Multiple sequence alignment - TraesCS1B01G114800

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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 TraesCS1B01G114800 chr1B 100.000 5390 0 0 1 5390 134571562 134576951 0.000000e+00 9954.0
1 TraesCS1B01G114800 chr1B 97.533 1986 43 3 446 2430 134642713 134644693 0.000000e+00 3391.0
2 TraesCS1B01G114800 chr1B 98.374 1784 15 6 3607 5390 134645377 134647146 0.000000e+00 3121.0
3 TraesCS1B01G114800 chr1B 93.849 2016 94 7 2841 4853 134436387 134438375 0.000000e+00 3009.0
4 TraesCS1B01G114800 chr1B 88.927 1174 104 14 1623 2792 134435091 134436242 0.000000e+00 1424.0
5 TraesCS1B01G114800 chr1B 93.841 552 19 7 4302 4853 134450213 134450749 0.000000e+00 817.0
6 TraesCS1B01G114800 chr1B 98.701 385 4 1 1 384 134642346 134642730 0.000000e+00 682.0
7 TraesCS1B01G114800 chr1B 90.189 530 29 11 4325 4853 134452391 134452898 0.000000e+00 669.0
8 TraesCS1B01G114800 chr1B 91.667 396 17 6 2 384 134430254 134430646 7.950000e-148 534.0
9 TraesCS1B01G114800 chr1B 91.379 348 16 2 796 1141 134434755 134435090 1.060000e-126 464.0
10 TraesCS1B01G114800 chr1B 98.214 224 4 0 2556 2779 134645042 134645265 5.060000e-105 392.0
11 TraesCS1B01G114800 chr1B 93.284 268 11 5 5124 5390 134438756 134439017 6.550000e-104 388.0
12 TraesCS1B01G114800 chr1B 93.284 268 11 5 5124 5390 134451130 134451391 6.550000e-104 388.0
13 TraesCS1B01G114800 chr1B 90.647 278 14 9 4846 5122 134438401 134438667 5.130000e-95 359.0
14 TraesCS1B01G114800 chr1B 90.288 278 15 9 4846 5122 134450775 134451041 2.390000e-93 353.0
15 TraesCS1B01G114800 chr1B 91.600 250 17 4 446 695 134430629 134430874 5.170000e-90 342.0
16 TraesCS1B01G114800 chr1B 94.798 173 8 1 5218 5390 134455839 134456010 8.900000e-68 268.0
17 TraesCS1B01G114800 chr1B 81.979 283 31 9 4846 5127 134452924 134453187 7.030000e-54 222.0
18 TraesCS1B01G114800 chr1B 79.323 266 50 3 2528 2792 13278921 13278660 1.190000e-41 182.0
19 TraesCS1B01G114800 chr1B 80.591 237 39 5 3346 3580 660013012 660012781 5.550000e-40 176.0
20 TraesCS1B01G114800 chr1B 95.876 97 3 1 709 804 134433114 134433210 7.230000e-34 156.0
21 TraesCS1B01G114800 chr1B 92.000 50 3 1 2772 2820 134645328 134645377 9.690000e-08 69.4
22 TraesCS1B01G114800 chr1D 98.984 2066 20 1 2772 4836 81286679 81288744 0.000000e+00 3698.0
23 TraesCS1B01G114800 chr1D 97.888 1989 39 3 446 2433 81283962 81285948 0.000000e+00 3437.0
24 TraesCS1B01G114800 chr1D 92.854 2029 105 8 2838 4853 81177266 81179267 0.000000e+00 2907.0
25 TraesCS1B01G114800 chr1D 88.079 1166 105 17 1640 2792 81175980 81177124 0.000000e+00 1352.0
