Multiple sequence alignment - TraesCS2D01G092800

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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 TraesCS2D01G092800 chr2D 100.000 3681 0 0 630 4310 44089541 44085861 0.000000e+00 6798.0
1 TraesCS2D01G092800 chr2D 87.165 1714 129 50 1832 3483 60752665 60754349 0.000000e+00 1862.0
2 TraesCS2D01G092800 chr2D 86.312 884 59 23 713 1592 60751548 60752373 0.000000e+00 905.0
3 TraesCS2D01G092800 chr2D 100.000 299 0 0 1 299 44090170 44089872 1.750000e-153 553.0
4 TraesCS2D01G092800 chr2D 86.538 260 24 8 21 280 60751284 60751532 4.250000e-70 276.0
5 TraesCS2D01G092800 chr2D 83.186 113 11 2 1634 1746 60752515 60752619 3.550000e-16 97.1
6 TraesCS2D01G092800 chr2A 96.823 1983 39 16 1960 3928 47919152 47917180 0.000000e+00 3291.0
7 TraesCS2D01G092800 chr2A 87.408 1366 109 36 2135 3483 61286431 61287750 0.000000e+00 1511.0
8 TraesCS2D01G092800 chr2A 94.567 773 13 6 711 1473 47919909 47919156 0.000000e+00 1168.0
9 TraesCS2D01G092800 chr2A 87.995 883 65 18 713 1592 61285008 61285852 0.000000e+00 1005.0
10 TraesCS2D01G092800 chr2A 81.231 650 53 22 950 1587 62918801 62919393 1.090000e-125 460.0
11 TraesCS2D01G092800 chr2A 92.946 241 11 3 4059 4294 47917095 47916856 3.190000e-91 346.0
12 TraesCS2D01G092800 chr2A 87.625 299 23 5 1837 2134 61286110 61286395 6.910000e-88 335.0
13 TraesCS2D01G092800 chr2A 95.968 124 4 1 157 280 61284870 61284992 2.630000e-47 200.0
14 TraesCS2D01G092800 chr2B 95.982 1742 17 5 1832 3555 69501606 69499900 0.000000e+00 2780.0
15 TraesCS2D01G092800 chr2B 90.812 1034 23 14 724 1746 69502695 69501723 0.000000e+00 1317.0
16 TraesCS2D01G092800 chr2B 96.073 713 25 1 2131 2843 94926715 94927424 0.000000e+00 1158.0
17 TraesCS2D01G092800 chr2B 87.864 824 51 18 782 1592 94925326 94926113 0.000000e+00 922.0
18 TraesCS2D01G092800 chr2B 87.270 707 82 8 2128 2831 601333874 601334575 0.000000e+00 800.0
19 TraesCS2D01G092800 chr2B 90.968 310 18 6 1832 2134 94926374 94926680 4.010000e-110 409.0
20 TraesCS2D01G092800 chr2B 96.296 243 7 2 4053 4294 69499455 69499214 8.680000e-107 398.0
21 TraesCS2D01G092800 chr2B 85.379 383 28 11 3082 3458 94927651 94928011 5.260000e-99 372.0
22 TraesCS2D01G092800 chr2B 98.571 210 2 1 1 209 69502899 69502690 1.890000e-98 370.0
23 TraesCS2D01G092800 chr2B 93.802 242 14 1 3582 3822 69499915 69499674 3.170000e-96 363.0
24 TraesCS2D01G092800 chr2B 88.502 287 25 5 1 280 94924710 94924995 1.480000e-89 340.0
25 TraesCS2D01G092800 chr2B 96.045 177 6 1 3886 4061 69499671 69499495 1.960000e-73 287.0
26 TraesCS2D01G092800 chr2B 95.714 70 3 0 1764 1833 69501650 69501719 3.520000e-21 113.0
27 TraesCS2D01G092800 chr2B 93.878 49 3 0 1750 1798 69501657 69501609 1.660000e-09 75.0
28 TraesCS2D01G092800 chr2B 86.441 59 8 0 1749 1807 760860353 760860295 1.000000e-06 65.8
