Multiple sequence alignment - TraesCS7B01G270500

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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 TraesCS7B01G270500 chr7B 100.000 4774 0 0 1 4774 495754435 495759208 0.000000e+00 8817.0
1 TraesCS7B01G270500 chr7D 95.775 4663 144 24 130 4774 471927789 471932416 0.000000e+00 7470.0
2 TraesCS7B01G270500 chr7D 89.655 58 4 1 1322 1377 538578631 538578688 6.630000e-09 73.1
3 TraesCS7B01G270500 chr7A 93.510 2003 93 18 735 2717 524643853 524641868 0.000000e+00 2944.0
4 TraesCS7B01G270500 chr7A 86.621 2063 129 60 2790 4774 524641794 524639801 0.000000e+00 2145.0
5 TraesCS7B01G270500 chr7A 84.541 621 87 6 1 616 524644658 524644042 1.470000e-169 606.0
6 TraesCS7B01G270500 chr7A 96.429 56 2 0 2727 2782 112776916 112776971 5.090000e-15 93.5
7 TraesCS7B01G270500 chr7A 94.915 59 3 0 2727 2785 112786310 112786252 5.090000e-15 93.5
8 TraesCS7B01G270500 chr6D 95.082 61 3 0 2727 2787 155253566 155253506 3.930000e-16 97.1
9 TraesCS7B01G270500 chr6D 73.401 297 56 15 2788 3078 62504364 62504085 6.580000e-14 89.8
10 TraesCS7B01G270500 chr1D 95.082 61 3 0 2727 2787 332956490 332956430 3.930000e-16 97.1
11 TraesCS7B01G270500 chr1D 90.909 66 6 0 2727 2792 415425000 415424935 6.580000e-14 89.8
12 TraesCS7B01G270500 chr5B 76.923 182 31 8 462 641 366525477 366525305 5.090000e-15 93.5
13 TraesCS7B01G270500 chr5B 96.429 56 2 0 2727 2782 567789516 567789571 5.090000e-15 93.5
14 TraesCS7B01G270500 chr3B 92.188 64 5 0 2727 2790 781397825 781397888 1.830000e-14 91.6
15 TraesCS7B01G270500 chr4D 89.855 69 7 0 2727 2795 15316066 15316134 6.580000e-14 89.8
16 TraesCS7B01G270500 chr6B 77.632 152 28 5 2788 2935 136119664 136119515 2.370000e-13 87.9
17 TraesCS7B01G270500 chr2D 89.655 58 4 1 1322 1377 166478080 166478137 6.630000e-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 TraesCS7B01G270500 chr7B 495754435 495759208 4773 False 8817.000000 8817 100.000 1 4774 1 chr7B.!!$F1 4773
1 TraesCS7B01G270500 chr7D 471927789 471932416 4627 False 7470.000000 7470 95.775 130 4774 1 chr7D.!!$F1 4644
2 TraesCS7B01G270500 chr7A 524639801 524644658 4857 True 1898.333333 2944 88.224 1 4774 3 chr7A.!!$R2 4773

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
770 878 0.400213 TGACAACTGGGCCTCGAAAT 59.600 50.0 4.53 0.0 0.00 2.17 F
