Multiple sequence alignment - TraesCS2B01G181600

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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 TraesCS2B01G181600 chr2B 100.000 3207 0 0 1 3207 156594091 156590885 0.000000e+00 5923
1 TraesCS2B01G181600 chr2B 100.000 521 0 0 3433 3953 156590659 156590139 0.000000e+00 963
2 TraesCS2B01G181600 chr2B 84.422 398 52 5 1470 1865 795318205 795317816 2.230000e-102 383
3 TraesCS2B01G181600 chr2B 87.755 196 22 2 1647 1840 156592301 156592106 1.110000e-55 228
4 TraesCS2B01G181600 chr2B 87.755 196 22 2 1791 1986 156592445 156592252 1.110000e-55 228
5 TraesCS2B01G181600 chr2D 92.906 2904 117 42 341 3207 106628661 106625810 0.000000e+00 4139
6 TraesCS2B01G181600 chr2D 88.390 534 32 11 3433 3953 106625755 106625239 2.020000e-172 616
7 TraesCS2B01G181600 chr2D 95.627 343 14 1 6 348 106629165 106628824 2.080000e-152 549
8 TraesCS2B01G181600 chr2D 85.533 394 48 4 1470 1861 622712191 622712577 1.710000e-108 403
9 TraesCS2B01G181600 chr2D 92.784 194 13 1 1791 1984 106627396 106627204 3.010000e-71 279
10 TraesCS2B01G181600 chr2D 89.583 192 19 1 1650 1840 106627247 106627056 3.950000e-60 243
11 TraesCS2B01G181600 chr2A 94.812 983 22 5 2253 3207 103099731 103098750 0.000000e+00 1506
12 TraesCS2B01G181600 chr2A 92.716 810 49 8 620 1424 103101292 103100488 0.000000e+00 1160
13 TraesCS2B01G181600 chr2A 90.168 773 68 3 1452 2222 103100490 103099724 0.000000e+00 1000
14 TraesCS2B01G181600 chr2A 90.590 542 28 9 3433 3953 103098701 103098162 0.000000e+00 697
15 TraesCS2B01G181600 chr2A 89.412 425 31 5 1007 1424 251390719 251391136 1.260000e-144 523
16 TraesCS2B01G181600 chr2A 88.020 409 37 9 1 398 103101878 103101471 1.290000e-129 473
17 TraesCS2B01G181600 chr2A 84.422 398 52 5 1470 1865 762079178 762079567 2.230000e-102 383
18 TraesCS2B01G181600 chr7D 90.597 787 65 4 1470 2254 475097436 475096657 0.000000e+00 1035
19 TraesCS2B01G181600 chr4D 89.814 805 68 8 1452 2254 46139514 46138722 0.000000e+00 1020
20 TraesCS2B01G181600 chr4D 93.810 420 20 1 1005 1424 46139925 46139512 9.330000e-176 627
21 TraesCS2B01G181600 chr4D 90.692 419 33 1 1006 1424 45005469 45005057 1.610000e-153 553
22 TraesCS2B01G181600 chr1A 89.737 419 37 1 1006 1424 570975257 570974845 7.520000e-147 531
23 TraesCS2B01G181600 chr1A 90.244 369 27 1 1886 2254 570974433 570974074 1.290000e-129 473
