Multiple sequence alignment - TraesCS2A01G336600

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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 TraesCS2A01G336600 chr2A 100.000 3972 0 0 1 3972 570191913 570195884 0.000000e+00 7336.0
1 TraesCS2A01G336600 chr2A 100.000 36 0 0 3424 3459 570195306 570195341 2.560000e-07 67.6
2 TraesCS2A01G336600 chr2A 100.000 36 0 0 3394 3429 570195336 570195371 2.560000e-07 67.6
3 TraesCS2A01G336600 chr2D 93.551 2636 96 30 732 3322 419783928 419781322 0.000000e+00 3858.0
4 TraesCS2A01G336600 chr2D 90.062 644 34 11 3350 3972 419781335 419780701 0.000000e+00 808.0
5 TraesCS2A01G336600 chr2D 89.739 575 35 12 1 553 419784674 419784102 0.000000e+00 713.0
6 TraesCS2A01G336600 chr2B 91.858 2530 126 39 826 3321 492148480 492145997 0.000000e+00 3458.0
7 TraesCS2A01G336600 chr2B 92.252 555 30 9 1 553 492149483 492148940 0.000000e+00 774.0
8 TraesCS2A01G336600 chr2B 88.975 644 37 17 3350 3972 492146009 492145379 0.000000e+00 765.0
9 TraesCS2A01G336600 chr7D 89.583 192 20 0 1052 1243 531553840 531554031 1.100000e-60 244.0
10 TraesCS2A01G336600 chr7A 84.400 250 31 7 1001 1243 611969535 611969783 5.130000e-59 239.0
11 TraesCS2A01G336600 chr7A 83.817 241 31 7 997 1230 611776746 611776985 5.170000e-54 222.0
12 TraesCS2A01G336600 chr5D 86.802 197 25 1 1047 1243 318059886 318060081 6.680000e-53 219.0
13 TraesCS2A01G336600 chr5A 86.802 197 25 1 1047 1243 412913483 412913678 6.680000e-53 219.0


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 TraesCS2A01G336600 chr2A 570191913 570195884 3971 False 2490.400000 7336 100.000000 1 3972 3 chr2A.!!$F1 3971
1 TraesCS2A01G336600 chr2D 419780701 419784674 3973 True 1793.000000 3858 91.117333 1 3972 3 chr2D.!!$R1 3971
2 TraesCS2A01G336600 chr2B 492145379 492149483 4104 True 1665.666667 3458 91.028333 1 3972 3 chr2B.!!$R1 3971

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
757 836 0.759346 CTCGGCCCATTACTAAGCCT 59.241 55.000 0.0 0.0 43.48 4.58 F
798 877 1.002868 CAAGAGCCCAGACCACAGG 60.003 63.158 0.0 0.0 0.00 4.00 F
1792 2131 0.171231 GGACGCCTGCTCATTTTTCC 59.829 55.000 0.0 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 2113 0.179189 CGGAAAAATGAGCAGGCGTC 60.179 55.000 0.00 0.00 0.00 5.19 R
2698 3056 1.138661 CTCTGCAAGGCTCTTCTAGGG 59.861 57.143 0.00 0.00 0.00 3.53 R
3570 3939 0.109551 GAGGCGCCTTGAGCTTTTTC 60.110 55.000 33.34 10.12 40.39 2.29 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
120 121 6.379988 GGTATTTCTCAACCCCACACATTATT 59.620 38.462 0.00 0.00 0.00 1.40
124 125 5.144100 TCTCAACCCCACACATTATTTGTT 58.856 37.500 0.00 0.00 36.00 2.83
145 146 4.177165 TGCTTAGGCACAATTTGACATG 57.823 40.909 2.79 0.00 44.28 3.21
147 148 4.463539 TGCTTAGGCACAATTTGACATGAT 59.536 37.500 0.00 0.00 44.28 2.45
151 165 3.698040 AGGCACAATTTGACATGATCCTC 59.302 43.478 0.00 0.00 34.40 3.71
159 173 7.281774 ACAATTTGACATGATCCTCACTGATAC 59.718 37.037 0.00 0.00 0.00 2.24
178 192 0.974383 CGGTGTAACTCTTCCAGGGT 59.026 55.000 0.00 0.00 36.74 4.34
181 195 2.105993 GGTGTAACTCTTCCAGGGTGTT 59.894 50.000 0.00 0.00 36.74 3.32
