Multiple sequence alignment - TraesCS2D01G177000

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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 TraesCS2D01G177000 chr2D 100.000 4171 0 0 1 4171 120550063 120554233 0.000000e+00 7703
1 TraesCS2D01G177000 chr2B 94.977 4201 139 23 1 4171 173463158 173467316 0.000000e+00 6523
2 TraesCS2D01G177000 chr2A 95.225 3309 115 21 313 3597 124377675 124380964 0.000000e+00 5195
3 TraesCS2D01G177000 chr2A 97.131 488 14 0 3684 4171 124380965 124381452 0.000000e+00 824
4 TraesCS2D01G177000 chr2A 92.130 216 14 2 103 315 124377375 124377590 6.780000e-78 302
5 TraesCS2D01G177000 chr2A 93.750 96 5 1 1 95 124377241 124377336 4.350000e-30 143
6 TraesCS2D01G177000 chr3A 83.778 2022 309 13 1164 3170 9606658 9604641 0.000000e+00 1899
7 TraesCS2D01G177000 chr3D 83.838 1980 302 12 1205 3170 4068298 4066323 0.000000e+00 1868
8 TraesCS2D01G177000 chrUn 82.330 2026 342 11 1155 3167 242439790 242441812 0.000000e+00 1744
9 TraesCS2D01G177000 chrUn 82.330 2026 342 11 1155 3167 242452825 242454847 0.000000e+00 1744
10 TraesCS2D01G177000 chr3B 82.330 2026 342 11 1158 3170 6309545 6307523 0.000000e+00 1744
11 TraesCS2D01G177000 chr3B 82.034 2026 348 11 1158 3170 6380871 6378849 0.000000e+00 1711


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 TraesCS2D01G177000 chr2D 120550063 120554233 4170 False 7703 7703 100.000 1 4171 1 chr2D.!!$F1 4170
1 TraesCS2D01G177000 chr2B 173463158 173467316 4158 False 6523 6523 94.977 1 4171 1 chr2B.!!$F1 4170
2 TraesCS2D01G177000 chr2A 124377241 124381452 4211 False 1616 5195 94.559 1 4171 4 chr2A.!!$F1 4170
3 TraesCS2D01G177000 chr3A 9604641 9606658 2017 True 1899 1899 83.778 1164 3170 1 chr3A.!!$R1 2006
4 TraesCS2D01G177000 chr3D 4066323 4068298 1975 True 1868 1868 83.838 1205 3170 1 chr3D.!!$R1 1965
5 TraesCS2D01G177000 chrUn 242439790 242441812 2022 False 1744 1744 82.330 1155 3167 1 chrUn.!!$F1 2012
6 TraesCS2D01G177000 chrUn 242452825 242454847 2022 False 1744 1744 82.330 1155 3167 1 chrUn.!!$F2 2012
7 TraesCS2D01G177000 chr3B 6307523 6309545 2022 True 1744 1744 82.330 1158 3170 1 chr3B.!!$R1 2012
8 TraesCS2D01G177000 chr3B 6378849 6380871 2022 True 1711 1711 82.034 1158 3170 1 chr3B.!!$R2 2012

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
159 193 0.031716 ATAGCAGGCTGTCTCCCTCA 60.032 55.000 17.16 0.00 0.00 3.86 F
336 460 0.038159 AGTGAGTACTGGCAACGAGC 60.038 55.000 0.00 0.00 44.65 5.03 F
1052 1181 4.037923 TCAAGCCCTTGTAAAAAGAAGCTG 59.962 41.667 7.80 1.17 41.16 4.24 F
1518 1647 2.306847 GCCAAGAAGGTTGGAGTTGAA 58.693 47.619 7.99 0.00 42.06 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1062 1191 1.194772 GCCACAGAGTAAAGTCGCAAC 59.805 52.381 0.0 0.0 0.0 4.17 R
1151 1280 1.550524 TGATCAAGGGAGGAAGACACG 59.449 52.381 0.0 0.0 0.0 4.49 R
2406 2545 2.444766 CCAGGAATAGGAGGGCTTCATT 59.555 50.000 0.0 0.0 0.0 2.57 R
