Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005048.1 Hibiscus syriacus cultivar Beakdansim tig00011337_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: 58530
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:8383 original size:24 final size:24
Alignment explanation
Indices: 8356--8407 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
8346 AACGGATATA
*
8356 TCAAAAATCAAAACATAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
** * *
8380 TCAAGTATCAGATCAAAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
8404 TCAA
1 TCAA
8408 GTATTCGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAATCCAGG
Found at i:8436 original size:24 final size:25
Alignment explanation
Indices: 8372--8436 Score: 98
Period size: 24 Copynumber: 2.7 Consensus size: 25
8362 ATCAAAACAT
8372 AATCCAGGTCAAGTA-TCAGATCAA
1 AATCCAGGTCAAGTATTCAGATCAA
*
8396 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCAGGTCAAGTATTCAGATCAA
*
8420 AATCCAGGTCAGGTATT
1 AATCCAGGTCAAGTATT
8437 ATAATAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 36 0.95
25 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (25 bp):
AATCCAGGTCAAGTATTCAGATCAA
Found at i:11144 original size:22 final size:22
Alignment explanation
Indices: 11116--11158 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11106 CATGGTCTTG
*
11116 TGCATCGATGCATCAAATGCAC
1 TGCATCGATGCATAAAATGCAC
11138 TGCATCGATGCATAAAATGCA
1 TGCATCGATGCATAAAATGCA
11159 TTCGATGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (22 bp):
TGCATCGATGCATAAAATGCAC
Found at i:11590 original size:17 final size:17
Alignment explanation
Indices: 11568--11602 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
11558 ACACTTCTCC
11568 CTTTAAAAACATTGTAA
1 CTTTAAAAACATTGTAA
*
11585 CTTTAAAAGCATTGTAA
1 CTTTAAAAACATTGTAA
11602 C
1 C
11603 ACTTAACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (17 bp):
CTTTAAAAACATTGTAA
Found at i:13810 original size:23 final size:22
Alignment explanation
Indices: 13781--13860 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
13771 GCATGACCCC
13781 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * * *
13803 CGTGCATCGGTGTACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
13825 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
13847 ATGCATCGATGCAC
1 GTGCATCGATGCAC
13861 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 14 0.31
22 16 0.36
23 15 0.33
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:13835 original size:44 final size:42
Alignment explanation
Indices: 13759--13879 Score: 120
Period size: 43 Copynumber: 2.8 Consensus size: 42
13749 CAAAACCGAC
* ** *
13759 GGATGCATCGATGCA-TGACCCCGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACTG-TCAGGTGTATCGATGCACATTCAA
* * *
13801 GGCGTGCATCGGTGTACCT-TCATGGTGTATCGATGCACATTCAA
1 GG-ATGCATCGATGCA-CTGTCA-GGTGTATCGATGCACATTCAA
*
13845 GGATGCATCGATGCACTGTTAGGTGTATCGATGCA
1 GGATGCATCGATGCACTGTCAGGTGTATCGATGCA
13880 TGAAGCACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
42 18 0.29
43 23 0.37
44 21 0.33
45 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (42 bp):
GGATGCATCGATGCACTGTCAGGTGTATCGATGCACATTCAA
Found at i:13876 original size:20 final size:21
