Multiple sequence alignment - TraesCS5A01G558500

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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 TraesCS5A01G558500 chr5A 100.000 3037 0 0 3067 6103 709195237 709198273 0.000000e+00 5609.0
1 TraesCS5A01G558500 chr5A 97.197 3033 67 6 3074 6103 659340451 659337434 0.000000e+00 5114.0
2 TraesCS5A01G558500 chr5A 100.000 2749 0 0 1 2749 709192171 709194919 0.000000e+00 5077.0
3 TraesCS5A01G558500 chr5A 97.459 1928 24 11 810 2732 659342550 659340643 0.000000e+00 3265.0
4 TraesCS5A01G558500 chr5A 90.290 587 33 16 1 567 659343116 659342534 0.000000e+00 747.0
5 TraesCS5A01G558500 chr5A 98.585 212 1 2 616 826 709192721 709192931 2.080000e-99 374.0
6 TraesCS5A01G558500 chr5A 98.585 212 1 2 551 761 709192786 709192996 2.080000e-99 374.0
7 TraesCS5A01G558500 chr5A 98.639 147 1 1 681 826 709192721 709192867 6.070000e-65 259.0
8 TraesCS5A01G558500 chr5A 98.639 147 1 1 551 697 709192851 709192996 6.070000e-65 259.0
9 TraesCS5A01G558500 chr5A 98.780 82 1 0 745 826 709192721 709192802 4.930000e-31 147.0
10 TraesCS5A01G558500 chr5A 98.780 82 1 0 551 632 709192915 709192996 4.930000e-31 147.0
11 TraesCS5A01G558500 chr5A 90.909 55 4 1 3481 3534 709611150 709611096 8.490000e-09 73.1
12 TraesCS5A01G558500 chr4B 89.013 1966 197 8 3824 5783 671697560 671699512 0.000000e+00 2416.0
13 TraesCS5A01G558500 chr4B 83.774 1627 239 18 3536 5150 671706357 671707970 0.000000e+00 1519.0
14 TraesCS5A01G558500 chr4B 90.141 710 50 14 2048 2746 671695887 671696587 0.000000e+00 905.0
15 TraesCS5A01G558500 chr4B 84.308 701 62 26 3067 3729 671696630 671697320 5.160000e-180 641.0
16 TraesCS5A01G558500 chr4B 83.552 687 68 27 2046 2711 671705270 671705932 8.750000e-168 601.0
17 TraesCS5A01G558500 chr4B 80.464 819 89 36 810 1614 671703395 671704156 1.490000e-155 560.0
18 TraesCS5A01G558500 chr4B 92.562 363 23 1 1253 1615 671694539 671694897 9.070000e-143 518.0
19 TraesCS5A01G558500 chr4B 92.661 218 7 2 1 218 671693797 671694005 7.690000e-79 305.0
20 TraesCS5A01G558500 chr4B 87.209 258 18 9 960 1215 671694294 671694538 4.660000e-71 279.0
21 TraesCS5A01G558500 chr4B 92.228 193 10 1 1 193 671702718 671702905 1.010000e-67 268.0
22 TraesCS5A01G558500 chr4B 87.029 239 18 8 198 426 671703067 671703302 2.180000e-64 257.0
23 TraesCS5A01G558500 chr4B 89.744 156 6 5 810 962 671694118 671694266 2.250000e-44 191.0
24 TraesCS5A01G558500 chr4B 88.976 127 11 3 1052 1175 671776125 671775999 2.950000e-33 154.0
25 TraesCS5A01G558500 chr4B 89.516 124 6 1 451 567 671703288 671703411 3.810000e-32 150.0
26 TraesCS5A01G558500 chr4B 94.444 54 1 2 248 300 671693992 671694044 1.410000e-11 82.4
27 TraesCS5A01G558500 chr4B 95.745 47 2 0 521 567 671694088 671694134 6.560000e-10 76.8
28 TraesCS5A01G558500 chrUn 84.266 1627 228 24 3536 5150 28299696 28298086 0.000000e+00 1561.0
29 TraesCS5A01G558500 chrUn 80.742 836 85 42 810 1628 28302781 28302005 3.170000e-162 582.0
30 TraesCS5A01G558500 chrUn 82.994 688 71 27 2046 2711 28300900 28300237 1.140000e-161 580.0
31 TraesCS5A01G558500 chrUn 90.869 449 17 10 1 428 28303321 28302876 1.140000e-161 580.0
32 TraesCS5A01G558500 chrUn 94.886 176 7 2 1007 1181 100234002 100234176 2.170000e-69 274.0
33 TraesCS5A01G558500 chrUn 87.500 128 5 3 451 567 28302892 28302765 2.970000e-28 137.0
34 TraesCS5A01G558500 chrUn 90.385 52 5 0 874 925 100233700 100233751 1.100000e-07 69.4
35 TraesCS5A01G558500 chrUn 89.091 55 5 1 3481 3534 28955525 28955471 3.950000e-07 67.6
36 TraesCS5A01G558500 chr2D 83.236 686 71 25 2046 2711 639533233 639532572 1.890000e-164 590.0
