Multiple sequence alignment - TraesCS5D01G214700

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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 TraesCS5D01G214700 chr5D 100.000 4253 0 0 1 4253 324371392 324375644 0.000000e+00 7854.0
1 TraesCS5D01G214700 chr5D 96.764 618 20 0 1 618 27398158 27398775 0.000000e+00 1031.0
2 TraesCS5D01G214700 chr5D 94.516 620 34 0 2 621 27397451 27396832 0.000000e+00 957.0
3 TraesCS5D01G214700 chr5D 94.203 621 35 1 1 621 324370702 324370083 0.000000e+00 946.0
4 TraesCS5D01G214700 chr5B 95.249 3094 90 8 981 4020 375797591 375800681 0.000000e+00 4846.0
5 TraesCS5D01G214700 chr5B 90.840 262 10 2 4006 4253 375801881 375802142 5.270000e-89 339.0
6 TraesCS5D01G214700 chr5B 100.000 56 0 0 915 970 375797496 375797551 2.090000e-18 104.0
7 TraesCS5D01G214700 chr3D 92.639 883 47 12 1 870 32354337 32355214 0.000000e+00 1254.0
8 TraesCS5D01G214700 chr3D 92.414 145 11 0 728 872 562688803 562688947 1.550000e-49 207.0
9 TraesCS5D01G214700 chr3D 96.296 81 3 0 3611 3691 313178332 313178412 2.670000e-27 134.0
10 TraesCS5D01G214700 chr3D 94.048 84 5 0 3609 3692 489457442 489457525 1.240000e-25 128.0
11 TraesCS5D01G214700 chr1D 93.218 870 28 8 1 869 471616773 471615934 0.000000e+00 1251.0
12 TraesCS5D01G214700 chr1D 98.258 689 11 1 1 688 438282601 438283289 0.000000e+00 1205.0
13 TraesCS5D01G214700 chr1D 83.333 276 14 14 590 865 471617998 471618241 4.280000e-55 226.0
14 TraesCS5D01G214700 chr1D 93.182 88 5 1 3606 3693 348128523 348128609 1.240000e-25 128.0
15 TraesCS5D01G214700 chr2D 97.968 689 13 1 1 688 72112240 72111552 0.000000e+00 1194.0
16 TraesCS5D01G214700 chr2D 96.129 620 20 3 1 618 97084466 97085083 0.000000e+00 1009.0
17 TraesCS5D01G214700 chr2D 85.382 301 17 13 568 868 477296506 477296779 1.940000e-73 287.0
18 TraesCS5D01G214700 chr2D 88.571 140 15 1 555 693 543174815 543174954 7.310000e-38 169.0
19 TraesCS5D01G214700 chr2D 97.368 38 1 0 1139 1176 437642973 437643010 9.870000e-07 65.8
20 TraesCS5D01G214700 chr6D 94.049 689 37 2 1 688 32251568 32250883 0.000000e+00 1042.0
21 TraesCS5D01G214700 chr4A 87.363 641 50 11 228 868 456587221 456586612 0.000000e+00 706.0
22 TraesCS5D01G214700 chr4A 90.426 94 5 2 3599 3691 97531481 97531391 2.080000e-23 121.0
23 TraesCS5D01G214700 chr7B 82.857 280 20 10 590 869 93443888 93444139 4.280000e-55 226.0
24 TraesCS5D01G214700 chr2B 90.141 142 14 0 727 868 627048525 627048666 7.260000e-43 185.0
25 TraesCS5D01G214700 chr2B 95.000 100 4 1 590 688 655019240 655019339 5.690000e-34 156.0
26 TraesCS5D01G214700 chr3B 96.000 100 3 1 590 688 619057670 619057571 1.220000e-35 161.0
27 TraesCS5D01G214700 chr3B 91.579 95 5 3 3601 3693 556504494 556504587 1.240000e-25 128.0
28 TraesCS5D01G214700 chr4B 90.385 104 8 2 3601 3704 670403245 670403346 7.420000e-28 135.0
29 TraesCS5D01G214700 chr1A 83.803 142 20 3 726 866 66696630 66696769 9.600000e-27 132.0
30 TraesCS5D01G214700 chr3A 95.062 81 4 0 3611 3691 419336177 419336097 1.240000e-25 128.0
31 TraesCS5D01G214700 chr6B 93.976 83 5 0 3609 3691 58801816 58801734 4.460000e-25 126.0


