Multiple sequence alignment - TraesCS5D01G175200

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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 TraesCS5D01G175200 chr5D 100.000 4518 0 0 1 4518 274774998 274779515 0.000000e+00 8344
1 TraesCS5D01G175200 chr5D 89.821 1120 83 20 525 1631 275146488 275147589 0.000000e+00 1408
2 TraesCS5D01G175200 chr5D 93.123 698 44 2 2899 3592 275147588 275148285 0.000000e+00 1020
3 TraesCS5D01G175200 chr5D 90.830 578 45 3 1062 1631 275195267 275195844 0.000000e+00 767
4 TraesCS5D01G175200 chr5D 80.668 838 96 40 2078 2898 392072731 392073519 1.400000e-164 590
5 TraesCS5D01G175200 chr5D 92.399 421 21 5 34 448 394199868 394199453 1.400000e-164 590
6 TraesCS5D01G175200 chr5D 83.206 524 75 11 1105 1623 245715656 245716171 6.840000e-128 468
7 TraesCS5D01G175200 chr5D 81.305 567 93 10 1071 1631 274572450 274571891 8.920000e-122 448
8 TraesCS5D01G175200 chr5D 80.266 451 69 16 2899 3345 275195843 275196277 5.640000e-84 322
9 TraesCS5D01G175200 chr5D 92.202 218 14 2 3335 3552 275196825 275197039 5.680000e-79 305
10 TraesCS5D01G175200 chr5D 88.517 209 13 5 34 236 487671398 487671195 4.520000e-60 243
11 TraesCS5D01G175200 chr7D 96.443 1265 35 5 1634 2895 575904415 575903158 0.000000e+00 2078
12 TraesCS5D01G175200 chr7D 92.764 691 32 9 1634 2315 126705046 126704365 0.000000e+00 983
13 TraesCS5D01G175200 chr7D 93.027 588 41 0 2312 2899 126687462 126686875 0.000000e+00 859
14 TraesCS5D01G175200 chr7D 84.091 176 17 6 2084 2250 603353707 603353534 4.680000e-35 159
15 TraesCS5D01G175200 chr1D 95.811 1289 31 9 1634 2899 229878089 229879377 0.000000e+00 2060
16 TraesCS5D01G175200 chr6D 95.345 1289 36 4 1634 2898 412444280 412445568 0.000000e+00 2026
17 TraesCS5D01G175200 chr6D 93.564 202 10 2 1634 1832 412445568 412445367 9.500000e-77 298
18 TraesCS5D01G175200 chr5B 95.945 1159 39 7 480 1631 309816436 309817593 0.000000e+00 1873
19 TraesCS5D01G175200 chr5B 93.687 697 38 4 2899 3590 309817592 309818287 0.000000e+00 1038
20 TraesCS5D01G175200 chr5B 89.792 578 51 3 1062 1631 312261194 312261771 0.000000e+00 734
21 TraesCS5D01G175200 chr5B 96.032 378 8 4 1 372 309816066 309816442 3.860000e-170 608
22 TraesCS5D01G175200 chr5B 83.714 657 86 17 2899 3552 312261770 312262408 6.470000e-168 601
23 TraesCS5D01G175200 chr5B 83.410 651 88 16 2899 3546 310035491 310036124 1.810000e-163 586
24 TraesCS5D01G175200 chr5B 86.116 569 44 17 1071 1631 310034951 310035492 8.420000e-162 580
25 TraesCS5D01G175200 chr5B 83.585 530 80 6 1105 1631 312592515 312593040 1.460000e-134 490
26 TraesCS5D01G175200 chr5B 86.787 333 29 6 3987 4314 309819214 309819536 1.550000e-94 357
27 TraesCS5D01G175200 chr1B 86.605 1299 116 28 1634 2898 534242932 534244206 0.000000e+00 1382
28 TraesCS5D01G175200 chr3D 86.528 1299 120 28 1633 2898 185061086 185062362 0.000000e+00 1378
29 TraesCS5D01G175200 chr6B 85.890 1304 102 42 1637 2899 703364377 703363115 0.000000e+00 1314
30 TraesCS5D01G175200 chr6B 85.355 1311 111 33 1634 2898 256018326 256017051 0.000000e+00 1282
31 TraesCS5D01G175200 chr5A 95.330 728 30 4 3631 4355 363865082 363865808 0.000000e+00 1153
32 TraesCS5D01G175200 chr5A 94.860 681 30 5 956 1631 363919686 363920366 0.000000e+00 1059
