Multiple sequence alignment - TraesCS2D01G143500

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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 TraesCS2D01G143500 chr2D 100.000 2660 0 0 1 2660 84780111 84782770 0.000000e+00 4913
1 TraesCS2D01G143500 chr2D 96.451 479 13 3 1 476 85408496 85408973 0.000000e+00 787
2 TraesCS2D01G143500 chr2D 94.195 379 13 4 1 371 84937699 84938076 1.070000e-158 569
3 TraesCS2D01G143500 chr5D 94.495 1962 76 17 720 2660 44511946 44513896 0.000000e+00 2996
4 TraesCS2D01G143500 chr5D 91.314 449 29 4 224 669 283110319 283110760 2.930000e-169 604
5 TraesCS2D01G143500 chr3D 94.447 1963 80 12 720 2660 546485998 546487953 0.000000e+00 2994
6 TraesCS2D01G143500 chr3D 94.359 1950 66 18 720 2660 447973570 447971656 0.000000e+00 2952
7 TraesCS2D01G143500 chrUn 94.844 1920 74 13 757 2660 43407879 43409789 0.000000e+00 2974
8 TraesCS2D01G143500 chrUn 88.346 266 15 6 457 719 354326064 354326316 3.330000e-79 305
9 TraesCS2D01G143500 chr3B 94.076 1958 89 14 720 2660 370213884 370215831 0.000000e+00 2948
10 TraesCS2D01G143500 chr5A 93.135 1952 112 10 723 2660 650703516 650701573 0.000000e+00 2843
11 TraesCS2D01G143500 chr3A 92.992 1955 94 19 720 2660 235187482 235189407 0.000000e+00 2811
12 TraesCS2D01G143500 chr7D 93.463 1897 80 21 797 2660 605599928 605601813 0.000000e+00 2776
13 TraesCS2D01G143500 chr7D 93.699 1825 96 13 721 2528 623570823 623572645 0.000000e+00 2715
14 TraesCS2D01G143500 chr7D 94.725 1706 70 14 720 2414 94497474 94495778 0.000000e+00 2634
15 TraesCS2D01G143500 chr2B 93.579 732 21 10 1 723 136638685 136639399 0.000000e+00 1068
16 TraesCS2D01G143500 chr2B 93.750 480 22 6 1 476 137622202 137622677 0.000000e+00 713
17 TraesCS2D01G143500 chr2B 95.249 442 17 3 1 439 136814853 136815293 0.000000e+00 697
18 TraesCS2D01G143500 chr2B 92.946 482 26 6 1 475 137349019 137349499 0.000000e+00 695
19 TraesCS2D01G143500 chr2B 95.023 442 18 3 1 439 137014510 137014950 0.000000e+00 691
20 TraesCS2D01G143500 chr2B 90.465 430 29 5 720 1138 13181554 13181982 8.320000e-155 556
21 TraesCS2D01G143500 chr5B 92.741 675 35 6 1 669 321477939 321478605 0.000000e+00 963
22 TraesCS2D01G143500 chr2A 92.193 538 27 7 720 1246 695806749 695806216 0.000000e+00 747
23 TraesCS2D01G143500 chr2A 88.346 266 15 6 457 719 85613722 85613974 3.330000e-79 305
24 TraesCS2D01G143500 chr2A 88.346 266 15 6 457 719 85811240 85811492 3.330000e-79 305
25 TraesCS2D01G143500 chr2A 88.550 262 14 6 457 715 85927147 85927395 1.200000e-78 303
26 TraesCS2D01G143500 chr7A 93.578 436 22 3 1 433 618195048 618195480 0.000000e+00 645
27 TraesCS2D01G143500 chr7A 98.276 58 1 0 612 669 618195511 618195568 4.680000e-18 102
28 TraesCS2D01G143500 chr4A 88.346 266 15 6 457 719 349806775 349807027 3.330000e-79 305


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 TraesCS2D01G143500 chr2D 84780111 84782770 2659 False 4913.0 4913 100.000 1 2660 1 chr2D.!!$F1 2659
1 TraesCS2D01G143500 chr5D 44511946 44513896 1950 False 2996.0 2996 94.495 720 2660 1 chr5D.!!$F1 1940
