Multiple sequence alignment - TraesCS6B01G418200

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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 TraesCS6B01G418200 chr6B 100.000 2270 0 0 1 2270 690455913 690453644 0.000000e+00 4193
1 TraesCS6B01G418200 chr6B 96.028 1309 42 2 1 1299 177406696 177405388 0.000000e+00 2121
2 TraesCS6B01G418200 chr6B 95.000 680 24 2 632 1301 197738962 197738283 0.000000e+00 1059
3 TraesCS6B01G418200 chr6B 90.736 421 26 10 1303 1715 694626703 694626288 1.190000e-152 549
4 TraesCS6B01G418200 chr6B 88.859 368 25 11 1907 2270 694626013 694625658 2.680000e-119 438
5 TraesCS6B01G418200 chr6B 89.157 249 21 3 1840 2082 9021372 9021124 2.830000e-79 305
6 TraesCS6B01G418200 chr2B 92.525 1311 86 4 1 1300 296058432 296059741 0.000000e+00 1868
7 TraesCS6B01G418200 chr2B 91.111 1260 100 6 51 1300 109881570 109880313 0.000000e+00 1696
8 TraesCS6B01G418200 chr2B 91.859 823 60 4 2 817 774546788 774545966 0.000000e+00 1142
9 TraesCS6B01G418200 chr2B 88.235 578 40 14 1303 1857 721336 720764 0.000000e+00 665
10 TraesCS6B01G418200 chr2B 87.634 558 52 14 1303 1857 742656871 742657414 1.140000e-177 632
11 TraesCS6B01G418200 chr2B 87.778 360 31 8 1727 2076 682582391 682582747 2.100000e-110 409
12 TraesCS6B01G418200 chr2B 86.198 384 33 14 1894 2270 448926914 448927284 4.540000e-107 398
13 TraesCS6B01G418200 chr2B 85.079 382 36 11 1894 2270 8748967 8748602 9.900000e-99 370
14 TraesCS6B01G418200 chr2B 81.842 380 30 15 1894 2270 96148326 96147983 1.330000e-72 283
15 TraesCS6B01G418200 chr2B 85.932 263 22 9 2009 2270 31414351 31414103 1.340000e-67 267
16 TraesCS6B01G418200 chr4A 92.190 1306 92 2 1 1296 169683712 169682407 0.000000e+00 1838
17 TraesCS6B01G418200 chr4A 87.386 547 36 15 1303 1822 713871657 713871117 4.170000e-167 597
18 TraesCS6B01G418200 chr4A 77.980 713 112 30 1572 2270 34268915 34268234 2.720000e-109 405
19 TraesCS6B01G418200 chr7B 92.706 1275 83 2 1 1265 14773422 14774696 0.000000e+00 1831
20 TraesCS6B01G418200 chr7B 86.949 544 40 13 1303 1819 583368038 583368577 1.170000e-162 582
21 TraesCS6B01G418200 chr7B 89.167 240 18 5 1840 2073 9636467 9636230 2.210000e-75 292
22 TraesCS6B01G418200 chr7B 88.571 245 17 6 1840 2076 714601309 714601068 1.030000e-73 287
23 TraesCS6B01G418200 chr3B 91.857 1314 97 4 1 1304 384336616 384335303 0.000000e+00 1825
24 TraesCS6B01G418200 chr3B 87.153 576 46 14 1303 1857 662418537 662419105 1.480000e-176 628
25 TraesCS6B01G418200 chr3B 83.921 454 39 13 1522 1949 811982019 811982464 9.770000e-109 403
26 TraesCS6B01G418200 chr3B 89.121 239 20 5 1840 2076 803330280 803330046 2.210000e-75 292
27 TraesCS6B01G418200 chr3B 88.618 246 19 5 1840 2077 19741042 19741286 7.930000e-75 291
28 TraesCS6B01G418200 chr3B 85.000 200 24 4 1672 1866 820731959 820731761 4.950000e-47 198
