Multiple sequence alignment - TraesCS6B01G083500

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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 TraesCS6B01G083500 chr6B 100.000 3301 0 0 1 3301 60605573 60602273 0.000000e+00 6096
1 TraesCS6B01G083500 chr6B 90.811 1295 48 20 249 1500 563134689 563133423 0.000000e+00 1666
2 TraesCS6B01G083500 chr6B 88.692 1300 92 27 1500 2754 563133375 563132086 0.000000e+00 1535
3 TraesCS6B01G083500 chr6B 88.684 1299 89 28 1500 2753 563145268 563143983 0.000000e+00 1531
4 TraesCS6B01G083500 chr6B 89.033 1158 86 20 2 1135 25429385 25428245 0.000000e+00 1397
5 TraesCS6B01G083500 chr6B 89.014 1156 90 16 2 1135 25454677 25453537 0.000000e+00 1397
6 TraesCS6B01G083500 chr6B 88.383 1076 92 16 78 1135 25408091 25407031 0.000000e+00 1264
7 TraesCS6B01G083500 chr6B 91.189 908 37 9 618 1500 563146205 563145316 0.000000e+00 1194
8 TraesCS6B01G083500 chr6B 89.003 582 49 9 4 573 25398315 25397737 0.000000e+00 706
9 TraesCS6B01G083500 chr6D 97.231 1517 25 4 1 1500 29113849 29115365 0.000000e+00 2553
10 TraesCS6B01G083500 chr6D 92.534 1701 94 7 1500 3175 29115413 29117105 0.000000e+00 2407
11 TraesCS6B01G083500 chr6D 91.113 1294 49 18 249 1500 376946489 376945220 0.000000e+00 1692
12 TraesCS6B01G083500 chr6D 91.113 1294 49 18 249 1500 376975383 376974114 0.000000e+00 1692
13 TraesCS6B01G083500 chr6D 88.829 1298 84 29 1500 2754 376945172 376943893 0.000000e+00 1537
14 TraesCS6B01G083500 chr6D 88.829 1298 84 29 1500 2754 376974066 376972787 0.000000e+00 1537
15 TraesCS6B01G083500 chr6D 86.207 290 34 5 3 286 13958594 13958305 3.200000e-80 309
16 TraesCS6B01G083500 chr6D 86.643 277 17 7 1 257 376946870 376946594 4.170000e-74 289
17 TraesCS6B01G083500 chr6D 83.333 186 21 6 2793 2977 376943893 376943717 2.640000e-36 163
18 TraesCS6B01G083500 chr6D 83.333 186 21 6 2793 2977 376972787 376972611 2.640000e-36 163
19 TraesCS6B01G083500 chr6A 94.348 1504 49 14 1 1500 33294562 33293091 0.000000e+00 2274
20 TraesCS6B01G083500 chr6A 94.350 1292 39 7 1500 2762 33293043 33291757 0.000000e+00 1951
21 TraesCS6B01G083500 chr6A 90.502 1295 53 18 249 1500 518598878 518597611 0.000000e+00 1646
22 TraesCS6B01G083500 chr6A 90.123 1296 57 20 249 1500 518550786 518549518 0.000000e+00 1618
23 TraesCS6B01G083500 chr6A 88.829 1298 91 24 1500 2754 518549470 518548184 0.000000e+00 1544
24 TraesCS6B01G083500 chr6A 88.701 1301 90 24 1500 2754 518597563 518596274 0.000000e+00 1535
25 TraesCS6B01G083500 chr6A 89.699 864 78 10 6 865 14530866 14530010 0.000000e+00 1092
26 TraesCS6B01G083500 chr6A 87.730 652 40 9 862 1495 14522588 14521959 0.000000e+00 725
27 TraesCS6B01G083500 chr6A 84.774 243 30 2 2972 3207 33289789 33289547 1.530000e-58 237
28 TraesCS6B01G083500 chr6A 89.730 185 16 2 2756 2940 33291701 33291520 1.980000e-57 233
29 TraesCS6B01G083500 chr6A 84.277 159 22 1 2793 2951 518596274 518596119 5.710000e-33 152
30 TraesCS6B01G083500 chr6A 88.636 88 10 0 2793 2880 518548184 518548097 1.250000e-19 108
