Multiple sequence alignment - TraesCS7A01G207900

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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 TraesCS7A01G207900 chr7A 100.000 2651 0 0 1 2651 170594101 170591451 0.000000e+00 4896.0
1 TraesCS7A01G207900 chr7A 82.107 788 125 13 1777 2550 642090863 642090078 0.000000e+00 660.0
2 TraesCS7A01G207900 chr7A 78.808 302 64 0 1076 1377 636555328 636555027 1.240000e-48 204.0
3 TraesCS7A01G207900 chr7A 77.926 299 66 0 1079 1377 636312891 636312593 1.250000e-43 187.0
4 TraesCS7A01G207900 chr1B 90.690 1869 145 18 811 2651 318993459 318991592 0.000000e+00 2460.0
5 TraesCS7A01G207900 chr1B 93.789 1272 79 0 1380 2651 119134186 119132915 0.000000e+00 1912.0
6 TraesCS7A01G207900 chr1B 93.333 570 38 0 810 1379 119134783 119134214 0.000000e+00 843.0
7 TraesCS7A01G207900 chr1B 79.075 454 95 0 2198 2651 296764143 296764596 1.980000e-81 313.0
8 TraesCS7A01G207900 chr2B 93.526 1174 75 1 1478 2651 767657756 767658928 0.000000e+00 1746.0
9 TraesCS7A01G207900 chr2B 93.434 396 15 2 984 1379 767657363 767657747 6.360000e-161 577.0
10 TraesCS7A01G207900 chr2B 81.292 449 84 0 2203 2651 222243236 222242788 5.390000e-97 364.0
11 TraesCS7A01G207900 chr2B 100.000 29 0 0 1202 1230 379105311 379105339 1.000000e-03 54.7
12 TraesCS7A01G207900 chr2B 100.000 28 0 0 1203 1230 32648544 32648517 5.000000e-03 52.8
13 TraesCS7A01G207900 chr5A 78.362 1294 248 27 1379 2651 698220340 698221622 0.000000e+00 809.0
14 TraesCS7A01G207900 chr5A 82.007 578 92 10 809 1379 698219741 698220313 5.130000e-132 481.0
15 TraesCS7A01G207900 chr7B 81.675 573 95 8 810 1377 81696274 81696841 4.000000e-128 468.0
16 TraesCS7A01G207900 chr7B 85.714 385 51 4 2197 2579 81706618 81707000 1.140000e-108 403.0
17 TraesCS7A01G207900 chr7D 88.218 331 16 10 19 327 168263404 168263075 8.960000e-100 374.0
18 TraesCS7A01G207900 chr7D 87.449 247 12 2 525 757 168261422 168261181 1.560000e-67 267.0
19 TraesCS7A01G207900 chr7D 84.884 86 12 1 434 519 613914890 613914974 4.700000e-13 86.1
20 TraesCS7A01G207900 chrUn 87.915 331 17 9 19 327 91844990 91844661 4.170000e-98 368.0
21 TraesCS7A01G207900 chrUn 89.344 244 10 4 525 757 91842702 91842464 2.580000e-75 292.0
22 TraesCS7A01G207900 chr3D 74.480 913 179 41 814 1683 398281974 398282875 1.950000e-91 346.0
23 TraesCS7A01G207900 chr1A 82.838 303 52 0 2197 2499 554838455 554838757 3.360000e-69 272.0
24 TraesCS7A01G207900 chr6A 78.981 314 64 2 1065 1377 107831854 107832166 2.070000e-51 213.0
25 TraesCS7A01G207900 chr5B 75.068 365 86 5 1013 1377 640161498 640161139 5.870000e-37 165.0
26 TraesCS7A01G207900 chr5B 82.692 104 18 0 416 519 381759696 381759593 2.810000e-15 93.5
27 TraesCS7A01G207900 chr3B 78.922 204 38 3 1379 1578 530268382 530268584 1.660000e-27 134.0
28 TraesCS7A01G207900 chr3B 87.000 100 13 0 419 518 163367659 163367758 2.160000e-21 113.0
29 TraesCS7A01G207900 chr3A 86.842 76 10 0 436 511 138808975 138809050 4.700000e-13 86.1
30 TraesCS7A01G207900 chr5D 89.231 65 4 3 810 873 32932524 32932586 7.870000e-11 78.7
31 TraesCS7A01G207900 chr5D 94.737 38 2 0 903 940 513713195 513713158 2.850000e-05 60.2
32 TraesCS7A01G207900 chr2A 95.122 41 1 1 811 851 755471265 755471226 2.200000e-06 63.9
33 TraesCS7A01G207900 chr1D 88.462 52 5 1 1651 1702 488494521 488494571 7.920000e-06 62.1


