Multiple sequence alignment - TraesCS2B01G422900

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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 TraesCS2B01G422900 chr2B 100.000 5656 0 0 1 5656 608444401 608450056 0.000000e+00 10445.0
1 TraesCS2B01G422900 chr2A 94.393 2907 103 24 2644 5525 660512150 660515021 0.000000e+00 4410.0
2 TraesCS2B01G422900 chr2A 92.281 2306 108 25 377 2650 660509679 660511946 0.000000e+00 3208.0
3 TraesCS2B01G422900 chr2A 89.826 344 9 5 1 335 660509349 660509675 8.760000e-113 418.0
4 TraesCS2B01G422900 chr2A 93.985 133 5 2 5525 5656 660514973 660515103 1.240000e-46 198.0
5 TraesCS2B01G422900 chr2D 92.993 2683 106 19 1 2650 516703913 516706546 0.000000e+00 3838.0
6 TraesCS2B01G422900 chr2D 96.472 1559 40 6 2644 4196 516706764 516708313 0.000000e+00 2560.0
7 TraesCS2B01G422900 chr2D 91.818 1320 67 21 4195 5495 516708475 516709772 0.000000e+00 1801.0
8 TraesCS2B01G422900 chr2D 91.736 121 5 3 5537 5656 516811858 516811974 4.530000e-36 163.0
9 TraesCS2B01G422900 chr2D 92.857 98 4 3 5560 5656 516709771 516709866 7.640000e-29 139.0
10 TraesCS2B01G422900 chr3B 84.906 265 32 5 3499 3761 778446712 778446454 1.560000e-65 261.0
11 TraesCS2B01G422900 chr7D 78.491 265 44 9 3641 3894 619630720 619630982 1.630000e-35 161.0
12 TraesCS2B01G422900 chr6B 90.385 52 4 1 2662 2712 451927500 451927449 3.660000e-07 67.6


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 TraesCS2B01G422900 chr2B 608444401 608450056 5655 False 10445.0 10445 100.00000 1 5656 1 chr2B.!!$F1 5655
1 TraesCS2B01G422900 chr2A 660509349 660515103 5754 False 2058.5 4410 92.62125 1 5656 4 chr2A.!!$F1 5655
2 TraesCS2B01G422900 chr2D 516703913 516709866 5953 False 2084.5 3838 93.53500 1 5656 4 chr2D.!!$F2 5655

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
614 626 0.540830 ATTGCCCCAGGTTTTGCGTA 60.541 50.0 0.00 0.00 0.0 4.42 F
713 728 0.830648 CTAGATTGGGGCTGTCGGAA 59.169 55.0 0.00 0.00 0.0 4.30 F
1860 1900 0.965363 GCGGCTCCATTCCTCCAAAA 60.965 55.0 0.00 0.00 0.0 2.44 F
3168 3437 0.108898 AGACGCTCACAGCTAGCTTG 60.109 55.0 16.46 16.35 39.6 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 2271 0.329261 CAGATCCCAGAAAGGCACCA 59.671 55.000 0.00 0.0 35.39 4.17 R
2375 2416 1.134098 GGCTTGGCAGGCTATTGTAGA 60.134 52.381 21.41 0.0 42.53 2.59 R
3440 3714 2.092699 AGCAATCTCAGCTTAGGGTTCC 60.093 50.000 0.00 0.0 39.87 3.62 R
4776 5218 0.819259 AGCACACCGTGAACTTGCAT 60.819 50.000 5.28 0.0 35.23 3.96 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
50 51 3.748568 TGGTTTGCGCCCAAAATTAAATC 59.251 39.130 4.18 0.00 42.19 2.17
52 53 4.377943 GGTTTGCGCCCAAAATTAAATCAC 60.378 41.667 4.18 0.00 42.19 3.06
53 54 2.600731 TGCGCCCAAAATTAAATCACG 58.399 42.857 4.18 0.00 0.00 4.35
54 55 2.029828 TGCGCCCAAAATTAAATCACGT 60.030 40.909 4.18 0.00 0.00 4.49
55 56 2.344142 GCGCCCAAAATTAAATCACGTG 59.656 45.455 9.94 9.94 0.00 4.49
56 57 2.920490 CGCCCAAAATTAAATCACGTGG 59.080 45.455 17.00 0.00 0.00 4.94
57 58 3.366476 CGCCCAAAATTAAATCACGTGGA 60.366 43.478 17.00 2.69 0.00 4.02
58 59 4.561105 GCCCAAAATTAAATCACGTGGAA 58.439 39.130 17.00 5.68 0.00 3.53
59 60 4.991687 GCCCAAAATTAAATCACGTGGAAA 59.008 37.500 17.00 5.53 0.00 3.13
60 61 5.641636 GCCCAAAATTAAATCACGTGGAAAT 59.358 36.000 17.00 7.63 0.00 2.17
61 62 6.148645 GCCCAAAATTAAATCACGTGGAAATT 59.851 34.615 17.00 12.85 0.00 1.82
62 63 7.308288 GCCCAAAATTAAATCACGTGGAAATTT 60.308 33.333 17.00 16.03 0.00 1.82
