Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005324.1 Hibiscus syriacus cultivar Beakdansim tig00012049_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: 103570
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:938 original size:21 final size:21
Alignment explanation
Indices: 913--975 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
903 CATATGAAAT
*
913 TTGTCCC-AAGGACCTGTGAA
1 TTGTCCCAAAGGACCTATGAA
* *
933 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCAAAGGACCTATGAA
955 TTGTCCCAAAGGACCTATGAA
1 TTGTCCCAAAGGACCTATGAA
976 ACCCTCGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 1 0.03
21 24 0.65
22 12 0.32
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
TTGTCCCAAAGGACCTATGAA
Found at i:6963 original size:31 final size:32
Alignment explanation
Indices: 6901--6963 Score: 110
Period size: 33 Copynumber: 2.0 Consensus size: 32
6891 CCTCGAACCC
6901 GACCCGAATATCACACTTAAAAAAACCCGACCT
1 GACCCGAATATCACACTTAAAAAAA-CCGACCT
6934 GACCCGAATATCACACTTAAAAAAA-CGACC
1 GACCCGAATATCACACTTAAAAAAACCGACC
6964 CGAACAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 5 0.17
33 25 0.83
ACGTcount: A:0.44, C:0.32, G:0.10, T:0.14
Consensus pattern (32 bp):
GACCCGAATATCACACTTAAAAAAACCGACCT
Found at i:7697 original size:13 final size:13
Alignment explanation
Indices: 7679--7703 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7669 GAGTCGATCT
7679 AAATTAAAAAATA
1 AAATTAAAAAATA
7692 AAATTAAAAAAT
1 AAATTAAAAAAT
7704 TCGGGAAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATTAAAAAATA
Found at i:9705 original size:30 final size:30
Alignment explanation
Indices: 9639--9727 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
9629 GGGTTAATTT
*
9639 TTTTGACCTCTGAGTTTTAGA-G-AATA-CTA
1 TTTTGACCT-TGAATTTTAGATGAAATATC-A
*
9668 ATTTGACCTTGAATTTTAGATGAAATATCA
1 TTTTGACCTTGAATTTTAGATGAAATATCA
* * * *
9698 TTTTGACCGTAAACTTTAGATAAAATATCA
1 TTTTGACCTTGAATTTTAGATGAAATATCA
9728 AATTGATCCA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
28 10 0.20
29 9 0.18
30 30 0.60
31 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (30 bp):
TTTTGACCTTGAATTTTAGATGAAATATCA
Found at i:10447 original size:2 final size:2
Alignment explanation
Indices: 10410--10434 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10400 TTAAAGGAAG
10410 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10435 TTCAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21390 original size:25 final size:25
Alignment explanation
Indices: 21354--21406 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
21344 AATAAAACTT
* *
21354 TTATTTTCTAATAAGATCATATATA
1 TTATTTTATAATAAGATCAGATATA
*
21379 TTATTTTATAATAAGATCGGATATA
1 TTATTTTATAATAAGATCAGATATA
21404 TTA
1 TTA
21407 AATAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (25 bp):
TTATTTTATAATAAGATCAGATATA
Found at i:22301 original size:11 final size:11
Alignment explanation
Indices: 22285--22309 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22275 TACGGACACG
22285 CTGGGTCGGAT
1 CTGGGTCGGAT
22296 CTGGGTCGGAT
1 CTGGGTCGGAT
22307 CTG
1 CTG
22310 ACACGGGATC
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:0.08, C:0.20, G:0.44, T:0.28
Consensus pattern (11 bp):
CTGGGTCGGAT
Found at i:24872 original size:60 final size:57
Alignment explanation
Indices: 24746--24875 Score: 138
Period size: 60 Copynumber: 2.2 Consensus size: 57
24736 TATAGTCTTA
* **
24746 CGACTATTAAAAGGTATAAATTATTCTTGATTATAAGGTGTTATCTTATTGAGTCAT
