Multiple sequence alignment - TraesCS6D01G316600

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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 TraesCS6D01G316600 chr6D 100.000 4122 0 0 1 4122 425905186 425901065 0.000000e+00 7613.0
1 TraesCS6D01G316600 chr6D 93.878 98 6 0 506 603 425910598 425910501 9.230000e-32 148.0
2 TraesCS6D01G316600 chr6D 84.416 77 12 0 1566 1642 330157795 330157719 4.420000e-10 76.8
3 TraesCS6D01G316600 chr6B 89.861 3156 160 72 319 3397 640981008 640977936 0.000000e+00 3908.0
4 TraesCS6D01G316600 chr6B 91.995 737 42 13 3392 4122 640977759 640977034 0.000000e+00 1018.0
5 TraesCS6D01G316600 chr6B 88.060 201 14 5 22 214 640981386 640981188 3.210000e-56 230.0
6 TraesCS6D01G316600 chr6B 91.411 163 13 1 357 518 641022954 641022792 5.360000e-54 222.0
7 TraesCS6D01G316600 chr6B 84.242 165 6 8 3175 3335 640977933 640977785 4.300000e-30 143.0
8 TraesCS6D01G316600 chr6B 86.486 74 10 0 1557 1630 490255451 490255524 9.500000e-12 82.4
9 TraesCS6D01G316600 chr6B 100.000 28 0 0 1 28 640981420 640981393 7.000000e-03 52.8
10 TraesCS6D01G316600 chr6A 92.607 2029 104 27 2125 4122 570382840 570380827 0.000000e+00 2874.0
11 TraesCS6D01G316600 chr6A 90.936 2008 96 42 209 2157 570384836 570382856 0.000000e+00 2621.0
12 TraesCS6D01G316600 chr6A 84.250 400 37 11 217 603 570388357 570387971 2.340000e-97 366.0
13 TraesCS6D01G316600 chr6A 89.904 208 11 7 22 221 570385075 570384870 4.090000e-65 259.0
14 TraesCS6D01G316600 chr6A 82.584 178 17 7 233 406 570388584 570388417 1.190000e-30 145.0
15 TraesCS6D01G316600 chr6A 86.047 86 12 0 1557 1642 469432538 469432453 4.390000e-15 93.5
16 TraesCS6D01G316600 chr5D 86.733 505 38 12 2064 2557 39347732 39347246 6.070000e-148 534.0
17 TraesCS6D01G316600 chr5D 95.522 67 3 0 2626 2692 39347247 39347181 1.570000e-19 108.0
18 TraesCS6D01G316600 chr7A 86.079 431 51 8 2418 2842 119702674 119702247 4.860000e-124 455.0
19 TraesCS6D01G316600 chr7A 80.114 352 48 18 1303 1639 119703738 119703394 4.120000e-60 243.0
20 TraesCS6D01G316600 chr7A 83.770 191 26 5 2431 2618 561603388 561603200 4.230000e-40 176.0
21 TraesCS6D01G316600 chr7A 80.882 136 26 0 1140 1275 670004720 670004855 1.570000e-19 108.0
22 TraesCS6D01G316600 chr7D 85.814 430 54 6 2418 2842 115048475 115048048 2.260000e-122 449.0
23 TraesCS6D01G316600 chr7D 79.832 357 47 19 1303 1639 115049493 115049142 1.920000e-58 237.0
24 TraesCS6D01G316600 chr7D 83.770 191 26 5 2431 2618 495852001 495851813 4.230000e-40 176.0
25 TraesCS6D01G316600 chr7D 95.522 67 3 0 2626 2692 259964270 259964336 1.570000e-19 108.0
26 TraesCS6D01G316600 chr7B 85.615 431 53 8 2418 2842 74598517 74598090 1.050000e-120 444.0
27 TraesCS6D01G316600 chr7B 83.246 191 27 5 2431 2618 524228498 524228310 1.970000e-38 171.0
28 TraesCS6D01G316600 chr5B 87.500 296 25 4 2176 2463 679342786 679342495 8.540000e-87 331.0
29 TraesCS6D01G316600 chr5B 97.753 89 2 0 2751 2839 679342501 679342413 1.980000e-33 154.0
30 TraesCS6D01G316600 chr5B 95.652 92 4 0 2751 2842 545985475 545985566 9.230000e-32 148.0
