Multiple sequence alignment - TraesCS1A01G201000

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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 TraesCS1A01G201000 chr1A 100.000 4746 0 0 1 4746 362064135 362059390 0.000000e+00 8765.0
1 TraesCS1A01G201000 chr1A 87.000 200 17 8 4029 4225 566481167 566480974 2.880000e-52 217.0
2 TraesCS1A01G201000 chr1A 100.000 48 0 0 3825 3872 362060261 362060214 6.540000e-14 89.8
3 TraesCS1A01G201000 chr1A 100.000 48 0 0 3875 3922 362060311 362060264 6.540000e-14 89.8
4 TraesCS1A01G201000 chr1B 94.567 3479 88 38 828 4273 390882525 390879115 0.000000e+00 5284.0
5 TraesCS1A01G201000 chr1B 96.094 128 4 1 4269 4395 390878835 390878708 1.730000e-49 207.0
6 TraesCS1A01G201000 chr1B 95.833 48 1 1 4393 4440 390878592 390878546 5.090000e-10 76.8
7 TraesCS1A01G201000 chr1D 95.542 1660 46 9 825 2463 289600615 289598963 0.000000e+00 2630.0
8 TraesCS1A01G201000 chr1D 95.728 1381 28 6 2494 3847 289598968 289597592 0.000000e+00 2194.0
9 TraesCS1A01G201000 chr1D 96.008 501 13 4 3895 4395 289597619 289597126 0.000000e+00 808.0
10 TraesCS1A01G201000 chr1D 96.462 424 9 3 3972 4395 289532327 289531910 0.000000e+00 695.0
11 TraesCS1A01G201000 chr1D 96.226 424 10 3 3972 4395 289575315 289574898 0.000000e+00 689.0
12 TraesCS1A01G201000 chr1D 92.978 356 16 4 4393 4746 289574782 289574434 1.180000e-140 510.0
13 TraesCS1A01G201000 chr1D 92.717 357 16 5 4393 4746 289597010 289596661 1.520000e-139 507.0
14 TraesCS1A01G201000 chr1D 91.111 225 15 3 4524 4746 289519656 289519435 2.780000e-77 300.0
15 TraesCS1A01G201000 chr1D 94.030 134 4 1 4393 4526 289531794 289531665 2.900000e-47 200.0
16 TraesCS1A01G201000 chr1D 100.000 28 0 0 3845 3872 289597619 289597592 9.000000e-03 52.8
17 TraesCS1A01G201000 chr5A 94.203 828 43 4 1 825 505422001 505422826 0.000000e+00 1258.0
18 TraesCS1A01G201000 chr5A 80.868 507 52 17 2 472 58469225 58468728 1.620000e-94 357.0
19 TraesCS1A01G201000 chr5A 100.000 28 0 0 109 136 34825970 34825943 9.000000e-03 52.8
20 TraesCS1A01G201000 chr4D 92.633 828 37 12 1 826 206664177 206664982 0.000000e+00 1170.0
21 TraesCS1A01G201000 chr4B 91.727 834 56 6 1 828 576744138 576744964 0.000000e+00 1146.0
22 TraesCS1A01G201000 chr4B 94.799 423 19 3 405 825 601297239 601297660 0.000000e+00 656.0
23 TraesCS1A01G201000 chr4B 94.048 420 19 4 1 418 601295293 601295708 2.410000e-177 632.0
24 TraesCS1A01G201000 chr2D 85.890 652 50 10 2506 3156 107864357 107864967 0.000000e+00 656.0
25 TraesCS1A01G201000 chr2D 92.683 164 9 2 4029 4192 526525119 526524959 2.860000e-57 233.0
26 TraesCS1A01G201000 chr2B 84.655 391 37 13 448 836 183431732 183432101 7.500000e-98 368.0
27 TraesCS1A01G201000 chr2B 81.119 429 57 11 1 414 183411669 183412088 5.920000e-84 322.0
28 TraesCS1A01G201000 chr2B 92.727 165 11 1 4029 4193 769078167 769078004 2.210000e-58 237.0
29 TraesCS1A01G201000 chr2B 96.774 31 1 0 3610 3640 212024917 212024887 9.000000e-03 52.8
30 TraesCS1A01G201000 chr3B 91.566 166 11 2 4029 4194 428703821 428703659 4.780000e-55 226.0
31 TraesCS1A01G201000 chr3B 80.851 141 26 1 1674 1814 11211216 11211355 5.020000e-20 110.0
32 TraesCS1A01G201000 chr6B 90.230 174 13 3 4029 4201 548811087 548811257 1.720000e-54 224.0
