Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003871.1 Hibiscus syriacus cultivar Beakdansim tig00008341_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: 53325
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:694 original size:37 final size:36
Alignment explanation
Indices: 652--853 Score: 172
Period size: 37 Copynumber: 5.6 Consensus size: 36
642 TGAAATGTTT
652 TTTTAAAAACTATATATTATACGTATTTTCAAAAACG
1 TTTTAAAAACTATATATTATAC-TATTTTCAAAAACG
*
689 TTTTAAAAACTATATA--ATA-TATTTTCAAAAATG
1 TTTTAAAAACTATATATTATACTATTTTCAAAAACG
*
722 TCTTTAAAAACTATATATTACA-TATATTTC--AAACG
1 T-TTTAAAAACTATATATTATACTAT-TTTCAAAAACG
* *
757 TTTTTTAAAAACTATATAATATATAAAC-GTTTTCAAAAATG
1 --TTTTAAAAACTATAT-AT-TAT--ACTATTTTCAAAAACG
* *
798 TTTTCAAAACTATATATTATA-TAAGTTTTC-AAAA-T
1 TTTTAAAAACTATATATTATACT-A-TTTTCAAAAACG
*
833 TTTTTAAAACTATATATTATA
1 TTTTAAAAACTATATATTATA
854 TGTGTTTTTT
Statistics
Matches: 139, Mismatches: 10, Indels: 34
0.76 0.05 0.19
Matches are distributed among these distances:
33 14 0.10
34 15 0.11
35 28 0.20
36 23 0.17
37 31 0.22
38 4 0.03
39 18 0.13
40 2 0.01
41 4 0.03
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATACTATTTTCAAAAACG
Found at i:790 original size:109 final size:106
Alignment explanation
Indices: 650--851 Score: 268
Period size: 109 Copynumber: 1.9 Consensus size: 106
640 TCTGAAATGT
650 TTTTTTAAAAACTATATATTATACGTATTTTCAAAAACGTTTTAAAAACTATATA-ATAT-A-TT
1 TTTTTTAAAAACTATATATTATACG-ATTTTCAAAAACGTTTTAAAAACTATATATATATAAGTT
712 TTCAAAAATGTCTTTAAAAACTATATATTACATATATTTCAAACG
65 TTC-AAAAT-T-TTTAAAAACTATATATTACATATATTTCAAACG
* *
757 TTTTTTAAAAACTATATAATATATAAACG-TTTTCAAAAATGTTTTCAAAACTATATATTATATA
1 TTTTTTAAAAACTATAT-AT-TAT--ACGATTTTCAAAAACGTTTTAAAAACTATATA-TATATA
*
821 AGTTTTCAAAATTTTTTAAAACTATATATTA
61 AGTTTTCAAAATTTTTAAAAACTATATATTA
852 TATGTGTTTT
Statistics
Matches: 84, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
107 17 0.20
108 2 0.02
109 29 0.35
110 17 0.20
111 8 0.10
112 6 0.07
113 5 0.06
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (106 bp):
TTTTTTAAAAACTATATATTATACGATTTTCAAAAACGTTTTAAAAACTATATATATATAAGTTT
TCAAAATTTTTAAAAACTATATATTACATATATTTCAAACG
Found at i:792 original size:39 final size:37
Alignment explanation
Indices: 650--854 Score: 178
Period size: 36 Copynumber: 5.6 Consensus size: 37
640 TCTGAAATGT
***
650 TTTTTTAAAAACTATATATTATACGTA-TTTTCAAAAA
1 TTTTTTAAAAACTATATATTATATAAAGTTTTC-AAAA
**
687 CGTTTTAAAAACTATATA--ATAT--A-TTTTCAAAAA
1 TTTTTTAAAAACTATATATTATATAAAGTTTTC-AAAA
* * * *
720 TGTCTTTAAAAACTATATATTACATATA--TTTCAAACG
1 T-TTTTTAAAAACTATATATTATATAAAGTTTTCAAA-A
*
757 TTTTTTAAAAACTATATAATATATAAACGTTTTCAAAAA
1 TTTTTTAAAAACTATATATTATATAAA-GTTTTC-AAAA
* *
796 TGTTTTCAAAACTATATATTATAT-AAGTTTTCAAAA
1 TTTTTTAAAAACTATATATTATATAAAGTTTTCAAAA
832 TTTTTT-AAAACTATATATTATAT
1 TTTTTTAAAAACTATATATTATAT
855 GTGTTTTTTT
Statistics
Matches: 141, Mismatches: 17, Indels: 22
0.78 0.09 0.12
Matches are distributed among these distances:
33 11 0.08
34 15 0.11
35 20 0.14
36 37 0.26
37 27 0.19
38 3 0.02
39 25 0.18
40 3 0.02
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTTTTAAAAACTATATATTATATAAAGTTTTCAAAA
Found at i:870 original size:75 final size:76
Alignment explanation
