Multiple sequence alignment - TraesCS3B01G540500

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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 TraesCS3B01G540500 chr3B 100.000 2384 0 0 1 2384 779437742 779435359 0.000000e+00 4403.0
1 TraesCS3B01G540500 chr7B 91.928 1561 117 5 13 1568 471394509 471392953 0.000000e+00 2176.0
2 TraesCS3B01G540500 chr4B 89.798 990 82 13 970 1950 11739075 11738096 0.000000e+00 1251.0
3 TraesCS3B01G540500 chr4B 98.000 50 1 0 1954 2003 369521990 369522039 1.170000e-13 87.9
4 TraesCS3B01G540500 chr4D 89.980 988 69 20 3 968 447223216 447222237 0.000000e+00 1249.0
5 TraesCS3B01G540500 chr4D 89.617 992 75 14 970 1942 6576409 6575427 0.000000e+00 1236.0
6 TraesCS3B01G540500 chr4D 96.883 385 11 1 2001 2384 447221068 447220684 0.000000e+00 643.0
7 TraesCS3B01G540500 chr4D 98.000 50 1 0 1954 2003 298120197 298120148 1.170000e-13 87.9
8 TraesCS3B01G540500 chr4D 98.000 50 1 0 1954 2003 447221929 447221880 1.170000e-13 87.9
9 TraesCS3B01G540500 chr5D 88.574 989 80 20 3 968 398033248 398034226 0.000000e+00 1170.0
10 TraesCS3B01G540500 chr5D 92.808 723 36 8 3 712 557875934 557875215 0.000000e+00 1033.0
11 TraesCS3B01G540500 chr5D 91.123 721 48 8 3 712 16576968 16576253 0.000000e+00 963.0
12 TraesCS3B01G540500 chr5D 96.144 389 13 2 1998 2384 557864990 557864602 3.340000e-178 634.0
13 TraesCS3B01G540500 chr5D 95.887 389 13 3 1998 2384 16574776 16574389 5.590000e-176 627.0
14 TraesCS3B01G540500 chr5D 94.717 265 12 2 704 967 557875188 557874925 6.130000e-111 411.0
15 TraesCS3B01G540500 chr5D 92.481 266 18 2 704 968 16576226 16575962 1.730000e-101 379.0
16 TraesCS3B01G540500 chr5D 100.000 50 0 0 1954 2003 398034541 398034590 2.520000e-15 93.5
17 TraesCS3B01G540500 chr5D 100.000 50 0 0 1954 2003 557874611 557874562 2.520000e-15 93.5
18 TraesCS3B01G540500 chr3D 93.277 714 36 9 3 712 10526590 10525885 0.000000e+00 1042.0
19 TraesCS3B01G540500 chr3D 92.050 717 42 9 3 709 250972003 250972714 0.000000e+00 994.0
20 TraesCS3B01G540500 chr3D 97.409 386 8 2 2001 2384 250986555 250986940 0.000000e+00 656.0
21 TraesCS3B01G540500 chr3D 96.373 386 11 3 2001 2384 10524419 10524035 1.200000e-177 632.0
22 TraesCS3B01G540500 chr3D 93.962 265 15 1 704 968 10525858 10525595 1.330000e-107 399.0
23 TraesCS3B01G540500 chr3D 92.830 265 19 0 704 968 250972744 250973008 3.720000e-103 385.0
24 TraesCS3B01G540500 chr3D 100.000 50 0 0 1954 2003 10525280 10525231 2.520000e-15 93.5
25 TraesCS3B01G540500 chr3D 98.000 50 1 0 1954 2003 250985694 250985743 1.170000e-13 87.9
26 TraesCS3B01G540500 chr6A 91.922 718 43 6 3 709 211312689 211313402 0.000000e+00 990.0
27 TraesCS3B01G540500 chr7D 91.783 718 43 7 3 709 553871031 553871743 0.000000e+00 985.0
28 TraesCS3B01G540500 chr7D 96.364 385 13 1 2001 2384 553873212 553873596 1.200000e-177 632.0
29 TraesCS3B01G540500 chr7D 91.698 265 22 0 704 968 553871773 553872037 3.740000e-98 368.0
30 TraesCS3B01G540500 chr7D 97.917 48 1 0 1956 2003 553872354 553872401 1.520000e-12 84.2
31 TraesCS3B01G540500 chr7A 97.416 387 8 2 1998 2382 151593652 151593266 0.000000e+00 658.0