33 TraesCS1A01G201000 chr6A 87.050 139 12 4 1 139 29150814 29150946 8.230000e-33 152.0
34 TraesCS1A01G201000 chr5B 96.875 32 1 0 3364 3395 582974081 582974112 2.000000e-03 54.7
35 TraesCS1A01G201000 chr2A 100.000 28 0 0 3610 3637 145438939 145438966 9.000000e-03 52.8


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 TraesCS1A01G201000 chr1A 362059390 362064135 4745 True 2981.533333 8765 100.0000 1 4746 3 chr1A.!!$R2 4745
1 TraesCS1A01G201000 chr1B 390878546 390882525 3979 True 1855.933333 5284 95.4980 828 4440 3 chr1B.!!$R1 3612
2 TraesCS1A01G201000 chr1D 289596661 289600615 3954 True 1238.360000 2630 95.9990 825 4746 5 chr1D.!!$R4 3921
3 TraesCS1A01G201000 chr1D 289574434 289575315 881 True 599.500000 689 94.6020 3972 4746 2 chr1D.!!$R3 774
4 TraesCS1A01G201000 chr1D 289531665 289532327 662 True 447.500000 695 95.2460 3972 4526 2 chr1D.!!$R2 554
5 TraesCS1A01G201000 chr5A 505422001 505422826 825 False 1258.000000 1258 94.2030 1 825 1 chr5A.!!$F1 824
6 TraesCS1A01G201000 chr4D 206664177 206664982 805 False 1170.000000 1170 92.6330 1 826 1 chr4D.!!$F1 825
7 TraesCS1A01G201000 chr4B 576744138 576744964 826 False 1146.000000 1146 91.7270 1 828 1 chr4B.!!$F1 827
8 TraesCS1A01G201000 chr4B 601295293 601297660 2367 False 644.000000 656 94.4235 1 825 2 chr4B.!!$F2 824
9 TraesCS1A01G201000 chr2D 107864357 107864967 610 False 656.000000 656 85.8900 2506 3156 1 chr2D.!!$F1 650

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
808 2370 1.006832 ATGAATACCGCAGCAACGTC 58.993 50.000 0.0 0.0 0.00 4.34 F
1567 3154 0.874175 CACAGTTGCGACGAGAACCA 60.874 55.000 0.0 0.0 0.00 3.67 F
2173 3760 1.077501 TAACTCTGCTGCCCCATGC 60.078 57.895 0.0 0.0 41.77 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 3232 0.535335 GCCAATCAGTAGGTGTCCGA 59.465 55.0 0.0 0.0 0.00 4.55 R
3396 5009 1.619654 TGGCAATTCCAAGTGACCAG 58.380 50.0 0.0 0.0 43.21 4.00 R
3767 5385 2.368875 CCGTTTATATCCCACTCCAGCT 59.631 50.0 0.0 0.0 0.00 4.24 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
25 26 4.880696 GCTCCATTCTTAATCTCAACAGCT 59.119 41.667 0.00 0.00 0.00 4.24
73 74 2.762887 TCCAGCTTCTCTATGACACTGG 59.237 50.000 0.00 0.00 43.88 4.00
160 167 4.857251 GGTCCCAACCTCATAGCG 57.143 61.111 0.00 0.00 42.80 4.26
241 248 1.609783 CAGATCAGAACCCCCACCC 59.390 63.158 0.00 0.00 0.00 4.61
242 249 1.163309 AGATCAGAACCCCCACCCA 59.837 57.895 0.00 0.00 0.00 4.51
311 322 4.098914 TCTTAACTGCATTGGGTCAACT 57.901 40.909 0.00 0.00 0.00 3.16
356 367 6.319048 ACAGATCCCATTTAGACTTGATGT 57.681 37.500 0.00 0.00 0.00 3.06
808 2370 1.006832 ATGAATACCGCAGCAACGTC 58.993 50.000 0.00 0.00 0.00 4.34
828 2390 5.474876 ACGTCCGGGGTATTATCTAGTTTAG 59.525 44.000 0.00 0.00 0.00 1.85
829 2391 5.707298 CGTCCGGGGTATTATCTAGTTTAGA 59.293 44.000 0.00 0.00 39.50 2.10
830 2392 6.128063 CGTCCGGGGTATTATCTAGTTTAGAG 60.128 46.154 0.00 0.00 38.38 2.43
831 2393 6.944862 GTCCGGGGTATTATCTAGTTTAGAGA 59.055 42.308 0.00 0.00 38.38 3.10
832 2394 7.449704 GTCCGGGGTATTATCTAGTTTAGAGAA 59.550 40.741 0.00 0.00 39.96 2.87
872 2434 5.673818 GCGGGAGACAAGTAATTAAGCAAAG 60.674 44.000 0.00 0.00 0.00 2.77
878 2440 5.997385 ACAAGTAATTAAGCAAAGGTGACG 58.003 37.500 0.00 0.00 0.00 4.35
