Multiple sequence alignment - TraesCS2B01G559500

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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 TraesCS2B01G559500 chr2B 100.000 3926 0 0 1 3926 753633392 753629467 0.000000e+00 7251.0
1 TraesCS2B01G559500 chr2D 96.093 2508 89 4 1000 3500 617416288 617413783 0.000000e+00 4080.0
2 TraesCS2B01G559500 chr2D 90.842 546 22 12 3 540 617417402 617416877 0.000000e+00 706.0
3 TraesCS2B01G559500 chr2D 82.184 522 60 15 3258 3758 617889399 617889908 6.070000e-113 418.0
4 TraesCS2B01G559500 chr2D 87.356 261 30 3 3258 3517 617635931 617636189 2.970000e-76 296.0
5 TraesCS2B01G559500 chr2D 92.216 167 12 1 3760 3926 617413605 617413440 6.560000e-58 235.0
6 TraesCS2B01G559500 chr2D 84.906 159 21 3 3769 3926 617907106 617906950 1.460000e-34 158.0
7 TraesCS2B01G559500 chr2D 98.305 59 1 0 3700 3758 617413695 617413637 1.930000e-18 104.0
8 TraesCS2B01G559500 chr2A 92.817 2840 143 20 705 3527 747680796 747678001 0.000000e+00 4058.0
9 TraesCS2B01G559500 chr2A 93.360 497 20 9 73 560 747687056 747686564 0.000000e+00 723.0
10 TraesCS2B01G559500 chr2A 90.303 330 32 0 3258 3587 748287236 748287565 2.170000e-117 433.0
11 TraesCS2B01G559500 chr2A 82.342 521 58 16 3260 3758 748439648 748440156 4.690000e-114 422.0
12 TraesCS2B01G559500 chr2A 85.816 282 37 3 3258 3537 748501496 748501216 2.970000e-76 296.0
13 TraesCS2B01G559500 chr2A 85.771 253 16 4 3526 3758 747677918 747677666 2.340000e-62 250.0
14 TraesCS2B01G559500 chr2A 87.879 99 11 1 3828 3926 748287787 748287884 8.910000e-22 115.0
15 TraesCS2B01G559500 chr2A 100.000 29 0 0 599 627 747686560 747686532 2.000000e-03 54.7
16 TraesCS2B01G559500 chr1B 100.000 28 0 0 724 751 529513324 529513297 7.000000e-03 52.8


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 TraesCS2B01G559500 chr2B 753629467 753633392 3925 True 7251.00 7251 100.000 1 3926 1 chr2B.!!$R1 3925
1 TraesCS2B01G559500 chr2D 617413440 617417402 3962 True 1281.25 4080 94.364 3 3926 4 chr2D.!!$R2 3923
2 TraesCS2B01G559500 chr2D 617889399 617889908 509 False 418.00 418 82.184 3258 3758 1 chr2D.!!$F2 500
3 TraesCS2B01G559500 chr2A 747677666 747680796 3130 True 2154.00 4058 89.294 705 3758 2 chr2A.!!$R2 3053
4 TraesCS2B01G559500 chr2A 748439648 748440156 508 False 422.00 422 82.342 3260 3758 1 chr2A.!!$F1 498
5 TraesCS2B01G559500 chr2A 747686532 747687056 524 True 388.85 723 96.680 73 627 2 chr2A.!!$R3 554
6 TraesCS2B01G559500 chr2A 748287236 748287884 648 False 274.00 433 89.091 3258 3926 2 chr2A.!!$F2 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
657 673 0.106419 GGGAGGAGAGGACAGATCGT 60.106 60.0 0.0 0.0 0.00 3.73 F
1698 2124 0.249699 TGTTCGACGCAATGTCCACT 60.250 50.0 0.0 0.0 45.23 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2621 0.627451 TGAAATGGCCTCATCCAGCT 59.373 50.0 3.32 0.0 39.89 4.24 R
3640 4179 0.328450 TCATATGACCCCCAGGCCTT 60.328 55.0 0.00 0.0 36.11 4.35 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
63 67 4.803426 GCGGACGGCAGTGAGGAG 62.803 72.222 0.00 0.00 42.87 3.69
67 71 1.679305 GACGGCAGTGAGGAGGAGA 60.679 63.158 0.00 0.00 0.00 3.71
86 90 0.394080 ATGCCAGGAAGAGAAGCAGC 60.394 55.000 0.00 0.00 36.80 5.25
87 91 1.002868 GCCAGGAAGAGAAGCAGCA 60.003 57.895 0.00 0.00 0.00 4.41
88 92 1.025647 GCCAGGAAGAGAAGCAGCAG 61.026 60.000 0.00 0.00 0.00 4.24
89 93 1.025647 CCAGGAAGAGAAGCAGCAGC 61.026 60.000 0.00 0.00 42.56 5.25
92 96 1.646624 GGAAGAGAAGCAGCAGCAGC 61.647 60.000 3.17 0.46 45.49 5.25
125 129 1.215647 GGCGGCGAGAAGAAGAAGA 59.784 57.895 12.98 0.00 0.00 2.87
