Multiple sequence alignment - TraesCS5A01G000300

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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 TraesCS5A01G000300 chr5A 100.000 4275 0 0 1 4275 30889 26615 0.000000e+00 7895.0
1 TraesCS5A01G000300 chr5A 93.137 408 20 4 222 628 13387924 13388324 3.680000e-165 592.0
2 TraesCS5A01G000300 chr5A 95.833 144 6 0 1 144 13387762 13387905 2.570000e-57 233.0
3 TraesCS5A01G000300 chr1B 98.782 3612 26 4 669 4275 16462193 16458595 0.000000e+00 6410.0
4 TraesCS5A01G000300 chr1B 93.514 185 9 2 324 507 174596392 174596574 5.450000e-69 272.0
5 TraesCS5A01G000300 chr1B 94.574 129 7 0 9 137 174596263 174596391 2.610000e-47 200.0
6 TraesCS5A01G000300 chr1B 90.698 129 10 1 502 628 174596806 174596934 2.040000e-38 171.0
7 TraesCS5A01G000300 chr4A 98.780 3607 26 6 671 4275 641295292 641298882 0.000000e+00 6401.0
8 TraesCS5A01G000300 chr2B 99.020 3572 21 4 706 4275 587240865 587237306 0.000000e+00 6390.0
9 TraesCS5A01G000300 chr1A 98.559 3608 28 5 669 4275 111985459 111981875 0.000000e+00 6353.0
10 TraesCS5A01G000300 chr7B 98.152 3626 20 7 669 4275 5929449 5925852 0.000000e+00 6281.0
11 TraesCS5A01G000300 chr7B 96.748 123 4 0 3294 3416 581218823 581218701 5.600000e-49 206.0
12 TraesCS5A01G000300 chr3B 98.753 3288 29 2 677 3963 647898545 647901821 0.000000e+00 5834.0
13 TraesCS5A01G000300 chr3B 100.000 311 0 0 3965 4275 647902028 647902338 3.710000e-160 575.0
14 TraesCS5A01G000300 chr6A 94.672 1708 56 5 1597 3301 40918061 40916386 0.000000e+00 2617.0
15 TraesCS5A01G000300 chr6A 97.106 864 17 5 3415 4275 40916387 40915529 0.000000e+00 1450.0
16 TraesCS5A01G000300 chr6A 90.608 937 49 24 677 1601 40919002 40918093 0.000000e+00 1206.0
17 TraesCS5A01G000300 chr4D 96.738 1410 35 1 1597 3006 503520129 503518731 0.000000e+00 2338.0
18 TraesCS5A01G000300 chr4D 90.417 1200 91 13 2111 3304 417821231 417820050 0.000000e+00 1557.0
19 TraesCS5A01G000300 chr4D 97.448 862 17 3 3415 4275 503518054 503517197 0.000000e+00 1465.0
20 TraesCS5A01G000300 chr4D 97.097 310 7 2 2994 3301 503518362 503518053 4.900000e-144 521.0
21 TraesCS5A01G000300 chr4D 90.857 350 15 4 680 1026 503520587 503520252 1.810000e-123 453.0
22 TraesCS5A01G000300 chr4D 82.752 487 49 18 937 1389 188707750 188708235 6.660000e-108 401.0
23 TraesCS5A01G000300 chr4D 87.864 206 16 2 1388 1584 188708278 188708483 2.570000e-57 233.0
24 TraesCS5A01G000300 chr7D 90.333 1200 92 9 2111 3304 340200748 340199567 0.000000e+00 1552.0
25 TraesCS5A01G000300 chr7D 90.468 577 32 12 52 628 605163666 605164219 0.000000e+00 739.0
26 TraesCS5A01G000300 chr7D 93.961 414 22 2 216 628 37004590 37004179 1.310000e-174 623.0
27 TraesCS5A01G000300 chr7D 93.617 141 9 0 1 141 37004790 37004650 1.200000e-50 211.0
28 TraesCS5A01G000300 chr5B 99.172 604 5 0 61 664 1755156 1754553 0.000000e+00 1088.0
29 TraesCS5A01G000300 chr5B 100.000 34 0 0 1 34 1755189 1755156 3.570000e-06 63.9
30 TraesCS5A01G000300 chr3D 94.431 413 20 2 217 628 571688947 571689357 2.170000e-177 632.0
31 TraesCS5A01G000300 chr3D 95.035 141 7 0 1 141 571688784 571688924 5.560000e-54 222.0
