Multiple sequence alignment - TraesCS4A01G349600

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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 TraesCS4A01G349600 chr4A 100.000 2862 0 0 1 2862 626184790 626181929 0.000000e+00 5286
1 TraesCS4A01G349600 chr4A 84.280 1444 156 34 449 1866 627774203 627772805 0.000000e+00 1343
2 TraesCS4A01G349600 chr4A 81.197 468 55 15 1 441 627774984 627774523 2.110000e-91 346
3 TraesCS4A01G349600 chr5D 94.797 1134 58 1 280 1412 542980977 542982110 0.000000e+00 1766
4 TraesCS4A01G349600 chr5D 83.288 1484 171 41 449 1903 539959954 539958519 0.000000e+00 1295
5 TraesCS4A01G349600 chr5D 93.238 769 37 10 1549 2307 542982279 542983042 0.000000e+00 1118
6 TraesCS4A01G349600 chr5D 95.539 538 16 3 2325 2862 542983883 542984412 0.000000e+00 854
7 TraesCS4A01G349600 chr5D 92.857 266 6 3 1 266 542973526 542973778 9.680000e-100 374
8 TraesCS4A01G349600 chr5B 83.482 1453 171 35 449 1890 682166732 682165338 0.000000e+00 1290
9 TraesCS4A01G349600 chr5B 96.283 538 19 1 2325 2862 684440829 684441365 0.000000e+00 881
10 TraesCS4A01G349600 chr5B 79.957 469 59 17 1 441 682167516 682167055 2.140000e-81 313


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 TraesCS4A01G349600 chr4A 626181929 626184790 2861 True 5286.0 5286 100.000000 1 2862 1 chr4A.!!$R1 2861
1 TraesCS4A01G349600 chr4A 627772805 627774984 2179 True 844.5 1343 82.738500 1 1866 2 chr4A.!!$R2 1865
2 TraesCS4A01G349600 chr5D 539958519 539959954 1435 True 1295.0 1295 83.288000 449 1903 1 chr5D.!!$R1 1454
3 TraesCS4A01G349600 chr5D 542980977 542984412 3435 False 1246.0 1766 94.524667 280 2862 3 chr5D.!!$F2 2582
4 TraesCS4A01G349600 chr5B 684440829 684441365 536 False 881.0 881 96.283000 2325 2862 1 chr5B.!!$F1 537
5 TraesCS4A01G349600 chr5B 682165338 682167516 2178 True 801.5 1290 81.719500 1 1890 2 chr5B.!!$R1 1889

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
623 994 0.325933 CCACCATCAACTGAGGCAGA 59.674 55.0 0.82 0.0 35.18 4.26 F
1314 1685 0.035439 ATACAGTTCACCCCTTGGCG 60.035 55.0 0.00 0.0 33.59 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 2034 0.657840 GTGGATGATAAGCGTGGTGC 59.342 55.000 0.0 0.0 46.98 5.01 R
2323 2777 4.818534 GACATCAAGTCTGTCAGCAAAA 57.181 40.909 0.0 0.0 44.09 2.44 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
23 24 4.592942 TCTTCCATCTTAATTGCTGCACT 58.407 39.130 0.00 0.00 0.00 4.40
62 63 5.797434 GCAACAGTTTCTTGCTTTAGATAGC 59.203 40.000 0.00 0.00 40.79 2.97
72 73 4.507710 TGCTTTAGATAGCAGGTGTTCAG 58.492 43.478 0.00 0.00 45.72 3.02
128 134 1.826720 GTGTGGGATTACACCGGACTA 59.173 52.381 9.46 0.00 43.94 2.59
137 143 1.386533 ACACCGGACTAGGATACACG 58.613 55.000 9.46 0.00 41.41 4.49
145 151 3.814283 GGACTAGGATACACGAGGTACAG 59.186 52.174 0.00 0.00 41.41 2.74
156 162 1.333931 CGAGGTACAGCGCAAGAGATA 59.666 52.381 11.47 0.00 43.02 1.98
159 165 2.036475 AGGTACAGCGCAAGAGATATGG 59.964 50.000 11.47 0.00 43.02 2.74
176 182 6.856757 AGATATGGGCAAAGAATATCTTGGT 58.143 36.000 0.00 0.00 39.49 3.67
186 192 9.294030 GCAAAGAATATCTTGGTTATGTTTGAG 57.706 33.333 0.00 0.00 36.71 3.02
196 202 3.412386 GTTATGTTTGAGTGGGAGCTGT 58.588 45.455 0.00 0.00 0.00 4.40
202 208 3.788227 TTGAGTGGGAGCTGTTGTAAT 57.212 42.857 0.00 0.00 0.00 1.89
203 209 3.788227 TGAGTGGGAGCTGTTGTAATT 57.212 42.857 0.00 0.00 0.00 1.40
204 210 3.411446 TGAGTGGGAGCTGTTGTAATTG 58.589 45.455 0.00 0.00 0.00 2.32