26 TraesCS1B01G114800 chr1D 99.284 559 4 0 4832 5390 81293793 81294351 0.000000e+00 1011.0
27 TraesCS1B01G114800 chr1D 91.803 549 29 6 4302 4845 81185020 81185557 0.000000e+00 750.0
28 TraesCS1B01G114800 chr1D 91.039 558 26 12 4298 4853 81182488 81183023 0.000000e+00 732.0
29 TraesCS1B01G114800 chr1D 93.274 446 16 3 698 1141 81175329 81175762 0.000000e+00 645.0
30 TraesCS1B01G114800 chr1D 92.191 397 16 5 1 384 81174274 81174668 1.020000e-151 547.0
31 TraesCS1B01G114800 chr1D 98.473 262 2 2 125 384 81283718 81283979 1.370000e-125 460.0
32 TraesCS1B01G114800 chr1D 94.403 268 8 5 5124 5390 81179647 81179908 6.500000e-109 405.0
33 TraesCS1B01G114800 chr1D 93.600 250 13 3 446 695 81174651 81174897 2.370000e-98 370.0
34 TraesCS1B01G114800 chr1D 90.614 277 15 8 4846 5122 81179293 81179558 1.850000e-94 357.0
35 TraesCS1B01G114800 chr1D 90.909 275 11 6 5124 5390 81183405 81183673 1.850000e-94 357.0
36 TraesCS1B01G114800 chr1D 96.591 176 4 1 2604 2779 81286443 81286616 1.900000e-74 291.0
37 TraesCS1B01G114800 chr1D 82.699 289 27 13 4846 5127 81183049 81183321 9.030000e-58 235.0
38 TraesCS1B01G114800 chr1D 98.413 126 2 0 1 126 81283489 81283614 7.030000e-54 222.0
39 TraesCS1B01G114800 chr1D 83.978 181 29 0 3297 3477 474900612 474900432 2.000000e-39 174.0
40 TraesCS1B01G114800 chr1D 81.579 190 31 4 3294 3481 18165978 18165791 2.600000e-33 154.0
41 TraesCS1B01G114800 chr1D 84.211 95 15 0 4220 4314 469811279 469811373 5.750000e-15 93.5
42 TraesCS1B01G114800 chr1D 72.238 353 79 10 4049 4390 18079325 18078981 2.070000e-14 91.6
43 TraesCS1B01G114800 chr1A 92.667 2032 106 15 2838 4853 99904934 99906938 0.000000e+00 2887.0
44 TraesCS1B01G114800 chr1A 87.617 1171 107 18 1627 2792 99903655 99904792 0.000000e+00 1325.0
45 TraesCS1B01G114800 chr1A 91.928 446 22 3 698 1141 99903217 99903650 3.570000e-171 612.0
46 TraesCS1B01G114800 chr1A 91.940 397 17 5 1 384 99897004 99897398 4.750000e-150 542.0
47 TraesCS1B01G114800 chr1A 95.506 267 9 2 5124 5390 99907326 99907589 1.790000e-114 424.0
48 TraesCS1B01G114800 chr1A 93.502 277 15 3 4846 5122 99906964 99907237 5.030000e-110 409.0
49 TraesCS1B01G114800 chr1A 94.393 214 10 2 483 695 99900285 99900497 1.450000e-85 327.0
50 TraesCS1B01G114800 chr1A 80.263 228 39 4 3251 3478 570423305 570423084 3.340000e-37 167.0
51 TraesCS1B01G114800 chr1A 74.167 360 71 14 4048 4390 20236951 20236597 4.380000e-26 130.0
52 TraesCS1B01G114800 chr1A 73.016 441 90 21 3969 4390 20245220 20244790 1.580000e-25 128.0
53 TraesCS1B01G114800 chr1A 87.755 98 11 1 2910 3007 380993455 380993551 4.410000e-21 113.0
54 TraesCS1B01G114800 chr7B 82.047 674 91 11 3522 4190 33012333 33011685 1.020000e-151 547.0
