Multiple sequence alignment - TraesCS7B01G063800

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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 TraesCS7B01G063800 chr7B 100.000 3008 0 0 1 3008 69581204 69584211 0.000000e+00 5555.0
1 TraesCS7B01G063800 chr7B 96.011 727 29 0 1 727 494242430 494241704 0.000000e+00 1182.0
2 TraesCS7B01G063800 chr7B 95.873 727 30 0 1 727 640728261 640728987 0.000000e+00 1177.0
3 TraesCS7B01G063800 chr7A 92.281 2345 104 31 722 3008 115818473 115816148 0.000000e+00 3256.0
4 TraesCS7B01G063800 chr7A 96.011 727 29 0 1 727 499574990 499575716 0.000000e+00 1182.0
5 TraesCS7B01G063800 chr7A 96.011 727 29 0 1 727 705600228 705599502 0.000000e+00 1182.0
6 TraesCS7B01G063800 chr7A 91.304 69 4 2 724 790 115820210 115820142 3.190000e-15 93.5
7 TraesCS7B01G063800 chr7D 93.798 1564 52 12 721 2245 110566005 110567562 0.000000e+00 2309.0
8 TraesCS7B01G063800 chr7D 94.162 394 21 2 2616 3008 110567627 110568019 1.540000e-167 599.0
9 TraesCS7B01G063800 chr2B 96.149 727 28 0 1 727 601900001 601900727 0.000000e+00 1188.0
10 TraesCS7B01G063800 chr2B 96.011 727 29 0 1 727 626236416 626237142 0.000000e+00 1182.0
11 TraesCS7B01G063800 chr5A 96.011 727 29 0 1 727 514208697 514209423 0.000000e+00 1182.0
12 TraesCS7B01G063800 chr1B 96.011 727 29 0 1 727 117192116 117192842 0.000000e+00 1182.0
13 TraesCS7B01G063800 chr1A 95.873 727 30 0 1 727 67001604 67000878 0.000000e+00 1177.0


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 TraesCS7B01G063800 chr7B 69581204 69584211 3007 False 5555.00 5555 100.0000 1 3008 1 chr7B.!!$F1 3007
1 TraesCS7B01G063800 chr7B 494241704 494242430 726 True 1182.00 1182 96.0110 1 727 1 chr7B.!!$R1 726
2 TraesCS7B01G063800 chr7B 640728261 640728987 726 False 1177.00 1177 95.8730 1 727 1 chr7B.!!$F2 726
3 TraesCS7B01G063800 chr7A 115816148 115820210 4062 True 1674.75 3256 91.7925 722 3008 2 chr7A.!!$R2 2286
4 TraesCS7B01G063800 chr7A 499574990 499575716 726 False 1182.00 1182 96.0110 1 727 1 chr7A.!!$F1 726
5 TraesCS7B01G063800 chr7A 705599502 705600228 726 True 1182.00 1182 96.0110 1 727 1 chr7A.!!$R1 726
6 TraesCS7B01G063800 chr7D 110566005 110568019 2014 False 1454.00 2309 93.9800 721 3008 2 chr7D.!!$F1 2287
7 TraesCS7B01G063800 chr2B 601900001 601900727 726 False 1188.00 1188 96.1490 1 727 1 chr2B.!!$F1 726