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 TraesCS5D01G214700 chr5D 324371392 324375644 4252 False 7854 7854 100.000 1 4253 1 chr5D.!!$F2 4252
1 TraesCS5D01G214700 chr5D 27398158 27398775 617 False 1031 1031 96.764 1 618 1 chr5D.!!$F1 617
2 TraesCS5D01G214700 chr5D 27396832 27397451 619 True 957 957 94.516 2 621 1 chr5D.!!$R1 619
3 TraesCS5D01G214700 chr5D 324370083 324370702 619 True 946 946 94.203 1 621 1 chr5D.!!$R2 620
4 TraesCS5D01G214700 chr5B 375797496 375802142 4646 False 1763 4846 95.363 915 4253 3 chr5B.!!$F1 3338
5 TraesCS5D01G214700 chr3D 32354337 32355214 877 False 1254 1254 92.639 1 870 1 chr3D.!!$F1 869
6 TraesCS5D01G214700 chr1D 471615934 471616773 839 True 1251 1251 93.218 1 869 1 chr1D.!!$R1 868
7 TraesCS5D01G214700 chr1D 438282601 438283289 688 False 1205 1205 98.258 1 688 1 chr1D.!!$F2 687
8 TraesCS5D01G214700 chr2D 72111552 72112240 688 True 1194 1194 97.968 1 688 1 chr2D.!!$R1 687
9 TraesCS5D01G214700 chr2D 97084466 97085083 617 False 1009 1009 96.129 1 618 1 chr2D.!!$F1 617
10 TraesCS5D01G214700 chr6D 32250883 32251568 685 True 1042 1042 94.049 1 688 1 chr6D.!!$R1 687
11 TraesCS5D01G214700 chr4A 456586612 456587221 609 True 706 706 87.363 228 868 1 chr4A.!!$R2 640

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
715 822 0.109781 CACGCTGGACCGGAAAAATG 60.110 55.0 9.46 0.0 0.00 2.32 F
1602 1738 0.251916 TGGATGTCCGTGGGAATGAC 59.748 55.0 0.00 0.0 39.43 3.06 F
2600 2772 0.186386 ACCGGAGAGGAGGGACTATG 59.814 60.0 9.46 0.0 41.55 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1741 0.598158 TCACCCACGCGTTTGAGTAC 60.598 55.000 10.22 0.0 0.00 2.73 R
2896 3086 2.158534 TGGTTTGTTCTGTGGCCAGTAT 60.159 45.455 5.11 0.0 39.82 2.12 R
3720 3910 1.643286 TGTTATGGGATGGGCAAAGGA 59.357 47.619 0.00 0.0 0.00 3.36 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
575 611 1.699634 TGCAGCTCCTTTCAGTTAGGT 59.300 47.619 0.00 0.00 34.29 3.08
577 613 2.551071 GCAGCTCCTTTCAGTTAGGTGT 60.551 50.000 0.00 0.00 39.16 4.16
689 796 4.680237 CTGCCACGCTGGACCGAA 62.680 66.667 8.04 0.00 40.96 4.30
693 800 2.738521 CACGCTGGACCGAAGTGG 60.739 66.667 5.44 0.00 46.41 4.00
694 801 2.915659 ACGCTGGACCGAAGTGGA 60.916 61.111 0.00 0.00 42.00 4.02
695 802 2.432628 CGCTGGACCGAAGTGGAC 60.433 66.667 0.00 0.00 42.00 4.02
700 807 2.737376 GACCGAAGTGGACCACGC 60.737 66.667 18.93 13.78 42.00 5.34
701 808 3.222354 GACCGAAGTGGACCACGCT 62.222 63.158 18.93 10.37 42.00 5.07
702 809 2.738521 CCGAAGTGGACCACGCTG 60.739 66.667 18.93 11.80 40.51 5.18
703 810 2.738521 CGAAGTGGACCACGCTGG 60.739 66.667 18.93 8.03 45.02 4.85
704 811 2.741092 GAAGTGGACCACGCTGGA 59.259 61.111 18.93 0.00 40.96 3.86
705 812 1.668151 GAAGTGGACCACGCTGGAC 60.668 63.158 18.93 4.78 40.96 4.02
710 817 3.998672 GACCACGCTGGACCGGAA 61.999 66.667 9.46 0.00 40.96 4.30
711 818 3.524648 GACCACGCTGGACCGGAAA 62.525 63.158 9.46 0.00 40.96 3.13
712 819 2.281208 CCACGCTGGACCGGAAAA 60.281 61.111 9.46 0.00 40.96 2.29
713 820 1.894756 CCACGCTGGACCGGAAAAA 60.895 57.895 9.46 0.00 40.96 1.94
714 821 1.241315 CCACGCTGGACCGGAAAAAT 61.241 55.000 9.46 0.00 40.96 1.82
715 822 0.109781 CACGCTGGACCGGAAAAATG 60.110 55.000 9.46 0.00 0.00 2.32
716 823 0.536460 ACGCTGGACCGGAAAAATGT 60.536 50.000 9.46 0.00 0.00 2.71
