Multiple sequence alignment - TraesCS6B01G065700

Loading Multiple Alignment...

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 TraesCS6B01G065700 chr6B 100.000 5862 0 0 1 5862 43497741 43503602 0.000000e+00 10826.0
1 TraesCS6B01G065700 chr6B 91.933 2157 146 18 610 2748 43348081 43350227 0.000000e+00 2994.0
2 TraesCS6B01G065700 chr6B 89.396 2386 219 21 748 3117 43281551 43283918 0.000000e+00 2974.0
3 TraesCS6B01G065700 chr6B 86.787 2437 290 18 809 3229 44100142 44102562 0.000000e+00 2687.0
4 TraesCS6B01G065700 chr6B 89.537 1424 109 13 3274 4662 43350743 43352161 0.000000e+00 1768.0
5 TraesCS6B01G065700 chr6B 84.899 1384 154 28 3317 4661 43284214 43285581 0.000000e+00 1347.0
6 TraesCS6B01G065700 chr6B 81.176 1275 184 31 3425 4659 44102669 44103927 0.000000e+00 974.0
7 TraesCS6B01G065700 chr6B 84.398 532 32 12 5118 5640 43801211 43801700 5.320000e-130 475.0
8 TraesCS6B01G065700 chr6B 86.842 380 40 3 218 590 43347720 43348096 3.270000e-112 416.0
9 TraesCS6B01G065700 chr6B 88.387 155 13 4 5713 5862 43802246 43802400 1.300000e-41 182.0
10 TraesCS6B01G065700 chr6B 76.965 369 49 21 4904 5252 43285716 43286068 1.680000e-40 178.0
11 TraesCS6B01G065700 chr6B 86.331 139 14 3 447 580 43281319 43281457 4.730000e-31 147.0
12 TraesCS6B01G065700 chr6B 84.298 121 19 0 137 257 43280874 43280994 1.030000e-22 119.0
13 TraesCS6B01G065700 chr6B 81.915 94 6 7 308 399 44099609 44099693 1.050000e-07 69.4
14 TraesCS6B01G065700 chrUn 96.668 3421 99 7 610 4023 94220584 94223996 0.000000e+00 5672.0
15 TraesCS6B01G065700 chrUn 91.215 2675 173 21 610 3236 94179219 94181879 0.000000e+00 3581.0
16 TraesCS6B01G065700 chrUn 89.798 2382 211 24 753 3116 94047333 94049700 0.000000e+00 3024.0
17 TraesCS6B01G065700 chrUn 87.960 2284 248 16 817 3089 94818013 94820280 0.000000e+00 2669.0
18 TraesCS6B01G065700 chrUn 89.422 1437 110 17 3262 4662 94181964 94183394 0.000000e+00 1773.0
19 TraesCS6B01G065700 chrUn 85.275 1365 153 27 3319 4661 94049872 94051210 0.000000e+00 1363.0
20 TraesCS6B01G065700 chrUn 95.109 736 28 2 4025 4760 94224158 94224885 0.000000e+00 1153.0
21 TraesCS6B01G065700 chrUn 89.038 821 48 24 4948 5751 94517447 94518242 0.000000e+00 979.0
22 TraesCS6B01G065700 chrUn 89.238 604 27 7 4922 5517 94243195 94243768 0.000000e+00 721.0
23 TraesCS6B01G065700 chrUn 86.495 622 52 16 1 590 94219978 94220599 0.000000e+00 654.0
24 TraesCS6B01G065700 chrUn 84.081 691 89 17 3425 4094 94820454 94821144 0.000000e+00 647.0
25 TraesCS6B01G065700 chrUn 88.660 388 35 2 212 590 94178847 94179234 1.150000e-126 464.0
26 TraesCS6B01G065700 chrUn 90.462 346 26 3 5514 5852 94258836 94259181 3.220000e-122 449.0
