Multiple sequence alignment - TraesCS6D01G405000

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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 TraesCS6D01G405000 chr6D 100.000 7346 0 0 1 7346 472503283 472495938 0.000000e+00 13566.0
1 TraesCS6D01G405000 chr6D 92.308 611 43 3 5 613 75890105 75889497 0.000000e+00 865.0
2 TraesCS6D01G405000 chr6D 85.109 685 65 11 3931 4597 472427259 472426594 0.000000e+00 665.0
3 TraesCS6D01G405000 chr6D 82.861 776 75 21 2352 3094 472428685 472427935 1.730000e-180 643.0
4 TraesCS6D01G405000 chr6D 84.832 567 47 11 5225 5783 472425767 472425232 1.080000e-147 534.0
5 TraesCS6D01G405000 chr6D 79.564 734 86 28 735 1441 472430341 472429645 4.010000e-127 466.0
6 TraesCS6D01G405000 chr6D 83.368 487 54 12 3329 3811 472427934 472427471 6.810000e-115 425.0
7 TraesCS6D01G405000 chr6D 90.957 188 14 1 6020 6204 472423749 472423562 4.400000e-62 250.0
8 TraesCS6D01G405000 chr6D 91.772 158 13 0 1030 1187 472491908 472491751 3.450000e-53 220.0
9 TraesCS6D01G405000 chr6D 79.580 333 42 13 6198 6518 472423514 472423196 1.610000e-51 215.0
10 TraesCS6D01G405000 chr6D 95.556 90 4 0 4872 4961 472426448 472426359 2.140000e-30 145.0
11 TraesCS6D01G405000 chr6D 81.379 145 16 7 3792 3925 472427465 472427321 2.800000e-19 108.0
12 TraesCS6D01G405000 chr1A 97.537 2883 63 5 3647 6523 2645383 2642503 0.000000e+00 4924.0
13 TraesCS6D01G405000 chr1A 92.972 1921 104 15 718 2608 2648118 2646199 0.000000e+00 2771.0
14 TraesCS6D01G405000 chr1A 96.057 837 14 3 2704 3537 2646200 2645380 0.000000e+00 1345.0
15 TraesCS6D01G405000 chr1A 81.445 1412 174 50 1722 3094 2843035 2841673 0.000000e+00 1075.0
16 TraesCS6D01G405000 chr1A 85.088 684 68 10 3931 4597 2840997 2840331 0.000000e+00 667.0
17 TraesCS6D01G405000 chr1A 95.396 391 18 0 6878 7268 2642507 2642117 2.250000e-174 623.0
18 TraesCS6D01G405000 chr1A 79.728 883 126 26 2979 3811 2657983 2657104 2.280000e-164 590.0
19 TraesCS6D01G405000 chr1A 91.059 425 36 2 6846 7268 2695375 2694951 2.300000e-159 573.0
20 TraesCS6D01G405000 chr1A 84.982 566 46 19 5225 5782 2839469 2838935 8.390000e-149 538.0
21 TraesCS6D01G405000 chr1A 81.359 574 79 19 6198 6758 2653338 2652780 6.760000e-120 442.0
22 TraesCS6D01G405000 chr1A 85.126 437 57 4 1724 2160 2658460 2658032 2.430000e-119 440.0
23 TraesCS6D01G405000 chr1A 80.157 635 67 22 3329 3925 2841672 2841059 3.170000e-113 420.0
24 TraesCS6D01G405000 chr1A 82.888 374 54 8 5781 6151 2653817 2653451 1.980000e-85 327.0
25 TraesCS6D01G405000 chr1A 79.794 485 69 16 6579 7046 2836928 2836456 7.110000e-85 326.0
26 TraesCS6D01G405000 chr1A 99.048 105 1 0 618 722 2648269 2648165 9.730000e-44 189.0
27 TraesCS6D01G405000 chr1A 91.803 61 2 1 894 954 2659115 2659058 1.700000e-11 82.4
28 TraesCS6D01G405000 chr6B 89.593 2700 204 42 727 3393 717420688 717418033 0.000000e+00 3358.0
29 TraesCS6D01G405000 chr6B 91.128 1082 73 3 6210 7268 717415191 717414110 0.000000e+00 1445.0
30 TraesCS6D01G405000 chr6B 86.608 1135 84 23 3723 4810 717418026 717416913 0.000000e+00 1192.0
31 TraesCS6D01G405000 chr6B 89.290 859 35 13 4957 5813 717416512 717415709 0.000000e+00 1024.0
32 TraesCS6D01G405000 chr6B 82.746 1078 108 29 3928 4959 717401333 717400288 0.000000e+00 889.0
33 TraesCS6D01G405000 chr6B 84.270 801 85 20 2298 3094 717141647 717140884 0.000000e+00 743.0
34 TraesCS6D01G405000 chr6B 79.543 1139 140 44 1149 2237 717403952 717402857 0.000000e+00 726.0
35 TraesCS6D01G405000 chr6B 85.526 684 65 10 3931 4597 717140208 717139542 0.000000e+00 684.0
36 TraesCS6D01G405000 chr6B 92.373 354 25 1 5850 6203 717415603 717415252 3.060000e-138 503.0
37 TraesCS6D01G405000 chr6B 88.329 377 42 2 2281 2656 717402859 717402484 1.120000e-122 451.0
