Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008217.1 Hibiscus syriacus cultivar Beakdansim tig00110847_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: 2417150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2391076 original size:18 final size:18
Alignment explanation
Indices: 2391028--2391076 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
2391018 ATTATAAGTA
* *
2391028 GTCCTTCGTGACATAGTG
1 GTCCTTCGAGATATAGTG
*
2391046 GTCCTCCGAGATATAGTG
1 GTCCTTCGAGATATAGTG
*
2391064 GTCCTTCGGGATA
1 GTCCTTCGAGATA
2391077 AATTTTTAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (18 bp):
GTCCTTCGAGATATAGTG
Found at i:2392134 original size:32 final size:32
Alignment explanation
Indices: 2392093--2392176 Score: 125
Period size: 32 Copynumber: 2.6 Consensus size: 32
2392083 TGTAGGTTGT
*
2392093 AACCATATTTTAGGTT-AGAACTTGTTTAGTGC
1 AACCATATTTTAGGTTGA-AACTTGTTTAATGC
*
2392125 AACCATATTTTAGGTTGAAACTTTTTTAATGC
1 AACCATATTTTAGGTTGAAACTTGTTTAATGC
*
2392157 AACCATTTTTTAGGTTGAAA
1 AACCATATTTTAGGTTGAAA
2392177 TCTGAATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
32 47 0.98
33 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (32 bp):
AACCATATTTTAGGTTGAAACTTGTTTAATGC
Found at i:2392351 original size:40 final size:40
Alignment explanation
Indices: 2392302--2392429 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 40
2392292 TATGAGGTAT
* * *
2392302 ACACGTAAATATGAAAACGGTGATGTATCGTACGTGGTAC
1 ACACCTAAATATGAAAGCGGTGATGTATCGTACGTGATAC
** *
2392342 ACACCTAAATATGAAAGCGAAGATGTATCGTACGTAATAC
1 ACACCTAAATATGAAAGCGGTGATGTATCGTACGTGATAC
* * * * ** *
2392382 ACATCAAAATATGATAGCGGTGATCTATTATACGAGATAC
1 ACACCTAAATATGAAAGCGGTGATGTATCGTACGTGATAC
2392422 ACACCTAA
1 ACACCTAA
2392430 CTACACGCAA
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (40 bp):
ACACCTAAATATGAAAGCGGTGATGTATCGTACGTGATAC
Found at i:2392447 original size:80 final size:79
Alignment explanation
Indices: 2392379--2392529 Score: 203
Period size: 80 Copynumber: 1.9 Consensus size: 79
2392369 TCGTACGTAA
* * * * *
2392379 TACACATCAAAATATGATAGCGGTGATCTATTATACGAGATACACACCTAACTACACGCAAGATG
1 TACACATCAAAATATGAAAGCAGTAATCTATTATACGAGATACACACCCAACTACAAGCAAGATG
2392444 ATGTATCATACAAGG
66 ATGTATCATACAA-G
* * * * *
2392459 TACACATCTAAATATGAAAGCAGTAATGTATTGTATGGGATACACACCCAACTACAAGCAAGATG
1 TACACATCAAAATATGAAAGCAGTAATCTATTATACGAGATACACACCCAACTACAAGCAAGATG
2392524 ATGTAT
66 ATGTAT
2392530 GTAACATCCC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (79 bp):
TACACATCAAAATATGAAAGCAGTAATCTATTATACGAGATACACACCCAACTACAAGCAAGATG
ATGTATCATACAAG
Found at i:2394592 original size:40 final size:40
Alignment explanation
Indices: 2394548--2394783 Score: 160
Period size: 40 Copynumber: 5.9 Consensus size: 40
2394538 TATCTCACGA
*
2394548 GGTACACATCTAAATATAAAAGTGTTGATGTATTGTACGG
1 GGTACACATCTAAATATAAAAGTGATGATGTATTGTACGG
** *
2394588 GGTACACATCTAAATATGAAAACAG-TGATGTATTGTATGG
1 GGTACACATCTAAATAT-AAAAGTGATGATGTATTGTACGG
* * * ** * **
2394628 GATACACACCCAGCTACAAGTAA-T-ATGATGTATCATACGG
1 GGTACACATCTAAATATAA--AAGTGATGATGTATTGTACGG
* * * * *
2394668 GGTACACATTTAAATATGAAAGTGGTAATGTATTGTACTG
1 GGTACACATCTAAATATAAAAGTGATGATGTATTGTACGG
