Multiple sequence alignment - TraesCS5D01G086000

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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 TraesCS5D01G086000 chr5D 100.000 3635 0 0 1 3635 91408008 91404374 0.000000e+00 6713.0
1 TraesCS5D01G086000 chr5D 84.115 768 102 10 2830 3591 305849001 305849754 0.000000e+00 725.0
2 TraesCS5D01G086000 chr5B 92.186 2726 99 40 139 2829 96766610 96763964 0.000000e+00 3749.0
3 TraesCS5D01G086000 chr5B 82.770 296 40 6 2835 3125 350511852 350512141 1.680000e-63 254.0
4 TraesCS5D01G086000 chr5A 87.193 2116 96 49 32 2080 85166457 85164450 0.000000e+00 2244.0
5 TraesCS5D01G086000 chr5A 96.645 626 18 3 2165 2789 85164429 85163806 0.000000e+00 1037.0
6 TraesCS5D01G086000 chr5A 82.451 359 48 4 2165 2508 693673783 693673425 2.120000e-77 300.0
7 TraesCS5D01G086000 chr5A 91.146 192 12 2 1707 1893 693674463 693674272 4.660000e-64 255.0
8 TraesCS5D01G086000 chr5A 98.246 57 1 0 1232 1288 694758660 694758716 2.310000e-17 100.0
9 TraesCS5D01G086000 chr6A 86.522 460 55 5 3105 3562 97699759 97699305 1.950000e-137 499.0
10 TraesCS5D01G086000 chr6A 88.116 345 35 4 2168 2509 399722655 399722996 4.370000e-109 405.0
11 TraesCS5D01G086000 chr6A 84.946 279 36 3 2834 3107 97722232 97721955 9.940000e-71 278.0
12 TraesCS5D01G086000 chr6A 89.381 226 16 6 1644 1868 399722439 399722657 9.940000e-71 278.0
13 TraesCS5D01G086000 chr4B 83.789 549 62 12 2879 3421 7035950 7035423 2.520000e-136 496.0
14 TraesCS5D01G086000 chr4D 77.696 816 135 31 2835 3635 93344914 93344131 4.280000e-124 455.0
15 TraesCS5D01G086000 chr4D 91.667 192 11 2 1707 1893 508432376 508432185 1.000000e-65 261.0
16 TraesCS5D01G086000 chr6B 76.952 794 172 9 2827 3613 701506820 701507609 3.330000e-120 442.0
17 TraesCS5D01G086000 chr6B 76.716 816 163 17 2830 3635 171730977 171731775 2.590000e-116 429.0
18 TraesCS5D01G086000 chr6B 87.861 346 34 6 2168 2509 438386250 438385909 2.030000e-107 399.0
19 TraesCS5D01G086000 chr6B 89.381 226 16 5 1644 1868 438386466 438386248 9.940000e-71 278.0
20 TraesCS5D01G086000 chr2D 76.813 772 152 18 2874 3635 480166817 480166063 3.380000e-110 409.0
21 TraesCS5D01G086000 chr6D 87.246 345 38 4 2168 2509 276456218 276455877 4.400000e-104 388.0
22 TraesCS5D01G086000 chr6D 88.938 226 17 6 1644 1868 276456434 276456216 4.630000e-69 272.0
23 TraesCS5D01G086000 chr6D 77.488 422 80 13 3223 3635 386463694 386464109 4.690000e-59 239.0
24 TraesCS5D01G086000 chr3A 84.884 344 40 6 2168 2511 711218505 711218836 1.620000e-88 337.0
25 TraesCS5D01G086000 chr3A 82.609 345 46 8 2168 2511 711203626 711203957 3.550000e-75 292.0
26 TraesCS5D01G086000 chr3A 88.983 118 11 2 1395 1511 712572214 712572098 1.050000e-30 145.0
27 TraesCS5D01G086000 chr3D 84.302 344 42 6 2168 2511 575726541 575726872 3.500000e-85 326.0
28 TraesCS5D01G086000 chr3D 95.679 162 7 0 1707 1868 577264146 577263985 1.000000e-65 261.0
29 TraesCS5D01G086000 chr3D 88.136 118 12 2 1395 1511 577255581 577255465 4.890000e-29 139.0
30 TraesCS5D01G086000 chr3B 84.012 344 43 6 2168 2511 766631929 766632260 1.630000e-83 320.0
31 TraesCS5D01G086000 chr3B 87.719 228 20 4 1648 1868 766631705 766631931 3.600000e-65 259.0
32 TraesCS5D01G086000 chr7D 73.750 720 149 26 2936 3635 276541 277240 2.800000e-61 246.0
33 TraesCS5D01G086000 chr2B 74.149 646 136 20 2943 3572 209245839 209245209 4.690000e-59 239.0
