Multiple sequence alignment - TraesCS3B01G112700

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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 TraesCS3B01G112700 chr3B 100.000 2860 0 0 1 2860 78852871 78850012 0.000000e+00 5282.0
1 TraesCS3B01G112700 chr3B 100.000 774 0 0 1988 2761 66395619 66394846 0.000000e+00 1430.0
2 TraesCS3B01G112700 chr3B 99.617 784 1 2 1979 2761 78847602 78848384 0.000000e+00 1430.0
3 TraesCS3B01G112700 chr3B 100.000 103 0 0 2758 2860 66393430 66393328 1.050000e-44 191.0
4 TraesCS3B01G112700 chr3B 100.000 49 0 0 1942 1990 66392353 66392401 1.090000e-14 91.6
5 TraesCS3B01G112700 chr3B 96.875 32 0 1 1 32 715950218 715950248 5.000000e-03 52.8
6 TraesCS3B01G112700 chr3A 90.661 1756 76 40 250 1944 62435839 62434111 0.000000e+00 2254.0
7 TraesCS3B01G112700 chr3A 99.352 772 5 0 1988 2759 60292611 60291840 0.000000e+00 1399.0
8 TraesCS3B01G112700 chr3A 99.725 728 2 0 2034 2761 687495537 687496264 0.000000e+00 1334.0
9 TraesCS3B01G112700 chr3A 92.424 198 11 2 25 218 62436032 62435835 2.170000e-71 279.0
10 TraesCS3B01G112700 chr3A 100.000 103 0 0 2758 2860 60289541 60289439 1.050000e-44 191.0
11 TraesCS3B01G112700 chr3A 100.000 50 0 0 1941 1990 687499408 687499359 3.030000e-15 93.5
12 TraesCS3B01G112700 chr3A 100.000 49 0 0 1942 1990 60288464 60288512 1.090000e-14 91.6
13 TraesCS3B01G112700 chr3D 93.996 1066 44 8 888 1944 49541252 49540198 0.000000e+00 1596.0
14 TraesCS3B01G112700 chr3D 96.875 32 1 0 1 32 271484589 271484558 1.000000e-03 54.7
15 TraesCS3B01G112700 chr2A 99.871 774 1 0 1988 2761 100991694 100990921 0.000000e+00 1424.0
16 TraesCS3B01G112700 chr2A 95.305 426 11 7 1986 2411 12238674 12238258 0.000000e+00 667.0
17 TraesCS3B01G112700 chr2A 100.000 51 0 0 1940 1990 100988280 100988330 8.440000e-16 95.3
18 TraesCS3B01G112700 chr2A 100.000 29 0 0 1 29 21023428 21023400 1.000000e-03 54.7
19 TraesCS3B01G112700 chr2A 100.000 29 0 0 398 426 87060215 87060187 1.000000e-03 54.7
20 TraesCS3B01G112700 chr6B 96.799 781 11 7 1988 2761 5158694 5157921 0.000000e+00 1291.0
21 TraesCS3B01G112700 chr6B 96.671 781 12 7 1988 2761 5197253 5196480 0.000000e+00 1286.0
22 TraesCS3B01G112700 chr6B 95.281 445 20 1 2317 2761 2585836 2586279 0.000000e+00 704.0
23 TraesCS3B01G112700 chr6B 96.842 95 3 0 2766 2860 5155715 5155621 2.950000e-35 159.0
24 TraesCS3B01G112700 chr6B 83.523 176 20 4 2458 2633 2585836 2586002 3.820000e-34 156.0
25 TraesCS3B01G112700 chr6B 97.959 49 1 0 1942 1990 5109074 5109122 5.080000e-13 86.1
26 TraesCS3B01G112700 chrUn 95.382 498 9 4 1988 2478 302530249 302530739 0.000000e+00 780.0
27 TraesCS3B01G112700 chrUn 96.875 32 1 0 1 32 39801032 39801063 1.000000e-03 54.7
28 TraesCS3B01G112700 chrUn 96.875 32 1 0 1 32 300441808 300441839 1.000000e-03 54.7
29 TraesCS3B01G112700 chr5A 100.000 103 0 0 2758 2860 10558886 10558784 1.050000e-44 191.0
30 TraesCS3B01G112700 chr5A 100.000 50 0 0 1941 1990 10556922 10556971 3.030000e-15 93.5
31 TraesCS3B01G112700 chr5B 100.000 49 0 0 1942 1990 37114298 37114346 1.090000e-14 91.6
