Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001294.1 Hibiscus syriacus cultivar Beakdansim tig00002530_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: 54807
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Found at i:133 original size:11 final size:10
Alignment explanation
Indices: 113--150 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
103 TATTTGTTCA
113 TCATTTTTTT
1 TCATTTTTTT
123 TCATTTCTTTT
1 TCATTT-TTTT
134 TCA--TTTTT
1 TCATTTTTTT
142 TCATTTTTT
1 TCATTTTTT
151 CTCTTCAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 10 0.40
11 7 0.28
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (10 bp):
TCATTTTTTT
Found at i:3635 original size:9 final size:9
Alignment explanation
Indices: 3621--3651 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3611 AGAAATAATG
3621 AATGTAAAA
1 AATGTAAAA
3630 AATGTAAAA
1 AATGTAAAA
*
3639 AATGTAAAG
1 AATGTAAAA
3648 AATG
1 AATG
3652 ATTGTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (9 bp):
AATGTAAAA
Found at i:7359 original size:15 final size:15
Alignment explanation
Indices: 7339--7370 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7329 TGCAATGAAT
*
7339 AATGAATGTATGCAA
1 AATGAATGTAAGCAA
7354 AATGAATGTAAGCAA
1 AATGAATGTAAGCAA
7369 AA
1 AA
7371 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (15 bp):
AATGAATGTAAGCAA
Found at i:12119 original size:3 final size:3
Alignment explanation
Indices: 12113--12193 Score: 96
Period size: 3 Copynumber: 27.0 Consensus size: 3
12103 TATTATTTAT
12113 TAA TAA TAA TATA TAA TAA TAA TAA TAA T-A TATA TAAA TAA -AA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A T-AA TAA TAA TAA
* *
12159 TAC TAA TAA TAA TAA T-A TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12194 AAACAAATGG
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
2 6 0.09
3 54 0.79
4 7 0.10
5 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:13797 original size:19 final size:19
Alignment explanation
Indices: 13747--13798 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
13737 ATCATAAAGT
*
13747 ATAAATATTAGTTAATTAC
1 ATAAATATTAATTAATTAC
* *
13766 ATAATGTAATAATTAA-TAC
1 ATAA-ATATTAATTAATTAC
13785 ATAAACTATTAATT
1 ATAAA-TATTAATT
13799 TTAATTAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (19 bp):
ATAAATATTAATTAATTAC
Found at i:15081 original size:3 final size:3
Alignment explanation
Indices: 15073--15148 Score: 57
Period size: 3 Copynumber: 25.0 Consensus size: 3
15063 AATTTTTATT
* * * * *
15073 TAA TAA TAA CAT TAT TAA TAA T-A TATA TAA TAA TAA TAA CATG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA
*
15119 TTAA TAA TAA TAA TAA T-A TGA TAA TAA TAA
1 -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15149 CATGTATAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
2 4 0.07
3 48 0.81
4 7 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:15092 original size:15 final size:16
Alignment explanation
Indices: 15072--15175 Score: 70
Period size: 15 Copynumber: 6.2 Consensus size: 16
15062 TAATTTTTAT
15072 TTAATAATAACAT-TA
1 TTAATAATAACATATA
*
15087 TTAATAAT-ATATATA
1 TTAATAATAACATATA
* *
15102 ATAATAATAACATGTAA
1 TTAATAATAACATAT-A
*
15119 TTAATAATAATAATAATA
1 TTAATAATAA-CAT-ATA
*
15137 TGATAATAATAACATGTA
1 T--TAATAATAACATATA
*
15155 -TAATTAATATATATATA
1 TTAA-TAATA-ACATATA
15172 TTAA
1 TTAA
15176 AAACGGACAA
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
14 3 0.04
15 20 0.29
16 9 0.13
17 15 0.22
18 9 0.13
19 3 0.04
20 9 0.13
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TTAATAATAACATATA
Found at i:15129 original size:23 final size:23
Alignment explanation
Indices: 15099--15148 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
15089 AATAATATAT
15099 ATAATAATAATAACATG-TAATTA
1 ATAATAATAATAACATGATAA-TA
*
15122 ATAATAATAATAATATGATAATA
1 ATAATAATAATAACATGATAATA
15145 ATAA
1 ATAA
15149 CATGTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (23 bp):
ATAATAATAATAACATGATAATA
Found at i:15143 original size:20 final size:20
Alignment explanation
Indices: 15088--15148 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 20
15078 ATAACATTAT
15088 TAATAATAT-AT-ATAATAA
1 TAATAATATGATAATAATAA
*
15106 TAATAACATGTAATTAATAATAA
1 TAATAATATG--A-TAATAATAA
15129 TAATAATATGATAATAATAA
1 TAATAATATGATAATAATAA
15149 CATGTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 8 0.22
20 9 0.25
21 2 0.06
22 1 0.03
23 16 0.44
