Multiple sequence alignment - TraesCS3A01G517400

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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 TraesCS3A01G517400 chr3A 100.000 3103 0 0 354 3456 734444307 734441205 0.000000e+00 5731.0
1 TraesCS3A01G517400 chr3A 95.645 620 26 1 2837 3455 91017006 91016387 0.000000e+00 994.0
2 TraesCS3A01G517400 chr3A 100.000 108 0 0 1 108 734444660 734444553 2.100000e-47 200.0
3 TraesCS3A01G517400 chr3A 84.848 132 17 3 1086 1217 42641034 42641162 2.800000e-26 130.0
4 TraesCS3A01G517400 chr3D 90.206 2379 137 51 393 2713 604566585 604564245 0.000000e+00 3014.0
5 TraesCS3A01G517400 chr3D 100.000 45 0 0 64 108 604567016 604566972 2.210000e-12 84.2
6 TraesCS3A01G517400 chr3B 90.552 1810 85 36 396 2153 811546108 811544333 0.000000e+00 2316.0
7 TraesCS3A01G517400 chr3B 89.805 667 39 12 2146 2785 811544307 811543643 0.000000e+00 828.0
8 TraesCS3A01G517400 chr3B 92.857 42 3 0 354 395 811546165 811546124 1.040000e-05 62.1
9 TraesCS3A01G517400 chr1A 95.968 620 24 1 2837 3455 464809055 464808436 0.000000e+00 1005.0
10 TraesCS3A01G517400 chr1A 95.645 620 26 1 2837 3455 292063125 292062506 0.000000e+00 994.0
11 TraesCS3A01G517400 chr7A 95.806 620 25 1 2837 3455 319591991 319591372 0.000000e+00 1000.0
12 TraesCS3A01G517400 chr4A 95.806 620 25 1 2837 3455 438239444 438240063 0.000000e+00 1000.0
13 TraesCS3A01G517400 chr6A 95.645 620 26 1 2837 3455 410901516 410902135 0.000000e+00 994.0
14 TraesCS3A01G517400 chr4D 95.645 620 26 1 2837 3455 242938962 242938343 0.000000e+00 994.0
15 TraesCS3A01G517400 chr2A 95.645 620 26 1 2837 3455 578390486 578391105 0.000000e+00 994.0
16 TraesCS3A01G517400 chr2A 85.401 137 16 4 1086 1222 29885555 29885423 4.650000e-29 139.0
17 TraesCS3A01G517400 chr7D 95.095 632 28 3 2826 3455 465340573 465339943 0.000000e+00 992.0
18 TraesCS3A01G517400 chr2B 85.401 137 16 4 1086 1222 43676742 43676610 4.650000e-29 139.0
19 TraesCS3A01G517400 chr2D 85.606 132 16 3 1086 1217 27780247 27780119 6.020000e-28 135.0
20 TraesCS3A01G517400 chr5B 84.559 136 18 3 1087 1222 136631204 136631072 7.780000e-27 132.0
21 TraesCS3A01G517400 chr5A 84.559 136 18 3 1087 1222 137282407 137282275 7.780000e-27 132.0
22 TraesCS3A01G517400 chr5D 83.824 136 19 3 1087 1222 123888203 123888071 3.620000e-25 126.0


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 TraesCS3A01G517400 chr3A 734441205 734444660 3455 True 2965.5 5731 100.000000 1 3456 2 chr3A.!!$R2 3455
1 TraesCS3A01G517400 chr3A 91016387 91017006 619 True 994.0 994 95.645000 2837 3455 1 chr3A.!!$R1 618
2 TraesCS3A01G517400 chr3D 604564245 604567016 2771 True 1549.1 3014 95.103000 64 2713 2 chr3D.!!$R1 2649
3 TraesCS3A01G517400 chr3B 811543643 811546165 2522 True 1068.7 2316 91.071333 354 2785 3 chr3B.!!$R1 2431
4 TraesCS3A01G517400 chr1A 464808436 464809055 619 True 1005.0 1005 95.968000 2837 3455 1 chr1A.!!$R2 618
5 TraesCS3A01G517400 chr1A 292062506 292063125 619 True 994.0 994 95.645000 2837 3455 1 chr1A.!!$R1 618
6 TraesCS3A01G517400 chr7A 319591372 319591991 619 True 1000.0 1000 95.806000 2837 3455 1 chr7A.!!$R1 618
7 TraesCS3A01G517400 chr4A 438239444 438240063 619 False 1000.0 1000 95.806000 2837 3455 1 chr4A.!!$F1 618
8 TraesCS3A01G517400 chr6A 410901516 410902135 619 False 994.0 994 95.645000 2837 3455 1 chr6A.!!$F1 618
9 TraesCS3A01G517400 chr4D 242938343 242938962 619 True 994.0 994 95.645000 2837 3455 1 chr4D.!!$R1 618
10 TraesCS3A01G517400 chr2A 578390486 578391105 619 False 994.0 994 95.645000 2837 3455 1 chr2A.!!$F1 618
