Multiple sequence alignment - TraesCS2D01G593900

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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 TraesCS2D01G593900 chr2D 100.000 5078 0 0 1 5078 648127536 648122459 0.000000e+00 9378
1 TraesCS2D01G593900 chr2D 88.520 2256 212 19 876 3112 648115394 648113167 0.000000e+00 2687
2 TraesCS2D01G593900 chr2D 84.523 1583 187 27 758 2299 648352153 648353718 0.000000e+00 1513
3 TraesCS2D01G593900 chr2D 86.467 835 89 8 2301 3114 648353756 648354587 0.000000e+00 894
4 TraesCS2D01G593900 chr2D 81.550 542 81 10 3268 3798 648113113 648112580 3.630000e-116 429
5 TraesCS2D01G593900 chr2D 81.545 466 67 8 3268 3728 648354624 648355075 2.890000e-97 366
6 TraesCS2D01G593900 chr2D 76.297 713 93 40 50 745 648116091 648115438 1.370000e-80 311
7 TraesCS2D01G593900 chr2D 87.600 250 19 5 3839 4085 648112587 648112347 3.870000e-71 279
8 TraesCS2D01G593900 chr2D 83.333 144 22 2 3940 4082 648355146 648355288 1.150000e-26 132
9 TraesCS2D01G593900 chr2B 93.010 3648 182 44 256 3840 781789485 781793122 0.000000e+00 5256
10 TraesCS2D01G593900 chr2B 88.597 2245 206 25 896 3112 781801145 781803367 0.000000e+00 2682
11 TraesCS2D01G593900 chr2B 83.916 1660 195 42 690 2299 784273345 784274982 0.000000e+00 1520
12 TraesCS2D01G593900 chr2B 86.516 838 89 8 2301 3114 784275020 784275857 0.000000e+00 900
13 TraesCS2D01G593900 chr2B 92.172 511 34 3 3764 4271 781793088 781793595 0.000000e+00 717
14 TraesCS2D01G593900 chr2B 86.220 537 39 14 2 511 602238878 602238350 2.670000e-152 549
15 TraesCS2D01G593900 chr2B 81.481 513 79 9 3281 3782 781803434 781803941 1.700000e-109 407
16 TraesCS2D01G593900 chr2B 86.850 327 21 7 4751 5057 781794136 781794460 3.760000e-91 346
17 TraesCS2D01G593900 chr2B 80.645 465 73 8 3268 3728 784275894 784276345 1.350000e-90 344
18 TraesCS2D01G593900 chr2B 86.400 250 22 5 3839 4085 781803947 781804187 3.900000e-66 263
19 TraesCS2D01G593900 chr2B 90.909 132 6 4 1 130 781789362 781789489 6.760000e-39 172
20 TraesCS2D01G593900 chr2B 84.028 144 21 2 3940 4082 784276416 784276558 2.470000e-28 137
21 TraesCS2D01G593900 chr2B 89.412 85 9 0 4532 4616 781824568 781824652 1.930000e-19 108
22 TraesCS2D01G593900 chrUn 96.354 2962 108 0 1124 4085 31306614 31309575 0.000000e+00 4872
23 TraesCS2D01G593900 chrUn 87.006 2732 266 47 435 3113 31320253 31322948 0.000000e+00 2996
24 TraesCS2D01G593900 chrUn 84.153 1647 206 32 690 2299 31091909 31090281 0.000000e+00 1544
25 TraesCS2D01G593900 chrUn 87.132 917 78 20 1 893 31305229 31306129 0.000000e+00 1003
26 TraesCS2D01G593900 chrUn 86.993 838 82 9 2301 3114 31090243 31089409 0.000000e+00 918
27 TraesCS2D01G593900 chrUn 90.909 440 28 6 4084 4517 31309631 31310064 9.480000e-162 580
28 TraesCS2D01G593900 chrUn 90.462 346 11 8 4754 5078 31310964 31311308 2.170000e-118 436
29 TraesCS2D01G593900 chrUn 81.734 542 80 10 3268 3798 31323001 31323534 7.810000e-118 435
30 TraesCS2D01G593900 chrUn 80.645 465 73 8 3268 3728 31089372 31088921 1.350000e-90 344
31 TraesCS2D01G593900 chrUn 91.129 248 16 3 896 1137 31306332 31306579 1.050000e-86 331
32 TraesCS2D01G593900 chrUn 86.800 250 21 5 3839 4085 31323527 31323767 8.380000e-68 268
33 TraesCS2D01G593900 chrUn 81.633 147 25 2 3940 4085 31088850 31088705 2.480000e-23 121


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 TraesCS2D01G593900 chr2D 648122459 648127536 5077 True 9378.000000 9378 100.000000 1 5078 1 chr2D.!!$R1 5077