31 TraesCS6B01G083500 chrUn 91.477 833 51 10 315 1135 355299268 355298444 0.000000e+00 1127
32 TraesCS6B01G083500 chrUn 86.207 290 34 5 3 286 469507427 469507138 3.200000e-80 309
33 TraesCS6B01G083500 chrUn 92.638 163 9 3 1332 1494 394744281 394744440 7.120000e-57 231


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 TraesCS6B01G083500 chr6B 60602273 60605573 3300 True 6096.000000 6096 100.000000 1 3301 1 chr6B.!!$R5 3300
1 TraesCS6B01G083500 chr6B 563132086 563134689 2603 True 1600.500000 1666 89.751500 249 2754 2 chr6B.!!$R6 2505
2 TraesCS6B01G083500 chr6B 25428245 25429385 1140 True 1397.000000 1397 89.033000 2 1135 1 chr6B.!!$R3 1133
3 TraesCS6B01G083500 chr6B 25453537 25454677 1140 True 1397.000000 1397 89.014000 2 1135 1 chr6B.!!$R4 1133
4 TraesCS6B01G083500 chr6B 563143983 563146205 2222 True 1362.500000 1531 89.936500 618 2753 2 chr6B.!!$R7 2135
5 TraesCS6B01G083500 chr6B 25407031 25408091 1060 True 1264.000000 1264 88.383000 78 1135 1 chr6B.!!$R2 1057
6 TraesCS6B01G083500 chr6B 25397737 25398315 578 True 706.000000 706 89.003000 4 573 1 chr6B.!!$R1 569
7 TraesCS6B01G083500 chr6D 29113849 29117105 3256 False 2480.000000 2553 94.882500 1 3175 2 chr6D.!!$F1 3174
8 TraesCS6B01G083500 chr6D 376972611 376975383 2772 True 1130.666667 1692 87.758333 249 2977 3 chr6D.!!$R3 2728
9 TraesCS6B01G083500 chr6D 376943717 376946870 3153 True 920.250000 1692 87.479500 1 2977 4 chr6D.!!$R2 2976
10 TraesCS6B01G083500 chr6A 33289547 33294562 5015 True 1173.750000 2274 90.800500 1 3207 4 chr6A.!!$R3 3206
11 TraesCS6B01G083500 chr6A 518596119 518598878 2759 True 1111.000000 1646 87.826667 249 2951 3 chr6A.!!$R5 2702
12 TraesCS6B01G083500 chr6A 14530010 14530866 856 True 1092.000000 1092 89.699000 6 865 1 chr6A.!!$R2 859
13 TraesCS6B01G083500 chr6A 518548097 518550786 2689 True 1090.000000 1618 89.196000 249 2880 3 chr6A.!!$R4 2631
14 TraesCS6B01G083500 chr6A 14521959 14522588 629 True 725.000000 725 87.730000 862 1495 1 chr6A.!!$R1 633
15 TraesCS6B01G083500 chrUn 355298444 355299268 824 True 1127.000000 1127 91.477000 315 1135 1 chrUn.!!$R1 820

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
112 125 3.813166 TCGAAGGCAAGTTTAGAGTTTGG 59.187 43.478 0.0 0.0 0.00 3.28 F
865 1047 3.931907 TGCAGTATTTGATAGGGCAGT 57.068 42.857 0.0 0.0 0.00 4.40 F
1711 2047 2.769663 TGTGGTGTTCCAGTCTGTTAGT 59.230 45.455 0.0 0.0 45.24 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1478 1710 0.387202 TGTGTGCCCGTTTCAAATGG 59.613 50.000 0.73 0.73 37.31 3.16 R
1896 2236 1.300080 CAAAGTGGTTGCTTGGCGG 60.300 57.895 0.00 0.00 0.00 6.13 R
3243 5413 0.107993 CCTCGAAGATTGGAGCAGCA 60.108 55.000 0.00 0.00 33.89 4.41 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
84 97 5.522456 TCAAAATGAATGCTGTGTCAGTTC 58.478 37.500 0.00 0.00 31.32 3.01
112 125 3.813166 TCGAAGGCAAGTTTAGAGTTTGG 59.187 43.478 0.00 0.00 0.00 3.28
309 457 4.410099 TGCTCCATGAGAAAATCCTTTGT 58.590 39.130 0.00 0.00 0.00 2.83