63 64 8.227119 CCCAAAATTAAATCACGTGGAAATTTC 58.773 33.333 17.00 9.83 0.00 2.17
64 65 8.768955 CCAAAATTAAATCACGTGGAAATTTCA 58.231 29.630 19.49 6.62 0.00 2.69
209 221 3.953775 CCGGGCCACAGAACAGGT 61.954 66.667 4.39 0.00 0.00 4.00
407 419 5.070685 AGGTCAGCTTTCGTTTAAATCCTT 58.929 37.500 0.00 0.00 0.00 3.36
410 422 5.117135 GTCAGCTTTCGTTTAAATCCTTTGC 59.883 40.000 0.00 0.00 0.00 3.68
495 507 3.083997 CCCTCCACCTCCTTCCGG 61.084 72.222 0.00 0.00 0.00 5.14
522 534 0.894184 AGGACGAGGAAGTTGAGCGA 60.894 55.000 0.00 0.00 0.00 4.93
568 580 4.002316 TGCCGTTAGTTATTGTTGGTACC 58.998 43.478 4.43 4.43 0.00 3.34
614 626 0.540830 ATTGCCCCAGGTTTTGCGTA 60.541 50.000 0.00 0.00 0.00 4.42
644 656 3.669251 AGTTGCTCTCACTTGTACTCC 57.331 47.619 0.00 0.00 0.00 3.85
695 710 1.593006 CGAACTCAGCACGTTTTGTCT 59.407 47.619 0.00 0.00 0.00 3.41
713 728 0.830648 CTAGATTGGGGCTGTCGGAA 59.169 55.000 0.00 0.00 0.00 4.30
727 742 5.118510 GGCTGTCGGAAATTATGTTGTTTTG 59.881 40.000 0.00 0.00 0.00 2.44
728 743 5.689961 GCTGTCGGAAATTATGTTGTTTTGT 59.310 36.000 0.00 0.00 0.00 2.83
797 812 6.225926 ACAAACTTGTTTCTGCTCTGCAGG 62.226 45.833 15.13 5.82 46.89 4.85
823 838 3.641434 ACCATCAAGTGAGGATTCTGG 57.359 47.619 0.00 0.00 0.00 3.86
868 883 4.698304 GGAATTTGATTTGTCAGTCGGGTA 59.302 41.667 0.00 0.00 0.00 3.69
869 884 5.357032 GGAATTTGATTTGTCAGTCGGGTAT 59.643 40.000 0.00 0.00 0.00 2.73
875 890 5.186215 TGATTTGTCAGTCGGGTATTGTAGA 59.814 40.000 0.00 0.00 0.00 2.59
879 894 4.097437 TGTCAGTCGGGTATTGTAGACATC 59.903 45.833 0.00 0.00 36.18 3.06
923 938 2.304056 ATCTGGAGGTGCCCACTGG 61.304 63.158 0.00 0.00 34.97 4.00
940 955 2.048603 GGTGCAGGGAAGGTGATGC 61.049 63.158 0.00 0.00 39.14 3.91
1053 1068 1.323412 TGGCGCAATACAAAACACCT 58.677 45.000 10.83 0.00 0.00 4.00
1134 1149 7.615403 TGTACCTGATATTTGAGCATCTATCC 58.385 38.462 0.00 0.00 34.92 2.59
1166 1181 1.341209 CCCAGAGGTTTGTGCTTTTCC 59.659 52.381 0.00 0.00 0.00 3.13
1169 1184 1.947456 AGAGGTTTGTGCTTTTCCGTC 59.053 47.619 0.00 0.00 0.00 4.79
1191 1206 3.119884 CGCTGCACCTTGTCATGAATTTA 60.120 43.478 0.00 0.00 0.00 1.40
1192 1207 4.418392 GCTGCACCTTGTCATGAATTTAG 58.582 43.478 0.00 0.00 0.00 1.85
1193 1208 4.676196 GCTGCACCTTGTCATGAATTTAGG 60.676 45.833 0.00 4.60 0.00 2.69
1215 1230 3.334583 CCTAGTTCTGTTTGCTAGGCA 57.665 47.619 4.22 0.00 43.42 4.75
1450 1465 1.160329 GCATCTTGCGCGAGGGTTAT 61.160 55.000 24.31 7.76 31.71 1.89
1514 1529 7.620880 TGCATGTTTAGGTAAGTTCTGTCTAT 58.379 34.615 0.00 0.00 0.00 1.98
1515 1530 7.764443 TGCATGTTTAGGTAAGTTCTGTCTATC 59.236 37.037 0.00 0.00 0.00 2.08
1536 1551 3.120792 CGACATTGTCATAACCCCTACG 58.879 50.000 16.61 0.00 32.09 3.51
1553 1569 1.959226 CGTTGTTACCTGCCGCAGT 60.959 57.895 18.98 9.70 0.00 4.40
1588 1604 8.778358 GTTCTGGAATTGCATTTAGTATAGAGG 58.222 37.037 0.00 0.00 0.00 3.69
1665 1681 9.736023 AGCTGTTTCTTTACTTCACATTTAAAG 57.264 29.630 0.00 0.00 35.15 1.85
1764 1804 1.313091 GGGGTGGGTTTCTCAATCGC 61.313 60.000 0.00 0.00 0.00 4.58
1822 1862 3.008485 AGACTGGAATTTCCTGGAGTGAC 59.992 47.826 21.95 6.26 39.50 3.67
1860 1900 0.965363 GCGGCTCCATTCCTCCAAAA 60.965 55.000 0.00 0.00 0.00 2.44
1946 1986 5.580691 GGATGTTTATGACTGAACATGACGA 59.419 40.000 0.00 0.00 44.17 4.20
1980 2020 4.096682 AGAGTAGATTCCGCTTGTACACTC 59.903 45.833 0.00 0.00 0.00 3.51
1981 2021 4.017808 AGTAGATTCCGCTTGTACACTCT 58.982 43.478 0.00 0.00 0.00 3.24
1984 2024 5.401531 AGATTCCGCTTGTACACTCTTTA 57.598 39.130 0.00 0.00 0.00 1.85
