Multiple sequence alignment - TraesCS1B01G228100

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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 TraesCS1B01G228100 chr1B 100.000 4079 0 0 1 4079 409626893 409630971 0 7533
1 TraesCS1B01G228100 chr1A 95.301 4022 132 21 88 4079 377426619 377430613 0 6327
2 TraesCS1B01G228100 chr1D 93.794 4141 156 40 1 4079 302816426 302820527 0 6130


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 TraesCS1B01G228100 chr1B 409626893 409630971 4078 False 7533 7533 100.000 1 4079 1 chr1B.!!$F1 4078
1 TraesCS1B01G228100 chr1A 377426619 377430613 3994 False 6327 6327 95.301 88 4079 1 chr1A.!!$F1 3991
2 TraesCS1B01G228100 chr1D 302816426 302820527 4101 False 6130 6130 93.794 1 4079 1 chr1D.!!$F1 4078

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
30 31 0.179189 CCGATCAACAAAGAAGCCGC 60.179 55.0 0.00 0.00 0.00 6.53 F
210 211 0.602905 CTAAAGGCGCCGGGGATTAG 60.603 60.0 24.68 20.46 0.00 1.73 F
255 256 0.971386 CCATGTCAAAAAGGCCAGCT 59.029 50.0 5.01 0.00 0.00 4.24 F
2009 2065 0.542702 AACACCAGGGATTTGGGCTG 60.543 55.0 0.00 0.00 42.76 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 1165 0.338467 TGGGCCTGCTACTTCTCCTA 59.662 55.000 4.53 0.0 0.00 2.94 R
1991 2047 1.077265 CAGCCCAAATCCCTGGTGT 59.923 57.895 0.00 0.0 34.33 4.16 R
2017 2073 4.455190 ACAAACATTTGGGCATTAACATGC 59.545 37.500 9.09 0.0 46.21 4.06 R
3524 3582 1.632920 TGTCCACAGGATTACATGGCA 59.367 47.619 0.00 0.0 32.73 4.92 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 31 0.179189 CCGATCAACAAAGAAGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
59 60 1.230635 GCATGGCTCGCGACCATTAT 61.231 55.000 28.89 15.02 45.86 1.28
80 81 1.300233 GAGTAGAAGGATGCGCCCG 60.300 63.158 4.18 0.00 37.37 6.13
89 90 4.740822 ATGCGCCCGCCCTTTTCT 62.741 61.111 4.18 0.00 41.09 2.52
207 208 4.564110 GCTAAAGGCGCCGGGGAT 62.564 66.667 24.68 6.79 0.00 3.85
209 210 1.448497 CTAAAGGCGCCGGGGATTA 59.552 57.895 24.68 15.64 0.00 1.75
210 211 0.602905 CTAAAGGCGCCGGGGATTAG 60.603 60.000 24.68 20.46 0.00 1.73
211 212 1.049855 TAAAGGCGCCGGGGATTAGA 61.050 55.000 24.68 5.16 0.00 2.10
212 213 2.604299 AAAGGCGCCGGGGATTAGAC 62.604 60.000 24.68 2.49 0.00 2.59
213 214 3.547513 GGCGCCGGGGATTAGACT 61.548 66.667 24.68 0.00 0.00 3.24
214 215 2.280186 GCGCCGGGGATTAGACTG 60.280 66.667 24.68 0.00 0.00 3.51
222 223 1.913419 GGGGATTAGACTGGGTTCACA 59.087 52.381 0.00 0.00 0.00 3.58
255 256 0.971386 CCATGTCAAAAAGGCCAGCT 59.029 50.000 5.01 0.00 0.00 4.24
413 428 6.420913 TTTCACTGGTTAGTTAGCTCTTCT 57.579 37.500 0.00 0.00 34.07 2.85
432 447 3.153919 TCTGTTAAATTCTGGTGGTGGC 58.846 45.455 0.00 0.00 0.00 5.01
499 514 2.727123 TTGTTGTCTTGGGCTCTTGA 57.273 45.000 0.00 0.00 0.00 3.02
