Multiple sequence alignment - TraesCS1B01G289700

Loading Multiple Alignment...

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 TraesCS1B01G289700 chr1B 100.000 3778 0 0 1 3778 505109541 505113318 0.000000e+00 6977.0
1 TraesCS1B01G289700 chr1B 91.595 809 45 8 1038 1845 499734308 499733522 0.000000e+00 1096.0
2 TraesCS1B01G289700 chr1B 90.137 365 22 8 1894 2245 44998219 44997856 2.660000e-126 462.0
3 TraesCS1B01G289700 chr1D 89.939 2117 108 41 1 2071 377909517 377911574 0.000000e+00 2632.0
4 TraesCS1B01G289700 chr1D 89.427 558 55 3 2605 3161 377913497 377914051 0.000000e+00 701.0
5 TraesCS1B01G289700 chr1D 92.557 309 23 0 3470 3778 377915572 377915880 9.630000e-121 444.0
6 TraesCS1B01G289700 chr1D 93.962 265 14 2 2352 2615 377913212 377913475 2.110000e-107 399.0
7 TraesCS1B01G289700 chr1D 87.589 282 23 5 3198 3469 377914052 377914331 2.190000e-82 316.0
8 TraesCS1B01G289700 chr1D 95.882 170 4 2 2073 2242 377913041 377913207 4.810000e-69 272.0
9 TraesCS1B01G289700 chr1A 89.275 2014 102 39 301 2244 478450134 478452103 0.000000e+00 2418.0
10 TraesCS1B01G289700 chr1A 89.732 857 65 9 2941 3778 478459036 478459888 0.000000e+00 1074.0
11 TraesCS1B01G289700 chr1A 90.556 593 48 6 2352 2942 478452110 478452696 0.000000e+00 778.0
12 TraesCS1B01G289700 chr3B 93.292 805 39 7 1041 1845 764841485 764840696 0.000000e+00 1173.0
13 TraesCS1B01G289700 chr3B 95.567 203 9 0 2348 2550 757906713 757906915 3.640000e-85 326.0
14 TraesCS1B01G289700 chr3B 87.234 282 15 7 1984 2245 757906436 757906716 6.130000e-78 302.0
15 TraesCS1B01G289700 chrUn 90.137 365 22 8 1894 2245 219181503 219181866 2.660000e-126 462.0
16 TraesCS1B01G289700 chrUn 89.863 365 23 8 1894 2245 224087924 224087561 1.240000e-124 457.0
17 TraesCS1B01G289700 chrUn 95.074 203 10 0 2348 2550 219181863 219182065 1.690000e-83 320.0
18 TraesCS1B01G289700 chrUn 95.074 203 10 0 2348 2550 224087564 224087362 1.690000e-83 320.0
19 TraesCS1B01G289700 chr2B 89.818 275 15 5 1984 2245 263834762 263835036 1.300000e-89 340.0
20 TraesCS1B01G289700 chr2B 89.591 269 17 2 1984 2241 106852795 106853063 7.820000e-87 331.0
21 TraesCS1B01G289700 chr2B 95.122 205 9 1 2348 2552 772921229 772921026 4.710000e-84 322.0
22 TraesCS1B01G289700 chr2B 88.166 169 18 2 3123 3289 1766813 1766645 2.300000e-47 200.0
23 TraesCS1B01G289700 chr2B 86.982 169 20 2 3123 3289 1751649 1751481 4.980000e-44 189.0
24 TraesCS1B01G289700 chr2A 89.818 275 15 4 1984 2245 485222712 485222986 1.300000e-89 340.0
25 TraesCS1B01G289700 chr2A 89.455 275 16 4 1984 2245 485202148 485202422 6.050000e-88 335.0
26 TraesCS1B01G289700 chr2A 96.059 203 8 0 2348 2550 485202419 485202621 7.820000e-87 331.0
27 TraesCS1B01G289700 chr2A 96.059 203 8 0 2348 2550 687898012 687898214 7.820000e-87 331.0
28 TraesCS1B01G289700 chr2A 88.727 275 18 7 1984 2245 687897741 687898015 1.310000e-84 324.0
29 TraesCS1B01G289700 chr2A 100.000 28 0 0 3028 3055 529057813 529057840 7.000000e-03 52.8
30 TraesCS1B01G289700 chr5B 96.552 203 7 0 2348 2550 62738027 62737825 1.680000e-88 337.0
31 TraesCS1B01G289700 chr6B 89.455 275 16 7 1984 2245 95972242 95972516 6.050000e-88 335.0
32 TraesCS1B01G289700 chr6B 77.707 314 47 8 3432 3731 624226575 624226271 1.800000e-38 171.0
33 TraesCS1B01G289700 chr7B 87.234 282 14 9 1984 2245 697908482 697908761 6.130000e-78 302.0