32 TraesCS3B01G112700 chr5B 100.000 28 0 0 1 28 375947141 375947168 5.000000e-03 52.8
33 TraesCS3B01G112700 chr1A 97.727 44 1 0 1942 1985 12180141 12180184 3.060000e-10 76.8
34 TraesCS3B01G112700 chr7A 87.719 57 4 2 1918 1972 704674195 704674250 2.380000e-06 63.9
35 TraesCS3B01G112700 chr7B 100.000 29 0 0 1 29 488354617 488354589 1.000000e-03 54.7
36 TraesCS3B01G112700 chr6D 100.000 29 0 0 398 426 275879359 275879331 1.000000e-03 54.7
37 TraesCS3B01G112700 chr5D 100.000 29 0 0 398 426 109609924 109609896 1.000000e-03 54.7
38 TraesCS3B01G112700 chr2D 100.000 29 0 0 398 426 500037859 500037887 1.000000e-03 54.7
39 TraesCS3B01G112700 chr1D 100.000 29 0 0 398 426 353064980 353064952 1.000000e-03 54.7
40 TraesCS3B01G112700 chr4D 100.000 28 0 0 2 29 66566245 66566218 5.000000e-03 52.8
41 TraesCS3B01G112700 chr1B 96.875 32 0 1 1 32 414772691 414772661 5.000000e-03 52.8


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 TraesCS3B01G112700 chr3B 78850012 78852871 2859 True 5282.0 5282 100.0000 1 2860 1 chr3B.!!$R1 2859
1 TraesCS3B01G112700 chr3B 78847602 78848384 782 False 1430.0 1430 99.6170 1979 2761 1 chr3B.!!$F2 782
2 TraesCS3B01G112700 chr3B 66393328 66395619 2291 True 810.5 1430 100.0000 1988 2860 2 chr3B.!!$R2 872
3 TraesCS3B01G112700 chr3A 687495537 687496264 727 False 1334.0 1334 99.7250 2034 2761 1 chr3A.!!$F2 727
4 TraesCS3B01G112700 chr3A 62434111 62436032 1921 True 1266.5 2254 91.5425 25 1944 2 chr3A.!!$R3 1919
5 TraesCS3B01G112700 chr3A 60289439 60292611 3172 True 795.0 1399 99.6760 1988 2860 2 chr3A.!!$R2 872
6 TraesCS3B01G112700 chr3D 49540198 49541252 1054 True 1596.0 1596 93.9960 888 1944 1 chr3D.!!$R1 1056
7 TraesCS3B01G112700 chr2A 100990921 100991694 773 True 1424.0 1424 99.8710 1988 2761 1 chr2A.!!$R4 773
8 TraesCS3B01G112700 chr6B 5196480 5197253 773 True 1286.0 1286 96.6710 1988 2761 1 chr6B.!!$R1 773
9 TraesCS3B01G112700 chr6B 5155621 5158694 3073 True 725.0 1291 96.8205 1988 2860 2 chr6B.!!$R2 872

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
863 898 0.102844 TTTCGAACTTCGGTGGTCGT 59.897 50.0 11.21 0.0 40.88 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 1953 0.1078 CCCACTGTCATCTGCTCTGG 60.108 60.0 0.0 0.0 0.0 3.86 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
21 22 3.190878 GCCAAACGGCTGGAGATG 58.809 61.111 9.09 0.00 46.85 2.90
22 23 3.056313 GCCAAACGGCTGGAGATGC 62.056 63.158 9.09 0.00 46.85 3.91
23 24 1.377725 CCAAACGGCTGGAGATGCT 60.378 57.895 0.00 0.00 38.96 3.79
60 64 1.260544 AAGATTGCAAGGTTGGCTCC 58.739 50.000 4.94 0.00 0.00 4.70
104 108 5.452255 AGTGCATGGTGGATTCTAAATCAT 58.548 37.500 0.00 0.00 0.00 2.45
140 144 1.538047 ACCTAAACATGTGCAGCTGG 58.462 50.000 17.12 0.00 0.00 4.85
167 172 4.320202 GCTTGCGTCCTAAAAATTCAGTGA 60.320 41.667 0.00 0.00 0.00 3.41
169 174 3.188460 TGCGTCCTAAAAATTCAGTGAGC 59.812 43.478 0.00 0.00 0.00 4.26
178 183 6.998258 AAAAATTCAGTGAGCGAAGATTTG 57.002 33.333 0.00 0.00 0.00 2.32
223 228 9.423061 AGAATAATATTTCAACAAACACCTTGC 57.577 29.630 0.00 0.00 38.75 4.01
