Multiple sequence alignment - TraesCS3B01G307300

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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 TraesCS3B01G307300 chr3B 100.000 2899 0 0 1 2899 493583552 493586450 0.000000e+00 5354.0
1 TraesCS3B01G307300 chr3D 92.951 1447 44 16 722 2140 378529011 378530427 0.000000e+00 2054.0
2 TraesCS3B01G307300 chr3D 89.937 636 60 4 63 696 8512697 8513330 0.000000e+00 817.0
3 TraesCS3B01G307300 chr3D 86.969 353 17 6 2182 2525 378530423 378530755 1.270000e-98 370.0
4 TraesCS3B01G307300 chr3D 78.531 354 19 17 2528 2850 378531205 378531532 2.300000e-41 180.0
5 TraesCS3B01G307300 chr3A 90.568 1548 55 35 930 2441 502490306 502491798 0.000000e+00 1965.0
6 TraesCS3B01G307300 chr3A 87.500 160 12 5 2732 2883 502493535 502493694 8.250000e-41 178.0
7 TraesCS3B01G307300 chr6D 90.581 637 59 1 63 698 21902859 21903495 0.000000e+00 843.0
8 TraesCS3B01G307300 chr6D 91.283 608 52 1 95 701 54233378 54232771 0.000000e+00 828.0
9 TraesCS3B01G307300 chr5D 91.722 604 50 0 95 698 470046478 470045875 0.000000e+00 839.0
10 TraesCS3B01G307300 chr5D 89.796 637 59 3 63 698 510060805 510060174 0.000000e+00 811.0
11 TraesCS3B01G307300 chr5D 100.000 48 0 0 2352 2399 511208131 511208084 3.980000e-14 89.8
12 TraesCS3B01G307300 chr2B 90.424 637 61 0 62 698 374023234 374022598 0.000000e+00 839.0
13 TraesCS3B01G307300 chr2B 90.094 636 62 1 63 698 747813648 747814282 0.000000e+00 824.0
14 TraesCS3B01G307300 chr2B 87.585 588 23 14 1947 2525 342171214 342170668 1.130000e-178 636.0
15 TraesCS3B01G307300 chr2B 92.040 201 14 2 2526 2725 342170626 342170427 6.120000e-72 281.0
16 TraesCS3B01G307300 chr7D 89.498 638 64 3 63 698 562820048 562819412 0.000000e+00 804.0
17 TraesCS3B01G307300 chr4B 88.906 640 69 2 63 702 618686971 618687608 0.000000e+00 787.0
18 TraesCS3B01G307300 chr4B 86.513 608 32 14 1927 2525 162842933 162842367 8.820000e-175 623.0
19 TraesCS3B01G307300 chr4B 91.542 201 15 2 2526 2725 162842325 162842126 2.850000e-70 276.0
20 TraesCS3B01G307300 chr7B 87.500 608 26 13 1927 2525 399533267 399533833 0.000000e+00 656.0
21 TraesCS3B01G307300 chr7B 91.045 201 16 2 2523 2722 399533872 399534071 1.320000e-68 270.0
22 TraesCS3B01G307300 chr7B 96.154 78 1 2 1 77 599384438 599384514 3.030000e-25 126.0
23 TraesCS3B01G307300 chr6A 87.500 608 26 14 1927 2525 421534904 421535470 0.000000e+00 656.0
24 TraesCS3B01G307300 chr6A 92.040 201 14 2 2523 2722 421535509 421535708 6.120000e-72 281.0
25 TraesCS3B01G307300 chr7A 87.034 617 28 18 1927 2532 285046447 285047022 0.000000e+00 649.0
26 TraesCS3B01G307300 chr7A 92.537 201 13 2 2523 2722 285047052 285047251 1.310000e-73 287.0
27 TraesCS3B01G307300 chr1A 86.349 608 33 12 1927 2525 351140074 351139508 4.100000e-173 617.0
28 TraesCS3B01G307300 chr1A 75.393 764 119 46 1027 1758 528103039 528102313 3.630000e-79 305.0
29 TraesCS3B01G307300 chr1A 92.040 201 14 2 2526 2725 351139466 351139267 6.120000e-72 281.0
30 TraesCS3B01G307300 chr1A 96.154 78 1 2 1 77 354014905 354014981 3.030000e-25 126.0
31 TraesCS3B01G307300 chr1A 96.154 78 1 2 1 77 526368528 526368452 3.030000e-25 126.0
32 TraesCS3B01G307300 chr1A 96.154 78 1 2 1 77 562011031 562011107 3.030000e-25 126.0
33 TraesCS3B01G307300 chr1B 75.923 731 107 43 1027 1727 581596283 581595592 7.800000e-81 311.0
