Multiple sequence alignment - TraesCS5D01G112000

Loading Multiple Alignment...

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 TraesCS5D01G112000 chr5D 100.000 3652 0 0 1 3652 127261226 127257575 0.000000e+00 6745.0
1 TraesCS5D01G112000 chr5B 96.783 2176 52 9 810 2975 140736758 140734591 0.000000e+00 3615.0
2 TraesCS5D01G112000 chr5B 95.658 714 23 4 1 708 140739680 140738969 0.000000e+00 1140.0
3 TraesCS5D01G112000 chr5B 95.146 515 15 7 3145 3652 140734552 140734041 0.000000e+00 804.0
4 TraesCS5D01G112000 chr5B 78.922 204 39 4 412 613 599756963 599757164 6.360000e-28 135.0
5 TraesCS5D01G112000 chr5B 97.183 71 2 0 2856 2926 162772842 162772772 1.780000e-23 121.0
6 TraesCS5D01G112000 chr5B 87.156 109 10 1 3040 3148 603641207 603641103 1.780000e-23 121.0
7 TraesCS5D01G112000 chr5A 95.402 1892 69 10 949 2833 142847356 142845476 0.000000e+00 2996.0
8 TraesCS5D01G112000 chr5A 88.849 843 59 19 2817 3652 142844336 142843522 0.000000e+00 1003.0
9 TraesCS5D01G112000 chr2B 79.817 436 84 4 185 617 758142815 758142381 7.610000e-82 315.0
10 TraesCS5D01G112000 chr2B 80.488 369 67 5 248 613 758366158 758365792 9.990000e-71 278.0
11 TraesCS5D01G112000 chr3D 80.047 426 80 4 185 608 5046622 5046200 9.850000e-81 311.0
12 TraesCS5D01G112000 chr3D 76.728 434 90 11 182 609 27874420 27874848 7.890000e-57 231.0
13 TraesCS5D01G112000 chr3D 78.261 299 55 8 261 552 267283656 267283951 2.240000e-42 183.0
14 TraesCS5D01G112000 chr4A 80.612 294 48 8 186 475 290367043 290366755 6.140000e-53 219.0
15 TraesCS5D01G112000 chr4A 76.378 381 81 9 182 556 441826191 441826568 2.880000e-46 196.0
16 TraesCS5D01G112000 chr6D 76.640 381 76 11 240 613 79732379 79732005 8.000000e-47 198.0
17 TraesCS5D01G112000 chr7D 91.071 112 6 2 3040 3151 433012539 433012432 8.170000e-32 148.0
18 TraesCS5D01G112000 chr7D 98.485 66 1 0 2856 2921 632404615 632404680 2.300000e-22 117.0
19 TraesCS5D01G112000 chr7D 83.962 106 13 3 3040 3145 395358495 395358596 8.350000e-17 99.0
20 TraesCS5D01G112000 chr2D 90.909 110 5 2 3040 3148 138808290 138808185 3.800000e-30 143.0
21 TraesCS5D01G112000 chr2D 92.683 82 6 0 2856 2937 117843105 117843024 6.410000e-23 119.0
22 TraesCS5D01G112000 chr3B 89.189 111 8 2 3040 3150 528494284 528494390 6.360000e-28 135.0
23 TraesCS5D01G112000 chr6A 87.719 114 8 3 3040 3152 2229039 2229147 1.060000e-25 128.0
24 TraesCS5D01G112000 chr7A 88.571 105 8 1 3040 3144 37108401 37108501 1.380000e-24 124.0
25 TraesCS5D01G112000 chr7A 95.890 73 3 0 2856 2928 686371380 686371308 6.410000e-23 119.0
26 TraesCS5D01G112000 chr4D 87.387 111 10 1 3040 3150 128777145 128777251 1.380000e-24 124.0
27 TraesCS5D01G112000 chr4B 90.426 94 4 5 2856 2948 640009094 640009183 6.410000e-23 119.0
28 TraesCS5D01G112000 chr1A 94.667 75 4 0 2852 2926 576371149 576371075 2.300000e-22 117.0
29 TraesCS5D01G112000 chr7B 91.463 82 6 1 2845 2925 667453400 667453319 1.070000e-20 111.0
30 TraesCS5D01G112000 chr7B 81.319 91 13 3 3055 3145 39522800 39522886 1.820000e-08 71.3


