Multiple sequence alignment - TraesCS2A01G233000

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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 TraesCS2A01G233000 chr2A 100.000 6555 0 0 1 6555 277608859 277602305 0.000000e+00 12105.0
1 TraesCS2A01G233000 chr2A 92.677 792 23 3 1 790 32943202 32943960 0.000000e+00 1109.0
2 TraesCS2A01G233000 chr2A 80.964 394 57 16 193 577 32943447 32943831 4.970000e-76 296.0
3 TraesCS2A01G233000 chr2A 82.216 343 48 11 233 569 277608552 277608217 3.870000e-72 283.0
4 TraesCS2A01G233000 chr2D 93.664 3283 113 30 3301 6555 205616264 205619479 0.000000e+00 4822.0
5 TraesCS2A01G233000 chr2D 91.988 1922 87 26 834 2730 205613979 205615858 0.000000e+00 2634.0
6 TraesCS2A01G233000 chr2D 94.847 621 21 1 176 796 503572239 503572848 0.000000e+00 959.0
7 TraesCS2A01G233000 chr2D 95.283 318 14 1 2967 3283 205615856 205616173 2.730000e-138 503.0
8 TraesCS2A01G233000 chr2D 89.712 243 25 0 2726 2968 126046529 126046771 1.770000e-80 311.0
9 TraesCS2A01G233000 chr2D 89.669 242 25 0 2728 2969 78385629 78385388 6.380000e-80 309.0
10 TraesCS2A01G233000 chr2B 94.252 2488 115 13 834 3305 259775904 259778379 0.000000e+00 3777.0
11 TraesCS2A01G233000 chr2B 94.193 1257 52 16 3301 4552 259778458 259779698 0.000000e+00 1897.0
12 TraesCS2A01G233000 chr2B 91.545 1301 58 28 4592 5870 259780485 259781755 0.000000e+00 1746.0
13 TraesCS2A01G233000 chr2B 92.609 690 41 5 5868 6555 259782004 259782685 0.000000e+00 983.0
14 TraesCS2A01G233000 chr2B 89.091 55 4 1 90 142 580001136 580001082 4.240000e-07 67.6
15 TraesCS2A01G233000 chr1A 94.313 844 29 3 1 836 219383519 219384351 0.000000e+00 1275.0
16 TraesCS2A01G233000 chr1A 89.024 246 27 0 2724 2969 579953980 579954225 8.260000e-79 305.0
17 TraesCS2A01G233000 chr3A 94.293 841 29 3 1 833 614232644 614233473 0.000000e+00 1269.0
18 TraesCS2A01G233000 chr4A 93.972 846 29 8 1 842 56265868 56265041 0.000000e+00 1260.0
19 TraesCS2A01G233000 chr6D 93.341 841 34 5 1 833 365734158 365733332 0.000000e+00 1223.0
20 TraesCS2A01G233000 chr1D 93.152 847 37 5 1 838 224396989 224397823 0.000000e+00 1223.0
21 TraesCS2A01G233000 chr1D 89.344 244 26 0 2725 2968 378551665 378551908 2.300000e-79 307.0
22 TraesCS2A01G233000 chr5D 96.675 391 11 1 1 389 46088495 46088885 0.000000e+00 649.0
23 TraesCS2A01G233000 chr5D 91.494 482 22 4 364 839 46089136 46089604 0.000000e+00 645.0
24 TraesCS2A01G233000 chr5A 91.704 446 19 7 394 833 600355435 600355002 2.610000e-168 603.0
25 TraesCS2A01G233000 chr5A 85.120 457 55 10 1 449 600355631 600355180 7.750000e-124 455.0
26 TraesCS2A01G233000 chr3D 90.244 246 23 1 2723 2968 236629046 236628802 2.950000e-83 320.0
27 TraesCS2A01G233000 chr3D 89.069 247 25 2 2724 2968 339249294 339249540 8.260000e-79 305.0
28 TraesCS2A01G233000 chr7A 90.123 243 24 0 2726 2968 459619366 459619124 3.810000e-82 316.0
29 TraesCS2A01G233000 chr7A 84.375 96 13 2 556 651 69714082 69713989 7.000000e-15 93.5
30 TraesCS2A01G233000 chr4D 90.083 242 24 0 2727 2968 378745065 378744824 1.370000e-81 315.0
31 TraesCS2A01G233000 chr6A 83.696 92 10 5 4182 4271 19885458 19885546 1.510000e-11 82.4
32 TraesCS2A01G233000 chr7B 86.275 51 6 1 4242 4291 593642622 593642572 3.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G233000 chr2A 277602305 277608859 6554 True 6194.00 12105 91.10800 1 6555 2 chr2A.!!$R1 6554
1 TraesCS2A01G233000 chr2A 32943202 32943960 758 False 702.50 1109 86.82050 1 790 2 chr2A.!!$F1 789
