Multiple sequence alignment - TraesCS2A01G401800

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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 TraesCS2A01G401800 chr2A 100.000 2606 0 0 1 2606 655289046 655286441 0.000000e+00 4813.0
1 TraesCS2A01G401800 chr2D 97.113 866 15 3 855 1719 512099372 512098516 0.000000e+00 1452.0
2 TraesCS2A01G401800 chr2D 82.836 134 9 5 755 885 636546160 636546282 9.860000e-20 108.0
3 TraesCS2A01G401800 chr2B 95.972 869 19 6 832 1697 601391108 601390253 0.000000e+00 1397.0
4 TraesCS2A01G401800 chr2B 90.811 740 57 6 1738 2476 133939203 133938474 0.000000e+00 979.0
5 TraesCS2A01G401800 chr2B 87.688 796 76 16 1723 2515 30477349 30478125 0.000000e+00 907.0
6 TraesCS2A01G401800 chr2B 94.737 418 22 0 2059 2476 381546363 381545946 0.000000e+00 651.0
7 TraesCS2A01G401800 chr2B 82.331 266 42 5 1726 1988 381546844 381546581 2.610000e-55 226.0
8 TraesCS2A01G401800 chr2B 95.506 89 4 0 2469 2557 133938443 133938355 2.700000e-30 143.0
9 TraesCS2A01G401800 chr2B 95.506 89 4 0 2469 2557 381545915 381545827 2.700000e-30 143.0
10 TraesCS2A01G401800 chr2B 81.818 110 7 4 770 878 154838674 154838771 2.150000e-11 80.5
11 TraesCS2A01G401800 chr2B 92.857 42 3 0 1689 1730 601384362 601384321 7.790000e-06 62.1
12 TraesCS2A01G401800 chr2B 82.667 75 6 2 771 844 601391204 601391136 2.800000e-05 60.2
13 TraesCS2A01G401800 chr3A 97.185 746 20 1 1723 2468 634575221 634575965 0.000000e+00 1260.0
14 TraesCS2A01G401800 chr3A 88.426 216 25 0 1723 1938 437862175 437861960 7.150000e-66 261.0
15 TraesCS2A01G401800 chr3A 96.377 138 5 0 2469 2606 634576004 634576141 7.260000e-56 228.0
16 TraesCS2A01G401800 chr3A 91.781 73 5 1 173 244 593992837 593992765 1.650000e-17 100.0
17 TraesCS2A01G401800 chr1B 90.704 753 68 2 1720 2472 446619050 446619800 0.000000e+00 1002.0
18 TraesCS2A01G401800 chr1B 92.063 63 5 0 2469 2531 446619835 446619897 3.570000e-14 89.8
19 TraesCS2A01G401800 chr7D 97.179 390 11 0 2087 2476 557710323 557710712 0.000000e+00 660.0
20 TraesCS2A01G401800 chr7D 86.705 346 22 5 1 323 106597641 106597297 1.910000e-96 363.0
21 TraesCS2A01G401800 chr7D 97.826 138 3 0 2469 2606 557710743 557710880 3.350000e-59 239.0
22 TraesCS2A01G401800 chr7D 88.961 154 16 1 428 581 106584261 106584109 3.420000e-44 189.0
23 TraesCS2A01G401800 chr7D 93.636 110 5 1 326 435 106597042 106596935 2.080000e-36 163.0
24 TraesCS2A01G401800 chr5A 85.205 561 31 18 101 613 26400057 26399501 1.780000e-146 529.0
25 TraesCS2A01G401800 chr5A 91.781 73 5 1 173 244 558139413 558139485 1.650000e-17 100.0
26 TraesCS2A01G401800 chr5A 91.781 73 5 1 173 244 558143627 558143555 1.650000e-17 100.0
27 TraesCS2A01G401800 chr5A 81.034 116 9 5 767 881 355188251 355188148 2.150000e-11 80.5
28 TraesCS2A01G401800 chr5A 80.702 114 10 3 769 881 422040534 422040432 7.730000e-11 78.7
29 TraesCS2A01G401800 chrUn 87.037 216 28 0 1727 1942 320064 319849 7.200000e-61 244.0
30 TraesCS2A01G401800 chr7A 84.556 259 23 3 251 492 6789086 6789344 9.320000e-60 241.0
31 TraesCS2A01G401800 chr7A 95.312 64 3 0 178 241 6788663 6788726 4.590000e-18 102.0
32 TraesCS2A01G401800 chr4A 84.332 217 11 11 249 443 702580089 702579874 9.520000e-45 191.0
33 TraesCS2A01G401800 chr4A 82.063 223 30 9 1723 1942 494035944 494036159 5.730000e-42 182.0
34 TraesCS2A01G401800 chr1D 80.543 221 36 6 1723 1939 331285142 331285359 2.080000e-36 163.0
35 TraesCS2A01G401800 chr6B 83.077 130 8 7 755 881 667784292 667784410 3.550000e-19 106.0
36 TraesCS2A01G401800 chr6D 84.821 112 4 6 771 881 459267986 459268085 1.650000e-17 100.0