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 TraesCS5D01G112000 chr5D 127257575 127261226 3651 True 6745.0 6745 100.000000 1 3652 1 chr5D.!!$R1 3651
1 TraesCS5D01G112000 chr5B 140734041 140739680 5639 True 1853.0 3615 95.862333 1 3652 3 chr5B.!!$R3 3651
2 TraesCS5D01G112000 chr5A 142843522 142847356 3834 True 1999.5 2996 92.125500 949 3652 2 chr5A.!!$R1 2703

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
767 774 0.109458 GCGGTCAGACATACGTGTGA 60.109 55.0 19.87 0.93 42.72 3.58 F
1155 3280 0.038709 AGCTCATCTATCCGAAGCGC 60.039 55.0 0.00 0.00 0.00 5.92 F
2032 4157 1.067295 AGGGTGTGGAGCAAGATGAA 58.933 50.0 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 4506 0.104304 AAAGAGCCGTGACGAGTTGT 59.896 50.000 6.54 0.0 0.00 3.32 R
2460 4585 1.134995 TGTGACATAGCCTGCTTCTCG 60.135 52.381 0.00 0.0 0.00 4.04 R
3589 6882 0.108756 ACTAGGAAACGAGAAGCGCC 60.109 55.000 2.29 0.0 46.04 6.53 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
109 110 2.243810 AGAGCCGTTCATAGGAGATCC 58.756 52.381 0.00 0.00 0.00 3.36
161 162 2.695759 TAAGTTGCATTGGCGGCCG 61.696 57.895 24.05 24.05 45.35 6.13
163 164 4.776647 GTTGCATTGGCGGCCGTC 62.777 66.667 26.05 26.05 45.35 4.79
175 176 1.153349 GGCCGTCTGGTGGAAGATC 60.153 63.158 0.00 0.00 37.67 2.75
176 177 1.617947 GGCCGTCTGGTGGAAGATCT 61.618 60.000 0.00 0.00 37.67 2.75
177 178 1.112113 GCCGTCTGGTGGAAGATCTA 58.888 55.000 0.00 0.00 37.67 1.98
178 179 1.689273 GCCGTCTGGTGGAAGATCTAT 59.311 52.381 0.00 0.00 37.67 1.98
229 230 1.002274 CCTCCAGACCAGGGCTACT 59.998 63.158 0.00 0.00 0.00 2.57
336 337 2.955660 TGAACGAGTTTTTCCAAGGCAT 59.044 40.909 0.00 0.00 0.00 4.40
337 338 3.243367 TGAACGAGTTTTTCCAAGGCATG 60.243 43.478 0.00 0.00 0.00 4.06
351 352 1.134159 AGGCATGCATCTGACTCCTTC 60.134 52.381 21.36 0.00 22.79 3.46
398 399 1.021390 CACCCACTTTCTAGGCAGCG 61.021 60.000 0.00 0.00 0.00 5.18
399 400 1.296715 CCCACTTTCTAGGCAGCGT 59.703 57.895 0.00 0.00 0.00 5.07
403 404 0.969894 ACTTTCTAGGCAGCGTGACT 59.030 50.000 0.00 0.00 40.22 3.41
458 459 0.247301 GCTACAACGCATCGACTTGC 60.247 55.000 0.75 0.75 39.29 4.01
528 530 6.094186 CCTTATTTCTCTCCTGTTTGTTAGGC 59.906 42.308 0.00 0.00 35.23 3.93
554 556 2.032681 GCTCTTGTCCCAGCCGTT 59.967 61.111 0.00 0.00 0.00 4.44
590 592 4.522789 AGTTTGGATGTTGGTTGTATGGAC 59.477 41.667 0.00 0.00 0.00 4.02
593 595 3.073798 TGGATGTTGGTTGTATGGACTGT 59.926 43.478 0.00 0.00 0.00 3.55
612 614 9.104965 TGGACTGTTGATTTATCTATAAAACGG 57.895 33.333 0.00 2.36 36.02 4.44
615 617 8.827677 ACTGTTGATTTATCTATAAAACGGAGC 58.172 33.333 9.82 0.00 36.02 4.70
679 686 0.882927 GCACAAGTACCGGCTCAACA 60.883 55.000 0.00 0.00 0.00 3.33
708 715 1.339929 TGCACGAGAGCTTGACAACTA 59.660 47.619 0.00 0.00 34.99 2.24
709 716 2.223947 TGCACGAGAGCTTGACAACTAA 60.224 45.455 0.00 0.00 34.99 2.24
710 717 2.800544 GCACGAGAGCTTGACAACTAAA 59.199 45.455 0.00 0.00 0.00 1.85
711 718 3.247648 GCACGAGAGCTTGACAACTAAAA 59.752 43.478 0.00 0.00 0.00 1.52
712 719 4.762809 CACGAGAGCTTGACAACTAAAAC 58.237 43.478 0.00 0.00 0.00 2.43
713 720 4.508124 CACGAGAGCTTGACAACTAAAACT 59.492 41.667 0.00 0.00 0.00 2.66