32 TraesCS3B01G540500 chr7A 88.454 485 30 16 232 712 151595590 151595128 1.600000e-156 562.0
33 TraesCS3B01G540500 chr7A 100.000 50 0 0 1954 2003 151594509 151594460 2.520000e-15 93.5
34 TraesCS3B01G540500 chr1B 96.401 389 9 2 2001 2384 19017978 19018366 9.290000e-179 636.0
35 TraesCS3B01G540500 chr1B 96.364 385 13 1 2001 2384 602340025 602340409 1.200000e-177 632.0
36 TraesCS3B01G540500 chr1B 92.075 265 21 0 704 968 602338579 602338843 8.050000e-100 374.0
37 TraesCS3B01G540500 chr1B 82.353 136 4 3 582 709 19016798 19016921 1.510000e-17 100.0
38 TraesCS3B01G540500 chr4A 90.164 427 34 3 974 1394 596825231 596825655 1.250000e-152 549.0
39 TraesCS3B01G540500 chr4A 87.288 354 27 9 1445 1798 596825736 596826071 2.870000e-104 388.0
40 TraesCS3B01G540500 chr4A 86.709 158 15 4 1548 1704 453006746 453006594 1.130000e-38 171.0
41 TraesCS3B01G540500 chr4A 83.333 102 7 1 1287 1388 453007036 453006945 4.220000e-13 86.1
42 TraesCS3B01G540500 chr2B 87.137 241 19 6 1037 1265 365921 365681 1.820000e-66 263.0
43 TraesCS3B01G540500 chr5A 87.273 165 16 3 1548 1712 514080733 514080574 1.460000e-42 183.0
44 TraesCS3B01G540500 chr5A 100.000 49 0 0 1337 1385 514080979 514080931 9.070000e-15 91.6
45 TraesCS3B01G540500 chr5B 87.582 153 14 3 1548 1700 699284016 699284163 3.150000e-39 172.0


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 TraesCS3B01G540500 chr3B 779435359 779437742 2383 True 4403.000000 4403 100.000000 1 2384 1 chr3B.!!$R1 2383
1 TraesCS3B01G540500 chr7B 471392953 471394509 1556 True 2176.000000 2176 91.928000 13 1568 1 chr7B.!!$R1 1555
2 TraesCS3B01G540500 chr4B 11738096 11739075 979 True 1251.000000 1251 89.798000 970 1950 1 chr4B.!!$R1 980
3 TraesCS3B01G540500 chr4D 6575427 6576409 982 True 1236.000000 1236 89.617000 970 1942 1 chr4D.!!$R1 972
4 TraesCS3B01G540500 chr4D 447220684 447223216 2532 True 659.966667 1249 94.954333 3 2384 3 chr4D.!!$R3 2381
5 TraesCS3B01G540500 chr5D 16574389 16576968 2579 True 656.333333 963 93.163667 3 2384 3 chr5D.!!$R2 2381
6 TraesCS3B01G540500 chr5D 398033248 398034590 1342 False 631.750000 1170 94.287000 3 2003 2 chr5D.!!$F1 2000
7 TraesCS3B01G540500 chr5D 557874562 557875934 1372 True 512.500000 1033 95.841667 3 2003 3 chr5D.!!$R3 2000
8 TraesCS3B01G540500 chr3D 250972003 250973008 1005 False 689.500000 994 92.440000 3 968 2 chr3D.!!$F1 965
9 TraesCS3B01G540500 chr3D 10524035 10526590 2555 True 541.625000 1042 95.903000 3 2384 4 chr3D.!!$R1 2381
10 TraesCS3B01G540500 chr3D 250985694 250986940 1246 False 371.950000 656 97.704500 1954 2384 2 chr3D.!!$F2 430
11 TraesCS3B01G540500 chr6A 211312689 211313402 713 False 990.000000 990 91.922000 3 709 1 chr6A.!!$F1 706
12 TraesCS3B01G540500 chr7D 553871031 553873596 2565 False 517.300000 985 94.440500 3 2384 4 chr7D.!!$F1 2381
13 TraesCS3B01G540500 chr7A 151593266 151595590 2324 True 437.833333 658 95.290000 232 2382 3 chr7A.!!$R1 2150
14 TraesCS3B01G540500 chr1B 602338579 602340409 1830 False 503.000000 632 94.219500 704 2384 2 chr1B.!!$F2 1680