224 229 9.202273 GAATAATATTTCAACAAACACCTTGCA 57.798 29.630 0.00 0.00 38.75 4.08
225 230 8.761575 ATAATATTTCAACAAACACCTTGCAG 57.238 30.769 0.00 0.00 38.75 4.41
226 231 2.957491 TTCAACAAACACCTTGCAGG 57.043 45.000 1.16 1.16 42.49 4.85
227 232 0.459489 TCAACAAACACCTTGCAGGC 59.541 50.000 2.50 0.00 39.63 4.85
228 233 0.175302 CAACAAACACCTTGCAGGCA 59.825 50.000 2.50 0.00 39.63 4.75
229 234 0.901124 AACAAACACCTTGCAGGCAA 59.099 45.000 6.53 6.53 39.63 4.52
230 235 0.175531 ACAAACACCTTGCAGGCAAC 59.824 50.000 1.93 0.00 39.63 4.17
231 236 0.871163 CAAACACCTTGCAGGCAACG 60.871 55.000 1.93 2.07 39.63 4.10
232 237 1.319614 AAACACCTTGCAGGCAACGT 61.320 50.000 1.93 2.74 39.63 3.99
233 238 2.003658 AACACCTTGCAGGCAACGTG 62.004 55.000 24.58 24.58 43.48 4.49
234 239 2.186160 CACCTTGCAGGCAACGTGA 61.186 57.895 23.00 0.00 41.82 4.35
235 240 1.228245 ACCTTGCAGGCAACGTGAT 60.228 52.632 1.93 0.00 39.63 3.06
236 241 1.210931 CCTTGCAGGCAACGTGATG 59.789 57.895 1.93 0.00 46.39 3.07
237 242 1.443194 CTTGCAGGCAACGTGATGC 60.443 57.895 1.93 3.56 45.67 3.91
246 251 3.201726 GCAACGTGATGCATAAACAGT 57.798 42.857 7.34 1.83 45.70 3.55
247 252 3.564511 GCAACGTGATGCATAAACAGTT 58.435 40.909 7.34 7.61 45.70 3.16
248 253 4.717991 GCAACGTGATGCATAAACAGTTA 58.282 39.130 7.34 0.00 45.70 2.24
249 254 5.150683 GCAACGTGATGCATAAACAGTTAA 58.849 37.500 7.34 0.00 45.70 2.01
250 255 5.627367 GCAACGTGATGCATAAACAGTTAAA 59.373 36.000 7.34 0.00 45.70 1.52
251 256 6.143118 GCAACGTGATGCATAAACAGTTAAAA 59.857 34.615 7.34 0.00 45.70 1.52
252 257 7.490055 CAACGTGATGCATAAACAGTTAAAAC 58.510 34.615 0.00 0.00 0.00 2.43
253 258 6.730175 ACGTGATGCATAAACAGTTAAAACA 58.270 32.000 0.00 0.00 0.00 2.83
254 259 6.855914 ACGTGATGCATAAACAGTTAAAACAG 59.144 34.615 0.00 0.00 0.00 3.16
304 309 4.764679 TTGACCATGAAAAATCAGACGG 57.235 40.909 0.00 0.00 0.00 4.79
312 317 8.798402 ACCATGAAAAATCAGACGGTTTTAATA 58.202 29.630 0.00 0.00 0.00 0.98
328 333 8.948946 CGGTTTTAATAACAATTTGTTTTTGCC 58.051 29.630 19.15 15.40 41.45 4.52
329 334 8.948946 GGTTTTAATAACAATTTGTTTTTGCCG 58.051 29.630 19.15 0.00 41.45 5.69
330 335 9.704098 GTTTTAATAACAATTTGTTTTTGCCGA 57.296 25.926 19.15 0.95 41.45 5.54
331 336 9.922305 TTTTAATAACAATTTGTTTTTGCCGAG 57.078 25.926 19.15 0.00 41.45 4.63
334 339 4.335400 ACAATTTGTTTTTGCCGAGGAT 57.665 36.364 0.00 0.00 0.00 3.24
343 348 7.026631 TGTTTTTGCCGAGGATGATAATAAG 57.973 36.000 0.00 0.00 0.00 1.73
467 473 2.280592 GGGGTCGTTTGCGTGTCT 60.281 61.111 0.00 0.00 39.49 3.41
478 484 2.908073 GCGTGTCTGGGCCAAACTG 61.908 63.158 11.97 5.03 0.00 3.16
486 492 2.031120 CTGGGCCAAACTGTTCTTCAA 58.969 47.619 8.04 0.00 0.00 2.69
537 543 1.273886 ACAGAGGGAGAGAAAGCGTTC 59.726 52.381 3.99 3.99 0.00 3.95
541 547 1.550976 AGGGAGAGAAAGCGTTCGAAT 59.449 47.619 0.00 0.00 38.90 3.34
561 567 3.818787 CGAGCCACCCTGCAATGC 61.819 66.667 0.00 0.00 0.00 3.56
562 568 3.455469 GAGCCACCCTGCAATGCC 61.455 66.667 1.53 0.00 0.00 4.40
565 571 3.443045 CCACCCTGCAATGCCGTC 61.443 66.667 1.53 0.00 0.00 4.79
566 572 3.803082 CACCCTGCAATGCCGTCG 61.803 66.667 1.53 0.00 0.00 5.12
659 665 4.486574 TCGTCGGTTTCCCAATAAAAAC 57.513 40.909 0.00 0.00 35.19 2.43