714 721 4.508124 ACGAGAGCTTGACAACTAAAACTG 59.492 41.667 0.00 0.00 0.00 3.16
715 722 4.508124 CGAGAGCTTGACAACTAAAACTGT 59.492 41.667 0.00 0.00 0.00 3.55
716 723 5.690409 CGAGAGCTTGACAACTAAAACTGTA 59.310 40.000 0.00 0.00 0.00 2.74
717 724 6.200286 CGAGAGCTTGACAACTAAAACTGTAA 59.800 38.462 0.00 0.00 0.00 2.41
718 725 7.095607 CGAGAGCTTGACAACTAAAACTGTAAT 60.096 37.037 0.00 0.00 0.00 1.89
719 726 7.865707 AGAGCTTGACAACTAAAACTGTAATG 58.134 34.615 0.00 0.00 0.00 1.90
720 727 7.499232 AGAGCTTGACAACTAAAACTGTAATGT 59.501 33.333 0.00 0.00 0.00 2.71
721 728 7.417612 AGCTTGACAACTAAAACTGTAATGTG 58.582 34.615 0.00 0.00 0.00 3.21
722 729 7.067008 AGCTTGACAACTAAAACTGTAATGTGT 59.933 33.333 0.00 0.00 0.00 3.72
723 730 7.165812 GCTTGACAACTAAAACTGTAATGTGTG 59.834 37.037 0.00 0.00 0.00 3.82
724 731 7.851387 TGACAACTAAAACTGTAATGTGTGA 57.149 32.000 0.00 0.00 0.00 3.58
725 732 8.270080 TGACAACTAAAACTGTAATGTGTGAA 57.730 30.769 0.00 0.00 0.00 3.18
726 733 8.898761 TGACAACTAAAACTGTAATGTGTGAAT 58.101 29.630 0.00 0.00 0.00 2.57
727 734 9.730420 GACAACTAAAACTGTAATGTGTGAATT 57.270 29.630 0.00 0.00 0.00 2.17
728 735 9.730420 ACAACTAAAACTGTAATGTGTGAATTC 57.270 29.630 0.00 0.00 0.00 2.17
729 736 9.729023 CAACTAAAACTGTAATGTGTGAATTCA 57.271 29.630 3.38 3.38 0.00 2.57
730 737 9.950680 AACTAAAACTGTAATGTGTGAATTCAG 57.049 29.630 8.80 0.00 0.00 3.02
731 738 9.120538 ACTAAAACTGTAATGTGTGAATTCAGT 57.879 29.630 8.80 0.00 33.35 3.41
732 739 9.950680 CTAAAACTGTAATGTGTGAATTCAGTT 57.049 29.630 8.80 3.33 38.32 3.16
734 741 9.651913 AAAACTGTAATGTGTGAATTCAGTTTT 57.348 25.926 19.99 19.99 42.89 2.43
735 742 9.651913 AAACTGTAATGTGTGAATTCAGTTTTT 57.348 25.926 8.80 3.87 40.34 1.94
759 766 3.083997 GGGAGGGCGGTCAGACAT 61.084 66.667 2.17 0.00 0.00 3.06
760 767 1.760875 GGGAGGGCGGTCAGACATA 60.761 63.158 2.17 0.00 0.00 2.29
761 768 1.442148 GGAGGGCGGTCAGACATAC 59.558 63.158 2.17 0.00 0.00 2.39
762 769 1.065928 GAGGGCGGTCAGACATACG 59.934 63.158 2.17 0.00 0.00 3.06
763 770 1.664321 GAGGGCGGTCAGACATACGT 61.664 60.000 2.17 0.00 0.00 3.57
764 771 1.518572 GGGCGGTCAGACATACGTG 60.519 63.158 2.17 0.00 0.00 4.49
765 772 1.214589 GGCGGTCAGACATACGTGT 59.785 57.895 2.17 0.00 42.49 4.49
766 773 1.076533 GGCGGTCAGACATACGTGTG 61.077 60.000 11.09 11.09 39.09 3.82
767 774 0.109458 GCGGTCAGACATACGTGTGA 60.109 55.000 19.87 0.93 42.72 3.58
768 775 1.667756 GCGGTCAGACATACGTGTGAA 60.668 52.381 19.87 0.00 46.04 3.18
769 776 2.876091 CGGTCAGACATACGTGTGAAT 58.124 47.619 19.87 3.78 46.04 2.57
770 777 3.250744 CGGTCAGACATACGTGTGAATT 58.749 45.455 19.87 0.00 46.04 2.17
771 778 3.303495 CGGTCAGACATACGTGTGAATTC 59.697 47.826 19.87 6.30 46.04 2.17
772 779 4.242475 GGTCAGACATACGTGTGAATTCA 58.758 43.478 19.87 3.38 46.04 2.57
773 780 4.688879 GGTCAGACATACGTGTGAATTCAA 59.311 41.667 19.87 0.00 46.04 2.69
774 781 5.178623 GGTCAGACATACGTGTGAATTCAAA 59.821 40.000 19.87 0.76 46.04 2.69
775 782 6.128282 GGTCAGACATACGTGTGAATTCAAAT 60.128 38.462 19.87 0.00 46.04 2.32
776 783 7.064134 GGTCAGACATACGTGTGAATTCAAATA 59.936 37.037 19.87 0.00 46.04 1.40
