Multiple sequence alignment - TraesCS1B01G229600

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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 TraesCS1B01G229600 chr1B 100.000 4667 0 0 1 4667 412249138 412244472 0.000000e+00 8619
1 TraesCS1B01G229600 chr1A 94.727 3186 106 21 1 3134 382246393 382249568 0.000000e+00 4896
2 TraesCS1B01G229600 chr1A 93.677 1534 56 13 3155 4667 382250209 382251722 0.000000e+00 2257
3 TraesCS1B01G229600 chr1A 94.805 77 4 0 1 77 382245867 382245943 2.280000e-23 121
4 TraesCS1B01G229600 chr1D 95.751 1577 33 14 1591 3139 305224792 305226362 0.000000e+00 2510
5 TraesCS1B01G229600 chr1D 94.557 1525 43 10 3155 4667 305227030 305228526 0.000000e+00 2320
6 TraesCS1B01G229600 chr1D 95.756 966 27 8 640 1596 305223657 305224617 0.000000e+00 1544
7 TraesCS1B01G229600 chr1D 93.148 467 25 4 1 465 305223149 305223610 0.000000e+00 678
8 TraesCS1B01G229600 chr7B 91.250 80 6 1 3063 3142 369872711 369872789 1.780000e-19 108
9 TraesCS1B01G229600 chr6A 95.588 68 2 1 3072 3139 117350663 117350729 1.780000e-19 108
10 TraesCS1B01G229600 chr6B 93.056 72 5 0 3068 3139 537553837 537553908 6.390000e-19 106
11 TraesCS1B01G229600 chr6B 89.744 78 6 2 3064 3139 641305423 641305500 1.070000e-16 99
12 TraesCS1B01G229600 chr6D 92.958 71 5 0 3072 3142 386931471 386931401 2.300000e-18 104
13 TraesCS1B01G229600 chr2D 92.958 71 5 0 3072 3142 93080171 93080101 2.300000e-18 104
14 TraesCS1B01G229600 chr7A 90.909 77 6 1 3063 3139 421784998 421785073 8.260000e-18 102


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 TraesCS1B01G229600 chr1B 412244472 412249138 4666 True 8619.000000 8619 100.000 1 4667 1 chr1B.!!$R1 4666
1 TraesCS1B01G229600 chr1A 382245867 382251722 5855 False 2424.666667 4896 94.403 1 4667 3 chr1A.!!$F1 4666
2 TraesCS1B01G229600 chr1D 305223149 305228526 5377 False 1763.000000 2510 94.803 1 4667 4 chr1D.!!$F1 4666

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
237 767 1.209275 GACGACCGAGAATGCATCCG 61.209 60.000 0.0 4.34 0.0 4.18 F
1660 2390 1.200948 GCTGGGTGAGTGCATCTTTTC 59.799 52.381 0.0 0.00 0.0 2.29 F
2248 2978 3.441222 TCTGCTTACGTACCTGATTCGAA 59.559 43.478 0.0 0.00 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2714 0.666374 TGTGACGAGTTGCGAGAAGA 59.334 50.0 0.0 0.0 44.57 2.87 R