15 TraesCS3B01G540500 chr1B 19016798 19018366 1568 False 368.000000 636 89.377000 582 2384 2 chr1B.!!$F1 1802
16 TraesCS3B01G540500 chr4A 596825231 596826071 840 False 468.500000 549 88.726000 974 1798 2 chr4A.!!$F1 824

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
993 1112 0.900647 CACTCCCGACTTCCCTGACT 60.901 60.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2139 2.128535 TGTTCACCAACCCAGACCTAA 58.871 47.619 0.0 0.0 0.0 2.69 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
119 120 8.978472 ACTATGAGGTAGCTGTAGTTCAAATTA 58.022 33.333 0.00 0.00 33.47 1.40
133 134 5.104485 AGTTCAAATTAGACCCGCTTCCTAT 60.104 40.000 0.00 0.00 0.00 2.57
166 167 5.458779 CGGAATTTTGTCTTTTTCACCAGAC 59.541 40.000 0.00 0.00 40.03 3.51
179 180 6.922247 TTTCACCAGACGTGTATAAAAACA 57.078 33.333 0.00 0.00 43.51 2.83
306 311 5.358298 AAAACTCAATTTAGGCACTCGAC 57.642 39.130 0.00 0.00 41.75 4.20
641 661 3.414700 CCCGAAGCGTGTGTGCTC 61.415 66.667 0.00 0.00 46.60 4.26
642 662 3.767230 CCGAAGCGTGTGTGCTCG 61.767 66.667 0.00 0.00 46.60 5.03
652 672 4.771356 TGTGCTCGCCGCGTACTC 62.771 66.667 13.39 7.65 43.27 2.59
653 673 4.771356 GTGCTCGCCGCGTACTCA 62.771 66.667 13.39 4.00 43.27 3.41
654 674 4.045771 TGCTCGCCGCGTACTCAA 62.046 61.111 13.39 0.00 43.27 3.02
655 675 3.542742 GCTCGCCGCGTACTCAAC 61.543 66.667 13.39 0.00 0.00 3.18
862 980 3.431415 CGTACCAGATCCATCCATCCTA 58.569 50.000 0.00 0.00 0.00 2.94
926 1045 2.031314 TAGGTTTGCGCAGGCGAA 59.969 55.556 18.96 3.34 44.10 4.70
981 1100 3.691342 TGGCGACTTCCACTCCCG 61.691 66.667 0.00 0.00 0.00 5.14
993 1112 0.900647 CACTCCCGACTTCCCTGACT 60.901 60.000 0.00 0.00 0.00 3.41
1004 1123 1.990060 CCCTGACTGGACCGATGGT 60.990 63.158 0.00 0.00 39.44 3.55
1272 1418 4.821589 GCCTTCTCCGTGGCCGAG 62.822 72.222 0.00 0.00 43.11 4.63
1285 1431 2.646719 CCGAGTTCGACGGGTTCA 59.353 61.111 5.09 0.00 45.65 3.18
1305 1451 2.680352 ATCGTGCTCAGGACCCGT 60.680 61.111 0.00 0.00 0.00 5.28
1401 1551 1.591504 GAGCGATCCCCTCTCCGATC 61.592 65.000 0.00 0.00 33.06 3.69
1404 1554 1.247419 CGATCCCCTCTCCGATCCTG 61.247 65.000 0.00 0.00 32.83 3.86
1429 1582 8.576442 TGTTTTCTCACCATCCTTTTAGATTTC 58.424 33.333 0.00 0.00 0.00 2.17
1431 1584 6.387192 TCTCACCATCCTTTTAGATTTCCA 57.613 37.500 0.00 0.00 0.00 3.53
1432 1585 6.180472 TCTCACCATCCTTTTAGATTTCCAC 58.820 40.000 0.00 0.00 0.00 4.02
1433 1586 6.012508 TCTCACCATCCTTTTAGATTTCCACT 60.013 38.462 0.00 0.00 0.00 4.00
1434 1587 6.180472 TCACCATCCTTTTAGATTTCCACTC 58.820 40.000 0.00 0.00 0.00 3.51
1435 1588 6.012508 TCACCATCCTTTTAGATTTCCACTCT 60.013 38.462 0.00 0.00 0.00 3.24
1436 1589 7.182026 TCACCATCCTTTTAGATTTCCACTCTA 59.818 37.037 0.00 0.00 0.00 2.43
1438 1591 8.049721 ACCATCCTTTTAGATTTCCACTCTAAG 58.950 37.037 0.00 0.00 36.75 2.18
1443 1630 6.374417 TTTAGATTTCCACTCTAAGTGCCT 57.626 37.500 1.49 0.00 44.63 4.75
1456 1643 2.584835 AGTGCCTTGGCATTTGAGTA 57.415 45.000 17.86 0.00 0.00 2.59
1520 1707 5.612351 AGTAGGAGAACTGGAAAACAAGTC 58.388 41.667 0.00 0.00 0.00 3.01
1523 1710 4.080299 AGGAGAACTGGAAAACAAGTCTGT 60.080 41.667 0.00 0.00 37.39 3.41
1524 1711 4.035675 GGAGAACTGGAAAACAAGTCTGTG 59.964 45.833 0.00 0.00 35.37 3.66
