Multiple sequence alignment - TraesCS7D01G159600

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 TraesCS7D01G159600 chr7D 100.000 2483 0 0 1 2483 109145014 109142532 0.000000e+00 4586.0
1 TraesCS7D01G159600 chr7D 78.506 1098 165 32 10 1070 9354552 9355615 0.000000e+00 654.0
2 TraesCS7D01G159600 chr7D 79.054 296 39 11 2092 2368 10149310 10149019 5.460000e-42 182.0
3 TraesCS7D01G159600 chr7D 89.189 74 5 2 2374 2447 562474819 562474889 3.400000e-14 89.8
4 TraesCS7D01G159600 chr7D 94.444 54 3 0 238 291 109144723 109144670 1.580000e-12 84.2
5 TraesCS7D01G159600 chr7B 90.604 2384 164 22 1 2368 68160989 68158650 0.000000e+00 3107.0
6 TraesCS7D01G159600 chr7B 92.041 2224 136 21 1 2213 68223942 68221749 0.000000e+00 3088.0
7 TraesCS7D01G159600 chr7B 88.710 124 6 3 2252 2368 68218329 68218207 7.160000e-31 145.0
8 TraesCS7D01G159600 chr7A 91.300 1931 135 11 1 1918 114414689 114412779 0.000000e+00 2604.0
9 TraesCS7D01G159600 chr7A 90.589 1934 145 14 1 1916 114689056 114687142 0.000000e+00 2529.0
10 TraesCS7D01G159600 chr7A 81.265 1692 253 32 307 1972 10169953 10168300 0.000000e+00 1310.0
11 TraesCS7D01G159600 chr7A 78.374 1771 276 61 293 2006 9486675 9488395 0.000000e+00 1050.0
12 TraesCS7D01G159600 chr7A 89.391 509 31 11 1874 2368 114687140 114686641 9.760000e-174 619.0
13 TraesCS7D01G159600 chr7A 82.152 409 57 8 291 699 1526782 1526390 1.100000e-88 337.0
14 TraesCS7D01G159600 chr6D 92.693 1218 86 1 238 1455 84280064 84281278 0.000000e+00 1753.0
15 TraesCS7D01G159600 chr6D 89.970 658 39 12 1495 2139 84281277 84281920 0.000000e+00 824.0
16 TraesCS7D01G159600 chr6D 87.819 353 34 3 1 345 84279766 84280117 2.970000e-109 405.0
17 TraesCS7D01G159600 chr6D 94.667 75 2 1 2171 2245 84281923 84281995 5.610000e-22 115.0
18 TraesCS7D01G159600 chr6D 100.000 51 0 0 2433 2483 65518543 65518593 7.310000e-16 95.3
19 TraesCS7D01G159600 chr6D 100.000 51 0 0 2433 2483 309227766 309227716 7.310000e-16 95.3
20 TraesCS7D01G159600 chr6D 100.000 51 0 0 2433 2483 430001882 430001832 7.310000e-16 95.3
21 TraesCS7D01G159600 chr6D 89.474 76 4 4 2358 2429 313939141 313939216 2.630000e-15 93.5
22 TraesCS7D01G159600 chr6D 87.179 78 6 1 2373 2450 28402018 28401945 4.400000e-13 86.1
23 TraesCS7D01G159600 chr4B 81.004 1395 217 29 296 1658 654201948 654203326 0.000000e+00 1064.0
24 TraesCS7D01G159600 chr4A 83.220 1180 163 14 383 1535 728353003 728351832 0.000000e+00 1050.0
25 TraesCS7D01G159600 chr4A 78.411 1510 255 45 382 1855 729972588 729971114 0.000000e+00 917.0
26 TraesCS7D01G159600 chr4A 78.411 1510 247 50 382 1855 730456135 730457601 0.000000e+00 909.0
27 TraesCS7D01G159600 chr4A 76.772 1679 298 62 384 2008 729880937 729882577 0.000000e+00 856.0
28 TraesCS7D01G159600 chr4A 78.903 237 31 12 2092 2310 731099356 731099591 2.570000e-30 143.0
29 TraesCS7D01G159600 chr5A 80.664 1386 222 22 293 1647 691821001 691822371 0.000000e+00 1033.0
30 TraesCS7D01G159600 chrUn 100.000 51 0 0 2433 2483 99654798 99654848 7.310000e-16 95.3