34 TraesCS5D01G086000 chr1D 84.058 138 16 6 1383 1517 300719063 300718929 1.060000e-25 128.0
35 TraesCS5D01G086000 chr1D 81.356 118 21 1 1391 1507 300858727 300858844 1.070000e-15 95.3
36 TraesCS5D01G086000 chr1A 82.482 137 18 6 1384 1517 375113367 375113234 8.250000e-22 115.0
37 TraesCS5D01G086000 chr1B 82.203 118 20 1 1391 1507 406036126 406036243 2.310000e-17 100.0


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 TraesCS5D01G086000 chr5D 91404374 91408008 3634 True 6713.0 6713 100.0000 1 3635 1 chr5D.!!$R1 3634
1 TraesCS5D01G086000 chr5D 305849001 305849754 753 False 725.0 725 84.1150 2830 3591 1 chr5D.!!$F1 761
2 TraesCS5D01G086000 chr5B 96763964 96766610 2646 True 3749.0 3749 92.1860 139 2829 1 chr5B.!!$R1 2690
3 TraesCS5D01G086000 chr5A 85163806 85166457 2651 True 1640.5 2244 91.9190 32 2789 2 chr5A.!!$R1 2757
4 TraesCS5D01G086000 chr5A 693673425 693674463 1038 True 277.5 300 86.7985 1707 2508 2 chr5A.!!$R2 801
5 TraesCS5D01G086000 chr6A 399722439 399722996 557 False 341.5 405 88.7485 1644 2509 2 chr6A.!!$F1 865
6 TraesCS5D01G086000 chr4B 7035423 7035950 527 True 496.0 496 83.7890 2879 3421 1 chr4B.!!$R1 542
7 TraesCS5D01G086000 chr4D 93344131 93344914 783 True 455.0 455 77.6960 2835 3635 1 chr4D.!!$R1 800
8 TraesCS5D01G086000 chr6B 701506820 701507609 789 False 442.0 442 76.9520 2827 3613 1 chr6B.!!$F2 786
9 TraesCS5D01G086000 chr6B 171730977 171731775 798 False 429.0 429 76.7160 2830 3635 1 chr6B.!!$F1 805
10 TraesCS5D01G086000 chr6B 438385909 438386466 557 True 338.5 399 88.6210 1644 2509 2 chr6B.!!$R1 865
11 TraesCS5D01G086000 chr2D 480166063 480166817 754 True 409.0 409 76.8130 2874 3635 1 chr2D.!!$R1 761
12 TraesCS5D01G086000 chr6D 276455877 276456434 557 True 330.0 388 88.0920 1644 2509 2 chr6D.!!$R1 865
13 TraesCS5D01G086000 chr3B 766631705 766632260 555 False 289.5 320 85.8655 1648 2511 2 chr3B.!!$F1 863
14 TraesCS5D01G086000 chr7D 276541 277240 699 False 246.0 246 73.7500 2936 3635 1 chr7D.!!$F1 699
15 TraesCS5D01G086000 chr2B 209245209 209245839 630 True 239.0 239 74.1490 2943 3572 1 chr2B.!!$R1 629

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
27 28 0.034059 AAGAGCATATCGGGCTTCGG 59.966 55.0 0.00 0.00 42.78 4.30 F
29 30 0.667792 GAGCATATCGGGCTTCGGAC 60.668 60.0 0.00 0.00 42.78 4.79 F
1420 1525 0.041312 CTTGCGGGTTCAAGAACGTG 60.041 55.0 6.84 3.37 44.61 4.49 F
1625 1735 0.679002 CCCCAGACAGCCTGTGATTG 60.679 60.0 0.00 0.00 41.33 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1463 0.179009 CCTGCATCCCATCCGTGATT 60.179 55.0 0.00 0.0 0.0 2.57 R
1762 1879 0.607217 TGAGGTCGAAGTGGTAGCGA 60.607 55.0 0.00 0.0 0.0 4.93 R
2618 2981 0.102300 TGATCACACGGCCAGTATCG 59.898 55.0 2.24 0.0 0.0 2.92 R
3255 3648 0.112995 AGGGATGTTCTGCTTTGCCA 59.887 50.0 0.00 0.0 0.0 4.92 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
21 22 4.935885 GCTATTTGAAGAGCATATCGGG 57.064 45.455 5.54 0.00 42.55 5.14
22 23 3.126000 GCTATTTGAAGAGCATATCGGGC 59.874 47.826 5.54 0.00 42.55 6.13
23 24 3.498774 ATTTGAAGAGCATATCGGGCT 57.501 42.857 0.00 0.00 46.07 5.19
24 25 3.281727 TTTGAAGAGCATATCGGGCTT 57.718 42.857 0.00 0.00 42.78 4.35
25 26 2.533266 TGAAGAGCATATCGGGCTTC 57.467 50.000 0.00 0.00 42.78 3.86
26 27 1.269778 TGAAGAGCATATCGGGCTTCG 60.270 52.381 0.00 0.00 42.78 3.79
