Multiple sequence alignment - TraesCS3A01G056200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G056200 chr3A 100.000 2279 0 0 1 2279 32411888 32414166 0.000000e+00 4209.0
1 TraesCS3A01G056200 chr3A 81.693 437 45 18 434 856 707916669 707916254 4.690000e-87 331.0
2 TraesCS3A01G056200 chr6A 96.416 586 14 1 390 968 450088723 450088138 0.000000e+00 959.0
3 TraesCS3A01G056200 chr5A 96.252 587 15 1 389 968 552657879 552658465 0.000000e+00 955.0
4 TraesCS3A01G056200 chr5A 85.945 434 34 12 433 857 684651795 684651380 2.690000e-119 438.0
5 TraesCS3A01G056200 chr5A 95.556 45 2 0 390 434 684652057 684652013 3.140000e-09 73.1
6 TraesCS3A01G056200 chr4A 92.231 605 34 6 377 971 468435018 468435619 0.000000e+00 845.0
7 TraesCS3A01G056200 chr4A 80.185 540 72 22 448 968 575729914 575730437 2.760000e-99 372.0
8 TraesCS3A01G056200 chr4A 79.789 569 57 34 448 972 540021920 540021366 5.980000e-96 361.0
9 TraesCS3A01G056200 chr3B 81.809 1006 101 38 1309 2266 41040537 41039566 0.000000e+00 769.0
10 TraesCS3A01G056200 chr3B 91.049 391 35 0 1 391 42173241 42173631 1.550000e-146 529.0
11 TraesCS3A01G056200 chr3B 93.491 338 21 1 969 1305 42173623 42173960 3.380000e-138 501.0
12 TraesCS3A01G056200 chr3B 85.366 410 41 9 1 391 41069902 41069493 7.580000e-110 407.0
13 TraesCS3A01G056200 chr3B 94.915 177 9 0 974 1150 41069496 41069320 6.200000e-71 278.0
14 TraesCS3A01G056200 chr7B 84.331 568 60 11 433 972 92336397 92335831 1.550000e-146 529.0
15 TraesCS3A01G056200 chr5D 83.101 574 56 17 433 968 438685611 438685041 3.400000e-133 484.0
16 TraesCS3A01G056200 chr7A 82.948 563 66 13 433 969 569613728 569613170 4.400000e-132 481.0
17 TraesCS3A01G056200 chr7A 82.975 558 65 13 433 968 157202701 157203250 5.700000e-131 477.0
18 TraesCS3A01G056200 chr7A 92.308 52 3 1 387 438 300856518 300856468 3.140000e-09 73.1
19 TraesCS3A01G056200 chr7A 93.617 47 3 0 388 434 157202394 157202440 1.130000e-08 71.3
20 TraesCS3A01G056200 chr7D 82.927 574 57 17 433 968 32053550 32052980 1.580000e-131 479.0
21 TraesCS3A01G056200 chr4D 82.927 574 57 17 433 968 449046615 449047185 1.580000e-131 479.0
22 TraesCS3A01G056200 chr2D 82.261 575 61 17 433 969 598078556 598079127 2.060000e-125 459.0
23 TraesCS3A01G056200 chr1A 85.843 445 42 11 435 869 508866347 508865914 9.600000e-124 453.0
24 TraesCS3A01G056200 chrUn 93.878 49 2 1 390 438 87128427 87128474 3.140000e-09 73.1
25 TraesCS3A01G056200 chr4B 93.750 48 1 2 391 438 449229890 449229845 1.130000e-08 71.3
26 TraesCS3A01G056200 chr6D 89.286 56 4 2 391 444 37937744 37937799 4.060000e-08 69.4


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 TraesCS3A01G056200 chr3A 32411888 32414166 2278 False 4209.00 4209 100.0000 1 2279 1 chr3A.!!$F1 2278
1 TraesCS3A01G056200 chr6A 450088138 450088723 585 True 959.00 959 96.4160 390 968 1 chr6A.!!$R1 578
2 TraesCS3A01G056200 chr5A 552657879 552658465 586 False 955.00 955 96.2520 389 968 1 chr5A.!!$F1 579
3 TraesCS3A01G056200 chr5A 684651380 684652057 677 True 255.55 438 90.7505 390 857 2 chr5A.!!$R1 467
4 TraesCS3A01G056200 chr4A 468435018 468435619 601 False 845.00 845 92.2310 377 971 1 chr4A.!!$F1 594