777 784 8.440059 GTCAGACATACGTGTGAATTCAAATAA 58.560 33.333 19.87 0.00 46.04 1.40
778 785 8.440059 TCAGACATACGTGTGAATTCAAATAAC 58.560 33.333 19.87 5.82 42.06 1.89
779 786 8.443160 CAGACATACGTGTGAATTCAAATAACT 58.557 33.333 19.87 0.00 38.69 2.24
780 787 8.999431 AGACATACGTGTGAATTCAAATAACTT 58.001 29.630 19.87 3.33 39.09 2.66
781 788 8.948853 ACATACGTGTGAATTCAAATAACTTG 57.051 30.769 19.87 5.90 37.14 3.16
782 789 7.537306 ACATACGTGTGAATTCAAATAACTTGC 59.463 33.333 19.87 0.00 37.14 4.01
783 790 5.219633 ACGTGTGAATTCAAATAACTTGCC 58.780 37.500 10.35 0.00 34.76 4.52
784 791 5.009610 ACGTGTGAATTCAAATAACTTGCCT 59.990 36.000 10.35 0.00 34.76 4.75
785 792 5.343058 CGTGTGAATTCAAATAACTTGCCTG 59.657 40.000 10.35 0.00 34.76 4.85
788 2776 7.599998 GTGTGAATTCAAATAACTTGCCTGATT 59.400 33.333 10.35 0.00 34.76 2.57
851 2967 2.125912 AGGCCTCTGACATGGGGT 59.874 61.111 0.00 0.00 0.00 4.95
852 2968 1.542375 AGGCCTCTGACATGGGGTT 60.542 57.895 0.00 0.00 0.00 4.11
910 3026 1.602771 GGCCTTCCAGTACCAGTCC 59.397 63.158 0.00 0.00 0.00 3.85
911 3027 0.910088 GGCCTTCCAGTACCAGTCCT 60.910 60.000 0.00 0.00 0.00 3.85
912 3028 0.250513 GCCTTCCAGTACCAGTCCTG 59.749 60.000 0.00 0.00 0.00 3.86
1099 3224 1.825474 GAGTTGGAGGATCGAGTTCCA 59.175 52.381 7.77 9.16 39.16 3.53
1125 3250 4.717313 GGGGACACGCTGGGGAAC 62.717 72.222 0.00 0.00 0.00 3.62
1155 3280 0.038709 AGCTCATCTATCCGAAGCGC 60.039 55.000 0.00 0.00 0.00 5.92
1394 3519 2.974698 CCGCCCCGAATGCAGATC 60.975 66.667 0.00 0.00 0.00 2.75
1726 3851 1.836802 GATCAAGGAGCTCAGGAGGTT 59.163 52.381 17.19 0.00 39.57 3.50
1817 3942 2.275318 GCGGAGAAGGTCTTTGATCTG 58.725 52.381 0.00 0.00 0.00 2.90
2032 4157 1.067295 AGGGTGTGGAGCAAGATGAA 58.933 50.000 0.00 0.00 0.00 2.57
2129 4254 4.255126 GCAGAGTGCGTTTACGGA 57.745 55.556 4.29 0.00 40.23 4.69
2153 4278 1.148027 TGGGAGTCAGAGTCAGGAACT 59.852 52.381 7.59 0.00 42.42 3.01
2348 4473 1.808411 TGGAGTGCCTTAAGAAAGCG 58.192 50.000 3.36 0.00 34.31 4.68
2391 4516 1.098712 GCCAAACCCACAACTCGTCA 61.099 55.000 0.00 0.00 0.00 4.35
2460 4585 1.016653 GGAGCTCCTCGTTGTGCTTC 61.017 60.000 26.25 0.00 35.76 3.86
2582 4707 5.046735 CGAGGATAAGGTCTCAATGGATGAT 60.047 44.000 0.00 0.00 37.44 2.45
2706 4833 4.074259 TCCAGGATGTGATGTTTGTTGAG 58.926 43.478 0.00 0.00 0.00 3.02
2835 6118 4.709397 AGTCTCTCTGTGTCATCCTTTAGG 59.291 45.833 0.00 0.00 0.00 2.69
2852 6135 5.533903 CCTTTAGGTATAGCGAAGTACTCCA 59.466 44.000 15.29 0.00 0.00 3.86
2866 6149 6.563222 AAGTACTCCATCTATAAGAGCGTC 57.437 41.667 0.00 0.00 0.00 5.19
2877 6160 8.600625 CATCTATAAGAGCGTCTAGATCACTAC 58.399 40.741 0.00 0.00 37.82 2.73
2921 6206 9.425248 TCTTATATTTCTTTACGGAGGGAGTAA 57.575 33.333 0.00 0.00 32.84 2.24
3036 6323 6.938596 ACCCTTACATTCAAGTGTAAAGTACC 59.061 38.462 1.75 0.00 42.25 3.34
3037 6324 6.938030 CCCTTACATTCAAGTGTAAAGTACCA 59.062 38.462 1.75 0.00 42.25 3.25
3038 6325 7.446013 CCCTTACATTCAAGTGTAAAGTACCAA 59.554 37.037 1.75 0.00 42.25 3.67
3043 6330 7.226720 ACATTCAAGTGTAAAGTACCAACTCTG 59.773 37.037 0.00 0.00 33.75 3.35
3053 6340 9.101655 GTAAAGTACCAACTCTGTTCACTTTTA 57.898 33.333 14.09 2.32 36.47 1.52
