Multiple sequence alignment - TraesCS5D01G193300

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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 TraesCS5D01G193300 chr5D 100.000 4604 0 0 1 4604 297581144 297576541 0.000000e+00 8503.0
1 TraesCS5D01G193300 chr5B 95.544 4017 134 20 1 3991 337907747 337903750 0.000000e+00 6384.0
2 TraesCS5D01G193300 chr5B 81.292 449 31 14 3989 4407 337903669 337903244 9.620000e-82 315.0
3 TraesCS5D01G193300 chr5B 96.825 63 2 0 4443 4505 337877942 337877880 6.300000e-19 106.0
4 TraesCS5D01G193300 chr5A 95.679 2870 90 14 1 2857 401438216 401441064 0.000000e+00 4582.0
5 TraesCS5D01G193300 chr5A 89.501 1724 97 36 2842 4502 401441077 401442779 0.000000e+00 2104.0
6 TraesCS5D01G193300 chr4B 85.088 912 111 18 1650 2557 513726133 513725243 0.000000e+00 907.0
7 TraesCS5D01G193300 chr4B 88.000 400 44 4 1069 1466 513726816 513726419 1.940000e-128 470.0
8 TraesCS5D01G193300 chr4B 86.328 256 35 0 3350 3605 513724202 513723947 3.510000e-71 279.0
9 TraesCS5D01G193300 chr4B 87.582 153 17 2 2615 2765 513725138 513724986 4.730000e-40 176.0
10 TraesCS5D01G193300 chr4A 84.683 914 113 20 1650 2557 47390232 47391124 0.000000e+00 887.0
11 TraesCS5D01G193300 chr4A 88.946 389 39 4 1081 1466 47389670 47390057 1.160000e-130 477.0
12 TraesCS5D01G193300 chr4A 86.641 262 34 1 3344 3605 47392143 47392403 5.830000e-74 289.0
13 TraesCS5D01G193300 chr4A 87.179 156 18 2 2612 2765 47391218 47391373 4.730000e-40 176.0
14 TraesCS5D01G193300 chr4A 88.298 94 8 3 4512 4604 735038631 735038540 4.870000e-20 110.0
15 TraesCS5D01G193300 chr4D 84.320 912 126 16 1650 2557 416763170 416762272 0.000000e+00 876.0
16 TraesCS5D01G193300 chr4D 89.119 386 38 4 1084 1466 416763727 416763343 1.160000e-130 477.0
17 TraesCS5D01G193300 chr4D 87.500 256 32 0 3350 3605 416760680 416760425 3.480000e-76 296.0
18 TraesCS5D01G193300 chr4D 88.079 151 17 1 2616 2765 416762165 416762015 1.320000e-40 178.0
19 TraesCS5D01G193300 chr7A 80.000 390 51 15 2420 2795 1708295 1708671 3.530000e-66 263.0
20 TraesCS5D01G193300 chr2A 90.909 165 15 0 247 411 775658241 775658405 6.000000e-54 222.0
21 TraesCS5D01G193300 chr2D 77.892 389 29 18 36 412 649062626 649062283 6.080000e-44 189.0
22 TraesCS5D01G193300 chr2D 89.691 97 8 1 4508 4604 46780790 46780696 6.260000e-24 122.0
23 TraesCS5D01G193300 chr2D 88.421 95 9 1 4510 4604 75100287 75100379 3.760000e-21 113.0
24 TraesCS5D01G193300 chr1D 87.387 111 11 2 4494 4603 250135249 250135357 1.740000e-24 124.0
25 TraesCS5D01G193300 chr6A 88.298 94 8 3 4512 4604 598866617 598866526 4.870000e-20 110.0
26 TraesCS5D01G193300 chr2B 86.598 97 11 1 4508 4604 784202638 784202732 6.300000e-19 106.0
27 TraesCS5D01G193300 chr2B 83.077 130 8 2 212 341 784754981 784754866 6.300000e-19 106.0
28 TraesCS5D01G193300 chr6D 83.929 112 13 4 4493 4604 222716632 222716738 8.150000e-18 102.0
29 TraesCS5D01G193300 chr3D 83.505 97 14 1 4508 4604 555148003 555148097 6.340000e-14 89.8
30 TraesCS5D01G193300 chr7B 84.211 95 9 3 4510 4604 104249532 104249620 2.280000e-13 87.9


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 TraesCS5D01G193300 chr5D 297576541 297581144 4603 True 8503.00 8503 100.00000 1 4604 1 chr5D.!!$R1 4603
1 TraesCS5D01G193300 chr5B 337903244 337907747 4503 True 3349.50 6384 88.41800 1 4407 2 chr5B.!!$R2 4406
