Multiple sequence alignment - TraesCS3B01G148400

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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 TraesCS3B01G148400 chr3B 100.000 2768 0 0 1 2768 139776246 139779013 0.000000e+00 5112
1 TraesCS3B01G148400 chr3B 79.191 865 114 28 1874 2677 139832105 139832964 8.720000e-150 540
2 TraesCS3B01G148400 chr3B 95.082 122 5 1 683 804 790640589 790640709 1.010000e-44 191
3 TraesCS3B01G148400 chr3D 90.457 1991 101 38 820 2768 90371749 90373692 0.000000e+00 2542
4 TraesCS3B01G148400 chr3D 85.515 718 55 20 5 686 90371034 90371738 0.000000e+00 704
5 TraesCS3B01G148400 chr3D 78.272 764 94 27 1992 2687 90379476 90380235 2.550000e-115 425
6 TraesCS3B01G148400 chr3D 94.531 128 5 2 677 804 165446905 165447030 2.170000e-46 196
7 TraesCS3B01G148400 chr3D 84.828 145 18 4 1874 2016 90379331 90379473 2.870000e-30 143
8 TraesCS3B01G148400 chr3A 92.402 1066 53 14 803 1861 106659784 106660828 0.000000e+00 1495
9 TraesCS3B01G148400 chr3A 92.850 1035 54 11 1742 2768 106660825 106661847 0.000000e+00 1483
10 TraesCS3B01G148400 chr3A 88.906 640 61 7 46 681 106659165 106659798 0.000000e+00 780
11 TraesCS3B01G148400 chr3A 77.294 872 120 30 1874 2686 106676509 106677361 2.530000e-120 442
12 TraesCS3B01G148400 chr3A 81.648 267 44 5 1874 2137 106674416 106674680 1.670000e-52 217
13 TraesCS3B01G148400 chr1D 96.774 124 3 1 676 799 108838876 108838754 3.610000e-49 206
14 TraesCS3B01G148400 chr5A 95.968 124 4 1 682 804 581473541 581473664 1.680000e-47 200
15 TraesCS3B01G148400 chr2D 95.238 126 6 0 679 804 556022244 556022119 1.680000e-47 200
16 TraesCS3B01G148400 chr2D 93.023 129 8 1 676 804 558937198 558937071 1.310000e-43 187
17 TraesCS3B01G148400 chr5D 95.238 126 5 1 680 804 361399972 361400097 6.050000e-47 198
18 TraesCS3B01G148400 chr5D 89.928 139 11 2 666 804 528280099 528280234 2.830000e-40 176
19 TraesCS3B01G148400 chr4D 92.913 127 7 2 678 804 396195509 396195385 1.690000e-42 183


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 TraesCS3B01G148400 chr3B 139776246 139779013 2767 False 5112.000000 5112 100.000 1 2768 1 chr3B.!!$F1 2767
1 TraesCS3B01G148400 chr3B 139832105 139832964 859 False 540.000000 540 79.191 1874 2677 1 chr3B.!!$F2 803
2 TraesCS3B01G148400 chr3D 90371034 90373692 2658 False 1623.000000 2542 87.986 5 2768 2 chr3D.!!$F2 2763
3 TraesCS3B01G148400 chr3D 90379331 90380235 904 False 284.000000 425 81.550 1874 2687 2 chr3D.!!$F3 813
4 TraesCS3B01G148400 chr3A 106659165 106661847 2682 False 1252.666667 1495 91.386 46 2768 3 chr3A.!!$F1 2722
5 TraesCS3B01G148400 chr3A 106674416 106677361 2945 False 329.500000 442 79.471 1874 2686 2 chr3A.!!$F2 812

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
785 824 0.322816 TCCCATGCTTCAGACTTGCC 60.323 55.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2470 4761 0.318107 GATGGTTGCATGCATACGCC 60.318 55.0 23.37 20.18 37.32 5.68 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
35 36 4.507879 GCAATGCTGCCATGAACC 57.492 55.556 0.00 0.00 43.26 3.62
53 54 7.255381 CCATGAACCTTCTCCACATTTATCATC 60.255 40.741 0.00 0.00 0.00 2.92
63 64 8.363390 TCTCCACATTTATCATCATGTACTCTC 58.637 37.037 0.00 0.00 32.16 3.20
