Multiple sequence alignment - TraesCS6D01G227700

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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 TraesCS6D01G227700 chr6D 100.000 3372 0 0 1 3372 318957389 318960760 0.000000e+00 6228
1 TraesCS6D01G227700 chr6A 93.464 2861 100 16 153 2982 456759361 456762165 0.000000e+00 4167
2 TraesCS6D01G227700 chr6A 93.684 570 28 4 1 562 456757601 456758170 0.000000e+00 846
3 TraesCS6D01G227700 chr6A 94.915 354 10 3 3027 3372 456762161 456762514 6.360000e-152 547
4 TraesCS6D01G227700 chr6B 93.677 1550 88 3 940 2479 504310566 504309017 0.000000e+00 2311
5 TraesCS6D01G227700 chr6B 90.698 817 34 16 153 942 504311518 504310717 0.000000e+00 1050
6 TraesCS6D01G227700 chr5A 88.848 538 52 3 969 1506 609611385 609610856 0.000000e+00 654
7 TraesCS6D01G227700 chr5A 90.476 336 28 3 605 939 609611883 609611551 1.110000e-119 440
8 TraesCS6D01G227700 chr2B 88.043 92 11 0 2767 2858 765923121 765923030 3.560000e-20 110


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 TraesCS6D01G227700 chr6D 318957389 318960760 3371 False 6228.000000 6228 100.0000 1 3372 1 chr6D.!!$F1 3371
1 TraesCS6D01G227700 chr6A 456757601 456762514 4913 False 1853.333333 4167 94.0210 1 3372 3 chr6A.!!$F1 3371
2 TraesCS6D01G227700 chr6B 504309017 504311518 2501 True 1680.500000 2311 92.1875 153 2479 2 chr6B.!!$R1 2326
3 TraesCS6D01G227700 chr5A 609610856 609611883 1027 True 547.000000 654 89.6620 605 1506 2 chr5A.!!$R1 901

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
43 45 0.249238 GGTCAGCCAGTCGCATCTAG 60.249 60.0 0.0 0.0 41.38 2.43 F
683 2291 0.324830 AGGAAAGGAGGAGGAGACCG 60.325 60.0 0.0 0.0 34.73 4.79 F
1884 3667 0.249868 CCTGAAGCTTGGTCGTGTCA 60.250 55.0 2.1 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 3318 0.179100 CTGATCTCGTGCCCGATGTT 60.179 55.0 0.0 0.0 43.27 2.71 R
1922 3705 0.460109 TCTGTTCGATCACCGGCATG 60.460 55.0 0.0 0.0 39.14 4.06 R
3016 4815 0.322997 CGTGGACTCACCTCCTCTCT 60.323 60.0 0.0 0.0 40.65 3.10 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
30 32 2.570181 GCAGCAACCATGGTCAGC 59.430 61.111 26.54 26.54 34.35 4.26
43 45 0.249238 GGTCAGCCAGTCGCATCTAG 60.249 60.000 0.00 0.00 41.38 2.43
53 55 1.032794 TCGCATCTAGTACCAGCAGG 58.967 55.000 0.00 0.00 42.21 4.85
66 68 1.341209 CCAGCAGGCGATATACTGTCA 59.659 52.381 0.00 0.00 37.07 3.58
73 75 5.528870 CAGGCGATATACTGTCACATACAA 58.471 41.667 0.00 0.00 37.74 2.41
101 103 2.416202 CACGAGCATGCTTTGTGTATCA 59.584 45.455 30.76 0.00 32.07 2.15
113 115 6.880529 TGCTTTGTGTATCATCTCAGATTGAA 59.119 34.615 0.00 0.00 0.00 2.69
151 153 8.221965 TCTGAGAAGAAAATCATCAATCATGG 57.778 34.615 0.00 0.00 32.64 3.66