2 TraesCS2A01G233000 chr2D 205613979 205619479 5500 False 2653.00 4822 93.64500 834 6555 3 chr2D.!!$F3 5721
3 TraesCS2A01G233000 chr2D 503572239 503572848 609 False 959.00 959 94.84700 176 796 1 chr2D.!!$F2 620
4 TraesCS2A01G233000 chr2B 259775904 259782685 6781 False 2100.75 3777 93.14975 834 6555 4 chr2B.!!$F1 5721
5 TraesCS2A01G233000 chr1A 219383519 219384351 832 False 1275.00 1275 94.31300 1 836 1 chr1A.!!$F1 835
6 TraesCS2A01G233000 chr3A 614232644 614233473 829 False 1269.00 1269 94.29300 1 833 1 chr3A.!!$F1 832
7 TraesCS2A01G233000 chr4A 56265041 56265868 827 True 1260.00 1260 93.97200 1 842 1 chr4A.!!$R1 841
8 TraesCS2A01G233000 chr6D 365733332 365734158 826 True 1223.00 1223 93.34100 1 833 1 chr6D.!!$R1 832
9 TraesCS2A01G233000 chr1D 224396989 224397823 834 False 1223.00 1223 93.15200 1 838 1 chr1D.!!$F1 837
10 TraesCS2A01G233000 chr5D 46088495 46089604 1109 False 647.00 649 94.08450 1 839 2 chr5D.!!$F1 838
11 TraesCS2A01G233000 chr5A 600355002 600355631 629 True 529.00 603 88.41200 1 833 2 chr5A.!!$R1 832

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
392 715 1.160137 GAGTTGCAATGGAGCTTCGT 58.840 50.000 0.59 0.0 34.99 3.85 F
1020 1350 0.689412 AGAAGCCCTACTCTGCCTCC 60.689 60.000 0.00 0.0 0.00 4.30 F
1620 1963 0.622136 TGAATGGTGATGCTCTGGCT 59.378 50.000 0.00 0.0 39.59 4.75 F
2580 2938 0.037512 TCAGCTCTCTGACTGCAAGC 60.038 55.000 0.00 0.0 43.95 4.01 F
2633 2993 0.618458 TTGCATCTGTGTAGTCCCCC 59.382 55.000 0.00 0.0 0.00 5.40 F
2684 3044 1.777101 TGCTTAATTGGCGTGTTTGC 58.223 45.000 0.00 0.0 0.00 3.68 F
4541 5007 1.270826 CAGCTGAAGGTTCGTCTCTCA 59.729 52.381 8.42 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 1844 0.395686 TCAGAGAAGCAGCAGCAGTT 59.604 50.000 3.17 0.0 45.49 3.16 R
2108 2451 1.006922 GCAGCCCAACAGCAGTTTC 60.007 57.895 0.00 0.0 35.28 2.78 R
3217 3579 1.004610 CTGCACGCCATCTGTTTATCG 60.005 52.381 0.00 0.0 0.00 2.92 R
4011 4460 0.947244 AGGAGCAACAACAAGCTTCG 59.053 50.000 0.00 0.0 41.33 3.79 R
4541 5007 1.077068 CTCCCCGCAGAGAGAGAGT 60.077 63.158 0.00 0.0 35.82 3.24 R
4681 5891 1.168714 GAAGCACTTTGCCCCTACAG 58.831 55.000 0.00 0.0 46.52 2.74 R
6032 7518 1.597797 CTGTTTGGCGGCCACATGAT 61.598 55.000 23.78 0.0 30.78 2.45 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
123 124 3.133014 CGACCCCATGATCTCGCT 58.867 61.111 0.00 0.00 0.00 4.93
153 156 3.787676 CTGCAACGCGAATCGGCA 61.788 61.111 15.93 13.55 43.86 5.69
187 190 1.965930 GCAAGCGACATGTGACCCA 60.966 57.895 1.15 0.00 0.00 4.51
231 234 4.954118 TGGACCAGGTCGGGCTGT 62.954 66.667 13.80 0.00 45.62 4.40
293 318 2.044252 CAGGGCTGCAATGGAGCT 60.044 61.111 25.07 4.62 36.63 4.09
294 319 2.119655 CAGGGCTGCAATGGAGCTC 61.120 63.158 25.07 22.40 37.17 4.09
295 320 3.207669 GGGCTGCAATGGAGCTCG 61.208 66.667 25.07 0.00 36.63 5.03
296 321 2.124983 GGCTGCAATGGAGCTCGA 60.125 61.111 25.07 3.70 36.63 4.04
297 322 2.467826 GGCTGCAATGGAGCTCGAC 61.468 63.158 25.07 5.86 36.63 4.20
298 323 2.467826 GCTGCAATGGAGCTCGACC 61.468 63.158 19.55 0.00 33.37 4.79
299 324 2.125552 TGCAATGGAGCTCGACCG 60.126 61.111 7.83 0.00 34.99 4.79
300 325 2.892425 GCAATGGAGCTCGACCGG 60.892 66.667 7.83 0.00 0.00 5.28
301 326 2.892640 CAATGGAGCTCGACCGGA 59.107 61.111 9.46 0.00 0.00 5.14
302 327 1.227089 CAATGGAGCTCGACCGGAG 60.227 63.158 9.46 0.85 46.06 4.63
303 328 1.682684 AATGGAGCTCGACCGGAGT 60.683 57.895 9.46 0.00 45.03 3.85
304 329 1.258445 AATGGAGCTCGACCGGAGTT 61.258 55.000 9.46 0.00 45.03 3.01
305 330 1.949847 ATGGAGCTCGACCGGAGTTG 61.950 60.000 9.46 0.00 45.03 3.16
