Multiple sequence alignment - TraesCS2D01G562300

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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 TraesCS2D01G562300 chr2D 100.000 2980 0 0 1 2980 634164830 634161851 0.000000e+00 5504.0
1 TraesCS2D01G562300 chr2D 96.610 649 22 0 1 649 74525936 74526584 0.000000e+00 1077.0
2 TraesCS2D01G562300 chr2D 88.141 312 37 0 1 312 87429480 87429169 3.630000e-99 372.0
3 TraesCS2D01G562300 chr2D 85.577 312 45 0 1 312 523013687 523013998 7.960000e-86 327.0
4 TraesCS2D01G562300 chr2D 80.000 175 23 9 394 565 87429135 87428970 5.220000e-23 119.0
5 TraesCS2D01G562300 chr2A 92.391 1577 89 17 958 2513 779299933 779301499 0.000000e+00 2218.0
6 TraesCS2D01G562300 chr2A 95.994 649 26 0 1 649 766096916 766097564 0.000000e+00 1055.0
7 TraesCS2D01G562300 chr2A 85.371 957 81 30 1172 2112 779495284 779496197 0.000000e+00 937.0
8 TraesCS2D01G562300 chr2A 85.177 958 82 30 1172 2112 779602915 779603829 0.000000e+00 928.0
9 TraesCS2D01G562300 chr2A 88.860 763 61 15 1351 2097 779498906 779499660 0.000000e+00 917.0
10 TraesCS2D01G562300 chr2A 88.860 763 61 15 1351 2097 779606538 779607292 0.000000e+00 917.0
11 TraesCS2D01G562300 chr2A 89.871 464 43 3 2510 2970 779607894 779608356 7.110000e-166 593.0
12 TraesCS2D01G562300 chr2A 92.665 409 26 2 2099 2507 779607456 779607860 1.190000e-163 586.0
13 TraesCS2D01G562300 chr2A 89.172 471 46 4 2504 2970 779500255 779500724 1.540000e-162 582.0
14 TraesCS2D01G562300 chr2A 92.421 409 27 2 2099 2507 779499824 779500228 5.540000e-162 580.0
15 TraesCS2D01G562300 chr2A 88.235 476 48 4 2509 2980 779301526 779301997 2.010000e-156 562.0
16 TraesCS2D01G562300 chr2A 90.645 310 27 1 866 1175 779599600 779599907 7.690000e-111 411.0
17 TraesCS2D01G562300 chr2A 89.667 300 29 1 866 1165 779491961 779492258 6.030000e-102 381.0
18 TraesCS2D01G562300 chr2A 86.901 313 39 2 1 312 87542702 87542391 1.700000e-92 350.0
19 TraesCS2D01G562300 chr2A 84.615 312 47 1 1 312 668174342 668174652 2.880000e-80 309.0
20 TraesCS2D01G562300 chr2A 83.654 312 47 3 3 312 87537073 87536764 1.040000e-74 291.0
21 TraesCS2D01G562300 chr2A 94.286 105 4 1 737 839 779491873 779491977 3.070000e-35 159.0
22 TraesCS2D01G562300 chr2A 85.714 98 14 0 1199 1296 779498781 779498878 1.460000e-18 104.0
23 TraesCS2D01G562300 chr2A 85.714 98 14 0 1199 1296 779606413 779606510 1.460000e-18 104.0
24 TraesCS2D01G562300 chr2A 95.161 62 3 0 775 836 779299835 779299896 6.800000e-17 99.0
25 TraesCS2D01G562300 chr2B 89.762 1426 110 18 866 2271 777166862 777165453 0.000000e+00 1792.0
26 TraesCS2D01G562300 chr2B 83.974 312 46 3 3 312 140213093 140212784 2.250000e-76 296.0
27 TraesCS2D01G562300 chr2B 88.400 250 22 5 2264 2512 777162422 777162179 8.080000e-76 294.0
28 TraesCS2D01G562300 chr2B 85.769 260 37 0 1 260 140223877 140223618 2.930000e-70 276.0
29 TraesCS2D01G562300 chr2B 98.058 103 2 0 737 839 777166948 777166846 2.360000e-41 180.0
30 TraesCS2D01G562300 chr2B 85.821 134 11 6 2853 2980 776321881 776322012 5.180000e-28 135.0
31 TraesCS2D01G562300 chr2B 93.443 61 4 0 252 312 140221885 140221825 1.140000e-14 91.6
32 TraesCS2D01G562300 chr6B 89.516 124 8 3 2860 2978 43319515 43319638 5.140000e-33 152.0
33 TraesCS2D01G562300 chr6B 87.903 124 9 6 2863 2980 508532840 508532963 1.110000e-29 141.0
