Multiple sequence alignment - TraesCS2A01G248800

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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 TraesCS2A01G248800 chr2A 100.000 4527 0 0 1 4527 372738383 372733857 0.000000e+00 8360.0
1 TraesCS2A01G248800 chr2A 92.500 840 59 4 1 838 592464136 592464973 0.000000e+00 1199.0
2 TraesCS2A01G248800 chr2A 94.949 99 4 1 4086 4184 32986126 32986029 2.180000e-33 154.0
3 TraesCS2A01G248800 chr2A 100.000 54 0 0 4273 4326 372734058 372734005 2.880000e-17 100.0
4 TraesCS2A01G248800 chr2A 100.000 54 0 0 4326 4379 372734111 372734058 2.880000e-17 100.0
5 TraesCS2A01G248800 chr2D 97.664 1541 26 6 837 2368 298942928 298941389 0.000000e+00 2638.0
6 TraesCS2A01G248800 chr2D 89.796 1029 42 30 3315 4326 298938699 298937717 0.000000e+00 1260.0
7 TraesCS2A01G248800 chr2D 87.534 746 36 14 2372 3109 298941234 298940538 0.000000e+00 809.0
8 TraesCS2A01G248800 chr2D 93.467 199 13 0 4326 4524 298937770 298937572 3.420000e-76 296.0
9 TraesCS2A01G248800 chr2D 92.553 94 7 0 3107 3200 298939365 298939272 7.900000e-28 135.0
10 TraesCS2A01G248800 chr2D 89.474 95 9 1 3197 3291 298938786 298938693 7.960000e-23 119.0
11 TraesCS2A01G248800 chr2D 84.906 53 8 0 4202 4254 543276784 543276836 2.000000e-03 54.7
12 TraesCS2A01G248800 chr2B 94.579 1697 43 14 836 2504 356315926 356317601 0.000000e+00 2579.0
13 TraesCS2A01G248800 chr2B 89.296 1037 53 33 3305 4324 356318734 356319729 0.000000e+00 1247.0
14 TraesCS2A01G248800 chr2B 89.432 634 32 18 2488 3109 356317619 356318229 0.000000e+00 767.0
15 TraesCS2A01G248800 chr2B 91.457 199 13 2 4326 4524 356319681 356319875 2.080000e-68 270.0
16 TraesCS2A01G248800 chr2B 90.052 191 14 3 3104 3291 356318562 356318750 4.520000e-60 243.0
17 TraesCS2A01G248800 chr5B 85.200 1223 157 16 1104 2314 604143990 604142780 0.000000e+00 1234.0
18 TraesCS2A01G248800 chr5D 85.094 1221 159 16 1104 2314 490006699 490005492 0.000000e+00 1225.0
19 TraesCS2A01G248800 chr5A 84.918 1220 163 13 1104 2314 611632741 611631534 0.000000e+00 1214.0
20 TraesCS2A01G248800 chr5A 89.167 240 26 0 1930 2169 645413292 645413053 2.650000e-77 300.0
21 TraesCS2A01G248800 chr7A 92.381 840 60 4 1 838 261061728 261062565 0.000000e+00 1194.0
22 TraesCS2A01G248800 chr7A 92.024 840 64 3 1 838 261086839 261087677 0.000000e+00 1177.0
23 TraesCS2A01G248800 chr7A 91.381 847 69 4 1 846 701774183 701775026 0.000000e+00 1157.0
24 TraesCS2A01G248800 chr7A 95.098 102 5 0 1934 2035 83536090 83536191 1.300000e-35 161.0
25 TraesCS2A01G248800 chr7A 92.000 100 7 1 4085 4184 134067463 134067365 6.110000e-29 139.0
26 TraesCS2A01G248800 chr7A 91.919 99 7 1 4086 4184 56927656 56927559 2.200000e-28 137.0
27 TraesCS2A01G248800 chr4A 92.253 839 61 2 6 840 684037237 684036399 0.000000e+00 1186.0
28 TraesCS2A01G248800 chr4A 91.815 843 64 5 1 840 628845247 628846087 0.000000e+00 1170.0
29 TraesCS2A01G248800 chr4A 91.351 844 69 2 1 840 684017452 684016609 0.000000e+00 1151.0
30 TraesCS2A01G248800 chr4A 91.509 106 9 0 1930 2035 21864592 21864697 3.650000e-31 147.0
31 TraesCS2A01G248800 chr4A 90.741 54 5 0 4201 4254 604094450 604094503 6.280000e-09 73.1
32 TraesCS2A01G248800 chr1A 91.934 843 65 2 1 841 589187427 589188268 0.000000e+00 1177.0
33 TraesCS2A01G248800 chr1A 90.566 53 5 0 4202 4254 367025182 367025130 2.260000e-08 71.3
34 TraesCS2A01G248800 chr3A 91.885 838 68 0 1 838 509023356 509024193 0.000000e+00 1171.0
35 TraesCS2A01G248800 chr3A 78.899 436 72 15 1105 1536 12562523 12562942 1.240000e-70 278.0
36 TraesCS2A01G248800 chr3A 97.561 41 1 0 4202 4242 299529115 299529075 2.260000e-08 71.3
