Multiple sequence alignment - TraesCS2D01G439500

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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 TraesCS2D01G439500 chr2D 100.000 2830 0 0 1 2830 548895576 548898405 0.000000e+00 5227.0
1 TraesCS2D01G439500 chr2D 90.205 1317 106 10 541 1835 110057575 110056260 0.000000e+00 1696.0
2 TraesCS2D01G439500 chr2D 92.671 423 28 3 2003 2422 538391591 538392013 8.670000e-170 606.0
3 TraesCS2D01G439500 chr2D 92.891 211 15 0 2052 2262 110055732 110055522 9.850000e-80 307.0
4 TraesCS2D01G439500 chr2D 91.919 99 7 1 2388 2485 316642767 316642669 1.370000e-28 137.0
5 TraesCS2D01G439500 chr2D 91.111 90 6 2 2415 2504 110055529 110055442 1.380000e-23 121.0
6 TraesCS2D01G439500 chr7D 90.174 1842 118 20 1 1840 580777002 580778782 0.000000e+00 2340.0
7 TraesCS2D01G439500 chr7D 93.085 376 25 1 2011 2386 580058178 580057804 1.480000e-152 549.0
8 TraesCS2D01G439500 chr7D 91.892 296 22 2 2011 2306 407792189 407791896 2.030000e-111 412.0
9 TraesCS2D01G439500 chr7D 91.111 90 7 1 2415 2504 272825111 272825023 1.380000e-23 121.0
10 TraesCS2D01G439500 chr7B 89.691 1843 151 19 1 1840 648440610 648442416 0.000000e+00 2314.0
11 TraesCS2D01G439500 chr7B 88.251 1864 151 24 130 1948 715229284 715227444 0.000000e+00 2167.0
12 TraesCS2D01G439500 chr7B 89.568 1505 112 23 1 1482 209399283 209400765 0.000000e+00 1868.0
13 TraesCS2D01G439500 chr7B 92.881 295 15 5 2507 2801 209401956 209402244 9.370000e-115 424.0
14 TraesCS2D01G439500 chr7B 92.542 295 18 3 2507 2801 38785827 38785537 1.210000e-113 420.0
15 TraesCS2D01G439500 chr7B 91.864 295 21 3 2507 2801 511708599 511708308 2.620000e-110 409.0
16 TraesCS2D01G439500 chr7B 92.417 211 16 0 2052 2262 332400916 332401126 4.580000e-78 302.0
17 TraesCS2D01G439500 chr7B 90.698 172 12 2 2294 2461 715227054 715226883 2.840000e-55 226.0
18 TraesCS2D01G439500 chr7B 89.899 99 9 1 2388 2485 715226918 715226820 2.960000e-25 126.0
19 TraesCS2D01G439500 chr3B 88.200 1856 188 24 1 1840 493571054 493572894 0.000000e+00 2185.0
20 TraesCS2D01G439500 chr6B 89.993 1509 120 24 1 1482 559486602 559488106 0.000000e+00 1921.0
21 TraesCS2D01G439500 chr6B 92.227 952 63 7 541 1485 172268715 172267768 0.000000e+00 1338.0
22 TraesCS2D01G439500 chr6B 94.505 455 23 1 3 455 172269510 172269056 0.000000e+00 701.0
23 TraesCS2D01G439500 chr3D 90.066 1359 117 8 491 1835 189780289 189781643 0.000000e+00 1746.0
24 TraesCS2D01G439500 chr3D 94.725 455 23 1 1 455 189779677 189780130 0.000000e+00 706.0
25 TraesCS2D01G439500 chr3D 92.476 412 28 3 2011 2422 464060624 464060216 1.130000e-163 586.0
26 TraesCS2D01G439500 chr1B 88.757 1352 137 3 503 1840 439538880 439537530 0.000000e+00 1640.0
27 TraesCS2D01G439500 chr5A 92.055 944 68 6 541 1482 582941039 582941977 0.000000e+00 1321.0
28 TraesCS2D01G439500 chr5A 95.385 455 21 0 1 455 582940244 582940698 0.000000e+00 725.0
29 TraesCS2D01G439500 chr5A 94.945 455 21 2 1 455 616789090 616789542 0.000000e+00 712.0
30 TraesCS2D01G439500 chr5A 93.846 455 27 1 1 455 129148443 129148896 0.000000e+00 684.0
31 TraesCS2D01G439500 chr5A 89.316 468 47 2 1543 2010 42100151 42099687 4.060000e-163 584.0
32 TraesCS2D01G439500 chr5A 83.261 460 66 9 1383 1835 616790777 616791232 2.030000e-111 412.0
33 TraesCS2D01G439500 chr5A 98.571 70 1 0 491 560 129149326 129149395 1.060000e-24 124.0
34 TraesCS2D01G439500 chr4A 95.604 455 20 0 1 455 90327758 90328212 0.000000e+00 730.0
35 TraesCS2D01G439500 chr4A 92.453 212 15 1 2052 2262 95385973 95385762 4.580000e-78 302.0
36 TraesCS2D01G439500 chr4A 90.000 90 8 1 2415 2504 95385769 95385681 6.410000e-22 115.0