2 TraesCS2D01G143500 chr3D 546485998 546487953 1955 False 2994.0 2994 94.447 720 2660 1 chr3D.!!$F1 1940
3 TraesCS2D01G143500 chr3D 447971656 447973570 1914 True 2952.0 2952 94.359 720 2660 1 chr3D.!!$R1 1940
4 TraesCS2D01G143500 chrUn 43407879 43409789 1910 False 2974.0 2974 94.844 757 2660 1 chrUn.!!$F1 1903
5 TraesCS2D01G143500 chr3B 370213884 370215831 1947 False 2948.0 2948 94.076 720 2660 1 chr3B.!!$F1 1940
6 TraesCS2D01G143500 chr5A 650701573 650703516 1943 True 2843.0 2843 93.135 723 2660 1 chr5A.!!$R1 1937
7 TraesCS2D01G143500 chr3A 235187482 235189407 1925 False 2811.0 2811 92.992 720 2660 1 chr3A.!!$F1 1940
8 TraesCS2D01G143500 chr7D 605599928 605601813 1885 False 2776.0 2776 93.463 797 2660 1 chr7D.!!$F1 1863
9 TraesCS2D01G143500 chr7D 623570823 623572645 1822 False 2715.0 2715 93.699 721 2528 1 chr7D.!!$F2 1807
10 TraesCS2D01G143500 chr7D 94495778 94497474 1696 True 2634.0 2634 94.725 720 2414 1 chr7D.!!$R1 1694
11 TraesCS2D01G143500 chr2B 136638685 136639399 714 False 1068.0 1068 93.579 1 723 1 chr2B.!!$F2 722
12 TraesCS2D01G143500 chr5B 321477939 321478605 666 False 963.0 963 92.741 1 669 1 chr5B.!!$F1 668
13 TraesCS2D01G143500 chr2A 695806216 695806749 533 True 747.0 747 92.193 720 1246 1 chr2A.!!$R1 526
14 TraesCS2D01G143500 chr7A 618195048 618195568 520 False 373.5 645 95.927 1 669 2 chr7A.!!$F1 668

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
526 530 0.035439 GCCCTCGTTGATTTCCCAGA 60.035 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 1970 0.251787 ATTTGGCCCACAGAGGAACC 60.252 55.0 0.0 0.0 41.22 3.62 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
157 158 4.005472 CTTCGCCGCCATCGATGC 62.005 66.667 20.25 13.87 38.10 3.91
286 290 1.751924 GACTCGGATTACCAGCTGTCT 59.248 52.381 13.81 0.00 35.59 3.41
331 335 1.299648 CTCGAATTCACAGGGGGCA 59.700 57.895 6.22 0.00 0.00 5.36
332 336 0.322456 CTCGAATTCACAGGGGGCAA 60.322 55.000 6.22 0.00 0.00 4.52
335 339 1.607801 GAATTCACAGGGGGCAAGCC 61.608 60.000 1.52 1.52 0.00 4.35
351 355 2.046314 CCCTTGGCCGTGTACCAG 60.046 66.667 0.00 0.00 38.73 4.00
448 452 4.876701 GCTACGGCCATTCCATCA 57.123 55.556 2.24 0.00 34.01 3.07
449 453 2.621763 GCTACGGCCATTCCATCAG 58.378 57.895 2.24 0.00 34.01 2.90
450 454 1.510480 GCTACGGCCATTCCATCAGC 61.510 60.000 2.24 0.00 34.01 4.26
451 455 1.224069 CTACGGCCATTCCATCAGCG 61.224 60.000 2.24 0.00 34.01 5.18
452 456 2.658679 TACGGCCATTCCATCAGCGG 62.659 60.000 2.24 0.00 34.01 5.52
453 457 2.908940 GGCCATTCCATCAGCGGG 60.909 66.667 0.00 0.00 34.01 6.13
454 458 3.599704 GCCATTCCATCAGCGGGC 61.600 66.667 0.00 0.00 0.00 6.13
455 459 2.124193 CCATTCCATCAGCGGGCA 60.124 61.111 0.00 0.00 0.00 5.36
456 460 2.191513 CCATTCCATCAGCGGGCAG 61.192 63.158 0.00 0.00 0.00 4.85
457 461 2.191513 CATTCCATCAGCGGGCAGG 61.192 63.158 0.00 0.00 0.00 4.85
458 462 4.802051 TTCCATCAGCGGGCAGGC 62.802 66.667 0.00 0.00 0.00 4.85
475 479 2.496817 CGCAGGTACCTGAGCTCC 59.503 66.667 40.26 23.03 46.30 4.70
476 480 2.496817 GCAGGTACCTGAGCTCCG 59.503 66.667 40.26 16.62 46.30 4.63
477 481 2.496817 CAGGTACCTGAGCTCCGC 59.503 66.667 34.54 0.00 46.30 5.54
