Multiple sequence alignment - TraesCS7D01G325300

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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 TraesCS7D01G325300 chr7D 100.000 2948 0 0 1 2948 415683924 415680977 0.000000e+00 5445.0
1 TraesCS7D01G325300 chr7D 83.729 1180 176 16 755 1924 529472978 529471805 0.000000e+00 1101.0
2 TraesCS7D01G325300 chr7D 83.517 1177 187 7 752 1924 415395534 415394361 0.000000e+00 1092.0
3 TraesCS7D01G325300 chr7D 91.000 200 18 0 2178 2377 415650401 415650202 1.350000e-68 270.0
4 TraesCS7D01G325300 chr7B 94.895 1998 59 19 280 2248 429268579 429266596 0.000000e+00 3085.0
5 TraesCS7D01G325300 chr7B 83.065 1181 186 14 753 1924 567546603 567547778 0.000000e+00 1061.0
6 TraesCS7D01G325300 chr7B 87.179 195 20 5 2178 2370 620984265 620984456 1.780000e-52 217.0
7 TraesCS7D01G325300 chr7A 95.392 1758 49 17 335 2067 477810293 477808543 0.000000e+00 2769.0
8 TraesCS7D01G325300 chr7A 83.786 1178 184 7 752 1924 477187742 477186567 0.000000e+00 1110.0
9 TraesCS7D01G325300 chr7A 83.736 910 131 13 1029 1924 608903857 608904763 0.000000e+00 845.0
10 TraesCS7D01G325300 chr7A 91.498 247 18 2 1 245 477811958 477811713 1.310000e-88 337.0
11 TraesCS7D01G325300 chr7A 85.271 258 35 3 752 1007 608903136 608903392 2.250000e-66 263.0
12 TraesCS7D01G325300 chr7A 88.415 164 7 5 230 385 477810451 477810292 1.400000e-43 187.0
13 TraesCS7D01G325300 chr7A 80.469 256 27 13 928 1180 511696127 511695892 1.090000e-39 174.0
14 TraesCS7D01G325300 chr3B 88.553 760 85 2 2185 2943 157659524 157658766 0.000000e+00 920.0
15 TraesCS7D01G325300 chr2B 85.990 778 101 5 2170 2945 51726902 51727673 0.000000e+00 826.0
16 TraesCS7D01G325300 chr2B 82.497 777 111 17 2174 2945 357892992 357892236 0.000000e+00 658.0
17 TraesCS7D01G325300 chr2B 88.710 62 6 1 1117 1178 800457391 800457331 1.130000e-09 75.0
18 TraesCS7D01G325300 chr5B 85.104 772 107 7 2176 2945 268285491 268284726 0.000000e+00 782.0
19 TraesCS7D01G325300 chr5B 85.274 584 82 4 2363 2945 662944148 662944728 1.510000e-167 599.0
20 TraesCS7D01G325300 chr1D 85.195 770 86 9 2177 2945 487857761 487857019 0.000000e+00 765.0
21 TraesCS7D01G325300 chr2D 83.943 766 107 10 2178 2940 404379433 404378681 0.000000e+00 719.0
22 TraesCS7D01G325300 chr6D 82.902 772 116 11 2176 2944 445457606 445456848 0.000000e+00 680.0
23 TraesCS7D01G325300 chr5D 86.219 566 78 0 2380 2945 509682003 509682568 5.400000e-172 614.0
24 TraesCS7D01G325300 chr3D 86.727 550 73 0 2396 2945 478661517 478662066 1.940000e-171 612.0
25 TraesCS7D01G325300 chr5A 81.099 746 131 10 2204 2945 125992774 125993513 3.270000e-164 588.0
26 TraesCS7D01G325300 chr2A 75.916 764 132 37 2178 2917 17747533 17748268 7.820000e-91 344.0
27 TraesCS7D01G325300 chr1B 75.806 186 33 12 968 1144 137625515 137625697 1.880000e-12 84.2


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 TraesCS7D01G325300 chr7D 415680977 415683924 2947 True 5445.000000 5445 100.000000 1 2948 1 chr7D.!!$R3 2947