34 TraesCS2D01G562300 chr1D 87.200 125 11 4 2860 2980 72674935 72675058 1.440000e-28 137.0
35 TraesCS2D01G562300 chr1D 86.813 91 7 3 2526 2616 90513793 90513708 2.440000e-16 97.1
36 TraesCS2D01G562300 chr1D 86.667 90 9 1 2401 2490 486766042 486766128 2.440000e-16 97.1
37 TraesCS2D01G562300 chr4D 87.097 124 10 5 2863 2980 84754788 84754665 5.180000e-28 135.0
38 TraesCS2D01G562300 chr4A 86.719 128 10 5 2860 2980 733536110 733536237 5.180000e-28 135.0
39 TraesCS2D01G562300 chr4A 84.091 88 11 3 2401 2488 711691029 711690945 6.850000e-12 82.4
40 TraesCS2D01G562300 chr5D 87.778 90 8 3 2401 2490 461928356 461928270 5.260000e-18 102.0
41 TraesCS2D01G562300 chr7A 88.235 85 7 1 2406 2490 175697125 175697206 6.800000e-17 99.0
42 TraesCS2D01G562300 chr3D 87.059 85 8 1 2406 2490 19803949 19803868 3.160000e-15 93.5
43 TraesCS2D01G562300 chr3D 91.837 49 4 0 1972 2020 138889962 138889914 5.330000e-08 69.4
44 TraesCS2D01G562300 chr3D 90.698 43 4 0 1978 2020 566486684 566486642 1.150000e-04 58.4
45 TraesCS2D01G562300 chr3A 92.683 41 3 0 1978 2018 287329534 287329574 3.210000e-05 60.2


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 TraesCS2D01G562300 chr2D 634161851 634164830 2979 True 5504.000000 5504 100.000000 1 2980 1 chr2D.!!$R1 2979
1 TraesCS2D01G562300 chr2D 74525936 74526584 648 False 1077.000000 1077 96.610000 1 649 1 chr2D.!!$F1 648
2 TraesCS2D01G562300 chr2D 87428970 87429480 510 True 245.500000 372 84.070500 1 565 2 chr2D.!!$R2 564
3 TraesCS2D01G562300 chr2A 766096916 766097564 648 False 1055.000000 1055 95.994000 1 649 1 chr2A.!!$F2 648
4 TraesCS2D01G562300 chr2A 779299835 779301997 2162 False 959.666667 2218 91.929000 775 2980 3 chr2A.!!$F3 2205
5 TraesCS2D01G562300 chr2A 779599600 779608356 8756 False 589.833333 928 88.822000 866 2970 6 chr2A.!!$F5 2104
6 TraesCS2D01G562300 chr2A 779491873 779500724 8851 False 522.857143 937 89.355857 737 2970 7 chr2A.!!$F4 2233
7 TraesCS2D01G562300 chr2B 777162179 777166948 4769 True 755.333333 1792 92.073333 737 2512 3 chr2B.!!$R3 1775

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
674 680 0.097674 CGCAGGTACAGATTTGCAGC 59.902 55.0 0.0 0.0 36.37 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 12350 1.076923 GGAGTCCTGGACTAGCGGA 60.077 63.158 28.41 0.0 43.53 5.54 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
97 98 1.202302 CGAGGATAAGCTGAAGACGCA 60.202 52.381 0.00 0.00 0.00 5.24
114 115 0.671781 GCACGTCTTCATGCTCTGGT 60.672 55.000 0.00 0.00 38.84 4.00
125 126 3.867771 CTCTGGTTGAGCTCGCAC 58.132 61.111 9.64 8.27 35.84 5.34
137 138 1.443872 CTCGCACAGTACACCGGAC 60.444 63.158 9.46 0.00 0.00 4.79
159 160 0.818296 GAGCAAGAACTCGGCCTCTA 59.182 55.000 0.00 0.00 0.00 2.43
300 301 4.414337 AGGATTTCCTGTAGCATCTCAC 57.586 45.455 0.00 0.00 46.55 3.51
375 376 0.889186 ACGTCCCACTGCAAATGGAC 60.889 55.000 16.62 15.74 43.07 4.02
445 446 1.585521 GCATCGTACTCGGTGGACG 60.586 63.158 8.45 8.45 46.76 4.79
475 480 0.301687 CCGGCGACTCGAAATCAATG 59.698 55.000 9.30 0.00 0.00 2.82
515 520 6.979465 ACCCTAGACTTCGCATTTATACTAC 58.021 40.000 0.00 0.00 0.00 2.73
530 535 0.682209 ACTACAGGGCACGACCGTAT 60.682 55.000 0.00 0.00 40.62 3.06
626 632 2.046292 GGGCTCTAGGCTCAAGAAGAT 58.954 52.381 3.36 0.00 42.01 2.40
651 657 4.318949 GGTACCACCAACCGCGGT 62.319 66.667 28.70 28.70 41.07 5.68
