Multiple sequence alignment - TraesCS5D01G003100

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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 TraesCS5D01G003100 chr5D 100.000 3529 0 0 1 3529 3011448 3014976 0.000000e+00 6517.0
1 TraesCS5D01G003100 chr5D 89.588 1383 93 25 969 2324 3070500 3071858 0.000000e+00 1709.0
2 TraesCS5D01G003100 chr5D 84.531 1280 108 45 1082 2334 2797315 2798531 0.000000e+00 1184.0
3 TraesCS5D01G003100 chr5D 84.576 590 88 3 2807 3393 117197656 117197067 1.830000e-162 582.0
4 TraesCS5D01G003100 chr5D 90.909 99 9 0 3427 3525 117196738 117196640 2.210000e-27 134.0
5 TraesCS5D01G003100 chr5D 100.000 46 0 0 2686 2731 3014088 3014133 6.280000e-13 86.1
6 TraesCS5D01G003100 chr5D 100.000 43 0 0 2412 2454 2798566 2798608 2.920000e-11 80.5
7 TraesCS5D01G003100 chr5A 88.014 1435 133 25 969 2393 1759615 1758210 0.000000e+00 1661.0
8 TraesCS5D01G003100 chr5A 86.442 1335 108 44 1037 2324 1714393 1713085 0.000000e+00 1395.0
9 TraesCS5D01G003100 chr5A 83.475 1416 148 43 1070 2451 1834848 1833485 0.000000e+00 1240.0
10 TraesCS5D01G003100 chr5A 82.286 875 100 29 3 865 1804674 1803843 0.000000e+00 706.0
11 TraesCS5D01G003100 chr5A 85.753 365 34 6 1980 2340 1803132 1802782 1.550000e-98 370.0
12 TraesCS5D01G003100 chr5A 87.676 284 27 3 1040 1316 1336371 1336653 1.220000e-84 324.0
13 TraesCS5D01G003100 chr5A 85.926 135 8 3 2393 2516 1802652 1802518 2.210000e-27 134.0
14 TraesCS5D01G003100 chr5A 84.058 138 4 7 2393 2516 1757920 1757787 2.230000e-22 117.0
15 TraesCS5D01G003100 chr5A 100.000 44 0 0 971 1014 1714433 1714390 8.120000e-12 82.4
16 TraesCS5D01G003100 chr5B 88.897 1378 111 20 969 2324 2883455 2884812 0.000000e+00 1659.0
17 TraesCS5D01G003100 chr5B 84.873 1699 164 57 853 2516 2614554 2612914 0.000000e+00 1628.0
18 TraesCS5D01G003100 chr5B 83.765 1275 134 33 1080 2327 2805580 2806808 0.000000e+00 1140.0
19 TraesCS5D01G003100 chr5B 89.245 874 58 12 1 855 2615458 2614602 0.000000e+00 1061.0
20 TraesCS5D01G003100 chr1D 94.240 868 23 10 2686 3529 416541916 416541052 0.000000e+00 1301.0
21 TraesCS5D01G003100 chr1D 96.471 170 6 0 2517 2686 416542040 416541871 7.460000e-72 281.0
22 TraesCS5D01G003100 chr3D 86.792 742 62 16 2686 3393 589433159 589433898 0.000000e+00 795.0
23 TraesCS5D01G003100 chr3D 90.173 173 12 4 2513 2683 589433032 589433201 1.650000e-53 220.0
24 TraesCS5D01G003100 chr6D 86.523 742 64 14 2686 3393 272854424 272855163 0.000000e+00 784.0
25 TraesCS5D01G003100 chr6D 89.113 496 46 4 2904 3393 23830279 23829786 8.380000e-171 610.0
26 TraesCS5D01G003100 chr6D 89.535 172 18 0 2512 2683 272854295 272854466 5.930000e-53 219.0
27 TraesCS5D01G003100 chr4D 85.868 743 68 15 2686 3393 39595719 39594979 0.000000e+00 756.0
28 TraesCS5D01G003100 chr4D 90.643 171 16 0 2516 2686 39595844 39595674 9.860000e-56 228.0
29 TraesCS5D01G003100 chr4A 89.438 587 51 9 2815 3393 560752299 560752882 0.000000e+00 730.0
30 TraesCS5D01G003100 chr4A 88.095 168 20 0 2516 2683 560745475 560745642 2.150000e-47 200.0
31 TraesCS5D01G003100 chr6A 85.538 567 61 11 2965 3529 577847626 577848173 1.100000e-159 573.0
32 TraesCS5D01G003100 chr6A 90.698 172 16 0 2513 2684 577847257 577847428 2.740000e-56 230.0
33 TraesCS5D01G003100 chr6A 92.308 117 5 4 2686 2799 577847385 577847500 2.820000e-36 163.0