1 TraesCS2D01G593900 chr2D 648112347 648116091 3744 True 926.500000 2687 83.491750 50 4085 4 chr2D.!!$R2 4035
2 TraesCS2D01G593900 chr2D 648352153 648355288 3135 False 726.250000 1513 83.967000 758 4082 4 chr2D.!!$F1 3324
3 TraesCS2D01G593900 chr2B 781789362 781794460 5098 False 1622.750000 5256 90.735250 1 5057 4 chr2B.!!$F2 5056
4 TraesCS2D01G593900 chr2B 781801145 781804187 3042 False 1117.333333 2682 85.492667 896 4085 3 chr2B.!!$F3 3189
5 TraesCS2D01G593900 chr2B 784273345 784276558 3213 False 725.250000 1520 83.776250 690 4082 4 chr2B.!!$F4 3392
6 TraesCS2D01G593900 chr2B 602238350 602238878 528 True 549.000000 549 86.220000 2 511 1 chr2B.!!$R1 509
7 TraesCS2D01G593900 chrUn 31305229 31311308 6079 False 1444.400000 4872 91.197200 1 5078 5 chrUn.!!$F1 5077
8 TraesCS2D01G593900 chrUn 31320253 31323767 3514 False 1233.000000 2996 85.180000 435 4085 3 chrUn.!!$F2 3650
9 TraesCS2D01G593900 chrUn 31088705 31091909 3204 True 731.750000 1544 83.356000 690 4085 4 chrUn.!!$R1 3395

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
26 27 0.045008 TGGAGCCCTGGGGTACATAA 59.955 55.000 25.85 3.37 39.34 1.90 F
502 539 0.606096 TTAAGAGCGTAGGCAGCACA 59.394 50.000 10.48 0.00 43.41 4.57 F
2059 2461 0.392595 AAAGGAAATCGACCCGAGCC 60.393 55.000 0.00 0.00 39.91 4.70 F
3328 3817 1.144057 CCGCCCTACATCACCACTC 59.856 63.158 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1818 1.202818 GCCTCAACAGGACTGGACTTT 60.203 52.381 4.14 0.00 43.65 2.66 R
2076 2478 0.044092 TGTCCATGGCTAAGGGGAGA 59.956 55.000 6.96 0.00 0.00 3.71 R
3339 3828 0.449388 CGCATGGCAGAAAGAGTTCC 59.551 55.000 0.00 0.00 33.92 3.62 R
4603 5645 0.037139 TGCCAATGCATGCCAACTTC 60.037 50.000 16.68 0.57 44.23 3.01 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
26 27 0.045008 TGGAGCCCTGGGGTACATAA 59.955 55.000 25.85 3.37 39.34 1.90
157 161 1.908299 CCACTTGAACCCCCAAGGC 60.908 63.158 8.29 0.00 45.76 4.35
158 162 1.908299 CACTTGAACCCCCAAGGCC 60.908 63.158 0.00 0.00 45.76 5.19
160 164 1.908299 CTTGAACCCCCAAGGCCAC 60.908 63.158 5.01 0.00 39.74 5.01
186 201 0.821711 AACTAGCTGCCGTGCCAAAA 60.822 50.000 0.00 0.00 0.00 2.44
194 209 1.069823 TGCCGTGCCAAAATCAAACAT 59.930 42.857 0.00 0.00 0.00 2.71
212 227 3.623703 ACATGGCTGTCTCATTTATGCA 58.376 40.909 0.00 0.00 0.00 3.96
224 246 8.970020 TGTCTCATTTATGCATGTTCCTTTTAT 58.030 29.630 10.16 0.00 0.00 1.40
278 302 3.272574 ACACATCATCTGCCTCGATTT 57.727 42.857 0.00 0.00 0.00 2.17
344 374 6.995686 CACTAGCTAGATCTCAAGGTCTCTAA 59.004 42.308 27.45 0.00 0.00 2.10
370 400 5.663456 CCATTTGGGGAAGTGATTTATGTG 58.337 41.667 0.00 0.00 0.00 3.21
371 401 5.187576 CCATTTGGGGAAGTGATTTATGTGT 59.812 40.000 0.00 0.00 0.00 3.72
372 402 5.720371 TTTGGGGAAGTGATTTATGTGTG 57.280 39.130 0.00 0.00 0.00 3.82
373 403 3.088532 TGGGGAAGTGATTTATGTGTGC 58.911 45.455 0.00 0.00 0.00 4.57
415 445 0.675083 TGACTGCCAAATTGTGCTGG 59.325 50.000 14.06 1.30 35.67 4.85
501 538 1.000145 GTTAAGAGCGTAGGCAGCAC 59.000 55.000 10.48 0.00 43.41 4.40
502 539 0.606096 TTAAGAGCGTAGGCAGCACA 59.394 50.000 10.48 0.00 43.41 4.57
553 594 6.002062 AGAAAACTAGCAAGTACAATGCAC 57.998 37.500 21.20 7.36 46.22 4.57
704 759 4.888038 ACGTGTGTTCCTTTTAGTTTCC 57.112 40.909 0.00 0.00 0.00 3.13
725 781 3.063997 CCTGACTATCGAATTGTGCAACC 59.936 47.826 0.00 0.00 34.36 3.77
729 785 1.176527 ATCGAATTGTGCAACCTGGG 58.823 50.000 0.00 0.00 34.36 4.45
734 790 2.310930 ATTGTGCAACCTGGGGTGGT 62.311 55.000 6.81 0.00 43.11 4.16
