Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001971.1 Hibiscus syriacus cultivar Beakdansim tig00003982_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: 73901
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:493 original size:26 final size:26
Alignment explanation
Indices: 464--513 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
454 AAATATTAAT
*
464 ATATATTAATAATTTAT-TTTAAAAAA
1 ATATATT-ATAATATATATTTAAAAAA
*
490 ATATATTTTAATATATATTTAAAA
1 ATATATTATAATATATATTTAAAA
514 TTGTTCACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATATATTATAATATATATTTAAAAAA
Found at i:5063 original size:19 final size:19
Alignment explanation
Indices: 5039--5079 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
5029 CACAACCACT
5039 GCATCAAATCAATCACCCA
1 GCATCAAATCAATCACCCA
5058 GCATCAAATCAATCACCCA
1 GCATCAAATCAATCACCCA
5077 GCA
1 GCA
5080 AGAATAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.37, G:0.07, T:0.15
Consensus pattern (19 bp):
GCATCAAATCAATCACCCA
Found at i:12517 original size:30 final size:31
Alignment explanation
Indices: 12459--12518 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
12449 GATCTTAAAA
*
12459 AAAATTAAAAGTTCAGATACTAAAACATATC
1 AAAATTAAAAGTTAAGATACTAAAACATATC
*
12490 AAAATTAATAGTTTAAG-TACT-AAACATAT
1 AAAATTAAAAG-TTAAGATACTAAAACATAT
12519 AAATTACCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 14 0.54
32 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (31 bp):
AAAATTAAAAGTTAAGATACTAAAACATATC
Found at i:25882 original size:25 final size:24
Alignment explanation
Indices: 25828--25879 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
25818 ACATATGATA
25828 TAATTAACTATAAAAATTAATTAAT
1 TAATTAACTATAAAAA-TAATTAAT
* *
25853 TAATTAATTATAAATAA-AATTATT
1 TAATTAACTATAAA-AATAATTAAT
25877 TAA
1 TAA
25880 ATTCCAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 13 0.54
26 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATTAACTATAAAAATAATTAAT
Found at i:27002 original size:2 final size:2
Alignment explanation
Indices: 26995--27021 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26985 TAGACCGTAA
26995 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
27022 AATAGGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28607 original size:121 final size:121
Alignment explanation
Indices: 28393--28629 Score: 438
Period size: 121 Copynumber: 2.0 Consensus size: 121
28383 TGCAAAAGGT
* *
28393 AAGAAGCCAATGCAATAATTGTTGACAGATTTCTGTGTAGAACCGAACCCTCACAACTTTATTTA
1 AAGAAGCCAAAGCAATAATTGTTGACAGATTTCTGTGTAGAACCGAACCCTAACAACTTTATTTA
*
28458 TTCTTGTTTCCTTAGTTAATGAACAAGATGGACTGTAGAGGCTAGTTAGCTAATGG
66 TGCTTGTTTCCTTAGTTAATGAACAAGATGGACTGTAGAGGCTAGTTAGCTAATGG
28514 AAGAAGCCAAAGCAATAATTGTTGACAGATTTCTGTGTAGAACCGAACCCTAACAACTTTATTTA
1 AAGAAGCCAAAGCAATAATTGTTGACAGATTTCTGTGTAGAACCGAACCCTAACAACTTTATTTA
*
28579 TGCTTGTTTCCTTAGTTAATGAACAAGATGGATTGTAGAGGCTAGTTAGCT
66 TGCTTGTTTCCTTAGTTAATGAACAAGATGGACTGTAGAGGCTAGTTAGCT
28630 GGTGCAGCAA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 112 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (121 bp):
AAGAAGCCAAAGCAATAATTGTTGACAGATTTCTGTGTAGAACCGAACCCTAACAACTTTATTTA
TGCTTGTTTCCTTAGTTAATGAACAAGATGGACTGTAGAGGCTAGTTAGCTAATGG
