Multiple sequence alignment - TraesCS3B01G236400

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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 TraesCS3B01G236400 chr3B 100.000 3689 0 0 1 3689 368935450 368931762 0.000000e+00 6813.0
1 TraesCS3B01G236400 chr3B 97.109 588 17 0 3102 3689 41217445 41216858 0.000000e+00 992.0
2 TraesCS3B01G236400 chr3B 99.115 113 1 0 3577 3689 50949278 50949390 1.740000e-48 204.0
3 TraesCS3B01G236400 chr3B 98.485 66 1 0 3518 3583 50944303 50944368 2.330000e-22 117.0
4 TraesCS3B01G236400 chr3B 75.714 140 29 5 1 138 91425115 91425251 8.550000e-07 65.8
5 TraesCS3B01G236400 chr6B 98.215 2689 44 1 1001 3689 613576088 613578772 0.000000e+00 4697.0
6 TraesCS3B01G236400 chr4A 95.682 1598 68 1 1148 2745 596976122 596974526 0.000000e+00 2567.0
7 TraesCS3B01G236400 chr4A 95.446 549 24 1 3141 3689 678229079 678228532 0.000000e+00 874.0
8 TraesCS3B01G236400 chr4B 97.878 1414 29 1 966 2378 375396952 375398365 0.000000e+00 2444.0
9 TraesCS3B01G236400 chr4B 98.026 1317 26 0 2373 3689 375406497 375407813 0.000000e+00 2289.0
10 TraesCS3B01G236400 chr3A 79.979 934 171 6 1026 1945 435357153 435358084 0.000000e+00 675.0
11 TraesCS3B01G236400 chr3A 87.574 507 41 3 6 506 366855719 366855229 5.350000e-158 568.0
12 TraesCS3B01G236400 chr3A 92.628 312 20 1 560 868 366855221 366854910 2.610000e-121 446.0
13 TraesCS3B01G236400 chr3A 78.771 179 35 3 1 179 69057558 69057383 2.330000e-22 117.0
14 TraesCS3B01G236400 chr1D 79.872 934 178 9 1001 1929 104293414 104294342 0.000000e+00 675.0
15 TraesCS3B01G236400 chr1D 79.553 895 157 10 1067 1947 413778587 413777705 1.880000e-172 616.0
16 TraesCS3B01G236400 chr1A 78.409 968 185 16 1001 1947 299265159 299264195 3.150000e-170 608.0
17 TraesCS3B01G236400 chr2B 79.042 835 159 8 1122 1945 677677132 677676303 3.220000e-155 558.0
18 TraesCS3B01G236400 chr3D 94.194 310 15 2 561 867 280998049 280997740 1.550000e-128 470.0
19 TraesCS3B01G236400 chr3D 93.119 218 12 2 290 506 280998273 280998058 2.140000e-82 316.0
20 TraesCS3B01G236400 chr3D 92.547 161 12 0 7 167 280998504 280998344 7.970000e-57 231.0
21 TraesCS3B01G236400 chr6D 78.022 637 128 11 1299 1930 456452457 456453086 1.240000e-104 390.0
22 TraesCS3B01G236400 chr6A 96.023 176 7 0 3514 3689 94259983 94259808 1.680000e-73 287.0
23 TraesCS3B01G236400 chr7D 97.143 35 1 0 46 80 126705113 126705079 3.980000e-05 60.2
24 TraesCS3B01G236400 chr2A 94.595 37 1 1 3442 3477 621374517 621374481 5.150000e-04 56.5
25 TraesCS3B01G236400 chr2D 100.000 28 0 0 90 117 37383208 37383181 7.000000e-03 52.8


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 TraesCS3B01G236400 chr3B 368931762 368935450 3688 True 6813 6813 100.000000 1 3689 1 chr3B.!!$R2 3688
1 TraesCS3B01G236400 chr3B 41216858 41217445 587 True 992 992 97.109000 3102 3689 1 chr3B.!!$R1 587
2 TraesCS3B01G236400 chr6B 613576088 613578772 2684 False 4697 4697 98.215000 1001 3689 1 chr6B.!!$F1 2688
3 TraesCS3B01G236400 chr4A 596974526 596976122 1596 True 2567 2567 95.682000 1148 2745 1 chr4A.!!$R1 1597
4 TraesCS3B01G236400 chr4A 678228532 678229079 547 True 874 874 95.446000 3141 3689 1 chr4A.!!$R2 548
5 TraesCS3B01G236400 chr4B 375396952 375398365 1413 False 2444 2444 97.878000 966 2378 1 chr4B.!!$F1 1412
6 TraesCS3B01G236400 chr4B 375406497 375407813 1316 False 2289 2289 98.026000 2373 3689 1 chr4B.!!$F2 1316
7 TraesCS3B01G236400 chr3A 435357153 435358084 931 False 675 675 79.979000 1026 1945 1 chr3A.!!$F1 919
