Multiple sequence alignment - TraesCS4D01G036400

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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 TraesCS4D01G036400 chr4D 100.000 5401 0 0 1 5401 16236046 16230646 0.000000e+00 9974
1 TraesCS4D01G036400 chr4D 95.127 513 24 1 4889 5401 211354833 211355344 0.000000e+00 808
2 TraesCS4D01G036400 chr4A 92.188 3290 147 46 4 3273 584271936 584275135 0.000000e+00 4551
3 TraesCS4D01G036400 chr4A 94.382 801 32 4 4101 4888 584275942 584276742 0.000000e+00 1218
4 TraesCS4D01G036400 chr4A 94.783 690 34 2 3374 4062 584275148 584275836 0.000000e+00 1074
5 TraesCS4D01G036400 chr4B 93.951 2860 148 16 845 3694 28072915 28070071 0.000000e+00 4300
6 TraesCS4D01G036400 chr4B 93.168 805 37 7 4101 4888 28069679 28068876 0.000000e+00 1166
7 TraesCS4D01G036400 chr4B 85.610 820 52 28 1 797 28073900 28073124 0.000000e+00 800
8 TraesCS4D01G036400 chr4B 93.096 449 21 4 4441 4880 27977312 27976865 0.000000e+00 649
9 TraesCS4D01G036400 chr4B 88.710 496 44 8 4397 4887 28041314 28040826 3.600000e-166 595
10 TraesCS4D01G036400 chr4B 96.429 280 10 0 3786 4065 28070059 28069780 3.810000e-126 462
11 TraesCS4D01G036400 chr4B 92.760 221 14 1 4231 4449 27977945 27977725 8.730000e-83 318
12 TraesCS4D01G036400 chr4B 91.579 95 7 1 3696 3790 437940379 437940472 4.390000e-26 130
13 TraesCS4D01G036400 chr5B 83.853 898 143 2 1013 1909 2562565 2561669 0.000000e+00 854
14 TraesCS4D01G036400 chr1A 95.874 509 19 2 4892 5400 567519838 567520344 0.000000e+00 822
15 TraesCS4D01G036400 chr7D 95.481 509 23 0 4892 5400 255928590 255929098 0.000000e+00 813
16 TraesCS4D01G036400 chr7D 94.706 510 25 2 4892 5400 563297132 563297640 0.000000e+00 791
17 TraesCS4D01G036400 chr6D 95.490 510 22 1 4891 5400 363172665 363173173 0.000000e+00 813
18 TraesCS4D01G036400 chr6D 94.892 509 24 2 4892 5400 20092795 20093301 0.000000e+00 795
19 TraesCS4D01G036400 chr5D 95.490 510 22 1 4890 5399 285845308 285845816 0.000000e+00 813
20 TraesCS4D01G036400 chr5D 79.755 736 130 14 2237 2962 2669658 2668932 2.880000e-142 516
21 TraesCS4D01G036400 chr3A 95.098 510 25 0 4891 5400 749627855 749627346 0.000000e+00 804
22 TraesCS4D01G036400 chr5A 94.563 515 27 1 4886 5400 8536833 8537346 0.000000e+00 795
23 TraesCS4D01G036400 chr5A 78.990 733 144 9 2237 2962 2112173 2112902 4.860000e-135 492
24 TraesCS4D01G036400 chr5A 87.500 104 13 0 3696 3799 50752689 50752586 2.640000e-23 121
25 TraesCS4D01G036400 chr3B 80.825 897 172 0 1013 1909 720834042 720833146 0.000000e+00 704
26 TraesCS4D01G036400 chr3B 97.500 80 2 0 3696 3775 6673719 6673798 2.620000e-28 137
27 TraesCS4D01G036400 chr7A 93.548 93 6 0 3696 3788 431990905 431990997 7.290000e-29 139
28 TraesCS4D01G036400 chrUn 92.632 95 7 0 3695 3789 62690555 62690461 2.620000e-28 137
29 TraesCS4D01G036400 chr2B 94.253 87 5 0 3696 3782 478114376 478114462 3.390000e-27 134
30 TraesCS4D01G036400 chr6B 90.909 99 8 1 3688 3786 91307310 91307407 1.220000e-26 132