756 841 5.813672 GGTTCATGCGATTTACTGGTTACTA 59.186 40.000 0.00 0.00 0.00 1.82
776 861 2.391616 TAGGCAGCAGATTGTGTGAG 57.608 50.000 0.00 0.00 0.00 3.51
808 894 7.441458 GCGGATTAAGAGTGTAGGAAACATATT 59.559 37.037 0.00 0.00 41.10 1.28
841 927 5.865085 ACACTAGATTGCAAGGTTTCTACA 58.135 37.500 4.94 0.00 0.00 2.74
886 974 1.067846 CAAGGCGTCTGTGCTGTAGTA 60.068 52.381 0.00 0.00 34.52 1.82
891 1137 1.920574 CGTCTGTGCTGTAGTATGTGC 59.079 52.381 0.00 0.00 0.00 4.57
935 1223 6.751888 GCTGGTCATTCCATAATTGTGTTAAC 59.248 38.462 0.00 0.00 46.12 2.01
952 1278 6.764085 TGTGTTAACAACCGATCCTATATTGG 59.236 38.462 10.51 0.00 31.82 3.16
1190 1580 3.620719 GCTGTGGATCCTTGTGAAGATCA 60.621 47.826 14.23 0.00 0.00 2.92
1416 1818 4.442375 TGCGGAAAACTTTGTGAAGAAA 57.558 36.364 0.00 0.00 36.69 2.52
1432 1834 4.640201 TGAAGAAAAAGTCCAGTCCTGTTG 59.360 41.667 0.00 0.00 0.00 3.33
1916 2318 4.324471 TGCCACAGCAGCTATTGG 57.676 55.556 15.49 15.49 46.52 3.16
1970 2372 7.719871 AAACATTAGAGGTTAGAGTAGCTGA 57.280 36.000 0.00 0.00 0.00 4.26
1975 2377 7.778185 TTAGAGGTTAGAGTAGCTGAAGTTT 57.222 36.000 0.00 0.00 0.00 2.66
2027 2429 2.101750 TGCAGTCCGTGTCAGAAACTTA 59.898 45.455 0.00 0.00 0.00 2.24
2029 2431 2.724690 CAGTCCGTGTCAGAAACTTACG 59.275 50.000 0.00 0.00 34.78 3.18
2059 2461 0.392595 AAAGGAAATCGACCCGAGCC 60.393 55.000 0.00 0.00 39.91 4.70
2076 2478 3.012518 GAGCCACTTGTATGTCTGCAAT 58.987 45.455 0.00 0.00 0.00 3.56
2286 2688 7.437565 GGTAAAAAGATAGAGGTCCGATTGTAC 59.562 40.741 0.00 0.00 0.00 2.90
2291 2693 1.743958 AGAGGTCCGATTGTACGACAG 59.256 52.381 0.00 0.00 35.09 3.51
2309 2747 2.960688 GCTCTCCACCCAGACCCAC 61.961 68.421 0.00 0.00 0.00 4.61
2409 2847 2.276201 TCGCCATTTGGTAAGATCACG 58.724 47.619 0.00 0.00 37.57 4.35
2721 3183 5.735285 TGATCAATCTGGAGTATAGCCTG 57.265 43.478 0.00 0.00 0.00 4.85
2913 3384 1.662438 CCAACTTGTGTGTTGCCGGT 61.662 55.000 1.90 0.00 44.12 5.28
3016 3487 2.549349 GGGTATGGCATGGTTAGGTACG 60.549 54.545 10.98 0.00 0.00 3.67
3094 3565 1.623811 GAAGTACCCTGGCTGTGAGAA 59.376 52.381 0.00 0.00 0.00 2.87
3203 3689 2.101917 CTGCAACAAATCCCATGGATCC 59.898 50.000 15.22 4.20 42.27 3.36
3205 3691 2.956385 GCAACAAATCCCATGGATCCCT 60.956 50.000 15.22 0.00 42.27 4.20
3276 3765 1.606885 CCAATGGGCCGCAGAAACAT 61.607 55.000 0.00 0.00 0.00 2.71
3328 3817 1.144057 CCGCCCTACATCACCACTC 59.856 63.158 0.00 0.00 0.00 3.51
3339 3828 1.581934 TCACCACTCAAAAGCTGACG 58.418 50.000 0.00 0.00 0.00 4.35
3540 4029 0.546122 TCCATCAAAGCGCTATGGGT 59.454 50.000 28.88 9.88 40.53 4.51
3639 4134 1.039233 GGCCATACCATTGTGCTGCT 61.039 55.000 0.00 0.00 38.86 4.24
3815 4328 1.774639 CAACAGTTGTCAAGCCATGC 58.225 50.000 4.99 0.00 0.00 4.06
3816 4329 1.067364 CAACAGTTGTCAAGCCATGCA 59.933 47.619 4.99 0.00 0.00 3.96
3819 4332 1.067364 CAGTTGTCAAGCCATGCAACA 59.933 47.619 19.47 0.00 42.95 3.33
3893 4448 1.153086 GCTTCGAGCCCCATCATGT 60.153 57.895 0.00 0.00 34.48 3.21
3990 4548 1.925255 TCCATCCCCAAGAAAGATGCT 59.075 47.619 0.00 0.00 36.82 3.79
3998 4556 3.880846 GAAAGATGCTGCCGCCGG 61.881 66.667 0.00 0.00 34.43 6.13
4139 4754 9.807649 AAAATGAAAGATCCATGTGCTAATTAC 57.192 29.630 0.00 0.00 0.00 1.89
4195 4811 4.776308 AGTAGTAGACTTGGTTGGTTAGGG 59.224 45.833 0.00 0.00 33.13 3.53
4253 4869 7.007697 GCCAGCGTAATCGTATTGTTAATTAG 58.992 38.462 0.00 0.00 39.49 1.73
4273 4889 2.493278 AGCCTGCATGGTTATTTGTGAC 59.507 45.455 0.00 0.00 38.35 3.67
4295 4911 1.030457 CAGCTGATGGCCTCCATTTC 58.970 55.000 8.42 0.00 45.26 2.17