8 TraesCS3B01G236400 chr3A 366854910 366855719 809 True 507 568 90.101000 6 868 2 chr3A.!!$R2 862
9 TraesCS3B01G236400 chr1D 104293414 104294342 928 False 675 675 79.872000 1001 1929 1 chr1D.!!$F1 928
10 TraesCS3B01G236400 chr1D 413777705 413778587 882 True 616 616 79.553000 1067 1947 1 chr1D.!!$R1 880
11 TraesCS3B01G236400 chr1A 299264195 299265159 964 True 608 608 78.409000 1001 1947 1 chr1A.!!$R1 946
12 TraesCS3B01G236400 chr2B 677676303 677677132 829 True 558 558 79.042000 1122 1945 1 chr2B.!!$R1 823
13 TraesCS3B01G236400 chr3D 280997740 280998504 764 True 339 470 93.286667 7 867 3 chr3D.!!$R1 860
14 TraesCS3B01G236400 chr6D 456452457 456453086 629 False 390 390 78.022000 1299 1930 1 chr6D.!!$F1 631

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
144 145 0.033504 AACTGGACGCGTCTGTGAAT 59.966 50.0 35.50 17.89 0.00 2.57 F
949 960 0.108207 GTATCCATCAGCTGCAGCCT 59.892 55.0 34.39 19.10 43.38 4.58 F
950 961 0.395686 TATCCATCAGCTGCAGCCTC 59.604 55.0 34.39 8.53 43.38 4.70 F
2111 2155 1.091771 CCTTGCAGTATGGCGACTGG 61.092 60.0 17.87 4.86 45.85 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1863 1.301716 AAACTGTCGCCGCATGACT 60.302 52.632 0.00 0.0 37.26 3.41 R
2571 2615 1.004440 GAGCTTGAAGAGGGCACGT 60.004 57.895 0.00 0.0 0.00 4.49 R
2610 2654 3.065233 GTGCAATTATGGCATCTTCGACA 59.935 43.478 1.65 0.0 44.11 4.35 R
3229 3273 2.138179 GCGGTAGGCCCATAGACCA 61.138 63.158 0.00 0.0 34.80 4.02 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
43 44 9.987272 TCATCTCTACTAATCACATGTAAATGG 57.013 33.333 0.00 0.00 0.00 3.16
48 49 4.889409 ACTAATCACATGTAAATGGCAGGG 59.111 41.667 0.00 0.00 0.00 4.45
56 57 5.477984 ACATGTAAATGGCAGGGCATATAAG 59.522 40.000 8.86 1.07 0.00 1.73
90 91 5.858381 AGAAGTATGATTGTATGCACGGAT 58.142 37.500 0.00 0.00 0.00 4.18
137 138 2.092882 GGCACTAACTGGACGCGTC 61.093 63.158 30.67 30.67 0.00 5.19
144 145 0.033504 AACTGGACGCGTCTGTGAAT 59.966 50.000 35.50 17.89 0.00 2.57
155 156 3.987868 GCGTCTGTGAATGTTTAGTGAGA 59.012 43.478 0.00 0.00 0.00 3.27
174 175 2.505819 AGATGGATTTGCTAAGTCGGGT 59.494 45.455 0.00 0.00 0.00 5.28
209 210 7.741785 TCTAAGAACACCTCTGAATTTACCAA 58.258 34.615 0.00 0.00 33.37 3.67
214 215 6.391227 ACACCTCTGAATTTACCAACTTTG 57.609 37.500 0.00 0.00 0.00 2.77
233 234 5.351189 ACTTTGGAACTTTGCATGTTGTTTC 59.649 36.000 9.83 2.56 0.00 2.78
243 250 1.759445 CATGTTGTTTCCCACACCCAA 59.241 47.619 0.00 0.00 33.98 4.12
252 259 1.497286 TCCCACACCCAACTAAGCTTT 59.503 47.619 3.20 0.00 0.00 3.51
286 293 2.784347 AGCTTCTGTTTAGCTGGGAAC 58.216 47.619 0.00 0.00 46.71 3.62
287 294 2.553247 AGCTTCTGTTTAGCTGGGAACC 60.553 50.000 0.00 0.00 46.71 3.62
318 325 2.285083 TGCCATATGCTTGTCCGTTAC 58.715 47.619 0.00 0.00 42.00 2.50
320 327 2.680841 GCCATATGCTTGTCCGTTACAA 59.319 45.455 0.00 1.24 45.90 2.41
331 338 3.256631 TGTCCGTTACAACTAGGGAGTTC 59.743 47.826 0.00 0.00 44.39 3.01
375 382 4.322801 GCTAGCAAAGTAGGGAGAAAGACA 60.323 45.833 10.63 0.00 0.00 3.41
382 389 4.678256 AGTAGGGAGAAAGACAGATCACA 58.322 43.478 0.00 0.00 0.00 3.58
391 398 5.127519 AGAAAGACAGATCACATGGAGAGAG 59.872 44.000 0.00 0.00 0.00 3.20
395 402 3.953612 ACAGATCACATGGAGAGAGAGAC 59.046 47.826 0.00 0.00 0.00 3.36
400 407 2.094286 CACATGGAGAGAGAGACACACC 60.094 54.545 0.00 0.00 0.00 4.16
418 425 8.818860 AGACACACCCACATAGTTAACTATTAA 58.181 33.333 22.81 1.79 37.07 1.40
465 472 1.143305 CGCTCTCTGACTGTTTGTGG 58.857 55.000 0.00 0.00 0.00 4.17