216 220 5.648033 ACATGATTGATGATTCGAGAACG 57.352 39.130 0.00 0.00 37.02 3.95
273 277 3.978718 TTCAACGTGCACATTGATCAA 57.021 38.095 26.95 11.46 34.87 2.57
290 297 6.545504 TGATCAAGAAGCAAAGACAAGTAC 57.454 37.500 0.00 0.00 0.00 2.73
323 330 5.626142 AGGAAGACCTTTCTTTCTTTCTCC 58.374 41.667 0.00 0.00 44.38 3.71
342 354 6.089249 TCTCCCTTTTTCTTCATTTTCAGC 57.911 37.500 0.00 0.00 0.00 4.26
682 2290 1.273324 TGAGGAAAGGAGGAGGAGACC 60.273 57.143 0.00 0.00 0.00 3.85
683 2291 0.324830 AGGAAAGGAGGAGGAGACCG 60.325 60.000 0.00 0.00 34.73 4.79
685 2293 1.341778 GGAAAGGAGGAGGAGACCGTA 60.342 57.143 0.00 0.00 34.73 4.02
898 2528 1.079543 AGCATCCACTCTCGTGTGC 60.080 57.895 0.00 0.00 41.11 4.57
924 2554 3.345808 GCGCGCCAGTTGAGTTCA 61.346 61.111 23.24 0.00 0.00 3.18
1045 2828 2.649034 GAGTCGTGCGTGGGAGAA 59.351 61.111 0.00 0.00 0.00 2.87
1063 2846 2.743928 CTGAACCGCTGGTGAGGC 60.744 66.667 0.94 0.00 35.34 4.70
1080 2863 2.575993 CCTGTGCGTCCTCTCAGG 59.424 66.667 0.00 0.00 40.83 3.86
1414 3197 3.488489 CGATGCAGGTAAAAGGAAAACG 58.512 45.455 0.00 0.00 0.00 3.60
1417 3200 3.018149 TGCAGGTAAAAGGAAAACGTGT 58.982 40.909 0.00 0.00 32.92 4.49
1441 3224 4.190772 CACCCCAATGGCAATGTAATTTC 58.809 43.478 1.30 0.00 37.83 2.17
1535 3318 1.663379 CTCGGAGGTGCACATCGGTA 61.663 60.000 29.99 19.21 0.00 4.02
1564 3347 1.244816 ACGAGATCAGGACGTGTGAA 58.755 50.000 0.00 0.00 38.79 3.18
1573 3356 1.303317 GACGTGTGAAGGCCCCAAT 60.303 57.895 0.00 0.00 0.00 3.16
1579 3362 2.124320 GAAGGCCCCAATAGCGCA 60.124 61.111 11.47 0.00 0.00 6.09
1700 3483 1.765904 TGGTGCACAAGGAGAAGTACA 59.234 47.619 20.43 0.00 0.00 2.90
1701 3484 2.143925 GGTGCACAAGGAGAAGTACAC 58.856 52.381 20.43 0.00 32.54 2.90
1714 3497 1.750399 GTACACCGTCCCGAGGCTA 60.750 63.158 0.00 0.00 0.00 3.93
1884 3667 0.249868 CCTGAAGCTTGGTCGTGTCA 60.250 55.000 2.10 0.00 0.00 3.58
1893 3676 2.809601 GTCGTGTCAATCGCCGCT 60.810 61.111 0.00 0.00 0.00 5.52
1922 3705 1.443802 GAGTTCTGCTTGTACTGCCC 58.556 55.000 8.51 0.00 0.00 5.36
2030 3819 1.751351 TGAGGCTGATGAGGAAGTACG 59.249 52.381 0.00 0.00 0.00 3.67
2362 4151 2.320587 ACGCGACGAGTACGACCTT 61.321 57.895 15.93 0.00 42.66 3.50
2425 4220 1.269517 TGCATGTTTTTGAGTTCGCCC 60.270 47.619 0.00 0.00 0.00 6.13
2426 4221 1.269517 GCATGTTTTTGAGTTCGCCCA 60.270 47.619 0.00 0.00 0.00 5.36
2574 4373 4.789159 TCTAAGTCTGGGGAGAGAAGTCTA 59.211 45.833 0.00 0.00 30.97 2.59
2654 4453 6.183360 GGTTCAAATTTCACCCTCCAAGTTTA 60.183 38.462 5.12 0.00 0.00 2.01
2686 4485 7.709182 CGTTCATAATACAACCCTGAGATGTAA 59.291 37.037 0.00 0.00 33.63 2.41
2766 4565 6.180472 GTTCTCAGGACAAAATTCTCCCATA 58.820 40.000 0.00 0.00 0.00 2.74
2804 4603 4.021544 TGCATACTTTGAATTGGGGTCAAC 60.022 41.667 0.00 0.00 34.78 3.18
2817 4616 2.831526 GGGGTCAACATTGCTGGTTAAT 59.168 45.455 0.00 0.00 0.00 1.40