11 TraesCS3A01G517400 chr7D 465339943 465340573 630 True 992.0 992 95.095000 2826 3455 1 chr7D.!!$R1 629

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
530 635 1.135315 TGGAAGACGTACCATGTACGC 60.135 52.381 22.47 16.13 43.97 4.42 F
533 638 1.171308 AGACGTACCATGTACGCACT 58.829 50.000 22.47 18.74 43.97 4.40 F
1260 1397 1.219664 CTCGCCGTCCCATTGGTTA 59.780 57.895 1.20 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 1799 1.009829 GCAGCTTACCGATCAACCTG 58.990 55.000 0.0 0.0 0.00 4.00 R
1882 2040 1.271102 TGGGCGTTCAAATGTAAAGGC 59.729 47.619 0.0 0.0 35.97 4.35 R
3076 3299 0.907486 AGAAGCTCCAGTGCATAGCA 59.093 50.000 13.5 0.0 38.75 3.49 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
24 25 6.983906 ATCCTCCTTTGTGAGTTTTCATTT 57.016 33.333 0.00 0.00 35.39 2.32
26 27 8.655935 ATCCTCCTTTGTGAGTTTTCATTTAT 57.344 30.769 0.00 0.00 35.39 1.40
27 28 8.110860 TCCTCCTTTGTGAGTTTTCATTTATC 57.889 34.615 0.00 0.00 35.39 1.75
28 29 7.944554 TCCTCCTTTGTGAGTTTTCATTTATCT 59.055 33.333 0.00 0.00 35.39 1.98
29 30 8.579863 CCTCCTTTGTGAGTTTTCATTTATCTT 58.420 33.333 0.00 0.00 35.39 2.40
30 31 9.403110 CTCCTTTGTGAGTTTTCATTTATCTTG 57.597 33.333 0.00 0.00 35.39 3.02
31 32 9.130661 TCCTTTGTGAGTTTTCATTTATCTTGA 57.869 29.630 0.00 0.00 35.39 3.02
32 33 9.185192 CCTTTGTGAGTTTTCATTTATCTTGAC 57.815 33.333 0.00 0.00 35.39 3.18
33 34 9.734620 CTTTGTGAGTTTTCATTTATCTTGACA 57.265 29.630 0.00 0.00 35.39 3.58
35 36 9.734620 TTGTGAGTTTTCATTTATCTTGACAAG 57.265 29.630 9.03 9.03 35.39 3.16
36 37 7.862372 TGTGAGTTTTCATTTATCTTGACAAGC 59.138 33.333 10.50 0.00 35.39 4.01
37 38 7.862372 GTGAGTTTTCATTTATCTTGACAAGCA 59.138 33.333 10.50 0.37 35.39 3.91
38 39 8.579006 TGAGTTTTCATTTATCTTGACAAGCAT 58.421 29.630 10.50 7.65 0.00 3.79
39 40 8.976986 AGTTTTCATTTATCTTGACAAGCATC 57.023 30.769 10.50 0.00 0.00 3.91
40 41 8.579006 AGTTTTCATTTATCTTGACAAGCATCA 58.421 29.630 10.50 0.00 0.00 3.07
41 42 9.362539 GTTTTCATTTATCTTGACAAGCATCAT 57.637 29.630 10.50 1.62 0.00 2.45
42 43 9.577110 TTTTCATTTATCTTGACAAGCATCATC 57.423 29.630 10.50 0.00 0.00 2.92
43 44 7.868906 TCATTTATCTTGACAAGCATCATCA 57.131 32.000 10.50 0.00 0.00 3.07
44 45 8.459911 TCATTTATCTTGACAAGCATCATCAT 57.540 30.769 10.50 0.00 0.00 2.45
45 46 8.909923 TCATTTATCTTGACAAGCATCATCATT 58.090 29.630 10.50 0.00 0.00 2.57
46 47 8.968242 CATTTATCTTGACAAGCATCATCATTG 58.032 33.333 10.50 0.00 0.00 2.82
47 48 7.868906 TTATCTTGACAAGCATCATCATTGA 57.131 32.000 10.50 0.00 36.00 2.57
48 49 5.813080 TCTTGACAAGCATCATCATTGAG 57.187 39.130 10.50 0.00 34.73 3.02
49 50 5.250982 TCTTGACAAGCATCATCATTGAGT 58.749 37.500 10.50 0.00 34.73 3.41
50 51 6.408869 TCTTGACAAGCATCATCATTGAGTA 58.591 36.000 10.50 0.00 34.73 2.59
51 52 7.052248 TCTTGACAAGCATCATCATTGAGTAT 58.948 34.615 10.50 0.00 34.73 2.12
52 53 6.613755 TGACAAGCATCATCATTGAGTATG 57.386 37.500 6.64 6.64 34.73 2.39
53 54 6.117488 TGACAAGCATCATCATTGAGTATGT 58.883 36.000 10.86 0.00 34.73 2.29
54 55 7.274447 TGACAAGCATCATCATTGAGTATGTA 58.726 34.615 10.86 0.00 34.73 2.29
55 56 7.935210 TGACAAGCATCATCATTGAGTATGTAT 59.065 33.333 10.86 1.43 34.73 2.29
56 57 8.687292 ACAAGCATCATCATTGAGTATGTATT 57.313 30.769 10.86 5.80 34.73 1.89
57 58 9.783081 ACAAGCATCATCATTGAGTATGTATTA 57.217 29.630 10.86 0.00 34.73 0.98
490 595 7.305474 ACTCTAATTGTTGGTAAAATCAAGCG 58.695 34.615 0.00 0.00 0.00 4.68
491 596 6.090129 TCTAATTGTTGGTAAAATCAAGCGC 58.910 36.000 0.00 0.00 0.00 5.92
495 600 3.058293 TGTTGGTAAAATCAAGCGCTGAG 60.058 43.478 12.58 7.34 37.52 3.35
522 627 4.333372 TGTTGAAAAAGTGGAAGACGTACC 59.667 41.667 0.00 0.00 0.00 3.34
