Multiple sequence alignment - TraesCS1D01G142900

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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 TraesCS1D01G142900 chr1D 100.000 2582 0 0 1 2582 198173971 198171390 0.000000e+00 4769
1 TraesCS1D01G142900 chr2A 89.648 2560 208 31 58 2582 227446449 227448986 0.000000e+00 3206
2 TraesCS1D01G142900 chr2A 87.890 1891 177 28 721 2582 476057100 476058967 0.000000e+00 2176
3 TraesCS1D01G142900 chr2A 92.070 744 49 7 3 745 292620089 292619355 0.000000e+00 1038
4 TraesCS1D01G142900 chr7A 87.442 2596 262 41 1 2582 326974470 326971925 0.000000e+00 2929
5 TraesCS1D01G142900 chr3D 90.068 1903 141 20 3 1891 345887379 345889247 0.000000e+00 2423
6 TraesCS1D01G142900 chr3D 89.748 1824 167 12 770 2582 250518719 250520533 0.000000e+00 2314
7 TraesCS1D01G142900 chr3D 91.683 1551 117 8 1038 2582 285259366 285260910 0.000000e+00 2139
8 TraesCS1D01G142900 chr3D 89.842 886 54 20 1 884 285258139 285258990 0.000000e+00 1105
9 TraesCS1D01G142900 chr2D 89.542 1855 178 12 739 2582 256974339 256976188 0.000000e+00 2337
10 TraesCS1D01G142900 chr2D 87.253 1012 76 35 1 1009 323942328 323943289 0.000000e+00 1105
11 TraesCS1D01G142900 chr5B 89.385 1771 176 6 816 2579 430842586 430844351 0.000000e+00 2218
12 TraesCS1D01G142900 chr5B 90.754 822 48 13 1 803 430836992 430837804 0.000000e+00 1072
13 TraesCS1D01G142900 chr1B 88.064 1818 192 17 776 2582 174120107 174121910 0.000000e+00 2132
14 TraesCS1D01G142900 chr6D 87.850 1819 192 19 776 2582 284186999 284185198 0.000000e+00 2108
15 TraesCS1D01G142900 chr6A 88.514 1689 172 14 908 2582 230160657 230158977 0.000000e+00 2025
16 TraesCS1D01G142900 chr4A 87.287 1054 109 16 302 1345 254963827 254962789 0.000000e+00 1181
17 TraesCS1D01G142900 chr7D 89.020 765 66 14 3 761 169141040 169140288 0.000000e+00 931
18 TraesCS1D01G142900 chr7D 88.086 789 80 14 1 778 391382330 391383115 0.000000e+00 924
19 TraesCS1D01G142900 chr3B 90.361 249 19 4 777 1024 380463833 380464077 3.210000e-84 322


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 TraesCS1D01G142900 chr1D 198171390 198173971 2581 True 4769 4769 100.0000 1 2582 1 chr1D.!!$R1 2581
1 TraesCS1D01G142900 chr2A 227446449 227448986 2537 False 3206 3206 89.6480 58 2582 1 chr2A.!!$F1 2524
2 TraesCS1D01G142900 chr2A 476057100 476058967 1867 False 2176 2176 87.8900 721 2582 1 chr2A.!!$F2 1861
3 TraesCS1D01G142900 chr2A 292619355 292620089 734 True 1038 1038 92.0700 3 745 1 chr2A.!!$R1 742
