Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004830.1 Hibiscus syriacus cultivar Beakdansim tig00010878_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: 71979
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2332 original size:27 final size:27
Alignment explanation
Indices: 2295--2346 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
2285 AGCAATATAC
2295 CCCCTTACAAGAACCAGAAAACCAACA
1 CCCCTTACAAGAACCAGAAAACCAACA
2322 CCCCTTACAAGAACCAGAAAACCAA
1 CCCCTTACAAGAACCAGAAAACCAA
2347 AAAACAACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.37, G:0.08, T:0.08
Consensus pattern (27 bp):
CCCCTTACAAGAACCAGAAAACCAACA
Found at i:5543 original size:18 final size:18
Alignment explanation
Indices: 5520--5560 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
5510 TTAATTCCTT
5520 AATAGGTCTTTCAGTTTC
1 AATAGGTCTTTCAGTTTC
5538 AATAGGTCTTTCAGTTTC
1 AATAGGTCTTTCAGTTTC
5556 AATAG
1 AATAG
5561 TCGGTCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (18 bp):
AATAGGTCTTTCAGTTTC
Found at i:9605 original size:29 final size:29
Alignment explanation
Indices: 9554--9611 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
9544 GTGTTGGCCG
*
9554 TAGGTCGCCATGCCATCCGGGCGACCTAC
1 TAGGTCGCCATGCCATCCCGGCGACCTAC
** * *
9583 TAGGTCGCCATTTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCATCCCGGCGACCTAC
9612 GAGATATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCATCCCGGCGACCTAC
Found at i:10383 original size:18 final size:18
Alignment explanation
Indices: 10340--10385 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
10330 GCCTTAGTCT
*
10340 AGGGCAGCATGTTTGAGG
1 AGGGCATCATGTTTGAGG
10358 AGGGCATCATGTTTGAGG
1 AGGGCATCATGTTTGAGG
10376 -GGGACATCAT
1 AGGG-CATCAT
10386 TTTTCTAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.24, C:0.13, G:0.39, T:0.24
Consensus pattern (18 bp):
AGGGCATCATGTTTGAGG
Found at i:17211 original size:22 final size:23
Alignment explanation
Indices: 17159--17211 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
17149 CATACATTAT
17159 AATTATCTCTTACTATAAAAGCCCA
1 AATTATCTCTTACTATAAAA--CCA
* *
17184 AATTATCTTTTACTATAAAA-TA
1 AATTATCTCTTACTATAAAACCA
17206 AATTAT
1 AATTAT
17212 TATTTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 7 0.27
25 19 0.73
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.40
Consensus pattern (23 bp):
AATTATCTCTTACTATAAAACCA
Found at i:24868 original size:60 final size:60
Alignment explanation
Indices: 24804--24921 Score: 137
Period size: 60 Copynumber: 2.0 Consensus size: 60
24794 ACATAAATAT
* * * * * * *
24804 TTTCCAGATTATATGATATTGTTTTGTTGAGTTCGTCGATTATTAAAAGTTATAAAATGA
1 TTTCCAGACTATAGGATATTGCTTTGTTGAGTCCGTCAACTATTAAAAGTTACAAAATGA
* * * *
24864 TTTCCCGACTATAGGGTGTTGCTTTGTTGAGTCCTTCAACTATTAAAAGTTACAAAAT
1 TTTCCAGACTATAGGATATTGCTTTGTTGAGTCCGTCAACTATTAAAAGTTACAAAAT
24922 TGTCATCTAA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.42
Consensus pattern (60 bp):
TTTCCAGACTATAGGATATTGCTTTGTTGAGTCCGTCAACTATTAAAAGTTACAAAATGA
Found at i:25390 original size:22 final size:21
Alignment explanation
Indices: 25353--25394 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
25343 TCCAATATTA
25353 ATTCAATTTGATATCAGATTTG
1 ATTCAATTTGATATCA-ATTTG
25375 ATTCAATTTG-TCATCAATTT
1 ATTCAATTTGAT-ATCAATTT
25395 TAAATTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (21 bp):
ATTCAATTTGATATCAATTTG