33 TraesCS5D01G175200 chr5A 93.846 715 21 9 923 1631 363861818 363862515 0.000000e+00 1055
34 TraesCS5D01G175200 chr5A 93.094 695 44 2 2899 3589 363920365 363921059 0.000000e+00 1014
35 TraesCS5D01G175200 chr5A 91.037 569 43 5 1071 1631 364198654 364199222 0.000000e+00 761
36 TraesCS5D01G175200 chr5A 95.228 482 19 2 2899 3377 363862514 363862994 0.000000e+00 760
37 TraesCS5D01G175200 chr5A 83.664 655 87 17 2899 3549 364199221 364199859 2.330000e-167 599
38 TraesCS5D01G175200 chr5A 90.000 340 28 6 525 861 363856389 363856725 6.940000e-118 435
39 TraesCS5D01G175200 chr5A 96.996 233 5 2 3419 3649 363862995 363863227 1.520000e-104 390
40 TraesCS5D01G175200 chr5A 85.829 374 39 6 3987 4355 363921969 363922333 7.090000e-103 385
41 TraesCS5D01G175200 chr5A 98.113 159 3 0 1 159 363855887 363856045 1.240000e-70 278
42 TraesCS5D01G175200 chr5A 95.930 172 6 1 4347 4517 363865669 363865840 1.240000e-70 278
43 TraesCS5D01G175200 chr5A 86.056 251 20 7 195 442 363856048 363856286 5.800000e-64 255
44 TraesCS5D01G175200 chr5A 92.500 80 6 0 858 937 363858485 363858564 1.030000e-21 115
45 TraesCS5D01G175200 chr3B 80.595 840 95 38 2078 2898 30512941 30513731 1.810000e-163 586
46 TraesCS5D01G175200 chr2D 80.288 832 101 34 2084 2899 438012423 438011639 1.820000e-158 569


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 TraesCS5D01G175200 chr5D 274774998 274779515 4517 False 8344.000000 8344 100.000000 1 4518 1 chr5D.!!$F2 4517
1 TraesCS5D01G175200 chr5D 275146488 275148285 1797 False 1214.000000 1408 91.472000 525 3592 2 chr5D.!!$F4 3067
2 TraesCS5D01G175200 chr5D 392072731 392073519 788 False 590.000000 590 80.668000 2078 2898 1 chr5D.!!$F3 820
3 TraesCS5D01G175200 chr5D 245715656 245716171 515 False 468.000000 468 83.206000 1105 1623 1 chr5D.!!$F1 518
4 TraesCS5D01G175200 chr5D 275195267 275197039 1772 False 464.666667 767 87.766000 1062 3552 3 chr5D.!!$F5 2490
5 TraesCS5D01G175200 chr5D 274571891 274572450 559 True 448.000000 448 81.305000 1071 1631 1 chr5D.!!$R1 560
6 TraesCS5D01G175200 chr7D 575903158 575904415 1257 True 2078.000000 2078 96.443000 1634 2895 1 chr7D.!!$R3 1261
7 TraesCS5D01G175200 chr7D 126704365 126705046 681 True 983.000000 983 92.764000 1634 2315 1 chr7D.!!$R2 681
8 TraesCS5D01G175200 chr7D 126686875 126687462 587 True 859.000000 859 93.027000 2312 2899 1 chr7D.!!$R1 587
9 TraesCS5D01G175200 chr1D 229878089 229879377 1288 False 2060.000000 2060 95.811000 1634 2899 1 chr1D.!!$F1 1265
10 TraesCS5D01G175200 chr6D 412444280 412445568 1288 False 2026.000000 2026 95.345000 1634 2898 1 chr6D.!!$F1 1264
11 TraesCS5D01G175200 chr5B 309816066 309819536 3470 False 969.000000 1873 93.112750 1 4314 4 chr5B.!!$F2 4313
12 TraesCS5D01G175200 chr5B 312261194 312262408 1214 False 667.500000 734 86.753000 1062 3552 2 chr5B.!!$F4 2490
13 TraesCS5D01G175200 chr5B 310034951 310036124 1173 False 583.000000 586 84.763000 1071 3546 2 chr5B.!!$F3 2475
14 TraesCS5D01G175200 chr5B 312592515 312593040 525 False 490.000000 490 83.585000 1105 1631 1 chr5B.!!$F1 526
15 TraesCS5D01G175200 chr1B 534242932 534244206 1274 False 1382.000000 1382 86.605000 1634 2898 1 chr1B.!!$F1 1264
16 TraesCS5D01G175200 chr3D 185061086 185062362 1276 False 1378.000000 1378 86.528000 1633 2898 1 chr3D.!!$F1 1265
