Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003433.1 Hibiscus syriacus cultivar Beakdansim tig00007237_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: 63569
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:13733 original size:196 final size:196
Alignment explanation
Indices: 13222--13805 Score: 969
Period size: 197 Copynumber: 3.0 Consensus size: 196
13212 TCTCAGATTC
* * *
13222 AAAAGAAAAATATCCCATGAAATTGAAGAATGAGGAAAACCCAGATAGTAAATTTTAGCCAAGTT
1 AAAAGAAAAAGATCCCATGAAATTGAAGAATGAGAAAAACCCAGATA-TAAATTTTAGCTAAGTT
*
13287 GCAAGAACCCAAAAAGATGCACTTTTCATGATCATGAATAATTAAGCAAAAACATGTTCAGAACT
65 GCAAGAACCCAAAAAGATGTACTTTTCATGATCATGAATAATTAAGCAAAAACATGTTCAGAACT
* * *
13352 ACAAAGCTAGAGTCTTTACATGGAGCAGGGTAAAAAAAAACTTGAAACTTGAGTAGGTAAAACCT
130 ATAAAGCTAGAGTCTTTACATGGAGCAGGGTAAAAAAAAACTGGAAACTTGAGTAGCT-AAACCT
13417 TAA
194 TAA
*
13420 AAAAGAAAAAGATCTCATG-AATTGAAGAATGAGAAAAACCCAGATAATAAATTTTAGCTAAGTT
1 AAAAGAAAAAGATCCCATGAAATTGAAGAATGAGAAAAACCCAGAT-ATAAATTTTAGCTAAGTT
* *
13484 GCAAGAACCCAAAAAGATATTCTTTTCATGATCATGAATAATTAAGC-AAAACATGTTCAGAACT
65 GCAAGAACCCAAAAAGATGTACTTTTCATGATCATGAATAATTAAGCAAAAACATGTTCAGAACT
*
13548 ATAAAGCTAGAGT-ATTACATGGAGCAGGGTAAAAACAAAACTGGAAACTTGAGTAGCTAAACCT
130 ATAAAGCTAGAGTCTTTACATGGAGCAGGGTAAAAA-AAAACTGGAAACTTGAGTAGCTAAACCT
13612 TAA
194 TAA
*
13615 AAAAAAAAAAGATCCCATGAAATTGAAGAATGAGAAAAACCCAGATATAAATTTTAGCTAAGTTG
1 AAAAGAAAAAGATCCCATGAAATTGAAGAATGAGAAAAACCCAGATATAAATTTTAGCTAAGTTG
13680 CAAGAACCCAAAAAGATGTACTTTTCATGATCATGAATAATTAAGCAAAAACATGTTCAGAACTA
66 CAAGAACCCAAAAAGATGTACTTTTCATGATCATGAATAATTAAGCAAAAACATGTTCAGAACTA
*
13745 TAAAGCTAGAGTCTTTACATGGAACAGGGTGAAAAAAAAAACTGGAAAC-TGAGTAGCTAAA
131 TAAAGCTAGAGTCTTTACATGGAGCAGGGT--AAAAAAAAACTGGAAACTTGAGTAGCTAAA
13806 ACATTAAGAA
Statistics
Matches: 362, Mismatches: 17, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
195 110 0.30
196 105 0.29
197 112 0.31
198 30 0.08
199 5 0.01
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.23
Consensus pattern (196 bp):
AAAAGAAAAAGATCCCATGAAATTGAAGAATGAGAAAAACCCAGATATAAATTTTAGCTAAGTTG
CAAGAACCCAAAAAGATGTACTTTTCATGATCATGAATAATTAAGCAAAAACATGTTCAGAACTA
TAAAGCTAGAGTCTTTACATGGAGCAGGGTAAAAAAAAACTGGAAACTTGAGTAGCTAAACCTTA
A
Found at i:16138 original size:75 final size:75
Alignment explanation
Indices: 16005--16151 Score: 224
Period size: 75 Copynumber: 2.0 Consensus size: 75
15995 TAGTAGATCC
* * *
16005 ATTTATTATTTTCGCCCCTATCATATTTCATATTAATTTAACCCTCCAAGTTGTTCAATTACAT-
1 ATTTATCATTTTCGCCCCTATCATATTTCACATCAATTTAACCCTCCAAGTTGTTCAATTACATC
16069 ATTCTATACA
66 ATTCTATACA
* * *
16079 ATTTATCATTTTCGTCCCTATCGTATTTTCGCATCAATTTAACCCTCCAAGTTGTTCAATTACAT
1 ATTTATCATTTTCGCCCCTATCATA-TTTCACATCAATTTAACCCTCCAAGTTGTTCAATTACAT
16144 CATTCTAT
65 CATTCTAT
16152 TCCTACACCT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 22 0.34
75 36 0.55
76 7 0.11
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.44
Consensus pattern (75 bp):
ATTTATCATTTTCGCCCCTATCATATTTCACATCAATTTAACCCTCCAAGTTGTTCAATTACATC
ATTCTATACA