24 TraesCS2B01G181600 chr5B 89.286 420 39 1 1005 1424 236414536 236414949 4.530000e-144 521
25 TraesCS2B01G181600 chr5B 88.810 420 41 1 1005 1424 236737069 236737482 9.800000e-141 510
26 TraesCS2B01G181600 chr5A 88.571 420 36 4 1005 1424 669523780 669523373 2.120000e-137 499


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 TraesCS2B01G181600 chr2B 156590139 156594091 3952 True 1835.5 5923 93.8775 1 3953 4 chr2B.!!$R2 3952
1 TraesCS2B01G181600 chr2D 106625239 106629165 3926 True 1165.2 4139 91.8580 6 3953 5 chr2D.!!$R1 3947
2 TraesCS2B01G181600 chr2A 103098162 103101878 3716 True 967.2 1506 91.2612 1 3953 5 chr2A.!!$R1 3952
3 TraesCS2B01G181600 chr7D 475096657 475097436 779 True 1035.0 1035 90.5970 1470 2254 1 chr7D.!!$R1 784
4 TraesCS2B01G181600 chr4D 46138722 46139925 1203 True 823.5 1020 91.8120 1005 2254 2 chr4D.!!$R2 1249
5 TraesCS2B01G181600 chr1A 570974074 570975257 1183 True 502.0 531 89.9905 1006 2254 2 chr1A.!!$R1 1248

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
293 300 0.449388 GTGTGCTAGCCATGTCTTGC 59.551 55.0 13.29 3.15 35.81 4.01 F
601 811 0.451783 CAGTTGCGGTGGGCTTTATC 59.548 55.0 0.00 0.00 44.05 1.75 F
1479 1727 0.751277 TCGGCAATGCATGGTTAGGG 60.751 55.0 7.79 0.00 0.00 3.53 F
1790 2040 2.096013 GCTTGAACTAGGTCGAATTGGC 59.904 50.0 2.72 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1884 0.107165 ATTTACGAGGCCCCTGAAGC 60.107 55.000 0.0 0.0 0.00 3.86 R
1683 1932 1.375140 CGTCCATGCACAGCTCTGT 60.375 57.895 0.0 0.0 46.17 3.41 R
2502 2823 3.174987 CTGGGTGGTGGTGGTCCA 61.175 66.667 0.0 0.0 42.05 4.02 R
3572 3931 1.367599 ATCCGACTCGACCGTCTCAC 61.368 60.000 0.0 0.0 0.00 3.51 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
116 117 1.741706 AGCGAATGACATTTGAGCAGG 59.258 47.619 18.05 0.00 0.00 4.85
205 207 2.821378 TGATGTTTGGAGGAGCACAATG 59.179 45.455 0.00 0.00 0.00 2.82
248 250 2.723124 TTTTGGCAAAAGAGCGGATC 57.277 45.000 20.81 0.00 34.64 3.36
293 300 0.449388 GTGTGCTAGCCATGTCTTGC 59.551 55.000 13.29 3.15 35.81 4.01
318 330 2.151202 TGCATTCGAAACCTTGAGACC 58.849 47.619 0.00 0.00 0.00 3.85
416 623 5.385198 TGGGACTGGGATGCTATAAAATTC 58.615 41.667 0.00 0.00 0.00 2.17
432 639 2.414994 ATTCTGTGCTGCTGCTATGT 57.585 45.000 17.00 0.00 40.48 2.29
433 640 3.548745 ATTCTGTGCTGCTGCTATGTA 57.451 42.857 17.00 0.39 40.48 2.29
501 708 9.093970 GTTTTTACCACTTTCAACAAGCTAATT 57.906 29.630 0.00 0.00 0.00 1.40