27 TraesCS6B01G065700 chrUn 79.054 296 34 15 308 580 94046940 94047230 1.680000e-40 178.0
28 TraesCS6B01G065700 chrUn 82.741 197 30 4 5055 5251 94183779 94183971 7.810000e-39 172.0
29 TraesCS6B01G065700 chrUn 95.413 109 4 1 4828 4935 94224890 94224998 7.810000e-39 172.0
30 TraesCS6B01G065700 chrUn 87.879 132 13 2 438 566 94178530 94178661 1.020000e-32 152.0
31 TraesCS6B01G065700 chr6A 96.057 2663 89 7 611 3265 25017600 25020254 0.000000e+00 4322.0
32 TraesCS6B01G065700 chr6A 91.148 2666 174 26 610 3229 24853408 24856057 0.000000e+00 3559.0
33 TraesCS6B01G065700 chr6A 89.305 2431 213 23 703 3116 24838500 24840900 0.000000e+00 3005.0
34 TraesCS6B01G065700 chr6A 88.620 2188 230 9 912 3089 25631483 25633661 0.000000e+00 2643.0
35 TraesCS6B01G065700 chr6A 93.717 1687 69 20 3263 4920 25020289 25021967 0.000000e+00 2494.0
36 TraesCS6B01G065700 chr6A 89.599 1423 110 16 3274 4662 24856056 24857474 0.000000e+00 1773.0
37 TraesCS6B01G065700 chr6A 86.117 1347 141 26 3355 4661 24841082 24842422 0.000000e+00 1410.0
38 TraesCS6B01G065700 chr6A 88.804 911 61 27 4974 5862 25021958 25022849 0.000000e+00 1079.0
39 TraesCS6B01G065700 chr6A 86.111 612 54 14 1 590 25017012 25017614 1.070000e-176 630.0
40 TraesCS6B01G065700 chr6A 85.427 398 36 4 212 590 24853029 24853423 1.530000e-105 394.0
41 TraesCS6B01G065700 chr6A 76.230 366 38 26 4905 5246 24842593 24842933 1.320000e-31 148.0
42 TraesCS6B01G065700 chr6A 85.915 142 17 2 438 576 24852720 24852861 1.320000e-31 148.0
43 TraesCS6B01G065700 chr6A 77.519 258 47 8 6 262 24837035 24837282 1.700000e-30 145.0
44 TraesCS6B01G065700 chr6A 79.255 188 23 9 108 284 24852276 24852458 3.710000e-22 117.0
45 TraesCS6B01G065700 chr6A 83.158 95 7 5 308 399 25631011 25631099 1.750000e-10 78.7
46 TraesCS6B01G065700 chr3A 86.275 102 9 5 4737 4836 377144671 377144769 8.030000e-19 106.0
47 TraesCS6B01G065700 chr3A 95.000 40 1 1 4794 4832 466777893 466777932 1.760000e-05 62.1
48 TraesCS6B01G065700 chr5D 97.917 48 0 1 3215 3262 61045896 61045850 1.350000e-11 82.4
49 TraesCS6B01G065700 chr5D 92.000 50 4 0 3226 3275 547276005 547276054 2.930000e-08 71.3
50 TraesCS6B01G065700 chr4B 94.340 53 1 2 3228 3279 66801336 66801387 4.870000e-11 80.5
51 TraesCS6B01G065700 chr4B 100.000 29 0 0 4739 4767 499852256 499852284 3.000000e-03 54.7
52 TraesCS6B01G065700 chr4B 96.774 31 1 0 4801 4831 660686885 660686855 1.100000e-02 52.8
53 TraesCS6B01G065700 chr4A 87.302 63 8 0 4773 4835 673448701 673448639 8.150000e-09 73.1
54 TraesCS6B01G065700 chr6D 89.655 58 2 1 3226 3279 448686798 448686741 2.930000e-08 71.3