938 2500 1.407618 GGGACGTTTTCCTTGCACTTT 59.592 47.619 0.00 0.00 45.09 2.66
940 2502 3.113322 GGACGTTTTCCTTGCACTTTTC 58.887 45.455 0.00 0.00 41.95 2.29
941 2503 3.181490 GGACGTTTTCCTTGCACTTTTCT 60.181 43.478 0.00 0.00 41.95 2.52
1068 2642 1.219124 GGAGCAGCGTCAGGATCAA 59.781 57.895 0.00 0.00 0.00 2.57
1276 2850 6.151312 ACTCGTTTTCTACTTCTGATCTAGCA 59.849 38.462 0.00 0.00 0.00 3.49
1312 2886 0.887933 AGGCGCGGATTGAATTGTTT 59.112 45.000 8.83 0.00 0.00 2.83
1338 2912 3.647649 GATTGCTTGGGGGTTGCGC 62.648 63.158 0.00 0.00 0.00 6.09
1356 2930 2.307768 CGCTAGTGAGGGATGGTTCTA 58.692 52.381 0.00 0.00 37.85 2.10
1505 3092 3.873910 TGCTTCTACTTATTGACCCTGC 58.126 45.455 0.00 0.00 0.00 4.85
1508 3095 4.383118 GCTTCTACTTATTGACCCTGCTCA 60.383 45.833 0.00 0.00 0.00 4.26
1567 3154 0.874175 CACAGTTGCGACGAGAACCA 60.874 55.000 0.00 0.00 0.00 3.67
1757 3344 4.228912 AGGAAATTGCAAGAAGTTCACG 57.771 40.909 4.94 0.00 0.00 4.35
1768 3355 5.390885 GCAAGAAGTTCACGATGCTATTGAA 60.391 40.000 5.50 0.00 0.00 2.69
1829 3416 4.431416 TTCTCAGCTCCCAACTTTGTTA 57.569 40.909 0.00 0.00 0.00 2.41
1893 3480 9.224267 CACACTTGCAGCTTATTATTATATCCT 57.776 33.333 0.00 0.00 0.00 3.24
1930 3517 9.056005 CACAGTACATGCTTTTATGGTGTATAT 57.944 33.333 0.00 0.00 32.32 0.86
2030 3617 7.462571 ACTGACAAGTTTGAAAAGGTTACTT 57.537 32.000 0.00 0.00 33.12 2.24
2173 3760 1.077501 TAACTCTGCTGCCCCATGC 60.078 57.895 0.00 0.00 41.77 4.06
2229 3816 7.493320 AGTTCTGTTAATCGTTCAAACAGTACA 59.507 33.333 19.39 4.35 45.89 2.90
2631 4218 3.189285 CGGCCCAAAATCACAAATGATC 58.811 45.455 0.00 0.00 45.26 2.92
2788 4375 1.134580 AGTTGCTGATCTGACCGATGG 60.135 52.381 3.42 0.00 30.84 3.51
2856 4444 2.169352 CCAATATATCTCCGAGGGCCAG 59.831 54.545 6.18 0.00 0.00 4.85
3076 4685 3.412386 ACTACATTTTCTGGCCACAGTC 58.588 45.455 0.00 0.00 45.14 3.51
3295 4908 5.602628 TGGTTGGTTATTTGGCAGTTAAAC 58.397 37.500 0.00 0.00 0.00 2.01
3356 4969 9.116067 GCTATGGTTGTGTAAATAATGGAAGTA 57.884 33.333 0.00 0.00 0.00 2.24
3409 5022 0.546122 ACACTGCTGGTCACTTGGAA 59.454 50.000 0.00 0.00 0.00 3.53
3560 5176 3.709141 AGGAGAAAGCTGAGGAGGATAAC 59.291 47.826 0.00 0.00 0.00 1.89
3598 5214 4.891992 AGGTAGTGGTATATCATGTGCC 57.108 45.455 0.00 0.00 0.00 5.01
3767 5385 0.338814 GGTGGAAGACTAGGGAGGGA 59.661 60.000 0.00 0.00 0.00 4.20
3802 5420 7.604927 GGGATATAAACGGCTGTGTATATTTGA 59.395 37.037 23.58 4.18 40.20 2.69
3809 5427 4.574759 GGCTGTGTATATTTGACGAAACG 58.425 43.478 0.00 0.00 0.00 3.60
3840 5458 7.953005 TGTTAATATTTCAATTCTGGAGGCA 57.047 32.000 0.00 0.00 0.00 4.75
3841 5459 8.537728 TGTTAATATTTCAATTCTGGAGGCAT 57.462 30.769 0.00 0.00 0.00 4.40
3842 5460 8.632679 TGTTAATATTTCAATTCTGGAGGCATC 58.367 33.333 0.00 0.00 0.00 3.91
3843 5461 6.661304 AATATTTCAATTCTGGAGGCATCC 57.339 37.500 11.34 11.34 46.87 3.51
3844 5462 3.744940 TTTCAATTCTGGAGGCATCCT 57.255 42.857 19.75 0.00 46.80 3.24
3845 5463 4.860802 TTTCAATTCTGGAGGCATCCTA 57.139 40.909 19.75 3.77 46.80 2.94
3846 5464 4.428294 TTCAATTCTGGAGGCATCCTAG 57.572 45.455 19.75 13.94 46.80 3.02
3847 5465 3.387962 TCAATTCTGGAGGCATCCTAGT 58.612 45.455 19.75 0.57 46.80 2.57
3848 5466 3.389329 TCAATTCTGGAGGCATCCTAGTC 59.611 47.826 19.75 0.00 46.80 2.59
3849 5467 2.856760 TTCTGGAGGCATCCTAGTCT 57.143 50.000 19.75 0.00 46.80 3.24