34 TraesCS3B01G307300 chr1B 96.154 78 1 2 1 77 47415053 47415129 3.030000e-25 126.0
35 TraesCS3B01G307300 chr1B 96.154 78 1 2 1 77 136952204 136952128 3.030000e-25 126.0
36 TraesCS3B01G307300 chr1B 96.154 78 1 2 1 77 592083302 592083378 3.030000e-25 126.0
37 TraesCS3B01G307300 chr1D 75.753 730 111 41 1019 1717 430482143 430481449 1.010000e-79 307.0
38 TraesCS3B01G307300 chr5B 96.154 78 1 2 1 77 50868921 50868997 3.030000e-25 126.0
39 TraesCS3B01G307300 chr5B 96.154 78 1 2 1 77 184129117 184129041 3.030000e-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 TraesCS3B01G307300 chr3B 493583552 493586450 2898 False 5354.0 5354 100.000000 1 2899 1 chr3B.!!$F1 2898
1 TraesCS3B01G307300 chr3D 378529011 378531532 2521 False 868.0 2054 86.150333 722 2850 3 chr3D.!!$F2 2128
2 TraesCS3B01G307300 chr3D 8512697 8513330 633 False 817.0 817 89.937000 63 696 1 chr3D.!!$F1 633
3 TraesCS3B01G307300 chr3A 502490306 502493694 3388 False 1071.5 1965 89.034000 930 2883 2 chr3A.!!$F1 1953
4 TraesCS3B01G307300 chr6D 21902859 21903495 636 False 843.0 843 90.581000 63 698 1 chr6D.!!$F1 635
5 TraesCS3B01G307300 chr6D 54232771 54233378 607 True 828.0 828 91.283000 95 701 1 chr6D.!!$R1 606
6 TraesCS3B01G307300 chr5D 470045875 470046478 603 True 839.0 839 91.722000 95 698 1 chr5D.!!$R1 603
7 TraesCS3B01G307300 chr5D 510060174 510060805 631 True 811.0 811 89.796000 63 698 1 chr5D.!!$R2 635
8 TraesCS3B01G307300 chr2B 374022598 374023234 636 True 839.0 839 90.424000 62 698 1 chr2B.!!$R1 636
9 TraesCS3B01G307300 chr2B 747813648 747814282 634 False 824.0 824 90.094000 63 698 1 chr2B.!!$F1 635
10 TraesCS3B01G307300 chr2B 342170427 342171214 787 True 458.5 636 89.812500 1947 2725 2 chr2B.!!$R2 778
11 TraesCS3B01G307300 chr7D 562819412 562820048 636 True 804.0 804 89.498000 63 698 1 chr7D.!!$R1 635
12 TraesCS3B01G307300 chr4B 618686971 618687608 637 False 787.0 787 88.906000 63 702 1 chr4B.!!$F1 639
13 TraesCS3B01G307300 chr4B 162842126 162842933 807 True 449.5 623 89.027500 1927 2725 2 chr4B.!!$R1 798
14 TraesCS3B01G307300 chr7B 399533267 399534071 804 False 463.0 656 89.272500 1927 2722 2 chr7B.!!$F2 795
15 TraesCS3B01G307300 chr6A 421534904 421535708 804 False 468.5 656 89.770000 1927 2722 2 chr6A.!!$F1 795
16 TraesCS3B01G307300 chr7A 285046447 285047251 804 False 468.0 649 89.785500 1927 2722 2 chr7A.!!$F1 795
17 TraesCS3B01G307300 chr1A 351139267 351140074 807 True 449.0 617 89.194500 1927 2725 2 chr1A.!!$R3 798
18 TraesCS3B01G307300 chr1A 528102313 528103039 726 True 305.0 305 75.393000 1027 1758 1 chr1A.!!$R2 731
19 TraesCS3B01G307300 chr1B 581595592 581596283 691 True 311.0 311 75.923000 1027 1727 1 chr1B.!!$R2 700
20 TraesCS3B01G307300 chr1D 430481449 430482143 694 True 307.0 307 75.753000 1019 1717 1 chr1D.!!$R1 698

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
875 906 0.043485 AACCTCCCTTCTCTCCCCTC 59.957 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2469 2598 0.041926 GGGCGTTGTTCGTGTTGTAC 60.042 55.0 0.0 0.0 42.13 2.9 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
60 61 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
108 109 3.409856 GCACACACTGCACTTCGT 58.590 55.556 0.00 0.00 46.29 3.85
112 113 2.661866 ACACTGCACTTCGTCGCC 60.662 61.111 0.00 0.00 0.00 5.54
