Multiple sequence alignment - TraesCS4D01G268300

Loading Multiple Alignment...

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 TraesCS4D01G268300 chr4D 100.000 3379 0 0 1 3379 439690251 439693629 0.000000e+00 6240.0
1 TraesCS4D01G268300 chr4A 89.118 2380 117 61 1079 3379 29021648 29023964 0.000000e+00 2830.0
2 TraesCS4D01G268300 chr4A 86.152 751 72 14 1 738 29020446 29021177 0.000000e+00 782.0
3 TraesCS4D01G268300 chr4A 89.434 265 10 5 723 983 29021304 29021554 5.440000e-83 318.0
4 TraesCS4D01G268300 chr4A 98.039 51 1 0 976 1026 29021584 29021634 4.640000e-14 89.8
5 TraesCS4D01G268300 chr4B 86.935 2610 188 84 220 2756 544036291 544038820 0.000000e+00 2789.0
6 TraesCS4D01G268300 chr4B 91.313 518 37 6 2867 3379 544039137 544039651 0.000000e+00 701.0
7 TraesCS4D01G268300 chr4B 96.591 88 3 0 118 205 495532482 495532395 2.720000e-31 147.0
8 TraesCS4D01G268300 chrUn 96.591 88 3 0 118 205 357881909 357881996 2.720000e-31 147.0
9 TraesCS4D01G268300 chrUn 96.591 88 3 0 118 205 417449748 417449661 2.720000e-31 147.0
10 TraesCS4D01G268300 chrUn 96.591 88 3 0 118 205 430333676 430333589 2.720000e-31 147.0
11 TraesCS4D01G268300 chrUn 96.591 88 3 0 118 205 439482732 439482645 2.720000e-31 147.0
12 TraesCS4D01G268300 chr7D 96.591 88 3 0 118 205 578996046 578996133 2.720000e-31 147.0
13 TraesCS4D01G268300 chr6D 96.591 88 3 0 118 205 283192711 283192798 2.720000e-31 147.0
14 TraesCS4D01G268300 chr1D 96.591 88 3 0 118 205 212434134 212434221 2.720000e-31 147.0
15 TraesCS4D01G268300 chr1D 96.591 88 3 0 118 205 351062958 351062871 2.720000e-31 147.0
16 TraesCS4D01G268300 chr5A 80.000 120 18 4 1 115 331341897 331342015 2.160000e-12 84.2


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 TraesCS4D01G268300 chr4D 439690251 439693629 3378 False 6240.00 6240 100.00000 1 3379 1 chr4D.!!$F1 3378
1 TraesCS4D01G268300 chr4A 29020446 29023964 3518 False 1004.95 2830 90.68575 1 3379 4 chr4A.!!$F1 3378
2 TraesCS4D01G268300 chr4B 544036291 544039651 3360 False 1745.00 2789 89.12400 220 3379 2 chr4B.!!$F1 3159

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
129 139 0.037303 TTACCCGACTCACGAGGACT 59.963 55.0 0.0 0.0 45.77 3.85 F
1010 1215 0.099613 CCAGACGAGATGACGGACTG 59.900 60.0 0.0 0.0 39.38 3.51 F
2113 2435 0.328258 CGTCCCCACCATTCCTCTTT 59.672 55.0 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1066 1271 0.108804 TTCGTGCCCTTCATCTCGTC 60.109 55.0 0.0 0.0 0.00 4.20 R
2226 2554 0.185901 AGAAGGGCAGGAGCAAAACA 59.814 50.0 0.0 0.0 44.61 2.83 R
3151 3736 0.748450 TATCCCGTAAGTTGCCTCCG 59.252 55.0 0.0 0.0 0.00 4.63 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
27 28 6.803807 GCTCTAATTGAGTCAAATTCCACAAC 59.196 38.462 10.14 0.00 44.41 3.32
28 29 7.522073 GCTCTAATTGAGTCAAATTCCACAACA 60.522 37.037 10.14 0.00 44.41 3.33
29 30 8.231692 TCTAATTGAGTCAAATTCCACAACAA 57.768 30.769 10.14 0.00 32.16 2.83
30 31 8.859090 TCTAATTGAGTCAAATTCCACAACAAT 58.141 29.630 10.14 0.00 32.16 2.71
33 34 8.991243 ATTGAGTCAAATTCCACAACAATATG 57.009 30.769 10.14 0.00 0.00 1.78
34 35 6.389091 TGAGTCAAATTCCACAACAATATGC 58.611 36.000 0.00 0.00 0.00 3.14
35 36 6.209192 TGAGTCAAATTCCACAACAATATGCT 59.791 34.615 0.00 0.00 0.00 3.79
64 74 3.568007 CCTCTCCATTTTTCACCGTGAAA 59.432 43.478 20.42 20.42 43.84 2.69