652 658 2.281002 GTACCACCAACCGCGGTT 60.281 61.111 36.96 36.96 37.07 4.44
653 659 2.030862 TACCACCAACCGCGGTTC 59.969 61.111 39.38 0.00 37.07 3.62
654 660 2.804912 TACCACCAACCGCGGTTCA 61.805 57.895 39.38 17.59 37.07 3.18
655 661 2.992607 TACCACCAACCGCGGTTCAC 62.993 60.000 39.38 0.00 37.07 3.18
665 671 3.856508 CGGTTCACGCAGGTACAG 58.143 61.111 0.00 0.00 34.82 2.74
666 672 1.287815 CGGTTCACGCAGGTACAGA 59.712 57.895 0.00 0.00 34.82 3.41
667 673 0.108804 CGGTTCACGCAGGTACAGAT 60.109 55.000 0.00 0.00 34.82 2.90
668 674 1.671850 CGGTTCACGCAGGTACAGATT 60.672 52.381 0.00 0.00 34.82 2.40
669 675 2.423577 GGTTCACGCAGGTACAGATTT 58.576 47.619 0.00 0.00 0.00 2.17
670 676 2.159627 GGTTCACGCAGGTACAGATTTG 59.840 50.000 0.00 0.00 0.00 2.32
671 677 1.438651 TCACGCAGGTACAGATTTGC 58.561 50.000 0.00 0.00 0.00 3.68
672 678 1.155889 CACGCAGGTACAGATTTGCA 58.844 50.000 0.00 0.00 36.37 4.08
673 679 1.129251 CACGCAGGTACAGATTTGCAG 59.871 52.381 0.00 0.00 36.37 4.41
674 680 0.097674 CGCAGGTACAGATTTGCAGC 59.902 55.000 0.00 0.00 36.37 5.25
675 681 1.167851 GCAGGTACAGATTTGCAGCA 58.832 50.000 0.00 0.00 36.59 4.41
676 682 1.747355 GCAGGTACAGATTTGCAGCAT 59.253 47.619 0.00 0.00 36.59 3.79
677 683 2.945008 GCAGGTACAGATTTGCAGCATA 59.055 45.455 0.00 0.00 36.59 3.14
678 684 3.242870 GCAGGTACAGATTTGCAGCATAC 60.243 47.826 0.00 0.00 36.59 2.39
679 685 3.313526 CAGGTACAGATTTGCAGCATACC 59.686 47.826 11.33 11.33 0.00 2.73
680 686 3.054434 AGGTACAGATTTGCAGCATACCA 60.054 43.478 18.68 0.00 34.31 3.25
681 687 3.065371 GGTACAGATTTGCAGCATACCAC 59.935 47.826 13.61 0.00 32.52 4.16
682 688 3.077484 ACAGATTTGCAGCATACCACT 57.923 42.857 0.00 0.00 0.00 4.00
683 689 4.220693 ACAGATTTGCAGCATACCACTA 57.779 40.909 0.00 0.00 0.00 2.74
684 690 3.941483 ACAGATTTGCAGCATACCACTAC 59.059 43.478 0.00 0.00 0.00 2.73
685 691 4.194640 CAGATTTGCAGCATACCACTACT 58.805 43.478 0.00 0.00 0.00 2.57
686 692 4.034858 CAGATTTGCAGCATACCACTACTG 59.965 45.833 0.00 0.00 0.00 2.74
687 693 2.401583 TTGCAGCATACCACTACTGG 57.598 50.000 0.00 0.00 44.26 4.00
688 694 1.567357 TGCAGCATACCACTACTGGA 58.433 50.000 0.00 0.00 40.55 3.86
689 695 1.905894 TGCAGCATACCACTACTGGAA 59.094 47.619 0.00 0.00 40.55 3.53
690 696 2.304470 TGCAGCATACCACTACTGGAAA 59.696 45.455 0.00 0.00 40.55 3.13
691 697 3.244735 TGCAGCATACCACTACTGGAAAA 60.245 43.478 0.00 0.00 40.55 2.29
692 698 3.756434 GCAGCATACCACTACTGGAAAAA 59.244 43.478 0.00 0.00 40.55 1.94
693 699 4.399303 GCAGCATACCACTACTGGAAAAAT 59.601 41.667 0.00 0.00 40.55 1.82
694 700 5.449177 GCAGCATACCACTACTGGAAAAATC 60.449 44.000 0.00 0.00 40.55 2.17
695 701 5.647658 CAGCATACCACTACTGGAAAAATCA 59.352 40.000 0.00 0.00 40.55 2.57
696 702 5.648092 AGCATACCACTACTGGAAAAATCAC 59.352 40.000 0.00 0.00 40.55 3.06
697 703 5.447279 GCATACCACTACTGGAAAAATCACG 60.447 44.000 0.00 0.00 40.55 4.35
698 704 4.345859 ACCACTACTGGAAAAATCACGA 57.654 40.909 0.00 0.00 40.55 4.35
699 705 4.906618 ACCACTACTGGAAAAATCACGAT 58.093 39.130 0.00 0.00 40.55 3.73
700 706 5.313712 ACCACTACTGGAAAAATCACGATT 58.686 37.500 0.00 0.00 40.55 3.34
701 707 6.469410 ACCACTACTGGAAAAATCACGATTA 58.531 36.000 0.00 0.00 40.55 1.75
702 708 6.594159 ACCACTACTGGAAAAATCACGATTAG 59.406 38.462 0.00 0.00 40.55 1.73
703 709 6.037172 CCACTACTGGAAAAATCACGATTAGG 59.963 42.308 0.00 0.00 40.55 2.69
704 710 4.965119 ACTGGAAAAATCACGATTAGGC 57.035 40.909 0.00 0.00 0.00 3.93