55 TraesCS6B01G065700 chr3D 93.750 48 1 2 3219 3265 167036949 167036995 2.930000e-08 71.3
56 TraesCS6B01G065700 chr3D 95.000 40 1 1 4794 4832 347576638 347576677 1.760000e-05 62.1
57 TraesCS6B01G065700 chr3D 100.000 28 0 0 4740 4767 575865219 575865192 1.100000e-02 52.8
58 TraesCS6B01G065700 chr7D 93.333 45 2 1 3221 3265 46702738 46702695 1.360000e-06 65.8
59 TraesCS6B01G065700 chr3B 85.714 63 5 4 3227 3286 775259894 775259833 4.900000e-06 63.9
60 TraesCS6B01G065700 chr3B 94.444 36 1 1 4794 4828 637092977 637093012 3.000000e-03 54.7


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 TraesCS6B01G065700 chr6B 43497741 43503602 5861 False 10826.000000 10826 100.000000 1 5862 1 chr6B.!!$F1 5861
1 TraesCS6B01G065700 chr6B 43347720 43352161 4441 False 1726.000000 2994 89.437333 218 4662 3 chr6B.!!$F3 4444
2 TraesCS6B01G065700 chr6B 44099609 44103927 4318 False 1243.466667 2687 83.292667 308 4659 3 chr6B.!!$F5 4351
3 TraesCS6B01G065700 chr6B 43280874 43286068 5194 False 953.000000 2974 84.377800 137 5252 5 chr6B.!!$F2 5115
4 TraesCS6B01G065700 chr6B 43801211 43802400 1189 False 328.500000 475 86.392500 5118 5862 2 chr6B.!!$F4 744
5 TraesCS6B01G065700 chrUn 94219978 94224998 5020 False 1912.750000 5672 93.421250 1 4935 4 chrUn.!!$F6 4934
6 TraesCS6B01G065700 chrUn 94818013 94821144 3131 False 1658.000000 2669 86.020500 817 4094 2 chrUn.!!$F7 3277
7 TraesCS6B01G065700 chrUn 94046940 94051210 4270 False 1521.666667 3024 84.709000 308 4661 3 chrUn.!!$F4 4353
8 TraesCS6B01G065700 chrUn 94178530 94183971 5441 False 1228.400000 3581 87.983400 212 5251 5 chrUn.!!$F5 5039
9 TraesCS6B01G065700 chrUn 94517447 94518242 795 False 979.000000 979 89.038000 4948 5751 1 chrUn.!!$F3 803
10 TraesCS6B01G065700 chrUn 94243195 94243768 573 False 721.000000 721 89.238000 4922 5517 1 chrUn.!!$F1 595
11 TraesCS6B01G065700 chr6A 25017012 25022849 5837 False 2131.250000 4322 91.172250 1 5862 4 chr6A.!!$F3 5861
12 TraesCS6B01G065700 chr6A 25631011 25633661 2650 False 1360.850000 2643 85.889000 308 3089 2 chr6A.!!$F4 2781
13 TraesCS6B01G065700 chr6A 24852276 24857474 5198 False 1198.200000 3559 86.268800 108 4662 5 chr6A.!!$F2 4554
14 TraesCS6B01G065700 chr6A 24837035 24842933 5898 False 1177.000000 3005 82.292750 6 5246 4 chr6A.!!$F1 5240

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
57 58 0.106894 GCGAGGAATCGGAGGGAAAT 59.893 55.000 0.00 0.00 0.00 2.17 F
238 907 0.242555 GGTCCGTTTACCGTCGGTTA 59.757 55.000 24.36 11.31 45.88 2.85 F
829 2504 0.548031 TGGGCTGAGGCTCCAAATAG 59.452 55.000 12.86 3.07 38.37 1.73 F
2260 3954 0.810648 TGGGCAAGTGCAATTCGATC 59.189 50.000 5.52 0.00 44.36 3.69 F