172 173 2.677337 GTCCTACTACACTGGAGTCGTC 59.323 54.545 0.00 0.00 0.00 4.20
220 222 1.208776 TCTCATCCACTGCACTGATGG 59.791 52.381 12.82 5.63 37.17 3.51
292 295 1.666553 CACCGCAACTAGTTCGCCA 60.667 57.895 18.30 0.00 0.00 5.69
361 364 1.080772 GCTCGTCATGTCGGACACA 60.081 57.895 13.92 0.00 40.18 3.72
379 382 2.187946 GCGCCACAGCCACTATCT 59.812 61.111 0.00 0.00 34.57 1.98
420 423 1.335324 GCGCACACTGCATTTCTTCTT 60.335 47.619 0.30 0.00 45.36 2.52
446 449 4.468153 CCTTCCTCTGCTAGTTCTTAACCT 59.532 45.833 0.00 0.00 0.00 3.50
473 476 1.923204 CTAAGTGCAAGTGCTAGCTCG 59.077 52.381 17.23 1.78 42.66 5.03
482 485 4.926238 GCAAGTGCTAGCTCGTAATCATAT 59.074 41.667 17.23 0.00 38.21 1.78
556 559 2.457366 ACCAAACAACGTGCCAAAAA 57.543 40.000 0.00 0.00 0.00 1.94
698 701 0.748367 TACTGCAACCAAACACGCCA 60.748 50.000 0.00 0.00 0.00 5.69
702 705 0.109319 GCAACCAAACACGCCATAGG 60.109 55.000 0.00 0.00 0.00 2.57
703 706 0.109319 CAACCAAACACGCCATAGGC 60.109 55.000 0.00 0.00 46.75 3.93
714 717 2.192605 CCATAGGCAAGGCAACACC 58.807 57.895 0.00 0.00 41.41 4.16
715 718 1.656818 CCATAGGCAAGGCAACACCG 61.657 60.000 0.00 0.00 46.52 4.94
716 719 2.046285 ATAGGCAAGGCAACACCGC 61.046 57.895 0.00 0.00 46.52 5.68
723 726 2.357760 GGCAACACCGCCGAGTAA 60.358 61.111 0.00 0.00 43.52 2.24
724 727 2.388232 GGCAACACCGCCGAGTAAG 61.388 63.158 0.00 0.00 43.52 2.34
725 728 1.666872 GCAACACCGCCGAGTAAGT 60.667 57.895 0.00 0.00 0.00 2.24
726 729 0.388907 GCAACACCGCCGAGTAAGTA 60.389 55.000 0.00 0.00 0.00 2.24
727 730 1.343506 CAACACCGCCGAGTAAGTAC 58.656 55.000 0.00 0.00 0.00 2.73
736 739 4.143179 CCGCCGAGTAAGTACAAAAGAAAG 60.143 45.833 0.00 0.00 0.00 2.62
748 751 7.574607 AGTACAAAAGAAAGAGGAGAGGAAAA 58.425 34.615 0.00 0.00 0.00 2.29
749 752 6.951062 ACAAAAGAAAGAGGAGAGGAAAAG 57.049 37.500 0.00 0.00 0.00 2.27
778 781 3.966665 AGAAAATTGAGAAACCCCAGCAA 59.033 39.130 0.00 0.00 0.00 3.91
789 792 1.063266 ACCCCAGCAAGAAAAGGAACA 60.063 47.619 0.00 0.00 0.00 3.18
810 813 2.061740 AAGCTGAAGTAACGGACGTC 57.938 50.000 7.13 7.13 37.10 4.34
812 815 1.338973 AGCTGAAGTAACGGACGTCAA 59.661 47.619 18.91 0.00 44.51 3.18
813 816 2.129607 GCTGAAGTAACGGACGTCAAA 58.870 47.619 18.91 0.00 44.51 2.69
815 818 2.129607 TGAAGTAACGGACGTCAAAGC 58.870 47.619 18.91 3.17 42.63 3.51
816 819 2.129607 GAAGTAACGGACGTCAAAGCA 58.870 47.619 18.91 0.00 36.63 3.91
817 820 2.450609 AGTAACGGACGTCAAAGCAT 57.549 45.000 18.91 3.85 0.00 3.79
818 821 2.762745 AGTAACGGACGTCAAAGCATT 58.237 42.857 18.91 4.37 0.00 3.56
819 822 2.478894 AGTAACGGACGTCAAAGCATTG 59.521 45.455 18.91 0.00 37.92 2.82
820 823 1.305201 AACGGACGTCAAAGCATTGT 58.695 45.000 18.91 0.00 37.79 2.71
821 824 0.865769 ACGGACGTCAAAGCATTGTC 59.134 50.000 18.91 0.00 37.79 3.18
822 825 0.165944 CGGACGTCAAAGCATTGTCC 59.834 55.000 18.91 0.96 44.43 4.02
824 827 1.606668 GGACGTCAAAGCATTGTCCAA 59.393 47.619 18.91 0.00 46.55 3.53
827 830 2.687935 ACGTCAAAGCATTGTCCAAAGT 59.312 40.909 1.04 0.00 37.79 2.66
865 895 3.525199 ACAATGCATCTCTAACCTCCCTT 59.475 43.478 0.00 0.00 0.00 3.95
867 897 3.121929 TGCATCTCTAACCTCCCTTCT 57.878 47.619 0.00 0.00 0.00 2.85
874 905 1.292546 CTAACCTCCCTTCTCTCCCCT 59.707 57.143 0.00 0.00 0.00 4.79
875 906 0.043485 AACCTCCCTTCTCTCCCCTC 59.957 60.000 0.00 0.00 0.00 4.30
877 908 1.074850 CTCCCTTCTCTCCCCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