2772 3534 0.249953 TGCCTTTTCGAGTGCGGTTA 60.250 50.0 0.0 0.0 38.28 2.85 R
4215 5647 0.248907 ATCAACGACCGTCCTATGCG 60.249 55.0 0.0 0.0 0.00 4.73 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
139 669 3.303351 GGTCCCACCAATCATCAAGAT 57.697 47.619 0.00 0.00 38.42 2.40
147 677 3.758023 ACCAATCATCAAGATGCGACAAA 59.242 39.130 5.19 0.00 38.65 2.83
192 722 1.888512 GGGCTTGCATGAGAAAAGTCA 59.111 47.619 3.33 0.00 0.00 3.41
237 767 1.209275 GACGACCGAGAATGCATCCG 61.209 60.000 0.00 4.34 0.00 4.18
272 802 3.707102 GAGCTCCACCCTTACTAACTGAT 59.293 47.826 0.87 0.00 0.00 2.90
282 812 7.222224 CACCCTTACTAACTGATATTTGTCGAC 59.778 40.741 9.11 9.11 0.00 4.20
320 850 2.699281 GGGGGTAACTCATAGGGGTGAT 60.699 54.545 0.00 0.00 41.13 3.06
371 901 3.225104 GCCTTTGATCCATAGCCAATGA 58.775 45.455 0.00 0.00 37.86 2.57
486 1016 4.816385 TGAAGTCAAAGATGCGAGAAAACT 59.184 37.500 0.00 0.00 0.00 2.66
518 1048 7.293828 TGTAGATCTACTCATGATCTTCCAGT 58.706 38.462 28.53 0.00 45.74 4.00
519 1049 7.782168 TGTAGATCTACTCATGATCTTCCAGTT 59.218 37.037 28.53 0.00 45.74 3.16
613 1143 8.519526 TGTGAAATTTGTGATGTTCCTATAACC 58.480 33.333 0.00 0.00 0.00 2.85
616 1146 9.353999 GAAATTTGTGATGTTCCTATAACCAAC 57.646 33.333 0.00 0.00 0.00 3.77
624 1154 2.041701 TCCTATAACCAACGGCTACCC 58.958 52.381 0.00 0.00 0.00 3.69
625 1155 2.044758 CCTATAACCAACGGCTACCCT 58.955 52.381 0.00 0.00 0.00 4.34
721 1254 8.437274 TTTTCTCTAGGGATTTCTCTTACAGT 57.563 34.615 0.00 0.00 0.00 3.55
722 1255 8.437274 TTTCTCTAGGGATTTCTCTTACAGTT 57.563 34.615 0.00 0.00 0.00 3.16
728 1261 4.720273 GGGATTTCTCTTACAGTTCCCCTA 59.280 45.833 0.00 0.00 33.86 3.53
730 1263 6.292150 GGATTTCTCTTACAGTTCCCCTATG 58.708 44.000 0.00 0.00 0.00 2.23
763 1297 3.146847 CCGTGCTTTCTCTAGGGTTTTT 58.853 45.455 0.00 0.00 0.00 1.94
764 1298 4.202388 ACCGTGCTTTCTCTAGGGTTTTTA 60.202 41.667 0.00 0.00 28.95 1.52
768 1302 7.368059 CGTGCTTTCTCTAGGGTTTTTATTTT 58.632 34.615 0.00 0.00 0.00 1.82
772 1306 9.758651 GCTTTCTCTAGGGTTTTTATTTTGAAA 57.241 29.630 0.00 0.00 0.00 2.69
776 1310 8.562052 TCTCTAGGGTTTTTATTTTGAAACGAC 58.438 33.333 0.00 0.00 36.78 4.34
793 1327 1.967779 CGACAACCCCCTTCCATTTTT 59.032 47.619 0.00 0.00 0.00 1.94
824 1358 1.651240 GAACCGACCGTCCGATCTGA 61.651 60.000 0.00 0.00 0.00 3.27
827 1361 1.725557 CCGACCGTCCGATCTGACAT 61.726 60.000 16.29 4.67 34.88 3.06