1985 2025 5.169295 AGATTCCGCTTGTACACTCTTTAC 58.831 41.667 0.00 0.00 0.00 2.01
1994 2035 4.091549 TGTACACTCTTTACCTGGGGTAG 58.908 47.826 0.00 0.00 39.52 3.18
2006 2047 3.723154 ACCTGGGGTAGTTTGGAAAGTTA 59.277 43.478 0.00 0.00 32.11 2.24
2105 2146 2.496899 TGGTCAGCTTTCTGGGATTC 57.503 50.000 0.00 0.00 40.69 2.52
2135 2176 2.803133 GCAACAGCGAGCACCATAGATA 60.803 50.000 0.00 0.00 0.00 1.98
2149 2190 6.715718 GCACCATAGATAGTTGTACTCCTAGA 59.284 42.308 0.00 0.00 0.00 2.43
2189 2230 1.878775 GGAGCACACAACATCTGCC 59.121 57.895 0.00 0.00 0.00 4.85
2230 2271 3.766051 GGTTGCTGGGATCTTGAAGAAAT 59.234 43.478 0.00 0.00 0.00 2.17
2242 2283 4.279169 TCTTGAAGAAATGGTGCCTTTCTG 59.721 41.667 12.80 5.13 41.01 3.02
2314 2355 2.190578 GGGAACGGCCTCCTGATG 59.809 66.667 10.70 0.00 35.63 3.07
2375 2416 5.204409 TCTTTGCAGCAATTCACTTGATT 57.796 34.783 9.12 0.00 36.97 2.57
2451 2492 2.235016 TGGGTGTGTGCATTTACCTTC 58.765 47.619 13.62 2.36 33.71 3.46
2524 2565 7.121907 GCATTACTCTTCCTCTTTTCCTGAAAT 59.878 37.037 0.00 0.00 0.00 2.17
2826 3095 1.596954 CGTTTGGTGCAGCTTGTGTAC 60.597 52.381 18.08 5.23 40.87 2.90
2878 3147 6.014070 ACTGTGTGTGTTTATATGTAGGTGGA 60.014 38.462 0.00 0.00 0.00 4.02
3028 3297 1.871039 CGAATGGGGACGCGATTTTAT 59.129 47.619 15.93 0.00 0.00 1.40
3074 3343 3.181440 CCAATATGTATGTCCACTGCCCT 60.181 47.826 0.00 0.00 0.00 5.19
3168 3437 0.108898 AGACGCTCACAGCTAGCTTG 60.109 55.000 16.46 16.35 39.60 4.01
3313 3587 8.621532 AGTTGTTTATGCAGAAGAGTTCAATA 57.378 30.769 0.00 0.00 0.00 1.90
3355 3629 9.768662 AAATGTAGCTTTTTCATGTCATCTTTT 57.231 25.926 0.00 0.00 0.00 2.27
3429 3703 8.488308 TCATCAGAAAATCTATCCAGATCTCA 57.512 34.615 0.00 0.00 40.81 3.27
3430 3704 8.931568 TCATCAGAAAATCTATCCAGATCTCAA 58.068 33.333 0.00 0.00 40.81 3.02
3440 3714 4.767578 TCCAGATCTCAATCTTTCCCTG 57.232 45.455 0.00 0.00 40.38 4.45
3444 3718 4.880696 CAGATCTCAATCTTTCCCTGGAAC 59.119 45.833 0.00 0.00 40.38 3.62
3485 3759 8.110002 GCTGAATTAATTAATTGCTTTTCGGTG 58.890 33.333 24.60 8.36 36.13 4.94
3493 3767 5.637006 AATTGCTTTTCGGTGTGCTTATA 57.363 34.783 0.00 0.00 0.00 0.98
3522 3798 9.875675 GTTGCTTCATTTATCTTATAGCTCTTG 57.124 33.333 0.00 0.00 0.00 3.02
3565 3841 4.609301 ACCCTTATTTTGCTGCAATCCTA 58.391 39.130 16.77 5.54 0.00 2.94
3625 3901 2.546899 TGGTACACAGCTACCAAGGAT 58.453 47.619 3.50 0.00 42.74 3.24
3831 4107 2.430332 TCTTTCCAAGTTGGCCTGTTTG 59.570 45.455 17.68 5.50 37.47 2.93
3832 4108 2.151502 TTCCAAGTTGGCCTGTTTGA 57.848 45.000 17.68 0.00 37.47 2.69
3852 4128 8.691797 TGTTTGATAAAGTTTCCTTAGCTTTGT 58.308 29.630 0.00 0.00 34.69 2.83
3895 4171 7.011763 CCATCATGTTTCTGTGATTACCTGTAG 59.988 40.741 0.00 0.00 32.98 2.74
3976 4252 3.844211 TCTATGTGTTCCCTGCTAAACCT 59.156 43.478 0.00 0.00 0.00 3.50
3998 4274 5.598830 CCTTATGAGCTCTTAGGTAACCAGA 59.401 44.000 16.19 0.00 37.17 3.86
4153 4429 3.119101 ACATAAAGGAGAGTGTTCGCGAT 60.119 43.478 10.88 0.00 0.00 4.58
4171 4447 1.686052 GATTTTGTGGTTGGCAGTGGA 59.314 47.619 0.00 0.00 0.00 4.02
4240 4679 9.642312 CAATACACTTCATTTTATCATGTCTCG 57.358 33.333 0.00 0.00 0.00 4.04
4373 4812 7.399245 TTTTAAGTTCACTGTTAACCAAGCT 57.601 32.000 2.48 0.00 0.00 3.74
4575 5014 2.679837 AGAGTTGTCAACACAGTTGCTG 59.320 45.455 17.78 0.00 37.52 4.41
4577 5016 1.133025 GTTGTCAACACAGTTGCTGCT 59.867 47.619 10.93 0.00 34.37 4.24
4675 5117 2.091541 ACGATTTAACCATGTGCAGGG 58.908 47.619 0.92 0.92 38.43 4.45
4688 5130 5.335113 CCATGTGCAGGGTTGATATATTTCG 60.335 44.000 0.00 0.00 0.00 3.46