37 TraesCS2A01G401800 chr6D 97.917 48 1 0 607 654 7328736 7328689 1.660000e-12 84.2
38 TraesCS2A01G401800 chr6D 97.872 47 1 0 608 654 365029485 365029439 5.980000e-12 82.4
39 TraesCS2A01G401800 chr6D 97.826 46 1 0 610 655 324736158 324736113 2.150000e-11 80.5
40 TraesCS2A01G401800 chr4B 87.356 87 11 0 2471 2557 437384786 437384700 1.650000e-17 100.0
41 TraesCS2A01G401800 chr1A 90.411 73 6 1 173 244 186707460 186707532 7.680000e-16 95.3
42 TraesCS2A01G401800 chr1A 98.039 51 1 0 607 657 399424808 399424758 3.570000e-14 89.8
43 TraesCS2A01G401800 chr1A 97.959 49 1 0 607 655 551187689 551187737 4.620000e-13 86.1
44 TraesCS2A01G401800 chr1A 97.917 48 1 0 607 654 17786453 17786406 1.660000e-12 84.2
45 TraesCS2A01G401800 chr3D 96.000 50 2 0 607 656 10715344 10715295 5.980000e-12 82.4
46 TraesCS2A01G401800 chr3D 94.340 53 3 0 2554 2606 136756494 136756442 5.980000e-12 82.4
47 TraesCS2A01G401800 chr5D 95.918 49 2 0 607 655 243873435 243873387 2.150000e-11 80.5
48 TraesCS2A01G401800 chr5D 92.857 56 2 2 597 652 520905599 520905652 2.150000e-11 80.5


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 TraesCS2A01G401800 chr2A 655286441 655289046 2605 True 4813.0 4813 100.0000 1 2606 1 chr2A.!!$R1 2605
1 TraesCS2A01G401800 chr2D 512098516 512099372 856 True 1452.0 1452 97.1130 855 1719 1 chr2D.!!$R1 864
2 TraesCS2A01G401800 chr2B 30477349 30478125 776 False 907.0 907 87.6880 1723 2515 1 chr2B.!!$F1 792
3 TraesCS2A01G401800 chr2B 601390253 601391204 951 True 728.6 1397 89.3195 771 1697 2 chr2B.!!$R4 926
4 TraesCS2A01G401800 chr2B 133938355 133939203 848 True 561.0 979 93.1585 1738 2557 2 chr2B.!!$R2 819
5 TraesCS2A01G401800 chr2B 381545827 381546844 1017 True 340.0 651 90.8580 1726 2557 3 chr2B.!!$R3 831
6 TraesCS2A01G401800 chr3A 634575221 634576141 920 False 744.0 1260 96.7810 1723 2606 2 chr3A.!!$F1 883
7 TraesCS2A01G401800 chr1B 446619050 446619897 847 False 545.9 1002 91.3835 1720 2531 2 chr1B.!!$F1 811
8 TraesCS2A01G401800 chr7D 557710323 557710880 557 False 449.5 660 97.5025 2087 2606 2 chr7D.!!$F1 519
9 TraesCS2A01G401800 chr7D 106596935 106597641 706 True 263.0 363 90.1705 1 435 2 chr7D.!!$R2 434
10 TraesCS2A01G401800 chr5A 26399501 26400057 556 True 529.0 529 85.2050 101 613 1 chr5A.!!$R1 512

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
671 971 0.468585 GCCCATCTGCCATCCATGAA 60.469 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2628 0.238289 CGGTGTGCTTCGATTTTGCT 59.762 50.0 0.0 0.0 0.0 3.91 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
58 59 9.045223 TCATTTCAAATTGTCTAGATACATCCG 57.955 33.333 0.00 0.00 0.00 4.18
64 65 8.703336 CAAATTGTCTAGATACATCCGTATGTG 58.297 37.037 3.56 0.00 45.99 3.21
65 66 5.959618 TGTCTAGATACATCCGTATGTGG 57.040 43.478 3.56 0.00 45.99 4.17
76 77 7.455641 ACATCCGTATGTGGACAAATTTAAA 57.544 32.000 0.00 0.00 44.79 1.52
176 179 2.480642 AGCCTCCTTCTAACCTAGGG 57.519 55.000 14.81 0.00 32.20 3.53
249 252 3.415237 GCAATAATGTTGCACGGCA 57.585 47.368 9.84 0.00 44.34 5.69
387 675 1.758592 CACGGGAAAGGTCCTTCCA 59.241 57.895 4.10 0.00 45.86 3.53
393 681 2.308866 GGGAAAGGTCCTTCCATCAGAA 59.691 50.000 4.10 0.00 45.86 3.02
394 682 3.245264 GGGAAAGGTCCTTCCATCAGAAA 60.245 47.826 4.10 0.00 45.86 2.52
467 762 2.675844 CCGTAATCTGGAACGCATTGAA 59.324 45.455 0.00 0.00 37.78 2.69
499 796 7.613801 TGTGCTTTTATTGGGCTTCTAATCTAA 59.386 33.333 0.00 0.00 0.00 2.10
501 798 8.632679 TGCTTTTATTGGGCTTCTAATCTAATG 58.367 33.333 0.00 0.00 0.00 1.90