311 459 5.166398 GCTCCATGAGAAAATCCTTTGTTG 58.834 41.667 0.00 0.00 0.00 3.33
563 738 7.179269 ACTAGAAGAGTCTCACAACCTTCTAT 58.821 38.462 0.00 0.00 42.22 1.98
865 1047 3.931907 TGCAGTATTTGATAGGGCAGT 57.068 42.857 0.00 0.00 0.00 4.40
1185 1402 4.265904 TCGATTGCCTTTCTGTGTCTTA 57.734 40.909 0.00 0.00 0.00 2.10
1194 1411 6.818644 TGCCTTTCTGTGTCTTACATATCTTC 59.181 38.462 0.00 0.00 38.92 2.87
1347 1577 4.541705 TGGTCAGTTCCTTCCATTGAAAA 58.458 39.130 0.00 0.00 0.00 2.29
1541 1869 4.785346 ATTGGTTGCAGATATGTCTCCT 57.215 40.909 0.00 0.00 30.42 3.69
1597 1925 4.992951 AGAAATGTTGCAGAAAATTCAGGC 59.007 37.500 0.00 0.03 0.00 4.85
1640 1968 6.995091 CAGAGGATCCGAAGATAAAAATTCCT 59.005 38.462 5.98 0.00 33.66 3.36
1711 2047 2.769663 TGTGGTGTTCCAGTCTGTTAGT 59.230 45.455 0.00 0.00 45.24 2.24
1734 2070 3.814625 TGTGTGCCTTCATGTTTACTCA 58.185 40.909 0.00 0.00 0.00 3.41
1896 2236 5.512473 TGTGGTTACGCAGTTAAATTGTTC 58.488 37.500 0.00 0.00 37.78 3.18
2023 2363 6.213397 TCTCACCTTCTTGTATCTCATTTCCA 59.787 38.462 0.00 0.00 0.00 3.53
2255 2603 3.629398 GGTCGATCAATGAAGGCAAGATT 59.371 43.478 0.00 0.00 0.00 2.40
2256 2604 4.260948 GGTCGATCAATGAAGGCAAGATTC 60.261 45.833 0.00 0.00 0.00 2.52
2320 2668 3.006537 TGAACCTCAGCTACACAGGTAAC 59.993 47.826 6.32 5.41 39.80 2.50
2362 2710 0.820226 CACCTCTTCCTGATCGCTCA 59.180 55.000 0.00 0.00 0.00 4.26
2379 2727 5.111989 TCGCTCACCTTTCTTAATGATCTG 58.888 41.667 0.00 0.00 0.00 2.90
2395 2743 7.729124 AATGATCTGAATTTCTGAATGGGTT 57.271 32.000 9.65 0.00 0.00 4.11
2521 2878 5.189928 TCAAGTTGTGTGTATGTGGAAACT 58.810 37.500 2.11 0.00 0.00 2.66
2544 2916 3.619900 ACTATGCCTAGGTCTGGATGA 57.380 47.619 11.31 0.00 0.00 2.92
2551 2923 3.118261 GCCTAGGTCTGGATGATTGAACA 60.118 47.826 11.31 0.00 0.00 3.18
2626 3009 2.375174 TCTGAATTGCCAAGTGGTACCT 59.625 45.455 14.36 0.00 37.57 3.08
2645 3028 3.746949 GATGGTCTGGCTCGCCTGG 62.747 68.421 13.79 5.30 35.98 4.45
2841 3293 3.826729 GGCAGGTTGAATTTGTAGGTTCT 59.173 43.478 0.00 0.00 0.00 3.01
2874 3326 5.291128 AGCTAGAACGATTAACATTCCAACG 59.709 40.000 0.00 0.00 0.00 4.10
2875 3327 4.336532 AGAACGATTAACATTCCAACGC 57.663 40.909 0.00 0.00 0.00 4.84
2881 3334 6.613233 ACGATTAACATTCCAACGCAAAATA 58.387 32.000 0.00 0.00 0.00 1.40
2924 3377 3.629142 TTAGCAGTTTTAGGGCTCCTC 57.371 47.619 0.00 0.00 39.01 3.71
2962 3415 6.540551 GGAATCTAACAGGAGATTTTGAGGAC 59.459 42.308 0.50 0.00 44.46 3.85
3035 5198 4.525912 AATTCGTTTACGGTAGACCTGT 57.474 40.909 2.09 0.00 40.29 4.00
3037 5200 4.685169 TTCGTTTACGGTAGACCTGTAG 57.315 45.455 2.09 0.00 40.29 2.74
3038 5201 3.937814 TCGTTTACGGTAGACCTGTAGA 58.062 45.455 2.09 0.00 40.29 2.59
3039 5202 4.323417 TCGTTTACGGTAGACCTGTAGAA 58.677 43.478 2.09 0.00 40.29 2.10
3040 5203 4.759693 TCGTTTACGGTAGACCTGTAGAAA 59.240 41.667 2.09 0.00 40.29 2.52
3041 5204 5.240623 TCGTTTACGGTAGACCTGTAGAAAA 59.759 40.000 2.09 0.00 40.29 2.29
3042 5205 5.920273 CGTTTACGGTAGACCTGTAGAAAAA 59.080 40.000 3.54 0.00 35.37 1.94
3054 5224 5.158494 CCTGTAGAAAAATTTTGCGGTACC 58.842 41.667 3.73 0.16 0.00 3.34