660 666 3.059051 TCGTCGGTTTCCCAATAAAAACG 60.059 43.478 0.00 0.00 45.66 3.60
739 768 8.877864 AATTCCTGAATAAGAATAACACACCA 57.122 30.769 0.00 0.00 32.46 4.17
811 840 9.701098 ATAAAATATAAGTGAAATACGCCTCGA 57.299 29.630 0.00 0.00 0.00 4.04
859 894 3.249013 GTTCTTTTCGAACTTCGGTGG 57.751 47.619 11.21 0.82 46.74 4.61
860 895 2.607631 TCTTTTCGAACTTCGGTGGT 57.392 45.000 11.21 0.00 40.88 4.16
861 896 2.476821 TCTTTTCGAACTTCGGTGGTC 58.523 47.619 11.21 0.00 40.88 4.02
863 898 0.102844 TTTCGAACTTCGGTGGTCGT 59.897 50.000 11.21 0.00 40.88 4.34
864 899 0.102844 TTCGAACTTCGGTGGTCGTT 59.897 50.000 11.21 0.00 40.88 3.85
866 901 0.932399 CGAACTTCGGTGGTCGTTTT 59.068 50.000 3.06 0.00 40.32 2.43
915 956 2.995547 GTGTCCGGGCCCAACTAT 59.004 61.111 24.92 0.00 0.00 2.12
1312 1369 4.776322 CCATGCCGGGTTCTCGCA 62.776 66.667 2.18 0.00 0.00 5.10
1367 1424 6.091441 CCAAGATAATGGCTCTAATTACTCGC 59.909 42.308 0.00 0.00 32.78 5.03
1370 1427 7.093992 AGATAATGGCTCTAATTACTCGCTTC 58.906 38.462 0.00 0.00 0.00 3.86
1380 1437 3.853831 TTACTCGCTTCGTGTATCCAA 57.146 42.857 2.68 0.00 36.12 3.53
1408 1465 3.648067 TGGTCTGACATTCTTGTTCCTCT 59.352 43.478 10.38 0.00 35.79 3.69
1409 1466 4.249661 GGTCTGACATTCTTGTTCCTCTC 58.750 47.826 10.38 0.00 35.79 3.20
1410 1467 4.020662 GGTCTGACATTCTTGTTCCTCTCT 60.021 45.833 10.38 0.00 35.79 3.10
1411 1468 4.928615 GTCTGACATTCTTGTTCCTCTCTG 59.071 45.833 2.24 0.00 35.79 3.35
1412 1469 3.668447 TGACATTCTTGTTCCTCTCTGC 58.332 45.455 0.00 0.00 35.79 4.26
1413 1470 2.670414 GACATTCTTGTTCCTCTCTGCG 59.330 50.000 0.00 0.00 35.79 5.18
1414 1471 2.037772 ACATTCTTGTTCCTCTCTGCGT 59.962 45.455 0.00 0.00 29.55 5.24
1415 1472 3.258372 ACATTCTTGTTCCTCTCTGCGTA 59.742 43.478 0.00 0.00 29.55 4.42
1421 1478 2.028112 TGTTCCTCTCTGCGTATTTGCT 60.028 45.455 0.00 0.00 35.36 3.91
1422 1479 2.299993 TCCTCTCTGCGTATTTGCTG 57.700 50.000 0.00 0.00 35.36 4.41
1530 1587 2.260434 GCTTCGCCTCGTGGTACA 59.740 61.111 5.26 0.00 35.27 2.90
1533 1590 1.722011 CTTCGCCTCGTGGTACATTT 58.278 50.000 5.26 0.00 44.52 2.32
1534 1591 2.073816 CTTCGCCTCGTGGTACATTTT 58.926 47.619 5.26 0.00 44.52 1.82
1543 1600 3.579586 TCGTGGTACATTTTCTACACCCT 59.420 43.478 0.00 0.00 44.52 4.34
1544 1601 3.682858 CGTGGTACATTTTCTACACCCTG 59.317 47.826 0.00 0.00 44.52 4.45
1545 1602 3.439129 GTGGTACATTTTCTACACCCTGC 59.561 47.826 0.00 0.00 44.52 4.85
1546 1603 3.073209 TGGTACATTTTCTACACCCTGCA 59.927 43.478 0.00 0.00 0.00 4.41
1549 1614 3.832527 ACATTTTCTACACCCTGCACTT 58.167 40.909 0.00 0.00 0.00 3.16
1567 1632 3.125829 CACTTGTGCTGCGATCTGTAAAT 59.874 43.478 0.00 0.00 0.00 1.40
1572 1637 0.583438 CTGCGATCTGTAAATGGCCG 59.417 55.000 0.00 0.00 30.14 6.13
1604 1670 2.030371 TGCATTGGTGACTGCAAGAAA 58.970 42.857 0.00 0.00 44.87 2.52
1605 1671 2.629137 TGCATTGGTGACTGCAAGAAAT 59.371 40.909 0.00 0.00 44.87 2.17
1614 1680 5.210715 GTGACTGCAAGAAATCAAGAACAG 58.789 41.667 0.00 0.00 37.43 3.16
1870 1936 7.259290 TCTTCAACAAGTAGGAAATGTGTTC 57.741 36.000 0.00 0.00 30.20 3.18
1879 1945 6.402222 AGTAGGAAATGTGTTCACTGAGATC 58.598 40.000 4.59 0.00 0.00 2.75