37 TraesCS2A01G248800 chr3D 87.160 257 29 4 1104 1358 7969831 7969577 5.730000e-74 289.0
38 TraesCS2A01G248800 chr3B 87.603 242 26 4 1119 1358 10172041 10171802 1.240000e-70 278.0
39 TraesCS2A01G248800 chrUn 94.949 99 4 1 4086 4184 12876690 12876787 2.180000e-33 154.0
40 TraesCS2A01G248800 chrUn 94.949 99 4 1 4086 4184 274067711 274067808 2.180000e-33 154.0
41 TraesCS2A01G248800 chrUn 88.000 50 6 0 4205 4254 1995174 1995125 4.890000e-05 60.2
42 TraesCS2A01G248800 chr4D 91.262 103 7 2 4085 4186 335890598 335890699 6.110000e-29 139.0
43 TraesCS2A01G248800 chr4D 90.196 51 5 0 4204 4254 408572567 408572517 2.920000e-07 67.6
44 TraesCS2A01G248800 chr7B 91.176 102 7 2 4084 4184 11657421 11657521 2.200000e-28 137.0
45 TraesCS2A01G248800 chr7B 91.000 100 8 1 4085 4184 186821953 186821855 2.840000e-27 134.0
46 TraesCS2A01G248800 chr7B 88.679 53 6 0 4202 4254 158366789 158366841 1.050000e-06 65.8
47 TraesCS2A01G248800 chr1D 75.197 254 38 9 1104 1355 108361828 108362058 3.730000e-16 97.1
48 TraesCS2A01G248800 chr1B 94.444 54 1 2 4202 4254 324356048 324356100 1.040000e-11 82.4
49 TraesCS2A01G248800 chr6B 92.308 52 4 0 4202 4253 135488313 135488364 1.750000e-09 75.0


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 TraesCS2A01G248800 chr2A 372733857 372738383 4526 True 8360.000000 8360 100.0000 1 4527 1 chr2A.!!$R2 4526
1 TraesCS2A01G248800 chr2A 592464136 592464973 837 False 1199.000000 1199 92.5000 1 838 1 chr2A.!!$F1 837
2 TraesCS2A01G248800 chr2D 298937572 298942928 5356 True 876.166667 2638 91.7480 837 4524 6 chr2D.!!$R1 3687
3 TraesCS2A01G248800 chr2B 356315926 356319875 3949 False 1021.200000 2579 90.9632 836 4524 5 chr2B.!!$F1 3688
4 TraesCS2A01G248800 chr5B 604142780 604143990 1210 True 1234.000000 1234 85.2000 1104 2314 1 chr5B.!!$R1 1210
5 TraesCS2A01G248800 chr5D 490005492 490006699 1207 True 1225.000000 1225 85.0940 1104 2314 1 chr5D.!!$R1 1210
6 TraesCS2A01G248800 chr5A 611631534 611632741 1207 True 1214.000000 1214 84.9180 1104 2314 1 chr5A.!!$R1 1210
7 TraesCS2A01G248800 chr7A 261061728 261062565 837 False 1194.000000 1194 92.3810 1 838 1 chr7A.!!$F2 837
8 TraesCS2A01G248800 chr7A 261086839 261087677 838 False 1177.000000 1177 92.0240 1 838 1 chr7A.!!$F3 837
9 TraesCS2A01G248800 chr7A 701774183 701775026 843 False 1157.000000 1157 91.3810 1 846 1 chr7A.!!$F4 845
10 TraesCS2A01G248800 chr4A 684036399 684037237 838 True 1186.000000 1186 92.2530 6 840 1 chr4A.!!$R2 834
11 TraesCS2A01G248800 chr4A 628845247 628846087 840 False 1170.000000 1170 91.8150 1 840 1 chr4A.!!$F3 839
12 TraesCS2A01G248800 chr4A 684016609 684017452 843 True 1151.000000 1151 91.3510 1 840 1 chr4A.!!$R1 839
13 TraesCS2A01G248800 chr1A 589187427 589188268 841 False 1177.000000 1177 91.9340 1 841 1 chr1A.!!$F1 840
14 TraesCS2A01G248800 chr3A 509023356 509024193 837 False 1171.000000 1171 91.8850 1 838 1 chr3A.!!$F2 837

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
582 587 0.686769 GGGGCGAAAGAGAGAGGGTA 60.687 60.0 0.0 0.0 0.00 3.69 F
2527 2746 0.607620 GGCACCCAAGCAAAGCAATA 59.392 50.0 0.0 0.0 35.83 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2529 2748 0.031994 ATTTTGTTGGTGAGGTGCGC 59.968 50.0 0.0 0.0 0.00 6.09 R
4437 6499 0.859232 GTGCGACAGACAATGAACGT 59.141 50.0 0.0 0.0 35.77 3.99 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
26 27 2.630580 GGGGTGTTGGCAAAGTAATCAA 59.369 45.455 0.00 0.00 0.00 2.57
33 34 7.367285 GTGTTGGCAAAGTAATCAACATAGAA 58.633 34.615 0.00 0.00 46.96 2.10
37 38 6.939730 TGGCAAAGTAATCAACATAGAACAGA 59.060 34.615 0.00 0.00 0.00 3.41
68 69 3.365265 CCCTGTTGCGGTTCAGGC 61.365 66.667 5.77 0.00 46.83 4.85
