Multiple sequence alignment - TraesCS5B01G196500

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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 TraesCS5B01G196500 chr5B 100.000 2303 0 0 1 2303 354236552 354238854 0.000000e+00 4253
1 TraesCS5B01G196500 chr5B 98.197 610 11 0 717 1326 521395747 521396356 0.000000e+00 1066
2 TraesCS5B01G196500 chr5B 92.017 714 53 3 1 711 243413771 243414483 0.000000e+00 1000
3 TraesCS5B01G196500 chr1B 93.007 715 41 5 1 712 338012548 338013256 0.000000e+00 1035
4 TraesCS5B01G196500 chr1B 96.916 616 19 0 712 1327 684735284 684735899 0.000000e+00 1033
5 TraesCS5B01G196500 chr1B 92.391 184 14 0 1329 1512 338013239 338013422 1.750000e-66 263
6 TraesCS5B01G196500 chr7D 92.737 716 43 9 1 712 631607306 631606596 0.000000e+00 1026
7 TraesCS5B01G196500 chr7D 92.896 183 12 1 1329 1510 27811125 27810943 4.880000e-67 265
8 TraesCS5B01G196500 chr3D 92.598 716 49 4 1 712 482861124 482860409 0.000000e+00 1026
9 TraesCS5B01G196500 chr3D 96.272 617 22 1 712 1327 569381230 569381846 0.000000e+00 1011
10 TraesCS5B01G196500 chr3D 95.800 619 25 1 712 1330 264600233 264600850 0.000000e+00 998
11 TraesCS5B01G196500 chr3D 92.350 183 14 0 1329 1511 482860426 482860244 6.310000e-66 261
12 TraesCS5B01G196500 chr7B 92.697 712 49 2 1 709 740229373 740230084 0.000000e+00 1024
13 TraesCS5B01G196500 chr7B 92.556 712 49 4 1 709 639785376 639786086 0.000000e+00 1018
14 TraesCS5B01G196500 chr6B 92.697 712 49 2 1 709 149166060 149166771 0.000000e+00 1024
15 TraesCS5B01G196500 chr6B 92.308 182 14 0 1329 1510 319558859 319558678 2.270000e-65 259
16 TraesCS5B01G196500 chr2D 96.602 618 20 1 712 1329 126957878 126958494 0.000000e+00 1024
17 TraesCS5B01G196500 chr2D 92.707 713 47 5 1 709 452373054 452373765 0.000000e+00 1024
18 TraesCS5B01G196500 chr2D 92.286 713 50 4 1 709 446309350 446308639 0.000000e+00 1007
19 TraesCS5B01G196500 chr2D 92.350 183 13 1 1329 1510 508095072 508094890 2.270000e-65 259
20 TraesCS5B01G196500 chr6D 96.272 617 20 2 712 1328 60314237 60314850 0.000000e+00 1009
21 TraesCS5B01G196500 chr6D 96.104 616 23 1 712 1327 132392654 132393268 0.000000e+00 1003
22 TraesCS5B01G196500 chr6D 92.593 189 12 2 1329 1515 18424661 18424473 1.050000e-68 270
23 TraesCS5B01G196500 chr4D 95.820 622 26 0 715 1336 337468229 337467608 0.000000e+00 1005
24 TraesCS5B01G196500 chr4D 96.248 613 22 1 715 1327 28465009 28464398 0.000000e+00 1003
25 TraesCS5B01G196500 chr4D 91.979 187 13 2 1329 1513 503814425 503814239 6.310000e-66 261
26 TraesCS5B01G196500 chr5A 83.678 435 52 8 1867 2300 389073851 389073435 2.140000e-105 392
27 TraesCS5B01G196500 chr5A 85.994 357 44 5 1512 1868 389074430 389074080 6.010000e-101 377
28 TraesCS5B01G196500 chr5D 86.034 358 44 5 1512 1868 308992605 308992957 1.670000e-101 379
29 TraesCS5B01G196500 chr5D 91.892 185 14 1 1329 1512 345030384 345030568 8.160000e-65 257
30 TraesCS5B01G196500 chr1D 92.063 189 14 1 1329 1516 395968691 395968879 4.880000e-67 265


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 TraesCS5B01G196500 chr5B 354236552 354238854 2302 False 4253.0 4253 100.000 1 2303 1 chr5B.!!$F2 2302
1 TraesCS5B01G196500 chr5B 521395747 521396356 609 False 1066.0 1066 98.197 717 1326 1 chr5B.!!$F3 609
2 TraesCS5B01G196500 chr5B 243413771 243414483 712 False 1000.0 1000 92.017 1 711 1 chr5B.!!$F1 710