29 TraesCS6B01G418200 chr5B 91.826 1309 96 3 1 1299 666585845 666584538 0.000000e+00 1814
30 TraesCS6B01G418200 chr5B 86.053 380 36 7 1894 2270 367515678 367516043 2.110000e-105 392
31 TraesCS6B01G418200 chr5B 97.674 43 1 0 1260 1302 23351813 23351771 8.700000e-10 75
32 TraesCS6B01G418200 chrUn 90.291 1308 115 6 3 1299 336409519 336410825 0.000000e+00 1701
33 TraesCS6B01G418200 chrUn 82.794 587 51 22 1719 2270 35731599 35732170 1.580000e-131 479
34 TraesCS6B01G418200 chr5A 83.954 1315 197 9 3 1305 415261553 415260241 0.000000e+00 1247
35 TraesCS6B01G418200 chr4B 82.080 1317 214 11 3 1300 664171511 664172824 0.000000e+00 1105
36 TraesCS6B01G418200 chr4B 90.714 420 30 8 1303 1718 575607037 575606623 3.300000e-153 551
37 TraesCS6B01G418200 chr4B 86.387 382 34 9 1894 2270 637589285 637588917 3.510000e-108 401
38 TraesCS6B01G418200 chr4B 85.382 301 40 3 1776 2074 23817408 23817706 2.190000e-80 309
39 TraesCS6B01G418200 chr1B 87.211 563 52 13 1303 1857 334305093 334304543 6.890000e-175 623
40 TraesCS6B01G418200 chr1B 90.974 421 29 9 1303 1718 676798740 676799156 1.970000e-155 558
41 TraesCS6B01G418200 chr1B 87.632 380 30 8 1894 2270 416830066 416830431 2.080000e-115 425
42 TraesCS6B01G418200 chr1B 85.488 379 34 11 1894 2270 469167723 469168082 2.130000e-100 375
43 TraesCS6B01G418200 chr7D 75.480 677 82 32 1630 2269 20110533 20111162 1.040000e-63 254


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 TraesCS6B01G418200 chr6B 690453644 690455913 2269 True 4193.0 4193 100.0000 1 2270 1 chr6B.!!$R4 2269
1 TraesCS6B01G418200 chr6B 177405388 177406696 1308 True 2121.0 2121 96.0280 1 1299 1 chr6B.!!$R2 1298
2 TraesCS6B01G418200 chr6B 197738283 197738962 679 True 1059.0 1059 95.0000 632 1301 1 chr6B.!!$R3 669
3 TraesCS6B01G418200 chr6B 694625658 694626703 1045 True 493.5 549 89.7975 1303 2270 2 chr6B.!!$R5 967
4 TraesCS6B01G418200 chr2B 296058432 296059741 1309 False 1868.0 1868 92.5250 1 1300 1 chr2B.!!$F1 1299
5 TraesCS6B01G418200 chr2B 109880313 109881570 1257 True 1696.0 1696 91.1110 51 1300 1 chr2B.!!$R5 1249
6 TraesCS6B01G418200 chr2B 774545966 774546788 822 True 1142.0 1142 91.8590 2 817 1 chr2B.!!$R6 815
7 TraesCS6B01G418200 chr2B 720764 721336 572 True 665.0 665 88.2350 1303 1857 1 chr2B.!!$R1 554
8 TraesCS6B01G418200 chr2B 742656871 742657414 543 False 632.0 632 87.6340 1303 1857 1 chr2B.!!$F4 554
9 TraesCS6B01G418200 chr4A 169682407 169683712 1305 True 1838.0 1838 92.1900 1 1296 1 chr4A.!!$R2 1295
10 TraesCS6B01G418200 chr4A 713871117 713871657 540 True 597.0 597 87.3860 1303 1822 1 chr4A.!!$R3 519
11 TraesCS6B01G418200 chr4A 34268234 34268915 681 True 405.0 405 77.9800 1572 2270 1 chr4A.!!$R1 698