3275 3419 0.601057 TGTACAAGCTCGCTACAGCA 59.399 50.000 0.0 0.0 42.4 4.41 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
25 26 0.179029 CGGTAATTCCCCAATCGCCT 60.179 55.000 0.00 0.00 0.00 5.52
158 192 0.678950 GATAGCAGGCTGTCTCCCTC 59.321 60.000 17.16 7.98 32.48 4.30
159 193 0.031716 ATAGCAGGCTGTCTCCCTCA 60.032 55.000 17.16 0.00 0.00 3.86
160 194 0.972983 TAGCAGGCTGTCTCCCTCAC 60.973 60.000 17.16 0.00 0.00 3.51
162 196 1.908340 GCAGGCTGTCTCCCTCACAT 61.908 60.000 17.16 0.00 0.00 3.21
175 212 2.237143 CCCTCACATTCTCAGCCTACAA 59.763 50.000 0.00 0.00 0.00 2.41
228 265 6.708502 CGGGTTGATTTTCCAATAAAAGGTTT 59.291 34.615 0.00 0.00 0.00 3.27
239 276 4.678743 AAGGTTTGCCCCGGCTCC 62.679 66.667 7.35 7.11 42.51 4.70
257 294 2.125147 TTCGCAATCCTGGCTCCG 60.125 61.111 0.00 0.00 0.00 4.63
336 460 0.038159 AGTGAGTACTGGCAACGAGC 60.038 55.000 0.00 0.00 44.65 5.03
533 659 6.607689 TGTGTACAAATTAATTCTGCCGAAG 58.392 36.000 0.00 0.00 31.60 3.79
603 729 7.261325 TGTAGCTGCTCTCTTCTAACAATAAG 58.739 38.462 4.91 0.00 0.00 1.73
612 738 8.599055 TCTCTTCTAACAATAAGCATGCTATG 57.401 34.615 23.00 21.37 0.00 2.23
733 861 6.152831 GCTTTTAATCAGGTACAATGGTTCCT 59.847 38.462 0.00 0.00 44.75 3.36
766 894 9.683069 CTAAATTTAATCCTGCACCATATGTTC 57.317 33.333 1.24 0.00 0.00 3.18
783 911 7.869429 CCATATGTTCTGAAAACAGAAAGCTTT 59.131 33.333 12.53 12.53 42.12 3.51
800 928 4.802999 AGCTTTGATTTGTTGCTCTAAGC 58.197 39.130 8.72 8.72 44.88 3.09
838 966 7.632721 TGAGGATAACAGTTACAACGTTTTTC 58.367 34.615 0.00 0.00 31.66 2.29
850 979 5.175127 ACAACGTTTTTCTTTTGCAGGAAT 58.825 33.333 0.00 0.00 0.00 3.01
956 1085 4.293662 AGTGGACATTCTTCCTTCTTCC 57.706 45.455 0.00 0.00 36.51 3.46
1052 1181 4.037923 TCAAGCCCTTGTAAAAAGAAGCTG 59.962 41.667 7.80 1.17 41.16 4.24
1151 1280 6.905578 TCTTTTTCAGCGAGTATAAAAACCC 58.094 36.000 0.00 0.00 30.15 4.11
1326 1455 2.625314 CAGAGAGATCCGGTGCTTCATA 59.375 50.000 0.00 0.00 0.00 2.15
1439 1568 6.313905 ACATTACTACAAGTTCATGCTACAGC 59.686 38.462 0.00 0.00 42.50 4.40
1518 1647 2.306847 GCCAAGAAGGTTGGAGTTGAA 58.693 47.619 7.99 0.00 42.06 2.69
1614 1743 7.616528 TGATGATATGAATACTTCTGGTCCA 57.383 36.000 0.00 0.00 0.00 4.02
1800 1929 3.628008 ACATGTGTCATCTGCATGGAAT 58.372 40.909 0.00 0.00 42.89 3.01
1929 2058 2.428530 GTTTGATGGGATGAAGAAGGGC 59.571 50.000 0.00 0.00 0.00 5.19
2106 2245 4.961438 AAGGTTGAATTGGCATTTGACT 57.039 36.364 0.00 0.00 0.00 3.41
2170 2309 7.148755 CCACATAGTTTACAGCATTTTTCTTGC 60.149 37.037 0.00 0.00 40.45 4.01
2406 2545 4.305539 TTCAGCAAAGAAGGGATGATCA 57.694 40.909 0.00 0.00 0.00 2.92
2573 2712 4.333926 GGCTGTGTTCCTGATACTTTCATC 59.666 45.833 0.00 0.00 32.72 2.92
2801 2940 9.851686 AGGATTTTGTATACATCTCTTATTGCA 57.148 29.630 6.36 0.00 0.00 4.08
3107 3246 5.163468 ACCAGATGACAAGCTGAGTAGTATG 60.163 44.000 9.54 0.00 42.67 2.39
3201 3345 1.831106 TGTGCTCTATGGGTGAACGAT 59.169 47.619 0.00 0.00 0.00 3.73
