Multiple sequence alignment - TraesCS3A01G525100

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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 TraesCS3A01G525100 chr3A 100.000 3781 0 0 1 3781 739520127 739516347 0.000000e+00 6983
1 TraesCS3A01G525100 chr3A 74.247 598 72 36 1 588 743186475 743185950 3.880000e-40 176
2 TraesCS3A01G525100 chr3D 87.594 3184 216 92 7 3069 607066672 607063547 0.000000e+00 3526
3 TraesCS3A01G525100 chr3D 94.250 713 29 8 3074 3781 607063499 607062794 0.000000e+00 1079
4 TraesCS3A01G525100 chr3D 80.914 372 46 18 1799 2154 132031134 132030772 1.730000e-68 270
5 TraesCS3A01G525100 chr3D 74.315 584 81 29 10 588 609620751 609620232 2.320000e-42 183
6 TraesCS3A01G525100 chr3B 91.820 1198 75 12 7 1200 816521994 816520816 0.000000e+00 1648
7 TraesCS3A01G525100 chr3B 94.390 713 30 9 3073 3781 816518844 816518138 0.000000e+00 1086
8 TraesCS3A01G525100 chr3B 84.746 826 82 30 1229 2031 816520821 816520017 0.000000e+00 787
9 TraesCS3A01G525100 chr3B 82.109 844 65 39 2160 2922 816519842 816519004 0.000000e+00 643
10 TraesCS3A01G525100 chr3B 75.085 586 79 24 1 580 820499547 820499023 1.060000e-50 211
11 TraesCS3A01G525100 chr3B 94.068 118 5 1 2960 3077 816518999 816518884 1.080000e-40 178
12 TraesCS3A01G525100 chr4D 82.337 368 47 13 1799 2154 505006119 505005758 1.710000e-78 303
13 TraesCS3A01G525100 chr7B 77.133 586 70 28 1 580 709219833 709220360 8.000000e-72 281
14 TraesCS3A01G525100 chr1D 81.402 371 46 16 1799 2154 225721479 225721117 8.000000e-72 281
15 TraesCS3A01G525100 chr2B 81.030 369 50 15 1799 2154 407883425 407883786 3.720000e-70 276
16 TraesCS3A01G525100 chr2B 79.805 307 39 16 1862 2154 145540101 145539804 6.400000e-48 202
17 TraesCS3A01G525100 chr7D 81.285 358 48 13 1799 2143 185423346 185423697 4.810000e-69 272
18 TraesCS3A01G525100 chr2A 79.661 354 51 16 1799 2138 96606125 96606471 6.310000e-58 235
19 TraesCS3A01G525100 chr1A 93.902 82 5 0 3518 3599 12157669 12157750 1.430000e-24 124


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 TraesCS3A01G525100 chr3A 739516347 739520127 3780 True 6983.0 6983 100.0000 1 3781 1 chr3A.!!$R1 3780
1 TraesCS3A01G525100 chr3D 607062794 607066672 3878 True 2302.5 3526 90.9220 7 3781 2 chr3D.!!$R3 3774
2 TraesCS3A01G525100 chr3B 816518138 816521994 3856 True 868.4 1648 89.4266 7 3781 5 chr3B.!!$R2 3774
3 TraesCS3A01G525100 chr3B 820499023 820499547 524 True 211.0 211 75.0850 1 580 1 chr3B.!!$R1 579
4 TraesCS3A01G525100 chr7B 709219833 709220360 527 False 281.0 281 77.1330 1 580 1 chr7B.!!$F1 579

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
914 921 0.534873 GACAGAGAAGGCAGAGTCCC 59.465 60.0 0.0 0.0 0.00 4.46 F
2082 2135 0.842635 AGGGTGCAATCTGGAGATCC 59.157 55.0 0.0 0.0 32.75 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 2530 0.104725 TTTTTGGGGCCTGGAATGGT 60.105 50.0 0.84 0.0 0.00 3.55 R
3255 3541 0.981183 ATTTGTCCACTAGGCCGTCA 59.019 50.0 0.00 0.0 33.74 4.35 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
62 63 4.550577 CCACAAATTGGGCAAAACTTTC 57.449 40.909 0.00 0.00 42.54 2.62
69 70 8.093307 ACAAATTGGGCAAAACTTTCAATTTTT 58.907 25.926 8.89 2.39 42.48 1.94
196 200 2.887152 ACTGAATTGAGTGGCCACTTTC 59.113 45.455 37.98 33.23 42.66 2.62
343 347 2.403252 GCACCAGCATTACCACTAGT 57.597 50.000 0.00 0.00 41.58 2.57
344 348 3.536956 GCACCAGCATTACCACTAGTA 57.463 47.619 0.00 0.00 41.58 1.82
