Multiple sequence alignment - TraesCS4B01G102800

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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 TraesCS4B01G102800 chr4B 100.000 4308 0 0 1 4308 109050354 109046047 0.000000e+00 7956.0
1 TraesCS4B01G102800 chr4B 79.537 259 46 4 136 389 262714008 262714264 1.230000e-40 178.0
2 TraesCS4B01G102800 chr4B 96.667 60 0 1 3534 3591 45493400 45493341 9.860000e-17 99.0
3 TraesCS4B01G102800 chr4D 94.416 2883 116 12 604 3484 77025565 77028404 0.000000e+00 4390.0
4 TraesCS4B01G102800 chr4D 93.319 2784 128 14 631 3393 76611859 76609113 0.000000e+00 4058.0
5 TraesCS4B01G102800 chr4D 91.382 557 28 8 3625 4173 76605250 76604706 0.000000e+00 745.0
6 TraesCS4B01G102800 chr4D 86.441 590 57 12 1 577 77023818 77024397 3.660000e-175 625.0
7 TraesCS4B01G102800 chr4D 84.513 452 43 12 167 603 76613441 76613002 5.150000e-114 422.0
8 TraesCS4B01G102800 chr4D 84.984 313 11 6 3625 3935 77039858 77040136 7.050000e-73 285.0
9 TraesCS4B01G102800 chr4D 88.971 136 15 0 1 136 76622296 76622161 7.410000e-38 169.0
10 TraesCS4B01G102800 chr4D 92.035 113 9 0 3395 3507 76605413 76605301 4.460000e-35 159.0
11 TraesCS4B01G102800 chr4D 94.382 89 4 1 4195 4283 76604584 76604497 7.510000e-28 135.0
12 TraesCS4B01G102800 chr4D 93.258 89 5 1 4195 4283 77041221 77041308 3.500000e-26 130.0
13 TraesCS4B01G102800 chr4A 93.322 2336 107 24 598 2921 511079019 511081317 0.000000e+00 3404.0
14 TraesCS4B01G102800 chr4A 86.527 861 53 31 3330 4170 511131680 511132497 0.000000e+00 889.0
15 TraesCS4B01G102800 chr4A 82.196 601 73 14 1 575 511078371 511078963 1.800000e-133 486.0
16 TraesCS4B01G102800 chr4A 97.596 208 5 0 2917 3124 511084570 511084777 1.470000e-94 357.0
17 TraesCS4B01G102800 chr4A 95.495 222 10 0 3118 3339 511131309 511131530 5.300000e-94 355.0
18 TraesCS4B01G102800 chr4A 87.831 189 17 6 598 780 511076702 511076890 2.610000e-52 217.0
19 TraesCS4B01G102800 chr4A 80.870 115 12 7 4168 4280 511132526 511132632 9.930000e-12 82.4
20 TraesCS4B01G102800 chr5D 75.148 507 88 16 14 495 501441667 501441174 2.030000e-48 204.0
21 TraesCS4B01G102800 chr5D 94.030 67 3 1 3534 3600 298145822 298145757 2.740000e-17 100.0
22 TraesCS4B01G102800 chr5B 74.951 507 89 16 14 495 633265524 633266017 9.450000e-47 198.0
23 TraesCS4B01G102800 chr5B 80.488 82 16 0 502 583 292183945 292184026 3.600000e-06 63.9
24 TraesCS4B01G102800 chrUn 81.560 141 23 1 137 274 49155729 49155589 3.520000e-21 113.0
25 TraesCS4B01G102800 chr3B 74.219 256 54 9 136 383 168755975 168756226 3.550000e-16 97.1
26 TraesCS4B01G102800 chr3A 77.143 175 34 5 136 307 432381273 432381444 3.550000e-16 97.1
27 TraesCS4B01G102800 chr2A 88.889 81 5 2 3528 3604 17251808 17251888 3.550000e-16 97.1
28 TraesCS4B01G102800 chr1D 89.610 77 5 1 3530 3603 464799798 464799722 1.280000e-15 95.3
29 TraesCS4B01G102800 chr1D 88.000 75 5 2 3529 3603 48193881 48193811 7.680000e-13 86.1
30 TraesCS4B01G102800 chr7D 80.328 122 22 2 1079 1199 157099949 157100069 1.650000e-14 91.6
31 TraesCS4B01G102800 chr7D 87.342 79 5 3 3534 3607 46702663 46702741 7.680000e-13 86.1
32 TraesCS4B01G102800 chr2B 87.654 81 6 2 3528 3604 27088381 27088461 1.650000e-14 91.6
33 TraesCS4B01G102800 chr7A 89.041 73 7 1 3534 3605 135963906 135963978 5.930000e-14 89.8
