Multiple sequence alignment - TraesCS1D01G240300

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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 TraesCS1D01G240300 chr1D 100.000 2955 0 0 1 2955 330093384 330090430 0.000000e+00 5457.0
1 TraesCS1D01G240300 chr1D 87.373 491 40 12 2140 2626 483963887 483964359 7.200000e-151 544.0
2 TraesCS1D01G240300 chr1D 94.937 79 4 0 2875 2953 39968866 39968944 1.110000e-24 124.0
3 TraesCS1D01G240300 chr1A 90.139 2089 102 30 1 2026 427050261 427048214 0.000000e+00 2621.0
4 TraesCS1D01G240300 chr1A 91.429 105 8 1 2038 2141 427048136 427048032 3.070000e-30 143.0
5 TraesCS1D01G240300 chr1B 86.654 1641 92 54 581 2141 444937765 444936172 0.000000e+00 1700.0
6 TraesCS1D01G240300 chr1B 90.051 583 32 7 1 581 444942449 444941891 0.000000e+00 732.0
7 TraesCS1D01G240300 chr5D 88.980 490 46 6 2139 2626 451628088 451628571 1.520000e-167 599.0
8 TraesCS1D01G240300 chr5D 97.287 258 7 0 2621 2878 505213594 505213337 3.500000e-119 438.0
9 TraesCS1D01G240300 chr5D 91.358 81 7 0 2875 2955 129507872 129507792 8.660000e-21 111.0
10 TraesCS1D01G240300 chr5D 91.358 81 7 0 2875 2955 451629379 451629459 8.660000e-21 111.0
11 TraesCS1D01G240300 chr2D 88.548 489 48 5 2143 2626 627642543 627642058 1.180000e-163 586.0
12 TraesCS1D01G240300 chr2D 87.631 477 45 6 2139 2605 159600604 159600132 2.590000e-150 542.0
13 TraesCS1D01G240300 chr2D 87.216 485 47 9 2143 2626 598002831 598002361 3.350000e-149 538.0
14 TraesCS1D01G240300 chr2D 85.163 492 56 9 2139 2626 76870793 76870315 3.420000e-134 488.0
15 TraesCS1D01G240300 chr2D 95.349 258 12 0 2621 2878 627641623 627641366 7.620000e-111 411.0
16 TraesCS1D01G240300 chr2D 93.798 258 15 1 2621 2878 159599671 159599415 1.280000e-103 387.0
17 TraesCS1D01G240300 chr2D 94.937 79 4 0 2877 2955 627640264 627640186 1.110000e-24 124.0
18 TraesCS1D01G240300 chr2D 93.671 79 5 0 2875 2953 76869427 76869349 5.170000e-23 119.0
19 TraesCS1D01G240300 chr3D 88.260 477 40 8 2152 2626 86202531 86202069 9.250000e-155 556.0
20 TraesCS1D01G240300 chr3D 96.124 258 10 0 2621 2878 574436156 574436413 3.520000e-114 422.0
21 TraesCS1D01G240300 chr3D 88.451 355 27 7 2140 2492 574435711 574436053 1.640000e-112 416.0
22 TraesCS1D01G240300 chr5A 87.117 489 54 4 2139 2626 431047445 431046965 2.000000e-151 545.0
23 TraesCS1D01G240300 chr5A 94.841 252 13 0 2627 2878 431046525 431046274 7.680000e-106 394.0
24 TraesCS1D01G240300 chr5A 93.827 81 5 0 2875 2955 480342724 480342644 4.000000e-24 122.0
25 TraesCS1D01G240300 chr7A 86.382 492 55 9 2139 2624 293543703 293543218 7.250000e-146 527.0
26 TraesCS1D01G240300 chr7A 83.851 483 70 7 2145 2626 423551950 423551475 1.250000e-123 453.0
27 TraesCS1D01G240300 chr3A 85.714 497 52 11 2143 2626 414929072 414928582 9.450000e-140 507.0