4298 4914 1.030457 CTGATGGCCTCCATTTCAGC 58.970 55.000 3.32 0.00 45.26 4.26
4300 4916 1.030457 GATGGCCTCCATTTCAGCTG 58.970 55.000 7.63 7.63 45.26 4.24
4329 4945 6.564557 ATTAATGGTTCCATTTCCATGCTT 57.435 33.333 20.02 0.00 42.73 3.91
4345 4961 0.109412 GCTTGCTTGCTGGTGTGATC 60.109 55.000 0.00 0.00 0.00 2.92
4361 4978 6.206634 TGGTGTGATCCATTCTGAACTTTAAC 59.793 38.462 0.00 0.00 31.96 2.01
4380 4997 9.379791 ACTTTAACTATGCTAGTATTTGTCCAC 57.620 33.333 0.00 0.00 38.26 4.02
4381 4998 8.726870 TTTAACTATGCTAGTATTTGTCCACC 57.273 34.615 0.00 0.00 38.26 4.61
4383 5000 4.719773 ACTATGCTAGTATTTGTCCACCCA 59.280 41.667 0.00 0.00 37.23 4.51
4388 5005 5.190925 TGCTAGTATTTGTCCACCCAAGTAT 59.809 40.000 0.00 0.00 0.00 2.12
4395 5012 4.563140 TGTCCACCCAAGTATAAGTTCC 57.437 45.455 0.00 0.00 0.00 3.62
4406 5028 7.040961 CCCAAGTATAAGTTCCGTTTTCAGAAA 60.041 37.037 0.00 0.00 0.00 2.52
4463 5085 5.841810 ACACATAAGATGTTGGTTTTGTGG 58.158 37.500 9.44 0.00 42.70 4.17
4484 5106 0.835941 GGGGATCTGTGTGCTCTCAT 59.164 55.000 0.00 0.00 0.00 2.90
4489 5111 2.046988 TGTGTGCTCTCATGCCGG 60.047 61.111 0.00 0.00 0.00 6.13
4507 5129 3.120165 GCCGGAGATCTTTGAACAGAAAC 60.120 47.826 5.05 0.00 0.00 2.78
4517 5139 7.873719 TCTTTGAACAGAAACCATGTCTTTA 57.126 32.000 0.00 0.00 0.00 1.85
4518 5140 8.463930 TCTTTGAACAGAAACCATGTCTTTAT 57.536 30.769 0.00 0.00 0.00 1.40
4519 5141 9.567776 TCTTTGAACAGAAACCATGTCTTTATA 57.432 29.630 0.00 0.00 0.00 0.98
4523 5145 9.513906 TGAACAGAAACCATGTCTTTATAATCA 57.486 29.630 0.00 0.00 0.00 2.57
4529 5151 9.520204 GAAACCATGTCTTTATAATCATGTTGG 57.480 33.333 16.89 10.07 36.81 3.77
4530 5152 7.042797 ACCATGTCTTTATAATCATGTTGGC 57.957 36.000 16.89 0.00 36.81 4.52
4531 5153 6.144854 CCATGTCTTTATAATCATGTTGGCG 58.855 40.000 16.89 0.00 36.81 5.69
4532 5154 6.017192 CCATGTCTTTATAATCATGTTGGCGA 60.017 38.462 16.89 0.00 36.81 5.54
4533 5155 6.603237 TGTCTTTATAATCATGTTGGCGAG 57.397 37.500 0.00 0.00 0.00 5.03
4534 5156 6.112734 TGTCTTTATAATCATGTTGGCGAGT 58.887 36.000 0.00 0.00 0.00 4.18
4536 5158 7.931407 TGTCTTTATAATCATGTTGGCGAGTAT 59.069 33.333 0.00 0.00 0.00 2.12
4537 5159 8.774586 GTCTTTATAATCATGTTGGCGAGTATT 58.225 33.333 0.00 0.00 0.00 1.89
4539 5161 9.599322 CTTTATAATCATGTTGGCGAGTATTTC 57.401 33.333 0.00 0.00 0.00 2.17
4540 5162 8.902540 TTATAATCATGTTGGCGAGTATTTCT 57.097 30.769 0.00 0.00 0.00 2.52
4555 5597 7.839837 GCGAGTATTTCTTACGAGTAATTTGTG 59.160 37.037 0.00 0.00 35.84 3.33
4581 5623 4.734398 TGAATTTGTAATCATGGGTGGC 57.266 40.909 0.00 0.00 0.00 5.01
4591 5633 6.438741 TGTAATCATGGGTGGCAAAATCTTTA 59.561 34.615 0.00 0.00 0.00 1.85
4596 5638 5.652994 TGGGTGGCAAAATCTTTATACAC 57.347 39.130 0.00 0.00 0.00 2.90
4603 5645 8.915654 GTGGCAAAATCTTTATACACTTTCAAG 58.084 33.333 0.00 0.00 0.00 3.02
4634 5676 0.325933 CATTGGCACAGGACAGGAGA 59.674 55.000 0.00 0.00 42.39 3.71
4643 5685 3.380004 CACAGGACAGGAGACTTAGCTAG 59.620 52.174 0.00 0.00 40.21 3.42
4671 5714 8.494433 ACTGGATAGTTAGATTCAAATAAGGCA 58.506 33.333 0.00 0.00 31.66 4.75
4693 5736 1.068125 TGCATGTGTCAGCAAATCAGC 60.068 47.619 0.00 0.00 37.90 4.26
4694 5737 1.068125 GCATGTGTCAGCAAATCAGCA 60.068 47.619 0.00 0.00 36.85 4.41
4697 5740 3.082698 TGTGTCAGCAAATCAGCAAAC 57.917 42.857 0.00 0.00 36.85 2.93
4698 5741 2.223782 TGTGTCAGCAAATCAGCAAACC 60.224 45.455 0.00 0.00 36.85 3.27
4699 5742 2.035066 GTGTCAGCAAATCAGCAAACCT 59.965 45.455 0.00 0.00 36.85 3.50
4701 5744 2.035066 GTCAGCAAATCAGCAAACCTGT 59.965 45.455 0.00 0.00 42.38 4.00