130 134 2.417719 GGCGAGAAGAAGAAGAAGCAA 58.582 47.619 0.00 0.00 0.00 3.91
306 321 9.454585 GGTTAACATGTGTTCATATGAATGATG 57.545 33.333 20.65 21.05 41.73 3.07
556 572 2.031807 CAGTTCCGTCGTCGACAGATAT 59.968 50.000 24.13 8.00 39.71 1.63
560 576 1.194997 CCGTCGTCGACAGATATCTCC 59.805 57.143 24.13 0.00 39.71 3.71
562 578 2.496111 GTCGTCGACAGATATCTCCCT 58.504 52.381 20.28 0.00 32.09 4.20
563 579 2.481185 GTCGTCGACAGATATCTCCCTC 59.519 54.545 20.28 0.00 32.09 4.30
564 580 2.369203 TCGTCGACAGATATCTCCCTCT 59.631 50.000 17.16 0.00 0.00 3.69
565 581 2.739913 CGTCGACAGATATCTCCCTCTC 59.260 54.545 17.16 0.00 0.00 3.20
566 582 3.078837 GTCGACAGATATCTCCCTCTCC 58.921 54.545 11.55 0.00 0.00 3.71
567 583 2.040545 TCGACAGATATCTCCCTCTCCC 59.959 54.545 1.03 0.00 0.00 4.30
568 584 2.224892 CGACAGATATCTCCCTCTCCCA 60.225 54.545 1.03 0.00 0.00 4.37
569 585 3.161866 GACAGATATCTCCCTCTCCCAC 58.838 54.545 1.03 0.00 0.00 4.61
570 586 2.520120 ACAGATATCTCCCTCTCCCACA 59.480 50.000 1.03 0.00 0.00 4.17
571 587 3.164268 CAGATATCTCCCTCTCCCACAG 58.836 54.545 1.03 0.00 0.00 3.66
572 588 1.899142 GATATCTCCCTCTCCCACAGC 59.101 57.143 0.00 0.00 0.00 4.40
573 589 0.636647 TATCTCCCTCTCCCACAGCA 59.363 55.000 0.00 0.00 0.00 4.41
574 590 0.690411 ATCTCCCTCTCCCACAGCAG 60.690 60.000 0.00 0.00 0.00 4.24
575 591 1.305633 CTCCCTCTCCCACAGCAGA 60.306 63.158 0.00 0.00 0.00 4.26
576 592 0.906756 CTCCCTCTCCCACAGCAGAA 60.907 60.000 0.00 0.00 0.00 3.02
577 593 0.473694 TCCCTCTCCCACAGCAGAAA 60.474 55.000 0.00 0.00 0.00 2.52
578 594 0.401738 CCCTCTCCCACAGCAGAAAA 59.598 55.000 0.00 0.00 0.00 2.29
579 595 1.005215 CCCTCTCCCACAGCAGAAAAT 59.995 52.381 0.00 0.00 0.00 1.82
580 596 2.239654 CCCTCTCCCACAGCAGAAAATA 59.760 50.000 0.00 0.00 0.00 1.40
581 597 3.274288 CCTCTCCCACAGCAGAAAATAC 58.726 50.000 0.00 0.00 0.00 1.89
582 598 3.054802 CCTCTCCCACAGCAGAAAATACT 60.055 47.826 0.00 0.00 0.00 2.12
583 599 4.162320 CCTCTCCCACAGCAGAAAATACTA 59.838 45.833 0.00 0.00 0.00 1.82
584 600 5.344743 TCTCCCACAGCAGAAAATACTAG 57.655 43.478 0.00 0.00 0.00 2.57
585 601 4.162320 TCTCCCACAGCAGAAAATACTAGG 59.838 45.833 0.00 0.00 0.00 3.02
586 602 4.101114 TCCCACAGCAGAAAATACTAGGA 58.899 43.478 0.00 0.00 0.00 2.94
587 603 4.162320 TCCCACAGCAGAAAATACTAGGAG 59.838 45.833 0.00 0.00 0.00 3.69
588 604 4.080863 CCCACAGCAGAAAATACTAGGAGT 60.081 45.833 0.00 0.00 0.00 3.85
589 605 5.128827 CCCACAGCAGAAAATACTAGGAGTA 59.871 44.000 0.00 0.00 34.82 2.59
590 606 6.276847 CCACAGCAGAAAATACTAGGAGTAG 58.723 44.000 0.00 0.00 33.66 2.57
591 607 6.127310 CCACAGCAGAAAATACTAGGAGTAGT 60.127 42.308 0.00 0.00 42.49 2.73
592 608 7.068348 CCACAGCAGAAAATACTAGGAGTAGTA 59.932 40.741 0.00 0.00 44.26 1.82
593 609 7.916450 CACAGCAGAAAATACTAGGAGTAGTAC 59.084 40.741 0.00 0.00 43.19 2.73
594 610 7.133513 CAGCAGAAAATACTAGGAGTAGTACG 58.866 42.308 0.00 0.00 43.19 3.67
595 611 7.012138 CAGCAGAAAATACTAGGAGTAGTACGA 59.988 40.741 0.00 0.00 43.19 3.43
596 612 7.555554 AGCAGAAAATACTAGGAGTAGTACGAA 59.444 37.037 0.00 0.00 43.19 3.85
597 613 7.643371 GCAGAAAATACTAGGAGTAGTACGAAC 59.357 40.741 0.00 0.00 43.19 3.95
627 643 2.242572 CGAGGATGCATGGACGCTG 61.243 63.158 2.46 0.00 0.00 5.18
628 644 1.890979 GAGGATGCATGGACGCTGG 60.891 63.158 2.46 0.00 0.00 4.85
629 645 2.903855 GGATGCATGGACGCTGGG 60.904 66.667 2.46 0.00 0.00 4.45
630 646 3.589881 GATGCATGGACGCTGGGC 61.590 66.667 2.46 0.00 0.00 5.36
631 647 4.429522 ATGCATGGACGCTGGGCA 62.430 61.111 0.00 0.00 39.03 5.36
633 649 4.783621 GCATGGACGCTGGGCAGA 62.784 66.667 0.00 0.00 0.00 4.26