3338 3483 2.489329 CCTTGTGTATCAAAGTGGCCTG 59.511 50.000 3.32 0.00 35.48 4.85
3351 3496 2.240667 AGTGGCCTGAAGACATAAGCAT 59.759 45.455 3.32 0.00 0.00 3.79
3408 3558 7.750229 TGATAGTCAACTGAGAAGCATTTTT 57.250 32.000 0.00 0.00 0.00 1.94
3415 3565 8.292448 GTCAACTGAGAAGCATTTTTATTGAGA 58.708 33.333 0.00 0.00 0.00 3.27
3597 3747 7.812191 CAGGTTTGCAGCTGTTATATTGTTTTA 59.188 33.333 16.64 0.00 42.66 1.52
3821 3971 6.500684 TGTTTAATGAAATCAGAGCACCTC 57.499 37.500 0.00 0.00 0.00 3.85
3848 3998 4.051922 CCCTCTTTGTACGCATACTGATC 58.948 47.826 0.00 0.00 32.00 2.92
3865 4015 6.365970 ACTGATCTGTACATCTGTTTTCCT 57.634 37.500 3.02 0.00 32.61 3.36
3880 4030 6.887545 TCTGTTTTCCTGTTGAAAGTTTAGGA 59.112 34.615 1.37 1.37 43.57 2.94
4047 4197 6.713762 TGTCCATCATTTCAATACCATTCC 57.286 37.500 0.00 0.00 0.00 3.01
4084 4234 5.447624 ACTGGGTTAGTTTTTGCATGTAC 57.552 39.130 0.00 0.00 35.67 2.90
4085 4235 4.890581 ACTGGGTTAGTTTTTGCATGTACA 59.109 37.500 0.00 0.00 35.67 2.90
4086 4236 5.361285 ACTGGGTTAGTTTTTGCATGTACAA 59.639 36.000 0.00 0.00 35.67 2.41
4087 4237 5.837437 TGGGTTAGTTTTTGCATGTACAAG 58.163 37.500 0.00 0.00 0.00 3.16
4088 4238 4.684242 GGGTTAGTTTTTGCATGTACAAGC 59.316 41.667 15.94 15.94 0.00 4.01
4089 4239 5.285651 GGTTAGTTTTTGCATGTACAAGCA 58.714 37.500 21.06 21.06 39.32 3.91
4090 4240 5.925969 GGTTAGTTTTTGCATGTACAAGCAT 59.074 36.000 24.82 13.05 40.94 3.79
4091 4241 6.423604 GGTTAGTTTTTGCATGTACAAGCATT 59.576 34.615 24.82 11.68 40.94 3.56
4117 4275 6.270156 TCATTTGCAGCAATATTTCTGACA 57.730 33.333 17.83 12.13 32.26 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 109 4.514577 AACCTCTCATCGCCGCCG 62.515 66.667 0.00 0.00 0.00 6.46
101 110 2.892425 CAACCTCTCATCGCCGCC 60.892 66.667 0.00 0.00 0.00 6.13
105 139 2.125512 ACGGCAACCTCTCATCGC 60.126 61.111 0.00 0.00 0.00 4.58
141 175 0.972983 GTGAGGGAGACAGCCTGCTA 60.973 60.000 0.00 0.00 33.27 3.49
158 192 6.741992 TTAACATTGTAGGCTGAGAATGTG 57.258 37.500 16.52 2.72 41.14 3.21
159 193 6.258727 CGATTAACATTGTAGGCTGAGAATGT 59.741 38.462 12.29 12.29 43.13 2.71
160 194 6.479990 TCGATTAACATTGTAGGCTGAGAATG 59.520 38.462 0.00 5.40 36.43 2.67
162 196 5.972935 TCGATTAACATTGTAGGCTGAGAA 58.027 37.500 0.00 0.00 0.00 2.87
239 276 2.176273 CGGAGCCAGGATTGCGAAG 61.176 63.158 0.00 0.00 0.00 3.79
336 460 8.753497 AAACCTAGGCATCTTATAGGAAAAAG 57.247 34.615 9.30 0.00 38.73 2.27
366 490 5.354234 GGTAAATTATATGCAGTCGGATGGG 59.646 44.000 0.00 0.00 0.00 4.00
533 659 5.309323 TGCAAACATAGCAAGGATGTTAC 57.691 39.130 1.70 0.00 44.75 2.50
603 729 3.498927 AAAACAGCAGACATAGCATGC 57.501 42.857 10.51 10.51 40.29 4.06
733 861 4.774726 TGCAGGATTAAATTTAGGTTGGCA 59.225 37.500 10.13 10.13 0.00 4.92
800 928 0.534412 ATCCTCAGTGTCAAGGCTCG 59.466 55.000 0.00 0.00 32.37 5.03
838 966 8.369218 AGTTACATGAAAAATTCCTGCAAAAG 57.631 30.769 0.00 0.00 0.00 2.27
1062 1191 1.194772 GCCACAGAGTAAAGTCGCAAC 59.805 52.381 0.00 0.00 0.00 4.17
