Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004674.1 Hibiscus syriacus cultivar Beakdansim tig00010479_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: 55516
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:139 original size:13 final size:13
Alignment explanation
Indices: 103--161 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 13
93 ATATATATTA
*
103 ATATAATTTAAAT
1 ATATAATTAAAAT
116 AATAATAATTAAAAT
1 -AT-ATAATTAAAAT
*
131 ATTTAATTAAACAT
1 ATATAATTAAA-AT
*
145 ATAAAATTAAAAT
1 ATATAATTAAAAT
158 ATAT
1 ATAT
162 TTAAACAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
13 13 0.34
14 15 0.39
15 10 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAATTAAAAT
Found at i:1616 original size:3 final size:3
Alignment explanation
Indices: 1610--1656 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
1600 AAATATTATT
* * * *
1610 TAA TAA TAA TAA TTA TAA TAG TAA TTA TAA TAA TAA -AA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1657 ATGGGTAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1629 original size:12 final size:12
Alignment explanation
Indices: 1612--1645 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1602 ATATTATTTA
1612 ATAATAATAATT
1 ATAATAATAATT
*
1624 ATAATAGTAATT
1 ATAATAATAATT
1636 ATAATAATAA
1 ATAATAATAA
1646 AATAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:7943 original size:40 final size:40
Alignment explanation
Indices: 7899--8007 Score: 191
Period size: 40 Copynumber: 2.7 Consensus size: 40
7889 GGAAACTAAG
* *
7899 TGTATATGGTGGGCATGACCTTATGTGTAATACATTTCGA
1 TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGA
*
7939 TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGG
1 TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGA
7979 TGTATATGGTGGGCACGACCTTATGTGTA
1 TGTATATGGTGGGCACGACCTTATGTGTA
8008 GCACTACGGT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.35
Consensus pattern (40 bp):
TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGA
Found at i:11098 original size:2 final size:2
Alignment explanation
Indices: 11091--11142 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
11081 ACACATGGGC
11091 AT AT AT 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 AT AT AT
11133 AT AT AT AT AT
1 AT AT AT AT AT
11143 TACTCATCCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11943 original size:94 final size:94
Alignment explanation
Indices: 11782--11968 Score: 311
Period size: 94 Copynumber: 2.0 Consensus size: 94
11772 CCTAGACCCA
* * *
11782 GCCTGGACGTTATGCACAAATCTAGGCGGTTACATATCTTATTCAGAAATTTCTTTTCATATTTA
1 GCCTGGACATTATGCACAAATATAGGCAGTTACATATCTTATTCAGAAATTTCTTTTCATATTTA
* *
11847 AAACAACGTTAAAATCTATATAACAGTAC
66 AAACAACATTAAAATCCATATAACAGTAC
* *
11876 GCCTGTACATTATGCCCAAATATAGGCAGTTACATATCTTATTCAGAAATTTCTTTTCATATTTA
1 GCCTGGACATTATGCACAAATATAGGCAGTTACATATCTTATTCAGAAATTTCTTTTCATATTTA
11941 AAACAACATTAAAATCCATATAACAGTA
66 AAACAACATTAAAATCCATATAACAGTA
11969 TATTATGAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (94 bp):
GCCTGGACATTATGCACAAATATAGGCAGTTACATATCTTATTCAGAAATTTCTTTTCATATTTA
AAACAACATTAAAATCCATATAACAGTAC
Found at i:13110 original size:39 final size:39
Alignment explanation
Indices: 13035--13124 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
13025 AGGACCTGCG
*
13035 GTAAGGACTTACCCTGAGAAAAAAGAAGAGATGCATGCA
1 GTAAGGACTTACCCTAAGAAAAAAGAAGAGATGCATGCA
* * * *
13074 GTAATGACTTACCCTAAGCACAAAGCAGATGA-GCATGCA
1 GTAAGGACTTACCCTAAGAAAAAAGAAGA-GATGCATGCA
* *
13113 GTTAGGTCTTAC
1 GTAAGGACTTAC
13125 AAGTCATATA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 40 0.95
40 2 0.05
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (39 bp):
GTAAGGACTTACCCTAAGAAAAAAGAAGAGATGCATGCA
Found at i:16082 original size:47 final size:47
Alignment explanation
Indices: 16023--16141 Score: 125
Period size: 47 Copynumber: 2.6 Consensus size: 47
16013 ATAAACAACT
* * *
16023 AGTATGGTACATTTAGTGCCTAGTATGCAATATAAACAACTAGTAAC
1 AGTATGGCACATTCAGTGCCTAGTATGCAATATAAACAACTAGAAAC
* * * **
16070 AGTATGGCACATTCAGTGCC-CGTTATGTAGTATAAACTGCTAGAAAC
1 AGTATGGCACATTCAGTGCCTAG-TATGCAATATAAACAACTAGAAAC
* *
16117 A-TATGACACATTCAATGCCTAGTAT
1 AGTATGGCACATTCAGTGCCTAGTAT
16142 CAGTGAATGC