38 TraesCS6D01G405000 chr6B 88.127 379 24 2 5225 5603 717138671 717138314 1.460000e-116 431.0
39 TraesCS6D01G405000 chr6B 81.784 538 65 17 917 1437 717143210 717142689 3.170000e-113 420.0
40 TraesCS6D01G405000 chr6B 78.931 636 73 28 3329 3925 717140883 717140270 6.960000e-100 375.0
41 TraesCS6D01G405000 chr6B 78.102 548 95 20 6198 6740 717389724 717389197 2.560000e-84 324.0
42 TraesCS6D01G405000 chr6B 83.060 366 48 10 5781 6143 717399194 717398840 3.310000e-83 320.0
43 TraesCS6D01G405000 chr6B 90.783 217 18 1 4957 5173 717138889 717138675 9.330000e-74 289.0
44 TraesCS6D01G405000 chr6B 83.904 292 41 5 6979 7268 717389198 717388911 2.610000e-69 274.0
45 TraesCS6D01G405000 chr6B 90.957 188 14 1 6020 6204 717137670 717137483 4.400000e-62 250.0
46 TraesCS6D01G405000 chr6B 77.538 325 43 15 6208 6518 717137425 717137117 1.270000e-37 169.0
47 TraesCS6D01G405000 chr6B 96.667 90 3 0 4872 4961 717416819 717416730 4.590000e-32 150.0
48 TraesCS6D01G405000 chr6B 96.591 88 3 0 4872 4959 717139366 717139279 5.940000e-31 147.0
49 TraesCS6D01G405000 chr6B 96.471 85 3 0 7262 7346 9429246 9429330 2.760000e-29 141.0
50 TraesCS6D01G405000 chr6B 96.341 82 3 0 7265 7346 628238617 628238698 1.290000e-27 135.0
51 TraesCS6D01G405000 chr6B 91.429 70 6 0 6624 6693 717137068 717136999 6.070000e-16 97.1
52 TraesCS6D01G405000 chr6B 87.719 57 4 2 894 950 717404034 717403981 6.150000e-06 63.9
53 TraesCS6D01G405000 chr6A 91.733 2395 152 19 1561 3935 617318791 617321159 0.000000e+00 3284.0
54 TraesCS6D01G405000 chr6A 93.154 1373 80 10 4835 6204 617322028 617323389 0.000000e+00 2002.0
55 TraesCS6D01G405000 chr6A 91.158 1097 64 12 6198 7268 617323437 617324526 0.000000e+00 1458.0
56 TraesCS6D01G405000 chr6A 81.219 1411 169 56 1722 3094 617553236 617554588 0.000000e+00 1050.0
57 TraesCS6D01G405000 chr6A 90.439 774 33 13 3928 4685 617321190 617321938 0.000000e+00 981.0
58 TraesCS6D01G405000 chr6A 80.048 1248 140 58 3448 4616 617237217 617238434 0.000000e+00 824.0
59 TraesCS6D01G405000 chr6A 77.763 1475 192 75 1125 2525 617234888 617236300 0.000000e+00 782.0
60 TraesCS6D01G405000 chr6A 83.707 847 60 34 731 1532 617317979 617318792 0.000000e+00 728.0
61 TraesCS6D01G405000 chr6A 83.208 798 86 23 4186 4961 617350455 617351226 0.000000e+00 688.0
62 TraesCS6D01G405000 chr6A 81.362 896 107 20 3928 4787 617224323 617225194 0.000000e+00 675.0
63 TraesCS6D01G405000 chr6A 83.796 648 62 22 5175 5783 617351536 617352179 6.390000e-160 575.0
64 TraesCS6D01G405000 chr6A 85.159 566 44 11 5226 5783 617557081 617557614 1.800000e-150 544.0
65 TraesCS6D01G405000 chr6A 82.126 649 65 28 718 1323 617217232 617217872 6.580000e-140 508.0
66 TraesCS6D01G405000 chr6A 77.323 1001 131 51 1143 2094 617348294 617349247 3.060000e-138 503.0
67 TraesCS6D01G405000 chr6A 85.068 442 43 9 5778 6204 617239798 617240231 5.270000e-116 429.0
68 TraesCS6D01G405000 chr6A 78.611 720 83 28 2221 2900 617222870 617223558 1.910000e-110 411.0
69 TraesCS6D01G405000 chr6A 83.442 459 48 13 997 1441 617552412 617552856 1.150000e-107 401.0
70 TraesCS6D01G405000 chr6A 91.882 271 21 1 5412 5682 617239443 617239712 1.930000e-100 377.0
71 TraesCS6D01G405000 chr6A 84.198 424 28 16 6198 6594 617240279 617240690 6.960000e-100 375.0
72 TraesCS6D01G405000 chr6A 82.313 441 53 13 5778 6201 617352203 617352635 7.010000e-95 359.0
73 TraesCS6D01G405000 chr6A 82.338 385 36 18 2979 3337 617236723 617237101 9.260000e-79 305.0
74 TraesCS6D01G405000 chr6A 85.714 294 36 6 6979 7268 617354319 617354610 9.260000e-79 305.0
75 TraesCS6D01G405000 chr6A 89.286 224 24 0 6209 6432 617352697 617352920 1.560000e-71 281.0
