Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002389.1 Hibiscus syriacus cultivar Beakdansim tig00004887_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: 31788
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Found at i:6019 original size:6 final size:6
Alignment explanation
Indices: 6008--6035 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5998 AAATTAAATA
6008 GAAAGG GAAAGG GAAAGG GAAAGG GAAA
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAA
6036 TGAATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:8844 original size:19 final size:19
Alignment explanation
Indices: 8820--8884 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
8810 TCTATCACAA
8820 TGCGATTTTCCAAATTCGT
1 TGCGATTTTCCAAATTCGT
** *
8839 TGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATT--CGT
*
8860 TGCGATTTATTCTAAATTCGT
1 TGCGA-TT-TTCCAAATTCGT
8881 TGCG
1 TGCG
8885 TCGAAGTTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 13 0.37
21 15 0.43
22 1 0.03
23 6 0.17
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (19 bp):
TGCGATTTTCCAAATTCGT
Found at i:8862 original size:21 final size:19
Alignment explanation
Indices: 8828--9015 Score: 78
Period size: 21 Copynumber: 9.3 Consensus size: 19
8818 AATGCGATTT
*
8828 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
8847 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
* *
8870 TCTAAATTCGTTGC----G
1 TCCAAGTTCGTTGCGATAG
* *
8885 TCGAAGTTCTCGTTGCGATTTAT
1 TCCAAG-T-TCGTTGCGA--TAG
* *
8908 TCTAAGTTCGTTGCGTTAG
1 TCCAAGTTCGTTGCGATAG
* *
8927 TCGAAGTTCTCGTTGCGATTTAT
1 TCCAAG-T-TCGTTGCGA--TAG
*
8950 TCCAAGTTTGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
8969 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
8992 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
9011 TCCAA
1 TCCAA
9016 AATCGCAATG
Statistics
Matches: 126, Mismatches: 23, Indels: 40
0.67 0.12 0.21
Matches are distributed among these distances:
15 4 0.03
16 1 0.01
17 7 0.06
19 30 0.24
20 1 0.01
21 53 0.42
22 2 0.02
23 28 0.22
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:8880 original size:42 final size:42
Alignment explanation
Indices: 8820--9012 Score: 263
Period size: 42 Copynumber: 4.7 Consensus size: 42
8810 TCTATCACAA
*
8820 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* *
8860 TGCGATTTATTCTAAATTCGTTGC----GTCGAAGTTCTCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* * * *
8898 TGCGATTTATTCTAAGTTCGTTGCGTTAGTCGAAGTTCTCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* *
8940 TGCGATTTATTCCAAGTTTGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
8982 TGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TGCGATTTATTCCAAATTCGTTGCGATAGTC
9013 CAAAATCGCA
Statistics
Matches: 137, Mismatches: 10, Indels: 10
0.87 0.06 0.06
Matches are distributed among these distances:
38 35 0.26
40 5 0.04
41 2 0.01
42 95 0.69
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:9597 original size:39 final size:39
Alignment explanation
Indices: 9553--9632 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
9543 GTCTCGTGGT
9553 CGTGGTCGTGGTCGCAGTAATACGTGTCTTCGACACGTC
1 CGTGGTCGTGGTCGCAGTAATACGTGTCTTCGACACGTC
**
9592 CGTGGTCGTGGTCGTGGTAATACGTGTCTTCGACACGTC
1 CGTGGTCGTGGTCGCAGTAATACGTGTCTTCGACACGTC
9631 CG
1 CG
9633 CACGAATACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.14, C:0.25, G:0.33, T:0.29
Consensus pattern (39 bp):
CGTGGTCGTGGTCGCAGTAATACGTGTCTTCGACACGTC
Found at i:9732 original size:21 final size:21
Alignment explanation
Indices: 9706--9939 Score: 126
Period size: 21 Copynumber: 10.9 Consensus size: 21
9696 ATTTTGGATT
9706 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
9727 ATCGCAACGCGAACTTCGACTACGA
1 ATCGCAA--CGAATTTGGAATA--A
*
9752 CTATCGCAACGAATTTGTAATAA
1 --ATCGCAACGAATTTGGAATAA
* *
9775 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
9796 ATCGCAACCAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
9817 ATCGCAACGCGAACTTAGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
9838 ATCGCAACGAATTTGTAATAA
1 ATCGCAACGAATTTGGAATAA
** *
9859 ATCGCAACGCGAACGTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
9880 ATCGCAACAAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
*
9901 ATCGCAACGCGAACTT-GAACT--
1 ATCGCAA--CGAATTTGGAA-TAA
9922 ATCGCAACGAATTTGGAA
1 ATCGCAACGAATTTGGAA
9940 AATCGAAATG
Statistics
Matches: 159, Mismatches: 32, Indels: 45
