Multiple sequence alignment - TraesCS7A01G295400

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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 TraesCS7A01G295400 chr7A 100.000 5490 0 0 1 5490 385426213 385431702 0.000000e+00 10139.0
1 TraesCS7A01G295400 chr7B 97.004 4606 98 12 896 5490 348980772 348976196 0.000000e+00 7705.0
2 TraesCS7A01G295400 chr7D 97.368 3229 58 12 753 3964 319900462 319903680 0.000000e+00 5467.0
3 TraesCS7A01G295400 chr7D 95.568 1083 34 6 4412 5490 319904788 319905860 0.000000e+00 1722.0
4 TraesCS7A01G295400 chr7D 85.226 731 89 13 42 755 319899432 319900160 0.000000e+00 734.0
5 TraesCS7A01G295400 chr7D 97.602 417 8 1 3960 4374 319904023 319904439 0.000000e+00 713.0
6 TraesCS7A01G295400 chr7D 84.188 234 29 4 4994 5226 319905601 319905827 2.570000e-53 220.0
7 TraesCS7A01G295400 chr7D 81.034 174 28 3 5234 5403 319906325 319906497 3.450000e-27 134.0
8 TraesCS7A01G295400 chr2B 86.946 835 88 16 21 841 439345947 439346774 0.000000e+00 918.0
9 TraesCS7A01G295400 chr2B 84.009 863 107 19 1 841 516537372 516536519 0.000000e+00 800.0
10 TraesCS7A01G295400 chr2B 82.068 764 108 21 86 834 489822496 489821747 4.670000e-175 625.0
11 TraesCS7A01G295400 chr2B 94.000 50 2 1 4844 4892 587889673 587889624 2.120000e-09 75.0
12 TraesCS7A01G295400 chr2A 85.384 821 72 19 106 898 598940160 598939360 0.000000e+00 808.0
13 TraesCS7A01G295400 chr2A 90.000 50 4 1 4844 4892 687354587 687354538 4.590000e-06 63.9
14 TraesCS7A01G295400 chr5A 83.488 860 107 20 1 841 341097518 341098361 0.000000e+00 769.0
15 TraesCS7A01G295400 chr5A 79.225 645 93 13 1 635 386469827 386469214 1.420000e-110 411.0
16 TraesCS7A01G295400 chr5D 86.233 661 72 13 7 650 284144414 284145072 0.000000e+00 699.0
17 TraesCS7A01G295400 chr4B 82.368 760 90 28 113 840 178377724 178378471 6.040000e-174 621.0
18 TraesCS7A01G295400 chr4B 92.000 50 3 1 4844 4892 354741411 354741362 9.870000e-08 69.4
19 TraesCS7A01G295400 chr4B 90.000 50 4 1 4844 4892 80393670 80393719 4.590000e-06 63.9
20 TraesCS7A01G295400 chr3D 79.358 872 118 45 1 843 351131285 351132123 1.730000e-154 556.0
21 TraesCS7A01G295400 chr4A 81.667 420 52 21 438 839 661025404 661025816 5.300000e-85 326.0
22 TraesCS7A01G295400 chr5B 94.000 50 2 1 4844 4892 242765408 242765359 2.120000e-09 75.0
23 TraesCS7A01G295400 chr5B 89.831 59 4 2 4836 4892 477005177 477005235 2.120000e-09 75.0


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 TraesCS7A01G295400 chr7A 385426213 385431702 5489 False 10139.000000 10139 100.000000 1 5490 1 chr7A.!!$F1 5489
1 TraesCS7A01G295400 chr7B 348976196 348980772 4576 True 7705.000000 7705 97.004000 896 5490 1 chr7B.!!$R1 4594
2 TraesCS7A01G295400 chr7D 319899432 319906497 7065 False 1498.333333 5467 90.164333 42 5490 6 chr7D.!!$F1 5448