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 TraesCS7A01G207900 chr7A 170591451 170594101 2650 True 4896.0 4896 100.0000 1 2651 1 chr7A.!!$R1 2650
1 TraesCS7A01G207900 chr7A 642090078 642090863 785 True 660.0 660 82.1070 1777 2550 1 chr7A.!!$R4 773
2 TraesCS7A01G207900 chr1B 318991592 318993459 1867 True 2460.0 2460 90.6900 811 2651 1 chr1B.!!$R1 1840
3 TraesCS7A01G207900 chr1B 119132915 119134783 1868 True 1377.5 1912 93.5610 810 2651 2 chr1B.!!$R2 1841
4 TraesCS7A01G207900 chr2B 767657363 767658928 1565 False 1161.5 1746 93.4800 984 2651 2 chr2B.!!$F2 1667
5 TraesCS7A01G207900 chr5A 698219741 698221622 1881 False 645.0 809 80.1845 809 2651 2 chr5A.!!$F1 1842
6 TraesCS7A01G207900 chr7B 81696274 81696841 567 False 468.0 468 81.6750 810 1377 1 chr7B.!!$F1 567
7 TraesCS7A01G207900 chr7D 168261181 168263404 2223 True 320.5 374 87.8335 19 757 2 chr7D.!!$R1 738
8 TraesCS7A01G207900 chrUn 91842464 91844990 2526 True 330.0 368 88.6295 19 757 2 chrUn.!!$R1 738
9 TraesCS7A01G207900 chr3D 398281974 398282875 901 False 346.0 346 74.4800 814 1683 1 chr3D.!!$F1 869

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
486 509 0.17900 ATTGCTACTCCCAAGCCGAG 59.821 55.0 0.00 0.00 39.30 4.63 F
790 2596 0.31179 CACGAAGTTGGCATGCTTGT 59.688 50.0 18.92 4.17 41.61 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1431 3396 0.560688 TCCTGGAAGCCAAACCCTTT 59.439 50.0 0.00 0.0 30.8 3.11 R
1698 3664 0.734889 CAGCTAGCACAAAATCCCCG 59.265 55.0 18.83 0.0 0.0 5.73 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
27 28 2.652095 CCCTCCACCTTCGCGGTTA 61.652 63.158 6.13 0.00 46.37 2.85
39 40 0.502695 CGCGGTTATGTATGCGTGAG 59.497 55.000 0.00 0.00 45.12 3.51
53 54 4.074526 TGAGCGAGGTCAGGCTGC 62.075 66.667 10.34 4.94 40.16 5.25
98 99 6.292542 GCTTTTCTTGAATGCTTGTCTTTTCC 60.293 38.462 0.00 0.00 35.97 3.13
106 107 6.097554 TGAATGCTTGTCTTTTCCACCTTTTA 59.902 34.615 0.00 0.00 0.00 1.52
112 113 8.925700 GCTTGTCTTTTCCACCTTTTATTATTG 58.074 33.333 0.00 0.00 0.00 1.90
141 142 4.282703 GGCTACCCATACGGAAGAGATAAA 59.717 45.833 0.00 0.00 34.64 1.40
182 183 6.266168 TGGTGTGCATTTCTTAATTACCAG 57.734 37.500 0.00 0.00 32.42 4.00
252 274 8.773404 TCTATTTCTACAGTCTGTTTTAAGCC 57.227 34.615 11.54 0.00 0.00 4.35
365 388 8.588290 AGTAATGTGGGTTTTTATAGCATTCA 57.412 30.769 0.00 0.00 0.00 2.57
366 389 9.030452 AGTAATGTGGGTTTTTATAGCATTCAA 57.970 29.630 0.00 0.00 0.00 2.69
367 390 9.301153 GTAATGTGGGTTTTTATAGCATTCAAG 57.699 33.333 0.00 0.00 0.00 3.02
368 391 6.909550 TGTGGGTTTTTATAGCATTCAAGT 57.090 33.333 0.00 0.00 0.00 3.16
370 393 7.375053 TGTGGGTTTTTATAGCATTCAAGTTC 58.625 34.615 0.00 0.00 0.00 3.01
381 404 5.809001 AGCATTCAAGTTCTATTGTCTCCA 58.191 37.500 0.00 0.00 0.00 3.86
383 406 7.568349 AGCATTCAAGTTCTATTGTCTCCATA 58.432 34.615 0.00 0.00 0.00 2.74
413 436 7.971183 TTTTTGCCTATTGGGTACAAAATTC 57.029 32.000 9.64 0.00 40.55 2.17
414 437 4.974368 TGCCTATTGGGTACAAAATTCG 57.026 40.909 0.00 0.00 40.55 3.34
415 438 4.590918 TGCCTATTGGGTACAAAATTCGA 58.409 39.130 0.00 0.00 40.55 3.71
416 439 4.396790 TGCCTATTGGGTACAAAATTCGAC 59.603 41.667 0.00 0.00 40.55 4.20
417 440 4.201980 GCCTATTGGGTACAAAATTCGACC 60.202 45.833 0.00 0.00 40.55 4.79
418 441 4.034742 CCTATTGGGTACAAAATTCGACCG 59.965 45.833 0.00 0.00 40.55 4.79
419 442 2.835580 TGGGTACAAAATTCGACCGA 57.164 45.000 0.00 0.00 32.38 4.69
420 443 3.337694 TGGGTACAAAATTCGACCGAT 57.662 42.857 0.00 0.00 32.38 4.18
422 445 4.829968 TGGGTACAAAATTCGACCGATTA 58.170 39.130 0.00 0.00 32.38 1.75