32 TraesCS5A01G000300 chr7A 90.476 357 24 4 7 355 137830092 137829738 3.010000e-126 462.0
33 TraesCS5A01G000300 chr7A 90.152 132 13 0 495 626 137827496 137827365 5.680000e-39 172.0
34 TraesCS5A01G000300 chr4B 83.162 487 47 18 937 1389 203203866 203204351 3.080000e-111 412.0
35 TraesCS5A01G000300 chr4B 87.019 208 16 1 1388 1584 203204395 203204602 1.550000e-54 224.0
36 TraesCS5A01G000300 chr2D 83.591 323 33 11 669 973 450900738 450901058 7.000000e-73 285.0
37 TraesCS5A01G000300 chrUn 98.374 123 2 0 3294 3416 9343721 9343599 2.590000e-52 217.0
38 TraesCS5A01G000300 chrUn 97.561 123 3 0 3294 3416 9472224 9472346 1.200000e-50 211.0
39 TraesCS5A01G000300 chr6D 85.000 200 18 7 1200 1388 60311011 60310813 4.360000e-45 193.0


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 TraesCS5A01G000300 chr5A 26615 30889 4274 True 7895.000000 7895 100.000000 1 4275 1 chr5A.!!$R1 4274
1 TraesCS5A01G000300 chr5A 13387762 13388324 562 False 412.500000 592 94.485000 1 628 2 chr5A.!!$F1 627
2 TraesCS5A01G000300 chr1B 16458595 16462193 3598 True 6410.000000 6410 98.782000 669 4275 1 chr1B.!!$R1 3606
3 TraesCS5A01G000300 chr1B 174596263 174596934 671 False 214.333333 272 92.928667 9 628 3 chr1B.!!$F1 619
4 TraesCS5A01G000300 chr4A 641295292 641298882 3590 False 6401.000000 6401 98.780000 671 4275 1 chr4A.!!$F1 3604
5 TraesCS5A01G000300 chr2B 587237306 587240865 3559 True 6390.000000 6390 99.020000 706 4275 1 chr2B.!!$R1 3569
6 TraesCS5A01G000300 chr1A 111981875 111985459 3584 True 6353.000000 6353 98.559000 669 4275 1 chr1A.!!$R1 3606
7 TraesCS5A01G000300 chr7B 5925852 5929449 3597 True 6281.000000 6281 98.152000 669 4275 1 chr7B.!!$R1 3606
8 TraesCS5A01G000300 chr3B 647898545 647902338 3793 False 3204.500000 5834 99.376500 677 4275 2 chr3B.!!$F1 3598
9 TraesCS5A01G000300 chr6A 40915529 40919002 3473 True 1757.666667 2617 94.128667 677 4275 3 chr6A.!!$R1 3598
10 TraesCS5A01G000300 chr4D 417820050 417821231 1181 True 1557.000000 1557 90.417000 2111 3304 1 chr4D.!!$R1 1193
11 TraesCS5A01G000300 chr4D 503517197 503520587 3390 True 1194.250000 2338 95.535000 680 4275 4 chr4D.!!$R2 3595
12 TraesCS5A01G000300 chr4D 188707750 188708483 733 False 317.000000 401 85.308000 937 1584 2 chr4D.!!$F1 647
13 TraesCS5A01G000300 chr7D 340199567 340200748 1181 True 1552.000000 1552 90.333000 2111 3304 1 chr7D.!!$R1 1193
14 TraesCS5A01G000300 chr7D 605163666 605164219 553 False 739.000000 739 90.468000 52 628 1 chr7D.!!$F1 576
15 TraesCS5A01G000300 chr7D 37004179 37004790 611 True 417.000000 623 93.789000 1 628 2 chr7D.!!$R2 627
16 TraesCS5A01G000300 chr5B 1754553 1755189 636 True 575.950000 1088 99.586000 1 664 2 chr5B.!!$R1 663
17 TraesCS5A01G000300 chr3D 571688784 571689357 573 False 427.000000 632 94.733000 1 628 2 chr3D.!!$F1 627
18 TraesCS5A01G000300 chr7A 137827365 137830092 2727 True 317.000000 462 90.314000 7 626 2 chr7A.!!$R1 619
19 TraesCS5A01G000300 chr4B 203203866 203204602 736 False 318.000000 412 85.090500 937 1584 2 chr4B.!!$F1 647