1767 1887 0.107066 ATGCACATCATTGCCCGAGA 60.107 50.0 0.00 0.0 42.25 4.04 F
2135 2256 2.160417 GGTGAAGCAATCTCCAGTTTCG 59.840 50.0 5.93 0.0 40.69 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2256 0.949105 CACACTGACCCGGTTGCTAC 60.949 60.0 0.00 0.00 0.00 3.58 R
3578 3735 1.667236 GCCTGCAGCATGTGTATACA 58.333 50.0 8.66 0.08 42.97 2.29 R
3981 4169 0.394192 TCCTCTCAGGCACAACACAG 59.606 55.0 0.00 0.00 34.61 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
51 52 9.337396 TGTCTTCTGAATATGTTACACAACTTT 57.663 29.630 0.00 0.00 35.56 2.66
63 64 7.247728 TGTTACACAACTTTTCATCTTGTGAC 58.752 34.615 14.88 5.91 45.06 3.67
64 65 5.895636 ACACAACTTTTCATCTTGTGACA 57.104 34.783 14.88 0.00 45.06 3.58
182 185 4.164252 CGTCTGCCACGTTAGACC 57.836 61.111 15.03 2.98 44.07 3.85
211 214 2.604046 GCCTCGAGCCAAATCTCTTA 57.396 50.000 6.99 0.00 34.35 2.10
219 222 4.389077 CGAGCCAAATCTCTTAAAGACGTT 59.611 41.667 0.00 0.00 36.65 3.99
221 224 4.389077 AGCCAAATCTCTTAAAGACGTTCG 59.611 41.667 0.00 0.00 36.65 3.95
273 277 4.379174 GTCCACACAGACGCCATT 57.621 55.556 0.00 0.00 0.00 3.16
285 289 1.450134 CGCCATTGTAGCTCTGCCA 60.450 57.895 0.00 0.00 0.00 4.92
302 306 2.023788 GCCATCATACCCAACCCACAG 61.024 57.143 0.00 0.00 0.00 3.66
403 408 3.291101 TACGTGCAACTCCTCCGGC 62.291 63.158 0.00 0.00 31.75 6.13
476 481 5.437289 TCTTGAAATGCATCGACAACTTT 57.563 34.783 0.00 0.00 0.00 2.66
497 502 2.779430 TGAGATCAACAGGGGCATATGT 59.221 45.455 4.29 0.00 0.00 2.29
498 503 3.973305 TGAGATCAACAGGGGCATATGTA 59.027 43.478 4.29 0.00 0.00 2.29
499 504 4.040829 TGAGATCAACAGGGGCATATGTAG 59.959 45.833 4.29 0.00 0.00 2.74
500 505 3.976654 AGATCAACAGGGGCATATGTAGT 59.023 43.478 4.29 0.00 0.00 2.73
511 516 6.602009 AGGGGCATATGTAGTAACTTTTCAAC 59.398 38.462 4.29 0.00 0.00 3.18
526 531 6.265577 ACTTTTCAACAATCTTGTACAGCAC 58.734 36.000 0.00 0.00 41.31 4.40
538 543 2.239402 TGTACAGCACATGTGGATCCAT 59.761 45.455 26.55 0.00 43.80 3.41
550 555 5.314718 TGTGGATCCATGCTAGAAATCAT 57.685 39.130 19.62 0.00 0.00 2.45
582 587 6.899393 TCTTTATGTTTCAATCAAGCACCT 57.101 33.333 0.00 0.00 0.00 4.00
620 625 8.601845 AAGTTTGGGCTATGTATTTTTGAAAC 57.398 30.769 0.00 0.00 0.00 2.78
621 626 7.731054 AGTTTGGGCTATGTATTTTTGAAACA 58.269 30.769 0.00 0.00 0.00 2.83
662 770 1.585521 GGACCGCTGTCGACGTATG 60.586 63.158 11.62 2.24 42.73 2.39
693 801 4.151157 GGATTTGCAAAATGCTCTGACAAC 59.849 41.667 17.19 0.00 45.31 3.32
