Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007169.1 Hibiscus syriacus cultivar Beakdansim tig00018799_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: 51614
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:13430 original size:26 final size:26
Alignment explanation
Indices: 13401--13469 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
13391 TATTGTATAG
*
13401 TAATGTAATATATGAGTTAGTGCTTC
1 TAATGTAATATATGAGTTAATGCTTC
* * *
13427 TAATGTAATGTAGGAGTTAATGTTTC
1 TAATGTAATATATGAGTTAATGCTTC
* *
13453 TAATGAAACATATGAGT
1 TAATGTAATATATGAGT
13470 ACGCTTCAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (26 bp):
TAATGTAATATATGAGTTAATGCTTC
Found at i:18845 original size:21 final size:21
Alignment explanation
Indices: 18821--18889 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
18811 GAACTGTAAC
18821 CGGAGGGAGTTTAGGGACAAG
1 CGGAGGGAGTTTAGGGACAAG
*
18842 CGGAGGGAGTTCAGGGACAAG
1 CGGAGGGAGTTTAGGGACAAG
18863 CGGAGGGAGTTTAGGGACAAG
1 CGGAGGGAGTTTAGGGACAAG
18884 CGGAGG
1 CGGAGG
18890 CAAATTGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.28, C:0.12, G:0.49, T:0.12
Consensus pattern (21 bp):
CGGAGGGAGTTTAGGGACAAG
Found at i:20369 original size:23 final size:22
Alignment explanation
Indices: 20339--20394 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
20329 AAAATTTATT
20339 TTTATCTTTTAAAATTTTATAAA
1 TTTATC-TTTAAAATTTTATAAA
*
20362 TTTATC-TTAAAATTTTATAAT
1 TTTATCTTTAAAATTTTATAAA
20383 TTTATCTCTTAA
1 TTTATCT-TTAA
20395 CATAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 20 0.67
23 10 0.33
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATCTTTAAAATTTTATAAA
Found at i:22137 original size:186 final size:187
Alignment explanation
Indices: 21907--22265 Score: 433
Period size: 186 Copynumber: 1.9 Consensus size: 187
21897 TAGAAACTGA
* * *
21907 AAATGTTATGAATATATATAAGAAATACAGTTGTACTCAAGAATGTTATGCTTTATTAAAAAAAT
1 AAATGTTATGAATATATATAAGAAATACAGTTGTACTCAAGAATGTCATGATTTACT-AAAAAAT
* * * * * **
21972 AAGTTACAATATAGAATGTTAATATTTTTATTAATAAAATGGGTTG-AGCCCAAAAATGTCATGG
65 AAATTACAATATAGAATGTTAATACTTTTATTAATAAAATGAGTTGCA-CCAAAAAATATCATAA
* *
22036 TTCACTAAG-AAATAAGTTGTGATCTGAAAT-TTAATATTTTTATTAACATTACTCCTG
129 TTCACTAAGAAAATAAGTTGTGATATGAAATGTTAATATATTTATTAACATTACTCCTG
* *
22093 AAATGTTAT-AATTATATATAAGAAATACGGTT-TCAC-CTAAGAATGTCATGATTTACTAAGAA
1 AAATGTTATGAA-TATATATAAGAAATACAGTTGT-ACTC-AAGAATGTCATGATTTACTAAAAA
*** * *
22155 ATAAATTGTGATCTAGAATGTTAATACTTTTATTAATAAAATGAGTTGCACCAAAAAATATTATA
63 ATAAATTACAATATAGAATGTTAATACTTTTATTAATAAAATGAGTTGCACCAAAAAATATCATA
** *
22220 ATTCTTTATGAAAATAAGTTGTGATATGAAATGTTAATATATTTAT
128 ATTCACTAAGAAAATAAGTTGTGATATGAAATGTTAATATATTTAT
22266 CATAAAAAAG
Statistics
Matches: 145, Mismatches: 22, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
185 66 0.46
186 67 0.46
187 12 0.08
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.38
Consensus pattern (187 bp):
AAATGTTATGAATATATATAAGAAATACAGTTGTACTCAAGAATGTCATGATTTACTAAAAAATA
AATTACAATATAGAATGTTAATACTTTTATTAATAAAATGAGTTGCACCAAAAAATATCATAATT
CACTAAGAAAATAAGTTGTGATATGAAATGTTAATATATTTATTAACATTACTCCTG
Found at i:23266 original size:19 final size:19
Alignment explanation
Indices: 23244--23290 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
23234 ATATATTCAT
23244 AATATTTTCAATTTTTAAA
1 AATATTTTCAATTTTTAAA
*
23263 AATATTTTCAGTTTTTAAA
1 AATATTTTCAATTTTTAAA
23282 AATATTTTC
1 AATATTTTC
23291 TTATTGTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (19 bp):
AATATTTTCAATTTTTAAA
Found at i:24747 original size:10 final size:8
Alignment explanation
Indices: 24707--24806 Score: 58
Period size: 8 Copynumber: 12.1 Consensus size: 8
24697 AAATATATAT
*
24707 AAAAATAT
1 AAAAATAA
24715 AAAAATAA
1 AAAAATAA
24723 AAAAATAA
1 AAAAATAA
*
24731 GAAAA-AA
1 AAAAATAA
* * *
24738 TAACAGAA
1 AAAAATAA
*
24746 AAGAAATCGA
1 AA-AAAT-AA
* **
24756 AGATGTAA
1 AAAAATAA
24764 AAAAATAA
1 AAAAATAA
24772 AAAAATAA
1 AAAAATAA
24780 AAATATATAA