0.67 0.14 0.19
Matches are distributed among these distances:
19 31 0.19
20 3 0.02
21 63 0.40
22 3 0.02
23 42 0.26
25 10 0.06
27 7 0.04
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:9809 original size:42 final size:42
Alignment explanation
Indices: 9699--9970 Score: 368
Period size: 42 Copynumber: 6.4 Consensus size: 42
9689 CGTTGCGATT
*
9699 TTGGATTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
9741 TTCGACTACGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAAC
1 TT-G-----GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
9789 TTGGACTATCGCAACCAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
9831 TTAGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
9873 GTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * * *
9915 TTGAACTATCGCAACGAATTTGG-A-AAATCGAAATGCGAAT
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
9955 TTCGACTATCGCAACG
1 TTGGACTATCGCAACG
9971 CGAACTTGAA
Statistics
Matches: 205, Mismatches: 19, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
40 27 0.13
41 1 0.00
42 136 0.66
43 1 0.00
47 1 0.00
48 39 0.19
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:9965 original size:21 final size:21
Alignment explanation
Indices: 9901--9996 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
9891 TTTGGAATAA
* *
9901 ATCGCAACGCGAACTTGAACT
1 ATCGCAATGCGAATTTGAACT
*
9922 ATCGCAA--CGAATTTGGAA-A
1 ATCGCAATGCGAATTT-GAACT
*
9941 ATCGAAATGCGAATTTCG-ACT
1 ATCGCAATGCGAATTT-GAACT
* *
9962 ATCGCAACGCGAACTTGAACT
1 ATCGCAATGCGAATTTGAACT
9983 ATCGCAATGCGAAT
1 ATCGCAATGCGAAT
9997 ATGTAAATCG
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
19 12 0.20
20 5 0.08
21 43 0.72
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAATTTGAACT
Found at i:18225 original size:29 final size:30
Alignment explanation
Indices: 18183--18240 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
18173 ATGCTTTTTT
*
18183 TTTTAGTTTAGTGCCTAATGTTT-ATTTCG
1 TTTTAGTTTAGTGCCCAATGTTTCATTTCG
18212 TTTTAGTTTAGTGCCCAATGTTTCATTTC
1 TTTTAGTTTAGTGCCCAATGTTTCATTTC
18241 TTTACTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.53
Consensus pattern (30 bp):
TTTTAGTTTAGTGCCCAATGTTTCATTTCG
Found at i:18348 original size:25 final size:25
Alignment explanation
Indices: 18319--18366 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
18309 TGATTTTAAA
18319 AAAATTATATAAAATTTTAAAAAAT
1 AAAATTATATAAAATTTTAAAAAAT
* *
18344 AAAATTATATATATTTTTAAAAA
1 AAAATTATATAAAATTTTAAAAA
18367 GAAAACACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAATTATATAAAATTTTAAAAAAT
Found at i:25980 original size:258 final size:253
Alignment explanation
Indices: 25601--26098 Score: 822
Period size: 258 Copynumber: 1.9 Consensus size: 253
25591 ATTAGGTCAA
25601 ACCAACCTCCAAAAAGGTGCTAATGCTTCATGTATGAAATTACCAAAGGCAGCCCAAGACTTTAA
1 ACCAACCTCCAAAAAGGTGCTAATGCTTCATGTATGAAATTACCAAAGGCAGCCCAAGACTTTAA
*
25666 TATCGGCATGGCAATGCATAGGAGAAAGGTATTATGGGAAGTATACTATCATATAGAAATATTAA
66 TATCGGCATGGCAATGCATAGGAGAAAGGTATTATGAGAAGTATACTATCATATAGAAATATTAA
* *
25731 ACATTCAATGAAACCATATTGAGGATGATATTACAGCAGTTCATCAACTCCTGAATAATGAAACC
131 ACATTCAATGAAACCATATTGAAGATGATATTACAGCAGTTCATCAACTCCTAAATAATGAAACC
* *
25796 ATATCGAACATAAAGATATAGTCTTCAATCTAAAGAATTAGGTCAGACCTAAAGATTG
196 ATATCAAACATAAAGATATAGCCTTCAATCTAAAGAATTAGGTCAGACCTAAAGATTG
* *
25854 ACCAATCC-CCAAAAAGGTGCTAATTCTTCATGTATGAAATTACCAAAGGCAG-CC-AGATTTTA
1 ACCAA-CCTCCAAAAAGGTGCTAATGCTTCATGTATGAAATTACCAAAGGCAGCCCAAGACTTTA
* *
25916 ATATCGGCATGGCAAATGGCAATGCATAGGAGAAAGGTATTATGAGAAGTATACTGTTATATAGA
65 ATAT---C--GGC--ATGGCAATGCATAGGAGAAAGGTATTATGAGAAGTATACTATCATATAGA
25981 AATATTAAACATTCAATGAAACCATATTGAAGATGATATTACAGCAGTTCATCAACTCCTAAATA
123 AATATTAAACATTCAATGAAACCATATTGAAGATGATATTACAGCAGTTCATCAACTCCTAAATA
26046 ATGAAACCATATCAAACATAAAGATATAGCCTTCAATCTAAAGAATTAGGTCA
188 ATGAAACCATATCAAACATAAAGATATAGCCTTCAATCTAAAGAATTAGGTCA
26099 AACTACTTTT
Statistics
Matches: 228, Mismatches: 9, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
251 11 0.05
252 2 0.01
253 48 0.21
254 3 0.01
256 3 0.01
258 161 0.71
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (253 bp):
ACCAACCTCCAAAAAGGTGCTAATGCTTCATGTATGAAATTACCAAAGGCAGCCCAAGACTTTAA
TATCGGCATGGCAATGCATAGGAGAAAGGTATTATGAGAAGTATACTATCATATAGAAATATTAA
ACATTCAATGAAACCATATTGAAGATGATATTACAGCAGTTCATCAACTCCTAAATAATGAAACC
ATATCAAACATAAAGATATAGCCTTCAATCTAAAGAATTAGGTCAGACCTAAAGATTG
Done.