Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006377.1 Hibiscus syriacus cultivar Beakdansim tig00015342_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: 44607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:8345 original size:23 final size:24
Alignment explanation
Indices: 8282--8345 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
8272 AAACAAAAAG
8282 AAAGAAAAAGAA-G-AAAATGGAAA
1 AAAGAAAAA-AATGAAAAATGGAAA
*
8305 AAGGAAAAAAATGAAAAAT-GAAA
1 AAAGAAAAAAATGAAAAATGGAAA
*
8328 AAAGAGAAAAATGAAAAA
1 AAAGAAAAAAATGAAAAA
8346 AGAGAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.06
23 29 0.81
24 5 0.14
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAAATGAAAAATGGAAA
Found at i:8347 original size:16 final size:16
Alignment explanation
Indices: 8234--8352 Score: 84
Period size: 16 Copynumber: 7.2 Consensus size: 16
8224 AATAAAACGA
*
8234 AAAAATGAAAAACGA-
1 AAAAATGAAAAAAGAG
*
8249 AAAAATAATAAAAATGATGG
1 AAAAATGA-AAAAA-GA--G
** *
8269 AAAAAACAAAAAGAAAG
1 AAAAATGAAAAA-AGAG
8286 AAAAA-GAAGAAAATG-G
1 AAAAATGAA-AAAA-GAG
*
8302 AAAAAGGAAAAAA-ATG
1 AAAAATGAAAAAAGA-G
8318 AAAAATGAAAAAAGAG
1 AAAAATGAAAAAAGAG
8334 AAAAATGAAAAAAGAG
1 AAAAATGAAAAAAGAG
8350 AAA
1 AAA
8353 TAAAAGGAGG
Statistics
Matches: 84, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
15 7 0.08
16 50 0.60
17 15 0.18
19 5 0.06
20 7 0.08
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.08
Consensus pattern (16 bp):
AAAAATGAAAAAAGAG
Found at i:9728 original size:51 final size:51
Alignment explanation
Indices: 9667--9992 Score: 438
Period size: 51 Copynumber: 6.3 Consensus size: 51
9657 AAGCAAATTC
9667 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAA
*
9718 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAA
9769 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAA
* *
9820 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAA
* * * * * **
9871 GTTCGTTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCC
1 GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAA
* * * * * * *
9922 GTTTTATTAAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACAC
1 G-TTTGTTGAAGATTG----AGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAA
9978 GTTT-TATGAAGATTG
1 GTTTGT-TGAAGATTG
9993 TTCGAGTCTT
Statistics
Matches: 252, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
51 196 0.78
52 10 0.04
54 1 0.00
55 11 0.04
56 34 0.13
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (51 bp):
GTTTGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAA
Found at i:10043 original size:55 final size:54
Alignment explanation
Indices: 9681--10046 Score: 234
Period size: 51 Copynumber: 6.9 Consensus size: 54
9671 GTTGAAGATT
* * * *
9681 GAGTCCTATACTCTCTGAAAGAATAGGGAGC-GGACAAGTTTGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGG-CACGTTT-TTGAAGATTGTTC
* * * * *
9732 GAGTCCTATACTCTCTGAAAGAATAGGGAGCAGACAAGTTTGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTT-TTGAAGATTGTTC
* * * * *
9783 GAGTCCTATACTCTCTGAAAGAATAGGGAGC-GGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGG-CACGTT-TTTGAAGATTGTTC
* * * *
9834 GAGTCCTATACTCTCTGAAGGAATAGGGAGC-GGACAAGTTCGTTGAAGA----TC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGG-CACGTT-TTTGAAGATTGTTC
* *
9885 GAGTCTTATACTCTCTGAAGGAATAGAGAGC-GGACCCGTTTTATTAAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGG-CACG-TTT-TTGAAGATTGTTC
* * *
9941 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTTT-TGAAGATTGTTC
* * *
9996 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATTTGAAGATT
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAGGCACGT-TTTTGAAGATT
10047 TTTCAAGTAT
Statistics
Matches: 280, Mismatches: 21, Indels: 24