17 TraesCS5D01G175200 chr6B 703363115 703364377 1262 True 1314.000000 1314 85.890000 1637 2899 1 chr6B.!!$R2 1262
18 TraesCS5D01G175200 chr6B 256017051 256018326 1275 True 1282.000000 1282 85.355000 1634 2898 1 chr6B.!!$R1 1264
19 TraesCS5D01G175200 chr5A 363919686 363922333 2647 False 819.333333 1059 91.261000 956 4355 3 chr5A.!!$F2 3399
20 TraesCS5D01G175200 chr5A 364198654 364199859 1205 False 680.000000 761 87.350500 1071 3549 2 chr5A.!!$F3 2478
21 TraesCS5D01G175200 chr5A 363855887 363865840 9953 False 524.333333 1153 93.777667 1 4517 9 chr5A.!!$F1 4516
22 TraesCS5D01G175200 chr3B 30512941 30513731 790 False 586.000000 586 80.595000 2078 2898 1 chr3B.!!$F1 820
23 TraesCS5D01G175200 chr2D 438011639 438012423 784 True 569.000000 569 80.288000 2084 2899 1 chr2D.!!$R1 815

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
386 393 0.310854 GGTTGTGCCACTAGTTGTGC 59.689 55.000 0.00 0.00 44.92 4.57 F
387 394 0.310854 GTTGTGCCACTAGTTGTGCC 59.689 55.000 0.00 0.00 44.92 5.01 F
1542 6633 0.747283 CCAGGTACTACGTCGGCTCT 60.747 60.000 0.00 0.00 36.02 4.09 F
1966 7095 0.411452 AGCTCTTCCCTGAGGTGAGA 59.589 55.000 14.64 8.66 42.36 3.27 F
2727 7917 2.185867 GGAGCCGTTATGCCACGA 59.814 61.111 0.00 0.00 43.15 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 6891 0.029300 GAGCCGTTACGCCACGTATA 59.971 55.000 0.00 0.00 41.97 1.47 R
1966 7095 1.975407 GGAGTTGTGGCTGCAGCAT 60.975 57.895 37.63 16.98 44.36 3.79 R
2727 7917 0.391228 GTGGGTCCCGTTTTTGCATT 59.609 50.000 2.65 0.00 0.00 3.56 R
3001 8194 2.060980 CCAGTAGAGCTTCCCGGCT 61.061 63.158 0.00 0.00 46.11 5.52 R
4318 12653 1.607148 ACAGGTAAAGCAAAAGACCGC 59.393 47.619 0.00 0.00 37.04 5.68 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
168 174 6.262944 TGTGCTGCATGGTCCTATAATAAAAG 59.737 38.462 5.27 0.00 0.00 2.27
175 181 7.229506 GCATGGTCCTATAATAAAAGCAGAAGT 59.770 37.037 0.00 0.00 0.00 3.01
192 198 5.974751 GCAGAAGTGATTACTACTCTACTGC 59.025 44.000 0.00 0.00 39.65 4.40
193 199 6.183360 GCAGAAGTGATTACTACTCTACTGCT 60.183 42.308 0.00 0.00 41.17 4.24
235 241 5.795441 GTCAAATTGAGGTAGTGAAATTCGC 59.205 40.000 0.00 0.00 0.00 4.70
380 387 6.671614 TTTTATTATCGGTTGTGCCACTAG 57.328 37.500 0.00 0.00 36.97 2.57
381 388 3.906720 ATTATCGGTTGTGCCACTAGT 57.093 42.857 0.00 0.00 36.97 2.57
384 391 0.466543 TCGGTTGTGCCACTAGTTGT 59.533 50.000 0.00 0.00 36.97 3.32
385 392 0.586319 CGGTTGTGCCACTAGTTGTG 59.414 55.000 0.00 0.00 45.80 3.33
386 393 0.310854 GGTTGTGCCACTAGTTGTGC 59.689 55.000 0.00 0.00 44.92 4.57
387 394 0.310854 GTTGTGCCACTAGTTGTGCC 59.689 55.000 0.00 0.00 44.92 5.01
418 428 5.758296 TGGCACTAGAAGTTTCAAGTACTTG 59.242 40.000 26.60 26.60 41.71 3.16
419 429 5.989777 GGCACTAGAAGTTTCAAGTACTTGA 59.010 40.000 30.07 30.07 46.72 3.02
442 452 4.322057 AAATGCCATCCCTCTGTTAAGT 57.678 40.909 0.00 0.00 0.00 2.24
443 453 3.567478 ATGCCATCCCTCTGTTAAGTC 57.433 47.619 0.00 0.00 0.00 3.01
446 456 2.237392 GCCATCCCTCTGTTAAGTCTGT 59.763 50.000 0.00 0.00 0.00 3.41
448 458 3.265791 CATCCCTCTGTTAAGTCTGTGC 58.734 50.000 0.00 0.00 0.00 4.57
449 459 2.609747 TCCCTCTGTTAAGTCTGTGCT 58.390 47.619 0.00 0.00 0.00 4.40
450 460 2.972713 TCCCTCTGTTAAGTCTGTGCTT 59.027 45.455 0.00 0.00 0.00 3.91
