Multiple sequence alignment - TraesCS2B01G049800

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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 TraesCS2B01G049800 chr2B 100.000 4938 0 0 1 4938 24703724 24708661 0.000000e+00 9119.0
1 TraesCS2B01G049800 chr2B 91.048 3731 287 29 766 4468 24816904 24820615 0.000000e+00 4996.0
2 TraesCS2B01G049800 chr2B 78.014 1269 217 44 876 2117 24509237 24508004 0.000000e+00 741.0
3 TraesCS2B01G049800 chr2B 75.696 1473 276 53 2169 3602 24508017 24506588 0.000000e+00 662.0
4 TraesCS2B01G049800 chr2B 81.296 679 112 11 1156 1831 24835930 24836596 2.020000e-148 536.0
5 TraesCS2B01G049800 chr2B 78.283 792 133 25 2607 3379 24837920 24838691 1.610000e-129 473.0
6 TraesCS2B01G049800 chr2B 79.283 642 96 18 3599 4237 24505218 24504611 9.890000e-112 414.0
7 TraesCS2B01G049800 chr2B 81.737 334 37 17 4481 4794 24247338 24247009 1.760000e-64 257.0
8 TraesCS2B01G049800 chr2B 93.082 159 11 0 4481 4639 24692163 24692321 2.970000e-57 233.0
9 TraesCS2B01G049800 chr2A 96.266 4205 143 12 1 4198 15632551 15636748 0.000000e+00 6883.0
10 TraesCS2B01G049800 chr2A 95.288 764 29 3 4180 4938 15636759 15637520 0.000000e+00 1205.0
11 TraesCS2B01G049800 chr2D 93.118 2296 136 11 766 3055 13604843 13607122 0.000000e+00 3345.0
12 TraesCS2B01G049800 chr2D 94.211 1451 76 4 3022 4470 13607117 13608561 0.000000e+00 2207.0
13 TraesCS2B01G049800 chr2D 77.495 1964 350 66 2305 4218 13541767 13539846 0.000000e+00 1094.0
14 TraesCS2B01G049800 chr2D 82.129 1287 180 22 2962 4238 13616950 13618196 0.000000e+00 1057.0
15 TraesCS2B01G049800 chr2D 79.961 1033 166 28 876 1897 13543088 13542086 0.000000e+00 723.0
16 TraesCS2B01G049800 chr2D 81.790 324 42 6 4481 4788 13590900 13591222 6.340000e-64 255.0
17 TraesCS2B01G049800 chr7D 90.052 764 72 4 3 765 494291196 494290436 0.000000e+00 987.0
18 TraesCS2B01G049800 chr4D 89.062 768 76 6 1 765 9552923 9552161 0.000000e+00 946.0
19 TraesCS2B01G049800 chr4D 86.364 770 93 10 3 767 402216783 402216021 0.000000e+00 830.0
20 TraesCS2B01G049800 chr7B 88.542 768 84 3 1 765 107990388 107989622 0.000000e+00 928.0
21 TraesCS2B01G049800 chr7A 87.516 769 87 7 1 765 553409010 553409773 0.000000e+00 880.0
22 TraesCS2B01G049800 chr3B 87.126 769 85 9 3 765 523713848 523714608 0.000000e+00 859.0
23 TraesCS2B01G049800 chr3D 86.641 771 89 11 1 765 520954565 520955327 0.000000e+00 841.0
24 TraesCS2B01G049800 chr3D 88.679 53 6 0 2117 2169 178528789 178528841 1.150000e-06 65.8
25 TraesCS2B01G049800 chr1B 86.310 767 95 6 1 765 413490189 413489431 0.000000e+00 826.0
26 TraesCS2B01G049800 chr5B 70.904 1007 249 36 2938 3922 6624913 6625897 3.900000e-46 196.0