2 TraesCS5D01G193300 chr5A 401438216 401442779 4563 False 3343.00 4582 92.59000 1 4502 2 chr5A.!!$F1 4501
3 TraesCS5D01G193300 chr4B 513723947 513726816 2869 True 458.00 907 86.74950 1069 3605 4 chr4B.!!$R1 2536
4 TraesCS5D01G193300 chr4A 47389670 47392403 2733 False 457.25 887 86.86225 1081 3605 4 chr4A.!!$F1 2524
5 TraesCS5D01G193300 chr4D 416760425 416763727 3302 True 456.75 876 87.25450 1084 3605 4 chr4D.!!$R1 2521

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
536 541 0.036732 TAGGCCGATGGGAATGATGC 59.963 55.000 0.00 0.00 34.06 3.91 F
744 750 0.102481 TCTGAGCGGTCTAATTCGGC 59.898 55.000 16.64 0.00 0.00 5.54 F
895 902 1.811359 AGCTGAGCAAGAAATCTGTGC 59.189 47.619 7.39 8.56 38.59 4.57 F
1585 1709 1.811965 TGCGGTGAATGACCAATGAAG 59.188 47.619 0.00 0.00 46.55 3.02 F
1959 2090 3.758554 CTGTTGCTAGTTGGCTTATGGTT 59.241 43.478 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2309 3.947834 CACGGAAGCCTTGGAAATAGATT 59.052 43.478 0.00 0.0 0.00 2.40 R
2360 2505 5.104527 TGCAAATGCTCACCCTACTATAGTT 60.105 40.000 11.40 0.0 42.66 2.24 R
2857 3080 2.159841 CCGCACGTGAAAACAGACATAG 60.160 50.000 22.23 0.0 0.00 2.23 R
3055 3636 0.846015 CCCCAACATCAGGCTGGATA 59.154 55.000 15.73 0.0 31.38 2.59 R
3764 4991 0.041839 CTGAAGAACACACGCAGCAC 60.042 55.000 0.00 0.0 0.00 4.40 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
386 390 1.730902 CCTGCGTGTGTGTCTCGAG 60.731 63.158 5.93 5.93 35.42 4.04
452 457 1.521457 GCGTCCAGATCCATGCGAA 60.521 57.895 0.00 0.00 0.00 4.70
454 459 0.460109 CGTCCAGATCCATGCGAACA 60.460 55.000 0.00 0.00 0.00 3.18
467 472 0.038159 GCGAACATAGGATCCCGAGG 60.038 60.000 8.55 0.65 0.00 4.63
472 477 0.611062 CATAGGATCCCGAGGCCGTA 60.611 60.000 8.55 0.00 0.00 4.02
536 541 0.036732 TAGGCCGATGGGAATGATGC 59.963 55.000 0.00 0.00 34.06 3.91
537 542 1.228367 GGCCGATGGGAATGATGCT 60.228 57.895 0.00 0.00 34.06 3.79
583 588 1.304381 GCTTGATCCCAGGGTTGCA 60.304 57.895 5.01 0.00 0.00 4.08
605 610 3.412386 ACAGTTTCCTATTCTGGTGCAC 58.588 45.455 8.80 8.80 34.02 4.57
663 668 4.637276 TCTGGTCGCTTAGTTTTGAATGA 58.363 39.130 0.00 0.00 0.00 2.57
681 686 5.123820 TGAATGAACGCTAGCTAAATTGCTT 59.876 36.000 13.93 0.00 43.74 3.91
683 688 4.253685 TGAACGCTAGCTAAATTGCTTCT 58.746 39.130 13.93 0.00 43.74 2.85
744 750 0.102481 TCTGAGCGGTCTAATTCGGC 59.898 55.000 16.64 0.00 0.00 5.54
802 809 2.417933 CAGAATTGTAGCTGTCAGGCAC 59.582 50.000 1.14 0.00 34.17 5.01
804 811 2.867109 ATTGTAGCTGTCAGGCACTT 57.133 45.000 1.14 0.00 34.60 3.16
814 821 6.472887 AGCTGTCAGGCACTTATAAAAGTAA 58.527 36.000 1.14 0.00 44.28 2.24
816 823 7.119846 AGCTGTCAGGCACTTATAAAAGTAAAG 59.880 37.037 1.14 0.00 44.28 1.85
817 824 7.094762 GCTGTCAGGCACTTATAAAAGTAAAGT 60.095 37.037 1.14 0.00 44.28 2.66
895 902 1.811359 AGCTGAGCAAGAAATCTGTGC 59.189 47.619 7.39 8.56 38.59 4.57
962 969 7.495901 TGTTCATTTCTGTTTCAGCCAAATTA 58.504 30.769 0.00 0.00 0.00 1.40
965 972 7.370383 TCATTTCTGTTTCAGCCAAATTAGTC 58.630 34.615 0.00 0.00 0.00 2.59
979 986 5.300286 CCAAATTAGTCCATCAACCTGATCC 59.700 44.000 0.00 0.00 34.28 3.36
980 987 5.983333 AATTAGTCCATCAACCTGATCCT 57.017 39.130 0.00 0.00 34.28 3.24
983 990 7.639062 ATTAGTCCATCAACCTGATCCTAAT 57.361 36.000 0.00 0.00 34.28 1.73
1005 1012 5.848286 TCATGACTTAGGGGATAATGCAT 57.152 39.130 0.00 0.00 0.00 3.96