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
46 20 0.34
47 39 0.66
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (47 bp):
AGTATGGCACATTCAGTGCCTAGTATGCAATATAAACAACTAGAAAC
Found at i:18870 original size:17 final size:17
Alignment explanation
Indices: 18851--18882 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18841 TTATGTCCCT
18851 TTTTC-CTGTATTGTTA
1 TTTTCACTGTATTGTTA
18867 TTTTCACTGTATTGTT
1 TTTTCACTGTATTGTT
18883 CCATTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTTCACTGTATTGTTA
Found at i:18978 original size:16 final size:16
Alignment explanation
Indices: 18957--18988 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18947 AATGATGAGA
18957 ATATATGGCACTCGAG
1 ATATATGGCACTCGAG
18973 ATATATGGCACTCGAG
1 ATATATGGCACTCGAG
18989 TCAGTCATGA
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:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (16 bp):
ATATATGGCACTCGAG
Found at i:21659 original size:31 final size:31
Alignment explanation
Indices: 21624--21730 Score: 74
Period size: 31 Copynumber: 3.3 Consensus size: 31
21614 TTCGTAGCTA
21624 GTAATTCCTTGTATAGGTTTAGCACCGACTG
1 GTAATTCCTTGTATAGGTTTAGCACCGACTG
* ** * *
21655 GTAATTACTATCTGTGGCAAGTTTAGTC-CCTACTG
1 GTAATT-C-CT-TGT-ATAGGTTTAG-CACCGACTG
* *
21690 GTAATTCCTTTTATAGGTTCT-GCACCGACTA
1 GTAATTCCTTGTATAGGTT-TAGCACCGACTG
*
21721 ATAATTCCTT
1 GTAATTCCTT
21731 ATGGGCCTGA
Statistics
Matches: 56, Mismatches: 13, Indels: 14
0.67 0.16 0.17
Matches are distributed among these distances:
30 1 0.02
31 25 0.45
32 4 0.07
33 2 0.04
34 4 0.07
35 19 0.34
36 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (31 bp):
GTAATTCCTTGTATAGGTTTAGCACCGACTG
Found at i:24856 original size:47 final size:46
Alignment explanation
Indices: 24772--24892 Score: 116
Period size: 47 Copynumber: 2.6 Consensus size: 46
24762 TAACAATATG
* * * * ** *
24772 GCACATTCAGTGCCCAACATACAATACAAACTGCCAGTAATAGCATA
1 GCACATTCAGTG-CCAATATGCAGTATAAACAACCAGTAACAGCATA
* *
24819 GCACATTCAGTGCCTAATATGCAGTATAAACAACCAGTAACAGTATG
1 GCACATTCAGTGCC-AATATGCAGTATAAACAACCAGTAACAGCATA
* * *
24866 GCACAATCAATGCCAGTATGCAGTATA
1 GCACATTCAGTGCCAATATGCAGTATA
24893 TATTGCTAGT
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
46 14 0.23
47 47 0.77
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (46 bp):
GCACATTCAGTGCCAATATGCAGTATAAACAACCAGTAACAGCATA
Found at i:26880 original size:25 final size:24
Alignment explanation
Indices: 26852--26905 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
26842 TTCTTTTAAG
26852 ATTTCCAAT-TTAGGCATATTCACTA
1 ATTTCC-ATCTTA-GCATATTCACTA
* *
26877 ATTTGCATCCTTAGCTTATTCACTA
1 ATTTCCAT-CTTAGCATATTCACTA
26902 ATTT
1 ATTT
26906 TATTAGCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 2 0.08
25 20 0.80
26 3 0.12
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.44
Consensus pattern (24 bp):
ATTTCCATCTTAGCATATTCACTA
Found at i:33590 original size:13 final size:13
Alignment explanation
Indices: 33574--33635 Score: 97
Period size: 13 Copynumber: 4.8 Consensus size: 13
33564 GCTCAATGAA
33574 CGTCATAAATGTG
1 CGTCATAAATGTG
33587 CGTCATAAATGTG
1 CGTCATAAATGTG
*
33600 TGTCATAAATGTG
1 CGTCATAAATGTG
* *
33613 TGTCATAAATGCG
1 CGTCATAAATGTG
33626 CGTCATAAAT
1 CGTCATAAAT
33636 TTATGACACA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (13 bp):
CGTCATAAATGTG
Found at i:34451 original size:19 final size:19
Alignment explanation
Indices: 34295--34452 Score: 112
Period size: 19 Copynumber: 8.4 Consensus size: 19
34285 ATAACACATA
*
34295 TTTCCAACTTTAAAATA-GG
1 TTTCCAAC-CTAAAATATGG
*
34314 TTTCCAACCTAAAA-ACAGG
1 TTTCCAACCTAAAATA-TGG
*
34333 TTTGCAACCTAAAATATGG
1 TTTCCAACCTAAAATATGG
34352 TTTCCAACCT-AAA-ATGG
1 TTTCCAACCTAAAATATGG
* * * *
34369 GTTACAACCTAAAATCTGA
1 TTTCCAACCTAAAATATGG
* * *
34388 CTTACAACCTAAAATCTAGG
1 TTTCCAACCTAAAATAT-GG
* * *
34408 --TCGCAGCCTAAAATCTAG
1 TTTC-CAACCTAAAATATGG
*
34426 TTCCCAACCTAAAATATGG
1 TTTCCAACCTAAAATATGG
34445 TTTCCAAC
1 TTTCCAAC
34453 ACTTAATTCC
Statistics
Matches: 112, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
17 13 0.12
18 13 0.12
19 83 0.74
20 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.28
Consensus pattern (19 bp):
TTTCCAACCTAAAATATGG
Done.