884 915 0.996762 TCTCTCCCCTCCCCTCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
904 935 5.646215 TCTCTCTCTCTTCTTAACCAACCT 58.354 41.667 0.00 0.00 0.00 3.50
907 938 3.838903 TCTCTCTTCTTAACCAACCTCCC 59.161 47.826 0.00 0.00 0.00 4.30
908 939 2.910977 TCTCTTCTTAACCAACCTCCCC 59.089 50.000 0.00 0.00 0.00 4.81
909 940 2.642807 CTCTTCTTAACCAACCTCCCCA 59.357 50.000 0.00 0.00 0.00 4.96
925 956 0.539669 CCCACCCTTTTTCCTCGCTT 60.540 55.000 0.00 0.00 0.00 4.68
999 1035 2.568062 TCCCAACTCTAACCATACGCAA 59.432 45.455 0.00 0.00 0.00 4.85
1051 1087 2.003548 GTTCCTCCCCATGCCTCCT 61.004 63.158 0.00 0.00 0.00 3.69
1165 1201 2.429930 CACAACCTTCCGCCCTCA 59.570 61.111 0.00 0.00 0.00 3.86
1225 1261 4.003788 ACCACCTTCGTCCAGGCG 62.004 66.667 0.00 0.00 37.47 5.52
1287 1323 0.541998 TCCGAGCAGTCCTCCAAGAA 60.542 55.000 0.00 0.00 37.27 2.52
1492 1555 4.593864 GCGCCGGAGATCCTGTCC 62.594 72.222 10.31 0.00 0.00 4.02
1687 1768 4.148825 CTCCCGCTCTTCCCCGTG 62.149 72.222 0.00 0.00 0.00 4.94
1814 1895 3.900388 ATCTACGACTTCTACCATCGC 57.100 47.619 0.00 0.00 39.47 4.58
1815 1896 1.945394 TCTACGACTTCTACCATCGCC 59.055 52.381 0.00 0.00 39.47 5.54
1816 1897 1.674441 CTACGACTTCTACCATCGCCA 59.326 52.381 0.00 0.00 39.47 5.69
1817 1898 0.172803 ACGACTTCTACCATCGCCAC 59.827 55.000 0.00 0.00 39.47 5.01
1818 1899 0.527817 CGACTTCTACCATCGCCACC 60.528 60.000 0.00 0.00 0.00 4.61
1819 1900 0.527817 GACTTCTACCATCGCCACCG 60.528 60.000 0.00 0.00 0.00 4.94
1820 1901 1.883084 CTTCTACCATCGCCACCGC 60.883 63.158 0.00 0.00 0.00 5.68
1821 1902 3.379865 TTCTACCATCGCCACCGCC 62.380 63.158 0.00 0.00 0.00 6.13
1822 1903 4.910585 CTACCATCGCCACCGCCC 62.911 72.222 0.00 0.00 0.00 6.13
1847 1928 1.217882 GTATCATCGCCGTCCTTTGG 58.782 55.000 0.00 0.00 0.00 3.28
1865 1946 3.678056 TGGTCGCAGTTCTAGTTTCAT 57.322 42.857 0.00 0.00 0.00 2.57
1866 1947 4.794278 TGGTCGCAGTTCTAGTTTCATA 57.206 40.909 0.00 0.00 0.00 2.15
1867 1948 4.491676 TGGTCGCAGTTCTAGTTTCATAC 58.508 43.478 0.00 0.00 0.00 2.39
1868 1949 4.219944 TGGTCGCAGTTCTAGTTTCATACT 59.780 41.667 0.00 0.00 41.04 2.12
1869 1950 4.563184 GGTCGCAGTTCTAGTTTCATACTG 59.437 45.833 0.00 0.00 37.73 2.74
1879 1961 9.934190 GTTCTAGTTTCATACTGTAGTAGTAGC 57.066 37.037 0.00 0.00 44.69 3.58
1939 2024 3.637432 TGCTGTTGTAATTTTTGCTCCG 58.363 40.909 0.00 0.00 0.00 4.63
2023 2108 5.773239 TTACAGCTTATTTTCGACCTTCG 57.227 39.130 0.00 0.00 42.10 3.79
2076 2162 2.370349 TCTTTCGGTTGCTGTTTGGAA 58.630 42.857 0.00 0.00 0.00 3.53
2077 2163 2.955660 TCTTTCGGTTGCTGTTTGGAAT 59.044 40.909 0.00 0.00 0.00 3.01
2078 2164 3.383185 TCTTTCGGTTGCTGTTTGGAATT 59.617 39.130 0.00 0.00 0.00 2.17
2079 2165 2.791383 TCGGTTGCTGTTTGGAATTG 57.209 45.000 0.00 0.00 0.00 2.32
2080 2166 1.339610 TCGGTTGCTGTTTGGAATTGG 59.660 47.619 0.00 0.00 0.00 3.16
2081 2167 1.339610 CGGTTGCTGTTTGGAATTGGA 59.660 47.619 0.00 0.00 0.00 3.53
2111 2197 1.067846 TCTGAACTTCATCGACCACCG 60.068 52.381 0.00 0.00 40.25 4.94
2158 2244 0.810031 CGGCCTTGTAATCTCGTGGG 60.810 60.000 0.00 0.00 0.00 4.61
2168 2254 1.965754 ATCTCGTGGGAAGGAGCAGC 61.966 60.000 0.00 0.00 0.00 5.25
2250 2340 1.251251 GCTGCAATCCAAGTGAGGTT 58.749 50.000 0.00 0.00 0.00 3.50
2251 2341 1.068055 GCTGCAATCCAAGTGAGGTTG 60.068 52.381 0.00 0.00 0.00 3.77
2422 2543 0.683973 CAGTCCTGAACCAGCAGTCT 59.316 55.000 0.00 0.00 34.06 3.24
