Multiple sequence alignment - TraesCS2B01G277500

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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 TraesCS2B01G277500 chr2B 100.000 3261 0 0 1 3261 383354335 383357595 0.000000e+00 6023
1 TraesCS2B01G277500 chr2B 88.759 427 42 3 1154 1580 235062757 235063177 4.820000e-143 518
2 TraesCS2B01G277500 chr2B 88.525 427 43 3 1154 1580 235906143 235906563 2.240000e-141 512
3 TraesCS2B01G277500 chr2D 88.020 1803 106 38 847 2591 315424723 315426473 0.000000e+00 2032
4 TraesCS2B01G277500 chr2D 91.274 848 68 3 3 846 476339685 476338840 0.000000e+00 1151
5 TraesCS2B01G277500 chr2D 87.463 678 48 10 2611 3261 315486288 315486955 0.000000e+00 747
6 TraesCS2B01G277500 chr2D 89.227 427 40 3 1154 1580 178529162 178529582 2.230000e-146 529
7 TraesCS2B01G277500 chr2D 89.227 427 40 3 1154 1580 178696888 178697308 2.230000e-146 529
8 TraesCS2B01G277500 chr6D 91.962 846 61 4 3 844 433763936 433764778 0.000000e+00 1179
9 TraesCS2B01G277500 chr6D 82.883 222 33 5 2184 2403 357785318 357785100 9.230000e-46 195
10 TraesCS2B01G277500 chr4D 91.489 846 66 3 3 844 488130112 488129269 0.000000e+00 1158
11 TraesCS2B01G277500 chr3D 91.135 846 68 4 3 844 33191913 33191071 0.000000e+00 1140
12 TraesCS2B01G277500 chr1B 91.017 846 69 4 3 844 437867939 437868781 0.000000e+00 1134
13 TraesCS2B01G277500 chr1B 82.833 233 37 3 2166 2397 465702064 465702294 4.260000e-49 206
14 TraesCS2B01G277500 chr2A 85.302 1143 109 20 2160 3261 419474139 419473015 0.000000e+00 1125
15 TraesCS2B01G277500 chr2A 83.279 616 69 18 960 1573 193584878 193585461 1.330000e-148 536
16 TraesCS2B01G277500 chr2A 90.000 210 14 2 847 1049 419476291 419476082 6.940000e-67 265
17 TraesCS2B01G277500 chr2A 93.750 96 6 0 1111 1206 419476077 419475982 9.430000e-31 145
18 TraesCS2B01G277500 chr7A 90.577 849 73 4 1 844 162948795 162947949 0.000000e+00 1118
19 TraesCS2B01G277500 chr7A 90.577 849 73 3 1 844 688480279 688481125 0.000000e+00 1118
20 TraesCS2B01G277500 chr7A 90.342 849 75 3 1 844 688473641 688474487 0.000000e+00 1107
21 TraesCS2B01G277500 chr7A 80.195 308 50 11 2153 2454 422486415 422486717 1.520000e-53 220
22 TraesCS2B01G277500 chr3A 90.459 849 74 3 1 844 114691481 114690635 0.000000e+00 1112
23 TraesCS2B01G277500 chr4B 80.063 316 47 11 2167 2472 439317419 439317110 1.520000e-53 220
24 TraesCS2B01G277500 chr6B 82.490 257 32 10 1808 2060 79796451 79796204 2.550000e-51 213
25 TraesCS2B01G277500 chr4A 81.022 274 44 7 2184 2454 109427802 109427534 9.170000e-51 211
26 TraesCS2B01G277500 chr3B 81.857 237 34 8 2184 2416 382709331 382709100 1.190000e-44 191
27 TraesCS2B01G277500 chr5B 79.323 266 44 11 2133 2393 213259035 213258776 3.340000e-40 176
28 TraesCS2B01G277500 chr5B 84.932 73 11 0 1191 1263 606871107 606871035 1.250000e-09 75
29 TraesCS2B01G277500 chr6A 81.532 222 31 10 2184 2404 499820631 499820843 1.200000e-39 174
30 TraesCS2B01G277500 chr5D 85.915 71 9 1 1185 1255 490968665 490968734 1.250000e-09 75
