Multiple sequence alignment - TraesCS1A01G243900

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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 TraesCS1A01G243900 chr1A 100.000 2979 0 0 1 2979 432338268 432341246 0.000000e+00 5502.0
1 TraesCS1A01G243900 chr1A 94.244 1494 48 12 550 2009 432484889 432486378 0.000000e+00 2248.0
2 TraesCS1A01G243900 chr1A 79.972 719 115 19 1013 1718 432213014 432212312 1.230000e-138 503.0
3 TraesCS1A01G243900 chr1B 90.434 1683 116 17 69 1722 449850633 449852299 0.000000e+00 2174.0
4 TraesCS1A01G243900 chr1B 91.424 1166 61 16 584 1722 449977065 449978218 0.000000e+00 1563.0
5 TraesCS1A01G243900 chr1B 78.159 728 115 25 1013 1718 449737452 449736747 9.870000e-115 424.0
6 TraesCS1A01G243900 chr1B 96.016 251 8 1 1761 2009 449978318 449978568 9.940000e-110 407.0
7 TraesCS1A01G243900 chr1B 85.445 371 50 4 15 384 449976281 449976648 1.680000e-102 383.0
8 TraesCS1A01G243900 chr1B 94.378 249 12 2 1761 2009 449852400 449852646 6.030000e-102 381.0
9 TraesCS1A01G243900 chr1B 82.713 376 49 13 2010 2382 449852708 449853070 1.330000e-83 320.0
10 TraesCS1A01G243900 chr1D 93.484 1197 46 11 550 1722 334450794 334451982 0.000000e+00 1749.0
11 TraesCS1A01G243900 chr1D 92.000 600 45 3 2382 2979 345939029 345939627 0.000000e+00 839.0
12 TraesCS1A01G243900 chr1D 78.255 722 125 20 1013 1718 334336882 334336177 4.560000e-118 435.0
13 TraesCS1A01G243900 chr1D 96.400 250 8 1 1761 2009 334452086 334452335 7.690000e-111 411.0
14 TraesCS1A01G243900 chr1D 92.727 55 3 1 1712 1765 334452010 334452064 8.850000e-11 78.7
15 TraesCS1A01G243900 chr2D 92.079 606 45 3 2376 2979 468626211 468626815 0.000000e+00 850.0
16 TraesCS1A01G243900 chr2D 92.000 600 46 2 2381 2979 315603732 315604330 0.000000e+00 841.0
17 TraesCS1A01G243900 chr4D 92.180 601 44 3 2380 2979 506144660 506145258 0.000000e+00 846.0
18 TraesCS1A01G243900 chr6D 91.803 610 45 5 2373 2979 452225375 452225982 0.000000e+00 845.0
19 TraesCS1A01G243900 chr7D 91.914 606 44 5 2377 2979 134116014 134116617 0.000000e+00 843.0
20 TraesCS1A01G243900 chr3D 92.027 602 44 4 2379 2979 420068212 420068810 0.000000e+00 843.0
21 TraesCS1A01G243900 chr5D 92.013 601 44 3 2382 2979 229953307 229952708 0.000000e+00 841.0
22 TraesCS1A01G243900 chr5D 91.860 602 45 4 2379 2979 339959502 339958904 0.000000e+00 837.0
23 TraesCS1A01G243900 chr6B 79.186 221 37 9 2121 2336 495747251 495747035 8.610000e-31 145.0
24 TraesCS1A01G243900 chr5A 76.981 265 49 11 2093 2349 691819587 691819327 1.110000e-29 141.0
25 TraesCS1A01G243900 chr4B 84.298 121 16 3 2175 2295 654190102 654189985 6.750000e-22 115.0
26 TraesCS1A01G243900 chr7A 85.455 110 14 2 2176 2285 15751000 15751107 2.430000e-21 113.0


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 TraesCS1A01G243900 chr1A 432338268 432341246 2978 False 5502.000000 5502 100.000000 1 2979 1 chr1A.!!$F1 2978
1 TraesCS1A01G243900 chr1A 432484889 432486378 1489 False 2248.000000 2248 94.244000 550 2009 1 chr1A.!!$F2 1459
2 TraesCS1A01G243900 chr1A 432212312 432213014 702 True 503.000000 503 79.972000 1013 1718 1 chr1A.!!$R1 705
3 TraesCS1A01G243900 chr1B 449850633 449853070 2437 False 958.333333 2174 89.175000 69 2382 3 chr1B.!!$F1 2313
4 TraesCS1A01G243900 chr1B 449976281 449978568 2287 False 784.333333 1563 90.961667 15 2009 3 chr1B.!!$F2 1994