37 TraesCS5A01G558500 chr2D 80.552 833 87 41 810 1628 639535277 639534506 6.860000e-159 571.0
38 TraesCS5A01G558500 chr2D 89.189 444 30 8 1 431 639535803 639535365 6.960000e-149 538.0
39 TraesCS5A01G558500 chr2D 76.764 581 106 19 5357 5919 109733497 109732928 1.290000e-76 298.0
40 TraesCS5A01G558500 chr2D 76.506 332 65 10 5498 5819 546874097 546873769 1.050000e-37 169.0
41 TraesCS5A01G558500 chr2D 91.129 124 4 1 451 567 639535384 639535261 1.760000e-35 161.0
42 TraesCS5A01G558500 chr2D 85.600 125 10 3 1926 2044 373883559 373883437 2.310000e-24 124.0
43 TraesCS5A01G558500 chr4D 73.499 1166 234 42 3968 5092 381558645 381559776 7.470000e-99 372.0
44 TraesCS5A01G558500 chr4D 74.086 629 117 23 5498 6101 481411661 481412268 3.700000e-52 217.0
45 TraesCS5A01G558500 chr4D 92.632 95 7 0 1076 1170 490888678 490888772 2.970000e-28 137.0
46 TraesCS5A01G558500 chr4D 76.113 247 54 4 5847 6092 46305169 46305411 2.310000e-24 124.0
47 TraesCS5A01G558500 chr6A 75.037 677 135 22 5450 6101 473355083 473354416 3.600000e-72 283.0
48 TraesCS5A01G558500 chr6A 85.246 122 10 2 1926 2041 21574606 21574725 1.070000e-22 119.0
49 TraesCS5A01G558500 chr6A 87.931 58 5 2 3469 3525 115279284 115279340 3.950000e-07 67.6
50 TraesCS5A01G558500 chr2A 79.558 362 60 10 5468 5819 689708573 689708930 4.720000e-61 246.0
51 TraesCS5A01G558500 chr2A 79.121 364 60 11 5468 5819 690411642 690411283 2.840000e-58 237.0
52 TraesCS5A01G558500 chr2A 84.800 125 11 7 1926 2044 419206853 419206975 1.070000e-22 119.0
53 TraesCS5A01G558500 chr7D 79.179 341 58 11 5468 5801 68982116 68981782 2.210000e-54 224.0
54 TraesCS5A01G558500 chr7A 75.446 505 96 15 5599 6081 260024282 260024780 2.860000e-53 220.0
55 TraesCS5A01G558500 chr7A 75.630 476 88 22 5339 5802 70891251 70891710 1.720000e-50 211.0
56 TraesCS5A01G558500 chr5D 77.838 370 59 15 5282 5645 416877983 416878335 2.230000e-49 207.0
57 TraesCS5A01G558500 chr5D 84.000 125 12 3 1926 2044 526253958 526253836 5.000000e-21 113.0
58 TraesCS5A01G558500 chr5D 88.889 54 4 2 5342 5394 399848852 399848800 1.420000e-06 65.8
59 TraesCS5A01G558500 chr7B 77.656 273 47 11 5654 5924 219591001 219591261 2.950000e-33 154.0
60 TraesCS5A01G558500 chr7B 83.206 131 14 5 1926 2050 443741521 443741393 5.000000e-21 113.0
61 TraesCS5A01G558500 chr7B 84.058 69 10 1 3463 3531 684471669 684471736 1.420000e-06 65.8
62 TraesCS5A01G558500 chr3D 84.733 131 12 4 1926 2050 540564870 540564742 2.310000e-24 124.0
63 TraesCS5A01G558500 chr3D 100.000 29 0 0 2715 2743 586364365 586364337 3.000000e-03 54.7
64 TraesCS5A01G558500 chr6B 83.594 128 13 3 1926 2047 481857975 481857850 5.000000e-21 113.0
65 TraesCS5A01G558500 chr6B 90.385 52 5 0 3480 3531 112909185 112909134 1.100000e-07 69.4
66 TraesCS5A01G558500 chr6B 97.297 37 0 1 2711 2746 712179750 712179786 1.840000e-05 62.1
67 TraesCS5A01G558500 chr2B 84.127 126 10 5 1926 2044 25187133 25187255 5.000000e-21 113.0
68 TraesCS5A01G558500 chr2B 95.238 42 2 0 5342 5383 356304893 356304852 3.950000e-07 67.6
69 TraesCS5A01G558500 chr2B 92.857 42 3 0 5342 5383 356257820 356257779 1.840000e-05 62.1
70 TraesCS5A01G558500 chr1D 90.476 63 4 2 3481 3542 388640493 388640432 1.410000e-11 82.4
71 TraesCS5A01G558500 chr1B 90.476 63 4 2 3481 3542 522012338 522012277 1.410000e-11 82.4
72 TraesCS5A01G558500 chr1A 90.476 63 4 2 3481 3542 487730701 487730640 1.410000e-11 82.4
73 TraesCS5A01G558500 chr3A 96.970 33 1 0 2711 2743 202655893 202655861 8.550000e-04 56.5


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 TraesCS5A01G558500 chr5A 709192171 709198273 6102 False 1530.750000 5609 99.0010 1 6103 8 chr5A.!!$F1 6102