478 482 3.141488 AGGTACCTGAGCTCCGCG 61.141 66.667 15.42 0.00 0.00 6.46
479 483 4.208686 GGTACCTGAGCTCCGCGG 62.209 72.222 22.12 22.12 0.00 6.46
480 484 4.874977 GTACCTGAGCTCCGCGGC 62.875 72.222 23.51 10.29 0.00 6.53
496 500 2.976903 GCGCTGGCCATGGAGATC 60.977 66.667 18.40 1.69 0.00 2.75
497 501 2.827423 CGCTGGCCATGGAGATCT 59.173 61.111 18.40 0.00 0.00 2.75
498 502 1.147824 CGCTGGCCATGGAGATCTT 59.852 57.895 18.40 0.00 0.00 2.40
499 503 0.883814 CGCTGGCCATGGAGATCTTC 60.884 60.000 18.40 0.00 0.00 2.87
500 504 0.182061 GCTGGCCATGGAGATCTTCA 59.818 55.000 18.40 6.06 0.00 3.02
501 505 1.814634 GCTGGCCATGGAGATCTTCAG 60.815 57.143 18.40 10.95 0.00 3.02
502 506 0.841961 TGGCCATGGAGATCTTCAGG 59.158 55.000 18.40 9.44 0.00 3.86
503 507 0.842635 GGCCATGGAGATCTTCAGGT 59.157 55.000 18.40 0.00 0.00 4.00
504 508 1.476471 GGCCATGGAGATCTTCAGGTG 60.476 57.143 18.40 6.30 0.00 4.00
505 509 1.476471 GCCATGGAGATCTTCAGGTGG 60.476 57.143 18.40 16.64 0.00 4.61
506 510 1.476471 CCATGGAGATCTTCAGGTGGC 60.476 57.143 14.40 0.00 0.00 5.01
507 511 0.467384 ATGGAGATCTTCAGGTGGCG 59.533 55.000 10.13 0.00 0.00 5.69
508 512 1.522580 GGAGATCTTCAGGTGGCGC 60.523 63.158 0.00 0.00 0.00 6.53
509 513 1.522580 GAGATCTTCAGGTGGCGCC 60.523 63.158 22.73 22.73 37.58 6.53
510 514 2.514824 GATCTTCAGGTGGCGCCC 60.515 66.667 26.77 15.53 38.26 6.13
511 515 3.011517 ATCTTCAGGTGGCGCCCT 61.012 61.111 26.77 12.40 38.26 5.19
512 516 2.932130 GATCTTCAGGTGGCGCCCTC 62.932 65.000 26.77 17.16 38.26 4.30
518 522 4.778143 GGTGGCGCCCTCGTTGAT 62.778 66.667 26.77 0.00 38.14 2.57
519 523 2.746277 GTGGCGCCCTCGTTGATT 60.746 61.111 26.77 0.00 38.14 2.57
520 524 2.033448 TGGCGCCCTCGTTGATTT 59.967 55.556 26.77 0.00 38.14 2.17
521 525 2.038269 TGGCGCCCTCGTTGATTTC 61.038 57.895 26.77 0.00 38.14 2.17
522 526 2.761195 GGCGCCCTCGTTGATTTCC 61.761 63.158 18.11 0.00 38.14 3.13
523 527 2.761195 GCGCCCTCGTTGATTTCCC 61.761 63.158 0.00 0.00 38.14 3.97
524 528 1.376683 CGCCCTCGTTGATTTCCCA 60.377 57.895 0.00 0.00 0.00 4.37
525 529 1.369091 CGCCCTCGTTGATTTCCCAG 61.369 60.000 0.00 0.00 0.00 4.45
526 530 0.035439 GCCCTCGTTGATTTCCCAGA 60.035 55.000 0.00 0.00 0.00 3.86
527 531 2.014068 GCCCTCGTTGATTTCCCAGAG 61.014 57.143 0.00 0.00 0.00 3.35
528 532 1.555075 CCCTCGTTGATTTCCCAGAGA 59.445 52.381 0.00 0.00 0.00 3.10
529 533 2.171448 CCCTCGTTGATTTCCCAGAGAT 59.829 50.000 0.00 0.00 0.00 2.75
530 534 3.462021 CCTCGTTGATTTCCCAGAGATC 58.538 50.000 0.00 0.00 0.00 2.75
531 535 3.462021 CTCGTTGATTTCCCAGAGATCC 58.538 50.000 0.00 0.00 0.00 3.36
532 536 2.170607 TCGTTGATTTCCCAGAGATCCC 59.829 50.000 0.00 0.00 0.00 3.85
533 537 2.746472 CGTTGATTTCCCAGAGATCCCC 60.746 54.545 0.00 0.00 0.00 4.81
534 538 1.131638 TGATTTCCCAGAGATCCCCG 58.868 55.000 0.00 0.00 0.00 5.73
535 539 1.343985 TGATTTCCCAGAGATCCCCGA 60.344 52.381 0.00 0.00 0.00 5.14
536 540 1.768870 GATTTCCCAGAGATCCCCGAA 59.231 52.381 0.00 0.00 0.00 4.30
537 541 0.909623 TTTCCCAGAGATCCCCGAAC 59.090 55.000 0.00 0.00 0.00 3.95
538 542 0.252513 TTCCCAGAGATCCCCGAACA 60.253 55.000 0.00 0.00 0.00 3.18