31 TraesCS4D01G036400 chr2D 87.156 109 12 2 3688 3795 381063574 381063681 7.350000e-24 122


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 TraesCS4D01G036400 chr4D 16230646 16236046 5400 True 9974.0 9974 100.000000 1 5401 1 chr4D.!!$R1 5400
1 TraesCS4D01G036400 chr4D 211354833 211355344 511 False 808.0 808 95.127000 4889 5401 1 chr4D.!!$F1 512
2 TraesCS4D01G036400 chr4A 584271936 584276742 4806 False 2281.0 4551 93.784333 4 4888 3 chr4A.!!$F1 4884
3 TraesCS4D01G036400 chr4B 28068876 28073900 5024 True 1682.0 4300 92.289500 1 4888 4 chr4B.!!$R3 4887
4 TraesCS4D01G036400 chr4B 27976865 27977945 1080 True 483.5 649 92.928000 4231 4880 2 chr4B.!!$R2 649
5 TraesCS4D01G036400 chr5B 2561669 2562565 896 True 854.0 854 83.853000 1013 1909 1 chr5B.!!$R1 896
6 TraesCS4D01G036400 chr1A 567519838 567520344 506 False 822.0 822 95.874000 4892 5400 1 chr1A.!!$F1 508
7 TraesCS4D01G036400 chr7D 255928590 255929098 508 False 813.0 813 95.481000 4892 5400 1 chr7D.!!$F1 508
8 TraesCS4D01G036400 chr7D 563297132 563297640 508 False 791.0 791 94.706000 4892 5400 1 chr7D.!!$F2 508
9 TraesCS4D01G036400 chr6D 363172665 363173173 508 False 813.0 813 95.490000 4891 5400 1 chr6D.!!$F2 509
10 TraesCS4D01G036400 chr6D 20092795 20093301 506 False 795.0 795 94.892000 4892 5400 1 chr6D.!!$F1 508
11 TraesCS4D01G036400 chr5D 285845308 285845816 508 False 813.0 813 95.490000 4890 5399 1 chr5D.!!$F1 509
12 TraesCS4D01G036400 chr5D 2668932 2669658 726 True 516.0 516 79.755000 2237 2962 1 chr5D.!!$R1 725
13 TraesCS4D01G036400 chr3A 749627346 749627855 509 True 804.0 804 95.098000 4891 5400 1 chr3A.!!$R1 509
14 TraesCS4D01G036400 chr5A 8536833 8537346 513 False 795.0 795 94.563000 4886 5400 1 chr5A.!!$F2 514
15 TraesCS4D01G036400 chr5A 2112173 2112902 729 False 492.0 492 78.990000 2237 2962 1 chr5A.!!$F1 725
16 TraesCS4D01G036400 chr3B 720833146 720834042 896 True 704.0 704 80.825000 1013 1909 1 chr3B.!!$R1 896

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
50 51 0.237498 GGGCGAAAAGAAAGACCACG 59.763 55.000 0.0 0.0 0.00 4.94 F
52 53 0.385598 GCGAAAAGAAAGACCACGGC 60.386 55.000 0.0 0.0 0.00 5.68 F
1519 1718 0.617820 TGTGGAGCTAGGAAGGACCC 60.618 60.000 0.0 0.0 40.05 4.46 F
1587 1786 1.134670 AGTCTCCAGCTTTCGCATACC 60.135 52.381 0.0 0.0 39.10 2.73 F
2040 2239 1.135689 GCATGTGATGTTTCCACCGAC 60.136 52.381 0.0 0.0 33.80 4.79 F
3334 3546 0.508641 CACAGAACAAAGCGAGACCG 59.491 55.000 0.0 0.0 39.16 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 2125 0.602638 AGCGGCATTGTGTTCGAGAA 60.603 50.000 1.45 0.0 0.00 2.87 R
1927 2126 0.602638 AAGCGGCATTGTGTTCGAGA 60.603 50.000 1.45 0.0 0.00 4.04 R
3317 3529 1.063806 CTCGGTCTCGCTTTGTTCTG 58.936 55.000 0.00 0.0 36.13 3.02 R
3321 3533 1.272490 TCAATCTCGGTCTCGCTTTGT 59.728 47.619 0.00 0.0 36.13 2.83 R
3892 4107 0.035881 CTCCAGGCTGAGTTTGAGCA 59.964 55.000 17.94 0.0 38.27 4.26 R