66 76 3.004315 TCTCCATTTTTCACCGTGAAAGC 59.996 43.478 22.47 0.00 45.77 3.51
88 98 3.320610 TCTCTCAATCCCTCCCTACTG 57.679 52.381 0.00 0.00 0.00 2.74
101 111 1.679032 CCCTACTGCTTTCTTTCCCGG 60.679 57.143 0.00 0.00 0.00 5.73
102 112 1.278127 CCTACTGCTTTCTTTCCCGGA 59.722 52.381 0.73 0.00 0.00 5.14
108 118 1.523758 CTTTCTTTCCCGGACACAGG 58.476 55.000 0.73 0.00 0.00 4.00
109 119 0.841289 TTTCTTTCCCGGACACAGGT 59.159 50.000 0.73 0.00 0.00 4.00
116 126 1.375013 CCGGACACAGGTTTACCCG 60.375 63.158 0.00 0.00 38.74 5.28
122 132 1.069668 ACACAGGTTTACCCGACTCAC 59.930 52.381 0.00 0.00 38.74 3.51
129 139 0.037303 TTACCCGACTCACGAGGACT 59.963 55.000 0.00 0.00 45.77 3.85
132 142 1.213013 CCGACTCACGAGGACTTGG 59.787 63.158 0.00 0.00 45.77 3.61
148 158 6.360618 AGGACTTGGCTATTCAATAAAGGAG 58.639 40.000 0.00 0.00 0.00 3.69
152 162 5.310409 TGGCTATTCAATAAAGGAGGGAG 57.690 43.478 0.00 0.00 0.00 4.30
194 204 5.652014 GTCCAAGAATATTCCATTGGTGTCA 59.348 40.000 24.84 11.43 42.32 3.58
235 247 7.821846 GCCATGAAATTAAGAACATAAACCCAA 59.178 33.333 0.00 0.00 0.00 4.12
246 258 2.721425 TAAACCCAATAGCCCGGAAG 57.279 50.000 0.73 0.00 0.00 3.46
283 296 8.548721 GTCCAAACTCATTTCGTATTCGATAAT 58.451 33.333 0.00 0.00 45.65 1.28
287 300 8.657074 AACTCATTTCGTATTCGATAATCCAA 57.343 30.769 0.00 0.00 45.65 3.53
290 303 6.425721 TCATTTCGTATTCGATAATCCAACCC 59.574 38.462 0.00 0.00 45.65 4.11
313 326 6.127394 CCCTACAAGAAAGAGGGTACTAGTTC 60.127 46.154 0.00 0.00 44.42 3.01
321 334 1.755380 AGGGTACTAGTTCACGATGGC 59.245 52.381 0.00 0.00 0.00 4.40
417 430 1.677576 CGTGTTCGGTATAGGGTGCTA 59.322 52.381 0.00 0.00 0.00 3.49
421 434 1.888215 TCGGTATAGGGTGCTACTCG 58.112 55.000 0.00 0.00 0.00 4.18
426 439 0.260816 ATAGGGTGCTACTCGGGACA 59.739 55.000 0.00 0.00 0.00 4.02
440 453 3.809013 GACATGGGCATCCGGGGT 61.809 66.667 0.00 0.00 35.24 4.95
446 459 3.530260 GGCATCCGGGGTGCAATG 61.530 66.667 31.73 11.15 44.25 2.82
500 514 1.682684 CCTAGGCGTGGTCAGGTCT 60.683 63.158 0.00 3.32 35.19 3.85
540 557 4.696402 ACTCCTCTAGACGTTAAGAGTGTG 59.304 45.833 20.35 15.69 38.03 3.82
550 567 3.935203 CGTTAAGAGTGTGCATTGATCCT 59.065 43.478 0.00 0.00 0.00 3.24
584 601 2.110213 TGGTTGTGTGACGGAGGC 59.890 61.111 0.00 0.00 0.00 4.70
653 670 5.009854 AGTCTTAAGAGCTCAAGATCAGC 57.990 43.478 17.77 5.42 33.57 4.26
680 697 2.583593 GATGGCCACGACGAGCTC 60.584 66.667 8.16 2.73 0.00 4.09
682 699 3.649277 ATGGCCACGACGAGCTCAC 62.649 63.158 8.16 6.19 0.00 3.51
684 701 4.357947 GCCACGACGAGCTCACCA 62.358 66.667 15.40 0.00 0.00 4.17
685 702 2.338620 CCACGACGAGCTCACCAA 59.661 61.111 15.40 0.00 0.00 3.67
686 703 2.022129 CCACGACGAGCTCACCAAC 61.022 63.158 15.40 0.00 0.00 3.77
688 705 2.201022 ACGACGAGCTCACCAACCT 61.201 57.895 15.40 0.00 0.00 3.50
689 706 1.734477 CGACGAGCTCACCAACCTG 60.734 63.158 15.40 0.00 0.00 4.00
690 707 1.666011 GACGAGCTCACCAACCTGA 59.334 57.895 15.40 0.00 0.00 3.86
691 708 0.389166 GACGAGCTCACCAACCTGAG 60.389 60.000 15.40 0.00 40.73 3.35
692 709 1.115930 ACGAGCTCACCAACCTGAGT 61.116 55.000 15.40 0.00 40.03 3.41
700 717 1.003233 CACCAACCTGAGTAACCTCCC 59.997 57.143 0.00 0.00 36.86 4.30
707 724 0.895530 TGAGTAACCTCCCGCTCTTG 59.104 55.000 0.00 0.00 36.86 3.02
725 742 1.179152 TGGTCCGATCGAGTTTAGCA 58.821 50.000 18.66 9.15 0.00 3.49
789 953 1.303643 GCCCCACTAAAGTGCAGCT 60.304 57.895 4.53 0.00 44.34 4.24