530 635 1.135315 TGGAAGACGTACCATGTACGC 60.135 52.381 22.47 16.13 43.97 4.42
533 638 1.171308 AGACGTACCATGTACGCACT 58.829 50.000 22.47 18.74 43.97 4.40
534 639 2.358957 AGACGTACCATGTACGCACTA 58.641 47.619 22.47 0.00 43.97 2.74
547 652 7.308408 CCATGTACGCACTACATACATAGTACT 60.308 40.741 0.00 0.00 43.21 2.73
548 653 7.182361 TGTACGCACTACATACATAGTACTC 57.818 40.000 0.00 0.00 33.50 2.59
550 655 4.518211 ACGCACTACATACATAGTACTCCC 59.482 45.833 0.00 0.00 33.50 4.30
551 656 4.082895 CGCACTACATACATAGTACTCCCC 60.083 50.000 0.00 0.00 33.50 4.81
552 657 5.078256 GCACTACATACATAGTACTCCCCT 58.922 45.833 0.00 0.00 33.50 4.79
564 669 7.569111 ACATAGTACTCCCCTTATGTGAAGATT 59.431 37.037 0.00 0.00 0.00 2.40
580 693 1.586154 GATTGCACACCCCTTGTCGG 61.586 60.000 0.00 0.00 35.67 4.79
651 764 5.951148 TGGAATATGACTGGCTTTTCATGAA 59.049 36.000 3.38 3.38 34.28 2.57
763 877 2.107343 CCACGTCGTCCCACAACA 59.893 61.111 0.00 0.00 0.00 3.33
794 908 4.263572 CCTCGCACCCAACCACCA 62.264 66.667 0.00 0.00 0.00 4.17
808 922 2.989824 ACCACCTCCACGTCCTCG 60.990 66.667 0.00 0.00 43.34 4.63
848 965 1.995626 CCATCGGGTCTCCCACCTT 60.996 63.158 5.64 0.00 45.83 3.50
855 972 1.229529 GTCTCCCACCTTCCCTCCA 60.230 63.158 0.00 0.00 0.00 3.86
997 1128 2.335369 GGACGGATCGGACCATCG 59.665 66.667 15.11 0.78 0.00 3.84
1045 1179 3.844090 GTGGCGAGGAGGAGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
1239 1373 1.729470 CTACGCACGCATCCTCCTCT 61.729 60.000 0.00 0.00 0.00 3.69
1241 1375 2.895680 GCACGCATCCTCCTCTCA 59.104 61.111 0.00 0.00 0.00 3.27
1251 1388 2.750637 TCCTCTCACTCGCCGTCC 60.751 66.667 0.00 0.00 0.00 4.79
1252 1389 3.827898 CCTCTCACTCGCCGTCCC 61.828 72.222 0.00 0.00 0.00 4.46
1253 1390 3.062466 CTCTCACTCGCCGTCCCA 61.062 66.667 0.00 0.00 0.00 4.37
1254 1391 2.362503 TCTCACTCGCCGTCCCAT 60.363 61.111 0.00 0.00 0.00 4.00
1255 1392 1.949847 CTCTCACTCGCCGTCCCATT 61.950 60.000 0.00 0.00 0.00 3.16
1256 1393 1.811266 CTCACTCGCCGTCCCATTG 60.811 63.158 0.00 0.00 0.00 2.82
1257 1394 2.819595 CACTCGCCGTCCCATTGG 60.820 66.667 0.00 0.00 0.00 3.16
1258 1395 3.319198 ACTCGCCGTCCCATTGGT 61.319 61.111 1.20 0.00 0.00 3.67
1260 1397 1.219664 CTCGCCGTCCCATTGGTTA 59.780 57.895 1.20 0.00 0.00 2.85
1266 1404 2.093341 GCCGTCCCATTGGTTACTCTTA 60.093 50.000 1.20 0.00 0.00 2.10
1302 1444 1.531578 TCATCGATGATCGTCTCCGTC 59.468 52.381 23.99 0.00 41.35 4.79
1820 1976 6.879276 ATTAGTAATGCAGAGTACGAGCTA 57.121 37.500 0.00 0.00 0.00 3.32
1837 1995 7.856145 ACGAGCTAAATTTTGATCATCTTCT 57.144 32.000 16.09 0.00 0.00 2.85
1850 2008 8.954950 TTGATCATCTTCTTTTGAGGATCTAC 57.045 34.615 15.83 0.00 45.97 2.59
1875 2033 9.653287 ACTTTTGATCATTCTACTTTACGATCA 57.347 29.630 0.00 0.00 37.93 2.92
1926 2085 8.423349 CCAAGCAATATTCTTATTTCCCAATGA 58.577 33.333 0.00 0.00 0.00 2.57
1927 2086 9.991906 CAAGCAATATTCTTATTTCCCAATGAT 57.008 29.630 0.00 0.00 0.00 2.45
2018 2178 4.014569 TCAAATGTGAGTCAATCGGGAA 57.985 40.909 0.00 0.00 0.00 3.97
2019 2179 3.751175 TCAAATGTGAGTCAATCGGGAAC 59.249 43.478 0.00 0.00 0.00 3.62
2095 2257 4.245660 TCTACTGGAAAACAAGCATCTCG 58.754 43.478 0.00 0.00 0.00 4.04
2143 2305 3.607422 TGAACATTGCAGACGTTTCAG 57.393 42.857 0.00 0.00 0.00 3.02
2185 2380 3.988379 TTTGTCAAGTTCAGACATGCC 57.012 42.857 0.00 0.00 44.66 4.40
2187 2382 2.497138 TGTCAAGTTCAGACATGCCTG 58.503 47.619 2.03 2.03 40.80 4.85
2195 2390 1.205655 TCAGACATGCCTGCTGTACTC 59.794 52.381 3.81 0.00 34.28 2.59
2200 2395 1.741706 CATGCCTGCTGTACTCCAAAG 59.258 52.381 0.00 0.00 0.00 2.77
2230 2425 5.521372 GTCAAAAATTTCATAGGCTGGATGC 59.479 40.000 0.00 0.00 41.94 3.91
2251 2446 4.756135 TGCTTGGATTTTCAGCCAAATTTC 59.244 37.500 0.00 0.00 43.09 2.17