222 236 1.075601 ATCACCCCTGAAGGCAAGAA 58.924 50.000 0.00 0.00 0.00 2.52
247 261 5.282055 TCATCCTCAACTTTGCGAGATAT 57.718 39.130 0.00 0.00 0.00 1.63
376 399 3.599730 GCCTAAAAGCCAAGCAGATTT 57.400 42.857 0.00 0.00 0.00 2.17
379 402 4.440663 GCCTAAAAGCCAAGCAGATTTAGG 60.441 45.833 21.69 21.69 44.57 2.69
384 407 2.042979 AGCCAAGCAGATTTAGGGGAAA 59.957 45.455 0.00 0.00 0.00 3.13
385 408 3.033909 GCCAAGCAGATTTAGGGGAAAT 58.966 45.455 0.00 0.00 40.62 2.17
407 430 9.494271 GAAATGAATAAGGGAAAAAGAGCTTTT 57.506 29.630 2.51 2.51 43.88 2.27
487 510 7.447374 TGAACTTCATTCGGTCAATTATGTT 57.553 32.000 0.00 0.00 40.56 2.71
528 551 6.826231 TCTCAAATAATAAATCGGTGGAAGCA 59.174 34.615 0.00 0.00 0.00 3.91
533 556 1.168714 AAATCGGTGGAAGCAGAAGC 58.831 50.000 0.00 0.00 42.56 3.86
577 626 5.127845 TCAGACTTCAGAGTTCAGAGTGTTT 59.872 40.000 0.00 0.00 35.88 2.83
583 632 6.590234 TCAGAGTTCAGAGTGTTTGCTATA 57.410 37.500 0.00 0.00 0.00 1.31
596 645 7.390027 AGTGTTTGCTATATGTTCTCTGTTCT 58.610 34.615 0.00 0.00 0.00 3.01
602 651 6.818644 TGCTATATGTTCTCTGTTCTGGTTTC 59.181 38.462 0.00 0.00 0.00 2.78
617 666 2.175931 TGGTTTCTGCCTTTCCCAACTA 59.824 45.455 0.00 0.00 0.00 2.24
619 668 3.832490 GGTTTCTGCCTTTCCCAACTATT 59.168 43.478 0.00 0.00 0.00 1.73
704 753 7.867445 TTTGTTGTGTTGAGAAAAGACTTTC 57.133 32.000 0.00 0.00 41.19 2.62
715 764 6.126594 TGAGAAAAGACTTTCCCAACTCCTAA 60.127 38.462 0.00 0.00 41.72 2.69
720 769 5.622180 AGACTTTCCCAACTCCTAACTTTC 58.378 41.667 0.00 0.00 0.00 2.62
722 771 5.622180 ACTTTCCCAACTCCTAACTTTCTC 58.378 41.667 0.00 0.00 0.00 2.87
723 772 4.635699 TTCCCAACTCCTAACTTTCTCC 57.364 45.455 0.00 0.00 0.00 3.71
724 773 3.593942 TCCCAACTCCTAACTTTCTCCA 58.406 45.455 0.00 0.00 0.00 3.86
725 774 3.583086 TCCCAACTCCTAACTTTCTCCAG 59.417 47.826 0.00 0.00 0.00 3.86
727 776 3.339141 CAACTCCTAACTTTCTCCAGGC 58.661 50.000 0.00 0.00 0.00 4.85
728 777 1.909986 ACTCCTAACTTTCTCCAGGCC 59.090 52.381 0.00 0.00 0.00 5.19
729 778 2.192263 CTCCTAACTTTCTCCAGGCCT 58.808 52.381 0.00 0.00 0.00 5.19
730 779 2.573915 CTCCTAACTTTCTCCAGGCCTT 59.426 50.000 0.00 0.00 0.00 4.35
757 836 0.759346 CTCGGCCCATTACTAAGCCT 59.241 55.000 0.00 0.00 43.48 4.58
798 877 1.002868 CAAGAGCCCAGACCACAGG 60.003 63.158 0.00 0.00 0.00 4.00
947 1256 1.764571 CGTTCCCTTCCACCTGTCCA 61.765 60.000 0.00 0.00 0.00 4.02
1257 1581 1.492764 GGTAACTTCCGATCCCTCCA 58.507 55.000 0.00 0.00 0.00 3.86
1260 1584 1.196012 AACTTCCGATCCCTCCAGTC 58.804 55.000 0.00 0.00 0.00 3.51
1328 1652 6.534475 AACCGAGGTTACAATACAGATACA 57.466 37.500 5.60 0.00 36.46 2.29
1426 1752 1.215014 TGTCAGCGTTTGCAGAGACG 61.215 55.000 13.01 13.01 46.23 4.18
1485 1821 3.330998 TGGCGAGAGAGATTAGGGAGATA 59.669 47.826 0.00 0.00 0.00 1.98
1510 1846 1.147153 GCATGTACCCTGCCTCTCC 59.853 63.158 6.30 0.00 33.44 3.71
1522 1858 2.230025 CTGCCTCTCCGTATCTGTATGG 59.770 54.545 0.00 0.00 38.18 2.74
1525 1861 3.813240 GCCTCTCCGTATCTGTATGGGTA 60.813 52.174 0.00 0.00 37.54 3.69
1570 1908 6.936279 TCAACAGTAGATTAAGCTAGCAAGT 58.064 36.000 18.83 4.05 0.00 3.16
