Multiple sequence alignment - TraesCS2D01G506100

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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 TraesCS2D01G506100 chr2D 100.000 4757 0 0 1 4757 600036098 600040854 0.000000e+00 8785.0
1 TraesCS2D01G506100 chr2D 92.195 205 15 1 3032 3236 600054670 600054467 6.020000e-74 289.0
2 TraesCS2D01G506100 chr2D 79.688 320 27 12 4005 4322 618652908 618652625 3.760000e-46 196.0
3 TraesCS2D01G506100 chr2A 92.487 2968 122 24 1 2898 733715181 733718117 0.000000e+00 4152.0
4 TraesCS2D01G506100 chr2A 91.971 137 11 0 1365 1501 657106710 657106846 4.860000e-45 193.0
5 TraesCS2D01G506100 chr2A 94.737 38 1 1 1762 1798 681104360 681104397 1.850000e-04 58.4
6 TraesCS2D01G506100 chr7D 97.702 1523 17 1 3235 4757 186818852 186817348 0.000000e+00 2603.0
7 TraesCS2D01G506100 chr7D 82.994 835 101 22 3497 4320 38763497 38762693 0.000000e+00 717.0
8 TraesCS2D01G506100 chr7D 87.888 322 39 0 3375 3696 154377043 154376722 3.470000e-101 379.0
9 TraesCS2D01G506100 chr7D 96.891 193 6 0 3044 3236 186819096 186818904 1.650000e-84 324.0
10 TraesCS2D01G506100 chr7D 90.722 194 17 1 3043 3236 186815061 186815253 1.700000e-64 257.0
11 TraesCS2D01G506100 chr4A 94.822 1545 57 7 3235 4757 700539198 700537655 0.000000e+00 2388.0
12 TraesCS2D01G506100 chr4A 91.525 177 15 0 3060 3236 700539426 700539250 1.320000e-60 244.0
13 TraesCS2D01G506100 chr3A 95.245 1451 51 4 3321 4756 34247348 34245901 0.000000e+00 2281.0
14 TraesCS2D01G506100 chr3A 93.741 1454 66 6 3321 4756 34151140 34149694 0.000000e+00 2158.0
15 TraesCS2D01G506100 chr3A 92.626 1451 60 13 3321 4756 34049614 34048196 0.000000e+00 2043.0
16 TraesCS2D01G506100 chr3A 85.051 1077 116 33 1836 2883 582343538 582342478 0.000000e+00 1055.0
17 TraesCS2D01G506100 chr3A 92.670 191 14 0 3046 3236 34247627 34247437 4.690000e-70 276.0
18 TraesCS2D01G506100 chr3A 90.816 196 17 1 3041 3236 34045594 34045788 1.310000e-65 261.0
19 TraesCS2D01G506100 chr3A 90.816 196 17 1 3041 3236 34147121 34147315 1.310000e-65 261.0
20 TraesCS2D01G506100 chr3A 90.306 196 18 1 3041 3236 34243281 34243475 6.110000e-64 255.0
21 TraesCS2D01G506100 chr3A 100.000 29 0 0 4581 4609 34149835 34149807 2.000000e-03 54.7
22 TraesCS2D01G506100 chr2B 92.681 1380 58 12 1 1368 729955515 729956863 0.000000e+00 1949.0
23 TraesCS2D01G506100 chr2B 89.674 1443 101 30 1499 2898 729956876 729958313 0.000000e+00 1796.0
24 TraesCS2D01G506100 chr5A 95.255 1159 40 5 3609 4756 28415747 28416901 0.000000e+00 1821.0
25 TraesCS2D01G506100 chr5A 89.869 306 19 1 3321 3614 28397494 28397799 2.690000e-102 383.0
26 TraesCS2D01G506100 chr5A 90.052 191 18 1 3046 3236 28419514 28419325 3.680000e-61 246.0
27 TraesCS2D01G506100 chr5A 79.688 320 27 12 4005 4322 523133957 523133674 3.760000e-46 196.0
28 TraesCS2D01G506100 chr5A 93.182 44 3 0 587 630 504723940 504723897 1.110000e-06 65.8
29 TraesCS2D01G506100 chr3D 87.009 1070 104 24 1836 2883 441570757 441569701 0.000000e+00 1173.0
30 TraesCS2D01G506100 chr3D 80.825 412 38 15 790 1182 441571586 441571197 7.790000e-73 285.0
31 TraesCS2D01G506100 chr3D 89.855 138 13 1 1368 1505 589215769 589215905 4.890000e-40 176.0
32 TraesCS2D01G506100 chr3B 83.713 1228 144 41 1830 3014 578988288 578989502 0.000000e+00 1109.0