76 TraesCS6D01G405000 chr6A 80.758 343 41 10 6212 6532 617226838 617227177 2.050000e-60 244.0
77 TraesCS6D01G405000 chr6A 81.139 281 29 6 3329 3606 617554589 617554848 3.470000e-48 204.0
78 TraesCS6D01G405000 chr6A 83.744 203 32 1 1001 1202 617246649 617246851 2.710000e-44 191.0
79 TraesCS6D01G405000 chr6A 87.500 168 18 2 3645 3811 617555170 617555335 2.710000e-44 191.0
80 TraesCS6D01G405000 chr6A 86.932 176 14 6 6584 6758 617354139 617354306 9.730000e-44 189.0
81 TraesCS6D01G405000 chr6A 94.068 118 7 0 6434 6551 617353960 617354077 5.860000e-41 180.0
82 TraesCS6D01G405000 chr6A 76.946 334 44 12 6198 6518 617559307 617559620 7.630000e-35 159.0
83 TraesCS6D01G405000 chr6A 94.318 88 5 0 4872 4959 617556390 617556477 1.290000e-27 135.0
84 TraesCS6D01G405000 chr6A 94.203 69 4 0 3339 3407 617237159 617237227 1.010000e-18 106.0
85 TraesCS6D01G405000 chr6A 93.939 66 4 0 6596 6661 617240716 617240781 4.690000e-17 100.0
86 TraesCS6D01G405000 chr6A 92.063 63 4 1 3864 3925 617555423 617555485 3.650000e-13 87.9
87 TraesCS6D01G405000 chr2D 93.617 611 35 2 5 613 86524647 86525255 0.000000e+00 909.0
88 TraesCS6D01G405000 chr2D 91.857 614 43 4 1 613 429202361 429202968 0.000000e+00 850.0
89 TraesCS6D01G405000 chr2D 91.396 616 50 3 9 623 7275980 7276593 0.000000e+00 841.0
90 TraesCS6D01G405000 chr7D 92.683 615 45 0 1 615 170587332 170586718 0.000000e+00 887.0
91 TraesCS6D01G405000 chr7D 92.244 606 44 3 9 613 373243225 373243828 0.000000e+00 856.0
92 TraesCS6D01G405000 chr7D 80.000 545 81 18 2049 2576 194244100 194244633 1.930000e-100 377.0
93 TraesCS6D01G405000 chr7D 98.795 83 1 0 7264 7346 555059204 555059286 1.650000e-31 148.0
94 TraesCS6D01G405000 chr7D 96.341 82 3 0 7265 7346 22654148 22654067 1.290000e-27 135.0
95 TraesCS6D01G405000 chr3D 92.659 613 41 4 1 613 50542041 50542649 0.000000e+00 880.0
96 TraesCS6D01G405000 chr3D 91.928 607 47 2 10 615 580619197 580618592 0.000000e+00 848.0
97 TraesCS6D01G405000 chr3D 97.531 81 1 1 7267 7346 475549956 475549876 3.570000e-28 137.0
98 TraesCS6D01G405000 chr4D 91.721 616 39 4 1 615 488494354 488494958 0.000000e+00 845.0
99 TraesCS6D01G405000 chr7A 79.736 227 41 4 6208 6430 203968734 203968959 7.630000e-35 159.0
100 TraesCS6D01G405000 chr3B 97.561 82 2 0 7265 7346 755478791 755478710 2.760000e-29 141.0
101 TraesCS6D01G405000 chr3B 97.500 80 2 0 7267 7346 254192881 254192960 3.570000e-28 137.0
102 TraesCS6D01G405000 chr3B 95.122 82 4 0 7265 7346 807441466 807441385 5.980000e-26 130.0
103 TraesCS6D01G405000 chr4A 96.386 83 3 0 7264 7346 541366917 541366999 3.570000e-28 137.0


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 TraesCS6D01G405000 chr6D 472495938 472503283 7345 True 13566.000000 13566 100.000000 1 7346 1 chr6D.!!$R3 7345
1 TraesCS6D01G405000 chr6D 75889497 75890105 608 True 865.000000 865 92.308000 5 613 1 chr6D.!!$R1 608
2 TraesCS6D01G405000 chr6D 472423196 472430341 7145 True 383.444444 665 84.800667 735 6518 9 chr6D.!!$R4 5783
3 TraesCS6D01G405000 chr1A 2642117 2648269 6152 True 1970.400000 4924 96.202000 618 7268 5 chr1A.!!$R2 6650
4 TraesCS6D01G405000 chr1A 2836456 2843035 6579 True 605.200000 1075 82.293200 1722 7046 5 chr1A.!!$R4 5324
5 TraesCS6D01G405000 chr1A 2652780 2659115 6335 True 376.280000 590 84.180800 894 6758 5 chr1A.!!$R3 5864
6 TraesCS6D01G405000 chr6B 717414110 717420688 6578 True 1278.666667 3358 90.943167 727 7268 6 chr6B.!!$R4 6541
7 TraesCS6D01G405000 chr6B 717398840 717404034 5194 True 489.980000 889 84.279400 894 6143 5 chr6B.!!$R3 5249
8 TraesCS6D01G405000 chr6B 717136999 717143210 6211 True 360.510000 743 86.593600 917 6693 10 chr6B.!!$R1 5776
9 TraesCS6D01G405000 chr6B 717388911 717389724 813 True 299.000000 324 81.003000 6198 7268 2 chr6B.!!$R2 1070
