Multiple sequence alignment - TraesCS7B01G444500

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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 TraesCS7B01G444500 chr7B 100.000 3073 0 0 1 3073 708952335 708949263 0.000000e+00 5675
1 TraesCS7B01G444500 chr7A 86.574 2160 143 58 8 2060 708665760 708663641 0.000000e+00 2246
2 TraesCS7B01G444500 chr7D 90.577 1560 105 13 537 2060 615903458 615901905 0.000000e+00 2028
3 TraesCS7B01G444500 chr7D 90.086 464 40 4 81 538 615903950 615903487 5.670000e-167 597
4 TraesCS7B01G444500 chr7D 84.416 231 21 4 8 223 615904267 615904037 2.400000e-51 213
5 TraesCS7B01G444500 chr5D 97.013 837 25 0 2237 3073 378839841 378840677 0.000000e+00 1408
6 TraesCS7B01G444500 chr5D 77.888 303 63 2 1430 1730 379234801 379234501 5.230000e-43 185
7 TraesCS7B01G444500 chr5B 97.013 837 25 0 2237 3073 231809043 231808207 0.000000e+00 1408
8 TraesCS7B01G444500 chr5B 77.303 304 63 4 1430 1730 454907636 454907336 1.130000e-39 174
9 TraesCS7B01G444500 chr2B 96.894 837 26 0 2237 3073 743675452 743674616 0.000000e+00 1402
10 TraesCS7B01G444500 chr2B 96.655 837 28 0 2237 3073 90680765 90681601 0.000000e+00 1391
11 TraesCS7B01G444500 chr2B 96.416 837 30 0 2237 3073 712793753 712794589 0.000000e+00 1380
12 TraesCS7B01G444500 chr2D 96.774 837 27 0 2237 3073 613533603 613532767 0.000000e+00 1397
13 TraesCS7B01G444500 chr6B 96.301 838 30 1 2237 3073 6426463 6425626 0.000000e+00 1375
14 TraesCS7B01G444500 chr4B 96.296 837 31 0 2237 3073 19778046 19777210 0.000000e+00 1375
15 TraesCS7B01G444500 chr4A 96.195 841 28 1 2237 3073 733117378 733116538 0.000000e+00 1373
16 TraesCS7B01G444500 chr5A 75.137 728 143 31 1024 1730 479462498 479461788 1.070000e-79 307


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 TraesCS7B01G444500 chr7B 708949263 708952335 3072 True 5675 5675 100.000000 1 3073 1 chr7B.!!$R1 3072
1 TraesCS7B01G444500 chr7A 708663641 708665760 2119 True 2246 2246 86.574000 8 2060 1 chr7A.!!$R1 2052
2 TraesCS7B01G444500 chr7D 615901905 615904267 2362 True 946 2028 88.359667 8 2060 3 chr7D.!!$R1 2052
3 TraesCS7B01G444500 chr5D 378839841 378840677 836 False 1408 1408 97.013000 2237 3073 1 chr5D.!!$F1 836
4 TraesCS7B01G444500 chr5B 231808207 231809043 836 True 1408 1408 97.013000 2237 3073 1 chr5B.!!$R1 836
5 TraesCS7B01G444500 chr2B 743674616 743675452 836 True 1402 1402 96.894000 2237 3073 1 chr2B.!!$R1 836
6 TraesCS7B01G444500 chr2B 90680765 90681601 836 False 1391 1391 96.655000 2237 3073 1 chr2B.!!$F1 836
7 TraesCS7B01G444500 chr2B 712793753 712794589 836 False 1380 1380 96.416000 2237 3073 1 chr2B.!!$F2 836
8 TraesCS7B01G444500 chr2D 613532767 613533603 836 True 1397 1397 96.774000 2237 3073 1 chr2D.!!$R1 836
9 TraesCS7B01G444500 chr6B 6425626 6426463 837 True 1375 1375 96.301000 2237 3073 1 chr6B.!!$R1 836
10 TraesCS7B01G444500 chr4B 19777210 19778046 836 True 1375 1375 96.296000 2237 3073 1 chr4B.!!$R1 836
11 TraesCS7B01G444500 chr4A 733116538 733117378 840 True 1373 1373 96.195000 2237 3073 1 chr4A.!!$R1 836
12 TraesCS7B01G444500 chr5A 479461788 479462498 710 True 307 307 75.137000 1024 1730 1 chr5A.!!$R1 706

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
675 961 0.038166 GGCTTCAGGGTGGAACATCA 59.962 55.0 0.0 0.0 44.52 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2457 0.118346 TGGGTAGAAGAAGGCAGGGA 59.882 55.0 0.0 0.0 0.0 4.2 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 61 7.386299 CAGAATGTTTCTTAACTACTGTGAGCT 59.614 37.037 0.00 0.00 38.11 4.09