4702 5745 3.253188 GTCAGCAAATCAGCAAACCTGTA 59.747 43.478 0.00 0.00 42.38 2.74
4703 5746 3.503363 TCAGCAAATCAGCAAACCTGTAG 59.497 43.478 0.00 0.00 42.38 2.74
4704 5747 2.229784 AGCAAATCAGCAAACCTGTAGC 59.770 45.455 0.00 0.00 42.38 3.58
4706 5749 3.440173 GCAAATCAGCAAACCTGTAGCTA 59.560 43.478 0.00 0.00 42.38 3.32
4707 5750 4.082787 GCAAATCAGCAAACCTGTAGCTAA 60.083 41.667 0.00 0.00 42.38 3.09
4708 5751 5.393962 CAAATCAGCAAACCTGTAGCTAAC 58.606 41.667 0.00 0.00 42.38 2.34
4709 5752 2.683968 TCAGCAAACCTGTAGCTAACG 58.316 47.619 0.00 0.00 42.38 3.18
4710 5753 1.732259 CAGCAAACCTGTAGCTAACGG 59.268 52.381 0.00 1.06 36.73 4.44
4711 5754 1.346722 AGCAAACCTGTAGCTAACGGT 59.653 47.619 8.94 8.94 36.73 4.83
4712 5755 1.463444 GCAAACCTGTAGCTAACGGTG 59.537 52.381 14.14 6.07 35.87 4.94
4714 5757 2.735134 CAAACCTGTAGCTAACGGTGAC 59.265 50.000 14.14 0.00 35.87 3.67
4715 5758 1.624336 ACCTGTAGCTAACGGTGACA 58.376 50.000 12.97 0.00 34.88 3.58
4716 5759 1.271656 ACCTGTAGCTAACGGTGACAC 59.728 52.381 12.97 0.00 34.88 3.67
4718 5761 2.094182 CCTGTAGCTAACGGTGACACAT 60.094 50.000 8.08 0.00 31.96 3.21
4719 5762 3.129813 CCTGTAGCTAACGGTGACACATA 59.870 47.826 8.08 0.00 31.96 2.29
4720 5763 4.381185 CCTGTAGCTAACGGTGACACATAA 60.381 45.833 8.08 0.00 31.96 1.90
4721 5764 4.740268 TGTAGCTAACGGTGACACATAAG 58.260 43.478 8.08 0.39 0.00 1.73
4722 5765 4.460034 TGTAGCTAACGGTGACACATAAGA 59.540 41.667 8.08 0.00 0.00 2.10
4723 5766 4.737855 AGCTAACGGTGACACATAAGAT 57.262 40.909 8.08 0.00 0.00 2.40
4724 5767 5.847111 AGCTAACGGTGACACATAAGATA 57.153 39.130 8.08 0.00 0.00 1.98
4725 5768 6.406692 AGCTAACGGTGACACATAAGATAT 57.593 37.500 8.08 0.00 0.00 1.63
4726 5769 6.817184 AGCTAACGGTGACACATAAGATATT 58.183 36.000 8.08 0.00 0.00 1.28
4727 5770 6.701841 AGCTAACGGTGACACATAAGATATTG 59.298 38.462 8.08 0.00 0.00 1.90
4728 5771 6.073765 GCTAACGGTGACACATAAGATATTGG 60.074 42.308 8.08 0.00 0.00 3.16
4729 5772 5.353394 ACGGTGACACATAAGATATTGGT 57.647 39.130 8.08 0.00 0.00 3.67
4730 5773 5.741011 ACGGTGACACATAAGATATTGGTT 58.259 37.500 8.08 0.00 0.00 3.67
4731 5774 6.177610 ACGGTGACACATAAGATATTGGTTT 58.822 36.000 8.08 0.00 0.00 3.27
4732 5775 6.657541 ACGGTGACACATAAGATATTGGTTTT 59.342 34.615 8.08 0.00 0.00 2.43
4733 5776 6.966632 CGGTGACACATAAGATATTGGTTTTG 59.033 38.462 8.08 0.00 0.00 2.44
4734 5777 7.361713 CGGTGACACATAAGATATTGGTTTTGT 60.362 37.037 8.08 0.00 0.00 2.83
4735 5778 8.952278 GGTGACACATAAGATATTGGTTTTGTA 58.048 33.333 8.08 0.00 0.00 2.41
4736 5779 9.769093 GTGACACATAAGATATTGGTTTTGTAC 57.231 33.333 0.00 0.00 0.00 2.90
4737 5780 9.733556 TGACACATAAGATATTGGTTTTGTACT 57.266 29.630 0.00 0.00 0.00 2.73
4805 6126 5.441718 ACTGACCCATACATCTGTCAATT 57.558 39.130 0.00 0.00 37.29 2.32
4818 6139 7.661968 ACATCTGTCAATTATGTACTAGCGAT 58.338 34.615 0.00 0.00 32.21 4.58
4840 6161 4.460948 AATCGCCATTTTCAGAAAGCAT 57.539 36.364 6.46 0.00 0.00 3.79
4841 6162 3.220507 TCGCCATTTTCAGAAAGCATG 57.779 42.857 6.46 4.15 0.00 4.06
4855 6176 8.261492 TCAGAAAGCATGAGAGAATTCTTTAC 57.739 34.615 9.87 5.13 32.53 2.01
4967 6305 7.839680 AGTTTATTTTGTGGAAGACTGGAAT 57.160 32.000 0.00 0.00 0.00 3.01
5012 6351 6.756542 GGGAAGCGTGAATTTGCTAATAATTT 59.243 34.615 0.00 0.00 41.46 1.82
5013 6352 7.254084 GGGAAGCGTGAATTTGCTAATAATTTG 60.254 37.037 0.00 0.00 41.46 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.629796 CCAAAATTATGTACCCCAGGGCT 60.630 47.826 0.00 0.00 39.32 5.19
136 140 1.146152 CCTTGGGGGTTCAAGTGGTTA 59.854 52.381 0.00 0.00 41.72 2.85
