Multiple sequence alignment - TraesCS7A01G421400

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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 TraesCS7A01G421400 chr7A 100.000 7262 0 0 1 7262 612417882 612410621 0.000000e+00 13411
1 TraesCS7A01G421400 chr7B 94.589 4084 146 31 2363 6415 572420227 572416188 0.000000e+00 6248
2 TraesCS7A01G421400 chr7B 93.809 2342 97 13 12 2339 572422852 572420545 0.000000e+00 3478
3 TraesCS7A01G421400 chr7D 95.483 3343 78 22 3144 6415 531862059 531858719 0.000000e+00 5269
4 TraesCS7A01G421400 chr7D 94.384 3009 105 23 20 3003 531865031 531862062 0.000000e+00 4562
5 TraesCS7A01G421400 chr7D 87.814 837 95 4 6418 7247 562412030 562412866 0.000000e+00 974
6 TraesCS7A01G421400 chr2A 97.524 848 20 1 6416 7262 733510717 733511564 0.000000e+00 1448
7 TraesCS7A01G421400 chr6B 92.874 870 35 12 6416 7262 693516830 693515965 0.000000e+00 1238
8 TraesCS7A01G421400 chr6B 76.000 575 128 10 6674 7243 523508213 523508782 9.220000e-74 289
9 TraesCS7A01G421400 chr2D 91.981 848 67 1 6416 7262 528629956 528630803 0.000000e+00 1188
10 TraesCS7A01G421400 chrUn 91.863 848 68 1 6416 7262 35253297 35252450 0.000000e+00 1182
11 TraesCS7A01G421400 chrUn 72.835 508 123 13 6563 7063 46081582 46081083 7.540000e-35 159
12 TraesCS7A01G421400 chr1B 91.253 846 73 1 6418 7262 681503289 681504134 0.000000e+00 1151
13 TraesCS7A01G421400 chr1D 89.398 830 82 5 6423 7248 390863899 390863072 0.000000e+00 1040
14 TraesCS7A01G421400 chr6D 75.381 853 193 16 6418 7261 317017653 317016809 5.280000e-106 396


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 TraesCS7A01G421400 chr7A 612410621 612417882 7261 True 13411.0 13411 100.0000 1 7262 1 chr7A.!!$R1 7261
1 TraesCS7A01G421400 chr7B 572416188 572422852 6664 True 4863.0 6248 94.1990 12 6415 2 chr7B.!!$R1 6403
2 TraesCS7A01G421400 chr7D 531858719 531865031 6312 True 4915.5 5269 94.9335 20 6415 2 chr7D.!!$R1 6395
3 TraesCS7A01G421400 chr7D 562412030 562412866 836 False 974.0 974 87.8140 6418 7247 1 chr7D.!!$F1 829
4 TraesCS7A01G421400 chr2A 733510717 733511564 847 False 1448.0 1448 97.5240 6416 7262 1 chr2A.!!$F1 846
5 TraesCS7A01G421400 chr6B 693515965 693516830 865 True 1238.0 1238 92.8740 6416 7262 1 chr6B.!!$R1 846
6 TraesCS7A01G421400 chr6B 523508213 523508782 569 False 289.0 289 76.0000 6674 7243 1 chr6B.!!$F1 569
7 TraesCS7A01G421400 chr2D 528629956 528630803 847 False 1188.0 1188 91.9810 6416 7262 1 chr2D.!!$F1 846
8 TraesCS7A01G421400 chrUn 35252450 35253297 847 True 1182.0 1182 91.8630 6416 7262 1 chrUn.!!$R1 846
9 TraesCS7A01G421400 chr1B 681503289 681504134 845 False 1151.0 1151 91.2530 6418 7262 1 chr1B.!!$F1 844
10 TraesCS7A01G421400 chr1D 390863072 390863899 827 True 1040.0 1040 89.3980 6423 7248 1 chr1D.!!$R1 825