306 331 2.507324 GAGCTCGACCGGAGTTGC 60.507 66.667 9.46 7.35 45.03 4.17
307 332 3.282745 GAGCTCGACCGGAGTTGCA 62.283 63.158 9.46 0.00 45.03 4.08
308 333 2.357034 GCTCGACCGGAGTTGCAA 60.357 61.111 9.46 0.00 45.03 4.08
309 334 1.741770 GCTCGACCGGAGTTGCAAT 60.742 57.895 9.46 0.00 45.03 3.56
310 335 1.970917 GCTCGACCGGAGTTGCAATG 61.971 60.000 9.46 0.00 45.03 2.82
392 715 1.160137 GAGTTGCAATGGAGCTTCGT 58.840 50.000 0.59 0.00 34.99 3.85
424 747 4.988598 CTGCCTTGGACCACGCGT 62.989 66.667 5.58 5.58 0.00 6.01
537 860 3.753434 CGGAGCCGTCAGAGCTGT 61.753 66.667 0.00 0.00 41.75 4.40
668 991 1.647545 AATCAATCCGTGGTGCTGCG 61.648 55.000 0.00 0.00 0.00 5.18
669 992 2.803155 ATCAATCCGTGGTGCTGCGT 62.803 55.000 0.00 0.00 0.00 5.24
670 993 2.281484 AATCCGTGGTGCTGCGTT 60.281 55.556 0.00 0.00 0.00 4.84
671 994 2.616330 AATCCGTGGTGCTGCGTTG 61.616 57.895 0.00 0.00 0.00 4.10
674 997 3.716006 CGTGGTGCTGCGTTGGAG 61.716 66.667 0.00 0.00 0.00 3.86
675 998 4.030452 GTGGTGCTGCGTTGGAGC 62.030 66.667 3.15 3.15 36.95 4.70
676 999 4.254709 TGGTGCTGCGTTGGAGCT 62.255 61.111 11.54 0.00 37.35 4.09
677 1000 3.730761 GGTGCTGCGTTGGAGCTG 61.731 66.667 11.54 0.00 37.35 4.24
678 1001 2.974698 GTGCTGCGTTGGAGCTGT 60.975 61.111 11.54 0.00 37.35 4.40
776 1099 2.672996 GCCACCAGTGCACCGATT 60.673 61.111 14.63 0.00 0.00 3.34
1020 1350 0.689412 AGAAGCCCTACTCTGCCTCC 60.689 60.000 0.00 0.00 0.00 4.30
1042 1372 4.489771 CCCCGAATTGCCGCCTCT 62.490 66.667 0.00 0.00 0.00 3.69
1043 1373 2.897350 CCCGAATTGCCGCCTCTC 60.897 66.667 0.00 0.00 0.00 3.20
1044 1374 2.897350 CCGAATTGCCGCCTCTCC 60.897 66.667 0.00 0.00 0.00 3.71
1045 1375 2.187946 CGAATTGCCGCCTCTCCT 59.812 61.111 0.00 0.00 0.00 3.69
1046 1376 1.884926 CGAATTGCCGCCTCTCCTC 60.885 63.158 0.00 0.00 0.00 3.71
1047 1377 1.524482 GAATTGCCGCCTCTCCTCT 59.476 57.895 0.00 0.00 0.00 3.69
1169 1505 1.066143 CGGCCTCATCAAAGGTACTGT 60.066 52.381 0.00 0.00 40.86 3.55
1171 1507 2.027192 GGCCTCATCAAAGGTACTGTCA 60.027 50.000 0.00 0.00 40.86 3.58
1394 1737 1.949525 CTCTACAGCTCAGCTCTCTCC 59.050 57.143 0.00 0.00 36.40 3.71
1396 1739 0.749818 TACAGCTCAGCTCTCTCCCG 60.750 60.000 0.00 0.00 36.40 5.14
1398 1741 0.749818 CAGCTCAGCTCTCTCCCGTA 60.750 60.000 0.00 0.00 36.40 4.02
1418 1761 2.700773 GCCCTTGGTGAATCACGGC 61.701 63.158 12.82 12.82 34.83 5.68
1433 1776 2.297315 TCACGGCTGCTCATTCCTATAG 59.703 50.000 0.00 0.00 0.00 1.31
1501 1844 1.342174 GGAAGAACGGTGTGGTGAGTA 59.658 52.381 0.00 0.00 0.00 2.59
1518 1861 1.622811 AGTAACTGCTGCTGCTTCTCT 59.377 47.619 17.00 6.17 40.48 3.10
1541 1884 0.887387 TTGGGACGCTTACCTTGTGC 60.887 55.000 0.00 0.00 0.00 4.57
1599 1942 2.957402 AGGTTGAGTTGCTGAATCCA 57.043 45.000 0.00 0.00 0.00 3.41
1600 1943 3.446442 AGGTTGAGTTGCTGAATCCAT 57.554 42.857 0.00 0.00 0.00 3.41
1620 1963 0.622136 TGAATGGTGATGCTCTGGCT 59.378 50.000 0.00 0.00 39.59 4.75
1710 2053 2.095567 CCTCTTCAGAAAACATGCACCG 60.096 50.000 0.00 0.00 0.00 4.94
1738 2081 4.419522 ACCACGTAATTTTCACATGCTC 57.580 40.909 0.00 0.00 0.00 4.26
1779 2122 8.865420 ATAGATATCTTACCACACGTCTACAT 57.135 34.615 11.25 0.00 0.00 2.29
1788 2131 5.191426 ACCACACGTCTACATCTGTAGTAT 58.809 41.667 15.13 2.32 46.08 2.12
1789 2132 5.651139 ACCACACGTCTACATCTGTAGTATT 59.349 40.000 15.13 0.96 46.08 1.89
1790 2133 6.825213 ACCACACGTCTACATCTGTAGTATTA 59.175 38.462 15.13 0.00 46.08 0.98
1792 2135 7.856398 CCACACGTCTACATCTGTAGTATTAAG 59.144 40.741 15.13 3.62 46.08 1.85
1793 2136 8.396390 CACACGTCTACATCTGTAGTATTAAGT 58.604 37.037 15.13 4.14 46.08 2.24