33 TraesCS2D01G506100 chr3B 85.017 594 80 7 3497 4083 143988431 143989022 3.170000e-166 595.0
34 TraesCS2D01G506100 chr3B 77.327 591 64 34 790 1358 578987463 578988005 7.790000e-73 285.0
35 TraesCS2D01G506100 chr3B 91.729 133 11 0 1369 1501 397669198 397669066 8.130000e-43 185.0
36 TraesCS2D01G506100 chr3B 91.667 132 11 0 1370 1501 15040309 15040440 2.920000e-42 183.0
37 TraesCS2D01G506100 chr3B 81.609 174 23 4 4506 4678 144029960 144030125 8.300000e-28 135.0
38 TraesCS2D01G506100 chrUn 95.866 387 16 0 4370 4756 476685717 476686103 1.120000e-175 627.0
39 TraesCS2D01G506100 chr7B 86.646 322 43 0 3375 3696 116493555 116493234 1.630000e-94 357.0
40 TraesCS2D01G506100 chr7B 93.750 64 4 0 3235 3298 641528376 641528439 3.920000e-16 97.1
41 TraesCS2D01G506100 chr7B 90.698 43 3 1 1766 1808 2565304 2565345 6.650000e-04 56.5
42 TraesCS2D01G506100 chr7A 86.646 322 43 0 3375 3696 156268047 156267726 1.630000e-94 357.0
43 TraesCS2D01G506100 chr1A 91.791 134 11 0 1368 1501 335028425 335028292 2.260000e-43 187.0
44 TraesCS2D01G506100 chr1A 90.977 133 12 0 1369 1501 540669371 540669239 3.780000e-41 180.0
45 TraesCS2D01G506100 chr6A 91.241 137 9 1 1369 1502 420832765 420832629 2.920000e-42 183.0
46 TraesCS2D01G506100 chr4D 90.977 133 11 1 1369 1501 57689204 57689335 1.360000e-40 178.0
47 TraesCS2D01G506100 chr4B 85.246 61 8 1 577 637 3293723 3293782 1.430000e-05 62.1
48 TraesCS2D01G506100 chr5B 100.000 28 0 0 601 628 527017561 527017534 9.000000e-03 52.8


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 TraesCS2D01G506100 chr2D 600036098 600040854 4756 False 8785.00 8785 100.0000 1 4757 1 chr2D.!!$F1 4756
1 TraesCS2D01G506100 chr2A 733715181 733718117 2936 False 4152.00 4152 92.4870 1 2898 1 chr2A.!!$F3 2897
2 TraesCS2D01G506100 chr7D 186817348 186819096 1748 True 1463.50 2603 97.2965 3044 4757 2 chr7D.!!$R3 1713
3 TraesCS2D01G506100 chr7D 38762693 38763497 804 True 717.00 717 82.9940 3497 4320 1 chr7D.!!$R1 823
4 TraesCS2D01G506100 chr4A 700537655 700539426 1771 True 1316.00 2388 93.1735 3060 4757 2 chr4A.!!$R1 1697
5 TraesCS2D01G506100 chr3A 34048196 34049614 1418 True 2043.00 2043 92.6260 3321 4756 1 chr3A.!!$R1 1435
6 TraesCS2D01G506100 chr3A 34245901 34247627 1726 True 1278.50 2281 93.9575 3046 4756 2 chr3A.!!$R4 1710
7 TraesCS2D01G506100 chr3A 34149694 34151140 1446 True 1106.35 2158 96.8705 3321 4756 2 chr3A.!!$R3 1435
8 TraesCS2D01G506100 chr3A 582342478 582343538 1060 True 1055.00 1055 85.0510 1836 2883 1 chr3A.!!$R2 1047
9 TraesCS2D01G506100 chr2B 729955515 729958313 2798 False 1872.50 1949 91.1775 1 2898 2 chr2B.!!$F1 2897
10 TraesCS2D01G506100 chr5A 28415747 28416901 1154 False 1821.00 1821 95.2550 3609 4756 1 chr5A.!!$F2 1147
11 TraesCS2D01G506100 chr3D 441569701 441571586 1885 True 729.00 1173 83.9170 790 2883 2 chr3D.!!$R1 2093
12 TraesCS2D01G506100 chr3B 578987463 578989502 2039 False 697.00 1109 80.5200 790 3014 2 chr3B.!!$F4 2224
13 TraesCS2D01G506100 chr3B 143988431 143989022 591 False 595.00 595 85.0170 3497 4083 1 chr3B.!!$F2 586

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
904 953 0.388659 GCAGAGACTCATCGCAGGAT 59.611 55.000 5.02 0.00 0.0 3.24 F
1368 1433 1.400494 GGGTAAGTAAGCAACGCATGG 59.600 52.381 0.00 0.00 0.0 3.66 F
2511 2680 1.585521 GGCAGGTACGTGACGATCG 60.586 63.158 19.35 14.88 0.0 3.69 F