11 TraesCS7A01G421400 chr6D 317016809 317017653 844 True 396.0 396 75.3810 6418 7261 1 chr6D.!!$R1 843

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
598 618 0.322975 CACCTGTTCTCCACTGAGGG 59.677 60.000 0.00 0.00 39.23 4.30 F
861 881 0.388907 GCACATTTGCCGTCATGCTT 60.389 50.000 0.00 0.00 43.66 3.91 F
866 886 0.878416 TTTGCCGTCATGCTTACCAC 59.122 50.000 0.00 0.00 0.00 4.16 F
1116 1136 1.004918 GGTTGTGAGCTACGCAGGT 60.005 57.895 0.00 0.00 40.21 4.00 F
1122 1142 1.153745 GAGCTACGCAGGTGGAGTG 60.154 63.158 0.00 0.00 30.99 3.51 F
2883 3210 1.673920 TCGCCAAACTTCTCACCAAAC 59.326 47.619 0.00 0.00 0.00 2.93 F
4198 4528 1.278985 TGACTGGTGCTGGTATTCTGG 59.721 52.381 0.00 0.00 0.00 3.86 F
5377 5784 0.173935 CTGTCTGAGGCTCTGAGCTG 59.826 60.000 27.09 16.28 41.99 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2495 2817 0.244450 TTAGCATTGCTGTTGGCTGC 59.756 50.000 21.31 0.0 40.10 5.25 R
2830 3157 1.640069 CTGATCAATCGCTGCCACG 59.360 57.895 0.00 0.0 0.00 4.94 R
2898 3225 5.255397 ACTGTTGGTGGGAAGAATGATAA 57.745 39.130 0.00 0.0 0.00 1.75 R
3139 3466 2.104967 GGTTTATACACCCCAAAGGCC 58.895 52.381 0.00 0.0 40.58 5.19 R
3211 3538 5.223449 ACCCAGAGTTTTTCGATAACTGA 57.777 39.130 15.65 0.0 36.04 3.41 R
4447 4777 2.039084 ACCTAGACTCTTGGCTGTTTGG 59.961 50.000 6.46 0.0 29.74 3.28 R
5963 6383 0.108138 CGAGGGGATGTTGAGGTCAC 60.108 60.000 0.00 0.0 0.00 3.67 R
7177 7629 1.560923 CTCCACCTTTCATAGCGTCG 58.439 55.000 0.00 0.0 0.00 5.12 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.874245 TCCCCCACCTCCTCCTCA 60.874 66.667 0.00 0.00 0.00 3.86
27 28 0.539438 CTCCTCCTCATCCTCCTCCG 60.539 65.000 0.00 0.00 0.00 4.63
139 140 2.242043 CTCCCAGGTGATTTGCTTGTT 58.758 47.619 0.00 0.00 0.00 2.83
156 157 2.980568 TGTTTCCCGACTCGCATTATT 58.019 42.857 0.00 0.00 0.00 1.40
160 161 2.546778 TCCCGACTCGCATTATTTGTC 58.453 47.619 0.00 0.00 0.00 3.18
161 162 1.597663 CCCGACTCGCATTATTTGTCC 59.402 52.381 0.00 0.00 0.00 4.02
162 163 1.597663 CCGACTCGCATTATTTGTCCC 59.402 52.381 0.00 0.00 0.00 4.46
246 255 4.097437 GGGTTTTAATAGGGTGTTAGCAGC 59.903 45.833 0.00 0.00 41.99 5.25
313 322 4.992319 CCGCATTATCGGGAACAGTATAAA 59.008 41.667 0.00 0.00 45.38 1.40
354 363 2.162809 AGTTTCCTTCACGCGTTTTTGT 59.837 40.909 10.22 0.00 0.00 2.83
366 375 4.078346 CGCGTTTTTGTTTGAAAAACAGG 58.922 39.130 18.06 8.64 45.46 4.00
367 376 4.143305 CGCGTTTTTGTTTGAAAAACAGGA 60.143 37.500 18.06 0.00 45.46 3.86
368 377 5.445275 CGCGTTTTTGTTTGAAAAACAGGAT 60.445 36.000 18.06 0.00 45.46 3.24
369 378 6.310960 GCGTTTTTGTTTGAAAAACAGGATT 58.689 32.000 18.06 0.00 45.46 3.01
410 419 1.098050 GCGCCTTGGATCAAATGACT 58.902 50.000 0.00 0.00 0.00 3.41
417 426 0.734889 GGATCAAATGACTGGCCGTG 59.265 55.000 4.94 0.00 0.00 4.94