1794 2137 9.605275 ACACGTCTACATCTGTAGTATTAAGTA 57.395 33.333 15.13 0.00 46.08 2.24
1830 2173 6.590178 TGAAAAGTTCATCGCTCTTGTGCG 62.590 45.833 10.28 10.28 45.13 5.34
1860 2203 8.932610 TGGTGATATTGGCCAAATTGTATTTAT 58.067 29.630 24.71 12.88 0.00 1.40
1951 2294 3.057174 TCTGTTGCAAAAGAAAACACGGT 60.057 39.130 17.22 0.00 30.93 4.83
1988 2331 0.899717 GGCCATCAAGCACTTGGGAA 60.900 55.000 10.35 0.00 40.78 3.97
2029 2372 3.489355 TGCAGTTTTCATCTGTGGATGT 58.511 40.909 5.99 0.00 46.74 3.06
2051 2394 6.344500 TGTTGGTGAAAACTATGCAATGTTT 58.656 32.000 12.67 12.67 37.92 2.83
2091 2434 2.210116 ACCTTTAGCATGCGATTACCG 58.790 47.619 13.01 0.40 42.21 4.02
2106 2449 5.860182 GCGATTACCGAATACTGTATGCTTA 59.140 40.000 0.22 0.00 41.76 3.09
2108 2451 7.410513 GCGATTACCGAATACTGTATGCTTAAG 60.411 40.741 0.22 0.00 41.76 1.85
2131 2474 1.531128 TGCTGTTGGGCTGCATTCA 60.531 52.632 0.50 0.00 45.14 2.57
2321 2666 5.718649 TTTGACTTATTAGCTGACATCGC 57.281 39.130 0.00 0.00 0.00 4.58
2339 2684 5.353956 ACATCGCAGCAAACATTTATCTGTA 59.646 36.000 0.00 0.16 0.00 2.74
2538 2896 5.348179 TCTTGTTTGCTCAATGTTTGTGTTG 59.652 36.000 0.00 0.00 0.00 3.33
2580 2938 0.037512 TCAGCTCTCTGACTGCAAGC 60.038 55.000 0.00 0.00 43.95 4.01
2616 2976 5.010516 TGGGGTTTTGTTATGATGTCTGTTG 59.989 40.000 0.00 0.00 0.00 3.33
2633 2993 0.618458 TTGCATCTGTGTAGTCCCCC 59.382 55.000 0.00 0.00 0.00 5.40
2683 3043 4.447054 TCATTTGCTTAATTGGCGTGTTTG 59.553 37.500 0.00 0.00 0.00 2.93
2684 3044 1.777101 TGCTTAATTGGCGTGTTTGC 58.223 45.000 0.00 0.00 0.00 3.68
2748 3108 6.136857 TGCTACTCCCTCCATCCATATATAC 58.863 44.000 0.00 0.00 0.00 1.47
2760 3120 5.630415 TCCATATATACAGGGCCTAATGC 57.370 43.478 5.28 0.00 40.16 3.56
2761 3121 4.100963 TCCATATATACAGGGCCTAATGCG 59.899 45.833 5.28 0.00 42.61 4.73
2850 3211 2.795329 TCATTGGAAGCTCCTTTCACC 58.205 47.619 0.00 0.00 37.46 4.02
2868 3229 3.113322 CACCTACGAATGTGACGGTATG 58.887 50.000 0.00 0.00 34.37 2.39
2892 3253 5.569059 GCTTTGTGTAACTTGCATGTCATAC 59.431 40.000 5.61 6.66 38.04 2.39
2947 3308 2.750712 TGAAAAACGCATTAGGCCCTAC 59.249 45.455 0.00 0.00 40.31 3.18
2948 3309 2.801077 AAAACGCATTAGGCCCTACT 57.199 45.000 0.00 0.00 40.31 2.57
3217 3579 4.894784 TCCTTTGACATGAGAACAGGTAC 58.105 43.478 0.00 0.00 41.15 3.34
3231 3593 3.793559 ACAGGTACGATAAACAGATGGC 58.206 45.455 0.00 0.00 0.00 4.40
3250 3612 2.444351 GCGTGCAGTATCTTTCAATGC 58.556 47.619 0.00 0.00 37.40 3.56
3298 3660 6.260050 TGCCTTTTCTGTCTAGTGTTAAAGTG 59.740 38.462 0.00 0.00 0.00 3.16
3367 3812 6.892658 TCATGTTTGCTGTTTTGTATAGGT 57.107 33.333 0.00 0.00 0.00 3.08
3506 3954 9.534565 TTATCAGCATTTCTACATGTTAGAGTC 57.465 33.333 2.30 0.00 0.00 3.36
3507 3955 7.175347 TCAGCATTTCTACATGTTAGAGTCT 57.825 36.000 2.30 0.00 0.00 3.24
3658 4106 7.610331 ACAGTGTTGTGATTGGTGTGTACCT 62.610 44.000 0.00 0.00 41.04 3.08
3736 4184 2.803956 TCGATAGTTAGGCATCCGGAT 58.196 47.619 12.38 12.38 37.40 4.18
3757 4205 4.226427 TCTGCCTTTGATAGCATCTTGT 57.774 40.909 0.00 0.00 38.56 3.16
3765 4213 4.558226 TGATAGCATCTTGTGGTGAGTT 57.442 40.909 0.00 0.00 39.30 3.01
3774 4222 8.462016 AGCATCTTGTGGTGAGTTATAAATTTC 58.538 33.333 0.00 0.00 37.12 2.17
4048 4497 5.835257 GCTCCTTGCAATTAATTGATGCTA 58.165 37.500 28.33 12.29 40.14 3.49
4085 4534 3.058293 TGCTCTAATTGTTTTCTGGTGCG 60.058 43.478 0.00 0.00 0.00 5.34
4103 4554 3.663564 GTGCGTTTTGACATGTGTGTATG 59.336 43.478 1.15 0.00 39.09 2.39
4214 4665 6.825721 CCCTCCATATCAAACTATAAGATGCC 59.174 42.308 0.00 0.00 0.00 4.40
4324 4775 4.970003 GCAAGTTCATTTATACATGTCGGC 59.030 41.667 0.00 0.00 0.00 5.54
