Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007266.1 Hibiscus syriacus cultivar Beakdansim tig00019260_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: 72597
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1897 original size:21 final size:21
Alignment explanation
Indices: 1873--1919 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1863 AGTTAGATCT
1873 CATG-AATTTTTCATAAATATA
1 CATGCAATTTTTC-TAAATATA
*
1894 CATGCCATTTTTCTAAATA-A
1 CATGCAATTTTTCTAAATATA
1914 -ATGCAA
1 CATGCAA
1920 ACAAGTCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.22
20 1 0.04
21 10 0.43
22 7 0.30
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (21 bp):
CATGCAATTTTTCTAAATATA
Found at i:11793 original size:2 final size:2
Alignment explanation
Indices: 11786--11815 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11776 TCTTTTGAAC
11786 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
11816 GTATGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11820 original size:4 final size:4
Alignment explanation
Indices: 11813--11843 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
11803 TATATATATA
11813 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
11844 ACATTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:19112 original size:26 final size:26
Alignment explanation
Indices: 19083--19135 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
19073 ACTCATTATG
19083 TCGTCAAC-ATTATCATCATATCATCA
1 TCGTC-ACTATTATCATCATATCATCA
*
19109 TCGTCACTATTATTATCATATCATCA
1 TCGTCACTATTATCATCATATCATCA
19135 T
1 T
19136 TATCGTCGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (26 bp):
TCGTCACTATTATCATCATATCATCA
Found at i:24704 original size:31 final size:31
Alignment explanation
Indices: 24638--24706 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
24628 AAATTACTAT
* * ** *
24638 TTTGTTATAAATCGATAACGTTAGTGATTAT
1 TTTGTTACAAATCGATAACGTTAGTAACAAA
24669 TTTGTTACAAATCGATAACGTT-GTTAACAAA
1 TTTGTTACAAATCGATAACGTTAG-TAACAAA
24700 TTTGTTA
1 TTTGTTA
24707 GTTTTAAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.43
Consensus pattern (31 bp):
TTTGTTACAAATCGATAACGTTAGTAACAAA
Found at i:25452 original size:2 final size:2
Alignment explanation
Indices: 25447--25506 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
25437 CTCTCTCTCT
25447 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
25489 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
25507 GGGATAATGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29706 original size:2 final size:2
Alignment explanation
Indices: 29701--29732 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
29691 ATTTTCCCAT
*
29701 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29733 CTTTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29827 original size:10 final size:10
Alignment explanation
Indices: 29812--29842 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
29802 ATAATAAATA
29812 AAAAAATTAG
1 AAAAAATTAG
29822 AAAAAATTAG
1 AAAAAATTAG
*
29832 AATAAATTAG
1 AAAAAATTAG
29842 A
1 A
29843 TATAAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (10 bp):
AAAAAATTAG
Found at i:30501 original size:3 final size:3
Alignment explanation
Indices: 30495--30539 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
30485 TTTAAAAAAA
*
30495 TAT TATT TATT TATT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT
1 TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
30540 AGGTTTCATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 28 0.72
4 11 0.28
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:33577 original size:12 final size:12
Alignment explanation
Indices: 33560--33603 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
