Multiple sequence alignment - TraesCS2B01G059700

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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 TraesCS2B01G059700 chr2B 100.000 2264 0 0 1 2264 28920385 28922648 0.000000e+00 4181.0
1 TraesCS2B01G059700 chr2B 85.481 1226 113 27 869 2052 29046825 29048027 0.000000e+00 1218.0
2 TraesCS2B01G059700 chr2B 91.069 627 51 4 864 1489 29991368 29990746 0.000000e+00 843.0
3 TraesCS2B01G059700 chr2B 86.570 484 51 4 1569 2052 29990609 29990140 2.580000e-144 521.0
4 TraesCS2B01G059700 chr2B 86.340 388 49 4 61 447 29992365 29991981 9.670000e-114 420.0
5 TraesCS2B01G059700 chr2B 85.204 392 34 9 61 447 29045827 29046199 4.560000e-102 381.0
6 TraesCS2B01G059700 chr2B 92.713 247 16 2 630 876 29991988 29991744 2.770000e-94 355.0
7 TraesCS2B01G059700 chr2B 89.262 149 9 4 486 632 760142667 760142810 1.790000e-41 180.0
8 TraesCS2B01G059700 chr2D 95.534 627 27 1 864 1489 17312776 17313402 0.000000e+00 1002.0
9 TraesCS2B01G059700 chr2D 94.822 618 31 1 864 1480 17169664 17170281 0.000000e+00 963.0
10 TraesCS2B01G059700 chr2D 95.396 391 14 1 61 447 17168720 17169110 8.880000e-174 619.0
11 TraesCS2B01G059700 chr2D 89.744 390 11 3 61 445 17311781 17312146 2.630000e-129 472.0
12 TraesCS2B01G059700 chr2D 96.109 257 10 0 1480 1736 17170311 17170567 9.670000e-114 420.0
13 TraesCS2B01G059700 chr2D 95.331 257 12 0 1480 1736 17313423 17313679 2.090000e-110 409.0
14 TraesCS2B01G059700 chr2D 92.366 262 20 0 2003 2264 17170565 17170826 7.640000e-100 374.0
15 TraesCS2B01G059700 chr2D 91.221 262 21 2 2003 2264 17313677 17313936 2.770000e-94 355.0
16 TraesCS2B01G059700 chr2D 90.837 251 21 2 1106 1355 17208272 17208521 3.600000e-88 335.0
17 TraesCS2B01G059700 chr2D 91.770 243 15 4 630 869 17312141 17312381 1.300000e-87 333.0
18 TraesCS2B01G059700 chr2D 92.083 240 11 1 630 869 17169103 17169334 4.660000e-87 331.0
19 TraesCS2B01G059700 chr2A 94.896 627 31 1 864 1489 18636439 18637065 0.000000e+00 979.0
20 TraesCS2B01G059700 chr2A 91.733 629 49 2 864 1489 18586850 18587478 0.000000e+00 870.0
21 TraesCS2B01G059700 chr2A 94.474 380 17 1 72 447 18635433 18635812 1.170000e-162 582.0
22 TraesCS2B01G059700 chr2A 86.957 391 33 9 61 447 18585857 18586233 7.480000e-115 424.0
23 TraesCS2B01G059700 chr2A 95.720 257 11 0 1480 1736 18637086 18637342 4.500000e-112 414.0
24 TraesCS2B01G059700 chr2A 93.511 262 17 0 2003 2264 18637340 18637601 7.580000e-105 390.0
25 TraesCS2B01G059700 chr2A 93.750 240 15 0 630 869 18635805 18636044 5.940000e-96 361.0
26 TraesCS2B01G059700 chr2A 92.432 185 7 4 446 629 457354492 457354314 8.020000e-65 257.0
27 TraesCS2B01G059700 chr2A 80.108 186 24 8 448 629 134614892 134614716 2.360000e-25 126.0
28 TraesCS2B01G059700 chr2A 77.698 139 18 10 2059 2192 53056343 53056213 3.120000e-09 73.1
29 TraesCS2B01G059700 chr2A 76.978 139 19 10 2059 2192 53053461 53053331 1.450000e-07 67.6
30 TraesCS2B01G059700 chr5A 93.989 183 6 2 448 629 34304971 34305149 2.870000e-69 272.0
31 TraesCS2B01G059700 chr5A 92.405 79 4 2 1 77 433805180 433805102 6.610000e-21 111.0
32 TraesCS2B01G059700 chr5A 76.351 148 20 12 2056 2192 560479515 560479372 5.220000e-07 65.8
33 TraesCS2B01G059700 chr6B 93.407 182 6 3 448 629 51523630 51523805 4.790000e-67 265.0
34 TraesCS2B01G059700 chr6B 89.888 89 5 4 1 87 700668888 700668802 6.610000e-21 111.0
35 TraesCS2B01G059700 chr3B 92.432 185 6 3 448 629 648805415 648805236 8.020000e-65 257.0