1583 1921 4.467795 AGCTAGCAAGTGAGAATGGTTCTA 59.532 41.667 18.83 0.00 40.87 2.10
1613 1951 4.437930 GCTGTCAGAATTATGTCCAACTGC 60.438 45.833 3.32 3.31 0.00 4.40
1735 2074 9.383519 GTCATGACTACATATATTAACCATGGG 57.616 37.037 18.83 0.00 35.09 4.00
1749 2088 4.281102 TGGGACAGGTGTACGTGT 57.719 55.556 9.81 9.81 46.21 4.49
1774 2113 4.685169 ATCTTGCTTTGTTACATCGTGG 57.315 40.909 0.00 0.00 0.00 4.94
1788 2127 2.034879 CGTGGACGCCTGCTCATTT 61.035 57.895 0.00 0.00 0.00 2.32
1792 2131 0.171231 GGACGCCTGCTCATTTTTCC 59.829 55.000 0.00 0.00 0.00 3.13
1810 2149 0.800683 CCGCAGATTGCATTGCACAG 60.801 55.000 11.66 2.79 45.36 3.66
1815 2154 1.129879 GATTGCATTGCACAGACGCG 61.130 55.000 11.66 3.53 38.71 6.01
1828 2167 1.441515 GACGCGTCGCTGTCTAACA 60.442 57.895 25.19 0.00 32.57 2.41
1938 2278 0.812549 TAGACAAGTGCGCGGACATA 59.187 50.000 32.28 13.51 0.00 2.29
2047 2387 6.603201 TGGAGAATAATGCTTGTCCCTTTAAG 59.397 38.462 0.00 0.00 37.69 1.85
2057 2397 2.303022 TGTCCCTTTAAGCTGTGGAGAG 59.697 50.000 0.00 0.00 0.00 3.20
2111 2451 1.675483 GCCCACGAATGCATGATTGTA 59.325 47.619 0.00 0.00 0.00 2.41
2112 2452 2.098934 GCCCACGAATGCATGATTGTAA 59.901 45.455 0.00 0.00 0.00 2.41
2128 2468 9.582431 CATGATTGTAAAATTTTCTGATCTGCT 57.418 29.630 6.72 0.00 0.00 4.24
2162 2502 1.229690 TAGGTACCTGGCTGCCCAA 60.230 57.895 25.33 0.00 41.58 4.12
2281 2621 0.322816 CCAGATTCCCCCAGTGTGTG 60.323 60.000 0.00 0.00 0.00 3.82
2307 2647 0.466555 TTGCAGCCTAACCACCGTTT 60.467 50.000 0.00 0.00 33.17 3.60
2323 2663 5.808030 CCACCGTTTGTATTTTGACTTGTTT 59.192 36.000 0.00 0.00 0.00 2.83
2324 2664 6.973474 CCACCGTTTGTATTTTGACTTGTTTA 59.027 34.615 0.00 0.00 0.00 2.01
2481 2821 3.511540 TGACAAGCAGCTACTGACACTAT 59.488 43.478 0.00 0.00 32.44 2.12
2482 2822 3.854666 ACAAGCAGCTACTGACACTATG 58.145 45.455 0.00 0.00 32.44 2.23
2483 2823 3.259374 ACAAGCAGCTACTGACACTATGT 59.741 43.478 0.00 0.00 32.44 2.29
2484 2824 4.462834 ACAAGCAGCTACTGACACTATGTA 59.537 41.667 0.00 0.00 32.44 2.29
2485 2825 5.127845 ACAAGCAGCTACTGACACTATGTAT 59.872 40.000 0.00 0.00 32.44 2.29
2486 2826 5.860941 AGCAGCTACTGACACTATGTATT 57.139 39.130 0.00 0.00 32.44 1.89
2487 2827 5.595885 AGCAGCTACTGACACTATGTATTG 58.404 41.667 0.00 0.00 32.44 1.90
2488 2828 5.127845 AGCAGCTACTGACACTATGTATTGT 59.872 40.000 0.00 0.00 32.44 2.71
2489 2829 5.812642 GCAGCTACTGACACTATGTATTGTT 59.187 40.000 0.00 0.00 32.44 2.83
2490 2830 6.313905 GCAGCTACTGACACTATGTATTGTTT 59.686 38.462 0.00 0.00 32.44 2.83
2491 2831 7.148407 GCAGCTACTGACACTATGTATTGTTTT 60.148 37.037 0.00 0.00 32.44 2.43
2492 2832 8.721478 CAGCTACTGACACTATGTATTGTTTTT 58.279 33.333 0.00 0.00 32.44 1.94
2698 3056 4.542075 GGATTGGAGAAGCCGGAC 57.458 61.111 5.05 0.00 40.66 4.79
2791 3149 2.171448 GCCCTACATGTTCATCTCCACT 59.829 50.000 2.30 0.00 0.00 4.00
2866 3224 1.271856 TTGGCTACATCAAGGGTCGA 58.728 50.000 0.00 0.00 0.00 4.20
2938 3296 4.748679 GTTGCTTCTGCTGCGGCG 62.749 66.667 13.96 0.51 42.25 6.46
2942 3300 2.432456 CTTCTGCTGCGGCGTACA 60.432 61.111 13.96 4.43 42.25 2.90
3081 3444 9.467258 GCATTATATTACATTGCAATCAGTTGT 57.533 29.630 9.53 8.45 37.65 3.32