517 532 3.701205 TGATCTTGCTTTCAGCTGGTA 57.299 42.857 15.13 0.00 42.97 3.25
626 651 6.067217 AGTTCTTTATGTGCCCTTCAGTAT 57.933 37.500 0.00 0.00 0.00 2.12
631 656 9.555727 TTCTTTATGTGCCCTTCAGTATATAAC 57.444 33.333 0.00 0.00 0.00 1.89
753 795 2.774234 TGGGATTGGCTAGAGAAAGGAG 59.226 50.000 0.00 0.00 0.00 3.69
761 804 4.102524 TGGCTAGAGAAAGGAGTTTGTGAA 59.897 41.667 0.00 0.00 0.00 3.18
792 835 2.489329 AGATTTTCCATGACCTTGTGCG 59.511 45.455 0.00 0.00 0.00 5.34
830 873 1.896220 TGTGATTGGTCCAGCTTCAC 58.104 50.000 18.10 18.10 37.73 3.18
910 953 5.302568 TGCTTCCTGATTTTATAAGGCATGG 59.697 40.000 0.00 0.00 30.14 3.66
1034 1077 4.985538 TCTTCAACTAGGAGCCATGTTTT 58.014 39.130 0.00 0.00 0.00 2.43
1483 1535 4.761227 TGAGTTGAGTGATTGCTTGCAATA 59.239 37.500 19.11 7.00 0.00 1.90
1543 1595 4.099573 AGGCTGTACGTTGTGCTATAGATT 59.900 41.667 3.21 0.00 0.00 2.40
1634 1686 4.517075 GCTTCTTACCTGATCCATTTAGCC 59.483 45.833 0.00 0.00 0.00 3.93
1645 1697 1.338020 CCATTTAGCCGCCTTTGGATC 59.662 52.381 0.00 0.00 0.00 3.36
1649 1701 1.967319 TAGCCGCCTTTGGATCATTC 58.033 50.000 0.00 0.00 0.00 2.67
1684 1736 5.587043 TCCAAATCGTTGTCTACTGTTGTTT 59.413 36.000 0.00 0.00 32.40 2.83
1685 1737 5.681105 CCAAATCGTTGTCTACTGTTGTTTG 59.319 40.000 0.00 0.00 32.40 2.93
1686 1738 6.255215 CAAATCGTTGTCTACTGTTGTTTGT 58.745 36.000 0.00 0.00 0.00 2.83
1694 1746 9.480053 GTTGTCTACTGTTGTTTGTATTAGGTA 57.520 33.333 0.00 0.00 0.00 3.08
1743 1795 7.272978 AGTGTACATAAATGTAGCGGAAGATT 58.727 34.615 0.00 0.00 43.32 2.40
1784 1840 7.606073 GGACATTTTTACTTTAAACCCATGCAT 59.394 33.333 0.00 0.00 0.00 3.96
1785 1841 8.321650 ACATTTTTACTTTAAACCCATGCATG 57.678 30.769 20.19 20.19 0.00 4.06
1786 1842 6.793492 TTTTTACTTTAAACCCATGCATGC 57.207 33.333 21.69 11.82 0.00 4.06
1787 1843 2.652941 ACTTTAAACCCATGCATGCG 57.347 45.000 21.69 15.67 0.00 4.73
1807 1863 3.662186 GCGTTCAGAAAACATTTACCGTG 59.338 43.478 0.00 0.00 0.00 4.94
1826 1882 3.118186 CGTGGTACCATCCCTTTCCATTA 60.118 47.826 19.72 0.00 0.00 1.90
1829 1885 3.203487 GGTACCATCCCTTTCCATTACCA 59.797 47.826 7.15 0.00 0.00 3.25
1836 1892 8.464322 ACCATCCCTTTCCATTACCATAATTAT 58.536 33.333 0.00 0.00 0.00 1.28
1871 1927 9.452287 TGTCCAAATTAGGTATTTACAAGGTAC 57.548 33.333 0.00 0.00 34.69 3.34
2009 2065 0.542702 AACACCAGGGATTTGGGCTG 60.543 55.000 0.00 0.00 42.76 4.85
2017 2073 1.369625 GGATTTGGGCTGTACTGACG 58.630 55.000 3.61 0.00 0.00 4.35
2080 2136 1.215173 CTGATGGCCTGGTTTGGGATA 59.785 52.381 3.32 0.00 0.00 2.59
2297 2353 6.980051 AGTCCAAAATTAGTTACCGCTAAG 57.020 37.500 0.00 0.00 34.83 2.18
2458 2514 8.056407 AGGAAAATAGTTCAATAGGAAGCAAC 57.944 34.615 0.00 0.00 35.82 4.17
2473 2529 1.160137 GCAACTGTAACTGGGAGCAG 58.840 55.000 0.00 0.00 35.31 4.24