208 214 3.189287 GTGGGAGCTGTTGTAATTGTCTG 59.811 47.826 0.00 0.00 0.00 3.51
210 216 3.437049 GGGAGCTGTTGTAATTGTCTGAC 59.563 47.826 0.00 0.00 0.00 3.51
211 217 4.065088 GGAGCTGTTGTAATTGTCTGACA 58.935 43.478 6.36 6.36 0.00 3.58
212 218 4.083802 GGAGCTGTTGTAATTGTCTGACAC 60.084 45.833 10.56 0.00 0.00 3.67
213 219 3.815401 AGCTGTTGTAATTGTCTGACACC 59.185 43.478 10.56 0.00 0.00 4.16
214 220 3.563808 GCTGTTGTAATTGTCTGACACCA 59.436 43.478 10.56 0.00 0.00 4.17
216 222 5.278463 GCTGTTGTAATTGTCTGACACCATT 60.278 40.000 10.56 11.01 0.00 3.16
217 223 6.707440 TGTTGTAATTGTCTGACACCATTT 57.293 33.333 10.56 5.06 0.00 2.32
218 224 6.502652 TGTTGTAATTGTCTGACACCATTTG 58.497 36.000 10.56 0.00 0.00 2.32
219 225 6.096141 TGTTGTAATTGTCTGACACCATTTGT 59.904 34.615 10.56 0.00 43.10 2.83
224 244 3.138304 TGTCTGACACCATTTGTACTGC 58.862 45.455 6.36 0.00 39.17 4.40
235 255 6.968904 CACCATTTGTACTGCTTCATTGATAC 59.031 38.462 0.00 0.00 0.00 2.24
236 256 6.658816 ACCATTTGTACTGCTTCATTGATACA 59.341 34.615 0.00 0.00 0.00 2.29
237 257 7.340232 ACCATTTGTACTGCTTCATTGATACAT 59.660 33.333 0.00 0.00 0.00 2.29
238 258 7.646526 CCATTTGTACTGCTTCATTGATACATG 59.353 37.037 0.00 0.00 0.00 3.21
239 259 7.920160 TTTGTACTGCTTCATTGATACATGA 57.080 32.000 0.00 0.00 0.00 3.07
240 260 8.510243 TTTGTACTGCTTCATTGATACATGAT 57.490 30.769 0.00 0.00 0.00 2.45
241 261 9.612066 TTTGTACTGCTTCATTGATACATGATA 57.388 29.630 0.00 0.00 0.00 2.15
242 262 9.612066 TTGTACTGCTTCATTGATACATGATAA 57.388 29.630 0.00 0.00 0.00 1.75
243 263 9.612066 TGTACTGCTTCATTGATACATGATAAA 57.388 29.630 0.00 0.00 0.00 1.40
244 264 9.869844 GTACTGCTTCATTGATACATGATAAAC 57.130 33.333 0.00 0.00 0.00 2.01
261 281 7.369803 TGATAAACTTTGCTTTGTTTTTGCA 57.630 28.000 6.79 0.00 37.53 4.08
301 334 4.862018 GCTTTGCAACTCACTTTTGTTACA 59.138 37.500 0.00 0.00 0.00 2.41
379 412 5.698832 TGTTTAGCCTGATGTTTGATTTCG 58.301 37.500 0.00 0.00 0.00 3.46
408 441 4.620723 ACTACCTCACTCCATACCAATGA 58.379 43.478 0.00 0.00 34.84 2.57
594 944 0.598680 GCAGGCATGTAGGAGTAGCG 60.599 60.000 0.00 0.00 0.00 4.26
623 994 0.325933 CCACCATCAACTGAGGCAGA 59.674 55.000 0.82 0.00 35.18 4.26
624 995 1.064906 CCACCATCAACTGAGGCAGAT 60.065 52.381 0.82 0.00 35.18 2.90
625 996 2.619849 CCACCATCAACTGAGGCAGATT 60.620 50.000 0.82 0.00 35.18 2.40
626 997 2.681848 CACCATCAACTGAGGCAGATTC 59.318 50.000 0.82 0.00 35.18 2.52
627 998 2.295885 CCATCAACTGAGGCAGATTCC 58.704 52.381 0.82 0.00 35.18 3.01
628 999 2.356432 CCATCAACTGAGGCAGATTCCA 60.356 50.000 0.82 0.00 35.18 3.53
629 1000 3.552875 CATCAACTGAGGCAGATTCCAT 58.447 45.455 0.82 0.00 35.18 3.41
630 1001 3.726557 TCAACTGAGGCAGATTCCATT 57.273 42.857 0.82 0.00 35.18 3.16
631 1002 3.349927 TCAACTGAGGCAGATTCCATTG 58.650 45.455 0.82 0.00 35.18 2.82
632 1003 2.426024 CAACTGAGGCAGATTCCATTGG 59.574 50.000 0.82 0.00 35.18 3.16
633 1004 1.064166 ACTGAGGCAGATTCCATTGGG 60.064 52.381 2.09 0.00 35.18 4.12
634 1005 1.002069 TGAGGCAGATTCCATTGGGT 58.998 50.000 2.09 0.00 34.93 4.51
635 1006 2.173356 CTGAGGCAGATTCCATTGGGTA 59.827 50.000 2.09 0.00 32.44 3.69
636 1007 2.785269 TGAGGCAGATTCCATTGGGTAT 59.215 45.455 2.09 0.00 34.93 2.73
637 1008 3.980022 TGAGGCAGATTCCATTGGGTATA 59.020 43.478 2.09 0.00 34.93 1.47
638 1009 4.202461 TGAGGCAGATTCCATTGGGTATAC 60.202 45.833 2.09 0.00 34.93 1.47
639 1010 3.983410 AGGCAGATTCCATTGGGTATACT 59.017 43.478 2.09 0.00 34.93 2.12
640 1011 4.416848 AGGCAGATTCCATTGGGTATACTT 59.583 41.667 2.09 0.00 34.93 2.24
