Multiple sequence alignment - TraesCS1A01G261900

Loading Multiple Alignment...

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 TraesCS1A01G261900 chr1A 100.000 2590 0 0 1 2590 456650005 456652594 0.000000e+00 4783.0
1 TraesCS1A01G261900 chr1A 85.006 907 99 27 706 1597 541381076 541381960 0.000000e+00 887.0
2 TraesCS1A01G261900 chr1A 86.240 734 64 25 706 1434 542358199 542358900 0.000000e+00 761.0
3 TraesCS1A01G261900 chr1D 88.389 1645 83 45 210 1788 355824494 355826096 0.000000e+00 1881.0
4 TraesCS1A01G261900 chr1D 84.590 1233 112 43 733 1919 446436834 446438034 0.000000e+00 1153.0
5 TraesCS1A01G261900 chr1D 85.061 897 88 31 705 1586 446558190 446559055 0.000000e+00 872.0
6 TraesCS1A01G261900 chr1D 84.400 891 91 29 706 1584 445387273 445386419 0.000000e+00 832.0
7 TraesCS1A01G261900 chr1D 95.278 360 12 2 2231 2590 355826633 355826987 1.350000e-157 566.0
8 TraesCS1A01G261900 chr1D 92.391 276 9 6 1928 2203 355826374 355826637 1.450000e-102 383.0
9 TraesCS1A01G261900 chr1D 92.941 255 18 0 1 255 355824235 355824489 3.150000e-99 372.0
10 TraesCS1A01G261900 chr1D 84.783 368 29 12 2235 2590 446438448 446438800 6.860000e-91 344.0
11 TraesCS1A01G261900 chr1D 87.544 281 24 7 1929 2204 445384590 445384316 5.380000e-82 315.0
12 TraesCS1A01G261900 chr1D 79.216 510 51 30 1441 1927 445385242 445384765 1.160000e-78 303.0
13 TraesCS1A01G261900 chr1D 81.408 355 47 9 210 554 81510582 81510927 3.280000e-69 272.0
14 TraesCS1A01G261900 chr1D 79.272 357 37 20 2243 2584 445384310 445383976 5.610000e-52 215.0
15 TraesCS1A01G261900 chr1D 87.425 167 15 5 698 859 445317306 445317471 1.220000e-43 187.0
16 TraesCS1A01G261900 chr1D 85.128 195 15 8 2016 2200 446438256 446438446 1.220000e-43 187.0
17 TraesCS1A01G261900 chr1D 86.607 112 4 3 1815 1926 355826095 355826195 2.110000e-21 113.0
18 TraesCS1A01G261900 chr1B 86.034 1253 87 34 711 1922 608054128 608052923 0.000000e+00 1264.0
19 TraesCS1A01G261900 chr1B 84.756 984 71 33 992 1912 607429557 607428590 0.000000e+00 913.0
20 TraesCS1A01G261900 chr1B 84.901 861 82 28 733 1587 611131219 611132037 0.000000e+00 826.0
21 TraesCS1A01G261900 chr1B 89.867 602 54 5 992 1587 606839875 606840475 0.000000e+00 767.0
22 TraesCS1A01G261900 chr1B 86.984 630 52 7 1086 1687 608355308 608354681 0.000000e+00 682.0
23 TraesCS1A01G261900 chr1B 91.103 281 19 5 1928 2204 608354426 608354148 2.430000e-100 375.0
24 TraesCS1A01G261900 chr1B 84.783 368 29 10 2235 2590 610562107 610562459 6.860000e-91 344.0
25 TraesCS1A01G261900 chr1B 78.591 369 41 15 2243 2584 607428200 607427843 2.610000e-50 209.0
26 TraesCS1A01G261900 chr1B 84.158 202 16 1 1930 2131 608052747 608052562 5.690000e-42 182.0
27 TraesCS1A01G261900 chr1B 80.556 144 10 6 2320 2447 608051834 608051693 7.630000e-16 95.3
