Multiple sequence alignment - TraesCS2D01G108600

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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 TraesCS2D01G108600 chr2D 100.000 3443 0 0 1 3443 60168592 60165150 0.000000e+00 6359.0
1 TraesCS2D01G108600 chr2D 89.419 964 87 12 1545 2504 59724572 59725524 0.000000e+00 1201.0
2 TraesCS2D01G108600 chr2D 83.246 573 74 15 658 1227 59723587 59724140 1.100000e-139 507.0
3 TraesCS2D01G108600 chr2D 90.741 378 28 5 2133 2504 59836613 59836989 6.640000e-137 497.0
4 TraesCS2D01G108600 chr2D 87.778 180 16 4 57 234 59721977 59722152 4.500000e-49 206.0
5 TraesCS2D01G108600 chr2B 94.966 1907 77 6 1545 3443 94251106 94249211 0.000000e+00 2972.0
6 TraesCS2D01G108600 chr2B 92.120 2094 124 19 1373 3443 94090137 94088062 0.000000e+00 2915.0
7 TraesCS2D01G108600 chr2B 91.070 963 67 8 1490 2448 94099425 94098478 0.000000e+00 1284.0
8 TraesCS2D01G108600 chr2B 89.189 962 87 11 1558 2510 93408785 93409738 0.000000e+00 1184.0
9 TraesCS2D01G108600 chr2B 87.192 851 94 10 1669 2511 93109161 93110004 0.000000e+00 953.0
10 TraesCS2D01G108600 chr2B 92.796 583 26 6 389 968 94091174 94090605 0.000000e+00 830.0
11 TraesCS2D01G108600 chr2B 91.935 496 21 9 747 1225 94252010 94251517 0.000000e+00 676.0
12 TraesCS2D01G108600 chr2B 92.695 397 26 2 1 396 94092727 94092333 1.390000e-158 569.0
13 TraesCS2D01G108600 chr2B 93.041 388 27 0 963 1350 94090577 94090190 4.990000e-158 568.0
14 TraesCS2D01G108600 chr2B 82.558 602 75 19 658 1253 93407763 93408340 1.430000e-138 503.0
15 TraesCS2D01G108600 chr2B 82.024 573 81 14 658 1227 93108139 93108692 5.200000e-128 468.0
16 TraesCS2D01G108600 chr2B 94.561 239 11 1 1 239 94102671 94102435 5.430000e-98 368.0
17 TraesCS2D01G108600 chr2B 88.492 252 12 5 1 239 94252794 94252547 4.350000e-74 289.0
18 TraesCS2D01G108600 chr2B 84.483 290 33 6 908 1192 94101842 94101560 3.380000e-70 276.0
19 TraesCS2D01G108600 chr2B 84.082 245 21 6 453 687 94252255 94252019 1.610000e-53 220.0
20 TraesCS2D01G108600 chr2B 89.172 157 7 7 1289 1435 94100005 94099849 1.630000e-43 187.0
21 TraesCS2D01G108600 chr2B 81.197 117 12 3 479 586 94252889 94252774 6.120000e-13 86.1
22 TraesCS2D01G108600 chr2B 89.831 59 2 1 2515 2573 93409770 93409824 4.770000e-09 73.1
23 TraesCS2D01G108600 chr2B 88.333 60 3 1 2511 2570 93110023 93110078 6.170000e-08 69.4
24 TraesCS2D01G108600 chr2B 83.117 77 5 1 518 586 94102727 94102651 2.870000e-06 63.9
25 TraesCS2D01G108600 chr2B 100.000 34 0 0 241 274 579568642 579568675 2.870000e-06 63.9
26 TraesCS2D01G108600 chr2A 92.890 1505 48 16 1 1486 60762146 60760682 0.000000e+00 2132.0
27 TraesCS2D01G108600 chr2A 96.247 1279 35 4 1434 2712 60283657 60282392 0.000000e+00 2084.0
28 TraesCS2D01G108600 chr2A 95.802 1215 38 4 1473 2687 60760366 60759165 0.000000e+00 1949.0
29 TraesCS2D01G108600 chr2A 90.731 971 80 8 1545 2510 59718141 59719106 0.000000e+00 1286.0
30 TraesCS2D01G108600 chr2A 93.210 648 35 5 2804 3443 60281104 60280458 0.000000e+00 944.0
31 TraesCS2D01G108600 chr2A 93.034 646 36 4 2807 3443 60759177 60758532 0.000000e+00 935.0
32 TraesCS2D01G108600 chr2A 82.975 558 72 15 674 1227 59717169 59717707 1.860000e-132 483.0
33 TraesCS2D01G108600 chr2A 87.990 408 27 9 453 858 60284662 60284275 2.420000e-126 462.0
34 TraesCS2D01G108600 chr2A 84.944 445 42 16 875 1303 60284140 60283705 8.830000e-116 427.0
35 TraesCS2D01G108600 chr2A 88.889 180 14 4 57 234 59812994 59813169 2.080000e-52 217.0
36 TraesCS2D01G108600 chr2A 100.000 43 0 0 241 283 612844610 612844652 2.850000e-11 80.5
37 TraesCS2D01G108600 chr2A 88.889 63 3 1 2511 2573 59719126 59719184 1.330000e-09 75.0
38 TraesCS2D01G108600 chr2A 86.765 68 5 3 3341 3406 115436448 115436513 4.770000e-09 73.1
39 TraesCS2D01G108600 chr2A 93.182 44 3 0 543 586 60762169 60762126 7.980000e-07 65.8
40 TraesCS2D01G108600 chr7A 83.696 184 27 3 3258 3440 677887318 677887137 1.640000e-38 171.0
41 TraesCS2D01G108600 chr3D 81.675 191 28 4 3251 3440 333397385 333397569 5.950000e-33 152.0
42 TraesCS2D01G108600 chr3D 95.745 47 2 0 241 287 81695017 81695063 3.680000e-10 76.8
43 TraesCS2D01G108600 chr4D 91.667 48 4 0 234 281 398666171 398666218 2.220000e-07 67.6