31 TraesCS7D01G159600 chrUn 100.000 51 0 0 2433 2483 110368309 110368359 7.310000e-16 95.3
32 TraesCS7D01G159600 chr4D 100.000 51 0 0 2433 2483 68727386 68727436 7.310000e-16 95.3
33 TraesCS7D01G159600 chr4D 100.000 51 0 0 2433 2483 411274637 411274687 7.310000e-16 95.3
34 TraesCS7D01G159600 chr1D 100.000 51 0 0 2433 2483 5738038 5738088 7.310000e-16 95.3
35 TraesCS7D01G159600 chr1D 93.750 64 3 1 2366 2429 136583392 136583330 7.310000e-16 95.3
36 TraesCS7D01G159600 chr1D 92.308 65 5 0 2374 2438 92549937 92550001 2.630000e-15 93.5
37 TraesCS7D01G159600 chr3B 89.474 76 5 3 2355 2429 57427546 57427619 2.630000e-15 93.5
38 TraesCS7D01G159600 chr3B 94.737 57 3 0 2373 2429 767276205 767276149 3.400000e-14 89.8
39 TraesCS7D01G159600 chr2D 92.424 66 3 2 2374 2438 9289575 9289511 2.630000e-15 93.5
40 TraesCS7D01G159600 chr2D 89.855 69 4 3 2416 2483 496901236 496901170 4.400000e-13 86.1
41 TraesCS7D01G159600 chr5D 94.737 57 3 0 2374 2430 370353542 370353598 3.400000e-14 89.8


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 TraesCS7D01G159600 chr7D 109142532 109145014 2482 True 2335.10 4586 97.22200 1 2483 2 chr7D.!!$R2 2482
1 TraesCS7D01G159600 chr7D 9354552 9355615 1063 False 654.00 654 78.50600 10 1070 1 chr7D.!!$F1 1060
2 TraesCS7D01G159600 chr7B 68158650 68160989 2339 True 3107.00 3107 90.60400 1 2368 1 chr7B.!!$R1 2367
3 TraesCS7D01G159600 chr7B 68218207 68223942 5735 True 1616.50 3088 90.37550 1 2368 2 chr7B.!!$R2 2367
4 TraesCS7D01G159600 chr7A 114412779 114414689 1910 True 2604.00 2604 91.30000 1 1918 1 chr7A.!!$R3 1917
5 TraesCS7D01G159600 chr7A 114686641 114689056 2415 True 1574.00 2529 89.99000 1 2368 2 chr7A.!!$R4 2367
6 TraesCS7D01G159600 chr7A 10168300 10169953 1653 True 1310.00 1310 81.26500 307 1972 1 chr7A.!!$R2 1665
7 TraesCS7D01G159600 chr7A 9486675 9488395 1720 False 1050.00 1050 78.37400 293 2006 1 chr7A.!!$F1 1713
8 TraesCS7D01G159600 chr6D 84279766 84281995 2229 False 774.25 1753 91.28725 1 2245 4 chr6D.!!$F3 2244
9 TraesCS7D01G159600 chr4B 654201948 654203326 1378 False 1064.00 1064 81.00400 296 1658 1 chr4B.!!$F1 1362
10 TraesCS7D01G159600 chr4A 728351832 728353003 1171 True 1050.00 1050 83.22000 383 1535 1 chr4A.!!$R1 1152
11 TraesCS7D01G159600 chr4A 729971114 729972588 1474 True 917.00 917 78.41100 382 1855 1 chr4A.!!$R2 1473
12 TraesCS7D01G159600 chr4A 730456135 730457601 1466 False 909.00 909 78.41100 382 1855 1 chr4A.!!$F2 1473
13 TraesCS7D01G159600 chr4A 729880937 729882577 1640 False 856.00 856 76.77200 384 2008 1 chr4A.!!$F1 1624
14 TraesCS7D01G159600 chr5A 691821001 691822371 1370 False 1033.00 1033 80.66400 293 1647 1 chr5A.!!$F1 1354

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
149 158 0.118346 TAGAGGACCACCACCACCAT 59.882 55.0 0.0 0.0 38.94 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1815 0.76489 AGCAGGAGTACAAGCACCAA 59.235 50.0 0.0 0.0 0.0 3.67 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