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
613 616 0.172578 CTCGCGTAGAACCATGTCCA 59.827 55.000 5.77 0.0 0.0 4.02 F
614 617 0.821517 TCGCGTAGAACCATGTCCAT 59.178 50.000 5.77 0.0 0.0 3.41 F
615 618 1.206132 TCGCGTAGAACCATGTCCATT 59.794 47.619 5.77 0.0 0.0 3.16 F
616 619 1.593006 CGCGTAGAACCATGTCCATTC 59.407 52.381 0.00 0.0 0.0 2.67 F
1171 1199 2.043801 ACCAAGAAGCTCCTCTACCTCT 59.956 50.000 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 3258 0.034059 CCTCGTGAGCTTGTGTCCTT 59.966 55.000 0.0 0.0 0.00 3.36 R
2640 3425 4.180377 ACATATCGGAGTGGAGTTAGGA 57.820 45.455 0.0 0.0 0.00 2.94 R
2939 3775 3.069289 CCTGCTCAAATTTCCCTTTTGC 58.931 45.455 0.0 0.0 34.73 3.68 R
2944 3780 3.168292 CCTTTCCTGCTCAAATTTCCCT 58.832 45.455 0.0 0.0 0.00 4.20 R
3311 6344 9.613428 ATCTATTTCAATGACAAGTATTTCCGA 57.387 29.630 0.0 0.0 0.00 4.55 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
43 44 1.302832 GAGGTGTGCCAGGTGAAGG 60.303 63.158 0.00 0.00 37.19 3.46
478 480 2.092914 GCAGTGGGGCTTACTCACTTAT 60.093 50.000 0.00 0.00 39.43 1.73
495 498 6.582636 TCACTTATTGGCTGTGGAATACTAG 58.417 40.000 0.00 0.00 33.04 2.57
510 513 6.946583 TGGAATACTAGGCCTATACTACACTG 59.053 42.308 14.30 0.16 0.00 3.66
511 514 7.173722 GGAATACTAGGCCTATACTACACTGA 58.826 42.308 14.30 0.00 0.00 3.41
512 515 7.668886 GGAATACTAGGCCTATACTACACTGAA 59.331 40.741 14.30 0.00 0.00 3.02
513 516 8.638629 AATACTAGGCCTATACTACACTGAAG 57.361 38.462 14.30 0.23 0.00 3.02
514 517 4.828387 ACTAGGCCTATACTACACTGAAGC 59.172 45.833 14.30 0.00 0.00 3.86
515 518 3.643237 AGGCCTATACTACACTGAAGCA 58.357 45.455 1.29 0.00 0.00 3.91
516 519 3.639094 AGGCCTATACTACACTGAAGCAG 59.361 47.826 1.29 0.00 37.52 4.24
517 520 3.385111 GGCCTATACTACACTGAAGCAGT 59.615 47.826 0.00 0.00 46.51 4.40
526 529 2.627515 ACTGAAGCAGTGCTGAGAAA 57.372 45.000 20.55 1.86 43.63 2.52
527 530 3.137446 ACTGAAGCAGTGCTGAGAAAT 57.863 42.857 20.55 0.28 43.63 2.17
528 531 4.277515 ACTGAAGCAGTGCTGAGAAATA 57.722 40.909 20.55 0.00 43.63 1.40
529 532 4.252073 ACTGAAGCAGTGCTGAGAAATAG 58.748 43.478 20.55 11.35 43.63 1.73
530 533 4.020751 ACTGAAGCAGTGCTGAGAAATAGA 60.021 41.667 20.55 0.00 43.63 1.98
531 534 5.095145 TGAAGCAGTGCTGAGAAATAGAT 57.905 39.130 20.55 0.00 39.62 1.98
532 535 4.874396 TGAAGCAGTGCTGAGAAATAGATG 59.126 41.667 20.55 0.00 39.62 2.90
533 536 4.484537 AGCAGTGCTGAGAAATAGATGT 57.515 40.909 18.98 0.00 37.57 3.06
534 537 5.604758 AGCAGTGCTGAGAAATAGATGTA 57.395 39.130 18.98 0.00 37.57 2.29
535 538 5.355596 AGCAGTGCTGAGAAATAGATGTAC 58.644 41.667 18.98 0.00 37.57 2.90
536 539 4.208047 GCAGTGCTGAGAAATAGATGTACG 59.792 45.833 8.18 0.00 0.00 3.67
537 540 4.742167 CAGTGCTGAGAAATAGATGTACGG 59.258 45.833 0.00 0.00 0.00 4.02
538 541 4.051922 GTGCTGAGAAATAGATGTACGGG 58.948 47.826 0.00 0.00 0.00 5.28
539 542 3.060602 GCTGAGAAATAGATGTACGGGC 58.939 50.000 0.00 0.00 0.00 6.13
540 543 3.243907 GCTGAGAAATAGATGTACGGGCT 60.244 47.826 0.00 0.00 0.00 5.19
541 544 4.302455 CTGAGAAATAGATGTACGGGCTG 58.698 47.826 0.00 0.00 0.00 4.85
542 545 3.069586 TGAGAAATAGATGTACGGGCTGG 59.930 47.826 0.00 0.00 0.00 4.85