60 69 7.773149 TCTTAACTACTGTGAGCTCTAATTCC 58.227 38.462 16.19 0.00 0.00 3.01
155 171 8.244113 GGATTTGTTCTTCCAAACCTGTTATAG 58.756 37.037 0.00 0.00 37.16 1.31
170 186 7.541122 CCTGTTATAGGCAGTTCTCTTTAAC 57.459 40.000 5.90 0.00 40.38 2.01
174 190 9.162764 TGTTATAGGCAGTTCTCTTTAACATTC 57.837 33.333 0.00 0.00 34.74 2.67
176 192 4.985538 AGGCAGTTCTCTTTAACATTCCA 58.014 39.130 0.00 0.00 0.00 3.53
359 606 2.912956 ACCACACCCTGATCATACACTT 59.087 45.455 0.00 0.00 0.00 3.16
364 611 3.452264 CACCCTGATCATACACTTGGAGA 59.548 47.826 0.00 0.00 0.00 3.71
400 649 2.326428 TGACCGGAGAAGAAAGTCCTT 58.674 47.619 9.46 0.00 0.00 3.36
434 687 1.157870 AGGAAACCGTGTGAGTTGCG 61.158 55.000 0.00 0.00 0.00 4.85
550 833 0.563173 TGTCTAGGATAGGCCCTGCT 59.437 55.000 0.00 0.00 44.38 4.24
576 859 5.362430 TCCAATTCCAGCTTGTAAGTTGTTT 59.638 36.000 7.52 0.00 35.74 2.83
615 898 2.664851 TGAAGTTGTCGGCCTGCG 60.665 61.111 0.00 0.00 0.00 5.18
630 916 0.847670 CTGCGTGTTGTTGTGCATTG 59.152 50.000 0.00 0.00 36.64 2.82
631 917 0.172127 TGCGTGTTGTTGTGCATTGT 59.828 45.000 0.00 0.00 31.31 2.71
639 925 5.748152 GTGTTGTTGTGCATTGTGTAGAATT 59.252 36.000 0.00 0.00 0.00 2.17
675 961 0.038166 GGCTTCAGGGTGGAACATCA 59.962 55.000 0.00 0.00 44.52 3.07
680 966 0.452987 CAGGGTGGAACATCAATGCG 59.547 55.000 0.00 0.00 44.52 4.73
719 1005 2.730715 CGCCGTTCTTCTTCTGAGAGAG 60.731 54.545 0.00 0.00 32.44 3.20
734 1020 6.102663 TCTGAGAGAGAATTTCGGTTTCATC 58.897 40.000 0.00 0.00 0.00 2.92
745 1031 3.655486 TCGGTTTCATCGTTGAGCTTAA 58.345 40.909 0.00 0.00 32.27 1.85
755 1041 8.317891 TCATCGTTGAGCTTAATTAGTTTTGA 57.682 30.769 0.00 0.00 0.00 2.69
804 1123 2.012673 CTGCAGCCTCCTGTTAATGTC 58.987 52.381 0.00 0.00 41.26 3.06
864 1194 1.320507 TGTGACATGTTGCTGCACAT 58.679 45.000 11.98 6.86 37.93 3.21
906 1236 5.119125 GCATGTCTGTTCCAACAAAATTAGC 59.881 40.000 0.00 0.00 38.66 3.09
928 1258 3.751518 GGTTGGTATTTGGAGTGTGTCT 58.248 45.455 0.00 0.00 0.00 3.41
929 1259 4.561938 CGGTTGGTATTTGGAGTGTGTCTA 60.562 45.833 0.00 0.00 0.00 2.59
930 1260 5.497474 GGTTGGTATTTGGAGTGTGTCTAT 58.503 41.667 0.00 0.00 0.00 1.98
931 1261 5.354234 GGTTGGTATTTGGAGTGTGTCTATG 59.646 44.000 0.00 0.00 0.00 2.23
932 1262 4.513442 TGGTATTTGGAGTGTGTCTATGC 58.487 43.478 0.00 0.00 0.00 3.14
933 1263 4.019771 TGGTATTTGGAGTGTGTCTATGCA 60.020 41.667 0.00 0.00 0.00 3.96
934 1264 4.332819 GGTATTTGGAGTGTGTCTATGCAC 59.667 45.833 0.00 0.00 39.65 4.57
935 1265 2.078849 TTGGAGTGTGTCTATGCACG 57.921 50.000 0.00 0.00 41.94 5.34
936 1266 0.246360 TGGAGTGTGTCTATGCACGG 59.754 55.000 0.00 0.00 41.94 4.94
938 1268 1.630148 GAGTGTGTCTATGCACGGAC 58.370 55.000 12.33 12.33 41.94 4.79
939 1269 0.966179 AGTGTGTCTATGCACGGACA 59.034 50.000 16.48 16.48 41.94 4.02
1242 1601 1.153489 CCTCGTCCTCGTCGGTCTA 60.153 63.158 0.00 0.00 38.33 2.59
1269 1628 1.000612 GGACCTCCGGGAAGTCTCT 59.999 63.158 21.82 0.00 36.25 3.10
1287 1646 2.202756 GACACGATCACCTCCCGC 60.203 66.667 0.00 0.00 0.00 6.13
1377 1745 3.081804 GTTCACTCAGGTTTGGGGTATG 58.918 50.000 0.00 0.00 0.00 2.39
1384 1752 0.107361 GGTTTGGGGTATGTCGGAGG 60.107 60.000 0.00 0.00 0.00 4.30
1414 1782 3.052082 CCTGCAGGCACTTGACGG 61.052 66.667 22.33 0.00 34.60 4.79
1546 1914 2.434359 GGCGTTCTTCCACGAGGG 60.434 66.667 0.00 0.00 43.15 4.30
1547 1915 3.119096 GCGTTCTTCCACGAGGGC 61.119 66.667 0.00 0.00 43.15 5.19