423 432 0.324943 AATGACTGGCCGTGTAGCTT 59.675 50.000 4.94 0.00 0.00 3.74
432 441 2.608090 GGCCGTGTAGCTTCAGATTAAC 59.392 50.000 0.00 0.00 0.00 2.01
435 444 4.113354 CCGTGTAGCTTCAGATTAACCTC 58.887 47.826 0.00 0.00 0.00 3.85
436 445 4.142138 CCGTGTAGCTTCAGATTAACCTCT 60.142 45.833 0.00 0.00 0.00 3.69
437 446 5.038033 CGTGTAGCTTCAGATTAACCTCTC 58.962 45.833 0.00 0.00 0.00 3.20
438 447 5.393135 CGTGTAGCTTCAGATTAACCTCTCA 60.393 44.000 0.00 0.00 0.00 3.27
439 448 5.808030 GTGTAGCTTCAGATTAACCTCTCAC 59.192 44.000 0.00 0.00 0.00 3.51
462 471 2.413371 GCTTTTCGGCTGTGATTCACTC 60.413 50.000 17.26 9.19 35.11 3.51
488 497 1.270571 TGTTCGCACTGCACTCCATAA 60.271 47.619 1.11 0.00 0.00 1.90
529 539 8.568794 CGTAATCCAGAGATCTTTACTGATGTA 58.431 37.037 10.68 0.00 34.07 2.29
570 590 8.436200 GCAGTATACTGTTAAGTTTCAACTGAG 58.564 37.037 28.95 2.83 45.45 3.35
598 618 0.322975 CACCTGTTCTCCACTGAGGG 59.677 60.000 0.00 0.00 39.23 4.30
664 684 0.465705 CTCGCTCTGAAGGGCCATTA 59.534 55.000 0.73 0.00 35.49 1.90
667 687 2.703536 TCGCTCTGAAGGGCCATTAATA 59.296 45.455 0.73 0.00 35.49 0.98
695 715 3.215151 GGCAGCCTAATTTAAGAGGTCC 58.785 50.000 3.29 0.00 35.08 4.46
786 806 2.961424 GGGACCATTCCTGTTGTGG 58.039 57.895 0.00 0.00 42.38 4.17
861 881 0.388907 GCACATTTGCCGTCATGCTT 60.389 50.000 0.00 0.00 43.66 3.91
862 882 1.135431 GCACATTTGCCGTCATGCTTA 60.135 47.619 0.00 0.00 43.66 3.09
866 886 0.878416 TTTGCCGTCATGCTTACCAC 59.122 50.000 0.00 0.00 0.00 4.16
878 898 2.024464 TGCTTACCACCTAATGCCCAAT 60.024 45.455 0.00 0.00 0.00 3.16
893 913 3.074390 TGCCCAATAGCTGCCACTATTAT 59.926 43.478 0.00 0.00 40.14 1.28
894 914 3.441572 GCCCAATAGCTGCCACTATTATG 59.558 47.826 0.00 4.57 40.14 1.90
895 915 4.807303 GCCCAATAGCTGCCACTATTATGA 60.807 45.833 0.00 0.00 40.14 2.15
896 916 5.316167 CCCAATAGCTGCCACTATTATGAA 58.684 41.667 0.00 0.00 40.14 2.57
897 917 5.948162 CCCAATAGCTGCCACTATTATGAAT 59.052 40.000 0.00 0.00 40.14 2.57
898 918 6.435277 CCCAATAGCTGCCACTATTATGAATT 59.565 38.462 0.00 0.00 40.14 2.17
899 919 7.611467 CCCAATAGCTGCCACTATTATGAATTA 59.389 37.037 0.00 0.00 40.14 1.40
900 920 9.182214 CCAATAGCTGCCACTATTATGAATTAT 57.818 33.333 0.00 0.00 40.14 1.28
901 921 9.999009 CAATAGCTGCCACTATTATGAATTATG 57.001 33.333 0.00 0.00 40.14 1.90
902 922 9.964354 AATAGCTGCCACTATTATGAATTATGA 57.036 29.630 0.00 0.00 40.30 2.15
904 924 8.874744 AGCTGCCACTATTATGAATTATGATT 57.125 30.769 0.00 0.00 0.00 2.57
905 925 8.954350 AGCTGCCACTATTATGAATTATGATTC 58.046 33.333 3.31 3.31 41.67 2.52
906 926 8.954350 GCTGCCACTATTATGAATTATGATTCT 58.046 33.333 11.13 0.86 41.80 2.40
948 968 5.640783 TCATGTTAAGTGCTTGTCTCTGATG 59.359 40.000 0.00 0.00 0.00 3.07
992 1012 2.807967 GCAGTGTTGCTGTTCTGACATA 59.192 45.455 0.00 0.00 46.95 2.29
1088 1108 5.810095 TGATGTGTACATTGTTACCATGGA 58.190 37.500 21.47 0.00 36.57 3.41