2253 2448 5.413523 GCTTGGATTTTCAGCCAAATTTCAT 59.586 36.000 0.00 0.00 43.09 2.57
2254 2449 6.594937 GCTTGGATTTTCAGCCAAATTTCATA 59.405 34.615 0.00 0.00 43.09 2.15
2256 2451 7.243604 TGGATTTTCAGCCAAATTTCATAGT 57.756 32.000 0.00 0.00 0.00 2.12
2257 2452 7.678837 TGGATTTTCAGCCAAATTTCATAGTT 58.321 30.769 0.00 0.00 0.00 2.24
2258 2453 7.818930 TGGATTTTCAGCCAAATTTCATAGTTC 59.181 33.333 0.00 0.00 0.00 3.01
2259 2454 8.037166 GGATTTTCAGCCAAATTTCATAGTTCT 58.963 33.333 0.00 0.00 0.00 3.01
2260 2455 8.767478 ATTTTCAGCCAAATTTCATAGTTCTG 57.233 30.769 0.00 0.00 0.00 3.02
2262 2457 6.500684 TCAGCCAAATTTCATAGTTCTGAC 57.499 37.500 0.00 0.00 0.00 3.51
2294 2502 1.613925 TGGAGTTTCCTCTGACTGACG 59.386 52.381 0.00 0.00 37.46 4.35
2315 2524 7.030768 TGACGTGATCGATGTAACTTATTTGA 58.969 34.615 0.54 0.00 40.62 2.69
2466 2675 9.237846 GAAGCAACCTAAATAGTTAATTGATGC 57.762 33.333 9.58 6.08 0.00 3.91
2504 2717 3.246936 GGTTAATTCGATTAGTCCCGTGC 59.753 47.826 0.00 0.00 0.00 5.34
2545 2758 1.207329 GGGTGTCCATCGACTAAGCTT 59.793 52.381 3.48 3.48 39.94 3.74
2559 2773 5.975939 CGACTAAGCTTACTTGTATGTACCC 59.024 44.000 0.86 0.00 36.57 3.69
2637 2855 7.809238 TCATGTCTGATTTCTCCTTTGGATAT 58.191 34.615 0.00 0.00 0.00 1.63
2661 2879 8.907222 ATTTGTGCTCTTTGAATGGTTAATTT 57.093 26.923 0.00 0.00 0.00 1.82
2664 2882 6.183360 TGTGCTCTTTGAATGGTTAATTTGGT 60.183 34.615 0.00 0.00 0.00 3.67
2673 2891 8.804688 TGAATGGTTAATTTGGTTTTACTTCG 57.195 30.769 0.00 0.00 0.00 3.79
2746 2968 2.546795 CGATTTCGCTAGGGCTGAGATT 60.547 50.000 1.02 0.00 36.09 2.40
2751 2973 0.599728 GCTAGGGCTGAGATTGAGCG 60.600 60.000 0.00 0.00 37.32 5.03
2769 2991 1.082117 CGATGTCGCCCACTAACCAC 61.082 60.000 0.00 0.00 0.00 4.16
2770 2992 1.079405 ATGTCGCCCACTAACCACG 60.079 57.895 0.00 0.00 0.00 4.94
2771 2993 1.537814 ATGTCGCCCACTAACCACGA 61.538 55.000 0.00 0.00 0.00 4.35
2776 2998 1.135527 CGCCCACTAACCACGATAAGA 59.864 52.381 0.00 0.00 0.00 2.10
2785 3007 6.538742 CACTAACCACGATAAGATTGTTCCAT 59.461 38.462 0.00 0.00 0.00 3.41
2786 3008 5.818136 AACCACGATAAGATTGTTCCATG 57.182 39.130 0.00 0.00 0.00 3.66
2787 3009 4.199310 ACCACGATAAGATTGTTCCATGG 58.801 43.478 4.97 4.97 0.00 3.66
2788 3010 3.003689 CCACGATAAGATTGTTCCATGGC 59.996 47.826 6.96 0.00 0.00 4.40
2789 3011 3.003689 CACGATAAGATTGTTCCATGGCC 59.996 47.826 6.96 0.00 0.00 5.36
2790 3012 2.554032 CGATAAGATTGTTCCATGGCCC 59.446 50.000 6.96 0.00 0.00 5.80
2791 3013 3.748668 CGATAAGATTGTTCCATGGCCCT 60.749 47.826 6.96 0.00 0.00 5.19
2792 3014 2.149973 AAGATTGTTCCATGGCCCTC 57.850 50.000 6.96 0.00 0.00 4.30
2793 3015 0.107017 AGATTGTTCCATGGCCCTCG 60.107 55.000 6.96 0.00 0.00 4.63
2794 3016 1.076777 ATTGTTCCATGGCCCTCGG 60.077 57.895 6.96 0.00 0.00 4.63
2825 3047 6.983906 AAAAAGGATGTTCCACAGAAAGAT 57.016 33.333 0.00 0.00 39.61 2.40
2827 3049 8.655935 AAAAAGGATGTTCCACAGAAAGATAT 57.344 30.769 0.00 0.00 39.61 1.63
2828 3050 7.636150 AAAGGATGTTCCACAGAAAGATATG 57.364 36.000 0.00 0.00 39.61 1.78
2829 3051 5.128919 AGGATGTTCCACAGAAAGATATGC 58.871 41.667 0.00 0.00 39.61 3.14
2830 3052 4.276926 GGATGTTCCACAGAAAGATATGCC 59.723 45.833 0.00 0.00 36.28 4.40
2831 3053 4.299586 TGTTCCACAGAAAGATATGCCA 57.700 40.909 0.00 0.00 32.58 4.92
2832 3054 4.858850 TGTTCCACAGAAAGATATGCCAT 58.141 39.130 0.00 0.00 32.58 4.40
2833 3055 5.263599 TGTTCCACAGAAAGATATGCCATT 58.736 37.500 0.00 0.00 32.58 3.16
2834 3056 5.357878 TGTTCCACAGAAAGATATGCCATTC 59.642 40.000 0.00 0.00 32.58 2.67
2849 3071 5.528043 TGCCATTCTACAACAACAACAAT 57.472 34.783 0.00 0.00 0.00 2.71