2441 2562 3.003897 GTCTTCGAGGCAGGATGTACTAG 59.996 52.174 0.00 0.00 39.31 2.57
2482 2611 2.030893 CGGAGGTAGTACAACACGAACA 60.031 50.000 2.06 0.00 0.00 3.18
2504 2645 1.545582 CGCCCCATGTTTTTCAGTGAT 59.454 47.619 0.00 0.00 0.00 3.06
2529 2670 5.140747 ACTCAGTAGTCCTTGATGTTGAC 57.859 43.478 0.00 0.00 0.00 3.18
2530 2671 4.588951 ACTCAGTAGTCCTTGATGTTGACA 59.411 41.667 0.00 0.00 0.00 3.58
2531 2672 5.247110 ACTCAGTAGTCCTTGATGTTGACAT 59.753 40.000 0.00 0.00 39.70 3.06
2533 2674 7.124901 ACTCAGTAGTCCTTGATGTTGACATAT 59.875 37.037 0.00 0.00 36.57 1.78
2534 2675 7.851228 TCAGTAGTCCTTGATGTTGACATATT 58.149 34.615 0.00 0.00 36.57 1.28
2540 4040 7.830697 AGTCCTTGATGTTGACATATTTGATCA 59.169 33.333 0.00 0.00 36.57 2.92
2612 4201 5.509498 TCAAGGAAGGATTGGTGAAATAGG 58.491 41.667 0.00 0.00 0.00 2.57
2668 4270 0.663568 GTAGCGTGTGTGCGAGAAGT 60.664 55.000 0.00 0.00 40.67 3.01
2728 4330 4.685169 CACACTTGGTGGACATTCATAC 57.315 45.455 2.75 0.00 44.04 2.39
2729 4331 3.125146 CACACTTGGTGGACATTCATACG 59.875 47.826 2.75 0.00 44.04 3.06
2730 4332 2.095853 CACTTGGTGGACATTCATACGC 59.904 50.000 0.00 0.00 0.00 4.42
2834 4466 2.367202 GGAGCTGGATTGGACGGGA 61.367 63.158 0.00 0.00 0.00 5.14
2855 4487 4.753662 CGGGAGGGAGGGACGACA 62.754 72.222 0.00 0.00 0.00 4.35
2856 4488 3.075641 GGGAGGGAGGGACGACAC 61.076 72.222 0.00 0.00 0.00 3.67
2883 4519 1.274703 TAGGGTAGGGTCCGTCGTCT 61.275 60.000 0.00 0.00 0.00 4.18
2884 4520 1.680314 GGGTAGGGTCCGTCGTCTT 60.680 63.158 0.00 0.00 0.00 3.01
2885 4521 0.394352 GGGTAGGGTCCGTCGTCTTA 60.394 60.000 0.00 0.00 0.00 2.10
2886 4522 1.020437 GGTAGGGTCCGTCGTCTTAG 58.980 60.000 0.00 0.00 0.00 2.18
2887 4523 0.380024 GTAGGGTCCGTCGTCTTAGC 59.620 60.000 0.00 0.00 0.00 3.09
2888 4524 0.749454 TAGGGTCCGTCGTCTTAGCC 60.749 60.000 0.00 0.00 0.00 3.93
2889 4525 2.101770 GGTCCGTCGTCTTAGCCG 59.898 66.667 0.00 0.00 0.00 5.52
2890 4526 2.101770 GTCCGTCGTCTTAGCCGG 59.898 66.667 0.00 0.00 41.75 6.13
2891 4527 3.136123 TCCGTCGTCTTAGCCGGG 61.136 66.667 2.18 0.00 40.78 5.73
2892 4528 4.867599 CCGTCGTCTTAGCCGGGC 62.868 72.222 12.11 12.11 36.84 6.13
2893 4529 4.867599 CGTCGTCTTAGCCGGGCC 62.868 72.222 17.02 0.00 0.00 5.80
2894 4530 3.766691 GTCGTCTTAGCCGGGCCA 61.767 66.667 17.02 0.00 0.00 5.36
2895 4531 2.762459 TCGTCTTAGCCGGGCCAT 60.762 61.111 17.02 0.00 0.00 4.40
2896 4532 2.189521 CGTCTTAGCCGGGCCATT 59.810 61.111 17.02 0.00 0.00 3.16
2897 4533 1.451387 CGTCTTAGCCGGGCCATTT 60.451 57.895 17.02 0.00 0.00 2.32
2898 4534 1.436983 CGTCTTAGCCGGGCCATTTC 61.437 60.000 17.02 3.24 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.437682 TGTTGGAAATATGCCCTAGAGG 57.562 45.455 0.00 0.00 39.47 3.69
40 41 5.474876 GGATTGTTGGAAATATGCCCTAGAG 59.525 44.000 0.00 0.00 0.00 2.43
41 42 5.134339 AGGATTGTTGGAAATATGCCCTAGA 59.866 40.000 0.00 0.00 0.00 2.43
42 43 5.388654 AGGATTGTTGGAAATATGCCCTAG 58.611 41.667 0.00 0.00 0.00 3.02
43 44 5.385198 GAGGATTGTTGGAAATATGCCCTA 58.615 41.667 0.00 0.00 0.00 3.53
44 45 4.218312 GAGGATTGTTGGAAATATGCCCT 58.782 43.478 0.00 0.00 0.00 5.19
45 46 3.321968 GGAGGATTGTTGGAAATATGCCC 59.678 47.826 0.00 0.00 0.00 5.36
46 47 4.218312 AGGAGGATTGTTGGAAATATGCC 58.782 43.478 0.00 0.00 0.00 4.40
47 48 6.016777 CAGTAGGAGGATTGTTGGAAATATGC 60.017 42.308 0.00 0.00 0.00 3.14
48 49 6.016777 GCAGTAGGAGGATTGTTGGAAATATG 60.017 42.308 0.00 0.00 0.00 1.78