2912 4711 4.164988 AGTGAGCTAGTCCAAAGGCATAAT 59.835 41.667 0.00 0.00 0.00 1.28
2947 4746 8.696374 TGTTTGGTTTTTATCTTTCCACACATA 58.304 29.630 0.00 0.00 35.07 2.29
2989 4788 2.716217 CTCACATTTGAGTTCCCTCCC 58.284 52.381 0.40 0.00 43.95 4.30
2990 4789 1.354368 TCACATTTGAGTTCCCTCCCC 59.646 52.381 0.00 0.00 36.86 4.81
2991 4790 1.075374 CACATTTGAGTTCCCTCCCCA 59.925 52.381 0.00 0.00 36.86 4.96
2992 4791 1.075536 ACATTTGAGTTCCCTCCCCAC 59.924 52.381 0.00 0.00 36.86 4.61
2993 4792 1.355720 CATTTGAGTTCCCTCCCCACT 59.644 52.381 0.00 0.00 36.86 4.00
2994 4793 0.771127 TTTGAGTTCCCTCCCCACTG 59.229 55.000 0.00 0.00 36.86 3.66
2995 4794 1.779061 TTGAGTTCCCTCCCCACTGC 61.779 60.000 0.00 0.00 36.86 4.40
2996 4795 2.936032 AGTTCCCTCCCCACTGCC 60.936 66.667 0.00 0.00 0.00 4.85
2997 4796 4.410400 GTTCCCTCCCCACTGCCG 62.410 72.222 0.00 0.00 0.00 5.69
3018 4817 3.133014 GCTGGAGCGGCAGATAGA 58.867 61.111 1.45 0.00 35.55 1.98
3019 4818 1.006337 GCTGGAGCGGCAGATAGAG 60.006 63.158 1.45 0.00 35.55 2.43
3020 4819 1.459455 GCTGGAGCGGCAGATAGAGA 61.459 60.000 1.45 0.00 35.55 3.10
3021 4820 0.597568 CTGGAGCGGCAGATAGAGAG 59.402 60.000 1.45 0.00 0.00 3.20
3022 4821 0.825425 TGGAGCGGCAGATAGAGAGG 60.825 60.000 1.45 0.00 0.00 3.69
3023 4822 0.538516 GGAGCGGCAGATAGAGAGGA 60.539 60.000 1.45 0.00 0.00 3.71
3024 4823 0.881118 GAGCGGCAGATAGAGAGGAG 59.119 60.000 1.45 0.00 0.00 3.69
3025 4824 0.539438 AGCGGCAGATAGAGAGGAGG 60.539 60.000 1.45 0.00 0.00 4.30
3026 4825 0.825840 GCGGCAGATAGAGAGGAGGT 60.826 60.000 0.00 0.00 0.00 3.85
3027 4826 0.958091 CGGCAGATAGAGAGGAGGTG 59.042 60.000 0.00 0.00 0.00 4.00
3028 4827 1.477740 CGGCAGATAGAGAGGAGGTGA 60.478 57.143 0.00 0.00 0.00 4.02
3029 4828 2.238521 GGCAGATAGAGAGGAGGTGAG 58.761 57.143 0.00 0.00 0.00 3.51
3030 4829 2.424234 GGCAGATAGAGAGGAGGTGAGT 60.424 54.545 0.00 0.00 0.00 3.41
3072 4871 1.484240 CTCGAGGGAAGGAAGCTTCAT 59.516 52.381 27.02 18.73 35.19 2.57
3106 4905 2.436542 CACCGTGGTAGGGGAATGAATA 59.563 50.000 0.00 0.00 36.61 1.75
3197 4996 8.032045 AGATGAATGTACTCCTTCATGAATCT 57.968 34.615 8.96 1.15 41.07 2.40
3207 5006 4.880120 TCCTTCATGAATCTGATGCAGTTC 59.120 41.667 8.96 0.00 32.61 3.01
3269 5076 0.723981 GCTGTTGCCACTCGAGAATC 59.276 55.000 21.68 7.50 0.00 2.52
3281 5088 3.669354 GAGAATCGCCGAATGGAGT 57.331 52.632 0.00 0.00 37.49 3.85
3284 5091 1.776034 GAATCGCCGAATGGAGTGCC 61.776 60.000 0.00 0.00 37.49 5.01
3329 5136 2.839486 TGAGCTTCAGGTTCGTCATT 57.161 45.000 0.00 0.00 0.00 2.57
3360 5167 2.430921 GTCCACTGTCGAGCCACG 60.431 66.667 0.00 0.00 44.09 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.592400 CTGACCATGGTTGCTGCCAG 61.592 60.000 20.85 16.17 42.47 4.85