34 TraesCS1B01G289700 chr3A 82.528 269 30 4 3509 3762 746458520 746458786 1.770000e-53 220.0
35 TraesCS1B01G289700 chr4A 94.872 117 5 1 2236 2352 595657949 595657834 8.340000e-42 182.0
36 TraesCS1B01G289700 chr4D 92.500 120 8 1 2237 2356 329002408 329002290 1.800000e-38 171.0
37 TraesCS1B01G289700 chr6D 82.558 86 4 4 2254 2338 414115950 414116025 8.760000e-07 65.8


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 TraesCS1B01G289700 chr1B 505109541 505113318 3777 False 6977.0 6977 100.000000 1 3778 1 chr1B.!!$F1 3777
1 TraesCS1B01G289700 chr1B 499733522 499734308 786 True 1096.0 1096 91.595000 1038 1845 1 chr1B.!!$R2 807
2 TraesCS1B01G289700 chr1D 377909517 377915880 6363 False 794.0 2632 91.559333 1 3778 6 chr1D.!!$F1 3777
3 TraesCS1B01G289700 chr1A 478450134 478452696 2562 False 1598.0 2418 89.915500 301 2942 2 chr1A.!!$F2 2641
4 TraesCS1B01G289700 chr1A 478459036 478459888 852 False 1074.0 1074 89.732000 2941 3778 1 chr1A.!!$F1 837
5 TraesCS1B01G289700 chr3B 764840696 764841485 789 True 1173.0 1173 93.292000 1041 1845 1 chr3B.!!$R1 804
6 TraesCS1B01G289700 chrUn 219181503 219182065 562 False 391.0 462 92.605500 1894 2550 2 chrUn.!!$F1 656
7 TraesCS1B01G289700 chrUn 224087362 224087924 562 True 388.5 457 92.468500 1894 2550 2 chrUn.!!$R1 656

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
608 637 0.042131 TCCACCCCATCTACCGACTT 59.958 55.0 0.0 0.0 0.00 3.01 F
968 1039 0.315251 CACGTGAGAGGAGAAGCACA 59.685 55.0 10.9 0.0 0.00 4.57 F
1483 1574 1.140312 TGGACTGACTGGCTTTTCCT 58.860 50.0 0.0 0.0 35.26 3.36 F
1757 1852 1.639298 GGCAATCCTCACGTCACTGC 61.639 60.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 3889 0.110509 CATGTCGCAGTTGTGAGTGC 60.111 55.0 0.0 0.0 46.54 4.40 R
2318 3894 0.241749 ATTGCCATGTCGCAGTTGTG 59.758 50.0 0.0 0.0 40.53 3.33 R
2325 3901 0.304705 CCGAGTAATTGCCATGTCGC 59.695 55.0 0.0 0.0 0.00 5.19 R
3105 4715 0.323360 ATATGCTTGCGGTTGGGTGT 60.323 50.0 0.0 0.0 0.00 4.16 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
106 111 2.252072 TAGTCCCTTCCGGCATGCAC 62.252 60.000 21.36 8.08 0.00 4.57
131 136 3.551887 ATGTGCGTGTCTGCGACGA 62.552 57.895 0.00 0.00 39.21 4.20
169 174 4.143333 CCCCGGTCACGTGGCTAG 62.143 72.222 21.13 14.13 38.78 3.42
239 247 5.413833 GCCCGATGAAATACAGATCATGAAT 59.586 40.000 0.00 0.00 36.45 2.57
251 259 5.530171 ACAGATCATGAATAGCCAACATCAC 59.470 40.000 0.00 0.00 0.00 3.06
272 280 1.082300 CTGAGCTGTGCGTGCAAAG 60.082 57.895 7.68 7.68 34.50 2.77
277 285 1.280746 CTGTGCGTGCAAAGGAGTG 59.719 57.895 4.02 0.00 0.00 3.51
279 287 2.186826 GTGCGTGCAAAGGAGTGGT 61.187 57.895 0.00 0.00 0.00 4.16
287 295 2.079925 GCAAAGGAGTGGTTGCTAGAG 58.920 52.381 0.00 0.00 45.34 2.43
299 308 4.079787 TGGTTGCTAGAGCCATAAAAGGAT 60.080 41.667 0.00 0.00 41.18 3.24
308 317 2.289002 GCCATAAAAGGATGCTCGTGAG 59.711 50.000 0.00 0.00 0.00 3.51
316 325 1.207390 GATGCTCGTGAGATGTCTGC 58.793 55.000 0.00 0.00 40.84 4.26
320 329 0.248417 CTCGTGAGATGTCTGCCTCG 60.248 60.000 0.00 0.00 40.84 4.63
338 347 2.270923 TCGTCGCAAATCCTGAAGATG 58.729 47.619 0.00 0.00 34.56 2.90
340 349 1.064654 GTCGCAAATCCTGAAGATGGC 59.935 52.381 0.00 0.00 34.56 4.40
387 400 0.107456 AATGTCCGCTGAGCTATGGG 59.893 55.000 1.78 0.00 0.00 4.00
423 436 0.977627 ATCACATGCAGAGGACCCGA 60.978 55.000 0.00 0.00 0.00 5.14