1608 1795 4.301628 CCTGAAACTTGTTTGCTTCATCC 58.698 43.478 3.27 0.00 0.00 3.51
1620 1807 2.040145 TGCTTCATCCCAATCTGTCACA 59.960 45.455 0.00 0.00 0.00 3.58
1657 1844 0.679321 TGCAGTGTGCTTGTGGTGAA 60.679 50.000 0.00 0.00 45.31 3.18
1661 1848 2.164219 CAGTGTGCTTGTGGTGAACTTT 59.836 45.455 0.00 0.00 0.00 2.66
1705 1892 4.152223 GCTGTTGGGTTTATGCATGTTTTC 59.848 41.667 10.16 0.00 0.00 2.29
1712 1899 5.279456 GGGTTTATGCATGTTTTCTGTCCTT 60.279 40.000 10.16 0.00 0.00 3.36
1713 1900 6.071616 GGGTTTATGCATGTTTTCTGTCCTTA 60.072 38.462 10.16 0.00 0.00 2.69
1714 1901 7.029563 GGTTTATGCATGTTTTCTGTCCTTAG 58.970 38.462 10.16 0.00 0.00 2.18
1717 1904 5.437289 TGCATGTTTTCTGTCCTTAGTTG 57.563 39.130 0.00 0.00 0.00 3.16
1735 1922 8.881262 CCTTAGTTGGGATAACTTATGATAGGT 58.119 37.037 0.00 0.00 0.00 3.08
1766 1953 8.243961 ACTAGTGATGTTAGCTTATCATGTCT 57.756 34.615 10.08 6.68 35.91 3.41
1776 1963 9.587772 GTTAGCTTATCATGTCTAAGTTCTTGA 57.412 33.333 14.82 0.00 0.00 3.02
1777 1964 9.809096 TTAGCTTATCATGTCTAAGTTCTTGAG 57.191 33.333 14.82 0.00 0.00 3.02
1788 1975 2.606378 AGTTCTTGAGACGGGGTTAGT 58.394 47.619 0.00 0.00 0.00 2.24
1789 1976 2.970640 AGTTCTTGAGACGGGGTTAGTT 59.029 45.455 0.00 0.00 0.00 2.24
1790 1977 3.006644 AGTTCTTGAGACGGGGTTAGTTC 59.993 47.826 0.00 0.00 0.00 3.01
1791 1978 2.600790 TCTTGAGACGGGGTTAGTTCA 58.399 47.619 0.00 0.00 0.00 3.18
1792 1979 2.561419 TCTTGAGACGGGGTTAGTTCAG 59.439 50.000 0.00 0.00 0.00 3.02
1793 1980 0.606604 TGAGACGGGGTTAGTTCAGC 59.393 55.000 0.00 0.00 0.00 4.26
1794 1981 0.896226 GAGACGGGGTTAGTTCAGCT 59.104 55.000 0.00 0.00 0.00 4.24
1795 1982 2.097825 GAGACGGGGTTAGTTCAGCTA 58.902 52.381 0.00 0.00 0.00 3.32
1796 1983 2.694109 GAGACGGGGTTAGTTCAGCTAT 59.306 50.000 0.00 0.00 0.00 2.97
1797 1984 2.431057 AGACGGGGTTAGTTCAGCTATG 59.569 50.000 0.00 0.00 0.00 2.23
1798 1985 1.134491 ACGGGGTTAGTTCAGCTATGC 60.134 52.381 0.00 0.00 0.00 3.14
1799 1986 1.134521 CGGGGTTAGTTCAGCTATGCA 60.135 52.381 0.00 0.00 0.00 3.96
1800 1987 2.485479 CGGGGTTAGTTCAGCTATGCAT 60.485 50.000 3.79 3.79 0.00 3.96
1801 1988 3.555966 GGGGTTAGTTCAGCTATGCATT 58.444 45.455 3.54 0.00 0.00 3.56
1802 1989 3.954258 GGGGTTAGTTCAGCTATGCATTT 59.046 43.478 3.54 0.00 0.00 2.32
1803 1990 4.036852 GGGGTTAGTTCAGCTATGCATTTC 59.963 45.833 3.54 0.00 0.00 2.17
1804 1991 4.640201 GGGTTAGTTCAGCTATGCATTTCA 59.360 41.667 3.54 0.00 0.00 2.69
1805 1992 5.300286 GGGTTAGTTCAGCTATGCATTTCAT 59.700 40.000 3.54 0.00 39.17 2.57
1806 1993 6.183360 GGGTTAGTTCAGCTATGCATTTCATT 60.183 38.462 3.54 0.00 36.63 2.57
1807 1994 7.260603 GGTTAGTTCAGCTATGCATTTCATTT 58.739 34.615 3.54 0.00 36.63 2.32
1808 1995 7.433425 GGTTAGTTCAGCTATGCATTTCATTTC 59.567 37.037 3.54 0.00 36.63 2.17
1809 1996 6.770746 AGTTCAGCTATGCATTTCATTTCT 57.229 33.333 3.54 0.00 36.63 2.52
1810 1997 6.561614 AGTTCAGCTATGCATTTCATTTCTG 58.438 36.000 3.54 2.70 36.63 3.02
1811 1998 4.928601 TCAGCTATGCATTTCATTTCTGC 58.071 39.130 3.54 0.00 35.32 4.26
1821 2008 8.582433 TGCATTTCATTTCTGCAACATATATG 57.418 30.769 11.29 11.29 42.53 1.78
1822 2009 8.198778 TGCATTTCATTTCTGCAACATATATGT 58.801 29.630 12.75 12.75 42.53 2.29