3074 5244 2.771762 GAGGCCCCATGAGCTCCT 60.772 66.667 12.15 0.00 0.00 3.69
3090 5260 5.250774 TGAGCTCCTAGGTTATTCCTTTTGT 59.749 40.000 12.15 0.00 45.67 2.83
3118 5288 2.914097 GCCACAGCTTGCCCAAGT 60.914 61.111 9.53 0.00 40.45 3.16
3150 5320 8.343168 ACATGGAATTCATTTTGCAAATCAAT 57.657 26.923 13.65 8.59 32.01 2.57
3155 5325 7.911727 GGAATTCATTTTGCAAATCAATTAGGC 59.088 33.333 13.65 6.27 34.12 3.93
3159 5329 6.935771 TCATTTTGCAAATCAATTAGGCTGTT 59.064 30.769 13.65 0.00 34.12 3.16
3164 5334 6.855836 TGCAAATCAATTAGGCTGTTAGAAG 58.144 36.000 0.00 0.00 0.00 2.85
3207 5377 6.223852 TGTGAAGGAGTTGTTGATACTCTTC 58.776 40.000 0.00 0.00 41.37 2.87
3208 5378 5.346281 GTGAAGGAGTTGTTGATACTCTTCG 59.654 44.000 0.00 0.00 41.37 3.79
3209 5379 4.457834 AGGAGTTGTTGATACTCTTCGG 57.542 45.455 0.00 0.00 41.37 4.30
3210 5380 3.195825 AGGAGTTGTTGATACTCTTCGGG 59.804 47.826 0.00 0.00 41.37 5.14
3211 5381 3.194968 GGAGTTGTTGATACTCTTCGGGA 59.805 47.826 0.00 0.00 41.37 5.14
3212 5382 4.174762 GAGTTGTTGATACTCTTCGGGAC 58.825 47.826 0.00 0.00 39.12 4.46
3213 5383 3.576982 AGTTGTTGATACTCTTCGGGACA 59.423 43.478 0.00 0.00 0.00 4.02
3214 5384 3.587797 TGTTGATACTCTTCGGGACAC 57.412 47.619 0.00 0.00 0.00 3.67
3215 5385 3.162666 TGTTGATACTCTTCGGGACACT 58.837 45.455 0.00 0.00 0.00 3.55
3216 5386 3.192844 TGTTGATACTCTTCGGGACACTC 59.807 47.826 0.00 0.00 0.00 3.51
3217 5387 3.367646 TGATACTCTTCGGGACACTCT 57.632 47.619 0.00 0.00 0.00 3.24
3218 5388 3.698289 TGATACTCTTCGGGACACTCTT 58.302 45.455 0.00 0.00 0.00 2.85
3219 5389 3.695060 TGATACTCTTCGGGACACTCTTC 59.305 47.826 0.00 0.00 0.00 2.87
3220 5390 0.882474 ACTCTTCGGGACACTCTTCG 59.118 55.000 0.00 0.00 0.00 3.79
3221 5391 0.171455 CTCTTCGGGACACTCTTCGG 59.829 60.000 0.00 0.00 0.00 4.30
3222 5392 1.215647 CTTCGGGACACTCTTCGGG 59.784 63.158 0.00 0.00 0.00 5.14
3223 5393 1.228644 TTCGGGACACTCTTCGGGA 60.229 57.895 0.00 0.00 0.00 5.14
3224 5394 1.530013 TTCGGGACACTCTTCGGGAC 61.530 60.000 0.00 0.00 0.00 4.46
3237 5407 2.577593 GGGACGAAGGGTTCTCCG 59.422 66.667 0.00 0.00 41.52 4.63
3238 5408 1.980772 GGGACGAAGGGTTCTCCGA 60.981 63.158 0.00 0.00 41.52 4.55
3239 5409 1.214853 GGACGAAGGGTTCTCCGAC 59.785 63.158 0.00 0.00 41.52 4.79
3240 5410 1.530013 GGACGAAGGGTTCTCCGACA 61.530 60.000 0.00 0.00 41.52 4.35
3241 5411 0.531200 GACGAAGGGTTCTCCGACAT 59.469 55.000 0.00 0.00 41.52 3.06
3242 5412 0.974383 ACGAAGGGTTCTCCGACATT 59.026 50.000 0.00 0.00 41.52 2.71
3243 5413 1.346722 ACGAAGGGTTCTCCGACATTT 59.653 47.619 0.00 0.00 41.52 2.32
3244 5414 1.732259 CGAAGGGTTCTCCGACATTTG 59.268 52.381 0.00 0.00 41.52 2.32
3245 5415 1.468914 GAAGGGTTCTCCGACATTTGC 59.531 52.381 0.00 0.00 41.52 3.68
3246 5416 0.693049 AGGGTTCTCCGACATTTGCT 59.307 50.000 0.00 0.00 41.52 3.91
3247 5417 0.804989 GGGTTCTCCGACATTTGCTG 59.195 55.000 0.00 0.00 33.83 4.41
3248 5418 0.169009 GGTTCTCCGACATTTGCTGC 59.831 55.000 0.00 0.00 0.00 5.25
3249 5419 1.160137 GTTCTCCGACATTTGCTGCT 58.840 50.000 0.00 0.00 0.00 4.24
3250 5420 1.129437 GTTCTCCGACATTTGCTGCTC 59.871 52.381 0.00 0.00 0.00 4.26
