTTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 12 0.44
14 11 0.41
15 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTTAATAATAA
Found at i:8933 original size:24 final size:26
Alignment explanation
Indices: 8906--8957 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
8896 AAATTTTATG
*
8906 TTAAAGGG-GC-GAACTTCTAAAATT
1 TTAAAGGGAGCTGAACTTATAAAATT
8930 TT-AAGGGAGCTGAACTTATAAAATT
1 TTAAAGGGAGCTGAACTTATAAAATT
8955 TTA
1 TTA
8958 CGGGTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 4 0.17
25 15 0.62
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (26 bp):
TTAAAGGGAGCTGAACTTATAAAATT
Found at i:9723 original size:14 final size:15
Alignment explanation
Indices: 9694--9726 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
9684 TATAAATACC
9694 TTTAAACTTTAATAT
1 TTTAAACTTTAATAT
*
9709 TTTAAA-TTTATTAT
1 TTTAAACTTTAATAT
9723 TTTA
1 TTTA
9727 TTACTCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAAACTTTAATAT
Found at i:15543 original size:6 final size:6
Alignment explanation
Indices: 15532--15578 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
15522 CGCAGTTTTG
* *
15532 AAAAGA AAAAG- -AAAGA AAAAGGA AAAAGA AGAAGA AGAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA AAAAGA
15579 GAGAAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 4 0.11
6 26 0.72
7 6 0.17
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:15548 original size:10 final size:9
Alignment explanation
Indices: 15534--15586 Score: 65
Period size: 10 Copynumber: 5.9 Consensus size: 9
15524 CAGTTTTGAA
15534 AAGAAAAAG
1 AAGAAAAAG
15543 AAAGAAAAAG
1 -AAGAAAAAG
15553 --GAAAAAG
1 AAGAAAAAG
*
15560 AAGAAGAAG
1 AAGAAAAAG
15569 AAGAAAAAG
1 AAGAAAAAG
15578 AGAGAAAAA
1 A-AGAAAAA
15587 TTAAAGTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
7 7 0.18
9 15 0.39
10 16 0.42
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:15551 original size:16 final size:16
Alignment explanation
Indices: 15532--15586 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
15522 CGCAGTTTTG
15532 AAAAGAAAAAGAAAGA
1 AAAAGAAAAAGAAAGA
15548 AAAAGGAAAAAGAAGAAGA
1 AAAA-GAAAAAG-A-AAGA
* *
15567 AGAAGAAAAAGAGAGA
1 AAAAGAAAAAGAAAGA
15583 AAAA
1 AAAA
15587 TTAAAGTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 10 0.30
17 8 0.24
18 8 0.24
19 7 0.21
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAGA
Found at i:16220 original size:43 final size:42
Alignment explanation
Indices: 16098--16263 Score: 138
Period size: 43 Copynumber: 3.8 Consensus size: 42
16088 AGTGTCAATT
* * * *
16098 TTTTGCTCGATTCTTCACATAAGGAGTTGAATCAGCATAAACTTA
1 TTTTGCTTGATTCTTCACAGAAGGAGTTGGATCA-CATAGAC--A
** * * *
16143 TTTTGCCGGATTCTATCACAGAACGAGGTAGATCATCATAGACA
1 TTTTGCTTGATTCT-TCACAGAAGGAGTTGGATCA-CATAGACA
* *
16187 TTTTGTTTGATTCTTCACAGAAGGAGTTGGATCA-ATGGTATC-
1 TTTTGCTTGATTCTTCACAGAAGGAGTTGGATCACATAG-A-CA
*
16229 TTTTCGCTTGATTCTTCACATAAGGAGTTGGATCA
1 TTTT-GCTTGATTCTTCACAGAAGGAGTTGGATCA
16264 ACGTAACCTT
Statistics
Matches: 99, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 3 0.03
42 5 0.05
43 46 0.46
44 12 0.12
45 12 0.12
46 21 0.21
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (42 bp):
TTTTGCTTGATTCTTCACAGAAGGAGTTGGATCACATAGACA
Found at i:53748 original size:23 final size:23
Alignment explanation
Indices: 53722--53767 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
53712 ATACTATCTA
53722 ATTTTTTTAAAGCATTTTGTTCT
1 ATTTTTTTAAAGCATTTTGTTCT
*
53745 ATTTTTTTAAAGTATTTTGTTCT
1 ATTTTTTTAAAGCATTTTGTTCT
53768 CCCAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.63
Consensus pattern (23 bp):
ATTTTTTTAAAGCATTTTGTTCT
Found at i:59906 original size:21 final size:21
Alignment explanation
Indices: 59877--59920 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
59867 AATATGTAAA
59877 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
59898 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
59919 TC
1 TC
59921 ACAACGCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:59929 original size:21 final size:21
Alignment explanation
Indices: 59884--59934 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
59874 AAATCGCATT
* ***
59884 GCGATTTTCCAAATTCGCGTT
1 GCGATTTTCCAAATTCACAAC
59905 GCGATTTTCCAAATTCACAAC
1 GCGATTTTCCAAATTCACAAC
59926 GCGAATTTT
1 GCG-ATTTT
59935 TAAATCGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (21 bp):
GCGATTTTCCAAATTCACAAC
Found at i:60136 original size:22 final size:23
Alignment explanation
Indices: 60089--60136 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
60079 GGCAACATCC
*
60089 GTCCCCATCTCCGACGAAAATTT
1 GTCCCCATCTCCGACGAAAATCT
*
60112 GTCCCCATTTCCGACG-AAATCT
1 GTCCCCATCTCCGACGAAAATCT
60134 GTC
1 GTC
60137 TATCTCCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.27
Consensus pattern (23 bp):
GTCCCCATCTCCGACGAAAATCT
Found at i:61612 original size:20 final size:20
Alignment explanation
Indices: 61589--61650 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
61579 AATAAGCGTT
61589 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
* *
61609 GCGAAAGTCAAATTCGCTAC
1 GCGATAGTCAAATTCGCAAC
61629 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
61649 GC
1 GC
61651 TTATTTCGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:61987 original size:18 final size:18
Alignment explanation
Indices: 61964--61999 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61954 AAGCCGGTTG
*
61964 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
61982 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
62000 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Done.