634 650 2.821366 CATGGACGCTGGGCAGAC 60.821 66.667 0.00 0.00 0.00 3.51
635 651 4.101448 ATGGACGCTGGGCAGACC 62.101 66.667 0.00 0.00 40.81 3.85
644 660 4.741239 GGGCAGACCAGGGGAGGA 62.741 72.222 0.00 0.00 39.85 3.71
645 661 3.086600 GGCAGACCAGGGGAGGAG 61.087 72.222 0.00 0.00 35.26 3.69
646 662 2.039624 GCAGACCAGGGGAGGAGA 59.960 66.667 0.00 0.00 0.00 3.71
647 663 2.063378 GCAGACCAGGGGAGGAGAG 61.063 68.421 0.00 0.00 0.00 3.20
648 664 1.382420 CAGACCAGGGGAGGAGAGG 60.382 68.421 0.00 0.00 0.00 3.69
649 665 1.547755 AGACCAGGGGAGGAGAGGA 60.548 63.158 0.00 0.00 0.00 3.71
650 666 1.382009 GACCAGGGGAGGAGAGGAC 60.382 68.421 0.00 0.00 0.00 3.85
651 667 2.169590 GACCAGGGGAGGAGAGGACA 62.170 65.000 0.00 0.00 0.00 4.02
652 668 1.382420 CCAGGGGAGGAGAGGACAG 60.382 68.421 0.00 0.00 0.00 3.51
653 669 1.700368 CAGGGGAGGAGAGGACAGA 59.300 63.158 0.00 0.00 0.00 3.41
654 670 0.264359 CAGGGGAGGAGAGGACAGAT 59.736 60.000 0.00 0.00 0.00 2.90
655 671 0.560688 AGGGGAGGAGAGGACAGATC 59.439 60.000 0.00 0.00 0.00 2.75
656 672 0.825840 GGGGAGGAGAGGACAGATCG 60.826 65.000 0.00 0.00 0.00 3.69
657 673 0.106419 GGGAGGAGAGGACAGATCGT 60.106 60.000 0.00 0.00 0.00 3.73
658 674 1.686741 GGGAGGAGAGGACAGATCGTT 60.687 57.143 0.00 0.00 0.00 3.85
659 675 1.679153 GGAGGAGAGGACAGATCGTTC 59.321 57.143 0.00 0.00 0.00 3.95
660 676 2.370349 GAGGAGAGGACAGATCGTTCA 58.630 52.381 0.00 0.00 0.00 3.18
661 677 2.357637 GAGGAGAGGACAGATCGTTCAG 59.642 54.545 0.00 0.00 0.00 3.02
673 689 4.384247 CAGATCGTTCAGAGTTGAGACAAC 59.616 45.833 6.53 6.53 34.15 3.32
677 693 6.812879 TCGTTCAGAGTTGAGACAACTATA 57.187 37.500 15.50 3.80 34.15 1.31
683 768 8.298729 TCAGAGTTGAGACAACTATACATGAT 57.701 34.615 15.50 0.00 0.00 2.45
704 789 5.472478 TGATAGATGATGCTTCATTGCCTTC 59.528 40.000 15.56 9.59 42.73 3.46
705 790 2.957006 AGATGATGCTTCATTGCCTTCC 59.043 45.455 15.56 2.48 42.73 3.46
706 791 2.219080 TGATGCTTCATTGCCTTCCA 57.781 45.000 0.00 0.00 0.00 3.53
708 793 3.900971 TGATGCTTCATTGCCTTCCATA 58.099 40.909 0.00 0.00 0.00 2.74
710 795 5.633117 TGATGCTTCATTGCCTTCCATATA 58.367 37.500 0.00 0.00 0.00 0.86
711 796 5.474532 TGATGCTTCATTGCCTTCCATATAC 59.525 40.000 0.00 0.00 0.00 1.47
712 797 5.052693 TGCTTCATTGCCTTCCATATACT 57.947 39.130 0.00 0.00 0.00 2.12
713 798 6.186420 TGCTTCATTGCCTTCCATATACTA 57.814 37.500 0.00 0.00 0.00 1.82
714 799 5.997746 TGCTTCATTGCCTTCCATATACTAC 59.002 40.000 0.00 0.00 0.00 2.73
715 800 6.183361 TGCTTCATTGCCTTCCATATACTACT 60.183 38.462 0.00 0.00 0.00 2.57
722 807 5.588648 TGCCTTCCATATACTACTTTGTTGC 59.411 40.000 0.00 0.00 0.00 4.17
724 809 6.990349 GCCTTCCATATACTACTTTGTTGCTA 59.010 38.462 0.00 0.00 0.00 3.49
731 816 8.875803 CATATACTACTTTGTTGCTAAAACGGA 58.124 33.333 0.00 0.00 0.00 4.69
743 828 3.060473 GCTAAAACGGATGTATCGAGCAC 60.060 47.826 0.00 0.00 0.00 4.40
755 840 2.273370 TCGAGCACTGAAATACGTCC 57.727 50.000 0.00 0.00 0.00 4.79
757 842 1.731424 CGAGCACTGAAATACGTCCGT 60.731 52.381 0.00 0.00 0.00 4.69
761 846 3.192001 AGCACTGAAATACGTCCGTCTAA 59.808 43.478 0.00 0.00 0.00 2.10
762 847 3.922240 GCACTGAAATACGTCCGTCTAAA 59.078 43.478 0.00 0.00 0.00 1.85
763 848 4.201561 GCACTGAAATACGTCCGTCTAAAC 60.202 45.833 0.00 0.00 0.00 2.01
764 849 4.919168 CACTGAAATACGTCCGTCTAAACA 59.081 41.667 0.00 0.00 0.00 2.83
765 850 5.060569 CACTGAAATACGTCCGTCTAAACAG 59.939 44.000 0.00 4.40 0.00 3.16
766 851 4.487948 TGAAATACGTCCGTCTAAACAGG 58.512 43.478 0.00 0.00 0.00 4.00
767 852 3.515330 AATACGTCCGTCTAAACAGGG 57.485 47.619 0.00 0.00 0.00 4.45