1133 1262 3.255725 CACGGGTTTTTATACTCGCTGA 58.744 45.455 0.00 0.00 45.73 4.26
1151 1280 1.550524 TGATCAAGGGAGGAAGACACG 59.449 52.381 0.00 0.00 0.00 4.49
1326 1455 3.436704 CACAGTAATCAACAATGCTCCGT 59.563 43.478 0.00 0.00 0.00 4.69
1439 1568 4.277423 ACAACTCTACAAAAACCCGAATGG 59.723 41.667 0.00 0.00 41.37 3.16
1701 1830 3.674753 CGCCTTTCATTTCCATTTCACAC 59.325 43.478 0.00 0.00 0.00 3.82
2106 2245 4.787551 TGTTCTTTGAGCCTCCTAAACAA 58.212 39.130 0.00 0.00 0.00 2.83
2195 2334 3.263425 TCCAAAGGTCATAGACAACCTCC 59.737 47.826 0.00 0.00 45.21 4.30
2406 2545 2.444766 CCAGGAATAGGAGGGCTTCATT 59.555 50.000 0.00 0.00 0.00 2.57
2801 2940 5.621197 TGTTTGAACGCTTACAATAGCAT 57.379 34.783 0.00 0.00 41.28 3.79
3107 3246 2.500910 TCCATCATTGCCAAATCCCAAC 59.499 45.455 0.00 0.00 0.00 3.77
3178 3317 3.009723 CGTTCACCCATAGAGCACAATT 58.990 45.455 0.00 0.00 0.00 2.32
3183 3322 3.704566 AGTAATCGTTCACCCATAGAGCA 59.295 43.478 0.00 0.00 0.00 4.26
3201 3345 5.654650 ACCACCAGTGAATTGTTGAAAGTAA 59.345 36.000 0.00 0.00 0.00 2.24
3275 3419 0.601057 TGTACAAGCTCGCTACAGCA 59.399 50.000 0.00 0.00 42.40 4.41
3297 3442 2.329379 GCCCTCGCAATTCTAGTATCG 58.671 52.381 0.00 0.00 34.03 2.92
3351 3496 7.414222 AACTTAAGGAATACGTGGATAGACA 57.586 36.000 7.53 0.00 0.00 3.41
3398 3548 8.470040 TGCTTTCATCTCAATAAAAATGCTTC 57.530 30.769 0.00 0.00 0.00 3.86
3408 3558 5.349061 TGCTCTCTGCTTTCATCTCAATA 57.651 39.130 0.00 0.00 43.37 1.90
3415 3565 0.743701 CGGCTGCTCTCTGCTTTCAT 60.744 55.000 0.00 0.00 43.37 2.57
3618 3768 4.487948 CCGACAGTAGAATTTCGGTGTAA 58.512 43.478 5.94 0.00 44.90 2.41
3619 3769 4.100707 CCGACAGTAGAATTTCGGTGTA 57.899 45.455 5.94 0.00 44.90 2.90
3625 3775 6.089150 GTGTAGAACACCGACAGTAGAATTTC 59.911 42.308 0.00 0.00 43.05 2.17
3764 3914 5.867174 TGTATGAAACTCACCAACTCATACG 59.133 40.000 13.09 0.00 46.15 3.06
3821 3971 0.320374 TGCGTACAAAGAGGGTCCAG 59.680 55.000 0.00 0.00 0.00 3.86
3848 3998 6.618287 TTCAACAGGAAAACAGATGTACAG 57.382 37.500 0.33 0.00 30.98 2.74
3865 4015 8.990163 AACTAAATCCTCCTAAACTTTCAACA 57.010 30.769 0.00 0.00 0.00 3.33
4047 4197 8.012957 ACTAACCCAGTAGAGATAGAAACATG 57.987 38.462 0.00 0.00 34.98 3.21
4084 4234 3.258228 TGCTGCAAATGATGAATGCTTG 58.742 40.909 0.00 0.00 40.66 4.01
4085 4235 3.603158 TGCTGCAAATGATGAATGCTT 57.397 38.095 0.00 0.00 40.66 3.91
4086 4236 3.603158 TTGCTGCAAATGATGAATGCT 57.397 38.095 13.51 0.00 40.66 3.79
4087 4237 6.539649 AATATTGCTGCAAATGATGAATGC 57.460 33.333 20.06 0.00 40.45 3.56
4088 4238 8.275632 CAGAAATATTGCTGCAAATGATGAATG 58.724 33.333 20.06 8.06 0.00 2.67
4089 4239 8.201464 TCAGAAATATTGCTGCAAATGATGAAT 58.799 29.630 20.06 2.54 32.27 2.57
4090 4240 7.490079 GTCAGAAATATTGCTGCAAATGATGAA 59.510 33.333 20.06 0.00 32.27 2.57
4091 4241 6.976349 GTCAGAAATATTGCTGCAAATGATGA 59.024 34.615 20.06 14.84 32.27 2.92


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

AutoCloner maintained by Alex Coulton.