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 TraesCS2B01G049800 chr2B 24703724 24708661 4937 False 9119.000000 9119 100.000000 1 4938 1 chr2B.!!$F2 4937
1 TraesCS2B01G049800 chr2B 24816904 24820615 3711 False 4996.000000 4996 91.048000 766 4468 1 chr2B.!!$F3 3702
2 TraesCS2B01G049800 chr2B 24504611 24509237 4626 True 605.666667 741 77.664333 876 4237 3 chr2B.!!$R2 3361
3 TraesCS2B01G049800 chr2B 24835930 24838691 2761 False 504.500000 536 79.789500 1156 3379 2 chr2B.!!$F4 2223
4 TraesCS2B01G049800 chr2A 15632551 15637520 4969 False 4044.000000 6883 95.777000 1 4938 2 chr2A.!!$F1 4937
5 TraesCS2B01G049800 chr2D 13604843 13608561 3718 False 2776.000000 3345 93.664500 766 4470 2 chr2D.!!$F3 3704
6 TraesCS2B01G049800 chr2D 13616950 13618196 1246 False 1057.000000 1057 82.129000 2962 4238 1 chr2D.!!$F2 1276
7 TraesCS2B01G049800 chr2D 13539846 13543088 3242 True 908.500000 1094 78.728000 876 4218 2 chr2D.!!$R1 3342
8 TraesCS2B01G049800 chr7D 494290436 494291196 760 True 987.000000 987 90.052000 3 765 1 chr7D.!!$R1 762
9 TraesCS2B01G049800 chr4D 9552161 9552923 762 True 946.000000 946 89.062000 1 765 1 chr4D.!!$R1 764
10 TraesCS2B01G049800 chr4D 402216021 402216783 762 True 830.000000 830 86.364000 3 767 1 chr4D.!!$R2 764
11 TraesCS2B01G049800 chr7B 107989622 107990388 766 True 928.000000 928 88.542000 1 765 1 chr7B.!!$R1 764
12 TraesCS2B01G049800 chr7A 553409010 553409773 763 False 880.000000 880 87.516000 1 765 1 chr7A.!!$F1 764
13 TraesCS2B01G049800 chr3B 523713848 523714608 760 False 859.000000 859 87.126000 3 765 1 chr3B.!!$F1 762
14 TraesCS2B01G049800 chr3D 520954565 520955327 762 False 841.000000 841 86.641000 1 765 1 chr3D.!!$F2 764
15 TraesCS2B01G049800 chr1B 413489431 413490189 758 True 826.000000 826 86.310000 1 765 1 chr1B.!!$R1 764

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
397 400 0.771755 GGACTCCCCTGTTGGTTTCT 59.228 55.0 0.00 0.00 0.0 2.52 F
1126 1143 0.744874 CGATCCAGGGTGTACACGAT 59.255 55.0 19.41 15.46 0.0 3.73 F
1141 1158 0.753262 ACGATCACCTCCACCTATGC 59.247 55.0 0.00 0.00 0.0 3.14 F
2950 3719 2.163818 TTCCACAGGACTACTTTGCG 57.836 50.0 0.00 0.00 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 1357 0.307760 GGGCACAGTGAACTCAAACG 59.692 55.000 4.15 0.0 0.0 3.60 R
2950 3719 0.553333 CCCCCTCTTCTCCCCATTTC 59.447 60.000 0.00 0.0 0.0 2.17 R
3021 3791 7.175104 TCTAACCTCATTTCCAAGTAAGCATT 58.825 34.615 0.00 0.0 0.0 3.56 R
4501 6728 0.034896 TCTTTCTCCTTGCCACCGTC 59.965 55.000 0.00 0.0 0.0 4.79 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
218 221 5.658198 TCTAGCTACTAACTATGGACCCA 57.342 43.478 0.00 0.00 0.00 4.51
248 251 5.294356 TGTGGTAAACTACTCACACATCAC 58.706 41.667 0.00 0.00 36.02 3.06
292 295 3.268023 AGAACCCCTTTGTGATCGATC 57.732 47.619 18.72 18.72 0.00 3.69