1138 1147 4.770874 GGCGGCTTTCGGGTGCTA 62.771 66.667 0.00 0.00 39.69 3.49
1487 1496 7.989826 AGTATTTGCGAAAATAGCAGAATCTT 58.010 30.769 8.92 0.00 46.01 2.40
1585 1709 1.811965 TGCGGTGAATGACCAATGAAG 59.188 47.619 0.00 0.00 46.55 3.02
1589 1713 4.516698 GCGGTGAATGACCAATGAAGATAT 59.483 41.667 0.00 0.00 46.55 1.63
1601 1727 7.486647 ACCAATGAAGATATTAAAGCTTGCTG 58.513 34.615 0.00 0.00 0.00 4.41
1959 2090 3.758554 CTGTTGCTAGTTGGCTTATGGTT 59.241 43.478 0.00 0.00 0.00 3.67
2178 2309 5.580998 ACTGTCCTGGTCTTTCTCATAGTA 58.419 41.667 0.00 0.00 0.00 1.82
2360 2505 9.775539 ATAGGCTTCTGTTCCAGATCTATAATA 57.224 33.333 0.00 0.00 40.39 0.98
2363 2508 8.371699 GGCTTCTGTTCCAGATCTATAATAACT 58.628 37.037 0.00 0.00 40.39 2.24
2468 2635 6.096423 GTGGAAACTTTCTGGTTAACCTTCTT 59.904 38.462 24.78 8.84 36.82 2.52
2817 3040 8.301252 TGTCTGGTTACTCTTACATATAGCAA 57.699 34.615 0.00 0.00 0.00 3.91
2933 3188 8.028938 GCATATCACCAAAGATTTGTACAAACT 58.971 33.333 22.78 17.61 36.45 2.66
2934 3189 9.912634 CATATCACCAAAGATTTGTACAAACTT 57.087 29.630 22.78 21.54 36.45 2.66
2938 3193 7.038659 CACCAAAGATTTGTACAAACTTCCAA 58.961 34.615 22.78 0.00 36.45 3.53
2972 3227 5.055265 TCTTCCATCCACTGTTTAAACCA 57.945 39.130 15.59 3.48 0.00 3.67
2973 3228 5.450453 TCTTCCATCCACTGTTTAAACCAA 58.550 37.500 15.59 0.00 0.00 3.67
3009 3264 8.960591 GGTATAGGATCCATTCATAAAACATGG 58.039 37.037 15.82 0.00 39.17 3.66
3055 3636 9.530633 GTTTGTCTCTCGTAGGATGTTTATAAT 57.469 33.333 0.00 0.00 0.00 1.28
3106 3806 7.277760 GCAGTACTTATCATGTGTAATGTGACA 59.722 37.037 0.00 0.00 35.53 3.58
3110 3810 7.530010 ACTTATCATGTGTAATGTGACAAAGC 58.470 34.615 0.00 0.00 0.00 3.51
3111 3811 5.963176 ATCATGTGTAATGTGACAAAGCA 57.037 34.783 0.00 0.00 0.00 3.91
3289 4516 7.702348 GTGATTCATTAGCTATTTTTGGTGACC 59.298 37.037 0.00 0.00 0.00 4.02
3326 4553 2.833794 AGACTGTTTTACGCAAGAGCA 58.166 42.857 0.00 0.00 42.27 4.26
3332 4559 4.062293 TGTTTTACGCAAGAGCATACTGT 58.938 39.130 0.00 0.00 42.27 3.55
3408 4635 1.872952 CATCGTGAGTCAAACCTGCAA 59.127 47.619 0.00 0.00 0.00 4.08
3576 4803 2.584673 CTTCGAGAAGGAGAGGGCA 58.415 57.895 4.99 0.00 34.87 5.36
3650 4877 1.936547 GTTATGGCTACAGCACAGCTC 59.063 52.381 3.24 0.00 44.36 4.09
3659 4886 1.202580 ACAGCACAGCTCGAGTCTTTT 60.203 47.619 15.13 0.00 36.40 2.27
3932 5159 4.769488 TGGTATATGTTTTTCTTGCCTGCA 59.231 37.500 0.00 0.00 0.00 4.41
3974 5201 5.932303 TGATACTTTCAACTGTTGAGTAGGC 59.068 40.000 25.31 19.03 41.38 3.93
3986 5213 4.574828 TGTTGAGTAGGCTTTTCTGTGTTC 59.425 41.667 0.00 0.00 0.00 3.18
4012 5322 3.960102 AGAACAAAAATGCTTGACCCAGA 59.040 39.130 0.00 0.00 0.00 3.86
4019 5329 3.550437 ATGCTTGACCCAGACTCATAC 57.450 47.619 0.00 0.00 0.00 2.39
4022 5332 3.701542 TGCTTGACCCAGACTCATACTAG 59.298 47.826 0.00 0.00 0.00 2.57
4023 5333 3.702045 GCTTGACCCAGACTCATACTAGT 59.298 47.826 0.00 0.00 0.00 2.57
4024 5334 4.888239 GCTTGACCCAGACTCATACTAGTA 59.112 45.833 4.77 4.77 0.00 1.82
4085 5402 5.351465 ACGTGTTCATATTGAGGTGAATGAC 59.649 40.000 0.00 0.00 36.79 3.06
4093 5410 1.338105 TGAGGTGAATGACTTCTGGCG 60.338 52.381 0.00 0.00 31.84 5.69
4097 5433 0.396435 TGAATGACTTCTGGCGGTGT 59.604 50.000 0.00 0.00 32.29 4.16
4098 5434 1.202758 TGAATGACTTCTGGCGGTGTT 60.203 47.619 0.00 0.00 32.29 3.32
4101 5437 1.300697 GACTTCTGGCGGTGTTCGT 60.301 57.895 0.00 0.00 41.72 3.85