5 TraesCS3A01G056200 chr4A 575729914 575730437 523 False 372.00 372 80.1850 448 968 1 chr4A.!!$F2 520
6 TraesCS3A01G056200 chr4A 540021366 540021920 554 True 361.00 361 79.7890 448 972 1 chr4A.!!$R1 524
7 TraesCS3A01G056200 chr3B 41039566 41040537 971 True 769.00 769 81.8090 1309 2266 1 chr3B.!!$R1 957
8 TraesCS3A01G056200 chr3B 42173241 42173960 719 False 515.00 529 92.2700 1 1305 2 chr3B.!!$F1 1304
9 TraesCS3A01G056200 chr3B 41069320 41069902 582 True 342.50 407 90.1405 1 1150 2 chr3B.!!$R2 1149
10 TraesCS3A01G056200 chr7B 92335831 92336397 566 True 529.00 529 84.3310 433 972 1 chr7B.!!$R1 539
11 TraesCS3A01G056200 chr5D 438685041 438685611 570 True 484.00 484 83.1010 433 968 1 chr5D.!!$R1 535
12 TraesCS3A01G056200 chr7A 569613170 569613728 558 True 481.00 481 82.9480 433 969 1 chr7A.!!$R2 536
13 TraesCS3A01G056200 chr7A 157202394 157203250 856 False 274.15 477 88.2960 388 968 2 chr7A.!!$F1 580
14 TraesCS3A01G056200 chr7D 32052980 32053550 570 True 479.00 479 82.9270 433 968 1 chr7D.!!$R1 535
15 TraesCS3A01G056200 chr4D 449046615 449047185 570 False 479.00 479 82.9270 433 968 1 chr4D.!!$F1 535
16 TraesCS3A01G056200 chr2D 598078556 598079127 571 False 459.00 459 82.2610 433 969 1 chr2D.!!$F1 536

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
982 1360 0.53578 CACTGTCCAGCTGCCTTTCA 60.536 55.0 8.66 1.56 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 2630 0.258774 AGCACCTATTCCGCCCAATT 59.741 50.0 0.0 0.0 0.0 2.32 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
27 28 2.530701 ACGATGAGTTCCACCTTCTCT 58.469 47.619 0.00 0.00 0.00 3.10
29 30 4.282496 ACGATGAGTTCCACCTTCTCTAT 58.718 43.478 0.00 0.00 0.00 1.98
74 75 3.385384 CTGCAGAGGCCGTGGAGA 61.385 66.667 20.58 0.00 40.13 3.71
132 133 0.951040 GCTGAAGCTGCCGTACAAGT 60.951 55.000 0.00 0.00 38.21 3.16
152 153 1.593209 GTTCAACGACGACAGCCCA 60.593 57.895 0.00 0.00 0.00 5.36
172 173 2.388232 CGGCGTACAACTCCAAGCC 61.388 63.158 0.00 0.00 41.03 4.35
176 177 2.740826 TACAACTCCAAGCCGCGC 60.741 61.111 0.00 0.00 0.00 6.86
203 204 1.550524 CTTCCCGAGTTCTCCATGTGA 59.449 52.381 0.00 0.00 0.00 3.58
247 248 1.153349 GCCTAAGGAGCTTGGTCGG 60.153 63.158 0.00 0.00 0.00 4.79
248 249 1.522569 CCTAAGGAGCTTGGTCGGG 59.477 63.158 0.00 0.00 0.00 5.14
340 360 1.542492 CTGCCCAAGTTCAAGCTGAT 58.458 50.000 0.00 0.00 0.00 2.90
352 372 5.764686 AGTTCAAGCTGATGTACATGAACAA 59.235 36.000 27.13 7.09 43.06 2.83
757 1095 9.459640 GTAATTTGTAGATCAAGCGATACAGTA 57.540 33.333 0.00 0.00 37.35 2.74
896 1269 2.813172 TCAACGACGTGGTACATAGACA 59.187 45.455 2.83 0.00 44.52 3.41
982 1360 0.535780 CACTGTCCAGCTGCCTTTCA 60.536 55.000 8.66 1.56 0.00 2.69
984 1362 0.595095 CTGTCCAGCTGCCTTTCAAC 59.405 55.000 8.66 0.00 0.00 3.18
988 1366 3.357079 AGCTGCCTTTCAACCGCG 61.357 61.111 0.00 0.00 0.00 6.46
1044 1422 1.959226 GTCGGTCGTGCCATTGTGT 60.959 57.895 0.39 0.00 36.97 3.72
1152 1530 1.053424 TGGGGTTCTCGCTTTACTGT 58.947 50.000 0.00 0.00 0.00 3.55
1163 1541 4.163552 TCGCTTTACTGTGATTACGAGTG 58.836 43.478 0.00 0.00 0.00 3.51
1164 1542 3.918591 CGCTTTACTGTGATTACGAGTGT 59.081 43.478 0.00 0.00 0.00 3.55
1242 1620 1.346068 GTTGAGGAGACTTCAGGCACT 59.654 52.381 0.00 0.00 44.43 4.40