27 28 0.034059 AAGAGCATATCGGGCTTCGG 59.966 55.000 0.00 0.00 42.78 4.30
28 29 0.827925 AGAGCATATCGGGCTTCGGA 60.828 55.000 0.00 0.00 42.78 4.55
29 30 0.667792 GAGCATATCGGGCTTCGGAC 60.668 60.000 0.00 0.00 42.78 4.79
30 31 2.022129 GCATATCGGGCTTCGGACG 61.022 63.158 0.75 0.00 39.77 4.79
38 39 3.723348 GCTTCGGACGTGTTGGGC 61.723 66.667 0.00 0.00 0.00 5.36
45 46 0.893727 GGACGTGTTGGGCCAAGAAT 60.894 55.000 21.62 10.36 0.00 2.40
59 60 6.597280 TGGGCCAAGAATAAATATTTGTTTGC 59.403 34.615 2.13 10.92 0.00 3.68
64 65 9.545611 CCAAGAATAAATATTTGTTTGCTTTGC 57.454 29.630 11.05 0.00 0.00 3.68
92 93 1.577736 AGCCCACTAGTGCTGATTCT 58.422 50.000 17.86 4.47 36.23 2.40
96 97 3.869912 GCCCACTAGTGCTGATTCTCAAA 60.870 47.826 17.86 0.00 0.00 2.69
119 120 2.466846 AGAAAGAGAGAGGAGAAGCCC 58.533 52.381 0.00 0.00 37.37 5.19
232 236 0.731417 CCTCTGCCATTTCTTCAGCG 59.269 55.000 0.00 0.00 0.00 5.18
364 374 1.215647 CTACAGCTCCGTGACCACC 59.784 63.158 0.00 0.00 0.00 4.61
371 381 3.556306 CCGTGACCACCCACCAGT 61.556 66.667 0.00 0.00 33.67 4.00
372 382 2.030562 CGTGACCACCCACCAGTC 59.969 66.667 0.00 0.00 33.67 3.51
373 383 2.507854 CGTGACCACCCACCAGTCT 61.508 63.158 0.00 0.00 33.67 3.24
374 384 1.071471 GTGACCACCCACCAGTCTG 59.929 63.158 0.00 0.00 0.00 3.51
375 385 2.146724 TGACCACCCACCAGTCTGG 61.147 63.158 17.88 17.88 45.02 3.86
401 411 4.779966 TCTCGCTCTCGCCGGAGT 62.780 66.667 5.05 0.00 41.26 3.85
402 412 4.244802 CTCGCTCTCGCCGGAGTC 62.245 72.222 5.05 0.00 41.26 3.36
403 413 4.779966 TCGCTCTCGCCGGAGTCT 62.780 66.667 5.05 0.00 41.26 3.24
421 431 4.203226 AGTCTCACATCGATCTGCTTCTA 58.797 43.478 0.00 0.00 0.00 2.10
708 747 2.359975 TGCTCTCTGTCTCCGCGA 60.360 61.111 8.23 0.00 0.00 5.87
709 748 2.101380 GCTCTCTGTCTCCGCGAC 59.899 66.667 8.23 0.00 43.14 5.19
710 749 2.795297 CTCTCTGTCTCCGCGACC 59.205 66.667 8.23 0.00 42.13 4.79
711 750 3.102107 CTCTCTGTCTCCGCGACCG 62.102 68.421 8.23 0.00 42.13 4.79
712 751 4.838486 CTCTGTCTCCGCGACCGC 62.838 72.222 8.23 4.06 42.13 5.68
726 765 2.359478 CCGCGTAGGCCAAGGTTT 60.359 61.111 5.01 0.00 35.02 3.27
831 870 2.046892 CCCTGTCACAGCTTCCGG 60.047 66.667 0.00 0.00 0.00 5.14
1044 1117 3.357079 GCCCGTGTGGTTGCTCTG 61.357 66.667 0.00 0.00 36.04 3.35
1104 1177 2.297315 CTGCGGTTATCTGCCTGATCTA 59.703 50.000 2.16 0.00 44.62 1.98
1131 1204 3.569210 CCACCTCCACCACCTGCA 61.569 66.667 0.00 0.00 0.00 4.41
1143 1216 2.118076 CCTGCACCCACCACCAAT 59.882 61.111 0.00 0.00 0.00 3.16
1144 1217 2.277591 CCTGCACCCACCACCAATG 61.278 63.158 0.00 0.00 0.00 2.82
1145 1218 1.531365 CTGCACCCACCACCAATGT 60.531 57.895 0.00 0.00 0.00 2.71
1146 1219 1.526575 CTGCACCCACCACCAATGTC 61.527 60.000 0.00 0.00 0.00 3.06
1147 1220 2.275380 GCACCCACCACCAATGTCC 61.275 63.158 0.00 0.00 0.00 4.02
1148 1221 1.606313 CACCCACCACCAATGTCCC 60.606 63.158 0.00 0.00 0.00 4.46
1149 1222 2.037208 CCCACCACCAATGTCCCC 59.963 66.667 0.00 0.00 0.00 4.81
1150 1223 2.850290 CCACCACCAATGTCCCCA 59.150 61.111 0.00 0.00 0.00 4.96
1151 1224 1.606313 CCACCACCAATGTCCCCAC 60.606 63.158 0.00 0.00 0.00 4.61
1152 1225 1.606313 CACCACCAATGTCCCCACC 60.606 63.158 0.00 0.00 0.00 4.61
1153 1226 2.088096 ACCACCAATGTCCCCACCA 61.088 57.895 0.00 0.00 0.00 4.17
1154 1227 1.606313 CCACCAATGTCCCCACCAC 60.606 63.158 0.00 0.00 0.00 4.16
1155 1228 1.606313 CACCAATGTCCCCACCACC 60.606 63.158 0.00 0.00 0.00 4.61