85 86 6.546034 TCTCAACTTTCCTCTTTTAACCTTGG 59.454 38.462 0.00 0.00 0.00 3.61
156 157 1.984026 CCGCCCATTCCAAAAGGCT 60.984 57.895 0.00 0.00 43.48 4.58
195 214 5.163652 ACAACAGTTTGGCTTACTCTTTGTC 60.164 40.000 8.80 0.00 37.00 3.18
207 228 3.813443 ACTCTTTGTCTGTCAATGTGCT 58.187 40.909 0.00 0.00 35.84 4.40
209 230 5.368145 ACTCTTTGTCTGTCAATGTGCTAA 58.632 37.500 0.00 0.00 35.84 3.09
230 251 9.547753 TGCTAATTCTCTTATGTATGAAGTTCC 57.452 33.333 0.00 0.00 0.00 3.62
255 276 5.978322 ACTTCTCGACAAGTAAAACTGACTC 59.022 40.000 4.07 0.00 34.70 3.36
259 280 2.132762 ACAAGTAAAACTGACTCGGCG 58.867 47.619 0.00 0.00 0.00 6.46
261 282 2.061740 AGTAAAACTGACTCGGCGAC 57.938 50.000 4.99 0.00 0.00 5.19
262 283 1.612463 AGTAAAACTGACTCGGCGACT 59.388 47.619 4.99 0.00 0.00 4.18
269 290 0.817654 TGACTCGGCGACTGATTCAT 59.182 50.000 4.99 0.00 0.00 2.57
389 410 0.533308 AAACAAAGCCGTAGCGACCA 60.533 50.000 0.00 0.00 46.67 4.02
446 468 6.670077 TTAAAACTTCAAAACCAATGCACC 57.330 33.333 0.00 0.00 0.00 5.01
462 484 4.063529 CCAGACATGGCGTGTGTT 57.936 55.556 18.67 2.11 42.36 3.32
464 486 0.603707 CCAGACATGGCGTGTGTTCT 60.604 55.000 18.67 5.34 42.36 3.01
523 546 6.317140 GTGAACTCTTTGGCAGATGATAATCA 59.683 38.462 0.00 0.00 0.00 2.57
530 553 4.769688 TGGCAGATGATAATCAGTTTCGT 58.230 39.130 0.00 0.00 0.00 3.85
547 571 1.798223 TCGTGTGCATTTCTTTCTCCG 59.202 47.619 0.00 0.00 0.00 4.63
551 575 3.251004 GTGTGCATTTCTTTCTCCGAACT 59.749 43.478 0.00 0.00 0.00 3.01
563 600 2.037136 CCGAACTGCTGGCTGGAAG 61.037 63.158 4.64 0.00 0.00 3.46
600 639 1.065709 TGCTCCGTTTGGTCCTAATCC 60.066 52.381 0.00 0.00 36.30 3.01
603 642 0.538118 CCGTTTGGTCCTAATCCGGA 59.462 55.000 6.61 6.61 36.12 5.14
604 643 1.472728 CCGTTTGGTCCTAATCCGGAG 60.473 57.143 11.34 0.00 36.12 4.63
605 644 1.479323 CGTTTGGTCCTAATCCGGAGA 59.521 52.381 11.34 0.00 32.70 3.71
618 657 3.330766 CGGAGAGGCTCTACGTTTG 57.669 57.895 35.38 12.57 45.40 2.93
623 662 4.677250 CGGAGAGGCTCTACGTTTGTAATT 60.677 45.833 35.38 2.17 45.40 1.40
665 704 3.425713 CGAATGCAGGCGCTGTGT 61.426 61.111 7.64 0.00 39.64 3.72
681 720 5.059710 GCGCTGTGTTTCTCATGTAATTTTC 59.940 40.000 0.00 0.00 0.00 2.29
691 730 9.814899 TTTCTCATGTAATTTTCTTTTTGAGCA 57.185 25.926 0.00 0.00 31.63 4.26
692 731 9.985730 TTCTCATGTAATTTTCTTTTTGAGCAT 57.014 25.926 0.00 0.00 31.63 3.79
693 732 9.630098 TCTCATGTAATTTTCTTTTTGAGCATC 57.370 29.630 0.00 0.00 31.63 3.91
756 795 9.347240 ACATAATGATGAAGAATAAAGTCAGGG 57.653 33.333 0.00 0.00 36.48 4.45
757 796 9.565090 CATAATGATGAAGAATAAAGTCAGGGA 57.435 33.333 0.00 0.00 34.73 4.20
759 798 8.461249 AATGATGAAGAATAAAGTCAGGGATG 57.539 34.615 0.00 0.00 0.00 3.51
760 799 7.199167 TGATGAAGAATAAAGTCAGGGATGA 57.801 36.000 0.00 0.00 0.00 2.92
761 800 7.050377 TGATGAAGAATAAAGTCAGGGATGAC 58.950 38.462 0.06 0.06 39.00 3.06
762 801 6.373005 TGAAGAATAAAGTCAGGGATGACA 57.627 37.500 10.72 0.00 41.02 3.58
763 802 6.409704 TGAAGAATAAAGTCAGGGATGACAG 58.590 40.000 10.72 0.00 41.02 3.51
764 803 6.013379 TGAAGAATAAAGTCAGGGATGACAGT 60.013 38.462 10.72 1.04 41.02 3.55
765 804 6.380079 AGAATAAAGTCAGGGATGACAGTT 57.620 37.500 10.72 6.81 41.02 3.16
766 805 6.784031 AGAATAAAGTCAGGGATGACAGTTT 58.216 36.000 10.72 6.13 41.02 2.66
767 806 6.881602 AGAATAAAGTCAGGGATGACAGTTTC 59.118 38.462 10.72 7.77 41.02 2.78