212 213 6.751888 ACAAAGAAAGTGATGGAAGAAAAACG 59.248 34.615 0.00 0.00 0.00 3.60
233 234 1.405821 CGTCTCCACTGTCCATACCTC 59.594 57.143 0.00 0.00 0.00 3.85
289 290 1.592669 CGAAGAGGCCGCGATGATT 60.593 57.895 8.23 0.00 0.00 2.57
301 302 1.835121 CGATGATTACCTCGACGCAA 58.165 50.000 0.00 0.00 36.54 4.85
344 345 4.400961 GGCCGCTGTGGAGCTCTT 62.401 66.667 14.64 0.00 43.77 2.85
582 587 0.686769 GGGGCGAAAGAGAGAGGGTA 60.687 60.000 0.00 0.00 0.00 3.69
615 620 3.291497 GGAGGGACTGCTAGTGTCT 57.709 57.895 14.49 0.66 45.87 3.41
617 622 1.617263 GGAGGGACTGCTAGTGTCTCA 60.617 57.143 16.41 0.00 45.87 3.27
623 628 3.078097 GACTGCTAGTGTCTCAGACAGA 58.922 50.000 8.09 0.00 43.57 3.41
707 717 1.959226 GAGCGCAAGTTTGGGTCGA 60.959 57.895 11.47 0.00 42.44 4.20
717 727 0.838554 TTTGGGTCGAGGATGGGTCA 60.839 55.000 0.00 0.00 0.00 4.02
724 734 3.343617 GTCGAGGATGGGTCAAAAATGA 58.656 45.455 0.00 0.00 0.00 2.57
763 773 2.304401 CGTTTGTGACCGTGCGCTA 61.304 57.895 9.73 0.00 0.00 4.26
813 824 2.202756 GACGGAGGCGGACATGAC 60.203 66.667 0.00 0.00 0.00 3.06
906 925 2.582052 GTGAACCCCACTCATGTTTCA 58.418 47.619 0.00 0.00 42.44 2.69
940 962 2.650322 TCCCAAAGAAAAGAACGCACT 58.350 42.857 0.00 0.00 0.00 4.40
955 977 2.109387 ACTACCACCGCAAACGCA 59.891 55.556 0.00 0.00 38.22 5.24
971 993 3.594775 CAAGCAGCAACCGCACCA 61.595 61.111 0.00 0.00 42.27 4.17
1638 1669 1.597854 CAGGACGCACAGGCTGAAA 60.598 57.895 23.66 0.00 38.10 2.69
2311 2345 2.995872 AAGCTCCGACGAGGTCAGC 61.996 63.158 0.00 0.00 46.12 4.26
2324 2358 3.305131 CGAGGTCAGCACAGTAACTTGTA 60.305 47.826 0.00 0.00 0.00 2.41
2410 2595 1.275291 AGAATGGTCGTGTCGATGGTT 59.725 47.619 0.00 0.00 38.42 3.67
2419 2604 4.792189 GTCGTGTCGATGGTTAGTAGAAAG 59.208 45.833 0.00 0.00 38.42 2.62
2420 2605 4.696877 TCGTGTCGATGGTTAGTAGAAAGA 59.303 41.667 0.00 0.00 0.00 2.52
2421 2606 5.181811 TCGTGTCGATGGTTAGTAGAAAGAA 59.818 40.000 0.00 0.00 0.00 2.52
2422 2607 5.860182 CGTGTCGATGGTTAGTAGAAAGAAA 59.140 40.000 0.00 0.00 0.00 2.52
2423 2608 6.033619 CGTGTCGATGGTTAGTAGAAAGAAAG 59.966 42.308 0.00 0.00 0.00 2.62
2424 2609 7.088905 GTGTCGATGGTTAGTAGAAAGAAAGA 58.911 38.462 0.00 0.00 0.00 2.52
2425 2610 7.597743 GTGTCGATGGTTAGTAGAAAGAAAGAA 59.402 37.037 0.00 0.00 0.00 2.52
2440 2625 3.056328 GAAGAGGGTTGTGCGGGC 61.056 66.667 0.00 0.00 0.00 6.13
2525 2744 2.820973 GGCACCCAAGCAAAGCAA 59.179 55.556 0.00 0.00 35.83 3.91
2526 2745 1.372307 GGCACCCAAGCAAAGCAAT 59.628 52.632 0.00 0.00 35.83 3.56
2527 2746 0.607620 GGCACCCAAGCAAAGCAATA 59.392 50.000 0.00 0.00 35.83 1.90
2528 2747 1.207811 GGCACCCAAGCAAAGCAATAT 59.792 47.619 0.00 0.00 35.83 1.28
2529 2748 2.273557 GCACCCAAGCAAAGCAATATG 58.726 47.619 0.00 0.00 0.00 1.78
2530 2749 2.273557 CACCCAAGCAAAGCAATATGC 58.726 47.619 0.00 0.00 45.46 3.14
2661 2883 3.090219 GCCCGGCGAGTTGGATAGT 62.090 63.158 9.30 0.00 0.00 2.12
2688 2910 2.940410 CCGCGTGTAAGGGTGAAATTAT 59.060 45.455 4.92 0.00 0.00 1.28
2701 2923 7.715482 AGGGTGAAATTATTTAAGGGGTACTT 58.285 34.615 0.00 0.00 43.28 2.24
2702 2924 8.848830 AGGGTGAAATTATTTAAGGGGTACTTA 58.151 33.333 0.00 0.00 40.64 2.24
2703 2925 8.906867 GGGTGAAATTATTTAAGGGGTACTTAC 58.093 37.037 0.00 0.00 41.24 2.34
2727 2949 2.604046 AGTAGGAGTAAATGCCGCAG 57.396 50.000 0.00 0.00 0.00 5.18
2826 3060 2.702441 GGGTGGGGAGGGGAGTAATAAT 60.702 54.545 0.00 0.00 0.00 1.28
2827 3061 3.441961 GGGTGGGGAGGGGAGTAATAATA 60.442 52.174 0.00 0.00 0.00 0.98
2828 3062 4.245308 GGTGGGGAGGGGAGTAATAATAA 58.755 47.826 0.00 0.00 0.00 1.40
2829 3063 4.856182 GGTGGGGAGGGGAGTAATAATAAT 59.144 45.833 0.00 0.00 0.00 1.28
2830 3064 6.034003 GGTGGGGAGGGGAGTAATAATAATA 58.966 44.000 0.00 0.00 0.00 0.98