34 TraesCS4B01G102800 chr7A 79.365 126 24 2 1075 1199 159699876 159699752 2.130000e-13 87.9
35 TraesCS4B01G102800 chr3D 93.333 60 4 0 14 73 366805070 366805011 5.930000e-14 89.8
36 TraesCS4B01G102800 chr2D 86.420 81 7 2 3528 3604 15196275 15196355 7.680000e-13 86.1
37 TraesCS4B01G102800 chr1A 81.731 104 17 2 1079 1181 463231454 463231556 7.680000e-13 86.1
38 TraesCS4B01G102800 chr7B 79.630 108 20 2 1075 1181 119582945 119583051 4.620000e-10 76.8
39 TraesCS4B01G102800 chr6B 100.000 28 0 0 556 583 299595500 299595473 8.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G102800 chr4B 109046047 109050354 4307 True 7956.000000 7956 100.000000 1 4308 1 chr4B.!!$R2 4307
1 TraesCS4B01G102800 chr4D 77023818 77028404 4586 False 2507.500000 4390 90.428500 1 3484 2 chr4D.!!$F1 3483
2 TraesCS4B01G102800 chr4D 76604497 76613441 8944 True 1103.800000 4058 91.126200 167 4283 5 chr4D.!!$R2 4116
3 TraesCS4B01G102800 chr4D 77039858 77041308 1450 False 207.500000 285 89.121000 3625 4283 2 chr4D.!!$F2 658
4 TraesCS4B01G102800 chr4A 511076702 511084777 8075 False 1116.000000 3404 90.236250 1 3124 4 chr4A.!!$F1 3123
5 TraesCS4B01G102800 chr4A 511131309 511132632 1323 False 442.133333 889 87.630667 3118 4280 3 chr4A.!!$F2 1162

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
302 1987 0.031449 CGGATTTTGCCACGGTTTGT 59.969 50.000 0.0 0.0 0.00 2.83 F
951 4899 0.102481 CATGCCTGATCTTTGCTGGC 59.898 55.000 0.0 0.0 46.72 4.85 F
1114 5062 1.339055 TGCAGCATGTACTGTCCTTCC 60.339 52.381 0.0 0.0 39.96 3.46 F
2901 6868 0.630673 ATCTAGGCCCCAATTGCACA 59.369 50.000 0.0 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 5487 0.475906 AGCAACCCCTCATCCATAGC 59.524 55.000 0.00 0.0 0.00 2.97 R
1829 5777 1.532868 GCACACAATCTCCACTGTCAC 59.467 52.381 0.00 0.0 0.00 3.67 R
3099 10323 1.075601 AACTTGGATCTGCCCCAGAA 58.924 50.000 0.00 0.0 44.04 3.02 R
4227 16266 1.301479 GCGAAGACGGTCAAAGGGT 60.301 57.895 11.27 0.0 40.15 4.34 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
64 1734 7.443575 ACATGAGCTATTATCTTTGTGATGGTC 59.556 37.037 0.00 0.00 36.65 4.02
74 1744 6.373005 TCTTTGTGATGGTCTCAATCCTTA 57.627 37.500 0.00 0.00 35.07 2.69
106 1776 4.804108 CTTCATCAGGACCATCTACGATC 58.196 47.826 0.00 0.00 0.00 3.69
112 1782 1.270358 GGACCATCTACGATCCAAGGC 60.270 57.143 0.00 0.00 0.00 4.35
113 1783 1.412710 GACCATCTACGATCCAAGGCA 59.587 52.381 0.00 0.00 0.00 4.75
136 1806 8.473219 GGCATGAGAAAAGATCTTATTTTTCCT 58.527 33.333 8.75 0.00 41.79 3.36
213 1898 3.365472 GAGGACCTGCAAAAATATGGGT 58.635 45.455 0.00 0.00 0.00 4.51
237 1922 1.072331 AGACATGTTGTGGGAGGTGAC 59.928 52.381 0.00 0.00 0.00 3.67
243 1928 1.822990 GTTGTGGGAGGTGACGATAGA 59.177 52.381 0.00 0.00 41.38 1.98
248 1933 3.104512 TGGGAGGTGACGATAGATTGTT 58.895 45.455 0.00 0.00 41.38 2.83
254 1939 6.984474 GGAGGTGACGATAGATTGTTTGATAA 59.016 38.462 0.00 0.00 41.38 1.75
276 1961 6.817765 AAACAACATTATTGTCGAGGATGT 57.182 33.333 0.00 0.00 34.06 3.06
287 1972 0.175760 CGAGGATGTTGGTGACGGAT 59.824 55.000 0.00 0.00 0.00 4.18
290 1975 3.081804 GAGGATGTTGGTGACGGATTTT 58.918 45.455 0.00 0.00 0.00 1.82
302 1987 0.031449 CGGATTTTGCCACGGTTTGT 59.969 50.000 0.00 0.00 0.00 2.83
327 2012 0.601311 GAGCGCATGGGTGATCCTAC 60.601 60.000 11.47 0.00 33.96 3.18