3189 3552 6.702282 GGATAAAATACTTGCGAACTAGCTCT 59.298 38.462 0.00 0.00 38.13 4.09
3230 3598 8.621532 AGATGTCAAGTAAAGTGAAATTAGCA 57.378 30.769 0.00 0.00 0.00 3.49
3287 3655 4.158384 GACCATATCAAGCACACGTTTTG 58.842 43.478 0.00 0.00 0.00 2.44
3288 3656 2.916716 CCATATCAAGCACACGTTTTGC 59.083 45.455 10.38 10.38 40.52 3.68
3305 3673 1.123861 TGCTGCAGACTGGGACTCTT 61.124 55.000 20.43 0.00 0.00 2.85
3306 3674 0.898320 GCTGCAGACTGGGACTCTTA 59.102 55.000 20.43 0.00 0.00 2.10
3308 3676 2.741228 GCTGCAGACTGGGACTCTTATG 60.741 54.545 20.43 0.00 0.00 1.90
3309 3677 1.833630 TGCAGACTGGGACTCTTATGG 59.166 52.381 4.26 0.00 0.00 2.74
3310 3678 1.139853 GCAGACTGGGACTCTTATGGG 59.860 57.143 4.26 0.00 0.00 4.00
3311 3679 2.472029 CAGACTGGGACTCTTATGGGT 58.528 52.381 0.00 0.00 0.00 4.51
3312 3680 3.643237 CAGACTGGGACTCTTATGGGTA 58.357 50.000 0.00 0.00 0.00 3.69
3313 3681 4.030913 CAGACTGGGACTCTTATGGGTAA 58.969 47.826 0.00 0.00 0.00 2.85
3314 3682 4.469945 CAGACTGGGACTCTTATGGGTAAA 59.530 45.833 0.00 0.00 0.00 2.01
3315 3683 4.470304 AGACTGGGACTCTTATGGGTAAAC 59.530 45.833 0.00 0.00 0.00 2.01
3316 3684 4.436079 ACTGGGACTCTTATGGGTAAACT 58.564 43.478 0.00 0.00 0.00 2.66
3317 3685 4.850386 ACTGGGACTCTTATGGGTAAACTT 59.150 41.667 0.00 0.00 0.00 2.66
3318 3686 6.027482 ACTGGGACTCTTATGGGTAAACTTA 58.973 40.000 0.00 0.00 0.00 2.24
3319 3687 6.677076 ACTGGGACTCTTATGGGTAAACTTAT 59.323 38.462 0.00 0.00 0.00 1.73
3320 3688 6.895782 TGGGACTCTTATGGGTAAACTTATG 58.104 40.000 0.00 0.00 0.00 1.90
3321 3689 6.126594 TGGGACTCTTATGGGTAAACTTATGG 60.127 42.308 0.00 0.00 0.00 2.74
3322 3690 6.126565 GGGACTCTTATGGGTAAACTTATGGT 60.127 42.308 0.00 0.00 0.00 3.55
3323 3691 6.990939 GGACTCTTATGGGTAAACTTATGGTC 59.009 42.308 0.00 0.00 0.00 4.02
3324 3692 7.147532 GGACTCTTATGGGTAAACTTATGGTCT 60.148 40.741 0.00 0.00 0.00 3.85
3325 3693 8.849543 ACTCTTATGGGTAAACTTATGGTCTA 57.150 34.615 0.00 0.00 0.00 2.59
3326 3694 9.448587 ACTCTTATGGGTAAACTTATGGTCTAT 57.551 33.333 0.00 0.00 0.00 1.98
3327 3695 9.712305 CTCTTATGGGTAAACTTATGGTCTATG 57.288 37.037 0.00 0.00 0.00 2.23
3328 3696 8.656806 TCTTATGGGTAAACTTATGGTCTATGG 58.343 37.037 0.00 0.00 0.00 2.74
3329 3697 8.570038 TTATGGGTAAACTTATGGTCTATGGA 57.430 34.615 0.00 0.00 0.00 3.41
3330 3698 6.894735 TGGGTAAACTTATGGTCTATGGAA 57.105 37.500 0.00 0.00 0.00 3.53
3331 3699 6.895782 TGGGTAAACTTATGGTCTATGGAAG 58.104 40.000 0.00 0.00 0.00 3.46
3332 3700 6.445786 TGGGTAAACTTATGGTCTATGGAAGT 59.554 38.462 0.00 0.00 31.79 3.01
3333 3701 7.037153 TGGGTAAACTTATGGTCTATGGAAGTT 60.037 37.037 0.00 0.00 41.01 2.66
3334 3702 8.488668 GGGTAAACTTATGGTCTATGGAAGTTA 58.511 37.037 0.00 0.00 38.94 2.24
3335 3703 9.322773 GGTAAACTTATGGTCTATGGAAGTTAC 57.677 37.037 0.00 0.00 38.94 2.50
3387 3755 7.592885 AAGTTACTGTTCTACCACAACTAGA 57.407 36.000 0.00 0.00 0.00 2.43
3410 3778 8.261349 AGATTTAGATAGAAGAAGCCATGAGT 57.739 34.615 0.00 0.00 0.00 3.41
3433 3801 9.980780 GAGTTAGAACAAAATCATAGAAGAAGC 57.019 33.333 0.00 0.00 0.00 3.86
3434 3802 8.951243 AGTTAGAACAAAATCATAGAAGAAGCC 58.049 33.333 0.00 0.00 0.00 4.35
