Multiple sequence alignment - TraesCS6B01G349100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G349100 chr6B 100.000 3153 0 0 1 3153 613609173 613612325 0.000000e+00 5823.0
1 TraesCS6B01G349100 chr6B 85.596 1326 101 50 123 1385 614126528 614127826 0.000000e+00 1308.0
2 TraesCS6B01G349100 chr6B 92.484 785 45 3 1395 2165 614127881 614128665 0.000000e+00 1110.0
3 TraesCS6B01G349100 chr6B 92.523 535 30 6 2268 2796 71498336 71498866 0.000000e+00 758.0
4 TraesCS6B01G349100 chr6B 87.321 418 19 7 2769 3153 71559730 71560146 6.200000e-122 448.0
5 TraesCS6B01G349100 chr6B 98.182 110 2 0 18 127 156651546 156651437 3.210000e-45 193.0
6 TraesCS6B01G349100 chr6B 96.364 110 4 0 18 127 679979076 679978967 6.950000e-42 182.0
7 TraesCS6B01G349100 chr6B 94.231 52 2 1 2266 2317 2669934 2669984 9.380000e-11 78.7
8 TraesCS6B01G349100 chr6D 95.051 1273 46 11 122 1389 408944640 408945900 0.000000e+00 1986.0
9 TraesCS6B01G349100 chr6D 90.979 1042 58 11 1152 2165 409288096 409289129 0.000000e+00 1371.0
10 TraesCS6B01G349100 chr6D 95.256 801 38 0 1395 2195 408945953 408946753 0.000000e+00 1269.0
11 TraesCS6B01G349100 chr6D 86.094 827 69 29 355 1151 409287253 409288063 0.000000e+00 848.0
12 TraesCS6B01G349100 chr6D 85.526 228 19 11 123 345 409286901 409287119 3.160000e-55 226.0
13 TraesCS6B01G349100 chr6D 93.902 82 3 1 2191 2270 408946909 408946990 4.270000e-24 122.0
14 TraesCS6B01G349100 chr6A 93.082 1142 52 10 1152 2270 554716151 554717288 0.000000e+00 1646.0
15 TraesCS6B01G349100 chr6A 85.274 1331 111 52 123 1387 554786380 554787691 0.000000e+00 1293.0
16 TraesCS6B01G349100 chr6A 92.611 785 44 5 1395 2165 554787744 554788528 0.000000e+00 1116.0
17 TraesCS6B01G349100 chr6A 86.645 629 48 17 535 1150 554715515 554716120 0.000000e+00 664.0
18 TraesCS6B01G349100 chr6A 81.308 321 37 17 123 432 554715056 554715364 4.060000e-59 239.0
19 TraesCS6B01G349100 chr7D 94.366 710 27 4 2274 2977 70181892 70182594 0.000000e+00 1077.0
20 TraesCS6B01G349100 chr7D 77.076 602 108 25 1213 1805 135357575 135358155 1.410000e-83 320.0
21 TraesCS6B01G349100 chr7D 92.486 173 11 2 2981 3153 70182629 70182799 2.430000e-61 246.0
22 TraesCS6B01G349100 chr7D 92.308 130 7 3 12 140 364631241 364631114 6.950000e-42 182.0
23 TraesCS6B01G349100 chr3B 86.536 661 59 10 2341 2988 240791675 240792318 0.000000e+00 701.0
24 TraesCS6B01G349100 chr3B 75.804 591 112 21 2265 2832 682170031 682169449 1.440000e-68 270.0
25 TraesCS6B01G349100 chr3B 99.099 111 0 1 18 127 50046416 50046526 6.900000e-47 198.0
26 TraesCS6B01G349100 chr3B 97.727 44 1 0 2274 2317 764318704 764318747 3.370000e-10 76.8
27 TraesCS6B01G349100 chr7B 75.574 827 155 41 997 1805 97192164 97192961 6.430000e-97 364.0
28 TraesCS6B01G349100 chr7B 95.763 118 5 0 16 133 380869619 380869736 1.150000e-44 191.0
29 TraesCS6B01G349100 chr7B 93.478 46 1 2 2272 2316 567987081 567987125 2.030000e-07 67.6
30 TraesCS6B01G349100 chr7A 75.361 832 149 47 997 1805 134491241 134492039 1.800000e-92 350.0
31 TraesCS6B01G349100 chr5B 98.214 112 1 1 18 128 610658969 610659080 8.920000e-46 195.0
32 TraesCS6B01G349100 chr5B 85.507 69 10 0 2274 2342 83697745 83697813 4.360000e-09 73.1
33 TraesCS6B01G349100 chrUn 94.958 119 6 0 17 135 15981934 15981816 1.490000e-43 187.0
34 TraesCS6B01G349100 chr3A 94.872 117 6 0 11 127 57873976 57873860 1.930000e-42 183.0
35 TraesCS6B01G349100 chr3A 95.349 43 0 2 2272 2313 506402520 506402479 2.030000e-07 67.6