1 AAA-A-ATAA
*
24790 AAAAATAT
1 AAAAATAA
*
24798 AATAATAA
1 AAAAATAA
24806 A
1 A
24807 TATATAAAAT
Statistics
Matches: 69, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
7 5 0.07
8 49 0.71
9 6 0.09
10 9 0.13
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:24790 original size:26 final size:26
Alignment explanation
Indices: 24696--24815 Score: 93
Period size: 26 Copynumber: 4.5 Consensus size: 26
24686 AAAGAGGAAG
* *
24696 AAAATATATATAAAAATATAAAAATA
1 AAAATATATAAAAAAATAAAAAAATA
* *
24722 AAAAAATA-AGAAAAAATAACAGAAAAGA
1 AAAATATATA-AAAAAATAA-A-AAAATA
* *
24750 AATCGAAGATGTAAAAAAATAAAAAAATA
1 AA---AATATATAAAAAAATAAAAAAATA
* *
24779 AAAATATATAAAAAAATATAATAAT-
1 AAAATATATAAAAAAATAAAAAAATA
24804 -AAATATATAAAA
1 AAAATATATAAAA
24816 TATATATACA
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
24 12 0.16
25 1 0.01
26 33 0.43
27 1 0.01
28 7 0.09
29 7 0.09
30 1 0.01
31 13 0.17
32 1 0.01
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (26 bp):
AAAATATATAAAAAAATAAAAAAATA
Found at i:24795 original size:12 final size:12
Alignment explanation
Indices: 24778--24815 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
24768 ATAAAAAAAT
24778 AAAAATATATAA
1 AAAAATATATAA
24790 AAAAATATA-ATA
1 AAAAATATATA-A
*
24802 ATAAATATATAA
1 AAAAATATATAA
24814 AA
1 AA
24816 TATATATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATATATAA
Found at i:24799 original size:20 final size:21
Alignment explanation
Indices: 24768--24819 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
24758 ATGTAAAAAA
*
24768 ATAAAAAA-ATAAAAATATAT
1 ATAAAAAATATAAAAATAAAT
*
24788 A-AAAAAATATAATAATAAAT
1 ATAAAAAATATAAAAATAAAT
*
24808 ATATAAAATATA
1 ATAAAAAATATA
24820 TATACAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.22
20 12 0.44
21 9 0.33
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAAAAAATATAAAAATAAAT
Found at i:27030 original size:58 final size:58
Alignment explanation
Indices: 26940--27082 Score: 223
Period size: 58 Copynumber: 2.5 Consensus size: 58
26930 CCTTCAATTG
* *
26940 GATATTCTTCTTCGTGAAGTTGAAATCCAATCTAAGGATAGGTATTGTTGGTGGACAC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAGGATAGGTATTGTTGGTGGACAC
* * *
26998 GATATCCTTCGTCGTTAAGTTGAAATCCAATCTAAGGATGGGTGTTGTTGGTGGACAC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAGGATAGGTATTGTTGGTGGACAC
* *
27056 AATATCCTTCGTCGTGAAGTTAAAATC
1 GATATCCTTCGTCGTGAAGTTGAAATC
27083 TTGGATGGCC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 77 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (58 bp):
GATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAGGATAGGTATTGTTGGTGGACAC
Found at i:27123 original size:182 final size:173
Alignment explanation
Indices: 26819--27200 Score: 475
Period size: 182 Copynumber: 2.2 Consensus size: 173
26809 CTTTGAATTA
* * * *
26819 GATATCCTTCTTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTGGTTGTGGGCACGATATCCTTC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTGGAGTAAGTTGGTTGTGGACACAATATCCTTC
*
26884 ATCGTGAAGTTGAAATTGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTCAATTGGATATTC-T
66 ATCGTGAAGTTAAAATTGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTCAATTGGATA-TCAT
* *
26948 TCTTCGTGAAGTTGAAATCCAATCTAAGGATAGGTATTGTTGGTG-GACAC
130 TCTTCGTGAAATTGAAATCCAATCT---GA-A--TATTGCTGGTGTG-CAC
* ** *
26998 GATATCCTTCGTCGTTAAGTTGAAATCCAATCTAAGGA-TGGGTGTTGTTGGTGGACACAATATC
1 GATATCCTTCGTCGTGAAGTTGAAATCCAATCT--GGAGTAAGT-TGGTT-GTGGACACAATATC
* * * *
27062 CTTCGTCGTGAAGTTAAAATCT-TGGATGGCCTCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
62 CTTCATCGTGAAGTTAAAAT-TGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTCAATTGGATA
*
27126 TCATTCTTCGTGAAATTGAAATCCAATCTGAATGTTGCTGGTGTGCAC
126 TCATTCTTCGTGAAATTGAAATCCAATCTGAATATTGCTGGTGTGCAC
27174 GATATCCTTCGTCGTGAAGTTGAAATC
1 GATATCCTTCGTCGTGAAGTTGAAATC
27201 GTGGATGGCC
Statistics
Matches: 179, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
176 38 0.21