836 1370 3.628032 GTCCGATCTGACATCTGTAGACA 59.372 47.826 11.95 0.00 35.29 3.41
1244 1789 3.807209 GCTAACGAGGATAGGGTACGGTA 60.807 52.174 0.00 0.00 0.00 4.02
1269 1814 2.224209 TGATGTGCAGCAGATCGATGAT 60.224 45.455 23.64 0.00 37.02 2.45
1625 2355 1.666189 GTCGGAATAGTTGCTGCCTTC 59.334 52.381 0.00 0.00 0.00 3.46
1660 2390 1.200948 GCTGGGTGAGTGCATCTTTTC 59.799 52.381 0.00 0.00 0.00 2.29
2248 2978 3.441222 TCTGCTTACGTACCTGATTCGAA 59.559 43.478 0.00 0.00 0.00 3.71
2338 3068 6.680810 TGATGATGGTTTGAAGTTGATGAAC 58.319 36.000 0.00 0.00 0.00 3.18
2371 3128 5.163258 TGGAAAGCATGGTTTTATGGTTGTT 60.163 36.000 22.77 0.00 45.13 2.83
2599 3356 4.380531 TGCTGATTAAAGATCCTAAGCGG 58.619 43.478 5.33 5.33 32.09 5.52
2965 3727 2.368439 CCAAGAATCTGGATTTCGGCA 58.632 47.619 0.00 0.00 38.96 5.69
3053 3815 4.591321 TCTTCCTGAGGTTTATGGCATT 57.409 40.909 4.78 0.00 0.00 3.56
3662 5080 4.623932 ACAGAAGATACAGGCAAAGACA 57.376 40.909 0.00 0.00 0.00 3.41
3960 5378 4.795962 GCCTGTTAGTTCATGTTTGGTTGG 60.796 45.833 0.00 0.00 0.00 3.77
4064 5490 6.884295 ACCTGTCCGAGATTTCAAATTTGATA 59.116 34.615 21.10 16.72 37.00 2.15
4102 5530 1.672356 CTGCAGGTGTAGGGTGTGC 60.672 63.158 5.57 0.00 34.62 4.57
4128 5556 1.680735 CAGGTTTACAGGCAGCACAAA 59.319 47.619 0.00 0.00 0.00 2.83
4151 5579 2.814336 GTTCGTTTCTTCCATGAGGCTT 59.186 45.455 0.00 0.00 33.74 4.35
4187 5619 1.946768 TGCTTTTGTTCTGAACCCTCG 59.053 47.619 17.26 5.56 0.00 4.63
4204 5636 0.323629 TCGTGAATTCACACCCTCCC 59.676 55.000 32.06 8.58 46.75 4.30
4205 5637 0.324943 CGTGAATTCACACCCTCCCT 59.675 55.000 32.06 0.00 46.75 4.20
4206 5638 1.676014 CGTGAATTCACACCCTCCCTC 60.676 57.143 32.06 7.25 46.75 4.30
4208 5640 1.630369 TGAATTCACACCCTCCCTCAG 59.370 52.381 3.38 0.00 0.00 3.35
4359 5795 5.671493 AGTCAATCAAATTACCGACCTAGG 58.329 41.667 7.41 7.41 37.30 3.02
4382 5818 4.309950 CCGCACCCCGCCCTATAC 62.310 72.222 0.00 0.00 37.30 1.47
4383 5819 3.542676 CGCACCCCGCCCTATACA 61.543 66.667 0.00 0.00 37.30 2.29
4384 5820 2.110420 GCACCCCGCCCTATACAC 59.890 66.667 0.00 0.00 32.94 2.90
4385 5821 2.826702 CACCCCGCCCTATACACC 59.173 66.667 0.00 0.00 0.00 4.16
4386 5822 2.447186 ACCCCGCCCTATACACCC 60.447 66.667 0.00 0.00 0.00 4.61
4387 5823 2.122547 CCCCGCCCTATACACCCT 60.123 66.667 0.00 0.00 0.00 4.34