425 448 6.183360 TGGGTACAAAATTCGACCGATTAATG 60.183 38.462 0.00 0.00 32.38 1.90
441 464 6.599437 CGATTAATGGTCGGTTGATTAATCC 58.401 40.000 12.90 0.00 41.70 3.01
442 465 6.203915 CGATTAATGGTCGGTTGATTAATCCA 59.796 38.462 12.90 2.78 41.70 3.41
443 466 6.935741 TTAATGGTCGGTTGATTAATCCAG 57.064 37.500 12.90 0.00 0.00 3.86
444 467 3.992943 TGGTCGGTTGATTAATCCAGT 57.007 42.857 12.90 0.00 0.00 4.00
445 468 4.295141 TGGTCGGTTGATTAATCCAGTT 57.705 40.909 12.90 0.00 0.00 3.16
446 469 5.423704 TGGTCGGTTGATTAATCCAGTTA 57.576 39.130 12.90 0.00 0.00 2.24
447 470 5.806818 TGGTCGGTTGATTAATCCAGTTAA 58.193 37.500 12.90 0.00 36.75 2.01
448 471 6.419791 TGGTCGGTTGATTAATCCAGTTAAT 58.580 36.000 12.90 0.00 43.86 1.40
449 472 7.566569 TGGTCGGTTGATTAATCCAGTTAATA 58.433 34.615 12.90 0.00 41.82 0.98
450 473 7.713507 TGGTCGGTTGATTAATCCAGTTAATAG 59.286 37.037 12.90 0.02 41.82 1.73
452 475 7.929785 GTCGGTTGATTAATCCAGTTAATAGGA 59.070 37.037 12.90 1.84 41.82 2.94
453 476 8.656806 TCGGTTGATTAATCCAGTTAATAGGAT 58.343 33.333 12.90 5.97 46.33 3.24
454 477 8.721478 CGGTTGATTAATCCAGTTAATAGGATG 58.279 37.037 12.90 0.00 43.67 3.51
455 478 9.793259 GGTTGATTAATCCAGTTAATAGGATGA 57.207 33.333 12.90 3.04 43.67 2.92
463 486 7.539034 TCCAGTTAATAGGATGATTCATCGA 57.461 36.000 18.09 10.52 41.35 3.59
464 487 8.138928 TCCAGTTAATAGGATGATTCATCGAT 57.861 34.615 18.09 12.09 41.35 3.59
465 488 8.597167 TCCAGTTAATAGGATGATTCATCGATT 58.403 33.333 18.09 19.46 41.35 3.34
466 489 9.875691 CCAGTTAATAGGATGATTCATCGATTA 57.124 33.333 18.09 18.68 41.35 1.75
472 495 9.458727 AATAGGATGATTCATCGATTAATTGCT 57.541 29.630 18.09 9.93 41.35 3.91
474 497 8.261492 AGGATGATTCATCGATTAATTGCTAC 57.739 34.615 18.09 2.53 41.35 3.58
476 499 8.386606 GGATGATTCATCGATTAATTGCTACTC 58.613 37.037 18.09 0.00 41.35 2.59
478 501 6.650807 TGATTCATCGATTAATTGCTACTCCC 59.349 38.462 6.29 0.00 0.00 4.30
479 502 5.545063 TCATCGATTAATTGCTACTCCCA 57.455 39.130 0.00 0.00 0.00 4.37
480 503 5.924356 TCATCGATTAATTGCTACTCCCAA 58.076 37.500 0.00 0.00 0.00 4.12
481 504 5.991606 TCATCGATTAATTGCTACTCCCAAG 59.008 40.000 0.00 0.00 0.00 3.61
482 505 4.127171 TCGATTAATTGCTACTCCCAAGC 58.873 43.478 0.00 0.00 40.50 4.01
483 506 3.251004 CGATTAATTGCTACTCCCAAGCC 59.749 47.826 0.00 0.00 39.30 4.35
484 507 2.325583 TAATTGCTACTCCCAAGCCG 57.674 50.000 0.00 0.00 39.30 5.52
485 508 0.618458 AATTGCTACTCCCAAGCCGA 59.382 50.000 0.00 0.00 39.30 5.54
486 509 0.179000 ATTGCTACTCCCAAGCCGAG 59.821 55.000 0.00 0.00 39.30 4.63
487 510 2.202946 GCTACTCCCAAGCCGAGC 60.203 66.667 0.00 0.00 33.73 5.03
488 511 2.105128 CTACTCCCAAGCCGAGCG 59.895 66.667 0.00 0.00 0.00 5.03
489 512 2.361992 TACTCCCAAGCCGAGCGA 60.362 61.111 0.00 0.00 0.00 4.93
490 513 2.343163 CTACTCCCAAGCCGAGCGAG 62.343 65.000 0.00 0.00 0.00 5.03
491 514 3.764466 CTCCCAAGCCGAGCGAGT 61.764 66.667 0.00 0.00 0.00 4.18
492 515 2.361992 TCCCAAGCCGAGCGAGTA 60.362 61.111 0.00 0.00 0.00 2.59
493 516 2.105128 CCCAAGCCGAGCGAGTAG 59.895 66.667 0.00 0.00 0.00 2.57
494 517 2.105128 CCAAGCCGAGCGAGTAGG 59.895 66.667 0.00 0.00 0.00 3.18
496 1783 1.381928 CCAAGCCGAGCGAGTAGGTA 61.382 60.000 0.00 0.00 0.00 3.08
498 1785 1.382692 AAGCCGAGCGAGTAGGTACC 61.383 60.000 2.73 2.73 0.00 3.34
503 1790 2.283298 CGAGCGAGTAGGTACCAGTTA 58.717 52.381 15.94 0.00 0.00 2.24
504 1791 2.679837 CGAGCGAGTAGGTACCAGTTAA 59.320 50.000 15.94 0.00 0.00 2.01