344 347 2.161855 CCAGATGGGATCTCTCGAGAG 58.838 57.143 32.43 32.43 41.33 3.20
397 400 0.771755 GGACTCCCCTGTTGGTTTCT 59.228 55.000 0.00 0.00 0.00 2.52
436 439 1.550976 AGAGGCGGAGTTAGGTCAAAG 59.449 52.381 0.00 0.00 0.00 2.77
440 443 1.002773 GCGGAGTTAGGTCAAAGGGAA 59.997 52.381 0.00 0.00 0.00 3.97
504 511 4.115199 GGCCCATGCTCCCTCGTT 62.115 66.667 0.00 0.00 37.74 3.85
828 845 2.594882 TCGCCTAGCTAGCCTCCG 60.595 66.667 15.74 13.62 0.00 4.63
1084 1101 8.387190 TCTCATCACTGCAATAATCATTAAGG 57.613 34.615 0.00 0.00 0.00 2.69
1107 1124 3.494045 GCAAATGCAAGAGTTACCTCC 57.506 47.619 0.00 0.00 38.58 4.30
1126 1143 0.744874 CGATCCAGGGTGTACACGAT 59.255 55.000 19.41 15.46 0.00 3.73
1141 1158 0.753262 ACGATCACCTCCACCTATGC 59.247 55.000 0.00 0.00 0.00 3.14
1149 1166 5.402630 TCACCTCCACCTATGCTCAATATA 58.597 41.667 0.00 0.00 0.00 0.86
1340 1357 3.198417 TCCGAGGTTTCCCAAGGTAATAC 59.802 47.826 0.00 0.00 33.00 1.89
1777 1811 6.375455 AGGAACCTAATTTGCTACTTCATGTG 59.625 38.462 0.00 0.00 0.00 3.21
1921 1956 9.047371 TGTGACTTTTTATGACAAATTCGTCTA 57.953 29.630 0.00 0.00 36.82 2.59
1932 1969 4.935808 ACAAATTCGTCTACAGTCCAATCC 59.064 41.667 0.00 0.00 0.00 3.01
2105 2170 6.872020 ACACAATTTAGAGCACTACATACGTT 59.128 34.615 0.00 0.00 0.00 3.99
2293 2375 6.255020 CACTTTGTCCTTATATGTCGGTGTAC 59.745 42.308 0.00 0.00 0.00 2.90
2405 2488 8.567948 ACAACTATCAAAACAAAGGTGATACAG 58.432 33.333 0.00 0.00 34.01 2.74
2777 3541 8.040727 AGTGTTACATGTAGTTCATTAGCATGA 58.959 33.333 5.56 0.00 39.21 3.07
2821 3585 6.357367 TCATTATTCAAGCCTTCCCTAGAAC 58.643 40.000 0.00 0.00 0.00 3.01
2840 3604 8.077991 CCTAGAACGTTATGGTATTTCACGATA 58.922 37.037 5.52 0.00 34.90 2.92
2904 3672 8.818057 GCTATATATGTTAATTCAACTAGCCGG 58.182 37.037 0.00 0.00 38.05 6.13
2922 3691 2.223144 CCGGCGTTGTCATAATGTATGG 59.777 50.000 6.01 0.00 36.81 2.74
2950 3719 2.163818 TTCCACAGGACTACTTTGCG 57.836 50.000 0.00 0.00 0.00 4.85
3021 3791 3.044235 ACTCATGTTGATCGCAAGTCA 57.956 42.857 0.00 0.00 34.01 3.41
3238 4035 1.687494 GCCGTGTCGAGCAAGATGTC 61.687 60.000 0.00 0.00 0.00 3.06
3276 4073 5.128919 GGACTCTAGGTATAAAGACGGTCA 58.871 45.833 11.27 0.00 0.00 4.02
3532 4335 1.517832 GCATCCAGCGACACTAGGT 59.482 57.895 0.00 0.00 0.00 3.08
3577 4380 7.453393 AGAATATCACTGTGAGGACAAAAGAA 58.547 34.615 16.46 0.00 0.00 2.52
3643 5819 9.953565 AATCTTGTAATGCTAACCAGTAAGTTA 57.046 29.630 0.00 0.00 0.00 2.24
4068 6263 7.436118 AGGTCACGTTATTTGTAACTTGAGTA 58.564 34.615 7.49 0.00 38.37 2.59
4363 6590 8.861086 ACAACCTATATCCTAGATGTACTGTTG 58.139 37.037 12.49 12.49 34.58 3.33
4472 6699 0.750911 CCTTACGCTCTCCGGGTACT 60.751 60.000 0.00 0.00 40.30 2.73
4473 6700 0.381089 CTTACGCTCTCCGGGTACTG 59.619 60.000 0.00 0.00 40.30 2.74
