Multiple sequence alignment - TraesCS1A01G152300

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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 TraesCS1A01G152300 chr1A 100.000 6155 0 0 1 6155 262008577 262014731 0.000000 11367.0
1 TraesCS1A01G152300 chr1D 96.512 6164 186 14 1 6155 205474852 205480995 0.000000 10165.0
2 TraesCS1A01G152300 chr1B 95.455 5324 215 12 38 5339 301248814 301254132 0.000000 8466.0
3 TraesCS1A01G152300 chr1B 94.699 830 35 4 5334 6155 301255721 301256549 0.000000 1280.0
4 TraesCS1A01G152300 chr1B 100.000 30 0 0 5510 5539 32987829 32987858 0.000862 56.5
5 TraesCS1A01G152300 chr2A 100.000 30 0 0 541 570 509546288 509546317 0.000862 56.5


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 TraesCS1A01G152300 chr1A 262008577 262014731 6154 False 11367 11367 100.000 1 6155 1 chr1A.!!$F1 6154
1 TraesCS1A01G152300 chr1D 205474852 205480995 6143 False 10165 10165 96.512 1 6155 1 chr1D.!!$F1 6154
2 TraesCS1A01G152300 chr1B 301248814 301256549 7735 False 4873 8466 95.077 38 6155 2 chr1B.!!$F2 6117

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 2.110967 CAGCGTGGCCCTCATCTTG 61.111 63.158 0.00 0.00 0.00 3.02 F
1338 1356 0.761323 TTGTCCACCGGGTGAAGAGA 60.761 55.000 28.36 13.80 35.23 3.10 F
2302 2320 0.032815 TGCTGGAACAACGATCGACA 59.967 50.000 24.34 9.29 38.70 4.35 F
3240 3258 0.690744 TCCCAAGATGGATCGAGGCA 60.691 55.000 0.00 0.00 40.96 4.75 F
4629 4647 0.179018 AAGAAGCCAGTTTCGCAGGT 60.179 50.000 0.00 0.00 32.33 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1782 0.473694 TCTGGAGAAGGTTCCTGCCA 60.474 55.0 7.69 7.69 38.12 4.92 R
2589 2607 0.035915 GTGGAGGGTTGAGCTCTTCC 60.036 60.0 16.19 16.02 0.00 3.46 R
3632 3650 0.374758 CAGCTTATGCATGCGACGTT 59.625 50.0 14.09 0.00 42.74 3.99 R
4846 4864 0.787787 GCATTGTCGTTGTCAGCGTA 59.212 50.0 9.00 0.00 0.00 4.42 R
6042 7675 0.112412 GGGGAAGAACAAGGGCAGAA 59.888 55.0 0.00 0.00 0.00 3.02 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 2.110967 CAGCGTGGCCCTCATCTTG 61.111 63.158 0.00 0.00 0.00 3.02
164 165 7.457380 TCCTCTTTATTCTCTTCCATCCAAT 57.543 36.000 0.00 0.00 0.00 3.16
597 598 4.380531 TGCCTCTGACTTGAACAAACTAG 58.619 43.478 0.00 0.00 0.00 2.57
768 774 2.499205 CGGAACCTGCAGGCGATA 59.501 61.111 33.06 0.00 39.32 2.92
1203 1212 1.215647 GTTCCTGCTCGTGGTCGAT 59.784 57.895 0.00 0.00 45.21 3.59
1338 1356 0.761323 TTGTCCACCGGGTGAAGAGA 60.761 55.000 28.36 13.80 35.23 3.10
1345 1363 1.536073 CCGGGTGAAGAGACTCAGCA 61.536 60.000 5.02 0.00 44.01 4.41
1411 1429 1.886585 GACGAGAGCCAGCTGAAGA 59.113 57.895 17.39 0.00 0.00 2.87
1982 2000 2.971330 AGAGCATCCTGAATTCGGAGAT 59.029 45.455 16.17 12.91 31.33 2.75