28 TraesCS1A01G261900 chr1B 95.833 48 2 0 619 666 608054186 608054139 7.680000e-11 78.7
29 TraesCS1A01G261900 chr2B 83.222 1049 85 49 906 1919 161026370 161027362 0.000000e+00 878.0
30 TraesCS1A01G261900 chr2B 86.142 267 20 12 1945 2204 161027507 161027763 3.280000e-69 272.0
31 TraesCS1A01G261900 chr2B 83.761 117 6 5 2243 2348 161027769 161027883 5.900000e-17 99.0
32 TraesCS1A01G261900 chr2A 93.119 218 14 1 8 225 773404412 773404628 4.160000e-83 318.0
33 TraesCS1A01G261900 chr3A 91.538 130 11 0 9 138 61483272 61483143 2.050000e-41 180.0
34 TraesCS1A01G261900 chr3D 90.769 130 12 0 9 138 49010109 49009980 9.530000e-40 174.0
35 TraesCS1A01G261900 chr3B 90.769 130 12 0 9 138 78607069 78606940 9.530000e-40 174.0
36 TraesCS1A01G261900 chr6D 85.156 128 8 2 119 246 277850336 277850220 1.260000e-23 121.0
37 TraesCS1A01G261900 chr2D 85.600 125 7 2 119 243 637509629 637509742 1.260000e-23 121.0
38 TraesCS1A01G261900 chr4D 97.826 46 0 1 124 169 318925686 318925642 7.680000e-11 78.7
39 TraesCS1A01G261900 chr4B 97.826 46 0 1 124 169 396449424 396449380 7.680000e-11 78.7


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 TraesCS1A01G261900 chr1A 456650005 456652594 2589 False 4783.000000 4783 100.000000 1 2590 1 chr1A.!!$F1 2589
1 TraesCS1A01G261900 chr1A 541381076 541381960 884 False 887.000000 887 85.006000 706 1597 1 chr1A.!!$F2 891
2 TraesCS1A01G261900 chr1A 542358199 542358900 701 False 761.000000 761 86.240000 706 1434 1 chr1A.!!$F3 728
3 TraesCS1A01G261900 chr1D 446558190 446559055 865 False 872.000000 872 85.061000 705 1586 1 chr1D.!!$F3 881
4 TraesCS1A01G261900 chr1D 355824235 355826987 2752 False 663.000000 1881 91.121200 1 2590 5 chr1D.!!$F4 2589
5 TraesCS1A01G261900 chr1D 446436834 446438800 1966 False 561.333333 1153 84.833667 733 2590 3 chr1D.!!$F5 1857
6 TraesCS1A01G261900 chr1D 445383976 445387273 3297 True 416.250000 832 82.608000 706 2584 4 chr1D.!!$R1 1878
7 TraesCS1A01G261900 chr1B 611131219 611132037 818 False 826.000000 826 84.901000 733 1587 1 chr1B.!!$F3 854
8 TraesCS1A01G261900 chr1B 606839875 606840475 600 False 767.000000 767 89.867000 992 1587 1 chr1B.!!$F1 595
9 TraesCS1A01G261900 chr1B 607427843 607429557 1714 True 561.000000 913 81.673500 992 2584 2 chr1B.!!$R1 1592
10 TraesCS1A01G261900 chr1B 608354148 608355308 1160 True 528.500000 682 89.043500 1086 2204 2 chr1B.!!$R3 1118
11 TraesCS1A01G261900 chr1B 608051693 608054186 2493 True 405.000000 1264 86.645250 619 2447 4 chr1B.!!$R2 1828
12 TraesCS1A01G261900 chr2B 161026370 161027883 1513 False 416.333333 878 84.375000 906 2348 3 chr2B.!!$F1 1442

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
575 652 0.032912 AAAAGGTGTTTGGGGGTCGT 60.033 50.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 3184 0.26023 TCAGAGGCAGCTAGCTAGGT 59.74 55.0 18.86 19.65 44.79 3.08 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
