Multiple sequence alignment - TraesCS2A01G305400

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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 TraesCS2A01G305400 chr2A 100.000 2888 0 0 1 2888 524954285 524951398 0.000000e+00 5334.0
1 TraesCS2A01G305400 chr2D 94.959 1706 41 20 639 2331 388482340 388480667 0.000000e+00 2632.0
2 TraesCS2A01G305400 chr2D 93.199 544 21 4 2318 2847 388480644 388480103 0.000000e+00 785.0
3 TraesCS2A01G305400 chr2D 96.328 463 13 3 30 489 388482901 388482440 0.000000e+00 758.0
4 TraesCS2A01G305400 chr2B 93.870 1566 55 13 723 2278 460551916 460550382 0.000000e+00 2322.0
5 TraesCS2A01G305400 chr2B 95.085 468 21 1 22 489 460552554 460552089 0.000000e+00 736.0
6 TraesCS2A01G305400 chr2B 87.285 582 23 15 2270 2847 460550104 460549570 4.090000e-173 617.0
7 TraesCS2A01G305400 chr3D 80.142 141 25 1 1068 1205 305622296 305622436 5.090000e-18 102.0
8 TraesCS2A01G305400 chr3A 80.142 141 25 1 1068 1205 423671786 423671926 5.090000e-18 102.0
9 TraesCS2A01G305400 chr3B 79.433 141 26 1 1068 1205 416135829 416135689 2.370000e-16 97.1
10 TraesCS2A01G305400 chr3B 95.652 46 2 0 531 576 545669767 545669812 1.110000e-09 75.0
11 TraesCS2A01G305400 chr6B 78.378 148 19 6 1069 1205 539195669 539195524 1.840000e-12 84.2
12 TraesCS2A01G305400 chr6A 78.378 148 19 6 1069 1205 499955051 499955196 1.840000e-12 84.2
13 TraesCS2A01G305400 chr4A 97.778 45 1 0 533 577 65467342 65467386 8.580000e-11 78.7
14 TraesCS2A01G305400 chr4A 95.918 49 1 1 529 577 594687861 594687908 8.580000e-11 78.7
15 TraesCS2A01G305400 chr4A 97.727 44 1 0 534 577 38825132 38825089 3.090000e-10 76.8
16 TraesCS2A01G305400 chr1B 97.727 44 1 0 534 577 402068616 402068659 3.090000e-10 76.8
17 TraesCS2A01G305400 chrUn 95.455 44 2 0 534 577 6217867 6217910 1.440000e-08 71.3
18 TraesCS2A01G305400 chr7B 95.455 44 2 0 534 577 135982296 135982339 1.440000e-08 71.3
19 TraesCS2A01G305400 chr5A 88.333 60 4 2 519 577 541600928 541600871 5.160000e-08 69.4
20 TraesCS2A01G305400 chr5A 85.714 63 6 2 516 577 541845824 541845884 2.400000e-06 63.9
21 TraesCS2A01G305400 chr1D 97.500 40 1 0 1162 1201 74929951 74929912 5.160000e-08 69.4
22 TraesCS2A01G305400 chr1A 97.500 40 1 0 1162 1201 75256107 75256068 5.160000e-08 69.4


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 TraesCS2A01G305400 chr2A 524951398 524954285 2887 True 5334.000000 5334 100.000000 1 2888 1 chr2A.!!$R1 2887
1 TraesCS2A01G305400 chr2D 388480103 388482901 2798 True 1391.666667 2632 94.828667 30 2847 3 chr2D.!!$R1 2817
2 TraesCS2A01G305400 chr2B 460549570 460552554 2984 True 1225.000000 2322 92.080000 22 2847 3 chr2B.!!$R1 2825

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
833 881 0.043334 TAGCTCCTCCCTTCCTTGCT 59.957 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2666 3069 0.539518 GGACAAGGAGAAGGGAGAGC 59.46 60.0 0.0 0.0 0.0 4.09 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
28 29 5.878116 TGTGACAATAACCTACTAACATGGC 59.122 40.000 0.00 0.00 0.00 4.40
39 40 1.737793 CTAACATGGCCACCGAAGTTC 59.262 52.381 8.16 0.00 0.00 3.01
114 115 5.512788 CCGTGTAATTAAATCAGCTGCAAAG 59.487 40.000 9.47 0.00 0.00 2.77
117 118 7.485913 CGTGTAATTAAATCAGCTGCAAAGATT 59.514 33.333 9.47 8.95 33.68 2.40
138 139 8.076910 AGATTGTGATCTAATTGACAGAGAGT 57.923 34.615 0.00 0.00 40.84 3.24
140 144 9.809096 GATTGTGATCTAATTGACAGAGAGTAA 57.191 33.333 0.00 0.00 0.00 2.24
322 326 0.316522 ATCATCATCTGACGCCGAGG 59.683 55.000 0.00 0.00 36.48 4.63
422 426 1.623081 CGACACGTTGCCGCTGTTAT 61.623 55.000 0.00 0.00 37.70 1.89