1 TraesCS7D01G325300 chr7D 529471805 529472978 1173 True 1101.000000 1101 83.729000 755 1924 1 chr7D.!!$R4 1169
2 TraesCS7D01G325300 chr7D 415394361 415395534 1173 True 1092.000000 1092 83.517000 752 1924 1 chr7D.!!$R1 1172
3 TraesCS7D01G325300 chr7B 429266596 429268579 1983 True 3085.000000 3085 94.895000 280 2248 1 chr7B.!!$R1 1968
4 TraesCS7D01G325300 chr7B 567546603 567547778 1175 False 1061.000000 1061 83.065000 753 1924 1 chr7B.!!$F1 1171
5 TraesCS7D01G325300 chr7A 477186567 477187742 1175 True 1110.000000 1110 83.786000 752 1924 1 chr7A.!!$R1 1172
6 TraesCS7D01G325300 chr7A 477808543 477811958 3415 True 1097.666667 2769 91.768333 1 2067 3 chr7A.!!$R3 2066
7 TraesCS7D01G325300 chr7A 608903136 608904763 1627 False 554.000000 845 84.503500 752 1924 2 chr7A.!!$F1 1172
8 TraesCS7D01G325300 chr3B 157658766 157659524 758 True 920.000000 920 88.553000 2185 2943 1 chr3B.!!$R1 758
9 TraesCS7D01G325300 chr2B 51726902 51727673 771 False 826.000000 826 85.990000 2170 2945 1 chr2B.!!$F1 775
10 TraesCS7D01G325300 chr2B 357892236 357892992 756 True 658.000000 658 82.497000 2174 2945 1 chr2B.!!$R1 771
11 TraesCS7D01G325300 chr5B 268284726 268285491 765 True 782.000000 782 85.104000 2176 2945 1 chr5B.!!$R1 769
12 TraesCS7D01G325300 chr5B 662944148 662944728 580 False 599.000000 599 85.274000 2363 2945 1 chr5B.!!$F1 582
13 TraesCS7D01G325300 chr1D 487857019 487857761 742 True 765.000000 765 85.195000 2177 2945 1 chr1D.!!$R1 768
14 TraesCS7D01G325300 chr2D 404378681 404379433 752 True 719.000000 719 83.943000 2178 2940 1 chr2D.!!$R1 762
15 TraesCS7D01G325300 chr6D 445456848 445457606 758 True 680.000000 680 82.902000 2176 2944 1 chr6D.!!$R1 768
16 TraesCS7D01G325300 chr5D 509682003 509682568 565 False 614.000000 614 86.219000 2380 2945 1 chr5D.!!$F1 565
17 TraesCS7D01G325300 chr3D 478661517 478662066 549 False 612.000000 612 86.727000 2396 2945 1 chr3D.!!$F1 549
18 TraesCS7D01G325300 chr5A 125992774 125993513 739 False 588.000000 588 81.099000 2204 2945 1 chr5A.!!$F1 741
19 TraesCS7D01G325300 chr2A 17747533 17748268 735 False 344.000000 344 75.916000 2178 2917 1 chr2A.!!$F1 739

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
802 2157 1.001974 CACATCCACTCGGACCTTGAA 59.998 52.381 0.0 0.0 46.79 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2410 4246 0.322187 TTAAGGGCTTTCGGTCCAGC 60.322 55.0 0.0 0.0 43.45 4.85 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
35 36 8.860780 AGAGAAATATTTAATCAGCCAGATCC 57.139 34.615 0.00 0.00 35.39 3.36
38 39 7.389053 AGAAATATTTAATCAGCCAGATCCGAC 59.611 37.037 0.00 0.00 35.39 4.79
61 62 4.504132 GCGAGGCGACTGATCTTT 57.496 55.556 0.00 0.00 44.43 2.52
62 63 2.755929 GCGAGGCGACTGATCTTTT 58.244 52.632 0.00 0.00 44.43 2.27
85 87 2.086251 AAAACGTCTGCCGACCCGTA 62.086 55.000 2.40 0.00 40.70 4.02
101 103 3.181475 ACCCGTAACACTGCTCATATGAG 60.181 47.826 25.64 25.64 44.75 2.90
174 176 8.181573 ACGTATATTTCCTTTTGTAGCACAATG 58.818 33.333 0.00 1.13 38.00 2.82
186 188 1.608109 AGCACAATGACATTTCACGCA 59.392 42.857 0.00 0.00 33.38 5.24