28 29 1.817941 AGCGTCCGTGCTGTTGTTT 60.818 52.632 0.00 0.00 45.28 2.83
106 112 1.611592 CCGTCGCTGTCGTAAACCAC 61.612 60.000 0.00 0.00 36.96 4.16
116 122 3.118482 TGTCGTAAACCACACCAAGGTAA 60.118 43.478 0.00 0.00 38.76 2.85
132 138 3.797451 GGTAACTTTCCGACTCCCTAG 57.203 52.381 0.00 0.00 0.00 3.02
149 158 0.118346 TAGAGGACCACCACCACCAT 59.882 55.000 0.00 0.00 38.94 3.55
150 159 0.772124 AGAGGACCACCACCACCATT 60.772 55.000 0.00 0.00 38.94 3.16
179 188 0.182061 ATTCGCAGCCAGATCCATGT 59.818 50.000 0.00 0.00 0.00 3.21
220 230 2.920912 TGACCTGACCGTGTCCCC 60.921 66.667 2.23 0.00 0.00 4.81
414 532 0.395862 ACGTCGACCTCATCCTGGAT 60.396 55.000 10.58 2.57 0.00 3.41
527 645 0.178873 AAGCTACCCCAGACCCTTGA 60.179 55.000 0.00 0.00 0.00 3.02
567 688 3.723235 CTGCAGCAGCGGGTATCGT 62.723 63.158 10.14 0.00 46.23 3.73
641 768 3.545703 CTTACCTGCATCCTAACAAGGG 58.454 50.000 0.00 0.00 0.00 3.95
720 886 2.566952 GCAACAGGCATGATTACCAC 57.433 50.000 4.84 0.00 43.97 4.16
805 989 4.523173 AGGAGACGATGAACAGACTTAACA 59.477 41.667 0.00 0.00 0.00 2.41
1164 1363 6.405508 GCTTACACTATGTTGTAGCTCCTGTA 60.406 42.308 0.00 0.00 33.50 2.74
1340 1539 1.135972 CGACACAATTTTCCTGGCTCG 60.136 52.381 0.00 0.00 0.00 5.03
1447 1659 7.112779 ACAGAAATTTCTACCCTATGTTCCTG 58.887 38.462 20.07 6.57 35.34 3.86
1557 1777 5.112220 TCATCTGAACAATTTGTCTGTGC 57.888 39.130 1.83 0.00 0.00 4.57
1604 1824 1.550072 CCCCCTATTTGTTGGTGCTTG 59.450 52.381 0.00 0.00 0.00 4.01
1651 1879 2.161855 CAGAGCAATGCCTGGTAAACA 58.838 47.619 13.50 0.00 35.35 2.83
1653 1881 3.019564 AGAGCAATGCCTGGTAAACATC 58.980 45.455 0.00 0.00 35.35 3.06
1654 1882 2.754552 GAGCAATGCCTGGTAAACATCA 59.245 45.455 0.00 0.00 35.35 3.07
1655 1883 2.756760 AGCAATGCCTGGTAAACATCAG 59.243 45.455 0.00 0.00 32.70 2.90
1656 1884 2.736400 GCAATGCCTGGTAAACATCAGC 60.736 50.000 0.00 0.00 0.00 4.26
1661 1889 4.535781 TGCCTGGTAAACATCAGCATTAT 58.464 39.130 0.00 0.00 0.00 1.28
1662 1890 4.955450 TGCCTGGTAAACATCAGCATTATT 59.045 37.500 0.00 0.00 0.00 1.40
1664 1892 5.979517 GCCTGGTAAACATCAGCATTATTTC 59.020 40.000 0.00 0.00 0.00 2.17
1665 1893 6.405731 GCCTGGTAAACATCAGCATTATTTCA 60.406 38.462 0.00 0.00 0.00 2.69
1666 1894 7.685155 GCCTGGTAAACATCAGCATTATTTCAT 60.685 37.037 0.00 0.00 0.00 2.57
1675 1903 9.932207 ACATCAGCATTATTTCATTTTCAAAGA 57.068 25.926 0.00 0.00 0.00 2.52
1678 1906 8.914654 TCAGCATTATTTCATTTTCAAAGAACG 58.085 29.630 0.00 0.00 0.00 3.95
1679 1907 8.164153 CAGCATTATTTCATTTTCAAAGAACGG 58.836 33.333 0.00 0.00 0.00 4.44
1794 2052 6.440965 ACTGTAATAGGCCCTCTTATCCATAC 59.559 42.308 0.00 0.00 0.00 2.39
1858 2125 5.867716 CGTCAACCTGCTAGTGTACTAAAAT 59.132 40.000 0.00 0.00 0.00 1.82
2011 2328 3.686726 GCTGACCACAGAGAAATTGTAGG 59.313 47.826 0.00 0.00 46.03 3.18
2012 2329 4.563580 GCTGACCACAGAGAAATTGTAGGA 60.564 45.833 0.00 0.00 46.03 2.94
2188 2514 6.367983 AGAAATGTAGTGGCCATGAACATAT 58.632 36.000 23.10 13.74 30.85 1.78
2189 2515 7.517320 AGAAATGTAGTGGCCATGAACATATA 58.483 34.615 23.10 5.78 30.85 0.86