3435 3803 8.730680 GTTAGAACAAAATCATAGAAGAAGCCA 58.269 33.333 0.00 0.00 0.00 4.75
3436 3804 7.951347 AGAACAAAATCATAGAAGAAGCCAT 57.049 32.000 0.00 0.00 0.00 4.40
3437 3805 7.769220 AGAACAAAATCATAGAAGAAGCCATG 58.231 34.615 0.00 0.00 0.00 3.66
3438 3806 7.613022 AGAACAAAATCATAGAAGAAGCCATGA 59.387 33.333 0.00 0.00 32.32 3.07
3439 3807 7.330900 ACAAAATCATAGAAGAAGCCATGAG 57.669 36.000 0.00 0.00 31.35 2.90
3440 3808 6.888632 ACAAAATCATAGAAGAAGCCATGAGT 59.111 34.615 0.00 0.00 31.35 3.41
3443 3811 8.674263 AAATCATAGAAGAAGCCATGAGTTAG 57.326 34.615 0.00 0.00 34.87 2.34
3446 3815 7.268586 TCATAGAAGAAGCCATGAGTTAGAAC 58.731 38.462 0.00 0.00 0.00 3.01
3471 3840 8.774586 ACAAAATCATAGAATATGCCTTACGAC 58.225 33.333 0.00 0.00 0.00 4.34
3476 3845 6.806739 TCATAGAATATGCCTTACGACGATTG 59.193 38.462 0.00 0.00 0.00 2.67
3486 3855 2.399396 ACGACGATTGCAGGTTTTTG 57.601 45.000 0.00 0.00 0.00 2.44
3500 3869 5.452636 GCAGGTTTTTGAACTATCAACCCAA 60.453 40.000 0.00 0.00 45.01 4.12
3501 3870 6.215845 CAGGTTTTTGAACTATCAACCCAAG 58.784 40.000 0.00 0.00 45.01 3.61
3544 3913 5.072055 TGAGCAAGGAGAATCATTTGAACA 58.928 37.500 0.00 0.00 34.12 3.18
3573 3942 6.648879 AGCAACCAATACTGCTAAAAGAAA 57.351 33.333 0.00 0.00 46.92 2.52
3574 3943 7.049799 AGCAACCAATACTGCTAAAAGAAAA 57.950 32.000 0.00 0.00 46.92 2.29
3575 3944 7.496747 AGCAACCAATACTGCTAAAAGAAAAA 58.503 30.769 0.00 0.00 46.92 1.94
3621 3990 6.655078 ATTTTCAAGTAAACATCTGCCACT 57.345 33.333 0.00 0.00 0.00 4.00
3685 4067 0.106015 ATGTAGGCTTTCCCCATGCC 60.106 55.000 0.00 0.00 44.69 4.40
3749 4131 6.434028 AGCAATATTTGTCTGCCTAAACTTGA 59.566 34.615 0.00 0.00 36.73 3.02
3760 4142 5.570320 TGCCTAAACTTGAAGAGCCTAATT 58.430 37.500 0.00 0.00 0.00 1.40
3801 4190 2.226912 CGGAGATCGATGGTTCTCTACC 59.773 54.545 0.54 0.00 43.98 3.18
3862 4251 6.540995 ACCTTATCTATCGTGGTAGCTCTTA 58.459 40.000 0.00 0.00 0.00 2.10
3910 4299 4.439057 TGATCAGTGAAGTATAAACGCCC 58.561 43.478 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.079127 AGTTCATCGTGCGGGAAGG 60.079 57.895 0.00 0.00 0.00 3.46
14 15 1.461127 GTGACTTCCAGTTCATCGTGC 59.539 52.381 0.00 0.00 0.00 5.34
145 146 4.338682 AGTTACACCGTATCAGTGAGGATC 59.661 45.833 4.00 0.00 38.63 3.36
147 148 3.693085 GAGTTACACCGTATCAGTGAGGA 59.307 47.826 4.00 0.00 38.63 3.71
151 165 4.082408 TGGAAGAGTTACACCGTATCAGTG 60.082 45.833 0.00 0.00 41.15 3.66
159 173 0.974383 ACCCTGGAAGAGTTACACCG 59.026 55.000 0.00 0.00 34.07 4.94
178 192 1.694150 CTCTCTGGGTGGAACTGAACA 59.306 52.381 0.00 0.00 36.74 3.18
181 195 0.471780 TGCTCTCTGGGTGGAACTGA 60.472 55.000 0.00 0.00 36.74 3.41
222 236 4.326826 TCTCGCAAAGTTGAGGATGATTT 58.673 39.130 0.00 0.00 33.00 2.17
247 261 1.686587 TGCTTCTCAAACTCCTCGACA 59.313 47.619 0.00 0.00 0.00 4.35
376 399 7.714500 TCTTTTTCCCTTATTCATTTCCCCTA 58.286 34.615 0.00 0.00 0.00 3.53
379 402 6.155221 AGCTCTTTTTCCCTTATTCATTTCCC 59.845 38.462 0.00 0.00 0.00 3.97
407 430 1.626686 ACCAAACGAATGGCAATGGA 58.373 45.000 10.48 0.00 44.75 3.41
409 432 3.023946 TGAACCAAACGAATGGCAATG 57.976 42.857 10.48 0.00 44.75 2.82
410 433 3.959535 ATGAACCAAACGAATGGCAAT 57.040 38.095 10.48 0.00 44.75 3.56