2871 3093 6.987403 ATAAAGCCTTTAGTCCCAAACAAA 57.013 33.333 2.98 0.00 0.00 2.83
2893 3116 3.130734 TGGGTAGGCTAGAGGTGAAAT 57.869 47.619 0.00 0.00 0.00 2.17
2900 3123 5.975988 AGGCTAGAGGTGAAATCCATAAA 57.024 39.130 0.00 0.00 0.00 1.40
2933 3156 1.725557 CTCATGGCTCTGGCACATGC 61.726 60.000 10.11 0.00 41.84 4.06
2937 3160 0.034283 TGGCTCTGGCACATGCATAA 60.034 50.000 0.00 0.00 44.36 1.90
2951 3174 0.804989 GCATAACAAGCTTCCACGCT 59.195 50.000 0.00 0.00 43.31 5.07
2952 3175 2.006888 GCATAACAAGCTTCCACGCTA 58.993 47.619 0.00 0.00 39.86 4.26
2954 3177 3.262420 CATAACAAGCTTCCACGCTACT 58.738 45.455 0.00 0.00 39.86 2.57
2984 3207 6.463614 CCATAGCTAGCTCTTTGGTGATACTT 60.464 42.308 23.26 0.00 32.65 2.24
3076 3299 2.809601 CGCACGCTTTAGCCGTCT 60.810 61.111 0.00 0.00 37.91 4.18
3118 3341 1.895707 GCCTGCGCTGAATATGCCT 60.896 57.895 16.65 0.00 0.00 4.75
3146 3369 2.628178 TCTCAGACGATGTTGGACAAGT 59.372 45.455 0.00 0.00 0.00 3.16
3158 3381 6.377327 TGTTGGACAAGTTTCTCTTCAATC 57.623 37.500 0.00 0.00 33.63 2.67
3236 3459 1.285667 TGGCCACACATCCATCTCAAT 59.714 47.619 0.00 0.00 0.00 2.57
3249 3472 4.772100 TCCATCTCAATATACGCATCTCCA 59.228 41.667 0.00 0.00 0.00 3.86
3273 3496 4.338118 CCACACCTAACTGTTGAACATGTT 59.662 41.667 11.78 11.78 0.00 2.71
3280 3503 4.045636 ACTGTTGAACATGTTGCCTTTC 57.954 40.909 17.58 0.26 0.00 2.62
3455 3678 3.367280 TCATCAATACCCCCATCCTCT 57.633 47.619 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.115490 AGATAAATGAAAACTCACAAAGGAGG 57.885 34.615 0.00 0.00 39.27 4.30
5 6 9.130661 TCAAGATAAATGAAAACTCACAAAGGA 57.869 29.630 0.00 0.00 0.00 3.36
7 8 9.734620 TGTCAAGATAAATGAAAACTCACAAAG 57.265 29.630 0.00 0.00 0.00 2.77
9 10 9.734620 CTTGTCAAGATAAATGAAAACTCACAA 57.265 29.630 6.76 0.00 0.00 3.33
10 11 7.862372 GCTTGTCAAGATAAATGAAAACTCACA 59.138 33.333 16.99 0.00 0.00 3.58
11 12 7.862372 TGCTTGTCAAGATAAATGAAAACTCAC 59.138 33.333 16.99 0.00 0.00 3.51
12 13 7.939782 TGCTTGTCAAGATAAATGAAAACTCA 58.060 30.769 16.99 0.00 0.00 3.41
13 14 8.976986 ATGCTTGTCAAGATAAATGAAAACTC 57.023 30.769 16.99 0.00 0.00 3.01
14 15 8.579006 TGATGCTTGTCAAGATAAATGAAAACT 58.421 29.630 16.99 0.00 0.00 2.66
15 16 8.746922 TGATGCTTGTCAAGATAAATGAAAAC 57.253 30.769 16.99 0.00 0.00 2.43
16 17 9.577110 GATGATGCTTGTCAAGATAAATGAAAA 57.423 29.630 16.99 0.00 0.00 2.29
17 18 8.741841 TGATGATGCTTGTCAAGATAAATGAAA 58.258 29.630 16.99 0.00 0.00 2.69
18 19 8.283699 TGATGATGCTTGTCAAGATAAATGAA 57.716 30.769 16.99 0.00 0.00 2.57
19 20 7.868906 TGATGATGCTTGTCAAGATAAATGA 57.131 32.000 16.99 0.00 0.00 2.57
20 21 8.968242 CAATGATGATGCTTGTCAAGATAAATG 58.032 33.333 16.99 0.00 0.00 2.32
21 22 8.909923 TCAATGATGATGCTTGTCAAGATAAAT 58.090 29.630 16.99 4.14 0.00 1.40
22 23 8.283699 TCAATGATGATGCTTGTCAAGATAAA 57.716 30.769 16.99 0.00 0.00 1.40
23 24 7.555195 ACTCAATGATGATGCTTGTCAAGATAA 59.445 33.333 16.99 1.34 34.37 1.75
24 25 7.052248 ACTCAATGATGATGCTTGTCAAGATA 58.948 34.615 16.99 4.69 34.37 1.98
25 26 5.886474 ACTCAATGATGATGCTTGTCAAGAT 59.114 36.000 16.99 6.96 34.37 2.40
26 27 5.250982 ACTCAATGATGATGCTTGTCAAGA 58.749 37.500 16.99 2.23 34.37 3.02
27 28 5.562506 ACTCAATGATGATGCTTGTCAAG 57.437 39.130 8.31 8.31 34.37 3.02
28 29 6.600427 ACATACTCAATGATGATGCTTGTCAA 59.400 34.615 4.90 0.00 39.07 3.18
29 30 6.117488 ACATACTCAATGATGATGCTTGTCA 58.883 36.000 4.90 0.00 39.07 3.58
30 31 6.615264 ACATACTCAATGATGATGCTTGTC 57.385 37.500 4.90 0.00 39.07 3.18
31 32 8.687292 AATACATACTCAATGATGATGCTTGT 57.313 30.769 4.90 0.00 39.07 3.16
40 41 9.920946 ACCTGGTTTTAATACATACTCAATGAT 57.079 29.630 0.00 0.00 39.07 2.45
41 42 9.173021 CACCTGGTTTTAATACATACTCAATGA 57.827 33.333 0.00 0.00 39.07 2.57