0.86 0.06 0.07
Matches are distributed among these distances:
50 2 0.01
51 176 0.63
52 9 0.03
54 2 0.01
55 54 0.19
56 36 0.13
57 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (54 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGGCACGTTTTTGAAGATTGTTC
Found at i:21065 original size:502 final size:502
Alignment explanation
Indices: 20123--21127 Score: 2010
Period size: 502 Copynumber: 2.0 Consensus size: 502
20113 ACCGAACTTG
20123 CTCGAAGAAGAGAACTTGAACTACAACCCGTAGAGGAAGTCTCTCGTTCTGTGCAGCATGCATAG
1 CTCGAAGAAGAGAACTTGAACTACAACCCGTAGAGGAAGTCTCTCGTTCTGTGCAGCATGCATAG
20188 ACGCATCCATTGTGAGCTTCTTGACATCCATCAGCCCACACATTTTCTTTCTTTCAGCCTTGGTC
66 ACGCATCCATTGTGAGCTTCTTGACATCCATCAGCCCACACATTTTCTTTCTTTCAGCCTTGGTC
20253 AAGTCCGGATGCCCCTGCAAACAAAATAAACCCGTTTTTACACAATCCGAATGACTTCGTCGGAA
131 AAGTCCGGATGCCCCTGCAAACAAAATAAACCCGTTTTTACACAATCCGAATGACTTCGTCGGAA
20318 AGGTTTCTGTTTCTCATTATATAATAGTGACAGGCATTATGAAAAACCAATAAATATCTGTATAA
196 AGGTTTCTGTTTCTCATTATATAATAGTGACAGGCATTATGAAAAACCAATAAATATCTGTATAA
20383 TTTTGTTGCTAGATGACTTGATAGCCGAAAAGCCTACCTTCAGGTAGATGTCAATGGCTTTATAG
261 TTTTGTTGCTAGATGACTTGATAGCCGAAAAGCCTACCTTCAGGTAGATGTCAATGGCTTTATAG
20448 AGTCCATCATGAACTGGTCTAGCTAACTCAGAGATAGACCGAGACAAGTCGATGAAACTGGCTAC
326 AGTCCATCATGAACTGGTCTAGCTAACTCAGAGATAGACCGAGACAAGTCGATGAAACTGGCTAC
20513 AGAAAGGTTTGGGTCGTATGCGATTTCTTGAAGATAACCATCGATCAGTTTACCAACGTATATCA
391 AGAAAGGTTTGGGTCGTATGCGATTTCTTGAAGATAACCATCGATCAGTTTACCAACGTATATCA
20578 AGGATCCATGCCCTAGCACATAACCGGTATGTCCCATCTCATTCTTT
456 AGGATCCATGCCCTAGCACATAACCGGTATGTCCCATCTCATTCTTT
20625 CTCGAAGAAGAGAACTTGAACTACAACCCGTAGAGGAAGTCTCTCGTTCTGTGCAGCATGCATAG
1 CTCGAAGAAGAGAACTTGAACTACAACCCGTAGAGGAAGTCTCTCGTTCTGTGCAGCATGCATAG
20690 ACGCATCCATTGTGAGCTTCTTGACATCCATCAGCCCACACATTTTCTTTCTTTCAGCCTTGGTC
66 ACGCATCCATTGTGAGCTTCTTGACATCCATCAGCCCACACATTTTCTTTCTTTCAGCCTTGGTC
20755 AAGTCCGGATGCCCCTGCAAACAAAATAAACCCGTTTTTACACAATCCGAATGACTTCGTCGGAA
131 AAGTCCGGATGCCCCTGCAAACAAAATAAACCCGTTTTTACACAATCCGAATGACTTCGTCGGAA
20820 AGGTTTCTGTTTCTCATTATATAATAGTGACAGGCATTATGAAAAACCAATAAATATCTGTATAA
196 AGGTTTCTGTTTCTCATTATATAATAGTGACAGGCATTATGAAAAACCAATAAATATCTGTATAA
20885 TTTTGTTGCTAGATGACTTGATAGCCGAAAAGCCTACCTTCAGGTAGATGTCAATGGCTTTATAG
261 TTTTGTTGCTAGATGACTTGATAGCCGAAAAGCCTACCTTCAGGTAGATGTCAATGGCTTTATAG
20950 AGTCCATCATGAACTGGTCTAGCTAACTCAGAGATAGACCGAGACAAGTCGATGAAACTGGCTAC
326 AGTCCATCATGAACTGGTCTAGCTAACTCAGAGATAGACCGAGACAAGTCGATGAAACTGGCTAC
21015 AGAAAGGTTTGGGTCGTATGCGATTTCTTGAAGATAACCATCGATCAGTTTACCAACGTATATCA
391 AGAAAGGTTTGGGTCGTATGCGATTTCTTGAAGATAACCATCGATCAGTTTACCAACGTATATCA
21080 AGGATCCATGCCCTAGCACATAACCGGTATGTCCCATCTCATTCTTT
456 AGGATCCATGCCCTAGCACATAACCGGTATGTCCCATCTCATTCTTT
21127 C
1 C
21128 CAAGCTCTAC
Statistics
Matches: 503, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
502 503 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (502 bp):
CTCGAAGAAGAGAACTTGAACTACAACCCGTAGAGGAAGTCTCTCGTTCTGTGCAGCATGCATAG
ACGCATCCATTGTGAGCTTCTTGACATCCATCAGCCCACACATTTTCTTTCTTTCAGCCTTGGTC
AAGTCCGGATGCCCCTGCAAACAAAATAAACCCGTTTTTACACAATCCGAATGACTTCGTCGGAA
AGGTTTCTGTTTCTCATTATATAATAGTGACAGGCATTATGAAAAACCAATAAATATCTGTATAA
TTTTGTTGCTAGATGACTTGATAGCCGAAAAGCCTACCTTCAGGTAGATGTCAATGGCTTTATAG
AGTCCATCATGAACTGGTCTAGCTAACTCAGAGATAGACCGAGACAAGTCGATGAAACTGGCTAC
AGAAAGGTTTGGGTCGTATGCGATTTCTTGAAGATAACCATCGATCAGTTTACCAACGTATATCA
AGGATCCATGCCCTAGCACATAACCGGTATGTCCCATCTCATTCTTT
Found at i:26016 original size:31 final size:29
Alignment explanation
Indices: 25981--26039 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 29
25971 AAATTACATA
25981 TTTAATACTTAAATTATTATTATTATTTTAT
1 TTTAATACTTAAATT-TTATTATT-TTTTAT
*