768 807 3.425162 AAGTCAGGGATGACAGTTTCC 57.575 47.619 10.72 0.00 41.02 3.13
774 813 2.134789 GGATGACAGTTTCCCATGCT 57.865 50.000 0.00 0.00 0.00 3.79
775 814 2.450476 GGATGACAGTTTCCCATGCTT 58.550 47.619 0.00 0.00 0.00 3.91
776 815 2.424956 GGATGACAGTTTCCCATGCTTC 59.575 50.000 0.00 0.00 0.00 3.86
777 816 2.655090 TGACAGTTTCCCATGCTTCA 57.345 45.000 0.00 0.00 0.00 3.02
778 817 2.507484 TGACAGTTTCCCATGCTTCAG 58.493 47.619 0.00 0.00 0.00 3.02
779 818 2.106338 TGACAGTTTCCCATGCTTCAGA 59.894 45.455 0.00 0.00 0.00 3.27
780 819 2.485814 GACAGTTTCCCATGCTTCAGAC 59.514 50.000 0.00 0.00 0.00 3.51
781 820 2.107204 ACAGTTTCCCATGCTTCAGACT 59.893 45.455 0.00 0.00 0.00 3.24
782 821 3.152341 CAGTTTCCCATGCTTCAGACTT 58.848 45.455 0.00 0.00 0.00 3.01
783 822 3.057736 CAGTTTCCCATGCTTCAGACTTG 60.058 47.826 0.00 0.00 0.00 3.16
784 823 1.538047 TTCCCATGCTTCAGACTTGC 58.462 50.000 0.00 0.00 0.00 4.01
785 824 0.322816 TCCCATGCTTCAGACTTGCC 60.323 55.000 0.00 0.00 0.00 4.52
786 825 0.609957 CCCATGCTTCAGACTTGCCA 60.610 55.000 0.00 0.00 0.00 4.92
787 826 0.809385 CCATGCTTCAGACTTGCCAG 59.191 55.000 0.00 0.00 0.00 4.85
788 827 1.612462 CCATGCTTCAGACTTGCCAGA 60.612 52.381 0.00 0.00 0.00 3.86
789 828 2.156917 CATGCTTCAGACTTGCCAGAA 58.843 47.619 0.00 0.00 0.00 3.02
790 829 1.597742 TGCTTCAGACTTGCCAGAAC 58.402 50.000 0.00 0.00 0.00 3.01
791 830 1.141657 TGCTTCAGACTTGCCAGAACT 59.858 47.619 0.00 0.00 0.00 3.01
792 831 2.368548 TGCTTCAGACTTGCCAGAACTA 59.631 45.455 0.00 0.00 0.00 2.24
793 832 3.181455 TGCTTCAGACTTGCCAGAACTAA 60.181 43.478 0.00 0.00 0.00 2.24
794 833 4.006319 GCTTCAGACTTGCCAGAACTAAT 58.994 43.478 0.00 0.00 0.00 1.73
795 834 5.178797 GCTTCAGACTTGCCAGAACTAATA 58.821 41.667 0.00 0.00 0.00 0.98
796 835 5.064071 GCTTCAGACTTGCCAGAACTAATAC 59.936 44.000 0.00 0.00 0.00 1.89
797 836 5.738619 TCAGACTTGCCAGAACTAATACA 57.261 39.130 0.00 0.00 0.00 2.29
798 837 6.109156 TCAGACTTGCCAGAACTAATACAA 57.891 37.500 0.00 0.00 0.00 2.41
799 838 5.932303 TCAGACTTGCCAGAACTAATACAAC 59.068 40.000 0.00 0.00 0.00 3.32
800 839 4.929808 AGACTTGCCAGAACTAATACAACG 59.070 41.667 0.00 0.00 0.00 4.10
801 840 4.638304 ACTTGCCAGAACTAATACAACGT 58.362 39.130 0.00 0.00 0.00 3.99
802 841 5.061179 ACTTGCCAGAACTAATACAACGTT 58.939 37.500 0.00 0.00 0.00 3.99
803 842 5.529800 ACTTGCCAGAACTAATACAACGTTT 59.470 36.000 0.00 0.00 0.00 3.60
804 843 5.600908 TGCCAGAACTAATACAACGTTTC 57.399 39.130 0.00 0.00 0.00 2.78
805 844 5.302360 TGCCAGAACTAATACAACGTTTCT 58.698 37.500 0.00 0.00 0.00 2.52
806 845 5.407387 TGCCAGAACTAATACAACGTTTCTC 59.593 40.000 0.00 0.00 0.00 2.87
807 846 5.407387 GCCAGAACTAATACAACGTTTCTCA 59.593 40.000 0.00 0.00 0.00 3.27
808 847 6.092259 GCCAGAACTAATACAACGTTTCTCAT 59.908 38.462 0.00 0.00 0.00 2.90
809 848 7.456253 CCAGAACTAATACAACGTTTCTCATG 58.544 38.462 0.00 0.00 0.00 3.07
810 849 7.117812 CCAGAACTAATACAACGTTTCTCATGT 59.882 37.037 0.00 0.00 0.00 3.21
811 850 9.135843 CAGAACTAATACAACGTTTCTCATGTA 57.864 33.333 0.00 0.00 33.24 2.29
812 851 9.701098 AGAACTAATACAACGTTTCTCATGTAA 57.299 29.630 0.00 0.00 32.53 2.41
874 913 1.873270 CTGCAAGCCCGTTTTACCCC 61.873 60.000 0.00 0.00 0.00 4.95
945 984 1.338200 GCCTTCGGCTCTGAAGAGAAA 60.338 52.381 17.54 1.65 46.64 2.52
946 985 2.679349 GCCTTCGGCTCTGAAGAGAAAT 60.679 50.000 17.54 0.00 46.64 2.17
