Multiple sequence alignment - TraesCS1D01G437700

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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 TraesCS1D01G437700 chr1D 100.000 4771 0 0 1 4771 485052754 485057524 0.000000e+00 8811.0
1 TraesCS1D01G437700 chr1D 85.967 905 81 25 3164 4053 485099368 485100241 0.000000e+00 926.0
2 TraesCS1D01G437700 chr1D 83.305 587 55 17 1871 2436 485089021 485089585 7.130000e-138 501.0
3 TraesCS1D01G437700 chr1D 80.430 419 45 11 2631 3043 485089777 485090164 7.810000e-73 285.0
4 TraesCS1D01G437700 chr1D 89.744 117 12 0 3161 3277 485090482 485090598 2.970000e-32 150.0
5 TraesCS1D01G437700 chr1A 90.281 2778 152 48 433 3152 582276160 582278877 0.000000e+00 3526.0
6 TraesCS1D01G437700 chr1A 94.201 914 36 11 3164 4065 582278965 582279873 0.000000e+00 1378.0
7 TraesCS1D01G437700 chr1A 88.394 965 71 23 2197 3150 582292258 582293192 0.000000e+00 1123.0
8 TraesCS1D01G437700 chr1A 92.188 448 31 3 1 445 582275235 582275681 8.710000e-177 630.0
9 TraesCS1D01G437700 chr1A 94.089 406 20 4 3212 3615 582293307 582293710 8.780000e-172 614.0
10 TraesCS1D01G437700 chr1A 82.345 759 82 24 3310 4053 582412065 582412786 3.160000e-171 612.0
11 TraesCS1D01G437700 chr1A 86.486 481 34 14 4315 4771 582280236 582280709 2.560000e-137 499.0
12 TraesCS1D01G437700 chr1A 82.927 533 56 14 2631 3156 582358357 582358861 9.420000e-122 448.0
13 TraesCS1D01G437700 chr1A 92.606 284 14 4 3695 3974 582293713 582293993 7.440000e-108 401.0
14 TraesCS1D01G437700 chr1A 80.068 592 59 31 1864 2436 582357633 582358184 7.490000e-103 385.0
15 TraesCS1D01G437700 chr1A 91.078 269 19 4 4061 4327 582279956 582280221 4.540000e-95 359.0
16 TraesCS1D01G437700 chr1A 92.070 227 16 2 3166 3391 582411558 582411783 7.700000e-83 318.0
17 TraesCS1D01G437700 chr1A 90.598 117 11 0 3161 3277 582358947 582359063 6.390000e-34 156.0
18 TraesCS1D01G437700 chr1A 86.765 136 9 5 3030 3156 582411350 582411485 4.980000e-30 143.0
19 TraesCS1D01G437700 chr1A 90.526 95 7 1 155 249 146629922 146630014 1.800000e-24 124.0
20 TraesCS1D01G437700 chr1A 78.894 199 29 7 952 1146 172895285 172895096 6.480000e-24 122.0
21 TraesCS1D01G437700 chr1A 78.641 206 25 10 954 1146 37395811 37396010 8.390000e-23 119.0
22 TraesCS1D01G437700 chr1B 90.365 1671 115 22 1518 3156 675374500 675376156 0.000000e+00 2152.0
23 TraesCS1D01G437700 chr1B 92.484 918 47 10 3164 4061 675376240 675377155 0.000000e+00 1293.0
24 TraesCS1D01G437700 chr1B 84.965 1011 51 46 566 1522 675373510 675374473 0.000000e+00 931.0
25 TraesCS1D01G437700 chr1B 89.204 741 38 20 4061 4770 675377242 675377971 0.000000e+00 887.0
26 TraesCS1D01G437700 chr1B 88.686 548 53 4 1 539 675372967 675373514 0.000000e+00 660.0
27 TraesCS1D01G437700 chr1B 82.339 419 51 11 2631 3043 675542785 675543186 4.570000e-90 342.0
28 TraesCS1D01G437700 chr1B 92.760 221 14 2 3166 3385 675552680 675552899 7.700000e-83 318.0
29 TraesCS1D01G437700 chr1B 88.412 233 23 4 3165 3396 675543538 675543767 1.310000e-70 278.0