26012 TTTAATACTTAAGTTTTATTATTTTTTA
1 TTTAATACTTAAATTTTATTATTTTTTA
26040 ATCATACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.19
30 8 0.30
31 14 0.52
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTAATACTTAAATTTTATTATTTTTTAT
Found at i:29706 original size:13 final size:13
Alignment explanation
Indices: 29690--29715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29680 TGTCTAACAC
29690 CTAAGATTAATGA
1 CTAAGATTAATGA
29703 CTAAGATTAATGA
1 CTAAGATTAATGA
29716 AGGGGTTGAA
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
CTAAGATTAATGA
Found at i:30101 original size:36 final size:36
Alignment explanation
Indices: 29997--30102 Score: 94
Period size: 36 Copynumber: 2.9 Consensus size: 36
29987 TTTTACATTA
* *
29997 AAATTTAAACTGAATTTTAAATTAGATAAAAAAA-ATT
1 AAATTTAAA-TTAAATTTAAA-TAGATAAAAAAATATT
* *
30034 AAATTTAAATTAAA-TTGAATA-ACGTATAAAAATA-T
1 AAATTTAAATTAAATTTAAATAGA--TAAAAAAATATT
*
30069 AATATTTGAATTAAATTTAAATAGATAAAAAAAT
1 AA-ATTTAAATTAAATTTAAATAGATAAAAAAAT
30103 TCACCTGATC
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
33 1 0.02
34 2 0.04
35 14 0.25
36 23 0.41
37 15 0.27
38 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (36 bp):
AAATTTAAATTAAATTTAAATAGATAAAAAAATATT
Found at i:34728 original size:17 final size:17
Alignment explanation
Indices: 34706--34741 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
34696 AAAAATTCAA
*
34706 GAGCTCGATTGAAGCTC
1 GAGCTCGATTAAAGCTC
34723 GAGCTCGATTAAAGCTC
1 GAGCTCGATTAAAGCTC
34740 GA
1 GA
34742 ACTCAAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (17 bp):
GAGCTCGATTAAAGCTC
Found at i:34854 original size:29 final size:27
Alignment explanation
Indices: 34822--34875 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
34812 TCCCTCAATT
34822 ATTTAAATTTTAGCTTAAATTAGTCTCAC
1 ATTTAAATTTT--CTTAAATTAGTCTCAC
* *
34851 ATTTAGATTTTCTTAATTTAGTCTC
1 ATTTAAATTTTCTTAAATTAGTCTC
34876 TGTTTTATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 13 0.57
29 10 0.43
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (27 bp):
ATTTAAATTTTCTTAAATTAGTCTCAC
Found at i:35393 original size:12 final size:11
Alignment explanation
Indices: 35361--35396 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
35351 TATTCATCAA
*
35361 TAATGTATTTT
1 TAATATATTTT
35372 TAATATATTTT
1 TAATATATTTT
*
35383 TAATATAATTT
1 TAATATATTTT
35394 TAA
1 TAA
35397 AAATATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
TAATATATTTT
Found at i:35809 original size:16 final size:16
Alignment explanation
Indices: 35763--35816 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
35753 ATCTAAAAAA
*
35763 TCAGATATCCGAAAAT
1 TCAGATATCCGAAATT
* *
35779 TCGGATATCCAAAATT
1 TCAGATATCCGAAATT
35795 TCAGATATCCGAAATT
1 TCAGATATCCGAAATT
*
35811 TTAGAT
1 TCAGAT
35817 CAGATATCCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (16 bp):
TCAGATATCCGAAATT
Found at i:41926 original size:21 final size:21
Alignment explanation
Indices: 41889--41943 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
41879 ATTAGTGTAA
* *
41889 TATAATTTTATTTTTTTAGTTT
1 TATAATTTCA-TTTTTTACTTT
41911 TATAATTTCATTTTTTACTTT
1 TATAATTTCATTTTTTACTTT
41932 TATAATTTCATT
1 TATAATTTCATT
41944 AGTTAATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.67
Consensus pattern (21 bp):
TATAATTTCATTTTTTACTTT
Found at i:43594 original size:12 final size:12
Alignment explanation
Indices: 43577--43601 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43567 TTTTCAGATT
43577 CTCTTGCAGTTC
1 CTCTTGCAGTTC
43589 CTCTTGCAGTTC
1 CTCTTGCAGTTC
43601 C
1 C
43602 ACTCCAACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.36, G:0.16, T:0.40
Consensus pattern (12 bp):
CTCTTGCAGTTC
Done.