34 TraesCS5D01G003100 chr6A 90.588 85 7 1 2807 2890 577847539 577847623 1.040000e-20 111.0
35 TraesCS5D01G003100 chr2B 83.548 620 69 13 2686 3273 782454519 782453901 1.850000e-152 549.0
36 TraesCS5D01G003100 chr2B 89.222 167 17 1 2514 2679 782454647 782454481 1.280000e-49 207.0
37 TraesCS5D01G003100 chr2B 79.137 139 17 5 488 620 283183977 283183845 6.280000e-13 86.1
38 TraesCS5D01G003100 chr7B 91.126 293 26 0 3237 3529 745627951 745628243 7.100000e-107 398.0
39 TraesCS5D01G003100 chr1B 89.216 306 32 1 3062 3366 301775600 301775295 7.150000e-102 381.0
40 TraesCS5D01G003100 chr1B 85.326 368 20 13 2686 3019 301776235 301775868 2.020000e-92 350.0
41 TraesCS5D01G003100 chr1B 89.017 173 17 2 2515 2686 301776361 301776190 2.760000e-51 213.0
42 TraesCS5D01G003100 chr1B 78.814 118 16 5 488 603 426779577 426779467 1.760000e-08 71.3
43 TraesCS5D01G003100 chr2D 89.116 147 16 0 2521 2667 631957283 631957137 2.160000e-42 183.0
44 TraesCS5D01G003100 chr3B 83.133 83 7 4 522 603 733894853 733894777 6.320000e-08 69.4
45 TraesCS5D01G003100 chr6B 76.596 141 21 5 488 622 672920010 672919876 2.270000e-07 67.6


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 TraesCS5D01G003100 chr5D 3011448 3014976 3528 False 3301.550000 6517 100.0000 1 3529 2 chr5D.!!$F3 3528
1 TraesCS5D01G003100 chr5D 3070500 3071858 1358 False 1709.000000 1709 89.5880 969 2324 1 chr5D.!!$F1 1355
2 TraesCS5D01G003100 chr5D 2797315 2798608 1293 False 632.250000 1184 92.2655 1082 2454 2 chr5D.!!$F2 1372
3 TraesCS5D01G003100 chr5D 117196640 117197656 1016 True 358.000000 582 87.7425 2807 3525 2 chr5D.!!$R1 718
4 TraesCS5D01G003100 chr5A 1833485 1834848 1363 True 1240.000000 1240 83.4750 1070 2451 1 chr5A.!!$R1 1381
5 TraesCS5D01G003100 chr5A 1757787 1759615 1828 True 889.000000 1661 86.0360 969 2516 2 chr5A.!!$R3 1547
6 TraesCS5D01G003100 chr5A 1713085 1714433 1348 True 738.700000 1395 93.2210 971 2324 2 chr5A.!!$R2 1353
7 TraesCS5D01G003100 chr5A 1802518 1804674 2156 True 403.333333 706 84.6550 3 2516 3 chr5A.!!$R4 2513
8 TraesCS5D01G003100 chr5B 2883455 2884812 1357 False 1659.000000 1659 88.8970 969 2324 1 chr5B.!!$F2 1355
9 TraesCS5D01G003100 chr5B 2612914 2615458 2544 True 1344.500000 1628 87.0590 1 2516 2 chr5B.!!$R1 2515
10 TraesCS5D01G003100 chr5B 2805580 2806808 1228 False 1140.000000 1140 83.7650 1080 2327 1 chr5B.!!$F1 1247
11 TraesCS5D01G003100 chr1D 416541052 416542040 988 True 791.000000 1301 95.3555 2517 3529 2 chr1D.!!$R1 1012
12 TraesCS5D01G003100 chr3D 589433032 589433898 866 False 507.500000 795 88.4825 2513 3393 2 chr3D.!!$F1 880
13 TraesCS5D01G003100 chr6D 272854295 272855163 868 False 501.500000 784 88.0290 2512 3393 2 chr6D.!!$F1 881
14 TraesCS5D01G003100 chr4D 39594979 39595844 865 True 492.000000 756 88.2555 2516 3393 2 chr4D.!!$R1 877
15 TraesCS5D01G003100 chr4A 560752299 560752882 583 False 730.000000 730 89.4380 2815 3393 1 chr4A.!!$F2 578
16 TraesCS5D01G003100 chr6A 577847257 577848173 916 False 269.250000 573 89.7830 2513 3529 4 chr6A.!!$F1 1016
17 TraesCS5D01G003100 chr2B 782453901 782454647 746 True 378.000000 549 86.3850 2514 3273 2 chr2B.!!$R2 759
18 TraesCS5D01G003100 chr1B 301775295 301776361 1066 True 314.666667 381 87.8530 2515 3366 3 chr1B.!!$R2 851