451 461 4.157246 TCCCTCTGTTAAGTCTGTGCTTA 58.843 43.478 0.00 0.00 0.00 3.09
452 462 4.220821 TCCCTCTGTTAAGTCTGTGCTTAG 59.779 45.833 0.00 0.00 33.16 2.18
454 464 5.279506 CCCTCTGTTAAGTCTGTGCTTAGAA 60.280 44.000 0.00 0.00 33.16 2.10
455 465 6.223852 CCTCTGTTAAGTCTGTGCTTAGAAA 58.776 40.000 0.00 0.00 33.16 2.52
457 467 8.035394 CCTCTGTTAAGTCTGTGCTTAGAAATA 58.965 37.037 0.00 0.00 33.16 1.40
458 468 8.988064 TCTGTTAAGTCTGTGCTTAGAAATAG 57.012 34.615 0.00 0.00 33.16 1.73
459 469 8.585881 TCTGTTAAGTCTGTGCTTAGAAATAGT 58.414 33.333 0.00 0.00 33.16 2.12
460 470 8.534333 TGTTAAGTCTGTGCTTAGAAATAGTG 57.466 34.615 0.00 0.00 33.16 2.74
461 471 7.602644 TGTTAAGTCTGTGCTTAGAAATAGTGG 59.397 37.037 0.00 0.00 33.16 4.00
462 472 4.508662 AGTCTGTGCTTAGAAATAGTGGC 58.491 43.478 0.00 0.00 0.00 5.01
463 473 4.020218 AGTCTGTGCTTAGAAATAGTGGCA 60.020 41.667 0.00 0.00 0.00 4.92
464 474 4.331168 GTCTGTGCTTAGAAATAGTGGCAG 59.669 45.833 0.00 0.00 0.00 4.85
465 475 4.222810 TCTGTGCTTAGAAATAGTGGCAGA 59.777 41.667 0.00 0.00 0.00 4.26
466 476 4.905429 TGTGCTTAGAAATAGTGGCAGAA 58.095 39.130 0.00 0.00 0.00 3.02
467 477 4.695455 TGTGCTTAGAAATAGTGGCAGAAC 59.305 41.667 0.00 0.00 0.00 3.01
469 479 4.937620 TGCTTAGAAATAGTGGCAGAACTG 59.062 41.667 0.00 0.00 0.00 3.16
471 481 5.819901 GCTTAGAAATAGTGGCAGAACTGAT 59.180 40.000 5.97 0.00 0.00 2.90
472 482 6.317391 GCTTAGAAATAGTGGCAGAACTGATT 59.683 38.462 5.97 0.00 0.00 2.57
473 483 7.495934 GCTTAGAAATAGTGGCAGAACTGATTA 59.504 37.037 5.97 0.00 0.00 1.75
474 484 9.553064 CTTAGAAATAGTGGCAGAACTGATTAT 57.447 33.333 5.97 0.00 0.00 1.28
481 491 7.158099 AGTGGCAGAACTGATTATAAAAACC 57.842 36.000 5.97 0.00 0.00 3.27
482 492 6.027749 GTGGCAGAACTGATTATAAAAACCG 58.972 40.000 5.97 0.00 0.00 4.44
486 496 6.526674 GCAGAACTGATTATAAAAACCGTTGG 59.473 38.462 5.97 0.00 0.00 3.77
488 498 5.319140 ACTGATTATAAAAACCGTTGGCC 57.681 39.130 0.00 0.00 0.00 5.36
490 500 3.757493 TGATTATAAAAACCGTTGGCCGT 59.243 39.130 0.00 0.00 33.66 5.68
530 565 1.825191 CAGTCAATGGGCCGATGGG 60.825 63.158 0.00 0.00 0.00 4.00
618 654 3.568007 TGGCAAAATGAAGTAGTGTGACC 59.432 43.478 0.00 0.00 0.00 4.02
851 889 4.217334 TGAGTGCTGTGTCAAGTTCAAAAA 59.783 37.500 0.00 0.00 0.00 1.94
852 890 5.105797 TGAGTGCTGTGTCAAGTTCAAAAAT 60.106 36.000 0.00 0.00 0.00 1.82
854 894 6.498304 AGTGCTGTGTCAAGTTCAAAAATAG 58.502 36.000 0.00 0.00 0.00 1.73
855 895 6.318648 AGTGCTGTGTCAAGTTCAAAAATAGA 59.681 34.615 0.00 0.00 0.00 1.98
918 2721 0.749454 CCTTCCCAAAGCCTGATCCG 60.749 60.000 0.00 0.00 0.00 4.18
985 6057 1.524482 CCTGCTACTGCTCCTTCCC 59.476 63.158 0.00 0.00 40.48 3.97
1123 6198 2.482333 ATTCTCCGTCGCCTCTCCG 61.482 63.158 0.00 0.00 0.00 4.63
1542 6633 0.747283 CCAGGTACTACGTCGGCTCT 60.747 60.000 0.00 0.00 36.02 4.09
1643 6734 1.405121 GGGTCGCGGAGAGTAAATTGT 60.405 52.381 6.13 0.00 0.00 2.71
1681 6774 3.639561 AGGGTTAGGTTTGCGAAAAACAT 59.360 39.130 6.70 6.62 32.04 2.71
1797 6891 1.746787 GACAGGTGGTTCCGTTTTTGT 59.253 47.619 0.00 0.00 41.99 2.83
1883 6981 5.705400 TGGGTCTTCTCCAATTCTTCTTTT 58.295 37.500 0.00 0.00 0.00 2.27
1966 7095 0.411452 AGCTCTTCCCTGAGGTGAGA 59.589 55.000 14.64 8.66 42.36 3.27
2370 7530 3.465403 CTGCTCCTCCTGGTCGGG 61.465 72.222 0.00 0.00 34.23 5.14