14 15 1.604308 TGGCTGACCATGGTTGCTG 60.604 57.895 29.93 19.49 42.67 4.41
30 32 1.269309 GCTGGTACTAGATGCGACTGG 60.269 57.143 10.90 0.00 0.00 4.00
43 45 2.296471 ACAGTATATCGCCTGCTGGTAC 59.704 50.000 11.69 5.48 35.27 3.34
53 55 6.475727 AGTTGTTGTATGTGACAGTATATCGC 59.524 38.462 0.00 0.00 39.88 4.58
66 68 3.985008 TGCTCGTGTAGTTGTTGTATGT 58.015 40.909 0.00 0.00 0.00 2.29
73 75 2.169832 AAGCATGCTCGTGTAGTTGT 57.830 45.000 22.93 0.00 0.00 3.32
141 143 4.166246 ACACAGAGCATCCATGATTGAT 57.834 40.909 0.00 0.00 33.66 2.57
151 153 5.261209 ACTGAGAAGATACACAGAGCATC 57.739 43.478 0.00 0.00 33.86 3.91
216 220 1.135699 CGATGTTCGCTGGCATTTGC 61.136 55.000 0.00 0.00 34.72 3.68
273 277 5.918608 TCTTCAGTACTTGTCTTTGCTTCT 58.081 37.500 0.00 0.00 0.00 2.85
323 330 4.919754 CGAGGCTGAAAATGAAGAAAAAGG 59.080 41.667 0.00 0.00 0.00 3.11
682 2290 3.689649 CCCCAGAGTCCAGAAAAATTACG 59.310 47.826 0.00 0.00 0.00 3.18
683 2291 4.663334 ACCCCAGAGTCCAGAAAAATTAC 58.337 43.478 0.00 0.00 0.00 1.89
685 2293 3.903530 ACCCCAGAGTCCAGAAAAATT 57.096 42.857 0.00 0.00 0.00 1.82
924 2554 0.320771 AAGGCGATTTGACGAGCAGT 60.321 50.000 0.00 0.00 35.09 4.40
983 2766 2.350388 GGCATTTCATCGAACACGTTGT 60.350 45.455 0.00 0.00 0.00 3.32
1045 2828 2.743718 CCTCACCAGCGGTTCAGT 59.256 61.111 0.00 0.00 31.02 3.41
1063 2846 2.575993 CCTGAGAGGACGCACAGG 59.424 66.667 5.31 5.31 42.71 4.00
1371 3154 3.329889 ACCGGGATGGCAGCTTCA 61.330 61.111 6.32 0.00 43.94 3.02
1414 3197 1.204467 CATTGCCATTGGGGTGTACAC 59.796 52.381 18.01 18.01 39.65 2.90
1417 3200 3.458044 TTACATTGCCATTGGGGTGTA 57.542 42.857 4.53 0.00 39.65 2.90
1441 3224 0.896940 AGACCATGGCTGTGCAAAGG 60.897 55.000 13.04 0.00 0.00 3.11
1535 3318 0.179100 CTGATCTCGTGCCCGATGTT 60.179 55.000 0.00 0.00 43.27 2.71
1573 3356 0.752009 AGGAGTTCCTCGATGCGCTA 60.752 55.000 9.73 0.00 44.77 4.26
1884 3667 2.359850 TTTGAGGCAGCGGCGATT 60.360 55.556 12.98 0.00 42.47 3.34
1922 3705 0.460109 TCTGTTCGATCACCGGCATG 60.460 55.000 0.00 0.00 39.14 4.06
2007 3796 1.830477 ACTTCCTCATCAGCCTCACTC 59.170 52.381 0.00 0.00 0.00 3.51
2158 3947 1.550130 GGTTCAGGGGGACGATGTCA 61.550 60.000 0.00 0.00 33.68 3.58
2425 4220 1.229975 TTGTGCAGCTCCGACATGTG 61.230 55.000 1.15 0.00 0.00 3.21
2426 4221 0.952497 CTTGTGCAGCTCCGACATGT 60.952 55.000 0.00 0.00 0.00 3.21
2574 4373 2.986728 AGACAAGTTCAGGGGGTAATGT 59.013 45.455 0.00 0.00 0.00 2.71
2654 4453 5.014202 AGGGTTGTATTATGAACGGCTTTT 58.986 37.500 0.00 0.00 0.00 2.27
2766 4565 9.502091 TCAAAGTATGCAAACACTCTTACTAAT 57.498 29.630 0.00 0.00 0.00 1.73
2835 4634 2.294512 CACTTCCTTGGCTGAGAAAACC 59.705 50.000 0.00 0.00 0.00 3.27
2912 4711 8.950007 AAGATAAAAACCAAACAGATCCCTAA 57.050 30.769 0.00 0.00 0.00 2.69
3001 4800 1.006337 CTCTATCTGCCGCTCCAGC 60.006 63.158 0.00 0.00 32.87 4.85