17 18 3.872431 AGCCTACATCTACGGCCC 58.128 61.111 0.00 0.00 44.84 5.80
26 27 4.910585 CTACGGCCCGGGCATGAC 62.911 72.222 44.46 27.17 44.11 3.06
33 34 4.429212 CCGGGCATGACGTCGTCA 62.429 66.667 28.75 28.75 46.90 4.35
50 51 1.737735 CAACGACTGCCATCTCGCA 60.738 57.895 0.00 0.00 37.19 5.10
120 121 2.357034 AGCACGTTGTACTGCCGG 60.357 61.111 0.00 0.00 33.57 6.13
124 125 2.740826 CGTTGTACTGCCGGGTGG 60.741 66.667 2.18 0.00 38.77 4.61
323 389 1.449246 GCTGTGCTTGCGGAGAGAT 60.449 57.895 0.00 0.00 0.00 2.75
326 392 1.406898 CTGTGCTTGCGGAGAGATAGA 59.593 52.381 0.00 0.00 0.00 1.98
327 393 1.406898 TGTGCTTGCGGAGAGATAGAG 59.593 52.381 0.00 0.00 0.00 2.43
328 394 1.407258 GTGCTTGCGGAGAGATAGAGT 59.593 52.381 0.00 0.00 0.00 3.24
329 395 1.406898 TGCTTGCGGAGAGATAGAGTG 59.593 52.381 0.00 0.00 0.00 3.51
333 399 3.790089 TGCGGAGAGATAGAGTGGATA 57.210 47.619 0.00 0.00 0.00 2.59
334 400 4.308526 TGCGGAGAGATAGAGTGGATAT 57.691 45.455 0.00 0.00 0.00 1.63
335 401 5.437191 TGCGGAGAGATAGAGTGGATATA 57.563 43.478 0.00 0.00 0.00 0.86
380 455 2.124942 GGGCCGAGCAGAAAGAGG 60.125 66.667 0.00 0.00 0.00 3.69
399 474 0.033601 GGAGGAGAGAGGCTGACTGA 60.034 60.000 0.00 0.00 0.00 3.41
426 502 2.158559 TGACCATGCACAAAATAGCGT 58.841 42.857 0.00 0.00 0.00 5.07
472 549 1.535202 TTGGGTTTGGCATGGGGTC 60.535 57.895 0.00 0.00 0.00 4.46
485 562 3.236233 GGGTCGCCGGGGCTATTA 61.236 66.667 14.85 0.00 39.32 0.98
488 565 0.953960 GGTCGCCGGGGCTATTATTG 60.954 60.000 14.85 0.00 39.32 1.90
489 566 0.250166 GTCGCCGGGGCTATTATTGT 60.250 55.000 14.85 0.00 39.32 2.71
492 569 2.104451 TCGCCGGGGCTATTATTGTTTA 59.896 45.455 14.85 0.00 39.32 2.01
496 573 5.181622 CGCCGGGGCTATTATTGTTTAAATA 59.818 40.000 5.22 0.00 39.32 1.40
497 574 6.127842 CGCCGGGGCTATTATTGTTTAAATAT 60.128 38.462 5.22 0.00 39.32 1.28
499 576 7.094118 GCCGGGGCTATTATTGTTTAAATATGA 60.094 37.037 2.18 0.00 38.26 2.15
519 596 6.741992 ATGACGCAAAATGATGTCTTAAGA 57.258 33.333 0.00 0.00 32.64 2.10
520 597 6.552859 TGACGCAAAATGATGTCTTAAGAA 57.447 33.333 6.78 0.00 32.64 2.52
521 598 6.370593 TGACGCAAAATGATGTCTTAAGAAC 58.629 36.000 6.78 2.60 32.64 3.01
522 599 6.017523 TGACGCAAAATGATGTCTTAAGAACA 60.018 34.615 6.78 8.33 32.64 3.18
526 603 7.699391 CGCAAAATGATGTCTTAAGAACATGAT 59.301 33.333 18.99 15.08 0.00 2.45
575 652 0.032912 AAAAGGTGTTTGGGGGTCGT 60.033 50.000 0.00 0.00 0.00 4.34
576 653 0.032912 AAAGGTGTTTGGGGGTCGTT 60.033 50.000 0.00 0.00 0.00 3.85
577 654 0.845337 AAGGTGTTTGGGGGTCGTTA 59.155 50.000 0.00 0.00 0.00 3.18
578 655 0.109153 AGGTGTTTGGGGGTCGTTAC 59.891 55.000 0.00 0.00 0.00 2.50
579 656 1.229975 GGTGTTTGGGGGTCGTTACG 61.230 60.000 0.00 0.00 0.00 3.18
580 657 1.071128 TGTTTGGGGGTCGTTACGG 59.929 57.895 4.53 0.00 0.00 4.02