641 1012 4.762251 GGCAGATTCCATTGGGTATACTTC 59.238 45.833 2.09 0.00 34.93 3.01
642 1013 5.376625 GCAGATTCCATTGGGTATACTTCA 58.623 41.667 2.09 0.00 34.93 3.02
643 1014 5.471456 GCAGATTCCATTGGGTATACTTCAG 59.529 44.000 2.09 0.00 34.93 3.02
649 1020 5.366768 TCCATTGGGTATACTTCAGAGGAAG 59.633 44.000 2.09 3.06 44.66 3.46
799 1170 8.952278 TCAACGCTTATTTAAACTGATGGTTAT 58.048 29.630 0.00 0.00 37.12 1.89
881 1252 3.100671 GGTGGAGTTATCCTCAGAGTGT 58.899 50.000 0.00 0.00 46.80 3.55
897 1268 6.044682 TCAGAGTGTGATTATATGCACAGTG 58.955 40.000 16.23 0.00 45.76 3.66
906 1277 4.596311 TGCACAGTGGAGCATACG 57.404 55.556 8.26 0.00 35.63 3.06
908 1279 0.536724 TGCACAGTGGAGCATACGAT 59.463 50.000 8.26 0.00 35.63 3.73
961 1332 1.209504 CTTCTGGTCCGATTGCCCTAA 59.790 52.381 0.00 0.00 0.00 2.69
977 1348 3.883489 GCCCTAATTCCAATAGGTGACAC 59.117 47.826 0.00 0.00 35.89 3.67
1042 1413 3.800261 GCGCCATAAGTCAATGAGCTCTA 60.800 47.826 16.19 1.49 31.83 2.43
1111 1482 1.000827 CGCATCCCAGCTCTAGTAGTG 60.001 57.143 0.00 0.00 0.00 2.74
1229 1600 4.952262 TCTTTGAGAGAATGGCATTTCG 57.048 40.909 14.93 2.11 0.00 3.46
1237 1608 2.890311 AGAATGGCATTTCGGTTGTCAA 59.110 40.909 14.93 0.00 31.53 3.18
1275 1646 4.695217 TTATGTTTCAAAAGGGCTAGCG 57.305 40.909 9.00 0.00 0.00 4.26
1314 1685 0.035439 ATACAGTTCACCCCTTGGCG 60.035 55.000 0.00 0.00 33.59 5.69
1383 1754 7.371159 CAAAAGTTATTTCTGAGGGAGTTTCC 58.629 38.462 0.00 0.00 35.23 3.13
1384 1755 5.843019 AGTTATTTCTGAGGGAGTTTCCA 57.157 39.130 0.00 0.00 38.64 3.53
1392 1763 0.482446 AGGGAGTTTCCATTGGTGCA 59.518 50.000 1.86 0.00 38.64 4.57
1393 1764 1.133199 AGGGAGTTTCCATTGGTGCAA 60.133 47.619 1.86 0.00 38.64 4.08
1398 1769 5.351458 GGAGTTTCCATTGGTGCAAATATC 58.649 41.667 1.86 0.16 36.28 1.63
1401 1772 3.289407 TCCATTGGTGCAAATATCGGA 57.711 42.857 1.86 0.00 0.00 4.55
1416 1816 8.251721 GCAAATATCGGAGATGTAAGTACCTAT 58.748 37.037 0.00 0.00 45.12 2.57
1417 1817 9.574458 CAAATATCGGAGATGTAAGTACCTATG 57.426 37.037 0.00 0.00 45.12 2.23
1418 1818 8.880991 AATATCGGAGATGTAAGTACCTATGT 57.119 34.615 0.00 0.00 45.12 2.29
1420 1820 6.387041 TCGGAGATGTAAGTACCTATGTTG 57.613 41.667 0.00 0.00 0.00 3.33
1421 1821 5.889853 TCGGAGATGTAAGTACCTATGTTGT 59.110 40.000 0.00 0.00 0.00 3.32
1454 1872 7.148355 GATACCACTGTATCCTAGCTTCTAC 57.852 44.000 0.00 0.00 45.07 2.59
1463 1881 7.730084 TGTATCCTAGCTTCTACGAGTAACTA 58.270 38.462 0.00 0.00 0.00 2.24
1467 1885 8.830201 TCCTAGCTTCTACGAGTAACTATTAG 57.170 38.462 0.00 0.00 0.00 1.73
1468 1886 8.646004 TCCTAGCTTCTACGAGTAACTATTAGA 58.354 37.037 0.00 0.00 0.00 2.10
1469 1887 9.439500 CCTAGCTTCTACGAGTAACTATTAGAT 57.561 37.037 0.00 0.00 0.00 1.98
1492 1910 9.838339 AGATTATATTGAGGAACTGGTTAAGTG 57.162 33.333 0.00 0.00 41.55 3.16
1493 1911 7.859325 TTATATTGAGGAACTGGTTAAGTGC 57.141 36.000 0.00 0.00 41.55 4.40
1494 1912 3.569194 TTGAGGAACTGGTTAAGTGCA 57.431 42.857 0.00 0.00 41.55 4.57
1495 1913 3.569194 TGAGGAACTGGTTAAGTGCAA 57.431 42.857 0.00 0.00 41.55 4.08
1496 1914 3.476552 TGAGGAACTGGTTAAGTGCAAG 58.523 45.455 0.00 0.00 41.55 4.01
1497 1915 2.226674 GAGGAACTGGTTAAGTGCAAGC 59.773 50.000 0.00 0.00 41.55 4.01
1498 1916 1.953686 GGAACTGGTTAAGTGCAAGCA 59.046 47.619 0.00 0.00 39.81 3.91
1499 1917 2.360801 GGAACTGGTTAAGTGCAAGCAA 59.639 45.455 0.00 0.00 39.81 3.91
1500 1918 3.181480 GGAACTGGTTAAGTGCAAGCAAA 60.181 43.478 0.00 0.00 39.81 3.68