508 1795 3.065925 GCGAGTAGGTACCAGTTAACGAT 59.934 47.826 15.94 0.00 0.00 3.73
512 1799 5.173664 AGTAGGTACCAGTTAACGATTTGC 58.826 41.667 15.94 0.00 0.00 3.68
516 1803 4.453136 GGTACCAGTTAACGATTTGCTCAA 59.547 41.667 7.15 0.00 0.00 3.02
517 1804 4.483476 ACCAGTTAACGATTTGCTCAAC 57.517 40.909 0.00 0.00 0.00 3.18
523 1810 5.295787 AGTTAACGATTTGCTCAACACTCAA 59.704 36.000 0.00 0.00 0.00 3.02
606 2412 1.487976 TGGCCTTGCAATTTTGGACAA 59.512 42.857 8.49 0.00 34.20 3.18
757 2563 2.799917 GCCGCACCTAGACAATAGACAG 60.800 54.545 0.00 0.00 0.00 3.51
758 2564 2.688446 CCGCACCTAGACAATAGACAGA 59.312 50.000 0.00 0.00 0.00 3.41
759 2565 3.489398 CCGCACCTAGACAATAGACAGAC 60.489 52.174 0.00 0.00 0.00 3.51
760 2566 3.378742 CGCACCTAGACAATAGACAGACT 59.621 47.826 0.00 0.00 0.00 3.24
761 2567 4.496673 CGCACCTAGACAATAGACAGACTC 60.497 50.000 0.00 0.00 0.00 3.36
762 2568 4.496673 GCACCTAGACAATAGACAGACTCG 60.497 50.000 0.00 0.00 0.00 4.18
763 2569 3.628487 ACCTAGACAATAGACAGACTCGC 59.372 47.826 0.00 0.00 0.00 5.03
764 2570 3.628032 CCTAGACAATAGACAGACTCGCA 59.372 47.826 0.00 0.00 0.00 5.10
765 2571 3.495670 AGACAATAGACAGACTCGCAC 57.504 47.619 0.00 0.00 0.00 5.34
766 2572 3.085533 AGACAATAGACAGACTCGCACT 58.914 45.455 0.00 0.00 0.00 4.40
767 2573 4.262617 AGACAATAGACAGACTCGCACTA 58.737 43.478 0.00 0.00 0.00 2.74
768 2574 4.700692 AGACAATAGACAGACTCGCACTAA 59.299 41.667 0.00 0.00 0.00 2.24
769 2575 5.183331 AGACAATAGACAGACTCGCACTAAA 59.817 40.000 0.00 0.00 0.00 1.85
770 2576 5.403246 ACAATAGACAGACTCGCACTAAAG 58.597 41.667 0.00 0.00 0.00 1.85
771 2577 2.355717 AGACAGACTCGCACTAAAGC 57.644 50.000 0.00 0.00 0.00 3.51
772 2578 1.613925 AGACAGACTCGCACTAAAGCA 59.386 47.619 0.00 0.00 0.00 3.91
773 2579 1.721926 GACAGACTCGCACTAAAGCAC 59.278 52.381 0.00 0.00 0.00 4.40
774 2580 0.710567 CAGACTCGCACTAAAGCACG 59.289 55.000 0.00 0.00 0.00 5.34
775 2581 0.596577 AGACTCGCACTAAAGCACGA 59.403 50.000 0.00 0.00 0.00 4.35
776 2582 1.000607 AGACTCGCACTAAAGCACGAA 60.001 47.619 0.00 0.00 33.61 3.85
777 2583 1.387084 GACTCGCACTAAAGCACGAAG 59.613 52.381 0.00 0.00 33.61 3.79
779 2585 1.792949 CTCGCACTAAAGCACGAAGTT 59.207 47.619 0.00 0.00 41.61 2.66
780 2586 1.525197 TCGCACTAAAGCACGAAGTTG 59.475 47.619 0.00 0.00 41.61 3.16
781 2587 1.398451 CGCACTAAAGCACGAAGTTGG 60.398 52.381 0.00 0.00 41.61 3.77
782 2588 1.663161 GCACTAAAGCACGAAGTTGGC 60.663 52.381 0.00 0.00 41.61 4.52
783 2589 1.601903 CACTAAAGCACGAAGTTGGCA 59.398 47.619 0.00 0.00 41.61 4.92
784 2590 2.226437 CACTAAAGCACGAAGTTGGCAT 59.774 45.455 0.00 0.00 41.61 4.40
785 2591 2.226437 ACTAAAGCACGAAGTTGGCATG 59.774 45.455 0.00 0.00 41.61 4.06
786 2592 0.318955 AAAGCACGAAGTTGGCATGC 60.319 50.000 9.90 9.90 41.61 4.06
787 2593 1.601759 AGCACGAAGTTGGCATGCT 60.602 52.632 18.92 5.24 41.61 3.79
788 2594 1.174712 AGCACGAAGTTGGCATGCTT 61.175 50.000 18.92 3.22 44.01 3.91
789 2595 1.005294 GCACGAAGTTGGCATGCTTG 61.005 55.000 18.92 3.46 41.61 4.01
790 2596 0.311790 CACGAAGTTGGCATGCTTGT 59.688 50.000 18.92 4.17 41.61 3.16
791 2597 1.032014 ACGAAGTTGGCATGCTTGTT 58.968 45.000 18.92 6.25 37.78 2.83
792 2598 2.031245 CACGAAGTTGGCATGCTTGTTA 60.031 45.455 18.92 0.00 41.61 2.41
793 2599 2.226437 ACGAAGTTGGCATGCTTGTTAG 59.774 45.455 18.92 9.01 37.78 2.34
794 2600 2.226437 CGAAGTTGGCATGCTTGTTAGT 59.774 45.455 18.92 0.00 0.00 2.24
795 2601 3.304659 CGAAGTTGGCATGCTTGTTAGTT 60.305 43.478 18.92 7.60 0.00 2.24