8 TraesCS7B01G063800 chr2B 626236416 626237142 726 False 1182.00 1182 96.0110 1 727 1 chr2B.!!$F2 726
9 TraesCS7B01G063800 chr5A 514208697 514209423 726 False 1182.00 1182 96.0110 1 727 1 chr5A.!!$F1 726
10 TraesCS7B01G063800 chr1B 117192116 117192842 726 False 1182.00 1182 96.0110 1 727 1 chr1B.!!$F1 726
11 TraesCS7B01G063800 chr1A 67000878 67001604 726 True 1177.00 1177 95.8730 1 727 1 chr1A.!!$R1 726

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
34 35 0.327924 TGCCCAGAAATCGTCCACAT 59.672 50.000 0.0 0.0 0.00 3.21 F
129 130 0.385751 GCCACGCAGCTCTAGTATGA 59.614 55.000 0.0 0.0 0.00 2.15 F
1562 3318 1.134580 CAACCAGATGATCCTGCTCGT 60.135 52.381 0.0 0.0 32.97 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 3223 0.037697 CCACGAACTCGACCATGGAA 60.038 55.000 21.47 2.13 43.02 3.53 R
1806 3562 0.682852 CGAGGGTGTACAGGAAACCA 59.317 55.000 0.00 0.00 35.56 3.67 R
2582 4376 1.549170 ACCATACTCCCTTCGTGTCAC 59.451 52.381 0.00 0.00 0.00 3.67 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
34 35 0.327924 TGCCCAGAAATCGTCCACAT 59.672 50.000 0.00 0.00 0.00 3.21
71 72 1.952296 GATTTGCAAGATCGCCTCCAT 59.048 47.619 0.00 0.00 0.00 3.41
129 130 0.385751 GCCACGCAGCTCTAGTATGA 59.614 55.000 0.00 0.00 0.00 2.15
132 133 2.294512 CCACGCAGCTCTAGTATGATCA 59.705 50.000 0.00 0.00 0.00 2.92
156 157 2.349886 CAGATCAGAAACTAGTTGCGGC 59.650 50.000 9.34 0.00 0.00 6.53
193 194 3.094386 GCCACCGGCTTCATCATTA 57.906 52.632 0.00 0.00 46.69 1.90
345 346 3.399440 AGTTGAGCTTCAAGGACTGAG 57.601 47.619 0.00 0.00 37.00 3.35
354 355 1.171308 CAAGGACTGAGCATTGTGGG 58.829 55.000 0.00 0.00 0.00 4.61
404 405 5.010922 CACTAAGAGAGGAGGGATCATTCAG 59.989 48.000 0.00 0.00 0.00 3.02
441 442 2.875933 CCGAGACAAAAGTGCCAAGTTA 59.124 45.455 0.00 0.00 0.00 2.24
540 541 1.356124 TCCTCTTGCCTCTCTTGCTT 58.644 50.000 0.00 0.00 0.00 3.91
590 591 4.935808 CGTAATACTTTCACAAAGGCCTCT 59.064 41.667 5.23 0.00 42.82 3.69
656 657 5.574188 AGCCACAGATTTTATGAGAACCTT 58.426 37.500 0.00 0.00 0.00 3.50
665 666 8.166726 AGATTTTATGAGAACCTTCTTTCCTGT 58.833 33.333 0.00 0.00 37.73 4.00
744 745 9.647797 CGTAAATATATATGCAACCTCTTACCA 57.352 33.333 0.00 0.00 0.00 3.25
812 2541 4.627467 CGATTGGAGGACACACTTTAAGAG 59.373 45.833 0.00 0.00 0.00 2.85
825 2554 8.749354 ACACACTTTAAGAGAAGGAAATGTTTT 58.251 29.630 0.00 0.00 0.00 2.43