2514 2700 0.445043 CAGGTACGTGACGATCGACA 59.555 55.000 24.34 19.93 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2288 2440 0.468585 GCATCCATCCATTGGCAGGA 60.469 55.000 15.5 15.5 46.01 3.86 R
2514 2700 0.681733 AGACCAGTTGTGCAGTCGAT 59.318 50.000 0.0 0.0 34.41 3.59 R
3460 3744 2.031919 ATGGACGGCTTCAACGCA 59.968 55.556 0.0 0.0 34.00 5.24 R
4365 4700 3.383505 TCGGTACATGAGATTGATTCGGT 59.616 43.478 0.0 0.0 0.00 4.69 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
87 88 1.080569 GGGAGCAAAACATGTGGCG 60.081 57.895 0.00 0.00 0.00 5.69
142 143 0.606401 TGACTGGCTGCTTACAAGGC 60.606 55.000 0.00 0.00 0.00 4.35
148 149 1.220749 CTGCTTACAAGGCCGCCTA 59.779 57.895 13.73 0.00 31.13 3.93
155 156 2.215942 ACAAGGCCGCCTATCTTTTT 57.784 45.000 13.73 0.00 31.13 1.94
197 203 4.100707 AGTATACTTAACAGCGCGAACA 57.899 40.909 12.10 0.00 0.00 3.18
263 269 2.905075 CACGCAGATAAACCATGGAGA 58.095 47.619 21.47 2.74 0.00 3.71
300 306 3.709653 TGTTACTGAGACAGACCCTGTTT 59.290 43.478 5.76 0.00 45.44 2.83
340 346 4.821805 TGCTCTTCAGGGTGAAAACTAAAG 59.178 41.667 0.00 0.00 35.73 1.85
344 350 6.837312 TCTTCAGGGTGAAAACTAAAGATCA 58.163 36.000 0.00 0.00 35.73 2.92
351 357 8.166726 AGGGTGAAAACTAAAGATCAAATCTCT 58.833 33.333 0.00 0.00 39.08 3.10
472 484 5.703592 TGTATGCTTTAGTTTGGTTCGACAT 59.296 36.000 0.00 0.00 0.00 3.06
552 564 3.380320 TGTGTGTATCCTCGTCATGTAGG 59.620 47.826 0.00 0.00 0.00 3.18
555 567 4.707934 TGTGTATCCTCGTCATGTAGGAAA 59.292 41.667 15.05 5.21 44.87 3.13
564 576 0.802494 CATGTAGGAAACGGGTGCAC 59.198 55.000 8.80 8.80 0.00 4.57
572 584 1.670811 GAAACGGGTGCACATCCATAG 59.329 52.381 20.43 1.77 0.00 2.23
581 593 4.809426 GGTGCACATCCATAGTACTTGTAC 59.191 45.833 20.43 0.69 0.00 2.90
585 597 6.154534 TGCACATCCATAGTACTTGTACTCTT 59.845 38.462 15.65 4.10 0.00 2.85
637 649 5.595133 ACACCCTTTATCGGAAAGAAAAACA 59.405 36.000 11.05 0.00 0.00 2.83
643 655 8.347035 CCTTTATCGGAAAGAAAAACAGTGTTA 58.653 33.333 9.37 0.00 0.00 2.41
644 656 9.724839 CTTTATCGGAAAGAAAAACAGTGTTAA 57.275 29.630 9.37 0.00 0.00 2.01
645 657 9.724839 TTTATCGGAAAGAAAAACAGTGTTAAG 57.275 29.630 9.37 0.00 0.00 1.85
646 658 5.575019 TCGGAAAGAAAAACAGTGTTAAGC 58.425 37.500 9.37 1.49 0.00 3.09
647 659 4.738252 CGGAAAGAAAAACAGTGTTAAGCC 59.262 41.667 9.37 3.81 0.00 4.35
648 660 5.656480 GGAAAGAAAAACAGTGTTAAGCCA 58.344 37.500 9.37 0.00 0.00 4.75
649 661 6.103330 GGAAAGAAAAACAGTGTTAAGCCAA 58.897 36.000 9.37 0.00 0.00 4.52
650 662 6.761242 GGAAAGAAAAACAGTGTTAAGCCAAT 59.239 34.615 9.37 0.00 0.00 3.16
651 663 7.042725 GGAAAGAAAAACAGTGTTAAGCCAATC 60.043 37.037 9.37 3.36 0.00 2.67
652 664 6.463995 AGAAAAACAGTGTTAAGCCAATCA 57.536 33.333 9.37 0.00 0.00 2.57
653 665 6.872920 AGAAAAACAGTGTTAAGCCAATCAA 58.127 32.000 9.37 0.00 0.00 2.57
654 666 6.980397 AGAAAAACAGTGTTAAGCCAATCAAG 59.020 34.615 9.37 0.00 0.00 3.02
655 667 5.852282 AAACAGTGTTAAGCCAATCAAGT 57.148 34.783 9.37 0.00 0.00 3.16
656 668 6.952773 AAACAGTGTTAAGCCAATCAAGTA 57.047 33.333 9.37 0.00 0.00 2.24
657 669 6.952773 AACAGTGTTAAGCCAATCAAGTAA 57.047 33.333 6.75 0.00 0.00 2.24
658 670 6.952773 ACAGTGTTAAGCCAATCAAGTAAA 57.047 33.333 0.00 0.00 0.00 2.01
659 671 7.524717 ACAGTGTTAAGCCAATCAAGTAAAT 57.475 32.000 0.00 0.00 0.00 1.40
660 672 8.630054 ACAGTGTTAAGCCAATCAAGTAAATA 57.370 30.769 0.00 0.00 0.00 1.40