3850 5468 2.856760 TCTGGAGGCATCCTAGTCTT 57.143 50.000 19.75 0.00 46.80 3.01
3851 5469 3.121929 TCTGGAGGCATCCTAGTCTTT 57.878 47.619 19.75 0.00 46.80 2.52
3852 5470 3.034635 TCTGGAGGCATCCTAGTCTTTC 58.965 50.000 19.75 0.00 46.80 2.62
3853 5471 2.768527 CTGGAGGCATCCTAGTCTTTCA 59.231 50.000 19.75 0.00 46.80 2.69
3854 5472 3.181329 TGGAGGCATCCTAGTCTTTCAA 58.819 45.455 19.75 0.00 46.80 2.69
3855 5473 3.782523 TGGAGGCATCCTAGTCTTTCAAT 59.217 43.478 19.75 0.00 46.80 2.57
3856 5474 4.228210 TGGAGGCATCCTAGTCTTTCAATT 59.772 41.667 19.75 0.00 46.80 2.32
3857 5475 4.819088 GGAGGCATCCTAGTCTTTCAATTC 59.181 45.833 10.91 0.00 42.94 2.17
3858 5476 5.397334 GGAGGCATCCTAGTCTTTCAATTCT 60.397 44.000 10.91 0.00 42.94 2.40
3859 5477 5.435291 AGGCATCCTAGTCTTTCAATTCTG 58.565 41.667 0.00 0.00 28.47 3.02
3860 5478 4.578105 GGCATCCTAGTCTTTCAATTCTGG 59.422 45.833 0.00 0.00 0.00 3.86
3861 5479 5.431765 GCATCCTAGTCTTTCAATTCTGGA 58.568 41.667 0.00 0.00 0.00 3.86
3862 5480 5.526846 GCATCCTAGTCTTTCAATTCTGGAG 59.473 44.000 0.00 0.00 0.00 3.86
3863 5481 5.683876 TCCTAGTCTTTCAATTCTGGAGG 57.316 43.478 0.00 0.00 0.00 4.30
3864 5482 4.080863 TCCTAGTCTTTCAATTCTGGAGGC 60.081 45.833 0.00 0.00 0.00 4.70
3865 5483 3.795688 AGTCTTTCAATTCTGGAGGCA 57.204 42.857 0.00 0.00 0.00 4.75
3866 5484 4.313020 AGTCTTTCAATTCTGGAGGCAT 57.687 40.909 0.00 0.00 0.00 4.40
3867 5485 4.268359 AGTCTTTCAATTCTGGAGGCATC 58.732 43.478 0.00 0.00 0.00 3.91
3868 5486 3.379688 GTCTTTCAATTCTGGAGGCATCC 59.620 47.826 11.34 11.34 46.87 3.51
3869 5487 3.267812 TCTTTCAATTCTGGAGGCATCCT 59.732 43.478 19.75 0.00 46.80 3.24
3870 5488 4.474651 TCTTTCAATTCTGGAGGCATCCTA 59.525 41.667 19.75 3.77 46.80 2.94
3871 5489 4.428294 TTCAATTCTGGAGGCATCCTAG 57.572 45.455 19.75 13.94 46.80 3.02
3872 5490 3.387962 TCAATTCTGGAGGCATCCTAGT 58.612 45.455 19.75 0.57 46.80 2.57
3873 5491 3.389329 TCAATTCTGGAGGCATCCTAGTC 59.611 47.826 19.75 0.00 46.80 2.59
3874 5492 2.856760 TTCTGGAGGCATCCTAGTCT 57.143 50.000 19.75 0.00 46.80 3.24
3875 5493 2.856760 TCTGGAGGCATCCTAGTCTT 57.143 50.000 19.75 0.00 46.80 3.01
3876 5494 3.121929 TCTGGAGGCATCCTAGTCTTT 57.878 47.619 19.75 0.00 46.80 2.52
3877 5495 3.034635 TCTGGAGGCATCCTAGTCTTTC 58.965 50.000 19.75 0.00 46.80 2.62
3878 5496 2.768527 CTGGAGGCATCCTAGTCTTTCA 59.231 50.000 19.75 0.00 46.80 2.69
3879 5497 3.181329 TGGAGGCATCCTAGTCTTTCAA 58.819 45.455 19.75 0.00 46.80 2.69
3880 5498 3.782523 TGGAGGCATCCTAGTCTTTCAAT 59.217 43.478 19.75 0.00 46.80 2.57
3881 5499 4.228210 TGGAGGCATCCTAGTCTTTCAATT 59.772 41.667 19.75 0.00 46.80 2.32
3882 5500 4.819088 GGAGGCATCCTAGTCTTTCAATTC 59.181 45.833 10.91 0.00 42.94 2.17
3883 5501 5.397334 GGAGGCATCCTAGTCTTTCAATTCT 60.397 44.000 10.91 0.00 42.94 2.40
3884 5502 5.435291 AGGCATCCTAGTCTTTCAATTCTG 58.565 41.667 0.00 0.00 28.47 3.02
3885 5503 4.578105 GGCATCCTAGTCTTTCAATTCTGG 59.422 45.833 0.00 0.00 0.00 3.86
3886 5504 5.431765 GCATCCTAGTCTTTCAATTCTGGA 58.568 41.667 0.00 0.00 0.00 3.86
3887 5505 5.526846 GCATCCTAGTCTTTCAATTCTGGAG 59.473 44.000 0.00 0.00 0.00 3.86
3888 5506 5.683876 TCCTAGTCTTTCAATTCTGGAGG 57.316 43.478 0.00 0.00 0.00 4.30
3889 5507 4.080863 TCCTAGTCTTTCAATTCTGGAGGC 60.081 45.833 0.00 0.00 0.00 4.70