2536 7697 2.284995 GCCACTCCTCCCAGGTCT 60.285 66.667 0.00 0.00 36.53 3.85
2584 7755 3.122613 CGAGACACGTCGTACTACTTCTT 59.877 47.826 0.00 0.00 35.14 2.52
2727 7917 2.185867 GGAGCCGTTATGCCACGA 59.814 61.111 0.00 0.00 43.15 4.35
2839 8032 6.636454 ATGGTGTCTTCTACAGGGAAAATA 57.364 37.500 0.00 0.00 39.29 1.40
3050 8243 2.004808 CTCCTACCGCATGCTCGTGA 62.005 60.000 17.13 4.98 0.00 4.35
3258 8454 1.042229 CTGGAGAGGGAGATGCTCAG 58.958 60.000 0.00 0.00 31.08 3.35
3652 11308 7.766738 TGATAGGTGCATTCGATTTAGTTTACA 59.233 33.333 0.00 0.00 0.00 2.41
3671 11327 2.358615 TGCTGGCGTTGGTAGCAG 60.359 61.111 0.00 0.00 42.05 4.24
3752 11408 0.673022 CCTCTGAAGCCACTGTGCTC 60.673 60.000 1.29 0.00 41.80 4.26
3790 11447 9.715121 AAATGTGAAGCAATCATTCAAAATACT 57.285 25.926 0.00 0.00 40.97 2.12
3967 11643 6.037172 GTCTGTCATATTTCGCATACCAAAGT 59.963 38.462 0.00 0.00 0.00 2.66
3971 11647 7.540400 TGTCATATTTCGCATACCAAAGTTTTG 59.460 33.333 0.00 0.00 37.90 2.44
3989 11665 6.121590 AGTTTTGGCAATTTGATGGAGTTTT 58.878 32.000 0.00 0.00 0.00 2.43
4032 12365 5.793457 GCTATTTGTTACAGCCGTTAACAAG 59.207 40.000 6.39 0.00 42.35 3.16
4213 12548 5.760253 TGGTCACTTAGAAGAGCAAAGAAAG 59.240 40.000 8.32 0.00 39.09 2.62
4241 12576 9.541143 TTAATTATGTTCATCGTCTCATTAGCA 57.459 29.630 0.00 0.00 0.00 3.49
4252 12587 9.035607 CATCGTCTCATTAGCACTTAAATAGTT 57.964 33.333 0.00 0.00 33.85 2.24
4280 12615 4.942761 TCCGCGGAAGTACCTTATATTT 57.057 40.909 28.99 0.00 36.31 1.40
4285 12620 6.204108 CCGCGGAAGTACCTTATATTTTGAAT 59.796 38.462 24.07 0.00 36.31 2.57
4314 12649 8.192068 TGATTGCTTGAAATCATTAAATGCTG 57.808 30.769 0.12 0.00 40.72 4.41
4315 12650 7.820386 TGATTGCTTGAAATCATTAAATGCTGT 59.180 29.630 0.12 0.00 40.72 4.40
4316 12651 7.585286 TTGCTTGAAATCATTAAATGCTGTC 57.415 32.000 0.00 0.00 0.00 3.51
4317 12652 6.689554 TGCTTGAAATCATTAAATGCTGTCA 58.310 32.000 0.00 0.00 0.00 3.58
4318 12653 6.809689 TGCTTGAAATCATTAAATGCTGTCAG 59.190 34.615 0.00 0.00 0.00 3.51
4319 12654 6.237755 GCTTGAAATCATTAAATGCTGTCAGC 60.238 38.462 18.32 18.32 42.82 4.26
4320 12655 5.334319 TGAAATCATTAAATGCTGTCAGCG 58.666 37.500 19.68 3.95 46.26 5.18
4321 12656 3.976793 ATCATTAAATGCTGTCAGCGG 57.023 42.857 19.68 3.78 46.26 5.52
4322 12657 2.710377 TCATTAAATGCTGTCAGCGGT 58.290 42.857 19.68 8.44 46.26 5.68
4323 12658 2.677836 TCATTAAATGCTGTCAGCGGTC 59.322 45.455 19.68 0.00 46.26 4.79
4324 12659 2.472695 TTAAATGCTGTCAGCGGTCT 57.527 45.000 19.68 7.00 46.26 3.85
4325 12660 2.472695 TAAATGCTGTCAGCGGTCTT 57.527 45.000 19.68 11.86 46.26 3.01
4326 12661 1.609208 AAATGCTGTCAGCGGTCTTT 58.391 45.000 19.68 12.94 46.26 2.52
4327 12662 1.609208 AATGCTGTCAGCGGTCTTTT 58.391 45.000 19.68 4.14 46.26 2.27
4328 12663 0.877071 ATGCTGTCAGCGGTCTTTTG 59.123 50.000 19.68 0.00 46.26 2.44
4329 12664 1.081840 GCTGTCAGCGGTCTTTTGC 60.082 57.895 9.53 0.00 0.00 3.68
4330 12665 1.510480 GCTGTCAGCGGTCTTTTGCT 61.510 55.000 9.53 0.00 43.58 3.91
4331 12666 0.947244 CTGTCAGCGGTCTTTTGCTT 59.053 50.000 0.00 0.00 40.03 3.91
4332 12667 1.334869 CTGTCAGCGGTCTTTTGCTTT 59.665 47.619 0.00 0.00 40.03 3.51
4333 12668 2.548057 CTGTCAGCGGTCTTTTGCTTTA 59.452 45.455 0.00 0.00 40.03 1.85
4334 12669 2.289547 TGTCAGCGGTCTTTTGCTTTAC 59.710 45.455 0.00 0.00 40.03 2.01
4335 12670 1.877443 TCAGCGGTCTTTTGCTTTACC 59.123 47.619 0.00 0.00 40.03 2.85
