Multiple sequence alignment - TraesCS2D01G472100

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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 TraesCS2D01G472100 chr2D 100.000 3138 0 0 1 3138 575827288 575830425 0.000000e+00 5795
1 TraesCS2D01G472100 chr2A 92.792 1637 91 13 849 2480 714029899 714031513 0.000000e+00 2344
2 TraesCS2D01G472100 chr2B 91.196 1488 78 19 849 2321 692111241 692112690 0.000000e+00 1973
3 TraesCS2D01G472100 chr2B 91.989 724 41 7 1 708 421077390 421078112 0.000000e+00 1000
4 TraesCS2D01G472100 chr2B 89.632 733 53 12 2412 3123 692127060 692127790 0.000000e+00 911
5 TraesCS2D01G472100 chr2B 91.469 211 14 3 2046 2253 692126602 692126811 1.420000e-73 287
6 TraesCS2D01G472100 chr2B 86.923 130 11 2 2251 2375 692126934 692127062 1.170000e-29 141
7 TraesCS2D01G472100 chr7B 93.379 725 30 6 1 708 707963308 707964031 0.000000e+00 1057
8 TraesCS2D01G472100 chr7B 92.000 725 39 9 1 709 547267462 547266741 0.000000e+00 1000
9 TraesCS2D01G472100 chr6B 93.671 711 37 5 1 708 678533143 678533848 0.000000e+00 1057
10 TraesCS2D01G472100 chr5B 92.552 725 36 10 1 708 492107358 492108081 0.000000e+00 1024
11 TraesCS2D01G472100 chr5B 90.858 711 58 5 1 707 617670722 617670015 0.000000e+00 946
12 TraesCS2D01G472100 chr1B 92.127 724 41 7 1 709 600980402 600979680 0.000000e+00 1007
13 TraesCS2D01G472100 chr3B 91.575 724 45 8 1 709 753267537 753268259 0.000000e+00 985
14 TraesCS2D01G472100 chr4B 93.353 662 42 2 1 661 562615371 562616031 0.000000e+00 977
15 TraesCS2D01G472100 chr4A 89.271 727 48 13 1 708 673441731 673441016 0.000000e+00 883


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 TraesCS2D01G472100 chr2D 575827288 575830425 3137 False 5795.000000 5795 100.000000 1 3138 1 chr2D.!!$F1 3137
1 TraesCS2D01G472100 chr2A 714029899 714031513 1614 False 2344.000000 2344 92.792000 849 2480 1 chr2A.!!$F1 1631
2 TraesCS2D01G472100 chr2B 692111241 692112690 1449 False 1973.000000 1973 91.196000 849 2321 1 chr2B.!!$F2 1472
3 TraesCS2D01G472100 chr2B 421077390 421078112 722 False 1000.000000 1000 91.989000 1 708 1 chr2B.!!$F1 707
4 TraesCS2D01G472100 chr2B 692126602 692127790 1188 False 446.333333 911 89.341333 2046 3123 3 chr2B.!!$F3 1077
5 TraesCS2D01G472100 chr7B 707963308 707964031 723 False 1057.000000 1057 93.379000 1 708 1 chr7B.!!$F1 707
6 TraesCS2D01G472100 chr7B 547266741 547267462 721 True 1000.000000 1000 92.000000 1 709 1 chr7B.!!$R1 708
7 TraesCS2D01G472100 chr6B 678533143 678533848 705 False 1057.000000 1057 93.671000 1 708 1 chr6B.!!$F1 707
8 TraesCS2D01G472100 chr5B 492107358 492108081 723 False 1024.000000 1024 92.552000 1 708 1 chr5B.!!$F1 707
9 TraesCS2D01G472100 chr5B 617670015 617670722 707 True 946.000000 946 90.858000 1 707 1 chr5B.!!$R1 706
10 TraesCS2D01G472100 chr1B 600979680 600980402 722 True 1007.000000 1007 92.127000 1 709 1 chr1B.!!$R1 708
11 TraesCS2D01G472100 chr3B 753267537 753268259 722 False 985.000000 985 91.575000 1 709 1 chr3B.!!$F1 708
12 TraesCS2D01G472100 chr4B 562615371 562616031 660 False 977.000000 977 93.353000 1 661 1 chr4B.!!$F1 660
13 TraesCS2D01G472100 chr4A 673441016 673441731 715 True 883.000000 883 89.271000 1 708 1 chr4A.!!$R1 707

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