4388 5824 1.156803 CCCCGCCCTATACACCCTA 59.843 63.158 0.00 0.00 0.00 3.53
4389 5825 1.190178 CCCCGCCCTATACACCCTAC 61.190 65.000 0.00 0.00 0.00 3.18
4390 5826 1.530013 CCCGCCCTATACACCCTACG 61.530 65.000 0.00 0.00 0.00 3.51
4391 5827 1.530013 CCGCCCTATACACCCTACGG 61.530 65.000 0.00 0.00 0.00 4.02
4407 5843 3.416880 GGGGCGGAGGGAATGGAA 61.417 66.667 0.00 0.00 0.00 3.53
4430 5866 6.442513 AAAGTTCAAGGTTGAGAAGAACAG 57.557 37.500 0.00 0.00 40.63 3.16
4542 5978 3.357079 CAGTGTTCTGTGGCGCCC 61.357 66.667 26.77 16.24 36.97 6.13
4543 5979 3.872603 AGTGTTCTGTGGCGCCCA 61.873 61.111 26.77 20.19 0.00 5.36
4544 5980 3.357079 GTGTTCTGTGGCGCCCAG 61.357 66.667 28.82 28.82 32.34 4.45
4545 5981 4.641645 TGTTCTGTGGCGCCCAGG 62.642 66.667 31.68 19.82 32.34 4.45
4546 5982 4.329545 GTTCTGTGGCGCCCAGGA 62.330 66.667 31.68 25.88 32.34 3.86
4551 5987 3.140814 GTGGCGCCCAGGAATTCC 61.141 66.667 26.77 17.31 32.34 3.01
4552 5988 3.656280 TGGCGCCCAGGAATTCCA 61.656 61.111 26.77 0.00 38.89 3.53
4553 5989 2.123726 GGCGCCCAGGAATTCCAT 60.124 61.111 26.22 8.81 38.89 3.41
4584 6031 8.684386 TTCATACTACAAACAGTTCAATTCCA 57.316 30.769 0.00 0.00 0.00 3.53
4653 6101 3.621794 CAGCAACTGTAAAACTCACAGC 58.378 45.455 2.51 0.00 45.96 4.40
4656 6104 3.065371 GCAACTGTAAAACTCACAGCACT 59.935 43.478 2.51 0.00 45.96 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.367695 TGGTATGTCTTTGTCAATCACTAACG 59.632 38.462 0.00 0.00 0.00 3.18
68 71 4.643334 AGGGTAAATCCTTGGCGTATTTTC 59.357 41.667 0.00 0.00 32.13 2.29
192 722 6.861065 ATTATAACGACGCTTCAAATCCAT 57.139 33.333 0.00 0.00 0.00 3.41
224 754 1.493950 GACAGCCGGATGCATTCTCG 61.494 60.000 21.97 5.86 44.83 4.04
237 767 1.759445 TGGAGCTCTAAGATGACAGCC 59.241 52.381 14.64 0.00 31.81 4.85
282 812 7.180587 AGTTACCCCCTCTTCTTTTCTACTTAG 59.819 40.741 0.00 0.00 0.00 2.18
415 945 2.094417 GTCACCATAGTCGCTTTCTTGC 59.906 50.000 0.00 0.00 0.00 4.01
475 1005 8.851145 AGATCTACATATCTTAGTTTTCTCGCA 58.149 33.333 0.00 0.00 32.09 5.10
508 1038 6.820656 AGATATGTGTGTCAAACTGGAAGATC 59.179 38.462 0.00 0.00 37.43 2.75
510 1040 6.114187 AGATATGTGTGTCAAACTGGAAGA 57.886 37.500 0.00 0.00 37.43 2.87
518 1048 4.284829 TGCAGGAGATATGTGTGTCAAA 57.715 40.909 0.00 0.00 0.00 2.69
519 1049 3.979101 TGCAGGAGATATGTGTGTCAA 57.021 42.857 0.00 0.00 0.00 3.18
594 1124 5.413213 CCGTTGGTTATAGGAACATCACAAA 59.587 40.000 0.00 0.00 0.00 2.83