3251 5421 0.391661 TCTCCGACATTTGCTGCTCC 60.392 55.000 0.00 0.00 0.00 4.70
3252 5422 0.674581 CTCCGACATTTGCTGCTCCA 60.675 55.000 0.00 0.00 0.00 3.86
3253 5423 0.250684 TCCGACATTTGCTGCTCCAA 60.251 50.000 0.00 0.00 0.00 3.53
3254 5424 0.813184 CCGACATTTGCTGCTCCAAT 59.187 50.000 0.00 0.00 0.00 3.16
3255 5425 1.202222 CCGACATTTGCTGCTCCAATC 60.202 52.381 0.00 0.00 0.00 2.67
3256 5426 1.741706 CGACATTTGCTGCTCCAATCT 59.258 47.619 0.00 0.00 0.00 2.40
3257 5427 2.163010 CGACATTTGCTGCTCCAATCTT 59.837 45.455 0.00 0.00 0.00 2.40
3258 5428 3.730061 CGACATTTGCTGCTCCAATCTTC 60.730 47.826 0.00 0.00 0.00 2.87
3259 5429 2.163010 ACATTTGCTGCTCCAATCTTCG 59.837 45.455 0.00 0.00 0.00 3.79
3260 5430 2.183478 TTTGCTGCTCCAATCTTCGA 57.817 45.000 0.00 0.00 0.00 3.71
3261 5431 1.730501 TTGCTGCTCCAATCTTCGAG 58.269 50.000 0.00 0.00 0.00 4.04
3262 5432 0.107993 TGCTGCTCCAATCTTCGAGG 60.108 55.000 0.00 0.00 0.00 4.63
3263 5433 0.176680 GCTGCTCCAATCTTCGAGGA 59.823 55.000 0.00 0.00 0.00 3.71
3264 5434 1.933247 CTGCTCCAATCTTCGAGGAC 58.067 55.000 0.00 0.00 0.00 3.85
3265 5435 1.205655 CTGCTCCAATCTTCGAGGACA 59.794 52.381 0.00 0.00 0.00 4.02
3266 5436 1.833630 TGCTCCAATCTTCGAGGACAT 59.166 47.619 0.00 0.00 0.00 3.06
3267 5437 2.237143 TGCTCCAATCTTCGAGGACATT 59.763 45.455 0.00 0.00 0.00 2.71
3268 5438 2.869192 GCTCCAATCTTCGAGGACATTC 59.131 50.000 0.00 0.00 0.00 2.67
3269 5439 3.119291 CTCCAATCTTCGAGGACATTCG 58.881 50.000 0.00 0.00 41.79 3.34
3270 5440 2.496070 TCCAATCTTCGAGGACATTCGT 59.504 45.455 0.00 0.00 41.22 3.85
3271 5441 3.697542 TCCAATCTTCGAGGACATTCGTA 59.302 43.478 0.00 0.00 41.22 3.43
3272 5442 4.341235 TCCAATCTTCGAGGACATTCGTAT 59.659 41.667 0.00 0.00 41.22 3.06
3273 5443 5.050490 CCAATCTTCGAGGACATTCGTATT 58.950 41.667 0.00 0.00 41.22 1.89
3274 5444 5.175856 CCAATCTTCGAGGACATTCGTATTC 59.824 44.000 0.00 0.00 41.22 1.75
3275 5445 4.976224 TCTTCGAGGACATTCGTATTCA 57.024 40.909 0.00 0.00 41.22 2.57
3276 5446 4.921547 TCTTCGAGGACATTCGTATTCAG 58.078 43.478 0.00 0.00 41.22 3.02
3277 5447 4.638865 TCTTCGAGGACATTCGTATTCAGA 59.361 41.667 0.00 0.00 41.22 3.27
3278 5448 4.288670 TCGAGGACATTCGTATTCAGAC 57.711 45.455 0.00 0.00 41.22 3.51
3279 5449 3.945921 TCGAGGACATTCGTATTCAGACT 59.054 43.478 0.00 0.00 41.22 3.24
3280 5450 5.121105 TCGAGGACATTCGTATTCAGACTA 58.879 41.667 0.00 0.00 41.22 2.59
3281 5451 5.587443 TCGAGGACATTCGTATTCAGACTAA 59.413 40.000 0.00 0.00 41.22 2.24
3282 5452 5.681982 CGAGGACATTCGTATTCAGACTAAC 59.318 44.000 0.00 0.00 35.91 2.34
3283 5453 6.458478 CGAGGACATTCGTATTCAGACTAACT 60.458 42.308 0.00 0.00 35.91 2.24
3284 5454 6.797454 AGGACATTCGTATTCAGACTAACTC 58.203 40.000 0.00 0.00 0.00 3.01
3285 5455 6.603997 AGGACATTCGTATTCAGACTAACTCT 59.396 38.462 0.00 0.00 0.00 3.24
3286 5456 7.122948 AGGACATTCGTATTCAGACTAACTCTT 59.877 37.037 0.00 0.00 0.00 2.85
3287 5457 7.760340 GGACATTCGTATTCAGACTAACTCTTT 59.240 37.037 0.00 0.00 0.00 2.52
3288 5458 9.141400 GACATTCGTATTCAGACTAACTCTTTT 57.859 33.333 0.00 0.00 0.00 2.27
