Multiple sequence alignment - TraesCS5A01G537900

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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 TraesCS5A01G537900 chr5A 100.000 9485 0 0 1 9485 694571029 694580513 0.000000e+00 17442.0
1 TraesCS5A01G537900 chr5A 99.218 2815 22 0 6671 9485 694556168 694558982 0.000000e+00 5077.0
2 TraesCS5A01G537900 chr5A 99.890 2737 2 1 1 2736 694530227 694532963 0.000000e+00 5036.0
3 TraesCS5A01G537900 chr5A 99.817 2737 4 1 1 2736 694550658 694553394 0.000000e+00 5025.0
4 TraesCS5A01G537900 chr5A 99.151 2710 22 1 6776 9485 694535868 694538576 0.000000e+00 4876.0
5 TraesCS5A01G537900 chr5A 96.490 1966 54 4 2714 4675 694533026 694534980 0.000000e+00 3234.0
6 TraesCS5A01G537900 chr5A 85.620 1975 253 18 6677 8635 704369961 704371920 0.000000e+00 2045.0
7 TraesCS5A01G537900 chr5A 89.633 1254 121 3 1101 2345 704368586 704369839 0.000000e+00 1587.0
8 TraesCS5A01G537900 chr5A 99.213 762 6 0 4686 5447 671396171 671396932 0.000000e+00 1375.0
9 TraesCS5A01G537900 chr5A 81.865 1373 210 23 1000 2338 708848074 708849441 0.000000e+00 1120.0
10 TraesCS5A01G537900 chr5A 87.654 405 48 2 5906 6310 430028007 430028409 4.010000e-128 470.0
11 TraesCS5A01G537900 chr5A 92.063 252 17 2 670 919 704367642 704367892 1.520000e-92 351.0
12 TraesCS5A01G537900 chr5A 88.583 254 27 2 6407 6660 430028711 430028962 3.330000e-79 307.0
13 TraesCS5A01G537900 chr5A 93.333 180 11 1 2392 2570 229211656 229211835 2.030000e-66 265.0
14 TraesCS5A01G537900 chr5A 96.178 157 6 0 4516 4672 626130301 626130457 3.400000e-64 257.0
15 TraesCS5A01G537900 chr5A 97.143 35 1 0 942 976 704368549 704368583 1.030000e-04 60.2
16 TraesCS5A01G537900 chrUn 99.899 1977 0 1 4686 6660 360700196 360702172 0.000000e+00 3639.0
17 TraesCS5A01G537900 chrUn 94.571 1805 92 4 2714 4514 82678659 82680461 0.000000e+00 2785.0
18 TraesCS5A01G537900 chrUn 89.101 1413 135 11 6678 8076 264519337 264520744 0.000000e+00 1738.0
19 TraesCS5A01G537900 chrUn 99.084 764 7 0 4690 5453 380913930 380913167 0.000000e+00 1373.0
20 TraesCS5A01G537900 chrUn 88.939 895 99 0 1447 2341 264518339 264519233 0.000000e+00 1105.0
21 TraesCS5A01G537900 chrUn 85.242 454 53 7 8177 8620 264520826 264521275 1.120000e-123 455.0
22 TraesCS5A01G537900 chrUn 82.895 152 26 0 9082 9233 264521418 264521569 4.620000e-28 137.0
23 TraesCS5A01G537900 chr4B 99.899 1977 0 1 4686 6660 189798378 189796402 0.000000e+00 3639.0
24 TraesCS5A01G537900 chr4B 86.098 1971 209 37 6678 8620 659499463 659497530 0.000000e+00 2061.0
25 TraesCS5A01G537900 chr4B 88.818 1413 138 11 6678 8075 659483929 659482522 0.000000e+00 1716.0
26 TraesCS5A01G537900 chr4B 86.315 1308 163 8 1048 2341 659485338 659484033 0.000000e+00 1410.0