490 500 0.108585 CCCCAACCATAGGACCGATG 59.891 60.0 7.58 7.58 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2588 0.250727 ATGTTCCACACCTTCCCGTG 60.251 55.0 0.0 0.0 39.75 4.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.067295 TCACTTGCCTCTGGAACCAT 58.933 50.000 0.00 0.00 0.00 3.55
97 104 3.417275 CTCGAAGCGGCTCCATCGT 62.417 63.158 18.68 0.00 36.70 3.73
121 128 3.793144 GCAGCTTTGCGGACCTCG 61.793 66.667 0.00 0.00 42.76 4.63
210 218 2.625790 GCCATCGAACTCTAGATCTGGT 59.374 50.000 5.18 0.00 0.00 4.00
217 225 3.887916 ACTCTAGATCTGGTACCCCTC 57.112 52.381 10.07 3.37 0.00 4.30
264 273 0.677731 CACACCTGCCATCCACGAAT 60.678 55.000 0.00 0.00 0.00 3.34
490 500 0.108585 CCCCAACCATAGGACCGATG 59.891 60.000 7.58 7.58 0.00 3.84
509 519 0.250640 GGCCTCGTCGGAGTAGGATA 60.251 60.000 9.25 0.00 38.70 2.59
679 741 4.699522 GGCGGCGTGGGAAACTCT 62.700 66.667 9.37 0.00 0.00 3.24
709 771 3.756117 AGGTCGCCTTTTCTTTCTTCAT 58.244 40.909 0.00 0.00 0.00 2.57
710 772 3.753797 AGGTCGCCTTTTCTTTCTTCATC 59.246 43.478 0.00 0.00 0.00 2.92
711 773 3.502211 GGTCGCCTTTTCTTTCTTCATCA 59.498 43.478 0.00 0.00 0.00 3.07
712 774 4.023193 GGTCGCCTTTTCTTTCTTCATCAA 60.023 41.667 0.00 0.00 0.00 2.57
713 775 4.912187 GTCGCCTTTTCTTTCTTCATCAAC 59.088 41.667 0.00 0.00 0.00 3.18
714 776 4.821805 TCGCCTTTTCTTTCTTCATCAACT 59.178 37.500 0.00 0.00 0.00 3.16
715 777 5.299279 TCGCCTTTTCTTTCTTCATCAACTT 59.701 36.000 0.00 0.00 0.00 2.66
716 778 6.485313 TCGCCTTTTCTTTCTTCATCAACTTA 59.515 34.615 0.00 0.00 0.00 2.24
717 779 7.012894 TCGCCTTTTCTTTCTTCATCAACTTAA 59.987 33.333 0.00 0.00 0.00 1.85
718 780 7.324616 CGCCTTTTCTTTCTTCATCAACTTAAG 59.675 37.037 0.00 0.00 0.00 1.85
719 781 7.115520 GCCTTTTCTTTCTTCATCAACTTAAGC 59.884 37.037 1.29 0.00 0.00 3.09
720 782 8.355913 CCTTTTCTTTCTTCATCAACTTAAGCT 58.644 33.333 1.29 0.00 0.00 3.74
723 785 8.902540 TTCTTTCTTCATCAACTTAAGCTACA 57.097 30.769 1.29 0.00 0.00 2.74
724 786 8.539770 TCTTTCTTCATCAACTTAAGCTACAG 57.460 34.615 1.29 0.00 0.00 2.74
725 787 7.604164 TCTTTCTTCATCAACTTAAGCTACAGG 59.396 37.037 1.29 0.00 0.00 4.00
726 788 6.360370 TCTTCATCAACTTAAGCTACAGGT 57.640 37.500 1.29 0.00 0.00 4.00
727 789 6.398918 TCTTCATCAACTTAAGCTACAGGTC 58.601 40.000 1.29 0.00 0.00 3.85
728 790 6.211584 TCTTCATCAACTTAAGCTACAGGTCT 59.788 38.462 1.29 0.00 0.00 3.85
729 791 7.396339 TCTTCATCAACTTAAGCTACAGGTCTA 59.604 37.037 1.29 0.00 0.00 2.59
730 792 6.864342 TCATCAACTTAAGCTACAGGTCTAC 58.136 40.000 1.29 0.00 0.00 2.59
731 793 6.663953 TCATCAACTTAAGCTACAGGTCTACT 59.336 38.462 1.29 0.00 0.00 2.57
732 794 6.512342 TCAACTTAAGCTACAGGTCTACTC 57.488 41.667 1.29 0.00 0.00 2.59
733 795 6.008331 TCAACTTAAGCTACAGGTCTACTCA 58.992 40.000 1.29 0.00 0.00 3.41
734 796 6.492429 TCAACTTAAGCTACAGGTCTACTCAA 59.508 38.462 1.29 0.00 0.00 3.02
735 797 6.912951 ACTTAAGCTACAGGTCTACTCAAA 57.087 37.500 1.29 0.00 0.00 2.69
736 798 6.689554 ACTTAAGCTACAGGTCTACTCAAAC 58.310 40.000 1.29 0.00 0.00 2.93
737 799 6.267014 ACTTAAGCTACAGGTCTACTCAAACA 59.733 38.462 1.29 0.00 0.00 2.83
738 800 5.546621 AAGCTACAGGTCTACTCAAACAA 57.453 39.130 0.00 0.00 0.00 2.83
739 801 5.140747 AGCTACAGGTCTACTCAAACAAG 57.859 43.478 0.00 0.00 0.00 3.16
740 802 4.589374 AGCTACAGGTCTACTCAAACAAGT 59.411 41.667 0.00 0.00 0.00 3.16