1501 1919 4.429108 GAACTGGTTAAGTGCAAGCAAAA 58.571 39.130 0.00 0.00 39.81 2.44
1502 1920 4.045636 ACTGGTTAAGTGCAAGCAAAAG 57.954 40.909 0.00 0.00 37.88 2.27
1503 1921 3.699038 ACTGGTTAAGTGCAAGCAAAAGA 59.301 39.130 0.00 0.00 37.88 2.52
1504 1922 4.342092 ACTGGTTAAGTGCAAGCAAAAGAT 59.658 37.500 0.00 0.00 37.88 2.40
1505 1923 4.619973 TGGTTAAGTGCAAGCAAAAGATG 58.380 39.130 0.00 0.00 33.23 2.90
1506 1924 4.099266 TGGTTAAGTGCAAGCAAAAGATGT 59.901 37.500 0.00 0.00 33.23 3.06
1507 1925 4.445385 GGTTAAGTGCAAGCAAAAGATGTG 59.555 41.667 0.00 0.00 0.00 3.21
1508 1926 3.806625 AAGTGCAAGCAAAAGATGTGT 57.193 38.095 0.00 0.00 0.00 3.72
1509 1927 4.916983 AAGTGCAAGCAAAAGATGTGTA 57.083 36.364 0.00 0.00 0.00 2.90
1532 1954 0.725686 CTGGTCATTCAGCAAGCTCG 59.274 55.000 0.00 0.00 30.08 5.03
1534 1956 0.445436 GGTCATTCAGCAAGCTCGTG 59.555 55.000 0.00 0.00 0.00 4.35
1539 1961 3.125829 TCATTCAGCAAGCTCGTGATTTC 59.874 43.478 0.00 0.00 0.00 2.17
1546 1987 4.997395 AGCAAGCTCGTGATTTCTTTCTTA 59.003 37.500 0.00 0.00 0.00 2.10
1589 2030 8.978874 ATCACCATCTTGCATATTGTAGTTAA 57.021 30.769 0.00 0.00 0.00 2.01
1590 2031 8.800370 TCACCATCTTGCATATTGTAGTTAAA 57.200 30.769 0.00 0.00 0.00 1.52
1592 2033 8.458052 CACCATCTTGCATATTGTAGTTAAACA 58.542 33.333 0.00 0.00 0.00 2.83
1593 2034 8.677300 ACCATCTTGCATATTGTAGTTAAACAG 58.323 33.333 0.00 0.00 0.00 3.16
1599 2051 6.027749 GCATATTGTAGTTAAACAGCACCAC 58.972 40.000 0.00 0.00 0.00 4.16
1601 2053 1.868498 TGTAGTTAAACAGCACCACGC 59.132 47.619 0.00 0.00 42.91 5.34
1633 2085 4.803613 CACAGCAAACTAACCAAACCTTTC 59.196 41.667 0.00 0.00 0.00 2.62
1657 2110 6.714810 TCTTGGTTTTTCAGCTATCTTTGCTA 59.285 34.615 0.00 0.00 38.92 3.49
1661 2114 7.014230 TGGTTTTTCAGCTATCTTTGCTAAGTT 59.986 33.333 7.77 2.48 38.92 2.66
1678 2131 3.543680 AGTTGGTATGAGAATGACCGG 57.456 47.619 0.00 0.00 0.00 5.28
1682 2135 3.371034 TGGTATGAGAATGACCGGAAGA 58.629 45.455 9.46 0.00 0.00 2.87
1753 2206 2.466867 CGTTGATTTCGGACCCCTG 58.533 57.895 0.00 0.00 0.00 4.45
1768 2221 1.211457 CCCCTGAATGTGCTAAGAGCT 59.789 52.381 0.00 0.00 42.97 4.09
1798 2251 2.104792 CCATGGGGCCCAGTATATATCG 59.895 54.545 31.98 9.70 36.75 2.92
1801 2254 0.104304 GGGCCCAGTATATATCGCCG 59.896 60.000 19.95 0.00 37.26 6.46
1804 2257 1.679680 GCCCAGTATATATCGCCGCTA 59.320 52.381 0.00 0.00 0.00 4.26
1821 2274 6.708949 TCGCCGCTAAAAAGGAATATAATCTT 59.291 34.615 0.00 0.00 0.00 2.40
1933 2386 2.501723 AGTATGGTGTACTCTGGGCTTG 59.498 50.000 0.00 0.00 0.00 4.01
1938 2391 1.621814 GTGTACTCTGGGCTTGTACCA 59.378 52.381 0.00 0.00 36.63 3.25
1959 2412 9.379791 GTACCAATGAGTATTTTAAGCTAGTGT 57.620 33.333 0.00 0.00 0.00 3.55
2041 2494 7.646884 ACCAAATAAAATGAGATCTCCTTCCT 58.353 34.615 20.03 9.70 0.00 3.36
2060 2513 5.042463 TCCTGGTGTTGTTAGAATGTTCA 57.958 39.130 0.00 0.00 0.00 3.18
2081 2534 4.971282 TCATTGGATCCAGTTCCACTATCT 59.029 41.667 15.53 0.00 45.42 1.98
2110 2563 2.158827 TGAGTAGTTTGCTTGCAGTGGA 60.159 45.455 0.00 0.00 0.00 4.02
2134 2588 7.308049 GGAAAGTGCCTTTTTGTTTGTTTGTTA 60.308 33.333 2.33 0.00 33.49 2.41
2159 2613 6.147328 AGTTTTCTTATCCTGCGAAGTTGTAC 59.853 38.462 0.00 0.00 0.00 2.90
2160 2614 4.794278 TCTTATCCTGCGAAGTTGTACA 57.206 40.909 0.00 0.00 0.00 2.90
2161 2615 4.744570 TCTTATCCTGCGAAGTTGTACAG 58.255 43.478 0.00 0.00 0.00 2.74
2164 2618 3.293311 TCCTGCGAAGTTGTACAGTAC 57.707 47.619 3.49 3.49 0.00 2.73
2264 2718 1.075525 CCATGGAGGTCCCGTCCTA 60.076 63.158 5.56 0.00 38.02 2.94