796 2602 3.648339 AGTTGGCATGCTTGTTAGTTG 57.352 42.857 18.92 0.00 0.00 3.16
797 2603 2.958355 AGTTGGCATGCTTGTTAGTTGT 59.042 40.909 18.92 0.00 0.00 3.32
798 2604 3.004734 AGTTGGCATGCTTGTTAGTTGTC 59.995 43.478 18.92 0.00 0.00 3.18
799 2605 1.885887 TGGCATGCTTGTTAGTTGTCC 59.114 47.619 18.92 0.00 0.00 4.02
800 2606 1.202348 GGCATGCTTGTTAGTTGTCCC 59.798 52.381 18.92 0.00 0.00 4.46
801 2607 2.162681 GCATGCTTGTTAGTTGTCCCT 58.837 47.619 11.37 0.00 0.00 4.20
802 2608 3.343617 GCATGCTTGTTAGTTGTCCCTA 58.656 45.455 11.37 0.00 0.00 3.53
803 2609 3.127030 GCATGCTTGTTAGTTGTCCCTAC 59.873 47.826 11.37 0.00 0.00 3.18
804 2610 3.034721 TGCTTGTTAGTTGTCCCTACG 57.965 47.619 0.00 0.00 0.00 3.51
805 2611 2.289195 TGCTTGTTAGTTGTCCCTACGG 60.289 50.000 0.00 0.00 0.00 4.02
806 2612 2.028748 GCTTGTTAGTTGTCCCTACGGA 60.029 50.000 0.00 0.00 35.01 4.69
807 2613 3.555586 GCTTGTTAGTTGTCCCTACGGAA 60.556 47.826 0.00 0.00 40.92 4.30
847 2653 2.165845 ACCTAGGGTTTCGACATCTTCG 59.834 50.000 14.81 0.00 40.52 3.79
856 2663 3.665675 GACATCTTCGGGCGCCACT 62.666 63.158 30.85 1.93 0.00 4.00
981 2801 1.137479 CCGATTGGGTAAGAAGGCGTA 59.863 52.381 0.00 0.00 0.00 4.42
1032 2853 0.950836 CGAGATCGCAGAGGAGACAT 59.049 55.000 0.00 0.00 43.63 3.06
1402 3367 2.176273 GCGCAGATTCATCGCCTGT 61.176 57.895 0.30 0.00 42.71 4.00
1431 3396 0.751277 TCCTTATCGAACCGGCGGTA 60.751 55.000 34.37 18.33 33.12 4.02
1476 3441 2.180276 GAGGTGGAAGAGGTTCAGCTA 58.820 52.381 0.00 0.00 33.93 3.32
1649 3615 3.916359 TTGTGGTGAGTTTGGTCACTA 57.084 42.857 4.14 0.00 45.34 2.74
1698 3664 5.659426 CACGATGAAACAAAGTTTGAATGC 58.341 37.500 22.23 9.48 0.00 3.56
1726 3692 6.128742 GGATTTTGTGCTAGCTGACAATTTTG 60.129 38.462 18.24 0.00 32.27 2.44
1878 3844 6.240894 ACCAATGCAGTCAGAAGAGAATAAA 58.759 36.000 0.00 0.00 0.00 1.40
2003 3969 0.324943 AATGCTACGAGCCCAACAGT 59.675 50.000 0.00 0.00 41.51 3.55
2043 4024 4.680237 TCCCTTGCGCTGGTGACG 62.680 66.667 9.73 0.00 0.00 4.35
2052 4033 1.525077 GCTGGTGACGGTGGAACAA 60.525 57.895 0.00 0.00 44.16 2.83
2083 4064 0.971959 TCCACTACCGCCGGTGTATT 60.972 55.000 21.20 2.40 36.19 1.89
2135 4116 1.985895 GAAGGGAGGGAAGGAACAAGA 59.014 52.381 0.00 0.00 0.00 3.02
2165 4146 2.561187 TGATGGGTCCCTGAAGATCAA 58.439 47.619 10.00 0.00 0.00 2.57
2168 4149 1.290134 GGGTCCCTGAAGATCAAGGT 58.710 55.000 0.00 0.00 30.08 3.50
2349 4330 7.418337 ACCCTCTTTTGTATTGTTGAAACTT 57.582 32.000 0.00 0.00 0.00 2.66
2412 4393 9.448438 GTATTGGTTATGACAATGGATATGCTA 57.552 33.333 0.00 0.00 38.84 3.49
2485 4470 8.147704 TCCAATAAAAATTGAGGTTCTTGGTTC 58.852 33.333 0.00 0.00 33.87 3.62
2533 4518 1.063567 AGAGGAACCTGGTAGCGATCT 60.064 52.381 0.00 0.46 0.00 2.75
2540 4525 1.393603 CTGGTAGCGATCTGTGGAGA 58.606 55.000 0.00 0.00 0.00 3.71
2550 4535 4.678044 GCGATCTGTGGAGAATGACACTTA 60.678 45.833 0.00 0.00 38.39 2.24
2639 4624 2.646175 CGATCTCCCGTGGGTGTGT 61.646 63.158 4.53 0.00 36.47 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.249073 GACCTCGCTCACGCATACAT 60.249 55.000 0.00 0.00 39.84 2.29
53 54 1.586028 CATGTTGGTCCCAAAGGCG 59.414 57.895 0.00 0.00 37.70 5.52
98 99 4.398044 AGCCCGTGACAATAATAAAAGGTG 59.602 41.667 0.00 0.00 0.00 4.00
106 107 2.632987 GGGTAGCCCGTGACAATAAT 57.367 50.000 0.00 0.00 32.13 1.28
141 142 1.877443 CCAAAATCACCTCGTTTCGGT 59.123 47.619 0.00 0.00 34.38 4.69
230 252 8.465273 AAAGGCTTAAAACAGACTGTAGAAAT 57.535 30.769 8.91 0.00 29.84 2.17
340 363 8.588290 TGAATGCTATAAAAACCCACATTACT 57.412 30.769 0.00 0.00 0.00 2.24
