Multiple sequence alignment - TraesCS2B01G409600

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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 TraesCS2B01G409600 chr2B 100.000 4079 0 0 811 4889 583068789 583064711 0.000000e+00 7533.0
1 TraesCS2B01G409600 chr2B 100.000 445 0 0 1 445 583069599 583069155 0.000000e+00 822.0
2 TraesCS2B01G409600 chr2B 93.182 132 9 0 1085 1216 762867262 762867131 1.390000e-45 195.0
3 TraesCS2B01G409600 chr2B 100.000 29 0 0 1249 1277 583068264 583068236 2.000000e-03 54.7
4 TraesCS2B01G409600 chr2B 100.000 29 0 0 1336 1364 583068351 583068323 2.000000e-03 54.7
5 TraesCS2B01G409600 chr2D 96.347 4106 107 15 816 4889 495405192 495401098 0.000000e+00 6711.0
6 TraesCS2B01G409600 chr2D 90.065 463 23 11 1 445 495405729 495405272 3.280000e-161 579.0
7 TraesCS2B01G409600 chr2D 81.548 168 22 6 4485 4649 620203534 620203373 3.970000e-26 130.0
8 TraesCS2B01G409600 chr2D 90.000 60 5 1 4485 4543 650258495 650258554 5.250000e-10 76.8
9 TraesCS2B01G409600 chr2D 100.000 29 0 0 1249 1277 495404681 495404653 2.000000e-03 54.7
10 TraesCS2B01G409600 chr2D 100.000 29 0 0 1336 1364 495404768 495404740 2.000000e-03 54.7
11 TraesCS2B01G409600 chr2A 96.813 3326 73 11 1594 4889 638306318 638309640 0.000000e+00 5524.0
12 TraesCS2B01G409600 chr2A 92.142 929 52 8 813 1732 638305402 638306318 0.000000e+00 1291.0
13 TraesCS2B01G409600 chr2A 89.286 448 25 12 1 445 638304898 638305325 1.550000e-149 540.0
14 TraesCS2B01G409600 chr2A 97.674 43 1 0 4486 4528 177664629 177664587 1.890000e-09 75.0
15 TraesCS2B01G409600 chr2A 96.875 32 1 0 1333 1364 638305832 638305863 2.000000e-03 54.7
16 TraesCS2B01G409600 chr7D 91.500 400 24 8 813 1212 100648933 100649322 4.300000e-150 542.0
17 TraesCS2B01G409600 chr7D 77.199 307 33 17 4336 4638 486060317 486060044 1.420000e-30 145.0
18 TraesCS2B01G409600 chr6D 90.250 400 28 9 813 1212 262759992 262760380 3.380000e-141 512.0
19 TraesCS2B01G409600 chr6D 94.318 176 9 1 1037 1212 159023480 159023306 8.070000e-68 268.0
20 TraesCS2B01G409600 chr4D 83.226 155 21 5 4486 4637 67277022 67276870 2.370000e-28 137.0
21 TraesCS2B01G409600 chr4A 83.226 155 21 5 4486 4637 516444614 516444462 2.370000e-28 137.0
22 TraesCS2B01G409600 chr3D 87.500 104 11 1 4546 4647 3002965 3003068 8.600000e-23 119.0
23 TraesCS2B01G409600 chr5D 88.542 96 8 3 4550 4645 44603288 44603380 4.000000e-21 113.0
24 TraesCS2B01G409600 chrUn 87.234 94 11 1 4546 4638 32136901 32136994 6.690000e-19 106.0
25 TraesCS2B01G409600 chr4B 97.674 43 0 1 4485 4527 581070472 581070513 6.790000e-09 73.1