452 465 2.515057 TTCCCGTGCACGCAAACT 60.515 55.556 33.17 0.00 38.18 2.66
575 604 1.301623 CCGCAGTTTCCCACCCATA 59.698 57.895 0.00 0.00 0.00 2.74
608 637 0.042131 TCCACCCCATCTACCGACTT 59.958 55.000 0.00 0.00 0.00 3.01
768 808 4.680237 CGCGCCACCTTCTGGTCA 62.680 66.667 0.00 0.00 46.60 4.02
769 809 3.050275 GCGCCACCTTCTGGTCAC 61.050 66.667 0.00 0.00 46.60 3.67
770 810 2.738521 CGCCACCTTCTGGTCACG 60.739 66.667 0.00 0.00 46.60 4.35
771 811 3.050275 GCCACCTTCTGGTCACGC 61.050 66.667 0.00 0.00 46.60 5.34
772 812 2.358737 CCACCTTCTGGTCACGCC 60.359 66.667 0.00 0.00 46.60 5.68
780 820 1.375396 CTGGTCACGCCGATCCAAA 60.375 57.895 0.00 0.00 41.21 3.28
813 877 4.696172 CGTCGCACGCGGTGAAAC 62.696 66.667 12.47 7.32 37.86 2.78
814 878 4.696172 GTCGCACGCGGTGAAACG 62.696 66.667 12.47 4.64 37.86 3.60
928 999 1.651987 CCCACACTACAGGCATTACG 58.348 55.000 0.00 0.00 0.00 3.18
966 1037 1.967535 CCACGTGAGAGGAGAAGCA 59.032 57.895 19.30 0.00 45.46 3.91
968 1039 0.315251 CACGTGAGAGGAGAAGCACA 59.685 55.000 10.90 0.00 0.00 4.57
992 1063 1.220206 CTGGTGCTTGAGCGGATCT 59.780 57.895 0.00 0.00 45.83 2.75
1206 1277 2.292794 GATCCCGTAAGCGCTCCACA 62.293 60.000 12.06 0.00 36.67 4.17
1209 1280 2.430244 CGTAAGCGCTCCACACGT 60.430 61.111 12.06 0.00 0.00 4.49
1210 1281 2.434134 CGTAAGCGCTCCACACGTC 61.434 63.158 12.06 0.00 0.00 4.34
1212 1283 2.273179 TAAGCGCTCCACACGTCCT 61.273 57.895 12.06 0.00 0.00 3.85
1213 1284 2.209064 TAAGCGCTCCACACGTCCTC 62.209 60.000 12.06 0.00 0.00 3.71
1451 1537 4.230314 TCCTCTGATTTGATCGATCGAC 57.770 45.455 22.06 14.65 0.00 4.20
1478 1568 1.280421 GGAAGATGGACTGACTGGCTT 59.720 52.381 0.00 0.00 0.00 4.35
1479 1569 2.290577 GGAAGATGGACTGACTGGCTTT 60.291 50.000 0.00 0.00 0.00 3.51
1483 1574 1.140312 TGGACTGACTGGCTTTTCCT 58.860 50.000 0.00 0.00 35.26 3.36
1671 1766 2.421073 ACATGTGCGATTCTTGGTCATG 59.579 45.455 0.00 0.00 37.68 3.07
1757 1852 1.639298 GGCAATCCTCACGTCACTGC 61.639 60.000 0.00 0.00 0.00 4.40
2071 2182 2.919043 CCTACCTGGGTGGCATCC 59.081 66.667 10.69 10.69 40.22 3.51
2132 3708 8.338259 GTGGTATTAAAATGCTCATGTAGACAG 58.662 37.037 0.00 0.00 0.00 3.51
2199 3775 4.389992 ACAGTGTTTGTGCTATTCGAGATG 59.610 41.667 0.00 0.00 38.99 2.90
2262 3838 6.976636 TTTTTGAAACGAAGGCAAAAGATT 57.023 29.167 0.00 0.00 41.02 2.40
2263 3839 6.976636 TTTTGAAACGAAGGCAAAAGATTT 57.023 29.167 0.00 0.00 36.80 2.17
2264 3840 5.964887 TTGAAACGAAGGCAAAAGATTTG 57.035 34.783 0.00 0.00 0.00 2.32
2265 3841 3.801594 TGAAACGAAGGCAAAAGATTTGC 59.198 39.130 17.18 17.18 44.22 3.68
2287 3863 9.762381 TTTGCCTCTTTAATTAAATAAGGGAGA 57.238 29.630 25.87 20.42 33.34 3.71
2288 3864 8.980481 TGCCTCTTTAATTAAATAAGGGAGAG 57.020 34.615 25.87 19.36 32.71 3.20
2289 3865 8.778059 TGCCTCTTTAATTAAATAAGGGAGAGA 58.222 33.333 25.87 12.67 32.71 3.10
2290 3866 9.628500 GCCTCTTTAATTAAATAAGGGAGAGAA 57.372 33.333 25.87 1.34 32.71 2.87
2302 3878 9.495382 AAATAAGGGAGAGAATAGTGTAGAGTT 57.505 33.333 0.00 0.00 0.00 3.01
2303 3879 9.495382 AATAAGGGAGAGAATAGTGTAGAGTTT 57.505 33.333 0.00 0.00 0.00 2.66
2304 3880 7.800300 AAGGGAGAGAATAGTGTAGAGTTTT 57.200 36.000 0.00 0.00 0.00 2.43
2305 3881 7.800300 AGGGAGAGAATAGTGTAGAGTTTTT 57.200 36.000 0.00 0.00 0.00 1.94
2324 3900 4.688511 TTTTTACAACGCACTCACAACT 57.311 36.364 0.00 0.00 0.00 3.16
2325 3901 3.666883 TTTACAACGCACTCACAACTG 57.333 42.857 0.00 0.00 0.00 3.16