37 TraesCS2D01G439500 chr1D 95.154 454 18 2 2 455 442117968 442117519 0.000000e+00 713.0
38 TraesCS2D01G439500 chr1D 87.389 452 45 3 1401 1840 442107962 442107511 2.520000e-140 508.0
39 TraesCS2D01G439500 chr1D 96.970 33 1 0 1954 1986 47708210 47708242 3.940000e-04 56.5
40 TraesCS2D01G439500 chr5B 88.889 468 52 0 1543 2010 56551154 56551621 6.800000e-161 577.0
41 TraesCS2D01G439500 chr5B 87.668 446 43 3 1402 1835 473281920 473281475 2.520000e-140 508.0
42 TraesCS2D01G439500 chr5B 95.000 200 10 0 2011 2210 434923342 434923143 5.890000e-82 315.0
43 TraesCS2D01G439500 chr5D 88.248 468 55 0 1543 2010 53874933 53875400 6.850000e-156 560.0
44 TraesCS2D01G439500 chr2B 90.634 363 29 3 2103 2461 177889822 177890183 7.090000e-131 477.0
45 TraesCS2D01G439500 chr2B 92.157 102 7 1 2385 2485 177890145 177890246 2.940000e-30 143.0
46 TraesCS2D01G439500 chr4D 95.890 73 2 1 2415 2487 60873540 60873611 1.780000e-22 117.0
47 TraesCS2D01G439500 chr2A 84.158 101 9 4 2290 2384 64626899 64626800 1.080000e-14 91.6
48 TraesCS2D01G439500 chr2A 82.178 101 11 4 2290 2384 15915568 15915469 2.340000e-11 80.5
49 TraesCS2D01G439500 chr1A 84.000 100 10 4 2290 2383 242689556 242689457 1.080000e-14 91.6
50 TraesCS2D01G439500 chr7A 84.524 84 2 2 2566 2649 692022800 692022728 3.910000e-09 73.1


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 TraesCS2D01G439500 chr2D 548895576 548898405 2829 False 5227.000000 5227 100.000000 1 2830 1 chr2D.!!$F2 2829
1 TraesCS2D01G439500 chr2D 110055442 110057575 2133 True 708.000000 1696 91.402333 541 2504 3 chr2D.!!$R2 1963
2 TraesCS2D01G439500 chr7D 580777002 580778782 1780 False 2340.000000 2340 90.174000 1 1840 1 chr7D.!!$F1 1839
3 TraesCS2D01G439500 chr7B 648440610 648442416 1806 False 2314.000000 2314 89.691000 1 1840 1 chr7B.!!$F2 1839
4 TraesCS2D01G439500 chr7B 209399283 209402244 2961 False 1146.000000 1868 91.224500 1 2801 2 chr7B.!!$F3 2800
5 TraesCS2D01G439500 chr7B 715226820 715229284 2464 True 839.666667 2167 89.616000 130 2485 3 chr7B.!!$R3 2355
6 TraesCS2D01G439500 chr3B 493571054 493572894 1840 False 2185.000000 2185 88.200000 1 1840 1 chr3B.!!$F1 1839
7 TraesCS2D01G439500 chr6B 559486602 559488106 1504 False 1921.000000 1921 89.993000 1 1482 1 chr6B.!!$F1 1481
8 TraesCS2D01G439500 chr6B 172267768 172269510 1742 True 1019.500000 1338 93.366000 3 1485 2 chr6B.!!$R1 1482
9 TraesCS2D01G439500 chr3D 189779677 189781643 1966 False 1226.000000 1746 92.395500 1 1835 2 chr3D.!!$F1 1834
10 TraesCS2D01G439500 chr1B 439537530 439538880 1350 True 1640.000000 1640 88.757000 503 1840 1 chr1B.!!$R1 1337
11 TraesCS2D01G439500 chr5A 582940244 582941977 1733 False 1023.000000 1321 93.720000 1 1482 2 chr5A.!!$F2 1481
12 TraesCS2D01G439500 chr5A 616789090 616791232 2142 False 562.000000 712 89.103000 1 1835 2 chr5A.!!$F3 1834
13 TraesCS2D01G439500 chr5A 129148443 129149395 952 False 404.000000 684 96.208500 1 560 2 chr5A.!!$F1 559

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
663 1282 0.984230 AAGAGCTCAATGGAACCCGA 59.016 50.000 17.77 0.0 0.0 5.14 F
670 1289 1.422024 TCAATGGAACCCGACTTTGGA 59.578 47.619 0.00 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 2282 0.036199 CTCCTGCTCTGCTTGCTTCT 60.036 55.0 0.00 0.00 0.0 2.85 R
2524 4211 0.251922 TAGCACCCGGGAGTAGTTGT 60.252 55.0 32.02 7.14 0.0 3.32 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
186 187 4.999311 GGAACAACGTATTAGGGAACACTT 59.001 41.667 0.00 0.00 0.00 3.16
429 454 4.462483 GTGAAGAAGCCATCACCCAAAATA 59.538 41.667 0.00 0.00 40.00 1.40
663 1282 0.984230 AAGAGCTCAATGGAACCCGA 59.016 50.000 17.77 0.00 0.00 5.14