1887 1953 3.368236 GTGTTCACTGAGATCGTTTAGCC 59.632 47.826 0.00 0.00 0.00 3.93
1903 1970 1.601171 GCCCAGAGCAGATGACAGT 59.399 57.895 0.00 0.00 42.97 3.55
1907 1974 0.743701 CAGAGCAGATGACAGTGGGC 60.744 60.000 0.00 0.00 0.00 5.36
1910 1977 1.153289 GCAGATGACAGTGGGCGAT 60.153 57.895 0.00 0.00 0.00 4.58
1950 2017 9.660180 GATTTATGATTATGAACTACTCCCTCC 57.340 37.037 0.00 0.00 0.00 4.30
1951 2018 8.798975 TTTATGATTATGAACTACTCCCTCCT 57.201 34.615 0.00 0.00 0.00 3.69
1952 2019 8.798975 TTATGATTATGAACTACTCCCTCCTT 57.201 34.615 0.00 0.00 0.00 3.36
1953 2020 6.732896 TGATTATGAACTACTCCCTCCTTC 57.267 41.667 0.00 0.00 0.00 3.46
1954 2021 5.602978 TGATTATGAACTACTCCCTCCTTCC 59.397 44.000 0.00 0.00 0.00 3.46
1955 2022 3.491766 ATGAACTACTCCCTCCTTCCA 57.508 47.619 0.00 0.00 0.00 3.53
1956 2023 3.491766 TGAACTACTCCCTCCTTCCAT 57.508 47.619 0.00 0.00 0.00 3.41
1957 2024 3.375699 TGAACTACTCCCTCCTTCCATC 58.624 50.000 0.00 0.00 0.00 3.51
1958 2025 3.012959 TGAACTACTCCCTCCTTCCATCT 59.987 47.826 0.00 0.00 0.00 2.90
1959 2026 4.232122 TGAACTACTCCCTCCTTCCATCTA 59.768 45.833 0.00 0.00 0.00 1.98
1960 2027 5.103043 TGAACTACTCCCTCCTTCCATCTAT 60.103 44.000 0.00 0.00 0.00 1.98
1961 2028 6.104243 TGAACTACTCCCTCCTTCCATCTATA 59.896 42.308 0.00 0.00 0.00 1.31
1962 2029 6.744802 ACTACTCCCTCCTTCCATCTATAT 57.255 41.667 0.00 0.00 0.00 0.86
1963 2030 7.848821 ACTACTCCCTCCTTCCATCTATATA 57.151 40.000 0.00 0.00 0.00 0.86
1964 2031 8.245929 ACTACTCCCTCCTTCCATCTATATAA 57.754 38.462 0.00 0.00 0.00 0.98
1965 2032 8.340757 ACTACTCCCTCCTTCCATCTATATAAG 58.659 40.741 0.00 0.00 0.00 1.73
1966 2033 6.507568 ACTCCCTCCTTCCATCTATATAAGG 58.492 44.000 0.00 0.00 39.93 2.69
1967 2034 5.281314 TCCCTCCTTCCATCTATATAAGGC 58.719 45.833 0.00 0.00 38.70 4.35
1968 2035 4.410555 CCCTCCTTCCATCTATATAAGGCC 59.589 50.000 0.00 0.00 38.70 5.19
1969 2036 5.284582 CCTCCTTCCATCTATATAAGGCCT 58.715 45.833 0.00 0.00 38.70 5.19
1970 2037 6.444704 CCTCCTTCCATCTATATAAGGCCTA 58.555 44.000 5.16 0.00 38.70 3.93
1971 2038 6.903534 CCTCCTTCCATCTATATAAGGCCTAA 59.096 42.308 5.16 0.00 38.70 2.69
1972 2039 7.070571 CCTCCTTCCATCTATATAAGGCCTAAG 59.929 44.444 5.16 0.39 38.70 2.18
1973 2040 7.488205 TCCTTCCATCTATATAAGGCCTAAGT 58.512 38.462 5.16 0.00 38.70 2.24
1974 2041 7.962003 TCCTTCCATCTATATAAGGCCTAAGTT 59.038 37.037 5.16 0.00 38.70 2.66
1975 2042 8.606830 CCTTCCATCTATATAAGGCCTAAGTTT 58.393 37.037 5.16 0.00 32.66 2.66
1977 2044 9.793259 TTCCATCTATATAAGGCCTAAGTTTTG 57.207 33.333 5.16 0.00 0.00 2.44
1978 2045 9.166222 TCCATCTATATAAGGCCTAAGTTTTGA 57.834 33.333 5.16 0.00 0.00 2.69
1979 2046 9.793259 CCATCTATATAAGGCCTAAGTTTTGAA 57.207 33.333 5.16 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.372087 GAGCATCTCCAGCCGTTTGG 61.372 60.000 0.00 0.00 39.70 3.28
7 8 4.625800 GAGCATCTCCAGCCGTTT 57.374 55.556 0.00 0.00 0.00 3.60
23 24 8.267183 TGCAATCTTAATGTCCTCTTGATAAGA 58.733 33.333 0.00 0.00 34.84 2.10
60 64 5.064834 CACTTGATCCATTCAGTCATGTCTG 59.935 44.000 13.06 13.06 35.27 3.51
140 144 0.040781 TTTTTAGGACGCAAGCGCAC 60.041 50.000 15.09 7.60 44.19 5.34