1156 1229 2.088096 ACCAATGTCCCCACCACCA 61.088 57.895 0.00 0.00 0.00 4.17
1157 1230 1.154921 CCAATGTCCCCACCACCAA 59.845 57.895 0.00 0.00 0.00 3.67
1303 1390 3.633235 GGTACGACTGCTATCATGTCTG 58.367 50.000 0.00 0.00 0.00 3.51
1306 1393 2.493675 ACGACTGCTATCATGTCTGTGT 59.506 45.455 0.00 0.00 0.00 3.72
1359 1446 2.100584 TGCTGATTGCGGTTCTTGTTTT 59.899 40.909 0.00 0.00 46.63 2.43
1360 1447 2.726241 GCTGATTGCGGTTCTTGTTTTC 59.274 45.455 0.00 0.00 0.00 2.29
1361 1448 3.795150 GCTGATTGCGGTTCTTGTTTTCA 60.795 43.478 0.00 0.00 0.00 2.69
1362 1449 4.358851 CTGATTGCGGTTCTTGTTTTCAA 58.641 39.130 0.00 0.00 38.21 2.69
1363 1450 4.942852 TGATTGCGGTTCTTGTTTTCAAT 58.057 34.783 0.00 0.00 39.22 2.57
1364 1451 6.078202 TGATTGCGGTTCTTGTTTTCAATA 57.922 33.333 0.00 0.00 39.22 1.90
1365 1452 6.507900 TGATTGCGGTTCTTGTTTTCAATAA 58.492 32.000 0.00 0.00 39.22 1.40
1366 1453 6.980978 TGATTGCGGTTCTTGTTTTCAATAAA 59.019 30.769 0.00 0.00 39.22 1.40
1367 1454 7.655328 TGATTGCGGTTCTTGTTTTCAATAAAT 59.345 29.630 0.00 0.00 39.22 1.40
1368 1455 9.134734 GATTGCGGTTCTTGTTTTCAATAAATA 57.865 29.630 0.00 0.00 39.22 1.40
1369 1456 7.861176 TGCGGTTCTTGTTTTCAATAAATAC 57.139 32.000 0.00 0.00 39.22 1.89
1370 1457 6.579292 TGCGGTTCTTGTTTTCAATAAATACG 59.421 34.615 0.00 0.00 39.22 3.06
1371 1458 6.579666 GCGGTTCTTGTTTTCAATAAATACGT 59.420 34.615 0.00 0.00 39.22 3.57
1372 1459 7.745594 GCGGTTCTTGTTTTCAATAAATACGTA 59.254 33.333 0.00 0.00 39.22 3.57
1373 1460 9.043678 CGGTTCTTGTTTTCAATAAATACGTAC 57.956 33.333 0.00 0.00 39.22 3.67
1374 1461 9.333497 GGTTCTTGTTTTCAATAAATACGTACC 57.667 33.333 0.00 0.00 39.22 3.34
1375 1462 9.881529 GTTCTTGTTTTCAATAAATACGTACCA 57.118 29.630 0.00 0.00 39.22 3.25
1420 1525 0.041312 CTTGCGGGTTCAAGAACGTG 60.041 55.000 6.84 3.37 44.61 4.49
1441 1546 3.589654 CTGGCCGCCTTTCTCGTCA 62.590 63.158 11.61 0.00 0.00 4.35
1624 1734 0.842030 TCCCCAGACAGCCTGTGATT 60.842 55.000 0.00 0.00 41.33 2.57
1625 1735 0.679002 CCCCAGACAGCCTGTGATTG 60.679 60.000 0.00 0.00 41.33 2.67
1627 1737 1.064906 CCCAGACAGCCTGTGATTGAT 60.065 52.381 0.00 0.00 41.33 2.57
1628 1738 2.014857 CCAGACAGCCTGTGATTGATG 58.985 52.381 0.00 0.00 41.33 3.07
1629 1739 2.617276 CCAGACAGCCTGTGATTGATGT 60.617 50.000 0.00 0.00 41.33 3.06
1635 1746 6.435277 AGACAGCCTGTGATTGATGTAATTTT 59.565 34.615 0.00 0.00 0.00 1.82
1642 1753 9.520204 CCTGTGATTGATGTAATTTTATTCCAC 57.480 33.333 0.00 0.00 0.00 4.02
1762 1879 3.288964 CATGAACTACTACCCGGTCTCT 58.711 50.000 0.00 0.00 0.00 3.10
2057 2307 3.688694 TGCACATCCTAACTTTACGGT 57.311 42.857 0.00 0.00 0.00 4.83
2084 2339 5.495926 AAGATCCATAATCTAGTGGCAGG 57.504 43.478 0.00 0.00 44.26 4.85
2085 2340 3.262915 AGATCCATAATCTAGTGGCAGGC 59.737 47.826 0.00 0.00 43.17 4.85
2088 2343 4.167319 TCCATAATCTAGTGGCAGGCATA 58.833 43.478 0.00 0.00 35.43 3.14
2090 2345 4.019860 CCATAATCTAGTGGCAGGCATACT 60.020 45.833 0.00 3.17 0.00 2.12
2104 2359 4.209703 CAGGCATACTGCTTTTTGTTTGTG 59.790 41.667 0.00 0.00 44.28 3.33
2127 2382 0.813610 CTTGGTTGCTCGTGTGGTGA 60.814 55.000 0.00 0.00 0.00 4.02
2129 2384 1.522806 GGTTGCTCGTGTGGTGACA 60.523 57.895 0.00 0.00 38.70 3.58
2540 2903 0.740868 ATGTCGCTTGTCACATCCGG 60.741 55.000 0.00 0.00 0.00 5.14
2618 2981 0.584876 GTGTGGCCTTGTGTACGTTC 59.415 55.000 3.32 0.00 0.00 3.95
2644 3007 1.709147 GGCCGTGTGATCATCTGCAC 61.709 60.000 0.00 1.02 35.63 4.57