4457 5169 2.000048 AGGCACAAAATTAGAGGGGGA 59.000 47.619 0.00 0.0 0.00 4.81 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
31 32 2.989253 GTGGGGACAAAAGCGGGG 60.989 66.667 0.00 0.00 46.06 5.73
32 33 4.293671 TGGGGACAAAAGCGGGGG 62.294 66.667 0.00 0.00 37.44 5.40
50 51 0.237498 GGGCGAAAAGAAAGACCACG 59.763 55.000 0.00 0.00 0.00 4.94
51 52 0.237498 GGCGAAAAGAAAGACCACGG 59.763 55.000 0.00 0.00 0.00 4.94
52 53 0.385598 GCGAAAAGAAAGACCACGGC 60.386 55.000 0.00 0.00 0.00 5.68
53 54 0.941542 CGAAAAGAAAGACCACGGCA 59.058 50.000 0.00 0.00 0.00 5.69
54 55 1.333791 CGAAAAGAAAGACCACGGCAC 60.334 52.381 0.00 0.00 0.00 5.01
191 192 2.432628 GACGACTTCACTGCCCCG 60.433 66.667 0.00 0.00 0.00 5.73
409 434 4.400529 TCTGGGTTTTCTTTTCTTTGGC 57.599 40.909 0.00 0.00 0.00 4.52
410 435 4.030216 TCTGGGTTTTCTTTTCTTTGGCT 58.970 39.130 0.00 0.00 0.00 4.75
438 463 1.228245 GGGCTTGCTGTGGTCAAGA 60.228 57.895 6.89 0.00 42.52 3.02
443 473 0.819259 TTGCTGTGGTCAAGAGGTGC 60.819 55.000 0.00 0.00 0.00 5.01
567 598 3.537874 GGGCGGGTGCTCGATAGT 61.538 66.667 0.00 0.00 42.25 2.12
568 599 2.279517 GGCGGGTGCTCGATAGTG 60.280 66.667 0.00 0.00 42.25 2.74
575 606 4.971125 GCTCGATAGTGCGGGGCC 62.971 72.222 0.00 0.00 46.23 5.80
576 607 4.647615 CTCGATAGTGCGGGGCCG 62.648 72.222 0.00 0.00 39.08 6.13
618 649 1.000771 GAGTGGGGAAAGGGGAAGC 60.001 63.158 0.00 0.00 0.00 3.86
624 655 2.343426 GGAAAGGGGAAGCGGCTTG 61.343 63.158 21.70 0.00 0.00 4.01
648 680 1.841663 GACACGCGGTGCTGAAATGT 61.842 55.000 12.47 1.13 36.98 2.71
650 682 1.891919 ACGCGGTGCTGAAATGTGT 60.892 52.632 12.47 0.00 0.00 3.72
678 710 6.022163 AGTGCTGAAATTCAGGAAATCTTG 57.978 37.500 22.73 0.00 46.30 3.02
704 736 3.350833 GAAATTCAGAGATGCCAGTGGT 58.649 45.455 11.74 0.00 0.00 4.16
716 748 1.755179 CCAGTGGTAGGCAAGATTGG 58.245 55.000 0.00 0.00 0.00 3.16
753 785 2.230508 CACTTGCAGATGGTTGATTGCT 59.769 45.455 0.00 0.00 37.45 3.91
756 788 1.820519 TGCAGATGGTTGATTGCTTCC 59.179 47.619 0.00 0.00 37.45 3.46
760 792 3.128242 CAGATGGTTGATTGCTTCCTGTC 59.872 47.826 0.00 0.00 0.00 3.51
774 806 1.151777 CCTGTCGTGTGTTTGAGCGT 61.152 55.000 0.00 0.00 0.00 5.07
797 829 7.244898 CGTTCTACTCCTATGCTATATGTGTC 58.755 42.308 0.00 0.00 0.00 3.67
798 830 7.094762 CGTTCTACTCCTATGCTATATGTGTCA 60.095 40.741 0.00 0.00 0.00 3.58
799 831 7.689446 TCTACTCCTATGCTATATGTGTCAC 57.311 40.000 0.00 0.00 0.00 3.67
806 838 4.301637 TGCTATATGTGTCACGACGAAT 57.698 40.909 0.00 0.00 0.00 3.34
817 849 3.000674 GTCACGACGAATATTCAGTGCTG 60.001 47.826 21.33 13.93 31.37 4.41
870 1066 7.712797 ACACAGTTCCTGTTATTTTAAAGTGG 58.287 34.615 0.00 0.00 42.59 4.00
886 1082 4.423625 AAGTGGTATATGAACCTCCTGC 57.576 45.455 0.00 0.00 40.44 4.85
887 1083 3.658725 AGTGGTATATGAACCTCCTGCT 58.341 45.455 0.00 0.00 40.44 4.24
935 1134 1.271001 TGAGTGGGTTGAGCATGACTG 60.271 52.381 0.00 0.00 0.00 3.51
947 1146 4.095932 TGAGCATGACTGATTTCTGCATTC 59.904 41.667 0.00 0.00 35.32 2.67
991 1190 1.878088 ACAACTGATGCAGTGCTGAAG 59.122 47.619 17.60 12.62 44.62 3.02