10 TraesCS6D01G405000 chr6A 617317979 617324526 6547 False 1690.600000 3284 90.038200 731 7268 5 chr6A.!!$F5 6537
11 TraesCS6D01G405000 chr6A 617217232 617217872 640 False 508.000000 508 82.126000 718 1323 1 chr6A.!!$F1 605
12 TraesCS6D01G405000 chr6A 617222870 617227177 4307 False 443.333333 675 80.243667 2221 6532 3 chr6A.!!$F3 4311
13 TraesCS6D01G405000 chr6A 617234888 617240781 5893 False 412.250000 824 86.179875 1125 6661 8 chr6A.!!$F4 5536
14 TraesCS6D01G405000 chr6A 617348294 617354610 6316 False 385.000000 688 85.330000 1143 7268 8 chr6A.!!$F6 6125
15 TraesCS6D01G405000 chr6A 617552412 617559620 7208 False 346.487500 1050 85.223250 997 6518 8 chr6A.!!$F7 5521
16 TraesCS6D01G405000 chr2D 86524647 86525255 608 False 909.000000 909 93.617000 5 613 1 chr2D.!!$F2 608
17 TraesCS6D01G405000 chr2D 429202361 429202968 607 False 850.000000 850 91.857000 1 613 1 chr2D.!!$F3 612
18 TraesCS6D01G405000 chr2D 7275980 7276593 613 False 841.000000 841 91.396000 9 623 1 chr2D.!!$F1 614
19 TraesCS6D01G405000 chr7D 170586718 170587332 614 True 887.000000 887 92.683000 1 615 1 chr7D.!!$R2 614
20 TraesCS6D01G405000 chr7D 373243225 373243828 603 False 856.000000 856 92.244000 9 613 1 chr7D.!!$F2 604
21 TraesCS6D01G405000 chr7D 194244100 194244633 533 False 377.000000 377 80.000000 2049 2576 1 chr7D.!!$F1 527
22 TraesCS6D01G405000 chr3D 50542041 50542649 608 False 880.000000 880 92.659000 1 613 1 chr3D.!!$F1 612
23 TraesCS6D01G405000 chr3D 580618592 580619197 605 True 848.000000 848 91.928000 10 615 1 chr3D.!!$R2 605
24 TraesCS6D01G405000 chr4D 488494354 488494958 604 False 845.000000 845 91.721000 1 615 1 chr4D.!!$F1 614

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
823 904 0.250467 TGAAGAGCTTGGACACAGCC 60.250 55.000 0.00 0.00 0.00 4.85 F
1781 2329 0.107459 GGTCCATTGCCTCTGTCCTC 60.107 60.000 0.00 0.00 0.00 3.71 F
1788 2336 2.355193 GCCTCTGTCCTCGAAGCCT 61.355 63.158 0.00 0.00 0.00 4.58 F
2945 3760 2.340337 GAATCAAACTGCAATGGTGGC 58.660 47.619 0.00 0.00 0.00 5.01 F
3653 4896 5.222631 CAAAGAAGTGACTGGGTATTTTGC 58.777 41.667 0.00 0.00 0.00 3.68 F
3962 5342 1.421268 TGTGTCTGCCTGAGTTGGATT 59.579 47.619 0.00 0.00 0.00 3.01 F
4462 5873 2.624364 TGTAAAGGTGTGAGACTGCGTA 59.376 45.455 0.00 0.00 0.00 4.42 F
5668 9129 2.180276 GGTCCTGGAGCTTCAGTTCTA 58.820 52.381 20.85 0.51 33.14 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2545 0.752009 TAAAGGGCGCACAAACCACA 60.752 50.000 14.57 0.0 0.00 4.17 R
2635 3361 0.986019 ACTCCCCAACACACAGGACA 60.986 55.000 0.00 0.0 0.00 4.02 R
3083 3918 2.412429 TGTCGCGCGTTGTATGTTATTT 59.588 40.909 30.98 0.0 0.00 1.40 R
3815 5123 0.968901 ACGAGTCCGGGTCTGCAATA 60.969 55.000 0.00 0.0 40.78 1.90 R
4548 5959 2.113860 TGTGAGATGCTAACTTGCCC 57.886 50.000 0.00 0.0 0.00 5.36 R
4955 7312 5.378292 TGCATTGCTTTTATGGTCGTTTA 57.622 34.783 10.49 0.0 0.00 2.01 R
6090 10929 1.715519 CACGCGAAAAGAAATGCCAAG 59.284 47.619 15.93 0.0 0.00 3.61 R
7030 13093 1.270839 CCGCCATTATCCCGATGAAGT 60.271 52.381 0.00 0.0 0.00 3.01 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
251 252 2.317609 CCTCTGGAACACGGCGTTG 61.318 63.158 11.19 8.99 38.19 4.10
359 360 5.361100 GCGTCGTCTAGTTTTTAGTGTTTC 58.639 41.667 0.00 0.00 0.00 2.78
615 630 1.745653 GCCCATTGGAGTTGCTCTTAC 59.254 52.381 3.62 0.00 0.00 2.34
616 631 2.879756 GCCCATTGGAGTTGCTCTTACA 60.880 50.000 3.62 0.00 0.00 2.41
621 636 3.423539 TGGAGTTGCTCTTACATTGCT 57.576 42.857 0.00 0.00 0.00 3.91
759 825 6.195700 TGTTTTTATCCGGGGGAATTAATGA 58.804 36.000 0.00 0.00 34.34 2.57
807 873 3.196913 TAGGTCGCGTGCGTGTGAA 62.197 57.895 14.47 0.00 40.74 3.18
821 902 1.869767 GTGTGAAGAGCTTGGACACAG 59.130 52.381 14.02 0.00 41.09 3.66