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (20 bp):
TAATAATATGATAATAATAA
Found at i:25701 original size:90 final size:89
Alignment explanation
Indices: 25543--25719 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
25533 CCTAACACAC
* *
25543 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTTAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
* *
25608 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATTAAAATTAAATAAT
* *
25632 CCTTTTATATCCAAGTTACCCTAATCATATTAGAGATTTTATTATTTCAAATTAATTAAGTCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAG-GATTTTATTATTTCAAATTAATTAAATCTAT
25697 ATTTAATTAATTAAAATTAAATA
65 ATTTAATTAATTAAAATTAAATA
25720 TTTGGGATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 32 0.40
90 49 0.60
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTAAAATTAAATAAT
Found at i:32105 original size:3 final size:3
Alignment explanation
Indices: 32099--32172 Score: 55
Period size: 3 Copynumber: 25.0 Consensus size: 3
32089 TAATATTATT
* * * * *
32099 TAA TAA TAA TAA TAT TAA TAA T-A TAT TTA T-A TAA TAA TAA CATG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
*
32143 TAA TTAA TAA TAA TAA T-A TGA TAA TAA TAA
1 TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
32173 CATATATAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
2 6 0.11
3 46 0.82
4 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:32137 original size:31 final size:30
Alignment explanation
Indices: 32089--32172 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
32079 TTTGGGCTTG
*
32089 TAAT-ATTATTTAATAATAATAAT-ATTAA
1 TAATAATTATATAATAATAATAATAATTAA
* *
32117 TAATATATTTATATAATAATAACATGTAATTAA
1 TAATA-A-TTATATAATAATAATA-ATAATTAA
* *
32150 TAATAATAATATGATAATAATAA
1 TAATAATTATATAATAATAATAA
32173 CATATATAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
28 4 0.09
30 1 0.02
31 27 0.61
32 2 0.05
33 10 0.23
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (30 bp):
TAATAATTATATAATAATAATAATAATTAA
Found at i:32154 original size:20 final size:20
Alignment explanation
Indices: 32129--32172 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
32119 ATATATTTAT
32129 ATAATAATAACATG-TAATTA
1 ATAATAATAACATGATAA-TA
*
32149 ATAATAATAATATGATAATA
1 ATAATAATAACATGATAATA
32169 ATAA
1 ATAA
32173 CATATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (20 bp):
ATAATAATAACATGATAATA
Found at i:32167 original size:17 final size:17
Alignment explanation
Indices: 32099--32172 Score: 61
Period size: 20 Copynumber: 4.5 Consensus size: 17
32089 TAATATTATT
32099 TAATAATAATAATAT--
1 TAATAATAATAATATGA
*
32114 TAATAAT-AT-AT-TTA
1 TAATAATAATAATATGA
*
32128 T-ATAATAATAACATGTAA
1 TAATAATAATAATATG--A
32146 TTAATAATAATAATATGA
1 -TAATAATAATAATATGA
32164 TAATAATAA
1 TAATAATAA
32173 CATATATAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
12 1 0.02
13 7 0.15
14 5 0.11
15 8 0.17
16 1 0.02
17 9 0.19
18 2 0.04
19 1 0.02
20 13 0.28
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (17 bp):
TAATAATAATAATATGA
Found at i:32183 original size:36 final size:33
Alignment explanation
Indices: 32089--32178 Score: 96
Period size: 34 Copynumber: 2.8 Consensus size: 33
32079 TTTGGGCTTG
* * *
32089 TAATATTATTTAATAATAATA-AT-ATTAATAA
1 TAATAATATATAATAATAACATATAATTAATAA
* *
32120 T-ATATTTATATAATAATAACATGTAATTAATAA
1 TAATA-ATATATAATAATAACATATAATTAATAA
32153 TAATAATATGATAATAATAACATATA
1 TAATAATAT-ATAATAATAACATATA
32179 TAATTCATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
30 3 0.06
31 15 0.31
32 1 0.02
33 12 0.24
34 18 0.37
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (33 bp):
TAATAATATATAATAATAACATATAATTAATAA
Found at i:37956 original size:21 final size:22
Alignment explanation
Indices: 37930--37972 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
37920 AGGTAAAAAA
*
37930 TAATAATAT-ATTTTTATTTTT
1 TAATAATATAAATTTTATTTTT
*
37951 TAATAATTTAAATTTTATTTTT
1 TAATAATATAAATTTTATTTTT
37973 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TAATAATATAAATTTTATTTTT
Found at i:37985 original size:5 final size:6
Alignment explanation
Indices: 37963--37999 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
37953 ATAATTTAAA
37963 TTTTATT TTTATAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTA-T TTT-TAT TTTTAT TTTTAT TTTTAT TTTTA
38000 AAAATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 20 0.69
7 7 0.24
8 2 0.07
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:37986 original size:20 final size:20