144 148 3.914364 CACTGAATTTTTAGGACGCAAGC 59.086 43.478 0.00 0.00 45.62 4.01
147 151 3.188460 GCTCACTGAATTTTTAGGACGCA 59.812 43.478 0.00 0.00 0.00 5.24
149 153 3.678072 TCGCTCACTGAATTTTTAGGACG 59.322 43.478 0.00 0.00 0.00 4.79
167 172 1.505353 GCTGCAGCAAATCTTCGCT 59.495 52.632 33.36 0.00 41.59 4.93
219 224 1.443194 GCATCACGTTGCCTGCAAG 60.443 57.895 4.52 2.68 36.52 4.01
220 225 1.525718 ATGCATCACGTTGCCTGCAA 61.526 50.000 9.62 0.00 46.59 4.08
221 226 2.594013 TGCATCACGTTGCCTGCA 60.594 55.556 9.62 8.15 42.06 4.41
222 227 0.451383 TTATGCATCACGTTGCCTGC 59.549 50.000 0.19 5.73 42.06 4.85
223 228 2.095314 TGTTTATGCATCACGTTGCCTG 60.095 45.455 0.19 0.00 42.06 4.85
224 229 2.158559 TGTTTATGCATCACGTTGCCT 58.841 42.857 0.19 2.75 42.06 4.75
225 230 2.095263 ACTGTTTATGCATCACGTTGCC 60.095 45.455 0.19 0.00 42.06 4.52
226 231 3.201726 ACTGTTTATGCATCACGTTGC 57.798 42.857 0.19 5.26 43.07 4.17
227 232 7.166638 TGTTTTAACTGTTTATGCATCACGTTG 59.833 33.333 0.19 0.00 0.00 4.10
228 233 7.197017 TGTTTTAACTGTTTATGCATCACGTT 58.803 30.769 0.19 12.05 0.00 3.99
229 234 6.730175 TGTTTTAACTGTTTATGCATCACGT 58.270 32.000 0.19 1.89 0.00 4.49
230 235 6.305399 CCTGTTTTAACTGTTTATGCATCACG 59.695 38.462 0.19 1.27 0.00 4.35
231 236 7.326063 GTCCTGTTTTAACTGTTTATGCATCAC 59.674 37.037 0.19 1.70 0.00 3.06
232 237 7.230510 AGTCCTGTTTTAACTGTTTATGCATCA 59.769 33.333 0.19 0.00 0.00 3.07
233 238 7.593825 AGTCCTGTTTTAACTGTTTATGCATC 58.406 34.615 0.19 0.00 0.00 3.91
234 239 7.524717 AGTCCTGTTTTAACTGTTTATGCAT 57.475 32.000 3.79 3.79 0.00 3.96
235 240 6.952773 AGTCCTGTTTTAACTGTTTATGCA 57.047 33.333 0.00 0.00 0.00 3.96
236 241 7.378728 GTGAAGTCCTGTTTTAACTGTTTATGC 59.621 37.037 0.00 0.00 0.00 3.14
237 242 8.621286 AGTGAAGTCCTGTTTTAACTGTTTATG 58.379 33.333 0.00 0.00 0.00 1.90
238 243 8.747538 AGTGAAGTCCTGTTTTAACTGTTTAT 57.252 30.769 0.00 0.00 0.00 1.40
239 244 9.101655 GTAGTGAAGTCCTGTTTTAACTGTTTA 57.898 33.333 0.00 0.00 0.00 2.01
240 245 7.608761 TGTAGTGAAGTCCTGTTTTAACTGTTT 59.391 33.333 0.00 0.00 0.00 2.83
241 246 7.107542 TGTAGTGAAGTCCTGTTTTAACTGTT 58.892 34.615 0.00 0.00 0.00 3.16
242 247 6.646267 TGTAGTGAAGTCCTGTTTTAACTGT 58.354 36.000 0.00 0.00 0.00 3.55
243 248 7.548196 TTGTAGTGAAGTCCTGTTTTAACTG 57.452 36.000 0.00 0.00 0.00 3.16
244 249 8.747538 ATTTGTAGTGAAGTCCTGTTTTAACT 57.252 30.769 0.00 0.00 0.00 2.24
245 250 8.837389 AGATTTGTAGTGAAGTCCTGTTTTAAC 58.163 33.333 0.00 0.00 0.00 2.01
246 251 8.974060 AGATTTGTAGTGAAGTCCTGTTTTAA 57.026 30.769 0.00 0.00 0.00 1.52
247 252 8.208224 TGAGATTTGTAGTGAAGTCCTGTTTTA 58.792 33.333 0.00 0.00 0.00 1.52
248 253 7.012421 GTGAGATTTGTAGTGAAGTCCTGTTTT 59.988 37.037 0.00 0.00 0.00 2.43
249 254 6.483640 GTGAGATTTGTAGTGAAGTCCTGTTT 59.516 38.462 0.00 0.00 0.00 2.83
250 255 5.992217 GTGAGATTTGTAGTGAAGTCCTGTT 59.008 40.000 0.00 0.00 0.00 3.16
251 256 5.305644 AGTGAGATTTGTAGTGAAGTCCTGT 59.694 40.000 0.00 0.00 0.00 4.00
252 257 5.788450 AGTGAGATTTGTAGTGAAGTCCTG 58.212 41.667 0.00 0.00 0.00 3.86
253 258 5.336055 CGAGTGAGATTTGTAGTGAAGTCCT 60.336 44.000 0.00 0.00 0.00 3.85
