Multiple sequence alignment - TraesCS7D01G419900

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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 TraesCS7D01G419900 chr7D 100.000 3078 0 0 1 3078 539135556 539132479 0.000000e+00 5685.0
1 TraesCS7D01G419900 chr7D 80.550 545 76 25 1038 1576 538662115 538662635 2.880000e-105 392.0
2 TraesCS7D01G419900 chr7D 82.380 437 49 18 1144 1576 538333156 538332744 3.770000e-94 355.0
3 TraesCS7D01G419900 chr7D 91.071 224 19 1 1353 1576 538595122 538595344 4.990000e-78 302.0
4 TraesCS7D01G419900 chr7D 78.333 420 64 22 1665 2066 538140184 538139774 2.370000e-61 246.0
5 TraesCS7D01G419900 chr7D 77.990 418 69 21 1665 2066 538595415 538595825 1.100000e-59 241.0
6 TraesCS7D01G419900 chr7D 78.043 419 67 22 1665 2066 538603311 538603721 1.100000e-59 241.0
7 TraesCS7D01G419900 chr7D 77.273 418 72 20 1665 2066 538662733 538663143 1.110000e-54 224.0
8 TraesCS7D01G419900 chr7D 77.103 428 64 28 1665 2066 538332640 538332221 1.860000e-52 217.0
9 TraesCS7D01G419900 chr7D 82.243 214 35 3 1053 1264 538818777 538818565 6.780000e-42 182.0
10 TraesCS7D01G419900 chr7A 87.961 2874 137 74 104 2877 620751328 620748564 0.000000e+00 3197.0
11 TraesCS7D01G419900 chr7A 77.264 1038 156 61 1058 2066 619576607 619575621 1.260000e-148 536.0
12 TraesCS7D01G419900 chr7A 77.763 751 116 40 1353 2066 620171919 620172655 6.140000e-112 414.0
13 TraesCS7D01G419900 chr7A 81.025 527 65 25 1058 1576 619633979 619633480 1.340000e-103 387.0
14 TraesCS7D01G419900 chr7A 80.989 526 67 24 1058 1576 619907219 619907718 1.340000e-103 387.0
15 TraesCS7D01G419900 chr7A 80.492 528 69 26 1058 1576 620171639 620172141 1.040000e-99 374.0
16 TraesCS7D01G419900 chr7A 92.308 221 16 1 1354 1574 619166638 619166419 2.300000e-81 313.0
17 TraesCS7D01G419900 chr7A 77.831 415 75 13 1665 2066 619907772 619908182 1.100000e-59 241.0
18 TraesCS7D01G419900 chr7A 77.804 419 68 20 1665 2066 619166335 619165925 5.130000e-58 235.0
19 TraesCS7D01G419900 chr7A 76.123 423 77 17 1665 2066 619633426 619633007 1.870000e-47 200.0
20 TraesCS7D01G419900 chr7A 82.569 218 35 3 1053 1268 620371185 620370969 4.050000e-44 189.0
21 TraesCS7D01G419900 chr7A 82.243 214 35 3 1053 1264 620487135 620487347 6.780000e-42 182.0
22 TraesCS7D01G419900 chr7A 94.937 79 4 0 2892 2970 620748577 620748499 1.160000e-24 124.0
23 TraesCS7D01G419900 chr7A 92.405 79 6 0 3000 3078 620748233 620748155 2.510000e-21 113.0
24 TraesCS7D01G419900 chr7B 91.922 1795 85 30 926 2686 581894491 581892723 0.000000e+00 2457.0
25 TraesCS7D01G419900 chr7B 83.541 881 64 33 2 854 581895332 581894505 0.000000e+00 749.0
26 TraesCS7D01G419900 chr7B 76.789 1034 174 53 1058 2066 580885611 580884619 1.260000e-143 520.0
27 TraesCS7D01G419900 chr7B 92.202 218 17 0 1359 1576 580969969 580969752 2.980000e-80 309.0
28 TraesCS7D01G419900 chr7B 92.202 218 17 0 1359 1576 581333772 581333989 2.980000e-80 309.0