2831 3065 6.506413 GGTGGGGAGGGGAGTAATAATAATAA 59.494 42.308 0.00 0.00 0.00 1.40
2976 3211 2.310233 CCCGCGTTGTCAGTGTCAG 61.310 63.158 4.92 0.00 0.00 3.51
3006 3247 0.111253 CAGGGAGGGCCATTATCACC 59.889 60.000 6.18 0.00 35.15 4.02
3023 3264 2.496070 TCACCACTACATACAGCTGTCC 59.504 50.000 25.56 0.00 0.00 4.02
3053 3296 2.128507 CCCGTGGGCTAGACTCTCC 61.129 68.421 0.00 0.00 0.00 3.71
3060 3303 0.818296 GGCTAGACTCTCCGCTTTGA 59.182 55.000 0.00 0.00 0.00 2.69
3070 3313 2.622942 TCTCCGCTTTGATTGCTTGTTT 59.377 40.909 0.00 0.00 0.00 2.83
3157 4702 3.126831 GTCGAGATGGAGCATAGGTTTG 58.873 50.000 0.00 0.00 0.00 2.93
3237 5271 0.802494 GTGCACCTGTAAATGGGACG 59.198 55.000 5.22 0.00 0.00 4.79
3254 5288 2.978010 GCACCACCCAACACCGAG 60.978 66.667 0.00 0.00 0.00 4.63
3269 5303 2.095059 CACCGAGGCCTGAAAATGAAAG 60.095 50.000 12.00 0.00 0.00 2.62
3298 5332 9.981114 AAAACATAGACATAACTTTCTTTTGGG 57.019 29.630 0.00 0.00 0.00 4.12
3299 5333 7.158099 ACATAGACATAACTTTCTTTTGGGC 57.842 36.000 0.00 0.00 0.00 5.36
3300 5334 6.719370 ACATAGACATAACTTTCTTTTGGGCA 59.281 34.615 0.00 0.00 0.00 5.36
3301 5335 5.712152 AGACATAACTTTCTTTTGGGCAG 57.288 39.130 0.00 0.00 0.00 4.85
3302 5336 5.140454 AGACATAACTTTCTTTTGGGCAGT 58.860 37.500 0.00 0.00 0.00 4.40
3303 5337 5.010012 AGACATAACTTTCTTTTGGGCAGTG 59.990 40.000 0.00 0.00 0.00 3.66
3309 5343 4.892934 ACTTTCTTTTGGGCAGTGAACATA 59.107 37.500 0.00 0.00 0.00 2.29
3313 5347 3.500448 TTTGGGCAGTGAACATAGACA 57.500 42.857 0.00 0.00 0.00 3.41
3324 5358 7.584108 CAGTGAACATAGACATAACTTTGCAA 58.416 34.615 0.00 0.00 0.00 4.08
3331 5365 8.796475 ACATAGACATAACTTTGCAACTCATTT 58.204 29.630 0.00 0.00 0.00 2.32
3513 5553 0.605319 GGTGGGCGATCACACTTCAA 60.605 55.000 10.74 0.00 39.27 2.69
3761 5803 5.474876 TCAGATCGACATCAGTGTATAGCAT 59.525 40.000 0.00 0.00 39.09 3.79
3766 5808 8.887036 ATCGACATCAGTGTATAGCATTTTTA 57.113 30.769 0.00 0.00 39.09 1.52
3812 5855 8.807948 ATTTGTGGTTTAAGATGCTACATACT 57.192 30.769 0.00 0.00 0.00 2.12
3897 5940 3.287867 TCTCTGCATTTTGATCCTCCC 57.712 47.619 0.00 0.00 0.00 4.30
3908 5951 1.008327 TGATCCTCCCTGCCTTCTACA 59.992 52.381 0.00 0.00 0.00 2.74
3911 5954 0.539051 CCTCCCTGCCTTCTACACTG 59.461 60.000 0.00 0.00 0.00 3.66
4001 6052 1.241485 AAGGAGTTCCCCCTTGGTTT 58.759 50.000 0.00 0.00 42.10 3.27
4010 6061 3.506398 TCCCCCTTGGTTTCATCTTTTC 58.494 45.455 0.00 0.00 34.77 2.29
4011 6062 2.567169 CCCCCTTGGTTTCATCTTTTCC 59.433 50.000 0.00 0.00 0.00 3.13
4012 6063 3.238597 CCCCTTGGTTTCATCTTTTCCA 58.761 45.455 0.00 0.00 0.00 3.53
4013 6064 3.840078 CCCCTTGGTTTCATCTTTTCCAT 59.160 43.478 0.00 0.00 0.00 3.41
4014 6065 4.286808 CCCCTTGGTTTCATCTTTTCCATT 59.713 41.667 0.00 0.00 0.00 3.16
4015 6066 5.240121 CCCTTGGTTTCATCTTTTCCATTG 58.760 41.667 0.00 0.00 0.00 2.82
4016 6067 5.011943 CCCTTGGTTTCATCTTTTCCATTGA 59.988 40.000 0.00 0.00 0.00 2.57
4017 6068 6.296030 CCCTTGGTTTCATCTTTTCCATTGAT 60.296 38.462 0.00 0.00 0.00 2.57
4018 6069 6.592607 CCTTGGTTTCATCTTTTCCATTGATG 59.407 38.462 0.00 0.00 38.97 3.07
4019 6070 6.914654 TGGTTTCATCTTTTCCATTGATGA 57.085 33.333 0.00 0.00 43.02 2.92
4057 6108 6.232581 TCCATTGATGAAACCAAACAAACT 57.767 33.333 0.00 0.00 0.00 2.66
4064 6115 5.238006 TGAAACCAAACAAACTAGGTTCG 57.762 39.130 0.00 0.00 43.17 3.95
4287 6349 6.038161 CAGACAACATCAAGTCTAACAACCAA 59.962 38.462 0.00 0.00 42.87 3.67
4326 6388 8.590719 TTACTGACGACAACATACATAAAACA 57.409 30.769 0.00 0.00 0.00 2.83
4327 6389 7.485418 ACTGACGACAACATACATAAAACAA 57.515 32.000 0.00 0.00 0.00 2.83
4328 6390 7.572759 ACTGACGACAACATACATAAAACAAG 58.427 34.615 0.00 0.00 0.00 3.16
4329 6391 7.225931 ACTGACGACAACATACATAAAACAAGT 59.774 33.333 0.00 0.00 0.00 3.16