2307 2761 0.896940 TACGTTTCTCCTCACCGCCT 60.897 55.000 0.00 0.00 0.00 5.52
2309 2763 1.291877 CGTTTCTCCTCACCGCCTTG 61.292 60.000 0.00 0.00 0.00 3.61
2310 2764 0.034896 GTTTCTCCTCACCGCCTTGA 59.965 55.000 0.00 0.00 0.00 3.02
2311 2765 0.984230 TTTCTCCTCACCGCCTTGAT 59.016 50.000 0.00 0.00 0.00 2.57
2312 2766 0.250234 TTCTCCTCACCGCCTTGATG 59.750 55.000 0.00 0.00 0.00 3.07
2314 2768 0.460987 CTCCTCACCGCCTTGATGTC 60.461 60.000 0.00 0.00 0.00 3.06
2315 2769 0.904865 TCCTCACCGCCTTGATGTCT 60.905 55.000 0.00 0.00 0.00 3.41
2318 2772 0.976641 TCACCGCCTTGATGTCTCTT 59.023 50.000 0.00 0.00 0.00 2.85
2319 2773 2.166459 CTCACCGCCTTGATGTCTCTTA 59.834 50.000 0.00 0.00 0.00 2.10
2321 2775 2.673368 CACCGCCTTGATGTCTCTTAAC 59.327 50.000 0.00 0.00 0.00 2.01
2322 2776 2.301870 ACCGCCTTGATGTCTCTTAACA 59.698 45.455 0.00 0.00 0.00 2.41
2323 2777 3.055094 ACCGCCTTGATGTCTCTTAACAT 60.055 43.478 0.00 0.00 42.49 2.71
2357 3634 2.134201 TGATGTCTGTATAAGCCGCG 57.866 50.000 0.00 0.00 0.00 6.46
2358 3635 1.407618 TGATGTCTGTATAAGCCGCGT 59.592 47.619 4.92 0.00 0.00 6.01
2521 3798 6.349033 GCGTTCACCCTTTCTTAATACAACAT 60.349 38.462 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 3.441222 TCAATGCTTATGCTGAACACCTG 59.559 43.478 1.96 0.00 40.48 4.00
63 64 3.689347 TCAATGCTTATGCTGAACACCT 58.311 40.909 1.96 0.00 40.48 4.00
99 105 1.557832 GTAATCCCACACCTACCAGCA 59.442 52.381 0.00 0.00 0.00 4.41
122 128 1.964552 ACCTCGTGTATCCTAGTCCG 58.035 55.000 0.00 0.00 0.00 4.79
128 134 1.022735 CGCTGTACCTCGTGTATCCT 58.977 55.000 0.00 0.00 0.00 3.24
137 143 3.312828 CATATCTCTTGCGCTGTACCTC 58.687 50.000 9.73 0.00 0.00 3.85
145 151 1.002033 CTTTGCCCATATCTCTTGCGC 60.002 52.381 0.00 0.00 0.00 6.09
156 162 6.840705 ACATAACCAAGATATTCTTTGCCCAT 59.159 34.615 0.00 0.00 33.78 4.00
159 165 8.250332 TCAAACATAACCAAGATATTCTTTGCC 58.750 33.333 0.00 0.00 33.78 4.52
176 182 3.788227 ACAGCTCCCACTCAAACATAA 57.212 42.857 0.00 0.00 0.00 1.90
186 192 3.189287 CAGACAATTACAACAGCTCCCAC 59.811 47.826 0.00 0.00 0.00 4.61
196 202 6.707440 ACAAATGGTGTCAGACAATTACAA 57.293 33.333 4.32 0.00 34.38 2.41
202 208 3.563808 GCAGTACAAATGGTGTCAGACAA 59.436 43.478 4.32 0.00 41.98 3.18
203 209 3.138304 GCAGTACAAATGGTGTCAGACA 58.862 45.455 0.00 0.00 41.98 3.41
204 210 3.403038 AGCAGTACAAATGGTGTCAGAC 58.597 45.455 0.00 0.00 41.98 3.51
208 214 5.048782 TCAATGAAGCAGTACAAATGGTGTC 60.049 40.000 0.00 0.00 41.98 3.67
210 216 5.375417 TCAATGAAGCAGTACAAATGGTG 57.625 39.130 0.00 0.00 0.00 4.17
211 217 6.658816 TGTATCAATGAAGCAGTACAAATGGT 59.341 34.615 0.00 0.00 0.00 3.55
212 218 7.087409 TGTATCAATGAAGCAGTACAAATGG 57.913 36.000 0.00 0.00 0.00 3.16
213 219 8.400186 TCATGTATCAATGAAGCAGTACAAATG 58.600 33.333 0.00 0.00 33.63 2.32
214 220 8.510243 TCATGTATCAATGAAGCAGTACAAAT 57.490 30.769 0.00 0.00 33.63 2.32
216 222 9.612066 TTATCATGTATCAATGAAGCAGTACAA 57.388 29.630 0.00 0.00 39.90 2.41
217 223 9.612066 TTTATCATGTATCAATGAAGCAGTACA 57.388 29.630 0.00 0.00 39.90 2.90
218 224 9.869844 GTTTATCATGTATCAATGAAGCAGTAC 57.130 33.333 0.00 0.00 39.90 2.73
219 225 9.836864 AGTTTATCATGTATCAATGAAGCAGTA 57.163 29.630 0.00 0.00 39.90 2.74
235 255 7.909121 TGCAAAAACAAAGCAAAGTTTATCATG 59.091 29.630 0.00 0.00 36.98 3.07
236 256 7.983307 TGCAAAAACAAAGCAAAGTTTATCAT 58.017 26.923 0.00 0.00 36.98 2.45
237 257 7.369803 TGCAAAAACAAAGCAAAGTTTATCA 57.630 28.000 0.00 0.00 36.98 2.15
238 258 8.735837 CAATGCAAAAACAAAGCAAAGTTTATC 58.264 29.630 0.00 0.00 42.15 1.75