741 803 4.924462 GCTACAGGTCTACTCAAACAAGTC 59.076 45.833 0.00 0.00 0.00 3.01
742 804 5.509163 GCTACAGGTCTACTCAAACAAGTCA 60.509 44.000 0.00 0.00 0.00 3.41
743 805 4.950050 ACAGGTCTACTCAAACAAGTCAG 58.050 43.478 0.00 0.00 0.00 3.51
744 806 4.202264 ACAGGTCTACTCAAACAAGTCAGG 60.202 45.833 0.00 0.00 0.00 3.86
745 807 3.967987 AGGTCTACTCAAACAAGTCAGGT 59.032 43.478 0.00 0.00 0.00 4.00
746 808 5.010719 CAGGTCTACTCAAACAAGTCAGGTA 59.989 44.000 0.00 0.00 0.00 3.08
747 809 5.010820 AGGTCTACTCAAACAAGTCAGGTAC 59.989 44.000 0.00 0.00 0.00 3.34
748 810 5.010820 GGTCTACTCAAACAAGTCAGGTACT 59.989 44.000 0.00 0.00 41.49 2.73
749 811 6.208204 GGTCTACTCAAACAAGTCAGGTACTA 59.792 42.308 0.00 0.00 37.50 1.82
750 812 7.255730 GGTCTACTCAAACAAGTCAGGTACTAA 60.256 40.741 0.00 0.00 37.50 2.24
751 813 8.139989 GTCTACTCAAACAAGTCAGGTACTAAA 58.860 37.037 0.00 0.00 37.50 1.85
752 814 8.867097 TCTACTCAAACAAGTCAGGTACTAAAT 58.133 33.333 0.00 0.00 37.50 1.40
755 817 9.841295 ACTCAAACAAGTCAGGTACTAAATAAA 57.159 29.630 0.00 0.00 37.50 1.40
757 819 9.841295 TCAAACAAGTCAGGTACTAAATAAAGT 57.159 29.630 0.00 0.00 37.50 2.66
789 851 4.139183 GGTACGTACGAGCTATAACTGG 57.861 50.000 24.41 0.00 0.00 4.00
790 852 3.561725 GGTACGTACGAGCTATAACTGGT 59.438 47.826 24.41 0.00 32.92 4.00
791 853 3.687572 ACGTACGAGCTATAACTGGTG 57.312 47.619 24.41 0.00 30.66 4.17
792 854 3.012518 ACGTACGAGCTATAACTGGTGT 58.987 45.455 24.41 0.00 30.66 4.16
793 855 4.191544 ACGTACGAGCTATAACTGGTGTA 58.808 43.478 24.41 0.00 30.66 2.90
794 856 4.818546 ACGTACGAGCTATAACTGGTGTAT 59.181 41.667 24.41 0.00 30.66 2.29
795 857 5.145059 CGTACGAGCTATAACTGGTGTATG 58.855 45.833 10.44 0.00 30.66 2.39
796 858 5.277683 CGTACGAGCTATAACTGGTGTATGT 60.278 44.000 10.44 0.00 30.66 2.29
797 859 6.073602 CGTACGAGCTATAACTGGTGTATGTA 60.074 42.308 10.44 0.00 30.66 2.29
798 860 6.896021 ACGAGCTATAACTGGTGTATGTAT 57.104 37.500 0.00 0.00 0.00 2.29
799 861 7.286215 ACGAGCTATAACTGGTGTATGTATT 57.714 36.000 0.00 0.00 0.00 1.89
800 862 7.723324 ACGAGCTATAACTGGTGTATGTATTT 58.277 34.615 0.00 0.00 0.00 1.40
801 863 8.202137 ACGAGCTATAACTGGTGTATGTATTTT 58.798 33.333 0.00 0.00 0.00 1.82
802 864 9.687210 CGAGCTATAACTGGTGTATGTATTTTA 57.313 33.333 0.00 0.00 0.00 1.52
824 886 9.624697 TTTTATTTTCAAATGGATTCTGTCTCG 57.375 29.630 0.00 0.00 0.00 4.04
825 887 8.560355 TTATTTTCAAATGGATTCTGTCTCGA 57.440 30.769 0.00 0.00 0.00 4.04
826 888 5.862924 TTTCAAATGGATTCTGTCTCGAC 57.137 39.130 0.00 0.00 0.00 4.20
827 889 4.808414 TCAAATGGATTCTGTCTCGACT 57.192 40.909 0.00 0.00 0.00 4.18
828 890 4.748892 TCAAATGGATTCTGTCTCGACTC 58.251 43.478 0.00 0.00 0.00 3.36
829 891 4.220602 TCAAATGGATTCTGTCTCGACTCA 59.779 41.667 0.00 0.00 0.00 3.41
830 892 4.808414 AATGGATTCTGTCTCGACTCAA 57.192 40.909 0.00 0.00 0.00 3.02
831 893 4.808414 ATGGATTCTGTCTCGACTCAAA 57.192 40.909 0.00 0.00 0.00 2.69
832 894 4.600692 TGGATTCTGTCTCGACTCAAAA 57.399 40.909 0.00 0.00 0.00 2.44
833 895 4.956085 TGGATTCTGTCTCGACTCAAAAA 58.044 39.130 0.00 0.00 0.00 1.94
941 1007 2.292569 CGGATGCATGGAAATCTCCTTG 59.707 50.000 2.46 0.00 45.57 3.61
942 1008 2.626743 GGATGCATGGAAATCTCCTTGG 59.373 50.000 2.46 0.00 43.85 3.61
954 1020 6.579243 GGAAATCTCCTTGGTAGTTCCAGATT 60.579 42.308 14.30 5.78 38.65 2.40
1093 1164 1.437772 GAACGCCGATCTCTCCTCGA 61.438 60.000 0.00 0.00 38.38 4.04