3 TraesCS7A01G295400 chr2B 439345947 439346774 827 False 918.000000 918 86.946000 21 841 1 chr2B.!!$F1 820
4 TraesCS7A01G295400 chr2B 516536519 516537372 853 True 800.000000 800 84.009000 1 841 1 chr2B.!!$R2 840
5 TraesCS7A01G295400 chr2B 489821747 489822496 749 True 625.000000 625 82.068000 86 834 1 chr2B.!!$R1 748
6 TraesCS7A01G295400 chr2A 598939360 598940160 800 True 808.000000 808 85.384000 106 898 1 chr2A.!!$R1 792
7 TraesCS7A01G295400 chr5A 341097518 341098361 843 False 769.000000 769 83.488000 1 841 1 chr5A.!!$F1 840
8 TraesCS7A01G295400 chr5A 386469214 386469827 613 True 411.000000 411 79.225000 1 635 1 chr5A.!!$R1 634
9 TraesCS7A01G295400 chr5D 284144414 284145072 658 False 699.000000 699 86.233000 7 650 1 chr5D.!!$F1 643
10 TraesCS7A01G295400 chr4B 178377724 178378471 747 False 621.000000 621 82.368000 113 840 1 chr4B.!!$F2 727
11 TraesCS7A01G295400 chr3D 351131285 351132123 838 False 556.000000 556 79.358000 1 843 1 chr3D.!!$F1 842

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
308 344 0.813184 CTACCTACCGCCTCGTCAAA 59.187 55.0 0.0 0.0 0.00 2.69 F
1365 1767 0.031585 TTCTCGGATATTGTCGGGCG 59.968 55.0 0.0 0.0 0.00 6.13 F
2588 2990 0.178953 AGGTGCAAGCCAAATGAGGT 60.179 50.0 0.0 0.0 32.25 3.85 F
2841 3243 0.960861 GTGCTAACTTGACCCCTGGC 60.961 60.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 1989 1.181786 CGAGAAGAACCTCTGCCTCT 58.818 55.000 0.00 0.00 29.98 3.69 R
3073 3475 2.614057 CCTTCCGCAATAGACCATCAAC 59.386 50.000 0.00 0.00 0.00 3.18 R
4362 5118 2.483106 CACATCCTTCAGTGCACAAGAG 59.517 50.000 21.04 12.51 0.00 2.85 R
4761 5828 1.342674 ACCCTATCGAGGTTACTGGCA 60.343 52.381 0.00 0.00 41.95 4.92 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
25 26 2.034066 CCCAACCGCACACTCCAT 59.966 61.111 0.00 0.00 0.00 3.41
55 56 2.762459 TACCTCGAGGGCGGCAAT 60.762 61.111 34.04 14.70 40.27 3.56
78 86 2.515290 TCGCTCGAGTATCCGGCA 60.515 61.111 15.13 0.00 0.00 5.69
84 92 3.161450 GAGTATCCGGCAGCCCCA 61.161 66.667 5.63 0.00 0.00 4.96
153 183 2.428085 GGCGGTTCCTCCTCCTCTC 61.428 68.421 0.00 0.00 38.03 3.20
157 187 0.935194 GGTTCCTCCTCCTCTCCCTA 59.065 60.000 0.00 0.00 0.00 3.53
273 303 1.675641 GTCATCAACAAGGGCGGCT 60.676 57.895 9.56 0.00 0.00 5.52
295 331 1.844839 CCTCCTCGGCTCCTACCTA 59.155 63.158 0.00 0.00 0.00 3.08
308 344 0.813184 CTACCTACCGCCTCGTCAAA 59.187 55.000 0.00 0.00 0.00 2.69
486 527 2.106332 CGCGATAAGGGAGGCGTT 59.894 61.111 0.00 0.00 43.36 4.84
639 696 1.677217 CCTTTAGCAAGCTCTTCGGCT 60.677 52.381 0.00 0.00 45.30 5.52
729 797 2.223386 GCAAAACGCCTAAATATCGCCA 60.223 45.455 0.00 0.00 32.94 5.69
737 805 6.636705 ACGCCTAAATATCGCCAAATCTATA 58.363 36.000 0.00 0.00 0.00 1.31
