Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000016.1 Hibiscus syriacus cultivar Beakdansim tig00000031_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: 84441
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4962 original size:13 final size:13
Alignment explanation
Indices: 4944--4970 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4934 GCGCGAGGCT
4944 GCCATTTATTAAA
1 GCCATTTATTAAA
4957 GCCATTTATTAAA
1 GCCATTTATTAAA
4970 G
1 G
4971 AGAGTTCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (13 bp):
GCCATTTATTAAA
Found at i:11465 original size:21 final size:21
Alignment explanation
Indices: 11436--11477 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11426 TGAGCTATGG
* *
11436 CTTTGAAGTAAGGCGCCTTGA
1 CTTTAAAGTAAAGCGCCTTGA
*
11457 CTTTAAAGTAAAGCTCCTTGA
1 CTTTAAAGTAAAGCGCCTTGA
11478 TTCTTAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (21 bp):
CTTTAAAGTAAAGCGCCTTGA
Found at i:22603 original size:17 final size:18
Alignment explanation
Indices: 22579--22625 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
22569 CAACGGTCAA
*
22579 CGGGTCGGGTGAACGGGT
1 CGGGTCGGGTCAACGGGT
22597 C-GGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
22614 CGGGTCGGGTCA
1 CGGGTCGGGTCA
22626 GGTTGTAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.11, C:0.21, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:23745 original size:15 final size:15
Alignment explanation
Indices: 23725--23762 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
23715 ATGATAACAC
23725 TAGTGCCATTGCAAT
1 TAGTGCCATTGCAAT
23740 TAGTGCCATTGCAAT
1 TAGTGCCATTGCAAT
*
23755 GAGTGCCA
1 TAGTGCCA
23763 ACCCGGTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (15 bp):
TAGTGCCATTGCAAT
Found at i:28520 original size:42 final size:41
Alignment explanation
Indices: 28473--28611 Score: 124
Period size: 42 Copynumber: 3.4 Consensus size: 41
28463 AAAATGATAT
* *
28473 TTTAGCGGCGTTTTTCTAACAAATGCCACAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTCTAACAAACGCCGCAATAGAGT-GTAA
* * * *
28515 TTTAGCAGCGTTTATTGCT-A-AAACGTCGGAATAGAGCTGT-T
1 TTTAGCGGCGTTT-TT-CTAACAAACGCCGCAATAGAG-TGTAA
* * *
28556 TTTAGTGGCTTTTTTC-AACAAACGCCGCAATATAGTAGTAA
1 TTTAGCGGCGTTTTTCTAACAAACGCCGCAATAGAGT-GTAA
28597 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
28612 ATATAAACGC
Statistics
Matches: 75, Mismatches: 15, Indels: 15
0.71 0.14 0.14
Matches are distributed among these distances:
39 3 0.04
40 17 0.23
41 23 0.31
42 26 0.35
43 4 0.05
44 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTCTAACAAACGCCGCAATAGAGTGTAA
Found at i:28658 original size:82 final size:81
Alignment explanation
Indices: 28552--28874 Score: 324
Period size: 82 Copynumber: 3.9 Consensus size: 81
28542 GGAATAGAGC
* * * * * * *
28552 TGTTTTTAGTGGCTTTTTTC-AACAAACGCCGCAATATAGTAGTAATTTAGCGGCGTTTTTATAT
1 TGTTTATAGTGGCGTTTGTCAAACAAACGCCGCTATATAGAAGTAATTTAGCGGCATTTTTATAC
*
28616 AAACGCTGCAACAGTAT
66 AAACGCCGCAACAG-AT
* * * * *
28633 TGTTTATAGTGGTGTTTGTCAAACAAATGCCACTATACAGAAGTAATTTAACGGCATTTTTATAC
1 TGTTTATAGTGGCGTTTGTCAAACAAACGCCGCTATATAGAAGTAATTTAGCGGCATTTTTATAC
*
28698 AAACGCCACAACAGGAT
66 AAACGCCGCAACA-GAT
* ** * * *
28715 TGTTTATAGTGGCATTTGTCAAACAAACGCCGCTATATAGAAGTAATTTAGTAGCGTTTATCAAA