705 711 3.694566 ACTGGAAAAATCACGATTAGGCC 59.305 43.478 0.00 0.00 0.00 5.19
706 712 3.020984 TGGAAAAATCACGATTAGGCCC 58.979 45.455 0.00 0.00 0.00 5.80
707 713 3.288092 GGAAAAATCACGATTAGGCCCT 58.712 45.455 0.00 0.00 0.00 5.19
708 714 3.699538 GGAAAAATCACGATTAGGCCCTT 59.300 43.478 0.00 0.00 0.00 3.95
709 715 4.159693 GGAAAAATCACGATTAGGCCCTTT 59.840 41.667 0.00 0.00 0.00 3.11
710 716 5.337250 GGAAAAATCACGATTAGGCCCTTTT 60.337 40.000 0.00 0.00 0.00 2.27
711 717 4.983671 AAATCACGATTAGGCCCTTTTC 57.016 40.909 0.00 0.00 0.00 2.29
712 718 3.644966 ATCACGATTAGGCCCTTTTCA 57.355 42.857 0.00 0.00 0.00 2.69
713 719 2.985896 TCACGATTAGGCCCTTTTCAG 58.014 47.619 0.00 0.00 0.00 3.02
714 720 2.304761 TCACGATTAGGCCCTTTTCAGT 59.695 45.455 0.00 0.00 0.00 3.41
715 721 2.420022 CACGATTAGGCCCTTTTCAGTG 59.580 50.000 0.00 0.00 0.00 3.66
716 722 2.039879 ACGATTAGGCCCTTTTCAGTGT 59.960 45.455 0.00 0.00 0.00 3.55
717 723 3.081804 CGATTAGGCCCTTTTCAGTGTT 58.918 45.455 0.00 0.00 0.00 3.32
718 724 3.506067 CGATTAGGCCCTTTTCAGTGTTT 59.494 43.478 0.00 0.00 0.00 2.83
719 725 4.379499 CGATTAGGCCCTTTTCAGTGTTTC 60.379 45.833 0.00 0.00 0.00 2.78
720 726 2.452600 AGGCCCTTTTCAGTGTTTCA 57.547 45.000 0.00 0.00 0.00 2.69
721 727 2.031870 AGGCCCTTTTCAGTGTTTCAC 58.968 47.619 0.00 0.00 34.10 3.18
722 728 2.031870 GGCCCTTTTCAGTGTTTCACT 58.968 47.619 0.00 0.00 46.51 3.41
762 768 3.473093 AGTCGTCGTATTCACTCACAG 57.527 47.619 0.00 0.00 0.00 3.66
822 830 1.226323 CCAACTCGGCTACGACTCG 60.226 63.158 0.00 0.00 45.59 4.18
823 831 1.226323 CAACTCGGCTACGACTCGG 60.226 63.158 2.98 0.00 45.59 4.63
824 832 1.376424 AACTCGGCTACGACTCGGA 60.376 57.895 2.98 0.00 45.59 4.55
825 833 0.957395 AACTCGGCTACGACTCGGAA 60.957 55.000 2.98 0.00 45.59 4.30
826 834 1.062206 CTCGGCTACGACTCGGAAC 59.938 63.158 2.98 0.00 45.59 3.62
827 835 2.101770 CGGCTACGACTCGGAACC 59.898 66.667 2.98 0.00 44.60 3.62
828 836 2.101770 GGCTACGACTCGGAACCG 59.898 66.667 6.94 6.94 41.35 4.44
829 837 2.101770 GCTACGACTCGGAACCGG 59.898 66.667 13.29 0.00 40.25 5.28
830 838 2.101770 CTACGACTCGGAACCGGC 59.898 66.667 13.29 3.04 40.25 6.13
831 839 3.407046 CTACGACTCGGAACCGGCC 62.407 68.421 13.29 0.00 40.25 6.13
832 840 3.925630 TACGACTCGGAACCGGCCT 62.926 63.158 13.29 0.00 40.25 5.19
833 841 4.796231 CGACTCGGAACCGGCCTG 62.796 72.222 13.29 0.00 40.25 4.85
834 842 3.379445 GACTCGGAACCGGCCTGA 61.379 66.667 13.29 3.21 40.25 3.86
835 843 3.644399 GACTCGGAACCGGCCTGAC 62.644 68.421 13.29 0.00 40.25 3.51
836 844 3.382832 CTCGGAACCGGCCTGACT 61.383 66.667 13.29 0.00 40.25 3.41
837 845 2.920912 TCGGAACCGGCCTGACTT 60.921 61.111 13.29 0.00 40.25 3.01
838 846 2.032071 CGGAACCGGCCTGACTTT 59.968 61.111 0.00 0.00 35.56 2.66
839 847 1.599797 CGGAACCGGCCTGACTTTT 60.600 57.895 0.00 0.00 35.56 2.27
840 848 1.170290 CGGAACCGGCCTGACTTTTT 61.170 55.000 0.00 0.00 35.56 1.94
1038 1049 1.800655 GCAAGATCTGAGCACGACGAT 60.801 52.381 13.83 0.00 0.00 3.73
1050 1061 3.310251 GACGATACGCGACGCACC 61.310 66.667 21.35 4.25 44.57 5.01
1054 1065 1.587876 GATACGCGACGCACCATGA 60.588 57.895 21.35 0.00 0.00 3.07
1059 1070 2.997869 CGACGCACCATGATGTCG 59.002 61.111 12.21 12.21 46.57 4.35
1096 1107 4.933064 CACCTCGCTCGATCGGGC 62.933 72.222 30.02 30.02 38.46 6.13
1141 1152 3.129871 CGACCTTTTACCCGTACAAACA 58.870 45.455 0.00 0.00 0.00 2.83
1142 1153 3.559242 CGACCTTTTACCCGTACAAACAA 59.441 43.478 0.00 0.00 0.00 2.83