31 TraesCS2B01G277500 chr5A 85.915 71 9 1 1185 1255 613457319 613457388 1.250000e-09 75


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 TraesCS2B01G277500 chr2B 383354335 383357595 3260 False 6023.000000 6023 100.000 1 3261 1 chr2B.!!$F3 3260
1 TraesCS2B01G277500 chr2D 315424723 315426473 1750 False 2032.000000 2032 88.020 847 2591 1 chr2D.!!$F3 1744
2 TraesCS2B01G277500 chr2D 476338840 476339685 845 True 1151.000000 1151 91.274 3 846 1 chr2D.!!$R1 843
3 TraesCS2B01G277500 chr2D 315486288 315486955 667 False 747.000000 747 87.463 2611 3261 1 chr2D.!!$F4 650
4 TraesCS2B01G277500 chr6D 433763936 433764778 842 False 1179.000000 1179 91.962 3 844 1 chr6D.!!$F1 841
5 TraesCS2B01G277500 chr4D 488129269 488130112 843 True 1158.000000 1158 91.489 3 844 1 chr4D.!!$R1 841
6 TraesCS2B01G277500 chr3D 33191071 33191913 842 True 1140.000000 1140 91.135 3 844 1 chr3D.!!$R1 841
7 TraesCS2B01G277500 chr1B 437867939 437868781 842 False 1134.000000 1134 91.017 3 844 1 chr1B.!!$F1 841
8 TraesCS2B01G277500 chr2A 193584878 193585461 583 False 536.000000 536 83.279 960 1573 1 chr2A.!!$F1 613
9 TraesCS2B01G277500 chr2A 419473015 419476291 3276 True 511.666667 1125 89.684 847 3261 3 chr2A.!!$R1 2414
10 TraesCS2B01G277500 chr7A 162947949 162948795 846 True 1118.000000 1118 90.577 1 844 1 chr7A.!!$R1 843
11 TraesCS2B01G277500 chr7A 688480279 688481125 846 False 1118.000000 1118 90.577 1 844 1 chr7A.!!$F3 843
12 TraesCS2B01G277500 chr7A 688473641 688474487 846 False 1107.000000 1107 90.342 1 844 1 chr7A.!!$F2 843
13 TraesCS2B01G277500 chr3A 114690635 114691481 846 True 1112.000000 1112 90.459 1 844 1 chr3A.!!$R1 843

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
471 476 0.106519 CTATGGGGCTTGGTGAAGGG 60.107 60.000 0.0 0.0 0.0 3.95 F
635 640 0.250553 TGGGACGAAAGGAACGCAAT 60.251 50.000 0.0 0.0 0.0 3.56 F
732 738 0.406361 TAGGGGCGAAACATTTGGGT 59.594 50.000 0.0 0.0 0.0 4.51 F
1593 1812 1.002011 GCTTCCAGTTCCACCCTCC 60.002 63.158 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1801 0.035820 TACAATGCGGAGGGTGGAAC 60.036 55.0 0.00 0.00 0.00 3.62 R
1583 1802 0.035820 GTACAATGCGGAGGGTGGAA 60.036 55.0 0.00 0.00 0.00 3.53 R
2131 3205 0.179056 CATTTACCGGGAGCGGATGT 60.179 55.0 6.32 0.00 0.00 3.06 R
2612 3725 0.249699 ACGATGCTCACGTGGTTTCA 60.250 50.0 17.00 8.88 42.37 2.69 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
52 53 0.407139 AGGTCAGGGAAGCTTTGCAT 59.593 50.000 0.00 0.00 0.00 3.96
54 55 2.019984 GGTCAGGGAAGCTTTGCATAG 58.980 52.381 0.00 0.00 0.00 2.23
80 81 5.014808 AGCATGGATTAGCAAAATCAACC 57.985 39.130 12.28 0.00 0.00 3.77
86 87 4.638865 GGATTAGCAAAATCAACCCTACGT 59.361 41.667 12.28 0.00 0.00 3.57
145 146 2.668632 TGGACTTCCATCCACGGC 59.331 61.111 0.00 0.00 44.14 5.68
165 166 3.474600 GCATTAGTCTGGATGAGCATGT 58.525 45.455 0.00 0.00 0.00 3.21
172 173 0.749049 TGGATGAGCATGTCGAGGAG 59.251 55.000 0.00 0.00 0.00 3.69
210 211 4.021894 GCATACGGTCTCAGGAGAATACAT 60.022 45.833 0.00 0.00 39.48 2.29
223 224 4.194640 GAGAATACATTGCTTCCTCTGCA 58.805 43.478 0.00 0.00 38.80 4.41