4541 5007 1.270826 CAGCTGAAGGTTCGTCTCTCA 59.729 52.381 8.42 0.00 0.00 3.27
4574 5050 4.879545 TGCGGGGAGTTTCTTATGTATTTC 59.120 41.667 0.00 0.00 0.00 2.17
4641 5851 3.580895 TGGTAAGTTATGTGAGAGTGGCA 59.419 43.478 0.00 0.00 0.00 4.92
4681 5891 2.677836 TGTTATCTCGAATGGTGCTTGC 59.322 45.455 0.00 0.00 0.00 4.01
4686 5896 1.662629 CTCGAATGGTGCTTGCTGTAG 59.337 52.381 0.00 0.00 0.00 2.74
4702 5913 0.965866 GTAGGGGCAAAGTGCTTCCC 60.966 60.000 6.48 6.48 42.85 3.97
4996 6223 5.649831 AGAAGAATGTATTGGTTGAAGAGGC 59.350 40.000 0.00 0.00 0.00 4.70
5066 6296 4.213059 GCAGTCAGAAAGGACAAGAAGAAG 59.787 45.833 0.00 0.00 40.29 2.85
5078 6308 7.216494 AGGACAAGAAGAAGAAGAAGAAGAAG 58.784 38.462 0.00 0.00 0.00 2.85
5079 6309 7.070571 AGGACAAGAAGAAGAAGAAGAAGAAGA 59.929 37.037 0.00 0.00 0.00 2.87
5080 6310 7.713073 GGACAAGAAGAAGAAGAAGAAGAAGAA 59.287 37.037 0.00 0.00 0.00 2.52
5081 6311 8.661352 ACAAGAAGAAGAAGAAGAAGAAGAAG 57.339 34.615 0.00 0.00 0.00 2.85
5082 6312 8.482128 ACAAGAAGAAGAAGAAGAAGAAGAAGA 58.518 33.333 0.00 0.00 0.00 2.87
5083 6313 9.323985 CAAGAAGAAGAAGAAGAAGAAGAAGAA 57.676 33.333 0.00 0.00 0.00 2.52
5084 6314 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
5085 6315 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
5086 6316 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
5087 6317 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
5088 6318 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
5089 6319 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
5090 6320 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
5091 6321 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
5092 6322 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
5093 6323 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
5094 6324 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
5095 6325 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
5123 6353 7.923344 ACTGTTATAGAGGATGATGAAGAAACG 59.077 37.037 0.00 0.00 0.00 3.60
5137 6367 0.872388 GAAACGCAAATGGTCGACCT 59.128 50.000 33.39 17.38 36.82 3.85
5146 6376 1.866015 ATGGTCGACCTGGATGAAGA 58.134 50.000 33.39 11.97 36.82 2.87
5230 6460 1.407989 GGAAGGAACTCAGATGGCTGG 60.408 57.143 0.00 0.00 42.53 4.85
5553 6785 9.924650 GAACGGTATGGTTCATTTATACTATCT 57.075 33.333 0.88 0.00 44.44 1.98
5554 6786 9.924650 AACGGTATGGTTCATTTATACTATCTC 57.075 33.333 0.00 0.00 0.00 2.75
5569 6801 7.744087 ATACTATCTCATCTGACTCTGTGTC 57.256 40.000 3.03 3.03 45.54 3.67
5615 6847 6.331061 CGAAGTAGCAATGGTCTAGTTTAGT 58.669 40.000 0.00 0.00 31.75 2.24
5659 6891 5.708948 TGGTGTAGTGAAATTAATGCAAGC 58.291 37.500 0.00 0.00 0.00 4.01
5718 6950 4.785346 ATGTGTAGGATCTCTGCCAATT 57.215 40.909 0.00 0.00 0.00 2.32
5757 6989 2.503331 TGTATGCAAGTGTTGGGTGAG 58.497 47.619 0.00 0.00 0.00 3.51
5776 7008 5.183331 GGTGAGCATATAAGATACGGAGTCA 59.817 44.000 0.00 0.00 43.93 3.41
5821 7053 8.511604 AACCATTTCGATAATTTCATGAGACT 57.488 30.769 0.00 0.00 0.00 3.24
5848 7080 9.097257 AGTTGACCAAAATTGATTTTTACACAG 57.903 29.630 0.00 0.00 37.86 3.66
5849 7081 8.878769 GTTGACCAAAATTGATTTTTACACAGT 58.121 29.630 0.00 0.00 37.86 3.55
5930 7416 5.582665 CCTTTGCTCTCACCTGTATAAACTC 59.417 44.000 0.00 0.00 0.00 3.01
5932 7418 3.117046 GCTCTCACCTGTATAAACTCGC 58.883 50.000 0.00 0.00 0.00 5.03
5952 7438 5.670485 TCGCATTAACTTGTCTCCATATGT 58.330 37.500 1.24 0.00 0.00 2.29
5985 7471 9.566432 GGAAGGATTCTGTCAATCTTATTATGT 57.434 33.333 0.00 0.00 46.56 2.29
6009 7495 5.893255 TGACAGCCAAGCCATATAATTTTCT 59.107 36.000 0.00 0.00 0.00 2.52