* * * *
2394708 GATACACA-CTCAACTATAGCAA-T-ATGATGTATCGTACGG
1 GGTACACATCT-AAATATA-AAAGTGATGATGTATTGTACGG
* * * *
2394747 GGTACATATCTAAATATGAAAGTGGTGATGTTTTGTA
1 GGTACACATCTAAATATAAAAGTGATGATGTATTGTA
2394784 AATGATACAC
Statistics
Matches: 142, Mismatches: 43, Indels: 22
0.69 0.21 0.11
Matches are distributed among these distances:
38 4 0.03
39 28 0.20
40 101 0.71
41 9 0.06
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (40 bp):
GGTACACATCTAAATATAAAAGTGATGATGTATTGTACGG
Found at i:2394668 original size:80 final size:79
Alignment explanation
Indices: 2394573--2394825 Score: 267
Period size: 80 Copynumber: 3.2 Consensus size: 79
2394563 ATAAAAGTGT
* *
2394573 TGATGTATTGTACGGGGTACACATCTAAATATGAAAACAGTGATGTATTGTA-TGGGATACACAC
1 TGATGTATCGTACGGGGTACACATCTAAATATGAAAACAGTAATGTATTGTACT-GGATACACAC
* *
2394637 CCAGCTACAAGTAATA
65 CCAACTA-AAGCAATA
* * *** *
2394653 TGATGTATCATACGGGGTACACATTTAAATATGAAAGTGGTAATGTATTGTACTGGATACACACT
1 TGATGTATCGTACGGGGTACACATCTAAATATGAAAACAGTAATGTATTGTACTGGATACACACC
*
2394718 CAACTATAGCAATA
66 CAACTAAAGCAATA
* *** * * *
2394732 TGATGTATCGTACGGGGTACATATCTAAATATGAAAGTGGTGATGTTTTGTAAAT-GATACACAC
1 TGATGTATCGTACGGGGTACACATCTAAATATGAAAACAGTAATGTATTGT-ACTGGATACACAC
* **
2394796 CCAATTATAAGCAAGG
65 CCAACTA-AAGCAATA
2394812 TGATGTATCGTACG
1 TGATGTATCGTACG
2394826 AAGTACAAAT
Statistics
Matches: 148, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
79 66 0.45
80 81 0.55
81 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (79 bp):
TGATGTATCGTACGGGGTACACATCTAAATATGAAAACAGTAATGTATTGTACTGGATACACACC
CAACTAAAGCAATA
Found at i:2396507 original size:31 final size:31
Alignment explanation
Indices: 2396449--2396507 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2396439 TTTGTTTCAT
* * *
2396449 TTTAGTACCCGATGTTATAAAACTTAACTCG
1 TTTAGTACCCGACGATAAAAAACTTAACTCG
*
2396480 TTTAGTACCCGACGATAAAAAATTTAAC
1 TTTAGTACCCGACGATAAAAAACTTAAC
2396508 GCTTAGTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (31 bp):
TTTAGTACCCGACGATAAAAAACTTAACTCG
Found at i:2405618 original size:60 final size:59
Alignment explanation
Indices: 2405495--2405663 Score: 171
Period size: 60 Copynumber: 2.8 Consensus size: 59
2405485 TCCTTCAACT
* * *
2405495 ATGATCCTT-ATTCTAAATTGGTCCCAAAACTTTTAAATATTCCAATTTAATCCATAAACC
1 ATGAT-CTTCATTCTAAATTGGTCCC-AAACTTTTAAATATTCCAATTTAATCAACAAAAC
* * ** * *
2405555 ATGA-CTATCATTCTAAATTAGTCCTCAAACTTTTGAATATTTTATTTTCATCAACAAAAC
1 ATGATCT-TCATTCTAAATTGGTCC-CAAACTTTTAAATATTCCAATTTAATCAACAAAAC
* *
2405615 ATGATCTTCATTCTAAATTGGTCCCCAAACTTTTTAAACATTTCAATTT
1 ATGATCTTCATTCTAAATTGGT-CCCAAAC-TTTTAAATATTCCAATTT
2405664 CATCCCAAAT
Statistics
Matches: 89, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 67 0.75
61 19 0.21
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (59 bp):
ATGATCTTCATTCTAAATTGGTCCCAAACTTTTAAATATTCCAATTTAATCAACAAAAC
Found at i:2405920 original size:3 final size:3
Alignment explanation
Indices: 2405912--2405941 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2405902 CTCGAAAGCT
2405912 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2405942 ACGTTGGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2409113 original size:22 final size:22