581 658 2.032376 TTTGGGGGTCGTTACGGC 59.968 61.111 4.53 1.78 0.00 5.68
592 669 1.153881 GTTACGGCCGAGTGGAGAC 60.154 63.158 35.90 14.48 37.49 3.36
600 677 0.170561 CCGAGTGGAGACGGTGTAAG 59.829 60.000 0.00 0.00 43.53 2.34
602 679 1.542492 GAGTGGAGACGGTGTAAGGA 58.458 55.000 0.00 0.00 0.00 3.36
604 681 1.617357 AGTGGAGACGGTGTAAGGAAC 59.383 52.381 0.00 0.00 0.00 3.62
605 682 0.599558 TGGAGACGGTGTAAGGAACG 59.400 55.000 0.00 0.00 0.00 3.95
606 683 0.108945 GGAGACGGTGTAAGGAACGG 60.109 60.000 0.00 0.00 0.00 4.44
607 684 0.883833 GAGACGGTGTAAGGAACGGA 59.116 55.000 0.00 0.00 0.00 4.69
608 685 1.475682 GAGACGGTGTAAGGAACGGAT 59.524 52.381 0.00 0.00 0.00 4.18
609 686 1.475682 AGACGGTGTAAGGAACGGATC 59.524 52.381 0.00 0.00 0.00 3.36
610 687 0.171903 ACGGTGTAAGGAACGGATCG 59.828 55.000 0.00 0.00 0.00 3.69
611 688 0.452987 CGGTGTAAGGAACGGATCGA 59.547 55.000 0.00 0.00 0.00 3.59
612 689 1.135315 CGGTGTAAGGAACGGATCGAA 60.135 52.381 0.00 0.00 0.00 3.71
613 690 2.265683 GGTGTAAGGAACGGATCGAAC 58.734 52.381 0.00 0.00 0.00 3.95
614 691 1.916000 GTGTAAGGAACGGATCGAACG 59.084 52.381 10.78 10.78 37.36 3.95
615 692 0.919300 GTAAGGAACGGATCGAACGC 59.081 55.000 12.06 0.00 34.00 4.84
616 693 0.527113 TAAGGAACGGATCGAACGCA 59.473 50.000 12.06 0.00 34.00 5.24
617 694 0.736325 AAGGAACGGATCGAACGCAG 60.736 55.000 12.06 0.00 34.00 5.18
618 695 2.695646 GAACGGATCGAACGCAGC 59.304 61.111 12.06 0.00 34.00 5.25
619 696 3.126722 GAACGGATCGAACGCAGCG 62.127 63.158 14.82 14.82 34.00 5.18
620 697 3.620300 AACGGATCGAACGCAGCGA 62.620 57.895 24.65 0.00 42.48 4.93
665 742 2.642254 CGGCCCTGTTCTGTACCGA 61.642 63.158 0.00 0.00 43.19 4.69
666 743 1.079336 GGCCCTGTTCTGTACCGAC 60.079 63.158 0.00 0.00 0.00 4.79
667 744 1.445582 GCCCTGTTCTGTACCGACG 60.446 63.158 0.00 0.00 0.00 5.12
670 747 1.162698 CCTGTTCTGTACCGACGAGA 58.837 55.000 0.00 0.00 0.00 4.04
678 755 3.058432 TCTGTACCGACGAGAAGTGAAAG 60.058 47.826 0.00 0.00 0.00 2.62
801 883 0.036388 AAATCTGACCGTCCACGCAT 60.036 50.000 0.00 0.00 38.18 4.73
832 915 1.519719 GCTCCACGCTCATCTTCCT 59.480 57.895 0.00 0.00 35.14 3.36
950 1052 0.693049 TTCTTCCTCTTCACCCCAGC 59.307 55.000 0.00 0.00 0.00 4.85
953 1055 4.101448 CCTCTTCACCCCAGCCCG 62.101 72.222 0.00 0.00 0.00 6.13
1498 2941 0.667993 CGGTGGAAATGTGTGTGCTT 59.332 50.000 0.00 0.00 0.00 3.91
1518 2987 2.778299 TGTAGTGTTCTTGCCATGGTC 58.222 47.619 14.67 6.41 0.00 4.02
1590 3068 4.455533 GGAAATGAAAAATGTTGGCTTCCC 59.544 41.667 0.00 0.00 0.00 3.97
1644 3123 3.209410 CCAACTTGTCAGAGTTCTTGCT 58.791 45.455 0.00 0.00 37.76 3.91
1645 3124 4.380531 CCAACTTGTCAGAGTTCTTGCTA 58.619 43.478 0.00 0.00 37.76 3.49
1795 3323 3.340928 TCGTCTTCAGTTCCGTCTATCA 58.659 45.455 0.00 0.00 0.00 2.15
1798 3326 4.615223 CGTCTTCAGTTCCGTCTATCAACA 60.615 45.833 0.00 0.00 0.00 3.33
1812 3340 2.780065 TCAACAAGTTGCATGACAGC 57.220 45.000 8.04 0.00 40.24 4.40