29 TraesCS7D01G419900 chr7B 76.526 426 70 23 1665 2066 580969663 580969244 4.020000e-49 206.0
30 TraesCS7D01G419900 chr7B 85.882 85 11 1 2793 2877 581890860 581890777 4.230000e-14 89.8


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 TraesCS7D01G419900 chr7D 539132479 539135556 3077 True 5685.000000 5685 100.000000 1 3078 1 chr7D.!!$R3 3077
1 TraesCS7D01G419900 chr7D 538662115 538663143 1028 False 308.000000 392 78.911500 1038 2066 2 chr7D.!!$F3 1028
2 TraesCS7D01G419900 chr7D 538332221 538333156 935 True 286.000000 355 79.741500 1144 2066 2 chr7D.!!$R4 922
3 TraesCS7D01G419900 chr7D 538595122 538595825 703 False 271.500000 302 84.530500 1353 2066 2 chr7D.!!$F2 713
4 TraesCS7D01G419900 chr7A 620748155 620751328 3173 True 1144.666667 3197 91.767667 104 3078 3 chr7A.!!$R5 2974
5 TraesCS7D01G419900 chr7A 619575621 619576607 986 True 536.000000 536 77.264000 1058 2066 1 chr7A.!!$R1 1008
6 TraesCS7D01G419900 chr7A 620171639 620172655 1016 False 394.000000 414 79.127500 1058 2066 2 chr7A.!!$F3 1008
7 TraesCS7D01G419900 chr7A 619907219 619908182 963 False 314.000000 387 79.410000 1058 2066 2 chr7A.!!$F2 1008
8 TraesCS7D01G419900 chr7A 619633007 619633979 972 True 293.500000 387 78.574000 1058 2066 2 chr7A.!!$R4 1008
9 TraesCS7D01G419900 chr7A 619165925 619166638 713 True 274.000000 313 85.056000 1354 2066 2 chr7A.!!$R3 712
10 TraesCS7D01G419900 chr7B 581890777 581895332 4555 True 1098.600000 2457 87.115000 2 2877 3 chr7B.!!$R3 2875
11 TraesCS7D01G419900 chr7B 580884619 580885611 992 True 520.000000 520 76.789000 1058 2066 1 chr7B.!!$R1 1008
12 TraesCS7D01G419900 chr7B 580969244 580969969 725 True 257.500000 309 84.364000 1359 2066 2 chr7B.!!$R2 707

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
905 1004 0.110104 CCAATCCATCCAGCTCCTCC 59.89 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
2107 2331 0.096976 GATGACGGGTTCATGCGTTG 59.903 55.0 0.0 0.0 45.67 4.1 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
45 55 2.942376 ACACAATGCACCGTATGTATGG 59.058 45.455 0.00 0.00 33.32 2.74
62 72 0.250553 TGGCCGTAAGAAACCCACTG 60.251 55.000 0.00 0.00 43.02 3.66
77 87 1.408127 CCACTGACCACTCAACCACAA 60.408 52.381 0.00 0.00 0.00 3.33
81 91 3.181465 ACTGACCACTCAACCACAAGTAG 60.181 47.826 0.00 0.00 0.00 2.57
82 92 2.104111 TGACCACTCAACCACAAGTAGG 59.896 50.000 0.00 0.00 0.00 3.18
83 93 2.367567 GACCACTCAACCACAAGTAGGA 59.632 50.000 0.00 0.00 0.00 2.94
84 94 2.368875 ACCACTCAACCACAAGTAGGAG 59.631 50.000 0.00 0.00 36.54 3.69
85 95 2.368875 CCACTCAACCACAAGTAGGAGT 59.631 50.000 0.00 0.00 41.46 3.85
86 96 3.576982 CCACTCAACCACAAGTAGGAGTA 59.423 47.826 0.00 0.00 39.79 2.59
87 97 4.557205 CACTCAACCACAAGTAGGAGTAC 58.443 47.826 0.00 0.00 39.79 2.73
88 98 4.281182 CACTCAACCACAAGTAGGAGTACT 59.719 45.833 0.00 0.00 39.79 2.73
89 99 5.475909 CACTCAACCACAAGTAGGAGTACTA 59.524 44.000 0.00 0.00 39.79 1.82
101 111 4.089408 AGGAGTACTACTGCTACCTAGC 57.911 50.000 6.88 0.00 45.38 3.42