55 TraesCS1B01G114800 chr7B 83.681 288 38 5 3247 3526 33065379 33065093 4.140000e-66 263.0
56 TraesCS1B01G114800 chr7B 84.896 192 25 4 797 987 33066615 33066427 1.980000e-44 191.0
57 TraesCS1B01G114800 chr7B 82.081 173 31 0 1693 1865 33065544 33065372 1.210000e-31 148.0
58 TraesCS1B01G114800 chr4D 84.615 416 53 9 2838 3249 442885535 442885943 2.340000e-108 403.0
59 TraesCS1B01G114800 chr4D 84.135 416 55 7 2838 3249 442876248 442875840 5.060000e-105 392.0
60 TraesCS1B01G114800 chr6B 77.586 638 108 21 2165 2792 157792023 157792635 2.390000e-93 353.0
61 TraesCS1B01G114800 chr6B 92.105 76 5 1 377 452 439400484 439400558 7.380000e-19 106.0
62 TraesCS1B01G114800 chr7D 76.504 532 78 30 2264 2792 491859918 491860405 4.170000e-61 246.0
63 TraesCS1B01G114800 chr5A 77.512 418 64 20 2826 3241 79714427 79714816 1.950000e-54 224.0
64 TraesCS1B01G114800 chr5A 95.652 69 2 1 384 452 225602145 225602212 5.710000e-20 110.0
65 TraesCS1B01G114800 chr5D 82.105 190 34 0 2553 2742 446900959 446901148 4.320000e-36 163.0
66 TraesCS1B01G114800 chr5D 92.000 75 4 2 379 452 370419912 370419985 2.660000e-18 104.0
67 TraesCS1B01G114800 chr5D 89.062 64 7 0 2936 2999 495314665 495314728 4.480000e-11 80.5
68 TraesCS1B01G114800 chr2B 82.738 168 28 1 2525 2692 32866922 32866756 1.210000e-31 148.0
69 TraesCS1B01G114800 chr2B 74.919 307 58 10 2288 2591 777737780 777737490 7.330000e-24 122.0
70 TraesCS1B01G114800 chr6D 88.525 122 9 3 2932 3048 430039856 430039977 5.630000e-30 143.0
71 TraesCS1B01G114800 chr6D 91.250 80 3 4 374 452 268345760 268345836 7.380000e-19 106.0
72 TraesCS1B01G114800 chr3A 98.551 69 1 0 384 452 498783416 498783348 7.330000e-24 122.0
73 TraesCS1B01G114800 chr2D 97.101 69 2 0 384 452 236111642 236111710 3.410000e-22 117.0
74 TraesCS1B01G114800 chr2A 85.000 120 9 6 3132 3249 475364886 475364998 4.410000e-21 113.0
75 TraesCS1B01G114800 chr2A 95.652 69 2 1 384 452 419203463 419203396 5.710000e-20 110.0
76 TraesCS1B01G114800 chr2A 93.243 74 3 2 380 452 306162444 306162516 2.050000e-19 108.0
77 TraesCS1B01G114800 chr3B 93.421 76 3 2 377 452 312188321 312188248 1.590000e-20 111.0
78 TraesCS1B01G114800 chr4A 86.364 88 10 2 2921 3007 440931028 440930942 1.600000e-15 95.3
79 TraesCS1B01G114800 chr4A 82.609 92 11 3 3161 3248 207290692 207290782 5.790000e-10 76.8
80 TraesCS1B01G114800 chr7A 80.328 122 17 5 3129 3249 287488788 287488903 9.620000e-13 86.1
81 TraesCS1B01G114800 chr5B 78.689 122 18 6 3129 3248 357112582 357112697 2.080000e-09 75.0


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 TraesCS1B01G114800 chr1B 134571562 134576951 5389 False 9954.000000 9954 100.000000 1 5390 1 chr1B.!!$F1 5389
