Multiple sequence alignment - TraesCS6A01G017300

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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 TraesCS6A01G017300 chr6A 100.000 3083 0 0 1 3083 8608094 8611176 0.000000e+00 5694
1 TraesCS6A01G017300 chr6A 87.259 2488 202 48 237 2649 8387216 8389663 0.000000e+00 2732
2 TraesCS6A01G017300 chr6A 92.181 243 19 0 1 243 8384209 8384451 8.180000e-91 344
3 TraesCS6A01G017300 chr6A 80.112 357 51 15 2285 2632 29120032 29120377 6.600000e-62 248
4 TraesCS6A01G017300 chr6A 90.323 124 12 0 2960 3083 132477555 132477678 2.460000e-36 163
5 TraesCS6A01G017300 chr6D 95.749 2964 111 7 1 2961 8139598 8142549 0.000000e+00 4761
6 TraesCS6A01G017300 chr6D 85.294 1768 212 18 537 2272 1540282 1538531 0.000000e+00 1781
7 TraesCS6A01G017300 chr6D 91.304 161 11 3 2107 2264 3618463 3618303 1.860000e-52 217
8 TraesCS6A01G017300 chr6D 89.431 123 13 0 2960 3082 293716457 293716579 4.120000e-34 156
9 TraesCS6A01G017300 chr6B 90.952 2343 165 21 1 2323 15105093 15107408 0.000000e+00 3109
10 TraesCS6A01G017300 chr6B 83.579 1766 242 21 538 2276 5715712 5713968 0.000000e+00 1611
11 TraesCS6A01G017300 chr6B 87.650 583 56 10 2378 2958 15107509 15108077 0.000000e+00 664
12 TraesCS6A01G017300 chr6B 90.323 124 12 0 2960 3083 58059232 58059109 2.460000e-36 163
13 TraesCS6A01G017300 chr6B 89.516 124 13 0 2960 3083 569138974 569138851 1.140000e-34 158
14 TraesCS6A01G017300 chr5B 84.522 1809 210 39 504 2272 132587779 132589557 0.000000e+00 1725
15 TraesCS6A01G017300 chr5D 84.322 1837 207 40 504 2272 119658763 119660586 0.000000e+00 1722
16 TraesCS6A01G017300 chr5D 84.500 200 30 1 1019 1218 515094285 515094087 2.430000e-46 196
17 TraesCS6A01G017300 chr5A 84.225 1813 220 33 504 2272 129749073 129750863 0.000000e+00 1703
18 TraesCS6A01G017300 chr7D 85.182 1370 164 17 537 1886 558888744 558887394 0.000000e+00 1369
19 TraesCS6A01G017300 chr3A 78.355 693 129 16 1559 2237 623942449 623943134 2.200000e-116 429
20 TraesCS6A01G017300 chr3A 89.516 124 13 0 2960 3083 734992242 734992365 1.140000e-34 158
21 TraesCS6A01G017300 chr3B 77.910 670 123 17 1559 2213 642094655 642095314 8.010000e-106 394
22 TraesCS6A01G017300 chr3B 83.249 197 31 2 1019 1214 798408852 798408657 2.440000e-41 180
23 TraesCS6A01G017300 chr7A 78.814 472 81 14 887 1350 8381145 8381605 1.800000e-77 300
24 TraesCS6A01G017300 chr3D 85.338 266 30 6 2281 2543 510859321 510859580 1.820000e-67 267
25 TraesCS6A01G017300 chrUn 81.073 354 48 15 2287 2632 71742347 71742689 6.560000e-67 265
26 TraesCS6A01G017300 chrUn 89.516 124 13 0 2960 3083 154681479 154681602 1.140000e-34 158