489 493 4.988598 CGCTTCCACGTGGCACCT 62.989 66.667 30.25 0.00 34.44 4.00
490 494 2.345991 GCTTCCACGTGGCACCTA 59.654 61.111 30.25 9.53 34.44 3.08
491 495 2.033194 GCTTCCACGTGGCACCTAC 61.033 63.158 30.25 11.48 34.44 3.18
492 496 1.369692 CTTCCACGTGGCACCTACA 59.630 57.895 30.25 7.86 34.44 2.74
493 497 0.250124 CTTCCACGTGGCACCTACAA 60.250 55.000 30.25 15.49 34.44 2.41
494 498 0.180642 TTCCACGTGGCACCTACAAA 59.819 50.000 30.25 13.25 34.44 2.83
496 500 1.574428 CACGTGGCACCTACAAAGC 59.426 57.895 12.86 0.00 0.00 3.51
498 502 0.250727 ACGTGGCACCTACAAAGCAT 60.251 50.000 12.86 0.00 0.00 3.79
499 503 1.002659 ACGTGGCACCTACAAAGCATA 59.997 47.619 12.86 0.00 0.00 3.14
500 504 1.665679 CGTGGCACCTACAAAGCATAG 59.334 52.381 12.86 0.00 0.00 2.23
501 505 1.401905 GTGGCACCTACAAAGCATAGC 59.598 52.381 6.29 0.00 0.00 2.97
502 506 1.025041 GGCACCTACAAAGCATAGCC 58.975 55.000 0.00 0.00 0.00 3.93
505 509 2.680805 GCACCTACAAAGCATAGCCTCA 60.681 50.000 0.00 0.00 0.00 3.86
506 510 3.201290 CACCTACAAAGCATAGCCTCAG 58.799 50.000 0.00 0.00 0.00 3.35
507 511 2.840651 ACCTACAAAGCATAGCCTCAGT 59.159 45.455 0.00 0.00 0.00 3.41
509 513 3.133721 CCTACAAAGCATAGCCTCAGTCT 59.866 47.826 0.00 0.00 0.00 3.24
510 514 3.258971 ACAAAGCATAGCCTCAGTCTC 57.741 47.619 0.00 0.00 0.00 3.36
511 515 2.836981 ACAAAGCATAGCCTCAGTCTCT 59.163 45.455 0.00 0.00 0.00 3.10
512 516 3.196463 CAAAGCATAGCCTCAGTCTCTG 58.804 50.000 0.00 0.00 0.00 3.35
513 517 2.450867 AGCATAGCCTCAGTCTCTGA 57.549 50.000 0.00 0.00 38.25 3.27
529 533 7.872993 TCAGTCTCTGAGTAAATTGGTTAACAG 59.127 37.037 8.10 0.00 35.39 3.16
531 535 8.598041 AGTCTCTGAGTAAATTGGTTAACAGAT 58.402 33.333 8.10 0.00 37.07 2.90
532 536 8.660373 GTCTCTGAGTAAATTGGTTAACAGATG 58.340 37.037 8.10 0.00 37.07 2.90
533 537 8.593679 TCTCTGAGTAAATTGGTTAACAGATGA 58.406 33.333 8.10 0.00 37.07 2.92
535 539 7.606456 TCTGAGTAAATTGGTTAACAGATGACC 59.394 37.037 8.10 0.00 34.91 4.02
536 540 7.227873 TGAGTAAATTGGTTAACAGATGACCA 58.772 34.615 8.10 0.00 41.46 4.02
537 541 7.888021 TGAGTAAATTGGTTAACAGATGACCAT 59.112 33.333 8.10 0.00 42.59 3.55
538 542 8.055279 AGTAAATTGGTTAACAGATGACCATG 57.945 34.615 8.10 0.00 42.59 3.66
539 543 4.989279 ATTGGTTAACAGATGACCATGC 57.011 40.909 8.10 0.00 42.59 4.06
540 544 2.355197 TGGTTAACAGATGACCATGCG 58.645 47.619 8.10 0.00 38.47 4.73
541 545 2.027653 TGGTTAACAGATGACCATGCGA 60.028 45.455 8.10 0.00 38.47 5.10
544 548 2.183478 AACAGATGACCATGCGACAA 57.817 45.000 0.00 0.00 0.00 3.18
545 549 1.730501 ACAGATGACCATGCGACAAG 58.269 50.000 0.00 0.00 0.00 3.16
556 560 3.361443 GCGACAAGCGTGGTAAAAG 57.639 52.632 4.26 0.00 43.41 2.27
557 561 0.724785 GCGACAAGCGTGGTAAAAGC 60.725 55.000 4.26 0.00 43.41 3.51
558 562 0.584396 CGACAAGCGTGGTAAAAGCA 59.416 50.000 4.26 0.00 35.46 3.91
559 563 1.003331 CGACAAGCGTGGTAAAAGCAA 60.003 47.619 4.26 0.00 35.46 3.91
560 564 2.350388 CGACAAGCGTGGTAAAAGCAAT 60.350 45.455 4.26 0.00 35.46 3.56
561 565 3.234386 GACAAGCGTGGTAAAAGCAATC 58.766 45.455 4.26 0.00 35.46 2.67
562 566 2.884639 ACAAGCGTGGTAAAAGCAATCT 59.115 40.909 4.26 0.00 35.46 2.40
563 567 3.058224 ACAAGCGTGGTAAAAGCAATCTC 60.058 43.478 4.26 0.00 35.46 2.75
564 568 2.778299 AGCGTGGTAAAAGCAATCTCA 58.222 42.857 0.00 0.00 35.46 3.27
565 569 3.146066 AGCGTGGTAAAAGCAATCTCAA 58.854 40.909 0.00 0.00 35.46 3.02
566 570 3.568007 AGCGTGGTAAAAGCAATCTCAAA 59.432 39.130 0.00 0.00 35.46 2.69
567 571 4.218417 AGCGTGGTAAAAGCAATCTCAAAT 59.782 37.500 0.00 0.00 35.46 2.32
568 572 4.923281 GCGTGGTAAAAGCAATCTCAAATT 59.077 37.500 0.00 0.00 32.90 1.82
569 573 5.164061 GCGTGGTAAAAGCAATCTCAAATTG 60.164 40.000 0.00 0.00 32.90 2.32