2326 3902 0.934496 TACAACGCACTCACAACTGC 59.066 50.000 0.00 0.00 0.00 4.40
2330 3906 3.717899 GCACTCACAACTGCGACA 58.282 55.556 0.00 0.00 0.00 4.35
2331 3907 2.238353 GCACTCACAACTGCGACAT 58.762 52.632 0.00 0.00 0.00 3.06
2332 3908 0.110509 GCACTCACAACTGCGACATG 60.111 55.000 0.00 0.00 0.00 3.21
2333 3909 0.514255 CACTCACAACTGCGACATGG 59.486 55.000 0.00 0.00 0.00 3.66
2334 3910 1.230635 ACTCACAACTGCGACATGGC 61.231 55.000 0.00 0.00 0.00 4.40
2335 3911 1.227793 TCACAACTGCGACATGGCA 60.228 52.632 0.00 0.00 41.45 4.92
2336 3912 0.817229 TCACAACTGCGACATGGCAA 60.817 50.000 0.00 0.00 43.39 4.52
2337 3913 0.241749 CACAACTGCGACATGGCAAT 59.758 50.000 0.00 0.00 43.39 3.56
2338 3914 0.961019 ACAACTGCGACATGGCAATT 59.039 45.000 0.00 0.00 43.39 2.32
2339 3915 2.095314 CACAACTGCGACATGGCAATTA 60.095 45.455 0.00 0.00 43.39 1.40
2340 3916 2.095263 ACAACTGCGACATGGCAATTAC 60.095 45.455 0.00 0.00 43.39 1.89
2341 3917 2.113860 ACTGCGACATGGCAATTACT 57.886 45.000 0.00 0.00 43.39 2.24
2342 3918 2.009774 ACTGCGACATGGCAATTACTC 58.990 47.619 0.00 0.00 43.39 2.59
2343 3919 1.004610 CTGCGACATGGCAATTACTCG 60.005 52.381 0.00 0.00 43.39 4.18
2344 3920 0.304705 GCGACATGGCAATTACTCGG 59.695 55.000 0.00 0.00 0.00 4.63
2345 3921 1.934589 CGACATGGCAATTACTCGGA 58.065 50.000 0.00 0.00 0.00 4.55
2346 3922 1.593006 CGACATGGCAATTACTCGGAC 59.407 52.381 0.00 0.00 0.00 4.79
2347 3923 2.627945 GACATGGCAATTACTCGGACA 58.372 47.619 0.00 0.00 0.00 4.02
2348 3924 3.206150 GACATGGCAATTACTCGGACAT 58.794 45.455 0.00 0.00 0.00 3.06
2349 3925 3.620488 ACATGGCAATTACTCGGACATT 58.380 40.909 0.00 0.00 0.00 2.71
2350 3926 4.776349 ACATGGCAATTACTCGGACATTA 58.224 39.130 0.00 0.00 0.00 1.90
2419 3995 5.091261 AGTTATCTTGATGAGTGTCCACC 57.909 43.478 0.00 0.00 0.00 4.61
2421 3997 5.249393 AGTTATCTTGATGAGTGTCCACCTT 59.751 40.000 0.00 0.00 0.00 3.50
2536 4113 0.036388 GATTCACCAGGCTCGGTCAA 60.036 55.000 5.76 0.93 37.07 3.18
2621 4230 4.481368 TTGATACCTGTAGGCGAACATT 57.519 40.909 0.00 0.00 39.32 2.71
2627 4236 3.244422 ACCTGTAGGCGAACATTTGAGAA 60.244 43.478 0.00 0.00 39.32 2.87
2628 4237 3.125316 CCTGTAGGCGAACATTTGAGAAC 59.875 47.826 0.00 0.00 0.00 3.01
2631 4240 4.759693 TGTAGGCGAACATTTGAGAACAAT 59.240 37.500 0.00 0.00 35.85 2.71
2639 4249 6.038161 CGAACATTTGAGAACAATATGGCCTA 59.962 38.462 3.32 0.00 35.85 3.93
2652 4262 6.265422 ACAATATGGCCTAAACAGATTTAGCC 59.735 38.462 3.32 10.68 44.12 3.93
2659 4269 6.546034 GGCCTAAACAGATTTAGCCTATTCAA 59.454 38.462 0.00 0.00 44.12 2.69
2689 4299 3.747976 CCCTTTTCTTGCCCGGCG 61.748 66.667 4.58 0.00 0.00 6.46
2714 4324 1.988107 TGCAGGATTCTTCTGGGAAGT 59.012 47.619 7.09 0.00 33.16 3.01
2730 4340 2.482490 GGAAGTGTGACCAACTACGTGT 60.482 50.000 0.00 0.00 0.00 4.49
2789 4399 1.140161 CCGTTAGGTTCGCCATCGA 59.860 57.895 0.00 0.00 43.89 3.59
2836 4446 4.299547 TGCTCCGTTGCTGCGTCT 62.300 61.111 0.00 0.00 0.00 4.18
2891 4501 3.996825 CGCAGGTTTGGCAGATTAC 57.003 52.632 0.00 0.00 0.00 1.89
2896 4506 3.756434 GCAGGTTTGGCAGATTACTGTAA 59.244 43.478 2.26 2.26 45.04 2.41
2927 4537 6.000891 TGTTTCTGAACATTTGGATTCGAG 57.999 37.500 0.00 0.00 40.71 4.04
3001 4611 4.394920 GGACGACCAAATGATTTGCTCTAA 59.605 41.667 12.26 0.00 39.31 2.10
3008 4618 8.712285 ACCAAATGATTTGCTCTAATTTCATG 57.288 30.769 12.26 0.00 39.31 3.07
3009 4619 7.279313 ACCAAATGATTTGCTCTAATTTCATGC 59.721 33.333 12.26 0.00 39.31 4.06