4336 12671 1.880027 CAGCGGTCTTTTGCTTTACCT 59.120 47.619 0.00 0.00 40.03 3.08
4337 12672 1.880027 AGCGGTCTTTTGCTTTACCTG 59.120 47.619 0.00 0.00 38.57 4.00
4338 12673 1.607148 GCGGTCTTTTGCTTTACCTGT 59.393 47.619 0.00 0.00 0.00 4.00
4339 12674 2.809696 GCGGTCTTTTGCTTTACCTGTA 59.190 45.455 0.00 0.00 0.00 2.74
4340 12675 3.364664 GCGGTCTTTTGCTTTACCTGTAC 60.365 47.826 0.00 0.00 0.00 2.90
4341 12676 3.810941 CGGTCTTTTGCTTTACCTGTACA 59.189 43.478 0.00 0.00 0.00 2.90
4342 12677 4.454504 CGGTCTTTTGCTTTACCTGTACAT 59.545 41.667 0.00 0.00 0.00 2.29
4343 12678 5.616866 CGGTCTTTTGCTTTACCTGTACATG 60.617 44.000 0.00 0.00 0.00 3.21
4344 12679 5.335661 GGTCTTTTGCTTTACCTGTACATGG 60.336 44.000 0.00 2.79 0.00 3.66
4345 12680 4.764823 TCTTTTGCTTTACCTGTACATGGG 59.235 41.667 13.68 7.74 0.00 4.00
4346 12681 2.122783 TGCTTTACCTGTACATGGGC 57.877 50.000 13.68 8.82 0.00 5.36
4347 12682 1.633432 TGCTTTACCTGTACATGGGCT 59.367 47.619 13.68 0.78 0.00 5.19
4348 12683 2.041081 TGCTTTACCTGTACATGGGCTT 59.959 45.455 13.68 0.00 0.00 4.35
4349 12684 3.264706 TGCTTTACCTGTACATGGGCTTA 59.735 43.478 13.68 0.00 0.00 3.09
4350 12685 4.263550 TGCTTTACCTGTACATGGGCTTAA 60.264 41.667 13.68 3.77 0.00 1.85
4351 12686 4.887655 GCTTTACCTGTACATGGGCTTAAT 59.112 41.667 13.68 0.00 0.00 1.40
4511 12847 3.659786 TCGCAGTTTGCTTGTACATAGT 58.340 40.909 0.00 0.00 42.25 2.12
4517 12853 5.412594 CAGTTTGCTTGTACATAGTCATGGT 59.587 40.000 0.00 0.00 36.39 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 174 5.974751 GCAGTAGAGTAGTAATCACTTCTGC 59.025 44.000 14.87 14.87 37.81 4.26
175 181 9.504708 GTCCTATTAGCAGTAGAGTAGTAATCA 57.495 37.037 0.00 0.00 0.00 2.57
192 198 8.970859 ATTTGACAATCTTCCTGTCCTATTAG 57.029 34.615 0.82 0.00 42.13 1.73
193 199 9.177608 CAATTTGACAATCTTCCTGTCCTATTA 57.822 33.333 0.82 0.00 42.13 0.98
235 241 9.438291 GTTAATGATCCTGATTTCATGTTAACG 57.562 33.333 0.26 0.00 33.01 3.18
387 394 7.492344 ACTTGAAACTTCTAGTGCCAAAATTTG 59.508 33.333 5.87 0.00 40.74 2.32
418 428 5.185828 ACTTAACAGAGGGATGGCATTTTTC 59.814 40.000 0.00 0.00 0.00 2.29
419 429 5.086621 ACTTAACAGAGGGATGGCATTTTT 58.913 37.500 0.00 0.00 0.00 1.94
442 452 4.222810 TCTGCCACTATTTCTAAGCACAGA 59.777 41.667 0.00 0.00 0.00 3.41
443 453 4.507710 TCTGCCACTATTTCTAAGCACAG 58.492 43.478 0.00 0.00 0.00 3.66
446 456 4.937620 CAGTTCTGCCACTATTTCTAAGCA 59.062 41.667 0.00 0.00 0.00 3.91
448 458 7.856145 AATCAGTTCTGCCACTATTTCTAAG 57.144 36.000 0.00 0.00 0.00 2.18
451 461 9.905713 TTTATAATCAGTTCTGCCACTATTTCT 57.094 29.630 0.00 0.00 0.00 2.52
455 465 8.903820 GGTTTTTATAATCAGTTCTGCCACTAT 58.096 33.333 0.00 0.00 0.00 2.12
457 467 6.128007 CGGTTTTTATAATCAGTTCTGCCACT 60.128 38.462 0.00 0.00 0.00 4.00
458 468 6.027749 CGGTTTTTATAATCAGTTCTGCCAC 58.972 40.000 0.00 0.00 0.00 5.01
459 469 5.708230 ACGGTTTTTATAATCAGTTCTGCCA 59.292 36.000 0.00 0.00 0.00 4.92
460 470 6.190954 ACGGTTTTTATAATCAGTTCTGCC 57.809 37.500 0.00 0.00 0.00 4.85
461 471 6.526674 CCAACGGTTTTTATAATCAGTTCTGC 59.473 38.462 0.00 0.00 0.00 4.26
462 472 6.526674 GCCAACGGTTTTTATAATCAGTTCTG 59.473 38.462 0.00 0.00 0.00 3.02
463 473 6.349860 GGCCAACGGTTTTTATAATCAGTTCT 60.350 38.462 0.00 0.00 0.00 3.01
464 474 5.803461 GGCCAACGGTTTTTATAATCAGTTC 59.197 40.000 0.00 0.00 0.00 3.01