1 TraesCS1B01G114800 chr1B 134642346 134647146 4800 False 1531.080000 3391 96.964400 1 5390 5 chr1B.!!$F4 5389
2 TraesCS1B01G114800 chr1B 134430254 134439017 8763 False 834.500000 3009 92.153625 2 5390 8 chr1B.!!$F2 5388
3 TraesCS1B01G114800 chr1B 134450213 134456010 5797 False 452.833333 817 90.729833 4302 5390 6 chr1B.!!$F3 1088
4 TraesCS1B01G114800 chr1D 81283489 81288744 5255 False 1621.600000 3698 98.069800 1 4836 5 chr1D.!!$F4 4835
5 TraesCS1B01G114800 chr1D 81293793 81294351 558 False 1011.000000 1011 99.284000 4832 5390 1 chr1D.!!$F1 558
6 TraesCS1B01G114800 chr1D 81174274 81185557 11283 False 787.000000 2907 91.042273 1 5390 11 chr1D.!!$F3 5389
7 TraesCS1B01G114800 chr1A 99897004 99907589 10585 False 932.285714 2887 92.507571 1 5390 7 chr1A.!!$F2 5389
8 TraesCS1B01G114800 chr7B 33011685 33012333 648 True 547.000000 547 82.047000 3522 4190 1 chr7B.!!$R1 668
9 TraesCS1B01G114800 chr7B 33065093 33066615 1522 True 200.666667 263 83.552667 797 3526 3 chr7B.!!$R2 2729
10 TraesCS1B01G114800 chr6B 157792023 157792635 612 False 353.000000 353 77.586000 2165 2792 1 chr6B.!!$F1 627

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
852 8126 1.839994 TGGACCAAATTGTTGCCCAAA 59.160 42.857 0.0 0.0 36.44 3.28 F
1555 9055 0.036388 CACCTGCACGGGTTGACTAT 60.036 55.000 0.0 0.0 37.52 2.12 F
2509 10274 0.109532 TGGGTGTGTGTGTGTATGGG 59.890 55.000 0.0 0.0 0.00 4.00 F
2510 10275 0.608035 GGGTGTGTGTGTGTATGGGG 60.608 60.000 0.0 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2523 10288 0.326264 CTCCCAACACCTCTCCCAAG 59.674 60.000 0.00 0.0 0.0 3.61 R
2676 10763 2.664851 CTGACCGCCGACAAAGCA 60.665 61.111 0.00 0.0 0.0 3.91 R
3967 12184 2.043115 TCCCCTCTGTGTCTACTGTGAT 59.957 50.000 0.00 0.0 0.0 3.06 R
5122 13378 2.417933 AGACTTGACAATCGCAATGCTC 59.582 45.455 2.94 0.0 0.0 4.26 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
384 504 9.590451 CAGCAAATGTGATCCTTTTGTATTATT 57.410 29.630 16.56 0.00 39.30 1.40
391 511 9.443323 TGTGATCCTTTTGTATTATTTTCGAGA 57.557 29.630 0.00 0.00 0.00 4.04
396 516 9.601971 TCCTTTTGTATTATTTTCGAGAAAACG 57.398 29.630 12.51 0.00 42.32 3.60
397 517 8.363029 CCTTTTGTATTATTTTCGAGAAAACGC 58.637 33.333 12.51 3.78 42.32 4.84
398 518 8.783999 TTTTGTATTATTTTCGAGAAAACGCA 57.216 26.923 12.51 5.85 42.32 5.24
399 519 8.783999 TTTGTATTATTTTCGAGAAAACGCAA 57.216 26.923 12.51 10.29 42.32 4.85
400 520 8.783999 TTGTATTATTTTCGAGAAAACGCAAA 57.216 26.923 12.51 6.46 42.32 3.68
401 521 8.783999 TGTATTATTTTCGAGAAAACGCAAAA 57.216 26.923 12.51 4.48 42.32 2.44
402 522 8.897809 TGTATTATTTTCGAGAAAACGCAAAAG 58.102 29.630 12.51 0.00 42.32 2.27