452 475 5.278808 CCGAATGAAGTTCATACGGGATCTA 60.279 44.000 18.56 0.00 35.76 1.98
487 510 0.039437 GAGAAAGAGCACCACGACGA 60.039 55.000 0.00 0.00 0.00 4.20
549 572 6.016693 CACTCTGAACTCTGAAGTCTGAAGTA 60.017 42.308 0.00 0.00 33.48 2.24
550 573 4.892934 ACTCTGAACTCTGAAGTCTGAAGT 59.107 41.667 0.00 0.00 33.48 3.01
577 626 5.939764 ACCAGAACAGAGAACATATAGCA 57.060 39.130 0.00 0.00 0.00 3.49
583 632 3.817647 GCAGAAACCAGAACAGAGAACAT 59.182 43.478 0.00 0.00 0.00 2.71
596 645 1.063266 AGTTGGGAAAGGCAGAAACCA 60.063 47.619 0.00 0.00 0.00 3.67
678 727 8.655651 AAAGTCTTTTCTCAACACAACAAAAA 57.344 26.923 0.00 0.00 0.00 1.94
679 728 7.383843 GGAAAGTCTTTTCTCAACACAACAAAA 59.616 33.333 0.00 0.00 41.92 2.44
680 729 6.866248 GGAAAGTCTTTTCTCAACACAACAAA 59.134 34.615 0.00 0.00 41.92 2.83
681 730 6.386654 GGAAAGTCTTTTCTCAACACAACAA 58.613 36.000 0.00 0.00 41.92 2.83
682 731 5.105917 GGGAAAGTCTTTTCTCAACACAACA 60.106 40.000 3.58 0.00 42.31 3.33
683 732 5.340803 GGGAAAGTCTTTTCTCAACACAAC 58.659 41.667 3.58 0.00 42.31 3.32
684 733 5.576447 GGGAAAGTCTTTTCTCAACACAA 57.424 39.130 3.58 0.00 42.31 3.33
691 740 4.720046 AGGAGTTGGGAAAGTCTTTTCTC 58.280 43.478 3.58 5.59 42.92 2.87
692 741 4.797912 AGGAGTTGGGAAAGTCTTTTCT 57.202 40.909 3.58 0.00 41.92 2.52
693 742 6.062749 AGTTAGGAGTTGGGAAAGTCTTTTC 58.937 40.000 0.00 0.00 41.59 2.29
694 743 6.014771 AGTTAGGAGTTGGGAAAGTCTTTT 57.985 37.500 0.00 0.00 0.00 2.27
698 747 5.622180 AGAAAGTTAGGAGTTGGGAAAGTC 58.378 41.667 0.00 0.00 0.00 3.01
699 748 5.456330 GGAGAAAGTTAGGAGTTGGGAAAGT 60.456 44.000 0.00 0.00 0.00 2.66
701 750 4.414182 TGGAGAAAGTTAGGAGTTGGGAAA 59.586 41.667 0.00 0.00 0.00 3.13
704 753 3.307762 CCTGGAGAAAGTTAGGAGTTGGG 60.308 52.174 0.00 0.00 31.91 4.12
715 764 1.349357 GTCAGAAGGCCTGGAGAAAGT 59.651 52.381 5.69 0.00 43.12 2.66
720 769 1.078567 GCTGTCAGAAGGCCTGGAG 60.079 63.158 5.69 0.00 43.12 3.86
722 771 1.078567 GAGCTGTCAGAAGGCCTGG 60.079 63.158 5.69 0.00 43.12 4.45
723 772 1.447489 CGAGCTGTCAGAAGGCCTG 60.447 63.158 5.69 0.00 44.27 4.85
724 773 2.654079 CCGAGCTGTCAGAAGGCCT 61.654 63.158 0.00 0.00 0.00 5.19
725 774 2.125350 CCGAGCTGTCAGAAGGCC 60.125 66.667 3.32 0.00 0.00 5.19
727 776 2.125350 GGCCGAGCTGTCAGAAGG 60.125 66.667 3.32 4.24 0.00 3.46
728 777 2.125350 GGGCCGAGCTGTCAGAAG 60.125 66.667 3.32 0.00 0.00 2.85
729 778 1.841302 AATGGGCCGAGCTGTCAGAA 61.841 55.000 3.32 0.00 0.00 3.02
730 779 0.975556 TAATGGGCCGAGCTGTCAGA 60.976 55.000 3.32 0.00 0.00 3.27
757 836 1.040646 CTACTGGGCCTTCGCTCATA 58.959 55.000 4.53 0.00 46.97 2.15
947 1256 2.995872 GCCGACAAGCGAGAGAGGT 61.996 63.158 0.00 0.00 44.57 3.85
1257 1581 5.085107 TTGAGAAGCAAAGCAGAGGGACT 62.085 47.826 0.00 0.00 35.25 3.85
1260 1584 1.901591 TTGAGAAGCAAAGCAGAGGG 58.098 50.000 0.00 0.00 32.46 4.30
1328 1652 2.612212 ACGCGTGTTGAGAAAACAATCT 59.388 40.909 12.93 0.00 32.36 2.40
1338 1662 1.846648 GTCAGACACGCGTGTTGAG 59.153 57.895 41.67 31.87 45.05 3.02
1366 1690 7.570140 GCGCGATCTGTACTATAGTTAGTTACA 60.570 40.741 12.10 7.91 39.42 2.41
1426 1752 0.743701 CAGAGTGCCAGAGTCCATGC 60.744 60.000 0.00 0.00 0.00 4.06
