Multiple sequence alignment - TraesCS5D01G087500

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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 TraesCS5D01G087500 chr5D 100.000 1309 0 0 1 1309 92466629 92465321 0.000000e+00 2418.0
1 TraesCS5D01G087500 chr5D 100.000 1249 0 0 2020 3268 92464610 92463362 0.000000e+00 2307.0
2 TraesCS5D01G087500 chr5A 89.757 1318 53 30 1 1256 86184314 86183017 0.000000e+00 1611.0
3 TraesCS5D01G087500 chr5A 94.654 636 32 2 2023 2656 86181831 86181196 0.000000e+00 985.0
4 TraesCS5D01G087500 chr5A 81.435 237 21 15 3030 3247 86180909 86180677 4.340000e-39 172.0
5 TraesCS5D01G087500 chr5A 85.938 128 8 5 2717 2844 86181089 86180972 9.520000e-26 128.0
6 TraesCS5D01G087500 chr5A 90.000 50 1 3 588 637 660208367 660208412 9.790000e-06 62.1
7 TraesCS5D01G087500 chr5B 90.532 1109 62 18 235 1309 98521290 98520191 0.000000e+00 1426.0
8 TraesCS5D01G087500 chr5B 92.460 504 11 5 1 477 98521678 98521175 0.000000e+00 695.0
9 TraesCS5D01G087500 chr5B 90.224 491 26 12 2023 2496 98519221 98518736 3.580000e-174 621.0
10 TraesCS5D01G087500 chr5B 87.500 72 7 2 269 340 687948145 687948076 7.520000e-12 82.4
11 TraesCS5D01G087500 chr6A 93.519 324 21 0 986 1309 55709393 55709716 1.760000e-132 483.0
12 TraesCS5D01G087500 chr6A 90.698 344 32 0 966 1309 55893231 55892888 2.970000e-125 459.0
13 TraesCS5D01G087500 chr6A 93.333 45 3 0 588 632 53448393 53448437 2.100000e-07 67.6
14 TraesCS5D01G087500 chr6A 95.349 43 1 1 588 629 104056654 104056696 2.100000e-07 67.6
15 TraesCS5D01G087500 chr7D 93.711 318 20 0 992 1309 562149195 562148878 8.200000e-131 477.0
16 TraesCS5D01G087500 chr7D 84.565 460 55 15 2029 2484 562148508 562148061 2.990000e-120 442.0
17 TraesCS5D01G087500 chr7D 85.446 426 56 5 887 1309 562424760 562425182 3.870000e-119 438.0
18 TraesCS5D01G087500 chr7D 84.233 463 49 20 2023 2472 562389891 562390342 2.330000e-116 429.0
19 TraesCS5D01G087500 chr7D 83.871 465 56 15 2023 2478 562425713 562426167 3.010000e-115 425.0
20 TraesCS5D01G087500 chr7D 85.894 397 45 10 919 1309 562401466 562401857 2.350000e-111 412.0
21 TraesCS5D01G087500 chr6B 92.593 324 24 0 986 1309 92532742 92532419 1.780000e-127 466.0
22 TraesCS5D01G087500 chr7B 90.173 346 34 0 964 1309 611742396 611742051 4.970000e-123 451.0
23 TraesCS5D01G087500 chr7B 82.645 484 55 23 2029 2499 612006436 612005969 5.080000e-108 401.0
24 TraesCS5D01G087500 chr7A 84.989 453 49 16 2029 2474 647934067 647933627 2.990000e-120 442.0
25 TraesCS5D01G087500 chr7A 84.579 428 47 19 2020 2436 647315394 647314975 1.090000e-109 407.0
26 TraesCS5D01G087500 chrUn 89.404 302 28 2 2029 2330 20922975 20922678 8.560000e-101 377.0
27 TraesCS5D01G087500 chrUn 93.182 44 3 0 589 632 32482751 32482794 7.570000e-07 65.8
28 TraesCS5D01G087500 chr6D 80.864 162 20 9 157 310 53538601 53538443 2.060000e-22 117.0
29 TraesCS5D01G087500 chr6D 88.462 52 5 1 588 638 354357740 354357689 9.790000e-06 62.1
30 TraesCS5D01G087500 chr2D 91.935 62 5 0 260 321 584516025 584516086 1.620000e-13 87.9
31 TraesCS5D01G087500 chr3D 95.238 42 2 0 588 629 486750863 486750904 2.100000e-07 67.6
32 TraesCS5D01G087500 chr3A 91.667 48 1 3 588 634 628192061 628192106 2.720000e-06 63.9


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 TraesCS5D01G087500 chr5D 92463362 92466629 3267 True 2362.5 2418 100.0000 1 3268 2 chr5D.!!$R1 3267
1 TraesCS5D01G087500 chr5A 86180677 86184314 3637 True 724.0 1611 87.9460 1 3247 4 chr5A.!!$R1 3246