345 349 4.073293 GCACCAGCATTACCACTAGTAT 57.927 45.455 0.00 0.00 41.58 2.12
346 350 4.451900 GCACCAGCATTACCACTAGTATT 58.548 43.478 0.00 0.00 41.58 1.89
353 357 9.391006 CCAGCATTACCACTAGTATTTTCTTTA 57.609 33.333 0.00 0.00 0.00 1.85
375 379 2.245159 TGTTTGCAGAGAGTGGAGTG 57.755 50.000 0.00 0.00 0.00 3.51
389 393 1.754226 TGGAGTGGCAAAAACAACTCC 59.246 47.619 10.60 10.60 42.83 3.85
421 425 5.419788 TCCTTGTTTACTCGCTAACCTATCA 59.580 40.000 0.00 0.00 0.00 2.15
456 462 1.893137 GAATGGTGACCAGGTTTTCCC 59.107 52.381 11.23 0.00 41.86 3.97
462 468 1.491332 TGACCAGGTTTTCCCGAAGAA 59.509 47.619 0.00 0.00 41.86 2.52
510 516 2.570302 ACGGGTGGTATCTTGCTACTTT 59.430 45.455 0.00 0.00 0.00 2.66
673 680 2.291741 GCCAAGGCAGTGATATGCTTAC 59.708 50.000 6.14 0.00 45.75 2.34
674 681 3.544684 CCAAGGCAGTGATATGCTTACA 58.455 45.455 0.00 0.00 45.75 2.41
696 703 5.593095 ACAACTTCTAGGAAACAGGGTTTTC 59.407 40.000 0.00 0.00 35.13 2.29
724 731 7.564793 TCAACTCATACCAGCAACATAACTAT 58.435 34.615 0.00 0.00 0.00 2.12
725 732 8.700973 TCAACTCATACCAGCAACATAACTATA 58.299 33.333 0.00 0.00 0.00 1.31
726 733 9.494271 CAACTCATACCAGCAACATAACTATAT 57.506 33.333 0.00 0.00 0.00 0.86
752 759 6.381994 ACCATACTACGAAATTCCTAGTTCCA 59.618 38.462 9.31 0.00 0.00 3.53
757 764 8.265165 ACTACGAAATTCCTAGTTCCAATTTC 57.735 34.615 12.26 12.26 40.69 2.17
770 777 1.602191 CAATTTCCGTCGGCGAAAAG 58.398 50.000 12.93 6.21 41.33 2.27
778 785 1.463444 CGTCGGCGAAAAGAATTCCTT 59.537 47.619 12.92 0.00 41.33 3.36
780 787 2.225727 GTCGGCGAAAAGAATTCCTTGT 59.774 45.455 12.92 0.00 34.79 3.16
781 788 2.225491 TCGGCGAAAAGAATTCCTTGTG 59.775 45.455 7.35 0.00 34.79 3.33
783 790 2.328473 GCGAAAAGAATTCCTTGTGCC 58.672 47.619 0.65 0.00 34.79 5.01
836 843 1.772836 ATGCATCCTCCTTTTGCCTC 58.227 50.000 0.00 0.00 35.51 4.70
843 850 1.895798 CCTCCTTTTGCCTCCTTTTCC 59.104 52.381 0.00 0.00 0.00 3.13
875 882 4.701956 ACTTTTGAGTCACCAACAACAG 57.298 40.909 0.00 0.00 0.00 3.16
878 885 2.620251 TGAGTCACCAACAACAGAGG 57.380 50.000 0.00 0.00 0.00 3.69
885 892 5.422012 AGTCACCAACAACAGAGGAAAATTT 59.578 36.000 0.00 0.00 0.00 1.82
889 896 8.141268 TCACCAACAACAGAGGAAAATTTAATC 58.859 33.333 0.00 0.00 0.00 1.75
911 918 0.972883 GTGGACAGAGAAGGCAGAGT 59.027 55.000 0.00 0.00 0.00 3.24
914 921 0.534873 GACAGAGAAGGCAGAGTCCC 59.465 60.000 0.00 0.00 0.00 4.46
931 938 2.422832 GTCCCCGAGAGCCGTATATAAG 59.577 54.545 0.00 0.00 36.31 1.73
932 939 2.040813 TCCCCGAGAGCCGTATATAAGT 59.959 50.000 0.00 0.00 36.31 2.24
935 942 2.095532 CCGAGAGCCGTATATAAGTCGG 59.904 54.545 9.76 9.76 45.94 4.79
967 977 1.902508 GAGGAGTTGTGATCCACCTCA 59.097 52.381 0.00 0.00 42.11 3.86
995 1005 4.042062 TCCAATTCCTCTGTGATCACTTGT 59.958 41.667 25.55 3.47 0.00 3.16
1041 1051 1.308326 CCCGTCTCCTCCTCTTCCT 59.692 63.158 0.00 0.00 0.00 3.36
1133 1143 2.078665 GCTATGGCTTCCTCCCCCA 61.079 63.158 0.00 0.00 35.22 4.96
1158 1168 3.733709 GCACCAGCCCTATTATGCT 57.266 52.632 0.00 0.00 38.67 3.79
1200 1210 3.498774 ATGTTGTTCCTTGCTCTCTGT 57.501 42.857 0.00 0.00 0.00 3.41
1246 1256 1.410004 TTCACTCTGAGAACACCCGT 58.590 50.000 12.44 0.00 0.00 5.28
1294 1304 2.151202 TGCCGTTTGGTTTCTGATCTC 58.849 47.619 0.00 0.00 37.67 2.75
1334 1344 4.714308 TGGTTTATTGGGTCCATTCATTCC 59.286 41.667 0.00 0.00 0.00 3.01
1363 1376 8.567285 TTTCTCTTGAGAAGAAACTTGTTCTT 57.433 30.769 12.11 1.06 40.41 2.52
1366 1379 5.882557 TCTTGAGAAGAAACTTGTTCTTGCT 59.117 36.000 6.08 3.97 40.41 3.91