3289 5459 8.926710 ACATTCGTATTCAGACTAACTCTTTTG 58.073 33.333 0.00 0.00 0.00 2.44
3290 5460 9.140286 CATTCGTATTCAGACTAACTCTTTTGA 57.860 33.333 0.00 0.00 0.00 2.69
3291 5461 8.516811 TTCGTATTCAGACTAACTCTTTTGAC 57.483 34.615 0.00 0.00 0.00 3.18
3292 5462 7.654568 TCGTATTCAGACTAACTCTTTTGACA 58.345 34.615 0.00 0.00 0.00 3.58
3293 5463 7.808381 TCGTATTCAGACTAACTCTTTTGACAG 59.192 37.037 0.00 0.00 0.00 3.51
3294 5464 7.808381 CGTATTCAGACTAACTCTTTTGACAGA 59.192 37.037 0.00 0.00 0.00 3.41
3295 5465 7.954788 ATTCAGACTAACTCTTTTGACAGAC 57.045 36.000 0.00 0.00 0.00 3.51
3296 5466 6.716934 TCAGACTAACTCTTTTGACAGACT 57.283 37.500 0.00 0.00 0.00 3.24
3297 5467 7.113658 TCAGACTAACTCTTTTGACAGACTT 57.886 36.000 0.00 0.00 0.00 3.01
3298 5468 7.556844 TCAGACTAACTCTTTTGACAGACTTT 58.443 34.615 0.00 0.00 0.00 2.66
3299 5469 8.041323 TCAGACTAACTCTTTTGACAGACTTTT 58.959 33.333 0.00 0.00 0.00 2.27
3300 5470 8.119226 CAGACTAACTCTTTTGACAGACTTTTG 58.881 37.037 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 97 0.307760 AAACTTGCCTTCGAACGCTG 59.692 50.000 17.94 13.33 0.00 5.18
88 101 5.205565 CAAACTCTAAACTTGCCTTCGAAC 58.794 41.667 0.00 0.00 0.00 3.95
513 682 8.968242 GTCAAATGATTCTTTACTGGAACAAAC 58.032 33.333 0.00 0.00 38.70 2.93
563 738 3.876914 CCAAGATAAGTATTTGGCGAGCA 59.123 43.478 0.00 0.00 35.41 4.26
1152 1369 8.826710 CAGAAAGGCAATCGATTGTATAACTAA 58.173 33.333 32.52 0.00 39.88 2.24
1478 1710 0.387202 TGTGTGCCCGTTTCAAATGG 59.613 50.000 0.73 0.73 37.31 3.16
1597 1925 7.415592 TCCTCTGATAAGATAGCCATATGTG 57.584 40.000 1.24 0.00 0.00 3.21
1665 1993 9.781834 CATAAACAATTATTAGCGGAACAGAAA 57.218 29.630 0.00 0.00 29.08 2.52
1668 2001 7.643764 CCACATAAACAATTATTAGCGGAACAG 59.356 37.037 0.00 0.00 29.08 3.16
1711 2047 4.642437 TGAGTAAACATGAAGGCACACAAA 59.358 37.500 0.00 0.00 0.00 2.83
1734 2070 3.034924 TGCCGGTGCAAGAAGAAAT 57.965 47.368 1.90 0.00 46.66 2.17
1896 2236 1.300080 CAAAGTGGTTGCTTGGCGG 60.300 57.895 0.00 0.00 0.00 6.13
2023 2363 5.421056 ACAAGCCATTTCATGTTGAGATGAT 59.579 36.000 9.01 0.00 40.29 2.45
2191 2533 1.538047 TGGATTTTGCAGGACTGAGC 58.462 50.000 3.00 0.00 0.00 4.26
2255 2603 3.081409 GCTGTAAGGGCCTCCGGA 61.081 66.667 6.46 2.93 38.33 5.14
2256 2604 4.176752 GGCTGTAAGGGCCTCCGG 62.177 72.222 6.46 7.11 45.57 5.14
2320 2668 2.097036 GTTCAAAGATTTACCCCCGGG 58.903 52.381 15.80 15.80 42.03 5.73
2328 2676 5.768164 GGAAGAGGTGTGGTTCAAAGATTTA 59.232 40.000 0.00 0.00 0.00 1.40
2362 2710 9.745018 TCAGAAATTCAGATCATTAAGAAAGGT 57.255 29.630 0.00 0.00 0.00 3.50
2448 2796 1.583556 TCCATACACCACAGAGGCAT 58.416 50.000 0.00 0.00 43.14 4.40
2451 2799 3.634397 AACATCCATACACCACAGAGG 57.366 47.619 0.00 0.00 45.67 3.69
2521 2878 3.965470 TCCAGACCTAGGCATAGTACA 57.035 47.619 9.30 0.00 0.00 2.90
2544 2916 7.653311 GCTAGTTTCCAAAAGTCAATGTTCAAT 59.347 33.333 0.00 0.00 0.00 2.57
2551 2923 4.584325 TGCAGCTAGTTTCCAAAAGTCAAT 59.416 37.500 0.00 0.00 0.00 2.57
2626 3009 2.685017 AGGCGAGCCAGACCATCA 60.685 61.111 17.18 0.00 38.92 3.07
