Multiple sequence alignment - TraesCS7D01G317200

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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 TraesCS7D01G317200 chr7D 100.000 3422 0 0 1 3422 403764032 403767453 0.000000e+00 6320.0
1 TraesCS7D01G317200 chr7A 93.748 3439 116 47 1 3422 462327849 462331205 0.000000e+00 5068.0
2 TraesCS7D01G317200 chr7B 96.031 2671 78 18 765 3422 413095171 413097826 0.000000e+00 4320.0
3 TraesCS7D01G317200 chr7B 91.304 621 37 11 53 670 413094289 413094895 0.000000e+00 832.0
4 TraesCS7D01G317200 chr7B 97.674 43 1 0 1 43 413094260 413094302 1.320000e-09 75.0
5 TraesCS7D01G317200 chr4B 78.012 332 31 17 1035 1364 562287 561996 1.630000e-38 171.0
6 TraesCS7D01G317200 chr6B 86.429 140 15 3 467 606 600782900 600783035 2.130000e-32 150.0
7 TraesCS7D01G317200 chr6B 83.824 68 10 1 21 88 367367209 367367143 2.850000e-06 63.9


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 TraesCS7D01G317200 chr7D 403764032 403767453 3421 False 6320.000000 6320 100.000 1 3422 1 chr7D.!!$F1 3421
1 TraesCS7D01G317200 chr7A 462327849 462331205 3356 False 5068.000000 5068 93.748 1 3422 1 chr7A.!!$F1 3421
2 TraesCS7D01G317200 chr7B 413094260 413097826 3566 False 1742.333333 4320 95.003 1 3422 3 chr7B.!!$F1 3421

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
690 705 1.557832 CTCCCTCCGTCCCATAAAACA 59.442 52.381 0.00 0.00 0.0 2.83 F
1905 2169 1.450312 CCGGCTCATTGAGGACACC 60.450 63.158 15.28 6.86 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 2193 0.98423 TCAGGGTGTCCTTAGCCTTG 59.016 55.0 0.00 0.0 45.88 3.61 R
3100 3369 2.93964 GCCTTTATCAGCGAAGGTTCCA 60.940 50.0 4.28 0.0 43.47 3.53 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
42 43 9.970395 ATAATTTGTGCTATTTCACATACATGG 57.030 29.630 0.00 0.00 45.26 3.66
43 44 7.643569 ATTTGTGCTATTTCACATACATGGA 57.356 32.000 0.00 0.00 45.26 3.41
277 284 3.065655 TGCTTTATTGTTTGCACCATGC 58.934 40.909 0.00 0.00 45.29 4.06
392 400 9.705290 ATTACAAAGTTTACATTTTGGACCATC 57.295 29.630 0.00 0.00 38.33 3.51
461 471 8.542132 CATGGCGATTTTACTTTTTATCCAATG 58.458 33.333 0.00 0.00 0.00 2.82
526 536 6.153067 TGGAACATGGCAAACTTTATTAACG 58.847 36.000 0.00 0.00 0.00 3.18
565 575 1.575419 ATGCTTTGGACCATGGCAAT 58.425 45.000 20.66 10.33 36.49 3.56
607 617 5.105752 TGGGCATATTTTATGTTGAAACGC 58.894 37.500 0.00 0.00 0.00 4.84
613 623 9.039500 GCATATTTTATGTTGAAACGCTTTTTG 57.961 29.630 0.00 0.00 0.00 2.44
687 702 2.023695 ACTACTCCCTCCGTCCCATAAA 60.024 50.000 0.00 0.00 0.00 1.40
688 703 1.961133 ACTCCCTCCGTCCCATAAAA 58.039 50.000 0.00 0.00 0.00 1.52
689 704 1.558294 ACTCCCTCCGTCCCATAAAAC 59.442 52.381 0.00 0.00 0.00 2.43
690 705 1.557832 CTCCCTCCGTCCCATAAAACA 59.442 52.381 0.00 0.00 0.00 2.83
691 706 2.172717 CTCCCTCCGTCCCATAAAACAT 59.827 50.000 0.00 0.00 0.00 2.71
692 707 2.171870 TCCCTCCGTCCCATAAAACATC 59.828 50.000 0.00 0.00 0.00 3.06
693 708 2.572290 CCTCCGTCCCATAAAACATCC 58.428 52.381 0.00 0.00 0.00 3.51
694 709 2.172717 CCTCCGTCCCATAAAACATCCT 59.827 50.000 0.00 0.00 0.00 3.24