30 TraesCS1D01G437700 chr1B 88.128 219 20 5 2935 3152 675543200 675543413 6.130000e-64 255.0
31 TraesCS1D01G437700 chr1B 86.486 185 18 7 3876 4053 675552955 675553139 3.770000e-46 196.0
32 TraesCS1D01G437700 chr1B 86.765 136 9 5 3030 3156 675552473 675552608 4.980000e-30 143.0
33 TraesCS1D01G437700 chr1B 89.655 87 8 1 4114 4199 675553300 675553386 5.050000e-20 110.0
34 TraesCS1D01G437700 chr2B 89.503 181 14 5 2977 3156 94929763 94929587 1.730000e-54 224.0
35 TraesCS1D01G437700 chr2B 93.103 87 6 0 156 242 215925392 215925306 1.390000e-25 128.0
36 TraesCS1D01G437700 chr2B 91.304 92 8 0 156 247 777546613 777546704 5.010000e-25 126.0
37 TraesCS1D01G437700 chr3D 84.135 208 14 6 952 1146 327309501 327309702 2.930000e-42 183.0
38 TraesCS1D01G437700 chr3D 90.625 96 9 0 153 248 606566357 606566452 1.390000e-25 128.0
39 TraesCS1D01G437700 chr3D 89.583 96 10 0 153 248 606595372 606595467 6.480000e-24 122.0
40 TraesCS1D01G437700 chr4A 82.692 208 17 6 952 1146 610429284 610429083 2.950000e-37 167.0
41 TraesCS1D01G437700 chr4A 88.983 118 6 3 1380 1490 175692766 175692649 6.440000e-29 139.0
42 TraesCS1D01G437700 chrUn 81.910 199 19 12 952 1145 114952549 114952735 8.270000e-33 152.0
43 TraesCS1D01G437700 chr7B 80.676 207 22 10 952 1146 699507199 699507399 1.380000e-30 145.0
44 TraesCS1D01G437700 chr7B 79.612 206 24 8 953 1146 431281695 431281894 1.080000e-26 132.0
45 TraesCS1D01G437700 chr5B 88.350 103 11 1 149 250 443276391 443276493 6.480000e-24 122.0
46 TraesCS1D01G437700 chr2A 90.323 93 9 0 155 247 611336580 611336672 6.480000e-24 122.0
47 TraesCS1D01G437700 chr2A 80.240 167 23 6 983 1146 132705492 132705651 3.020000e-22 117.0
48 TraesCS1D01G437700 chr5A 90.769 65 6 0 1582 1646 622224980 622225044 2.370000e-13 87.9


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 TraesCS1D01G437700 chr1D 485052754 485057524 4770 False 8811.000000 8811 100.000000 1 4771 1 chr1D.!!$F1 4770
1 TraesCS1D01G437700 chr1D 485099368 485100241 873 False 926.000000 926 85.967000 3164 4053 1 chr1D.!!$F2 889
2 TraesCS1D01G437700 chr1D 485089021 485090598 1577 False 312.000000 501 84.493000 1871 3277 3 chr1D.!!$F3 1406
3 TraesCS1D01G437700 chr1A 582275235 582280709 5474 False 1278.400000 3526 90.846800 1 4771 5 chr1A.!!$F3 4770
4 TraesCS1D01G437700 chr1A 582292258 582293993 1735 False 712.666667 1123 91.696333 2197 3974 3 chr1A.!!$F4 1777
5 TraesCS1D01G437700 chr1A 582411350 582412786 1436 False 357.666667 612 87.060000 3030 4053 3 chr1A.!!$F6 1023
6 TraesCS1D01G437700 chr1A 582357633 582359063 1430 False 329.666667 448 84.531000 1864 3277 3 chr1A.!!$F5 1413
7 TraesCS1D01G437700 chr1B 675372967 675377971 5004 False 1184.600000 2152 89.140800 1 4770 5 chr1B.!!$F1 4769
8 TraesCS1D01G437700 chr1B 675542785 675543767 982 False 291.666667 342 86.293000 2631 3396 3 chr1B.!!$F2 765

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
743 1266 0.248702 GCCTACTCTACGAGCAGCAC 60.249 60.0 0.00 0.0 32.04 4.40 F
1288 1826 0.616891 AATTCTTACCGCCCCGAAGT 59.383 50.0 0.00 0.0 0.00 3.01 F
2583 3238 0.392060 AGCGCTGATGCAGAATGACA 60.392 50.0 10.39 0.0 39.69 3.58 F