2055 2073 0.249955 TCACGAGGCTGCATCATCAA 59.750 50.000 15.07 0.00 0.00 2.57
2179 2197 0.465705 GGCGATTCCAGAGTCCATCA 59.534 55.000 0.00 0.00 34.01 3.07
2280 2298 0.985490 GGGGGCTCAGAGACCTTGAT 60.985 60.000 22.69 0.00 45.15 2.57
2292 2310 2.373169 AGACCTTGATCTTGCTGGAACA 59.627 45.455 0.00 0.00 0.00 3.18
2302 2320 0.032815 TGCTGGAACAACGATCGACA 59.967 50.000 24.34 9.29 38.70 4.35
2303 2321 1.337728 TGCTGGAACAACGATCGACAT 60.338 47.619 24.34 4.44 38.70 3.06
2304 2322 1.732259 GCTGGAACAACGATCGACATT 59.268 47.619 24.34 11.98 38.70 2.71
2377 2395 1.973812 GTGGCCAGCAAAGAGGACC 60.974 63.158 5.11 0.00 29.23 4.46
2382 2400 2.529389 AGCAAAGAGGACCGGGGT 60.529 61.111 6.32 0.00 0.00 4.95
2446 2464 2.338577 ACTCCATGTGCATAAGCTCC 57.661 50.000 0.00 0.00 42.74 4.70
2454 2472 0.984961 TGCATAAGCTCCAGAGGGCT 60.985 55.000 0.00 0.00 42.74 5.19
2541 2559 1.073216 CATCCAGCGACGACACTGTC 61.073 60.000 0.00 0.00 35.49 3.51
2553 2571 2.029666 ACTGTCAGTCTGCCGCAC 59.970 61.111 0.00 0.00 0.00 5.34
2589 2607 2.943690 CAGGAAGATTGAGGATGTGCTG 59.056 50.000 0.00 0.00 0.00 4.41
2634 2652 2.480416 CCTCGAGTCGCTAAAGATTGCT 60.480 50.000 12.31 0.00 0.00 3.91
2646 2664 5.163519 GCTAAAGATTGCTGGCTATTTTGGA 60.164 40.000 0.00 0.00 0.00 3.53
2696 2714 1.819632 CCCTCCCAAATCTTCGCCG 60.820 63.158 0.00 0.00 0.00 6.46
2917 2935 1.902508 GGATGGATATCGAGGCAGGAA 59.097 52.381 0.00 0.00 33.98 3.36
3001 3019 0.891373 CCTCAGACACGTGACATCCT 59.109 55.000 25.01 7.86 0.00 3.24
3126 3144 1.704628 TCAGACATGCCTTCCCTTGAA 59.295 47.619 0.00 0.00 0.00 2.69
3163 3181 1.227943 TGCCCAGTGTTGCAGACTC 60.228 57.895 0.75 0.00 32.77 3.36
3240 3258 0.690744 TCCCAAGATGGATCGAGGCA 60.691 55.000 0.00 0.00 40.96 4.75
3242 3260 0.877649 CCAAGATGGATCGAGGCACG 60.878 60.000 0.00 0.00 40.96 5.34
3246 3264 4.794439 TGGATCGAGGCACGTGCG 62.794 66.667 32.35 19.91 43.26 5.34
3285 3303 2.483877 GGATGTCACAAGCACGATCAAA 59.516 45.455 0.00 0.00 0.00 2.69
3465 3483 1.932511 GCTGCTTCTGATAGTGCTGAC 59.067 52.381 0.00 0.00 0.00 3.51
3511 3529 3.096092 GCCAATCAAGATGTTGGGGTTA 58.904 45.455 2.33 0.00 43.98 2.85
3632 3650 4.640771 ACACAGAAAGGAGAAATAGCCA 57.359 40.909 0.00 0.00 0.00 4.75
3708 3726 3.008330 AGATGCAGATTCAGTTGTGCTC 58.992 45.455 0.00 0.00 36.84 4.26
3716 3734 3.558931 TTCAGTTGTGCTCTTTCCTGA 57.441 42.857 0.00 0.00 0.00 3.86
3722 3740 2.897436 TGTGCTCTTTCCTGATCATCG 58.103 47.619 0.00 0.00 0.00 3.84
3732 3750 5.535753 TTCCTGATCATCGAGCTAAATCA 57.464 39.130 0.00 0.00 0.00 2.57
3973 3991 5.449314 CGTGAAGGATCTCGAGTAATCAACT 60.449 44.000 13.13 0.20 43.35 3.16
4018 4036 3.106242 ACATCAGTGTACGTCAAAGCA 57.894 42.857 0.00 0.00 36.63 3.91
4077 4095 3.261897 ACATCAGTAAACAGACCAGGAGG 59.738 47.826 0.00 0.00 42.21 4.30