102 112 3.717913 AGGAGTACTACTGCTACCTAGCT 59.282 47.826 6.88 0.00 45.38 3.32
120 130 5.360714 CCTAGCTAAAATTCAGCCCAATGAA 59.639 40.000 8.07 0.00 43.04 2.57
259 302 3.243053 TTCGGCGAGGGGGAAACA 61.243 61.111 10.46 0.00 0.00 2.83
489 554 4.146156 TCCGCCCATCTACCCCGA 62.146 66.667 0.00 0.00 0.00 5.14
490 555 3.925090 CCGCCCATCTACCCCGAC 61.925 72.222 0.00 0.00 0.00 4.79
491 556 3.925090 CGCCCATCTACCCCGACC 61.925 72.222 0.00 0.00 0.00 4.79
492 557 3.557290 GCCCATCTACCCCGACCC 61.557 72.222 0.00 0.00 0.00 4.46
493 558 2.847715 CCCATCTACCCCGACCCC 60.848 72.222 0.00 0.00 0.00 4.95
494 559 3.231736 CCATCTACCCCGACCCCG 61.232 72.222 0.00 0.00 0.00 5.73
758 848 2.676471 ACTTGCCCGTTGGATGCC 60.676 61.111 0.00 0.00 0.00 4.40
759 849 2.676121 CTTGCCCGTTGGATGCCA 60.676 61.111 0.00 0.00 0.00 4.92
760 850 2.988684 TTGCCCGTTGGATGCCAC 60.989 61.111 0.00 0.00 30.78 5.01
761 851 3.505790 TTGCCCGTTGGATGCCACT 62.506 57.895 0.00 0.00 30.78 4.00
810 900 1.575447 ATCCAAACCAGCCTCCCTCC 61.575 60.000 0.00 0.00 0.00 4.30
835 934 2.158784 GGCCGTATAAATACCACCACCA 60.159 50.000 0.00 0.00 0.00 4.17
859 958 1.064832 TGCCCGATCAATCCATCAACA 60.065 47.619 0.00 0.00 0.00 3.33
861 960 2.426738 GCCCGATCAATCCATCAACAAA 59.573 45.455 0.00 0.00 0.00 2.83
866 965 4.858692 CGATCAATCCATCAACAAACCAAC 59.141 41.667 0.00 0.00 0.00 3.77
867 966 4.599047 TCAATCCATCAACAAACCAACC 57.401 40.909 0.00 0.00 0.00 3.77
868 967 3.323403 TCAATCCATCAACAAACCAACCC 59.677 43.478 0.00 0.00 0.00 4.11
869 968 2.461300 TCCATCAACAAACCAACCCA 57.539 45.000 0.00 0.00 0.00 4.51
871 970 2.432510 TCCATCAACAAACCAACCCAAC 59.567 45.455 0.00 0.00 0.00 3.77
873 972 1.938585 TCAACAAACCAACCCAACCA 58.061 45.000 0.00 0.00 0.00 3.67
874 973 1.827969 TCAACAAACCAACCCAACCAG 59.172 47.619 0.00 0.00 0.00 4.00
875 974 0.539518 AACAAACCAACCCAACCAGC 59.460 50.000 0.00 0.00 0.00 4.85
876 975 0.616111 ACAAACCAACCCAACCAGCA 60.616 50.000 0.00 0.00 0.00 4.41
877 976 0.539051 CAAACCAACCCAACCAGCAA 59.461 50.000 0.00 0.00 0.00 3.91
878 977 1.140652 CAAACCAACCCAACCAGCAAT 59.859 47.619 0.00 0.00 0.00 3.56
884 983 0.611896 ACCCAACCAGCAATAGCCAC 60.612 55.000 0.00 0.00 43.56 5.01
885 984 1.322538 CCCAACCAGCAATAGCCACC 61.323 60.000 0.00 0.00 43.56 4.61
896 995 0.779997 ATAGCCACCCCAATCCATCC 59.220 55.000 0.00 0.00 0.00 3.51
897 996 0.625980 TAGCCACCCCAATCCATCCA 60.626 55.000 0.00 0.00 0.00 3.41
898 997 1.456331 GCCACCCCAATCCATCCAG 60.456 63.158 0.00 0.00 0.00 3.86
900 999 1.616921 CACCCCAATCCATCCAGCT 59.383 57.895 0.00 0.00 0.00 4.24
901 1000 0.466922 CACCCCAATCCATCCAGCTC 60.467 60.000 0.00 0.00 0.00 4.09
902 1001 1.152368 CCCCAATCCATCCAGCTCC 59.848 63.158 0.00 0.00 0.00 4.70
903 1002 1.358830 CCCCAATCCATCCAGCTCCT 61.359 60.000 0.00 0.00 0.00 3.69
905 1004 0.110104 CCAATCCATCCAGCTCCTCC 59.890 60.000 0.00 0.00 0.00 4.30
906 1005 0.841961 CAATCCATCCAGCTCCTCCA 59.158 55.000 0.00 0.00 0.00 3.86