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
340 343 0.180406 GGTGATGGCTATCGGTGGTT 59.820 55.0 5.52 0.00 36.04 3.67 F
560 571 0.385974 GTGTGGTGTTTCGCATGAGC 60.386 55.0 0.00 0.00 37.42 4.26 F
1816 2611 0.322277 ACACCAGAAGCAGAGCATGG 60.322 55.0 0.00 6.42 35.84 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 2535 0.035725 CCACCATGCTCTGCTTCTGA 60.036 55.0 0.0 0.0 0.00 3.27 R
1821 2616 0.037882 CCACGTCATGCTGAGACTGT 60.038 55.0 0.0 0.0 33.89 3.55 R
2653 3867 0.108019 AAAAGGCGTTCGGGAGACTT 59.892 50.0 0.0 0.0 39.59 3.01 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
72 73 8.026607 TGCAATAGTATTAAAAGGAGTTTGTGC 58.973 33.333 0.00 0.00 0.00 4.57
83 84 1.943693 GTTTGTGCGCGCAACATGT 60.944 52.632 38.24 0.00 0.00 3.21
144 145 1.603306 GGTGGTATGGTTGCGGGTA 59.397 57.895 0.00 0.00 0.00 3.69
170 171 1.482593 CATAGGGATACGATGGAGGGC 59.517 57.143 0.00 0.00 37.60 5.19
221 224 0.250727 GTTGTACTGGGCAGAGGCAA 60.251 55.000 0.00 0.00 43.71 4.52
250 253 1.070108 GCGAACGTTGTTTCCTTCCTC 60.070 52.381 5.00 0.00 0.00 3.71
259 262 1.346722 GTTTCCTTCCTCGAGGTTCCA 59.653 52.381 30.17 9.08 38.04 3.53
262 265 1.195115 CCTTCCTCGAGGTTCCATCA 58.805 55.000 30.17 7.04 36.34 3.07
265 268 0.611062 TCCTCGAGGTTCCATCACGT 60.611 55.000 30.17 0.00 36.34 4.49
271 274 2.767505 GAGGTTCCATCACGTTGTTCT 58.232 47.619 0.00 0.00 0.00 3.01
340 343 0.180406 GGTGATGGCTATCGGTGGTT 59.820 55.000 5.52 0.00 36.04 3.67
349 352 2.346803 CTATCGGTGGTTGTGTCCTTG 58.653 52.381 0.00 0.00 0.00 3.61
381 384 2.260481 GTCTTGTAGTGCTTACTCCGC 58.740 52.381 0.00 0.00 33.23 5.54
389 392 2.098831 GCTTACTCCGCCGTTGTCC 61.099 63.158 0.00 0.00 0.00 4.02
402 405 1.537348 CGTTGTCCGTCTCACCTTTCA 60.537 52.381 0.00 0.00 0.00 2.69
409 412 2.029020 CCGTCTCACCTTTCATCTGTGA 60.029 50.000 0.00 0.00 37.45 3.58
486 489 1.786937 ATTTGCTTGGTGGTTGTGGA 58.213 45.000 0.00 0.00 0.00 4.02
560 571 0.385974 GTGTGGTGTTTCGCATGAGC 60.386 55.000 0.00 0.00 37.42 4.26
650 669 3.197333 AGGAGTGATCATCTGGTGTGAAG 59.803 47.826 0.00 0.00 0.00 3.02
658 677 4.065088 TCATCTGGTGTGAAGTTTGCTAC 58.935 43.478 0.00 0.00 0.00 3.58
735 755 4.648651 AGGCGACACAAAACCTAATAAGT 58.351 39.130 0.00 0.00 0.00 2.24
793 813 5.163519 ACAGCAAATAAAGCACAAGACAGTT 60.164 36.000 0.00 0.00 0.00 3.16
812 832 6.162777 ACAGTTAGATTCTTGAGCTGAAGAC 58.837 40.000 15.68 5.30 31.53 3.01
855 879 1.490490 TCCCATTGACATCCAGCTACC 59.510 52.381 0.00 0.00 0.00 3.18
856 880 1.212688 CCCATTGACATCCAGCTACCA 59.787 52.381 0.00 0.00 0.00 3.25
857 881 2.357050 CCCATTGACATCCAGCTACCAA 60.357 50.000 0.00 0.00 0.00 3.67
858 882 3.559069 CCATTGACATCCAGCTACCAAT 58.441 45.455 0.00 0.00 0.00 3.16
860 884 4.403432 CCATTGACATCCAGCTACCAATTT 59.597 41.667 0.00 0.00 0.00 1.82
861 885 5.593909 CCATTGACATCCAGCTACCAATTTA 59.406 40.000 0.00 0.00 0.00 1.40
862 886 6.460123 CCATTGACATCCAGCTACCAATTTAC 60.460 42.308 0.00 0.00 0.00 2.01
864 888 6.553953 TGACATCCAGCTACCAATTTACTA 57.446 37.500 0.00 0.00 0.00 1.82
865 889 6.582636 TGACATCCAGCTACCAATTTACTAG 58.417 40.000 0.00 0.00 0.00 2.57
935 1569 7.439157 TGTTCTTTCTTGTATTCCAGACATG 57.561 36.000 0.00 0.00 0.00 3.21
941 1575 5.664457 TCTTGTATTCCAGACATGCTAGTG 58.336 41.667 0.00 0.00 0.00 2.74
945 1579 4.679373 ATTCCAGACATGCTAGTGGTAG 57.321 45.455 0.00 0.00 0.00 3.18