Found at i:28678 original size:12 final size:13
Alignment explanation
Indices: 28658--28770 Score: 80
Period size: 12 Copynumber: 9.3 Consensus size: 13
28648 TCAAAACATA
28658 ATCCAGGTCAAGT
1 ATCCAGGTCAAGT
*
28671 AT-CAGGTCAA-A
1 ATCCAGGTCAAGT
28682 ATCCAGGTCAAGT
1 ATCCAGGTCAAGT
* * *
28695 ATTC-GATC-AGA
1 ATCCAGGTCAAGT
*
28706 ATCCATGTCAAGT
1 ATCCAGGTCAAGT
* *
28719 ATCC-GATC-AGA
1 ATCCAGGTCAAGT
28730 ATCCAGGTCAAGT
1 ATCCAGGTCAAGT
* *
28743 ATCC-GATC-AGA
1 ATCCAGGTCAAGT
*
28754 ATCCAGGTCAAAT
1 ATCCAGGTCAAGT
28767 ATCC
1 ATCC
28771 GATCAGAATC
Statistics
Matches: 73, Mismatches: 19, Indels: 16
0.68 0.18 0.15
Matches are distributed among these distances:
11 19 0.26
12 32 0.44
13 22 0.30
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (13 bp):
ATCCAGGTCAAGT
Found at i:28684 original size:24 final size:24
Alignment explanation
Indices: 28657--28792 Score: 200
Period size: 24 Copynumber: 5.7 Consensus size: 24
28647 ATCAAAACAT
* * *
28657 AATCCAGGTCAAGTATCAGGTCAA
1 AATCCAGGTCAAGTATCCGATCAG
*
28681 AATCCAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
28705 AATCCATGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
28729 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
28753 AATCCAGGTCAAATATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
* *
28777 AATCTAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
28793 TATAATAGAA
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 101 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:31391 original size:21 final size:21
Alignment explanation
Indices: 31365--31414 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
31355 CCATCCCCAC
31365 GCGCAGTGGC-AGCGCGTAGGG
1 GCGCAGTGGCGA-CGCGTAGGG
*
31386 GCGCAGTGGCGACGCGTGGGG
1 GCGCAGTGGCGACGCGTAGGG
31407 GCGC-GTGG
1 GCGCAGTGG
31415 AGCCCCTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 22 0.81
22 1 0.04
ACGTcount: A:0.10, C:0.24, G:0.56, T:0.10
Consensus pattern (21 bp):
GCGCAGTGGCGACGCGTAGGG
Found at i:32786 original size:38 final size:38
Alignment explanation
Indices: 32744--32820 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
32734 GTTCGTCCCT
* *
32744 GATCATAGAAGGATAATATTAAAAAAATCCAATCAAAA
1 GATCATAGAAGAAAAATATTAAAAAAATCCAATCAAAA
32782 GATCATAGAAGAAAAATATTAAAAAAATCCAATCAAAA
1 GATCATAGAAGAAAAATATTAAAAAAATCCAATCAAAA
32820 G
1 G
32821 TTTGAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.19
Consensus pattern (38 bp):
GATCATAGAAGAAAAATATTAAAAAAATCCAATCAAAA
Found at i:32839 original size:40 final size:38
Alignment explanation
Indices: 32758--32839 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 38
32748 ATAGAAGGAT
* *
32758 AATATTAAAAAAATCCAATCAAAAGATCATAGAAGAAA
1 AATATTAAAAAAATCCAATCAAAAGATAATAAAAGAAA
* *
32796 AATATTAAAAAAATCCAATCAAAAGTTTGAATAAAAGATA
1 AATATTAAAAAAATCCAATCAAAAG-AT-AATAAAAGAAA
32836 AATA
1 AATA
32840 CGAAAAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 25 0.66
39 1 0.03
40 12 0.32
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (38 bp):
AATATTAAAAAAATCCAATCAAAAGATAATAAAAGAAA
Found at i:34388 original size:16 final size:17
Alignment explanation
Indices: 34367--34400 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34357 ATAATATATG
34367 ATGATCG-ACAATATAA
1 ATGATCGAACAATATAA
*
34383 ATGATCGAATAATATAA
1 ATGATCGAACAATATAA
34400 A
1 A
34401 ATACATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (17 bp):