3058 6345 7.745620 ACCAACTCTGTTCACTTTTATAAGG 57.254 36.000 0.00 0.00 35.61 2.69
3059 6346 7.287810 ACCAACTCTGTTCACTTTTATAAGGT 58.712 34.615 0.00 0.00 35.61 3.50
3060 6347 7.228706 ACCAACTCTGTTCACTTTTATAAGGTG 59.771 37.037 11.87 11.87 35.61 4.00
3063 6350 8.154649 ACTCTGTTCACTTTTATAAGGTGTTG 57.845 34.615 15.45 8.31 35.61 3.33
3064 6351 7.773690 ACTCTGTTCACTTTTATAAGGTGTTGT 59.226 33.333 15.45 7.86 35.61 3.32
3065 6352 9.268268 CTCTGTTCACTTTTATAAGGTGTTGTA 57.732 33.333 15.45 0.80 35.61 2.41
3070 6357 9.787435 TTCACTTTTATAAGGTGTTGTAGACAT 57.213 29.630 15.45 0.00 36.37 3.06
3071 6358 9.787435 TCACTTTTATAAGGTGTTGTAGACATT 57.213 29.630 15.45 0.00 36.37 2.71
3080 6367 7.907214 AGGTGTTGTAGACATTTCAGATAAC 57.093 36.000 0.00 0.00 41.10 1.89
3081 6368 6.590292 AGGTGTTGTAGACATTTCAGATAACG 59.410 38.462 0.00 0.00 41.10 3.18
3082 6369 6.367969 GGTGTTGTAGACATTTCAGATAACGT 59.632 38.462 0.00 0.00 41.10 3.99
3083 6370 7.227461 GTGTTGTAGACATTTCAGATAACGTG 58.773 38.462 0.00 0.00 41.10 4.49
3084 6371 6.128661 TGTTGTAGACATTTCAGATAACGTGC 60.129 38.462 0.00 0.00 32.00 5.34
3085 6372 5.474825 TGTAGACATTTCAGATAACGTGCA 58.525 37.500 0.00 0.00 0.00 4.57
3086 6373 5.929415 TGTAGACATTTCAGATAACGTGCAA 59.071 36.000 0.00 0.00 0.00 4.08
3087 6374 5.940192 AGACATTTCAGATAACGTGCAAA 57.060 34.783 0.00 0.00 0.00 3.68
3088 6375 6.312399 AGACATTTCAGATAACGTGCAAAA 57.688 33.333 0.00 0.00 0.00 2.44
3089 6376 6.142817 AGACATTTCAGATAACGTGCAAAAC 58.857 36.000 0.00 0.00 0.00 2.43
3090 6377 5.826586 ACATTTCAGATAACGTGCAAAACA 58.173 33.333 0.00 0.00 0.00 2.83
3091 6378 6.269315 ACATTTCAGATAACGTGCAAAACAA 58.731 32.000 0.00 0.00 0.00 2.83
3092 6379 6.198216 ACATTTCAGATAACGTGCAAAACAAC 59.802 34.615 0.00 0.00 0.00 3.32
3093 6380 5.493133 TTCAGATAACGTGCAAAACAACT 57.507 34.783 0.00 0.00 0.00 3.16
3095 6382 4.572795 TCAGATAACGTGCAAAACAACTCA 59.427 37.500 0.00 0.00 0.00 3.41
3096 6383 5.065346 TCAGATAACGTGCAAAACAACTCAA 59.935 36.000 0.00 0.00 0.00 3.02
3098 6385 6.417635 CAGATAACGTGCAAAACAACTCAATT 59.582 34.615 0.00 0.00 0.00 2.32
3100 6387 5.448926 AACGTGCAAAACAACTCAATTTC 57.551 34.783 0.00 0.00 0.00 2.17
3102 6389 4.562394 ACGTGCAAAACAACTCAATTTCAG 59.438 37.500 0.00 0.00 0.00 3.02
3103 6390 4.562394 CGTGCAAAACAACTCAATTTCAGT 59.438 37.500 0.00 0.00 0.00 3.41
3104 6391 5.062058 CGTGCAAAACAACTCAATTTCAGTT 59.938 36.000 0.00 0.00 34.24 3.16
3119 6406 3.153676 TCAGTTGTCTGAAACGAACGA 57.846 42.857 0.14 0.00 46.17 3.85
3123 6410 3.306166 AGTTGTCTGAAACGAACGACTTG 59.694 43.478 0.14 0.00 35.13 3.16
3135 6422 4.191161 CGAACGACTTGTAAAAGTGAACG 58.809 43.478 2.08 3.44 32.22 3.95
3303 6592 4.201950 CGGAAGGAACAAGCTTCCATAATG 60.202 45.833 2.71 0.00 44.95 1.90
3321 6612 7.967854 TCCATAATGATTGCAGAAAAGTTAACG 59.032 33.333 0.00 0.00 0.00 3.18
3462 6753 1.258982 GTCAACTTGACACAGCAGACG 59.741 52.381 15.77 0.00 46.22 4.18
3574 6867 6.324512 AGACATCTATATGCATCAGGGAGATC 59.675 42.308 0.19 0.69 36.50 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 1.291132 GAACGGCTCTAGTGAATGCC 58.709 55.000 0.00 0.00 41.76 4.40