3049 3878 0.330604 ATGCTTCTGCCCTGTCATGT 59.669 50.0 0.00 0.0 38.71 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 2454 0.457853 CGCGTGTAGCTGAAGCCTAA 60.458 55.000 0.00 0.00 45.59 2.69 R
3017 3726 3.129988 GCAGAAGCATGTGCCTTTCTTAT 59.870 43.478 0.00 0.00 39.82 1.73 R
3573 4907 1.956477 AGATTGCGCAAACAAAGGAGT 59.044 42.857 28.81 6.89 32.27 3.85 R
4690 6189 0.895559 CTGCAGGTCAAGGAAACCCC 60.896 60.000 5.57 0.00 37.52 4.95 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
93 96 1.067295 TGAGTCATTTGCCCCTCTGT 58.933 50.000 0.00 0.00 0.00 3.41
232 235 5.846714 AGTGTATGATGCTACCTCCCTAATT 59.153 40.000 0.00 0.00 0.00 1.40
239 242 6.842280 TGATGCTACCTCCCTAATTTGTAGTA 59.158 38.462 0.00 0.00 33.20 1.82
341 344 5.995282 TGCAATTATCCGGAACCAGTATTAG 59.005 40.000 9.01 0.00 0.00 1.73
395 400 5.050769 AGCATTAGTTACAGAATCAATCGCG 60.051 40.000 0.00 0.00 0.00 5.87
396 401 5.670097 CATTAGTTACAGAATCAATCGCGG 58.330 41.667 6.13 0.00 0.00 6.46
459 958 2.591923 TGGAAACAACATTAGCTGCCA 58.408 42.857 0.00 0.00 37.44 4.92
492 994 1.002792 GAGACCAAAAGACGCAACACC 60.003 52.381 0.00 0.00 0.00 4.16
503 1009 1.372997 GCAACACCTCTTCGAGCGA 60.373 57.895 0.00 0.00 0.00 4.93
514 1020 0.601057 TTCGAGCGATGTCACTTCCA 59.399 50.000 0.00 0.00 0.00 3.53
532 1038 1.481772 CCACCAATCGAAAATGGCCAT 59.518 47.619 14.09 14.09 40.51 4.40
558 1064 4.650754 ATACCGACACACTTCATACCTC 57.349 45.455 0.00 0.00 0.00 3.85
563 1069 4.280461 CGACACACTTCATACCTCGTATC 58.720 47.826 0.00 0.00 0.00 2.24
564 1070 4.608951 GACACACTTCATACCTCGTATCC 58.391 47.826 0.00 0.00 0.00 2.59
565 1071 4.021229 ACACACTTCATACCTCGTATCCA 58.979 43.478 0.00 0.00 0.00 3.41
649 1168 1.589779 CACATCACATCACACGGATCG 59.410 52.381 0.00 0.00 32.57 3.69
656 1176 1.739338 ATCACACGGATCGGAGAGGC 61.739 60.000 7.35 0.00 43.63 4.70
694 1214 3.905249 GGATGTTTCCTCGGCACC 58.095 61.111 0.00 0.00 39.14 5.01
743 1266 0.248702 GCCTACTCTACGAGCAGCAC 60.249 60.000 0.00 0.00 32.04 4.40
783 1306 1.298041 CACACGTGCCGGTCAAAAC 60.298 57.895 17.22 0.00 0.00 2.43
850 1373 4.379243 CGCCTCGCCTCACCAACT 62.379 66.667 0.00 0.00 0.00 3.16
852 1375 1.153549 GCCTCGCCTCACCAACTAG 60.154 63.158 0.00 0.00 0.00 2.57
853 1376 1.517832 CCTCGCCTCACCAACTAGG 59.482 63.158 0.00 0.00 45.67 3.02
859 1383 1.448540 CTCACCAACTAGGCTGGCG 60.449 63.158 11.95 4.34 43.14 5.69
995 1522 2.764547 CGACCCCTTCCTCCCTCC 60.765 72.222 0.00 0.00 0.00 4.30
997 1524 4.040198 ACCCCTTCCTCCCTCCCC 62.040 72.222 0.00 0.00 0.00 4.81
998 1525 3.711782 CCCCTTCCTCCCTCCCCT 61.712 72.222 0.00 0.00 0.00 4.79
999 1526 2.367512 CCCTTCCTCCCTCCCCTG 60.368 72.222 0.00 0.00 0.00 4.45
1233 1770 4.457496 CGCACCATCTCGGGCACT 62.457 66.667 0.00 0.00 40.22 4.40
1286 1824 2.701951 AGATAATTCTTACCGCCCCGAA 59.298 45.455 0.00 0.00 0.00 4.30
1288 1826 0.616891 AATTCTTACCGCCCCGAAGT 59.383 50.000 0.00 0.00 0.00 3.01
1322 1860 3.761445 TTCCGTCGATTAGGCCGCG 62.761 63.158 0.00 0.00 0.00 6.46
1324 1862 4.260355 CGTCGATTAGGCCGCGGA 62.260 66.667 33.48 8.40 0.00 5.54
