Multiple sequence alignment - TraesCS2B01G626800

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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 TraesCS2B01G626800 chr2B 100.000 1667 0 0 1 1667 798755203 798756869 0.000000e+00 3079
1 TraesCS2B01G626800 chr2B 100.000 1282 0 0 1881 3162 798757083 798758364 0.000000e+00 2368
2 TraesCS2B01G626800 chr2B 98.625 291 4 0 603 893 798769911 798770201 1.680000e-142 516
3 TraesCS2B01G626800 chr2B 98.851 261 3 0 2902 3162 510048343 510048603 1.720000e-127 466
4 TraesCS2B01G626800 chr2B 98.851 261 3 0 2902 3162 798765177 798765437 1.720000e-127 466
5 TraesCS2B01G626800 chr2B 80.099 608 73 21 10 602 729645056 729644482 2.940000e-110 409
6 TraesCS2B01G626800 chr2B 82.292 192 31 1 959 1147 797943458 797943649 2.520000e-36 163
7 TraesCS2B01G626800 chr4B 88.827 1074 115 3 597 1667 486997533 486998604 0.000000e+00 1314
8 TraesCS2B01G626800 chr4B 89.289 1027 88 5 1881 2901 486998642 486999652 0.000000e+00 1267
9 TraesCS2B01G626800 chr4B 98.467 261 4 0 2902 3162 613605837 613605577 7.990000e-126 460
10 TraesCS2B01G626800 chr4B 89.078 293 28 4 603 893 487002635 487002925 8.340000e-96 361
11 TraesCS2B01G626800 chr7A 88.281 1024 114 1 1884 2901 565358961 565357938 0.000000e+00 1221
12 TraesCS2B01G626800 chr7A 86.932 1056 123 12 618 1665 565360052 565359004 0.000000e+00 1171
13 TraesCS2B01G626800 chr7A 82.825 623 67 22 8 602 177049266 177048656 3.610000e-144 521
14 TraesCS2B01G626800 chr7A 76.111 360 74 12 1314 1667 618176601 618176248 9.010000e-41 178
15 TraesCS2B01G626800 chr3D 85.687 1034 139 6 1881 2905 94130386 94131419 0.000000e+00 1081
16 TraesCS2B01G626800 chr3D 85.590 1034 139 8 1881 2905 341468605 341469637 0.000000e+00 1075
17 TraesCS2B01G626800 chr3D 85.618 1043 127 14 634 1667 341467540 341468568 0.000000e+00 1074
18 TraesCS2B01G626800 chr3D 85.057 1044 132 15 634 1667 94129319 94130348 0.000000e+00 1042
19 TraesCS2B01G626800 chr6A 84.468 1043 140 12 634 1667 2878018 2879047 0.000000e+00 1009
20 TraesCS2B01G626800 chr6A 84.741 793 97 15 634 1417 147257468 147258245 0.000000e+00 773
21 TraesCS2B01G626800 chr6A 89.328 253 27 0 1415 1667 147270540 147270792 5.090000e-83 318
22 TraesCS2B01G626800 chr6A 90.769 130 12 0 1881 2010 147270829 147270958 1.170000e-39 174
23 TraesCS2B01G626800 chr6B 89.142 571 46 6 14 568 647162559 647161989 0.000000e+00 697
24 TraesCS2B01G626800 chr6B 86.688 616 47 24 20 602 23350937 23350324 0.000000e+00 651
25 TraesCS2B01G626800 chr6B 90.909 429 38 1 1 428 583589634 583590062 2.740000e-160 575
26 TraesCS2B01G626800 chrUn 86.054 588 65 10 1 576 100187384 100187966 1.610000e-172 616
27 TraesCS2B01G626800 chrUn 87.565 386 45 1 1001 1383 480265419 480265804 8.050000e-121 444
28 TraesCS2B01G626800 chr2A 85.142 599 78 9 8 599 203664289 203664883 1.250000e-168 603
29 TraesCS2B01G626800 chr4D 86.535 557 62 11 54 602 465009422 465008871 4.510000e-168 601
30 TraesCS2B01G626800 chr4D 73.137 1020 234 35 1882 2881 499531069 499530070 2.350000e-86 329
31 TraesCS2B01G626800 chr3B 84.477 612 73 14 1 602 21952970 21953569 4.540000e-163 584
32 TraesCS2B01G626800 chr3B 89.347 291 31 0 603 893 662520007 662520297 1.790000e-97 366
33 TraesCS2B01G626800 chr3B 91.748 206 13 3 404 608 658963960 658963758 1.860000e-72 283
34 TraesCS2B01G626800 chr3B 78.717 343 61 11 1329 1665 689671107 689671443 5.310000e-53 219
35 TraesCS2B01G626800 chr7B 90.676 429 39 1 1 428 144104207 144104635 1.270000e-158 569