194 196 3.580731 TGACATTTCACGCACGAGAATA 58.419 40.909 3.84 0.00 0.00 1.75
224 226 1.375908 GGGAGCGTGACATGCAGAA 60.376 57.895 21.34 0.00 31.07 3.02
234 236 4.794762 CGTGACATGCAGAAAATAACATGG 59.205 41.667 0.00 0.00 43.28 3.66
489 1842 8.232913 TCATCATACTACAATGTGCTGTACTA 57.767 34.615 0.00 0.00 0.00 1.82
802 2157 1.001974 CACATCCACTCGGACCTTGAA 59.998 52.381 0.00 0.00 46.79 2.69
1440 3243 3.667282 CGGTCGTGGTCGGTGAGT 61.667 66.667 0.00 0.00 37.69 3.41
1551 3354 4.682334 TACTGGCCCGTCGACCCA 62.682 66.667 10.58 10.82 0.00 4.51
1553 3356 4.323477 CTGGCCCGTCGACCCAAA 62.323 66.667 10.58 0.00 0.00 3.28
1734 3545 3.065306 CTCCGGTACAAGCCCACA 58.935 61.111 0.00 0.00 0.00 4.17
1899 3710 2.068821 GGAGAGGGAGATGGCTGCA 61.069 63.158 0.50 0.00 33.56 4.41
1926 3737 3.744660 AGAGGATGTGCGAAGAAAAGTT 58.255 40.909 0.00 0.00 0.00 2.66
1936 3747 7.030165 TGTGCGAAGAAAAGTTGTTAAAATGA 58.970 30.769 0.00 0.00 0.00 2.57
2140 3965 4.164221 TCCAAAGGAAGCCTGAACCTATAG 59.836 45.833 0.00 0.00 32.13 1.31
2157 3982 4.570874 GCCCCCGCTTCCTGGATC 62.571 72.222 0.00 0.00 0.00 3.36
2162 3987 1.528824 CCGCTTCCTGGATCCATGT 59.471 57.895 16.63 0.00 0.00 3.21
2174 3999 3.648067 TGGATCCATGTGTCCCTAATCTC 59.352 47.826 11.44 0.00 33.45 2.75
2206 4031 1.316651 GAAGAGAGGGATTGCATGCC 58.683 55.000 16.68 0.00 41.75 4.40
2232 4059 3.829886 AATTTCATTGATCGTGCACGT 57.170 38.095 35.74 24.06 40.80 4.49
2252 4080 8.745590 TGCACGTGGTACATATATAGATACAAT 58.254 33.333 18.88 0.00 44.52 2.71
2275 4104 4.526650 TGAGTGCACCTAATGTCTTGTCTA 59.473 41.667 14.63 0.00 0.00 2.59
2317 4152 0.333312 AGGGGAGAGAGACGTGACAT 59.667 55.000 0.00 0.00 0.00 3.06
2427 4263 2.034221 GCTGGACCGAAAGCCCTT 59.966 61.111 0.00 0.00 33.12 3.95
2472 4312 1.533129 CGTCATGACATCGGCGAACTA 60.533 52.381 24.93 0.75 0.00 2.24
2496 4336 1.451927 CGGTGGGCACATGCAGTAT 60.452 57.895 6.15 0.00 44.36 2.12
2633 4473 3.264193 ACAGTAGACAATCATGGCCTTGA 59.736 43.478 22.42 22.42 33.81 3.02
2723 4564 0.537188 CCAGTACTCCGCCTCAACAT 59.463 55.000 0.00 0.00 0.00 2.71
2725 4566 2.167693 CCAGTACTCCGCCTCAACATTA 59.832 50.000 0.00 0.00 0.00 1.90
2731 4572 1.154205 CCGCCTCAACATTAGAGCGG 61.154 60.000 6.86 6.86 42.08 5.52
2795 4636 2.433436 GCCCAAGGTAAACACAGTAGG 58.567 52.381 0.00 0.00 0.00 3.18
2815 4656 1.025113 CAGAGGTGGAGCGACGAGTA 61.025 60.000 0.00 0.00 0.00 2.59
2868 4709 4.570663 GACGAGATCGGTGGCGGG 62.571 72.222 7.22 0.00 44.95 6.13
2919 4760 1.337447 GGTGCCACGTATATACCGCAT 60.337 52.381 15.87 0.00 0.00 4.73
2931 4772 9.642327 ACGTATATACCGCATAATACATTTCAA 57.358 29.630 7.30 0.00 0.00 2.69
2945 4786 3.256631 ACATTTCAACAGAGCCCAATGAC 59.743 43.478 0.00 0.00 0.00 3.06
2946 4787 2.957402 TTCAACAGAGCCCAATGACT 57.043 45.000 0.00 0.00 0.00 3.41
2947 4788 4.365514 TTTCAACAGAGCCCAATGACTA 57.634 40.909 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.171476 CGTCGGATCTGGCTGATTAAATAT 58.829 41.667 8.36 0.00 35.14 1.28
73 75 1.736645 CAGTGTTACGGGTCGGCAG 60.737 63.158 0.00 0.00 0.00 4.85
74 76 2.340809 CAGTGTTACGGGTCGGCA 59.659 61.111 0.00 0.00 0.00 5.69