1 TraesCS5A01G558500 chr5A 659337434 659343116 5682 True 3042.000000 5114 94.9820 1 6103 3 chr5A.!!$R2 6102
2 TraesCS5A01G558500 chr4B 671693797 671707970 14173 False 584.613333 2416 88.8260 1 5783 15 chr4B.!!$F1 5782
3 TraesCS5A01G558500 chrUn 28298086 28303321 5235 True 688.000000 1561 85.2742 1 5150 5 chrUn.!!$R2 5149
4 TraesCS5A01G558500 chr2D 639532572 639535803 3231 True 465.000000 590 86.0265 1 2711 4 chr2D.!!$R4 2710
5 TraesCS5A01G558500 chr2D 109732928 109733497 569 True 298.000000 298 76.7640 5357 5919 1 chr2D.!!$R1 562
6 TraesCS5A01G558500 chr4D 381558645 381559776 1131 False 372.000000 372 73.4990 3968 5092 1 chr4D.!!$F2 1124
7 TraesCS5A01G558500 chr4D 481411661 481412268 607 False 217.000000 217 74.0860 5498 6101 1 chr4D.!!$F3 603
8 TraesCS5A01G558500 chr6A 473354416 473355083 667 True 283.000000 283 75.0370 5450 6101 1 chr6A.!!$R1 651

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
610 671 0.037512 CGGGCCTCTGCATCAGATAG 60.038 60.0 0.84 0.0 39.92 2.08 F
804 865 0.037512 CGGGCCTCTGCATCAGATAG 60.038 60.0 0.84 0.0 39.92 2.08 F
864 925 1.030488 TCCTCTCTAACGGGAGCACG 61.030 60.0 0.00 0.0 40.31 5.34 F
2618 4187 0.261696 CCCACCCCTCCCAAATTAGG 59.738 60.0 0.00 0.0 0.00 2.69 F
3974 5949 0.916086 ACAATGTCGCCAAGGGGATA 59.084 50.0 9.20 7.1 39.24 2.59 F
4658 6660 0.918983 GGGGATCCATGAGGTTGTCA 59.081 55.0 15.23 0.0 40.38 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 2480 0.656259 CTGAATGCACGCATCTCCAG 59.344 55.000 4.73 9.25 35.31 3.86 R
2593 4162 1.844296 TTGGGAGGGGTGGGGAGTAT 61.844 60.000 0.00 0.00 0.00 2.12 R
3124 4700 7.648510 CACTTACGAAGGATTCTACATAAGTCC 59.351 40.741 0.00 0.00 44.75 3.85 R
4803 6805 0.591170 CACCCGTGTCATCAACAACC 59.409 55.000 0.00 0.00 40.31 3.77 R
4918 6920 2.125512 GTTGGTGCGATCGAGGCT 60.126 61.111 21.57 0.00 0.00 4.58 R
5632 7656 4.232188 AGAGTCTACGGATACAAGGACA 57.768 45.455 0.00 0.00 32.52 4.02 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
248 253 2.035066 GGACTTTTGCATTGTGTCTGCT 59.965 45.455 0.00 0.00 40.34 4.24
422 460 4.981806 TGCCTTAAATGGAGTATGTTGC 57.018 40.909 0.00 0.00 0.00 4.17
555 616 6.966534 ATATAACTTGCCTTGGATTCTTGG 57.033 37.500 0.00 0.00 0.00 3.61
556 617 1.260544 ACTTGCCTTGGATTCTTGGC 58.739 50.000 0.00 0.00 45.10 4.52
557 618 0.533951 CTTGCCTTGGATTCTTGGCC 59.466 55.000 0.00 0.00 44.32 5.36
558 619 0.114954 TTGCCTTGGATTCTTGGCCT 59.885 50.000 3.32 0.00 44.32 5.19
559 620 0.612732 TGCCTTGGATTCTTGGCCTG 60.613 55.000 3.32 0.00 44.32 4.85
560 621 0.613012 GCCTTGGATTCTTGGCCTGT 60.613 55.000 3.32 0.00 39.49 4.00
561 622 1.928868 CCTTGGATTCTTGGCCTGTT 58.071 50.000 3.32 0.00 0.00 3.16
562 623 2.250924 CCTTGGATTCTTGGCCTGTTT 58.749 47.619 3.32 0.00 0.00 2.83
563 624 2.634453 CCTTGGATTCTTGGCCTGTTTT 59.366 45.455 3.32 0.00 0.00 2.43
564 625 3.306294 CCTTGGATTCTTGGCCTGTTTTC 60.306 47.826 3.32 0.00 0.00 2.29
565 626 1.885887 TGGATTCTTGGCCTGTTTTCG 59.114 47.619 3.32 0.00 0.00 3.46
566 627 1.886542 GGATTCTTGGCCTGTTTTCGT 59.113 47.619 3.32 0.00 0.00 3.85
567 628 2.296190 GGATTCTTGGCCTGTTTTCGTT 59.704 45.455 3.32 0.00 0.00 3.85
568 629 3.243737 GGATTCTTGGCCTGTTTTCGTTT 60.244 43.478 3.32 0.00 0.00 3.60
569 630 3.878160 TTCTTGGCCTGTTTTCGTTTT 57.122 38.095 3.32 0.00 0.00 2.43
570 631 3.878160 TCTTGGCCTGTTTTCGTTTTT 57.122 38.095 3.32 0.00 0.00 1.94
603 664 3.801997 CTTCCCGGGCCTCTGCAT 61.802 66.667 18.49 0.00 40.13 3.96
604 665 3.764160 CTTCCCGGGCCTCTGCATC 62.764 68.421 18.49 0.00 40.13 3.91
606 667 4.559063 CCCGGGCCTCTGCATCAG 62.559 72.222 8.08 0.00 40.13 2.90