254 259 4.859798 CGAGTGAGATTTGTAGTGAAGTCC 59.140 45.833 0.00 0.00 0.00 3.85
304 309 9.704098 TCGGCAAAAACAAATTGTTATTAAAAC 57.296 25.926 12.11 0.00 40.14 2.43
312 317 4.130286 TCCTCGGCAAAAACAAATTGTT 57.870 36.364 5.41 5.41 43.41 2.83
325 330 7.956328 ACTATACTTATTATCATCCTCGGCA 57.044 36.000 0.00 0.00 0.00 5.69
417 423 6.787085 AAAGAACTCGAGGTGTATTTTCTG 57.213 37.500 18.41 0.00 0.00 3.02
418 424 6.145696 CGAAAAGAACTCGAGGTGTATTTTCT 59.854 38.462 26.41 18.46 38.61 2.52
460 466 2.594592 AGTTTGGCCCAGACACGC 60.595 61.111 7.22 0.00 0.00 5.34
467 473 2.031120 CTTGAAGAACAGTTTGGCCCA 58.969 47.619 0.00 0.00 0.00 5.36
537 543 1.982073 GCAGGGTGGCTCGAAATTCG 61.982 60.000 9.38 9.38 42.10 3.34
541 547 1.074775 ATTGCAGGGTGGCTCGAAA 59.925 52.632 0.00 0.00 34.04 3.46
570 576 3.041940 GACTGACCACGTTGGCGG 61.042 66.667 0.00 0.00 42.67 6.13
798 827 4.490479 CGAAAAGAACTCGAGGCGTATTTC 60.490 45.833 18.41 17.11 38.61 2.17
883 924 0.305617 GACACGAAAACGACCCCAAC 59.694 55.000 0.00 0.00 0.00 3.77
884 925 0.814812 GGACACGAAAACGACCCCAA 60.815 55.000 0.00 0.00 0.00 4.12
915 956 2.662006 CTCAGATGGAGCGTGAAGAA 57.338 50.000 0.00 0.00 36.69 2.52
1312 1369 1.456705 GAGAGGGGATCGCCTGAGT 60.457 63.158 34.05 18.68 0.00 3.41
1380 1437 4.147321 ACAAGAATGTCAGACCAAGCAAT 58.853 39.130 0.00 0.00 33.41 3.56
1408 1465 4.711892 TGCCAGCAAATACGCAGA 57.288 50.000 0.00 0.00 0.00 4.26
1410 1467 0.804364 CTTCTGCCAGCAAATACGCA 59.196 50.000 0.00 0.00 0.00 5.24
1411 1468 0.099436 CCTTCTGCCAGCAAATACGC 59.901 55.000 0.00 0.00 0.00 4.42
1412 1469 1.737838 TCCTTCTGCCAGCAAATACG 58.262 50.000 0.00 0.00 0.00 3.06
1413 1470 2.289002 CGATCCTTCTGCCAGCAAATAC 59.711 50.000 0.00 0.00 0.00 1.89
1414 1471 2.170397 TCGATCCTTCTGCCAGCAAATA 59.830 45.455 0.00 0.00 0.00 1.40
1415 1472 1.065199 TCGATCCTTCTGCCAGCAAAT 60.065 47.619 0.00 0.00 0.00 2.32
1421 1478 0.615331 AAAGCTCGATCCTTCTGCCA 59.385 50.000 0.00 0.00 0.00 4.92
1422 1479 1.012841 CAAAGCTCGATCCTTCTGCC 58.987 55.000 0.00 0.00 0.00 4.85
1530 1587 3.569701 CACAAGTGCAGGGTGTAGAAAAT 59.430 43.478 0.00 0.00 0.00 1.82
1533 1590 2.254546 CACAAGTGCAGGGTGTAGAA 57.745 50.000 0.00 0.00 0.00 2.10
1545 1602 1.713597 TACAGATCGCAGCACAAGTG 58.286 50.000 0.00 0.00 0.00 3.16
1546 1603 2.455674 TTACAGATCGCAGCACAAGT 57.544 45.000 0.00 0.00 0.00 3.16
1549 1614 2.009051 CCATTTACAGATCGCAGCACA 58.991 47.619 0.00 0.00 0.00 4.57
1567 1632 2.604686 AGGAGAAGAGCACGGCCA 60.605 61.111 2.24 0.00 0.00 5.36
1572 1637 1.093159 CCAATGCAGGAGAAGAGCAC 58.907 55.000 0.00 0.00 41.60 4.40
1604 1670 4.882427 CCAGATTCAGATGCTGTTCTTGAT 59.118 41.667 0.00 0.00 32.61 2.57
1605 1671 4.259356 CCAGATTCAGATGCTGTTCTTGA 58.741 43.478 0.00 0.00 32.61 3.02
1649 1715 1.630244 CCTGAAAGAAGGAGCACGCG 61.630 60.000 3.53 3.53 40.02 6.01
1728 1794 1.299976 GCCCCAAGAACCTGACGAT 59.700 57.895 0.00 0.00 0.00 3.73
1821 1887 0.762418 TTCAGTCCAAGCTTCGGGAA 59.238 50.000 7.08 4.64 34.34 3.97
1870 1936 2.166459 TCTGGGCTAAACGATCTCAGTG 59.834 50.000 0.00 0.00 0.00 3.66
1879 1945 1.134699 TCATCTGCTCTGGGCTAAACG 60.135 52.381 0.00 0.00 42.39 3.60