Found at i:18068 original size:21 final size:20
Alignment explanation
Indices: 18031--18070 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
18021 TGATATTTAA
*
18031 TTTTAAATACCGATTAATTT
1 TTTTAAATACCCATTAATTT
*
18051 TTTTAATATACCCTTTAATT
1 TTTTAA-ATACCCATTAATT
18071 AAAGTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTAAATACCCATTAATTT
Found at i:18108 original size:37 final size:34
Alignment explanation
Indices: 18047--18116 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 34
18037 ATACCGATTA
18047 ATTTTTTTAATATACCCTTTAATTAAAGTAAAAT
1 ATTTTTTTAATATACCCTTTAATTAAAGTAAAAT
* *
18081 ATTTTTTTGAATAATTATCCTTTAATTACAGTAAAA
1 ATTTTTTT-AAT-A-TACCCTTTAATTAAAGTAAAA
18117 ATTAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 8 0.26
35 3 0.10
36 1 0.03
37 19 0.61
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (34 bp):
ATTTTTTTAATATACCCTTTAATTAAAGTAAAAT
Found at i:18259 original size:21 final size:20
Alignment explanation
Indices: 18205--18259 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
18195 CTTCTGTTGA
*
18205 TTTAAAATTATATTTGATGAT
1 TTTAAAATT-TATGTGATGAT
18226 TTTAAAATATTATGTGATGAT
1 TTTAAAAT-TTATGTGATGAT
*
18247 TTTGAGAATTTAT
1 TTT-AAAATTTAT
18260 AAAATGACGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
TTTAAAATTTATGTGATGAT
Found at i:21070 original size:58 final size:57
Alignment explanation
Indices: 20936--21077 Score: 132
Period size: 58 Copynumber: 2.5 Consensus size: 57
20926 TATCAATGTT
* *
20936 CTCAAATATGACCCTCATTTTAAATTGATCTCTAAATTTTTAAATTTCAACTTCATTC
1 CTCAAATATGACCTTCATTTTAAATTAATCTCTAAATTTTT-AATTTCAACTTCATTC
* * *
20994 CT-AAATTATGA-TTATCATTTTAAATTAATCATC-AACTTTGATT-ATTTCAATTTCA-TC
1 CTCAAA-TATGACCT-TCATTTTAAATTAATC-TCTAAATTT--TTAATTTCAACTTCATTC
*
21051 CTCAAACTATGACCTTCATTCTAAATT
1 CTCAAA-TATGACCTTCATTTTAAATT
21078 GGTCCCAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
57 7 0.10
58 57 0.83
59 3 0.04
60 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.44
Consensus pattern (57 bp):
CTCAAATATGACCTTCATTTTAAATTAATCTCTAAATTTTTAATTTCAACTTCATTC
Found at i:23183 original size:23 final size:23
Alignment explanation
Indices: 23152--23196 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
23142 TCAGCTCATC
*
23152 TTTACCATCGCCGCCTGCCGTCG
1 TTTACCATCGCCGCCCGCCGTCG
*
23175 TTTATCATCGCCGCCCGCCGTC
1 TTTACCATCGCCGCCCGCCGTC
23197 TTCCGTCCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.44, G:0.20, T:0.27
Consensus pattern (23 bp):
TTTACCATCGCCGCCCGCCGTCG
Found at i:23220 original size:22 final size:22
Alignment explanation
Indices: 23192--23234 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
23182 TCGCCGCCCG
*
23192 CCGTCTTCCGTCCGTCTTCCGT
1 CCGTCTTCCGTCCGTCATCCGT
*
23214 CCGTCTTCCGTCTGTCATCCG
1 CCGTCTTCCGTCCGTCATCCG
23235 CTGTCTGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.02, C:0.44, G:0.19, T:0.35
Consensus pattern (22 bp):
CCGTCTTCCGTCCGTCATCCGT
Found at i:23234 original size:11 final size:11
Alignment explanation
Indices: 23192--23225 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