109 110 3.541831 CGACCAACGACATCCGCG 61.542 66.667 0.00 0.00 45.77 6.46
136 137 2.599659 GCCAATGCAACTTACTGCTTC 58.400 47.619 0.00 0.00 43.07 3.86
161 162 3.742640 GCACCATAGATCTTCCACCAGAC 60.743 52.174 0.00 0.00 0.00 3.51
163 164 2.486191 GGCACCATAGATCTTCCACCAG 60.486 54.545 0.00 0.00 0.00 4.00
166 167 2.486191 CCAGGCACCATAGATCTTCCAC 60.486 54.545 0.00 0.00 0.00 4.02
168 169 1.072965 CCCAGGCACCATAGATCTTCC 59.927 57.143 0.00 0.00 0.00 3.46
336 337 4.012374 GGAATTTGAAGGAGTCAGATGCA 58.988 43.478 0.00 0.00 37.61 3.96
337 338 4.268359 AGGAATTTGAAGGAGTCAGATGC 58.732 43.478 0.00 0.00 37.61 3.91
351 352 5.403466 GTGCTGCAGAAAAGTAAGGAATTTG 59.597 40.000 20.43 0.00 0.00 2.32
398 399 4.141846 TGAGCCCAAGATAATCTCAGTCAC 60.142 45.833 0.00 0.00 31.07 3.67
399 400 4.033009 TGAGCCCAAGATAATCTCAGTCA 58.967 43.478 0.00 0.00 31.07 3.41
403 404 3.393609 AGCATGAGCCCAAGATAATCTCA 59.606 43.478 0.00 0.00 43.56 3.27
458 459 0.163788 CAAGCGGCACTACAAAGACG 59.836 55.000 1.45 0.00 0.00 4.18
528 530 2.422479 CTGGGACAAGAGCACAATCATG 59.578 50.000 0.00 0.00 38.70 3.07
554 556 7.148154 CCAACATCCAAACTTCGAACCATAATA 60.148 37.037 0.00 0.00 0.00 0.98
590 592 8.004344 CGCTCCGTTTTATAGATAAATCAACAG 58.996 37.037 0.00 0.00 32.78 3.16
593 595 6.346279 CGCGCTCCGTTTTATAGATAAATCAA 60.346 38.462 5.56 0.00 32.78 2.57
742 749 1.760875 TATGTCTGACCGCCCTCCC 60.761 63.158 5.17 0.00 0.00 4.30
743 750 1.442148 GTATGTCTGACCGCCCTCC 59.558 63.158 5.17 0.00 0.00 4.30
744 751 1.065928 CGTATGTCTGACCGCCCTC 59.934 63.158 5.17 0.00 0.00 4.30
745 752 1.681327 ACGTATGTCTGACCGCCCT 60.681 57.895 5.17 0.00 0.00 5.19
746 753 1.518572 CACGTATGTCTGACCGCCC 60.519 63.158 5.17 0.00 0.00 6.13
747 754 1.076533 CACACGTATGTCTGACCGCC 61.077 60.000 5.17 0.00 36.72 6.13
748 755 0.109458 TCACACGTATGTCTGACCGC 60.109 55.000 5.17 0.00 36.72 5.68
749 756 2.341318 TTCACACGTATGTCTGACCG 57.659 50.000 5.17 4.43 36.72 4.79
750 757 4.242475 TGAATTCACACGTATGTCTGACC 58.758 43.478 3.38 0.00 36.72 4.02
751 758 5.839262 TTGAATTCACACGTATGTCTGAC 57.161 39.130 7.89 0.00 36.72 3.51
752 759 8.440059 GTTATTTGAATTCACACGTATGTCTGA 58.560 33.333 7.89 0.00 36.72 3.27
753 760 8.443160 AGTTATTTGAATTCACACGTATGTCTG 58.557 33.333 7.89 0.00 36.72 3.51
754 761 8.547967 AGTTATTTGAATTCACACGTATGTCT 57.452 30.769 7.89 0.00 36.72 3.41
755 762 9.051027 CAAGTTATTTGAATTCACACGTATGTC 57.949 33.333 7.89 0.00 39.21 3.06
756 763 7.537306 GCAAGTTATTTGAATTCACACGTATGT 59.463 33.333 7.89 0.00 39.21 2.29
757 764 7.008266 GGCAAGTTATTTGAATTCACACGTATG 59.992 37.037 7.89 4.02 39.21 2.39
758 765 7.027161 GGCAAGTTATTTGAATTCACACGTAT 58.973 34.615 7.89 0.17 39.21 3.06
759 766 6.205853 AGGCAAGTTATTTGAATTCACACGTA 59.794 34.615 7.89 0.00 39.21 3.57
760 767 5.009610 AGGCAAGTTATTTGAATTCACACGT 59.990 36.000 7.89 0.00 39.21 4.49
761 768 5.343058 CAGGCAAGTTATTTGAATTCACACG 59.657 40.000 7.89 0.00 39.21 4.49
762 769 6.446318 TCAGGCAAGTTATTTGAATTCACAC 58.554 36.000 7.89 3.08 39.21 3.82
763 770 6.647334 TCAGGCAAGTTATTTGAATTCACA 57.353 33.333 7.89 1.31 39.21 3.58