3 TraesCS5B01G196500 chr1B 684735284 684735899 615 False 1033.0 1033 96.916 712 1327 1 chr1B.!!$F1 615
4 TraesCS5B01G196500 chr1B 338012548 338013422 874 False 649.0 1035 92.699 1 1512 2 chr1B.!!$F2 1511
5 TraesCS5B01G196500 chr7D 631606596 631607306 710 True 1026.0 1026 92.737 1 712 1 chr7D.!!$R2 711
6 TraesCS5B01G196500 chr3D 569381230 569381846 616 False 1011.0 1011 96.272 712 1327 1 chr3D.!!$F2 615
7 TraesCS5B01G196500 chr3D 264600233 264600850 617 False 998.0 998 95.800 712 1330 1 chr3D.!!$F1 618
8 TraesCS5B01G196500 chr3D 482860244 482861124 880 True 643.5 1026 92.474 1 1511 2 chr3D.!!$R1 1510
9 TraesCS5B01G196500 chr7B 740229373 740230084 711 False 1024.0 1024 92.697 1 709 1 chr7B.!!$F2 708
10 TraesCS5B01G196500 chr7B 639785376 639786086 710 False 1018.0 1018 92.556 1 709 1 chr7B.!!$F1 708
11 TraesCS5B01G196500 chr6B 149166060 149166771 711 False 1024.0 1024 92.697 1 709 1 chr6B.!!$F1 708
12 TraesCS5B01G196500 chr2D 126957878 126958494 616 False 1024.0 1024 96.602 712 1329 1 chr2D.!!$F1 617
13 TraesCS5B01G196500 chr2D 452373054 452373765 711 False 1024.0 1024 92.707 1 709 1 chr2D.!!$F2 708
14 TraesCS5B01G196500 chr2D 446308639 446309350 711 True 1007.0 1007 92.286 1 709 1 chr2D.!!$R1 708
15 TraesCS5B01G196500 chr6D 60314237 60314850 613 False 1009.0 1009 96.272 712 1328 1 chr6D.!!$F1 616
16 TraesCS5B01G196500 chr6D 132392654 132393268 614 False 1003.0 1003 96.104 712 1327 1 chr6D.!!$F2 615
17 TraesCS5B01G196500 chr4D 337467608 337468229 621 True 1005.0 1005 95.820 715 1336 1 chr4D.!!$R2 621
18 TraesCS5B01G196500 chr4D 28464398 28465009 611 True 1003.0 1003 96.248 715 1327 1 chr4D.!!$R1 612
19 TraesCS5B01G196500 chr5A 389073435 389074430 995 True 384.5 392 84.836 1512 2300 2 chr5A.!!$R1 788

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
329 333 0.391661 TTCTTGGAGATGCACTCGGC 60.392 55.0 0.0 0.0 45.76 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2284 0.104855 TACAATGCTAGAGCCTGCGG 59.895 55.0 0.0 0.0 41.18 5.69 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
43 44 2.048503 GCTGTTGCGGTAGGTCGT 60.049 61.111 0.00 0.00 0.00 4.34
220 222 2.766263 AGGCATCATCGAGGTGAAACTA 59.234 45.455 0.00 0.00 36.74 2.24
329 333 0.391661 TTCTTGGAGATGCACTCGGC 60.392 55.000 0.00 0.00 45.76 5.54
332 336 1.841302 TTGGAGATGCACTCGGCCTT 61.841 55.000 0.00 0.00 45.76 4.35
446 451 1.717937 GTCAGATGTGTGGCGATGC 59.282 57.895 0.00 0.00 0.00 3.91
469 474 2.504244 CGCAGGAGGTCGACGTTC 60.504 66.667 12.67 10.58 0.00 3.95
504 509 2.888863 GTCGGCAGCAGCTAGACT 59.111 61.111 17.69 0.00 41.54 3.24
521 526 0.698238 ACTGGGCAAGGTAGATGCAA 59.302 50.000 0.00 0.00 45.60 4.08
612 618 2.665185 GAGCACGCCGGACTGTTT 60.665 61.111 5.05 0.00 0.00 2.83
616 622 1.301087 CACGCCGGACTGTTTGGTA 60.301 57.895 5.05 0.00 0.00 3.25
712 719 5.163237 GGTATTAGGCCCAGACTATCAACAA 60.163 44.000 0.00 0.00 0.00 2.83
713 720 4.919774 TTAGGCCCAGACTATCAACAAA 57.080 40.909 0.00 0.00 0.00 2.83
968 976 1.614996 TGTGCGGATGTTTTGATGGT 58.385 45.000 0.00 0.00 0.00 3.55
1089 1097 2.553028 GCAGGAAGGAGGACAATCAACA 60.553 50.000 0.00 0.00 0.00 3.33
1159 1167 6.811665 TGATTTTGTCACGACTAGATTCGAAT 59.188 34.615 11.20 11.20 41.78 3.34
1366 1374 9.896645 TCAATATCCCTTCATCAATTAGATAGC 57.103 33.333 0.00 0.00 34.43 2.97
1392 1400 2.479837 CGACAGTTTGTTGCCTAGACA 58.520 47.619 0.00 0.00 0.00 3.41