1551 1919 1.906824 TTCTTCCACGAGGGCGACT 60.907 57.895 0.00 0.00 41.64 4.18
2057 2431 3.786918 GAGATCGTCGACGGCGTCC 62.787 68.421 35.05 18.93 40.29 4.79
2067 2441 2.739287 CGGCGTCCGCAAACCTTA 60.739 61.111 14.19 0.00 41.17 2.69
2068 2442 2.319096 CGGCGTCCGCAAACCTTAA 61.319 57.895 14.19 0.00 41.17 1.85
2069 2443 1.208358 GGCGTCCGCAAACCTTAAC 59.792 57.895 14.19 0.00 44.11 2.01
2070 2444 1.232621 GGCGTCCGCAAACCTTAACT 61.233 55.000 14.19 0.00 44.11 2.24
2071 2445 1.431496 GCGTCCGCAAACCTTAACTA 58.569 50.000 6.82 0.00 41.49 2.24
2072 2446 1.799994 GCGTCCGCAAACCTTAACTAA 59.200 47.619 6.82 0.00 41.49 2.24
2073 2447 2.223845 GCGTCCGCAAACCTTAACTAAA 59.776 45.455 6.82 0.00 41.49 1.85
2074 2448 3.120095 GCGTCCGCAAACCTTAACTAAAT 60.120 43.478 6.82 0.00 41.49 1.40
2075 2449 4.644954 CGTCCGCAAACCTTAACTAAATC 58.355 43.478 0.00 0.00 0.00 2.17
2076 2450 4.152759 CGTCCGCAAACCTTAACTAAATCA 59.847 41.667 0.00 0.00 0.00 2.57
2077 2451 5.334260 CGTCCGCAAACCTTAACTAAATCAA 60.334 40.000 0.00 0.00 0.00 2.57
2078 2452 6.440436 GTCCGCAAACCTTAACTAAATCAAA 58.560 36.000 0.00 0.00 0.00 2.69
2079 2453 6.919115 GTCCGCAAACCTTAACTAAATCAAAA 59.081 34.615 0.00 0.00 0.00 2.44
2080 2454 6.919115 TCCGCAAACCTTAACTAAATCAAAAC 59.081 34.615 0.00 0.00 0.00 2.43
2081 2455 6.921307 CCGCAAACCTTAACTAAATCAAAACT 59.079 34.615 0.00 0.00 0.00 2.66
2082 2456 7.436970 CCGCAAACCTTAACTAAATCAAAACTT 59.563 33.333 0.00 0.00 0.00 2.66
2083 2457 8.813282 CGCAAACCTTAACTAAATCAAAACTTT 58.187 29.630 0.00 0.00 0.00 2.66
2086 2460 9.826574 AAACCTTAACTAAATCAAAACTTTCCC 57.173 29.630 0.00 0.00 0.00 3.97
2087 2461 8.777578 ACCTTAACTAAATCAAAACTTTCCCT 57.222 30.769 0.00 0.00 0.00 4.20
2088 2462 8.638873 ACCTTAACTAAATCAAAACTTTCCCTG 58.361 33.333 0.00 0.00 0.00 4.45
2089 2463 7.598869 CCTTAACTAAATCAAAACTTTCCCTGC 59.401 37.037 0.00 0.00 0.00 4.85
2090 2464 5.468540 ACTAAATCAAAACTTTCCCTGCC 57.531 39.130 0.00 0.00 0.00 4.85
2091 2465 5.147767 ACTAAATCAAAACTTTCCCTGCCT 58.852 37.500 0.00 0.00 0.00 4.75
2092 2466 5.602561 ACTAAATCAAAACTTTCCCTGCCTT 59.397 36.000 0.00 0.00 0.00 4.35
2093 2467 4.607293 AATCAAAACTTTCCCTGCCTTC 57.393 40.909 0.00 0.00 0.00 3.46
2094 2468 3.312736 TCAAAACTTTCCCTGCCTTCT 57.687 42.857 0.00 0.00 0.00 2.85
2095 2469 3.642141 TCAAAACTTTCCCTGCCTTCTT 58.358 40.909 0.00 0.00 0.00 2.52
2096 2470 3.636764 TCAAAACTTTCCCTGCCTTCTTC 59.363 43.478 0.00 0.00 0.00 2.87
2097 2471 3.602205 AAACTTTCCCTGCCTTCTTCT 57.398 42.857 0.00 0.00 0.00 2.85
2098 2472 4.724279 AAACTTTCCCTGCCTTCTTCTA 57.276 40.909 0.00 0.00 0.00 2.10
2099 2473 3.704800 ACTTTCCCTGCCTTCTTCTAC 57.295 47.619 0.00 0.00 0.00 2.59
2100 2474 2.306219 ACTTTCCCTGCCTTCTTCTACC 59.694 50.000 0.00 0.00 0.00 3.18
2101 2475 1.286248 TTCCCTGCCTTCTTCTACCC 58.714 55.000 0.00 0.00 0.00 3.69
2102 2476 0.118346 TCCCTGCCTTCTTCTACCCA 59.882 55.000 0.00 0.00 0.00 4.51
2103 2477 1.216990 CCCTGCCTTCTTCTACCCAT 58.783 55.000 0.00 0.00 0.00 4.00
2104 2478 2.022428 TCCCTGCCTTCTTCTACCCATA 60.022 50.000 0.00 0.00 0.00 2.74
2105 2479 2.982488 CCCTGCCTTCTTCTACCCATAT 59.018 50.000 0.00 0.00 0.00 1.78
2106 2480 3.008485 CCCTGCCTTCTTCTACCCATATC 59.992 52.174 0.00 0.00 0.00 1.63
2107 2481 3.008485 CCTGCCTTCTTCTACCCATATCC 59.992 52.174 0.00 0.00 0.00 2.59
2108 2482 3.648067 CTGCCTTCTTCTACCCATATCCA 59.352 47.826 0.00 0.00 0.00 3.41
2109 2483 4.044308 TGCCTTCTTCTACCCATATCCAA 58.956 43.478 0.00 0.00 0.00 3.53
2110 2484 4.476846 TGCCTTCTTCTACCCATATCCAAA 59.523 41.667 0.00 0.00 0.00 3.28