341 364 9.301153 CTTGAATGCTATAAAAACCCACATTAC 57.699 33.333 0.00 0.00 0.00 1.89
342 365 9.030452 ACTTGAATGCTATAAAAACCCACATTA 57.970 29.630 0.00 0.00 0.00 1.90
343 366 7.906327 ACTTGAATGCTATAAAAACCCACATT 58.094 30.769 0.00 0.00 0.00 2.71
344 367 7.480760 ACTTGAATGCTATAAAAACCCACAT 57.519 32.000 0.00 0.00 0.00 3.21
346 369 7.602753 AGAACTTGAATGCTATAAAAACCCAC 58.397 34.615 0.00 0.00 0.00 4.61
356 379 7.568349 TGGAGACAATAGAACTTGAATGCTAT 58.432 34.615 0.00 0.00 37.44 2.97
358 381 5.809001 TGGAGACAATAGAACTTGAATGCT 58.191 37.500 0.00 0.00 37.44 3.79
395 418 4.034742 CGGTCGAATTTTGTACCCAATAGG 59.965 45.833 0.00 0.00 43.78 2.57
396 419 4.871557 TCGGTCGAATTTTGTACCCAATAG 59.128 41.667 0.00 0.00 0.00 1.73
398 421 3.677190 TCGGTCGAATTTTGTACCCAAT 58.323 40.909 0.00 0.00 0.00 3.16
400 423 2.835580 TCGGTCGAATTTTGTACCCA 57.164 45.000 0.00 0.00 0.00 4.51
402 425 6.183360 ACCATTAATCGGTCGAATTTTGTACC 60.183 38.462 0.00 0.00 27.30 3.34
403 426 6.778108 ACCATTAATCGGTCGAATTTTGTAC 58.222 36.000 0.00 0.00 27.30 2.90
405 428 5.875930 GACCATTAATCGGTCGAATTTTGT 58.124 37.500 16.33 0.00 43.36 2.83
417 440 6.203915 TGGATTAATCAACCGACCATTAATCG 59.796 38.462 17.07 0.00 43.95 3.34
418 441 7.228706 ACTGGATTAATCAACCGACCATTAATC 59.771 37.037 17.07 12.31 43.11 1.75
419 442 7.060421 ACTGGATTAATCAACCGACCATTAAT 58.940 34.615 17.07 0.00 36.05 1.40
420 443 6.419791 ACTGGATTAATCAACCGACCATTAA 58.580 36.000 17.07 0.00 0.00 1.40
422 445 4.855340 ACTGGATTAATCAACCGACCATT 58.145 39.130 17.07 0.00 0.00 3.16
425 448 6.937436 ATTAACTGGATTAATCAACCGACC 57.063 37.500 17.07 0.00 38.88 4.79
428 451 8.721478 CATCCTATTAACTGGATTAATCAACCG 58.279 37.037 17.07 4.73 41.66 4.44
429 452 9.793259 TCATCCTATTAACTGGATTAATCAACC 57.207 33.333 17.07 1.34 41.66 3.77
436 459 9.875691 CGATGAATCATCCTATTAACTGGATTA 57.124 33.333 16.71 2.67 40.76 1.75
437 460 8.597167 TCGATGAATCATCCTATTAACTGGATT 58.403 33.333 16.71 0.00 40.76 3.01
438 461 8.138928 TCGATGAATCATCCTATTAACTGGAT 57.861 34.615 16.71 5.50 43.23 3.41
439 462 7.539034 TCGATGAATCATCCTATTAACTGGA 57.461 36.000 16.71 2.44 37.57 3.86
440 463 8.783833 AATCGATGAATCATCCTATTAACTGG 57.216 34.615 16.71 0.15 37.57 4.00
446 469 9.458727 AGCAATTAATCGATGAATCATCCTATT 57.541 29.630 16.71 17.02 37.57 1.73
448 471 9.371136 GTAGCAATTAATCGATGAATCATCCTA 57.629 33.333 16.71 6.53 37.57 2.94
449 472 8.099537 AGTAGCAATTAATCGATGAATCATCCT 58.900 33.333 16.71 7.65 37.57 3.24
450 473 8.261492 AGTAGCAATTAATCGATGAATCATCC 57.739 34.615 16.71 0.62 37.57 3.51
452 475 7.335422 GGGAGTAGCAATTAATCGATGAATCAT 59.665 37.037 8.50 0.00 0.00 2.45
453 476 6.650807 GGGAGTAGCAATTAATCGATGAATCA 59.349 38.462 8.50 0.00 0.00 2.57
454 477 6.650807 TGGGAGTAGCAATTAATCGATGAATC 59.349 38.462 8.50 0.00 0.00 2.52
455 478 6.533730 TGGGAGTAGCAATTAATCGATGAAT 58.466 36.000 1.78 1.78 0.00 2.57
456 479 5.924356 TGGGAGTAGCAATTAATCGATGAA 58.076 37.500 0.00 0.00 0.00 2.57
457 480 5.545063 TGGGAGTAGCAATTAATCGATGA 57.455 39.130 0.00 0.00 0.00 2.92
458 481 5.334414 GCTTGGGAGTAGCAATTAATCGATG 60.334 44.000 0.00 0.00 38.51 3.84
459 482 4.757149 GCTTGGGAGTAGCAATTAATCGAT 59.243 41.667 0.00 0.00 38.51 3.59
460 483 4.127171 GCTTGGGAGTAGCAATTAATCGA 58.873 43.478 0.00 0.00 38.51 3.59
461 484 3.251004 GGCTTGGGAGTAGCAATTAATCG 59.749 47.826 0.00 0.00 40.42 3.34
463 486 3.118038 TCGGCTTGGGAGTAGCAATTAAT 60.118 43.478 0.00 0.00 40.42 1.40