49 50 6.064717 GCAGTAGGAGGATTGTTGGAAATAT 58.935 40.000 0.00 0.00 0.00 1.28
50 51 5.045213 TGCAGTAGGAGGATTGTTGGAAATA 60.045 40.000 0.00 0.00 0.00 1.40
51 52 4.263905 TGCAGTAGGAGGATTGTTGGAAAT 60.264 41.667 0.00 0.00 0.00 2.17
52 53 3.073798 TGCAGTAGGAGGATTGTTGGAAA 59.926 43.478 0.00 0.00 0.00 3.13
53 54 2.642311 TGCAGTAGGAGGATTGTTGGAA 59.358 45.455 0.00 0.00 0.00 3.53
54 55 2.027192 GTGCAGTAGGAGGATTGTTGGA 60.027 50.000 0.00 0.00 0.00 3.53
55 56 2.026822 AGTGCAGTAGGAGGATTGTTGG 60.027 50.000 0.00 0.00 0.00 3.77
56 57 3.005554 CAGTGCAGTAGGAGGATTGTTG 58.994 50.000 0.00 0.00 0.00 3.33
57 58 2.906389 TCAGTGCAGTAGGAGGATTGTT 59.094 45.455 0.00 0.00 0.00 2.83
58 59 2.234908 GTCAGTGCAGTAGGAGGATTGT 59.765 50.000 0.00 0.00 0.00 2.71
59 60 2.736719 CGTCAGTGCAGTAGGAGGATTG 60.737 54.545 0.00 0.00 0.00 2.67
60 61 1.478510 CGTCAGTGCAGTAGGAGGATT 59.521 52.381 0.00 0.00 0.00 3.01
172 173 3.470520 GAGATGATCGACGCTGGAG 57.529 57.895 0.00 0.00 0.00 3.86
220 222 2.622903 TAGTGCTCGCGCCATGGTAC 62.623 60.000 14.67 4.76 34.43 3.34
379 382 1.376683 GACCATGGCAACTGCGGTA 60.377 57.895 13.04 0.00 43.26 4.02
420 423 1.362932 AGAACTAGCAGAGGAAGGGGA 59.637 52.381 0.00 0.00 0.00 4.81
473 476 3.599343 TGCCCGCATGAGATATGATTAC 58.401 45.455 0.00 0.00 0.00 1.89
482 485 1.228398 TTTGGTTGCCCGCATGAGA 60.228 52.632 0.00 0.00 0.00 3.27
633 636 2.575279 ACATCTCAATCCAGTCTGGCTT 59.425 45.455 14.64 8.17 37.47 4.35
645 648 6.060136 AGCTGCATTGTATACACATCTCAAT 58.940 36.000 4.68 0.00 33.76 2.57
698 701 2.046285 GCGGTGTTGCCTTGCCTAT 61.046 57.895 0.00 0.00 34.25 2.57
707 710 0.388907 TACTTACTCGGCGGTGTTGC 60.389 55.000 7.21 0.00 0.00 4.17
708 711 1.336148 TGTACTTACTCGGCGGTGTTG 60.336 52.381 7.21 6.15 0.00 3.33
709 712 0.961019 TGTACTTACTCGGCGGTGTT 59.039 50.000 7.21 0.00 0.00 3.32
710 713 0.961019 TTGTACTTACTCGGCGGTGT 59.039 50.000 7.21 9.41 0.00 4.16
711 714 2.068837 TTTGTACTTACTCGGCGGTG 57.931 50.000 7.21 2.81 0.00 4.94
712 715 2.297033 TCTTTTGTACTTACTCGGCGGT 59.703 45.455 7.21 6.66 0.00 5.68
713 716 2.950433 TCTTTTGTACTTACTCGGCGG 58.050 47.619 7.21 0.00 0.00 6.13
714 717 4.682860 TCTTTCTTTTGTACTTACTCGGCG 59.317 41.667 0.00 0.00 0.00 6.46
715 718 5.120363 CCTCTTTCTTTTGTACTTACTCGGC 59.880 44.000 0.00 0.00 0.00 5.54
716 719 6.453092 TCCTCTTTCTTTTGTACTTACTCGG 58.547 40.000 0.00 0.00 0.00 4.63
717 720 7.368833 TCTCCTCTTTCTTTTGTACTTACTCG 58.631 38.462 0.00 0.00 0.00 4.18
718 721 7.815549 CCTCTCCTCTTTCTTTTGTACTTACTC 59.184 40.741 0.00 0.00 0.00 2.59
719 722 7.509659 TCCTCTCCTCTTTCTTTTGTACTTACT 59.490 37.037 0.00 0.00 0.00 2.24
720 723 7.668492 TCCTCTCCTCTTTCTTTTGTACTTAC 58.332 38.462 0.00 0.00 0.00 2.34
721 724 7.850935 TCCTCTCCTCTTTCTTTTGTACTTA 57.149 36.000 0.00 0.00 0.00 2.24
722 725 6.749036 TCCTCTCCTCTTTCTTTTGTACTT 57.251 37.500 0.00 0.00 0.00 2.24
723 726 6.749036 TTCCTCTCCTCTTTCTTTTGTACT 57.251 37.500 0.00 0.00 0.00 2.73
724 727 7.041030 CCTTTTCCTCTCCTCTTTCTTTTGTAC 60.041 40.741 0.00 0.00 0.00 2.90
725 728 6.998673 CCTTTTCCTCTCCTCTTTCTTTTGTA 59.001 38.462 0.00 0.00 0.00 2.41
726 729 5.830457 CCTTTTCCTCTCCTCTTTCTTTTGT 59.170 40.000 0.00 0.00 0.00 2.83
727 730 6.016693 GTCCTTTTCCTCTCCTCTTTCTTTTG 60.017 42.308 0.00 0.00 0.00 2.44
736 739 2.425668 CTCTCGTCCTTTTCCTCTCCTC 59.574 54.545 0.00 0.00 0.00 3.71
748 751 4.998033 GGTTTCTCAATTTTCTCTCGTCCT 59.002 41.667 0.00 0.00 0.00 3.85