915 1083 4.785453 GCTGCACCGGCCTAGCTT 62.785 66.667 14.94 0.00 36.44 3.74
936 1104 0.234625 AAACGCGTCGTACGTCTACA 59.765 50.000 14.44 0.00 44.30 2.74
971 1139 1.002011 GGCTTCCGCTTTTCTCCCT 60.002 57.895 0.00 0.00 36.09 4.20
976 1144 1.131303 TCCGCTTTTCTCCCTTCCCA 61.131 55.000 0.00 0.00 0.00 4.37
1010 1215 0.099613 CCAGACGAGATGACGGACTG 59.900 60.000 0.00 0.00 39.38 3.51
1027 1232 4.719369 GCACCGACTCGCCGTCTT 62.719 66.667 0.00 0.00 40.59 3.01
1028 1233 2.805353 CACCGACTCGCCGTCTTG 60.805 66.667 0.00 0.00 40.59 3.02
1029 1234 4.719369 ACCGACTCGCCGTCTTGC 62.719 66.667 0.00 0.00 40.59 4.01
1032 1237 4.719369 GACTCGCCGTCTTGCCGT 62.719 66.667 0.00 0.00 39.61 5.68
1038 1243 4.680237 CCGTCTTGCCGTGCTGGA 62.680 66.667 0.00 0.00 42.00 3.86
1073 1278 3.532155 GGAGCGGCCAGACGAGAT 61.532 66.667 2.24 0.00 36.34 2.75
1074 1279 2.279120 GAGCGGCCAGACGAGATG 60.279 66.667 2.24 0.00 35.47 2.90
1075 1280 2.755876 AGCGGCCAGACGAGATGA 60.756 61.111 2.24 0.00 35.47 2.92
1076 1281 2.184322 GCGGCCAGACGAGATGAA 59.816 61.111 2.24 0.00 35.47 2.57
1077 1282 1.880340 GCGGCCAGACGAGATGAAG 60.880 63.158 2.24 0.00 35.47 3.02
1164 1369 4.292178 CTGGGGCTCGAGATCCGC 62.292 72.222 18.75 17.16 38.37 5.54
1336 1555 3.257933 GCGACAGCAAGGTTCCTG 58.742 61.111 0.00 0.00 44.35 3.86
1346 1565 2.680339 GCAAGGTTCCTGCTCAACTATC 59.320 50.000 0.00 0.00 0.00 2.08
1347 1566 3.620966 GCAAGGTTCCTGCTCAACTATCT 60.621 47.826 0.00 0.00 0.00 1.98
1348 1567 4.383118 GCAAGGTTCCTGCTCAACTATCTA 60.383 45.833 0.00 0.00 0.00 1.98
1377 1628 4.305001 CGATAGAATCGCATGCTCTTTC 57.695 45.455 17.13 14.43 46.55 2.62
1378 1629 3.986572 CGATAGAATCGCATGCTCTTTCT 59.013 43.478 22.14 22.14 46.55 2.52
1379 1630 4.447054 CGATAGAATCGCATGCTCTTTCTT 59.553 41.667 23.08 14.84 46.55 2.52
1410 1661 3.632145 TGTGTTCCTTTCTTTCTTGGCTC 59.368 43.478 0.00 0.00 0.00 4.70
1467 1727 1.550524 TCCTGGCCATATACAGATCGC 59.449 52.381 5.51 0.00 36.86 4.58
1565 1825 1.084370 CGACGCCTTGGTCAAGATCC 61.084 60.000 11.87 0.47 40.79 3.36
1659 1919 4.748600 CCAGGTATATATGATGCATCTGCG 59.251 45.833 26.32 4.97 45.83 5.18
1662 1922 2.766345 TATATGATGCATCTGCGGCA 57.234 45.000 26.32 7.11 46.66 5.69
1681 1941 2.807108 GCAGGAGTCCGTCTTTGTTTCT 60.807 50.000 2.76 0.00 0.00 2.52
1726 2008 3.622612 TCATGGTGATGCGACTAACAATG 59.377 43.478 0.00 0.00 0.00 2.82
1727 2009 3.326836 TGGTGATGCGACTAACAATGA 57.673 42.857 0.00 0.00 0.00 2.57
1729 2011 4.260985 TGGTGATGCGACTAACAATGAAT 58.739 39.130 0.00 0.00 0.00 2.57
1730 2012 4.094739 TGGTGATGCGACTAACAATGAATG 59.905 41.667 0.00 0.00 0.00 2.67
1787 2080 0.750546 TCCGAGCGGTACAGTGCTAT 60.751 55.000 8.96 0.00 42.60 2.97
1791 2084 2.464865 GAGCGGTACAGTGCTATTCAG 58.535 52.381 6.49 0.00 42.60 3.02
1852 2145 3.417101 TGCAACGATGTTATTCCAAGGT 58.583 40.909 0.00 0.00 0.00 3.50
1853 2146 4.580868 TGCAACGATGTTATTCCAAGGTA 58.419 39.130 0.00 0.00 0.00 3.08
1854 2147 5.004448 TGCAACGATGTTATTCCAAGGTAA 58.996 37.500 0.00 0.00 0.00 2.85
1891 2191 4.877823 TGGTTGATCTTGATTTCTCCATCG 59.122 41.667 0.00 0.00 0.00 3.84
1905 2205 3.315470 TCTCCATCGTAGGTTTCGATCTG 59.685 47.826 0.00 0.00 44.49 2.90
1906 2206 2.128035 CCATCGTAGGTTTCGATCTGC 58.872 52.381 0.00 0.00 44.49 4.26
1914 2214 3.024547 AGGTTTCGATCTGCAGCTACTA 58.975 45.455 9.47 0.00 0.00 1.82
1915 2215 3.117046 GGTTTCGATCTGCAGCTACTAC 58.883 50.000 9.47 2.64 0.00 2.73