2690 3053 2.519013 AGATTGAACCTGGAGTTTGGC 58.481 47.619 0.00 0.00 39.40 4.52
2782 3145 3.811722 TGCAACGATCACTTGTGATTC 57.188 42.857 16.15 9.42 0.00 2.52
2820 3190 2.811431 TGCCTCGTATTTTTGTCACCTG 59.189 45.455 0.00 0.00 0.00 4.00
2830 3200 8.026607 CGTATTTTTGTCACCTGGTATGATTTT 58.973 33.333 0.00 0.00 0.00 1.82
2861 3231 7.518161 TGTTTGAGAAAGTATGCTTGTATTCG 58.482 34.615 0.00 0.00 34.71 3.34
2903 3276 0.931702 TTCAACCGTACAAGCACACG 59.068 50.000 0.00 0.00 37.89 4.49
2963 3337 7.390718 AGCACCCTAACACAACTAGAAAAATAG 59.609 37.037 0.00 0.00 0.00 1.73
2987 3361 2.094286 AGATCTTTGGAGCTCTGTGTCG 60.094 50.000 14.64 0.00 32.09 4.35
3032 3407 7.086685 AGACCCCTACAACAAAAGAATCTAA 57.913 36.000 0.00 0.00 0.00 2.10
3036 3411 7.081976 CCCCTACAACAAAAGAATCTAAAACG 58.918 38.462 0.00 0.00 0.00 3.60
3071 3456 6.885918 ACATCATCTTCAACCACAACATCATA 59.114 34.615 0.00 0.00 0.00 2.15
3088 3473 0.530650 ATAATCGCCACACTGCTCCG 60.531 55.000 0.00 0.00 0.00 4.63
3103 3488 1.528129 CTCCGCCTTTTCTTTGCTCT 58.472 50.000 0.00 0.00 0.00 4.09
3144 3530 3.476552 CACACCTGTGTATCCAACAAGT 58.523 45.455 2.05 0.00 42.83 3.16
3165 3552 1.375908 GCACCAGCCTTCGTCATCA 60.376 57.895 0.00 0.00 33.58 3.07
3176 3563 2.542020 TCGTCATCAGTGGCTTTGAA 57.458 45.000 0.00 0.00 0.00 2.69
3190 3577 3.304659 GGCTTTGAATACCGCCATATGTG 60.305 47.826 1.24 0.00 42.06 3.21
3191 3578 3.853307 GCTTTGAATACCGCCATATGTGC 60.853 47.826 1.24 4.17 0.00 4.57
3192 3579 2.928801 TGAATACCGCCATATGTGCT 57.071 45.000 12.45 0.78 0.00 4.40
3201 3588 0.184451 CCATATGTGCTGCCCCTTCT 59.816 55.000 1.24 0.00 0.00 2.85
3352 3749 3.706086 GAGGAAGAAGAAGCTCCATCTCT 59.294 47.826 0.00 0.00 0.00 3.10
3418 3815 1.834263 GACCTTGAGACACCATAGCCT 59.166 52.381 0.00 0.00 0.00 4.58
3432 3829 0.175760 TAGCCTGCGACCTCAATGAC 59.824 55.000 0.00 0.00 0.00 3.06
3468 3865 3.477224 CTCGCTGGCTCCTAGACGC 62.477 68.421 0.00 0.00 0.00 5.19
3472 3869 1.754621 CTGGCTCCTAGACGCAGGA 60.755 63.158 0.00 1.50 42.62 3.86
3480 3877 0.532573 CTAGACGCAGGAAAGAGCCA 59.467 55.000 0.00 0.00 0.00 4.75
3485 3882 3.121030 CAGGAAAGAGCCACGCCG 61.121 66.667 0.00 0.00 0.00 6.46
3523 3920 4.635765 CCCGAGAAAACTTATTCAGATGCA 59.364 41.667 0.00 0.00 0.00 3.96
3565 3962 1.204941 CAACGTCTCCCTCAACCCTAG 59.795 57.143 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.126000 GCCCGATATGCTCTTCAAATAGC 59.874 47.826 0.00 0.00 39.25 2.97
1 2 4.573900 AGCCCGATATGCTCTTCAAATAG 58.426 43.478 0.00 0.00 32.41 1.73
3 4 3.498774 AGCCCGATATGCTCTTCAAAT 57.501 42.857 0.00 0.00 32.41 2.32
4 5 3.206150 GAAGCCCGATATGCTCTTCAAA 58.794 45.455 0.00 0.00 38.34 2.69
7 8 1.423395 CGAAGCCCGATATGCTCTTC 58.577 55.000 0.00 0.00 41.76 2.87
8 9 0.034059 CCGAAGCCCGATATGCTCTT 59.966 55.000 0.00 0.00 41.76 2.85
9 10 0.827925 TCCGAAGCCCGATATGCTCT 60.828 55.000 0.00 0.00 41.76 4.09
10 11 0.667792 GTCCGAAGCCCGATATGCTC 60.668 60.000 0.00 0.00 41.76 4.26
11 12 1.367840 GTCCGAAGCCCGATATGCT 59.632 57.895 0.00 0.00 41.76 3.79
12 13 2.022129 CGTCCGAAGCCCGATATGC 61.022 63.158 0.00 0.00 41.76 3.14
13 14 0.939577 CACGTCCGAAGCCCGATATG 60.940 60.000 0.00 0.00 41.76 1.78
14 15 1.362717 CACGTCCGAAGCCCGATAT 59.637 57.895 0.00 0.00 41.76 1.63
15 16 1.597797 AACACGTCCGAAGCCCGATA 61.598 55.000 0.00 0.00 41.76 2.92
16 17 2.939261 AACACGTCCGAAGCCCGAT 61.939 57.895 0.00 0.00 41.76 4.18
17 18 3.608662 AACACGTCCGAAGCCCGA 61.609 61.111 0.00 0.00 41.76 5.14