403 523 4.692371 ATTTTCGAGAAAACGCAAAAGC 57.308 36.364 12.51 0.00 42.32 3.51
404 524 3.414549 TTTCGAGAAAACGCAAAAGCT 57.585 38.095 0.00 0.00 0.00 3.74
405 525 3.414549 TTCGAGAAAACGCAAAAGCTT 57.585 38.095 0.00 0.00 0.00 3.74
406 526 3.414549 TCGAGAAAACGCAAAAGCTTT 57.585 38.095 5.69 5.69 0.00 3.51
407 527 3.105203 TCGAGAAAACGCAAAAGCTTTG 58.895 40.909 13.54 8.26 0.00 2.77
408 528 2.346649 CGAGAAAACGCAAAAGCTTTGC 60.347 45.455 13.54 16.43 41.71 3.68
416 536 3.656651 GCAAAAGCTTTGCGTTTCTTT 57.343 38.095 13.54 0.00 38.06 2.52
417 537 4.002267 GCAAAAGCTTTGCGTTTCTTTT 57.998 36.364 13.54 0.00 38.06 2.27
418 538 4.021822 GCAAAAGCTTTGCGTTTCTTTTC 58.978 39.130 13.54 0.00 38.06 2.29
419 539 4.435386 GCAAAAGCTTTGCGTTTCTTTTCA 60.435 37.500 13.54 0.00 38.06 2.69
420 540 5.727515 GCAAAAGCTTTGCGTTTCTTTTCAT 60.728 36.000 13.54 0.00 38.06 2.57
421 541 6.250089 CAAAAGCTTTGCGTTTCTTTTCATT 58.750 32.000 13.54 0.00 38.06 2.57
422 542 5.393902 AAGCTTTGCGTTTCTTTTCATTG 57.606 34.783 0.00 0.00 0.00 2.82
423 543 4.681744 AGCTTTGCGTTTCTTTTCATTGA 58.318 34.783 0.00 0.00 0.00 2.57
424 544 5.108517 AGCTTTGCGTTTCTTTTCATTGAA 58.891 33.333 0.00 0.00 0.00 2.69
425 545 5.580297 AGCTTTGCGTTTCTTTTCATTGAAA 59.420 32.000 7.74 7.74 0.00 2.69
426 546 6.091986 AGCTTTGCGTTTCTTTTCATTGAAAA 59.908 30.769 20.33 20.33 38.90 2.29
437 557 6.405278 TTTTCATTGAAAAGGGAGAGGTTC 57.595 37.500 18.29 0.00 36.73 3.62
438 558 4.722526 TCATTGAAAAGGGAGAGGTTCA 57.277 40.909 0.00 0.00 0.00 3.18
439 559 4.655963 TCATTGAAAAGGGAGAGGTTCAG 58.344 43.478 0.00 0.00 31.98 3.02
440 560 4.104738 TCATTGAAAAGGGAGAGGTTCAGT 59.895 41.667 0.00 0.00 31.98 3.41
441 561 4.519906 TTGAAAAGGGAGAGGTTCAGTT 57.480 40.909 0.00 0.00 31.98 3.16
442 562 5.640158 TTGAAAAGGGAGAGGTTCAGTTA 57.360 39.130 0.00 0.00 31.98 2.24
443 563 4.969484 TGAAAAGGGAGAGGTTCAGTTAC 58.031 43.478 0.00 0.00 0.00 2.50
444 564 4.410883 TGAAAAGGGAGAGGTTCAGTTACA 59.589 41.667 0.00 0.00 0.00 2.41
445 565 4.625607 AAAGGGAGAGGTTCAGTTACAG 57.374 45.455 0.00 0.00 0.00 2.74
446 566 3.261818 AGGGAGAGGTTCAGTTACAGT 57.738 47.619 0.00 0.00 0.00 3.55
447 567 3.166679 AGGGAGAGGTTCAGTTACAGTC 58.833 50.000 0.00 0.00 0.00 3.51
448 568 2.897969 GGGAGAGGTTCAGTTACAGTCA 59.102 50.000 0.00 0.00 0.00 3.41
449 569 3.515901 GGGAGAGGTTCAGTTACAGTCAT 59.484 47.826 0.00 0.00 0.00 3.06
450 570 4.382147 GGGAGAGGTTCAGTTACAGTCATC 60.382 50.000 0.00 0.00 0.00 2.92
451 571 4.382147 GGAGAGGTTCAGTTACAGTCATCC 60.382 50.000 0.00 0.00 0.00 3.51
452 572 4.421131 AGAGGTTCAGTTACAGTCATCCT 58.579 43.478 0.00 0.00 0.00 3.24
453 573 4.841246 AGAGGTTCAGTTACAGTCATCCTT 59.159 41.667 0.00 0.00 0.00 3.36