1407 1415 2.540265 AGACAGTGGCTTCAGTCTTG 57.460 50.000 0.00 0.00 38.08 3.02
1487 1495 4.804420 AGATGCAGAGGCCGGGGA 62.804 66.667 2.18 0.00 40.13 4.81
1495 1503 4.109656 AGGCCGGGGATCCTCCTT 62.110 66.667 12.58 0.00 36.57 3.36
1551 1559 6.985188 TGAAATACATTCAGTTCTACCTGC 57.015 37.500 0.00 0.00 43.08 4.85
1552 1560 6.472016 TGAAATACATTCAGTTCTACCTGCA 58.528 36.000 0.00 0.00 43.08 4.41
1553 1561 7.112122 TGAAATACATTCAGTTCTACCTGCAT 58.888 34.615 0.00 0.00 43.08 3.96
1554 1562 7.611467 TGAAATACATTCAGTTCTACCTGCATT 59.389 33.333 0.00 0.00 43.08 3.56
1555 1563 7.559590 AATACATTCAGTTCTACCTGCATTC 57.440 36.000 0.00 0.00 32.32 2.67
1556 1564 4.910195 ACATTCAGTTCTACCTGCATTCA 58.090 39.130 0.00 0.00 32.32 2.57
1557 1565 5.316167 ACATTCAGTTCTACCTGCATTCAA 58.684 37.500 0.00 0.00 32.32 2.69
1558 1566 5.769662 ACATTCAGTTCTACCTGCATTCAAA 59.230 36.000 0.00 0.00 32.32 2.69
1567 1575 3.592059 ACCTGCATTCAAATTGACATGC 58.408 40.909 23.41 23.41 39.28 4.06
1597 1605 7.735917 TCTGGTGTATTAGCTATTGCAGTAAT 58.264 34.615 6.66 0.92 42.74 1.89
1639 1647 8.015185 TCTAATACCCTAGTGTTGGACATAAC 57.985 38.462 0.00 0.00 31.22 1.89
1658 1666 1.333619 ACATTGCACACGGTTCTTGAC 59.666 47.619 0.00 0.00 0.00 3.18
1685 1693 2.987821 GTCGTCAGCCTTGAACTCTAAC 59.012 50.000 0.00 0.00 34.49 2.34
1686 1694 2.626266 TCGTCAGCCTTGAACTCTAACA 59.374 45.455 0.00 0.00 34.49 2.41
1687 1695 3.258372 TCGTCAGCCTTGAACTCTAACAT 59.742 43.478 0.00 0.00 34.49 2.71
1696 1704 2.672874 TGAACTCTAACATCGCACATGC 59.327 45.455 0.00 0.00 37.78 4.06
1707 1715 3.610786 TCGCACATGCTTCGTTTAAAA 57.389 38.095 1.82 0.00 39.32 1.52
1708 1716 3.293262 TCGCACATGCTTCGTTTAAAAC 58.707 40.909 1.82 0.00 39.32 2.43
1709 1717 3.039405 CGCACATGCTTCGTTTAAAACA 58.961 40.909 1.82 0.00 39.32 2.83
1710 1718 3.117832 CGCACATGCTTCGTTTAAAACAG 59.882 43.478 1.82 0.00 39.32 3.16
1711 1719 3.121362 GCACATGCTTCGTTTAAAACAGC 60.121 43.478 0.00 7.33 38.21 4.40
1713 1721 4.379793 CACATGCTTCGTTTAAAACAGCTC 59.620 41.667 13.06 0.00 33.12 4.09
1714 1722 3.247563 TGCTTCGTTTAAAACAGCTCG 57.752 42.857 13.06 2.67 33.12 5.03
1715 1723 2.867368 TGCTTCGTTTAAAACAGCTCGA 59.133 40.909 13.06 4.68 33.12 4.04
1716 1724 3.216031 GCTTCGTTTAAAACAGCTCGAC 58.784 45.455 7.10 0.00 30.28 4.20
1718 1726 2.730069 TCGTTTAAAACAGCTCGACGA 58.270 42.857 0.00 0.00 35.93 4.20
1719 1727 3.311106 TCGTTTAAAACAGCTCGACGAT 58.689 40.909 0.00 0.00 33.73 3.73
1725 1733 2.126914 AACAGCTCGACGATGATAGC 57.873 50.000 5.50 1.84 32.18 2.97
1729 1737 1.132588 GCTCGACGATGATAGCCAAC 58.867 55.000 0.00 0.00 0.00 3.77
1737 1745 3.802722 GATGATAGCCAACTTCATCGC 57.197 47.619 0.00 0.00 37.21 4.58
1744 1752 1.466360 GCCAACTTCATCGCACACATC 60.466 52.381 0.00 0.00 0.00 3.06
1745 1753 1.131126 CCAACTTCATCGCACACATCC 59.869 52.381 0.00 0.00 0.00 3.51
1759 1767 5.220586 CGCACACATCCGTACAAAGATAATT 60.221 40.000 0.00 0.00 0.00 1.40
1760 1768 5.965334 GCACACATCCGTACAAAGATAATTG 59.035 40.000 0.00 0.00 36.37 2.32
1772 1780 6.003950 ACAAAGATAATTGTGTGCTAGTGGT 58.996 36.000 0.00 0.00 41.78 4.16
1773 1781 6.490040 ACAAAGATAATTGTGTGCTAGTGGTT 59.510 34.615 0.00 0.00 41.78 3.67
1795 1803 7.068839 TGGTTTCCACATTACACACAATTAGTT 59.931 33.333 0.00 0.00 0.00 2.24
1796 1804 7.923878 GGTTTCCACATTACACACAATTAGTTT 59.076 33.333 0.00 0.00 0.00 2.66
1821 1829 9.493206 TTTGAAAAACTGTATTCGAACTACAAC 57.507 29.630 0.00 0.00 0.00 3.32
1830 1838 4.959631 TTCGAACTACAACAACATCGTC 57.040 40.909 0.00 0.00 0.00 4.20