Alignment explanation
Indices: 37938--37998 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
37928 AATAATAATA
*
37938 TATTTTTATTTTTTAATAATTT
1 TATTTTTA-TTTTT-ATATTTT
* *
37960 AAATTTTATTTTTATATTTT
1 TATTTTTATTTTTATATTTT
37980 TATTTTTATTTTTAT-TTTT
1 TATTTTTATTTTTATATTTT
37999 AAAAATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 4 0.12
20 19 0.56
21 5 0.15
22 6 0.18
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TATTTTTATTTTTATATTTT
Found at i:38602 original size:25 final size:25
Alignment explanation
Indices: 38568--38617 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
38558 AACCAGTGAA
* *
38568 CCTTAGGGAAGCTTTAGTAGTTGAG
1 CCTTAGGGAAACTTTAGCAGTTGAG
38593 CCTTAGGGAAACTTTAGCAGTTGAG
1 CCTTAGGGAAACTTTAGCAGTTGAG
38618 TCTCTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (25 bp):
CCTTAGGGAAACTTTAGCAGTTGAG
Found at i:38738 original size:11 final size:11
Alignment explanation
Indices: 38712--38744 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
38702 AAAAGGTGTT
38712 CATAT-ATATG
1 CATATAATATG
38722 CAATATAATATG
1 C-ATATAATATG
38734 CATATAATATG
1 CATATAATATG
38745 GAGTAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (11 bp):
CATATAATATG
Found at i:41820 original size:42 final size:43
Alignment explanation
Indices: 41754--41881 Score: 161
Period size: 43 Copynumber: 3.0 Consensus size: 43
41744 AAATATAAAA
*
41754 ATCAATAAAACAGAATCATA-ACTAAGATAGAAAAAGATATTAG
1 ATCAATAAAACAGAATCA-ACACTAAGATAAAAAAAGATATTAG
* * * *
41797 ATCAA-CAAACAGAACCAACACTAAAATAAAAAATATATATTAG
1 ATCAATAAAACAGAATCAACACTAAGATAAAAAA-AGATATTAG
* *
41840 ATCAATAAAACAGATTCAACAGTAAGATAAAAAAAGATATTA
1 ATCAATAAAACAGAATCAACACTAAGATAAAAAAAGATATTA
41882 TTTTAGAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 22 0.31
43 25 0.35
44 23 0.32
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.20
Consensus pattern (43 bp):
ATCAATAAAACAGAATCAACACTAAGATAAAAAAAGATATTAG
Found at i:42358 original size:15 final size:14
Alignment explanation
Indices: 42325--42368 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
42315 TAAACAACTT
*
42325 ATATTTATATAATTC
1 ATATTTAAATAA-TC
42340 ATATTTAAATAATC
1 ATATTTAAATAATC
42354 AATATTTTAAATAAT
1 -ATA-TTTAAATAAT
42369 TAGTGGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 2 0.08
15 14 0.54
16 10 0.38
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATTTAAATAATC
Found at i:47685 original size:14 final size:14
Alignment explanation
Indices: 47655--47695 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
47645 GAATGGAAGG
47655 AGACAAGGTAA-GA
1 AGACAAGGTAATGA
47668 AGACAAGGTAATGA
1 AGACAAGGTAATGA
*
47682 AGACAAGGAAATGA
1 AGACAAGGTAATGA
47696 GGATACCGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.54, C:0.07, G:0.29, T:0.10
Consensus pattern (14 bp):
AGACAAGGTAATGA
Found at i:48690 original size:34 final size:35
Alignment explanation
Indices: 48646--48723 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 35
48636 GTTAAATTGG
* *
48646 AAAAGATGAAATAATTTGATCATATTTGACTTTTC
1 AAAAGATGAAATAATTTGATAATATTTCACTTTTC
*
48681 -AAAGATGAAATAATTTGATAATGTTTCACTTTTC
1 AAAAGATGAAATAATTTGATAATATTTCACTTTTC
48715 AAAAGATGA
1 AAAAGATGA
48724 TAAGTTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
34 31 0.79
35 8 0.21
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (35 bp):
AAAAGATGAAATAATTTGATAATATTTCACTTTTC
Found at i:49487 original size:30 final size:31
Alignment explanation
Indices: 49442--49509 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
49432 CAGGCCTTAG
* * *
49442 AAAGATTTGGGGACC-ATTTGGTAATTTTTGA
1 AAAG-TTTAGGGACCAAATTGGTAATTATTGA
*
49473 AAAGTTTAGGGACCAAATTGTTAATTATTGA
1 AAAGTTTAGGGACCAAATTGGTAATTATTGA
49504 AAAGTT
1 AAAGTT
49510 ATGGGTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (31 bp):
AAAGTTTAGGGACCAAATTGGTAATTATTGA
Found at i:50388 original size:59 final size:59
Alignment explanation
Indices: 50287--50400 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
50277 TAGCAGGTTG
* * ** *
50287 CATATTCAGGATTGCACTAAAGTATAACTAGTGTATAAGGTGGGCACGACCTTATGTGT
1 CATATTCAGGACTGCACTAAAGCATAACTAGTACATAAGGTGGACACGACCTTATGTGT
* * * *
50346 CATATTCAGGACTGTACTTAAGCATACCTAGTACATATGGTGGACACGACCTTAT
1 CATATTCAGGACTGCACTAAAGCATAACTAGTACATAAGGTGGACACGACCTTAT
50401 AAGTCATACT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (59 bp):
CATATTCAGGACTGCACTAAAGCATAACTAGTACATAAGGTGGACACGACCTTATGTGT
Done.