2645 3028 4.035017 CCACAACAACAGTTTTCATCGTC 58.965 43.478 0.00 0.00 0.00 4.20
2779 3231 7.913297 CGTCTACAGAAAACAAAATCCTTTTCA 59.087 33.333 5.84 0.00 38.38 2.69
2841 3293 2.728690 TCGTTCTAGCTAAAACGGCA 57.271 45.000 27.14 10.48 46.14 5.69
2905 3358 1.838077 GGAGGAGCCCTAAAACTGCTA 59.162 52.381 0.00 0.00 34.41 3.49
2954 3407 7.785028 TGCTCTAAGGATCTATAAGTCCTCAAA 59.215 37.037 6.14 0.00 43.94 2.69
2978 5141 1.365633 CCGGACCTGCTAGAGATGC 59.634 63.158 0.00 0.00 0.00 3.91
3007 5170 1.538075 ACCGTAAACGAATTTGCAGGG 59.462 47.619 3.65 0.00 43.02 4.45
3090 5260 3.391736 GCTGTGGCTGCATCTATCA 57.608 52.632 0.50 0.00 35.22 2.15
3118 5288 8.347004 TGCAAAATGAATTCCATGTAGAACTA 57.653 30.769 2.27 0.00 35.24 2.24
3150 5320 2.903784 TGACCAGCTTCTAACAGCCTAA 59.096 45.455 0.00 0.00 41.12 2.69
3155 5325 3.616956 TGGATGACCAGCTTCTAACAG 57.383 47.619 0.00 0.00 41.77 3.16
3185 5355 5.470368 CGAAGAGTATCAACAACTCCTTCA 58.530 41.667 0.00 0.00 43.64 3.02
3187 5357 4.322801 CCCGAAGAGTATCAACAACTCCTT 60.323 45.833 0.00 0.00 43.64 3.36
3207 5377 2.572284 GTCCCGAAGAGTGTCCCG 59.428 66.667 0.00 0.00 0.00 5.14
3208 5378 1.530013 TTCGTCCCGAAGAGTGTCCC 61.530 60.000 0.00 0.00 41.05 4.46
3209 5379 1.962144 TTCGTCCCGAAGAGTGTCC 59.038 57.895 0.00 0.00 41.05 4.02
3217 5387 1.538687 GGAGAACCCTTCGTCCCGAA 61.539 60.000 0.00 0.00 43.75 4.30
3218 5388 1.980772 GGAGAACCCTTCGTCCCGA 60.981 63.158 0.00 0.00 34.02 5.14
3219 5389 2.577593 GGAGAACCCTTCGTCCCG 59.422 66.667 0.00 0.00 34.02 5.14
3220 5390 1.980772 TCGGAGAACCCTTCGTCCC 60.981 63.158 0.00 0.00 42.03 4.46
3221 5391 1.214853 GTCGGAGAACCCTTCGTCC 59.785 63.158 0.00 0.00 42.03 4.79
3222 5392 0.531200 ATGTCGGAGAACCCTTCGTC 59.469 55.000 0.00 0.00 42.03 4.20
3223 5393 0.974383 AATGTCGGAGAACCCTTCGT 59.026 50.000 0.00 0.00 42.03 3.85
3224 5394 1.732259 CAAATGTCGGAGAACCCTTCG 59.268 52.381 0.00 0.00 42.73 3.79
3225 5395 1.468914 GCAAATGTCGGAGAACCCTTC 59.531 52.381 0.00 0.00 39.69 3.46
3226 5396 1.073923 AGCAAATGTCGGAGAACCCTT 59.926 47.619 0.00 0.00 39.69 3.95
3227 5397 0.693049 AGCAAATGTCGGAGAACCCT 59.307 50.000 0.00 0.00 39.69 4.34
3228 5398 0.804989 CAGCAAATGTCGGAGAACCC 59.195 55.000 0.00 0.00 39.69 4.11
3229 5399 0.169009 GCAGCAAATGTCGGAGAACC 59.831 55.000 0.00 0.00 39.69 3.62
3230 5400 1.129437 GAGCAGCAAATGTCGGAGAAC 59.871 52.381 0.00 0.00 39.69 3.01
3231 5401 1.442769 GAGCAGCAAATGTCGGAGAA 58.557 50.000 0.00 0.00 39.69 2.87
3232 5402 0.391661 GGAGCAGCAAATGTCGGAGA 60.392 55.000 0.00 0.00 0.00 3.71
3233 5403 0.674581 TGGAGCAGCAAATGTCGGAG 60.675 55.000 0.00 0.00 0.00 4.63
3234 5404 0.250684 TTGGAGCAGCAAATGTCGGA 60.251 50.000 0.00 0.00 0.00 4.55
3235 5405 0.813184 ATTGGAGCAGCAAATGTCGG 59.187 50.000 0.00 0.00 0.00 4.79
3236 5406 1.741706 AGATTGGAGCAGCAAATGTCG 59.258 47.619 0.00 0.00 0.00 4.35
3237 5407 3.730061 CGAAGATTGGAGCAGCAAATGTC 60.730 47.826 0.00 0.00 0.00 3.06
3238 5408 2.163010 CGAAGATTGGAGCAGCAAATGT 59.837 45.455 0.00 0.00 0.00 2.71
3239 5409 2.421073 TCGAAGATTGGAGCAGCAAATG 59.579 45.455 0.00 0.00 0.00 2.32