947 986 2.935201 CCTTCGGCTCTGAAGAGAAATG 59.065 50.000 17.54 0.00 46.64 2.32
949 988 3.961480 TCGGCTCTGAAGAGAAATGAA 57.039 42.857 11.56 0.00 44.74 2.57
950 989 3.854666 TCGGCTCTGAAGAGAAATGAAG 58.145 45.455 11.56 0.00 44.74 3.02
953 992 4.009002 GGCTCTGAAGAGAAATGAAGCTT 58.991 43.478 11.56 0.00 44.74 3.74
954 993 4.142643 GGCTCTGAAGAGAAATGAAGCTTG 60.143 45.833 2.10 0.00 44.74 4.01
955 994 4.142643 GCTCTGAAGAGAAATGAAGCTTGG 60.143 45.833 2.10 0.00 44.74 3.61
988 1027 3.433709 CACAGCAGATACACGAGAGAAG 58.566 50.000 0.00 0.00 0.00 2.85
1048 1090 2.105930 GCTACAGCTCGCCCTCTG 59.894 66.667 0.00 0.00 38.21 3.35
1049 1091 2.105930 CTACAGCTCGCCCTCTGC 59.894 66.667 0.00 0.00 33.80 4.26
1050 1092 3.438017 CTACAGCTCGCCCTCTGCC 62.438 68.421 0.00 0.00 36.24 4.85
1411 1453 2.298163 GTCGAGAAGGACAGGTAACCAA 59.702 50.000 0.00 0.00 36.91 3.67
1412 1454 2.967201 TCGAGAAGGACAGGTAACCAAA 59.033 45.455 0.00 0.00 37.17 3.28
1413 1455 3.064931 CGAGAAGGACAGGTAACCAAAC 58.935 50.000 0.00 0.00 37.17 2.93
1415 1457 2.148768 GAAGGACAGGTAACCAAACCG 58.851 52.381 0.00 0.00 44.77 4.44
1416 1458 1.426751 AGGACAGGTAACCAAACCGA 58.573 50.000 0.00 0.00 44.77 4.69
1417 1459 1.346722 AGGACAGGTAACCAAACCGAG 59.653 52.381 0.00 0.00 44.77 4.63
1418 1460 1.071228 GGACAGGTAACCAAACCGAGT 59.929 52.381 0.00 0.00 44.77 4.18
1419 1461 2.410939 GACAGGTAACCAAACCGAGTC 58.589 52.381 6.11 6.11 44.77 3.36
1420 1462 2.036862 GACAGGTAACCAAACCGAGTCT 59.963 50.000 11.77 0.00 44.77 3.24
1421 1463 2.224209 ACAGGTAACCAAACCGAGTCTG 60.224 50.000 0.00 0.00 44.77 3.51
1422 1464 1.346722 AGGTAACCAAACCGAGTCTGG 59.653 52.381 0.00 0.00 44.77 3.86
1425 1467 0.249741 AACCAAACCGAGTCTGGTCG 60.250 55.000 2.49 0.94 42.72 4.79
1437 1479 4.074526 TGGTCGAGCTGCTCTGCC 62.075 66.667 25.59 24.41 0.00 4.85
1438 1480 3.768922 GGTCGAGCTGCTCTGCCT 61.769 66.667 25.59 0.00 0.00 4.75
1444 1486 1.303155 AGCTGCTCTGCCTTTGTCC 60.303 57.895 0.00 0.00 0.00 4.02
1447 1489 1.093159 CTGCTCTGCCTTTGTCCATC 58.907 55.000 0.00 0.00 0.00 3.51
1462 1504 1.512996 CCATCGACATCAGCCATGGC 61.513 60.000 30.12 30.12 37.12 4.40
1464 1506 1.986632 ATCGACATCAGCCATGGCCA 61.987 55.000 33.14 20.64 37.18 5.36
1466 1508 1.721664 CGACATCAGCCATGGCCAAG 61.722 60.000 33.14 22.48 37.18 3.61
1467 1509 0.682209 GACATCAGCCATGGCCAAGT 60.682 55.000 33.14 24.71 43.17 3.16
1468 1510 0.968901 ACATCAGCCATGGCCAAGTG 60.969 55.000 33.14 25.83 43.17 3.16
1469 1511 0.968901 CATCAGCCATGGCCAAGTGT 60.969 55.000 33.14 10.96 43.17 3.55
1470 1512 0.968901 ATCAGCCATGGCCAAGTGTG 60.969 55.000 33.14 22.62 43.17 3.82
1483 1525 4.228912 CCAAGTGTGGTGAGAAATGTTC 57.771 45.455 0.00 0.00 40.42 3.18
1488 1530 4.044426 GTGTGGTGAGAAATGTTCTTTGC 58.956 43.478 0.00 0.00 40.87 3.68
1489 1531 3.068024 TGTGGTGAGAAATGTTCTTTGCC 59.932 43.478 0.00 0.00 40.87 4.52
1490 1532 2.627699 TGGTGAGAAATGTTCTTTGCCC 59.372 45.455 0.00 0.00 40.87 5.36
1491 1533 2.029020 GGTGAGAAATGTTCTTTGCCCC 60.029 50.000 0.00 0.00 40.87 5.80
1587 1630 1.618343 CGTTCCTCAAAATTGCCCCTT 59.382 47.619 0.00 0.00 0.00 3.95
1612 1655 2.642427 AGCTCAATTCACACACACACA 58.358 42.857 0.00 0.00 0.00 3.72
1613 1656 2.355756 AGCTCAATTCACACACACACAC 59.644 45.455 0.00 0.00 0.00 3.82