Alignment explanation
Indices: 13785--13879 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 21
13775 GACCCCGTGC
*
13785 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * * *
13808 ATCGGTGTACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
13829 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
13851 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
13871 ATCGATGCA
1 ATCGATGCA
13880 TGAAGCACAA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 11 0.19
21 21 0.36
22 14 0.24
23 12 0.21
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:19337 original size:26 final size:26
Alignment explanation
Indices: 19306--19375 Score: 140
Period size: 26 Copynumber: 2.7 Consensus size: 26
19296 TTGAAAAAGC
19306 CTGAGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATCAAATGCA
19332 CTGAGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATCAAATGCA
19358 CTGAGTGCATCGATGCAT
1 CTGAGTGCATCGATGCAT
19376 GGTATGTGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (26 bp):
CTGAGTGCATCGATGCATCAAATGCA
Found at i:19450 original size:20 final size:20
Alignment explanation
Indices: 19422--19460 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19412 CAAGAAATTA
19422 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
19442 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
19461 CCTTTGAAAA
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:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:23046 original size:141 final size:141
Alignment explanation
Indices: 22833--23242 Score: 484
Period size: 141 Copynumber: 2.9 Consensus size: 141
22823 TAAGGAATGC
* *** * * * * *
22833 GGAAGACTCTTAATAGGATTGAAGGAAAGATCAAGAATCTTGAGTTCATTCGTAT-CATCGAAGA
1 GGAAGACTCTTGATAGGATTTCTGGAAAGATCAAGAACCTTGAGTCCATCCATATGC-TTGAAGA
* * ** * * *
22897 AGCTTTCTGGAATACTTTCTATAAGACAATGACAAAACAACAATGTTGTGAGCCAGGGACACTTC
65 ACCCTTCTGGAATACTCGCTATATGACAATGAGACAACAACAATGTTGTGAGCCAGGGACACTTC
*
22962 GACAAGGAAATT
130 GACAAAGAAATT
* *
22974 GGAAGACTCTTGATAGGATTTCTGGAAAGATCAAGAACCTTGAGTGCATCCATATGCTTGAAAAA
1 GGAAGACTCTTGATAGGATTTCTGGAAAGATCAAGAACCTTGAGTCCATCCATATGCTTGAAGAA
* * * *
23039 TCGTTCTGGAATACTCGCTATATTG-CATTGAGACAACAACAATGTTGTGAGCCCGGGACACTTC
66 CCCTTCTGGAATACTCGCTATA-TGACAATGAGACAACAACAATGTTGTGAGCCAGGGACACTTC
23103 GACAAAGAAATT
130 GACAAAGAAATT
* * *
23115 GGAAGACTCTTGATAGGATTTCTGGAAAGATCAAGAATCC-TAAGCCCATGCATATGCTTGAAGA
1 GGAAGACTCTTGATAGGATTTCTGGAAAGATCAAGAA-CCTTGAGTCCATCCATATGCTTGAAGA
* * * * * *
23179 ACCCTTCCGGAATACTCGCTATATCACAATCAGACAACAGCAATGTTGTGAGCCTGGGGCACTT
65 ACCCTTCTGGAATACTCGCTATATGACAATGAGACAACAACAATGTTGTGAGCCAGGGACACTT
23243 TGGGGGTGAC
Statistics
Matches: 231, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
140 1 0.00
141 226 0.98
142 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (141 bp):
GGAAGACTCTTGATAGGATTTCTGGAAAGATCAAGAACCTTGAGTCCATCCATATGCTTGAAGAA
CCCTTCTGGAATACTCGCTATATGACAATGAGACAACAACAATGTTGTGAGCCAGGGACACTTCG
ACAAAGAAATT
Found at i:24047 original size:36 final size:36
Alignment explanation
Indices: 23998--24069 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
23988 CCATTTGACG
*
23998 GCTCAGGATTTCCTATTCTCTCAAGTGAAACCTTCT
1 GCTCAGGAATTCCTATTCTCTCAAGTGAAACCTTCT
