Multiple sequence alignment - TraesCS3A01G121400

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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 TraesCS3A01G121400 chr3A 100.000 4733 0 0 1 4733 95526560 95531292 0.000000e+00 8741.0
1 TraesCS3A01G121400 chr3A 98.319 119 1 1 4166 4284 95530654 95530771 1.730000e-49 207.0
2 TraesCS3A01G121400 chr3A 98.319 119 1 1 4095 4212 95530725 95530843 1.730000e-49 207.0
3 TraesCS3A01G121400 chr3A 97.872 47 0 1 4238 4284 95530654 95530699 3.930000e-11 80.5
4 TraesCS3A01G121400 chr3A 97.872 47 0 1 4095 4140 95530797 95530843 3.930000e-11 80.5
5 TraesCS3A01G121400 chr3D 94.012 4075 164 37 695 4733 81363762 81367792 0.000000e+00 6100.0
6 TraesCS3A01G121400 chr3D 94.606 482 19 4 197 677 81363053 81363528 0.000000e+00 739.0
7 TraesCS3A01G121400 chr3D 87.850 214 17 8 1 207 81360865 81361076 4.730000e-60 243.0
8 TraesCS3A01G121400 chr3D 91.089 101 8 1 3016 3116 545547894 545547795 8.260000e-28 135.0
9 TraesCS3A01G121400 chr3D 95.000 60 2 1 4153 4212 81367283 81367341 5.040000e-15 93.5
10 TraesCS3A01G121400 chr3D 97.826 46 1 0 4095 4140 81367296 81367341 3.930000e-11 80.5
11 TraesCS3A01G121400 chr3B 93.003 4059 204 55 710 4733 127289562 127293575 0.000000e+00 5849.0
12 TraesCS3A01G121400 chr3B 90.806 707 48 7 6 709 127288674 127289366 0.000000e+00 929.0
13 TraesCS3A01G121400 chr3B 93.333 60 3 1 4153 4212 127293068 127293126 2.350000e-13 87.9
14 TraesCS3A01G121400 chr3B 95.652 46 2 0 4095 4140 127293081 127293126 1.830000e-09 75.0
15 TraesCS3A01G121400 chr1D 81.576 939 165 6 1165 2096 115578017 115577080 0.000000e+00 769.0
16 TraesCS3A01G121400 chr1A 81.363 939 167 6 1165 2096 126858358 126857421 0.000000e+00 758.0
17 TraesCS3A01G121400 chr6D 94.624 93 5 0 3024 3116 146072815 146072907 1.370000e-30 145.0
18 TraesCS3A01G121400 chr4A 94.444 90 5 0 3031 3120 253419831 253419742 6.390000e-29 139.0
19 TraesCS3A01G121400 chr7B 92.708 96 6 1 3021 3116 131572578 131572484 2.300000e-28 137.0
20 TraesCS3A01G121400 chr5A 91.837 98 7 1 3023 3119 300120179 300120082 8.260000e-28 135.0
21 TraesCS3A01G121400 chr6A 91.667 96 8 0 3028 3123 1090372 1090277 2.970000e-27 134.0
22 TraesCS3A01G121400 chr2D 90.291 103 8 2 3022 3124 622355879 622355979 2.970000e-27 134.0
23 TraesCS3A01G121400 chr5D 84.892 139 11 9 3024 3156 238555763 238555629 1.070000e-26 132.0


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 TraesCS3A01G121400 chr3A 95526560 95531292 4732 False 1863.200 8741 98.4764 1 4733 5 chr3A.!!$F1 4732
1 TraesCS3A01G121400 chr3D 81360865 81367792 6927 False 1451.200 6100 93.8588 1 4733 5 chr3D.!!$F1 4732
2 TraesCS3A01G121400 chr3B 127288674 127293575 4901 False 1735.225 5849 93.1985 6 4733 4 chr3B.!!$F1 4727
3 TraesCS3A01G121400 chr1D 115577080 115578017 937 True 769.000 769 81.5760 1165 2096 1 chr1D.!!$R1 931
4 TraesCS3A01G121400 chr1A 126857421 126858358 937 True 758.000 758 81.3630 1165 2096 1 chr1A.!!$R1 931

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
790 3200 0.038166 TGCCCGAGAGCAAGGAATTT 59.962 50.0 0.00 0.0 40.56 1.82 F
791 3201 0.453390 GCCCGAGAGCAAGGAATTTG 59.547 55.0 0.00 0.0 39.88 2.32 F