23182 TCGCCGCCCG
23192 CCGTCTTCCGT
1 CCGTCTTCCGT
23203 CCGTCTTCCGT
1 CCGTCTTCCGT
23214 CCGTCTTCCGT
1 CCGTCTTCCGT
23225 C
1 C
23226 TGTCATCCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.47, G:0.18, T:0.35
Consensus pattern (11 bp):
CCGTCTTCCGT
Found at i:26480 original size:17 final size:17
Alignment explanation
Indices: 26460--26494 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
26450 CCTAATATAT
*
26460 ATATTAAACTAAACCTA
1 ATATTAAAATAAACCTA
26477 ATATTAAAATAAACCTA
1 ATATTAAAATAAACCTA
26494 A
1 A
26495 CTACAAACAT
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:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (17 bp):
ATATTAAAATAAACCTA
Found at i:28461 original size:18 final size:18
Alignment explanation
Indices: 28438--28479 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
28428 TTATGTGTAC
28438 TTGTTTTCTAGTTATATT
1 TTGTTTTCTAGTTATATT
28456 TTGTTTTCTAGTTATATT
1 TTGTTTTCTAGTTATATT
28474 TTGTTT
1 TTGTTT
28480 CCTACGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.05, G:0.12, T:0.69
Consensus pattern (18 bp):
TTGTTTTCTAGTTATATT
Found at i:29975 original size:16 final size:16
Alignment explanation
Indices: 29946--29986 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
29936 CAGACTTGTT
29946 TGTTTTCT--ACAGTC
1 TGTTTTCTACACAGTC
29960 TGTTTTCTACACAGTC
1 TGTTTTCTACACAGTC
29976 TGTTTTCTACA
1 TGTTTTCTACA
29987 TGGTATCAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.32
16 17 0.68
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (16 bp):
TGTTTTCTACACAGTC
Found at i:31805 original size:51 final size:51
Alignment explanation
Indices: 31729--31830 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
31719 TCAGGGGGAG
* *
31729 AGTTATAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTATT
31780 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTATT
31831 CTTTCCTTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTATT
Found at i:34061 original size:14 final size:14
Alignment explanation
Indices: 34042--34069 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34032 AATAGACTTG
34042 TCTGTTTTCTACAA
1 TCTGTTTTCTACAA
34056 TCTGTTTTCTACAA
1 TCTGTTTTCTACAA
34070 AATTGTTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
TCTGTTTTCTACAA
Found at i:35004 original size:42 final size:42
Alignment explanation
Indices: 34945--35030 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
34935 TCTGCATGTG
34945 CCATGCACATCCCCAACACCCCAACAAAGGTCGCCATGCACT
1 CCATGCACATCCCCAACACCCCAACAAAGGTCGCCATGCACT
* *
34987 CCATGCACGTCCCCAACACCCCAACACAGGTCGCCATGCACT
1 CCATGCACATCCCCAACACCCCAACAAAGGTCGCCATGCACT
35029 CC
1 CC
35031 CAGCAACCTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.48, G:0.13, T:0.12
Consensus pattern (42 bp):
CCATGCACATCCCCAACACCCCAACAAAGGTCGCCATGCACT
Found at i:36760 original size:24 final size:24
Alignment explanation
Indices: 36731--36784 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
36721 AATGGTTCAG
*
36731 GGCGCATAAATCTTTATTGCCTCA