3010 4620 7.254658 CCAAATGATTTGCTCTAATTTCATGCC 60.255 37.037 12.26 0.00 39.31 4.40
3056 4666 3.938963 TGCAACGAGAGAAACAAACTCTT 59.061 39.130 0.00 0.00 43.55 2.85
3065 4675 1.111277 AACAAACTCTTGTGCACCCC 58.889 50.000 15.69 0.00 45.25 4.95
3103 4713 2.664568 CGTTGGTATAAGTGTCCACGTG 59.335 50.000 9.08 9.08 36.20 4.49
3105 4715 4.309099 GTTGGTATAAGTGTCCACGTGAA 58.691 43.478 19.30 0.00 36.20 3.18
3121 4731 2.441164 AACACCCAACCGCAAGCA 60.441 55.556 0.00 0.00 0.00 3.91
3134 4744 5.323371 ACCGCAAGCATATGTTAAACAAT 57.677 34.783 4.29 0.00 0.00 2.71
3137 4747 5.804473 CCGCAAGCATATGTTAAACAATCAA 59.196 36.000 4.29 0.00 0.00 2.57
3138 4748 6.020440 CCGCAAGCATATGTTAAACAATCAAG 60.020 38.462 4.29 0.00 0.00 3.02
3156 4766 2.556622 CAAGCGGGTCCACTAAATGTTT 59.443 45.455 0.00 0.00 0.00 2.83
3167 4777 9.406828 GGTCCACTAAATGTTTAAGAAATGAAC 57.593 33.333 0.00 0.00 0.00 3.18
3170 4780 7.061789 CCACTAAATGTTTAAGAAATGAACGGC 59.938 37.037 0.00 0.00 30.42 5.68
3190 4800 1.542492 CTTGCCTTGGAGCTTGTGAT 58.458 50.000 0.00 0.00 0.00 3.06
3192 4802 1.250328 TGCCTTGGAGCTTGTGATTG 58.750 50.000 0.00 0.00 0.00 2.67
3195 4805 0.529378 CTTGGAGCTTGTGATTGGGC 59.471 55.000 0.00 0.00 0.00 5.36
3200 4810 0.823356 AGCTTGTGATTGGGCGTTGT 60.823 50.000 0.00 0.00 0.00 3.32
3213 4823 2.752903 GGGCGTTGTTTCAGGTTCATAT 59.247 45.455 0.00 0.00 0.00 1.78
3259 4869 8.929827 TTTATTATGTGCCATGTCATCAAAAG 57.070 30.769 0.00 0.00 0.00 2.27
3270 4880 6.401394 CATGTCATCAAAAGAGTCTAGGTGA 58.599 40.000 0.00 0.00 0.00 4.02
3305 4920 4.386954 CGATGATACGATTGTTGGAGATGG 59.613 45.833 0.00 0.00 35.09 3.51
3312 4927 4.102524 ACGATTGTTGGAGATGGCCTAATA 59.897 41.667 3.32 0.00 0.00 0.98
3347 4962 6.548441 TTTCTTTTTGTACCATCGTCGATT 57.452 33.333 4.63 0.00 0.00 3.34
3406 5033 4.630644 AGACTGTGAGTTTGGTCATCAT 57.369 40.909 0.00 0.00 0.00 2.45
3417 5044 7.443272 TGAGTTTGGTCATCATAATCTAGCATG 59.557 37.037 0.00 0.00 0.00 4.06
3646 6515 3.655615 TTACCACGCCCATTTATTCCT 57.344 42.857 0.00 0.00 0.00 3.36
3651 6520 3.066760 CCACGCCCATTTATTCCTTCTTC 59.933 47.826 0.00 0.00 0.00 2.87
3723 6599 1.152694 ATCGGCCCATCCAACCATG 60.153 57.895 0.00 0.00 34.01 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 111 2.023771 AGACACGCACATGCTGACG 61.024 57.895 1.82 2.21 39.32 4.35
131 136 4.996434 GGCACTGTGTCGGCTGCT 62.996 66.667 9.86 0.00 0.00 4.24
225 233 7.389884 GTGATGTTGGCTATTCATGATCTGTAT 59.610 37.037 0.00 0.00 0.00 2.29
226 234 6.707608 GTGATGTTGGCTATTCATGATCTGTA 59.292 38.462 0.00 0.00 0.00 2.74
227 235 5.530171 GTGATGTTGGCTATTCATGATCTGT 59.470 40.000 0.00 0.00 0.00 3.41
239 247 1.676916 GCTCAGCTGTGATGTTGGCTA 60.677 52.381 19.61 0.00 33.43 3.93
268 276 2.079925 GCTCTAGCAACCACTCCTTTG 58.920 52.381 0.00 0.00 41.59 2.77
272 280 0.543749 ATGGCTCTAGCAACCACTCC 59.456 55.000 4.07 0.00 44.36 3.85
277 285 3.886123 TCCTTTTATGGCTCTAGCAACC 58.114 45.455 4.07 0.00 44.36 3.77
279 287 3.885297 GCATCCTTTTATGGCTCTAGCAA 59.115 43.478 4.07 0.00 44.36 3.91
287 295 2.288666 TCACGAGCATCCTTTTATGGC 58.711 47.619 0.00 0.00 0.00 4.40
299 308 1.216444 GGCAGACATCTCACGAGCA 59.784 57.895 0.00 0.00 0.00 4.26
308 317 1.014044 TTTGCGACGAGGCAGACATC 61.014 55.000 0.00 0.00 44.94 3.06
316 325 1.002366 CTTCAGGATTTGCGACGAGG 58.998 55.000 0.00 0.00 0.00 4.63
320 329 1.064654 GCCATCTTCAGGATTTGCGAC 59.935 52.381 0.00 0.00 31.27 5.19