995 1194 1.540267 CTGATGCAGTGCTGAAGCTTT 59.460 47.619 17.60 0.00 42.66 3.51
1041 1240 4.457496 CCGCTGTGGCCGACTGAT 62.457 66.667 13.67 0.00 34.44 2.90
1050 1249 1.109920 GGCCGACTGATGAGCTCCTA 61.110 60.000 12.15 0.00 0.00 2.94
1257 1456 1.671054 AAAGACCGTCGCCATGGTG 60.671 57.895 19.75 19.75 42.59 4.17
1380 1579 6.488006 AGCTGTTTCTGAAGAATAAAGCTGAA 59.512 34.615 17.20 0.00 40.12 3.02
1519 1718 0.617820 TGTGGAGCTAGGAAGGACCC 60.618 60.000 0.00 0.00 40.05 4.46
1587 1786 1.134670 AGTCTCCAGCTTTCGCATACC 60.135 52.381 0.00 0.00 39.10 2.73
1680 1879 5.321102 AGCAATCGGGCAATTATAATACCA 58.679 37.500 15.71 1.59 35.83 3.25
2008 2207 4.500716 GGTGAATGGTGTTTAAGGTGTTGG 60.501 45.833 0.00 0.00 0.00 3.77
2040 2239 1.135689 GCATGTGATGTTTCCACCGAC 60.136 52.381 0.00 0.00 33.80 4.79
2072 2271 8.885494 TCTTCAACTGGGAAATGTTTTATTTG 57.115 30.769 0.00 0.00 0.00 2.32
2118 2317 4.340381 GGGCTTCTGCAAATAACATCAGAT 59.660 41.667 0.00 0.00 41.91 2.90
2119 2318 5.506982 GGGCTTCTGCAAATAACATCAGATC 60.507 44.000 0.00 0.00 41.91 2.75
2120 2319 5.298777 GGCTTCTGCAAATAACATCAGATCT 59.701 40.000 0.00 0.00 41.91 2.75
2121 2320 6.428799 GCTTCTGCAAATAACATCAGATCTC 58.571 40.000 0.00 0.00 39.41 2.75
2622 2825 8.398665 GTTTTCAAAGAGGTCGCAATATTATCT 58.601 33.333 0.00 0.00 0.00 1.98
2951 3163 7.487189 GCAAGTGATGACCATTTCTATTTGAAG 59.513 37.037 0.00 0.00 35.89 3.02
3086 3298 1.446907 CCCTGTGCATCTTCAGTCAC 58.553 55.000 0.00 0.00 0.00 3.67
3134 3346 5.207768 GCATGTATGAAATTAGCCACTTCG 58.792 41.667 0.00 0.00 0.00 3.79
3137 3349 5.680619 TGTATGAAATTAGCCACTTCGGAT 58.319 37.500 0.00 0.00 36.56 4.18
3150 3362 5.934625 GCCACTTCGGATCATTACTTATCAT 59.065 40.000 0.00 0.00 36.56 2.45
3206 3418 1.265635 CGGCTGGAATGTTTCGTCAAA 59.734 47.619 0.00 0.00 0.00 2.69
3220 3432 7.132213 TGTTTCGTCAAATCATCTTCAAGTTC 58.868 34.615 0.00 0.00 0.00 3.01
3264 3476 4.829492 CAGATGTTTTTCCAGTTCTCCCTT 59.171 41.667 0.00 0.00 0.00 3.95
3292 3504 3.267031 GCTATACCATAGGGGCCATCTTT 59.733 47.826 4.39 0.00 42.05 2.52
3294 3506 5.045140 GCTATACCATAGGGGCCATCTTTTA 60.045 44.000 4.39 0.00 42.05 1.52
3301 3513 4.197559 AGGGGCCATCTTTTATTGCATA 57.802 40.909 4.39 0.00 0.00 3.14
3305 3517 6.101588 AGGGGCCATCTTTTATTGCATATTTT 59.898 34.615 4.39 0.00 0.00 1.82
3306 3518 6.205270 GGGGCCATCTTTTATTGCATATTTTG 59.795 38.462 4.39 0.00 0.00 2.44
3327 3539 2.345341 GTGCAACAACACAGAACAAAGC 59.655 45.455 0.00 0.00 40.40 3.51
3334 3546 0.508641 CACAGAACAAAGCGAGACCG 59.491 55.000 0.00 0.00 39.16 4.79
3349 3561 3.490933 CGAGACCGAGATTGAATTAGCCA 60.491 47.826 0.00 0.00 38.22 4.75
3415 3630 3.288092 GAGACAGAAACCCAAACCAACT 58.712 45.455 0.00 0.00 0.00 3.16
3437 3652 2.073117 TCGCGTTCTCAACTATGCAA 57.927 45.000 5.77 0.00 0.00 4.08
3705 3920 6.157820 TGATGTGTAATCATTTACTCCCTCCA 59.842 38.462 0.00 0.00 38.81 3.86
3706 3921 6.381498 TGTGTAATCATTTACTCCCTCCAA 57.619 37.500 0.00 0.00 38.81 3.53
3722 3937 4.127171 CCTCCAACCCATAATGTAAGACG 58.873 47.826 0.00 0.00 0.00 4.18