12 TraesCS6B01G418200 chr7B 14773422 14774696 1274 False 1831.0 1831 92.7060 1 1265 1 chr7B.!!$F1 1264
13 TraesCS6B01G418200 chr7B 583368038 583368577 539 False 582.0 582 86.9490 1303 1819 1 chr7B.!!$F2 516
14 TraesCS6B01G418200 chr3B 384335303 384336616 1313 True 1825.0 1825 91.8570 1 1304 1 chr3B.!!$R1 1303
15 TraesCS6B01G418200 chr3B 662418537 662419105 568 False 628.0 628 87.1530 1303 1857 1 chr3B.!!$F2 554
16 TraesCS6B01G418200 chr5B 666584538 666585845 1307 True 1814.0 1814 91.8260 1 1299 1 chr5B.!!$R2 1298
17 TraesCS6B01G418200 chrUn 336409519 336410825 1306 False 1701.0 1701 90.2910 3 1299 1 chrUn.!!$F2 1296
18 TraesCS6B01G418200 chrUn 35731599 35732170 571 False 479.0 479 82.7940 1719 2270 1 chrUn.!!$F1 551
19 TraesCS6B01G418200 chr5A 415260241 415261553 1312 True 1247.0 1247 83.9540 3 1305 1 chr5A.!!$R1 1302
20 TraesCS6B01G418200 chr4B 664171511 664172824 1313 False 1105.0 1105 82.0800 3 1300 1 chr4B.!!$F2 1297
21 TraesCS6B01G418200 chr1B 334304543 334305093 550 True 623.0 623 87.2110 1303 1857 1 chr1B.!!$R1 554
22 TraesCS6B01G418200 chr7D 20110533 20111162 629 False 254.0 254 75.4800 1630 2269 1 chr7D.!!$F1 639

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
979 987 1.131883 GCATGATCTTTGCGCAACTCT 59.868 47.619 24.99 9.94 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 2592 0.039165 CTTTCCAAAAGAGGCACGCC 60.039 55.0 0.0 0.0 0.0 5.68 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
208 209 2.839228 ACTCTAGCCTGGTCTTTGGAT 58.161 47.619 0.00 0.00 0.00 3.41
262 263 2.061773 CGTTCTCTTGTGACTCGCAAT 58.938 47.619 5.49 0.00 33.31 3.56
416 417 8.529476 GGATTTTACCTGACTCTACTACTTTGA 58.471 37.037 0.00 0.00 0.00 2.69
490 491 3.679980 ACGAAGACATGTTACATGCACTC 59.320 43.478 23.43 14.32 0.00 3.51
643 644 9.217278 GACAGATGCAAGATTATCACTATCATT 57.783 33.333 0.00 0.00 0.00 2.57
644 645 9.570468 ACAGATGCAAGATTATCACTATCATTT 57.430 29.630 0.00 0.00 0.00 2.32
979 987 1.131883 GCATGATCTTTGCGCAACTCT 59.868 47.619 24.99 9.94 0.00 3.24
1037 1048 5.558818 CTTGGAGCTAGATCTATGGCATTT 58.441 41.667 4.78 0.00 0.00 2.32
1061 1072 0.883833 GGCAACACCAGATCAGTTGG 59.116 55.000 16.64 9.39 42.07 3.77
1187 1205 2.034878 CCTAGCTAGCACACTGGATGA 58.965 52.381 18.83 0.00 0.00 2.92
1194 1212 1.627329 AGCACACTGGATGACACTGAT 59.373 47.619 0.00 0.00 0.00 2.90
1421 1441 6.480285 GTTTTCGGCTTTTTAAAAGGGTTTC 58.520 36.000 17.68 2.21 0.00 2.78
1477 1502 3.713826 TTCCCTAGCTTTTCGACCAAT 57.286 42.857 0.00 0.00 0.00 3.16
1600 1631 2.358737 CACGGGTGTGCCTCTTCC 60.359 66.667 0.00 0.00 39.67 3.46
1601 1632 4.003788 ACGGGTGTGCCTCTTCCG 62.004 66.667 0.00 0.00 45.42 4.30
1602 1633 4.760047 CGGGTGTGCCTCTTCCGG 62.760 72.222 0.00 0.00 37.35 5.14
1604 1635 2.747686 GGTGTGCCTCTTCCGGAA 59.252 61.111 17.73 17.73 0.00 4.30
1605 1636 1.072505 GGTGTGCCTCTTCCGGAAA 59.927 57.895 19.39 8.50 0.00 3.13