749 752 4.154375 GGGTTTCTCAATTTTCTCTCGTCC 59.846 45.833 0.00 0.00 0.00 4.79
778 781 5.921962 ACTTCAGCTTTTGTTCCTTTTCT 57.078 34.783 0.00 0.00 0.00 2.52
789 792 2.798847 GACGTCCGTTACTTCAGCTTTT 59.201 45.455 3.51 0.00 0.00 2.27
810 813 4.311816 ACTGACTTTGGACAATGCTTTG 57.688 40.909 10.58 10.58 38.86 2.77
812 815 3.953612 TGAACTGACTTTGGACAATGCTT 59.046 39.130 0.00 0.00 0.00 3.91
813 816 3.316308 GTGAACTGACTTTGGACAATGCT 59.684 43.478 0.00 0.00 0.00 3.79
815 818 4.498009 GGTGTGAACTGACTTTGGACAATG 60.498 45.833 0.00 0.00 0.00 2.82
816 819 3.632145 GGTGTGAACTGACTTTGGACAAT 59.368 43.478 0.00 0.00 0.00 2.71
817 820 3.013921 GGTGTGAACTGACTTTGGACAA 58.986 45.455 0.00 0.00 0.00 3.18
818 821 2.026729 TGGTGTGAACTGACTTTGGACA 60.027 45.455 0.00 0.00 0.00 4.02
819 822 2.639065 TGGTGTGAACTGACTTTGGAC 58.361 47.619 0.00 0.00 0.00 4.02
820 823 3.013921 GTTGGTGTGAACTGACTTTGGA 58.986 45.455 0.00 0.00 0.00 3.53
821 824 2.752354 TGTTGGTGTGAACTGACTTTGG 59.248 45.455 0.00 0.00 0.00 3.28
822 825 4.165779 GTTGTTGGTGTGAACTGACTTTG 58.834 43.478 0.00 0.00 0.00 2.77
824 827 3.417101 TGTTGTTGGTGTGAACTGACTT 58.583 40.909 0.00 0.00 0.00 3.01
827 830 3.428725 GCATTGTTGTTGGTGTGAACTGA 60.429 43.478 0.00 0.00 0.00 3.41
865 895 0.996762 GAGAGAGGGGAGGGGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
867 897 0.996762 GAGAGAGAGGGGAGGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
874 905 2.858644 AGAAGAGAGAGAGAGAGGGGA 58.141 52.381 0.00 0.00 0.00 4.81
875 906 3.669939 AAGAAGAGAGAGAGAGAGGGG 57.330 52.381 0.00 0.00 0.00 4.79
877 908 5.505780 TGGTTAAGAAGAGAGAGAGAGAGG 58.494 45.833 0.00 0.00 0.00 3.69
884 915 4.081365 GGGAGGTTGGTTAAGAAGAGAGAG 60.081 50.000 0.00 0.00 0.00 3.20
904 935 1.765074 CGAGGAAAAAGGGTGGGGA 59.235 57.895 0.00 0.00 0.00 4.81
907 938 0.881796 GAAGCGAGGAAAAAGGGTGG 59.118 55.000 0.00 0.00 0.00 4.61
908 939 1.604604 TGAAGCGAGGAAAAAGGGTG 58.395 50.000 0.00 0.00 0.00 4.61
909 940 2.358322 TTGAAGCGAGGAAAAAGGGT 57.642 45.000 0.00 0.00 0.00 4.34
925 956 2.668850 AGGGGGAGAAGAGGATTTGA 57.331 50.000 0.00 0.00 0.00 2.69
999 1035 0.883833 CTCCATTGAAGCCTTGCGTT 59.116 50.000 0.00 0.00 0.00 4.84
1051 1087 2.204090 GGGGAGTTGGGGTCCTGA 60.204 66.667 0.00 0.00 34.16 3.86
1141 1177 1.153046 CGGAAGGTTGTGTGGGTGT 60.153 57.895 0.00 0.00 0.00 4.16
1225 1261 0.606673 GCTTGAAGGAGGTGGTGTCC 60.607 60.000 0.00 0.00 0.00 4.02
1492 1555 3.358076 GAAGTCCAGGACGCTCGGG 62.358 68.421 14.32 0.00 37.67 5.14
1519 1582 4.711949 ACCGGGCTGCTGAGCTTG 62.712 66.667 6.32 0.00 45.44 4.01
1678 1759 4.821589 GGCGAGCTCACGGGGAAG 62.822 72.222 15.40 0.00 0.00 3.46
1687 1768 4.925861 GCCATCCTGGGCGAGCTC 62.926 72.222 2.73 2.73 45.40 4.09
1817 1898 1.373497 GATGATACAGCGAGGGCGG 60.373 63.158 0.00 0.00 46.35 6.13
1818 1899 1.730902 CGATGATACAGCGAGGGCG 60.731 63.158 3.34 0.00 46.56 6.13
1819 1900 2.024319 GCGATGATACAGCGAGGGC 61.024 63.158 13.25 0.00 46.56 5.19
1820 1901 1.373497 GGCGATGATACAGCGAGGG 60.373 63.158 13.25 0.00 46.56 4.30
1821 1902 1.730902 CGGCGATGATACAGCGAGG 60.731 63.158 13.25 0.37 46.56 4.63
1822 1903 0.999228 GACGGCGATGATACAGCGAG 60.999 60.000 16.62 8.32 46.56 5.03
1847 1928 5.162075 ACAGTATGAAACTAGAACTGCGAC 58.838 41.667 0.00 0.00 40.94 5.19
1865 1946 6.684686 CAAACACCTTGCTACTACTACAGTA 58.315 40.000 0.00 0.00 38.80 2.74