36 TraesCS2B01G626800 chr2D 86.391 507 53 11 1 497 102276765 102276265 9.980000e-150 540
37 TraesCS2B01G626800 chr3A 82.534 584 87 10 23 599 630810974 630811549 1.690000e-137 499
38 TraesCS2B01G626800 chr1B 98.113 265 5 0 2898 3162 296266310 296266574 2.220000e-126 462
39 TraesCS2B01G626800 chr1B 98.467 261 4 0 2902 3162 296273280 296273540 7.990000e-126 460
40 TraesCS2B01G626800 chr1B 98.467 261 4 0 2902 3162 299990524 299990264 7.990000e-126 460
41 TraesCS2B01G626800 chr1B 96.691 272 8 1 2891 3162 450033014 450033284 4.810000e-123 451
42 TraesCS2B01G626800 chr5B 98.467 261 4 0 2902 3162 272293522 272293262 7.990000e-126 460
43 TraesCS2B01G626800 chr5B 98.467 261 4 0 2902 3162 275324489 275324229 7.990000e-126 460
44 TraesCS2B01G626800 chr1A 72.431 798 194 23 1882 2663 17854096 17853309 6.820000e-57 231
45 TraesCS2B01G626800 chr7D 78.632 351 67 8 1319 1665 572017529 572017183 3.170000e-55 226
46 TraesCS2B01G626800 chr5A 81.461 178 25 7 936 1108 684710258 684710432 4.250000e-29 139


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 TraesCS2B01G626800 chr2B 798755203 798758364 3161 False 2723.500000 3079 100.000000 1 3162 2 chr2B.!!$F5 3161
1 TraesCS2B01G626800 chr2B 729644482 729645056 574 True 409.000000 409 80.099000 10 602 1 chr2B.!!$R1 592
2 TraesCS2B01G626800 chr4B 486997533 487002925 5392 False 980.666667 1314 89.064667 597 2901 3 chr4B.!!$F1 2304
3 TraesCS2B01G626800 chr7A 565357938 565360052 2114 True 1196.000000 1221 87.606500 618 2901 2 chr7A.!!$R3 2283
4 TraesCS2B01G626800 chr7A 177048656 177049266 610 True 521.000000 521 82.825000 8 602 1 chr7A.!!$R1 594
5 TraesCS2B01G626800 chr3D 341467540 341469637 2097 False 1074.500000 1075 85.604000 634 2905 2 chr3D.!!$F2 2271
6 TraesCS2B01G626800 chr3D 94129319 94131419 2100 False 1061.500000 1081 85.372000 634 2905 2 chr3D.!!$F1 2271
7 TraesCS2B01G626800 chr6A 2878018 2879047 1029 False 1009.000000 1009 84.468000 634 1667 1 chr6A.!!$F1 1033
8 TraesCS2B01G626800 chr6A 147257468 147258245 777 False 773.000000 773 84.741000 634 1417 1 chr6A.!!$F2 783
9 TraesCS2B01G626800 chr6B 647161989 647162559 570 True 697.000000 697 89.142000 14 568 1 chr6B.!!$R2 554
10 TraesCS2B01G626800 chr6B 23350324 23350937 613 True 651.000000 651 86.688000 20 602 1 chr6B.!!$R1 582
11 TraesCS2B01G626800 chrUn 100187384 100187966 582 False 616.000000 616 86.054000 1 576 1 chrUn.!!$F1 575
12 TraesCS2B01G626800 chr2A 203664289 203664883 594 False 603.000000 603 85.142000 8 599 1 chr2A.!!$F1 591
13 TraesCS2B01G626800 chr4D 465008871 465009422 551 True 601.000000 601 86.535000 54 602 1 chr4D.!!$R1 548
14 TraesCS2B01G626800 chr4D 499530070 499531069 999 True 329.000000 329 73.137000 1882 2881 1 chr4D.!!$R2 999
15 TraesCS2B01G626800 chr3B 21952970 21953569 599 False 584.000000 584 84.477000 1 602 1 chr3B.!!$F1 601
16 TraesCS2B01G626800 chr2D 102276265 102276765 500 True 540.000000 540 86.391000 1 497 1 chr2D.!!$R1 496
17 TraesCS2B01G626800 chr3A 630810974 630811549 575 False 499.000000 499 82.534000 23 599 1 chr3A.!!$F1 576
18 TraesCS2B01G626800 chr1A 17853309 17854096 787 True 231.000000 231 72.431000 1882 2663 1 chr1A.!!$R1 781

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
294 346 0.608130 TACATCGACCTGTGCAGCTT 59.392 50.0 1.88 0.00 0.00 3.74 F
1478 1574 0.546747 GGGGATCGGGGATATCACCA 60.547 60.0 23.86 11.28 44.93 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 1730 0.039618 TTGGGAGGATTGGAGCCAAC 59.960 55.0 3.7 0.0 38.88 3.77 R