33550 AACGAACAAG
33560 CTCGTTTATCAA
1 CTCGTTTATCAA
33572 CTCGTTTA-CAA
1 CTCGTTTATCAA
*
33583 GCTCGTTTATCGA
1 -CTCGTTTATCAA
33596 CTCGTTTA
1 CTCGTTTA
33604 CAAGCTCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 3 0.10
12 24 0.83
13 2 0.07
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (12 bp):
CTCGTTTATCAA
Found at i:33584 original size:24 final size:24
Alignment explanation
Indices: 33555--33610 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
33545 ATATTAACGA
33555 ACAAGCTCGTTTATCAACTCGTTT
1 ACAAGCTCGTTTATCAACTCGTTT
*
33579 ACAAGCTCGTTTATCGACTCGTTT
1 ACAAGCTCGTTTATCAACTCGTTT
33603 ACAAGCTC
1 ACAAGCTC
33611 ATTTTAAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (24 bp):
ACAAGCTCGTTTATCAACTCGTTT
Found at i:33786 original size:23 final size:23
Alignment explanation
Indices: 33760--33816 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
33750 TTTTGGTTAT
33760 CGAACATGTTCACGAA-CGTTAAA
1 CGAACATGTTCAC-AAGCGTTAAA
*
33783 CGAATATGTTCACAAGCGTTAAA
1 CGAACATGTTCACAAGCGTTAAA
*
33806 TGAACATGTTC
1 CGAACATGTTC
33817 TTAAATGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (23 bp):
CGAACATGTTCACAAGCGTTAAA
Found at i:34579 original size:21 final size:21
Alignment explanation
Indices: 34531--34584 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
34521 GTTGTTATTG
*
34531 AAATCCCTAAATCTTAATACCA
1 AAATCCCTAAATC-TAAAACCA
*
34553 AAATCCCTAAATC-AAAACTCT
1 AAATCCCTAAATCTAAAAC-CA
34574 AAATCCCTAAA
1 AAATCCCTAAA
34585 AATCAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 12 0.41
22 13 0.45
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATCCCTAAATCTAAAACCA
Found at i:35349 original size:16 final size:16
Alignment explanation
Indices: 35328--35359 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35318 TGATATCATT
35328 AAAAATGGGTCGAGGG
1 AAAAATGGGTCGAGGG
35344 AAAAATGGGTCGAGGG
1 AAAAATGGGTCGAGGG
35360 GTGGGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.44, T:0.12
Consensus pattern (16 bp):
AAAAATGGGTCGAGGG
Found at i:36127 original size:25 final size:25
Alignment explanation
Indices: 36093--36143 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
36083 ATATTACGCC
36093 AAAGTCCATAGTCATCATACACGTA
1 AAAGTCCATAGTCATCATACACGTA
36118 AAAGTCCATAGTCATCATACACGTA
1 AAAGTCCATAGTCATCATACACGTA
36143 A
1 A
36144 TCATTATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (25 bp):
AAAGTCCATAGTCATCATACACGTA
Found at i:37844 original size:182 final size:181
Alignment explanation
Indices: 37516--38127 Score: 612
Period size: 179 Copynumber: 3.4 Consensus size: 181
37506 GATACAAATA
* * ** * * ** * *
37516 AAAAATGTATCGCTCCATAGCAATATAACAGGTAAAAATATGATAAAACCGGT-T-TTATTAATA
1 AAAAATGTATCGATCTATAATAATATAACAGGT-AAAATATGACAAAACAGGTATCAAAATGATA
** ** * * * * *
37579 AAACCGGTAAACCGCTACTGGATATATCGAAAGTATCGATTAGATTTAA-ATAAGTATCGATACT
65 AAACCAATAAAAAGCTACCGGATATATTGAAAGTGTC-AATA-AATTAATATAAGTATCGATACT
*
37643 TTTGAAATTTAAAAGAGAAGAAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
128 TTTGAAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
* * * * * *
37697 AAAAACGTATCGATCTATAACAATGTAACATGTATAAGTATGACAAAACCGGTAAT-AAAATGAT
1 AAAAATGTATCGATCTATAATAATATAACAGGTA-AAATATGACAAAACAGGT-ATCAAAATGAT
* * * * *
37761 AAAACCAATAAAGAGCTACCTGATATATTGAAAGTGTCAATACATTAATATAAATATCGACACTT
64 AAAACCAATAAAAAGCTACCGGATATATTGAAAGTGTCAATAAATTAATATAAGTATCGATAC-T
37826 TTTG-AATTT-AAA-AG-AGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
128 TTTGAAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
* * * * *
37876 ACAAATGTATAGATCTATAATAATATAACAGGTAAGAATATGACAAAACATGTCTCGAAATGATA
1 AAAAATGTATCGATCTATAATAATATAACAGGTAA-AATATGACAAAACAGGTATCAAAATGATA