1510 1846 5.223449 ACCCAATTACCCATACAGATACG 57.777 43.478 0.00 0.00 0.00 3.06
1570 1908 2.169352 GCAGGAGCTAGAACCATTCTCA 59.831 50.000 0.00 0.00 41.14 3.27
1613 1951 5.980698 CAGTACTGCATTCTACTCCATTG 57.019 43.478 10.54 0.00 0.00 2.82
1727 2066 0.323629 CGTACACCTGTCCCATGGTT 59.676 55.000 11.73 0.00 33.75 3.67
1735 2074 3.650139 AGATTCAACACGTACACCTGTC 58.350 45.455 0.00 0.00 0.00 3.51
1749 2088 6.142139 CACGATGTAACAAAGCAAGATTCAA 58.858 36.000 0.00 0.00 0.00 2.69
1774 2113 0.179189 CGGAAAAATGAGCAGGCGTC 60.179 55.000 0.00 0.00 0.00 5.19
1810 2149 1.396543 CTGTTAGACAGCGACGCGTC 61.397 60.000 28.96 28.96 39.62 5.19
1828 2167 6.420913 TGAGGCTAAAGTAAAGAACAGACT 57.579 37.500 0.00 0.00 0.00 3.24
2047 2387 2.495270 TGATCTTGTCTCTCTCCACAGC 59.505 50.000 0.00 0.00 0.00 4.40
2057 2397 9.334693 GAATTGTAAACAATGTGATCTTGTCTC 57.665 33.333 9.01 0.00 45.06 3.36
2111 2451 6.385033 GCACAGTAGCAGATCAGAAAATTTT 58.615 36.000 2.28 2.28 0.00 1.82
2112 2452 5.105997 GGCACAGTAGCAGATCAGAAAATTT 60.106 40.000 0.00 0.00 35.83 1.82
2162 2502 1.186200 TGTAGTGATCTGCCTCGCTT 58.814 50.000 0.00 0.00 37.23 4.68
2281 2621 2.225727 GTGGTTAGGCTGCAAGTTACAC 59.774 50.000 0.50 0.00 35.30 2.90
2323 2663 7.910584 TCAGCAGCCTCTGAATTATCATTATA 58.089 34.615 3.30 0.00 39.89 0.98
2324 2664 6.776744 TCAGCAGCCTCTGAATTATCATTAT 58.223 36.000 3.30 0.00 39.89 1.28
2332 2672 3.280295 CAATCTCAGCAGCCTCTGAATT 58.720 45.455 6.91 7.00 41.99 2.17
2492 2832 9.462174 CAATACATAGTGCTTCTCAAACAAAAA 57.538 29.630 0.00 0.00 0.00 1.94
2493 2833 8.629158 ACAATACATAGTGCTTCTCAAACAAAA 58.371 29.630 0.00 0.00 0.00 2.44
2494 2834 8.165239 ACAATACATAGTGCTTCTCAAACAAA 57.835 30.769 0.00 0.00 0.00 2.83
2495 2835 7.744087 ACAATACATAGTGCTTCTCAAACAA 57.256 32.000 0.00 0.00 0.00 2.83
2496 2836 7.744087 AACAATACATAGTGCTTCTCAAACA 57.256 32.000 0.00 0.00 0.00 2.83
2497 2837 8.507249 AGAAACAATACATAGTGCTTCTCAAAC 58.493 33.333 0.43 0.00 33.16 2.93
2498 2838 8.506437 CAGAAACAATACATAGTGCTTCTCAAA 58.494 33.333 2.84 0.00 35.38 2.69
2499 2839 7.877612 TCAGAAACAATACATAGTGCTTCTCAA 59.122 33.333 2.84 0.00 35.38 3.02
2500 2840 7.386059 TCAGAAACAATACATAGTGCTTCTCA 58.614 34.615 2.84 0.00 35.38 3.27
2501 2841 7.834068 TCAGAAACAATACATAGTGCTTCTC 57.166 36.000 2.84 0.00 35.38 2.87
2502 2842 8.671921 CAATCAGAAACAATACATAGTGCTTCT 58.328 33.333 0.43 0.43 37.23 2.85
2503 2843 8.454106 ACAATCAGAAACAATACATAGTGCTTC 58.546 33.333 0.00 0.00 29.48 3.86
2504 2844 8.340618 ACAATCAGAAACAATACATAGTGCTT 57.659 30.769 0.00 0.00 0.00 3.91
2505 2845 7.928307 ACAATCAGAAACAATACATAGTGCT 57.072 32.000 0.00 0.00 0.00 4.40
2506 2846 8.883731 AGTACAATCAGAAACAATACATAGTGC 58.116 33.333 0.00 0.00 0.00 4.40
2555 2895 3.827008 TTCAGTCTTGACAGCTCTGTT 57.173 42.857 3.83 0.00 45.05 3.16
2698 3056 1.138661 CTCTGCAAGGCTCTTCTAGGG 59.861 57.143 0.00 0.00 0.00 3.53
2791 3149 3.315142 GAGCATGGCGTCCTGGACA 62.315 63.158 25.42 7.78 32.09 4.02
2938 3296 0.811616 CAGCCTTCGCCATCCTGTAC 60.812 60.000 0.00 0.00 34.57 2.90
2942 3300 2.270205 CACAGCCTTCGCCATCCT 59.730 61.111 0.00 0.00 34.57 3.24