843 1227 2.750237 GATCACCCCCACGCCAAC 60.750 66.667 0.00 0.00 0.00 3.77
844 1228 4.360405 ATCACCCCCACGCCAACC 62.360 66.667 0.00 0.00 0.00 3.77
874 1270 3.279875 GGCGCTATTTCCAGCCGG 61.280 66.667 7.64 0.00 40.17 6.13
876 1272 3.279875 CGCTATTTCCAGCCGGGC 61.280 66.667 12.11 12.11 38.37 6.13
877 1273 2.907407 GCTATTTCCAGCCGGGCC 60.907 66.667 17.02 0.00 35.40 5.80
879 1275 3.084646 TATTTCCAGCCGGGCCGA 61.085 61.111 30.79 9.01 36.21 5.54
880 1276 2.602746 CTATTTCCAGCCGGGCCGAA 62.603 60.000 30.79 13.29 36.21 4.30
1002 1404 3.832237 AATAGCCCTCCGCGCCATG 62.832 63.158 0.00 0.00 44.76 3.66
1105 1507 2.174876 CTCCCACCTCCTCCTCACCT 62.175 65.000 0.00 0.00 0.00 4.00
1365 1767 0.031585 TTCTCGGATATTGTCGGGCG 59.968 55.000 0.00 0.00 0.00 6.13
1446 1848 1.136305 ACTGTGTTCACGTACACTGCT 59.864 47.619 21.46 10.87 46.67 4.24
1680 2082 1.105457 TTGATGGCTACTGCAATGCC 58.895 50.000 14.95 14.95 46.26 4.40
1731 2133 2.975489 TGAGAGGATGGATCTTAAGGGC 59.025 50.000 1.85 0.00 0.00 5.19
1827 2229 2.109126 GCTGTTCAGCCGGATGGTC 61.109 63.158 21.53 13.55 37.67 4.02
1938 2340 4.147701 CAATCGATGGAGGCCACC 57.852 61.111 13.09 13.09 35.80 4.61
2052 2454 7.256012 GGGTCTCTTATACAGAAAGGATACAGG 60.256 44.444 0.00 0.00 41.41 4.00
2317 2719 2.112190 AGCTTGTTAGGGAGCTAGGAC 58.888 52.381 0.00 0.00 46.78 3.85
2429 2831 2.130193 TCATGAGGGAAGGATGGAAGG 58.870 52.381 0.00 0.00 0.00 3.46
2550 2952 4.571984 GCCAGTCAAGCATTTTCAGTTTTT 59.428 37.500 0.00 0.00 0.00 1.94
2588 2990 0.178953 AGGTGCAAGCCAAATGAGGT 60.179 50.000 0.00 0.00 32.25 3.85
2841 3243 0.960861 GTGCTAACTTGACCCCTGGC 60.961 60.000 0.00 0.00 0.00 4.85
3057 3459 8.956446 TGGAGGAATACAACTATGATGAGATA 57.044 34.615 0.00 0.00 0.00 1.98
3073 3475 7.278135 TGATGAGATAGTTTGGAAGATTCTGG 58.722 38.462 0.00 0.00 0.00 3.86
3289 3691 3.484524 GCCGAGGCATATGCATTTG 57.515 52.632 28.07 18.19 44.36 2.32
3375 3780 6.261603 CAGGCTTTCAGCAATGTATAGAATCA 59.738 38.462 0.00 0.00 44.75 2.57
3637 4043 2.296752 GGGCTTTAACCCGTTTGCTTAA 59.703 45.455 0.00 0.00 40.98 1.85
4087 4840 2.725637 TGTATGTGTCAGGCATGCAAT 58.274 42.857 21.36 4.13 36.34 3.56
4253 5007 2.819608 GTTGCCAACTATTGCTTCCTCA 59.180 45.455 0.00 0.00 0.00 3.86
4310 5064 2.210116 TGAGACAACTTCCTTCGTTGC 58.790 47.619 3.08 0.00 44.15 4.17
4362 5118 1.299089 GCCCTGTGCAACGTTTGTC 60.299 57.895 0.00 0.00 42.39 3.18
4387 5143 3.023119 TGTGCACTGAAGGATGTGTTTT 58.977 40.909 19.41 0.00 36.63 2.43
4423 5490 7.125659 CCCAAGGGTATTTTATTTGTCAGGATT 59.874 37.037 0.00 0.00 0.00 3.01
4491 5558 7.992180 AGTTGAATTGTTTGTTGAGTTGATC 57.008 32.000 0.00 0.00 0.00 2.92
4567 5634 9.613428 TTGACAATTATCTAAGTATGTTCCAGG 57.387 33.333 0.00 0.00 0.00 4.45
4751 5818 4.082190 GTCAGCTTCTGTATATATGCCGGA 60.082 45.833 5.05 0.00 32.61 5.14
4761 5828 9.588096 TCTGTATATATGCCGGATCATAATACT 57.412 33.333 5.05 0.00 33.19 2.12