3890 5508 3.795688 AGTCTTTCAATTCTGGAGGCA 57.204 42.857 0.00 0.00 0.00 4.75
3891 5509 4.313020 AGTCTTTCAATTCTGGAGGCAT 57.687 40.909 0.00 0.00 0.00 4.40
3892 5510 4.268359 AGTCTTTCAATTCTGGAGGCATC 58.732 43.478 0.00 0.00 0.00 3.91
3893 5511 3.379688 GTCTTTCAATTCTGGAGGCATCC 59.620 47.826 11.34 11.34 46.87 3.51
3932 5575 3.761752 GAGGCATCCTAGAGAGTGGTATC 59.238 52.174 0.00 0.00 31.76 2.24
3970 5613 9.716556 TTTGGTTTAAGATGGGCCTATTTATAA 57.283 29.630 1.86 0.76 0.00 0.98
4085 5729 8.783660 AGATCCCACTATAAAGACTACATTCA 57.216 34.615 0.00 0.00 0.00 2.57
4316 6246 1.352352 CAAGTGGGAGTGGGATGTTCT 59.648 52.381 0.00 0.00 0.00 3.01
4395 6326 2.740055 CTGCACACCTGAGCGGTC 60.740 66.667 7.89 7.89 44.93 4.79
4396 6327 3.231889 CTGCACACCTGAGCGGTCT 62.232 63.158 16.64 0.00 44.93 3.85
4451 6500 5.068987 AGCTAAGACCAACATTTTCTTTGCA 59.931 36.000 15.79 0.00 45.07 4.08
4452 6501 5.175673 GCTAAGACCAACATTTTCTTTGCAC 59.824 40.000 10.69 0.00 43.35 4.57
4453 6502 4.734398 AGACCAACATTTTCTTTGCACA 57.266 36.364 0.00 0.00 0.00 4.57
4454 6503 5.280654 AGACCAACATTTTCTTTGCACAT 57.719 34.783 0.00 0.00 0.00 3.21
4468 6517 2.691927 TGCACATAGTCACTGAAGCAG 58.308 47.619 0.00 0.00 37.52 4.24
4545 6596 6.429078 TGAACATGAGATGACTTTTCTTCCAG 59.571 38.462 0.00 0.00 0.00 3.86
4556 6607 0.773644 TTCTTCCAGGCTCCAGCTTT 59.226 50.000 0.00 0.00 41.70 3.51
4559 6610 0.620556 TTCCAGGCTCCAGCTTTAGG 59.379 55.000 0.00 0.00 41.70 2.69
4574 6625 5.527582 CAGCTTTAGGTACCATTGGTGATAC 59.472 44.000 18.83 8.56 36.19 2.24
4685 6737 0.749454 GTTGCCAGGCGATTCAGGAT 60.749 55.000 4.08 0.00 0.00 3.24
4687 6739 1.340399 TGCCAGGCGATTCAGGATCT 61.340 55.000 7.03 0.00 32.30 2.75
4694 6746 4.635765 CAGGCGATTCAGGATCTGTTAAAA 59.364 41.667 0.00 0.00 32.61 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 3.550437 ACTCATGTTGGAGATAGGTGC 57.450 47.619 0.00 0.00 38.30 5.01
160 167 6.429538 TTTAGCTTCATGCGCTAACAGCAC 62.430 45.833 21.37 0.54 46.30 4.40
182 189 2.158900 AGCATTCCGGATTCGTCTCATT 60.159 45.455 4.15 0.00 33.95 2.57
356 367 9.474313 AATTAGGTCTGCAGGAACAAAAATATA 57.526 29.630 15.13 0.00 33.21 0.86
776 2338 4.213270 GCGGTATTCATAGTGCAAGCAATA 59.787 41.667 4.61 4.61 0.00 1.90
808 2370 7.771927 TTCTCTAAACTAGATAATACCCCGG 57.228 40.000 0.00 0.00 33.66 5.73
828 2390 1.809869 GCCCCGCCATCTTTTTCTC 59.190 57.895 0.00 0.00 0.00 2.87
829 2391 4.018409 GCCCCGCCATCTTTTTCT 57.982 55.556 0.00 0.00 0.00 2.52
1009 2571 4.415332 GCGTCCGCGACTTCCAGA 62.415 66.667 8.23 0.00 41.33 3.86
1219 2793 1.521681 GACATACGGTGCAGAGCCC 60.522 63.158 0.00 0.00 0.00 5.19
1276 2850 2.546795 CGCCTTTTCTGTCAGACAGTCT 60.547 50.000 26.65 0.00 46.03 3.24
1312 2886 0.958091 CCCCAAGCAATCGACAAACA 59.042 50.000 0.00 0.00 0.00 2.83
1338 2912 5.941555 AAACTAGAACCATCCCTCACTAG 57.058 43.478 0.00 0.00 35.11 2.57
1356 2930 8.000709 TGAAATTCATAGGGATGCAGATAAACT 58.999 33.333 0.00 0.00 32.62 2.66
1486 3073 5.344743 TGAGCAGGGTCAATAAGTAGAAG 57.655 43.478 0.00 0.00 0.00 2.85
1567 3154 6.183360 GCAACTTATTTAAGTGCGAGACAGAT 60.183 38.462 3.84 0.00 45.17 2.90
1645 3232 0.535335 GCCAATCAGTAGGTGTCCGA 59.465 55.000 0.00 0.00 0.00 4.55
1757 3344 5.119898 CCTCAAGATAGCGTTCAATAGCATC 59.880 44.000 0.00 0.00 35.48 3.91