4477 6704 0.100146 CGCTCTCCGGGTACTGTTAC 59.900 60.000 0.00 0.00 0.00 2.50
4534 6761 0.804989 GAAAGACACCAAGATGGCCG 59.195 55.000 0.00 0.00 42.67 6.13
4536 6763 2.359850 GACACCAAGATGGCCGCA 60.360 61.111 0.00 0.00 42.67 5.69
4582 6809 4.268644 ACGATATGTTTCAGTCATTCAGCG 59.731 41.667 0.00 0.00 0.00 5.18
4606 6833 2.526120 GCCTGCCGCGATACTTCAC 61.526 63.158 8.23 0.00 0.00 3.18
4616 6843 2.030946 GCGATACTTCACAGGCACAATC 59.969 50.000 0.00 0.00 0.00 2.67
4627 6854 1.226295 GCACAATCGTTTAGGCCGC 60.226 57.895 0.00 0.00 0.00 6.53
4662 6889 4.452753 TCGTTGCTCGACGATCAC 57.547 55.556 8.17 0.00 46.09 3.06
4673 6900 2.422479 TCGACGATCACGAAATCTTCCT 59.578 45.455 9.08 0.00 42.66 3.36
4697 6924 6.530120 TGTTGTGTCAGATTATTACCAGTGT 58.470 36.000 0.00 0.00 0.00 3.55
4698 6925 6.426633 TGTTGTGTCAGATTATTACCAGTGTG 59.573 38.462 0.00 0.00 0.00 3.82
4814 7045 5.821204 AGTTTGATTTCTTGTTCGAACTGG 58.179 37.500 27.32 19.16 42.37 4.00
4823 7054 4.748102 TCTTGTTCGAACTGGTATGTCAAC 59.252 41.667 27.32 0.00 0.00 3.18
4846 7077 4.515191 CCACTAAATGATAACCGGTCATGG 59.485 45.833 8.04 2.06 36.49 3.66
4868 7099 2.774774 CGCGCTTCTCTTCTGTGC 59.225 61.111 5.56 0.00 0.00 4.57
4888 7119 2.158841 GCGCTTTCCTGTTCGTATTTCA 59.841 45.455 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 163 6.256539 TCTCTCGATGTTTCTCAATACAATGC 59.743 38.462 0.00 0.00 0.00 3.56
218 221 5.715279 TGTGAGTAGTTTACCACAGAGCTAT 59.285 40.000 0.00 0.00 36.02 2.97
344 347 2.175322 GCTGTCGCAAGCTTCTGC 59.825 61.111 0.00 0.00 40.20 4.26
357 360 4.825085 TCCAAGAAATACTTTTTCCGCTGT 59.175 37.500 0.00 0.00 36.61 4.40
397 400 7.827236 CCGCCTCTATAAATACCCATAAATCAA 59.173 37.037 0.00 0.00 0.00 2.57
436 439 4.048470 GGGGCCCACAGAGTTCCC 62.048 72.222 26.86 0.00 36.25 3.97
557 567 3.736433 CGAAGTCCAAATGCCACAAAACA 60.736 43.478 0.00 0.00 0.00 2.83
701 713 8.517878 CCATGCTATTAAAGTATCAATCTTGGG 58.482 37.037 0.00 0.00 0.00 4.12
828 845 3.932545 TGTGGTCACCAAAATGCATAC 57.067 42.857 0.00 0.00 34.18 2.39
914 931 4.253685 CTCGATAAACTTCATGGGTGTGT 58.746 43.478 0.00 0.00 0.00 3.72
915 932 4.253685 ACTCGATAAACTTCATGGGTGTG 58.746 43.478 0.00 0.00 0.00 3.82
920 937 8.697846 TTGTTACTACTCGATAAACTTCATGG 57.302 34.615 0.00 0.00 0.00 3.66
979 996 2.755650 AGTTTCTGTCGGTACTGCAAG 58.244 47.619 0.00 0.00 42.29 4.01
1107 1124 0.744874 ATCGTGTACACCCTGGATCG 59.255 55.000 20.11 6.18 0.00 3.69
1126 1143 1.951209 TTGAGCATAGGTGGAGGTGA 58.049 50.000 0.00 0.00 0.00 4.02
1149 1166 7.021998 AGGTAAGAGTTTTAGGAGAGCAATT 57.978 36.000 0.00 0.00 0.00 2.32
1340 1357 0.307760 GGGCACAGTGAACTCAAACG 59.692 55.000 4.15 0.00 0.00 3.60
1555 1574 7.417612 GTTGGTTATTTGATAGTACTGCATGG 58.582 38.462 5.39 0.00 0.00 3.66
1594 1613 9.860898 AAAACAAGTCATCTATTTAGAAATGGC 57.139 29.630 0.00 0.00 35.69 4.40