1823 2010 9.681692 GCATTTCATTTCTGCAACATATATGTA 57.318 29.630 18.56 2.84 40.80 2.29
1845 2032 7.847487 TGTACAAATTTTTCTGTAGACTGTCG 58.153 34.615 1.52 0.00 0.00 4.35
1846 2033 6.920569 ACAAATTTTTCTGTAGACTGTCGT 57.079 33.333 1.52 0.00 0.00 4.34
1847 2034 6.715464 ACAAATTTTTCTGTAGACTGTCGTG 58.285 36.000 1.52 0.00 0.00 4.35
1848 2035 4.992381 ATTTTTCTGTAGACTGTCGTGC 57.008 40.909 1.52 0.00 0.00 5.34
1849 2036 3.446310 TTTTCTGTAGACTGTCGTGCA 57.554 42.857 1.52 2.44 0.00 4.57
1861 2048 4.505301 CTGTCGTGCAGTATGTGTATTG 57.495 45.455 0.00 0.00 40.27 1.90
1862 2049 2.670905 TGTCGTGCAGTATGTGTATTGC 59.329 45.455 0.00 0.00 42.14 3.56
1873 2060 7.641760 CAGTATGTGTATTGCAATATGCTTGA 58.358 34.615 21.52 4.46 45.31 3.02
1874 2061 8.294577 CAGTATGTGTATTGCAATATGCTTGAT 58.705 33.333 21.52 10.67 45.31 2.57
1879 2066 8.848182 TGTGTATTGCAATATGCTTGATTATGA 58.152 29.630 21.52 0.00 45.31 2.15
1880 2067 9.121517 GTGTATTGCAATATGCTTGATTATGAC 57.878 33.333 21.52 7.26 45.31 3.06
1881 2068 8.298854 TGTATTGCAATATGCTTGATTATGACC 58.701 33.333 21.52 4.35 45.31 4.02
1888 2075 8.789762 CAATATGCTTGATTATGACCAGATTGA 58.210 33.333 0.00 0.00 35.23 2.57
1891 2078 6.358991 TGCTTGATTATGACCAGATTGATCA 58.641 36.000 0.00 0.00 0.00 2.92
1893 2080 6.485984 GCTTGATTATGACCAGATTGATCAGT 59.514 38.462 0.00 0.00 0.00 3.41
1899 2086 8.722480 TTATGACCAGATTGATCAGTTTGTAG 57.278 34.615 7.78 0.00 0.00 2.74
1901 2088 7.239763 TGACCAGATTGATCAGTTTGTAGTA 57.760 36.000 7.78 0.00 0.00 1.82
1902 2089 7.097192 TGACCAGATTGATCAGTTTGTAGTAC 58.903 38.462 7.78 0.00 0.00 2.73
1903 2090 6.100004 ACCAGATTGATCAGTTTGTAGTACG 58.900 40.000 7.78 0.00 0.00 3.67
1904 2091 6.071560 ACCAGATTGATCAGTTTGTAGTACGA 60.072 38.462 7.78 0.00 0.00 3.43
1905 2092 6.980978 CCAGATTGATCAGTTTGTAGTACGAT 59.019 38.462 7.78 0.00 0.00 3.73
1907 2094 8.959058 CAGATTGATCAGTTTGTAGTACGATAC 58.041 37.037 0.00 0.00 0.00 2.24
1908 2095 8.904834 AGATTGATCAGTTTGTAGTACGATACT 58.095 33.333 0.00 0.00 42.68 2.12
1910 2097 8.683550 TTGATCAGTTTGTAGTACGATACTTG 57.316 34.615 0.00 0.00 40.14 3.16
1912 2099 8.301720 TGATCAGTTTGTAGTACGATACTTGTT 58.698 33.333 0.00 0.00 40.14 2.83
1913 2100 9.136952 GATCAGTTTGTAGTACGATACTTGTTT 57.863 33.333 0.00 0.00 40.14 2.83
1914 2101 8.289440 TCAGTTTGTAGTACGATACTTGTTTG 57.711 34.615 0.00 0.00 40.14 2.93
1915 2102 7.007697 CAGTTTGTAGTACGATACTTGTTTGC 58.992 38.462 0.00 0.00 40.14 3.68
1917 2104 7.440255 AGTTTGTAGTACGATACTTGTTTGCTT 59.560 33.333 0.00 0.00 40.14 3.91
1918 2105 8.702438 GTTTGTAGTACGATACTTGTTTGCTTA 58.298 33.333 0.00 0.00 40.14 3.09
1919 2106 8.815141 TTGTAGTACGATACTTGTTTGCTTAA 57.185 30.769 0.00 0.00 40.14 1.85
1920 2107 8.991243 TGTAGTACGATACTTGTTTGCTTAAT 57.009 30.769 0.00 0.00 40.14 1.40
1924 2111 6.254281 ACGATACTTGTTTGCTTAATGCTT 57.746 33.333 0.00 0.00 43.37 3.91
1925 2112 6.677913 ACGATACTTGTTTGCTTAATGCTTT 58.322 32.000 0.00 0.00 43.37 3.51
1928 2115 7.114811 CGATACTTGTTTGCTTAATGCTTTTGT 59.885 33.333 0.00 0.00 43.37 2.83
1930 2117 7.376435 ACTTGTTTGCTTAATGCTTTTGTTT 57.624 28.000 0.00 0.00 43.37 2.83
1932 2119 7.334171 ACTTGTTTGCTTAATGCTTTTGTTTCT 59.666 29.630 0.00 0.00 43.37 2.52