2554 2610 3.644966 TCTTTTGTGTGGGTTCTGAGT 57.355 42.857 0.00 0.00 0.00 3.41
2823 2879 9.557338 TGTGTTTATACGGTTTATGTAAATTGC 57.443 29.630 0.00 0.00 0.00 3.56
2847 2904 6.042777 CGTTGCTATCTCTCTGATTGGTTTA 58.957 40.000 0.00 0.00 36.65 2.01
2913 2970 3.571590 TGGCATACAGTTTGGTTTCCTT 58.428 40.909 0.00 0.00 0.00 3.36
2955 3012 6.881065 TGTCTACTTTTGCTGCTGAAATCTAT 59.119 34.615 0.00 0.00 0.00 1.98
3113 3170 1.321474 CAGACTTGAAGGCTTTGGCA 58.679 50.000 0.00 0.00 40.87 4.92
3219 3276 9.679661 TGCTTCTTTAAGATATTTGATGTACCA 57.320 29.630 0.00 0.00 34.37 3.25
3243 3300 1.952990 ACGTTGTTGAACATGATGGCA 59.047 42.857 0.00 0.00 31.78 4.92
3246 3303 3.989167 CGTTGTTGAACATGATGGCATTT 59.011 39.130 0.00 0.00 30.68 2.32
3394 3451 6.109156 TGTATCACCTGTAGAAGCAAAAGA 57.891 37.500 0.00 0.00 0.00 2.52
3435 3493 8.673711 GTTTATGGATTAGCTTTGTCACACATA 58.326 33.333 0.00 0.00 0.00 2.29
3615 3673 8.264347 TGCAAGGTATCTGTACATCATTTTCTA 58.736 33.333 0.00 0.00 32.25 2.10
3682 3759 7.925043 TTGTACCTACAAACTTTCAAGTGAA 57.075 32.000 0.00 0.00 42.66 3.18
3683 3760 8.514330 TTGTACCTACAAACTTTCAAGTGAAT 57.486 30.769 0.00 0.00 42.66 2.57
3684 3761 7.925993 TGTACCTACAAACTTTCAAGTGAATG 58.074 34.615 5.61 5.61 39.66 2.67
3685 3762 7.554835 TGTACCTACAAACTTTCAAGTGAATGT 59.445 33.333 6.73 6.73 42.05 2.71
3686 3763 9.048446 GTACCTACAAACTTTCAAGTGAATGTA 57.952 33.333 11.63 8.38 40.22 2.29
3687 3764 8.154649 ACCTACAAACTTTCAAGTGAATGTAG 57.845 34.615 20.68 20.68 42.94 2.74
3688 3765 7.078228 CCTACAAACTTTCAAGTGAATGTAGC 58.922 38.462 21.43 0.00 42.55 3.58
3767 3844 4.061596 TGTGACATGACAAAGCGATGTTA 58.938 39.130 0.00 0.00 32.57 2.41
3873 3952 4.019321 TCCCTCTTCCTTCAATTACACCAG 60.019 45.833 0.00 0.00 0.00 4.00
3886 3965 4.335647 ACCAGGCCCAGCAGAACG 62.336 66.667 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.391523 CGGCTTCTTTGTTGATCGGATTTAA 60.392 40.000 0.00 0.00 0.00 1.52
17 18 3.146066 TGTATCTTGCGGCTTCTTTGTT 58.854 40.909 0.00 0.00 0.00 2.83
30 31 1.224075 CGAGCCATGCCTGTATCTTG 58.776 55.000 0.00 0.00 0.00 3.02
55 56 4.380655 GGCGCATCCTTCTACTCGTATAAT 60.381 45.833 10.83 0.00 0.00 1.28
59 60 0.666913 GGCGCATCCTTCTACTCGTA 59.333 55.000 10.83 0.00 0.00 3.43
80 81 2.391389 CGCCGTCTCAGAAAAGGGC 61.391 63.158 6.23 6.23 41.80 5.19
86 87 0.856641 CGTTTTTCGCCGTCTCAGAA 59.143 50.000 0.00 0.00 0.00 3.02
89 90 1.216941 GGTCGTTTTTCGCCGTCTCA 61.217 55.000 0.00 0.00 39.67 3.27
206 207 9.449719 CTAAACTAATTGTGAACCCAGTCTAAT 57.550 33.333 0.00 0.00 0.00 1.73
207 208 8.434392 ACTAAACTAATTGTGAACCCAGTCTAA 58.566 33.333 0.00 0.00 0.00 2.10
209 210 6.710744 CACTAAACTAATTGTGAACCCAGTCT 59.289 38.462 0.00 0.00 32.72 3.24
210 211 6.485648 ACACTAAACTAATTGTGAACCCAGTC 59.514 38.462 0.00 0.00 34.81 3.51