1266 1644 2.282391 TTCGCTGGGCATGTGCTT 60.282 55.556 4.84 0.00 41.70 3.91
1276 1654 1.133976 GGCATGTGCTTGATCCTACCT 60.134 52.381 4.84 0.00 41.70 3.08
1299 1678 1.067821 GAAGAGTAGACTCCGGGCATG 59.932 57.143 0.00 0.00 43.88 4.06
1305 1684 1.043116 AGACTCCGGGCATGATCGAA 61.043 55.000 0.00 0.00 0.00 3.71
1306 1685 0.034059 GACTCCGGGCATGATCGAAT 59.966 55.000 0.00 0.00 0.00 3.34
1307 1686 0.469917 ACTCCGGGCATGATCGAATT 59.530 50.000 0.00 0.00 0.00 2.17
1315 1694 0.377905 CATGATCGAATTGTGCCGCA 59.622 50.000 0.00 0.00 0.00 5.69
1324 1703 2.352503 ATTGTGCCGCATCACTTTTC 57.647 45.000 0.00 0.00 37.81 2.29
1332 1711 3.705604 CCGCATCACTTTTCAGTTTTGT 58.294 40.909 0.00 0.00 0.00 2.83
1339 1718 7.594758 GCATCACTTTTCAGTTTTGTAAGCATA 59.405 33.333 0.00 0.00 0.00 3.14
1340 1719 8.905702 CATCACTTTTCAGTTTTGTAAGCATAC 58.094 33.333 0.00 0.00 0.00 2.39
1390 1769 6.597672 TGCGACTATATGTTTTGGTCTGAAAT 59.402 34.615 0.00 0.00 0.00 2.17
1402 1781 7.861176 TTTGGTCTGAAATTTTACGTAATGC 57.139 32.000 9.18 0.00 0.00 3.56
1417 1796 5.974108 ACGTAATGCTATTTAGAGGTGTGT 58.026 37.500 0.00 0.00 0.00 3.72
1419 1798 6.534079 ACGTAATGCTATTTAGAGGTGTGTTC 59.466 38.462 0.00 0.00 0.00 3.18
1420 1799 6.533723 CGTAATGCTATTTAGAGGTGTGTTCA 59.466 38.462 0.00 0.00 0.00 3.18
1421 1800 6.992063 AATGCTATTTAGAGGTGTGTTCAG 57.008 37.500 0.00 0.00 0.00 3.02
1422 1801 5.483685 TGCTATTTAGAGGTGTGTTCAGT 57.516 39.130 0.00 0.00 0.00 3.41
1423 1802 5.237815 TGCTATTTAGAGGTGTGTTCAGTG 58.762 41.667 0.00 0.00 0.00 3.66
1425 1804 2.543777 TTAGAGGTGTGTTCAGTGGC 57.456 50.000 0.00 0.00 0.00 5.01
1426 1805 1.419381 TAGAGGTGTGTTCAGTGGCA 58.581 50.000 0.00 0.00 0.00 4.92
1427 1806 0.179045 AGAGGTGTGTTCAGTGGCAC 60.179 55.000 10.29 10.29 36.26 5.01
1431 1820 1.065551 GGTGTGTTCAGTGGCACTTTC 59.934 52.381 19.43 11.56 36.63 2.62
1437 1826 2.612212 GTTCAGTGGCACTTTCGAAAGA 59.388 45.455 37.54 17.43 39.31 2.52
1448 1837 6.029607 GCACTTTCGAAAGATGATAATTGCA 58.970 36.000 37.54 0.53 41.60 4.08
1455 1844 7.630458 TCGAAAGATGATAATTGCAGTGGCAT 61.630 38.462 0.00 0.00 42.90 4.40
1477 1866 4.676196 ATTCATCTGAATCGGCAAAGTTGC 60.676 41.667 7.51 7.51 45.72 4.17
1500 1889 5.106157 GCAGTGGCACTTATCTGTTTAACAT 60.106 40.000 19.43 0.00 40.72 2.71
1501 1890 6.317088 CAGTGGCACTTATCTGTTTAACATG 58.683 40.000 19.43 0.00 0.00 3.21
1528 1923 9.472995 GTACAATTGAAGATGTTAACATACACG 57.527 33.333 20.83 13.25 36.57 4.49
1530 1925 6.735678 ATTGAAGATGTTAACATACACGCA 57.264 33.333 20.83 11.79 36.57 5.24
1538 1933 4.389382 TGTTAACATACACGCACATACACC 59.611 41.667 3.59 0.00 0.00 4.16
1577 1974 0.466189 AGCACACAACACCTCCAAGG 60.466 55.000 0.00 0.00 42.49 3.61
1603 2000 6.544197 TGCTGAACCCGCATAATATTTTAAGA 59.456 34.615 0.00 0.00 31.40 2.10
1629 2026 3.312973 ACGAAGTCATCATAGACGTCTCC 59.687 47.826 23.89 2.58 42.41 3.71
1637 2034 5.527951 TCATCATAGACGTCTCCTAGTTGAC 59.472 44.000 23.89 3.17 0.00 3.18
1645 2042 4.705337 GTCTCCTAGTTGACGAAGATGT 57.295 45.455 0.00 0.00 0.00 3.06
1655 2052 3.625853 TGACGAAGATGTCATCTCTCCT 58.374 45.455 15.75 0.00 43.62 3.69
1656 2053 4.781934 TGACGAAGATGTCATCTCTCCTA 58.218 43.478 15.75 1.05 43.62 2.94
1657 2054 4.576873 TGACGAAGATGTCATCTCTCCTAC 59.423 45.833 15.75 6.74 43.62 3.18
