Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002162.1 Hibiscus syriacus cultivar Beakdansim tig00004414_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: 64949
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1855 original size:18 final size:18
Alignment explanation
Indices: 1816--1851 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1806 TTAAAAAGAA
*
1816 TAATAGTTTATTGAAAAT
1 TAATAATTTATTGAAAAT
1834 TAATAATTTATT-AAAAT
1 TAATAATTTATTGAAAAT
1851 T
1 T
1852 TAATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TAATAATTTATTGAAAAT
Found at i:3270 original size:21 final size:22
Alignment explanation
Indices: 3248--3301 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
3238 AAACTTATTA
3248 AATTAATTATTATTTTTAATAAA-
1 AATTAATTA--ATTTTTAATAAAT
3271 AATTAAATTAATTTTTAATAAAT
1 AATT-AATTAATTTTTAATAAAT
*
3294 AAATAATT
1 AATTAATT
3302 TTTAAGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 16 0.57
23 7 0.25
24 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTAATTAATTTTTAATAAAT
Found at i:3304 original size:19 final size:21
Alignment explanation
Indices: 3259--3306 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 21
3249 ATTAATTATT
3259 ATTTTTAATAAAAATTAAATTA
1 ATTTTTAAT-AAAATTAAATTA
3281 ATTTTTAAT-AAA-TAAA-TA
1 ATTTTTAATAAAATTAAATTA
3299 ATTTTTAA
1 ATTTTTAA
3307 GAAACTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.38
19 4 0.15
20 3 0.12
22 9 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTTTAATAAAATTAAATTA
Found at i:3570 original size:2 final size:2
Alignment explanation
Indices: 3563--3601 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3553 AAGCTCAACC
3563 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
3602 CCGAAGCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24831 original size:22 final size:22
Alignment explanation
Indices: 24801--24848 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
24791 AATTATAATT
24801 ATAAAATT-ATAAAAAAAATTAA
1 ATAAAATTAAT-AAAAAAATTAA
* * *
24823 ATAATATTAATTATAAAATTAA
1 ATAAAATTAATAAAAAAATTAA
24845 ATAA
1 ATAA
24849 CGTAATTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAAATTAATAAAAAAATTAA
Found at i:24856 original size:21 final size:22
Alignment explanation
Indices: 24815--24856 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
24805 AATTATAAAA
*
24815 AAAATTAAATAATATTAATTAT
1 AAAATTAAATAATAGTAATTAT
*
24837 AAAATTAAATAA-CGTAATTA
1 AAAATTAAATAATAGTAATTA
24857 GAAATATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATTAAATAATAGTAATTAT
Found at i:25918 original size:29 final size:29
Alignment explanation
Indices: 25871--25936 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
25861 AACTTCCAAA
*
25871 TAAACAATAATTCAATTCTGGGAAATTGT
1 TAAAAAATAATTCAATTCTGGGAAATTGT
*
25900 TCAAAAATAATTCAATTCTGGGAAATTGT
1 TAAAAAATAATTCAATTCTGGGAAATTGT
25929 TAAAAAAT
1 TAAAAAAT
25937 TATTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (29 bp):
TAAAAAATAATTCAATTCTGGGAAATTGT
Found at i:26216 original size:28 final size:28
Alignment explanation
Indices: 26184--26238 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
26174 AAAGTAACCC
26184 ATGCCGTTCGAGACATGAACGAAATAAT
1 ATGCCGTTCGAGACATGAACGAAATAAT
26212 ATGCCGTTCGAGACATGAACGAAATAA
1 ATGCCGTTCGAGACATGAACGAAATAA
26239 GTAATTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (28 bp):
ATGCCGTTCGAGACATGAACGAAATAAT
Found at i:28818 original size:17 final size:17
Alignment explanation
Indices: 28798--28835 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
28788 TTTTTTAAAA
28798 AAATAATTATTTTTTAT
1 AAATAATTATTTTTTAT
*
28815 AAAT-ATTTTTTTTTAT
1 AAATAATTATTTTTTAT
28831 AAATA
1 AAATA
28836 TATAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATAATTATTTTTTAT
Found at i:33411 original size:59 final size:59
Alignment explanation
Indices: 33302--33413 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
33292 AAATATTAAA
* * * *
33302 ATAATCAAATAATTATTTTATAATTTTTAATAATTATTAACTCAATAAAATAATATTCT
1 ATAATCAAAAAATTATTTTATAACTTTTAATAATTATGAACTCAAAAAAATAATATTCT
* *
33361 ATAATCAAAAAATTATTTTATAACTTTTAATAGTTA-GAATTCAACAAAAATAA
1 ATAATCAAAAAATTATTTTATAACTTTTAATAATTATGAACTCAA-AAAAATAA
33414 CATCATAGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 6 0.13
59 40 0.87
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (59 bp):
ATAATCAAAAAATTATTTTATAACTTTTAATAATTATGAACTCAAAAAAATAATATTCT
Found at i:43476 original size:66 final size:67
Alignment explanation
Indices: 43370--43504 Score: 263
Period size: 66 Copynumber: 2.0 Consensus size: 67
43360 AGCAGAAGTT
43370 AACCACTGCCATTCAAAAGAAGGGGTTAACTAAATTATTGGGCTTGGATTATGCTATTC-ATACA
1 AACCACTGCCATTCAAAAGAAGGGGTTAACTAAATTATTGGGCTTGGATTATGCTATTCAATACA
43434 GA
66 GA
43436 AACCACTGCCATTCAAAAGAAGGGGTTAACTAAATTATTGGGCTTGGATTATGCTATTCAATACA