717 824 0.109781 CGCTGGACCGGAAAAATGTG 60.110 55.000 9.46 0.00 0.00 3.21
718 825 0.388520 GCTGGACCGGAAAAATGTGC 60.389 55.000 9.46 0.00 0.00 4.57
719 826 0.958091 CTGGACCGGAAAAATGTGCA 59.042 50.000 9.46 0.00 0.00 4.57
720 827 1.339610 CTGGACCGGAAAAATGTGCAA 59.660 47.619 9.46 0.00 29.78 4.08
721 828 1.067821 TGGACCGGAAAAATGTGCAAC 59.932 47.619 9.46 0.00 37.35 4.17
788 895 2.029964 GGGTGCCACTCGAAACGA 59.970 61.111 0.00 0.00 0.00 3.85
802 909 2.926200 CGAAACGATCAGCTCAGTGAAT 59.074 45.455 0.00 0.00 0.00 2.57
849 956 5.588648 TGTGAATTCTTTTCGTCCTCAAGTT 59.411 36.000 7.05 0.00 0.00 2.66
885 992 2.193306 CCGACAAATGGCAATGCTAC 57.807 50.000 4.82 0.00 0.00 3.58
886 993 1.745087 CCGACAAATGGCAATGCTACT 59.255 47.619 4.82 0.00 0.00 2.57
887 994 2.164219 CCGACAAATGGCAATGCTACTT 59.836 45.455 4.82 0.00 0.00 2.24
888 995 3.429085 CGACAAATGGCAATGCTACTTC 58.571 45.455 4.82 0.00 0.00 3.01
889 996 3.731867 CGACAAATGGCAATGCTACTTCC 60.732 47.826 4.82 0.00 0.00 3.46
890 997 3.434309 ACAAATGGCAATGCTACTTCCT 58.566 40.909 4.82 0.00 0.00 3.36
891 998 3.445096 ACAAATGGCAATGCTACTTCCTC 59.555 43.478 4.82 0.00 0.00 3.71
892 999 3.659183 AATGGCAATGCTACTTCCTCT 57.341 42.857 4.82 0.00 0.00 3.69
893 1000 2.698855 TGGCAATGCTACTTCCTCTC 57.301 50.000 4.82 0.00 0.00 3.20
894 1001 1.210478 TGGCAATGCTACTTCCTCTCC 59.790 52.381 4.82 0.00 0.00 3.71
895 1002 1.210478 GGCAATGCTACTTCCTCTCCA 59.790 52.381 4.82 0.00 0.00 3.86
896 1003 2.158696 GGCAATGCTACTTCCTCTCCAT 60.159 50.000 4.82 0.00 0.00 3.41
897 1004 3.549794 GCAATGCTACTTCCTCTCCATT 58.450 45.455 0.00 0.00 0.00 3.16
898 1005 3.950395 GCAATGCTACTTCCTCTCCATTT 59.050 43.478 0.00 0.00 0.00 2.32
899 1006 4.036144 GCAATGCTACTTCCTCTCCATTTC 59.964 45.833 0.00 0.00 0.00 2.17
900 1007 3.914426 TGCTACTTCCTCTCCATTTCC 57.086 47.619 0.00 0.00 0.00 3.13
901 1008 3.181329 TGCTACTTCCTCTCCATTTCCA 58.819 45.455 0.00 0.00 0.00 3.53
902 1009 3.587061 TGCTACTTCCTCTCCATTTCCAA 59.413 43.478 0.00 0.00 0.00 3.53
903 1010 4.195416 GCTACTTCCTCTCCATTTCCAAG 58.805 47.826 0.00 0.00 0.00 3.61
904 1011 4.323868 GCTACTTCCTCTCCATTTCCAAGT 60.324 45.833 0.00 0.00 0.00 3.16
905 1012 4.293662 ACTTCCTCTCCATTTCCAAGTC 57.706 45.455 0.00 0.00 0.00 3.01
906 1013 3.913163 ACTTCCTCTCCATTTCCAAGTCT 59.087 43.478 0.00 0.00 0.00 3.24
907 1014 3.988976 TCCTCTCCATTTCCAAGTCTG 57.011 47.619 0.00 0.00 0.00 3.51
908 1015 3.520696 TCCTCTCCATTTCCAAGTCTGA 58.479 45.455 0.00 0.00 0.00 3.27
909 1016 3.517100 TCCTCTCCATTTCCAAGTCTGAG 59.483 47.826 0.00 0.00 0.00 3.35
910 1017 3.269178 CTCTCCATTTCCAAGTCTGAGC 58.731 50.000 0.00 0.00 0.00 4.26
911 1018 2.026822 TCTCCATTTCCAAGTCTGAGCC 60.027 50.000 0.00 0.00 0.00 4.70
912 1019 1.004745 TCCATTTCCAAGTCTGAGCCC 59.995 52.381 0.00 0.00 0.00 5.19
913 1020 1.272092 CCATTTCCAAGTCTGAGCCCA 60.272 52.381 0.00 0.00 0.00 5.36
970 1077 0.614979 TCCTTCTCCCCTGGTTCGAG 60.615 60.000 0.00 0.00 0.00 4.04
972 1079 2.564553 CTTCTCCCCTGGTTCGAGCG 62.565 65.000 0.00 0.00 0.00 5.03
974 1081 2.602267 TCCCCTGGTTCGAGCGAA 60.602 61.111 0.55 0.55 0.00 4.70
975 1082 2.125512 CCCCTGGTTCGAGCGAAG 60.126 66.667 5.46 0.00 34.49 3.79