3192 4929 1.142870 AGAGCAGTGGCCAGTTAACAA 59.857 47.619 11.44 0.00 42.56 2.83 F
3829 5880 1.470632 CGGTCAAGGCTAAGAGCTCTG 60.471 57.143 19.06 6.88 41.99 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 3006 1.203038 TCATTGCCACCACTCCACAAT 60.203 47.619 0.00 0.0 0.00 2.71 R
1695 3380 3.818773 TCCTTTTAGCGTTGGAAGGAAAG 59.181 43.478 13.26 0.0 43.35 2.62 R
2773 4499 0.807496 GCATCAAACTCCTGCAGGAC 59.193 55.000 32.00 15.4 39.78 3.85 R
4187 6426 0.613012 AGTCCCTTGGAAATGCCTGC 60.613 55.000 0.00 0.0 37.63 4.85 R
4501 6740 0.321671 CCGCCTCTCCTTGTTCTTCA 59.678 55.000 0.00 0.0 0.00 3.02 R
5381 7787 0.029567 GTCGCATCTCAGACCTACCG 59.970 60.000 0.00 0.0 0.00 4.02 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
32 33 2.207229 GCCCGCCTTTTCTTTGGGT 61.207 57.895 0.00 0.00 42.10 4.51
34 35 0.756294 CCCGCCTTTTCTTTGGGTTT 59.244 50.000 0.00 0.00 35.05 3.27
57 58 0.106894 GCGAGGAATCGGAGGGAAAT 59.893 55.000 0.00 0.00 0.00 2.17
61 62 1.771255 AGGAATCGGAGGGAAATCTGG 59.229 52.381 0.00 0.00 0.00 3.86
115 116 1.247567 GCCCTGCTTGCTTTCTGTTA 58.752 50.000 0.00 0.00 0.00 2.41
118 119 2.229792 CCTGCTTGCTTTCTGTTACCA 58.770 47.619 0.00 0.00 0.00 3.25
210 228 2.064762 CTGGTCTCGTTTCAGCTCTTG 58.935 52.381 0.00 0.00 0.00 3.02
211 229 1.270305 TGGTCTCGTTTCAGCTCTTGG 60.270 52.381 0.00 0.00 0.00 3.61
212 230 1.000955 GGTCTCGTTTCAGCTCTTGGA 59.999 52.381 0.00 0.00 0.00 3.53
213 231 2.354203 GGTCTCGTTTCAGCTCTTGGAT 60.354 50.000 0.00 0.00 0.00 3.41
214 232 2.670414 GTCTCGTTTCAGCTCTTGGATG 59.330 50.000 0.00 0.00 0.00 3.51
219 888 2.662006 TTCAGCTCTTGGATGTCTCG 57.338 50.000 0.00 0.00 32.48 4.04
238 907 0.242555 GGTCCGTTTACCGTCGGTTA 59.757 55.000 24.36 11.31 45.88 2.85
242 911 1.339711 CGTTTACCGTCGGTTACTGG 58.660 55.000 24.36 5.04 37.09 4.00
251 920 2.423577 GTCGGTTACTGGAAATGTGCT 58.576 47.619 0.00 0.00 0.00 4.40
258 927 1.880027 ACTGGAAATGTGCTCGAAACC 59.120 47.619 0.00 0.00 0.00 3.27
511 1552 3.559171 GCTTCCACTCAAGGACCACATTA 60.559 47.826 0.00 0.00 37.42 1.90
594 2240 9.574516 AGTGTTATAAATCAGAAACATATCCCC 57.425 33.333 0.00 0.00 34.62 4.81
595 2241 8.504005 GTGTTATAAATCAGAAACATATCCCCG 58.496 37.037 0.00 0.00 34.62 5.73
597 2243 3.576078 AATCAGAAACATATCCCCGCA 57.424 42.857 0.00 0.00 0.00 5.69
600 2246 3.691575 TCAGAAACATATCCCCGCAAAA 58.308 40.909 0.00 0.00 0.00 2.44
666 2316 8.966194 GCTTACTAGATTCGGTGTATTTACTTC 58.034 37.037 0.00 0.00 0.00 3.01
685 2335 4.443394 ACTTCGTGTGTTTAGTCGAATCAC 59.557 41.667 0.00 0.00 40.53 3.06
723 2376 4.458989 TCAAGTTGCTTTTCCTTGCGATAT 59.541 37.500 0.00 0.00 36.41 1.63
724 2377 5.048083 TCAAGTTGCTTTTCCTTGCGATATT 60.048 36.000 0.00 0.00 36.41 1.28