1614 1657 2.355756 GCTCAATTCACACACACACACT 59.644 45.455 0.00 0.00 0.00 3.55
1778 1948 4.387598 GAGATACTCTGAATTGCTGCCAT 58.612 43.478 0.00 0.00 0.00 4.40
1872 2047 3.683340 CAGATATGAGATGGCATGAACCG 59.317 47.826 3.81 0.00 0.00 4.44
1883 2060 1.949525 GCATGAACCGCCATCATTACT 59.050 47.619 0.00 0.00 35.38 2.24
1895 2072 5.106555 CGCCATCATTACTACCAATCCAATC 60.107 44.000 0.00 0.00 0.00 2.67
1918 2096 1.910722 CACTGCTACCCTGCCTCAT 59.089 57.895 0.00 0.00 0.00 2.90
1953 2131 8.471052 ACCTACGGTAAGCATTTCTGCACTTA 62.471 42.308 0.00 0.00 42.25 2.24
1996 2175 1.920574 CTATGTTCACAACGGAGAGCG 59.079 52.381 0.00 0.00 0.00 5.03
2111 4371 1.761174 GTTGGCCCAAGAGAGGTCA 59.239 57.895 0.00 0.00 37.17 4.02
2216 4476 0.317160 TGTTGATGAACCTCGCGTCT 59.683 50.000 5.77 0.00 0.00 4.18
2326 4617 0.944386 CACCCGTTCTGGACAGTTTG 59.056 55.000 0.00 0.00 42.00 2.93
2349 4640 0.623723 GGGGGCAATAGAACTGGTCA 59.376 55.000 0.00 0.00 0.00 4.02
2445 4736 6.131264 TCCCTGCATTTCTCATAACATCATT 58.869 36.000 0.00 0.00 0.00 2.57
2470 4761 9.621629 TTATAAGTTTGGGGAACATACTACATG 57.378 33.333 0.00 0.00 39.94 3.21
2472 4763 3.290948 TTGGGGAACATACTACATGGC 57.709 47.619 0.00 0.00 0.00 4.40
2473 4764 1.140052 TGGGGAACATACTACATGGCG 59.860 52.381 0.00 0.00 0.00 5.69
2474 4765 1.140252 GGGGAACATACTACATGGCGT 59.860 52.381 0.00 0.00 0.00 5.68
2475 4766 2.366266 GGGGAACATACTACATGGCGTA 59.634 50.000 0.00 0.00 0.00 4.42
2608 4943 7.201444 CGTACTAAAGAAGTTGCAGTTGGATAG 60.201 40.741 0.00 0.00 39.80 2.08
2680 5018 3.748048 CCCACACTACACAACAAGATCAG 59.252 47.826 0.00 0.00 0.00 2.90
2693 5032 3.823304 ACAAGATCAGAAAAGCCACCTTC 59.177 43.478 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.450137 GCATTGCTGGCCAAGATATATGATC 60.450 44.000 7.01 0.00 36.76 2.92
1 2 4.401519 GCATTGCTGGCCAAGATATATGAT 59.598 41.667 7.01 0.00 36.76 2.45
2 3 3.760151 GCATTGCTGGCCAAGATATATGA 59.240 43.478 7.01 0.00 36.76 2.15
3 4 3.762288 AGCATTGCTGGCCAAGATATATG 59.238 43.478 11.09 6.26 37.57 1.78
21 22 1.684248 GGAGAAGGTTCATGGCAGCAT 60.684 52.381 0.00 0.00 0.00 3.79
35 36 8.899427 AGTACATGATGATAAATGTGGAGAAG 57.101 34.615 0.00 0.00 37.57 2.85
53 54 7.736447 AAAAGAGGAAAGTTGAGAGTACATG 57.264 36.000 0.00 0.00 0.00 3.21
63 64 6.127451 ACACCAAGGTTAAAAGAGGAAAGTTG 60.127 38.462 0.00 0.00 0.00 3.16
85 86 5.127194 TGGATGTCCTAATCTCTACACACAC 59.873 44.000 0.09 0.00 36.82 3.82
156 157 7.929785 CCAAACTGTTGTTACTCTCTTACCTTA 59.070 37.037 0.00 0.00 34.96 2.69
195 214 8.206325 ACATAAGAGAATTAGCACATTGACAG 57.794 34.615 0.00 0.00 0.00 3.51
230 251 5.749109 AGTCAGTTTTACTTGTCGAGAAGTG 59.251 40.000 31.71 17.35 36.80 3.16
235 256 3.669122 CCGAGTCAGTTTTACTTGTCGAG 59.331 47.826 0.00 0.00 28.74 4.04
236 257 3.635331 CCGAGTCAGTTTTACTTGTCGA 58.365 45.455 0.00 0.00 28.74 4.20
237 258 2.155155 GCCGAGTCAGTTTTACTTGTCG 59.845 50.000 0.00 0.00 0.00 4.35
238 259 2.155155 CGCCGAGTCAGTTTTACTTGTC 59.845 50.000 0.00 0.00 0.00 3.18
243 264 1.719780 CAGTCGCCGAGTCAGTTTTAC 59.280 52.381 0.00 0.00 0.00 2.01
255 276 0.807275 TCTGCATGAATCAGTCGCCG 60.807 55.000 0.00 0.00 33.48 6.46
259 280 7.153315 TCTATCTCAATCTGCATGAATCAGTC 58.847 38.462 0.00 0.00 33.48 3.51
261 282 7.156000 ACTCTATCTCAATCTGCATGAATCAG 58.844 38.462 0.00 0.00 0.00 2.90
262 283 7.063934 ACTCTATCTCAATCTGCATGAATCA 57.936 36.000 0.00 0.00 0.00 2.57