29 TraesCS2D01G092800 chr2B 92.857 42 1 2 3445 3484 601334716 601334757 4.650000e-05 60.2
30 TraesCS2D01G092800 chr5B 84.831 1035 117 27 1838 2857 457989517 457990526 0.000000e+00 1005.0
31 TraesCS2D01G092800 chr5B 91.304 46 4 0 1760 1805 15661227 15661182 3.600000e-06 63.9
32 TraesCS2D01G092800 chr3D 85.605 653 45 25 950 1587 473415338 473414720 1.310000e-179 640.0
33 TraesCS2D01G092800 chr6B 87.203 547 64 6 2306 2850 157480015 157479473 6.120000e-173 617.0
34 TraesCS2D01G092800 chr6B 90.152 132 13 0 2232 2363 157480137 157480006 5.730000e-39 172.0
35 TraesCS2D01G092800 chr6B 100.000 36 0 0 3449 3484 157476418 157476383 2.780000e-07 67.6
36 TraesCS2D01G092800 chr6B 100.000 36 0 0 3449 3484 157478548 157478513 2.780000e-07 67.6
37 TraesCS2D01G092800 chr6B 100.000 36 0 0 3449 3484 157479397 157479362 2.780000e-07 67.6
38 TraesCS2D01G092800 chr4D 84.816 652 51 22 950 1587 499921221 499920604 2.850000e-171 612.0
39 TraesCS2D01G092800 chr4D 92.029 138 10 1 985 1121 295434961 295434824 4.400000e-45 193.0
40 TraesCS2D01G092800 chr5A 83.359 649 58 23 954 1587 232875101 232874488 4.870000e-154 555.0
41 TraesCS2D01G092800 chr5A 83.129 652 59 22 950 1587 612651936 612652550 8.150000e-152 547.0
42 TraesCS2D01G092800 chr5A 97.368 38 1 0 3447 3484 299615547 299615584 1.000000e-06 65.8
43 TraesCS2D01G092800 chr1A 82.875 654 61 23 950 1587 414218133 414218751 1.360000e-149 540.0
44 TraesCS2D01G092800 chr4A 92.084 379 27 3 2481 2857 703283578 703283201 8.210000e-147 531.0
45 TraesCS2D01G092800 chr4A 90.132 152 10 4 972 1118 196571398 196571549 4.400000e-45 193.0
46 TraesCS2D01G092800 chr7B 86.329 395 42 7 1204 1587 619205893 619206286 1.850000e-113 420.0
47 TraesCS2D01G092800 chr7B 80.534 262 16 15 950 1208 619196852 619197081 7.410000e-38 169.0
48 TraesCS2D01G092800 chr7B 94.000 50 3 0 1749 1798 60366514 60366563 4.620000e-10 76.8
49 TraesCS2D01G092800 chr4B 85.714 168 14 6 949 1107 364151916 364152082 7.410000e-38 169.0
50 TraesCS2D01G092800 chr4B 94.000 50 3 0 1749 1798 59873784 59873735 4.620000e-10 76.8
51 TraesCS2D01G092800 chr1B 97.436 78 2 0 1013 1090 608864147 608864070 2.700000e-27 134.0
52 TraesCS2D01G092800 chr7A 97.368 38 1 0 3447 3484 46896967 46897004 1.000000e-06 65.8


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 TraesCS2D01G092800 chr2D 44085861 44090170 4309 True 3675.500000 6798 100.000000 1 4310 2 chr2D.!!$R1 4309
1 TraesCS2D01G092800 chr2D 60751284 60754349 3065 False 785.025000 1862 85.800250 21 3483 4 chr2D.!!$F1 3462
2 TraesCS2D01G092800 chr2A 47916856 47919909 3053 True 1601.666667 3291 94.778667 711 4294 3 chr2A.!!$R1 3583
3 TraesCS2D01G092800 chr2A 61284870 61287750 2880 False 762.750000 1511 89.749000 157 3483 4 chr2A.!!$F2 3326