834 2589 2.820178 AGGAAATGTTTTAGGCCCAGG 58.180 47.619 0.00 0.00 0.00 4.45
835 2590 1.207089 GGAAATGTTTTAGGCCCAGGC 59.793 52.381 0.00 0.00 41.06 4.85
937 2692 1.704641 ACTTTTCCCCTGTTTGCTCC 58.295 50.000 0.00 0.00 0.00 4.70
951 2706 3.887621 TTGCTCCATCACTACTGTACC 57.112 47.619 0.00 0.00 0.00 3.34
1016 2772 2.142761 CCATGGCGATCTCCTCCCA 61.143 63.158 0.00 0.00 0.00 4.37
1095 2851 4.069232 CTGGTCGGCGAGCTCCAA 62.069 66.667 34.79 17.28 0.00 3.53
1562 3318 1.134580 CAACCAGATGATCCTGCTCGT 60.135 52.381 0.00 0.00 32.97 4.18
1593 3349 1.301009 GATCTCCATCCCGTTCGGC 60.301 63.158 5.66 0.00 0.00 5.54
1680 3436 2.613730 TCGTCTACTTCTTCAGCGTG 57.386 50.000 0.00 0.00 0.00 5.34
1806 3562 2.597510 GCAGAGGGGTTTGCCGTT 60.598 61.111 0.00 0.00 34.28 4.44
1992 3748 1.322442 GCATTCATACCTTCTGGCCC 58.678 55.000 0.00 0.00 36.63 5.80
2036 3792 0.874175 CAACCGGCGATCGATGCTTA 60.874 55.000 21.57 0.00 42.43 3.09
2092 3848 8.964476 ATCTCTTCTTTCTCTTGTTGTACAAA 57.036 30.769 10.51 0.00 37.69 2.83
2093 3849 8.964476 TCTCTTCTTTCTCTTGTTGTACAAAT 57.036 30.769 10.51 0.00 37.69 2.32
2094 3850 8.830580 TCTCTTCTTTCTCTTGTTGTACAAATG 58.169 33.333 10.51 3.77 37.69 2.32
2127 3899 5.482006 TCGAATATTGGGCATGATGAGTAG 58.518 41.667 0.00 0.00 0.00 2.57
2129 3901 6.210584 TCGAATATTGGGCATGATGAGTAGTA 59.789 38.462 0.00 0.00 0.00 1.82
2130 3902 7.044181 CGAATATTGGGCATGATGAGTAGTAT 58.956 38.462 0.00 0.00 0.00 2.12
2131 3903 8.197439 CGAATATTGGGCATGATGAGTAGTATA 58.803 37.037 0.00 0.00 0.00 1.47
2175 3947 7.022055 TCTCGTTAGATGAGTCAGAGAATTC 57.978 40.000 0.00 0.00 33.10 2.17
2183 3955 6.885376 AGATGAGTCAGAGAATTCAGCATTTT 59.115 34.615 8.44 0.00 0.00 1.82
2213 3985 5.703592 TGGTTGTATAGCTGAAACGAAATGT 59.296 36.000 0.00 0.00 0.00 2.71
2214 3986 6.021596 GGTTGTATAGCTGAAACGAAATGTG 58.978 40.000 0.00 0.00 0.00 3.21
2221 3993 1.876799 TGAAACGAAATGTGCACCGAT 59.123 42.857 15.69 2.00 0.00 4.18
2223 3995 3.243234 TGAAACGAAATGTGCACCGATTT 60.243 39.130 15.69 14.31 0.00 2.17
2237 4009 7.443879 TGTGCACCGATTTATAATGTCATATGT 59.556 33.333 15.69 0.00 0.00 2.29
2257 4029 8.916654 CATATGTGATTCTCCGACTGTAATAAC 58.083 37.037 0.00 0.00 0.00 1.89
2261 4033 6.696148 GTGATTCTCCGACTGTAATAACGAAT 59.304 38.462 0.00 0.00 0.00 3.34
2304 4076 4.929198 CTGCTGGTTTTGTCGCAG 57.071 55.556 0.00 0.00 43.10 5.18