1 CGACTATTAAAAAGTATAAATTATTCTTGATTATAAGACGTTATCTTATTGAGTCAT
* * *
24803 CATATTATTAAAAAGTATGAAATTTTATT-TTGATTATATGACGTTA-CTTTATTGGAGTCAT
1 C-GACTATTAAAAAGTAT-AAA--TTATTCTTGATTATAAGACGTTATC-TTATT-GAGTCAT
24864 CGACTATTAAAA
1 CGACTATTAAAA
24876 GTTACTATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
57 1 0.02
58 13 0.22
59 4 0.07
60 28 0.47
61 13 0.22
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.42
Consensus pattern (57 bp):
CGACTATTAAAAAGTATAAATTATTCTTGATTATAAGACGTTATCTTATTGAGTCAT
Found at i:27797 original size:2 final size:2
Alignment explanation
Indices: 27784--27831 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
27774 ATATTTATCT
*
27784 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27826 TA TA TA
1 TA TA TA
27832 ATACTTTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39662 original size:23 final size:24
Alignment explanation
Indices: 39615--39666 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
39605 GAAATATGTC
39615 AAAAGACAGACGAAAATGTATCAT
1 AAAAGACAGACGAAAATGTATCAT
39639 AAAA-ACAGA-GAAAAT-TATACCAT
1 AAAAGACAGACGAAAATGTAT--CAT
39662 AAAAG
1 AAAAG
39667 CAAAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 3 0.12
22 6 0.24
23 12 0.48
24 4 0.16
ACGTcount: A:0.60, C:0.12, G:0.13, T:0.15
Consensus pattern (24 bp):
AAAAGACAGACGAAAATGTATCAT
Found at i:40966 original size:20 final size:20
Alignment explanation
Indices: 40943--40981 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40933 TAAACTACGT
*
40943 TTTTTATTATTTAATTTTTG
1 TTTTGATTATTTAATTTTTG
*
40963 TTTTGATTATTTGATTTTT
1 TTTTGATTATTTAATTTTT
40982 AATTTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (20 bp):
TTTTGATTATTTAATTTTTG
Found at i:41922 original size:18 final size:18
Alignment explanation
Indices: 41911--41946 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41901 TAGCAGTCCA
*
41911 AGGTTAATTAGCTGTAAG
1 AGGTTAATTAGCAGTAAG
*
41929 AGGTTAATTAGCTGTAAG
1 AGGTTAATTAGCAGTAAG
41947 CCAAGCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (18 bp):
AGGTTAATTAGCAGTAAG
Found at i:42803 original size:2 final size:2
Alignment explanation
Indices: 42796--42829 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42786 TCCTTTAATC
42796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42830 ATAATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42962 original size:14 final size:15
Alignment explanation
Indices: 42919--42965 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
42909 ATCTAATAAA
42919 ATTA-AATA-TTAAT
1 ATTATAATATTTAAT
*
42932 A-TACAATATTTAA-
1 ATTATAATATTTAAT
42945 ATTATAAT-TTTAAT
1 ATTATAATATTTAAT
42959 ATTATAA
1 ATTATAA
42966 ATAGAATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 2 0.07
13 11 0.38
14 16 0.55
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAATATTTAAT
Found at i:48030 original size:2 final size:2
Alignment explanation
Indices: 48019--48052 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
48009 CACATATTTG
48019 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48053 TAATTTATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54548 original size:11 final size:11
Alignment explanation
Indices: 54532--54576 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
54522 AAACGTCCCT
54532 GGTACGGGGAC
1 GGTACGGGGAC
54543 GGTACGGGGAC
1 GGTACGGGGAC
54554 GGT-CGGGGTAC
1 GGTACGGGG-AC
54565 -GTACCGGGGAC
1 GGTA-CGGGGAC
54576 G
1 G
54577 TGCCACTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.23
11 18 0.60
12 5 0.17