694 802 3.797451 TTGCAAAATGCTCTGACAACA 57.203 38.095 0.00 0.00 45.31 3.33
695 803 3.797451 TGCAAAATGCTCTGACAACAA 57.203 38.095 3.78 0.00 45.31 2.83
696 804 3.708890 TGCAAAATGCTCTGACAACAAG 58.291 40.909 3.78 0.00 45.31 3.16
713 821 4.123497 ACAAGGAAAAGAAAACTGTGCC 57.877 40.909 0.00 0.00 0.00 5.01
716 824 3.631250 AGGAAAAGAAAACTGTGCCAGA 58.369 40.909 8.91 0.00 35.18 3.86
770 878 0.400213 TGACAACTGGGCCTCGAAAT 59.600 50.000 4.53 0.00 0.00 2.17
1089 1208 3.299977 CAGGTCACGGACGTCCCA 61.300 66.667 28.52 10.23 32.65 4.37
1147 1266 2.164865 CTTCTGCGACAGCTGGAGGT 62.165 60.000 19.93 0.00 42.29 3.85
1230 1349 4.508128 CGCGCGTACATGGAGGGT 62.508 66.667 24.19 0.00 0.00 4.34
1448 1568 0.799534 GCATTGATTGTGCGTGCTCC 60.800 55.000 0.00 0.00 32.29 4.70
1540 1660 9.787435 TTTGTGTGAACTCATAACTACCTTAAT 57.213 29.630 0.00 0.00 0.00 1.40
1642 1762 2.945668 GTCTGAAGCCTGACAAAACAGT 59.054 45.455 0.00 0.00 39.93 3.55
1751 1871 1.892474 TGTTTTACCTGAAGGGCATGC 59.108 47.619 9.90 9.90 40.27 4.06
1767 1887 0.107066 ATGCACATCATTGCCCGAGA 60.107 50.000 0.00 0.00 42.25 4.04
1930 2050 2.275134 TTTCACAGCAATCTGGCTCA 57.725 45.000 0.00 0.00 43.68 4.26
1967 2088 3.260931 CAACGCATGCTGCAGACT 58.739 55.556 20.43 0.00 45.36 3.24
2135 2256 2.160417 GGTGAAGCAATCTCCAGTTTCG 59.840 50.000 5.93 0.00 40.69 3.46
2782 2917 4.105697 ACACTTATTTTGGGACAGAGGGAA 59.894 41.667 0.00 0.00 42.39 3.97
2839 2975 8.752187 AGCCATTTGTCTTGTTCATAATATGTT 58.248 29.630 0.00 0.00 0.00 2.71
2904 3040 7.085601 ACCTCCTAATCTCTCCTCCAATAATT 58.914 38.462 0.00 0.00 0.00 1.40
2987 3123 8.367911 TGTTAATTCTAGGTACATAGCTCATGG 58.632 37.037 9.70 0.00 39.13 3.66
3184 3322 3.134804 GCTAGTCCATAGAAAGCTCCCAA 59.865 47.826 0.00 0.00 32.83 4.12
3193 3331 6.547141 CCATAGAAAGCTCCCAATGAATTGTA 59.453 38.462 2.55 0.00 36.06 2.41
3262 3400 5.183904 AGGAGTGTTGCCAAAATTCTATCAC 59.816 40.000 0.00 0.00 0.00 3.06
3386 3527 2.839486 TCTCCGACTTTGAGTTGCAT 57.161 45.000 0.00 0.00 0.00 3.96
3387 3528 3.953712 TCTCCGACTTTGAGTTGCATA 57.046 42.857 0.00 0.00 0.00 3.14
3388 3529 4.471904 TCTCCGACTTTGAGTTGCATAT 57.528 40.909 0.00 0.00 0.00 1.78
3389 3530 5.592104 TCTCCGACTTTGAGTTGCATATA 57.408 39.130 0.00 0.00 0.00 0.86
3390 3531 5.592054 TCTCCGACTTTGAGTTGCATATAG 58.408 41.667 0.00 0.00 0.00 1.31
3391 3532 5.359860 TCTCCGACTTTGAGTTGCATATAGA 59.640 40.000 0.00 0.00 0.00 1.98