2310 2427 1.022735 GCCAGCTTGTCATCATGAGG 58.977 55.0 0.0 0.0 0.00 3.86 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
104 105 4.051167 TCGGGCCCGAGGACTACA 62.051 66.667 42.66 19.15 44.01 2.74
111 115 1.035932 CCCGAGGACTACATCACGGT 61.036 60.000 0.00 0.00 43.03 4.83
116 120 3.018149 GAGGACTACATCACGGTCTTCT 58.982 50.000 0.00 0.00 34.63 2.85
294 346 0.608130 TACATCGACCTGTGCAGCTT 59.392 50.000 1.88 0.00 0.00 3.74
330 382 4.148825 GTCGCTCGGCCTCCACAT 62.149 66.667 0.00 0.00 0.00 3.21
391 445 4.042684 CCGACCCCCTCTACTACTAGTTAT 59.957 50.000 0.00 0.00 0.00 1.89
457 545 6.265196 TGAACTATGTTTGTGCAATTTCTCCT 59.735 34.615 0.00 0.00 0.00 3.69
542 631 2.739932 CGACCCGCAAATGAGATCTTCT 60.740 50.000 0.00 0.00 0.00 2.85
599 688 0.615850 GGGGTCTGCTAGAGTTGCTT 59.384 55.000 0.00 0.00 0.00 3.91
613 702 1.813786 GTTGCTTTATGTTACGGCCCA 59.186 47.619 0.00 0.00 0.00 5.36
766 856 2.507102 CTGCGCGAGGTGACGATT 60.507 61.111 12.10 0.00 35.09 3.34
780 870 6.588204 AGGTGACGATTATGTAATTGGCTAA 58.412 36.000 7.25 0.00 36.29 3.09
830 920 1.133294 CCTCCTCCCTCTAGAACTCCC 60.133 61.905 0.00 0.00 0.00 4.30
835 925 2.107552 CTCCCTCTAGAACTCCCGATCT 59.892 54.545 0.00 0.00 0.00 2.75
839 929 3.078837 CTCTAGAACTCCCGATCTAGCC 58.921 54.545 5.20 0.00 43.09 3.93
855 945 5.201713 TCTAGCCGAATTCTTGTATCCTG 57.798 43.478 3.52 0.00 0.00 3.86
860 950 3.118408 CCGAATTCTTGTATCCTGGACCA 60.118 47.826 0.00 0.00 0.00 4.02
867 957 2.902608 TGTATCCTGGACCAAGTGAGT 58.097 47.619 0.00 0.00 0.00 3.41
877 967 4.141505 TGGACCAAGTGAGTGAATTCTTGA 60.142 41.667 7.05 0.00 39.39 3.02
946 1038 3.628832 TTTTTCTCCCCACCCTCAATT 57.371 42.857 0.00 0.00 0.00 2.32
966 1058 3.518068 GCCGGCCATTTCCCTTCG 61.518 66.667 18.11 0.00 0.00 3.79
1029 1121 0.694771 TCAACAAGGCTCTGGCTGAT 59.305 50.000 0.00 0.00 38.81 2.90
1092 1187 4.803426 CACCCCGTGCTCGAGCTC 62.803 72.222 35.27 30.32 42.66 4.09
1260 1356 4.435970 TCCGACCTGCCGCCTCTA 62.436 66.667 0.00 0.00 0.00 2.43
1271 1367 2.187163 GCCTCTACTTCCGGCCAC 59.813 66.667 2.24 0.00 37.86 5.01
1311 1407 2.360350 CCAGGCGAGCAACCACAT 60.360 61.111 0.00 0.00 0.00 3.21
1387 1483 0.679960 GGGGAAATCGGTGGGTGAAG 60.680 60.000 0.00 0.00 0.00 3.02
1442 1538 2.159476 CGTCTGATTTCCTTCCGTACGA 60.159 50.000 18.76 0.00 0.00 3.43
1464 1560 1.139853 GAGCAATCGTTCTCTGGGGAT 59.860 52.381 0.00 0.00 0.00 3.85
1478 1574 0.546747 GGGGATCGGGGATATCACCA 60.547 60.000 23.86 11.28 44.93 4.17
1540 1636 1.534729 GATGAACCCGAAAGCTTGGT 58.465 50.000 0.00 0.00 0.00 3.67
1560 1656 7.575720 GCTTGGTGTCTTAAATGTGAAGCTTAT 60.576 37.037 0.00 0.00 32.42 1.73
1597 1693 1.145571 TAGCCCTGACACTTGGGTTT 58.854 50.000 0.00 0.00 45.06 3.27
1634 1730 2.756840 TTCACAGATGGAGCACTCAG 57.243 50.000 0.00 0.00 0.00 3.35
1656 1752 1.454663 GCTCCAATCCTCCCAAGCC 60.455 63.158 0.00 0.00 0.00 4.35
1939 2035 5.105351 GGCAGTTTAATAGGTTGAGGCAAAT 60.105 40.000 0.00 0.00 0.00 2.32
1947 2043 4.615170 TGAGGCAAATGGGCACAA 57.385 50.000 0.00 0.00 46.44 3.33
1949 2045 1.350071 TGAGGCAAATGGGCACAATT 58.650 45.000 0.00 0.00 46.44 2.32
2072 2168 1.084037 GCGTGATATTCGTGCAGCG 60.084 57.895 0.00 0.00 43.01 5.18
2075 2171 1.847818 GTGATATTCGTGCAGCGGTA 58.152 50.000 8.46 3.98 41.72 4.02
2162 2258 2.715624 GCATTTCGGCGGGATGAC 59.284 61.111 21.60 12.15 0.00 3.06
2310 2427 1.652563 GACAACAACAAGACCGCCC 59.347 57.895 0.00 0.00 0.00 6.13
2378 2495 2.345244 CTCTGCTTCACCTGCGGT 59.655 61.111 0.00 0.00 37.96 5.68
2465 2582 0.887933 AAATGCTACAAGGCCAACCG 59.112 50.000 5.01 0.00 42.76 4.44