1110 1181 4.430765 ACGAAGCGGTACCTGCGG 62.431 66.667 18.63 15.08 38.21 5.69
1299 1370 4.286320 GGATCGCCGGTGCTCGAT 62.286 66.667 11.05 12.50 46.62 3.59
1494 1568 1.430632 GATGCACAACCTGATGGCG 59.569 57.895 0.00 0.00 36.63 5.69
1509 1583 3.561429 GCGATGTGCGAGTGGAAA 58.439 55.556 0.00 0.00 44.57 3.13
1702 1776 8.880750 GCAATTTCTCCCTTATTATATACCGTC 58.119 37.037 0.00 0.00 0.00 4.79
1703 1777 9.379791 CAATTTCTCCCTTATTATATACCGTCC 57.620 37.037 0.00 0.00 0.00 4.79
1704 1778 6.764308 TTCTCCCTTATTATATACCGTCCG 57.236 41.667 0.00 0.00 0.00 4.79
1705 1779 5.819991 TCTCCCTTATTATATACCGTCCGT 58.180 41.667 0.00 0.00 0.00 4.69
1716 1790 0.947180 ACCGTCCGTGTTTGATTCCG 60.947 55.000 0.00 0.00 0.00 4.30
1786 1860 0.796312 TGTTTCCTTTGCTCGCGATC 59.204 50.000 10.36 6.00 0.00 3.69
1787 1861 0.247301 GTTTCCTTTGCTCGCGATCG 60.247 55.000 10.36 11.69 0.00 3.69
1788 1862 0.389296 TTTCCTTTGCTCGCGATCGA 60.389 50.000 21.57 1.26 43.28 3.59
1813 1887 1.679311 GATGCAGGTGACAGGGACA 59.321 57.895 0.00 0.00 0.00 4.02
1884 1958 1.755393 AAGGCGACCTCGTTGTTCCT 61.755 55.000 0.00 0.00 42.22 3.36
1958 2032 2.111972 TGGGGCCTTCTCCTATACCTAG 59.888 54.545 0.84 0.00 0.00 3.02
1964 2038 4.027437 CCTTCTCCTATACCTAGCCATCC 58.973 52.174 0.00 0.00 0.00 3.51
2024 2098 0.318762 AGACTCTTGGCTCGACAACC 59.681 55.000 0.00 0.00 0.00 3.77
2071 2145 2.107953 GTCTCCTGGATCTGCCGC 59.892 66.667 0.00 0.00 40.66 6.53
2128 2202 0.749454 AATCCGCATGGCTCAACTCC 60.749 55.000 0.00 0.00 34.14 3.85
2141 2217 6.166279 TGGCTCAACTCCGATATATGATTTC 58.834 40.000 0.00 0.00 0.00 2.17
2143 2219 6.820656 GGCTCAACTCCGATATATGATTTCAT 59.179 38.462 0.00 0.00 40.22 2.57
2196 2278 0.661187 TTCGTTCGTCCCTTCGTTCG 60.661 55.000 0.00 0.00 0.00 3.95
2241 2323 1.457346 CATCAAGGAGGTTGGAGTGC 58.543 55.000 0.00 0.00 36.71 4.40
2286 2498 5.400066 TGATTTAGGGCAAGTTTTTAGGC 57.600 39.130 0.00 0.00 0.00 3.93
2364 2576 2.985282 CGCTGTTGTGGTGCCCAT 60.985 61.111 0.00 0.00 35.28 4.00
2376 2588 1.351350 GGTGCCCATAGAACCCTATCC 59.649 57.143 0.00 0.00 33.47 2.59
2382 2594 2.605257 CATAGAACCCTATCCACGGGA 58.395 52.381 1.44 0.00 44.90 5.14
2388 2600 0.981277 CCCTATCCACGGGAAGGTGT 60.981 60.000 14.17 0.00 44.90 4.16
2393 2605 4.058797 CACGGGAAGGTGTGGAAC 57.941 61.111 0.00 0.00 33.24 3.62
2405 2617 0.174845 TGTGGAACATCGATCGACCC 59.825 55.000 22.06 18.38 45.67 4.46
2437 2649 2.741092 GCGTTGTCTCCTCCCACA 59.259 61.111 0.00 0.00 0.00 4.17
2482 2694 1.360931 CGCTGACATCGACATTGGCA 61.361 55.000 0.00 0.00 0.00 4.92
2498 2710 2.499205 CAAGTGATAGGCGCCGGA 59.501 61.111 23.20 14.39 0.00 5.14
2518 2730 2.981350 GCCGGCCCAAACTTTCGA 60.981 61.111 18.11 0.00 0.00 3.71
2522 2734 1.852067 CGGCCCAAACTTTCGACCAG 61.852 60.000 0.00 0.00 0.00 4.00
2525 2737 1.961793 CCCAAACTTTCGACCAGTCA 58.038 50.000 0.00 0.00 0.00 3.41
2590 2803 2.740256 GCGTCATCTTCCTCTCTTTCCC 60.740 54.545 0.00 0.00 0.00 3.97
2605 2818 4.974399 TCTTTCCCTGTCTTCCTTCTTTC 58.026 43.478 0.00 0.00 0.00 2.62
2625 2838 0.393077 CCCCGAACGCTATTGATCCT 59.607 55.000 0.00 0.00 0.00 3.24
2637 2850 5.251764 GCTATTGATCCTTGCTATGGATGT 58.748 41.667 9.73 1.17 43.68 3.06
2657 2870 4.373116 GACCTCGAAGCACCGCCA 62.373 66.667 0.00 0.00 0.00 5.69
2743 2957 0.108520 CCCCATGCAGCAAATCACAC 60.109 55.000 0.00 0.00 0.00 3.82
