Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000045.1 Hibiscus syriacus cultivar Beakdansim tig00000071_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: 77343
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:3973 original size:31 final size:31
Alignment explanation
Indices: 3938--4000 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
3928 AAGTTTTAAA
3938 ATGGATAATGAGAATAAT-GGAAATCAAACTC
1 ATGGATAATGAG-ATAATGGGAAATCAAACTC
3969 ATGGATAATGAGATAATGGGAAATCAAACTC
1 ATGGATAATGAGATAATGGGAAATCAAACTC
4000 A
1 A
4001 AACCGACACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.22
Consensus pattern (31 bp):
ATGGATAATGAGATAATGGGAAATCAAACTC
Found at i:3987 original size:15 final size:15
Alignment explanation
Indices: 3937--3987 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3927 TAAGTTTTAA
3937 AATGGATAATGAGAAT
1 AATGGATAATGAG-AT
* *
3953 AATGGA-AATCAAACT
1 AATGGATAATGAGA-T
*
3968 CATGGATAATGAGAT
1 AATGGATAATGAGAT
3983 AATGG
1 AATGG
3988 GAAATCAAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
14 1 0.04
15 15 0.56
16 11 0.41
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.24
Consensus pattern (15 bp):
AATGGATAATGAGAT
Found at i:9003 original size:12 final size:12
Alignment explanation
Indices: 8986--9028 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
8976 AAATAGGTAT
8986 AAATATATTTTA
1 AAATATATTTTA
*
8998 AAATATATTATTT
1 AAATATATT-TTA
*
9011 TAAT-TATTTTA
1 AAATATATTTTA
9022 AAATATA
1 AAATATA
9029 AATATATTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 5 0.20
12 15 0.60
13 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AAATATATTTTA
Found at i:14795 original size:31 final size:32
Alignment explanation
Indices: 14741--14882 Score: 110
Period size: 31 Copynumber: 4.5 Consensus size: 32
14731 AGCGATAAAT
* *
14741 TTTGATAAATTTAAGGATTATTTTATGAC-AA
1 TTTGATAAATTTAATGATCATTTTATGACTAA
* * * *
14772 TTTGATAAATTTAATGACCATTTTCTTACTAC
1 TTTGATAAATTTAATGATCATTTTATGACTAA
* * * **
14804 TTTGTTAAAATTTAATGATCATTTCAT-AATGG
1 TTTGAT-AAATTTAATGATCATTTTATGACTAA
** *
14836 TTCAATAAATTTAATGATCATTTTGT-ACTAA
1 TTTGATAAATTTAATGATCATTTTATGACTAA
*
14867 TTTAATAAAATTTAAT
1 TTTGAT-AAATTTAAT
14883 AATTATTTAA
Statistics
Matches: 86, Mismatches: 22, Indels: 5
0.76 0.19 0.04
Matches are distributed among these distances:
31 49 0.57
32 20 0.23
33 17 0.20
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (32 bp):
TTTGATAAATTTAATGATCATTTTATGACTAA
Found at i:15011 original size:31 final size:30
Alignment explanation
Indices: 14915--15011 Score: 79
Period size: 32 Copynumber: 3.1 Consensus size: 30
14905 AGAATTTAAA
* *
14915 ATAATAATTCAATAAGTTT-ATAATCATTTT
1 ATAATAATTTAATAAATTTAATAAT-ATTTT
* * * * * *
14945 ATACTAAATTGATAAAGTATAATGATTATTCT
1 ATAATAATTTAATAAA-TTTAAT-AATATTTT
14977 ATAATAATTTAATAAATTTAATAACTATTTT
1 ATAATAATTTAATAAATTTAATAA-TATTTT
15008 ATAA
1 ATAA
15012 CATCCAAAAA
Statistics
Matches: 49, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