2 TraesCS5D01G087500 chr5B 98518736 98521678 2942 True 914.0 1426 91.0720 1 2496 3 chr5B.!!$R2 2495
3 TraesCS5D01G087500 chr7D 562148061 562149195 1134 True 459.5 477 89.1380 992 2484 2 chr7D.!!$R1 1492
4 TraesCS5D01G087500 chr7D 562424760 562426167 1407 False 431.5 438 84.6585 887 2478 2 chr7D.!!$F3 1591

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
352 367 0.320374 AGTTGATTCCGCTCGTTCCA 59.680 50.000 0.0 0.0 0.00 3.53 F
916 1111 1.306141 TCCCTCTTGGATCGTGGCT 60.306 57.895 0.0 0.0 38.61 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1464 0.456995 CCGAAGACTCAACCTCGAGC 60.457 60.0 6.99 0.00 36.42 5.03 R
2631 3680 0.095935 CCGTTGAAGCTGAGCATTCG 59.904 55.0 7.39 3.99 0.00 3.34 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
22 23 1.519751 TTCCCCGAAATTGCGTGGTG 61.520 55.000 7.26 2.30 30.53 4.17
26 27 1.501741 CGAAATTGCGTGGTGGAGG 59.498 57.895 0.00 0.00 0.00 4.30
116 117 4.075793 CCCCTCCCGTCTCCTCCA 62.076 72.222 0.00 0.00 0.00 3.86
195 199 0.737715 CAAGGCTTTCTCGTCCTCCG 60.738 60.000 0.00 0.00 38.13 4.63
310 325 3.417069 TTATGCCTGGATTATCGGGTG 57.583 47.619 0.00 0.00 35.63 4.61
311 326 1.434188 ATGCCTGGATTATCGGGTGA 58.566 50.000 0.00 0.00 35.63 4.02
352 367 0.320374 AGTTGATTCCGCTCGTTCCA 59.680 50.000 0.00 0.00 0.00 3.53
482 647 6.811954 TGTTGATTATGTTCATCTAGGCGTA 58.188 36.000 0.00 0.00 0.00 4.42
504 669 4.471904 TGTAGTTGATTGATTCCGCTCT 57.528 40.909 0.00 0.00 0.00 4.09
659 841 4.324331 GGCCTAGTAGTTGTTTGGAGGATT 60.324 45.833 0.00 0.00 0.00 3.01
762 945 4.567959 GCTTGCTGTGTCAAAACTTGAAAT 59.432 37.500 0.00 0.00 42.15 2.17
860 1050 9.624373 ACTTGAACATCAATCTGCTATCTAATT 57.376 29.630 0.00 0.00 35.59 1.40
880 1074 9.383519 TCTAATTGTTCCTATTGAGATGTTCAC 57.616 33.333 0.00 0.00 34.94 3.18
900 1095 8.511321 TGTTCACACATAGTTACAATTTCATCC 58.489 33.333 0.00 0.00 0.00 3.51
916 1111 1.306141 TCCCTCTTGGATCGTGGCT 60.306 57.895 0.00 0.00 38.61 4.75
921 1116 2.168521 CCTCTTGGATCGTGGCTTTCTA 59.831 50.000 0.00 0.00 34.57 2.10
1239 1434 1.667724 CGTGGTGGAATGCAGATCTTC 59.332 52.381 0.00 0.00 0.00 2.87
1269 1464 2.047274 ACCGGCAAGACCATCACG 60.047 61.111 0.00 0.00 39.03 4.35
1284 1479 0.889638 TCACGCTCGAGGTTGAGTCT 60.890 55.000 15.58 0.00 38.28 3.24
1296 1491 2.232941 GGTTGAGTCTTCGGACACCATA 59.767 50.000 0.00 0.00 46.67 2.74
1305 1500 1.200716 TCGGACACCATAGACAACGTC 59.799 52.381 0.00 0.00 0.00 4.34
2078 3087 2.034879 CGGCAAGACCATCACGCTT 61.035 57.895 0.00 0.00 39.03 4.68
2311 3320 0.681733 GTCTCTGGGCTCACAAGTCA 59.318 55.000 0.00 0.00 0.00 3.41
2455 3503 5.775686 CAGCAGATTTGGATGAACTTGAAA 58.224 37.500 0.00 0.00 0.00 2.69
2486 3534 0.670162 CCCTGAACTTGTGCCTGTTG 59.330 55.000 0.00 0.00 0.00 3.33
2524 3573 0.442699 GCAGTTCCTAAACCTTCGCG 59.557 55.000 0.00 0.00 35.92 5.87
2539 3588 3.488047 CCTTCGCGATTGCATTTGATCTT 60.488 43.478 10.88 0.00 42.97 2.40
2546 3595 4.731961 CGATTGCATTTGATCTTCTTTCGG 59.268 41.667 0.00 0.00 0.00 4.30
2562 3611 9.974980 TCTTCTTTCGGTGCTTTATTTTAAATT 57.025 25.926 0.00 0.00 0.00 1.82
2620 3669 9.965824 AACATTTTATACTGAACTGAAACCAAG 57.034 29.630 0.00 0.00 0.00 3.61
2631 3680 7.257722 TGAACTGAAACCAAGAAAATCTGAAC 58.742 34.615 0.00 0.00 0.00 3.18
2656 3705 2.949106 CAGCTTCAACGGGTGCTG 59.051 61.111 0.00 0.00 45.15 4.41
2658 3707 1.302033 AGCTTCAACGGGTGCTGAG 60.302 57.895 0.00 0.00 34.19 3.35
2659 3708 1.598130 GCTTCAACGGGTGCTGAGT 60.598 57.895 0.00 0.00 0.00 3.41
2660 3709 1.166531 GCTTCAACGGGTGCTGAGTT 61.167 55.000 0.00 0.00 0.00 3.01
2661 3710 0.868406 CTTCAACGGGTGCTGAGTTC 59.132 55.000 0.00 0.00 0.00 3.01