492 499 1.405821 TGACAATTTTGTTTCGGGCGT 59.594 42.857 0.00 0.00 42.43 5.68
506 514 3.023119 TCGGGCGTGGATACTAGTTTAA 58.977 45.455 0.00 0.00 37.61 1.52
508 516 3.181483 CGGGCGTGGATACTAGTTTAAGT 60.181 47.826 0.00 0.00 37.61 2.24
511 519 6.340522 GGGCGTGGATACTAGTTTAAGTTTA 58.659 40.000 0.00 0.00 37.61 2.01
512 520 6.818142 GGGCGTGGATACTAGTTTAAGTTTAA 59.182 38.462 0.00 0.00 37.61 1.52
513 521 7.010830 GGGCGTGGATACTAGTTTAAGTTTAAG 59.989 40.741 0.00 0.00 37.61 1.85
514 522 7.010830 GGCGTGGATACTAGTTTAAGTTTAAGG 59.989 40.741 0.00 0.00 37.61 2.69
515 523 7.547019 GCGTGGATACTAGTTTAAGTTTAAGGT 59.453 37.037 0.00 0.00 37.61 3.50
516 524 9.428097 CGTGGATACTAGTTTAAGTTTAAGGTT 57.572 33.333 0.00 0.00 37.61 3.50
529 537 7.578310 AAGTTTAAGGTTTTCAAGTACTCCC 57.422 36.000 0.00 0.00 0.00 4.30
530 538 6.665695 AGTTTAAGGTTTTCAAGTACTCCCA 58.334 36.000 0.00 0.00 0.00 4.37
531 539 7.120716 AGTTTAAGGTTTTCAAGTACTCCCAA 58.879 34.615 0.00 0.00 0.00 4.12
532 540 7.616542 AGTTTAAGGTTTTCAAGTACTCCCAAA 59.383 33.333 0.00 0.00 0.00 3.28
533 541 7.957992 TTAAGGTTTTCAAGTACTCCCAAAA 57.042 32.000 0.00 0.00 0.00 2.44
534 542 6.860790 AAGGTTTTCAAGTACTCCCAAAAA 57.139 33.333 0.00 0.00 0.00 1.94
572 580 2.099427 GGACGGAGGAAGTACATCTGAC 59.901 54.545 0.00 0.00 37.83 3.51
623 631 0.909610 CCAGCACTCCTTGGGTCCTA 60.910 60.000 0.00 0.00 0.00 2.94
644 652 8.394121 GTCCTACTGCAAGAAATTCATCTTAAG 58.606 37.037 0.00 0.00 37.56 1.85
645 653 8.321353 TCCTACTGCAAGAAATTCATCTTAAGA 58.679 33.333 7.82 7.82 37.56 2.10
675 683 3.953542 AGAGTTTTGACAGGGTTCCTT 57.046 42.857 0.00 0.00 0.00 3.36
686 694 4.172807 ACAGGGTTCCTTCATGGTTACTA 58.827 43.478 0.00 0.00 37.07 1.82
718 726 5.807909 ACTAGTTAAATTAACCTTCCCGCA 58.192 37.500 11.83 0.00 39.47 5.69
726 734 0.618458 AACCTTCCCGCAGCATTCTA 59.382 50.000 0.00 0.00 0.00 2.10
771 779 5.643348 TGAGATTAAGTCACATGCGTCAAAT 59.357 36.000 0.00 0.00 0.00 2.32
800 808 0.392193 CAGCACTAAGTCCTGCCAGG 60.392 60.000 3.69 3.69 36.46 4.45
834 845 1.883275 CCGCCAGGTGTTTTGTTATCA 59.117 47.619 0.00 0.00 0.00 2.15
881 892 6.012962 GCTTTATAGCGAAAATGCTGTTTG 57.987 37.500 0.00 0.00 46.70 2.93
882 893 5.004726 GCTTTATAGCGAAAATGCTGTTTGG 59.995 40.000 0.00 0.00 46.70 3.28
883 894 5.888691 TTATAGCGAAAATGCTGTTTGGA 57.111 34.783 0.00 0.00 46.70 3.53
884 895 2.712057 AGCGAAAATGCTGTTTGGAG 57.288 45.000 0.00 0.00 45.28 3.86
885 896 1.270550 AGCGAAAATGCTGTTTGGAGG 59.729 47.619 0.00 0.00 45.28 4.30
886 897 1.701704 CGAAAATGCTGTTTGGAGGC 58.298 50.000 0.00 0.00 0.00 4.70
887 898 1.669795 CGAAAATGCTGTTTGGAGGCC 60.670 52.381 0.00 0.00 0.00 5.19
888 899 0.318120 AAAATGCTGTTTGGAGGCCG 59.682 50.000 0.00 0.00 0.00 6.13
889 900 0.539438 AAATGCTGTTTGGAGGCCGA 60.539 50.000 0.00 0.00 0.00 5.54
890 901 0.323725 AATGCTGTTTGGAGGCCGAT 60.324 50.000 0.00 0.00 0.00 4.18
891 902 0.749454 ATGCTGTTTGGAGGCCGATC 60.749 55.000 0.00 0.00 0.00 3.69
892 903 2.464459 GCTGTTTGGAGGCCGATCG 61.464 63.158 8.51 8.51 0.00 3.69
893 904 1.218047 CTGTTTGGAGGCCGATCGA 59.782 57.895 18.66 0.00 0.00 3.59
894 905 0.807667 CTGTTTGGAGGCCGATCGAG 60.808 60.000 18.66 8.00 0.00 4.04
895 906 2.174319 GTTTGGAGGCCGATCGAGC 61.174 63.158 18.66 17.69 0.00 5.03
896 907 2.359169 TTTGGAGGCCGATCGAGCT 61.359 57.895 18.66 8.24 0.00 4.09
897 908 2.298158 TTTGGAGGCCGATCGAGCTC 62.298 60.000 18.66 15.41 0.00 4.09
898 909 3.984749 GGAGGCCGATCGAGCTCC 61.985 72.222 18.66 19.54 0.00 4.70
899 910 3.219928 GAGGCCGATCGAGCTCCA 61.220 66.667 18.66 0.00 0.00 3.86