464 487 2.237643 TCGGCTTGGGAGTAGCAATTAA 59.762 45.455 0.00 0.00 40.42 1.40
465 488 1.834896 TCGGCTTGGGAGTAGCAATTA 59.165 47.619 0.00 0.00 40.42 1.40
466 489 0.618458 TCGGCTTGGGAGTAGCAATT 59.382 50.000 0.00 0.00 40.42 2.32
470 493 2.202946 GCTCGGCTTGGGAGTAGC 60.203 66.667 0.00 0.00 37.91 3.58
472 495 2.361992 TCGCTCGGCTTGGGAGTA 60.362 61.111 0.00 0.00 34.00 2.59
473 496 3.764466 CTCGCTCGGCTTGGGAGT 61.764 66.667 10.80 0.00 38.94 3.85
474 497 2.343163 CTACTCGCTCGGCTTGGGAG 62.343 65.000 15.29 15.29 45.92 4.30
476 499 2.105128 CTACTCGCTCGGCTTGGG 59.895 66.667 0.00 0.00 0.00 4.12
478 501 0.248539 GTACCTACTCGCTCGGCTTG 60.249 60.000 0.00 0.00 0.00 4.01
479 502 1.382692 GGTACCTACTCGCTCGGCTT 61.383 60.000 4.06 0.00 0.00 4.35
480 503 1.823041 GGTACCTACTCGCTCGGCT 60.823 63.158 4.06 0.00 0.00 5.52
481 504 2.061182 CTGGTACCTACTCGCTCGGC 62.061 65.000 14.36 0.00 0.00 5.54
482 505 0.747283 ACTGGTACCTACTCGCTCGG 60.747 60.000 14.36 0.00 0.00 4.63
483 506 1.093159 AACTGGTACCTACTCGCTCG 58.907 55.000 14.36 0.00 0.00 5.03
484 507 3.486542 CGTTAACTGGTACCTACTCGCTC 60.487 52.174 14.36 0.00 0.00 5.03
485 508 2.421424 CGTTAACTGGTACCTACTCGCT 59.579 50.000 14.36 0.00 0.00 4.93
486 509 2.420022 TCGTTAACTGGTACCTACTCGC 59.580 50.000 14.36 0.00 0.00 5.03
487 510 4.889832 ATCGTTAACTGGTACCTACTCG 57.110 45.455 14.36 10.34 0.00 4.18
488 511 5.290400 GCAAATCGTTAACTGGTACCTACTC 59.710 44.000 14.36 0.00 0.00 2.59
489 512 5.046807 AGCAAATCGTTAACTGGTACCTACT 60.047 40.000 14.36 0.00 0.00 2.57
490 513 5.173664 AGCAAATCGTTAACTGGTACCTAC 58.826 41.667 14.36 2.90 0.00 3.18
491 514 5.047164 TGAGCAAATCGTTAACTGGTACCTA 60.047 40.000 14.36 0.00 0.00 3.08
492 515 4.251268 GAGCAAATCGTTAACTGGTACCT 58.749 43.478 14.36 0.00 0.00 3.08
493 516 3.998341 TGAGCAAATCGTTAACTGGTACC 59.002 43.478 4.43 4.43 0.00 3.34
494 517 5.049954 TGTTGAGCAAATCGTTAACTGGTAC 60.050 40.000 3.71 0.00 0.00 3.34
496 1783 3.880490 TGTTGAGCAAATCGTTAACTGGT 59.120 39.130 3.71 0.37 0.00 4.00
498 1785 5.095691 AGTGTTGAGCAAATCGTTAACTG 57.904 39.130 3.71 0.00 0.00 3.16
503 1790 4.630894 TTTGAGTGTTGAGCAAATCGTT 57.369 36.364 0.00 0.00 0.00 3.85
504 1791 4.630894 TTTTGAGTGTTGAGCAAATCGT 57.369 36.364 0.00 0.00 32.27 3.73
523 1810 9.790389 TCACAAACAAATGATACGTAACTTTTT 57.210 25.926 12.18 6.34 0.00 1.94
532 2324 5.059587 GCACATGTCACAAACAAATGATACG 59.940 40.000 0.00 0.00 42.37 3.06
543 2335 7.715657 AGAAGAAAAATAGCACATGTCACAAA 58.284 30.769 0.00 0.00 0.00 2.83
606 2412 2.248248 TCTGTTCCTCGTGTCTTGGAT 58.752 47.619 0.00 0.00 0.00 3.41
671 2477 7.063898 GCTTTGTGCTTCTTTTCTTTTTCTTCT 59.936 33.333 0.00 0.00 38.95 2.85
672 2478 7.176075 GCTTTGTGCTTCTTTTCTTTTTCTTC 58.824 34.615 0.00 0.00 38.95 2.87
673 2479 7.065216 GCTTTGTGCTTCTTTTCTTTTTCTT 57.935 32.000 0.00 0.00 38.95 2.52
674 2480 6.653273 GCTTTGTGCTTCTTTTCTTTTTCT 57.347 33.333 0.00 0.00 38.95 2.52
757 2563 1.387084 CTTCGTGCTTTAGTGCGAGTC 59.613 52.381 0.00 0.00 34.78 3.36
758 2564 1.269621 ACTTCGTGCTTTAGTGCGAGT 60.270 47.619 0.00 0.00 34.78 4.18
759 2565 1.419374 ACTTCGTGCTTTAGTGCGAG 58.581 50.000 0.00 0.00 34.78 5.03
760 2566 1.525197 CAACTTCGTGCTTTAGTGCGA 59.475 47.619 0.00 0.00 35.36 5.10
761 2567 1.398451 CCAACTTCGTGCTTTAGTGCG 60.398 52.381 0.00 0.00 35.36 5.34
762 2568 1.663161 GCCAACTTCGTGCTTTAGTGC 60.663 52.381 0.00 0.00 0.00 4.40
763 2569 1.601903 TGCCAACTTCGTGCTTTAGTG 59.398 47.619 0.00 0.00 0.00 2.74