157 161 1.517832 CAGCTAGTTCCCTCCGTGG 59.482 63.158 0.00 0.00 0.00 4.94
158 162 1.153549 GCAGCTAGTTCCCTCCGTG 60.154 63.158 0.00 0.00 0.00 4.94
160 164 2.501610 GGCAGCTAGTTCCCTCCG 59.498 66.667 0.00 0.00 0.00 4.63
167 182 0.821711 TTTTGGCACGGCAGCTAGTT 60.822 50.000 0.00 0.00 34.17 2.24
186 201 6.682113 GCATAAATGAGACAGCCATGTTTGAT 60.682 38.462 0.00 0.00 40.68 2.57
194 209 3.623703 ACATGCATAAATGAGACAGCCA 58.376 40.909 0.00 0.00 0.00 4.75
212 227 6.654582 GCCATCCACAAAAATAAAAGGAACAT 59.345 34.615 0.00 0.00 0.00 2.71
224 246 3.964031 ACTTTGGTAGCCATCCACAAAAA 59.036 39.130 0.00 0.00 34.45 1.94
278 302 5.298989 TGTTTTCCTACACTCTTAAGCCA 57.701 39.130 0.00 0.00 0.00 4.75
344 374 2.555732 ATCACTTCCCCAAATGGCAT 57.444 45.000 0.00 0.00 0.00 4.40
370 400 3.857093 ACAAAACTGAAATGAACACGCAC 59.143 39.130 0.00 0.00 0.00 5.34
371 401 4.103365 ACAAAACTGAAATGAACACGCA 57.897 36.364 0.00 0.00 0.00 5.24
372 402 5.164002 ACAAACAAAACTGAAATGAACACGC 60.164 36.000 0.00 0.00 0.00 5.34
373 403 6.088749 TCACAAACAAAACTGAAATGAACACG 59.911 34.615 0.00 0.00 0.00 4.49
415 445 7.171678 GTGAGTAATCACTTAGCCCATATCAAC 59.828 40.741 15.79 0.00 37.62 3.18
443 473 0.657368 GTGTTTGCGTGCACTACAGC 60.657 55.000 16.19 11.38 33.22 4.40
553 594 3.790089 AAACTAGTTCCCTTGTGGAGG 57.210 47.619 8.95 0.00 46.24 4.30
572 617 6.811170 GTCTTGTGTGATTTGGTTCTGAAAAA 59.189 34.615 0.00 0.00 0.00 1.94
580 627 2.362077 GCTGGTCTTGTGTGATTTGGTT 59.638 45.455 0.00 0.00 0.00 3.67
590 637 1.310933 GCTCCCATGCTGGTCTTGTG 61.311 60.000 0.00 0.00 35.17 3.33
648 697 2.552268 CGTTTACCACAACCGCGG 59.448 61.111 26.86 26.86 0.00 6.46
704 759 3.935203 AGGTTGCACAATTCGATAGTCAG 59.065 43.478 0.00 0.00 37.40 3.51
725 781 0.680921 AATCGCATGAACCACCCCAG 60.681 55.000 0.00 0.00 0.00 4.45
729 785 2.097466 CCAGTAAATCGCATGAACCACC 59.903 50.000 0.00 0.00 0.00 4.61
734 790 7.870954 CCTATAGTAACCAGTAAATCGCATGAA 59.129 37.037 0.00 0.00 0.00 2.57
756 841 2.238144 ACTCACACAATCTGCTGCCTAT 59.762 45.455 0.00 0.00 0.00 2.57
776 861 2.810650 ACACTCTTAATCCGCATCGAC 58.189 47.619 0.00 0.00 0.00 4.20
808 894 3.002791 GCAATCTAGTGTAAGCTGCACA 58.997 45.455 19.62 10.21 39.17 4.57
841 927 4.961438 AAAAATGACAAATGTGCTCCCT 57.039 36.364 0.00 0.00 0.00 4.20
873 961 3.511540 AGAAGCACATACTACAGCACAGA 59.488 43.478 0.00 0.00 0.00 3.41
875 963 3.961480 AGAAGCACATACTACAGCACA 57.039 42.857 0.00 0.00 0.00 4.57
876 964 4.328440 CAGAAGAAGCACATACTACAGCAC 59.672 45.833 0.00 0.00 0.00 4.40
886 974 6.459298 GCAAACATATAGCAGAAGAAGCACAT 60.459 38.462 0.00 0.00 0.00 3.21
891 1137 5.587844 ACCAGCAAACATATAGCAGAAGAAG 59.412 40.000 0.00 0.00 0.00 2.85
935 1223 5.299279 AGCAAAACCAATATAGGATCGGTTG 59.701 40.000 0.00 0.00 39.83 3.77
952 1278 8.951243 ACAGAGGAGAAGATTATTTAGCAAAAC 58.049 33.333 0.00 0.00 0.00 2.43
993 1323 0.396060 TTTTGCACCCCATTCTTGCC 59.604 50.000 0.00 0.00 35.26 4.52
1190 1580 2.620108 GCCTCCTCTTCTTCTGCCAAAT 60.620 50.000 0.00 0.00 0.00 2.32
1416 1818 1.202818 GCCTCAACAGGACTGGACTTT 60.203 52.381 4.14 0.00 43.65 2.66
1432 1834 6.375455 TCATTTTGTTCCTTCTTGATAGCCTC 59.625 38.462 0.00 0.00 0.00 4.70
1626 2028 4.734266 ACTGAGCTTTCCTTTTCTCCAAT 58.266 39.130 0.00 0.00 0.00 3.16
1970 2372 4.170468 ACTGATGGTGGAACTGAAACTT 57.830 40.909 0.00 0.00 36.74 2.66
1975 2377 3.449918 TGGATACTGATGGTGGAACTGA 58.550 45.455 0.00 0.00 34.75 3.41
1979 2381 3.785325 TGGATTGGATACTGATGGTGGAA 59.215 43.478 0.00 0.00 37.61 3.53
2027 2429 1.415672 TTCCTTTGAGGGCAGACCGT 61.416 55.000 0.00 0.00 46.96 4.83