695 710 3.389983 CCTCCGTCCCATAAAACATCCTA 59.610 47.826 0.00 0.00 0.00 2.94
1302 1566 4.162690 GCCATCGACGCCTTCCCT 62.163 66.667 0.00 0.00 0.00 4.20
1905 2169 1.450312 CCGGCTCATTGAGGACACC 60.450 63.158 15.28 6.86 0.00 4.16
1915 2179 3.901797 GAGGACACCAGGGTTGCCG 62.902 68.421 0.00 0.00 0.00 5.69
1929 2193 3.056328 GCCGCCACCAAGTTCTCC 61.056 66.667 0.00 0.00 0.00 3.71
1968 2232 4.487804 TGATTGTCAGGAAATTTGGGGAA 58.512 39.130 0.00 0.00 0.00 3.97
1998 2262 5.623956 CAGGGAATTACTGGTACCATGTA 57.376 43.478 16.75 16.21 32.38 2.29
2050 2314 2.534019 CCACGCCATGCCATACGTC 61.534 63.158 0.00 0.00 36.45 4.34
2076 2340 4.232221 CACCAAGTTTGATGAGCATTGTC 58.768 43.478 0.00 0.00 0.00 3.18
2417 2681 1.878656 AAGAAGGTCGAGGTGCTCCG 61.879 60.000 0.00 0.00 39.05 4.63
2424 2688 1.448540 CGAGGTGCTCCGCTGATTT 60.449 57.895 6.97 0.00 39.05 2.17
2439 2703 5.236047 CCGCTGATTTCTTCTCCAAGATAAG 59.764 44.000 0.00 0.00 38.50 1.73
2499 2763 5.100259 CGTGTATAGACCGTGTCTGAATTT 58.900 41.667 14.50 1.05 43.30 1.82
2515 2779 6.417930 GTCTGAATTTTGTTGTCAGGTTTAGC 59.582 38.462 0.00 0.00 39.42 3.09
2523 2787 5.647589 TGTTGTCAGGTTTAGCGTATAGAG 58.352 41.667 0.00 0.00 0.00 2.43
2524 2788 5.184479 TGTTGTCAGGTTTAGCGTATAGAGT 59.816 40.000 0.00 0.00 0.00 3.24
2543 2807 5.334421 AGAGTATCCAGTCAGTACCACTTT 58.666 41.667 0.00 0.00 33.66 2.66
2545 2809 4.838986 AGTATCCAGTCAGTACCACTTTGT 59.161 41.667 0.00 0.00 0.00 2.83
2828 3094 5.796350 AGTGACGCACAAAAGTATAATCC 57.204 39.130 11.58 0.00 36.74 3.01
2966 3232 8.604890 GGAAACTGAAATATAGCTGTAAGACAC 58.395 37.037 0.00 0.00 34.07 3.67
2967 3233 9.151471 GAAACTGAAATATAGCTGTAAGACACA 57.849 33.333 0.00 0.00 34.07 3.72
3060 3326 4.635765 TCTTTTGTGGTCTGACTGAAACTG 59.364 41.667 7.85 1.78 0.00 3.16
3093 3362 7.011109 GTGCCATATTGACGTACTTTACATTCT 59.989 37.037 0.00 0.00 0.00 2.40
3100 3369 9.871238 ATTGACGTACTTTACATTCTGTTCTAT 57.129 29.630 0.00 0.00 0.00 1.98
3116 3385 4.945246 GTTCTATGGAACCTTCGCTGATA 58.055 43.478 10.68 0.00 44.24 2.15
3133 3402 5.287035 CGCTGATAAAGGCTTCATTTTTCAC 59.713 40.000 0.00 0.00 0.00 3.18
3144 3413 7.040686 AGGCTTCATTTTTCACGTACATTTACT 60.041 33.333 0.00 0.00 0.00 2.24
3376 3646 7.141363 GCAATACGGCATCTCTGAAATTTATT 58.859 34.615 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.811655 GCCTTGCTTTGTATAAAAGAAATTTTC 57.188 29.630 0.66 0.66 32.27 2.29
43 44 9.336171 TGCCTTGCTTTGTATAAAAGAAATTTT 57.664 25.926 2.10 0.00 32.27 1.82
58 59 6.601741 TTGAAGTAAAATTGCCTTGCTTTG 57.398 33.333 0.00 0.00 30.13 2.77
136 137 6.751888 AGTAGAATGAACAGCACAAAAACAAC 59.248 34.615 0.00 0.00 0.00 3.32
137 138 6.862209 AGTAGAATGAACAGCACAAAAACAA 58.138 32.000 0.00 0.00 0.00 2.83
138 139 6.449635 AGTAGAATGAACAGCACAAAAACA 57.550 33.333 0.00 0.00 0.00 2.83
139 140 7.755582 AAAGTAGAATGAACAGCACAAAAAC 57.244 32.000 0.00 0.00 0.00 2.43
140 141 8.770438 AAAAAGTAGAATGAACAGCACAAAAA 57.230 26.923 0.00 0.00 0.00 1.94
141 142 9.296400 GTAAAAAGTAGAATGAACAGCACAAAA 57.704 29.630 0.00 0.00 0.00 2.44
142 143 8.462811 TGTAAAAAGTAGAATGAACAGCACAAA 58.537 29.630 0.00 0.00 0.00 2.83