27 TraesCS6A01G017300 chr1B 79.710 345 57 10 2285 2624 647543906 647543570 1.430000e-58 237
28 TraesCS6A01G017300 chr4A 72.911 742 149 39 506 1224 657194627 657195339 3.120000e-50 209
29 TraesCS6A01G017300 chr2B 91.129 124 11 0 2960 3083 643267572 643267449 5.290000e-38 169
30 TraesCS6A01G017300 chr4B 89.516 124 13 0 2960 3083 46871989 46872112 1.140000e-34 158
31 TraesCS6A01G017300 chr4B 89.062 128 13 1 2957 3083 626638043 626638170 1.140000e-34 158


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 TraesCS6A01G017300 chr6A 8608094 8611176 3082 False 5694.0 5694 100.000 1 3083 1 chr6A.!!$F1 3082
1 TraesCS6A01G017300 chr6A 8384209 8389663 5454 False 1538.0 2732 89.720 1 2649 2 chr6A.!!$F4 2648
2 TraesCS6A01G017300 chr6D 8139598 8142549 2951 False 4761.0 4761 95.749 1 2961 1 chr6D.!!$F1 2960
3 TraesCS6A01G017300 chr6D 1538531 1540282 1751 True 1781.0 1781 85.294 537 2272 1 chr6D.!!$R1 1735
4 TraesCS6A01G017300 chr6B 15105093 15108077 2984 False 1886.5 3109 89.301 1 2958 2 chr6B.!!$F1 2957
5 TraesCS6A01G017300 chr6B 5713968 5715712 1744 True 1611.0 1611 83.579 538 2276 1 chr6B.!!$R1 1738
6 TraesCS6A01G017300 chr5B 132587779 132589557 1778 False 1725.0 1725 84.522 504 2272 1 chr5B.!!$F1 1768
7 TraesCS6A01G017300 chr5D 119658763 119660586 1823 False 1722.0 1722 84.322 504 2272 1 chr5D.!!$F1 1768
8 TraesCS6A01G017300 chr5A 129749073 129750863 1790 False 1703.0 1703 84.225 504 2272 1 chr5A.!!$F1 1768
9 TraesCS6A01G017300 chr7D 558887394 558888744 1350 True 1369.0 1369 85.182 537 1886 1 chr7D.!!$R1 1349
10 TraesCS6A01G017300 chr3A 623942449 623943134 685 False 429.0 429 78.355 1559 2237 1 chr3A.!!$F1 678
11 TraesCS6A01G017300 chr3B 642094655 642095314 659 False 394.0 394 77.910 1559 2213 1 chr3B.!!$F1 654
12 TraesCS6A01G017300 chr4A 657194627 657195339 712 False 209.0 209 72.911 506 1224 1 chr4A.!!$F1 718

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
719 3504 0.320771 GACGGTCCAATGTGTGCTCT 60.321 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 5233 0.320771 GTGGACTACACTGCCCACTG 60.321 60.0 0.0 0.0 46.72 3.66 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
142 143 2.294979 GTTCAACGGTTCCTTGGTCTT 58.705 47.619 0.00 0.00 0.00 3.01
349 3128 6.381481 TGAACCGAGAAACGATAAGCTATA 57.619 37.500 0.00 0.00 45.77 1.31
427 3206 1.385528 TGCTCGTCAATACTAGCCGA 58.614 50.000 0.00 0.00 42.30 5.54
473 3252 5.879237 ACAACACAGGAATTATTGTATGCG 58.121 37.500 0.00 0.00 31.88 4.73
488 3267 4.505217 GCGTGCGCATGAAGACCG 62.505 66.667 32.94 20.87 41.49 4.79
699 3483 4.989279 TGCATGCGCTAGATATAGATCA 57.011 40.909 14.09 0.00 39.64 2.92
719 3504 0.320771 GACGGTCCAATGTGTGCTCT 60.321 55.000 0.00 0.00 0.00 4.09