257 258 5.936686 ATTTCTATCCATCATTCGCACAG 57.063 39.130 0.00 0.00 0.00 3.66
283 284 1.134220 TGCAAGGTCGTTTGGAAGACT 60.134 47.619 0.00 0.00 37.52 3.24
320 325 0.238289 CAAATTCCTCGCGTGTGCTT 59.762 50.000 5.77 0.00 39.65 3.91
330 335 2.159558 TCGCGTGTGCTTTACAAAACAA 60.160 40.909 5.77 0.00 41.89 2.83
331 336 2.594654 CGCGTGTGCTTTACAAAACAAA 59.405 40.909 0.00 0.00 41.89 2.83
358 363 2.909965 GCTGACCGGTTGGCCAAA 60.910 61.111 22.47 1.73 39.70 3.28
396 401 1.228552 GCCCTTGTCCTCTTTGCCA 60.229 57.895 0.00 0.00 0.00 4.92
399 404 1.548582 CCCTTGTCCTCTTTGCCACAT 60.549 52.381 0.00 0.00 0.00 3.21
402 407 0.770499 TGTCCTCTTTGCCACATGGA 59.230 50.000 0.87 0.00 37.39 3.41
414 419 2.359900 CCACATGGACCTAGAAACTGC 58.640 52.381 0.00 0.00 37.39 4.40
434 439 1.301677 CGAGCACCTCTTCTTTGGCC 61.302 60.000 0.00 0.00 0.00 5.36
451 456 4.476410 CGCCGCTACACGCTGAGA 62.476 66.667 0.00 0.00 41.76 3.27
471 476 0.106519 CTATGGGGCTTGGTGAAGGG 60.107 60.000 0.00 0.00 0.00 3.95
476 481 2.436109 GCTTGGTGAAGGGCTGGA 59.564 61.111 0.00 0.00 0.00 3.86
481 486 0.776810 TGGTGAAGGGCTGGATTCAA 59.223 50.000 0.00 0.00 37.19 2.69
486 491 1.203287 GAAGGGCTGGATTCAACTTGC 59.797 52.381 0.00 0.00 0.00 4.01
505 510 1.447317 CCAGCTTGGACGTTGCAGTT 61.447 55.000 0.00 0.00 40.96 3.16
506 511 0.381801 CAGCTTGGACGTTGCAGTTT 59.618 50.000 0.00 0.00 0.00 2.66
507 512 1.102978 AGCTTGGACGTTGCAGTTTT 58.897 45.000 0.00 0.00 0.00 2.43
535 540 5.335819 GCGAACTATAGGAGTATCAAGGACC 60.336 48.000 4.43 0.00 37.44 4.46
615 620 2.455674 TGCTAGTGTGCAAGTCGATT 57.544 45.000 0.00 0.00 40.29 3.34
635 640 0.250553 TGGGACGAAAGGAACGCAAT 60.251 50.000 0.00 0.00 0.00 3.56
653 658 3.850374 GCAATGGTTTTTCGACGCAACTA 60.850 43.478 0.00 0.00 0.00 2.24
732 738 0.406361 TAGGGGCGAAACATTTGGGT 59.594 50.000 0.00 0.00 0.00 4.51
742 748 5.393027 GCGAAACATTTGGGTCACATTCTAT 60.393 40.000 0.00 0.00 0.00 1.98
748 754 4.561500 TTGGGTCACATTCTATCGGAAA 57.438 40.909 0.00 0.00 37.49 3.13
759 765 2.100252 TCTATCGGAAAAGTAGTGCGGG 59.900 50.000 0.00 0.00 0.00 6.13
791 797 1.478105 CCCCATGCTTGAGGCTTTTAC 59.522 52.381 0.22 0.00 42.39 2.01
820 826 5.984725 TGTCCTCTGTAACTTTGAAAGACA 58.015 37.500 12.53 5.65 0.00 3.41
828 836 7.559897 TCTGTAACTTTGAAAGACATTTCCCTT 59.440 33.333 12.53 0.00 43.56 3.95
831 839 7.423844 AACTTTGAAAGACATTTCCCTTTCT 57.576 32.000 12.53 0.00 45.05 2.52
874 882 1.264826 GCTGCCGTCTAGTAGTAGCTC 59.735 57.143 0.00 0.00 0.00 4.09
1031 1051 2.510238 GCTTCGCTGCTGGACGAT 60.510 61.111 0.00 0.00 38.25 3.73
1042 1062 2.159099 TGCTGGACGATATCTCCAACAC 60.159 50.000 18.61 13.60 37.36 3.32
1045 1065 2.829120 TGGACGATATCTCCAACACACA 59.171 45.455 16.82 0.00 34.70 3.72
1247 1272 1.067749 CCAGCGATCTCTGCTCCAG 59.932 63.158 7.21 0.00 41.72 3.86
1577 1796 1.551883 GATGGCAAGGGTTTGAATGCT 59.448 47.619 0.00 0.00 38.79 3.79
1578 1797 1.422531 TGGCAAGGGTTTGAATGCTT 58.577 45.000 0.00 0.00 38.79 3.91
1579 1798 1.344114 TGGCAAGGGTTTGAATGCTTC 59.656 47.619 0.00 0.00 38.79 3.86
1580 1799 1.338105 GGCAAGGGTTTGAATGCTTCC 60.338 52.381 0.00 0.00 38.79 3.46