3002 4801 0.597568 CTCTCTATCTGCCGCTCCAG 59.402 60.000 0.00 0.00 0.00 3.86
3003 4802 0.825425 CCTCTCTATCTGCCGCTCCA 60.825 60.000 0.00 0.00 0.00 3.86
3004 4803 0.538516 TCCTCTCTATCTGCCGCTCC 60.539 60.000 0.00 0.00 0.00 4.70
3005 4804 0.881118 CTCCTCTCTATCTGCCGCTC 59.119 60.000 0.00 0.00 0.00 5.03
3006 4805 0.539438 CCTCCTCTCTATCTGCCGCT 60.539 60.000 0.00 0.00 0.00 5.52
3007 4806 0.825840 ACCTCCTCTCTATCTGCCGC 60.826 60.000 0.00 0.00 0.00 6.53
3008 4807 0.958091 CACCTCCTCTCTATCTGCCG 59.042 60.000 0.00 0.00 0.00 5.69
3009 4808 2.238521 CTCACCTCCTCTCTATCTGCC 58.761 57.143 0.00 0.00 0.00 4.85
3010 4809 2.884639 GACTCACCTCCTCTCTATCTGC 59.115 54.545 0.00 0.00 0.00 4.26
3011 4810 3.117701 TGGACTCACCTCCTCTCTATCTG 60.118 52.174 0.00 0.00 39.86 2.90
3012 4811 3.117663 GTGGACTCACCTCCTCTCTATCT 60.118 52.174 0.00 0.00 37.92 1.98
3013 4812 3.219281 GTGGACTCACCTCCTCTCTATC 58.781 54.545 0.00 0.00 37.92 2.08
3014 4813 2.422235 CGTGGACTCACCTCCTCTCTAT 60.422 54.545 0.00 0.00 40.65 1.98
3015 4814 1.065345 CGTGGACTCACCTCCTCTCTA 60.065 57.143 0.00 0.00 40.65 2.43
3016 4815 0.322997 CGTGGACTCACCTCCTCTCT 60.323 60.000 0.00 0.00 40.65 3.10
3017 4816 1.316706 CCGTGGACTCACCTCCTCTC 61.317 65.000 0.00 0.00 40.65 3.20
3018 4817 1.304547 CCGTGGACTCACCTCCTCT 60.305 63.158 0.00 0.00 40.65 3.69
3019 4818 2.352032 CCCGTGGACTCACCTCCTC 61.352 68.421 0.00 0.00 40.65 3.71
3020 4819 2.283966 CCCGTGGACTCACCTCCT 60.284 66.667 0.00 0.00 40.65 3.69
3021 4820 4.083862 GCCCGTGGACTCACCTCC 62.084 72.222 0.00 0.00 40.65 4.30
3022 4821 2.997897 AGCCCGTGGACTCACCTC 60.998 66.667 0.00 0.00 40.65 3.85
3023 4822 2.997897 GAGCCCGTGGACTCACCT 60.998 66.667 0.00 0.00 40.65 4.00
3024 4823 2.579684 GATGAGCCCGTGGACTCACC 62.580 65.000 7.08 0.00 45.19 4.02
3025 4824 1.153549 GATGAGCCCGTGGACTCAC 60.154 63.158 7.08 0.00 45.19 3.51
3026 4825 2.710902 CGATGAGCCCGTGGACTCA 61.711 63.158 7.39 7.39 46.34 3.41
3027 4826 2.105128 CGATGAGCCCGTGGACTC 59.895 66.667 0.00 0.00 0.00 3.36
3028 4827 3.461773 CCGATGAGCCCGTGGACT 61.462 66.667 0.00 0.00 0.00 3.85
3090 4889 3.838317 CCGATCTATTCATTCCCCTACCA 59.162 47.826 0.00 0.00 0.00 3.25
3093 4892 6.296026 CAAAACCGATCTATTCATTCCCCTA 58.704 40.000 0.00 0.00 0.00 3.53
3106 4905 1.803334 TACGCAAGCAAAACCGATCT 58.197 45.000 0.00 0.00 45.62 2.75
3197 4996 2.610433 GATCTGTCACGAACTGCATCA 58.390 47.619 0.00 0.00 0.00 3.07
3207 5006 3.378427 TGACTACATGAGGATCTGTCACG 59.622 47.826 0.00 0.00 34.92 4.35
3269 5076 4.473520 AGGGCACTCCATTCGGCG 62.474 66.667 0.00 0.00 38.24 6.46
3284 5091 1.026718 GCGATCTCACCCCAAACAGG 61.027 60.000 0.00 0.00 37.03 4.00


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

AutoCloner maintained by Alex Coulton.