42 43 7.915397 GCACCTGGTTTTAATACATACTCAATG 59.085 37.037 0.00 0.00 41.74 2.82
43 44 7.613801 TGCACCTGGTTTTAATACATACTCAAT 59.386 33.333 0.00 0.00 0.00 2.57
44 45 6.943146 TGCACCTGGTTTTAATACATACTCAA 59.057 34.615 0.00 0.00 0.00 3.02
45 46 6.477253 TGCACCTGGTTTTAATACATACTCA 58.523 36.000 0.00 0.00 0.00 3.41
46 47 6.995511 TGCACCTGGTTTTAATACATACTC 57.004 37.500 0.00 0.00 0.00 2.59
47 48 7.116075 TCATGCACCTGGTTTTAATACATACT 58.884 34.615 0.00 0.00 0.00 2.12
48 49 7.328277 TCATGCACCTGGTTTTAATACATAC 57.672 36.000 0.00 0.00 0.00 2.39
49 50 7.777440 TGATCATGCACCTGGTTTTAATACATA 59.223 33.333 0.00 0.00 0.00 2.29
50 51 6.606796 TGATCATGCACCTGGTTTTAATACAT 59.393 34.615 0.00 0.00 0.00 2.29
51 52 5.948758 TGATCATGCACCTGGTTTTAATACA 59.051 36.000 0.00 0.00 0.00 2.29
52 53 6.449635 TGATCATGCACCTGGTTTTAATAC 57.550 37.500 0.00 0.00 0.00 1.89
53 54 7.039434 TGTTTGATCATGCACCTGGTTTTAATA 60.039 33.333 0.00 0.00 0.00 0.98
54 55 5.999205 TTGATCATGCACCTGGTTTTAAT 57.001 34.783 0.00 0.00 0.00 1.40
55 56 5.069648 TGTTTGATCATGCACCTGGTTTTAA 59.930 36.000 0.00 0.00 0.00 1.52
56 57 4.586421 TGTTTGATCATGCACCTGGTTTTA 59.414 37.500 0.00 0.00 0.00 1.52
57 58 3.387374 TGTTTGATCATGCACCTGGTTTT 59.613 39.130 0.00 0.00 0.00 2.43
58 59 2.964464 TGTTTGATCATGCACCTGGTTT 59.036 40.909 0.00 0.00 0.00 3.27
59 60 2.596346 TGTTTGATCATGCACCTGGTT 58.404 42.857 0.00 0.00 0.00 3.67
60 61 2.291209 TGTTTGATCATGCACCTGGT 57.709 45.000 0.00 0.00 0.00 4.00
61 62 2.494471 ACATGTTTGATCATGCACCTGG 59.506 45.455 0.00 0.00 46.15 4.45
62 63 3.861276 ACATGTTTGATCATGCACCTG 57.139 42.857 0.00 0.49 46.15 4.00
399 502 7.721402 ACACAAAAATGATAAGTTGCAAGGTA 58.279 30.769 0.00 0.00 0.00 3.08
489 594 5.122239 TCCACTTTTTCAACATATCTCAGCG 59.878 40.000 0.00 0.00 0.00 5.18
490 595 6.500684 TCCACTTTTTCAACATATCTCAGC 57.499 37.500 0.00 0.00 0.00 4.26
491 596 8.233190 GTCTTCCACTTTTTCAACATATCTCAG 58.767 37.037 0.00 0.00 0.00 3.35
495 600 6.899114 ACGTCTTCCACTTTTTCAACATATC 58.101 36.000 0.00 0.00 0.00 1.63
530 635 8.740906 CATAAGGGGAGTACTATGTATGTAGTG 58.259 40.741 0.00 0.00 36.39 2.74
533 638 8.450434 TCACATAAGGGGAGTACTATGTATGTA 58.550 37.037 6.42 1.04 31.51 2.29
534 639 7.302948 TCACATAAGGGGAGTACTATGTATGT 58.697 38.462 6.42 8.23 32.57 2.29
547 652 3.010027 TGTGCAATCTTCACATAAGGGGA 59.990 43.478 0.00 0.00 39.29 4.81
548 653 3.129287 GTGTGCAATCTTCACATAAGGGG 59.871 47.826 0.00 0.00 44.96 4.79
550 655 3.129287 GGGTGTGCAATCTTCACATAAGG 59.871 47.826 6.71 0.00 44.96 2.69
551 656 3.129287 GGGGTGTGCAATCTTCACATAAG 59.871 47.826 6.71 0.00 44.96 1.73
552 657 3.088532 GGGGTGTGCAATCTTCACATAA 58.911 45.455 6.71 0.00 44.96 1.90
763 877 1.941999 GCGAGGGGTACGTAGCAGTT 61.942 60.000 24.76 10.37 34.01 3.16
808 922 4.158949 GGAGACCACCTAGAAGAAGAAGAC 59.841 50.000 0.00 0.00 0.00 3.01
848 965 0.263468 TACACGATGGGATGGAGGGA 59.737 55.000 0.00 0.00 0.00 4.20
855 972 0.309922 CGTAGCGTACACGATGGGAT 59.690 55.000 5.84 0.00 41.91 3.85
952 1077 3.003482 CCTACGTACCTACTTAGCAGCAG 59.997 52.174 0.00 0.00 29.57 4.24
953 1078 2.947652 CCTACGTACCTACTTAGCAGCA 59.052 50.000 0.00 0.00 29.57 4.41
954 1079 2.292845 CCCTACGTACCTACTTAGCAGC 59.707 54.545 0.00 0.00 29.57 5.25
1221 1355 1.725557 GAGAGGAGGATGCGTGCGTA 61.726 60.000 0.00 0.00 0.00 4.42
1239 1373 2.264480 CAATGGGACGGCGAGTGA 59.736 61.111 16.62 0.00 0.00 3.41
1241 1375 1.546589 TAACCAATGGGACGGCGAGT 61.547 55.000 16.62 0.00 38.05 4.18
1251 1388 4.441634 CCGAGGAGTAAGAGTAACCAATGG 60.442 50.000 0.00 0.00 0.00 3.16
1252 1389 4.683832 CCGAGGAGTAAGAGTAACCAATG 58.316 47.826 0.00 0.00 0.00 2.82