2540 4958 0.319813 GTTCTGGTGCAATTGGTGGC 60.320 55.0 7.72 0.0 0.00 5.01 F
3310 5731 1.039856 TCTCTTGCAGTTTTTGGCCC 58.960 50.0 0.00 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2494 4912 1.404035 GGCGAACAACTGAGGTGTTTT 59.596 47.619 17.98 0.0 0.00 2.43 R
2789 5207 1.554617 GGGTGGTTGCAGCCATAATTT 59.445 47.619 26.00 0.0 41.08 1.82 R
3672 6102 1.007387 CGCTTTGGCTGGTTGGAAC 60.007 57.895 0.00 0.0 36.09 3.62 R
4586 7105 1.076024 ACATGCCACCCTGAGAACAAT 59.924 47.619 0.00 0.0 0.00 2.71 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
30 31 0.872388 CGACAAGCACCACTAAACCC 59.128 55.000 0.00 0.00 0.00 4.11
46 47 2.341846 ACCCAAAGAACGAAGCTTGA 57.658 45.000 2.10 0.00 0.00 3.02
50 51 3.751175 CCCAAAGAACGAAGCTTGATACA 59.249 43.478 2.10 0.00 0.00 2.29
52 53 5.278266 CCCAAAGAACGAAGCTTGATACAAA 60.278 40.000 2.10 0.00 0.00 2.83
88 94 3.379445 GAAGACGAGCCCGGTCCA 61.379 66.667 0.00 0.00 40.78 4.02
261 2258 4.789012 AAAATGAACTGCCGAATGACAT 57.211 36.364 0.00 0.00 0.00 3.06
364 2361 0.244178 GAGGAAAGAACCGCTCGACT 59.756 55.000 0.00 0.00 34.73 4.18
375 2372 1.591863 GCTCGACTATCCAACGGCC 60.592 63.158 0.00 0.00 0.00 6.13
481 2478 0.755698 ACTGTCGTCCTCCAGTGTGT 60.756 55.000 0.00 0.00 40.30 3.72
482 2479 0.319040 CTGTCGTCCTCCAGTGTGTG 60.319 60.000 0.00 0.00 0.00 3.82
483 2480 1.040893 TGTCGTCCTCCAGTGTGTGT 61.041 55.000 0.00 0.00 0.00 3.72
484 2481 0.318784 GTCGTCCTCCAGTGTGTGTC 60.319 60.000 0.00 0.00 0.00 3.67
549 2546 4.715523 TTCTGCGCCCTTTCCCCG 62.716 66.667 4.18 0.00 0.00 5.73
596 2593 3.882326 CATCCATGGCCGCCTCCT 61.882 66.667 11.61 0.00 0.00 3.69
731 3141 2.764251 CTTTCTTGGCGGTGCGTTCG 62.764 60.000 0.00 0.00 0.00 3.95
790 3200 0.038166 TGCCCGAGAGCAAGGAATTT 59.962 50.000 0.00 0.00 40.56 1.82
791 3201 0.453390 GCCCGAGAGCAAGGAATTTG 59.547 55.000 0.00 0.00 39.88 2.32
811 3221 2.725008 CTGAGATCTCCGGTCGCC 59.275 66.667 20.03 0.00 0.00 5.54
895 3305 7.088272 AGGTGCGTCTTTTACATAAAATTTCC 58.912 34.615 0.00 0.00 34.95 3.13
912 3322 3.870606 CGCGAGGAATTTCACGGT 58.129 55.556 0.00 0.00 0.00 4.83
919 3329 0.800631 GGAATTTCACGGTCGGTTCC 59.199 55.000 0.00 0.00 0.00 3.62
921 3331 0.607217 AATTTCACGGTCGGTTCCCC 60.607 55.000 0.00 0.00 0.00 4.81
1415 3828 2.046892 CAAGGTCCGGTCAGGCAG 60.047 66.667 0.00 0.00 40.77 4.85
1555 3971 3.958798 GGCTAGGAAGTATGTGGACAGTA 59.041 47.826 0.00 0.00 0.00 2.74
1556 3972 4.404715 GGCTAGGAAGTATGTGGACAGTAA 59.595 45.833 0.00 0.00 0.00 2.24
1557 3973 5.105064 GGCTAGGAAGTATGTGGACAGTAAA 60.105 44.000 0.00 0.00 0.00 2.01
1566 3982 7.851228 AGTATGTGGACAGTAAATTCATCTCA 58.149 34.615 0.00 0.00 0.00 3.27
1744 4160 1.271054 ACAATGGGATATCCGAGCTGC 60.271 52.381 15.69 1.17 38.76 5.25
1953 4369 1.429463 GTCTGTTGAAGTACTGGCCG 58.571 55.000 0.00 0.00 0.00 6.13
2019 4435 6.002704 AGAAGAAGTGCTTGAGTTGATTGAT 58.997 36.000 0.00 0.00 36.83 2.57
2297 4714 7.064134 TCACCATTATTTTGTAGAGTAGTTGCG 59.936 37.037 0.00 0.00 0.00 4.85
2355 4772 4.215613 AGGTTTTTAGTCGAAGAATGTGCC 59.784 41.667 0.00 0.00 39.69 5.01
2494 4912 2.582052 CTTGTTGGCTAAAGTGGGACA 58.418 47.619 0.00 0.00 0.00 4.02
2511 4929 3.181490 GGGACAAAACACCTCAGTTGTTC 60.181 47.826 0.00 0.00 34.44 3.18
2540 4958 0.319813 GTTCTGGTGCAATTGGTGGC 60.320 55.000 7.72 0.00 0.00 5.01