502 799 8.084684 GCTTTTATTGGGCTTCTAATCTAATGG 58.915 37.037 0.00 0.00 0.00 3.16
562 862 2.181125 TCAGTATTGGGCTTGTACGGA 58.819 47.619 0.00 0.00 0.00 4.69
596 896 7.178712 GCCTTTAGCAAGCGTATATATATGG 57.821 40.000 12.81 2.56 42.97 2.74
597 897 6.761714 GCCTTTAGCAAGCGTATATATATGGT 59.238 38.462 10.27 10.27 42.97 3.55
598 898 7.042658 GCCTTTAGCAAGCGTATATATATGGTC 60.043 40.741 15.27 6.08 42.97 4.02
599 899 8.198109 CCTTTAGCAAGCGTATATATATGGTCT 58.802 37.037 15.27 11.89 0.00 3.85
600 900 8.926715 TTTAGCAAGCGTATATATATGGTCTG 57.073 34.615 15.27 15.10 0.00 3.51
601 901 5.907207 AGCAAGCGTATATATATGGTCTGG 58.093 41.667 15.27 10.16 0.00 3.86
602 902 5.050490 GCAAGCGTATATATATGGTCTGGG 58.950 45.833 15.27 8.24 0.00 4.45
603 903 5.395324 GCAAGCGTATATATATGGTCTGGGT 60.395 44.000 15.27 0.00 0.00 4.51
604 904 6.273825 CAAGCGTATATATATGGTCTGGGTC 58.726 44.000 15.27 0.00 0.00 4.46
605 905 4.579340 AGCGTATATATATGGTCTGGGTCG 59.421 45.833 10.27 0.47 0.00 4.79
606 906 4.261489 GCGTATATATATGGTCTGGGTCGG 60.261 50.000 12.81 0.00 0.00 4.79
607 907 4.277672 CGTATATATATGGTCTGGGTCGGG 59.722 50.000 5.44 0.00 0.00 5.14
608 908 1.952621 ATATATGGTCTGGGTCGGGG 58.047 55.000 0.00 0.00 0.00 5.73
609 909 0.834687 TATATGGTCTGGGTCGGGGC 60.835 60.000 0.00 0.00 0.00 5.80
610 910 7.940186 TATATATATGGTCTGGGTCGGGGCC 62.940 52.000 5.44 0.00 0.00 5.80
664 964 4.534824 GCCCTGCCCATCTGCCAT 62.535 66.667 0.00 0.00 0.00 4.40
665 965 2.203451 CCCTGCCCATCTGCCATC 60.203 66.667 0.00 0.00 0.00 3.51
666 966 2.203451 CCTGCCCATCTGCCATCC 60.203 66.667 0.00 0.00 0.00 3.51
667 967 2.599032 CTGCCCATCTGCCATCCA 59.401 61.111 0.00 0.00 0.00 3.41
668 968 1.153061 CTGCCCATCTGCCATCCAT 59.847 57.895 0.00 0.00 0.00 3.41
669 969 1.152631 TGCCCATCTGCCATCCATG 60.153 57.895 0.00 0.00 0.00 3.66
670 970 1.152138 GCCCATCTGCCATCCATGA 59.848 57.895 0.00 0.00 0.00 3.07
671 971 0.468585 GCCCATCTGCCATCCATGAA 60.469 55.000 0.00 0.00 0.00 2.57
672 972 1.325355 CCCATCTGCCATCCATGAAC 58.675 55.000 0.00 0.00 0.00 3.18
673 973 1.133575 CCCATCTGCCATCCATGAACT 60.134 52.381 0.00 0.00 0.00 3.01
674 974 2.107031 CCCATCTGCCATCCATGAACTA 59.893 50.000 0.00 0.00 0.00 2.24
675 975 3.245158 CCCATCTGCCATCCATGAACTAT 60.245 47.826 0.00 0.00 0.00 2.12
676 976 4.019051 CCCATCTGCCATCCATGAACTATA 60.019 45.833 0.00 0.00 0.00 1.31
677 977 5.515359 CCCATCTGCCATCCATGAACTATAA 60.515 44.000 0.00 0.00 0.00 0.98
678 978 6.005823 CCATCTGCCATCCATGAACTATAAA 58.994 40.000 0.00 0.00 0.00 1.40
679 979 6.072286 CCATCTGCCATCCATGAACTATAAAC 60.072 42.308 0.00 0.00 0.00 2.01
680 980 5.376625 TCTGCCATCCATGAACTATAAACC 58.623 41.667 0.00 0.00 0.00 3.27
681 981 4.469657 TGCCATCCATGAACTATAAACCC 58.530 43.478 0.00 0.00 0.00 4.11
682 982 4.079500 TGCCATCCATGAACTATAAACCCA 60.080 41.667 0.00 0.00 0.00 4.51
683 983 4.892934 GCCATCCATGAACTATAAACCCAA 59.107 41.667 0.00 0.00 0.00 4.12
684 984 5.221244 GCCATCCATGAACTATAAACCCAAC 60.221 44.000 0.00 0.00 0.00 3.77
685 985 5.890985 CCATCCATGAACTATAAACCCAACA 59.109 40.000 0.00 0.00 0.00 3.33
686 986 6.183360 CCATCCATGAACTATAAACCCAACAC 60.183 42.308 0.00 0.00 0.00 3.32
687 987 5.882040 TCCATGAACTATAAACCCAACACA 58.118 37.500 0.00 0.00 0.00 3.72
688 988 5.708230 TCCATGAACTATAAACCCAACACAC 59.292 40.000 0.00 0.00 0.00 3.82
689 989 5.475220 CCATGAACTATAAACCCAACACACA 59.525 40.000 0.00 0.00 0.00 3.72
690 990 6.152661 CCATGAACTATAAACCCAACACACAT 59.847 38.462 0.00 0.00 0.00 3.21
691 991 7.309744 CCATGAACTATAAACCCAACACACATT 60.310 37.037 0.00 0.00 0.00 2.71
692 992 7.589958 TGAACTATAAACCCAACACACATTT 57.410 32.000 0.00 0.00 0.00 2.32