4 TraesCS1D01G142900 chr7A 326971925 326974470 2545 True 2929 2929 87.4420 1 2582 1 chr7A.!!$R1 2581
5 TraesCS1D01G142900 chr3D 345887379 345889247 1868 False 2423 2423 90.0680 3 1891 1 chr3D.!!$F2 1888
6 TraesCS1D01G142900 chr3D 250518719 250520533 1814 False 2314 2314 89.7480 770 2582 1 chr3D.!!$F1 1812
7 TraesCS1D01G142900 chr3D 285258139 285260910 2771 False 1622 2139 90.7625 1 2582 2 chr3D.!!$F3 2581
8 TraesCS1D01G142900 chr2D 256974339 256976188 1849 False 2337 2337 89.5420 739 2582 1 chr2D.!!$F1 1843
9 TraesCS1D01G142900 chr2D 323942328 323943289 961 False 1105 1105 87.2530 1 1009 1 chr2D.!!$F2 1008
10 TraesCS1D01G142900 chr5B 430842586 430844351 1765 False 2218 2218 89.3850 816 2579 1 chr5B.!!$F2 1763
11 TraesCS1D01G142900 chr5B 430836992 430837804 812 False 1072 1072 90.7540 1 803 1 chr5B.!!$F1 802
12 TraesCS1D01G142900 chr1B 174120107 174121910 1803 False 2132 2132 88.0640 776 2582 1 chr1B.!!$F1 1806
13 TraesCS1D01G142900 chr6D 284185198 284186999 1801 True 2108 2108 87.8500 776 2582 1 chr6D.!!$R1 1806
14 TraesCS1D01G142900 chr6A 230158977 230160657 1680 True 2025 2025 88.5140 908 2582 1 chr6A.!!$R1 1674
15 TraesCS1D01G142900 chr4A 254962789 254963827 1038 True 1181 1181 87.2870 302 1345 1 chr4A.!!$R1 1043
16 TraesCS1D01G142900 chr7D 169140288 169141040 752 True 931 931 89.0200 3 761 1 chr7D.!!$R1 758
17 TraesCS1D01G142900 chr7D 391382330 391383115 785 False 924 924 88.0860 1 778 1 chr7D.!!$F1 777

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
985 1125 0.24928 GCTCTTTCTAGCCTCGCCTC 60.249 60.0 0.0 0.0 36.45 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2432 0.110486 ATGTCCCCAATATCCCGTGC 59.89 55.0 0.0 0.0 0.0 5.34 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
77 78 3.223435 GTCTTCCATGGTCTCGGATCTA 58.777 50.000 12.58 0.00 0.00 1.98
137 138 2.628178 TCGTGGACAATGAACTGACTCT 59.372 45.455 0.00 0.00 0.00 3.24
230 231 6.286240 TGAATCTCTTAGCAGTACATGTGT 57.714 37.500 9.11 0.00 0.00 3.72
236 237 7.090808 TCTCTTAGCAGTACATGTGTAGTTTG 58.909 38.462 9.11 0.00 32.19 2.93
336 338 6.653320 TGTCCAACAGAATATCACCTTGTAAC 59.347 38.462 0.00 0.00 0.00 2.50
395 397 3.616956 TCTTCATCTGCAACCAGTAGG 57.383 47.619 0.00 0.00 40.09 3.18
397 399 1.951209 TCATCTGCAACCAGTAGGGA 58.049 50.000 0.00 0.00 40.09 4.20
415 418 3.269381 AGGGAGGCAAATGATGGAAAGTA 59.731 43.478 0.00 0.00 0.00 2.24
463 468 3.236816 GTTGCACGAAACATCAAGATGG 58.763 45.455 14.04 0.00 42.91 3.51