239 259 8.242739 ACAATGCAAAAACAAAGCAAAGTTTAT 58.757 25.926 0.00 0.00 42.15 1.40
240 260 7.536622 CACAATGCAAAAACAAAGCAAAGTTTA 59.463 29.630 0.00 0.00 42.15 2.01
241 261 6.362820 CACAATGCAAAAACAAAGCAAAGTTT 59.637 30.769 0.00 0.00 42.15 2.66
242 262 5.857517 CACAATGCAAAAACAAAGCAAAGTT 59.142 32.000 0.00 0.00 42.15 2.66
243 263 5.392286 CACAATGCAAAAACAAAGCAAAGT 58.608 33.333 0.00 0.00 42.15 2.66
244 264 4.794246 CCACAATGCAAAAACAAAGCAAAG 59.206 37.500 0.00 0.00 42.15 2.77
259 279 1.336240 GCACCTTGTTCTCCACAATGC 60.336 52.381 0.00 0.00 44.72 3.56
261 281 2.664402 AGCACCTTGTTCTCCACAAT 57.336 45.000 0.00 0.00 44.72 2.71
301 334 5.238650 CGTTGGAAAAGACAGACCTGTAAAT 59.761 40.000 2.23 0.00 45.05 1.40
379 412 5.185442 GGTATGGAGTGAGGTAGTATTAGGC 59.815 48.000 0.00 0.00 0.00 3.93
497 847 6.790319 AGGTCTTCCTTTTGCTCCTAATAAA 58.210 36.000 0.00 0.00 42.12 1.40
527 877 2.599408 TCGGGTAGGGTAGATCATCC 57.401 55.000 0.00 0.00 0.00 3.51
594 944 0.038166 TTGATGGTGGCTTCACTCCC 59.962 55.000 0.00 0.00 41.00 4.30
623 994 5.911178 TCCTCTGAAGTATACCCAATGGAAT 59.089 40.000 0.00 0.00 34.81 3.01
624 995 5.285401 TCCTCTGAAGTATACCCAATGGAA 58.715 41.667 0.00 0.00 34.81 3.53
625 996 4.890988 TCCTCTGAAGTATACCCAATGGA 58.109 43.478 0.00 5.99 34.81 3.41
626 997 5.615289 CTTCCTCTGAAGTATACCCAATGG 58.385 45.833 0.00 0.00 42.55 3.16
639 1010 3.759581 ACTACGGTGTACTTCCTCTGAA 58.240 45.455 0.00 0.00 0.00 3.02
640 1011 3.430042 ACTACGGTGTACTTCCTCTGA 57.570 47.619 0.00 0.00 0.00 3.27
641 1012 4.260170 ACTACTACGGTGTACTTCCTCTG 58.740 47.826 0.00 0.00 0.00 3.35
642 1013 4.566426 ACTACTACGGTGTACTTCCTCT 57.434 45.455 0.00 0.00 0.00 3.69
643 1014 5.397326 CAAACTACTACGGTGTACTTCCTC 58.603 45.833 0.00 0.00 0.00 3.71
649 1020 5.346011 GCTTAACCAAACTACTACGGTGTAC 59.654 44.000 0.00 0.00 0.00 2.90
653 1024 4.879197 AGCTTAACCAAACTACTACGGT 57.121 40.909 0.00 0.00 0.00 4.83
759 1130 4.846779 AGCGTTGAAAGGCAATAAAGAA 57.153 36.364 10.07 0.00 41.92 2.52
773 1144 6.811253 ACCATCAGTTTAAATAAGCGTTGA 57.189 33.333 0.00 0.00 0.00 3.18
799 1170 2.023404 TGGAACCATCAGCTCCTACCTA 60.023 50.000 0.00 0.00 0.00 3.08
850 1221 3.506067 GGATAACTCCACCCAGTTGTTTG 59.494 47.826 0.00 0.00 41.64 2.93
881 1252 4.420522 TGCTCCACTGTGCATATAATCA 57.579 40.909 1.29 0.00 36.15 2.57
897 1268 2.917971 GTCATTCGCTATCGTATGCTCC 59.082 50.000 1.24 0.00 41.36 4.70
906 1277 2.222678 CCATGCACAGTCATTCGCTATC 59.777 50.000 0.00 0.00 0.00 2.08
908 1279 1.655484 CCATGCACAGTCATTCGCTA 58.345 50.000 0.00 0.00 0.00 4.26
977 1348 4.769688 TGTCCACACTATATTGCTGAAGG 58.230 43.478 0.00 0.00 0.00 3.46
1042 1413 6.507023 GGTTCACTGACATCACAAAATCTTT 58.493 36.000 0.00 0.00 0.00 2.52
1140 1511 0.659427 CTGCAGTATGTCCAATGCCG 59.341 55.000 5.25 0.00 39.31 5.69
1211 1582 3.071874 ACCGAAATGCCATTCTCTCAA 57.928 42.857 0.00 0.00 0.00 3.02
1229 1600 2.496871 TGGGAATGCATCATTGACAACC 59.503 45.455 0.00 0.00 33.90 3.77
1237 1608 6.928348 AACATAATCATGGGAATGCATCAT 57.072 33.333 0.00 0.00 36.39 2.45
1275 1646 1.012841 GAGCAGCATCACCAACTAGC 58.987 55.000 0.00 0.00 0.00 3.42
1314 1685 0.321346 CCAAATTGACACCTTGGCCC 59.679 55.000 0.00 0.00 33.65 5.80
1317 1688 3.836365 AAACCCAAATTGACACCTTGG 57.164 42.857 7.50 7.50 39.51 3.61
1374 1745 1.337118 TTGCACCAATGGAAACTCCC 58.663 50.000 6.16 0.00 35.03 4.30
1383 1754 4.276678 ACATCTCCGATATTTGCACCAATG 59.723 41.667 0.00 0.00 0.00 2.82