2765 5183 8.946085 GTTAGGATGATCACAACTGTTTGATAA 58.054 33.333 0.00 9.92 36.48 1.75
2932 5350 6.153340 ACCACAGAACCATGATTTGATTAAGG 59.847 38.462 0.00 0.00 0.00 2.69
2938 5356 3.631686 CCATGATTTGATTAAGGGCGTCA 59.368 43.478 0.00 0.00 0.00 4.35
3065 5483 7.925993 TGTCCCATAATATAAGAGCGTTTTTG 58.074 34.615 0.00 0.00 0.00 2.44
3069 5487 8.567948 CCCATAATATAAGAGCGTTTTTGACAT 58.432 33.333 0.00 0.00 0.00 3.06
3070 5488 9.950680 CCATAATATAAGAGCGTTTTTGACATT 57.049 29.630 0.00 0.00 0.00 2.71
3091 5509 9.382244 GACATTAGTGTAGTGTCAAAAACATTC 57.618 33.333 5.08 0.00 42.77 2.67
3183 5604 1.479709 ACTGTCTTCTCCCCATCGAG 58.520 55.000 0.00 0.00 0.00 4.04
3239 5660 4.895224 TGAATGACCTAGTAGCACTACG 57.105 45.455 2.29 0.00 40.80 3.51
3310 5731 1.039856 TCTCTTGCAGTTTTTGGCCC 58.960 50.000 0.00 0.00 0.00 5.80
3312 5733 1.138661 CTCTTGCAGTTTTTGGCCCAA 59.861 47.619 0.00 0.00 0.00 4.12
3567 5988 2.736719 CGACATGGACGAGAGATTGCTT 60.737 50.000 8.49 0.00 0.00 3.91
3571 5992 1.895798 TGGACGAGAGATTGCTTCTGT 59.104 47.619 0.00 0.00 33.74 3.41
3660 6081 2.035442 GGAGCAACTGGAGCGGAAC 61.035 63.158 0.00 0.00 37.01 3.62
3677 6107 4.680237 CGCTGACCCTGCGTTCCA 62.680 66.667 9.51 0.00 44.43 3.53
3687 6117 1.733402 CTGCGTTCCAACCAGCCAAA 61.733 55.000 0.00 0.00 0.00 3.28
3691 6121 1.454847 TTCCAACCAGCCAAAGCGT 60.455 52.632 0.00 0.00 46.67 5.07
3699 6129 3.062466 GCCAAAGCGTCCCCTTCC 61.062 66.667 0.00 0.00 0.00 3.46
3700 6130 2.746277 CCAAAGCGTCCCCTTCCG 60.746 66.667 0.00 0.00 0.00 4.30
3735 6165 1.198094 TCCCCACCGTGACATGACAT 61.198 55.000 0.00 0.00 0.00 3.06
3742 6172 0.036483 CGTGACATGACATGGGTCCA 60.036 55.000 19.39 8.75 43.65 4.02
4022 6456 2.348666 GGCGCTACTGACTTTGTATGTG 59.651 50.000 7.64 0.00 0.00 3.21
4136 6573 6.545666 TCTGAACAAAATGCCTTCTCTAACAA 59.454 34.615 0.00 0.00 0.00 2.83
4161 6677 7.816640 ACATATGCAAGTTACTGTACCTTTTG 58.183 34.615 1.58 0.00 0.00 2.44
4169 6685 8.621286 CAAGTTACTGTACCTTTTGTTGAGATT 58.379 33.333 0.00 0.00 0.00 2.40
4208 6724 6.545666 TCTGAACAAAATGCCTTCTCTAACAA 59.454 34.615 0.00 0.00 0.00 2.83
4209 6725 6.503524 TGAACAAAATGCCTTCTCTAACAAC 58.496 36.000 0.00 0.00 0.00 3.32
4210 6726 6.096141 TGAACAAAATGCCTTCTCTAACAACA 59.904 34.615 0.00 0.00 0.00 3.33
4211 6727 6.655078 ACAAAATGCCTTCTCTAACAACAT 57.345 33.333 0.00 0.00 0.00 2.71
4212 6728 7.759489 ACAAAATGCCTTCTCTAACAACATA 57.241 32.000 0.00 0.00 0.00 2.29
4213 6729 8.353423 ACAAAATGCCTTCTCTAACAACATAT 57.647 30.769 0.00 0.00 0.00 1.78
4214 6730 8.246180 ACAAAATGCCTTCTCTAACAACATATG 58.754 33.333 0.00 0.00 0.00 1.78
4215 6731 6.382869 AATGCCTTCTCTAACAACATATGC 57.617 37.500 1.58 0.00 0.00 3.14
4216 6732 4.842574 TGCCTTCTCTAACAACATATGCA 58.157 39.130 1.58 0.00 0.00 3.96
4217 6733 5.252547 TGCCTTCTCTAACAACATATGCAA 58.747 37.500 1.58 0.00 0.00 4.08
4218 6734 5.355071 TGCCTTCTCTAACAACATATGCAAG 59.645 40.000 1.58 0.00 0.00 4.01
4219 6735 5.355350 GCCTTCTCTAACAACATATGCAAGT 59.645 40.000 1.58 0.00 0.00 3.16
4220 6736 6.127897 GCCTTCTCTAACAACATATGCAAGTT 60.128 38.462 1.58 7.81 0.00 2.66
4221 6737 7.065803 GCCTTCTCTAACAACATATGCAAGTTA 59.934 37.037 1.58 8.52 0.00 2.24
4222 6738 8.391106 CCTTCTCTAACAACATATGCAAGTTAC 58.609 37.037 1.58 0.00 0.00 2.50