539 543 0.687757 TCCCAGAGATCCCCGAACAG 60.688 60.000 0.00 0.00 0.00 3.16
540 544 1.144936 CCAGAGATCCCCGAACAGC 59.855 63.158 0.00 0.00 0.00 4.40
541 545 1.617018 CCAGAGATCCCCGAACAGCA 61.617 60.000 0.00 0.00 0.00 4.41
542 546 0.179089 CAGAGATCCCCGAACAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
543 547 1.522580 GAGATCCCCGAACAGCAGC 60.523 63.158 0.00 0.00 0.00 5.25
544 548 1.965754 GAGATCCCCGAACAGCAGCT 61.966 60.000 0.00 0.00 0.00 4.24
545 549 1.522580 GATCCCCGAACAGCAGCTC 60.523 63.158 0.00 0.00 0.00 4.09
546 550 2.932130 GATCCCCGAACAGCAGCTCC 62.932 65.000 0.00 0.00 0.00 4.70
547 551 4.785453 CCCCGAACAGCAGCTCCC 62.785 72.222 0.00 0.00 0.00 4.30
548 552 4.785453 CCCGAACAGCAGCTCCCC 62.785 72.222 0.00 0.00 0.00 4.81
549 553 3.710722 CCGAACAGCAGCTCCCCT 61.711 66.667 0.00 0.00 0.00 4.79
550 554 2.125350 CGAACAGCAGCTCCCCTC 60.125 66.667 0.00 0.00 0.00 4.30
551 555 2.125350 GAACAGCAGCTCCCCTCG 60.125 66.667 0.00 0.00 0.00 4.63
552 556 3.672295 GAACAGCAGCTCCCCTCGG 62.672 68.421 0.00 0.00 0.00 4.63
571 575 4.742201 GCGAGGAAGACGGCTGCA 62.742 66.667 0.00 0.00 0.00 4.41
572 576 2.185350 CGAGGAAGACGGCTGCAT 59.815 61.111 0.00 0.00 0.00 3.96
573 577 1.880340 CGAGGAAGACGGCTGCATC 60.880 63.158 0.00 0.00 0.00 3.91
574 578 1.522580 GAGGAAGACGGCTGCATCC 60.523 63.158 0.00 0.00 0.00 3.51
575 579 2.514824 GGAAGACGGCTGCATCCC 60.515 66.667 0.00 0.00 0.00 3.85
576 580 2.586792 GAAGACGGCTGCATCCCT 59.413 61.111 0.00 0.00 0.00 4.20
577 581 1.522580 GAAGACGGCTGCATCCCTC 60.523 63.158 0.00 0.00 0.00 4.30
578 582 2.932130 GAAGACGGCTGCATCCCTCC 62.932 65.000 0.00 0.00 0.00 4.30
579 583 4.554036 GACGGCTGCATCCCTCCC 62.554 72.222 0.00 0.00 0.00 4.30
584 588 4.247380 CTGCATCCCTCCCGGCTC 62.247 72.222 0.00 0.00 0.00 4.70
664 668 4.443266 GCGCGGCTCTGTTCCTCT 62.443 66.667 8.83 0.00 0.00 3.69
665 669 2.507992 CGCGGCTCTGTTCCTCTG 60.508 66.667 0.00 0.00 0.00 3.35
666 670 2.659610 GCGGCTCTGTTCCTCTGT 59.340 61.111 0.00 0.00 0.00 3.41
667 671 1.004440 GCGGCTCTGTTCCTCTGTT 60.004 57.895 0.00 0.00 0.00 3.16
668 672 1.016653 GCGGCTCTGTTCCTCTGTTC 61.017 60.000 0.00 0.00 0.00 3.18
669 673 0.390472 CGGCTCTGTTCCTCTGTTCC 60.390 60.000 0.00 0.00 0.00 3.62
670 674 0.980423 GGCTCTGTTCCTCTGTTCCT 59.020 55.000 0.00 0.00 0.00 3.36
671 675 1.349357 GGCTCTGTTCCTCTGTTCCTT 59.651 52.381 0.00 0.00 0.00 3.36
672 676 2.224646 GGCTCTGTTCCTCTGTTCCTTT 60.225 50.000 0.00 0.00 0.00 3.11
673 677 3.070748 GCTCTGTTCCTCTGTTCCTTTC 58.929 50.000 0.00 0.00 0.00 2.62
674 678 3.244387 GCTCTGTTCCTCTGTTCCTTTCT 60.244 47.826 0.00 0.00 0.00 2.52
675 679 4.745172 GCTCTGTTCCTCTGTTCCTTTCTT 60.745 45.833 0.00 0.00 0.00 2.52
676 680 4.708177 TCTGTTCCTCTGTTCCTTTCTTG 58.292 43.478 0.00 0.00 0.00 3.02
677 681 3.817647 CTGTTCCTCTGTTCCTTTCTTGG 59.182 47.826 0.00 0.00 0.00 3.61
678 682 2.554462 GTTCCTCTGTTCCTTTCTTGGC 59.446 50.000 0.00 0.00 0.00 4.52
679 683 2.057922 TCCTCTGTTCCTTTCTTGGCT 58.942 47.619 0.00 0.00 0.00 4.75
680 684 2.039084 TCCTCTGTTCCTTTCTTGGCTC 59.961 50.000 0.00 0.00 0.00 4.70
681 685 2.431454 CTCTGTTCCTTTCTTGGCTCC 58.569 52.381 0.00 0.00 0.00 4.70