4 TraesCS2D01G092800 chr2A 62918801 62919393 592 False 460.000000 460 81.231000 950 1587 1 chr2A.!!$F1 637
5 TraesCS2D01G092800 chr2B 69499214 69502899 3685 True 798.571429 2780 95.055143 1 4294 7 chr2B.!!$R2 4293
6 TraesCS2D01G092800 chr2B 94924710 94928011 3301 False 640.200000 1158 89.757200 1 3458 5 chr2B.!!$F2 3457
7 TraesCS2D01G092800 chr2B 601333874 601334757 883 False 430.100000 800 90.063500 2128 3484 2 chr2B.!!$F3 1356
8 TraesCS2D01G092800 chr5B 457989517 457990526 1009 False 1005.000000 1005 84.831000 1838 2857 1 chr5B.!!$F1 1019
9 TraesCS2D01G092800 chr3D 473414720 473415338 618 True 640.000000 640 85.605000 950 1587 1 chr3D.!!$R1 637
10 TraesCS2D01G092800 chr4D 499920604 499921221 617 True 612.000000 612 84.816000 950 1587 1 chr4D.!!$R2 637
11 TraesCS2D01G092800 chr5A 232874488 232875101 613 True 555.000000 555 83.359000 954 1587 1 chr5A.!!$R1 633
12 TraesCS2D01G092800 chr5A 612651936 612652550 614 False 547.000000 547 83.129000 950 1587 1 chr5A.!!$F2 637
13 TraesCS2D01G092800 chr1A 414218133 414218751 618 False 540.000000 540 82.875000 950 1587 1 chr1A.!!$F1 637

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
970 1197 0.034896 ACAACCAGACGGCAGGTAAG 59.965 55.0 5.45 4.56 37.07 2.34 F
1131 1386 0.263468 GTAAGAGCCTCCCCCTCTCT 59.737 60.0 0.00 0.00 38.67 3.10 F
1145 1404 0.478942 CTCTCTCCACCCCTATCGGA 59.521 60.0 0.00 0.00 0.00 4.55 F
1800 2252 0.706433 ACGGTACAGAGGGGGTAGAA 59.294 55.0 0.00 0.00 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 2282 3.498774 ACACTGAAACCAGCTTCATCT 57.501 42.857 0.0 0.0 34.86 2.90 R
2018 2484 5.133221 AGCAACAACTGAACCTTAACAGAT 58.867 37.500 0.0 0.0 37.54 2.90 R
2468 3012 7.329962 TCACAGGTTACAACACAAATATCTACG 59.670 37.037 0.0 0.0 0.00 3.51 R
3639 4311 0.249031 AGCAAAAGCGTTTCAGGTGC 60.249 50.000 0.0 0.0 0.00 5.01 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
51 56 9.127277 AGTACTCAAAATCTCTCTACCTCATAC 57.873 37.037 0.00 0.00 0.00 2.39
251 278 1.321474 CCAAGCTTGCTTGGTTGAGA 58.679 50.000 34.02 0.00 46.45 3.27
261 288 2.687935 GCTTGGTTGAGAAGTTTGACCA 59.312 45.455 0.00 0.00 38.54 4.02
280 307 5.360999 TGACCATTGATCGAGATGTCTACTT 59.639 40.000 0.00 0.00 0.00 2.24
283 310 6.097554 ACCATTGATCGAGATGTCTACTTCTT 59.902 38.462 0.00 0.00 31.50 2.52
286 313 5.193679 TGATCGAGATGTCTACTTCTTCCA 58.806 41.667 0.00 0.00 31.50 3.53
287 314 5.830457 TGATCGAGATGTCTACTTCTTCCAT 59.170 40.000 0.00 0.00 31.50 3.41
288 315 5.506686 TCGAGATGTCTACTTCTTCCATG 57.493 43.478 0.63 0.00 31.50 3.66
289 316 5.193679 TCGAGATGTCTACTTCTTCCATGA 58.806 41.667 0.00 0.00 31.50 3.07
290 317 5.298026 TCGAGATGTCTACTTCTTCCATGAG 59.702 44.000 0.00 0.00 31.50 2.90
291 318 5.275067 AGATGTCTACTTCTTCCATGAGC 57.725 43.478 0.00 0.00 0.00 4.26
292 319 4.961730 AGATGTCTACTTCTTCCATGAGCT 59.038 41.667 0.00 0.00 0.00 4.09