506 713 5.241506 CCACTTTCAACAAGCTAATTCCTCA 59.758 40.000 0.00 0.00 0.00 3.86
510 717 8.257306 ACTTTCAACAAGCTAATTCCTCAAAAA 58.743 29.630 0.00 0.00 0.00 1.94
589 799 0.588252 CCACTTCACTTCCAGTTGCG 59.412 55.000 0.00 0.00 0.00 4.85
601 811 0.451783 CAGTTGCGGTGGGCTTTATC 59.548 55.000 0.00 0.00 44.05 1.75
735 982 4.615588 TCCCATCCAATTCCAACAAAAC 57.384 40.909 0.00 0.00 0.00 2.43
783 1031 3.067091 CTGGCCTCTCACACTGCT 58.933 61.111 3.32 0.00 0.00 4.24
809 1057 1.307343 CCACACCCCCTCTCATCCT 60.307 63.158 0.00 0.00 0.00 3.24
811 1059 1.418334 CACACCCCCTCTCATCCTAG 58.582 60.000 0.00 0.00 0.00 3.02
830 1078 3.214696 AGCCCCAGAAAAATATCTCCG 57.785 47.619 0.00 0.00 0.00 4.63
832 1080 1.873591 CCCCAGAAAAATATCTCCGCG 59.126 52.381 0.00 0.00 0.00 6.46
833 1081 2.484770 CCCCAGAAAAATATCTCCGCGA 60.485 50.000 8.23 0.00 0.00 5.87
834 1082 2.802816 CCCAGAAAAATATCTCCGCGAG 59.197 50.000 8.23 3.02 0.00 5.03
884 1132 2.111878 CTGGCCGTCCATCCATCC 59.888 66.667 0.00 0.00 42.51 3.51
885 1133 3.814615 CTGGCCGTCCATCCATCCG 62.815 68.421 0.00 0.00 42.51 4.18
889 1137 3.550431 CGTCCATCCATCCGCCCT 61.550 66.667 0.00 0.00 0.00 5.19
945 1193 1.377333 CTCACCCCTTTCCCTTCGC 60.377 63.158 0.00 0.00 0.00 4.70
1362 1610 5.855045 GAGATGGTCGAGGTATAATTTGGT 58.145 41.667 0.00 0.00 0.00 3.67
1374 1622 6.040616 AGGTATAATTTGGTACTCTCTGGTCG 59.959 42.308 0.00 0.00 0.00 4.79
1390 1638 5.045215 TCTGGTCGTGTTAACTAACAGTTG 58.955 41.667 15.91 0.00 45.82 3.16
1424 1672 7.115805 GCAAGTTGTAATGGGCTAAAGTTAAAC 59.884 37.037 4.48 0.00 0.00 2.01
1466 1714 2.509569 TGGTAAAATTCTGCTCGGCAA 58.490 42.857 0.35 0.00 38.41 4.52
1479 1727 0.751277 TCGGCAATGCATGGTTAGGG 60.751 55.000 7.79 0.00 0.00 3.53
1513 1761 3.999663 GAGTCAGGACATTCTGTTTCAGG 59.000 47.826 1.84 0.00 36.25 3.86
1528 1776 4.202284 TGTTTCAGGGTAGTGTCAGGTTAC 60.202 45.833 0.00 0.00 0.00 2.50
1554 1802 5.391843 CGATGGATGTTGAATTGTTGCTGTA 60.392 40.000 0.00 0.00 0.00 2.74
1616 1865 6.815641 ACTGTAAATTGTCTCAGCATAGAGTG 59.184 38.462 0.00 0.00 36.97 3.51
1634 1883 4.039245 AGAGTGAGTTCGAATTGGTTCAGA 59.961 41.667 0.00 0.00 33.86 3.27
1635 1884 4.310769 AGTGAGTTCGAATTGGTTCAGAG 58.689 43.478 0.00 0.00 33.86 3.35
1725 1974 7.094032 ACGTGGAGTTATTATACCAGTATAGGC 60.094 40.741 0.00 0.00 32.89 3.93
1779 2028 5.712152 AAAATGGTCTTGGCTTGAACTAG 57.288 39.130 0.00 0.00 0.00 2.57
1790 2040 2.096013 GCTTGAACTAGGTCGAATTGGC 59.904 50.000 2.72 0.00 0.00 4.52