385 2071 9.188588 GATGATTTTATCGAAATGCATCAACAT 57.811 29.630 0.00 0.00 39.24 2.71
391 2077 9.449550 TTTATCGAAATGCATCAACATATTCAC 57.550 29.630 0.00 0.00 0.00 3.18
392 2078 6.682423 TCGAAATGCATCAACATATTCACT 57.318 33.333 0.00 0.00 0.00 3.41
393 2079 7.784633 TCGAAATGCATCAACATATTCACTA 57.215 32.000 0.00 0.00 0.00 2.74
394 2080 8.382030 TCGAAATGCATCAACATATTCACTAT 57.618 30.769 0.00 0.00 0.00 2.12
395 2081 8.839343 TCGAAATGCATCAACATATTCACTATT 58.161 29.630 0.00 0.00 0.00 1.73
396 2082 9.454585 CGAAATGCATCAACATATTCACTATTT 57.545 29.630 0.00 0.00 0.00 1.40
430 2121 5.065602 TGAGTAATTCATGAGCAGCAATGAC 59.934 40.000 9.69 0.00 0.00 3.06
614 4551 6.195700 AGTGCTTAGATAGTAACCCTCAGAA 58.804 40.000 0.00 0.00 0.00 3.02
615 4552 6.668283 AGTGCTTAGATAGTAACCCTCAGAAA 59.332 38.462 0.00 0.00 0.00 2.52
616 4553 7.345914 AGTGCTTAGATAGTAACCCTCAGAAAT 59.654 37.037 0.00 0.00 0.00 2.17
657 4600 2.485795 CCTCTTCCTCCCTCGCTCG 61.486 68.421 0.00 0.00 0.00 5.03
709 4652 6.479001 GCATCTAGACCTAAGAATTTACGCAA 59.521 38.462 0.00 0.00 0.00 4.85
726 4669 2.864471 AACCCAGTCCACCGTCGAC 61.864 63.158 5.18 5.18 0.00 4.20
771 4715 0.526524 CGGATGCTGACGTTCTCCTC 60.527 60.000 0.00 0.00 0.00 3.71
780 4724 0.966370 ACGTTCTCCTCGGAGGAAGG 60.966 60.000 25.95 19.36 45.28 3.46
786 4730 3.839432 CTCGGAGGAAGGTCGGCC 61.839 72.222 0.00 0.00 0.00 6.13
791 4735 3.393360 AGGAAGGTCGGCCTCAAG 58.607 61.111 10.20 0.00 46.33 3.02
793 4737 0.836400 AGGAAGGTCGGCCTCAAGAA 60.836 55.000 10.20 0.00 46.33 2.52
798 4742 1.371558 GTCGGCCTCAAGAACTGGT 59.628 57.895 0.00 0.00 0.00 4.00
805 4749 1.284982 CTCAAGAACTGGTGACGGCG 61.285 60.000 4.80 4.80 41.93 6.46
809 4753 4.250305 AACTGGTGACGGCGGCTT 62.250 61.111 16.45 0.00 41.93 4.35
834 4778 3.361158 TGCCACGCAATTCCACCG 61.361 61.111 0.00 0.00 34.76 4.94
844 4788 2.432444 CAATTCCACCGCTACTCCAAA 58.568 47.619 0.00 0.00 0.00 3.28
886 4830 4.060038 ACGATCCACGAGCTCATAATTT 57.940 40.909 15.40 0.00 45.77 1.82
905 4849 2.111999 TTTCACTCCGAGGCACCAGG 62.112 60.000 0.00 0.00 0.00 4.45
947 4895 0.379669 CGTCCATGCCTGATCTTTGC 59.620 55.000 0.00 0.00 0.00 3.68
951 4899 0.102481 CATGCCTGATCTTTGCTGGC 59.898 55.000 0.00 0.00 46.72 4.85
1084 5032 3.889044 GGATCGACGCTCTGCCGA 61.889 66.667 0.00 0.00 36.72 5.54
1114 5062 1.339055 TGCAGCATGTACTGTCCTTCC 60.339 52.381 0.00 0.00 39.96 3.46
1402 5350 2.733858 GCTCGAGTCCTCAGTGTTCATC 60.734 54.545 15.13 0.00 0.00 2.92
1425 5373 3.886123 AGGCCGTGATAACAATAGCTTT 58.114 40.909 0.00 0.00 0.00 3.51
1460 5408 4.244802 GCCTCTCGTCTCTCCGCG 62.245 72.222 0.00 0.00 0.00 6.46
1462 5410 4.244802 CTCTCGTCTCTCCGCGCC 62.245 72.222 0.00 0.00 0.00 6.53
1647 5595 2.761767 TCCAAATGAACGGACTCGGATA 59.238 45.455 0.00 0.00 41.39 2.59
1669 5617 7.069578 GGATATCTGTCCCAAGTCTAGTTACAA 59.930 40.741 2.05 0.00 31.82 2.41
1728 5676 4.642445 TGAAAGCATGCCATCATTAGTG 57.358 40.909 15.66 0.00 0.00 2.74
1793 5741 2.117941 GAAGCTGGTGGTTCGTGTGC 62.118 60.000 0.00 0.00 40.24 4.57
1883 5831 1.470494 GTCAGAGGCTAAAAGCTTGGC 59.530 52.381 0.00 5.21 41.99 4.52
1937 5885 6.701340 TGCATCTACTTCTTTTCTCAGCTTA 58.299 36.000 0.00 0.00 0.00 3.09
2181 6143 7.225784 TGGCCAATTATACATATTCGCATTT 57.774 32.000 0.61 0.00 0.00 2.32
2285 6247 2.785713 TTTCGCTTTGGTTACAAGCC 57.214 45.000 2.53 0.00 37.97 4.35
2286 6248 1.975660 TTCGCTTTGGTTACAAGCCT 58.024 45.000 2.53 0.00 37.97 4.58