293 320 6.132658 AGATGTCTACTTCTTCCATGAGCTA 58.867 40.000 0.00 0.00 0.00 3.32
294 321 6.609212 AGATGTCTACTTCTTCCATGAGCTAA 59.391 38.462 0.00 0.00 0.00 3.09
295 322 6.605471 TGTCTACTTCTTCCATGAGCTAAA 57.395 37.500 0.00 0.00 0.00 1.85
296 323 7.004555 TGTCTACTTCTTCCATGAGCTAAAA 57.995 36.000 0.00 0.00 0.00 1.52
297 324 7.624549 TGTCTACTTCTTCCATGAGCTAAAAT 58.375 34.615 0.00 0.00 0.00 1.82
298 325 7.550551 TGTCTACTTCTTCCATGAGCTAAAATG 59.449 37.037 0.00 0.00 0.00 2.32
715 907 5.465724 AGGAAAACTTCTACGTAGCTTGTTG 59.534 40.000 18.00 6.30 0.00 3.33
763 955 4.382754 CGTGGTTTCATAGCAAAGAAAAGC 59.617 41.667 0.00 0.00 35.71 3.51
777 969 4.681978 AAGCCGGACACCGCTGAC 62.682 66.667 5.05 0.00 46.86 3.51
790 1015 1.543802 CCGCTGACATCTATCCTCTCC 59.456 57.143 0.00 0.00 0.00 3.71
962 1189 3.583276 TAGCGCCACAACCAGACGG 62.583 63.158 2.29 0.00 38.77 4.79
965 1192 3.357079 GCCACAACCAGACGGCAG 61.357 66.667 0.00 0.00 44.25 4.85
966 1193 2.669569 CCACAACCAGACGGCAGG 60.670 66.667 0.00 0.00 34.57 4.85
967 1194 2.111043 CACAACCAGACGGCAGGT 59.889 61.111 0.00 0.00 40.61 4.00
968 1195 1.369692 CACAACCAGACGGCAGGTA 59.630 57.895 5.45 0.00 37.07 3.08
969 1196 0.250124 CACAACCAGACGGCAGGTAA 60.250 55.000 5.45 0.00 37.07 2.85
970 1197 0.034896 ACAACCAGACGGCAGGTAAG 59.965 55.000 5.45 4.56 37.07 2.34
971 1198 0.673644 CAACCAGACGGCAGGTAAGG 60.674 60.000 5.45 0.00 37.07 2.69
972 1199 1.838073 AACCAGACGGCAGGTAAGGG 61.838 60.000 5.45 0.00 37.07 3.95
973 1200 1.987855 CCAGACGGCAGGTAAGGGA 60.988 63.158 0.00 0.00 0.00 4.20
1050 1283 1.581954 CTCGAGCGTCCTCAAGTGT 59.418 57.895 0.00 0.00 38.00 3.55
1131 1386 0.263468 GTAAGAGCCTCCCCCTCTCT 59.737 60.000 0.00 0.00 38.67 3.10
1143 1402 0.540830 CCCTCTCTCCACCCCTATCG 60.541 65.000 0.00 0.00 0.00 2.92
1144 1403 0.540830 CCTCTCTCCACCCCTATCGG 60.541 65.000 0.00 0.00 0.00 4.18
1145 1404 0.478942 CTCTCTCCACCCCTATCGGA 59.521 60.000 0.00 0.00 0.00 4.55
1335 1606 4.277174 AGCTGAGTATCTAGACGGAACATG 59.723 45.833 0.00 0.00 34.92 3.21
1556 1827 7.971168 TGTTAAATTTACTGATTTGTATGCGGG 59.029 33.333 0.00 0.00 31.96 6.13
1608 1975 9.075519 CATATTGGTAAACTGCAAAACATGTAG 57.924 33.333 0.00 0.00 46.19 2.74
1709 2096 6.387513 TCCATTAGCCTAACCATGGTAACTAA 59.612 38.462 20.12 21.03 37.92 2.24
1742 2129 6.997239 TCTACTGTTGAAGCTAATCGAGTA 57.003 37.500 0.00 0.00 0.00 2.59
1794 2246 3.703052 ACAACTATTACGGTACAGAGGGG 59.297 47.826 0.00 0.00 0.00 4.79
1798 2250 2.442236 TTACGGTACAGAGGGGGTAG 57.558 55.000 0.00 0.00 0.00 3.18
1799 2251 1.595311 TACGGTACAGAGGGGGTAGA 58.405 55.000 0.00 0.00 0.00 2.59
1800 2252 0.706433 ACGGTACAGAGGGGGTAGAA 59.294 55.000 0.00 0.00 0.00 2.10
1801 2253 1.341778 ACGGTACAGAGGGGGTAGAAG 60.342 57.143 0.00 0.00 0.00 2.85
1802 2254 1.341778 CGGTACAGAGGGGGTAGAAGT 60.342 57.143 0.00 0.00 0.00 3.01
1803 2255 2.830293 GGTACAGAGGGGGTAGAAGTT 58.170 52.381 0.00 0.00 0.00 2.66