30 12 0.24
31 16 0.33
32 19 0.39
33 2 0.04
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (30 bp):
ATAATAATTTAATAAATTTAATAATATTTT
Found at i:23805 original size:27 final size:28
Alignment explanation
Indices: 23747--23805 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
23737 GGTTACAAAA
* *
23747 ATGAGTTTGATGACTATGAAGATGATAG
1 ATGAGTTTGATGACGACGAAGATGATAG
*
23775 -TGAGTTTGTTGACGACGAAGATGA-AG
1 ATGAGTTTGATGACGACGAAGATGATAG
23801 ATGAG
1 ATGAG
23806 GCCGACCACG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.29
Consensus pattern (28 bp):
ATGAGTTTGATGACGACGAAGATGATAG
Found at i:23832 original size:30 final size:30
Alignment explanation
Indices: 23791--23856 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
23781 TGTTGACGAC
* *
23791 GAAGATGAAGATGAGGCCGACCACGACTGG
1 GAAGATAAAGATGAGGCCGACAACGACTGG
*
23821 GAAGATAAAGATGAGGCCGTCAACGACTGG
1 GAAGATAAAGATGAGGCCGACAACGACTGG
23851 GAAGAT
1 GAAGAT
23857 GATGACTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.36, C:0.17, G:0.35, T:0.12
Consensus pattern (30 bp):
GAAGATAAAGATGAGGCCGACAACGACTGG
Found at i:35454 original size:16 final size:16
Alignment explanation
Indices: 35407--35459 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
35397 CATATCCAAT
*
35407 CCGAACTGAAAGCAAC
1 CCGAACCGAAAGCAAC
* * *
35423 CCGGACCAAAATCAAC
1 CCGAACCGAAAGCAAC
*
35439 CTGAACCGAAAGCAAC
1 CCGAACCGAAAGCAAC
35455 CCGAA
1 CCGAA
35460 TTTAATTTAC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.43, C:0.34, G:0.17, T:0.06
Consensus pattern (16 bp):
CCGAACCGAAAGCAAC
Found at i:35778 original size:26 final size:30
Alignment explanation
Indices: 35725--35778 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
35715 ATTATTTAAA
*
35725 AATTATTTATATTAATATTTATTCAAATAT
1 AATTATTTATATTAATATTTATTAAAATAT
35755 AATTA-TTATATT-AT-TTT-TTAAAAT
1 AATTATTTATATTAATATTTATTAAAAT
35779 TCAATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 6 0.26
27 3 0.13
28 2 0.09
29 7 0.30
30 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (30 bp):
AATTATTTATATTAATATTTATTAAAATAT
Found at i:38075 original size:12 final size:13
Alignment explanation
Indices: 38053--38078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38043 TTTATTTAAA
38053 AATGAAAAAAAAT
1 AATGAAAAAAAAT
38066 AATGAAAAAAAAT
1 AATGAAAAAAAAT
38079 CGAGTTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AATGAAAAAAAAT
Found at i:41214 original size:2 final size:2
Alignment explanation
Indices: 41207--41254 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
41197 AAAAGTTATG
41207 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
41249 AT AT AT
1 AT AT AT
41255 TTACGTAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42755 original size:22 final size:21
Alignment explanation
Indices: 42717--42763 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
42707 TATTAATGTG
42717 TAATTAAATATTGATATTAAAA
1 TAATTAAATATTGATA-TAAAA
* *
42739 TAATTCAAT-TTGAATATAAAT
1 TAATTAAATATTG-ATATAAAA
42760 TAAT