1452 1466 3.571401 AGTTGCTGTTGAATCTTTCCTGG 59.429 43.478 0.00 0.00 0.00 4.45
1499 1513 1.404035 ACTTCTGTTTTCGTGGTTGCC 59.596 47.619 0.00 0.00 0.00 4.52
1549 1563 5.618640 GCTTTTGGTCATGTCTTGATCAGAC 60.619 44.000 14.67 14.67 46.01 3.51
1566 1580 8.610248 TGATCAGACGTAACAAGGAAAAATAA 57.390 30.769 0.00 0.00 0.00 1.40
1663 1680 3.623960 TCATGAAAAAGTTTCCACGTCGT 59.376 39.130 0.00 0.00 0.00 4.34
1720 1738 5.997384 AATTACTCTACGACAGAAGGGTT 57.003 39.130 0.00 0.00 31.12 4.11
1721 1739 7.472334 AAATTACTCTACGACAGAAGGGTTA 57.528 36.000 0.00 0.00 31.12 2.85
1732 1750 6.039941 ACGACAGAAGGGTTAGATTAGATCAG 59.960 42.308 0.00 0.00 0.00 2.90
1733 1751 6.263392 CGACAGAAGGGTTAGATTAGATCAGA 59.737 42.308 0.00 0.00 0.00 3.27
1734 1752 7.040062 CGACAGAAGGGTTAGATTAGATCAGAT 60.040 40.741 0.00 0.00 0.00 2.90
1735 1753 8.560124 ACAGAAGGGTTAGATTAGATCAGATT 57.440 34.615 0.00 0.00 0.00 2.40
1736 1754 8.428063 ACAGAAGGGTTAGATTAGATCAGATTG 58.572 37.037 0.00 0.00 0.00 2.67
1737 1755 7.877097 CAGAAGGGTTAGATTAGATCAGATTGG 59.123 40.741 0.00 0.00 0.00 3.16
1738 1756 7.791766 AGAAGGGTTAGATTAGATCAGATTGGA 59.208 37.037 0.00 0.00 0.00 3.53
1842 1863 0.853530 ACTTCCCTTGCCCTTTCTGT 59.146 50.000 0.00 0.00 0.00 3.41
1871 1892 1.943340 GGTCGAAATGCCCTTCATCTC 59.057 52.381 0.00 0.00 33.40 2.75
1923 1944 4.573900 ACACCAGAAATGCTGTAAGAGAG 58.426 43.478 0.00 0.00 43.33 3.20
1924 1945 4.040952 ACACCAGAAATGCTGTAAGAGAGT 59.959 41.667 0.00 0.00 43.33 3.24
1925 1946 4.629200 CACCAGAAATGCTGTAAGAGAGTC 59.371 45.833 0.00 0.00 43.33 3.36
1926 1947 4.530161 ACCAGAAATGCTGTAAGAGAGTCT 59.470 41.667 0.00 0.00 43.33 3.24
1927 1948 5.108517 CCAGAAATGCTGTAAGAGAGTCTC 58.891 45.833 12.54 12.54 43.33 3.36
1928 1949 5.105392 CCAGAAATGCTGTAAGAGAGTCTCT 60.105 44.000 17.30 17.30 41.87 3.10
1929 1950 6.035843 CAGAAATGCTGTAAGAGAGTCTCTC 58.964 44.000 22.86 20.50 38.65 3.20
1930 1951 6.127647 CAGAAATGCTGTAAGAGAGTCTCTCT 60.128 42.308 24.25 24.25 46.14 3.10
1955 1976 5.982890 TTTTCCCTTTTGCCTTCTATCTG 57.017 39.130 0.00 0.00 0.00 2.90
1959 1980 3.703052 CCCTTTTGCCTTCTATCTGCAAT 59.297 43.478 0.00 0.00 43.78 3.56
1962 1983 3.788333 TTGCCTTCTATCTGCAATTGC 57.212 42.857 23.69 23.69 39.86 3.56
1980 2001 7.502177 CAATTGCTTGCTTGAAATACTACAG 57.498 36.000 0.00 0.00 0.00 2.74
1982 2003 6.633500 TTGCTTGCTTGAAATACTACAGTT 57.367 33.333 0.00 0.00 0.00 3.16
1983 2004 6.633500 TGCTTGCTTGAAATACTACAGTTT 57.367 33.333 0.00 0.00 0.00 2.66
1984 2005 7.038154 TGCTTGCTTGAAATACTACAGTTTT 57.962 32.000 0.00 0.00 0.00 2.43
1985 2006 6.917477 TGCTTGCTTGAAATACTACAGTTTTG 59.083 34.615 0.00 0.00 0.00 2.44
1988 2009 9.334693 CTTGCTTGAAATACTACAGTTTTGATC 57.665 33.333 0.00 0.00 0.00 2.92
2018 2067 2.489329 GCTTGAGCCAATAAGCTGTTCA 59.511 45.455 0.00 0.00 45.15 3.18
2032 2081 2.602878 CTGTTCATGCTGGAAATGCAC 58.397 47.619 0.00 0.00 43.59 4.57
2040 2089 4.439305 TGCTGGAAATGCACTTACAATC 57.561 40.909 0.00 0.00 35.31 2.67
2041 2090 3.825585 TGCTGGAAATGCACTTACAATCA 59.174 39.130 0.00 0.00 35.31 2.57
2043 2092 5.651576 TGCTGGAAATGCACTTACAATCATA 59.348 36.000 0.00 0.00 35.31 2.15
2047 2096 7.761409 TGGAAATGCACTTACAATCATAAGAC 58.239 34.615 0.00 0.00 35.96 3.01
2048 2097 7.611467 TGGAAATGCACTTACAATCATAAGACT 59.389 33.333 0.00 0.00 35.96 3.24
2049 2098 8.125448 GGAAATGCACTTACAATCATAAGACTC 58.875 37.037 0.00 0.00 35.96 3.36
2050 2099 8.798859 AAATGCACTTACAATCATAAGACTCT 57.201 30.769 0.00 0.00 35.96 3.24