543 546 3.039011 AGAAATAGATGTACGGGCTGGT 58.961 45.455 0.00 0.00 0.00 4.00
544 547 3.454812 AGAAATAGATGTACGGGCTGGTT 59.545 43.478 0.00 0.00 0.00 3.67
545 548 2.910688 ATAGATGTACGGGCTGGTTG 57.089 50.000 0.00 0.00 0.00 3.77
546 549 1.563924 TAGATGTACGGGCTGGTTGT 58.436 50.000 0.00 0.00 0.00 3.32
547 550 1.563924 AGATGTACGGGCTGGTTGTA 58.436 50.000 0.00 0.00 0.00 2.41
548 551 1.206371 AGATGTACGGGCTGGTTGTAC 59.794 52.381 0.00 0.00 39.08 2.90
549 552 2.438730 TGTACGGGCTGGTTGTACA 58.561 52.632 0.00 0.00 44.36 2.90
550 553 0.757512 TGTACGGGCTGGTTGTACAA 59.242 50.000 3.59 3.59 43.81 2.41
551 554 1.140452 TGTACGGGCTGGTTGTACAAA 59.860 47.619 10.51 0.00 43.81 2.83
552 555 2.224572 TGTACGGGCTGGTTGTACAAAT 60.225 45.455 10.51 0.00 43.81 2.32
553 556 2.863132 ACGGGCTGGTTGTACAAATA 57.137 45.000 10.51 1.31 0.00 1.40
554 557 2.429478 ACGGGCTGGTTGTACAAATAC 58.571 47.619 10.51 4.63 0.00 1.89
555 558 2.039348 ACGGGCTGGTTGTACAAATACT 59.961 45.455 10.51 0.00 32.00 2.12
556 559 3.261390 ACGGGCTGGTTGTACAAATACTA 59.739 43.478 10.51 0.00 32.00 1.82
557 560 3.619929 CGGGCTGGTTGTACAAATACTAC 59.380 47.826 10.51 0.00 36.61 2.73
558 561 4.581868 GGGCTGGTTGTACAAATACTACA 58.418 43.478 10.51 2.54 38.38 2.74
559 562 4.393990 GGGCTGGTTGTACAAATACTACAC 59.606 45.833 10.51 0.00 38.38 2.90
560 563 4.092383 GGCTGGTTGTACAAATACTACACG 59.908 45.833 10.51 0.00 38.38 4.49
561 564 4.925054 GCTGGTTGTACAAATACTACACGA 59.075 41.667 10.51 0.00 38.38 4.35
562 565 5.406175 GCTGGTTGTACAAATACTACACGAA 59.594 40.000 10.51 0.00 38.38 3.85
563 566 6.091713 GCTGGTTGTACAAATACTACACGAAT 59.908 38.462 10.51 0.00 38.38 3.34
564 567 7.585286 TGGTTGTACAAATACTACACGAATC 57.415 36.000 10.51 0.00 38.38 2.52
565 568 7.153315 TGGTTGTACAAATACTACACGAATCA 58.847 34.615 10.51 0.00 38.38 2.57
566 569 7.116662 TGGTTGTACAAATACTACACGAATCAC 59.883 37.037 10.51 0.00 38.38 3.06
567 570 6.858104 TGTACAAATACTACACGAATCACG 57.142 37.500 0.00 0.00 38.87 4.35
568 571 6.380995 TGTACAAATACTACACGAATCACGT 58.619 36.000 0.00 0.00 42.99 4.49
576 579 2.021793 CGAATCACGTGCGCATGG 59.978 61.111 31.55 20.59 37.22 3.66
577 580 2.451990 CGAATCACGTGCGCATGGA 61.452 57.895 31.55 24.56 37.22 3.41
578 581 1.060937 GAATCACGTGCGCATGGAC 59.939 57.895 31.55 10.18 0.00 4.02
584 587 4.760047 GTGCGCATGGACGGAGGT 62.760 66.667 15.91 0.00 32.64 3.85
585 588 4.758251 TGCGCATGGACGGAGGTG 62.758 66.667 5.66 0.00 0.00 4.00
586 589 4.451150 GCGCATGGACGGAGGTGA 62.451 66.667 0.30 0.00 0.00 4.02
587 590 2.501128 CGCATGGACGGAGGTGAT 59.499 61.111 0.00 0.00 0.00 3.06
588 591 1.153369 CGCATGGACGGAGGTGATT 60.153 57.895 0.00 0.00 0.00 2.57
589 592 1.154205 CGCATGGACGGAGGTGATTC 61.154 60.000 0.00 0.00 0.00 2.52
590 593 0.815615 GCATGGACGGAGGTGATTCC 60.816 60.000 0.00 0.00 0.00 3.01
591 594 0.541392 CATGGACGGAGGTGATTCCA 59.459 55.000 0.00 0.00 42.34 3.53
592 595 1.511613 ATGGACGGAGGTGATTCCAT 58.488 50.000 0.00 0.00 42.88 3.41
593 596 1.285280 TGGACGGAGGTGATTCCATT 58.715 50.000 0.00 0.00 37.05 3.16
594 597 1.209504 TGGACGGAGGTGATTCCATTC 59.790 52.381 0.00 0.00 37.05 2.67
595 598 1.486726 GGACGGAGGTGATTCCATTCT 59.513 52.381 0.00 0.00 37.05 2.40