1916 2216 3.181485 GGTTTCGATCTGCAGCTACTACT 60.181 47.826 9.47 0.00 0.00 2.57
1917 2217 4.036498 GGTTTCGATCTGCAGCTACTACTA 59.964 45.833 9.47 0.00 0.00 1.82
1918 2218 4.815040 TTCGATCTGCAGCTACTACTAC 57.185 45.455 9.47 0.00 0.00 2.73
1919 2219 4.074627 TCGATCTGCAGCTACTACTACT 57.925 45.455 9.47 0.00 0.00 2.57
1926 2242 6.887013 TCTGCAGCTACTACTACTAAGTACT 58.113 40.000 9.47 0.00 37.15 2.73
1928 2244 8.481314 TCTGCAGCTACTACTACTAAGTACTAA 58.519 37.037 9.47 0.00 37.15 2.24
1937 2253 7.821846 ACTACTACTAAGTACTAACGCTTCACT 59.178 37.037 0.00 0.00 37.15 3.41
1947 2263 5.302360 ACTAACGCTTCACTTGAACCATTA 58.698 37.500 0.00 0.00 0.00 1.90
2101 2423 3.327404 GAAGAAGCCCCGTCCCCA 61.327 66.667 0.00 0.00 0.00 4.96
2111 2433 1.995626 CCGTCCCCACCATTCCTCT 60.996 63.158 0.00 0.00 0.00 3.69
2113 2435 0.328258 CGTCCCCACCATTCCTCTTT 59.672 55.000 0.00 0.00 0.00 2.52
2166 2491 2.357637 GCTCAGCAAACACAGGTAAACA 59.642 45.455 0.00 0.00 0.00 2.83
2210 2538 0.461961 GACTCCCAAGTGATCGGAGG 59.538 60.000 15.47 3.12 46.32 4.30
2214 2542 1.599047 CCAAGTGATCGGAGGCTGT 59.401 57.895 0.00 0.00 0.00 4.40
2215 2543 0.460987 CCAAGTGATCGGAGGCTGTC 60.461 60.000 0.00 0.00 0.00 3.51
2216 2544 0.534412 CAAGTGATCGGAGGCTGTCT 59.466 55.000 0.00 0.00 0.00 3.41
2217 2545 0.534412 AAGTGATCGGAGGCTGTCTG 59.466 55.000 0.00 0.00 0.00 3.51
2280 2610 3.974871 AACAACGCACGGTTTTTCTAT 57.025 38.095 0.00 0.00 36.49 1.98
2287 2617 4.023536 ACGCACGGTTTTTCTATGATTTGT 60.024 37.500 0.00 0.00 0.00 2.83
2340 2673 3.357079 GCACCCAGTTGCAGGACG 61.357 66.667 0.00 0.00 42.49 4.79
2341 2674 3.357079 CACCCAGTTGCAGGACGC 61.357 66.667 0.00 0.00 42.89 5.19
2342 2675 4.988598 ACCCAGTTGCAGGACGCG 62.989 66.667 3.53 3.53 46.97 6.01
2343 2676 4.680237 CCCAGTTGCAGGACGCGA 62.680 66.667 15.93 0.00 46.97 5.87
2344 2677 2.434884 CCAGTTGCAGGACGCGAT 60.435 61.111 15.93 0.00 46.97 4.58
2345 2678 2.034879 CCAGTTGCAGGACGCGATT 61.035 57.895 15.93 0.00 46.97 3.34
2346 2679 1.421485 CAGTTGCAGGACGCGATTC 59.579 57.895 15.93 0.00 46.97 2.52
2347 2680 1.005037 AGTTGCAGGACGCGATTCA 60.005 52.632 15.93 0.00 46.97 2.57
2348 2681 1.016130 AGTTGCAGGACGCGATTCAG 61.016 55.000 15.93 0.00 46.97 3.02
2440 2773 3.133901 AGATGCCATACACGGTACATTCA 59.866 43.478 0.00 0.00 0.00 2.57
2443 2776 3.437395 TGCCATACACGGTACATTCAAAC 59.563 43.478 0.00 0.00 0.00 2.93
2444 2777 3.437395 GCCATACACGGTACATTCAAACA 59.563 43.478 0.00 0.00 0.00 2.83
2445 2778 4.083217 GCCATACACGGTACATTCAAACAA 60.083 41.667 0.00 0.00 0.00 2.83
2446 2779 5.392595 GCCATACACGGTACATTCAAACAAT 60.393 40.000 0.00 0.00 0.00 2.71
2576 2910 4.261741 GCATTGCCCAATGGTAGTAGATTG 60.262 45.833 19.31 0.00 46.14 2.67
2590 2924 6.018994 GGTAGTAGATTGTTGGAAATGTAGCG 60.019 42.308 0.00 0.00 0.00 4.26
2610 2944 2.596112 CGCGATCTCGAAGCAGATTTTG 60.596 50.000 0.00 0.00 43.02 2.44
2761 3095 5.104735 AGGTCAGAGTTAAAGCTGGATTAGG 60.105 44.000 0.00 0.00 33.05 2.69
2829 3402 4.937620 TCTTTTCATGCTAGTGATGGTGAC 59.062 41.667 0.00 0.00 0.00 3.67
2842 3415 0.104120 TGGTGACTCGTCCACAAGTG 59.896 55.000 0.00 0.00 36.31 3.16
2859 3433 4.224433 CAAGTGTGCTGCTATTTGAGTTG 58.776 43.478 0.00 0.00 0.00 3.16
2860 3434 3.743521 AGTGTGCTGCTATTTGAGTTGA 58.256 40.909 0.00 0.00 0.00 3.18
2861 3435 3.750130 AGTGTGCTGCTATTTGAGTTGAG 59.250 43.478 0.00 0.00 0.00 3.02
2862 3436 3.076621 TGTGCTGCTATTTGAGTTGAGG 58.923 45.455 0.00 0.00 0.00 3.86