976 1083 2.657237 CCCTGGTTCGAGCGAAGT 59.343 61.111 5.46 0.00 34.49 3.01
979 1086 1.284982 CCTGGTTCGAGCGAAGTGTG 61.285 60.000 5.46 0.00 34.49 3.82
1007 1143 2.505982 CGGAGGGGCGATGACAAT 59.494 61.111 0.00 0.00 0.00 2.71
1393 1529 0.689412 CCTCCACTCCTCCCTCTTCC 60.689 65.000 0.00 0.00 0.00 3.46
1416 1552 3.050275 GCCCAACTCACGCACCTC 61.050 66.667 0.00 0.00 0.00 3.85
1423 1559 2.666190 TCACGCACCTCAAGCTGC 60.666 61.111 0.00 0.00 0.00 5.25
1424 1560 2.974148 CACGCACCTCAAGCTGCA 60.974 61.111 1.02 0.00 32.57 4.41
1428 1564 2.195567 GCACCTCAAGCTGCACCAA 61.196 57.895 1.02 0.00 33.31 3.67
1481 1617 0.259938 GGATTCCCCATGCTCAAGGT 59.740 55.000 0.00 0.00 34.14 3.50
1492 1628 4.142816 CCATGCTCAAGGTTCTAAAACTCG 60.143 45.833 0.00 0.00 35.61 4.18
1495 1631 2.742589 CTCAAGGTTCTAAAACTCGGCC 59.257 50.000 0.00 0.00 35.61 6.13
1503 1639 2.232941 TCTAAAACTCGGCCTTGTCGAT 59.767 45.455 0.00 0.00 39.46 3.59
1508 1644 1.078708 TCGGCCTTGTCGATTTCCC 60.079 57.895 0.00 0.00 33.73 3.97
1554 1690 0.739813 CGATTCTTGTCGGGTCACCC 60.740 60.000 1.06 1.06 41.09 4.61
1588 1724 4.157289 CCCTGAATCTTCACTTTGTGGATG 59.843 45.833 0.00 0.00 33.87 3.51
1599 1735 0.695924 TTGTGGATGTCCGTGGGAAT 59.304 50.000 0.00 0.00 39.43 3.01
1602 1738 0.251916 TGGATGTCCGTGGGAATGAC 59.748 55.000 0.00 0.00 39.43 3.06
1603 1739 0.810031 GGATGTCCGTGGGAATGACG 60.810 60.000 0.00 0.00 31.38 4.35
1605 1741 3.186047 GTCCGTGGGAATGACGCG 61.186 66.667 3.53 3.53 41.15 6.01
1614 1750 1.392510 GGGAATGACGCGTACTCAAAC 59.607 52.381 13.97 4.79 0.00 2.93
1658 1794 1.269998 CCTCCGGAGCCTAACGATAAG 59.730 57.143 26.87 3.64 0.00 1.73
1665 1801 4.361420 GGAGCCTAACGATAAGTTCTGAC 58.639 47.826 0.00 0.00 43.06 3.51
1671 1807 6.535508 GCCTAACGATAAGTTCTGACTTTGAT 59.464 38.462 0.00 0.00 43.48 2.57
1700 1836 1.133790 GCAAGTTAAGGAGCTGCCATG 59.866 52.381 0.00 0.00 40.02 3.66
1702 1838 0.329261 AGTTAAGGAGCTGCCATGCA 59.671 50.000 0.00 0.00 40.02 3.96
1708 1844 1.574925 GAGCTGCCATGCATCGATG 59.425 57.895 21.27 21.27 38.13 3.84
1712 1848 1.306148 CTGCCATGCATCGATGAAGT 58.694 50.000 29.20 10.46 38.13 3.01
1780 1916 2.027897 TTGCCAGCTTTGCGCAAG 59.972 55.556 23.68 17.61 42.61 4.01
1797 1939 3.733684 CGCAAGTTAGGAAGCTCTCTCTC 60.734 52.174 0.00 0.00 0.00 3.20
1810 1952 0.523519 CTCTCTCTGTGCGTGCTACA 59.476 55.000 0.00 0.00 0.00 2.74
1987 2130 1.416401 GAGTTTGACCCTCTGGACACA 59.584 52.381 0.00 0.00 36.01 3.72
1991 2134 2.859165 TGACCCTCTGGACACATTTC 57.141 50.000 0.00 0.00 31.12 2.17
1994 2137 3.260884 TGACCCTCTGGACACATTTCTAC 59.739 47.826 0.00 0.00 31.12 2.59
1997 2140 3.056107 CCCTCTGGACACATTTCTACGAA 60.056 47.826 0.00 0.00 0.00 3.85
2002 2145 3.438781 TGGACACATTTCTACGAAATGCC 59.561 43.478 22.39 17.41 40.35 4.40
2004 2147 4.437390 GGACACATTTCTACGAAATGCCTG 60.437 45.833 22.39 17.74 40.35 4.85
2009 2152 3.552132 TTCTACGAAATGCCTGCCATA 57.448 42.857 0.00 0.00 32.67 2.74
2025 2168 4.148838 TGCCATAGTGTTAACCTTTTGCT 58.851 39.130 2.48 0.00 0.00 3.91
2037 2180 8.573035 TGTTAACCTTTTGCTTACTAAGGAATG 58.427 33.333 2.48 1.54 40.71 2.67
2103 2246 2.747446 ACCGCCTTGCAAACTATTGTAG 59.253 45.455 0.00 0.00 38.85 2.74
2104 2247 2.747446 CCGCCTTGCAAACTATTGTAGT 59.253 45.455 0.00 0.00 41.73 2.73