900 911 2.522923 AGGCCGATCGAGCTCCAT 60.523 61.111 18.66 0.00 0.00 3.41
901 912 2.356793 GGCCGATCGAGCTCCATG 60.357 66.667 18.66 0.00 0.00 3.66
902 913 3.040763 GCCGATCGAGCTCCATGC 61.041 66.667 18.66 4.69 43.29 4.06
903 914 2.418777 CCGATCGAGCTCCATGCA 59.581 61.111 18.66 0.00 45.94 3.96
904 915 1.664017 CCGATCGAGCTCCATGCAG 60.664 63.158 18.66 0.00 45.94 4.41
905 916 1.067084 CGATCGAGCTCCATGCAGT 59.933 57.895 10.26 0.00 45.94 4.40
906 917 0.529337 CGATCGAGCTCCATGCAGTT 60.529 55.000 10.26 0.00 45.94 3.16
907 918 1.216122 GATCGAGCTCCATGCAGTTC 58.784 55.000 8.47 0.00 45.94 3.01
908 919 0.529337 ATCGAGCTCCATGCAGTTCG 60.529 55.000 15.96 15.96 45.53 3.95
909 920 1.446792 CGAGCTCCATGCAGTTCGT 60.447 57.895 14.11 0.00 45.94 3.85
910 921 1.016130 CGAGCTCCATGCAGTTCGTT 61.016 55.000 14.11 0.00 45.94 3.85
911 922 1.735700 CGAGCTCCATGCAGTTCGTTA 60.736 52.381 14.11 0.00 45.94 3.18
912 923 1.661112 GAGCTCCATGCAGTTCGTTAC 59.339 52.381 0.87 0.00 45.94 2.50
913 924 0.727398 GCTCCATGCAGTTCGTTACC 59.273 55.000 0.00 0.00 42.31 2.85
914 925 1.676014 GCTCCATGCAGTTCGTTACCT 60.676 52.381 0.00 0.00 42.31 3.08
915 926 2.699954 CTCCATGCAGTTCGTTACCTT 58.300 47.619 0.00 0.00 0.00 3.50
916 927 2.416547 CTCCATGCAGTTCGTTACCTTG 59.583 50.000 0.00 0.00 0.00 3.61
917 928 1.468520 CCATGCAGTTCGTTACCTTGG 59.531 52.381 0.00 0.00 0.00 3.61
918 929 2.151202 CATGCAGTTCGTTACCTTGGT 58.849 47.619 0.00 0.00 0.00 3.67
919 930 1.588674 TGCAGTTCGTTACCTTGGTG 58.411 50.000 2.03 0.00 0.00 4.17
920 931 0.872388 GCAGTTCGTTACCTTGGTGG 59.128 55.000 2.03 0.00 42.93 4.61
930 941 3.217242 CCTTGGTGGTCAGTTCTCG 57.783 57.895 0.00 0.00 0.00 4.04
931 942 0.393077 CCTTGGTGGTCAGTTCTCGT 59.607 55.000 0.00 0.00 0.00 4.18
932 943 1.616865 CCTTGGTGGTCAGTTCTCGTA 59.383 52.381 0.00 0.00 0.00 3.43
933 944 2.233922 CCTTGGTGGTCAGTTCTCGTAT 59.766 50.000 0.00 0.00 0.00 3.06
934 945 3.512680 CTTGGTGGTCAGTTCTCGTATC 58.487 50.000 0.00 0.00 0.00 2.24
935 946 1.822990 TGGTGGTCAGTTCTCGTATCC 59.177 52.381 0.00 0.00 0.00 2.59
936 947 1.822990 GGTGGTCAGTTCTCGTATCCA 59.177 52.381 0.00 0.00 0.00 3.41
937 948 2.431057 GGTGGTCAGTTCTCGTATCCAT 59.569 50.000 0.00 0.00 0.00 3.41
938 949 3.491104 GGTGGTCAGTTCTCGTATCCATC 60.491 52.174 0.00 0.00 0.00 3.51
939 950 3.130516 GTGGTCAGTTCTCGTATCCATCA 59.869 47.826 0.00 0.00 0.00 3.07
940 951 3.381590 TGGTCAGTTCTCGTATCCATCAG 59.618 47.826 0.00 0.00 0.00 2.90
941 952 3.376540 GTCAGTTCTCGTATCCATCAGC 58.623 50.000 0.00 0.00 0.00 4.26
942 953 3.067461 GTCAGTTCTCGTATCCATCAGCT 59.933 47.826 0.00 0.00 0.00 4.24
943 954 3.067320 TCAGTTCTCGTATCCATCAGCTG 59.933 47.826 7.63 7.63 0.00 4.24
944 955 2.131183 GTTCTCGTATCCATCAGCTGC 58.869 52.381 9.47 0.00 0.00 5.25
945 956 1.402787 TCTCGTATCCATCAGCTGCA 58.597 50.000 9.47 0.00 0.00 4.41
946 957 1.339291 TCTCGTATCCATCAGCTGCAG 59.661 52.381 10.11 10.11 0.00 4.41
947 958 0.249615 TCGTATCCATCAGCTGCAGC 60.250 55.000 31.53 31.53 42.49 5.25
948 959 1.226686 CGTATCCATCAGCTGCAGCC 61.227 60.000 34.39 17.05 43.38 4.85
949 960 0.108207 GTATCCATCAGCTGCAGCCT 59.892 55.000 34.39 19.10 43.38 4.58
950 961 0.395686 TATCCATCAGCTGCAGCCTC 59.604 55.000 34.39 8.53 43.38 4.70
951 962 2.661840 ATCCATCAGCTGCAGCCTCG 62.662 60.000 34.39 22.81 43.38 4.63
952 963 3.574445 CATCAGCTGCAGCCTCGC 61.574 66.667 34.39 11.30 43.38 5.03
960 971 4.537433 GCAGCCTCGCGGGAAGAT 62.537 66.667 8.08 0.00 37.23 2.40
961 972 2.587194 CAGCCTCGCGGGAAGATG 60.587 66.667 8.08 2.32 37.23 2.90