26 TraesCS2B01G409600 chr3A 93.878 49 1 2 4485 4531 645564918 645564870 6.790000e-09 73.1


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 TraesCS2B01G409600 chr2B 583064711 583069599 4888 True 2116.100 7533 100.000 1 4889 4 chr2B.!!$R2 4888
1 TraesCS2B01G409600 chr2D 495401098 495405729 4631 True 1849.850 6711 96.603 1 4889 4 chr2D.!!$R2 4888
2 TraesCS2B01G409600 chr2A 638304898 638309640 4742 False 1852.425 5524 93.779 1 4889 4 chr2A.!!$F1 4888

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
123 130 0.534412 CGAGTGGAGCTGGAATCACT 59.466 55.0 0.00 0.0 42.37 3.41 F
1284 1322 0.179134 CGACCATGAAGAGGACCGAC 60.179 60.0 0.00 0.0 0.00 4.79 F
1992 2168 0.170339 GTGCTAACACGGGAAATGGC 59.830 55.0 0.00 0.0 36.98 4.40 F
3411 3587 0.324275 CCAAATCGATGGGTTGGGGT 60.324 55.0 16.47 0.0 38.52 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 1517 0.582005 GTGTGTGTCTCTTGAACGGC 59.418 55.000 0.0 0.0 0.0 5.68 R
2298 2474 0.321671 CTGCTCGGGTTTCCTTCTCA 59.678 55.000 0.0 0.0 0.0 3.27 R
3613 3789 1.269206 CGCATCAACAGCAAAACCAGT 60.269 47.619 0.0 0.0 0.0 4.00 R
4775 4985 3.698029 AGTTGTTATCCATTCATGCGC 57.302 42.857 0.0 0.0 0.0 6.09 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
123 130 0.534412 CGAGTGGAGCTGGAATCACT 59.466 55.000 0.00 0.00 42.37 3.41
124 131 1.738365 CGAGTGGAGCTGGAATCACTG 60.738 57.143 0.00 0.00 40.13 3.66
149 156 2.871453 ACAAATTCGTAAACCAGCCCT 58.129 42.857 0.00 0.00 0.00 5.19
189 198 1.318576 GCCCACCCTAAATCAATCGG 58.681 55.000 0.00 0.00 0.00 4.18
190 199 1.409661 GCCCACCCTAAATCAATCGGT 60.410 52.381 0.00 0.00 0.00 4.69
198 207 4.384208 CCCTAAATCAATCGGTCCAGTTCT 60.384 45.833 0.00 0.00 0.00 3.01
200 209 3.981071 AATCAATCGGTCCAGTTCTGA 57.019 42.857 1.00 0.00 0.00 3.27
207 216 2.831526 TCGGTCCAGTTCTGATCATCAA 59.168 45.455 0.00 0.00 0.00 2.57
263 284 3.461831 CTCCAATAATAACCCACCCTGGA 59.538 47.826 0.00 0.00 40.96 3.86
358 379 2.558313 GCGGTTGCTGTGCTTCTC 59.442 61.111 0.00 0.00 38.39 2.87
367 388 0.820226 CTGTGCTTCTCCATCTCGGA 59.180 55.000 0.00 0.00 43.61 4.55
368 389 1.411977 CTGTGCTTCTCCATCTCGGAT 59.588 52.381 0.00 0.00 45.19 4.18
369 390 1.410517 TGTGCTTCTCCATCTCGGATC 59.589 52.381 0.00 0.00 45.19 3.36
370 391 1.043816 TGCTTCTCCATCTCGGATCC 58.956 55.000 0.00 0.00 45.19 3.36
405 434 4.675303 CCCTCACCTCCCCACCCA 62.675 72.222 0.00 0.00 0.00 4.51
406 435 3.330720 CCTCACCTCCCCACCCAC 61.331 72.222 0.00 0.00 0.00 4.61
407 436 3.330720 CTCACCTCCCCACCCACC 61.331 72.222 0.00 0.00 0.00 4.61
408 437 4.995058 TCACCTCCCCACCCACCC 62.995 72.222 0.00 0.00 0.00 4.61
850 879 1.262640 AATCAGGTACGCCCCGTCTT 61.263 55.000 0.00 0.00 41.54 3.01