3892 4107 8.608185 ATCTACCCCATGTATTCACAAAATTT 57.392 30.769 0.00 0.00 38.42 1.82
4004 4219 5.357314 CGATCTCCTTACTTGTAGACCTTCA 59.643 44.000 0.00 0.00 0.00 3.02
4031 4246 7.119262 AGAGTGTATGTTATTGTGCTTGGTAAC 59.881 37.037 0.00 0.00 0.00 2.50
4062 4277 4.388485 TCTTGAAGCAGCACACAAAGATA 58.612 39.130 0.00 0.00 0.00 1.98
4065 4280 6.314648 TCTTGAAGCAGCACACAAAGATATAG 59.685 38.462 0.00 0.00 0.00 1.31
4067 4282 6.639563 TGAAGCAGCACACAAAGATATAGTA 58.360 36.000 0.00 0.00 0.00 1.82
4068 4283 7.275183 TGAAGCAGCACACAAAGATATAGTAT 58.725 34.615 0.00 0.00 0.00 2.12
4069 4284 8.421002 TGAAGCAGCACACAAAGATATAGTATA 58.579 33.333 0.00 0.00 0.00 1.47
4070 4285 9.429359 GAAGCAGCACACAAAGATATAGTATAT 57.571 33.333 2.12 2.12 0.00 0.86
4071 4286 8.768957 AGCAGCACACAAAGATATAGTATATG 57.231 34.615 7.41 0.00 0.00 1.78
4072 4287 8.370940 AGCAGCACACAAAGATATAGTATATGT 58.629 33.333 7.41 0.58 0.00 2.29
4085 4300 6.896021 ATAGTATATGTTACTGTGCTCGGT 57.104 37.500 5.45 5.45 37.00 4.69
4086 4301 7.991084 ATAGTATATGTTACTGTGCTCGGTA 57.009 36.000 3.33 3.33 34.68 4.02
4092 4307 3.570926 TTACTGTGCTCGGTAACTCTG 57.429 47.619 14.63 0.00 39.56 3.35
4093 4308 0.038159 ACTGTGCTCGGTAACTCTGC 60.038 55.000 0.00 0.00 0.00 4.26
4094 4309 0.244994 CTGTGCTCGGTAACTCTGCT 59.755 55.000 0.00 0.00 0.00 4.24
4095 4310 0.243907 TGTGCTCGGTAACTCTGCTC 59.756 55.000 0.00 0.00 0.00 4.26
4097 4312 0.243907 TGCTCGGTAACTCTGCTCAC 59.756 55.000 0.00 0.00 0.00 3.51
4099 4314 1.067495 GCTCGGTAACTCTGCTCACTT 60.067 52.381 0.00 0.00 0.00 3.16
4138 4423 6.645415 GTGAATCACTCTTTCTAAAACTCGGA 59.355 38.462 6.07 0.00 0.00 4.55
4140 4425 7.385205 TGAATCACTCTTTCTAAAACTCGGAAG 59.615 37.037 0.00 0.00 0.00 3.46
4141 4426 4.989168 TCACTCTTTCTAAAACTCGGAAGC 59.011 41.667 0.00 0.00 0.00 3.86
4143 4428 4.202326 ACTCTTTCTAAAACTCGGAAGCCA 60.202 41.667 0.00 0.00 0.00 4.75
4211 4497 1.676384 GCTGGACAGTGAAGGAGCT 59.324 57.895 0.00 0.00 0.00 4.09
4415 4703 8.460428 AGAAGTGTATGAGCTAGTGTAAACTAC 58.540 37.037 0.00 0.00 0.00 2.73
4457 5169 3.577415 AGGGAGTCGTAGCTAGTTTTGTT 59.423 43.478 0.00 0.00 0.00 2.83
4558 5271 2.270352 TGCAGTTAAGTTCCTGGGTG 57.730 50.000 0.00 0.00 0.00 4.61
4615 5328 3.798337 GTCAGCCAATTTGCATATTTCGG 59.202 43.478 4.12 1.29 0.00 4.30
4619 5332 2.865551 CCAATTTGCATATTTCGGGTGC 59.134 45.455 0.00 0.00 39.26 5.01
4642 5355 2.351835 CGTGAGCCCGGTTATATCAGAG 60.352 54.545 0.00 0.00 0.00 3.35
4683 5408 6.039941 TGGAAACCATGTGTAAAAGTTTCGAT 59.960 34.615 12.36 0.00 44.52 3.59
4914 5648 3.336509 TTTTGGAAAATGGGGGACTCA 57.663 42.857 0.00 0.00 0.00 3.41
5075 5809 2.038387 ACCGGCTAGCATAACAAAGG 57.962 50.000 18.24 8.36 0.00 3.11
5184 5918 0.605589 AGTAACCAAACGCTCCCTGC 60.606 55.000 0.00 0.00 38.57 4.85
5234 5968 3.706563 GATCAGCGCAGTGGCTCGA 62.707 63.158 11.47 5.92 42.53 4.04
5297 6032 4.612264 AGCCAAATCATTTCTGCAGTTT 57.388 36.364 14.67 2.57 0.00 2.66
5305 6040 8.339714 CAAATCATTTCTGCAGTTTCAAATTGT 58.660 29.630 14.67 0.91 0.00 2.71