454 574 5.308237 AGAGGTTCAGTTACAGTCATCCTTT 59.692 40.000 0.00 0.00 0.00 3.11
455 575 5.941788 AGGTTCAGTTACAGTCATCCTTTT 58.058 37.500 0.00 0.00 0.00 2.27
456 576 5.765182 AGGTTCAGTTACAGTCATCCTTTTG 59.235 40.000 0.00 0.00 0.00 2.44
457 577 5.531287 GGTTCAGTTACAGTCATCCTTTTGT 59.469 40.000 0.00 0.00 0.00 2.83
458 578 6.708949 GGTTCAGTTACAGTCATCCTTTTGTA 59.291 38.462 0.00 0.00 0.00 2.41
459 579 7.390718 GGTTCAGTTACAGTCATCCTTTTGTAT 59.609 37.037 0.00 0.00 0.00 2.29
460 580 8.784043 GTTCAGTTACAGTCATCCTTTTGTATT 58.216 33.333 0.00 0.00 0.00 1.89
462 582 9.653287 TCAGTTACAGTCATCCTTTTGTATTAG 57.347 33.333 0.00 0.00 0.00 1.73
744 6465 4.726825 TCTATTTCCCTTATTCAGCCACCT 59.273 41.667 0.00 0.00 0.00 4.00
852 8126 1.839994 TGGACCAAATTGTTGCCCAAA 59.160 42.857 0.00 0.00 36.44 3.28
927 8201 3.531538 TCAGTCGTAATCAATTCCTGCC 58.468 45.455 0.00 0.00 0.00 4.85
1555 9055 0.036388 CACCTGCACGGGTTGACTAT 60.036 55.000 0.00 0.00 37.52 2.12
1691 9444 1.064621 CAAGGATTTGATGCCGCCG 59.935 57.895 0.00 0.00 36.36 6.46
1962 9722 2.470362 CGCTAGAGGAAGCCGTCGA 61.470 63.158 0.00 0.00 39.43 4.20
2075 9836 4.028490 GGTGGTGGGTGGATGCGA 62.028 66.667 0.00 0.00 0.00 5.10
2497 10262 1.004918 GGAGTCGAGGTTGGGTGTG 60.005 63.158 0.00 0.00 0.00 3.82
2498 10263 1.746517 GAGTCGAGGTTGGGTGTGT 59.253 57.895 0.00 0.00 0.00 3.72
2499 10264 0.600255 GAGTCGAGGTTGGGTGTGTG 60.600 60.000 0.00 0.00 0.00 3.82
2500 10265 1.145377 GTCGAGGTTGGGTGTGTGT 59.855 57.895 0.00 0.00 0.00 3.72
2502 10267 1.153249 CGAGGTTGGGTGTGTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
2503 10268 1.436195 CGAGGTTGGGTGTGTGTGTG 61.436 60.000 0.00 0.00 0.00 3.82
2504 10269 0.393808 GAGGTTGGGTGTGTGTGTGT 60.394 55.000 0.00 0.00 0.00 3.72
2505 10270 0.913205 AGGTTGGGTGTGTGTGTGTA 59.087 50.000 0.00 0.00 0.00 2.90
2506 10271 1.493022 AGGTTGGGTGTGTGTGTGTAT 59.507 47.619 0.00 0.00 0.00 2.29
2507 10272 1.606668 GGTTGGGTGTGTGTGTGTATG 59.393 52.381 0.00 0.00 0.00 2.39
2508 10273 1.606668 GTTGGGTGTGTGTGTGTATGG 59.393 52.381 0.00 0.00 0.00 2.74
2509 10274 0.109532 TGGGTGTGTGTGTGTATGGG 59.890 55.000 0.00 0.00 0.00 4.00
2510 10275 0.608035 GGGTGTGTGTGTGTATGGGG 60.608 60.000 0.00 0.00 0.00 4.96
2511 10276 0.608035 GGTGTGTGTGTGTATGGGGG 60.608 60.000 0.00 0.00 0.00 5.40
2536 10301 1.837051 TGACGCTTGGGAGAGGTGT 60.837 57.895 0.00 0.00 0.00 4.16
2668 10755 4.094684 CGATCTGGTCGTTCTGGC 57.905 61.111 1.33 0.00 45.19 4.85
2913 11105 1.966451 CTTTCCCTTCGCCGTGCTT 60.966 57.895 0.00 0.00 0.00 3.91
3002 11194 1.611673 CCATCTTGGAGCTCACGGTTT 60.612 52.381 17.19 0.00 40.96 3.27
3744 11958 8.105829 CCTCCTAATCCTATACAATTGCAAGAT 58.894 37.037 4.94 0.00 0.00 2.40