596 599 2.483889 GGACGGAGGTGATTCCATTCTC 60.484 54.545 0.00 0.00 37.05 2.87
597 600 1.137086 ACGGAGGTGATTCCATTCTCG 59.863 52.381 0.00 0.00 37.05 4.04
598 601 1.587547 GGAGGTGATTCCATTCTCGC 58.412 55.000 0.00 0.00 39.02 5.03
599 602 1.212616 GAGGTGATTCCATTCTCGCG 58.787 55.000 0.00 0.00 39.02 5.87
600 603 0.537188 AGGTGATTCCATTCTCGCGT 59.463 50.000 5.77 0.00 39.02 6.01
601 604 1.754803 AGGTGATTCCATTCTCGCGTA 59.245 47.619 5.77 0.00 39.02 4.42
602 605 2.128035 GGTGATTCCATTCTCGCGTAG 58.872 52.381 5.77 2.22 35.97 3.51
603 606 2.223735 GGTGATTCCATTCTCGCGTAGA 60.224 50.000 5.77 4.97 35.97 2.59
605 608 3.243177 GTGATTCCATTCTCGCGTAGAAC 59.757 47.826 18.70 9.12 46.90 3.01
606 609 2.288961 TTCCATTCTCGCGTAGAACC 57.711 50.000 18.70 0.00 46.90 3.62
607 610 1.179152 TCCATTCTCGCGTAGAACCA 58.821 50.000 18.70 7.13 46.90 3.67
608 611 1.754803 TCCATTCTCGCGTAGAACCAT 59.245 47.619 18.70 5.49 46.90 3.55
609 612 1.860950 CCATTCTCGCGTAGAACCATG 59.139 52.381 18.70 14.29 46.90 3.66
610 613 2.540515 CATTCTCGCGTAGAACCATGT 58.459 47.619 18.70 4.92 46.90 3.21
611 614 2.273370 TTCTCGCGTAGAACCATGTC 57.727 50.000 5.77 0.00 39.36 3.06
612 615 0.454600 TCTCGCGTAGAACCATGTCC 59.545 55.000 5.77 0.00 0.00 4.02
613 616 0.172578 CTCGCGTAGAACCATGTCCA 59.827 55.000 5.77 0.00 0.00 4.02
614 617 0.821517 TCGCGTAGAACCATGTCCAT 59.178 50.000 5.77 0.00 0.00 3.41
615 618 1.206132 TCGCGTAGAACCATGTCCATT 59.794 47.619 5.77 0.00 0.00 3.16
616 619 1.593006 CGCGTAGAACCATGTCCATTC 59.407 52.381 0.00 0.00 0.00 2.67
617 620 1.593006 GCGTAGAACCATGTCCATTCG 59.407 52.381 0.00 0.00 0.00 3.34
618 621 2.888594 CGTAGAACCATGTCCATTCGT 58.111 47.619 0.00 0.00 0.00 3.85
619 622 3.735820 GCGTAGAACCATGTCCATTCGTA 60.736 47.826 0.00 0.00 0.00 3.43
620 623 4.426416 CGTAGAACCATGTCCATTCGTAA 58.574 43.478 0.00 0.00 0.00 3.18
621 624 5.047847 CGTAGAACCATGTCCATTCGTAAT 58.952 41.667 0.00 0.00 0.00 1.89
622 625 5.522460 CGTAGAACCATGTCCATTCGTAATT 59.478 40.000 0.00 0.00 0.00 1.40
623 626 6.698329 CGTAGAACCATGTCCATTCGTAATTA 59.302 38.462 0.00 0.00 0.00 1.40
624 627 7.384115 CGTAGAACCATGTCCATTCGTAATTAT 59.616 37.037 0.00 0.00 0.00 1.28
625 628 9.052759 GTAGAACCATGTCCATTCGTAATTATT 57.947 33.333 0.00 0.00 0.00 1.40
626 629 8.154649 AGAACCATGTCCATTCGTAATTATTC 57.845 34.615 0.00 0.00 0.00 1.75
627 630 6.539649 ACCATGTCCATTCGTAATTATTCG 57.460 37.500 0.00 0.00 0.00 3.34
628 631 6.285224 ACCATGTCCATTCGTAATTATTCGA 58.715 36.000 0.00 0.00 0.00 3.71
629 632 6.934645 ACCATGTCCATTCGTAATTATTCGAT 59.065 34.615 0.00 0.00 36.01 3.59
630 633 7.117812 ACCATGTCCATTCGTAATTATTCGATC 59.882 37.037 0.00 0.00 36.01 3.69
631 634 7.331934 CCATGTCCATTCGTAATTATTCGATCT 59.668 37.037 0.00 0.00 36.01 2.75
632 635 9.353999 CATGTCCATTCGTAATTATTCGATCTA 57.646 33.333 0.00 0.00 36.01 1.98
634 637 9.569167 TGTCCATTCGTAATTATTCGATCTATC 57.431 33.333 0.00 0.00 36.01 2.08
635 638 9.790389 GTCCATTCGTAATTATTCGATCTATCT 57.210 33.333 0.00 0.00 36.01 1.98
640 643 9.458727 TTCGTAATTATTCGATCTATCTACCCT 57.541 33.333 0.00 0.00 36.01 4.34
769 772 2.642154 TTCAACCCGCAGTCCTTTTA 57.358 45.000 0.00 0.00 0.00 1.52