2315 6035 2.328473 GCAAGGAAGAAAAATCACCGC 58.672 47.619 0.00 0.00 0.00 5.68
2318 6038 1.804748 AGGAAGAAAAATCACCGCGTC 59.195 47.619 4.92 0.00 0.00 5.19
2319 6039 1.533731 GGAAGAAAAATCACCGCGTCA 59.466 47.619 4.92 0.00 0.00 4.35
2337 6063 3.306364 CGTCAAGACTCCCAGATTCTGTT 60.306 47.826 12.54 0.00 0.00 3.16
2342 6068 7.391833 GTCAAGACTCCCAGATTCTGTTAAAAT 59.608 37.037 12.54 0.00 0.00 1.82
2389 6117 8.773404 TCTTATTGTCACTACTAGGAAAAAGC 57.227 34.615 0.00 0.00 0.00 3.51
2390 6118 7.822822 TCTTATTGTCACTACTAGGAAAAAGCC 59.177 37.037 0.00 0.00 0.00 4.35
2391 6119 5.562298 TTGTCACTACTAGGAAAAAGCCT 57.438 39.130 0.00 0.00 42.15 4.58
2392 6120 4.894784 TGTCACTACTAGGAAAAAGCCTG 58.105 43.478 0.00 0.00 39.08 4.85
2393 6121 4.347000 TGTCACTACTAGGAAAAAGCCTGT 59.653 41.667 0.00 0.00 39.08 4.00
2394 6122 5.163237 TGTCACTACTAGGAAAAAGCCTGTT 60.163 40.000 0.00 0.00 39.08 3.16
2395 6123 6.042322 TGTCACTACTAGGAAAAAGCCTGTTA 59.958 38.462 0.00 0.00 39.08 2.41
2396 6124 6.590677 GTCACTACTAGGAAAAAGCCTGTTAG 59.409 42.308 0.00 0.00 39.08 2.34
2397 6125 6.269307 TCACTACTAGGAAAAAGCCTGTTAGT 59.731 38.462 0.00 0.00 39.08 2.24
2398 6126 6.369065 CACTACTAGGAAAAAGCCTGTTAGTG 59.631 42.308 13.93 13.93 42.26 2.74
2399 6127 5.562298 ACTAGGAAAAAGCCTGTTAGTGA 57.438 39.130 0.00 0.00 39.08 3.41
2400 6128 5.306394 ACTAGGAAAAAGCCTGTTAGTGAC 58.694 41.667 0.00 0.00 39.08 3.67
2401 6129 3.139077 AGGAAAAAGCCTGTTAGTGACG 58.861 45.455 0.00 0.00 36.76 4.35
2402 6130 2.350484 GGAAAAAGCCTGTTAGTGACGC 60.350 50.000 0.00 0.00 0.00 5.19
2403 6131 1.961793 AAAAGCCTGTTAGTGACGCA 58.038 45.000 0.00 0.00 0.00 5.24
2404 6132 1.226746 AAAGCCTGTTAGTGACGCAC 58.773 50.000 2.28 2.28 34.10 5.34
2405 6133 0.602905 AAGCCTGTTAGTGACGCACC 60.603 55.000 6.39 0.00 34.49 5.01
2406 6134 1.004918 GCCTGTTAGTGACGCACCT 60.005 57.895 6.39 0.00 34.49 4.00
2407 6135 1.291877 GCCTGTTAGTGACGCACCTG 61.292 60.000 6.39 0.00 34.49 4.00
2408 6136 0.033504 CCTGTTAGTGACGCACCTGT 59.966 55.000 6.39 0.00 34.49 4.00
2409 6137 1.540363 CCTGTTAGTGACGCACCTGTT 60.540 52.381 6.39 0.00 34.49 3.16
2410 6138 2.210116 CTGTTAGTGACGCACCTGTTT 58.790 47.619 6.39 0.00 34.49 2.83
2411 6139 2.612212 CTGTTAGTGACGCACCTGTTTT 59.388 45.455 6.39 0.00 34.49 2.43
2412 6140 2.353269 TGTTAGTGACGCACCTGTTTTG 59.647 45.455 6.39 0.00 34.49 2.44
2413 6141 0.941542 TAGTGACGCACCTGTTTTGC 59.058 50.000 6.39 0.00 34.49 3.68
2414 6142 1.299089 GTGACGCACCTGTTTTGCC 60.299 57.895 0.00 0.00 36.57 4.52
2415 6143 1.453015 TGACGCACCTGTTTTGCCT 60.453 52.632 0.00 0.00 36.57 4.75
2416 6144 0.179043 TGACGCACCTGTTTTGCCTA 60.179 50.000 0.00 0.00 36.57 3.93
2417 6145 0.237498 GACGCACCTGTTTTGCCTAC 59.763 55.000 0.00 0.00 36.57 3.18
2418 6146 0.179029 ACGCACCTGTTTTGCCTACT 60.179 50.000 0.00 0.00 36.57 2.57
2419 6147 1.071071 ACGCACCTGTTTTGCCTACTA 59.929 47.619 0.00 0.00 36.57 1.82
2420 6148 2.147958 CGCACCTGTTTTGCCTACTAA 58.852 47.619 0.00 0.00 36.57 2.24