768 853 2.198827 TACGTCCGTCTAAACAGGGA 57.801 50.000 0.00 0.00 0.00 4.20
769 854 0.600057 ACGTCCGTCTAAACAGGGAC 59.400 55.000 2.80 2.80 44.60 4.46
772 857 2.489329 CGTCCGTCTAAACAGGGACTAA 59.511 50.000 9.88 0.00 45.47 2.24
789 874 4.152938 GGACTAATTGTTGTCCCGTGTTAC 59.847 45.833 13.02 0.00 45.03 2.50
797 882 1.270947 TGTCCCGTGTTACCCATGAAC 60.271 52.381 0.00 0.00 31.20 3.18
799 884 0.678684 CCCGTGTTACCCATGAACCC 60.679 60.000 0.00 0.00 31.20 4.11
805 890 4.259356 GTGTTACCCATGAACCCTAGAAC 58.741 47.826 0.00 0.00 0.00 3.01
806 891 3.055675 TGTTACCCATGAACCCTAGAACG 60.056 47.826 0.00 0.00 0.00 3.95
837 923 3.623060 TCGATCCAGCAGCATAGTTTTTC 59.377 43.478 0.00 0.00 0.00 2.29
838 924 3.624861 CGATCCAGCAGCATAGTTTTTCT 59.375 43.478 0.00 0.00 0.00 2.52
840 926 4.292186 TCCAGCAGCATAGTTTTTCTCT 57.708 40.909 0.00 0.00 0.00 3.10
841 927 4.655963 TCCAGCAGCATAGTTTTTCTCTT 58.344 39.130 0.00 0.00 0.00 2.85
842 928 4.456911 TCCAGCAGCATAGTTTTTCTCTTG 59.543 41.667 0.00 0.00 0.00 3.02
843 929 4.456911 CCAGCAGCATAGTTTTTCTCTTGA 59.543 41.667 0.00 0.00 0.00 3.02
844 930 5.048504 CCAGCAGCATAGTTTTTCTCTTGAA 60.049 40.000 0.00 0.00 0.00 2.69
845 931 6.441274 CAGCAGCATAGTTTTTCTCTTGAAA 58.559 36.000 0.00 0.00 40.08 2.69
846 932 6.919662 CAGCAGCATAGTTTTTCTCTTGAAAA 59.080 34.615 0.00 0.49 46.63 2.29
930 1350 0.403271 AGGCAGTGGCAGAACAGAAT 59.597 50.000 20.04 0.00 43.71 2.40
967 1387 4.449161 CGCACGCTCGTTTCGTCG 62.449 66.667 0.00 0.00 38.19 5.12
982 1402 4.373116 TCGAACACCTCTGCCGCC 62.373 66.667 0.00 0.00 0.00 6.13
1393 1813 2.745100 TCGGCTGCTACGTCTCGT 60.745 61.111 0.00 0.00 44.35 4.18
1575 2001 4.385405 GACGAGCTGCTGTGGGCT 62.385 66.667 7.01 0.00 42.39 5.19
1676 2102 2.738521 CCTTGACACCGCCGTCAG 60.739 66.667 5.45 1.79 46.14 3.51
1698 2124 0.249699 TGTTCGACGCAATGTCCACT 60.250 50.000 0.00 0.00 45.23 4.00
1807 2233 1.071385 GGCTCGATCACATGAGGGAAT 59.929 52.381 0.00 0.00 32.78 3.01
1808 2234 2.141517 GCTCGATCACATGAGGGAATG 58.858 52.381 0.00 0.00 32.78 2.67
1836 2262 1.134367 CTCTCGCCCGACAAGATAACA 59.866 52.381 0.00 0.00 0.00 2.41
2088 2514 4.637387 TGATTCAATGGGCAAATTTGGT 57.363 36.364 19.47 0.00 0.00 3.67
2094 2520 2.704190 TGGGCAAATTTGGTAGGGAA 57.296 45.000 19.47 0.00 0.00 3.97
2129 2555 5.167845 GTCACTCTTTGAGAGGATGAAGAC 58.832 45.833 9.55 4.38 46.45 3.01
2130 2556 4.221703 TCACTCTTTGAGAGGATGAAGACC 59.778 45.833 9.55 0.00 46.45 3.85
2154 2580 2.430921 CTTGAGCTCGACGCGGTT 60.431 61.111 12.47 0.00 45.59 4.44
2195 2621 2.494530 GCTTGTGCCGGTTTGGGAA 61.495 57.895 1.90 0.00 41.26 3.97
2364 2790 1.467342 GGTTTTGTGCCGGACTCATAC 59.533 52.381 5.05 5.58 0.00 2.39
2367 2793 0.973632 TTGTGCCGGACTCATACTGT 59.026 50.000 5.05 0.00 0.00 3.55
2382 2808 5.956642 TCATACTGTTACAACGTGCTGATA 58.043 37.500 0.00 0.00 0.00 2.15
2391 2817 2.315925 ACGTGCTGATAGATGGGTTG 57.684 50.000 0.00 0.00 0.00 3.77
2409 2835 1.064003 TGGCTAAAGCAGGAAGGACA 58.936 50.000 4.07 0.00 44.36 4.02
2421 2847 1.674962 GGAAGGACAGATGATGCTTGC 59.325 52.381 0.00 0.00 0.00 4.01
2436 2862 0.798776 CTTGCGCCTTGTACAAGAGG 59.201 55.000 32.50 23.82 42.71 3.69
2559 2985 1.272490 GCGATGATCGACAAGGGGATA 59.728 52.381 20.25 0.00 43.74 2.59
2775 3201 0.179054 GAAAGGGCCGTGAGATACCC 60.179 60.000 0.00 0.00 43.17 3.69
2835 3261 1.402984 GCGGGGAATACTGATCTAGCG 60.403 57.143 0.00 0.00 0.00 4.26
3024 3450 2.125178 GCCATAGGCTACACCGAGT 58.875 57.895 0.00 0.00 46.69 4.18
3088 3515 3.636764 ACCAACAGGAGGAATTTTGACAC 59.363 43.478 0.00 0.00 0.00 3.67
3146 3573 5.115480 GTTTTGAGCAATCAAAGGGAAACA 58.885 37.500 3.88 0.00 40.20 2.83