1831 1839 3.967401 TCGAACTACAACAACATCGTCA 58.033 40.909 0.00 0.00 0.00 4.35
1833 1841 4.804665 TCGAACTACAACAACATCGTCAAA 59.195 37.500 0.00 0.00 0.00 2.69
1843 1851 9.128107 ACAACAACATCGTCAAAAATTGATATC 57.872 29.630 0.00 0.00 42.47 1.63
1869 2107 4.465632 AATTGTCTGCAATGCATCATGT 57.534 36.364 8.91 1.42 43.89 3.21
1873 2111 2.947652 GTCTGCAATGCATCATGTAGGT 59.052 45.455 8.91 0.00 38.13 3.08
1877 2115 3.878699 TGCAATGCATCATGTAGGTACAG 59.121 43.478 2.72 0.00 34.76 2.74
1880 2118 1.480545 TGCATCATGTAGGTACAGCGT 59.519 47.619 0.00 0.00 39.92 5.07
1889 2127 2.025418 GGTACAGCGTTGGTGGTCG 61.025 63.158 3.74 0.00 35.13 4.79
1895 2133 4.444024 CGTTGGTGGTCGCATGCG 62.444 66.667 33.61 33.61 41.35 4.73
1896 2134 4.101790 GTTGGTGGTCGCATGCGG 62.102 66.667 37.18 20.26 40.25 5.69
1915 2153 4.704833 GCCTTGGGTGCTCGCTGA 62.705 66.667 4.41 0.00 0.00 4.26
1918 2156 2.031012 TTGGGTGCTCGCTGACAG 59.969 61.111 0.00 0.00 0.00 3.51
1929 2167 1.159285 CGCTGACAGCTCAAATGGAA 58.841 50.000 24.36 0.00 39.60 3.53
1930 2168 1.741706 CGCTGACAGCTCAAATGGAAT 59.258 47.619 24.36 0.00 39.60 3.01
1943 2181 7.709613 AGCTCAAATGGAATTTTCATCTATTGC 59.290 33.333 0.00 0.00 46.10 3.56
1944 2182 7.493320 GCTCAAATGGAATTTTCATCTATTGCA 59.507 33.333 0.00 0.00 46.10 4.08
1955 2193 0.988832 TCTATTGCAAGGGGAACGGT 59.011 50.000 4.94 0.00 0.00 4.83
1961 2199 0.252197 GCAAGGGGAACGGTCATAGT 59.748 55.000 1.31 0.00 0.00 2.12
1966 2204 3.716431 AGGGGAACGGTCATAGTAAGAA 58.284 45.455 1.31 0.00 0.00 2.52
1984 2222 0.602905 AAGGTGTTCGTGGTGCTAGC 60.603 55.000 8.10 8.10 0.00 3.42
2015 2253 3.198068 CGACATTGATGAGTAAGGGGTG 58.802 50.000 0.00 0.00 0.00 4.61
2024 2262 0.766674 AGTAAGGGGTGCACCAGTGA 60.767 55.000 35.78 16.30 42.91 3.41
2028 2266 1.678970 GGGGTGCACCAGTGATTCC 60.679 63.158 35.78 22.10 42.91 3.01
2029 2267 1.678970 GGGTGCACCAGTGATTCCC 60.679 63.158 35.78 12.94 39.85 3.97
2031 2269 1.380302 GTGCACCAGTGATTCCCCT 59.620 57.895 5.22 0.00 0.00 4.79
2032 2270 0.962356 GTGCACCAGTGATTCCCCTG 60.962 60.000 5.22 0.00 0.00 4.45
2033 2271 2.048603 GCACCAGTGATTCCCCTGC 61.049 63.158 0.99 0.00 0.00 4.85
2034 2272 1.379916 CACCAGTGATTCCCCTGCA 59.620 57.895 0.00 0.00 0.00 4.41
2035 2273 0.962356 CACCAGTGATTCCCCTGCAC 60.962 60.000 0.00 0.00 0.00 4.57
2038 2276 0.679002 CAGTGATTCCCCTGCACCAG 60.679 60.000 0.00 0.00 33.14 4.00
2039 2277 1.136329 AGTGATTCCCCTGCACCAGT 61.136 55.000 0.00 0.00 33.14 4.00
2040 2278 0.962356 GTGATTCCCCTGCACCAGTG 60.962 60.000 0.00 0.00 0.00 3.66
2042 2280 0.257039 GATTCCCCTGCACCAGTGAT 59.743 55.000 0.99 0.00 0.00 3.06
2043 2281 0.706433 ATTCCCCTGCACCAGTGATT 59.294 50.000 0.99 0.00 0.00 2.57
2044 2282 0.038166 TTCCCCTGCACCAGTGATTC 59.962 55.000 0.99 0.00 0.00 2.52
2046 2284 1.379044 CCCTGCACCAGTGATTCCC 60.379 63.158 0.99 0.00 0.00 3.97
2047 2285 1.379044 CCTGCACCAGTGATTCCCC 60.379 63.158 0.99 0.00 0.00 4.81
2048 2286 1.746615 CTGCACCAGTGATTCCCCG 60.747 63.158 0.99 0.00 0.00 5.73
2049 2287 3.134127 GCACCAGTGATTCCCCGC 61.134 66.667 0.99 0.00 0.00 6.13
2050 2288 2.350895 CACCAGTGATTCCCCGCA 59.649 61.111 0.00 0.00 0.00 5.69
2051 2289 1.746615 CACCAGTGATTCCCCGCAG 60.747 63.158 0.00 0.00 0.00 5.18
2063 2301 3.728474 CCGCAGGCTCTAGCATTG 58.272 61.111 4.07 3.10 46.14 2.82
2064 2302 1.153289 CCGCAGGCTCTAGCATTGT 60.153 57.895 4.07 0.00 46.14 2.71