36 TraesCS6B01G349100 chr1D 94.215 121 6 1 11 131 45399308 45399189 1.930000e-42 183.0
37 TraesCS6B01G349100 chr1D 91.071 56 3 1 2262 2317 16495988 16496041 1.210000e-09 75.0
38 TraesCS6B01G349100 chr2D 86.290 124 11 5 1224 1344 627974070 627974190 2.550000e-26 130.0
39 TraesCS6B01G349100 chr2B 87.255 102 11 2 1224 1324 771043285 771043385 7.150000e-22 115.0
40 TraesCS6B01G349100 chr1B 81.356 118 22 0 1430 1547 615744798 615744681 2.590000e-16 97.1
41 TraesCS6B01G349100 chr1B 92.727 55 2 2 2263 2316 466663904 466663851 9.380000e-11 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G349100 chr6B 613609173 613612325 3152 False 5823.000000 5823 100.000000 1 3153 1 chr6B.!!$F4 3152
1 TraesCS6B01G349100 chr6B 614126528 614128665 2137 False 1209.000000 1308 89.040000 123 2165 2 chr6B.!!$F5 2042
2 TraesCS6B01G349100 chr6B 71498336 71498866 530 False 758.000000 758 92.523000 2268 2796 1 chr6B.!!$F2 528
3 TraesCS6B01G349100 chr6D 408944640 408946990 2350 False 1125.666667 1986 94.736333 122 2270 3 chr6D.!!$F1 2148
4 TraesCS6B01G349100 chr6D 409286901 409289129 2228 False 815.000000 1371 87.533000 123 2165 3 chr6D.!!$F2 2042
5 TraesCS6B01G349100 chr6A 554786380 554788528 2148 False 1204.500000 1293 88.942500 123 2165 2 chr6A.!!$F2 2042
6 TraesCS6B01G349100 chr6A 554715056 554717288 2232 False 849.666667 1646 87.011667 123 2270 3 chr6A.!!$F1 2147
7 TraesCS6B01G349100 chr7D 70181892 70182799 907 False 661.500000 1077 93.426000 2274 3153 2 chr7D.!!$F2 879
8 TraesCS6B01G349100 chr7D 135357575 135358155 580 False 320.000000 320 77.076000 1213 1805 1 chr7D.!!$F1 592
9 TraesCS6B01G349100 chr3B 240791675 240792318 643 False 701.000000 701 86.536000 2341 2988 1 chr3B.!!$F2 647
10 TraesCS6B01G349100 chr3B 682169449 682170031 582 True 270.000000 270 75.804000 2265 2832 1 chr3B.!!$R1 567
11 TraesCS6B01G349100 chr7B 97192164 97192961 797 False 364.000000 364 75.574000 997 1805 1 chr7B.!!$F1 808
12 TraesCS6B01G349100 chr7A 134491241 134492039 798 False 350.000000 350 75.361000 997 1805 1 chr7A.!!$F1 808

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
33 34 0.033796 ACATACTCCCTCCGTTCGGA 60.034 55.0 13.34 13.34 0.0 4.55 F
662 895 0.111061 TGACTGCTGATTGCCCAAGT 59.889 50.0 0.00 0.00 42.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 2064 0.828762 TTTGCTGCCTGGACTGCATT 60.829 50.0 17.95 0.0 42.94 3.56 R
2249 2829 0.331278 TTGAAGATCCGGCAACCCAT 59.669 50.0 0.00 0.0 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.845781 CTGCTGGTCCCATTACATACT 57.154 47.619 0.00 0.00 0.00 2.12
21 22 3.733337 CTGCTGGTCCCATTACATACTC 58.267 50.000 0.00 0.00 0.00 2.59
22 23 2.438021 TGCTGGTCCCATTACATACTCC 59.562 50.000 0.00 0.00 0.00 3.85
23 24 2.224548 GCTGGTCCCATTACATACTCCC 60.225 54.545 0.00 0.00 0.00 4.30
24 25 3.318313 CTGGTCCCATTACATACTCCCT 58.682 50.000 0.00 0.00 0.00 4.20
25 26 3.314693 TGGTCCCATTACATACTCCCTC 58.685 50.000 0.00 0.00 0.00 4.30
26 27 2.638363 GGTCCCATTACATACTCCCTCC 59.362 54.545 0.00 0.00 0.00 4.30
27 28 2.299297 GTCCCATTACATACTCCCTCCG 59.701 54.545 0.00 0.00 0.00 4.63
28 29 2.090943 TCCCATTACATACTCCCTCCGT 60.091 50.000 0.00 0.00 0.00 4.69
29 30 2.704065 CCCATTACATACTCCCTCCGTT 59.296 50.000 0.00 0.00 0.00 4.44
30 31 3.244112 CCCATTACATACTCCCTCCGTTC 60.244 52.174 0.00 0.00 0.00 3.95
31 32 3.552273 CCATTACATACTCCCTCCGTTCG 60.552 52.174 0.00 0.00 0.00 3.95