682 686 1.160137 CTGTTCCTTTCTTGGCTCCG 58.840 55.000 0.00 0.00 0.00 4.63
683 687 0.762418 TGTTCCTTTCTTGGCTCCGA 59.238 50.000 0.00 0.00 0.00 4.55
684 688 1.157585 GTTCCTTTCTTGGCTCCGAC 58.842 55.000 0.00 0.00 0.00 4.79
685 689 0.036306 TTCCTTTCTTGGCTCCGACC 59.964 55.000 0.00 0.00 0.00 4.79
686 690 0.836400 TCCTTTCTTGGCTCCGACCT 60.836 55.000 0.00 0.00 0.00 3.85
687 691 0.391793 CCTTTCTTGGCTCCGACCTC 60.392 60.000 0.00 0.00 0.00 3.85
688 692 0.610687 CTTTCTTGGCTCCGACCTCT 59.389 55.000 0.00 0.00 0.00 3.69
689 693 0.608640 TTTCTTGGCTCCGACCTCTC 59.391 55.000 0.00 0.00 0.00 3.20
690 694 1.595993 TTCTTGGCTCCGACCTCTCG 61.596 60.000 0.00 0.00 39.83 4.04
698 702 2.487428 CGACCTCTCGGACTGCTG 59.513 66.667 0.00 0.00 36.16 4.41
699 703 2.183046 GACCTCTCGGACTGCTGC 59.817 66.667 0.00 0.00 0.00 5.25
700 704 2.283532 ACCTCTCGGACTGCTGCT 60.284 61.111 0.00 0.00 0.00 4.24
701 705 2.183811 CCTCTCGGACTGCTGCTG 59.816 66.667 4.89 4.89 0.00 4.41
702 706 2.508887 CTCTCGGACTGCTGCTGC 60.509 66.667 8.89 8.89 40.20 5.25
703 707 4.074526 TCTCGGACTGCTGCTGCC 62.075 66.667 13.47 7.95 38.71 4.85
828 835 1.334779 CGACTCGTTCCGTGAACTCTT 60.335 52.381 12.80 0.24 40.05 2.85
871 878 0.834687 TGACTCGGCCCTTACAGGTT 60.835 55.000 0.00 0.00 31.93 3.50
1047 1088 1.831106 AGAGAGAGAGAGAGAGCACGA 59.169 52.381 0.00 0.00 0.00 4.35
1052 1093 1.022451 AGAGAGAGAGCACGACGGTC 61.022 60.000 0.00 0.00 42.76 4.79
1092 1135 4.162690 GGCGGCGTTGAGATCCCT 62.163 66.667 9.37 0.00 0.00 4.20
1353 1438 0.884259 TGGTGTTCATGCAGGTGACG 60.884 55.000 0.00 0.00 0.00 4.35
1671 1773 5.082425 GGAAAGGCATGAATTATGGAGGAT 58.918 41.667 0.00 0.00 37.26 3.24
1690 1792 6.091305 GGAGGATTTTGTAAGCTTGAAATTGC 59.909 38.462 9.86 9.50 0.00 3.56
1695 1797 7.783090 TTTTGTAAGCTTGAAATTGCATGAA 57.217 28.000 9.86 0.00 0.00 2.57
1702 1804 6.595794 AGCTTGAAATTGCATGAAAAATTCG 58.404 32.000 3.47 0.00 0.00 3.34
1728 1830 7.381408 GCCTAGTTTAAATGTTGGTCAAAGTTC 59.619 37.037 0.00 0.00 0.00 3.01
1944 2128 3.686227 ACATCCAATTAGGCCCATTCA 57.314 42.857 0.00 0.00 37.29 2.57
2022 2209 9.545105 AAATCATAATGCTGAAACTTTTTGTGA 57.455 25.926 0.00 0.00 0.00 3.58
2208 2397 4.931002 CACCTGGTGCCAAAATAAATGAAG 59.069 41.667 14.87 0.00 0.00 3.02
2299 2489 2.366153 ATTGGTGCGGTTGGGGACTT 62.366 55.000 0.00 0.00 0.00 3.01
2360 2550 1.134560 CTGGTAACCGCTAGGACAGAC 59.865 57.143 0.00 0.00 41.02 3.51
2549 2778 3.501062 GGTTAGAGTGGCACTTGGTTTAC 59.499 47.826 22.98 13.27 0.00 2.01
2553 2782 2.151202 AGTGGCACTTGGTTTACGATG 58.849 47.619 15.88 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 158 0.179073 AGATCCAATCCAAGACGCGG 60.179 55.000 12.47 0.00 0.00 6.46
160 161 1.475751 CCCCAGATCCAATCCAAGACG 60.476 57.143 0.00 0.00 0.00 4.18
197 198 1.140407 CGGCTCCAACTCGATTCGTC 61.140 60.000 5.89 0.00 0.00 4.20
286 290 0.690192 TCATTTCCAGTTCAGCCGGA 59.310 50.000 5.05 0.00 0.00 5.14
335 339 2.746277 GCTGGTACACGGCCAAGG 60.746 66.667 2.24 0.00 46.06 3.61
431 435 1.510480 GCTGATGGAATGGCCGTAGC 61.510 60.000 0.00 0.00 40.66 3.58
432 436 1.224069 CGCTGATGGAATGGCCGTAG 61.224 60.000 0.00 0.00 40.66 3.51