4102 5438 0.878961 GACTTCTGGCGGTGTTCGTT 60.879 55.000 0.00 0.00 41.72 3.85
4113 5449 3.904234 GCGGTGTTCGTTAGAAATGAAAC 59.096 43.478 0.00 0.00 38.08 2.78
4122 5458 6.775139 TTCGTTAGAAATGAAACGTCACGTTC 60.775 38.462 17.54 10.52 40.28 3.95
4134 5470 4.817517 ACGTCACGTTCTCAAATAATCCT 58.182 39.130 0.00 0.00 36.35 3.24
4135 5471 5.235516 ACGTCACGTTCTCAAATAATCCTT 58.764 37.500 0.00 0.00 36.35 3.36
4136 5472 5.120208 ACGTCACGTTCTCAAATAATCCTTG 59.880 40.000 0.00 0.00 36.35 3.61
4137 5473 5.347635 CGTCACGTTCTCAAATAATCCTTGA 59.652 40.000 0.00 0.00 0.00 3.02
4278 5618 1.137086 AGGTAGATCGCGCTTTGATGT 59.863 47.619 5.56 1.95 0.00 3.06
4290 5630 4.736793 GCGCTTTGATGTCATCCTATTTTG 59.263 41.667 10.36 0.00 0.00 2.44
4292 5632 5.967674 CGCTTTGATGTCATCCTATTTTGTC 59.032 40.000 10.36 0.00 0.00 3.18
4409 5771 2.437850 GCAACTTTGATGCCTTGCG 58.562 52.632 0.00 0.00 37.85 4.85
4410 5772 0.318955 GCAACTTTGATGCCTTGCGT 60.319 50.000 0.00 0.00 37.85 5.24
4415 5786 1.851021 TTTGATGCCTTGCGTCGTGG 61.851 55.000 4.05 0.00 46.39 4.94
4430 5801 4.386652 GCGTCGTGGATTGACTTAACTTTA 59.613 41.667 0.00 0.00 34.17 1.85
4502 5891 8.040727 GGTGCATTGGAGAACCTTAATTTAAAT 58.959 33.333 0.00 0.00 37.04 1.40
4505 5894 9.249457 GCATTGGAGAACCTTAATTTAAATAGC 57.751 33.333 0.01 0.00 37.04 2.97
4525 5914 8.716646 AATAGCAAAATATTTAAGTGGCAACC 57.283 30.769 0.01 0.00 0.00 3.77
4526 5915 5.167845 AGCAAAATATTTAAGTGGCAACCG 58.832 37.500 0.01 0.00 0.00 4.44
4527 5916 4.926832 GCAAAATATTTAAGTGGCAACCGT 59.073 37.500 0.01 0.00 0.00 4.83
4528 5917 5.164002 GCAAAATATTTAAGTGGCAACCGTG 60.164 40.000 0.01 0.00 0.00 4.94
4529 5918 5.968528 AAATATTTAAGTGGCAACCGTGA 57.031 34.783 0.00 0.00 0.00 4.35
4530 5919 5.560966 AATATTTAAGTGGCAACCGTGAG 57.439 39.130 0.00 0.00 0.00 3.51
4531 5920 2.623878 TTTAAGTGGCAACCGTGAGA 57.376 45.000 0.00 0.00 0.00 3.27
4532 5921 1.873698 TTAAGTGGCAACCGTGAGAC 58.126 50.000 0.00 0.00 0.00 3.36
4533 5922 0.753867 TAAGTGGCAACCGTGAGACA 59.246 50.000 0.00 0.00 0.00 3.41
4534 5923 0.532862 AAGTGGCAACCGTGAGACAG 60.533 55.000 0.00 0.00 0.00 3.51
4535 5924 1.069090 GTGGCAACCGTGAGACAGA 59.931 57.895 0.00 0.00 0.00 3.41
4536 5925 0.320771 GTGGCAACCGTGAGACAGAT 60.321 55.000 0.00 0.00 0.00 2.90
4537 5926 0.396435 TGGCAACCGTGAGACAGATT 59.604 50.000 0.00 0.00 0.00 2.40
4538 5927 0.798776 GGCAACCGTGAGACAGATTG 59.201 55.000 0.00 0.00 0.00 2.67
4539 5928 0.166814 GCAACCGTGAGACAGATTGC 59.833 55.000 0.00 0.00 36.07 3.56
4540 5929 1.511850 CAACCGTGAGACAGATTGCA 58.488 50.000 0.00 0.00 0.00 4.08
4541 5930 1.872952 CAACCGTGAGACAGATTGCAA 59.127 47.619 0.00 0.00 0.00 4.08
4542 5931 2.254546 ACCGTGAGACAGATTGCAAA 57.745 45.000 1.71 0.00 0.00 3.68
4543 5932 2.571212 ACCGTGAGACAGATTGCAAAA 58.429 42.857 1.71 0.00 0.00 2.44
4544 5933 2.290641 ACCGTGAGACAGATTGCAAAAC 59.709 45.455 1.71 0.47 0.00 2.43
4545 5934 2.549754 CCGTGAGACAGATTGCAAAACT 59.450 45.455 1.71 3.20 0.00 2.66
4551 5940 2.512485 CAGATTGCAAAACTGCCACA 57.488 45.000 18.94 0.00 39.88 4.17
4552 5941 2.129607 CAGATTGCAAAACTGCCACAC 58.870 47.619 18.94 0.00 39.88 3.82
4553 5942 1.130955 GATTGCAAAACTGCCACACG 58.869 50.000 1.71 0.00 0.00 4.49
4554 5943 0.875474 ATTGCAAAACTGCCACACGC 60.875 50.000 1.71 0.00 38.31 5.34
4562 5951 4.639906 TGCCACACGCATCCAGCA 62.640 61.111 0.00 0.00 44.64 4.41