2065 2303 0.104855 CCGCAGGCTCTAGCATTGTA 59.895 55.000 4.07 0.00 46.14 2.41
2066 2304 1.495878 CGCAGGCTCTAGCATTGTAG 58.504 55.000 4.07 0.00 44.36 2.74
2067 2305 1.224965 GCAGGCTCTAGCATTGTAGC 58.775 55.000 4.07 0.00 44.36 3.58
2068 2306 1.495878 CAGGCTCTAGCATTGTAGCG 58.504 55.000 4.07 0.00 44.36 4.26
2069 2307 0.390860 AGGCTCTAGCATTGTAGCGG 59.609 55.000 4.07 0.00 44.36 5.52
2070 2308 0.105039 GGCTCTAGCATTGTAGCGGT 59.895 55.000 4.07 0.00 44.36 5.68
2073 2311 2.482142 GCTCTAGCATTGTAGCGGTTCT 60.482 50.000 0.00 0.00 41.59 3.01
2076 2314 5.531122 TCTAGCATTGTAGCGGTTCTAAT 57.469 39.130 0.00 0.00 40.15 1.73
2090 2328 7.450074 AGCGGTTCTAATAATATGGTGAATGA 58.550 34.615 0.00 0.00 0.00 2.57
2102 2340 5.717078 ATGGTGAATGATGCAATATGACC 57.283 39.130 0.00 0.00 0.00 4.02
2129 2367 0.537143 GTGTGGAATGGCAGTGGTCA 60.537 55.000 0.00 0.00 0.00 4.02
2133 2371 1.133513 TGGAATGGCAGTGGTCAGTTT 60.134 47.619 0.00 0.00 28.09 2.66
2134 2372 1.963515 GGAATGGCAGTGGTCAGTTTT 59.036 47.619 0.00 0.00 28.09 2.43
2148 2386 4.304110 GTCAGTTTTACACCGAGACATGA 58.696 43.478 0.00 0.00 0.00 3.07
2150 2388 5.408604 GTCAGTTTTACACCGAGACATGAAT 59.591 40.000 0.00 0.00 0.00 2.57
2151 2389 5.408299 TCAGTTTTACACCGAGACATGAATG 59.592 40.000 0.00 0.00 0.00 2.67
2152 2390 5.408299 CAGTTTTACACCGAGACATGAATGA 59.592 40.000 0.00 0.00 0.00 2.57
2205 2443 3.019564 GGAAAGATGTCCCACCAATCTG 58.980 50.000 0.00 0.00 0.00 2.90
2217 2455 3.506067 CCACCAATCTGTTTGTACCCTTC 59.494 47.826 0.00 0.00 33.15 3.46
2225 2463 4.642885 TCTGTTTGTACCCTTCTGTTTTGG 59.357 41.667 0.00 0.00 0.00 3.28
2232 2470 1.547372 CCCTTCTGTTTTGGCATGGAG 59.453 52.381 0.00 0.00 0.00 3.86
2245 2483 0.105593 CATGGAGTGCTAGCGGATGT 59.894 55.000 10.77 0.00 0.00 3.06
2249 2487 0.173481 GAGTGCTAGCGGATGTGACA 59.827 55.000 10.77 0.00 0.00 3.58
2256 2494 2.315925 AGCGGATGTGACAATCGAAT 57.684 45.000 13.49 0.69 0.00 3.34
2257 2495 1.935873 AGCGGATGTGACAATCGAATG 59.064 47.619 13.49 0.00 0.00 2.67
2300 2538 1.202486 AGAACACGCTTCAAGTTCGGA 60.202 47.619 0.00 0.00 44.67 4.55
2301 2539 0.935196 AACACGCTTCAAGTTCGGAC 59.065 50.000 0.00 0.00 0.00 4.79
2302 2540 1.213094 ACACGCTTCAAGTTCGGACG 61.213 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.394712 GTGCCACCGTAGCAGCCT 62.395 66.667 0.00 0.00 41.87 4.58
12 13 3.121030 CAGCAGTGCCACCGTAGC 61.121 66.667 12.58 0.00 0.00 3.58
171 173 4.170468 AGGAAACGATGATAAGGGCATT 57.830 40.909 0.00 0.00 0.00 3.56
220 222 0.778479 AGGTATTGGGTGGGGTTGGT 60.778 55.000 0.00 0.00 0.00 3.67
252 254 4.023963 TCGTCATCCGATCAACTGATCTAC 60.024 45.833 15.79 6.90 46.58 2.59
329 333 2.895424 AACCGCTGGTCCCTCAAGG 61.895 63.158 0.69 0.00 33.12 3.61
332 336 3.636231 CCAACCGCTGGTCCCTCA 61.636 66.667 0.69 0.00 40.78 3.86
354 358 0.393077 AGAAACACCACTCCACCGAG 59.607 55.000 0.00 0.00 42.32 4.63
467 472 2.338620 CACCACGACGCCAGAGAA 59.661 61.111 0.00 0.00 0.00 2.87
504 509 0.403655 TGTTGCATCTACCTTGCCCA 59.596 50.000 0.00 0.00 39.39 5.36
521 526 3.435275 TCCATCTTCAGAGCTGTACTGT 58.565 45.455 0.00 0.00 36.81 3.55
568 573 2.125269 GACGCTTGCCGGGTATGT 60.125 61.111 2.18 0.00 42.52 2.29
616 622 3.467226 CGTCTGCCGGGTATGGGT 61.467 66.667 2.18 0.00 0.00 4.51
662 668 0.321653 ACCTCGCAGCCAAACCTAAG 60.322 55.000 0.00 0.00 0.00 2.18
712 719 6.954487 TGCTATCTGATTTGCATTCTGATT 57.046 33.333 18.35 8.38 34.71 2.57
713 720 6.954487 TTGCTATCTGATTTGCATTCTGAT 57.046 33.333 17.67 17.67 36.27 2.90