607 668 3.473647 CCGGGCCTCTGCATCAGA 61.474 66.667 0.84 0.00 38.25 3.27
608 669 2.815945 CCGGGCCTCTGCATCAGAT 61.816 63.158 0.84 0.00 39.92 2.90
609 670 1.475169 CCGGGCCTCTGCATCAGATA 61.475 60.000 0.84 0.00 39.92 1.98
610 671 0.037512 CGGGCCTCTGCATCAGATAG 60.038 60.000 0.84 0.00 39.92 2.08
611 672 1.346062 GGGCCTCTGCATCAGATAGA 58.654 55.000 0.84 0.00 39.92 1.98
612 673 1.907936 GGGCCTCTGCATCAGATAGAT 59.092 52.381 0.84 0.00 39.92 1.98
622 683 3.336468 CATCAGATAGATGCTCTTGGCC 58.664 50.000 0.00 0.00 46.90 5.36
623 684 2.687297 TCAGATAGATGCTCTTGGCCT 58.313 47.619 3.32 0.00 40.92 5.19
624 685 2.367894 TCAGATAGATGCTCTTGGCCTG 59.632 50.000 3.32 0.00 40.92 4.85
625 686 2.104451 CAGATAGATGCTCTTGGCCTGT 59.896 50.000 3.32 0.00 40.92 4.00
626 687 2.776536 AGATAGATGCTCTTGGCCTGTT 59.223 45.455 3.32 0.00 40.92 3.16
627 688 3.201708 AGATAGATGCTCTTGGCCTGTTT 59.798 43.478 3.32 0.00 40.92 2.83
628 689 2.299326 AGATGCTCTTGGCCTGTTTT 57.701 45.000 3.32 0.00 40.92 2.43
629 690 2.165998 AGATGCTCTTGGCCTGTTTTC 58.834 47.619 3.32 0.00 40.92 2.29
630 691 0.883833 ATGCTCTTGGCCTGTTTTCG 59.116 50.000 3.32 0.00 40.92 3.46
631 692 0.465460 TGCTCTTGGCCTGTTTTCGT 60.465 50.000 3.32 0.00 40.92 3.85
632 693 0.668535 GCTCTTGGCCTGTTTTCGTT 59.331 50.000 3.32 0.00 34.27 3.85
633 694 1.067060 GCTCTTGGCCTGTTTTCGTTT 59.933 47.619 3.32 0.00 34.27 3.60
634 695 2.481276 GCTCTTGGCCTGTTTTCGTTTT 60.481 45.455 3.32 0.00 34.27 2.43
635 696 3.780902 CTCTTGGCCTGTTTTCGTTTTT 58.219 40.909 3.32 0.00 0.00 1.94
668 729 3.801997 CTTCCCGGGCCTCTGCAT 61.802 66.667 18.49 0.00 40.13 3.96
669 730 3.764160 CTTCCCGGGCCTCTGCATC 62.764 68.421 18.49 0.00 40.13 3.91
671 732 4.559063 CCCGGGCCTCTGCATCAG 62.559 72.222 8.08 0.00 40.13 2.90
672 733 3.473647 CCGGGCCTCTGCATCAGA 61.474 66.667 0.84 0.00 38.25 3.27
673 734 2.815945 CCGGGCCTCTGCATCAGAT 61.816 63.158 0.84 0.00 39.92 2.90
674 735 1.475169 CCGGGCCTCTGCATCAGATA 61.475 60.000 0.84 0.00 39.92 1.98
675 736 0.037512 CGGGCCTCTGCATCAGATAG 60.038 60.000 0.84 0.00 39.92 2.08
676 737 1.346062 GGGCCTCTGCATCAGATAGA 58.654 55.000 0.84 0.00 39.92 1.98
677 738 1.907936 GGGCCTCTGCATCAGATAGAT 59.092 52.381 0.84 0.00 39.92 1.98
687 748 3.336468 CATCAGATAGATGCTCTTGGCC 58.664 50.000 0.00 0.00 46.90 5.36
688 749 2.687297 TCAGATAGATGCTCTTGGCCT 58.313 47.619 3.32 0.00 40.92 5.19
689 750 2.367894 TCAGATAGATGCTCTTGGCCTG 59.632 50.000 3.32 0.00 40.92 4.85
690 751 2.104451 CAGATAGATGCTCTTGGCCTGT 59.896 50.000 3.32 0.00 40.92 4.00
691 752 2.776536 AGATAGATGCTCTTGGCCTGTT 59.223 45.455 3.32 0.00 40.92 3.16
692 753 3.201708 AGATAGATGCTCTTGGCCTGTTT 59.798 43.478 3.32 0.00 40.92 2.83
693 754 2.299326 AGATGCTCTTGGCCTGTTTT 57.701 45.000 3.32 0.00 40.92 2.43
694 755 2.165998 AGATGCTCTTGGCCTGTTTTC 58.834 47.619 3.32 0.00 40.92 2.29
695 756 0.883833 ATGCTCTTGGCCTGTTTTCG 59.116 50.000 3.32 0.00 40.92 3.46
696 757 0.465460 TGCTCTTGGCCTGTTTTCGT 60.465 50.000 3.32 0.00 40.92 3.85
697 758 0.668535 GCTCTTGGCCTGTTTTCGTT 59.331 50.000 3.32 0.00 34.27 3.85
698 759 1.067060 GCTCTTGGCCTGTTTTCGTTT 59.933 47.619 3.32 0.00 34.27 3.60
699 760 2.481276 GCTCTTGGCCTGTTTTCGTTTT 60.481 45.455 3.32 0.00 34.27 2.43
700 761 3.780902 CTCTTGGCCTGTTTTCGTTTTT 58.219 40.909 3.32 0.00 0.00 1.94
716 777 2.375014 TTTTTCTCGAAAAGGGGGCT 57.625 45.000 5.15 0.00 40.83 5.19
717 778 2.375014 TTTTCTCGAAAAGGGGGCTT 57.625 45.000 0.93 0.00 35.57 4.35
718 779 1.905637 TTTCTCGAAAAGGGGGCTTC 58.094 50.000 0.00 0.00 0.00 3.86
719 780 0.037734 TTCTCGAAAAGGGGGCTTCC 59.962 55.000 0.00 0.00 0.00 3.46
732 793 3.801997 CTTCCCGGGCCTCTGCAT 61.802 66.667 18.49 0.00 40.13 3.96