2287 6249 1.519408 TCGCTTTGGTTACAAGCCTC 58.481 50.000 2.53 0.00 37.97 4.70
2288 6250 1.071699 TCGCTTTGGTTACAAGCCTCT 59.928 47.619 2.53 0.00 37.97 3.69
2289 6251 1.880027 CGCTTTGGTTACAAGCCTCTT 59.120 47.619 2.53 0.00 37.97 2.85
2290 6252 2.293399 CGCTTTGGTTACAAGCCTCTTT 59.707 45.455 2.53 0.00 37.97 2.52
2291 6253 3.243401 CGCTTTGGTTACAAGCCTCTTTT 60.243 43.478 2.53 0.00 37.97 2.27
2292 6254 4.693283 GCTTTGGTTACAAGCCTCTTTTT 58.307 39.130 0.00 0.00 37.97 1.94
2549 6513 3.322541 TCCAACATACACCTGTTCTCGAA 59.677 43.478 0.00 0.00 37.25 3.71
2604 6568 9.935241 ATGCTTCGTAAATCTGATATATGTTCT 57.065 29.630 0.00 0.00 0.00 3.01
2901 6868 0.630673 ATCTAGGCCCCAATTGCACA 59.369 50.000 0.00 0.00 0.00 4.57
3099 10323 0.179089 CAACAGCAGATCCTAGCGCT 60.179 55.000 17.26 17.26 35.48 5.92
3138 10362 1.625315 TGAACAGCAGCAGGTCATAGT 59.375 47.619 0.43 0.00 0.00 2.12
3224 10448 2.032620 TCTTGACTCGGATCTTAGCCC 58.967 52.381 0.00 0.00 0.00 5.19
3225 10449 1.757118 CTTGACTCGGATCTTAGCCCA 59.243 52.381 0.00 0.00 0.00 5.36
3296 10520 0.831288 AGGCTCAGCTCACACAGAGT 60.831 55.000 0.00 0.00 46.47 3.24
3309 10533 3.027412 ACACAGAGTGTCTTGAGTGACT 58.973 45.455 0.00 0.00 43.92 3.41
3393 14484 7.097192 TGTCAGTTTATCTGTTAGGCACTTAG 58.903 38.462 0.00 0.00 43.97 2.18
3458 14549 4.019174 GGTGAATGGGATTATGCTATGGG 58.981 47.826 0.00 0.00 0.00 4.00
3459 14550 3.445096 GTGAATGGGATTATGCTATGGGC 59.555 47.826 0.00 0.00 42.22 5.36
3467 14558 1.583556 TATGCTATGGGCGATGGGAT 58.416 50.000 5.21 5.21 45.43 3.85
3551 14664 4.687262 ATATACTCCCTCCGTCCCATAA 57.313 45.455 0.00 0.00 0.00 1.90
3554 14667 2.890814 ACTCCCTCCGTCCCATAATAG 58.109 52.381 0.00 0.00 0.00 1.73
3555 14668 2.179424 ACTCCCTCCGTCCCATAATAGT 59.821 50.000 0.00 0.00 0.00 2.12
3556 14669 2.563179 CTCCCTCCGTCCCATAATAGTG 59.437 54.545 0.00 0.00 0.00 2.74
3557 14670 2.090943 TCCCTCCGTCCCATAATAGTGT 60.091 50.000 0.00 0.00 0.00 3.55
3560 14673 4.150359 CCTCCGTCCCATAATAGTGTAGT 58.850 47.826 0.00 0.00 0.00 2.73
3563 14676 4.581824 TCCGTCCCATAATAGTGTAGTGTC 59.418 45.833 0.00 0.00 0.00 3.67
3564 14677 4.340097 CCGTCCCATAATAGTGTAGTGTCA 59.660 45.833 0.00 0.00 0.00 3.58
3565 14678 5.163488 CCGTCCCATAATAGTGTAGTGTCAA 60.163 44.000 0.00 0.00 0.00 3.18
3566 14679 6.334989 CGTCCCATAATAGTGTAGTGTCAAA 58.665 40.000 0.00 0.00 0.00 2.69
3567 14680 6.814644 CGTCCCATAATAGTGTAGTGTCAAAA 59.185 38.462 0.00 0.00 0.00 2.44
3570 14683 7.332430 TCCCATAATAGTGTAGTGTCAAAAACG 59.668 37.037 0.00 0.00 0.00 3.60
3573 14686 5.840940 ATAGTGTAGTGTCAAAAACGCTC 57.159 39.130 0.00 0.00 45.69 5.03
3575 14688 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
3576 14689 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
3578 14691 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
3579 14692 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
3580 14693 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
3581 14694 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
3584 14697 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
3585 14698 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
3586 14699 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
3587 14700 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
3588 14701 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