2111 2485 5.134339 TGCCTTCTTCTACCCATATCCAAAT 59.866 40.000 0.00 0.00 0.00 2.32
2112 2486 5.707764 GCCTTCTTCTACCCATATCCAAATC 59.292 44.000 0.00 0.00 0.00 2.17
2113 2487 6.691491 GCCTTCTTCTACCCATATCCAAATCA 60.691 42.308 0.00 0.00 0.00 2.57
2114 2488 7.290061 CCTTCTTCTACCCATATCCAAATCAA 58.710 38.462 0.00 0.00 0.00 2.57
2115 2489 7.779798 CCTTCTTCTACCCATATCCAAATCAAA 59.220 37.037 0.00 0.00 0.00 2.69
2116 2490 9.359653 CTTCTTCTACCCATATCCAAATCAAAT 57.640 33.333 0.00 0.00 0.00 2.32
2117 2491 9.713684 TTCTTCTACCCATATCCAAATCAAATT 57.286 29.630 0.00 0.00 0.00 1.82
2151 2525 8.190784 ACCAAAAATCAGAAATATGATCGTTCC 58.809 33.333 0.00 0.00 39.00 3.62
2152 2526 8.190122 CCAAAAATCAGAAATATGATCGTTCCA 58.810 33.333 0.00 0.00 39.00 3.53
2153 2527 9.571810 CAAAAATCAGAAATATGATCGTTCCAA 57.428 29.630 0.00 0.00 39.00 3.53
2154 2528 9.793252 AAAAATCAGAAATATGATCGTTCCAAG 57.207 29.630 0.00 0.00 39.00 3.61
2155 2529 8.737168 AAATCAGAAATATGATCGTTCCAAGA 57.263 30.769 0.00 0.00 39.00 3.02
2156 2530 8.915057 AATCAGAAATATGATCGTTCCAAGAT 57.085 30.769 0.00 0.00 39.00 2.40
2157 2531 8.915057 ATCAGAAATATGATCGTTCCAAGATT 57.085 30.769 0.00 0.00 34.84 2.40
2158 2532 8.737168 TCAGAAATATGATCGTTCCAAGATTT 57.263 30.769 0.00 0.00 0.00 2.17
2159 2533 9.830975 TCAGAAATATGATCGTTCCAAGATTTA 57.169 29.630 0.00 0.00 0.00 1.40
2164 2538 5.966636 TGATCGTTCCAAGATTTATGTCG 57.033 39.130 0.00 0.00 0.00 4.35
2165 2539 4.270084 TGATCGTTCCAAGATTTATGTCGC 59.730 41.667 0.00 0.00 0.00 5.19
2166 2540 3.591023 TCGTTCCAAGATTTATGTCGCA 58.409 40.909 0.00 0.00 0.00 5.10
2167 2541 3.369756 TCGTTCCAAGATTTATGTCGCAC 59.630 43.478 0.00 0.00 0.00 5.34
2168 2542 3.124466 CGTTCCAAGATTTATGTCGCACA 59.876 43.478 0.00 0.00 0.00 4.57
2169 2543 4.403453 GTTCCAAGATTTATGTCGCACAC 58.597 43.478 0.00 0.00 0.00 3.82
2170 2544 2.670905 TCCAAGATTTATGTCGCACACG 59.329 45.455 0.00 0.00 42.01 4.49
2206 2580 7.996098 ACCAGTAAAATATGTATGTATGCCC 57.004 36.000 0.00 0.00 0.00 5.36
2207 2581 6.946009 ACCAGTAAAATATGTATGTATGCCCC 59.054 38.462 0.00 0.00 0.00 5.80
2208 2582 6.945435 CCAGTAAAATATGTATGTATGCCCCA 59.055 38.462 0.00 0.00 0.00 4.96
2209 2583 7.450014 CCAGTAAAATATGTATGTATGCCCCAA 59.550 37.037 0.00 0.00 0.00 4.12
2210 2584 9.023962 CAGTAAAATATGTATGTATGCCCCAAT 57.976 33.333 0.00 0.00 0.00 3.16
2211 2585 9.600432 AGTAAAATATGTATGTATGCCCCAATT 57.400 29.630 0.00 0.00 0.00 2.32
2212 2586 9.638239 GTAAAATATGTATGTATGCCCCAATTG 57.362 33.333 0.00 0.00 0.00 2.32
2213 2587 5.920193 ATATGTATGTATGCCCCAATTGC 57.080 39.130 0.00 0.00 0.00 3.56
2214 2588 3.023939 TGTATGTATGCCCCAATTGCA 57.976 42.857 0.00 0.00 43.97 4.08
2215 2589 3.369175 TGTATGTATGCCCCAATTGCAA 58.631 40.909 0.00 0.00 42.92 4.08
2216 2590 3.966006 TGTATGTATGCCCCAATTGCAAT 59.034 39.130 5.99 5.99 42.92 3.56
2217 2591 2.983907 TGTATGCCCCAATTGCAATG 57.016 45.000 13.82 7.26 42.92 2.82
2218 2592 1.134461 TGTATGCCCCAATTGCAATGC 60.134 47.619 13.82 12.43 42.92 3.56
2219 2593 1.134461 GTATGCCCCAATTGCAATGCA 60.134 47.619 20.42 20.42 42.92 3.96
2220 2594 0.548989 ATGCCCCAATTGCAATGCAT 59.451 45.000 22.49 22.49 42.92 3.96
2221 2595 0.393132 TGCCCCAATTGCAATGCATG 60.393 50.000 13.82 5.17 38.76 4.06
2222 2596 0.393267 GCCCCAATTGCAATGCATGT 60.393 50.000 13.82 0.00 38.76 3.21
2223 2597 1.134461 GCCCCAATTGCAATGCATGTA 60.134 47.619 13.82 0.00 38.76 2.29
2224 2598 2.680221 GCCCCAATTGCAATGCATGTAA 60.680 45.455 13.82 0.87 38.76 2.41