1384 1755 4.464008 ACATCTCCGATATTTGCACCAAT 58.536 39.130 0.00 0.00 0.00 3.16
1392 1763 9.310449 ACATAGGTACTTACATCTCCGATATTT 57.690 33.333 0.00 0.00 41.75 1.40
1393 1764 8.880991 ACATAGGTACTTACATCTCCGATATT 57.119 34.615 0.00 0.00 41.75 1.28
1398 1769 6.145338 ACAACATAGGTACTTACATCTCCG 57.855 41.667 0.00 0.00 41.75 4.63
1416 1816 5.767665 ACAGTGGTATCTGCATAAAACAACA 59.232 36.000 0.00 0.00 38.84 3.33
1417 1817 6.254281 ACAGTGGTATCTGCATAAAACAAC 57.746 37.500 0.00 0.00 38.84 3.32
1467 1885 8.560374 GCACTTAACCAGTTCCTCAATATAATC 58.440 37.037 0.00 0.00 30.92 1.75
1468 1886 8.052748 TGCACTTAACCAGTTCCTCAATATAAT 58.947 33.333 0.00 0.00 30.92 1.28
1469 1887 7.398829 TGCACTTAACCAGTTCCTCAATATAA 58.601 34.615 0.00 0.00 30.92 0.98
1471 1889 5.815581 TGCACTTAACCAGTTCCTCAATAT 58.184 37.500 0.00 0.00 30.92 1.28
1472 1890 5.235850 TGCACTTAACCAGTTCCTCAATA 57.764 39.130 0.00 0.00 30.92 1.90
1473 1891 4.098914 TGCACTTAACCAGTTCCTCAAT 57.901 40.909 0.00 0.00 30.92 2.57
1474 1892 3.569194 TGCACTTAACCAGTTCCTCAA 57.431 42.857 0.00 0.00 30.92 3.02
1475 1893 3.476552 CTTGCACTTAACCAGTTCCTCA 58.523 45.455 0.00 0.00 30.92 3.86
1476 1894 2.226674 GCTTGCACTTAACCAGTTCCTC 59.773 50.000 0.00 0.00 30.92 3.71
1477 1895 2.230660 GCTTGCACTTAACCAGTTCCT 58.769 47.619 0.00 0.00 30.92 3.36
1478 1896 1.953686 TGCTTGCACTTAACCAGTTCC 59.046 47.619 0.00 0.00 30.92 3.62
1479 1897 3.708563 TTGCTTGCACTTAACCAGTTC 57.291 42.857 0.00 0.00 30.92 3.01
1480 1898 4.159506 TCTTTTGCTTGCACTTAACCAGTT 59.840 37.500 0.00 0.00 30.92 3.16
1481 1899 3.699038 TCTTTTGCTTGCACTTAACCAGT 59.301 39.130 0.00 0.00 35.35 4.00
1482 1900 4.305989 TCTTTTGCTTGCACTTAACCAG 57.694 40.909 0.00 0.00 0.00 4.00
1483 1901 4.099266 ACATCTTTTGCTTGCACTTAACCA 59.901 37.500 0.00 0.00 0.00 3.67
1484 1902 4.445385 CACATCTTTTGCTTGCACTTAACC 59.555 41.667 0.00 0.00 0.00 2.85
1485 1903 5.043248 ACACATCTTTTGCTTGCACTTAAC 58.957 37.500 0.00 0.00 0.00 2.01
1486 1904 5.261209 ACACATCTTTTGCTTGCACTTAA 57.739 34.783 0.00 0.00 0.00 1.85
1487 1905 4.916983 ACACATCTTTTGCTTGCACTTA 57.083 36.364 0.00 0.00 0.00 2.24
1488 1906 3.806625 ACACATCTTTTGCTTGCACTT 57.193 38.095 0.00 0.00 0.00 3.16
1489 1907 4.136796 TCTACACATCTTTTGCTTGCACT 58.863 39.130 0.00 0.00 0.00 4.40
1490 1908 4.470462 CTCTACACATCTTTTGCTTGCAC 58.530 43.478 0.00 0.00 0.00 4.57
1491 1909 3.058016 GCTCTACACATCTTTTGCTTGCA 60.058 43.478 0.00 0.00 0.00 4.08
1492 1910 3.190118 AGCTCTACACATCTTTTGCTTGC 59.810 43.478 0.00 0.00 0.00 4.01
1493 1911 4.379186 CCAGCTCTACACATCTTTTGCTTG 60.379 45.833 0.00 0.00 0.00 4.01
1494 1912 3.755378 CCAGCTCTACACATCTTTTGCTT 59.245 43.478 0.00 0.00 0.00 3.91
1495 1913 3.244700 ACCAGCTCTACACATCTTTTGCT 60.245 43.478 0.00 0.00 0.00 3.91
1496 1914 3.077359 ACCAGCTCTACACATCTTTTGC 58.923 45.455 0.00 0.00 0.00 3.68
1497 1915 4.318332 TGACCAGCTCTACACATCTTTTG 58.682 43.478 0.00 0.00 0.00 2.44
1498 1916 4.623932 TGACCAGCTCTACACATCTTTT 57.376 40.909 0.00 0.00 0.00 2.27
1499 1917 4.833478 ATGACCAGCTCTACACATCTTT 57.167 40.909 0.00 0.00 0.00 2.52
1500 1918 4.223700 TGAATGACCAGCTCTACACATCTT 59.776 41.667 0.00 0.00 0.00 2.40
1501 1919 3.771479 TGAATGACCAGCTCTACACATCT 59.229 43.478 0.00 0.00 0.00 2.90
1502 1920 4.118410 CTGAATGACCAGCTCTACACATC 58.882 47.826 0.00 0.00 0.00 3.06
1503 1921 4.134379 CTGAATGACCAGCTCTACACAT 57.866 45.455 0.00 0.00 0.00 3.21
1504 1922 3.599730 CTGAATGACCAGCTCTACACA 57.400 47.619 0.00 0.00 0.00 3.72