*
24034 GCTCAGGAATTCCTATTTTCTCAAGTGAAACCTTCT
1 GCTCAGGAATTCCTATTCTCTCAAGTGAAACCTTCT
24070 CCCATAGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (36 bp):
GCTCAGGAATTCCTATTCTCTCAAGTGAAACCTTCT
Found at i:28581 original size:120 final size:120
Alignment explanation
Indices: 28368--28611 Score: 488
Period size: 120 Copynumber: 2.0 Consensus size: 120
28358 TCATCCGTGA
28368 GTGACAGAATTAAGAGCCAAATGGAAAGACGGATGAGCAGATGCAGGGACATTATCTAATGCCCG
1 GTGACAGAATTAAGAGCCAAATGGAAAGACGGATGAGCAGATGCAGGGACATTATCTAATGCCCG
28433 CCTGCTTCTTTTAATATTTTCCAATGTTTTCAAAATCGGACCGGACATTGAACCG
66 CCTGCTTCTTTTAATATTTTCCAATGTTTTCAAAATCGGACCGGACATTGAACCG
28488 GTGACAGAATTAAGAGCCAAATGGAAAGACGGATGAGCAGATGCAGGGACATTATCTAATGCCCG
1 GTGACAGAATTAAGAGCCAAATGGAAAGACGGATGAGCAGATGCAGGGACATTATCTAATGCCCG
28553 CCTGCTTCTTTTAATATTTTCCAATGTTTTCAAAATCGGACCGGACATTGAACCG
66 CCTGCTTCTTTTAATATTTTCCAATGTTTTCAAAATCGGACCGGACATTGAACCG
28608 GTGA
1 GTGA
28612 AGGTATTAGT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 124 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (120 bp):
GTGACAGAATTAAGAGCCAAATGGAAAGACGGATGAGCAGATGCAGGGACATTATCTAATGCCCG
CCTGCTTCTTTTAATATTTTCCAATGTTTTCAAAATCGGACCGGACATTGAACCG
Found at i:29193 original size:24 final size:24
Alignment explanation
Indices: 29161--29216 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
29151 CTATTCTTTC
29161 GCTTCAATTGAGCTAAAATTTTAG
1 GCTTCAATTGAGCTAAAATTTTAG
*
29185 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTAAAATTTTAG
29209 GCTTCAAT
1 GCTTCAAT
29217 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTAAAATTTTAG
Found at i:30778 original size:22 final size:22
Alignment explanation
Indices: 30734--30781 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
30724 GTTCAATTCA
*
30734 TTTATGTTCATAAACAAGTTCG
1 TTTATGTTCATAAACAAGCTCG
*
30756 TTTATGTTCATGAACCAA-CTCG
1 TTTATGTTCAT-AAACAAGCTCG
30778 TTTA
1 TTTA
30782 GAAGATCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (22 bp):
TTTATGTTCATAAACAAGCTCG
Found at i:32246 original size:25 final size:25
Alignment explanation
Indices: 32192--32247 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
32182 GTTAGGAGAT
*
32192 AAATATATAAAATTTTAGAGGAAAAT
1 AAATATATAAAATTTTAGA-GAAAAA
* *
32218 AAATTTATAAATTTTTAGA-AAATAA
1 AAATATATAAAATTTTAGAGAAA-AA
32243 AAATA
1 AAATA
32248 AATTATCGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 3 0.12
25 5 0.20
26 17 0.68
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (25 bp):
AAATATATAAAATTTTAGAGAAAAA
Found at i:33561 original size:101 final size:101
Alignment explanation
Indices: 33386--33585 Score: 400
Period size: 101 Copynumber: 2.0 Consensus size: 101
33376 TTAACAGAAC
33386 CTCCAAAAACGTGCACAGATGAGGAACAACAAGAACAAAGAAGAGATATATAATCAGAGAATGAT
1 CTCCAAAAACGTGCACAGATGAGGAACAACAAGAACAAAGAAGAGATATATAATCAGAGAATGAT
33451 ACAATATTATGCATTTCAAGATTCAGTCAAAATAAG
66 ACAATATTATGCATTTCAAGATTCAGTCAAAATAAG
33487 CTCCAAAAACGTGCACAGATGAGGAACAACAAGAACAAAGAAGAGATATATAATCAGAGAATGAT
1 CTCCAAAAACGTGCACAGATGAGGAACAACAAGAACAAAGAAGAGATATATAATCAGAGAATGAT
33552 ACAATATTATGCATTTCAAGATTCAGTCAAAATA
66 ACAATATTATGCATTTCAAGATTCAGTCAAAATA
33586 TTAGTTAAAC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (101 bp):