3240 5410 2.681848 CTCGAAGATTGGAGCAGCAAAT 59.318 45.455 0.00 0.00 33.89 2.32
3241 5411 2.079158 CTCGAAGATTGGAGCAGCAAA 58.921 47.619 0.00 0.00 33.89 3.68
3242 5412 1.676916 CCTCGAAGATTGGAGCAGCAA 60.677 52.381 0.00 0.00 33.89 3.91
3243 5413 0.107993 CCTCGAAGATTGGAGCAGCA 60.108 55.000 0.00 0.00 33.89 4.41
3244 5414 0.176680 TCCTCGAAGATTGGAGCAGC 59.823 55.000 0.00 0.00 33.89 5.25
3245 5415 1.205655 TGTCCTCGAAGATTGGAGCAG 59.794 52.381 0.00 0.00 31.23 4.24
3246 5416 1.266178 TGTCCTCGAAGATTGGAGCA 58.734 50.000 0.00 0.00 31.23 4.26
3247 5417 2.611225 ATGTCCTCGAAGATTGGAGC 57.389 50.000 0.00 0.00 31.23 4.70
3248 5418 3.119291 CGAATGTCCTCGAAGATTGGAG 58.881 50.000 0.00 0.00 41.44 3.86
3249 5419 2.496070 ACGAATGTCCTCGAAGATTGGA 59.504 45.455 0.00 0.00 41.44 3.53
3250 5420 2.893637 ACGAATGTCCTCGAAGATTGG 58.106 47.619 0.00 0.00 41.44 3.16
3251 5421 5.748630 TGAATACGAATGTCCTCGAAGATTG 59.251 40.000 0.00 0.00 41.44 2.67
3252 5422 5.902681 TGAATACGAATGTCCTCGAAGATT 58.097 37.500 0.00 0.00 41.44 2.40
3253 5423 5.299531 TCTGAATACGAATGTCCTCGAAGAT 59.700 40.000 0.00 0.00 41.44 2.40
3254 5424 4.638865 TCTGAATACGAATGTCCTCGAAGA 59.361 41.667 0.00 0.00 41.44 2.87
3255 5425 4.735822 GTCTGAATACGAATGTCCTCGAAG 59.264 45.833 0.00 0.00 41.44 3.79
3256 5426 4.398358 AGTCTGAATACGAATGTCCTCGAA 59.602 41.667 0.00 0.00 41.44 3.71
3257 5427 3.945921 AGTCTGAATACGAATGTCCTCGA 59.054 43.478 0.00 0.00 41.44 4.04
3258 5428 4.294416 AGTCTGAATACGAATGTCCTCG 57.706 45.455 0.00 0.00 44.50 4.63
3259 5429 6.797454 AGTTAGTCTGAATACGAATGTCCTC 58.203 40.000 0.00 0.00 0.00 3.71
3260 5430 6.603997 AGAGTTAGTCTGAATACGAATGTCCT 59.396 38.462 0.00 0.00 32.57 3.85
3261 5431 6.797454 AGAGTTAGTCTGAATACGAATGTCC 58.203 40.000 0.00 0.00 32.57 4.02
3262 5432 8.690680 AAAGAGTTAGTCTGAATACGAATGTC 57.309 34.615 0.00 0.00 34.84 3.06
3263 5433 8.926710 CAAAAGAGTTAGTCTGAATACGAATGT 58.073 33.333 0.00 0.00 34.84 2.71
3264 5434 9.140286 TCAAAAGAGTTAGTCTGAATACGAATG 57.860 33.333 0.00 0.00 34.84 2.67
3265 5435 9.141400 GTCAAAAGAGTTAGTCTGAATACGAAT 57.859 33.333 0.00 0.00 34.84 3.34
3266 5436 8.139350 TGTCAAAAGAGTTAGTCTGAATACGAA 58.861 33.333 0.00 0.00 34.84 3.85
3267 5437 7.654568 TGTCAAAAGAGTTAGTCTGAATACGA 58.345 34.615 0.00 0.00 34.84 3.43
3268 5438 7.808381 TCTGTCAAAAGAGTTAGTCTGAATACG 59.192 37.037 0.00 0.00 34.84 3.06
3269 5439 8.917655 GTCTGTCAAAAGAGTTAGTCTGAATAC 58.082 37.037 0.00 0.00 34.84 1.89
3270 5440 8.861086 AGTCTGTCAAAAGAGTTAGTCTGAATA 58.139 33.333 0.00 0.00 34.84 1.75
3271 5441 7.731054 AGTCTGTCAAAAGAGTTAGTCTGAAT 58.269 34.615 0.00 0.00 34.84 2.57
3272 5442 7.113658 AGTCTGTCAAAAGAGTTAGTCTGAA 57.886 36.000 0.00 0.00 34.84 3.02
3273 5443 6.716934 AGTCTGTCAAAAGAGTTAGTCTGA 57.283 37.500 0.00 0.00 34.84 3.27
3274 5444 7.778470 AAAGTCTGTCAAAAGAGTTAGTCTG 57.222 36.000 0.00 0.00 38.60 3.51
3275 5445 8.202745 CAAAAGTCTGTCAAAAGAGTTAGTCT 57.797 34.615 0.00 0.00 38.60 3.24


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

AutoCloner maintained by Alex Coulton.