854 883 2.050934 GGTACGCCCCGTCTTCTCT 61.051 63.158 0.00 0.00 41.54 3.10
863 892 1.328430 CCGTCTTCTCTACCCACCCC 61.328 65.000 0.00 0.00 0.00 4.95
865 894 1.880941 GTCTTCTCTACCCACCCCAT 58.119 55.000 0.00 0.00 0.00 4.00
866 895 1.763545 GTCTTCTCTACCCACCCCATC 59.236 57.143 0.00 0.00 0.00 3.51
938 967 1.136774 GCGCGATTTGTTTCCTCCC 59.863 57.895 12.10 0.00 0.00 4.30
939 968 1.800681 CGCGATTTGTTTCCTCCCC 59.199 57.895 0.00 0.00 0.00 4.81
1027 1056 4.832608 GGGAGGCCGCGGTACAAG 62.833 72.222 28.70 0.00 0.00 3.16
1028 1057 4.832608 GGAGGCCGCGGTACAAGG 62.833 72.222 28.70 0.00 0.00 3.61
1070 1099 1.522569 GGAGGTACAAGGCGCTCAT 59.477 57.895 7.64 0.00 0.00 2.90
1115 1144 0.322008 GTCAGGAACCAGGCCAAGAG 60.322 60.000 5.01 0.00 0.00 2.85
1235 1273 3.857764 GGGAGATCCGTCGGATGT 58.142 61.111 31.02 26.91 43.27 3.06
1284 1322 0.179134 CGACCATGAAGAGGACCGAC 60.179 60.000 0.00 0.00 0.00 4.79
1369 1407 0.684535 TGCGACCATGAAGAACTCCA 59.315 50.000 0.00 0.00 0.00 3.86
1441 1479 3.129502 GCTCCGGCGGGGTTAAAC 61.130 66.667 29.03 6.07 37.00 2.01
1455 1493 1.286354 TTAAACTGGAGAACGGCGCG 61.286 55.000 6.90 0.00 0.00 6.86
1479 1517 1.506262 CGGTGCCGGAAAGGATTTG 59.494 57.895 5.05 0.00 45.00 2.32
1618 1656 0.179097 GACCACGAGGAGCTCCAATC 60.179 60.000 33.90 22.07 38.89 2.67
1662 1838 2.046314 ACCGGTGCCGAAATGGAG 60.046 61.111 6.12 0.00 42.00 3.86
1764 1940 0.171455 CAGACTACAGCGGTGTCCTC 59.829 60.000 25.54 18.55 38.19 3.71
1927 2103 3.161866 GGGAATGGGTTAAAGAGCAACA 58.838 45.455 0.00 0.00 0.00 3.33
1992 2168 0.170339 GTGCTAACACGGGAAATGGC 59.830 55.000 0.00 0.00 36.98 4.40
2092 2268 3.127425 GCAGAGGGCGGAAAGTAATAT 57.873 47.619 0.00 0.00 0.00 1.28
2093 2269 3.067833 GCAGAGGGCGGAAAGTAATATC 58.932 50.000 0.00 0.00 0.00 1.63
2181 2357 4.039973 TCACTTGAAACTCCGGAATACAGT 59.960 41.667 5.23 0.00 0.00 3.55
2298 2474 2.578480 GGATTTCTCCTCAGGGAAAGGT 59.422 50.000 11.60 0.00 41.69 3.50
2314 2490 0.977395 AGGTGAGAAGGAAACCCGAG 59.023 55.000 0.00 0.00 34.29 4.63
2532 2708 2.290641 CAGGTTCCTTGCACAGTGTAAC 59.709 50.000 0.00 0.00 0.00 2.50
2861 3037 4.701651 TGGTTTCACCATTCATGCTAAGAG 59.298 41.667 0.00 0.00 44.79 2.85
3102 3278 5.677319 TCCCGATATCTGTTTTGAACTCT 57.323 39.130 0.34 0.00 0.00 3.24
3384 3560 2.704725 TCAAATTTCGGCTGCAAGTC 57.295 45.000 0.50 0.00 35.30 3.01
3411 3587 0.324275 CCAAATCGATGGGTTGGGGT 60.324 55.000 16.47 0.00 38.52 4.95
3424 3600 2.650322 GTTGGGGTGTGAAAACTCTCA 58.350 47.619 0.00 0.00 0.00 3.27
3613 3789 3.328343 TGGTCCGGGTAAAGATGAAGAAA 59.672 43.478 0.00 0.00 0.00 2.52
3633 3809 1.269206 ACTGGTTTTGCTGTTGATGCG 60.269 47.619 0.00 0.00 0.00 4.73