2421 6149 2.747446 CGCACCTGTTTTGCCTACTAAT 59.253 45.455 0.00 0.00 36.57 1.73
2422 6150 3.426159 CGCACCTGTTTTGCCTACTAATG 60.426 47.826 0.00 0.00 36.57 1.90
2423 6151 3.119495 GCACCTGTTTTGCCTACTAATGG 60.119 47.826 0.00 0.00 33.58 3.16
2429 6157 3.732470 GCCTACTAATGGCGCACC 58.268 61.111 10.83 0.00 41.03 5.01
2430 6158 1.146263 GCCTACTAATGGCGCACCT 59.854 57.895 10.83 0.00 41.03 4.00
2431 6159 1.160329 GCCTACTAATGGCGCACCTG 61.160 60.000 10.83 0.00 41.03 4.00
2432 6160 0.178068 CCTACTAATGGCGCACCTGT 59.822 55.000 10.83 3.52 36.63 4.00
2433 6161 1.406887 CCTACTAATGGCGCACCTGTT 60.407 52.381 10.83 0.00 36.63 3.16
2434 6162 2.356135 CTACTAATGGCGCACCTGTTT 58.644 47.619 10.83 0.00 36.63 2.83
2435 6163 1.616159 ACTAATGGCGCACCTGTTTT 58.384 45.000 10.83 0.00 36.63 2.43
2436 6164 1.269448 ACTAATGGCGCACCTGTTTTG 59.731 47.619 10.83 0.00 36.63 2.44
2437 6165 0.038709 TAATGGCGCACCTGTTTTGC 60.039 50.000 10.83 0.00 36.63 3.68
2438 6166 2.025767 AATGGCGCACCTGTTTTGCA 62.026 50.000 10.83 0.00 40.20 4.08
2439 6167 2.355009 GGCGCACCTGTTTTGCAG 60.355 61.111 10.83 0.00 44.63 4.41
2440 6168 2.412937 GCGCACCTGTTTTGCAGT 59.587 55.556 0.30 0.00 43.55 4.40
2441 6169 1.945662 GCGCACCTGTTTTGCAGTG 60.946 57.895 0.30 0.00 43.55 3.66
2442 6170 1.945662 CGCACCTGTTTTGCAGTGC 60.946 57.895 14.59 14.59 43.55 4.40
2443 6171 1.945662 GCACCTGTTTTGCAGTGCG 60.946 57.895 11.20 0.00 43.55 5.34
2444 6172 1.945662 CACCTGTTTTGCAGTGCGC 60.946 57.895 11.20 0.00 43.55 6.09
2445 6173 2.355009 CCTGTTTTGCAGTGCGCC 60.355 61.111 11.20 0.00 43.55 6.53
2446 6174 2.412525 CTGTTTTGCAGTGCGCCA 59.587 55.556 11.20 3.27 41.33 5.69
2447 6175 1.945662 CTGTTTTGCAGTGCGCCAC 60.946 57.895 11.20 7.01 41.33 5.01
2448 6176 2.340453 CTGTTTTGCAGTGCGCCACT 62.340 55.000 11.20 5.73 46.51 4.00
2449 6177 1.098129 TGTTTTGCAGTGCGCCACTA 61.098 50.000 11.20 0.00 43.43 2.74
2450 6178 0.030101 GTTTTGCAGTGCGCCACTAA 59.970 50.000 11.20 0.00 43.43 2.24
2451 6179 0.741326 TTTTGCAGTGCGCCACTAAA 59.259 45.000 11.20 4.57 43.43 1.85
2452 6180 0.310543 TTTGCAGTGCGCCACTAAAG 59.689 50.000 11.20 0.00 43.43 1.85
2453 6181 0.817634 TTGCAGTGCGCCACTAAAGT 60.818 50.000 11.20 0.00 43.43 2.66
2454 6182 1.207593 GCAGTGCGCCACTAAAGTG 59.792 57.895 4.18 3.02 43.43 3.16
2455 6183 1.207593 CAGTGCGCCACTAAAGTGC 59.792 57.895 4.18 0.32 43.43 4.40
2456 6184 1.071471 AGTGCGCCACTAAAGTGCT 59.929 52.632 4.18 0.00 43.46 4.40
2457 6185 1.207593 GTGCGCCACTAAAGTGCTG 59.792 57.895 4.18 0.67 44.34 4.41
2458 6186 1.965930 TGCGCCACTAAAGTGCTGG 60.966 57.895 4.18 0.00 44.34 4.85
2459 6187 2.690778 GCGCCACTAAAGTGCTGGG 61.691 63.158 0.00 2.45 44.34 4.45
2460 6188 1.302511 CGCCACTAAAGTGCTGGGT 60.303 57.895 4.53 0.00 44.34 4.51
2461 6189 1.577328 CGCCACTAAAGTGCTGGGTG 61.577 60.000 4.53 0.00 44.34 4.61
2462 6190 2.946947 CCACTAAAGTGCTGGGTGG 58.053 57.895 4.53 0.00 44.34 4.61
2463 6191 0.110486 CCACTAAAGTGCTGGGTGGT 59.890 55.000 4.53 0.00 44.34 4.16
2464 6192 1.238439 CACTAAAGTGCTGGGTGGTG 58.762 55.000 0.00 0.00 39.39 4.17