2054 2103 8.506437 TGCACTTACAATCATAAGACTCTTTTG 58.494 33.333 0.00 0.00 35.96 2.44
2080 2133 4.166725 TGAATAAGGGTGCAATCTGGAGAT 59.833 41.667 0.00 0.00 36.07 2.75
2081 2134 2.725221 AAGGGTGCAATCTGGAGATC 57.275 50.000 0.00 0.00 32.75 2.75
2082 2135 0.842635 AGGGTGCAATCTGGAGATCC 59.157 55.000 0.00 0.00 32.75 3.36
2083 2136 0.842635 GGGTGCAATCTGGAGATCCT 59.157 55.000 0.00 0.00 36.82 3.24
2084 2137 2.050144 GGGTGCAATCTGGAGATCCTA 58.950 52.381 0.00 0.00 36.82 2.94
2085 2138 2.038295 GGGTGCAATCTGGAGATCCTAG 59.962 54.545 0.00 0.00 36.82 3.02
2086 2139 2.703007 GGTGCAATCTGGAGATCCTAGT 59.297 50.000 0.00 0.00 36.82 2.57
2087 2140 3.898123 GGTGCAATCTGGAGATCCTAGTA 59.102 47.826 0.00 0.00 36.82 1.82
2088 2141 4.530161 GGTGCAATCTGGAGATCCTAGTAT 59.470 45.833 0.00 0.00 36.82 2.12
2089 2142 5.477510 GTGCAATCTGGAGATCCTAGTATG 58.522 45.833 0.00 2.51 36.82 2.39
2090 2143 4.020751 TGCAATCTGGAGATCCTAGTATGC 60.021 45.833 0.00 10.52 36.82 3.14
2091 2144 4.222588 GCAATCTGGAGATCCTAGTATGCT 59.777 45.833 0.00 0.00 36.82 3.79
2092 2145 5.420421 GCAATCTGGAGATCCTAGTATGCTA 59.580 44.000 0.00 0.00 36.82 3.49
2093 2146 6.405731 GCAATCTGGAGATCCTAGTATGCTAG 60.406 46.154 10.66 10.66 38.10 3.42
2096 2149 7.517898 TCTGGAGATCCTAGTATGCTAGTAT 57.482 40.000 15.63 6.37 42.35 2.12
2099 2152 7.699878 TGGAGATCCTAGTATGCTAGTATTGA 58.300 38.462 15.63 6.97 42.35 2.57
2106 2159 9.764363 TCCTAGTATGCTAGTATTGAATGTTTG 57.236 33.333 15.63 0.00 42.35 2.93
2124 2177 8.980143 AATGTTTGTTTATAGAATCCCAAACG 57.020 30.769 0.00 0.00 42.64 3.60
2144 2201 9.823647 CCAAACGGATTATATAGCTCTTGATAT 57.176 33.333 0.00 0.00 0.00 1.63
2171 2292 7.830739 ACAATAAAACAGAGTGGATTGATTCC 58.169 34.615 0.00 0.00 45.69 3.01
2234 2388 4.862371 TGAATCACTAATGGGGGTTTACC 58.138 43.478 0.00 0.00 39.11 2.85
2311 2465 2.867429 CGCATTTCAGATTCCAACACC 58.133 47.619 0.00 0.00 0.00 4.16
2333 2487 4.284746 CCCCCATCTTCTCAAGGTACTATC 59.715 50.000 0.00 0.00 38.49 2.08
2334 2488 4.284746 CCCCATCTTCTCAAGGTACTATCC 59.715 50.000 0.00 0.00 38.49 2.59
2336 2490 4.901849 CCATCTTCTCAAGGTACTATCCCA 59.098 45.833 0.00 0.00 38.49 4.37
2338 2492 5.934402 TCTTCTCAAGGTACTATCCCAAC 57.066 43.478 0.00 0.00 38.49 3.77
2342 2511 4.016479 TCTCAAGGTACTATCCCAACTCCT 60.016 45.833 0.00 0.00 38.49 3.69
2349 2518 4.628661 ACTATCCCAACTCCTTCCTACT 57.371 45.455 0.00 0.00 0.00 2.57
2351 2520 4.963628 ACTATCCCAACTCCTTCCTACTTC 59.036 45.833 0.00 0.00 0.00 3.01
2355 2524 3.055747 CCCAACTCCTTCCTACTTCAGAC 60.056 52.174 0.00 0.00 0.00 3.51
2359 2528 3.009253 ACTCCTTCCTACTTCAGACTCGA 59.991 47.826 0.00 0.00 0.00 4.04
2361 2530 3.082548 CCTTCCTACTTCAGACTCGACA 58.917 50.000 0.00 0.00 0.00 4.35
2365 2534 2.755655 CCTACTTCAGACTCGACACCAT 59.244 50.000 0.00 0.00 0.00 3.55
2369 2538 1.627864 TCAGACTCGACACCATTCCA 58.372 50.000 0.00 0.00 0.00 3.53
2373 2542 1.450312 CTCGACACCATTCCAGGCC 60.450 63.158 0.00 0.00 0.00 5.19
2375 2544 2.043953 GACACCATTCCAGGCCCC 60.044 66.667 0.00 0.00 0.00 5.80
2387 2556 1.550869 CCAGGCCCCAAAAACTCATCT 60.551 52.381 0.00 0.00 0.00 2.90
2388 2557 1.547372 CAGGCCCCAAAAACTCATCTG 59.453 52.381 0.00 0.00 0.00 2.90
2389 2558 1.428912 AGGCCCCAAAAACTCATCTGA 59.571 47.619 0.00 0.00 0.00 3.27
2487 2669 3.181329 TGTGAACCCCTACATGATGAGT 58.819 45.455 0.00 0.00 0.00 3.41
2520 2702 3.775654 GACCCTGAGCCTGACCCG 61.776 72.222 0.00 0.00 0.00 5.28
2632 2838 1.484240 CCCAGAGGTGAGGAAGATGAC 59.516 57.143 0.00 0.00 0.00 3.06