2807 3039 4.954970 CCACCTGCTGGGCACGTT 62.955 66.667 14.82 0.00 39.10 3.99
2820 3052 2.661866 ACGTTGTCGCAGCTCCAC 60.662 61.111 0.00 0.00 41.18 4.02
2829 3061 2.662596 CAGCTCCACCCGTTGCTA 59.337 61.111 0.00 0.00 34.10 3.49
2830 3062 1.448540 CAGCTCCACCCGTTGCTAG 60.449 63.158 0.00 0.00 34.10 3.42
2837 3069 1.599797 ACCCGTTGCTAGTGGTTGC 60.600 57.895 0.00 0.00 0.00 4.17
2840 3072 1.207593 CGTTGCTAGTGGTTGCAGC 59.792 57.895 0.00 0.00 40.46 5.25
2869 3101 2.494445 CATCGTAGCTCGCCACCA 59.506 61.111 0.00 0.00 39.67 4.17
2872 3104 2.407846 ATCGTAGCTCGCCACCATCG 62.408 60.000 0.00 0.00 39.67 3.84
2873 3105 2.494918 GTAGCTCGCCACCATCGT 59.505 61.111 0.00 0.00 0.00 3.73
2875 3107 2.049767 TAGCTCGCCACCATCGTCA 61.050 57.895 0.00 0.00 0.00 4.35
2880 3112 0.533085 TCGCCACCATCGTCAAACAA 60.533 50.000 0.00 0.00 0.00 2.83
2919 3151 1.738099 CTCTGGTCGCCGGTTGAAG 60.738 63.158 1.90 0.00 0.00 3.02
2920 3152 2.742372 CTGGTCGCCGGTTGAAGG 60.742 66.667 1.90 0.00 0.00 3.46
2926 3158 0.664224 TCGCCGGTTGAAGGTTTTTC 59.336 50.000 1.90 0.00 0.00 2.29
2936 3168 6.549061 GGTTGAAGGTTTTTCCATATACGAC 58.451 40.000 0.00 0.00 39.02 4.34
2938 3170 6.978343 TGAAGGTTTTTCCATATACGACTG 57.022 37.500 0.00 0.00 39.02 3.51
2974 3206 2.422832 ACGGTTGCAACTTTTTCGGTTA 59.577 40.909 27.64 0.00 0.00 2.85
2975 3207 3.067040 ACGGTTGCAACTTTTTCGGTTAT 59.933 39.130 27.64 5.08 0.00 1.89
2976 3208 3.423867 CGGTTGCAACTTTTTCGGTTATG 59.576 43.478 27.64 0.00 0.00 1.90
2977 3209 4.364860 GGTTGCAACTTTTTCGGTTATGT 58.635 39.130 27.64 0.00 0.00 2.29
3015 3247 1.403814 TCTCTATCGCTGGTTGGAGG 58.596 55.000 0.00 0.00 0.00 4.30
3020 3253 1.247567 ATCGCTGGTTGGAGGTTTTG 58.752 50.000 0.00 0.00 0.00 2.44
3049 3282 4.396790 ACGGTCAAAGCTTTTCTGTAAACA 59.603 37.500 18.38 0.00 0.00 2.83
3065 3298 2.602257 AACAGTTGCAGCTTTTTCCC 57.398 45.000 0.00 0.00 0.00 3.97
3096 3329 3.049912 CAGCGCCTGGTTAAAAACTTTC 58.950 45.455 2.29 0.00 0.00 2.62
3098 3331 3.004419 AGCGCCTGGTTAAAAACTTTCTC 59.996 43.478 2.29 0.00 0.00 2.87
3100 3333 4.214758 GCGCCTGGTTAAAAACTTTCTCTA 59.785 41.667 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.650281 TTCCTTTGATGGCTGCTATGA 57.350 42.857 2.27 0.00 0.00 2.15
210 218 2.440409 GTCTTAGTCGTGTGAGGGGTA 58.560 52.381 0.00 0.00 0.00 3.69
217 225 1.800315 CCGGCGTCTTAGTCGTGTG 60.800 63.158 6.01 0.00 37.56 3.82
264 273 2.094757 ATCGTGTGCTGGGTTCGTGA 62.095 55.000 0.00 0.00 0.00 4.35
404 414 1.873270 CGACATCCTCGTGGTGGACA 61.873 60.000 2.99 0.00 37.64 4.02
490 500 0.250640 TATCCTACTCCGACGAGGCC 60.251 60.000 0.00 0.00 40.77 5.19
509 519 4.437390 CGGCGCTGAATAAAGTTTCTTCAT 60.437 41.667 11.90 0.00 0.00 2.57
584 595 4.925054 CGTGTGGATCGGTTTTTACTCTAA 59.075 41.667 0.00 0.00 0.00 2.10
709 771 6.008331 TGAGTAGACCTGTAGCTTAAGTTGA 58.992 40.000 4.02 0.00 0.00 3.18
710 772 6.268825 TGAGTAGACCTGTAGCTTAAGTTG 57.731 41.667 4.02 0.00 0.00 3.16
711 773 6.912951 TTGAGTAGACCTGTAGCTTAAGTT 57.087 37.500 4.02 0.00 0.00 2.66
712 774 6.267014 TGTTTGAGTAGACCTGTAGCTTAAGT 59.733 38.462 4.02 0.00 0.00 2.24
713 775 6.688578 TGTTTGAGTAGACCTGTAGCTTAAG 58.311 40.000 0.00 0.00 0.00 1.85
714 776 6.659745 TGTTTGAGTAGACCTGTAGCTTAA 57.340 37.500 0.00 0.00 0.00 1.85
715 777 6.267014 ACTTGTTTGAGTAGACCTGTAGCTTA 59.733 38.462 0.00 0.00 0.00 3.09
716 778 5.070580 ACTTGTTTGAGTAGACCTGTAGCTT 59.929 40.000 0.00 0.00 0.00 3.74