982 3798 3.760035 CGTCCTCCACCACCTCCG 61.760 72.222 0.00 0.00 0.00 4.63
1117 3955 1.212688 AGACCATCCGCCAAATGATCA 59.787 47.619 0.00 0.00 0.00 2.92
1257 4104 2.257371 GCTGCGTCTGACACCGTA 59.743 61.111 8.73 0.00 0.00 4.02
1343 4190 0.763223 ACCCACTTCGACCTCAACCT 60.763 55.000 0.00 0.00 0.00 3.50
1444 4293 4.617520 TGGGCTTGCGCGTCTTGA 62.618 61.111 8.43 0.00 36.88 3.02
1583 4438 0.385390 GCCGGCCATACAAAATCCTG 59.615 55.000 18.11 0.00 0.00 3.86
1608 4463 5.603170 AAATTGGTTAGGGCATCATCTTG 57.397 39.130 0.00 0.00 0.00 3.02
1609 4464 3.737559 TTGGTTAGGGCATCATCTTGT 57.262 42.857 0.00 0.00 0.00 3.16
1610 4465 3.003394 TGGTTAGGGCATCATCTTGTG 57.997 47.619 0.00 0.00 0.00 3.33
1670 4530 4.477302 TGCGTAACCTTTGAAGCTTTAC 57.523 40.909 0.00 0.00 0.00 2.01
1873 4776 7.132694 TGTAACACATCTTAATGCAAGACAG 57.867 36.000 0.00 0.00 46.01 3.51
2004 4916 0.478072 TGTTGGACCTGACTTGCCAT 59.522 50.000 0.00 0.00 0.00 4.40
2111 5038 1.096416 GACGATCCGTGGAGAGAACT 58.904 55.000 0.00 0.00 41.37 3.01
2252 5182 4.326826 AGGTGGTGTCAGTGAACATATTG 58.673 43.478 0.00 0.00 0.00 1.90
2302 5233 3.691118 TCATTGTCTTTACATGAGGCTGC 59.309 43.478 0.00 0.00 34.97 5.25
2338 5269 0.764890 CACGGGGTGGTATGATCCAT 59.235 55.000 0.00 0.00 39.81 3.41
2379 5356 2.840651 CTCTAGGGTGGATGGTGAAGTT 59.159 50.000 0.00 0.00 0.00 2.66
2382 5359 1.995542 AGGGTGGATGGTGAAGTTCAT 59.004 47.619 9.18 0.00 0.00 2.57
2463 5440 6.894339 AAGGAGGTTCGTAAATTTGTCAAT 57.106 33.333 0.00 0.00 0.00 2.57
2498 5475 3.820467 AGAGATTGTTGCGACCAATGAAA 59.180 39.130 0.45 0.00 32.84 2.69
2584 5562 6.093771 GTCAAGATCAAATCAGCACAGAAGAT 59.906 38.462 0.00 0.00 0.00 2.40
2585 5563 6.093633 TCAAGATCAAATCAGCACAGAAGATG 59.906 38.462 0.00 0.00 0.00 2.90
2704 5684 5.356470 AGTGTCCGAGTAGTAGTATGGTTTC 59.644 44.000 0.00 0.00 0.00 2.78
2876 5857 2.479837 CAGTGAGTTGTAACTTGGCGA 58.520 47.619 0.00 0.00 39.88 5.54
2933 5914 4.440880 CACATGTTCCTTTGGCAAAAAGA 58.559 39.130 14.43 10.81 0.00 2.52
2948 5929 4.737765 GCAAAAAGATTTTGTGCACGTCTA 59.262 37.500 13.13 0.00 35.85 2.59
2961 5942 7.229228 TGTGCACGTCTATTTTGTGATATAC 57.771 36.000 13.13 0.00 35.66 1.47
2962 5943 6.814146 TGTGCACGTCTATTTTGTGATATACA 59.186 34.615 13.13 0.00 35.66 2.29
2979 5960 9.574516 GTGATATACACCCTCTATTCCAAAATT 57.425 33.333 0.00 0.00 43.05 1.82
2980 5961 9.793259 TGATATACACCCTCTATTCCAAAATTC 57.207 33.333 0.00 0.00 0.00 2.17
2983 5964 6.840780 ACACCCTCTATTCCAAAATTCTTG 57.159 37.500 0.00 0.00 0.00 3.02
2984 5965 6.314917 ACACCCTCTATTCCAAAATTCTTGT 58.685 36.000 0.00 0.00 0.00 3.16
2985 5966 6.782494 ACACCCTCTATTCCAAAATTCTTGTT 59.218 34.615 0.00 0.00 0.00 2.83