613 1143 1.806623 GCTGACATAGGGTAGCCGTTG 60.807 57.143 5.06 9.76 0.00 4.10
616 1146 0.681733 ATGCTGACATAGGGTAGCCG 59.318 55.000 5.06 0.00 33.67 5.52
625 1155 9.665719 TTGAAATGTTAACTCTATGCTGACATA 57.334 29.630 7.22 0.00 37.74 2.29
739 1273 2.100989 ACCCTAGAGAAAGCACGGTAG 58.899 52.381 0.00 0.00 0.00 3.18
741 1275 1.349067 AACCCTAGAGAAAGCACGGT 58.651 50.000 0.00 0.00 0.00 4.83
743 1277 6.496338 AATAAAAACCCTAGAGAAAGCACG 57.504 37.500 0.00 0.00 0.00 5.34
763 1297 3.834938 AGGGGGTTGTCGTTTCAAAATA 58.165 40.909 0.00 0.00 0.00 1.40
764 1298 2.673258 AGGGGGTTGTCGTTTCAAAAT 58.327 42.857 0.00 0.00 0.00 1.82
768 1302 0.179012 GGAAGGGGGTTGTCGTTTCA 60.179 55.000 0.00 0.00 0.00 2.69
772 1306 0.481128 AAATGGAAGGGGGTTGTCGT 59.519 50.000 0.00 0.00 0.00 4.34
793 1327 1.228831 TCGGTTCGACCCACCCTAA 60.229 57.895 0.00 0.00 33.75 2.69
836 1370 0.613777 GGAAGATCCCACGGTTCTGT 59.386 55.000 0.00 0.00 32.71 3.41
1209 1754 4.728102 TTAGCACCCGACGCCACG 62.728 66.667 0.00 0.00 0.00 4.94
1244 1789 1.676746 GATCTGCTGCACATCACCAT 58.323 50.000 12.23 0.00 0.00 3.55
1269 1814 3.916544 CGCAGCCTCCTCCGCATA 61.917 66.667 0.00 0.00 0.00 3.14
1336 1884 3.243101 CGACTAGACAGATTACCATGCGT 60.243 47.826 0.00 0.00 0.00 5.24
1589 2139 0.937304 CGACAACCAACCACACAGAG 59.063 55.000 0.00 0.00 0.00 3.35
1625 2355 1.135083 CCCAGCACCTACAAGTACTCG 60.135 57.143 0.00 0.00 0.00 4.18
1660 2390 5.291371 TGAAATGAACAAACACACAATGCTG 59.709 36.000 0.00 0.00 0.00 4.41
1790 2520 1.701847 CTGCCTAGCCCATGATTAGGT 59.298 52.381 14.59 1.98 37.00 3.08
1818 2548 1.153978 CGGTCCTGCTTTACGCGTA 60.154 57.895 16.41 16.41 43.27 4.42
1984 2714 0.666374 TGTGACGAGTTGCGAGAAGA 59.334 50.000 0.00 0.00 44.57 2.87
2025 2755 9.210329 TGTTGACGCTAGAAAATAACATTCTAA 57.790 29.630 0.00 0.00 38.53 2.10
2026 2756 8.766000 TGTTGACGCTAGAAAATAACATTCTA 57.234 30.769 0.00 0.00 38.13 2.10
2027 2757 7.667043 TGTTGACGCTAGAAAATAACATTCT 57.333 32.000 0.00 0.00 40.18 2.40
2041 2771 3.980646 AAAGTGCAATTGTTGACGCTA 57.019 38.095 7.40 0.00 30.98 4.26
2174 2904 4.415596 TGATTTGGGGCATTCTTTAGTGT 58.584 39.130 0.00 0.00 0.00 3.55
2182 2912 4.675976 TCATGATTGATTTGGGGCATTC 57.324 40.909 0.00 0.00 0.00 2.67
2338 3068 5.587388 AACCATGCTTTCCATAGAACATG 57.413 39.130 0.00 0.00 36.74 3.21