2662 3711 0.534203 TTCAACGGGTGCTGAGTTCC 60.534 55.000 0.00 0.00 0.00 3.62
2663 3712 1.966451 CAACGGGTGCTGAGTTCCC 60.966 63.158 4.46 4.46 37.98 3.97
2664 3713 3.192103 AACGGGTGCTGAGTTCCCC 62.192 63.158 8.11 1.74 38.09 4.81
2666 3715 4.410400 GGGTGCTGAGTTCCCCGG 62.410 72.222 0.00 0.00 35.52 5.73
2667 3716 3.637273 GGTGCTGAGTTCCCCGGT 61.637 66.667 0.00 0.00 0.00 5.28
2668 3717 2.358737 GTGCTGAGTTCCCCGGTG 60.359 66.667 0.00 0.00 0.00 4.94
2682 3793 0.106719 CCGGTGCATCTACCCCATTT 60.107 55.000 0.00 0.00 37.44 2.32
2683 3794 1.684869 CCGGTGCATCTACCCCATTTT 60.685 52.381 0.00 0.00 37.44 1.82
2685 3796 3.283751 CGGTGCATCTACCCCATTTTTA 58.716 45.455 0.00 0.00 37.44 1.52
2687 3798 4.023193 CGGTGCATCTACCCCATTTTTATC 60.023 45.833 0.00 0.00 37.44 1.75
2688 3799 5.140454 GGTGCATCTACCCCATTTTTATCT 58.860 41.667 0.00 0.00 34.56 1.98
2690 3801 6.775629 GGTGCATCTACCCCATTTTTATCTTA 59.224 38.462 0.00 0.00 34.56 2.10
2691 3802 7.040409 GGTGCATCTACCCCATTTTTATCTTAG 60.040 40.741 0.00 0.00 34.56 2.18
2692 3803 7.719633 GTGCATCTACCCCATTTTTATCTTAGA 59.280 37.037 0.00 0.00 0.00 2.10
2693 3804 7.719633 TGCATCTACCCCATTTTTATCTTAGAC 59.280 37.037 0.00 0.00 0.00 2.59
2697 3808 9.681062 TCTACCCCATTTTTATCTTAGACAAAG 57.319 33.333 0.00 0.00 36.45 2.77
2698 3809 9.462606 CTACCCCATTTTTATCTTAGACAAAGT 57.537 33.333 0.00 0.00 36.51 2.66
2699 3810 8.721133 ACCCCATTTTTATCTTAGACAAAGTT 57.279 30.769 0.00 0.00 36.51 2.66
2700 3811 9.154632 ACCCCATTTTTATCTTAGACAAAGTTT 57.845 29.630 0.00 0.00 36.51 2.66
2701 3812 9.423061 CCCCATTTTTATCTTAGACAAAGTTTG 57.577 33.333 14.13 14.13 36.51 2.93
2772 3883 6.843069 TTTGCAAATTTGAAGAAGGTTAGC 57.157 33.333 22.31 2.19 0.00 3.09
2773 3884 5.528043 TGCAAATTTGAAGAAGGTTAGCA 57.472 34.783 22.31 4.91 0.00 3.49
2774 3885 5.911752 TGCAAATTTGAAGAAGGTTAGCAA 58.088 33.333 22.31 0.00 0.00 3.91
2775 3886 5.984926 TGCAAATTTGAAGAAGGTTAGCAAG 59.015 36.000 22.31 0.00 0.00 4.01
2776 3887 5.985530 GCAAATTTGAAGAAGGTTAGCAAGT 59.014 36.000 22.31 0.00 0.00 3.16
2777 3888 6.479990 GCAAATTTGAAGAAGGTTAGCAAGTT 59.520 34.615 22.31 0.00 0.00 2.66
2778 3889 7.651704 GCAAATTTGAAGAAGGTTAGCAAGTTA 59.348 33.333 22.31 0.00 0.00 2.24
2779 3890 9.528018 CAAATTTGAAGAAGGTTAGCAAGTTAA 57.472 29.630 13.08 0.00 0.00 2.01
2845 3956 9.492730 AAAGATATTCATGGATTTAACACCCTT 57.507 29.630 0.00 0.00 0.00 3.95
2852 3963 8.073467 TCATGGATTTAACACCCTTAAAATCC 57.927 34.615 15.49 15.49 0.00 3.01
2853 3964 7.898636 TCATGGATTTAACACCCTTAAAATCCT 59.101 33.333 20.43 8.57 31.04 3.24
2854 3965 7.475137 TGGATTTAACACCCTTAAAATCCTG 57.525 36.000 20.43 0.00 31.04 3.86
2855 3966 6.439058 TGGATTTAACACCCTTAAAATCCTGG 59.561 38.462 20.43 0.00 31.04 4.45
2856 3967 6.439375 GGATTTAACACCCTTAAAATCCTGGT 59.561 38.462 15.20 0.00 0.00 4.00
2857 3968 6.904463 TTTAACACCCTTAAAATCCTGGTC 57.096 37.500 0.00 0.00 0.00 4.02
2858 3969 4.741928 AACACCCTTAAAATCCTGGTCT 57.258 40.909 0.00 0.00 0.00 3.85
2859 3970 5.853572 AACACCCTTAAAATCCTGGTCTA 57.146 39.130 0.00 0.00 0.00 2.59
2860 3971 5.853572 ACACCCTTAAAATCCTGGTCTAA 57.146 39.130 0.00 0.00 0.00 2.10
2861 3972 5.816682 ACACCCTTAAAATCCTGGTCTAAG 58.183 41.667 0.00 0.00 0.00 2.18
2862 3973 4.640647 CACCCTTAAAATCCTGGTCTAAGC 59.359 45.833 0.00 0.00 0.00 3.09
2863 3974 3.877508 CCCTTAAAATCCTGGTCTAAGCG 59.122 47.826 0.00 0.00 0.00 4.68
2864 3975 4.383770 CCCTTAAAATCCTGGTCTAAGCGA 60.384 45.833 0.00 0.00 0.00 4.93
2865 3976 4.571176 CCTTAAAATCCTGGTCTAAGCGAC 59.429 45.833 0.00 0.00 42.07 5.19