764 771 8.538409 AAATCAGGCAAGTTATTTGAATTCAC 57.462 30.769 7.89 0.00 39.21 3.18
765 772 9.558396 AAAAATCAGGCAAGTTATTTGAATTCA 57.442 25.926 3.38 3.38 39.21 2.57
798 2786 5.841783 AGGCAAGTTATTTACCCCTCAAAAA 59.158 36.000 0.00 0.00 0.00 1.94
802 2790 3.589735 TCAGGCAAGTTATTTACCCCTCA 59.410 43.478 0.00 0.00 0.00 3.86
803 2791 4.230745 TCAGGCAAGTTATTTACCCCTC 57.769 45.455 0.00 0.00 0.00 4.30
804 2792 4.536765 CATCAGGCAAGTTATTTACCCCT 58.463 43.478 0.00 0.00 0.00 4.79
805 2793 3.068165 GCATCAGGCAAGTTATTTACCCC 59.932 47.826 0.00 0.00 43.97 4.95
806 2794 4.307443 GCATCAGGCAAGTTATTTACCC 57.693 45.455 0.00 0.00 43.97 3.69
852 2968 2.463047 AAGGGCTGTGGGTACAAAAA 57.537 45.000 0.00 0.00 36.14 1.94
897 3013 2.671145 CAGCAGGACTGGTACTGGA 58.329 57.895 13.98 0.00 41.84 3.86
910 3026 1.747924 TCTCGGATGACTTCTCAGCAG 59.252 52.381 0.00 0.00 34.21 4.24
911 3027 1.839424 TCTCGGATGACTTCTCAGCA 58.161 50.000 0.00 0.00 34.21 4.41
912 3028 3.818210 TCTATCTCGGATGACTTCTCAGC 59.182 47.826 0.00 0.00 31.51 4.26
942 3058 2.706890 TGGAACTAACGGGCTTCATTC 58.293 47.619 0.00 0.00 0.00 2.67
1125 3250 1.446907 AGATGAGCTTCAGCAAACGG 58.553 50.000 0.75 0.00 45.16 4.44
1297 3422 1.809619 GCTAGGTGCAACGCGATGA 60.810 57.895 21.39 2.44 42.31 2.92
1394 3519 1.226802 CGTCCTCATCCACTCGCAG 60.227 63.158 0.00 0.00 0.00 5.18
1726 3851 4.152248 CCAGGTCTGGGATGGTGA 57.848 61.111 9.08 0.00 46.81 4.02
1817 3942 3.274288 GACCACCCTGTCATCTTTCATC 58.726 50.000 0.00 0.00 35.29 2.92
1960 4085 2.239400 ACATGGTGAGAAGTGACGAGA 58.761 47.619 0.00 0.00 0.00 4.04
1964 4089 1.993370 GCGTACATGGTGAGAAGTGAC 59.007 52.381 0.00 0.00 0.00 3.67
2032 4157 4.399303 CACTGAACTTCCTGAAGGTTTGTT 59.601 41.667 11.34 1.82 38.71 2.83
2129 4254 2.043664 TCCTGACTCTGACTCCCATTCT 59.956 50.000 0.00 0.00 0.00 2.40
2153 4278 5.183228 GTGTTCGGGATCCTTGAATCTTTA 58.817 41.667 18.67 5.63 0.00 1.85
2307 4432 1.038280 ACTTTGTCCGTCCTCTCGTT 58.962 50.000 0.00 0.00 0.00 3.85
2348 4473 3.305608 CCCATTTCTCCAAGCTTGACAAC 60.306 47.826 28.05 0.00 0.00 3.32
2381 4506 0.104304 AAAGAGCCGTGACGAGTTGT 59.896 50.000 6.54 0.00 0.00 3.32
2460 4585 1.134995 TGTGACATAGCCTGCTTCTCG 60.135 52.381 0.00 0.00 0.00 4.04
2465 4590 1.625315 TCAGTTGTGACATAGCCTGCT 59.375 47.619 0.00 0.00 0.00 4.24
2582 4707 7.117812 GTCGATTTCAACAATCTCCTAGTTTCA 59.882 37.037 0.00 0.00 0.00 2.69
2819 6102 5.009710 TCGCTATACCTAAAGGATGACACAG 59.990 44.000 2.23 0.00 38.94 3.66
2835 6118 9.381033 TCTTATAGATGGAGTACTTCGCTATAC 57.619 37.037 17.08 0.00 0.00 1.47
2852 6135 8.537016 AGTAGTGATCTAGACGCTCTTATAGAT 58.463 37.037 10.41 0.00 37.62 1.98
3036 6323 8.154649 ACACCTTATAAAAGTGAACAGAGTTG 57.845 34.615 17.79 0.00 0.00 3.16
3037 6324 8.621286 CAACACCTTATAAAAGTGAACAGAGTT 58.379 33.333 17.79 2.46 0.00 3.01
3038 6325 7.773690 ACAACACCTTATAAAAGTGAACAGAGT 59.226 33.333 17.79 7.33 0.00 3.24
3043 6330 9.048446 TGTCTACAACACCTTATAAAAGTGAAC 57.952 33.333 17.79 8.94 31.20 3.18
3058 6345 7.227461 CACGTTATCTGAAATGTCTACAACAC 58.773 38.462 0.00 0.00 41.75 3.32
3059 6346 6.128661 GCACGTTATCTGAAATGTCTACAACA 60.129 38.462 0.00 0.00 43.51 3.33