2539 2656 1.203287 GTCCAAGGAAGCCATTGAAGC 59.797 52.381 0.00 0.00 0.00 3.86
2664 2781 0.610232 GGCTCAACATCTGCAAGGGT 60.610 55.000 0.00 0.00 0.00 4.34
2669 2786 1.962807 CAACATCTGCAAGGGTTCCAA 59.037 47.619 0.00 0.00 31.22 3.53
2673 2790 0.106268 TCTGCAAGGGTTCCAAAGCA 60.106 50.000 0.00 0.00 0.00 3.91
2771 2889 1.825641 CGTTCCCAGGGGGTCAAATTT 60.826 52.381 5.33 0.00 44.74 1.82
2849 2967 2.421314 CTGGCGTGTCACAGTCCA 59.579 61.111 3.42 6.16 0.00 4.02
2861 2979 3.563808 GTCACAGTCCAATGCAAGTACAA 59.436 43.478 0.00 0.00 0.00 2.41
2901 3019 4.263816 TGGATTTCCAATACAACGGGGTTA 60.264 41.667 0.00 0.00 44.35 2.85
2905 3023 2.905085 TCCAATACAACGGGGTTACTGA 59.095 45.455 0.00 0.00 0.00 3.41
2906 3024 3.327172 TCCAATACAACGGGGTTACTGAA 59.673 43.478 0.00 0.00 0.00 3.02
2907 3025 3.687698 CCAATACAACGGGGTTACTGAAG 59.312 47.826 0.00 0.00 0.00 3.02
2909 3027 4.895668 ATACAACGGGGTTACTGAAGAA 57.104 40.909 0.00 0.00 0.00 2.52
2910 3028 3.564053 ACAACGGGGTTACTGAAGAAA 57.436 42.857 0.00 0.00 0.00 2.52
2911 3029 3.888583 ACAACGGGGTTACTGAAGAAAA 58.111 40.909 0.00 0.00 0.00 2.29
2912 3030 4.466827 ACAACGGGGTTACTGAAGAAAAT 58.533 39.130 0.00 0.00 0.00 1.82
2913 3031 5.623169 ACAACGGGGTTACTGAAGAAAATA 58.377 37.500 0.00 0.00 0.00 1.40
2914 3032 6.243148 ACAACGGGGTTACTGAAGAAAATAT 58.757 36.000 0.00 0.00 0.00 1.28
2915 3033 6.150474 ACAACGGGGTTACTGAAGAAAATATG 59.850 38.462 0.00 0.00 0.00 1.78
2916 3034 4.638865 ACGGGGTTACTGAAGAAAATATGC 59.361 41.667 0.00 0.00 0.00 3.14
2917 3035 4.036380 CGGGGTTACTGAAGAAAATATGCC 59.964 45.833 0.00 0.00 0.00 4.40
2918 3036 4.341235 GGGGTTACTGAAGAAAATATGCCC 59.659 45.833 0.00 0.00 0.00 5.36
2919 3037 5.201243 GGGTTACTGAAGAAAATATGCCCT 58.799 41.667 0.00 0.00 0.00 5.19
2920 3038 6.362248 GGGTTACTGAAGAAAATATGCCCTA 58.638 40.000 0.00 0.00 0.00 3.53
2921 3039 6.486993 GGGTTACTGAAGAAAATATGCCCTAG 59.513 42.308 0.00 0.00 0.00 3.02
2922 3040 7.280356 GGTTACTGAAGAAAATATGCCCTAGA 58.720 38.462 0.00 0.00 0.00 2.43
2923 3041 7.442666 GGTTACTGAAGAAAATATGCCCTAGAG 59.557 40.741 0.00 0.00 0.00 2.43
2924 3042 5.934781 ACTGAAGAAAATATGCCCTAGAGG 58.065 41.667 0.00 0.00 39.47 3.69
3000 3118 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
3001 3119 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
3002 3120 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
3003 3121 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
3004 3122 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
3006 3124 7.855904 GCTAGAATTGTATTAACCGGAAACATG 59.144 37.037 9.46 0.00 0.00 3.21
3008 3126 8.519799 AGAATTGTATTAACCGGAAACATGAT 57.480 30.769 9.46 0.00 0.00 2.45
3009 3127 9.621629 AGAATTGTATTAACCGGAAACATGATA 57.378 29.630 9.46 0.00 0.00 2.15
3010 3128 9.659830 GAATTGTATTAACCGGAAACATGATAC 57.340 33.333 9.46 7.13 0.00 2.24
3016 3134 3.950397 ACCGGAAACATGATACATGTGT 58.050 40.909 9.46 11.88 31.80 3.72
3017 3135 3.689161 ACCGGAAACATGATACATGTGTG 59.311 43.478 9.46 4.81 31.80 3.82
3018 3136 3.938334 CCGGAAACATGATACATGTGTGA 59.062 43.478 16.29 0.00 31.80 3.58
3019 3137 4.394610 CCGGAAACATGATACATGTGTGAA 59.605 41.667 16.29 0.00 31.80 3.18
3022 3140 7.125755 CGGAAACATGATACATGTGTGAATAC 58.874 38.462 16.29 1.40 31.80 1.89
3023 3141 7.201600 CGGAAACATGATACATGTGTGAATACA 60.202 37.037 16.29 0.00 34.63 2.29
3024 3142 8.623903 GGAAACATGATACATGTGTGAATACAT 58.376 33.333 16.29 0.00 41.77 2.29
3027 3145 9.836864 AACATGATACATGTGTGAATACATAGT 57.163 29.630 16.29 0.75 39.17 2.12
3028 3146 9.481340 ACATGATACATGTGTGAATACATAGTC 57.519 33.333 15.11 0.00 39.17 2.59