1658 2055 4.787551 ACGAAGATGTCATCTCTCCTACT 58.212 43.478 15.75 0.00 39.08 2.57
1659 2056 5.931294 ACGAAGATGTCATCTCTCCTACTA 58.069 41.667 15.75 0.00 39.08 1.82
1661 2058 6.829298 ACGAAGATGTCATCTCTCCTACTAAA 59.171 38.462 15.75 0.00 39.08 1.85
1662 2059 7.339721 ACGAAGATGTCATCTCTCCTACTAAAA 59.660 37.037 15.75 0.00 39.08 1.52
1664 2061 7.962995 AGATGTCATCTCTCCTACTAAAACA 57.037 36.000 9.68 0.00 33.42 2.83
1665 2062 8.546083 AGATGTCATCTCTCCTACTAAAACAT 57.454 34.615 9.68 0.00 33.42 2.71
1666 2063 9.647918 AGATGTCATCTCTCCTACTAAAACATA 57.352 33.333 9.68 0.00 33.42 2.29
1667 2064 9.906660 GATGTCATCTCTCCTACTAAAACATAG 57.093 37.037 5.52 0.00 0.00 2.23
1668 2065 8.824756 TGTCATCTCTCCTACTAAAACATAGT 57.175 34.615 0.00 0.00 0.00 2.12
1688 2085 8.477256 ACATAGTACAAAAATTTGCCATGCTAT 58.523 29.630 5.82 3.61 41.79 2.97
1704 2101 9.306777 TGCCATGCTATAATCATAAATTTACCA 57.693 29.630 0.00 0.00 0.00 3.25
1785 2182 6.648192 AGAGAGAAAAGAACCCACATCTATG 58.352 40.000 0.00 0.00 0.00 2.23
1798 2214 5.755375 CCCACATCTATGTCTGTTATGTGAC 59.245 44.000 13.72 0.00 46.57 3.67
1804 2220 1.003118 TGTCTGTTATGTGACTGGGCC 59.997 52.381 0.00 0.00 34.57 5.80
1812 2228 2.847234 TGACTGGGCCTTGTCCGT 60.847 61.111 21.27 0.55 32.67 4.69
1813 2229 2.047179 GACTGGGCCTTGTCCGTC 60.047 66.667 15.93 2.24 0.00 4.79
1836 2252 3.714798 GACATATAGGAGGGGGTGTCAAA 59.285 47.826 0.00 0.00 36.78 2.69
1863 2279 5.825532 TGACATTGTGATCAAATTAGGGGA 58.174 37.500 0.00 0.00 37.11 4.81
1872 2288 6.378280 GTGATCAAATTAGGGGAGTGAATGTT 59.622 38.462 0.00 0.00 0.00 2.71
1886 2302 6.094186 GGAGTGAATGTTATTCTCCCAAGTTC 59.906 42.308 0.00 0.00 38.81 3.01
1888 2304 6.656693 AGTGAATGTTATTCTCCCAAGTTCAG 59.343 38.462 3.53 0.00 0.00 3.02
1889 2305 5.415701 TGAATGTTATTCTCCCAAGTTCAGC 59.584 40.000 3.53 0.00 0.00 4.26
1890 2306 4.365514 TGTTATTCTCCCAAGTTCAGCA 57.634 40.909 0.00 0.00 0.00 4.41
1891 2307 4.724399 TGTTATTCTCCCAAGTTCAGCAA 58.276 39.130 0.00 0.00 0.00 3.91
1892 2308 5.324409 TGTTATTCTCCCAAGTTCAGCAAT 58.676 37.500 0.00 0.00 0.00 3.56
1893 2309 5.183713 TGTTATTCTCCCAAGTTCAGCAATG 59.816 40.000 0.00 0.00 0.00 2.82
1894 2310 2.957402 TCTCCCAAGTTCAGCAATGT 57.043 45.000 0.00 0.00 0.00 2.71
1895 2311 2.783135 TCTCCCAAGTTCAGCAATGTC 58.217 47.619 0.00 0.00 0.00 3.06
1896 2312 1.815003 CTCCCAAGTTCAGCAATGTCC 59.185 52.381 0.00 0.00 0.00 4.02
1897 2313 1.144708 TCCCAAGTTCAGCAATGTCCA 59.855 47.619 0.00 0.00 0.00 4.02
1898 2314 2.173519 CCCAAGTTCAGCAATGTCCAT 58.826 47.619 0.00 0.00 0.00 3.41
1899 2315 2.094390 CCCAAGTTCAGCAATGTCCATG 60.094 50.000 0.00 0.00 0.00 3.66
1900 2316 2.559668 CCAAGTTCAGCAATGTCCATGT 59.440 45.455 0.00 0.00 0.00 3.21
1901 2317 3.006110 CCAAGTTCAGCAATGTCCATGTT 59.994 43.478 0.00 0.00 0.00 2.71
1902 2318 4.218200 CCAAGTTCAGCAATGTCCATGTTA 59.782 41.667 0.00 0.00 0.00 2.41
1903 2319 5.105635 CCAAGTTCAGCAATGTCCATGTTAT 60.106 40.000 0.00 0.00 0.00 1.89
1904 2320 5.571784 AGTTCAGCAATGTCCATGTTATG 57.428 39.130 0.00 0.00 0.00 1.90
1905 2321 5.012239 AGTTCAGCAATGTCCATGTTATGT 58.988 37.500 0.00 0.00 0.00 2.29
1906 2322 5.477984 AGTTCAGCAATGTCCATGTTATGTT 59.522 36.000 0.00 0.00 0.00 2.71
1907 2323 5.981088 TCAGCAATGTCCATGTTATGTTT 57.019 34.783 0.00 0.00 0.00 2.83