1606 1637 0.955919 GGTGTGCCTCTTCCGGAAAG 60.956 60.000 19.39 16.97 36.22 2.62
1607 1638 0.955919 GTGTGCCTCTTCCGGAAAGG 60.956 60.000 27.66 27.66 42.97 3.11
1651 1682 4.813296 TTTTTCTTCTTTCGTGAGAGGC 57.187 40.909 0.00 0.00 43.69 4.70
1652 1683 3.469008 TTTCTTCTTTCGTGAGAGGCA 57.531 42.857 0.00 0.00 43.69 4.75
1653 1684 2.440539 TCTTCTTTCGTGAGAGGCAC 57.559 50.000 0.00 0.00 43.69 5.01
1661 1692 1.282875 GTGAGAGGCACGGTTTTGC 59.717 57.895 0.00 0.00 42.18 3.68
1662 1693 1.148273 TGAGAGGCACGGTTTTGCT 59.852 52.632 0.00 0.00 42.56 3.91
1663 1694 0.465460 TGAGAGGCACGGTTTTGCTT 60.465 50.000 0.00 0.00 42.56 3.91
1664 1695 0.238553 GAGAGGCACGGTTTTGCTTC 59.761 55.000 0.28 0.28 46.31 3.86
1665 1696 1.172812 AGAGGCACGGTTTTGCTTCC 61.173 55.000 4.54 0.00 46.96 3.46
1670 1701 2.725008 CGGTTTTGCTTCCGCCAA 59.275 55.556 0.00 0.00 40.28 4.52
1671 1702 1.066587 CGGTTTTGCTTCCGCCAAA 59.933 52.632 0.00 0.00 40.28 3.28
1672 1703 0.939106 CGGTTTTGCTTCCGCCAAAG 60.939 55.000 0.00 0.00 40.28 2.77
1673 1704 0.599991 GGTTTTGCTTCCGCCAAAGG 60.600 55.000 0.00 0.00 32.23 3.11
1696 1727 0.721718 GGTTGTGATTTCGCGAGAGG 59.278 55.000 9.59 0.00 43.69 3.69
1702 1733 4.735132 TTTCGCGAGAGGCACGGG 62.735 66.667 9.59 0.00 43.84 5.28
1714 1745 3.423154 CACGGGCGTGCCTCTTTC 61.423 66.667 11.25 0.00 39.39 2.62
1725 1756 3.181520 CGTGCCTCTTTCGGACTATTTTG 60.182 47.826 0.00 0.00 0.00 2.44
1752 2403 2.251642 GCGAGAGGCACGGTTTTGT 61.252 57.895 0.00 0.00 42.87 2.83
1755 2406 1.064952 CGAGAGGCACGGTTTTGTTTT 59.935 47.619 0.00 0.00 0.00 2.43
1819 2555 3.552273 GCCTCTTTCGGAAAGGGAAAAAC 60.552 47.826 27.71 10.56 41.66 2.43
1820 2556 3.634910 CCTCTTTCGGAAAGGGAAAAACA 59.365 43.478 27.71 7.78 41.66 2.83
1821 2557 4.499188 CCTCTTTCGGAAAGGGAAAAACAC 60.499 45.833 27.71 0.00 41.66 3.32
1822 2558 3.065648 TCTTTCGGAAAGGGAAAAACACG 59.934 43.478 25.66 1.87 39.01 4.49
1823 2559 2.041251 TCGGAAAGGGAAAAACACGT 57.959 45.000 0.00 0.00 0.00 4.49
1824 2560 2.367486 TCGGAAAGGGAAAAACACGTT 58.633 42.857 0.00 0.00 0.00 3.99
1825 2561 2.754002 TCGGAAAGGGAAAAACACGTTT 59.246 40.909 0.00 0.00 0.00 3.60
1826 2562 3.193056 TCGGAAAGGGAAAAACACGTTTT 59.807 39.130 2.06 2.06 43.88 2.43
1852 2588 9.099454 TCTATTTATTTTTCTTTCTCGAGAGGC 57.901 33.333 15.94 0.00 0.00 4.70
1853 2589 7.687941 ATTTATTTTTCTTTCTCGAGAGGCA 57.312 32.000 15.94 0.00 0.00 4.75
1854 2590 6.481954 TTATTTTTCTTTCTCGAGAGGCAC 57.518 37.500 15.94 0.00 0.00 5.01
1855 2591 2.065993 TTTCTTTCTCGAGAGGCACG 57.934 50.000 15.94 0.00 0.00 5.34
1856 2592 0.243907 TTCTTTCTCGAGAGGCACGG 59.756 55.000 15.94 4.00 0.00 4.94
1857 2593 1.153745 CTTTCTCGAGAGGCACGGG 60.154 63.158 15.94 0.00 0.00 5.28
1858 2594 3.296709 TTTCTCGAGAGGCACGGGC 62.297 63.158 15.94 0.00 40.13 6.13
1869 2605 2.978010 CACGGGCGTGCCTCTTTT 60.978 61.111 11.25 0.00 39.39 2.27