725 2378 4.986622 AGTTGCTTTTCCTTGCGATATTC 58.013 39.130 0.00 0.00 0.00 1.75
726 2379 4.458989 AGTTGCTTTTCCTTGCGATATTCA 59.541 37.500 0.00 0.00 0.00 2.57
727 2380 5.126061 AGTTGCTTTTCCTTGCGATATTCAT 59.874 36.000 0.00 0.00 0.00 2.57
728 2381 4.923893 TGCTTTTCCTTGCGATATTCATG 58.076 39.130 0.00 0.00 0.00 3.07
781 2439 8.552865 CAATTGCTTCATTCAAAGTGATTTTCA 58.447 29.630 0.00 0.00 0.00 2.69
802 2472 6.090483 TCACTTCTTTGTTGTTGTTTTCCA 57.910 33.333 0.00 0.00 0.00 3.53
805 2477 5.925969 ACTTCTTTGTTGTTGTTTTCCACAG 59.074 36.000 0.00 0.00 36.48 3.66
807 2479 3.667497 TTGTTGTTGTTTTCCACAGCA 57.333 38.095 0.00 0.00 44.27 4.41
829 2504 0.548031 TGGGCTGAGGCTCCAAATAG 59.452 55.000 12.86 3.07 38.37 1.73
984 2666 2.172717 ACAAGTGTCCAGTAGCCTTTGT 59.827 45.455 0.00 0.00 0.00 2.83
1078 2760 2.494059 TCTGCAAGAGTTTAGCCACAC 58.506 47.619 0.00 0.00 38.67 3.82
1695 3380 6.147864 TGCAAAATATCCTACAAGATTGGC 57.852 37.500 0.00 0.00 0.00 4.52
1875 3560 0.819259 TTGCAACTGACTGGCTGTCC 60.819 55.000 19.97 6.45 44.75 4.02
1986 3674 9.525826 AACTCAAAGATGAATAATTTGGTCTCT 57.474 29.630 0.00 0.00 34.49 3.10
2260 3954 0.810648 TGGGCAAGTGCAATTCGATC 59.189 50.000 5.52 0.00 44.36 3.69
2411 4105 4.173290 AGCCTCCTAATACTTCTCTCGT 57.827 45.455 0.00 0.00 0.00 4.18
2496 4190 4.218417 GTCTTTCCTTCTAATGCCAAGCAA 59.782 41.667 0.00 0.00 43.62 3.91
2910 4636 7.411912 CCGGTTAAAGAGCATATAACATCATCG 60.412 40.741 0.00 0.00 32.47 3.84
3192 4929 1.142870 AGAGCAGTGGCCAGTTAACAA 59.857 47.619 11.44 0.00 42.56 2.83
3555 5604 4.586001 ACATTTTGTTCTGAGGCATGACTT 59.414 37.500 0.41 0.00 0.00 3.01
3592 5643 1.590238 CTGCTCGCAGGAGAAAATACG 59.410 52.381 10.98 0.00 43.27 3.06
3744 5795 4.576053 TGATGACCTGAAAAATAGCGATGG 59.424 41.667 0.00 0.00 0.00 3.51
3829 5880 1.470632 CGGTCAAGGCTAAGAGCTCTG 60.471 57.143 19.06 6.88 41.99 3.35
3943 5994 5.047660 ACTGTTTTTGTCAACCTACTGCAAA 60.048 36.000 0.00 0.00 0.00 3.68
4136 6351 4.083110 GCAACTGTTCTTGCACATATCTGT 60.083 41.667 0.00 0.00 45.07 3.41
4177 6415 7.867403 ACAAATCAAAATGTAGCACCTTACAAG 59.133 33.333 0.00 0.00 37.13 3.16
4187 6426 4.074970 AGCACCTTACAAGTTCATTCTGG 58.925 43.478 0.00 0.00 0.00 3.86
4313 6552 2.281484 GGGGAGTGCGCAACTGAA 60.281 61.111 14.00 0.00 40.07 3.02
4501 6740 3.801997 CCATGGGAAGGAGCCGCT 61.802 66.667 2.85 0.00 0.00 5.52
4763 7064 6.699575 ACTCCCTCCGATTCAAATTAATTG 57.300 37.500 0.39 0.00 40.58 2.32
4799 7111 4.193865 ACAAAGTTGTACTAAGTTGGCGT 58.806 39.130 0.00 0.00 40.16 5.68
4803 7115 4.056050 AGTTGTACTAAGTTGGCGTCAAG 58.944 43.478 0.75 0.00 32.92 3.02
4810 7122 5.997385 ACTAAGTTGGCGTCAAGTAATTTG 58.003 37.500 11.10 4.03 35.64 2.32