3029 3147 9.480053 CATGATACATGTGTGAATACATAGTCA 57.520 33.333 9.11 0.00 39.17 3.41
3031 3149 9.883142 TGATACATGTGTGAATACATAGTCAAA 57.117 29.630 9.11 0.00 39.17 2.69
3036 3154 7.977789 TGTGTGAATACATAGTCAAACACAT 57.022 32.000 8.01 0.00 41.82 3.21
3039 3157 9.151471 GTGTGAATACATAGTCAAACACATAGT 57.849 33.333 5.07 0.00 38.16 2.12
3041 3159 9.366216 GTGAATACATAGTCAAACACATAGTCA 57.634 33.333 0.00 0.00 31.64 3.41
3043 3161 9.587772 GAATACATAGTCAAACACATAGTCACT 57.412 33.333 0.00 0.00 0.00 3.41
3050 3168 7.036220 AGTCAAACACATAGTCACTAGTATGC 58.964 38.462 0.00 0.00 41.09 3.14
3051 3169 6.255887 GTCAAACACATAGTCACTAGTATGCC 59.744 42.308 0.00 0.00 41.09 4.40
3052 3170 6.154534 TCAAACACATAGTCACTAGTATGCCT 59.845 38.462 0.00 0.00 41.09 4.75
3053 3171 5.776173 ACACATAGTCACTAGTATGCCTC 57.224 43.478 0.00 0.00 41.09 4.70
3054 3172 5.450453 ACACATAGTCACTAGTATGCCTCT 58.550 41.667 0.00 0.00 41.09 3.69
3055 3173 6.602278 ACACATAGTCACTAGTATGCCTCTA 58.398 40.000 0.00 0.00 41.09 2.43
3056 3174 6.487331 ACACATAGTCACTAGTATGCCTCTAC 59.513 42.308 0.00 0.00 41.09 2.59
3057 3175 6.712998 CACATAGTCACTAGTATGCCTCTACT 59.287 42.308 0.00 0.00 41.09 2.57
3059 3177 8.438373 ACATAGTCACTAGTATGCCTCTACTTA 58.562 37.037 0.00 0.00 41.09 2.24
3061 3179 7.571080 AGTCACTAGTATGCCTCTACTTAAC 57.429 40.000 0.00 0.00 33.96 2.01
3062 3180 7.348033 AGTCACTAGTATGCCTCTACTTAACT 58.652 38.462 0.00 0.00 33.96 2.24
3064 3182 8.776470 GTCACTAGTATGCCTCTACTTAACTAG 58.224 40.741 0.00 0.00 33.96 2.57
3065 3183 7.444792 TCACTAGTATGCCTCTACTTAACTAGC 59.555 40.741 0.00 0.00 33.96 3.42
3066 3184 7.446013 CACTAGTATGCCTCTACTTAACTAGCT 59.554 40.741 0.00 0.00 33.96 3.32
3067 3185 6.887626 AGTATGCCTCTACTTAACTAGCTC 57.112 41.667 0.00 0.00 0.00 4.09
3068 3186 6.366340 AGTATGCCTCTACTTAACTAGCTCA 58.634 40.000 0.00 0.00 0.00 4.26
3069 3187 7.007723 AGTATGCCTCTACTTAACTAGCTCAT 58.992 38.462 0.00 0.00 0.00 2.90
3071 3189 7.841282 ATGCCTCTACTTAACTAGCTCATTA 57.159 36.000 0.00 0.00 0.00 1.90
3072 3190 7.655521 TGCCTCTACTTAACTAGCTCATTAA 57.344 36.000 0.00 0.00 0.00 1.40
3073 3191 8.251383 TGCCTCTACTTAACTAGCTCATTAAT 57.749 34.615 0.00 0.00 0.00 1.40
3074 3192 8.361139 TGCCTCTACTTAACTAGCTCATTAATC 58.639 37.037 0.00 0.00 0.00 1.75
3075 3193 8.361139 GCCTCTACTTAACTAGCTCATTAATCA 58.639 37.037 0.00 0.00 0.00 2.57
3083 3201 9.905713 TTAACTAGCTCATTAATCAAAGATGGT 57.094 29.630 0.00 0.00 0.00 3.55
3084 3202 8.814038 AACTAGCTCATTAATCAAAGATGGTT 57.186 30.769 0.00 4.29 33.49 3.67
3085 3203 9.905713 AACTAGCTCATTAATCAAAGATGGTTA 57.094 29.630 0.00 0.00 28.92 2.85
3089 3207 9.193806 AGCTCATTAATCAAAGATGGTTATGTT 57.806 29.630 0.00 0.00 32.32 2.71
3103 3239 5.741011 TGGTTATGTTTCCTGACCATAGAC 58.259 41.667 0.00 0.00 35.58 2.59
3106 3242 6.260936 GGTTATGTTTCCTGACCATAGACATG 59.739 42.308 0.00 0.00 0.00 3.21
3108 3244 4.578871 TGTTTCCTGACCATAGACATGTG 58.421 43.478 1.15 0.00 0.00 3.21
3112 3248 3.582647 TCCTGACCATAGACATGTGTTGT 59.417 43.478 1.15 0.00 42.79 3.32
3128 4654 6.907853 TGTGTTGTCATTTGATTAATGGGA 57.092 33.333 0.00 0.00 43.19 4.37
3134 4660 7.901283 TGTCATTTGATTAATGGGATCACAT 57.099 32.000 4.06 4.06 43.19 3.21
3135 4661 7.944061 TGTCATTTGATTAATGGGATCACATC 58.056 34.615 11.76 0.00 43.19 3.06
3137 4663 8.582437 GTCATTTGATTAATGGGATCACATCAT 58.418 33.333 11.76 6.60 43.19 2.45
3138 4664 9.150028 TCATTTGATTAATGGGATCACATCATT 57.850 29.630 11.76 9.08 43.19 2.57
3141 4667 8.640063 TTGATTAATGGGATCACATCATTAGG 57.360 34.615 11.76 0.00 35.59 2.69