Indices: 710--854 Score: 208
Period size: 75 Copynumber: 1.9 Consensus size: 76
700 ATATAATATA
*
710 TTTTCAAAAATGTCTTTAAAAACTATATATTACATATATTTCAAACGTTTTTTAAAAACTATATA
1 TTTTCAAAAATGTCTTTAAAAACTATATATTACATATATTTCAAACATTTTTTAAAAACTATATA
775 ATATATAAACG
66 ATATATAAACG
* *
786 TTTTCAAAAATGT-TTTCAAAACTATATATTATATA-AGTTTTCAAA-ATTTTTT-AAAACTATA
1 TTTTCAAAAATGTCTTTAAAAACTATATATTACATATA--TTTCAAACATTTTTTAAAAACTATA
*
847 TATTATAT
64 TAATATAT
855 GTGTTTTTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
74 17 0.27
75 26 0.41
76 20 0.32
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.44
Consensus pattern (76 bp):
TTTTCAAAAATGTCTTTAAAAACTATATATTACATATATTTCAAACATTTTTTAAAAACTATATA
ATATATAAACG
Found at i:897 original size:2 final size:2
Alignment explanation
Indices: 890--920 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
880 CAAACTATTA
*
890 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
921 AAAATATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2390 original size:3 final size:3
Alignment explanation
Indices: 2382--2445 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
2372 TTGTGTTACA
2382 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2430 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
2446 GTATTTCCAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6619 original size:17 final size:17
Alignment explanation
Indices: 6597--6664 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 17
6587 TTATTATATA
6597 TATATTTTAAATATTTT
1 TATATTTTAAATATTTT
*
6614 TATATTTTAAAT-TTTA
1 TATATTTTAAATATTTT
* *
6630 AATATTTT-TATA-TTT
1 TATATTTTAAATATTTT
* *
6645 TAAATTTTAAACATTTT
1 TATATTTTAAATATTTT
6662 TAT
1 TAT
6665 TTAAAAAATC
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
15 10 0.26
16 12 0.31
17 17 0.44
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTTTAAATATTTT
Found at i:6673 original size:24 final size:24
Alignment explanation
Indices: 6600--6664 Score: 121
Period size: 24 Copynumber: 2.7 Consensus size: 24
6590 TTATATATAT
6600 ATTTTAAATATTTTTATATTTTAA
1 ATTTTAAATATTTTTATATTTTAA
6624 ATTTTAAATATTTTTATATTTTAA
1 ATTTTAAATATTTTTATATTTTAA
*
6648 ATTTTAAACATTTTTAT
1 ATTTTAAATATTTTTAT
6665 TTAAAAAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTAAATATTTTTATATTTTAA
Found at i:9016 original size:16 final size:16
Alignment explanation
Indices: 8995--9026 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8985 ATAAATAAAC
8995 GAACATAAACAAACAA
1 GAACATAAACAAACAA
*
9011 GAACATAAACGAACAA
1 GAACATAAACAAACAA
9027 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.19, G:0.09, T:0.06
Consensus pattern (16 bp):
GAACATAAACAAACAA
Found at i:9167 original size:23 final size:23
Alignment explanation
Indices: 9094--9167 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
9084 TTTAAATAAT
*
9094 AAACAAATATAAACGAACACGAAC
1 AAACGAATATAAACGAACAC-AAC
* * *
9118 GAACGAACATAAACGAACACAAT
1 AAACGAATATAAACGAACACAAC
9141 AAACGAATATAAACGAACA-ACAC
1 AAACGAATATAAACGAACACA-AC
9164 AAAC
1 AAAC
9168 AAAAAAAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.02
23 24 0.57
24 17 0.40
ACGTcount: A:0.61, C:0.22, G:0.09, T:0.08
Consensus pattern (23 bp):
AAACGAATATAAACGAACACAAC
Found at i:9440 original size:14 final size:14