834 842 8.257306 TCAAAAGAGGCTTCAACATTAAGTTTT 58.743 29.630 0.00 0.00 38.74 2.43
849 857 7.058525 TCAACATATCATGATCAAAAGAGGCT 58.941 34.615 12.53 0.00 0.00 4.58
1101 1109 4.556233 GGTAACAATCCTCAAAAACTGCC 58.444 43.478 0.00 0.00 0.00 4.85
1330 1338 4.287067 TGAAGGGATATTGATACTCTGGGC 59.713 45.833 0.00 0.00 0.00 5.36
1343 1351 9.055689 ACTGCTATCTAATTGATGAAGGGATAT 57.944 33.333 0.00 0.00 36.65 1.63
1344 1352 8.441311 ACTGCTATCTAATTGATGAAGGGATA 57.559 34.615 0.00 0.00 36.65 2.59
1360 1368 3.193691 ACAAACTGTCGCTACTGCTATCT 59.806 43.478 0.00 0.00 36.97 1.98
1366 1374 1.069906 GGCAACAAACTGTCGCTACTG 60.070 52.381 0.00 0.00 29.61 2.74
1407 1415 5.701290 AGACCTTACAAAGTCATACAACAGC 59.299 40.000 0.00 0.00 0.00 4.40
1536 1544 7.177216 TCAATTTGAATGCAGGTAGAACTGAAT 59.823 33.333 0.00 0.00 38.40 2.57
1544 1552 4.802039 GCATGTCAATTTGAATGCAGGTAG 59.198 41.667 25.17 7.83 38.98 3.18
1545 1553 4.220163 TGCATGTCAATTTGAATGCAGGTA 59.780 37.500 27.01 12.69 41.36 3.08
1546 1554 3.007074 TGCATGTCAATTTGAATGCAGGT 59.993 39.130 27.01 2.35 41.36 4.00
1547 1555 3.591023 TGCATGTCAATTTGAATGCAGG 58.409 40.909 27.01 15.44 41.36 4.85
1548 1556 5.794687 AATGCATGTCAATTTGAATGCAG 57.205 34.783 30.24 13.65 44.98 4.41
1549 1557 6.428465 AGAAAATGCATGTCAATTTGAATGCA 59.572 30.769 29.70 29.70 45.37 3.96
1550 1558 6.740905 CAGAAAATGCATGTCAATTTGAATGC 59.259 34.615 24.29 24.29 39.28 3.56
1551 1559 7.094975 ACCAGAAAATGCATGTCAATTTGAATG 60.095 33.333 0.00 8.47 28.48 2.67
1552 1560 6.938030 ACCAGAAAATGCATGTCAATTTGAAT 59.062 30.769 0.00 0.00 28.48 2.57
1553 1561 6.203145 CACCAGAAAATGCATGTCAATTTGAA 59.797 34.615 0.00 0.00 28.48 2.69
1554 1562 5.697178 CACCAGAAAATGCATGTCAATTTGA 59.303 36.000 0.00 0.00 28.48 2.69
1555 1563 5.467399 ACACCAGAAAATGCATGTCAATTTG 59.533 36.000 0.00 0.00 28.48 2.32
1556 1564 5.613329 ACACCAGAAAATGCATGTCAATTT 58.387 33.333 0.00 0.00 30.86 1.82
1557 1565 5.217978 ACACCAGAAAATGCATGTCAATT 57.782 34.783 0.00 0.00 0.00 2.32
1558 1566 4.877378 ACACCAGAAAATGCATGTCAAT 57.123 36.364 0.00 0.00 0.00 2.57
1567 1575 7.706159 TGCAATAGCTAATACACCAGAAAATG 58.294 34.615 0.00 0.00 42.74 2.32
1621 1629 4.096382 GCAATGTTATGTCCAACACTAGGG 59.904 45.833 0.00 0.00 41.02 3.53
1626 1634 3.980775 GTGTGCAATGTTATGTCCAACAC 59.019 43.478 0.00 0.00 41.02 3.32
1639 1647 1.660052 CGTCAAGAACCGTGTGCAATG 60.660 52.381 0.00 0.00 0.00 2.82
1666 1674 3.026630 TGTTAGAGTTCAAGGCTGACG 57.973 47.619 0.00 0.00 0.00 4.35
1668 1676 3.849911 CGATGTTAGAGTTCAAGGCTGA 58.150 45.455 0.00 0.00 0.00 4.26
1674 1682 3.125146 GCATGTGCGATGTTAGAGTTCAA 59.875 43.478 0.00 0.00 0.00 2.69
1675 1683 2.672874 GCATGTGCGATGTTAGAGTTCA 59.327 45.455 0.00 0.00 0.00 3.18
1696 1704 3.180980 TCGTCGAGCTGTTTTAAACGAAG 59.819 43.478 0.00 0.00 35.06 3.79
1707 1715 0.312416 GGCTATCATCGTCGAGCTGT 59.688 55.000 0.00 0.00 35.23 4.40
1708 1716 0.312102 TGGCTATCATCGTCGAGCTG 59.688 55.000 0.00 0.00 35.23 4.24
1709 1717 1.032794 TTGGCTATCATCGTCGAGCT 58.967 50.000 0.00 0.00 35.23 4.09
1710 1718 1.132588 GTTGGCTATCATCGTCGAGC 58.867 55.000 0.00 0.00 0.00 5.03
1711 1719 2.783828 AGTTGGCTATCATCGTCGAG 57.216 50.000 0.00 0.00 0.00 4.04
1713 1721 2.809446 TGAAGTTGGCTATCATCGTCG 58.191 47.619 0.00 0.00 0.00 5.12
1714 1722 4.981389 GATGAAGTTGGCTATCATCGTC 57.019 45.455 0.00 0.00 39.84 4.20
1718 1726 2.874701 GTGCGATGAAGTTGGCTATCAT 59.125 45.455 0.00 0.00 36.54 2.45