2636 2842 1.550976 GAGGTGAGGAAGATGACGGTT 59.449 52.381 0.00 0.00 0.00 4.44
2671 2878 2.363683 AGATTTGCTGTGGCTAAGCTC 58.636 47.619 12.16 3.47 43.77 4.09
2741 2949 0.326427 AGGAGAGGCTGCAGAGGATT 60.326 55.000 20.43 0.00 0.00 3.01
2750 2958 2.617532 GCTGCAGAGGATTGAGTTCCTT 60.618 50.000 20.43 0.00 46.35 3.36
2759 2967 5.292815 AGGATTGAGTTCCTTAGGGAGATT 58.707 41.667 0.00 0.00 43.88 2.40
2768 2976 5.984695 TCCTTAGGGAGATTATCACATCG 57.015 43.478 0.00 0.00 36.57 3.84
2783 2991 8.786826 TTATCACATCGACCATTCTTTAGTTT 57.213 30.769 0.00 0.00 0.00 2.66
2947 3188 7.524717 AAGTTAATGTGCTTCTTTGGTGTAT 57.475 32.000 0.00 0.00 0.00 2.29
2948 3189 6.913170 AGTTAATGTGCTTCTTTGGTGTATG 58.087 36.000 0.00 0.00 0.00 2.39
3002 3243 4.009675 TGTTCCATTGAGATTTTCCCGAG 58.990 43.478 0.00 0.00 0.00 4.63
3093 3351 8.153550 AGAGTAAAATGGGAGAAGCATATACAG 58.846 37.037 0.00 0.00 0.00 2.74
3120 3403 8.436778 AGCAAAAAGGGAGGTAACAAAATTAAT 58.563 29.630 0.00 0.00 41.41 1.40
3167 3450 8.573035 TGTATGCTCTACACGTATCATCAATAA 58.427 33.333 0.00 0.00 0.00 1.40
3244 3527 1.840635 GGACAGGGAGGATTAACAGCT 59.159 52.381 0.00 0.00 0.00 4.24
3246 3529 2.237392 GACAGGGAGGATTAACAGCTGT 59.763 50.000 15.25 15.25 0.00 4.40
3249 3532 3.118112 CAGGGAGGATTAACAGCTGTGAT 60.118 47.826 22.49 17.48 0.00 3.06
3255 3541 7.390027 GGAGGATTAACAGCTGTGATGTATAT 58.610 38.462 22.49 2.04 0.00 0.86
3286 3572 2.030628 GTGGACAAATGTTACGTTGGGG 60.031 50.000 0.00 0.00 0.00 4.96
3361 3647 1.916181 TGGAAGATCCCCCACTCTTTC 59.084 52.381 0.00 0.00 35.03 2.62
3407 3693 4.388499 GCGCCTTCCCGTTCTCCA 62.388 66.667 0.00 0.00 0.00 3.86
3418 3704 1.472662 CGTTCTCCACCTGTCCCTGT 61.473 60.000 0.00 0.00 0.00 4.00
3466 3752 5.811796 TGGTAGTAAGTGCTAGGTTTTGA 57.188 39.130 0.00 0.00 0.00 2.69
3485 3771 2.785269 TGATGTTCTATGATGGGGCCTT 59.215 45.455 0.84 0.00 0.00 4.35
3617 3903 5.581085 AGGCTGCAAAGAGTAAATACGTTAG 59.419 40.000 0.50 0.00 0.00 2.34
3660 3946 6.926272 AGATGGTCGAGAGCTATTTAAATGAC 59.074 38.462 11.05 7.36 0.00 3.06
3662 3948 7.342769 TGGTCGAGAGCTATTTAAATGACTA 57.657 36.000 11.05 3.22 0.00 2.59
3713 4000 9.479549 AGAAATATATCAATGTTTGACAAGGGT 57.520 29.630 0.00 0.00 43.48 4.34
3754 4041 4.828939 ACACATTTCCTCAGAGCAAAATCA 59.171 37.500 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.028748 ACTTTTCACCATTCTGGCATGC 60.029 45.455 9.90 9.90 42.67 4.06
69 70 6.442541 TGGACACCTTTATTTACCTCAAGA 57.557 37.500 0.00 0.00 0.00 3.02
196 200 3.120060 CCAGACCTGCAGAAAGAAAATCG 60.120 47.826 17.39 0.00 0.00 3.34
342 346 9.334693 CTCTCTGCAAACATGTAAAGAAAATAC 57.665 33.333 0.00 0.00 0.00 1.89
343 347 9.066892 ACTCTCTGCAAACATGTAAAGAAAATA 57.933 29.630 0.00 0.00 0.00 1.40
344 348 7.864379 CACTCTCTGCAAACATGTAAAGAAAAT 59.136 33.333 0.00 0.00 0.00 1.82
345 349 7.195646 CACTCTCTGCAAACATGTAAAGAAAA 58.804 34.615 0.00 0.00 0.00 2.29
346 350 6.238731 CCACTCTCTGCAAACATGTAAAGAAA 60.239 38.462 0.00 0.00 0.00 2.52
353 357 2.105477 ACTCCACTCTCTGCAAACATGT 59.895 45.455 0.00 0.00 0.00 3.21
358 362 0.250467 GCCACTCCACTCTCTGCAAA 60.250 55.000 0.00 0.00 0.00 3.68
359 363 1.372683 GCCACTCCACTCTCTGCAA 59.627 57.895 0.00 0.00 0.00 4.08
389 393 3.975035 GCGAGTAAACAAGGAAAGCAAAG 59.025 43.478 0.00 0.00 0.00 2.77
421 425 2.695666 ACCATTCTCCAAGATCGTCGAT 59.304 45.455 7.63 7.63 0.00 3.59
510 516 3.078837 GCGGAAATTAACTTCTCCACCA 58.921 45.455 0.00 0.00 0.00 4.17
673 680 6.073327 GAAAACCCTGTTTCCTAGAAGTTG 57.927 41.667 0.00 0.00 32.36 3.16