32 33 1.683943 TACATACTCCCTCCGTTCGG 58.316 55.000 4.74 4.74 0.00 4.30
33 34 0.033796 ACATACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
34 35 1.108776 CATACTCCCTCCGTTCGGAA 58.891 55.000 14.79 0.00 33.41 4.30
35 36 1.687123 CATACTCCCTCCGTTCGGAAT 59.313 52.381 14.79 2.14 33.41 3.01
36 37 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
37 38 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
38 39 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
39 40 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
40 41 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
41 42 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
42 43 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
43 44 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
44 45 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
45 46 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
46 47 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87
47 48 1.987770 GTTCGGAATTACTTGTCGCGA 59.012 47.619 3.71 3.71 0.00 5.87
48 49 2.350899 TCGGAATTACTTGTCGCGAA 57.649 45.000 12.06 0.00 0.00 4.70
49 50 2.674954 TCGGAATTACTTGTCGCGAAA 58.325 42.857 12.06 0.54 0.00 3.46
50 51 3.058450 TCGGAATTACTTGTCGCGAAAA 58.942 40.909 12.06 12.01 0.00 2.29
51 52 3.680937 TCGGAATTACTTGTCGCGAAAAT 59.319 39.130 13.05 5.74 0.00 1.82
52 53 3.778718 CGGAATTACTTGTCGCGAAAATG 59.221 43.478 13.05 9.32 0.00 2.32
53 54 4.095610 GGAATTACTTGTCGCGAAAATGG 58.904 43.478 13.05 4.35 0.00 3.16
54 55 4.142773 GGAATTACTTGTCGCGAAAATGGA 60.143 41.667 13.05 0.56 0.00 3.41
55 56 5.448632 GGAATTACTTGTCGCGAAAATGGAT 60.449 40.000 13.05 3.91 0.00 3.41
56 57 2.900122 ACTTGTCGCGAAAATGGATG 57.100 45.000 13.05 2.76 0.00 3.51
57 58 2.151202 ACTTGTCGCGAAAATGGATGT 58.849 42.857 13.05 3.46 0.00 3.06
58 59 3.331150 ACTTGTCGCGAAAATGGATGTA 58.669 40.909 13.05 0.00 0.00 2.29
59 60 3.938963 ACTTGTCGCGAAAATGGATGTAT 59.061 39.130 13.05 0.00 0.00 2.29
60 61 4.034048 ACTTGTCGCGAAAATGGATGTATC 59.966 41.667 13.05 0.00 0.00 2.24
61 62 3.792401 TGTCGCGAAAATGGATGTATCT 58.208 40.909 12.06 0.00 0.00 1.98
62 63 4.939271 TGTCGCGAAAATGGATGTATCTA 58.061 39.130 12.06 0.00 0.00 1.98
63 64 4.982295 TGTCGCGAAAATGGATGTATCTAG 59.018 41.667 12.06 0.00 0.00 2.43
64 65 5.220381 GTCGCGAAAATGGATGTATCTAGA 58.780 41.667 12.06 0.00 0.00 2.43
65 66 5.117287 GTCGCGAAAATGGATGTATCTAGAC 59.883 44.000 12.06 0.00 0.00 2.59
66 67 4.088638 CGCGAAAATGGATGTATCTAGACG 59.911 45.833 0.00 0.00 0.00 4.18
67 68 4.982916 GCGAAAATGGATGTATCTAGACGT 59.017 41.667 0.00 0.00 0.00 4.34
68 69 6.147581 GCGAAAATGGATGTATCTAGACGTA 58.852 40.000 0.00 0.00 0.00 3.57
69 70 6.807230 GCGAAAATGGATGTATCTAGACGTAT 59.193 38.462 0.00 0.00 0.00 3.06
70 71 7.328737 GCGAAAATGGATGTATCTAGACGTATT 59.671 37.037 0.00 0.00 0.00 1.89
71 72 9.193133 CGAAAATGGATGTATCTAGACGTATTT 57.807 33.333 0.00 0.00 0.00 1.40
100 101 8.919777 TTCTAGATACATCTATTTCCGAGACA 57.080 34.615 0.00 0.00 38.60 3.41
101 102 8.919777 TCTAGATACATCTATTTCCGAGACAA 57.080 34.615 0.00 0.00 38.60 3.18
102 103 9.004717 TCTAGATACATCTATTTCCGAGACAAG 57.995 37.037 0.00 0.00 38.60 3.16
103 104 7.589958 AGATACATCTATTTCCGAGACAAGT 57.410 36.000 0.00 0.00 34.85 3.16
104 105 8.693120 AGATACATCTATTTCCGAGACAAGTA 57.307 34.615 0.00 0.00 34.85 2.24
105 106 9.132923 AGATACATCTATTTCCGAGACAAGTAA 57.867 33.333 0.00 0.00 34.85 2.24
106 107 9.915629 GATACATCTATTTCCGAGACAAGTAAT 57.084 33.333 0.00 0.00 0.00 1.89