1155 1166 0.233590 CAAACAAATCGACGCGGACA 59.766 50.000 12.47 0.00 0.00 4.02
1266 4300 1.224039 GAAGGAGCTGCTGCAGGAT 59.776 57.895 29.05 10.43 42.74 3.24
1358 4398 3.130160 GGCAGCTGGAGAAAGCCG 61.130 66.667 17.12 0.00 44.68 5.52
1793 8301 1.672881 GCATGCATAGAACCTGTGACC 59.327 52.381 14.21 0.00 0.00 4.02
1844 8355 2.704572 CAGCGGAGGAAGAAATCAAGT 58.295 47.619 0.00 0.00 0.00 3.16
2043 8563 6.647229 TCATGTTCATGTAGAAGCTGAATCT 58.353 36.000 11.73 0.00 36.78 2.40
2070 8590 2.827652 TGTTGTGCGTCACAGACATAA 58.172 42.857 11.48 0.00 45.39 1.90
2092 8614 6.817765 AAGAGTGTTTGAAAGTTGAGTTCA 57.182 33.333 0.00 0.00 33.21 3.18
2097 8781 5.795441 GTGTTTGAAAGTTGAGTTCAGTGTC 59.205 40.000 0.00 0.00 36.41 3.67
2107 8791 6.870965 AGTTGAGTTCAGTGTCAGATTGTATC 59.129 38.462 0.00 0.00 0.00 2.24
2132 8816 6.072112 ACACACATGCTAAAAGGTAAGTTG 57.928 37.500 0.00 0.00 0.00 3.16
2174 8858 3.782046 AGCATGCATGAGAAATTTCAGC 58.218 40.909 30.64 16.62 0.00 4.26
2360 12083 7.309770 TGTAGAGGGGCAAATTGTAAAAATT 57.690 32.000 0.00 0.00 0.00 1.82
2361 12084 8.423906 TGTAGAGGGGCAAATTGTAAAAATTA 57.576 30.769 0.00 0.00 0.00 1.40
2459 12185 4.162509 ACCAGAGGCTTAGGATAACAAGAC 59.837 45.833 12.43 0.00 0.00 3.01
2593 12350 4.219507 GTCGGGAGATGATGTGATGAGTAT 59.780 45.833 0.00 0.00 43.27 2.12
2596 12353 4.381398 GGGAGATGATGTGATGAGTATCCG 60.381 50.000 0.00 0.00 32.09 4.18
2667 12425 2.743928 GCAACTGTCGGCAGAGGG 60.744 66.667 26.48 13.21 45.28 4.30
2689 12447 2.125552 CATCGCGTCTTGGAGGCA 60.126 61.111 5.77 1.46 42.60 4.75
2698 12456 0.961019 TCTTGGAGGCATTGTTGTGC 59.039 50.000 0.00 0.00 44.31 4.57
2736 12494 3.057033 GGCGTTGTACTCAGTTCTTCCTA 60.057 47.826 0.00 0.00 0.00 2.94
2747 12505 8.196378 ACTCAGTTCTTCCTACAGTCTATTTT 57.804 34.615 0.00 0.00 0.00 1.82
2773 12531 1.078759 GTAGTCGCGTGCATCTTGCT 61.079 55.000 5.77 0.00 45.31 3.91
2794 12552 4.340381 GCTTGATGCAGTTATTCTGGGAAT 59.660 41.667 0.00 0.00 43.78 3.01
2824 12582 3.713826 TGAGGGTTACCCATCACTTTC 57.286 47.619 23.87 9.83 46.17 2.62
2826 12584 3.009033 TGAGGGTTACCCATCACTTTCTG 59.991 47.826 23.87 0.00 46.17 3.02
2972 12733 1.767289 AACGACGACTACAAGCACTG 58.233 50.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 1.344438 TCAACCAGAGCATGAAGACGT 59.656 47.619 0.00 0.00 0.00 4.34
114 115 0.319555 GGTGTACTGTGCGAGCTCAA 60.320 55.000 15.40 0.00 0.00 3.02
125 126 1.215647 GCTCCTGTCCGGTGTACTG 59.784 63.158 0.00 0.00 0.00 2.74
137 138 1.743252 GGCCGAGTTCTTGCTCCTG 60.743 63.158 0.00 0.00 32.11 3.86
375 376 4.489810 GATGGTCTACAGTCACAAGTCTG 58.510 47.826 0.00 0.00 37.02 3.51
461 462 4.690748 TCACAAGTCCATTGATTTCGAGTC 59.309 41.667 0.00 0.00 41.83 3.36
475 480 2.932261 AGGGTCAAAACTCACAAGTCC 58.068 47.619 0.00 0.00 33.48 3.85
515 520 1.226974 CTCATACGGTCGTGCCCTG 60.227 63.158 6.25 0.00 0.00 4.45
530 535 1.138069 TGACTCAAACTCGGCAACTCA 59.862 47.619 0.00 0.00 0.00 3.41
596 602 3.430497 TAGAGCCCCTCGCCTCCT 61.430 66.667 0.00 0.00 38.78 3.69
626 632 0.971386 GTTGGTGGTACCGGAGAAGA 59.029 55.000 9.46 0.00 42.58 2.87
649 655 2.094762 AATCTGTACCTGCGTGAACC 57.905 50.000 0.00 0.00 0.00 3.62
650 656 2.412847 GCAAATCTGTACCTGCGTGAAC 60.413 50.000 0.00 0.00 0.00 3.18
651 657 1.804151 GCAAATCTGTACCTGCGTGAA 59.196 47.619 0.00 0.00 0.00 3.18
652 658 1.270571 TGCAAATCTGTACCTGCGTGA 60.271 47.619 0.00 0.00 37.62 4.35