907 1006 1.213678 CAATCCATCCAGCTCCTCCAA 59.786 52.381 0.00 0.00 0.00 3.53
908 1007 1.138568 ATCCATCCAGCTCCTCCAAG 58.861 55.000 0.00 0.00 0.00 3.61
909 1008 1.153005 CCATCCAGCTCCTCCAAGC 60.153 63.158 0.00 0.00 42.82 4.01
915 1014 4.613929 GCTCCTCCAAGCTCAGTG 57.386 61.111 0.00 0.00 39.27 3.66
916 1015 1.676384 GCTCCTCCAAGCTCAGTGT 59.324 57.895 0.00 0.00 39.27 3.55
917 1016 0.390998 GCTCCTCCAAGCTCAGTGTC 60.391 60.000 0.00 0.00 39.27 3.67
918 1017 0.248843 CTCCTCCAAGCTCAGTGTCC 59.751 60.000 0.00 0.00 0.00 4.02
919 1018 1.079543 CCTCCAAGCTCAGTGTCCG 60.080 63.158 0.00 0.00 0.00 4.79
958 1057 1.967066 ACACTTCACTCAGTAGCAGCT 59.033 47.619 0.00 0.00 0.00 4.24
959 1058 3.057245 CACACTTCACTCAGTAGCAGCTA 60.057 47.826 0.00 0.00 0.00 3.32
962 1062 1.095600 TCACTCAGTAGCAGCTACCG 58.904 55.000 26.20 18.03 37.65 4.02
985 1085 5.560375 CGGTAGCGAGAAAGAAAGATCGATA 60.560 44.000 9.07 0.00 37.35 2.92
987 1087 5.508200 AGCGAGAAAGAAAGATCGATAGT 57.492 39.130 0.00 0.00 37.35 2.12
991 1091 5.250235 AGAAAGAAAGATCGATAGTGCGA 57.750 39.130 0.00 0.00 45.22 5.10
992 1092 5.038033 AGAAAGAAAGATCGATAGTGCGAC 58.962 41.667 0.00 0.00 43.79 5.19
1015 1115 4.470170 CGATGACGACGGTGGCGA 62.470 66.667 0.00 0.00 42.66 5.54
1017 1117 1.357690 GATGACGACGGTGGCGATA 59.642 57.895 0.00 0.00 0.00 2.92
1280 1384 4.111375 ACGTAAGCATCTTCAGTAGTGG 57.889 45.455 0.00 0.00 45.62 4.00
1281 1385 2.860735 CGTAAGCATCTTCAGTAGTGGC 59.139 50.000 0.00 0.00 0.00 5.01
1282 1386 3.676049 CGTAAGCATCTTCAGTAGTGGCA 60.676 47.826 0.00 0.00 0.00 4.92
1369 1498 3.002862 GGTTCTTTGTGTGTGTGCGAATA 59.997 43.478 0.00 0.00 0.00 1.75
1473 1605 1.348938 CACCAACGTGTTCGCGAAA 59.651 52.632 25.24 11.28 41.18 3.46
1629 1790 0.597118 TGCGCATGTTGTTTTGAGCC 60.597 50.000 5.66 0.00 37.79 4.70
2105 2329 0.394938 TCCCGCAGCTTACAAGAACA 59.605 50.000 0.00 0.00 0.00 3.18
2106 2330 1.202710 TCCCGCAGCTTACAAGAACAA 60.203 47.619 0.00 0.00 0.00 2.83
2107 2331 1.069227 CCCGCAGCTTACAAGAACAAC 60.069 52.381 0.00 0.00 0.00 3.32
2124 2352 0.816018 AACAACGCATGAACCCGTCA 60.816 50.000 0.00 0.00 41.67 4.35
2139 2367 3.244561 ACCCGTCATCTGAGATGTGTTTT 60.245 43.478 20.82 3.07 0.00 2.43
2168 2396 3.990546 TCGATCCGTGAGAACGAAG 57.009 52.632 0.00 0.00 45.51 3.79
2272 2509 2.278989 CGTTGTCACACGGGTCGT 60.279 61.111 0.00 0.00 42.36 4.34
2329 2566 5.838521 AGTTCCTTTTAGCCTTGAAAATCCA 59.161 36.000 0.00 0.00 0.00 3.41
2333 2570 5.371115 TTTTAGCCTTGAAAATCCAGACG 57.629 39.130 0.00 0.00 0.00 4.18
2402 2642 1.552792 GGCACAGAGCTAGAAGAAGGT 59.447 52.381 0.00 0.00 44.79 3.50
2426 2666 0.482446 AAAGTGGGCTTGGACATGGA 59.518 50.000 0.00 0.00 34.71 3.41
2472 2712 3.528078 GGAAGGGAAGGGGAAGTTTATCT 59.472 47.826 0.00 0.00 0.00 1.98
2567 2808 1.768275 AGGGCCGACATTCATGTATCA 59.232 47.619 0.00 0.00 41.95 2.15
2623 2864 2.095059 TCCAGCGGTAACTAAACTCGTC 60.095 50.000 0.00 0.00 0.00 4.20
2690 4724 1.507141 GCAATACGCCGCCAGCTAAT 61.507 55.000 0.00 0.00 40.39 1.73