1768 3355 1.437986 GCGGTCCTCAAGATAGCGT 59.562 57.895 0.00 0.00 36.56 5.07
1893 3480 5.800296 AGCATGTACTGTGTAACCATGTTA 58.200 37.500 0.00 0.00 35.88 2.41
1930 3517 6.909550 ATTGTGATTAGGTTTTGTTGCCTA 57.090 33.333 0.00 0.00 36.38 3.93
1931 3518 5.806654 ATTGTGATTAGGTTTTGTTGCCT 57.193 34.783 0.00 0.00 38.81 4.75
2173 3760 6.533723 TGGTCTCGCTACAACAATATTTAGTG 59.466 38.462 0.00 0.00 0.00 2.74
2214 3801 5.986741 TGCTCTTATTGTACTGTTTGAACGA 59.013 36.000 0.00 0.00 0.00 3.85
2229 3816 4.960938 TCACAACTCAGTGTGCTCTTATT 58.039 39.130 0.41 0.00 46.97 1.40
2631 4218 4.346129 GCATTTCACTATGGCTTTCTTCG 58.654 43.478 0.00 0.00 0.00 3.79
2788 4375 8.662781 TCATGTGCTAGATCCTAAAATAACAC 57.337 34.615 0.00 0.00 0.00 3.32
2856 4444 7.881775 AGTGAAATTGAAATGATAGTACCCC 57.118 36.000 0.00 0.00 0.00 4.95
3056 4665 2.749621 GGACTGTGGCCAGAAAATGTAG 59.250 50.000 5.11 0.00 41.50 2.74
3076 4685 4.816385 ACATTTGCACGTATATCTTCCAGG 59.184 41.667 0.00 0.00 0.00 4.45
3295 4908 3.951663 AGTTACAAAAGAGGGGGAATCG 58.048 45.455 0.00 0.00 0.00 3.34
3356 4969 2.290641 TGTTGGGGTGCTTCATACGAAT 60.291 45.455 0.00 0.00 0.00 3.34
3396 5009 1.619654 TGGCAATTCCAAGTGACCAG 58.380 50.000 0.00 0.00 43.21 4.00
3409 5022 3.949754 CACTACAACATCCAGATGGCAAT 59.050 43.478 12.10 0.00 42.91 3.56
3560 5176 8.304596 ACCACTACCTTGAACATATATCGTATG 58.695 37.037 0.00 0.00 0.00 2.39
3739 5357 4.019681 CCCTAGTCTTCCACCATTTACACA 60.020 45.833 0.00 0.00 0.00 3.72
3767 5385 2.368875 CCGTTTATATCCCACTCCAGCT 59.631 50.000 0.00 0.00 0.00 4.24
3819 5437 7.529555 AGGATGCCTCCAGAATTGAAATATTA 58.470 34.615 10.92 0.00 44.79 0.98
3820 5438 6.379579 AGGATGCCTCCAGAATTGAAATATT 58.620 36.000 10.92 0.00 44.79 1.28
3821 5439 5.961897 AGGATGCCTCCAGAATTGAAATAT 58.038 37.500 10.92 0.00 44.79 1.28
3822 5440 5.393068 AGGATGCCTCCAGAATTGAAATA 57.607 39.130 10.92 0.00 44.79 1.40
3823 5441 4.261411 AGGATGCCTCCAGAATTGAAAT 57.739 40.909 10.92 0.00 44.79 2.17
3824 5442 3.744940 AGGATGCCTCCAGAATTGAAA 57.255 42.857 10.92 0.00 44.79 2.69
3825 5443 3.782523 ACTAGGATGCCTCCAGAATTGAA 59.217 43.478 10.92 0.00 44.79 2.69
3826 5444 3.387962 ACTAGGATGCCTCCAGAATTGA 58.612 45.455 10.92 0.00 44.79 2.57
3827 5445 3.390639 AGACTAGGATGCCTCCAGAATTG 59.609 47.826 10.92 0.00 44.79 2.32
3828 5446 3.663198 AGACTAGGATGCCTCCAGAATT 58.337 45.455 10.92 0.00 44.79 2.17
3829 5447 3.342926 AGACTAGGATGCCTCCAGAAT 57.657 47.619 10.92 0.00 44.79 2.40
3830 5448 2.856760 AGACTAGGATGCCTCCAGAA 57.143 50.000 10.92 0.00 44.79 3.02
3831 5449 2.856760 AAGACTAGGATGCCTCCAGA 57.143 50.000 10.92 0.00 44.79 3.86
3832 5450 2.768527 TGAAAGACTAGGATGCCTCCAG 59.231 50.000 10.92 8.10 44.79 3.86
3833 5451 2.832838 TGAAAGACTAGGATGCCTCCA 58.167 47.619 10.92 0.00 44.79 3.86
3834 5452 3.914426 TTGAAAGACTAGGATGCCTCC 57.086 47.619 0.00 0.00 42.43 4.30
3835 5453 5.526846 CAGAATTGAAAGACTAGGATGCCTC 59.473 44.000 0.00 0.00 34.61 4.70
3836 5454 5.435291 CAGAATTGAAAGACTAGGATGCCT 58.565 41.667 0.00 0.00 37.71 4.75
3837 5455 4.578105 CCAGAATTGAAAGACTAGGATGCC 59.422 45.833 0.00 0.00 0.00 4.40
3838 5456 5.431765 TCCAGAATTGAAAGACTAGGATGC 58.568 41.667 0.00 0.00 0.00 3.91
3839 5457 6.054295 CCTCCAGAATTGAAAGACTAGGATG 58.946 44.000 0.00 0.00 0.00 3.51
3840 5458 5.397334 GCCTCCAGAATTGAAAGACTAGGAT 60.397 44.000 0.00 0.00 0.00 3.24
