Multiple sequence alignment - TraesCS3B01G423100

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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 TraesCS3B01G423100 chr3B 100.000 2339 0 0 1 2339 660332195 660334533 0.000000e+00 4320
1 TraesCS3B01G423100 chr3D 95.441 2347 84 9 1 2339 499597675 499600006 0.000000e+00 3720
2 TraesCS3B01G423100 chr3D 94.216 1141 53 6 1 1135 225357596 225358729 0.000000e+00 1729
3 TraesCS3B01G423100 chr3D 84.971 1364 188 13 3 1359 300565481 300566834 0.000000e+00 1367
4 TraesCS3B01G423100 chr3D 87.054 224 18 4 1472 1684 499594000 499593777 2.320000e-60 243
5 TraesCS3B01G423100 chr5D 93.933 1368 74 6 2 1362 117351130 117352495 0.000000e+00 2058
6 TraesCS3B01G423100 chr6D 93.050 1367 85 7 3 1362 158872462 158871099 0.000000e+00 1989
7 TraesCS3B01G423100 chr6D 85.777 1364 186 7 3 1362 48683473 48682114 0.000000e+00 1437
8 TraesCS3B01G423100 chr2B 91.387 1370 104 11 3 1362 361567414 361568779 0.000000e+00 1864
9 TraesCS3B01G423100 chr2B 83.871 124 19 1 1561 1684 182845744 182845866 1.470000e-22 117
10 TraesCS3B01G423100 chr1D 86.404 1368 171 12 3 1362 216023919 216022559 0.000000e+00 1482
11 TraesCS3B01G423100 chr2D 85.359 1366 185 15 3 1362 574398710 574397354 0.000000e+00 1400
12 TraesCS3B01G423100 chr6B 91.768 656 42 3 1685 2339 295781466 295782110 0.000000e+00 902
13 TraesCS3B01G423100 chr7B 91.077 650 48 1 1690 2339 679174035 679173396 0.000000e+00 870
14 TraesCS3B01G423100 chr5B 90.382 655 52 2 1685 2339 139195378 139194735 0.000000e+00 850
15 TraesCS3B01G423100 chr5B 84.545 110 15 2 1577 1685 549123676 549123568 8.840000e-20 108
16 TraesCS3B01G423100 chr5B 80.420 143 23 5 1543 1684 549165412 549165550 1.140000e-18 104
17 TraesCS3B01G423100 chr3A 86.350 652 74 7 1688 2339 375744129 375743493 0.000000e+00 697
18 TraesCS3B01G423100 chr3A 83.019 159 26 1 1822 1979 511997834 511997676 2.420000e-30 143
19 TraesCS3B01G423100 chr7D 86.239 109 15 0 1577 1685 638400294 638400402 4.080000e-23 119
20 TraesCS3B01G423100 chr7D 82.069 145 18 8 1543 1684 459895472 459895611 1.470000e-22 117
21 TraesCS3B01G423100 chr6A 78.431 204 27 10 1496 1686 92886745 92886546 1.470000e-22 117
22 TraesCS3B01G423100 chr7A 83.065 124 20 1 1561 1684 617979749 617979627 6.830000e-21 111


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 TraesCS3B01G423100 chr3B 660332195 660334533 2338 False 4320 4320 100.000 1 2339 1 chr3B.!!$F1 2338
1 TraesCS3B01G423100 chr3D 499597675 499600006 2331 False 3720 3720 95.441 1 2339 1 chr3D.!!$F3 2338
2 TraesCS3B01G423100 chr3D 225357596 225358729 1133 False 1729 1729 94.216 1 1135 1 chr3D.!!$F1 1134
3 TraesCS3B01G423100 chr3D 300565481 300566834 1353 False 1367 1367 84.971 3 1359 1 chr3D.!!$F2 1356
4 TraesCS3B01G423100 chr5D 117351130 117352495 1365 False 2058 2058 93.933 2 1362 1 chr5D.!!$F1 1360
5 TraesCS3B01G423100 chr6D 158871099 158872462 1363 True 1989 1989 93.050 3 1362 1 chr6D.!!$R2 1359
6 TraesCS3B01G423100 chr6D 48682114 48683473 1359 True 1437 1437 85.777 3 1362 1 chr6D.!!$R1 1359
7 TraesCS3B01G423100 chr2B 361567414 361568779 1365 False 1864 1864 91.387 3 1362 1 chr2B.!!$F2 1359
8 TraesCS3B01G423100 chr1D 216022559 216023919 1360 True 1482 1482 86.404 3 1362 1 chr1D.!!$R1 1359
9 TraesCS3B01G423100 chr2D 574397354 574398710 1356 True 1400 1400 85.359 3 1362 1 chr2D.!!$R1 1359
10 TraesCS3B01G423100 chr6B 295781466 295782110 644 False 902 902 91.768 1685 2339 1 chr6B.!!$F1 654
11 TraesCS3B01G423100 chr7B 679173396 679174035 639 True 870 870 91.077 1690 2339 1 chr7B.!!$R1 649
12 TraesCS3B01G423100 chr5B 139194735 139195378 643 True 850 850 90.382 1685 2339 1 chr5B.!!$R1 654
13 TraesCS3B01G423100 chr3A 375743493 375744129 636 True 697 697 86.350 1688 2339 1 chr3A.!!$R1 651