4775 5217 2.355007 GCTGGCCAATTTTGTTGCCTAT 60.355 45.455 7.01 0.00 44.32 2.57
4776 5218 3.118811 GCTGGCCAATTTTGTTGCCTATA 60.119 43.478 7.01 0.00 44.32 1.31
4862 5304 7.330700 GTCTCTGTGCATAGCCTATTATTTCTC 59.669 40.741 5.44 0.00 0.00 2.87
4883 5325 2.812011 CCTTTCCAAAAGGACTGGTACG 59.188 50.000 12.19 0.00 39.81 3.67
4912 5354 7.656707 ATTGATTGTTACAACTTCAATTGGC 57.343 32.000 16.58 0.00 38.29 4.52
4922 5364 2.289694 ACTTCAATTGGCGCTACTCAGT 60.290 45.455 7.64 0.00 0.00 3.41
4973 5415 2.602676 GCCCCTCTACAACTGCCCA 61.603 63.158 0.00 0.00 0.00 5.36
5019 5462 7.534085 TCTTGTGATATTATTGTTCGGACAC 57.466 36.000 0.00 0.00 34.98 3.67
5027 5470 8.974060 ATATTATTGTTCGGACACCATACTTT 57.026 30.769 0.00 0.00 34.98 2.66
5055 5498 6.485171 ACTGTAAAGAGCTGGTGGAAATAAT 58.515 36.000 0.00 0.00 0.00 1.28
5120 5563 5.843673 TTTTTGCATGAACTGTTAGTCCA 57.156 34.783 0.00 0.00 0.00 4.02
5121 5564 6.403866 TTTTTGCATGAACTGTTAGTCCAT 57.596 33.333 0.00 0.00 0.00 3.41
5122 5565 7.517614 TTTTTGCATGAACTGTTAGTCCATA 57.482 32.000 0.00 0.00 0.00 2.74
5123 5566 7.701539 TTTTGCATGAACTGTTAGTCCATAT 57.298 32.000 0.00 0.00 0.00 1.78
5140 5584 6.203530 AGTCCATATATCTTGCGTGTGAAATG 59.796 38.462 0.00 0.00 0.00 2.32
5305 5766 4.494484 ACACTTTCAGTTGGTTCTTTTGC 58.506 39.130 0.00 0.00 0.00 3.68
5332 5804 9.059023 GGGGTATTTTATTATGGACCTATCTCT 57.941 37.037 0.00 0.00 0.00 3.10
5337 5809 8.418597 TTTTATTATGGACCTATCTCTAGCGT 57.581 34.615 0.00 0.00 0.00 5.07
5338 5810 5.906113 ATTATGGACCTATCTCTAGCGTG 57.094 43.478 0.00 0.00 0.00 5.34
5339 5811 2.730934 TGGACCTATCTCTAGCGTGT 57.269 50.000 0.00 0.00 0.00 4.49
5340 5812 2.573369 TGGACCTATCTCTAGCGTGTC 58.427 52.381 0.00 0.00 0.00 3.67
5341 5813 2.172930 TGGACCTATCTCTAGCGTGTCT 59.827 50.000 0.00 0.00 0.00 3.41
5342 5814 2.809696 GGACCTATCTCTAGCGTGTCTC 59.190 54.545 0.00 0.00 0.00 3.36
5355 5827 1.000607 CGTGTCTCAGGACGGAAAAGA 60.001 52.381 0.00 0.00 44.83 2.52
5394 5866 2.228822 CCTTGTCTTGCCGCATAAAAGT 59.771 45.455 0.00 0.00 0.00 2.66
5401 5873 2.671596 TGCCGCATAAAAGTTTGAAGC 58.328 42.857 0.00 0.00 0.00 3.86
5402 5874 2.295909 TGCCGCATAAAAGTTTGAAGCT 59.704 40.909 0.00 0.00 0.00 3.74
5403 5875 3.504134 TGCCGCATAAAAGTTTGAAGCTA 59.496 39.130 0.00 0.00 0.00 3.32
5443 5915 5.122239 CGAGATGTAAAATGGTTGAAGCTGA 59.878 40.000 0.00 0.00 0.00 4.26
5446 5918 5.689383 TGTAAAATGGTTGAAGCTGACTC 57.311 39.130 0.00 0.00 0.00 3.36
5448 5920 5.470098 TGTAAAATGGTTGAAGCTGACTCTC 59.530 40.000 0.00 0.00 0.00 3.20
5452 5924 1.271102 GGTTGAAGCTGACTCTCGTCT 59.729 52.381 0.00 0.00 40.86 4.18
5494 5966 5.422145 GTGATTTGCATGGGCTTATTTCTT 58.578 37.500 0.00 0.00 41.91 2.52
5503 5975 6.672147 CATGGGCTTATTTCTTACTATGTGC 58.328 40.000 0.00 0.00 0.00 4.57
5508 5980 5.177696 GCTTATTTCTTACTATGTGCCCTCG 59.822 44.000 0.00 0.00 0.00 4.63
5543 6015 7.848223 AAAAATGCATGGGCTTATTTCTTAC 57.152 32.000 0.00 0.00 41.91 2.34
5544 6016 6.796785 AAATGCATGGGCTTATTTCTTACT 57.203 33.333 0.00 0.00 41.91 2.24
5545 6017 7.896383 AAATGCATGGGCTTATTTCTTACTA 57.104 32.000 0.00 0.00 41.91 1.82
5546 6018 6.884280 ATGCATGGGCTTATTTCTTACTAC 57.116 37.500 0.00 0.00 41.91 2.73
5547 6019 4.814234 TGCATGGGCTTATTTCTTACTACG 59.186 41.667 0.00 0.00 41.91 3.51
5548 6020 4.814771 GCATGGGCTTATTTCTTACTACGT 59.185 41.667 0.00 0.00 36.96 3.57
5549 6021 5.277345 GCATGGGCTTATTTCTTACTACGTG 60.277 44.000 0.00 0.00 36.96 4.49
5550 6022 4.186159 TGGGCTTATTTCTTACTACGTGC 58.814 43.478 0.00 0.00 0.00 5.34