570 574 6.148948 CGTGGTAAAAGCAATCTCAAATTGA 58.851 36.000 0.00 0.00 0.00 2.57
571 575 6.088085 CGTGGTAAAAGCAATCTCAAATTGAC 59.912 38.462 2.07 0.00 0.00 3.18
572 576 6.922957 GTGGTAAAAGCAATCTCAAATTGACA 59.077 34.615 2.07 0.00 0.00 3.58
573 577 7.437862 GTGGTAAAAGCAATCTCAAATTGACAA 59.562 33.333 2.07 0.00 0.00 3.18
574 578 7.984050 TGGTAAAAGCAATCTCAAATTGACAAA 59.016 29.630 2.07 0.00 0.00 2.83
575 579 8.825745 GGTAAAAGCAATCTCAAATTGACAAAA 58.174 29.630 2.07 0.00 0.00 2.44
579 583 9.724839 AAAGCAATCTCAAATTGACAAAAATTG 57.275 25.926 2.07 0.00 30.21 2.32
580 584 7.867752 AGCAATCTCAAATTGACAAAAATTGG 58.132 30.769 2.07 4.25 34.12 3.16
581 585 7.499895 AGCAATCTCAAATTGACAAAAATTGGT 59.500 29.630 2.07 1.41 34.12 3.67
582 586 8.130469 GCAATCTCAAATTGACAAAAATTGGTT 58.870 29.630 2.07 3.78 34.12 3.67
586 590 9.658799 TCTCAAATTGACAAAAATTGGTTAACA 57.341 25.926 8.10 0.00 34.12 2.41
587 591 9.919348 CTCAAATTGACAAAAATTGGTTAACAG 57.081 29.630 8.10 0.00 34.12 3.16
588 592 9.658799 TCAAATTGACAAAAATTGGTTAACAGA 57.341 25.926 8.10 0.00 34.12 3.41
591 595 9.829507 AATTGACAAAAATTGGTTAACAGATGA 57.170 25.926 8.10 0.00 34.12 2.92
592 596 8.870160 TTGACAAAAATTGGTTAACAGATGAG 57.130 30.769 8.10 0.00 34.12 2.90
593 597 6.922957 TGACAAAAATTGGTTAACAGATGAGC 59.077 34.615 8.10 0.00 34.12 4.26
594 598 7.054491 ACAAAAATTGGTTAACAGATGAGCT 57.946 32.000 8.10 0.00 34.12 4.09
595 599 7.500141 ACAAAAATTGGTTAACAGATGAGCTT 58.500 30.769 8.10 0.00 34.12 3.74
596 600 7.653311 ACAAAAATTGGTTAACAGATGAGCTTC 59.347 33.333 8.10 0.00 34.12 3.86
597 601 6.899393 AAATTGGTTAACAGATGAGCTTCA 57.101 33.333 8.10 0.00 0.00 3.02
598 602 5.886960 ATTGGTTAACAGATGAGCTTCAC 57.113 39.130 8.10 0.00 0.00 3.18
599 603 4.623932 TGGTTAACAGATGAGCTTCACT 57.376 40.909 8.10 0.00 0.00 3.41
600 604 4.973168 TGGTTAACAGATGAGCTTCACTT 58.027 39.130 8.10 0.00 0.00 3.16
601 605 6.109156 TGGTTAACAGATGAGCTTCACTTA 57.891 37.500 8.10 0.00 0.00 2.24
602 606 5.932303 TGGTTAACAGATGAGCTTCACTTAC 59.068 40.000 8.10 0.00 0.00 2.34
603 607 6.166982 GGTTAACAGATGAGCTTCACTTACT 58.833 40.000 8.10 0.00 0.00 2.24
604 608 6.091441 GGTTAACAGATGAGCTTCACTTACTG 59.909 42.308 8.10 0.00 32.89 2.74
605 609 4.881019 ACAGATGAGCTTCACTTACTGT 57.119 40.909 0.00 0.00 34.15 3.55
606 610 5.984695 ACAGATGAGCTTCACTTACTGTA 57.015 39.130 0.00 0.00 35.84 2.74
607 611 5.715070 ACAGATGAGCTTCACTTACTGTAC 58.285 41.667 0.00 0.00 35.84 2.90
608 612 4.795795 CAGATGAGCTTCACTTACTGTACG 59.204 45.833 0.00 0.00 0.00 3.67
609 613 4.700692 AGATGAGCTTCACTTACTGTACGA 59.299 41.667 0.00 0.00 0.00 3.43
610 614 4.156664 TGAGCTTCACTTACTGTACGAC 57.843 45.455 0.00 0.00 0.00 4.34
611 615 3.162068 GAGCTTCACTTACTGTACGACG 58.838 50.000 0.00 0.00 0.00 5.12
613 617 3.748048 AGCTTCACTTACTGTACGACGTA 59.252 43.478 2.97 2.97 0.00 3.57
616 620 5.399301 GCTTCACTTACTGTACGACGTAAAA 59.601 40.000 9.72 0.32 0.00 1.52
619 623 9.117145 CTTCACTTACTGTACGACGTAAAAATA 57.883 33.333 9.72 0.00 0.00 1.40
621 625 9.457110 TCACTTACTGTACGACGTAAAAATAAA 57.543 29.630 9.72 0.00 0.00 1.40
672 695 8.718102 ATTGCTTTTACTATGTGTAGGTACTG 57.282 34.615 0.00 0.00 41.52 2.74
673 696 6.103997 TGCTTTTACTATGTGTAGGTACTGC 58.896 40.000 0.00 0.00 41.52 4.40
674 697 5.522824 GCTTTTACTATGTGTAGGTACTGCC 59.477 44.000 0.00 0.00 41.53 4.85
675 698 6.608539 TTTTACTATGTGTAGGTACTGCCA 57.391 37.500 0.00 0.00 41.53 4.92
676 699 5.847111 TTACTATGTGTAGGTACTGCCAG 57.153 43.478 0.00 0.00 41.53 4.85
677 700 3.709587 ACTATGTGTAGGTACTGCCAGT 58.290 45.455 1.54 1.54 41.53 4.00
678 701 4.863548 ACTATGTGTAGGTACTGCCAGTA 58.136 43.478 0.00 0.00 41.53 2.74