Alignment explanation
Indices: 9421--9449 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9411 GTCTTCTGTT
9421 CGAACATAAATGAA
1 CGAACATAAATGAA
9435 CGAACATAAATGAA
1 CGAACATAAATGAA
9449 C
1 C
9450 AAATAAACAA
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:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:9465 original size:10 final size:10
Alignment explanation
Indices: 9452--9503 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
9442 AAATGAACAA
9452 ATAAACAAAC
1 ATAAACAAAC
9462 ATAAACAAAC
1 ATAAACAAAC
9472 ATAAACAAAC
1 ATAAACAAAC
9482 ATATAATCAAAC
1 ATA-AA-CAAAC
* *
9494 GTAAATAAAC
1 ATAAACAAAC
9504 GAACGAGCCC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 27 0.71
11 4 0.11
12 7 0.18
ACGTcount: A:0.65, C:0.17, G:0.02, T:0.15
Consensus pattern (10 bp):
ATAAACAAAC
Found at i:9476 original size:32 final size:32
Alignment explanation
Indices: 9437--9503 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
9427 TAAATGAACG
**
9437 AACATAAATGAACAAATAAACAAACATAAACA
1 AACATAAACAAACAAATAAACAAACATAAACA
* * * *
9469 AACATAAACAAACATATAATCAAACGTAAATA
1 AACATAAACAAACAAATAAACAAACATAAACA
9501 AAC
1 AAC
9504 GAACGAGCCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.66, C:0.16, G:0.03, T:0.15
Consensus pattern (32 bp):
AACATAAACAAACAAATAAACAAACATAAACA
Found at i:15300 original size:121 final size:123
Alignment explanation
Indices: 15083--15325 Score: 350
Period size: 121 Copynumber: 2.0 Consensus size: 123
15073 TGTAATGAGA
* * **
15083 ACAACTTTTACTATTTGCTTCATCATGGCTTGTAGCAATAATAGTGCTTGGCTTGCATTTCTTGA
1 ACAACTTTTACTATTT-CTTCATCATGGCTTGTAGCAACAATAATGCTTAACTTGCATTTCTTGA
**
15148 TCCATTATCATGAGTTACTATTCATCTTTGTTTTGGTGTTGTAGGGAATCTTGAATGCT
65 TCCATTATCATGAGTTACTATTCATCTTTGTTTTGGTGTTACAGGGAATCTTGAATGCT
* * *
15207 ACAACTTTTACTA-TT-TTCATCATGGCTTGTAGGAACAATAAT-TTTAAACTTGTATTTCTTGA
1 ACAACTTTTACTATTTCTTCATCATGGCTTGTAGCAACAATAATGCTT-AACTTGCATTTCTTGA
15269 TCCATTATCATGTA-TTACTATTCATCTTTGTTTTGGTGTTACAGGGAATCTTGAATG
65 TCCATTATCATG-AGTTACTATTCATCTTTGTTTTGGTGTTACAGGGAATCTTGAATG
15326 TTTTTCCACA
Statistics
Matches: 108, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
120 2 0.02
121 90 0.83
122 1 0.01
123 2 0.02
124 13 0.12
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.44
Consensus pattern (123 bp):
ACAACTTTTACTATTTCTTCATCATGGCTTGTAGCAACAATAATGCTTAACTTGCATTTCTTGAT
CCATTATCATGAGTTACTATTCATCTTTGTTTTGGTGTTACAGGGAATCTTGAATGCT
Found at i:27825 original size:23 final size:21
Alignment explanation
Indices: 27771--27854 Score: 73
Period size: 21 Copynumber: 3.9 Consensus size: 21
27761 TTTTGGTGCA
27771 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAATCGATTCCCCCCAT
* **
27791 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCAT
27812 GAAGGGGAATCGATTCCCCCCCA-
1 G-A-GGGAATCGATT-CCCCCCAT
* *
27835 CAGGGGAATCGATACCCCCC
1 GA-GGGAATCGATTCCCCCC
27855 TGGGGTTCTG
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 10 0.19
21 14 0.27
22 13 0.25
23 10 0.19
24 5 0.10
ACGTcount: A:0.24, C:0.36, G:0.25, T:0.15
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCAT
Found at i:32445 original size:20 final size:22
Alignment explanation
Indices: 32422--32502 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 22