CTCCAAAAACGTGCACAGATGAGGAACAACAAGAACAAAGAAGAGATATATAATCAGAGAATGAT
ACAATATTATGCATTTCAAGATTCAGTCAAAATAAG
Found at i:37229 original size:13 final size:13
Alignment explanation
Indices: 37208--37238 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
37198 TATTGAGTGA
37208 TGTTGAACATACT
1 TGTTGAACATACT
*
37221 TGTTTAACATACT
1 TGTTGAACATACT
37234 TGTTG
1 TGTTG
37239 CATCCCATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (13 bp):
TGTTGAACATACT
Found at i:40570 original size:141 final size:141
Alignment explanation
Indices: 40343--40615 Score: 325
Period size: 141 Copynumber: 1.9 Consensus size: 141
40333 TAAGGAATGC
** ** * * * * *
40343 GGAAGACTCTTGATAGGATTGGAGGAAAGATCAAGAGTCTTGAGCTCATTCGTATCATCGAAGAA
1 GGAAGACTCTTGATAGGATTCCAGGAAAGATCAAGAACCCTAAGCCCATGCATATCATCGAAGAA
* * * * **
40408 GCTTTCTGGAATACTTTCTATA-CGACAACCACACAACAACAATGTTGTGAGCCCGGGACACTTC
66 CCCTTCAGGAAGACTCGCTATATC-ACAACCACACAACAACAATGTTGTGAGCCCGGGACACTTC
40472 GACAAGGAAATT
130 GACAAGGAAATT
*
40484 GGAAGACTCTTGATAGGATTCCAGGAAAGATCAAGAACCCTAAGCCCATGCATATGC-TTGAAGA
1 GGAAGACTCTTGATAGGATTCCAGGAAAGATCAAGAACCCTAAGCCCATGCATAT-CATCGAAGA
* * * * *
40548 ACCCTTCAGGAAGACTCGCTATATCACAATCAGACAACAACAATGTTGTGAGTCTGGGGCACTTC
65 ACCCTTCAGGAAGACTCGCTATATCACAACCACACAACAACAATGTTGTGAGCCCGGGACACTTC
40613 GAC
130 GAC
40616 GGTGACATTT
Statistics
Matches: 109, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
141 107 0.98
142 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (141 bp):
GGAAGACTCTTGATAGGATTCCAGGAAAGATCAAGAACCCTAAGCCCATGCATATCATCGAAGAA
CCCTTCAGGAAGACTCGCTATATCACAACCACACAACAACAATGTTGTGAGCCCGGGACACTTCG
ACAAGGAAATT
Found at i:46244 original size:22 final size:22
Alignment explanation
Indices: 46200--46247 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
46190 GTTCAATTCA
*
46200 TTTATGTTCATAAACAAGTTCG
1 TTTATGTTCATAAACAAGCTCG
*
46222 TTTATGTTCATGAACCAA-CTCG
1 TTTATGTTCAT-AAACAAGCTCG
46244 TTTA
1 TTTA
46248 GAATATTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (22 bp):
TTTATGTTCATAAACAAGCTCG
Found at i:47246 original size:9 final size:10
Alignment explanation
Indices: 47222--47247 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
47212 TAACAAAAAA
47222 TAAAAAAATC
1 TAAAAAAATC
47232 TAAAAAAATC
1 TAAAAAAATC
47242 TAAAAA
1 TAAAAA
47248 TTTTAAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (10 bp):
TAAAAAAATC
Found at i:48687 original size:18 final size:18
Alignment explanation
Indices: 48664--48704 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
48654 GTTTTGCTCG
48664 CCCCGTCCCCGAACCC-AT
1 CCCCGTCCCCG-ACCCGAT
48682 CCCCGTCCCCGACCCGAT
1 CCCCGTCCCCGACCCGAT
48700 CCCCG
1 CCCCG
48705 ATAGGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.12, C:0.63, G:0.15, T:0.10
Consensus pattern (18 bp):
CCCCGTCCCCGACCCGAT
Found at i:49474 original size:16 final size:16
Alignment explanation
Indices: 49453--49496 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
49443 GGAAACAGTC
49453 TTGAATAAGACCAAAG
1 TTGAATAAGACCAAAG
49469 TTGAATAAGACCAAAG
1 TTGAATAAGACCAAAG
49485 TTGAATAAGACC
1 TTGAATAAGACC
49497 TTCCTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (16 bp):
TTGAATAAGACCAAAG
Done.