1325 1863 2.354773 GTCGATTAGGCCGCGGAG 60.355 66.667 33.48 10.10 0.00 4.63
1328 1866 2.932234 CGATTAGGCCGCGGAGGAT 61.932 63.158 33.48 16.43 45.00 3.24
1508 2083 9.712305 GTGATATTTATATGTTACCTGCTCTGT 57.288 33.333 0.00 0.00 0.00 3.41
1542 2148 6.346096 TGTTTCCACCATAACTAGATACAGC 58.654 40.000 0.00 0.00 0.00 4.40
1549 2155 5.780282 ACCATAACTAGATACAGCTGCCATA 59.220 40.000 15.27 0.00 0.00 2.74
1613 2219 4.789075 CCGTTCATCGTCGCCGGT 62.789 66.667 1.90 0.00 37.94 5.28
1661 2267 1.424493 CGCTGAAGGTTCTCGATGCC 61.424 60.000 0.00 0.00 0.00 4.40
1703 2309 2.506438 GGCGTGCCGTACTCTGAC 60.506 66.667 0.00 0.00 0.00 3.51
1747 2353 7.276218 TGTTATTCAGGTACGCTACAATGTTAC 59.724 37.037 0.00 0.00 0.00 2.50
1751 2357 6.267817 TCAGGTACGCTACAATGTTACATAC 58.732 40.000 0.00 0.00 0.00 2.39
1752 2358 6.037726 CAGGTACGCTACAATGTTACATACA 58.962 40.000 0.00 0.00 41.97 2.29
1755 2361 6.477688 GGTACGCTACAATGTTACATACACAT 59.522 38.462 0.00 0.00 40.19 3.21
1756 2362 6.583912 ACGCTACAATGTTACATACACATC 57.416 37.500 0.00 0.00 40.19 3.06
1758 2364 7.485810 ACGCTACAATGTTACATACACATCTA 58.514 34.615 0.00 0.00 40.19 1.98
1759 2365 7.648112 ACGCTACAATGTTACATACACATCTAG 59.352 37.037 0.00 0.00 40.19 2.43
1773 2394 9.457110 CATACACATCTAGTATTGTCTTCTGTC 57.543 37.037 0.00 0.00 30.08 3.51
1789 2410 7.814587 TGTCTTCTGTCTGTAGTATTCATGTTG 59.185 37.037 0.00 0.00 0.00 3.33
1799 2420 8.251750 TGTAGTATTCATGTTGTTCAGCTTAC 57.748 34.615 0.00 0.00 0.00 2.34
1800 2421 7.875554 TGTAGTATTCATGTTGTTCAGCTTACA 59.124 33.333 0.00 0.00 0.00 2.41
1802 2423 6.710295 AGTATTCATGTTGTTCAGCTTACACA 59.290 34.615 0.00 1.99 0.00 3.72
1842 2463 9.499479 TTTTTATTGCATCATTTTTAGGCTTCA 57.501 25.926 0.00 0.00 0.00 3.02
1929 2550 1.537397 TGAGCTGTCCTGCCCTCTT 60.537 57.895 0.00 0.00 0.00 2.85
1986 2607 0.517316 GTGTCGCCAACTTCATGTCC 59.483 55.000 0.00 0.00 0.00 4.02
2086 2707 4.631131 TGCCATTTCTACTCATATGGTCG 58.369 43.478 2.13 0.00 39.75 4.79
2126 2747 7.440198 TGAATTCTGAAACATGGCATTGTTTA 58.560 30.769 20.32 10.77 46.84 2.01
2152 2774 9.988815 ATCCTGCATATCTTAGTTTTACTAGTG 57.011 33.333 5.39 0.00 31.47 2.74
2153 2775 7.926555 TCCTGCATATCTTAGTTTTACTAGTGC 59.073 37.037 5.39 0.00 31.47 4.40
2154 2776 7.928706 CCTGCATATCTTAGTTTTACTAGTGCT 59.071 37.037 5.39 1.25 31.47 4.40
2155 2777 8.648557 TGCATATCTTAGTTTTACTAGTGCTG 57.351 34.615 5.39 0.00 31.47 4.41
2156 2778 8.258007 TGCATATCTTAGTTTTACTAGTGCTGT 58.742 33.333 5.39 0.00 31.47 4.40
2157 2779 9.745880 GCATATCTTAGTTTTACTAGTGCTGTA 57.254 33.333 5.39 0.00 31.47 2.74
2200 2822 7.745620 AGACGATTGAGGATTAAAAAGTTGT 57.254 32.000 0.00 0.00 0.00 3.32
2446 3092 7.336176 TCTCTTTGGCATTATCATCTATCATGC 59.664 37.037 0.00 0.00 42.23 4.06
2576 3231 9.778993 ATATTTATTATTTAAGCGCTGATGCAG 57.221 29.630 12.58 0.00 39.64 4.41
2582 3237 0.731417 AAGCGCTGATGCAGAATGAC 59.269 50.000 12.58 0.00 39.69 3.06
2583 3238 0.392060 AGCGCTGATGCAGAATGACA 60.392 50.000 10.39 0.00 39.69 3.58
2630 3285 8.129840 TGCTTTGCTGTAATTTTAAACTTCGTA 58.870 29.630 0.00 0.00 0.00 3.43
2631 3286 8.960075 GCTTTGCTGTAATTTTAAACTTCGTAA 58.040 29.630 0.00 0.00 0.00 3.18