147 154 7.593825 ACCATGTAAAAAGTAGAATGAACAGC 58.406 34.615 0.00 0.00 0.00 4.40
392 400 6.098124 TCCATGCCCTTAAGTATGAATTTTGG 59.902 38.462 0.97 0.00 32.15 3.28
607 617 2.700371 AGAAGGAACCTTGGCCAAAAAG 59.300 45.455 20.91 13.57 36.26 2.27
613 623 2.290960 ACACATAGAAGGAACCTTGGCC 60.291 50.000 11.02 0.00 36.26 5.36
688 703 9.653516 CTCCCTATGTCTCATAATATAGGATGT 57.346 37.037 9.99 0.00 43.03 3.06
689 704 9.653516 ACTCCCTATGTCTCATAATATAGGATG 57.346 37.037 9.99 5.64 43.03 3.51
708 723 7.947782 AAAAATGGATCCATACTACTCCCTA 57.052 36.000 27.54 0.00 35.31 3.53
743 758 9.889128 TGTATATTGAAACTGTCATCAAGATGA 57.111 29.630 18.69 8.61 44.83 2.92
945 1208 2.595655 GGTCTGGCATACACCCCC 59.404 66.667 5.34 0.00 0.00 5.40
1819 2083 4.543590 ACTGTCTTTCCTCGATGATGTT 57.456 40.909 0.00 0.00 0.00 2.71
1915 2179 1.527433 GCCTTGGAGAACTTGGTGGC 61.527 60.000 0.00 0.00 0.00 5.01
1929 2193 0.984230 TCAGGGTGTCCTTAGCCTTG 59.016 55.000 0.00 0.00 45.88 3.61
1968 2232 1.482593 CAGTAATTCCCTGGCTCGACT 59.517 52.381 0.00 0.00 0.00 4.18
1998 2262 2.284625 TCCGCCTCACCCTCACAT 60.285 61.111 0.00 0.00 0.00 3.21
2034 2298 1.521457 CAGACGTATGGCATGGCGT 60.521 57.895 24.43 24.43 40.44 5.68
2050 2314 1.068055 GCTCATCAAACTTGGTGCCAG 60.068 52.381 0.00 0.00 39.14 4.85
2090 2354 6.312918 GGAATCGAAGTCTTGTTGCATACTTA 59.687 38.462 0.00 0.00 32.51 2.24
2417 2681 7.498570 ACATCTTATCTTGGAGAAGAAATCAGC 59.501 37.037 8.36 0.00 42.01 4.26
2424 2688 6.874278 TCCAACATCTTATCTTGGAGAAGA 57.126 37.500 7.00 7.00 42.71 2.87
2439 2703 1.131126 CATGCCGTGTTCTCCAACATC 59.869 52.381 0.00 0.00 44.47 3.06
2499 2763 6.028146 TCTATACGCTAAACCTGACAACAA 57.972 37.500 0.00 0.00 0.00 2.83
2515 2779 6.147492 GTGGTACTGACTGGATACTCTATACG 59.853 46.154 0.00 0.00 37.61 3.06
2523 2787 4.929808 CACAAAGTGGTACTGACTGGATAC 59.070 45.833 0.00 0.00 0.00 2.24
2524 2788 4.836175 TCACAAAGTGGTACTGACTGGATA 59.164 41.667 0.00 0.00 33.87 2.59
2543 2807 4.576873 TGCTGGTTACGAAAATTTCTCACA 59.423 37.500 4.09 0.00 0.00 3.58
2545 2809 5.957842 ATGCTGGTTACGAAAATTTCTCA 57.042 34.783 4.09 0.00 0.00 3.27
2594 2858 8.209917 ACTAATTGATCGGAACAGGTATTTTC 57.790 34.615 0.00 0.00 0.00 2.29
2597 2861 6.766467 GGAACTAATTGATCGGAACAGGTATT 59.234 38.462 0.00 0.00 0.00 1.89
2783 3049 7.121168 CACTTAAAGAATAGATGCCCAGAACAA 59.879 37.037 0.00 0.00 0.00 2.83
2966 3232 3.181503 GGTCAAGCAGCACATACAGATTG 60.182 47.826 0.00 0.00 0.00 2.67
2967 3233 3.012518 GGTCAAGCAGCACATACAGATT 58.987 45.455 0.00 0.00 0.00 2.40
3060 3326 6.444633 AGTACGTCAATATGGCACTATGTAC 58.555 40.000 0.00 0.30 0.00 2.90
3100 3369 2.939640 GCCTTTATCAGCGAAGGTTCCA 60.940 50.000 4.28 0.00 43.47 3.53
3116 3385 5.508200 TGTACGTGAAAAATGAAGCCTTT 57.492 34.783 0.00 0.00 0.00 3.11
3144 3413 6.491745 TGATGCTGGGTTAACATAAGTGAAAA 59.508 34.615 8.10 0.00 0.00 2.29
3214 3484 6.112734 TCAAGGAGATAGCGCATAAAGAAAA 58.887 36.000 11.47 0.00 0.00 2.29
3215 3485 5.670485 TCAAGGAGATAGCGCATAAAGAAA 58.330 37.500 11.47 0.00 0.00 2.52
3281 3551 7.472334 AACAAAGAAGCATAACATCTGGAAT 57.528 32.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.