5361 6096 4.577283 GTCTAGCTGTTTCGGACTCTATCT 59.423 45.833 0.00 0.00 0.00 1.98
5369 6104 4.720649 TTCGGACTCTATCTCAACAAGG 57.279 45.455 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.237498 CGTGGTCTTTCTTTTCGCCC 59.763 55.000 0.00 0.00 0.00 6.13
32 33 0.237498 CCGTGGTCTTTCTTTTCGCC 59.763 55.000 0.00 0.00 0.00 5.54
89 90 4.037923 AGCAGAAAAAGAAAGGAAATGCGA 59.962 37.500 0.00 0.00 36.31 5.10
280 302 2.435410 GGTTGTACGGCGGGGAAG 60.435 66.667 13.24 0.00 0.00 3.46
281 303 2.453379 GAAGGTTGTACGGCGGGGAA 62.453 60.000 13.24 0.00 0.00 3.97
282 304 2.924101 AAGGTTGTACGGCGGGGA 60.924 61.111 13.24 0.00 0.00 4.81
382 407 3.503748 AGAAAAGAAAACCCAGATCTGCG 59.496 43.478 17.76 11.70 0.00 5.18
438 463 1.693606 CAAAAATCAACCCCTGCACCT 59.306 47.619 0.00 0.00 0.00 4.00
443 473 0.324614 GCCCCAAAAATCAACCCCTG 59.675 55.000 0.00 0.00 0.00 4.45
558 589 4.971125 GGCCCCGCACTATCGAGC 62.971 72.222 0.00 0.00 0.00 5.03
577 608 4.034258 CAACACGCAGCAGCCCAG 62.034 66.667 0.00 0.00 37.52 4.45
578 609 3.848301 ATCAACACGCAGCAGCCCA 62.848 57.895 0.00 0.00 37.52 5.36
579 610 3.058160 ATCAACACGCAGCAGCCC 61.058 61.111 0.00 0.00 37.52 5.19
580 611 2.177531 CATCAACACGCAGCAGCC 59.822 61.111 0.00 0.00 37.52 4.85
581 612 1.154338 GACATCAACACGCAGCAGC 60.154 57.895 0.00 0.00 37.42 5.25
582 613 1.131218 CGACATCAACACGCAGCAG 59.869 57.895 0.00 0.00 0.00 4.24
618 649 2.551270 GCGTGTCACTTCAAGCCG 59.449 61.111 0.65 0.00 36.97 5.52
621 652 1.564622 CACCGCGTGTCACTTCAAG 59.435 57.895 4.92 0.00 0.00 3.02
624 655 2.661866 AGCACCGCGTGTCACTTC 60.662 61.111 4.92 0.00 35.75 3.01
648 680 1.071542 TGAATTTCAGCACTCCCGACA 59.928 47.619 0.00 0.00 0.00 4.35
650 682 1.339055 CCTGAATTTCAGCACTCCCGA 60.339 52.381 19.04 0.00 42.98 5.14
678 710 2.679837 TGGCATCTCTGAATTTCGAAGC 59.320 45.455 0.00 0.00 0.00 3.86
704 736 2.507058 AGCTCATGACCAATCTTGCCTA 59.493 45.455 0.00 0.00 31.52 3.93
712 744 4.018960 AGTGGTTCTTAGCTCATGACCAAT 60.019 41.667 11.98 9.20 0.00 3.16
713 745 3.327757 AGTGGTTCTTAGCTCATGACCAA 59.672 43.478 11.98 0.00 0.00 3.67
716 748 3.126000 GCAAGTGGTTCTTAGCTCATGAC 59.874 47.826 0.00 0.00 34.66 3.06
745 777 1.872952 CACACGACAGGAAGCAATCAA 59.127 47.619 0.00 0.00 0.00 2.57
746 778 1.202639 ACACACGACAGGAAGCAATCA 60.203 47.619 0.00 0.00 0.00 2.57
753 785 1.295792 GCTCAAACACACGACAGGAA 58.704 50.000 0.00 0.00 0.00 3.36
756 788 0.650512 AACGCTCAAACACACGACAG 59.349 50.000 0.00 0.00 0.00 3.51
760 792 2.124903 AGTAGAACGCTCAAACACACG 58.875 47.619 0.00 0.00 0.00 4.49
774 806 7.094762 CGTGACACATATAGCATAGGAGTAGAA 60.095 40.741 6.37 0.00 0.00 2.10
797 829 2.923655 ACAGCACTGAATATTCGTCGTG 59.076 45.455 19.68 19.68 0.00 4.35
798 830 3.232213 ACAGCACTGAATATTCGTCGT 57.768 42.857 10.80 5.21 0.00 4.34
799 831 4.584029 AAACAGCACTGAATATTCGTCG 57.416 40.909 10.80 4.63 0.00 5.12
870 1066 4.408182 ACACAGCAGGAGGTTCATATAC 57.592 45.455 0.00 0.00 0.00 1.47
882 1078 1.334869 GAACTCCAACAACACAGCAGG 59.665 52.381 0.00 0.00 0.00 4.85