1866 1947 5.539048 CAAACACCTTGCTACTACTACAGT 58.461 41.667 0.00 0.00 41.62 3.55
1879 1961 0.732571 ACGACACAGCAAACACCTTG 59.267 50.000 0.00 0.00 38.15 3.61
1939 2024 3.073209 ACTCCCCTCTTCCTTTCAAGAAC 59.927 47.826 0.00 0.00 31.86 3.01
2023 2108 5.086104 TGGGAAAAGATCTACTAGCACAC 57.914 43.478 0.00 0.00 0.00 3.82
2080 2166 5.236047 CGATGAAGTTCAGAGGGAATCAATC 59.764 44.000 11.91 0.00 37.93 2.67
2081 2167 5.104776 TCGATGAAGTTCAGAGGGAATCAAT 60.105 40.000 11.91 0.00 37.93 2.57
2158 2244 3.797546 GCACTGCGCTGCTCCTTC 61.798 66.667 14.80 0.00 37.77 3.46
2168 2254 4.460505 CATATGTATTCACATGCACTGCG 58.539 43.478 0.00 0.00 45.17 5.18
2210 2296 0.108851 GCAAACGCCGGATTTTGGAT 60.109 50.000 22.63 0.00 33.97 3.41
2250 2340 0.976641 AGACTCGAGGCATGTTTCCA 59.023 50.000 22.94 0.00 0.00 3.53
2251 2341 2.003301 GAAGACTCGAGGCATGTTTCC 58.997 52.381 22.94 0.00 0.00 3.13
2252 2342 2.966050 AGAAGACTCGAGGCATGTTTC 58.034 47.619 22.94 15.25 0.00 2.78
2253 2343 3.007398 AGAAGAAGACTCGAGGCATGTTT 59.993 43.478 22.94 5.47 0.00 2.83
2254 2344 2.564947 AGAAGAAGACTCGAGGCATGTT 59.435 45.455 22.94 14.18 0.00 2.71
2255 2345 2.165437 GAGAAGAAGACTCGAGGCATGT 59.835 50.000 22.94 3.53 0.00 3.21
2256 2346 2.426738 AGAGAAGAAGACTCGAGGCATG 59.573 50.000 22.94 0.00 39.12 4.06
2257 2347 2.426738 CAGAGAAGAAGACTCGAGGCAT 59.573 50.000 22.94 8.94 39.12 4.40
2422 2543 3.014304 ACTAGTACATCCTGCCTCGAA 57.986 47.619 0.00 0.00 0.00 3.71
2441 2562 0.466124 GGGCAGATGAGTCCAGGTAC 59.534 60.000 0.00 0.00 0.00 3.34
2469 2598 0.041926 GGGCGTTGTTCGTGTTGTAC 60.042 55.000 0.00 0.00 42.13 2.90
2482 2611 1.068434 CACTGAAAAACATGGGGCGTT 59.932 47.619 0.00 0.00 0.00 4.84
2525 2666 8.089597 ACATTTTGCTGTGATCAAATATGTCAA 58.910 29.630 0.00 0.00 34.30 3.18
2527 2668 8.377681 CAACATTTTGCTGTGATCAAATATGTC 58.622 33.333 11.76 0.00 36.02 3.06
2529 2670 8.468720 TCAACATTTTGCTGTGATCAAATATG 57.531 30.769 0.00 2.08 33.94 1.78
2530 2671 9.146984 CTTCAACATTTTGCTGTGATCAAATAT 57.853 29.630 0.00 0.00 33.94 1.28
2531 2672 8.143193 ACTTCAACATTTTGCTGTGATCAAATA 58.857 29.630 0.00 0.00 33.94 1.40
2533 2674 6.339730 ACTTCAACATTTTGCTGTGATCAAA 58.660 32.000 0.00 0.00 32.17 2.69
2534 2675 5.904941 ACTTCAACATTTTGCTGTGATCAA 58.095 33.333 0.00 0.00 32.17 2.57
2540 4040 6.034470 CGTGTTTTACTTCAACATTTTGCTGT 59.966 34.615 0.00 0.00 36.54 4.40
2668 4270 1.834263 CCCCAACCCAAACAAACAAGA 59.166 47.619 0.00 0.00 0.00 3.02
2741 4356 2.003672 CCAACGAGGATTTACGCCG 58.996 57.895 0.00 0.00 41.22 6.46
2742 4357 1.712018 GGCCAACGAGGATTTACGCC 61.712 60.000 0.00 0.00 41.22 5.68
2846 4478 1.852157 TACCCTACCGTGTCGTCCCT 61.852 60.000 0.00 0.00 0.00 4.20
2847 4479 1.378514 TACCCTACCGTGTCGTCCC 60.379 63.158 0.00 0.00 0.00 4.46
2848 4480 1.379642 CCTACCCTACCGTGTCGTCC 61.380 65.000 0.00 0.00 0.00 4.79
2849 4481 1.379642 CCCTACCCTACCGTGTCGTC 61.380 65.000 0.00 0.00 0.00 4.20
2850 4482 1.379044 CCCTACCCTACCGTGTCGT 60.379 63.158 0.00 0.00 0.00 4.34
2851 4483 0.107214 TACCCTACCCTACCGTGTCG 60.107 60.000 0.00 0.00 0.00 4.35
2853 4485 0.259938 CCTACCCTACCCTACCGTGT 59.740 60.000 0.00 0.00 0.00 4.49
2854 4486 0.468771 CCCTACCCTACCCTACCGTG 60.469 65.000 0.00 0.00 0.00 4.94
2855 4487 0.926220 ACCCTACCCTACCCTACCGT 60.926 60.000 0.00 0.00 0.00 4.83
2856 4488 0.178978 GACCCTACCCTACCCTACCG 60.179 65.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.