1581 1800 1.344114 GCAAGGGTTTGAATGCTTCCA 59.656 47.619 0.00 0.00 36.36 3.53
1582 1801 2.611224 GCAAGGGTTTGAATGCTTCCAG 60.611 50.000 0.00 0.00 36.36 3.86
1583 1802 2.629617 CAAGGGTTTGAATGCTTCCAGT 59.370 45.455 0.00 0.00 36.36 4.00
1585 1804 2.893489 AGGGTTTGAATGCTTCCAGTTC 59.107 45.455 0.00 0.00 0.00 3.01
1593 1812 1.002011 GCTTCCAGTTCCACCCTCC 60.002 63.158 0.00 0.00 0.00 4.30
1604 1823 2.125269 ACCCTCCGCATTGTACGC 60.125 61.111 0.00 0.00 0.00 4.42
1661 1887 1.374125 TATGTGCTTGCGTGCGTCT 60.374 52.632 0.00 0.00 35.36 4.18
1675 1901 2.971452 GTCTCCGTCTGTCCACCC 59.029 66.667 0.00 0.00 0.00 4.61
1756 2309 7.170773 TCATTCATTCGAGTTAAATTCGTTCG 58.829 34.615 9.60 0.00 39.05 3.95
1758 2311 6.074398 TCATTCGAGTTAAATTCGTTCGTC 57.926 37.500 9.60 0.00 39.05 4.20
1769 2322 3.693300 TTCGTTCGTCAAGTTATTCGC 57.307 42.857 0.00 0.00 0.00 4.70
1770 2323 2.663808 TCGTTCGTCAAGTTATTCGCA 58.336 42.857 0.00 0.00 0.00 5.10
1772 2325 3.060230 TCGTTCGTCAAGTTATTCGCATG 59.940 43.478 0.00 0.00 0.00 4.06
1774 2327 4.665645 CGTTCGTCAAGTTATTCGCATGTT 60.666 41.667 0.00 0.00 0.00 2.71
1775 2328 4.320667 TCGTCAAGTTATTCGCATGTTG 57.679 40.909 0.00 0.00 0.00 3.33
1790 2343 1.311651 TGTTGCCATGGTGGTATGCG 61.312 55.000 14.67 0.00 40.46 4.73
1791 2344 2.413963 TTGCCATGGTGGTATGCGC 61.414 57.895 14.67 0.00 40.46 6.09
1816 2369 6.261158 CCATGCATTTGGATGATAAATTGCAA 59.739 34.615 12.94 0.00 45.22 4.08
1868 2421 9.775854 ACATCTAGATCCAATCAGTTAATCTTG 57.224 33.333 1.03 0.00 0.00 3.02
1988 2555 7.726291 TGGGTCACCTTAACAATAGAATTTTCA 59.274 33.333 0.00 0.00 37.76 2.69
1989 2556 8.581578 GGGTCACCTTAACAATAGAATTTTCAA 58.418 33.333 0.00 0.00 0.00 2.69
2039 2703 1.416401 TCCTTGGTCCAGGCGATTATC 59.584 52.381 0.00 0.00 33.35 1.75
2062 2727 7.556733 TCGCCTATATTTTCGGTATTTTTGT 57.443 32.000 0.00 0.00 0.00 2.83
2079 2756 7.759489 ATTTTTGTTGTAGTCCAGCAGATTA 57.241 32.000 0.00 0.00 35.57 1.75
2116 3190 6.015688 TGAGGCCTAATTATCGACGACTATTT 60.016 38.462 4.42 0.66 0.00 1.40
2131 3205 4.500887 CGACTATTTATTTCTGAGCCGGGA 60.501 45.833 2.18 0.00 0.00 5.14
2136 3212 0.181350 ATTTCTGAGCCGGGACATCC 59.819 55.000 2.18 0.00 0.00 3.51
2162 3238 7.321908 GCTCCCGGTAAATGGTAAATTAAAAA 58.678 34.615 0.00 0.00 0.00 1.94
2211 3306 2.715532 AAGTGCGTGATGTCCGTGCT 62.716 55.000 0.00 0.00 0.00 4.40
2228 3323 4.536065 CGTGCTAAATTTCAGCTTGTTCA 58.464 39.130 15.79 0.00 39.83 3.18
2252 3347 1.004560 CTGAGGAGCTCGTGGCAAA 60.005 57.895 14.78 0.00 44.79 3.68
2280 3379 5.446143 AAATTCAGTCCAAACAATGCGTA 57.554 34.783 0.00 0.00 0.00 4.42
2293 3392 7.305763 CCAAACAATGCGTAAACAGTAAACTTC 60.306 37.037 0.00 0.00 0.00 3.01
2309 3408 6.726764 AGTAAACTTCTCTCACAGACCCTAAT 59.273 38.462 0.00 0.00 0.00 1.73
2312 3411 5.799213 ACTTCTCTCACAGACCCTAATTTG 58.201 41.667 0.00 0.00 0.00 2.32
2313 3412 5.308237 ACTTCTCTCACAGACCCTAATTTGT 59.692 40.000 0.00 0.00 0.00 2.83
2314 3413 5.152623 TCTCTCACAGACCCTAATTTGTG 57.847 43.478 0.18 0.18 41.64 3.33
2315 3414 4.593206 TCTCTCACAGACCCTAATTTGTGT 59.407 41.667 5.78 0.00 41.19 3.72
2374 3486 3.305267 CGAAATTTGGCATGGACTTCACA 60.305 43.478 0.00 0.00 0.00 3.58