4330 6392 7.569297 TGACGACAACATACATAAAACAAGTC 58.431 34.615 0.00 0.00 0.00 3.01
4331 6393 7.439955 TGACGACAACATACATAAAACAAGTCT 59.560 33.333 0.00 0.00 0.00 3.24
4332 6394 8.821147 ACGACAACATACATAAAACAAGTCTA 57.179 30.769 0.00 0.00 0.00 2.59
4333 6395 9.263538 ACGACAACATACATAAAACAAGTCTAA 57.736 29.630 0.00 0.00 0.00 2.10
4334 6396 9.525007 CGACAACATACATAAAACAAGTCTAAC 57.475 33.333 0.00 0.00 0.00 2.34
4339 6401 9.344772 ACATACATAAAACAAGTCTAACAACCA 57.655 29.630 0.00 0.00 0.00 3.67
4343 6405 9.528018 ACATAAAACAAGTCTAACAACCAATTG 57.472 29.630 0.00 0.00 41.98 2.32
4344 6406 9.743057 CATAAAACAAGTCTAACAACCAATTGA 57.257 29.630 7.12 0.00 39.30 2.57
4345 6407 9.965824 ATAAAACAAGTCTAACAACCAATTGAG 57.034 29.630 7.12 0.00 39.30 3.02
4346 6408 6.391227 AACAAGTCTAACAACCAATTGAGG 57.609 37.500 7.12 0.00 39.30 3.86
4347 6409 4.278419 ACAAGTCTAACAACCAATTGAGGC 59.722 41.667 7.12 0.00 39.30 4.70
4348 6410 4.373156 AGTCTAACAACCAATTGAGGCT 57.627 40.909 7.12 0.00 39.30 4.58
4349 6411 4.729868 AGTCTAACAACCAATTGAGGCTT 58.270 39.130 7.12 0.00 39.30 4.35
4350 6412 5.876357 AGTCTAACAACCAATTGAGGCTTA 58.124 37.500 7.12 0.00 39.30 3.09
4351 6413 6.485171 AGTCTAACAACCAATTGAGGCTTAT 58.515 36.000 7.12 0.00 39.30 1.73
4352 6414 6.948309 AGTCTAACAACCAATTGAGGCTTATT 59.052 34.615 7.12 0.00 39.30 1.40
4353 6415 8.107095 AGTCTAACAACCAATTGAGGCTTATTA 58.893 33.333 7.12 0.00 39.30 0.98
4354 6416 8.903820 GTCTAACAACCAATTGAGGCTTATTAT 58.096 33.333 7.12 0.00 39.30 1.28
4355 6417 9.474313 TCTAACAACCAATTGAGGCTTATTATT 57.526 29.630 7.12 0.00 39.30 1.40
4358 6420 8.823220 ACAACCAATTGAGGCTTATTATTACT 57.177 30.769 7.12 0.00 39.30 2.24
4359 6421 8.686334 ACAACCAATTGAGGCTTATTATTACTG 58.314 33.333 7.12 0.00 39.30 2.74
4360 6422 8.902806 CAACCAATTGAGGCTTATTATTACTGA 58.097 33.333 7.12 0.00 38.15 3.41
4361 6423 8.451908 ACCAATTGAGGCTTATTATTACTGAC 57.548 34.615 7.12 0.00 0.00 3.51
4404 6466 1.761449 ACACCACACACATTGCTCAA 58.239 45.000 0.00 0.00 0.00 3.02
4437 6499 1.297968 TGGAGATCAGGGATTGGCAA 58.702 50.000 0.68 0.68 0.00 4.52
4499 6561 1.089920 CAACATGAAGAAGCTCCCCG 58.910 55.000 0.00 0.00 0.00 5.73
4501 6563 1.078214 CATGAAGAAGCTCCCCGCA 60.078 57.895 0.00 0.00 42.61 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.108138 GGCCACGCTCTGTTCTATGT 60.108 55.000 0.00 0.00 0.00 2.29
37 38 4.390556 AGGGAGAGAGGCCACGCT 62.391 66.667 6.06 6.06 0.00 5.07
87 88 1.164313 TCCTCGGTATAGGGGGTCAT 58.836 55.000 0.00 0.00 37.24 3.06
97 98 1.614241 AACGGCAGCTTCCTCGGTAT 61.614 55.000 0.00 0.00 0.00 2.73
182 183 7.587037 TCTTCCATCACTTTCTTTGTTCATT 57.413 32.000 0.00 0.00 0.00 2.57
212 213 0.179108 GGTATGGACAGTGGAGACGC 60.179 60.000 0.00 0.00 42.66 5.19
289 290 2.642254 CCCCTGTTGCGTCGAGGTA 61.642 63.158 7.01 0.00 0.00 3.08
301 302 4.265056 GCCGACAACCACCCCTGT 62.265 66.667 0.00 0.00 0.00 4.00
344 345 3.062466 CCTCGACAGCTCCCGACA 61.062 66.667 3.12 0.00 0.00 4.35
559 560 3.775654 CTCTCTTTCGCCCCGCCT 61.776 66.667 0.00 0.00 0.00 5.52
570 571 2.494073 CAACGCTTCTACCCTCTCTCTT 59.506 50.000 0.00 0.00 0.00 2.85
582 587 1.374758 CTCCGCTTCCAACGCTTCT 60.375 57.895 0.00 0.00 0.00 2.85
615 620 3.680786 CGTGGCCCGTCTGTCTGA 61.681 66.667 0.00 0.00 0.00 3.27
707 717 2.825532 CCGTTCATTTTTGACCCATCCT 59.174 45.455 0.00 0.00 0.00 3.24
717 727 3.150767 TGTCCGGATTCCGTTCATTTTT 58.849 40.909 22.83 0.00 46.80 1.94
724 734 2.081462 GACAAATGTCCGGATTCCGTT 58.919 47.619 22.83 8.48 46.80 4.44
751 761 4.435436 CAGCCTAGCGCACGGTCA 62.435 66.667 11.47 0.00 41.38 4.02
803 814 2.509336 CGACCCTGTCATGTCCGC 60.509 66.667 0.00 0.00 32.09 5.54
906 925 1.415672 TTGGGAAGAAGGCGGAGTGT 61.416 55.000 0.00 0.00 0.00 3.55