2873 3984 3.590127 GTCTAAGCGACCCCATAGC 57.410 57.895 0.00 0.00 36.62 2.97
2874 3985 1.041437 GTCTAAGCGACCCCATAGCT 58.959 55.000 0.00 0.00 41.72 3.32
2876 3987 1.687123 TCTAAGCGACCCCATAGCTTC 59.313 52.381 5.14 0.00 45.14 3.86
2877 3988 1.689273 CTAAGCGACCCCATAGCTTCT 59.311 52.381 5.14 0.00 45.14 2.85
2878 3989 0.179000 AAGCGACCCCATAGCTTCTG 59.821 55.000 0.00 0.00 45.14 3.02
2879 3990 0.687757 AGCGACCCCATAGCTTCTGA 60.688 55.000 0.00 0.00 35.42 3.27
2880 3991 0.530870 GCGACCCCATAGCTTCTGAC 60.531 60.000 0.00 0.00 0.00 3.51
2881 3992 0.249073 CGACCCCATAGCTTCTGACG 60.249 60.000 0.00 0.00 0.00 4.35
2882 3993 0.530870 GACCCCATAGCTTCTGACGC 60.531 60.000 0.00 0.00 0.00 5.19
2883 3994 1.264749 ACCCCATAGCTTCTGACGCA 61.265 55.000 8.91 0.00 0.00 5.24
2884 3995 0.811616 CCCCATAGCTTCTGACGCAC 60.812 60.000 8.91 0.00 0.00 5.34
2885 3996 0.811616 CCCATAGCTTCTGACGCACC 60.812 60.000 8.91 0.00 0.00 5.01
2886 3997 0.108186 CCATAGCTTCTGACGCACCA 60.108 55.000 8.91 0.00 0.00 4.17
2887 3998 1.284657 CATAGCTTCTGACGCACCAG 58.715 55.000 8.91 0.00 35.55 4.00
2888 3999 0.176680 ATAGCTTCTGACGCACCAGG 59.823 55.000 8.91 0.00 34.99 4.45
2889 4000 2.507110 TAGCTTCTGACGCACCAGGC 62.507 60.000 8.91 0.36 39.90 4.85
2898 4009 3.461773 GCACCAGGCGGCTCTAGA 61.462 66.667 9.32 0.00 34.57 2.43
2899 4010 3.019003 GCACCAGGCGGCTCTAGAA 62.019 63.158 9.32 0.00 34.57 2.10
2900 4011 1.142748 CACCAGGCGGCTCTAGAAG 59.857 63.158 9.32 0.00 34.57 2.85
2901 4012 2.060980 ACCAGGCGGCTCTAGAAGG 61.061 63.158 9.32 9.10 34.57 3.46
2902 4013 2.060980 CCAGGCGGCTCTAGAAGGT 61.061 63.158 9.32 0.00 0.00 3.50
2903 4014 1.617947 CCAGGCGGCTCTAGAAGGTT 61.618 60.000 9.32 0.00 0.00 3.50
2904 4015 0.250513 CAGGCGGCTCTAGAAGGTTT 59.749 55.000 9.32 0.00 0.00 3.27
2905 4016 0.537653 AGGCGGCTCTAGAAGGTTTC 59.462 55.000 5.25 0.00 0.00 2.78
2906 4017 0.249398 GGCGGCTCTAGAAGGTTTCA 59.751 55.000 0.00 0.00 0.00 2.69
2907 4018 1.134371 GGCGGCTCTAGAAGGTTTCAT 60.134 52.381 0.00 0.00 0.00 2.57
2908 4019 2.633488 GCGGCTCTAGAAGGTTTCATT 58.367 47.619 0.00 0.00 0.00 2.57
2909 4020 2.352960 GCGGCTCTAGAAGGTTTCATTG 59.647 50.000 0.00 0.00 0.00 2.82
2910 4021 2.939103 CGGCTCTAGAAGGTTTCATTGG 59.061 50.000 0.00 0.00 0.00 3.16
2911 4022 3.619979 CGGCTCTAGAAGGTTTCATTGGT 60.620 47.826 0.00 0.00 0.00 3.67
2912 4023 3.691609 GGCTCTAGAAGGTTTCATTGGTG 59.308 47.826 0.00 0.00 0.00 4.17
2913 4024 4.565652 GGCTCTAGAAGGTTTCATTGGTGA 60.566 45.833 0.00 0.00 0.00 4.02
2914 4025 5.189180 GCTCTAGAAGGTTTCATTGGTGAT 58.811 41.667 0.00 0.00 33.56 3.06
2915 4026 5.065731 GCTCTAGAAGGTTTCATTGGTGATG 59.934 44.000 0.00 0.00 37.08 3.07
2916 4027 6.126863 TCTAGAAGGTTTCATTGGTGATGT 57.873 37.500 0.00 0.00 37.06 3.06
2917 4028 6.542821 TCTAGAAGGTTTCATTGGTGATGTT 58.457 36.000 0.00 0.00 37.06 2.71
2918 4029 5.458041 AGAAGGTTTCATTGGTGATGTTG 57.542 39.130 0.00 0.00 37.06 3.33
2919 4030 3.665745 AGGTTTCATTGGTGATGTTGC 57.334 42.857 0.00 0.00 37.06 4.17
2920 4031 2.964464 AGGTTTCATTGGTGATGTTGCA 59.036 40.909 0.00 0.00 37.06 4.08
2921 4032 3.059166 GGTTTCATTGGTGATGTTGCAC 58.941 45.455 0.00 0.00 37.06 4.57
2928 4039 3.525619 GTGATGTTGCACCGGTAGA 57.474 52.632 6.87 0.00 32.68 2.59
2929 4040 2.024176 GTGATGTTGCACCGGTAGAT 57.976 50.000 6.87 0.00 32.68 1.98
2930 4041 1.665679 GTGATGTTGCACCGGTAGATG 59.334 52.381 6.87 0.00 32.68 2.90
2931 4042 1.552792 TGATGTTGCACCGGTAGATGA 59.447 47.619 6.87 0.00 0.00 2.92
2932 4043 2.170397 TGATGTTGCACCGGTAGATGAT 59.830 45.455 6.87 0.00 0.00 2.45