4763 5830 8.088365 TGTATATATGCCGGATCATAATACTGC 58.912 37.037 5.05 0.00 33.19 4.40
4793 5860 2.099592 TCGATAGGGTTTCACGCGTAAT 59.900 45.455 13.44 0.00 36.04 1.89
4940 6007 3.837731 TGTGGTGTACAATGGAGAGATCA 59.162 43.478 0.00 0.00 36.06 2.92
5047 6114 0.762418 AATGTTCCAGGTCGGTGACA 59.238 50.000 0.00 0.00 36.70 3.58
5064 6131 4.364686 ACCGGGGTGGGGATCCTT 62.365 66.667 12.58 0.00 44.64 3.36
5187 6254 2.528797 CGACTTTTGGTCTGTCGGG 58.471 57.895 6.83 0.00 46.45 5.14
5188 6255 0.249741 CGACTTTTGGTCTGTCGGGT 60.250 55.000 6.83 0.00 46.45 5.28
5189 6256 1.226746 GACTTTTGGTCTGTCGGGTG 58.773 55.000 0.00 0.00 41.46 4.61
5190 6257 0.544697 ACTTTTGGTCTGTCGGGTGT 59.455 50.000 0.00 0.00 0.00 4.16
5191 6258 1.226746 CTTTTGGTCTGTCGGGTGTC 58.773 55.000 0.00 0.00 0.00 3.67
5192 6259 0.531090 TTTTGGTCTGTCGGGTGTCG 60.531 55.000 0.00 0.00 40.90 4.35
5243 6310 2.623416 GCCCCATTGTATCCTTGCTTAC 59.377 50.000 0.00 0.00 0.00 2.34
5305 6376 0.911525 CCTGGGTGGTGATCCTCTGT 60.912 60.000 0.00 0.00 34.23 3.41
5425 6497 1.371558 GACTTCCGGTCTGCTGGTT 59.628 57.895 0.00 0.00 41.89 3.67
5472 6544 3.770040 CCCCGAGTGCGTCATGGA 61.770 66.667 0.00 0.00 35.23 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.672996 GGCATGGAGTGTGCGGTT 60.673 61.111 0.00 0.00 43.40 4.44
25 26 2.353958 AGGTACTCGAGGACGGCA 59.646 61.111 21.39 0.00 40.21 5.69
140 161 2.180308 GGAATAGGGAGAGGAGGAGGAA 59.820 54.545 0.00 0.00 0.00 3.36
153 183 1.723288 GAGTGGGAGGAGGAATAGGG 58.277 60.000 0.00 0.00 0.00 3.53
157 187 0.030603 GGAGGAGTGGGAGGAGGAAT 60.031 60.000 0.00 0.00 0.00 3.01
295 331 3.154584 TTCGGTTTGACGAGGCGGT 62.155 57.895 0.00 0.00 44.47 5.68
308 344 3.470888 CCCGGCTCCATCTTCGGT 61.471 66.667 0.00 0.00 40.78 4.69
333 369 2.049063 GTGCTCGCTCTTCACGGT 60.049 61.111 0.00 0.00 0.00 4.83
431 470 4.478371 TCCTCTAGGGCGTCGCGA 62.478 66.667 3.71 3.71 35.41 5.87
435 474 0.032815 GCAATCTCCTCTAGGGCGTC 59.967 60.000 0.00 0.00 35.41 5.19
639 696 4.998400 TTGCTGCCGCGCCTACAA 62.998 61.111 0.00 0.00 39.65 2.41
710 778 4.705337 TTTGGCGATATTTAGGCGTTTT 57.295 36.364 0.00 0.00 35.52 2.43
817 1188 1.207488 TGGGGGTGATCTGGTTCCAG 61.207 60.000 12.20 12.20 35.54 3.86
825 1209 2.933287 TTGGCGTGGGGGTGATCT 60.933 61.111 0.00 0.00 0.00 2.75
851 1247 2.973052 GGAAATAGCGCCGCCCTC 60.973 66.667 4.98 0.00 0.00 4.30
877 1273 2.107141 GAGCATCTCCGGGGTTCG 59.893 66.667 0.00 0.00 38.88 3.95
961 1363 0.039035 TGGTGGGTTATGAAGGTGGC 59.961 55.000 0.00 0.00 0.00 5.01
1056 1458 1.300931 GTCTGCAGTTGAGGACGCA 60.301 57.895 14.67 0.00 36.71 5.24
1105 1507 2.453054 GGGGAGTGGGGTGTAGGA 59.547 66.667 0.00 0.00 0.00 2.94
1446 1848 2.226315 ACACAGCCCATGGAGCAGA 61.226 57.895 22.33 0.00 0.00 4.26
1587 1989 1.181786 CGAGAAGAACCTCTGCCTCT 58.818 55.000 0.00 0.00 29.98 3.69