2644 3329 5.382618 AACTTCGTAATACTCGTCAGGTT 57.617 39.130 0.00 0.00 0.00 3.50
2780 3469 3.194005 ACACCAACTACACCAACAGAG 57.806 47.619 0.00 0.00 0.00 3.35
2875 3565 4.008074 TGCTCCCTTAAACTCTGTTCTG 57.992 45.455 0.00 0.00 0.00 3.02
2876 3566 3.244561 TGCTCCCTTAAACTCTGTTCTGG 60.245 47.826 0.00 0.00 0.00 3.86
2890 3580 6.070538 ACTCTGTTCTGGTATAGCACATTCTT 60.071 38.462 0.00 0.00 32.13 2.52
2925 3615 7.814264 ATAAGAAAGTTCTCATAATGGCCAG 57.186 36.000 13.05 0.00 36.28 4.85
2934 3624 2.093181 TCATAATGGCCAGCGTAGTGTT 60.093 45.455 13.05 0.00 0.00 3.32
2938 3628 2.257691 TGGCCAGCGTAGTGTTTTTA 57.742 45.000 0.00 0.00 0.00 1.52
2939 3629 2.785562 TGGCCAGCGTAGTGTTTTTAT 58.214 42.857 0.00 0.00 0.00 1.40
2947 3656 7.479603 GCCAGCGTAGTGTTTTTATAACTTAAC 59.520 37.037 0.00 0.00 0.00 2.01
3039 3868 0.886563 AGAAAGGCACATGCTTCTGC 59.113 50.000 7.38 0.00 41.70 4.26
3049 3878 0.330604 ATGCTTCTGCCCTGTCATGT 59.669 50.000 0.00 0.00 38.71 3.21
3294 4256 1.900486 ACTACTGGAGTTACTGGCACC 59.100 52.381 0.00 0.00 33.13 5.01
3371 4696 9.181805 GGTTTGCTAAGTCTTTTCTTTATTGTC 57.818 33.333 0.00 0.00 0.00 3.18
3374 4699 9.730420 TTGCTAAGTCTTTTCTTTATTGTCAAC 57.270 29.630 0.00 0.00 0.00 3.18
3375 4700 9.120538 TGCTAAGTCTTTTCTTTATTGTCAACT 57.879 29.630 0.00 0.00 0.00 3.16
3376 4701 9.600646 GCTAAGTCTTTTCTTTATTGTCAACTC 57.399 33.333 0.00 0.00 0.00 3.01
3399 4724 4.932200 CAGGAACTAGTTTTGGTCTGCTAG 59.068 45.833 10.02 0.00 36.02 3.42
3454 4779 6.426980 TGCTTATAGAACATTGTCTGCTTG 57.573 37.500 0.00 0.00 0.00 4.01
3794 5138 9.107177 TGAAACATGCATTTTTATCTTTTGTGT 57.893 25.926 10.70 0.00 0.00 3.72
3873 5218 7.124750 AGCATTACATTCCTGGCTTTAGATTTT 59.875 33.333 0.00 0.00 0.00 1.82
3990 5337 4.287067 AGAAAGCATCTTTCTGTCCCAGTA 59.713 41.667 17.91 0.00 37.37 2.74
3999 5346 0.744414 CTGTCCCAGTACCATTGCCG 60.744 60.000 0.00 0.00 0.00 5.69
4020 5367 4.461081 CCGTTTCAATGATTTCCTGGGTTA 59.539 41.667 0.00 0.00 0.00 2.85
4042 5391 8.798153 GGTTATTATTTTTCTGAACAGCATTCG 58.202 33.333 0.00 0.00 0.00 3.34
4099 5535 9.866655 ATTCCAGCTTAATATTCCTGTCATTTA 57.133 29.630 0.00 0.00 0.00 1.40
4134 5570 9.496873 GCTATAAAAACCCCAACACTAATTTTT 57.503 29.630 0.00 0.00 34.56 1.94
4138 5574 7.618502 AAAACCCCAACACTAATTTTTGTTC 57.381 32.000 2.24 0.00 33.59 3.18
4199 5635 3.685139 TCAAGTCACTTCCTGGATGAC 57.315 47.619 18.50 18.50 42.54 3.06
4466 5951 7.556996 TGTTACCTAATGTTTTGTTGTGGTACT 59.443 33.333 0.00 0.00 0.00 2.73
4467 5952 6.385649 ACCTAATGTTTTGTTGTGGTACTG 57.614 37.500 0.00 0.00 0.00 2.74
4468 5953 5.889289 ACCTAATGTTTTGTTGTGGTACTGT 59.111 36.000 0.00 0.00 0.00 3.55
4469 5954 6.183360 ACCTAATGTTTTGTTGTGGTACTGTG 60.183 38.462 0.00 0.00 0.00 3.66
4470 5955 4.647424 ATGTTTTGTTGTGGTACTGTGG 57.353 40.909 0.00 0.00 0.00 4.17
4471 5956 3.422796 TGTTTTGTTGTGGTACTGTGGT 58.577 40.909 0.00 0.00 0.00 4.16
4472 5957 4.586884 TGTTTTGTTGTGGTACTGTGGTA 58.413 39.130 0.00 0.00 0.00 3.25
4473 5958 4.395542 TGTTTTGTTGTGGTACTGTGGTAC 59.604 41.667 0.00 0.00 45.38 3.34
4531 6016 7.698506 AAATTGAGATGAATCTGAAGAAGCA 57.301 32.000 0.00 0.00 37.25 3.91