717 779 4.589374 ACTTGTTTGAGTAGACCTGTAGCT 59.411 41.667 0.00 0.00 0.00 3.32
718 780 4.884247 ACTTGTTTGAGTAGACCTGTAGC 58.116 43.478 0.00 0.00 0.00 3.58
719 781 6.085555 TGACTTGTTTGAGTAGACCTGTAG 57.914 41.667 0.00 0.00 0.00 2.74
720 782 5.010719 CCTGACTTGTTTGAGTAGACCTGTA 59.989 44.000 0.00 0.00 0.00 2.74
721 783 4.202264 CCTGACTTGTTTGAGTAGACCTGT 60.202 45.833 0.00 0.00 0.00 4.00
722 784 4.202264 ACCTGACTTGTTTGAGTAGACCTG 60.202 45.833 0.00 0.00 0.00 4.00
723 785 3.967987 ACCTGACTTGTTTGAGTAGACCT 59.032 43.478 0.00 0.00 0.00 3.85
724 786 4.338379 ACCTGACTTGTTTGAGTAGACC 57.662 45.455 0.00 0.00 0.00 3.85
725 787 6.086785 AGTACCTGACTTGTTTGAGTAGAC 57.913 41.667 0.00 0.00 33.13 2.59
726 788 7.828508 TTAGTACCTGACTTGTTTGAGTAGA 57.171 36.000 0.00 0.00 39.81 2.59
729 791 9.841295 TTTATTTAGTACCTGACTTGTTTGAGT 57.159 29.630 0.00 0.00 39.81 3.41
731 793 9.841295 ACTTTATTTAGTACCTGACTTGTTTGA 57.159 29.630 0.00 0.00 39.81 2.69
752 814 9.681692 TCGTACGTACCGTATATAAGTACTTTA 57.318 33.333 19.67 6.70 44.12 1.85
753 815 8.583810 TCGTACGTACCGTATATAAGTACTTT 57.416 34.615 19.67 4.61 44.12 2.66
754 816 7.148787 GCTCGTACGTACCGTATATAAGTACTT 60.149 40.741 19.67 13.68 44.12 2.24
755 817 6.308282 GCTCGTACGTACCGTATATAAGTACT 59.692 42.308 19.67 0.00 44.12 2.73
756 818 6.308282 AGCTCGTACGTACCGTATATAAGTAC 59.692 42.308 19.67 11.70 44.12 2.73
757 819 6.387465 AGCTCGTACGTACCGTATATAAGTA 58.613 40.000 19.67 0.00 44.12 2.24
758 820 5.230942 AGCTCGTACGTACCGTATATAAGT 58.769 41.667 19.67 0.00 44.12 2.24
759 821 5.769967 AGCTCGTACGTACCGTATATAAG 57.230 43.478 19.67 8.24 44.12 1.73
760 822 8.804743 GTTATAGCTCGTACGTACCGTATATAA 58.195 37.037 19.67 17.56 44.12 0.98
761 823 8.188799 AGTTATAGCTCGTACGTACCGTATATA 58.811 37.037 19.67 13.53 44.12 0.86
762 824 7.009631 CAGTTATAGCTCGTACGTACCGTATAT 59.990 40.741 19.67 14.38 44.12 0.86
763 825 6.308041 CAGTTATAGCTCGTACGTACCGTATA 59.692 42.308 19.67 11.91 44.12 1.47
764 826 5.119279 CAGTTATAGCTCGTACGTACCGTAT 59.881 44.000 19.67 12.77 44.12 3.06
765 827 4.444388 CAGTTATAGCTCGTACGTACCGTA 59.556 45.833 19.67 6.77 41.54 4.02
766 828 3.246226 CAGTTATAGCTCGTACGTACCGT 59.754 47.826 19.67 4.77 44.35 4.83
767 829 3.363378 CCAGTTATAGCTCGTACGTACCG 60.363 52.174 19.67 14.34 0.00 4.02
768 830 3.561725 ACCAGTTATAGCTCGTACGTACC 59.438 47.826 19.67 6.26 0.00 3.34
769 831 4.034510 ACACCAGTTATAGCTCGTACGTAC 59.965 45.833 15.90 15.90 0.00 3.67
770 832 4.191544 ACACCAGTTATAGCTCGTACGTA 58.808 43.478 16.05 0.32 0.00 3.57
771 833 3.012518 ACACCAGTTATAGCTCGTACGT 58.987 45.455 16.05 0.00 0.00 3.57
772 834 3.687572 ACACCAGTTATAGCTCGTACG 57.312 47.619 9.53 9.53 0.00 3.67
773 835 6.069684 ACATACACCAGTTATAGCTCGTAC 57.930 41.667 0.00 0.00 0.00 3.67
774 836 7.991084 ATACATACACCAGTTATAGCTCGTA 57.009 36.000 0.00 0.00 0.00 3.43
775 837 6.896021 ATACATACACCAGTTATAGCTCGT 57.104 37.500 0.00 0.00 0.00 4.18
776 838 8.589335 AAAATACATACACCAGTTATAGCTCG 57.411 34.615 0.00 0.00 0.00 5.03
798 860 9.624697 CGAGACAGAATCCATTTGAAAATAAAA 57.375 29.630 0.00 0.00 0.00 1.52
799 861 9.008965 TCGAGACAGAATCCATTTGAAAATAAA 57.991 29.630 0.00 0.00 0.00 1.40
800 862 8.450964 GTCGAGACAGAATCCATTTGAAAATAA 58.549 33.333 0.00 0.00 0.00 1.40
801 863 7.824289 AGTCGAGACAGAATCCATTTGAAAATA 59.176 33.333 5.99 0.00 0.00 1.40