32412 TTGGTGCAGA
*
32422 GGGAATCGAT-CCCCCCATGA-
1 GGGAACCGATACCCCCCATGAG
* **
32442 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCCCATG-AG
* *
32465 GGGAACCGATCCCCCCCA-CAG
1 GGGAACCGATACCCCCCATGAG
*
32486 GGGAATCGATACCCCCC
1 GGGAACCGATACCCCCC
32503 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.18
21 24 0.49
22 1 0.02
23 15 0.31
ACGTcount: A:0.23, C:0.38, G:0.25, T:0.14
Consensus pattern (22 bp):
GGGAACCGATACCCCCCATGAG
Found at i:36080 original size:216 final size:218
Alignment explanation
Indices: 35660--36090 Score: 706
Period size: 216 Copynumber: 2.0 Consensus size: 218
35650 GTAAGGTTAT
* * * *
35660 CTCTTTGGCCTCAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAAATCCTTAGTGTGGATAGCT
1 CTCTTTGGCCTCAAAAGAAAGAACAAATTAGTGAATTTGATGGAAAATCCTCAGTATGGATAACT
* *
35725 AAGGTAGTGGACGTAGACTTTGATTGAGAAAGTCGAACCACTCTAAATCGCTGTGCAAATCTTTT
66 AAGGTAGTGGACGTAGACTTTGATTGAGAAAGTCGAACCACTCTAAATCGCTGTGAAAATATTTT
* * *
35790 CAATTTTCTGCAAAAGCTTCCACCGAATTTTTAATTGCCAATTCACCCCCCTCTTGGCTAATTCC
131 CAATTTTCTGCAAAAGCTTCCACCGAAATTTTAATTGCCAATTCACCACCCTCTTGGCCAATTCC
35855 GTCGATCGATTAACTCAACATTA
196 GTCGATCGATTAACTCAACATTA
* *
35878 CTCTTTGTCCTCAAAAGAAAG-ACAAATTAGTGAATTT-ATGGAAAATTCTCAGTATGGATAACT
1 CTCTTTGGCCTCAAAAGAAAGAACAAATTAGTGAATTTGATGGAAAATCCTCAGTATGGATAACT
* *
35941 AAGGTAGTGGATGTAGACTTTGGTTGAGAAAGTCGAACCACTCTAAATCGCTGTGAAAATATTTT
66 AAGGTAGTGGACGTAGACTTTGATTGAGAAAGTCGAACCACTCTAAATCGCTGTGAAAATATTTT
36006 CAATTTTCTGCAAAAGCTTCCACCGAAATTTTAATTGCCAATTCACCACCCTCTTGGCCATATT-
131 CAATTTTCTGCAAAAGCTTCCACCGAAATTTTAATTGCCAATTCACCACCCTCTTGGCCA-ATTC
*
36070 CGTTGATCGATTAACTCAACA
195 CGTCGATCGATTAACTCAACA
36091 ATTGGTATCA
Statistics
Matches: 198, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
216 159 0.80
217 19 0.10
218 20 0.10
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (218 bp):
CTCTTTGGCCTCAAAAGAAAGAACAAATTAGTGAATTTGATGGAAAATCCTCAGTATGGATAACT
AAGGTAGTGGACGTAGACTTTGATTGAGAAAGTCGAACCACTCTAAATCGCTGTGAAAATATTTT
CAATTTTCTGCAAAAGCTTCCACCGAAATTTTAATTGCCAATTCACCACCCTCTTGGCCAATTCC
GTCGATCGATTAACTCAACATTA
Found at i:41949 original size:15 final size:15
Alignment explanation
Indices: 41929--41958 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41919 TAACAAAAAG
41929 GGGGAGAAGTGTTAA
1 GGGGAGAAGTGTTAA
41944 GGGGAGAAGTGTTAA
1 GGGGAGAAGTGTTAA
41959 AGTAAGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.47, T:0.20
Consensus pattern (15 bp):
GGGGAGAAGTGTTAA
Found at i:42370 original size:19 final size:19
Alignment explanation
Indices: 42346--42391 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
42336 TTTTGTGTAC
42346 CGATGCACATACTATGCAT
1 CGATGCACATACTATGCAT
42365 CGATGCACATACTATGCAT
1 CGATGCACATACTATGCAT
42384 CGATGCAC
1 CGATGCAC
42392 TCCATGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (19 bp):
CGATGCACATACTATGCAT
Found at i:48960 original size:22 final size:22
Alignment explanation
Indices: 48932--48973 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
48922 GCCATTTGGA
48932 AAATGCCATGTGATAATGTTCC
1 AAATGCCATGTGATAATGTTCC
48954 AAATGCCATGTGATAATGTT
1 AAATGCCATGTGATAATGTT
48974 GATATGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (22 bp):
AAATGCCATGTGATAATGTTCC
Done.