1740 2142 3.306166 GCTCAGTATACGTTCGCACATTT 59.694 43.478 0.00 0.00 0.00 2.32
1743 2145 1.471287 AGCTCAGTATACGTTCGCACA 59.529 47.619 0.00 0.00 0.00 4.57
1827 2229 2.747855 GGAGCCAAACCAGCCTCG 60.748 66.667 0.00 0.00 0.00 4.63
1938 2340 1.258445 ACTCACTAGGAACCAGCCCG 61.258 60.000 0.00 0.00 0.00 6.13
2052 2454 4.832248 TGGTGTAGACAATCTCATTCACC 58.168 43.478 0.00 0.00 42.72 4.02
2317 2719 8.848474 TTAAGTATCTTCTTTGAACCTTCAGG 57.152 34.615 0.00 0.00 38.61 3.86
2429 2831 5.565592 TTCAACCATCATATGTTCAGCAC 57.434 39.130 1.90 0.00 0.00 4.40
3057 3459 4.768968 CCATCAACCAGAATCTTCCAAACT 59.231 41.667 0.00 0.00 0.00 2.66
3073 3475 2.614057 CCTTCCGCAATAGACCATCAAC 59.386 50.000 0.00 0.00 0.00 3.18
3416 3821 9.645059 ATTATGAACATATTCCACTAGACATCG 57.355 33.333 0.00 0.00 33.49 3.84
4087 4840 7.451731 AGTTCCCAATACCATTGAGAATCTA 57.548 36.000 0.46 0.00 34.92 1.98
4214 4968 6.037098 TGGCAACTAAACACAACATAAACAC 58.963 36.000 0.00 0.00 37.61 3.32
4362 5118 2.483106 CACATCCTTCAGTGCACAAGAG 59.517 50.000 21.04 12.51 0.00 2.85
4397 5153 5.955355 TCCTGACAAATAAAATACCCTTGGG 59.045 40.000 3.77 3.77 0.00 4.12
4398 5154 7.660030 ATCCTGACAAATAAAATACCCTTGG 57.340 36.000 0.00 0.00 0.00 3.61
4400 5156 9.421399 CCTAATCCTGACAAATAAAATACCCTT 57.579 33.333 0.00 0.00 0.00 3.95
4401 5157 8.004801 CCCTAATCCTGACAAATAAAATACCCT 58.995 37.037 0.00 0.00 0.00 4.34
4402 5158 8.002459 TCCCTAATCCTGACAAATAAAATACCC 58.998 37.037 0.00 0.00 0.00 3.69
4403 5159 8.990163 TCCCTAATCCTGACAAATAAAATACC 57.010 34.615 0.00 0.00 0.00 2.73
4423 5490 7.292356 TCTTCAAGCAGGTAATTGATATCCCTA 59.708 37.037 0.00 0.00 35.47 3.53
4491 5558 5.607119 AGTAATTTCACCAAGTTACAGCG 57.393 39.130 3.79 0.00 37.23 5.18
4567 5634 2.863137 CAAGTATTCTTCGAGGAGCAGC 59.137 50.000 0.00 0.00 0.00 5.25
4662 5729 8.494433 AGAATTTGACTATCCTATTTACCTGCA 58.506 33.333 0.00 0.00 0.00 4.41
4751 5818 5.538813 TCGAGGTTACTGGCAGTATTATGAT 59.461 40.000 26.71 10.82 29.64 2.45
4761 5828 1.342674 ACCCTATCGAGGTTACTGGCA 60.343 52.381 0.00 0.00 41.95 4.92
4793 5860 1.378762 CTCCCTTTTGGCCTTCCGA 59.621 57.895 3.32 0.00 38.58 4.55
4864 5931 4.755266 TTCAATCAAGTAGGAGTAGGGC 57.245 45.455 0.00 0.00 0.00 5.19
4940 6007 5.382616 TGGATACACCTACGTGATCATAGT 58.617 41.667 0.00 5.33 46.17 2.12
5047 6114 4.364686 AAGGATCCCCACCCCGGT 62.365 66.667 8.55 0.00 33.88 5.28
5064 6131 1.304217 GCTATCCCGGGGATCTCGA 60.304 63.158 31.46 13.70 42.11 4.04
5243 6310 1.657804 AACCCTAGGTCTTGTCCCTG 58.342 55.000 8.29 0.00 33.12 4.45
5305 6376 0.399949 ACAAGCTATCCCGGGGATCA 60.400 55.000 31.46 16.50 42.11 2.92
5425 6497 2.420827 CGATGCCATGTACCAAGGGTAA 60.421 50.000 0.00 0.00 40.12 2.85
5472 6544 4.120244 ACCCAGATGCAGTCGAGT 57.880 55.556 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.