36 TraesCS2B01G059700 chr3B 83.422 187 25 6 447 631 754454792 754454610 3.870000e-38 169.0
37 TraesCS2B01G059700 chr3B 77.931 145 16 12 2050 2182 727796458 727796318 2.410000e-10 76.8
38 TraesCS2B01G059700 chr5B 91.935 186 7 4 447 629 691156851 691157031 1.040000e-63 254.0
39 TraesCS2B01G059700 chr5B 83.784 185 24 4 446 629 518291744 518291565 1.080000e-38 171.0
40 TraesCS2B01G059700 chr5B 93.671 79 1 4 1 76 424455366 424455289 5.110000e-22 115.0
41 TraesCS2B01G059700 chr1B 83.784 185 19 8 448 629 250062643 250062819 5.000000e-37 165.0
42 TraesCS2B01G059700 chr7A 90.323 93 6 3 1 91 193593937 193593846 3.950000e-23 119.0
43 TraesCS2B01G059700 chr4A 97.143 70 2 0 1 70 692479976 692479907 3.950000e-23 119.0
44 TraesCS2B01G059700 chr4A 93.506 77 3 2 1 76 728473378 728473303 1.840000e-21 113.0
45 TraesCS2B01G059700 chr7B 90.909 88 5 3 1 87 576109558 576109643 5.110000e-22 115.0
46 TraesCS2B01G059700 chr7B 94.595 74 3 1 1 74 41234773 41234845 1.840000e-21 113.0
47 TraesCS2B01G059700 chrUn 91.358 81 4 2 1 80 288923615 288923693 8.550000e-20 108.0
48 TraesCS2B01G059700 chr6A 97.727 44 0 1 2051 2093 77899550 77899507 8.670000e-10 75.0
49 TraesCS2B01G059700 chr6A 97.727 44 0 1 2051 2093 78033824 78033781 8.670000e-10 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G059700 chr2B 28920385 28922648 2263 False 4181.00 4181 100.0000 1 2264 1 chr2B.!!$F1 2263
1 TraesCS2B01G059700 chr2B 29045827 29048027 2200 False 799.50 1218 85.3425 61 2052 2 chr2B.!!$F3 1991
2 TraesCS2B01G059700 chr2B 29990140 29992365 2225 True 534.75 843 89.1730 61 2052 4 chr2B.!!$R1 1991
3 TraesCS2B01G059700 chr2D 17168720 17170826 2106 False 541.40 963 94.1552 61 2264 5 chr2D.!!$F2 2203
4 TraesCS2B01G059700 chr2D 17311781 17313936 2155 False 514.20 1002 92.7200 61 2264 5 chr2D.!!$F3 2203
5 TraesCS2B01G059700 chr2A 18585857 18587478 1621 False 647.00 870 89.3450 61 1489 2 chr2A.!!$F1 1428
6 TraesCS2B01G059700 chr2A 18635433 18637601 2168 False 545.20 979 94.4702 72 2264 5 chr2A.!!$F2 2192

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
20 21 0.034477 ATGGAACCGGCACTAAAGGG 60.034 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1274 1696 0.318762 GGGCGAACAGAACAGTCTCT 59.681 55.0 0.0 0.0 28.78 3.1 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
19 20 2.702592 TATGGAACCGGCACTAAAGG 57.297 50.000 0.00 0.00 0.00 3.11
20 21 0.034477 ATGGAACCGGCACTAAAGGG 60.034 55.000 0.00 0.00 0.00 3.95
21 22 2.044555 GGAACCGGCACTAAAGGGC 61.045 63.158 0.00 0.00 0.00 5.19
22 23 2.035155 AACCGGCACTAAAGGGCC 59.965 61.111 13.51 13.51 46.80 5.80
27 28 2.776659 GGCACTAAAGGGCCTTACG 58.223 57.895 21.25 15.66 46.74 3.18
28 29 0.251073 GGCACTAAAGGGCCTTACGA 59.749 55.000 21.25 7.25 46.74 3.43
29 30 1.339342 GGCACTAAAGGGCCTTACGAA 60.339 52.381 21.25 4.81 46.74 3.85
30 31 1.736126 GCACTAAAGGGCCTTACGAAC 59.264 52.381 21.25 5.99 0.00 3.95
31 32 2.353323 CACTAAAGGGCCTTACGAACC 58.647 52.381 21.25 0.00 0.00 3.62
32 33 1.066645 ACTAAAGGGCCTTACGAACCG 60.067 52.381 21.25 5.60 0.00 4.44
33 34 0.249955 TAAAGGGCCTTACGAACCGG 59.750 55.000 21.25 0.00 0.00 5.28
34 35 1.771783 AAAGGGCCTTACGAACCGGT 61.772 55.000 21.25 0.00 0.00 5.28
35 36 2.435410 GGGCCTTACGAACCGGTG 60.435 66.667 8.52 0.00 0.00 4.94
36 37 3.122971 GGCCTTACGAACCGGTGC 61.123 66.667 8.52 4.53 0.00 5.01
37 38 2.047560 GCCTTACGAACCGGTGCT 60.048 61.111 8.52 0.00 0.00 4.40