3142 4668 7.987820 TGATTAATGGGATCACATCATTAGGA 58.012 34.615 11.76 0.00 35.59 2.94
3144 4670 7.631510 TTAATGGGATCACATCATTAGGAGA 57.368 36.000 11.76 0.00 35.59 3.71
3145 4671 6.520021 AATGGGATCACATCATTAGGAGAA 57.480 37.500 11.76 0.00 30.35 2.87
3146 4672 6.715350 ATGGGATCACATCATTAGGAGAAT 57.285 37.500 4.06 0.00 0.00 2.40
3147 4673 5.872963 TGGGATCACATCATTAGGAGAATG 58.127 41.667 0.00 0.00 0.00 2.67
3148 4674 5.608015 TGGGATCACATCATTAGGAGAATGA 59.392 40.000 0.00 2.66 40.50 2.57
3149 4675 6.273965 TGGGATCACATCATTAGGAGAATGAT 59.726 38.462 0.00 6.90 45.40 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.683933 GGGCTCCTCCTTCACCGA 60.684 66.667 0.00 0.00 34.39 4.69
104 105 1.432251 CGGCGTAGAAGACCGTGAT 59.568 57.895 0.00 0.00 42.01 3.06
111 115 2.483745 CAGCGACGGCGTAGAAGA 59.516 61.111 24.18 0.00 46.35 2.87
173 196 3.749064 GAGCTCCTCGACGTGGCA 61.749 66.667 11.08 0.25 0.00 4.92
228 274 1.079543 CGCCACTCCTCAGTCTTGG 60.080 63.158 0.00 0.00 0.00 3.61
262 308 1.153628 GATGTACTTCGCCGCCTGT 60.154 57.895 0.00 0.00 0.00 4.00
294 346 1.667154 CGCTCAATCCTCCTCACCGA 61.667 60.000 0.00 0.00 0.00 4.69
329 381 1.977594 GCGGCAAAATGGACGACGAT 61.978 55.000 0.00 0.00 43.61 3.73
330 382 2.673114 GCGGCAAAATGGACGACGA 61.673 57.895 0.00 0.00 43.61 4.20
391 445 8.056407 AGCATAGATCATACTAAATGCTACGA 57.944 34.615 5.86 0.00 37.12 3.43
599 688 4.968370 GCCTGGGCCGTAACATAA 57.032 55.556 0.00 0.00 34.56 1.90
623 712 2.746277 GCAGTAGTGGTTGGGCCG 60.746 66.667 0.00 0.00 41.21 6.13
661 750 2.915659 TGACTTGTCGACGGGGCT 60.916 61.111 11.62 0.00 0.00 5.19
761 851 4.451096 CCGCTTAGCCAATTACATAATCGT 59.549 41.667 0.00 0.00 0.00 3.73
764 854 3.188460 CGCCGCTTAGCCAATTACATAAT 59.812 43.478 0.00 0.00 0.00 1.28
766 856 2.139917 CGCCGCTTAGCCAATTACATA 58.860 47.619 0.00 0.00 0.00 2.29
791 881 1.384643 AAAGGGGATCGGGAGAGGG 60.385 63.158 0.00 0.00 45.48 4.30
830 920 4.859798 GGATACAAGAATTCGGCTAGATCG 59.140 45.833 0.00 0.00 0.00 3.69
835 925 3.964688 TCCAGGATACAAGAATTCGGCTA 59.035 43.478 0.00 0.00 41.41 3.93
839 929 4.137116 TGGTCCAGGATACAAGAATTCG 57.863 45.455 0.00 0.00 41.41 3.34
855 945 4.389374 TCAAGAATTCACTCACTTGGTCC 58.611 43.478 8.44 0.00 39.74 4.46
860 950 4.823989 CCCACTTCAAGAATTCACTCACTT 59.176 41.667 8.44 0.00 0.00 3.16
867 957 3.507162 TGCTCCCACTTCAAGAATTCA 57.493 42.857 8.44 0.00 0.00 2.57
877 967 2.795329 CCACTTGTTATGCTCCCACTT 58.205 47.619 0.00 0.00 0.00 3.16
966 1058 2.022129 CCGCCGCGTCTGGATAATC 61.022 63.158 12.58 0.00 0.00 1.75
1029 1121 4.193334 CTGATCGCCGCCGTCAGA 62.193 66.667 11.17 0.00 41.14 3.27
1354 1450 2.595750 TTCCCCCGAATTTCATGTGT 57.404 45.000 0.00 0.00 0.00 3.72
1387 1483 1.579429 GCAATCGTGGGGTGTGAAC 59.421 57.895 0.00 0.00 0.00 3.18
1464 1560 1.202879 GGCAAATGGTGATATCCCCGA 60.203 52.381 0.00 0.00 0.00 5.14
1523 1619 0.106918 ACACCAAGCTTTCGGGTTCA 60.107 50.000 4.25 0.00 32.86 3.18
1533 1629 4.022849 GCTTCACATTTAAGACACCAAGCT 60.023 41.667 0.00 0.00 32.69 3.74
1540 1636 8.296713 GTGGAAATAAGCTTCACATTTAAGACA 58.703 33.333 0.00 0.00 0.00 3.41
1560 1656 2.866460 GCTAAGAGTGCAGACGTGGAAA 60.866 50.000 0.00 0.00 0.00 3.13
1634 1730 0.039618 TTGGGAGGATTGGAGCCAAC 59.960 55.000 3.70 0.00 38.88 3.77
1949 2045 7.986889 TGAGTAAATTGCTCTACATATTCTGCA 59.013 33.333 12.07 0.00 34.30 4.41
2072 2168 3.615224 TGGGGTCGATGTAAAACTACC 57.385 47.619 0.00 0.00 0.00 3.18
2075 2171 4.070009 GAGTTTGGGGTCGATGTAAAACT 58.930 43.478 14.98 14.98 39.77 2.66
2162 2258 1.300620 TGGAAACGAGTGACGCCTG 60.301 57.895 0.00 0.00 46.94 4.85