822 903 0.871057 GTGAAGAGCTTGGACACAGC 59.129 55.000 0.00 0.00 0.00 4.40
823 904 0.250467 TGAAGAGCTTGGACACAGCC 60.250 55.000 0.00 0.00 0.00 4.85
824 905 1.294659 GAAGAGCTTGGACACAGCCG 61.295 60.000 0.00 0.00 0.00 5.52
825 906 3.426568 GAGCTTGGACACAGCCGC 61.427 66.667 0.00 0.00 0.00 6.53
826 907 3.890936 GAGCTTGGACACAGCCGCT 62.891 63.158 0.00 0.00 31.89 5.52
827 908 2.047274 GCTTGGACACAGCCGCTA 60.047 61.111 0.00 0.00 0.00 4.26
828 909 2.103042 GCTTGGACACAGCCGCTAG 61.103 63.158 0.00 0.00 0.00 3.42
829 910 1.293498 CTTGGACACAGCCGCTAGT 59.707 57.895 0.00 0.00 0.00 2.57
830 911 1.005037 TTGGACACAGCCGCTAGTG 60.005 57.895 16.59 16.59 41.40 2.74
915 1039 4.157289 CACTGGTAACGTAAGCTTCTCCTA 59.843 45.833 0.00 0.00 45.62 2.94
946 1070 3.249752 CCTCTCCATCTCCATCTCCATT 58.750 50.000 0.00 0.00 0.00 3.16
954 1078 4.701651 TCTCCATCTCCATTTCCATCTG 57.298 45.455 0.00 0.00 0.00 2.90
965 1098 2.898729 TTCCATCTGCGAGGAATCTC 57.101 50.000 0.00 0.00 38.91 2.75
966 1099 1.780503 TCCATCTGCGAGGAATCTCA 58.219 50.000 0.00 0.00 39.95 3.27
967 1100 1.410517 TCCATCTGCGAGGAATCTCAC 59.589 52.381 0.00 0.00 39.95 3.51
969 1102 0.387202 ATCTGCGAGGAATCTCACCG 59.613 55.000 0.00 0.00 39.95 4.94
970 1103 1.880340 CTGCGAGGAATCTCACCGC 60.880 63.158 0.00 0.00 45.28 5.68
972 1105 2.278857 CGAGGAATCTCACCGCGG 60.279 66.667 26.86 26.86 44.39 6.46
1003 1151 1.152881 GCAGCCAGGGGAACTATGG 60.153 63.158 0.00 0.00 39.33 2.74
1013 1161 3.697439 GAACTATGGCGGGGCAGCA 62.697 63.158 6.53 0.00 39.27 4.41
1224 1376 0.390603 CGTACGTTGCCCAAGATCCA 60.391 55.000 7.22 0.00 0.00 3.41
1225 1377 1.816074 GTACGTTGCCCAAGATCCAA 58.184 50.000 0.00 0.00 0.00 3.53
1493 1830 5.594317 ACATGATGGTCTATTTGGTAAAGGC 59.406 40.000 0.00 0.00 0.00 4.35
1497 1834 5.514500 TGGTCTATTTGGTAAAGGCTTCT 57.486 39.130 0.00 0.00 0.00 2.85
1527 1878 2.126882 AGTTATGCATAGCCTCACCCA 58.873 47.619 16.04 0.00 0.00 4.51
1781 2329 0.107459 GGTCCATTGCCTCTGTCCTC 60.107 60.000 0.00 0.00 0.00 3.71
1788 2336 2.355193 GCCTCTGTCCTCGAAGCCT 61.355 63.158 0.00 0.00 0.00 4.58
1874 2422 4.553351 GCAGGCAAAATTTTCAACTCAAGC 60.553 41.667 0.00 0.00 0.00 4.01
1934 2483 5.381757 TGTAGTTCTTTGTATTTGTGGGCT 58.618 37.500 0.00 0.00 0.00 5.19
2044 2600 3.653164 TCATAACTCTAGGCCACATGGA 58.347 45.455 5.01 0.00 37.39 3.41
2173 2732 4.445735 GGGAATATTTCTTCGGATGGTGGA 60.446 45.833 0.00 0.00 0.00 4.02
2231 2796 8.844865 TGGAGCATGGTATGAAGATATATACT 57.155 34.615 0.00 0.00 31.92 2.12
2283 2907 4.967036 TCATGTCACATGTGGTCTGTTTA 58.033 39.130 25.16 0.44 0.00 2.01
2635 3361 7.116376 CGACTCATCTAACTTTGTGTTGTACAT 59.884 37.037 0.00 0.00 39.48 2.29
2945 3760 2.340337 GAATCAAACTGCAATGGTGGC 58.660 47.619 0.00 0.00 0.00 5.01
3641 4599 5.289595 GGAAATGAAACCCAAAGAAGTGAC 58.710 41.667 0.00 0.00 0.00 3.67
3653 4896 5.222631 CAAAGAAGTGACTGGGTATTTTGC 58.777 41.667 0.00 0.00 0.00 3.68
3962 5342 1.421268 TGTGTCTGCCTGAGTTGGATT 59.579 47.619 0.00 0.00 0.00 3.01
4187 5591 5.633655 TGTACAAACCTTCCTGTCCTAAA 57.366 39.130 0.00 0.00 0.00 1.85
4462 5873 2.624364 TGTAAAGGTGTGAGACTGCGTA 59.376 45.455 0.00 0.00 0.00 4.42
4548 5959 3.871594 ACGACTTCTTTTCACCTGACTTG 59.128 43.478 0.00 0.00 0.00 3.16
4601 6315 7.433708 TTCATGTCTTCGTGAAACATTATGT 57.566 32.000 0.00 0.00 43.74 2.29
4602 6316 7.433708 TCATGTCTTCGTGAAACATTATGTT 57.566 32.000 4.56 4.56 43.41 2.71
4603 6317 7.297391 TCATGTCTTCGTGAAACATTATGTTG 58.703 34.615 11.60 0.00 40.14 3.33
4604 6318 5.996219 TGTCTTCGTGAAACATTATGTTGG 58.004 37.500 11.60 2.42 40.14 3.77
4605 6319 4.851558 GTCTTCGTGAAACATTATGTTGGC 59.148 41.667 11.60 7.66 40.14 4.52
4606 6320 3.840890 TCGTGAAACATTATGTTGGCC 57.159 42.857 11.60 0.00 40.14 5.36
4611 6325 5.296748 GTGAAACATTATGTTGGCCAGTTT 58.703 37.500 11.60 14.75 40.14 2.66