2698 4732 0.683973 CCGCCAGCTAATCCTGAGAT 59.316 55.000 0.00 0.00 34.77 2.75
2705 4739 1.609320 GCTAATCCTGAGATTCGGGCC 60.609 57.143 0.00 0.00 42.73 5.80
2767 4804 3.041701 CAAACCGTGCAGTGCCAT 58.958 55.556 13.72 0.00 0.00 4.40
2768 4805 2.252556 CAAACCGTGCAGTGCCATA 58.747 52.632 13.72 0.00 0.00 2.74
2770 4807 0.960364 AAACCGTGCAGTGCCATAGG 60.960 55.000 13.72 12.63 0.00 2.57
2771 4808 2.514592 CCGTGCAGTGCCATAGGG 60.515 66.667 13.72 5.43 37.18 3.53
2772 4809 2.514592 CGTGCAGTGCCATAGGGG 60.515 66.667 13.72 0.00 40.85 4.79
2773 4810 2.998097 GTGCAGTGCCATAGGGGA 59.002 61.111 13.72 0.00 40.01 4.81
2937 4974 8.506168 TCACAACATGATCTTTTTATACCTCC 57.494 34.615 0.00 0.00 29.99 4.30
2961 4998 6.809689 CCGTAGTCAGTACACAAATGTAATCA 59.190 38.462 0.00 0.00 42.99 2.57
2966 5003 8.939929 AGTCAGTACACAAATGTAATCATCTTG 58.060 33.333 0.00 0.00 42.99 3.02
2970 5007 9.394767 AGTACACAAATGTAATCATCTTGCATA 57.605 29.630 0.00 0.00 42.99 3.14
2971 5008 9.655769 GTACACAAATGTAATCATCTTGCATAG 57.344 33.333 0.00 0.00 42.99 2.23
2972 5009 8.284945 ACACAAATGTAATCATCTTGCATAGT 57.715 30.769 0.00 0.00 37.26 2.12
2973 5010 8.186163 ACACAAATGTAATCATCTTGCATAGTG 58.814 33.333 14.14 14.14 37.26 2.74
2974 5011 8.186163 CACAAATGTAATCATCTTGCATAGTGT 58.814 33.333 0.00 6.49 32.10 3.55
2975 5012 9.394767 ACAAATGTAATCATCTTGCATAGTGTA 57.605 29.630 0.00 0.00 32.56 2.90
2979 5016 9.881649 ATGTAATCATCTTGCATAGTGTATAGG 57.118 33.333 0.00 0.00 0.00 2.57
2980 5017 8.314021 TGTAATCATCTTGCATAGTGTATAGGG 58.686 37.037 0.00 0.00 0.00 3.53
2981 5018 5.745312 TCATCTTGCATAGTGTATAGGGG 57.255 43.478 0.00 0.00 0.00 4.79
2982 5019 4.532126 TCATCTTGCATAGTGTATAGGGGG 59.468 45.833 0.00 0.00 0.00 5.40
2983 5020 4.207698 TCTTGCATAGTGTATAGGGGGA 57.792 45.455 0.00 0.00 0.00 4.81
2984 5021 4.160329 TCTTGCATAGTGTATAGGGGGAG 58.840 47.826 0.00 0.00 0.00 4.30
2985 5022 3.630625 TGCATAGTGTATAGGGGGAGT 57.369 47.619 0.00 0.00 0.00 3.85
2986 5023 3.507411 TGCATAGTGTATAGGGGGAGTC 58.493 50.000 0.00 0.00 0.00 3.36
2987 5024 2.832733 GCATAGTGTATAGGGGGAGTCC 59.167 54.545 0.00 0.00 0.00 3.85
2988 5025 3.757461 GCATAGTGTATAGGGGGAGTCCA 60.757 52.174 12.30 0.00 37.22 4.02
2989 5026 4.689062 CATAGTGTATAGGGGGAGTCCAT 58.311 47.826 12.30 0.00 37.22 3.41
2990 5027 2.977808 AGTGTATAGGGGGAGTCCATG 58.022 52.381 12.30 0.00 37.22 3.66
2991 5028 1.978580 GTGTATAGGGGGAGTCCATGG 59.021 57.143 12.30 4.97 37.22 3.66
2992 5029 0.984995 GTATAGGGGGAGTCCATGGC 59.015 60.000 12.30 2.00 37.22 4.40
2993 5030 0.874594 TATAGGGGGAGTCCATGGCT 59.125 55.000 12.30 7.71 37.22 4.75
2994 5031 0.474660 ATAGGGGGAGTCCATGGCTC 60.475 60.000 21.31 21.31 37.22 4.70
2998 5035 2.914289 GGAGTCCATGGCTCCCTG 59.086 66.667 30.32 0.92 45.05 4.45
3013 5286 1.227764 CCTGCCATCTGATCCACCG 60.228 63.158 0.00 0.00 0.00 4.94
3018 5291 0.179073 CCATCTGATCCACCGTCACC 60.179 60.000 0.00 0.00 0.00 4.02
3036 5309 0.101759 CCGACGATATTCACCACCGT 59.898 55.000 0.00 0.00 36.08 4.83