4815 7127 2.675844 TGGCGTCAAGTAATTTGGATCG 59.324 45.455 0.00 0.00 37.39 3.69
4943 7257 4.291249 ACTGTATTTTGGGGGATACTGTGT 59.709 41.667 5.58 0.00 38.58 3.72
4957 7272 0.861837 CTGTGTCGGTTCAGACTTGC 59.138 55.000 4.95 0.00 41.47 4.01
5048 7388 1.320344 TGCAGCGGACCGAGTCTATT 61.320 55.000 20.50 0.00 32.47 1.73
5085 7456 5.556915 TGCCTGTAGTTTGTAGCACTAAAT 58.443 37.500 0.00 0.00 0.00 1.40
5246 7651 6.435904 AGCCATAAAAATGTGTTAGCACCTTA 59.564 34.615 7.29 1.11 44.65 2.69
5252 7657 3.120321 TGTGTTAGCACCTTACACAGG 57.880 47.619 11.71 0.00 45.03 4.00
5253 7658 2.701423 TGTGTTAGCACCTTACACAGGA 59.299 45.455 11.71 0.00 45.03 3.86
5254 7659 3.244078 TGTGTTAGCACCTTACACAGGAG 60.244 47.826 11.71 0.00 45.03 3.69
5255 7660 5.478912 TGTGTTAGCACCTTACACAGGAGA 61.479 45.833 11.71 0.00 45.03 3.71
5256 7661 6.913917 TGTGTTAGCACCTTACACAGGAGAA 61.914 44.000 11.71 0.00 45.03 2.87
5257 7662 8.315437 TGTGTTAGCACCTTACACAGGAGAAA 62.315 42.308 11.71 0.00 45.03 2.52
5258 7663 9.531964 TGTGTTAGCACCTTACACAGGAGAAAT 62.532 40.741 11.71 0.00 45.03 2.17
5322 7727 4.401202 TCCAGTTTTTGTTTCTCCAACTCC 59.599 41.667 0.00 0.00 36.21 3.85
5332 7737 2.265367 TCTCCAACTCCATGCCTACAA 58.735 47.619 0.00 0.00 0.00 2.41
5381 7787 2.494059 TGCTGCAACTGTACTCTTTCC 58.506 47.619 0.00 0.00 0.00 3.13
5464 7882 2.606308 GCAAGACAAATGCACTGGACTG 60.606 50.000 0.00 0.00 43.29 3.51
5480 7901 2.493675 GGACTGCAAAGAGGAAATTCCC 59.506 50.000 8.66 0.31 37.19 3.97
5565 7986 0.323999 TAGCGGAGTGGTAGGCAGAA 60.324 55.000 0.00 0.00 0.00 3.02
5624 8045 5.912892 TGTAAAAGCATCGATACATCTCCA 58.087 37.500 0.00 0.00 0.00 3.86
5625 8046 5.753438 TGTAAAAGCATCGATACATCTCCAC 59.247 40.000 0.00 0.00 0.00 4.02
5691 8120 8.739972 GGAAGAGTCTTTTTCCTATGCAAAATA 58.260 33.333 6.88 0.00 39.78 1.40
5782 8702 0.034059 ACCAAGAGTCGTTCAGCAGG 59.966 55.000 0.00 0.00 0.00 4.85
5791 8715 0.669318 CGTTCAGCAGGGCGTTTCTA 60.669 55.000 0.00 0.00 0.00 2.10
5803 8727 1.474017 CGTTTCTAGGATACGCCACG 58.526 55.000 0.00 0.00 46.39 4.94
5809 8733 0.396139 TAGGATACGCCACGGGTCTT 60.396 55.000 0.00 0.00 46.39 3.01
5818 8742 2.344025 GCCACGGGTCTTACAGTAAAG 58.656 52.381 0.00 0.00 0.00 1.85
5820 8744 2.301009 CCACGGGTCTTACAGTAAAGGT 59.699 50.000 0.00 0.00 0.00 3.50
5821 8745 3.511146 CCACGGGTCTTACAGTAAAGGTA 59.489 47.826 0.00 0.00 0.00 3.08
5825 8750 4.498241 GGGTCTTACAGTAAAGGTAACGG 58.502 47.826 0.00 0.00 46.39 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.100682 CTCCGATTCCTCGCTCGAAA 59.899 55.000 0.00 0.00 43.66 3.46
34 35 2.187493 CCTCCGATTCCTCGCTCGA 61.187 63.158 0.00 0.00 43.66 4.04
57 58 0.178903 AGCCACAGGAAGTACCCAGA 60.179 55.000 0.00 0.00 40.05 3.86