4601 6100 6.604735 TTTCGTTTCTTTCTTCTCCTTCTG 57.395 37.500 0.00 0.00 0.00 3.02
4624 6123 9.159364 TCTGTCAAGATTCAAATACTCATCAAG 57.841 33.333 0.00 0.00 0.00 3.02
4636 6135 4.851639 ACTCATCAAGATAAAGGGCTGT 57.148 40.909 0.00 0.00 0.00 4.40
4640 6139 3.350219 TCAAGATAAAGGGCTGTCCAC 57.650 47.619 0.00 0.00 38.24 4.02
4709 6208 0.895559 GGGGTTTCCTTGACCTGCAG 60.896 60.000 6.78 6.78 37.34 4.41
4733 6232 6.326583 AGGGTCAATTCTGATCGTCCTAAATA 59.673 38.462 0.00 0.00 32.99 1.40
4734 6233 6.990349 GGGTCAATTCTGATCGTCCTAAATAA 59.010 38.462 0.00 0.00 32.99 1.40
4735 6234 7.497909 GGGTCAATTCTGATCGTCCTAAATAAA 59.502 37.037 0.00 0.00 32.99 1.40
4736 6235 9.057089 GGTCAATTCTGATCGTCCTAAATAAAT 57.943 33.333 0.00 0.00 33.05 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.019094 GGCCAAATTACCGTAATACATGTATTC 58.981 37.037 29.68 20.46 37.07 1.75
46 49 3.637769 TGATAACAGGGGCCAAATTACC 58.362 45.455 4.39 0.00 0.00 2.85
143 146 1.560923 CAGCCTTAGATCGACGGTTG 58.439 55.000 1.34 1.34 0.00 3.77
341 344 9.109393 TCCAAGATTATCTACAGTTAATGCAAC 57.891 33.333 0.00 0.00 37.41 4.17
395 400 5.598417 AGATTAATGTTGTCCCCAAATAGCC 59.402 40.000 0.00 0.00 30.94 3.93
396 401 6.321181 TGAGATTAATGTTGTCCCCAAATAGC 59.679 38.462 0.00 0.00 30.94 2.97
459 958 0.106708 TGGTCTCAGCTTCTTTGCGT 59.893 50.000 0.00 0.00 38.13 5.24
503 1009 3.417069 TTCGATTGGTGGAAGTGACAT 57.583 42.857 0.00 0.00 0.00 3.06
514 1020 2.166254 GTCATGGCCATTTTCGATTGGT 59.834 45.455 17.92 0.00 35.34 3.67
532 1038 3.737032 TGAAGTGTGTCGGTATTGTCA 57.263 42.857 0.00 0.00 0.00 3.58
558 1064 8.462143 AAAGCGTTTAGATATATGTGGATACG 57.538 34.615 0.00 0.00 42.51 3.06
602 1108 2.556622 CCCGGCAAGACATTTTGTACTT 59.443 45.455 0.00 0.00 0.00 2.24
615 1124 1.077501 ATGTGATGGACCCGGCAAG 60.078 57.895 0.00 0.00 0.00 4.01
656 1176 2.881352 GAAGAAGCCGTCGCCTCG 60.881 66.667 0.00 0.00 34.57 4.63
743 1266 0.167251 GTGGATGGCGTTTTACGTGG 59.833 55.000 0.00 0.00 44.73 4.94
859 1383 2.516225 GGGTTGGTGATAGGGCGC 60.516 66.667 0.00 0.00 0.00 6.53
1233 1770 1.214175 TGCTCCTTGAGGTTGGTGAAA 59.786 47.619 0.00 0.00 36.34 2.69
1286 1824 0.944386 AATCAAAACACGCGCAGACT 59.056 45.000 5.73 0.00 0.00 3.24
1288 1826 0.237235 GGAATCAAAACACGCGCAGA 59.763 50.000 5.73 0.00 0.00 4.26
1369 1908 5.433526 TGGCCACTAAGACAACCATTATAC 58.566 41.667 0.00 0.00 0.00 1.47
1372 1911 4.263727 ACATGGCCACTAAGACAACCATTA 60.264 41.667 8.16 0.00 35.76 1.90
1373 1912 2.969821 TGGCCACTAAGACAACCATT 57.030 45.000 0.00 0.00 0.00 3.16
1374 1913 2.041620 ACATGGCCACTAAGACAACCAT 59.958 45.455 8.16 0.00 38.42 3.55
1376 1915 2.200373 ACATGGCCACTAAGACAACC 57.800 50.000 8.16 0.00 0.00 3.77
1377 1916 4.760204 AGTAAACATGGCCACTAAGACAAC 59.240 41.667 8.16 0.00 0.00 3.32
1508 2083 3.694043 TGGTGGAAACAGATCGAATCA 57.306 42.857 0.00 0.00 44.46 2.57
1542 2148 6.311935 CCATCAGAACACAAAAATTATGGCAG 59.688 38.462 0.00 0.00 0.00 4.85
1549 2155 6.183360 GCAAACACCATCAGAACACAAAAATT 60.183 34.615 0.00 0.00 0.00 1.82
1661 2267 3.236632 TCGATCACATCAGAACCACAG 57.763 47.619 0.00 0.00 0.00 3.66
1735 2341 8.873215 ACTAGATGTGTATGTAACATTGTAGC 57.127 34.615 0.00 0.00 41.10 3.58