946 1580 2.388735 TCCAGACATGCTAGTGGTAGG 58.611 52.381 0.00 0.00 0.00 3.18
948 1582 2.363680 CCAGACATGCTAGTGGTAGGAG 59.636 54.545 0.00 0.00 28.84 3.69
967 1604 2.817844 GAGTACATCACAAACCCCAACC 59.182 50.000 0.00 0.00 0.00 3.77
1014 1658 2.765135 CCACCTCACTCATCTCACTCAT 59.235 50.000 0.00 0.00 0.00 2.90
1016 1660 4.431809 CACCTCACTCATCTCACTCATTC 58.568 47.826 0.00 0.00 0.00 2.67
1017 1661 4.081807 CACCTCACTCATCTCACTCATTCA 60.082 45.833 0.00 0.00 0.00 2.57
1021 1665 5.668471 TCACTCATCTCACTCATTCATTCC 58.332 41.667 0.00 0.00 0.00 3.01
1022 1666 5.424573 TCACTCATCTCACTCATTCATTCCT 59.575 40.000 0.00 0.00 0.00 3.36
1026 1670 4.750021 TCTCACTCATTCATTCCTCCAG 57.250 45.455 0.00 0.00 0.00 3.86
1042 1698 1.376424 CAGCACCGCCATCTCACTT 60.376 57.895 0.00 0.00 0.00 3.16
1231 1909 3.632080 ATGCCCCGTCCGACAACA 61.632 61.111 0.00 0.00 0.00 3.33
1248 1926 4.586235 AACTGCGCCACCAAGCCT 62.586 61.111 4.18 0.00 0.00 4.58
1256 1934 2.435586 CACCAAGCCTGAGCCTCG 60.436 66.667 0.00 0.00 41.25 4.63
1755 2457 2.125350 GCCTCGGCCTCTGTTCTG 60.125 66.667 0.00 0.00 34.56 3.02
1761 2535 1.903877 CGGCCTCTGTTCTGGACCAT 61.904 60.000 0.00 0.00 0.00 3.55
1801 2596 1.174712 ACAGCCACAGCATGAACACC 61.175 55.000 0.00 0.00 43.56 4.16
1803 2598 0.892358 AGCCACAGCATGAACACCAG 60.892 55.000 0.00 0.00 43.56 4.00
1805 2600 1.608055 CCACAGCATGAACACCAGAA 58.392 50.000 0.00 0.00 39.69 3.02
1806 2601 1.538512 CCACAGCATGAACACCAGAAG 59.461 52.381 0.00 0.00 39.69 2.85
1807 2602 1.068748 CACAGCATGAACACCAGAAGC 60.069 52.381 0.00 0.00 39.69 3.86
1809 2604 1.199327 CAGCATGAACACCAGAAGCAG 59.801 52.381 0.00 0.00 39.69 4.24
1810 2605 1.072806 AGCATGAACACCAGAAGCAGA 59.927 47.619 0.00 0.00 0.00 4.26
1811 2606 1.467734 GCATGAACACCAGAAGCAGAG 59.532 52.381 0.00 0.00 0.00 3.35
1812 2607 1.467734 CATGAACACCAGAAGCAGAGC 59.532 52.381 0.00 0.00 0.00 4.09
1813 2608 0.469494 TGAACACCAGAAGCAGAGCA 59.531 50.000 0.00 0.00 0.00 4.26
1815 2610 1.467734 GAACACCAGAAGCAGAGCATG 59.532 52.381 0.00 0.00 0.00 4.06
1816 2611 0.322277 ACACCAGAAGCAGAGCATGG 60.322 55.000 0.00 6.42 35.84 3.66
1817 2612 0.322277 CACCAGAAGCAGAGCATGGT 60.322 55.000 0.00 0.00 40.78 3.55
1818 2613 0.322277 ACCAGAAGCAGAGCATGGTG 60.322 55.000 0.00 0.00 39.44 4.17
1819 2614 1.654954 CCAGAAGCAGAGCATGGTGC 61.655 60.000 0.00 0.00 45.46 5.01
1829 2624 2.632643 GCATGGTGCAACAGTCTCA 58.367 52.632 11.62 0.00 44.26 3.27
1830 2625 0.520404 GCATGGTGCAACAGTCTCAG 59.480 55.000 11.62 0.00 44.26 3.35
1831 2626 0.520404 CATGGTGCAACAGTCTCAGC 59.480 55.000 11.62 0.00 39.98 4.26
1832 2627 0.109153 ATGGTGCAACAGTCTCAGCA 59.891 50.000 11.62 8.70 41.55 4.41
1833 2628 0.109153 TGGTGCAACAGTCTCAGCAT 59.891 50.000 0.00 0.00 39.98 3.79
1834 2629 0.520404 GGTGCAACAGTCTCAGCATG 59.480 55.000 0.00 0.00 39.98 4.06
1835 2630 1.516161 GTGCAACAGTCTCAGCATGA 58.484 50.000 0.00 0.00 39.43 3.07
1839 2634 1.458445 CAACAGTCTCAGCATGACGTG 59.542 52.381 0.00 0.00 42.56 4.49
1842 2637 0.969149 AGTCTCAGCATGACGTGGAA 59.031 50.000 0.00 0.00 42.56 3.53
2242 3061 3.580100 GAGCTGGTGCAGAGCGTGA 62.580 63.158 11.14 0.00 41.61 4.35
2368 3187 2.559440 GGGCTAGCTTGAGAATGTCAG 58.441 52.381 15.72 0.00 36.21 3.51
2519 3733 9.849166 AAGTTAATATGACAACAATTTTACGGG 57.151 29.630 0.00 0.00 0.00 5.28
2615 3829 3.582647 ACACATCTTGACACACCATCCTA 59.417 43.478 0.00 0.00 0.00 2.94