2933 4044 2.022764 TGTTGCACCGGTAGATGATG 57.977 50.000 6.87 0.00 0.00 3.07
2934 4045 1.299541 GTTGCACCGGTAGATGATGG 58.700 55.000 6.87 0.00 0.00 3.51
2935 4046 0.463654 TTGCACCGGTAGATGATGGC 60.464 55.000 6.87 4.20 0.00 4.40
2936 4047 1.337384 TGCACCGGTAGATGATGGCT 61.337 55.000 6.87 0.00 0.00 4.75
2937 4048 0.179045 GCACCGGTAGATGATGGCTT 60.179 55.000 6.87 0.00 0.00 4.35
2938 4049 1.747206 GCACCGGTAGATGATGGCTTT 60.747 52.381 6.87 0.00 0.00 3.51
2939 4050 1.942657 CACCGGTAGATGATGGCTTTG 59.057 52.381 6.87 0.00 0.00 2.77
2940 4051 1.837439 ACCGGTAGATGATGGCTTTGA 59.163 47.619 4.49 0.00 0.00 2.69
2941 4052 2.213499 CCGGTAGATGATGGCTTTGAC 58.787 52.381 0.00 0.00 0.00 3.18
2942 4053 2.419990 CCGGTAGATGATGGCTTTGACA 60.420 50.000 0.00 0.00 0.00 3.58
2943 4054 3.270027 CGGTAGATGATGGCTTTGACAA 58.730 45.455 0.00 0.00 0.00 3.18
2944 4055 3.879295 CGGTAGATGATGGCTTTGACAAT 59.121 43.478 0.00 0.00 0.00 2.71
2945 4056 4.260907 CGGTAGATGATGGCTTTGACAATG 60.261 45.833 0.00 0.00 0.00 2.82
2946 4057 4.641989 GGTAGATGATGGCTTTGACAATGT 59.358 41.667 3.32 0.00 0.00 2.71
2947 4058 5.126061 GGTAGATGATGGCTTTGACAATGTT 59.874 40.000 3.32 0.00 0.00 2.71
2948 4059 6.318648 GGTAGATGATGGCTTTGACAATGTTA 59.681 38.462 3.32 0.00 0.00 2.41
2949 4060 6.446781 AGATGATGGCTTTGACAATGTTAG 57.553 37.500 3.32 0.00 0.00 2.34
2953 4064 3.485394 TGGCTTTGACAATGTTAGCAGA 58.515 40.909 14.67 2.45 33.60 4.26
2968 4079 3.760580 AGCAGAGTTTCTGTAAGCACT 57.239 42.857 7.80 0.00 45.94 4.40
2969 4080 3.397482 AGCAGAGTTTCTGTAAGCACTG 58.603 45.455 7.80 0.00 45.94 3.66
2970 4081 3.134458 GCAGAGTTTCTGTAAGCACTGT 58.866 45.455 7.80 0.00 45.94 3.55
2990 4105 7.647715 GCACTGTGTATTTGTTCTTGTTGTAAT 59.352 33.333 9.86 0.00 0.00 1.89
3011 4126 9.214957 TGTAATATGTTGATCGATGTAATTCCC 57.785 33.333 0.54 0.00 0.00 3.97
3012 4127 9.214957 GTAATATGTTGATCGATGTAATTCCCA 57.785 33.333 0.54 0.00 0.00 4.37
3013 4128 7.912056 ATATGTTGATCGATGTAATTCCCAG 57.088 36.000 0.54 0.00 0.00 4.45
3014 4129 3.876914 TGTTGATCGATGTAATTCCCAGC 59.123 43.478 0.54 0.00 0.00 4.85
3015 4130 3.836365 TGATCGATGTAATTCCCAGCA 57.164 42.857 0.54 0.00 0.00 4.41
3016 4131 4.356405 TGATCGATGTAATTCCCAGCAT 57.644 40.909 0.54 0.00 0.00 3.79
3017 4132 4.067192 TGATCGATGTAATTCCCAGCATG 58.933 43.478 0.54 0.00 0.00 4.06
3038 4153 6.680810 CATGGTTTCATTAACTCAAAGCAGA 58.319 36.000 11.14 0.00 39.97 4.26
3047 4162 4.827304 AACTCAAAGCAGAGCTCTTTTC 57.173 40.909 15.27 6.39 38.25 2.29
3129 4246 3.831715 CTTTACTGGCAAAGCTGTACC 57.168 47.619 0.00 0.00 0.00 3.34
3136 4253 2.576191 TGGCAAAGCTGTACCTAATCCT 59.424 45.455 0.00 0.00 0.00 3.24
3141 4258 5.163713 GCAAAGCTGTACCTAATCCTTGAAG 60.164 44.000 0.00 0.00 0.00 3.02
3144 4261 4.962995 AGCTGTACCTAATCCTTGAAGCTA 59.037 41.667 0.00 0.00 36.75 3.32
3145 4262 5.604650 AGCTGTACCTAATCCTTGAAGCTAT 59.395 40.000 0.00 0.00 36.75 2.97
3146 4263 5.929415 GCTGTACCTAATCCTTGAAGCTATC 59.071 44.000 0.00 0.00 0.00 2.08
3147 4264 6.239458 GCTGTACCTAATCCTTGAAGCTATCT 60.239 42.308 0.00 0.00 0.00 1.98
3179 4313 2.941453 TCATTGTCTCACGGCTAGAC 57.059 50.000 0.00 7.02 43.04 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.959596 GAGCGATGCGAGGCCTCC 62.960 72.222 27.20 19.25 0.00 4.30
116 117 1.216990 GGGAGGATTGGATGAGTGGT 58.783 55.000 0.00 0.00 0.00 4.16
195 199 0.248949 GTCTGGGATTCGCGTACCTC 60.249 60.000 5.77 0.00 0.00 3.85
310 325 3.068873 AGACACCTCTAATCGGCAGATTC 59.931 47.826 15.61 0.00 45.21 2.52
352 367 8.613060 ACAGCAATCGATCAACAAATCTATAT 57.387 30.769 0.00 0.00 0.00 0.86