540 545 7.287927 CCTTATCTGTAAATGTGGAGAGAGGTA 59.712 40.741 0.00 0.00 0.00 3.08
548 555 2.228925 GTGGAGAGAGGTACGGGTATC 58.771 57.143 0.00 0.00 0.00 2.24
597 607 8.244802 GCTTTCTATCCGTTAGCTATAGATCAA 58.755 37.037 3.21 0.00 33.44 2.57
850 974 1.509923 GACGTCGGGAAAGGATCGT 59.490 57.895 0.00 0.00 0.00 3.73
975 1115 2.024825 GCTCTCTCCCCGCTCTTTCTA 61.025 57.143 0.00 0.00 0.00 2.10
984 1124 1.819905 GCTCTTTCTAGCCTCGCCT 59.180 57.895 0.00 0.00 36.45 5.52
985 1125 0.249280 GCTCTTTCTAGCCTCGCCTC 60.249 60.000 0.00 0.00 36.45 4.70
1131 1542 4.309950 GACACCGCCCACGAGGTT 62.310 66.667 0.00 0.00 40.72 3.50
1598 2036 9.453325 CGAGGAGTAGTTGAACTATCTATTTTC 57.547 37.037 8.46 0.98 32.65 2.29
1971 2432 3.709987 CAAAGGAGCAACAAAGACCAAG 58.290 45.455 0.00 0.00 0.00 3.61
1998 2459 4.104738 GGGATATTGGGGACATCTTCAAGA 59.895 45.833 0.00 0.00 42.32 3.02
2003 2464 2.370519 TGGGGACATCTTCAAGAAACGA 59.629 45.455 0.00 0.00 33.40 3.85
2057 2518 6.232692 TGTAAACCGAGCTTTGGTAAGTAAT 58.767 36.000 11.56 0.00 39.29 1.89
2088 2549 5.346822 TCAATTACTTTCGTTTAGCCTCGTC 59.653 40.000 0.00 0.00 0.00 4.20
2138 2608 4.058817 CTGTTTCTCTTAGCCTCGTGTTT 58.941 43.478 0.00 0.00 0.00 2.83
2141 2611 5.205565 GTTTCTCTTAGCCTCGTGTTTTTG 58.794 41.667 0.00 0.00 0.00 2.44
2239 2709 9.362151 TCACCTTGGAGTCTGTTTTTATATTTT 57.638 29.630 0.00 0.00 0.00 1.82
2269 2739 6.025749 TGAATTCACTTCTACGAGTCATGT 57.974 37.500 3.38 0.00 34.75 3.21
2317 2787 4.225942 TCTGGGTTGCTCTGAGTATTGATT 59.774 41.667 6.53 0.00 0.00 2.57
2439 2909 1.418637 GGTGCCCGTTCCCTAATGATA 59.581 52.381 0.00 0.00 0.00 2.15
2441 2911 1.418637 TGCCCGTTCCCTAATGATACC 59.581 52.381 0.00 0.00 0.00 2.73
2495 2965 1.200020 GCTGGATTACACACAAGCCAC 59.800 52.381 0.00 0.00 39.00 5.01
2517 2987 1.268896 TGGAGTCGTCAACTGTTCGTC 60.269 52.381 0.00 0.00 38.74 4.20
2527 2997 0.822532 ACTGTTCGTCTCCTCGTGGT 60.823 55.000 2.99 0.00 34.23 4.16
2548 3018 6.147985 GTGGTTCTAGTAAAGGCTGAAAGAAG 59.852 42.308 0.00 0.00 34.07 2.85
2554 3024 0.179018 AAGGCTGAAAGAAGGCGTGT 60.179 50.000 0.00 0.00 46.86 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.255667 GGGAAGAGGCTCCGTGTACA 61.256 60.000 11.71 0.00 36.21 2.90
77 78 2.048503 CGTCGGCTTTCGGGAAGT 60.049 61.111 0.00 0.00 37.69 3.01
230 231 7.662669 GGGTAGGTATGAACAAAACTCAAACTA 59.337 37.037 0.00 0.00 0.00 2.24
236 237 6.235664 TGAAGGGTAGGTATGAACAAAACTC 58.764 40.000 0.00 0.00 0.00 3.01
336 338 2.534298 CAATACAGGAGCGACTCACAG 58.466 52.381 8.71 1.67 31.08 3.66