2658 3872 3.069318 GGGACGAGGGCGAAGTCT 61.069 66.667 0.00 0.00 41.64 3.24
2659 3873 2.490685 GGACGAGGGCGAAGTCTC 59.509 66.667 0.00 0.00 41.64 3.36
2660 3874 2.490685 GACGAGGGCGAAGTCTCC 59.509 66.667 0.00 0.00 41.64 3.71
2661 3875 3.066233 GACGAGGGCGAAGTCTCCC 62.066 68.421 0.00 0.00 41.20 4.30
2662 3876 4.194720 CGAGGGCGAAGTCTCCCG 62.195 72.222 0.68 0.00 45.44 5.14
2663 3877 2.754658 GAGGGCGAAGTCTCCCGA 60.755 66.667 0.68 0.00 45.44 5.14
2664 3878 2.283676 AGGGCGAAGTCTCCCGAA 60.284 61.111 0.68 0.00 45.44 4.30
2665 3879 2.125633 GGGCGAAGTCTCCCGAAC 60.126 66.667 0.00 0.00 30.24 3.95
2666 3880 2.506438 GGCGAAGTCTCCCGAACG 60.506 66.667 0.00 0.00 0.00 3.95
2667 3881 3.179939 GCGAAGTCTCCCGAACGC 61.180 66.667 0.00 0.00 39.33 4.84
2668 3882 2.506438 CGAAGTCTCCCGAACGCC 60.506 66.667 0.00 0.00 0.00 5.68
2669 3883 2.971452 GAAGTCTCCCGAACGCCT 59.029 61.111 0.00 0.00 0.00 5.52
2670 3884 1.292541 GAAGTCTCCCGAACGCCTT 59.707 57.895 0.00 0.00 0.00 4.35
2671 3885 0.320508 GAAGTCTCCCGAACGCCTTT 60.321 55.000 0.00 0.00 0.00 3.11
2672 3886 0.108019 AAGTCTCCCGAACGCCTTTT 59.892 50.000 0.00 0.00 0.00 2.27
2673 3887 0.320508 AGTCTCCCGAACGCCTTTTC 60.321 55.000 0.00 0.00 0.00 2.29
2674 3888 0.320508 GTCTCCCGAACGCCTTTTCT 60.321 55.000 0.00 0.00 0.00 2.52
2675 3889 0.395312 TCTCCCGAACGCCTTTTCTT 59.605 50.000 0.00 0.00 0.00 2.52
2676 3890 1.202722 TCTCCCGAACGCCTTTTCTTT 60.203 47.619 0.00 0.00 0.00 2.52
2677 3891 1.607148 CTCCCGAACGCCTTTTCTTTT 59.393 47.619 0.00 0.00 0.00 2.27
2678 3892 2.025898 TCCCGAACGCCTTTTCTTTTT 58.974 42.857 0.00 0.00 0.00 1.94
2679 3893 2.033675 TCCCGAACGCCTTTTCTTTTTC 59.966 45.455 0.00 0.00 0.00 2.29
2680 3894 2.223618 CCCGAACGCCTTTTCTTTTTCA 60.224 45.455 0.00 0.00 0.00 2.69
2681 3895 2.787129 CCGAACGCCTTTTCTTTTTCAC 59.213 45.455 0.00 0.00 0.00 3.18
2682 3896 3.488553 CCGAACGCCTTTTCTTTTTCACT 60.489 43.478 0.00 0.00 0.00 3.41
2683 3897 3.724257 CGAACGCCTTTTCTTTTTCACTC 59.276 43.478 0.00 0.00 0.00 3.51
2684 3898 3.334272 ACGCCTTTTCTTTTTCACTCG 57.666 42.857 0.00 0.00 0.00 4.18
2685 3899 2.044135 CGCCTTTTCTTTTTCACTCGC 58.956 47.619 0.00 0.00 0.00 5.03
2686 3900 2.044135 GCCTTTTCTTTTTCACTCGCG 58.956 47.619 0.00 0.00 0.00 5.87
2687 3901 2.650608 CCTTTTCTTTTTCACTCGCGG 58.349 47.619 6.13 0.00 0.00 6.46
2688 3902 2.604614 CCTTTTCTTTTTCACTCGCGGG 60.605 50.000 3.27 3.27 0.00 6.13
2689 3903 1.956297 TTTCTTTTTCACTCGCGGGA 58.044 45.000 15.95 1.66 0.00 5.14
2690 3904 1.223187 TTCTTTTTCACTCGCGGGAC 58.777 50.000 15.95 0.00 0.00 4.46
2871 4133 2.827423 CGATGAGCTGCCTGGGAT 59.173 61.111 0.00 0.00 0.00 3.85
3097 4588 2.680352 GTCGACAGGGGAGCTCCA 60.680 66.667 33.29 8.97 37.91 3.86
3176 4669 2.711922 CCGTCTCCAACTCCCCGAG 61.712 68.421 0.00 0.00 35.52 4.63
3460 5256 1.078567 CTGCTCCTCAAGTCTGGGC 60.079 63.158 0.00 0.00 0.00 5.36
3513 5309 2.480419 CGACTGCGATTTCAAGGTCTTT 59.520 45.455 0.00 0.00 40.82 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 4.979013 GCACATGTTGCGCGCACA 62.979 61.111 36.72 31.94 42.79 4.57
85 86 1.016130 CCGCACCTGAGCAAGTAGTG 61.016 60.000 0.00 0.00 0.00 2.74
86 87 1.293498 CCGCACCTGAGCAAGTAGT 59.707 57.895 0.00 0.00 0.00 2.73
87 88 1.448540 CCCGCACCTGAGCAAGTAG 60.449 63.158 0.00 0.00 0.00 2.57