1089 1109 6.241645 TGATGTGTACATTGTTACCATGGAA 58.758 36.000 21.47 5.58 36.57 3.53
1111 1131 1.445582 GACCCGGTTGTGAGCTACG 60.446 63.158 0.00 0.00 0.00 3.51
1116 1136 1.004918 GGTTGTGAGCTACGCAGGT 60.005 57.895 0.00 0.00 40.21 4.00
1122 1142 1.153745 GAGCTACGCAGGTGGAGTG 60.154 63.158 0.00 0.00 30.99 3.51
1222 1242 3.193267 TGGCCATGTCTCTTAACATTTGC 59.807 43.478 0.00 0.00 37.78 3.68
1364 1384 5.104900 TGGAACTACCCTCTCTAATTGAAGC 60.105 44.000 0.00 0.00 38.00 3.86
1564 1584 4.470462 GTTTGCAGTTCACATGTCATCTC 58.530 43.478 0.00 0.00 0.00 2.75
1581 1601 2.923121 TCTCTGCAGGTATTTGGCATC 58.077 47.619 15.13 0.00 36.87 3.91
1594 1614 7.712205 AGGTATTTGGCATCATAAATTTTCTGC 59.288 33.333 0.00 1.00 0.00 4.26
1595 1615 7.495279 GGTATTTGGCATCATAAATTTTCTGCA 59.505 33.333 0.00 0.00 0.00 4.41
1596 1616 6.971527 TTTGGCATCATAAATTTTCTGCAG 57.028 33.333 7.63 7.63 0.00 4.41
1597 1617 5.664294 TGGCATCATAAATTTTCTGCAGT 57.336 34.783 14.67 0.00 0.00 4.40
1598 1618 6.040209 TGGCATCATAAATTTTCTGCAGTT 57.960 33.333 14.67 2.42 0.00 3.16
1615 1637 6.716628 TCTGCAGTTCATATGTTTTCCTTTCT 59.283 34.615 14.67 0.00 0.00 2.52
2015 2038 2.014068 GCTGCTGGAGCGTTTAATCCT 61.014 52.381 5.14 0.00 45.83 3.24
2075 2098 3.114606 TGGAAGGTAATGCTCCTGATGA 58.885 45.455 0.00 0.00 35.27 2.92
2079 2102 5.221722 GGAAGGTAATGCTCCTGATGATACA 60.222 44.000 0.00 0.00 35.27 2.29
2083 2106 5.698545 GGTAATGCTCCTGATGATACACTTC 59.301 44.000 0.00 0.00 0.00 3.01
2084 2107 5.363562 AATGCTCCTGATGATACACTTCA 57.636 39.130 0.00 0.00 0.00 3.02
2170 2197 5.626142 TGCTTATAACTTCCAAACCTGTGA 58.374 37.500 0.00 0.00 0.00 3.58
2277 2304 2.724977 TTGCAACGTTGGTTTTGACA 57.275 40.000 28.33 13.63 32.98 3.58
2312 2339 2.030363 GTCATGTGAAAAATGGCACGGA 60.030 45.455 0.00 0.00 35.79 4.69
2386 2708 1.702182 TTGCTGCTGGAAACAATGGA 58.298 45.000 0.00 0.00 42.06 3.41
2495 2817 8.702163 ATTTCTGAACAAAGTTAAACCTTGTG 57.298 30.769 0.00 0.00 0.00 3.33
2521 2843 4.381932 GCCAACAGCAATGCTAAATTACCT 60.382 41.667 7.70 0.00 42.97 3.08
2536 2858 7.388224 GCTAAATTACCTACCTCAAAGATAGGC 59.612 40.741 0.00 0.00 34.62 3.93
2582 2904 5.808366 TGACTAGCATTATCCTGTTAGGG 57.192 43.478 0.00 0.00 35.10 3.53
2830 3157 4.380841 TGGTGGTTATGTATCTGACGTC 57.619 45.455 9.11 9.11 0.00 4.34
2883 3210 1.673920 TCGCCAAACTTCTCACCAAAC 59.326 47.619 0.00 0.00 0.00 2.93
2949 3276 7.722728 ACCGTACTTGATATTGAGTAGATACCA 59.277 37.037 0.00 0.00 0.00 3.25
3050 3377 5.130292 ACATTGTTCATTTGCTTGAGAGG 57.870 39.130 0.00 0.00 0.00 3.69
3069 3396 6.490040 TGAGAGGTTGACTGAAAAATAAAGGG 59.510 38.462 0.00 0.00 0.00 3.95
3086 3413 9.555411 AAATAAAGGGATGGTTGGTAAACTATT 57.445 29.630 0.00 0.00 37.59 1.73
3089 3416 7.949690 AAGGGATGGTTGGTAAACTATTAAC 57.050 36.000 0.00 0.00 37.59 2.01
