Multiple sequence alignment - TraesCS7D01G002000

Loading Multiple Alignment...

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 TraesCS7D01G002000 chr7D 100.000 3772 0 0 1 3772 1463656 1467427 0 6966
1 TraesCS7D01G002000 chr7D 96.970 2871 80 4 1 2869 580137557 580134692 0 4813
2 TraesCS7D01G002000 chr7D 98.644 885 12 0 2888 3772 1479678 1480562 0 1568
3 TraesCS7D01G002000 chr7D 96.384 885 32 0 2888 3772 83912086 83911202 0 1458
4 TraesCS7D01G002000 chr7D 96.384 885 32 0 2888 3772 230684521 230685405 0 1458
5 TraesCS7D01G002000 chr7D 96.284 888 33 0 2885 3772 460066622 460067509 0 1458
6 TraesCS7D01G002000 chr2D 97.248 2871 73 4 1 2869 481529466 481532332 0 4859
7 TraesCS7D01G002000 chr2D 97.109 2871 77 5 1 2869 411644018 411646884 0 4837
8 TraesCS7D01G002000 chr2D 96.723 885 29 0 2888 3772 161005845 161006729 0 1474
9 TraesCS7D01G002000 chr2D 96.271 885 33 0 2888 3772 460679148 460680032 0 1452
10 TraesCS7D01G002000 chr3D 96.972 2873 76 6 1 2869 591901101 591898236 0 4813
11 TraesCS7D01G002000 chr3D 96.692 2872 88 4 1 2869 80463070 80465937 0 4771
12 TraesCS7D01G002000 chr4D 96.830 2871 82 6 1 2869 68755957 68758820 0 4789
13 TraesCS7D01G002000 chr6D 96.696 2875 86 7 1 2869 448264691 448261820 0 4774
14 TraesCS7D01G002000 chr5D 96.656 2871 91 4 1 2869 449467416 449470283 0 4765
15 TraesCS7D01G002000 chr5D 96.723 885 29 0 2888 3772 404283092 404283976 0 1474
16 TraesCS7D01G002000 chr5D 96.384 885 32 0 2888 3772 209924669 209925553 0 1458
17 TraesCS7D01G002000 chr1D 96.657 2872 84 7 1 2869 421632577 421635439 0 4761
18 TraesCS7D01G002000 chr1D 96.045 885 35 0 2888 3772 422591152 422590268 0 1441


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 TraesCS7D01G002000 chr7D 1463656 1467427 3771 False 6966 6966 100.000 1 3772 1 chr7D.!!$F1 3771
1 TraesCS7D01G002000 chr7D 580134692 580137557 2865 True 4813 4813 96.970 1 2869 1 chr7D.!!$R2 2868
2 TraesCS7D01G002000 chr7D 1479678 1480562 884 False 1568 1568 98.644 2888 3772 1 chr7D.!!$F2 884
3 TraesCS7D01G002000 chr7D 83911202 83912086 884 True 1458 1458 96.384 2888 3772 1 chr7D.!!$R1 884
4 TraesCS7D01G002000 chr7D 230684521 230685405 884 False 1458 1458 96.384 2888 3772 1 chr7D.!!$F3 884
5 TraesCS7D01G002000 chr7D 460066622 460067509 887 False 1458 1458 96.284 2885 3772 1 chr7D.!!$F4 887
6 TraesCS7D01G002000 chr2D 481529466 481532332 2866 False 4859 4859 97.248 1 2869 1 chr2D.!!$F4 2868
7 TraesCS7D01G002000 chr2D 411644018 411646884 2866 False 4837 4837 97.109 1 2869 1 chr2D.!!$F2 2868
8 TraesCS7D01G002000 chr2D 161005845 161006729 884 False 1474 1474 96.723 2888 3772 1 chr2D.!!$F1 884
9 TraesCS7D01G002000 chr2D 460679148 460680032 884 False 1452 1452 96.271 2888 3772 1 chr2D.!!$F3 884