38 39 1.216178 GCCTTACGAACCGGTGCTA 59.784 57.895 8.52 0.00 0.00 3.49
39 40 0.179092 GCCTTACGAACCGGTGCTAT 60.179 55.000 8.52 0.00 0.00 2.97
40 41 1.741394 GCCTTACGAACCGGTGCTATT 60.741 52.381 8.52 0.00 0.00 1.73
41 42 1.931172 CCTTACGAACCGGTGCTATTG 59.069 52.381 8.52 0.00 0.00 1.90
42 43 1.326548 CTTACGAACCGGTGCTATTGC 59.673 52.381 8.52 0.00 40.20 3.56
43 44 0.460635 TACGAACCGGTGCTATTGCC 60.461 55.000 8.52 0.00 38.71 4.52
44 45 2.469516 CGAACCGGTGCTATTGCCC 61.470 63.158 8.52 0.00 38.71 5.36
45 46 2.437716 AACCGGTGCTATTGCCCG 60.438 61.111 8.52 17.41 45.75 6.13
48 49 2.437716 CGGTGCTATTGCCCGGTT 60.438 61.111 16.86 0.00 43.94 4.44
49 50 2.469516 CGGTGCTATTGCCCGGTTC 61.470 63.158 16.86 0.00 43.94 3.62
50 51 1.077716 GGTGCTATTGCCCGGTTCT 60.078 57.895 0.00 0.00 38.71 3.01
51 52 1.376609 GGTGCTATTGCCCGGTTCTG 61.377 60.000 0.00 0.00 38.71 3.02
52 53 1.748879 TGCTATTGCCCGGTTCTGC 60.749 57.895 0.00 0.00 38.71 4.26
53 54 1.748879 GCTATTGCCCGGTTCTGCA 60.749 57.895 0.00 0.00 35.27 4.41
54 55 1.993369 GCTATTGCCCGGTTCTGCAC 61.993 60.000 0.00 0.00 37.18 4.57
55 56 0.392998 CTATTGCCCGGTTCTGCACT 60.393 55.000 0.00 0.00 37.18 4.40
56 57 0.906066 TATTGCCCGGTTCTGCACTA 59.094 50.000 0.00 0.00 37.18 2.74
57 58 0.392998 ATTGCCCGGTTCTGCACTAG 60.393 55.000 0.00 0.00 37.18 2.57
58 59 1.764571 TTGCCCGGTTCTGCACTAGT 61.765 55.000 0.00 0.00 37.18 2.57
59 60 1.741770 GCCCGGTTCTGCACTAGTG 60.742 63.158 18.93 18.93 0.00 2.74
211 220 4.517453 TGTCCTTTGGTTCAGTATTTTCGG 59.483 41.667 0.00 0.00 0.00 4.30
443 453 0.609131 AAATGCCCAAGGGTCACGAG 60.609 55.000 7.05 0.00 37.65 4.18
444 454 1.779061 AATGCCCAAGGGTCACGAGT 61.779 55.000 7.05 0.00 37.65 4.18
445 455 0.907704 ATGCCCAAGGGTCACGAGTA 60.908 55.000 7.05 0.00 37.65 2.59
446 456 1.218316 GCCCAAGGGTCACGAGTAG 59.782 63.158 7.05 0.00 37.65 2.57
447 457 1.218316 CCCAAGGGTCACGAGTAGC 59.782 63.158 0.00 0.00 0.00 3.58
448 458 1.541310 CCCAAGGGTCACGAGTAGCA 61.541 60.000 0.00 0.00 0.00 3.49
449 459 0.108615 CCAAGGGTCACGAGTAGCAG 60.109 60.000 0.00 0.00 0.00 4.24
450 460 0.603569 CAAGGGTCACGAGTAGCAGT 59.396 55.000 0.00 0.00 0.00 4.40
451 461 0.603569 AAGGGTCACGAGTAGCAGTG 59.396 55.000 0.00 0.00 39.55 3.66
452 462 1.215647 GGGTCACGAGTAGCAGTGG 59.784 63.158 0.00 0.00 38.77 4.00
453 463 1.446272 GGTCACGAGTAGCAGTGGC 60.446 63.158 0.00 0.00 41.78 5.01
471 481 4.299796 GGAGCTTTGTGGGGGCCA 62.300 66.667 4.39 0.00 0.00 5.36
472 482 2.203625 GAGCTTTGTGGGGGCCAA 60.204 61.111 4.39 0.00 34.18 4.52
473 483 2.524148 AGCTTTGTGGGGGCCAAC 60.524 61.111 4.39 3.36 34.18 3.77
474 484 3.625897 GCTTTGTGGGGGCCAACC 61.626 66.667 4.39 6.97 34.18 3.77
475 485 2.201210 CTTTGTGGGGGCCAACCT 59.799 61.111 15.84 0.00 40.03 3.50
476 486 2.123077 TTTGTGGGGGCCAACCTG 60.123 61.111 15.84 0.00 40.03 4.00
477 487 3.765257 TTTGTGGGGGCCAACCTGG 62.765 63.158 15.84 0.00 41.55 4.45
507 517 4.647564 CCCCCAGCTCATAAGAATACAT 57.352 45.455 0.00 0.00 0.00 2.29
508 518 4.330250 CCCCCAGCTCATAAGAATACATG 58.670 47.826 0.00 0.00 0.00 3.21
509 519 4.202503 CCCCCAGCTCATAAGAATACATGT 60.203 45.833 2.69 2.69 0.00 3.21
510 520 5.013079 CCCCCAGCTCATAAGAATACATGTA 59.987 44.000 8.27 8.27 0.00 2.29
511 521 6.296662 CCCCCAGCTCATAAGAATACATGTAT 60.297 42.308 12.75 12.75 0.00 2.29
512 522 7.092891 CCCCCAGCTCATAAGAATACATGTATA 60.093 40.741 18.56 3.69 0.00 1.47
513 523 8.489489 CCCCAGCTCATAAGAATACATGTATAT 58.511 37.037 18.56 10.59 0.00 0.86
572 582 7.766219 ATCAGCTGAAAATAATCATGTTTGC 57.234 32.000 22.50 0.00 0.00 3.68