2206 2523 7.122948 TGGTACATTACATGGGTTTAAATGACC 59.877 37.037 0.00 7.41 36.41 4.02
2214 2531 4.735369 TGGGTTTAAATGACCATCTGTGT 58.265 39.130 5.45 0.00 38.98 3.72
2502 2823 3.837399 AGACCTCTCAGGGTTAACTCT 57.163 47.619 0.85 0.85 40.58 3.24
2794 3118 1.069378 CGACGGCGTGGTAAGTTCTC 61.069 60.000 21.19 0.00 0.00 2.87
2872 3221 3.833706 GCTAATTGAGCGCATGGTC 57.166 52.632 11.47 0.00 42.62 4.02
2892 3241 3.444388 GTCTTGTTCTGTAGGACCTCGAT 59.556 47.826 0.00 0.00 0.00 3.59
2977 3326 2.025155 TCCTGACGCTGGTTAGAGATC 58.975 52.381 0.00 0.00 31.74 2.75
2989 3338 6.457934 GCTGGTTAGAGATCAATCATGTGTTG 60.458 42.308 0.00 7.10 0.00 3.33
3111 3460 0.815095 TCGTTGCGCCTCTTGATAGA 59.185 50.000 4.18 0.00 0.00 1.98
3460 3810 6.012858 TGCCTTTTTCTAGATGAAGTCCCTAA 60.013 38.462 12.17 0.00 35.89 2.69
3461 3811 6.884836 GCCTTTTTCTAGATGAAGTCCCTAAA 59.115 38.462 12.17 0.00 35.89 1.85
3542 3901 5.607119 AACCACACTAAATTGTCATCGAC 57.393 39.130 0.00 0.00 0.00 4.20
3614 3978 3.958798 CGATGGTCTAACCCTCTTCCTAA 59.041 47.826 0.00 0.00 37.50 2.69
3627 3991 5.046014 CCCTCTTCCTAATCCGATCATCAAT 60.046 44.000 0.00 0.00 0.00 2.57
3674 4038 2.180159 GAAGCCAGTTCAGCCGGGTA 62.180 60.000 5.47 0.00 34.97 3.69
3718 4082 2.466571 GCGTGTACGTACATGACATAGC 59.533 50.000 39.18 25.65 44.02 2.97
3719 4083 3.791122 GCGTGTACGTACATGACATAGCT 60.791 47.826 39.18 0.00 44.02 3.32
3834 4206 1.194781 ACTCGACCATGGCTCAGGTT 61.195 55.000 13.04 0.00 38.50 3.50
3925 4297 1.519719 GACCATCAGCTCGCCTCTT 59.480 57.895 0.00 0.00 0.00 2.85
3936 4308 0.740868 TCGCCTCTTCAAGCAATCCG 60.741 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 2.932498 TGCGAATCTGAAAACATGTGC 58.068 42.857 0.00 0.00 0.00 4.57
205 207 2.436417 ACAATCACCACAGCCATGTAC 58.564 47.619 0.00 0.00 37.65 2.90
245 247 5.044558 AGATTTTCTCTCGGCTAAACGATC 58.955 41.667 0.00 0.00 42.62 3.69
248 250 4.389077 ACAAGATTTTCTCTCGGCTAAACG 59.611 41.667 0.00 0.00 31.03 3.60
293 300 4.631377 TCTCAAGGTTTCGAATGCATACTG 59.369 41.667 0.00 0.00 0.00 2.74
318 330 8.338259 CCATAGAATGATACAAAGTTCCGAAAG 58.662 37.037 0.00 0.00 0.00 2.62
371 553 3.658757 GCTGTCAGCCCAAAATACAAA 57.341 42.857 14.27 0.00 34.48 2.83
416 623 2.306341 ACTACATAGCAGCAGCACAG 57.694 50.000 3.17 0.00 45.49 3.66
432 639 6.745907 CGAAACAACAACGAGATGAGATACTA 59.254 38.462 0.00 0.00 0.00 1.82
433 640 5.573282 CGAAACAACAACGAGATGAGATACT 59.427 40.000 0.00 0.00 0.00 2.12
501 708 8.314751 TCAAGGTAAACACAAAATTTTTGAGGA 58.685 29.630 24.73 7.43 0.00 3.71