696 703 2.290260 TGTTGCTGGTATGAGTTGAGGG 60.290 50.000 0.00 0.00 0.00 4.30
725 732 8.583296 GGAACTAGGAATTTCGTAGTATGGTAT 58.417 37.037 24.44 12.86 44.43 2.73
726 733 7.560991 TGGAACTAGGAATTTCGTAGTATGGTA 59.439 37.037 24.44 11.91 44.43 3.25
727 734 6.381994 TGGAACTAGGAATTTCGTAGTATGGT 59.618 38.462 24.44 13.69 44.43 3.55
728 735 6.812998 TGGAACTAGGAATTTCGTAGTATGG 58.187 40.000 24.44 6.52 44.43 2.74
735 742 5.123344 CGGAAATTGGAACTAGGAATTTCGT 59.877 40.000 16.80 0.00 42.88 3.85
736 743 5.123344 ACGGAAATTGGAACTAGGAATTTCG 59.877 40.000 16.80 15.11 42.88 3.46
741 748 3.592059 CGACGGAAATTGGAACTAGGAA 58.408 45.455 0.00 0.00 0.00 3.36
747 754 1.133869 CGCCGACGGAAATTGGAAC 59.866 57.895 20.50 0.00 34.97 3.62
752 759 1.515081 TCTTTTCGCCGACGGAAATT 58.485 45.000 20.50 0.00 45.45 1.82
757 764 0.096454 GGAATTCTTTTCGCCGACGG 59.904 55.000 10.29 10.29 40.63 4.79
770 777 0.387239 GTGTGCGGCACAAGGAATTC 60.387 55.000 34.78 18.16 46.28 2.17
783 790 0.179215 GATTTTCAGGCTCGTGTGCG 60.179 55.000 0.00 0.00 39.92 5.34
791 798 3.760684 GAGACAACATGGATTTTCAGGCT 59.239 43.478 0.00 0.00 0.00 4.58
836 843 0.256177 GTAGGAGCAGGGGGAAAAGG 59.744 60.000 0.00 0.00 0.00 3.11
843 850 1.630878 ACTCAAAAGTAGGAGCAGGGG 59.369 52.381 0.00 0.00 34.48 4.79
875 882 8.055279 TCTGTCCACATGATTAAATTTTCCTC 57.945 34.615 0.00 0.00 0.00 3.71
878 885 9.565213 CTTCTCTGTCCACATGATTAAATTTTC 57.435 33.333 0.00 0.00 0.00 2.29
885 892 3.519107 TGCCTTCTCTGTCCACATGATTA 59.481 43.478 0.00 0.00 0.00 1.75
889 896 1.277273 TCTGCCTTCTCTGTCCACATG 59.723 52.381 0.00 0.00 0.00 3.21
911 918 2.040813 ACTTATATACGGCTCTCGGGGA 59.959 50.000 0.00 0.00 44.45 4.81
914 921 2.095532 CCGACTTATATACGGCTCTCGG 59.904 54.545 0.00 2.85 44.45 4.63
967 977 4.043310 TGATCACAGAGGAATTGGAGGTTT 59.957 41.667 0.00 0.00 0.00 3.27
995 1005 2.346766 ACTGACACAGCACATCCAAA 57.653 45.000 0.00 0.00 34.37 3.28
1041 1051 2.755655 CTCTTTACTCTTCTCCTCGGCA 59.244 50.000 0.00 0.00 0.00 5.69
1080 1090 3.411114 ATCCACCTCCATGGCTGCG 62.411 63.158 6.96 0.00 39.85 5.18
1083 1093 2.280404 CTGCATCCACCTCCATGGCT 62.280 60.000 6.96 0.00 39.85 4.75
1158 1168 2.450243 GGTGGAGGAGGAGGTGGA 59.550 66.667 0.00 0.00 0.00 4.02
1200 1210 6.885376 TGAAACCAAACAACAGTTAGTAGGAA 59.115 34.615 11.11 0.00 0.00 3.36
1246 1256 1.355796 CCTCATAACGAAACGGCGCA 61.356 55.000 10.83 0.00 33.86 6.09
1294 1304 5.473066 AAACCATGAAGAAACCAAGGATG 57.527 39.130 0.00 0.00 0.00 3.51
1334 1344 6.038050 ACAAGTTTCTTCTCAAGAGAAAGCAG 59.962 38.462 13.04 2.64 45.75 4.24
1363 1376 2.203480 GGGCAACAGGAACCAGCA 60.203 61.111 0.00 0.00 39.74 4.41
1366 1379 1.152777 CACAGGGCAACAGGAACCA 60.153 57.895 0.00 0.00 39.74 3.67
1490 1504 4.823276 TTTTTGCAGGCAACCACG 57.177 50.000 6.14 0.00 35.46 4.94
1511 1525 2.476821 CAAAAGCAAGGCTCCAAGTTG 58.523 47.619 0.00 0.00 38.25 3.16
1663 1680 4.060900 GTGCAGTCAACTTCTCAATCTCA 58.939 43.478 0.00 0.00 0.00 3.27
1699 1717 6.421485 TCTAACCCTTCTGTCGTAGAGTAAT 58.579 40.000 0.00 0.00 36.95 1.89
1700 1718 5.809001 TCTAACCCTTCTGTCGTAGAGTAA 58.191 41.667 0.00 0.00 36.95 2.24
1701 1719 5.426689 TCTAACCCTTCTGTCGTAGAGTA 57.573 43.478 0.00 0.00 36.95 2.59
1702 1720 4.298103 TCTAACCCTTCTGTCGTAGAGT 57.702 45.455 0.00 0.00 36.95 3.24
1703 1721 5.838531 AATCTAACCCTTCTGTCGTAGAG 57.161 43.478 0.00 0.00 36.95 2.43
1704 1722 6.656902 TCTAATCTAACCCTTCTGTCGTAGA 58.343 40.000 0.00 0.00 0.00 2.59
1705 1723 6.939132 TCTAATCTAACCCTTCTGTCGTAG 57.061 41.667 0.00 0.00 0.00 3.51