482 647 4.813161 CAGAGCGGAATCAATCAACTACAT 59.187 41.667 0.00 0.00 0.00 2.29
504 669 0.750249 TGAACGACTCAGCAGGAACA 59.250 50.000 0.00 0.00 0.00 3.18
625 807 5.013808 ACAACTACTAGGCCCAACAACTAAT 59.986 40.000 0.00 0.00 0.00 1.73
659 841 1.153329 AACCGGTGCACAAGAACGA 60.153 52.632 20.43 0.00 0.00 3.85
762 945 6.701340 AGAACTGATGCACAAGTACAGATAA 58.299 36.000 3.66 0.00 33.53 1.75
828 1018 5.300034 AGCAGATTGATGTTCAAGTTTGACA 59.700 36.000 0.00 0.00 40.05 3.58
860 1050 5.863965 TGTGTGAACATCTCAATAGGAACA 58.136 37.500 0.00 0.00 35.22 3.18
878 1072 7.554118 AGAGGGATGAAATTGTAACTATGTGTG 59.446 37.037 0.00 0.00 0.00 3.82
879 1073 7.633789 AGAGGGATGAAATTGTAACTATGTGT 58.366 34.615 0.00 0.00 0.00 3.72
880 1074 8.400947 CAAGAGGGATGAAATTGTAACTATGTG 58.599 37.037 0.00 0.00 0.00 3.21
900 1095 1.065854 AGAAAGCCACGATCCAAGAGG 60.066 52.381 0.00 0.00 0.00 3.69
921 1116 8.681486 TGCAGAACATAAAGCATATATGAACT 57.319 30.769 17.10 2.01 35.28 3.01
1227 1422 3.265791 GGTCTTGACGAAGATCTGCATT 58.734 45.455 0.51 0.00 40.40 3.56
1239 1434 2.261671 CCGGTGAGGGTCTTGACG 59.738 66.667 0.00 0.00 35.97 4.35
1269 1464 0.456995 CCGAAGACTCAACCTCGAGC 60.457 60.000 6.99 0.00 36.42 5.03
1284 1479 1.614903 ACGTTGTCTATGGTGTCCGAA 59.385 47.619 0.00 0.00 0.00 4.30
2019 2214 2.505982 CATACCACCCCTGAGGCG 59.494 66.667 0.00 0.00 40.58 5.52
2020 2215 2.193248 GCATACCACCCCTGAGGC 59.807 66.667 0.00 0.00 40.58 4.70
2021 2216 0.982852 TCTGCATACCACCCCTGAGG 60.983 60.000 0.00 0.00 43.78 3.86
2311 3320 3.132289 TCGAAGGACACAGAAAGACAACT 59.868 43.478 0.00 0.00 0.00 3.16
2455 3503 4.042187 ACAAGTTCAGGGCTCACTTATTCT 59.958 41.667 0.00 0.00 0.00 2.40
2486 3534 4.027572 TGCAGAAGTACAAACAGCAAAC 57.972 40.909 0.00 0.00 0.00 2.93
2524 3573 5.514204 CACCGAAAGAAGATCAAATGCAATC 59.486 40.000 0.00 0.00 0.00 2.67
2578 3627 8.969260 ATAAAATGTTCTCACATCAGCTCATA 57.031 30.769 0.00 0.00 43.34 2.15
2620 3669 4.142730 AGCTGAGCATTCGTTCAGATTTTC 60.143 41.667 7.39 0.00 45.43 2.29
2631 3680 0.095935 CCGTTGAAGCTGAGCATTCG 59.904 55.000 7.39 3.99 0.00 3.34
2656 3705 0.179081 GTAGATGCACCGGGGAACTC 60.179 60.000 8.67 0.00 0.00 3.01
2658 3707 1.153229 GGTAGATGCACCGGGGAAC 60.153 63.158 8.67 0.00 0.00 3.62
2659 3708 2.372074 GGGTAGATGCACCGGGGAA 61.372 63.158 8.67 0.00 39.69 3.97
2660 3709 2.766651 GGGTAGATGCACCGGGGA 60.767 66.667 8.67 0.00 39.69 4.81
2661 3710 3.873812 GGGGTAGATGCACCGGGG 61.874 72.222 6.32 0.84 39.69 5.73
2662 3711 1.994885 AATGGGGTAGATGCACCGGG 61.995 60.000 6.32 0.00 39.69 5.73
2663 3712 0.106719 AAATGGGGTAGATGCACCGG 60.107 55.000 0.00 0.00 39.69 5.28
2664 3713 1.762708 AAAATGGGGTAGATGCACCG 58.237 50.000 0.00 0.00 39.69 4.94
2665 3714 5.140454 AGATAAAAATGGGGTAGATGCACC 58.860 41.667 0.00 0.00 37.91 5.01
2666 3715 6.715347 AAGATAAAAATGGGGTAGATGCAC 57.285 37.500 0.00 0.00 0.00 4.57
2667 3716 7.719633 GTCTAAGATAAAAATGGGGTAGATGCA 59.280 37.037 0.00 0.00 0.00 3.96
2668 3717 7.719633 TGTCTAAGATAAAAATGGGGTAGATGC 59.280 37.037 0.00 0.00 0.00 3.91
2856 3967 1.687123 GAAGCTATGGGGTCGCTTAGA 59.313 52.381 10.60 0.00 43.42 2.10
2857 3968 1.689273 AGAAGCTATGGGGTCGCTTAG 59.311 52.381 0.00 4.37 43.42 2.18
2858 3969 1.412710 CAGAAGCTATGGGGTCGCTTA 59.587 52.381 0.00 0.00 43.42 3.09
2859 3970 0.179000 CAGAAGCTATGGGGTCGCTT 59.821 55.000 0.00 0.00 45.79 4.68
2860 3971 0.687757 TCAGAAGCTATGGGGTCGCT 60.688 55.000 0.00 0.00 35.09 4.93
2861 3972 0.530870 GTCAGAAGCTATGGGGTCGC 60.531 60.000 0.00 0.00 0.00 5.19
2862 3973 0.249073 CGTCAGAAGCTATGGGGTCG 60.249 60.000 0.00 0.00 0.00 4.79