962 973 3.854669 AGCCTCGCGGGAAGATGG 61.855 66.667 8.08 2.17 37.23 3.51
963 974 4.162690 GCCTCGCGGGAAGATGGT 62.163 66.667 8.08 0.00 37.23 3.55
964 975 2.202932 CCTCGCGGGAAGATGGTG 60.203 66.667 8.08 0.00 37.23 4.17
1234 1258 3.387091 CGTCCCATGACCGGTCCA 61.387 66.667 31.19 19.32 38.32 4.02
1261 1285 4.082523 CGCCGGTGGAGATGGTGT 62.083 66.667 7.26 0.00 0.00 4.16
1819 1863 1.493022 ACCAAACACCAACCAGCTCTA 59.507 47.619 0.00 0.00 0.00 2.43
2037 2081 2.291153 CCCAGGATTTGAAGCTTCTCCA 60.291 50.000 26.48 13.51 0.00 3.86
2111 2155 1.091771 CCTTGCAGTATGGCGACTGG 61.092 60.000 17.87 4.86 45.85 4.00
2491 2535 2.717639 AGGAATCGTCAAAGATGGGG 57.282 50.000 0.00 0.00 0.00 4.96
2571 2615 1.596752 CACGGTGTTGGCTGCACTA 60.597 57.895 0.50 0.00 37.07 2.74
3019 3063 0.820871 GTGTGCCTCCAGGAGACTAG 59.179 60.000 19.21 1.79 40.21 2.57
3127 3171 2.301583 GTGGAGGGATCCTTATGCTCTC 59.698 54.545 12.58 7.51 31.76 3.20
3132 3176 1.273886 GGATCCTTATGCTCTCGGACC 59.726 57.143 3.84 0.00 0.00 4.46
3229 3273 4.649674 TGACTCCCGCTTCAAGATAACTAT 59.350 41.667 0.00 0.00 0.00 2.12
3568 3612 0.749649 CTACATGCGCTCTCCTCCTT 59.250 55.000 9.73 0.00 0.00 3.36
3672 3716 0.842905 TTCCATCCCGGGTTTCTCCA 60.843 55.000 22.86 0.00 38.11 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.899502 AGATGAAGAGCGAGAAAGGAAAA 58.100 39.130 0.00 0.00 0.00 2.29
1 2 4.221703 AGAGATGAAGAGCGAGAAAGGAAA 59.778 41.667 0.00 0.00 0.00 3.13
2 3 3.766591 AGAGATGAAGAGCGAGAAAGGAA 59.233 43.478 0.00 0.00 0.00 3.36
3 4 3.360867 AGAGATGAAGAGCGAGAAAGGA 58.639 45.455 0.00 0.00 0.00 3.36
4 5 3.799281 AGAGATGAAGAGCGAGAAAGG 57.201 47.619 0.00 0.00 0.00 3.11
21 22 7.172190 CCTGCCATTTACATGTGATTAGTAGAG 59.828 40.741 9.11 0.00 0.00 2.43
40 41 1.637553 CTCCCTTATATGCCCTGCCAT 59.362 52.381 0.00 0.00 0.00 4.40
43 44 3.508845 TTTCTCCCTTATATGCCCTGC 57.491 47.619 0.00 0.00 0.00 4.85
48 49 9.732130 ATACTTCTCATTTTCTCCCTTATATGC 57.268 33.333 0.00 0.00 0.00 3.14
56 57 7.872113 ACAATCATACTTCTCATTTTCTCCC 57.128 36.000 0.00 0.00 0.00 4.30
90 91 2.027837 GTCCGTTTTGAGCCCCTACTTA 60.028 50.000 0.00 0.00 0.00 2.24
137 138 7.621428 AATCCATCTCACTAAACATTCACAG 57.379 36.000 0.00 0.00 0.00 3.66
144 145 7.168219 ACTTAGCAAATCCATCTCACTAAACA 58.832 34.615 0.00 0.00 0.00 2.83
155 156 3.016736 CAACCCGACTTAGCAAATCCAT 58.983 45.455 0.00 0.00 0.00 3.41
174 175 5.533903 AGAGGTGTTCTTAGAACGTCTACAA 59.466 40.000 18.64 0.00 37.30 2.41
209 210 4.470334 ACAACATGCAAAGTTCCAAAGT 57.530 36.364 5.05 0.00 0.00 2.66
214 215 3.130633 GGGAAACAACATGCAAAGTTCC 58.869 45.455 5.05 5.85 0.00 3.62
218 219 2.865551 GTGTGGGAAACAACATGCAAAG 59.134 45.455 0.00 0.00 41.57 2.77
233 234 1.613437 CAAAGCTTAGTTGGGTGTGGG 59.387 52.381 0.00 0.00 0.00 4.61
243 250 1.975680 TCTTCCCGACCAAAGCTTAGT 59.024 47.619 0.00 0.00 0.00 2.24
252 259 1.892209 GAAGCTTTTCTTCCCGACCA 58.108 50.000 0.00 0.00 44.22 4.02
280 287 1.410083 GCATAAGGCATCTGGTTCCCA 60.410 52.381 0.00 0.00 43.97 4.37
281 288 1.322442 GCATAAGGCATCTGGTTCCC 58.678 55.000 0.00 0.00 43.97 3.97
282 289 1.410083 TGGCATAAGGCATCTGGTTCC 60.410 52.381 0.00 0.00 46.46 3.62
283 290 2.057137 TGGCATAAGGCATCTGGTTC 57.943 50.000 0.00 0.00 46.46 3.62
318 325 4.487019 GAGTCGAAAGAACTCCCTAGTTG 58.513 47.826 0.00 0.00 46.09 3.16
320 327 3.090790 GGAGTCGAAAGAACTCCCTAGT 58.909 50.000 10.56 0.00 45.01 2.57
375 382 3.953612 GTGTCTCTCTCTCCATGTGATCT 59.046 47.826 0.00 0.00 0.00 2.75
382 389 1.077828 TGGGTGTGTCTCTCTCTCCAT 59.922 52.381 0.00 0.00 0.00 3.41