905 1101 3.684908 TCAACCCACTCATACACATTGG 58.315 45.455 0.00 0.00 0.00 3.16
935 1134 5.288543 ACAGAAGAACGAATGCAGAAATC 57.711 39.130 0.00 0.00 0.00 2.17
947 1146 4.152402 CACAACATTCCCTACAGAAGAACG 59.848 45.833 0.00 0.00 0.00 3.95
991 1190 0.248215 CATCGTTCCATCGCCAAAGC 60.248 55.000 0.00 0.00 0.00 3.51
995 1194 2.889988 CGCATCGTTCCATCGCCA 60.890 61.111 0.00 0.00 0.00 5.69
1041 1240 4.353777 ACTGGTACTTGATTAGGAGCTCA 58.646 43.478 17.19 0.00 36.11 4.26
1050 1249 4.954202 TCGGAGATGTACTGGTACTTGATT 59.046 41.667 11.44 0.00 37.00 2.57
1257 1456 0.958822 AAACCTTGGCAACCGTCATC 59.041 50.000 0.00 0.00 0.00 2.92
1380 1579 1.202330 CCATCTCCCAGTCAAGCTCT 58.798 55.000 0.00 0.00 0.00 4.09
1519 1718 1.372087 GCGCATTCTTCCAGACCCAG 61.372 60.000 0.30 0.00 0.00 4.45
1587 1786 1.973281 AGTGATTTGGTGGCGCAGG 60.973 57.895 10.83 0.00 0.00 4.85
1680 1879 0.827507 GTGCCAAAGGGGATGTGTGT 60.828 55.000 0.00 0.00 40.01 3.72
1926 2125 0.602638 AGCGGCATTGTGTTCGAGAA 60.603 50.000 1.45 0.00 0.00 2.87
1927 2126 0.602638 AAGCGGCATTGTGTTCGAGA 60.603 50.000 1.45 0.00 0.00 4.04
2034 2233 2.294791 AGTTGAAGAGTCTCTGTCGGTG 59.705 50.000 2.28 0.00 0.00 4.94
2040 2239 4.342862 TTTCCCAGTTGAAGAGTCTCTG 57.657 45.455 2.28 0.00 0.00 3.35
2072 2271 6.863126 CCCTTGAACAATTCATAGTTGTGAAC 59.137 38.462 0.00 0.00 40.60 3.18
2264 2467 4.631377 CACGCATGGACTCTTCAAGAATAA 59.369 41.667 0.00 0.00 0.00 1.40
3086 3298 3.942829 TGTTGAGCAAAGGTATCTCCAG 58.057 45.455 0.00 0.00 39.02 3.86
3168 3380 1.656652 CGAGATTTCGGATGTGCCTT 58.343 50.000 0.00 0.00 43.05 4.35
3194 3406 7.206981 ACTTGAAGATGATTTGACGAAACAT 57.793 32.000 0.00 0.00 0.00 2.71
3206 3418 7.932491 CAGTCATATGGAGAACTTGAAGATGAT 59.068 37.037 0.00 0.00 0.00 2.45
3220 3432 4.474394 TGGACCTAGACAGTCATATGGAG 58.526 47.826 2.66 0.00 35.89 3.86
3281 3493 5.488262 AATATGCAATAAAAGATGGCCCC 57.512 39.130 0.00 0.00 29.06 5.80
3305 3517 3.573598 CTTTGTTCTGTGTTGTTGCACA 58.426 40.909 0.00 0.00 45.85 4.57
3306 3518 2.345341 GCTTTGTTCTGTGTTGTTGCAC 59.655 45.455 0.00 0.00 39.65 4.57
3312 3524 2.286418 GGTCTCGCTTTGTTCTGTGTTG 60.286 50.000 0.00 0.00 0.00 3.33
3317 3529 1.063806 CTCGGTCTCGCTTTGTTCTG 58.936 55.000 0.00 0.00 36.13 3.02
3321 3533 1.272490 TCAATCTCGGTCTCGCTTTGT 59.728 47.619 0.00 0.00 36.13 2.83
3326 3538 2.473235 GCTAATTCAATCTCGGTCTCGC 59.527 50.000 0.00 0.00 36.13 5.03
3327 3539 3.053455 GGCTAATTCAATCTCGGTCTCG 58.947 50.000 0.00 0.00 37.82 4.04
3355 3567 7.215789 TCATGTTTCCATTTAATGCTGTGTTT 58.784 30.769 0.00 0.00 0.00 2.83
3356 3568 6.757237 TCATGTTTCCATTTAATGCTGTGTT 58.243 32.000 0.00 0.00 0.00 3.32
3362 3574 4.268405 CCGCTTCATGTTTCCATTTAATGC 59.732 41.667 0.00 0.00 0.00 3.56
3384 3598 3.335579 GGTTTCTGTCTCATGTACCACC 58.664 50.000 0.00 0.00 0.00 4.61
3415 3630 2.193447 GCATAGTTGAGAACGCGATGA 58.807 47.619 15.93 0.00 36.23 2.92
3437 3652 8.942338 TTGTTGTTATATCTTAACATCGCTCT 57.058 30.769 0.00 0.00 37.29 4.09
3474 3689 9.611284 TGATGAAATGTTCTTTTAACTGAATCG 57.389 29.630 0.00 0.00 0.00 3.34