2863 3437 3.077359 GTGCTGCTATTTGAGTTGAGGT 58.923 45.455 0.00 0.00 0.00 3.85
2864 3438 3.126000 GTGCTGCTATTTGAGTTGAGGTC 59.874 47.826 0.00 0.00 0.00 3.85
2865 3439 2.680339 GCTGCTATTTGAGTTGAGGTCC 59.320 50.000 0.00 0.00 0.00 4.46
2870 3444 3.710209 ATTTGAGTTGAGGTCCTGGAG 57.290 47.619 0.00 0.00 0.00 3.86
2877 3451 3.328050 AGTTGAGGTCCTGGAGTTTAAGG 59.672 47.826 0.00 0.00 34.65 2.69
2880 3454 4.094476 TGAGGTCCTGGAGTTTAAGGTAG 58.906 47.826 0.00 0.00 34.94 3.18
2885 3466 5.267587 GTCCTGGAGTTTAAGGTAGAGGTA 58.732 45.833 0.00 0.00 34.94 3.08
2933 3514 0.036022 AAGTCAGCCTCACCTGCTTC 59.964 55.000 0.00 0.00 36.81 3.86
2981 3562 3.356290 GGTTAATGAACTGGCAGGTGAT 58.644 45.455 20.34 9.51 35.74 3.06
3015 3596 2.172717 GCAATAGGAACTTCCCCAGCTA 59.827 50.000 4.01 0.00 41.75 3.32
3051 3632 0.473755 TGGAAACAAGCAGAGCTCCA 59.526 50.000 10.93 0.00 38.25 3.86
3081 3666 7.807977 AGAGATAAGAAACAGCAGACAAAAA 57.192 32.000 0.00 0.00 0.00 1.94
3096 3681 5.576774 CAGACAAAAAGAAGTCCAAACCAAC 59.423 40.000 0.00 0.00 35.38 3.77
3124 3709 9.567848 AGGTTGCAACAATTTATTTTATACTCG 57.432 29.630 29.55 0.00 0.00 4.18
3151 3736 5.638234 AGCCACTAGAATCACTTAACGTTTC 59.362 40.000 5.91 0.00 0.00 2.78
3284 3869 5.073965 AGGGGTTTATGTACAGAGGACAAAA 59.926 40.000 0.33 0.00 0.00 2.44
3331 3916 1.029681 AAGTGCAAAAGGACGGGTTC 58.970 50.000 0.00 0.00 0.00 3.62
3356 3942 5.048643 CGTCGTGATCCTTAGATTGGATACT 60.049 44.000 0.00 0.00 43.68 2.12
3358 3944 7.308408 CGTCGTGATCCTTAGATTGGATACTAA 60.308 40.741 0.00 0.00 43.68 2.24
3373 3959 5.747545 TGGATACTAACAAAGCAAGGCTTCA 60.748 40.000 3.67 0.00 43.14 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 50 3.146066 CACGGTGAAAAATGGAGAGGAA 58.854 45.455 0.74 0.00 0.00 3.36
41 51 2.370519 TCACGGTGAAAAATGGAGAGGA 59.629 45.455 8.68 0.00 0.00 3.71
44 54 3.004315 GCTTTCACGGTGAAAAATGGAGA 59.996 43.478 29.76 11.44 44.69 3.71
64 74 1.009429 AGGGAGGGATTGAGAGAAGCT 59.991 52.381 0.00 0.00 0.00 3.74
66 76 3.640967 CAGTAGGGAGGGATTGAGAGAAG 59.359 52.174 0.00 0.00 0.00 2.85
88 98 0.875059 CTGTGTCCGGGAAAGAAAGC 59.125 55.000 0.00 0.00 0.00 3.51
101 111 1.342174 TGAGTCGGGTAAACCTGTGTC 59.658 52.381 7.83 6.62 43.01 3.67
102 112 1.069668 GTGAGTCGGGTAAACCTGTGT 59.930 52.381 7.83 0.00 43.01 3.72
108 118 0.883833 TCCTCGTGAGTCGGGTAAAC 59.116 55.000 0.00 0.00 38.54 2.01
109 119 0.883833 GTCCTCGTGAGTCGGGTAAA 59.116 55.000 0.00 0.00 38.54 2.01
116 126 1.174783 TAGCCAAGTCCTCGTGAGTC 58.825 55.000 0.00 0.00 0.00 3.36
122 132 5.237344 CCTTTATTGAATAGCCAAGTCCTCG 59.763 44.000 0.00 0.00 0.00 4.63
129 139 5.193728 ACTCCCTCCTTTATTGAATAGCCAA 59.806 40.000 0.00 0.00 0.00 4.52
132 142 5.930135 TGACTCCCTCCTTTATTGAATAGC 58.070 41.667 0.00 0.00 0.00 2.97
148 158 0.606604 TAAGGCTCACGTTGACTCCC 59.393 55.000 0.00 0.00 0.00 4.30
152 162 0.320697 ACCCTAAGGCTCACGTTGAC 59.679 55.000 0.00 0.00 36.11 3.18
176 186 7.516198 AATAGCTGACACCAATGGAATATTC 57.484 36.000 6.16 6.93 0.00 1.75
208 218 6.475402 GGGTTTATGTTCTTAATTTCATGGCG 59.525 38.462 0.00 0.00 0.00 5.69
209 219 7.327214 TGGGTTTATGTTCTTAATTTCATGGC 58.673 34.615 0.00 0.00 0.00 4.40
214 224 9.529325 GGCTATTGGGTTTATGTTCTTAATTTC 57.471 33.333 0.00 0.00 0.00 2.17
217 227 6.264518 CGGGCTATTGGGTTTATGTTCTTAAT 59.735 38.462 0.00 0.00 0.00 1.40
255 267 5.697178 TCGAATACGAAATGAGTTTGGACAA 59.303 36.000 0.00 0.00 45.74 3.18