338 347 2.014128 TGCTTAAACAAGATAGGCGCC 58.986 47.619 21.89 21.89 0.00 6.53
340 349 4.558860 GCTTTTGCTTAAACAAGATAGGCG 59.441 41.667 0.00 0.00 43.35 5.52
423 436 2.158871 TGCACGGGAACAGTTTCTTACT 60.159 45.455 0.00 0.00 37.68 2.24
452 465 0.824595 TTGAGAGGTTCCGTGGTCGA 60.825 55.000 0.00 0.00 39.71 4.20
763 803 1.375396 CTTTGGATCGGCGTGACCA 60.375 57.895 6.85 12.26 39.03 4.02
764 804 2.750888 GCTTTGGATCGGCGTGACC 61.751 63.158 6.85 9.67 0.00 4.02
765 805 2.750888 GGCTTTGGATCGGCGTGAC 61.751 63.158 6.85 0.00 0.00 3.67
766 806 2.435938 GGCTTTGGATCGGCGTGA 60.436 61.111 6.85 0.00 0.00 4.35
767 807 3.508840 GGGCTTTGGATCGGCGTG 61.509 66.667 6.85 0.00 0.00 5.34
768 808 4.796495 GGGGCTTTGGATCGGCGT 62.796 66.667 6.85 0.00 0.00 5.68
770 810 3.774599 ATCGGGGCTTTGGATCGGC 62.775 63.158 0.00 0.00 0.00 5.54
771 811 1.893808 CATCGGGGCTTTGGATCGG 60.894 63.158 0.00 0.00 0.00 4.18
772 812 2.546494 GCATCGGGGCTTTGGATCG 61.546 63.158 0.00 0.00 0.00 3.69
827 891 4.394712 GGTGGGAGCACACGGGAG 62.395 72.222 0.00 0.00 42.23 4.30
914 978 2.081462 GTTTGCCGTAATGCCTGTAGT 58.919 47.619 0.00 0.00 0.00 2.73
915 979 2.080693 TGTTTGCCGTAATGCCTGTAG 58.919 47.619 0.00 0.00 0.00 2.74
992 1063 4.794648 CGCCGGCCATCCTTTCCA 62.795 66.667 23.46 0.00 0.00 3.53
1033 1104 3.492353 CATGGCCACCCCGATCCT 61.492 66.667 8.16 0.00 35.87 3.24
1173 1244 2.674754 GATCCGGACTTGGCCCAA 59.325 61.111 6.12 0.00 0.00 4.12
1206 1277 2.207924 GGGTGTGTGAGGAGGACGT 61.208 63.158 0.00 0.00 0.00 4.34
1209 1280 1.841556 GGTGGGTGTGTGAGGAGGA 60.842 63.158 0.00 0.00 0.00 3.71
1210 1281 2.750350 GGTGGGTGTGTGAGGAGG 59.250 66.667 0.00 0.00 0.00 4.30
1212 1283 2.852075 GGGGTGGGTGTGTGAGGA 60.852 66.667 0.00 0.00 0.00 3.71
1213 1284 2.854032 AGGGGTGGGTGTGTGAGG 60.854 66.667 0.00 0.00 0.00 3.86
1214 1285 1.843376 AGAGGGGTGGGTGTGTGAG 60.843 63.158 0.00 0.00 0.00 3.51
1282 1357 3.199290 CTCGGACAGAGGGATGAGT 57.801 57.895 0.00 0.00 43.20 3.41
1451 1537 2.121948 TCAGTCCATCTTCCTCCATGG 58.878 52.381 4.97 4.97 41.04 3.66
1478 1568 1.562942 AGCTGATCATCAGGCAGGAAA 59.437 47.619 16.70 0.00 44.43 3.13
1479 1569 1.134189 CAGCTGATCATCAGGCAGGAA 60.134 52.381 16.70 0.00 44.43 3.36
1483 1574 1.134189 CCTTCAGCTGATCATCAGGCA 60.134 52.381 19.04 0.00 44.43 4.75
1604 1695 2.025605 AGTGTCGTACCTCTGGATGGTA 60.026 50.000 0.00 0.00 38.88 3.25
1622 1713 4.516698 AGCAACATTTTGACAGGAGTAGTG 59.483 41.667 0.00 0.00 34.24 2.74
1671 1766 4.066418 CGATTTCGTGCTCTGGGAAACC 62.066 54.545 0.00 0.00 42.66 3.27
2071 2182 2.746904 TGACCACACAAATAATCTGGCG 59.253 45.455 0.00 0.00 0.00 5.69
2132 3708 8.263940 TCTACACCATTCTAATGCTTAAACAC 57.736 34.615 0.00 0.00 35.08 3.32
2199 3775 7.019774 TCTGATGAACACTTATTTATGCTGC 57.980 36.000 0.00 0.00 0.00 5.25
2244 3820 4.374990 GCAAATCTTTTGCCTTCGTTTC 57.625 40.909 12.74 0.00 39.38 2.78
2261 3837 9.762381 TCTCCCTTATTTAATTAAAGAGGCAAA 57.238 29.630 24.50 16.21 34.06 3.68
2262 3838 9.408648 CTCTCCCTTATTTAATTAAAGAGGCAA 57.591 33.333 24.50 17.72 34.06 4.52
2263 3839 8.778059 TCTCTCCCTTATTTAATTAAAGAGGCA 58.222 33.333 24.50 16.29 34.06 4.75
2264 3840 9.628500 TTCTCTCCCTTATTTAATTAAAGAGGC 57.372 33.333 24.50 0.00 34.06 4.70
2276 3852 9.495382 AACTCTACACTATTCTCTCCCTTATTT 57.505 33.333 0.00 0.00 0.00 1.40
2277 3853 9.495382 AAACTCTACACTATTCTCTCCCTTATT 57.505 33.333 0.00 0.00 0.00 1.40