31 TraesCS6D01G316600 chr4B 84.175 297 20 10 2063 2350 626050618 626050340 3.160000e-66 263.0
32 TraesCS6D01G316600 chr3B 81.126 302 18 16 2063 2351 87483882 87483607 5.400000e-49 206.0
33 TraesCS6D01G316600 chr3B 79.402 301 25 13 2063 2351 308418346 308418621 1.180000e-40 178.0
34 TraesCS6D01G316600 chr2B 97.802 91 2 0 2751 2841 18322827 18322737 1.530000e-34 158.0
35 TraesCS6D01G316600 chr1B 95.652 92 4 0 2751 2842 617704876 617704785 9.230000e-32 148.0
36 TraesCS6D01G316600 chr1B 85.075 134 12 3 2223 2348 78315837 78315970 3.340000e-26 130.0
37 TraesCS6D01G316600 chr3D 81.884 138 18 7 2546 2680 609739091 609738958 4.360000e-20 110.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G316600 chr6D 425901065 425905186 4121 True 7613.00 7613 100.0000 1 4122 1 chr6D.!!$R2 4121
1 TraesCS6D01G316600 chr6B 640977034 640981420 4386 True 1070.36 3908 90.8316 1 4122 5 chr6B.!!$R2 4121
2 TraesCS6D01G316600 chr6A 570380827 570388584 7757 True 1253.00 2874 88.0562 22 4122 5 chr6A.!!$R2 4100
3 TraesCS6D01G316600 chr5D 39347181 39347732 551 True 321.00 534 91.1275 2064 2692 2 chr5D.!!$R1 628
4 TraesCS6D01G316600 chr7A 119702247 119703738 1491 True 349.00 455 83.0965 1303 2842 2 chr7A.!!$R2 1539
5 TraesCS6D01G316600 chr7D 115048048 115049493 1445 True 343.00 449 82.8230 1303 2842 2 chr7D.!!$R2 1539

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
676 4291 0.037590 CTCCATCCGACCAACCCAAA 59.962 55.0 0.00 0.0 0.0 3.28 F
1636 5289 0.103208 ACATCCTGCTCGAATCGGTC 59.897 55.0 1.76 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 5294 0.031111 TGGTAGGGATGGTGGAGGAG 60.031 60.0 0.0 0.0 0.0 3.69 R
3140 7181 0.459585 AACTCACGCACACACGAACT 60.460 50.0 0.0 0.0 36.7 3.01 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
19 20 2.880963 CCAAACGCTTCCTTTCCAAA 57.119 45.000 0.00 0.00 0.00 3.28
21 22 3.123050 CCAAACGCTTCCTTTCCAAAAG 58.877 45.455 0.00 0.00 0.00 2.27
22 23 2.509052 AACGCTTCCTTTCCAAAAGC 57.491 45.000 0.00 0.00 41.51 3.51
25 26 2.338140 GCTTCCTTTCCAAAAGCGAG 57.662 50.000 0.00 0.00 36.41 5.03
26 27 1.880027 GCTTCCTTTCCAAAAGCGAGA 59.120 47.619 0.00 0.00 36.41 4.04
27 28 2.095516 GCTTCCTTTCCAAAAGCGAGAG 60.096 50.000 0.00 0.00 36.41 3.20
28 29 2.930826 TCCTTTCCAAAAGCGAGAGT 57.069 45.000 0.00 0.00 0.00 3.24
29 30 3.208747 TCCTTTCCAAAAGCGAGAGTT 57.791 42.857 0.00 0.00 0.00 3.01
33 3526 0.762418 TCCAAAAGCGAGAGTTCCCA 59.238 50.000 0.00 0.00 0.00 4.37
35 3528 0.875059 CAAAAGCGAGAGTTCCCACC 59.125 55.000 0.00 0.00 0.00 4.61
94 3590 9.031360 CATTTTCTTCCATCATCATCATCAAAC 57.969 33.333 0.00 0.00 0.00 2.93
193 3695 1.000506 GACGTTGCCAGTTACCTCAGA 59.999 52.381 0.00 0.00 0.00 3.27
197 3699 1.352083 TGCCAGTTACCTCAGAAGCT 58.648 50.000 0.00 0.00 0.00 3.74
199 3701 2.233922 TGCCAGTTACCTCAGAAGCTAC 59.766 50.000 0.00 0.00 0.00 3.58
200 3702 2.498078 GCCAGTTACCTCAGAAGCTACT 59.502 50.000 0.00 0.00 0.00 2.57
202 3704 3.131400 CCAGTTACCTCAGAAGCTACTCC 59.869 52.174 0.00 0.00 0.00 3.85
214 3716 1.905215 AGCTACTCCAAGATGCAGTGT 59.095 47.619 0.00 0.00 0.00 3.55