1253 1390 3.132467 GCCGAGGAGTAAGAGTAACCAAT 59.868 47.826 0.00 0.00 0.00 3.16
1254 1391 2.494870 GCCGAGGAGTAAGAGTAACCAA 59.505 50.000 0.00 0.00 0.00 3.67
1255 1392 2.097825 GCCGAGGAGTAAGAGTAACCA 58.902 52.381 0.00 0.00 0.00 3.67
1256 1393 2.097825 TGCCGAGGAGTAAGAGTAACC 58.902 52.381 0.00 0.00 0.00 2.85
1257 1394 4.142227 TGAATGCCGAGGAGTAAGAGTAAC 60.142 45.833 0.00 0.00 0.00 2.50
1258 1395 4.021229 TGAATGCCGAGGAGTAAGAGTAA 58.979 43.478 0.00 0.00 0.00 2.24
1260 1397 2.457598 TGAATGCCGAGGAGTAAGAGT 58.542 47.619 0.00 0.00 0.00 3.24
1266 1404 2.804572 CGATGATTGAATGCCGAGGAGT 60.805 50.000 0.00 0.00 0.00 3.85
1491 1641 3.827898 GAGGTCGAGCTGGTCCCG 61.828 72.222 23.97 0.00 0.00 5.14
1649 1799 1.009829 GCAGCTTACCGATCAACCTG 58.990 55.000 0.00 0.00 0.00 4.00
1686 1836 4.680237 CACCGCCCAGTCGAGCAA 62.680 66.667 0.00 0.00 0.00 3.91
1837 1995 9.745018 AGAATGATCAAAAGTAGATCCTCAAAA 57.255 29.630 0.00 0.00 40.87 2.44
1862 2020 7.772332 AAGGCTGTAAATGATCGTAAAGTAG 57.228 36.000 0.00 0.00 0.00 2.57
1873 2031 7.081349 CGTTCAAATGTAAAGGCTGTAAATGA 58.919 34.615 0.00 0.00 0.00 2.57
1875 2033 5.861787 GCGTTCAAATGTAAAGGCTGTAAAT 59.138 36.000 0.00 0.00 34.38 1.40
1882 2040 1.271102 TGGGCGTTCAAATGTAAAGGC 59.729 47.619 0.00 0.00 35.97 4.35
1946 2105 8.096414 CCAAGTAAAATGACTGAATTTTCCCAT 58.904 33.333 8.38 0.00 39.73 4.00
2063 2223 7.276878 GCTTGTTTTCCAGTAGAGATTAGACTC 59.723 40.741 0.00 0.00 37.19 3.36
2067 2227 7.768120 AGATGCTTGTTTTCCAGTAGAGATTAG 59.232 37.037 0.00 0.00 0.00 1.73
2095 2257 6.287525 TCTTTTGGTGGATTTGATTGGAAAC 58.712 36.000 0.00 0.00 0.00 2.78
2143 2305 9.353999 ACAAAAGTTTTGAAGTCTGACAAATAC 57.646 29.630 30.20 6.90 36.21 1.89
2185 2380 3.316308 ACAAAAGCTTTGGAGTACAGCAG 59.684 43.478 20.65 0.00 35.88 4.24
2187 2382 3.315191 TGACAAAAGCTTTGGAGTACAGC 59.685 43.478 20.65 5.19 0.00 4.40
2195 2390 9.654417 CTATGAAATTTTTGACAAAAGCTTTGG 57.346 29.630 13.54 12.85 35.30 3.28
2200 2395 7.293018 CAGCCTATGAAATTTTTGACAAAAGC 58.707 34.615 12.84 9.76 35.30 3.51
2230 2425 7.820872 ACTATGAAATTTGGCTGAAAATCCAAG 59.179 33.333 0.00 0.00 42.62 3.61
2251 2446 7.064609 TCCAGCTTTAAATTCGTCAGAACTATG 59.935 37.037 0.00 0.00 39.48 2.23
2253 2448 6.460781 TCCAGCTTTAAATTCGTCAGAACTA 58.539 36.000 0.00 0.00 39.48 2.24
2254 2449 5.305585 TCCAGCTTTAAATTCGTCAGAACT 58.694 37.500 0.00 0.00 39.48 3.01
2256 2451 5.305585 ACTCCAGCTTTAAATTCGTCAGAA 58.694 37.500 0.00 0.00 41.13 3.02
2257 2452 4.894784 ACTCCAGCTTTAAATTCGTCAGA 58.105 39.130 0.00 0.00 0.00 3.27
2258 2453 5.613358 AACTCCAGCTTTAAATTCGTCAG 57.387 39.130 0.00 0.00 0.00 3.51
2259 2454 5.048991 GGAAACTCCAGCTTTAAATTCGTCA 60.049 40.000 0.00 0.00 36.28 4.35
2260 2455 5.181433 AGGAAACTCCAGCTTTAAATTCGTC 59.819 40.000 0.00 0.00 39.61 4.20
2262 2457 5.629079 AGGAAACTCCAGCTTTAAATTCG 57.371 39.130 0.00 0.00 39.61 3.34
2294 2502 7.359264 CCGGATCAAATAAGTTACATCGATCAC 60.359 40.741 0.00 0.00 31.70 3.06
2466 2675 4.497473 TTAACCAAAGCGTCAATCAAGG 57.503 40.909 0.00 0.00 0.00 3.61
2504 2717 7.075741 CACCCAACTGAACGAAATTAACTAAG 58.924 38.462 0.00 0.00 0.00 2.18
2545 2758 3.022557 AGGCTCGGGTACATACAAGTA 57.977 47.619 0.00 0.00 0.00 2.24
2559 2773 1.152735 TGGGTCCTAGCTAGGCTCG 60.153 63.158 31.76 11.31 43.31 5.03
2637 2855 7.226325 CCAAATTAACCATTCAAAGAGCACAAA 59.774 33.333 0.00 0.00 0.00 2.83
2661 2879 3.002038 ACACAACCCGAAGTAAAACCA 57.998 42.857 0.00 0.00 0.00 3.67
2664 2882 7.160049 TGACATATACACAACCCGAAGTAAAA 58.840 34.615 0.00 0.00 0.00 1.52
2672 2890 2.475111 GCGATGACATATACACAACCCG 59.525 50.000 0.00 0.00 0.00 5.28
2673 2891 3.247648 GTGCGATGACATATACACAACCC 59.752 47.826 9.10 0.00 0.00 4.11