5551 6023 3.558829 GGGCTTATTTCTTACTACGTGCC 59.441 47.826 0.00 0.00 36.27 5.01
5552 6024 3.558829 GGCTTATTTCTTACTACGTGCCC 59.441 47.826 0.00 0.00 0.00 5.36
5553 6025 4.439968 GCTTATTTCTTACTACGTGCCCT 58.560 43.478 0.00 0.00 0.00 5.19
5554 6026 4.507021 GCTTATTTCTTACTACGTGCCCTC 59.493 45.833 0.00 0.00 0.00 4.30
5555 6027 5.681695 GCTTATTTCTTACTACGTGCCCTCT 60.682 44.000 0.00 0.00 0.00 3.69
5556 6028 3.587797 TTTCTTACTACGTGCCCTCTG 57.412 47.619 0.00 0.00 0.00 3.35
5557 6029 2.502142 TCTTACTACGTGCCCTCTGA 57.498 50.000 0.00 0.00 0.00 3.27
5558 6030 3.014304 TCTTACTACGTGCCCTCTGAT 57.986 47.619 0.00 0.00 0.00 2.90
5559 6031 3.362706 TCTTACTACGTGCCCTCTGATT 58.637 45.455 0.00 0.00 0.00 2.57
5560 6032 3.767673 TCTTACTACGTGCCCTCTGATTT 59.232 43.478 0.00 0.00 0.00 2.17
5561 6033 4.222145 TCTTACTACGTGCCCTCTGATTTT 59.778 41.667 0.00 0.00 0.00 1.82
5562 6034 2.699954 ACTACGTGCCCTCTGATTTTG 58.300 47.619 0.00 0.00 0.00 2.44
5563 6035 1.398390 CTACGTGCCCTCTGATTTTGC 59.602 52.381 0.00 0.00 0.00 3.68
5564 6036 1.244019 ACGTGCCCTCTGATTTTGCC 61.244 55.000 0.00 0.00 0.00 4.52
5565 6037 0.962356 CGTGCCCTCTGATTTTGCCT 60.962 55.000 0.00 0.00 0.00 4.75
5566 6038 1.678728 CGTGCCCTCTGATTTTGCCTA 60.679 52.381 0.00 0.00 0.00 3.93
5567 6039 2.446435 GTGCCCTCTGATTTTGCCTAA 58.554 47.619 0.00 0.00 0.00 2.69
5568 6040 2.825532 GTGCCCTCTGATTTTGCCTAAA 59.174 45.455 0.00 0.00 0.00 1.85
5569 6041 3.258123 GTGCCCTCTGATTTTGCCTAAAA 59.742 43.478 0.00 0.00 39.86 1.52
5570 6042 3.900601 TGCCCTCTGATTTTGCCTAAAAA 59.099 39.130 0.00 0.00 41.88 1.94
5618 6090 6.049955 TCCATTTTTACAGTGGAGTAGAGG 57.950 41.667 0.00 0.00 37.12 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 5.977129 ACTTTCACGTGATTGAAATTTCCAC 59.023 36.000 20.80 14.13 43.03 4.02
54 55 6.142818 ACTTTCACGTGATTGAAATTTCCA 57.857 33.333 20.80 5.01 43.03 3.53
55 56 6.581166 GGTACTTTCACGTGATTGAAATTTCC 59.419 38.462 20.80 8.31 43.03 3.13
56 57 7.136119 TGGTACTTTCACGTGATTGAAATTTC 58.864 34.615 20.80 11.41 43.03 2.17
57 58 7.033530 TGGTACTTTCACGTGATTGAAATTT 57.966 32.000 20.80 3.47 43.03 1.82
58 59 6.293955 CCTGGTACTTTCACGTGATTGAAATT 60.294 38.462 20.80 7.40 43.03 1.82
59 60 5.181245 CCTGGTACTTTCACGTGATTGAAAT 59.819 40.000 20.80 3.17 43.03 2.17
60 61 4.513692 CCTGGTACTTTCACGTGATTGAAA 59.486 41.667 20.80 9.68 42.04 2.69
61 62 4.062293 CCTGGTACTTTCACGTGATTGAA 58.938 43.478 20.80 10.07 33.55 2.69
62 63 3.659786 CCTGGTACTTTCACGTGATTGA 58.340 45.455 20.80 7.81 0.00 2.57
63 64 2.159627 GCCTGGTACTTTCACGTGATTG 59.840 50.000 20.80 16.85 0.00 2.67
64 65 2.423577 GCCTGGTACTTTCACGTGATT 58.576 47.619 20.80 9.49 0.00 2.57
65 66 1.338769 GGCCTGGTACTTTCACGTGAT 60.339 52.381 20.80 7.28 0.00 3.06
66 67 0.034337 GGCCTGGTACTTTCACGTGA 59.966 55.000 15.76 15.76 0.00 4.35
67 68 0.953960 GGGCCTGGTACTTTCACGTG 60.954 60.000 9.94 9.94 0.00 4.49
139 148 4.138487 AGATTTAACCGGCTGTCTTAGG 57.862 45.455 0.00 0.00 0.00 2.69
203 215 1.227853 GCGGTCTGTTCCACCTGTT 60.228 57.895 0.00 0.00 0.00 3.16
311 323 2.666526 GCGGATCGAGGCAATCCC 60.667 66.667 7.68 0.00 39.71 3.85
312 324 2.666526 GGCGGATCGAGGCAATCC 60.667 66.667 8.20 0.45 39.51 3.01
313 325 3.038417 CGGCGGATCGAGGCAATC 61.038 66.667 0.00 0.00 0.00 2.67
410 422 0.453282 CACGGAACATCTTGCTTGCG 60.453 55.000 0.00 0.00 37.26 4.85
475 487 1.229853 GGAAGGAGGTGGAGGGGAA 60.230 63.158 0.00 0.00 0.00 3.97
495 507 1.070289 ACTTCCTCGTCCTGGAAACAC 59.930 52.381 0.00 0.00 42.29 3.32