3921 12138 3.772025 AGACTCCTATTGGTCTTCCTGTG 59.228 47.826 0.00 0.00 39.44 3.66
4460 12679 1.338020 GCAACACCTAGCAACAGCTTT 59.662 47.619 0.00 0.00 39.77 3.51
4697 12916 6.607019 TCTTTTATGGACAACTTGTTACCCT 58.393 36.000 0.00 0.00 0.00 4.34
5122 13378 5.341872 TGCATTTTCCCATCATAAACCTG 57.658 39.130 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
397 517 5.202046 TGAAAAGAAACGCAAAGCTTTTG 57.798 34.783 9.53 7.81 39.77 2.44
398 518 6.091986 TCAATGAAAAGAAACGCAAAGCTTTT 59.908 30.769 9.53 0.00 41.65 2.27
399 519 5.580297 TCAATGAAAAGAAACGCAAAGCTTT 59.420 32.000 5.69 5.69 32.38 3.51
400 520 5.108517 TCAATGAAAAGAAACGCAAAGCTT 58.891 33.333 0.00 0.00 0.00 3.74
401 521 4.681744 TCAATGAAAAGAAACGCAAAGCT 58.318 34.783 0.00 0.00 0.00 3.74
402 522 5.388225 TTCAATGAAAAGAAACGCAAAGC 57.612 34.783 0.00 0.00 0.00 3.51
414 534 5.896678 TGAACCTCTCCCTTTTCAATGAAAA 59.103 36.000 18.68 18.68 38.90 2.29
415 535 5.454062 TGAACCTCTCCCTTTTCAATGAAA 58.546 37.500 4.03 4.03 0.00 2.69
416 536 5.060427 TGAACCTCTCCCTTTTCAATGAA 57.940 39.130 0.00 0.00 0.00 2.57
417 537 4.104738 ACTGAACCTCTCCCTTTTCAATGA 59.895 41.667 0.00 0.00 0.00 2.57
418 538 4.401925 ACTGAACCTCTCCCTTTTCAATG 58.598 43.478 0.00 0.00 0.00 2.82
419 539 4.731313 ACTGAACCTCTCCCTTTTCAAT 57.269 40.909 0.00 0.00 0.00 2.57
420 540 4.519906 AACTGAACCTCTCCCTTTTCAA 57.480 40.909 0.00 0.00 0.00 2.69
421 541 4.410883 TGTAACTGAACCTCTCCCTTTTCA 59.589 41.667 0.00 0.00 0.00 2.69
422 542 4.969484 TGTAACTGAACCTCTCCCTTTTC 58.031 43.478 0.00 0.00 0.00 2.29
423 543 4.412528 ACTGTAACTGAACCTCTCCCTTTT 59.587 41.667 0.00 0.00 0.00 2.27
424 544 3.974642 ACTGTAACTGAACCTCTCCCTTT 59.025 43.478 0.00 0.00 0.00 3.11
425 545 3.579151 GACTGTAACTGAACCTCTCCCTT 59.421 47.826 0.00 0.00 0.00 3.95
426 546 3.166679 GACTGTAACTGAACCTCTCCCT 58.833 50.000 0.00 0.00 0.00 4.20
427 547 2.897969 TGACTGTAACTGAACCTCTCCC 59.102 50.000 0.00 0.00 0.00 4.30
428 548 4.382147 GGATGACTGTAACTGAACCTCTCC 60.382 50.000 0.00 0.00 0.00 3.71
429 549 4.464597 AGGATGACTGTAACTGAACCTCTC 59.535 45.833 0.00 0.00 0.00 3.20
430 550 4.421131 AGGATGACTGTAACTGAACCTCT 58.579 43.478 0.00 0.00 0.00 3.69
431 551 4.810191 AGGATGACTGTAACTGAACCTC 57.190 45.455 0.00 0.00 0.00 3.85
432 552 5.568620 AAAGGATGACTGTAACTGAACCT 57.431 39.130 0.00 0.00 0.00 3.50
433 553 5.531287 ACAAAAGGATGACTGTAACTGAACC 59.469 40.000 0.00 0.00 0.00 3.62
434 554 6.619801 ACAAAAGGATGACTGTAACTGAAC 57.380 37.500 0.00 0.00 0.00 3.18
435 555 8.918202 AATACAAAAGGATGACTGTAACTGAA 57.082 30.769 0.00 0.00 0.00 3.02
436 556 9.653287 CTAATACAAAAGGATGACTGTAACTGA 57.347 33.333 0.00 0.00 0.00 3.41
437 557 8.391106 GCTAATACAAAAGGATGACTGTAACTG 58.609 37.037 0.00 0.00 0.00 3.16