2278 3854 9.495382 AAAACTCTACACTATTCTCTCCCTTAT 57.505 33.333 0.00 0.00 0.00 1.73
2279 3855 8.896722 AAAACTCTACACTATTCTCTCCCTTA 57.103 34.615 0.00 0.00 0.00 2.69
2280 3856 7.800300 AAAACTCTACACTATTCTCTCCCTT 57.200 36.000 0.00 0.00 0.00 3.95
2281 3857 7.800300 AAAAACTCTACACTATTCTCTCCCT 57.200 36.000 0.00 0.00 0.00 4.20
2303 3879 4.407818 CAGTTGTGAGTGCGTTGTAAAAA 58.592 39.130 0.00 0.00 0.00 1.94
2304 3880 3.729462 GCAGTTGTGAGTGCGTTGTAAAA 60.729 43.478 0.00 0.00 41.95 1.52
2305 3881 2.223157 GCAGTTGTGAGTGCGTTGTAAA 60.223 45.455 0.00 0.00 41.95 2.01
2306 3882 1.329292 GCAGTTGTGAGTGCGTTGTAA 59.671 47.619 0.00 0.00 41.95 2.41
2307 3883 0.934496 GCAGTTGTGAGTGCGTTGTA 59.066 50.000 0.00 0.00 41.95 2.41
2308 3884 1.721487 GCAGTTGTGAGTGCGTTGT 59.279 52.632 0.00 0.00 41.95 3.32
2309 3885 4.595629 GCAGTTGTGAGTGCGTTG 57.404 55.556 0.00 0.00 41.95 4.10
2313 3889 0.110509 CATGTCGCAGTTGTGAGTGC 60.111 55.000 0.00 0.00 46.54 4.40
2314 3890 0.514255 CCATGTCGCAGTTGTGAGTG 59.486 55.000 0.00 0.00 34.93 3.51
2315 3891 1.230635 GCCATGTCGCAGTTGTGAGT 61.231 55.000 0.00 0.00 34.93 3.41
2316 3892 1.229975 TGCCATGTCGCAGTTGTGAG 61.230 55.000 0.00 0.00 34.93 3.51
2317 3893 0.817229 TTGCCATGTCGCAGTTGTGA 60.817 50.000 0.00 0.00 40.53 3.58
2318 3894 0.241749 ATTGCCATGTCGCAGTTGTG 59.758 50.000 0.00 0.00 40.53 3.33
2319 3895 0.961019 AATTGCCATGTCGCAGTTGT 59.039 45.000 4.34 0.00 40.53 3.32
2320 3896 2.162208 AGTAATTGCCATGTCGCAGTTG 59.838 45.455 12.73 0.00 38.88 3.16
2321 3897 2.420022 GAGTAATTGCCATGTCGCAGTT 59.580 45.455 9.10 9.10 41.09 3.16
2322 3898 2.009774 GAGTAATTGCCATGTCGCAGT 58.990 47.619 0.00 0.00 40.53 4.40
2323 3899 1.004610 CGAGTAATTGCCATGTCGCAG 60.005 52.381 0.00 0.00 40.53 5.18
2324 3900 1.006086 CGAGTAATTGCCATGTCGCA 58.994 50.000 0.00 0.00 36.85 5.10
2325 3901 0.304705 CCGAGTAATTGCCATGTCGC 59.695 55.000 0.00 0.00 0.00 5.19
2326 3902 1.593006 GTCCGAGTAATTGCCATGTCG 59.407 52.381 0.00 0.00 0.00 4.35
2327 3903 2.627945 TGTCCGAGTAATTGCCATGTC 58.372 47.619 0.00 0.00 0.00 3.06
2328 3904 2.779755 TGTCCGAGTAATTGCCATGT 57.220 45.000 0.00 0.00 0.00 3.21
2329 3905 5.947228 ATAATGTCCGAGTAATTGCCATG 57.053 39.130 0.00 0.00 0.00 3.66
2330 3906 6.205464 CAGAATAATGTCCGAGTAATTGCCAT 59.795 38.462 0.00 0.00 0.00 4.40
2331 3907 5.527214 CAGAATAATGTCCGAGTAATTGCCA 59.473 40.000 0.00 0.00 0.00 4.92
2332 3908 5.049405 CCAGAATAATGTCCGAGTAATTGCC 60.049 44.000 0.00 0.00 0.00 4.52
2333 3909 5.758296 TCCAGAATAATGTCCGAGTAATTGC 59.242 40.000 0.00 0.00 0.00 3.56
2334 3910 7.875041 AGATCCAGAATAATGTCCGAGTAATTG 59.125 37.037 0.00 0.00 0.00 2.32
2335 3911 7.967908 AGATCCAGAATAATGTCCGAGTAATT 58.032 34.615 0.00 0.00 0.00 1.40
2336 3912 7.546250 AGATCCAGAATAATGTCCGAGTAAT 57.454 36.000 0.00 0.00 0.00 1.89
2337 3913 6.978674 AGATCCAGAATAATGTCCGAGTAA 57.021 37.500 0.00 0.00 0.00 2.24
2338 3914 7.888546 TCATAGATCCAGAATAATGTCCGAGTA 59.111 37.037 0.00 0.00 0.00 2.59
2339 3915 6.721668 TCATAGATCCAGAATAATGTCCGAGT 59.278 38.462 0.00 0.00 0.00 4.18
2340 3916 7.032580 GTCATAGATCCAGAATAATGTCCGAG 58.967 42.308 0.00 0.00 0.00 4.63
2341 3917 6.721668 AGTCATAGATCCAGAATAATGTCCGA 59.278 38.462 0.00 0.00 0.00 4.55
2342 3918 6.929625 AGTCATAGATCCAGAATAATGTCCG 58.070 40.000 0.00 0.00 0.00 4.79
2343 3919 7.543868 CGAAGTCATAGATCCAGAATAATGTCC 59.456 40.741 0.00 0.00 0.00 4.02