2225 2599 3.199677 CCCCAATTGCAATGCATGTAAG 58.800 45.455 13.82 0.00 38.76 2.34
2226 2600 3.118702 CCCCAATTGCAATGCATGTAAGA 60.119 43.478 13.82 0.00 38.76 2.10
2227 2601 4.443739 CCCCAATTGCAATGCATGTAAGAT 60.444 41.667 13.82 0.00 38.76 2.40
2228 2602 4.748102 CCCAATTGCAATGCATGTAAGATC 59.252 41.667 13.82 0.00 38.76 2.75
2229 2603 5.452776 CCCAATTGCAATGCATGTAAGATCT 60.453 40.000 13.82 0.00 38.76 2.75
2230 2604 5.690409 CCAATTGCAATGCATGTAAGATCTC 59.310 40.000 13.82 0.00 38.76 2.75
2231 2605 6.461092 CCAATTGCAATGCATGTAAGATCTCT 60.461 38.462 13.82 0.00 38.76 3.10
2232 2606 6.710597 ATTGCAATGCATGTAAGATCTCTT 57.289 33.333 12.09 0.00 38.76 2.85
2233 2607 7.812690 ATTGCAATGCATGTAAGATCTCTTA 57.187 32.000 12.09 0.00 38.76 2.10
2234 2608 7.812690 TTGCAATGCATGTAAGATCTCTTAT 57.187 32.000 9.39 0.00 38.32 1.73
2235 2609 8.907222 TTGCAATGCATGTAAGATCTCTTATA 57.093 30.769 9.39 1.42 38.32 0.98
2367 2742 3.831911 TCAAGAAAGAATCCCGCCAATTT 59.168 39.130 0.00 0.00 0.00 1.82
2407 2782 2.798680 CGATCTTGTGGTAGGAGTTCG 58.201 52.381 0.00 0.00 0.00 3.95
2410 2785 4.566987 GATCTTGTGGTAGGAGTTCGTTT 58.433 43.478 0.00 0.00 0.00 3.60
2484 2863 8.408043 AATGAAACTCAACAGAAATGATGGTA 57.592 30.769 0.00 0.00 0.00 3.25
2901 3280 1.410882 TGGTGCGGTGATGATCGATTA 59.589 47.619 0.00 0.00 0.00 1.75
2943 3322 6.767524 TTTATTCATGTCCGCATAGGTTTT 57.232 33.333 0.00 0.00 41.99 2.43
2962 3341 3.671008 TTGGGATCTTTTCGTCTCGAA 57.329 42.857 0.40 0.40 44.28 3.71
3006 3385 3.935203 CGCTCAAGCTTAATCTCCAGAAA 59.065 43.478 0.00 0.00 39.32 2.52
3054 3433 9.850628 GCATGCATAACTCATCAATTACATTAT 57.149 29.630 14.21 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 5.441718 AAATCAGTGGGAATTAGAGCTCA 57.558 39.130 17.77 0.00 0.00 4.26
52 61 7.831691 TTTGTGAAAATCAGTGGGAATTAGA 57.168 32.000 0.00 0.00 0.00 2.10
87 96 5.926542 GGGGCAGAAAAGAACTAAAACATTC 59.073 40.000 0.00 0.00 0.00 2.67
88 97 5.365314 TGGGGCAGAAAAGAACTAAAACATT 59.635 36.000 0.00 0.00 0.00 2.71
155 171 5.904362 ATGGAATGTTAAAGAGAACTGCC 57.096 39.130 0.00 0.00 0.00 4.85
216 463 5.459532 CCAAGTGGATGCTGCAAACAGAG 62.460 52.174 6.36 1.94 41.48 3.35
400 649 4.457466 GGTTTCCTCTTTACAAGTGTCCA 58.543 43.478 0.00 0.00 0.00 4.02
444 697 3.132139 AGAATGCTGGCGCTGCTG 61.132 61.111 21.88 6.80 36.97 4.41
542 825 2.054453 GGAATTGGACAGCAGGGCC 61.054 63.158 0.00 0.00 0.00 5.80
550 833 4.098914 ACTTACAAGCTGGAATTGGACA 57.901 40.909 0.00 0.00 31.76 4.02
563 846 5.140177 GCTCATCGACAAACAACTTACAAG 58.860 41.667 0.00 0.00 0.00 3.16
576 859 2.181777 GCTCACCGCTCATCGACA 59.818 61.111 0.00 0.00 41.67 4.35
602 885 3.276846 AACACGCAGGCCGACAAC 61.277 61.111 0.00 0.00 41.02 3.32
615 898 4.285807 TCTACACAATGCACAACAACAC 57.714 40.909 0.00 0.00 0.00 3.32
631 917 9.231297 CCTAATCACAAGGAGAAAAATTCTACA 57.769 33.333 5.20 0.00 43.38 2.74
639 925 5.630121 TGAAGCCTAATCACAAGGAGAAAA 58.370 37.500 0.00 0.00 36.08 2.29
675 961 0.927537 TCGAAATCGAATCGCGCATT 59.072 45.000 16.47 6.49 46.30 3.56
699 985 2.490115 TCTCTCTCAGAAGAAGAACGGC 59.510 50.000 0.00 0.00 0.00 5.68
700 986 4.775058 TTCTCTCTCAGAAGAAGAACGG 57.225 45.455 0.00 0.00 36.08 4.44
701 987 6.033407 CGAAATTCTCTCTCAGAAGAAGAACG 59.967 42.308 5.78 6.59 44.71 3.95
719 1005 3.846335 GCTCAACGATGAAACCGAAATTC 59.154 43.478 0.00 0.00 34.49 2.17
734 1020 8.948853 TCAATCAAAACTAATTAAGCTCAACG 57.051 30.769 0.00 0.00 0.00 4.10
755 1041 6.709397 CCACTGAATGTATACATCTGCTCAAT 59.291 38.462 18.52 6.16 35.10 2.57