76 78 1.445582 GAGCAGTGTTACGGGTCGG 60.446 63.158 0.00 0.00 31.90 4.79
78 80 2.953466 TATGAGCAGTGTTACGGGTC 57.047 50.000 4.71 4.71 40.37 4.46
81 83 4.307443 TCTCATATGAGCAGTGTTACGG 57.693 45.455 25.27 1.23 41.80 4.02
85 87 8.743085 AATGTAAATCTCATATGAGCAGTGTT 57.257 30.769 25.27 16.00 41.80 3.32
128 130 2.939103 GTGGATAGTGAACAGATGTGCC 59.061 50.000 0.00 0.00 0.00 5.01
174 176 4.577687 TTATTCTCGTGCGTGAAATGTC 57.422 40.909 12.01 0.00 32.50 3.06
186 188 7.974501 CGCTCCCTAACATTATATTATTCTCGT 59.025 37.037 0.00 0.00 0.00 4.18
194 196 6.169557 TGTCACGCTCCCTAACATTATATT 57.830 37.500 0.00 0.00 0.00 1.28
258 1537 6.671614 CATTTTGTGCTACCTACGGAAATA 57.328 37.500 0.00 0.00 0.00 1.40
489 1842 2.648059 GCATGTACAAGCAGAGGGATT 58.352 47.619 17.73 0.00 0.00 3.01
1543 3346 1.226746 CACTTGTCCTTTGGGTCGAC 58.773 55.000 7.13 7.13 0.00 4.20
1551 3354 3.660111 GCGCGGCACTTGTCCTTT 61.660 61.111 8.83 0.00 0.00 3.11
1899 3710 0.984230 TTCGCACATCCTCTTCCCTT 59.016 50.000 0.00 0.00 0.00 3.95
1926 3737 4.043561 TGCTACCTCCCCTTCATTTTAACA 59.956 41.667 0.00 0.00 0.00 2.41
1936 3747 2.692741 GGGCTGCTACCTCCCCTT 60.693 66.667 0.00 0.00 34.59 3.95
1999 3824 4.344679 TGTTCCATTTGGTTGATCTTGCTT 59.655 37.500 0.00 0.00 36.34 3.91
2035 3860 8.940768 AAATACTCTAAGCTTGTCTTCATCTC 57.059 34.615 9.86 0.00 36.25 2.75
2117 3942 1.149101 AGGTTCAGGCTTCCTTTGGA 58.851 50.000 0.00 0.00 0.00 3.53
2118 3943 2.879103 TAGGTTCAGGCTTCCTTTGG 57.121 50.000 7.75 0.00 33.34 3.28
2140 3965 4.570874 GATCCAGGAAGCGGGGGC 62.571 72.222 0.00 0.00 0.00 5.80
2157 3982 4.848357 ACAAAGAGATTAGGGACACATGG 58.152 43.478 0.00 0.00 0.00 3.66
2162 3987 7.676893 TCCTAACTTACAAAGAGATTAGGGACA 59.323 37.037 7.76 0.00 39.34 4.02
2174 3999 6.607004 TCCCTCTCTTCCTAACTTACAAAG 57.393 41.667 0.00 0.00 0.00 2.77
2206 4031 5.842843 GTGCACGATCAATGAAATTATCGAG 59.157 40.000 11.83 6.18 39.70 4.04
2252 4080 3.324846 AGACAAGACATTAGGTGCACTCA 59.675 43.478 17.98 1.36 0.00 3.41
2254 4082 4.322801 GGTAGACAAGACATTAGGTGCACT 60.323 45.833 17.98 5.41 0.00 4.40
2275 4104 7.159372 CCTCTGTAACTTGTATGTAACTTGGT 58.841 38.462 0.00 0.00 0.00 3.67
2317 4152 3.998341 GTCTGGGTTTTATACTTCGCACA 59.002 43.478 0.00 0.00 0.00 4.57
2371 4207 2.820767 CTTCGACTGCGGGGAGTGTC 62.821 65.000 0.00 0.00 38.28 3.67
2410 4246 0.322187 TTAAGGGCTTTCGGTCCAGC 60.322 55.000 0.00 0.00 43.45 4.85
2427 4263 4.273318 GGGACTACCTACCTCGACTTTTA 58.727 47.826 0.00 0.00 35.85 1.52
2472 4312 1.078214 CATGTGCCCACCGATCAGT 60.078 57.895 0.00 0.00 0.00 3.41
2633 4473 2.509964 AGGAGTTGTTGGTTGAGGTTCT 59.490 45.455 0.00 0.00 0.00 3.01
2706 4547 3.362706 TCTAATGTTGAGGCGGAGTACT 58.637 45.455 0.00 0.00 0.00 2.73
2731 4572 1.096967 AACGACAACCCACGGTTTCC 61.097 55.000 0.00 0.00 44.33 3.13
2795 4636 3.691744 CTCGTCGCTCCACCTCTGC 62.692 68.421 0.00 0.00 0.00 4.26
2842 4683 3.920144 CGATCTCGTCGCCTACTTT 57.080 52.632 0.00 0.00 44.33 2.66
2868 4709 1.194781 TCTCACCCTGACAGCTTCCC 61.195 60.000 0.00 0.00 0.00 3.97
2919 4760 6.889177 TCATTGGGCTCTGTTGAAATGTATTA 59.111 34.615 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.