3081 3444 4.890581 GGAGGAACAGACTAGCTTCATCTA 59.109 45.833 0.00 0.00 0.00 1.98
3189 3552 6.530019 TGACATCTCAGTTCAGCTTACATA 57.470 37.500 0.00 0.00 0.00 2.29
3287 3655 0.898320 TAAGAGTCCCAGTCTGCAGC 59.102 55.000 9.47 4.26 0.00 5.25
3288 3656 2.158986 CCATAAGAGTCCCAGTCTGCAG 60.159 54.545 7.63 7.63 0.00 4.41
3305 3673 8.570038 TTCCATAGACCATAAGTTTACCCATA 57.430 34.615 0.00 0.00 0.00 2.74
3306 3674 7.128883 ACTTCCATAGACCATAAGTTTACCCAT 59.871 37.037 0.00 0.00 0.00 4.00
3308 3676 6.896883 ACTTCCATAGACCATAAGTTTACCC 58.103 40.000 0.00 0.00 0.00 3.69
3309 3677 9.322773 GTAACTTCCATAGACCATAAGTTTACC 57.677 37.037 0.00 0.00 40.07 2.85
3341 3709 5.786264 TTCATAAGTTTACCCCGCAAAAA 57.214 34.783 0.00 0.00 0.00 1.94
3342 3710 5.302313 ACTTTCATAAGTTTACCCCGCAAAA 59.698 36.000 0.00 0.00 41.85 2.44
3343 3711 4.828387 ACTTTCATAAGTTTACCCCGCAAA 59.172 37.500 0.00 0.00 41.85 3.68
3344 3712 4.400120 ACTTTCATAAGTTTACCCCGCAA 58.600 39.130 0.00 0.00 41.85 4.85
3345 3713 4.023726 ACTTTCATAAGTTTACCCCGCA 57.976 40.909 0.00 0.00 41.85 5.69
3387 3755 9.995003 CTAACTCATGGCTTCTTCTATCTAAAT 57.005 33.333 0.00 0.00 0.00 1.40
3392 3760 7.268586 TGTTCTAACTCATGGCTTCTTCTATC 58.731 38.462 0.00 0.00 0.00 2.08
3410 3778 8.862325 TGGCTTCTTCTATGATTTTGTTCTAA 57.138 30.769 0.00 0.00 0.00 2.10
3429 3797 6.913170 TGATTTTGTTCTAACTCATGGCTTC 58.087 36.000 0.00 0.00 0.00 3.86
3431 3799 8.049117 TCTATGATTTTGTTCTAACTCATGGCT 58.951 33.333 0.00 0.00 0.00 4.75
3432 3800 8.213518 TCTATGATTTTGTTCTAACTCATGGC 57.786 34.615 0.00 0.00 0.00 4.40
3443 3811 9.599322 CGTAAGGCATATTCTATGATTTTGTTC 57.401 33.333 0.00 0.00 0.00 3.18
3471 3840 5.698832 TGATAGTTCAAAAACCTGCAATCG 58.301 37.500 0.00 0.00 35.92 3.34
3476 3845 4.038642 TGGGTTGATAGTTCAAAAACCTGC 59.961 41.667 0.00 0.00 43.29 4.85
3486 3855 4.081420 TCTCTCAGCTTGGGTTGATAGTTC 60.081 45.833 0.00 0.00 32.52 3.01
3500 3869 2.099405 GGCAACTCTACTCTCTCAGCT 58.901 52.381 0.00 0.00 0.00 4.24
3501 3870 2.577449 GGCAACTCTACTCTCTCAGC 57.423 55.000 0.00 0.00 0.00 4.26
3570 3939 0.109551 GAGGCGCCTTGAGCTTTTTC 60.110 55.000 33.34 10.12 40.39 2.29
3573 3942 1.673665 CTGAGGCGCCTTGAGCTTT 60.674 57.895 33.34 5.00 40.39 3.51
3574 3943 2.046507 CTGAGGCGCCTTGAGCTT 60.047 61.111 33.34 5.97 40.39 3.74
3575 3944 1.908340 ATTCTGAGGCGCCTTGAGCT 61.908 55.000 33.34 18.43 40.39 4.09
3586 3955 9.748708 TGTTTACTTGAAAATTGAATTCTGAGG 57.251 29.630 7.05 0.00 0.00 3.86
3659 4028 3.149981 GGGGAAAGCCTACATGCTATTC 58.850 50.000 0.00 0.00 41.80 1.75
3686 4068 0.784778 GGATACATACTTCGCAGCGC 59.215 55.000 10.87 0.00 0.00 5.92
3699 4081 0.561184 ACTCCTCGATGGGGGATACA 59.439 55.000 0.00 0.00 41.89 2.29
3700 4082 0.969894 CACTCCTCGATGGGGGATAC 59.030 60.000 0.00 0.00 41.89 2.24
3701 4083 0.178932 CCACTCCTCGATGGGGGATA 60.179 60.000 0.00 0.00 41.89 2.59
3801 4190 5.067936 ACATCTTATGAGTACTTCCTCACCG 59.932 44.000 0.00 0.00 43.86 4.94
3862 4251 3.891049 ACTTGTCAAGAAGAAACCAGCT 58.109 40.909 19.53 0.00 0.00 4.24
3910 4299 3.967332 AAAGGAATGGTGCCAGATTTG 57.033 42.857 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.