589 799 2.128771 TGCTGAAGATAAAGCCCACC 57.871 50.000 0.00 0.00 38.71 4.61
647 890 2.270923 CTAGCAAGCATCGTTAGCACA 58.729 47.619 0.00 0.00 0.00 4.57
697 944 5.821470 GGATGGGATAATGCACTATCATCAG 59.179 44.000 16.38 0.00 31.01 2.90
704 951 5.163001 TGGAATTGGATGGGATAATGCACTA 60.163 40.000 0.00 0.00 0.00 2.74
735 982 2.977405 GCTGGAAACTAGCTGTGTTG 57.023 50.000 0.00 0.00 38.14 3.33
790 1038 2.592308 GATGAGAGGGGGTGTGGC 59.408 66.667 0.00 0.00 0.00 5.01
809 1057 3.496160 GCGGAGATATTTTTCTGGGGCTA 60.496 47.826 0.00 0.00 0.00 3.93
811 1059 1.609072 GCGGAGATATTTTTCTGGGGC 59.391 52.381 0.00 0.00 0.00 5.80
830 1078 1.845809 CGGCTGGATATTTGCCTCGC 61.846 60.000 11.14 0.00 44.09 5.03
832 1080 1.334869 CAACGGCTGGATATTTGCCTC 59.665 52.381 0.00 0.00 44.09 4.70
833 1081 1.392589 CAACGGCTGGATATTTGCCT 58.607 50.000 0.00 0.00 44.09 4.75
834 1082 3.944871 CAACGGCTGGATATTTGCC 57.055 52.632 0.00 0.00 42.94 4.52
884 1132 3.200483 GGGTTTTATAGTGTACAGGGCG 58.800 50.000 0.00 0.00 0.00 6.13
885 1133 3.548770 GGGGTTTTATAGTGTACAGGGC 58.451 50.000 0.00 0.00 0.00 5.19
889 1137 4.225717 GTGGAGGGGGTTTTATAGTGTACA 59.774 45.833 0.00 0.00 0.00 2.90
1357 1605 2.313317 ACACGACCAGAGAGTACCAAA 58.687 47.619 0.00 0.00 0.00 3.28
1361 1609 4.762956 AGTTAACACGACCAGAGAGTAC 57.237 45.455 8.61 0.00 0.00 2.73
1362 1610 5.764686 TGTTAGTTAACACGACCAGAGAGTA 59.235 40.000 8.61 0.00 40.93 2.59
1374 1622 5.038683 GCCAAACCAACTGTTAGTTAACAC 58.961 41.667 8.61 0.00 40.93 3.32
1390 1638 2.058057 CATTACAACTTGCGCCAAACC 58.942 47.619 4.18 0.00 0.00 3.27
1443 1691 3.509575 TGCCGAGCAGAATTTTACCAATT 59.490 39.130 0.00 0.00 33.32 2.32
1445 1693 2.509569 TGCCGAGCAGAATTTTACCAA 58.490 42.857 0.00 0.00 33.32 3.67
1447 1695 3.438360 CATTGCCGAGCAGAATTTTACC 58.562 45.455 0.00 0.00 40.61 2.85
1466 1714 3.658725 AGTCTCTACCCTAACCATGCAT 58.341 45.455 0.00 0.00 0.00 3.96
1504 1752 2.368875 ACCTGACACTACCCTGAAACAG 59.631 50.000 0.00 0.00 0.00 3.16
1528 1776 3.772932 CAACAATTCAACATCCATCGGG 58.227 45.455 0.00 0.00 0.00 5.14
1603 1851 4.362932 TTCGAACTCACTCTATGCTGAG 57.637 45.455 0.00 0.00 39.95 3.35
1606 1855 4.081420 ACCAATTCGAACTCACTCTATGCT 60.081 41.667 0.00 0.00 0.00 3.79
1616 1865 3.330267 AGCTCTGAACCAATTCGAACTC 58.670 45.455 0.00 0.00 37.69 3.01
1634 1883 1.198759 TTTACGAGGCCCCTGAAGCT 61.199 55.000 0.00 0.00 0.00 3.74
1635 1884 0.107165 ATTTACGAGGCCCCTGAAGC 60.107 55.000 0.00 0.00 0.00 3.86