1706 1724 7.058525 TGATCTAATCTAACCCTTCTGTCGTA 58.941 38.462 0.00 0.00 0.00 3.43
1708 1726 6.263392 TCTGATCTAATCTAACCCTTCTGTCG 59.737 42.308 0.00 0.00 0.00 4.35
1718 1736 9.956640 ATCCAATCCAATCTGATCTAATCTAAC 57.043 33.333 0.00 0.00 0.00 2.34
1721 1739 7.823310 CGAATCCAATCCAATCTGATCTAATCT 59.177 37.037 0.00 0.00 0.00 2.40
1732 1750 5.192327 AGCAAATCGAATCCAATCCAATC 57.808 39.130 0.00 0.00 0.00 2.67
1733 1751 5.603170 AAGCAAATCGAATCCAATCCAAT 57.397 34.783 0.00 0.00 0.00 3.16
1734 1752 5.417266 TGTAAGCAAATCGAATCCAATCCAA 59.583 36.000 0.00 0.00 0.00 3.53
1735 1753 4.946772 TGTAAGCAAATCGAATCCAATCCA 59.053 37.500 0.00 0.00 0.00 3.41
1736 1754 5.499139 TGTAAGCAAATCGAATCCAATCC 57.501 39.130 0.00 0.00 0.00 3.01
1932 1953 5.279456 GCAGATAGAAGGCAAAAGGGAAAAA 60.279 40.000 0.00 0.00 0.00 1.94
1933 1954 4.220602 GCAGATAGAAGGCAAAAGGGAAAA 59.779 41.667 0.00 0.00 0.00 2.29
1959 1980 6.633500 AACTGTAGTATTTCAAGCAAGCAA 57.367 33.333 0.00 0.00 0.00 3.91
1962 1983 9.334693 GATCAAAACTGTAGTATTTCAAGCAAG 57.665 33.333 0.00 0.00 0.00 4.01
1979 2000 6.571150 GCTCAAGCCTATGTTTGATCAAAACT 60.571 38.462 22.07 14.28 40.34 2.66
1980 2001 5.574443 GCTCAAGCCTATGTTTGATCAAAAC 59.426 40.000 22.07 15.86 40.34 2.43
1982 2003 5.314923 GCTCAAGCCTATGTTTGATCAAA 57.685 39.130 16.91 16.91 40.34 2.69
1983 2004 4.970662 GCTCAAGCCTATGTTTGATCAA 57.029 40.909 3.38 3.38 40.34 2.57
1997 2046 2.489329 TGAACAGCTTATTGGCTCAAGC 59.511 45.455 9.35 9.35 46.03 4.01
2005 2054 4.707030 TTCCAGCATGAACAGCTTATTG 57.293 40.909 0.00 0.00 41.14 1.90
2011 2060 1.067425 TGCATTTCCAGCATGAACAGC 60.067 47.619 0.00 0.00 39.69 4.40
2018 2067 4.463539 TGATTGTAAGTGCATTTCCAGCAT 59.536 37.500 0.00 0.00 44.79 3.79
2032 2081 9.817365 CACACAAAAGAGTCTTATGATTGTAAG 57.183 33.333 16.52 10.36 33.85 2.34
2040 2089 8.454106 CCCTTATTCACACAAAAGAGTCTTATG 58.546 37.037 5.65 7.86 0.00 1.90
2041 2090 8.164070 ACCCTTATTCACACAAAAGAGTCTTAT 58.836 33.333 5.65 0.00 0.00 1.73
2043 2092 6.263168 CACCCTTATTCACACAAAAGAGTCTT 59.737 38.462 0.00 0.00 0.00 3.01
2047 2096 4.278170 TGCACCCTTATTCACACAAAAGAG 59.722 41.667 0.00 0.00 0.00 2.85
2048 2097 4.211125 TGCACCCTTATTCACACAAAAGA 58.789 39.130 0.00 0.00 0.00 2.52
2049 2098 4.582701 TGCACCCTTATTCACACAAAAG 57.417 40.909 0.00 0.00 0.00 2.27
2050 2099 5.304101 AGATTGCACCCTTATTCACACAAAA 59.696 36.000 0.00 0.00 0.00 2.44
2054 2103 3.129287 CCAGATTGCACCCTTATTCACAC 59.871 47.826 0.00 0.00 0.00 3.82
2099 2152 8.032451 CCGTTTGGGATTCTATAAACAAACATT 58.968 33.333 15.49 0.00 44.57 2.71
2192 2346 5.582689 TCAGCATCGTAGAGAGAAAATCA 57.417 39.130 0.00 0.00 43.63 2.57
2311 2465 4.284746 GGATAGTACCTTGAGAAGATGGGG 59.715 50.000 0.00 0.00 0.00 4.96
2333 2487 3.055747 GTCTGAAGTAGGAAGGAGTTGGG 60.056 52.174 0.00 0.00 0.00 4.12
2334 2488 3.835395 AGTCTGAAGTAGGAAGGAGTTGG 59.165 47.826 0.00 0.00 0.00 3.77
2336 2490 3.759618 CGAGTCTGAAGTAGGAAGGAGTT 59.240 47.826 0.00 0.00 0.00 3.01
2338 2492 3.375922 GTCGAGTCTGAAGTAGGAAGGAG 59.624 52.174 0.00 0.00 0.00 3.69
2342 2511 2.818432 GGTGTCGAGTCTGAAGTAGGAA 59.182 50.000 0.00 0.00 0.00 3.36
2349 2518 1.967779 TGGAATGGTGTCGAGTCTGAA 59.032 47.619 0.00 0.00 0.00 3.02
2351 2520 1.404717 CCTGGAATGGTGTCGAGTCTG 60.405 57.143 0.00 0.00 0.00 3.51
2355 2524 1.450312 GGCCTGGAATGGTGTCGAG 60.450 63.158 0.00 0.00 0.00 4.04
2359 2528 2.029892 TTTGGGGCCTGGAATGGTGT 62.030 55.000 0.84 0.00 0.00 4.16