2324 4096 3.941483 CAGAATTACTTTGGGACGCATCT 59.059 43.478 0.00 0.00 0.00 2.90
2328 4100 1.270907 ACTTTGGGACGCATCTCTCT 58.729 50.000 0.00 0.00 0.00 3.10
2340 4112 4.097286 ACGCATCTCTCTACTTCTTTCCTC 59.903 45.833 0.00 0.00 0.00 3.71
2354 4126 6.434652 ACTTCTTTCCTCGATTCTGAAGACTA 59.565 38.462 16.54 0.00 35.05 2.59
2361 4133 7.054751 TCCTCGATTCTGAAGACTAAGTATGA 58.945 38.462 0.00 0.00 0.00 2.15
2430 4224 1.520342 GCTCCCTCAGCGTCATCAC 60.520 63.158 0.00 0.00 38.76 3.06
2449 4243 7.702348 GTCATCACCAGTTAATCATTTTAAGGC 59.298 37.037 0.00 0.00 0.00 4.35
2451 4245 7.716799 TCACCAGTTAATCATTTTAAGGCAT 57.283 32.000 0.00 0.00 0.00 4.40
2480 4274 9.273137 CCATGGATATAGGAAAACCTATCTACT 57.727 37.037 5.56 0.00 35.07 2.57
2517 4311 9.551734 TGGAATCATAATTCTAGATTCACTGTG 57.448 33.333 20.08 0.17 45.82 3.66
2567 4361 9.962759 GCACTTTTATTTCAAGAAGCATATTTG 57.037 29.630 0.00 0.00 0.00 2.32
2578 4372 5.054477 AGAAGCATATTTGAATTGGCATGC 58.946 37.500 9.90 9.90 39.19 4.06
2580 4374 4.771903 AGCATATTTGAATTGGCATGCAA 58.228 34.783 21.36 4.92 40.89 4.08
2652 4461 7.707624 ATGTGATGACTTTGATGGTGTAATT 57.292 32.000 0.00 0.00 0.00 1.40
2751 4560 9.820725 AATTCACAATTTGTTATGTATGGGATG 57.179 29.630 0.00 0.00 0.00 3.51
2754 4563 8.898761 TCACAATTTGTTATGTATGGGATGTAC 58.101 33.333 0.00 0.00 0.00 2.90
2833 4644 8.856490 ATTGTATTTATTTCGGTCAAGCATTC 57.144 30.769 0.00 0.00 0.00 2.67
2865 4676 2.100197 TCACCTAGATTCACGTCCTGG 58.900 52.381 0.00 0.00 0.00 4.45
2888 4699 3.068590 ACAATTGACCTTTTGTCCTGCAG 59.931 43.478 13.59 6.78 43.78 4.41
3001 4812 5.986004 AACTAGAAGTTCTTGAACGGTTG 57.014 39.130 19.28 2.71 31.77 3.77
3003 4814 3.553828 AGAAGTTCTTGAACGGTTGGA 57.446 42.857 0.00 0.00 0.00 3.53
3004 4815 3.467803 AGAAGTTCTTGAACGGTTGGAG 58.532 45.455 0.00 0.00 0.00 3.86
3005 4816 3.118371 AGAAGTTCTTGAACGGTTGGAGT 60.118 43.478 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.617935 TGGACGATTTCTGGGCATGA 59.382 50.000 0.00 0.00 0.00 3.07
34 35 4.063967 CCCGCTCTGTACACGGCA 62.064 66.667 15.89 0.00 45.58 5.69
129 130 6.257411 CGCAACTAGTTTCTGATCTGATTGAT 59.743 38.462 5.07 0.00 38.27 2.57
132 133 4.872691 CCGCAACTAGTTTCTGATCTGATT 59.127 41.667 5.07 0.00 0.00 2.57
345 346 4.595762 AGCATCATATTTCCCACAATGC 57.404 40.909 0.00 0.00 38.58 3.56
354 355 8.758715 GCACAAATCCTTAAAGCATCATATTTC 58.241 33.333 0.00 0.00 0.00 2.17