395 397 5.859205 AATACTTTCCATCATTTGCCTCC 57.141 39.130 0.00 0.00 0.00 4.30
397 399 8.593945 TCTAAAATACTTTCCATCATTTGCCT 57.406 30.769 0.00 0.00 0.00 4.75
415 418 5.509498 TGGGCATCTTGCTAGTTCTAAAAT 58.491 37.500 0.00 0.00 44.28 1.82
540 545 7.513371 TGACAATTTTACAAAAGATACCCGT 57.487 32.000 0.00 0.00 0.00 5.28
597 607 6.169557 TGCCATCTTGTAATATAGACCGTT 57.830 37.500 0.00 0.00 0.00 4.44
902 1032 3.132160 TGGATTTTATAAATCGCGCCGA 58.868 40.909 0.00 2.55 41.13 5.54
1139 1550 4.105733 ATGTCGCCGCGTCGTACA 62.106 61.111 10.12 13.01 0.00 2.90
1255 1688 3.541831 CCGGTTGCGACGATCGTG 61.542 66.667 28.12 18.27 42.81 4.35
1257 1690 2.949678 CTCCGGTTGCGACGATCG 60.950 66.667 14.88 14.88 43.89 3.69
1952 2413 1.683385 GCTTGGTCTTTGTTGCTCCTT 59.317 47.619 0.00 0.00 0.00 3.36
1961 2422 2.107950 TATCCCGTGCTTGGTCTTTG 57.892 50.000 0.00 0.00 0.00 2.77
1962 2423 3.016736 CAATATCCCGTGCTTGGTCTTT 58.983 45.455 0.00 0.00 0.00 2.52
1971 2432 0.110486 ATGTCCCCAATATCCCGTGC 59.890 55.000 0.00 0.00 0.00 5.34
1998 2459 4.065789 CTCCTCTTTAACTTGCCTCGTTT 58.934 43.478 0.00 0.00 0.00 3.60
2003 2464 2.877708 GCAGCTCCTCTTTAACTTGCCT 60.878 50.000 0.00 0.00 0.00 4.75
2167 2637 7.395190 AGCTAACAATGAAAGCATTATGACA 57.605 32.000 12.43 0.00 42.66 3.58
2171 2641 8.472413 ACATCAAGCTAACAATGAAAGCATTAT 58.528 29.630 12.43 0.00 42.66 1.28
2185 2655 4.192317 CCCACTTCCTACATCAAGCTAAC 58.808 47.826 0.00 0.00 0.00 2.34
2239 2709 6.990349 ACTCGTAGAAGTGAATTCAAAAGGAA 59.010 34.615 10.35 0.00 40.67 3.36
2259 2729 6.692486 AGAAGACAGATAAAACATGACTCGT 58.308 36.000 0.00 0.00 0.00 4.18
2269 2739 9.798994 GATCCGTTTAGTAGAAGACAGATAAAA 57.201 33.333 0.00 0.00 0.00 1.52
2290 2760 0.179089 CTCAGAGCAACCCAGATCCG 60.179 60.000 0.00 0.00 0.00 4.18
2360 2830 3.581332 TCGAGGTTGACCATACTTTCCTT 59.419 43.478 2.56 0.00 38.89 3.36
2364 2834 4.466370 TGATCTCGAGGTTGACCATACTTT 59.534 41.667 13.56 0.00 38.89 2.66
2439 2909 1.338769 GCACCTTGTGTCTAATCCGGT 60.339 52.381 0.00 0.00 35.75 5.28
2441 2911 2.093306 TGCACCTTGTGTCTAATCCG 57.907 50.000 0.00 0.00 35.75 4.18
2495 2965 1.129326 GAACAGTTGACGACTCCACG 58.871 55.000 0.00 0.00 36.10 4.94
2517 2987 3.429135 GCCTTTACTAGAACCACGAGGAG 60.429 52.174 5.68 0.00 38.69 3.69
2527 2997 5.246307 GCCTTCTTTCAGCCTTTACTAGAA 58.754 41.667 0.00 0.00 0.00 2.10
2548 3018 3.127533 CAAGGGCTGCTACACGCC 61.128 66.667 0.00 0.00 45.55 5.68
2554 3024 2.158900 GCTACATTCTCAAGGGCTGCTA 60.159 50.000 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.