3090 3417 7.280044 AGGGATGGTTGGTAAACTATTAACT 57.720 36.000 0.00 0.00 37.59 2.24
3091 3418 8.396619 AGGGATGGTTGGTAAACTATTAACTA 57.603 34.615 0.00 0.00 37.59 2.24
3092 3419 9.010767 AGGGATGGTTGGTAAACTATTAACTAT 57.989 33.333 0.00 0.00 37.59 2.12
3136 3463 7.070946 AGGATTGATCATCTAAGTGACACAGAT 59.929 37.037 8.59 5.51 31.67 2.90
3137 3464 7.714377 GGATTGATCATCTAAGTGACACAGATT 59.286 37.037 8.59 0.00 31.67 2.40
3138 3465 9.107177 GATTGATCATCTAAGTGACACAGATTT 57.893 33.333 8.59 0.00 0.00 2.17
3139 3466 7.838771 TGATCATCTAAGTGACACAGATTTG 57.161 36.000 8.59 0.00 0.00 2.32
3140 3467 6.820152 TGATCATCTAAGTGACACAGATTTGG 59.180 38.462 8.59 0.00 0.00 3.28
3141 3468 4.937620 TCATCTAAGTGACACAGATTTGGC 59.062 41.667 8.59 0.00 0.00 4.52
3142 3469 3.674997 TCTAAGTGACACAGATTTGGCC 58.325 45.455 8.59 0.00 0.00 5.36
3211 3538 9.178758 CTAAATCAAGTGGGAGCTATTAACTTT 57.821 33.333 0.00 0.00 0.00 2.66
3235 3562 5.699458 TCAGTTATCGAAAAACTCTGGGTTC 59.301 40.000 12.23 0.00 37.12 3.62
3294 3622 8.767478 AATTTTAGAGTTCCATTTCATGCAAG 57.233 30.769 0.00 0.00 0.00 4.01
3303 3631 8.408601 AGTTCCATTTCATGCAAGATATACAAC 58.591 33.333 0.00 0.00 0.00 3.32
3583 3911 3.693807 TCTCAATCCTTTTGATGCAGCT 58.306 40.909 2.53 0.00 32.68 4.24
3679 4007 2.381911 GTGTCATTCAGCCCATGGATT 58.618 47.619 15.22 0.00 0.00 3.01
3931 4261 4.260784 GCTGTCATAAAAGTATCCTTGGCG 60.261 45.833 0.00 0.00 0.00 5.69
3957 4287 5.701290 GCCCCACACTTATTTATAGTGCTAG 59.299 44.000 0.00 0.00 45.38 3.42
4198 4528 1.278985 TGACTGGTGCTGGTATTCTGG 59.721 52.381 0.00 0.00 0.00 3.86
4447 4777 3.365364 CGGCTTCAATCAAGAAAGTGTCC 60.365 47.826 0.00 0.00 33.29 4.02
4504 4834 9.502091 TTTGTTGTTGCTGTAGAAGATAGTTAT 57.498 29.630 0.00 0.00 0.00 1.89
4733 5078 8.984891 TTTAAGTTCACATGCATTAGAATTGG 57.015 30.769 12.29 0.00 0.00 3.16
4822 5206 8.625651 TGCTGCTGTTGTAGAATTAGTTAAAAA 58.374 29.630 0.00 0.00 0.00 1.94
5153 5543 2.076863 ACAGATGAAGCAAACTACGCC 58.923 47.619 0.00 0.00 0.00 5.68
5209 5599 3.635331 CACACAAGCTTGTTTCAGGATG 58.365 45.455 29.23 17.23 39.91 3.51
5377 5784 0.173935 CTGTCTGAGGCTCTGAGCTG 59.826 60.000 27.09 16.28 41.99 4.24
5704 6118 9.548208 GTTCTAGATGCAAGTAAGTTGATTTTC 57.452 33.333 0.00 0.00 38.60 2.29
5747 6161 0.898320 TCTCTTCTGCCCTACTGTGC 59.102 55.000 0.00 0.00 0.00 4.57
5768 6182 3.000523 GCATTTGTGTTGCAAGTCTGTTG 59.999 43.478 0.00 0.00 39.90 3.33
5777 6191 7.700234 TGTGTTGCAAGTCTGTTGTTAAATAAG 59.300 33.333 0.00 0.00 0.00 1.73
5778 6192 6.695278 TGTTGCAAGTCTGTTGTTAAATAAGC 59.305 34.615 0.00 0.00 0.00 3.09
5991 6411 1.068083 CATCCCCTCGATCACGGTG 59.932 63.158 0.56 0.56 40.21 4.94
6008 6428 0.308993 GTGTCACAGCTCAAAGGCAC 59.691 55.000 0.00 0.00 34.17 5.01
6009 6429 0.107263 TGTCACAGCTCAAAGGCACA 60.107 50.000 0.00 0.00 34.17 4.57
6259 6679 1.004745 CAGTGGTTGCTATGGGGTTCT 59.995 52.381 0.00 0.00 0.00 3.01