733 794 3.764160 CTTCCCGGGCCTCTGCATC 62.764 68.421 18.49 0.00 40.13 3.91
735 796 4.559063 CCCGGGCCTCTGCATCAG 62.559 72.222 8.08 0.00 40.13 2.90
736 797 3.473647 CCGGGCCTCTGCATCAGA 61.474 66.667 0.84 0.00 38.25 3.27
737 798 2.815945 CCGGGCCTCTGCATCAGAT 61.816 63.158 0.84 0.00 39.92 2.90
738 799 1.475169 CCGGGCCTCTGCATCAGATA 61.475 60.000 0.84 0.00 39.92 1.98
739 800 0.037512 CGGGCCTCTGCATCAGATAG 60.038 60.000 0.84 0.00 39.92 2.08
740 801 1.346062 GGGCCTCTGCATCAGATAGA 58.654 55.000 0.84 0.00 39.92 1.98
741 802 1.907936 GGGCCTCTGCATCAGATAGAT 59.092 52.381 0.84 0.00 39.92 1.98
751 812 3.336468 CATCAGATAGATGCTCTTGGCC 58.664 50.000 0.00 0.00 46.90 5.36
752 813 2.687297 TCAGATAGATGCTCTTGGCCT 58.313 47.619 3.32 0.00 40.92 5.19
753 814 2.367894 TCAGATAGATGCTCTTGGCCTG 59.632 50.000 3.32 0.00 40.92 4.85
754 815 2.104451 CAGATAGATGCTCTTGGCCTGT 59.896 50.000 3.32 0.00 40.92 4.00
755 816 2.776536 AGATAGATGCTCTTGGCCTGTT 59.223 45.455 3.32 0.00 40.92 3.16
756 817 3.201708 AGATAGATGCTCTTGGCCTGTTT 59.798 43.478 3.32 0.00 40.92 2.83
757 818 2.299326 AGATGCTCTTGGCCTGTTTT 57.701 45.000 3.32 0.00 40.92 2.43
758 819 2.165998 AGATGCTCTTGGCCTGTTTTC 58.834 47.619 3.32 0.00 40.92 2.29
759 820 0.883833 ATGCTCTTGGCCTGTTTTCG 59.116 50.000 3.32 0.00 40.92 3.46
760 821 0.465460 TGCTCTTGGCCTGTTTTCGT 60.465 50.000 3.32 0.00 40.92 3.85
761 822 0.668535 GCTCTTGGCCTGTTTTCGTT 59.331 50.000 3.32 0.00 34.27 3.85
762 823 1.067060 GCTCTTGGCCTGTTTTCGTTT 59.933 47.619 3.32 0.00 34.27 3.60
763 824 2.481276 GCTCTTGGCCTGTTTTCGTTTT 60.481 45.455 3.32 0.00 34.27 2.43
764 825 3.780902 CTCTTGGCCTGTTTTCGTTTTT 58.219 40.909 3.32 0.00 0.00 1.94
797 858 3.801997 CTTCCCGGGCCTCTGCAT 61.802 66.667 18.49 0.00 40.13 3.96
798 859 3.764160 CTTCCCGGGCCTCTGCATC 62.764 68.421 18.49 0.00 40.13 3.91
800 861 4.559063 CCCGGGCCTCTGCATCAG 62.559 72.222 8.08 0.00 40.13 2.90
801 862 3.473647 CCGGGCCTCTGCATCAGA 61.474 66.667 0.84 0.00 38.25 3.27
802 863 2.815945 CCGGGCCTCTGCATCAGAT 61.816 63.158 0.84 0.00 39.92 2.90
803 864 1.475169 CCGGGCCTCTGCATCAGATA 61.475 60.000 0.84 0.00 39.92 1.98
804 865 0.037512 CGGGCCTCTGCATCAGATAG 60.038 60.000 0.84 0.00 39.92 2.08
805 866 1.346062 GGGCCTCTGCATCAGATAGA 58.654 55.000 0.84 0.00 39.92 1.98
806 867 1.907936 GGGCCTCTGCATCAGATAGAT 59.092 52.381 0.84 0.00 39.92 1.98
864 925 1.030488 TCCTCTCTAACGGGAGCACG 61.030 60.000 0.00 0.00 40.31 5.34
1022 1160 1.402062 GCAGGAAACAGCAAAGCTAGC 60.402 52.381 6.62 6.62 43.31 3.42
1027 1165 1.856265 AACAGCAAAGCTAGCGTGGC 61.856 55.000 21.01 21.01 36.40 5.01
1046 1184 1.605710 GCAATCAATGGCGCTATCAGT 59.394 47.619 6.75 0.00 0.00 3.41
1047 1185 2.807967 GCAATCAATGGCGCTATCAGTA 59.192 45.455 6.75 0.00 0.00 2.74
1048 1186 3.438087 GCAATCAATGGCGCTATCAGTAT 59.562 43.478 6.75 0.00 0.00 2.12
1050 1188 4.541973 ATCAATGGCGCTATCAGTATCA 57.458 40.909 6.75 0.00 0.00 2.15
1051 1189 3.917988 TCAATGGCGCTATCAGTATCAG 58.082 45.455 6.75 0.00 0.00 2.90
1248 1386 9.148104 CATCCATACAGAGTACATTCATGTATG 57.852 37.037 18.86 18.86 46.82 2.39
1251 1389 8.526218 CATACAGAGTACATTCATGTATGGAC 57.474 38.462 17.56 17.56 44.99 4.02
1566 1708 2.582978 GGGAAGCCGAGTGGTACC 59.417 66.667 4.43 4.43 37.67 3.34
1689 2480 4.210746 GCGCCCTAGCTAGTTTAATTGTAC 59.789 45.833 19.31 0.00 36.60 2.90
1909 2882 7.902087 AGCTAGTCTCTTGTACTTCTTTTGAT 58.098 34.615 0.00 0.00 0.00 2.57
2371 3931 3.894427 TGTGCCTTCTAGATCTCTGATCC 59.106 47.826 0.00 0.00 0.00 3.36
2593 4162 6.642707 ATTAGTGACGGTTTCAATTTCCAA 57.357 33.333 0.00 0.00 35.39 3.53
2618 4187 0.261696 CCCACCCCTCCCAAATTAGG 59.738 60.000 0.00 0.00 0.00 2.69