3589 14702 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
3590 14703 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
3591 14704 4.525487 ACGCTCTTATATTATGGGACGGAA 59.475 41.667 0.00 0.00 0.00 4.30
3592 14705 5.103000 CGCTCTTATATTATGGGACGGAAG 58.897 45.833 0.00 0.00 0.00 3.46
3593 14706 5.420409 GCTCTTATATTATGGGACGGAAGG 58.580 45.833 0.00 0.00 0.00 3.46
3594 14707 5.046520 GCTCTTATATTATGGGACGGAAGGT 60.047 44.000 0.00 0.00 0.00 3.50
3595 14708 6.354794 TCTTATATTATGGGACGGAAGGTG 57.645 41.667 0.00 0.00 0.00 4.00
3596 14709 5.842328 TCTTATATTATGGGACGGAAGGTGT 59.158 40.000 0.00 0.00 0.00 4.16
3597 14710 6.328148 TCTTATATTATGGGACGGAAGGTGTT 59.672 38.462 0.00 0.00 0.00 3.32
3598 14711 2.483014 TTATGGGACGGAAGGTGTTG 57.517 50.000 0.00 0.00 0.00 3.33
3601 14714 1.129917 TGGGACGGAAGGTGTTGTTA 58.870 50.000 0.00 0.00 0.00 2.41
3609 14722 6.009115 ACGGAAGGTGTTGTTATGATTTTC 57.991 37.500 0.00 0.00 0.00 2.29
3611 14724 6.086222 CGGAAGGTGTTGTTATGATTTTCAG 58.914 40.000 0.00 0.00 0.00 3.02
3615 14728 6.738114 AGGTGTTGTTATGATTTTCAGTGTG 58.262 36.000 0.00 0.00 0.00 3.82
3633 14746 5.067153 CAGTGTGAGGGTGTTGTTTTGATTA 59.933 40.000 0.00 0.00 0.00 1.75
3662 14775 7.446001 TGTGATGATATTAACTGTTGCACAA 57.554 32.000 2.69 0.00 30.61 3.33
3778 14892 5.608437 TGTCAGATTCTCCTAGGGCATAAAT 59.392 40.000 9.46 2.10 0.00 1.40
3849 14963 2.507484 TGGAAACAGTCTCTTGCCATG 58.493 47.619 0.00 0.00 35.01 3.66
4080 15814 7.899648 ACTACTCCTACCATATATGCATACC 57.100 40.000 8.99 0.00 0.00 2.73
4082 15816 6.546428 ACTCCTACCATATATGCATACCAC 57.454 41.667 8.99 0.00 0.00 4.16
4084 15818 6.381420 ACTCCTACCATATATGCATACCACTC 59.619 42.308 8.99 0.00 0.00 3.51
4085 15819 5.661312 TCCTACCATATATGCATACCACTCC 59.339 44.000 8.99 0.00 0.00 3.85
4086 15820 5.425217 CCTACCATATATGCATACCACTCCA 59.575 44.000 8.99 0.00 0.00 3.86
4088 15822 4.846367 ACCATATATGCATACCACTCCAGT 59.154 41.667 8.99 0.00 0.00 4.00
4089 15823 5.310594 ACCATATATGCATACCACTCCAGTT 59.689 40.000 8.99 0.00 0.00 3.16
4115 16055 3.514645 GCAAACTGCAAGAACCCATATG 58.485 45.455 0.00 0.00 44.26 1.78
4143 16083 7.665145 ACAAATTAATCCCCAAAATCAACCAAG 59.335 33.333 0.00 0.00 0.00 3.61
4170 16110 6.801539 TCGTTTGTTTCTAGCAGATCAATT 57.198 33.333 0.00 0.00 0.00 2.32
4184 16205 8.218338 AGCAGATCAATTAACTATCCTTGTTG 57.782 34.615 0.00 0.00 0.00 3.33
4199 16220 1.334160 TGTTGAGGTAGGCGAACTCA 58.666 50.000 11.55 11.55 39.31 3.41
4200 16221 1.272490 TGTTGAGGTAGGCGAACTCAG 59.728 52.381 14.99 0.00 41.71 3.35
4227 16266 2.026636 CCAAAGATTCCCACTCCGGTTA 60.027 50.000 0.00 0.00 0.00 2.85
4231 16270 0.253020 ATTCCCACTCCGGTTACCCT 60.253 55.000 0.00 0.00 0.00 4.34
4232 16271 0.474273 TTCCCACTCCGGTTACCCTT 60.474 55.000 0.00 0.00 0.00 3.95
4297 16336 4.082523 GGCCGCTGCTGGTACTGA 62.083 66.667 0.00 0.00 37.74 3.41
4298 16337 2.815647 GCCGCTGCTGGTACTGAC 60.816 66.667 11.14 0.00 33.53 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 1700 8.483218 CAAAGATAATAGCTCATGTTGTAGTCG 58.517 37.037 0.00 0.00 0.00 4.18
64 1734 4.510167 AGGTCACCCATTAAGGATTGAG 57.490 45.455 0.00 0.00 41.22 3.02
74 1744 2.814805 CCTGATGAAGGTCACCCATT 57.185 50.000 0.00 0.00 41.74 3.16
102 1772 3.273434 TCTTTTCTCATGCCTTGGATCG 58.727 45.455 0.00 0.00 0.00 3.69
106 1776 6.956202 ATAAGATCTTTTCTCATGCCTTGG 57.044 37.500 14.36 0.00 31.78 3.61