670 1289 1.422024 TCAATGGAACCCGACTTTGGA 59.578 47.619 0.00 0.00 0.00 3.53
714 1333 4.350368 TCAGGAGCACAACACTTCATAA 57.650 40.909 0.00 0.00 0.00 1.90
722 1341 4.941263 GCACAACACTTCATAACATAGGGA 59.059 41.667 0.00 0.00 0.00 4.20
732 1351 6.463995 TCATAACATAGGGAACAAAATGGC 57.536 37.500 0.00 0.00 0.00 4.40
803 1422 7.850193 AGATATGGCCACACAAATTTTACAAT 58.150 30.769 8.16 0.00 0.00 2.71
884 1503 2.021722 GCAAACAGAGCGGTGTCAA 58.978 52.632 0.00 0.00 0.00 3.18
906 1525 5.207110 ACTGGAGCTATCATACACACATC 57.793 43.478 0.00 0.00 0.00 3.06
914 1533 8.358582 AGCTATCATACACACATCATAGATGA 57.641 34.615 13.46 0.75 41.70 2.92
1081 1707 4.689612 ATACAGTCGTGGCCAGAAATAT 57.310 40.909 5.11 0.00 0.00 1.28
1121 1747 4.657013 CCTTTTCCCCTCTATGATAAGCC 58.343 47.826 0.00 0.00 0.00 4.35
1204 1836 9.974980 TTTGTTGACCTTTATAATGAGTTTTCC 57.025 29.630 0.04 0.00 0.00 3.13
1331 1968 5.427806 TGATCATGAAGTGGAAAGAGAGGAT 59.572 40.000 0.00 0.00 0.00 3.24
1391 2028 9.445878 GATGATTTACACATGTATGATGATCCT 57.554 33.333 0.00 0.00 0.00 3.24
1476 2167 2.636830 CCCCAAGTGATGCTACTCAAG 58.363 52.381 0.00 0.00 0.00 3.02
1482 2173 4.993029 AGTGATGCTACTCAAGTAGGTC 57.007 45.455 16.77 4.18 46.07 3.85
1488 2179 3.526430 TGCTACTCAAGTAGGTCCTCCTA 59.474 47.826 16.77 0.00 46.07 2.94
1502 2196 9.145442 GTAGGTCCTCCTAGTAGTTCAAATAAT 57.855 37.037 0.00 0.00 45.75 1.28
1507 2201 9.435570 TCCTCCTAGTAGTTCAAATAATAAGCT 57.564 33.333 0.00 0.00 0.00 3.74
1596 2296 0.109689 CAAGCAGAAGCAAGCAGAGC 60.110 55.000 0.00 0.00 45.49 4.09
1650 2350 2.686118 GCCCAAGAATTCTCCATCAGCT 60.686 50.000 8.78 0.00 0.00 4.24
1703 2403 3.188100 CGCCGCGATGAAAGAGCA 61.188 61.111 8.23 0.00 0.00 4.26
1707 2407 0.528466 CCGCGATGAAAGAGCAGCTA 60.528 55.000 8.23 0.00 0.00 3.32
1760 2461 5.702670 TCGTGAGATTTTTCTCAATTCTGCT 59.297 36.000 7.23 0.00 46.81 4.24
1763 2464 5.242171 TGAGATTTTTCTCAATTCTGCTGCA 59.758 36.000 0.88 0.88 43.03 4.41
1780 2481 3.368220 GCTGCAGAAGATGAAGAGAGTGA 60.368 47.826 20.43 0.00 36.54 3.41
1785 2487 5.642919 GCAGAAGATGAAGAGAGTGATGTTT 59.357 40.000 0.00 0.00 0.00 2.83
1853 2555 7.151694 AGGTAAGCTACTTATGACTCTAGGA 57.848 40.000 0.00 0.00 0.00 2.94
1874 2908 7.404671 AGGACAGTAAATTGTTTGTTGTTCT 57.595 32.000 0.00 0.00 0.00 3.01
1893 2927 9.738832 GTTGTTCTAGATCAGTAATCCTCTTAC 57.261 37.037 3.80 0.00 34.67 2.34
1910 2944 4.914983 TCTTACGACTCTAGGTCCTTCAA 58.085 43.478 0.00 0.00 41.64 2.69
1912 2946 5.771666 TCTTACGACTCTAGGTCCTTCAAAA 59.228 40.000 0.00 0.00 41.64 2.44
1919 2953 7.041372 CGACTCTAGGTCCTTCAAAATTTGAAA 60.041 37.037 19.95 5.78 42.63 2.69
1937 2972 1.435256 AAGATGGCCGCTATACCCTT 58.565 50.000 0.00 0.00 0.00 3.95
1948 2983 5.705905 GCCGCTATACCCTTATTCAATCTTT 59.294 40.000 0.00 0.00 0.00 2.52
1949 2984 6.206829 GCCGCTATACCCTTATTCAATCTTTT 59.793 38.462 0.00 0.00 0.00 2.27
1950 2985 7.389607 GCCGCTATACCCTTATTCAATCTTTTA 59.610 37.037 0.00 0.00 0.00 1.52
1951 2986 8.936864 CCGCTATACCCTTATTCAATCTTTTAG 58.063 37.037 0.00 0.00 0.00 1.85
1952 2987 9.706691 CGCTATACCCTTATTCAATCTTTTAGA 57.293 33.333 0.00 0.00 0.00 2.10
1980 3015 7.848223 TGTATGATACATGTTTCTTCCACAG 57.152 36.000 15.92 0.00 32.89 3.66
1988 3023 1.546029 GTTTCTTCCACAGCCCATTCC 59.454 52.381 0.00 0.00 0.00 3.01
1996 3031 2.025887 CCACAGCCCATTCCTTTCTAGT 60.026 50.000 0.00 0.00 0.00 2.57
2004 3039 5.316987 CCCATTCCTTTCTAGTTGAACTGT 58.683 41.667 8.33 0.00 33.88 3.55
2005 3040 5.770162 CCCATTCCTTTCTAGTTGAACTGTT 59.230 40.000 8.33 0.00 33.88 3.16
2013 3048 8.889717 CCTTTCTAGTTGAACTGTTGTTTAAGA 58.110 33.333 8.33 0.00 36.39 2.10
2025 3060 9.927668 AACTGTTGTTTAAGAAATATTCATGGG 57.072 29.630 0.00 0.00 31.37 4.00