1935 2122 7.548780 TGTTTGCTTAATGCTTTTGTTTCTCTT 59.451 29.630 0.00 0.00 43.37 2.85
1937 2124 7.698836 TGCTTAATGCTTTTGTTTCTCTTTC 57.301 32.000 0.00 0.00 43.37 2.62
1938 2125 7.491682 TGCTTAATGCTTTTGTTTCTCTTTCT 58.508 30.769 0.00 0.00 43.37 2.52
1940 2127 9.122613 GCTTAATGCTTTTGTTTCTCTTTCTAG 57.877 33.333 0.00 0.00 38.95 2.43
1946 2133 7.285401 TGCTTTTGTTTCTCTTTCTAGTTGGAT 59.715 33.333 0.00 0.00 0.00 3.41
1947 2134 8.138074 GCTTTTGTTTCTCTTTCTAGTTGGATT 58.862 33.333 0.00 0.00 0.00 3.01
2031 3346 4.763073 TGATCTCTTCGCATCAATTCTGT 58.237 39.130 0.00 0.00 0.00 3.41
2125 3516 2.203337 GCGGCTTATGGGATGCCA 60.203 61.111 9.00 9.00 46.60 4.92
2155 3546 0.318762 GATATCTCCTGGGTCGTGGC 59.681 60.000 0.00 0.00 0.00 5.01
2216 3611 2.309528 TCTGTGCGACAACTTTGAGT 57.690 45.000 0.00 0.00 0.00 3.41
2238 3633 9.607988 TGAGTATTGGATTATAACGTGAATTGT 57.392 29.630 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.254508 AGTATCTATTAAATCGGAGAAGCATCC 58.745 37.037 0.00 0.00 43.58 3.51
119 120 2.987232 GTTTCAATAGGAAGCGGGTCT 58.013 47.619 0.00 0.00 36.72 3.85
133 134 4.886247 AGACAAAATTCCGTCGTTTCAA 57.114 36.364 0.00 0.00 37.23 2.69
179 180 8.744568 ATTGACAAAATGGTTGGTTGTAAAAT 57.255 26.923 0.00 0.00 35.67 1.82
567 578 4.144727 GAGAGCGAGGGGAGGGGA 62.145 72.222 0.00 0.00 0.00 4.81
638 658 3.542742 GTTGAGTACGCGGCGAGC 61.543 66.667 30.94 19.73 43.95 5.03
639 659 3.238241 CGTTGAGTACGCGGCGAG 61.238 66.667 30.94 11.17 44.26 5.03
647 667 3.065095 AGCGTTATCCTCTCGTTGAGTAC 59.935 47.826 7.25 0.00 41.11 2.73
648 668 3.276857 AGCGTTATCCTCTCGTTGAGTA 58.723 45.455 7.25 0.00 41.11 2.59
649 669 2.093106 AGCGTTATCCTCTCGTTGAGT 58.907 47.619 7.25 0.00 41.11 3.41
650 670 2.541999 GGAGCGTTATCCTCTCGTTGAG 60.542 54.545 2.13 2.13 42.30 3.02
651 671 1.404391 GGAGCGTTATCCTCTCGTTGA 59.596 52.381 0.00 0.00 36.35 3.18
652 672 1.536284 GGGAGCGTTATCCTCTCGTTG 60.536 57.143 3.92 0.00 39.50 4.10
653 673 0.745468 GGGAGCGTTATCCTCTCGTT 59.255 55.000 3.92 0.00 39.50 3.85
654 674 1.108132 GGGGAGCGTTATCCTCTCGT 61.108 60.000 3.92 0.00 36.84 4.18
655 675 1.107538 TGGGGAGCGTTATCCTCTCG 61.108 60.000 5.18 0.00 40.86 4.04
656 676 0.389757 GTGGGGAGCGTTATCCTCTC 59.610 60.000 5.18 0.00 40.86 3.20
657 677 1.049289 GGTGGGGAGCGTTATCCTCT 61.049 60.000 5.18 0.00 40.86 3.69
658 678 1.049289 AGGTGGGGAGCGTTATCCTC 61.049 60.000 3.92 0.68 40.62 3.71
659 679 1.003051 AGGTGGGGAGCGTTATCCT 59.997 57.895 3.92 0.00 39.50 3.24
660 680 1.049289 AGAGGTGGGGAGCGTTATCC 61.049 60.000 0.00 0.00 38.76 2.59
661 681 0.831307 AAGAGGTGGGGAGCGTTATC 59.169 55.000 0.00 0.00 0.00 1.75
662 682 0.831307 GAAGAGGTGGGGAGCGTTAT 59.169 55.000 0.00 0.00 0.00 1.89
663 683 0.252103 AGAAGAGGTGGGGAGCGTTA 60.252 55.000 0.00 0.00 0.00 3.18
664 684 1.536662 AGAAGAGGTGGGGAGCGTT 60.537 57.895 0.00 0.00 0.00 4.84
665 685 1.985116 GAGAAGAGGTGGGGAGCGT 60.985 63.158 0.00 0.00 0.00 5.07
666 686 2.726351 GGAGAAGAGGTGGGGAGCG 61.726 68.421 0.00 0.00 0.00 5.03
697 746 4.436998 GCGGGGAGTGACGACTGG 62.437 72.222 0.00 0.00 30.16 4.00
839 957 1.276421 GATGGATGGATCTGGTACGGG 59.724 57.143 0.00 0.00 33.92 5.28