269 290 4.033009 TCCCAACTCTATCTCAATCTGCA 58.967 43.478 0.00 0.00 0.00 4.41
446 468 1.069703 CAAGAACACACGCCATGTCTG 60.070 52.381 0.00 0.00 40.64 3.51
464 486 9.919348 GACACTACGAAAATACAAGTTAAACAA 57.081 29.630 0.00 0.00 0.00 2.83
523 546 4.261197 GGAGAAAGAAATGCACACGAAACT 60.261 41.667 0.00 0.00 0.00 2.66
530 553 3.250762 CAGTTCGGAGAAAGAAATGCACA 59.749 43.478 0.00 0.00 45.90 4.57
547 571 2.185004 TTACTTCCAGCCAGCAGTTC 57.815 50.000 0.00 0.00 0.00 3.01
551 575 3.439857 AAAGATTACTTCCAGCCAGCA 57.560 42.857 0.00 0.00 35.05 4.41
563 600 3.153735 GAGCACACGCGAAAAAGATTAC 58.846 45.455 15.93 0.00 45.49 1.89
600 639 0.526662 ACAAACGTAGAGCCTCTCCG 59.473 55.000 5.05 5.05 0.00 4.63
603 642 5.995897 ACAAAATTACAAACGTAGAGCCTCT 59.004 36.000 0.00 0.00 0.00 3.69
604 643 6.237313 ACAAAATTACAAACGTAGAGCCTC 57.763 37.500 0.00 0.00 0.00 4.70
605 644 6.261381 TCAACAAAATTACAAACGTAGAGCCT 59.739 34.615 0.00 0.00 0.00 4.58
656 695 1.438651 TACATGAGAAACACAGCGCC 58.561 50.000 2.29 0.00 0.00 6.53
665 704 9.814899 TGCTCAAAAAGAAAATTACATGAGAAA 57.185 25.926 0.00 0.00 36.11 2.52
730 769 9.347240 CCCTGACTTTATTCTTCATCATTATGT 57.653 33.333 0.00 0.00 34.50 2.29
731 770 9.565090 TCCCTGACTTTATTCTTCATCATTATG 57.435 33.333 0.00 0.00 0.00 1.90
733 772 9.565090 CATCCCTGACTTTATTCTTCATCATTA 57.435 33.333 0.00 0.00 0.00 1.90
734 773 8.277197 TCATCCCTGACTTTATTCTTCATCATT 58.723 33.333 0.00 0.00 0.00 2.57
735 774 7.718753 GTCATCCCTGACTTTATTCTTCATCAT 59.281 37.037 0.00 0.00 46.84 2.45
736 775 7.050377 GTCATCCCTGACTTTATTCTTCATCA 58.950 38.462 0.00 0.00 46.84 3.07
737 776 7.489574 GTCATCCCTGACTTTATTCTTCATC 57.510 40.000 0.00 0.00 46.84 2.92
755 794 2.134789 AGCATGGGAAACTGTCATCC 57.865 50.000 0.00 4.46 34.85 3.51
756 795 3.084039 TGAAGCATGGGAAACTGTCATC 58.916 45.455 0.00 0.00 0.00 2.92
757 796 3.087031 CTGAAGCATGGGAAACTGTCAT 58.913 45.455 0.00 0.00 0.00 3.06
758 797 2.106338 TCTGAAGCATGGGAAACTGTCA 59.894 45.455 0.00 0.00 0.00 3.58
759 798 2.485814 GTCTGAAGCATGGGAAACTGTC 59.514 50.000 0.00 0.00 0.00 3.51
760 799 2.107204 AGTCTGAAGCATGGGAAACTGT 59.893 45.455 0.00 0.00 0.00 3.55
761 800 2.787994 AGTCTGAAGCATGGGAAACTG 58.212 47.619 0.00 0.00 0.00 3.16
762 801 3.152341 CAAGTCTGAAGCATGGGAAACT 58.848 45.455 0.00 0.00 0.00 2.66
763 802 2.352127 GCAAGTCTGAAGCATGGGAAAC 60.352 50.000 0.00 0.00 0.00 2.78
764 803 1.888512 GCAAGTCTGAAGCATGGGAAA 59.111 47.619 0.00 0.00 0.00 3.13
765 804 1.538047 GCAAGTCTGAAGCATGGGAA 58.462 50.000 0.00 0.00 0.00 3.97
766 805 0.322816 GGCAAGTCTGAAGCATGGGA 60.323 55.000 0.00 0.00 0.00 4.37
767 806 0.609957 TGGCAAGTCTGAAGCATGGG 60.610 55.000 0.00 0.00 0.00 4.00
768 807 0.809385 CTGGCAAGTCTGAAGCATGG 59.191 55.000 0.00 0.00 0.00 3.66
769 808 1.817357 TCTGGCAAGTCTGAAGCATG 58.183 50.000 0.00 0.00 0.00 4.06
770 809 2.157738 GTTCTGGCAAGTCTGAAGCAT 58.842 47.619 0.00 0.00 0.00 3.79
771 810 1.141657 AGTTCTGGCAAGTCTGAAGCA 59.858 47.619 0.00 0.00 0.00 3.91
772 811 1.889545 AGTTCTGGCAAGTCTGAAGC 58.110 50.000 0.00 0.00 0.00 3.86
773 812 6.166279 TGTATTAGTTCTGGCAAGTCTGAAG 58.834 40.000 0.00 0.00 0.00 3.02
774 813 6.109156 TGTATTAGTTCTGGCAAGTCTGAA 57.891 37.500 0.00 0.00 0.00 3.02
775 814 5.738619 TGTATTAGTTCTGGCAAGTCTGA 57.261 39.130 0.00 0.00 0.00 3.27