237 3787 4.605640 AAAAATGGCTACAGTGTGCATT 57.394 36.364 5.88 7.52 0.00 3.56
254 3804 0.109643 ATTACAGCGCGACACGTACA 60.110 50.000 12.10 0.00 46.11 2.90
258 3808 0.795358 CAGCGCGACACGTACATACA 60.795 55.000 12.10 0.00 46.11 2.29
273 3824 7.438160 CACGTACATACAACATCCTTGTCATAT 59.562 37.037 0.00 0.00 34.06 1.78
274 3825 8.635328 ACGTACATACAACATCCTTGTCATATA 58.365 33.333 0.00 0.00 34.06 0.86
275 3826 9.639601 CGTACATACAACATCCTTGTCATATAT 57.360 33.333 0.00 0.00 34.06 0.86
293 3845 8.410912 GTCATATATACATACTGGCCGATTGTA 58.589 37.037 0.00 4.15 0.00 2.41
294 3846 8.410912 TCATATATACATACTGGCCGATTGTAC 58.589 37.037 0.00 0.00 0.00 2.90
295 3847 4.948341 ATACATACTGGCCGATTGTACA 57.052 40.909 0.00 0.00 0.00 2.90
332 3884 4.021822 CGAAATTGCAGTATACTTGCACG 58.978 43.478 21.82 18.62 38.37 5.34
446 4037 2.776312 TTTCCTACAGCTAGCGATCG 57.224 50.000 11.69 11.69 0.00 3.69
447 4038 1.963172 TTCCTACAGCTAGCGATCGA 58.037 50.000 21.57 0.00 0.00 3.59
486 4077 1.675720 AACCCAAGCCAGCACACAAC 61.676 55.000 0.00 0.00 0.00 3.32
487 4078 2.126596 CCCAAGCCAGCACACAACA 61.127 57.895 0.00 0.00 0.00 3.33
646 4261 2.036731 TGACCACGACCCGATCCT 59.963 61.111 0.00 0.00 0.00 3.24
647 4262 2.050350 TGACCACGACCCGATCCTC 61.050 63.158 0.00 0.00 0.00 3.71
648 4263 2.758737 ACCACGACCCGATCCTCC 60.759 66.667 0.00 0.00 0.00 4.30
675 4290 1.682849 CTCCATCCGACCAACCCAA 59.317 57.895 0.00 0.00 0.00 4.12
676 4291 0.037590 CTCCATCCGACCAACCCAAA 59.962 55.000 0.00 0.00 0.00 3.28
680 4295 0.186386 ATCCGACCAACCCAAAACCA 59.814 50.000 0.00 0.00 0.00 3.67
691 4306 5.278266 CCAACCCAAAACCACGCTATATATG 60.278 44.000 0.00 0.00 0.00 1.78
755 4370 3.071874 TCTTGTCAACCCATCATCCAC 57.928 47.619 0.00 0.00 0.00 4.02
759 4374 0.918983 TCAACCCATCATCCACTCCC 59.081 55.000 0.00 0.00 0.00 4.30
760 4375 0.625316 CAACCCATCATCCACTCCCA 59.375 55.000 0.00 0.00 0.00 4.37
766 4383 2.039480 CCATCATCCACTCCCATCGATT 59.961 50.000 0.00 0.00 0.00 3.34
777 4399 1.956477 CCCATCGATTCCCATTCCAAC 59.044 52.381 0.00 0.00 0.00 3.77
780 4402 3.446873 CCATCGATTCCCATTCCAACAAA 59.553 43.478 0.00 0.00 0.00 2.83
781 4403 4.423732 CATCGATTCCCATTCCAACAAAC 58.576 43.478 0.00 0.00 0.00 2.93
782 4404 2.823154 TCGATTCCCATTCCAACAAACC 59.177 45.455 0.00 0.00 0.00 3.27
783 4405 2.560542 CGATTCCCATTCCAACAAACCA 59.439 45.455 0.00 0.00 0.00 3.67
784 4406 3.367292 CGATTCCCATTCCAACAAACCAG 60.367 47.826 0.00 0.00 0.00 4.00
785 4407 3.320610 TTCCCATTCCAACAAACCAGA 57.679 42.857 0.00 0.00 0.00 3.86
786 4408 2.875296 TCCCATTCCAACAAACCAGAG 58.125 47.619 0.00 0.00 0.00 3.35
787 4409 1.895131 CCCATTCCAACAAACCAGAGG 59.105 52.381 0.00 0.00 0.00 3.69
791 4413 3.943671 TTCCAACAAACCAGAGGAAGA 57.056 42.857 0.00 0.00 33.69 2.87
793 4415 4.453480 TCCAACAAACCAGAGGAAGAAT 57.547 40.909 0.00 0.00 0.00 2.40
794 4416 4.398319 TCCAACAAACCAGAGGAAGAATC 58.602 43.478 0.00 0.00 0.00 2.52
809 4431 2.417719 AGAATCCAGTTCGTTGCACTC 58.582 47.619 0.00 0.00 41.84 3.51
810 4432 1.126846 GAATCCAGTTCGTTGCACTCG 59.873 52.381 4.38 4.38 0.00 4.18