1908 2324 5.953183 TCAGCAATGTCCATGTTATGTTTC 58.047 37.500 0.00 0.00 0.00 2.78
1909 2325 5.711506 TCAGCAATGTCCATGTTATGTTTCT 59.288 36.000 0.00 0.00 0.00 2.52
1910 2326 6.209192 TCAGCAATGTCCATGTTATGTTTCTT 59.791 34.615 0.00 0.00 0.00 2.52
1911 2327 6.869913 CAGCAATGTCCATGTTATGTTTCTTT 59.130 34.615 0.00 0.00 0.00 2.52
1986 2405 1.136141 GCAGTCTTGTGAACATGAGCG 60.136 52.381 0.00 0.00 31.81 5.03
1994 2413 4.678509 TGTGAACATGAGCGTAAATTCC 57.321 40.909 0.00 0.00 0.00 3.01
1995 2414 4.068599 TGTGAACATGAGCGTAAATTCCA 58.931 39.130 0.00 0.00 0.00 3.53
1997 2416 5.163764 TGTGAACATGAGCGTAAATTCCATC 60.164 40.000 0.00 0.00 0.00 3.51
2006 2425 6.036577 AGCGTAAATTCCATCCATTTTTGT 57.963 33.333 0.00 0.00 0.00 2.83
2008 2427 7.607250 AGCGTAAATTCCATCCATTTTTGTAA 58.393 30.769 0.00 0.00 0.00 2.41
2027 2446 7.469537 TTGTAATATTTCGGTTTGGAATGGT 57.530 32.000 0.00 0.00 0.00 3.55
2028 2447 8.577048 TTGTAATATTTCGGTTTGGAATGGTA 57.423 30.769 0.00 0.00 0.00 3.25
2044 2467 1.095228 GGTACGTGTGATGCATGGGG 61.095 60.000 2.46 0.00 38.39 4.96
2054 2477 0.855598 ATGCATGGGGTTAGATGGCT 59.144 50.000 0.00 0.00 0.00 4.75
2057 2480 1.972872 CATGGGGTTAGATGGCTGAC 58.027 55.000 0.00 0.00 0.00 3.51
2075 2498 2.091499 TGACTCCCCTATCGGTGTATGT 60.091 50.000 0.00 0.00 29.85 2.29
2098 2521 3.466836 GACGTATCCGCGAATATTTTGC 58.533 45.455 8.23 4.10 37.70 3.68
2111 2534 6.676578 GCGAATATTTTGCGGTGTTTAATTTG 59.323 34.615 0.00 0.00 0.00 2.32
2115 2538 1.705873 TGCGGTGTTTAATTTGGGGT 58.294 45.000 0.00 0.00 0.00 4.95
2124 2547 7.561251 GGTGTTTAATTTGGGGTATGCTAAAT 58.439 34.615 0.00 0.00 0.00 1.40
2132 2555 7.979786 TTTGGGGTATGCTAAATTGGAAATA 57.020 32.000 0.00 0.00 0.00 1.40
2143 2566 7.891183 TGCTAAATTGGAAATACCCTAAGAACA 59.109 33.333 0.00 0.00 38.00 3.18
2157 2580 5.105146 CCCTAAGAACAACTCTAGCAGATGT 60.105 44.000 0.00 0.00 39.76 3.06
2173 2598 4.466828 CAGATGTTGCAAAGAGTTTACGG 58.533 43.478 0.00 0.00 0.00 4.02
2182 2607 3.320673 AAGAGTTTACGGCTCCTCTTG 57.679 47.619 8.33 0.00 41.45 3.02
2186 2611 3.400255 AGTTTACGGCTCCTCTTGAAAC 58.600 45.455 0.00 0.00 0.00 2.78
2187 2612 2.074547 TTACGGCTCCTCTTGAAACG 57.925 50.000 0.00 0.00 0.00 3.60
2188 2613 1.250328 TACGGCTCCTCTTGAAACGA 58.750 50.000 0.00 0.00 0.00 3.85
2194 2619 4.332819 CGGCTCCTCTTGAAACGAATTTAT 59.667 41.667 0.00 0.00 0.00 1.40
2198 2623 6.494893 TCCTCTTGAAACGAATTTATGGTG 57.505 37.500 0.00 0.00 0.00 4.17
2204 2629 1.010125 CGAATTTATGGTGCCGCGG 60.010 57.895 24.05 24.05 0.00 6.46
2205 2630 1.433053 CGAATTTATGGTGCCGCGGA 61.433 55.000 33.48 11.82 0.00 5.54
2206 2631 0.736053 GAATTTATGGTGCCGCGGAA 59.264 50.000 33.48 19.06 0.00 4.30
2208 2633 1.398692 ATTTATGGTGCCGCGGAATT 58.601 45.000 33.48 10.67 0.00 2.17
2209 2634 0.453793 TTTATGGTGCCGCGGAATTG 59.546 50.000 33.48 0.95 0.00 2.32
2210 2635 1.380403 TTATGGTGCCGCGGAATTGG 61.380 55.000 33.48 0.01 0.00 3.16
2218 2645 4.150994 GCGGAATTGGGCGGAATA 57.849 55.556 0.00 0.00 0.00 1.75
2224 2651 0.258774 AATTGGGCGGAATAGGTGCT 59.741 50.000 0.00 0.00 0.00 4.40
2226 2653 2.902343 GGGCGGAATAGGTGCTGC 60.902 66.667 0.00 0.00 0.00 5.25
2239 2666 0.317519 GTGCTGCAAAACCGTACCAC 60.318 55.000 2.77 0.00 0.00 4.16