1531 1953 7.541783 TGCATCCAAATTAAGAAAGAAATCACG 59.458 33.333 0.00 0.00 0.00 4.35
1532 1954 8.761575 TGCATCCAAATTAAGAAAGAAATCAC 57.238 30.769 0.00 0.00 0.00 3.06
1546 1987 9.715121 GATGGTGATAAATAATGCATCCAAATT 57.285 29.630 0.00 0.00 0.00 1.82
1560 2001 9.578576 ACTACAATATGCAAGATGGTGATAAAT 57.421 29.630 0.00 0.00 0.00 1.40
1593 2034 0.657840 GTGGATGATAAGCGTGGTGC 59.342 55.000 0.00 0.00 46.98 5.01
1599 2051 2.679837 AGTTTGCTGTGGATGATAAGCG 59.320 45.455 0.00 0.00 38.53 4.68
1601 2053 5.647658 TGGTTAGTTTGCTGTGGATGATAAG 59.352 40.000 0.00 0.00 0.00 1.73
1633 2085 5.776744 AGCAAAGATAGCTGAAAAACCAAG 58.223 37.500 0.00 0.00 41.61 3.61
1657 2110 3.517901 TCCGGTCATTCTCATACCAACTT 59.482 43.478 0.00 0.00 32.55 2.66
1661 2114 3.132289 GTCTTCCGGTCATTCTCATACCA 59.868 47.826 0.00 0.00 32.55 3.25
1678 2131 0.874390 TCGCAACATTGGCAGTCTTC 59.126 50.000 0.00 0.00 0.00 2.87
1682 2135 1.885157 CCATCGCAACATTGGCAGT 59.115 52.632 0.00 0.00 0.00 4.40
1702 2155 1.906574 TGGAAACCATCTAGAACCGCT 59.093 47.619 0.00 0.00 0.00 5.52
1705 2158 5.422214 TCTTCTGGAAACCATCTAGAACC 57.578 43.478 0.00 0.00 46.90 3.62
1753 2206 1.063764 GCAGCAGCTCTTAGCACATTC 59.936 52.381 0.00 0.00 45.56 2.67
1768 2221 2.760799 GCCCCATGGAATGCAGCA 60.761 61.111 15.22 0.00 44.97 4.41
1835 2288 9.829507 CTATGAGAATAGAGGAGATTGTTTGTT 57.170 33.333 0.00 0.00 0.00 2.83
1841 2294 6.602410 TGCCTATGAGAATAGAGGAGATTG 57.398 41.667 0.00 0.00 30.53 2.67
1933 2386 9.379791 ACACTAGCTTAAAATACTCATTGGTAC 57.620 33.333 0.00 0.00 0.00 3.34
1959 2412 4.512198 TCTTAACATTTCTCCGCGAAACAA 59.488 37.500 8.23 0.00 43.90 2.83
2041 2494 5.830457 TCCAATGAACATTCTAACAACACCA 59.170 36.000 0.00 0.00 0.00 4.17
2134 2588 5.063880 ACAACTTCGCAGGATAAGAAAACT 58.936 37.500 0.00 0.00 0.00 2.66
2181 2635 9.224267 CTCCATTTCTTTTCTTCAGTTAGATGA 57.776 33.333 0.00 0.00 0.00 2.92
2307 2761 7.013178 TGTCAGCAAAATGTTAAGAGACATCAA 59.987 33.333 0.00 0.00 39.25 2.57
2309 2763 6.902341 TGTCAGCAAAATGTTAAGAGACATC 58.098 36.000 0.00 0.00 39.25 3.06
2310 2764 6.712095 TCTGTCAGCAAAATGTTAAGAGACAT 59.288 34.615 0.00 0.00 41.83 3.06
2311 2765 6.017934 GTCTGTCAGCAAAATGTTAAGAGACA 60.018 38.462 0.00 0.00 33.11 3.41
2312 2766 6.203723 AGTCTGTCAGCAAAATGTTAAGAGAC 59.796 38.462 0.00 0.00 0.00 3.36
2314 2768 6.551385 AGTCTGTCAGCAAAATGTTAAGAG 57.449 37.500 0.00 0.00 0.00 2.85
2315 2769 6.542005 TCAAGTCTGTCAGCAAAATGTTAAGA 59.458 34.615 0.00 0.00 0.00 2.10
2318 2772 6.262944 ACATCAAGTCTGTCAGCAAAATGTTA 59.737 34.615 0.00 0.00 0.00 2.41
2319 2773 5.068198 ACATCAAGTCTGTCAGCAAAATGTT 59.932 36.000 0.00 0.00 0.00 2.71
2321 2775 5.117355 ACATCAAGTCTGTCAGCAAAATG 57.883 39.130 0.00 0.00 0.00 2.32
2322 2776 5.368256 GACATCAAGTCTGTCAGCAAAAT 57.632 39.130 0.00 0.00 44.09 1.82
2323 2777 4.818534 GACATCAAGTCTGTCAGCAAAA 57.181 40.909 0.00 0.00 44.09 2.44
2452 3729 6.275335 CGATAAATCAAATCAAACCATGGCT 58.725 36.000 13.04 0.00 0.00 4.75
2552 3830 9.683069 GTTTCATTGTCTGTGACTTGAAATAAT 57.317 29.630 20.53 3.55 41.79 1.28
2553 3831 8.902806 AGTTTCATTGTCTGTGACTTGAAATAA 58.097 29.630 20.53 7.24 41.79 1.40
2554 3832 8.450578 AGTTTCATTGTCTGTGACTTGAAATA 57.549 30.769 20.53 7.69 41.79 1.40
2555 3833 7.338800 AGTTTCATTGTCTGTGACTTGAAAT 57.661 32.000 20.53 13.00 41.79 2.17
2558 3836 7.011389 CAGTTAGTTTCATTGTCTGTGACTTGA 59.989 37.037 0.00 0.77 33.15 3.02


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

AutoCloner maintained by Alex Coulton.