688 711 1.512926 ACTGCCAGTACTTCTTTGCG 58.487 50.000 0.00 0.00 0.00 4.85
710 752 6.320164 TGCGGTGCCTATAGTCAAATTAATTT 59.680 34.615 7.64 7.64 0.00 1.82
711 753 7.499563 TGCGGTGCCTATAGTCAAATTAATTTA 59.500 33.333 12.98 0.00 0.00 1.40
757 805 5.371344 AGTCGTCGCATTAATTAACGAAG 57.629 39.130 14.73 12.71 43.13 3.79
762 810 7.521899 GTCGTCGCATTAATTAACGAAGTAATC 59.478 37.037 17.26 4.99 45.00 1.75
825 873 1.838656 AAACCCCCTAGCTCCTCCCT 61.839 60.000 0.00 0.00 0.00 4.20
831 879 1.127343 CCTAGCTCCTCCCTTCCTTG 58.873 60.000 0.00 0.00 0.00 3.61
832 880 0.467804 CTAGCTCCTCCCTTCCTTGC 59.532 60.000 0.00 0.00 0.00 4.01
833 881 0.043334 TAGCTCCTCCCTTCCTTGCT 59.957 55.000 0.00 0.00 0.00 3.91
834 882 0.844221 AGCTCCTCCCTTCCTTGCTT 60.844 55.000 0.00 0.00 0.00 3.91
893 941 2.079925 CGCCTTCCTTTCCTTCTTCTG 58.920 52.381 0.00 0.00 0.00 3.02
897 945 1.348064 TCCTTTCCTTCTTCTGGCGA 58.652 50.000 0.00 0.00 0.00 5.54
898 946 1.276421 TCCTTTCCTTCTTCTGGCGAG 59.724 52.381 0.00 0.00 0.00 5.03
899 947 1.677217 CCTTTCCTTCTTCTGGCGAGG 60.677 57.143 0.00 0.00 0.00 4.63
900 948 0.324943 TTTCCTTCTTCTGGCGAGGG 59.675 55.000 0.00 0.00 0.00 4.30
967 1015 2.915869 GTGAGTGGTGGTGGTGGT 59.084 61.111 0.00 0.00 0.00 4.16
968 1016 1.525995 GTGAGTGGTGGTGGTGGTG 60.526 63.158 0.00 0.00 0.00 4.17
969 1017 2.113139 GAGTGGTGGTGGTGGTGG 59.887 66.667 0.00 0.00 0.00 4.61
970 1018 3.491598 GAGTGGTGGTGGTGGTGGG 62.492 68.421 0.00 0.00 0.00 4.61
971 1019 3.494254 GTGGTGGTGGTGGTGGGA 61.494 66.667 0.00 0.00 0.00 4.37
972 1020 3.494254 TGGTGGTGGTGGTGGGAC 61.494 66.667 0.00 0.00 0.00 4.46
1724 1772 2.615227 ATCGGCATCAACCCAGGAGC 62.615 60.000 0.00 0.00 0.00 4.70
1921 1969 4.557097 GCTAGCTAATGAGTACCGAGTTCC 60.557 50.000 7.70 0.00 0.00 3.62
1929 1977 5.334724 TGAGTACCGAGTTCCTTTAATCC 57.665 43.478 0.00 0.00 0.00 3.01
1956 2004 7.869429 CCAGGGCTTTAGATTTAATTAATGCAG 59.131 37.037 0.00 0.00 33.83 4.41
2108 2157 4.460873 GGCGCCGCTGTTTGTAGC 62.461 66.667 12.58 0.00 40.29 3.58
2152 2210 7.830099 TGCTTTAATCCTAGTACTACTACCC 57.170 40.000 0.00 0.00 0.00 3.69
2236 2300 2.374184 CCGCATTAATTTGTCCCTGGA 58.626 47.619 0.00 0.00 0.00 3.86
2554 2957 0.745128 TCGAACGTTGCCCTTGTGTT 60.745 50.000 5.00 0.00 0.00 3.32
2589 2992 0.036010 AGTTGTCTCATCGGCTTGGG 60.036 55.000 0.00 0.00 0.00 4.12
2590 2993 0.036388 GTTGTCTCATCGGCTTGGGA 60.036 55.000 0.00 0.00 0.00 4.37
2625 3028 2.588034 GGCGATTAGGCACGGTCC 60.588 66.667 0.00 0.00 45.92 4.46
2666 3069 0.236187 GATCCGACACGATCTCTCCG 59.764 60.000 0.00 0.00 36.51 4.63
2681 3084 0.686112 CTCCGCTCTCCCTTCTCCTT 60.686 60.000 0.00 0.00 0.00 3.36
2708 3111 2.897350 GGGATTTGGCCTCTCGCG 60.897 66.667 3.32 0.00 38.94 5.87
2733 3136 1.069227 GTGGTTTTGCTGTCGCCTAAG 60.069 52.381 0.00 0.00 34.43 2.18
2737 3141 1.604604 TTTGCTGTCGCCTAAGCTTT 58.395 45.000 3.20 0.00 40.21 3.51
2740 3144 0.166814 GCTGTCGCCTAAGCTTTGTG 59.833 55.000 3.20 3.41 36.47 3.33
2745 3149 1.648467 CGCCTAAGCTTTGTGGCTCC 61.648 60.000 24.97 7.25 42.24 4.70
2847 3251 2.740447 GGTTTGGCTAGGTTTGAGTACG 59.260 50.000 0.00 0.00 0.00 3.67
2848 3252 3.555586 GGTTTGGCTAGGTTTGAGTACGA 60.556 47.826 0.00 0.00 0.00 3.43
2849 3253 3.587797 TTGGCTAGGTTTGAGTACGAG 57.412 47.619 0.00 0.00 0.00 4.18
2850 3254 1.203994 TGGCTAGGTTTGAGTACGAGC 59.796 52.381 0.00 0.00 0.00 5.03
2851 3255 1.203994 GGCTAGGTTTGAGTACGAGCA 59.796 52.381 0.00 0.00 32.36 4.26
2852 3256 2.260481 GCTAGGTTTGAGTACGAGCAC 58.740 52.381 0.00 0.00 31.55 4.40
2853 3257 2.516923 CTAGGTTTGAGTACGAGCACG 58.483 52.381 0.76 0.76 45.75 5.34
2872 3276 2.691836 CGTACTCGTCTAGTCTTTCGC 58.308 52.381 0.00 0.00 39.80 4.70