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
953 962 1.193323 AGAGATGACAGAGGCAGGTG 58.807 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 2320 1.456892 ATATGGTGGTCCTCGGCGA 60.457 57.895 10.14 10.14 34.23 5.54 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
31 32 8.842280 GGGAACGGACATAACATTAATATTTGA 58.158 33.333 0.00 0.00 0.00 2.69
205 206 4.516652 AAGGATTCTCTCAATTCCCCTG 57.483 45.455 0.00 0.00 0.00 4.45
248 249 3.530265 TCGTTGCCTGGAATTATACGT 57.470 42.857 0.00 0.00 0.00 3.57
346 348 2.512974 GGTATGGGGCGAACCACG 60.513 66.667 0.25 0.00 45.43 4.94
389 391 9.494271 GTAAGATATGGAAATTAGCATGTCTGA 57.506 33.333 0.00 0.00 0.00 3.27
390 392 8.985315 AAGATATGGAAATTAGCATGTCTGAA 57.015 30.769 0.00 0.00 0.00 3.02
587 589 5.872963 TGGGACTGGATGATATCATTGAAG 58.127 41.667 19.11 17.24 36.57 3.02
661 663 5.249393 ACTCCTACCAGATCAAGATTTGTGT 59.751 40.000 0.00 1.59 0.00 3.72
724 726 2.639839 AGCATGGTACCTATGATGGGAC 59.360 50.000 21.45 0.00 40.20 4.46
803 808 3.252554 TCCTTGCCCTTACCACATTTT 57.747 42.857 0.00 0.00 0.00 1.82
850 859 3.711704 TCTGTGAAGGAGAGTTGGTCTTT 59.288 43.478 0.00 0.00 34.71 2.52
878 887 5.299279 TCCAAGAGGTTTTGTTAAGCTCAAG 59.701 40.000 16.23 9.32 44.67 3.02
913 922 6.006449 CCTTTGATCATGACCTTATTAGGGG 58.994 44.000 0.00 0.00 46.58 4.79
953 962 1.193323 AGAGATGACAGAGGCAGGTG 58.807 55.000 0.00 0.00 0.00 4.00
1108 1118 7.862274 ATGGAGGTGATTGACTCTATGAATA 57.138 36.000 0.00 0.00 34.24 1.75
1219 1229 7.396055 AGCACTGTAATAGGGAAGCAAATAAAA 59.604 33.333 0.00 0.00 0.00 1.52
1263 1273 8.134895 AGATTAGCTAGATTCTCTTTGACTTCG 58.865 37.037 0.00 0.00 0.00 3.79
1516 1528 4.632688 GCTTTCTGCAAAAATATGTGCCAT 59.367 37.500 0.00 0.00 40.14 4.40
1527 1539 0.401356 ATGTGCCATGTGTCACCTGA 59.599 50.000 9.59 0.00 32.51 3.86
1752 1764 3.785859 CAAGCTAGGGAGGCGGCA 61.786 66.667 13.08 0.00 34.52 5.69
1797 1809 1.086067 CAGCTACCTACCGACGACGA 61.086 60.000 9.28 0.00 42.66 4.20
1803 1815 0.027716 CCTACCGACGACGACATCAG 59.972 60.000 9.28 0.00 42.66 2.90
1973 1986 3.613877 TTCCAACCATGCGCCGCTA 62.614 57.895 11.67 0.00 0.00 4.26
2038 2051 2.031163 GGTCCAGCTGCTGTTCGT 59.969 61.111 26.41 0.00 0.00 3.85
2068 2081 2.987547 GCCAGCCTGCATGTGTGT 60.988 61.111 0.00 0.00 0.00 3.72
2114 2127 1.004979 AGTAGGTGCTTCTCTCCGTCT 59.995 52.381 0.00 0.00 33.65 4.18
2204 2217 1.609061 GGCTACTGTTGCTGCTTCTCA 60.609 52.381 13.54 0.00 0.00 3.27
2206 2219 2.746362 GCTACTGTTGCTGCTTCTCATT 59.254 45.455 6.98 0.00 0.00 2.57
2222 2235 1.004628 TCATTGGCACCACATACTGCT 59.995 47.619 0.00 0.00 33.63 4.24
2237 2250 1.138464 ACTGCTGATGATGATGCTCGT 59.862 47.619 0.00 0.00 0.00 4.18