211 212 6.362248 ACACTAAACTAATTGTGAACCCAGT 58.638 36.000 0.00 0.00 34.81 4.00
212 213 6.072673 GGACACTAAACTAATTGTGAACCCAG 60.073 42.308 0.00 0.00 34.81 4.45
213 214 5.766174 GGACACTAAACTAATTGTGAACCCA 59.234 40.000 0.00 0.00 34.81 4.51
214 215 5.766174 TGGACACTAAACTAATTGTGAACCC 59.234 40.000 0.00 0.00 34.81 4.11
222 223 9.965824 CTTTTTGACATGGACACTAAACTAATT 57.034 29.630 0.00 0.00 0.00 1.40
255 256 3.580458 AGAAGAGAAGCTAGTGCAAAGGA 59.420 43.478 0.00 0.00 42.74 3.36
261 262 3.601443 TTCCAGAAGAGAAGCTAGTGC 57.399 47.619 0.00 0.00 40.05 4.40
413 428 3.153919 GAGCCACCACCAGAATTTAACA 58.846 45.455 0.00 0.00 0.00 2.41
439 454 6.282930 TCAAAATCCAAAAGAAGAGCCAAAG 58.717 36.000 0.00 0.00 0.00 2.77
517 532 3.468071 TCATACGCAGGGATAGGGTAT 57.532 47.619 0.00 0.00 43.29 2.73
553 568 7.147776 ACACATGGGGTACTGAACTAACTATAC 60.148 40.741 0.00 0.00 0.00 1.47
626 651 9.914834 AAGGTGAAAATAACATAGCTGGTTATA 57.085 29.630 19.67 7.30 39.77 0.98
631 656 7.378181 ACAAAAGGTGAAAATAACATAGCTGG 58.622 34.615 0.00 0.00 0.00 4.85
761 804 9.631257 AAGGTCATGGAAAATCTTTTTGAAAAT 57.369 25.926 0.00 0.00 0.00 1.82
781 824 4.160814 ACATATTAGTACCGCACAAGGTCA 59.839 41.667 0.00 0.00 44.68 4.02
830 873 4.814967 AGATTGGGGGTATATTTGTTGGG 58.185 43.478 0.00 0.00 0.00 4.12
910 953 4.108699 TCAAAATCAATCGCCACCAATC 57.891 40.909 0.00 0.00 0.00 2.67
1034 1077 2.679342 CCCAGCCGATTCCCCTCAA 61.679 63.158 0.00 0.00 0.00 3.02
1122 1165 0.338467 TGGGCCTGCTACTTCTCCTA 59.662 55.000 4.53 0.00 0.00 2.94
1237 1280 1.263484 CAAAGCCGAGCTATCAGCATG 59.737 52.381 0.38 0.00 45.56 4.06
1543 1595 8.677300 GGAAAGCATAGACATGTTCATTTTAGA 58.323 33.333 0.00 0.00 34.40 2.10
1634 1686 1.447317 CCCCGAATGATCCAAAGGCG 61.447 60.000 0.00 0.00 0.00 5.52
1645 1697 3.343941 TTTGGAGAGTTACCCCGAATG 57.656 47.619 0.00 0.00 0.00 2.67
1649 1701 1.206371 ACGATTTGGAGAGTTACCCCG 59.794 52.381 0.00 0.00 0.00 5.73
1709 1761 9.032420 GCTACATTTATGTACACTAAGGAAGAC 57.968 37.037 0.00 0.00 41.97 3.01
1743 1795 4.387026 AATGTCCCCTGAACTTTCATCA 57.613 40.909 0.00 0.00 36.46 3.07
1784 1840 3.312973 ACGGTAAATGTTTTCTGAACGCA 59.687 39.130 0.00 0.00 0.00 5.24
1785 1841 3.662186 CACGGTAAATGTTTTCTGAACGC 59.338 43.478 0.00 0.00 0.00 4.84
1786 1842 4.215965 CCACGGTAAATGTTTTCTGAACG 58.784 43.478 0.00 0.00 0.00 3.95
1787 1843 5.177725 ACCACGGTAAATGTTTTCTGAAC 57.822 39.130 0.00 0.00 0.00 3.18
1807 1863 3.203487 TGGTAATGGAAAGGGATGGTACC 59.797 47.826 4.43 4.43 0.00 3.34
1991 2047 1.077265 CAGCCCAAATCCCTGGTGT 59.923 57.895 0.00 0.00 34.33 4.16
2017 2073 4.455190 ACAAACATTTGGGCATTAACATGC 59.545 37.500 9.09 0.00 46.21 4.06
2080 2136 5.122396 GTGCCGAATGTCAGTCTTAAAGATT 59.878 40.000 0.00 0.00 0.00 2.40