3451 3592 9.351570 GTCTACAGTGTAACCATCTAGTTTTAC 57.648 37.037 4.21 0.00 37.80 2.01
3514 3655 7.360438 GCTCTCACTATACACAAAAGGAAAGTG 60.360 40.741 0.00 0.00 39.12 3.16
3528 3671 5.488262 AGGAAAGTGCAGGCATTAAAAAT 57.512 34.783 0.00 0.00 0.00 1.82
3578 3735 9.760077 CCAGTTTGTATTAATCGGAAGTATACT 57.240 33.333 0.00 0.00 0.00 2.12
3937 4123 4.535526 GGTACCAATGAATTTGCCAGTT 57.464 40.909 7.15 0.00 33.73 3.16
3938 4124 4.244862 GGTACCAATGAATTTGCCAGTTG 58.755 43.478 7.15 0.00 33.73 3.16
3939 4125 2.769893 ACCAATGAATTTGCCAGTTGC 58.230 42.857 0.00 0.00 41.77 4.17
3940 4126 2.078392 CCAATGAATTTGCCAGTTGCC 58.922 47.619 0.00 0.00 40.16 4.52
3941 4127 2.550423 CCAATGAATTTGCCAGTTGCCA 60.550 45.455 0.00 0.00 40.16 4.92
3944 4130 2.591923 TGAATTTGCCAGTTGCCACTA 58.408 42.857 0.00 0.00 40.16 2.74
3976 4164 6.301486 TGGATATATTGCTCAGAAGTGCATT 58.699 36.000 0.00 0.00 43.05 3.56
3981 4169 3.631145 TGCTCAGAAGTGCATTGTTTC 57.369 42.857 0.00 0.00 39.15 2.78
4006 4194 1.067295 TGTGCCTGAGAGGATTGGTT 58.933 50.000 0.00 0.00 37.67 3.67
4118 4308 8.454106 ACATTAAGCTTTGTTGATTACTGCTAG 58.546 33.333 3.20 0.00 31.81 3.42
4147 4337 2.292016 TGCCAAACGTTGTGTATTCAGG 59.708 45.455 0.00 0.00 0.00 3.86
4265 4465 4.019174 AGCAAATTGTCCTCGGAATCATT 58.981 39.130 0.00 0.00 0.00 2.57
4381 4584 2.419297 GGCAGACGAAGACATGGAATCT 60.419 50.000 0.00 0.00 0.00 2.40
4398 4601 4.018324 GGAATCTTGGGGGTACTCTTTCTT 60.018 45.833 0.00 0.00 0.00 2.52
4515 4722 2.047274 TTGCTCTGGTACGCAGGC 60.047 61.111 10.33 11.89 37.46 4.85
4615 4832 2.457598 TCTTCCCTATCGTCTTGCTGT 58.542 47.619 0.00 0.00 0.00 4.40
4722 4942 2.478894 GCATTTGACGTCGGAAAGAGAA 59.521 45.455 11.62 0.00 0.00 2.87
4728 4948 3.005472 TGACGTCGGAAAGAGAAGTGAAT 59.995 43.478 11.62 0.00 30.91 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 5.624159 AGAACCTTGATGTCACAAGATGAA 58.376 37.500 13.50 0.00 46.85 2.57
56 57 7.819415 TGATTACTAGAACCTTGATGTCACAAG 59.181 37.037 0.00 0.00 44.50 3.16
63 64 7.504403 AGATGGTGATTACTAGAACCTTGATG 58.496 38.462 0.00 0.00 33.65 3.07
64 65 7.682787 AGATGGTGATTACTAGAACCTTGAT 57.317 36.000 0.00 0.00 33.65 2.57
177 180 2.753043 GGCCCTGTCGTCGGTCTA 60.753 66.667 0.00 0.00 0.00 2.59
182 185 4.180946 CTCGAGGCCCTGTCGTCG 62.181 72.222 12.10 8.03 43.28 5.12
211 214 1.352156 GGCAGATCGCGAACGTCTTT 61.352 55.000 15.24 0.00 43.84 2.52