886 1216 4.226761 CCGCTAATTTTGTTGGAACAGAC 58.773 43.478 0.00 0.00 42.39 3.51
906 1236 2.482721 GACACACTCCAAATACCAACCG 59.517 50.000 0.00 0.00 0.00 4.44
939 1269 5.230942 CAGTTTTGTAGTAGCAGTAGCACT 58.769 41.667 0.00 0.00 45.49 4.40
1036 1395 4.459089 GAGGACGGCCAGCCAGAC 62.459 72.222 11.69 2.35 36.29 3.51
1263 1622 2.088423 GAGGTGATCGTGTCAGAGACT 58.912 52.381 0.00 0.00 37.56 3.24
1269 1628 3.001902 GCGGGAGGTGATCGTGTCA 62.002 63.158 0.00 0.00 0.00 3.58
1536 1904 2.342279 CAAGTCGCCCTCGTGGAA 59.658 61.111 4.76 0.00 35.39 3.53
1546 1914 2.879462 CGTACGCCTCCAAGTCGC 60.879 66.667 0.52 0.00 0.00 5.19
1547 1915 1.800315 CACGTACGCCTCCAAGTCG 60.800 63.158 16.72 0.00 0.00 4.18
1773 2141 4.778415 CTGCACGTCGACCCCTCG 62.778 72.222 10.58 0.00 41.65 4.63
1831 2199 4.070552 GCCAGACCGCCGAGAAGT 62.071 66.667 0.00 0.00 0.00 3.01
2018 2386 2.649034 GACGTGTTCCTCTGCCGA 59.351 61.111 0.00 0.00 0.00 5.54
2057 2431 7.924103 AGTTTTGATTTAGTTAAGGTTTGCG 57.076 32.000 0.00 0.00 0.00 4.85
2060 2434 9.826574 GGGAAAGTTTTGATTTAGTTAAGGTTT 57.173 29.630 0.00 0.00 0.00 3.27
2061 2435 9.209048 AGGGAAAGTTTTGATTTAGTTAAGGTT 57.791 29.630 0.00 0.00 0.00 3.50
2062 2436 8.638873 CAGGGAAAGTTTTGATTTAGTTAAGGT 58.361 33.333 0.00 0.00 0.00 3.50
2063 2437 7.598869 GCAGGGAAAGTTTTGATTTAGTTAAGG 59.401 37.037 0.00 0.00 0.00 2.69
2064 2438 7.598869 GGCAGGGAAAGTTTTGATTTAGTTAAG 59.401 37.037 0.00 0.00 0.00 1.85
2065 2439 7.289084 AGGCAGGGAAAGTTTTGATTTAGTTAA 59.711 33.333 0.00 0.00 0.00 2.01
2066 2440 6.780522 AGGCAGGGAAAGTTTTGATTTAGTTA 59.219 34.615 0.00 0.00 0.00 2.24
2067 2441 5.602561 AGGCAGGGAAAGTTTTGATTTAGTT 59.397 36.000 0.00 0.00 0.00 2.24
2068 2442 5.147767 AGGCAGGGAAAGTTTTGATTTAGT 58.852 37.500 0.00 0.00 0.00 2.24
2069 2443 5.728637 AGGCAGGGAAAGTTTTGATTTAG 57.271 39.130 0.00 0.00 0.00 1.85
2070 2444 5.838521 AGAAGGCAGGGAAAGTTTTGATTTA 59.161 36.000 0.00 0.00 0.00 1.40
2071 2445 4.655649 AGAAGGCAGGGAAAGTTTTGATTT 59.344 37.500 0.00 0.00 0.00 2.17
2072 2446 4.226384 AGAAGGCAGGGAAAGTTTTGATT 58.774 39.130 0.00 0.00 0.00 2.57
2073 2447 3.849527 AGAAGGCAGGGAAAGTTTTGAT 58.150 40.909 0.00 0.00 0.00 2.57
2074 2448 3.312736 AGAAGGCAGGGAAAGTTTTGA 57.687 42.857 0.00 0.00 0.00 2.69
2075 2449 3.638627 AGAAGAAGGCAGGGAAAGTTTTG 59.361 43.478 0.00 0.00 0.00 2.44
2076 2450 3.916035 AGAAGAAGGCAGGGAAAGTTTT 58.084 40.909 0.00 0.00 0.00 2.43
2077 2451 3.602205 AGAAGAAGGCAGGGAAAGTTT 57.398 42.857 0.00 0.00 0.00 2.66
2078 2452 3.244946 GGTAGAAGAAGGCAGGGAAAGTT 60.245 47.826 0.00 0.00 0.00 2.66
2079 2453 2.306219 GGTAGAAGAAGGCAGGGAAAGT 59.694 50.000 0.00 0.00 0.00 2.66
2080 2454 2.356227 GGGTAGAAGAAGGCAGGGAAAG 60.356 54.545 0.00 0.00 0.00 2.62
2081 2455 1.633945 GGGTAGAAGAAGGCAGGGAAA 59.366 52.381 0.00 0.00 0.00 3.13
2082 2456 1.286248 GGGTAGAAGAAGGCAGGGAA 58.714 55.000 0.00 0.00 0.00 3.97
2083 2457 0.118346 TGGGTAGAAGAAGGCAGGGA 59.882 55.000 0.00 0.00 0.00 4.20
2084 2458 1.216990 ATGGGTAGAAGAAGGCAGGG 58.783 55.000 0.00 0.00 0.00 4.45
2085 2459 3.008485 GGATATGGGTAGAAGAAGGCAGG 59.992 52.174 0.00 0.00 0.00 4.85
2086 2460 3.648067 TGGATATGGGTAGAAGAAGGCAG 59.352 47.826 0.00 0.00 0.00 4.85
2087 2461 3.664320 TGGATATGGGTAGAAGAAGGCA 58.336 45.455 0.00 0.00 0.00 4.75
2088 2462 4.706842 TTGGATATGGGTAGAAGAAGGC 57.293 45.455 0.00 0.00 0.00 4.35
2089 2463 6.841601 TGATTTGGATATGGGTAGAAGAAGG 58.158 40.000 0.00 0.00 0.00 3.46
2090 2464 8.752005 TTTGATTTGGATATGGGTAGAAGAAG 57.248 34.615 0.00 0.00 0.00 2.85