283 296 2.642807 CCCTCTTTCTTGTAGGGTTGGA 59.357 50.000 0.00 0.00 44.34 3.53
290 303 7.314393 GTGAACTAGTACCCTCTTTCTTGTAG 58.686 42.308 0.00 0.00 0.00 2.74
321 334 2.516930 ATCAAGGGATTGCCGCCG 60.517 61.111 0.00 0.00 33.83 6.46
328 341 3.703052 GACAATGGCTTCATCAAGGGATT 59.297 43.478 0.00 0.00 0.00 3.01
371 384 2.158249 TCAACATCCCCATTCCAAACCA 60.158 45.455 0.00 0.00 0.00 3.67
403 416 0.879765 CCGAGTAGCACCCTATACCG 59.120 60.000 0.00 0.00 0.00 4.02
409 422 1.001760 ATGTCCCGAGTAGCACCCT 59.998 57.895 0.00 0.00 0.00 4.34
417 430 2.746375 GGATGCCCATGTCCCGAGT 61.746 63.158 0.00 0.00 0.00 4.18
421 434 4.586235 CCCGGATGCCCATGTCCC 62.586 72.222 0.73 0.00 0.00 4.46
446 459 1.554042 AACCGTCGACGATGTTGCAC 61.554 55.000 37.65 0.00 43.02 4.57
500 514 0.470766 AGTCGGCAAGTGGGTTGTAA 59.529 50.000 0.00 0.00 38.55 2.41
550 567 1.210967 ACCACAACTCCAAAACCGAGA 59.789 47.619 0.00 0.00 0.00 4.04
680 697 1.003233 GGGAGGTTACTCAGGTTGGTG 59.997 57.143 0.00 0.00 45.81 4.17
682 699 0.249398 CGGGAGGTTACTCAGGTTGG 59.751 60.000 0.00 0.00 45.81 3.77
684 701 0.544595 AGCGGGAGGTTACTCAGGTT 60.545 55.000 0.00 0.00 45.81 3.50
685 702 0.971447 GAGCGGGAGGTTACTCAGGT 60.971 60.000 0.00 0.00 45.81 4.00
686 703 0.684805 AGAGCGGGAGGTTACTCAGG 60.685 60.000 0.00 0.00 45.81 3.86
688 705 0.895530 CAAGAGCGGGAGGTTACTCA 59.104 55.000 0.00 0.00 45.81 3.41
689 706 0.175989 CCAAGAGCGGGAGGTTACTC 59.824 60.000 0.00 0.00 43.00 2.59
690 707 0.544595 ACCAAGAGCGGGAGGTTACT 60.545 55.000 0.00 0.00 43.00 2.24
691 708 0.108281 GACCAAGAGCGGGAGGTTAC 60.108 60.000 0.00 0.00 43.00 2.50
692 709 1.262640 GGACCAAGAGCGGGAGGTTA 61.263 60.000 0.00 0.00 43.00 2.85
707 724 2.223735 TGATGCTAAACTCGATCGGACC 60.224 50.000 16.41 0.00 0.00 4.46
789 953 2.988684 GGGATTGCGGTTGGTGCA 60.989 61.111 0.00 0.00 41.38 4.57
898 1066 4.785453 AAGCTAGGCCGGTGCAGC 62.785 66.667 17.31 5.64 40.13 5.25
900 1068 2.404566 TTTGAAGCTAGGCCGGTGCA 62.405 55.000 17.31 3.64 40.13 4.57
901 1069 1.674322 TTTGAAGCTAGGCCGGTGC 60.674 57.895 1.90 9.17 0.00 5.01
902 1070 1.635663 CGTTTGAAGCTAGGCCGGTG 61.636 60.000 1.90 0.00 0.00 4.94
903 1071 1.375523 CGTTTGAAGCTAGGCCGGT 60.376 57.895 1.90 0.00 0.00 5.28
904 1072 2.750888 GCGTTTGAAGCTAGGCCGG 61.751 63.158 0.00 0.00 0.00 6.13
905 1073 2.785258 GCGTTTGAAGCTAGGCCG 59.215 61.111 0.00 0.00 0.00 6.13
906 1074 1.967597 GACGCGTTTGAAGCTAGGCC 61.968 60.000 15.53 0.00 0.00 5.19
907 1075 1.420312 GACGCGTTTGAAGCTAGGC 59.580 57.895 15.53 0.00 0.00 3.93
908 1076 1.007336 ACGACGCGTTTGAAGCTAGG 61.007 55.000 15.53 0.00 36.35 3.02
909 1077 1.316735 GTACGACGCGTTTGAAGCTAG 59.683 52.381 15.53 0.00 41.54 3.42
910 1078 1.330306 GTACGACGCGTTTGAAGCTA 58.670 50.000 15.53 0.00 41.54 3.32
911 1079 1.602877 CGTACGACGCGTTTGAAGCT 61.603 55.000 15.53 0.00 41.54 3.74
1056 1261 3.532155 ATCTCGTCTGGCCGCTCC 61.532 66.667 0.00 0.00 0.00 4.70
1058 1263 2.290122 CTTCATCTCGTCTGGCCGCT 62.290 60.000 0.00 0.00 0.00 5.52
1059 1264 1.880340 CTTCATCTCGTCTGGCCGC 60.880 63.158 0.00 0.00 0.00 6.53
1060 1265 1.227089 CCTTCATCTCGTCTGGCCG 60.227 63.158 0.00 0.00 0.00 6.13
1062 1267 1.522580 GCCCTTCATCTCGTCTGGC 60.523 63.158 0.00 0.00 0.00 4.85
1063 1268 0.460987 GTGCCCTTCATCTCGTCTGG 60.461 60.000 0.00 0.00 0.00 3.86
1064 1269 0.803768 CGTGCCCTTCATCTCGTCTG 60.804 60.000 0.00 0.00 0.00 3.51