4563 5952 4.107051 GCCACACGCATCCAGCAC 62.107 66.667 0.00 0.00 46.13 4.40
4564 5953 3.792047 CCACACGCATCCAGCACG 61.792 66.667 0.00 0.00 46.13 5.34
4565 5954 3.792047 CACACGCATCCAGCACGG 61.792 66.667 0.00 0.00 46.13 4.94
4566 5955 4.314440 ACACGCATCCAGCACGGT 62.314 61.111 0.00 0.00 46.13 4.83
4567 5956 3.792047 CACGCATCCAGCACGGTG 61.792 66.667 3.15 3.15 46.13 4.94
4568 5957 4.002506 ACGCATCCAGCACGGTGA 62.003 61.111 13.29 0.00 46.13 4.02
4569 5958 3.490759 CGCATCCAGCACGGTGAC 61.491 66.667 13.29 3.33 46.13 3.67
4570 5959 2.046892 GCATCCAGCACGGTGACT 60.047 61.111 13.29 5.79 44.79 3.41
4571 5960 2.393768 GCATCCAGCACGGTGACTG 61.394 63.158 13.29 17.03 44.79 3.51
4572 5961 1.004560 CATCCAGCACGGTGACTGT 60.005 57.895 22.13 0.00 35.57 3.55
4573 5962 0.603707 CATCCAGCACGGTGACTGTT 60.604 55.000 22.13 12.26 35.57 3.16
4574 5963 0.108585 ATCCAGCACGGTGACTGTTT 59.891 50.000 22.13 12.01 35.57 2.83
4575 5964 0.531974 TCCAGCACGGTGACTGTTTC 60.532 55.000 22.13 2.70 35.57 2.78
4576 5965 1.564622 CAGCACGGTGACTGTTTCG 59.435 57.895 13.29 0.00 0.00 3.46
4577 5966 1.594293 AGCACGGTGACTGTTTCGG 60.594 57.895 13.29 0.00 0.00 4.30
4578 5967 1.885850 GCACGGTGACTGTTTCGGT 60.886 57.895 13.29 0.00 0.00 4.69
4579 5968 1.828331 GCACGGTGACTGTTTCGGTC 61.828 60.000 13.29 2.20 39.93 4.79
4580 5969 1.299620 ACGGTGACTGTTTCGGTCG 60.300 57.895 0.00 0.00 42.18 4.79
4581 5970 2.654912 CGGTGACTGTTTCGGTCGC 61.655 63.158 12.16 12.16 46.03 5.19
4582 5971 3.241177 GTGACTGTTTCGGTCGCC 58.759 61.111 10.12 0.00 42.42 5.54
4583 5972 2.029964 TGACTGTTTCGGTCGCCC 59.970 61.111 4.61 0.00 42.18 6.13
4584 5973 2.342648 GACTGTTTCGGTCGCCCT 59.657 61.111 0.00 0.00 29.77 5.19
4585 5974 1.737008 GACTGTTTCGGTCGCCCTC 60.737 63.158 0.00 0.00 29.77 4.30
4586 5975 2.434359 CTGTTTCGGTCGCCCTCC 60.434 66.667 0.00 0.00 0.00 4.30
4587 5976 3.234630 CTGTTTCGGTCGCCCTCCA 62.235 63.158 0.00 0.00 0.00 3.86
4588 5977 2.434359 GTTTCGGTCGCCCTCCAG 60.434 66.667 0.00 0.00 0.00 3.86
4589 5978 2.602267 TTTCGGTCGCCCTCCAGA 60.602 61.111 0.00 0.00 0.00 3.86
4590 5979 1.987855 TTTCGGTCGCCCTCCAGAT 60.988 57.895 0.00 0.00 0.00 2.90
4591 5980 1.956629 TTTCGGTCGCCCTCCAGATC 61.957 60.000 0.00 0.00 0.00 2.75
4592 5981 2.835431 CGGTCGCCCTCCAGATCT 60.835 66.667 0.00 0.00 0.00 2.75
4593 5982 2.851071 CGGTCGCCCTCCAGATCTC 61.851 68.421 0.00 0.00 0.00 2.75
4594 5983 2.503382 GGTCGCCCTCCAGATCTCC 61.503 68.421 0.00 0.00 0.00 3.71
4595 5984 1.456705 GTCGCCCTCCAGATCTCCT 60.457 63.158 0.00 0.00 0.00 3.69
4596 5985 1.045911 GTCGCCCTCCAGATCTCCTT 61.046 60.000 0.00 0.00 0.00 3.36
4597 5986 0.757188 TCGCCCTCCAGATCTCCTTC 60.757 60.000 0.00 0.00 0.00 3.46
4598 5987 1.753368 CGCCCTCCAGATCTCCTTCC 61.753 65.000 0.00 0.00 0.00 3.46
4599 5988 0.399806 GCCCTCCAGATCTCCTTCCT 60.400 60.000 0.00 0.00 0.00 3.36
4600 5989 1.974197 GCCCTCCAGATCTCCTTCCTT 60.974 57.143 0.00 0.00 0.00 3.36
4601 5990 2.486716 CCCTCCAGATCTCCTTCCTTT 58.513 52.381 0.00 0.00 0.00 3.11
4602 5991 2.437651 CCCTCCAGATCTCCTTCCTTTC 59.562 54.545 0.00 0.00 0.00 2.62
4603 5992 2.437651 CCTCCAGATCTCCTTCCTTTCC 59.562 54.545 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
270 271 2.604299 GAATCGGGGGAAAGGACGGG 62.604 65.000 0.00 0.00 0.00 5.28
369 371 0.999228 GACTCGAGACACACACGCAG 60.999 60.000 21.68 0.00 33.00 5.18
372 374 0.992263 CACGACTCGAGACACACACG 60.992 60.000 21.68 13.79 0.00 4.49
