Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004999.1 Hibiscus syriacus cultivar Beakdansim tig00011220_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: 74331
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2107 original size:33 final size:33
Alignment explanation
Indices: 2065--2133 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2055 GTTGATGAAT
*
2065 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
2098 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
2131 GAA
1 GAA
2134 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:2138 original size:13 final size:12
Alignment explanation
Indices: 2119--2215 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
2109 TTATTGGCGT
2119 GATATGGTGATG
1 GATATGGTGATG
2131 GAATATGGTGAT-
1 G-ATATGGTGATG
*
2143 GATATAGGCG-T-
1 GATAT-GGTGATG
2154 GATAATGGTGATG
1 GAT-ATGGTGATG
2167 GACTATGGTGAT-
1 GA-TATGGTGATG
*
2179 GATATAGGCG-T-
1 GATAT-GGTGATG
*
2190 GATAATGGAGATG
1 GAT-ATGGTGATG
2203 GATTATGGTGATG
1 GA-TATGGTGATG
2216 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:2174 original size:36 final size:36
Alignment explanation
Indices: 2104--2216 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
2094 AATGGAAGGA
* *
2104 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
2139 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
2175 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
2211 TGATGA
1 TGATGA
2217 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:4220 original size:35 final size:37
Alignment explanation
Indices: 4151--4228 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 37
4141 ATACTATTTC
*
4151 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
4188 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
4223 CATCAC
1 CATCAC
4229 AAAATTCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 20 0.51
36 3 0.08
37 16 0.41
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:18143 original size:22 final size:25
Alignment explanation
Indices: 18091--18143 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
18081 TGTTTTTCTT
18091 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
*
18116 TTTCTT-C-TTTTGAGTGCTTT-GA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
18138 TTTCTT
1 TTTCTT
18144 TGTTGGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 7 0.26
23 13 0.48
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.60
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:18189 original size:11 final size:11
Alignment explanation
Indices: 18175--18201 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
18165 TTTCACTTTT
18175 CACTTCACTTG
1 CACTTCACTTG
18186 CACTTCACTTG
1 CACTTCACTTG
18197 CACTT
1 CACTT
18202 TGTTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.37, G:0.07, T:0.37
Consensus pattern (11 bp):
CACTTCACTTG
Found at i:19472 original size:11 final size:11
Alignment explanation
Indices: 19452--19492 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
19442 GTGCTGGAAC
*
19452 AAGATAAAAAT
1 AAGATAAAAAA
*
19463 AAGATTAAAAA
1 AAGATAAAAAA
19474 AAGATAAAAAA
1 AAGATAAAAAA
19485 AAGATAAA
1 AAGATAAA
19493 TGAATTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (11 bp):
AAGATAAAAAA
Found at i:20362 original size:33 final size:33
Alignment explanation
Indices: 20320--20388 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
20310 GTTGATGAAT
*
20320 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
20353 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
20386 GAA
1 GAA
20389 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:24323 original size:33 final size:33
Alignment explanation
Indices: 24281--24349 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
24271 GTTGATGAAT
*
24281 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
24314 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
24347 GAA
1 GAA
24350 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:29759 original size:13 final size:11