2026 3061 9.308000 ACTGTTGTTTAAGAAATATTCATGGGA 57.692 29.630 0.00 0.00 0.00 4.37
2027 3062 9.573133 CTGTTGTTTAAGAAATATTCATGGGAC 57.427 33.333 0.00 0.00 0.00 4.46
2029 3064 9.573133 GTTGTTTAAGAAATATTCATGGGACTG 57.427 33.333 0.00 0.00 0.00 3.51
2030 3065 7.771183 TGTTTAAGAAATATTCATGGGACTGC 58.229 34.615 0.00 0.00 0.00 4.40
2031 3066 6.959639 TTAAGAAATATTCATGGGACTGCC 57.040 37.500 0.00 0.00 0.00 4.85
2042 3077 3.346426 GGACTGCCCAGTGAATGTT 57.654 52.632 5.53 0.00 42.66 2.71
2043 3078 0.883833 GGACTGCCCAGTGAATGTTG 59.116 55.000 5.53 0.00 42.66 3.33
2046 3081 1.956477 ACTGCCCAGTGAATGTTGAAC 59.044 47.619 0.00 0.00 40.75 3.18
2143 3787 7.661536 TTGTACCTCTTGATGTAGCTCTAAT 57.338 36.000 0.00 0.00 0.00 1.73
2197 3841 9.271828 CTTTATTGTACTTTTCCCTTTGCAAAT 57.728 29.630 13.23 0.00 0.00 2.32
2222 3866 1.871080 ACAGCCTCTGAAGTTGAACG 58.129 50.000 0.29 0.00 35.18 3.95
2223 3867 1.151668 CAGCCTCTGAAGTTGAACGG 58.848 55.000 0.00 0.00 32.44 4.44
2225 3869 1.001406 AGCCTCTGAAGTTGAACGGAG 59.999 52.381 0.00 0.00 38.71 4.63
2229 3873 3.467803 CTCTGAAGTTGAACGGAGGTTT 58.532 45.455 0.00 0.00 36.24 3.27
2234 3878 2.572290 AGTTGAACGGAGGTTTCCTTG 58.428 47.619 0.00 0.00 41.67 3.61
2241 3885 1.610886 CGGAGGTTTCCTTGGTTCTCC 60.611 57.143 0.00 0.00 41.67 3.71
2271 3915 5.643379 TTTGTATTTTGTGATGGAGGAGC 57.357 39.130 0.00 0.00 0.00 4.70
2272 3916 4.574674 TGTATTTTGTGATGGAGGAGCT 57.425 40.909 0.00 0.00 0.00 4.09
2273 3917 5.692115 TGTATTTTGTGATGGAGGAGCTA 57.308 39.130 0.00 0.00 0.00 3.32
2274 3918 6.252599 TGTATTTTGTGATGGAGGAGCTAT 57.747 37.500 0.00 0.00 0.00 2.97
2275 3919 7.373617 TGTATTTTGTGATGGAGGAGCTATA 57.626 36.000 0.00 0.00 0.00 1.31
2276 3920 7.445121 TGTATTTTGTGATGGAGGAGCTATAG 58.555 38.462 0.00 0.00 0.00 1.31
2277 3921 5.957771 TTTTGTGATGGAGGAGCTATAGT 57.042 39.130 0.84 0.00 0.00 2.12
2278 3922 5.957771 TTTGTGATGGAGGAGCTATAGTT 57.042 39.130 0.84 0.00 0.00 2.24
2279 3923 5.537300 TTGTGATGGAGGAGCTATAGTTC 57.463 43.478 8.01 8.01 0.00 3.01
2280 3924 3.898123 TGTGATGGAGGAGCTATAGTTCC 59.102 47.826 24.16 24.16 44.60 3.62
2281 3925 3.898123 GTGATGGAGGAGCTATAGTTCCA 59.102 47.826 30.49 22.21 46.37 3.53
2283 3927 5.717178 GTGATGGAGGAGCTATAGTTCCATA 59.283 44.000 30.49 19.04 45.94 2.74
2284 3928 6.382570 GTGATGGAGGAGCTATAGTTCCATAT 59.617 42.308 30.49 21.98 45.94 1.78
2285 3929 6.382282 TGATGGAGGAGCTATAGTTCCATATG 59.618 42.308 30.49 0.00 45.94 1.78
2286 3930 4.467795 TGGAGGAGCTATAGTTCCATATGC 59.532 45.833 30.49 18.89 46.37 3.14
2287 3931 4.467795 GGAGGAGCTATAGTTCCATATGCA 59.532 45.833 30.49 0.00 46.37 3.96
2288 3932 5.413309 AGGAGCTATAGTTCCATATGCAC 57.587 43.478 30.49 7.54 46.37 4.57
2289 3933 4.081972 AGGAGCTATAGTTCCATATGCACG 60.082 45.833 30.49 0.00 46.37 5.34
2290 3934 4.082190 GGAGCTATAGTTCCATATGCACGA 60.082 45.833 25.98 0.00 43.82 4.35
2291 3935 5.394663 GGAGCTATAGTTCCATATGCACGAT 60.395 44.000 25.98 1.19 43.82 3.73
2292 3936 5.655488 AGCTATAGTTCCATATGCACGATC 58.345 41.667 0.84 0.00 0.00 3.69
2308 3952 6.627243 TGCACGATCTATAGTTGTTAGTTGT 58.373 36.000 0.00 0.00 0.00 3.32
2395 4039 9.745018 AGGTCGATGATCCATTTCATATAATTT 57.255 29.630 0.00 0.00 36.48 1.82
2487 4174 5.197451 TGCAAGGGAAAAGTCTCTTTGTTA 58.803 37.500 0.00 0.00 42.26 2.41
2489 4176 5.278512 GCAAGGGAAAAGTCTCTTTGTTAGG 60.279 44.000 0.00 0.00 42.26 2.69
2490 4177 4.399219 AGGGAAAAGTCTCTTTGTTAGGC 58.601 43.478 0.00 0.00 25.56 3.93
2493 4180 4.083961 GGAAAAGTCTCTTTGTTAGGCGAC 60.084 45.833 0.00 0.00 0.00 5.19
2495 4182 3.963428 AGTCTCTTTGTTAGGCGACAT 57.037 42.857 0.00 0.00 31.37 3.06
2504 4191 5.446143 TTGTTAGGCGACATGAATTTTGT 57.554 34.783 0.00 0.00 0.00 2.83
2505 4192 6.561737 TTGTTAGGCGACATGAATTTTGTA 57.438 33.333 0.00 0.00 0.00 2.41