2290 2386 1.433837 GGCGGTCTTGTTGTTGTCGT 61.434 55.000 0.00 0.00 0.00 4.34
2310 2427 1.022735 GCCAGCTTGTCATCATGAGG 58.977 55.000 0.00 0.00 0.00 3.86
2378 2495 3.263503 CTCGCGACTCCACCGTTCA 62.264 63.158 3.71 0.00 0.00 3.18
2465 2582 2.278330 CCCTTGCCCTTGCTTGGTC 61.278 63.158 0.00 0.00 38.71 4.02
2516 2633 1.180029 CAATGGCTTCCTTGGACAGG 58.820 55.000 0.00 0.00 45.64 4.00
2771 2889 4.072131 GCAAAACCTTGAGATCAGTGGTA 58.928 43.478 9.13 0.00 34.87 3.25
2849 2967 4.406456 TCTCCAACCATTGTACTTGCATT 58.594 39.130 0.00 0.00 0.00 3.56
2861 2979 2.187958 TCCATCGTCTTCTCCAACCAT 58.812 47.619 0.00 0.00 0.00 3.55
2901 3019 5.934781 CCTCTAGGGCATATTTTCTTCAGT 58.065 41.667 0.00 0.00 0.00 3.41
2915 3033 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
2973 3091 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
2974 3092 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
2975 3093 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
2976 3094 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
2977 3095 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
2978 3096 7.554835 TGTTTCCGGTTAATACAATTCTAGCAT 59.445 33.333 0.00 0.00 0.00 3.79
2979 3097 6.879993 TGTTTCCGGTTAATACAATTCTAGCA 59.120 34.615 0.00 0.00 0.00 3.49
2980 3098 7.311364 TGTTTCCGGTTAATACAATTCTAGC 57.689 36.000 0.00 0.00 0.00 3.42
2981 3099 9.104965 TCATGTTTCCGGTTAATACAATTCTAG 57.895 33.333 0.00 0.00 0.00 2.43
2982 3100 9.621629 ATCATGTTTCCGGTTAATACAATTCTA 57.378 29.630 0.00 0.00 0.00 2.10
2984 3102 9.659830 GTATCATGTTTCCGGTTAATACAATTC 57.340 33.333 0.00 0.00 0.00 2.17
2985 3103 9.179909 TGTATCATGTTTCCGGTTAATACAATT 57.820 29.630 0.00 0.00 0.00 2.32
2988 3106 7.771361 ACATGTATCATGTTTCCGGTTAATACA 59.229 33.333 0.00 7.97 34.10 2.29
2989 3107 8.067784 CACATGTATCATGTTTCCGGTTAATAC 58.932 37.037 11.89 2.60 0.00 1.89
2990 3108 7.771361 ACACATGTATCATGTTTCCGGTTAATA 59.229 33.333 11.89 0.00 0.00 0.98
2991 3109 6.601613 ACACATGTATCATGTTTCCGGTTAAT 59.398 34.615 11.89 0.00 0.00 1.40
2993 3111 5.352846 CACACATGTATCATGTTTCCGGTTA 59.647 40.000 11.89 0.00 0.00 2.85
2995 3113 3.689161 CACACATGTATCATGTTTCCGGT 59.311 43.478 11.89 5.17 0.00 5.28
2996 3114 3.938334 TCACACATGTATCATGTTTCCGG 59.062 43.478 11.89 0.00 0.00 5.14
2997 3115 5.544136 TTCACACATGTATCATGTTTCCG 57.456 39.130 11.89 4.94 0.00 4.30
3001 3119 9.836864 ACTATGTATTCACACATGTATCATGTT 57.163 29.630 11.89 1.93 39.46 2.71
3002 3120 9.481340 GACTATGTATTCACACATGTATCATGT 57.519 33.333 9.21 9.21 39.46 3.21
3003 3121 9.480053 TGACTATGTATTCACACATGTATCATG 57.520 33.333 0.00 7.99 39.46 3.07
3008 3126 8.931775 GTGTTTGACTATGTATTCACACATGTA 58.068 33.333 0.00 0.00 39.46 2.29
3009 3127 7.443879 TGTGTTTGACTATGTATTCACACATGT 59.556 33.333 0.00 0.00 39.46 3.21
3010 3128 7.805700 TGTGTTTGACTATGTATTCACACATG 58.194 34.615 0.00 0.00 39.46 3.21
3016 3134 9.366216 GTGACTATGTGTTTGACTATGTATTCA 57.634 33.333 0.00 0.00 0.00 2.57
3017 3135 9.587772 AGTGACTATGTGTTTGACTATGTATTC 57.412 33.333 0.00 0.00 0.00 1.75
3024 3142 8.188799 GCATACTAGTGACTATGTGTTTGACTA 58.811 37.037 5.39 0.00 0.00 2.59
3026 3144 6.255887 GGCATACTAGTGACTATGTGTTTGAC 59.744 42.308 5.39 0.00 0.00 3.18
3027 3145 6.154534 AGGCATACTAGTGACTATGTGTTTGA 59.845 38.462 5.39 0.00 35.12 2.69
3028 3146 6.341316 AGGCATACTAGTGACTATGTGTTTG 58.659 40.000 5.39 0.00 35.12 2.93
3029 3147 6.381420 AGAGGCATACTAGTGACTATGTGTTT 59.619 38.462 5.39 0.00 37.66 2.83
3031 3149 5.450453 AGAGGCATACTAGTGACTATGTGT 58.550 41.667 5.39 0.00 37.66 3.72
3032 3150 6.712998 AGTAGAGGCATACTAGTGACTATGTG 59.287 42.308 5.39 0.00 37.66 3.21