18 19 3.411351 CAACACGTCCGAAGCCCG 61.411 66.667 0.00 0.00 38.18 6.13
19 20 3.047877 CCAACACGTCCGAAGCCC 61.048 66.667 0.00 0.00 0.00 5.19
20 21 3.047877 CCCAACACGTCCGAAGCC 61.048 66.667 0.00 0.00 0.00 4.35
21 22 3.723348 GCCCAACACGTCCGAAGC 61.723 66.667 0.00 0.00 0.00 3.86
22 23 3.047877 GGCCCAACACGTCCGAAG 61.048 66.667 0.00 0.00 0.00 3.79
23 24 3.402095 TTGGCCCAACACGTCCGAA 62.402 57.895 0.00 0.00 0.00 4.30
24 25 3.818121 CTTGGCCCAACACGTCCGA 62.818 63.158 0.00 0.00 0.00 4.55
25 26 3.353836 CTTGGCCCAACACGTCCG 61.354 66.667 0.00 0.00 0.00 4.79
26 27 0.893727 ATTCTTGGCCCAACACGTCC 60.894 55.000 0.00 0.00 0.00 4.79
27 28 1.816074 TATTCTTGGCCCAACACGTC 58.184 50.000 0.00 0.00 0.00 4.34
28 29 2.279935 TTATTCTTGGCCCAACACGT 57.720 45.000 0.00 0.00 0.00 4.49
29 30 3.866883 ATTTATTCTTGGCCCAACACG 57.133 42.857 0.00 0.00 0.00 4.49
30 31 7.102993 ACAAATATTTATTCTTGGCCCAACAC 58.897 34.615 0.00 0.00 0.00 3.32
38 39 9.545611 GCAAAGCAAACAAATATTTATTCTTGG 57.454 29.630 0.00 0.00 0.00 3.61
64 65 1.741706 CACTAGTGGGCTTTGATGCAG 59.258 52.381 15.49 0.00 34.04 4.41
65 66 1.825090 CACTAGTGGGCTTTGATGCA 58.175 50.000 15.49 0.00 34.04 3.96
96 97 4.263287 GGGCTTCTCCTCTCTCTTTCTTTT 60.263 45.833 0.00 0.00 34.39 2.27
106 107 1.220477 GCACTGGGCTTCTCCTCTC 59.780 63.158 0.00 0.00 40.25 3.20
116 117 2.594592 ACGTTCCAAGCACTGGGC 60.595 61.111 0.00 0.00 46.44 5.36
119 120 0.249868 TGAGGACGTTCCAAGCACTG 60.250 55.000 6.78 0.00 39.61 3.66
291 301 2.267961 GGTGGCTGGGTACGAAGG 59.732 66.667 0.00 0.00 0.00 3.46
371 381 0.328592 AGCGAGACCAGAGTACCAGA 59.671 55.000 0.00 0.00 0.00 3.86
372 382 0.736053 GAGCGAGACCAGAGTACCAG 59.264 60.000 0.00 0.00 0.00 4.00
373 383 0.328592 AGAGCGAGACCAGAGTACCA 59.671 55.000 0.00 0.00 0.00 3.25
374 384 1.018910 GAGAGCGAGACCAGAGTACC 58.981 60.000 0.00 0.00 0.00 3.34
375 385 0.653636 CGAGAGCGAGACCAGAGTAC 59.346 60.000 0.00 0.00 40.82 2.73
376 386 3.067074 CGAGAGCGAGACCAGAGTA 57.933 57.895 0.00 0.00 40.82 2.59
377 387 3.897936 CGAGAGCGAGACCAGAGT 58.102 61.111 0.00 0.00 40.82 3.24
401 411 4.558296 GCATAGAAGCAGATCGATGTGAGA 60.558 45.833 25.37 5.85 35.59 3.27
402 412 3.674281 GCATAGAAGCAGATCGATGTGAG 59.326 47.826 25.37 0.96 35.59 3.51
403 413 3.646946 GCATAGAAGCAGATCGATGTGA 58.353 45.455 25.37 5.07 35.59 3.58
432 442 1.080501 GTCTGAGCAGTGCAGCGTA 60.081 57.895 19.20 0.00 40.15 4.42
433 443 2.356793 GTCTGAGCAGTGCAGCGT 60.357 61.111 19.20 0.00 40.15 5.07
708 747 2.685804 AAAACCTTGGCCTACGCGGT 62.686 55.000 12.47 0.00 35.02 5.68
709 748 1.969589 AAAACCTTGGCCTACGCGG 60.970 57.895 12.47 0.00 35.02 6.46
710 749 1.209127 CAAAACCTTGGCCTACGCG 59.791 57.895 3.53 3.53 35.02 6.01
711 750 1.584495 CCAAAACCTTGGCCTACGC 59.416 57.895 3.32 0.00 45.67 4.42
726 765 2.203056 CGCATCAGATCCGGCCAA 60.203 61.111 2.24 0.00 0.00 4.52
779 818 2.255406 AGGATAGGAGCTATGCCACTG 58.745 52.381 0.00 0.00 35.78 3.66
863 902 2.993038 GATTCCTCCCCTCCCCTCCC 62.993 70.000 0.00 0.00 0.00 4.30
864 903 1.462432 GATTCCTCCCCTCCCCTCC 60.462 68.421 0.00 0.00 0.00 4.30
865 904 1.057275 GTGATTCCTCCCCTCCCCTC 61.057 65.000 0.00 0.00 0.00 4.30
866 905 1.004891 GTGATTCCTCCCCTCCCCT 59.995 63.158 0.00 0.00 0.00 4.79
867 906 2.444256 CGTGATTCCTCCCCTCCCC 61.444 68.421 0.00 0.00 0.00 4.81
1044 1117 2.035442 GGCAGCGACCAGGAAGAAC 61.035 63.158 0.00 0.00 0.00 3.01
1104 1177 1.633945 GGTGGAGGTGGGTAACAGAAT 59.366 52.381 0.00 0.00 39.74 2.40