1 AACCACTGCCATTCAAAAGAAGGGGTTAACTAAATTATTGGGCTTGGATTATGCTATTCAATACA
43501 GA
66 GA
43503 AA
1 AA
43505 AGGTAAATCC
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 59 0.87
67 9 0.13
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28
Consensus pattern (67 bp):
AACCACTGCCATTCAAAAGAAGGGGTTAACTAAATTATTGGGCTTGGATTATGCTATTCAATACA
GA
Found at i:49925 original size:16 final size:17
Alignment explanation
Indices: 49904--49938 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
49894 GAAAGGGAAA
*
49904 GGAGGAGG-GATTTGAG
1 GGAGGAGGAGAGTTGAG
49920 GGAGGAGGAGAGTTGAG
1 GGAGGAGGAGAGTTGAG
49937 GG
1 GG
49939 GGTTGGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.60, T:0.14
Consensus pattern (17 bp):
GGAGGAGGAGAGTTGAG
Found at i:51392 original size:2 final size:2
Alignment explanation
Indices: 51385--51429 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
51375 CTTAATATGT
* * *
51385 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TG TA TA TG TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51426 TA TA
1 TA TA
51430 GTATTGAGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51406 original size:12 final size:12
Alignment explanation
Indices: 51385--51429 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
51375 CTTAATATGT
*
51385 TATATATATATA
1 TATATGTATATA
51397 TATATGTATATA
1 TATATGTATATA
*
51409 TATATGTATATG
1 TATATGTATATA
51421 TATAT-TATA
1 TATATGTATA
51430 GTATTGAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 4 0.13
12 27 0.87
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (12 bp):
TATATGTATATA
Found at i:54742 original size:31 final size:31
Alignment explanation
Indices: 54690--54755 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
54680 AAATTTAAAT
54690 TGGTCACGAACATTATCGATTTGTAACAAAA
1 TGGTCACGAACATTATCGATTTGTAACAAAA
* * *
54721 TGGTCACTAACGTTATTGATTTGTAACAAAA
1 TGGTCACGAACATTATCGATTTGTAACAAAA
54752 TGGT
1 TGGT
54756 AACTTCACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (31 bp):
TGGTCACGAACATTATCGATTTGTAACAAAA
Found at i:54975 original size:25 final size:24
Alignment explanation
Indices: 54947--54996 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
54937 TTAATAAATT
54947 TTAAAA-AAAATTAAAACATTAAAAG
1 TTAAAATAAAATT-AAA-ATTAAAAG
54972 TTAAAATTAAAATTAAAATTAAAAG
1 TTAAAA-TAAAATTAAAATTAAAAG
54997 ATCTTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 14 0.61
26 3 0.13
27 6 0.26
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (24 bp):
TTAAAATAAAATTAAAATTAAAAG
Found at i:54981 original size:6 final size:6
Alignment explanation
Indices: 54953--54995 Score: 59
Period size: 6 Copynumber: 6.7 Consensus size: 6
54943 AATTTTAAAA
54953 AAAATT AAAACATT AAAAGTT AAAATT AAAATT AAAATT AAAA
1 AAAATT -AAA-ATT AAAA-TT AAAATT AAAATT AAAATT AAAA
54996 GATCTTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.56
7 12 0.35
8 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (6 bp):
AAAATT
Found at i:55213 original size:8 final size:8
Alignment explanation
Indices: 55190--55229 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
55180 ACTCGTTACC
55190 TTTTTAGAT
1 TTTTTA-AT
*
55199 ATTTTAAT
1 TTTTTAAT
55207 TTTTTAAT
1 TTTTTAAT
55215 TTTTTAAT
1 TTTTTAAT
55223 ATTTTTA
1 -TTTTTA
55230 TAGATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 17 0.61
9 11 0.39
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (8 bp):
TTTTTAAT
Found at i:55219 original size:16 final size:18
Alignment explanation
Indices: 55190--55229 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
55180 ACTCGTTACC
55190 TTTTTAGATATTTTAAT-
1 TTTTTAGATATTTTAATA
*
55207 TTTTTA-ATTTTTTAATA
1 TTTTTAGATATTTTAATA
55224 TTTTTA
1 TTTTTA
55230 TAGATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTTAGATATTTTAATA
Found at i:55238 original size:20 final size:18
Alignment explanation
Indices: 55204--55246 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
55194 TAGATATTTT
55204 AATTTTTTAATTTTTTAA
1 AATTTTTTAATTTTTTAA
*
55222 TATTTTTATAGATTTTTTAA
1 AATTTTT-TA-ATTTTTTAA
55242 AATTT
1 AATTT
55247 ATTCAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 2 0.10
20 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
AATTTTTTAATTTTTTAA
Found at i:55498 original size:31 final size:31
Alignment explanation
Indices: 55424--55501 Score: 113
Period size: 30 Copynumber: 2.5 Consensus size: 31
55414 ATGACGATAG
* *
55424 AGTGATCATTTTGTTATAAATGGATAACGTT
1 AGTGATCATTTTGTTACAAATGGATAACATT
*
55455 -GTGATCATTTTGTTACAAATTGATAACATT
1 AGTGATCATTTTGTTACAAATGGATAACATT
*
55485 AGTGATCAATTTGTTAC
1 AGTGATCATTTTGTTAC
55502 TTTTGAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 27 0.64
31 15 0.36
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (31 bp):
AGTGATCATTTTGTTACAAATGGATAACATT
Done.