27 TraesCS5A01G537900 chr4B 86.236 1315 157 13 1048 2341 659513648 659512337 0.000000e+00 1404.0
28 TraesCS5A01G537900 chr4B 85.920 1321 156 17 1048 2341 659500884 659499567 0.000000e+00 1382.0
29 TraesCS5A01G537900 chr4B 94.839 465 22 2 5435 5899 258987860 258988322 0.000000e+00 725.0
30 TraesCS5A01G537900 chr4B 94.468 470 24 2 5435 5904 365087073 365086606 0.000000e+00 723.0
31 TraesCS5A01G537900 chr4B 83.810 525 56 16 8111 8620 659482522 659482012 1.110000e-128 472.0
32 TraesCS5A01G537900 chr4B 96.203 237 9 0 9249 9485 242249091 242248855 1.160000e-103 388.0
33 TraesCS5A01G537900 chr4B 91.111 180 15 1 2392 2570 29934478 29934299 9.520000e-60 243.0
34 TraesCS5A01G537900 chr4B 85.526 152 22 0 9082 9233 659481869 659481718 9.860000e-35 159.0
35 TraesCS5A01G537900 chr4B 82.895 152 25 1 9082 9233 659497390 659497240 1.660000e-27 135.0
36 TraesCS5A01G537900 chr3B 99.899 1977 0 1 4686 6660 802913614 802915590 0.000000e+00 3639.0
37 TraesCS5A01G537900 chr3B 93.669 537 30 4 5829 6365 481336590 481336058 0.000000e+00 800.0
38 TraesCS5A01G537900 chr3B 93.542 480 31 0 5408 5887 696518630 696518151 0.000000e+00 715.0
39 TraesCS5A01G537900 chr3B 88.396 293 34 0 6368 6660 481336013 481335721 4.210000e-93 353.0
40 TraesCS5A01G537900 chr1A 99.899 1977 0 1 4686 6660 100103544 100101568 0.000000e+00 3639.0
41 TraesCS5A01G537900 chr1A 92.381 210 11 2 1 208 557995085 557995291 2.590000e-75 294.0
42 TraesCS5A01G537900 chr1A 91.111 180 15 1 2392 2570 126539680 126539859 9.520000e-60 243.0
43 TraesCS5A01G537900 chr1A 92.727 110 8 0 476 585 535324237 535324128 9.860000e-35 159.0
44 TraesCS5A01G537900 chr7A 94.681 1805 90 4 2717 4517 95235714 95233912 0.000000e+00 2796.0
45 TraesCS5A01G537900 chr7A 94.460 1805 95 3 2717 4517 95228539 95226736 0.000000e+00 2774.0
46 TraesCS5A01G537900 chr7A 93.407 1805 113 4 2717 4517 571812574 571814376 0.000000e+00 2669.0
47 TraesCS5A01G537900 chr7A 93.352 1805 113 5 2714 4516 694613714 694615513 0.000000e+00 2662.0
48 TraesCS5A01G537900 chr7A 99.084 764 7 0 4690 5453 655940243 655939480 0.000000e+00 1373.0
49 TraesCS5A01G537900 chr7A 91.753 194 14 1 2379 2570 315530404 315530597 1.570000e-67 268.0
50 TraesCS5A01G537900 chr7A 95.541 157 7 0 4516 4672 116512076 116512232 1.580000e-62 252.0
51 TraesCS5A01G537900 chr7A 93.750 144 9 0 2566 2709 640634769 640634626 5.770000e-52 217.0
52 TraesCS5A01G537900 chr7A 100.000 31 0 0 2706 2736 79741002 79740972 3.700000e-04 58.4
53 TraesCS5A01G537900 chr6A 94.358 1790 93 6 2732 4517 104451485 104449700 0.000000e+00 2739.0
54 TraesCS5A01G537900 chr6A 93.968 1807 100 7 2714 4514 602741458 602743261 0.000000e+00 2724.0
55 TraesCS5A01G537900 chr6A 92.925 212 10 2 1 210 189198529 189198321 4.300000e-78 303.0