2873 3277 2.348059 CGTACTCGTCTAGTCTTTCGCT 59.652 50.000 0.00 0.00 39.80 4.93
2874 3278 2.904011 ACTCGTCTAGTCTTTCGCTG 57.096 50.000 0.00 0.00 30.33 5.18
2875 3279 1.135632 ACTCGTCTAGTCTTTCGCTGC 60.136 52.381 0.00 0.00 30.33 5.25
2876 3280 1.131504 CTCGTCTAGTCTTTCGCTGCT 59.868 52.381 0.00 0.00 0.00 4.24
2877 3281 1.130749 TCGTCTAGTCTTTCGCTGCTC 59.869 52.381 0.00 0.00 0.00 4.26
2878 3282 1.540407 GTCTAGTCTTTCGCTGCTCG 58.460 55.000 0.00 0.00 40.15 5.03
2879 3283 0.179161 TCTAGTCTTTCGCTGCTCGC 60.179 55.000 0.00 0.00 38.27 5.03
2880 3284 1.142778 CTAGTCTTTCGCTGCTCGCC 61.143 60.000 0.00 0.00 38.27 5.54
2881 3285 1.873270 TAGTCTTTCGCTGCTCGCCA 61.873 55.000 0.00 0.00 38.27 5.69
2882 3286 2.103042 GTCTTTCGCTGCTCGCCAT 61.103 57.895 0.00 0.00 38.27 4.40
2883 3287 1.375908 TCTTTCGCTGCTCGCCATT 60.376 52.632 0.00 0.00 38.27 3.16
2884 3288 0.955428 TCTTTCGCTGCTCGCCATTT 60.955 50.000 0.00 0.00 38.27 2.32
2885 3289 0.795735 CTTTCGCTGCTCGCCATTTG 60.796 55.000 0.00 0.00 38.27 2.32
2886 3290 1.514678 TTTCGCTGCTCGCCATTTGT 61.515 50.000 0.00 0.00 38.27 2.83
2887 3291 2.186350 TTCGCTGCTCGCCATTTGTG 62.186 55.000 0.00 0.00 38.27 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.647797 CATGTTAGTAGGTTATTGTCACACTAA 57.352 33.333 0.00 0.00 0.00 2.24
1 2 8.255206 CCATGTTAGTAGGTTATTGTCACACTA 58.745 37.037 0.00 0.00 0.00 2.74
2 3 7.103641 CCATGTTAGTAGGTTATTGTCACACT 58.896 38.462 0.00 0.00 0.00 3.55
3 4 6.183360 GCCATGTTAGTAGGTTATTGTCACAC 60.183 42.308 0.00 0.00 0.00 3.82
4 5 5.878116 GCCATGTTAGTAGGTTATTGTCACA 59.122 40.000 0.00 0.00 0.00 3.58
5 6 5.296035 GGCCATGTTAGTAGGTTATTGTCAC 59.704 44.000 0.00 0.00 0.00 3.67
6 7 5.045505 TGGCCATGTTAGTAGGTTATTGTCA 60.046 40.000 0.00 0.00 0.00 3.58
7 8 5.296035 GTGGCCATGTTAGTAGGTTATTGTC 59.704 44.000 9.72 0.00 0.00 3.18
8 9 5.190677 GTGGCCATGTTAGTAGGTTATTGT 58.809 41.667 9.72 0.00 0.00 2.71
9 10 4.578928 GGTGGCCATGTTAGTAGGTTATTG 59.421 45.833 9.72 0.00 0.00 1.90
10 11 4.685030 CGGTGGCCATGTTAGTAGGTTATT 60.685 45.833 9.72 0.00 0.00 1.40
11 12 3.181458 CGGTGGCCATGTTAGTAGGTTAT 60.181 47.826 9.72 0.00 0.00 1.89
12 13 2.168936 CGGTGGCCATGTTAGTAGGTTA 59.831 50.000 9.72 0.00 0.00 2.85
13 14 1.065709 CGGTGGCCATGTTAGTAGGTT 60.066 52.381 9.72 0.00 0.00 3.50
14 15 0.539986 CGGTGGCCATGTTAGTAGGT 59.460 55.000 9.72 0.00 0.00 3.08
15 16 0.828022 TCGGTGGCCATGTTAGTAGG 59.172 55.000 9.72 0.00 0.00 3.18
16 17 2.093658 ACTTCGGTGGCCATGTTAGTAG 60.094 50.000 9.72 4.94 0.00 2.57
17 18 1.903860 ACTTCGGTGGCCATGTTAGTA 59.096 47.619 9.72 0.00 0.00 1.82
18 19 0.690762 ACTTCGGTGGCCATGTTAGT 59.309 50.000 9.72 8.26 0.00 2.24
19 20 1.737793 GAACTTCGGTGGCCATGTTAG 59.262 52.381 9.72 7.55 0.00 2.34
20 21 1.816074 GAACTTCGGTGGCCATGTTA 58.184 50.000 9.72 0.00 0.00 2.41
28 29 2.000447 GGATTTCTCGAACTTCGGTGG 59.000 52.381 11.21 3.03 40.88 4.61
39 40 1.645034 ATGTCAGCGTGGATTTCTCG 58.355 50.000 0.00 0.00 0.00 4.04
114 115 9.809096 TTACTCTCTGTCAATTAGATCACAATC 57.191 33.333 0.00 0.00 0.00 2.67
117 118 8.122472 TGTTACTCTCTGTCAATTAGATCACA 57.878 34.615 0.00 0.00 0.00 3.58
138 139 4.080526 GGGGTTCTAGCTCCAATCTTGTTA 60.081 45.833 0.00 0.00 0.00 2.41
140 144 2.239907 GGGGTTCTAGCTCCAATCTTGT 59.760 50.000 0.00 0.00 0.00 3.16
190 194 1.204146 TACCTGATCTTCTGTGCCCC 58.796 55.000 0.00 0.00 0.00 5.80
322 326 2.047560 GGGTGCCGTGGTGTACTC 60.048 66.667 0.00 0.00 0.00 2.59
422 426 1.975407 GGGACTCGACGAAGGGTGA 60.975 63.158 0.00 0.00 0.00 4.02
489 493 4.026744 AGAGACTGAGGCTATGCTTTGTA 58.973 43.478 0.00 0.00 0.00 2.41
490 494 2.836981 AGAGACTGAGGCTATGCTTTGT 59.163 45.455 0.00 0.00 0.00 2.83