693 706 2.160205 TCAGATCGACTCAAGACGGTT 58.840 47.619 0.00 0.00 34.25 4.44
713 726 7.039882 ACGGTTAATGGCTAGGATTATATTCG 58.960 38.462 0.00 0.00 0.00 3.34
721 734 7.156673 TGGCTAGGATTATATTCGTGTTTACC 58.843 38.462 0.00 0.00 0.00 2.85
772 788 6.606395 AGGTACCGAGTATTGAGTATTGACTT 59.394 38.462 6.18 0.00 35.45 3.01
832 848 7.172875 CCAAAGAAAATCAGATCGAGATGCTAT 59.827 37.037 4.74 0.00 0.00 2.97
833 849 7.655236 AAGAAAATCAGATCGAGATGCTATG 57.345 36.000 4.74 0.00 0.00 2.23
834 850 5.638657 AGAAAATCAGATCGAGATGCTATGC 59.361 40.000 4.74 0.00 0.00 3.14
835 851 4.804868 AATCAGATCGAGATGCTATGCT 57.195 40.909 4.74 0.00 0.00 3.79
836 852 5.911378 AATCAGATCGAGATGCTATGCTA 57.089 39.130 4.74 0.00 0.00 3.49
904 953 0.388659 GCAGAGACTCATCGCAGGAT 59.611 55.000 5.02 0.00 0.00 3.24
969 1019 1.471287 TGATCTGTTCGGTACCTGACG 59.529 52.381 10.90 5.43 0.00 4.35
1305 1362 5.648960 TCCCAGGAAAAACATACGGTTAATC 59.351 40.000 0.00 0.00 39.29 1.75
1368 1433 1.400494 GGGTAAGTAAGCAACGCATGG 59.600 52.381 0.00 0.00 0.00 3.66
1432 1497 2.596346 TGCTTCAGGAAAAAGCCATCA 58.404 42.857 5.48 0.00 46.81 3.07
1477 1542 5.174761 GTGTTTGATGACTTTTGCGCAATTA 59.825 36.000 25.64 14.18 0.00 1.40
1535 1602 6.540914 GGCACCTAATTAGCTGTTTGTGTATA 59.459 38.462 6.99 0.00 0.00 1.47
1536 1603 7.407337 GCACCTAATTAGCTGTTTGTGTATAC 58.593 38.462 6.99 0.00 0.00 1.47
1549 1616 5.804692 TTGTGTATACGCAACAAATAGGG 57.195 39.130 24.38 0.00 40.93 3.53
1559 1632 4.279169 CGCAACAAATAGGGGATGAATGAT 59.721 41.667 0.00 0.00 0.00 2.45
1682 1769 1.831106 TGGTCACCTTCATCATAGCGT 59.169 47.619 0.00 0.00 0.00 5.07
1807 1936 8.763984 TGGAATAGAGGGAGTACTAAAGTTAG 57.236 38.462 0.00 0.00 36.82 2.34
1953 2102 1.944676 CGCCATCGCCTTCTACGTC 60.945 63.158 0.00 0.00 0.00 4.34
2288 2440 7.308469 GCTTCTCAATTCTCTGTCTTGACAATT 60.308 37.037 4.95 0.00 0.00 2.32
2289 2441 7.664082 TCTCAATTCTCTGTCTTGACAATTC 57.336 36.000 4.95 0.00 0.00 2.17
2341 2510 3.947196 GACTGATGTATGCATGGGTTGAA 59.053 43.478 10.16 0.00 35.07 2.69
2343 2512 4.957954 ACTGATGTATGCATGGGTTGAATT 59.042 37.500 10.16 0.00 35.07 2.17
2511 2680 1.585521 GGCAGGTACGTGACGATCG 60.586 63.158 19.35 14.88 0.00 3.69
2514 2700 0.445043 CAGGTACGTGACGATCGACA 59.555 55.000 24.34 19.93 0.00 4.35
2793 2982 1.732259 AGCACGATAAAGAAGCAACGG 59.268 47.619 0.00 0.00 0.00 4.44
2837 3026 4.821805 TGATTTGATCGATTAAAGGAGGCC 59.178 41.667 18.65 0.00 0.00 5.19
2874 3068 6.992063 GGATGCATCCATTATTCGAGTAAT 57.008 37.500 35.93 7.32 46.38 1.89
2884 3078 9.389755 TCCATTATTCGAGTAATTGTGAATTCA 57.610 29.630 10.20 3.38 33.42 2.57
2898 3092 6.713762 TGTGAATTCAGTCCAATTTGAACT 57.286 33.333 8.80 0.00 36.26 3.01
2899 3093 7.111247 TGTGAATTCAGTCCAATTTGAACTT 57.889 32.000 8.80 0.00 36.26 2.66
2900 3094 6.979817 TGTGAATTCAGTCCAATTTGAACTTG 59.020 34.615 8.80 0.00 36.26 3.16
2901 3095 5.984926 TGAATTCAGTCCAATTTGAACTTGC 59.015 36.000 3.38 0.00 36.26 4.01
2903 3097 5.534207 TTCAGTCCAATTTGAACTTGCAT 57.466 34.783 0.00 0.00 0.00 3.96
2904 3098 5.125100 TCAGTCCAATTTGAACTTGCATC 57.875 39.130 0.00 0.00 0.00 3.91
2905 3099 4.022068 TCAGTCCAATTTGAACTTGCATCC 60.022 41.667 0.00 0.00 0.00 3.51
2906 3100 3.896888 AGTCCAATTTGAACTTGCATCCA 59.103 39.130 0.00 0.00 0.00 3.41
2907 3101 4.529377 AGTCCAATTTGAACTTGCATCCAT 59.471 37.500 0.00 0.00 0.00 3.41
2908 3102 5.012354 AGTCCAATTTGAACTTGCATCCATT 59.988 36.000 0.00 0.00 0.00 3.16