3037 5310 1.474017 CGACGATATTCACCACCGTC 58.526 55.000 0.00 0.00 44.06 4.79
3042 5315 2.319890 ATATTCACCACCGTCGGGGC 62.320 60.000 17.28 0.00 40.62 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.616774 TCTGTTTTTGAATTTGAAATGGCC 57.383 33.333 0.00 0.00 0.00 5.36
45 55 1.154197 GTCAGTGGGTTTCTTACGGC 58.846 55.000 0.00 0.00 0.00 5.68
62 72 2.367567 TCCTACTTGTGGTTGAGTGGTC 59.632 50.000 0.00 0.00 0.00 4.02
93 103 5.036117 TGGGCTGAATTTTAGCTAGGTAG 57.964 43.478 12.30 0.00 40.92 3.18
94 104 5.444744 TTGGGCTGAATTTTAGCTAGGTA 57.555 39.130 12.30 0.00 40.92 3.08
95 105 4.316025 TTGGGCTGAATTTTAGCTAGGT 57.684 40.909 12.30 0.00 40.92 3.08
96 106 4.889409 TCATTGGGCTGAATTTTAGCTAGG 59.111 41.667 12.30 2.20 40.92 3.02
97 107 6.455360 TTCATTGGGCTGAATTTTAGCTAG 57.545 37.500 12.30 0.00 40.92 3.42
98 108 6.350949 GGTTTCATTGGGCTGAATTTTAGCTA 60.351 38.462 12.30 0.00 40.92 3.32
99 109 5.482006 GTTTCATTGGGCTGAATTTTAGCT 58.518 37.500 12.30 0.00 40.92 3.32
100 110 4.631377 GGTTTCATTGGGCTGAATTTTAGC 59.369 41.667 4.66 4.66 40.41 3.09
101 111 6.041423 AGGTTTCATTGGGCTGAATTTTAG 57.959 37.500 0.00 0.00 35.20 1.85
102 112 5.541868 TGAGGTTTCATTGGGCTGAATTTTA 59.458 36.000 0.00 0.00 35.20 1.52
120 130 1.754380 TACGTGCAGCTGGTGAGGTT 61.754 55.000 17.12 0.00 0.00 3.50
227 270 4.468689 GAAGGAAGGGACGCCGGG 62.469 72.222 2.18 0.00 33.06 5.73
306 359 1.227674 GGGTGCGTGATCTGATCCC 60.228 63.158 14.71 8.05 0.00 3.85
547 612 4.386088 CCCAATATCCCATCTCATCCCATC 60.386 50.000 0.00 0.00 0.00 3.51
548 613 3.530564 CCCAATATCCCATCTCATCCCAT 59.469 47.826 0.00 0.00 0.00 4.00
549 614 2.921612 CCCAATATCCCATCTCATCCCA 59.078 50.000 0.00 0.00 0.00 4.37
550 615 3.192944 TCCCAATATCCCATCTCATCCC 58.807 50.000 0.00 0.00 0.00 3.85
551 616 4.386088 CCATCCCAATATCCCATCTCATCC 60.386 50.000 0.00 0.00 0.00 3.51
552 617 4.476113 TCCATCCCAATATCCCATCTCATC 59.524 45.833 0.00 0.00 0.00 2.92
553 618 4.229123 GTCCATCCCAATATCCCATCTCAT 59.771 45.833 0.00 0.00 0.00 2.90
554 619 3.588842 GTCCATCCCAATATCCCATCTCA 59.411 47.826 0.00 0.00 0.00 3.27
555 620 3.369892 CGTCCATCCCAATATCCCATCTC 60.370 52.174 0.00 0.00 0.00 2.75
556 621 2.573462 CGTCCATCCCAATATCCCATCT 59.427 50.000 0.00 0.00 0.00 2.90
758 848 1.735920 GCGAGGCAGTGAGTGAGTG 60.736 63.158 0.00 0.00 0.00 3.51
759 849 2.653702 GCGAGGCAGTGAGTGAGT 59.346 61.111 0.00 0.00 0.00 3.41
760 850 2.125753 GGCGAGGCAGTGAGTGAG 60.126 66.667 0.00 0.00 0.00 3.51
761 851 2.917227 TGGCGAGGCAGTGAGTGA 60.917 61.111 0.00 0.00 0.00 3.41
810 900 0.686224 TGGTATTTATACGGCCGGGG 59.314 55.000 31.76 1.36 34.11 5.73
835 934 2.639347 TGATGGATTGATCGGGCAGTAT 59.361 45.455 0.00 0.00 0.00 2.12
859 958 1.506025 ATTGCTGGTTGGGTTGGTTT 58.494 45.000 0.00 0.00 0.00 3.27
861 960 1.923356 CTATTGCTGGTTGGGTTGGT 58.077 50.000 0.00 0.00 0.00 3.67
866 965 1.322538 GGTGGCTATTGCTGGTTGGG 61.323 60.000 0.00 0.00 39.59 4.12
867 966 1.322538 GGGTGGCTATTGCTGGTTGG 61.323 60.000 0.00 0.00 39.59 3.77