1887 1953 0.107800 CCCACTGTCATCTGCTCTGG 60.108 60.000 0.00 0.00 0.00 3.86
1895 1961 1.000283 CCTAGATCGCCCACTGTCATC 60.000 57.143 0.00 0.00 0.00 2.92
1903 1970 2.693591 CAAACTAGACCTAGATCGCCCA 59.306 50.000 10.74 0.00 36.97 5.36
1940 2007 7.782644 CCTTATATAGATGGAAGGAGGGAGTAG 59.217 44.444 0.00 0.00 40.88 2.57
1944 2011 5.281314 GCCTTATATAGATGGAAGGAGGGA 58.719 45.833 3.56 0.00 40.88 4.20
1945 2012 4.410555 GGCCTTATATAGATGGAAGGAGGG 59.589 50.000 0.00 0.00 40.88 4.30
1946 2013 5.284582 AGGCCTTATATAGATGGAAGGAGG 58.715 45.833 0.00 0.00 40.88 4.30
1947 2014 7.621683 ACTTAGGCCTTATATAGATGGAAGGAG 59.378 40.741 12.58 0.00 40.88 3.69
1948 2015 7.488205 ACTTAGGCCTTATATAGATGGAAGGA 58.512 38.462 12.58 0.00 40.88 3.36
1949 2016 7.741554 ACTTAGGCCTTATATAGATGGAAGG 57.258 40.000 12.58 0.00 41.26 3.46
1951 2018 9.793259 CAAAACTTAGGCCTTATATAGATGGAA 57.207 33.333 12.58 0.00 0.00 3.53
1952 2019 9.166222 TCAAAACTTAGGCCTTATATAGATGGA 57.834 33.333 12.58 0.00 0.00 3.41
1953 2020 9.793259 TTCAAAACTTAGGCCTTATATAGATGG 57.207 33.333 12.58 0.00 0.00 3.51
1961 2028 8.773216 ACTAGAGATTCAAAACTTAGGCCTTAT 58.227 33.333 12.58 0.00 0.00 1.73
1962 2029 8.147244 ACTAGAGATTCAAAACTTAGGCCTTA 57.853 34.615 12.58 0.00 0.00 2.69
1963 2030 7.021998 ACTAGAGATTCAAAACTTAGGCCTT 57.978 36.000 12.58 0.00 0.00 4.35
1964 2031 6.628644 ACTAGAGATTCAAAACTTAGGCCT 57.371 37.500 11.78 11.78 0.00 5.19
1965 2032 7.557724 AGTACTAGAGATTCAAAACTTAGGCC 58.442 38.462 0.00 0.00 0.00 5.19
1966 2033 7.707464 GGAGTACTAGAGATTCAAAACTTAGGC 59.293 40.741 0.00 0.00 0.00 3.93
1967 2034 8.198778 GGGAGTACTAGAGATTCAAAACTTAGG 58.801 40.741 0.00 0.00 0.00 2.69
1968 2035 8.973182 AGGGAGTACTAGAGATTCAAAACTTAG 58.027 37.037 0.00 0.00 0.00 2.18
1969 2036 8.896722 AGGGAGTACTAGAGATTCAAAACTTA 57.103 34.615 0.00 0.00 0.00 2.24
1970 2037 7.093245 GGAGGGAGTACTAGAGATTCAAAACTT 60.093 40.741 0.00 0.00 0.00 2.66
1971 2038 6.381707 GGAGGGAGTACTAGAGATTCAAAACT 59.618 42.308 0.00 0.00 0.00 2.66
1972 2039 6.381707 AGGAGGGAGTACTAGAGATTCAAAAC 59.618 42.308 0.00 0.00 0.00 2.43
1973 2040 6.503944 AGGAGGGAGTACTAGAGATTCAAAA 58.496 40.000 0.00 0.00 0.00 2.44
1974 2041 6.093617 AGGAGGGAGTACTAGAGATTCAAA 57.906 41.667 0.00 0.00 0.00 2.69
1975 2042 5.735733 AGGAGGGAGTACTAGAGATTCAA 57.264 43.478 0.00 0.00 0.00 2.69
1976 2043 5.399267 GGAAGGAGGGAGTACTAGAGATTCA 60.399 48.000 0.00 0.00 0.00 2.57
1977 2044 5.074804 GGAAGGAGGGAGTACTAGAGATTC 58.925 50.000 0.00 0.00 0.00 2.52
1978 2045 4.482772 TGGAAGGAGGGAGTACTAGAGATT 59.517 45.833 0.00 0.00 0.00 2.40
1979 2046 4.055820 TGGAAGGAGGGAGTACTAGAGAT 58.944 47.826 0.00 0.00 0.00 2.75
1980 2047 3.471879 TGGAAGGAGGGAGTACTAGAGA 58.528 50.000 0.00 0.00 0.00 3.10
1981 2048 3.955524 TGGAAGGAGGGAGTACTAGAG 57.044 52.381 0.00 0.00 0.00 2.43
1982 2049 4.055820 AGATGGAAGGAGGGAGTACTAGA 58.944 47.826 0.00 0.00 0.00 2.43
1983 2050 4.463050 AGATGGAAGGAGGGAGTACTAG 57.537 50.000 0.00 0.00 0.00 2.57
1984 2051 7.848821 ATATAGATGGAAGGAGGGAGTACTA 57.151 40.000 0.00 0.00 0.00 1.82
1985 2052 6.744802 ATATAGATGGAAGGAGGGAGTACT 57.255 41.667 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.