1065 1270 0.965866 TCGTGCCCTTCATCTCGTCT 60.966 55.000 0.00 0.00 0.00 4.18
1066 1271 0.108804 TTCGTGCCCTTCATCTCGTC 60.109 55.000 0.00 0.00 0.00 4.20
1067 1272 0.389948 GTTCGTGCCCTTCATCTCGT 60.390 55.000 0.00 0.00 0.00 4.18
1068 1273 1.413767 CGTTCGTGCCCTTCATCTCG 61.414 60.000 0.00 0.00 0.00 4.04
1069 1274 1.084370 CCGTTCGTGCCCTTCATCTC 61.084 60.000 0.00 0.00 0.00 2.75
1070 1275 1.079127 CCGTTCGTGCCCTTCATCT 60.079 57.895 0.00 0.00 0.00 2.90
1071 1276 2.750888 GCCGTTCGTGCCCTTCATC 61.751 63.158 0.00 0.00 0.00 2.92
1072 1277 2.746277 GCCGTTCGTGCCCTTCAT 60.746 61.111 0.00 0.00 0.00 2.57
1164 1369 3.764466 AGACGCAGGAAGGGCTCG 61.764 66.667 0.00 0.00 0.00 5.03
1336 1555 4.550422 TCGATGTGCATAGATAGTTGAGC 58.450 43.478 0.00 0.00 0.00 4.26
1376 1627 5.714806 AGAAAGGAACACAAAGAAACCAAGA 59.285 36.000 0.00 0.00 0.00 3.02
1377 1628 5.965922 AGAAAGGAACACAAAGAAACCAAG 58.034 37.500 0.00 0.00 0.00 3.61
1378 1629 5.993748 AGAAAGGAACACAAAGAAACCAA 57.006 34.783 0.00 0.00 0.00 3.67
1379 1630 5.993748 AAGAAAGGAACACAAAGAAACCA 57.006 34.783 0.00 0.00 0.00 3.67
1410 1661 9.956720 AGAAGATAACAATCAACAAAACAAGAG 57.043 29.630 0.00 0.00 0.00 2.85
1565 1825 2.636830 GATGTTGGACCAGAGGATGTG 58.363 52.381 0.00 0.00 0.00 3.21
1615 1875 0.171231 TCCTCAGCGTGTCGAATCTG 59.829 55.000 0.00 0.00 0.00 2.90
1659 1919 0.250338 AACAAAGACGGACTCCTGCC 60.250 55.000 0.00 0.00 0.00 4.85
1662 1922 2.037381 GGAGAAACAAAGACGGACTCCT 59.963 50.000 0.00 0.00 39.20 3.69
1681 1941 6.215431 TGATGATCCTCTCTGTTTAAAAGGGA 59.785 38.462 3.59 2.55 0.00 4.20
1787 2080 1.303074 CTTGCTGCTGGAGGCTGAA 60.303 57.895 0.00 0.00 41.52 3.02
1791 2084 3.441290 CTGCTTGCTGCTGGAGGC 61.441 66.667 11.93 11.93 43.37 4.70
1853 2146 9.071276 CAAGATCAACCATGGCTTACTATTATT 57.929 33.333 13.04 0.00 0.00 1.40
1854 2147 8.439971 TCAAGATCAACCATGGCTTACTATTAT 58.560 33.333 13.04 0.00 0.00 1.28
1891 2191 2.301577 AGCTGCAGATCGAAACCTAC 57.698 50.000 20.43 0.00 0.00 3.18
1905 2205 7.563270 CGTTAGTACTTAGTAGTAGTAGCTGC 58.437 42.308 0.00 0.00 41.49 5.25
1906 2206 7.437862 AGCGTTAGTACTTAGTAGTAGTAGCTG 59.562 40.741 20.88 7.88 41.49 4.24
1914 2214 7.173907 TCAAGTGAAGCGTTAGTACTTAGTAGT 59.826 37.037 0.00 5.02 38.44 2.73
1915 2215 7.524912 TCAAGTGAAGCGTTAGTACTTAGTAG 58.475 38.462 0.00 0.00 31.01 2.57
1916 2216 7.439157 TCAAGTGAAGCGTTAGTACTTAGTA 57.561 36.000 0.00 0.00 31.01 1.82
1917 2217 6.323203 TCAAGTGAAGCGTTAGTACTTAGT 57.677 37.500 0.00 0.00 31.01 2.24
1918 2218 6.089150 GGTTCAAGTGAAGCGTTAGTACTTAG 59.911 42.308 0.00 0.00 41.76 2.18
1919 2219 5.922544 GGTTCAAGTGAAGCGTTAGTACTTA 59.077 40.000 0.00 0.00 41.76 2.24
1947 2263 4.664688 AAGGTCCTGGAGATTGAACAAT 57.335 40.909 0.00 0.00 0.00 2.71
2101 2423 2.040544 CGCGCCAAAGAGGAATGGT 61.041 57.895 0.00 0.00 41.22 3.55
2166 2491 5.819991 TGGAGAATGACCAGAATTTTAGCT 58.180 37.500 0.00 0.00 33.22 3.32
2226 2554 0.185901 AGAAGGGCAGGAGCAAAACA 59.814 50.000 0.00 0.00 44.61 2.83
2280 2610 0.472471 GGATCGGCCCCTACAAATCA 59.528 55.000 0.00 0.00 0.00 2.57
2304 2637 1.687123 GCCCCAGTACTCATGATACGT 59.313 52.381 0.00 0.00 0.00 3.57
2342 2675 3.123804 ACGAATATGTGCCGACTGAATC 58.876 45.455 0.00 0.00 0.00 2.52
2343 2676 3.179443 ACGAATATGTGCCGACTGAAT 57.821 42.857 0.00 0.00 0.00 2.57
2344 2677 2.665649 ACGAATATGTGCCGACTGAA 57.334 45.000 0.00 0.00 0.00 3.02
2345 2678 2.536365 GAACGAATATGTGCCGACTGA 58.464 47.619 0.00 0.00 0.00 3.41