573 583 6.101332 TCAGCTGAAAATAATCATGTTTGCC 58.899 36.000 15.67 0.00 0.00 4.52
574 584 5.292589 CAGCTGAAAATAATCATGTTTGCCC 59.707 40.000 8.42 0.00 0.00 5.36
575 585 4.571984 GCTGAAAATAATCATGTTTGCCCC 59.428 41.667 0.00 0.00 0.00 5.80
576 586 5.096443 TGAAAATAATCATGTTTGCCCCC 57.904 39.130 0.00 0.00 0.00 5.40
610 620 2.603008 CCCCCGCCCATGATTTCT 59.397 61.111 0.00 0.00 0.00 2.52
611 621 1.843421 CCCCCGCCCATGATTTCTA 59.157 57.895 0.00 0.00 0.00 2.10
612 622 0.537371 CCCCCGCCCATGATTTCTAC 60.537 60.000 0.00 0.00 0.00 2.59
613 623 0.474184 CCCCGCCCATGATTTCTACT 59.526 55.000 0.00 0.00 0.00 2.57
614 624 1.543429 CCCCGCCCATGATTTCTACTC 60.543 57.143 0.00 0.00 0.00 2.59
615 625 1.140852 CCCGCCCATGATTTCTACTCA 59.859 52.381 0.00 0.00 0.00 3.41
616 626 2.421388 CCCGCCCATGATTTCTACTCAA 60.421 50.000 0.00 0.00 0.00 3.02
617 627 2.874701 CCGCCCATGATTTCTACTCAAG 59.125 50.000 0.00 0.00 0.00 3.02
618 628 2.289002 CGCCCATGATTTCTACTCAAGC 59.711 50.000 0.00 0.00 0.00 4.01
619 629 3.549794 GCCCATGATTTCTACTCAAGCT 58.450 45.455 0.00 0.00 0.00 3.74
620 630 3.563390 GCCCATGATTTCTACTCAAGCTC 59.437 47.826 0.00 0.00 0.00 4.09
621 631 4.685575 GCCCATGATTTCTACTCAAGCTCT 60.686 45.833 0.00 0.00 0.00 4.09
622 632 4.815308 CCCATGATTTCTACTCAAGCTCTG 59.185 45.833 0.00 0.00 0.00 3.35
623 633 4.272991 CCATGATTTCTACTCAAGCTCTGC 59.727 45.833 0.00 0.00 0.00 4.26
624 634 3.866651 TGATTTCTACTCAAGCTCTGCC 58.133 45.455 0.00 0.00 0.00 4.85
625 635 3.261643 TGATTTCTACTCAAGCTCTGCCA 59.738 43.478 0.00 0.00 0.00 4.92
626 636 2.751166 TTCTACTCAAGCTCTGCCAC 57.249 50.000 0.00 0.00 0.00 5.01
627 637 1.930251 TCTACTCAAGCTCTGCCACT 58.070 50.000 0.00 0.00 0.00 4.00
628 638 1.547820 TCTACTCAAGCTCTGCCACTG 59.452 52.381 0.00 0.00 0.00 3.66
629 639 1.547820 CTACTCAAGCTCTGCCACTGA 59.452 52.381 0.00 0.00 0.00 3.41
630 640 0.034616 ACTCAAGCTCTGCCACTGAC 59.965 55.000 0.00 0.00 0.00 3.51
631 641 1.005748 TCAAGCTCTGCCACTGACG 60.006 57.895 0.00 0.00 0.00 4.35
632 642 1.005748 CAAGCTCTGCCACTGACGA 60.006 57.895 0.00 0.00 0.00 4.20
710 723 8.484214 AAGAGCTCAATGACTCCACTAATATA 57.516 34.615 17.77 0.00 33.18 0.86
724 737 8.651589 TCCACTAATATATGTCCTTCTACCTG 57.348 38.462 0.00 0.00 0.00 4.00
734 747 4.097437 TGTCCTTCTACCTGTATGCTTACG 59.903 45.833 5.40 1.17 0.00 3.18
793 806 5.185056 AGCGGTTGAGTTAAAATTTAGGCAT 59.815 36.000 0.00 0.00 0.00 4.40
813 826 6.275618 AGGCATGGTTATTCTCCACCTATAAT 59.724 38.462 0.00 0.00 37.81 1.28
815 828 7.451566 GGCATGGTTATTCTCCACCTATAATTT 59.548 37.037 0.00 0.00 37.81 1.82
837 850 0.316772 ATATGAAGTCGTCGTCGCGG 60.317 55.000 6.13 0.00 36.96 6.46
853 866 0.649628 GCGGCGTCGTAATAAAAGCG 60.650 55.000 12.58 0.00 38.89 4.68
912 1334 6.363577 TGACTCTTTGTTCAAGCTAGTTTG 57.636 37.500 12.74 12.74 31.70 2.93
913 1335 5.175090 ACTCTTTGTTCAAGCTAGTTTGC 57.825 39.130 13.99 2.64 31.70 3.68
954 1376 9.918630 ATCTTTCATTCTTTGACCATTAACTTG 57.081 29.630 0.00 0.00 32.84 3.16
992 1414 6.318648 TGCTTGTGTCTCTGTCAAGTTAATTT 59.681 34.615 0.00 0.00 40.14 1.82
1023 1445 3.696051 TGAAAGAGCAACTGAAAGCAAGT 59.304 39.130 0.00 0.00 37.60 3.16
1035 1457 8.734386 CAACTGAAAGCAAGTAGGATTAAGATT 58.266 33.333 0.00 0.00 37.60 2.40
1274 1696 4.973168 ACAAAGAACTAGTGCCATTCTCA 58.027 39.130 0.00 0.00 31.44 3.27
1300 1724 2.673368 CTGTTCTGTTCGCCCAAGATAC 59.327 50.000 0.00 0.00 0.00 2.24
1411 1835 6.642707 AGGGAAGAGTAATGTCGAAGATAG 57.357 41.667 0.00 0.00 40.67 2.08