1804 2256 3.625716 CGGTACAGAGGGGGTAGAAGTTA 60.626 52.174 0.00 0.00 0.00 2.24
1805 2257 4.554683 GGTACAGAGGGGGTAGAAGTTAT 58.445 47.826 0.00 0.00 0.00 1.89
1806 2258 4.967442 GGTACAGAGGGGGTAGAAGTTATT 59.033 45.833 0.00 0.00 0.00 1.40
1807 2259 5.163332 GGTACAGAGGGGGTAGAAGTTATTG 60.163 48.000 0.00 0.00 0.00 1.90
1808 2260 3.200165 ACAGAGGGGGTAGAAGTTATTGC 59.800 47.826 0.00 0.00 0.00 3.56
1809 2261 3.199946 CAGAGGGGGTAGAAGTTATTGCA 59.800 47.826 0.00 0.00 0.00 4.08
1810 2262 4.047883 AGAGGGGGTAGAAGTTATTGCAT 58.952 43.478 0.00 0.00 0.00 3.96
1811 2263 4.137543 GAGGGGGTAGAAGTTATTGCATG 58.862 47.826 0.00 0.00 0.00 4.06
1812 2264 3.527665 AGGGGGTAGAAGTTATTGCATGT 59.472 43.478 0.00 0.00 0.00 3.21
1813 2265 3.632145 GGGGGTAGAAGTTATTGCATGTG 59.368 47.826 0.00 0.00 0.00 3.21
1814 2266 4.523083 GGGGTAGAAGTTATTGCATGTGA 58.477 43.478 0.00 0.00 0.00 3.58
1815 2267 4.947388 GGGGTAGAAGTTATTGCATGTGAA 59.053 41.667 0.00 0.00 0.00 3.18
1816 2268 5.066505 GGGGTAGAAGTTATTGCATGTGAAG 59.933 44.000 0.00 0.00 0.00 3.02
1817 2269 5.066505 GGGTAGAAGTTATTGCATGTGAAGG 59.933 44.000 0.00 0.00 0.00 3.46
1818 2270 5.648092 GGTAGAAGTTATTGCATGTGAAGGT 59.352 40.000 0.00 0.00 0.00 3.50
1819 2271 6.821665 GGTAGAAGTTATTGCATGTGAAGGTA 59.178 38.462 0.00 0.00 0.00 3.08
1820 2272 7.335924 GGTAGAAGTTATTGCATGTGAAGGTAA 59.664 37.037 0.00 0.00 0.00 2.85
1821 2273 7.759489 AGAAGTTATTGCATGTGAAGGTAAA 57.241 32.000 0.00 0.00 0.00 2.01
1822 2274 7.820648 AGAAGTTATTGCATGTGAAGGTAAAG 58.179 34.615 0.00 0.00 0.00 1.85
1823 2275 6.515272 AGTTATTGCATGTGAAGGTAAAGG 57.485 37.500 0.00 0.00 0.00 3.11
1824 2276 6.245408 AGTTATTGCATGTGAAGGTAAAGGA 58.755 36.000 0.00 0.00 0.00 3.36
1825 2277 6.719370 AGTTATTGCATGTGAAGGTAAAGGAA 59.281 34.615 0.00 0.00 0.00 3.36
1826 2278 4.846779 TTGCATGTGAAGGTAAAGGAAC 57.153 40.909 0.00 0.00 0.00 3.62
1827 2279 3.826524 TGCATGTGAAGGTAAAGGAACA 58.173 40.909 0.00 0.00 0.00 3.18
1828 2280 4.406456 TGCATGTGAAGGTAAAGGAACAT 58.594 39.130 0.00 0.00 0.00 2.71
1829 2281 4.832266 TGCATGTGAAGGTAAAGGAACATT 59.168 37.500 0.00 0.00 0.00 2.71
1830 2282 6.007076 TGCATGTGAAGGTAAAGGAACATTA 58.993 36.000 0.00 0.00 0.00 1.90
2018 2484 6.941857 TGTAATTCATGTACCAGCAGTCTTA 58.058 36.000 0.00 0.00 0.00 2.10
2448 2992 5.474189 TGGTTAGTAGCCGCAACTTTAATTT 59.526 36.000 0.00 0.00 0.00 1.82
2963 3605 1.638589 TGGGGCTTGCTATACTTGGTT 59.361 47.619 0.00 0.00 0.00 3.67
3032 3674 2.480037 TCGTGTTGAATGTAGCAAGCTG 59.520 45.455 4.53 0.00 0.00 4.24
3260 3905 5.865552 CGTTCCGTTTTATCTTACCTTCTCA 59.134 40.000 0.00 0.00 0.00 3.27
3538 4210 7.537306 GTGCAAATTTATGTACCTACTGTGTTG 59.463 37.037 0.00 0.00 30.71 3.33
3550 4222 5.222048 ACCTACTGTGTTGGTGATGGTAATT 60.222 40.000 3.28 0.00 39.88 1.40
3623 4295 9.243637 GCACAAAAAGTAGATTTACATCACAAA 57.756 29.630 0.00 0.00 31.96 2.83