2266 2693 4.708726 AAATCATTTCCTCTTCCTTGCG 57.291 40.909 0.00 0.00 0.00 4.85
2267 2694 2.859165 TCATTTCCTCTTCCTTGCGT 57.141 45.000 0.00 0.00 0.00 5.24
2268 2695 2.699954 TCATTTCCTCTTCCTTGCGTC 58.300 47.619 0.00 0.00 0.00 5.19
2269 2696 2.038426 TCATTTCCTCTTCCTTGCGTCA 59.962 45.455 0.00 0.00 0.00 4.35
2270 2697 2.169832 TTTCCTCTTCCTTGCGTCAG 57.830 50.000 0.00 0.00 0.00 3.51
2271 2698 0.321671 TTCCTCTTCCTTGCGTCAGG 59.678 55.000 0.00 0.00 34.86 3.86
2272 2699 1.743252 CCTCTTCCTTGCGTCAGGC 60.743 63.158 0.00 0.00 43.96 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.900546 AGAGAAGGTGGAACTCATCGTT 59.099 45.455 0.00 0.00 38.91 3.85
27 28 0.251634 TTGTCCACGATGCTGCCATA 59.748 50.000 0.00 0.00 0.00 2.74
29 30 1.672030 CTTGTCCACGATGCTGCCA 60.672 57.895 0.00 0.00 0.00 4.92
74 75 0.175760 ACGCGATCTGCTGGTACATT 59.824 50.000 15.93 0.00 43.27 2.71
98 99 2.847234 AGCACCCTGAACCCGTCA 60.847 61.111 0.00 0.00 34.17 4.35
152 153 1.005394 CTTGGAGTTGTACGCCGGT 60.005 57.895 1.90 0.00 41.28 5.28
185 186 3.374318 TCACATGGAGAACTCGGGA 57.626 52.632 0.00 0.00 0.00 5.14
233 234 2.294078 CCTCCCGACCAAGCTCCTT 61.294 63.158 0.00 0.00 0.00 3.36
234 235 2.537714 ATCCTCCCGACCAAGCTCCT 62.538 60.000 0.00 0.00 0.00 3.69
267 268 1.000955 CAGGTGCTCGTGTAGGAACTT 59.999 52.381 0.42 0.00 41.58 2.66
340 360 2.772287 TGCGGATGTTGTTCATGTACA 58.228 42.857 0.00 0.00 36.83 2.90
352 372 1.148310 CTTGAGAACGTTGCGGATGT 58.852 50.000 5.00 0.00 0.00 3.06
757 1095 4.941873 GTCCAAAATCCCTTAACTGATCGT 59.058 41.667 0.00 0.00 0.00 3.73
896 1269 1.281419 TGTACGACATTGACCCCCAT 58.719 50.000 0.00 0.00 0.00 4.00
971 1349 3.357079 CGCGGTTGAAAGGCAGCT 61.357 61.111 0.00 0.00 0.00 4.24
982 1360 3.284449 GTTGGCCAGAACGCGGTT 61.284 61.111 12.47 1.69 0.00 4.44
984 1362 3.055719 ATGTTGGCCAGAACGCGG 61.056 61.111 12.47 0.00 0.00 6.46
1005 1383 2.131709 GTCATCCCCGACGATCCCA 61.132 63.158 0.00 0.00 0.00 4.37
1038 1416 2.806244 GACAACCTCGCTTACACACAAT 59.194 45.455 0.00 0.00 0.00 2.71
1044 1422 0.753867 TGTGGACAACCTCGCTTACA 59.246 50.000 0.00 0.00 37.04 2.41
1164 1542 2.194597 GTTGGAGGTGGTGGCACA 59.805 61.111 20.82 2.61 0.00 4.57
1242 1620 1.528076 ATGCCCAGCGAACACAACA 60.528 52.632 0.00 0.00 0.00 3.33
1248 1626 2.629656 AAGCACATGCCCAGCGAAC 61.630 57.895 0.00 0.00 43.38 3.95
1266 1644 6.043474 GAGTCTACTCTTCCTAGGTAGGATCA 59.957 46.154 14.84 0.00 42.17 2.92
1276 1654 1.133853 GCCCGGAGTCTACTCTTCCTA 60.134 57.143 0.73 0.00 42.48 2.94
1299 1678 0.657312 TGATGCGGCACAATTCGATC 59.343 50.000 4.03 0.00 0.00 3.69
1305 1684 1.612950 TGAAAAGTGATGCGGCACAAT 59.387 42.857 4.03 2.03 41.19 2.71
1306 1685 1.001487 CTGAAAAGTGATGCGGCACAA 60.001 47.619 4.03 0.00 41.19 3.33
1307 1686 0.592637 CTGAAAAGTGATGCGGCACA 59.407 50.000 4.03 2.71 41.19 4.57
1315 1694 8.850156 AGTATGCTTACAAAACTGAAAAGTGAT 58.150 29.630 11.89 0.00 0.00 3.06
1390 1769 8.875803 CACACCTCTAAATAGCATTACGTAAAA 58.124 33.333 12.81 0.00 0.00 1.52
1402 1781 4.631813 GCCACTGAACACACCTCTAAATAG 59.368 45.833 0.00 0.00 0.00 1.73
1417 1796 2.912771 TCTTTCGAAAGTGCCACTGAA 58.087 42.857 31.29 11.18 37.31 3.02
1419 1798 2.807967 TCATCTTTCGAAAGTGCCACTG 59.192 45.455 31.29 20.38 37.31 3.66
1420 1799 3.126001 TCATCTTTCGAAAGTGCCACT 57.874 42.857 31.29 12.08 37.31 4.00