2465 6193 0.537371 ACTAAAGTGCTGGGTGGTGC 60.537 55.000 0.00 0.00 0.00 5.01
2466 6194 1.577328 CTAAAGTGCTGGGTGGTGCG 61.577 60.000 0.00 0.00 0.00 5.34
2478 6206 2.585876 TGGTGCGCCACTAGTATGA 58.414 52.632 16.89 0.00 40.46 2.15
2479 6207 0.899019 TGGTGCGCCACTAGTATGAA 59.101 50.000 16.89 0.00 40.46 2.57
2480 6208 1.484653 TGGTGCGCCACTAGTATGAAT 59.515 47.619 16.89 0.00 40.46 2.57
2481 6209 2.696187 TGGTGCGCCACTAGTATGAATA 59.304 45.455 16.89 0.00 40.46 1.75
2482 6210 3.323691 TGGTGCGCCACTAGTATGAATAT 59.676 43.478 16.89 0.00 40.46 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.148027 ACTTCTCAGAGGACAGTGGGA 59.852 52.381 0.00 0.00 0.00 4.37
106 112 3.064931 GAGTCGGAAAGTTACCTTGGTG 58.935 50.000 2.03 0.00 0.00 4.17
116 122 1.639628 TCCTCTAGGGAGTCGGAAAGT 59.360 52.381 0.00 0.00 39.58 2.66
130 136 0.118346 ATGGTGGTGGTGGTCCTCTA 59.882 55.000 0.00 0.00 34.23 2.43
132 138 0.609131 CAATGGTGGTGGTGGTCCTC 60.609 60.000 0.00 0.00 34.23 3.71
149 158 3.357203 TGGCTGCGAATAATTAACCCAA 58.643 40.909 0.00 0.00 0.00 4.12
150 159 2.948979 CTGGCTGCGAATAATTAACCCA 59.051 45.455 0.00 0.00 0.00 4.51
160 169 0.182061 ACATGGATCTGGCTGCGAAT 59.818 50.000 0.00 0.00 0.00 3.34
164 173 1.135721 GGAAAACATGGATCTGGCTGC 59.864 52.381 0.00 0.00 0.00 5.25
179 188 4.371624 TCTGCAAATGGAGAGAGGAAAA 57.628 40.909 0.01 0.00 37.60 2.29
220 230 1.383803 AGGAGGAAGGGCTAGGCAG 60.384 63.158 19.14 0.00 0.00 4.85
380 498 2.594303 CGTTGAACAGGCTGGCCA 60.594 61.111 20.34 4.71 38.92 5.36
414 532 2.373338 CTGGGAGGCGGGAGAGGATA 62.373 65.000 0.00 0.00 0.00 2.59
527 645 1.593296 GGTCGTGTAGAGGAAGCCGT 61.593 60.000 0.00 0.00 0.00 5.68
567 688 1.595929 GAAACCGGCGAAGTGGTGA 60.596 57.895 9.30 0.00 38.34 4.02
720 886 1.769733 CGGGATTGCACACAACAAAG 58.230 50.000 0.00 0.00 38.99 2.77
805 989 2.499303 AAAGCCAGGCCTGCGGTATT 62.499 55.000 28.39 17.25 0.00 1.89
1283 1482 1.978580 CAACCACCCTGTACTTCTCCT 59.021 52.381 0.00 0.00 0.00 3.69
1425 1637 9.628500 AATACAGGAACATAGGGTAGAAATTTC 57.372 33.333 10.33 10.33 0.00 2.17
1447 1659 3.005897 TCTGCTAATGGCTCCGAGAATAC 59.994 47.826 0.00 0.00 42.39 1.89
1589 1809 4.759693 CAGGAGTACAAGCACCAACAAATA 59.240 41.667 0.00 0.00 0.00 1.40
1595 1815 0.764890 AGCAGGAGTACAAGCACCAA 59.235 50.000 0.00 0.00 0.00 3.67
1604 1824 3.127721 GGAAATCAAGCAAGCAGGAGTAC 59.872 47.826 0.00 0.00 0.00 2.73
1653 1881 8.164153 CCGTTCTTTGAAAATGAAATAATGCTG 58.836 33.333 0.00 0.00 40.94 4.41
1654 1882 8.087750 TCCGTTCTTTGAAAATGAAATAATGCT 58.912 29.630 0.00 0.00 40.94 3.79
1655 1883 8.238481 TCCGTTCTTTGAAAATGAAATAATGC 57.762 30.769 0.00 0.00 40.94 3.56
1661 1889 8.709386 TGAAAATCCGTTCTTTGAAAATGAAA 57.291 26.923 0.00 0.00 40.94 2.69
1662 1890 8.709386 TTGAAAATCCGTTCTTTGAAAATGAA 57.291 26.923 0.00 0.00 37.61 2.57
1664 1892 8.816144 TCTTTGAAAATCCGTTCTTTGAAAATG 58.184 29.630 0.00 0.00 0.00 2.32
1665 1893 8.940768 TCTTTGAAAATCCGTTCTTTGAAAAT 57.059 26.923 0.00 0.00 0.00 1.82
1666 1894 8.764524 TTCTTTGAAAATCCGTTCTTTGAAAA 57.235 26.923 0.00 0.00 0.00 2.29