1870 2606 2.978010 ACGGGCGTGCCTCTTTTG 60.978 61.111 11.25 0.00 36.10 2.44
1871 2607 3.737172 CGGGCGTGCCTCTTTTGG 61.737 66.667 11.25 0.00 36.10 3.28
1872 2608 2.282180 GGGCGTGCCTCTTTTGGA 60.282 61.111 11.25 0.00 36.10 3.53
1873 2609 1.901464 GGGCGTGCCTCTTTTGGAA 60.901 57.895 11.25 0.00 36.10 3.53
1874 2610 1.460273 GGGCGTGCCTCTTTTGGAAA 61.460 55.000 11.25 0.00 36.10 3.13
1875 2611 0.039165 GGCGTGCCTCTTTTGGAAAG 60.039 55.000 2.98 0.00 0.00 2.62
1876 2612 0.039165 GCGTGCCTCTTTTGGAAAGG 60.039 55.000 1.04 0.00 0.00 3.11
1877 2613 0.598065 CGTGCCTCTTTTGGAAAGGG 59.402 55.000 1.04 0.00 0.00 3.95
1878 2614 1.817740 CGTGCCTCTTTTGGAAAGGGA 60.818 52.381 1.96 0.00 0.00 4.20
1879 2615 2.316108 GTGCCTCTTTTGGAAAGGGAA 58.684 47.619 1.96 0.00 31.86 3.97
1880 2616 2.698274 GTGCCTCTTTTGGAAAGGGAAA 59.302 45.455 1.96 0.00 31.86 3.13
1881 2617 3.133901 GTGCCTCTTTTGGAAAGGGAAAA 59.866 43.478 1.96 0.00 31.86 2.29
1882 2618 3.777522 TGCCTCTTTTGGAAAGGGAAAAA 59.222 39.130 1.96 0.00 0.00 1.94
1883 2619 4.127171 GCCTCTTTTGGAAAGGGAAAAAC 58.873 43.478 1.96 0.00 0.00 2.43
1884 2620 4.368315 CCTCTTTTGGAAAGGGAAAAACG 58.632 43.478 1.96 0.00 0.00 3.60
1885 2621 3.787785 TCTTTTGGAAAGGGAAAAACGC 58.212 40.909 1.04 0.00 0.00 4.84
1886 2622 2.211353 TTTGGAAAGGGAAAAACGCG 57.789 45.000 3.53 3.53 36.53 6.01
1887 2623 1.104630 TTGGAAAGGGAAAAACGCGT 58.895 45.000 5.58 5.58 36.53 6.01
1888 2624 1.104630 TGGAAAGGGAAAAACGCGTT 58.895 45.000 20.79 20.79 36.12 4.84
1889 2625 1.477295 TGGAAAGGGAAAAACGCGTTT 59.523 42.857 30.36 30.36 34.04 3.60
1890 2626 2.094130 TGGAAAGGGAAAAACGCGTTTT 60.094 40.909 36.93 36.93 43.88 2.43
1914 2650 3.240203 TTTTTCGCGAGAGGCACG 58.760 55.556 9.59 0.00 43.84 5.34
1915 2651 2.314647 TTTTTCGCGAGAGGCACGG 61.315 57.895 9.59 0.00 43.84 4.94
1916 2652 2.981977 TTTTTCGCGAGAGGCACGGT 62.982 55.000 9.59 0.00 43.84 4.83
1917 2653 2.981977 TTTTCGCGAGAGGCACGGTT 62.982 55.000 9.59 0.00 43.84 4.44
1918 2654 4.717629 TCGCGAGAGGCACGGTTG 62.718 66.667 3.71 0.00 43.84 3.77
1928 2664 3.882668 CACGGTTGTGTTTTCGCG 58.117 55.556 0.00 0.00 41.34 5.87
1929 2665 1.348938 CACGGTTGTGTTTTCGCGA 59.651 52.632 3.71 3.71 41.34 5.87
1930 2666 0.653323 CACGGTTGTGTTTTCGCGAG 60.653 55.000 9.59 0.00 41.34 5.03
1931 2667 0.806884 ACGGTTGTGTTTTCGCGAGA 60.807 50.000 9.59 0.43 39.20 4.04
1932 2668 0.111266 CGGTTGTGTTTTCGCGAGAG 60.111 55.000 9.59 0.00 43.69 3.20
1933 2669 0.234884 GGTTGTGTTTTCGCGAGAGG 59.765 55.000 9.59 0.00 43.69 3.69
1934 2670 0.384353 GTTGTGTTTTCGCGAGAGGC 60.384 55.000 9.59 2.53 43.69 4.70
1935 2671 0.812014 TTGTGTTTTCGCGAGAGGCA 60.812 50.000 9.59 5.38 43.84 4.75
1936 2672 0.602638 TGTGTTTTCGCGAGAGGCAT 60.603 50.000 9.59 0.00 43.84 4.40
1937 2673 0.179215 GTGTTTTCGCGAGAGGCATG 60.179 55.000 9.59 0.00 43.84 4.06