10 TraesCS7D01G002000 chr3D 591898236 591901101 2865 True 4813 4813 96.972 1 2869 1 chr3D.!!$R1 2868
11 TraesCS7D01G002000 chr3D 80463070 80465937 2867 False 4771 4771 96.692 1 2869 1 chr3D.!!$F1 2868
12 TraesCS7D01G002000 chr4D 68755957 68758820 2863 False 4789 4789 96.830 1 2869 1 chr4D.!!$F1 2868
13 TraesCS7D01G002000 chr6D 448261820 448264691 2871 True 4774 4774 96.696 1 2869 1 chr6D.!!$R1 2868
14 TraesCS7D01G002000 chr5D 449467416 449470283 2867 False 4765 4765 96.656 1 2869 1 chr5D.!!$F3 2868
15 TraesCS7D01G002000 chr5D 404283092 404283976 884 False 1474 1474 96.723 2888 3772 1 chr5D.!!$F2 884
16 TraesCS7D01G002000 chr5D 209924669 209925553 884 False 1458 1458 96.384 2888 3772 1 chr5D.!!$F1 884
17 TraesCS7D01G002000 chr1D 421632577 421635439 2862 False 4761 4761 96.657 1 2869 1 chr1D.!!$F1 2868
18 TraesCS7D01G002000 chr1D 422590268 422591152 884 True 1441 1441 96.045 2888 3772 1 chr1D.!!$R1 884

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
195 196 1.143305 CTTTCCGCATATCGCTCCTG 58.857 55.0 0.0 0.0 39.08 3.86 F
1366 1378 0.391130 TGGCGTACAAGGAGATGCAC 60.391 55.0 0.0 0.0 0.00 4.57 F
1974 1989 0.462047 ACAATCCCGAATCCTCGCAC 60.462 55.0 0.0 0.0 44.04 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 1750 0.107897 TGGAGATTGTGCCGCGTAAT 60.108 50.0 4.92 0.0 0.00 1.89 R
2195 2210 1.087771 GTCCAATACGCCGGGTTCAG 61.088 60.0 2.18 0.0 0.00 3.02 R
3378 3394 0.179137 CAGGTGCATTAGCTCGACGA 60.179 55.0 0.00 0.0 42.74 4.20 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
64 65 6.993902 ACTAACAAATCTTCCAACCGACTAAA 59.006 34.615 0.00 0.00 0.00 1.85
104 105 1.308047 GACCATCCATGCGCATTACA 58.692 50.000 22.81 7.72 0.00 2.41
195 196 1.143305 CTTTCCGCATATCGCTCCTG 58.857 55.000 0.00 0.00 39.08 3.86
241 242 3.141488 CAGAGGTAGCCGTCGCCT 61.141 66.667 0.00 0.00 34.57 5.52
342 343 5.419542 TCCCATCTCTTGAAACGTTCATAG 58.580 41.667 0.00 0.00 39.84 2.23
407 409 2.615447 AGAGATGCCATATTTGTGTGCG 59.385 45.455 0.00 0.00 0.00 5.34
430 432 5.874810 CGAGATCTTTGGTATTTGTTCCTGA 59.125 40.000 0.00 0.00 0.00 3.86
431 433 6.036517 CGAGATCTTTGGTATTTGTTCCTGAG 59.963 42.308 0.00 0.00 0.00 3.35
445 447 5.947663 TGTTCCTGAGGGATTAGTTTTTCA 58.052 37.500 0.00 0.00 41.87 2.69
634 637 8.573885 ACTGGATTACTATGAATGATTTGCATG 58.426 33.333 0.00 0.00 37.28 4.06
823 831 3.740115 AGATGTGGCGTACAAAGACTTT 58.260 40.909 0.00 0.00 43.77 2.66
886 894 7.284034 AGTTGCTGGATTATTTAGGACTGATTG 59.716 37.037 0.00 0.00 0.00 2.67
957 965 2.676076 GCGTTTGCTGGAAATTCATGT 58.324 42.857 0.00 0.00 38.39 3.21
958 966 3.059166 GCGTTTGCTGGAAATTCATGTT 58.941 40.909 0.00 0.00 38.39 2.71
1171 1180 4.812476 CGCCGGGAGATTGACGCA 62.812 66.667 2.18 0.00 0.00 5.24