862 980 3.394719 GAACGGAAAGCAGAGAGAAAGT 58.605 45.455 0.00 0.00 0.00 2.66
981 1100 0.898789 TCGGTCCAGTCAGGGAAGTC 60.899 60.000 0.00 0.00 39.05 3.01
993 1112 1.671166 CAGTGTCACCATCGGTCCA 59.329 57.895 0.00 0.00 31.02 4.02
1004 1123 1.134250 TGTGGTTTAGCTGCAGTGTCA 60.134 47.619 16.64 3.14 0.00 3.58
1008 1127 1.442769 CGATGTGGTTTAGCTGCAGT 58.557 50.000 16.64 4.79 0.00 4.40
1062 1185 0.895530 CCAGCACCTCCTCGTAGAAA 59.104 55.000 0.00 0.00 34.09 2.52
1105 1228 1.686110 CCTGGAAGCCGGAGTAGGT 60.686 63.158 5.05 0.00 29.82 3.08
1272 1418 0.921347 CGATGATGAACCCGTCGAAC 59.079 55.000 0.00 0.00 43.50 3.95
1285 1431 1.826024 GGGTCCTGAGCACGATGAT 59.174 57.895 0.00 0.00 0.00 2.45
1305 1451 1.112916 TCTCGAACAGCTGGGTGTCA 61.113 55.000 19.93 0.00 0.00 3.58
1389 1539 0.912486 AAAACAGGATCGGAGAGGGG 59.088 55.000 0.00 0.00 43.63 4.79
1401 1551 6.003950 TCTAAAAGGATGGTGAGAAAACAGG 58.996 40.000 0.00 0.00 0.00 4.00
1404 1554 8.029522 GGAAATCTAAAAGGATGGTGAGAAAAC 58.970 37.037 0.00 0.00 0.00 2.43
1443 1630 6.372937 TCGACACAATATTACTCAAATGCCAA 59.627 34.615 0.00 0.00 0.00 4.52
1456 1643 8.601243 GAATTTCGTCAATTCGACACAATATT 57.399 30.769 6.95 0.00 45.70 1.28
1520 1707 4.326826 TCAAGCCACTCCTAAAATCACAG 58.673 43.478 0.00 0.00 0.00 3.66
1523 1710 5.185635 CCATTTCAAGCCACTCCTAAAATCA 59.814 40.000 0.00 0.00 0.00 2.57
1524 1711 5.394553 CCCATTTCAAGCCACTCCTAAAATC 60.395 44.000 0.00 0.00 0.00 2.17
1608 1795 5.106038 ACAAATAGCACATGTGACAGATTGG 60.106 40.000 29.80 18.84 0.00 3.16
1620 1807 4.801891 CTGCAAGTTCACAAATAGCACAT 58.198 39.130 0.00 0.00 0.00 3.21
1705 1892 7.792032 TCATAAGTTATCCCAACTAAGGACAG 58.208 38.462 0.00 0.00 35.85 3.51
1766 1953 4.154942 ACTAACCCCGTCTCAAGAACTTA 58.845 43.478 0.00 0.00 0.00 2.24
1776 1963 2.226962 TAGCTGAACTAACCCCGTCT 57.773 50.000 0.00 0.00 0.00 4.18
1777 1964 2.822764 CATAGCTGAACTAACCCCGTC 58.177 52.381 0.00 0.00 33.57 4.79
1788 1975 5.105675 TGCAGAAATGAAATGCATAGCTGAA 60.106 36.000 0.00 0.00 44.56 3.02
1789 1976 4.399934 TGCAGAAATGAAATGCATAGCTGA 59.600 37.500 0.00 0.00 44.56 4.26
1790 1977 4.678622 TGCAGAAATGAAATGCATAGCTG 58.321 39.130 0.00 1.65 44.56 4.24
1791 1978 4.994907 TGCAGAAATGAAATGCATAGCT 57.005 36.364 0.00 0.00 44.56 3.32
1797 1984 8.583810 ACATATATGTTGCAGAAATGAAATGC 57.416 30.769 12.75 0.00 37.90 3.56
1819 2006 8.495949 CGACAGTCTACAGAAAAATTTGTACAT 58.504 33.333 0.00 0.00 0.00 2.29
1820 2007 7.493320 ACGACAGTCTACAGAAAAATTTGTACA 59.507 33.333 0.00 0.00 0.00 2.90
1821 2008 7.792508 CACGACAGTCTACAGAAAAATTTGTAC 59.207 37.037 0.00 0.00 0.00 2.90
1822 2009 7.517734 GCACGACAGTCTACAGAAAAATTTGTA 60.518 37.037 0.00 0.00 0.00 2.41
1823 2010 6.715464 CACGACAGTCTACAGAAAAATTTGT 58.285 36.000 0.00 0.00 0.00 2.83
1824 2011 5.621228 GCACGACAGTCTACAGAAAAATTTG 59.379 40.000 0.00 0.00 0.00 2.32
1825 2012 5.295787 TGCACGACAGTCTACAGAAAAATTT 59.704 36.000 0.00 0.00 0.00 1.82
1826 2013 4.814234 TGCACGACAGTCTACAGAAAAATT 59.186 37.500 0.00 0.00 0.00 1.82
1827 2014 4.377021 TGCACGACAGTCTACAGAAAAAT 58.623 39.130 0.00 0.00 0.00 1.82
1828 2015 3.787785 TGCACGACAGTCTACAGAAAAA 58.212 40.909 0.00 0.00 0.00 1.94