1747 1781 9.528489 TGAAGTAGCAAATTAGGTTCCTTAATT 57.472 29.630 0.00 0.00 0.00 1.40
1921 1956 9.533831 AGTATTAGAATTTTTGGATTGGACTGT 57.466 29.630 0.00 0.00 0.00 3.55
2267 2349 4.570772 CACCGACATATAAGGACAAAGTGG 59.429 45.833 0.00 0.00 0.00 4.00
2293 2375 7.641411 CGATAGCATCCAAATTTCTGTGTAAAG 59.359 37.037 0.00 0.00 0.00 1.85
2777 3541 1.804151 AGCGTATTGTGCAATCGTGTT 59.196 42.857 0.18 0.00 33.85 3.32
2840 3604 7.491372 CACCACGAGTTTGTCTACACATATAAT 59.509 37.037 0.00 0.00 30.55 1.28
2950 3719 0.553333 CCCCCTCTTCTCCCCATTTC 59.447 60.000 0.00 0.00 0.00 2.17
3021 3791 7.175104 TCTAACCTCATTTCCAAGTAAGCATT 58.825 34.615 0.00 0.00 0.00 3.56
3238 4035 4.500499 AGAGTCCATCAATTTCTGGAGG 57.500 45.455 6.07 0.00 42.10 4.30
3276 4073 1.076533 CGCCGCTTCTGTTGTACGAT 61.077 55.000 0.00 0.00 0.00 3.73
3532 4335 4.748892 TCTTTTGTGTTTGGCGAATCAAA 58.251 34.783 13.14 13.14 34.64 2.69
3577 4380 2.224621 CGGGATGCCATATTCAGTTCCT 60.225 50.000 3.39 0.00 0.00 3.36
3643 5819 4.042809 TCAGGGTCCTTGTAAATGTGTGAT 59.957 41.667 0.20 0.00 0.00 3.06
4103 6298 1.221840 CATAGCAGGGCCGACAAGT 59.778 57.895 0.00 0.00 0.00 3.16
4385 6612 0.322098 TGGTGGCAACGATGGGTAAG 60.322 55.000 0.00 0.00 42.51 2.34
4459 6686 1.472188 AGTAACAGTACCCGGAGAGC 58.528 55.000 0.73 0.00 0.00 4.09
4472 6699 6.091718 TGTTGCACACTGAGTATAGTAACA 57.908 37.500 9.41 9.41 0.00 2.41
4473 6700 6.020599 CGATGTTGCACACTGAGTATAGTAAC 60.021 42.308 0.00 0.00 0.00 2.50
4477 6704 4.500837 GTCGATGTTGCACACTGAGTATAG 59.499 45.833 0.00 0.00 0.00 1.31
4501 6728 0.034896 TCTTTCTCCTTGCCACCGTC 59.965 55.000 0.00 0.00 0.00 4.79
4534 6761 0.524862 CAGTGGAAGCTTGATGGTGC 59.475 55.000 2.10 0.00 0.00 5.01
4536 6763 1.004044 CCTCAGTGGAAGCTTGATGGT 59.996 52.381 2.10 0.00 38.35 3.55
4593 6820 1.153647 TGCCTGTGAAGTATCGCGG 60.154 57.895 6.13 0.00 41.27 6.46
4596 6823 2.282555 CGATTGTGCCTGTGAAGTATCG 59.717 50.000 0.00 0.00 0.00 2.92
4606 6833 0.451783 GGCCTAAACGATTGTGCCTG 59.548 55.000 11.22 0.00 35.08 4.85
4616 6843 2.125991 TACACCGCGGCCTAAACG 60.126 61.111 28.58 7.50 0.00 3.60
4627 6854 2.809601 GCACTCACGCCTACACCG 60.810 66.667 0.00 0.00 0.00 4.94
4662 6889 4.058124 TCTGACACAACAGGAAGATTTCG 58.942 43.478 0.00 0.00 38.31 3.46
4673 6900 6.426633 CACACTGGTAATAATCTGACACAACA 59.573 38.462 0.00 0.00 0.00 3.33
4814 7045 7.254658 CCGGTTATCATTTAGTGGTTGACATAC 60.255 40.741 0.00 0.00 0.00 2.39
4823 7054 4.515191 CCATGACCGGTTATCATTTAGTGG 59.485 45.833 9.42 2.31 34.49 4.00
4846 7077 2.029844 AGAAGAGAAGCGCGCAACC 61.030 57.895 35.10 20.83 0.00 3.77
4868 7099 3.991069 CTGAAATACGAACAGGAAAGCG 58.009 45.455 0.00 0.00 0.00 4.68
4902 7133 8.929260 AACTATCCATCTGCATTTCATAATCA 57.071 30.769 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.