4223 6739 9.155975 CTTCTCTAACAACATATGCAAGTTACT 57.844 33.333 1.58 0.00 0.00 2.24
4224 6740 8.479313 TCTCTAACAACATATGCAAGTTACTG 57.521 34.615 1.58 3.99 0.00 2.74
4225 6741 8.094548 TCTCTAACAACATATGCAAGTTACTGT 58.905 33.333 1.58 0.00 0.00 3.55
4226 6742 9.366216 CTCTAACAACATATGCAAGTTACTGTA 57.634 33.333 1.58 0.00 0.00 2.74
4227 6743 9.146984 TCTAACAACATATGCAAGTTACTGTAC 57.853 33.333 1.58 0.00 0.00 2.90
4228 6744 6.403333 ACAACATATGCAAGTTACTGTACG 57.597 37.500 1.58 0.00 0.00 3.67
4229 6745 5.929992 ACAACATATGCAAGTTACTGTACGT 59.070 36.000 1.58 0.00 0.00 3.57
4230 6746 6.425721 ACAACATATGCAAGTTACTGTACGTT 59.574 34.615 1.58 0.00 0.00 3.99
4231 6747 7.041644 ACAACATATGCAAGTTACTGTACGTTT 60.042 33.333 1.58 0.00 0.00 3.60
4232 6748 7.429636 ACATATGCAAGTTACTGTACGTTTT 57.570 32.000 1.58 0.00 0.00 2.43
4233 6749 7.295201 ACATATGCAAGTTACTGTACGTTTTG 58.705 34.615 1.58 0.00 0.00 2.44
4234 6750 5.744666 ATGCAAGTTACTGTACGTTTTGT 57.255 34.783 0.00 0.00 0.00 2.83
4235 6751 5.548706 TGCAAGTTACTGTACGTTTTGTT 57.451 34.783 0.00 0.00 0.00 2.83
4236 6752 5.325494 TGCAAGTTACTGTACGTTTTGTTG 58.675 37.500 0.00 0.00 0.00 3.33
4237 6753 5.121925 TGCAAGTTACTGTACGTTTTGTTGA 59.878 36.000 0.00 0.00 0.00 3.18
4238 6754 5.675444 GCAAGTTACTGTACGTTTTGTTGAG 59.325 40.000 0.00 0.00 0.00 3.02
4239 6755 6.455913 GCAAGTTACTGTACGTTTTGTTGAGA 60.456 38.462 0.00 0.00 0.00 3.27
4240 6756 7.627340 CAAGTTACTGTACGTTTTGTTGAGAT 58.373 34.615 0.00 0.00 0.00 2.75
4241 6757 7.781548 AGTTACTGTACGTTTTGTTGAGATT 57.218 32.000 0.00 0.00 0.00 2.40
4242 6758 8.205131 AGTTACTGTACGTTTTGTTGAGATTT 57.795 30.769 0.00 0.00 0.00 2.17
4243 6759 8.333186 AGTTACTGTACGTTTTGTTGAGATTTC 58.667 33.333 0.00 0.00 0.00 2.17
4244 6760 6.671614 ACTGTACGTTTTGTTGAGATTTCA 57.328 33.333 0.00 0.00 0.00 2.69
4245 6761 6.483687 ACTGTACGTTTTGTTGAGATTTCAC 58.516 36.000 0.00 0.00 31.71 3.18
4246 6762 6.315393 ACTGTACGTTTTGTTGAGATTTCACT 59.685 34.615 0.00 0.00 31.71 3.41
4247 6763 7.079182 TGTACGTTTTGTTGAGATTTCACTT 57.921 32.000 0.00 0.00 31.71 3.16
4248 6764 6.964370 TGTACGTTTTGTTGAGATTTCACTTG 59.036 34.615 0.00 0.00 31.71 3.16
4249 6765 5.949735 ACGTTTTGTTGAGATTTCACTTGT 58.050 33.333 0.00 0.00 31.71 3.16
4250 6766 6.386654 ACGTTTTGTTGAGATTTCACTTGTT 58.613 32.000 0.00 0.00 31.71 2.83
4251 6767 6.866248 ACGTTTTGTTGAGATTTCACTTGTTT 59.134 30.769 0.00 0.00 31.71 2.83
4252 6768 7.148820 ACGTTTTGTTGAGATTTCACTTGTTTG 60.149 33.333 0.00 0.00 31.71 2.93
4253 6769 7.148820 CGTTTTGTTGAGATTTCACTTGTTTGT 60.149 33.333 0.00 0.00 31.71 2.83
4254 6770 8.495148 GTTTTGTTGAGATTTCACTTGTTTGTT 58.505 29.630 0.00 0.00 31.71 2.83
4255 6771 8.600449 TTTGTTGAGATTTCACTTGTTTGTTT 57.400 26.923 0.00 0.00 31.71 2.83
4256 6772 7.810766 TGTTGAGATTTCACTTGTTTGTTTC 57.189 32.000 0.00 0.00 31.71 2.78
4257 6773 7.601856 TGTTGAGATTTCACTTGTTTGTTTCT 58.398 30.769 0.00 0.00 31.71 2.52
4258 6774 7.541783 TGTTGAGATTTCACTTGTTTGTTTCTG 59.458 33.333 0.00 0.00 31.71 3.02
4259 6775 7.389803 TGAGATTTCACTTGTTTGTTTCTGA 57.610 32.000 0.00 0.00 0.00 3.27
4260 6776 7.825681 TGAGATTTCACTTGTTTGTTTCTGAA 58.174 30.769 0.00 0.00 0.00 3.02
4261 6777 7.754924 TGAGATTTCACTTGTTTGTTTCTGAAC 59.245 33.333 0.00 0.00 36.29 3.18