1456 1880 6.970484 TCACAGAAGGAAAAAGCTATGTTTC 58.030 36.000 8.31 8.31 33.78 2.78
1464 1888 6.918022 AGGAAAAAGCTATGTTTCGTTTGAAG 59.082 34.615 9.91 0.00 35.08 3.02
1476 1900 9.884465 ATGTTTCGTTTGAAGAATAAAGAAGAG 57.116 29.630 0.00 0.00 35.06 2.85
1477 1901 7.855904 TGTTTCGTTTGAAGAATAAAGAAGAGC 59.144 33.333 0.00 0.00 35.06 4.09
1478 1902 7.730364 TTCGTTTGAAGAATAAAGAAGAGCT 57.270 32.000 0.00 0.00 0.00 4.09
1495 1950 5.483685 AGAGCTATGTGTGTAAGGAAACA 57.516 39.130 0.00 0.00 0.00 2.83
1556 2012 4.293415 CTGCAATCTGTTGTTCAGGAAAC 58.707 43.478 0.00 0.00 43.76 2.78
1670 2152 4.388378 ACTAAGGGCAACTCTAATCGAC 57.612 45.455 0.00 0.00 0.00 4.20
1681 2163 4.670347 ACTCTAATCGACGCCTAAAACTC 58.330 43.478 0.00 0.00 0.00 3.01
1689 2171 3.514645 GACGCCTAAAACTCAATACCGA 58.485 45.455 0.00 0.00 0.00 4.69
1713 2195 1.686587 CTCCACCCCCAAAACTGAAAC 59.313 52.381 0.00 0.00 0.00 2.78
1743 2225 2.068831 TTCTGGGTATTGGGAGGGTT 57.931 50.000 0.00 0.00 0.00 4.11
1750 2232 2.369394 GTATTGGGAGGGTTGCTTCTG 58.631 52.381 0.00 0.00 0.00 3.02
1758 2240 3.614092 GAGGGTTGCTTCTGAATGATGA 58.386 45.455 0.00 0.00 0.00 2.92
1775 2257 5.269554 TGATGACCAAAACTTAATCCCCT 57.730 39.130 0.00 0.00 0.00 4.79
1779 2261 7.898636 TGATGACCAAAACTTAATCCCCTAAAT 59.101 33.333 0.00 0.00 0.00 1.40
1817 2301 3.988379 TCTCCAACTTTGTGCATTCAC 57.012 42.857 0.00 0.00 43.40 3.18
1829 2313 7.874016 ACTTTGTGCATTCACATGAACATATTT 59.126 29.630 0.00 0.00 46.78 1.40
1868 2352 6.647481 ACACATGAACATCATTTGAACATTGG 59.353 34.615 12.11 0.00 36.85 3.16
1902 2386 8.402472 GTTAAGCACAATGCCAACTACATAATA 58.598 33.333 0.00 0.00 46.52 0.98
2054 2548 0.178068 TTGCGAGCCTCCTCATTACC 59.822 55.000 0.00 0.00 38.00 2.85
2113 2607 4.843728 ACCATTACCGATCACAGAACATT 58.156 39.130 0.00 0.00 0.00 2.71
2144 2638 3.444742 TGAATAGCACATCAAGCCCAAAG 59.555 43.478 0.00 0.00 0.00 2.77
2147 2641 0.529378 GCACATCAAGCCCAAAGGAG 59.471 55.000 0.00 0.00 33.47 3.69
2177 2671 6.809630 AAGAGAAGAGAAACTAATGCCAAC 57.190 37.500 0.00 0.00 0.00 3.77
2178 2672 5.869579 AGAGAAGAGAAACTAATGCCAACA 58.130 37.500 0.00 0.00 0.00 3.33
2182 2676 4.385825 AGAGAAACTAATGCCAACAACGA 58.614 39.130 0.00 0.00 0.00 3.85
2189 2683 1.674359 ATGCCAACAACGACAACTCA 58.326 45.000 0.00 0.00 0.00 3.41
2193 2687 1.267832 CCAACAACGACAACTCAACGG 60.268 52.381 0.00 0.00 0.00 4.44
2197 2691 1.931172 CAACGACAACTCAACGGAACT 59.069 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.210967 CCCTTTAGTGCCGGTTCCATA 59.789 52.381 1.90 0.00 0.00 2.74
1 2 0.034477 CCCTTTAGTGCCGGTTCCAT 60.034 55.000 1.90 0.00 0.00 3.41
2 3 1.377229 CCCTTTAGTGCCGGTTCCA 59.623 57.895 1.90 0.00 0.00 3.53
3 4 2.044555 GCCCTTTAGTGCCGGTTCC 61.045 63.158 1.90 0.00 0.00 3.62
4 5 2.044555 GGCCCTTTAGTGCCGGTTC 61.045 63.158 1.90 0.00 38.00 3.62
10 11 1.736126 GTTCGTAAGGCCCTTTAGTGC 59.264 52.381 0.00 0.00 38.47 4.40
11 12 2.353323 GGTTCGTAAGGCCCTTTAGTG 58.647 52.381 0.00 0.00 38.47 2.74
12 13 1.066645 CGGTTCGTAAGGCCCTTTAGT 60.067 52.381 0.00 0.00 38.47 2.24
13 14 1.648504 CGGTTCGTAAGGCCCTTTAG 58.351 55.000 0.00 0.00 38.47 1.85
14 15 0.249955 CCGGTTCGTAAGGCCCTTTA 59.750 55.000 0.00 0.00 38.47 1.85
15 16 1.002990 CCGGTTCGTAAGGCCCTTT 60.003 57.895 0.00 0.00 38.47 3.11
16 17 2.219164 ACCGGTTCGTAAGGCCCTT 61.219 57.895 0.00 0.00 38.47 3.95
17 18 2.605601 ACCGGTTCGTAAGGCCCT 60.606 61.111 0.00 0.00 38.47 5.19
18 19 2.435410 CACCGGTTCGTAAGGCCC 60.435 66.667 2.97 0.00 38.47 5.80
19 20 2.229690 TAGCACCGGTTCGTAAGGCC 62.230 60.000 2.97 0.00 38.47 5.19
