Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004191.1 Hibiscus syriacus cultivar Beakdansim tig00009169_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: 85111
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:619 original size:15 final size:14
Alignment explanation
Indices: 594--634 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
584 AATTATAAAA
594 GGTTTAAGGTTTAG
1 GGTTTAAGGTTTAG
608 GGTTTAAAGGTTTAG
1 GGTTT-AAGGTTTAG
* *
623 GGGTTAGGGTTT
1 GGTTTAAGGTTT
635 GTATTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (14 bp):
GGTTTAAGGTTTAG
Found at i:619 original size:22 final size:22
Alignment explanation
Indices: 591--634 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
581 AATAATTATA
*
591 AAAGGTTTAAGGTTTAGGGTTT
1 AAAGGTTTAAGGGTTAGGGTTT
*
613 AAAGGTTTAGGGGTTAGGGTTT
1 AAAGGTTTAAGGGTTAGGGTTT
635 GTATTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (22 bp):
AAAGGTTTAAGGGTTAGGGTTT
Found at i:678 original size:21 final size:21
Alignment explanation
Indices: 638--677 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
628 AGGGTTTGTA
638 TTATATAAATTAATATAAAAT
1 TTATATAAATTAATATAAAAT
659 TTATATATAA-TAAT-TAAAA
1 TTATATA-AATTAATATAAAA
678 AAATAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 11 0.61
22 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTATATAAATTAATATAAAAT
Found at i:686 original size:20 final size:21
Alignment explanation
Indices: 640--717 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 21
630 GGTTTGTATT
* **
640 ATATAAATTAATATAAAATTTA
1 ATAT-AATAAATATAAAAAATA
*
662 TATATAATAATTA-AAAAAATA
1 -ATATAATAAATATAAAAAATA
*
683 ATAT-ATAAATATAAAATATA
1 ATATAATAAATATAAAAAATA
703 ATATATATATAATAT
1 ATATA-ATA-AATAT
718 CGGGCGGATA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 6 0.13
20 15 0.33
21 6 0.13
22 9 0.20
23 9 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAATAAATATAAAAAATA
Found at i:7801 original size:39 final size:39
Alignment explanation
Indices: 7747--7823 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
7737 ATTTAGCTGT
7747 ATATTACTTAATTCTCGAGTTCATTAAAGTTTCATAATA
1 ATATTACTTAATTCTCGAGTTCATTAAAGTTTCATAATA
7786 ATATTACTTAATTCTCGAGTTCATTAAAGTTTCATAAT
1 ATATTACTTAATTCTCGAGTTCATTAAAGTTTCATAAT
7824 TCTGTAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (39 bp):
ATATTACTTAATTCTCGAGTTCATTAAAGTTTCATAATA
Found at i:19250 original size:3 final size:3
Alignment explanation
Indices: 19242--19267 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19232 CCAAAAACCT
19242 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
19268 TACTATTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:24267 original size:6 final size:6
Alignment explanation
Indices: 24194--24266 Score: 92
Period size: 6 Copynumber: 11.8 Consensus size: 6
24184 GAAACAAGGT
* * *
24194 GTGTGC GTGTGT GTGTGCGC GTGTGC GTGCGC GTGTGC GTGCGC GTGTGC
1 GTGTGC GTGTGC GTGT--GC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
*
24244 GTGTGC GTGTGC GTGTGT GTGTG
1 GTGTGC GTGTGC GTGTGC GTGTG
24267 TTAGGTCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 53 0.91
8 5 0.09
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GTGTGC
Found at i:40016 original size:21 final size:21
Alignment explanation
Indices: 39974--40016 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39964 TTTCTGGGCT
* *
39974 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
39995 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
40016 A
1 A
40017 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:40112 original size:16 final size:17
Alignment explanation
Indices: 40087--40118 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
40077 CCCATATAAA
40087 AAAAAGAAAAGAAGAAG
1 AAAAAGAAAAGAAGAAG
40104 AAAAA-AAAAGAAGAA
1 AAAAAGAAAAGAAGAA
40119 AGACTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAGAAG
Found at i:46224 original size:4 final size:4
Alignment explanation
Indices: 46215--46239 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
46205 TATTTTCTGG
46215 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
46240 GTTTACACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:47673 original size:36 final size:36
Alignment explanation
Indices: 47616--47686 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
47606 CAGCAAGATT
*
47616 GTGCATTGGCATCTTGGTTGCTCGCATCAATTAGTA
1 GTGCATTGGCATCTTGATTGCTCGCATCAATTAGTA
*
47652 GTGCGTTGGCATCTTGATTGCTCGCATCAATTAGT
1 GTGCATTGGCATCTTGATTGCTCGCATCAATTAGT
47687 CCCTCCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (36 bp):
GTGCATTGGCATCTTGATTGCTCGCATCAATTAGTA
Found at i:48762 original size:36 final size:36
Alignment explanation
Indices: 48710--49001 Score: 343
Period size: 36 Copynumber: 8.0 Consensus size: 36
48700 AGAAATACAA
*
48710 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
*
48746 GAATGGAAGGAGGCATCGGCACTTCCGTTTCTGATTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTT-C----C-GATTCAAGTC