1264 1273 5.926542 GCTTAAGGATGAGCGTGTTGATATA 59.073 40.000 4.29 0.00 0.00 0.86
1366 1378 0.391130 TGGCGTACAAGGAGATGCAC 60.391 55.000 0.00 0.00 0.00 4.57
1434 1446 0.944311 GAGCGTGTCAACATGGACGT 60.944 55.000 0.00 0.00 40.72 4.34
1456 1468 3.585990 GTGTTGCAGGCACGTGCT 61.586 61.111 36.84 21.66 44.32 4.40
1484 1496 1.352352 ACATTAGGCTGCAACAGGAGT 59.648 47.619 0.50 0.00 31.21 3.85
1620 1632 1.471676 GCATGTCTTCAGTACTCCCCG 60.472 57.143 0.00 0.00 0.00 5.73
1682 1694 8.570488 TCACGACCGATATTGTGTATTAATAGT 58.430 33.333 0.00 0.00 35.71 2.12
1683 1695 9.188588 CACGACCGATATTGTGTATTAATAGTT 57.811 33.333 0.00 0.00 30.41 2.24
1735 1750 3.632643 TCATATGCAGTCCAAGAAGCA 57.367 42.857 0.00 0.00 41.73 3.91
1758 1773 1.577328 CGCGGCACAATCTCCAAACT 61.577 55.000 0.00 0.00 0.00 2.66
1925 1940 3.043586 GTGTAACTCTATGTCGGCGATG 58.956 50.000 14.79 4.31 0.00 3.84
1974 1989 0.462047 ACAATCCCGAATCCTCGCAC 60.462 55.000 0.00 0.00 44.04 5.34
2106 2121 5.008811 GTGAGATACTCGTATGTAGGTGCTT 59.991 44.000 0.00 0.00 32.35 3.91
2195 2210 5.033589 AGACCCATTGAGATGAGATTGTC 57.966 43.478 0.00 0.00 35.16 3.18
2240 2255 7.771927 ATGATTTTCTCATGAAAGAAGTGGT 57.228 32.000 0.00 0.00 43.15 4.16
2253 2268 6.657541 TGAAAGAAGTGGTTGGATATGGTTAC 59.342 38.462 0.00 0.00 0.00 2.50
2380 2395 1.571460 CTGAACGGCAGCAAGACAC 59.429 57.895 0.00 0.00 37.90 3.67
2476 2491 7.989741 AGGTTCCTATTCTTCATGTTACATCAG 59.010 37.037 0.00 0.00 0.00 2.90
2600 2615 2.884639 GCTTGAGGCAAAGGAACAACTA 59.115 45.455 2.66 0.00 41.35 2.24
2626 2641 7.735326 ACTCCTTAGGTTACATTGATGTACT 57.265 36.000 3.42 2.32 42.48 2.73
2775 2790 9.877178 TTAAATGTTTTAAGCTGGAGACAAAAA 57.123 25.926 0.00 0.00 42.06 1.94
2869 2885 8.814235 CATTTTTGCTAGAATGTGATTTCCATC 58.186 33.333 0.00 0.00 0.00 3.51
2870 2886 7.465353 TTTTGCTAGAATGTGATTTCCATCA 57.535 32.000 0.00 0.00 37.05 3.07
2871 2887 7.465353 TTTGCTAGAATGTGATTTCCATCAA 57.535 32.000 0.00 0.00 41.30 2.57
2872 2888 6.688637 TGCTAGAATGTGATTTCCATCAAG 57.311 37.500 0.00 0.00 41.30 3.02
2873 2889 5.066893 TGCTAGAATGTGATTTCCATCAAGC 59.933 40.000 0.00 0.00 41.30 4.01
2874 2890 5.066893 GCTAGAATGTGATTTCCATCAAGCA 59.933 40.000 0.00 0.00 41.30 3.91
2875 2891 5.320549 AGAATGTGATTTCCATCAAGCAC 57.679 39.130 0.00 0.00 41.30 4.40
2876 2892 5.014858 AGAATGTGATTTCCATCAAGCACT 58.985 37.500 3.74 0.00 41.30 4.40
2877 2893 5.479375 AGAATGTGATTTCCATCAAGCACTT 59.521 36.000 3.74 0.00 41.30 3.16
2878 2894 4.771590 TGTGATTTCCATCAAGCACTTC 57.228 40.909 3.74 0.00 41.30 3.01
2879 2895 4.143543 TGTGATTTCCATCAAGCACTTCA 58.856 39.130 3.74 0.00 41.30 3.02
2880 2896 4.768448 TGTGATTTCCATCAAGCACTTCAT 59.232 37.500 3.74 0.00 41.30 2.57
2881 2897 5.100259 GTGATTTCCATCAAGCACTTCATG 58.900 41.667 0.00 0.00 41.30 3.07