2346 2679 1.593006 GGAACGAATATGTGCCGACTG 59.407 52.381 0.00 0.00 0.00 3.51
2347 2680 1.480954 AGGAACGAATATGTGCCGACT 59.519 47.619 0.00 0.00 42.97 4.18
2348 2681 1.935933 AGGAACGAATATGTGCCGAC 58.064 50.000 0.00 0.00 42.97 4.79
2410 2743 4.100344 ACCGTGTATGGCATCTATACAACA 59.900 41.667 1.65 0.00 41.26 3.33
2423 2756 5.614923 TTGTTTGAATGTACCGTGTATGG 57.385 39.130 0.00 0.00 0.00 2.74
2440 2773 5.850557 TGTGACAAGACCATTGATTGTTT 57.149 34.783 0.00 0.00 37.29 2.83
2443 2776 6.499234 TGTATGTGACAAGACCATTGATTG 57.501 37.500 0.00 0.00 34.15 2.67
2501 2834 4.154228 TCGTTTTCGTTTATATGACGCG 57.846 40.909 3.53 3.53 44.46 6.01
2576 2910 1.933853 AGATCGCGCTACATTTCCAAC 59.066 47.619 5.56 0.00 0.00 3.77
2590 2924 2.966509 CAAAATCTGCTTCGAGATCGC 58.033 47.619 0.00 0.00 39.60 4.58
2610 2944 3.309954 GGTCAGATCGTCCAAATTGTAGC 59.690 47.826 0.00 0.00 0.00 3.58
2617 2951 0.613260 CCCAGGTCAGATCGTCCAAA 59.387 55.000 6.63 0.00 0.00 3.28
2761 3095 6.645700 TTTTTGTTCTTTCACAACTGCATC 57.354 33.333 0.00 0.00 36.36 3.91
2829 3402 1.835483 GCAGCACACTTGTGGACGAG 61.835 60.000 11.27 0.00 45.72 4.18
2842 3415 3.077359 ACCTCAACTCAAATAGCAGCAC 58.923 45.455 0.00 0.00 0.00 4.40
2859 3433 4.351127 TCTACCTTAAACTCCAGGACCTC 58.649 47.826 0.00 0.00 33.90 3.85
2860 3434 4.354662 CTCTACCTTAAACTCCAGGACCT 58.645 47.826 0.00 0.00 33.90 3.85
2861 3435 3.451540 CCTCTACCTTAAACTCCAGGACC 59.548 52.174 0.00 0.00 33.90 4.46
2862 3436 4.095211 ACCTCTACCTTAAACTCCAGGAC 58.905 47.826 0.00 0.00 33.90 3.85
2863 3437 4.415224 ACCTCTACCTTAAACTCCAGGA 57.585 45.455 0.00 0.00 33.90 3.86
2864 3438 5.270794 AGTACCTCTACCTTAAACTCCAGG 58.729 45.833 0.00 0.00 36.10 4.45
2865 3439 6.095720 CAGAGTACCTCTACCTTAAACTCCAG 59.904 46.154 0.00 0.00 38.99 3.86
2870 3444 7.407393 ACATCAGAGTACCTCTACCTTAAAC 57.593 40.000 0.00 0.00 38.99 2.01
2877 3451 2.032722 CGCGACATCAGAGTACCTCTAC 60.033 54.545 0.00 0.00 38.99 2.59
2880 3454 1.015109 TCGCGACATCAGAGTACCTC 58.985 55.000 3.71 0.00 0.00 3.85
2885 3466 2.159240 TGCTAAATCGCGACATCAGAGT 60.159 45.455 12.93 0.00 0.00 3.24
2933 3514 1.582502 GACGTCCAGAAGTTTATCGCG 59.417 52.381 3.51 0.00 0.00 5.87
2981 3562 3.653164 TCCTATTGCCTATGTGGTGAGA 58.347 45.455 0.00 0.00 38.35 3.27
3015 3596 2.278245 TCCAAGGTTCCCTGATGATGT 58.722 47.619 0.00 0.00 32.13 3.06
3051 3632 6.648725 GTCTGCTGTTTCTTATCTCTTGACTT 59.351 38.462 0.00 0.00 0.00 3.01
3124 3709 5.638234 ACGTTAAGTGATTCTAGTGGCTTTC 59.362 40.000 0.00 0.00 0.00 2.62
3131 3716 6.017400 TCCGAAACGTTAAGTGATTCTAGT 57.983 37.500 0.00 0.00 0.00 2.57
3151 3736 0.748450 TATCCCGTAAGTTGCCTCCG 59.252 55.000 0.00 0.00 0.00 4.63
3209 3794 0.959372 CACCTGCTGAGCTTGAAGGG 60.959 60.000 16.31 6.95 31.98 3.95
3284 3869 4.095932 TCTTGCTCGAACATACGTCATACT 59.904 41.667 0.00 0.00 34.70 2.12
3331 3916 2.361119 TCCAATCTAAGGATCACGACGG 59.639 50.000 0.00 0.00 0.00 4.79
3333 3918 6.334102 AGTATCCAATCTAAGGATCACGAC 57.666 41.667 0.00 0.00 44.54 4.34
3334 3919 7.504574 TGTTAGTATCCAATCTAAGGATCACGA 59.495 37.037 0.00 0.00 44.54 4.35
3335 3920 7.658261 TGTTAGTATCCAATCTAAGGATCACG 58.342 38.462 0.00 0.00 44.54 4.35
3336 3921 9.832445 TTTGTTAGTATCCAATCTAAGGATCAC 57.168 33.333 0.00 0.00 44.54 3.06
3341 3927 8.506168 TTGCTTTGTTAGTATCCAATCTAAGG 57.494 34.615 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.