5 TraesCS1A01G243900 chr1B 449736747 449737452 705 True 424.000000 424 78.159000 1013 1718 1 chr1B.!!$R1 705
6 TraesCS1A01G243900 chr1D 345939029 345939627 598 False 839.000000 839 92.000000 2382 2979 1 chr1D.!!$F1 597
7 TraesCS1A01G243900 chr1D 334450794 334452335 1541 False 746.233333 1749 94.203667 550 2009 3 chr1D.!!$F2 1459
8 TraesCS1A01G243900 chr1D 334336177 334336882 705 True 435.000000 435 78.255000 1013 1718 1 chr1D.!!$R1 705
9 TraesCS1A01G243900 chr2D 468626211 468626815 604 False 850.000000 850 92.079000 2376 2979 1 chr2D.!!$F2 603
10 TraesCS1A01G243900 chr2D 315603732 315604330 598 False 841.000000 841 92.000000 2381 2979 1 chr2D.!!$F1 598
11 TraesCS1A01G243900 chr4D 506144660 506145258 598 False 846.000000 846 92.180000 2380 2979 1 chr4D.!!$F1 599
12 TraesCS1A01G243900 chr6D 452225375 452225982 607 False 845.000000 845 91.803000 2373 2979 1 chr6D.!!$F1 606
13 TraesCS1A01G243900 chr7D 134116014 134116617 603 False 843.000000 843 91.914000 2377 2979 1 chr7D.!!$F1 602
14 TraesCS1A01G243900 chr3D 420068212 420068810 598 False 843.000000 843 92.027000 2379 2979 1 chr3D.!!$F1 600
15 TraesCS1A01G243900 chr5D 229952708 229953307 599 True 841.000000 841 92.013000 2382 2979 1 chr5D.!!$R1 597
16 TraesCS1A01G243900 chr5D 339958904 339959502 598 True 837.000000 837 91.860000 2379 2979 1 chr5D.!!$R2 600

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
53 54 0.256464 ACACACGGTTCCCTTTCCAA 59.744 50.0 0.0 0.0 0.0 3.53 F
951 1284 0.603569 TCCTTCTTGTGGCGTCTCTC 59.396 55.0 0.0 0.0 0.0 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1010 1352 0.464373 GGCATGGCGAAATGGAGAGA 60.464 55.0 2.41 0.0 0.00 3.10 R
2056 2602 0.101040 CATTGTGGCTATTGCACGGG 59.899 55.0 0.66 0.0 41.91 5.28 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
19 20 4.272100 GCATTTGCCAGCCAAGTG 57.728 55.556 0.00 0.00 42.25 3.16
30 31 2.564721 GCCAAGTGGTGTGCCCTTC 61.565 63.158 0.00 0.00 37.57 3.46
33 34 1.331214 CAAGTGGTGTGCCCTTCATT 58.669 50.000 0.00 0.00 0.00 2.57
38 39 1.143889 TGGTGTGCCCTTCATTACACA 59.856 47.619 0.00 0.00 43.82 3.72
40 41 1.518325 TGTGCCCTTCATTACACACG 58.482 50.000 0.00 0.00 38.07 4.49
50 51 3.404899 TCATTACACACGGTTCCCTTTC 58.595 45.455 0.00 0.00 0.00 2.62
53 54 0.256464 ACACACGGTTCCCTTTCCAA 59.744 50.000 0.00 0.00 0.00 3.53
65 66 2.506644 CCCTTTCCAAAATCATGCCCAT 59.493 45.455 0.00 0.00 0.00 4.00
67 68 4.163839 CCCTTTCCAAAATCATGCCCATTA 59.836 41.667 0.00 0.00 0.00 1.90
73 74 5.898397 TCCAAAATCATGCCCATTAGATCAA 59.102 36.000 0.00 0.00 0.00 2.57
78 79 4.806892 TCATGCCCATTAGATCAACCATT 58.193 39.130 0.00 0.00 0.00 3.16
104 105 3.077229 TGTTTCATTTTCTGGCACACG 57.923 42.857 0.00 0.00 0.00 4.49
105 106 2.223688 TGTTTCATTTTCTGGCACACGG 60.224 45.455 0.00 0.00 0.00 4.94
152 153 3.429822 GCCTGCATTGCACATAGTTCAAT 60.430 43.478 7.38 0.00 33.79 2.57
180 181 2.350458 ATGGGGTTGTGATTGGCGC 61.350 57.895 0.00 0.00 0.00 6.53
183 184 2.126888 GGTTGTGATTGGCGCGTG 60.127 61.111 8.43 0.00 0.00 5.34
186 187 0.996727 GTTGTGATTGGCGCGTGTTC 60.997 55.000 8.43 0.48 0.00 3.18
187 188 2.123988 TTGTGATTGGCGCGTGTTCC 62.124 55.000 8.43 0.00 0.00 3.62
212 213 3.865446 CATCATTCTGCACTAGTGACCA 58.135 45.455 27.08 14.34 0.00 4.02
239 240 3.201266 AGGGGCGACATAGTTTTTATGGA 59.799 43.478 0.00 0.00 0.00 3.41
242 243 3.625764 GGCGACATAGTTTTTATGGAGCA 59.374 43.478 13.75 0.00 35.06 4.26