433 437 1.227527 CGCTGATGGAATGGCCGTA 60.228 57.895 0.00 0.00 40.66 4.02
434 438 2.514592 CGCTGATGGAATGGCCGT 60.515 61.111 0.00 0.00 40.66 5.68
435 439 3.282157 CCGCTGATGGAATGGCCG 61.282 66.667 0.00 0.00 40.66 6.13
436 440 2.908940 CCCGCTGATGGAATGGCC 60.909 66.667 0.00 0.00 37.10 5.36
437 441 3.599704 GCCCGCTGATGGAATGGC 61.600 66.667 0.00 0.00 0.00 4.40
438 442 2.124193 TGCCCGCTGATGGAATGG 60.124 61.111 0.00 0.00 0.00 3.16
439 443 2.191513 CCTGCCCGCTGATGGAATG 61.192 63.158 0.00 0.00 0.00 2.67
440 444 2.194056 CCTGCCCGCTGATGGAAT 59.806 61.111 0.00 0.00 0.00 3.01
441 445 4.802051 GCCTGCCCGCTGATGGAA 62.802 66.667 0.00 0.00 0.00 3.53
455 459 3.775654 GCTCAGGTACCTGCGCCT 61.776 66.667 36.42 4.36 45.74 5.52
458 462 2.496817 GGAGCTCAGGTACCTGCG 59.503 66.667 33.39 29.05 43.31 5.18
459 463 2.496817 CGGAGCTCAGGTACCTGC 59.503 66.667 33.39 24.10 43.31 4.85
479 483 2.955022 AAGATCTCCATGGCCAGCGC 62.955 60.000 13.05 0.00 0.00 5.92
480 484 0.883814 GAAGATCTCCATGGCCAGCG 60.884 60.000 13.05 4.50 0.00 5.18
481 485 0.182061 TGAAGATCTCCATGGCCAGC 59.818 55.000 13.05 0.00 0.00 4.85
482 486 1.202782 CCTGAAGATCTCCATGGCCAG 60.203 57.143 13.05 3.10 0.00 4.85
483 487 0.841961 CCTGAAGATCTCCATGGCCA 59.158 55.000 8.56 8.56 0.00 5.36
484 488 0.842635 ACCTGAAGATCTCCATGGCC 59.157 55.000 6.96 0.00 0.00 5.36
485 489 1.476471 CCACCTGAAGATCTCCATGGC 60.476 57.143 6.96 0.00 0.00 4.40
486 490 1.476471 GCCACCTGAAGATCTCCATGG 60.476 57.143 4.97 4.97 0.00 3.66
487 491 1.809271 CGCCACCTGAAGATCTCCATG 60.809 57.143 0.00 0.00 0.00 3.66
488 492 0.467384 CGCCACCTGAAGATCTCCAT 59.533 55.000 0.00 0.00 0.00 3.41
489 493 1.900351 CGCCACCTGAAGATCTCCA 59.100 57.895 0.00 0.00 0.00 3.86
490 494 1.522580 GCGCCACCTGAAGATCTCC 60.523 63.158 0.00 0.00 0.00 3.71
491 495 1.522580 GGCGCCACCTGAAGATCTC 60.523 63.158 24.80 0.00 34.51 2.75
492 496 2.586792 GGCGCCACCTGAAGATCT 59.413 61.111 24.80 0.00 34.51 2.75
493 497 2.514824 GGGCGCCACCTGAAGATC 60.515 66.667 30.85 1.84 39.10 2.75
494 498 3.011517 AGGGCGCCACCTGAAGAT 61.012 61.111 30.85 0.00 40.04 2.40
495 499 3.706373 GAGGGCGCCACCTGAAGA 61.706 66.667 30.85 0.00 42.10 2.87
501 505 4.778143 ATCAACGAGGGCGCCACC 62.778 66.667 30.85 18.01 42.48 4.61
502 506 2.253414 GAAATCAACGAGGGCGCCAC 62.253 60.000 30.85 20.30 42.48 5.01
503 507 2.033448 AAATCAACGAGGGCGCCA 59.967 55.556 30.85 5.63 42.48 5.69
504 508 2.761195 GGAAATCAACGAGGGCGCC 61.761 63.158 21.18 21.18 42.48 6.53
505 509 2.761195 GGGAAATCAACGAGGGCGC 61.761 63.158 0.00 0.00 42.48 6.53
506 510 1.369091 CTGGGAAATCAACGAGGGCG 61.369 60.000 0.00 0.00 44.79 6.13
507 511 0.035439 TCTGGGAAATCAACGAGGGC 60.035 55.000 0.00 0.00 0.00 5.19
508 512 1.555075 TCTCTGGGAAATCAACGAGGG 59.445 52.381 0.00 0.00 0.00 4.30
509 513 3.462021 GATCTCTGGGAAATCAACGAGG 58.538 50.000 0.00 0.00 0.00 4.63
510 514 3.462021 GGATCTCTGGGAAATCAACGAG 58.538 50.000 0.00 0.00 0.00 4.18
511 515 2.170607 GGGATCTCTGGGAAATCAACGA 59.829 50.000 0.00 0.00 0.00 3.85
512 516 2.565841 GGGATCTCTGGGAAATCAACG 58.434 52.381 0.00 0.00 0.00 4.10