522 534 3.314541 AAAAGAGTACGCGATTCAGGT 57.685 42.857 15.93 0.00 0.00 4.00
568 580 4.617875 CGAAGCCAACCTACCCAG 57.382 61.111 0.00 0.00 0.00 4.45
614 626 0.179936 GAGAGCAACTAGGCCAGCAT 59.820 55.000 5.01 0.00 0.00 3.79
695 710 1.281419 TTTCCGACAGCCCCAATCTA 58.719 50.000 0.00 0.00 0.00 1.98
727 742 7.657761 ACTCCAAACAATCTATCGATTATCCAC 59.342 37.037 1.71 0.00 37.77 4.02
728 743 7.735917 ACTCCAAACAATCTATCGATTATCCA 58.264 34.615 1.71 0.00 37.77 3.41
751 766 3.034635 AGTTCTGAACCTGTCACTGACT 58.965 45.455 16.48 0.00 33.15 3.41
752 767 3.460857 AGTTCTGAACCTGTCACTGAC 57.539 47.619 16.48 1.86 31.13 3.51
797 812 6.758886 CAGAATCCTCACTTGATGGTTACTAC 59.241 42.308 0.00 0.00 0.00 2.73
923 938 1.001641 AGCATCACCTTCCCTGCAC 60.002 57.895 0.00 0.00 37.09 4.57
940 955 1.005242 CACGCGCTCAAGATCAATCAG 60.005 52.381 5.73 0.00 0.00 2.90
1053 1068 1.983481 GACCAATGTGGCCCATGCA 60.983 57.895 0.00 0.00 42.67 3.96
1134 1149 1.086696 CCTCTGGGTTGTTGTATGCG 58.913 55.000 0.00 0.00 0.00 4.73
1166 1181 2.029288 ATGACAAGGTGCAGCGACG 61.029 57.895 10.78 5.50 0.00 5.12
1169 1184 0.806868 ATTCATGACAAGGTGCAGCG 59.193 50.000 10.78 0.00 0.00 5.18
1191 1206 3.515901 CCTAGCAAACAGAACTAGGTCCT 59.484 47.826 3.53 0.00 45.36 3.85
1192 1207 3.863041 CCTAGCAAACAGAACTAGGTCC 58.137 50.000 3.53 0.00 45.36 4.46
1514 1529 3.181484 CGTAGGGGTTATGACAATGTCGA 60.181 47.826 9.00 0.00 34.95 4.20
1515 1530 3.120792 CGTAGGGGTTATGACAATGTCG 58.879 50.000 9.00 0.00 34.95 4.35
1536 1551 1.463444 CTAACTGCGGCAGGTAACAAC 59.537 52.381 31.38 0.00 32.93 3.32
1553 1569 3.894427 TGCAATTCCAGAACCAAAGCTAA 59.106 39.130 0.00 0.00 0.00 3.09
1588 1604 5.593095 GGGTAAACCTTTAATCATCCTCCAC 59.407 44.000 0.00 0.00 35.85 4.02
1665 1681 3.061403 CGCATCGTTTATCCGACAGTAAC 60.061 47.826 0.00 0.00 40.08 2.50
1699 1717 3.924576 AGGCACTTCCACAAGGTTT 57.075 47.368 0.00 0.00 37.29 3.27
1822 1862 2.416547 CGCTTGTACCTTTGACTCCATG 59.583 50.000 0.00 0.00 0.00 3.66
1914 1954 3.374058 CAGTCATAAACATCCGGTTCACC 59.626 47.826 0.00 0.00 39.29 4.02
1927 1967 6.565811 GCAAAGTCGTCATGTTCAGTCATAAA 60.566 38.462 0.00 0.00 0.00 1.40
1946 1986 5.411781 CGGAATCTACTCTGTAAGCAAAGT 58.588 41.667 0.00 0.00 0.00 2.66
1980 2020 4.376225 TTCCAAACTACCCCAGGTAAAG 57.624 45.455 0.00 0.00 37.76 1.85
1981 2021 4.168479 ACTTTCCAAACTACCCCAGGTAAA 59.832 41.667 0.00 0.00 37.76 2.01
1984 2024 2.141067 ACTTTCCAAACTACCCCAGGT 58.859 47.619 0.00 0.00 40.16 4.00
1985 2025 2.971901 ACTTTCCAAACTACCCCAGG 57.028 50.000 0.00 0.00 0.00 4.45
1994 2035 3.400255 ACCTCTCGCTAACTTTCCAAAC 58.600 45.455 0.00 0.00 0.00 2.93
2006 2047 1.133730 CCTAGGACCTTACCTCTCGCT 60.134 57.143 1.05 0.00 41.00 4.93
2105 2146 3.716006 CGCTGTTGCTGGGTGTCG 61.716 66.667 0.00 0.00 36.97 4.35
2135 2176 4.227754 TGCTAGGAGTCTAGGAGTACAACT 59.772 45.833 0.00 0.00 42.41 3.16
2149 2190 2.354203 GCTGTTGCTACTTGCTAGGAGT 60.354 50.000 9.25 0.00 43.37 3.85
2189 2230 4.974792 CGAGGCCCATGATACTCG 57.025 61.111 15.00 15.00 45.34 4.18
2230 2271 0.329261 CAGATCCCAGAAAGGCACCA 59.671 55.000 0.00 0.00 35.39 4.17
2242 2283 2.159043 TCGTGAATCAGAAGCAGATCCC 60.159 50.000 0.00 0.00 0.00 3.85
2375 2416 1.134098 GGCTTGGCAGGCTATTGTAGA 60.134 52.381 21.41 0.00 42.53 2.59
2481 2522 7.994911 AGAGTAATGCAATTGGACAGATTATCA 59.005 33.333 7.72 0.00 36.99 2.15
2733 3002 8.877864 AGTGAAATCAAACAATAATGGTAGGA 57.122 30.769 0.00 0.00 0.00 2.94
2774 3043 2.710377 AGTCACAACAGCAAACAGACA 58.290 42.857 0.00 0.00 0.00 3.41