3300 3728 1.693606 AGGGTGTTGCTGGAAAAATGG 59.306 47.619 0.00 0.00 0.00 3.16
3441 3870 5.635700 GCACATAAAATTGCTTCCGGTAAAA 59.364 36.000 0.00 0.00 35.74 1.52
3459 3888 5.855235 GTAAAATACCAGCGTTCTGAGAAC 58.145 41.667 15.12 15.12 42.95 3.01
3537 4051 5.292101 GGTATTCACTCATAGCTGACACAAC 59.708 44.000 0.00 0.00 0.00 3.32
3538 4052 4.335400 TTCACTCATAGCTGACACAACA 57.665 40.909 0.00 0.00 0.00 3.33
3640 4179 9.968870 ACGTTCAAAATTAAAATAACAAGCCTA 57.031 25.926 0.00 0.00 0.00 3.93
3685 4256 4.524053 TCAGAAGGCGTAACTCTGATCTA 58.476 43.478 5.41 0.00 33.17 1.98
3686 4257 4.335874 TCAGAAGGCGTAACTCTGATCTAC 59.664 45.833 5.41 0.00 33.17 2.59
3748 4321 3.327757 TCAGAGTATCCAAGTTTGTGGCT 59.672 43.478 0.00 0.00 38.68 4.75
3758 4331 4.819630 CCAAGTTTGTGGCTAAGTACTTGA 59.180 41.667 18.56 1.90 42.99 3.02
3802 4405 3.414700 GCGTGACCAAGGAGTGCG 61.415 66.667 0.00 0.00 0.00 5.34
3888 4491 6.073276 CCTCTCTCTGTCGATGATAGTTACTG 60.073 46.154 0.00 0.00 0.00 2.74
3890 4493 6.258947 TCTCTCTGTCGATGATAGTTACTGTG 59.741 42.308 0.00 0.00 0.00 3.66
3896 4499 6.751888 TGTCGATGATAGTTACTGTGATGTTG 59.248 38.462 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 59 0.690411 CCTGGCATCTCCTCCTCACT 60.690 60.000 0.00 0.00 35.26 3.41
63 67 1.474855 GCTTCTCTTCCTGGCATCTCC 60.475 57.143 0.00 0.00 0.00 3.71
67 71 0.394080 GCTGCTTCTCTTCCTGGCAT 60.394 55.000 0.00 0.00 32.39 4.40
89 93 2.125229 ATCACCGCTCTGCTGCTG 60.125 61.111 0.00 0.00 0.00 4.41
92 96 3.200593 GCCATCACCGCTCTGCTG 61.201 66.667 0.00 0.00 0.00 4.41
125 129 3.260632 GTCCTCTTCTCCTTCTCTTGCTT 59.739 47.826 0.00 0.00 0.00 3.91
130 134 2.891191 ACGTCCTCTTCTCCTTCTCT 57.109 50.000 0.00 0.00 0.00 3.10
279 287 7.693020 TCATTCATATGAACACATGTTAACCG 58.307 34.615 20.19 0.00 37.83 4.44
294 305 6.377429 CCCTCCCAAGAATCATCATTCATATG 59.623 42.308 0.00 0.00 41.03 1.78
306 321 2.170607 TGACGAATCCCTCCCAAGAATC 59.829 50.000 0.00 0.00 0.00 2.52
307 322 2.171448 CTGACGAATCCCTCCCAAGAAT 59.829 50.000 0.00 0.00 0.00 2.40
308 323 1.555075 CTGACGAATCCCTCCCAAGAA 59.445 52.381 0.00 0.00 0.00 2.52
502 517 2.270986 GGCAGCAGACACCCAAAGG 61.271 63.158 0.00 0.00 40.04 3.11
512 527 1.145738 AGGAAAGAAAAGGGCAGCAGA 59.854 47.619 0.00 0.00 0.00 4.26
513 528 1.271656 CAGGAAAGAAAAGGGCAGCAG 59.728 52.381 0.00 0.00 0.00 4.24
556 572 1.305633 CTGCTGTGGGAGAGGGAGA 60.306 63.158 0.00 0.00 32.36 3.71
560 576 2.503895 ATTTTCTGCTGTGGGAGAGG 57.496 50.000 0.00 0.00 40.83 3.69
562 578 4.162320 CCTAGTATTTTCTGCTGTGGGAGA 59.838 45.833 0.00 0.00 38.14 3.71
563 579 4.162320 TCCTAGTATTTTCTGCTGTGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
564 580 4.101114 TCCTAGTATTTTCTGCTGTGGGA 58.899 43.478 0.00 0.00 0.00 4.37
565 581 4.080863 ACTCCTAGTATTTTCTGCTGTGGG 60.081 45.833 0.00 0.00 0.00 4.61
566 582 5.091261 ACTCCTAGTATTTTCTGCTGTGG 57.909 43.478 0.00 0.00 0.00 4.17
567 583 6.868622 ACTACTCCTAGTATTTTCTGCTGTG 58.131 40.000 0.00 0.00 30.81 3.66
568 584 7.201714 CGTACTACTCCTAGTATTTTCTGCTGT 60.202 40.741 0.00 0.00 37.70 4.40
569 585 7.012138 TCGTACTACTCCTAGTATTTTCTGCTG 59.988 40.741 0.00 0.00 37.70 4.41
570 586 7.052873 TCGTACTACTCCTAGTATTTTCTGCT 58.947 38.462 0.00 0.00 37.70 4.24
571 587 7.256756 TCGTACTACTCCTAGTATTTTCTGC 57.743 40.000 0.00 0.00 37.70 4.26
572 588 7.850003 CGTTCGTACTACTCCTAGTATTTTCTG 59.150 40.741 0.00 0.00 37.70 3.02
573 589 7.766278 TCGTTCGTACTACTCCTAGTATTTTCT 59.234 37.037 0.00 0.00 37.70 2.52
574 590 7.910304 TCGTTCGTACTACTCCTAGTATTTTC 58.090 38.462 0.00 0.00 37.70 2.29
575 591 7.849804 TCGTTCGTACTACTCCTAGTATTTT 57.150 36.000 0.00 0.00 37.70 1.82