2863 3974 0.530870 GCGTCAGAAGCTATGGGGTC 60.531 60.000 0.37 0.00 0.00 4.46
2864 3975 1.264749 TGCGTCAGAAGCTATGGGGT 61.265 55.000 9.88 0.00 35.28 4.95
2865 3976 0.811616 GTGCGTCAGAAGCTATGGGG 60.812 60.000 9.88 0.00 35.28 4.96
2866 3977 0.811616 GGTGCGTCAGAAGCTATGGG 60.812 60.000 9.88 0.00 35.28 4.00
2867 3978 0.108186 TGGTGCGTCAGAAGCTATGG 60.108 55.000 9.88 0.00 35.28 2.74
2868 3979 1.284657 CTGGTGCGTCAGAAGCTATG 58.715 55.000 9.88 0.00 36.93 2.23
2869 3980 0.176680 CCTGGTGCGTCAGAAGCTAT 59.823 55.000 9.88 0.00 36.93 2.97
2870 3981 1.591703 CCTGGTGCGTCAGAAGCTA 59.408 57.895 9.88 0.00 36.93 3.32
2871 3982 2.345244 CCTGGTGCGTCAGAAGCT 59.655 61.111 9.88 0.00 36.93 3.74
2872 3983 3.426568 GCCTGGTGCGTCAGAAGC 61.427 66.667 0.65 0.65 36.93 3.86
2881 3992 2.914777 CTTCTAGAGCCGCCTGGTGC 62.915 65.000 0.55 1.73 37.67 5.01
2882 3993 1.142748 CTTCTAGAGCCGCCTGGTG 59.857 63.158 0.00 0.00 37.67 4.17
2883 3994 2.060980 CCTTCTAGAGCCGCCTGGT 61.061 63.158 0.00 0.00 37.67 4.00
2884 3995 1.617947 AACCTTCTAGAGCCGCCTGG 61.618 60.000 0.00 0.00 38.77 4.45
2885 3996 0.250513 AAACCTTCTAGAGCCGCCTG 59.749 55.000 0.00 0.00 0.00 4.85
2886 3997 0.537653 GAAACCTTCTAGAGCCGCCT 59.462 55.000 0.00 0.00 0.00 5.52
2887 3998 0.249398 TGAAACCTTCTAGAGCCGCC 59.751 55.000 0.00 0.00 0.00 6.13
2888 3999 2.317530 ATGAAACCTTCTAGAGCCGC 57.682 50.000 0.00 0.00 0.00 6.53
2889 4000 2.939103 CCAATGAAACCTTCTAGAGCCG 59.061 50.000 0.00 0.00 0.00 5.52
2890 4001 3.691609 CACCAATGAAACCTTCTAGAGCC 59.308 47.826 0.00 0.00 0.00 4.70
2891 4002 4.579869 TCACCAATGAAACCTTCTAGAGC 58.420 43.478 0.00 0.00 0.00 4.09
2892 4003 6.176183 ACATCACCAATGAAACCTTCTAGAG 58.824 40.000 0.00 0.00 38.69 2.43
2893 4004 6.126863 ACATCACCAATGAAACCTTCTAGA 57.873 37.500 0.00 0.00 38.69 2.43
2894 4005 6.615088 CAACATCACCAATGAAACCTTCTAG 58.385 40.000 0.00 0.00 38.69 2.43
2895 4006 5.048083 GCAACATCACCAATGAAACCTTCTA 60.048 40.000 0.00 0.00 38.69 2.10
2896 4007 4.262164 GCAACATCACCAATGAAACCTTCT 60.262 41.667 0.00 0.00 38.69 2.85
2897 4008 3.989817 GCAACATCACCAATGAAACCTTC 59.010 43.478 0.00 0.00 38.69 3.46
2898 4009 3.387374 TGCAACATCACCAATGAAACCTT 59.613 39.130 0.00 0.00 38.69 3.50
2899 4010 2.964464 TGCAACATCACCAATGAAACCT 59.036 40.909 0.00 0.00 38.69 3.50
2900 4011 3.059166 GTGCAACATCACCAATGAAACC 58.941 45.455 0.00 0.00 38.69 3.27
2910 4021 1.665679 CATCTACCGGTGCAACATCAC 59.334 52.381 19.93 0.00 39.98 3.06
2911 4022 1.552792 TCATCTACCGGTGCAACATCA 59.447 47.619 19.93 0.00 39.98 3.07
2912 4023 2.309528 TCATCTACCGGTGCAACATC 57.690 50.000 19.93 0.00 39.98 3.06
2913 4024 2.564771 CATCATCTACCGGTGCAACAT 58.435 47.619 19.93 0.32 39.98 2.71
2914 4025 1.406751 CCATCATCTACCGGTGCAACA 60.407 52.381 19.93 0.00 39.98 3.33
2915 4026 1.299541 CCATCATCTACCGGTGCAAC 58.700 55.000 19.93 0.00 0.00 4.17
2916 4027 0.463654 GCCATCATCTACCGGTGCAA 60.464 55.000 19.93 2.03 0.00 4.08
2917 4028 1.146041 GCCATCATCTACCGGTGCA 59.854 57.895 19.93 2.98 0.00 4.57
2918 4029 0.179045 AAGCCATCATCTACCGGTGC 60.179 55.000 19.93 9.52 0.00 5.01
2919 4030 1.942657 CAAAGCCATCATCTACCGGTG 59.057 52.381 19.93 7.59 0.00 4.94
2920 4031 1.837439 TCAAAGCCATCATCTACCGGT 59.163 47.619 13.98 13.98 0.00 5.28
2921 4032 2.213499 GTCAAAGCCATCATCTACCGG 58.787 52.381 0.00 0.00 0.00 5.28
2922 4033 2.905075 TGTCAAAGCCATCATCTACCG 58.095 47.619 0.00 0.00 0.00 4.02
2923 4034 4.641989 ACATTGTCAAAGCCATCATCTACC 59.358 41.667 0.00 0.00 0.00 3.18
2924 4035 5.824904 ACATTGTCAAAGCCATCATCTAC 57.175 39.130 0.00 0.00 0.00 2.59