108 109 8.649973 ACATCTATTTCCGAGACAAGTAATTC 57.350 34.615 0.00 0.00 0.00 2.17
109 110 7.711339 ACATCTATTTCCGAGACAAGTAATTCC 59.289 37.037 0.00 0.00 0.00 3.01
110 111 6.270815 TCTATTTCCGAGACAAGTAATTCCG 58.729 40.000 0.00 0.00 0.00 4.30
111 112 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
112 113 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
113 114 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
114 115 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
115 116 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
116 117 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
117 118 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
118 119 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
119 120 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
120 121 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
237 239 8.904834 TCTCTGAAACCTGTGATACTCTATAAC 58.095 37.037 0.00 0.00 0.00 1.89
289 313 7.545265 ACAATGTTGCCAATACAATATCAACAC 59.455 33.333 7.61 0.00 44.01 3.32
300 328 4.641989 ACAATATCAACACATCTTGAGGCC 59.358 41.667 0.00 0.00 33.65 5.19
353 381 7.254852 TGAAGTTGTTGAAATTGTACCACTTC 58.745 34.615 16.62 16.62 41.36 3.01
393 545 1.003233 CAGTACACTTCCAGGAACCCC 59.997 57.143 0.00 0.00 0.00 4.95
403 555 1.547901 CCAGGAACCCCCTTCTGAAAC 60.548 57.143 0.00 0.00 44.85 2.78
457 648 3.316029 TGCCAGCAAGCAATCACATATAC 59.684 43.478 0.00 0.00 40.56 1.47
660 893 0.178995 TGTGACTGCTGATTGCCCAA 60.179 50.000 0.00 0.00 42.00 4.12
661 894 0.524862 GTGACTGCTGATTGCCCAAG 59.475 55.000 0.00 0.00 42.00 3.61
662 895 0.111061 TGACTGCTGATTGCCCAAGT 59.889 50.000 0.00 0.00 42.00 3.16
690 923 1.661112 GCTAGCGGCTTAAGTCAACAG 59.339 52.381 8.26 1.44 38.06 3.16
759 998 1.523711 CCCGGCGCTTGACATGTAT 60.524 57.895 7.64 0.00 0.00 2.29
760 999 1.498865 CCCGGCGCTTGACATGTATC 61.499 60.000 7.64 0.00 0.00 2.24
761 1000 1.559814 CGGCGCTTGACATGTATCG 59.440 57.895 7.64 1.11 0.00 2.92
763 1002 1.428370 GGCGCTTGACATGTATCGCA 61.428 55.000 24.46 8.02 43.72 5.10
764 1003 0.583438 GCGCTTGACATGTATCGCAT 59.417 50.000 20.86 0.00 41.84 4.73
766 1005 2.410262 GCGCTTGACATGTATCGCATAC 60.410 50.000 20.86 0.45 41.84 2.39
767 1006 3.052745 CGCTTGACATGTATCGCATACT 58.947 45.455 0.00 0.00 35.74 2.12
769 1008 3.120286 GCTTGACATGTATCGCATACTCG 59.880 47.826 0.00 0.00 35.74 4.18
770 1009 2.661594 TGACATGTATCGCATACTCGC 58.338 47.619 0.00 0.00 35.74 5.03
771 1010 2.034053 TGACATGTATCGCATACTCGCA 59.966 45.455 0.00 0.00 35.74 5.10
772 1011 3.245797 GACATGTATCGCATACTCGCAT 58.754 45.455 0.00 0.00 35.74 4.73
773 1012 4.083003 TGACATGTATCGCATACTCGCATA 60.083 41.667 0.00 0.00 35.74 3.14
776 1015 2.094906 TGTATCGCATACTCGCATACCC 60.095 50.000 7.50 0.00 36.70 3.69
791 1030 3.689649 GCATACCCAATTATCTAAGGGCG 59.310 47.826 0.00 0.00 45.45 6.13
822 1062 8.101419 AGTCCTTTCCACTCGAATAAACTAATT 58.899 33.333 0.00 0.00 0.00 1.40
829 1069 6.258068 CCACTCGAATAAACTAATTCTGACCC 59.742 42.308 0.00 0.00 34.34 4.46
837 1077 9.462606 AATAAACTAATTCTGACCCAGGTTTAG 57.537 33.333 0.00 0.00 31.85 1.85
844 1084 0.327259 GACCCAGGTTTAGGACACCC 59.673 60.000 0.00 0.00 34.44 4.61
845 1085 0.402272 ACCCAGGTTTAGGACACCCA 60.402 55.000 0.00 0.00 34.44 4.51
851 1091 3.190535 CAGGTTTAGGACACCCAATTTCG 59.809 47.826 0.00 0.00 34.44 3.46
852 1092 2.094906 GGTTTAGGACACCCAATTTCGC 60.095 50.000 0.00 0.00 33.88 4.70