2144 2287 5.870433 TCATCATTGCTATTTTTGGTGCTTG 59.130 36.000 0.00 0.00 0.00 4.01
2584 2756 6.452242 TGTGCTACCATTATTGTCTATACCG 58.548 40.000 0.00 0.00 0.00 4.02
2596 2768 1.704070 TCTATACCGGAGAGGAGGGAC 59.296 57.143 9.46 0.00 45.00 4.46
2600 2772 0.186386 ACCGGAGAGGAGGGACTATG 59.814 60.000 9.46 0.00 41.55 2.23
2623 2795 6.122277 TGGATGGAAATAGGATGAACACTTC 58.878 40.000 0.00 0.00 0.00 3.01
2630 2802 7.361286 GGAAATAGGATGAACACTTCTGTCAAC 60.361 40.741 0.00 0.00 0.00 3.18
2840 3029 1.946745 CTGCCTTTACTCTAGCAGCC 58.053 55.000 0.00 0.00 45.44 4.85
2896 3086 9.202273 GGACAAACATTAAGTGCAAATTATCAA 57.798 29.630 0.00 0.00 0.00 2.57
2921 3111 1.067060 GGCCACAGAACAAACCACTTC 59.933 52.381 0.00 0.00 0.00 3.01
2938 3128 7.448748 ACCACTTCGTGATAATTTAGCTTTT 57.551 32.000 0.00 0.00 35.23 2.27
3026 3216 5.163754 GGGACAAAAAGTTGATAGTGATCCG 60.164 44.000 0.00 0.00 38.20 4.18
3088 3278 6.320418 TCTTCATGCTTCACTGAATGCATTAT 59.680 34.615 12.97 0.00 43.24 1.28
3125 3315 1.001048 ACACGTGCTGCTACTTCGTTA 60.001 47.619 17.22 0.00 32.47 3.18
3260 3450 6.261118 CAGGTAAAATGAAATGAGCTGCTAC 58.739 40.000 0.15 0.00 0.00 3.58
3603 3793 6.006275 AGTGGGATAGTAGCAATGACAAAT 57.994 37.500 0.00 0.00 0.00 2.32
3738 3928 3.704545 ATTCCTTTGCCCATCCCATAA 57.295 42.857 0.00 0.00 0.00 1.90
3746 3936 2.176581 TGCCCATCCCATAACATTAGCA 59.823 45.455 0.00 0.00 0.00 3.49
3775 3965 7.255070 GCAACATGCCTTGGAAAAATTAAAAGA 60.255 33.333 0.00 0.00 37.42 2.52
3794 3984 3.290710 AGAAGCAGGAGAAAAGCAACAA 58.709 40.909 0.00 0.00 0.00 2.83
4125 5543 1.832883 TGTGCAACACAGTGTCCTTT 58.167 45.000 6.67 0.00 45.67 3.11
4195 5613 8.641498 ATGTGGATTCTTTTCATTCTTGTACT 57.359 30.769 0.00 0.00 0.00 2.73
4196 5614 7.874940 TGTGGATTCTTTTCATTCTTGTACTG 58.125 34.615 0.00 0.00 0.00 2.74
4199 5617 9.958180 TGGATTCTTTTCATTCTTGTACTGATA 57.042 29.630 0.00 0.00 0.00 2.15
4209 5627 9.936759 TCATTCTTGTACTGATATTTGTACACA 57.063 29.630 16.40 0.00 45.59 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 180 8.565896 ACATGTTCATTTCTTGCATCTAAGTA 57.434 30.769 0.00 0.00 0.00 2.24
212 213 3.705579 TGCCTATGCTTGCCATGTTAATT 59.294 39.130 0.00 0.00 38.71 1.40
532 533 1.135199 GTGTAGTGCAGCGCCTAACTA 60.135 52.381 2.29 6.69 0.00 2.24
689 796 3.626924 GGTCCAGCGTGGTCCACT 61.627 66.667 19.82 0.00 43.84 4.00
693 800 2.999739 TTTTCCGGTCCAGCGTGGTC 63.000 60.000 0.00 0.00 39.03 4.02
694 801 2.612095 TTTTTCCGGTCCAGCGTGGT 62.612 55.000 0.00 0.00 39.03 4.16
695 802 1.241315 ATTTTTCCGGTCCAGCGTGG 61.241 55.000 0.00 0.00 39.43 4.94
697 804 0.536460 ACATTTTTCCGGTCCAGCGT 60.536 50.000 0.00 0.00 0.00 5.07
698 805 0.109781 CACATTTTTCCGGTCCAGCG 60.110 55.000 0.00 0.00 0.00 5.18
699 806 0.388520 GCACATTTTTCCGGTCCAGC 60.389 55.000 0.00 0.00 0.00 4.85
700 807 0.958091 TGCACATTTTTCCGGTCCAG 59.042 50.000 0.00 0.00 0.00 3.86
701 808 1.067821 GTTGCACATTTTTCCGGTCCA 59.932 47.619 0.00 0.00 0.00 4.02
702 809 1.067821 TGTTGCACATTTTTCCGGTCC 59.932 47.619 0.00 0.00 0.00 4.46
703 810 2.500509 TGTTGCACATTTTTCCGGTC 57.499 45.000 0.00 0.00 0.00 4.79
704 811 3.613910 GCTATGTTGCACATTTTTCCGGT 60.614 43.478 0.00 0.00 39.88 5.28
705 812 2.923020 GCTATGTTGCACATTTTTCCGG 59.077 45.455 0.00 0.00 39.88 5.14