28 TraesCS1D01G240300 chr3A 88.618 246 21 4 2143 2381 11798024 11797779 2.880000e-75 292.0
29 TraesCS1D01G240300 chr6D 86.429 420 23 13 2215 2626 465569360 465568967 2.100000e-116 429.0
30 TraesCS1D01G240300 chr6D 95.736 258 11 0 2621 2878 156435871 156436128 1.640000e-112 416.0
31 TraesCS1D01G240300 chr6D 93.798 258 16 0 2621 2878 178847360 178847103 3.570000e-104 388.0
32 TraesCS1D01G240300 chr6D 93.411 258 17 0 2621 2878 314515387 314515130 1.660000e-102 383.0
33 TraesCS1D01G240300 chr6D 92.593 81 6 0 2875 2955 156436327 156436407 1.860000e-22 117.0
34 TraesCS1D01G240300 chr6D 92.593 81 6 0 2875 2955 178846904 178846824 1.860000e-22 117.0
35 TraesCS1D01G240300 chr7D 93.411 258 17 0 2621 2878 555424478 555424221 1.660000e-102 383.0
36 TraesCS1D01G240300 chr7D 91.358 81 7 0 2875 2955 581799049 581798969 8.660000e-21 111.0
37 TraesCS1D01G240300 chr2B 82.778 180 28 3 1 179 650784421 650784244 1.100000e-34 158.0
38 TraesCS1D01G240300 chr4B 77.778 108 23 1 287 394 606996427 606996533 6.840000e-07 65.8


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 TraesCS1D01G240300 chr1D 330090430 330093384 2954 True 5457.000000 5457 100.000000 1 2955 1 chr1D.!!$R1 2954
1 TraesCS1D01G240300 chr1A 427048032 427050261 2229 True 1382.000000 2621 90.784000 1 2141 2 chr1A.!!$R1 2140
2 TraesCS1D01G240300 chr1B 444936172 444937765 1593 True 1700.000000 1700 86.654000 581 2141 1 chr1B.!!$R1 1560
3 TraesCS1D01G240300 chr1B 444941891 444942449 558 True 732.000000 732 90.051000 1 581 1 chr1B.!!$R2 580
4 TraesCS1D01G240300 chr5D 451628088 451629459 1371 False 355.000000 599 90.169000 2139 2955 2 chr5D.!!$F1 816
5 TraesCS1D01G240300 chr2D 159599415 159600604 1189 True 464.500000 542 90.714500 2139 2878 2 chr2D.!!$R3 739
6 TraesCS1D01G240300 chr2D 627640186 627642543 2357 True 373.666667 586 92.944667 2143 2955 3 chr2D.!!$R4 812
7 TraesCS1D01G240300 chr2D 76869349 76870793 1444 True 303.500000 488 89.417000 2139 2953 2 chr2D.!!$R2 814
8 TraesCS1D01G240300 chr3D 574435711 574436413 702 False 419.000000 422 92.287500 2140 2878 2 chr3D.!!$F1 738
9 TraesCS1D01G240300 chr5A 431046274 431047445 1171 True 469.500000 545 90.979000 2139 2878 2 chr5A.!!$R2 739
10 TraesCS1D01G240300 chr6D 156435871 156436407 536 False 266.500000 416 94.164500 2621 2955 2 chr6D.!!$F1 334
11 TraesCS1D01G240300 chr6D 178846824 178847360 536 True 252.500000 388 93.195500 2621 2955 2 chr6D.!!$R3 334

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
964 988 0.037590 AATTTCAGGTGCACGCCCTA 59.962 50.0 11.45 0.0 0.00 3.53 F
1697 1748 0.934496 CGCCGCCGATTTTGATTAGA 59.066 50.0 0.00 0.0 36.29 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1877 1.074248 GGAAAAGGCACGGGGAAGA 59.926 57.895 0.0 0.0 0.00 2.87 R
2559 2757 2.792599 GACAGCGACGAGGACGAT 59.207 61.111 0.0 0.0 42.66 3.73 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