2909 3103 6.211184 AGTCCAATTTGAACTTGCATCCATTA 59.789 34.615 0.00 0.00 0.00 1.90
2910 3104 7.043565 GTCCAATTTGAACTTGCATCCATTAT 58.956 34.615 0.00 0.00 0.00 1.28
2912 3106 7.042950 CCAATTTGAACTTGCATCCATTATCA 58.957 34.615 0.00 0.00 0.00 2.15
2952 3152 9.989869 CTTTAGCTAATTCTTAGTTGCTTAACC 57.010 33.333 7.08 0.00 35.66 2.85
2956 3157 9.078990 AGCTAATTCTTAGTTGCTTAACCTTTT 57.921 29.630 0.00 0.00 35.66 2.27
2965 3166 6.755206 AGTTGCTTAACCTTTTACAAATCCC 58.245 36.000 0.00 0.00 0.00 3.85
2967 3168 4.218852 TGCTTAACCTTTTACAAATCCCGG 59.781 41.667 0.00 0.00 0.00 5.73
2974 3175 4.566070 CCTTTTACAAATCCCGGTCACCTA 60.566 45.833 0.00 0.00 0.00 3.08
2977 3178 2.786777 ACAAATCCCGGTCACCTAAAC 58.213 47.619 0.00 0.00 0.00 2.01
2985 3186 2.676342 CCGGTCACCTAAACTTGCATAC 59.324 50.000 0.00 0.00 0.00 2.39
2988 3189 4.565564 CGGTCACCTAAACTTGCATACTAC 59.434 45.833 0.00 0.00 0.00 2.73
2989 3190 5.623824 CGGTCACCTAAACTTGCATACTACT 60.624 44.000 0.00 0.00 0.00 2.57
2990 3191 5.581085 GGTCACCTAAACTTGCATACTACTG 59.419 44.000 0.00 0.00 0.00 2.74
2991 3192 6.395629 GTCACCTAAACTTGCATACTACTGA 58.604 40.000 0.00 0.00 0.00 3.41
2992 3193 6.531948 GTCACCTAAACTTGCATACTACTGAG 59.468 42.308 0.00 0.00 0.00 3.35
2999 3206 5.411781 ACTTGCATACTACTGAGCTTACAC 58.588 41.667 0.00 0.00 0.00 2.90
3006 3213 4.058817 ACTACTGAGCTTACACTGCAAAC 58.941 43.478 0.00 0.00 0.00 2.93
3014 3221 4.044426 GCTTACACTGCAAACTTTGAAGG 58.956 43.478 13.27 5.69 40.87 3.46
3015 3222 4.440112 GCTTACACTGCAAACTTTGAAGGT 60.440 41.667 13.27 10.34 40.87 3.50
3016 3223 5.220970 GCTTACACTGCAAACTTTGAAGGTA 60.221 40.000 13.27 9.54 40.87 3.08
3017 3224 6.515035 GCTTACACTGCAAACTTTGAAGGTAT 60.515 38.462 13.27 2.13 40.87 2.73
3018 3225 5.186996 ACACTGCAAACTTTGAAGGTATG 57.813 39.130 13.27 5.92 40.87 2.39
3019 3226 3.983344 CACTGCAAACTTTGAAGGTATGC 59.017 43.478 13.27 9.34 40.87 3.14
3020 3227 3.636300 ACTGCAAACTTTGAAGGTATGCA 59.364 39.130 13.27 14.91 40.87 3.96
3021 3228 4.099266 ACTGCAAACTTTGAAGGTATGCAA 59.901 37.500 13.27 0.00 40.87 4.08
3022 3229 4.367450 TGCAAACTTTGAAGGTATGCAAC 58.633 39.130 5.65 0.00 37.06 4.17
3023 3230 4.099266 TGCAAACTTTGAAGGTATGCAACT 59.901 37.500 5.65 0.00 37.06 3.16
3024 3231 5.049828 GCAAACTTTGAAGGTATGCAACTT 58.950 37.500 5.65 0.00 33.18 2.66
3025 3232 5.523552 GCAAACTTTGAAGGTATGCAACTTT 59.476 36.000 5.65 0.00 33.18 2.66
3026 3233 6.037062 GCAAACTTTGAAGGTATGCAACTTTT 59.963 34.615 5.65 0.00 33.18 2.27
3027 3234 7.223777 GCAAACTTTGAAGGTATGCAACTTTTA 59.776 33.333 5.65 0.00 33.18 1.52
3028 3235 8.755018 CAAACTTTGAAGGTATGCAACTTTTAG 58.245 33.333 0.00 0.00 0.00 1.85
3029 3236 7.582667 ACTTTGAAGGTATGCAACTTTTAGT 57.417 32.000 0.00 0.00 0.00 2.24
3030 3237 7.649057 ACTTTGAAGGTATGCAACTTTTAGTC 58.351 34.615 0.00 0.00 0.00 2.59
3031 3238 6.569179 TTGAAGGTATGCAACTTTTAGTCC 57.431 37.500 0.00 0.00 0.00 3.85
3032 3239 5.626142 TGAAGGTATGCAACTTTTAGTCCA 58.374 37.500 0.00 0.00 0.00 4.02
3033 3240 6.245408 TGAAGGTATGCAACTTTTAGTCCAT 58.755 36.000 0.00 0.00 0.00 3.41
3034 3241 7.398829 TGAAGGTATGCAACTTTTAGTCCATA 58.601 34.615 0.00 0.00 0.00 2.74
3035 3242 8.052748 TGAAGGTATGCAACTTTTAGTCCATAT 58.947 33.333 0.00 0.00 0.00 1.78
3036 3243 9.555727 GAAGGTATGCAACTTTTAGTCCATATA 57.444 33.333 0.00 0.00 0.00 0.86
3088 3295 3.494223 GCCTAAACTTGCCACCAATGTTT 60.494 43.478 0.00 0.00 36.80 2.83