2631 4200 8.683615 CCTCCCAAATTAGGTTGTATAGTTTTC 58.316 37.037 0.00 0.00 0.00 2.29
2746 4322 5.582269 ACATCTACTAACAGCTACGAACGTA 59.418 40.000 6.87 6.87 0.00 3.57
2747 4323 6.259608 ACATCTACTAACAGCTACGAACGTAT 59.740 38.462 7.50 0.00 0.00 3.06
2748 4324 6.279227 TCTACTAACAGCTACGAACGTATC 57.721 41.667 7.50 4.03 0.00 2.24
3101 4677 4.289410 TCTTCCTCCATCTCCAATCACAAA 59.711 41.667 0.00 0.00 0.00 2.83
3137 4713 5.339008 AATCACGCAGGACTTATGTAGAA 57.661 39.130 0.00 0.00 0.00 2.10
3324 4924 3.243941 TGTTAGCTTTGTAGGAGCGACAA 60.244 43.478 0.00 0.00 44.71 3.18
3616 5442 4.458989 TGTCAACAATTATCCTTCACAGGC 59.541 41.667 0.00 0.00 40.58 4.85
3621 5447 4.702131 ACAATTATCCTTCACAGGCACTTC 59.298 41.667 0.00 0.00 40.58 3.01
3742 5572 2.632537 ACTGTAGGACACAATTCCCCT 58.367 47.619 0.00 0.00 36.48 4.79
3901 5876 2.037144 GCCAAGCTCCAATCCATCAAT 58.963 47.619 0.00 0.00 0.00 2.57
3974 5949 0.916086 ACAATGTCGCCAAGGGGATA 59.084 50.000 9.20 7.10 39.24 2.59
4487 6486 8.039603 TCTTCTTCGCAAATTACATACATTGT 57.960 30.769 0.00 0.00 42.62 2.71
4658 6660 0.918983 GGGGATCCATGAGGTTGTCA 59.081 55.000 15.23 0.00 40.38 3.58
4716 6718 2.303175 GAAGGTGCTAGAGACGGAGAT 58.697 52.381 0.00 0.00 0.00 2.75
4803 6805 2.825836 GCAGTGCCGATGGAAGGG 60.826 66.667 2.85 0.00 0.00 3.95
4918 6920 7.631909 ATCTCAAGATACGAGCTACTCAGCAA 61.632 42.308 0.00 0.00 40.76 3.91
5132 7140 8.806429 ATTAATATCAACAACATGACCTGACA 57.194 30.769 0.00 0.00 30.82 3.58
5133 7141 8.806429 TTAATATCAACAACATGACCTGACAT 57.194 30.769 0.00 0.00 30.82 3.06
5134 7142 7.707624 AATATCAACAACATGACCTGACATT 57.292 32.000 0.00 0.00 30.82 2.71
5135 7143 4.834357 TCAACAACATGACCTGACATTG 57.166 40.909 0.00 0.00 0.00 2.82
5136 7144 3.569277 TCAACAACATGACCTGACATTGG 59.431 43.478 0.00 0.00 0.00 3.16
5137 7145 3.228188 ACAACATGACCTGACATTGGT 57.772 42.857 0.00 0.00 41.07 3.67
5138 7146 4.365514 ACAACATGACCTGACATTGGTA 57.634 40.909 0.00 0.00 38.03 3.25
5139 7147 4.326826 ACAACATGACCTGACATTGGTAG 58.673 43.478 0.00 0.00 38.03 3.18
5140 7148 3.634397 ACATGACCTGACATTGGTAGG 57.366 47.619 0.00 6.85 38.03 3.18
5141 7149 2.239654 ACATGACCTGACATTGGTAGGG 59.760 50.000 0.00 1.05 38.03 3.53
5280 7299 3.056536 TCTGATGGAGCACTTGTCTACAC 60.057 47.826 0.00 0.00 0.00 2.90
5344 7363 5.130350 TGGTCCAAAACTTAGAAAGTGAGG 58.870 41.667 0.00 0.00 41.91 3.86
5418 7437 8.377034 TGGTTGGAATTGATGATTGAAAGAAAT 58.623 29.630 0.00 0.00 0.00 2.17
5578 7602 7.484140 TGTGAACAAGTTACAATTGTGCAATA 58.516 30.769 21.42 0.00 45.52 1.90
6094 13804 5.068636 AGATGGATCACAATCATGTTAGGC 58.931 41.667 0.00 0.00 37.82 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
309 347 0.103930 TCCATATTAGCCCCAGCCCT 60.104 55.000 0.00 0.00 41.25 5.19
446 496 3.197983 ACACCTAGCAACATACTCTTCCC 59.802 47.826 0.00 0.00 0.00 3.97
586 647 3.764160 GATGCAGAGGCCCGGGAAG 62.764 68.421 29.31 9.33 40.13 3.46
587 648 3.797353 GATGCAGAGGCCCGGGAA 61.797 66.667 29.31 0.00 40.13 3.97
589 650 4.559063 CTGATGCAGAGGCCCGGG 62.559 72.222 19.09 19.09 40.13 5.73
590 651 1.475169 TATCTGATGCAGAGGCCCGG 61.475 60.000 0.00 0.00 44.08 5.73
591 652 0.037512 CTATCTGATGCAGAGGCCCG 60.038 60.000 0.00 0.00 44.08 6.13
592 653 1.346062 TCTATCTGATGCAGAGGCCC 58.654 55.000 0.00 0.00 44.08 5.80
593 654 2.975266 CATCTATCTGATGCAGAGGCC 58.025 52.381 0.00 0.00 44.08 5.19
610 671 1.135575 CGAAAACAGGCCAAGAGCATC 60.136 52.381 5.01 0.00 46.50 3.91
611 672 0.883833 CGAAAACAGGCCAAGAGCAT 59.116 50.000 5.01 0.00 46.50 3.79
612 673 0.465460 ACGAAAACAGGCCAAGAGCA 60.465 50.000 5.01 0.00 46.50 4.26
613 674 0.668535 AACGAAAACAGGCCAAGAGC 59.331 50.000 5.01 0.00 42.60 4.09