3662 4334 1.270550 CCTGAAACGCTTTTGCTCCAT 59.729 47.619 0.00 0.00 44.80 3.41
3721 4393 5.467399 CCATTGCAAACTTGATCAAACATGT 59.533 36.000 9.88 0.74 0.00 3.21
3736 4408 9.334693 GATCAAACATGTAAGACATTTGAAGTC 57.665 33.333 10.09 2.75 39.24 3.01
3848 4521 9.378551 TGATGTAACATAATCACACTTTAGTCC 57.621 33.333 0.00 0.00 0.00 3.85
3944 4618 0.251341 AACCGCCAGAAGCATTTCCT 60.251 50.000 0.00 0.00 44.04 3.36
3952 4626 4.640201 GCCAGAAGCATTTCCTGTGTATTA 59.360 41.667 0.00 0.00 42.97 0.98
4054 4728 5.637810 ACGCGAAAGAGATATGAACAAGAAA 59.362 36.000 15.93 0.00 33.96 2.52
4148 4877 6.729690 TTTGAAATGTGAAGGATTGGTTCT 57.270 33.333 0.00 0.00 0.00 3.01
4287 5016 4.452455 AGTGATTTGTTCTGTTCTTAGCCG 59.548 41.667 0.00 0.00 0.00 5.52
4288 5017 4.451096 GTGATTTGTTCTGTTCTTAGCCGA 59.549 41.667 0.00 0.00 0.00 5.54
4289 5018 5.122396 GTGATTTGTTCTGTTCTTAGCCGAT 59.878 40.000 0.00 0.00 0.00 4.18
4290 5019 5.122239 TGATTTGTTCTGTTCTTAGCCGATG 59.878 40.000 0.00 0.00 0.00 3.84
4291 5020 2.972625 TGTTCTGTTCTTAGCCGATGG 58.027 47.619 0.00 0.00 0.00 3.51
4302 5031 4.838152 CCGATGGCACCCGTCAGG 62.838 72.222 9.70 3.03 39.36 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 56 0.547712 TGGTCTTCCTTGGGGAGAGG 60.548 60.000 0.00 0.00 43.29 3.69
243 270 4.531854 TCAATGGTCAAACTTCTCAACCA 58.468 39.130 0.00 0.00 43.68 3.67
251 278 5.248640 ACATCTCGATCAATGGTCAAACTT 58.751 37.500 0.00 0.00 0.00 2.66
261 288 6.322456 TGGAAGAAGTAGACATCTCGATCAAT 59.678 38.462 0.00 0.00 0.00 2.57
686 713 8.553696 CAAGCTACGTAGAAGTTTTCCTAAAAA 58.446 33.333 26.53 0.00 31.13 1.94
687 714 7.712205 ACAAGCTACGTAGAAGTTTTCCTAAAA 59.288 33.333 26.53 0.00 0.00 1.52
690 717 6.336842 ACAAGCTACGTAGAAGTTTTCCTA 57.663 37.500 26.53 0.00 0.00 2.94
692 719 5.235831 ACAACAAGCTACGTAGAAGTTTTCC 59.764 40.000 26.53 5.65 0.00 3.13
693 720 6.283161 ACAACAAGCTACGTAGAAGTTTTC 57.717 37.500 26.53 6.40 0.00 2.29
695 722 4.748600 GGACAACAAGCTACGTAGAAGTTT 59.251 41.667 26.53 14.81 0.00 2.66
696 723 4.038883 AGGACAACAAGCTACGTAGAAGTT 59.961 41.667 26.53 20.73 0.00 2.66
697 724 3.573110 AGGACAACAAGCTACGTAGAAGT 59.427 43.478 26.53 16.42 0.00 3.01
698 725 4.167268 GAGGACAACAAGCTACGTAGAAG 58.833 47.826 26.53 15.80 0.00 2.85
699 726 3.570975 TGAGGACAACAAGCTACGTAGAA 59.429 43.478 26.53 0.00 0.00 2.10
700 727 3.057736 GTGAGGACAACAAGCTACGTAGA 60.058 47.826 26.53 0.00 0.00 2.59
701 728 3.243336 GTGAGGACAACAAGCTACGTAG 58.757 50.000 18.47 18.47 0.00 3.51
702 729 2.624364 TGTGAGGACAACAAGCTACGTA 59.376 45.455 0.00 0.00 0.00 3.57
703 730 1.411246 TGTGAGGACAACAAGCTACGT 59.589 47.619 0.00 0.00 0.00 3.57
705 732 3.467803 ACTTGTGAGGACAACAAGCTAC 58.532 45.455 14.49 0.00 43.15 3.58
706 733 3.838244 ACTTGTGAGGACAACAAGCTA 57.162 42.857 14.49 0.00 43.15 3.32
708 735 3.378427 AGAAACTTGTGAGGACAACAAGC 59.622 43.478 14.49 1.46 43.15 4.01