56 TraesCS5A01G537900 chr6A 92.019 213 11 2 1 210 194459118 194459327 2.590000e-75 294.0
57 TraesCS5A01G537900 chr6A 77.095 179 32 7 7557 7731 609154390 609154563 2.820000e-15 95.3
58 TraesCS5A01G537900 chr3A 93.622 1803 103 6 2717 4514 171126848 171125053 0.000000e+00 2682.0
59 TraesCS5A01G537900 chr3A 100.000 314 0 0 5829 6142 46040036 46039723 1.780000e-161 580.0
60 TraesCS5A01G537900 chr3A 95.851 241 9 1 9246 9485 465692551 465692791 1.160000e-103 388.0
61 TraesCS5A01G537900 chr2A 93.481 1810 102 11 2713 4514 76515808 76514007 0.000000e+00 2675.0
62 TraesCS5A01G537900 chr2A 94.937 158 8 0 4516 4673 362453603 362453446 2.050000e-61 248.0
63 TraesCS5A01G537900 chr2A 95.105 143 6 1 2565 2706 654337741 654337883 3.450000e-54 224.0
64 TraesCS5A01G537900 chr2A 93.750 144 9 0 2563 2706 689530129 689530272 5.770000e-52 217.0
65 TraesCS5A01G537900 chr4D 90.422 1681 146 11 670 2349 508339232 508340898 0.000000e+00 2198.0
66 TraesCS5A01G537900 chr4D 86.350 1978 235 17 6677 8635 508341016 508342977 0.000000e+00 2124.0
67 TraesCS5A01G537900 chr4D 91.844 1361 109 1 1023 2381 504518201 504519561 0.000000e+00 1897.0
68 TraesCS5A01G537900 chr4D 90.960 1239 105 4 6682 7916 504520349 504521584 0.000000e+00 1661.0
69 TraesCS5A01G537900 chr4D 89.623 742 76 1 7971 8711 504521584 504522325 0.000000e+00 942.0
70 TraesCS5A01G537900 chr4D 96.104 154 6 0 4516 4669 85684107 85683954 1.580000e-62 252.0
71 TraesCS5A01G537900 chr4D 91.061 179 16 0 2392 2570 104153251 104153073 9.520000e-60 243.0
72 TraesCS5A01G537900 chr4D 91.111 180 15 1 2392 2570 214923944 214924123 9.520000e-60 243.0
73 TraesCS5A01G537900 chr7B 99.519 832 4 0 5829 6660 72331426 72332257 0.000000e+00 1515.0
74 TraesCS5A01G537900 chr7B 99.219 768 6 0 4686 5453 108457782 108457015 0.000000e+00 1386.0
75 TraesCS5A01G537900 chr7B 96.203 237 9 0 9249 9485 313036922 313037158 1.160000e-103 388.0
76 TraesCS5A01G537900 chr7B 92.453 265 17 2 8717 8978 574415162 574415426 8.990000e-100 375.0
77 TraesCS5A01G537900 chr2B 98.647 813 11 0 5848 6660 102877901 102877089 0.000000e+00 1441.0
78 TraesCS5A01G537900 chr2B 94.255 470 27 0 5407 5876 289639268 289638799 0.000000e+00 719.0
79 TraesCS5A01G537900 chr2B 91.958 286 19 2 1 282 361646052 361646337 1.920000e-106 398.0
80 TraesCS5A01G537900 chr2B 78.075 187 41 0 7539 7725 20147053 20147239 1.670000e-22 119.0
81 TraesCS5A01G537900 chr5B 99.089 768 7 0 4686 5453 471936601 471937368 0.000000e+00 1380.0
82 TraesCS5A01G537900 chr1D 94.363 479 26 1 5407 5885 372470247 372470724 0.000000e+00 734.0
83 TraesCS5A01G537900 chr1D 96.753 154 5 0 4516 4669 483105310 483105463 3.400000e-64 257.0
84 TraesCS5A01G537900 chr1D 94.964 139 7 0 2568 2706 377577483 377577621 1.600000e-52 219.0