4232 4250 2.278792 CGATCATGCTGACGCCGA 60.279 61.111 0.00 0.00 34.43 5.54
4526 4544 6.954487 TCATGAAGAATCTAAAGCATGCAT 57.046 33.333 21.98 4.57 34.64 3.96
4629 4647 0.179018 AAGAAGCCAGTTTCGCAGGT 60.179 50.000 0.00 0.00 32.33 4.00
4675 4693 4.096833 CCATCAAGAAAATTCCTCGCATGA 59.903 41.667 0.00 0.00 0.00 3.07
4773 4791 1.722011 ACACCGATCCACATTCGAAC 58.278 50.000 0.00 0.00 38.88 3.95
4846 4864 2.111878 GACACCACACCAGCAGCT 59.888 61.111 0.00 0.00 0.00 4.24
4851 4869 2.047844 CACACCAGCAGCTACGCT 60.048 61.111 0.00 0.00 45.21 5.07
5229 5251 6.690194 ATGCTAATACTTTGCTCCTTTCTG 57.310 37.500 0.00 0.00 0.00 3.02
5318 5343 5.396362 CACGCTAATTCGCTTAATTGATTGG 59.604 40.000 0.08 0.00 38.29 3.16
5348 6967 2.758089 GCTGCTGCGATTGTCCAGG 61.758 63.158 0.00 0.00 0.00 4.45
5354 6973 2.289002 GCTGCGATTGTCCAGGATAAAG 59.711 50.000 2.21 1.96 0.00 1.85
5381 7000 3.499338 ACACATTCCTGCCAAGAAATGA 58.501 40.909 0.00 0.00 0.00 2.57
5583 7205 5.126384 CGCCTAGTGATTTTATCCCCAAAAA 59.874 40.000 0.00 0.00 31.54 1.94
5931 7558 3.000819 AGTCGCCGATGGGGAACA 61.001 61.111 3.99 0.00 45.99 3.18
6019 7652 0.898320 AGATCGTCAGGGTCACCAAG 59.102 55.000 0.00 0.00 40.13 3.61
6048 7681 2.158957 TCAGGGTATCAATCGTTCTGCC 60.159 50.000 0.00 0.00 0.00 4.85
6050 7683 1.141053 GGGTATCAATCGTTCTGCCCT 59.859 52.381 0.00 0.00 32.47 5.19
6051 7684 2.421529 GGGTATCAATCGTTCTGCCCTT 60.422 50.000 0.00 0.00 32.47 3.95
6052 7685 2.614057 GGTATCAATCGTTCTGCCCTTG 59.386 50.000 0.00 0.00 0.00 3.61
6054 7687 2.270352 TCAATCGTTCTGCCCTTGTT 57.730 45.000 0.00 0.00 0.00 2.83
6055 7688 2.151202 TCAATCGTTCTGCCCTTGTTC 58.849 47.619 0.00 0.00 0.00 3.18
6062 7696 1.304464 CTGCCCTTGTTCTTCCCCC 60.304 63.158 0.00 0.00 0.00 5.40
6065 7699 0.702316 GCCCTTGTTCTTCCCCCTTA 59.298 55.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.393077 ATGAGGGCCACGCTGTATAC 59.607 55.000 6.18 0.00 0.00 1.47
12 13 0.679505 GATGAGGGCCACGCTGTATA 59.320 55.000 6.18 0.00 0.00 1.47
85 86 9.450807 AACTAATAATTCAGAATGTAATTGCGC 57.549 29.630 0.00 0.00 36.07 6.09
184 185 4.950926 TGTTTCGTTCGTTCGTTTGTTTA 58.049 34.783 2.67 0.00 0.00 2.01
185 186 3.808095 TGTTTCGTTCGTTCGTTTGTTT 58.192 36.364 2.67 0.00 0.00 2.83
188 189 3.234284 CAGTTGTTTCGTTCGTTCGTTTG 59.766 43.478 2.67 0.00 0.00 2.93
189 190 3.120580 ACAGTTGTTTCGTTCGTTCGTTT 60.121 39.130 2.67 0.00 0.00 3.60
190 191 2.412770 ACAGTTGTTTCGTTCGTTCGTT 59.587 40.909 2.67 0.00 0.00 3.85
193 194 3.598670 CGAGACAGTTGTTTCGTTCGTTC 60.599 47.826 14.75 0.00 44.42 3.95
559 560 2.305405 GCAGTAATCTCGCCTGCTG 58.695 57.895 3.75 0.00 46.23 4.41
560 561 4.844420 GCAGTAATCTCGCCTGCT 57.156 55.556 3.75 0.00 46.23 4.24
597 598 1.270274 TGCAATGCAACAGTGTGATCC 59.730 47.619 5.01 0.00 34.76 3.36