247 248 6.346120 CGACATAGTTTTTATGGAGCATCTCG 60.346 42.308 0.00 0.00 33.73 4.04
277 278 3.238441 GCTCACTCAACTTCGACTACAG 58.762 50.000 0.00 0.00 0.00 2.74
284 285 0.803740 ACTTCGACTACAGCCTCGAC 59.196 55.000 0.00 0.00 38.61 4.20
286 287 0.671472 TTCGACTACAGCCTCGACGA 60.671 55.000 0.00 0.00 38.61 4.20
320 321 4.437930 GCTTTGGCTACTTTGCTCTATGTG 60.438 45.833 0.00 0.00 35.22 3.21
359 361 0.957395 AGATGTTGTTGCGCTGGAGG 60.957 55.000 9.73 0.00 0.00 4.30
368 370 2.193536 GCGCTGGAGGTTTTGGTGT 61.194 57.895 0.00 0.00 0.00 4.16
395 697 4.674101 CGTCTGTCATGAACTCTCTCTTCC 60.674 50.000 0.00 0.00 0.00 3.46
415 717 2.358957 CGACATGTGTCATTGGTCCAT 58.641 47.619 1.15 0.00 44.99 3.41
420 722 6.000246 ACATGTGTCATTGGTCCATATACA 58.000 37.500 0.00 0.00 0.00 2.29
434 736 6.459066 GTCCATATACATGTGTGCTAGATGT 58.541 40.000 9.11 8.78 44.58 3.06
441 743 3.319137 TGTGTGCTAGATGTTCCTGAC 57.681 47.619 0.00 0.00 0.00 3.51
467 769 2.049888 TATGCGATTTGCCATGTCCA 57.950 45.000 0.00 0.00 45.60 4.02
480 782 5.939447 TGCCATGTCCATAATCTTGTGATA 58.061 37.500 0.00 0.00 31.70 2.15
481 783 5.999600 TGCCATGTCCATAATCTTGTGATAG 59.000 40.000 0.00 0.00 31.70 2.08
497 799 9.330063 TCTTGTGATAGTGCTAATTTGGATTAG 57.670 33.333 2.57 2.57 44.94 1.73
500 802 8.052748 TGTGATAGTGCTAATTTGGATTAGGTT 58.947 33.333 7.92 0.00 43.22 3.50
501 803 8.903820 GTGATAGTGCTAATTTGGATTAGGTTT 58.096 33.333 7.92 0.00 43.22 3.27
506 808 9.084533 AGTGCTAATTTGGATTAGGTTTAAACA 57.915 29.630 19.57 0.00 43.22 2.83
507 809 9.699703 GTGCTAATTTGGATTAGGTTTAAACAA 57.300 29.630 19.57 7.08 43.22 2.83
508 810 9.699703 TGCTAATTTGGATTAGGTTTAAACAAC 57.300 29.630 19.57 3.74 43.22 3.32
515 817 9.699703 TTGGATTAGGTTTAAACAACAATTAGC 57.300 29.630 19.57 0.00 0.00 3.09
516 818 8.024285 TGGATTAGGTTTAAACAACAATTAGCG 58.976 33.333 19.57 0.00 0.00 4.26
517 819 8.238631 GGATTAGGTTTAAACAACAATTAGCGA 58.761 33.333 19.57 0.00 0.00 4.93
518 820 9.615295 GATTAGGTTTAAACAACAATTAGCGAA 57.385 29.630 19.57 2.77 0.00 4.70
519 821 9.620660 ATTAGGTTTAAACAACAATTAGCGAAG 57.379 29.630 19.57 0.00 0.00 3.79
520 822 7.266922 AGGTTTAAACAACAATTAGCGAAGA 57.733 32.000 19.57 0.00 0.00 2.87
537 848 7.138692 AGCGAAGAATATTTCTATTGCCATC 57.861 36.000 0.00 0.00 39.61 3.51
709 1025 1.866015 CCACTACTCCACTCCATCCA 58.134 55.000 0.00 0.00 0.00 3.41
711 1027 2.366916 CCACTACTCCACTCCATCCATC 59.633 54.545 0.00 0.00 0.00 3.51
747 1076 4.625028 TCTTCCATGTATTGCGATGAGAG 58.375 43.478 0.00 0.00 0.00 3.20
819 1148 1.764134 TGTTCCAACCGACAACTACCT 59.236 47.619 0.00 0.00 0.00 3.08
824 1153 3.135167 TCCAACCGACAACTACCTTCTTT 59.865 43.478 0.00 0.00 0.00 2.52
951 1284 0.603569 TCCTTCTTGTGGCGTCTCTC 59.396 55.000 0.00 0.00 0.00 3.20
999 1341 1.538075 CAATTACACCAACCGTCACCC 59.462 52.381 0.00 0.00 0.00 4.61
1009 1351 4.675029 CGTCACCCCCACCGTGTC 62.675 72.222 0.00 0.00 32.86 3.67
1010 1352 3.239253 GTCACCCCCACCGTGTCT 61.239 66.667 0.00 0.00 32.86 3.41
1011 1353 2.920912 TCACCCCCACCGTGTCTC 60.921 66.667 0.00 0.00 32.86 3.36
1028 1370 0.942962 CTCTCTCCATTTCGCCATGC 59.057 55.000 0.00 0.00 0.00 4.06
1096 1438 2.048127 GGCTCTCTGTTCGCCGTT 60.048 61.111 0.00 0.00 33.64 4.44
1149 1491 2.202756 GCTACCGTTCGCTCCCAG 60.203 66.667 0.00 0.00 0.00 4.45
1312 1675 2.847234 ACCAAGGTGGAGCCGACA 60.847 61.111 0.18 0.00 40.96 4.35
2009 2494 6.291377 AGCATGTCTGTTTTCTAACTTCAGA 58.709 36.000 0.00 0.00 35.24 3.27