3370 3654 2.992689 TCAAGTAGGACGGCGGCA 60.993 61.111 17.61 0.00 0.00 5.69
3531 3815 2.258591 CTGCCACAGCTCGTACGT 59.741 61.111 16.05 0.00 40.80 3.57
4191 4526 1.284491 TGGCAGGTCCTGATGCATTTA 59.716 47.619 23.77 0.00 44.37 1.40
4362 4697 7.448161 TGTCAATTTCATGTACAACAATCTCCT 59.552 33.333 0.00 0.00 0.00 3.69
4363 4698 7.752239 GTCAATTTCATGTACAACAATCTCCTG 59.248 37.037 0.00 0.00 0.00 3.86
4364 4699 7.448161 TCAATTTCATGTACAACAATCTCCTGT 59.552 33.333 0.00 0.00 0.00 4.00
4365 4700 8.729756 CAATTTCATGTACAACAATCTCCTGTA 58.270 33.333 0.00 0.00 0.00 2.74
4366 4701 7.667043 TTTCATGTACAACAATCTCCTGTAC 57.333 36.000 0.00 4.95 43.67 2.90
4367 4702 5.730550 TCATGTACAACAATCTCCTGTACC 58.269 41.667 0.00 0.00 43.05 3.34
4368 4703 4.182693 TGTACAACAATCTCCTGTACCG 57.817 45.455 8.63 0.00 43.05 4.02
4369 4704 3.827876 TGTACAACAATCTCCTGTACCGA 59.172 43.478 8.63 0.00 43.05 4.69
4370 4705 4.281435 TGTACAACAATCTCCTGTACCGAA 59.719 41.667 8.63 0.00 43.05 4.30
4371 4706 4.553330 ACAACAATCTCCTGTACCGAAT 57.447 40.909 0.00 0.00 0.00 3.34
4372 4707 4.504858 ACAACAATCTCCTGTACCGAATC 58.495 43.478 0.00 0.00 0.00 2.52
4373 4708 4.020573 ACAACAATCTCCTGTACCGAATCA 60.021 41.667 0.00 0.00 0.00 2.57
4374 4709 4.819105 ACAATCTCCTGTACCGAATCAA 57.181 40.909 0.00 0.00 0.00 2.57
4375 4710 5.359194 ACAATCTCCTGTACCGAATCAAT 57.641 39.130 0.00 0.00 0.00 2.57
4376 4711 5.360591 ACAATCTCCTGTACCGAATCAATC 58.639 41.667 0.00 0.00 0.00 2.67
4377 4712 5.129485 ACAATCTCCTGTACCGAATCAATCT 59.871 40.000 0.00 0.00 0.00 2.40
4378 4713 4.920640 TCTCCTGTACCGAATCAATCTC 57.079 45.455 0.00 0.00 0.00 2.75
4379 4714 4.278310 TCTCCTGTACCGAATCAATCTCA 58.722 43.478 0.00 0.00 0.00 3.27
4629 5019 5.531634 TCAGTGCCAAATTTTGACAAGATC 58.468 37.500 10.72 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 3.737172 GCCTCGCGCCACATGTTT 61.737 61.111 0.00 0.00 0.00 2.83
87 88 4.096732 AGTCAAATTAACAATGCCTCGC 57.903 40.909 0.00 0.00 0.00 5.03
142 143 1.651987 TCGCAGAAAAAGATAGGCGG 58.348 50.000 0.00 0.00 44.14 6.13
148 149 8.178313 GCTACTTAAGATTTCGCAGAAAAAGAT 58.822 33.333 10.09 0.21 45.90 2.40
155 156 5.479306 ACTTGCTACTTAAGATTTCGCAGA 58.521 37.500 10.09 1.82 0.00 4.26
237 243 0.734889 GGTTTATCTGCGTGCATGCT 59.265 50.000 29.83 13.96 35.36 3.79
263 269 5.900425 TCAGTAACAACACAAACATGCATT 58.100 33.333 0.00 0.00 0.00 3.56
300 306 2.226437 GAGCAAATCCGAGCAAACTCAA 59.774 45.455 0.00 0.00 43.66 3.02
340 346 5.064558 AGATCCATGCACAGAGATTTGATC 58.935 41.667 0.00 0.00 0.00 2.92
344 350 4.813161 CGTTAGATCCATGCACAGAGATTT 59.187 41.667 0.00 0.00 0.00 2.17
351 357 1.066215 ACAGCGTTAGATCCATGCACA 60.066 47.619 8.93 0.00 0.00 4.57
401 407 1.073964 CAATGACAGCACTCGGACTG 58.926 55.000 0.00 0.00 39.86 3.51
472 484 2.702592 AACGTGACCCTCAAAAGTCA 57.297 45.000 0.00 0.00 40.61 3.41
552 564 1.670811 CTATGGATGTGCACCCGTTTC 59.329 52.381 15.69 3.50 0.00 2.78
555 567 1.138266 GTACTATGGATGTGCACCCGT 59.862 52.381 15.69 12.99 0.00 5.28
564 576 9.823647 ATCAAAAGAGTACAAGTACTATGGATG 57.176 33.333 12.50 9.68 45.63 3.51
602 614 8.866970 TCCGATAAAGGGTGTTTTTATTAACT 57.133 30.769 0.00 0.00 32.42 2.24
612 624 6.097129 TGTTTTTCTTTCCGATAAAGGGTGTT 59.903 34.615 9.45 0.00 0.00 3.32
614 626 6.079424 TGTTTTTCTTTCCGATAAAGGGTG 57.921 37.500 9.45 0.00 0.00 4.61