4616 6330 8.916628 AAACATTATGTTGGCCAGTTTATTTT 57.083 26.923 11.60 3.17 40.14 1.82
4678 6454 6.073112 CCATTTTCCTTTTGTTATGCACTTGG 60.073 38.462 0.00 0.00 0.00 3.61
5524 8019 2.669569 TGCCGCTGCAGGTTTCTC 60.670 61.111 17.12 0.00 44.23 2.87
5668 9129 2.180276 GGTCCTGGAGCTTCAGTTCTA 58.820 52.381 20.85 0.51 33.14 2.10
5819 9323 3.819564 ATAAATGAGTAGCTCGCCACA 57.180 42.857 0.00 0.00 32.35 4.17
5983 10522 9.983024 TTGATGGGGAAGAATAGTGTAAAATAA 57.017 29.630 0.00 0.00 0.00 1.40
6304 11252 0.476338 TGCCCCAAACAGTGAAGCTA 59.524 50.000 0.00 0.00 0.00 3.32
6442 12429 1.143684 AGGATGGTTGCTGTTGACTGT 59.856 47.619 0.00 0.00 0.00 3.55
6580 12586 3.810623 TCCTTCAGTACACCCCCTTAAT 58.189 45.455 0.00 0.00 0.00 1.40
6598 12645 8.704668 CCCCTTAATAGAAAATATTGGCAGTTT 58.295 33.333 0.00 0.00 0.00 2.66
6769 12817 5.569355 TCTCCTTTCATCTGCCAATTAACA 58.431 37.500 0.00 0.00 0.00 2.41
6869 12927 5.876612 GCTGATGGAGAAGCTAATATTGG 57.123 43.478 0.00 0.00 36.47 3.16
6870 12928 5.312079 GCTGATGGAGAAGCTAATATTGGT 58.688 41.667 0.00 0.00 36.47 3.67
6871 12929 6.467677 GCTGATGGAGAAGCTAATATTGGTA 58.532 40.000 0.00 0.00 36.47 3.25
6873 12931 8.260818 GCTGATGGAGAAGCTAATATTGGTATA 58.739 37.037 0.00 0.00 36.47 1.47
7088 13151 7.601856 TGACCGCTTTTTATGAATCAGATTTT 58.398 30.769 0.00 0.00 0.00 1.82
7268 13333 8.243426 ACAATAATATGTGCAACTGTGTTTAGG 58.757 33.333 0.00 0.00 38.04 2.69
7269 13334 5.643379 AATATGTGCAACTGTGTTTAGGG 57.357 39.130 0.00 0.00 38.04 3.53
7270 13335 1.028905 TGTGCAACTGTGTTTAGGGC 58.971 50.000 0.00 0.00 38.04 5.19
7271 13336 1.318576 GTGCAACTGTGTTTAGGGCT 58.681 50.000 0.00 0.00 0.00 5.19
7272 13337 1.266989 GTGCAACTGTGTTTAGGGCTC 59.733 52.381 0.00 0.00 0.00 4.70
7273 13338 0.881796 GCAACTGTGTTTAGGGCTCC 59.118 55.000 0.00 0.00 0.00 4.70
7274 13339 1.545651 GCAACTGTGTTTAGGGCTCCT 60.546 52.381 0.00 0.00 37.71 3.69
7275 13340 2.863809 CAACTGTGTTTAGGGCTCCTT 58.136 47.619 0.00 0.00 34.61 3.36
7276 13341 3.222603 CAACTGTGTTTAGGGCTCCTTT 58.777 45.455 0.00 0.00 34.61 3.11
7277 13342 2.863809 ACTGTGTTTAGGGCTCCTTTG 58.136 47.619 0.00 0.00 34.61 2.77
7278 13343 2.441750 ACTGTGTTTAGGGCTCCTTTGA 59.558 45.455 0.00 0.00 34.61 2.69
7279 13344 3.074538 ACTGTGTTTAGGGCTCCTTTGAT 59.925 43.478 0.00 0.00 34.61 2.57
7280 13345 4.082125 CTGTGTTTAGGGCTCCTTTGATT 58.918 43.478 0.00 0.00 34.61 2.57
7281 13346 4.079253 TGTGTTTAGGGCTCCTTTGATTC 58.921 43.478 0.00 0.00 34.61 2.52
7282 13347 4.079253 GTGTTTAGGGCTCCTTTGATTCA 58.921 43.478 0.00 0.00 34.61 2.57
7283 13348 4.522789 GTGTTTAGGGCTCCTTTGATTCAA 59.477 41.667 0.00 0.00 34.61 2.69
7284 13349 5.010617 GTGTTTAGGGCTCCTTTGATTCAAA 59.989 40.000 11.19 11.19 34.61 2.69
7298 13363 8.792830 CTTTGATTCAAAGGACTTACATAGGA 57.207 34.615 25.14 0.00 44.75 2.94
7299 13364 9.231297 CTTTGATTCAAAGGACTTACATAGGAA 57.769 33.333 25.14 0.00 44.75 3.36
7300 13365 9.753674 TTTGATTCAAAGGACTTACATAGGAAT 57.246 29.630 7.74 0.00 0.00 3.01
7301 13366 9.753674 TTGATTCAAAGGACTTACATAGGAATT 57.246 29.630 0.00 0.00 0.00 2.17
7302 13367 9.753674 TGATTCAAAGGACTTACATAGGAATTT 57.246 29.630 0.00 0.00 0.00 1.82
7305 13370 8.348285 TCAAAGGACTTACATAGGAATTTTGG 57.652 34.615 0.00 0.00 0.00 3.28
7306 13371 8.167392 TCAAAGGACTTACATAGGAATTTTGGA 58.833 33.333 0.00 0.00 0.00 3.53
7307 13372 8.462016 CAAAGGACTTACATAGGAATTTTGGAG 58.538 37.037 0.00 0.00 0.00 3.86
7308 13373 6.663734 AGGACTTACATAGGAATTTTGGAGG 58.336 40.000 0.00 0.00 0.00 4.30
7309 13374 6.447084 AGGACTTACATAGGAATTTTGGAGGA 59.553 38.462 0.00 0.00 0.00 3.71
7310 13375 7.129504 AGGACTTACATAGGAATTTTGGAGGAT 59.870 37.037 0.00 0.00 0.00 3.24
7311 13376 7.445707 GGACTTACATAGGAATTTTGGAGGATC 59.554 40.741 0.00 0.00 0.00 3.36