994 1242 6.150332 TCCTACCCCAATTCTATCTCAATCA 58.850 40.000 0.00 0.00 0.00 2.57
1029 1277 1.347817 CTCCTTGCTGCGACGAGAAC 61.348 60.000 9.50 0.00 0.00 3.01
1086 1334 2.093973 CCAGAAGCTCACGGACTACATT 60.094 50.000 0.00 0.00 0.00 2.71
1098 1346 3.430790 CGGACTACATTGAGAAGCATGGA 60.431 47.826 0.00 0.00 0.00 3.41
1139 1387 1.965930 CCAAGCTTGCAGGTACGCA 60.966 57.895 21.43 0.00 41.03 5.24
1373 1722 3.686726 CACACCTATCAAACCTCTTGCTC 59.313 47.826 0.00 0.00 0.00 4.26
1407 1806 9.195411 CTTCAAAAACATATTGCTAACACACAT 57.805 29.630 0.00 0.00 0.00 3.21
1600 2003 1.958205 GCTCATCGCGCTAGCCAAT 60.958 57.895 9.66 0.00 41.18 3.16
1644 2047 3.777925 CTGCGACGACCAAAGCGG 61.778 66.667 0.00 0.00 42.50 5.52
1690 2093 0.539051 AGGCAGCAAAGCTCGAGTAT 59.461 50.000 15.13 0.00 36.40 2.12
1759 2162 0.172578 CCAGCAGCATCAACACCATG 59.827 55.000 0.00 0.00 0.00 3.66
1807 2213 1.203287 CTGAGTCCTTCGCAGATGTCA 59.797 52.381 0.00 0.00 44.72 3.58
1820 2226 3.677148 GCAGATGTCATCCTTGTCTTCGA 60.677 47.826 9.29 0.00 0.00 3.71
1906 2312 5.073827 TGACATCCAGATACCTAGTAGCTCT 59.926 44.000 0.00 0.00 32.11 4.09
1946 2352 5.589855 CAGGCTATCATCAATTGTACCAACA 59.410 40.000 5.13 0.00 0.00 3.33
2040 2458 2.420022 CACTTGCCGACTTCCCTATTTG 59.580 50.000 0.00 0.00 0.00 2.32
2249 2829 5.940192 AAAATCTGTGCAAAGTGATACGA 57.060 34.783 3.21 0.00 0.00 3.43
2250 2830 6.500684 AAAATCTGTGCAAAGTGATACGAT 57.499 33.333 3.21 0.00 0.00 3.73
2329 2909 1.204704 CTCACGCATCCACACTCCTTA 59.795 52.381 0.00 0.00 0.00 2.69
2376 2956 0.539986 ATGGCCGTCCGATACACTTT 59.460 50.000 0.00 0.00 34.14 2.66
2382 2962 2.422479 CCGTCCGATACACTTTCTCTCA 59.578 50.000 0.00 0.00 0.00 3.27
2397 2977 2.046988 TCATGTGTGGGCTGCTCG 60.047 61.111 0.00 0.00 0.00 5.03
2496 3078 0.669077 CTCGGATGGACGGTAAGGAG 59.331 60.000 0.00 0.00 0.00 3.69
2545 3130 0.398098 TCTCTAATCCCACCCCCGAC 60.398 60.000 0.00 0.00 0.00 4.79
2547 3132 2.367242 TAATCCCACCCCCGACCC 60.367 66.667 0.00 0.00 0.00 4.46
2729 3316 4.263639 TGCAACAGGGATCATCTCTTTCTT 60.264 41.667 0.00 0.00 0.00 2.52
2765 3353 2.446848 ATCCCCAGATCGGTGGCAG 61.447 63.158 0.00 0.00 36.11 4.85
2915 3520 2.435693 GGCTCAGGGCAGGTATCGT 61.436 63.158 0.00 0.00 44.01 3.73
3026 3661 0.464373 CCAGCGAATGCATACAGGGT 60.464 55.000 0.00 0.00 46.23 4.34
3037 3672 3.054655 TGCATACAGGGTAAAGAGGGAAC 60.055 47.826 0.00 0.00 0.00 3.62
3043 3678 4.263506 ACAGGGTAAAGAGGGAACATTGAG 60.264 45.833 0.00 0.00 0.00 3.02
3046 3681 4.263771 GGGTAAAGAGGGAACATTGAGGAA 60.264 45.833 0.00 0.00 0.00 3.36
3063 3698 4.162320 TGAGGAACCATATTCTCTGTCCAC 59.838 45.833 0.00 0.00 0.00 4.02
3073 3708 3.944055 TCTCTGTCCACTTTGCTCTAC 57.056 47.619 0.00 0.00 0.00 2.59
3074 3709 3.230976 TCTCTGTCCACTTTGCTCTACA 58.769 45.455 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.495100 GGAGTATGTAATGGGACCAGCAG 60.495 52.174 0.00 0.00 0.00 4.24
1 2 2.438021 GGAGTATGTAATGGGACCAGCA 59.562 50.000 0.00 0.00 0.00 4.41
3 4 3.318313 AGGGAGTATGTAATGGGACCAG 58.682 50.000 0.00 0.00 0.00 4.00
4 5 3.314693 GAGGGAGTATGTAATGGGACCA 58.685 50.000 0.00 0.00 0.00 4.02
6 7 2.299297 CGGAGGGAGTATGTAATGGGAC 59.701 54.545 0.00 0.00 0.00 4.46
8 9 2.326428 ACGGAGGGAGTATGTAATGGG 58.674 52.381 0.00 0.00 0.00 4.00
9 10 3.552273 CGAACGGAGGGAGTATGTAATGG 60.552 52.174 0.00 0.00 0.00 3.16
10 11 3.552273 CCGAACGGAGGGAGTATGTAATG 60.552 52.174 7.53 0.00 37.50 1.90
11 12 2.626743 CCGAACGGAGGGAGTATGTAAT 59.373 50.000 7.53 0.00 37.50 1.89
12 13 2.026641 CCGAACGGAGGGAGTATGTAA 58.973 52.381 7.53 0.00 37.50 2.41