614 675 3.436700 AAAACGAAAACAGGCCAAGAG 57.563 42.857 5.01 0.00 0.00 2.85
615 676 3.878160 AAAAACGAAAACAGGCCAAGA 57.122 38.095 5.01 0.00 0.00 3.02
651 712 3.764160 GATGCAGAGGCCCGGGAAG 62.764 68.421 29.31 9.33 40.13 3.46
652 713 3.797353 GATGCAGAGGCCCGGGAA 61.797 66.667 29.31 0.00 40.13 3.97
654 715 4.559063 CTGATGCAGAGGCCCGGG 62.559 72.222 19.09 19.09 40.13 5.73
655 716 1.475169 TATCTGATGCAGAGGCCCGG 61.475 60.000 0.00 0.00 44.08 5.73
656 717 0.037512 CTATCTGATGCAGAGGCCCG 60.038 60.000 0.00 0.00 44.08 6.13
657 718 1.346062 TCTATCTGATGCAGAGGCCC 58.654 55.000 0.00 0.00 44.08 5.80
658 719 2.975266 CATCTATCTGATGCAGAGGCC 58.025 52.381 0.00 0.00 44.08 5.19
675 736 1.135575 CGAAAACAGGCCAAGAGCATC 60.136 52.381 5.01 0.00 46.50 3.91
676 737 0.883833 CGAAAACAGGCCAAGAGCAT 59.116 50.000 5.01 0.00 46.50 3.79
677 738 0.465460 ACGAAAACAGGCCAAGAGCA 60.465 50.000 5.01 0.00 46.50 4.26
678 739 0.668535 AACGAAAACAGGCCAAGAGC 59.331 50.000 5.01 0.00 42.60 4.09
679 740 3.436700 AAAACGAAAACAGGCCAAGAG 57.563 42.857 5.01 0.00 0.00 2.85
680 741 3.878160 AAAAACGAAAACAGGCCAAGA 57.122 38.095 5.01 0.00 0.00 3.02
697 758 2.375014 AGCCCCCTTTTCGAGAAAAA 57.625 45.000 11.50 0.00 39.49 1.94
698 759 2.235891 GAAGCCCCCTTTTCGAGAAAA 58.764 47.619 10.17 10.17 37.90 2.29
699 760 1.546998 GGAAGCCCCCTTTTCGAGAAA 60.547 52.381 0.00 0.00 0.00 2.52
700 761 0.037734 GGAAGCCCCCTTTTCGAGAA 59.962 55.000 0.00 0.00 0.00 2.87
701 762 1.683441 GGAAGCCCCCTTTTCGAGA 59.317 57.895 0.00 0.00 0.00 4.04
702 763 4.320910 GGAAGCCCCCTTTTCGAG 57.679 61.111 0.00 0.00 0.00 4.04
715 776 3.764160 GATGCAGAGGCCCGGGAAG 62.764 68.421 29.31 9.33 40.13 3.46
716 777 3.797353 GATGCAGAGGCCCGGGAA 61.797 66.667 29.31 0.00 40.13 3.97
718 779 4.559063 CTGATGCAGAGGCCCGGG 62.559 72.222 19.09 19.09 40.13 5.73
719 780 1.475169 TATCTGATGCAGAGGCCCGG 61.475 60.000 0.00 0.00 44.08 5.73
720 781 0.037512 CTATCTGATGCAGAGGCCCG 60.038 60.000 0.00 0.00 44.08 6.13
721 782 1.346062 TCTATCTGATGCAGAGGCCC 58.654 55.000 0.00 0.00 44.08 5.80
722 783 2.975266 CATCTATCTGATGCAGAGGCC 58.025 52.381 0.00 0.00 44.08 5.19
739 800 1.135575 CGAAAACAGGCCAAGAGCATC 60.136 52.381 5.01 0.00 46.50 3.91
740 801 0.883833 CGAAAACAGGCCAAGAGCAT 59.116 50.000 5.01 0.00 46.50 3.79
741 802 0.465460 ACGAAAACAGGCCAAGAGCA 60.465 50.000 5.01 0.00 46.50 4.26
742 803 0.668535 AACGAAAACAGGCCAAGAGC 59.331 50.000 5.01 0.00 42.60 4.09
743 804 3.436700 AAAACGAAAACAGGCCAAGAG 57.563 42.857 5.01 0.00 0.00 2.85
744 805 3.878160 AAAAACGAAAACAGGCCAAGA 57.122 38.095 5.01 0.00 0.00 3.02
780 841 3.764160 GATGCAGAGGCCCGGGAAG 62.764 68.421 29.31 9.33 40.13 3.46
781 842 3.797353 GATGCAGAGGCCCGGGAA 61.797 66.667 29.31 0.00 40.13 3.97
783 844 4.559063 CTGATGCAGAGGCCCGGG 62.559 72.222 19.09 19.09 40.13 5.73
784 845 1.475169 TATCTGATGCAGAGGCCCGG 61.475 60.000 0.00 0.00 44.08 5.73
785 846 0.037512 CTATCTGATGCAGAGGCCCG 60.038 60.000 0.00 0.00 44.08 6.13
786 847 1.346062 TCTATCTGATGCAGAGGCCC 58.654 55.000 0.00 0.00 44.08 5.80
787 848 2.975266 CATCTATCTGATGCAGAGGCC 58.025 52.381 0.00 0.00 44.08 5.19
804 865 1.135575 CGAAAACAGGCCAAGAGCATC 60.136 52.381 5.01 0.00 46.50 3.91
805 866 0.883833 CGAAAACAGGCCAAGAGCAT 59.116 50.000 5.01 0.00 46.50 3.79
806 867 0.465460 ACGAAAACAGGCCAAGAGCA 60.465 50.000 5.01 0.00 46.50 4.26
807 868 1.519408 TACGAAAACAGGCCAAGAGC 58.481 50.000 5.01 0.00 42.60 4.09
808 869 5.177696 GCTATATACGAAAACAGGCCAAGAG 59.822 44.000 5.01 0.00 0.00 2.85
809 870 5.054477 GCTATATACGAAAACAGGCCAAGA 58.946 41.667 5.01 0.00 0.00 3.02
810 871 4.814234 TGCTATATACGAAAACAGGCCAAG 59.186 41.667 5.01 0.00 0.00 3.61