7312 13377 7.872138 ACTTACATAGGAATTTTGGAGGATCA 58.128 34.615 0.00 0.00 36.25 2.92
7313 13378 8.506083 ACTTACATAGGAATTTTGGAGGATCAT 58.494 33.333 0.00 0.00 36.25 2.45
7317 13382 9.525826 ACATAGGAATTTTGGAGGATCATAATC 57.474 33.333 0.00 0.00 36.25 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 3.224324 GTCGCCCCGAGCCAGATA 61.224 66.667 0.00 0.00 36.23 1.98
464 479 4.114997 CCATTTTTCCGGCGCGCT 62.115 61.111 32.29 4.96 0.00 5.92
473 488 0.526211 GCTGGTCCGACCCATTTTTC 59.474 55.000 15.24 0.00 37.50 2.29
508 523 2.186160 CAGCGCTGTGTTTGGGTCA 61.186 57.895 29.24 0.00 0.00 4.02
615 630 4.142609 TGAGCTTACTTCCCTAGCAATG 57.857 45.455 0.00 0.00 37.37 2.82
616 631 4.518249 GTTGAGCTTACTTCCCTAGCAAT 58.482 43.478 0.00 0.00 37.37 3.56
621 636 2.667473 GCGTTGAGCTTACTTCCCTA 57.333 50.000 0.00 0.00 44.04 3.53
807 873 2.345244 CGGCTGTGTCCAAGCTCT 59.655 61.111 0.00 0.00 0.00 4.09
823 904 4.473520 CTGGGGGTGGCACTAGCG 62.474 72.222 18.45 0.00 43.41 4.26
824 905 1.345715 ATACTGGGGGTGGCACTAGC 61.346 60.000 18.45 0.11 41.10 3.42
825 906 1.213296 AATACTGGGGGTGGCACTAG 58.787 55.000 18.45 12.81 0.00 2.57
826 907 1.283613 CAAATACTGGGGGTGGCACTA 59.716 52.381 18.45 0.65 0.00 2.74
827 908 0.039618 CAAATACTGGGGGTGGCACT 59.960 55.000 18.45 0.00 0.00 4.40
828 909 1.604147 GCAAATACTGGGGGTGGCAC 61.604 60.000 9.70 9.70 0.00 5.01
829 910 1.304879 GCAAATACTGGGGGTGGCA 60.305 57.895 0.00 0.00 0.00 4.92
830 911 0.687427 ATGCAAATACTGGGGGTGGC 60.687 55.000 0.00 0.00 0.00 5.01
836 917 2.792500 TGCCGATGCAAATACTGGG 58.208 52.632 0.00 0.00 46.66 4.45
854 935 3.392228 TCCAAGCTGGATCACGCT 58.608 55.556 2.46 2.46 42.67 5.07
892 1008 3.056749 AGGAGAAGCTTACGTTACCAGTG 60.057 47.826 0.00 0.00 0.00 3.66
915 1039 2.553438 GATGGAGAGGGGTGGGAGGT 62.553 65.000 0.00 0.00 0.00 3.85
946 1070 2.110578 TGAGATTCCTCGCAGATGGAA 58.889 47.619 0.00 0.00 43.81 3.53
954 1078 2.956964 CGCGGTGAGATTCCTCGC 60.957 66.667 0.00 0.00 46.43 5.03
984 1132 1.639635 CCATAGTTCCCCTGGCTGCT 61.640 60.000 0.00 0.00 0.00 4.24
1085 1233 3.818787 CAGGACGCTTGGGCATGC 61.819 66.667 9.90 9.90 38.60 4.06
1224 1376 9.475620 TCCATACGTATAGATCCTGATTGTATT 57.524 33.333 7.96 0.00 0.00 1.89
1225 1377 9.647918 ATCCATACGTATAGATCCTGATTGTAT 57.352 33.333 10.26 0.00 0.00 2.29
1459 1796 9.591792 CAAATAGACCATCATGTATCATCGTAT 57.408 33.333 0.00 0.00 0.00 3.06
1527 1878 3.672503 GGGACCCCTGCACCCAAT 61.673 66.667 0.00 0.00 42.81 3.16
1781 2329 6.072452 GGAATATCCCAAATTAAGAGGCTTCG 60.072 42.308 0.00 0.00 0.00 3.79
1788 2336 7.060421 GTGTCCTGGAATATCCCAAATTAAGA 58.940 38.462 0.00 0.00 35.03 2.10
1874 2422 1.094785 CCAGAACCCGCCAACATTAG 58.905 55.000 0.00 0.00 0.00 1.73
1934 2483 1.256895 CGCGACGACAAACTTTGAAGA 59.743 47.619 0.00 0.00 0.00 2.87
1996 2545 0.752009 TAAAGGGCGCACAAACCACA 60.752 50.000 14.57 0.00 0.00 4.17
2044 2600 8.522178 TCTAAACGACAAACACAAAAATTGTT 57.478 26.923 0.00 0.00 43.23 2.83
2053 2609 8.885722 ACTAAAATCTTCTAAACGACAAACACA 58.114 29.630 0.00 0.00 0.00 3.72
2173 2732 3.701040 ACTTTGCTTCAAACTGGACATGT 59.299 39.130 0.00 0.00 0.00 3.21
2231 2796 8.827832 ACATGAAGGAGGAAATGATGAAATAA 57.172 30.769 0.00 0.00 0.00 1.40
2283 2907 9.337396 ACGTGGAAAATTATATCACATACACAT 57.663 29.630 0.00 0.00 0.00 3.21
2346 2985 6.677781 TGTAAAACTGAAAGGTTCACTCAG 57.322 37.500 0.00 0.00 43.11 3.35
2609 3309 5.907197 ACAACACAAAGTTAGATGAGTCG 57.093 39.130 0.00 0.00 38.74 4.18
2635 3361 0.986019 ACTCCCCAACACACAGGACA 60.986 55.000 0.00 0.00 0.00 4.02
2945 3760 3.259064 CATTTCCAAGCTGGCATGAAAG 58.741 45.455 0.00 0.00 37.47 2.62
3083 3918 2.412429 TGTCGCGCGTTGTATGTTATTT 59.588 40.909 30.98 0.00 0.00 1.40
3128 3968 6.788243 TGACATCATGATTATGACAAGCAAC 58.212 36.000 5.16 0.00 45.54 4.17
3489 4440 4.080526 ACAATTAACGCCCTTCATCTAGGT 60.081 41.667 0.00 0.00 33.17 3.08