2024 2570 6.481954 AACTTCAGACAATTTAACGGCTAG 57.518 37.500 0.00 0.00 0.00 3.42
2055 2601 5.715070 TCTTAGAGCAACTCTAGCAAAGTC 58.285 41.667 4.64 0.00 42.92 3.01
2056 2602 3.326836 AGAGCAACTCTAGCAAAGTCC 57.673 47.619 0.00 0.00 39.28 3.85
2057 2603 2.027653 AGAGCAACTCTAGCAAAGTCCC 60.028 50.000 0.00 0.00 39.28 4.46
2058 2604 1.003696 AGCAACTCTAGCAAAGTCCCC 59.996 52.381 0.00 0.00 0.00 4.81
2059 2605 1.726853 CAACTCTAGCAAAGTCCCCG 58.273 55.000 0.00 0.00 0.00 5.73
2063 2609 1.003839 CTAGCAAAGTCCCCGTGCA 60.004 57.895 0.00 0.00 40.83 4.57
2066 2612 0.037590 AGCAAAGTCCCCGTGCAATA 59.962 50.000 0.00 0.00 40.83 1.90
2073 2619 1.677300 CCCCGTGCAATAGCCACAA 60.677 57.895 0.00 0.00 41.13 3.33
2077 2623 0.862701 CGTGCAATAGCCACAATGCG 60.863 55.000 0.00 0.00 41.61 4.73
2080 2626 1.400142 TGCAATAGCCACAATGCGTAC 59.600 47.619 0.00 0.00 41.61 3.67
2085 2631 1.226018 GCCACAATGCGTACGAAGC 60.226 57.895 21.65 3.71 0.00 3.86
2091 2637 3.780693 TGCGTACGAAGCATGCTC 58.219 55.556 22.93 13.44 40.01 4.26
2112 2658 2.496871 CCATTTGCATTTGGAGGCTACA 59.503 45.455 9.32 0.00 34.81 2.74
2113 2659 3.133362 CCATTTGCATTTGGAGGCTACAT 59.867 43.478 0.00 0.00 34.81 2.29
2115 2661 5.163426 CCATTTGCATTTGGAGGCTACATAA 60.163 40.000 0.00 0.00 34.81 1.90
2117 2663 4.235079 TGCATTTGGAGGCTACATAAGT 57.765 40.909 0.00 0.00 32.80 2.24
2131 2677 2.094906 ACATAAGTAGCACGCGAACTCA 60.095 45.455 15.93 0.00 0.00 3.41
2133 2679 0.596577 AAGTAGCACGCGAACTCAGA 59.403 50.000 15.93 0.00 0.00 3.27
2134 2680 0.169230 AGTAGCACGCGAACTCAGAG 59.831 55.000 15.93 0.00 0.00 3.35
2135 2681 0.109689 GTAGCACGCGAACTCAGAGT 60.110 55.000 15.93 0.00 0.00 3.24
2136 2682 0.168348 TAGCACGCGAACTCAGAGTC 59.832 55.000 15.93 0.00 0.00 3.36
2137 2683 2.429351 GCACGCGAACTCAGAGTCG 61.429 63.158 15.93 10.35 0.00 4.18
2138 2684 1.082038 CACGCGAACTCAGAGTCGT 60.082 57.895 15.93 14.25 0.00 4.34
2139 2685 1.060726 CACGCGAACTCAGAGTCGTC 61.061 60.000 15.93 2.97 0.00 4.20
2140 2686 1.206831 CGCGAACTCAGAGTCGTCA 59.793 57.895 17.96 0.00 0.00 4.35
2141 2687 0.179187 CGCGAACTCAGAGTCGTCAT 60.179 55.000 17.96 0.00 0.00 3.06
2151 2697 4.270008 TCAGAGTCGTCATATCTTCACCA 58.730 43.478 0.00 0.00 0.00 4.17
2158 2704 7.901029 AGTCGTCATATCTTCACCATCATAAT 58.099 34.615 0.00 0.00 0.00 1.28
2160 2706 8.993121 GTCGTCATATCTTCACCATCATAATTT 58.007 33.333 0.00 0.00 0.00 1.82
2193 2739 3.077359 CACAAACACTCAGATTCCCTCC 58.923 50.000 0.00 0.00 0.00 4.30
2195 2741 3.138283 ACAAACACTCAGATTCCCTCCAA 59.862 43.478 0.00 0.00 0.00 3.53
2197 2743 4.664688 AACACTCAGATTCCCTCCAAAT 57.335 40.909 0.00 0.00 0.00 2.32
2204 2750 6.139679 TCAGATTCCCTCCAAATGTAAACT 57.860 37.500 0.00 0.00 0.00 2.66
2230 2776 3.068448 AGCACATCAAGAAAACATGCACA 59.932 39.130 0.00 0.00 34.03 4.57
2238 2784 8.767085 CATCAAGAAAACATGCACATAGTTTTT 58.233 29.630 16.95 9.34 43.26 1.94
2252 2798 5.463061 ACATAGTTTTTGACAAGTTGCATGC 59.537 36.000 11.82 11.82 0.00 4.06
2270 2816 4.903016 GCATGCACAAAAACATTTAAACCG 59.097 37.500 14.21 0.00 0.00 4.44
2272 2818 3.309954 TGCACAAAAACATTTAAACCGGC 59.690 39.130 0.00 0.00 0.00 6.13
2278 2824 3.363341 AACATTTAAACCGGCACACAG 57.637 42.857 0.00 0.00 0.00 3.66
2292 2838 3.556213 GGCACACAGGTACAAGTCACATA 60.556 47.826 0.00 0.00 0.00 2.29
2296 2842 4.695455 ACACAGGTACAAGTCACATATTGC 59.305 41.667 0.00 0.00 0.00 3.56
2297 2843 4.694982 CACAGGTACAAGTCACATATTGCA 59.305 41.667 0.00 0.00 0.00 4.08