*
48788 GAACGGAATGAGGCATCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
* * *
48824 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
* * *
48860 GAACGGAAGGAAGCATCGGCACCTCCGAGTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
* * * *
48896 GAACGGAATGAGGCATCAGCCCTTCCGAGTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
* **
48932 GAATGGAAGGAGGCATCAACACTTCCGATTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
* * **
48968 GAACGGAATGAGGCGTC-GCACTTTTGATTCAAGT
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGT
49002 GTTCATTTTT
Statistics
Matches: 222, Mismatches: 28, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
35 14 0.06
36 172 0.77
37 2 0.01
41 2 0.01
42 32 0.14
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.20
Consensus pattern (36 bp):
GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
Found at i:49755 original size:18 final size:18
Alignment explanation
Indices: 49732--49771 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
49722 TTACTCAGCA
49732 TTTTAAACTTTTATTTAT
1 TTTTAAACTTTTATTTAT
*
49750 TTTT-AAGTTTTATTTAT
1 TTTTAAACTTTTATTTAT
49767 TTTTA
1 TTTTA
49772 TTTTTTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTAAACTTTTATTTAT
Found at i:55524 original size:2 final size:2
Alignment explanation
Indices: 55517--55541 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55507 GATTCTGGTG
55517 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 A
55542 GAAAAATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57267 original size:2 final size:2
Alignment explanation
Indices: 57260--57286 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57250 TGATTTTTCT
57260 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
57287 CACCTAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60945 original size:13 final size:13
Alignment explanation
Indices: 60927--60979 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
60917 CCGGCGAACA
60927 CTAAAATGTGTTT
1 CTAAAATGTGTTT
**
60940 CTAAAATGTGTCG
1 CTAAAATGTGTTT
* * *
60953 ATGACA-GTGTTT
1 CTAAAATGTGTTT
60965 CTAAAATGTGTTT
1 CTAAAATGTGTTT
60978 CT
1 CT
60980 CAAAGGTATG
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
12 7 0.24
13 22 0.76
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (13 bp):
CTAAAATGTGTTT
Found at i:63890 original size:23 final size:24
Alignment explanation
Indices: 63833--63890 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 24
63823 GATTTTATCA
*
63833 TAATTTTGTTTTATATATTTAAAT
1 TAATTTTATTTTATATATTTAAAT
* * *
63857 T-ATGTTATTTTATTTGTTT-AAT
1 TAATTTTATTTTATATATTTAAAT
*
63879 TAATTTTCTTTT
1 TAATTTTATTTT
63891 CTTTTCATGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 4 0.15
23 22 0.81
24 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (24 bp):
TAATTTTATTTTATATATTTAAAT
Found at i:73600 original size:3 final size:3
Alignment explanation
Indices: 73592--73640 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
73582 CTTTAAAAAT
73592 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
73640 T
1 T
73641 GTGTCATCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:75044 original size:2 final size:2
Alignment explanation
Indices: 75037--75119 Score: 110
Period size: 2 Copynumber: 45.5 Consensus size: 2
75027 GATTTCGTCA
75037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75075 AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75113 AT AT AT A
1 AT AT AT A
75120 ATGGGACTTG
Statistics
Matches: 73, Mismatches: 0, Indels: 16
0.82 0.00 0.18
Matches are distributed among these distances:
1 8 0.11
2 65 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:75084 original size:32 final size:32
Alignment explanation
Indices: 75043--75119 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
75033 GTCAATATAT
75043 ATATATATATATATATATATATATAATTATTA
1 ATATATATATATATATATATATATAATTATTA
75075 ATATATATATATATATATATATATAATTATTA
1 ATATATATATATATATATATATATAATTATTA
75107 ATATATATATATA
1 ATATATATATATA
75120 ATGGGACTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
ATATATATATATATATATATATATAATTATTA
Found at i:77089 original size:22 final size:20
Alignment explanation
Indices: 77049--77092 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
77039 TTGATTCATG
*
77049 TAAAAATAAATATTTAAATT
1 TAAAAATAAAAATTTAAATT
77069 TAAAAATATAAAATTTAAAATT
1 TAAAAATA-AAAATTT-AAATT
77091 TA
1 TA
77093 TTAAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 6 0.29
22 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAAATAAAAATTTAAATT
Found at i:79226 original size:15 final size:17
Alignment explanation
Indices: 79193--79226 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
79183 CGTATCCAAT
79193 AGTTCCAGATTATTAGA
1 AGTTCCAGATTATTAGA
79210 AGTTCCA-ATTA-TAGA
1 AGTTCCAGATTATTAGA
79225 AG
1 AG
79227 CTTCTTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (17 bp):
AGTTCCAGATTATTAGA
Done.