404 405 4.394920 TGTCTCGGCAAATTTGGAGATTAC 59.605 41.667 22.18 14.46 37.80 1.89
441 442 5.544176 TGGCTTTCGGGATATAGAGATCTTT 59.456 40.000 0.00 0.00 0.00 2.52
540 541 4.339748 TCATTCGTCAATTTTGATGGGGA 58.660 39.130 11.53 5.53 42.90 4.81
590 591 5.359860 TCGATGTCTTGCTTCAGATTACCTA 59.640 40.000 0.00 0.00 0.00 3.08
656 657 7.993183 AGAAACTTTTATCAGTGACAGGAAAGA 59.007 33.333 18.52 0.00 0.00 2.52
665 666 6.778821 TGGATGGAGAAACTTTTATCAGTGA 58.221 36.000 0.00 0.00 30.33 3.41
744 745 0.830648 TTAGCACTGCGAATAGGCCT 59.169 50.000 11.78 11.78 0.00 5.19
803 2532 8.577296 GCCTAAAACATTTCCTTCTCTTAAAGT 58.423 33.333 0.00 0.00 0.00 2.66
812 2541 3.195610 CCTGGGCCTAAAACATTTCCTTC 59.804 47.826 4.53 0.00 0.00 3.46
834 2589 1.672030 GGTTGCAATGGGCCAAAGC 60.672 57.895 22.28 22.28 43.89 3.51
835 2590 0.037046 GAGGTTGCAATGGGCCAAAG 60.037 55.000 11.89 7.35 43.89 2.77
951 2706 2.663852 ACCGACGGCGAAAACTGG 60.664 61.111 15.16 8.07 40.82 4.00
1012 2768 4.075793 CGGGAGGAGGAGGTGGGA 62.076 72.222 0.00 0.00 0.00 4.37
1016 2772 4.467107 GGAGCGGGAGGAGGAGGT 62.467 72.222 0.00 0.00 0.00 3.85
1467 3223 0.037697 CCACGAACTCGACCATGGAA 60.038 55.000 21.47 2.13 43.02 3.53
1562 3318 1.362584 TGGAGATCAGGAACAGGAGGA 59.637 52.381 0.00 0.00 0.00 3.71
1593 3349 3.498121 CCCCTTCCATGATCCTCTTGATG 60.498 52.174 0.00 0.00 32.41 3.07
1680 3436 2.189521 CCGTACATGCCCCCTGAC 59.810 66.667 0.00 0.00 0.00 3.51
1806 3562 0.682852 CGAGGGTGTACAGGAAACCA 59.317 55.000 0.00 0.00 35.56 3.67
1992 3748 4.579869 ACAACATTTACCTCCAGCTACTG 58.420 43.478 0.00 0.00 0.00 2.74
2036 3792 2.962859 ACCTCTGCAACCAAAGGAAAT 58.037 42.857 5.93 0.00 32.99 2.17
2091 3847 7.986320 TGCCCAATATTCGAATTGAAAATCATT 59.014 29.630 17.19 4.39 40.71 2.57
2092 3848 7.499292 TGCCCAATATTCGAATTGAAAATCAT 58.501 30.769 17.19 0.00 40.71 2.45
2093 3849 6.871844 TGCCCAATATTCGAATTGAAAATCA 58.128 32.000 17.19 4.47 40.71 2.57
2094 3850 7.652909 TCATGCCCAATATTCGAATTGAAAATC 59.347 33.333 17.19 1.94 40.71 2.17
2105 3875 5.240891 ACTACTCATCATGCCCAATATTCG 58.759 41.667 0.00 0.00 0.00 3.34
2146 3918 4.399303 TCTGACTCATCTAACGAGATTGCA 59.601 41.667 0.00 0.00 40.68 4.08
2175 3947 6.256321 GCTATACAACCATTTCCAAAATGCTG 59.744 38.462 6.85 8.34 0.00 4.41
2183 3955 5.123186 CGTTTCAGCTATACAACCATTTCCA 59.877 40.000 0.00 0.00 0.00 3.53