706 813 2.923020 GGCTATGTTGCACATTTTTCCG 59.077 45.455 7.02 0.00 39.88 4.30
707 814 4.192429 AGGCTATGTTGCACATTTTTCC 57.808 40.909 7.02 4.76 39.88 3.13
708 815 6.620678 TCTTAGGCTATGTTGCACATTTTTC 58.379 36.000 7.24 0.00 39.88 2.29
709 816 6.588719 TCTTAGGCTATGTTGCACATTTTT 57.411 33.333 7.24 0.00 39.88 1.94
710 817 5.393461 GCTCTTAGGCTATGTTGCACATTTT 60.393 40.000 16.47 0.00 39.88 1.82
711 818 4.096984 GCTCTTAGGCTATGTTGCACATTT 59.903 41.667 16.47 0.00 39.88 2.32
712 819 3.629398 GCTCTTAGGCTATGTTGCACATT 59.371 43.478 16.47 0.00 39.88 2.71
713 820 3.209410 GCTCTTAGGCTATGTTGCACAT 58.791 45.455 16.47 6.93 42.35 3.21
714 821 2.632377 GCTCTTAGGCTATGTTGCACA 58.368 47.619 16.47 0.00 34.04 4.57
715 822 1.943340 GGCTCTTAGGCTATGTTGCAC 59.057 52.381 20.00 11.63 37.85 4.57
716 823 1.559219 TGGCTCTTAGGCTATGTTGCA 59.441 47.619 20.00 0.00 41.96 4.08
717 824 2.216898 CTGGCTCTTAGGCTATGTTGC 58.783 52.381 7.24 11.57 41.96 4.17
718 825 2.843701 CCTGGCTCTTAGGCTATGTTG 58.156 52.381 7.24 3.86 41.96 3.33
820 927 7.158697 TGAGGACGAAAAGAATTCACAATCTA 58.841 34.615 8.44 0.00 0.00 1.98
870 977 3.698040 AGAGGAAGTAGCATTGCCATTTG 59.302 43.478 4.70 0.00 0.00 2.32
871 978 3.950395 GAGAGGAAGTAGCATTGCCATTT 59.050 43.478 4.70 0.00 0.00 2.32
872 979 3.549794 GAGAGGAAGTAGCATTGCCATT 58.450 45.455 4.70 0.00 0.00 3.16
873 980 2.158696 GGAGAGGAAGTAGCATTGCCAT 60.159 50.000 4.70 0.00 0.00 4.40
874 981 1.210478 GGAGAGGAAGTAGCATTGCCA 59.790 52.381 4.70 0.00 0.00 4.92
875 982 1.210478 TGGAGAGGAAGTAGCATTGCC 59.790 52.381 4.70 0.00 0.00 4.52
876 983 2.698855 TGGAGAGGAAGTAGCATTGC 57.301 50.000 0.00 0.00 0.00 3.56
877 984 4.578105 GGAAATGGAGAGGAAGTAGCATTG 59.422 45.833 0.00 0.00 0.00 2.82
878 985 4.228210 TGGAAATGGAGAGGAAGTAGCATT 59.772 41.667 0.00 0.00 0.00 3.56
879 986 3.782523 TGGAAATGGAGAGGAAGTAGCAT 59.217 43.478 0.00 0.00 0.00 3.79
880 987 3.181329 TGGAAATGGAGAGGAAGTAGCA 58.819 45.455 0.00 0.00 0.00 3.49
881 988 3.914426 TGGAAATGGAGAGGAAGTAGC 57.086 47.619 0.00 0.00 0.00 3.58
882 989 5.188751 AGACTTGGAAATGGAGAGGAAGTAG 59.811 44.000 0.00 0.00 0.00 2.57
883 990 5.046304 CAGACTTGGAAATGGAGAGGAAGTA 60.046 44.000 0.00 0.00 0.00 2.24
884 991 3.913163 AGACTTGGAAATGGAGAGGAAGT 59.087 43.478 0.00 0.00 0.00 3.01
885 992 4.019860 TCAGACTTGGAAATGGAGAGGAAG 60.020 45.833 0.00 0.00 0.00 3.46
886 993 3.909995 TCAGACTTGGAAATGGAGAGGAA 59.090 43.478 0.00 0.00 0.00 3.36
887 994 3.517100 CTCAGACTTGGAAATGGAGAGGA 59.483 47.826 0.00 0.00 0.00 3.71
888 995 3.871485 CTCAGACTTGGAAATGGAGAGG 58.129 50.000 0.00 0.00 0.00 3.69
889 996 3.269178 GCTCAGACTTGGAAATGGAGAG 58.731 50.000 0.00 0.00 0.00 3.20
890 997 2.026822 GGCTCAGACTTGGAAATGGAGA 60.027 50.000 0.00 0.00 0.00 3.71
891 998 2.363683 GGCTCAGACTTGGAAATGGAG 58.636 52.381 0.00 0.00 0.00 3.86
892 999 1.004745 GGGCTCAGACTTGGAAATGGA 59.995 52.381 0.00 0.00 0.00 3.41
893 1000 1.272092 TGGGCTCAGACTTGGAAATGG 60.272 52.381 0.00 0.00 0.00 3.16
894 1001 1.815003 GTGGGCTCAGACTTGGAAATG 59.185 52.381 0.00 0.00 0.00 2.32
895 1002 1.272147 GGTGGGCTCAGACTTGGAAAT 60.272 52.381 0.00 0.00 0.00 2.17
896 1003 0.110486 GGTGGGCTCAGACTTGGAAA 59.890 55.000 0.00 0.00 0.00 3.13