219 222 2.786495 GGAAGAGGGCAGATCGCGA 61.786 63.158 13.09 13.09 43.84 5.87
221 224 0.107459 AAAGGAAGAGGGCAGATCGC 60.107 55.000 1.55 1.55 41.28 4.58
273 277 1.694150 GGGTATGATGGCAGAGCTACA 59.306 52.381 0.00 0.00 34.37 2.74
285 289 0.107214 CGCTGTGGGTTGGGTATGAT 60.107 55.000 0.00 0.00 0.00 2.45
334 339 4.856801 GATGGCGGCATGGTCGGT 62.857 66.667 30.87 3.36 0.00 4.69
356 361 0.813610 CATCCGGTGCCAGCGAATTA 60.814 55.000 19.13 0.38 42.41 1.40
358 363 2.514592 CATCCGGTGCCAGCGAAT 60.515 61.111 19.13 0.00 42.41 3.34
403 408 1.419374 CGAGACGGACTTGAACTTGG 58.581 55.000 0.00 0.00 31.94 3.61
476 481 2.779430 ACATATGCCCCTGTTGATCTCA 59.221 45.455 1.58 0.00 0.00 3.27
498 503 8.129211 GCTGTACAAGATTGTTGAAAAGTTACT 58.871 33.333 3.14 0.00 42.35 2.24
499 504 7.913297 TGCTGTACAAGATTGTTGAAAAGTTAC 59.087 33.333 3.14 0.00 42.35 2.50
500 505 7.913297 GTGCTGTACAAGATTGTTGAAAAGTTA 59.087 33.333 3.14 0.00 42.35 2.24
511 516 3.752747 TCCACATGTGCTGTACAAGATTG 59.247 43.478 20.81 2.04 43.77 2.67
574 579 7.538303 ACTTAAAATTTGTTCAAGGTGCTTG 57.462 32.000 0.00 0.00 42.25 4.01
582 587 9.050601 CATAGCCCAAACTTAAAATTTGTTCAA 57.949 29.630 9.75 0.00 35.65 2.69
596 601 7.731054 TGTTTCAAAAATACATAGCCCAAACT 58.269 30.769 0.00 0.00 0.00 2.66
627 632 4.747605 GCGGTCCACACACAAAAATAAAAT 59.252 37.500 0.00 0.00 0.00 1.82
636 641 1.522806 GACAGCGGTCCACACACAA 60.523 57.895 5.60 0.00 38.12 3.33
644 649 1.585521 CATACGTCGACAGCGGTCC 60.586 63.158 17.16 0.00 41.13 4.46
662 770 1.253100 TTTTGCAAATCCGTCCTCCC 58.747 50.000 13.65 0.00 0.00 4.30
693 801 4.122143 TGGCACAGTTTTCTTTTCCTTG 57.878 40.909 0.00 0.00 0.00 3.61
713 821 9.703892 ATTATCTCAATAATTCCTTCGTCTCTG 57.296 33.333 0.00 0.00 35.01 3.35
770 878 2.692368 GGAGGATGGCCCCACAGA 60.692 66.667 0.00 0.00 34.66 3.41
967 1080 0.264657 TGGCTAGGTATCTGGCTCCA 59.735 55.000 11.49 0.00 45.37 3.86
974 1087 0.603569 CGGCGATTGGCTAGGTATCT 59.396 55.000 0.00 0.00 42.94 1.98
1147 1266 3.998672 GGCCGTCTCCACCGACAA 61.999 66.667 0.00 0.00 33.54 3.18
1429 1549 0.799534 GGAGCACGCACAATCAATGC 60.800 55.000 0.00 0.00 39.81 3.56
1448 1568 5.670097 CCAATAACAGCGACTGATTAATCG 58.330 41.667 10.80 8.09 41.32 3.34
1751 1871 2.545526 GTGTATCTCGGGCAATGATGTG 59.454 50.000 0.00 0.00 0.00 3.21
1767 1887 6.403866 TTGTTTCTTGCAATGAAGGTGTAT 57.596 33.333 0.00 0.00 31.23 2.29