709 736 4.878397 AGAGAAACTTGTGAGGACAACAAG 59.122 41.667 13.30 13.30 44.43 3.16
715 907 5.241949 TGTCTCTAGAGAAACTTGTGAGGAC 59.758 44.000 23.96 8.31 39.48 3.85
777 969 3.058570 CGTTCAGTCGGAGAGGATAGATG 60.059 52.174 0.00 0.00 36.95 2.90
790 1015 3.047877 GGTTGGCCCGTTCAGTCG 61.048 66.667 0.00 0.00 0.00 4.18
962 1189 1.051556 CCTCCTCCTCCCTTACCTGC 61.052 65.000 0.00 0.00 0.00 4.85
963 1190 0.637195 TCCTCCTCCTCCCTTACCTG 59.363 60.000 0.00 0.00 0.00 4.00
964 1191 0.938192 CTCCTCCTCCTCCCTTACCT 59.062 60.000 0.00 0.00 0.00 3.08
965 1192 0.105401 CCTCCTCCTCCTCCCTTACC 60.105 65.000 0.00 0.00 0.00 2.85
966 1193 0.935194 TCCTCCTCCTCCTCCCTTAC 59.065 60.000 0.00 0.00 0.00 2.34
967 1194 1.236708 CTCCTCCTCCTCCTCCCTTA 58.763 60.000 0.00 0.00 0.00 2.69
968 1195 0.556380 TCTCCTCCTCCTCCTCCCTT 60.556 60.000 0.00 0.00 0.00 3.95
969 1196 0.998945 CTCTCCTCCTCCTCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
970 1197 1.541672 CTCTCCTCCTCCTCCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
971 1198 1.152546 GCTCTCCTCCTCCTCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
972 1199 1.528309 CGCTCTCCTCCTCCTCCTC 60.528 68.421 0.00 0.00 0.00 3.71
973 1200 2.600731 CGCTCTCCTCCTCCTCCT 59.399 66.667 0.00 0.00 0.00 3.69
1050 1283 2.115910 CAGACCTTGCCCTTGCCA 59.884 61.111 0.00 0.00 36.33 4.92
1242 1503 1.136147 CACAAGCAAGCATCGCTCC 59.864 57.895 0.00 0.00 38.25 4.70
1267 1528 1.065701 ACACATCCGATCTACGAGCAC 59.934 52.381 0.00 0.00 45.77 4.40
1556 1827 7.063544 GGATACATACTATCAATTCAGCGGTTC 59.936 40.741 0.00 0.00 0.00 3.62
1608 1975 8.658499 TCTTAACTAGGTTCAAACTCTTGTTC 57.342 34.615 11.31 0.00 34.96 3.18
1709 2096 9.944376 TTAGCTTCAACAGTAGAATAACTTGAT 57.056 29.630 0.00 0.00 0.00 2.57
1794 2246 5.648092 ACCTTCACATGCAATAACTTCTACC 59.352 40.000 0.00 0.00 0.00 3.18
1798 2250 7.029563 CCTTTACCTTCACATGCAATAACTTC 58.970 38.462 0.00 0.00 0.00 3.01
1799 2251 6.719370 TCCTTTACCTTCACATGCAATAACTT 59.281 34.615 0.00 0.00 0.00 2.66
1800 2252 6.245408 TCCTTTACCTTCACATGCAATAACT 58.755 36.000 0.00 0.00 0.00 2.24
1801 2253 6.509418 TCCTTTACCTTCACATGCAATAAC 57.491 37.500 0.00 0.00 0.00 1.89
1802 2254 6.491745 TGTTCCTTTACCTTCACATGCAATAA 59.508 34.615 0.00 0.00 0.00 1.40
1803 2255 6.007076 TGTTCCTTTACCTTCACATGCAATA 58.993 36.000 0.00 0.00 0.00 1.90
1804 2256 4.832266 TGTTCCTTTACCTTCACATGCAAT 59.168 37.500 0.00 0.00 0.00 3.56
1805 2257 4.211125 TGTTCCTTTACCTTCACATGCAA 58.789 39.130 0.00 0.00 0.00 4.08
1806 2258 3.826524 TGTTCCTTTACCTTCACATGCA 58.173 40.909 0.00 0.00 0.00 3.96
1807 2259 5.391312 AATGTTCCTTTACCTTCACATGC 57.609 39.130 0.00 0.00 0.00 4.06
1808 2260 7.921786 TCTAATGTTCCTTTACCTTCACATG 57.078 36.000 0.00 0.00 0.00 3.21
1809 2261 8.328758 TCATCTAATGTTCCTTTACCTTCACAT 58.671 33.333 0.00 0.00 0.00 3.21