776 815 5.163953 CGTTGTATTAGTTCTGGCAAGTCTG 60.164 44.000 0.00 0.00 0.00 3.51
777 816 4.929808 CGTTGTATTAGTTCTGGCAAGTCT 59.070 41.667 0.00 0.00 0.00 3.24
778 817 4.689345 ACGTTGTATTAGTTCTGGCAAGTC 59.311 41.667 0.00 0.00 0.00 3.01
779 818 4.638304 ACGTTGTATTAGTTCTGGCAAGT 58.362 39.130 0.00 0.00 0.00 3.16
780 819 5.607119 AACGTTGTATTAGTTCTGGCAAG 57.393 39.130 0.00 0.00 0.00 4.01
781 820 5.761234 AGAAACGTTGTATTAGTTCTGGCAA 59.239 36.000 0.00 0.00 0.00 4.52
782 821 5.302360 AGAAACGTTGTATTAGTTCTGGCA 58.698 37.500 0.00 0.00 0.00 4.92
783 822 5.407387 TGAGAAACGTTGTATTAGTTCTGGC 59.593 40.000 0.00 0.00 0.00 4.85
784 823 7.117812 ACATGAGAAACGTTGTATTAGTTCTGG 59.882 37.037 0.00 0.00 0.00 3.86
785 824 8.018677 ACATGAGAAACGTTGTATTAGTTCTG 57.981 34.615 0.00 0.00 0.00 3.02
786 825 9.701098 TTACATGAGAAACGTTGTATTAGTTCT 57.299 29.630 0.00 0.00 0.00 3.01
797 836 9.458374 CCAAACTAAAATTACATGAGAAACGTT 57.542 29.630 0.00 0.00 0.00 3.99
798 837 8.842280 TCCAAACTAAAATTACATGAGAAACGT 58.158 29.630 0.00 0.00 0.00 3.99
799 838 9.672086 TTCCAAACTAAAATTACATGAGAAACG 57.328 29.630 0.00 0.00 0.00 3.60
812 851 9.492973 CCAGAATTTCACATTCCAAACTAAAAT 57.507 29.630 0.00 0.00 0.00 1.82
813 852 8.700051 TCCAGAATTTCACATTCCAAACTAAAA 58.300 29.630 0.00 0.00 0.00 1.52
814 853 8.243961 TCCAGAATTTCACATTCCAAACTAAA 57.756 30.769 0.00 0.00 0.00 1.85
815 854 7.831691 TCCAGAATTTCACATTCCAAACTAA 57.168 32.000 0.00 0.00 0.00 2.24
816 855 7.523709 GCTTCCAGAATTTCACATTCCAAACTA 60.524 37.037 0.00 0.00 0.00 2.24
874 913 0.734597 GCAACGGGTAATTTTGGCCG 60.735 55.000 0.00 0.00 0.00 6.13
927 966 3.854666 TCATTTCTCTTCAGAGCCGAAG 58.145 45.455 0.00 2.49 43.17 3.79
936 975 4.717877 TGTCCAAGCTTCATTTCTCTTCA 58.282 39.130 0.00 0.00 0.00 3.02
953 992 1.526686 CTGTGCAGTGGCTTGTCCA 60.527 57.895 0.00 0.00 44.18 4.02
954 993 2.912624 GCTGTGCAGTGGCTTGTCC 61.913 63.158 0.00 0.00 41.91 4.02
955 994 2.188829 TGCTGTGCAGTGGCTTGTC 61.189 57.895 0.00 0.00 41.91 3.18
988 1027 4.918201 CGCCATCGCCTCCTTCCC 62.918 72.222 0.00 0.00 0.00 3.97
1185 1227 1.801913 CTGGAAGAACTCGGCGTCG 60.802 63.158 1.15 1.15 34.07 5.12
1411 1453 1.604023 AGCTCGACCAGACTCGGTT 60.604 57.895 0.00 0.00 40.22 4.44
1412 1454 2.034376 AGCTCGACCAGACTCGGT 59.966 61.111 0.00 0.00 43.91 4.69
1413 1455 2.487428 CAGCTCGACCAGACTCGG 59.513 66.667 0.00 0.00 34.27 4.63
1415 1457 1.138671 GAGCAGCTCGACCAGACTC 59.861 63.158 6.67 0.00 0.00 3.36
1416 1458 1.304052 AGAGCAGCTCGACCAGACT 60.304 57.895 16.99 0.00 35.36 3.24
1417 1459 1.153862 CAGAGCAGCTCGACCAGAC 60.154 63.158 16.99 0.00 35.36 3.51
1418 1460 2.999485 GCAGAGCAGCTCGACCAGA 61.999 63.158 16.99 0.00 35.36 3.86
1419 1461 2.508887 GCAGAGCAGCTCGACCAG 60.509 66.667 16.99 7.06 35.36 4.00
1420 1462 4.074526 GGCAGAGCAGCTCGACCA 62.075 66.667 24.47 0.00 35.36 4.02
1421 1463 2.794820 AAAGGCAGAGCAGCTCGACC 62.795 60.000 22.81 22.81 35.36 4.79
1422 1464 1.375268 AAAGGCAGAGCAGCTCGAC 60.375 57.895 16.99 13.67 35.36 4.20
1425 1467 1.304509 GGACAAAGGCAGAGCAGCTC 61.305 60.000 15.25 15.25 34.17 4.09
1444 1486 1.512996 GGCCATGGCTGATGTCGATG 61.513 60.000 34.70 0.00 41.60 3.84
1447 1489 1.721664 CTTGGCCATGGCTGATGTCG 61.722 60.000 34.70 13.34 41.60 4.35
1462 1504 3.885297 AGAACATTTCTCACCACACTTGG 59.115 43.478 0.00 0.00 42.03 3.61