1938 2674 1.298157 TGTTTTCGCGAGAGGCATGG 61.298 55.000 9.59 0.00 43.84 3.66
1939 2675 1.745115 TTTTCGCGAGAGGCATGGG 60.745 57.895 9.59 0.00 43.84 4.00
1940 2676 4.838152 TTCGCGAGAGGCATGGGC 62.838 66.667 9.59 0.00 43.84 5.36
1950 2686 2.125952 GCATGGGCGTGCCTTTTC 60.126 61.111 11.25 0.00 39.18 2.29
1951 2687 2.573340 CATGGGCGTGCCTTTTCC 59.427 61.111 11.25 0.00 36.10 3.13
1952 2688 3.061848 ATGGGCGTGCCTTTTCCG 61.062 61.111 11.25 0.00 36.10 4.30
1955 2691 2.981350 GGCGTGCCTTTTCCGGAA 60.981 61.111 14.35 14.35 0.00 4.30
1956 2692 2.557372 GGCGTGCCTTTTCCGGAAA 61.557 57.895 25.67 25.67 0.00 3.13
1957 2693 1.081442 GCGTGCCTTTTCCGGAAAG 60.081 57.895 27.48 18.90 43.57 2.62
2007 2744 1.785951 GCGAGAGGTACGGTTTTGC 59.214 57.895 0.00 0.00 0.00 3.68
2011 2748 2.609737 CGAGAGGTACGGTTTTGCTTCT 60.610 50.000 0.00 0.00 0.00 2.85
2014 2751 0.240145 GGTACGGTTTTGCTTCTGCC 59.760 55.000 0.00 0.00 38.71 4.85
2037 2774 3.882668 CACGGTTGTGTTTTCGCG 58.117 55.556 0.00 0.00 41.34 5.87
2066 2803 1.512156 GGCGTGCCTCTTTCGGAAAA 61.512 55.000 2.98 0.00 0.00 2.29
2067 2804 0.110192 GCGTGCCTCTTTCGGAAAAG 60.110 55.000 4.53 5.42 42.77 2.27
2161 2898 9.810545 TTCCTGAAATAAAAACTTCGTCAAAAT 57.189 25.926 0.00 0.00 0.00 1.82
2201 2938 1.614385 TTTGAAGATCTCGACGCGAC 58.386 50.000 15.93 5.54 0.00 5.19
2244 2981 2.097728 GATTTGGACGCGCGGTTC 59.902 61.111 35.22 22.98 0.00 3.62
2252 2989 1.352156 GACGCGCGGTTCAAGAGATT 61.352 55.000 35.22 7.97 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.126883 CCCTAGGTTTCAGTGTGGTCATATTA 60.127 42.308 8.29 0.00 0.00 0.98
208 209 2.453521 ACAGTGTAGATGCCCGACTTA 58.546 47.619 0.00 0.00 0.00 2.24
416 417 4.585955 ACGGCTTGATATGACGATAACT 57.414 40.909 0.00 0.00 38.36 2.24
643 644 2.034179 CCGTGACGTCCAGATGCTATAA 59.966 50.000 14.12 0.00 0.00 0.98
644 645 1.607148 CCGTGACGTCCAGATGCTATA 59.393 52.381 14.12 0.00 0.00 1.31
652 653 0.249322 AGTTGTTCCGTGACGTCCAG 60.249 55.000 14.12 6.75 0.00 3.86
979 987 3.570540 TGATCACATGTGAAAAACCCCA 58.429 40.909 31.00 16.47 43.58 4.96
1061 1072 2.159170 AGTTCACTCAAGATAGGCGCTC 60.159 50.000 7.64 0.00 0.00 5.03
1187 1205 4.292186 ACATCAAGCCAACTATCAGTGT 57.708 40.909 0.00 0.00 0.00 3.55
1441 1465 1.888512 GGGAAAACCGGTAGAAAACCC 59.111 52.381 8.00 11.77 46.62 4.11
1589 1620 1.374947 CCTTTCCGGAAGAGGCACA 59.625 57.895 23.65 7.26 37.57 4.57
1633 1664 2.755650 GTGCCTCTCACGAAAGAAGAA 58.244 47.619 0.00 0.00 35.76 2.52
1644 1675 0.465460 AAGCAAAACCGTGCCTCTCA 60.465 50.000 0.00 0.00 46.14 3.27
1667 1698 0.673437 AATCACAACCGTGCCTTTGG 59.327 50.000 0.00 0.00 43.28 3.28
1668 1699 2.393764 GAAATCACAACCGTGCCTTTG 58.606 47.619 0.00 0.00 43.28 2.77
1669 1700 1.001815 CGAAATCACAACCGTGCCTTT 60.002 47.619 0.00 0.00 43.28 3.11
1670 1701 0.591170 CGAAATCACAACCGTGCCTT 59.409 50.000 0.00 0.00 43.28 4.35