2882 2898 4.768448 TGATTTCCATCAAGCACTTCATGT 59.232 37.500 0.00 0.00 36.41 3.21
2883 2899 5.244402 TGATTTCCATCAAGCACTTCATGTT 59.756 36.000 0.00 0.00 36.41 2.71
2886 2902 3.890756 TCCATCAAGCACTTCATGTTTGT 59.109 39.130 3.86 0.00 46.54 2.83
2912 2928 1.554160 CAGGACTCTTGCTGAGATGGT 59.446 52.381 12.88 0.00 43.79 3.55
3075 3091 7.360113 ACCCAATGTGAGTTATTTCAAAGTT 57.640 32.000 0.00 0.00 0.00 2.66
3199 3215 5.068198 ACCTACAGAGTCTTCAACAACGTTA 59.932 40.000 0.00 0.00 0.00 3.18
3220 3236 7.066043 ACGTTATTCACAAGGTTGTTGAAACTA 59.934 33.333 9.98 0.00 39.91 2.24
3378 3394 6.176183 AGAATTCATTCCAGAACGTGAAGAT 58.824 36.000 8.44 0.00 37.51 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 2.356741 CCGTCCATGATTTTAGGGTGGT 60.357 50.000 0.00 0.00 0.00 4.16
104 105 9.952188 CCGTGATATCTGACGATATATTTACAT 57.048 33.333 15.12 0.00 41.70 2.29
195 196 0.608308 ACTTTCTGGGCGGTTAAGGC 60.608 55.000 0.00 0.00 0.00 4.35
241 242 0.969149 AGAGCGATGGCGATTATCCA 59.031 50.000 0.00 0.00 46.35 3.41
348 350 3.146066 CCTTTTTGGTCCAATCGACAGA 58.854 45.455 4.80 0.00 43.95 3.41
407 409 6.317391 CCTCAGGAACAAATACCAAAGATCTC 59.683 42.308 0.00 0.00 0.00 2.75
430 432 5.816682 ACCTTCGATGAAAAACTAATCCCT 58.183 37.500 0.00 0.00 0.00 4.20
431 433 6.822170 AGTACCTTCGATGAAAAACTAATCCC 59.178 38.462 0.00 0.00 0.00 3.85
445 447 4.839121 TGCACCAAAATAGTACCTTCGAT 58.161 39.130 0.00 0.00 0.00 3.59
634 637 6.071952 TGCATAAAATTCTTCACTCCAACCTC 60.072 38.462 0.00 0.00 0.00 3.85
823 831 8.311836 CACCTCCTTTACTGTAGTATTGAGAAA 58.688 37.037 11.44 0.00 0.00 2.52
886 894 3.644966 TGGTATGAACAACCTCATCCC 57.355 47.619 0.00 0.00 37.27 3.85
957 965 5.432645 TGGTATGTGTGAGACAAACTGAAA 58.567 37.500 0.00 0.00 38.36 2.69
958 966 5.029807 TGGTATGTGTGAGACAAACTGAA 57.970 39.130 0.00 0.00 38.36 3.02
1165 1174 1.433053 CGTGTTGGACCTTTGCGTCA 61.433 55.000 0.00 0.00 34.24 4.35
1171 1180 1.011333 CACGTTCGTGTTGGACCTTT 58.989 50.000 15.81 0.00 0.00 3.11
1264 1273 4.989797 CGCATCTGCTTAATCTTCTGAGAT 59.010 41.667 0.09 0.00 40.68 2.75
1320 1332 2.286365 TTTCTTTTCCATGGCCTCGT 57.714 45.000 6.96 0.00 0.00 4.18
1366 1378 3.257127 TCCGGTCCTTTTGCAATTTAAGG 59.743 43.478 18.56 18.56 39.82 2.69
1434 1446 1.100463 ACGTGCCTGCAACACATTCA 61.100 50.000 17.08 0.00 37.93 2.57
1456 1468 5.689835 TGTTGCAGCCTAATGTCCATATTA 58.310 37.500 0.00 0.00 0.00 0.98
1484 1496 2.290260 CCTTGTAGTCCATGTCCTTGCA 60.290 50.000 0.00 0.00 0.00 4.08
1587 1599 2.350522 AGACATGCTCTTGCGGTTTAG 58.649 47.619 0.00 0.00 43.34 1.85
1589 1601 1.537202 GAAGACATGCTCTTGCGGTTT 59.463 47.619 13.14 0.00 39.53 3.27
1620 1632 1.860676 TCGTTGCAAGGTACTCACAC 58.139 50.000 17.96 0.00 38.49 3.82
1690 1703 5.986004 AGCTTACACAAAGTTACTCACAC 57.014 39.130 0.00 0.00 37.53 3.82