136 1806 1.754555 GCCCTCTCGTCATCCTTCCTA 60.755 57.143 0.00 0.00 0.00 2.94
138 1808 1.330655 TGCCCTCTCGTCATCCTTCC 61.331 60.000 0.00 0.00 0.00 3.46
139 1809 0.755686 ATGCCCTCTCGTCATCCTTC 59.244 55.000 0.00 0.00 0.00 3.46
213 1898 1.608055 CTCCCACAACATGTCTGCAA 58.392 50.000 0.00 0.00 0.00 4.08
248 1933 8.554835 TCCTCGACAATAATGTTGTTTATCAA 57.445 30.769 0.00 0.00 40.74 2.57
254 1939 6.611381 CAACATCCTCGACAATAATGTTGTT 58.389 36.000 15.02 0.00 46.06 2.83
268 1953 0.175760 ATCCGTCACCAACATCCTCG 59.824 55.000 0.00 0.00 0.00 4.63
276 1961 0.671251 GTGGCAAAATCCGTCACCAA 59.329 50.000 0.00 0.00 32.77 3.67
287 1972 4.755411 TCAAATTACAAACCGTGGCAAAA 58.245 34.783 0.00 0.00 0.00 2.44
290 1975 2.287909 GCTCAAATTACAAACCGTGGCA 60.288 45.455 0.00 0.00 0.00 4.92
302 1987 2.121291 TCACCCATGCGCTCAAATTA 57.879 45.000 9.73 0.00 0.00 1.40
327 2012 6.322491 GTCGGATTTTGATTTGAAAGTAGGG 58.678 40.000 0.00 0.00 0.00 3.53
330 2015 6.788684 TCGTCGGATTTTGATTTGAAAGTA 57.211 33.333 0.00 0.00 0.00 2.24
338 2023 5.682943 TCAAACTTCGTCGGATTTTGATT 57.317 34.783 13.41 0.00 33.20 2.57
410 2096 4.337274 CAGGTCATTGCTGCTCATGAATTA 59.663 41.667 14.17 0.00 0.00 1.40
430 2121 1.067915 CCCACAAATACGCAAACCAGG 60.068 52.381 0.00 0.00 0.00 4.45
614 4551 1.630878 GGAGAGGCGATGGGGATTATT 59.369 52.381 0.00 0.00 0.00 1.40
615 4552 1.280457 GGAGAGGCGATGGGGATTAT 58.720 55.000 0.00 0.00 0.00 1.28
616 4553 0.105194 TGGAGAGGCGATGGGGATTA 60.105 55.000 0.00 0.00 0.00 1.75
709 4652 3.300765 GTCGACGGTGGACTGGGT 61.301 66.667 14.98 0.00 0.00 4.51
780 4724 0.951040 CACCAGTTCTTGAGGCCGAC 60.951 60.000 0.00 0.00 0.00 4.79
786 4730 1.284982 CGCCGTCACCAGTTCTTGAG 61.285 60.000 0.00 0.00 0.00 3.02
791 4735 4.681978 AGCCGCCGTCACCAGTTC 62.682 66.667 0.00 0.00 0.00 3.01
793 4737 4.988598 CAAGCCGCCGTCACCAGT 62.989 66.667 0.00 0.00 0.00 4.00
798 4742 4.451150 CCTAGCAAGCCGCCGTCA 62.451 66.667 0.00 0.00 44.04 4.35
809 4753 2.762969 AATTGCGTGGCACCCTAGCA 62.763 55.000 12.86 12.87 38.71 3.49
834 4778 2.561478 TCTTGTGGGTTTGGAGTAGC 57.439 50.000 0.00 0.00 0.00 3.58
844 4788 4.322499 CGTTTACCTGTAGATCTTGTGGGT 60.322 45.833 0.00 7.49 0.00 4.51
886 4830 1.371183 CTGGTGCCTCGGAGTGAAA 59.629 57.895 4.02 0.00 0.00 2.69
905 4849 1.136147 CTTGGCTTCGCTGCATCAC 59.864 57.895 0.00 0.00 34.04 3.06
919 4863 2.438434 GCATGGACGGACCCTTGG 60.438 66.667 0.00 0.00 38.00 3.61
920 4864 2.438434 GGCATGGACGGACCCTTG 60.438 66.667 0.00 0.00 38.00 3.61
921 4865 2.610859 AGGCATGGACGGACCCTT 60.611 61.111 0.00 0.00 38.00 3.95
922 4866 3.402681 CAGGCATGGACGGACCCT 61.403 66.667 0.00 0.00 38.00 4.34
923 4867 2.666596 GATCAGGCATGGACGGACCC 62.667 65.000 0.00 0.00 38.00 4.46
924 4868 1.227674 GATCAGGCATGGACGGACC 60.228 63.158 0.00 0.00 39.54 4.46
925 4869 0.179000 AAGATCAGGCATGGACGGAC 59.821 55.000 0.00 0.00 0.00 4.79
926 4870 0.911769 AAAGATCAGGCATGGACGGA 59.088 50.000 0.00 0.00 0.00 4.69
927 4871 1.019673 CAAAGATCAGGCATGGACGG 58.980 55.000 0.00 0.00 0.00 4.79
928 4872 0.379669 GCAAAGATCAGGCATGGACG 59.620 55.000 0.00 0.00 0.00 4.79
947 4895 1.134226 CGCTGAAAAGCAAAAGCCAG 58.866 50.000 0.00 0.00 31.84 4.85
951 4899 0.249405 TGGCCGCTGAAAAGCAAAAG 60.249 50.000 0.00 0.00 34.41 2.27
1084 5032 3.397439 ATGCTGCAGGACCTCGCT 61.397 61.111 17.12 0.00 0.00 4.93
1211 5159 2.267642 CCCGCCGGTTCAGAATCA 59.732 61.111 1.90 0.00 0.00 2.57