653 659 1.129251 CTGCAAATCTGTACCTGCGTG 59.871 52.381 0.00 0.00 37.62 5.34
654 660 1.442769 CTGCAAATCTGTACCTGCGT 58.557 50.000 0.00 0.00 37.62 5.24
655 661 0.097674 GCTGCAAATCTGTACCTGCG 59.902 55.000 0.00 0.00 37.62 5.18
656 662 1.167851 TGCTGCAAATCTGTACCTGC 58.832 50.000 0.00 0.00 35.32 4.85
657 663 3.313526 GGTATGCTGCAAATCTGTACCTG 59.686 47.826 16.67 0.00 0.00 4.00
658 664 3.054434 TGGTATGCTGCAAATCTGTACCT 60.054 43.478 21.73 0.86 33.13 3.08
659 665 3.065371 GTGGTATGCTGCAAATCTGTACC 59.935 47.826 16.97 16.97 0.00 3.34
660 666 3.941483 AGTGGTATGCTGCAAATCTGTAC 59.059 43.478 6.36 3.22 0.00 2.90
661 667 4.220693 AGTGGTATGCTGCAAATCTGTA 57.779 40.909 6.36 0.00 0.00 2.74
662 668 3.077484 AGTGGTATGCTGCAAATCTGT 57.923 42.857 6.36 0.00 0.00 3.41
663 669 4.034858 CAGTAGTGGTATGCTGCAAATCTG 59.965 45.833 6.36 3.86 0.00 2.90
664 670 4.194640 CAGTAGTGGTATGCTGCAAATCT 58.805 43.478 6.36 4.12 0.00 2.40
665 671 3.313526 CCAGTAGTGGTATGCTGCAAATC 59.686 47.826 6.36 0.00 39.30 2.17
666 672 3.054434 TCCAGTAGTGGTATGCTGCAAAT 60.054 43.478 16.36 0.00 45.28 2.32
667 673 2.304470 TCCAGTAGTGGTATGCTGCAAA 59.696 45.455 16.36 0.00 45.28 3.68
668 674 1.905894 TCCAGTAGTGGTATGCTGCAA 59.094 47.619 16.36 0.00 45.28 4.08
669 675 1.567357 TCCAGTAGTGGTATGCTGCA 58.433 50.000 16.36 4.13 45.28 4.41
670 676 2.691409 TTCCAGTAGTGGTATGCTGC 57.309 50.000 16.36 0.00 45.28 5.25
671 677 5.647658 TGATTTTTCCAGTAGTGGTATGCTG 59.352 40.000 16.36 0.00 45.28 4.41
672 678 5.648092 GTGATTTTTCCAGTAGTGGTATGCT 59.352 40.000 16.36 0.43 45.28 3.79
673 679 5.447279 CGTGATTTTTCCAGTAGTGGTATGC 60.447 44.000 16.36 3.76 45.28 3.14
674 680 5.872617 TCGTGATTTTTCCAGTAGTGGTATG 59.127 40.000 16.36 2.31 45.28 2.39
675 681 6.045072 TCGTGATTTTTCCAGTAGTGGTAT 57.955 37.500 16.36 6.29 45.28 2.73
676 682 5.471556 TCGTGATTTTTCCAGTAGTGGTA 57.528 39.130 16.36 3.96 45.28 3.25
677 683 4.345859 TCGTGATTTTTCCAGTAGTGGT 57.654 40.909 16.36 0.00 45.28 4.16
678 684 5.880054 AATCGTGATTTTTCCAGTAGTGG 57.120 39.130 10.66 10.66 46.63 4.00
679 685 6.456988 GCCTAATCGTGATTTTTCCAGTAGTG 60.457 42.308 0.00 0.00 32.50 2.74
680 686 5.585047 GCCTAATCGTGATTTTTCCAGTAGT 59.415 40.000 0.00 0.00 32.50 2.73
681 687 5.007724 GGCCTAATCGTGATTTTTCCAGTAG 59.992 44.000 0.00 0.00 32.50 2.57
682 688 4.879545 GGCCTAATCGTGATTTTTCCAGTA 59.120 41.667 0.00 0.00 32.50 2.74
683 689 3.694566 GGCCTAATCGTGATTTTTCCAGT 59.305 43.478 0.00 0.00 32.50 4.00
684 690 3.066760 GGGCCTAATCGTGATTTTTCCAG 59.933 47.826 0.84 0.00 32.50 3.86
685 691 3.020984 GGGCCTAATCGTGATTTTTCCA 58.979 45.455 0.84 0.00 32.50 3.53
686 692 3.288092 AGGGCCTAATCGTGATTTTTCC 58.712 45.455 2.82 0.36 32.50 3.13
687 693 4.983671 AAGGGCCTAATCGTGATTTTTC 57.016 40.909 6.41 0.00 32.50 2.29
688 694 5.245075 TGAAAAGGGCCTAATCGTGATTTTT 59.755 36.000 6.41 0.00 32.50 1.94
689 695 4.770010 TGAAAAGGGCCTAATCGTGATTTT 59.230 37.500 6.41 0.00 32.50 1.82
690 696 4.340617 TGAAAAGGGCCTAATCGTGATTT 58.659 39.130 6.41 0.00 32.50 2.17
691 697 3.947834 CTGAAAAGGGCCTAATCGTGATT 59.052 43.478 6.41 0.22 34.93 2.57
692 698 3.054361 ACTGAAAAGGGCCTAATCGTGAT 60.054 43.478 6.41 0.00 0.00 3.06
693 699 2.304761 ACTGAAAAGGGCCTAATCGTGA 59.695 45.455 6.41 0.00 0.00 4.35
694 700 2.420022 CACTGAAAAGGGCCTAATCGTG 59.580 50.000 6.41 15.56 0.00 4.35
695 701 2.039879 ACACTGAAAAGGGCCTAATCGT 59.960 45.455 6.41 8.14 0.00 3.73
