Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004330.1 Hibiscus syriacus cultivar Beakdansim tig00009497_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: 77794
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:7336 original size:60 final size:61
Alignment explanation
Indices: 7246--7372 Score: 179
Period size: 60 Copynumber: 2.1 Consensus size: 61
7236 TTTATATTTT
*
7246 AAAG-TACACAAATAGTACTCCAACTATAAGGTATTGTTTTGTTGAGTCTCCCAACCATTA
1 AAAGTTACACAAATAGTACTCCAACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTA
* * * *
7306 AAAGTTACA-AAATGGT-CTCCTAACTATAAGGTATTGCTTTGTTGAGTCTCTCGACTATTA
1 AAAGTTACACAAATAGTACTCC-AACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTA
7366 AAAGTTA
1 AAAGTTA
7373 TAAATTGATC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
59 4 0.07
60 52 0.87
61 4 0.07
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (61 bp):
AAAGTTACACAAATAGTACTCCAACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTA
Found at i:7390 original size:60 final size:60
Alignment explanation
Indices: 7267--7392 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 60
7257 ATAGTACTCC
* * * *
7267 AACTATAAGGTATTGTTTTGTTGAGTCTCCCAACCATTAAAAGTTACAAAATGGTCTCCT
1 AACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTAAAAGTTACAAAATGATCACAT
* * * * *
7327 AACTATAAGGTATTGCTTTGTTGAGTCTCTCGACTATTAAAAGTTATAAATTGATCACAT
1 AACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTAAAAGTTACAAAATGATCACAT
7387 AACTAT
1 AACTAT
7393 TCATATGTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (60 bp):
AACTATAAGGTATTGCTTTGTTGAGTCTCCCAACCATTAAAAGTTACAAAATGATCACAT
Found at i:7908 original size:60 final size:60
Alignment explanation
Indices: 7837--7954 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
7827 AAATAGAACT
7837 CCAACTATAAGGTATTA-TCTTGTTCAGTCCTC-CAACCATTAAAAGTTACAAAATGATCTC
1 CCAACTATAAGGTATTACT-TTGTTCAG-CCTCTCAACCATTAAAAGTTACAAAATGATCTC
* * * *
7897 CCAACTATAAGGTGTTACTTTGTTGAGCCTCTCAACTATTAAAAGTTATAAAATGATC
1 CCAACTATAAGGTATTACTTTGTTCAGCCTCTCAACCATTAAAAGTTACAAAATGATC
7955 ACATGACTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
59 4 0.08
60 47 0.90
61 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (60 bp):
CCAACTATAAGGTATTACTTTGTTCAGCCTCTCAACCATTAAAAGTTACAAAATGATCTC
Found at i:8343 original size:21 final size:22
Alignment explanation
Indices: 8313--8358 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
8303 TGAAATTTCC
* *
8313 TAAAATTCGAA-TTTTCTTCTT
1 TAAAACTCGAAGTTTTCTTCAT
8334 TAAAACTCGAAGTTTTCTTCAT
1 TAAAACTCGAAGTTTTCTTCAT
8356 TAA
1 TAA
8359 TATACACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (22 bp):
TAAAACTCGAAGTTTTCTTCAT
Found at i:10831 original size:18 final size:18
Alignment explanation
Indices: 10808--10847 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
10798 AGAAAGACAC
10808 GAAAAGGAGAAGGAACGT
1 GAAAAGGAGAAGGAACGT
10826 GAAAAGGAGAAGGAACGT
1 GAAAAGGAGAAGGAACGT
10844 GAAA
1 GAAA
10848 TGGAAAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.05, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAAAGGAGAAGGAACGT
Found at i:22949 original size:37 final size:37
Alignment explanation
Indices: 22899--22980 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
22889 TTTAAAAATT
* *
22899 ATATATGAATTTTATCTAAAAAGAATAACTATGTGTA
1 ATATATAAATTTTATCTAAAAAGAATAACTATGTGCA
*
22936 ATATATAAATTTTATCTAAAAAGAATAATTATGTGCA
1 ATATATAAATTTTATCTAAAAAGAATAACTATGTGCA
22973 ATATATAA
1 ATATATAA
22981 CAAAGACAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.38
Consensus pattern (37 bp):
ATATATAAATTTTATCTAAAAAGAATAACTATGTGCA
Found at i:28508 original size:35 final size:35
Alignment explanation
Indices: 28440--28530 Score: 128
Period size: 35 Copynumber: 2.5 Consensus size: 35
28430 AACATCTATT
* * *
28440 AAACTTTGAAAAACTATTTTTCAAAGAAGCATTTACC
1 AAACTTTG-AAAACCA-TTTTCAAAAAAACATTTACC
28477 AAACTTTGAAAACCATTTTCAAAAAAACATTTACC
1 AAACTTTGAAAACCATTTTCAAAAAAACATTTACC
*
28512 AAACTTTGAAAATCATTTT
1 AAACTTTGAAAACCATTTT
28531 TTCAAAGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 36 0.72
36 6 0.12
37 8 0.16
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.33
Consensus pattern (35 bp):
AAACTTTGAAAACCATTTTCAAAAAAACATTTACC
Found at i:32630 original size:16 final size:17
Alignment explanation
Indices: 32602--32635 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
32592 TATCACCGAT
32602 AAAATTACACTATTCAC
1 AAAATTACACTATTCAC
32619 AAAATT-CACTATTCAC
1 AAAATTACACTATTCAC
32635 A
1 A