2344 3920 7.543868 CCGAAGTCATAGATCCAGAATAATGTC 59.456 40.741 0.00 0.00 0.00 3.06
2345 3921 7.015682 ACCGAAGTCATAGATCCAGAATAATGT 59.984 37.037 0.00 0.00 0.00 2.71
2346 3922 7.382110 ACCGAAGTCATAGATCCAGAATAATG 58.618 38.462 0.00 0.00 0.00 1.90
2347 3923 7.546250 ACCGAAGTCATAGATCCAGAATAAT 57.454 36.000 0.00 0.00 0.00 1.28
2348 3924 6.978674 ACCGAAGTCATAGATCCAGAATAA 57.021 37.500 0.00 0.00 0.00 1.40
2349 3925 6.738731 GCAACCGAAGTCATAGATCCAGAATA 60.739 42.308 0.00 0.00 0.00 1.75
2350 3926 5.605534 CAACCGAAGTCATAGATCCAGAAT 58.394 41.667 0.00 0.00 0.00 2.40
2536 4113 0.982852 TGCCCAAGGATCAGACCGAT 60.983 55.000 0.00 0.00 36.91 4.18
2606 4183 2.972625 TCTCAAATGTTCGCCTACAGG 58.027 47.619 0.00 0.00 38.53 4.00
2621 4230 6.480763 TCTGTTTAGGCCATATTGTTCTCAA 58.519 36.000 5.01 0.00 37.98 3.02
2627 4236 7.277174 GCTAAATCTGTTTAGGCCATATTGT 57.723 36.000 5.01 0.00 44.48 2.71
2652 4262 4.396166 AGGGCGTCAGTGAAATTTGAATAG 59.604 41.667 0.00 0.00 0.00 1.73
2659 4269 3.222603 AGAAAAGGGCGTCAGTGAAATT 58.777 40.909 0.00 0.00 0.00 1.82
2689 4299 1.093159 CAGAAGAATCCTGCAGCACC 58.907 55.000 8.66 0.00 0.00 5.01
2836 4446 7.573710 ACACAATAGGCTCCATACTTTATTCA 58.426 34.615 0.00 0.00 0.00 2.57
2925 4535 3.728845 TGGCAGACACTTTACTGAACTC 58.271 45.455 0.00 0.00 36.38 3.01
2927 4537 4.127171 TCTTGGCAGACACTTTACTGAAC 58.873 43.478 0.00 0.00 36.38 3.18
3001 4611 3.081061 TGTTTGCTAGTCGGCATGAAAT 58.919 40.909 0.00 0.00 42.09 2.17
3008 4618 2.864343 ACGAATATGTTTGCTAGTCGGC 59.136 45.455 5.07 0.00 40.03 5.54
3009 4619 3.302480 GCACGAATATGTTTGCTAGTCGG 60.302 47.826 5.07 0.00 40.03 4.79
3010 4620 3.599339 CGCACGAATATGTTTGCTAGTCG 60.599 47.826 0.00 0.00 41.11 4.18
3056 4666 2.546899 ACATACTCTTAGGGGTGCACA 58.453 47.619 20.43 0.00 0.00 4.57
3103 4713 1.805428 ATGCTTGCGGTTGGGTGTTC 61.805 55.000 0.00 0.00 0.00 3.18
3105 4715 0.323360 ATATGCTTGCGGTTGGGTGT 60.323 50.000 0.00 0.00 0.00 4.16
3121 4731 5.067283 GGACCCGCTTGATTGTTTAACATAT 59.933 40.000 0.00 0.00 0.00 1.78
3134 4744 1.349688 ACATTTAGTGGACCCGCTTGA 59.650 47.619 7.49 0.00 37.92 3.02
3137 4747 2.579410 AAACATTTAGTGGACCCGCT 57.421 45.000 7.34 7.34 40.24 5.52
3138 4748 4.004982 TCTTAAACATTTAGTGGACCCGC 58.995 43.478 0.00 0.00 0.00 6.13
3156 4766 1.816224 GGCAAGGCCGTTCATTTCTTA 59.184 47.619 0.00 0.00 39.62 2.10
3170 4780 0.538057 TCACAAGCTCCAAGGCAAGG 60.538 55.000 0.00 0.00 34.17 3.61
3190 4800 0.741915 GAACCTGAAACAACGCCCAA 59.258 50.000 0.00 0.00 0.00 4.12
3192 4802 0.958822 ATGAACCTGAAACAACGCCC 59.041 50.000 0.00 0.00 0.00 6.13
3195 4805 7.304735 TGAAATCATATGAACCTGAAACAACG 58.695 34.615 9.99 0.00 0.00 4.10
3200 4810 9.690913 AGAGAATGAAATCATATGAACCTGAAA 57.309 29.630 9.99 0.00 35.10 2.69
3270 4880 7.065324 ACAATCGTATCATCGTTGGTAAATTGT 59.935 33.333 16.00 16.00 34.92 2.71
3305 4920 9.923143 AAAAGAAAAGGTAACAACATATTAGGC 57.077 29.630 0.00 0.00 41.41 3.93
3312 4927 8.532819 TGGTACAAAAAGAAAAGGTAACAACAT 58.467 29.630 0.00 0.00 33.73 2.71
3347 4962 4.908601 AATAGATGGACAAGTGACCACA 57.091 40.909 4.61 0.00 42.19 4.17
3389 5016 6.763135 GCTAGATTATGATGACCAAACTCACA 59.237 38.462 0.00 0.00 0.00 3.58
3646 6515 8.760980 TCCAAAAGGAACTGAAATTAGAAGAA 57.239 30.769 0.00 0.00 40.86 2.52
3651 6520 6.152379 GTGCTCCAAAAGGAACTGAAATTAG 58.848 40.000 0.00 0.00 40.86 1.73


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

AutoCloner maintained by Alex Coulton.