1233 5181 3.135712 TCACAAACTTGTTGAGCCTCCTA 59.864 43.478 0.00 0.00 39.91 2.94
1316 5264 4.963318 TCATCCTGGCTATGGAAAGTAG 57.037 45.455 0.00 0.00 37.13 2.57
1402 5350 4.258702 AGCTATTGTTATCACGGCCTAG 57.741 45.455 0.00 0.00 0.00 3.02
1425 5373 2.121385 AGGTCCTCCAGCAGCTCA 59.879 61.111 0.00 0.00 35.89 4.26
1460 5408 2.435059 GCTCCAACCTCGTCAGGC 60.435 66.667 0.00 0.00 45.05 4.85
1462 5410 1.151668 CAAAGCTCCAACCTCGTCAG 58.848 55.000 0.00 0.00 0.00 3.51
1539 5487 0.475906 AGCAACCCCTCATCCATAGC 59.524 55.000 0.00 0.00 0.00 2.97
1647 5595 6.352222 CCATTGTAACTAGACTTGGGACAGAT 60.352 42.308 0.00 0.00 42.39 2.90
1669 5617 4.716287 CCCCCAACACTCAATTAATTCCAT 59.284 41.667 0.00 0.00 0.00 3.41
1728 5676 3.743396 CGGCAAGCTTAATAGATCCTGTC 59.257 47.826 0.00 0.00 0.00 3.51
1793 5741 5.818136 ACAATTTTCACAGGTATCATCGG 57.182 39.130 0.00 0.00 0.00 4.18
1829 5777 1.532868 GCACACAATCTCCACTGTCAC 59.467 52.381 0.00 0.00 0.00 3.67
1883 5831 3.067106 ACACAAGGTTCAGCTATCAACG 58.933 45.455 0.00 0.00 0.00 4.10
2196 6158 7.537596 CCCCCTGCATAACATATAAAAATGA 57.462 36.000 0.00 0.00 0.00 2.57
2289 6251 1.916181 TGGTTTGGCCAAAGGGAAAAA 59.084 42.857 31.09 4.41 45.94 1.94
2290 6252 1.584724 TGGTTTGGCCAAAGGGAAAA 58.415 45.000 31.09 5.27 45.94 2.29
2291 6253 3.324246 TGGTTTGGCCAAAGGGAAA 57.676 47.368 31.09 12.07 45.94 3.13
2295 6257 6.795254 AGCAAAATCTGGTTTGGCCAAAGG 62.795 45.833 31.09 21.96 46.10 3.11
2716 6680 5.109903 AGTACCTTAAGCTTGTTAGATGCG 58.890 41.667 9.86 0.00 0.00 4.73
2901 6868 9.953697 GATCGTTCTAGTTACTAATCAACAGAT 57.046 33.333 0.00 5.15 0.00 2.90
3099 10323 1.075601 AACTTGGATCTGCCCCAGAA 58.924 50.000 0.00 0.00 44.04 3.02
3138 10362 1.767088 CTTGGATCTCCTCCTGATGCA 59.233 52.381 0.00 0.00 45.21 3.96
3224 10448 3.401182 GAGCTGAATATTCCTGGAGCTG 58.599 50.000 24.81 2.68 34.29 4.24
3225 10449 2.036992 CGAGCTGAATATTCCTGGAGCT 59.963 50.000 21.64 21.64 36.09 4.09
3296 10520 0.880278 GCGCCAAGTCACTCAAGACA 60.880 55.000 0.00 0.00 40.98 3.41
3309 10533 0.890542 AGTCTCTGCAAATGCGCCAA 60.891 50.000 4.18 0.00 45.83 4.52
3393 14484 3.706698 GTTTTCTCCAACTTCCAACAGC 58.293 45.455 0.00 0.00 0.00 4.40
3458 14549 1.151668 GACACAGCATATCCCATCGC 58.848 55.000 0.00 0.00 0.00 4.58
3459 14550 2.531522 TGACACAGCATATCCCATCG 57.468 50.000 0.00 0.00 0.00 3.84
3551 14664 5.539048 AGAGCGTTTTTGACACTACACTAT 58.461 37.500 0.00 0.00 0.00 2.12
3554 14667 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
3555 14668 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
3560 14673 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
3563 14676 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
3564 14677 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
3565 14678 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
3566 14679 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
3567 14680 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
3570 14683 5.046520 ACCTTCCGTCCCATAATATAAGAGC 60.047 44.000 0.00 0.00 0.00 4.09
3573 14686 6.110411 ACACCTTCCGTCCCATAATATAAG 57.890 41.667 0.00 0.00 0.00 1.73
3575 14688 5.367352 ACAACACCTTCCGTCCCATAATATA 59.633 40.000 0.00 0.00 0.00 0.86
3576 14689 4.165372 ACAACACCTTCCGTCCCATAATAT 59.835 41.667 0.00 0.00 0.00 1.28
3578 14691 2.307686 ACAACACCTTCCGTCCCATAAT 59.692 45.455 0.00 0.00 0.00 1.28