1421 1800 5.545658 TTATCATCTTTCGAAAGTGCCAC 57.454 39.130 31.29 0.00 37.31 5.01
1422 1801 6.554419 CAATTATCATCTTTCGAAAGTGCCA 58.446 36.000 31.29 16.78 37.31 4.92
1423 1802 5.456822 GCAATTATCATCTTTCGAAAGTGCC 59.543 40.000 31.29 14.94 37.31 5.01
1425 1804 7.217636 CACTGCAATTATCATCTTTCGAAAGTG 59.782 37.037 31.29 26.73 37.31 3.16
1426 1805 7.246311 CACTGCAATTATCATCTTTCGAAAGT 58.754 34.615 31.29 18.96 37.31 2.66
1427 1806 6.690098 CCACTGCAATTATCATCTTTCGAAAG 59.310 38.462 28.26 28.26 37.36 2.62
1431 1820 4.201940 TGCCACTGCAATTATCATCTTTCG 60.202 41.667 0.00 0.00 46.66 3.46
1448 1837 2.569059 CCGATTCAGATGAATGCCACT 58.431 47.619 12.62 0.00 44.14 4.00
1455 1844 4.424061 CAACTTTGCCGATTCAGATGAA 57.576 40.909 0.00 0.00 38.56 2.57
1477 1866 5.940192 TGTTAAACAGATAAGTGCCACTG 57.060 39.130 0.00 0.00 36.58 3.66
1478 1867 5.415701 CCATGTTAAACAGATAAGTGCCACT 59.584 40.000 0.00 0.00 0.00 4.00
1500 1889 9.508642 TGTATGTTAACATCTTCAATTGTACCA 57.491 29.630 24.00 0.00 37.76 3.25
1501 1890 9.769093 GTGTATGTTAACATCTTCAATTGTACC 57.231 33.333 24.00 5.95 37.76 3.34
1511 1906 6.592220 TGTATGTGCGTGTATGTTAACATCTT 59.408 34.615 24.00 4.86 37.76 2.40
1522 1917 2.101917 GGGTAGGTGTATGTGCGTGTAT 59.898 50.000 0.00 0.00 0.00 2.29
1528 1923 4.682778 TCATAAGGGTAGGTGTATGTGC 57.317 45.455 0.00 0.00 0.00 4.57
1530 1925 4.442472 GCGTTCATAAGGGTAGGTGTATGT 60.442 45.833 0.00 0.00 0.00 2.29
1538 1933 2.930040 CTGTGTGCGTTCATAAGGGTAG 59.070 50.000 0.00 0.00 0.00 3.18
1603 2000 6.230849 GACGTCTATGATGACTTCGTCTAT 57.769 41.667 8.70 0.00 41.48 1.98
1637 2034 6.869315 TTAGTAGGAGAGATGACATCTTCG 57.131 41.667 18.89 0.00 40.38 3.79
1641 2038 9.906660 CTATGTTTTAGTAGGAGAGATGACATC 57.093 37.037 7.39 7.39 0.00 3.06
1643 2040 8.824756 ACTATGTTTTAGTAGGAGAGATGACA 57.175 34.615 0.00 0.00 0.00 3.58
1645 2042 9.916360 TGTACTATGTTTTAGTAGGAGAGATGA 57.084 33.333 0.00 0.00 31.41 2.92
1659 2056 8.288913 GCATGGCAAATTTTTGTACTATGTTTT 58.711 29.630 0.00 0.00 40.24 2.43
1661 2058 7.160726 AGCATGGCAAATTTTTGTACTATGTT 58.839 30.769 0.00 0.00 40.24 2.71
1662 2059 6.700352 AGCATGGCAAATTTTTGTACTATGT 58.300 32.000 0.00 0.00 40.24 2.29
1666 2063 9.533253 GATTATAGCATGGCAAATTTTTGTACT 57.467 29.630 0.00 0.00 40.24 2.73
1667 2064 9.311916 TGATTATAGCATGGCAAATTTTTGTAC 57.688 29.630 0.00 0.00 40.24 2.90
1764 2161 6.314896 CAGACATAGATGTGGGTTCTTTTCTC 59.685 42.308 0.00 0.00 41.95 2.87
1785 2182 1.279271 AGGCCCAGTCACATAACAGAC 59.721 52.381 0.00 0.00 35.02 3.51
1798 2214 3.691342 TCGACGGACAAGGCCCAG 61.691 66.667 0.00 0.00 0.00 4.45
1812 2228 1.502039 ACACCCCCTCCTATATGTCGA 59.498 52.381 0.00 0.00 0.00 4.20
1813 2229 1.893801 GACACCCCCTCCTATATGTCG 59.106 57.143 0.00 0.00 0.00 4.35
1836 2252 7.503566 CCCCTAATTTGATCACAATGTCATACT 59.496 37.037 0.00 0.00 35.85 2.12
1863 2279 6.542821 TGAACTTGGGAGAATAACATTCACT 58.457 36.000 2.03 0.00 0.00 3.41
1872 2288 4.922206 ACATTGCTGAACTTGGGAGAATA 58.078 39.130 0.00 0.00 0.00 1.75
1886 2302 5.957798 AGAAACATAACATGGACATTGCTG 58.042 37.500 0.00 0.00 33.60 4.41
1888 2304 6.867816 TCAAAGAAACATAACATGGACATTGC 59.132 34.615 0.00 0.00 33.60 3.56
1889 2305 8.815141 TTCAAAGAAACATAACATGGACATTG 57.185 30.769 0.00 0.00 33.60 2.82