2280 2293 0.171455 GGCACCTAGTCACGACTCAG 59.829 60.000 2.26 0.00 42.54 3.35
2300 2313 0.898789 CGTGGTCACTGGGAGGTAGT 60.899 60.000 0.00 0.00 0.00 2.73
2307 2320 1.828660 CTGGGAGGTAGTCGGCGAT 60.829 63.158 14.79 4.89 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.600058 TTGGGATCCAGGCATCTTCT 58.400 50.000 15.23 0.00 33.81 2.85
131 132 4.552883 TCAGGTCTCCATCCCAAGTATA 57.447 45.455 0.00 0.00 0.00 1.47
205 206 3.438087 AGTCTTGCATATCATATTGCGGC 59.562 43.478 0.00 0.00 41.80 6.53
309 311 8.739039 CCATACCATTAGAGTGTTTCAATTTGA 58.261 33.333 0.00 0.00 0.00 2.69
587 589 1.929836 ACGATCAATCTCGCAAGCTTC 59.070 47.619 0.00 0.00 42.35 3.86
661 663 3.131933 GCACATTGTGGCAACCCAATATA 59.868 43.478 18.05 0.00 44.33 0.86
724 726 4.035091 TCATTGTGAACCAACTTTCGTCTG 59.965 41.667 0.00 0.00 35.44 3.51
765 767 3.985127 AGGATTCCCATTGAAATCTGCA 58.015 40.909 0.00 0.00 36.33 4.41
821 827 0.318441 TCTCCTTCACAGACGCCTTG 59.682 55.000 0.00 0.00 0.00 3.61
872 881 1.831580 AGGAAGCATCAACCTTGAGC 58.168 50.000 0.00 0.00 41.08 4.26
878 887 4.400251 TCATGATCAAAGGAAGCATCAACC 59.600 41.667 0.00 0.00 0.00 3.77
913 922 0.324645 AGCATTGGTCCCATTGTCCC 60.325 55.000 9.31 0.00 32.01 4.46
953 962 3.389329 TCTCTCATTCCCTCCAGCAATAC 59.611 47.826 0.00 0.00 0.00 1.89
1108 1118 4.473520 CGCCGACTGCCCTCCATT 62.474 66.667 0.00 0.00 36.24 3.16
1130 1140 1.177895 TTTGAAGATTGCTGCCGCCA 61.178 50.000 0.00 0.00 34.43 5.69
1251 1261 4.515191 TCAAACCAATCCGAAGTCAAAGAG 59.485 41.667 0.00 0.00 0.00 2.85
1263 1273 2.222227 AAGGCTCCTCAAACCAATCC 57.778 50.000 0.00 0.00 0.00 3.01
1364 1376 0.170561 CCTCTACACTACACGCGCTT 59.829 55.000 5.73 0.00 0.00 4.68
1396 1408 4.552365 CGAGCCCCCGCATCACAT 62.552 66.667 0.00 0.00 37.52 3.21
1410 1422 2.585247 GGGATTCGAACCGGCGAG 60.585 66.667 9.30 0.06 41.79 5.03
1456 1468 4.916870 CGTAATCACGTAGATGTCCTTCA 58.083 43.478 0.00 0.00 43.31 3.02
1575 1587 4.935352 AGAGCCTAATTGTTGCAAAACA 57.065 36.364 0.00 0.00 0.00 2.83
1797 1809 3.717294 GGTGGGGCGGTCTGATGT 61.717 66.667 0.00 0.00 0.00 3.06
2021 2034 2.029844 GACGAACAGCAGCTGGACC 61.030 63.158 26.38 13.15 35.51 4.46
2058 2071 2.743664 GCATAGAGTCAACACACATGCA 59.256 45.455 0.00 0.00 37.74 3.96
2068 2081 5.510349 GCATCCATCTAGTGCATAGAGTCAA 60.510 44.000 10.34 0.55 43.78 3.18
2204 2217 3.985410 AGCAGTATGTGGTGCCAAT 57.015 47.368 0.00 0.00 40.81 3.16
2222 2235 1.861971 GCTGACGAGCATCATCATCA 58.138 50.000 0.00 0.00 45.46 3.07
2280 2293 2.227089 CTACCTCCCAGTGACCACGC 62.227 65.000 0.00 0.00 36.20 5.34
2307 2320 1.456892 ATATGGTGGTCCTCGGCGA 60.457 57.895 10.14 10.14 34.23 5.54


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

AutoCloner maintained by Alex Coulton.