768 774 4.749310 CGGCGCTGCTTCCTCAGT 62.749 66.667 7.64 0.00 36.49 3.41
856 862 2.663188 GACGATGCCGGGATCAGC 60.663 66.667 31.91 20.34 40.78 4.26
864 870 3.853330 CTTGTGCCGACGATGCCG 61.853 66.667 0.00 0.00 42.50 5.69
1764 1782 0.473694 TCTGGAGAAGGTTCCTGCCA 60.474 55.000 7.69 7.69 38.12 4.92
1982 2000 4.521075 GCAGCAGCGTCCTTATCA 57.479 55.556 0.00 0.00 0.00 2.15
2179 2197 1.708993 TTCAGGCTCCACAGGTTGCT 61.709 55.000 0.00 0.00 0.00 3.91
2280 2298 1.000394 TCGATCGTTGTTCCAGCAAGA 60.000 47.619 15.94 0.00 0.00 3.02
2292 2310 2.798501 CGCGGCAATGTCGATCGTT 61.799 57.895 12.84 0.00 29.41 3.85
2302 2320 1.449601 CTACCCTGAACGCGGCAAT 60.450 57.895 12.47 0.00 0.00 3.56
2303 2321 2.047655 CTACCCTGAACGCGGCAA 60.048 61.111 12.47 0.00 0.00 4.52
2304 2322 4.077184 CCTACCCTGAACGCGGCA 62.077 66.667 12.47 7.49 0.00 5.69
2439 2457 1.383248 GGGAGCCCTCTGGAGCTTA 60.383 63.158 0.00 0.00 40.11 3.09
2472 2490 2.647297 GCAAGTGCCACTTCAGCC 59.353 61.111 7.22 0.00 36.03 4.85
2541 2559 3.349006 GGTGTGTGCGGCAGACTG 61.349 66.667 27.35 0.00 40.76 3.51
2553 2571 3.345808 CTGACCGCCGTTGGTGTG 61.346 66.667 0.00 0.00 44.01 3.82
2565 2583 3.539604 CACATCCTCAATCTTCCTGACC 58.460 50.000 0.00 0.00 0.00 4.02
2589 2607 0.035915 GTGGAGGGTTGAGCTCTTCC 60.036 60.000 16.19 16.02 0.00 3.46
2646 2664 2.437897 CAGCTGGGGAACTTGGCT 59.562 61.111 5.57 0.00 0.00 4.75
2882 2900 7.360691 CGATATCCATCCATGTTTCAAGCTTAG 60.361 40.741 0.00 0.00 0.00 2.18
2917 2935 1.898574 CCTGCAAAGAGGGCAACGT 60.899 57.895 0.00 0.00 41.39 3.99
3126 3144 2.370189 GCAGTGGGATATGCTAAGGTCT 59.630 50.000 0.00 0.00 39.38 3.85
3154 3172 1.000163 GACGTTCTCCAGAGTCTGCAA 60.000 52.381 15.10 4.13 0.00 4.08
3163 3181 1.444553 GGCTGTCGACGTTCTCCAG 60.445 63.158 11.62 1.65 0.00 3.86
3194 3212 6.124340 TCCTGCAACTGATGATCAAATATGT 58.876 36.000 0.00 0.00 0.00 2.29
3235 3253 4.389576 CTTTGCCGCACGTGCCTC 62.390 66.667 33.23 24.30 37.91 4.70
3285 3303 1.374190 CAGGCACCTCTTGAGCAGT 59.626 57.895 0.00 0.00 0.00 4.40
3465 3483 2.736995 TTTTCTGCCGACGCCTCG 60.737 61.111 0.00 0.00 39.83 4.63
3511 3529 5.685075 GCATATAACCAGTACCTGAAGCTGT 60.685 44.000 0.00 0.00 32.44 4.40
3632 3650 0.374758 CAGCTTATGCATGCGACGTT 59.625 50.000 14.09 0.00 42.74 3.99
3708 3726 5.987953 TGATTTAGCTCGATGATCAGGAAAG 59.012 40.000 0.09 0.00 0.00 2.62
3716 3734 5.176406 CGTGAATGTGATTTAGCTCGATGAT 59.824 40.000 0.00 0.00 0.00 2.45
3722 3740 4.033358 CCACTCGTGAATGTGATTTAGCTC 59.967 45.833 0.00 0.00 36.38 4.09
3732 3750 3.393800 CTGTTTCTCCACTCGTGAATGT 58.606 45.455 0.00 0.00 0.00 2.71
3957 3975 7.392494 TTCAGTACAGTTGATTACTCGAGAT 57.608 36.000 21.68 2.18 33.85 2.75
3973 3991 9.515020 GTTTGAATTTTGATCAGTTTCAGTACA 57.485 29.630 13.40 1.99 0.00 2.90