2826 3095 6.249192 AGAAAGAGAAATACAGAAAAGGGGG 58.751 40.000 0.00 0.00 0.00 5.40
2827 3096 7.767250 AAGAAAGAGAAATACAGAAAAGGGG 57.233 36.000 0.00 0.00 0.00 4.79
3168 3437 7.135467 CACCAAAAGCTTCTAGAAAAAGAGAC 58.865 38.462 6.63 0.00 0.00 3.36
3429 3703 3.309193 GCTTAGGGTTCCAGGGAAAGATT 60.309 47.826 1.58 0.00 35.75 2.40
3430 3704 2.242452 GCTTAGGGTTCCAGGGAAAGAT 59.758 50.000 1.58 0.00 35.75 2.40
3440 3714 2.092699 AGCAATCTCAGCTTAGGGTTCC 60.093 50.000 0.00 0.00 39.87 3.62
3444 3718 2.996249 TCAGCAATCTCAGCTTAGGG 57.004 50.000 0.00 0.00 41.14 3.53
3485 3759 9.956720 AGATAAATGAAGCAACATTATAAGCAC 57.043 29.630 8.39 0.00 39.19 4.40
3522 3798 6.208204 AGGGTATCTGCATCAAAAAGATATGC 59.792 38.462 0.00 0.00 44.94 3.14
3565 3841 4.104579 AGGGCCCAAAATTGACTGAAATTT 59.895 37.500 27.56 0.00 40.60 1.82
3625 3901 6.096705 CCAGAGGTTTTATATGTGCCAATTCA 59.903 38.462 0.00 0.00 0.00 2.57
3852 4128 8.893563 ACATGATGGAGGGTATTTCTTAAAAA 57.106 30.769 0.00 0.00 0.00 1.94
3866 4142 5.297776 GGTAATCACAGAAACATGATGGAGG 59.702 44.000 0.00 0.00 35.71 4.30
3895 4171 3.377346 AGACACGATGCCATCAGATAC 57.623 47.619 5.40 0.00 0.00 2.24
3976 4252 5.955959 TGTCTGGTTACCTAAGAGCTCATAA 59.044 40.000 17.77 3.62 0.00 1.90
3998 4274 3.117512 AGGACTGAAATGTTTCCAGGTGT 60.118 43.478 3.26 0.00 36.36 4.16
4153 4429 1.110442 CTCCACTGCCAACCACAAAA 58.890 50.000 0.00 0.00 0.00 2.44
4277 4716 4.835615 AGAACAGAGAACCATACTGTGAGT 59.164 41.667 0.00 0.00 42.81 3.41
4373 4812 3.220999 CTTCTCCACCGGTCGCACA 62.221 63.158 2.59 0.00 0.00 4.57
4564 5003 3.282157 CCGCAGCAGCAACTGTGT 61.282 61.111 15.66 0.00 44.84 3.72
4575 5014 1.227674 CTCCCCAACTATCCGCAGC 60.228 63.158 0.00 0.00 0.00 5.25
4577 5016 1.306654 ACCTCCCCAACTATCCGCA 60.307 57.895 0.00 0.00 0.00 5.69
4675 5117 8.545420 ACGTGTTATGGTTCGAAATATATCAAC 58.455 33.333 0.00 0.47 0.00 3.18
4688 5130 4.273969 TCCTTGTTTCACGTGTTATGGTTC 59.726 41.667 16.51 0.14 0.00 3.62
4775 5217 0.871722 GCACACCGTGAACTTGCATA 59.128 50.000 5.28 0.00 35.23 3.14
4776 5218 0.819259 AGCACACCGTGAACTTGCAT 60.819 50.000 5.28 0.00 35.23 3.96
4883 5325 6.339587 TGAAGTTGTAACAATCAATTCCCC 57.660 37.500 0.00 0.00 0.00 4.81
4922 5364 7.608153 TGTACGGAACAAGATTCTTCTCAATA 58.392 34.615 0.00 0.00 34.29 1.90
4973 5415 8.889717 CAAGATTAGGTACATCGGTAAACAAAT 58.110 33.333 0.00 0.00 0.00 2.32
5019 5462 7.148407 CCAGCTCTTTACAGTAACAAAGTATGG 60.148 40.741 0.00 1.59 34.17 2.74
5027 5470 3.644265 TCCACCAGCTCTTTACAGTAACA 59.356 43.478 0.00 0.00 0.00 2.41
5115 5558 4.937201 TCACACGCAAGATATATGGACT 57.063 40.909 0.00 0.00 43.62 3.85
5116 5559 5.984233 TTTCACACGCAAGATATATGGAC 57.016 39.130 0.00 0.00 43.62 4.02
5118 5561 6.544038 TCATTTCACACGCAAGATATATGG 57.456 37.500 0.00 0.00 43.62 2.74
5121 5564 9.325198 ACTAATTCATTTCACACGCAAGATATA 57.675 29.630 0.00 0.00 43.62 0.86
5122 5565 8.124823 CACTAATTCATTTCACACGCAAGATAT 58.875 33.333 0.00 0.00 43.62 1.63
5123 5566 7.119116 ACACTAATTCATTTCACACGCAAGATA 59.881 33.333 0.00 0.00 43.62 1.98
5251 5707 4.678256 ACACTATGAGAAACAGGAGGAGA 58.322 43.478 0.00 0.00 0.00 3.71
5252 5708 6.511416 CATACACTATGAGAAACAGGAGGAG 58.489 44.000 0.00 0.00 38.45 3.69
5254 5710 5.053145 GCATACACTATGAGAAACAGGAGG 58.947 45.833 0.00 0.00 38.45 4.30
5291 5747 0.396556 ACCCCGCAAAAGAACCAACT 60.397 50.000 0.00 0.00 0.00 3.16
5292 5748 1.320507 TACCCCGCAAAAGAACCAAC 58.679 50.000 0.00 0.00 0.00 3.77
5305 5766 7.858498 AGATAGGTCCATAATAAAATACCCCG 58.142 38.462 0.00 0.00 0.00 5.73