811 4433 0.317160 ATCCAGTTCGTTGCACTCGA 59.683 50.000 8.76 8.76 35.50 4.04
812 4434 0.596600 TCCAGTTCGTTGCACTCGAC 60.597 55.000 11.83 8.21 37.05 4.20
985 4622 1.228154 AGGGCGTCCACCAAGAAAC 60.228 57.895 9.71 0.00 34.83 2.78
1386 5023 1.590792 GTACGAGTACATGGCCCGC 60.591 63.158 0.00 0.00 36.15 6.13
1486 5139 7.616935 ACATGGTTACTGATCTTGGATGATTTT 59.383 33.333 0.00 0.00 0.00 1.82
1488 5141 7.829725 TGGTTACTGATCTTGGATGATTTTTG 58.170 34.615 0.00 0.00 0.00 2.44
1490 5143 8.306761 GGTTACTGATCTTGGATGATTTTTGTT 58.693 33.333 0.00 0.00 0.00 2.83
1491 5144 9.132521 GTTACTGATCTTGGATGATTTTTGTTG 57.867 33.333 0.00 0.00 0.00 3.33
1492 5145 6.161381 ACTGATCTTGGATGATTTTTGTTGC 58.839 36.000 0.00 0.00 0.00 4.17
1636 5289 0.103208 ACATCCTGCTCGAATCGGTC 59.897 55.000 1.76 0.00 0.00 4.79
1640 5293 0.803768 CCTGCTCGAATCGGTCAGTG 60.804 60.000 18.05 9.85 0.00 3.66
1641 5294 1.416813 CTGCTCGAATCGGTCAGTGC 61.417 60.000 1.76 0.00 0.00 4.40
1642 5295 1.153745 GCTCGAATCGGTCAGTGCT 60.154 57.895 1.76 0.00 0.00 4.40
1643 5296 1.142778 GCTCGAATCGGTCAGTGCTC 61.143 60.000 1.76 0.00 0.00 4.26
1648 5301 0.904865 AATCGGTCAGTGCTCCTCCA 60.905 55.000 3.43 0.00 0.00 3.86
1690 5343 4.156455 GGGCATATCATATCCCGTTCAT 57.844 45.455 0.00 0.00 0.00 2.57
1691 5344 5.290493 GGGCATATCATATCCCGTTCATA 57.710 43.478 0.00 0.00 0.00 2.15
1692 5345 5.057149 GGGCATATCATATCCCGTTCATAC 58.943 45.833 0.00 0.00 0.00 2.39
1711 5365 2.765502 ACCTCCATACCTCCTTTCCTC 58.234 52.381 0.00 0.00 0.00 3.71
1745 5592 1.881602 GACTAGTTCGTCGGTGCCT 59.118 57.895 0.00 0.00 0.00 4.75
1753 5600 4.767255 GTCGGTGCCTCCCAGCAG 62.767 72.222 0.00 0.00 45.14 4.24
1775 5622 6.149633 CAGATACGATTTGATATGACGACCA 58.850 40.000 0.00 0.00 0.00 4.02
1779 5626 4.984785 ACGATTTGATATGACGACCATCTG 59.015 41.667 0.00 0.00 36.71 2.90
1815 5671 2.804647 GTGCCAGCACGTTTTAAAACT 58.195 42.857 24.57 11.89 37.19 2.66
1816 5672 2.533942 GTGCCAGCACGTTTTAAAACTG 59.466 45.455 24.57 21.09 37.19 3.16
1820 5676 3.042887 CAGCACGTTTTAAAACTGGCTC 58.957 45.455 28.61 15.38 41.08 4.70
1897 5754 1.082104 CGTTGAACGAGCAAAGCCC 60.082 57.895 13.13 0.00 46.05 5.19
1899 5756 1.519408 GTTGAACGAGCAAAGCCCTA 58.481 50.000 0.00 0.00 0.00 3.53
1914 5771 6.648725 GCAAAGCCCTAGACTTAATCTCTATG 59.351 42.308 0.00 0.00 39.04 2.23
1920 5782 7.094118 GCCCTAGACTTAATCTCTATGGTAGTG 60.094 44.444 0.00 0.00 39.04 2.74
2040 5911 4.336433 CGGGATCAGACAAGCATAAATGTT 59.664 41.667 0.00 0.00 0.00 2.71
2041 5912 5.585390 GGGATCAGACAAGCATAAATGTTG 58.415 41.667 0.00 0.00 0.00 3.33
2059 5930 0.321919 TGCTGTCATTGTGAGGAGGC 60.322 55.000 0.00 0.00 0.00 4.70
2103 5974 2.908688 ACAAAATTGGCCAGTTGGTC 57.091 45.000 15.02 0.00 41.09 4.02
2113 5986 2.814336 GGCCAGTTGGTCTGTTCTTAAG 59.186 50.000 0.00 0.00 42.19 1.85
2182 6106 1.830408 CTGTAGGAGCTAGCCGGCT 60.830 63.158 34.85 34.85 46.11 5.52
2215 6140 3.186409 CACCTGTCTAAATCAACCACACG 59.814 47.826 0.00 0.00 0.00 4.49
2218 6143 4.625742 CCTGTCTAAATCAACCACACGTAG 59.374 45.833 0.00 0.00 0.00 3.51
2219 6144 3.991773 TGTCTAAATCAACCACACGTAGC 59.008 43.478 0.00 0.00 0.00 3.58