955 977 1.747325 ATTTGGTGCGGTTGCTGCTT 61.747 50.000 0.00 0.00 43.34 3.91
971 993 2.092699 GGTTCTAGCTGGCTCTGGATTT 60.093 50.000 0.00 0.00 0.00 2.17
2115 2146 3.636313 CTCGCCGTGCCCGAACTTA 62.636 63.158 0.00 0.00 35.63 2.24
2368 2402 7.270757 TCTTGCTCAATCTCTACATCTACTC 57.729 40.000 0.00 0.00 0.00 2.59
2410 2595 7.442656 CACAACCCTCTTCTTTCTTTCTACTA 58.557 38.462 0.00 0.00 0.00 1.82
2419 2604 0.875059 CCGCACAACCCTCTTCTTTC 59.125 55.000 0.00 0.00 0.00 2.62
2420 2605 0.537371 CCCGCACAACCCTCTTCTTT 60.537 55.000 0.00 0.00 0.00 2.52
2421 2606 1.073199 CCCGCACAACCCTCTTCTT 59.927 57.895 0.00 0.00 0.00 2.52
2422 2607 2.750350 CCCGCACAACCCTCTTCT 59.250 61.111 0.00 0.00 0.00 2.85
2423 2608 3.056328 GCCCGCACAACCCTCTTC 61.056 66.667 0.00 0.00 0.00 2.87
2512 2731 1.563111 CGCATATTGCTTTGCTTGGG 58.437 50.000 0.00 0.00 42.25 4.12
2525 2744 0.035534 TGTTGGTGAGGTGCGCATAT 60.036 50.000 15.91 4.87 0.00 1.78
2526 2745 0.250510 TTGTTGGTGAGGTGCGCATA 60.251 50.000 15.91 0.00 0.00 3.14
2527 2746 1.106351 TTTGTTGGTGAGGTGCGCAT 61.106 50.000 15.91 0.00 0.00 4.73
2528 2747 1.315981 TTTTGTTGGTGAGGTGCGCA 61.316 50.000 5.66 5.66 0.00 6.09
2529 2748 0.031994 ATTTTGTTGGTGAGGTGCGC 59.968 50.000 0.00 0.00 0.00 6.09
2530 2749 2.507339 AATTTTGTTGGTGAGGTGCG 57.493 45.000 0.00 0.00 0.00 5.34
2531 2750 3.309410 CACAAATTTTGTTGGTGAGGTGC 59.691 43.478 12.02 0.00 43.23 5.01
2532 2751 3.870419 CCACAAATTTTGTTGGTGAGGTG 59.130 43.478 12.02 0.00 43.23 4.00
2533 2752 3.517500 ACCACAAATTTTGTTGGTGAGGT 59.482 39.130 23.64 18.28 43.23 3.85
2688 2910 9.069086 TCCTACTAGTAGTAAGTACCCCTTAAA 57.931 37.037 24.84 0.00 37.39 1.52
2701 2923 5.471456 GCGGCATTTACTCCTACTAGTAGTA 59.529 44.000 24.84 13.31 33.62 1.82
2702 2924 4.277921 GCGGCATTTACTCCTACTAGTAGT 59.722 45.833 24.84 14.26 33.62 2.73
2703 2925 4.277672 TGCGGCATTTACTCCTACTAGTAG 59.722 45.833 21.11 21.11 33.62 2.57
2727 2949 2.418976 GTGCTTCAACGAATTCTACCCC 59.581 50.000 3.52 0.00 0.00 4.95
2739 2961 3.408150 GAATCGAATGACGTGCTTCAAC 58.592 45.455 0.00 0.00 43.13 3.18
2740 2962 2.092055 CGAATCGAATGACGTGCTTCAA 59.908 45.455 0.00 0.00 43.13 2.69
2826 3060 4.124238 CGCCTCCGTTGGATTCTTTATTA 58.876 43.478 0.00 0.00 0.00 0.98
2827 3061 2.943033 CGCCTCCGTTGGATTCTTTATT 59.057 45.455 0.00 0.00 0.00 1.40
2828 3062 2.561569 CGCCTCCGTTGGATTCTTTAT 58.438 47.619 0.00 0.00 0.00 1.40
2829 3063 2.010043 GCGCCTCCGTTGGATTCTTTA 61.010 52.381 0.00 0.00 36.67 1.85
2830 3064 1.305930 GCGCCTCCGTTGGATTCTTT 61.306 55.000 0.00 0.00 36.67 2.52
2831 3065 1.745489 GCGCCTCCGTTGGATTCTT 60.745 57.895 0.00 0.00 36.67 2.52
2884 3118 3.532155 ATCGCTCGCTGTCTCCCC 61.532 66.667 0.00 0.00 0.00 4.81
2976 3211 1.849823 CCTCCCTGGATCCATCCCC 60.850 68.421 16.63 0.00 46.59 4.81
3006 3247 2.530177 CACGGACAGCTGTATGTAGTG 58.470 52.381 21.73 19.56 36.36 2.74
3042 3285 2.863137 CAATCAAAGCGGAGAGTCTAGC 59.137 50.000 11.05 11.05 0.00 3.42
3045 3288 1.277557 AGCAATCAAAGCGGAGAGTCT 59.722 47.619 0.00 0.00 37.01 3.24
3047 3290 1.808945 CAAGCAATCAAAGCGGAGAGT 59.191 47.619 0.00 0.00 37.01 3.24
3053 3296 2.219216 CACCAAACAAGCAATCAAAGCG 59.781 45.455 0.00 0.00 37.01 4.68
3060 3303 2.102757 TGTCATGCACCAAACAAGCAAT 59.897 40.909 0.00 0.00 42.15 3.56
3070 3313 0.250252 ACATGTCGTGTCATGCACCA 60.250 50.000 12.62 7.73 46.15 4.17
3098 3341 2.268298 GGCGCATTACTCTTCTTCGAA 58.732 47.619 10.83 0.00 0.00 3.71
3103 3346 2.472695 TGTTGGCGCATTACTCTTCT 57.527 45.000 10.83 0.00 0.00 2.85
3157 4702 0.765510 ACAAGGAGAGGACACCAACC 59.234 55.000 0.00 0.00 0.00 3.77
3237 5271 2.978010 CTCGGTGTTGGGTGGTGC 60.978 66.667 0.00 0.00 0.00 5.01
3276 5310 7.094205 ACTGCCCAAAAGAAAGTTATGTCTATG 60.094 37.037 0.00 0.00 0.00 2.23