61 62 2.789409 ATCAAGCCACAGGAAGTACC 57.211 50.000 0.00 0.00 39.35 3.34
118 119 1.546476 CAAAGAGTAGAGCGACCCAGT 59.454 52.381 0.00 0.00 0.00 4.00
205 223 0.101399 CGGACCGAGACATCCAAGAG 59.899 60.000 8.64 0.00 34.35 2.85
210 228 1.470458 GGTAAACGGACCGAGACATCC 60.470 57.143 23.38 10.88 0.00 3.51
211 229 1.918595 GGTAAACGGACCGAGACATC 58.081 55.000 23.38 5.53 0.00 3.06
238 907 1.880027 GGTTTCGAGCACATTTCCAGT 59.120 47.619 0.00 0.00 0.00 4.00
242 911 2.487762 TCATGGGTTTCGAGCACATTTC 59.512 45.455 4.36 0.00 0.00 2.17
251 920 2.230992 CCAGCATTTTCATGGGTTTCGA 59.769 45.455 0.00 0.00 0.00 3.71
258 927 2.940410 GCAAATCCCAGCATTTTCATGG 59.060 45.455 0.00 0.00 0.00 3.66
276 945 1.299014 CGGCAAACAAAGAGCGCAA 60.299 52.632 11.47 0.00 0.00 4.85
359 1302 4.560035 CAGACAGCAAACAAACAAACAGAG 59.440 41.667 0.00 0.00 0.00 3.35
431 1466 6.863126 CAGATTCCAGTTTCCAACACATAAAC 59.137 38.462 0.00 0.00 34.13 2.01
493 1534 3.703001 AGTAATGTGGTCCTTGAGTGG 57.297 47.619 0.00 0.00 0.00 4.00
511 1552 4.723309 AGCATCCAAGAAAGTCAAGAAGT 58.277 39.130 0.00 0.00 0.00 3.01
571 2199 7.174253 TGCGGGGATATGTTTCTGATTTATAAC 59.826 37.037 0.00 0.00 0.00 1.89
666 2316 3.121279 CAGGTGATTCGACTAAACACACG 59.879 47.826 0.00 0.00 41.37 4.49
685 2335 4.320057 GCAACTTGAGAGAACAATGACAGG 60.320 45.833 0.00 0.00 0.00 4.00
723 2376 2.639970 CCGCTGGGTTGAACATGAA 58.360 52.632 0.00 0.00 0.00 2.57
724 2377 4.395519 CCGCTGGGTTGAACATGA 57.604 55.556 0.00 0.00 0.00 3.07
781 2439 5.848406 TGTGGAAAACAACAACAAAGAAGT 58.152 33.333 0.00 0.00 35.24 3.01
805 2477 2.421399 GGAGCCTCAGCCCAAATGC 61.421 63.158 0.00 0.00 41.25 3.56
807 2479 0.114954 TTTGGAGCCTCAGCCCAAAT 59.885 50.000 13.32 0.00 45.96 2.32
829 2504 7.042335 ACATAGTCCATGTAAAAGAGTAGCAC 58.958 38.462 0.00 0.00 46.34 4.40
877 2552 5.673337 ATGTTATCGTGATACCAATGCAC 57.327 39.130 0.00 0.00 0.00 4.57
1078 2760 2.332063 ATATTCACAACAGGAGGCCG 57.668 50.000 0.00 0.00 0.00 6.13
1209 2891 9.143631 CAATTTGTATCCTTGATTTGAACCTTC 57.856 33.333 0.00 0.00 0.00 3.46
1323 3006 1.203038 TCATTGCCACCACTCCACAAT 60.203 47.619 0.00 0.00 0.00 2.71
1695 3380 3.818773 TCCTTTTAGCGTTGGAAGGAAAG 59.181 43.478 13.26 0.00 43.35 2.62
1986 3674 5.440234 TTTTACTTTGCGTGCTCCATTTA 57.560 34.783 0.00 0.00 0.00 1.40
2260 3954 2.359900 GTGAATGAGGTTGCCTACAGG 58.640 52.381 0.00 0.00 31.76 4.00
2773 4499 0.807496 GCATCAAACTCCTGCAGGAC 59.193 55.000 32.00 15.40 39.78 3.85
3192 4929 9.331282 GTAATCACTAGATGCTTCATTTAGGTT 57.669 33.333 0.00 4.45 34.25 3.50
3744 5795 4.149598 ACCAACTTGGAAACCAATAGGAC 58.850 43.478 15.14 0.00 43.07 3.85
3829 5880 1.467342 GCGTATTCTTGTGGTGAACCC 59.533 52.381 0.00 0.00 34.29 4.11