391 398 5.148651 AGTTAACTATGTGGGTGTGTCTC 57.851 43.478 6.26 0.00 0.00 3.36
395 402 9.314321 CTCTTAATAGTTAACTATGTGGGTGTG 57.686 37.037 25.21 11.81 39.02 3.82
418 425 8.830915 TCCTCTCTCAAACTTCATTATACTCT 57.169 34.615 0.00 0.00 0.00 3.24
428 435 3.855858 AGCGAATCCTCTCTCAAACTTC 58.144 45.455 0.00 0.00 0.00 3.01
455 462 3.351740 TGTCAACACATCCACAAACAGT 58.648 40.909 0.00 0.00 0.00 3.55
465 472 5.051106 CCCGAAACAAAATTGTCAACACATC 60.051 40.000 0.00 0.00 41.31 3.06
506 514 6.665695 TGGGAGTACTTGAAAACCTTAAACT 58.334 36.000 0.00 0.00 0.00 2.66
508 516 7.957992 TTTGGGAGTACTTGAAAACCTTAAA 57.042 32.000 0.00 0.00 0.00 1.52
511 519 6.860790 TTTTTGGGAGTACTTGAAAACCTT 57.139 33.333 0.00 0.00 0.00 3.50
531 539 9.675464 TCCGTCCTAATAATGTAAGACATTTTT 57.325 29.630 9.92 10.64 45.80 1.94
532 540 9.326413 CTCCGTCCTAATAATGTAAGACATTTT 57.674 33.333 9.92 7.31 45.80 1.82
533 541 7.931948 CCTCCGTCCTAATAATGTAAGACATTT 59.068 37.037 9.92 0.00 45.80 2.32
535 543 6.781014 TCCTCCGTCCTAATAATGTAAGACAT 59.219 38.462 0.00 0.00 41.31 3.06
536 544 6.131264 TCCTCCGTCCTAATAATGTAAGACA 58.869 40.000 0.00 0.00 0.00 3.41
537 545 6.645790 TCCTCCGTCCTAATAATGTAAGAC 57.354 41.667 0.00 0.00 0.00 3.01
538 546 6.837568 ACTTCCTCCGTCCTAATAATGTAAGA 59.162 38.462 0.00 0.00 0.00 2.10
539 547 7.052142 ACTTCCTCCGTCCTAATAATGTAAG 57.948 40.000 0.00 0.00 0.00 2.34
540 548 7.560991 TGTACTTCCTCCGTCCTAATAATGTAA 59.439 37.037 0.00 0.00 0.00 2.41
541 549 7.062322 TGTACTTCCTCCGTCCTAATAATGTA 58.938 38.462 0.00 0.00 0.00 2.29
542 550 5.895534 TGTACTTCCTCCGTCCTAATAATGT 59.104 40.000 0.00 0.00 0.00 2.71
543 551 6.401047 TGTACTTCCTCCGTCCTAATAATG 57.599 41.667 0.00 0.00 0.00 1.90
544 552 7.011382 AGATGTACTTCCTCCGTCCTAATAAT 58.989 38.462 5.19 0.00 0.00 1.28
545 553 6.264744 CAGATGTACTTCCTCCGTCCTAATAA 59.735 42.308 5.19 0.00 0.00 1.40
546 554 5.768662 CAGATGTACTTCCTCCGTCCTAATA 59.231 44.000 5.19 0.00 0.00 0.98
547 555 4.585162 CAGATGTACTTCCTCCGTCCTAAT 59.415 45.833 5.19 0.00 0.00 1.73
548 556 3.952323 CAGATGTACTTCCTCCGTCCTAA 59.048 47.826 5.19 0.00 0.00 2.69
549 557 3.201487 TCAGATGTACTTCCTCCGTCCTA 59.799 47.826 5.19 0.00 0.00 2.94
550 558 2.025226 TCAGATGTACTTCCTCCGTCCT 60.025 50.000 5.19 0.00 0.00 3.85
551 559 2.099427 GTCAGATGTACTTCCTCCGTCC 59.901 54.545 5.19 0.00 0.00 4.79
552 560 2.753452 TGTCAGATGTACTTCCTCCGTC 59.247 50.000 5.19 0.00 0.00 4.79
553 561 2.492484 GTGTCAGATGTACTTCCTCCGT 59.508 50.000 5.19 0.00 0.00 4.69
554 562 2.492088 TGTGTCAGATGTACTTCCTCCG 59.508 50.000 5.19 0.00 0.00 4.63
555 563 3.258372 TGTGTGTCAGATGTACTTCCTCC 59.742 47.826 5.19 0.00 0.00 4.30
556 564 4.521130 TGTGTGTCAGATGTACTTCCTC 57.479 45.455 5.19 0.00 0.00 3.71
557 565 5.489792 AATGTGTGTCAGATGTACTTCCT 57.510 39.130 5.19 0.00 0.00 3.36
558 566 5.288712 CGTAATGTGTGTCAGATGTACTTCC 59.711 44.000 5.19 0.00 0.00 3.46
623 631 8.169977 TGTTCTTAAGATGAATTTCTTGCAGT 57.830 30.769 5.89 0.00 36.63 4.40
644 652 6.017852 CCCTGTCAAAACTCTTACTTCTGTTC 60.018 42.308 0.00 0.00 0.00 3.18
645 653 5.823045 CCCTGTCAAAACTCTTACTTCTGTT 59.177 40.000 0.00 0.00 0.00 3.16
664 672 2.986728 AGTAACCATGAAGGAACCCTGT 59.013 45.455 0.00 0.00 41.22 4.00
675 683 8.074613 ACTAGTTAAGCACATAGTAACCATGA 57.925 34.615 0.00 0.00 0.00 3.07
718 726 6.548622 ACAAGATGCCAACATTATAGAATGCT 59.451 34.615 9.97 0.00 45.52 3.79
726 734 3.378112 CACCGACAAGATGCCAACATTAT 59.622 43.478 0.00 0.00 36.35 1.28
771 779 5.183331 CAGGACTTAGTGCTGTCTAGTAACA 59.817 44.000 22.90 0.00 44.86 2.41