2375 3487 4.630111 GAAATTTGGCATGGACTTCACAA 58.370 39.130 0.00 0.00 0.00 3.33
2377 3489 4.686191 ATTTGGCATGGACTTCACAAAA 57.314 36.364 0.00 0.00 32.44 2.44
2454 3567 8.623310 AATTAAAACAGTTTTAGTGTTCACCG 57.377 30.769 16.30 0.00 40.60 4.94
2536 3649 6.596497 TGTTAAACACTAATAAGGCAGCCTAC 59.404 38.462 16.56 4.69 31.13 3.18
2564 3677 4.250464 TGGATCAACATACTTTGACGGTC 58.750 43.478 0.00 0.00 38.31 4.79
2567 3680 5.163854 GGATCAACATACTTTGACGGTCAAG 60.164 44.000 21.47 17.53 38.31 3.02
2568 3681 4.951254 TCAACATACTTTGACGGTCAAGA 58.049 39.130 21.47 12.71 37.70 3.02
2569 3682 5.547465 TCAACATACTTTGACGGTCAAGAT 58.453 37.500 21.47 16.24 37.70 2.40
2570 3683 5.995282 TCAACATACTTTGACGGTCAAGATT 59.005 36.000 21.47 13.11 37.70 2.40
2591 3704 5.440234 TTAGATGGAGACTTTAGCGCTAG 57.560 43.478 17.98 11.64 0.00 3.42
2594 3707 5.317808 AGATGGAGACTTTAGCGCTAGATA 58.682 41.667 17.98 6.52 0.00 1.98
2601 3714 5.463724 AGACTTTAGCGCTAGATATGTTTGC 59.536 40.000 17.98 0.90 0.00 3.68
2628 3741 2.229792 ACATTGAAACCACGTGAGCAT 58.770 42.857 19.30 0.00 0.00 3.79
2629 3742 2.226437 ACATTGAAACCACGTGAGCATC 59.774 45.455 19.30 10.12 0.00 3.91
2652 3765 9.995957 CATCGTAGGATTAGAGATATGTACAAG 57.004 37.037 0.00 0.00 0.00 3.16
2675 3788 5.705441 AGTAAGATTGATTTGGTTCTTCGCA 59.295 36.000 0.00 0.00 31.29 5.10
2707 3820 8.566260 TGCTTTTACGAGGATAGTAGATAGAAC 58.434 37.037 0.00 0.00 0.00 3.01
2714 3830 7.110810 CGAGGATAGTAGATAGAACCCATGTA 58.889 42.308 0.00 0.00 0.00 2.29
2744 3860 8.713708 ATAAGGTAGTAGATGCACTTGTCTAT 57.286 34.615 0.00 0.00 30.35 1.98
2746 3862 4.985409 GGTAGTAGATGCACTTGTCTATGC 59.015 45.833 0.00 0.00 42.40 3.14
2766 3882 8.427276 TCTATGCATCTACAATCAGACAAATCT 58.573 33.333 0.19 0.00 34.57 2.40
2769 3885 7.532571 TGCATCTACAATCAGACAAATCTTTG 58.467 34.615 1.19 1.19 43.62 2.77
2799 3915 9.032420 CCGTTTTATATGAGACTAGAGAAAACC 57.968 37.037 0.00 0.00 33.88 3.27
2825 3941 9.768662 CTTCATTCCATTTTATTTGGGATTAGG 57.231 33.333 0.00 0.00 29.40 2.69
2869 3986 0.179113 AGGGCTGTTGCAAAAACACG 60.179 50.000 0.00 0.00 41.91 4.49
2897 4014 1.592669 CCTCGAGTATGCGCAAGGG 60.593 63.158 17.11 3.43 38.28 3.95
2900 4017 1.269723 CTCGAGTATGCGCAAGGGATA 59.730 52.381 17.11 0.00 38.28 2.59
2902 4019 1.792949 CGAGTATGCGCAAGGGATAAC 59.207 52.381 17.11 4.33 30.10 1.89
2945 4062 9.480053 ACAAATGTTCCAAGATCAAACAATAAG 57.520 29.630 0.00 0.00 36.57 1.73
3006 4140 1.001597 GAGCGGTATAAGGTGAGACGG 60.002 57.143 0.00 0.00 0.00 4.79
3119 4260 3.268023 AGTAGAGCCTGAAAATTCCCG 57.732 47.619 0.00 0.00 0.00 5.14
3120 4261 2.572104 AGTAGAGCCTGAAAATTCCCGT 59.428 45.455 0.00 0.00 0.00 5.28
3128 4269 6.530120 AGCCTGAAAATTCCCGTAAAAATTT 58.470 32.000 0.00 0.00 36.81 1.82
3129 4270 7.672240 AGCCTGAAAATTCCCGTAAAAATTTA 58.328 30.769 0.00 0.00 34.78 1.40
3171 4312 3.132289 TGGTGGTCTCATCTTAATCGGAC 59.868 47.826 0.00 0.00 0.00 4.79
3207 4348 8.145767 CCATTAGATTTATGTAACCGTGTCCTA 58.854 37.037 0.00 0.00 0.00 2.94
3239 4380 4.881273 TGGACCTTACAATCATGCACATAC 59.119 41.667 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 6.602803 TGATTTTGCTAATCCATGCTTCACTA 59.397 34.615 8.88 0.00 0.00 2.74