3277 5311 6.948309 ACTGCCCAAAAGAAAGTTATGTCTAT 59.052 34.615 0.00 0.00 0.00 1.98
3279 5313 5.010012 CACTGCCCAAAAGAAAGTTATGTCT 59.990 40.000 0.00 0.00 0.00 3.41
3280 5314 5.009610 TCACTGCCCAAAAGAAAGTTATGTC 59.990 40.000 0.00 0.00 0.00 3.06
3282 5316 5.452078 TCACTGCCCAAAAGAAAGTTATG 57.548 39.130 0.00 0.00 0.00 1.90
3283 5317 5.362430 TGTTCACTGCCCAAAAGAAAGTTAT 59.638 36.000 0.00 0.00 0.00 1.89
3284 5318 4.707448 TGTTCACTGCCCAAAAGAAAGTTA 59.293 37.500 0.00 0.00 0.00 2.24
3285 5319 3.513515 TGTTCACTGCCCAAAAGAAAGTT 59.486 39.130 0.00 0.00 0.00 2.66
3286 5320 3.096092 TGTTCACTGCCCAAAAGAAAGT 58.904 40.909 0.00 0.00 0.00 2.66
3287 5321 3.799281 TGTTCACTGCCCAAAAGAAAG 57.201 42.857 0.00 0.00 0.00 2.62
3288 5322 5.009610 GTCTATGTTCACTGCCCAAAAGAAA 59.990 40.000 0.00 0.00 0.00 2.52
3289 5323 4.518970 GTCTATGTTCACTGCCCAAAAGAA 59.481 41.667 0.00 0.00 0.00 2.52
3290 5324 4.072131 GTCTATGTTCACTGCCCAAAAGA 58.928 43.478 0.00 0.00 0.00 2.52
3291 5325 3.820467 TGTCTATGTTCACTGCCCAAAAG 59.180 43.478 0.00 0.00 0.00 2.27
3292 5326 3.826524 TGTCTATGTTCACTGCCCAAAA 58.173 40.909 0.00 0.00 0.00 2.44
3293 5327 3.500448 TGTCTATGTTCACTGCCCAAA 57.500 42.857 0.00 0.00 0.00 3.28
3294 5328 3.719268 ATGTCTATGTTCACTGCCCAA 57.281 42.857 0.00 0.00 0.00 4.12
3295 5329 4.225042 AGTTATGTCTATGTTCACTGCCCA 59.775 41.667 0.00 0.00 0.00 5.36
3296 5330 4.770795 AGTTATGTCTATGTTCACTGCCC 58.229 43.478 0.00 0.00 0.00 5.36
3297 5331 6.546395 CAAAGTTATGTCTATGTTCACTGCC 58.454 40.000 0.00 0.00 0.00 4.85
3298 5332 6.024049 GCAAAGTTATGTCTATGTTCACTGC 58.976 40.000 0.00 0.00 0.00 4.40
3299 5333 7.132694 TGCAAAGTTATGTCTATGTTCACTG 57.867 36.000 0.00 0.00 0.00 3.66
3300 5334 7.445402 AGTTGCAAAGTTATGTCTATGTTCACT 59.555 33.333 0.00 0.00 0.00 3.41
3301 5335 7.584987 AGTTGCAAAGTTATGTCTATGTTCAC 58.415 34.615 0.00 0.00 0.00 3.18
3302 5336 7.443879 TGAGTTGCAAAGTTATGTCTATGTTCA 59.556 33.333 0.00 0.00 0.00 3.18
3303 5337 7.806690 TGAGTTGCAAAGTTATGTCTATGTTC 58.193 34.615 0.00 0.00 0.00 3.18
3309 5343 9.846248 GATTAAATGAGTTGCAAAGTTATGTCT 57.154 29.630 0.00 0.00 0.00 3.41
3354 5390 1.069227 GTGCCACCGACAATTGAGTTC 60.069 52.381 13.59 0.00 0.00 3.01
3403 5442 6.857848 AGATGGTAAGATGAGAGAGTCCATA 58.142 40.000 0.00 0.00 35.06 2.74
3513 5553 1.693062 CCATGATCTACTGGCAGCTCT 59.307 52.381 15.89 0.00 0.00 4.09
3707 5749 6.127591 CCGTATAAACAAATTTCCATCCACCA 60.128 38.462 0.00 0.00 0.00 4.17
3855 5898 1.202639 ACAAACTGATGAGTGGTCGCA 60.203 47.619 0.00 0.00 30.61 5.10
3897 5940 4.318332 TGATTTGACAGTGTAGAAGGCAG 58.682 43.478 0.00 0.00 0.00 4.85
3908 5951 6.655078 AAAATAAGTGGCTGATTTGACAGT 57.345 33.333 0.00 0.00 39.73 3.55
3937 5983 7.478520 ACAATTTGTTATATACTGTCTCCGC 57.521 36.000 0.00 0.00 0.00 5.54
3970 6021 5.013079 GGGGGAACTCCTTTCATTCAAAAAT 59.987 40.000 0.00 0.00 35.70 1.82
3986 6037 2.073776 AGATGAAACCAAGGGGGAACT 58.926 47.619 0.00 0.00 41.15 3.01
4018 6069 8.036575 TCATCAATGGAAAAGATGAAACCATTC 58.963 33.333 0.00 0.00 45.60 2.67
4020 6071 7.484993 TCATCAATGGAAAAGATGAAACCAT 57.515 32.000 0.00 0.00 43.56 3.55
4021 6072 6.914654 TCATCAATGGAAAAGATGAAACCA 57.085 33.333 0.00 0.00 43.56 3.67
4026 6077 6.914654 TGGTTTCATCAATGGAAAAGATGA 57.085 33.333 0.00 0.00 44.50 2.92
4027 6078 7.441760 TGTTTGGTTTCATCAATGGAAAAGATG 59.558 33.333 0.00 0.00 40.29 2.90
4028 6079 7.507829 TGTTTGGTTTCATCAATGGAAAAGAT 58.492 30.769 0.00 0.00 36.14 2.40
4029 6080 6.882656 TGTTTGGTTTCATCAATGGAAAAGA 58.117 32.000 0.00 0.00 36.14 2.52
4030 6081 7.551035 TTGTTTGGTTTCATCAATGGAAAAG 57.449 32.000 0.00 0.00 36.14 2.27
4031 6082 7.609532 AGTTTGTTTGGTTTCATCAATGGAAAA 59.390 29.630 0.00 0.00 36.14 2.29