811 872 4.771903 TGCTATATACGAAAACAGGCCAA 58.228 39.130 5.01 0.00 0.00 4.52
812 873 4.100344 TCTGCTATATACGAAAACAGGCCA 59.900 41.667 5.01 0.00 0.00 5.36
813 874 4.628074 TCTGCTATATACGAAAACAGGCC 58.372 43.478 0.00 0.00 0.00 5.19
864 925 0.714439 GCAAGAAGAGCCGTACGTTC 59.286 55.000 15.21 11.09 0.00 3.95
1014 1152 1.533625 TTGATTGCCACGCTAGCTTT 58.466 45.000 13.93 0.00 0.00 3.51
1015 1153 1.402968 CATTGATTGCCACGCTAGCTT 59.597 47.619 13.93 0.00 0.00 3.74
1022 1160 1.713937 TAGCGCCATTGATTGCCACG 61.714 55.000 2.29 0.00 0.00 4.94
1027 1165 4.692155 TGATACTGATAGCGCCATTGATTG 59.308 41.667 2.29 0.00 0.00 2.67
1065 1203 4.748144 GGTTCCTGCTGGCCCTGG 62.748 72.222 0.00 0.00 0.00 4.45
1248 1386 2.289694 ACTTGTGACCAGCTATGTGTCC 60.290 50.000 0.00 0.00 0.00 4.02
1249 1387 3.045601 ACTTGTGACCAGCTATGTGTC 57.954 47.619 0.00 0.00 0.00 3.67
1250 1388 3.492102 AACTTGTGACCAGCTATGTGT 57.508 42.857 0.00 0.00 0.00 3.72
1251 1389 3.565482 ACAAACTTGTGACCAGCTATGTG 59.435 43.478 0.00 0.00 40.49 3.21
1566 1708 4.187594 CATAAGTCATGCTTAGCGTGTG 57.812 45.455 23.52 11.98 44.84 3.82
1689 2480 0.656259 CTGAATGCACGCATCTCCAG 59.344 55.000 4.73 9.25 35.31 3.86
2371 3931 2.827322 TGAAAAATGTGATCCAGCTGGG 59.173 45.455 32.23 14.13 35.41 4.45
2593 4162 1.844296 TTGGGAGGGGTGGGGAGTAT 61.844 60.000 0.00 0.00 0.00 2.12
3124 4700 7.648510 CACTTACGAAGGATTCTACATAAGTCC 59.351 40.741 0.00 0.00 44.75 3.85
3137 4713 3.871594 GCAATGCTACACTTACGAAGGAT 59.128 43.478 0.00 0.00 0.00 3.24
3545 5371 4.537288 ATGTATCTCATATGCATGGGGACA 59.463 41.667 10.16 4.02 39.04 4.02
3546 5372 4.558226 TGTATCTCATATGCATGGGGAC 57.442 45.455 10.16 0.00 33.01 4.46
3681 5510 4.935352 ACCTTGTGCACAAAACACATAT 57.065 36.364 30.62 9.22 46.72 1.78
3742 5572 9.109393 GTAGCACTTCATTAATGTGGATAAAGA 57.891 33.333 14.97 0.00 32.85 2.52
3815 5650 2.040947 TGTGCCAATCTGGTTCACCATA 59.959 45.455 0.00 0.00 46.46 2.74
3901 5876 0.895530 CCTGTTCCCTGCTTCGTCTA 59.104 55.000 0.00 0.00 0.00 2.59
3974 5949 1.211456 CCTCCCCAAGCTCAGAGATT 58.789 55.000 0.00 0.00 0.00 2.40
4658 6660 0.908198 AGCTTGATCTTCTTCCCGCT 59.092 50.000 0.00 0.00 0.00 5.52
4803 6805 0.591170 CACCCGTGTCATCAACAACC 59.409 55.000 0.00 0.00 40.31 3.77
4918 6920 2.125512 GTTGGTGCGATCGAGGCT 60.126 61.111 21.57 0.00 0.00 4.58
5131 7139 3.297134 AGTACCAATGCCCTACCAATG 57.703 47.619 0.00 0.00 0.00 2.82
5132 7140 5.663158 ATAAGTACCAATGCCCTACCAAT 57.337 39.130 0.00 0.00 0.00 3.16
5133 7141 6.773583 ATATAAGTACCAATGCCCTACCAA 57.226 37.500 0.00 0.00 0.00 3.67
5134 7142 6.240060 GGAATATAAGTACCAATGCCCTACCA 60.240 42.308 0.00 0.00 0.00 3.25
5135 7143 6.178324 GGAATATAAGTACCAATGCCCTACC 58.822 44.000 0.00 0.00 0.00 3.18
5136 7144 6.178324 GGGAATATAAGTACCAATGCCCTAC 58.822 44.000 0.00 0.00 0.00 3.18
5137 7145 5.852807 TGGGAATATAAGTACCAATGCCCTA 59.147 40.000 10.33 0.00 33.07 3.53
5138 7146 4.667858 TGGGAATATAAGTACCAATGCCCT 59.332 41.667 10.33 0.00 33.07 5.19
5139 7147 4.993028 TGGGAATATAAGTACCAATGCCC 58.007 43.478 0.00 0.00 0.00 5.36
5140 7148 4.459337 GCTGGGAATATAAGTACCAATGCC 59.541 45.833 0.00 0.00 0.00 4.40
5141 7149 5.316987 AGCTGGGAATATAAGTACCAATGC 58.683 41.667 0.00 0.00 0.00 3.56
5168 7187 3.700538 ACTGTGTCCACATGGCATAAAT 58.299 40.909 0.00 0.00 41.01 1.40
5280 7299 3.428870 GTGTGTAGGTGACGTTCATTGAG 59.571 47.826 0.00 0.00 0.00 3.02
5632 7656 4.232188 AGAGTCTACGGATACAAGGACA 57.768 45.455 0.00 0.00 32.52 4.02
5686 7710 7.180766 TGGATATGCATGATGGATAGTTGTCTA 59.819 37.037 10.16 0.92 34.20 2.59
5762 7793 9.566432 AGCTGGAGGTAAAGAGAATAAATTATG 57.434 33.333 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.