438 558 8.100791 TGCTAATACAAAAGGATGACTGTAACT 58.899 33.333 0.00 0.00 0.00 2.24
439 559 8.263940 TGCTAATACAAAAGGATGACTGTAAC 57.736 34.615 0.00 0.00 0.00 2.50
440 560 8.100791 ACTGCTAATACAAAAGGATGACTGTAA 58.899 33.333 0.00 0.00 0.00 2.41
441 561 7.620880 ACTGCTAATACAAAAGGATGACTGTA 58.379 34.615 0.00 0.00 0.00 2.74
442 562 6.476378 ACTGCTAATACAAAAGGATGACTGT 58.524 36.000 0.00 0.00 0.00 3.55
443 563 6.992063 ACTGCTAATACAAAAGGATGACTG 57.008 37.500 0.00 0.00 0.00 3.51
444 564 8.267894 ACATACTGCTAATACAAAAGGATGACT 58.732 33.333 0.33 0.00 33.62 3.41
445 565 8.338259 CACATACTGCTAATACAAAAGGATGAC 58.662 37.037 0.33 0.00 33.62 3.06
446 566 8.264347 TCACATACTGCTAATACAAAAGGATGA 58.736 33.333 0.33 0.00 33.62 2.92
447 567 8.437360 TCACATACTGCTAATACAAAAGGATG 57.563 34.615 0.00 0.00 35.66 3.51
448 568 9.632638 ATTCACATACTGCTAATACAAAAGGAT 57.367 29.630 0.00 0.00 0.00 3.24
449 569 9.461312 AATTCACATACTGCTAATACAAAAGGA 57.539 29.630 0.00 0.00 0.00 3.36
744 6465 9.264719 CATGCTTACTCATAAGAATGTGATACA 57.735 33.333 6.81 0.00 44.75 2.29
852 8126 2.496899 ACATGTTTCGAATCCAGGCT 57.503 45.000 0.00 0.00 0.00 4.58
1385 8871 7.952637 GTGTGTTAATTTTTCAAAAGCGAAACA 59.047 29.630 0.00 0.00 34.68 2.83
1391 8877 8.439286 TGTGAAGTGTGTTAATTTTTCAAAAGC 58.561 29.630 0.00 0.00 0.00 3.51
1555 9055 3.495377 CACGACTTATTTTCCCGACACAA 59.505 43.478 0.00 0.00 0.00 3.33
1691 9444 1.383803 ATGCTCACCTCCTCCTCCC 60.384 63.158 0.00 0.00 0.00 4.30
1913 9673 2.447572 TGGACAGGAGGTGTGGCA 60.448 61.111 0.00 0.00 40.56 4.92
2240 10004 1.247419 CCAACATGGCCGCTACCAAA 61.247 55.000 0.00 0.00 44.65 3.28
2459 10224 0.954449 CGGCCTGGATCTGCATCATC 60.954 60.000 0.00 0.00 0.00 2.92
2460 10225 1.072678 CGGCCTGGATCTGCATCAT 59.927 57.895 0.00 0.00 0.00 2.45
2461 10226 2.507452 CGGCCTGGATCTGCATCA 59.493 61.111 0.00 0.00 0.00 3.07
2523 10288 0.326264 CTCCCAACACCTCTCCCAAG 59.674 60.000 0.00 0.00 0.00 3.61
2536 10301 3.897122 GCCACCCACCACTCCCAA 61.897 66.667 0.00 0.00 0.00 4.12
2676 10763 2.664851 CTGACCGCCGACAAAGCA 60.665 61.111 0.00 0.00 0.00 3.91
2913 11105 4.097741 CCAATGGTCCAGATTTTTATGCGA 59.902 41.667 0.00 0.00 0.00 5.10
2916 11108 6.441274 CGATCCAATGGTCCAGATTTTTATG 58.559 40.000 0.00 0.00 0.00 1.90
3002 11194 3.069586 AGAGGTGAAGTTGAATGTCGACA 59.930 43.478 22.48 22.48 33.17 4.35
3744 11958 4.275196 TCTTCGACTTCTTCTTCGTCTTCA 59.725 41.667 0.00 0.00 36.60 3.02
3921 12138 5.391312 AATGCAAAGTACCATTCAGGAAC 57.609 39.130 0.00 0.00 41.22 3.62
3967 12184 2.043115 TCCCCTCTGTGTCTACTGTGAT 59.957 50.000 0.00 0.00 0.00 3.06
5122 13378 2.417933 AGACTTGACAATCGCAATGCTC 59.582 45.455 2.94 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.