1884 2004 9.403583 TCCAACACTTAATTTAATAGGCTTAGG 57.596 33.333 0.00 0.00 0.00 2.69
1967 2088 5.222130 GGAAAGGAGGGGATATAATCTTGCA 60.222 44.000 0.00 0.00 0.00 4.08
2135 2256 0.949105 CACACTGACCCGGTTGCTAC 60.949 60.000 0.00 0.00 0.00 3.58
2227 2348 6.645790 ATTATCACATCATCTGCCCTTTTC 57.354 37.500 0.00 0.00 0.00 2.29
2839 2975 7.733773 TCTTAAGTCCTTGGATCTGTGATTA 57.266 36.000 1.63 0.00 0.00 1.75
2841 2977 6.627087 TTCTTAAGTCCTTGGATCTGTGAT 57.373 37.500 1.63 0.00 0.00 3.06
2842 2978 6.627087 ATTCTTAAGTCCTTGGATCTGTGA 57.373 37.500 1.63 0.00 0.00 3.58
2843 2979 7.011857 GCTAATTCTTAAGTCCTTGGATCTGTG 59.988 40.741 1.63 0.00 0.00 3.66
2844 2980 7.051000 GCTAATTCTTAAGTCCTTGGATCTGT 58.949 38.462 1.63 0.00 0.00 3.41
3193 3331 8.796475 ACACATTGCTAGAAGTTAAATTGTGAT 58.204 29.630 7.00 0.00 0.00 3.06
3262 3400 6.159293 TCAAAGTACAGCAGAGTTCTATGTG 58.841 40.000 0.00 2.15 0.00 3.21
3419 3560 5.418209 AGATGGTTACACTGTAGACTGTACC 59.582 44.000 0.00 4.14 0.00 3.34
3514 3655 9.546428 AATGGAGTAATTATTTTTAATGCCTGC 57.454 29.630 0.00 0.00 0.00 4.85
3578 3735 1.667236 GCCTGCAGCATGTGTATACA 58.333 50.000 8.66 0.08 42.97 2.29
3734 3891 5.722021 TTGGATTTGGAAGCTTAAAGGAC 57.278 39.130 0.00 0.00 0.00 3.85
3935 4121 9.672673 AATATATCCATAGACATTAGTGGCAAC 57.327 33.333 0.00 0.00 35.06 4.17
3936 4122 9.671279 CAATATATCCATAGACATTAGTGGCAA 57.329 33.333 0.00 0.00 35.06 4.52
3937 4123 7.770433 GCAATATATCCATAGACATTAGTGGCA 59.230 37.037 0.00 0.00 35.06 4.92
3938 4124 7.989741 AGCAATATATCCATAGACATTAGTGGC 59.010 37.037 0.00 0.00 0.00 5.01
3939 4125 9.539825 GAGCAATATATCCATAGACATTAGTGG 57.460 37.037 0.00 0.00 0.00 4.00
3944 4130 9.887629 CTTCTGAGCAATATATCCATAGACATT 57.112 33.333 0.00 0.00 0.00 2.71
3976 4164 2.016318 CTCAGGCACAACACAGAAACA 58.984 47.619 0.00 0.00 0.00 2.83
3981 4169 0.394192 TCCTCTCAGGCACAACACAG 59.606 55.000 0.00 0.00 34.61 3.66
4006 4194 8.893219 TGTGGTGCAATTTTTGAATTTGTATA 57.107 26.923 0.00 0.00 0.00 1.47
4118 4308 1.199624 CAACGTTTGGCACTTTCAGC 58.800 50.000 0.00 0.00 0.00 4.26
4147 4337 5.801947 CAGACATTTGGTTAGTTAGCAATGC 59.198 40.000 0.00 0.00 43.26 3.56
4265 4465 4.522789 TGATAACTGCATATGCTCGGTCTA 59.477 41.667 27.13 16.18 42.66 2.59
4381 4584 2.910977 GAGGAAGAAAGAGTACCCCCAA 59.089 50.000 0.00 0.00 0.00 4.12
4615 4832 0.250295 CTTCACGTTCAAGGGCCTCA 60.250 55.000 6.46 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.