2986 5967 7.290014 ACACCCTCTATTCCAAAATTCTTGTTT 59.710 33.333 0.00 0.00 0.00 2.83
2987 5968 8.150296 CACCCTCTATTCCAAAATTCTTGTTTT 58.850 33.333 0.00 0.00 0.00 2.43
2988 5969 9.374711 ACCCTCTATTCCAAAATTCTTGTTTTA 57.625 29.630 0.00 0.00 30.56 1.52
2989 5970 9.639601 CCCTCTATTCCAAAATTCTTGTTTTAC 57.360 33.333 0.00 0.00 30.56 2.01
2997 5978 9.883142 TCCAAAATTCTTGTTTTACATTTGTCT 57.117 25.926 0.00 0.00 30.56 3.41
3042 6023 8.506168 ACTAAAATGTGATTTGATACATCCGT 57.494 30.769 0.00 0.00 36.56 4.69
3043 6024 9.607988 ACTAAAATGTGATTTGATACATCCGTA 57.392 29.630 0.00 0.00 36.56 4.02
3077 6058 9.463443 AAATTTAAGACAAGAATTTTGAGACGG 57.537 29.630 0.00 0.00 31.00 4.79
3078 6059 7.795482 TTTAAGACAAGAATTTTGAGACGGA 57.205 32.000 7.18 0.00 0.00 4.69
3079 6060 5.931441 AAGACAAGAATTTTGAGACGGAG 57.069 39.130 7.18 0.00 0.00 4.63
3080 6061 4.319177 AGACAAGAATTTTGAGACGGAGG 58.681 43.478 7.18 0.00 0.00 4.30
3081 6062 3.412386 ACAAGAATTTTGAGACGGAGGG 58.588 45.455 7.18 0.00 0.00 4.30
3082 6063 3.072476 ACAAGAATTTTGAGACGGAGGGA 59.928 43.478 7.18 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 1.159285 CAAACTGCAGCTCGGATGAA 58.841 50.000 15.27 0.00 0.00 2.57
326 3105 3.587797 AGCTTATCGTTTCTCGGTTCA 57.412 42.857 0.00 0.00 40.32 3.18
473 3252 2.742372 ACCGGTCTTCATGCGCAC 60.742 61.111 14.90 0.00 0.00 5.34
699 3483 0.320771 GAGCACACATTGGACCGTCT 60.321 55.000 0.00 0.00 0.00 4.18
982 3798 1.055040 ATCACTGCTAGATCTGGGCC 58.945 55.000 5.18 0.00 0.00 5.80
1044 3860 0.463204 ACTCCATGCCGTCAGATGAG 59.537 55.000 0.00 0.00 0.00 2.90
1117 3955 2.125512 GTCGGCGCACTCATCCTT 60.126 61.111 10.83 0.00 0.00 3.36
1146 3984 3.849574 TCTTGGAGTTGATGTTGGGGATA 59.150 43.478 0.00 0.00 0.00 2.59
1234 4081 3.121030 GTCAGACGCAGCGGCATT 61.121 61.111 25.80 0.00 37.34 3.56
1235 4082 4.377708 TGTCAGACGCAGCGGCAT 62.378 61.111 25.80 4.90 37.34 4.40
1276 4123 2.192263 GTCCCAGATCTTGAGGTCCTT 58.808 52.381 0.00 0.00 0.00 3.36
1343 4190 6.042666 TGGTCGAATTGAAGGATATCATACCA 59.957 38.462 4.83 2.80 0.00 3.25
1402 4250 3.003173 CCGAGTGCCAGAAGGGGA 61.003 66.667 0.00 0.00 37.04 4.81
1544 4398 1.327460 CCAATGTCCACGTCGCTAATG 59.673 52.381 0.00 0.00 0.00 1.90
1583 4438 5.140454 AGATGATGCCCTAACCAATTTACC 58.860 41.667 0.00 0.00 0.00 2.85
1608 4463 7.712639 ACATATCAGTGAAACATATCAGACCAC 59.287 37.037 0.00 0.00 41.43 4.16
1609 4464 7.712205 CACATATCAGTGAAACATATCAGACCA 59.288 37.037 0.00 0.00 42.05 4.02
1610 4465 7.307632 GCACATATCAGTGAAACATATCAGACC 60.308 40.741 0.00 0.00 42.05 3.85
1670 4530 7.647318 CAGCTAGTAAGTTCACACTGATCATAG 59.353 40.741 0.00 0.00 31.60 2.23
1799 4699 3.155501 AGTGACCTCCCGTGCTATATAC 58.844 50.000 0.00 0.00 0.00 1.47