3496 4450 5.155278 TCTCTAACAATTAACGCCCTTCA 57.845 39.130 0.00 0.00 0.00 3.02
3641 4599 4.036380 GGGTCGATAAAGCAAAATACCCAG 59.964 45.833 0.00 0.00 43.95 4.45
3653 4896 5.390991 GCTTGTGAAGAAAGGGTCGATAAAG 60.391 44.000 0.00 0.00 0.00 1.85
3786 5068 8.137745 TCCTGGCTATTCATTGAAAAAGAAAT 57.862 30.769 13.47 0.00 37.07 2.17
3815 5123 0.968901 ACGAGTCCGGGTCTGCAATA 60.969 55.000 0.00 0.00 40.78 1.90
4187 5591 4.721776 ACCACTCCTAACCACATGTATCAT 59.278 41.667 0.00 0.00 0.00 2.45
4361 5768 8.488651 TTCCTGAAATTTCTCCGTAGATAAAC 57.511 34.615 18.64 0.00 0.00 2.01
4462 5873 2.138320 CACAGCGACACATTGAAGAGT 58.862 47.619 0.00 0.00 0.00 3.24
4548 5959 2.113860 TGTGAGATGCTAACTTGCCC 57.886 50.000 0.00 0.00 0.00 5.36
4596 6310 6.211584 TGGCTAAAATAAACTGGCCAACATAA 59.788 34.615 7.01 0.00 45.16 1.90
4597 6311 5.717178 TGGCTAAAATAAACTGGCCAACATA 59.283 36.000 7.01 0.00 45.16 2.29
4598 6312 4.530161 TGGCTAAAATAAACTGGCCAACAT 59.470 37.500 7.01 0.00 45.16 2.71
4599 6313 3.898123 TGGCTAAAATAAACTGGCCAACA 59.102 39.130 7.01 0.00 45.16 3.33
4600 6314 4.529109 TGGCTAAAATAAACTGGCCAAC 57.471 40.909 7.01 0.00 45.16 3.77
4602 6316 3.257127 GTGTGGCTAAAATAAACTGGCCA 59.743 43.478 4.71 4.71 45.81 5.36
4603 6317 3.257127 TGTGTGGCTAAAATAAACTGGCC 59.743 43.478 0.00 0.00 39.93 5.36
4604 6318 4.513198 TGTGTGGCTAAAATAAACTGGC 57.487 40.909 0.00 0.00 0.00 4.85
4605 6319 8.250332 ACATATTGTGTGGCTAAAATAAACTGG 58.750 33.333 0.00 0.00 40.28 4.00
4865 6813 8.723942 ATACAAACAAGAAATAGAGCTGTAGG 57.276 34.615 0.00 0.00 0.00 3.18
4955 7312 5.378292 TGCATTGCTTTTATGGTCGTTTA 57.622 34.783 10.49 0.00 0.00 2.01
5819 9323 5.962031 GGTTTTAATGGGTAGGGAAAGGATT 59.038 40.000 0.00 0.00 0.00 3.01
6090 10929 1.715519 CACGCGAAAAGAAATGCCAAG 59.284 47.619 15.93 0.00 0.00 3.61
6304 11252 2.877786 TGTCGTCATGTGCTTCATTTGT 59.122 40.909 0.00 0.00 34.09 2.83
6580 12586 9.995003 AAATGACAAAACTGCCAATATTTTCTA 57.005 25.926 0.00 0.00 0.00 2.10
6670 12717 8.830915 ATCCTTATTCCACGAGATGTATAGAT 57.169 34.615 0.00 0.00 0.00 1.98
6769 12817 5.939764 AAAAAGAAGGAAAACAAGGAGCT 57.060 34.783 0.00 0.00 0.00 4.09
6799 12857 3.700539 TGGTGGCAAATCGATCAAATGAT 59.299 39.130 0.00 0.00 37.51 2.45
6869 12927 8.718102 ATGTCATTAGTTGTCAAGTGGTATAC 57.282 34.615 2.99 0.00 0.00 1.47
6871 12929 9.905713 AATATGTCATTAGTTGTCAAGTGGTAT 57.094 29.630 2.99 0.00 0.00 2.73
6873 12931 8.514594 CAAATATGTCATTAGTTGTCAAGTGGT 58.485 33.333 2.99 0.00 0.00 4.16
7030 13093 1.270839 CCGCCATTATCCCGATGAAGT 60.271 52.381 0.00 0.00 0.00 3.01
7274 13339 9.753674 ATTCCTATGTAAGTCCTTTGAATCAAA 57.246 29.630 8.25 8.25 0.00 2.69
7275 13340 9.753674 AATTCCTATGTAAGTCCTTTGAATCAA 57.246 29.630 0.00 0.00 0.00 2.57
7276 13341 9.753674 AAATTCCTATGTAAGTCCTTTGAATCA 57.246 29.630 0.00 0.00 0.00 2.57
7279 13344 8.802267 CCAAAATTCCTATGTAAGTCCTTTGAA 58.198 33.333 0.00 0.00 0.00 2.69
7280 13345 8.167392 TCCAAAATTCCTATGTAAGTCCTTTGA 58.833 33.333 0.00 0.00 0.00 2.69
7281 13346 8.348285 TCCAAAATTCCTATGTAAGTCCTTTG 57.652 34.615 0.00 0.00 0.00 2.77
7282 13347 7.615757 CCTCCAAAATTCCTATGTAAGTCCTTT 59.384 37.037 0.00 0.00 0.00 3.11
7283 13348 7.036863 TCCTCCAAAATTCCTATGTAAGTCCTT 60.037 37.037 0.00 0.00 0.00 3.36
7284 13349 6.447084 TCCTCCAAAATTCCTATGTAAGTCCT 59.553 38.462 0.00 0.00 0.00 3.85
7285 13350 6.659824 TCCTCCAAAATTCCTATGTAAGTCC 58.340 40.000 0.00 0.00 0.00 3.85
7286 13351 7.993183 TGATCCTCCAAAATTCCTATGTAAGTC 59.007 37.037 0.00 0.00 0.00 3.01
7287 13352 7.872138 TGATCCTCCAAAATTCCTATGTAAGT 58.128 34.615 0.00 0.00 0.00 2.24
7288 13353 8.930846 ATGATCCTCCAAAATTCCTATGTAAG 57.069 34.615 0.00 0.00 0.00 2.34
7291 13356 9.525826 GATTATGATCCTCCAAAATTCCTATGT 57.474 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.