2458 2514 0.610174 TCAGCTGCTCCCAGTTACAG 59.390 55.000 9.47 0.00 41.26 2.74
2473 2529 3.996480 AGTCCTAGTGTTGACTTTCAGC 58.004 45.455 0.00 0.00 38.67 4.26
2554 2610 5.529430 CACCTTTATTATGGCCAACACGATA 59.471 40.000 10.96 0.99 0.00 2.92
2823 2879 4.052159 ACCAATCAGAGAGATAGCAACG 57.948 45.455 0.00 0.00 35.39 4.10
2847 2904 6.651225 GCTTTGTATTCACCTACAGAAAGACT 59.349 38.462 0.00 0.00 33.38 3.24
3066 3123 9.851686 AATACTTCATGAAGCTATTGGTAATGA 57.148 29.630 30.95 0.65 41.99 2.57
3158 3215 7.567622 TCCCTAGAAAAGCCTAACTATGTATGT 59.432 37.037 0.00 0.00 0.00 2.29
3218 3275 5.088068 CCATCATGTTCAACAACGTACATG 58.912 41.667 17.02 17.02 45.69 3.21
3219 3276 4.379394 GCCATCATGTTCAACAACGTACAT 60.379 41.667 0.00 0.00 34.95 2.29
3220 3277 3.058570 GCCATCATGTTCAACAACGTACA 60.059 43.478 0.00 0.00 34.95 2.90
3221 3278 3.058570 TGCCATCATGTTCAACAACGTAC 60.059 43.478 0.00 0.00 34.95 3.67
3222 3279 3.142174 TGCCATCATGTTCAACAACGTA 58.858 40.909 0.00 0.00 34.95 3.57
3223 3280 1.952990 TGCCATCATGTTCAACAACGT 59.047 42.857 0.00 0.00 34.95 3.99
3224 3281 2.702898 TGCCATCATGTTCAACAACG 57.297 45.000 0.00 0.00 34.95 4.10
3243 3300 4.877251 ACAAACATGTTTCTGCTGCAAAAT 59.123 33.333 20.85 0.00 0.00 1.82
3246 3303 3.523606 ACAAACATGTTTCTGCTGCAA 57.476 38.095 20.85 0.00 0.00 4.08
3356 3413 7.019418 CAGGTGATACATTCATTTCATATGCG 58.981 38.462 0.00 0.00 36.54 4.73
3385 3442 6.598850 ACATGGATGTTGTTTTTCTTTTGCTT 59.401 30.769 0.00 0.00 37.90 3.91
3435 3493 9.979578 AATCATGTATGTTGTTTGTGTACAAAT 57.020 25.926 12.72 0.55 46.12 2.32
3524 3582 1.632920 TGTCCACAGGATTACATGGCA 59.367 47.619 0.00 0.00 32.73 4.92
3615 3673 3.213206 TCTGCATCTGTGTCCAGTTTT 57.787 42.857 0.00 0.00 39.82 2.43
3679 3756 7.603963 TTACTATTTTTCTGCGCTACATTCA 57.396 32.000 9.73 0.00 0.00 2.57
3680 3757 7.112148 GCATTACTATTTTTCTGCGCTACATTC 59.888 37.037 9.73 0.00 0.00 2.67
3681 3758 6.912591 GCATTACTATTTTTCTGCGCTACATT 59.087 34.615 9.73 0.00 0.00 2.71
3682 3759 6.260936 AGCATTACTATTTTTCTGCGCTACAT 59.739 34.615 9.73 0.00 34.89 2.29
3683 3760 5.584649 AGCATTACTATTTTTCTGCGCTACA 59.415 36.000 9.73 0.00 34.89 2.74
3684 3761 5.904080 CAGCATTACTATTTTTCTGCGCTAC 59.096 40.000 9.73 0.00 34.89 3.58
3685 3762 5.815222 TCAGCATTACTATTTTTCTGCGCTA 59.185 36.000 9.73 0.00 34.89 4.26
3686 3763 4.635765 TCAGCATTACTATTTTTCTGCGCT 59.364 37.500 9.73 0.00 34.89 5.92
3687 3764 4.908736 TCAGCATTACTATTTTTCTGCGC 58.091 39.130 0.00 0.00 34.89 6.09
3688 3765 4.966366 GCTCAGCATTACTATTTTTCTGCG 59.034 41.667 0.00 0.00 34.89 5.18
3767 3844 5.801947 GCGATTTCACAAATATTGTCAAGCT 59.198 36.000 0.00 0.00 43.23 3.74
3886 3965 2.439156 GGACCTGCAGACATGGGC 60.439 66.667 17.39 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.