693 993 7.653647 TGAACTATAAACCCAACACACATTTC 58.346 34.615 0.00 0.00 0.00 2.17
694 994 7.285629 TGAACTATAAACCCAACACACATTTCA 59.714 33.333 0.00 0.00 0.00 2.69
695 995 7.775053 ACTATAAACCCAACACACATTTCAT 57.225 32.000 0.00 0.00 0.00 2.57
696 996 7.826690 ACTATAAACCCAACACACATTTCATC 58.173 34.615 0.00 0.00 0.00 2.92
697 997 6.662865 ATAAACCCAACACACATTTCATCA 57.337 33.333 0.00 0.00 0.00 3.07
698 998 5.549742 AAACCCAACACACATTTCATCAT 57.450 34.783 0.00 0.00 0.00 2.45
699 999 4.789012 ACCCAACACACATTTCATCATC 57.211 40.909 0.00 0.00 0.00 2.92
700 1000 4.410099 ACCCAACACACATTTCATCATCT 58.590 39.130 0.00 0.00 0.00 2.90
701 1001 4.834496 ACCCAACACACATTTCATCATCTT 59.166 37.500 0.00 0.00 0.00 2.40
702 1002 5.305128 ACCCAACACACATTTCATCATCTTT 59.695 36.000 0.00 0.00 0.00 2.52
703 1003 5.865552 CCCAACACACATTTCATCATCTTTC 59.134 40.000 0.00 0.00 0.00 2.62
704 1004 6.448852 CCAACACACATTTCATCATCTTTCA 58.551 36.000 0.00 0.00 0.00 2.69
705 1005 6.924612 CCAACACACATTTCATCATCTTTCAA 59.075 34.615 0.00 0.00 0.00 2.69
706 1006 7.438757 CCAACACACATTTCATCATCTTTCAAA 59.561 33.333 0.00 0.00 0.00 2.69
707 1007 8.984764 CAACACACATTTCATCATCTTTCAAAT 58.015 29.630 0.00 0.00 0.00 2.32
709 1009 9.630098 ACACACATTTCATCATCTTTCAAATAC 57.370 29.630 0.00 0.00 0.00 1.89
710 1010 9.079833 CACACATTTCATCATCTTTCAAATACC 57.920 33.333 0.00 0.00 0.00 2.73
711 1011 7.970061 ACACATTTCATCATCTTTCAAATACCG 59.030 33.333 0.00 0.00 0.00 4.02
712 1012 7.970061 CACATTTCATCATCTTTCAAATACCGT 59.030 33.333 0.00 0.00 0.00 4.83
713 1013 8.522830 ACATTTCATCATCTTTCAAATACCGTT 58.477 29.630 0.00 0.00 0.00 4.44
718 1018 8.128582 TCATCATCTTTCAAATACCGTTAATGC 58.871 33.333 0.00 0.00 0.00 3.56
719 1019 7.384439 TCATCTTTCAAATACCGTTAATGCA 57.616 32.000 0.00 0.00 0.00 3.96
720 1020 7.471721 TCATCTTTCAAATACCGTTAATGCAG 58.528 34.615 0.00 0.00 0.00 4.41
721 1021 7.335673 TCATCTTTCAAATACCGTTAATGCAGA 59.664 33.333 0.00 0.00 0.00 4.26
722 1022 6.837992 TCTTTCAAATACCGTTAATGCAGAC 58.162 36.000 0.00 0.00 0.00 3.51
723 1023 5.554822 TTCAAATACCGTTAATGCAGACC 57.445 39.130 0.00 0.00 0.00 3.85
724 1024 4.580868 TCAAATACCGTTAATGCAGACCA 58.419 39.130 0.00 0.00 0.00 4.02
725 1025 4.393680 TCAAATACCGTTAATGCAGACCAC 59.606 41.667 0.00 0.00 0.00 4.16
726 1026 3.620427 ATACCGTTAATGCAGACCACA 57.380 42.857 0.00 0.00 0.00 4.17
727 1027 2.264005 ACCGTTAATGCAGACCACAA 57.736 45.000 0.00 0.00 0.00 3.33
728 1028 2.790433 ACCGTTAATGCAGACCACAAT 58.210 42.857 0.00 0.00 0.00 2.71
729 1029 2.747446 ACCGTTAATGCAGACCACAATC 59.253 45.455 0.00 0.00 0.00 2.67
730 1030 3.009723 CCGTTAATGCAGACCACAATCT 58.990 45.455 0.00 0.00 0.00 2.40
738 1038 2.602878 CAGACCACAATCTGCATTTGC 58.397 47.619 8.91 0.00 39.77 3.68
739 1039 2.230508 CAGACCACAATCTGCATTTGCT 59.769 45.455 8.91 0.00 39.77 3.91
740 1040 2.895404 AGACCACAATCTGCATTTGCTT 59.105 40.909 8.91 0.00 42.66 3.91
741 1041 3.057033 AGACCACAATCTGCATTTGCTTC 60.057 43.478 8.91 4.36 42.66 3.86
742 1042 2.895404 ACCACAATCTGCATTTGCTTCT 59.105 40.909 8.91 0.00 42.66 2.85
743 1043 3.250744 CCACAATCTGCATTTGCTTCTG 58.749 45.455 8.91 0.00 42.66 3.02
744 1044 3.250744 CACAATCTGCATTTGCTTCTGG 58.749 45.455 8.91 0.00 42.66 3.86
745 1045 3.057104 CACAATCTGCATTTGCTTCTGGA 60.057 43.478 8.91 0.00 42.66 3.86
746 1046 3.057033 ACAATCTGCATTTGCTTCTGGAC 60.057 43.478 8.91 0.00 42.66 4.02
747 1047 2.574006 TCTGCATTTGCTTCTGGACT 57.426 45.000 3.94 0.00 42.66 3.85
748 1048 3.701205 TCTGCATTTGCTTCTGGACTA 57.299 42.857 3.94 0.00 42.66 2.59
749 1049 4.226427 TCTGCATTTGCTTCTGGACTAT 57.774 40.909 3.94 0.00 42.66 2.12