897 1004 1.761174 GGTGGGCTCAGACTTGGAA 59.239 57.895 0.00 0.00 0.00 3.53
898 1005 2.224159 GGGTGGGCTCAGACTTGGA 61.224 63.158 0.00 0.00 0.00 3.53
899 1006 2.352805 GGGTGGGCTCAGACTTGG 59.647 66.667 0.00 0.00 0.00 3.61
900 1007 2.046892 CGGGTGGGCTCAGACTTG 60.047 66.667 0.00 0.00 0.00 3.16
901 1008 2.526873 ACGGGTGGGCTCAGACTT 60.527 61.111 0.00 0.00 0.00 3.01
902 1009 2.997897 GACGGGTGGGCTCAGACT 60.998 66.667 0.00 0.00 0.00 3.24
903 1010 1.327690 TATGACGGGTGGGCTCAGAC 61.328 60.000 0.00 0.00 0.00 3.51
904 1011 1.001120 TATGACGGGTGGGCTCAGA 59.999 57.895 0.00 0.00 0.00 3.27
905 1012 1.144057 GTATGACGGGTGGGCTCAG 59.856 63.158 0.00 0.00 0.00 3.35
906 1013 1.305802 AGTATGACGGGTGGGCTCA 60.306 57.895 0.00 0.00 0.00 4.26
907 1014 1.144057 CAGTATGACGGGTGGGCTC 59.856 63.158 0.00 0.00 39.69 4.70
908 1015 3.031417 GCAGTATGACGGGTGGGCT 62.031 63.158 0.00 0.00 39.69 5.19
909 1016 2.513897 GCAGTATGACGGGTGGGC 60.514 66.667 0.00 0.00 39.69 5.36
910 1017 1.144057 GAGCAGTATGACGGGTGGG 59.856 63.158 0.00 0.00 39.69 4.61
911 1018 0.179100 CAGAGCAGTATGACGGGTGG 60.179 60.000 0.00 0.00 39.69 4.61
912 1019 0.179100 CCAGAGCAGTATGACGGGTG 60.179 60.000 0.00 0.00 39.69 4.61
913 1020 0.324368 TCCAGAGCAGTATGACGGGT 60.324 55.000 0.00 0.00 39.69 5.28
970 1077 1.741770 CCTGTAGCCCACACTTCGC 60.742 63.158 0.00 0.00 32.33 4.70
972 1079 1.377333 GCCCTGTAGCCCACACTTC 60.377 63.158 0.00 0.00 32.33 3.01
974 1081 3.706373 CGCCCTGTAGCCCACACT 61.706 66.667 0.00 0.00 32.33 3.55
975 1082 4.778143 CCGCCCTGTAGCCCACAC 62.778 72.222 0.00 0.00 32.33 3.82
1088 1224 4.899239 CGAGGCGGGTGAGGATGC 62.899 72.222 0.00 0.00 0.00 3.91
1340 1476 0.815615 GCATCGGAGGTTGATGGACC 60.816 60.000 5.25 0.00 42.73 4.46
1393 1529 3.398920 CGTGAGTTGGGCGCATAG 58.601 61.111 10.83 0.00 0.00 2.23
1481 1617 2.036217 TCGACAAGGCCGAGTTTTAGAA 59.964 45.455 0.00 0.00 0.00 2.10
1492 1628 2.112815 CCGGGAAATCGACAAGGCC 61.113 63.158 0.00 0.00 0.00 5.19
1495 1631 2.000447 GTTCTCCGGGAAATCGACAAG 59.000 52.381 0.00 0.00 35.51 3.16
1508 1644 3.839432 GGCTCTCCCCGTTCTCCG 61.839 72.222 0.00 0.00 0.00 4.63
1554 1690 4.279169 TGAAGATTCAGGGTTTCAAGCAAG 59.721 41.667 0.00 0.00 32.50 4.01
1588 1724 2.546645 TACGCGTCATTCCCACGGAC 62.547 60.000 18.63 0.00 37.74 4.79
1605 1741 0.598158 TCACCCACGCGTTTGAGTAC 60.598 55.000 10.22 0.00 0.00 2.73
1658 1794 5.412594 TGCCAGTCATAATCAAAGTCAGAAC 59.587 40.000 0.00 0.00 0.00 3.01
1665 1801 7.121168 TCCTTAACTTGCCAGTCATAATCAAAG 59.879 37.037 0.00 0.00 30.45 2.77
1671 1807 4.019321 AGCTCCTTAACTTGCCAGTCATAA 60.019 41.667 0.00 0.00 30.45 1.90
1715 1851 4.875536 TCACATAGTTTCCAACATCGATGG 59.124 41.667 28.09 13.66 39.41 3.51
1740 1876 9.113838 GCAAGAAATCCTCTGAACTTGATATTA 57.886 33.333 0.00 0.00 34.85 0.98
1741 1877 7.067981 GGCAAGAAATCCTCTGAACTTGATATT 59.932 37.037 0.00 0.00 34.85 1.28
1742 1878 6.545298 GGCAAGAAATCCTCTGAACTTGATAT 59.455 38.462 0.00 0.00 34.85 1.63
1749 1885 2.163211 GCTGGCAAGAAATCCTCTGAAC 59.837 50.000 0.00 0.00 33.37 3.18
1780 1916 3.428862 GCACAGAGAGAGAGCTTCCTAAC 60.429 52.174 0.00 0.00 0.00 2.34
1810 1952 6.938030 TGGTAAGAACAGAAAATTACCGATGT 59.062 34.615 8.09 0.00 46.67 3.06
1857 1999 4.523558 TCAATGCAAATGTGGATCAGAACA 59.476 37.500 0.00 0.00 34.17 3.18