85 TraesCS5A01G537900 chr1D 90.000 110 11 0 476 585 439068362 439068253 9.930000e-30 143.0
86 TraesCS5A01G537900 chr7D 93.727 271 15 2 8703 8972 41057251 41057520 1.150000e-108 405.0
87 TraesCS5A01G537900 chr7D 91.549 284 19 3 1 279 10652344 10652627 4.150000e-103 387.0
88 TraesCS5A01G537900 chr7D 96.178 157 6 0 4516 4672 444357077 444356921 3.400000e-64 257.0
89 TraesCS5A01G537900 chr7D 90.957 188 15 2 2385 2570 119016619 119016432 1.580000e-62 252.0
90 TraesCS5A01G537900 chr7D 95.139 144 7 0 2566 2709 207910944 207910801 2.660000e-55 228.0
91 TraesCS5A01G537900 chr7D 93.750 144 8 1 2567 2709 432695202 432695059 2.070000e-51 215.0
92 TraesCS5A01G537900 chr2D 92.527 281 19 1 1 279 290742806 290743086 1.480000e-107 401.0
93 TraesCS5A01G537900 chr2D 96.203 237 9 0 9249 9485 299096728 299096964 1.160000e-103 388.0
94 TraesCS5A01G537900 chr2D 93.182 264 17 1 8708 8971 37526875 37526613 4.150000e-103 387.0
95 TraesCS5A01G537900 chr2D 92.996 257 18 0 8719 8975 583317276 583317020 8.990000e-100 375.0
96 TraesCS5A01G537900 chr2D 95.484 155 7 0 4516 4670 76640590 76640744 2.050000e-61 248.0
97 TraesCS5A01G537900 chr2D 77.033 209 48 0 7529 7737 12626168 12625960 4.650000e-23 121.0
98 TraesCS5A01G537900 chr6B 92.527 281 16 2 1 279 270780247 270780524 1.920000e-106 398.0
99 TraesCS5A01G537900 chr6B 89.439 303 26 6 8709 9008 4953243 4952944 2.500000e-100 377.0
100 TraesCS5A01G537900 chr6B 89.439 303 26 6 8709 9008 4975625 4975326 2.500000e-100 377.0
101 TraesCS5A01G537900 chr6B 91.209 273 21 2 10 279 270817462 270817734 1.500000e-97 368.0
102 TraesCS5A01G537900 chr6B 88.779 303 28 6 8709 9008 5033020 5032721 5.410000e-97 366.0
103 TraesCS5A01G537900 chr5D 96.218 238 8 1 9249 9485 406247777 406247540 1.160000e-103 388.0
104 TraesCS5A01G537900 chr5D 94.326 141 8 0 2569 2709 284116797 284116657 5.770000e-52 217.0
105 TraesCS5A01G537900 chr5D 85.859 99 10 4 6263 6360 175297288 175297193 1.690000e-17 102.0
106 TraesCS5A01G537900 chr1B 96.203 237 9 0 9249 9485 161974683 161974919 1.160000e-103 388.0
107 TraesCS5A01G537900 chr1B 96.203 237 9 0 9249 9485 615218803 615218567 1.160000e-103 388.0
108 TraesCS5A01G537900 chr1B 91.818 110 9 0 476 585 595331554 595331445 4.590000e-33 154.0
109 TraesCS5A01G537900 chr6D 94.737 247 12 1 9239 9485 439669670 439669915 5.370000e-102 383.0
110 TraesCS5A01G537900 chr6D 93.023 258 17 1 8713 8970 270874221 270873965 8.990000e-100 375.0
111 TraesCS5A01G537900 chr6D 96.078 153 6 0 4516 4668 123976564 123976716 5.690000e-62 250.0
112 TraesCS5A01G537900 chr6D 75.912 137 32 1 7595 7731 462394300 462394435 1.710000e-07 69.4
113 TraesCS5A01G537900 chr3D 95.000 160 8 0 4514 4673 111763004 111763163 1.580000e-62 252.0