Found at i:32613 original size:3 final size:3
Alignment explanation
Indices: 32605--32642 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
32595 TTTTTATCTT
32605 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TT
32643 TTCATCTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:32649 original size:15 final size:15
Alignment explanation
Indices: 32598--32651 Score: 67
Period size: 15 Copynumber: 3.5 Consensus size: 15
32588 TTTTTCTTTT
32598 TTATCTTTTATTATTA
1 TTATC-TTTATTATTA
32614 TTAT-TATTATTATTA
1 TTATCT-TTATTATTA
32629 TTATCTTTATTATT-
1 TTATCTTTATTATTA
32643 TTCATCTTT
1 TT-ATCTTT
32652 CTTTTTGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.09
15 27 0.77
16 5 0.14
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATCTTTATTATTA
Found at i:35122 original size:30 final size:32
Alignment explanation
Indices: 35069--35146 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
35059 TATTGAAAAT
*
35069 TTAAAATTATTA-TATATTTTATATA-TTTTTA
1 TTAAAATT-TTATTTTATTTTATATATTTTTTA
35100 TTAAAATTTTATTTTA-TTTATATATTTTTTA
1 TTAAAATTTTATTTTATTTTATATATTTTTTA
35131 TTAAAAATTTTATTTT
1 TT-AAAATTTTATTTT
35147 CATCTTTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
30 11 0.26
31 19 0.44
32 13 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TTAAAATTTTATTTTATTTTATATATTTTTTA
Found at i:43495 original size:2 final size:2
Alignment explanation
Indices: 43488--43523 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
43478 TTCAGTATTA
43488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43524 CAATTCCGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44913 original size:75 final size:74
Alignment explanation
Indices: 44776--44924 Score: 187
Period size: 75 Copynumber: 2.0 Consensus size: 74
44766 GGCAAGCATA
* * * *
44776 AATAAAATTTTAGGTTGAAACTATCAATAAAATGAGTCATTAATCGAAGAAAATTGAGATTTCAA
1 AATAAAATTTTAGGATGAAACTATCAATAAAATAAATCATTAATCGAAGAAAATCGAGATTTC-A
44841 GG-TGGACAC
65 GGATGGACAC
* *
44850 AATAAAATTTTAGGAT-ATACATCATCAATAAAATAAATGATTAATCGAAGAAAATCCGA-ATTT
1 AATAAAATTTTAGGATGAAAC-T-ATCAATAAAATAAATCATTAATCGAAGAAAAT-CGAGATTT
44913 CAGGATGGACAC
63 CAGGATGGACAC
44925 GTGTTTACGC
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
73 3 0.05
74 19 0.29
75 41 0.63
76 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (74 bp):
AATAAAATTTTAGGATGAAACTATCAATAAAATAAATCATTAATCGAAGAAAATCGAGATTTCAG
GATGGACAC
Found at i:46831 original size:17 final size:18
Alignment explanation
Indices: 46811--46846 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46801 TTAATTAATA
*
46811 ATTTTT-ATTAAAAAAAT
1 ATTTTTGATAAAAAAAAT
46828 ATTTTTGATAAAAAAAAT
1 ATTTTTGATAAAAAAAAT
46846 A
1 A
46847 ACGGTTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTTTTGATAAAAAAAAT
Found at i:46833 original size:18 final size:18
Alignment explanation
Indices: 46807--46847 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
46797 ATTGTTAATT
* *
46807 AATAATTTTTATTAAAAA
1 AATAATTTTGATAAAAAA
*
46825 AATATTTTTGATAAAAAA
1 AATAATTTTGATAAAAAA
46843 AATAA
1 AATAA
46848 CGGTTAAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AATAATTTTGATAAAAAA
Found at i:49989 original size:159 final size:160