1719 1727 2.279741 GTGCGATGAAGTTGGCTATCA 58.720 47.619 0.00 0.00 0.00 2.15
1725 1733 1.131126 GGATGTGTGCGATGAAGTTGG 59.869 52.381 0.00 0.00 0.00 3.77
1729 1737 1.588404 GTACGGATGTGTGCGATGAAG 59.412 52.381 0.00 0.00 42.26 3.02
1737 1745 6.960992 CACAATTATCTTTGTACGGATGTGTG 59.039 38.462 14.28 14.28 37.73 3.82
1744 1752 5.545658 AGCACACAATTATCTTTGTACGG 57.454 39.130 0.00 0.00 37.73 4.02
1745 1753 7.173419 CACTAGCACACAATTATCTTTGTACG 58.827 38.462 0.00 0.00 37.73 3.67
1772 1780 9.307121 CAAAACTAATTGTGTGTAATGTGGAAA 57.693 29.630 0.00 0.00 0.00 3.13
1773 1781 8.687242 TCAAAACTAATTGTGTGTAATGTGGAA 58.313 29.630 0.00 0.00 0.00 3.53
1795 1803 9.493206 GTTGTAGTTCGAATACAGTTTTTCAAA 57.507 29.630 0.00 0.00 34.76 2.69
1796 1804 8.666573 TGTTGTAGTTCGAATACAGTTTTTCAA 58.333 29.630 0.00 0.00 34.76 2.69
1808 1816 4.986034 TGACGATGTTGTTGTAGTTCGAAT 59.014 37.500 0.00 0.00 0.00 3.34
1812 1820 7.908193 ATTTTTGACGATGTTGTTGTAGTTC 57.092 32.000 0.00 0.00 0.00 3.01
1821 1829 9.726232 ATCAGATATCAATTTTTGACGATGTTG 57.274 29.630 5.32 0.00 43.48 3.33
1842 1850 5.591067 TGATGCATTGCAGACAATTATCAGA 59.409 36.000 17.52 0.00 44.21 3.27
1843 1851 5.827666 TGATGCATTGCAGACAATTATCAG 58.172 37.500 17.52 0.00 44.21 2.90
1858 1866 3.133691 CGCTGTACCTACATGATGCATT 58.866 45.455 0.00 0.00 35.36 3.56
1869 2107 0.604578 GACCACCAACGCTGTACCTA 59.395 55.000 0.00 0.00 0.00 3.08
1880 2118 4.634703 ACCGCATGCGACCACCAA 62.635 61.111 39.90 0.00 42.83 3.67
1915 2153 6.600882 AGATGAAAATTCCATTTGAGCTGT 57.399 33.333 0.00 0.00 31.77 4.40
1918 2156 7.493320 TGCAATAGATGAAAATTCCATTTGAGC 59.507 33.333 0.00 0.00 31.77 4.26
1929 2167 5.163519 CGTTCCCCTTGCAATAGATGAAAAT 60.164 40.000 0.00 0.00 0.00 1.82
1930 2168 4.157656 CGTTCCCCTTGCAATAGATGAAAA 59.842 41.667 0.00 0.00 0.00 2.29
1943 2181 3.449737 TCTTACTATGACCGTTCCCCTTG 59.550 47.826 0.00 0.00 0.00 3.61
1944 2182 3.716431 TCTTACTATGACCGTTCCCCTT 58.284 45.455 0.00 0.00 0.00 3.95
1955 2193 4.525487 ACCACGAACACCTTCTTACTATGA 59.475 41.667 0.00 0.00 0.00 2.15
1961 2199 1.414919 AGCACCACGAACACCTTCTTA 59.585 47.619 0.00 0.00 0.00 2.10
1966 2204 1.004918 GCTAGCACCACGAACACCT 60.005 57.895 10.63 0.00 0.00 4.00
1984 2222 4.330894 ACTCATCAATGTCGTATGTTGCTG 59.669 41.667 0.00 0.00 0.00 4.41
1989 2227 5.453339 CCCCTTACTCATCAATGTCGTATGT 60.453 44.000 0.00 0.00 0.00 2.29
1991 2229 4.654262 ACCCCTTACTCATCAATGTCGTAT 59.346 41.667 0.00 0.00 0.00 3.06
1994 2232 3.198068 CACCCCTTACTCATCAATGTCG 58.802 50.000 0.00 0.00 0.00 4.35
2015 2253 2.048603 GCAGGGGAATCACTGGTGC 61.049 63.158 6.38 0.00 35.30 5.01
2024 2262 0.706433 AATCACTGGTGCAGGGGAAT 59.294 50.000 0.00 0.00 35.28 3.01
2028 2266 1.379044 GGGAATCACTGGTGCAGGG 60.379 63.158 0.00 0.00 36.00 4.45
2029 2267 1.379044 GGGGAATCACTGGTGCAGG 60.379 63.158 0.00 0.00 35.51 4.85
2031 2269 2.350895 CGGGGAATCACTGGTGCA 59.649 61.111 0.00 0.00 0.00 4.57
2032 2270 3.134127 GCGGGGAATCACTGGTGC 61.134 66.667 0.00 0.00 0.00 5.01
2033 2271 1.746615 CTGCGGGGAATCACTGGTG 60.747 63.158 0.00 0.00 0.00 4.17
2034 2272 2.671070 CTGCGGGGAATCACTGGT 59.329 61.111 0.00 0.00 0.00 4.00
2035 2273 2.124570 CCTGCGGGGAATCACTGG 60.125 66.667 2.57 0.00 37.23 4.00
2038 2276 1.686325 TAGAGCCTGCGGGGAATCAC 61.686 60.000 15.02 0.00 37.23 3.06
2039 2277 1.382557 TAGAGCCTGCGGGGAATCA 60.383 57.895 15.02 0.00 37.23 2.57
2040 2278 1.369321 CTAGAGCCTGCGGGGAATC 59.631 63.158 15.02 3.63 37.23 2.52