1 TGTTTATAGTGGCGTTTGTCAAACAAACGCCGCTATATAGAAGTAATTTAGCGGCATTT-TTATA
* * *
28780 CAAATGCCGAAACAGGT
65 CAAACGCCGCAACAGAT
* * * * * *
28797 TGTTTATGGTGGCGTTTGTACAAAAAAACACCGCTATAAAGTAGTAATTTAGCTGCATTTTTACT
1 TGTTTATAGTGGCGTTTGT-CAAACAAACGCCGCTATATAGAAGTAATTTAGCGGCATTTTTA-T
*
28862 ACAAACGTCGCAA
64 ACAAACGCCGCAA
28875 TATGGTTGCT
Statistics
Matches: 194, Mismatches: 43, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
81 16 0.08
82 120 0.62
83 58 0.30
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (81 bp):
TGTTTATAGTGGCGTTTGTCAAACAAACGCCGCTATATAGAAGTAATTTAGCGGCATTTTTATAC
AAACGCCGCAACAGAT
Found at i:28741 original size:41 final size:41
Alignment explanation
Indices: 28624--28745 Score: 106
Period size: 41 Copynumber: 3.0 Consensus size: 41
28614 ATAAACGCTG
* ** *
28624 CAACAGTATTGTTTATAGTGGTGTTTGTCAAACAAATGCCA
1 CAACAGAATTGTTTATAGTGGCATTTGTCAAACAAACGCCA
** * * *
28665 CTATACAGAAGTAATTTA-A-CGGCATTT-TTATACAAACGCCA
1 C-A-ACAGAA-TTGTTTATAGTGGCATTTGTCAAACAAACGCCA
*
28706 CAACAGGATTGTTTATAGTGGCATTTGTCAAACAAACGCC
1 CAACAGAATTGTTTATAGTGGCATTTGTCAAACAAACGCC
28746 GCTATATAGA
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
38 5 0.08
39 6 0.10
40 8 0.13
41 24 0.40
42 6 0.10
43 6 0.10
44 5 0.08
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (41 bp):
CAACAGAATTGTTTATAGTGGCATTTGTCAAACAAACGCCA
Found at i:28762 original size:164 final size:165
Alignment explanation
Indices: 28552--28868 Score: 379
Period size: 164 Copynumber: 1.9 Consensus size: 165
28542 GGAATAGAGC
* * * * * * * *
28552 TGTTTTTAGTGGCTTTTTTCAACAAACGCCGCAATATAGTAGTAATTTAGCGGCGTTT-TTATAT
1 TGTTTATAGTGGCATTTGTCAACAAACGCCGCAATATAGAAGTAATTTAGCAGCGTTTATCAAAC
* * * * ** *
28616 AAACGCTGCAACAGTATTGTTTATAGTGGTGTTTGT-CAAACAAATGCCACTATACAGAAGTAAT
66 AAACGCCGAAACAG-ATTGTTTATAGTGGCGTTTGTACAAAAAAACACCACTATAAAGAAGTAAT
28680 TTAACGGCATTTTTA-TACAAACGCCACAACAGGAT
130 TTAACGGCATTTTTACTACAAACGCCACAACAGGAT
* *
28715 TGTTTATAGTGGCATTTGTCAAACAAACGCCGCTATATAGAAGTAATTTAGTAGCGTTTATCAAA
1 TGTTTATAGTGGCATTTGTC-AACAAACGCCGCAATATAGAAGTAATTTAGCAGCGTTTATCAAA
* * * * *
28780 CAAATGCCGAAACAGGTTGTTTATGGTGGCGTTTGTACAAAAAAACACCGCTATAAAGTAGTAAT
65 CAAACGCCGAAACAGATTGTTTATAGTGGCGTTTGTACAAAAAAACACCACTATAAAGAAGTAAT
* *
28845 TTAGCTGCATTTTTACTACAAACG
130 TTAACGGCATTTTTACTACAAACG
28869 TCGCAATATG
Statistics
Matches: 126, Mismatches: 24, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
163 17 0.13
164 52 0.41
165 49 0.39
166 8 0.06
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (165 bp):
TGTTTATAGTGGCATTTGTCAACAAACGCCGCAATATAGAAGTAATTTAGCAGCGTTTATCAAAC
AAACGCCGAAACAGATTGTTTATAGTGGCGTTTGTACAAAAAAACACCACTATAAAGAAGTAATT
TAACGGCATTTTTACTACAAACGCCACAACAGGAT
Found at i:29371 original size:22 final size:22
Alignment explanation
Indices: 29340--29414 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
29330 GTGTTTTTCT
* *
29340 GCTTTCGAATAGAAAAATAATA
1 GCTTTTGAATAGGAAAATAATA
29362 GCTTTTGAATAGGAAAATAATA
1 GCTTTTGAATAGGAAAATAATA
29384 GCTTTTGAATAGGAAAATAATA
1 GCTTTTGAATAGGAAAATAATA
29406 GCTTTTGAA
1 GCTTTTGAA
29415 AACCCGAACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (22 bp):
GCTTTTGAATAGGAAAATAATA
Found at i:34293 original size:21 final size:21
Alignment explanation
Indices: 34269--34334 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