4018 4036 6.664816 TCTCCTTTATTCAATGTGCATTCCTT 59.335 34.615 0.00 0.00 0.00 3.36
4077 4095 3.189287 CCTTACTTGCAGTGTCATGAACC 59.811 47.826 0.00 0.00 0.00 3.62
4150 4168 6.115446 TGATAGCAGGTGAACTATTTTCAGG 58.885 40.000 0.00 0.00 0.00 3.86
4232 4250 5.957842 AATTGTGTTCGGTGAATGTACAT 57.042 34.783 1.41 1.41 0.00 2.29
4454 4472 2.103771 CTGTCCTCCATATGACCACCAG 59.896 54.545 3.65 1.15 0.00 4.00
4526 4544 0.942410 GCACGTGGTTTCAGTAGCGA 60.942 55.000 18.88 0.00 0.00 4.93
4629 4647 4.488136 CCTATGCCACCGCCTGCA 62.488 66.667 0.00 0.00 42.52 4.41
4675 4693 4.014406 ACTTTCTCCGAGGTTTTGTTTGT 58.986 39.130 0.00 0.00 0.00 2.83
4795 4813 1.885887 TGCTTCAGTTGTACCAATGGC 59.114 47.619 0.00 0.00 0.00 4.40
4800 4818 2.719531 TGGTTGCTTCAGTTGTACCA 57.280 45.000 0.00 0.00 33.54 3.25
4846 4864 0.787787 GCATTGTCGTTGTCAGCGTA 59.212 50.000 9.00 0.00 0.00 4.42
4851 4869 3.814842 AGAAATGAGCATTGTCGTTGTCA 59.185 39.130 0.00 0.00 0.00 3.58
4855 4873 3.411446 TGGAGAAATGAGCATTGTCGTT 58.589 40.909 0.00 0.00 0.00 3.85
5013 5034 4.910585 GCCCTACGGTGGCGATGG 62.911 72.222 0.00 0.00 39.48 3.51
5021 5042 4.430765 CGTGCTTCGCCCTACGGT 62.431 66.667 0.00 0.00 43.89 4.83
5229 5251 6.619801 AAAGATAACAACAAGTGAGACACC 57.380 37.500 0.00 0.00 34.49 4.16
5339 5364 9.920946 ATGTGTTTATACTTTATCCTGGACAAT 57.079 29.630 0.00 0.00 0.00 2.71
5340 5365 9.747898 AATGTGTTTATACTTTATCCTGGACAA 57.252 29.630 0.00 0.00 0.00 3.18
5348 6967 8.220755 TGGCAGGAATGTGTTTATACTTTATC 57.779 34.615 0.00 0.00 0.00 1.75
5354 6973 6.509418 TTCTTGGCAGGAATGTGTTTATAC 57.491 37.500 8.09 0.00 0.00 1.47
5381 7000 7.810282 CGCAAGAGCACAAGATAGTACTATTAT 59.190 37.037 16.46 6.32 42.27 1.28
5875 7502 2.360844 GAAGGCAAGGGTTAGAGAAGC 58.639 52.381 0.00 0.00 0.00 3.86
5876 7503 2.028020 ACGAAGGCAAGGGTTAGAGAAG 60.028 50.000 0.00 0.00 0.00 2.85
5931 7558 2.593420 CCGGCGGGTAGGGATTTT 59.407 61.111 20.56 0.00 0.00 1.82
5961 7594 0.179108 CGGGGAGTTCGGAATCTCAC 60.179 60.000 16.57 14.23 33.80 3.51
6042 7675 0.112412 GGGGAAGAACAAGGGCAGAA 59.888 55.000 0.00 0.00 0.00 3.02
6048 7681 1.350019 ACGTAAGGGGGAAGAACAAGG 59.650 52.381 0.00 0.00 46.39 3.61
6050 7683 2.048601 TGACGTAAGGGGGAAGAACAA 58.951 47.619 0.00 0.00 46.39 2.83
6051 7684 1.345415 GTGACGTAAGGGGGAAGAACA 59.655 52.381 0.00 0.00 46.39 3.18
6052 7685 1.670967 CGTGACGTAAGGGGGAAGAAC 60.671 57.143 0.00 0.00 46.39 3.01
6054 7687 1.880819 GCGTGACGTAAGGGGGAAGA 61.881 60.000 6.91 0.00 46.39 2.87
6055 7688 1.447314 GCGTGACGTAAGGGGGAAG 60.447 63.158 6.91 0.00 46.39 3.46
6065 7699 1.371389 GAACGGAGAAGCGTGACGT 60.371 57.895 6.91 0.00 39.74 4.34


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

AutoCloner maintained by Alex Coulton.