2299 2845 3.941483 AGGTACAAGTCACATATTGCAGC 59.059 43.478 0.00 0.00 0.00 5.25
2323 2869 1.002069 TGCACCATCCCATCCTTCTT 58.998 50.000 0.00 0.00 0.00 2.52
2324 2870 1.358787 TGCACCATCCCATCCTTCTTT 59.641 47.619 0.00 0.00 0.00 2.52
2325 2871 2.225343 TGCACCATCCCATCCTTCTTTT 60.225 45.455 0.00 0.00 0.00 2.27
2326 2872 2.167075 GCACCATCCCATCCTTCTTTTG 59.833 50.000 0.00 0.00 0.00 2.44
2345 2891 2.202650 GTGTGCATTGCGCCATCC 60.203 61.111 18.87 0.00 41.33 3.51
2349 2895 2.025156 GCATTGCGCCATCCTTCG 59.975 61.111 4.18 0.00 32.94 3.79
2355 2901 2.174319 GCGCCATCCTTCGAGGTTC 61.174 63.158 0.00 0.00 36.53 3.62
2359 2905 0.179000 CCATCCTTCGAGGTTCCTGG 59.821 60.000 0.00 0.00 36.53 4.45
2363 2909 0.389948 CCTTCGAGGTTCCTGGAACG 60.390 60.000 28.08 19.42 42.78 3.95
2416 2963 4.647611 AGACACATCCGTAACATTTTGGA 58.352 39.130 0.00 0.00 34.45 3.53
2424 2971 2.577450 GTAACATTTTGGACCGAACGC 58.423 47.619 0.00 0.00 0.00 4.84
2478 3025 9.605955 TTCTATGACAATAATTGTGACAAAACG 57.394 29.630 0.62 0.00 45.52 3.60
2485 3032 2.672188 TTGTGACAAAACGCGGTATG 57.328 45.000 12.47 8.48 0.00 2.39
2498 3045 2.600420 CGCGGTATGATCATAGATGTGC 59.400 50.000 15.83 13.21 0.00 4.57
2511 3059 2.269940 AGATGTGCTGGGTCCTACTTT 58.730 47.619 0.00 0.00 0.00 2.66
2559 3107 1.964373 GCTTTTCGTTCTGGGCGGA 60.964 57.895 0.00 0.00 0.00 5.54
2560 3108 1.305930 GCTTTTCGTTCTGGGCGGAT 61.306 55.000 0.00 0.00 0.00 4.18
2595 3143 1.545582 CATGACATTCTTTGGGCCGTT 59.454 47.619 0.00 0.00 0.00 4.44
2636 3185 3.433740 GGTAGAAATGAGGGCGAGGAAAT 60.434 47.826 0.00 0.00 0.00 2.17
2659 3208 3.059099 GGGTGTTCCCGGTTACGA 58.941 61.111 0.00 0.00 44.74 3.43
2666 3215 0.903924 TTCCCGGTTACGATGGGTGA 60.904 55.000 0.00 0.00 43.75 4.02
2682 3231 2.423446 GATCGGGGCAGAGCGATT 59.577 61.111 0.00 0.00 0.00 3.34
2707 3258 2.120355 TTCTCTCGTACACGCACGCA 62.120 55.000 0.00 0.00 41.67 5.24
2740 3291 2.614734 GGCGTTGGGCTCTAACTAAACT 60.615 50.000 0.00 0.00 42.94 2.66
2756 3307 0.038251 AACTCGAGCGATTGCACTGA 60.038 50.000 13.61 0.71 46.23 3.41
2790 3341 1.359117 GAACCCGAGCGATCGATCA 59.641 57.895 30.28 0.00 34.64 2.92
2795 3346 1.010935 CCGAGCGATCGATCAATGGG 61.011 60.000 30.28 20.02 34.64 4.00
2826 3377 1.137086 ACCCGATCGAGTGATTCCTTG 59.863 52.381 18.66 0.00 34.09 3.61
2886 3438 3.132111 TGGATGAATAGTGAGCGTTGCTA 59.868 43.478 0.00 0.00 39.88 3.49
2904 3457 2.358195 GCTAGGGGGTTTGGATGAACAT 60.358 50.000 0.00 0.00 0.00 2.71
2906 3459 2.539302 AGGGGGTTTGGATGAACATTG 58.461 47.619 0.00 0.00 0.00 2.82
2931 3484 0.552367 TGGGGGTGGATGAACAGGAT 60.552 55.000 0.00 0.00 0.00 3.24
2933 3486 0.918983 GGGGTGGATGAACAGGATCA 59.081 55.000 0.00 0.00 0.00 2.92
2945 3498 1.667830 AGGATCACGTGGTGTTGCG 60.668 57.895 17.00 0.00 34.79 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.375013 CCACTTGGCTGGCAAATGC 60.375 57.895 18.38 0.00 41.14 3.56
3 4 0.320073 CACCACTTGGCTGGCAAATG 60.320 55.000 17.09 17.09 39.32 2.32
4 5 0.760189 ACACCACTTGGCTGGCAAAT 60.760 50.000 17.66 4.93 39.32 2.32
5 6 1.381056 ACACCACTTGGCTGGCAAA 60.381 52.632 17.66 2.39 39.32 3.68
7 8 2.519063 CACACCACTTGGCTGGCA 60.519 61.111 0.00 0.00 39.32 4.92
8 9 3.982241 GCACACCACTTGGCTGGC 61.982 66.667 0.00 0.00 39.32 4.85
9 10 3.297620 GGCACACCACTTGGCTGG 61.298 66.667 0.00 0.00 39.32 4.85
10 11 3.297620 GGGCACACCACTTGGCTG 61.298 66.667 0.00 0.00 39.45 4.85
11 12 2.983725 GAAGGGCACACCACTTGGCT 62.984 60.000 0.00 0.00 43.89 4.75