3654 3830 2.893489 GTCAAAGATGGGGAACTTTGCT 59.107 45.455 12.74 0.00 46.86 3.91
3768 3944 1.202698 GCCTGCGAAGATATTCCACCT 60.203 52.381 0.00 0.00 0.00 4.00
4118 4297 7.498900 ACGATAATTCTTGGACATAGCATCAAA 59.501 33.333 0.00 0.00 0.00 2.69
4119 4298 8.344831 CGATAATTCTTGGACATAGCATCAAAA 58.655 33.333 0.00 0.00 0.00 2.44
4233 4412 8.948401 TCTCTTGATAGAAATATCCTAGCACT 57.052 34.615 3.44 0.00 32.96 4.40
4273 4454 9.120538 GGAGATTACTGGAGCATTGTAAAAATA 57.879 33.333 0.00 0.00 31.25 1.40
4349 4533 6.974932 TGCTTTGAAAATTTGTTGCAACTA 57.025 29.167 28.61 19.86 0.00 2.24
4589 4797 0.675633 GGCATGATGGGTTGGCATAC 59.324 55.000 0.00 0.00 38.23 2.39
4775 4985 8.183536 TGATTTCCGTTATGATGTGAAAGAATG 58.816 33.333 0.00 0.00 0.00 2.67
4867 5077 7.733773 TCATTGAAATGGAAGTAGTAGGAGA 57.266 36.000 3.31 0.00 37.03 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.074412 GGATATAAATGTGGCGGTCAGG 58.926 50.000 0.00 0.00 0.00 3.86
123 130 4.319911 GCTGGTTTACGAATTTGTACAGCA 60.320 41.667 26.78 22.95 39.68 4.41
124 131 4.156182 GCTGGTTTACGAATTTGTACAGC 58.844 43.478 21.80 21.80 35.90 4.40
189 198 3.372206 CCGTTTGATGATCAGAACTGGAC 59.628 47.826 0.09 0.00 0.00 4.02
190 199 3.599343 CCGTTTGATGATCAGAACTGGA 58.401 45.455 0.09 0.00 0.00 3.86
198 207 1.486310 CCTCTCCCCGTTTGATGATCA 59.514 52.381 0.00 0.00 0.00 2.92
200 209 0.181350 GCCTCTCCCCGTTTGATGAT 59.819 55.000 0.00 0.00 0.00 2.45
207 216 2.757077 CCTTTGCCTCTCCCCGTT 59.243 61.111 0.00 0.00 0.00 4.44
279 300 2.511600 GCTGGTGAATCGGACGGG 60.512 66.667 0.00 0.00 0.00 5.28
367 388 1.697754 GGGGACTGGGTGGATGGAT 60.698 63.158 0.00 0.00 0.00 3.41
368 389 2.286121 GGGGACTGGGTGGATGGA 60.286 66.667 0.00 0.00 0.00 3.41
369 390 3.420482 GGGGGACTGGGTGGATGG 61.420 72.222 0.00 0.00 0.00 3.51
370 391 2.613696 TGGGGGACTGGGTGGATG 60.614 66.667 0.00 0.00 0.00 3.51
376 397 4.675303 TGAGGGTGGGGGACTGGG 62.675 72.222 0.00 0.00 0.00 4.45
850 879 1.218196 GAGAGATGGGGTGGGTAGAGA 59.782 57.143 0.00 0.00 0.00 3.10
854 883 1.218196 GAGAGAGAGATGGGGTGGGTA 59.782 57.143 0.00 0.00 0.00 3.69
863 892 1.782752 AGGGGGAGAGAGAGAGAGATG 59.217 57.143 0.00 0.00 0.00 2.90
865 894 1.010793 AGAGGGGGAGAGAGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
866 895 1.421646 GAGAGGGGGAGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
1228 1266 1.472878 CTTCTTCGACTGGACATCCGA 59.527 52.381 0.00 0.00 39.43 4.55
1233 1271 2.029828 GCTTCTCTTCTTCGACTGGACA 60.030 50.000 0.00 0.00 0.00 4.02
1235 1273 2.029828 GTGCTTCTCTTCTTCGACTGGA 60.030 50.000 0.00 0.00 0.00 3.86
1369 1407 1.822990 CAGGCAATCCATTTCAGCACT 59.177 47.619 0.00 0.00 33.74 4.40