3841 5459 4.080863 GCCTCCAGAATTGAAAGACTAGGA 60.081 45.833 0.00 0.00 0.00 2.94
3842 5460 4.195416 GCCTCCAGAATTGAAAGACTAGG 58.805 47.826 0.00 0.00 0.00 3.02
3843 5461 4.836825 TGCCTCCAGAATTGAAAGACTAG 58.163 43.478 0.00 0.00 0.00 2.57
3844 5462 4.908601 TGCCTCCAGAATTGAAAGACTA 57.091 40.909 0.00 0.00 0.00 2.59
3845 5463 3.795688 TGCCTCCAGAATTGAAAGACT 57.204 42.857 0.00 0.00 0.00 3.24
3846 5464 3.379688 GGATGCCTCCAGAATTGAAAGAC 59.620 47.826 2.72 0.00 41.64 3.01
3847 5465 3.267812 AGGATGCCTCCAGAATTGAAAGA 59.732 43.478 10.92 0.00 44.79 2.52
3848 5466 3.629087 AGGATGCCTCCAGAATTGAAAG 58.371 45.455 10.92 0.00 44.79 2.62
3849 5467 3.744940 AGGATGCCTCCAGAATTGAAA 57.255 42.857 10.92 0.00 44.79 2.69
3850 5468 3.782523 ACTAGGATGCCTCCAGAATTGAA 59.217 43.478 10.92 0.00 44.79 2.69
3851 5469 3.387962 ACTAGGATGCCTCCAGAATTGA 58.612 45.455 10.92 0.00 44.79 2.57
3852 5470 3.390639 AGACTAGGATGCCTCCAGAATTG 59.609 47.826 10.92 0.00 44.79 2.32
3853 5471 3.663198 AGACTAGGATGCCTCCAGAATT 58.337 45.455 10.92 0.00 44.79 2.17
3854 5472 3.342926 AGACTAGGATGCCTCCAGAAT 57.657 47.619 10.92 0.00 44.79 2.40
3855 5473 2.856760 AGACTAGGATGCCTCCAGAA 57.143 50.000 10.92 0.00 44.79 3.02
3856 5474 2.856760 AAGACTAGGATGCCTCCAGA 57.143 50.000 10.92 0.00 44.79 3.86
3857 5475 2.768527 TGAAAGACTAGGATGCCTCCAG 59.231 50.000 10.92 8.10 44.79 3.86
3858 5476 2.832838 TGAAAGACTAGGATGCCTCCA 58.167 47.619 10.92 0.00 44.79 3.86
3859 5477 3.914426 TTGAAAGACTAGGATGCCTCC 57.086 47.619 0.00 0.00 42.43 4.30
3860 5478 5.526846 CAGAATTGAAAGACTAGGATGCCTC 59.473 44.000 0.00 0.00 34.61 4.70
3861 5479 5.435291 CAGAATTGAAAGACTAGGATGCCT 58.565 41.667 0.00 0.00 37.71 4.75
3862 5480 4.578105 CCAGAATTGAAAGACTAGGATGCC 59.422 45.833 0.00 0.00 0.00 4.40
3863 5481 5.431765 TCCAGAATTGAAAGACTAGGATGC 58.568 41.667 0.00 0.00 0.00 3.91
3864 5482 6.054295 CCTCCAGAATTGAAAGACTAGGATG 58.946 44.000 0.00 0.00 0.00 3.51
3865 5483 5.397334 GCCTCCAGAATTGAAAGACTAGGAT 60.397 44.000 0.00 0.00 0.00 3.24
3866 5484 4.080863 GCCTCCAGAATTGAAAGACTAGGA 60.081 45.833 0.00 0.00 0.00 2.94
3867 5485 4.195416 GCCTCCAGAATTGAAAGACTAGG 58.805 47.826 0.00 0.00 0.00 3.02
3868 5486 4.836825 TGCCTCCAGAATTGAAAGACTAG 58.163 43.478 0.00 0.00 0.00 2.57
3869 5487 4.908601 TGCCTCCAGAATTGAAAGACTA 57.091 40.909 0.00 0.00 0.00 2.59
3870 5488 3.795688 TGCCTCCAGAATTGAAAGACT 57.204 42.857 0.00 0.00 0.00 3.24
3871 5489 3.379688 GGATGCCTCCAGAATTGAAAGAC 59.620 47.826 2.72 0.00 41.64 3.01
3872 5490 3.267812 AGGATGCCTCCAGAATTGAAAGA 59.732 43.478 10.92 0.00 44.79 2.52
3873 5491 3.629087 AGGATGCCTCCAGAATTGAAAG 58.371 45.455 10.92 0.00 44.79 2.62
3874 5492 3.744940 AGGATGCCTCCAGAATTGAAA 57.255 42.857 10.92 0.00 44.79 2.69
3875 5493 3.782523 ACTAGGATGCCTCCAGAATTGAA 59.217 43.478 10.92 0.00 44.79 2.69
3876 5494 3.387962 ACTAGGATGCCTCCAGAATTGA 58.612 45.455 10.92 0.00 44.79 2.57
3877 5495 3.390639 AGACTAGGATGCCTCCAGAATTG 59.609 47.826 10.92 0.00 44.79 2.32
3878 5496 3.663198 AGACTAGGATGCCTCCAGAATT 58.337 45.455 10.92 0.00 44.79 2.17
3879 5497 3.342926 AGACTAGGATGCCTCCAGAAT 57.657 47.619 10.92 0.00 44.79 2.40
3880 5498 2.856760 AGACTAGGATGCCTCCAGAA 57.143 50.000 10.92 0.00 44.79 3.02