2029 2431 2.095461 GATTTCCTTTGAGGGCAGACC 58.905 52.381 0.00 0.00 35.59 3.85
2059 2461 3.624861 GGGAGATTGCAGACATACAAGTG 59.375 47.826 0.00 0.00 0.00 3.16
2076 2478 0.044092 TGTCCATGGCTAAGGGGAGA 59.956 55.000 6.96 0.00 0.00 3.71
2286 2688 1.979155 TCTGGGTGGAGAGCTGTCG 60.979 63.158 4.57 0.00 0.00 4.35
2291 2693 2.607750 TGGGTCTGGGTGGAGAGC 60.608 66.667 0.00 0.00 39.35 4.09
2309 2747 0.740737 GGCCATGTCGATTTCCTTGG 59.259 55.000 0.00 0.00 0.00 3.61
2409 2847 1.367599 CTGCTGCCACTCTAGCTTGC 61.368 60.000 0.00 0.00 40.52 4.01
2576 3038 1.221840 GGAGAGGCAATTGGCGAGA 59.778 57.895 24.49 0.00 46.16 4.04
2721 3183 2.797156 CGCTACATCTGCATAGAACACC 59.203 50.000 0.00 0.00 36.32 4.16
2913 3384 1.449726 CGGTCATCGTCGGTGGGATA 61.450 60.000 5.50 0.00 0.00 2.59
2946 3417 0.462047 CGTATGGCCGGAAAAGCTCT 60.462 55.000 5.05 0.00 0.00 4.09
3203 3689 1.137404 GCATTTGTGGCAGCGTAGG 59.863 57.895 0.00 0.00 0.00 3.18
3205 3691 1.305219 GGAGCATTTGTGGCAGCGTA 61.305 55.000 0.00 0.00 0.00 4.42
3276 3765 8.082242 CAGACATATAAGTTGGTCATGTCGATA 58.918 37.037 7.21 0.00 46.40 2.92
3328 3817 3.561725 AGAAAGAGTTCCGTCAGCTTTTG 59.438 43.478 0.00 0.00 33.92 2.44
3339 3828 0.449388 CGCATGGCAGAAAGAGTTCC 59.551 55.000 0.00 0.00 33.92 3.62
3540 4029 1.227645 GAGATGCGCCATGTAGCCA 60.228 57.895 4.18 0.00 0.00 4.75
3639 4134 4.020307 TGGTTCTCAGTGTATGCTGATTCA 60.020 41.667 0.00 0.00 43.61 2.57
3815 4328 3.982475 TGCTGAGAACTAGTGTCTGTTG 58.018 45.455 10.94 4.41 0.00 3.33
3816 4329 3.553922 GCTGCTGAGAACTAGTGTCTGTT 60.554 47.826 10.94 0.00 0.00 3.16
3819 4332 2.230992 CTGCTGCTGAGAACTAGTGTCT 59.769 50.000 0.00 1.53 0.00 3.41
3887 4442 3.588906 CCGCCGCATGCACATGAT 61.589 61.111 19.57 0.00 41.20 2.45
3893 4448 4.819761 GAGAGACCGCCGCATGCA 62.820 66.667 19.57 0.00 41.33 3.96
3925 4480 1.972198 CCCAAGGTACTGCTGACGA 59.028 57.895 0.00 0.00 40.86 4.20
3998 4556 1.395635 ACGTTGGGAAGGTTTTGTCC 58.604 50.000 0.00 0.00 0.00 4.02
4016 4574 1.457346 CAGATGGACCTTGGAGCAAC 58.543 55.000 0.00 0.00 0.00 4.17
4195 4811 0.099436 CATTTTACCAGCCAGCTCGC 59.901 55.000 0.00 0.00 0.00 5.03
4253 4869 2.731968 CGTCACAAATAACCATGCAGGC 60.732 50.000 0.00 0.00 43.14 4.85
4292 4908 4.832248 ACCATTAATCGTCTCAGCTGAAA 58.168 39.130 18.85 0.21 0.00 2.69
4295 4911 3.557595 GGAACCATTAATCGTCTCAGCTG 59.442 47.826 7.63 7.63 0.00 4.24
4298 4914 6.238484 GGAAATGGAACCATTAATCGTCTCAG 60.238 42.308 17.73 0.00 44.86 3.35
4300 4916 5.588648 TGGAAATGGAACCATTAATCGTCTC 59.411 40.000 17.73 10.42 44.86 3.36
4329 4945 0.038599 ATGGATCACACCAGCAAGCA 59.961 50.000 0.00 0.00 43.49 3.91
4361 4978 5.290493 TGGGTGGACAAATACTAGCATAG 57.710 43.478 0.00 0.00 46.50 2.23
4377 4994 3.622166 ACGGAACTTATACTTGGGTGG 57.378 47.619 0.00 0.00 0.00 4.61
4380 4997 5.935789 TCTGAAAACGGAACTTATACTTGGG 59.064 40.000 0.00 0.00 0.00 4.12
4381 4998 7.429636 TTCTGAAAACGGAACTTATACTTGG 57.570 36.000 0.00 0.00 0.00 3.61
4406 5028 4.018597 ACTGGAATCTGATGCTCTCCTTTT 60.019 41.667 7.43 0.00 0.00 2.27
4436 5058 8.514594 CACAAAACCAACATCTTATGTGTAGAT 58.485 33.333 0.00 0.00 44.07 1.98
4437 5059 7.040755 CCACAAAACCAACATCTTATGTGTAGA 60.041 37.037 0.00 0.00 44.07 2.59
4438 5060 7.083858 CCACAAAACCAACATCTTATGTGTAG 58.916 38.462 0.00 0.00 44.07 2.74
4439 5061 6.547880 ACCACAAAACCAACATCTTATGTGTA 59.452 34.615 0.00 0.00 44.07 2.90
4440 5062 5.362430 ACCACAAAACCAACATCTTATGTGT 59.638 36.000 0.00 0.00 44.07 3.72
4441 5063 5.691305 CACCACAAAACCAACATCTTATGTG 59.309 40.000 0.00 0.00 44.07 3.21