815 826 3.848272 ATGATAACAAAACACCTGGCG 57.152 42.857 0.00 0.00 0.00 5.69
868 879 1.669795 CGGCCTCCAAACAGCATTTTC 60.670 52.381 0.00 0.00 0.00 2.29
869 880 0.318120 CGGCCTCCAAACAGCATTTT 59.682 50.000 0.00 0.00 0.00 1.82
870 881 0.539438 TCGGCCTCCAAACAGCATTT 60.539 50.000 0.00 0.00 0.00 2.32
871 882 0.323725 ATCGGCCTCCAAACAGCATT 60.324 50.000 0.00 0.00 0.00 3.56
872 883 0.749454 GATCGGCCTCCAAACAGCAT 60.749 55.000 0.00 0.00 0.00 3.79
873 884 1.377202 GATCGGCCTCCAAACAGCA 60.377 57.895 0.00 0.00 0.00 4.41
874 885 2.464459 CGATCGGCCTCCAAACAGC 61.464 63.158 7.38 0.00 0.00 4.40
875 886 0.807667 CTCGATCGGCCTCCAAACAG 60.808 60.000 16.41 0.00 0.00 3.16
876 887 1.218047 CTCGATCGGCCTCCAAACA 59.782 57.895 16.41 0.00 0.00 2.83
877 888 2.174319 GCTCGATCGGCCTCCAAAC 61.174 63.158 16.41 0.00 0.00 2.93
878 889 2.186903 GCTCGATCGGCCTCCAAA 59.813 61.111 16.41 0.00 0.00 3.28
879 890 2.759973 AGCTCGATCGGCCTCCAA 60.760 61.111 16.41 0.00 0.00 3.53
880 891 3.219928 GAGCTCGATCGGCCTCCA 61.220 66.667 16.41 0.00 0.00 3.86
881 892 3.984749 GGAGCTCGATCGGCCTCC 61.985 72.222 27.29 27.29 0.00 4.30
882 893 2.569354 ATGGAGCTCGATCGGCCTC 61.569 63.158 16.41 18.99 0.00 4.70
883 894 2.522923 ATGGAGCTCGATCGGCCT 60.523 61.111 16.41 11.59 0.00 5.19
884 895 2.356793 CATGGAGCTCGATCGGCC 60.357 66.667 16.41 12.12 0.00 6.13
885 896 3.040763 GCATGGAGCTCGATCGGC 61.041 66.667 16.41 17.03 41.15 5.54
886 897 1.664017 CTGCATGGAGCTCGATCGG 60.664 63.158 16.41 7.26 45.94 4.18
887 898 0.529337 AACTGCATGGAGCTCGATCG 60.529 55.000 14.95 9.36 45.94 3.69
888 899 1.216122 GAACTGCATGGAGCTCGATC 58.784 55.000 14.95 4.95 45.94 3.69
889 900 0.529337 CGAACTGCATGGAGCTCGAT 60.529 55.000 29.23 6.51 45.94 3.59
890 901 1.153765 CGAACTGCATGGAGCTCGA 60.154 57.895 29.23 3.70 45.94 4.04
891 902 1.016130 AACGAACTGCATGGAGCTCG 61.016 55.000 30.56 30.56 45.94 5.03
892 903 1.661112 GTAACGAACTGCATGGAGCTC 59.339 52.381 14.95 10.95 45.94 4.09
893 904 1.676014 GGTAACGAACTGCATGGAGCT 60.676 52.381 14.95 0.88 45.94 4.09
894 905 0.727398 GGTAACGAACTGCATGGAGC 59.273 55.000 14.95 0.00 45.96 4.70
895 906 2.386661 AGGTAACGAACTGCATGGAG 57.613 50.000 13.34 13.34 46.39 3.86
896 907 2.422597 CAAGGTAACGAACTGCATGGA 58.577 47.619 0.00 0.00 46.39 3.41
897 908 1.468520 CCAAGGTAACGAACTGCATGG 59.531 52.381 0.00 0.00 46.39 3.66
898 909 2.095768 CACCAAGGTAACGAACTGCATG 60.096 50.000 0.00 0.00 46.39 4.06
899 910 2.151202 CACCAAGGTAACGAACTGCAT 58.849 47.619 0.00 0.00 46.39 3.96
900 911 1.588674 CACCAAGGTAACGAACTGCA 58.411 50.000 0.00 0.00 46.39 4.41
901 912 0.872388 CCACCAAGGTAACGAACTGC 59.128 55.000 0.00 0.00 46.39 4.40
912 923 0.393077 ACGAGAACTGACCACCAAGG 59.607 55.000 0.00 0.00 45.67 3.61
913 924 3.512680 GATACGAGAACTGACCACCAAG 58.487 50.000 0.00 0.00 0.00 3.61
914 925 2.232941 GGATACGAGAACTGACCACCAA 59.767 50.000 0.00 0.00 0.00 3.67
915 926 1.822990 GGATACGAGAACTGACCACCA 59.177 52.381 0.00 0.00 0.00 4.17
916 927 1.822990 TGGATACGAGAACTGACCACC 59.177 52.381 0.00 0.00 42.51 4.61
917 928 3.130516 TGATGGATACGAGAACTGACCAC 59.869 47.826 0.00 0.00 42.51 4.16
918 929 3.361786 TGATGGATACGAGAACTGACCA 58.638 45.455 0.00 0.00 42.51 4.02
919 930 3.797184 GCTGATGGATACGAGAACTGACC 60.797 52.174 0.00 0.00 42.51 4.02
920 931 3.067461 AGCTGATGGATACGAGAACTGAC 59.933 47.826 0.00 0.00 42.51 3.51
921 932 3.067320 CAGCTGATGGATACGAGAACTGA 59.933 47.826 8.42 0.00 42.51 3.41
922 933 3.379240 CAGCTGATGGATACGAGAACTG 58.621 50.000 8.42 0.00 42.51 3.16