ATGATCGAACAATATAA
Found at i:40527 original size:35 final size:35
Alignment explanation
Indices: 40481--40550 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
40471 TCACCGGGAA
40481 ACATGTACAATTATAGCAGCATATGCTGTGTTTCG
1 ACATGTACAATTATAGCAGCATATGCTGTGTTTCG
40516 ACATGTACAATTATAGCAGCATATGCTGTGTTTCG
1 ACATGTACAATTATAGCAGCATATGCTGTGTTTCG
40551 TGATGATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (35 bp):
ACATGTACAATTATAGCAGCATATGCTGTGTTTCG
Found at i:43360 original size:30 final size:30
Alignment explanation
Indices: 43324--43410 Score: 174
Period size: 30 Copynumber: 2.9 Consensus size: 30
43314 CTTTTTTAAC
43324 AAGATCTAGGACTAATATGAAAAATAAAAT
1 AAGATCTAGGACTAATATGAAAAATAAAAT
43354 AAGATCTAGGACTAATATGAAAAATAAAAT
1 AAGATCTAGGACTAATATGAAAAATAAAAT
43384 AAGATCTAGGACTAATATGAAAAATAA
1 AAGATCTAGGACTAATATGAAAAATAA
43411 GATTAATACA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (30 bp):
AAGATCTAGGACTAATATGAAAAATAAAAT
Found at i:44905 original size:14 final size:14
Alignment explanation
Indices: 44871--44899 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44861 ATTATATAAG
44871 AAGAAA-AATACAT
1 AAGAAATAATACAT
44884 AAGAAATAATACAT
1 AAGAAATAATACAT
44898 AA
1 AA
44900 CGAATATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (14 bp):
AAGAAATAATACAT
Found at i:50141 original size:42 final size:42
Alignment explanation
Indices: 50094--50189 Score: 192
Period size: 42 Copynumber: 2.3 Consensus size: 42
50084 TTACATGGGC
50094 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
1 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
50136 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
1 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
50178 TCAACAGCAGCA
1 TCAACAGCAGCA
50190 GCAATCCCTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (42 bp):
TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
Found at i:50209 original size:45 final size:42
Alignment explanation
Indices: 50094--50211 Score: 121
Period size: 42 Copynumber: 2.7 Consensus size: 42
50084 TTACATGGGC
* * **
50094 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
1 TCAACAGCAGCAAATCCAGCAGCAATTGCAGACTCCTTTAAA
* * **
50136 TCAACAGCAGCAACTTCAGCAGTTATTGCAGACTCCTTTAAA
1 TCAACAGCAGCAAATCCAGCAGCAATTGCAGACTCCTTTAAA
50178 TCAACAGCAGCAGCAATCCCTA-CAGCAATTGCAG
1 TCAACAGCAGCA--AAT-CC-AGCAGCAATTGCAG
50212 CGACATCAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
42 54 0.79
44 2 0.03
45 11 0.16
46 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (42 bp):
TCAACAGCAGCAAATCCAGCAGCAATTGCAGACTCCTTTAAA
Found at i:61103 original size:12 final size:12
Alignment explanation
Indices: 61086--61110 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61076 TTTTTCATCT
61086 ATGAGAACCACC
1 ATGAGAACCACC
61098 ATGAGAACCACC
1 ATGAGAACCACC
61110 A
1 A
61111 CCAAAAAGAA
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:0.44, C:0.32, G:0.16, T:0.08
Consensus pattern (12 bp):
ATGAGAACCACC
Found at i:64743 original size:21 final size:20
Alignment explanation
Indices: 64715--64753 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
64705 TATTCATTAA
64715 AGTTTTAAAATTTA-CAAAAT
1 AGTTTT-AAATTTATCAAAAT
64735 AGTTATTAAATTTATCAAA
1 AGTT-TTAAATTTATCAAA
64754 TTATTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (20 bp):
AGTTTTAAATTTATCAAAAT
Done.