6322 6742 9.436957 CTGAGGAGTGTTGTAATATTTTGTAGT 57.563 33.333 0.00 0.00 0.00 2.73
6472 6894 3.923017 AAGGCAGAATTTTCTTCACCG 57.077 42.857 0.00 0.00 34.74 4.94
6710 7156 3.228453 ACCCAAAGTACGAGTCTTCTGA 58.772 45.455 0.00 0.00 0.00 3.27
6715 7161 2.447443 AGTACGAGTCTTCTGATGGCA 58.553 47.619 0.00 0.00 0.00 4.92
6948 7395 2.743664 TGCTCGATGACATGTTTTCTGG 59.256 45.455 0.00 0.00 0.00 3.86
6960 7407 3.482436 TGTTTTCTGGCGACATAAGGTT 58.518 40.909 0.00 0.00 41.51 3.50
7177 7629 2.032550 CACAGATGGTGCGATCAATTCC 59.967 50.000 0.00 0.00 41.36 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.257541 GATGAGGAGGAGGTGGGGGA 62.258 65.000 0.00 0.00 0.00 4.81
1 2 1.768077 GATGAGGAGGAGGTGGGGG 60.768 68.421 0.00 0.00 0.00 5.40
2 3 1.768077 GGATGAGGAGGAGGTGGGG 60.768 68.421 0.00 0.00 0.00 4.96
3 4 0.762461 GAGGATGAGGAGGAGGTGGG 60.762 65.000 0.00 0.00 0.00 4.61
4 5 0.762461 GGAGGATGAGGAGGAGGTGG 60.762 65.000 0.00 0.00 0.00 4.61
5 6 0.264359 AGGAGGATGAGGAGGAGGTG 59.736 60.000 0.00 0.00 0.00 4.00
6 7 0.560688 GAGGAGGATGAGGAGGAGGT 59.439 60.000 0.00 0.00 0.00 3.85
7 8 0.178935 GGAGGAGGATGAGGAGGAGG 60.179 65.000 0.00 0.00 0.00 4.30
8 9 0.539438 CGGAGGAGGATGAGGAGGAG 60.539 65.000 0.00 0.00 0.00 3.69
9 10 1.539165 CGGAGGAGGATGAGGAGGA 59.461 63.158 0.00 0.00 0.00 3.71
10 11 4.189539 CGGAGGAGGATGAGGAGG 57.810 66.667 0.00 0.00 0.00 4.30
139 140 2.933906 GACAAATAATGCGAGTCGGGAA 59.066 45.455 15.52 0.00 0.00 3.97
197 198 4.668576 TGCAGAAGTAAATCGAAAGCAG 57.331 40.909 0.00 0.00 0.00 4.24
246 255 1.003839 TGGCCGGTTCTAAGCTGTG 60.004 57.895 1.90 0.00 0.00 3.66
313 322 8.947115 GGAAACTGTTAAATCTTATGCTACAGT 58.053 33.333 0.00 0.00 44.57 3.55
336 345 2.917971 CAAACAAAAACGCGTGAAGGAA 59.082 40.909 14.98 0.00 0.00 3.36
410 419 0.613260 AATCTGAAGCTACACGGCCA 59.387 50.000 2.24 0.00 0.00 5.36
417 426 6.039616 CAGTGAGAGGTTAATCTGAAGCTAC 58.960 44.000 0.00 0.00 37.29 3.58
423 432 5.489792 AAAGCAGTGAGAGGTTAATCTGA 57.510 39.130 0.00 0.00 0.00 3.27
432 441 0.321122 AGCCGAAAAGCAGTGAGAGG 60.321 55.000 0.00 0.00 34.23 3.69
435 444 2.621763 ACAGCCGAAAAGCAGTGAG 58.378 52.632 0.00 0.00 30.48 3.51
436 445 4.876701 ACAGCCGAAAAGCAGTGA 57.123 50.000 0.00 0.00 30.48 3.41
437 446 4.929198 CACAGCCGAAAAGCAGTG 57.071 55.556 0.00 0.00 42.68 3.66
438 447 1.537202 GAATCACAGCCGAAAAGCAGT 59.463 47.619 0.00 0.00 31.96 4.40
439 448 1.536766 TGAATCACAGCCGAAAAGCAG 59.463 47.619 0.00 0.00 34.23 4.24
529 539 1.356124 ACTGCTCCACTGAGAATGGT 58.644 50.000 0.00 0.00 41.42 3.55
570 590 0.603975 GAGAACAGGTGGGCACTCAC 60.604 60.000 0.00 0.00 36.95 3.51
598 618 3.876914 TGCATTTCGTATCACTCCATTCC 59.123 43.478 0.00 0.00 0.00 3.01
664 684 1.136828 TTAGGCTGCCCGGTGATATT 58.863 50.000 16.57 0.00 35.76 1.28