3695 3910 3.743132 ACATTATGGGTTGGAGGGAGTA 58.257 45.455 0.00 0.00 0.00 2.59
3770 3985 9.154847 GAAAATTGCTAAACAAATATTGCCTCT 57.845 29.630 0.00 0.00 42.86 3.69
3892 4107 0.035881 CTCCAGGCTGAGTTTGAGCA 59.964 55.000 17.94 0.00 38.27 4.26
4004 4219 6.003950 ACCAAGCACAATAACATACACTCTT 58.996 36.000 0.00 0.00 0.00 2.85
4062 4277 6.896021 ACCGAGCACAGTAACATATACTAT 57.104 37.500 0.00 0.00 0.00 2.12
4065 4280 6.501781 AGTTACCGAGCACAGTAACATATAC 58.498 40.000 18.59 0.00 46.95 1.47
4067 4282 5.360144 AGAGTTACCGAGCACAGTAACATAT 59.640 40.000 18.59 2.77 46.95 1.78
4068 4283 4.703575 AGAGTTACCGAGCACAGTAACATA 59.296 41.667 18.59 0.00 46.95 2.29
4069 4284 3.510360 AGAGTTACCGAGCACAGTAACAT 59.490 43.478 18.59 7.45 46.95 2.71
4070 4285 2.889045 AGAGTTACCGAGCACAGTAACA 59.111 45.455 18.59 0.00 46.95 2.41
4071 4286 3.243336 CAGAGTTACCGAGCACAGTAAC 58.757 50.000 11.19 11.19 45.60 2.50
4072 4287 2.352421 GCAGAGTTACCGAGCACAGTAA 60.352 50.000 0.00 0.00 0.00 2.24
4075 4290 0.244994 AGCAGAGTTACCGAGCACAG 59.755 55.000 0.00 0.00 0.00 3.66
4076 4291 0.243907 GAGCAGAGTTACCGAGCACA 59.756 55.000 0.00 0.00 0.00 4.57
4077 4292 0.243907 TGAGCAGAGTTACCGAGCAC 59.756 55.000 0.00 0.00 0.00 4.40
4079 4294 0.528470 AGTGAGCAGAGTTACCGAGC 59.472 55.000 0.00 0.00 0.00 5.03
4080 4295 2.600731 CAAGTGAGCAGAGTTACCGAG 58.399 52.381 0.00 0.00 0.00 4.63
4082 4297 1.000955 ACCAAGTGAGCAGAGTTACCG 59.999 52.381 0.00 0.00 0.00 4.02
4083 4298 2.841442 ACCAAGTGAGCAGAGTTACC 57.159 50.000 0.00 0.00 0.00 2.85
4085 4300 4.689612 AAGAACCAAGTGAGCAGAGTTA 57.310 40.909 0.00 0.00 0.00 2.24
4086 4301 3.567478 AAGAACCAAGTGAGCAGAGTT 57.433 42.857 0.00 0.00 0.00 3.01
4097 4312 7.162082 AGTGATTCACTAGGTTAAGAACCAAG 58.838 38.462 17.63 0.00 46.04 3.61
4099 4314 6.681729 AGTGATTCACTAGGTTAAGAACCA 57.318 37.500 17.63 0.00 46.04 3.67
4118 4403 4.989168 GCTTCCGAGTTTTAGAAAGAGTGA 59.011 41.667 0.00 0.00 0.00 3.41
4124 4409 5.181245 CAGAATGGCTTCCGAGTTTTAGAAA 59.819 40.000 0.00 0.00 31.27 2.52
4138 4423 4.957954 TGCATAGGATTTTCAGAATGGCTT 59.042 37.500 0.00 0.00 36.16 4.35
4140 4425 4.868067 CTGCATAGGATTTTCAGAATGGC 58.132 43.478 0.00 0.00 36.16 4.40
4211 4497 4.704833 GCCGTGCAGCCTCTTCCA 62.705 66.667 0.00 0.00 0.00 3.53
4457 5169 2.000048 AGGCACAAAATTAGAGGGGGA 59.000 47.619 0.00 0.00 0.00 4.81
4795 5526 7.656137 TCAAGTACTGTTTCTGGAACAAGATAC 59.344 37.037 2.68 6.28 46.99 2.24
4914 5648 2.293318 TTCTGATGCAGAGGCCGGT 61.293 57.895 1.90 0.00 41.75 5.28
5004 5738 2.659016 CTCTCCGTGAGCTTGCCA 59.341 61.111 0.00 0.00 35.84 4.92
5075 5809 6.587206 AGGATAGGCGATTAGTTTACCTAC 57.413 41.667 0.00 0.00 35.88 3.18
5268 6003 6.935771 TGCAGAAATGATTTGGCTTTTAACAT 59.064 30.769 11.04 0.00 0.00 2.71
5297 6032 4.180057 GTGCTTTGTTGTGGACAATTTGA 58.820 39.130 2.79 0.00 46.99 2.69
5305 6040 3.146066 GGAGTATGTGCTTTGTTGTGGA 58.854 45.455 0.00 0.00 0.00 4.02
5361 6096 1.464734 TTTGGAACGTGCCTTGTTGA 58.535 45.000 15.35 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.