2524 4211 5.235850 TGTAGGTTCATTAGGTGCAGAAA 57.764 39.130 0.00 0.00 0.00 2.52
2535 4222 2.152016 GGTGCAGAAACAACTACTCCC 58.848 52.381 0.00 0.00 0.00 4.30
2537 4224 1.270625 TGCAGAAACAACTACTCCCGG 60.271 52.381 0.00 0.00 0.00 5.73
2569 4256 0.813184 ATTGCTCGGTGGAAATGCTG 59.187 50.000 0.00 0.00 0.00 4.41
2584 4271 3.996150 ATGCTGTCTTGTTCTGGTTTG 57.004 42.857 0.00 0.00 0.00 2.93
2596 4283 4.578516 TGTTCTGGTTTGTGAATGTGTAGG 59.421 41.667 0.00 0.00 0.00 3.18
2603 4290 6.013725 TGGTTTGTGAATGTGTAGGAGACTAT 60.014 38.462 0.00 0.00 46.56 2.12
2639 4326 9.197694 GTGTCCATAAGCAAATACTAGTATCAG 57.802 37.037 15.72 11.94 0.00 2.90
2695 4382 5.063880 GTGATGTATAAATCCTGTCACCCC 58.936 45.833 0.23 0.00 0.00 4.95
2696 4383 3.830744 TGTATAAATCCTGTCACCCCG 57.169 47.619 0.00 0.00 0.00 5.73
2697 4384 2.158871 TGTATAAATCCTGTCACCCCGC 60.159 50.000 0.00 0.00 0.00 6.13
2746 4433 4.887748 ACTTGACCGATATATCAGGCAAG 58.112 43.478 30.68 30.68 38.49 4.01
2748 4435 4.955811 TGACCGATATATCAGGCAAGTT 57.044 40.909 17.95 4.37 0.00 2.66
2750 4437 5.680619 TGACCGATATATCAGGCAAGTTTT 58.319 37.500 17.95 3.31 0.00 2.43
2751 4438 5.527214 TGACCGATATATCAGGCAAGTTTTG 59.473 40.000 17.95 0.00 0.00 2.44
2753 4440 5.885912 ACCGATATATCAGGCAAGTTTTGTT 59.114 36.000 17.95 0.00 0.00 2.83
2754 4441 6.038271 ACCGATATATCAGGCAAGTTTTGTTC 59.962 38.462 17.95 0.00 0.00 3.18
2755 4442 6.260936 CCGATATATCAGGCAAGTTTTGTTCT 59.739 38.462 13.11 0.00 0.00 3.01
2756 4443 7.441157 CCGATATATCAGGCAAGTTTTGTTCTA 59.559 37.037 13.11 0.00 0.00 2.10
2776 4463 0.034186 CAATACTTGCCTGCCTCCCA 60.034 55.000 0.00 0.00 0.00 4.37
2777 4464 0.257039 AATACTTGCCTGCCTCCCAG 59.743 55.000 0.00 0.00 41.41 4.45
2788 4475 4.384868 GCCTGCCTCCCAGTTTACTTATTA 60.385 45.833 0.00 0.00 40.06 0.98
2789 4476 5.123936 CCTGCCTCCCAGTTTACTTATTAC 58.876 45.833 0.00 0.00 40.06 1.89
2803 4490 9.840427 GTTTACTTATTACCTACGAGTTACACA 57.160 33.333 0.00 0.00 0.00 3.72
2812 4499 9.740239 TTACCTACGAGTTACACATATGATTTC 57.260 33.333 10.38 0.00 0.00 2.17
2813 4500 8.008513 ACCTACGAGTTACACATATGATTTCT 57.991 34.615 10.38 1.16 0.00 2.52
2814 4501 7.921214 ACCTACGAGTTACACATATGATTTCTG 59.079 37.037 10.38 0.00 0.00 3.02
2815 4502 7.921214 CCTACGAGTTACACATATGATTTCTGT 59.079 37.037 10.38 5.44 0.00 3.41
2816 4503 7.525688 ACGAGTTACACATATGATTTCTGTG 57.474 36.000 10.38 0.00 44.51 3.66
2817 4504 6.036083 ACGAGTTACACATATGATTTCTGTGC 59.964 38.462 10.38 1.50 43.13 4.57
2818 4505 6.035975 CGAGTTACACATATGATTTCTGTGCA 59.964 38.462 10.38 0.00 43.13 4.57
2819 4506 7.076842 AGTTACACATATGATTTCTGTGCAC 57.923 36.000 10.75 10.75 43.13 4.57
2820 4507 6.881065 AGTTACACATATGATTTCTGTGCACT 59.119 34.615 19.41 6.92 43.13 4.40
2821 4508 7.391554 AGTTACACATATGATTTCTGTGCACTT 59.608 33.333 19.41 0.00 43.13 3.16
2822 4509 6.579666 ACACATATGATTTCTGTGCACTTT 57.420 33.333 19.41 0.00 43.13 2.66
2823 4510 6.985117 ACACATATGATTTCTGTGCACTTTT 58.015 32.000 19.41 0.00 43.13 2.27
2824 4511 6.864685 ACACATATGATTTCTGTGCACTTTTG 59.135 34.615 19.41 5.93 43.13 2.44
2825 4512 6.309494 CACATATGATTTCTGTGCACTTTTGG 59.691 38.462 19.41 3.44 34.47 3.28
2826 4513 4.942761 ATGATTTCTGTGCACTTTTGGT 57.057 36.364 19.41 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 173 7.758820 TCATCCCTTAAAGTGTTCCCTAATA 57.241 36.000 0.00 0.00 0.00 0.98
173 174 6.652205 TCATCCCTTAAAGTGTTCCCTAAT 57.348 37.500 0.00 0.00 0.00 1.73
186 187 3.698539 TGCATTGCGATTTCATCCCTTAA 59.301 39.130 3.84 0.00 0.00 1.85
663 1282 3.054728 CCACCAAACCCTTTTTCCAAAGT 60.055 43.478 0.00 0.00 38.22 2.66
670 1289 4.616553 AGTAACTCCACCAAACCCTTTTT 58.383 39.130 0.00 0.00 0.00 1.94