513 517 2.746472 CGGGGATCTCTGGGAAATCAAC 60.746 54.545 0.00 0.00 0.00 3.18
514 518 1.490490 CGGGGATCTCTGGGAAATCAA 59.510 52.381 0.00 0.00 0.00 2.57
515 519 1.131638 CGGGGATCTCTGGGAAATCA 58.868 55.000 0.00 0.00 0.00 2.57
516 520 1.424638 TCGGGGATCTCTGGGAAATC 58.575 55.000 0.36 0.00 0.00 2.17
517 521 1.490910 GTTCGGGGATCTCTGGGAAAT 59.509 52.381 0.36 0.00 0.00 2.17
518 522 0.909623 GTTCGGGGATCTCTGGGAAA 59.090 55.000 0.36 0.00 0.00 3.13
519 523 0.252513 TGTTCGGGGATCTCTGGGAA 60.253 55.000 0.36 0.00 0.00 3.97
520 524 0.687757 CTGTTCGGGGATCTCTGGGA 60.688 60.000 0.36 0.00 0.00 4.37
521 525 1.826024 CTGTTCGGGGATCTCTGGG 59.174 63.158 0.36 0.00 0.00 4.45
522 526 1.144936 GCTGTTCGGGGATCTCTGG 59.855 63.158 0.36 0.00 0.00 3.86
523 527 0.179089 CTGCTGTTCGGGGATCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
524 528 1.965754 GCTGCTGTTCGGGGATCTCT 61.966 60.000 0.00 0.00 0.00 3.10
525 529 1.522580 GCTGCTGTTCGGGGATCTC 60.523 63.158 0.00 0.00 0.00 2.75
526 530 1.965754 GAGCTGCTGTTCGGGGATCT 61.966 60.000 7.01 0.00 0.00 2.75
527 531 1.522580 GAGCTGCTGTTCGGGGATC 60.523 63.158 7.01 0.00 0.00 3.36
528 532 2.586792 GAGCTGCTGTTCGGGGAT 59.413 61.111 7.01 0.00 0.00 3.85
529 533 3.706373 GGAGCTGCTGTTCGGGGA 61.706 66.667 7.01 0.00 0.00 4.81
530 534 4.785453 GGGAGCTGCTGTTCGGGG 62.785 72.222 7.01 0.00 0.00 5.73
531 535 4.785453 GGGGAGCTGCTGTTCGGG 62.785 72.222 7.01 0.00 0.00 5.14
532 536 3.672295 GAGGGGAGCTGCTGTTCGG 62.672 68.421 7.01 0.00 0.00 4.30
533 537 2.125350 GAGGGGAGCTGCTGTTCG 60.125 66.667 7.01 0.00 0.00 3.95
534 538 2.125350 CGAGGGGAGCTGCTGTTC 60.125 66.667 7.01 0.00 0.00 3.18
535 539 3.710722 CCGAGGGGAGCTGCTGTT 61.711 66.667 7.01 0.00 34.06 3.16
554 558 4.742201 TGCAGCCGTCTTCCTCGC 62.742 66.667 0.00 0.00 0.00 5.03
555 559 1.880340 GATGCAGCCGTCTTCCTCG 60.880 63.158 0.00 0.00 0.00 4.63
556 560 1.522580 GGATGCAGCCGTCTTCCTC 60.523 63.158 4.62 0.00 0.00 3.71
557 561 2.586792 GGATGCAGCCGTCTTCCT 59.413 61.111 4.62 0.00 0.00 3.36
558 562 2.514824 GGGATGCAGCCGTCTTCC 60.515 66.667 16.15 2.95 0.00 3.46
559 563 1.522580 GAGGGATGCAGCCGTCTTC 60.523 63.158 30.94 15.31 39.21 2.87
560 564 2.586792 GAGGGATGCAGCCGTCTT 59.413 61.111 30.94 10.71 39.21 3.01
561 565 3.474570 GGAGGGATGCAGCCGTCT 61.475 66.667 34.71 20.01 41.40 4.18
562 566 4.554036 GGGAGGGATGCAGCCGTC 62.554 72.222 30.57 30.57 41.04 4.79
647 651 4.443266 AGAGGAACAGAGCCGCGC 62.443 66.667 0.00 0.00 0.00 6.86
648 652 2.507992 CAGAGGAACAGAGCCGCG 60.508 66.667 0.00 0.00 0.00 6.46
649 653 1.004440 AACAGAGGAACAGAGCCGC 60.004 57.895 0.00 0.00 0.00 6.53
650 654 0.390472 GGAACAGAGGAACAGAGCCG 60.390 60.000 0.00 0.00 0.00 5.52
651 655 0.980423 AGGAACAGAGGAACAGAGCC 59.020 55.000 0.00 0.00 0.00 4.70
652 656 2.849294 AAGGAACAGAGGAACAGAGC 57.151 50.000 0.00 0.00 0.00 4.09
653 657 4.615588 AGAAAGGAACAGAGGAACAGAG 57.384 45.455 0.00 0.00 0.00 3.35
654 658 4.444876 CCAAGAAAGGAACAGAGGAACAGA 60.445 45.833 0.00 0.00 0.00 3.41
655 659 3.817647 CCAAGAAAGGAACAGAGGAACAG 59.182 47.826 0.00 0.00 0.00 3.16
656 660 3.820557 CCAAGAAAGGAACAGAGGAACA 58.179 45.455 0.00 0.00 0.00 3.18
