Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000616.1 Hibiscus syriacus cultivar Beakdansim tig00001194_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: 50946
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:3569 original size:22 final size:21
Alignment explanation
Indices: 3532--3573 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3522 ACTATTTTCA
3532 TATTTTATTTTTGTTTTGTTT
1 TATTTTATTTTTGTTTTGTTT
3553 TATTTT-TTTCTTCGTTTTGTT
1 TATTTTATTT-TT-GTTTTGTT
3574 CATGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.07, C:0.05, G:0.10, T:0.79
Consensus pattern (21 bp):
TATTTTATTTTTGTTTTGTTT
Found at i:8602 original size:21 final size:21
Alignment explanation
Indices: 8576--8644 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
8566 GGACCTACCA
8576 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTAATCTGTG
* *
8597 TCCCGAA-G--G--ACCTGTCA
1 TCCCGAAGGATGTAATCTGT-G
8614 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTAATCTGTG
*
8635 TCCCGTAGGA
1 TCCCGAAGGA
8645 CCTATCATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
16 5 0.14
17 7 0.19
18 2 0.05
20 2 0.05
21 16 0.43
22 5 0.14
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (21 bp):
TCCCGAAGGATGTAATCTGTG
Found at i:8608 original size:38 final size:38
Alignment explanation
Indices: 8557--8648 Score: 157
Period size: 38 Copynumber: 2.4 Consensus size: 38
8547 CTCGTACAAA
8557 TGTCCCGAAGGACCTACCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTACCATCCCGAAGGATGTAATCTG
**
8595 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTACCATCCCGAAGGATGTAATCTG
*
8633 TGTCCCGTAGGACCTA
1 TGTCCCGAAGGACCTA
8649 TCATATGTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (38 bp):
TGTCCCGAAGGACCTACCATCCCGAAGGATGTAATCTG
Found at i:8860 original size:46 final size:46
Alignment explanation
Indices: 8803--8907 Score: 185
Period size: 46 Copynumber: 2.3 Consensus size: 46
8793 ATGTGTAACC
8803 ATGT-ATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
8848 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
8894 ATATCATTTCATAT
1 ATGTCATTTCATAT
8908 AGTCACATAG
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 4 0.07
46 53 0.93
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
Found at i:12713 original size:2 final size:2
Alignment explanation
Indices: 12685--12772 Score: 141
Period size: 2 Copynumber: 46.5 Consensus size: 2
12675 TCAATCAAAT
12685 TA TA T- TA TA T- TA T- TA T- TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12764 TA TA TA TA T
1 TA TA TA TA T
12773 TCCAATGATA
Statistics
Matches: 81, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
1 5 0.06
2 76 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:14673 original size:3 final size:3
Alignment explanation
Indices: 14665--14691 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
14655 TATATTTCAA
14665 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
14692 CCCATGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:14818 original size:21 final size:21
Alignment explanation
Indices: 14792--14860 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
14782 TGACCTATCA
14792 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
14813 TCCCGAAGGA---C--CTGTCA
1 TCCCGAAGGATGTCATCTGT-G
*
14830 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
14851 TCCCGTAGGA
1 TCCCGAAGGA
14861 CCTATCATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.25
Consensus pattern (21 bp):
TCCCGAAGGATGTCATCTGTG
Found at i:14825 original size:38 final size:38
Alignment explanation
Indices: 14773--14868 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
14763 CTCGTACAAA
* *
14773 TGTCCCGAATGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
14811 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
14849 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
14869 ATGTCTTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:15075 original size:46 final size:46
Alignment explanation
Indices: 15018--15122 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
15008 GTGTGTAACC
15018 ATGT-ATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
* *
15063 ATGTCATTTCATATCATATCACATGTATCACTTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