1171 1199 2.043801 ACCAAGAAGCTCCTCTACCTCT 59.956 50.000 0.00 0.00 0.00 3.69
1777 2426 3.771160 GGGAGTGATGGCGTCGGT 61.771 66.667 1.67 0.00 0.00 4.69
2461 3246 2.359850 GGATTCGCAGTGGCACCA 60.360 61.111 15.27 0.00 41.24 4.17
2640 3425 7.950684 TCCAGGTATATAGCAGTAACATCTCTT 59.049 37.037 14.11 0.00 0.00 2.85
2939 3775 9.003658 TCAATTTGCTCTTAAGTAAAAGGAGAG 57.996 33.333 1.63 0.00 39.96 3.20
3311 6344 7.854337 TGAAACTAAATTATACTCCCTCCGTT 58.146 34.615 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.732941 TTGGGCGACATATGTGACAC 58.267 50.000 14.43 6.55 0.00 3.67
421 423 7.015974 ACACTGATCCATGCTATTGATTAGAGA 59.984 37.037 7.40 0.00 0.00 3.10
478 480 1.211949 GGCCTAGTATTCCACAGCCAA 59.788 52.381 0.00 0.00 38.98 4.52
495 498 3.385111 ACTGCTTCAGTGTAGTATAGGCC 59.615 47.826 0.00 0.00 43.63 5.19
510 513 4.874966 ACATCTATTTCTCAGCACTGCTTC 59.125 41.667 0.00 0.00 36.40 3.86
511 514 4.841422 ACATCTATTTCTCAGCACTGCTT 58.159 39.130 0.00 0.00 36.40 3.91
512 515 4.484537 ACATCTATTTCTCAGCACTGCT 57.515 40.909 0.00 0.00 40.77 4.24
513 516 4.208047 CGTACATCTATTTCTCAGCACTGC 59.792 45.833 0.00 0.00 0.00 4.40
514 517 4.742167 CCGTACATCTATTTCTCAGCACTG 59.258 45.833 0.00 0.00 0.00 3.66
515 518 4.202161 CCCGTACATCTATTTCTCAGCACT 60.202 45.833 0.00 0.00 0.00 4.40
516 519 4.051922 CCCGTACATCTATTTCTCAGCAC 58.948 47.826 0.00 0.00 0.00 4.40
517 520 3.492656 GCCCGTACATCTATTTCTCAGCA 60.493 47.826 0.00 0.00 0.00 4.41
518 521 3.060602 GCCCGTACATCTATTTCTCAGC 58.939 50.000 0.00 0.00 0.00 4.26
519 522 4.302455 CAGCCCGTACATCTATTTCTCAG 58.698 47.826 0.00 0.00 0.00 3.35
520 523 3.069586 CCAGCCCGTACATCTATTTCTCA 59.930 47.826 0.00 0.00 0.00 3.27
521 524 3.069729 ACCAGCCCGTACATCTATTTCTC 59.930 47.826 0.00 0.00 0.00 2.87
522 525 3.039011 ACCAGCCCGTACATCTATTTCT 58.961 45.455 0.00 0.00 0.00 2.52
523 526 3.470645 ACCAGCCCGTACATCTATTTC 57.529 47.619 0.00 0.00 0.00 2.17
524 527 3.054655 ACAACCAGCCCGTACATCTATTT 60.055 43.478 0.00 0.00 0.00 1.40
525 528 2.504175 ACAACCAGCCCGTACATCTATT 59.496 45.455 0.00 0.00 0.00 1.73
526 529 2.116238 ACAACCAGCCCGTACATCTAT 58.884 47.619 0.00 0.00 0.00 1.98
527 530 1.563924 ACAACCAGCCCGTACATCTA 58.436 50.000 0.00 0.00 0.00 1.98
528 531 1.206371 GTACAACCAGCCCGTACATCT 59.794 52.381 0.00 0.00 36.38 2.90
529 532 1.066716 TGTACAACCAGCCCGTACATC 60.067 52.381 0.00 0.00 40.29 3.06
530 533 0.978151 TGTACAACCAGCCCGTACAT 59.022 50.000 0.00 0.00 40.29 2.29
531 534 0.757512 TTGTACAACCAGCCCGTACA 59.242 50.000 3.59 0.00 42.70 2.90
532 535 1.881591 TTTGTACAACCAGCCCGTAC 58.118 50.000 8.07 0.00 36.79 3.67
533 536 2.863132 ATTTGTACAACCAGCCCGTA 57.137 45.000 8.07 0.00 0.00 4.02
534 537 2.039348 AGTATTTGTACAACCAGCCCGT 59.961 45.455 8.07 0.00 0.00 5.28
535 538 2.706890 AGTATTTGTACAACCAGCCCG 58.293 47.619 8.07 0.00 0.00 6.13
536 539 4.393990 GTGTAGTATTTGTACAACCAGCCC 59.606 45.833 8.07 0.00 32.23 5.19
537 540 4.092383 CGTGTAGTATTTGTACAACCAGCC 59.908 45.833 8.07 0.00 32.23 4.85
538 541 4.925054 TCGTGTAGTATTTGTACAACCAGC 59.075 41.667 8.07 0.00 32.23 4.85
539 542 7.329962 TGATTCGTGTAGTATTTGTACAACCAG 59.670 37.037 8.07 0.00 32.23 4.00