667 687 0.258774 AAATTAGGCTGCCCGGTGAT 59.741 50.000 16.57 0.00 35.76 3.06
786 806 4.722700 ATCACACACCGCCCCAGC 62.723 66.667 0.00 0.00 0.00 4.85
861 881 3.053077 AGCTATTGGGCATTAGGTGGTA 58.947 45.455 0.00 0.00 34.17 3.25
862 882 1.852965 AGCTATTGGGCATTAGGTGGT 59.147 47.619 0.00 0.00 34.17 4.16
866 886 1.251251 GGCAGCTATTGGGCATTAGG 58.749 55.000 0.00 0.00 34.17 2.69
878 898 9.964354 AATCATAATTCATAATAGTGGCAGCTA 57.036 29.630 0.00 0.00 0.00 3.32
948 968 4.994217 CAGAACCTTTCAAGAAGAGAGACC 59.006 45.833 0.00 0.00 30.18 3.85
986 1006 3.455910 CCCCTTCATCTTCACCTATGTCA 59.544 47.826 0.00 0.00 0.00 3.58
987 1007 3.745797 GCCCCTTCATCTTCACCTATGTC 60.746 52.174 0.00 0.00 0.00 3.06
992 1012 0.915364 GAGCCCCTTCATCTTCACCT 59.085 55.000 0.00 0.00 0.00 4.00
1088 1108 3.530910 CTCACAACCGGGTCGCCTT 62.531 63.158 6.32 0.00 0.00 4.35
1089 1109 4.003788 CTCACAACCGGGTCGCCT 62.004 66.667 6.32 0.00 0.00 5.52
1111 1131 0.329596 AATCCTTCCACTCCACCTGC 59.670 55.000 0.00 0.00 0.00 4.85
1222 1242 1.068895 TGAATGCCAGGCAACACAAAG 59.931 47.619 20.84 0.00 43.62 2.77
1564 1584 5.518848 TTTATGATGCCAAATACCTGCAG 57.481 39.130 6.78 6.78 38.58 4.41
1596 1616 9.129209 GCAAACTAGAAAGGAAAACATATGAAC 57.871 33.333 10.38 0.00 0.00 3.18
1597 1617 8.855110 TGCAAACTAGAAAGGAAAACATATGAA 58.145 29.630 10.38 0.00 0.00 2.57
1598 1618 8.402798 TGCAAACTAGAAAGGAAAACATATGA 57.597 30.769 10.38 0.00 0.00 2.15
1615 1637 8.439993 TTTAGCCACGATAATAATGCAAACTA 57.560 30.769 0.00 0.00 0.00 2.24
2015 2038 3.753815 TGGAGATGCAAACTCAACATCA 58.246 40.909 20.41 9.87 42.12 3.07
2170 2197 6.070995 ACCATCATCATTTGAAACAAGATGCT 60.071 34.615 10.26 1.59 38.03 3.79
2277 2304 5.233083 TCACATGACCAGAATGACTTTCT 57.767 39.130 0.00 0.00 45.83 2.52
2386 2708 2.960968 TGCATTCGCACCGCAATT 59.039 50.000 0.00 0.00 45.36 2.32
2495 2817 0.244450 TTAGCATTGCTGTTGGCTGC 59.756 50.000 21.31 0.00 40.10 5.25
2521 2843 5.179452 AGCAAAAGCCTATCTTTGAGGTA 57.821 39.130 0.00 0.00 43.84 3.08
2536 2858 9.897744 TCATACAAAGATAGAACAAAGCAAAAG 57.102 29.630 0.00 0.00 0.00 2.27
2830 3157 1.640069 CTGATCAATCGCTGCCACG 59.360 57.895 0.00 0.00 0.00 4.94
2897 3224 5.640147 ACTGTTGGTGGGAAGAATGATAAA 58.360 37.500 0.00 0.00 0.00 1.40
2898 3225 5.255397 ACTGTTGGTGGGAAGAATGATAA 57.745 39.130 0.00 0.00 0.00 1.75
2949 3276 6.180472 CCATAACAGTCATAAAGTTGTCCCT 58.820 40.000 0.00 0.00 0.00 4.20
3050 3377 6.993079 ACCATCCCTTTATTTTTCAGTCAAC 58.007 36.000 0.00 0.00 0.00 3.18
3087 3414 9.220906 TCCTACCAAGTACCAAATGATATAGTT 57.779 33.333 0.00 0.00 0.00 2.24
3088 3415 8.792830 TCCTACCAAGTACCAAATGATATAGT 57.207 34.615 0.00 0.00 0.00 2.12
3091 3418 8.723365 TCAATCCTACCAAGTACCAAATGATAT 58.277 33.333 0.00 0.00 0.00 1.63
3092 3419 8.096621 TCAATCCTACCAAGTACCAAATGATA 57.903 34.615 0.00 0.00 0.00 2.15