750 1050 4.194640 TCTGCATTTGCTTCTGGACTATC 58.805 43.478 3.94 0.00 42.66 2.08
751 1051 4.080695 TCTGCATTTGCTTCTGGACTATCT 60.081 41.667 3.94 0.00 42.66 1.98
752 1052 4.592942 TGCATTTGCTTCTGGACTATCTT 58.407 39.130 3.94 0.00 42.66 2.40
753 1053 5.012239 TGCATTTGCTTCTGGACTATCTTT 58.988 37.500 3.94 0.00 42.66 2.52
754 1054 5.477984 TGCATTTGCTTCTGGACTATCTTTT 59.522 36.000 3.94 0.00 42.66 2.27
755 1055 6.658816 TGCATTTGCTTCTGGACTATCTTTTA 59.341 34.615 3.94 0.00 42.66 1.52
756 1056 7.176515 TGCATTTGCTTCTGGACTATCTTTTAA 59.823 33.333 3.94 0.00 42.66 1.52
757 1057 8.028938 GCATTTGCTTCTGGACTATCTTTTAAA 58.971 33.333 0.00 0.00 38.21 1.52
758 1058 9.912634 CATTTGCTTCTGGACTATCTTTTAAAA 57.087 29.630 0.00 0.00 0.00 1.52
762 1062 9.733556 TGCTTCTGGACTATCTTTTAAAATACA 57.266 29.630 0.09 0.00 0.00 2.29
763 1063 9.989869 GCTTCTGGACTATCTTTTAAAATACAC 57.010 33.333 0.09 0.00 0.00 2.90
775 1075 9.834628 TCTTTTAAAATACACAATTCATCGGTC 57.165 29.630 0.09 0.00 0.00 4.79
776 1076 8.662369 TTTTAAAATACACAATTCATCGGTCG 57.338 30.769 0.00 0.00 0.00 4.79
781 1081 4.141855 ACACAATTCATCGGTCGTTTTC 57.858 40.909 0.00 0.00 0.00 2.29
786 1086 5.470777 ACAATTCATCGGTCGTTTTCCTTTA 59.529 36.000 0.00 0.00 0.00 1.85
787 1087 4.996062 TTCATCGGTCGTTTTCCTTTAC 57.004 40.909 0.00 0.00 0.00 2.01
797 1097 5.454554 GTCGTTTTCCTTTACAGCTCAAAAC 59.545 40.000 0.00 0.00 32.71 2.43
896 1231 1.202065 CGGCCGAAGTTTGTGATGATG 60.202 52.381 24.07 0.00 0.00 3.07
914 1249 2.597340 CCCCATCAACCGCATCCT 59.403 61.111 0.00 0.00 0.00 3.24
942 1277 1.228154 GGCCGTTGACCAAAGGAGT 60.228 57.895 16.85 0.00 41.56 3.85
989 1324 4.572389 AGCTGCGGATAAGATAAACTTGTG 59.428 41.667 0.00 0.00 39.38 3.33
1624 1959 3.887621 AGTCCGATGCTACAGCTTTTA 57.112 42.857 2.44 0.00 42.66 1.52
1719 2056 6.994221 TGCTTTTAACTCTAGTCTAGCAACT 58.006 36.000 1.60 0.00 0.00 3.16
1720 2057 8.118976 TGCTTTTAACTCTAGTCTAGCAACTA 57.881 34.615 1.60 0.00 0.00 2.24
1721 2058 8.244802 TGCTTTTAACTCTAGTCTAGCAACTAG 58.755 37.037 10.90 10.90 46.72 2.57
1729 2066 6.670617 TCTAGTCTAGCAACTAGTACCCAAT 58.329 40.000 14.92 0.00 45.89 3.16
2004 2342 4.435436 CTGTCGTGCGGCAGGCTA 62.435 66.667 17.24 7.93 43.49 3.93
2143 2628 3.003173 CGTCTCTGGAAGGCCCCA 61.003 66.667 0.00 0.00 34.52 4.96
2313 2798 4.307908 GTTGCTGCCGCGTTTCGT 62.308 61.111 4.92 0.00 39.65 3.85
2387 2872 3.246112 TGCCCCAGCACCGTTACT 61.246 61.111 0.00 0.00 46.52 2.24
2452 2937 3.011818 TCGTCAATGATGCATCTTGCTT 58.988 40.909 26.32 12.22 45.31 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.045223 CGGATGTATCTAGACAATTTGAAATGA 57.955 33.333 2.79 0.00 31.83 2.57
36 37 9.476202 CATACGGATGTATCTAGACAATTTGAA 57.524 33.333 0.00 0.00 39.28 2.69
76 77 8.129496 ACAACTTCCGTCCCAAATTATTTATT 57.871 30.769 0.00 0.00 0.00 1.40
202 205 2.348411 ACTCCAAAGTTGAGGTGTGG 57.652 50.000 2.54 0.00 31.00 4.17
249 252 1.508632 CTTCGTTTCCCGTCACACAT 58.491 50.000 0.00 0.00 37.94 3.21
272 295 1.515952 CTTCACTCGCTCAGGCTCG 60.516 63.158 0.00 0.00 36.09 5.03
274 297 0.901124 AATCTTCACTCGCTCAGGCT 59.099 50.000 0.00 0.00 36.09 4.58
365 653 0.838987 AAGGACCTTTCCCGTGGCTA 60.839 55.000 0.00 0.00 44.10 3.93
425 713 0.036483 TCGGCTGTACATGTGTGCAT 60.036 50.000 9.11 0.00 39.79 3.96
467 762 4.344104 AGCCCAATAAAAGCACACATAGT 58.656 39.130 0.00 0.00 0.00 2.12
499 796 2.505819 GAGGCCCATCCGTAATATCCAT 59.494 50.000 0.00 0.00 40.77 3.41
501 798 2.168728 GAGAGGCCCATCCGTAATATCC 59.831 54.545 0.00 0.00 40.77 2.59
502 799 2.832129 TGAGAGGCCCATCCGTAATATC 59.168 50.000 0.00 0.00 40.77 1.63
507 804 1.457643 CCTGAGAGGCCCATCCGTA 60.458 63.158 0.00 0.00 40.77 4.02