13 14 1.212688 TCCGAACGGAGGGAGTATGTA 59.787 52.381 12.04 0.00 39.76 2.29
14 15 0.033796 TCCGAACGGAGGGAGTATGT 60.034 55.000 12.04 0.00 39.76 2.29
15 16 1.108776 TTCCGAACGGAGGGAGTATG 58.891 55.000 15.34 0.00 46.06 2.39
16 17 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
17 18 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
18 19 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
19 20 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
20 21 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
21 22 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
22 23 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
23 24 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
24 25 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
25 26 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
26 27 1.266211 CGCGACAAGTAATTCCGAACG 60.266 52.381 0.00 0.00 0.00 3.95
27 28 1.987770 TCGCGACAAGTAATTCCGAAC 59.012 47.619 3.71 0.00 0.00 3.95
28 29 2.350899 TCGCGACAAGTAATTCCGAA 57.649 45.000 3.71 0.00 0.00 4.30
29 30 2.350899 TTCGCGACAAGTAATTCCGA 57.649 45.000 9.15 0.00 0.00 4.55
30 31 3.443054 TTTTCGCGACAAGTAATTCCG 57.557 42.857 9.15 0.00 0.00 4.30
31 32 4.095610 CCATTTTCGCGACAAGTAATTCC 58.904 43.478 9.15 0.00 0.00 3.01
32 33 4.965062 TCCATTTTCGCGACAAGTAATTC 58.035 39.130 9.15 0.00 0.00 2.17
33 34 5.106317 ACATCCATTTTCGCGACAAGTAATT 60.106 36.000 9.15 0.00 0.00 1.40
34 35 4.394920 ACATCCATTTTCGCGACAAGTAAT 59.605 37.500 9.15 0.42 0.00 1.89
35 36 3.749088 ACATCCATTTTCGCGACAAGTAA 59.251 39.130 9.15 0.00 0.00 2.24
36 37 3.331150 ACATCCATTTTCGCGACAAGTA 58.669 40.909 9.15 0.00 0.00 2.24
37 38 2.151202 ACATCCATTTTCGCGACAAGT 58.849 42.857 9.15 0.00 0.00 3.16
38 39 2.900122 ACATCCATTTTCGCGACAAG 57.100 45.000 9.15 2.84 0.00 3.16
39 40 4.188462 AGATACATCCATTTTCGCGACAA 58.812 39.130 9.15 9.93 0.00 3.18
40 41 3.792401 AGATACATCCATTTTCGCGACA 58.208 40.909 9.15 0.00 0.00 4.35
41 42 5.117287 GTCTAGATACATCCATTTTCGCGAC 59.883 44.000 9.15 0.00 0.00 5.19
42 43 5.220381 GTCTAGATACATCCATTTTCGCGA 58.780 41.667 3.71 3.71 0.00 5.87
43 44 4.088638 CGTCTAGATACATCCATTTTCGCG 59.911 45.833 0.00 0.00 0.00 5.87
44 45 4.982916 ACGTCTAGATACATCCATTTTCGC 59.017 41.667 0.00 0.00 0.00 4.70
45 46 8.744008 AATACGTCTAGATACATCCATTTTCG 57.256 34.615 0.00 0.00 0.00 3.46
74 75 9.521841 TGTCTCGGAAATAGATGTATCTAGAAT 57.478 33.333 0.00 0.00 42.20 2.40
75 76 8.919777 TGTCTCGGAAATAGATGTATCTAGAA 57.080 34.615 0.00 0.00 42.20 2.10
76 77 8.919777 TTGTCTCGGAAATAGATGTATCTAGA 57.080 34.615 7.57 0.00 42.20 2.43
77 78 8.788806 ACTTGTCTCGGAAATAGATGTATCTAG 58.211 37.037 7.57 0.00 42.20 2.43
78 79 8.693120 ACTTGTCTCGGAAATAGATGTATCTA 57.307 34.615 4.22 4.22 43.00 1.98
79 80 7.589958 ACTTGTCTCGGAAATAGATGTATCT 57.410 36.000 0.00 0.00 40.86 1.98
80 81 9.915629 ATTACTTGTCTCGGAAATAGATGTATC 57.084 33.333 0.00 0.00 0.00 2.24
82 83 9.745880 GAATTACTTGTCTCGGAAATAGATGTA 57.254 33.333 0.00 0.00 0.00 2.29
83 84 7.711339 GGAATTACTTGTCTCGGAAATAGATGT 59.289 37.037 0.00 0.00 0.00 3.06
84 85 7.096023 CGGAATTACTTGTCTCGGAAATAGATG 60.096 40.741 0.00 0.00 0.00 2.90
85 86 6.924060 CGGAATTACTTGTCTCGGAAATAGAT 59.076 38.462 0.00 0.00 0.00 1.98
86 87 6.095860 TCGGAATTACTTGTCTCGGAAATAGA 59.904 38.462 0.00 0.00 0.00 1.98
87 88 6.270815 TCGGAATTACTTGTCTCGGAAATAG 58.729 40.000 0.00 0.00 0.00 1.73
88 89 6.211587 TCGGAATTACTTGTCTCGGAAATA 57.788 37.500 0.00 0.00 0.00 1.40