Alignment explanation
Indices: 49696--49990 Score: 400
Period size: 159 Copynumber: 1.9 Consensus size: 160
49686 CCCGACAAAG
* * * * * *
49696 CATGGTAAATAATAGGGTATTAAATTAGACTAAAATTGATAGTTTTAGTAATTATATTTTTAATT
1 CATGGTAAATAATAGGGTACTAAATTAGACCAAAATCGATAATTTTAATAATTACATTTTTAATT
* * * * *
49761 TTAGTTCATTTTAATACTTAAATTTTTATTTTTAAAAATTATATTTACAATTTAATTTTTATTTT
66 TTAATCCATTTTAATACCTAAATTTTTATTTTTAAAAATTATACTTACAATTTAATTTTTATTTC
49826 ATTTTAGTGTTTTTGTTCAAAATGTAACAT
131 ATTTTAGTGTTTTTGTTCAAAATGTAACAT
*
49856 CATGGTAAATAATA-GGTACTAAATT-GAACCAAAATCGATAATTTTAATATTTACATTTTTAAT
1 CATGGTAAATAATAGGGTACTAAATTAG-ACCAAAATCGATAATTTTAATAATTACATTTTTAAT
* * *
49919 TTTAATCCGTTTTAATACCT-AATTTTTTTATTTTAAAAGTTATACTTA-AATTTTAATTTTTAT
65 TTTAATCCATTTTAATACCTAAATTTTTAT-TTTTAAAAATTATACTTACAA-TTTAATTTTTAT
49982 TTCATTTTA
128 TTCATTTTA
49991 ATTCTTCTAT
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
158 11 0.09
159 92 0.79
160 14 0.12
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.50
Consensus pattern (160 bp):
CATGGTAAATAATAGGGTACTAAATTAGACCAAAATCGATAATTTTAATAATTACATTTTTAATT
TTAATCCATTTTAATACCTAAATTTTTATTTTTAAAAATTATACTTACAATTTAATTTTTATTTC
ATTTTAGTGTTTTTGTTCAAAATGTAACAT
Found at i:58934 original size:60 final size:60
Alignment explanation
Indices: 58842--58998 Score: 171
Period size: 60 Copynumber: 2.6 Consensus size: 60
58832 GTATATGAGT
* * * * * *
58842 ATAGTTT-GGGATAAAATTGGAACGTTCAAAAAGTTTAGGGACCAATTTAGAATGA-AGGTC
1 ATAGTTTAGGGATGAAATTGAAACATT-TAAAAGTTTAAGGACCAATGTAGAATGATA-GTC
*
58902 ATAGTTT-GGGAATGAAATT-AAA-ATGATTAAAAGTTTAAGGACTAATGTAGAATGATAGTC
1 ATAGTTTAGGG-ATGAAATTGAAACAT--TTAAAAGTTTAAGGACCAATGTAGAATGATAGTC
58962 ATAGTTTAGGGATGAAATTGAAACATTTAAAAGTTTA
1 ATAGTTTAGGGATGAAATTGAAACATTTAAAAGTTTA
58999 TATACCAGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
59 1 0.01
60 65 0.78
61 15 0.18
62 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.31
Consensus pattern (60 bp):
ATAGTTTAGGGATGAAATTGAAACATTTAAAAGTTTAAGGACCAATGTAGAATGATAGTC
Found at i:60154 original size:40 final size:42
Alignment explanation
Indices: 60110--60187 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
60100 GATTTACATA
60110 TTCGCATTGCGATTT-TT-CAAATTCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
* *
60150 TTCGCGTTGCGATTTATTCCAAATTCGTTGTGATAGTC
1 TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTC
60188 CAAAATCGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 14 0.41
41 2 0.06
42 18 0.53
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (42 bp):
TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
Found at i:60178 original size:21 final size:21
Alignment explanation
Indices: 60116--60179 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
60106 CATATTCGCA
60116 TTGCGATTT-TT-CAAATTCG
1 TTGCGATTTATTCCAAATTCG
* * *
60135 TTGCGA--TAGTCGAAGTTCGCG
1 TTGCGATTTATTCCAAATT--CG
60156 TTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAATTCG
60177 TTG
1 TTG
60180 TGATAGTCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 1 0.03
18 1 0.03
19 10 0.30
21 13 0.39
23 8 0.24
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (21 bp):
TTGCGATTTATTCCAAATTCG
Found at i:60822 original size:6 final size:6