1671 1702 1.852067 GCGAAATCACAACCGTGCCT 61.852 55.000 0.00 0.00 43.28 4.75
1672 1703 1.442017 GCGAAATCACAACCGTGCC 60.442 57.895 0.00 0.00 43.28 5.01
1673 1704 1.792057 CGCGAAATCACAACCGTGC 60.792 57.895 0.00 0.00 43.28 5.34
1702 1733 0.179108 ATAGTCCGAAAGAGGCACGC 60.179 55.000 0.00 0.00 0.00 5.34
1712 1743 5.445845 GCGAAGAAAACAAAATAGTCCGAA 58.554 37.500 0.00 0.00 0.00 4.30
1713 1744 4.376615 CGCGAAGAAAACAAAATAGTCCGA 60.377 41.667 0.00 0.00 0.00 4.55
1714 1745 3.838550 CGCGAAGAAAACAAAATAGTCCG 59.161 43.478 0.00 0.00 0.00 4.79
1715 1746 5.025986 TCGCGAAGAAAACAAAATAGTCC 57.974 39.130 6.20 0.00 0.00 3.85
1716 1747 5.912528 TCTCGCGAAGAAAACAAAATAGTC 58.087 37.500 11.33 0.00 0.00 2.59
1725 1756 0.164002 GTGCCTCTCGCGAAGAAAAC 59.836 55.000 11.33 2.51 42.08 2.43
1826 2562 9.099454 GCCTCTCGAGAAAGAAAAATAAATAGA 57.901 33.333 17.36 0.00 0.00 1.98
1827 2563 8.883731 TGCCTCTCGAGAAAGAAAAATAAATAG 58.116 33.333 17.36 0.00 0.00 1.73
1828 2564 8.665685 GTGCCTCTCGAGAAAGAAAAATAAATA 58.334 33.333 17.36 0.00 0.00 1.40
1829 2565 7.530863 GTGCCTCTCGAGAAAGAAAAATAAAT 58.469 34.615 17.36 0.00 0.00 1.40
1830 2566 6.347402 CGTGCCTCTCGAGAAAGAAAAATAAA 60.347 38.462 17.36 0.00 0.00 1.40
1831 2567 5.120208 CGTGCCTCTCGAGAAAGAAAAATAA 59.880 40.000 17.36 0.00 0.00 1.40
1832 2568 4.625742 CGTGCCTCTCGAGAAAGAAAAATA 59.374 41.667 17.36 0.00 0.00 1.40
1833 2569 3.433615 CGTGCCTCTCGAGAAAGAAAAAT 59.566 43.478 17.36 0.00 0.00 1.82
1834 2570 2.800544 CGTGCCTCTCGAGAAAGAAAAA 59.199 45.455 17.36 0.00 0.00 1.94
1835 2571 2.404215 CGTGCCTCTCGAGAAAGAAAA 58.596 47.619 17.36 0.00 0.00 2.29
1836 2572 1.336887 CCGTGCCTCTCGAGAAAGAAA 60.337 52.381 17.36 0.71 0.00 2.52
1837 2573 0.243907 CCGTGCCTCTCGAGAAAGAA 59.756 55.000 17.36 2.38 0.00 2.52
1838 2574 1.595993 CCCGTGCCTCTCGAGAAAGA 61.596 60.000 17.36 0.00 0.00 2.52
1839 2575 1.153745 CCCGTGCCTCTCGAGAAAG 60.154 63.158 17.36 11.91 0.00 2.62
1840 2576 2.970639 CCCGTGCCTCTCGAGAAA 59.029 61.111 17.36 2.17 0.00 2.52
1841 2577 3.760035 GCCCGTGCCTCTCGAGAA 61.760 66.667 17.36 0.00 0.00 2.87
1853 2589 2.978010 CAAAAGAGGCACGCCCGT 60.978 61.111 3.95 0.00 39.21 5.28
1854 2590 3.737172 CCAAAAGAGGCACGCCCG 61.737 66.667 3.95 0.00 39.21 6.13
1855 2591 1.460273 TTTCCAAAAGAGGCACGCCC 61.460 55.000 3.95 0.00 36.58 6.13
1856 2592 0.039165 CTTTCCAAAAGAGGCACGCC 60.039 55.000 0.00 0.00 0.00 5.68
1857 2593 0.039165 CCTTTCCAAAAGAGGCACGC 60.039 55.000 1.06 0.00 0.00 5.34
1858 2594 0.598065 CCCTTTCCAAAAGAGGCACG 59.402 55.000 1.06 0.00 0.00 5.34
1859 2595 1.995376 TCCCTTTCCAAAAGAGGCAC 58.005 50.000 1.06 0.00 0.00 5.01
1860 2596 2.765689 TTCCCTTTCCAAAAGAGGCA 57.234 45.000 1.06 0.00 0.00 4.75
1861 2597 4.127171 GTTTTTCCCTTTCCAAAAGAGGC 58.873 43.478 1.06 0.00 0.00 4.70