51 52 6.768483 TCAAGTCTATGGTCAAGACAAATCA 58.232 36.000 6.06 0.00 44.77 2.57
111 112 0.837272 GCAGGAGTAGGGTATTGCCA 59.163 55.000 0.00 0.00 39.65 4.92
300 302 4.522022 CCTCTCAACTGAAATTTGCCTTCT 59.478 41.667 0.00 0.00 0.00 2.85
402 404 3.004629 CACCATGCAAGTAAAAGCTGACA 59.995 43.478 0.00 0.00 0.00 3.58
425 427 3.066760 GCCACGAAAATCAATCCCCTTAG 59.933 47.826 0.00 0.00 0.00 2.18
426 428 4.523083 CCACGAAAATCAATCCCCTTAGA 58.477 43.478 0.00 0.00 0.00 2.10
427 429 5.133221 CCACGAAAATCAATCCCCTTAGAT 58.867 41.667 0.00 0.00 0.00 1.98
428 430 5.239525 CCACGAAAATCAATCCCCTTAGATC 59.760 44.000 0.00 0.00 0.00 2.75
429 431 5.050091 CACGAAAATCAATCCCCTTAGATCG 60.050 44.000 0.00 0.00 0.00 3.69
430 432 5.163343 ACGAAAATCAATCCCCTTAGATCGA 60.163 40.000 0.00 0.00 0.00 3.59
431 433 5.177696 CGAAAATCAATCCCCTTAGATCGAC 59.822 44.000 0.00 0.00 0.00 4.20
432 434 5.896073 AAATCAATCCCCTTAGATCGACT 57.104 39.130 0.00 0.00 0.00 4.18
433 435 6.996180 AAATCAATCCCCTTAGATCGACTA 57.004 37.500 0.00 0.00 0.00 2.59
610 613 9.383578 ACCACATTATATTCCATCCATTTGAAT 57.616 29.630 0.00 0.00 33.54 2.57
746 758 6.765989 CCCTCCAAATCATTCGTTTCATACTA 59.234 38.462 0.00 0.00 0.00 1.82
747 759 7.445402 CCCTCCAAATCATTCGTTTCATACTAT 59.555 37.037 0.00 0.00 0.00 2.12
786 804 3.181490 GCGGTTCCTTGTTTCTCAACTTT 60.181 43.478 0.00 0.00 33.58 2.66
791 809 6.972901 GGTTCCTTGTTTCTCAACTTTACTTG 59.027 38.462 0.00 0.00 33.58 3.16
852 870 2.654877 CAAGCCAGCCAAAGCCAG 59.345 61.111 0.00 0.00 41.25 4.85
950 974 1.605232 ACCACACGGAACCGAAATTTC 59.395 47.619 20.14 8.20 42.83 2.17
964 988 0.037590 AATTTCAGGTGCACGCCCTA 59.962 50.000 11.45 0.00 0.00 3.53
985 1009 4.472310 CCCCCTCCCCTCCCCAAT 62.472 72.222 0.00 0.00 0.00 3.16
986 1010 2.778717 CCCCTCCCCTCCCCAATC 60.779 72.222 0.00 0.00 0.00 2.67
1004 1029 2.361610 CATCCCCAAACCAGCGCT 60.362 61.111 2.64 2.64 0.00 5.92
1057 1087 4.926162 GGGTTTGGCGGGTTGGGT 62.926 66.667 0.00 0.00 0.00 4.51
1130 1160 2.281761 CATGTATGCGGGAGGGGC 60.282 66.667 0.00 0.00 0.00 5.80
1270 1300 1.975407 GTCTTCGTCGGGTGGAGGA 60.975 63.158 0.00 0.00 37.75 3.71
1271 1301 1.677966 TCTTCGTCGGGTGGAGGAG 60.678 63.158 0.00 0.00 40.37 3.69
1272 1302 1.677966 CTTCGTCGGGTGGAGGAGA 60.678 63.158 0.00 0.00 40.37 3.71
1273 1303 1.658686 CTTCGTCGGGTGGAGGAGAG 61.659 65.000 0.00 0.00 40.37 3.20
1274 1304 3.141488 CGTCGGGTGGAGGAGAGG 61.141 72.222 0.00 0.00 32.22 3.69
1275 1305 3.462678 GTCGGGTGGAGGAGAGGC 61.463 72.222 0.00 0.00 0.00 4.70
1658 1709 2.570068 CCGAAGACGACGACGACG 60.570 66.667 17.60 17.60 42.66 5.12
1659 1710 2.467223 CGAAGACGACGACGACGA 59.533 61.111 25.15 0.00 41.06 4.20
1660 1711 1.852351 CGAAGACGACGACGACGAC 60.852 63.158 25.15 18.88 41.06 4.34
1697 1748 0.934496 CGCCGCCGATTTTGATTAGA 59.066 50.000 0.00 0.00 36.29 2.10
1706 1757 3.809832 CGATTTTGATTAGATGCCCGTCT 59.190 43.478 0.00 0.00 0.00 4.18