Alignment explanation
Indices: 29730--29769 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
29720 TAAATTTTGG
29730 TTTTTTTGTTT
1 TTTTTTTGTTT
*
29741 TTTTTGTGTTT
1 TTTTTTTGTTT
*
29752 TATTTTTGTTT
1 TTTTTTTGTTT
29763 TTTTTTT
1 TTTTTTT
29770 ACCTTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.88
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:30143 original size:11 final size:11
Alignment explanation
Indices: 30108--30143 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
30098 TTGGTGCTGG
30108 AAACAAGATAA
1 AAACAAGATAA
* *
30119 AAATAAGATTA
1 AAACAAGATAA
30130 AAACAAGATAA
1 AAACAAGATAA
30141 AAA
1 AAA
30144 GAGATAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:36858 original size:23 final size:23
Alignment explanation
Indices: 36832--36875 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
36822 AAATCCAGCA
36832 AAGAAAATCAAAGCACTCAAAAT
1 AAGAAAATCAAAGCACTCAAAAT
* *
36855 AAGAAATTGAAAGCACTCAAA
1 AAGAAAATCAAAGCACTCAAA
36876 GAGGAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAT
Found at i:45089 original size:15 final size:16
Alignment explanation
Indices: 45069--45105 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
45059 GATTAGAATA
45069 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
45084 AAATAAATAAAAGATG
1 AAATAAACAAAAGATG
45100 AAATAA
1 AAATAA
45106 GATAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:45103 original size:16 final size:15
Alignment explanation
Indices: 45069--45110 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
45059 GATTAGAATA
*
45069 AAATAAACAAAAGAT
1 AAATAAATAAAAGAT
45084 AAATAAATAAAAGAT
1 AAATAAATAAAAGAT
45099 GAAATAAGATAA
1 -AAATAA-ATAA
45111 TAAAGAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 6 0.25
17 4 0.17
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (15 bp):
AAATAAATAAAAGAT
Found at i:49404 original size:8 final size:8
Alignment explanation
Indices: 49393--49442 Score: 57
Period size: 8 Copynumber: 6.0 Consensus size: 8
49383 TTTTTGGCTC
49393 TTTTTTTG
1 TTTTTTTG
49401 TTTTTTTG
1 TTTTTTTG
49409 CCTTTTTTT-
1 --TTTTTTTG
*
49418 TTTTTTTCC
1 TTTTTTT-G
49427 TTTTTTTG
1 TTTTTTTG
49435 TTTTTTTG
1 TTTTTTTG
49443 AAAAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
7 7 0.19
8 16 0.43
9 7 0.19
10 7 0.19
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:49404 original size:18 final size:17
Alignment explanation
Indices: 49382--49440 Score: 75
Period size: 16 Copynumber: 3.4 Consensus size: 17
49372 AAATTTTGGC
49382 TTTTTTGGCTCTTTTTTTG
1 TTTTTT-GC-CTTTTTTTG
49401 TTTTTTTGCCTTTTTTT-
1 -TTTTTTGCCTTTTTTTG
*
49418 TTTTTTTCCTTTTTTTG
1 TTTTTTGCCTTTTTTTG
49435 TTTTTT
1 TTTTTT
49441 TGAAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 15 0.41
17 6 0.16
18 8 0.22
19 2 0.05
20 6 0.16
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.81
Consensus pattern (17 bp):
TTTTTTGCCTTTTTTTG
Found at i:49441 original size:18 final size:18
Alignment explanation
Indices: 49382--49442 Score: 90
Period size: 17 Copynumber: 3.4 Consensus size: 18
49372 AAATTTTGGC
*
49382 TTTTTTGGCTCTTTTTTTG
1 TTTTTTTGC-CTTTTTTTG
49401 TTTTTTTGCCTTTTTTT-
1 TTTTTTTGCCTTTTTTTG
49418 TTTTTTT-CCTTTTTTTG
1 TTTTTTTGCCTTTTTTTG
49435 TTTTTTTG
1 TTTTTTTG
49443 AAAAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
16 9 0.23
17 14 0.36
18 8 0.21
19 8 0.21
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (18 bp):
TTTTTTTGCCTTTTTTTG
Found at i:49816 original size:15 final size:16
Alignment explanation
Indices: 49796--49832 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
49786 GATTAGAATA
49796 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
49811 AAATAAATAAAAGATG
1 AAATAAACAAAAGATG
49827 AAATAA
1 AAATAA
49833 GATAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:49830 original size:16 final size:15
Alignment explanation
Indices: 49796--49837 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