1131 1204 2.851045 GGGACATTGGTGGTGGGT 59.149 61.111 0.00 0.00 0.00 4.51
1143 1216 1.458486 GACATTGGTGGTGGGGACA 59.542 57.895 0.00 0.00 38.70 4.02
1144 1217 1.304134 GGACATTGGTGGTGGGGAC 60.304 63.158 0.00 0.00 0.00 4.46
1145 1218 2.543797 GGGACATTGGTGGTGGGGA 61.544 63.158 0.00 0.00 0.00 4.81
1146 1219 2.037208 GGGACATTGGTGGTGGGG 59.963 66.667 0.00 0.00 0.00 4.96
1147 1220 2.037208 GGGGACATTGGTGGTGGG 59.963 66.667 0.00 0.00 0.00 4.61
1148 1221 2.361104 CGGGGACATTGGTGGTGG 60.361 66.667 0.00 0.00 0.00 4.61
1149 1222 3.061848 GCGGGGACATTGGTGGTG 61.062 66.667 0.00 0.00 0.00 4.17
1150 1223 4.360405 GGCGGGGACATTGGTGGT 62.360 66.667 0.00 0.00 0.00 4.16
1151 1224 4.358841 TGGCGGGGACATTGGTGG 62.359 66.667 0.00 0.00 0.00 4.61
1152 1225 3.061848 GTGGCGGGGACATTGGTG 61.062 66.667 0.00 0.00 0.00 4.17
1153 1226 4.360405 GGTGGCGGGGACATTGGT 62.360 66.667 0.00 0.00 0.00 3.67
1154 1227 3.877344 TTGGTGGCGGGGACATTGG 62.877 63.158 0.00 0.00 0.00 3.16
1155 1228 2.282816 TTGGTGGCGGGGACATTG 60.283 61.111 0.00 0.00 0.00 2.82
1156 1229 2.282887 GTTGGTGGCGGGGACATT 60.283 61.111 0.00 0.00 0.00 2.71
1157 1230 4.715523 CGTTGGTGGCGGGGACAT 62.716 66.667 0.00 0.00 0.00 3.06
1303 1390 3.934579 GCAATTGGAATTGGAATCCACAC 59.065 43.478 0.00 0.00 46.37 3.82
1359 1446 7.040494 TCCGTGATTTGGTACGTATTTATTGA 58.960 34.615 0.00 0.00 38.56 2.57
1360 1447 7.236674 TCCGTGATTTGGTACGTATTTATTG 57.763 36.000 0.00 0.00 38.56 1.90
1361 1448 7.041644 CCATCCGTGATTTGGTACGTATTTATT 60.042 37.037 0.00 0.00 38.56 1.40
1362 1449 6.425721 CCATCCGTGATTTGGTACGTATTTAT 59.574 38.462 0.00 0.00 38.56 1.40
1363 1450 5.754406 CCATCCGTGATTTGGTACGTATTTA 59.246 40.000 0.00 0.00 38.56 1.40
1364 1451 4.573201 CCATCCGTGATTTGGTACGTATTT 59.427 41.667 0.00 0.00 38.56 1.40
1365 1452 4.124238 CCATCCGTGATTTGGTACGTATT 58.876 43.478 0.00 0.00 38.56 1.89
1366 1453 3.493699 CCCATCCGTGATTTGGTACGTAT 60.494 47.826 0.00 0.00 38.56 3.06
1367 1454 2.159071 CCCATCCGTGATTTGGTACGTA 60.159 50.000 0.00 0.00 38.56 3.57
1368 1455 1.406341 CCCATCCGTGATTTGGTACGT 60.406 52.381 0.00 0.00 38.56 3.57
1369 1456 1.134640 TCCCATCCGTGATTTGGTACG 60.135 52.381 0.00 0.00 39.83 3.67
1370 1457 2.702592 TCCCATCCGTGATTTGGTAC 57.297 50.000 0.00 0.00 0.00 3.34
1371 1458 2.748132 GCATCCCATCCGTGATTTGGTA 60.748 50.000 0.00 0.00 0.00 3.25
1372 1459 2.023788 GCATCCCATCCGTGATTTGGT 61.024 52.381 0.00 0.00 0.00 3.67
1373 1460 0.670162 GCATCCCATCCGTGATTTGG 59.330 55.000 0.00 0.00 0.00 3.28
1374 1461 1.335810 CTGCATCCCATCCGTGATTTG 59.664 52.381 0.00 0.00 0.00 2.32
1375 1462 1.683943 CTGCATCCCATCCGTGATTT 58.316 50.000 0.00 0.00 0.00 2.17
1376 1463 0.179009 CCTGCATCCCATCCGTGATT 60.179 55.000 0.00 0.00 0.00 2.57
1377 1464 1.348008 ACCTGCATCCCATCCGTGAT 61.348 55.000 0.00 0.00 0.00 3.06
1420 1525 2.391389 CGAGAAAGGCGGCCAGTTC 61.391 63.158 23.09 22.10 0.00 3.01
1441 1546 2.663520 TTGCCGCACGACGTCATT 60.664 55.556 17.16 0.00 41.42 2.57
1541 1646 6.803154 ACTGTGAAAAGTAAGTATCAAGCC 57.197 37.500 0.00 0.00 0.00 4.35
1624 1734 8.620416 CAAGATCCGTGGAATAAAATTACATCA 58.380 33.333 0.00 0.00 0.00 3.07
1625 1735 8.076178 CCAAGATCCGTGGAATAAAATTACATC 58.924 37.037 7.16 0.00 38.54 3.06
1627 1737 7.113437 TCCAAGATCCGTGGAATAAAATTACA 58.887 34.615 12.32 0.00 42.29 2.41
1628 1738 7.562454 TCCAAGATCCGTGGAATAAAATTAC 57.438 36.000 12.32 0.00 42.29 1.89