114 TraesCS5A01G537900 chr3D 93.750 144 9 0 2566 2709 24203406 24203263 5.770000e-52 217.0
115 TraesCS5A01G537900 chr4A 91.111 180 15 1 2392 2570 538737723 538737544 9.520000e-60 243.0


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 TraesCS5A01G537900 chr5A 694571029 694580513 9484 False 17442.000000 17442 100.000000 1 9485 1 chr5A.!!$F4 9484
1 TraesCS5A01G537900 chr5A 694550658 694558982 8324 False 5051.000000 5077 99.517500 1 9485 2 chr5A.!!$F8 9484
2 TraesCS5A01G537900 chr5A 694530227 694538576 8349 False 4382.000000 5036 98.510333 1 9485 3 chr5A.!!$F7 9484
3 TraesCS5A01G537900 chr5A 671396171 671396932 761 False 1375.000000 1375 99.213000 4686 5447 1 chr5A.!!$F3 761
4 TraesCS5A01G537900 chr5A 708848074 708849441 1367 False 1120.000000 1120 81.865000 1000 2338 1 chr5A.!!$F5 1338
5 TraesCS5A01G537900 chr5A 704367642 704371920 4278 False 1010.800000 2045 91.114750 670 8635 4 chr5A.!!$F9 7965
6 TraesCS5A01G537900 chr5A 430028007 430028962 955 False 388.500000 470 88.118500 5906 6660 2 chr5A.!!$F6 754
7 TraesCS5A01G537900 chrUn 360700196 360702172 1976 False 3639.000000 3639 99.899000 4686 6660 1 chrUn.!!$F2 1974
8 TraesCS5A01G537900 chrUn 82678659 82680461 1802 False 2785.000000 2785 94.571000 2714 4514 1 chrUn.!!$F1 1800
9 TraesCS5A01G537900 chrUn 380913167 380913930 763 True 1373.000000 1373 99.084000 4690 5453 1 chrUn.!!$R1 763
10 TraesCS5A01G537900 chrUn 264518339 264521569 3230 False 858.750000 1738 86.544250 1447 9233 4 chrUn.!!$F3 7786
11 TraesCS5A01G537900 chr4B 189796402 189798378 1976 True 3639.000000 3639 99.899000 4686 6660 1 chr4B.!!$R2 1974
12 TraesCS5A01G537900 chr4B 659512337 659513648 1311 True 1404.000000 1404 86.236000 1048 2341 1 chr4B.!!$R5 1293
13 TraesCS5A01G537900 chr4B 659497240 659500884 3644 True 1192.666667 2061 84.971000 1048 9233 3 chr4B.!!$R7 8185
14 TraesCS5A01G537900 chr4B 659481718 659485338 3620 True 939.250000 1716 86.117250 1048 9233 4 chr4B.!!$R6 8185
15 TraesCS5A01G537900 chr3B 802913614 802915590 1976 False 3639.000000 3639 99.899000 4686 6660 1 chr3B.!!$F1 1974
16 TraesCS5A01G537900 chr3B 481335721 481336590 869 True 576.500000 800 91.032500 5829 6660 2 chr3B.!!$R2 831
17 TraesCS5A01G537900 chr1A 100101568 100103544 1976 True 3639.000000 3639 99.899000 4686 6660 1 chr1A.!!$R1 1974
18 TraesCS5A01G537900 chr7A 95233912 95235714 1802 True 2796.000000 2796 94.681000 2717 4517 1 chr7A.!!$R3 1800
19 TraesCS5A01G537900 chr7A 95226736 95228539 1803 True 2774.000000 2774 94.460000 2717 4517 1 chr7A.!!$R2 1800
20 TraesCS5A01G537900 chr7A 571812574 571814376 1802 False 2669.000000 2669 93.407000 2717 4517 1 chr7A.!!$F3 1800