491 495 3.118847 TCAGAGACTGAGGCTATGCTTTG 60.119 47.826 4.76 0.00 35.39 2.77
492 496 3.102972 TCAGAGACTGAGGCTATGCTTT 58.897 45.455 4.76 0.00 35.39 3.51
493 497 2.744760 TCAGAGACTGAGGCTATGCTT 58.255 47.619 4.76 0.00 35.39 3.91
494 498 2.450867 TCAGAGACTGAGGCTATGCT 57.549 50.000 4.76 0.00 35.39 3.79
505 509 7.963532 TCTGTTAACCAATTTACTCAGAGACT 58.036 34.615 3.79 0.00 32.07 3.24
506 510 8.660373 CATCTGTTAACCAATTTACTCAGAGAC 58.340 37.037 3.79 0.00 35.83 3.36
507 511 8.593679 TCATCTGTTAACCAATTTACTCAGAGA 58.406 33.333 3.79 0.00 35.83 3.10
509 513 7.606456 GGTCATCTGTTAACCAATTTACTCAGA 59.394 37.037 2.48 0.00 36.33 3.27
510 514 7.390440 TGGTCATCTGTTAACCAATTTACTCAG 59.610 37.037 2.48 0.00 40.04 3.35
511 515 7.227873 TGGTCATCTGTTAACCAATTTACTCA 58.772 34.615 2.48 0.00 40.04 3.41
512 516 7.681939 TGGTCATCTGTTAACCAATTTACTC 57.318 36.000 2.48 0.00 40.04 2.59
513 517 7.362920 GCATGGTCATCTGTTAACCAATTTACT 60.363 37.037 2.48 0.00 45.65 2.24
514 518 6.751888 GCATGGTCATCTGTTAACCAATTTAC 59.248 38.462 2.48 0.00 45.65 2.01
515 519 6.404184 CGCATGGTCATCTGTTAACCAATTTA 60.404 38.462 2.48 0.00 45.65 1.40
516 520 5.622007 CGCATGGTCATCTGTTAACCAATTT 60.622 40.000 2.48 0.00 45.65 1.82
517 521 4.142403 CGCATGGTCATCTGTTAACCAATT 60.142 41.667 2.48 0.00 45.65 2.32
520 524 2.027653 TCGCATGGTCATCTGTTAACCA 60.028 45.455 2.48 0.00 46.51 3.67
521 525 2.351726 GTCGCATGGTCATCTGTTAACC 59.648 50.000 2.48 0.00 0.00 2.85
522 526 3.000041 TGTCGCATGGTCATCTGTTAAC 59.000 45.455 0.00 0.00 0.00 2.01
523 527 3.326836 TGTCGCATGGTCATCTGTTAA 57.673 42.857 0.00 0.00 0.00 2.01
526 530 1.730501 CTTGTCGCATGGTCATCTGT 58.269 50.000 0.00 0.00 0.00 3.41
529 533 1.349627 CGCTTGTCGCATGGTCATC 59.650 57.895 0.00 0.00 39.08 2.92
531 535 2.030412 ACGCTTGTCGCATGGTCA 59.970 55.556 0.00 0.00 43.23 4.02
532 536 2.476051 CACGCTTGTCGCATGGTC 59.524 61.111 0.00 0.00 43.23 4.02
533 537 2.443260 TACCACGCTTGTCGCATGGT 62.443 55.000 9.68 9.68 45.68 3.55
535 539 0.515127 TTTACCACGCTTGTCGCATG 59.485 50.000 0.00 0.00 43.23 4.06
536 540 1.196808 CTTTTACCACGCTTGTCGCAT 59.803 47.619 0.00 0.00 43.23 4.73
537 541 0.584396 CTTTTACCACGCTTGTCGCA 59.416 50.000 0.00 0.00 43.23 5.10
538 542 0.724785 GCTTTTACCACGCTTGTCGC 60.725 55.000 0.00 0.00 43.23 5.19
539 543 0.584396 TGCTTTTACCACGCTTGTCG 59.416 50.000 0.00 0.00 45.38 4.35
540 544 2.766970 TTGCTTTTACCACGCTTGTC 57.233 45.000 0.00 0.00 0.00 3.18
541 545 2.884639 AGATTGCTTTTACCACGCTTGT 59.115 40.909 0.00 0.00 0.00 3.16
544 548 2.778299 TGAGATTGCTTTTACCACGCT 58.222 42.857 0.00 0.00 0.00 5.07
545 549 3.552604 TTGAGATTGCTTTTACCACGC 57.447 42.857 0.00 0.00 0.00 5.34
546 550 6.088085 GTCAATTTGAGATTGCTTTTACCACG 59.912 38.462 0.00 0.00 0.00 4.94
547 551 6.922957 TGTCAATTTGAGATTGCTTTTACCAC 59.077 34.615 0.00 0.00 0.00 4.16
548 552 7.048629 TGTCAATTTGAGATTGCTTTTACCA 57.951 32.000 0.00 0.00 0.00 3.25
549 553 7.945033 TTGTCAATTTGAGATTGCTTTTACC 57.055 32.000 0.00 0.00 0.00 2.85
553 557 9.724839 CAATTTTTGTCAATTTGAGATTGCTTT 57.275 25.926 0.00 0.00 0.00 3.51
554 558 8.347035 CCAATTTTTGTCAATTTGAGATTGCTT 58.653 29.630 0.00 0.00 0.00 3.91
555 559 7.499895 ACCAATTTTTGTCAATTTGAGATTGCT 59.500 29.630 0.00 0.00 0.00 3.91
556 560 7.641760 ACCAATTTTTGTCAATTTGAGATTGC 58.358 30.769 0.00 0.00 0.00 3.56
560 564 9.658799 TGTTAACCAATTTTTGTCAATTTGAGA 57.341 25.926 2.48 0.00 0.00 3.27
561 565 9.919348 CTGTTAACCAATTTTTGTCAATTTGAG 57.081 29.630 2.48 0.00 0.00 3.02
562 566 9.658799 TCTGTTAACCAATTTTTGTCAATTTGA 57.341 25.926 2.48 0.00 0.00 2.69
565 569 9.829507 TCATCTGTTAACCAATTTTTGTCAATT 57.170 25.926 2.48 0.00 0.00 2.32