34259 AGCAGCATTG
34269 GAAGCAGAGACAACACAGAGA
1 GAAGCAGAGACAACACAGAGA
* * *
34290 GAAGTAGCAG-TAGCACAGAGA
1 GAAGCAG-AGACAACACAGAGA
*
34311 GAAGCA-ACAGCAACACAGAGA
1 GAAGCAGAGA-CAACACAGAGA
34332 GAA
1 GAA
34335 TCAACATATC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 1 0.03
21 32 0.91
22 2 0.06
ACGTcount: A:0.50, C:0.18, G:0.29, T:0.03
Consensus pattern (21 bp):
GAAGCAGAGACAACACAGAGA
Found at i:34339 original size:21 final size:21
Alignment explanation
Indices: 34279--34340 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
34269 GAAGCAGAGA
*
34279 CAACACAGAGAGAAGT-AGCAG
1 CAACACAGAGAGAA-TCAACAG
* * *
34300 TAGCACAGAGAGAAGCAACAG
1 CAACACAGAGAGAATCAACAG
34321 CAACACAGAGAGAATCAACA
1 CAACACAGAGAGAATCAACA
34341 TATCAGTAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.50, C:0.21, G:0.24, T:0.05
Consensus pattern (21 bp):
CAACACAGAGAGAATCAACAG
Found at i:34725 original size:44 final size:43
Alignment explanation
Indices: 34662--34819 Score: 158
Period size: 44 Copynumber: 3.6 Consensus size: 43
34652 ATGCTTTTTG
* * *
34662 GCGGCGTTTGTA-ACAAAAAATGCCGCTATATACCATACATTTT
1 GCGGCGTTTGTATCCAAAAAATGCCGCTATATACCAGAC-TTTA
* * * *
34705 GTGGCGTTTGTATCCTAAAAACT-CCTCTATAAACCAGACCTTTA
1 GCGGCGTTTGTATCC-AAAAAATGCCGCTATATACCAGA-CTTTA
** * *
34749 GCGGCGTTTGTATCCTCAAAACGCTGCTATATACCAGATCTTTA
1 GCGGCGTTTGTATCCAAAAAATGCCGCTATATACCAGA-CTTTA
*
34793 GCGGCGATTGTATCCAAAAAATGCCGC
1 GCGGCGTTTGTATCCAAAAAATGCCGC
34820 GAAATTTCTT
Statistics
Matches: 90, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
43 14 0.16
44 69 0.77
45 7 0.08
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAAATGCCGCTATATACCAGACTTTA
Found at i:35012 original size:42 final size:42
Alignment explanation
Indices: 34964--35143 Score: 148
Period size: 43 Copynumber: 4.2 Consensus size: 42
34954 ATGGTATATA
*
34964 GCGGCGTTTGTGAGAAAACGCCGCTAATTATCAACACCTATT
1 GCGGCGTTTGTGAGAAAACGCCGCTAAATATCAACACCTATT
* * * * ** * *
35006 GCGGCGTTTTTGGGGAAAATGCTGCTAAACCTTAATACCTATT
1 GCGGCGTTTGT-GAGAAAACGCCGCTAAATATCAACACCTATT
* * * *
35049 GCGGCGTTTATAAGACAAACGCCGCTAAATATCGACACCCATT
1 GCGGCGTTTGTGAGA-AAACGCCGCTAAATATCAACACCTATT
** * *
35092 GCGGCGTTTGTTGA-ACAAACATCGCTATATATC-GCTACCTATT
1 GCGGCGTTTG-TGAGA-AAACGCCGCTAAATATCAAC-ACCTATT
35135 GCGGCGTTT
1 GCGGCGTTT
35144 TGTGTGACCA
Statistics
Matches: 107, Mismatches: 27, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
42 13 0.12
43 92 0.86
44 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (42 bp):
GCGGCGTTTGTGAGAAAACGCCGCTAAATATCAACACCTATT
Found at i:38018 original size:64 final size:65
Alignment explanation
Indices: 37921--38085 Score: 190
Period size: 65 Copynumber: 2.5 Consensus size: 65
37911 TTTCAAAGAG
* * * **
37921 ATGTACCGATGCACTAGTCCATGCATCGATGCACTC-TCAATTAAATTG-AATTTCGAATGCATT
1 ATGTACCGATGCACTA-TCTATGCATCGATGCACTCTTCAA-CAAATAGAAACATCGAATGCATT
*
37984 TA
64 CA
* * *
37986 GTGTACCGATGCACTCTCTATGCATCGATGCACTCTTGAACAAATAGAAACATCGAATGCATTCA
1 ATGTACCGATGCACTATCTATGCATCGATGCACTCTTCAACAAATAGAAACATCGAATGCATTCA
* * *
38051 ATGTACCGTTGCACAAGCTATGCATCGATGCACTC
1 ATGTACCGATGCACTATCTATGCATCGATGCACTC
38086 AGGCTATTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 23 0.27
65 61 0.73
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (65 bp):