21 TraesCS5A01G537900 chr7A 694613714 694615513 1799 False 2662.000000 2662 93.352000 2714 4516 1 chr7A.!!$F4 1802
22 TraesCS5A01G537900 chr7A 655939480 655940243 763 True 1373.000000 1373 99.084000 4690 5453 1 chr7A.!!$R5 763
23 TraesCS5A01G537900 chr6A 104449700 104451485 1785 True 2739.000000 2739 94.358000 2732 4517 1 chr6A.!!$R1 1785
24 TraesCS5A01G537900 chr6A 602741458 602743261 1803 False 2724.000000 2724 93.968000 2714 4514 1 chr6A.!!$F2 1800
25 TraesCS5A01G537900 chr3A 171125053 171126848 1795 True 2682.000000 2682 93.622000 2717 4514 1 chr3A.!!$R2 1797
26 TraesCS5A01G537900 chr2A 76514007 76515808 1801 True 2675.000000 2675 93.481000 2713 4514 1 chr2A.!!$R1 1801
27 TraesCS5A01G537900 chr4D 508339232 508342977 3745 False 2161.000000 2198 88.386000 670 8635 2 chr4D.!!$F3 7965
28 TraesCS5A01G537900 chr4D 504518201 504522325 4124 False 1500.000000 1897 90.809000 1023 8711 3 chr4D.!!$F2 7688
29 TraesCS5A01G537900 chr7B 72331426 72332257 831 False 1515.000000 1515 99.519000 5829 6660 1 chr7B.!!$F1 831
30 TraesCS5A01G537900 chr7B 108457015 108457782 767 True 1386.000000 1386 99.219000 4686 5453 1 chr7B.!!$R1 767
31 TraesCS5A01G537900 chr2B 102877089 102877901 812 True 1441.000000 1441 98.647000 5848 6660 1 chr2B.!!$R1 812
32 TraesCS5A01G537900 chr5B 471936601 471937368 767 False 1380.000000 1380 99.089000 4686 5453 1 chr5B.!!$F1 767

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
2841 3620 4.506886 TCGGCCAAACACGATAAATTTT 57.493 36.364 2.24 0.00 33.69 1.82 F
3175 3961 0.760567 ATCGCTATGGAGTCCCTGCA 60.761 55.000 6.74 0.00 36.05 4.41 F
4627 5450 1.059994 GTTCAGATTCTGCTGCGCG 59.940 57.895 8.89 0.00 35.86 6.86 F
4628 5451 2.102438 TTCAGATTCTGCTGCGCGG 61.102 57.895 13.18 13.18 35.86 6.46 F
6838 9661 0.462581 ACTCATATGCGTGGTGCCTG 60.463 55.000 0.00 0.00 45.60 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4567 5390 3.266510 TCCGATTCCAGAAATCCACTG 57.733 47.619 0.00 0.0 40.69 3.66 R
4633 5456 3.454375 TCAGCTTTTATCGACGGATTCC 58.546 45.455 0.00 0.0 34.00 3.01 R
6838 9661 4.591072 ACCTCTAGAGCCATAGATCCAAAC 59.409 45.833 14.73 0.0 31.50 2.93 R
7411 10247 6.401394 AGTAATCCAAACTTCGGTTAGGTAC 58.599 40.000 0.00 0.0 37.14 3.34 R
9168 12078 1.398041 CGTGTCGCCATCATTGATGTT 59.602 47.619 21.95 0.0 38.28 2.71 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
2841 3620 4.506886 TCGGCCAAACACGATAAATTTT 57.493 36.364 2.24 0.00 33.69 1.82
3175 3961 0.760567 ATCGCTATGGAGTCCCTGCA 60.761 55.000 6.74 0.00 36.05 4.41
3443 4262 1.684450 GAAGATCGGGAGGAGGAAGAC 59.316 57.143 0.00 0.00 0.00 3.01
3544 4363 4.368808 CAACAGCGGGTCGTTGCG 62.369 66.667 4.20 0.00 41.50 4.85
3855 4675 2.997315 CGCTGAGTCTCCACCCCA 60.997 66.667 0.00 0.00 0.00 4.96
4028 4848 1.997040 GAGAGATAGAGGGAGGGGCTA 59.003 57.143 0.00 0.00 0.00 3.93