566 570 9.480053 CTCATCTGTTAACCAATTTTTGTCAAT 57.520 29.630 2.48 0.00 0.00 2.57
567 571 7.437862 GCTCATCTGTTAACCAATTTTTGTCAA 59.562 33.333 2.48 0.00 0.00 3.18
568 572 6.922957 GCTCATCTGTTAACCAATTTTTGTCA 59.077 34.615 2.48 0.00 0.00 3.58
569 573 7.147976 AGCTCATCTGTTAACCAATTTTTGTC 58.852 34.615 2.48 0.00 0.00 3.18
570 574 7.054491 AGCTCATCTGTTAACCAATTTTTGT 57.946 32.000 2.48 0.00 0.00 2.83
571 575 7.652909 TGAAGCTCATCTGTTAACCAATTTTTG 59.347 33.333 2.48 0.00 0.00 2.44
572 576 7.653311 GTGAAGCTCATCTGTTAACCAATTTTT 59.347 33.333 2.48 0.00 0.00 1.94
573 577 7.014615 AGTGAAGCTCATCTGTTAACCAATTTT 59.985 33.333 2.48 0.00 0.00 1.82
574 578 6.491403 AGTGAAGCTCATCTGTTAACCAATTT 59.509 34.615 2.48 0.00 0.00 1.82
575 579 6.006449 AGTGAAGCTCATCTGTTAACCAATT 58.994 36.000 2.48 0.00 0.00 2.32
576 580 5.564550 AGTGAAGCTCATCTGTTAACCAAT 58.435 37.500 2.48 0.00 0.00 3.16
577 581 4.973168 AGTGAAGCTCATCTGTTAACCAA 58.027 39.130 2.48 0.00 0.00 3.67
578 582 4.623932 AGTGAAGCTCATCTGTTAACCA 57.376 40.909 2.48 0.00 0.00 3.67
579 583 6.091441 CAGTAAGTGAAGCTCATCTGTTAACC 59.909 42.308 2.48 0.00 0.00 2.85
580 584 6.647067 ACAGTAAGTGAAGCTCATCTGTTAAC 59.353 38.462 0.00 0.00 29.95 2.01
581 585 6.759272 ACAGTAAGTGAAGCTCATCTGTTAA 58.241 36.000 0.00 0.00 29.95 2.01
582 586 6.346477 ACAGTAAGTGAAGCTCATCTGTTA 57.654 37.500 0.00 0.00 29.95 2.41
583 587 5.220710 ACAGTAAGTGAAGCTCATCTGTT 57.779 39.130 0.00 0.00 29.95 3.16
584 588 4.881019 ACAGTAAGTGAAGCTCATCTGT 57.119 40.909 0.00 0.00 0.00 3.41
585 589 4.795795 CGTACAGTAAGTGAAGCTCATCTG 59.204 45.833 0.00 0.00 0.00 2.90
586 590 4.700692 TCGTACAGTAAGTGAAGCTCATCT 59.299 41.667 0.00 0.00 0.00 2.90
587 591 4.794246 GTCGTACAGTAAGTGAAGCTCATC 59.206 45.833 0.00 0.00 0.00 2.92
588 592 4.672024 CGTCGTACAGTAAGTGAAGCTCAT 60.672 45.833 0.00 0.00 0.00 2.90
589 593 3.364664 CGTCGTACAGTAAGTGAAGCTCA 60.365 47.826 0.00 0.00 0.00 4.26
590 594 3.162068 CGTCGTACAGTAAGTGAAGCTC 58.838 50.000 0.00 0.00 0.00 4.09
591 595 2.551459 ACGTCGTACAGTAAGTGAAGCT 59.449 45.455 0.00 0.00 0.00 3.74
592 596 2.926165 ACGTCGTACAGTAAGTGAAGC 58.074 47.619 0.00 0.00 0.00 3.86
593 597 6.974677 TTTTACGTCGTACAGTAAGTGAAG 57.025 37.500 4.17 0.00 34.75 3.02
594 598 7.928908 ATTTTTACGTCGTACAGTAAGTGAA 57.071 32.000 4.17 0.00 34.75 3.18
595 599 9.457110 TTTATTTTTACGTCGTACAGTAAGTGA 57.543 29.630 4.17 0.00 34.75 3.41
626 630 7.024768 GCAATATTTTTACGTCTACCAGCAAA 58.975 34.615 0.00 0.00 0.00 3.68
627 631 6.373216 AGCAATATTTTTACGTCTACCAGCAA 59.627 34.615 0.00 0.00 0.00 3.91
668 691 2.611971 CCGCAAAGAAGTACTGGCAGTA 60.612 50.000 22.96 22.96 32.39 2.74
669 692 1.512926 CGCAAAGAAGTACTGGCAGT 58.487 50.000 25.34 25.34 32.39 4.40
670 693 0.798776 CCGCAAAGAAGTACTGGCAG 59.201 55.000 14.16 14.16 32.39 4.85
671 694 0.107831 ACCGCAAAGAAGTACTGGCA 59.892 50.000 0.00 0.00 32.39 4.92
672 695 0.517316 CACCGCAAAGAAGTACTGGC 59.483 55.000 0.00 0.00 0.00 4.85
673 696 0.517316 GCACCGCAAAGAAGTACTGG 59.483 55.000 0.00 0.00 0.00 4.00
674 697 0.517316 GGCACCGCAAAGAAGTACTG 59.483 55.000 0.00 0.00 0.00 2.74
675 698 0.396811 AGGCACCGCAAAGAAGTACT 59.603 50.000 0.00 0.00 0.00 2.73
676 699 2.088950 TAGGCACCGCAAAGAAGTAC 57.911 50.000 0.00 0.00 0.00 2.73
677 700 3.449737 ACTATAGGCACCGCAAAGAAGTA 59.550 43.478 4.43 0.00 0.00 2.24
678 701 2.236395 ACTATAGGCACCGCAAAGAAGT 59.764 45.455 4.43 0.00 0.00 3.01
710 752 4.907269 TGGCCCTGATACAGAATGAGAATA 59.093 41.667 0.00 0.00 39.69 1.75
711 753 3.718434 TGGCCCTGATACAGAATGAGAAT 59.282 43.478 0.00 0.00 39.69 2.40
713 755 2.763039 TGGCCCTGATACAGAATGAGA 58.237 47.619 0.00 0.00 39.69 3.27