1813 3341 2.022934 TCAACAAGTTGCATGACAGCA 58.977 42.857 8.04 0.00 43.99 4.41
1876 3404 5.251764 AGCATCCATATTCTGCCTGATTAC 58.748 41.667 0.00 0.00 36.56 1.89
1889 3417 3.091545 CCTGATTACATTGCAACCCTGT 58.908 45.455 0.00 5.21 0.00 4.00
1923 3487 7.764443 TGAACCATGCTCTAAACTAAGTACATC 59.236 37.037 0.00 0.00 0.00 3.06
1974 3743 4.854399 TGTTTGCTTTATGTTCTGTTCCG 58.146 39.130 0.00 0.00 0.00 4.30
2046 3840 4.153117 CAGGAGTGTAAAGAGAACATGTGC 59.847 45.833 0.00 0.00 0.00 4.57
2082 3876 1.239347 GAAGTGACCTGCCAGTTTCC 58.761 55.000 0.00 0.00 30.45 3.13
2120 3917 8.889849 TTAATTGCTTCGATTTTGTAGCTTAC 57.110 30.769 6.14 0.00 33.86 2.34
2178 4061 0.034863 TATTCCGGTTGGTTGCCTCC 60.035 55.000 0.00 0.00 36.30 4.30
2201 4084 5.118990 CGAACCTGGATGAACAGATGTAAT 58.881 41.667 0.00 0.00 40.97 1.89
2202 4085 6.280643 CGAACCTGGATGAACAGATGTAATA 58.719 40.000 0.00 0.00 40.97 0.98
2203 4086 6.201044 CGAACCTGGATGAACAGATGTAATAC 59.799 42.308 0.00 0.00 40.97 1.89
2204 4087 6.814954 ACCTGGATGAACAGATGTAATACT 57.185 37.500 0.00 0.00 40.97 2.12
2205 4088 6.821388 ACCTGGATGAACAGATGTAATACTC 58.179 40.000 0.00 0.00 40.97 2.59
2206 4089 6.183361 ACCTGGATGAACAGATGTAATACTCC 60.183 42.308 0.00 0.00 40.97 3.85
2207 4090 6.042552 CCTGGATGAACAGATGTAATACTCCT 59.957 42.308 0.00 0.00 40.97 3.69
2208 4091 6.820335 TGGATGAACAGATGTAATACTCCTG 58.180 40.000 9.72 9.72 0.00 3.86
2209 4092 6.611236 TGGATGAACAGATGTAATACTCCTGA 59.389 38.462 15.46 0.00 0.00 3.86
2210 4093 7.125659 TGGATGAACAGATGTAATACTCCTGAA 59.874 37.037 15.46 5.42 0.00 3.02
2211 4094 7.439655 GGATGAACAGATGTAATACTCCTGAAC 59.560 40.741 15.46 10.55 0.00 3.18
2212 4095 7.239763 TGAACAGATGTAATACTCCTGAACA 57.760 36.000 15.46 12.16 0.00 3.18
2213 4096 7.323420 TGAACAGATGTAATACTCCTGAACAG 58.677 38.462 15.46 0.00 0.00 3.16
2214 4097 7.178451 TGAACAGATGTAATACTCCTGAACAGA 59.822 37.037 15.46 0.00 0.00 3.41
2215 4098 7.667575 ACAGATGTAATACTCCTGAACAGAT 57.332 36.000 15.46 0.00 0.00 2.90
2216 4099 7.495901 ACAGATGTAATACTCCTGAACAGATG 58.504 38.462 15.46 0.00 0.00 2.90
2217 4100 7.124901 ACAGATGTAATACTCCTGAACAGATGT 59.875 37.037 15.46 4.57 0.00 3.06
2218 4101 7.651304 CAGATGTAATACTCCTGAACAGATGTC 59.349 40.741 3.19 0.00 0.00 3.06
2219 4102 6.850752 TGTAATACTCCTGAACAGATGTCA 57.149 37.500 3.19 0.00 0.00 3.58
2220 4103 7.239763 TGTAATACTCCTGAACAGATGTCAA 57.760 36.000 3.19 0.00 0.00 3.18
2221 4104 7.676004 TGTAATACTCCTGAACAGATGTCAAA 58.324 34.615 3.19 0.00 0.00 2.69
2222 4105 8.154203 TGTAATACTCCTGAACAGATGTCAAAA 58.846 33.333 3.19 0.00 0.00 2.44
2223 4106 9.167311 GTAATACTCCTGAACAGATGTCAAAAT 57.833 33.333 3.19 0.00 0.00 1.82
2224 4107 8.641498 AATACTCCTGAACAGATGTCAAAATT 57.359 30.769 3.19 0.00 0.00 1.82
2225 4108 6.566197 ACTCCTGAACAGATGTCAAAATTC 57.434 37.500 3.19 0.00 0.00 2.17