386 390 0.996727 GCCGCATGAACAAACACGAC 60.997 55.000 0.00 0.00 0.00 4.34
452 457 1.908793 CGGCCTCGGGATCCTATGT 60.909 63.158 12.58 0.00 0.00 2.29
454 459 0.323542 CTACGGCCTCGGGATCCTAT 60.324 60.000 12.58 0.00 41.39 2.57
461 466 4.609018 CCATGCTACGGCCTCGGG 62.609 72.222 0.00 0.00 41.39 5.14
583 588 3.821033 GTGCACCAGAATAGGAAACTGTT 59.179 43.478 5.22 0.00 45.30 3.16
605 610 6.086222 ACGCTTTGCTTAAACACATATCAAG 58.914 36.000 0.00 0.00 0.00 3.02
663 668 3.375299 CCAGAAGCAATTTAGCTAGCGTT 59.625 43.478 9.55 0.45 45.89 4.84
681 686 1.883678 TCCATCAGCTTGGATCCAGA 58.116 50.000 15.53 9.27 40.90 3.86
744 750 1.270358 GGCGGCCTATCCAGAAAGTAG 60.270 57.143 12.87 0.00 34.01 2.57
895 902 8.822652 AGCAGACAAAGGAATAAAATGAAAAG 57.177 30.769 0.00 0.00 0.00 2.27
962 969 4.971282 TGATTAGGATCAGGTTGATGGACT 59.029 41.667 0.00 0.00 37.20 3.85
965 972 5.704515 GTCATGATTAGGATCAGGTTGATGG 59.295 44.000 0.00 0.00 45.01 3.51
979 986 7.397221 TGCATTATCCCCTAAGTCATGATTAG 58.603 38.462 0.00 8.09 0.00 1.73
980 987 7.328404 TGCATTATCCCCTAAGTCATGATTA 57.672 36.000 0.00 0.00 0.00 1.75
983 990 5.310331 TCATGCATTATCCCCTAAGTCATGA 59.690 40.000 0.00 0.00 38.40 3.07
1005 1012 3.896888 ACTTCACAGCAATTCCCATTTCA 59.103 39.130 0.00 0.00 0.00 2.69
1053 1060 7.696755 TGTACAATGCACATGACAATCTTATC 58.303 34.615 0.00 0.00 0.00 1.75
1054 1061 7.628769 TGTACAATGCACATGACAATCTTAT 57.371 32.000 0.00 0.00 0.00 1.73
1055 1062 7.628769 ATGTACAATGCACATGACAATCTTA 57.371 32.000 0.00 0.00 35.33 2.10
1056 1063 5.963176 TGTACAATGCACATGACAATCTT 57.037 34.783 0.00 0.00 0.00 2.40
1057 1064 7.628769 TTATGTACAATGCACATGACAATCT 57.371 32.000 9.23 0.00 37.22 2.40
1138 1147 1.366319 AGAAGGGCCTGACAAGATGT 58.634 50.000 6.92 0.00 0.00 3.06
1508 1517 6.743575 ACAGAGCACTTATCAACATTAACC 57.256 37.500 0.00 0.00 0.00 2.85
1589 1713 7.829725 ACAACATATGAATCAGCAAGCTTTAA 58.170 30.769 10.38 0.00 0.00 1.52
1601 1727 7.734924 TTGCTGGAGATACAACATATGAATC 57.265 36.000 10.38 6.83 0.00 2.52
1897 2028 9.566624 CAATCAACAAGTAACAAAAATAAAGCG 57.433 29.630 0.00 0.00 0.00 4.68
2178 2309 3.947834 CACGGAAGCCTTGGAAATAGATT 59.052 43.478 0.00 0.00 0.00 2.40
2360 2505 5.104527 TGCAAATGCTCACCCTACTATAGTT 60.105 40.000 11.40 0.00 42.66 2.24
2363 2508 5.308014 CATGCAAATGCTCACCCTACTATA 58.692 41.667 6.97 0.00 42.66 1.31
2791 3007 8.301252 TGCTATATGTAAGAGTAACCAGACAA 57.699 34.615 0.00 0.00 0.00 3.18
2857 3080 2.159841 CCGCACGTGAAAACAGACATAG 60.160 50.000 22.23 0.00 0.00 2.23
2933 3188 5.078949 TGGAAGAGATGAAATTGCTTGGAA 58.921 37.500 0.00 0.00 0.00 3.53
2934 3189 4.665451 TGGAAGAGATGAAATTGCTTGGA 58.335 39.130 0.00 0.00 0.00 3.53
2938 3193 4.643784 GTGGATGGAAGAGATGAAATTGCT 59.356 41.667 0.00 0.00 0.00 3.91
2973 3228 9.265862 TGAATGGATCCTATACCAAAACAATTT 57.734 29.630 14.23 0.00 39.69 1.82
3009 3264 9.865484 GACAAACAAGTTCTAGAAACAGATAAC 57.135 33.333 6.78 0.00 0.00 1.89
3055 3636 0.846015 CCCCAACATCAGGCTGGATA 59.154 55.000 15.73 0.00 31.38 2.59
3076 3657 3.535561 ACACATGATAAGTACTGCTGGC 58.464 45.455 0.00 0.00 0.00 4.85
3085 3666 7.174772 TGCTTTGTCACATTACACATGATAAGT 59.825 33.333 0.00 0.00 0.00 2.24
3091 3672 8.427012 GTTAAATGCTTTGTCACATTACACATG 58.573 33.333 0.00 0.00 35.49 3.21
3106 3806 7.944729 ACATGTCATCCTAGTTAAATGCTTT 57.055 32.000 0.00 0.00 0.00 3.51