4262 6778 7.601856 AGATTTCACTTGTTTGTTTCTGAACA 58.398 30.769 0.00 0.00 43.73 3.18
4273 6789 5.596836 TGTTTCTGAACAAAATGCCTTCT 57.403 34.783 0.00 0.00 42.54 2.85
4274 6790 5.591099 TGTTTCTGAACAAAATGCCTTCTC 58.409 37.500 0.00 0.00 42.54 2.87
4275 6791 5.360714 TGTTTCTGAACAAAATGCCTTCTCT 59.639 36.000 0.00 0.00 42.54 3.10
4276 6792 6.545666 TGTTTCTGAACAAAATGCCTTCTCTA 59.454 34.615 0.00 0.00 42.54 2.43
4277 6793 7.068103 TGTTTCTGAACAAAATGCCTTCTCTAA 59.932 33.333 0.00 0.00 42.54 2.10
4278 6794 6.560253 TCTGAACAAAATGCCTTCTCTAAC 57.440 37.500 0.00 0.00 0.00 2.34
4279 6795 6.061441 TCTGAACAAAATGCCTTCTCTAACA 58.939 36.000 0.00 0.00 0.00 2.41
4280 6796 6.545666 TCTGAACAAAATGCCTTCTCTAACAA 59.454 34.615 0.00 0.00 0.00 2.83
4286 6802 6.899393 AAATGCCTTCTCTAACAACATGAA 57.101 33.333 0.00 0.00 0.00 2.57
4382 6898 3.322254 GCTTAGGCTATCCACTTGCTCTA 59.678 47.826 0.00 0.00 35.22 2.43
4383 6899 4.020662 GCTTAGGCTATCCACTTGCTCTAT 60.021 45.833 0.00 0.00 35.22 1.98
4384 6900 5.512232 GCTTAGGCTATCCACTTGCTCTATT 60.512 44.000 0.00 0.00 35.22 1.73
4468 6984 9.626045 CTCAAAGGGTTATGTAAAGAAAACATC 57.374 33.333 0.00 0.00 38.49 3.06
4555 7074 4.697756 CCCCGCCAACTCTTCGCA 62.698 66.667 0.00 0.00 0.00 5.10
4567 7086 1.514811 CTCTTCGCAGTTATCGCTTCG 59.485 52.381 0.00 0.00 0.00 3.79
4586 7105 4.212913 GCGAGGCCTGATCAGCGA 62.213 66.667 12.00 0.00 0.00 4.93
4639 7158 5.188327 GCCTGAGCTTGAGTTTAGTTTTT 57.812 39.130 0.00 0.00 35.50 1.94
4718 7246 1.219773 ACCATGGATGCCATCTGACT 58.780 50.000 21.47 0.00 43.15 3.41
4719 7247 1.133884 ACCATGGATGCCATCTGACTG 60.134 52.381 21.47 0.00 43.15 3.51
4720 7248 1.142262 CCATGGATGCCATCTGACTGA 59.858 52.381 5.56 0.00 43.15 3.41
4721 7249 2.219458 CATGGATGCCATCTGACTGAC 58.781 52.381 4.41 0.00 43.15 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.176910 TGGTGCTTGTCGAAGTGTCA 59.823 50.000 0.00 0.00 0.00 3.58
30 31 7.678194 TTTTTGTATCAAGCTTCGTTCTTTG 57.322 32.000 0.00 0.00 0.00 2.77
58 59 1.550524 TCGTCTTCCTCCCTGTCAATG 59.449 52.381 0.00 0.00 0.00 2.82
65 71 2.364448 GGGCTCGTCTTCCTCCCT 60.364 66.667 0.00 0.00 34.19 4.20
66 72 3.839432 CGGGCTCGTCTTCCTCCC 61.839 72.222 0.00 0.00 0.00 4.30
105 111 0.693049 ATAATCATCTGGGGTCCCGC 59.307 55.000 0.48 0.00 39.42 6.13
107 113 5.520748 AATACATAATCATCTGGGGTCCC 57.479 43.478 0.00 0.00 0.00 4.46
167 176 5.492895 TGATGGAAGTATGGCGTCTTTTTA 58.507 37.500 0.00 0.00 0.00 1.52
184 194 7.661027 TCACTGCGATTAATTAATCATGATGGA 59.339 33.333 28.90 18.65 41.59 3.41
261 2258 1.144969 GCAACGGTCGAGAAATGTCA 58.855 50.000 0.00 0.00 0.00 3.58
408 2405 2.202892 GGACGGTTCGGCTCATCC 60.203 66.667 0.00 0.00 34.07 3.51
414 2411 2.823829 GATGCATGGACGGTTCGGC 61.824 63.158 2.46 0.00 0.00 5.54
549 2546 4.890306 GAGGGAGGGGAGGGGAGC 62.890 77.778 0.00 0.00 0.00 4.70
716 3126 3.573489 GAACGAACGCACCGCCAAG 62.573 63.158 0.00 0.00 0.00 3.61
731 3141 2.140717 ACGGATCAAGAACCAACGAAC 58.859 47.619 0.00 0.00 0.00 3.95
766 3176 4.441695 TTGCTCTCGGGCAGCTCG 62.442 66.667 8.94 8.94 43.39 5.03
811 3221 2.027625 GGGGACTTCGACAGCAACG 61.028 63.158 0.00 0.00 0.00 4.10
832 3242 3.145551 GCAATGGCAGGCAGGGAG 61.146 66.667 1.89 0.00 40.72 4.30
895 3305 1.708027 GACCGTGAAATTCCTCGCG 59.292 57.895 0.00 0.00 46.36 5.87