88 89 2.662596 CCCGCACCTGAGCAAGTA 59.337 61.111 0.00 0.00 0.00 2.24
144 145 2.168521 CCATCGTATCCCTATGCCGAAT 59.831 50.000 0.00 0.00 0.00 3.34
170 171 4.056125 TGCACTCCGGCTCTCACG 62.056 66.667 0.00 0.00 34.04 4.35
213 216 3.799753 CGGATTCCGTTGCCTCTG 58.200 61.111 17.08 0.00 42.73 3.35
233 236 2.480845 CTCGAGGAAGGAAACAACGTT 58.519 47.619 3.91 0.00 0.00 3.99
250 253 1.459592 GAACAACGTGATGGAACCTCG 59.540 52.381 0.00 0.00 0.00 4.63
259 262 3.753294 AGGAAGTGAGAACAACGTGAT 57.247 42.857 0.00 0.00 0.00 3.06
262 265 3.374058 CACAAAGGAAGTGAGAACAACGT 59.626 43.478 0.00 0.00 39.30 3.99
265 268 6.177610 AGTAACACAAAGGAAGTGAGAACAA 58.822 36.000 0.00 0.00 40.16 2.83
271 274 6.655930 ACCTAAAGTAACACAAAGGAAGTGA 58.344 36.000 0.00 0.00 40.16 3.41
349 352 1.732259 CTACAAGACCGTGCATCCAAC 59.268 52.381 0.00 0.00 0.00 3.77
389 392 3.303881 TCACAGATGAAAGGTGAGACG 57.696 47.619 0.00 0.00 36.69 4.18
402 405 1.134280 CCCCGAGAGCAATTCACAGAT 60.134 52.381 0.00 0.00 0.00 2.90
409 412 1.208165 AACCTCCCCCGAGAGCAATT 61.208 55.000 0.00 0.00 38.52 2.32
450 453 3.548818 GCAAATTACATAGGCGCCAAGAG 60.549 47.826 31.54 17.63 0.00 2.85
486 489 4.016706 GGCACCGCTACACCACCT 62.017 66.667 0.00 0.00 0.00 4.00
504 507 4.201910 CCAAGGCAAAATACATAGGTGTCG 60.202 45.833 0.00 0.00 39.77 4.35
506 509 4.023291 CCCAAGGCAAAATACATAGGTGT 58.977 43.478 0.00 0.00 42.39 4.16
560 571 5.371115 ACCATCAAACAATCCGTTACAAG 57.629 39.130 0.00 0.00 36.59 3.16
615 634 6.994421 TGATCACTCCTTAATGCTATACCA 57.006 37.500 0.00 0.00 0.00 3.25
616 635 7.763528 CAGATGATCACTCCTTAATGCTATACC 59.236 40.741 0.00 0.00 0.00 2.73
623 642 5.526479 CACACCAGATGATCACTCCTTAATG 59.474 44.000 0.00 0.00 0.00 1.90
630 649 4.199432 ACTTCACACCAGATGATCACTC 57.801 45.455 0.00 0.00 0.00 3.51
634 653 3.755378 AGCAAACTTCACACCAGATGATC 59.245 43.478 0.00 0.00 0.00 2.92
674 693 4.318050 GGAACTGAAAAACATTTGCGCTTC 60.318 41.667 9.73 1.41 0.00 3.86
678 698 2.470999 CGGGAACTGAAAAACATTTGCG 59.529 45.455 0.00 0.00 36.31 4.85
735 755 4.766373 TGCTAGCATCTTGGAAATTCAACA 59.234 37.500 14.93 0.00 0.00 3.33
793 813 3.429547 GGCGTCTTCAGCTCAAGAATCTA 60.430 47.826 0.00 0.00 34.11 1.98
812 832 4.516698 AGACAGCAATGAATATAAAGGGCG 59.483 41.667 0.00 0.00 0.00 6.13
927 1561 2.363680 CTCCTACCACTAGCATGTCTGG 59.636 54.545 0.00 0.00 0.00 3.86
935 1569 3.952323 TGTGATGTACTCCTACCACTAGC 59.048 47.826 0.00 0.00 0.00 3.42
941 1575 3.370209 GGGGTTTGTGATGTACTCCTACC 60.370 52.174 0.00 0.00 29.48 3.18
945 1579 2.817844 GTTGGGGTTTGTGATGTACTCC 59.182 50.000 0.00 0.00 32.85 3.85
946 1580 2.817844 GGTTGGGGTTTGTGATGTACTC 59.182 50.000 0.00 0.00 0.00 2.59
948 1582 2.588620 TGGTTGGGGTTTGTGATGTAC 58.411 47.619 0.00 0.00 0.00 2.90
967 1604 2.158370 GGGGGTTGGGAGGGTATTTATG 60.158 54.545 0.00 0.00 0.00 1.90
1014 1658 1.377202 GCGGTGCTGGAGGAATGAA 60.377 57.895 0.00 0.00 0.00 2.57
1016 1660 2.825836 GGCGGTGCTGGAGGAATG 60.826 66.667 0.00 0.00 0.00 2.67
1017 1661 2.615227 GATGGCGGTGCTGGAGGAAT 62.615 60.000 0.00 0.00 0.00 3.01
1021 1665 2.202987 GAGATGGCGGTGCTGGAG 60.203 66.667 0.00 0.00 0.00 3.86
1022 1666 3.002583 TGAGATGGCGGTGCTGGA 61.003 61.111 0.00 0.00 0.00 3.86
1026 1670 1.599542 GAATAAGTGAGATGGCGGTGC 59.400 52.381 0.00 0.00 0.00 5.01
1042 1698 3.782523 AGATGAAGGTTGCTGGAGGAATA 59.217 43.478 0.00 0.00 0.00 1.75