714 756 3.565764 TTGGCCCTGATACAGAATGAG 57.434 47.619 0.00 0.00 39.69 2.90
715 757 3.266772 ACTTTGGCCCTGATACAGAATGA 59.733 43.478 0.00 0.00 39.69 2.57
716 758 3.624777 ACTTTGGCCCTGATACAGAATG 58.375 45.455 0.00 0.00 46.00 2.67
717 759 3.682718 CGACTTTGGCCCTGATACAGAAT 60.683 47.826 0.00 0.00 32.44 2.40
718 760 2.354704 CGACTTTGGCCCTGATACAGAA 60.355 50.000 0.00 0.00 32.44 3.02
719 761 1.207089 CGACTTTGGCCCTGATACAGA 59.793 52.381 0.00 0.00 32.44 3.41
721 763 0.981183 ACGACTTTGGCCCTGATACA 59.019 50.000 0.00 0.00 0.00 2.29
726 774 3.423154 GCGACGACTTTGGCCCTG 61.423 66.667 0.00 0.00 0.00 4.45
757 805 5.468072 CCATCAGGTGTGAAGCATAGATTAC 59.532 44.000 0.00 0.00 35.88 1.89
762 810 2.569059 CCCATCAGGTGTGAAGCATAG 58.431 52.381 0.00 0.00 35.88 2.23
825 873 2.597217 CACCGGCCAAGCAAGGAA 60.597 61.111 0.00 0.00 33.41 3.36
877 925 1.697432 TCGCCAGAAGAAGGAAAGGAA 59.303 47.619 0.00 0.00 0.00 3.36
878 926 1.276421 CTCGCCAGAAGAAGGAAAGGA 59.724 52.381 0.00 0.00 0.00 3.36
879 927 1.677217 CCTCGCCAGAAGAAGGAAAGG 60.677 57.143 0.00 0.00 0.00 3.11
880 928 1.677217 CCCTCGCCAGAAGAAGGAAAG 60.677 57.143 0.00 0.00 0.00 2.62
881 929 0.324943 CCCTCGCCAGAAGAAGGAAA 59.675 55.000 0.00 0.00 0.00 3.13
897 945 3.137459 CACTCTCGCTCGCTCCCT 61.137 66.667 0.00 0.00 0.00 4.20
898 946 4.200283 CCACTCTCGCTCGCTCCC 62.200 72.222 0.00 0.00 0.00 4.30
899 947 4.863925 GCCACTCTCGCTCGCTCC 62.864 72.222 0.00 0.00 0.00 4.70
900 948 4.863925 GGCCACTCTCGCTCGCTC 62.864 72.222 0.00 0.00 0.00 5.03
969 1017 3.894947 GAGAGCTCGCTCCCGTCC 61.895 72.222 14.83 0.00 43.70 4.79
1921 1969 4.519906 TCTAAAGCCCTGGGGATTAAAG 57.480 45.455 16.03 10.34 43.82 1.85
1929 1977 7.154656 GCATTAATTAAATCTAAAGCCCTGGG 58.845 38.462 8.86 8.86 0.00 4.45
1956 2004 1.939974 TGCTCACAACTGACTGACAC 58.060 50.000 0.00 0.00 0.00 3.67
2152 2210 4.025563 CAGCTACTACACTAGTCTAGCACG 60.026 50.000 6.81 0.00 40.14 5.34
2236 2300 1.781786 ATCCCGATGCACTCTACTGT 58.218 50.000 0.00 0.00 0.00 3.55
2331 2720 3.426117 ATTACGAGGTGGCGCTCCG 62.426 63.158 7.64 6.63 34.14 4.63
2336 2725 2.960129 GCCGATTACGAGGTGGCG 60.960 66.667 0.00 0.00 42.66 5.69
2589 2992 2.079158 CCATCATCACACACCACACTC 58.921 52.381 0.00 0.00 0.00 3.51
2590 2993 1.883638 GCCATCATCACACACCACACT 60.884 52.381 0.00 0.00 0.00 3.55
2666 3069 0.539518 GGACAAGGAGAAGGGAGAGC 59.460 60.000 0.00 0.00 0.00 4.09
2681 3084 1.682849 CCAAATCCCACCGAGGACA 59.317 57.895 0.00 0.00 39.24 4.02
2708 3111 4.264638 ACAGCAAAACCACGCGGC 62.265 61.111 12.47 1.26 34.57 6.53
2711 3114 2.725815 GCGACAGCAAAACCACGC 60.726 61.111 0.00 0.00 44.35 5.34
2722 3125 0.798776 CCACAAAGCTTAGGCGACAG 59.201 55.000 0.00 0.00 44.37 3.51
2852 3256 2.348059 AGCGAAAGACTAGACGAGTACG 59.652 50.000 0.00 0.00 39.06 3.67
2853 3257 3.672310 CAGCGAAAGACTAGACGAGTAC 58.328 50.000 0.00 0.00 39.06 2.73
2854 3258 2.095532 GCAGCGAAAGACTAGACGAGTA 59.904 50.000 0.00 0.00 39.06 2.59
2855 3259 1.135632 GCAGCGAAAGACTAGACGAGT 60.136 52.381 0.00 0.00 42.90 4.18
2856 3260 1.131504 AGCAGCGAAAGACTAGACGAG 59.868 52.381 0.00 0.00 0.00 4.18
2857 3261 1.130749 GAGCAGCGAAAGACTAGACGA 59.869 52.381 0.00 0.00 0.00 4.20
2858 3262 1.540407 GAGCAGCGAAAGACTAGACG 58.460 55.000 0.00 0.00 0.00 4.18
2859 3263 1.540407 CGAGCAGCGAAAGACTAGAC 58.460 55.000 0.00 0.00 44.57 2.59
2860 3264 0.179161 GCGAGCAGCGAAAGACTAGA 60.179 55.000 0.00 0.00 44.57 2.43
2861 3265 2.283254 GCGAGCAGCGAAAGACTAG 58.717 57.895 3.02 0.00 44.57 2.57
2862 3266 4.478195 GCGAGCAGCGAAAGACTA 57.522 55.556 3.02 0.00 44.57 2.59


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

AutoCloner maintained by Alex Coulton.