ACGTcount: A:0.16, C:0.20, G:0.53, T:0.11
Consensus pattern (11 bp):
GGTACGGGGAC
Found at i:57197 original size:2 final size:2
Alignment explanation
Indices: 57190--57214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57180 GAAAACAGGA
57190 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
57215 ATGGGTTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57814 original size:299 final size:300
Alignment explanation
Indices: 57273--57875 Score: 1118
Period size: 299 Copynumber: 2.0 Consensus size: 300
57263 TGGCCAAGTC
*
57273 GATGAGCTCTAGCCATTGCTTGTAAATCAGTATGAGGATTCCAATCACTGTAGAGACAGGACCCA
1 GATGAGCTCTAGCCATTGCTTGTAAATCAGCATGAGGATTCCAATCACTGTAGAGACAGGACCCA
*
57338 TATTTTCACTTTTCAATTGAACGAAACCAAAGGGAGCATGTAATATACCTAAACCTTAAAATATT
66 TA-TTTCACTTTTCAATTGAACGAAACCAAAGGGAGCATGCAATATACCTAAACCTTAAAATATT
57403 ACACAAACAAATAAACAAACTGAAAGTCACCAAAAAAAGGTTTCAACATCACATCAGCAAACGGG
130 ACACAAACAAATAAACAAACTGAAAGTCACCAAAAAAAGGTTTCAACATCACATCAGCAAACGGG
57468 CAATAGTTCGTGATATTGTAACCTTCATACCATTCGCTCTACAATATGAGAAACCTAATATTCTG
195 CAATAGTTCGTGATATTGTAACCTTCATACCATTCGCTCTACAATATGAGAAACCTAATATTCTG
57533 ACACATGGTACTGAAAAGGCAATATCAGGTTTGTGCTTCTT
260 ACACATGGTACTGAAAAGGCAATATCAGGTTTGTGCTTCTT
*
57574 GATGAGCTCTAGCCATTGCTTGTAAATCAGCATGAGGATTCCAATCACTGTAGAGGCAGGACCCA
1 GATGAGCTCTAGCCATTGCTTGTAAATCAGCATGAGGATTCCAATCACTGTAGAGACAGGACCCA
57639 TA-TTCACTTTTCAATTGAACGAAACCAAAGGGAGCATGCAATATACCTAAACCTTAAAATATTA
66 TATTTCACTTTTCAATTGAACGAAACCAAAGGGAGCATGCAATATACCTAAACCTTAAAATATTA
*
57703 CACAAACAAATAAACAAACTGAAAGTCACCAAAAAAAGGTTTCAACATTACATCAGCAAACGGGC
131 CACAAACAAATAAACAAACTGAAAGTCACCAAAAAAAGGTTTCAACATCACATCAGCAAACGGGC
* * *
57768 AATAGTTCGTGATATTGTAACCTTTATACCATTCGCTCTGCAATATGAGAAACCTAATATTCTGT
196 AATAGTTCGTGATATTGTAACCTTCATACCATTCGCTCTACAATATGAGAAACCTAATATTCTGA
*
57833 CACATGGTACTGTAAAGGCAATATCAGGTTTGTGCTTCTT
261 CACATGGTACTGAAAAGGCAATATCAGGTTTGTGCTTCTT
57873 GAT
1 GAT
57876 CATTCGGGTT
Statistics
Matches: 294, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
299 229 0.78
301 65 0.22
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (300 bp):
GATGAGCTCTAGCCATTGCTTGTAAATCAGCATGAGGATTCCAATCACTGTAGAGACAGGACCCA
TATTTCACTTTTCAATTGAACGAAACCAAAGGGAGCATGCAATATACCTAAACCTTAAAATATTA
CACAAACAAATAAACAAACTGAAAGTCACCAAAAAAAGGTTTCAACATCACATCAGCAAACGGGC
AATAGTTCGTGATATTGTAACCTTCATACCATTCGCTCTACAATATGAGAAACCTAATATTCTGA
CACATGGTACTGAAAAGGCAATATCAGGTTTGTGCTTCTT
Found at i:73091 original size:13 final size:13
Alignment explanation
Indices: 73073--73117 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
73063 GTCATAAATC
73073 TATGACGCGCATT
1 TATGACGCGCATT
* *
73086 TATGACACGTATT
1 TATGACGCGCATT
*
73099 TATGACGCACATT
1 TATGACGCGCATT
73112 TATGAC
1 TATGAC
73118 TTACATTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:80650 original size:14 final size:15
Alignment explanation
Indices: 80625--80653 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
80615 CTTTTAGGTA
80625 TGTTTATTATTAATT
1 TGTTTATTATTAATT
80640 TGTTT-TTATTAATT
1 TGTTTATTATTAATT
80654 ATTGCTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
TGTTTATTATTAATT
Found at i:81025 original size:14 final size:15
Alignment explanation
Indices: 80987--81026 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
80977 ATGAATAGTC
80987 CATCTTTTAAAAGTA
1 CATCTTTTAAAAGTA
81002 CATCTTTTAAAAGTA
1 CATCTTTTAAAAGTA
81017 CAT-TTTTAAA
1 CATCTTTTAAA
81027 GACGAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (15 bp):
CATCTTTTAAAAGTA
Done.