540 543 7.116662 GTGATTCGTGTAGTATTTGTACAACCA 59.883 37.037 8.07 0.00 32.23 3.67
541 544 7.450627 GTGATTCGTGTAGTATTTGTACAACC 58.549 38.462 8.07 0.00 32.23 3.77
542 545 7.162246 CGTGATTCGTGTAGTATTTGTACAAC 58.838 38.462 8.07 0.00 32.23 3.32
543 546 7.268186 CGTGATTCGTGTAGTATTTGTACAA 57.732 36.000 3.59 3.59 32.23 2.41
544 547 6.858104 CGTGATTCGTGTAGTATTTGTACA 57.142 37.500 0.00 0.00 34.52 2.90
559 562 2.021793 CCATGCGCACGTGATTCG 59.978 61.111 22.23 14.82 46.00 3.34
560 563 1.060937 GTCCATGCGCACGTGATTC 59.939 57.895 22.23 7.47 34.49 2.52
561 564 2.739704 CGTCCATGCGCACGTGATT 61.740 57.895 22.23 0.00 34.49 2.57
562 565 3.188100 CGTCCATGCGCACGTGAT 61.188 61.111 22.23 0.02 34.49 3.06
567 570 4.760047 ACCTCCGTCCATGCGCAC 62.760 66.667 14.90 0.00 0.00 5.34
568 571 4.758251 CACCTCCGTCCATGCGCA 62.758 66.667 14.96 14.96 0.00 6.09
569 572 3.740128 ATCACCTCCGTCCATGCGC 62.740 63.158 0.00 0.00 0.00 6.09
570 573 1.153369 AATCACCTCCGTCCATGCG 60.153 57.895 0.00 0.00 0.00 4.73
571 574 0.815615 GGAATCACCTCCGTCCATGC 60.816 60.000 0.00 0.00 35.41 4.06
572 575 0.541392 TGGAATCACCTCCGTCCATG 59.459 55.000 0.00 0.00 38.44 3.66
573 576 1.511613 ATGGAATCACCTCCGTCCAT 58.488 50.000 0.00 0.00 43.91 3.41
574 577 1.209504 GAATGGAATCACCTCCGTCCA 59.790 52.381 0.00 0.00 44.07 4.02
575 578 1.486726 AGAATGGAATCACCTCCGTCC 59.513 52.381 0.00 0.00 38.44 4.79
576 579 2.799917 CGAGAATGGAATCACCTCCGTC 60.800 54.545 0.00 0.00 38.44 4.79
577 580 1.137086 CGAGAATGGAATCACCTCCGT 59.863 52.381 0.00 0.00 38.44 4.69
578 581 1.858091 CGAGAATGGAATCACCTCCG 58.142 55.000 0.00 0.00 38.44 4.63
579 582 1.587547 GCGAGAATGGAATCACCTCC 58.412 55.000 0.00 0.00 39.86 4.30
580 583 1.212616 CGCGAGAATGGAATCACCTC 58.787 55.000 0.00 0.00 39.86 3.85
581 584 0.537188 ACGCGAGAATGGAATCACCT 59.463 50.000 15.93 0.00 39.86 4.00
582 585 2.128035 CTACGCGAGAATGGAATCACC 58.872 52.381 15.93 0.00 39.54 4.02
583 586 3.079960 TCTACGCGAGAATGGAATCAC 57.920 47.619 15.93 0.00 0.00 3.06
584 587 3.444916 GTTCTACGCGAGAATGGAATCA 58.555 45.455 15.93 0.00 45.96 2.57
585 588 2.795470 GGTTCTACGCGAGAATGGAATC 59.205 50.000 15.93 0.00 45.96 2.52
586 589 2.167693 TGGTTCTACGCGAGAATGGAAT 59.832 45.455 15.93 0.00 45.96 3.01
587 590 1.546923 TGGTTCTACGCGAGAATGGAA 59.453 47.619 15.93 0.04 45.96 3.53
588 591 1.179152 TGGTTCTACGCGAGAATGGA 58.821 50.000 15.93 0.00 45.96 3.41
589 592 1.860950 CATGGTTCTACGCGAGAATGG 59.139 52.381 15.93 5.34 45.96 3.16
590 593 2.535984 GACATGGTTCTACGCGAGAATG 59.464 50.000 15.93 14.39 45.96 2.67
591 594 2.481449 GGACATGGTTCTACGCGAGAAT 60.481 50.000 15.93 2.14 45.96 2.40
592 595 1.135199 GGACATGGTTCTACGCGAGAA 60.135 52.381 15.93 14.87 42.13 2.87
593 596 0.454600 GGACATGGTTCTACGCGAGA 59.545 55.000 15.93 8.82 0.00 4.04
594 597 0.172578 TGGACATGGTTCTACGCGAG 59.827 55.000 15.93 6.12 0.00 5.03
595 598 0.821517 ATGGACATGGTTCTACGCGA 59.178 50.000 15.93 0.00 0.00 5.87
596 599 1.593006 GAATGGACATGGTTCTACGCG 59.407 52.381 3.53 3.53 0.00 6.01
597 600 1.593006 CGAATGGACATGGTTCTACGC 59.407 52.381 0.00 0.00 0.00 4.42