576 592 7.011857 CCTTCGTTCGTACTACTCCTAGTATTT 59.988 40.741 0.00 0.00 37.70 1.40
577 593 6.481644 CCTTCGTTCGTACTACTCCTAGTATT 59.518 42.308 0.00 0.00 37.70 1.89
578 594 5.988561 CCTTCGTTCGTACTACTCCTAGTAT 59.011 44.000 0.00 0.00 37.70 2.12
579 595 5.127194 TCCTTCGTTCGTACTACTCCTAGTA 59.873 44.000 0.00 0.00 34.79 1.82
580 596 4.081420 TCCTTCGTTCGTACTACTCCTAGT 60.081 45.833 0.00 0.00 37.04 2.57
581 597 4.269844 GTCCTTCGTTCGTACTACTCCTAG 59.730 50.000 0.00 0.00 0.00 3.02
582 598 4.184629 GTCCTTCGTTCGTACTACTCCTA 58.815 47.826 0.00 0.00 0.00 2.94
583 599 3.006247 GTCCTTCGTTCGTACTACTCCT 58.994 50.000 0.00 0.00 0.00 3.69
584 600 2.096657 GGTCCTTCGTTCGTACTACTCC 59.903 54.545 0.00 0.00 0.00 3.85
585 601 2.222908 CGGTCCTTCGTTCGTACTACTC 60.223 54.545 0.00 0.00 0.00 2.59
586 602 1.734465 CGGTCCTTCGTTCGTACTACT 59.266 52.381 0.00 0.00 0.00 2.57
587 603 1.732259 TCGGTCCTTCGTTCGTACTAC 59.268 52.381 0.00 0.00 0.00 2.73
588 604 2.093306 TCGGTCCTTCGTTCGTACTA 57.907 50.000 0.00 0.00 0.00 1.82
589 605 1.399791 GATCGGTCCTTCGTTCGTACT 59.600 52.381 0.00 0.00 0.00 2.73
590 606 1.820092 GATCGGTCCTTCGTTCGTAC 58.180 55.000 0.00 0.00 0.00 3.67
591 607 0.374758 CGATCGGTCCTTCGTTCGTA 59.625 55.000 7.38 0.00 43.20 3.43
592 608 1.136147 CGATCGGTCCTTCGTTCGT 59.864 57.895 7.38 0.00 43.20 3.85
593 609 0.589229 CTCGATCGGTCCTTCGTTCG 60.589 60.000 16.41 10.25 46.88 3.95
594 610 0.248539 CCTCGATCGGTCCTTCGTTC 60.249 60.000 16.41 0.00 36.74 3.95
595 611 0.679002 TCCTCGATCGGTCCTTCGTT 60.679 55.000 16.41 0.00 36.74 3.85
596 612 0.465824 ATCCTCGATCGGTCCTTCGT 60.466 55.000 16.41 0.00 36.74 3.85
597 613 0.039978 CATCCTCGATCGGTCCTTCG 60.040 60.000 16.41 5.05 36.72 3.79
627 643 4.741239 TCCTCCCCTGGTCTGCCC 62.741 72.222 0.00 0.00 0.00 5.36
628 644 3.086600 CTCCTCCCCTGGTCTGCC 61.087 72.222 0.00 0.00 0.00 4.85
629 645 2.039624 TCTCCTCCCCTGGTCTGC 59.960 66.667 0.00 0.00 0.00 4.26
630 646 1.382420 CCTCTCCTCCCCTGGTCTG 60.382 68.421 0.00 0.00 0.00 3.51
631 647 1.547755 TCCTCTCCTCCCCTGGTCT 60.548 63.158 0.00 0.00 0.00 3.85
632 648 1.382009 GTCCTCTCCTCCCCTGGTC 60.382 68.421 0.00 0.00 0.00 4.02
633 649 2.174876 CTGTCCTCTCCTCCCCTGGT 62.175 65.000 0.00 0.00 0.00 4.00
634 650 1.382420 CTGTCCTCTCCTCCCCTGG 60.382 68.421 0.00 0.00 0.00 4.45
635 651 0.264359 ATCTGTCCTCTCCTCCCCTG 59.736 60.000 0.00 0.00 0.00 4.45
636 652 0.560688 GATCTGTCCTCTCCTCCCCT 59.439 60.000 0.00 0.00 0.00 4.79
637 653 0.825840 CGATCTGTCCTCTCCTCCCC 60.826 65.000 0.00 0.00 0.00 4.81
638 654 0.106419 ACGATCTGTCCTCTCCTCCC 60.106 60.000 0.00 0.00 0.00 4.30
639 655 1.679153 GAACGATCTGTCCTCTCCTCC 59.321 57.143 0.00 0.00 0.00 4.30
640 656 2.357637 CTGAACGATCTGTCCTCTCCTC 59.642 54.545 0.00 0.00 0.00 3.71
641 657 2.025793 TCTGAACGATCTGTCCTCTCCT 60.026 50.000 0.00 0.00 0.00 3.69
642 658 2.357637 CTCTGAACGATCTGTCCTCTCC 59.642 54.545 0.00 0.00 0.00 3.71
643 659 3.013921 ACTCTGAACGATCTGTCCTCTC 58.986 50.000 0.00 0.00 0.00 3.20
644 660 3.080300 ACTCTGAACGATCTGTCCTCT 57.920 47.619 0.00 0.00 0.00 3.69
645 661 3.191581 TCAACTCTGAACGATCTGTCCTC 59.808 47.826 0.00 0.00 0.00 3.71
646 662 3.157881 TCAACTCTGAACGATCTGTCCT 58.842 45.455 0.00 0.00 0.00 3.85
647 663 3.191581 TCTCAACTCTGAACGATCTGTCC 59.808 47.826 0.00 0.00 0.00 4.02
648 664 4.162812 GTCTCAACTCTGAACGATCTGTC 58.837 47.826 0.00 0.00 0.00 3.51
649 665 3.570125 TGTCTCAACTCTGAACGATCTGT 59.430 43.478 0.00 0.00 0.00 3.41
650 666 4.166187 TGTCTCAACTCTGAACGATCTG 57.834 45.455 0.00 0.00 0.00 2.90
651 667 4.279671 AGTTGTCTCAACTCTGAACGATCT 59.720 41.667 9.00 0.00 0.00 2.75