1412 1450 4.093291 CGGAGCTCTTGGCAGCCT 62.093 66.667 14.15 0.00 44.79 4.58
1430 1468 1.162698 GTTCTCCAGTTTAACCCCGC 58.837 55.000 0.00 0.00 0.00 6.13
1431 1469 1.435577 CGTTCTCCAGTTTAACCCCG 58.564 55.000 0.00 0.00 0.00 5.73
1479 1517 0.582005 GTGTGTGTCTCTTGAACGGC 59.418 55.000 0.00 0.00 0.00 5.68
1485 1523 1.787155 GTACTGCGTGTGTGTCTCTTG 59.213 52.381 0.00 0.00 0.00 3.02
1618 1656 6.346919 CGAGCATTGTTATCTATTTTCTCCCG 60.347 42.308 0.00 0.00 0.00 5.14
1629 1805 1.290203 CGGTGCGAGCATTGTTATCT 58.710 50.000 0.00 0.00 0.00 1.98
1662 1838 1.040339 TGGACTTGCCCAAACCACAC 61.040 55.000 0.00 0.00 34.97 3.82
1764 1940 6.754702 AAATTCTGGACATGTTCATCTCTG 57.245 37.500 7.44 0.00 0.00 3.35
1927 2103 4.096532 CACATGATCTGCAGCAGAAGAAAT 59.903 41.667 28.78 12.31 44.04 2.17
1992 2168 1.066573 ACATCACTCTCCTTGGAAGCG 60.067 52.381 0.00 0.00 0.00 4.68
2087 2263 2.976185 TGGAACCTCCATGGCGATATTA 59.024 45.455 6.96 0.00 42.67 0.98
2277 2453 2.578480 ACCTTTCCCTGAGGAGAAATCC 59.422 50.000 13.19 0.00 45.19 3.01
2298 2474 0.321671 CTGCTCGGGTTTCCTTCTCA 59.678 55.000 0.00 0.00 0.00 3.27
2314 2490 7.090173 TCAGTTTTCACCTTTTTATATGCTGC 58.910 34.615 0.00 0.00 0.00 5.25
2462 2638 1.985116 GCTCCTCCTTCCCGTGACT 60.985 63.158 0.00 0.00 0.00 3.41
2532 2708 1.428448 TGCCAACAAATCTCTCGTCG 58.572 50.000 0.00 0.00 0.00 5.12
2861 3037 1.743252 CTCTTCCGCTGGCTGTTCC 60.743 63.158 0.00 0.00 0.00 3.62
3384 3560 3.347216 ACCCATCGATTTGGTCTTGAAG 58.653 45.455 10.01 0.00 34.77 3.02
3411 3587 9.817809 GATGGTATATAGTTGAGAGTTTTCACA 57.182 33.333 0.00 0.00 0.00 3.58
3424 3600 6.267928 ACGAAGCTTCCAGATGGTATATAGTT 59.732 38.462 20.62 0.00 36.34 2.24
3613 3789 1.269206 CGCATCAACAGCAAAACCAGT 60.269 47.619 0.00 0.00 0.00 4.00
3654 3830 8.802267 GGGGTGCAGCTATGATTAATAAATTTA 58.198 33.333 16.65 0.00 0.00 1.40
3768 3944 4.868268 AGTGGTATACTAGCTCTTGACCA 58.132 43.478 2.25 0.00 38.04 4.02
4138 4317 1.886542 GAGAGGTTGCCGGAAAATGTT 59.113 47.619 5.05 0.00 0.00 2.71
4139 4318 1.202879 TGAGAGGTTGCCGGAAAATGT 60.203 47.619 5.05 0.00 0.00 2.71
4273 4454 7.157347 AGTGTACATCATGATATCGCAATTCT 58.843 34.615 8.15 0.00 0.00 2.40
4519 4724 6.013466 AGCCCAATAAGTCCAATTTTCAACAT 60.013 34.615 0.00 0.00 0.00 2.71
4526 4731 7.038373 ACACATTTAGCCCAATAAGTCCAATTT 60.038 33.333 0.00 0.00 0.00 1.82
4531 4738 5.914898 AACACATTTAGCCCAATAAGTCC 57.085 39.130 0.00 0.00 0.00 3.85
4589 4797 6.981762 ACTCTAATTCTCTCAACATGCAAG 57.018 37.500 0.00 0.00 0.00 4.01
4757 4967 4.661125 TGCGCATTCTTTCACATCATAAC 58.339 39.130 5.66 0.00 0.00 1.89
4775 4985 3.698029 AGTTGTTATCCATTCATGCGC 57.302 42.857 0.00 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.