657 661 2.554462 GCCAAGAAAGGAACAGAGGAAC 59.446 50.000 0.00 0.00 0.00 3.62
658 662 2.443255 AGCCAAGAAAGGAACAGAGGAA 59.557 45.455 0.00 0.00 0.00 3.36
659 663 2.039084 GAGCCAAGAAAGGAACAGAGGA 59.961 50.000 0.00 0.00 0.00 3.71
660 664 2.431454 GAGCCAAGAAAGGAACAGAGG 58.569 52.381 0.00 0.00 0.00 3.69
661 665 2.431454 GGAGCCAAGAAAGGAACAGAG 58.569 52.381 0.00 0.00 0.00 3.35
662 666 1.270839 CGGAGCCAAGAAAGGAACAGA 60.271 52.381 0.00 0.00 0.00 3.41
663 667 1.160137 CGGAGCCAAGAAAGGAACAG 58.840 55.000 0.00 0.00 0.00 3.16
664 668 0.762418 TCGGAGCCAAGAAAGGAACA 59.238 50.000 0.00 0.00 0.00 3.18
665 669 1.157585 GTCGGAGCCAAGAAAGGAAC 58.842 55.000 0.00 0.00 0.00 3.62
666 670 0.036306 GGTCGGAGCCAAGAAAGGAA 59.964 55.000 0.00 0.00 0.00 3.36
667 671 0.836400 AGGTCGGAGCCAAGAAAGGA 60.836 55.000 3.13 0.00 0.00 3.36
668 672 0.391793 GAGGTCGGAGCCAAGAAAGG 60.392 60.000 3.13 0.00 0.00 3.11
669 673 0.610687 AGAGGTCGGAGCCAAGAAAG 59.389 55.000 3.13 0.00 0.00 2.62
670 674 0.608640 GAGAGGTCGGAGCCAAGAAA 59.391 55.000 3.13 0.00 0.00 2.52
671 675 1.595993 CGAGAGGTCGGAGCCAAGAA 61.596 60.000 3.13 0.00 42.87 2.52
672 676 2.046864 CGAGAGGTCGGAGCCAAGA 61.047 63.158 3.13 0.00 42.87 3.02
673 677 2.492090 CGAGAGGTCGGAGCCAAG 59.508 66.667 3.13 0.00 42.87 3.61
685 689 2.508887 GCAGCAGCAGTCCGAGAG 60.509 66.667 0.00 0.00 41.58 3.20
686 690 4.074526 GGCAGCAGCAGTCCGAGA 62.075 66.667 2.65 0.00 44.61 4.04
716 720 8.093927 CAGTGAGGGCAAAAGGATAATTAAAAA 58.906 33.333 0.00 0.00 0.00 1.94
717 721 7.234577 ACAGTGAGGGCAAAAGGATAATTAAAA 59.765 33.333 0.00 0.00 0.00 1.52
718 722 6.723977 ACAGTGAGGGCAAAAGGATAATTAAA 59.276 34.615 0.00 0.00 0.00 1.52
740 744 3.189287 GGCAAAACTGAGTACATGGACAG 59.811 47.826 11.55 9.59 36.58 3.51
945 952 1.668919 CGCAACGGCTCTCTACTCAAA 60.669 52.381 0.00 0.00 38.10 2.69
951 958 2.678934 ACCCGCAACGGCTCTCTA 60.679 61.111 0.00 0.00 46.86 2.43
1000 1013 1.938657 CTCTCTGTCGCCGTGGTCAT 61.939 60.000 0.00 0.00 0.00 3.06
1047 1088 1.977544 ACAGCTAGCTTCCGACCGT 60.978 57.895 16.46 5.02 0.00 4.83
1052 1093 1.142748 CCTCCACAGCTAGCTTCCG 59.857 63.158 16.46 6.77 0.00 4.30
1353 1438 2.218603 TCGACCCAAAGAAAGAAGCAC 58.781 47.619 0.00 0.00 0.00 4.40
1671 1773 7.783090 TTCATGCAATTTCAAGCTTACAAAA 57.217 28.000 0.00 0.78 0.00 2.44
1690 1792 9.139174 ACATTTAAACTAGGCGAATTTTTCATG 57.861 29.630 0.00 0.00 0.00 3.07
1695 1797 7.438564 ACCAACATTTAAACTAGGCGAATTTT 58.561 30.769 0.00 0.00 0.00 1.82
1702 1804 6.745116 ACTTTGACCAACATTTAAACTAGGC 58.255 36.000 0.00 0.00 0.00 3.93
1861 1970 0.251787 ATTTGGCCCACAGAGGAACC 60.252 55.000 0.00 0.00 41.22 3.62
1944 2128 2.067365 AAAAACGCAAGAGAACCCCT 57.933 45.000 0.00 0.00 43.62 4.79
2022 2209 7.342799 TGGCTCTGGAATAATTCAATTAGCTTT 59.657 33.333 0.00 0.00 0.00 3.51
2299 2489 4.308458 CACGCGGTCCTGGGTTCA 62.308 66.667 12.47 0.00 32.02 3.18
2360 2550 2.504367 ACCCATGTCAAAGTCTTTCCG 58.496 47.619 0.00 0.00 0.00 4.30
2549 2778 7.706179 ACATGCAAATTTATTCCCTTTACATCG 59.294 33.333 0.00 0.00 0.00 3.84
2553 2782 9.869757 ACTAACATGCAAATTTATTCCCTTTAC 57.130 29.630 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.