4032 6083 7.108847 AGTTTGTTTGGTTTCATCAATGGAAA 58.891 30.769 0.00 0.00 32.18 3.13
4033 6084 6.648192 AGTTTGTTTGGTTTCATCAATGGAA 58.352 32.000 0.00 0.00 0.00 3.53
4034 6085 6.232581 AGTTTGTTTGGTTTCATCAATGGA 57.767 33.333 0.00 0.00 0.00 3.41
4035 6086 6.646240 CCTAGTTTGTTTGGTTTCATCAATGG 59.354 38.462 0.00 0.00 0.00 3.16
4057 6108 1.209621 AGCCTTAATGCCCGAACCTA 58.790 50.000 0.00 0.00 0.00 3.08
4064 6115 4.023980 AGAGGTTTTTAGCCTTAATGCCC 58.976 43.478 0.00 0.00 36.29 5.36
4268 6330 6.207417 CCTCAATTGGTTGTTAGACTTGATGT 59.793 38.462 5.42 0.00 36.69 3.06
4287 6349 7.497595 TGTCGTCAGTAATAATAAGCCTCAAT 58.502 34.615 0.00 0.00 0.00 2.57
4321 6383 7.264947 CCTCAATTGGTTGTTAGACTTGTTTT 58.735 34.615 5.42 0.00 36.69 2.43
4322 6384 6.682861 GCCTCAATTGGTTGTTAGACTTGTTT 60.683 38.462 5.42 0.00 36.69 2.83
4323 6385 5.221244 GCCTCAATTGGTTGTTAGACTTGTT 60.221 40.000 5.42 0.00 36.69 2.83
4324 6386 4.278419 GCCTCAATTGGTTGTTAGACTTGT 59.722 41.667 5.42 0.00 36.69 3.16
4325 6387 4.520492 AGCCTCAATTGGTTGTTAGACTTG 59.480 41.667 5.42 0.00 36.69 3.16
4326 6388 4.729868 AGCCTCAATTGGTTGTTAGACTT 58.270 39.130 5.42 0.00 36.69 3.01
4327 6389 4.373156 AGCCTCAATTGGTTGTTAGACT 57.627 40.909 5.42 0.00 36.69 3.24
4328 6390 6.759497 ATAAGCCTCAATTGGTTGTTAGAC 57.241 37.500 5.42 0.00 36.69 2.59
4329 6391 9.474313 AATAATAAGCCTCAATTGGTTGTTAGA 57.526 29.630 5.42 0.00 36.69 2.10
4332 6394 9.255029 AGTAATAATAAGCCTCAATTGGTTGTT 57.745 29.630 5.42 0.00 36.69 2.83
4333 6395 8.686334 CAGTAATAATAAGCCTCAATTGGTTGT 58.314 33.333 5.42 0.00 36.69 3.32
4334 6396 8.902806 TCAGTAATAATAAGCCTCAATTGGTTG 58.097 33.333 5.42 0.00 36.65 3.77
4335 6397 8.903820 GTCAGTAATAATAAGCCTCAATTGGTT 58.096 33.333 5.42 0.00 0.00 3.67
4336 6398 7.226720 CGTCAGTAATAATAAGCCTCAATTGGT 59.773 37.037 5.42 0.00 0.00 3.67
4337 6399 7.441157 TCGTCAGTAATAATAAGCCTCAATTGG 59.559 37.037 5.42 0.00 0.00 3.16
4338 6400 8.276325 GTCGTCAGTAATAATAAGCCTCAATTG 58.724 37.037 0.00 0.00 0.00 2.32
4339 6401 7.985184 TGTCGTCAGTAATAATAAGCCTCAATT 59.015 33.333 0.00 0.00 0.00 2.32
4340 6402 7.497595 TGTCGTCAGTAATAATAAGCCTCAAT 58.502 34.615 0.00 0.00 0.00 2.57
4341 6403 6.869695 TGTCGTCAGTAATAATAAGCCTCAA 58.130 36.000 0.00 0.00 0.00 3.02
4342 6404 6.459670 TGTCGTCAGTAATAATAAGCCTCA 57.540 37.500 0.00 0.00 0.00 3.86
4343 6405 6.755141 TGTTGTCGTCAGTAATAATAAGCCTC 59.245 38.462 0.00 0.00 0.00 4.70
4344 6406 6.636705 TGTTGTCGTCAGTAATAATAAGCCT 58.363 36.000 0.00 0.00 0.00 4.58
4345 6407 6.897259 TGTTGTCGTCAGTAATAATAAGCC 57.103 37.500 0.00 0.00 0.00 4.35
4346 6408 9.027129 TGTATGTTGTCGTCAGTAATAATAAGC 57.973 33.333 0.00 0.00 0.00 3.09
4353 6415 8.662141 GGTTTTATGTATGTTGTCGTCAGTAAT 58.338 33.333 0.00 0.00 0.00 1.89
4354 6416 7.148771 CGGTTTTATGTATGTTGTCGTCAGTAA 60.149 37.037 0.00 0.00 0.00 2.24
4355 6417 6.308524 CGGTTTTATGTATGTTGTCGTCAGTA 59.691 38.462 0.00 0.00 0.00 2.74
4356 6418 5.119588 CGGTTTTATGTATGTTGTCGTCAGT 59.880 40.000 0.00 0.00 0.00 3.41
4357 6419 5.346551 TCGGTTTTATGTATGTTGTCGTCAG 59.653 40.000 0.00 0.00 0.00 3.51
4358 6420 5.118971 GTCGGTTTTATGTATGTTGTCGTCA 59.881 40.000 0.00 0.00 0.00 4.35
4359 6421 5.118971 TGTCGGTTTTATGTATGTTGTCGTC 59.881 40.000 0.00 0.00 0.00 4.20
4360 6422 4.989797 TGTCGGTTTTATGTATGTTGTCGT 59.010 37.500 0.00 0.00 0.00 4.34
4361 6423 5.518529 TGTCGGTTTTATGTATGTTGTCG 57.481 39.130 0.00 0.00 0.00 4.35
4404 6466 5.533154 CCTGATCTCCAACTTCTACGTAGAT 59.467 44.000 25.17 9.48 31.40 1.98
4437 6499 0.859232 GTGCGACAGACAATGAACGT 59.141 50.000 0.00 0.00 35.77 3.99
4501 6563 4.779733 ATGAGGAGGACCGCCGGT 62.780 66.667 9.43 9.43 41.83 5.28


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

AutoCloner maintained by Alex Coulton.