921 3331 1.589196 GCGAGAAATCCGTCCTCCG 60.589 63.158 0.00 0.00 0.00 4.63
934 3344 3.191162 CCAATCAAAGAACCATTGCGAGA 59.809 43.478 0.00 0.00 0.00 4.04
1341 3754 3.188100 ACGCACGCCGACATCATG 61.188 61.111 2.93 0.00 41.02 3.07
1555 3971 5.467705 GTCAAGCAGCTTTGAGATGAATTT 58.532 37.500 4.38 0.00 37.72 1.82
1556 3972 4.082354 GGTCAAGCAGCTTTGAGATGAATT 60.082 41.667 4.38 0.00 37.72 2.17
1557 3973 3.442977 GGTCAAGCAGCTTTGAGATGAAT 59.557 43.478 4.38 0.00 37.72 2.57
1566 3982 2.378038 TCAAACAGGTCAAGCAGCTTT 58.622 42.857 4.38 0.00 0.00 3.51
1744 4160 2.620112 CGCTGCCAAACACCTCCAG 61.620 63.158 0.00 0.00 0.00 3.86
1953 4369 7.556844 TCATCTCCTTCTGACTATTTGTAACC 58.443 38.462 0.00 0.00 0.00 2.85
2019 4435 3.244526 TGCACTTCTGAAACTCAGCCATA 60.245 43.478 0.00 0.00 43.95 2.74
2297 4714 4.446371 AGAATGCACCAGTATACAGCTTC 58.554 43.478 5.50 8.79 0.00 3.86
2351 4768 3.004839 GGAAAAGGAAAGAGAACAGGCAC 59.995 47.826 0.00 0.00 0.00 5.01
2355 4772 4.339247 TGCAAGGAAAAGGAAAGAGAACAG 59.661 41.667 0.00 0.00 0.00 3.16
2494 4912 1.404035 GGCGAACAACTGAGGTGTTTT 59.596 47.619 17.98 0.00 0.00 2.43
2511 4929 1.654220 CACCAGAACCAACAAGGCG 59.346 57.895 0.00 0.00 43.14 5.52
2616 5034 7.102346 CACCCAGATATAAGATAGAGCCAAAG 58.898 42.308 0.00 0.00 0.00 2.77
2670 5088 4.158394 TCAAGTTATCTGCCTTTGGATTGC 59.842 41.667 0.00 0.00 0.00 3.56
2765 5183 7.432148 TGTACCATGACATGACCTTATAAGT 57.568 36.000 17.24 5.36 0.00 2.24
2789 5207 1.554617 GGGTGGTTGCAGCCATAATTT 59.445 47.619 26.00 0.00 41.08 1.82
2797 5215 2.829741 TTTATTTGGGTGGTTGCAGC 57.170 45.000 0.00 0.00 0.00 5.25
2938 5356 6.533730 TCTACTGTGATGTTTCAGTCCAAAT 58.466 36.000 1.08 0.00 42.77 2.32
3065 5483 9.382244 GAATGTTTTTGACACTACACTAATGTC 57.618 33.333 0.00 0.00 42.04 3.06
3087 5505 5.948162 CCCTCCATCCCACAATATAAGAATG 59.052 44.000 0.00 0.00 0.00 2.67
3091 5509 4.599241 ACTCCCTCCATCCCACAATATAAG 59.401 45.833 0.00 0.00 0.00 1.73
3099 5517 1.880941 AACTACTCCCTCCATCCCAC 58.119 55.000 0.00 0.00 0.00 4.61
3105 5523 4.880164 ACTGCTATTAACTACTCCCTCCA 58.120 43.478 0.00 0.00 0.00 3.86
3239 5660 5.335191 GGAATTGTCATGAACCAAGACAGTC 60.335 44.000 0.00 0.00 41.79 3.51
3348 5769 6.603599 GCCAAAAGACAGGGAATAGATTAACT 59.396 38.462 0.00 0.00 0.00 2.24
3615 6036 4.856607 CTTCGACGCTCCTCCGCC 62.857 72.222 0.00 0.00 0.00 6.13
3663 6084 2.112297 GGTTGGAACGCAGGGTCA 59.888 61.111 0.00 0.00 0.00 4.02
3672 6102 1.007387 CGCTTTGGCTGGTTGGAAC 60.007 57.895 0.00 0.00 36.09 3.62
3677 6107 2.597510 GGGACGCTTTGGCTGGTT 60.598 61.111 0.00 0.00 36.09 3.67
3699 6129 3.798954 GATTCTCGGAGGGGCTGCG 62.799 68.421 4.96 0.00 46.23 5.18
3700 6130 2.110006 GATTCTCGGAGGGGCTGC 59.890 66.667 4.96 0.00 0.00 5.25
3702 6132 2.446802 GGGATTCTCGGAGGGGCT 60.447 66.667 4.96 0.00 0.00 5.19
3715 6145 1.198094 TGTCATGTCACGGTGGGGAT 61.198 55.000 8.50 0.00 0.00 3.85
3735 6165 2.781174 GGGTGGAGTATATTTGGACCCA 59.219 50.000 0.00 0.00 41.17 4.51
3742 6172 3.462205 GGAAGGTGGGGTGGAGTATATTT 59.538 47.826 0.00 0.00 0.00 1.40
3907 6340 2.795175 TTCGCCGCAAAAATAACCAA 57.205 40.000 0.00 0.00 0.00 3.67
3908 6341 3.057174 AGAATTCGCCGCAAAAATAACCA 60.057 39.130 0.00 0.00 0.00 3.67
3909 6342 3.507786 AGAATTCGCCGCAAAAATAACC 58.492 40.909 0.00 0.00 0.00 2.85