1670 1898 7.698836 ACATTCTTTGAAAATCCGTTCTTTG 57.301 32.000 0.00 0.00 0.00 2.77
1671 1899 9.981114 ATAACATTCTTTGAAAATCCGTTCTTT 57.019 25.926 0.00 0.00 0.00 2.52
1672 1900 9.981114 AATAACATTCTTTGAAAATCCGTTCTT 57.019 25.926 0.00 0.00 0.00 2.52
1675 1903 9.634163 GGTAATAACATTCTTTGAAAATCCGTT 57.366 29.630 0.00 0.00 0.00 4.44
1676 1904 8.248253 GGGTAATAACATTCTTTGAAAATCCGT 58.752 33.333 0.00 0.00 0.00 4.69
1677 1905 8.466798 AGGGTAATAACATTCTTTGAAAATCCG 58.533 33.333 0.00 0.00 0.00 4.18
1705 1934 3.157087 CCAGTGGTAGGCAAACAAGAAT 58.843 45.455 0.00 0.00 0.00 2.40
1817 2081 6.823689 AGGTTGACGATATGCACTAAGATTTT 59.176 34.615 0.00 0.00 0.00 1.82
1834 2098 4.430137 TTAGTACACTAGCAGGTTGACG 57.570 45.455 0.00 0.00 0.00 4.35
1858 2125 4.161565 ACCAGTAACAAGTCTGACTGAACA 59.838 41.667 11.71 0.00 41.51 3.18
2156 2482 3.369471 GGCCACTACATTTCTAGCACAGA 60.369 47.826 0.00 0.00 0.00 3.41
2223 5943 1.156736 GGCTTCAGTTAAGAGCGCAA 58.843 50.000 11.47 0.00 37.38 4.85
2315 6035 2.232452 ACAGAATCTGGGAGTCTTGACG 59.768 50.000 15.38 0.00 34.68 4.35
2318 6038 7.693969 ATTTTAACAGAATCTGGGAGTCTTG 57.306 36.000 15.38 0.00 34.68 3.02
2319 6039 9.401058 CATATTTTAACAGAATCTGGGAGTCTT 57.599 33.333 15.38 1.18 34.68 3.01
2368 6096 5.940470 CAGGCTTTTTCCTAGTAGTGACAAT 59.060 40.000 0.00 0.00 33.95 2.71
2369 6097 5.163237 ACAGGCTTTTTCCTAGTAGTGACAA 60.163 40.000 0.00 0.00 33.95 3.18
2370 6098 4.347000 ACAGGCTTTTTCCTAGTAGTGACA 59.653 41.667 0.00 0.00 33.95 3.58
2371 6099 4.895961 ACAGGCTTTTTCCTAGTAGTGAC 58.104 43.478 0.00 0.00 33.95 3.67
2372 6100 5.562298 AACAGGCTTTTTCCTAGTAGTGA 57.438 39.130 0.00 0.00 33.95 3.41
2373 6101 6.369065 CACTAACAGGCTTTTTCCTAGTAGTG 59.631 42.308 13.21 13.21 41.39 2.74
2374 6102 6.269307 TCACTAACAGGCTTTTTCCTAGTAGT 59.731 38.462 0.00 0.00 36.34 2.73
2375 6103 6.590677 GTCACTAACAGGCTTTTTCCTAGTAG 59.409 42.308 0.00 0.00 33.95 2.57
2376 6104 6.461640 GTCACTAACAGGCTTTTTCCTAGTA 58.538 40.000 0.00 0.00 33.95 1.82
2377 6105 5.306394 GTCACTAACAGGCTTTTTCCTAGT 58.694 41.667 0.00 0.00 33.95 2.57
2378 6106 4.389077 CGTCACTAACAGGCTTTTTCCTAG 59.611 45.833 0.00 0.00 33.95 3.02
2379 6107 4.312443 CGTCACTAACAGGCTTTTTCCTA 58.688 43.478 0.00 0.00 33.95 2.94
2380 6108 3.139077 CGTCACTAACAGGCTTTTTCCT 58.861 45.455 0.00 0.00 36.78 3.36
2381 6109 2.350484 GCGTCACTAACAGGCTTTTTCC 60.350 50.000 0.00 0.00 0.00 3.13
2382 6110 2.289547 TGCGTCACTAACAGGCTTTTTC 59.710 45.455 0.00 0.00 0.00 2.29
2383 6111 2.032924 GTGCGTCACTAACAGGCTTTTT 59.967 45.455 0.00 0.00 0.00 1.94
2384 6112 1.602377 GTGCGTCACTAACAGGCTTTT 59.398 47.619 3.20 0.00 0.00 2.27
2385 6113 1.226746 GTGCGTCACTAACAGGCTTT 58.773 50.000 3.20 0.00 0.00 3.51
2386 6114 0.602905 GGTGCGTCACTAACAGGCTT 60.603 55.000 9.31 0.00 34.40 4.35
2387 6115 1.004918 GGTGCGTCACTAACAGGCT 60.005 57.895 9.31 0.00 34.40 4.58
2388 6116 1.004918 AGGTGCGTCACTAACAGGC 60.005 57.895 9.31 0.00 34.40 4.85
2389 6117 0.033504 ACAGGTGCGTCACTAACAGG 59.966 55.000 9.31 0.00 34.40 4.00