465 475 5.620429 CGGCCAACGGTTTTTATAATCAGTT 60.620 40.000 2.24 0.00 39.42 3.16
466 476 4.142556 CGGCCAACGGTTTTTATAATCAGT 60.143 41.667 2.24 0.00 39.42 3.41
467 477 4.347813 CGGCCAACGGTTTTTATAATCAG 58.652 43.478 2.24 0.00 39.42 2.90
482 492 0.896479 ACCCAAATACCACGGCCAAC 60.896 55.000 2.24 0.00 0.00 3.77
486 496 1.470051 AATGACCCAAATACCACGGC 58.530 50.000 0.00 0.00 0.00 5.68
488 498 3.756434 AGTGAAATGACCCAAATACCACG 59.244 43.478 0.00 0.00 0.00 4.94
490 500 4.202620 TGGAGTGAAATGACCCAAATACCA 60.203 41.667 0.00 0.00 0.00 3.25
530 565 1.453148 GTGCTCAAAAATGCAACTCGC 59.547 47.619 0.00 0.00 41.10 5.03
580 616 8.584157 TCATTTTGCCACTATAAGTTTCAACAT 58.416 29.630 0.00 0.00 0.00 2.71
773 811 9.498176 AATTTGAAATGCTCTGCTTAATTCTTT 57.502 25.926 0.00 0.00 0.00 2.52
851 889 5.084519 TGTTGACCAGACCACTTACTCTAT 58.915 41.667 0.00 0.00 0.00 1.98
852 890 4.476297 TGTTGACCAGACCACTTACTCTA 58.524 43.478 0.00 0.00 0.00 2.43
854 894 3.069729 ACTGTTGACCAGACCACTTACTC 59.930 47.826 0.00 0.00 44.49 2.59
855 895 3.039011 ACTGTTGACCAGACCACTTACT 58.961 45.455 0.00 0.00 44.49 2.24
918 2721 3.251571 ACGAAAAGAGCGGAGTACATTC 58.748 45.455 0.00 0.00 0.00 2.67
985 6057 3.220447 CCATGGTTTGGCTTTGCAG 57.780 52.632 2.57 0.00 39.09 4.41
1123 6198 3.745803 ACGGAGAAGGTCGGCGAC 61.746 66.667 30.72 30.72 0.00 5.19
1248 6323 1.307647 GGATGACTTGGGCATGGGT 59.692 57.895 0.00 0.00 0.00 4.51
1571 6662 2.202676 CGACCTCGAAGCAGAGCC 60.203 66.667 0.00 0.00 43.02 4.70
1623 6714 1.287425 CAATTTACTCTCCGCGACCC 58.713 55.000 8.23 0.00 0.00 4.46
1624 6715 2.005971 ACAATTTACTCTCCGCGACC 57.994 50.000 8.23 0.00 0.00 4.79
1626 6717 6.256321 GGTTTTATACAATTTACTCTCCGCGA 59.744 38.462 8.23 0.00 0.00 5.87
1627 6718 6.036300 TGGTTTTATACAATTTACTCTCCGCG 59.964 38.462 0.00 0.00 0.00 6.46
1628 6719 7.184779 GTGGTTTTATACAATTTACTCTCCGC 58.815 38.462 0.00 0.00 0.00 5.54
1643 6734 4.914177 AACCCTCGAAGGTGGTTTTATA 57.086 40.909 6.44 0.00 39.28 0.98
1657 6750 1.515081 TTTCGCAAACCTAACCCTCG 58.485 50.000 0.00 0.00 0.00 4.63
1681 6774 7.766278 GTCTTCTGCAGAGAAAATGTATCCTAA 59.234 37.037 17.43 0.00 37.77 2.69
1797 6891 0.029300 GAGCCGTTACGCCACGTATA 59.971 55.000 0.00 0.00 41.97 1.47
1893 7021 7.963532 AGAAAGCGGAGGTCTTTTCATATATA 58.036 34.615 0.00 0.00 37.06 0.86
1966 7095 1.975407 GGAGTTGTGGCTGCAGCAT 60.975 57.895 37.63 16.98 44.36 3.79
2727 7917 0.391228 GTGGGTCCCGTTTTTGCATT 59.609 50.000 2.65 0.00 0.00 3.56
2813 8005 6.636454 TTTCCCTGTAGAAGACACCATATT 57.364 37.500 0.00 0.00 33.31 1.28
2839 8032 5.944007 AGGTTTGCGAAAAACACTAGGATAT 59.056 36.000 6.70 0.00 32.04 1.63
3001 8194 2.060980 CCAGTAGAGCTTCCCGGCT 61.061 63.158 0.00 0.00 46.11 5.52
3050 8243 4.415150 CAGCGTGGCAGGGTCCAT 62.415 66.667 9.17 0.00 38.57 3.41
3209 8402 4.154347 GTCGCTCCCTCTGGCCTG 62.154 72.222 3.32 2.92 0.00 4.85
3258 8454 4.041917 CCCACACCACACGCATGC 62.042 66.667 7.91 7.91 0.00 4.06
3652 11308 2.358737 GCTACCAACGCCAGCAGT 60.359 61.111 0.00 0.00 35.35 4.40
3752 11408 5.347342 TGCTTCACATTTGTTACCACTTTG 58.653 37.500 0.00 0.00 0.00 2.77
3880 11556 9.781425 AGACTATGATCCATGTAGAGGAATAAT 57.219 33.333 0.00 0.00 38.93 1.28
3883 11559 7.477864 AGAGACTATGATCCATGTAGAGGAAT 58.522 38.462 0.00 0.00 38.93 3.01
4291 12626 7.820386 TGACAGCATTTAATGATTTCAAGCAAT 59.180 29.630 9.21 0.00 33.06 3.56