802 864 6.656693 AGTCGAGACAGAATCCATTTGAAAAT 59.343 34.615 5.99 0.00 0.00 1.82
803 865 5.997746 AGTCGAGACAGAATCCATTTGAAAA 59.002 36.000 5.99 0.00 0.00 2.29
804 866 5.551233 AGTCGAGACAGAATCCATTTGAAA 58.449 37.500 5.99 0.00 0.00 2.69
805 867 5.152623 AGTCGAGACAGAATCCATTTGAA 57.847 39.130 5.99 0.00 0.00 2.69
806 868 4.220602 TGAGTCGAGACAGAATCCATTTGA 59.779 41.667 5.99 0.00 34.68 2.69
807 869 4.498241 TGAGTCGAGACAGAATCCATTTG 58.502 43.478 5.99 0.00 34.68 2.32
808 870 4.808414 TGAGTCGAGACAGAATCCATTT 57.192 40.909 5.99 0.00 34.68 2.32
809 871 4.808414 TTGAGTCGAGACAGAATCCATT 57.192 40.909 5.99 0.00 34.68 3.16
810 872 4.808414 TTTGAGTCGAGACAGAATCCAT 57.192 40.909 5.99 0.00 34.68 3.41
811 873 4.600692 TTTTGAGTCGAGACAGAATCCA 57.399 40.909 5.99 0.00 34.68 3.41
840 902 9.614792 ACTACAAGTAGACAAAGACAGATTTTT 57.385 29.630 13.79 0.00 36.97 1.94
842 904 9.694137 GTACTACAAGTAGACAAAGACAGATTT 57.306 33.333 13.79 0.00 36.97 2.17
843 905 8.857098 TGTACTACAAGTAGACAAAGACAGATT 58.143 33.333 13.79 0.00 36.97 2.40
844 906 8.405418 TGTACTACAAGTAGACAAAGACAGAT 57.595 34.615 13.79 0.00 36.97 2.90
845 907 7.812690 TGTACTACAAGTAGACAAAGACAGA 57.187 36.000 13.79 0.00 36.97 3.41
862 924 8.228464 GCATGGTTTACTTTCTTCTTGTACTAC 58.772 37.037 0.00 0.00 0.00 2.73
863 925 7.934665 TGCATGGTTTACTTTCTTCTTGTACTA 59.065 33.333 0.00 0.00 0.00 1.82
864 926 6.770785 TGCATGGTTTACTTTCTTCTTGTACT 59.229 34.615 0.00 0.00 0.00 2.73
906 972 5.363101 CATGCATCCGCTGTTATATATCCT 58.637 41.667 0.00 0.00 39.64 3.24
941 1007 3.621715 CGGCTACAAAATCTGGAACTACC 59.378 47.826 0.00 0.00 39.54 3.18
942 1008 4.501071 TCGGCTACAAAATCTGGAACTAC 58.499 43.478 0.00 0.00 0.00 2.73
954 1020 1.331138 CGTTGGTGTTTCGGCTACAAA 59.669 47.619 0.00 0.00 0.00 2.83
1110 1181 1.673665 CAGCCTCAGCCACTTCCAC 60.674 63.158 0.00 0.00 41.25 4.02
1316 1387 1.145819 GAGGTCTCCTGCATCTGGC 59.854 63.158 0.00 0.00 45.13 4.85
1317 1388 1.828768 GGAGGTCTCCTGCATCTGG 59.171 63.158 9.64 0.00 46.16 3.86
1494 1568 1.195448 CACAGTTTCCACTCGCACATC 59.805 52.381 0.00 0.00 0.00 3.06
1671 1745 1.750193 TAAGGGAGAAATTGCTGGCG 58.250 50.000 0.00 0.00 0.00 5.69
1702 1776 3.498082 GGAAATTCGGAATCAAACACGG 58.502 45.455 3.28 0.00 0.00 4.94
1703 1777 3.120477 TCGGAAATTCGGAATCAAACACG 60.120 43.478 3.28 4.25 0.00 4.49
1704 1778 4.413495 TCGGAAATTCGGAATCAAACAC 57.587 40.909 3.28 0.00 0.00 3.32
1705 1779 6.036735 GTCTATCGGAAATTCGGAATCAAACA 59.963 38.462 7.32 0.00 29.49 2.83
1716 1790 2.662156 GCGATCGGTCTATCGGAAATTC 59.338 50.000 18.30 0.00 46.89 2.17
1787 1861 1.269257 TGTCACCTGCATCGATCGATC 60.269 52.381 27.20 20.56 31.62 3.69
1788 1862 0.746659 TGTCACCTGCATCGATCGAT 59.253 50.000 24.60 24.60 34.81 3.59
1794 1868 1.448540 GTCCCTGTCACCTGCATCG 60.449 63.158 0.00 0.00 0.00 3.84
1884 1958 2.268920 GGCTGTTCCTCGCATGGA 59.731 61.111 0.00 0.00 0.00 3.41
1964 2038 2.868583 CCTCTATGACGTGCTCCATTTG 59.131 50.000 0.00 0.00 0.00 2.32
1976 2050 4.156477 AGTTGGATAGCCTCCTCTATGAC 58.844 47.826 0.00 0.00 45.21 3.06
2128 2202 7.120285 AGCTGGGTCAAATGAAATCATATATCG 59.880 37.037 0.00 0.00 35.10 2.92
2141 2217 1.404391 GCAGATGAGCTGGGTCAAATG 59.596 52.381 0.00 9.19 45.03 2.32
2143 2219 0.694771 AGCAGATGAGCTGGGTCAAA 59.305 50.000 0.00 0.00 44.66 2.69