2091 2465 9.713684 AATTTGATTTGGATATGGGTAGAAGAA 57.286 29.630 0.00 0.00 0.00 2.52
2125 2499 8.190784 GGAACGATCATATTTCTGATTTTTGGT 58.809 33.333 0.00 0.00 36.01 3.67
2126 2500 8.190122 TGGAACGATCATATTTCTGATTTTTGG 58.810 33.333 0.00 0.00 36.01 3.28
2127 2501 9.571810 TTGGAACGATCATATTTCTGATTTTTG 57.428 29.630 0.00 0.00 36.01 2.44
2128 2502 9.793252 CTTGGAACGATCATATTTCTGATTTTT 57.207 29.630 0.00 0.00 36.01 1.94
2129 2503 9.177608 TCTTGGAACGATCATATTTCTGATTTT 57.822 29.630 0.00 0.00 36.01 1.82
2130 2504 8.737168 TCTTGGAACGATCATATTTCTGATTT 57.263 30.769 0.00 0.00 36.01 2.17
2131 2505 8.915057 ATCTTGGAACGATCATATTTCTGATT 57.085 30.769 0.00 0.00 36.01 2.57
2132 2506 8.915057 AATCTTGGAACGATCATATTTCTGAT 57.085 30.769 0.00 0.00 38.57 2.90
2133 2507 8.737168 AAATCTTGGAACGATCATATTTCTGA 57.263 30.769 0.00 0.00 0.00 3.27
2138 2512 8.712363 CGACATAAATCTTGGAACGATCATATT 58.288 33.333 0.00 0.00 0.00 1.28
2139 2513 7.148573 GCGACATAAATCTTGGAACGATCATAT 60.149 37.037 0.00 0.00 0.00 1.78
2140 2514 6.145534 GCGACATAAATCTTGGAACGATCATA 59.854 38.462 0.00 0.00 0.00 2.15
2141 2515 5.050091 GCGACATAAATCTTGGAACGATCAT 60.050 40.000 0.00 0.00 0.00 2.45
2142 2516 4.270084 GCGACATAAATCTTGGAACGATCA 59.730 41.667 0.00 0.00 0.00 2.92
2143 2517 4.270084 TGCGACATAAATCTTGGAACGATC 59.730 41.667 0.00 0.00 0.00 3.69
2144 2518 4.034048 GTGCGACATAAATCTTGGAACGAT 59.966 41.667 0.00 0.00 0.00 3.73
2145 2519 3.369756 GTGCGACATAAATCTTGGAACGA 59.630 43.478 0.00 0.00 0.00 3.85
2146 2520 3.124466 TGTGCGACATAAATCTTGGAACG 59.876 43.478 0.00 0.00 0.00 3.95
2147 2521 4.403453 GTGTGCGACATAAATCTTGGAAC 58.597 43.478 0.00 0.00 0.00 3.62
2148 2522 3.124466 CGTGTGCGACATAAATCTTGGAA 59.876 43.478 0.00 0.00 41.33 3.53
2149 2523 2.670905 CGTGTGCGACATAAATCTTGGA 59.329 45.455 0.00 0.00 41.33 3.53
2150 2524 2.670905 TCGTGTGCGACATAAATCTTGG 59.329 45.455 0.00 0.00 42.81 3.61
2151 2525 3.989705 TCGTGTGCGACATAAATCTTG 57.010 42.857 0.00 0.00 42.81 3.02
2180 2554 8.856103 GGGCATACATACATATTTTACTGGTTT 58.144 33.333 0.00 0.00 0.00 3.27
2181 2555 7.450323 GGGGCATACATACATATTTTACTGGTT 59.550 37.037 0.00 0.00 0.00 3.67
2182 2556 6.946009 GGGGCATACATACATATTTTACTGGT 59.054 38.462 0.00 0.00 0.00 4.00
2183 2557 6.945435 TGGGGCATACATACATATTTTACTGG 59.055 38.462 0.00 0.00 0.00 4.00
2184 2558 7.994425 TGGGGCATACATACATATTTTACTG 57.006 36.000 0.00 0.00 0.00 2.74
2185 2559 9.600432 AATTGGGGCATACATACATATTTTACT 57.400 29.630 0.00 0.00 0.00 2.24
2186 2560 9.638239 CAATTGGGGCATACATACATATTTTAC 57.362 33.333 0.00 0.00 0.00 2.01
2187 2561 8.310382 GCAATTGGGGCATACATACATATTTTA 58.690 33.333 7.72 0.00 0.00 1.52
2188 2562 7.160726 GCAATTGGGGCATACATACATATTTT 58.839 34.615 7.72 0.00 0.00 1.82
2189 2563 6.269538 TGCAATTGGGGCATACATACATATTT 59.730 34.615 7.72 0.00 36.11 1.40
2190 2564 5.779260 TGCAATTGGGGCATACATACATATT 59.221 36.000 7.72 0.00 36.11 1.28
2191 2565 5.331906 TGCAATTGGGGCATACATACATAT 58.668 37.500 7.72 0.00 36.11 1.78
2192 2566 4.734266 TGCAATTGGGGCATACATACATA 58.266 39.130 7.72 0.00 36.11 2.29
2193 2567 3.574749 TGCAATTGGGGCATACATACAT 58.425 40.909 7.72 0.00 36.11 2.29
2194 2568 3.023939 TGCAATTGGGGCATACATACA 57.976 42.857 7.72 0.00 36.11 2.29
2195 2569 4.309099 CATTGCAATTGGGGCATACATAC 58.691 43.478 9.83 0.00 41.58 2.39
2196 2570 3.244146 GCATTGCAATTGGGGCATACATA 60.244 43.478 9.83 0.00 41.58 2.29
2197 2571 2.485835 GCATTGCAATTGGGGCATACAT 60.486 45.455 9.83 0.00 41.58 2.29