ATGTACCGATGCACTATCTATGCATCGATGCACTCTTCAACAAATAGAAACATCGAATGCATTCA
Found at i:43933 original size:44 final size:44
Alignment explanation
Indices: 43847--43944 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
43837 TTTGTGCATA
* *
43847 ATGCATCGATACACTAAATAGTGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATACACTAAAGAGTGCACCGATGCATCCCTTTGAAT
*
43891 ATGCATCGATACATCATGAAGA-TGCACCGATGCA-CTCC-TTGAAT
1 ATGCATCGATACA-C-TAAAGAGTGCACCGATGCATC-CCTTTGAAT
*
43935 GTGCATCGAT
1 ATGCATCGAT
43945 GCACACTGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 29 0.62
45 14 0.30
46 4 0.09
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (44 bp):
ATGCATCGATACACTAAAGAGTGCACCGATGCATCCCTTTGAAT
Found at i:46221 original size:16 final size:16
Alignment explanation
Indices: 46200--46233 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
46190 ATTTAACAAA
46200 AAGGGGGAGAAGTGTT
1 AAGGGGGAGAAGTGTT
46216 AAGGGGGAGAAGTGTT
1 AAGGGGGAGAAGTGTT
46232 AA
1 AA
46234 AGTAAGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.47, T:0.18
Consensus pattern (16 bp):
AAGGGGGAGAAGTGTT
Found at i:53749 original size:26 final size:26
Alignment explanation
Indices: 53716--53768 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
53706 TTTGGCCTAC
53716 TCTCCTTTCCTTGTTAGCTTGGTCGG
1 TCTCCTTTCCTTGTTAGCTTGGTCGG
*
53742 TCTCCTTTCCTTGTTAGCTTTGTCGG
1 TCTCCTTTCCTTGTTAGCTTGGTCGG
53768 T
1 T
53769 TGGTAATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.04, C:0.26, G:0.21, T:0.49
Consensus pattern (26 bp):
TCTCCTTTCCTTGTTAGCTTGGTCGG
Found at i:55187 original size:30 final size:30
Alignment explanation
Indices: 55151--55210 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
55141 CATTCCTCGC
*
55151 TATTTTCTATTTTA-TTCACT-ATATTTTTAA
1 TATTTTCTAATTTAGTT-ACTGA-ATTTTTAA
55181 TATTTTCTAATTTAGTTACTGAATTTTTAA
1 TATTTTCTAATTTAGTTACTGAATTTTTAA
55211 AATTGTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.60
Consensus pattern (30 bp):
TATTTTCTAATTTAGTTACTGAATTTTTAA
Found at i:60259 original size:21 final size:21
Alignment explanation
Indices: 60235--60278 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
60225 AGACCATGCT
60235 TGAATCCCGAAAAAGAAATAA
1 TGAATCCCGAAAAAGAAATAA
60256 TGAATCCCGAAAAAGAAATAA
1 TGAATCCCGAAAAAGAAATAA
60277 TG
1 TG
60279 TTGTCAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (21 bp):
TGAATCCCGAAAAAGAAATAA
Found at i:72249 original size:26 final size:26
Alignment explanation
Indices: 72220--72281 Score: 115
Period size: 26 Copynumber: 2.3 Consensus size: 26
72210 GGGAGTGACA
72220 AGCTAGGCGTCCAAGAGGAGCTAGCG
1 AGCTAGGCGTCCAAGAGGAGCTAGCG
72246 AGCTAGGCGTCCAAGAGGAGCTAGCG
1 AGCTAGGCGTCCAAGAGGAGCTAGCG
72272 AGCTAAGGCG
1 AGCT-AGGCG
72282 ATTCATGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 30 0.86
27 5 0.14
ACGTcount: A:0.27, C:0.23, G:0.39, T:0.11
Consensus pattern (26 bp):
AGCTAGGCGTCCAAGAGGAGCTAGCG
Found at i:77919 original size:23 final size:23
Alignment explanation
Indices: 77876--77919 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
77866 TGTTTGTTTG
* *
77876 TTTATTTTTCTTTGTTTTATTTC
1 TTTATTTTTATTTGTTATATTTC
77899 TTTATTTTTATTT-TTAATATT
1 TTTATTTTTATTTGTT-ATATT
77920 AGTTTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTATTTTTATTTGTTATATTTC
Done.