652 668 4.551388 AGTTGTCTCAACTCTGAACGATC 58.449 43.478 9.00 0.00 0.00 3.69
653 669 4.592485 AGTTGTCTCAACTCTGAACGAT 57.408 40.909 9.00 0.00 0.00 3.73
654 670 5.707242 ATAGTTGTCTCAACTCTGAACGA 57.293 39.130 16.65 0.96 0.00 3.85
655 671 6.379386 TGTATAGTTGTCTCAACTCTGAACG 58.621 40.000 16.65 0.00 0.00 3.95
656 672 8.029522 TCATGTATAGTTGTCTCAACTCTGAAC 58.970 37.037 16.65 11.67 0.00 3.18
657 673 8.122472 TCATGTATAGTTGTCTCAACTCTGAA 57.878 34.615 16.65 2.55 0.00 3.02
658 674 7.703058 TCATGTATAGTTGTCTCAACTCTGA 57.297 36.000 16.65 10.95 0.00 3.27
659 675 9.676195 CTATCATGTATAGTTGTCTCAACTCTG 57.324 37.037 16.65 9.32 34.02 3.35
660 676 9.634021 TCTATCATGTATAGTTGTCTCAACTCT 57.366 33.333 16.65 10.94 38.99 3.24
677 693 5.183331 GGCAATGAAGCATCATCTATCATGT 59.817 40.000 4.66 0.00 45.60 3.21
683 768 4.139786 GGAAGGCAATGAAGCATCATCTA 58.860 43.478 4.66 0.00 45.60 1.98
704 789 8.120465 CCGTTTTAGCAACAAAGTAGTATATGG 58.880 37.037 0.00 0.00 0.00 2.74
705 790 8.875803 TCCGTTTTAGCAACAAAGTAGTATATG 58.124 33.333 0.00 0.00 0.00 1.78
706 791 9.609346 ATCCGTTTTAGCAACAAAGTAGTATAT 57.391 29.630 0.00 0.00 0.00 0.86
708 793 7.389607 ACATCCGTTTTAGCAACAAAGTAGTAT 59.610 33.333 0.00 0.00 0.00 2.12
710 795 5.529800 ACATCCGTTTTAGCAACAAAGTAGT 59.470 36.000 0.00 0.00 0.00 2.73
711 796 5.997385 ACATCCGTTTTAGCAACAAAGTAG 58.003 37.500 0.00 0.00 0.00 2.57
712 797 7.412129 CGATACATCCGTTTTAGCAACAAAGTA 60.412 37.037 0.00 0.00 0.00 2.24
713 798 4.911514 ACATCCGTTTTAGCAACAAAGT 57.088 36.364 0.00 0.00 0.00 2.66
714 799 5.732647 CGATACATCCGTTTTAGCAACAAAG 59.267 40.000 0.00 0.00 0.00 2.77
715 800 5.408909 TCGATACATCCGTTTTAGCAACAAA 59.591 36.000 0.00 0.00 0.00 2.83
722 807 4.207224 CAGTGCTCGATACATCCGTTTTAG 59.793 45.833 3.24 0.00 0.00 1.85
724 809 2.930040 CAGTGCTCGATACATCCGTTTT 59.070 45.455 3.24 0.00 0.00 2.43
731 816 4.933330 ACGTATTTCAGTGCTCGATACAT 58.067 39.130 0.00 0.00 0.00 2.29
743 828 4.561606 CCTGTTTAGACGGACGTATTTCAG 59.438 45.833 0.00 4.68 33.82 3.02
755 840 5.699458 ACAACAATTAGTCCCTGTTTAGACG 59.301 40.000 0.00 0.00 38.08 4.18
757 842 6.235664 GGACAACAATTAGTCCCTGTTTAGA 58.764 40.000 11.08 0.00 46.79 2.10
767 852 4.152938 GGTAACACGGGACAACAATTAGTC 59.847 45.833 0.00 0.00 0.00 2.59
768 853 4.067192 GGTAACACGGGACAACAATTAGT 58.933 43.478 0.00 0.00 0.00 2.24
769 854 3.437741 GGGTAACACGGGACAACAATTAG 59.562 47.826 0.00 0.00 39.74 1.73
772 857 1.143277 TGGGTAACACGGGACAACAAT 59.857 47.619 0.00 0.00 39.74 2.71
783 868 4.259356 GTTCTAGGGTTCATGGGTAACAC 58.741 47.826 0.00 0.00 39.74 3.32
785 870 3.055602 ACGTTCTAGGGTTCATGGGTAAC 60.056 47.826 0.00 0.00 0.00 2.50
789 874 2.781681 AACGTTCTAGGGTTCATGGG 57.218 50.000 0.00 0.00 0.00 4.00
837 923 4.072131 TCCAACGGAATCCTTTTCAAGAG 58.928 43.478 0.00 0.00 0.00 2.85
838 924 4.093472 TCCAACGGAATCCTTTTCAAGA 57.907 40.909 0.00 0.00 0.00 3.02
840 926 5.599999 TTTTCCAACGGAATCCTTTTCAA 57.400 34.783 0.00 0.00 41.71 2.69
841 927 5.799827 ATTTTCCAACGGAATCCTTTTCA 57.200 34.783 0.00 0.00 41.71 2.69
842 928 6.366061 CAGAATTTTCCAACGGAATCCTTTTC 59.634 38.462 0.00 0.00 41.71 2.29
843 929 6.183360 ACAGAATTTTCCAACGGAATCCTTTT 60.183 34.615 0.00 0.00 41.71 2.27
844 930 5.304357 ACAGAATTTTCCAACGGAATCCTTT 59.696 36.000 0.00 0.00 41.71 3.11
845 931 4.832823 ACAGAATTTTCCAACGGAATCCTT 59.167 37.500 0.00 0.00 41.71 3.36
846 932 4.407365 ACAGAATTTTCCAACGGAATCCT 58.593 39.130 0.00 0.00 41.71 3.24
847 933 4.783764 ACAGAATTTTCCAACGGAATCC 57.216 40.909 0.00 0.00 41.71 3.01
848 934 6.674066 TGTAACAGAATTTTCCAACGGAATC 58.326 36.000 0.00 0.00 41.71 2.52