714 1333 3.099141 CCAGCCATTTTGTTCCCTATGT 58.901 45.455 0.00 0.00 0.00 2.29
722 1341 3.030291 TCAGTTGACCAGCCATTTTGTT 58.970 40.909 0.00 0.00 0.00 2.83
732 1351 2.260844 TCCAAGCTTCAGTTGACCAG 57.739 50.000 0.00 0.00 0.00 4.00
803 1422 8.862325 TTTCTGTTTTTCCTGAATCTATAGCA 57.138 30.769 0.00 0.00 0.00 3.49
884 1503 4.651045 TGATGTGTGTATGATAGCTCCAGT 59.349 41.667 0.00 0.00 0.00 4.00
914 1533 1.246649 TTGCCAAAGATGTGCGTCAT 58.753 45.000 0.00 0.00 39.77 3.06
1081 1707 6.884836 GGAAAAGGCTTATTCTGGAACTTAGA 59.115 38.462 0.00 0.00 0.00 2.10
1121 1747 4.588106 ACTCACCATCATAGAGATCACCAG 59.412 45.833 0.00 0.00 33.72 4.00
1198 1825 1.480545 AGGCCACACAACAAGGAAAAC 59.519 47.619 5.01 0.00 0.00 2.43
1204 1836 4.582701 TCATTAAAGGCCACACAACAAG 57.417 40.909 5.01 0.00 0.00 3.16
1255 1892 8.463930 TGATGTGAAATTGAAGTTACCTTCTT 57.536 30.769 1.45 0.00 46.07 2.52
1331 1968 5.241403 TCAGGTCAAAAGAGAAGGCATTA 57.759 39.130 0.00 0.00 0.00 1.90
1391 2028 0.824109 CACTTGGGGCGACATCTCTA 59.176 55.000 0.00 0.00 0.00 2.43
1476 2167 8.530804 TTATTTGAACTACTAGGAGGACCTAC 57.469 38.462 6.98 0.00 45.83 3.18
1502 2196 7.403671 TCTTCTTAGTCTCCTTCACTAGCTTA 58.596 38.462 0.00 0.00 0.00 3.09
1507 2201 8.578151 GTTTCTTCTTCTTAGTCTCCTTCACTA 58.422 37.037 0.00 0.00 0.00 2.74
1582 2282 0.036199 CTCCTGCTCTGCTTGCTTCT 60.036 55.000 0.00 0.00 0.00 2.85
1596 2296 0.673022 GCCAACAGAGCAGACTCCTG 60.673 60.000 0.00 0.00 44.65 3.86
1703 2403 5.070580 ACTTCTGAACACTTTGTAGGTAGCT 59.929 40.000 0.00 0.00 0.00 3.32
1707 2407 3.877508 GCACTTCTGAACACTTTGTAGGT 59.122 43.478 0.00 0.00 0.00 3.08
1760 2461 4.222366 ACATCACTCTCTTCATCTTCTGCA 59.778 41.667 0.00 0.00 0.00 4.41
1763 2464 7.222872 ACAAAACATCACTCTCTTCATCTTCT 58.777 34.615 0.00 0.00 0.00 2.85
1780 2481 5.828299 TTCACTCCGAAGAAACAAAACAT 57.172 34.783 0.00 0.00 0.00 2.71
1785 2487 3.004315 GCCATTTCACTCCGAAGAAACAA 59.996 43.478 0.00 0.00 34.32 2.83
1893 2927 5.932303 TCAAATTTTGAAGGACCTAGAGTCG 59.068 40.000 9.36 0.00 40.74 4.18
1910 2944 5.221244 GGTATAGCGGCCATCTTTCAAATTT 60.221 40.000 2.24 0.00 0.00 1.82
1912 2946 3.821033 GGTATAGCGGCCATCTTTCAAAT 59.179 43.478 2.24 0.00 0.00 2.32
1919 2953 2.320681 TAAGGGTATAGCGGCCATCT 57.679 50.000 2.24 0.83 0.00 2.90
1953 2988 9.241919 TGTGGAAGAAACATGTATCATACATTT 57.758 29.630 7.64 1.92 46.69 2.32
1954 2989 8.806429 TGTGGAAGAAACATGTATCATACATT 57.194 30.769 7.64 0.00 46.69 2.71
1956 2991 6.316140 GCTGTGGAAGAAACATGTATCATACA 59.684 38.462 0.00 0.00 43.80 2.29
1957 2992 6.238484 GGCTGTGGAAGAAACATGTATCATAC 60.238 42.308 0.00 0.00 0.00 2.39
1958 2993 5.822519 GGCTGTGGAAGAAACATGTATCATA 59.177 40.000 0.00 0.00 0.00 2.15
1959 2994 4.641989 GGCTGTGGAAGAAACATGTATCAT 59.358 41.667 0.00 0.00 0.00 2.45
1960 2995 4.009675 GGCTGTGGAAGAAACATGTATCA 58.990 43.478 0.00 0.00 0.00 2.15
1961 2996 3.378427 GGGCTGTGGAAGAAACATGTATC 59.622 47.826 0.00 0.00 0.00 2.24
1962 2997 3.245229 TGGGCTGTGGAAGAAACATGTAT 60.245 43.478 0.00 0.00 0.00 2.29
1963 2998 2.107378 TGGGCTGTGGAAGAAACATGTA 59.893 45.455 0.00 0.00 0.00 2.29
1964 2999 1.133513 TGGGCTGTGGAAGAAACATGT 60.134 47.619 0.00 0.00 0.00 3.21
1965 3000 1.619654 TGGGCTGTGGAAGAAACATG 58.380 50.000 0.00 0.00 0.00 3.21
1966 3001 2.610438 ATGGGCTGTGGAAGAAACAT 57.390 45.000 0.00 0.00 0.00 2.71
1967 3002 2.238521 GAATGGGCTGTGGAAGAAACA 58.761 47.619 0.00 0.00 0.00 2.83
1968 3003 1.546029 GGAATGGGCTGTGGAAGAAAC 59.454 52.381 0.00 0.00 0.00 2.78
1969 3004 1.428912 AGGAATGGGCTGTGGAAGAAA 59.571 47.619 0.00 0.00 0.00 2.52
1970 3005 1.075601 AGGAATGGGCTGTGGAAGAA 58.924 50.000 0.00 0.00 0.00 2.52
1971 3006 1.075601 AAGGAATGGGCTGTGGAAGA 58.924 50.000 0.00 0.00 0.00 2.87