2226 4109 5.474876 ACTCCTGAACAGATGTCAAAATTCC 59.525 40.000 3.19 0.00 0.00 3.01
2227 4110 5.384336 TCCTGAACAGATGTCAAAATTCCA 58.616 37.500 3.19 0.00 0.00 3.53
2228 4111 5.832595 TCCTGAACAGATGTCAAAATTCCAA 59.167 36.000 3.19 0.00 0.00 3.53
2229 4112 6.323482 TCCTGAACAGATGTCAAAATTCCAAA 59.677 34.615 3.19 0.00 0.00 3.28
2230 4113 7.015487 TCCTGAACAGATGTCAAAATTCCAAAT 59.985 33.333 3.19 0.00 0.00 2.32
2231 4114 8.306038 CCTGAACAGATGTCAAAATTCCAAATA 58.694 33.333 3.19 0.00 0.00 1.40
2232 4115 9.695526 CTGAACAGATGTCAAAATTCCAAATAA 57.304 29.630 0.00 0.00 0.00 1.40
2233 4116 9.474920 TGAACAGATGTCAAAATTCCAAATAAC 57.525 29.630 0.00 0.00 0.00 1.89
2384 4773 7.063544 CCTCCGACTACAGTTTTTCTTGATTAG 59.936 40.741 0.00 0.00 0.00 1.73
2409 4798 0.173481 TATCGTGAGGCACACTGCTC 59.827 55.000 13.11 0.00 46.24 4.26
2410 4799 1.539560 ATCGTGAGGCACACTGCTCT 61.540 55.000 13.11 0.00 46.24 4.09
2411 4800 0.893727 TCGTGAGGCACACTGCTCTA 60.894 55.000 13.11 0.00 46.24 2.43
2527 4917 3.935872 GCGCACACACTTGACGCA 61.936 61.111 0.30 0.00 45.20 5.24
2531 4921 1.623359 GCACACACTTGACGCAAAAA 58.377 45.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.431771 TTGACGACGTCATGCCCG 60.432 61.111 29.60 3.17 42.40 6.13
33 34 2.656646 TGCGAGATGGCAGTCGTT 59.343 55.556 19.51 0.00 38.17 3.85
39 40 2.580815 CTGGTCTGCGAGATGGCA 59.419 61.111 0.00 0.00 41.45 4.92
99 100 2.763248 CAGTACAACGTGCTCGCG 59.237 61.111 8.29 0.00 41.18 5.87
184 185 3.408851 GACGAACGGGCCGTGAAC 61.409 66.667 34.87 24.16 39.99 3.18
368 434 1.756538 CTCTCCTCCCTCTTTCTGCTC 59.243 57.143 0.00 0.00 0.00 4.26
380 455 0.033601 TCAGTCAGCCTCTCTCCTCC 60.034 60.000 0.00 0.00 0.00 4.30
399 474 1.714541 TTGTGCATGGTCAAACCCAT 58.285 45.000 0.00 0.00 46.28 4.00
454 531 1.535202 GACCCCATGCCAAACCCAA 60.535 57.895 0.00 0.00 0.00 4.12
488 565 9.289303 AGACATCATTTTGCGTCATATTTAAAC 57.711 29.630 0.00 0.00 0.00 2.01
489 566 9.853555 AAGACATCATTTTGCGTCATATTTAAA 57.146 25.926 0.00 0.00 0.00 1.52
492 569 9.507280 CTTAAGACATCATTTTGCGTCATATTT 57.493 29.630 0.00 0.00 0.00 1.40
496 573 6.741992 TCTTAAGACATCATTTTGCGTCAT 57.258 33.333 0.00 0.00 0.00 3.06
497 574 6.017523 TGTTCTTAAGACATCATTTTGCGTCA 60.018 34.615 4.18 0.00 0.00 4.35
499 576 6.312399 TGTTCTTAAGACATCATTTTGCGT 57.688 33.333 4.18 0.00 0.00 5.24
560 637 1.229975 CGTAACGACCCCCAAACACC 61.230 60.000 0.00 0.00 0.00 4.16
561 638 1.229975 CCGTAACGACCCCCAAACAC 61.230 60.000 0.00 0.00 0.00 3.32
565 642 4.019312 GGCCGTAACGACCCCCAA 62.019 66.667 0.00 0.00 0.00 4.12
568 645 4.503314 CTCGGCCGTAACGACCCC 62.503 72.222 27.15 0.00 36.25 4.95
571 648 2.505557 CCACTCGGCCGTAACGAC 60.506 66.667 27.15 0.00 36.25 4.34
572 649 2.672651 TCCACTCGGCCGTAACGA 60.673 61.111 27.15 14.02 38.79 3.85
573 650 2.202570 CTCCACTCGGCCGTAACG 60.203 66.667 27.15 14.43 0.00 3.18
575 652 2.693762 CGTCTCCACTCGGCCGTAA 61.694 63.158 27.15 5.52 0.00 3.18