3881 5499 2.856760 AAGACTAGGATGCCTCCAGA 57.143 50.000 10.92 0.00 44.79 3.86
3882 5500 2.768527 TGAAAGACTAGGATGCCTCCAG 59.231 50.000 10.92 8.10 44.79 3.86
3883 5501 2.832838 TGAAAGACTAGGATGCCTCCA 58.167 47.619 10.92 0.00 44.79 3.86
3884 5502 3.914426 TTGAAAGACTAGGATGCCTCC 57.086 47.619 0.00 0.00 42.43 4.30
3885 5503 5.526846 CAGAATTGAAAGACTAGGATGCCTC 59.473 44.000 0.00 0.00 34.61 4.70
3886 5504 5.435291 CAGAATTGAAAGACTAGGATGCCT 58.565 41.667 0.00 0.00 37.71 4.75
3887 5505 4.578105 CCAGAATTGAAAGACTAGGATGCC 59.422 45.833 0.00 0.00 0.00 4.40
3888 5506 5.431765 TCCAGAATTGAAAGACTAGGATGC 58.568 41.667 0.00 0.00 0.00 3.91
3889 5507 6.054295 CCTCCAGAATTGAAAGACTAGGATG 58.946 44.000 0.00 0.00 0.00 3.51
3890 5508 5.397334 GCCTCCAGAATTGAAAGACTAGGAT 60.397 44.000 0.00 0.00 0.00 3.24
3891 5509 4.080863 GCCTCCAGAATTGAAAGACTAGGA 60.081 45.833 0.00 0.00 0.00 2.94
3892 5510 4.195416 GCCTCCAGAATTGAAAGACTAGG 58.805 47.826 0.00 0.00 0.00 3.02
3893 5511 4.836825 TGCCTCCAGAATTGAAAGACTAG 58.163 43.478 0.00 0.00 0.00 2.57
4027 5670 5.011840 ACTTATATTTAGGAACGGAGGGAGC 59.988 44.000 0.00 0.00 0.00 4.70
4064 5708 8.424918 ACATCTGAATGTAGTCTTTATAGTGGG 58.575 37.037 0.00 0.00 44.38 4.61
4099 5743 9.710818 TGAGTGAACCTATATACTCTAAAAGGT 57.289 33.333 0.00 0.00 40.07 3.50
4105 5750 9.982651 GCAAAATGAGTGAACCTATATACTCTA 57.017 33.333 0.00 0.00 40.07 2.43
4106 5751 8.709308 AGCAAAATGAGTGAACCTATATACTCT 58.291 33.333 0.00 0.00 40.07 3.24
4107 5752 8.894768 AGCAAAATGAGTGAACCTATATACTC 57.105 34.615 0.00 0.00 39.88 2.59
4108 5753 7.934120 GGAGCAAAATGAGTGAACCTATATACT 59.066 37.037 0.00 0.00 0.00 2.12
4109 5754 7.095607 CGGAGCAAAATGAGTGAACCTATATAC 60.096 40.741 0.00 0.00 0.00 1.47
4110 5755 6.929049 CGGAGCAAAATGAGTGAACCTATATA 59.071 38.462 0.00 0.00 0.00 0.86
4111 5756 5.760253 CGGAGCAAAATGAGTGAACCTATAT 59.240 40.000 0.00 0.00 0.00 0.86
4182 5827 3.048600 AGCAAAGCATATACTCCCTCCA 58.951 45.455 0.00 0.00 0.00 3.86
4395 6326 6.623767 GCTTGGGAAGAGCTAACAAACATTAG 60.624 42.308 0.00 0.00 37.18 1.73
4396 6327 5.183140 GCTTGGGAAGAGCTAACAAACATTA 59.817 40.000 0.00 0.00 37.18 1.90
4451 6500 3.499918 GCAAACTGCTTCAGTGACTATGT 59.500 43.478 0.00 0.00 44.62 2.29
4452 6501 3.120060 GGCAAACTGCTTCAGTGACTATG 60.120 47.826 0.00 0.00 44.62 2.23
4453 6502 3.077359 GGCAAACTGCTTCAGTGACTAT 58.923 45.455 0.00 0.00 44.62 2.12
4454 6503 2.158827 TGGCAAACTGCTTCAGTGACTA 60.159 45.455 0.00 0.00 44.62 2.59
4468 6517 1.713597 GGCTGCTAATTGTGGCAAAC 58.286 50.000 0.00 0.00 41.20 2.93
4545 6596 0.909623 TGGTACCTAAAGCTGGAGCC 59.090 55.000 14.36 0.00 43.38 4.70
4556 6607 3.385433 CCACGTATCACCAATGGTACCTA 59.615 47.826 14.36 0.00 38.98 3.08
4559 6610 3.192466 GTCCACGTATCACCAATGGTAC 58.808 50.000 3.85 0.00 38.82 3.34
4574 6625 3.433957 TCATCATTTAACGTTGGTCCACG 59.566 43.478 11.99 10.96 46.04 4.94
4587 6638 8.421249 AATGACTTTTTCACCCTCATCATTTA 57.579 30.769 0.00 0.00 36.92 1.40
4633 6685 6.075762 TGTTGATTTGGATGACAAGTTCTG 57.924 37.500 0.00 0.00 40.82 3.02
4717 6769 4.599047 TTTGCATTTCTTGGGTTCGATT 57.401 36.364 0.00 0.00 0.00 3.34
4718 6770 4.280677 TCTTTTGCATTTCTTGGGTTCGAT 59.719 37.500 0.00 0.00 0.00 3.59
4721 6773 4.751600 CCTTCTTTTGCATTTCTTGGGTTC 59.248 41.667 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.