3136 3463 3.544698 TTATACACCCCAAAGGCCAAA 57.455 42.857 5.01 0.00 40.58 3.28
3137 3464 3.166679 GTTTATACACCCCAAAGGCCAA 58.833 45.455 5.01 0.00 40.58 4.52
3138 3465 2.557901 GGTTTATACACCCCAAAGGCCA 60.558 50.000 5.01 0.00 40.58 5.36
3139 3466 2.104967 GGTTTATACACCCCAAAGGCC 58.895 52.381 0.00 0.00 40.58 5.19
3211 3538 5.223449 ACCCAGAGTTTTTCGATAACTGA 57.777 39.130 15.65 0.00 36.04 3.41
3235 3562 6.449698 ACTAGTGAATGCAAACCAGAATTTG 58.550 36.000 0.00 0.00 41.62 2.32
3294 3622 8.342634 ACCATTGCAAGTATTTCGTTGTATATC 58.657 33.333 4.94 0.00 0.00 1.63
3303 3631 8.447833 TCTAAAGTTACCATTGCAAGTATTTCG 58.552 33.333 4.94 0.00 0.00 3.46
3583 3911 3.498397 CAGCTTTTACGGCAGAAAGAAGA 59.502 43.478 8.01 0.00 35.41 2.87
3649 3977 2.225491 GCTGAATGACACCAGCGTTTTA 59.775 45.455 13.73 0.00 44.99 1.52
3679 4007 2.031919 CCAGCGGCAACAGTGGTA 59.968 61.111 1.45 0.00 0.00 3.25
3931 4261 4.515567 GCACTATAAATAAGTGTGGGGCTC 59.484 45.833 5.25 0.00 45.01 4.70
4198 4528 6.267496 ACCACAGGTAGAAATGTTAATTGC 57.733 37.500 0.00 0.00 32.11 3.56
4447 4777 2.039084 ACCTAGACTCTTGGCTGTTTGG 59.961 50.000 6.46 0.00 29.74 3.28
4504 4834 2.716424 AGGATCAAACTTTGTCCCTGGA 59.284 45.455 14.56 0.00 34.25 3.86
4733 5078 5.066593 AGTTGGTTCCTTGAGATTTGAGAC 58.933 41.667 0.00 0.00 0.00 3.36
4910 5300 2.564947 AGCCCAGTCTCTTGTTGTAGAG 59.435 50.000 0.00 0.00 42.46 2.43
5153 5543 5.350640 GGGATAAACTCTGACAAACTTACCG 59.649 44.000 0.00 0.00 0.00 4.02
5377 5784 1.135721 GGCATGCAGAGAATTTGGGTC 59.864 52.381 21.36 0.00 0.00 4.46
5459 5872 1.843368 ATTAGTGCTGCAATGCCAGT 58.157 45.000 13.47 0.00 35.28 4.00
5747 6161 4.175516 ACAACAGACTTGCAACACAAATG 58.824 39.130 0.00 0.00 37.96 2.32
5768 6182 6.507023 CATGGAAGGGACATGCTTATTTAAC 58.493 40.000 0.00 0.00 39.23 2.01
5957 6377 0.326264 GATGTTGAGGTCACAGGGCT 59.674 55.000 0.00 0.00 0.00 5.19
5963 6383 0.108138 CGAGGGGATGTTGAGGTCAC 60.108 60.000 0.00 0.00 0.00 3.67
5964 6384 0.252057 TCGAGGGGATGTTGAGGTCA 60.252 55.000 0.00 0.00 0.00 4.02
5991 6411 0.308993 GTGTGCCTTTGAGCTGTGAC 59.691 55.000 0.00 0.00 0.00 3.67
6027 6447 3.598715 TCGGCCACGTTCGTGACT 61.599 61.111 23.84 0.00 41.85 3.41
6054 6474 2.158900 CCTGGTCATGATGGTGTAGGTC 60.159 54.545 0.00 0.00 0.00 3.85
6177 6597 2.038837 GCCGAAACTGTAGGTGCCC 61.039 63.158 0.00 0.00 0.00 5.36
6322 6742 5.413523 GTCGGCTCTTATTTTTCCTACCAAA 59.586 40.000 0.00 0.00 0.00 3.28
6472 6894 5.545588 TGTTCAATATAGCCTCTGCATCTC 58.454 41.667 0.00 0.00 41.13 2.75
6710 7156 4.411540 AGAATACCTCTCAAGACATGCCAT 59.588 41.667 0.00 0.00 0.00 4.40
6948 7395 7.225931 TGGTAATAATCTTGAACCTTATGTCGC 59.774 37.037 0.00 0.00 0.00 5.19
6960 7407 8.217111 TGGAGTGCATAATGGTAATAATCTTGA 58.783 33.333 0.00 0.00 0.00 3.02
7177 7629 1.560923 CTCCACCTTTCATAGCGTCG 58.439 55.000 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.