3289 4516 6.124088 ACAGTCTTTGCAAGTTGAAACTAG 57.876 37.500 7.16 0.00 38.57 2.57
3314 4541 6.978343 ATTTAACAGTATGCTCTTGCGTAA 57.022 33.333 0.00 0.00 42.53 3.18
3315 4542 6.978343 AATTTAACAGTATGCTCTTGCGTA 57.022 33.333 0.00 0.00 42.53 4.42
3387 4614 1.069978 TGCAGGTTTGACTCACGATGA 59.930 47.619 0.00 0.00 0.00 2.92
3408 4635 5.251700 AGGGATGTATCTGTTCAGTTCCTTT 59.748 40.000 0.00 0.00 0.00 3.11
3576 4803 2.222027 CCGAAGAAACCAAGCTCTGTT 58.778 47.619 0.00 0.00 0.00 3.16
3650 4877 3.305964 TGCGACTGTCTAAAAAGACTCG 58.694 45.455 6.21 10.90 38.60 4.18
3764 4991 0.041839 CTGAAGAACACACGCAGCAC 60.042 55.000 0.00 0.00 0.00 4.40
3966 5193 4.141711 ACAGAACACAGAAAAGCCTACTCA 60.142 41.667 0.00 0.00 0.00 3.41
3986 5213 5.221224 TGGGTCAAGCATTTTTGTTCTACAG 60.221 40.000 0.00 0.00 0.00 2.74
4003 5313 5.651139 GTGTACTAGTATGAGTCTGGGTCAA 59.349 44.000 5.75 0.00 0.00 3.18
4012 5322 5.895928 CACATGCAGTGTACTAGTATGAGT 58.104 41.667 5.75 0.00 43.40 3.41
4085 5402 1.068474 CTAACGAACACCGCCAGAAG 58.932 55.000 0.00 0.00 43.32 2.85
4113 5449 5.347635 TCAAGGATTATTTGAGAACGTGACG 59.652 40.000 2.24 2.24 31.35 4.35
4132 5468 4.463891 ACAAGGTTTTATGCATCCTCAAGG 59.536 41.667 0.19 0.00 0.00 3.61
4133 5469 5.047802 ACACAAGGTTTTATGCATCCTCAAG 60.048 40.000 0.19 0.42 0.00 3.02
4134 5470 4.832266 ACACAAGGTTTTATGCATCCTCAA 59.168 37.500 0.19 0.00 0.00 3.02
4135 5471 4.406456 ACACAAGGTTTTATGCATCCTCA 58.594 39.130 0.19 0.00 0.00 3.86
4136 5472 5.648092 ACTACACAAGGTTTTATGCATCCTC 59.352 40.000 0.19 0.00 0.00 3.71
4137 5473 5.570320 ACTACACAAGGTTTTATGCATCCT 58.430 37.500 0.19 0.00 0.00 3.24
4253 5589 1.090052 AAGCGCGATCTACCTTTGCC 61.090 55.000 12.10 0.00 0.00 4.52
4261 5597 2.577449 TGACATCAAAGCGCGATCTA 57.423 45.000 12.10 0.00 0.00 1.98
4407 5769 2.334838 AGTTAAGTCAATCCACGACGC 58.665 47.619 0.00 0.00 38.46 5.19
4408 5770 4.985044 AAAGTTAAGTCAATCCACGACG 57.015 40.909 0.00 0.00 38.46 5.12
4409 5771 6.426025 AGGTTAAAGTTAAGTCAATCCACGAC 59.574 38.462 0.00 0.00 0.00 4.34
4410 5772 6.527423 AGGTTAAAGTTAAGTCAATCCACGA 58.473 36.000 0.00 0.00 0.00 4.35
4456 5845 3.008049 ACCGTGCTCCAAAATTAGACTCT 59.992 43.478 0.00 0.00 0.00 3.24
4457 5846 3.125316 CACCGTGCTCCAAAATTAGACTC 59.875 47.826 0.00 0.00 0.00 3.36
4458 5847 3.074412 CACCGTGCTCCAAAATTAGACT 58.926 45.455 0.00 0.00 0.00 3.24
4459 5848 2.414161 GCACCGTGCTCCAAAATTAGAC 60.414 50.000 16.51 0.00 40.96 2.59
4460 5849 1.810151 GCACCGTGCTCCAAAATTAGA 59.190 47.619 16.51 0.00 40.96 2.10
4461 5850 1.539388 TGCACCGTGCTCCAAAATTAG 59.461 47.619 23.52 0.00 45.31 1.73
4462 5851 1.610363 TGCACCGTGCTCCAAAATTA 58.390 45.000 23.52 0.00 45.31 1.40
4502 5891 6.071840 ACGGTTGCCACTTAAATATTTTGCTA 60.072 34.615 5.91 0.00 0.00 3.49
4503 5892 5.167845 CGGTTGCCACTTAAATATTTTGCT 58.832 37.500 5.91 0.00 0.00 3.91
4504 5893 4.926832 ACGGTTGCCACTTAAATATTTTGC 59.073 37.500 5.91 3.25 0.00 3.68
4505 5894 6.153067 TCACGGTTGCCACTTAAATATTTTG 58.847 36.000 5.91 2.97 0.00 2.44
4506 5895 6.207810 TCTCACGGTTGCCACTTAAATATTTT 59.792 34.615 5.91 0.00 0.00 1.82
4507 5896 5.708230 TCTCACGGTTGCCACTTAAATATTT 59.292 36.000 5.89 5.89 0.00 1.40
4508 5897 5.123344 GTCTCACGGTTGCCACTTAAATATT 59.877 40.000 0.00 0.00 0.00 1.28
4509 5898 4.634443 GTCTCACGGTTGCCACTTAAATAT 59.366 41.667 0.00 0.00 0.00 1.28
4510 5899 3.998341 GTCTCACGGTTGCCACTTAAATA 59.002 43.478 0.00 0.00 0.00 1.40