2390 6118 1.865865 AACAGGTGCGTCACTAACAG 58.134 50.000 9.31 0.46 34.40 3.16
2391 6119 2.319136 AAACAGGTGCGTCACTAACA 57.681 45.000 9.31 0.00 34.40 2.41
2392 6120 2.853281 GCAAAACAGGTGCGTCACTAAC 60.853 50.000 9.31 0.00 34.40 2.34
2393 6121 1.332375 GCAAAACAGGTGCGTCACTAA 59.668 47.619 9.31 0.00 34.40 2.24
2394 6122 0.941542 GCAAAACAGGTGCGTCACTA 59.058 50.000 9.31 0.00 34.40 2.74
2395 6123 1.724582 GGCAAAACAGGTGCGTCACT 61.725 55.000 9.31 0.00 43.18 3.41
2396 6124 1.299089 GGCAAAACAGGTGCGTCAC 60.299 57.895 1.92 1.92 43.18 3.67
2397 6125 0.179043 TAGGCAAAACAGGTGCGTCA 60.179 50.000 0.00 0.00 43.18 4.35
2398 6126 0.237498 GTAGGCAAAACAGGTGCGTC 59.763 55.000 0.00 0.00 43.18 5.19
2399 6127 0.179029 AGTAGGCAAAACAGGTGCGT 60.179 50.000 0.00 0.00 43.18 5.24
2400 6128 1.803334 TAGTAGGCAAAACAGGTGCG 58.197 50.000 0.00 0.00 43.18 5.34
2401 6129 3.119495 CCATTAGTAGGCAAAACAGGTGC 60.119 47.826 0.00 0.00 41.45 5.01
2402 6130 4.701956 CCATTAGTAGGCAAAACAGGTG 57.298 45.455 0.00 0.00 0.00 4.00
2413 6141 0.178068 ACAGGTGCGCCATTAGTAGG 59.822 55.000 20.59 0.00 37.19 3.18
2414 6142 2.024176 AACAGGTGCGCCATTAGTAG 57.976 50.000 20.59 1.48 37.19 2.57
2415 6143 2.483014 AAACAGGTGCGCCATTAGTA 57.517 45.000 20.59 0.00 37.19 1.82
2416 6144 1.269448 CAAAACAGGTGCGCCATTAGT 59.731 47.619 20.59 8.46 37.19 2.24
2417 6145 1.981254 CAAAACAGGTGCGCCATTAG 58.019 50.000 20.59 7.78 37.19 1.73
2418 6146 0.038709 GCAAAACAGGTGCGCCATTA 60.039 50.000 20.59 0.00 37.19 1.90
2419 6147 1.300853 GCAAAACAGGTGCGCCATT 60.301 52.632 20.59 9.66 37.19 3.16
2420 6148 2.339712 GCAAAACAGGTGCGCCAT 59.660 55.556 20.59 2.62 37.19 4.40
2421 6149 3.136345 CTGCAAAACAGGTGCGCCA 62.136 57.895 20.59 0.00 45.27 5.69
2422 6150 2.355009 CTGCAAAACAGGTGCGCC 60.355 61.111 8.71 8.71 45.27 6.53
2436 6164 1.207593 CACTTTAGTGGCGCACTGC 59.792 57.895 18.70 2.75 45.01 4.40
2437 6165 1.207593 GCACTTTAGTGGCGCACTG 59.792 57.895 18.70 8.01 45.01 3.66
2439 6167 1.207593 CAGCACTTTAGTGGCGCAC 59.792 57.895 10.83 5.73 45.72 5.34
2440 6168 1.965930 CCAGCACTTTAGTGGCGCA 60.966 57.895 10.83 0.00 45.72 6.09
2441 6169 2.690778 CCCAGCACTTTAGTGGCGC 61.691 63.158 11.55 0.00 45.72 6.53
2442 6170 1.302511 ACCCAGCACTTTAGTGGCG 60.303 57.895 11.55 2.24 45.72 5.69
2443 6171 1.244019 CCACCCAGCACTTTAGTGGC 61.244 60.000 11.55 4.51 45.72 5.01
2444 6172 2.946947 CCACCCAGCACTTTAGTGG 58.053 57.895 11.55 0.00 45.72 4.00
2446 6174 0.537371 GCACCACCCAGCACTTTAGT 60.537 55.000 0.00 0.00 0.00 2.24
2447 6175 1.577328 CGCACCACCCAGCACTTTAG 61.577 60.000 0.00 0.00 0.00 1.85
2448 6176 1.599518 CGCACCACCCAGCACTTTA 60.600 57.895 0.00 0.00 0.00 1.85
2449 6177 2.906897 CGCACCACCCAGCACTTT 60.907 61.111 0.00 0.00 0.00 2.66
2460 6188 0.899019 TTCATACTAGTGGCGCACCA 59.101 50.000 10.83 0.00 46.51 4.17
2461 6189 2.240493 ATTCATACTAGTGGCGCACC 57.760 50.000 10.83 0.00 34.49 5.01


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

AutoCloner maintained by Alex Coulton.