12 13 2.521708 AAGGGCACACCACTTGGC 60.522 61.111 0.00 0.00 43.89 4.52
13 14 0.540365 ATGAAGGGCACACCACTTGG 60.540 55.000 0.00 0.00 43.89 3.61
19 20 1.904287 TGTGTAATGAAGGGCACACC 58.096 50.000 0.00 0.00 40.41 4.16
50 51 5.794726 TGATCTAATGGGCATGATTTTGG 57.205 39.130 0.00 0.00 0.00 3.28
53 54 5.210430 TGGTTGATCTAATGGGCATGATTT 58.790 37.500 0.00 0.00 0.00 2.17
65 66 5.981088 AACATGTGCAATGGTTGATCTAA 57.019 34.783 0.00 0.00 0.00 2.10
67 68 4.281435 TGAAACATGTGCAATGGTTGATCT 59.719 37.500 14.29 0.00 0.00 2.75
73 74 5.467399 CAGAAAATGAAACATGTGCAATGGT 59.533 36.000 0.00 4.29 0.00 3.55
78 79 3.181468 TGCCAGAAAATGAAACATGTGCA 60.181 39.130 0.00 0.94 0.00 4.57
138 139 2.355197 CCCGACATTGAACTATGTGCA 58.645 47.619 6.61 0.00 38.80 4.57
139 140 1.670811 CCCCGACATTGAACTATGTGC 59.329 52.381 6.61 0.00 38.80 4.57
152 153 2.530661 AACCCCATGTCCCCGACA 60.531 61.111 0.00 0.00 46.90 4.35
180 181 2.286294 GCAGAATGATGCTAGGAACACG 59.714 50.000 0.00 0.00 43.07 4.49
183 184 3.539604 AGTGCAGAATGATGCTAGGAAC 58.460 45.455 4.25 0.00 46.63 3.62
186 187 4.056740 CACTAGTGCAGAATGATGCTAGG 58.943 47.826 10.54 0.00 46.63 3.02
187 188 4.744137 GTCACTAGTGCAGAATGATGCTAG 59.256 45.833 18.45 0.00 46.63 3.42
212 213 1.794714 AACTATGTCGCCCCTCATCT 58.205 50.000 0.00 0.00 0.00 2.90
239 240 4.862092 CAGTCGCGCCGAGATGCT 62.862 66.667 0.00 0.00 36.23 3.79
242 243 4.560856 GAGCAGTCGCGCCGAGAT 62.561 66.667 0.00 0.00 45.49 2.75
247 248 4.724602 TGAGTGAGCAGTCGCGCC 62.725 66.667 0.00 0.00 45.49 6.53
284 285 2.357517 AAAGCAGGCCGACAGTCG 60.358 61.111 16.50 16.50 40.07 4.18
286 287 2.281761 CCAAAGCAGGCCGACAGT 60.282 61.111 0.00 0.00 0.00 3.55
310 311 1.067142 GTTGTCGTCCCACATAGAGCA 60.067 52.381 0.00 0.00 0.00 4.26
320 321 2.040544 CAGCCATGGTTGTCGTCCC 61.041 63.158 19.77 0.00 0.00 4.46
359 361 1.865340 GACAGACGAGGACACCAAAAC 59.135 52.381 0.00 0.00 0.00 2.43
368 370 2.750166 GAGAGTTCATGACAGACGAGGA 59.250 50.000 0.00 0.00 0.00 3.71
415 717 6.323739 TCAGGAACATCTAGCACACATGTATA 59.676 38.462 0.00 0.00 30.37 1.47
420 722 3.369892 GGTCAGGAACATCTAGCACACAT 60.370 47.826 0.00 0.00 0.00 3.21
434 736 2.107366 TCGCATATGACAGGTCAGGAA 58.893 47.619 6.97 0.00 43.61 3.36
441 743 1.948834 TGGCAAATCGCATATGACAGG 59.051 47.619 6.97 0.00 45.17 4.00
467 769 9.851686 TCCAAATTAGCACTATCACAAGATTAT 57.148 29.630 0.00 0.00 35.67 1.28
480 782 9.084533 TGTTTAAACCTAATCCAAATTAGCACT 57.915 29.630 15.59 0.00 42.03 4.40
481 783 9.699703 TTGTTTAAACCTAATCCAAATTAGCAC 57.300 29.630 15.59 0.00 42.03 4.40
497 799 7.917720 TTCTTCGCTAATTGTTGTTTAAACC 57.082 32.000 15.59 1.97 0.00 3.27
507 809 9.884465 GCAATAGAAATATTCTTCGCTAATTGT 57.116 29.630 0.00 0.00 41.14 2.71
508 810 9.334693 GGCAATAGAAATATTCTTCGCTAATTG 57.665 33.333 0.00 3.09 41.14 2.32
511 813 8.621532 ATGGCAATAGAAATATTCTTCGCTAA 57.378 30.769 0.00 0.00 41.14 3.09
512 814 8.097038 AGATGGCAATAGAAATATTCTTCGCTA 58.903 33.333 0.00 0.00 41.14 4.26
514 816 7.118971 AGAGATGGCAATAGAAATATTCTTCGC 59.881 37.037 0.00 0.00 41.14 4.70
515 817 8.545229 AGAGATGGCAATAGAAATATTCTTCG 57.455 34.615 0.00 0.00 41.14 3.79
529 840 6.466885 ACTACGTAGTTTAGAGATGGCAAT 57.533 37.500 22.45 0.00 37.78 3.56
532 843 5.762218 TCCTACTACGTAGTTTAGAGATGGC 59.238 44.000 31.58 0.00 37.78 4.40
537 848 9.054922 AGCTTAATCCTACTACGTAGTTTAGAG 57.945 37.037 31.58 21.85 37.78 2.43