625 637 5.656480 TGGCTTAACACTGTTTTTCTTTCC 58.344 37.500 0.00 0.00 0.00 3.13
637 649 8.244113 GCTTATTTACTTGATTGGCTTAACACT 58.756 33.333 0.00 0.00 0.00 3.55
643 655 6.603940 TTGGCTTATTTACTTGATTGGCTT 57.396 33.333 0.00 0.00 0.00 4.35
644 656 6.437162 TCTTTGGCTTATTTACTTGATTGGCT 59.563 34.615 0.00 0.00 0.00 4.75
645 657 6.630071 TCTTTGGCTTATTTACTTGATTGGC 58.370 36.000 0.00 0.00 0.00 4.52
646 658 9.487790 TTTTCTTTGGCTTATTTACTTGATTGG 57.512 29.630 0.00 0.00 0.00 3.16
650 662 9.912634 CTGATTTTCTTTGGCTTATTTACTTGA 57.087 29.630 0.00 0.00 0.00 3.02
651 663 9.912634 TCTGATTTTCTTTGGCTTATTTACTTG 57.087 29.630 0.00 0.00 0.00 3.16
654 666 9.226345 CGATCTGATTTTCTTTGGCTTATTTAC 57.774 33.333 0.00 0.00 0.00 2.01
655 667 9.173021 TCGATCTGATTTTCTTTGGCTTATTTA 57.827 29.630 0.00 0.00 0.00 1.40
656 668 7.970614 GTCGATCTGATTTTCTTTGGCTTATTT 59.029 33.333 0.00 0.00 0.00 1.40
657 669 7.337942 AGTCGATCTGATTTTCTTTGGCTTATT 59.662 33.333 0.00 0.00 0.00 1.40
658 670 6.825721 AGTCGATCTGATTTTCTTTGGCTTAT 59.174 34.615 0.00 0.00 0.00 1.73
659 671 6.173339 AGTCGATCTGATTTTCTTTGGCTTA 58.827 36.000 0.00 0.00 0.00 3.09
660 672 5.006386 AGTCGATCTGATTTTCTTTGGCTT 58.994 37.500 0.00 0.00 0.00 4.35
713 726 5.710984 TCGAAAGAGAGATCTGGTAAACAC 58.289 41.667 0.00 0.00 34.84 3.32
721 734 5.691305 CCAGCTAATTCGAAAGAGAGATCTG 59.309 44.000 0.00 5.24 43.69 2.90
772 788 1.540363 GGAAACGACCTGCACTTCTCA 60.540 52.381 0.00 0.00 0.00 3.27
832 848 2.095461 CACTGAGCTGGAGTAGTAGCA 58.905 52.381 0.00 0.00 42.29 3.49
833 849 2.096248 ACACTGAGCTGGAGTAGTAGC 58.904 52.381 0.00 0.00 40.18 3.58
834 850 3.314080 GCTACACTGAGCTGGAGTAGTAG 59.686 52.174 16.29 16.81 39.50 2.57
835 851 3.280295 GCTACACTGAGCTGGAGTAGTA 58.720 50.000 16.29 10.77 39.50 1.82
836 852 2.096248 GCTACACTGAGCTGGAGTAGT 58.904 52.381 16.29 10.38 39.50 2.73
904 953 2.949644 TGAATCGATTGTCGCCTCTCTA 59.050 45.455 16.96 0.00 40.21 2.43
1401 1466 7.062722 GCTTTTTCCTGAAGCATTGATAACTTC 59.937 37.037 4.13 0.00 46.67 3.01
1432 1497 3.136260 ACCCACCAAAATGCATGTTTTCT 59.864 39.130 0.00 0.00 0.00 2.52
1535 1602 2.799126 TCATCCCCTATTTGTTGCGT 57.201 45.000 0.00 0.00 0.00 5.24
1536 1603 3.631686 TCATTCATCCCCTATTTGTTGCG 59.368 43.478 0.00 0.00 0.00 4.85
1549 1616 9.770503 CTGAAAATATCGATCAATCATTCATCC 57.229 33.333 0.00 0.00 0.00 3.51
1559 1632 9.613428 AAATGTAGTCCTGAAAATATCGATCAA 57.387 29.630 0.00 0.00 0.00 2.57
1682 1769 4.330250 ACTAGTTCGTACCTCAGCAGTAA 58.670 43.478 0.00 0.00 0.00 2.24
1759 1887 7.446013 TCCATAATTCTTGTCGTGGTTTAGTTT 59.554 33.333 0.00 0.00 0.00 2.66
1807 1936 7.708998 AGGTACGTACTACTACTACTACTGAC 58.291 42.308 24.07 2.50 0.00 3.51
2288 2440 0.468585 GCATCCATCCATTGGCAGGA 60.469 55.000 15.50 15.50 46.01 3.86
2289 2441 0.757561 TGCATCCATCCATTGGCAGG 60.758 55.000 0.00 2.32 46.01 4.85
2341 2510 1.271707 CCGTCACCACAAACCCCTAAT 60.272 52.381 0.00 0.00 0.00 1.73
2343 2512 1.756024 CCGTCACCACAAACCCCTA 59.244 57.895 0.00 0.00 0.00 3.53
2511 2680 0.792640 CCAGTTGTGCAGTCGATGTC 59.207 55.000 0.00 0.00 0.00 3.06
2514 2700 0.681733 AGACCAGTTGTGCAGTCGAT 59.318 50.000 0.00 0.00 34.41 3.59
2517 2703 3.257393 CTGATAGACCAGTTGTGCAGTC 58.743 50.000 0.00 0.00 0.00 3.51
2793 2982 1.661112 GACTTGTTCAGCAGGCGATAC 59.339 52.381 0.00 0.00 0.00 2.24
2874 3068 7.111247 AGTTCAAATTGGACTGAATTCACAA 57.889 32.000 6.05 8.18 34.26 3.33