15109 ATATCATTTCATAT
1 ATGTCATTTCATAT
15123 AGTCACATAG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 4 0.07
46 52 0.93
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
Found at i:15114 original size:22 final size:21
Alignment explanation
Indices: 15042--15114 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 21
15032 ATATCACATG
*
15042 TATCACGTATTACATATTCATA
1 TATCACTTATT-CATATTCATA
* * * *
15064 TGTCATTTCATATCATATCACATG
1 TATCACTT-AT-TCATAT-TCATA
15088 TATCACTTATTGCATATTCATA
1 TATCACTTATT-CATATTCATA
15110 TATCA
1 TATCA
15115 TTTCATATAG
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
22 14 0.37
23 14 0.37
24 10 0.26
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.42
Consensus pattern (21 bp):
TATCACTTATTCATATTCATA
Found at i:15564 original size:19 final size:20
Alignment explanation
Indices: 15527--15564 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15517 TTTTCCTTTA
*
15527 GGGGGAATCGATTCCCCCTG
1 GGGGGAATCGATTACCCCTG
15547 GGGGGAATCGA-TACCCCT
1 GGGGGAATCGATTACCCCT
15565 TAAACATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.18, C:0.29, G:0.34, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGATTACCCCTG
Found at i:25928 original size:5 final size:5
Alignment explanation
Indices: 25918--25964 Score: 62
Period size: 5 Copynumber: 9.4 Consensus size: 5
25908 ATCTACAAAA
25918 ATATT ATATT ATATT ATATT ATATT -TATT -TATT ATTATT ATTATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT A-TATT A-TATT AT
25965 TAATAATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 8 0.20
5 21 0.52
6 11 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
ATATT
Found at i:25954 original size:3 final size:3
Alignment explanation
Indices: 25919--25966 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
25909 TCTACAAAAA
25919 TAT TA- TAT TA- TAT TA- TAT TA- TATT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT
25962 TAT TA
1 TAT TA
25967 ATAATATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.20
3 26 0.65
4 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:25961 original size:32 final size:31
Alignment explanation
Indices: 25919--25985 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
25909 TCTACAAAAA
*
25919 TATTATATTA-TATTATATTATATTTATTTAT
1 TATTATATTATTATTA-ATAATATTTATTTAT
*
25950 TATTATTATTATTATTAATAATATTTATTTTT
1 TATTA-TATTATTATTAATAATATTTATTTAT
25982 TATT
1 TATT
25986 TTTTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 5 0.16
32 22 0.69
33 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TATTATATTATTATTAATAATATTTATTTAT
Found at i:26121 original size:33 final size:33
Alignment explanation
Indices: 26053--26125 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
26043 ATCAACATAA
* * *
26053 TTGAGTCCTATTGAAACACTAAAACCAACGTAT
1 TTGAGTCATATTAAAACACTAAAACCAACGCAT
* *
26086 TTGAGTCATATTAAAATACTAAAACTGAA-GCAT
1 TTGAGTCATATTAAAACACTAAAAC-CAACGCAT
26119 TTGAGTC
1 TTGAGTC
26126 CAAGTAGGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (33 bp):
TTGAGTCATATTAAAACACTAAAACCAACGCAT
Found at i:26522 original size:22 final size:21
Alignment explanation
Indices: 26483--26555 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 21
26473 TTTTACATTG
26483 TTATATATATATATATATATATTTA
1 TTAT-TATAT-TA-ATAT-TATTTA
* *
26508 TTTTTTTATTAATATTATTATA
1 TTATTATATTAATATTATT-TA
*
26530 TTATTATATTAATATTTTTTA
1 TTATTATATTAATATTATTTA
26551 TTATT
1 TTATT
26556 CTTTTCTCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
21 11 0.26
22 22 0.52
23 2 0.05
24 4 0.10
25 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTATATTAATATTATTTA
Found at i:26530 original size:8 final size:8
Alignment explanation
Indices: 26465--26540 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 8
26455 TTTAATATTT
26465 TTATT-TA
1 TTATTATA
* *
26472 TTTTTACA
1 TTATTATA
*
26480 TTGTTATA
1 TTATTATA
26488 -TA-TATA
1 TTATTATA
26494 TATATATATA
1 T-TAT-TATA
* *
26504 TTTATTTTT
1 -TTATTATA
26513 TTATTAATA
1 TTATT-ATA
26522 TTATTATA
1 TTATTATA
26530 TTATTATA
1 TTATTATA
26538 TTA
1 TTA
26541 ATATTTTTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
6 4 0.08
7 5 0.09
8 28 0.53
9 8 0.15
10 7 0.13
11 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (8 bp):