2925 4036 6.038603 GCTAACATTGTCAAAGCCATCATCTA 59.961 38.462 7.25 0.00 0.00 1.98
2926 4037 5.163581 GCTAACATTGTCAAAGCCATCATCT 60.164 40.000 7.25 0.00 0.00 2.90
2927 4038 5.039333 GCTAACATTGTCAAAGCCATCATC 58.961 41.667 7.25 0.00 0.00 2.92
2928 4039 4.463539 TGCTAACATTGTCAAAGCCATCAT 59.536 37.500 13.18 0.00 32.14 2.45
2929 4040 3.825585 TGCTAACATTGTCAAAGCCATCA 59.174 39.130 13.18 0.00 32.14 3.07
2930 4041 4.156556 TCTGCTAACATTGTCAAAGCCATC 59.843 41.667 13.18 0.00 32.14 3.51
2931 4042 4.081406 TCTGCTAACATTGTCAAAGCCAT 58.919 39.130 13.18 0.00 32.14 4.40
2932 4043 3.485394 TCTGCTAACATTGTCAAAGCCA 58.515 40.909 13.18 4.62 32.14 4.75
2933 4044 3.503748 ACTCTGCTAACATTGTCAAAGCC 59.496 43.478 13.18 1.37 32.14 4.35
2934 4045 4.756084 ACTCTGCTAACATTGTCAAAGC 57.244 40.909 10.29 10.29 0.00 3.51
2935 4046 6.854892 CAGAAACTCTGCTAACATTGTCAAAG 59.145 38.462 0.00 0.00 37.72 2.77
2936 4047 6.728200 CAGAAACTCTGCTAACATTGTCAAA 58.272 36.000 0.00 0.00 37.72 2.69
2937 4048 6.304356 CAGAAACTCTGCTAACATTGTCAA 57.696 37.500 0.00 0.00 37.72 3.18
2938 4049 5.929697 CAGAAACTCTGCTAACATTGTCA 57.070 39.130 0.00 0.00 37.72 3.58
2953 4064 6.542370 ACAAATACACAGTGCTTACAGAAACT 59.458 34.615 0.00 0.00 0.00 2.66
2990 4105 5.700832 GCTGGGAATTACATCGATCAACATA 59.299 40.000 0.00 0.00 0.00 2.29
3009 4124 3.763360 TGAGTTAATGAAACCATGCTGGG 59.237 43.478 7.06 0.29 43.37 4.45
3010 4125 5.389859 TTGAGTTAATGAAACCATGCTGG 57.610 39.130 1.16 1.16 45.02 4.85
3011 4126 5.346822 GCTTTGAGTTAATGAAACCATGCTG 59.653 40.000 0.00 0.00 39.03 4.41
3012 4127 5.010922 TGCTTTGAGTTAATGAAACCATGCT 59.989 36.000 0.00 0.00 39.03 3.79
3013 4128 5.229423 TGCTTTGAGTTAATGAAACCATGC 58.771 37.500 0.00 0.00 39.03 4.06
3014 4129 6.680810 TCTGCTTTGAGTTAATGAAACCATG 58.319 36.000 0.00 0.00 39.03 3.66
3015 4130 6.571150 GCTCTGCTTTGAGTTAATGAAACCAT 60.571 38.462 0.00 0.00 39.03 3.55
3016 4131 5.278463 GCTCTGCTTTGAGTTAATGAAACCA 60.278 40.000 0.00 0.00 39.03 3.67
3017 4132 5.048434 AGCTCTGCTTTGAGTTAATGAAACC 60.048 40.000 0.00 0.00 35.24 3.27
3018 4133 6.006759 AGCTCTGCTTTGAGTTAATGAAAC 57.993 37.500 0.00 0.00 33.89 2.78
3019 4134 6.000219 AGAGCTCTGCTTTGAGTTAATGAAA 59.000 36.000 17.42 0.00 39.88 2.69
3020 4135 5.555017 AGAGCTCTGCTTTGAGTTAATGAA 58.445 37.500 17.42 0.00 39.88 2.57
3021 4136 5.157940 AGAGCTCTGCTTTGAGTTAATGA 57.842 39.130 17.42 0.00 39.88 2.57
3022 4137 5.876612 AAGAGCTCTGCTTTGAGTTAATG 57.123 39.130 19.06 0.00 39.88 1.90
3023 4138 6.348050 CGAAAAGAGCTCTGCTTTGAGTTAAT 60.348 38.462 19.06 0.00 39.88 1.40
3024 4139 5.050091 CGAAAAGAGCTCTGCTTTGAGTTAA 60.050 40.000 19.06 0.00 39.88 2.01
3025 4140 4.449068 CGAAAAGAGCTCTGCTTTGAGTTA 59.551 41.667 19.06 0.00 39.88 2.24
3026 4141 3.249559 CGAAAAGAGCTCTGCTTTGAGTT 59.750 43.478 19.06 1.63 39.88 3.01
3027 4142 2.805099 CGAAAAGAGCTCTGCTTTGAGT 59.195 45.455 19.06 0.00 39.88 3.41
3028 4143 3.062763 TCGAAAAGAGCTCTGCTTTGAG 58.937 45.455 19.06 10.98 39.88 3.02
3109 4226 3.412386 AGGTACAGCTTTGCCAGTAAAG 58.588 45.455 9.80 4.10 39.95 1.85
3112 4229 4.383770 GGATTAGGTACAGCTTTGCCAGTA 60.384 45.833 9.80 0.00 0.00 2.74
3118 4235 5.163713 GCTTCAAGGATTAGGTACAGCTTTG 60.164 44.000 0.00 0.00 0.00 2.77
3147 4264 9.476202 CCGTGAGACAATGATGTTATCTATTAA 57.524 33.333 0.00 0.00 40.74 1.40
3153 4287 4.122776 AGCCGTGAGACAATGATGTTATC 58.877 43.478 0.00 0.00 40.74 1.75
3179 4313 6.540189 ACGTTGGATATCCTTTGAGATTTCAG 59.460 38.462 22.35 2.81 33.91 3.02


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

AutoCloner maintained by Alex Coulton.