2599 3356 1.988467 GCAAAAGAAAGAAGATGCCGC 59.012 47.619 0.00 0.00 0.00 6.53
2772 3534 0.249953 TGCCTTTTCGAGTGCGGTTA 60.250 50.000 0.00 0.00 38.28 2.85
3053 3815 5.105310 GGGAGTACTAAAACAGCAGATGAGA 60.105 44.000 0.00 0.00 0.00 3.27
3128 3890 2.851263 TACGGGCTGAAATGTGTCTT 57.149 45.000 0.00 0.00 0.00 3.01
3142 3926 9.204570 CACCTAGAAAAATTCACTATATACGGG 57.795 37.037 0.00 0.00 0.00 5.28
3662 5080 0.394565 AGAAGTCGCAGCCTTTCAGT 59.605 50.000 0.00 0.00 0.00 3.41
3736 5154 8.612145 ACATAGGTTCATTCCTAAGGTAAAAGT 58.388 33.333 0.00 0.00 42.42 2.66
3960 5378 2.162408 GGAACATCACCAGCTAACAAGC 59.838 50.000 0.00 0.00 0.00 4.01
3993 5411 1.804746 CGGAAAACCAAAGGCAACCAC 60.805 52.381 0.00 0.00 37.17 4.16
4064 5490 0.389391 CGGCCATAAGGACTCGACAT 59.611 55.000 2.24 0.00 42.67 3.06
4102 5530 1.267806 CTGCCTGTAAACCTGCAACTG 59.732 52.381 0.00 0.00 32.58 3.16
4128 5556 2.876079 GCCTCATGGAAGAAACGAACCT 60.876 50.000 0.00 0.00 34.57 3.50
4151 5579 4.778213 AAAGCACCATAGCCAGAAGATA 57.222 40.909 0.00 0.00 34.23 1.98
4187 5619 1.351017 TGAGGGAGGGTGTGAATTCAC 59.649 52.381 28.10 28.10 46.59 3.18
4204 5636 2.028190 CTATGCGCCGGACCTGAG 59.972 66.667 5.05 0.00 0.00 3.35
4205 5637 3.536917 CCTATGCGCCGGACCTGA 61.537 66.667 5.05 0.00 0.00 3.86
4206 5638 3.536917 TCCTATGCGCCGGACCTG 61.537 66.667 5.05 0.00 0.00 4.00
4208 5640 4.944372 CGTCCTATGCGCCGGACC 62.944 72.222 25.40 13.71 45.41 4.46
4215 5647 0.248907 ATCAACGACCGTCCTATGCG 60.249 55.000 0.00 0.00 0.00 4.73
4330 5766 6.149807 GGTCGGTAATTTGATTGACTAACCAA 59.850 38.462 0.00 0.00 0.00 3.67
4386 5822 2.842936 ATTCCCTCCGCCCCGTAG 60.843 66.667 0.00 0.00 0.00 3.51
4387 5823 3.158648 CATTCCCTCCGCCCCGTA 61.159 66.667 0.00 0.00 0.00 4.02
4390 5826 2.508407 TTTTCCATTCCCTCCGCCCC 62.508 60.000 0.00 0.00 0.00 5.80
4391 5827 1.000145 TTTTCCATTCCCTCCGCCC 60.000 57.895 0.00 0.00 0.00 6.13
4392 5828 0.323451 ACTTTTCCATTCCCTCCGCC 60.323 55.000 0.00 0.00 0.00 6.13
4393 5829 1.472878 GAACTTTTCCATTCCCTCCGC 59.527 52.381 0.00 0.00 0.00 5.54
4407 5843 6.180472 TCTGTTCTTCTCAACCTTGAACTTT 58.820 36.000 0.00 0.00 38.17 2.66
4430 5866 9.557338 GTAACTAATGTCACTGGATACGATATC 57.443 37.037 0.00 0.00 42.51 1.63
4584 6031 2.565841 GTGAGTTTCACAGTTCCTGCT 58.434 47.619 4.42 0.00 46.22 4.24


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

AutoCloner maintained by Alex Coulton.