TTATTATA
Found at i:34816 original size:12 final size:12
Alignment explanation
Indices: 34799--34856 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
34789 AAATATGGTA
*
34799 TGAACAGTACCG
1 TGAACAATACCG
*
34811 TGAACAATA--A
1 TGAACAATACCG
**
34821 TGAACAATATTG
1 TGAACAATACCG
*
34833 TGAACAGTACCG
1 TGAACAATACCG
34845 TGAACAATACCG
1 TGAACAATACCG
34857 AATGTTAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
10 9 0.24
12 28 0.76
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (12 bp):
TGAACAATACCG
Found at i:34924 original size:21 final size:23
Alignment explanation
Indices: 34880--34925 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
34870 TTCCAGATTA
*
34880 CTTCAGGGGTATCGATTCCCCTG
1 CTTCAGGGGAATCGATTCCCCTG
34903 CTTCA-GGGAATCGATT-CCCTG
1 CTTCAGGGGAATCGATTCCCCTG
34924 CT
1 CT
34926 ACAGTACTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 10 0.45
23 5 0.23
ACGTcount: A:0.15, C:0.30, G:0.24, T:0.30
Consensus pattern (23 bp):
CTTCAGGGGAATCGATTCCCCTG
Found at i:35766 original size:32 final size:32
Alignment explanation
Indices: 35648--35771 Score: 128
Period size: 32 Copynumber: 3.9 Consensus size: 32
35638 CCTTGGCAAA
* * * *
35648 TGTCCATAGGTTTCGAAGAACCTAGGTAA-AC
1 TGTCCATATGTTCCGTAGAACATAGGTAATAC
* *
35679 TGTCCATATGTTCCTTAGAATATAGGGT-ATAC
1 TGTCCATATGTTCCGTAGAACATA-GGTAATAC
* * *
35711 TGTCCATATGTCCCG-AAAGACATAGGTAATTC
1 TGTCCATATGTTCCGTAGA-ACATAGGTAATAC
35743 TGTCCATATGTTCCGTAGAACATAGGTAA
1 TGTCCATATGTTCCGTAGAACATAGGTAA
35772 ACCCTCGACT
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
31 24 0.32
32 49 0.65
33 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (32 bp):
TGTCCATATGTTCCGTAGAACATAGGTAATAC
Found at i:36151 original size:2 final size:2
Alignment explanation
Indices: 36144--36183 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
36134 CACATAAACC
36144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
36184 CTTGTTCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46862 original size:28 final size:28
Alignment explanation
Indices: 46804--46872 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 28
46794 TAAAAAATAA
46804 ATAAAAACCCAAT--TTGTATTTTATAT
1 ATAAAAACCCAATAATTGTATTTTATAT
46830 ATAAAAACCCAATAATTGGT-TTTTATAT
1 ATAAAAACCCAATAATT-GTATTTTATAT
46858 ATAAAAACCCAATAA
1 ATAAAAACCCAATAA
46873 ATTATATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
26 13 0.32
28 25 0.62
29 2 0.05
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (28 bp):
ATAAAAACCCAATAATTGTATTTTATAT
Found at i:47258 original size:26 final size:26
Alignment explanation
Indices: 47224--47282 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
47214 TTAAATAATT
*
47224 ATAAATACATTATTTTCTACTCCCCG
1 ATAACTACATTATTTTCTACTCCCCG
47250 ATAACTACATTATTTTCTACTCCCCG
1 ATAACTACATTATTTTCTACTCCCCG
47276 ATAACTA
1 ATAACTA
47283 TACTGTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.37
Consensus pattern (26 bp):
ATAACTACATTATTTTCTACTCCCCG
Found at i:47976 original size:31 final size:30
Alignment explanation
Indices: 47941--48025 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 30
47931 ACTTTGTATA
*
47941 AAATATTAATTTGATCTTTCAATTTTAGAT
1 AAATATTAATTTGATCTTTCAATTTTAAAT
* *
47971 GAAATA-TAATTTTGATCCTTAAATTTTAAAT
1 -AAATATTAA-TTTGATCTTTCAATTTTAAAT
* *
48002 AAATATCAATTTGAACTTTCAATT
1 AAATATTAATTTGATCTTTCAATT
48026 CGATCAAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 20 0.44
31 25 0.56
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (30 bp):
AAATATTAATTTGATCTTTCAATTTTAAAT
Found at i:49419 original size:2 final size:2
Alignment explanation
Indices: 49408--49440 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
49398 TATTTTAGAA
*
49408 AT AT -T AT AT AT AT AT TT 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
49441 TATGAGGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:50583 original size:19 final size:20
Alignment explanation
Indices: 50555--50592 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
50545 AGTTTAGAGA
*
50555 GTTTAGGGTTTA-GGTTTAT
1 GTTTAAGGTTTAGGGTTTAT
50574 GTTTAAGGTTTAGGGTTTA
1 GTTTAAGGTTTAGGGTTTA
50593 GGATTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (20 bp):
GTTTAAGGTTTAGGGTTTAT
Done.