2236 6163 6.426328 ACACGTAGCCAGTATACATCTAGTAC 59.574 42.308 5.50 0.00 35.05 2.73
2248 6175 9.212641 GTATACATCTAGTACGATCACCTAACA 57.787 37.037 0.00 0.00 35.05 2.41
2264 6191 3.502211 CCTAACACAGCCACTTTACTTGG 59.498 47.826 0.00 0.00 37.17 3.61
2344 6323 2.544694 CCTAAAACAACCGTGCATGCAA 60.545 45.455 24.58 3.50 0.00 4.08
2387 6370 0.247974 CAGTACACGTCGATCGACCC 60.248 60.000 35.48 20.70 41.76 4.46
2407 6390 1.193203 CGTGATTCTGACTGTGTGTGC 59.807 52.381 0.00 0.00 0.00 4.57
2942 6980 4.438346 CCGACAAGGCCGATAAGG 57.562 61.111 0.00 0.00 44.97 2.69
3153 7194 2.539503 CGTGAGTTCGTGTGTGCG 59.460 61.111 0.00 0.00 0.00 5.34
3158 7199 0.870307 GAGTTCGTGTGTGCGTGAGT 60.870 55.000 0.00 0.00 0.00 3.41
3230 7271 6.721208 AGGATGTGTAATCTGTTGGTTGATTT 59.279 34.615 0.00 0.00 35.01 2.17
3292 7333 5.527582 ACACAAGAGCAAAAGGTGTTAGTAG 59.472 40.000 0.00 0.00 39.48 2.57
3348 7400 8.084590 TCTTTCTTGATTAAGACGTTCCTTTC 57.915 34.615 0.00 0.00 42.41 2.62
3349 7401 7.713507 TCTTTCTTGATTAAGACGTTCCTTTCA 59.286 33.333 0.00 0.00 42.41 2.69
3443 7680 5.646606 TGCTTTCAACTACCAACACTTTTC 58.353 37.500 0.00 0.00 0.00 2.29
3445 7682 4.886247 TTCAACTACCAACACTTTTCCG 57.114 40.909 0.00 0.00 0.00 4.30
3516 7754 2.559668 CAGGACATTTTGCCACAGATGT 59.440 45.455 0.00 0.00 35.57 3.06
3540 7778 2.509569 TCAATTTCGGGCAACTGCTTA 58.490 42.857 1.06 0.00 45.18 3.09
3544 7782 0.322456 TTCGGGCAACTGCTTAGCAT 60.322 50.000 7.58 0.00 45.18 3.79
3654 7892 4.235079 TGCTTTGGAACTGCATACCTAT 57.765 40.909 0.00 0.00 0.00 2.57
3655 7893 4.599041 TGCTTTGGAACTGCATACCTATT 58.401 39.130 0.00 0.00 0.00 1.73
3770 8012 0.035317 AACTGATCTTCACGGCAGCA 59.965 50.000 0.00 0.00 31.74 4.41
3849 8094 2.735663 CGCAGATGGATAGTGATGAAGC 59.264 50.000 0.00 0.00 0.00 3.86
3882 8127 4.019860 AGCTCCACATCCGCATAATCTATT 60.020 41.667 0.00 0.00 0.00 1.73
3897 8142 1.421268 TCTATTGCTGGGATGGCGATT 59.579 47.619 0.00 0.00 35.64 3.34
3900 8145 1.031571 TTGCTGGGATGGCGATTGAC 61.032 55.000 0.00 0.00 0.00 3.18
3924 8169 2.364632 TCCTCGGTCGAAAACGGTATA 58.635 47.619 5.73 0.00 0.00 1.47
3934 8179 3.181524 CGAAAACGGTATACTGCACCAAG 60.182 47.826 11.79 0.00 35.67 3.61
3953 8198 5.476599 ACCAAGCAAGCATCAAATGTAAGTA 59.523 36.000 0.00 0.00 0.00 2.24
3961 8206 9.409312 CAAGCATCAAATGTAAGTACAAAATCA 57.591 29.630 0.00 0.00 39.99 2.57
3970 8215 5.825679 TGTAAGTACAAAATCAGCAACCACT 59.174 36.000 0.00 0.00 32.40 4.00
3975 8220 7.777095 AGTACAAAATCAGCAACCACTTAAAA 58.223 30.769 0.00 0.00 0.00 1.52
3980 8225 9.206870 CAAAATCAGCAACCACTTAAAACATAT 57.793 29.630 0.00 0.00 0.00 1.78
3986 8231 6.493458 AGCAACCACTTAAAACATATTCCACT 59.507 34.615 0.00 0.00 0.00 4.00
3987 8232 7.015195 AGCAACCACTTAAAACATATTCCACTT 59.985 33.333 0.00 0.00 0.00 3.16
3989 8234 9.541143 CAACCACTTAAAACATATTCCACTTTT 57.459 29.630 0.00 0.00 0.00 2.27
3990 8235 9.541143 AACCACTTAAAACATATTCCACTTTTG 57.459 29.630 0.00 0.00 0.00 2.44
4009 8254 5.830900 TTTGACAAACAAAAACACGGAAG 57.169 34.783 0.00 0.00 44.16 3.46
4012 8257 4.918583 TGACAAACAAAAACACGGAAGTTC 59.081 37.500 0.00 0.00 46.40 3.01