2213 3985 7.659390 TCACATATGACATTATAAATCGGTGCA 59.341 33.333 10.38 0.00 0.00 4.57
2214 3986 8.028540 TCACATATGACATTATAAATCGGTGC 57.971 34.615 10.38 0.00 0.00 5.01
2223 3995 9.025041 AGTCGGAGAATCACATATGACATTATA 57.975 33.333 10.38 0.00 39.69 0.98
2237 4009 5.823209 TCGTTATTACAGTCGGAGAATCA 57.177 39.130 0.00 0.00 39.69 2.57
2300 4072 1.202031 GCGTCCCAAAGTAATTCTGCG 60.202 52.381 0.00 0.00 0.00 5.18
2301 4073 1.810151 TGCGTCCCAAAGTAATTCTGC 59.190 47.619 0.00 0.00 0.00 4.26
2304 4076 4.192317 AGAGATGCGTCCCAAAGTAATTC 58.808 43.478 1.23 0.00 0.00 2.17
2324 4096 6.181190 TCAGAATCGAGGAAAGAAGTAGAGA 58.819 40.000 0.00 0.00 0.00 3.10
2328 4100 6.434652 AGTCTTCAGAATCGAGGAAAGAAGTA 59.565 38.462 13.50 3.28 34.28 2.24
2340 4112 7.698628 TCTGTCATACTTAGTCTTCAGAATCG 58.301 38.462 0.00 0.00 0.00 3.34
2354 4126 8.057536 ACGAAAGAAGTCTATCTGTCATACTT 57.942 34.615 0.00 0.00 33.93 2.24
2361 4133 7.926555 TGAAAGAAACGAAAGAAGTCTATCTGT 59.073 33.333 0.00 0.00 0.00 3.41
2427 4199 7.395772 TCATGCCTTAAAATGATTAACTGGTGA 59.604 33.333 0.00 0.00 0.00 4.02
2430 4224 6.980397 GGTCATGCCTTAAAATGATTAACTGG 59.020 38.462 0.00 0.00 35.38 4.00
2449 4243 6.824305 GGTTTTCCTATATCCATGGTCATG 57.176 41.667 12.58 4.09 36.45 3.07
2567 4361 2.669434 GTGTCACATTGCATGCCAATTC 59.331 45.455 16.68 0.53 42.15 2.17
2578 4372 2.169832 ACTCCCTTCGTGTCACATTG 57.830 50.000 3.42 0.00 0.00 2.82
2580 4374 2.168521 CCATACTCCCTTCGTGTCACAT 59.831 50.000 3.42 0.00 0.00 3.21
2582 4376 1.549170 ACCATACTCCCTTCGTGTCAC 59.451 52.381 0.00 0.00 0.00 3.67
2583 4377 1.933021 ACCATACTCCCTTCGTGTCA 58.067 50.000 0.00 0.00 0.00 3.58
2584 4378 3.285484 TCTACCATACTCCCTTCGTGTC 58.715 50.000 0.00 0.00 0.00 3.67
2585 4379 3.288964 CTCTACCATACTCCCTTCGTGT 58.711 50.000 0.00 0.00 0.00 4.49
2586 4380 3.066900 CACTCTACCATACTCCCTTCGTG 59.933 52.174 0.00 0.00 0.00 4.35
2587 4381 3.288964 CACTCTACCATACTCCCTTCGT 58.711 50.000 0.00 0.00 0.00 3.85
2588 4382 2.623889 CCACTCTACCATACTCCCTTCG 59.376 54.545 0.00 0.00 0.00 3.79
2589 4383 3.644335 ACCACTCTACCATACTCCCTTC 58.356 50.000 0.00 0.00 0.00 3.46
2591 4385 3.140519 CCTACCACTCTACCATACTCCCT 59.859 52.174 0.00 0.00 0.00 4.20
2833 4644 6.366332 GTGAATCTAGGTGAAGGCAATATACG 59.634 42.308 0.00 0.00 0.00 3.06
2951 4762 5.652994 ACTCTTACTCTGACAAGACATCC 57.347 43.478 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.