696 702 2.711542 ACACTGAAAAGGGCCTAATCG 58.288 47.619 6.41 7.52 0.00 3.34
697 703 4.522789 TGAAACACTGAAAAGGGCCTAATC 59.477 41.667 6.41 9.18 0.00 1.75
698 704 4.280929 GTGAAACACTGAAAAGGGCCTAAT 59.719 41.667 6.41 0.00 36.32 1.73
699 705 3.634910 GTGAAACACTGAAAAGGGCCTAA 59.365 43.478 6.41 0.00 36.32 2.69
700 706 3.117663 AGTGAAACACTGAAAAGGGCCTA 60.118 43.478 6.41 0.00 43.63 3.93
701 707 2.031870 GTGAAACACTGAAAAGGGCCT 58.968 47.619 0.00 0.00 36.32 5.19
702 708 2.031870 AGTGAAACACTGAAAAGGGCC 58.968 47.619 0.00 0.00 43.63 5.80
712 718 3.196901 TGACCTGTACACAGTGAAACACT 59.803 43.478 7.81 0.00 46.51 3.55
713 719 3.308866 GTGACCTGTACACAGTGAAACAC 59.691 47.826 7.81 4.20 42.27 3.32
714 720 3.527533 GTGACCTGTACACAGTGAAACA 58.472 45.455 7.81 10.11 42.27 2.83
715 721 2.870411 GGTGACCTGTACACAGTGAAAC 59.130 50.000 7.81 5.73 42.27 2.78
716 722 2.482316 CGGTGACCTGTACACAGTGAAA 60.482 50.000 7.81 0.00 42.27 2.69
717 723 1.067974 CGGTGACCTGTACACAGTGAA 59.932 52.381 7.81 0.00 42.27 3.18
718 724 0.671796 CGGTGACCTGTACACAGTGA 59.328 55.000 7.81 0.00 42.27 3.41
719 725 0.387929 ACGGTGACCTGTACACAGTG 59.612 55.000 8.48 0.00 42.72 3.66
720 726 1.884579 CTACGGTGACCTGTACACAGT 59.115 52.381 8.48 0.00 45.18 3.55
721 727 1.884579 ACTACGGTGACCTGTACACAG 59.115 52.381 0.00 2.23 43.40 3.66
722 728 1.985473 ACTACGGTGACCTGTACACA 58.015 50.000 0.00 0.00 39.65 3.72
723 729 3.077359 ACTACTACGGTGACCTGTACAC 58.923 50.000 0.00 0.00 37.51 2.90
724 730 3.338249 GACTACTACGGTGACCTGTACA 58.662 50.000 0.00 0.00 0.00 2.90
725 731 2.349886 CGACTACTACGGTGACCTGTAC 59.650 54.545 0.00 0.00 0.00 2.90
726 732 2.028112 ACGACTACTACGGTGACCTGTA 60.028 50.000 0.00 3.18 34.93 2.74
727 733 1.271054 ACGACTACTACGGTGACCTGT 60.271 52.381 0.00 2.01 34.93 4.00
728 734 1.396301 GACGACTACTACGGTGACCTG 59.604 57.143 0.00 0.00 34.93 4.00
729 735 1.731720 GACGACTACTACGGTGACCT 58.268 55.000 0.00 0.00 34.93 3.85
730 736 0.371645 CGACGACTACTACGGTGACC 59.628 60.000 0.00 0.00 34.93 4.02
731 737 1.071605 ACGACGACTACTACGGTGAC 58.928 55.000 0.00 0.00 34.93 3.67
732 738 2.647529 TACGACGACTACTACGGTGA 57.352 50.000 0.00 0.00 34.93 4.02
733 739 3.306973 TGAATACGACGACTACTACGGTG 59.693 47.826 0.00 0.00 34.93 4.94
734 740 3.307242 GTGAATACGACGACTACTACGGT 59.693 47.826 0.00 0.00 34.93 4.83
735 741 3.553511 AGTGAATACGACGACTACTACGG 59.446 47.826 0.00 0.00 34.93 4.02
762 768 1.337823 TGCCTTGCCGACTAGAGTTTC 60.338 52.381 0.00 0.00 0.00 2.78
799 805 1.226323 CGTAGCCGAGTTGGAGTCG 60.226 63.158 0.00 0.00 42.00 4.18
822 830 2.728397 AAAAAGTCAGGCCGGTTCC 58.272 52.632 1.90 0.00 0.00 3.62
849 857 3.735514 CGGTTCCCTCGCAAAAAGAAAAA 60.736 43.478 0.00 0.00 0.00 1.94
850 858 2.223618 CGGTTCCCTCGCAAAAAGAAAA 60.224 45.455 0.00 0.00 0.00 2.29
851 859 1.335496 CGGTTCCCTCGCAAAAAGAAA 59.665 47.619 0.00 0.00 0.00 2.52
852 860 0.948678 CGGTTCCCTCGCAAAAAGAA 59.051 50.000 0.00 0.00 0.00 2.52
853 861 0.887387 CCGGTTCCCTCGCAAAAAGA 60.887 55.000 0.00 0.00 0.00 2.52
854 862 1.579429 CCGGTTCCCTCGCAAAAAG 59.421 57.895 0.00 0.00 0.00 2.27
855 863 2.557372 GCCGGTTCCCTCGCAAAAA 61.557 57.895 1.90 0.00 0.00 1.94
856 864 2.981350 GCCGGTTCCCTCGCAAAA 60.981 61.111 1.90 0.00 0.00 2.44
861 869 4.452733 GTCAGGCCGGTTCCCTCG 62.453 72.222 1.90 0.00 0.00 4.63
862 870 2.125766 AAAGTCAGGCCGGTTCCCTC 62.126 60.000 1.90 0.00 0.00 4.30
863 871 2.154074 AAAGTCAGGCCGGTTCCCT 61.154 57.895 1.90 0.00 0.00 4.20