4314 12649 2.350484 GGTAAAGCAAAAGACCGCTGAC 60.350 50.000 0.00 0.00 38.82 3.51
4315 12650 1.877443 GGTAAAGCAAAAGACCGCTGA 59.123 47.619 0.00 0.00 38.82 4.26
4316 12651 1.880027 AGGTAAAGCAAAAGACCGCTG 59.120 47.619 0.00 0.00 38.82 5.18
4317 12652 1.880027 CAGGTAAAGCAAAAGACCGCT 59.120 47.619 0.00 0.00 41.20 5.52
4318 12653 1.607148 ACAGGTAAAGCAAAAGACCGC 59.393 47.619 0.00 0.00 37.04 5.68
4319 12654 3.810941 TGTACAGGTAAAGCAAAAGACCG 59.189 43.478 0.00 0.00 37.04 4.79
4320 12655 5.335661 CCATGTACAGGTAAAGCAAAAGACC 60.336 44.000 6.79 0.00 0.00 3.85
4321 12656 5.335661 CCCATGTACAGGTAAAGCAAAAGAC 60.336 44.000 6.79 0.00 0.00 3.01
4322 12657 4.764823 CCCATGTACAGGTAAAGCAAAAGA 59.235 41.667 6.79 0.00 0.00 2.52
4323 12658 4.618227 GCCCATGTACAGGTAAAGCAAAAG 60.618 45.833 6.79 0.00 0.00 2.27
4324 12659 3.257127 GCCCATGTACAGGTAAAGCAAAA 59.743 43.478 6.79 0.00 0.00 2.44
4325 12660 2.823154 GCCCATGTACAGGTAAAGCAAA 59.177 45.455 6.79 0.00 0.00 3.68
4326 12661 2.041081 AGCCCATGTACAGGTAAAGCAA 59.959 45.455 6.79 0.00 0.00 3.91
4327 12662 1.633432 AGCCCATGTACAGGTAAAGCA 59.367 47.619 6.79 0.00 0.00 3.91
4328 12663 2.420058 AGCCCATGTACAGGTAAAGC 57.580 50.000 6.79 4.11 0.00 3.51
4329 12664 5.885912 ACATTAAGCCCATGTACAGGTAAAG 59.114 40.000 6.79 0.00 32.88 1.85
4330 12665 5.822204 ACATTAAGCCCATGTACAGGTAAA 58.178 37.500 6.79 0.00 32.88 2.01
4331 12666 5.444744 ACATTAAGCCCATGTACAGGTAA 57.555 39.130 6.79 0.00 32.88 2.85
4332 12667 5.189928 CAACATTAAGCCCATGTACAGGTA 58.810 41.667 6.79 0.00 33.54 3.08
4333 12668 4.016444 CAACATTAAGCCCATGTACAGGT 58.984 43.478 6.79 0.00 33.54 4.00
4334 12669 4.016444 ACAACATTAAGCCCATGTACAGG 58.984 43.478 0.33 0.00 33.54 4.00
4335 12670 5.182950 TGAACAACATTAAGCCCATGTACAG 59.817 40.000 0.33 0.00 33.54 2.74
4336 12671 5.073428 TGAACAACATTAAGCCCATGTACA 58.927 37.500 0.00 0.00 33.54 2.90
4337 12672 5.637006 TGAACAACATTAAGCCCATGTAC 57.363 39.130 0.00 0.00 33.54 2.90
4338 12673 5.948758 TGATGAACAACATTAAGCCCATGTA 59.051 36.000 0.00 0.00 39.56 2.29
4339 12674 4.771577 TGATGAACAACATTAAGCCCATGT 59.228 37.500 0.00 0.00 39.56 3.21
4340 12675 5.327616 TGATGAACAACATTAAGCCCATG 57.672 39.130 0.00 0.00 39.56 3.66
4341 12676 5.895534 AGATGATGAACAACATTAAGCCCAT 59.104 36.000 0.00 0.00 39.56 4.00
4342 12677 5.263599 AGATGATGAACAACATTAAGCCCA 58.736 37.500 0.00 0.00 39.56 5.36
4343 12678 5.357878 TGAGATGATGAACAACATTAAGCCC 59.642 40.000 0.00 0.00 39.56 5.19
4344 12679 6.441093 TGAGATGATGAACAACATTAAGCC 57.559 37.500 0.00 0.00 39.56 4.35
4345 12680 9.661187 CTAATGAGATGATGAACAACATTAAGC 57.339 33.333 0.00 0.00 39.56 3.09
4346 12681 9.661187 GCTAATGAGATGATGAACAACATTAAG 57.339 33.333 0.00 0.00 39.56 1.85
4347 12682 9.176460 TGCTAATGAGATGATGAACAACATTAA 57.824 29.630 0.00 0.00 39.56 1.40
4348 12683 8.615211 GTGCTAATGAGATGATGAACAACATTA 58.385 33.333 0.00 0.00 39.56 1.90
4349 12684 7.338703 AGTGCTAATGAGATGATGAACAACATT 59.661 33.333 0.00 0.00 39.56 2.71
4350 12685 6.827251 AGTGCTAATGAGATGATGAACAACAT 59.173 34.615 0.00 0.00 42.47 2.71
4351 12686 6.175471 AGTGCTAATGAGATGATGAACAACA 58.825 36.000 0.00 0.00 0.00 3.33
4451 12787 6.679392 GCCAGTGTACAAGTAAAGCAAAAGAA 60.679 38.462 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.