1972 3007 1.821136 GAAAGGAATGGGCTGTGGAAG 59.179 52.381 0.00 0.00 0.00 3.46
1973 3008 1.428912 AGAAAGGAATGGGCTGTGGAA 59.571 47.619 0.00 0.00 0.00 3.53
1974 3009 1.075601 AGAAAGGAATGGGCTGTGGA 58.924 50.000 0.00 0.00 0.00 4.02
1980 3015 4.156739 CAGTTCAACTAGAAAGGAATGGGC 59.843 45.833 0.00 0.00 38.13 5.36
2004 3039 8.250332 GCAGTCCCATGAATATTTCTTAAACAA 58.750 33.333 0.00 0.00 0.00 2.83
2005 3040 7.147915 GGCAGTCCCATGAATATTTCTTAAACA 60.148 37.037 0.00 0.00 0.00 2.83
2024 3059 0.883833 CAACATTCACTGGGCAGTCC 59.116 55.000 0.00 0.00 40.20 3.85
2025 3060 1.896220 TCAACATTCACTGGGCAGTC 58.104 50.000 0.00 0.00 40.20 3.51
2026 3061 1.956477 GTTCAACATTCACTGGGCAGT 59.044 47.619 0.00 0.00 43.61 4.40
2027 3062 1.069022 CGTTCAACATTCACTGGGCAG 60.069 52.381 0.00 0.00 0.00 4.85
2029 3064 0.951558 ACGTTCAACATTCACTGGGC 59.048 50.000 0.00 0.00 0.00 5.36
2030 3065 3.813166 AGTAACGTTCAACATTCACTGGG 59.187 43.478 2.82 0.00 0.00 4.45
2031 3066 5.204833 CAAGTAACGTTCAACATTCACTGG 58.795 41.667 2.82 0.00 0.00 4.00
2032 3067 4.670621 GCAAGTAACGTTCAACATTCACTG 59.329 41.667 2.82 0.00 0.00 3.66
2033 3068 4.551990 CGCAAGTAACGTTCAACATTCACT 60.552 41.667 2.82 0.00 0.00 3.41
2034 3069 3.657625 CGCAAGTAACGTTCAACATTCAC 59.342 43.478 2.82 0.00 0.00 3.18
2106 3625 6.990349 TCAAGAGGTACAAAACTACTTTCAGG 59.010 38.462 0.00 0.00 0.00 3.86
2174 3818 9.084533 ACTATTTGCAAAGGGAAAAGTACAATA 57.915 29.630 18.19 0.00 37.88 1.90
2197 3841 4.663334 TCAACTTCAGAGGCTGTAGACTA 58.337 43.478 7.86 0.00 33.94 2.59
2222 3866 1.705745 AGGAGAACCAAGGAAACCTCC 59.294 52.381 0.00 0.00 40.21 4.30
2223 3867 3.510531 AAGGAGAACCAAGGAAACCTC 57.489 47.619 0.00 0.00 38.94 3.85
2225 3869 6.665992 ATTAAAAGGAGAACCAAGGAAACC 57.334 37.500 0.00 0.00 38.94 3.27
2226 3870 8.826710 CAAAATTAAAAGGAGAACCAAGGAAAC 58.173 33.333 0.00 0.00 38.94 2.78
2229 3873 7.669089 ACAAAATTAAAAGGAGAACCAAGGA 57.331 32.000 0.00 0.00 38.94 3.36
2257 3901 4.345257 GGAACTATAGCTCCTCCATCACAA 59.655 45.833 13.97 0.00 0.00 3.33
2258 3902 3.898123 GGAACTATAGCTCCTCCATCACA 59.102 47.826 13.97 0.00 0.00 3.58
2259 3903 3.898123 TGGAACTATAGCTCCTCCATCAC 59.102 47.826 20.34 0.00 31.19 3.06
2260 3904 4.199002 TGGAACTATAGCTCCTCCATCA 57.801 45.455 20.34 0.00 31.19 3.07
2261 3905 6.685116 GCATATGGAACTATAGCTCCTCCATC 60.685 46.154 20.34 8.58 44.06 3.51
2262 3906 5.130145 GCATATGGAACTATAGCTCCTCCAT 59.870 44.000 20.34 20.74 46.28 3.41
2263 3907 4.467795 GCATATGGAACTATAGCTCCTCCA 59.532 45.833 20.34 16.44 40.36 3.86
2264 3908 4.467795 TGCATATGGAACTATAGCTCCTCC 59.532 45.833 20.34 12.12 31.72 4.30
2265 3909 5.415221 GTGCATATGGAACTATAGCTCCTC 58.585 45.833 20.34 7.52 31.72 3.71
2266 3910 4.081972 CGTGCATATGGAACTATAGCTCCT 60.082 45.833 20.34 10.34 31.72 3.69
2267 3911 4.082190 TCGTGCATATGGAACTATAGCTCC 60.082 45.833 14.31 14.31 0.00 4.70
2268 3912 5.060662 TCGTGCATATGGAACTATAGCTC 57.939 43.478 4.56 0.00 0.00 4.09
2269 3913 5.420421 AGATCGTGCATATGGAACTATAGCT 59.580 40.000 4.56 0.00 0.00 3.32
2270 3914 5.655488 AGATCGTGCATATGGAACTATAGC 58.345 41.667 4.56 0.00 0.00 2.97
2272 3916 9.628500 ACTATAGATCGTGCATATGGAACTATA 57.372 33.333 6.78 9.97 0.00 1.31
2273 3917 8.526667 ACTATAGATCGTGCATATGGAACTAT 57.473 34.615 6.78 9.42 0.00 2.12
2274 3918 7.939784 ACTATAGATCGTGCATATGGAACTA 57.060 36.000 6.78 2.83 0.00 2.24
2275 3919 6.842437 ACTATAGATCGTGCATATGGAACT 57.158 37.500 6.78 0.64 0.00 3.01
2276 3920 6.868864 ACAACTATAGATCGTGCATATGGAAC 59.131 38.462 6.78 0.00 0.00 3.62
2277 3921 6.993079 ACAACTATAGATCGTGCATATGGAA 58.007 36.000 6.78 0.00 0.00 3.53
2278 3922 6.590234 ACAACTATAGATCGTGCATATGGA 57.410 37.500 6.78 0.00 0.00 3.41