20 21 0.179092 ATAGCACCGGTTCGTAAGGC 60.179 55.000 2.97 2.83 38.47 4.35
21 22 1.931172 CAATAGCACCGGTTCGTAAGG 59.069 52.381 2.97 0.00 38.47 2.69
22 23 1.326548 GCAATAGCACCGGTTCGTAAG 59.673 52.381 2.97 0.00 41.58 2.34
23 24 1.361793 GCAATAGCACCGGTTCGTAA 58.638 50.000 2.97 0.00 41.58 3.18
24 25 0.460635 GGCAATAGCACCGGTTCGTA 60.461 55.000 2.97 0.00 44.61 3.43
25 26 1.743995 GGCAATAGCACCGGTTCGT 60.744 57.895 2.97 0.00 44.61 3.85
26 27 2.469516 GGGCAATAGCACCGGTTCG 61.470 63.158 2.97 0.00 44.61 3.95
27 28 2.469516 CGGGCAATAGCACCGGTTC 61.470 63.158 2.97 0.00 45.12 3.62
28 29 2.437716 CGGGCAATAGCACCGGTT 60.438 61.111 2.97 0.00 45.12 4.44
32 33 1.077716 AGAACCGGGCAATAGCACC 60.078 57.895 6.32 0.00 42.77 5.01
33 34 1.993369 GCAGAACCGGGCAATAGCAC 61.993 60.000 6.32 0.00 44.61 4.40
34 35 1.748879 GCAGAACCGGGCAATAGCA 60.749 57.895 6.32 0.00 44.61 3.49
35 36 1.748879 TGCAGAACCGGGCAATAGC 60.749 57.895 6.32 2.35 37.03 2.97
36 37 0.392998 AGTGCAGAACCGGGCAATAG 60.393 55.000 6.32 0.00 42.45 1.73
37 38 0.906066 TAGTGCAGAACCGGGCAATA 59.094 50.000 6.32 6.43 42.45 1.90
38 39 0.392998 CTAGTGCAGAACCGGGCAAT 60.393 55.000 6.32 7.58 42.45 3.56
39 40 1.003839 CTAGTGCAGAACCGGGCAA 60.004 57.895 6.32 0.00 42.45 4.52
40 41 2.214216 ACTAGTGCAGAACCGGGCA 61.214 57.895 6.32 1.81 37.77 5.36
41 42 1.741770 CACTAGTGCAGAACCGGGC 60.742 63.158 10.54 0.00 0.00 6.13
42 43 0.537188 ATCACTAGTGCAGAACCGGG 59.463 55.000 18.45 0.00 0.00 5.73
43 44 3.735237 ATATCACTAGTGCAGAACCGG 57.265 47.619 18.45 0.00 0.00 5.28
44 45 7.715265 AATTTATATCACTAGTGCAGAACCG 57.285 36.000 18.45 0.00 0.00 4.44
45 46 9.109393 TGAAATTTATATCACTAGTGCAGAACC 57.891 33.333 18.45 1.37 0.00 3.62
443 453 1.376037 AAAGCTCCGCCACTGCTAC 60.376 57.895 0.00 0.00 35.85 3.58
444 454 1.375908 CAAAGCTCCGCCACTGCTA 60.376 57.895 0.00 0.00 35.85 3.49
445 455 2.670934 CAAAGCTCCGCCACTGCT 60.671 61.111 0.00 0.00 38.87 4.24
446 456 2.980233 ACAAAGCTCCGCCACTGC 60.980 61.111 0.00 0.00 0.00 4.40
447 457 2.620112 CCACAAAGCTCCGCCACTG 61.620 63.158 0.00 0.00 0.00 3.66
448 458 2.281761 CCACAAAGCTCCGCCACT 60.282 61.111 0.00 0.00 0.00 4.00
449 459 3.365265 CCCACAAAGCTCCGCCAC 61.365 66.667 0.00 0.00 0.00 5.01
450 460 4.659172 CCCCACAAAGCTCCGCCA 62.659 66.667 0.00 0.00 0.00 5.69
454 464 3.826265 TTGGCCCCCACAAAGCTCC 62.826 63.158 0.00 0.00 30.78 4.70
455 465 2.203625 TTGGCCCCCACAAAGCTC 60.204 61.111 0.00 0.00 30.78 4.09
456 466 2.524148 GTTGGCCCCCACAAAGCT 60.524 61.111 0.00 0.00 30.78 3.74
457 467 3.625897 GGTTGGCCCCCACAAAGC 61.626 66.667 0.00 0.00 30.78 3.51
458 468 2.201210 AGGTTGGCCCCCACAAAG 59.799 61.111 10.93 0.00 30.78 2.77
459 469 2.123077 CAGGTTGGCCCCCACAAA 60.123 61.111 10.93 0.00 30.78 2.83
460 470 4.232061 CCAGGTTGGCCCCCACAA 62.232 66.667 10.93 0.00 30.78 3.33
486 496 4.202503 ACATGTATTCTTATGAGCTGGGGG 60.203 45.833 0.00 0.00 0.00 5.40
487 497 4.978099 ACATGTATTCTTATGAGCTGGGG 58.022 43.478 0.00 0.00 0.00 4.96
546 556 8.662141 GCAAACATGATTATTTTCAGCTGATTT 58.338 29.630 19.04 7.45 0.00 2.17
547 557 7.279313 GGCAAACATGATTATTTTCAGCTGATT 59.721 33.333 19.04 8.36 0.00 2.57
548 558 6.759827 GGCAAACATGATTATTTTCAGCTGAT 59.240 34.615 19.04 5.26 0.00 2.90
549 559 6.101332 GGCAAACATGATTATTTTCAGCTGA 58.899 36.000 13.74 13.74 0.00 4.26
550 560 5.292589 GGGCAAACATGATTATTTTCAGCTG 59.707 40.000 7.63 7.63 0.00 4.24
551 561 5.422145 GGGCAAACATGATTATTTTCAGCT 58.578 37.500 0.00 0.00 0.00 4.24