3060 6347 6.128661 TGCACGTTATCTGAAATGTCTACAAC 60.129 38.462 0.00 0.00 0.00 3.32
3063 6350 6.403333 TTGCACGTTATCTGAAATGTCTAC 57.597 37.500 0.00 0.00 0.00 2.59
3064 6351 7.041712 TGTTTTGCACGTTATCTGAAATGTCTA 60.042 33.333 0.00 0.00 0.00 2.59
3065 6352 5.940192 TTTGCACGTTATCTGAAATGTCT 57.060 34.783 0.00 0.00 0.00 3.41
3070 6357 5.885881 AGTTGTTTTGCACGTTATCTGAAA 58.114 33.333 0.00 0.00 0.00 2.69
3071 6358 5.065346 TGAGTTGTTTTGCACGTTATCTGAA 59.935 36.000 0.00 0.00 0.00 3.02
3073 6360 4.843147 TGAGTTGTTTTGCACGTTATCTG 58.157 39.130 0.00 0.00 0.00 2.90
3075 6362 6.747659 AATTGAGTTGTTTTGCACGTTATC 57.252 33.333 0.00 0.00 0.00 1.75
3078 6365 4.926238 TGAAATTGAGTTGTTTTGCACGTT 59.074 33.333 0.00 0.00 0.00 3.99
3079 6366 4.489810 TGAAATTGAGTTGTTTTGCACGT 58.510 34.783 0.00 0.00 0.00 4.49
3080 6367 4.562394 ACTGAAATTGAGTTGTTTTGCACG 59.438 37.500 0.00 0.00 0.00 5.34
3081 6368 6.242829 CAACTGAAATTGAGTTGTTTTGCAC 58.757 36.000 15.51 0.00 43.55 4.57
3082 6369 6.406093 CAACTGAAATTGAGTTGTTTTGCA 57.594 33.333 15.51 0.00 43.55 4.08
3100 6387 2.858344 AGTCGTTCGTTTCAGACAACTG 59.142 45.455 0.00 0.00 44.66 3.16
3102 6389 3.061697 ACAAGTCGTTCGTTTCAGACAAC 59.938 43.478 0.00 0.00 36.18 3.32
3103 6390 3.255725 ACAAGTCGTTCGTTTCAGACAA 58.744 40.909 0.00 0.00 36.18 3.18
3104 6391 2.883574 ACAAGTCGTTCGTTTCAGACA 58.116 42.857 0.00 0.00 36.18 3.41
3105 6392 5.379757 TTTACAAGTCGTTCGTTTCAGAC 57.620 39.130 0.00 0.00 0.00 3.51
3106 6393 5.577945 ACTTTTACAAGTCGTTCGTTTCAGA 59.422 36.000 0.00 0.00 39.15 3.27
3107 6394 5.671140 CACTTTTACAAGTCGTTCGTTTCAG 59.329 40.000 0.00 0.00 41.69 3.02
3108 6395 5.348179 TCACTTTTACAAGTCGTTCGTTTCA 59.652 36.000 0.00 0.00 41.69 2.69
3109 6396 5.788467 TCACTTTTACAAGTCGTTCGTTTC 58.212 37.500 0.00 0.00 41.69 2.78
3110 6397 5.783100 TCACTTTTACAAGTCGTTCGTTT 57.217 34.783 0.00 0.00 41.69 3.60
3111 6398 5.553721 GTTCACTTTTACAAGTCGTTCGTT 58.446 37.500 0.00 0.00 41.69 3.85
3112 6399 4.259530 CGTTCACTTTTACAAGTCGTTCGT 60.260 41.667 0.00 0.00 41.69 3.85
3113 6400 4.191161 CGTTCACTTTTACAAGTCGTTCG 58.809 43.478 0.00 0.00 41.69 3.95
3114 6401 4.268405 TCCGTTCACTTTTACAAGTCGTTC 59.732 41.667 0.00 0.00 41.69 3.95
3117 6404 3.183775 CCTCCGTTCACTTTTACAAGTCG 59.816 47.826 0.00 0.00 41.69 4.18
3119 6406 3.135167 TCCCTCCGTTCACTTTTACAAGT 59.865 43.478 0.00 0.00 44.72 3.16
3123 6410 3.397849 ACTCCCTCCGTTCACTTTTAC 57.602 47.619 0.00 0.00 0.00 2.01
3135 6422 7.939784 AATGAACAAATTTAGTACTCCCTCC 57.060 36.000 0.00 0.00 0.00 4.30
3303 6592 4.759516 TCCCGTTAACTTTTCTGCAATC 57.240 40.909 3.71 0.00 0.00 2.67
3321 6612 4.843220 AATCGAGCATGAATGATTTCCC 57.157 40.909 0.00 0.00 0.00 3.97
3461 6752 4.625742 AGATGTATCGTTTGGTCAACTTCG 59.374 41.667 0.00 0.00 32.53 3.79
3462 6753 5.637810 TCAGATGTATCGTTTGGTCAACTTC 59.362 40.000 0.00 0.00 32.53 3.01
3589 6882 0.108756 ACTAGGAAACGAGAAGCGCC 60.109 55.000 2.29 0.00 46.04 6.53
3590 6883 2.452105 CTACTAGGAAACGAGAAGCGC 58.548 52.381 0.00 0.00 46.04 5.92


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

AutoCloner maintained by Alex Coulton.