868 967 1.322538 GGGGTGGCTATTGCTGGTTG 61.323 60.000 0.00 0.00 39.59 3.77
869 968 1.000359 GGGGTGGCTATTGCTGGTT 60.000 57.895 0.00 0.00 39.59 3.67
871 970 0.397535 ATTGGGGTGGCTATTGCTGG 60.398 55.000 0.00 0.00 39.59 4.85
873 972 0.106015 GGATTGGGGTGGCTATTGCT 60.106 55.000 0.00 0.00 39.59 3.91
874 973 0.396974 TGGATTGGGGTGGCTATTGC 60.397 55.000 0.00 0.00 38.76 3.56
875 974 2.242043 GATGGATTGGGGTGGCTATTG 58.758 52.381 0.00 0.00 0.00 1.90
876 975 1.147817 GGATGGATTGGGGTGGCTATT 59.852 52.381 0.00 0.00 0.00 1.73
877 976 0.779997 GGATGGATTGGGGTGGCTAT 59.220 55.000 0.00 0.00 0.00 2.97
878 977 0.625980 TGGATGGATTGGGGTGGCTA 60.626 55.000 0.00 0.00 0.00 3.93
884 983 1.152368 GGAGCTGGATGGATTGGGG 59.848 63.158 0.00 0.00 0.00 4.96
885 984 0.110104 GAGGAGCTGGATGGATTGGG 59.890 60.000 0.00 0.00 0.00 4.12
898 997 0.390998 GACACTGAGCTTGGAGGAGC 60.391 60.000 0.00 0.00 43.02 4.70
900 999 1.536073 CGGACACTGAGCTTGGAGGA 61.536 60.000 0.00 0.00 0.00 3.71
901 1000 1.079543 CGGACACTGAGCTTGGAGG 60.080 63.158 0.00 0.00 0.00 4.30
902 1001 0.108898 CTCGGACACTGAGCTTGGAG 60.109 60.000 0.00 0.00 0.00 3.86
903 1002 1.967535 CTCGGACACTGAGCTTGGA 59.032 57.895 0.00 0.00 0.00 3.53
909 1008 1.153862 GCTGAGCTCGGACACTGAG 60.154 63.158 27.04 7.90 36.53 3.35
910 1009 1.590610 GAGCTGAGCTCGGACACTGA 61.591 60.000 27.04 0.00 45.85 3.41
912 1011 3.283303 GAGCTGAGCTCGGACACT 58.717 61.111 27.04 13.64 45.85 3.55
958 1057 3.084039 TCTTTCTTTCTCGCTACCGGTA 58.916 45.455 14.95 14.95 34.56 4.02
959 1058 1.891150 TCTTTCTTTCTCGCTACCGGT 59.109 47.619 13.98 13.98 34.56 5.28
962 1062 4.030134 TCGATCTTTCTTTCTCGCTACC 57.970 45.455 0.00 0.00 0.00 3.18
967 1067 4.145585 CGCACTATCGATCTTTCTTTCTCG 59.854 45.833 0.00 0.00 0.00 4.04
1004 1104 2.971428 AATGCCTATCGCCACCGTCG 62.971 60.000 0.00 0.00 36.24 5.12
1280 1384 2.158959 CGACCGACGGAGAATGTGC 61.159 63.158 23.38 0.00 38.46 4.57
1281 1385 2.158959 GCGACCGACGGAGAATGTG 61.159 63.158 23.38 2.80 42.83 3.21
1282 1386 2.181021 GCGACCGACGGAGAATGT 59.819 61.111 23.38 0.00 42.83 2.71
1369 1498 2.812609 CTGCGACGACAGCTGCAT 60.813 61.111 15.27 0.00 36.64 3.96
1629 1790 2.375766 GCCTTCACGTCAGCGACAG 61.376 63.158 8.91 4.90 42.00 3.51
2105 2329 0.816018 TGACGGGTTCATGCGTTGTT 60.816 50.000 0.00 0.00 0.00 2.83
2106 2330 0.605319 ATGACGGGTTCATGCGTTGT 60.605 50.000 0.00 0.00 43.87 3.32
2107 2331 0.096976 GATGACGGGTTCATGCGTTG 59.903 55.000 0.00 0.00 45.67 4.10
2124 2352 4.320494 GCCGAAACAAAACACATCTCAGAT 60.320 41.667 0.00 0.00 0.00 2.90
2168 2396 2.391389 CGCGCACTTCCTTCCTTCC 61.391 63.158 8.75 0.00 0.00 3.46
2304 2541 7.007723 TGGATTTTCAAGGCTAAAAGGAACTA 58.992 34.615 2.07 0.00 38.49 2.24
2329 2566 5.049405 GGAAAAGAACACATCAATCACGTCT 60.049 40.000 0.00 0.00 0.00 4.18
2333 2570 6.317789 TGAGGAAAAGAACACATCAATCAC 57.682 37.500 0.00 0.00 0.00 3.06
2426 2666 1.201429 GGTCCAGATCCACAGGGTGT 61.201 60.000 0.00 0.00 34.93 4.16
2472 2712 6.325545 TCCTCGGTTAGAATAATCTAAAGCCA 59.674 38.462 1.75 0.00 46.83 4.75