3033 3151 6.843752 AGTAGAGGCATACTAGTGACTATGT 58.156 40.000 5.39 0.00 37.66 2.29
3034 3152 7.753309 AAGTAGAGGCATACTAGTGACTATG 57.247 40.000 5.39 2.12 37.66 2.23
3035 3153 9.287373 GTTAAGTAGAGGCATACTAGTGACTAT 57.713 37.037 5.39 0.00 37.66 2.12
3036 3154 8.492782 AGTTAAGTAGAGGCATACTAGTGACTA 58.507 37.037 5.39 0.00 37.66 2.59
3039 3157 7.444792 GCTAGTTAAGTAGAGGCATACTAGTGA 59.555 40.741 19.55 0.00 37.18 3.41
3041 3159 7.519927 AGCTAGTTAAGTAGAGGCATACTAGT 58.480 38.462 19.55 0.00 37.18 2.57
3043 3161 7.515586 TGAGCTAGTTAAGTAGAGGCATACTA 58.484 38.462 19.55 0.00 34.90 1.82
3045 3163 6.636562 TGAGCTAGTTAAGTAGAGGCATAC 57.363 41.667 19.55 1.94 0.00 2.39
3048 3166 7.655521 TTAATGAGCTAGTTAAGTAGAGGCA 57.344 36.000 19.55 13.34 0.00 4.75
3049 3167 8.361139 TGATTAATGAGCTAGTTAAGTAGAGGC 58.639 37.037 19.55 6.71 0.00 4.70
3057 3175 9.905713 ACCATCTTTGATTAATGAGCTAGTTAA 57.094 29.630 0.00 5.72 0.00 2.01
3059 3177 8.814038 AACCATCTTTGATTAATGAGCTAGTT 57.186 30.769 0.00 0.00 0.00 2.24
3062 3180 9.851686 ACATAACCATCTTTGATTAATGAGCTA 57.148 29.630 0.00 0.00 0.00 3.32
3064 3182 9.807649 AAACATAACCATCTTTGATTAATGAGC 57.192 29.630 0.00 0.00 0.00 4.26
3069 3187 9.527157 TCAGGAAACATAACCATCTTTGATTAA 57.473 29.630 0.00 0.00 0.00 1.40
3071 3189 7.093771 GGTCAGGAAACATAACCATCTTTGATT 60.094 37.037 0.00 0.00 0.00 2.57
3072 3190 6.378280 GGTCAGGAAACATAACCATCTTTGAT 59.622 38.462 0.00 0.00 0.00 2.57
3073 3191 5.710099 GGTCAGGAAACATAACCATCTTTGA 59.290 40.000 0.00 0.00 0.00 2.69
3074 3192 5.476599 TGGTCAGGAAACATAACCATCTTTG 59.523 40.000 0.00 0.00 35.15 2.77
3075 3193 5.640147 TGGTCAGGAAACATAACCATCTTT 58.360 37.500 0.00 0.00 35.15 2.52
3077 3195 4.927267 TGGTCAGGAAACATAACCATCT 57.073 40.909 0.00 0.00 35.15 2.90
3078 3196 6.483640 GTCTATGGTCAGGAAACATAACCATC 59.516 42.308 8.50 0.00 45.30 3.51
3083 3201 6.823182 CACATGTCTATGGTCAGGAAACATAA 59.177 38.462 0.00 0.00 38.66 1.90
3084 3202 6.070251 ACACATGTCTATGGTCAGGAAACATA 60.070 38.462 0.00 0.00 38.66 2.29
3085 3203 5.188434 CACATGTCTATGGTCAGGAAACAT 58.812 41.667 0.00 0.00 38.66 2.71
3086 3204 4.041567 ACACATGTCTATGGTCAGGAAACA 59.958 41.667 0.00 0.00 38.66 2.83
3087 3205 4.579869 ACACATGTCTATGGTCAGGAAAC 58.420 43.478 0.00 0.00 38.66 2.78
3089 3207 4.041567 ACAACACATGTCTATGGTCAGGAA 59.958 41.667 0.00 0.00 37.96 3.36
3091 3209 3.942829 ACAACACATGTCTATGGTCAGG 58.057 45.455 0.00 0.00 37.96 3.86
3103 3239 7.321908 TCCCATTAATCAAATGACAACACATG 58.678 34.615 0.00 0.00 46.81 3.21
3106 3242 7.489113 GTGATCCCATTAATCAAATGACAACAC 59.511 37.037 0.00 0.00 46.81 3.32
3108 3244 7.546358 TGTGATCCCATTAATCAAATGACAAC 58.454 34.615 0.00 0.00 46.81 3.32
3112 3248 8.715190 ATGATGTGATCCCATTAATCAAATGA 57.285 30.769 0.00 0.00 46.81 2.57
3115 3251 9.081204 CCTAATGATGTGATCCCATTAATCAAA 57.919 33.333 0.00 0.00 35.04 2.69
3116 3252 8.447200 TCCTAATGATGTGATCCCATTAATCAA 58.553 33.333 0.00 0.00 35.04 2.57
3118 3254 8.324306 TCTCCTAATGATGTGATCCCATTAATC 58.676 37.037 0.00 0.00 33.84 1.75
3119 3255 8.223378 TCTCCTAATGATGTGATCCCATTAAT 57.777 34.615 0.00 0.00 33.84 1.40
3120 3256 7.631510 TCTCCTAATGATGTGATCCCATTAA 57.368 36.000 0.00 0.00 33.84 1.40
3134 4660 7.567458 TGTCAATCACATCATTCTCCTAATGA 58.433 34.615 3.13 3.13 40.50 2.57
3135 4661 7.797038 TGTCAATCACATCATTCTCCTAATG 57.203 36.000 0.00 0.00 0.00 1.90
3137 4663 7.797038 CATGTCAATCACATCATTCTCCTAA 57.203 36.000 0.00 0.00 44.60 2.69


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

AutoCloner maintained by Alex Coulton.