4451 5073 1.343142 GATCCCCACCACAAAACCAAC 59.657 52.381 0.00 0.00 0.00 3.77
4463 5085 0.107945 GAGAGCACACAGATCCCCAC 60.108 60.000 0.00 0.00 31.44 4.61
4484 5106 1.623311 TCTGTTCAAAGATCTCCGGCA 59.377 47.619 0.00 0.00 0.00 5.69
4489 5111 6.429385 AGACATGGTTTCTGTTCAAAGATCTC 59.571 38.462 0.00 0.00 0.00 2.75
4507 5129 6.017192 TCGCCAACATGATTATAAAGACATGG 60.017 38.462 22.39 14.15 42.66 3.66
4517 5139 7.807977 AAGAAATACTCGCCAACATGATTAT 57.192 32.000 0.00 0.00 0.00 1.28
4518 5140 7.042992 CGTAAGAAATACTCGCCAACATGATTA 60.043 37.037 0.00 0.00 43.02 1.75
4519 5141 6.238103 CGTAAGAAATACTCGCCAACATGATT 60.238 38.462 0.00 0.00 43.02 2.57
4520 5142 5.234329 CGTAAGAAATACTCGCCAACATGAT 59.766 40.000 0.00 0.00 43.02 2.45
4521 5143 4.565166 CGTAAGAAATACTCGCCAACATGA 59.435 41.667 0.00 0.00 43.02 3.07
4522 5144 4.822107 CGTAAGAAATACTCGCCAACATG 58.178 43.478 0.00 0.00 43.02 3.21
4539 5161 4.634004 TCATGGCCACAAATTACTCGTAAG 59.366 41.667 8.16 0.00 0.00 2.34
4540 5162 4.580868 TCATGGCCACAAATTACTCGTAA 58.419 39.130 8.16 0.00 0.00 3.18
4591 5633 5.565439 GCATGCCAACTTCTTGAAAGTGTAT 60.565 40.000 6.36 0.00 0.00 2.29
4596 5638 3.374220 TGCATGCCAACTTCTTGAAAG 57.626 42.857 16.68 0.00 0.00 2.62
4603 5645 0.037139 TGCCAATGCATGCCAACTTC 60.037 50.000 16.68 0.57 44.23 3.01
4623 5665 2.360801 GCTAGCTAAGTCTCCTGTCCTG 59.639 54.545 7.70 0.00 0.00 3.86
4634 5676 6.366340 TCTAACTATCCAGTGCTAGCTAAGT 58.634 40.000 17.23 5.90 34.36 2.24
4643 5685 8.778358 CCTTATTTGAATCTAACTATCCAGTGC 58.222 37.037 0.00 0.00 34.36 4.40
4671 5714 3.845178 CTGATTTGCTGACACATGCAAT 58.155 40.909 0.00 0.00 46.55 3.56
4691 5734 1.346722 ACCGTTAGCTACAGGTTTGCT 59.653 47.619 12.28 0.00 40.43 3.91
4693 5736 2.735134 GTCACCGTTAGCTACAGGTTTG 59.265 50.000 14.75 7.11 33.38 2.93
4694 5737 2.366266 TGTCACCGTTAGCTACAGGTTT 59.634 45.455 14.75 0.00 33.38 3.27
4697 5740 1.271379 TGTGTCACCGTTAGCTACAGG 59.729 52.381 11.13 11.13 0.00 4.00
4698 5741 2.717580 TGTGTCACCGTTAGCTACAG 57.282 50.000 0.00 0.00 0.00 2.74
4699 5742 4.460034 TCTTATGTGTCACCGTTAGCTACA 59.540 41.667 0.00 0.00 0.00 2.74
4701 5744 5.847111 ATCTTATGTGTCACCGTTAGCTA 57.153 39.130 0.00 0.00 0.00 3.32
4702 5745 4.737855 ATCTTATGTGTCACCGTTAGCT 57.262 40.909 0.00 0.00 0.00 3.32
4703 5746 6.073765 CCAATATCTTATGTGTCACCGTTAGC 60.074 42.308 0.00 0.00 0.00 3.09
4704 5747 6.984474 ACCAATATCTTATGTGTCACCGTTAG 59.016 38.462 0.00 0.00 0.00 2.34
4706 5749 5.741011 ACCAATATCTTATGTGTCACCGTT 58.259 37.500 0.00 0.00 0.00 4.44
4707 5750 5.353394 ACCAATATCTTATGTGTCACCGT 57.647 39.130 0.00 0.00 0.00 4.83
4708 5751 6.677781 AAACCAATATCTTATGTGTCACCG 57.322 37.500 0.00 0.00 0.00 4.94
4709 5752 7.826690 ACAAAACCAATATCTTATGTGTCACC 58.173 34.615 0.00 0.00 0.00 4.02
4710 5753 9.769093 GTACAAAACCAATATCTTATGTGTCAC 57.231 33.333 0.00 0.00 0.00 3.67
4711 5754 9.733556 AGTACAAAACCAATATCTTATGTGTCA 57.266 29.630 0.00 0.00 0.00 3.58
4818 6139 5.125257 TCATGCTTTCTGAAAATGGCGATTA 59.875 36.000 12.47 0.00 0.00 1.75
4832 6153 7.882271 ACAGTAAAGAATTCTCTCATGCTTTCT 59.118 33.333 8.78 0.00 0.00 2.52
4893 6231 3.960102 ACTTTCATGTGCTGGGAAAAAGA 59.040 39.130 5.14 0.00 30.87 2.52
4894 6232 4.326504 ACTTTCATGTGCTGGGAAAAAG 57.673 40.909 0.00 0.00 30.87 2.27
4967 6305 6.938698 TCCCCGGTTATATTAGCTATCAAA 57.061 37.500 0.00 0.00 0.00 2.69
5013 6352 2.632377 TCGAATGGAATGTGAGCTTCC 58.368 47.619 0.00 0.00 42.15 3.46


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

AutoCloner maintained by Alex Coulton.