4221 5041 2.450476 GTGAGGAATCAATGGCAAGGT 58.550 47.619 0.00 0.00 0.00 3.50
4340 5160 3.357079 CGCCAAAACAGCTCGCCT 61.357 61.111 0.00 0.00 0.00 5.52
4567 5390 2.476241 CGCTTTTGGTTCAGATTTTGGC 59.524 45.455 0.00 0.00 0.00 4.52
4619 5442 1.351017 TCGCCCTTTGGTTCAGATTCT 59.649 47.619 0.00 0.00 0.00 2.40
4626 5449 1.300971 TGGTTCAGATTCTGCTGCGC 61.301 55.000 8.89 0.00 35.86 6.09
4627 5450 1.059994 GTTCAGATTCTGCTGCGCG 59.940 57.895 8.89 0.00 35.86 6.86
4628 5451 2.102438 TTCAGATTCTGCTGCGCGG 61.102 57.895 13.18 13.18 35.86 6.46
4629 5452 4.233635 CAGATTCTGCTGCGCGGC 62.234 66.667 34.00 34.00 34.49 6.53
4630 5453 4.765449 AGATTCTGCTGCGCGGCA 62.765 61.111 39.10 39.10 40.15 5.69
6838 9661 0.462581 ACTCATATGCGTGGTGCCTG 60.463 55.000 0.00 0.00 45.60 4.85
7411 10247 9.061610 ACGAAAAGCTTTTGATTTATGAATACG 57.938 29.630 28.42 20.51 37.00 3.06
7563 10404 5.574188 AGAAAATCACTACTCAATTGGCCT 58.426 37.500 3.32 0.00 0.00 5.19
8711 11621 9.784531 CCAGTCATTCAATGGACTAACTAATAT 57.215 33.333 0.00 0.00 42.22 1.28
9024 11934 2.992543 CGTTTTCTTCTCCTCTCTGCTG 59.007 50.000 0.00 0.00 0.00 4.41
9070 11980 5.337813 GGGAGATTTGACAGGAAATTTGCAT 60.338 40.000 12.54 0.00 0.00 3.96
9128 12038 1.202256 CGACATGCACTTCTACGCCTA 60.202 52.381 0.00 0.00 0.00 3.93
9465 12376 5.567138 ATGATGGCAAAAGTAACAGTAGC 57.433 39.130 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2557 3249 1.448540 CAGGGCCTAAGCGTGAGTG 60.449 63.158 5.28 0.0 41.24 3.51
2841 3620 1.169661 AACTTCGCCGAAATGTGCCA 61.170 50.000 0.00 0.0 0.00 4.92
2949 3729 2.124942 CAAGGAGGAGAAGGCCGC 60.125 66.667 0.00 0.0 0.00 6.53
3443 4262 2.044252 TTCGGGTCCTCCTCCTCG 60.044 66.667 0.00 0.0 0.00 4.63
3548 4367 1.511464 CGTGCTGACGTACCTCGAC 60.511 63.158 0.00 0.0 40.91 4.20
4567 5390 3.266510 TCCGATTCCAGAAATCCACTG 57.733 47.619 0.00 0.0 40.69 3.66
4633 5456 3.454375 TCAGCTTTTATCGACGGATTCC 58.546 45.455 0.00 0.0 34.00 3.01
4634 5457 4.260253 GGTTCAGCTTTTATCGACGGATTC 60.260 45.833 0.00 0.0 34.00 2.52
4635 5458 3.621715 GGTTCAGCTTTTATCGACGGATT 59.378 43.478 0.00 0.0 34.00 3.01
6838 9661 4.591072 ACCTCTAGAGCCATAGATCCAAAC 59.409 45.833 14.73 0.0 31.50 2.93
7411 10247 6.401394 AGTAATCCAAACTTCGGTTAGGTAC 58.599 40.000 0.00 0.0 37.14 3.34
8711 11621 8.211116 TGTAGACTAAAACAAAACGAATGGAA 57.789 30.769 0.00 0.0 0.00 3.53
9070 11980 1.411787 GGGAGGCTAGCTCTAGGTTCA 60.412 57.143 15.72 0.0 33.87 3.18
9128 12038 2.069273 CATCGGCTCACTTCGAAAAGT 58.931 47.619 0.00 0.0 46.80 2.66
9168 12078 1.398041 CGTGTCGCCATCATTGATGTT 59.602 47.619 21.95 0.0 38.28 2.71
9415 12326 6.696148 CCGTTACTTCCATACTACTTTGCTAG 59.304 42.308 0.00 0.0 0.00 3.42


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

AutoCloner maintained by Alex Coulton.