1810 2262 7.685481 TCATCTAATGTTCCTTTACCTTCACA 58.315 34.615 0.00 0.00 0.00 3.58
1811 2263 8.561738 TTCATCTAATGTTCCTTTACCTTCAC 57.438 34.615 0.00 0.00 0.00 3.18
1812 2264 7.336931 GCTTCATCTAATGTTCCTTTACCTTCA 59.663 37.037 0.00 0.00 0.00 3.02
1813 2265 7.554476 AGCTTCATCTAATGTTCCTTTACCTTC 59.446 37.037 0.00 0.00 0.00 3.46
1814 2266 7.337942 CAGCTTCATCTAATGTTCCTTTACCTT 59.662 37.037 0.00 0.00 0.00 3.50
1815 2267 6.825721 CAGCTTCATCTAATGTTCCTTTACCT 59.174 38.462 0.00 0.00 0.00 3.08
1816 2268 6.038714 CCAGCTTCATCTAATGTTCCTTTACC 59.961 42.308 0.00 0.00 0.00 2.85
1817 2269 6.599638 ACCAGCTTCATCTAATGTTCCTTTAC 59.400 38.462 0.00 0.00 0.00 2.01
1818 2270 6.721318 ACCAGCTTCATCTAATGTTCCTTTA 58.279 36.000 0.00 0.00 0.00 1.85
1819 2271 5.574188 ACCAGCTTCATCTAATGTTCCTTT 58.426 37.500 0.00 0.00 0.00 3.11
1820 2272 5.184892 ACCAGCTTCATCTAATGTTCCTT 57.815 39.130 0.00 0.00 0.00 3.36
1821 2273 4.851639 ACCAGCTTCATCTAATGTTCCT 57.148 40.909 0.00 0.00 0.00 3.36
1822 2274 5.415701 TGAAACCAGCTTCATCTAATGTTCC 59.584 40.000 0.00 0.00 30.31 3.62
1823 2275 6.150140 ACTGAAACCAGCTTCATCTAATGTTC 59.850 38.462 0.00 0.00 34.86 3.18
1824 2276 6.006449 ACTGAAACCAGCTTCATCTAATGTT 58.994 36.000 0.00 0.00 34.86 2.71
1825 2277 5.413833 CACTGAAACCAGCTTCATCTAATGT 59.586 40.000 0.00 0.00 34.86 2.71
1826 2278 5.413833 ACACTGAAACCAGCTTCATCTAATG 59.586 40.000 0.00 0.00 34.86 1.90
1827 2279 5.564550 ACACTGAAACCAGCTTCATCTAAT 58.435 37.500 0.00 0.00 34.86 1.73
1828 2280 4.973168 ACACTGAAACCAGCTTCATCTAA 58.027 39.130 0.00 0.00 34.86 2.10
1829 2281 4.623932 ACACTGAAACCAGCTTCATCTA 57.376 40.909 0.00 0.00 34.86 1.98
1830 2282 3.498774 ACACTGAAACCAGCTTCATCT 57.501 42.857 0.00 0.00 34.86 2.90
2018 2484 5.133221 AGCAACAACTGAACCTTAACAGAT 58.867 37.500 0.00 0.00 37.54 2.90
2448 2992 8.110860 TCTACGAAGATGAATACTATCATGCA 57.889 34.615 0.00 0.00 40.08 3.96
2468 3012 7.329962 TCACAGGTTACAACACAAATATCTACG 59.670 37.037 0.00 0.00 0.00 3.51
3177 3822 2.887568 CTTACGCTGCTGCCGGAG 60.888 66.667 5.05 0.10 35.36 4.63
3180 3825 3.160557 GATGCTTACGCTGCTGCCG 62.161 63.158 10.24 7.82 36.97 5.69
3260 3905 3.006323 TGCCCTGTAAACGATGCAAATTT 59.994 39.130 0.00 0.00 0.00 1.82
3538 4210 1.750778 CCAGGCACAATTACCATCACC 59.249 52.381 0.00 0.00 0.00 4.02
3639 4311 0.249031 AGCAAAAGCGTTTCAGGTGC 60.249 50.000 0.00 0.00 0.00 5.01
3736 4408 7.587629 TGAAGCATAGAGATTTGTTGTTCAAG 58.412 34.615 0.00 0.00 37.35 3.02
3811 4484 9.936759 TGATTATGTTACATCAACTTCACACTA 57.063 29.630 0.00 0.00 38.05 2.74
3884 4557 7.698836 TCGATGTATCAATGGCATATTATCG 57.301 36.000 0.00 10.80 36.12 2.92
3929 4603 1.251251 ACACAGGAAATGCTTCTGGC 58.749 50.000 0.00 0.00 42.22 4.85
3952 4626 6.775939 CACGATGTGCATATATCTGACTTT 57.224 37.500 0.00 0.00 0.00 2.66
4148 4877 5.128171 ACGGATTCTTGTGCCTATGTAGTAA 59.872 40.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.