764 2570 1.961793 TGCCAACTTCGTGCTTTAGT 58.038 45.000 0.00 0.00 0.00 2.24
765 2571 2.855180 CATGCCAACTTCGTGCTTTAG 58.145 47.619 0.00 0.00 0.00 1.85
766 2572 1.068610 GCATGCCAACTTCGTGCTTTA 60.069 47.619 6.36 0.00 41.78 1.85
767 2573 0.318955 GCATGCCAACTTCGTGCTTT 60.319 50.000 6.36 0.00 41.78 3.51
768 2574 1.286880 GCATGCCAACTTCGTGCTT 59.713 52.632 6.36 0.00 41.78 3.91
769 2575 2.956987 GCATGCCAACTTCGTGCT 59.043 55.556 6.36 0.00 41.78 4.40
770 2576 1.005294 CAAGCATGCCAACTTCGTGC 61.005 55.000 15.66 0.00 44.47 5.34
771 2577 0.311790 ACAAGCATGCCAACTTCGTG 59.688 50.000 15.66 2.64 0.00 4.35
772 2578 1.032014 AACAAGCATGCCAACTTCGT 58.968 45.000 15.66 0.87 0.00 3.85
773 2579 2.226437 ACTAACAAGCATGCCAACTTCG 59.774 45.455 15.66 0.28 0.00 3.79
774 2580 3.923017 ACTAACAAGCATGCCAACTTC 57.077 42.857 15.66 0.00 0.00 3.01
775 2581 3.384467 ACAACTAACAAGCATGCCAACTT 59.616 39.130 15.66 0.00 0.00 2.66
776 2582 2.958355 ACAACTAACAAGCATGCCAACT 59.042 40.909 15.66 0.00 0.00 3.16
777 2583 3.308530 GACAACTAACAAGCATGCCAAC 58.691 45.455 15.66 0.00 0.00 3.77
778 2584 2.295909 GGACAACTAACAAGCATGCCAA 59.704 45.455 15.66 0.00 0.00 4.52
779 2585 1.885887 GGACAACTAACAAGCATGCCA 59.114 47.619 15.66 0.00 0.00 4.92
780 2586 1.202348 GGGACAACTAACAAGCATGCC 59.798 52.381 15.66 0.00 0.00 4.40
781 2587 2.162681 AGGGACAACTAACAAGCATGC 58.837 47.619 10.51 10.51 0.00 4.06
782 2588 3.370978 CGTAGGGACAACTAACAAGCATG 59.629 47.826 0.00 0.00 0.00 4.06
783 2589 3.596214 CGTAGGGACAACTAACAAGCAT 58.404 45.455 0.00 0.00 0.00 3.79
784 2590 3.034721 CGTAGGGACAACTAACAAGCA 57.965 47.619 0.00 0.00 0.00 3.91
953 2771 1.004979 CTTACCCAATCGGAAACCCCA 59.995 52.381 0.00 0.00 34.64 4.96
981 2801 3.708631 ACATCCTTTGAGATCCGATCTGT 59.291 43.478 15.85 3.03 40.38 3.41
1032 2853 0.967887 CCTCCGCTGACTCCTTCTCA 60.968 60.000 0.00 0.00 0.00 3.27
1431 3396 0.560688 TCCTGGAAGCCAAACCCTTT 59.439 50.000 0.00 0.00 30.80 3.11
1476 3441 4.383010 CCAAAGAAACCAGCAGGAAGTTTT 60.383 41.667 0.35 0.00 38.69 2.43
1649 3615 1.047596 ATCTCCGCACTCCTCATGCT 61.048 55.000 0.00 0.00 41.10 3.79
1698 3664 0.734889 CAGCTAGCACAAAATCCCCG 59.265 55.000 18.83 0.00 0.00 5.73
1726 3692 2.281276 ACCGGTCGGCTTGAAACC 60.281 61.111 0.00 0.00 39.32 3.27
1753 3719 2.674220 GGCCCCTCTGTCCTCCAAG 61.674 68.421 0.00 0.00 0.00 3.61
1864 3830 6.379703 CCTCCTGAGTCTTTATTCTCTTCTGA 59.620 42.308 0.00 0.00 0.00 3.27
1878 3844 0.907230 GTTCAGCCCCTCCTGAGTCT 60.907 60.000 0.00 0.00 42.34 3.24
2003 3969 1.127567 ACTTGCAGCCACCACCTCTA 61.128 55.000 0.00 0.00 0.00 2.43
2043 4024 1.782028 GCACTCCGTGTTGTTCCACC 61.782 60.000 0.00 0.00 35.75 4.61
2083 4064 2.708861 TGCACTCTTTTCTAGGGGACAA 59.291 45.455 0.00 0.00 0.00 3.18
2135 4116 4.915809 TCAGGGACCCATCAATATCTTCAT 59.084 41.667 14.60 0.00 0.00 2.57
2165 4146 1.988107 TCTCCTTCATGCTTTCCACCT 59.012 47.619 0.00 0.00 0.00 4.00
2168 4149 4.019051 TGATCTTCTCCTTCATGCTTTCCA 60.019 41.667 0.00 0.00 0.00 3.53
2379 4360 6.603201 CCATTGTCATAACCAATACTTCCAGT 59.397 38.462 0.00 0.00 31.52 4.00
2412 4393 5.198965 TCCGCTTCTACCTTGACTACTTAT 58.801 41.667 0.00 0.00 0.00 1.73
2533 4518 6.611236 TCCATAGATAAGTGTCATTCTCCACA 59.389 38.462 0.00 0.00 33.99 4.17
2540 4525 5.604231 TGCCTCTCCATAGATAAGTGTCATT 59.396 40.000 0.00 0.00 0.00 2.57
2550 4535 3.230134 GAGTCTGTGCCTCTCCATAGAT 58.770 50.000 0.00 0.00 35.79 1.98


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

AutoCloner maintained by Alex Coulton.