6012 7498 4.650588 AGCCAAGCCATATAATTTTCTGCA 59.349 37.500 0.00 0.00 0.00 4.41
6032 7518 4.870363 GCAATCTTTCTTTGCTACCACAA 58.130 39.130 1.36 0.00 44.71 3.33
6138 7624 2.289002 GGCGATGTCATGATTCTCAACC 59.711 50.000 0.00 0.00 0.00 3.77
6276 7762 3.264193 TCTCCTGTACAAAGTGATGGCAT 59.736 43.478 0.00 0.00 0.00 4.40
6304 7790 9.994432 CCAGTTACTCATCAGAAAAACATAATC 57.006 33.333 0.00 0.00 0.00 1.75
6334 7820 3.403038 AGTCCTCAACTTTTCATCACCG 58.597 45.455 0.00 0.00 33.03 4.94
6363 7849 7.973048 TGGTTGTGATAGTTAAGAGATACCT 57.027 36.000 0.00 0.00 0.00 3.08
6434 7921 2.562298 TCCATTGGTTTTGGCTGATGAC 59.438 45.455 1.86 0.00 34.06 3.06
6478 7965 3.006110 CCTGTTTCAAGTCATGGCATTGT 59.994 43.478 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 124 1.227118 TTGCAGCGTCACTTCGACA 60.227 52.632 0.00 0.00 45.70 4.35
289 314 2.507324 GCAACTCCGGTCGAGCTC 60.507 66.667 13.48 2.73 43.01 4.09
290 315 2.172483 ATTGCAACTCCGGTCGAGCT 62.172 55.000 13.48 0.00 43.01 4.09
291 316 1.741770 ATTGCAACTCCGGTCGAGC 60.742 57.895 0.00 4.06 43.01 5.03
292 317 1.361668 CCATTGCAACTCCGGTCGAG 61.362 60.000 0.00 0.00 44.95 4.04
293 318 1.375396 CCATTGCAACTCCGGTCGA 60.375 57.895 0.00 0.00 0.00 4.20
294 319 1.361668 CTCCATTGCAACTCCGGTCG 61.362 60.000 0.00 0.00 0.00 4.79
295 320 1.648467 GCTCCATTGCAACTCCGGTC 61.648 60.000 0.00 0.00 0.00 4.79
296 321 1.675641 GCTCCATTGCAACTCCGGT 60.676 57.895 0.00 0.00 0.00 5.28
297 322 0.962356 AAGCTCCATTGCAACTCCGG 60.962 55.000 0.00 0.00 34.99 5.14
298 323 0.449388 GAAGCTCCATTGCAACTCCG 59.551 55.000 0.00 0.00 34.99 4.63
299 324 0.449388 CGAAGCTCCATTGCAACTCC 59.551 55.000 0.00 0.00 34.99 3.85
300 325 3.984292 CGAAGCTCCATTGCAACTC 57.016 52.632 0.00 0.00 34.99 3.01
424 747 4.025858 GAGCTCCACTGCAGCCCA 62.026 66.667 15.27 0.00 37.63 5.36
668 991 0.536006 AGCTCCAACACAGCTCCAAC 60.536 55.000 0.00 0.00 44.25 3.77
669 992 0.535780 CAGCTCCAACACAGCTCCAA 60.536 55.000 0.00 0.00 44.25 3.53
670 993 1.071987 CAGCTCCAACACAGCTCCA 59.928 57.895 0.00 0.00 44.25 3.86
671 994 2.331132 GCAGCTCCAACACAGCTCC 61.331 63.158 0.00 0.00 44.25 4.70
672 995 2.675056 CGCAGCTCCAACACAGCTC 61.675 63.158 0.00 0.00 44.25 4.09
708 1031 1.438651 GAGTCAACGCAGCACCATTA 58.561 50.000 0.00 0.00 0.00 1.90
776 1099 0.825410 TCCGCCTATTTAGCCGTTCA 59.175 50.000 0.00 0.00 0.00 3.18
1020 1350 4.875713 CGGCAATTCGGGGGAGGG 62.876 72.222 0.00 0.00 0.00 4.30
1038 1368 0.478507 GGAGGAGAGGAGAGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
1039 1369 1.133792 GTGGAGGAGAGGAGAGGAGAG 60.134 61.905 0.00 0.00 0.00 3.20
1040 1370 0.923358 GTGGAGGAGAGGAGAGGAGA 59.077 60.000 0.00 0.00 0.00 3.71
1041 1371 0.106217 GGTGGAGGAGAGGAGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
1042 1372 1.927569 CGGTGGAGGAGAGGAGAGGA 61.928 65.000 0.00 0.00 0.00 3.71
1043 1373 1.454847 CGGTGGAGGAGAGGAGAGG 60.455 68.421 0.00 0.00 0.00 3.69
1044 1374 1.454847 CCGGTGGAGGAGAGGAGAG 60.455 68.421 0.00 0.00 0.00 3.20
1045 1375 1.929088 TCCGGTGGAGGAGAGGAGA 60.929 63.158 0.00 0.00 34.92 3.71
1046 1376 2.684104 TCCGGTGGAGGAGAGGAG 59.316 66.667 0.00 0.00 34.92 3.69
1169 1505 1.588082 GCGAAGTCGGGTAAGGTGA 59.412 57.895 2.47 0.00 40.23 4.02
1171 1507 2.976356 GGCGAAGTCGGGTAAGGT 59.024 61.111 2.47 0.00 40.23 3.50
1206 1542 2.331132 GGAACAGTGAGCAGCAGGC 61.331 63.158 0.00 0.00 45.30 4.85
1394 1737 1.339631 TGATTCACCAAGGGCTTACGG 60.340 52.381 0.00 0.00 0.00 4.02
1396 1739 1.737793 CGTGATTCACCAAGGGCTTAC 59.262 52.381 11.12 0.00 0.00 2.34
1398 1741 0.609131 CCGTGATTCACCAAGGGCTT 60.609 55.000 11.12 0.00 33.01 4.35