89 90 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
90 91 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
91 92 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
92 93 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
93 94 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
94 95 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
95 96 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
96 97 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
97 98 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
98 99 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
99 100 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
100 101 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
101 102 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
102 103 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
103 104 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
104 105 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
105 106 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
106 107 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
107 108 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
108 109 0.172803 CAAGTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
109 110 1.132643 CTCAAGTACTCCCTCCGTTCG 59.867 57.143 0.00 0.00 0.00 3.95
110 111 2.444421 TCTCAAGTACTCCCTCCGTTC 58.556 52.381 0.00 0.00 0.00 3.95
111 112 2.599408 TCTCAAGTACTCCCTCCGTT 57.401 50.000 0.00 0.00 0.00 4.44
112 113 2.041350 TCTTCTCAAGTACTCCCTCCGT 59.959 50.000 0.00 0.00 0.00 4.69
113 114 2.685897 CTCTTCTCAAGTACTCCCTCCG 59.314 54.545 0.00 0.00 0.00 4.63
114 115 3.028130 CCTCTTCTCAAGTACTCCCTCC 58.972 54.545 0.00 0.00 0.00 4.30
115 116 3.970842 TCCTCTTCTCAAGTACTCCCTC 58.029 50.000 0.00 0.00 0.00 4.30
116 117 4.618378 ATCCTCTTCTCAAGTACTCCCT 57.382 45.455 0.00 0.00 0.00 4.20
117 118 6.149807 CGTATATCCTCTTCTCAAGTACTCCC 59.850 46.154 0.00 0.00 0.00 4.30
118 119 6.149807 CCGTATATCCTCTTCTCAAGTACTCC 59.850 46.154 0.00 0.00 0.00 3.85
119 120 6.348704 GCCGTATATCCTCTTCTCAAGTACTC 60.349 46.154 0.00 0.00 0.00 2.59
120 121 5.474189 GCCGTATATCCTCTTCTCAAGTACT 59.526 44.000 0.00 0.00 0.00 2.73
237 239 4.198530 TGGCACATGACACCTACAATATG 58.801 43.478 0.00 0.00 0.00 1.78
289 313 1.009829 GTTGTAGCGGCCTCAAGATG 58.990 55.000 0.00 0.00 0.00 2.90
300 328 5.607119 AGTTTTGGAATGTAGTTGTAGCG 57.393 39.130 0.00 0.00 0.00 4.26
353 381 9.599866 TGTACTGTATCAATTCCAAAGACATAG 57.400 33.333 0.00 0.00 0.00 2.23
393 545 4.861102 ATGAGCAAAAGGTTTCAGAAGG 57.139 40.909 0.00 0.00 0.00 3.46
457 648 2.959507 TCATGTGACATGTCCTACCG 57.040 50.000 23.39 9.37 0.00 4.02
660 893 2.034607 GCCGCTAGCTGCTACTACT 58.965 57.895 22.29 0.00 40.11 2.57
661 894 4.637873 GCCGCTAGCTGCTACTAC 57.362 61.111 22.29 0.00 40.11 2.73
690 923 2.057137 TAAGGGCTGTTGATCCATGC 57.943 50.000 0.00 0.00 0.00 4.06
759 998 0.747852 TTGGGTATGCGAGTATGCGA 59.252 50.000 0.00 0.00 37.81 5.10
760 999 1.795768 ATTGGGTATGCGAGTATGCG 58.204 50.000 0.00 0.00 37.81 4.73
761 1000 5.178797 AGATAATTGGGTATGCGAGTATGC 58.821 41.667 0.00 0.00 0.00 3.14
763 1002 7.364762 CCCTTAGATAATTGGGTATGCGAGTAT 60.365 40.741 0.00 0.00 35.13 2.12
764 1003 6.070995 CCCTTAGATAATTGGGTATGCGAGTA 60.071 42.308 0.00 0.00 35.13 2.59
766 1005 5.178797 CCCTTAGATAATTGGGTATGCGAG 58.821 45.833 0.00 0.00 35.13 5.03
767 1006 4.564821 GCCCTTAGATAATTGGGTATGCGA 60.565 45.833 0.00 0.00 41.59 5.10