1642 1753 1.086696 ACGCAACAATCCAAGATCCG 58.913 50.000 0.00 0.00 0.00 4.18
1762 1879 0.607217 TGAGGTCGAAGTGGTAGCGA 60.607 55.000 0.00 0.00 0.00 4.93
1909 2031 5.554822 TGCCATGTCGGTTAAAGTTAATC 57.445 39.130 0.00 0.00 36.97 1.75
1910 2032 5.067283 GGATGCCATGTCGGTTAAAGTTAAT 59.933 40.000 0.00 0.00 36.97 1.40
2085 2340 7.524294 AGAAACACAAACAAAAAGCAGTATG 57.476 32.000 0.00 0.00 40.87 2.39
2088 2343 5.179182 CCAAGAAACACAAACAAAAAGCAGT 59.821 36.000 0.00 0.00 0.00 4.40
2090 2345 5.059833 ACCAAGAAACACAAACAAAAAGCA 58.940 33.333 0.00 0.00 0.00 3.91
2092 2347 5.850653 GCAACCAAGAAACACAAACAAAAAG 59.149 36.000 0.00 0.00 0.00 2.27
2093 2348 5.529060 AGCAACCAAGAAACACAAACAAAAA 59.471 32.000 0.00 0.00 0.00 1.94
2104 2359 1.268539 CCACACGAGCAACCAAGAAAC 60.269 52.381 0.00 0.00 0.00 2.78
2127 2382 3.308035 TCCCGGTATCTATCAGTGTGT 57.692 47.619 0.00 0.00 0.00 3.72
2129 2384 4.281182 GTCATTCCCGGTATCTATCAGTGT 59.719 45.833 0.00 0.00 0.00 3.55
2130 2385 4.616143 CGTCATTCCCGGTATCTATCAGTG 60.616 50.000 0.00 0.00 0.00 3.66
2133 2388 3.493334 ACGTCATTCCCGGTATCTATCA 58.507 45.455 0.00 0.00 0.00 2.15
2134 2389 4.456911 TGTACGTCATTCCCGGTATCTATC 59.543 45.833 0.00 0.00 0.00 2.08
2143 2399 1.364721 TGCAATGTACGTCATTCCCG 58.635 50.000 9.38 2.80 43.93 5.14
2618 2981 0.102300 TGATCACACGGCCAGTATCG 59.898 55.000 2.24 0.00 0.00 2.92
2690 3053 6.909909 TCACATACTACTACAACACAGACAG 58.090 40.000 0.00 0.00 0.00 3.51
2830 3200 7.816995 ACAAGCATACTTTCTCAAACAAACAAA 59.183 29.630 0.00 0.00 32.29 2.83
2833 3203 9.463443 AATACAAGCATACTTTCTCAAACAAAC 57.537 29.630 0.00 0.00 32.29 2.93
2841 3211 8.480853 GTGATACGAATACAAGCATACTTTCTC 58.519 37.037 0.00 0.00 32.29 2.87
2903 3276 8.464770 TTTTGCTTAATCATGATTGTGTTAGC 57.535 30.769 27.59 23.84 32.50 3.09
2963 3337 3.269178 CACAGAGCTCCAAAGATCTTCC 58.731 50.000 10.93 0.00 45.93 3.46
2987 3361 1.966451 CGCAAGGTTCAGGGGTGAC 60.966 63.158 0.00 0.00 0.00 3.67
3032 3407 2.839486 TGATGTCCTGCTTCTCGTTT 57.161 45.000 0.00 0.00 0.00 3.60
3036 3411 4.134379 TGAAGATGATGTCCTGCTTCTC 57.866 45.455 0.00 0.00 36.73 2.87
3071 3456 2.434884 CGGAGCAGTGTGGCGATT 60.435 61.111 0.00 0.00 39.27 3.34
3088 3473 0.387750 CGCCAGAGCAAAGAAAAGGC 60.388 55.000 0.00 0.00 39.83 4.35
3144 3530 1.830587 ATGACGAAGGCTGGTGCAGA 61.831 55.000 0.00 0.00 41.91 4.26
3176 3563 0.606401 GGCAGCACATATGGCGGTAT 60.606 55.000 7.80 0.00 36.08 2.73
3190 3577 2.677875 CCAACCAGAAGGGGCAGC 60.678 66.667 0.00 0.00 42.91 5.25
3191 3578 0.610232 CTTCCAACCAGAAGGGGCAG 60.610 60.000 0.00 0.00 42.91 4.85
3192 3579 1.065410 TCTTCCAACCAGAAGGGGCA 61.065 55.000 1.74 0.00 42.94 5.36
3201 3588 3.775316 GGATCCTAGTTCTCTTCCAACCA 59.225 47.826 3.84 0.00 0.00 3.67
3255 3648 0.112995 AGGGATGTTCTGCTTTGCCA 59.887 50.000 0.00 0.00 0.00 4.92
3266 3659 1.565759 TGCTAATGCTGGAGGGATGTT 59.434 47.619 0.00 0.00 40.48 2.71
3352 3749 1.617947 GGGTGGTTGGTGGTTTTGCA 61.618 55.000 0.00 0.00 0.00 4.08
3418 3815 0.460109 CGGATGTCATTGAGGTCGCA 60.460 55.000 0.00 0.00 0.00 5.10
3468 3865 3.121030 CGGCGTGGCTCTTTCCTG 61.121 66.667 0.00 0.00 0.00 3.86
3472 3869 4.699522 GGTCCGGCGTGGCTCTTT 62.700 66.667 6.01 0.00 37.80 2.52
3485 3882 2.125793 GGGCTTCGTACACGGTCC 60.126 66.667 1.39 1.28 40.29 4.46
3565 3962 1.235724 GGTTGTGTTCACAGTAGGGC 58.764 55.000 5.78 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.