1862 2598 4.368315 CGTTTTTCCCTTTCCAAAAGAGG 58.632 43.478 1.06 1.84 0.00 3.69
1863 2599 3.802139 GCGTTTTTCCCTTTCCAAAAGAG 59.198 43.478 1.06 0.00 0.00 2.85
1864 2600 3.735514 CGCGTTTTTCCCTTTCCAAAAGA 60.736 43.478 0.00 0.00 0.00 2.52
1865 2601 2.538037 CGCGTTTTTCCCTTTCCAAAAG 59.462 45.455 0.00 0.00 0.00 2.27
1866 2602 2.094130 ACGCGTTTTTCCCTTTCCAAAA 60.094 40.909 5.58 0.00 0.00 2.44
1867 2603 1.477295 ACGCGTTTTTCCCTTTCCAAA 59.523 42.857 5.58 0.00 0.00 3.28
1868 2604 1.104630 ACGCGTTTTTCCCTTTCCAA 58.895 45.000 5.58 0.00 0.00 3.53
1869 2605 1.104630 AACGCGTTTTTCCCTTTCCA 58.895 45.000 20.79 0.00 0.00 3.53
1870 2606 2.212869 AAACGCGTTTTTCCCTTTCC 57.787 45.000 30.36 0.00 0.00 3.13
1871 2607 3.829066 GAAAACGCGTTTTTCCCTTTC 57.171 42.857 40.53 26.85 45.19 2.62
1903 2639 3.414700 CACAACCGTGCCTCTCGC 61.415 66.667 0.00 0.00 36.06 5.03
1912 2648 0.806884 TCTCGCGAAAACACAACCGT 60.807 50.000 11.33 0.00 0.00 4.83
1913 2649 0.111266 CTCTCGCGAAAACACAACCG 60.111 55.000 11.33 0.00 0.00 4.44
1914 2650 0.234884 CCTCTCGCGAAAACACAACC 59.765 55.000 11.33 0.00 0.00 3.77
1915 2651 0.384353 GCCTCTCGCGAAAACACAAC 60.384 55.000 11.33 0.00 0.00 3.32
1916 2652 0.812014 TGCCTCTCGCGAAAACACAA 60.812 50.000 11.33 0.00 42.08 3.33
1917 2653 0.602638 ATGCCTCTCGCGAAAACACA 60.603 50.000 11.33 5.58 42.08 3.72
1918 2654 0.179215 CATGCCTCTCGCGAAAACAC 60.179 55.000 11.33 0.00 42.08 3.32
1919 2655 1.298157 CCATGCCTCTCGCGAAAACA 61.298 55.000 11.33 6.76 42.08 2.83
1920 2656 1.425428 CCATGCCTCTCGCGAAAAC 59.575 57.895 11.33 0.18 42.08 2.43
1921 2657 1.745115 CCCATGCCTCTCGCGAAAA 60.745 57.895 11.33 0.00 42.08 2.29
1922 2658 2.125147 CCCATGCCTCTCGCGAAA 60.125 61.111 11.33 0.00 42.08 3.46
1923 2659 4.838152 GCCCATGCCTCTCGCGAA 62.838 66.667 11.33 0.00 42.08 4.70
1933 2669 2.125952 GAAAAGGCACGCCCATGC 60.126 61.111 3.95 0.00 45.34 4.06
1934 2670 2.573340 GGAAAAGGCACGCCCATG 59.427 61.111 3.95 0.00 36.58 3.66
1935 2671 3.061848 CGGAAAAGGCACGCCCAT 61.062 61.111 3.95 0.00 36.58 4.00
1938 2674 2.472232 CTTTCCGGAAAAGGCACGCC 62.472 60.000 28.62 0.00 40.66 5.68
1939 2675 1.081442 CTTTCCGGAAAAGGCACGC 60.081 57.895 28.62 0.00 40.66 5.34
1997 2734 1.202710 TCTGGCAGAAGCAAAACCGTA 60.203 47.619 16.28 0.00 44.61 4.02
2076 2813 2.540157 GGAAACACGGGTTTTTCGTCTG 60.540 50.000 18.40 0.00 46.84 3.51
2078 2815 1.595246 CGGAAACACGGGTTTTTCGTC 60.595 52.381 18.40 3.71 46.84 4.20
2079 2816 0.377905 CGGAAACACGGGTTTTTCGT 59.622 50.000 18.40 0.00 46.84 3.85
2080 2817 3.151848 CGGAAACACGGGTTTTTCG 57.848 52.632 18.40 19.30 46.84 3.46
2150 2887 6.316140 TCCCATGTTGATAGATTTTGACGAAG 59.684 38.462 0.00 0.00 0.00 3.79
2161 2898 9.527157 TTCAAAACTAAATCCCATGTTGATAGA 57.473 29.630 0.00 0.00 0.00 1.98
2207 2944 0.239879 TCAAACCGCTTTCGCCATTC 59.760 50.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.