2042 2280 3.470888 GCTAGAGCCTGCGGGGAA 61.471 66.667 15.02 0.00 37.23 3.97
2043 2281 4.777854 TGCTAGAGCCTGCGGGGA 62.778 66.667 15.02 0.00 41.18 4.81
2044 2282 3.112205 AATGCTAGAGCCTGCGGGG 62.112 63.158 15.02 1.86 41.18 5.73
2046 2284 0.104855 TACAATGCTAGAGCCTGCGG 59.895 55.000 0.00 0.00 41.18 5.69
2047 2285 1.495878 CTACAATGCTAGAGCCTGCG 58.504 55.000 0.00 0.00 41.18 5.18
2048 2286 1.224965 GCTACAATGCTAGAGCCTGC 58.775 55.000 0.00 0.00 41.18 4.85
2049 2287 1.495878 CGCTACAATGCTAGAGCCTG 58.504 55.000 0.00 0.00 41.18 4.85
2050 2288 0.390860 CCGCTACAATGCTAGAGCCT 59.609 55.000 0.00 0.00 41.18 4.58
2051 2289 0.105039 ACCGCTACAATGCTAGAGCC 59.895 55.000 0.00 0.00 41.18 4.70
2053 2291 3.444703 AGAACCGCTACAATGCTAGAG 57.555 47.619 0.00 0.00 0.00 2.43
2054 2292 4.994907 TTAGAACCGCTACAATGCTAGA 57.005 40.909 0.00 0.00 0.00 2.43
2055 2293 7.891183 ATTATTAGAACCGCTACAATGCTAG 57.109 36.000 0.00 0.00 0.00 3.42
2056 2294 9.366216 CATATTATTAGAACCGCTACAATGCTA 57.634 33.333 0.00 0.00 0.00 3.49
2057 2295 7.334421 CCATATTATTAGAACCGCTACAATGCT 59.666 37.037 0.00 0.00 0.00 3.79
2058 2296 7.119262 ACCATATTATTAGAACCGCTACAATGC 59.881 37.037 0.00 0.00 0.00 3.56
2059 2297 8.443160 CACCATATTATTAGAACCGCTACAATG 58.557 37.037 0.00 0.00 0.00 2.82
2060 2298 8.372459 TCACCATATTATTAGAACCGCTACAAT 58.628 33.333 0.00 0.00 0.00 2.71
2061 2299 7.728148 TCACCATATTATTAGAACCGCTACAA 58.272 34.615 0.00 0.00 0.00 2.41
2062 2300 7.292713 TCACCATATTATTAGAACCGCTACA 57.707 36.000 0.00 0.00 0.00 2.74
2063 2301 8.656849 CATTCACCATATTATTAGAACCGCTAC 58.343 37.037 0.00 0.00 0.00 3.58
2064 2302 8.590204 TCATTCACCATATTATTAGAACCGCTA 58.410 33.333 0.00 0.00 0.00 4.26
2065 2303 7.450074 TCATTCACCATATTATTAGAACCGCT 58.550 34.615 0.00 0.00 0.00 5.52
2066 2304 7.667043 TCATTCACCATATTATTAGAACCGC 57.333 36.000 0.00 0.00 0.00 5.68
2067 2305 8.177663 GCATCATTCACCATATTATTAGAACCG 58.822 37.037 0.00 0.00 0.00 4.44
2068 2306 9.013229 TGCATCATTCACCATATTATTAGAACC 57.987 33.333 0.00 0.00 0.00 3.62
2076 2314 8.959548 GGTCATATTGCATCATTCACCATATTA 58.040 33.333 0.00 0.00 0.00 0.98
2090 2328 2.719376 GGCACGGGTCATATTGCAT 58.281 52.632 0.00 0.00 36.66 3.96
2121 2359 2.800544 CTCGGTGTAAAACTGACCACTG 59.199 50.000 0.00 0.00 39.36 3.66
2129 2367 5.547465 TCATTCATGTCTCGGTGTAAAACT 58.453 37.500 0.00 0.00 0.00 2.66
2133 2371 4.250464 GGTTCATTCATGTCTCGGTGTAA 58.750 43.478 0.00 0.00 0.00 2.41
2134 2372 3.369052 GGGTTCATTCATGTCTCGGTGTA 60.369 47.826 0.00 0.00 0.00 2.90
2148 2386 2.557452 CCACTGGCTTTAGGGGTTCATT 60.557 50.000 0.00 0.00 36.46 2.57
2150 2388 0.404040 CCACTGGCTTTAGGGGTTCA 59.596 55.000 0.00 0.00 36.46 3.18
2151 2389 0.965866 GCCACTGGCTTTAGGGGTTC 60.966 60.000 13.28 0.00 46.69 3.62
2152 2390 1.076727 GCCACTGGCTTTAGGGGTT 59.923 57.895 13.28 0.00 46.69 4.11
2205 2443 3.131400 TGCCAAAACAGAAGGGTACAAAC 59.869 43.478 0.00 0.00 0.00 2.93
2232 2470 1.594862 GATTGTCACATCCGCTAGCAC 59.405 52.381 16.45 3.75 0.00 4.40
2236 2474 2.951457 TTCGATTGTCACATCCGCTA 57.049 45.000 0.00 0.00 0.00 4.26
2267 2505 9.541143 TTGAAGCGTGTTCTAATCAATATATCA 57.459 29.630 2.04 0.00 0.00 2.15
2269 2507 9.547753 ACTTGAAGCGTGTTCTAATCAATATAT 57.452 29.630 0.00 0.00 0.00 0.86
2271 2509 7.849804 ACTTGAAGCGTGTTCTAATCAATAT 57.150 32.000 0.00 0.00 0.00 1.28
2273 2511 6.560253 AACTTGAAGCGTGTTCTAATCAAT 57.440 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.