4019 8264 2.320745 AACACGGAAGTTCGAAAGGT 57.679 45.000 0.00 0.00 46.40 3.50
4037 8282 2.554032 AGGTGCATTTTCTACAGTGTGC 59.446 45.455 5.88 0.00 0.00 4.57
4051 8296 3.006110 ACAGTGTGCTAAGCGGTAACTAA 59.994 43.478 0.00 0.00 0.00 2.24
4061 8306 6.959871 GCTAAGCGGTAACTAACAAGAAAATC 59.040 38.462 0.00 0.00 0.00 2.17
4063 8308 6.237313 AGCGGTAACTAACAAGAAAATCAC 57.763 37.500 0.00 0.00 0.00 3.06
4074 8319 7.440523 AACAAGAAAATCACAGCTACCTTAG 57.559 36.000 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.226674 GGAACTCTCGCTTTTGGAAAGG 59.773 50.000 2.95 0.00 0.00 3.11
11 12 2.226674 GGGAACTCTCGCTTTTGGAAAG 59.773 50.000 0.00 0.00 0.00 2.62
12 13 2.227194 GGGAACTCTCGCTTTTGGAAA 58.773 47.619 0.00 0.00 0.00 3.13
13 14 1.142060 TGGGAACTCTCGCTTTTGGAA 59.858 47.619 0.00 0.00 35.57 3.53
14 15 0.762418 TGGGAACTCTCGCTTTTGGA 59.238 50.000 0.00 0.00 35.57 3.53
16 17 0.875059 GGTGGGAACTCTCGCTTTTG 59.125 55.000 0.00 0.00 35.57 2.44
17 18 0.250770 GGGTGGGAACTCTCGCTTTT 60.251 55.000 0.00 0.00 35.57 2.27
18 19 1.375326 GGGTGGGAACTCTCGCTTT 59.625 57.895 0.00 0.00 35.57 3.51
19 20 2.943978 CGGGTGGGAACTCTCGCTT 61.944 63.158 0.00 0.00 41.31 4.68
23 24 2.047179 GTGCGGGTGGGAACTCTC 60.047 66.667 0.00 0.00 0.00 3.20
25 26 4.717313 GGGTGCGGGTGGGAACTC 62.717 72.222 0.00 0.00 0.00 3.01
105 3601 7.562454 TTGAGACGGAGAAATTAACAGTTTT 57.438 32.000 0.00 0.00 0.00 2.43
199 3701 5.865552 CCATTTTTAACACTGCATCTTGGAG 59.134 40.000 0.00 0.00 41.93 3.86
200 3702 5.782047 CCATTTTTAACACTGCATCTTGGA 58.218 37.500 0.00 0.00 0.00 3.53
202 3704 5.232463 AGCCATTTTTAACACTGCATCTTG 58.768 37.500 0.00 0.00 0.00 3.02
214 3716 5.720371 ATGCACACTGTAGCCATTTTTAA 57.280 34.783 0.00 0.00 0.00 1.52
237 3787 0.726256 TATGTACGTGTCGCGCTGTA 59.274 50.000 5.56 0.00 46.11 2.74
273 3824 6.183360 TGTTGTACAATCGGCCAGTATGTATA 60.183 38.462 12.26 1.99 0.00 1.47
274 3825 4.948341 TGTACAATCGGCCAGTATGTAT 57.052 40.909 2.24 0.00 0.00 2.29
275 3826 4.081586 TGTTGTACAATCGGCCAGTATGTA 60.082 41.667 12.26 3.46 0.00 2.29
277 3828 3.266636 TGTTGTACAATCGGCCAGTATG 58.733 45.455 12.26 0.00 0.00 2.39
315 3867 1.083489 GCCGTGCAAGTATACTGCAA 58.917 50.000 22.94 10.99 40.45 4.08
332 3884 0.037232 AGCTCGTGTACTTCTTGGCC 60.037 55.000 0.00 0.00 0.00 5.36
444 4035 0.100682 GGTGAATGCGACTAGCTCGA 59.899 55.000 15.79 0.00 46.14 4.04
648 4263 0.604780 GTCGGATGGAGCCATGGATG 60.605 60.000 18.40 0.00 36.70 3.51
658 4273 0.478942 TTTTGGGTTGGTCGGATGGA 59.521 50.000 0.00 0.00 0.00 3.41
755 4370 1.421268 TGGAATGGGAATCGATGGGAG 59.579 52.381 0.00 0.00 0.00 4.30
759 4374 4.423732 GTTTGTTGGAATGGGAATCGATG 58.576 43.478 0.00 0.00 0.00 3.84
760 4375 3.447229 GGTTTGTTGGAATGGGAATCGAT 59.553 43.478 0.00 0.00 0.00 3.59
766 4383 2.490718 CCTCTGGTTTGTTGGAATGGGA 60.491 50.000 0.00 0.00 0.00 4.37
777 4399 4.026356 ACTGGATTCTTCCTCTGGTTTG 57.974 45.455 0.00 0.00 43.07 2.93
780 4402 2.234908 CGAACTGGATTCTTCCTCTGGT 59.765 50.000 0.00 0.00 43.07 4.00
781 4403 2.234908 ACGAACTGGATTCTTCCTCTGG 59.765 50.000 0.00 0.00 43.07 3.86
782 4404 3.601443 ACGAACTGGATTCTTCCTCTG 57.399 47.619 0.00 0.00 43.07 3.35