2884 3078 3.896888 TGGATGCAAGTTCAAATTGGACT 59.103 39.130 0.06 0.06 30.41 3.85
2898 3092 9.695526 GCAGTAATAAATTGATAATGGATGCAA 57.304 29.630 0.00 0.00 0.00 4.08
2899 3093 9.081204 AGCAGTAATAAATTGATAATGGATGCA 57.919 29.630 0.00 0.00 0.00 3.96
2900 3094 9.565213 GAGCAGTAATAAATTGATAATGGATGC 57.435 33.333 0.00 0.00 0.00 3.91
2951 3151 2.490509 GGTGACCGGGATTTGTAAAAGG 59.509 50.000 6.32 0.00 0.00 3.11
2952 3152 3.418047 AGGTGACCGGGATTTGTAAAAG 58.582 45.455 6.32 0.00 0.00 2.27
2956 3157 3.583966 AGTTTAGGTGACCGGGATTTGTA 59.416 43.478 6.32 0.00 0.00 2.41
2965 3166 3.596214 AGTATGCAAGTTTAGGTGACCG 58.404 45.455 0.00 0.00 0.00 4.79
2967 3168 6.395629 TCAGTAGTATGCAAGTTTAGGTGAC 58.604 40.000 0.00 0.00 0.00 3.67
2974 3175 6.369065 GTGTAAGCTCAGTAGTATGCAAGTTT 59.631 38.462 0.00 0.00 0.00 2.66
2977 3178 5.518128 CAGTGTAAGCTCAGTAGTATGCAAG 59.482 44.000 0.00 0.00 0.00 4.01
2985 3186 4.310769 AGTTTGCAGTGTAAGCTCAGTAG 58.689 43.478 4.51 0.00 0.00 2.57
2988 3189 4.035558 TCAAAGTTTGCAGTGTAAGCTCAG 59.964 41.667 10.53 6.88 0.00 3.35
2989 3190 3.944650 TCAAAGTTTGCAGTGTAAGCTCA 59.055 39.130 10.53 0.00 0.00 4.26
2990 3191 4.552166 TCAAAGTTTGCAGTGTAAGCTC 57.448 40.909 10.53 0.00 0.00 4.09
2991 3192 4.202050 CCTTCAAAGTTTGCAGTGTAAGCT 60.202 41.667 10.90 4.51 0.00 3.74
2992 3193 4.044426 CCTTCAAAGTTTGCAGTGTAAGC 58.956 43.478 10.90 0.00 0.00 3.09
2999 3206 4.241590 TGCATACCTTCAAAGTTTGCAG 57.758 40.909 10.90 9.43 43.95 4.41
3006 3213 7.084486 GGACTAAAAGTTGCATACCTTCAAAG 58.916 38.462 0.00 0.00 0.00 2.77
3017 3224 9.674068 TGTTGTATATATGGACTAAAAGTTGCA 57.326 29.630 0.00 0.00 0.00 4.08
3038 3245 9.342308 CCATTGATGTAATTACCTCTATGTTGT 57.658 33.333 26.82 6.91 34.75 3.32
3039 3246 9.342308 ACCATTGATGTAATTACCTCTATGTTG 57.658 33.333 26.82 20.24 34.75 3.33
3040 3247 9.342308 CACCATTGATGTAATTACCTCTATGTT 57.658 33.333 26.82 18.75 34.75 2.71
3041 3248 7.445402 GCACCATTGATGTAATTACCTCTATGT 59.555 37.037 26.82 18.75 34.75 2.29
3042 3249 7.094634 GGCACCATTGATGTAATTACCTCTATG 60.095 40.741 24.56 24.56 35.55 2.23
3088 3295 4.632251 TCTTCAAGTTCGTGCACAAAACTA 59.368 37.500 26.15 14.50 33.08 2.24
3370 3654 3.003763 GTCACGGAGGAGGCCCTT 61.004 66.667 0.00 0.00 44.53 3.95
3460 3744 2.031919 ATGGACGGCTTCAACGCA 59.968 55.556 0.00 0.00 34.00 5.24
3573 3857 3.914984 GAGGTACTGCAGCAACTGA 57.085 52.632 9.87 0.00 41.55 3.41
4362 4697 5.597806 GGTACATGAGATTGATTCGGTACA 58.402 41.667 0.00 0.00 33.35 2.90
4363 4698 4.680110 CGGTACATGAGATTGATTCGGTAC 59.320 45.833 0.00 0.00 32.08 3.34
4364 4699 4.581409 TCGGTACATGAGATTGATTCGGTA 59.419 41.667 0.00 0.00 0.00 4.02
4365 4700 3.383505 TCGGTACATGAGATTGATTCGGT 59.616 43.478 0.00 0.00 0.00 4.69
4366 4701 3.977427 TCGGTACATGAGATTGATTCGG 58.023 45.455 0.00 0.00 0.00 4.30
4367 4702 6.200854 TCAATTCGGTACATGAGATTGATTCG 59.799 38.462 0.00 0.00 0.00 3.34
4368 4703 7.482654 TCAATTCGGTACATGAGATTGATTC 57.517 36.000 0.00 0.00 0.00 2.52
4369 4704 7.864108 TTCAATTCGGTACATGAGATTGATT 57.136 32.000 0.00 0.00 0.00 2.57
4370 4705 7.864108 TTTCAATTCGGTACATGAGATTGAT 57.136 32.000 0.00 0.00 0.00 2.57
4371 4706 7.864108 ATTTCAATTCGGTACATGAGATTGA 57.136 32.000 0.00 14.00 0.00 2.57
4375 4710 9.173021 ACAATAATTTCAATTCGGTACATGAGA 57.827 29.630 0.00 0.00 0.00 3.27
4376 4711 9.787532 AACAATAATTTCAATTCGGTACATGAG 57.212 29.630 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.