1464 1506 5.679638 GCAAAGAACATTTCTCACCACACTT 60.680 40.000 0.00 0.00 39.61 3.16
1466 1508 4.044426 GCAAAGAACATTTCTCACCACAC 58.956 43.478 0.00 0.00 39.61 3.82
1467 1509 3.068024 GGCAAAGAACATTTCTCACCACA 59.932 43.478 0.00 0.00 39.61 4.17
1468 1510 3.552890 GGGCAAAGAACATTTCTCACCAC 60.553 47.826 0.00 0.00 39.61 4.16
1469 1511 2.627699 GGGCAAAGAACATTTCTCACCA 59.372 45.455 0.00 0.00 39.61 4.17
1470 1512 2.029020 GGGGCAAAGAACATTTCTCACC 60.029 50.000 0.00 0.00 39.61 4.02
1488 1530 2.774234 ACTTGATGTATGACCTGAGGGG 59.226 50.000 2.38 0.00 41.89 4.79
1489 1531 3.708631 AGACTTGATGTATGACCTGAGGG 59.291 47.826 2.38 0.00 38.88 4.30
1490 1532 4.403752 TCAGACTTGATGTATGACCTGAGG 59.596 45.833 0.00 0.00 41.37 3.86
1491 1533 5.588958 TCAGACTTGATGTATGACCTGAG 57.411 43.478 0.00 0.00 41.37 3.35
1514 1557 1.224069 CCATTATCCTCAGCACGGCG 61.224 60.000 4.80 4.80 0.00 6.46
1587 1630 4.637977 TGTGTGTGTGAATTGAGCTTACAA 59.362 37.500 0.00 0.00 0.00 2.41
1612 1655 3.069872 TGGTTCAATTGAAAGCATGCAGT 59.930 39.130 22.07 6.66 35.58 4.40
1613 1656 3.430895 GTGGTTCAATTGAAAGCATGCAG 59.569 43.478 22.07 0.00 35.58 4.41
1614 1657 3.069872 AGTGGTTCAATTGAAAGCATGCA 59.930 39.130 22.07 0.00 35.58 3.96
1728 1776 2.154798 CTGTCTCTGACCGGCCGAAA 62.155 60.000 30.73 10.73 0.00 3.46
1825 1998 3.605634 TGCCTACAACTTCGCAATATGT 58.394 40.909 0.00 0.00 0.00 2.29
1830 2003 1.804151 GTCATGCCTACAACTTCGCAA 59.196 47.619 0.00 0.00 34.38 4.85
1831 2004 1.270571 TGTCATGCCTACAACTTCGCA 60.271 47.619 0.00 0.00 35.35 5.10
1832 2005 1.394917 CTGTCATGCCTACAACTTCGC 59.605 52.381 0.00 0.00 0.00 4.70
1833 2006 2.959516 TCTGTCATGCCTACAACTTCG 58.040 47.619 0.00 0.00 0.00 3.79
1872 2047 6.006449 AGATTGGATTGGTAGTAATGATGGC 58.994 40.000 0.00 0.00 0.00 4.40
1883 2060 4.080356 AGCAGTGCTAAGATTGGATTGGTA 60.080 41.667 18.11 0.00 36.99 3.25
1895 2072 0.462759 GGCAGGGTAGCAGTGCTAAG 60.463 60.000 26.04 16.41 43.07 2.18
1953 2131 2.763448 GCTTGGACATAGACAGAGGAGT 59.237 50.000 0.00 0.00 0.00 3.85
2005 2184 4.006357 TACGGTTCCGCGGCCTTT 62.006 61.111 23.51 9.05 0.00 3.11
2050 4310 4.383010 CCAAAATCCTAAATGCCCAAGGAC 60.383 45.833 0.00 0.00 42.08 3.85
2111 4371 2.292292 CGGGATTTTTCTCCACAACGTT 59.708 45.455 0.00 0.00 37.01 3.99
2142 4402 2.482296 ATCCTGTGCAGCAAAAGCGC 62.482 55.000 0.00 0.00 42.56 5.92
2349 4640 5.766670 TGAAGTACGGTATCCTATCGACATT 59.233 40.000 0.00 0.00 35.91 2.71
2445 4736 8.215050 CCATGTAGTATGTTCCCCAAACTTATA 58.785 37.037 0.00 0.00 38.76 0.98
2469 4760 1.036481 ATGGTTGCATGCATACGCCA 61.036 50.000 23.37 24.63 37.32 5.69
2470 4761 0.318107 GATGGTTGCATGCATACGCC 60.318 55.000 23.37 20.18 37.32 5.68
2472 4763 1.672363 ACTGATGGTTGCATGCATACG 59.328 47.619 23.37 11.15 0.00 3.06
2473 4764 3.441163 CAACTGATGGTTGCATGCATAC 58.559 45.455 23.37 20.50 46.89 2.39
2474 4765 3.786516 CAACTGATGGTTGCATGCATA 57.213 42.857 23.37 11.70 46.89 3.14
2475 4766 2.665649 CAACTGATGGTTGCATGCAT 57.334 45.000 23.37 6.15 46.89 3.96
2586 4921 6.428159 ACACTATCCAACTGCAACTTCTTTAG 59.572 38.462 0.00 0.00 0.00 1.85
2680 5018 2.893489 ACATTGAGGAAGGTGGCTTTTC 59.107 45.455 0.00 0.00 0.00 2.29
2693 5032 5.851720 AGTGAGTAGCATATCACATTGAGG 58.148 41.667 14.95 0.00 46.63 3.86


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

AutoCloner maintained by Alex Coulton.