1418 1761 4.837896 TCGTGACTATAGGAATGAGCAG 57.162 45.455 4.43 0.00 0.00 4.24
1433 1776 4.549599 CGCAACAAAATAGACAATCGTGAC 59.450 41.667 0.00 0.00 0.00 3.67
1501 1844 0.395686 TCAGAGAAGCAGCAGCAGTT 59.604 50.000 3.17 0.00 45.49 3.16
1518 1861 1.053424 AAGGTAAGCGTCCCAACTCA 58.947 50.000 0.00 0.00 0.00 3.41
1541 1884 6.040391 TGGAATTAACAACCAACTGAAAGAGG 59.960 38.462 0.00 0.00 37.43 3.69
1599 1942 2.029623 GCCAGAGCATCACCATTCAAT 58.970 47.619 0.00 0.00 37.82 2.57
1600 1943 1.005097 AGCCAGAGCATCACCATTCAA 59.995 47.619 0.00 0.00 43.56 2.69
1710 2053 6.303021 TGTGAAAATTACGTGGTTAAGTCC 57.697 37.500 0.00 0.00 0.00 3.85
1951 2294 1.412710 GCCCAACATCCGAGTCAGATA 59.587 52.381 0.00 0.00 0.00 1.98
1988 2331 3.818773 GCAATGTACCCTTGTTACACACT 59.181 43.478 7.01 0.00 0.00 3.55
2029 2372 5.757320 CCAAACATTGCATAGTTTTCACCAA 59.243 36.000 12.67 0.00 35.90 3.67
2051 2394 3.773119 GGTTATAGTCAACTCACCCTCCA 59.227 47.826 0.00 0.00 0.00 3.86
2091 2434 8.119226 CAGCAGTTTCTTAAGCATACAGTATTC 58.881 37.037 0.00 0.00 0.00 1.75
2106 2449 1.035139 CAGCCCAACAGCAGTTTCTT 58.965 50.000 0.00 0.00 35.28 2.52
2108 2451 1.006922 GCAGCCCAACAGCAGTTTC 60.007 57.895 0.00 0.00 35.28 2.78
2205 2548 9.136323 ACTTCCATACCATTCCTAAAATGAATC 57.864 33.333 0.00 0.00 30.16 2.52
2316 2661 4.665212 ACAGATAAATGTTTGCTGCGATG 58.335 39.130 0.00 0.00 31.38 3.84
2319 2664 8.786937 ATTAATACAGATAAATGTTTGCTGCG 57.213 30.769 0.00 0.00 34.56 5.18
2339 2684 9.822185 GGGCTGTGAGATCAAAATAAAATTAAT 57.178 29.630 0.00 0.00 0.00 1.40
2506 2853 8.579682 AACATTGAGCAAACAAGATTAAACTC 57.420 30.769 0.00 0.00 33.22 3.01
2508 2855 8.603181 ACAAACATTGAGCAAACAAGATTAAAC 58.397 29.630 0.00 0.00 33.22 2.01
2538 2896 8.655651 TGAACTGGTTAAATTTGTTGAATTCC 57.344 30.769 2.27 0.00 36.96 3.01
2580 2938 2.493278 CAAAACCCCATCAACTAGCAGG 59.507 50.000 0.00 0.00 0.00 4.85
2683 3043 4.156739 ACTGCCTAGCATAAAAGAAAGTGC 59.843 41.667 0.00 0.00 38.13 4.40
2684 3044 5.412594 TCACTGCCTAGCATAAAAGAAAGTG 59.587 40.000 0.00 0.00 38.13 3.16
2816 3177 9.674824 GAGCTTCCAATGATATAATTTTCACAG 57.325 33.333 0.00 0.00 0.00 3.66
2823 3184 8.854117 GTGAAAGGAGCTTCCAATGATATAATT 58.146 33.333 5.21 0.00 39.61 1.40
2850 3211 3.079960 AGCATACCGTCACATTCGTAG 57.920 47.619 0.00 0.00 0.00 3.51
2868 3229 3.963665 TGACATGCAAGTTACACAAAGC 58.036 40.909 0.00 0.00 0.00 3.51
2892 3253 7.864108 TTGACCACATGTTAGAGGAATAATG 57.136 36.000 6.93 0.00 0.00 1.90
2947 3308 5.712917 GTCCTACTCCCTCTATCCATGTAAG 59.287 48.000 0.00 0.00 0.00 2.34
2948 3309 5.459241 GGTCCTACTCCCTCTATCCATGTAA 60.459 48.000 0.00 0.00 0.00 2.41
3217 3579 1.004610 CTGCACGCCATCTGTTTATCG 60.005 52.381 0.00 0.00 0.00 2.92
3231 3593 3.745332 TGCATTGAAAGATACTGCACG 57.255 42.857 0.00 0.00 37.88 5.34
3250 3612 7.023575 GCACATGTTCCTAAAATACTCAGTTG 58.976 38.462 0.00 0.00 0.00 3.16
3264 3626 2.887152 GACAGAAAAGGCACATGTTCCT 59.113 45.455 11.66 11.66 0.00 3.36
3298 3660 2.770164 AGACTTGTGACACATAGGCC 57.230 50.000 9.55 0.00 0.00 5.19
3529 3977 2.496070 ACTAAGTGCTACGCAATCTCCA 59.504 45.455 0.00 0.00 41.47 3.86
3736 4184 3.943381 CACAAGATGCTATCAAAGGCAGA 59.057 43.478 0.00 0.00 41.88 4.26
4011 4460 0.947244 AGGAGCAACAACAAGCTTCG 59.053 50.000 0.00 0.00 41.33 3.79
4058 4507 8.405531 GCACCAGAAAACAATTAGAGCAATATA 58.594 33.333 0.00 0.00 0.00 0.86
4085 4534 9.457110 TTCATTTACATACACACATGTCAAAAC 57.543 29.630 0.00 0.00 39.77 2.43
4541 5007 1.077068 CTCCCCGCAGAGAGAGAGT 60.077 63.158 0.00 0.00 35.82 3.24