177 1 0.01
178 1 0.01
179 33 0.18
180 3 0.02
181 8 0.04
182 94 0.53
183 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (173 bp):
GATATCCTTCGTCGTGAAGTTGAAATCCAATCTGGAGTAAGTTGGTTGTGGACACAATATCCTTC
ATCGTGAAGTTAAAATTGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTCAATTGGATATCATT
CTTCGTGAAATTGAAATCCAATCTGAATATTGCTGGTGTGCAC
Found at i:27179 original size:118 final size:118
Alignment explanation
Indices: 27040--27270 Score: 347
Period size: 118 Copynumber: 2.0 Consensus size: 118
27030 TAAGGATGGG
* * * *
27040 TGTTGTTGGTGGACACAATATCCTTCGTCGTGAAGTTAAAATCTTGGATGGCCTCTTCGTTGTGA
1 TGTTGCTGGTGGACACAATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCCCCTTCATTGTGA
* *
27105 AGTTGAGCCTTGAATTGGATATCATTCTTCGTGAAATTGAAATCCAATCTGAA
66 AGTTGAGCCTTGAATTGGATATCATTCGTCATGAAATTGAAATCCAATCTGAA
* * *
27158 TGTTGCTGGTGTG-CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTTATTGTG
1 TGTTGCTGGTG-GACACAATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCCCCTTCATTGTG
* *
27222 AAGTTGAGCCTTGATTTGGATATCATTCGTCATGAAGTTGAAATCCAAT
65 AAGTTGAGCCTTGAATTGGATATCATTCGTCATGAAATTGAAATCCAAT
27271 ATTGTGTAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
118 100 0.99
119 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (118 bp):
TGTTGCTGGTGGACACAATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCCCCTTCATTGTGA
AGTTGAGCCTTGAATTGGATATCATTCGTCATGAAATTGAAATCCAATCTGAA
Found at i:28124 original size:13 final size:12
Alignment explanation
Indices: 28102--28131 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
28092 ACCCACCTTA
28102 TTTTTCTTTTTC
1 TTTTTCTTTTTC
28114 TTTTCTCTTTTTC
1 TTTT-TCTTTTTC
28127 TTTTT
1 TTTTT
28132 TCAATTTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:28133 original size:7 final size:6
Alignment explanation
Indices: 28102--28131 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
28092 ACCCACCTTA
28102 TTTTTC TTTTTC TTTTCTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTT-TC TTTTTC TTTTT
28132 TCAATTTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:38669 original size:14 final size:14
Alignment explanation
Indices: 38652--38686 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
38642 ATATATATAT
*
38652 AATAATAAAGACAA
1 AATAATAAAGAAAA
*
38666 AATAATAATGAAAA
1 AATAATAAAGAAAA
38680 AATAATA
1 AATAATA
38687 GAGTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (14 bp):
AATAATAAAGAAAA
Found at i:38746 original size:18 final size:19
Alignment explanation
Indices: 38723--38765 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
38713 GTAAAAAACT
*
38723 AATATACATAAATA-ATTA
1 AATATACATAAATATATAA
* *
38741 AATATATATACATATATAA
1 AATATACATAAATATATAA
38760 AATATA
1 AATATA
38766 TAACAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AATATACATAAATATATAA
Found at i:41143 original size:10 final size:10
Alignment explanation
Indices: 41128--41152 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41118 ATTACTGCAG
41128 TAACGATTGT
1 TAACGATTGT
41138 TAACGATTGT
1 TAACGATTGT
41148 TAACG
1 TAACG
41153 TTGAGTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (10 bp):
TAACGATTGT
Found at i:42021 original size:20 final size:20
Alignment explanation
Indices: 41996--42038 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41986 TCTAAAGTCC
41996 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
42016 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
42036 CAT
1 CAT
42039 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:49717 original size:21 final size:21
Alignment explanation
Indices: 49684--49733 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
49674 CCCTACCCCA
49684 CATTTTCACCTTTCACTTTCTAT
1 CATTTT-A-CTTTCACTTTCTAT
* *
49707 CTTTTTACTTTTACTTTCTAT
1 CATTTTACTTTCACTTTCTAT
49728 CATTTT
1 CATTTT
49734 CTTCTCCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 1 0.04
23 5 0.21
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (21 bp):
CATTTTACTTTCACTTTCTAT
Done.