769 1008 3.689649 CGCCCTTAGATAATTGGGTATGC 59.310 47.826 0.00 0.00 41.59 3.14
770 1009 4.019681 TCCGCCCTTAGATAATTGGGTATG 60.020 45.833 0.00 0.00 41.59 2.39
771 1010 4.172807 TCCGCCCTTAGATAATTGGGTAT 58.827 43.478 0.00 0.00 41.59 2.73
772 1011 3.589641 TCCGCCCTTAGATAATTGGGTA 58.410 45.455 0.00 0.00 41.59 3.69
773 1012 2.414612 TCCGCCCTTAGATAATTGGGT 58.585 47.619 0.00 0.00 41.59 4.51
776 1015 5.875359 GGACTAATCCGCCCTTAGATAATTG 59.125 44.000 0.00 0.00 34.48 2.32
791 1030 4.467198 TTCGAGTGGAAAGGACTAATCC 57.533 45.455 0.00 0.00 46.69 3.01
822 1062 1.975680 GTGTCCTAAACCTGGGTCAGA 59.024 52.381 0.00 0.00 32.44 3.27
829 1069 3.190535 CGAAATTGGGTGTCCTAAACCTG 59.809 47.826 0.00 0.00 37.85 4.00
837 1077 2.874751 CCGCGAAATTGGGTGTCC 59.125 61.111 8.23 0.00 0.00 4.02
844 1084 5.163854 CCTCTATATAAAGGCCGCGAAATTG 60.164 44.000 8.23 0.00 0.00 2.32
845 1085 4.935808 CCTCTATATAAAGGCCGCGAAATT 59.064 41.667 8.23 0.00 0.00 1.82
851 1091 3.055747 AGCTTCCTCTATATAAAGGCCGC 60.056 47.826 0.00 2.85 32.37 6.53
852 1092 4.021016 ACAGCTTCCTCTATATAAAGGCCG 60.021 45.833 0.00 0.00 32.37 6.13
1086 1334 1.211212 CTCCCATGTCCATGCTTCTCA 59.789 52.381 1.64 0.00 37.49 3.27
1098 1346 2.729479 CGCTCTCCAGCTCCCATGT 61.729 63.158 0.00 0.00 44.40 3.21
1407 1806 4.642437 TGGTTTGATCAGCACAACAGTTTA 59.358 37.500 9.57 0.00 0.00 2.01
1627 2030 3.777925 CCGCTTTGGTCGTCGCAG 61.778 66.667 0.00 0.00 0.00 5.18
1630 2033 3.777925 CTGCCGCTTTGGTCGTCG 61.778 66.667 0.00 0.00 41.21 5.12
1661 2064 0.828762 TTTGCTGCCTGGACTGCATT 60.829 50.000 17.95 0.00 42.94 3.56
1759 2162 2.697147 TTTGCTCCAGGTCAGTGGGC 62.697 60.000 0.00 0.00 38.26 5.36
1807 2213 2.755655 AGACGACATCGAAGACAAGGAT 59.244 45.455 8.54 0.00 42.51 3.24
1820 2226 2.103771 CCATGATCCTTGGAGACGACAT 59.896 50.000 6.00 0.00 36.26 3.06
1946 2352 7.148340 GCTGTTTGCACTATAATCTGAGTTCTT 60.148 37.037 0.00 0.00 42.31 2.52
2040 2458 3.127533 AAGCATCGCCGAGGTTGC 61.128 61.111 3.07 3.07 35.34 4.17
2249 2829 0.331278 TTGAAGATCCGGCAACCCAT 59.669 50.000 0.00 0.00 0.00 4.00
2250 2830 0.331278 ATTGAAGATCCGGCAACCCA 59.669 50.000 0.00 0.00 0.00 4.51
2329 2909 3.761897 TCAATCCAAGAAATCCAACGGT 58.238 40.909 0.00 0.00 0.00 4.83
2376 2956 1.196766 AGCAGCCCACACATGAGAGA 61.197 55.000 0.00 0.00 0.00 3.10
2382 2962 2.359107 CACGAGCAGCCCACACAT 60.359 61.111 0.00 0.00 0.00 3.21
2397 2977 1.966451 CAAAGGACAGTCGGCCCAC 60.966 63.158 0.00 0.00 0.00 4.61
2496 3078 1.572941 GTGGAACGGAAGGAAACGC 59.427 57.895 0.00 0.00 0.00 4.84
2505 3087 1.000019 AGAGATCGGGTGGAACGGA 60.000 57.895 0.00 0.00 38.12 4.69
2545 3130 1.687493 GTGGGTGAGAGAGGAGGGG 60.687 68.421 0.00 0.00 0.00 4.79
2547 3132 1.079256 TGGTGGGTGAGAGAGGAGG 59.921 63.158 0.00 0.00 0.00 4.30
2765 3353 1.412710 TCGGATACATGCTTCTGGGTC 59.587 52.381 0.00 0.00 0.00 4.46
2915 3520 0.965363 GCCATTCGAGCCCCTTGAAA 60.965 55.000 0.00 0.00 37.41 2.69
3005 3640 1.277739 CTGTATGCATTCGCTGGCG 59.722 57.895 3.54 8.80 39.64 5.69
3026 3661 4.352595 TGGTTCCTCAATGTTCCCTCTTTA 59.647 41.667 0.00 0.00 0.00 1.85
3037 3672 5.762218 GGACAGAGAATATGGTTCCTCAATG 59.238 44.000 0.00 0.00 0.00 2.82
3043 3678 4.762289 AGTGGACAGAGAATATGGTTCC 57.238 45.455 0.00 0.00 0.00 3.62
3046 3681 4.018960 AGCAAAGTGGACAGAGAATATGGT 60.019 41.667 0.00 0.00 0.00 3.55
3063 3698 3.364764 GCTTTCAGCACTGTAGAGCAAAG 60.365 47.826 13.63 6.84 41.89 2.77


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.