1683 1932 1.375140 CGTCCATGCACAGCTCTGT 60.375 57.895 0.00 0.00 46.17 3.41
1779 2028 3.938963 TGATTTACTGAGCCAATTCGACC 59.061 43.478 0.00 0.00 0.00 4.79
1790 2040 7.601073 TCATTTGCTGTACTGATTTACTGAG 57.399 36.000 3.61 0.00 0.00 3.35
1875 2183 9.606631 ACAACATCTTATCTTATCCTGAAGAAC 57.393 33.333 0.00 0.00 38.89 3.01
1929 2237 8.792633 TGCTGTAGTAATTTACTGAAGCAATTT 58.207 29.630 28.03 4.91 46.36 1.82
2502 2823 3.174987 CTGGGTGGTGGTGGTCCA 61.175 66.667 0.00 0.00 42.05 4.02
2794 3118 9.511144 TTGACACTATGAACACAGTAATATACG 57.489 33.333 0.00 0.00 0.00 3.06
2833 3157 6.536731 AGCATAGCTATTCAGAAAACATCG 57.463 37.500 2.64 0.00 36.99 3.84
2872 3221 3.429547 CCATCGAGGTCCTACAGAACAAG 60.430 52.174 0.00 0.00 33.03 3.16
2977 3326 4.145876 ACACTTACGCAACACATGATTG 57.854 40.909 0.00 4.85 0.00 2.67
2989 3338 7.170240 AGAAACTACAAACTAACACTTACGC 57.830 36.000 0.00 0.00 0.00 4.42
3437 3787 9.467796 AATTTAGGGACTTCATCTAGAAAAAGG 57.532 33.333 17.19 2.44 41.75 3.11
3516 3868 6.013085 CGATGACAATTTAGTGTGGTTTACG 58.987 40.000 0.00 0.00 0.00 3.18
3517 3869 7.013529 GTCGATGACAATTTAGTGTGGTTTAC 58.986 38.462 0.00 0.00 32.09 2.01
3518 3870 6.148150 GGTCGATGACAATTTAGTGTGGTTTA 59.852 38.462 0.00 0.00 33.68 2.01
3519 3871 5.048991 GGTCGATGACAATTTAGTGTGGTTT 60.049 40.000 0.00 0.00 33.68 3.27
3520 3872 4.454504 GGTCGATGACAATTTAGTGTGGTT 59.545 41.667 0.00 0.00 33.68 3.67
3522 3874 3.374058 GGGTCGATGACAATTTAGTGTGG 59.626 47.826 0.00 0.00 33.68 4.17
3523 3875 3.374058 GGGGTCGATGACAATTTAGTGTG 59.626 47.826 0.00 0.00 33.68 3.82
3569 3928 1.848932 CGACTCGACCGTCTCACCAA 61.849 60.000 3.64 0.00 0.00 3.67
3570 3929 2.322830 CGACTCGACCGTCTCACCA 61.323 63.158 3.64 0.00 0.00 4.17
3572 3931 1.367599 ATCCGACTCGACCGTCTCAC 61.368 60.000 0.00 0.00 0.00 3.51
3574 3933 1.642753 GATCCGACTCGACCGTCTC 59.357 63.158 0.00 0.00 0.00 3.36
3575 3934 2.172372 CGATCCGACTCGACCGTCT 61.172 63.158 0.00 0.00 41.12 4.18
3614 3978 4.070716 GGAAGAAGCATTGATGATCGGAT 58.929 43.478 0.00 0.00 0.00 4.18
3627 3991 2.871096 ATTAACGTGGGGAAGAAGCA 57.129 45.000 0.00 0.00 0.00 3.91
3674 4038 4.520874 CCATATATAGGCTCGTGATCCGAT 59.479 45.833 6.73 0.00 46.23 4.18
3850 4222 2.512286 CATGTCGATGGCGTGGCT 60.512 61.111 0.00 0.00 38.98 4.75
3925 4297 1.741401 CGTGGCTCGGATTGCTTGA 60.741 57.895 0.13 0.00 35.71 3.02


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

AutoCloner maintained by Alex Coulton.