547 858 9.530633 AGACAATTTTAGCTTAATCCTACTACG 57.469 33.333 0.00 0.00 0.00 3.51
709 1025 6.327365 ACATGGAAGAAAACAAAAGAAGGGAT 59.673 34.615 0.00 0.00 0.00 3.85
711 1027 5.917462 ACATGGAAGAAAACAAAAGAAGGG 58.083 37.500 0.00 0.00 0.00 3.95
747 1076 0.382515 CTCTCCGACTCCGATTCCAC 59.617 60.000 0.00 0.00 38.22 4.02
819 1148 2.351276 GCAGAGGCCGGGAAAGAA 59.649 61.111 2.18 0.00 0.00 2.52
861 1192 1.142870 TGTGTTGTGGGGAAGAAGAGG 59.857 52.381 0.00 0.00 0.00 3.69
999 1341 0.972983 ATGGAGAGAGACACGGTGGG 60.973 60.000 13.48 0.00 0.00 4.61
1008 1350 1.473965 GCATGGCGAAATGGAGAGAGA 60.474 52.381 0.00 0.00 0.00 3.10
1009 1351 0.942962 GCATGGCGAAATGGAGAGAG 59.057 55.000 0.00 0.00 0.00 3.20
1010 1352 0.464373 GGCATGGCGAAATGGAGAGA 60.464 55.000 2.41 0.00 0.00 3.10
1011 1353 0.465097 AGGCATGGCGAAATGGAGAG 60.465 55.000 14.30 0.00 0.00 3.20
1096 1438 3.327404 GGCTTCCCGGGTTCCTGA 61.327 66.667 22.86 0.00 0.00 3.86
1149 1491 2.588034 GGTACGCCGGCATCTTCC 60.588 66.667 28.98 16.51 0.00 3.46
1403 1766 3.391382 GGCGTACACCTCCAGCCT 61.391 66.667 0.00 0.00 44.06 4.58
1578 1941 2.670934 CCACACACTCCTGCTGCC 60.671 66.667 0.00 0.00 0.00 4.85
1591 1957 0.533308 GCACGTACTTTGGGACCACA 60.533 55.000 0.00 0.00 0.00 4.17
2009 2494 6.034161 AGACACTACTAGCCGTTAAATTGT 57.966 37.500 0.00 0.00 0.00 2.71
2010 2495 6.331061 AGAGACACTACTAGCCGTTAAATTG 58.669 40.000 0.00 0.00 0.00 2.32
2013 2498 5.972107 AAGAGACACTACTAGCCGTTAAA 57.028 39.130 0.00 0.00 0.00 1.52
2024 2570 5.890424 AGAGTTGCTCTAAGAGACACTAC 57.110 43.478 0.00 0.00 39.28 2.73
2055 2601 1.037030 ATTGTGGCTATTGCACGGGG 61.037 55.000 0.66 0.00 41.91 5.73
2056 2602 0.101040 CATTGTGGCTATTGCACGGG 59.899 55.000 0.66 0.00 41.91 5.28
2057 2603 0.526096 GCATTGTGGCTATTGCACGG 60.526 55.000 0.66 0.00 41.91 4.94
2058 2604 0.862701 CGCATTGTGGCTATTGCACG 60.863 55.000 0.66 0.00 41.91 5.34
2059 2605 0.171007 ACGCATTGTGGCTATTGCAC 59.829 50.000 0.66 0.00 41.91 4.57
2063 2609 2.303163 TCGTACGCATTGTGGCTATT 57.697 45.000 11.24 0.00 0.00 1.73
2066 2612 1.635663 GCTTCGTACGCATTGTGGCT 61.636 55.000 11.24 0.00 0.00 4.75
2077 2623 2.792542 GCAAATGGAGCATGCTTCGTAC 60.793 50.000 23.61 10.62 37.12 3.67
2080 2626 0.171679 TGCAAATGGAGCATGCTTCG 59.828 50.000 23.61 8.01 40.66 3.79
2091 2637 2.496871 TGTAGCCTCCAAATGCAAATGG 59.503 45.455 13.53 13.53 38.09 3.16
2108 2654 3.692576 AGTTCGCGTGCTACTTATGTAG 58.307 45.455 5.77 10.67 46.59 2.74
2112 2658 2.422479 TCTGAGTTCGCGTGCTACTTAT 59.578 45.455 5.77 0.00 0.00 1.73
2113 2659 1.808343 TCTGAGTTCGCGTGCTACTTA 59.192 47.619 5.77 2.16 0.00 2.24
2115 2661 0.169230 CTCTGAGTTCGCGTGCTACT 59.831 55.000 5.77 5.81 0.00 2.57
2117 2663 0.168348 GACTCTGAGTTCGCGTGCTA 59.832 55.000 12.27 0.00 0.00 3.49
2123 2669 2.826979 TATGACGACTCTGAGTTCGC 57.173 50.000 21.22 16.35 0.00 4.70
2125 2671 5.968848 GTGAAGATATGACGACTCTGAGTTC 59.031 44.000 12.27 7.14 0.00 3.01
2127 2673 4.336993 GGTGAAGATATGACGACTCTGAGT 59.663 45.833 10.66 10.66 0.00 3.41
2131 2677 4.889995 TGATGGTGAAGATATGACGACTCT 59.110 41.667 0.00 0.00 0.00 3.24
2133 2679 5.798125 ATGATGGTGAAGATATGACGACT 57.202 39.130 0.00 0.00 0.00 4.18
2134 2680 8.539770 AATTATGATGGTGAAGATATGACGAC 57.460 34.615 0.00 0.00 0.00 4.34
2169 2715 4.792068 AGGGAATCTGAGTGTTTGTGAAA 58.208 39.130 0.00 0.00 0.00 2.69
2170 2716 4.389374 GAGGGAATCTGAGTGTTTGTGAA 58.611 43.478 0.00 0.00 0.00 3.18