783 4405 3.866449 GCAACGAACTGGATTCTTCCTCT 60.866 47.826 0.00 0.00 43.07 3.69
784 4406 2.416893 GCAACGAACTGGATTCTTCCTC 59.583 50.000 0.00 0.00 43.07 3.71
785 4407 2.224523 TGCAACGAACTGGATTCTTCCT 60.225 45.455 0.00 0.00 43.07 3.36
786 4408 2.095718 GTGCAACGAACTGGATTCTTCC 60.096 50.000 0.00 0.00 42.94 3.46
787 4409 2.808543 AGTGCAACGAACTGGATTCTTC 59.191 45.455 0.00 0.00 45.86 2.87
791 4413 1.148310 CGAGTGCAACGAACTGGATT 58.852 50.000 8.56 0.00 45.86 3.01
793 4415 0.596600 GTCGAGTGCAACGAACTGGA 60.597 55.000 16.63 0.82 45.86 3.86
794 4416 1.557443 GGTCGAGTGCAACGAACTGG 61.557 60.000 20.33 1.78 45.86 4.00
810 4432 1.521681 CCTTCCTTGGCGATCGGTC 60.522 63.158 18.30 0.00 0.00 4.79
811 4433 1.550130 TTCCTTCCTTGGCGATCGGT 61.550 55.000 18.30 0.00 0.00 4.69
812 4434 1.090052 GTTCCTTCCTTGGCGATCGG 61.090 60.000 18.30 0.00 0.00 4.18
970 4607 1.104577 TTGGGTTTCTTGGTGGACGC 61.105 55.000 0.00 0.00 0.00 5.19
985 4622 1.002366 CGCATCGACTTCTTCTTGGG 58.998 55.000 0.00 0.00 0.00 4.12
1368 5005 1.590792 GCGGGCCATGTACTCGTAC 60.591 63.158 4.39 0.35 36.63 3.67
1636 5289 1.222936 GGATGGTGGAGGAGCACTG 59.777 63.158 0.00 0.00 34.04 3.66
1640 5293 1.411651 GGTAGGGATGGTGGAGGAGC 61.412 65.000 0.00 0.00 0.00 4.70
1641 5294 0.031111 TGGTAGGGATGGTGGAGGAG 60.031 60.000 0.00 0.00 0.00 3.69
1642 5295 0.419865 TTGGTAGGGATGGTGGAGGA 59.580 55.000 0.00 0.00 0.00 3.71
1643 5296 0.546598 GTTGGTAGGGATGGTGGAGG 59.453 60.000 0.00 0.00 0.00 4.30
1648 5301 0.981277 CCGGAGTTGGTAGGGATGGT 60.981 60.000 0.00 0.00 0.00 3.55
1690 5343 3.536434 AGAGGAAAGGAGGTATGGAGGTA 59.464 47.826 0.00 0.00 0.00 3.08
1691 5344 2.319438 AGAGGAAAGGAGGTATGGAGGT 59.681 50.000 0.00 0.00 0.00 3.85
1692 5345 2.703007 CAGAGGAAAGGAGGTATGGAGG 59.297 54.545 0.00 0.00 0.00 4.30
1711 5365 2.728015 TCGTGCGTGCGTGTACAG 60.728 61.111 0.00 0.00 0.00 2.74
1741 5588 0.760567 ATCGTATCTGCTGGGAGGCA 60.761 55.000 0.00 0.00 40.15 4.75
1745 5592 5.245977 TCATATCAAATCGTATCTGCTGGGA 59.754 40.000 0.00 0.00 0.00 4.37
1753 5600 7.008719 CAGATGGTCGTCATATCAAATCGTATC 59.991 40.741 0.00 0.00 35.97 2.24
1820 5676 1.874019 CGACAGAGATCGGCCAACG 60.874 63.158 2.24 0.00 46.11 4.10
1844 5700 8.412456 TCTCTGAGACATCATCATTAGAGAAAC 58.588 37.037 2.58 0.00 37.17 2.78
1866 5723 3.005472 TCGTTCAACGGATCAAAGTCTCT 59.995 43.478 10.69 0.00 42.81 3.10
1997 5859 2.128035 GTCCGAGGCATAGACAATTCG 58.872 52.381 0.00 0.00 0.00 3.34
2040 5911 0.321919 GCCTCCTCACAATGACAGCA 60.322 55.000 0.00 0.00 0.00 4.41
2041 5912 0.321919 TGCCTCCTCACAATGACAGC 60.322 55.000 0.00 0.00 0.00 4.40
2059 5930 1.738099 CTCGAGGGCACGTTTCCTG 60.738 63.158 10.83 4.67 32.74 3.86
2103 5974 6.385649 CTAGCCTAGGAGACTTAAGAACAG 57.614 45.833 14.75 0.00 43.67 3.16
2182 6106 5.648178 TTTAGACAGGTGCGACTATGTTA 57.352 39.130 0.00 0.00 0.00 2.41
2215 6140 7.548427 TGATCGTACTAGATGTATACTGGCTAC 59.452 40.741 4.17 0.00 33.23 3.58
2218 6143 6.403418 GGTGATCGTACTAGATGTATACTGGC 60.403 46.154 4.17 0.00 33.23 4.85
2219 6144 6.879993 AGGTGATCGTACTAGATGTATACTGG 59.120 42.308 4.17 0.00 33.23 4.00