923 934 2.223923 GCAGCTGATGGATACGAGAACT 60.224 50.000 20.43 0.00 42.51 3.01
924 935 2.131183 GCAGCTGATGGATACGAGAAC 58.869 52.381 20.43 0.00 42.51 3.01
925 936 1.756538 TGCAGCTGATGGATACGAGAA 59.243 47.619 20.43 0.00 42.51 2.87
926 937 1.339291 CTGCAGCTGATGGATACGAGA 59.661 52.381 20.43 0.00 42.51 4.04
927 938 1.780806 CTGCAGCTGATGGATACGAG 58.219 55.000 20.43 0.00 42.51 4.18
928 939 0.249615 GCTGCAGCTGATGGATACGA 60.250 55.000 31.33 0.00 37.50 3.43
929 940 1.226686 GGCTGCAGCTGATGGATACG 61.227 60.000 35.82 0.00 41.70 3.06
930 941 0.108207 AGGCTGCAGCTGATGGATAC 59.892 55.000 35.82 17.24 41.70 2.24
931 942 0.395686 GAGGCTGCAGCTGATGGATA 59.604 55.000 35.82 0.00 41.70 2.59
932 943 1.148723 GAGGCTGCAGCTGATGGAT 59.851 57.895 35.82 14.53 41.70 3.41
933 944 2.588439 GAGGCTGCAGCTGATGGA 59.412 61.111 35.82 0.00 41.70 3.41
934 945 2.895865 CGAGGCTGCAGCTGATGG 60.896 66.667 35.82 19.97 41.70 3.51
935 946 3.574445 GCGAGGCTGCAGCTGATG 61.574 66.667 35.82 23.57 41.70 3.07
948 959 2.202932 CCACCATCTTCCCGCGAG 60.203 66.667 8.23 0.00 0.00 5.03
949 960 2.287274 TTCCACCATCTTCCCGCGA 61.287 57.895 8.23 0.00 0.00 5.87
950 961 2.106683 GTTCCACCATCTTCCCGCG 61.107 63.158 0.00 0.00 0.00 6.46
951 962 1.026718 CAGTTCCACCATCTTCCCGC 61.027 60.000 0.00 0.00 0.00 6.13
952 963 0.324943 ACAGTTCCACCATCTTCCCG 59.675 55.000 0.00 0.00 0.00 5.14
953 964 2.162681 CAACAGTTCCACCATCTTCCC 58.837 52.381 0.00 0.00 0.00 3.97
954 965 2.863809 ACAACAGTTCCACCATCTTCC 58.136 47.619 0.00 0.00 0.00 3.46
955 966 5.063880 AGTTACAACAGTTCCACCATCTTC 58.936 41.667 0.00 0.00 0.00 2.87
956 967 5.048846 AGTTACAACAGTTCCACCATCTT 57.951 39.130 0.00 0.00 0.00 2.40
957 968 4.706842 AGTTACAACAGTTCCACCATCT 57.293 40.909 0.00 0.00 0.00 2.90
958 969 5.507315 CCAAAGTTACAACAGTTCCACCATC 60.507 44.000 0.00 0.00 0.00 3.51
959 970 4.340950 CCAAAGTTACAACAGTTCCACCAT 59.659 41.667 0.00 0.00 0.00 3.55
960 971 3.697045 CCAAAGTTACAACAGTTCCACCA 59.303 43.478 0.00 0.00 0.00 4.17
961 972 3.949113 TCCAAAGTTACAACAGTTCCACC 59.051 43.478 0.00 0.00 0.00 4.61
962 973 4.396790 TGTCCAAAGTTACAACAGTTCCAC 59.603 41.667 0.00 0.00 0.00 4.02
963 974 4.590918 TGTCCAAAGTTACAACAGTTCCA 58.409 39.130 0.00 0.00 0.00 3.53
964 975 5.767816 ATGTCCAAAGTTACAACAGTTCC 57.232 39.130 0.00 0.00 0.00 3.62
1819 1863 1.301716 AAACTGTCGCCGCATGACT 60.302 52.632 0.00 0.00 37.26 3.41
2037 2081 3.386237 GGGGCAGAGCTCGTCACT 61.386 66.667 8.37 0.00 0.00 3.41
2111 2155 4.259356 GGTAGTAGGGGAACAAACATCAC 58.741 47.826 0.00 0.00 0.00 3.06
2491 2535 1.623973 GCCGCCGCCGTTATATCTTC 61.624 60.000 0.00 0.00 0.00 2.87
2571 2615 1.004440 GAGCTTGAAGAGGGCACGT 60.004 57.895 0.00 0.00 0.00 4.49
2610 2654 3.065233 GTGCAATTATGGCATCTTCGACA 59.935 43.478 1.65 0.00 44.11 4.35
2892 2936 7.805071 CAGAAAGTTGATGGATTGTTCTAACAC 59.195 37.037 0.00 0.00 38.92 3.32
3019 3063 6.292596 GGTGAAGCGATCAATATCTTCAAGTC 60.293 42.308 5.26 0.00 44.19 3.01
3067 3111 3.512724 CCTCTGGGCAAAATGTTTCAGAT 59.487 43.478 0.00 0.00 31.93 2.90
3127 3171 3.452755 TGCTGACATAACTATGGTCCG 57.547 47.619 1.98 0.00 38.00 4.79
3132 3176 6.709397 ACATTGGAGATGCTGACATAACTATG 59.291 38.462 0.00 0.00 36.35 2.23
3206 3250 2.832129 AGTTATCTTGAAGCGGGAGTCA 59.168 45.455 0.00 0.00 0.00 3.41
3229 3273 2.138179 GCGGTAGGCCCATAGACCA 61.138 63.158 0.00 0.00 34.80 4.02
3568 3612 2.587247 GGGCAGTGGTCAGAGAGCA 61.587 63.158 0.00 0.00 37.74 4.26


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

AutoCloner maintained by Alex Coulton.