2713 2931 3.454375 AGCGAAATCGAACGGTCAATAT 58.546 40.909 7.06 0.00 43.02 1.28
2751 2973 1.082117 CGTGGTTAGTGGGCGACATC 61.082 60.000 1.61 0.00 0.00 3.06
2758 2980 4.766375 ACAATCTTATCGTGGTTAGTGGG 58.234 43.478 0.00 0.00 0.00 4.61
2811 3033 5.591877 AGAATGGCATATCTTTCTGTGGAAC 59.408 40.000 0.00 0.00 32.29 3.62
2812 3034 5.759059 AGAATGGCATATCTTTCTGTGGAA 58.241 37.500 0.00 0.00 32.29 3.53
2813 3035 5.378230 AGAATGGCATATCTTTCTGTGGA 57.622 39.130 0.00 0.00 32.29 4.02
2814 3036 6.057533 TGTAGAATGGCATATCTTTCTGTGG 58.942 40.000 14.42 0.00 34.42 4.17
2815 3037 7.066163 TGTTGTAGAATGGCATATCTTTCTGTG 59.934 37.037 14.42 0.00 34.42 3.66
2816 3038 7.112122 TGTTGTAGAATGGCATATCTTTCTGT 58.888 34.615 14.42 0.00 34.42 3.41
2817 3039 7.558161 TGTTGTAGAATGGCATATCTTTCTG 57.442 36.000 14.42 0.00 34.42 3.02
2818 3040 7.611467 TGTTGTTGTAGAATGGCATATCTTTCT 59.389 33.333 14.42 10.43 35.93 2.52
2819 3041 7.761409 TGTTGTTGTAGAATGGCATATCTTTC 58.239 34.615 14.42 4.04 0.00 2.62
2820 3042 7.701539 TGTTGTTGTAGAATGGCATATCTTT 57.298 32.000 14.42 0.00 0.00 2.52
2821 3043 7.176515 TGTTGTTGTTGTAGAATGGCATATCTT 59.823 33.333 14.42 0.00 0.00 2.40
2822 3044 6.658816 TGTTGTTGTTGTAGAATGGCATATCT 59.341 34.615 0.00 8.74 0.00 1.98
2823 3045 6.851609 TGTTGTTGTTGTAGAATGGCATATC 58.148 36.000 0.00 0.86 0.00 1.63
2824 3046 6.832520 TGTTGTTGTTGTAGAATGGCATAT 57.167 33.333 0.00 0.00 0.00 1.78
2825 3047 6.641169 TTGTTGTTGTTGTAGAATGGCATA 57.359 33.333 0.00 0.00 0.00 3.14
2826 3048 5.528043 TTGTTGTTGTTGTAGAATGGCAT 57.472 34.783 0.00 0.00 0.00 4.40
2827 3049 4.991153 TTGTTGTTGTTGTAGAATGGCA 57.009 36.364 0.00 0.00 0.00 4.92
2828 3050 7.359181 GCTTTATTGTTGTTGTTGTAGAATGGC 60.359 37.037 0.00 0.00 0.00 4.40
2829 3051 7.116233 GGCTTTATTGTTGTTGTTGTAGAATGG 59.884 37.037 0.00 0.00 0.00 3.16
2830 3052 7.867403 AGGCTTTATTGTTGTTGTTGTAGAATG 59.133 33.333 0.00 0.00 0.00 2.67
2831 3053 7.951591 AGGCTTTATTGTTGTTGTTGTAGAAT 58.048 30.769 0.00 0.00 0.00 2.40
2832 3054 7.341445 AGGCTTTATTGTTGTTGTTGTAGAA 57.659 32.000 0.00 0.00 0.00 2.10
2833 3055 6.952773 AGGCTTTATTGTTGTTGTTGTAGA 57.047 33.333 0.00 0.00 0.00 2.59
2834 3056 9.180678 CTAAAGGCTTTATTGTTGTTGTTGTAG 57.819 33.333 19.32 0.95 0.00 2.74
2849 3071 6.987403 ATTTGTTTGGGACTAAAGGCTTTA 57.013 33.333 18.11 18.11 0.00 1.85
2871 3093 2.868964 TCACCTCTAGCCTACCCAAT 57.131 50.000 0.00 0.00 0.00 3.16
2893 3116 6.703319 TGAGTTGGTTACGAGATTTTATGGA 58.297 36.000 0.00 0.00 0.00 3.41
2933 3156 3.262420 AGTAGCGTGGAAGCTTGTTATG 58.738 45.455 2.10 0.00 46.80 1.90
2937 3160 0.969894 AGAGTAGCGTGGAAGCTTGT 59.030 50.000 2.10 0.00 46.80 3.16
2951 3174 4.715534 AGAGCTAGCTATGGACAGAGTA 57.284 45.455 19.38 0.00 0.00 2.59
2952 3175 3.593442 AGAGCTAGCTATGGACAGAGT 57.407 47.619 19.38 0.00 0.00 3.24
2954 3177 3.386078 CCAAAGAGCTAGCTATGGACAGA 59.614 47.826 27.69 0.00 30.53 3.41
2984 3207 5.105716 CGTTAAGAGAGACCTGAAGGATTGA 60.106 44.000 2.62 0.00 38.94 2.57
3076 3299 0.907486 AGAAGCTCCAGTGCATAGCA 59.093 50.000 13.50 0.00 38.75 3.49
3118 3341 4.221924 TCCAACATCGTCTGAGATGGTTTA 59.778 41.667 16.20 3.67 45.46 2.01
3146 3369 3.596214 GGTAGCACCGATTGAAGAGAAA 58.404 45.455 0.00 0.00 0.00 2.52
3158 3381 1.068741 GATAGAGTTGGGGTAGCACCG 59.931 57.143 0.00 0.00 39.83 4.94
3236 3459 1.411246 GGTGTGGTGGAGATGCGTATA 59.589 52.381 0.00 0.00 0.00 1.47
3249 3472 3.637911 TGTTCAACAGTTAGGTGTGGT 57.362 42.857 0.00 0.00 35.97 4.16
3280 3503 2.320587 GCTGAGTGTTGGCCGACTG 61.321 63.158 23.87 9.82 0.00 3.51


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

AutoCloner maintained by Alex Coulton.