1 TAAT
42764 AATTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
TAATTAAATATTGATATAAAA
Found at i:48874 original size:276 final size:265
Alignment explanation
Indices: 48371--48910 Score: 676
Period size: 276 Copynumber: 2.0 Consensus size: 265
48361 TGCTGATAAT
* *
48371 TCTTTGTCGAATATATGCTTTAAAGTACTTTAAAAGGGATAAAAGAGCAGGATAAGTGATTTGAG
1 TCTTTGTCGAATATATGCTCTAAAGTACTTTAAAAGGGACAAAAGAGCAGGATAAGTGATTTGAG
* * * *
48436 TTAAACAGTCCTGGTTAGAAATCATAAGGGGAGTGTTAGTACCTTATGGTTTTCTTCCTTTTAGA
66 TTAAAAAGTCCTGGTTACAAATCATAAGGGGAGTGTTAGTACCCTATGGTGTTCTTCCTTTTAGA
* * * * *
48501 GGGGATGGATTTAAGTTCAAACTTGAAGATGCAGAATTGGGAAAAGGGCTGCGTGCTTTCTCTTT
131 GGGGATGGATTAAAGTTCAAACATGAAGAGGCAGAATTGGGAAAAGGGCTGCATGCTGTCTCTTT
* *
48566 CTAATTCTAGCCTTTATTTTTTGTACTGAAAATTTCGAAGATTGCATTTTGGGAATTTTCAACTT
196 CTAATTCTAGCCTTTATTTTTCGTACTGAAAATTTC---G-TTGCATTTTGGAAATTTTCAACTT
48631 CATCCTTTA
257 CATCCTTTA
48640 TCTTTG-CTGAATATATGCTCTAAAGTACTTT-AAAGGGACAAAAGAGCAGGATAAGTGATTTGA
1 TCTTTGTC-GAATATATGCTCTAAAGTACTTTAAAAGGGACAAAAGAGCAGGATAAGTGATTTGA
*
48703 GTTAAAAAGATTCCTGGTTTCAAATCATGAA-GGGAGTGGTAGTAGTGTGAACACCT-T-GTGTT
65 GTTAAAAAG--TCCTGGTTACAAATCAT-AAGGGGAGT-GT--TA--GT--AC-CCTATGGTGTT
* * * * *
48765 CTTCCTTTTAGAGGGGATGGGTTAAAGTTGAAACATGAAGAGGCGGAATTGGGAAAAGGGTTGTA
119 CTTCCTTTTAGAGGGGATGGATTAAAGTTCAAACATGAAGAGGCAGAATTGGGAAAAGGGCTGCA
* * * * *
48830 TGGTGTGTCTTTCTGATTCTAGCCTTTCTTTTTCGTATTGAAAATTTCGTTGCATTTTGGAAATT
184 TGCTGTCTCTTTCTAATTCTAGCCTTTATTTTTCGTACTGAAAATTTCGTTGCATTTTGGAAATT
*
48895 TTCAACTTCGTCCTTT
249 TTCAACTTCATCCTTT
48911 TTATCTTTTT
Statistics
Matches: 234, Mismatches: 25, Indels: 21
0.84 0.09 0.08
Matches are distributed among these distances:
268 40 0.17
269 28 0.12
270 21 0.09
271 4 0.02
272 30 0.13
273 3 0.01
275 2 0.01
276 101 0.43
277 3 0.01
278 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (265 bp):
TCTTTGTCGAATATATGCTCTAAAGTACTTTAAAAGGGACAAAAGAGCAGGATAAGTGATTTGAG
TTAAAAAGTCCTGGTTACAAATCATAAGGGGAGTGTTAGTACCCTATGGTGTTCTTCCTTTTAGA
GGGGATGGATTAAAGTTCAAACATGAAGAGGCAGAATTGGGAAAAGGGCTGCATGCTGTCTCTTT
CTAATTCTAGCCTTTATTTTTCGTACTGAAAATTTCGTTGCATTTTGGAAATTTTCAACTTCATC
CTTTA
Found at i:59816 original size:27 final size:27
Alignment explanation
Indices: 59778--59832 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
59768 AGCCTCAAAA
59778 ACTCTTTCAGGAGAGTAAATATTTTGT
1 ACTCTTTCAGGAGAGTAAATATTTTGT
59805 ACTCTTTCAGGAGAGTAAATATTTTGT
1 ACTCTTTCAGGAGAGTAAATATTTTGT
59832 A
1 A
59833 TACCAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (27 bp):
ACTCTTTCAGGAGAGTAAATATTTTGT
Found at i:60369 original size:25 final size:25
Alignment explanation
Indices: 60315--60374 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
60305 TTTTCAGTTA
*
60315 TTAATTATTTAAAATTGTATTATTG
1 TTAATTTTTTAAAATTGTATTATTG
*
60340 ATAATTTTTTAAAAATT-TATATATT-
1 TTAATTTTTT-AAAATTGTAT-TATTG
60365 TTAATTTTTT
1 TTAATTTTTT
60375 TAATGAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
TTAATTTTTTAAAATTGTATTATTG
Done.