54 55 5.653507 TGATTTTGCTAATCCATGCTTCAC 58.346 37.500 8.88 0.00 0.00 3.18
86 87 2.210116 GTGGTCAAAAGAGAACGCAGA 58.790 47.619 0.00 0.00 35.82 4.26
145 146 3.739810 CGACATGCTCATCCAGACTAATG 59.260 47.826 0.00 0.00 0.00 1.90
223 224 6.207221 TGATGGATAGAAATTGCGCATTGTAT 59.793 34.615 12.75 12.17 0.00 2.29
257 258 1.334960 CCAAACGACCTTGCACATGTC 60.335 52.381 0.00 0.00 0.00 3.06
271 272 1.574428 CGCCCAAGTCTTCCAAACG 59.426 57.895 0.00 0.00 0.00 3.60
320 325 7.064016 GTCAGCTGTCCAAATTTTGTTTTGTAA 59.936 33.333 14.67 0.00 35.30 2.41
330 335 1.247567 CCGGTCAGCTGTCCAAATTT 58.752 50.000 26.31 0.00 0.00 1.82
331 336 0.110486 ACCGGTCAGCTGTCCAAATT 59.890 50.000 26.31 7.20 0.00 1.82
358 363 2.201210 CAGTTTGGCCACCCCCTT 59.799 61.111 3.88 0.00 0.00 3.95
396 401 1.066143 CGGCAGTTTCTAGGTCCATGT 60.066 52.381 0.00 0.00 0.00 3.21
399 404 0.895530 CTCGGCAGTTTCTAGGTCCA 59.104 55.000 0.00 0.00 0.00 4.02
402 407 0.037232 GTGCTCGGCAGTTTCTAGGT 60.037 55.000 0.00 0.00 40.08 3.08
414 419 1.301677 GCCAAAGAAGAGGTGCTCGG 61.302 60.000 0.00 0.00 35.36 4.63
451 456 0.625849 CCTTCACCAAGCCCCATAGT 59.374 55.000 0.00 0.00 0.00 2.12
476 481 1.615392 GTCCAAGCTGGCAAGTTGAAT 59.385 47.619 7.16 0.00 37.47 2.57
481 486 1.152963 AACGTCCAAGCTGGCAAGT 60.153 52.632 0.00 0.00 37.47 3.16
486 491 1.447317 AACTGCAACGTCCAAGCTGG 61.447 55.000 0.00 0.00 39.43 4.85
505 510 5.364446 TGATACTCCTATAGTTCGCCCAAAA 59.636 40.000 0.00 0.00 39.80 2.44
506 511 4.897076 TGATACTCCTATAGTTCGCCCAAA 59.103 41.667 0.00 0.00 39.80 3.28
507 512 4.476297 TGATACTCCTATAGTTCGCCCAA 58.524 43.478 0.00 0.00 39.80 4.12
535 540 3.870606 GACCATGTCGAACCACCG 58.129 61.111 0.00 0.00 0.00 4.94
559 564 1.734655 GCCCTTCCATGGATCCTCTA 58.265 55.000 17.06 0.00 0.00 2.43
603 608 0.165944 CGTCCCAAATCGACTTGCAC 59.834 55.000 0.00 0.00 0.00 4.57
615 620 0.464013 TTGCGTTCCTTTCGTCCCAA 60.464 50.000 0.00 0.00 0.00 4.12
635 640 2.350007 GCATAGTTGCGTCGAAAAACCA 60.350 45.455 0.00 0.00 39.49 3.67
653 658 1.213926 GAAGGATGGTTGGAGGAGCAT 59.786 52.381 0.00 0.00 40.21 3.79
713 719 0.406361 ACCCAAATGTTTCGCCCCTA 59.594 50.000 0.00 0.00 0.00 3.53
714 720 0.898326 GACCCAAATGTTTCGCCCCT 60.898 55.000 0.00 0.00 0.00 4.79
732 738 5.810587 GCACTACTTTTCCGATAGAATGTGA 59.189 40.000 0.00 0.00 33.44 3.58
742 748 0.320073 CACCCGCACTACTTTTCCGA 60.320 55.000 0.00 0.00 0.00 4.55
748 754 2.695359 CATAACACACCCGCACTACTT 58.305 47.619 0.00 0.00 0.00 2.24
782 788 5.066593 CAGAGGACAAGAAAGTAAAAGCCT 58.933 41.667 0.00 0.00 0.00 4.58
791 797 7.553881 TTCAAAGTTACAGAGGACAAGAAAG 57.446 36.000 0.00 0.00 0.00 2.62
828 836 6.570764 GCCACCCACGTTTCATTAATTAAGAA 60.571 38.462 3.94 5.30 0.00 2.52
831 839 4.379603 CGCCACCCACGTTTCATTAATTAA 60.380 41.667 0.00 0.00 0.00 1.40
858 866 2.769893 GAGGGAGCTACTACTAGACGG 58.230 57.143 0.00 0.00 0.00 4.79
874 882 2.938539 GAATCCGACGAGTGCGAGGG 62.939 65.000 0.00 0.00 41.64 4.30
907 915 2.085320 GCAGACCTTCTCACTCTCGTA 58.915 52.381 0.00 0.00 0.00 3.43