1735 1750 0.107897 TGGAGATTGTGCCGCGTAAT 60.108 50.000 4.92 0.00 0.00 1.89
1758 1773 2.693591 CCGACATCACTAGGCCTTTAGA 59.306 50.000 12.58 6.90 0.00 2.10
1925 1940 2.288825 TGGATGCTTAGCCTACGTATGC 60.289 50.000 14.20 14.20 0.00 3.14
2106 2121 9.928618 TCCCTATGAATGTAAAATTCCATTACA 57.071 29.630 4.19 4.19 44.69 2.41
2195 2210 1.087771 GTCCAATACGCCGGGTTCAG 61.088 60.000 2.18 0.00 0.00 3.02
2240 2255 8.657387 TGAATCCTTTTTGTAACCATATCCAA 57.343 30.769 0.00 0.00 0.00 3.53
2253 2268 7.661040 AGTGGTACAAATCTGAATCCTTTTTG 58.339 34.615 0.00 0.00 44.16 2.44
2380 2395 8.332464 ACGATTATACACCAAATACAAATGACG 58.668 33.333 0.00 0.00 0.00 4.35
2412 2427 5.586243 CGACCACCACTCATAATCATCTTTT 59.414 40.000 0.00 0.00 0.00 2.27
2476 2491 4.965119 AAGGATGATGAAGCCGTAAAAC 57.035 40.909 0.00 0.00 0.00 2.43
2600 2615 8.603304 AGTACATCAATGTAACCTAAGGAGTTT 58.397 33.333 4.48 0.00 44.11 2.66
2626 2641 6.435904 CCCACCTTCTCCAATATTTTTACACA 59.564 38.462 0.00 0.00 0.00 3.72
2805 2821 5.066375 TCCATCGTGAATGAATTGTTCCATC 59.934 40.000 0.00 0.00 37.59 3.51
2869 2885 6.264832 TGTTCTTACAAACATGAAGTGCTTG 58.735 36.000 0.00 0.00 39.30 4.01
2870 2886 6.449635 TGTTCTTACAAACATGAAGTGCTT 57.550 33.333 0.00 0.00 34.31 3.91
2871 2887 5.009010 CCTGTTCTTACAAACATGAAGTGCT 59.991 40.000 0.00 0.00 38.41 4.40
2872 2888 5.008613 TCCTGTTCTTACAAACATGAAGTGC 59.991 40.000 0.00 0.00 38.41 4.40
2873 2889 6.260936 AGTCCTGTTCTTACAAACATGAAGTG 59.739 38.462 0.00 0.00 38.41 3.16
2874 2890 6.357367 AGTCCTGTTCTTACAAACATGAAGT 58.643 36.000 0.00 0.00 38.41 3.01
2875 2891 6.708054 AGAGTCCTGTTCTTACAAACATGAAG 59.292 38.462 0.00 0.00 38.41 3.02
2876 2892 6.591935 AGAGTCCTGTTCTTACAAACATGAA 58.408 36.000 0.00 0.00 38.41 2.57
2877 2893 6.174720 AGAGTCCTGTTCTTACAAACATGA 57.825 37.500 0.00 0.00 38.41 3.07
2878 2894 6.662616 CAAGAGTCCTGTTCTTACAAACATG 58.337 40.000 0.00 0.00 38.41 3.21
2879 2895 5.239525 GCAAGAGTCCTGTTCTTACAAACAT 59.760 40.000 0.00 0.00 38.41 2.71
2880 2896 4.574828 GCAAGAGTCCTGTTCTTACAAACA 59.425 41.667 0.00 0.00 37.56 2.83
2881 2897 4.816925 AGCAAGAGTCCTGTTCTTACAAAC 59.183 41.667 0.00 0.00 33.30 2.93
2882 2898 4.816385 CAGCAAGAGTCCTGTTCTTACAAA 59.184 41.667 0.00 0.00 33.30 2.83
2883 2899 4.100963 TCAGCAAGAGTCCTGTTCTTACAA 59.899 41.667 0.00 0.00 33.30 2.41
2886 2902 4.152647 TCTCAGCAAGAGTCCTGTTCTTA 58.847 43.478 6.15 0.00 44.98 2.10
2912 2928 7.920160 TTGTATTCATCAAGCATAGTGTGAA 57.080 32.000 0.00 0.00 0.00 3.18
3199 3215 8.918202 TCTATAGTTTCAACAACCTTGTGAAT 57.082 30.769 0.00 0.00 41.31 2.57
3220 3236 5.292765 AGTTTCATCGAATCGCACATCTAT 58.707 37.500 0.00 0.00 0.00 1.98
3378 3394 0.179137 CAGGTGCATTAGCTCGACGA 60.179 55.000 0.00 0.00 42.74 4.20


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

AutoCloner maintained by Alex Coulton.