3910 6343 3.237433 CGAGAATTCGCCGCAAAAATAAC 59.763 43.478 3.43 0.00 40.36 1.89
3913 6346 1.466950 TCGAGAATTCGCCGCAAAAAT 59.533 42.857 15.33 0.00 46.28 1.82
4120 6557 5.887598 TGCATATGTTGTTAGAGAAGGCATT 59.112 36.000 4.29 0.00 0.00 3.56
4136 6573 7.447238 ACAAAAGGTACAGTAACTTGCATATGT 59.553 33.333 11.83 9.21 35.51 2.29
4161 6677 7.754924 TCAGAAACAAACAAGTGAAATCTCAAC 59.245 33.333 0.00 0.00 31.88 3.18
4208 6724 7.041644 ACAAAACGTACAGTAACTTGCATATGT 60.042 33.333 4.29 0.00 0.00 2.29
4209 6725 7.295201 ACAAAACGTACAGTAACTTGCATATG 58.705 34.615 0.00 0.00 0.00 1.78
4210 6726 7.429636 ACAAAACGTACAGTAACTTGCATAT 57.570 32.000 0.00 0.00 0.00 1.78
4211 6727 6.847956 ACAAAACGTACAGTAACTTGCATA 57.152 33.333 0.00 0.00 0.00 3.14
4212 6728 5.744666 ACAAAACGTACAGTAACTTGCAT 57.255 34.783 0.00 0.00 0.00 3.96
4213 6729 5.121925 TCAACAAAACGTACAGTAACTTGCA 59.878 36.000 0.00 0.00 0.00 4.08
4214 6730 5.561993 TCAACAAAACGTACAGTAACTTGC 58.438 37.500 0.00 0.00 0.00 4.01
4215 6731 6.996106 TCTCAACAAAACGTACAGTAACTTG 58.004 36.000 0.00 0.98 0.00 3.16
4216 6732 7.781548 ATCTCAACAAAACGTACAGTAACTT 57.218 32.000 0.00 0.00 0.00 2.66
4217 6733 7.781548 AATCTCAACAAAACGTACAGTAACT 57.218 32.000 0.00 0.00 0.00 2.24
4218 6734 8.117988 TGAAATCTCAACAAAACGTACAGTAAC 58.882 33.333 0.00 0.00 0.00 2.50
4219 6735 8.117988 GTGAAATCTCAACAAAACGTACAGTAA 58.882 33.333 0.00 0.00 31.88 2.24
4220 6736 7.493320 AGTGAAATCTCAACAAAACGTACAGTA 59.507 33.333 0.00 0.00 31.88 2.74
4221 6737 6.315393 AGTGAAATCTCAACAAAACGTACAGT 59.685 34.615 0.00 0.00 31.88 3.55
4222 6738 6.715464 AGTGAAATCTCAACAAAACGTACAG 58.285 36.000 0.00 0.00 31.88 2.74
4223 6739 6.671614 AGTGAAATCTCAACAAAACGTACA 57.328 33.333 0.00 0.00 31.88 2.90
4224 6740 6.964934 ACAAGTGAAATCTCAACAAAACGTAC 59.035 34.615 0.00 0.00 31.88 3.67
4225 6741 7.079182 ACAAGTGAAATCTCAACAAAACGTA 57.921 32.000 0.00 0.00 31.88 3.57
4226 6742 5.949735 ACAAGTGAAATCTCAACAAAACGT 58.050 33.333 0.00 0.00 31.88 3.99
4227 6743 6.869421 AACAAGTGAAATCTCAACAAAACG 57.131 33.333 0.00 0.00 31.88 3.60
4228 6744 8.017587 ACAAACAAGTGAAATCTCAACAAAAC 57.982 30.769 0.00 0.00 31.88 2.43
4229 6745 8.600449 AACAAACAAGTGAAATCTCAACAAAA 57.400 26.923 0.00 0.00 31.88 2.44
4230 6746 8.600449 AAACAAACAAGTGAAATCTCAACAAA 57.400 26.923 0.00 0.00 31.88 2.83
4231 6747 8.087750 AGAAACAAACAAGTGAAATCTCAACAA 58.912 29.630 0.00 0.00 31.88 2.83
4232 6748 7.541783 CAGAAACAAACAAGTGAAATCTCAACA 59.458 33.333 0.00 0.00 31.88 3.33
4233 6749 7.754924 TCAGAAACAAACAAGTGAAATCTCAAC 59.245 33.333 0.00 0.00 31.88 3.18
4234 6750 7.825681 TCAGAAACAAACAAGTGAAATCTCAA 58.174 30.769 0.00 0.00 31.88 3.02
4235 6751 7.389803 TCAGAAACAAACAAGTGAAATCTCA 57.610 32.000 0.00 0.00 0.00 3.27
4236 6752 7.754924 TGTTCAGAAACAAACAAGTGAAATCTC 59.245 33.333 0.00 0.00 42.34 2.75
4237 6753 7.601856 TGTTCAGAAACAAACAAGTGAAATCT 58.398 30.769 0.00 0.00 42.34 2.40
4238 6754 7.810766 TGTTCAGAAACAAACAAGTGAAATC 57.189 32.000 0.00 0.00 42.34 2.17
4251 6767 5.360714 AGAGAAGGCATTTTGTTCAGAAACA 59.639 36.000 0.00 0.00 43.58 2.83
4252 6768 5.836347 AGAGAAGGCATTTTGTTCAGAAAC 58.164 37.500 0.00 0.00 35.85 2.78
4253 6769 7.068103 TGTTAGAGAAGGCATTTTGTTCAGAAA 59.932 33.333 0.00 0.00 0.00 2.52