**** * *
37941 AAATTGGTAAAAAGTTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGATACTTT
65 AAACCAATAAAAAGCTACCGGATATATTGAAAGTGTCAATAAATTAATATAAGTATCGATACTTT
* * * *
38006 CGTAATTTAAAAGATAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT
130 TGAAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
* * * * * *
38058 GAAAATGTATCGATCCATAATAATATAATAGGTAAAAATATGACAAAATC-GATATCGAAATGAC
1 AAAAATGTATCGATCTATAATAATATAACAGGT-AAAATATGACAAAA-CAGGTATCAAAATGAT
38122 AAAACC
64 AAAACC
38128 GGTAAAGTGC
Statistics
Matches: 356, Mismatches: 62, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
178 6 0.02
179 141 0.40
180 6 0.02
181 51 0.14
182 109 0.31
183 43 0.12
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (181 bp):
AAAAATGTATCGATCTATAATAATATAACAGGTAAAATATGACAAAACAGGTATCAAAATGATAA
AACCAATAAAAAGCTACCGGATATATTGAAAGTGTCAATAAATTAATATAAGTATCGATACTTTT
GAAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
Found at i:43620 original size:20 final size:20
Alignment explanation
Indices: 43586--43637 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
43576 TTTGACTCAC
43586 AAAATATAATTTTTTTT-AA
1 AAAATATAATTTTTTTTAAA
43605 AAAATATAATTTTTTTTAAA
1 AAAATATAATTTTTTTTAAA
*
43625 AAAATAAAATTTT
1 AAAATATAATTTT
43638 CATAATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAATATAATTTTTTTTAAA
Found at i:50671 original size:20 final size:20
Alignment explanation
Indices: 50646--50690 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
50636 TATAATCAAT
*
50646 AAAATAGGTAGTAATTGAAG
1 AAAATAAGTAGTAATTGAAG
50666 AAAATAAGTAGTAATTGAAG
1 AAAATAAGTAGTAATTGAAG
50686 AAAAT
1 AAAAT
50691 TCAATTCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (20 bp):
AAAATAAGTAGTAATTGAAG
Found at i:52441 original size:60 final size:60
Alignment explanation
Indices: 52367--52530 Score: 179
Period size: 60 Copynumber: 2.7 Consensus size: 60
52357 ATGAATTTGA
* * * ** *
52367 GGATGAATTTGGAATATTCAAAACTTTAGGGACCAATTTAGAAA-GAGGGTTGTAGTTTAG
1 GGATGAAATTGGAATATTTAAAACTTTAGGGACCAATTTA-AAATGAGAGTCATAATTTAG
* **
52427 GGATGAAATTGGAATATTTAAAAGTTTAAGGG-TTAATTTAAAATGAGAGTCATAATTTAG
1 GGATGAAATTGGAATATTTAAAACTTT-AGGGACCAATTTAAAATGAGAGTCATAATTTAG
* * * *
52487 GGATAAAATTAGAATATTTAAAATTTTAAGGACCAATTTAAAAT
1 GGATGAAATTGGAATATTTAAAACTTTAGGGACCAATTTAAAAT
52531 AAGAATTATA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
59 6 0.07
60 76 0.88
61 4 0.05
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (60 bp):
GGATGAAATTGGAATATTTAAAACTTTAGGGACCAATTTAAAATGAGAGTCATAATTTAG
Found at i:53726 original size:16 final size:16
Alignment explanation
Indices: 53705--53736 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53695 ACGCGTTTAG
53705 ATTTAAAATAAAAATT
1 ATTTAAAATAAAAATT
53721 ATTTAAAATAAAAATT
1 ATTTAAAATAAAAATT
53737 GTTAAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTAAAATAAAAATT
Found at i:53741 original size:15 final size:16
Alignment explanation
Indices: 53707--53742 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
53697 GCGTTTAGAT
*
53707 TTAAAATAAAAATTAT
1 TTAAAATAAAAATTAG
53723 TTAAAATAAAAATT-G
1 TTAAAATAAAAATTAG
53738 TTAAA
1 TTAAA
53743 TTCAAGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TTAAAATAAAAATTAG
Found at i:53830 original size:17 final size:17
Alignment explanation
Indices: 53789--53848 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
53779 ATTTAATTTT
*
53789 TATTTTTAGTATTTT-AT
1 TATTTTTA-TATTTTAAA
* *
53806 TATATTTACT-TTTTGAA
1 TATTTTTA-TATTTTAAA
53823 TATTTTTATATTTTAAA
1 TATTTTTATATTTTAAA
53840 TATTTTTAT
1 TATTTTTAT
53849 TTAAAAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 5 0.14
17 31 0.86
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (17 bp):
TATTTTTATATTTTAAA
Done.