5332 5804 0.607217 TTCCGTCCTGAGACACGCTA 60.607 55.000 0.00 0.00 43.73 4.26
5333 5805 1.461091 TTTCCGTCCTGAGACACGCT 61.461 55.000 0.00 0.00 43.73 5.07
5334 5806 0.599204 TTTTCCGTCCTGAGACACGC 60.599 55.000 0.00 0.00 43.73 5.34
5335 5807 1.000607 TCTTTTCCGTCCTGAGACACG 60.001 52.381 0.00 0.00 43.73 4.49
5336 5808 2.814280 TCTTTTCCGTCCTGAGACAC 57.186 50.000 0.00 0.00 43.73 3.67
5337 5809 4.620803 GCTATTCTTTTCCGTCCTGAGACA 60.621 45.833 0.00 0.00 43.73 3.41
5338 5810 3.866327 GCTATTCTTTTCCGTCCTGAGAC 59.134 47.826 0.00 0.00 39.83 3.36
5339 5811 3.513912 TGCTATTCTTTTCCGTCCTGAGA 59.486 43.478 0.00 0.00 0.00 3.27
5340 5812 3.861840 TGCTATTCTTTTCCGTCCTGAG 58.138 45.455 0.00 0.00 0.00 3.35
5341 5813 3.973206 TGCTATTCTTTTCCGTCCTGA 57.027 42.857 0.00 0.00 0.00 3.86
5342 5814 4.142600 CCTTTGCTATTCTTTTCCGTCCTG 60.143 45.833 0.00 0.00 0.00 3.86
5376 5848 3.316588 TCAAACTTTTATGCGGCAAGACA 59.683 39.130 6.82 0.00 0.00 3.41
5443 5915 2.653702 GCCAGTGCAGACGAGAGT 59.346 61.111 0.00 0.00 42.82 3.24
5446 5918 1.153745 GTAGGCCAGTGCAGACGAG 60.154 63.158 5.01 0.00 40.13 4.18
5448 5920 1.446792 CAGTAGGCCAGTGCAGACG 60.447 63.158 5.01 0.00 40.13 4.18
5494 5966 1.070134 GCAATCCGAGGGCACATAGTA 59.930 52.381 0.00 0.00 0.00 1.82
5524 5996 4.814234 CGTAGTAAGAAATAAGCCCATGCA 59.186 41.667 0.00 0.00 41.13 3.96
5525 5997 4.814771 ACGTAGTAAGAAATAAGCCCATGC 59.185 41.667 0.00 0.00 41.94 4.06
5526 5998 5.277345 GCACGTAGTAAGAAATAAGCCCATG 60.277 44.000 0.00 0.00 41.61 3.66
5527 5999 4.814771 GCACGTAGTAAGAAATAAGCCCAT 59.185 41.667 0.00 0.00 41.61 4.00
5528 6000 4.186159 GCACGTAGTAAGAAATAAGCCCA 58.814 43.478 0.00 0.00 41.61 5.36
5529 6001 3.558829 GGCACGTAGTAAGAAATAAGCCC 59.441 47.826 0.00 0.00 41.61 5.19
5530 6002 3.558829 GGGCACGTAGTAAGAAATAAGCC 59.441 47.826 0.00 0.00 41.61 4.35
5531 6003 4.439968 AGGGCACGTAGTAAGAAATAAGC 58.560 43.478 0.00 0.00 41.61 3.09
5532 6004 5.749109 CAGAGGGCACGTAGTAAGAAATAAG 59.251 44.000 0.00 0.00 41.61 1.73
5533 6005 5.419788 TCAGAGGGCACGTAGTAAGAAATAA 59.580 40.000 0.00 0.00 41.61 1.40
5534 6006 4.951715 TCAGAGGGCACGTAGTAAGAAATA 59.048 41.667 0.00 0.00 41.61 1.40
5535 6007 3.767673 TCAGAGGGCACGTAGTAAGAAAT 59.232 43.478 0.00 0.00 41.61 2.17
5536 6008 3.159472 TCAGAGGGCACGTAGTAAGAAA 58.841 45.455 0.00 0.00 41.61 2.52
5537 6009 2.799017 TCAGAGGGCACGTAGTAAGAA 58.201 47.619 0.00 0.00 41.61 2.52
5538 6010 2.502142 TCAGAGGGCACGTAGTAAGA 57.498 50.000 0.00 0.00 41.61 2.10
5539 6011 3.802948 AATCAGAGGGCACGTAGTAAG 57.197 47.619 0.00 0.00 41.61 2.34
5540 6012 4.250464 CAAAATCAGAGGGCACGTAGTAA 58.750 43.478 0.00 0.00 41.61 2.24
5541 6013 3.857052 CAAAATCAGAGGGCACGTAGTA 58.143 45.455 0.00 0.00 41.61 1.82
5543 6015 1.398390 GCAAAATCAGAGGGCACGTAG 59.602 52.381 0.00 0.00 0.00 3.51
5544 6016 1.448985 GCAAAATCAGAGGGCACGTA 58.551 50.000 0.00 0.00 0.00 3.57
5545 6017 1.244019 GGCAAAATCAGAGGGCACGT 61.244 55.000 0.00 0.00 0.00 4.49
5546 6018 0.962356 AGGCAAAATCAGAGGGCACG 60.962 55.000 0.00 0.00 0.00 5.34
5547 6019 2.128771 TAGGCAAAATCAGAGGGCAC 57.871 50.000 0.00 0.00 0.00 5.01
5548 6020 2.897271 TTAGGCAAAATCAGAGGGCA 57.103 45.000 0.00 0.00 0.00 5.36
5549 6021 4.535526 TTTTTAGGCAAAATCAGAGGGC 57.464 40.909 0.00 0.00 33.72 5.19
5568 6040 5.607119 CTGTAAGAGCACACGGTATTTTT 57.393 39.130 0.00 0.00 34.07 1.94
5618 6090 5.858581 GGAATATTTTCTTGTCGGCATATGC 59.141 40.000 19.79 19.79 34.63 3.14


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

AutoCloner maintained by Alex Coulton.