4254 6770 6.545666 TGTTAGAGAAGGCATTTTGTTCAGAA 59.454 34.615 0.00 0.00 0.00 3.02
4255 6771 6.061441 TGTTAGAGAAGGCATTTTGTTCAGA 58.939 36.000 0.00 0.00 0.00 3.27
4256 6772 6.317789 TGTTAGAGAAGGCATTTTGTTCAG 57.682 37.500 0.00 0.00 0.00 3.02
4257 6773 6.096141 TGTTGTTAGAGAAGGCATTTTGTTCA 59.904 34.615 0.00 0.00 0.00 3.18
4258 6774 6.503524 TGTTGTTAGAGAAGGCATTTTGTTC 58.496 36.000 0.00 0.00 0.00 3.18
4259 6775 6.463995 TGTTGTTAGAGAAGGCATTTTGTT 57.536 33.333 0.00 0.00 0.00 2.83
4260 6776 6.265196 TCATGTTGTTAGAGAAGGCATTTTGT 59.735 34.615 0.00 0.00 0.00 2.83
4261 6777 6.680810 TCATGTTGTTAGAGAAGGCATTTTG 58.319 36.000 0.00 0.00 0.00 2.44
4262 6778 6.899393 TCATGTTGTTAGAGAAGGCATTTT 57.101 33.333 0.00 0.00 0.00 1.82
4263 6779 6.265196 TGTTCATGTTGTTAGAGAAGGCATTT 59.735 34.615 0.00 0.00 0.00 2.32
4264 6780 5.769662 TGTTCATGTTGTTAGAGAAGGCATT 59.230 36.000 0.00 0.00 0.00 3.56
4265 6781 5.316167 TGTTCATGTTGTTAGAGAAGGCAT 58.684 37.500 0.00 0.00 0.00 4.40
4266 6782 4.713553 TGTTCATGTTGTTAGAGAAGGCA 58.286 39.130 0.00 0.00 0.00 4.75
4267 6783 5.689383 TTGTTCATGTTGTTAGAGAAGGC 57.311 39.130 0.00 0.00 0.00 4.35
4268 6784 7.080099 CACATTGTTCATGTTGTTAGAGAAGG 58.920 38.462 0.00 0.00 44.40 3.46
4269 6785 7.041167 TCCACATTGTTCATGTTGTTAGAGAAG 60.041 37.037 0.00 0.00 44.40 2.85
4270 6786 6.770303 TCCACATTGTTCATGTTGTTAGAGAA 59.230 34.615 0.00 0.00 44.40 2.87
4271 6787 6.295249 TCCACATTGTTCATGTTGTTAGAGA 58.705 36.000 0.00 0.00 44.40 3.10
4272 6788 6.205464 ACTCCACATTGTTCATGTTGTTAGAG 59.795 38.462 0.00 2.82 44.40 2.43
4273 6789 6.061441 ACTCCACATTGTTCATGTTGTTAGA 58.939 36.000 0.00 0.00 44.40 2.10
4274 6790 6.317789 ACTCCACATTGTTCATGTTGTTAG 57.682 37.500 0.00 0.00 44.40 2.34
4275 6791 7.220740 TCTACTCCACATTGTTCATGTTGTTA 58.779 34.615 0.00 0.00 44.40 2.41
4276 6792 6.061441 TCTACTCCACATTGTTCATGTTGTT 58.939 36.000 0.00 0.00 44.40 2.83
4277 6793 5.620206 TCTACTCCACATTGTTCATGTTGT 58.380 37.500 0.00 0.00 44.40 3.32
4278 6794 6.748333 ATCTACTCCACATTGTTCATGTTG 57.252 37.500 0.00 0.00 44.40 3.33
4279 6795 7.851228 TCTATCTACTCCACATTGTTCATGTT 58.149 34.615 0.00 0.00 44.40 2.71
4286 6802 6.436027 TCTTCCTCTATCTACTCCACATTGT 58.564 40.000 0.00 0.00 0.00 2.71
4302 6818 3.137360 AGCAACTCCTGTTTTCTTCCTCT 59.863 43.478 0.00 0.00 33.52 3.69
4382 6898 3.950395 GAGCATAGAAAAGGCACAGGAAT 59.050 43.478 0.00 0.00 0.00 3.01
4383 6899 3.244875 TGAGCATAGAAAAGGCACAGGAA 60.245 43.478 0.00 0.00 0.00 3.36
4384 6900 2.305635 TGAGCATAGAAAAGGCACAGGA 59.694 45.455 0.00 0.00 0.00 3.86
4435 6951 7.942341 TCTTTACATAACCCTTTGAGAATGTGT 59.058 33.333 0.00 0.00 0.00 3.72
4468 6984 6.988580 TGAGAATGACATAGCTTGTTCTATGG 59.011 38.462 13.36 0.00 46.27 2.74
4532 7051 1.694696 GAAGAGTTGGCGGGGATCTAT 59.305 52.381 0.00 0.00 0.00 1.98
4537 7056 4.388499 GCGAAGAGTTGGCGGGGA 62.388 66.667 0.00 0.00 0.00 4.81
4538 7057 4.697756 TGCGAAGAGTTGGCGGGG 62.698 66.667 0.00 0.00 37.17 5.73
4567 7086 2.894387 GCTGATCAGGCCTCGCAC 60.894 66.667 23.89 0.93 0.00 5.34
4586 7105 1.076024 ACATGCCACCCTGAGAACAAT 59.924 47.619 0.00 0.00 0.00 2.71
4639 7158 2.200373 GCTCAAGTAGCCTCCCAAAA 57.800 50.000 0.00 0.00 46.25 2.44


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

AutoCloner maintained by Alex Coulton.