3579 14692 1.700739 ACAACACCTTCCGTCCCATAA 59.299 47.619 0.00 0.00 0.00 1.90
3580 14693 1.354101 ACAACACCTTCCGTCCCATA 58.646 50.000 0.00 0.00 0.00 2.74
3581 14694 0.476771 AACAACACCTTCCGTCCCAT 59.523 50.000 0.00 0.00 0.00 4.00
3582 14695 1.129917 TAACAACACCTTCCGTCCCA 58.870 50.000 0.00 0.00 0.00 4.37
3583 14696 2.081462 CATAACAACACCTTCCGTCCC 58.919 52.381 0.00 0.00 0.00 4.46
3584 14697 3.048337 TCATAACAACACCTTCCGTCC 57.952 47.619 0.00 0.00 0.00 4.79
3585 14698 5.622770 AAATCATAACAACACCTTCCGTC 57.377 39.130 0.00 0.00 0.00 4.79
3586 14699 5.533154 TGAAAATCATAACAACACCTTCCGT 59.467 36.000 0.00 0.00 0.00 4.69
3587 14700 6.007936 TGAAAATCATAACAACACCTTCCG 57.992 37.500 0.00 0.00 0.00 4.30
3588 14701 6.863126 CACTGAAAATCATAACAACACCTTCC 59.137 38.462 0.00 0.00 0.00 3.46
3589 14702 7.379529 CACACTGAAAATCATAACAACACCTTC 59.620 37.037 0.00 0.00 0.00 3.46
3590 14703 7.068103 TCACACTGAAAATCATAACAACACCTT 59.932 33.333 0.00 0.00 0.00 3.50
3591 14704 6.545666 TCACACTGAAAATCATAACAACACCT 59.454 34.615 0.00 0.00 0.00 4.00
3592 14705 6.734137 TCACACTGAAAATCATAACAACACC 58.266 36.000 0.00 0.00 0.00 4.16
3593 14706 6.857964 CCTCACACTGAAAATCATAACAACAC 59.142 38.462 0.00 0.00 0.00 3.32
3594 14707 6.016360 CCCTCACACTGAAAATCATAACAACA 60.016 38.462 0.00 0.00 0.00 3.33
3595 14708 6.016276 ACCCTCACACTGAAAATCATAACAAC 60.016 38.462 0.00 0.00 0.00 3.32
3596 14709 6.016360 CACCCTCACACTGAAAATCATAACAA 60.016 38.462 0.00 0.00 0.00 2.83
3597 14710 5.473162 CACCCTCACACTGAAAATCATAACA 59.527 40.000 0.00 0.00 0.00 2.41
3598 14711 5.473504 ACACCCTCACACTGAAAATCATAAC 59.526 40.000 0.00 0.00 0.00 1.89
3601 14714 4.104383 ACACCCTCACACTGAAAATCAT 57.896 40.909 0.00 0.00 0.00 2.45
3609 14722 2.752354 TCAAAACAACACCCTCACACTG 59.248 45.455 0.00 0.00 0.00 3.66
3611 14724 4.385358 AATCAAAACAACACCCTCACAC 57.615 40.909 0.00 0.00 0.00 3.82
3615 14728 9.139174 CACATTAATAATCAAAACAACACCCTC 57.861 33.333 0.00 0.00 0.00 4.30
3778 14892 4.398988 AGACACTTGTTTGAAGCATCAACA 59.601 37.500 3.39 3.65 45.01 3.33
3849 14963 6.572509 CCATCTATGGTACTACAGTATGTGCC 60.573 46.154 0.49 9.10 46.59 5.01
3941 15060 5.471456 CAGTTTTCAGATTCCTGCACTAGTT 59.529 40.000 0.00 0.00 40.20 2.24
3944 15063 4.326826 CCAGTTTTCAGATTCCTGCACTA 58.673 43.478 0.00 0.00 40.20 2.74
4010 15129 8.213518 ACGTTGATTATCTATCATGTGCTTTT 57.786 30.769 0.00 0.00 42.69 2.27
4062 15793 5.425217 TGGAGTGGTATGCATATATGGTAGG 59.575 44.000 10.16 0.00 0.00 3.18
4086 15820 5.048013 GGGTTCTTGCAGTTTGCTTATAACT 60.048 40.000 2.48 0.00 45.31 2.24
4088 15822 4.830046 TGGGTTCTTGCAGTTTGCTTATAA 59.170 37.500 2.48 0.00 45.31 0.98
4089 15823 4.402829 TGGGTTCTTGCAGTTTGCTTATA 58.597 39.130 2.48 0.00 45.31 0.98
4115 16055 8.097662 TGGTTGATTTTGGGGATTAATTTGTAC 58.902 33.333 0.00 0.00 0.00 2.90
4143 16083 6.831769 TGATCTGCTAGAAACAAACGATTTC 58.168 36.000 0.00 0.00 36.49 2.17
4184 16205 1.338655 GGATCTGAGTTCGCCTACCTC 59.661 57.143 0.00 0.00 0.00 3.85
4199 16220 3.457749 GAGTGGGAATCTTTGGAGGATCT 59.542 47.826 0.00 0.00 33.73 2.75
4200 16221 3.434310 GGAGTGGGAATCTTTGGAGGATC 60.434 52.174 0.00 0.00 0.00 3.36
4227 16266 1.301479 GCGAAGACGGTCAAAGGGT 60.301 57.895 11.27 0.00 40.15 4.34


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

AutoCloner maintained by Alex Coulton.