3943 5994 1.303236 TGTGCCAGCTACCGCAATT 60.303 52.632 4.05 0.00 36.60 2.32
4119 6334 3.347216 ACCCACAGATATGTGCAAGAAC 58.653 45.455 15.08 0.00 38.40 3.01
4177 6415 2.417787 GGAAATGCCTGCCAGAATGAAC 60.418 50.000 0.00 0.00 39.69 3.18
4187 6426 0.613012 AGTCCCTTGGAAATGCCTGC 60.613 55.000 0.00 0.00 37.63 4.85
4501 6740 0.321671 CCGCCTCTCCTTGTTCTTCA 59.678 55.000 0.00 0.00 0.00 3.02
4763 7064 6.579491 ACAACTTTGTACTAAGTCAACGTC 57.421 37.500 20.50 0.00 40.16 4.34
4794 7106 2.675844 CGATCCAAATTACTTGACGCCA 59.324 45.455 0.00 0.00 37.17 5.69
4799 7111 3.778075 TCCCTCCGATCCAAATTACTTGA 59.222 43.478 0.00 0.00 37.17 3.02
4803 7115 3.840124 ACTCCCTCCGATCCAAATTAC 57.160 47.619 0.00 0.00 0.00 1.89
4810 7122 3.564264 ACTTTAGTACTCCCTCCGATCC 58.436 50.000 0.00 0.00 0.00 3.36
4864 7177 8.844244 ACAGGATGAGCATTTCAATATTTCTAC 58.156 33.333 0.00 0.00 39.69 2.59
5147 7522 2.864343 AGAGTACGTGAGCAACAACAAC 59.136 45.455 0.00 0.00 0.00 3.32
5153 7528 3.308866 ACAAAACAGAGTACGTGAGCAAC 59.691 43.478 0.00 0.00 0.00 4.17
5246 7651 6.051179 GGTCTTTACCTATTTCTCCTGTGT 57.949 41.667 0.00 0.00 43.08 3.72
5363 7769 2.069273 CCGGAAAGAGTACAGTTGCAG 58.931 52.381 0.00 0.00 0.00 4.41
5381 7787 0.029567 GTCGCATCTCAGACCTACCG 59.970 60.000 0.00 0.00 0.00 4.02
5464 7882 0.887933 TGCGGGAATTTCCTCTTTGC 59.112 50.000 14.95 11.36 36.57 3.68
5480 7901 0.458543 AGATGCACTACGAACCTGCG 60.459 55.000 0.00 0.00 33.35 5.18
5492 7913 2.796593 GCAAGAACCAAAACAGATGCAC 59.203 45.455 0.00 0.00 33.00 4.57
5565 7986 7.935210 AGAAGAAAAATGATGGTTTGATTTGCT 59.065 29.630 0.00 0.00 0.00 3.91
5616 8037 6.377146 ACAAATAAATTAAGCGGTGGAGATGT 59.623 34.615 0.00 0.00 0.00 3.06
5624 8045 7.826690 ACAGAATGACAAATAAATTAAGCGGT 58.173 30.769 0.00 0.00 39.69 5.68
5625 8046 8.687824 AACAGAATGACAAATAAATTAAGCGG 57.312 30.769 0.00 0.00 39.69 5.52
5707 8136 1.679139 TGCCTGCAATCGGAATTAGG 58.321 50.000 0.00 0.00 0.00 2.69
5778 8698 1.867166 GTATCCTAGAAACGCCCTGC 58.133 55.000 0.00 0.00 0.00 4.85
5791 8715 0.396139 TAAGACCCGTGGCGTATCCT 60.396 55.000 0.00 0.00 35.26 3.24
5803 8727 4.021104 ACCGTTACCTTTACTGTAAGACCC 60.021 45.833 0.00 0.00 37.43 4.46
5809 8733 5.981088 TCATCACCGTTACCTTTACTGTA 57.019 39.130 0.00 0.00 0.00 2.74
5818 8742 2.467566 ACCAGTTCATCACCGTTACC 57.532 50.000 0.00 0.00 0.00 2.85
5820 8744 4.074627 TGAAACCAGTTCATCACCGTTA 57.925 40.909 0.00 0.00 41.47 3.18
5821 8745 2.925724 TGAAACCAGTTCATCACCGTT 58.074 42.857 0.00 0.00 41.47 4.44
5825 8750 3.316308 ACAGCTTGAAACCAGTTCATCAC 59.684 43.478 0.00 0.00 45.71 3.06


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

AutoCloner maintained by Alex Coulton.