864 872 1.971695 CAAAGTCAGGCCGGTTCCC 60.972 63.158 1.90 0.00 0.00 3.97
1038 1049 1.876263 CATCATGGTGCGTCGCGTA 60.876 57.895 13.38 1.26 0.00 4.42
1059 1070 3.770040 GGGAATTTGCGGTGGCCC 61.770 66.667 0.00 0.00 38.85 5.80
1074 1085 1.519455 GATCGAGCGAGGTGTTGGG 60.519 63.158 0.00 0.00 0.00 4.12
1096 1107 1.519455 GTTCGCTCAGATCCACCGG 60.519 63.158 0.00 0.00 0.00 5.28
1098 1109 1.153349 GGGTTCGCTCAGATCCACC 60.153 63.158 0.00 0.00 39.86 4.61
1123 1134 5.049543 TCGATTTGTTTGTACGGGTAAAAGG 60.050 40.000 0.00 0.00 0.00 3.11
1141 1152 0.108804 ATCTGTGTCCGCGTCGATTT 60.109 50.000 4.92 0.00 0.00 2.17
1142 1153 0.802222 CATCTGTGTCCGCGTCGATT 60.802 55.000 4.92 0.00 0.00 3.34
1155 1166 3.118445 GCTTTAGCTCCTTCTCCATCTGT 60.118 47.826 0.00 0.00 38.21 3.41
1266 4300 4.021719 GGATCGAACCCCTTGTCGATTATA 60.022 45.833 9.64 0.00 44.01 0.98
1347 4387 0.253044 CTTCATCCCGGCTTTCTCCA 59.747 55.000 0.00 0.00 0.00 3.86
1358 4398 0.106967 GCTGGGGTCTTCTTCATCCC 60.107 60.000 0.00 0.00 39.22 3.85
1844 8355 1.267806 GGTAGTAGCGCGCCAACTATA 59.732 52.381 33.24 19.90 0.00 1.31
1999 8519 8.442632 ACATGAGTGATGTAAATGGTCTTATG 57.557 34.615 0.00 0.00 43.96 1.90
2043 8563 1.266989 TGTGACGCACAACAAAACACA 59.733 42.857 9.71 0.00 41.69 3.72
2070 8590 5.940470 ACTGAACTCAACTTTCAAACACTCT 59.060 36.000 0.00 0.00 32.61 3.24
2097 8781 3.867493 AGCATGTGTGTCGATACAATCTG 59.133 43.478 17.08 14.35 37.36 2.90
2107 8791 4.451096 ACTTACCTTTTAGCATGTGTGTCG 59.549 41.667 0.00 0.00 0.00 4.35
2132 8816 4.496507 GCTCACCTTTCAAACACTGAACTC 60.497 45.833 0.00 0.00 43.90 3.01
2174 8858 5.405935 TCCTATTGTATCATCCCATGACG 57.594 43.478 0.00 0.00 43.01 4.35
2333 12056 6.524101 TTTACAATTTGCCCCTCTACATTC 57.476 37.500 0.00 0.00 0.00 2.67
2381 12106 2.656560 ATAACTGTCGCAGGTGAGTC 57.343 50.000 7.53 0.00 35.51 3.36
2382 12107 3.699538 TGATATAACTGTCGCAGGTGAGT 59.300 43.478 7.53 0.00 35.51 3.41
2383 12108 4.307443 TGATATAACTGTCGCAGGTGAG 57.693 45.455 7.53 0.00 35.51 3.51
2386 12111 4.737855 AGTTGATATAACTGTCGCAGGT 57.262 40.909 10.80 7.13 35.51 4.00
2427 12153 6.912951 TCCTAAGCCTCTGGTACATTATAC 57.087 41.667 0.00 0.00 38.20 1.47
2428 12154 9.032624 GTTATCCTAAGCCTCTGGTACATTATA 57.967 37.037 0.00 0.00 38.20 0.98
2429 12155 7.512746 TGTTATCCTAAGCCTCTGGTACATTAT 59.487 37.037 0.00 0.00 38.20 1.28
2593 12350 1.076923 GGAGTCCTGGACTAGCGGA 60.077 63.158 28.41 0.00 43.53 5.54
2596 12353 1.686052 CTGATGGAGTCCTGGACTAGC 59.314 57.143 28.41 17.43 43.53 3.42
2644 12402 1.445518 TGCCGACAGTTGCAGAGAA 59.554 52.632 0.00 0.00 32.77 2.87
2667 12425 1.078759 CTCCAAGACGCGATGTGTCC 61.079 60.000 15.93 0.00 43.20 4.02
2689 12447 0.874390 CACCTACGCTGCACAACAAT 59.126 50.000 0.00 0.00 0.00 2.71
2698 12456 1.153628 GCCTACACCACCTACGCTG 60.154 63.158 0.00 0.00 0.00 5.18
2736 12494 5.648572 GACTACGCTACCAAAATAGACTGT 58.351 41.667 0.00 0.00 0.00 3.55
2773 12531 4.646040 CCATTCCCAGAATAACTGCATCAA 59.354 41.667 0.00 0.00 44.52 2.57
2780 12538 4.998051 ACAACACCATTCCCAGAATAACT 58.002 39.130 0.00 0.00 0.00 2.24
2794 12552 3.706600 GGTAACCCTCATACAACACCA 57.293 47.619 0.00 0.00 0.00 4.17
2824 12582 1.511464 GTACACGTCCGAGCGACAG 60.511 63.158 5.65 0.00 42.07 3.51
2826 12584 1.225963 GAGTACACGTCCGAGCGAC 60.226 63.158 5.65 0.00 38.21 5.19


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

AutoCloner maintained by Alex Coulton.