32636 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTACACTATTCAC
Found at i:33089 original size:37 final size:37
Alignment explanation
Indices: 33028--33149 Score: 153
Period size: 35 Copynumber: 3.4 Consensus size: 37
33018 TTATCCCATT
* *
33028 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAAA
1 ATCATTTTTCAAAAAAACATTTACCAAACTTTGAAAA
* *
33064 ATTATTTTTCAAAGAAACATTTACCAAACTTT-AAAA
1 ATCATTTTTCAAAAAAACATTTACCAAACTTTGAAAA
**
33100 GCCA-TTTTCAAAAAAACATTTACCAAACTTTG-AAA
1 ATCATTTTTCAAAAAAACATTTACCAAACTTTGAAAA
33135 ATCATTTTTTCAAAA
1 ATCA-TTTTTCAAAA
33150 TTGGTTGCCA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
35 31 0.42
36 14 0.19
37 28 0.38
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (37 bp):
ATCATTTTTCAAAAAAACATTTACCAAACTTTGAAAA
Found at i:36133 original size:38 final size:38
Alignment explanation
Indices: 36082--36164 Score: 157
Period size: 38 Copynumber: 2.2 Consensus size: 38
36072 GGAACATTAT
36082 CGTTTATGAACTTTTCAGGGCAAGAAAGACTTCAATGG
1 CGTTTATGAACTTTTCAGGGCAAGAAAGACTTCAATGG
36120 CGTTTATGAACTTTTCAGGGCAAGAAAGACTTCAATGG
1 CGTTTATGAACTTTTCAGGGCAAGAAAGACTTCAATGG
*
36158 CATTTAT
1 CGTTTAT
36165 AAAAGCTAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (38 bp):
CGTTTATGAACTTTTCAGGGCAAGAAAGACTTCAATGG
Found at i:36985 original size:21 final size:21
Alignment explanation
Indices: 36959--36998 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36949 TAAAATTTTG
36959 TTTTGAAAATAA-AATAAAATA
1 TTTTG-AAATAATAATAAAATA
*
36980 TTTTGATATAATAATAAAA
1 TTTTGAAATAATAATAAAA
36999 CATTCTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
TTTTGAAATAATAATAAAATA
Found at i:37568 original size:49 final size:49
Alignment explanation
Indices: 37515--37720 Score: 322
Period size: 49 Copynumber: 4.2 Consensus size: 49
37505 TTTATGTTGA
37515 AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
* *
37564 AAATGCACCGTTATGCATTTAACTTTTATTAGTGACACTTTTTATGCCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
* * *
37613 AAATGCACCGTTATGCATTTAATTTTCATTAGTGGCACATTTTATGCCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
* * * * *
37662 AAATGCACCGTTATACATTTAACTTTTATTAGCGGCACCTTTCATGCCG
1 AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
37711 AAATGCACCG
1 AAATGCACCG
37721 ATTTAAACAT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 145 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (49 bp):
AAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTATGCCG
Found at i:41045 original size:28 final size:27
Alignment explanation
Indices: 41014--41067 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
41004 GTTAGCTTTA
*
41014 TATTTTTTTACTTTCCTTAATTTTTCTT
1 TATTTTTTT-CTTTCATTAATTTTTCTT
* *
41042 TATTTTTTTTTTTCATTTATTTTTCT
1 TATTTTTTTCTTTCATTAATTTTTCT
41068 AGGTACATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (27 bp):
TATTTTTTTCTTTCATTAATTTTTCTT
Found at i:49739 original size:13 final size:13
Alignment explanation
Indices: 49721--49756 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
49711 CTGTATCCAG
49721 CTGTCCGAGAGCT
1 CTGTCCGAGAGCT
49734 CTGTCCGAGAGCT
1 CTGTCCGAGAGCT
*
49747 CTGCCCGAGA
1 CTGTCCGAGA
49757 AATCCACCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.19
Consensus pattern (13 bp):
CTGTCCGAGAGCT
Found at i:69730 original size:18 final size:18
Alignment explanation
Indices: 69696--69737 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
69686 AACCTAAAAA
*
69696 AACTCTCATTTTCCTCTC
1 AACTCTCATCTTCCTCTC
69714 AACTCTC-TCTTCTCTCTC
1 AACTCTCATCTTC-CTCTC
*
69732 TACTCT
1 AACTCT
69738 ACTAAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.14, C:0.40, G:0.00, T:0.45
Consensus pattern (18 bp):
AACTCTCATCTTCCTCTC
Found at i:70809 original size:36 final size:36
Alignment explanation
Indices: 70764--70857 Score: 179
Period size: 36 Copynumber: 2.6 Consensus size: 36
70754 AATATATGAA
*
70764 TTTTAATGTCGATAGCGTTTTTCATCGGACCCGGAT
1 TTTTAATGTCGATAGCGTTTTTCACCGGACCCGGAT
70800 TTTTAATGTCGATAGCGTTTTTCACCGGACCCGGAT
1 TTTTAATGTCGATAGCGTTTTTCACCGGACCCGGAT
70836 TTTTAATGTCGATAGCGTTTTT
1 TTTTAATGTCGATAGCGTTTTT
70858 GGATCCTGGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (36 bp):
TTTTAATGTCGATAGCGTTTTTCACCGGACCCGGAT
Found at i:75429 original size:2 final size:2
Alignment explanation
Indices: 75422--75455 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
75412 TTATTTTTAA
75422 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75456 GTACCTGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.