2279 3923 8.029522 ACTAACAACTATAGATCGTGCATATGG 58.970 37.037 6.78 0.00 0.00 2.74
2280 3924 8.972262 ACTAACAACTATAGATCGTGCATATG 57.028 34.615 6.78 0.00 0.00 1.78
2281 3925 9.411801 CAACTAACAACTATAGATCGTGCATAT 57.588 33.333 6.78 0.00 0.00 1.78
2282 3926 8.410912 ACAACTAACAACTATAGATCGTGCATA 58.589 33.333 6.78 0.00 0.00 3.14
2283 3927 7.265673 ACAACTAACAACTATAGATCGTGCAT 58.734 34.615 6.78 0.00 0.00 3.96
2284 3928 6.627243 ACAACTAACAACTATAGATCGTGCA 58.373 36.000 6.78 0.00 0.00 4.57
2285 3929 7.521509 AACAACTAACAACTATAGATCGTGC 57.478 36.000 6.78 0.00 0.00 5.34
2286 3930 9.784680 AGTAACAACTAACAACTATAGATCGTG 57.215 33.333 6.78 1.74 0.00 4.35
2409 4053 8.623903 GGAATATTAAGAGCACAACAATGATCA 58.376 33.333 0.00 0.00 37.47 2.92
2414 4058 8.579850 TCAAGGAATATTAAGAGCACAACAAT 57.420 30.769 0.00 0.00 0.00 2.71
2453 4140 6.410540 ACTTTTCCCTTGCATAAACAACAAA 58.589 32.000 0.00 0.00 0.00 2.83
2487 4174 3.686016 ACCTACAAAATTCATGTCGCCT 58.314 40.909 0.51 0.00 32.27 5.52
2489 4176 5.041951 TGAACCTACAAAATTCATGTCGC 57.958 39.130 0.51 0.00 32.27 5.19
2490 4177 7.910162 CCTAATGAACCTACAAAATTCATGTCG 59.090 37.037 0.51 0.00 41.17 4.35
2493 4180 7.489113 GCACCTAATGAACCTACAAAATTCATG 59.511 37.037 0.00 0.00 41.17 3.07
2495 4182 6.491745 TGCACCTAATGAACCTACAAAATTCA 59.508 34.615 0.00 0.00 36.81 2.57
2504 4191 5.235850 TGTTTCTGCACCTAATGAACCTA 57.764 39.130 0.00 0.00 0.00 3.08
2505 4192 4.098914 TGTTTCTGCACCTAATGAACCT 57.901 40.909 0.00 0.00 0.00 3.50
2524 4211 0.251922 TAGCACCCGGGAGTAGTTGT 60.252 55.000 32.02 7.14 0.00 3.32
2535 4222 3.546020 CGAGCAATTACAATTAGCACCCG 60.546 47.826 9.93 7.42 0.00 5.28
2537 4224 3.377172 ACCGAGCAATTACAATTAGCACC 59.623 43.478 9.93 3.67 0.00 5.01
2569 4256 5.036737 CACATTCACAAACCAGAACAAGAC 58.963 41.667 0.00 0.00 0.00 3.01
2584 4271 6.095580 TGACTCATAGTCTCCTACACATTCAC 59.904 42.308 8.42 0.00 45.27 3.18
2596 4283 4.160439 TGGACACCATTGACTCATAGTCTC 59.840 45.833 8.42 0.00 45.27 3.36
2603 4290 3.008923 TGCTTATGGACACCATTGACTCA 59.991 43.478 8.59 0.00 42.23 3.41
2639 4326 4.529109 AAAGAGAGGCTGACTAGTTGAC 57.471 45.455 0.00 0.00 0.00 3.18
2703 4390 6.038997 AGTAATCCAGAACTTACGAGCTTT 57.961 37.500 0.00 0.00 33.93 3.51
2704 4391 5.662674 AGTAATCCAGAACTTACGAGCTT 57.337 39.130 0.00 0.00 33.93 3.74
2705 4392 5.185249 TCAAGTAATCCAGAACTTACGAGCT 59.815 40.000 0.00 0.00 34.23 4.09
2706 4393 5.288952 GTCAAGTAATCCAGAACTTACGAGC 59.711 44.000 0.00 0.00 34.23 5.03
2707 4394 5.805994 GGTCAAGTAATCCAGAACTTACGAG 59.194 44.000 0.00 0.00 34.23 4.18
2708 4395 5.620654 CGGTCAAGTAATCCAGAACTTACGA 60.621 44.000 0.00 0.00 34.23 3.43
2767 4454 5.104485 AGGTAATAAGTAAACTGGGAGGCAG 60.104 44.000 0.00 0.00 0.00 4.85
2777 4464 9.840427 TGTGTAACTCGTAGGTAATAAGTAAAC 57.160 33.333 0.00 0.00 38.04 2.01
2788 4475 7.921214 CAGAAATCATATGTGTAACTCGTAGGT 59.079 37.037 1.90 0.00 38.04 3.08
2789 4476 7.921214 ACAGAAATCATATGTGTAACTCGTAGG 59.079 37.037 1.90 0.00 38.04 3.18
2801 4488 6.015180 ACCAAAAGTGCACAGAAATCATATGT 60.015 34.615 21.04 0.00 0.00 2.29
2802 4489 6.309494 CACCAAAAGTGCACAGAAATCATATG 59.691 38.462 21.04 0.00 40.28 1.78
2803 4490 6.209192 TCACCAAAAGTGCACAGAAATCATAT 59.791 34.615 21.04 0.00 46.81 1.78
2804 4491 5.534278 TCACCAAAAGTGCACAGAAATCATA 59.466 36.000 21.04 0.00 46.81 2.15
2805 4492 4.341806 TCACCAAAAGTGCACAGAAATCAT 59.658 37.500 21.04 0.00 46.81 2.45
2806 4493 3.698539 TCACCAAAAGTGCACAGAAATCA 59.301 39.130 21.04 0.00 46.81 2.57
2807 4494 4.305989 TCACCAAAAGTGCACAGAAATC 57.694 40.909 21.04 0.00 46.81 2.17
2808 4495 4.734398 TTCACCAAAAGTGCACAGAAAT 57.266 36.364 21.04 0.00 46.81 2.17


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

AutoCloner maintained by Alex Coulton.