562 862 3.193479 GCTTGCTAAAGGCTTTGGTACAT 59.807 43.478 22.32 0.00 39.42 2.29
569 869 8.883731 CATATATATACGCTTGCTAAAGGCTTT 58.116 33.333 17.76 17.76 42.39 3.51
585 885 4.587684 CCCCGACCCAGACCATATATATAC 59.412 50.000 0.00 0.00 0.00 1.47
592 892 2.766651 GCCCCGACCCAGACCATA 60.767 66.667 0.00 0.00 0.00 2.74
652 952 0.468585 TTCATGGATGGCAGATGGGC 60.469 55.000 0.00 0.00 43.73 5.36
653 953 1.133575 AGTTCATGGATGGCAGATGGG 60.134 52.381 0.00 0.00 0.00 4.00
654 954 2.359981 AGTTCATGGATGGCAGATGG 57.640 50.000 0.00 0.00 0.00 3.51
655 955 6.072286 GGTTTATAGTTCATGGATGGCAGATG 60.072 42.308 0.00 0.00 0.00 2.90
656 956 6.006449 GGTTTATAGTTCATGGATGGCAGAT 58.994 40.000 0.00 0.00 0.00 2.90
657 957 5.376625 GGTTTATAGTTCATGGATGGCAGA 58.623 41.667 0.00 0.00 0.00 4.26
658 958 4.520492 GGGTTTATAGTTCATGGATGGCAG 59.480 45.833 0.00 0.00 0.00 4.85
659 959 4.079500 TGGGTTTATAGTTCATGGATGGCA 60.080 41.667 0.00 0.00 0.00 4.92
660 960 4.469657 TGGGTTTATAGTTCATGGATGGC 58.530 43.478 0.00 0.00 0.00 4.40
661 961 5.890985 TGTTGGGTTTATAGTTCATGGATGG 59.109 40.000 0.00 0.00 0.00 3.51
662 962 6.376864 TGTGTTGGGTTTATAGTTCATGGATG 59.623 38.462 0.00 0.00 0.00 3.51
663 963 6.377146 GTGTGTTGGGTTTATAGTTCATGGAT 59.623 38.462 0.00 0.00 0.00 3.41
664 964 5.708230 GTGTGTTGGGTTTATAGTTCATGGA 59.292 40.000 0.00 0.00 0.00 3.41
665 965 5.475220 TGTGTGTTGGGTTTATAGTTCATGG 59.525 40.000 0.00 0.00 0.00 3.66
666 966 6.567687 TGTGTGTTGGGTTTATAGTTCATG 57.432 37.500 0.00 0.00 0.00 3.07
667 967 7.775053 AATGTGTGTTGGGTTTATAGTTCAT 57.225 32.000 0.00 0.00 0.00 2.57
668 968 7.285629 TGAAATGTGTGTTGGGTTTATAGTTCA 59.714 33.333 0.00 0.00 0.00 3.18
669 969 7.653647 TGAAATGTGTGTTGGGTTTATAGTTC 58.346 34.615 0.00 0.00 0.00 3.01
670 970 7.589958 TGAAATGTGTGTTGGGTTTATAGTT 57.410 32.000 0.00 0.00 0.00 2.24
671 971 7.450014 TGATGAAATGTGTGTTGGGTTTATAGT 59.550 33.333 0.00 0.00 0.00 2.12
672 972 7.825681 TGATGAAATGTGTGTTGGGTTTATAG 58.174 34.615 0.00 0.00 0.00 1.31
673 973 7.767250 TGATGAAATGTGTGTTGGGTTTATA 57.233 32.000 0.00 0.00 0.00 0.98
674 974 6.662865 TGATGAAATGTGTGTTGGGTTTAT 57.337 33.333 0.00 0.00 0.00 1.40
675 975 6.493115 AGATGATGAAATGTGTGTTGGGTTTA 59.507 34.615 0.00 0.00 0.00 2.01
676 976 5.305128 AGATGATGAAATGTGTGTTGGGTTT 59.695 36.000 0.00 0.00 0.00 3.27
677 977 4.834496 AGATGATGAAATGTGTGTTGGGTT 59.166 37.500 0.00 0.00 0.00 4.11
678 978 4.410099 AGATGATGAAATGTGTGTTGGGT 58.590 39.130 0.00 0.00 0.00 4.51
679 979 5.395682 AAGATGATGAAATGTGTGTTGGG 57.604 39.130 0.00 0.00 0.00 4.12
680 980 6.448852 TGAAAGATGATGAAATGTGTGTTGG 58.551 36.000 0.00 0.00 0.00 3.77
681 981 7.933728 TTGAAAGATGATGAAATGTGTGTTG 57.066 32.000 0.00 0.00 0.00 3.33
683 983 9.630098 GTATTTGAAAGATGATGAAATGTGTGT 57.370 29.630 0.00 0.00 0.00 3.72
684 984 9.079833 GGTATTTGAAAGATGATGAAATGTGTG 57.920 33.333 0.00 0.00 0.00 3.82
685 985 7.970061 CGGTATTTGAAAGATGATGAAATGTGT 59.030 33.333 0.00 0.00 0.00 3.72
686 986 7.970061 ACGGTATTTGAAAGATGATGAAATGTG 59.030 33.333 0.00 0.00 0.00 3.21
687 987 8.055279 ACGGTATTTGAAAGATGATGAAATGT 57.945 30.769 0.00 0.00 0.00 2.71
688 988 8.915871 AACGGTATTTGAAAGATGATGAAATG 57.084 30.769 0.00 0.00 0.00 2.32
692 992 8.128582 GCATTAACGGTATTTGAAAGATGATGA 58.871 33.333 0.00 0.00 0.00 2.92
693 993 7.914871 TGCATTAACGGTATTTGAAAGATGATG 59.085 33.333 0.00 0.00 0.00 3.07
694 994 7.995289 TGCATTAACGGTATTTGAAAGATGAT 58.005 30.769 0.00 0.00 0.00 2.45
695 995 7.335673 TCTGCATTAACGGTATTTGAAAGATGA 59.664 33.333 0.00 0.00 0.00 2.92
696 996 7.429340 GTCTGCATTAACGGTATTTGAAAGATG 59.571 37.037 0.00 0.00 0.00 2.90