576 653 3.129502 CGTCTCCACTCGGCCGTA 61.130 66.667 27.15 11.20 0.00 4.02
592 669 0.452987 TCGATCCGTTCCTTACACCG 59.547 55.000 0.00 0.00 0.00 4.94
594 671 1.916000 CGTTCGATCCGTTCCTTACAC 59.084 52.381 0.00 0.00 0.00 2.90
596 673 0.919300 GCGTTCGATCCGTTCCTTAC 59.081 55.000 6.83 0.00 0.00 2.34
597 674 0.527113 TGCGTTCGATCCGTTCCTTA 59.473 50.000 6.83 0.00 0.00 2.69
600 677 2.799540 GCTGCGTTCGATCCGTTCC 61.800 63.158 6.83 0.00 0.00 3.62
602 679 2.884087 ATCGCTGCGTTCGATCCGTT 62.884 55.000 22.48 0.00 42.28 4.44
604 681 2.655364 ATCGCTGCGTTCGATCCG 60.655 61.111 22.48 1.01 42.28 4.18
609 686 4.257376 CTGCGATCGCTGCGTTCG 62.257 66.667 36.71 36.71 46.97 3.95
665 742 0.321996 GGCTCCCTTTCACTTCTCGT 59.678 55.000 0.00 0.00 0.00 4.18
666 743 0.737715 CGGCTCCCTTTCACTTCTCG 60.738 60.000 0.00 0.00 0.00 4.04
667 744 0.391793 CCGGCTCCCTTTCACTTCTC 60.392 60.000 0.00 0.00 0.00 2.87
670 747 2.757077 CCCGGCTCCCTTTCACTT 59.243 61.111 0.00 0.00 0.00 3.16
678 755 2.032681 GATGTATGCCCGGCTCCC 59.967 66.667 11.61 0.00 0.00 4.30
801 883 0.602638 GTGGAGCGTTGGATGTGTGA 60.603 55.000 0.00 0.00 0.00 3.58
832 915 2.223386 CGTGAGTTTTGCTTTTCGGGAA 60.223 45.455 0.00 0.00 0.00 3.97
950 1052 0.394352 CTTGGAGATTTGGGGACGGG 60.394 60.000 0.00 0.00 0.00 5.28
953 1055 1.657751 GCGCTTGGAGATTTGGGGAC 61.658 60.000 0.00 0.00 0.00 4.46
1498 2941 2.778299 GACCATGGCAAGAACACTACA 58.222 47.619 13.04 0.00 0.00 2.74
1518 2987 1.004610 CAGATTAGGCACAACGCATCG 60.005 52.381 0.00 0.00 45.17 3.84
1590 3068 5.596268 TCAAACACAGATGAATGAGAACG 57.404 39.130 0.00 0.00 0.00 3.95
1645 3124 8.835439 GCAAAATAGAAAGAGCTAGCTAAATCT 58.165 33.333 19.38 21.14 0.00 2.40
1705 3184 0.260230 TCAGAGGCAGCTAGCTAGGT 59.740 55.000 18.86 19.65 44.79 3.08
1709 3206 0.617249 AGGTTCAGAGGCAGCTAGCT 60.617 55.000 12.68 12.68 44.79 3.32
1795 3323 1.067516 GGTGCTGTCATGCAACTTGTT 59.932 47.619 0.00 0.00 46.25 2.83
1865 3393 2.159198 GGGTTGCAATGTAATCAGGCAG 60.159 50.000 0.59 0.00 38.41 4.85
1876 3404 5.185454 TCATAGACTTACAGGGTTGCAATG 58.815 41.667 0.59 0.00 0.00 2.82
1889 3417 8.079211 AGTTTAGAGCATGGTTCATAGACTTA 57.921 34.615 0.00 0.00 0.00 2.24
1923 3487 1.669115 CGACAGGCAGAACCACAGG 60.669 63.158 0.00 0.00 43.14 4.00
2046 3840 2.092212 ACTTCACATGCTTGGGATAGGG 60.092 50.000 5.24 0.20 34.53 3.53
2082 3876 5.504755 CGAAGCAATTAAGAACAAAGTAGCG 59.495 40.000 0.00 0.00 0.00 4.26
2120 3917 7.940178 TGACACACTACTACAGTAACATTTG 57.060 36.000 0.00 0.00 34.98 2.32
2178 4061 2.977914 ACATCTGTTCATCCAGGTTCG 58.022 47.619 0.00 0.00 33.14 3.95
2201 4084 6.655003 GGAATTTTGACATCTGTTCAGGAGTA 59.345 38.462 0.00 0.00 0.00 2.59
2202 4085 5.474876 GGAATTTTGACATCTGTTCAGGAGT 59.525 40.000 0.00 0.00 0.00 3.85
2203 4086 5.474532 TGGAATTTTGACATCTGTTCAGGAG 59.525 40.000 0.00 0.00 0.00 3.69