4511 5900 2.812011 GTCTCACGGTTGCCACTTAAAT 59.188 45.455 0.00 0.00 0.00 1.40
4512 5901 2.215196 GTCTCACGGTTGCCACTTAAA 58.785 47.619 0.00 0.00 0.00 1.52
4513 5902 1.139256 TGTCTCACGGTTGCCACTTAA 59.861 47.619 0.00 0.00 0.00 1.85
4514 5903 0.753867 TGTCTCACGGTTGCCACTTA 59.246 50.000 0.00 0.00 0.00 2.24
4515 5904 0.532862 CTGTCTCACGGTTGCCACTT 60.533 55.000 0.00 0.00 0.00 3.16
4516 5905 1.069765 CTGTCTCACGGTTGCCACT 59.930 57.895 0.00 0.00 0.00 4.00
4517 5906 0.320771 ATCTGTCTCACGGTTGCCAC 60.321 55.000 0.00 0.00 0.00 5.01
4518 5907 0.396435 AATCTGTCTCACGGTTGCCA 59.604 50.000 0.00 0.00 0.00 4.92
4519 5908 0.798776 CAATCTGTCTCACGGTTGCC 59.201 55.000 0.00 0.00 0.00 4.52
4520 5909 0.166814 GCAATCTGTCTCACGGTTGC 59.833 55.000 0.00 0.00 35.79 4.17
4521 5910 1.511850 TGCAATCTGTCTCACGGTTG 58.488 50.000 0.00 0.00 0.00 3.77
4522 5911 2.254546 TTGCAATCTGTCTCACGGTT 57.745 45.000 0.00 0.00 0.00 4.44
4523 5912 2.254546 TTTGCAATCTGTCTCACGGT 57.745 45.000 0.00 0.00 0.00 4.83
4524 5913 2.549754 AGTTTTGCAATCTGTCTCACGG 59.450 45.455 0.00 0.00 0.00 4.94
4525 5914 3.548587 CAGTTTTGCAATCTGTCTCACG 58.451 45.455 18.17 0.00 0.00 4.35
4546 5935 4.107051 GTGCTGGATGCGTGTGGC 62.107 66.667 0.00 0.00 46.63 5.01
4547 5936 3.792047 CGTGCTGGATGCGTGTGG 61.792 66.667 0.00 0.00 46.63 4.17
4548 5937 3.792047 CCGTGCTGGATGCGTGTG 61.792 66.667 0.00 0.00 46.63 3.82
4549 5938 4.314440 ACCGTGCTGGATGCGTGT 62.314 61.111 2.38 0.00 46.63 4.49
4550 5939 3.792047 CACCGTGCTGGATGCGTG 61.792 66.667 2.38 0.00 46.63 5.34
4551 5940 4.002506 TCACCGTGCTGGATGCGT 62.003 61.111 2.38 0.00 46.63 5.24
4552 5941 3.490759 GTCACCGTGCTGGATGCG 61.491 66.667 2.38 0.00 46.63 4.73
4553 5942 2.046892 AGTCACCGTGCTGGATGC 60.047 61.111 2.38 0.00 42.00 3.91
4554 5943 0.603707 AACAGTCACCGTGCTGGATG 60.604 55.000 20.11 7.10 42.00 3.51
4555 5944 0.108585 AAACAGTCACCGTGCTGGAT 59.891 50.000 20.11 10.58 42.00 3.41
4556 5945 0.531974 GAAACAGTCACCGTGCTGGA 60.532 55.000 20.11 0.00 42.00 3.86
4557 5946 1.831389 CGAAACAGTCACCGTGCTGG 61.831 60.000 20.11 5.22 46.41 4.85
4558 5947 1.564622 CGAAACAGTCACCGTGCTG 59.435 57.895 16.59 16.59 38.58 4.41
4559 5948 1.594293 CCGAAACAGTCACCGTGCT 60.594 57.895 0.00 0.00 0.00 4.40
4560 5949 1.828331 GACCGAAACAGTCACCGTGC 61.828 60.000 0.00 0.00 34.27 5.34
4561 5950 1.545614 CGACCGAAACAGTCACCGTG 61.546 60.000 0.00 0.00 33.70 4.94
4562 5951 1.299620 CGACCGAAACAGTCACCGT 60.300 57.895 0.00 0.00 33.70 4.83
4563 5952 2.654912 GCGACCGAAACAGTCACCG 61.655 63.158 0.00 0.00 33.70 4.94
4564 5953 2.315386 GGCGACCGAAACAGTCACC 61.315 63.158 0.00 0.00 33.70 4.02
4565 5954 2.315386 GGGCGACCGAAACAGTCAC 61.315 63.158 0.00 0.00 43.64 3.67
4566 5955 2.029964 GGGCGACCGAAACAGTCA 59.970 61.111 0.00 0.00 43.64 3.41
4577 5966 1.045911 AAGGAGATCTGGAGGGCGAC 61.046 60.000 0.00 0.00 0.00 5.19
4578 5967 0.757188 GAAGGAGATCTGGAGGGCGA 60.757 60.000 0.00 0.00 0.00 5.54
4579 5968 1.745264 GAAGGAGATCTGGAGGGCG 59.255 63.158 0.00 0.00 0.00 6.13
4580 5969 0.399806 AGGAAGGAGATCTGGAGGGC 60.400 60.000 0.00 0.00 0.00 5.19
4581 5970 2.188818 AAGGAAGGAGATCTGGAGGG 57.811 55.000 0.00 0.00 0.00 4.30
4582 5971 2.437651 GGAAAGGAAGGAGATCTGGAGG 59.562 54.545 0.00 0.00 0.00 4.30
4583 5972 3.836365 GGAAAGGAAGGAGATCTGGAG 57.164 52.381 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.