697 997 7.415206 GGTCTGCATTAACGGTATTTGAAAGAT 60.415 37.037 0.00 0.00 0.00 2.40
698 998 6.128117 GGTCTGCATTAACGGTATTTGAAAGA 60.128 38.462 0.00 0.00 0.00 2.52
699 999 6.027749 GGTCTGCATTAACGGTATTTGAAAG 58.972 40.000 0.00 0.00 0.00 2.62
700 1000 5.473846 TGGTCTGCATTAACGGTATTTGAAA 59.526 36.000 0.00 0.00 0.00 2.69
701 1001 5.004448 TGGTCTGCATTAACGGTATTTGAA 58.996 37.500 0.00 0.00 0.00 2.69
702 1002 4.393680 GTGGTCTGCATTAACGGTATTTGA 59.606 41.667 0.00 0.00 0.00 2.69
703 1003 4.155099 TGTGGTCTGCATTAACGGTATTTG 59.845 41.667 0.00 0.00 0.00 2.32
704 1004 4.328536 TGTGGTCTGCATTAACGGTATTT 58.671 39.130 0.00 0.00 0.00 1.40
705 1005 3.945346 TGTGGTCTGCATTAACGGTATT 58.055 40.909 0.00 0.00 0.00 1.89
706 1006 3.620427 TGTGGTCTGCATTAACGGTAT 57.380 42.857 0.00 0.00 0.00 2.73
707 1007 3.404224 TTGTGGTCTGCATTAACGGTA 57.596 42.857 0.00 0.00 0.00 4.02
708 1008 2.264005 TTGTGGTCTGCATTAACGGT 57.736 45.000 0.00 0.00 0.00 4.83
709 1009 3.009723 AGATTGTGGTCTGCATTAACGG 58.990 45.455 0.00 0.00 0.00 4.44
710 1010 4.007282 CAGATTGTGGTCTGCATTAACG 57.993 45.455 0.00 0.00 39.19 3.18
718 1018 2.230508 AGCAAATGCAGATTGTGGTCTG 59.769 45.455 14.39 0.00 46.59 3.51
719 1019 2.522185 AGCAAATGCAGATTGTGGTCT 58.478 42.857 14.39 3.08 45.16 3.85
720 1020 3.057033 AGAAGCAAATGCAGATTGTGGTC 60.057 43.478 14.39 10.05 45.16 4.02
721 1021 2.895404 AGAAGCAAATGCAGATTGTGGT 59.105 40.909 14.39 0.00 45.16 4.16
722 1022 3.250744 CAGAAGCAAATGCAGATTGTGG 58.749 45.455 14.39 0.43 45.16 4.17
723 1023 3.057104 TCCAGAAGCAAATGCAGATTGTG 60.057 43.478 14.39 5.06 45.16 3.33
724 1024 3.057033 GTCCAGAAGCAAATGCAGATTGT 60.057 43.478 14.39 0.00 45.16 2.71
725 1025 3.192844 AGTCCAGAAGCAAATGCAGATTG 59.807 43.478 8.28 9.95 45.16 2.67
726 1026 3.428532 AGTCCAGAAGCAAATGCAGATT 58.571 40.909 8.28 0.00 45.16 2.40
727 1027 3.083122 AGTCCAGAAGCAAATGCAGAT 57.917 42.857 8.28 0.00 45.16 2.90
728 1028 2.574006 AGTCCAGAAGCAAATGCAGA 57.426 45.000 8.28 0.00 45.16 4.26
729 1029 4.197750 AGATAGTCCAGAAGCAAATGCAG 58.802 43.478 8.28 0.00 45.16 4.41
730 1030 4.226427 AGATAGTCCAGAAGCAAATGCA 57.774 40.909 8.28 0.00 45.16 3.96
731 1031 5.573337 AAAGATAGTCCAGAAGCAAATGC 57.427 39.130 0.00 0.00 42.49 3.56
732 1032 9.912634 TTTTAAAAGATAGTCCAGAAGCAAATG 57.087 29.630 0.00 0.00 0.00 2.32
736 1036 9.733556 TGTATTTTAAAAGATAGTCCAGAAGCA 57.266 29.630 6.79 0.00 0.00 3.91
737 1037 9.989869 GTGTATTTTAAAAGATAGTCCAGAAGC 57.010 33.333 6.79 0.00 0.00 3.86
749 1049 9.834628 GACCGATGAATTGTGTATTTTAAAAGA 57.165 29.630 6.79 0.00 0.00 2.52
750 1050 8.785101 CGACCGATGAATTGTGTATTTTAAAAG 58.215 33.333 6.79 0.00 0.00 2.27
751 1051 8.291032 ACGACCGATGAATTGTGTATTTTAAAA 58.709 29.630 2.51 2.51 0.00 1.52
752 1052 7.808672 ACGACCGATGAATTGTGTATTTTAAA 58.191 30.769 0.00 0.00 0.00 1.52
753 1053 7.367159 ACGACCGATGAATTGTGTATTTTAA 57.633 32.000 0.00 0.00 0.00 1.52
754 1054 6.971527 ACGACCGATGAATTGTGTATTTTA 57.028 33.333 0.00 0.00 0.00 1.52
755 1055 5.873179 ACGACCGATGAATTGTGTATTTT 57.127 34.783 0.00 0.00 0.00 1.82
756 1056 5.873179 AACGACCGATGAATTGTGTATTT 57.127 34.783 0.00 0.00 0.00 1.40
757 1057 5.873179 AAACGACCGATGAATTGTGTATT 57.127 34.783 0.00 0.00 0.00 1.89
758 1058 5.163794 GGAAAACGACCGATGAATTGTGTAT 60.164 40.000 0.00 0.00 0.00 2.29
759 1059 4.152759 GGAAAACGACCGATGAATTGTGTA 59.847 41.667 0.00 0.00 0.00 2.90
760 1060 3.058501 GGAAAACGACCGATGAATTGTGT 60.059 43.478 0.00 0.00 0.00 3.72
761 1061 3.188460 AGGAAAACGACCGATGAATTGTG 59.812 43.478 0.00 0.00 0.00 3.33
762 1062 3.408634 AGGAAAACGACCGATGAATTGT 58.591 40.909 0.00 0.00 0.00 2.71