1031 1051 1.555075 GGCCTCTGTGTGTTGGAGATA 59.445 52.381 0.00 0.00 0.00 1.98
1042 1062 2.738521 CCGAACACGGCCTCTGTG 60.739 66.667 0.00 4.17 42.99 3.66
1055 1075 0.108992 ACGATTAACTGCTCGCCGAA 60.109 50.000 0.00 0.00 38.42 4.30
1272 1297 1.736645 ATCAAAGGCCACGACGTCG 60.737 57.895 34.58 34.58 46.33 5.12
1314 1339 4.166888 AGCGTGATGGCCAGCGAT 62.167 61.111 24.92 18.57 34.34 4.58
1567 1786 3.552890 GGTGGAACTGGAAGCATTCAAAC 60.553 47.826 0.00 0.00 42.28 2.93
1577 1796 2.890766 GCGGAGGGTGGAACTGGAA 61.891 63.158 0.00 0.00 36.74 3.53
1578 1797 3.319198 GCGGAGGGTGGAACTGGA 61.319 66.667 0.00 0.00 36.74 3.86
1579 1798 2.484287 AATGCGGAGGGTGGAACTGG 62.484 60.000 0.00 0.00 36.74 4.00
1580 1799 1.002134 AATGCGGAGGGTGGAACTG 60.002 57.895 0.00 0.00 36.74 3.16
1581 1800 1.002134 CAATGCGGAGGGTGGAACT 60.002 57.895 0.00 0.00 36.74 3.01
1582 1801 0.035820 TACAATGCGGAGGGTGGAAC 60.036 55.000 0.00 0.00 0.00 3.62
1583 1802 0.035820 GTACAATGCGGAGGGTGGAA 60.036 55.000 0.00 0.00 0.00 3.53
1585 1804 1.813753 CGTACAATGCGGAGGGTGG 60.814 63.158 0.00 0.00 0.00 4.61
1604 1823 3.624326 CTCATCTGTAGAGCCTTCTCG 57.376 52.381 0.00 0.00 44.02 4.04
1626 1852 6.406370 AGCACATACTAGCACTAATTTCACA 58.594 36.000 0.00 0.00 0.00 3.58
1661 1887 1.458777 ACAAGGGTGGACAGACGGA 60.459 57.895 0.00 0.00 0.00 4.69
1675 1901 1.349026 ACACAGACCCTCCATCACAAG 59.651 52.381 0.00 0.00 0.00 3.16
1741 2294 9.247562 GAATAACTTGACGAACGAATTTAACTC 57.752 33.333 0.14 0.00 0.00 3.01
1756 2309 3.171277 GGCAACATGCGAATAACTTGAC 58.829 45.455 0.00 0.00 46.21 3.18
1758 2311 3.214697 TGGCAACATGCGAATAACTTG 57.785 42.857 0.00 0.00 46.21 3.16
1772 2325 1.433064 CGCATACCACCATGGCAAC 59.567 57.895 13.04 0.00 42.67 4.17
1774 2327 2.828095 GCGCATACCACCATGGCA 60.828 61.111 13.04 0.00 42.67 4.92
1775 2328 3.595758 GGCGCATACCACCATGGC 61.596 66.667 13.04 0.00 42.67 4.40
1790 2343 5.334569 GCAATTTATCATCCAAATGCATGGC 60.335 40.000 0.00 0.00 40.46 4.40
1791 2344 5.760743 TGCAATTTATCATCCAAATGCATGG 59.239 36.000 0.00 0.00 42.12 3.66
1816 2369 1.247567 CCGATTCACCAGCCAAAGTT 58.752 50.000 0.00 0.00 0.00 2.66
1868 2421 7.548427 GGTGGTAACTAGTGATAGGAAAAGAAC 59.452 40.741 0.00 0.00 37.61 3.01
1950 2517 4.927267 AGGTGACCCAAATCTTGTGATA 57.073 40.909 0.00 0.00 31.70 2.15
2039 2703 7.698970 ACAACAAAAATACCGAAAATATAGGCG 59.301 33.333 0.00 0.00 0.00 5.52
2052 2717 5.472137 TCTGCTGGACTACAACAAAAATACC 59.528 40.000 0.00 0.00 0.00 2.73
2062 2727 7.898014 TCTTCTATAATCTGCTGGACTACAA 57.102 36.000 0.00 0.00 0.00 2.41
2070 2735 8.881743 GCCTCATAATTCTTCTATAATCTGCTG 58.118 37.037 0.00 0.00 0.00 4.41
2116 3190 1.416401 GGATGTCCCGGCTCAGAAATA 59.584 52.381 0.00 0.00 0.00 1.40
2131 3205 0.179056 CATTTACCGGGAGCGGATGT 60.179 55.000 6.32 0.00 0.00 3.06
2136 3212 2.027003 TTTACCATTTACCGGGAGCG 57.973 50.000 6.32 0.00 0.00 5.03
2211 3306 7.587629 CAGATGTCTGAACAAGCTGAAATTTA 58.412 34.615 3.96 0.00 46.59 1.40
2228 3323 1.102154 CACGAGCTCCTCAGATGTCT 58.898 55.000 8.47 0.00 0.00 3.41
2252 3347 8.281893 CGCATTGTTTGGACTGAATTTATTTTT 58.718 29.630 0.00 0.00 0.00 1.94