49786 GATTAGAATA
*
49796 AAATAAACAAAAGAT
1 AAATAAATAAAAGAT
49811 AAATAAATAAAAGAT
1 AAATAAATAAAAGAT
49826 GAAATAAGATAA
1 -AAATAA-ATAA
49838 TAAAGAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 6 0.25
17 4 0.17
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (15 bp):
AAATAAATAAAAGAT
Found at i:60050 original size:33 final size:33
Alignment explanation
Indices: 60008--60076 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
59998 GTTGATGAAT
60008 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGTG-TGAAATGGTAATG
* * *
60041 GAAGGATGATGTTATTGGTGTGATATGGTGATG
1 GAAGGATGATGTTAATGGTGTGAAATGGTAATG
60074 GAA
1 GAA
60077 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGTGTGAAATGGTAATG
Found at i:60120 original size:36 final size:36
Alignment explanation
Indices: 60060--60159 Score: 148
Period size: 36 Copynumber: 2.8 Consensus size: 36
60050 TGTTATTGGT
60060 GTGAT-ATGGTGATGGAATATGGTGATGATATAGGC
1 GTGATAATGGTGATGGAATATGGTGATGATATAGGC
* * *
60095 GTGATAATTGTGATGGACTACGGTGATGATATAGGC
1 GTGATAATGGTGATGGAATATGGTGATGATATAGGC
* *
60131 GTGATAATGGAGATGGATTATGGTGATGA
1 GTGATAATGGTGATGGAATATGGTGATGA
60160 AAATAGTATC
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
35 5 0.09
36 52 0.91
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
GTGATAATGGTGATGGAATATGGTGATGATATAGGC
Found at i:65366 original size:17 final size:16
Alignment explanation
Indices: 65344--65386 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
65334 GTTGTAGGAG
65344 TCTTTTCTTTTCTTCTT
1 TCTTTTCTTTTCTT-TT
*
65361 TCTTTTTTTTTCTTTT
1 TCTTTTCTTTTCTTTT
65377 T-TTTTCTTTT
1 TCTTTTCTTTT
65387 TGTTGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.33
16 3 0.12
17 13 0.54
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TCTTTTCTTTTCTTTT
Found at i:65372 original size:10 final size:10
Alignment explanation
Indices: 65346--65387 Score: 66
Period size: 10 Copynumber: 4.0 Consensus size: 10
65336 TGTAGGAGTC
65346 TTTTCTTTTCT
1 TTTTCTTTT-T
65357 TCTTTCTTTTT
1 T-TTTCTTTTT
65368 TTTTCTTTTT
1 TTTTCTTTTT
65378 TTTTCTTTTT
1 TTTTCTTTTT
65388 GTTGCTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 19 0.63
11 3 0.10
12 8 0.27
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:65395 original size:20 final size:20
Alignment explanation
Indices: 65359--65396 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
65349 TCTTTTCTTC
* *
65359 TTTCTTTTTTTTTCTTTTTT
1 TTTCTTTTTGTTGCTTTTTT
65379 TTTCTTTTTGTTGCTTTT
1 TTTCTTTTTGTTGCTTTT
65397 GTTGCAGCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (20 bp):
TTTCTTTTTGTTGCTTTTTT
Found at i:65807 original size:13 final size:12
Alignment explanation
Indices: 65788--65852 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
65778 GTTATTGGCT
65788 GATATGGTGATG
1 GATATGGTGATG
65800 GAATATGGTGAT-
1 G-ATATGGTGATG
*
65812 GATATAGGCG-T-
1 GATAT-GGTGATG
65823 GATAATGGTGATG
1 GAT-ATGGTGATG
65836 GACTATGGTGAT-
1 GA-TATGGTGATG
65848 GATAT
1 GATAT
65853 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:65833 original size:36 final size:36
Alignment explanation
Indices: 65787--65885 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
65777 TGTTATTGGC
65787 TGAT-ATGGTGATGGAATATGGTGATGATATAGGCG
1 TGATAATGGTGATGGAATATGGTGATGATATAGGCG
*
65822 TGATAATGGTGATGGACTATGGTGATGATATAGGCG
1 TGATAATGGTGATGGAATATGGTGATGATATAGGCG
* * *
65858 TGATAATGGAGATGGATTATGGTCATGA
1 TGATAATGGTGATGGAATATGGTGATGA
65886 AAATATCTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 4 0.07
36 55 0.93
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.31
Consensus pattern (36 bp):
TGATAATGGTGATGGAATATGGTGATGATATAGGCG
Found at i:70882 original size:13 final size:13
Alignment explanation
Indices: 70866--70891 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
70856 TAAAACCTTT
70866 ACATACCTTTTCA
1 ACATACCTTTTCA
70879 ACATACCTTTTCA
1 ACATACCTTTTCA
70892 TCTTTGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Done.