1747 2353 9.457110 GACAGAAGACAATACTAGATGTGTATG 57.543 37.037 0.00 3.49 31.76 2.39
1751 2357 7.542890 ACAGACAGAAGACAATACTAGATGTG 58.457 38.462 0.00 0.00 0.00 3.21
1752 2358 7.710676 ACAGACAGAAGACAATACTAGATGT 57.289 36.000 0.00 0.00 0.00 3.06
1758 2364 9.244292 TGAATACTACAGACAGAAGACAATACT 57.756 33.333 0.00 0.00 0.00 2.12
1766 2387 8.539770 AACAACATGAATACTACAGACAGAAG 57.460 34.615 0.00 0.00 0.00 2.85
1773 2394 6.974932 AGCTGAACAACATGAATACTACAG 57.025 37.500 0.00 1.60 0.00 2.74
1780 2401 6.579666 ATGTGTAAGCTGAACAACATGAAT 57.420 33.333 0.00 0.00 0.00 2.57
1820 2441 6.097270 AGCTGAAGCCTAAAAATGATGCAATA 59.903 34.615 0.00 0.00 43.38 1.90
1823 2444 3.765511 AGCTGAAGCCTAAAAATGATGCA 59.234 39.130 0.00 0.00 43.38 3.96
1824 2445 4.382345 AGCTGAAGCCTAAAAATGATGC 57.618 40.909 0.00 0.00 43.38 3.91
1833 2454 0.457853 CGCGTGTAGCTGAAGCCTAA 60.458 55.000 0.00 0.00 45.59 2.69
1834 2455 1.138883 CGCGTGTAGCTGAAGCCTA 59.861 57.895 0.00 0.00 45.59 3.93
1929 2550 4.380023 GGGTTGTAATATGTGAAAAGCGCA 60.380 41.667 11.47 0.00 42.01 6.09
1986 2607 1.600485 ACACCGGCTTCTTTTACAACG 59.400 47.619 0.00 0.00 0.00 4.10
2126 2747 9.988815 CACTAGTAAAACTAAGATATGCAGGAT 57.011 33.333 0.00 0.00 29.00 3.24
2152 2774 3.375299 CCTGAAACCTTATGCACTACAGC 59.625 47.826 0.00 0.00 0.00 4.40
2153 2775 4.579869 ACCTGAAACCTTATGCACTACAG 58.420 43.478 0.00 0.00 0.00 2.74
2154 2776 4.634012 ACCTGAAACCTTATGCACTACA 57.366 40.909 0.00 0.00 0.00 2.74
2155 2777 5.811100 GTCTACCTGAAACCTTATGCACTAC 59.189 44.000 0.00 0.00 0.00 2.73
2156 2778 5.393787 CGTCTACCTGAAACCTTATGCACTA 60.394 44.000 0.00 0.00 0.00 2.74
2157 2779 4.620803 CGTCTACCTGAAACCTTATGCACT 60.621 45.833 0.00 0.00 0.00 4.40
2158 2780 3.617263 CGTCTACCTGAAACCTTATGCAC 59.383 47.826 0.00 0.00 0.00 4.57
2159 2781 3.512329 TCGTCTACCTGAAACCTTATGCA 59.488 43.478 0.00 0.00 0.00 3.96
2200 2822 4.097286 TGCGTATCTGTCTATGCTGTTACA 59.903 41.667 0.00 0.00 35.17 2.41
2474 3120 9.927668 CTATTTGGTTTAGACACAAAAATGGAT 57.072 29.630 0.00 0.00 37.60 3.41
2475 3121 8.364142 CCTATTTGGTTTAGACACAAAAATGGA 58.636 33.333 0.00 0.00 37.60 3.41
2477 3123 8.147704 ACCCTATTTGGTTTAGACACAAAAATG 58.852 33.333 0.00 0.00 37.60 2.32
2478 3124 8.257602 ACCCTATTTGGTTTAGACACAAAAAT 57.742 30.769 0.00 0.00 37.60 1.82
2630 3285 6.603997 AGACTAATCAGAACCTGACGAGTATT 59.396 38.462 10.67 0.23 43.63 1.89
2631 3286 6.038825 CAGACTAATCAGAACCTGACGAGTAT 59.961 42.308 10.67 6.87 43.63 2.12
2632 3287 5.354513 CAGACTAATCAGAACCTGACGAGTA 59.645 44.000 10.67 0.00 43.63 2.59
2633 3288 4.156922 CAGACTAATCAGAACCTGACGAGT 59.843 45.833 10.55 10.55 43.63 4.18
2634 3289 4.439426 CCAGACTAATCAGAACCTGACGAG 60.439 50.000 0.00 2.77 43.63 4.18
2635 3290 3.444034 CCAGACTAATCAGAACCTGACGA 59.556 47.826 0.00 0.00 43.63 4.20
2644 3329 9.993454 CATCTTCAATATTCCAGACTAATCAGA 57.007 33.333 0.00 0.00 0.00 3.27
2780 3469 6.118852 AGCCTTTGTAATTCTCTCCATTCTC 58.881 40.000 0.00 0.00 0.00 2.87
2875 3565 7.736447 AGCAATAAGAAGAATGTGCTATACC 57.264 36.000 0.00 0.00 40.40 2.73