2261 3360 4.096532 TGTTTACGCATTGTTTGGACTGAA 59.903 37.500 0.00 0.00 0.00 3.02
2264 3363 3.630312 ACTGTTTACGCATTGTTTGGACT 59.370 39.130 0.00 0.00 0.00 3.85
2274 3373 6.145696 GTGAGAGAAGTTTACTGTTTACGCAT 59.854 38.462 0.00 0.00 0.00 4.73
2280 3379 6.049790 GGTCTGTGAGAGAAGTTTACTGTTT 58.950 40.000 0.00 0.00 30.26 2.83
2293 3392 4.899502 ACACAAATTAGGGTCTGTGAGAG 58.100 43.478 11.62 0.00 41.35 3.20
2332 3444 2.350772 CGTGGAGTTTGGACATTTCAGC 60.351 50.000 0.00 0.00 0.00 4.26
2430 3543 7.067251 TCCGGTGAACACTAAAACTGTTTTAAT 59.933 33.333 21.99 12.92 34.93 1.40
2439 3552 3.725490 ACTCTCCGGTGAACACTAAAAC 58.275 45.455 7.75 0.00 0.00 2.43
2445 3558 2.234300 TTTGACTCTCCGGTGAACAC 57.766 50.000 7.75 2.99 0.00 3.32
2453 3566 0.600255 AGCGGTGTTTTGACTCTCCG 60.600 55.000 0.00 0.00 41.58 4.63
2454 3567 1.594331 AAGCGGTGTTTTGACTCTCC 58.406 50.000 0.00 0.00 0.00 3.71
2536 3649 6.307155 GTCAAAGTATGTTGATCCAAAGACG 58.693 40.000 0.00 0.00 39.61 4.18
2564 3677 5.176590 GCGCTAAAGTCTCCATCTAATCTTG 59.823 44.000 0.00 0.00 0.00 3.02
2567 3680 4.877282 AGCGCTAAAGTCTCCATCTAATC 58.123 43.478 8.99 0.00 0.00 1.75
2568 3681 4.946478 AGCGCTAAAGTCTCCATCTAAT 57.054 40.909 8.99 0.00 0.00 1.73
2569 3682 5.131067 TCTAGCGCTAAAGTCTCCATCTAA 58.869 41.667 19.37 0.00 0.00 2.10
2570 3683 4.715713 TCTAGCGCTAAAGTCTCCATCTA 58.284 43.478 19.37 0.00 0.00 1.98
2601 3714 3.974401 CACGTGGTTTCAATGTTTAGCAG 59.026 43.478 7.95 0.00 0.00 4.24
2612 3725 0.249699 ACGATGCTCACGTGGTTTCA 60.250 50.000 17.00 8.88 42.37 2.69
2652 3765 5.795441 GTGCGAAGAACCAAATCAATCTTAC 59.205 40.000 0.00 0.00 32.54 2.34
2690 3803 9.482175 AATACATGGGTTCTATCTACTATCCTC 57.518 37.037 0.00 0.00 0.00 3.71
2744 3860 7.391275 TCAAAGATTTGTCTGATTGTAGATGCA 59.609 33.333 5.29 0.00 39.18 3.96
2782 3898 7.038017 TGGAATGAAGGTTTTCTCTAGTCTCAT 60.038 37.037 0.00 0.00 34.31 2.90
2799 3915 9.768662 CCTAATCCCAAATAAAATGGAATGAAG 57.231 33.333 0.00 0.00 40.56 3.02
2825 3941 5.169295 CACTAACAGAGGTTTAGCTGTACC 58.831 45.833 10.27 10.27 44.06 3.34
2854 3970 1.199624 GAGGCGTGTTTTTGCAACAG 58.800 50.000 0.00 0.00 0.00 3.16
2869 3986 2.827652 CATACTCGAGGAAAAGGAGGC 58.172 52.381 18.41 0.00 32.11 4.70
2919 4036 9.480053 CTTATTGTTTGATCTTGGAACATTTGT 57.520 29.630 0.00 0.00 39.30 2.83
2991 4125 2.756760 TGTGACCCGTCTCACCTTATAC 59.243 50.000 7.13 0.00 40.02 1.47
2992 4126 3.090210 TGTGACCCGTCTCACCTTATA 57.910 47.619 7.13 0.00 40.02 0.98
3006 4140 8.149973 TGAAAACAAGTTAACTAGATGTGACC 57.850 34.615 8.92 3.79 0.00 4.02
3100 4235 2.987232 ACGGGAATTTTCAGGCTCTAC 58.013 47.619 0.00 0.00 0.00 2.59
3128 4269 8.887717 CCACCAAAAGAAATGTTCAATGTTTTA 58.112 29.630 0.00 0.00 0.00 1.52
3129 4270 7.392953 ACCACCAAAAGAAATGTTCAATGTTTT 59.607 29.630 0.00 0.00 0.00 2.43
3136 4277 4.952957 TGAGACCACCAAAAGAAATGTTCA 59.047 37.500 0.00 0.00 0.00 3.18
3137 4278 5.514274 TGAGACCACCAAAAGAAATGTTC 57.486 39.130 0.00 0.00 0.00 3.18
3207 4348 5.630121 TGATTGTAAGGTCCATTTGACAGT 58.370 37.500 0.00 0.00 46.38 3.55


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

AutoCloner maintained by Alex Coulton.