1925 2068 2.930826 GAAGTGTTTCCAGGAGACCA 57.069 50.000 7.67 0.00 0.00 4.02
1987 2130 2.722094 TGGCAGGCATTTCGTAGAAAT 58.278 42.857 0.00 2.49 45.90 2.17
1991 2134 2.545526 CACTATGGCAGGCATTTCGTAG 59.454 50.000 15.80 8.40 0.00 3.51
1994 2137 1.382522 ACACTATGGCAGGCATTTCG 58.617 50.000 15.80 6.89 0.00 3.46
1997 2140 3.023832 GGTTAACACTATGGCAGGCATT 58.976 45.455 15.80 0.00 0.00 3.56
2002 2145 4.218417 AGCAAAAGGTTAACACTATGGCAG 59.782 41.667 8.10 0.00 0.00 4.85
2004 2147 4.783764 AGCAAAAGGTTAACACTATGGC 57.216 40.909 8.10 3.83 0.00 4.40
2009 2152 7.284820 TCCTTAGTAAGCAAAAGGTTAACACT 58.715 34.615 8.10 1.56 40.58 3.55
2037 2180 8.956533 ATTTCAAGTTCTTCTAGATTAGGAGC 57.043 34.615 0.00 0.00 31.11 4.70
2046 2189 9.582431 TCATACCGTAATTTCAAGTTCTTCTAG 57.418 33.333 0.00 0.00 0.00 2.43
2103 2246 4.009675 TGATGACCTCCAAGCATAACAAC 58.990 43.478 0.00 0.00 0.00 3.32
2104 2247 4.299586 TGATGACCTCCAAGCATAACAA 57.700 40.909 0.00 0.00 0.00 2.83
2105 2248 3.998913 TGATGACCTCCAAGCATAACA 57.001 42.857 0.00 0.00 0.00 2.41
2115 2258 5.127682 ACCAAAAATAGCAATGATGACCTCC 59.872 40.000 0.00 0.00 0.00 4.30
2144 2287 9.701355 CATCACCAAAAATAAACAAAAAGTGTC 57.299 29.630 0.00 0.00 40.60 3.67
2148 2291 7.500559 TCCCCATCACCAAAAATAAACAAAAAG 59.499 33.333 0.00 0.00 0.00 2.27
2242 2396 7.718753 ACCAGCCAATATTTTTCATTTTCACAA 59.281 29.630 0.00 0.00 0.00 3.33
2539 2711 6.248433 CACATAATATATCAACCCAAGGGCT 58.752 40.000 4.70 0.00 39.32 5.19
2584 2756 2.534990 CATCCATAGTCCCTCCTCTCC 58.465 57.143 0.00 0.00 0.00 3.71
2596 2768 7.456725 AGTGTTCATCCTATTTCCATCCATAG 58.543 38.462 0.00 0.00 0.00 2.23
2600 2772 6.261826 CAGAAGTGTTCATCCTATTTCCATCC 59.738 42.308 0.00 0.00 0.00 3.51
2623 2795 5.678132 TCACATGTGATTTCTGTTGACAG 57.322 39.130 24.56 4.77 38.80 3.51
2896 3086 2.158534 TGGTTTGTTCTGTGGCCAGTAT 60.159 45.455 5.11 0.00 39.82 2.12
2921 3111 7.640240 GCCTTACTCAAAAGCTAAATTATCACG 59.360 37.037 0.00 0.00 0.00 4.35
2938 3128 4.853468 TTATCCCAATGTGCCTTACTCA 57.147 40.909 0.00 0.00 0.00 3.41
2984 3174 5.793817 TGTCCCATGAGATAAATCCATACG 58.206 41.667 0.00 0.00 0.00 3.06
3026 3216 2.993899 CCACTGTAATCGACAAGGTGTC 59.006 50.000 0.00 0.00 43.65 3.67
3111 3301 8.601476 ACAAAGTAATAATAACGAAGTAGCAGC 58.399 33.333 0.00 0.00 45.00 5.25
3260 3450 3.119291 GCATGGAAGACACGTCTCTATG 58.881 50.000 0.00 8.76 39.39 2.23
3720 3910 1.643286 TGTTATGGGATGGGCAAAGGA 59.357 47.619 0.00 0.00 0.00 3.36
3738 3928 2.564062 AGGCATGTTGCTTTGCTAATGT 59.436 40.909 0.00 0.00 44.28 2.71
3746 3936 3.557228 TTTTCCAAGGCATGTTGCTTT 57.443 38.095 0.00 0.00 43.75 3.51
3775 3965 3.026694 AGTTGTTGCTTTTCTCCTGCTT 58.973 40.909 0.00 0.00 0.00 3.91
4000 4190 5.733620 ACAAATGGAATGCAGTTTCAGAT 57.266 34.783 2.65 0.00 0.00 2.90
4008 4198 3.514645 GCAGGTAACAAATGGAATGCAG 58.485 45.455 0.00 0.00 41.41 4.41
4075 5479 7.730364 AACATCTATGCTCCCGTTAATTAAG 57.270 36.000 0.00 0.00 0.00 1.85
4125 5543 8.301002 CAACATAACCCGGATCTTAAAAGAAAA 58.699 33.333 0.73 0.00 38.77 2.29
4146 5564 9.970395 CATTTAGGAAATGTGCATATACAACAT 57.030 29.630 0.00 0.00 42.53 2.71
4199 5617 8.531146 CCCAATATTTTTCTCCTGTGTACAAAT 58.469 33.333 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.