1708 1759 3.627395 TTTGATTAGATGCCCGTCTGT 57.373 42.857 0.35 0.00 0.00 3.41
1724 1775 2.948134 GTCGATCCGCCGTTCGTC 60.948 66.667 6.59 0.00 36.74 4.20
1793 1847 8.943002 AGAAGGTATACACAGGTTTATTTTTCG 58.057 33.333 5.01 0.00 0.00 3.46
1823 1877 2.181021 GCGTCCGGTCGAGTTCAT 59.819 61.111 25.18 0.00 0.00 2.57
1927 2016 2.982470 GCCTTTTGCATCTTTTGTCTCG 59.018 45.455 0.00 0.00 40.77 4.04
1946 2035 1.674980 TCGCATGCCAATCAGTGCA 60.675 52.632 13.15 0.00 42.52 4.57
1995 2100 1.373246 CTTTGCATTGTGGCACGGG 60.373 57.895 13.77 5.89 44.86 5.28
1996 2101 3.512223 TTTGCATTGTGGCACGGGC 62.512 57.895 13.77 16.01 44.86 6.13
2073 2249 0.885196 TGTGCCTTTCGTATTTGGCC 59.115 50.000 0.00 0.00 44.32 5.36
2121 2298 7.250569 GTGTAGGTATGCACGTACTTTACTTA 58.749 38.462 8.18 0.00 43.36 2.24
2125 2302 6.759827 AGGTATGCACGTACTTTACTTATTGG 59.240 38.462 0.00 0.00 0.00 3.16
2141 2318 3.681473 GGGCTTCCCACGAAAAGG 58.319 61.111 0.00 0.00 44.65 3.11
2149 2326 0.322456 CCCACGAAAAGGGCATCTCA 60.322 55.000 0.00 0.00 39.96 3.27
2210 2387 0.179092 GGATGTACCGGCGCTAAACT 60.179 55.000 7.64 0.00 0.00 2.66
2250 2427 4.802051 CCCAGTCGCCACCCCATG 62.802 72.222 0.00 0.00 0.00 3.66
2252 2429 2.436646 CAGTCGCCACCCCATGTC 60.437 66.667 0.00 0.00 0.00 3.06
2253 2430 4.082523 AGTCGCCACCCCATGTCG 62.083 66.667 0.00 0.00 0.00 4.35
2257 2434 2.755469 GCCACCCCATGTCGCATT 60.755 61.111 0.00 0.00 0.00 3.56
2258 2435 3.067480 GCCACCCCATGTCGCATTG 62.067 63.158 0.00 0.00 0.00 2.82
2259 2436 1.678635 CCACCCCATGTCGCATTGT 60.679 57.895 0.00 0.00 0.00 2.71
2260 2437 1.507630 CACCCCATGTCGCATTGTG 59.492 57.895 0.00 0.00 0.00 3.33
2261 2438 1.678635 ACCCCATGTCGCATTGTGG 60.679 57.895 0.00 0.00 0.00 4.17
2306 2494 2.353208 GCCCCACATTCGCACAAATAAA 60.353 45.455 0.00 0.00 0.00 1.40
2333 2521 4.571372 AATTTAACCAAACTTCGGCGAA 57.429 36.364 22.33 22.33 0.00 4.70
2384 2573 0.395448 AGACACTACTAGACCCGCCC 60.395 60.000 0.00 0.00 0.00 6.13
2433 2622 0.543277 CCCTGAAGCTCTACATGCCA 59.457 55.000 0.00 0.00 0.00 4.92
2550 2748 2.446994 AGTGGGTTGGACGGTCCA 60.447 61.111 25.53 25.53 46.61 4.02
2559 2757 3.986006 GACGGTCCAGTGGCGTCA 61.986 66.667 27.41 1.07 37.84 4.35
2646 3293 3.036084 CGTCGGCGTTGTGCTTCT 61.036 61.111 6.85 0.00 45.43 2.85
2890 4641 1.135170 GTCCGGCGACTTATATAGGCC 60.135 57.143 9.30 0.00 40.36 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.568685 TGAGTCAACCTCTCTATTCTTCG 57.431 43.478 0.00 0.00 41.11 3.79
10 11 6.524101 GACTTGAGTCAACCTCTCTATTCT 57.476 41.667 0.08 0.00 44.18 2.40
51 52 3.684788 GTGTGAGCCGAGTGAATACAAAT 59.315 43.478 0.00 0.00 0.00 2.32
105 106 0.625849 CCCCCTGTTCTAGTGGCAAT 59.374 55.000 0.00 0.00 0.00 3.56
111 112 0.252103 TTCGAGCCCCCTGTTCTAGT 60.252 55.000 0.00 0.00 0.00 2.57
146 148 7.130303 TCTAGATACGAGATTTCACATACCG 57.870 40.000 0.00 0.00 0.00 4.02
148 150 8.952278 AGGATCTAGATACGAGATTTCACATAC 58.048 37.037 9.38 0.00 33.71 2.39