2204 4087 5.384336 TGGAATTTTGACATCTGTTCAGGA 58.616 37.500 0.00 0.00 0.00 3.86
2205 4088 5.710513 TGGAATTTTGACATCTGTTCAGG 57.289 39.130 0.00 0.00 0.00 3.86
2206 4089 9.695526 TTATTTGGAATTTTGACATCTGTTCAG 57.304 29.630 0.00 0.00 0.00 3.02
2207 4090 9.474920 GTTATTTGGAATTTTGACATCTGTTCA 57.525 29.630 0.00 0.00 0.00 3.18
2208 4091 9.696917 AGTTATTTGGAATTTTGACATCTGTTC 57.303 29.630 0.00 0.00 0.00 3.18
2212 4095 9.807649 GCATAGTTATTTGGAATTTTGACATCT 57.192 29.630 0.00 0.00 0.00 2.90
2213 4096 9.034544 GGCATAGTTATTTGGAATTTTGACATC 57.965 33.333 0.00 0.00 0.00 3.06
2214 4097 7.986889 GGGCATAGTTATTTGGAATTTTGACAT 59.013 33.333 0.00 0.00 0.00 3.06
2215 4098 7.038729 TGGGCATAGTTATTTGGAATTTTGACA 60.039 33.333 0.00 0.00 0.00 3.58
2216 4099 7.327214 TGGGCATAGTTATTTGGAATTTTGAC 58.673 34.615 0.00 0.00 0.00 3.18
2217 4100 7.487822 TGGGCATAGTTATTTGGAATTTTGA 57.512 32.000 0.00 0.00 0.00 2.69
2218 4101 8.735692 AATGGGCATAGTTATTTGGAATTTTG 57.264 30.769 0.00 0.00 0.00 2.44
2219 4102 8.547173 TGAATGGGCATAGTTATTTGGAATTTT 58.453 29.630 0.00 0.00 0.00 1.82
2220 4103 8.088463 TGAATGGGCATAGTTATTTGGAATTT 57.912 30.769 0.00 0.00 0.00 1.82
2221 4104 7.345392 ACTGAATGGGCATAGTTATTTGGAATT 59.655 33.333 0.00 0.00 0.00 2.17
2222 4105 6.840705 ACTGAATGGGCATAGTTATTTGGAAT 59.159 34.615 0.00 0.00 0.00 3.01
2223 4106 6.194235 ACTGAATGGGCATAGTTATTTGGAA 58.806 36.000 0.00 0.00 0.00 3.53
2224 4107 5.765510 ACTGAATGGGCATAGTTATTTGGA 58.234 37.500 0.00 0.00 0.00 3.53
2225 4108 6.096705 TGAACTGAATGGGCATAGTTATTTGG 59.903 38.462 0.00 0.00 33.83 3.28
2226 4109 7.099266 TGAACTGAATGGGCATAGTTATTTG 57.901 36.000 0.00 0.00 33.83 2.32
2227 4110 6.891908 ACTGAACTGAATGGGCATAGTTATTT 59.108 34.615 0.00 0.00 33.83 1.40
2228 4111 6.426587 ACTGAACTGAATGGGCATAGTTATT 58.573 36.000 0.00 0.00 33.83 1.40
2229 4112 6.006275 ACTGAACTGAATGGGCATAGTTAT 57.994 37.500 0.00 0.00 33.83 1.89
2230 4113 5.435686 ACTGAACTGAATGGGCATAGTTA 57.564 39.130 0.00 0.00 33.83 2.24
2231 4114 4.307032 ACTGAACTGAATGGGCATAGTT 57.693 40.909 0.00 0.00 36.18 2.24
2232 4115 4.307032 AACTGAACTGAATGGGCATAGT 57.693 40.909 0.00 0.00 0.00 2.12
2233 4116 5.047802 ACAAAACTGAACTGAATGGGCATAG 60.048 40.000 0.00 0.00 0.00 2.23
2300 4662 0.449388 GGATTGAGGCACTTTCAGCG 59.551 55.000 0.00 0.00 41.55 5.18
2384 4773 3.658351 GTGTGCCTCACGATAAACATC 57.342 47.619 0.00 0.00 37.14 3.06
2394 4783 2.428890 AGTATAGAGCAGTGTGCCTCAC 59.571 50.000 0.00 1.58 46.52 3.51
2495 4885 2.949678 CGCGCGCTAGTCGATGTT 60.950 61.111 30.48 0.00 41.67 2.71
2522 4912 3.423206 CAGAATGAACAGCTTTTTGCGTC 59.577 43.478 0.00 0.00 43.53 5.19
2527 4917 2.699846 TGCCCAGAATGAACAGCTTTTT 59.300 40.909 0.00 0.00 39.69 1.94
2531 4921 0.403271 ACTGCCCAGAATGAACAGCT 59.597 50.000 1.69 0.00 40.89 4.24


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

AutoCloner maintained by Alex Coulton.