1829 2016 3.381045 CTGCACGACAGTCTACAGAAAA 58.619 45.455 8.07 0.00 41.86 2.29
1830 2017 3.013276 CTGCACGACAGTCTACAGAAA 57.987 47.619 8.07 0.00 41.86 2.52
1831 2018 2.706555 CTGCACGACAGTCTACAGAA 57.293 50.000 8.07 0.00 41.86 3.02
1841 2028 2.670905 GCAATACACATACTGCACGACA 59.329 45.455 0.00 0.00 34.87 4.35
1842 2029 2.670905 TGCAATACACATACTGCACGAC 59.329 45.455 0.00 0.00 39.77 4.34
1843 2030 2.966050 TGCAATACACATACTGCACGA 58.034 42.857 0.00 0.00 39.77 4.35
1844 2031 3.738286 TTGCAATACACATACTGCACG 57.262 42.857 0.00 0.00 44.08 5.34
1845 2032 5.626543 GCATATTGCAATACACATACTGCAC 59.373 40.000 23.99 5.46 44.08 4.57
1846 2033 5.761003 GCATATTGCAATACACATACTGCA 58.239 37.500 23.99 3.93 44.26 4.41
1861 2048 6.564709 TCTGGTCATAATCAAGCATATTGC 57.435 37.500 0.00 0.00 45.46 3.56
1862 2049 8.789762 TCAATCTGGTCATAATCAAGCATATTG 58.210 33.333 0.00 0.00 38.11 1.90
1863 2050 8.929260 TCAATCTGGTCATAATCAAGCATATT 57.071 30.769 0.00 0.00 0.00 1.28
1873 2060 9.334947 CTACAAACTGATCAATCTGGTCATAAT 57.665 33.333 0.00 0.00 36.82 1.28
1874 2061 8.321353 ACTACAAACTGATCAATCTGGTCATAA 58.679 33.333 0.00 0.00 36.82 1.90
1877 2064 6.114187 ACTACAAACTGATCAATCTGGTCA 57.886 37.500 0.00 0.00 34.65 4.02
1879 2066 6.071560 TCGTACTACAAACTGATCAATCTGGT 60.072 38.462 0.00 0.00 0.00 4.00
1880 2067 6.330278 TCGTACTACAAACTGATCAATCTGG 58.670 40.000 0.00 0.00 0.00 3.86
1881 2068 7.993821 ATCGTACTACAAACTGATCAATCTG 57.006 36.000 0.00 0.00 0.00 2.90
1888 2075 8.922676 CAAACAAGTATCGTACTACAAACTGAT 58.077 33.333 0.00 0.00 38.26 2.90
1891 2078 6.927381 AGCAAACAAGTATCGTACTACAAACT 59.073 34.615 0.00 0.00 38.26 2.66
1893 2080 7.718272 AAGCAAACAAGTATCGTACTACAAA 57.282 32.000 0.00 0.00 38.26 2.83
1914 2101 7.936950 AGAAAGAGAAACAAAAGCATTAAGC 57.063 32.000 0.00 0.00 46.19 3.09
1917 2104 9.950680 CAACTAGAAAGAGAAACAAAAGCATTA 57.049 29.630 0.00 0.00 0.00 1.90
1918 2105 7.922811 CCAACTAGAAAGAGAAACAAAAGCATT 59.077 33.333 0.00 0.00 0.00 3.56
1919 2106 7.285401 TCCAACTAGAAAGAGAAACAAAAGCAT 59.715 33.333 0.00 0.00 0.00 3.79
1920 2107 6.601613 TCCAACTAGAAAGAGAAACAAAAGCA 59.398 34.615 0.00 0.00 0.00 3.91
1937 2124 8.881262 ACCCAGACCTAATAATAATCCAACTAG 58.119 37.037 0.00 0.00 0.00 2.57
1938 2125 8.808240 ACCCAGACCTAATAATAATCCAACTA 57.192 34.615 0.00 0.00 0.00 2.24
1940 2127 7.230712 CCAACCCAGACCTAATAATAATCCAAC 59.769 40.741 0.00 0.00 0.00 3.77
1942 2129 6.391649 ACCAACCCAGACCTAATAATAATCCA 59.608 38.462 0.00 0.00 0.00 3.41
1946 2133 6.894735 TCACCAACCCAGACCTAATAATAA 57.105 37.500 0.00 0.00 0.00 1.40
1947 2134 6.215841 TGTTCACCAACCCAGACCTAATAATA 59.784 38.462 0.00 0.00 0.00 0.98
1950 2137 3.911260 TGTTCACCAACCCAGACCTAATA 59.089 43.478 0.00 0.00 0.00 0.98
1951 2138 2.714250 TGTTCACCAACCCAGACCTAAT 59.286 45.455 0.00 0.00 0.00 1.73
1952 2139 2.128535 TGTTCACCAACCCAGACCTAA 58.871 47.619 0.00 0.00 0.00 2.69
2031 3346 4.037222 TCTAGGATTACTGGGATGTGCAA 58.963 43.478 0.00 0.00 0.00 4.08
2238 3633 4.783764 TGAGCGACAGAGTATCAGAAAA 57.216 40.909 0.00 0.00 37.82 2.29


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

AutoCloner maintained by Alex Coulton.