402 404 1.005924 AGGGGATTGATTTTCGTGGCT 59.994 47.619 0.00 0.00 0.00 4.75
452 454 3.756082 TCCTTAAAATCACCATGCCCT 57.244 42.857 0.00 0.00 0.00 5.19
490 492 2.348888 CGCTGGTCTTACGGGGACT 61.349 63.158 0.00 0.00 34.47 3.85
546 549 9.503427 CTAATATGACCGGTTCATTTTCTTTTC 57.497 33.333 19.94 0.19 42.87 2.29
610 613 7.522236 CGTTGTTAGATAGGAGTAGATGATGCA 60.522 40.741 0.00 0.00 0.00 3.96
697 709 7.222872 GGTGGATGAGTATCTGATGAGAAAAT 58.777 38.462 0.00 0.00 34.92 1.82
766 784 6.694877 AGTAAAGTTGAGAAACAAGGAACC 57.305 37.500 0.00 0.00 39.30 3.62
786 804 2.479837 CTTTCGTCACAGGTGCAAGTA 58.520 47.619 0.00 0.00 0.00 2.24
791 809 0.951040 CTCCCTTTCGTCACAGGTGC 60.951 60.000 0.00 0.00 0.00 5.01
902 926 2.248135 TGGTATTATTGCGGCCGCG 61.248 57.895 41.73 12.29 45.51 6.46
950 974 2.125512 GAGTAGGGCGTGCACCTG 60.126 66.667 12.15 0.00 39.12 4.00
983 1007 0.684153 CGCTGGTTTGGGGATGGATT 60.684 55.000 0.00 0.00 0.00 3.01
984 1008 1.076777 CGCTGGTTTGGGGATGGAT 60.077 57.895 0.00 0.00 0.00 3.41
985 1009 2.354729 CGCTGGTTTGGGGATGGA 59.645 61.111 0.00 0.00 0.00 3.41
986 1010 3.451894 GCGCTGGTTTGGGGATGG 61.452 66.667 0.00 0.00 0.00 3.51
1280 1310 2.044551 CTTCTTGGCTCCCCCTGC 60.045 66.667 0.00 0.00 0.00 4.85
1281 1311 2.044551 GCTTCTTGGCTCCCCCTG 60.045 66.667 0.00 0.00 0.00 4.45
1447 1489 4.862823 CCCTCCCCCTCCTCGACC 62.863 77.778 0.00 0.00 0.00 4.79
1448 1490 4.862823 CCCCTCCCCCTCCTCGAC 62.863 77.778 0.00 0.00 0.00 4.20
1697 1748 2.815308 GGATCGACAGACGGGCAT 59.185 61.111 0.00 0.00 42.82 4.40
1706 1757 3.672255 GACGAACGGCGGATCGACA 62.672 63.158 33.16 0.00 46.49 4.35
1708 1759 3.433453 TGACGAACGGCGGATCGA 61.433 61.111 33.16 16.40 46.49 3.59
1823 1877 1.074248 GGAAAAGGCACGGGGAAGA 59.926 57.895 0.00 0.00 0.00 2.87
1927 2016 1.226491 GCACTGATTGGCATGCGAC 60.226 57.895 12.44 0.00 0.00 5.19
1946 2035 6.039493 CACGGAGTAGTAGTAGTCAATCCAAT 59.961 42.308 13.31 0.00 41.61 3.16
1995 2100 2.742774 AGGCAATGTGAAAAAGTTCGC 58.257 42.857 0.00 0.00 43.35 4.70
1996 2101 4.610945 AGAAGGCAATGTGAAAAAGTTCG 58.389 39.130 0.00 0.00 36.46 3.95
2141 2318 3.056313 GCCAACGGCTTGAGATGCC 62.056 63.158 0.00 0.00 46.69 4.40
2166 2343 4.571257 GCGATTTTTAGCGCCTCG 57.429 55.556 2.29 4.74 46.93 4.63
2193 2370 1.087771 GCAGTTTAGCGCCGGTACAT 61.088 55.000 2.29 0.00 0.00 2.29
2210 2387 3.529341 ATCACGCCCTCAACACGCA 62.529 57.895 0.00 0.00 0.00 5.24
2306 2494 3.733727 CGAAGTTTGGTTAAATTTGCGCT 59.266 39.130 9.73 0.00 0.00 5.92
2433 2622 1.276421 ACGCAGTTCTACATGCTCCTT 59.724 47.619 0.00 0.00 37.78 3.36
2550 2748 2.885861 GAGGACGATGACGCCACT 59.114 61.111 0.00 0.00 43.96 4.00
2552 2750 3.047718 GACGAGGACGATGACGCCA 62.048 63.158 0.00 0.00 43.96 5.69
2559 2757 2.792599 GACAGCGACGAGGACGAT 59.207 61.111 0.00 0.00 42.66 3.73


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

AutoCloner maintained by Alex Coulton.