1 GGCGCATAAACCTTTATTGCCTCA
36755 GGCGCATAAACCTTTATTGCCTCA
1 GGCGCATAAACCTTTATTGCCTCA
36779 GGCGCA
1 GGCGCA
36785 AGGCACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (24 bp):
GGCGCATAAACCTTTATTGCCTCA
Found at i:40128 original size:17 final size:17
Alignment explanation
Indices: 40106--40144 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
40096 CACTGTTTTG
40106 TCATTTAAATATCTATT
1 TCATTTAAATATCTATT
40123 TCATTTAAATATCTATT
1 TCATTTAAATATCTATT
40140 TCATT
1 TCATT
40145 GATGAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (17 bp):
TCATTTAAATATCTATT
Found at i:41347 original size:20 final size:20
Alignment explanation
Indices: 41322--41366 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41312 GTCATCCAAT
*
41322 TTTTTAAACCCCATACCGGA
1 TTTTTAAACCCCAGACCGGA
*
41342 TTTTTAAACCCCAGACTGGA
1 TTTTTAAACCCCAGACCGGA
41362 TTTTT
1 TTTTT
41367 TTTCAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:42168 original size:14 final size:14
Alignment explanation
Indices: 42149--42177 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42139 ATCGTTAAGA
42149 AACGGTTAATCGTT
1 AACGGTTAATCGTT
42163 AACGGTTAATCGTT
1 AACGGTTAATCGTT
42177 A
1 A
42178 TTAACTGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (14 bp):
AACGGTTAATCGTT
Found at i:60599 original size:16 final size:16
Alignment explanation
Indices: 60578--60635 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
60568 TTAATAAAAA
*
60578 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
60594 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
60610 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
60626 ACGAACATAA
1 ACGAACATAA
60636 TGTTGGAGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:60916 original size:12 final size:12
Alignment explanation
Indices: 60896--60955 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
60886 AGCTCAATTT
60896 TTTTAAGCTCGA
1 TTTTAAGCTCGA
*
60908 TTTTGAGCTCGA
1 TTTTAAGCTCGA
*
60920 -TTCAAGCTCGA
1 TTTTAAGCTCGA
*
60931 TTTTGAGCTCGA
1 TTTTAAGCTCGA
*
60943 -TTCAAGCTCGA
1 TTTTAAGCTCGA
60954 TT
1 TT
60956 GACCCAGTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 18 0.46
12 21 0.54
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (12 bp):
TTTTAAGCTCGA
Found at i:60929 original size:11 final size:11
Alignment explanation
Indices: 60913--60955 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
60903 CTCGATTTTG
60913 AGCTCGATTCA
1 AGCTCGATTCA
**
60924 AGCTCGATTTTG
1 AGCTCGA-TTCA
60936 AGCTCGATTCA
1 AGCTCGATTCA
60947 AGCTCGATT
1 AGCTCGATT
60956 GACCCAGTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:60930 original size:23 final size:23
Alignment explanation
Indices: 60900--60955 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
60890 CAATTTTTTT
60900 AAGCTCGATTTTGAGCTCGATTC
1 AAGCTCGATTTTGAGCTCGATTC
60923 AAGCTCGATTTTGAGCTCGATTC
1 AAGCTCGATTTTGAGCTCGATTC
60946 AAGCTCGATT
1 AAGCTCGATT
60956 GACCCAGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (23 bp):
AAGCTCGATTTTGAGCTCGATTC
Done.