Alignment explanation
Indices: 60811--60841 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
60801 TCTCGGGTCG
*
60811 GGTAGT GGTAGT AGTAGT GGTAGT GGTAGT G
1 GGTAGT GGTAGT GGTAGT GGTAGT GGTAGT G
60842 CGTGTCTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.32
Consensus pattern (6 bp):
GGTAGT
Found at i:60947 original size:23 final size:21
Alignment explanation
Indices: 60921--61012 Score: 80
Period size: 21 Copynumber: 4.3 Consensus size: 21
60911 ACCAGTCGTT
60921 GCGAATTTGGAATAAATCGCAAC
1 GCGAATTTGGAAT--ATCGCAAC
* * *
60944 GCGAACTTCGACTATCGCAA-
1 GCGAATTTGGAATATCGCAAC
60964 -CGAATTTGGAATAAATCGCAAC
1 GCGAATTTGGAAT--ATCGCAAC
* * *
60986 GCGAACTTGGACTATCGCAAT
1 GCGAATTTGGAATATCGCAAC
61007 GCGAAT
1 GCGAAT
61013 ATGTAAATCG
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
19 9 0.16
21 26 0.47
23 20 0.36
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
GCGAATTTGGAATATCGCAAC
Found at i:60961 original size:21 final size:21
Alignment explanation
Indices: 60936--61011 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
60926 TTTGGAATAA
*
60936 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* *
60957 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
60976 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
*
60999 ATCGCAATGCGAA
1 ATCGCAACGCGAA
61012 TATGTAAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 9 0.20
21 26 0.58
23 10 0.22
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:60981 original size:42 final size:42
Alignment explanation
Indices: 60922--61005 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
60912 CCAGTCGTTG
60922 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
*
60964 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
61006 TGCGAATATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
Found at i:61049 original size:21 final size:21
Alignment explanation
Indices: 61020--61092 Score: 89
Period size: 21 Copynumber: 3.5 Consensus size: 21
61010 AATATGTAAA
61020 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
61041 TCGCGTTGCGA-A-TCACATA-T
1 TCGCATTGCGATAGTC-CA-AGT
61061 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
61082 TCGCGTTGCGA
1 TCGCATTGCGA
61093 ATCTGGAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.05
20 15 0.34
21 25 0.57
22 2 0.05
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:61051 original size:41 final size:41
Alignment explanation
Indices: 61018--61095 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
61008 CGAATATGTA
61018 AATCGCATTGCGATAGTCCAAGTTCGCGTTGCGAATCACAT
1 AATCGCATTGCGATAGTCCAAGTTCGCGTTGCGAATCACAT
*
61059 ATTCGCATTGCGATAGTCCAAGTTCGCGTTGCGAATC
1 AATCGCATTGCGATAGTCCAAGTTCGCGTTGCGAATC
61096 TGGAAACTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (41 bp):
AATCGCATTGCGATAGTCCAAGTTCGCGTTGCGAATCACAT
Found at i:72401 original size:15 final size:16
Alignment explanation
Indices: 72367--72401 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
72357 CTTCTAATTT
*
72367 TTTTTTGAGTTCAAGC
1 TTTTTCGAGTTCAAGC
72383 TTTTTCGAGTTCAAG-
1 TTTTTCGAGTTCAAGC
72398 TTTT
1 TTTT
72402 AATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (16 bp):
TTTTTCGAGTTCAAGC
Done.