2171 2717 3.244561 GGAGGGAATCTGAGTGTTTGTGA 60.245 47.826 0.00 0.00 0.00 3.58
2172 2718 3.077359 GGAGGGAATCTGAGTGTTTGTG 58.923 50.000 0.00 0.00 0.00 3.33
2173 2719 2.711009 TGGAGGGAATCTGAGTGTTTGT 59.289 45.455 0.00 0.00 0.00 2.83
2182 2728 6.840780 AAGTTTACATTTGGAGGGAATCTG 57.159 37.500 0.00 0.00 0.00 2.90
2184 2730 7.759886 GCTAAAAGTTTACATTTGGAGGGAATC 59.240 37.037 0.00 0.00 0.00 2.52
2193 2739 9.462174 TCTTGATGTGCTAAAAGTTTACATTTG 57.538 29.630 3.80 0.00 32.58 2.32
2197 2743 9.296400 GTTTTCTTGATGTGCTAAAAGTTTACA 57.704 29.630 0.00 0.00 0.00 2.41
2204 2750 6.200665 GTGCATGTTTTCTTGATGTGCTAAAA 59.799 34.615 0.00 0.00 32.67 1.52
2230 2776 5.463061 GTGCATGCAACTTGTCAAAAACTAT 59.537 36.000 24.58 0.00 0.00 2.12
2238 2784 2.955477 TTTGTGCATGCAACTTGTCA 57.045 40.000 24.58 12.40 0.00 3.58
2252 2798 4.330074 TGTGCCGGTTTAAATGTTTTTGTG 59.670 37.500 1.90 0.00 0.00 3.33
2270 2816 1.226746 GTGACTTGTACCTGTGTGCC 58.773 55.000 0.00 0.00 0.00 5.01
2272 2818 5.390885 GCAATATGTGACTTGTACCTGTGTG 60.391 44.000 0.00 0.00 0.00 3.82
2278 2824 3.065371 GGCTGCAATATGTGACTTGTACC 59.935 47.826 0.50 0.00 0.00 3.34
2296 2842 3.434319 GGATGGTGCACACGGCTG 61.434 66.667 20.43 0.00 45.15 4.85
2297 2843 4.722700 GGGATGGTGCACACGGCT 62.723 66.667 20.43 0.00 45.15 5.52
2299 2845 2.045045 ATGGGATGGTGCACACGG 60.045 61.111 20.43 0.00 0.00 4.94
2338 2884 1.521681 GGAACCTCGAAGGATGGCG 60.522 63.158 7.76 0.00 37.67 5.69
2345 2891 0.317479 ACGTTCCAGGAACCTCGAAG 59.683 55.000 24.33 12.82 39.14 3.79
2349 2895 3.132289 TGATCATACGTTCCAGGAACCTC 59.868 47.826 24.33 12.65 39.14 3.85
2355 2901 6.272822 TGAGATATGATCATACGTTCCAGG 57.727 41.667 17.60 0.00 0.00 4.45
2359 2905 6.810676 AGTGCATGAGATATGATCATACGTTC 59.189 38.462 17.60 14.56 35.64 3.95
2363 2909 8.992835 TTGTAGTGCATGAGATATGATCATAC 57.007 34.615 17.60 11.40 35.64 2.39
2406 2953 1.025812 TGCGTTCGGTCCAAAATGTT 58.974 45.000 0.00 0.00 0.00 2.71
2478 3025 3.615937 CAGCACATCTATGATCATACCGC 59.384 47.826 11.49 9.44 0.00 5.68
2485 3032 2.636893 AGGACCCAGCACATCTATGATC 59.363 50.000 0.00 0.00 0.00 2.92
2498 3045 7.519032 TTTTTGTCATAAAAGTAGGACCCAG 57.481 36.000 0.00 0.00 39.73 4.45
2550 3098 2.833582 GTCTCCGATCCGCCCAGA 60.834 66.667 0.00 0.00 0.00 3.86
2621 3170 2.289694 CCGATAATTTCCTCGCCCTCAT 60.290 50.000 0.00 0.00 33.63 2.90
2659 3208 2.366837 TCTGCCCCGATCACCCAT 60.367 61.111 0.00 0.00 0.00 4.00
2666 3215 2.423446 GAATCGCTCTGCCCCGAT 59.577 61.111 0.00 0.00 45.17 4.18
2682 3231 3.373020 GTGTACGAGAGAAACGCGA 57.627 52.632 15.93 0.00 44.01 5.87
2707 3258 3.920196 AACGCCTCGAACCCACGT 61.920 61.111 0.00 0.00 38.88 4.49
2715 3266 1.980232 TTAGAGCCCAACGCCTCGA 60.980 57.895 0.00 0.00 38.78 4.04
2736 3287 0.792640 CAGTGCAATCGCTCGAGTTT 59.207 50.000 15.13 2.98 39.64 2.66
2740 3291 0.737367 CCTTCAGTGCAATCGCTCGA 60.737 55.000 0.00 0.00 39.64 4.04
2795 3346 2.921754 CTCGATCGGGTTCAGTTAACAC 59.078 50.000 16.41 0.00 40.08 3.32
2826 3377 2.275318 CTTCAGTTAGCAGCAGTAGCC 58.725 52.381 0.00 0.00 43.56 3.93
2886 3438 2.539302 CAATGTTCATCCAAACCCCCT 58.461 47.619 0.00 0.00 0.00 4.79
2931 3484 1.880796 CAGACGCAACACCACGTGA 60.881 57.895 19.30 0.00 43.71 4.35
2933 3486 2.377628 ATCCAGACGCAACACCACGT 62.378 55.000 0.00 0.00 46.91 4.49
2945 3498 0.253327 GGGGTCCTGTTCATCCAGAC 59.747 60.000 0.00 0.00 34.23 3.51


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

AutoCloner maintained by Alex Coulton.