2361 2530 0.104725 TTTTTGGGGCCTGGAATGGT 60.105 50.000 0.84 0.00 0.00 3.55
2365 2534 0.263172 TGAGTTTTTGGGGCCTGGAA 59.737 50.000 0.84 0.00 0.00 3.53
2369 2538 1.428912 TCAGATGAGTTTTTGGGGCCT 59.571 47.619 0.84 0.00 0.00 5.19
2373 2542 5.067413 CCATGATCTCAGATGAGTTTTTGGG 59.933 44.000 9.56 3.14 42.60 4.12
2375 2544 5.124936 TGCCATGATCTCAGATGAGTTTTTG 59.875 40.000 9.56 4.73 42.60 2.44
2387 2556 1.062658 TCCTCCTCTGCCATGATCTCA 60.063 52.381 0.00 0.00 0.00 3.27
2388 2557 1.714541 TCCTCCTCTGCCATGATCTC 58.285 55.000 0.00 0.00 0.00 2.75
2389 2558 2.048601 CTTCCTCCTCTGCCATGATCT 58.951 52.381 0.00 0.00 0.00 2.75
2520 2702 0.540923 AGATGAACTGGGAGAGCAGC 59.459 55.000 0.00 0.00 0.00 5.25
2609 2812 0.252881 TCTTCCTCACCTCTGGGCAT 60.253 55.000 0.00 0.00 35.63 4.40
2612 2818 1.484240 GTCATCTTCCTCACCTCTGGG 59.516 57.143 0.00 0.00 38.88 4.45
2657 2864 3.495543 GCTGAGCTTAGCCACAGC 58.504 61.111 27.35 27.35 45.55 4.40
2659 2866 1.456296 CATTGCTGAGCTTAGCCACA 58.544 50.000 25.95 11.70 43.02 4.17
2660 2867 0.737219 CCATTGCTGAGCTTAGCCAC 59.263 55.000 25.95 1.43 43.02 5.01
2671 2878 0.393820 AAAAGGCACCACCATTGCTG 59.606 50.000 0.00 0.00 43.14 4.41
2741 2949 6.202331 TGTGATAATCTCCCTAAGGAACTCA 58.798 40.000 0.00 0.00 43.40 3.41
2750 2958 4.736473 TGGTCGATGTGATAATCTCCCTA 58.264 43.478 0.00 0.00 0.00 3.53
2759 2967 9.309516 GTAAACTAAAGAATGGTCGATGTGATA 57.690 33.333 0.00 0.00 0.00 2.15
2800 3008 6.010219 ACCATAAAACACAGGCTTAGAACAT 58.990 36.000 0.00 0.00 0.00 2.71
2920 3161 7.102993 ACACCAAAGAAGCACATTAACTTTTT 58.897 30.769 0.00 0.00 0.00 1.94
2921 3162 6.639563 ACACCAAAGAAGCACATTAACTTTT 58.360 32.000 0.00 0.00 0.00 2.27
2922 3163 6.220726 ACACCAAAGAAGCACATTAACTTT 57.779 33.333 0.00 0.00 0.00 2.66
2925 3166 6.677913 ACATACACCAAAGAAGCACATTAAC 58.322 36.000 0.00 0.00 0.00 2.01
2947 3188 7.239763 TGTTCATGTTAATCCTCTCAGTACA 57.760 36.000 0.00 0.00 0.00 2.90
2948 3189 7.981789 TGATGTTCATGTTAATCCTCTCAGTAC 59.018 37.037 0.00 0.00 0.00 2.73
3002 3243 2.988493 TCGCAAGCAAATGAAAATCAGC 59.012 40.909 0.00 0.00 37.18 4.26
3093 3351 4.929819 TTTGTTACCTCCCTTTTTGCTC 57.070 40.909 0.00 0.00 0.00 4.26
3167 3450 3.264193 TGAGCTTAGGTGAATGGTGATGT 59.736 43.478 0.00 0.00 0.00 3.06
3226 3509 2.026822 CACAGCTGTTAATCCTCCCTGT 60.027 50.000 18.94 0.00 32.79 4.00
3227 3510 2.237143 TCACAGCTGTTAATCCTCCCTG 59.763 50.000 18.94 0.95 0.00 4.45
3244 3527 4.022329 CACTAGGCCGTCATATACATCACA 60.022 45.833 0.00 0.00 0.00 3.58
3246 3529 3.509967 CCACTAGGCCGTCATATACATCA 59.490 47.826 0.00 0.00 0.00 3.07
3249 3532 2.889045 GTCCACTAGGCCGTCATATACA 59.111 50.000 0.00 0.00 33.74 2.29
3255 3541 0.981183 ATTTGTCCACTAGGCCGTCA 59.019 50.000 0.00 0.00 33.74 4.35
3407 3693 1.202651 CGAAAACTCACAGGGACAGGT 60.203 52.381 0.00 0.00 0.00 4.00
3418 3704 4.133820 TCATTCCTGCTTTCGAAAACTCA 58.866 39.130 12.41 9.10 0.00 3.41
3466 3752 2.515429 ACAAGGCCCCATCATAGAACAT 59.485 45.455 0.00 0.00 0.00 2.71
3551 3837 1.139734 CGACTCCCAGTGGATCGTG 59.860 63.158 11.95 0.00 40.80 4.35
3617 3903 7.412129 CGACCATCTTATCTCTATGTCTACGAC 60.412 44.444 0.00 0.00 0.00 4.34
3660 3946 9.828852 GACTACTTCCATCGATAACACTATTAG 57.171 37.037 0.00 0.00 0.00 1.73
3662 3948 8.234136 TGACTACTTCCATCGATAACACTATT 57.766 34.615 0.00 0.00 0.00 1.73
3672 3958 9.297037 TGATATATTTCTGACTACTTCCATCGA 57.703 33.333 0.00 0.00 0.00 3.59
3754 4041 1.381867 TGGTTCATGGATGGGGTCTT 58.618 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.