2903 3593 4.400567 GCTGGCCATTATGAGAACTTTCTT 59.599 41.667 5.51 0.00 37.73 2.52
2939 3629 9.762933 ACAAAATACCGTACTCTTGTTAAGTTA 57.237 29.630 0.00 0.00 0.00 2.24
2960 3669 9.760660 CCGTCAACAAATTTTAAAATGACAAAA 57.239 25.926 22.18 6.05 0.00 2.44
2975 3684 6.016360 TCAGATGACAAATTCCGTCAACAAAT 60.016 34.615 13.00 0.00 45.91 2.32
2984 3693 5.180117 AGTCAACTTCAGATGACAAATTCCG 59.820 40.000 16.83 0.00 46.28 4.30
3017 3726 3.129988 GCAGAAGCATGTGCCTTTCTTAT 59.870 43.478 0.00 0.00 39.82 1.73
3143 3983 7.598278 TGTCAATTCCATTTAGCGTACATTTT 58.402 30.769 0.00 0.00 0.00 1.82
3152 3992 6.532657 CCTCAACAATGTCAATTCCATTTAGC 59.467 38.462 0.00 0.00 30.28 3.09
3156 3996 6.041865 TCAACCTCAACAATGTCAATTCCATT 59.958 34.615 0.00 0.00 32.88 3.16
3157 3997 5.539574 TCAACCTCAACAATGTCAATTCCAT 59.460 36.000 0.00 0.00 0.00 3.41
3158 3998 4.892345 TCAACCTCAACAATGTCAATTCCA 59.108 37.500 0.00 0.00 0.00 3.53
3159 3999 5.452078 TCAACCTCAACAATGTCAATTCC 57.548 39.130 0.00 0.00 0.00 3.01
3162 4085 3.890756 TGCTCAACCTCAACAATGTCAAT 59.109 39.130 0.00 0.00 0.00 2.57
3371 4696 5.237344 CAGACCAAAACTAGTTCCTGAGTTG 59.763 44.000 8.95 8.38 36.05 3.16
3373 4698 4.743955 GCAGACCAAAACTAGTTCCTGAGT 60.744 45.833 8.95 9.34 0.00 3.41
3374 4699 3.748568 GCAGACCAAAACTAGTTCCTGAG 59.251 47.826 8.95 6.59 0.00 3.35
3375 4700 3.391296 AGCAGACCAAAACTAGTTCCTGA 59.609 43.478 8.95 0.00 0.00 3.86
3376 4701 3.744660 AGCAGACCAAAACTAGTTCCTG 58.255 45.455 8.95 9.37 0.00 3.86
3378 4703 3.685272 GCTAGCAGACCAAAACTAGTTCC 59.315 47.826 10.63 0.00 35.58 3.62
3454 4779 9.765795 ACAGCTTTATCTGTGACCTATAATAAC 57.234 33.333 0.00 0.00 44.88 1.89
3573 4907 1.956477 AGATTGCGCAAACAAAGGAGT 59.044 42.857 28.81 6.89 32.27 3.85
3794 5138 3.289407 TGGTATTCATGCGATTTCCCA 57.711 42.857 0.00 0.00 0.00 4.37
3824 5168 6.847792 GCTACACTGTAAAACGGAACTAAAAC 59.152 38.462 0.00 0.00 0.00 2.43
3834 5178 6.959311 GGAATGTAATGCTACACTGTAAAACG 59.041 38.462 0.00 0.00 40.84 3.60
3873 5218 4.777366 TCTATCACACAACAGGATCCTTCA 59.223 41.667 13.00 0.00 0.00 3.02
4020 5367 7.538678 GTGACGAATGCTGTTCAGAAAAATAAT 59.461 33.333 3.84 0.00 0.00 1.28
4099 5535 7.775561 TGTTGGGGTTTTTATAGCAAAACAAAT 59.224 29.630 12.55 0.00 45.00 2.32
4138 5574 9.303537 GCTCAACCTAGTAGTATTTCTAACTTG 57.696 37.037 0.00 0.00 0.00 3.16
4276 5714 4.515567 CGAATCTTCCTGGCTATTTAACCC 59.484 45.833 0.00 0.00 0.00 4.11
4504 5989 8.242053 GCTTCTTCAGATTCATCTCAATTTTGA 58.758 33.333 0.00 0.00 34.22 2.69
4531 6016 6.215636 ACCTTCACCCTGTTTCATAATCTAGT 59.784 38.462 0.00 0.00 0.00 2.57
4624 6123 1.682087 GGTGGTGGACAGCCCTTTATC 60.682 57.143 0.00 0.00 41.69 1.75
4636 6135 2.435663 CACATGGCAGGTGGTGGA 59.564 61.111 23.62 0.00 32.65 4.02
4672 6171 7.202102 GGAAACCCCTCATGAACATAGTATAGT 60.202 40.741 0.00 0.00 0.00 2.12
4677 6176 3.852578 AGGAAACCCCTCATGAACATAGT 59.147 43.478 0.00 0.00 43.31 2.12
4690 6189 0.895559 CTGCAGGTCAAGGAAACCCC 60.896 60.000 5.57 0.00 37.52 4.95
4709 6208 2.990066 AGGACGATCAGAATTGACCC 57.010 50.000 0.00 0.00 35.83 4.46


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

AutoCloner maintained by Alex Coulton.