552 562 4.571984 GGGGCAAACATGATTATTTTCAGC 59.428 41.667 0.00 0.00 0.00 4.26
553 563 5.118286 GGGGGCAAACATGATTATTTTCAG 58.882 41.667 0.00 0.00 0.00 3.02
554 564 5.096443 GGGGGCAAACATGATTATTTTCA 57.904 39.130 0.00 0.00 0.00 2.69
593 603 0.537371 GTAGAAATCATGGGCGGGGG 60.537 60.000 0.00 0.00 0.00 5.40
594 604 0.474184 AGTAGAAATCATGGGCGGGG 59.526 55.000 0.00 0.00 0.00 5.73
595 605 1.140852 TGAGTAGAAATCATGGGCGGG 59.859 52.381 0.00 0.00 0.00 6.13
596 606 2.620251 TGAGTAGAAATCATGGGCGG 57.380 50.000 0.00 0.00 0.00 6.13
597 607 2.289002 GCTTGAGTAGAAATCATGGGCG 59.711 50.000 0.00 0.00 0.00 6.13
598 608 3.549794 AGCTTGAGTAGAAATCATGGGC 58.450 45.455 0.00 0.00 0.00 5.36
599 609 4.815308 CAGAGCTTGAGTAGAAATCATGGG 59.185 45.833 0.00 0.00 0.00 4.00
600 610 4.272991 GCAGAGCTTGAGTAGAAATCATGG 59.727 45.833 0.00 0.00 0.00 3.66
601 611 4.272991 GGCAGAGCTTGAGTAGAAATCATG 59.727 45.833 0.00 0.00 0.00 3.07
602 612 4.080695 TGGCAGAGCTTGAGTAGAAATCAT 60.081 41.667 0.00 0.00 0.00 2.45
603 613 3.261643 TGGCAGAGCTTGAGTAGAAATCA 59.738 43.478 0.00 0.00 0.00 2.57
604 614 3.620821 GTGGCAGAGCTTGAGTAGAAATC 59.379 47.826 0.00 0.00 0.00 2.17
605 615 3.262915 AGTGGCAGAGCTTGAGTAGAAAT 59.737 43.478 0.00 0.00 0.00 2.17
606 616 2.634940 AGTGGCAGAGCTTGAGTAGAAA 59.365 45.455 0.00 0.00 0.00 2.52
607 617 2.028658 CAGTGGCAGAGCTTGAGTAGAA 60.029 50.000 0.00 0.00 0.00 2.10
608 618 1.547820 CAGTGGCAGAGCTTGAGTAGA 59.452 52.381 0.00 0.00 0.00 2.59
609 619 1.547820 TCAGTGGCAGAGCTTGAGTAG 59.452 52.381 0.00 0.00 0.00 2.57
610 620 1.273606 GTCAGTGGCAGAGCTTGAGTA 59.726 52.381 0.00 0.00 0.00 2.59
611 621 0.034616 GTCAGTGGCAGAGCTTGAGT 59.965 55.000 0.00 0.00 0.00 3.41
612 622 1.013005 CGTCAGTGGCAGAGCTTGAG 61.013 60.000 0.00 0.00 0.00 3.02
613 623 1.005748 CGTCAGTGGCAGAGCTTGA 60.006 57.895 0.00 0.00 0.00 3.02
614 624 1.005748 TCGTCAGTGGCAGAGCTTG 60.006 57.895 0.00 0.00 0.00 4.01
615 625 1.291588 CTCGTCAGTGGCAGAGCTT 59.708 57.895 0.00 0.00 0.00 3.74
616 626 0.609406 TACTCGTCAGTGGCAGAGCT 60.609 55.000 13.94 0.00 33.62 4.09
617 627 0.179150 CTACTCGTCAGTGGCAGAGC 60.179 60.000 13.94 0.00 33.62 4.09
618 628 1.169577 ACTACTCGTCAGTGGCAGAG 58.830 55.000 12.87 12.87 34.43 3.35
619 629 2.082231 GTACTACTCGTCAGTGGCAGA 58.918 52.381 0.00 0.00 34.43 4.26
620 630 2.085320 AGTACTACTCGTCAGTGGCAG 58.915 52.381 0.00 0.00 34.43 4.85
621 631 2.195741 AGTACTACTCGTCAGTGGCA 57.804 50.000 0.00 0.00 34.43 4.92
622 632 4.096081 ACAATAGTACTACTCGTCAGTGGC 59.904 45.833 4.31 0.00 34.43 5.01
623 633 5.814764 ACAATAGTACTACTCGTCAGTGG 57.185 43.478 4.31 0.00 37.15 4.00
624 634 6.839033 TCAACAATAGTACTACTCGTCAGTG 58.161 40.000 4.31 0.00 33.62 3.66
625 635 7.627298 ATCAACAATAGTACTACTCGTCAGT 57.373 36.000 4.31 0.00 36.55 3.41
626 636 9.999009 TTTATCAACAATAGTACTACTCGTCAG 57.001 33.333 4.31 0.65 0.00 3.51
627 637 9.778993 GTTTATCAACAATAGTACTACTCGTCA 57.221 33.333 4.31 0.00 32.54 4.35
628 638 9.778993 TGTTTATCAACAATAGTACTACTCGTC 57.221 33.333 4.31 0.00 40.10 4.20
632 642 9.884636 TGCATGTTTATCAACAATAGTACTACT 57.115 29.630 4.31 0.00 46.17 2.57
710 723 5.221263 CGTAAGCATACAGGTAGAAGGACAT 60.221 44.000 0.00 0.00 32.02 3.06
724 737 8.451748 TGTCATCATCTATCTACGTAAGCATAC 58.548 37.037 0.00 0.00 45.62 2.39
813 826 4.028268 CGCGACGACGACTTCATATTTAAA 60.028 41.667 12.29 0.00 42.66 1.52
815 828 3.031126 CGCGACGACGACTTCATATTTA 58.969 45.455 12.29 0.00 42.66 1.40
837 850 4.015331 GGTTTACGCTTTTATTACGACGC 58.985 43.478 0.00 0.00 0.00 5.19