1136 1802 3.878519 GAGGAGGAGCGACGTCGG 61.879 72.222 36.13 19.71 40.23 4.79
1137 1803 3.125573 TGAGGAGGAGCGACGTCG 61.126 66.667 32.57 32.57 43.27 5.12
1185 1863 2.359107 CACATGTCCAGCTGCCGT 60.359 61.111 8.66 0.00 0.00 5.68
1215 1893 3.862991 TTGTTGTCGGACGGGGCA 61.863 61.111 3.34 0.00 0.00 5.36
1222 1900 2.970324 GGCGCAGTTGTTGTCGGA 60.970 61.111 10.83 0.00 0.00 4.55
1231 1909 4.586235 AGGCTTGGTGGCGCAGTT 62.586 61.111 10.83 0.00 46.88 3.16
1410 2091 2.513259 ATCGTCGGTTGTGTGGGGT 61.513 57.895 0.00 0.00 0.00 4.95
1755 2457 0.251354 TGCTCTGCTTCTGATGGTCC 59.749 55.000 0.00 0.00 0.00 4.46
1761 2535 0.035725 CCACCATGCTCTGCTTCTGA 60.036 55.000 0.00 0.00 0.00 3.27
1801 2596 0.958876 TGCACCATGCTCTGCTTCTG 60.959 55.000 2.02 0.00 45.31 3.02
1803 2598 0.109412 GTTGCACCATGCTCTGCTTC 60.109 55.000 2.02 1.02 45.31 3.86
1805 2600 1.228337 TGTTGCACCATGCTCTGCT 60.228 52.632 2.02 0.00 45.31 4.24
1806 2601 1.211969 CTGTTGCACCATGCTCTGC 59.788 57.895 2.02 2.21 45.31 4.26
1807 2602 0.520404 GACTGTTGCACCATGCTCTG 59.480 55.000 2.02 2.96 45.31 3.35
1809 2604 0.801251 GAGACTGTTGCACCATGCTC 59.199 55.000 2.02 0.00 45.31 4.26
1810 2605 0.109153 TGAGACTGTTGCACCATGCT 59.891 50.000 2.02 0.00 45.31 3.79
1811 2606 0.520404 CTGAGACTGTTGCACCATGC 59.480 55.000 0.00 0.00 45.29 4.06
1812 2607 0.520404 GCTGAGACTGTTGCACCATG 59.480 55.000 0.00 0.00 0.00 3.66
1813 2608 0.109153 TGCTGAGACTGTTGCACCAT 59.891 50.000 0.00 0.00 0.00 3.55
1815 2610 0.520404 CATGCTGAGACTGTTGCACC 59.480 55.000 0.00 0.00 38.29 5.01
1816 2611 1.196354 GTCATGCTGAGACTGTTGCAC 59.804 52.381 0.00 0.00 38.29 4.57
1817 2612 1.516161 GTCATGCTGAGACTGTTGCA 58.484 50.000 0.00 0.00 39.83 4.08
1818 2613 0.441533 CGTCATGCTGAGACTGTTGC 59.558 55.000 0.00 0.00 33.89 4.17
1819 2614 1.458445 CACGTCATGCTGAGACTGTTG 59.542 52.381 0.00 0.00 33.89 3.33
1820 2615 1.606480 CCACGTCATGCTGAGACTGTT 60.606 52.381 0.00 0.00 33.89 3.16
1821 2616 0.037882 CCACGTCATGCTGAGACTGT 60.038 55.000 0.00 0.00 33.89 3.55
1822 2617 0.244721 TCCACGTCATGCTGAGACTG 59.755 55.000 0.00 0.00 33.89 3.51
1823 2618 0.969149 TTCCACGTCATGCTGAGACT 59.031 50.000 0.00 0.00 33.89 3.24
1824 2619 1.067565 TCTTCCACGTCATGCTGAGAC 60.068 52.381 0.00 0.00 0.00 3.36
1825 2620 1.203287 CTCTTCCACGTCATGCTGAGA 59.797 52.381 0.00 0.00 0.00 3.27
1826 2621 1.638133 CTCTTCCACGTCATGCTGAG 58.362 55.000 0.00 0.00 0.00 3.35
1827 2622 0.247460 CCTCTTCCACGTCATGCTGA 59.753 55.000 0.00 0.00 0.00 4.26
1828 2623 0.247460 TCCTCTTCCACGTCATGCTG 59.753 55.000 0.00 0.00 0.00 4.41
1829 2624 0.976641 TTCCTCTTCCACGTCATGCT 59.023 50.000 0.00 0.00 0.00 3.79
1830 2625 1.066858 TCTTCCTCTTCCACGTCATGC 60.067 52.381 0.00 0.00 0.00 4.06
1831 2626 3.056536 TCTTCTTCCTCTTCCACGTCATG 60.057 47.826 0.00 0.00 0.00 3.07
1832 2627 3.165875 TCTTCTTCCTCTTCCACGTCAT 58.834 45.455 0.00 0.00 0.00 3.06
1833 2628 2.594131 TCTTCTTCCTCTTCCACGTCA 58.406 47.619 0.00 0.00 0.00 4.35
1834 2629 3.256136 TCTTCTTCTTCCTCTTCCACGTC 59.744 47.826 0.00 0.00 0.00 4.34
1835 2630 3.231818 TCTTCTTCTTCCTCTTCCACGT 58.768 45.455 0.00 0.00 0.00 4.49
1839 2634 3.450817 CCTCCTCTTCTTCTTCCTCTTCC 59.549 52.174 0.00 0.00 0.00 3.46
1842 2637 3.309848 CCTCCTCCTCTTCTTCTTCCTCT 60.310 52.174 0.00 0.00 0.00 3.69
1935 2742 1.194218 TGATGACGATCCTGGAGCAA 58.806 50.000 13.04 0.00 0.00 3.91