1906 4809 6.404074 GGGTGTCAAAGAGAAGCATTAATCTG 60.404 42.308 0.00 0.00 0.00 2.90
2004 4916 2.355756 GCCACTAATCGTGTCGGTAGTA 59.644 50.000 6.28 0.00 42.20 1.82
2104 5031 3.584848 ACTGAAATGCCCACTAGTTCTCT 59.415 43.478 0.00 0.00 0.00 3.10
2111 5038 3.706594 CTCCTCTACTGAAATGCCCACTA 59.293 47.826 0.00 0.00 0.00 2.74
2252 5182 0.442310 TCACGCAAGCATAAACGCTC 59.558 50.000 0.00 0.00 42.89 5.03
2302 5233 0.320771 GTGGACTACACTGCCCACTG 60.321 60.000 0.00 0.00 46.72 3.66
2325 5256 3.617531 CGGCTCCTTATGGATCATACCAC 60.618 52.174 0.00 0.00 43.03 4.16
2338 5269 4.043059 AGAGAGATACATACCGGCTCCTTA 59.957 45.833 0.00 0.00 0.00 2.69
2349 5280 5.316183 ACCATCCACCCTAGAGAGATACATA 59.684 44.000 0.00 0.00 0.00 2.29
2463 5440 8.788806 TCGCAACAATCTCTCCTTAATTTTAAA 58.211 29.630 0.00 0.00 0.00 1.52
2472 5449 1.347707 TGGTCGCAACAATCTCTCCTT 59.652 47.619 0.00 0.00 0.00 3.36
2473 5450 0.976641 TGGTCGCAACAATCTCTCCT 59.023 50.000 0.00 0.00 0.00 3.69
2498 5475 7.526608 CACCACGACAAGTTAAATTGATATGT 58.473 34.615 21.48 10.74 34.20 2.29
2568 5546 7.223260 TGATTTTCATCTTCTGTGCTGATTT 57.777 32.000 0.00 0.00 0.00 2.17
2885 5866 9.120538 GCCTTCCTTTTTCCTCTTTTTATTTTT 57.879 29.630 0.00 0.00 0.00 1.94
2933 5914 5.826586 TCACAAAATAGACGTGCACAAAAT 58.173 33.333 18.64 1.29 0.00 1.82
2961 5942 6.840780 ACAAGAATTTTGGAATAGAGGGTG 57.159 37.500 5.68 0.00 0.00 4.61
2962 5943 7.855784 AAACAAGAATTTTGGAATAGAGGGT 57.144 32.000 5.68 0.00 0.00 4.34
2963 5944 9.639601 GTAAAACAAGAATTTTGGAATAGAGGG 57.360 33.333 5.68 0.00 33.80 4.30
2971 5952 9.883142 AGACAAATGTAAAACAAGAATTTTGGA 57.117 25.926 7.55 0.00 31.16 3.53
3016 5997 9.607988 ACGGATGTATCAAATCACATTTTAGTA 57.392 29.630 0.00 0.00 35.55 1.82
3017 5998 8.506168 ACGGATGTATCAAATCACATTTTAGT 57.494 30.769 0.00 0.00 35.55 2.24
3051 6032 9.463443 CCGTCTCAAAATTCTTGTCTTAAATTT 57.537 29.630 0.00 0.00 34.86 1.82
3052 6033 8.846211 TCCGTCTCAAAATTCTTGTCTTAAATT 58.154 29.630 0.00 0.00 0.00 1.82
3053 6034 8.391075 TCCGTCTCAAAATTCTTGTCTTAAAT 57.609 30.769 0.00 0.00 0.00 1.40
3054 6035 7.041372 CCTCCGTCTCAAAATTCTTGTCTTAAA 60.041 37.037 0.00 0.00 0.00 1.52
3055 6036 6.426937 CCTCCGTCTCAAAATTCTTGTCTTAA 59.573 38.462 0.00 0.00 0.00 1.85
3056 6037 5.932303 CCTCCGTCTCAAAATTCTTGTCTTA 59.068 40.000 0.00 0.00 0.00 2.10
3057 6038 4.757149 CCTCCGTCTCAAAATTCTTGTCTT 59.243 41.667 0.00 0.00 0.00 3.01
3058 6039 4.319177 CCTCCGTCTCAAAATTCTTGTCT 58.681 43.478 0.00 0.00 0.00 3.41
3059 6040 3.437049 CCCTCCGTCTCAAAATTCTTGTC 59.563 47.826 0.00 0.00 0.00 3.18
3060 6041 3.072476 TCCCTCCGTCTCAAAATTCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
3061 6042 3.674997 TCCCTCCGTCTCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.