2198 2572 1.134461 GCATTGCAATTGGGGCATACA 60.134 47.619 9.83 0.00 41.58 2.29
2199 2573 1.134461 TGCATTGCAATTGGGGCATAC 60.134 47.619 15.85 0.00 41.58 2.39
2200 2574 1.201424 TGCATTGCAATTGGGGCATA 58.799 45.000 15.85 0.00 41.58 3.14
2201 2575 0.548989 ATGCATTGCAATTGGGGCAT 59.451 45.000 22.49 22.49 43.62 4.40
2202 2576 0.393132 CATGCATTGCAATTGGGGCA 60.393 50.000 20.42 20.42 43.62 5.36
2203 2577 0.393267 ACATGCATTGCAATTGGGGC 60.393 50.000 16.46 10.81 43.62 5.80
2204 2578 2.983907 TACATGCATTGCAATTGGGG 57.016 45.000 16.46 0.00 43.62 4.96
2205 2579 4.126208 TCTTACATGCATTGCAATTGGG 57.874 40.909 16.46 6.68 43.62 4.12
2206 2580 5.597806 AGATCTTACATGCATTGCAATTGG 58.402 37.500 16.46 8.25 43.62 3.16
2207 2581 6.504398 AGAGATCTTACATGCATTGCAATTG 58.496 36.000 16.46 12.79 43.62 2.32
2208 2582 6.710597 AGAGATCTTACATGCATTGCAATT 57.289 33.333 16.46 7.96 43.62 2.32
2209 2583 6.710597 AAGAGATCTTACATGCATTGCAAT 57.289 33.333 16.46 5.99 36.87 3.56
2210 2584 7.812690 ATAAGAGATCTTACATGCATTGCAA 57.187 32.000 16.46 0.00 40.55 4.08
2211 2585 8.907222 TTATAAGAGATCTTACATGCATTGCA 57.093 30.769 14.72 14.72 41.03 4.08
2212 2586 9.985318 GATTATAAGAGATCTTACATGCATTGC 57.015 33.333 0.00 0.46 40.81 3.56
2214 2588 9.376075 CGGATTATAAGAGATCTTACATGCATT 57.624 33.333 0.00 0.00 40.81 3.56
2215 2589 8.753133 TCGGATTATAAGAGATCTTACATGCAT 58.247 33.333 4.47 0.00 40.81 3.96
2216 2590 8.029522 GTCGGATTATAAGAGATCTTACATGCA 58.970 37.037 4.47 0.00 40.81 3.96
2217 2591 7.219154 CGTCGGATTATAAGAGATCTTACATGC 59.781 40.741 4.47 5.17 40.81 4.06
2218 2592 7.219154 GCGTCGGATTATAAGAGATCTTACATG 59.781 40.741 4.47 0.00 40.81 3.21
2219 2593 7.121463 AGCGTCGGATTATAAGAGATCTTACAT 59.879 37.037 4.47 1.04 40.81 2.29
2220 2594 6.430308 AGCGTCGGATTATAAGAGATCTTACA 59.570 38.462 4.47 0.00 40.81 2.41
2221 2595 6.844254 AGCGTCGGATTATAAGAGATCTTAC 58.156 40.000 4.47 0.00 40.81 2.34
2222 2596 7.823310 AGTAGCGTCGGATTATAAGAGATCTTA 59.177 37.037 4.84 4.84 42.04 2.10
2223 2597 5.968528 AGCGTCGGATTATAAGAGATCTT 57.031 39.130 0.00 0.07 39.85 2.40
2224 2598 6.092944 CAGTAGCGTCGGATTATAAGAGATCT 59.907 42.308 0.00 0.00 0.00 2.75
2225 2599 6.252281 CAGTAGCGTCGGATTATAAGAGATC 58.748 44.000 0.00 0.00 0.00 2.75
2226 2600 5.124138 CCAGTAGCGTCGGATTATAAGAGAT 59.876 44.000 0.00 0.00 0.00 2.75
2227 2601 4.454847 CCAGTAGCGTCGGATTATAAGAGA 59.545 45.833 0.00 0.00 0.00 3.10
2228 2602 4.724303 CCAGTAGCGTCGGATTATAAGAG 58.276 47.826 0.00 0.00 0.00 2.85
2229 2603 3.057736 GCCAGTAGCGTCGGATTATAAGA 60.058 47.826 0.00 0.00 0.00 2.10
2230 2604 3.243336 GCCAGTAGCGTCGGATTATAAG 58.757 50.000 0.00 0.00 0.00 1.73
2231 2605 3.293311 GCCAGTAGCGTCGGATTATAA 57.707 47.619 0.00 0.00 0.00 0.98
2233 2607 3.888093 GCCAGTAGCGTCGGATTAT 57.112 52.632 0.00 0.00 0.00 1.28
2283 2657 7.125391 AGTTGATTTCAATTGCTAGGGGATTA 58.875 34.615 0.00 0.00 38.24 1.75
2407 2782 1.132640 GACGTGGCAGATGCGAAAC 59.867 57.895 0.00 0.00 43.26 2.78
2410 2785 0.459899 ATTAGACGTGGCAGATGCGA 59.540 50.000 0.00 0.00 43.26 5.10
2798 3177 1.269051 GCAGGGTTTGGAAACAGTTCG 60.269 52.381 4.71 0.00 44.54 3.95
2888 3267 9.478019 CAACAAGTAAGTTTAATCGATCATCAC 57.522 33.333 0.00 0.00 0.00 3.06
2890 3269 9.907576 CTCAACAAGTAAGTTTAATCGATCATC 57.092 33.333 0.00 0.00 0.00 2.92
2924 3303 2.752354 CCAAAACCTATGCGGACATGAA 59.248 45.455 0.00 0.00 37.04 2.57
2962 3341 4.468713 GGGGACTAGTAACCGTCTTAGAT 58.531 47.826 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.