Alignment explanation
Indices: 2409088--2409129 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2409078 TTCTGGTATT
*
2409088 GGATT-AAATGGTAATTATGGAA
1 GGATTGAAAGGGTAA-TATGGAA
2409110 GGATTGAAAGGGTAATATGG
1 GGATTGAAAGGGTAATATGG
2409130 TAATTTAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (22 bp):
GGATTGAAAGGGTAATATGGAA
Found at i:2409949 original size:26 final size:26
Alignment explanation
Indices: 2409910--2409981 Score: 117
Period size: 26 Copynumber: 2.8 Consensus size: 26
2409900 TCGAGGGTTT
* *
2409910 TATGTGGTCATTCGGGACATGTGTTC
1 TATGTGGTCCTTCGGGACATGTGCTC
*
2409936 TATGTGGTCCTTCGAGACATGTGCTC
1 TATGTGGTCCTTCGGGACATGTGCTC
2409962 TATGTGGTCCTTCGGGACAT
1 TATGTGGTCCTTCGGGACAT
2409982 AGTGGTCCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.15, C:0.19, G:0.29, T:0.36
Consensus pattern (26 bp):
TATGTGGTCCTTCGGGACATGTGCTC
Found at i:2411046 original size:60 final size:59
Alignment explanation
Indices: 2410953--2411110 Score: 147
Period size: 60 Copynumber: 2.7 Consensus size: 59
2410943 TGGAAGATTA
** * * ** *
2410953 AAAAGTTTGGGGACCAATTTAGAATGGGAGTCATAGTTTAAAGATGAAATTATAAAT-TTC
1 AAAAGTTTAAGGACTAATTTAAAATGAAAGTCATAGTTTAAAGATGAAA-T-GAAATGTTC
* * *** *
2411013 AAAAGTTTAAGTACTAATTTATAATGAAAGTCATAGTTTGGGGATGAAATGAAATGTTT
1 AAAAGTTTAAGGACTAATTTAAAATGAAAGTCATAGTTTAAAGATGAAATGAAATGTTC
* **
2411072 AAAAGTTTAAGGATTAATTTAAAATGAGGGTCATAGTTT
1 AAAAGTTTAAGGACTAATTTAAAATGAAAGTCATAGTTT
2411111 GGGGATATAT
Statistics
Matches: 80, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
58 4 0.05
59 37 0.46
60 39 0.49
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (59 bp):
AAAAGTTTAAGGACTAATTTAAAATGAAAGTCATAGTTTAAAGATGAAATGAAATGTTC
Found at i:2414672 original size:32 final size:31
Alignment explanation
Indices: 2414636--2414704 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
2414626 TATTTGAAAG
*
2414636 TACTACTGGTACTGTGCATTACCTAAATATAA
1 TACTACT-CTACTGTGCATTACCTAAATATAA
* * *
2414668 TACTAACTCTACTGTGCATTAGCTGAATGTAA
1 TACT-ACTCTACTGTGCATTACCTAAATATAA
2414700 TACTA
1 TACTA
2414705 ATACTACTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 1 0.03
32 28 0.88
33 3 0.09
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (31 bp):
TACTACTCTACTGTGCATTACCTAAATATAA
Found at i:2414712 original size:32 final size:32
Alignment explanation
Indices: 2414645--2414705 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2414635 GTACTACTGG
2414645 TACTGTGCATTACCTAAATATAATACTAACTC
1 TACTGTGCATTACCTAAATATAATACTAACTC
* * *
2414677 TACTGTGCATTAGCTGAATGTAATACTAA
1 TACTGTGCATTACCTAAATATAATACTAA
2414706 TACTACTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (32 bp):
TACTGTGCATTACCTAAATATAATACTAACTC
Found at i:2415919 original size:21 final size:21
Alignment explanation
Indices: 2415890--2415949 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
2415880 ATACTATAGG
*
2415890 GGCAATATCGATACTCTCTCT
1 GGCAGTATCGATACTCTCTCT
2415911 GGCAGTATCGATACTCTCTCT
1 GGCAGTATCGATACTCTCTCT
2415932 GGCAGTATCGATACTCTC
1 GGCAGTATCGATACTCTC
2415950 AGTATGAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (21 bp):
GGCAGTATCGATACTCTCTCT
Done.