4574 5050 5.235186 GCACATAACACAGAATAGCTACTGG 59.765 44.000 14.07 7.11 38.30 4.00
4652 5862 6.202762 GCACCATTCGAGATAACATGAATGTA 59.797 38.462 0.00 0.00 43.78 2.29
4681 5891 1.168714 GAAGCACTTTGCCCCTACAG 58.831 55.000 0.00 0.00 46.52 2.74
4702 5913 6.867662 AGTCAACATGTTTCAGTCCTAAAG 57.132 37.500 8.77 0.00 0.00 1.85
4766 5986 6.122964 AGTGTTCCAAGTAAAAAGAAGCTCT 58.877 36.000 0.00 0.00 0.00 4.09
4782 6009 3.181465 GGTCAGAACTCAGAAGTGTTCCA 60.181 47.826 6.76 0.00 45.00 3.53
4985 6212 1.339535 CCTTCCTCAGCCTCTTCAACC 60.340 57.143 0.00 0.00 0.00 3.77
4996 6223 3.755378 CACCATTTGAGTTCCTTCCTCAG 59.245 47.826 0.00 0.00 39.91 3.35
5057 6287 8.885494 TCTTCTTCTTCTTCTTCTTCTTCTTG 57.115 34.615 0.00 0.00 0.00 3.02
5066 6296 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
5083 6313 9.936759 CCTCTATAACAGTTTTCTTCTTCTTCT 57.063 33.333 0.00 0.00 0.00 2.85
5084 6314 9.930693 TCCTCTATAACAGTTTTCTTCTTCTTC 57.069 33.333 0.00 0.00 0.00 2.87
5086 6316 9.883142 CATCCTCTATAACAGTTTTCTTCTTCT 57.117 33.333 0.00 0.00 0.00 2.85
5087 6317 9.877178 TCATCCTCTATAACAGTTTTCTTCTTC 57.123 33.333 0.00 0.00 0.00 2.87
5089 6319 9.829507 CATCATCCTCTATAACAGTTTTCTTCT 57.170 33.333 0.00 0.00 0.00 2.85
5090 6320 9.823647 TCATCATCCTCTATAACAGTTTTCTTC 57.176 33.333 0.00 0.00 0.00 2.87
5092 6322 9.829507 CTTCATCATCCTCTATAACAGTTTTCT 57.170 33.333 0.00 0.00 0.00 2.52
5093 6323 9.823647 TCTTCATCATCCTCTATAACAGTTTTC 57.176 33.333 0.00 0.00 0.00 2.29
5104 6334 4.736126 TGCGTTTCTTCATCATCCTCTA 57.264 40.909 0.00 0.00 0.00 2.43
5123 6353 0.734889 CATCCAGGTCGACCATTTGC 59.265 55.000 35.00 8.29 38.89 3.68
5137 6367 3.002791 GTTTCAGCATCGTCTTCATCCA 58.997 45.455 0.00 0.00 0.00 3.41
5191 6421 1.005215 CCTCATCCTCTGCAACCCTTT 59.995 52.381 0.00 0.00 0.00 3.11
5230 6460 3.687572 CAGCATCACTGTCATTAAGGC 57.312 47.619 0.00 0.00 41.86 4.35
5255 6485 7.503566 TCAGATTTTATTCTCTTTGGGGCATAG 59.496 37.037 0.00 0.00 0.00 2.23
5458 6688 8.088365 ACAGCAGGTAATATTTCAAGGAAAAAC 58.912 33.333 0.00 0.00 35.11 2.43
5508 6740 8.889849 ACCGTTCAAGTTTGATAATATTTTCG 57.110 30.769 0.00 0.00 37.00 3.46
5569 6801 4.630069 CGGTACAAACTAACCAAGATGAGG 59.370 45.833 0.00 0.00 35.35 3.86
5659 6891 6.752168 AGTTCAAATTTCAAATGTCCAGGAG 58.248 36.000 0.00 0.00 0.00 3.69
5757 6989 6.183360 GCAACATGACTCCGTATCTTATATGC 60.183 42.308 0.00 0.00 0.00 3.14
5776 7008 4.855531 GTTTTTAACCTCGTCTGCAACAT 58.144 39.130 0.00 0.00 0.00 2.71
5848 7080 5.985911 TGAAGTGTATAGCCTTAAGGGAAC 58.014 41.667 23.06 6.58 37.23 3.62
5849 7081 6.615726 AGATGAAGTGTATAGCCTTAAGGGAA 59.384 38.462 23.06 0.00 37.23 3.97
5952 7438 6.388100 AGATTGACAGAATCCTTCCCTGATTA 59.612 38.462 0.00 0.00 32.74 1.75
5985 7471 5.893255 AGAAAATTATATGGCTTGGCTGTCA 59.107 36.000 0.00 0.00 0.00 3.58
6012 7498 6.899393 TGATTGTGGTAGCAAAGAAAGATT 57.101 33.333 0.00 0.00 31.63 2.40
6032 7518 1.597797 CTGTTTGGCGGCCACATGAT 61.598 55.000 23.78 0.00 30.78 2.45
6042 7528 2.336088 CAGTTGGGCTGTTTGGCG 59.664 61.111 0.00 0.00 42.84 5.69
6138 7624 1.738474 TCATCATCCCTGATCCTGGG 58.262 55.000 13.16 13.16 40.20 4.45
6248 7734 5.871396 TCACTTTGTACAGGAGAAAGAGT 57.129 39.130 9.29 0.00 40.15 3.24
6276 7762 9.567776 TTATGTTTTTCTGATGAGTAACTGGAA 57.432 29.630 0.00 0.00 0.00 3.53
6334 7820 6.698380 TCTCTTAACTATCACAACCAAGTCC 58.302 40.000 0.00 0.00 0.00 3.85
6363 7849 7.151308 CCTGCACATCACAAAGGTAAATTTAA 58.849 34.615 0.00 0.00 0.00 1.52
6434 7921 2.436292 GTGCAGCAGAGCTCCAGG 60.436 66.667 10.93 1.26 36.40 4.45


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

AutoCloner maintained by Alex Coulton.