912 1334 4.880120 TGAAAGATGATCATGACCAAGAGC 59.120 41.667 14.30 0.00 0.00 4.09
913 1335 7.499563 AGAATGAAAGATGATCATGACCAAGAG 59.500 37.037 14.30 0.00 37.58 2.85
954 1376 8.341173 CAGAGACACAAGCATAGGAATTTTATC 58.659 37.037 0.00 0.00 0.00 1.75
957 1379 6.006449 ACAGAGACACAAGCATAGGAATTTT 58.994 36.000 0.00 0.00 0.00 1.82
970 1392 9.042008 GTCTAAATTAACTTGACAGAGACACAA 57.958 33.333 0.00 0.00 32.82 3.33
992 1414 4.040339 TCAGTTGCTCTTTCATGGTGTCTA 59.960 41.667 0.00 0.00 0.00 2.59
1023 1445 5.129368 AGGCAGCCAAAATCTTAATCCTA 57.871 39.130 15.80 0.00 0.00 2.94
1035 1457 2.123338 ACCAGCAAGGCAGCCAAA 60.123 55.556 15.80 0.00 43.14 3.28
1274 1696 0.318762 GGGCGAACAGAACAGTCTCT 59.681 55.000 0.00 0.00 28.78 3.10
1318 1742 5.645067 GCTGCTGGCATCTATACAATATGAA 59.355 40.000 0.00 0.00 41.35 2.57
1376 1800 2.639839 ACTCTTCCCTTAAGCAGCTTCA 59.360 45.455 12.07 0.00 34.97 3.02
1377 1801 3.342377 ACTCTTCCCTTAAGCAGCTTC 57.658 47.619 12.07 0.00 34.97 3.86
1411 1835 8.208718 TGTGAGGATGTAAATAACAAGCATAC 57.791 34.615 0.00 0.00 42.70 2.39
1456 1880 8.660373 ACATAGCTCTTCTTTATTCTTCAAACG 58.340 33.333 0.00 0.00 0.00 3.60
1464 1888 8.821894 CCTTACACACATAGCTCTTCTTTATTC 58.178 37.037 0.00 0.00 0.00 1.75
1476 1900 6.494893 TGAATGTTTCCTTACACACATAGC 57.505 37.500 0.00 0.00 0.00 2.97
1477 1901 8.267620 TCATGAATGTTTCCTTACACACATAG 57.732 34.615 0.00 0.00 31.07 2.23
1478 1902 8.806429 ATCATGAATGTTTCCTTACACACATA 57.194 30.769 0.00 0.00 31.07 2.29
1495 1950 4.260985 TGACTGCCGTGTTAATCATGAAT 58.739 39.130 0.00 0.00 35.23 2.57
1556 2012 8.250332 ACCATAAGTATGCAGTTAATTTGGTTG 58.750 33.333 0.00 0.00 32.40 3.77
1670 2152 4.932268 TTTCGGTATTGAGTTTTAGGCG 57.068 40.909 0.00 0.00 0.00 5.52
1681 2163 2.089201 GGGGTGGAGTTTTCGGTATTG 58.911 52.381 0.00 0.00 0.00 1.90
1689 2171 2.115427 CAGTTTTGGGGGTGGAGTTTT 58.885 47.619 0.00 0.00 0.00 2.43
1743 2225 4.828939 AGTTTTGGTCATCATTCAGAAGCA 59.171 37.500 0.00 0.00 0.00 3.91
1750 2232 6.381133 AGGGGATTAAGTTTTGGTCATCATTC 59.619 38.462 0.00 0.00 0.00 2.67
1758 2240 9.610104 AACTAATTTAGGGGATTAAGTTTTGGT 57.390 29.630 8.26 0.00 0.00 3.67
1795 2279 4.681744 GTGAATGCACAAAGTTGGAGAAA 58.318 39.130 0.00 0.00 44.51 2.52
1868 2352 8.190784 AGTTGGCATTGTGCTTAACTATAAATC 58.809 33.333 17.07 0.00 43.35 2.17
1876 2360 4.497473 TGTAGTTGGCATTGTGCTTAAC 57.503 40.909 1.64 7.88 44.28 2.01
1881 2365 6.969366 TCATATTATGTAGTTGGCATTGTGC 58.031 36.000 3.67 0.00 44.08 4.57
1992 2486 3.955650 TCCTCCGACAAGGACTAAAAG 57.044 47.619 0.00 0.00 45.98 2.27
2089 2583 4.647611 TGTTCTGTGATCGGTAATGGTTT 58.352 39.130 0.00 0.00 0.00 3.27
2113 2607 0.403655 TGTGCTATTCACCCCAGCAA 59.596 50.000 0.00 0.00 46.18 3.91
2144 2638 6.993079 AGTTTCTCTTCTCTTTCTCTTCTCC 58.007 40.000 0.00 0.00 0.00 3.71
2147 2641 8.655970 GCATTAGTTTCTCTTCTCTTTCTCTTC 58.344 37.037 0.00 0.00 0.00 2.87
2177 2671 1.931172 AGTTCCGTTGAGTTGTCGTTG 59.069 47.619 0.00 0.00 0.00 4.10
2178 2672 2.199236 GAGTTCCGTTGAGTTGTCGTT 58.801 47.619 0.00 0.00 0.00 3.85
2182 2676 0.748450 TCCGAGTTCCGTTGAGTTGT 59.252 50.000 0.00 0.00 36.31 3.32
2189 2683 1.595357 GGGTCATCCGAGTTCCGTT 59.405 57.895 0.00 0.00 36.31 4.44
2213 2707 1.153862 GACTCTGGAGAGCGCAGTG 60.154 63.158 11.47 0.64 45.79 3.66
2214 2708 2.695759 CGACTCTGGAGAGCGCAGT 61.696 63.158 11.47 1.04 45.79 4.40
2215 2709 2.101965 CGACTCTGGAGAGCGCAG 59.898 66.667 11.47 0.00 45.79 5.18


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

AutoCloner maintained by Alex Coulton.