1892 2308 9.906660 GTATTTCAAAGAAACATAACATGGACA 57.093 29.630 0.00 0.00 33.60 4.02
1910 2326 9.635520 CGTTTCTTACTCCTCTAAGTATTTCAA 57.364 33.333 0.00 0.00 32.00 2.69
1911 2327 9.017509 TCGTTTCTTACTCCTCTAAGTATTTCA 57.982 33.333 0.00 0.00 32.00 2.69
1966 2385 1.136141 CGCTCATGTTCACAAGACTGC 60.136 52.381 0.00 0.00 0.00 4.40
1972 2391 4.517075 TGGAATTTACGCTCATGTTCACAA 59.483 37.500 0.00 0.00 0.00 3.33
1980 2399 6.469782 AAAATGGATGGAATTTACGCTCAT 57.530 33.333 0.00 0.00 0.00 2.90
1995 2414 9.377312 CCAAACCGAAATATTACAAAAATGGAT 57.623 29.630 0.00 0.00 0.00 3.41
1997 2416 8.764524 TCCAAACCGAAATATTACAAAAATGG 57.235 30.769 0.00 0.00 0.00 3.16
2006 2425 6.822676 ACGTACCATTCCAAACCGAAATATTA 59.177 34.615 0.00 0.00 0.00 0.98
2008 2427 5.065474 CACGTACCATTCCAAACCGAAATAT 59.935 40.000 0.00 0.00 0.00 1.28
2027 2446 0.326595 AACCCCATGCATCACACGTA 59.673 50.000 0.00 0.00 0.00 3.57
2028 2447 0.326595 TAACCCCATGCATCACACGT 59.673 50.000 0.00 0.00 0.00 4.49
2044 2467 1.501582 AGGGGAGTCAGCCATCTAAC 58.498 55.000 0.00 0.00 0.00 2.34
2086 2509 5.942325 ATTAAACACCGCAAAATATTCGC 57.058 34.783 0.00 0.00 0.00 4.70
2092 2515 4.068599 CCCCAAATTAAACACCGCAAAAT 58.931 39.130 0.00 0.00 0.00 1.82
2098 2521 3.445805 AGCATACCCCAAATTAAACACCG 59.554 43.478 0.00 0.00 0.00 4.94
2099 2522 6.532988 TTAGCATACCCCAAATTAAACACC 57.467 37.500 0.00 0.00 0.00 4.16
2111 2534 5.245301 GGGTATTTCCAATTTAGCATACCCC 59.755 44.000 15.93 0.00 45.91 4.95
2124 2547 7.086685 AGAGTTGTTCTTAGGGTATTTCCAA 57.913 36.000 0.00 0.00 32.59 3.53
2132 2555 4.417437 TCTGCTAGAGTTGTTCTTAGGGT 58.583 43.478 0.00 0.00 37.36 4.34
2157 2580 1.877443 GGAGCCGTAAACTCTTTGCAA 59.123 47.619 0.00 0.00 34.46 4.08
2166 2589 2.157085 CGTTTCAAGAGGAGCCGTAAAC 59.843 50.000 0.00 0.00 0.00 2.01
2167 2590 2.036217 TCGTTTCAAGAGGAGCCGTAAA 59.964 45.455 0.00 0.00 0.00 2.01
2173 2598 5.123979 ACCATAAATTCGTTTCAAGAGGAGC 59.876 40.000 0.00 0.00 0.00 4.70
2182 2607 2.182014 GCGGCACCATAAATTCGTTTC 58.818 47.619 0.00 0.00 0.00 2.78
2186 2611 1.010125 CCGCGGCACCATAAATTCG 60.010 57.895 14.67 0.00 0.00 3.34
2187 2612 0.736053 TTCCGCGGCACCATAAATTC 59.264 50.000 23.51 0.00 0.00 2.17
2188 2613 1.398692 ATTCCGCGGCACCATAAATT 58.601 45.000 23.51 0.00 0.00 1.82
2204 2629 0.668535 GCACCTATTCCGCCCAATTC 59.331 55.000 0.00 0.00 0.00 2.17
2205 2630 0.258774 AGCACCTATTCCGCCCAATT 59.741 50.000 0.00 0.00 0.00 2.32
2206 2631 0.466189 CAGCACCTATTCCGCCCAAT 60.466 55.000 0.00 0.00 0.00 3.16
2208 2633 2.589540 CAGCACCTATTCCGCCCA 59.410 61.111 0.00 0.00 0.00 5.36
2209 2634 2.902343 GCAGCACCTATTCCGCCC 60.902 66.667 0.00 0.00 0.00 6.13
2210 2635 1.312371 TTTGCAGCACCTATTCCGCC 61.312 55.000 0.00 0.00 0.00 6.13
2216 2643 2.081462 GTACGGTTTTGCAGCACCTAT 58.919 47.619 13.09 5.42 0.00 2.57
2218 2645 1.170290 GGTACGGTTTTGCAGCACCT 61.170 55.000 13.09 4.83 0.00 4.00
2224 2651 3.587797 TTTTTGTGGTACGGTTTTGCA 57.412 38.095 0.00 0.00 0.00 4.08
2246 2673 3.690460 ACGCAAGGAAGAGGAAATGATT 58.310 40.909 0.00 0.00 46.39 2.57
2247 2674 3.274288 GACGCAAGGAAGAGGAAATGAT 58.726 45.455 0.00 0.00 46.39 2.45


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

AutoCloner maintained by Alex Coulton.