849 935 6.642707 TGTAACAGAATTTTCCAACGGAAT 57.357 33.333 0.00 0.00 41.71 3.01
922 1342 1.093159 CAGGCTGGCTGATTCTGTTC 58.907 55.000 25.34 0.00 0.00 3.18
930 1350 2.659016 CGTTCTCAGGCTGGCTGA 59.341 61.111 28.96 28.96 0.00 4.26
951 1371 2.641783 TTCGACGAAACGAGCGTGC 61.642 57.895 8.05 0.00 42.77 5.34
959 1379 0.507358 GCAGAGGTGTTCGACGAAAC 59.493 55.000 12.67 12.16 0.00 2.78
983 1403 3.069980 ATCTCGCGGTGTGAGGAGC 62.070 63.158 6.13 0.00 40.20 4.70
984 1404 1.226802 CATCTCGCGGTGTGAGGAG 60.227 63.158 6.13 0.00 40.20 3.69
1336 1756 4.353437 GAGGTCGTCGGTGCCGTT 62.353 66.667 10.60 0.00 40.74 4.44
1393 1813 3.043713 CGCGAAGGAGTGCAGCAA 61.044 61.111 0.00 0.00 0.00 3.91
1698 2124 4.011517 GGGCGAACCGGGTCTTCA 62.012 66.667 19.34 0.00 36.48 3.02
1902 2328 3.560105 CATTCCCCTCTCTTCCATTTCC 58.440 50.000 0.00 0.00 0.00 3.13
2088 2514 0.988832 ACATTGCCTCGGTTTCCCTA 59.011 50.000 0.00 0.00 0.00 3.53
2094 2520 0.687354 AGAGTGACATTGCCTCGGTT 59.313 50.000 0.00 0.00 0.00 4.44
2130 2556 4.441695 TCGAGCTCAAGCCCGCTG 62.442 66.667 15.40 0.00 42.14 5.18
2151 2577 8.612619 CAGTTAACAATCACTCCATATGTAACC 58.387 37.037 8.61 0.00 0.00 2.85
2154 2580 7.564793 AGCAGTTAACAATCACTCCATATGTA 58.435 34.615 8.61 0.00 0.00 2.29
2195 2621 0.627451 TGAAATGGCCTCATCCAGCT 59.373 50.000 3.32 0.00 39.89 4.24
2364 2790 4.268644 CCATCTATCAGCACGTTGTAACAG 59.731 45.833 0.00 0.00 0.00 3.16
2367 2793 3.196901 ACCCATCTATCAGCACGTTGTAA 59.803 43.478 0.00 0.00 0.00 2.41
2382 2808 1.341383 CCTGCTTTAGCCAACCCATCT 60.341 52.381 0.00 0.00 41.18 2.90
2391 2817 1.279271 TCTGTCCTTCCTGCTTTAGCC 59.721 52.381 0.00 0.00 41.18 3.93
2421 2847 1.207089 TCCATCCTCTTGTACAAGGCG 59.793 52.381 30.35 21.93 38.88 5.52
2436 2862 3.204306 TCACAGCCATCATCTTCCATC 57.796 47.619 0.00 0.00 0.00 3.51
2559 2985 2.282040 GCTGCAGCTGTGGGAGTT 60.282 61.111 31.33 0.00 38.21 3.01
2775 3201 0.953471 TCATTGTTCGAACCCTGCCG 60.953 55.000 24.78 8.13 0.00 5.69
2835 3261 2.691409 TACTATGCACCAGCTTGACC 57.309 50.000 0.00 0.00 42.74 4.02
3107 3534 6.625873 CTCAAAACAGGAAGAGCTTTAAGT 57.374 37.500 0.00 0.00 0.00 2.24
3146 3573 4.060205 GACTCATGTGCCAAGCAATTTTT 58.940 39.130 0.00 0.00 41.47 1.94
3382 3811 4.019860 CCCTTTCCATGAGAAGAGAGACAA 60.020 45.833 0.00 0.00 35.40 3.18
3397 3826 3.076785 TGCTCCCTTAATTTCCCTTTCCA 59.923 43.478 0.00 0.00 0.00 3.53
3441 3870 3.673594 CGAAGTTCTCAGAACGCTGGTAT 60.674 47.826 12.01 0.00 42.53 2.73
3449 3878 2.062519 GTCAGCCGAAGTTCTCAGAAC 58.937 52.381 9.78 9.78 0.00 3.01
3459 3888 3.935203 ACTGTATCAATTGTCAGCCGAAG 59.065 43.478 19.43 7.24 0.00 3.79
3537 4051 1.076339 ACGGGTGGGGGCAATATTG 60.076 57.895 11.27 11.27 0.00 1.90
3538 4052 1.229076 GACGGGTGGGGGCAATATT 59.771 57.895 0.00 0.00 0.00 1.28
3640 4179 0.328450 TCATATGACCCCCAGGCCTT 60.328 55.000 0.00 0.00 36.11 4.35
3648 4187 4.455606 CCTTCTGAAACTCATATGACCCC 58.544 47.826 0.00 0.00 0.00 4.95
3685 4256 5.906113 TGTGTAACACATCCAAACTTTGT 57.094 34.783 0.00 0.00 45.67 2.83
3784 4387 3.414700 GCACTCCTTGGTCACGCG 61.415 66.667 3.53 3.53 0.00 6.01
3839 4442 2.426024 GCAGTGCATCAACCATCTCAAT 59.574 45.455 11.09 0.00 0.00 2.57
3840 4443 1.814394 GCAGTGCATCAACCATCTCAA 59.186 47.619 11.09 0.00 0.00 3.02
3863 4466 5.995282 AGTAACTATCATCGACAGAGAGAGG 59.005 44.000 15.72 0.00 0.00 3.69
3864 4467 6.481976 ACAGTAACTATCATCGACAGAGAGAG 59.518 42.308 15.72 8.25 0.00 3.20
3888 4491 8.398665 AGTTGAAGTTTTAAGAGTCAACATCAC 58.601 33.333 17.79 6.22 46.71 3.06


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

AutoCloner maintained by Alex Coulton.