763 1063 4.419522 AAGGAAAACGACCGATGAATTG 57.580 40.909 0.00 0.00 0.00 2.32
764 1064 5.470777 TGTAAAGGAAAACGACCGATGAATT 59.529 36.000 0.00 0.00 0.00 2.17
765 1065 4.998672 TGTAAAGGAAAACGACCGATGAAT 59.001 37.500 0.00 0.00 0.00 2.57
766 1066 4.378774 TGTAAAGGAAAACGACCGATGAA 58.621 39.130 0.00 0.00 0.00 2.57
767 1067 3.991773 CTGTAAAGGAAAACGACCGATGA 59.008 43.478 0.00 0.00 0.00 2.92
768 1068 3.424433 GCTGTAAAGGAAAACGACCGATG 60.424 47.826 0.00 0.00 0.00 3.84
769 1069 2.740447 GCTGTAAAGGAAAACGACCGAT 59.260 45.455 0.00 0.00 0.00 4.18
770 1070 2.137523 GCTGTAAAGGAAAACGACCGA 58.862 47.619 0.00 0.00 0.00 4.69
771 1071 2.140717 AGCTGTAAAGGAAAACGACCG 58.859 47.619 0.00 0.00 0.00 4.79
772 1072 3.135994 TGAGCTGTAAAGGAAAACGACC 58.864 45.455 0.00 0.00 0.00 4.79
773 1073 4.806342 TTGAGCTGTAAAGGAAAACGAC 57.194 40.909 0.00 0.00 0.00 4.34
774 1074 5.449451 GGTTTTGAGCTGTAAAGGAAAACGA 60.449 40.000 0.00 0.00 35.23 3.85
775 1075 4.738252 GGTTTTGAGCTGTAAAGGAAAACG 59.262 41.667 0.00 0.00 35.23 3.60
776 1076 5.656480 TGGTTTTGAGCTGTAAAGGAAAAC 58.344 37.500 0.00 0.00 34.18 2.43
781 1081 4.097892 ACACTTGGTTTTGAGCTGTAAAGG 59.902 41.667 0.00 0.00 0.00 3.11
786 1086 1.750778 CCACACTTGGTTTTGAGCTGT 59.249 47.619 0.00 0.00 38.23 4.40
787 1087 2.023673 TCCACACTTGGTTTTGAGCTG 58.976 47.619 0.00 0.00 44.35 4.24
797 1097 5.871396 ATACTAGTACCATCCACACTTGG 57.129 43.478 4.31 0.00 45.56 3.61
844 1144 8.520351 GGCATGGGGTATTTTTATACAGAATAC 58.480 37.037 0.00 0.00 36.17 1.89
846 1146 7.072562 TGGCATGGGGTATTTTTATACAGAAT 58.927 34.615 0.00 0.00 0.00 2.40
847 1147 6.436027 TGGCATGGGGTATTTTTATACAGAA 58.564 36.000 0.00 0.00 0.00 3.02
848 1148 6.019656 TGGCATGGGGTATTTTTATACAGA 57.980 37.500 0.00 0.00 0.00 3.41
896 1231 2.337879 TAGGATGCGGTTGATGGGGC 62.338 60.000 0.00 0.00 0.00 5.80
942 1277 2.217038 GGAGTGGTGGAGCACTGGA 61.217 63.158 15.89 0.00 34.40 3.86
989 1324 1.146358 GCCGCTCATCGTACAAGACC 61.146 60.000 0.00 0.00 36.19 3.85
1637 1973 2.806745 CGGTTGGTCACATTCTGTCACT 60.807 50.000 0.00 0.00 0.00 3.41
1638 1974 1.531149 CGGTTGGTCACATTCTGTCAC 59.469 52.381 0.00 0.00 0.00 3.67
1639 1975 1.414550 TCGGTTGGTCACATTCTGTCA 59.585 47.619 0.00 0.00 0.00 3.58
1640 1976 2.163818 TCGGTTGGTCACATTCTGTC 57.836 50.000 0.00 0.00 0.00 3.51
1641 1977 2.426522 CATCGGTTGGTCACATTCTGT 58.573 47.619 0.00 0.00 0.00 3.41
1642 1978 1.131126 GCATCGGTTGGTCACATTCTG 59.869 52.381 0.00 0.00 0.00 3.02
1644 1980 1.453155 AGCATCGGTTGGTCACATTC 58.547 50.000 0.00 0.00 0.00 2.67
1645 1981 1.909700 AAGCATCGGTTGGTCACATT 58.090 45.000 0.00 0.00 34.16 2.71
1719 2056 5.403512 CCTGGAATAGAGGATTGGGTACTA 58.596 45.833 0.00 0.00 31.48 1.82
1720 2057 4.235372 CCTGGAATAGAGGATTGGGTACT 58.765 47.826 0.00 0.00 31.48 2.73
1721 2058 3.244596 GCCTGGAATAGAGGATTGGGTAC 60.245 52.174 0.00 0.00 31.48 3.34
1729 2066 4.657814 AAACTTTGCCTGGAATAGAGGA 57.342 40.909 0.00 0.00 31.48 3.71
1880 2217 4.023193 CCCAAAGAAACATGACGCTAGTTT 60.023 41.667 0.00 0.00 38.10 2.66
2143 2628 0.238289 CGGTGTGCTTCGATTTTGCT 59.762 50.000 0.00 0.00 0.00 3.91
2313 2798 4.608514 TGGACTGGGGCTTGGGGA 62.609 66.667 0.00 0.00 0.00 4.81
2354 2839 1.327690 GGCAGACCTATGGACGGTGA 61.328 60.000 0.00 0.00 34.19 4.02
2387 2872 1.215382 CAATGACCGAGAGACGCCA 59.785 57.895 0.00 0.00 41.07 5.69
2452 2937 2.284331 TCCTTGCGGTCCTGCCTA 60.284 61.111 3.72 0.00 34.25 3.93
2518 3041 4.699522 GGGACTTCCGCAAGCCGT 62.700 66.667 0.00 0.00 36.71 5.68


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

AutoCloner maintained by Alex Coulton.