2196 2278 1.239296 TGCATGCTGAGTTGTGCTCC 61.239 55.000 20.33 0.00 43.48 4.70
2376 2588 0.250727 ATGTTCCACACCTTCCCGTG 60.251 55.000 0.00 0.00 39.75 4.94
2382 2594 1.548719 TCGATCGATGTTCCACACCTT 59.451 47.619 15.15 0.00 0.00 3.50
2388 2600 0.899019 TTGGGTCGATCGATGTTCCA 59.101 50.000 22.50 21.28 0.00 3.53
2391 2603 3.053831 AGTTTTGGGTCGATCGATGTT 57.946 42.857 22.50 0.00 0.00 2.71
2392 2604 2.762535 AGTTTTGGGTCGATCGATGT 57.237 45.000 22.50 0.00 0.00 3.06
2393 2605 3.059597 GCATAGTTTTGGGTCGATCGATG 60.060 47.826 22.50 12.04 0.00 3.84
2394 2606 3.131396 GCATAGTTTTGGGTCGATCGAT 58.869 45.455 22.50 0.00 0.00 3.59
2395 2607 2.546778 GCATAGTTTTGGGTCGATCGA 58.453 47.619 15.15 15.15 0.00 3.59
2396 2608 1.257936 CGCATAGTTTTGGGTCGATCG 59.742 52.381 9.36 9.36 0.00 3.69
2397 2609 2.546778 TCGCATAGTTTTGGGTCGATC 58.453 47.619 0.00 0.00 0.00 3.69
2405 2617 2.176369 CAACGCCATCGCATAGTTTTG 58.824 47.619 0.00 0.00 39.84 2.44
2482 2694 1.069765 CATCCGGCGCCTATCACTT 59.930 57.895 26.68 0.00 0.00 3.16
2498 2710 2.203773 AAAGTTTGGGCCGGCCAT 60.204 55.556 44.46 22.76 37.98 4.40
2590 2803 1.339151 CGGGGGAAAGAAGGAAGACAG 60.339 57.143 0.00 0.00 0.00 3.51
2605 2818 0.602905 GGATCAATAGCGTTCGGGGG 60.603 60.000 0.00 0.00 0.00 5.40
2625 2838 2.418609 CGAGGTCACACATCCATAGCAA 60.419 50.000 0.00 0.00 0.00 3.91
2637 2850 2.338620 CGGTGCTTCGAGGTCACA 59.661 61.111 18.48 0.00 32.69 3.58
2722 2936 2.360767 TGATTTGCTGCATGGGGGC 61.361 57.895 1.84 0.00 0.00 5.80
2743 2957 2.425143 TTTTGCTAGATCCAGGGCAG 57.575 50.000 0.00 0.00 36.06 4.85
2764 2978 1.033202 AACAACGAGTTTTGCCCGGT 61.033 50.000 0.00 0.00 37.03 5.28
2765 2979 0.593773 CAACAACGAGTTTTGCCCGG 60.594 55.000 0.00 0.00 38.74 5.73
2820 3052 1.577328 CTGCAACCACTAGCAACGGG 61.577 60.000 0.00 0.00 40.73 5.28
2824 3056 4.896402 TGCTGCAACCACTAGCAA 57.104 50.000 0.00 0.00 43.77 3.91
2829 3061 4.954970 CCCCGTGCTGCAACCACT 62.955 66.667 2.77 0.00 0.00 4.00
2856 3088 1.589196 GACGATGGTGGCGAGCTAC 60.589 63.158 2.84 2.84 0.00 3.58
2869 3101 0.604511 GGGGACCGTTGTTTGACGAT 60.605 55.000 0.00 0.00 45.47 3.73
2889 3121 1.734465 CGACCAGAGAGTTGATTTGCC 59.266 52.381 0.00 0.00 0.00 4.52
2919 3151 5.585047 AGCTTCAGTCGTATATGGAAAAACC 59.415 40.000 0.00 0.00 39.54 3.27
2920 3152 6.663944 AGCTTCAGTCGTATATGGAAAAAC 57.336 37.500 0.00 0.00 0.00 2.43
2926 3158 5.218885 CAGAGAAGCTTCAGTCGTATATGG 58.781 45.833 27.57 0.97 0.00 2.74
2936 3168 2.064762 CCGTTGACAGAGAAGCTTCAG 58.935 52.381 27.57 18.39 0.00 3.02
2938 3170 2.156343 ACCGTTGACAGAGAAGCTTC 57.844 50.000 19.11 19.11 0.00 3.86
2974 3206 8.270744 AGAGAAAGCTTCAACCAGATATTACAT 58.729 33.333 0.00 0.00 0.00 2.29
2975 3207 7.624549 AGAGAAAGCTTCAACCAGATATTACA 58.375 34.615 0.00 0.00 0.00 2.41
2976 3208 9.771534 ATAGAGAAAGCTTCAACCAGATATTAC 57.228 33.333 0.00 0.00 0.00 1.89
2977 3209 9.988815 GATAGAGAAAGCTTCAACCAGATATTA 57.011 33.333 0.00 0.00 0.00 0.98
3015 3247 2.393764 CTTTGACCGTGGATGCAAAAC 58.606 47.619 0.00 0.00 30.78 2.43
3020 3253 0.598065 AAAGCTTTGACCGTGGATGC 59.402 50.000 11.80 0.00 0.00 3.91
3025 3258 4.545823 TTACAGAAAAGCTTTGACCGTG 57.454 40.909 13.54 8.47 0.00 4.94
3049 3282 3.912496 AAAAGGGAAAAAGCTGCAACT 57.088 38.095 1.02 0.00 0.00 3.16
3065 3298 1.080974 CAGGCGCTGCTCCAAAAAG 60.081 57.895 11.76 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.