2018 2834 0.543883 TTCCTCAGCAGCTCTGGAGT 60.544 55.000 11.55 0.00 43.06 3.85
2148 2967 0.616111 TCTGGTCAGCCTCTTCCTCC 60.616 60.000 0.00 0.00 35.27 4.30
2380 3199 4.787598 CCACAGCAAGAACAAACTGATAC 58.212 43.478 0.00 0.00 34.25 2.24
2519 3733 3.303791 GGCACGTTCGGGATTTATTGATC 60.304 47.826 0.00 0.00 0.00 2.92
2615 3829 4.457496 CGCTGGGATGACGTGGCT 62.457 66.667 0.00 0.00 0.00 4.75
2652 3866 0.320508 AAAGGCGTTCGGGAGACTTC 60.321 55.000 0.00 0.00 39.59 3.01
2653 3867 0.108019 AAAAGGCGTTCGGGAGACTT 59.892 50.000 0.00 0.00 39.59 3.01
2654 3868 0.320508 GAAAAGGCGTTCGGGAGACT 60.321 55.000 0.00 0.00 39.59 3.24
2655 3869 0.320508 AGAAAAGGCGTTCGGGAGAC 60.321 55.000 0.00 0.00 39.59 3.36
2656 3870 0.395312 AAGAAAAGGCGTTCGGGAGA 59.605 50.000 0.00 0.00 32.50 3.71
2657 3871 1.235724 AAAGAAAAGGCGTTCGGGAG 58.764 50.000 0.00 0.00 32.50 4.30
2658 3872 1.682740 AAAAGAAAAGGCGTTCGGGA 58.317 45.000 0.00 0.00 32.50 5.14
2659 3873 2.223618 TGAAAAAGAAAAGGCGTTCGGG 60.224 45.455 0.00 0.00 32.50 5.14
2660 3874 2.787129 GTGAAAAAGAAAAGGCGTTCGG 59.213 45.455 0.00 0.00 32.50 4.30
2661 3875 3.691498 AGTGAAAAAGAAAAGGCGTTCG 58.309 40.909 0.00 0.00 32.50 3.95
2662 3876 3.724257 CGAGTGAAAAAGAAAAGGCGTTC 59.276 43.478 0.00 0.00 0.00 3.95
2663 3877 3.691498 CGAGTGAAAAAGAAAAGGCGTT 58.309 40.909 0.00 0.00 0.00 4.84
2664 3878 2.540973 GCGAGTGAAAAAGAAAAGGCGT 60.541 45.455 0.00 0.00 0.00 5.68
2665 3879 2.044135 GCGAGTGAAAAAGAAAAGGCG 58.956 47.619 0.00 0.00 0.00 5.52
2666 3880 2.044135 CGCGAGTGAAAAAGAAAAGGC 58.956 47.619 0.00 0.00 0.00 4.35
2667 3881 2.604614 CCCGCGAGTGAAAAAGAAAAGG 60.605 50.000 8.23 0.00 0.00 3.11
2668 3882 2.289547 TCCCGCGAGTGAAAAAGAAAAG 59.710 45.455 8.23 0.00 0.00 2.27
2669 3883 2.032426 GTCCCGCGAGTGAAAAAGAAAA 59.968 45.455 8.23 0.00 0.00 2.29
2670 3884 1.600485 GTCCCGCGAGTGAAAAAGAAA 59.400 47.619 8.23 0.00 0.00 2.52
2671 3885 1.223187 GTCCCGCGAGTGAAAAAGAA 58.777 50.000 8.23 0.00 0.00 2.52
2672 3886 0.942410 CGTCCCGCGAGTGAAAAAGA 60.942 55.000 8.23 0.00 44.77 2.52
2673 3887 0.942410 TCGTCCCGCGAGTGAAAAAG 60.942 55.000 8.23 0.00 45.68 2.27
2674 3888 1.067749 TCGTCCCGCGAGTGAAAAA 59.932 52.632 8.23 0.00 45.68 1.94
2675 3889 2.729455 TCGTCCCGCGAGTGAAAA 59.271 55.556 8.23 0.00 45.68 2.29
2685 3899 4.493747 GACTTCGCCCTCGTCCCG 62.494 72.222 0.00 0.00 36.96 5.14
2686 3900 3.066233 GAGACTTCGCCCTCGTCCC 62.066 68.421 0.00 0.00 36.96 4.46
2687 3901 2.490685 GAGACTTCGCCCTCGTCC 59.509 66.667 0.00 0.00 36.96 4.79
2688 3902 2.490685 GGAGACTTCGCCCTCGTC 59.509 66.667 0.00 0.00 36.96 4.20
2694 3908 2.506438 CGTTCGGGAGACTTCGCC 60.506 66.667 0.00 0.00 39.59 5.54
2695 3909 3.179939 GCGTTCGGGAGACTTCGC 61.180 66.667 0.00 0.00 42.65 4.70
2696 3910 2.488087 AAGGCGTTCGGGAGACTTCG 62.488 60.000 0.00 0.00 39.59 3.79
2893 4155 3.154473 TCCATCGCTTCTCCCCCG 61.154 66.667 0.00 0.00 0.00 5.73
2937 4201 1.754226 GAGGGAGATTCACTCTTCGCT 59.246 52.381 1.14 0.00 43.46 4.93
3051 4315 2.355115 GGGAACGATGGGGCAAGT 59.645 61.111 0.00 0.00 0.00 3.16
3097 4588 0.681243 GCCTCCTCCCGCAAAAATCT 60.681 55.000 0.00 0.00 0.00 2.40
3160 4653 0.688087 ATCCTCGGGGAGTTGGAGAC 60.688 60.000 11.27 0.00 45.86 3.36
3232 4733 4.406173 CACGCTCGAGTCAGCCGT 62.406 66.667 15.13 11.64 35.84 5.68


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

AutoCloner maintained by Alex Coulton.