598 601 2.888594 ACGAATGGACATGGTTCTACG 58.111 47.619 0.00 0.00 0.00 3.51
599 602 6.920569 AATTACGAATGGACATGGTTCTAC 57.079 37.500 0.00 0.00 0.00 2.59
600 603 9.268268 GAATAATTACGAATGGACATGGTTCTA 57.732 33.333 0.00 0.00 0.00 2.10
601 604 7.042051 CGAATAATTACGAATGGACATGGTTCT 60.042 37.037 0.00 0.00 0.00 3.01
602 605 7.042321 TCGAATAATTACGAATGGACATGGTTC 60.042 37.037 0.00 0.00 35.62 3.62
603 606 6.764085 TCGAATAATTACGAATGGACATGGTT 59.236 34.615 0.00 0.00 35.62 3.67
604 607 6.285224 TCGAATAATTACGAATGGACATGGT 58.715 36.000 0.00 0.00 35.62 3.55
605 608 6.779115 TCGAATAATTACGAATGGACATGG 57.221 37.500 0.00 0.00 35.62 3.66
606 609 8.244494 AGATCGAATAATTACGAATGGACATG 57.756 34.615 2.73 0.00 41.65 3.21
608 611 9.569167 GATAGATCGAATAATTACGAATGGACA 57.431 33.333 2.73 0.00 41.65 4.02
609 612 9.790389 AGATAGATCGAATAATTACGAATGGAC 57.210 33.333 2.73 0.00 41.65 4.02
614 617 9.458727 AGGGTAGATAGATCGAATAATTACGAA 57.541 33.333 2.73 0.00 41.65 3.85
647 650 9.213799 GAGAGAAGAGATTTTTATGGCGATTAT 57.786 33.333 0.00 0.00 0.00 1.28
648 651 7.657761 GGAGAGAAGAGATTTTTATGGCGATTA 59.342 37.037 0.00 0.00 0.00 1.75
649 652 6.484977 GGAGAGAAGAGATTTTTATGGCGATT 59.515 38.462 0.00 0.00 0.00 3.34
650 653 5.994668 GGAGAGAAGAGATTTTTATGGCGAT 59.005 40.000 0.00 0.00 0.00 4.58
651 654 5.360591 GGAGAGAAGAGATTTTTATGGCGA 58.639 41.667 0.00 0.00 0.00 5.54
652 655 4.513318 GGGAGAGAAGAGATTTTTATGGCG 59.487 45.833 0.00 0.00 0.00 5.69
653 656 5.689835 AGGGAGAGAAGAGATTTTTATGGC 58.310 41.667 0.00 0.00 0.00 4.40
654 657 8.028652 AGTAGGGAGAGAAGAGATTTTTATGG 57.971 38.462 0.00 0.00 0.00 2.74
661 664 9.150028 GGTTTATTAGTAGGGAGAGAAGAGATT 57.850 37.037 0.00 0.00 0.00 2.40
662 665 8.290277 TGGTTTATTAGTAGGGAGAGAAGAGAT 58.710 37.037 0.00 0.00 0.00 2.75
663 666 7.560626 GTGGTTTATTAGTAGGGAGAGAAGAGA 59.439 40.741 0.00 0.00 0.00 3.10
664 667 7.201929 GGTGGTTTATTAGTAGGGAGAGAAGAG 60.202 44.444 0.00 0.00 0.00 2.85
665 668 6.610425 GGTGGTTTATTAGTAGGGAGAGAAGA 59.390 42.308 0.00 0.00 0.00 2.87
666 669 6.461231 CGGTGGTTTATTAGTAGGGAGAGAAG 60.461 46.154 0.00 0.00 0.00 2.85
667 670 5.361857 CGGTGGTTTATTAGTAGGGAGAGAA 59.638 44.000 0.00 0.00 0.00 2.87
745 748 2.463752 AGGACTGCGGGTTGAATACTA 58.536 47.619 0.00 0.00 0.00 1.82
769 772 6.090898 CCTGATCGAAACGTTTTCTCACTTAT 59.909 38.462 15.89 0.73 0.00 1.73
1171 1199 3.545124 CTAACACGGCACCCAGGCA 62.545 63.158 0.00 0.00 44.47 4.75
1684 2333 1.004044 AGCTACAACTGAGGCAATGCT 59.996 47.619 4.82 0.00 0.00 3.79
2397 3182 8.934023 AAGAAGGATGGTACTGAAAACATTAA 57.066 30.769 0.00 0.00 0.00 1.40
2473 3258 0.034059 CCTCGTGAGCTTGTGTCCTT 59.966 55.000 0.00 0.00 0.00 3.36
2640 3425 4.180377 ACATATCGGAGTGGAGTTAGGA 57.820 45.455 0.00 0.00 0.00 2.94
2939 3775 3.069289 CCTGCTCAAATTTCCCTTTTGC 58.931 45.455 0.00 0.00 34.73 3.68
2944 3780 3.168292 CCTTTCCTGCTCAAATTTCCCT 58.832 45.455 0.00 0.00 0.00 4.20
3311 6344 9.613428 ATCTATTTCAATGACAAGTATTTCCGA 57.387 29.630 0.00 0.00 0.00 4.55
3833 6873 0.889186 GTGTGTGGCAACGGGAGATT 60.889 55.000 0.00 0.00 42.51 2.40


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

AutoCloner maintained by Alex Coulton.