2236 6163 1.066858 AGTGGCTGTGTTAGGTGATCG 60.067 52.381 0.00 0.00 0.00 3.69
2264 6191 2.426024 TCTACGTGGTTATCTGGAGTGC 59.574 50.000 0.00 0.00 0.00 4.40
2268 6195 5.186215 TGACATTTCTACGTGGTTATCTGGA 59.814 40.000 0.00 0.00 0.00 3.86
2387 6370 1.193203 GCACACACAGTCAGAATCACG 59.807 52.381 0.00 0.00 0.00 4.35
2407 6390 2.533266 AGTCCTGCAATACATAGGCG 57.467 50.000 0.00 0.00 0.00 5.52
2614 6640 4.753877 CGCTTGTCGACGCTCCGA 62.754 66.667 11.62 0.00 41.67 4.55
2995 7033 2.747855 CACTTCTTCCTGGCCGCC 60.748 66.667 1.04 1.04 0.00 6.13
3140 7181 0.459585 AACTCACGCACACACGAACT 60.460 50.000 0.00 0.00 36.70 3.01
3315 7358 7.876068 ACGTCTTAATCAAGAAAGAACACCATA 59.124 33.333 0.00 0.00 42.41 2.74
3370 7424 5.570205 TTAGTCCCTGTACCAAACAATCA 57.430 39.130 0.00 0.00 37.74 2.57
3435 7672 4.243270 CGTTCTAATCTCCGGAAAAGTGT 58.757 43.478 5.23 0.00 0.00 3.55
3443 7680 2.398498 CAGATGCGTTCTAATCTCCGG 58.602 52.381 0.00 0.00 30.62 5.14
3445 7682 3.460857 ACCAGATGCGTTCTAATCTCC 57.539 47.619 0.00 0.00 30.62 3.71
3516 7754 3.509575 AGCAGTTGCCCGAAATTGATTAA 59.490 39.130 0.00 0.00 43.38 1.40
3540 7778 9.502091 TGTACAAAGAATACTGTAGAAAATGCT 57.498 29.630 0.00 0.00 0.00 3.79
3654 7892 0.494551 TAGGGTGGAAGAGGGGTGAA 59.505 55.000 0.00 0.00 0.00 3.18
3655 7893 0.042731 CTAGGGTGGAAGAGGGGTGA 59.957 60.000 0.00 0.00 0.00 4.02
3770 8012 6.050432 TGTGTAATAGAACAACGAGGTTTGT 58.950 36.000 0.00 0.00 41.62 2.83
3849 8094 2.892425 GTGGAGCTGCCGGAATCG 60.892 66.667 5.05 0.00 40.66 3.34
3882 8127 1.451927 GTCAATCGCCATCCCAGCA 60.452 57.895 0.00 0.00 0.00 4.41
3897 8142 2.803956 GTTTTCGACCGAGGATTTGTCA 59.196 45.455 0.00 0.00 0.00 3.58
3934 8179 7.636259 TTTTGTACTTACATTTGATGCTTGC 57.364 32.000 0.00 0.00 35.89 4.01
3953 8198 6.402222 TGTTTTAAGTGGTTGCTGATTTTGT 58.598 32.000 0.00 0.00 0.00 2.83
3961 8206 6.493458 AGTGGAATATGTTTTAAGTGGTTGCT 59.507 34.615 0.00 0.00 0.00 3.91
3987 8232 5.290386 ACTTCCGTGTTTTTGTTTGTCAAA 58.710 33.333 0.00 0.00 43.24 2.69
3989 8234 4.506886 ACTTCCGTGTTTTTGTTTGTCA 57.493 36.364 0.00 0.00 0.00 3.58
3990 8235 4.029750 CGAACTTCCGTGTTTTTGTTTGTC 59.970 41.667 0.00 0.00 0.00 3.18
3997 8242 3.441222 ACCTTTCGAACTTCCGTGTTTTT 59.559 39.130 0.00 0.00 0.00 1.94
4006 8251 4.860072 AGAAAATGCACCTTTCGAACTTC 58.140 39.130 14.34 0.00 37.76 3.01
4009 8254 5.103290 TGTAGAAAATGCACCTTTCGAAC 57.897 39.130 14.34 15.56 37.76 3.95
4012 8257 4.024048 ACACTGTAGAAAATGCACCTTTCG 60.024 41.667 14.34 6.06 37.76 3.46
4019 8264 4.083324 GCTTAGCACACTGTAGAAAATGCA 60.083 41.667 0.00 0.00 35.51 3.96
4037 8282 7.955864 GTGATTTTCTTGTTAGTTACCGCTTAG 59.044 37.037 0.00 0.00 0.00 2.18
4051 8296 6.769512 TCTAAGGTAGCTGTGATTTTCTTGT 58.230 36.000 0.00 0.00 0.00 3.16
4061 8306 5.011431 TGGATGATGATCTAAGGTAGCTGTG 59.989 44.000 0.00 0.00 0.00 3.66
4063 8308 5.735285 TGGATGATGATCTAAGGTAGCTG 57.265 43.478 0.00 0.00 0.00 4.24
4074 8319 8.662141 CAAATTCCTTTTTGTTGGATGATGATC 58.338 33.333 0.00 0.00 32.99 2.92


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

AutoCloner maintained by Alex Coulton.