2550 2791 2.472861 CGAGTGATACATGAATGTCGGC 59.527 50.000 0.00 0.00 41.97 5.54
2567 2808 0.402504 TGGGTATTTTGGGTGCGAGT 59.597 50.000 0.00 0.00 0.00 4.18
2604 2845 2.660236 GTGACGAGTTTAGTTACCGCTG 59.340 50.000 0.00 0.00 0.00 5.18
2690 4724 3.154473 CCGGCCCGAATCTCAGGA 61.154 66.667 3.71 0.00 0.00 3.86
2718 4752 2.108976 CGATGGGTGTGGATCCGG 59.891 66.667 7.39 0.00 0.00 5.14
2760 4797 2.746375 CGCCTTCCCCTATGGCACT 61.746 63.158 0.00 0.00 46.48 4.40
2765 4802 2.189499 GCTTGCGCCTTCCCCTATG 61.189 63.158 4.18 0.00 0.00 2.23
2766 4803 2.193248 GCTTGCGCCTTCCCCTAT 59.807 61.111 4.18 0.00 0.00 2.57
2767 4804 2.819984 CTTGCTTGCGCCTTCCCCTA 62.820 60.000 4.18 0.00 34.43 3.53
2768 4805 4.284550 TTGCTTGCGCCTTCCCCT 62.285 61.111 4.18 0.00 34.43 4.79
2770 4807 3.752339 CCTTGCTTGCGCCTTCCC 61.752 66.667 4.18 0.00 34.43 3.97
2771 4808 4.426112 GCCTTGCTTGCGCCTTCC 62.426 66.667 4.18 0.00 34.43 3.46
2772 4809 4.426112 GGCCTTGCTTGCGCCTTC 62.426 66.667 4.18 0.00 39.70 3.46
2935 4972 4.859304 ACATTTGTGTACTGACTACGGA 57.141 40.909 0.00 0.00 0.00 4.69
2937 4974 7.806149 TGATTACATTTGTGTACTGACTACG 57.194 36.000 0.00 0.00 0.00 3.51
2961 4998 4.763355 TCCCCCTATACACTATGCAAGAT 58.237 43.478 0.00 0.00 0.00 2.40
2966 5003 2.832733 GGACTCCCCCTATACACTATGC 59.167 54.545 0.00 0.00 0.00 3.14
2970 5007 2.427889 CCATGGACTCCCCCTATACACT 60.428 54.545 5.56 0.00 0.00 3.55
2971 5008 1.978580 CCATGGACTCCCCCTATACAC 59.021 57.143 5.56 0.00 0.00 2.90
2972 5009 1.765025 GCCATGGACTCCCCCTATACA 60.765 57.143 18.40 0.00 0.00 2.29
2973 5010 0.984995 GCCATGGACTCCCCCTATAC 59.015 60.000 18.40 0.00 0.00 1.47
2974 5011 0.874594 AGCCATGGACTCCCCCTATA 59.125 55.000 18.40 0.00 0.00 1.31
2975 5012 0.474660 GAGCCATGGACTCCCCCTAT 60.475 60.000 18.40 0.00 0.00 2.57
2976 5013 1.074471 GAGCCATGGACTCCCCCTA 60.074 63.158 18.40 0.00 0.00 3.53
2977 5014 2.367512 GAGCCATGGACTCCCCCT 60.368 66.667 18.40 0.00 0.00 4.79
2978 5015 3.493303 GGAGCCATGGACTCCCCC 61.493 72.222 30.32 15.97 46.81 5.40
2982 5019 2.191641 GCAGGGAGCCATGGACTC 59.808 66.667 18.40 20.27 37.23 3.36
2991 5028 1.072852 GGATCAGATGGCAGGGAGC 59.927 63.158 0.00 0.00 44.65 4.70
2992 5029 0.108207 GTGGATCAGATGGCAGGGAG 59.892 60.000 0.00 0.00 0.00 4.30
2993 5030 1.348008 GGTGGATCAGATGGCAGGGA 61.348 60.000 0.00 0.00 0.00 4.20
2994 5031 1.150081 GGTGGATCAGATGGCAGGG 59.850 63.158 0.00 0.00 0.00 4.45
2995 5032 1.227764 CGGTGGATCAGATGGCAGG 60.228 63.158 0.00 0.00 0.00 4.85
2996 5033 0.531532 GACGGTGGATCAGATGGCAG 60.532 60.000 0.00 0.00 0.00 4.85
2997 5034 1.264045 TGACGGTGGATCAGATGGCA 61.264 55.000 0.00 0.00 0.00 4.92
2998 5035 0.811616 GTGACGGTGGATCAGATGGC 60.812 60.000 0.00 0.00 0.00 4.40
3013 5286 2.190981 GTGGTGAATATCGTCGGTGAC 58.809 52.381 0.00 0.00 0.00 3.67
3018 5291 1.474017 GACGGTGGTGAATATCGTCG 58.526 55.000 0.00 0.00 40.22 5.12
3042 5315 4.803426 GAGGCGAGCGAGGGTGTG 62.803 72.222 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.