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 TraesCS2D01G108600 chr2D 60165150 60168592 3442 True 6359.000000 6359 100.000000 1 3443 1 chr2D.!!$R1 3442
1 TraesCS2D01G108600 chr2D 59721977 59725524 3547 False 638.000000 1201 86.814333 57 2504 3 chr2D.!!$F2 2447
2 TraesCS2D01G108600 chr2B 94088062 94092727 4665 True 1220.500000 2915 92.663000 1 3443 4 chr2B.!!$R1 3442
3 TraesCS2D01G108600 chr2B 94249211 94252889 3678 True 848.620000 2972 88.134400 1 3443 5 chr2B.!!$R3 3442
4 TraesCS2D01G108600 chr2B 93407763 93409824 2061 False 586.700000 1184 87.192667 658 2573 3 chr2B.!!$F3 1915
5 TraesCS2D01G108600 chr2B 93108139 93110078 1939 False 496.800000 953 85.849667 658 2570 3 chr2B.!!$F2 1912
6 TraesCS2D01G108600 chr2B 94098478 94102727 4249 True 435.780000 1284 88.480600 1 2448 5 chr2B.!!$R2 2447
7 TraesCS2D01G108600 chr2A 60758532 60762169 3637 True 1270.450000 2132 93.727000 1 3443 4 chr2A.!!$R2 3442
8 TraesCS2D01G108600 chr2A 60280458 60284662 4204 True 979.250000 2084 90.597750 453 3443 4 chr2A.!!$R1 2990
9 TraesCS2D01G108600 chr2A 59717169 59719184 2015 False 614.666667 1286 87.531667 674 2573 3 chr2A.!!$F4 1899

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
164 274 0.179056 ACTGTTCACTGACCCCGTTG 60.179 55.000 0.0 0.0 0.00 4.10 F
651 2771 0.834612 AATGCTGCCCATTTCCCATG 59.165 50.000 0.0 0.0 41.29 3.66 F
745 3109 2.375845 CCTAGCCTACTAGCTACCCAGA 59.624 54.545 0.0 0.0 44.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1083 3629 0.608640 ACTTGGCGTAGAACTGAGGG 59.391 55.000 0.0 0.0 0.0 4.30 R
2337 7466 1.810412 GCGAAGTCCCTGTTGAACTGT 60.810 52.381 0.0 0.0 0.0 3.55 R
2462 7592 2.435938 GTCGCCTTTGATCGCCCA 60.436 61.111 0.0 0.0 0.0 5.36 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
120 229 6.705302 CAGCTAATTGGCCATCTCTATCTAA 58.295 40.000 6.09 0.00 0.00 2.10
164 274 0.179056 ACTGTTCACTGACCCCGTTG 60.179 55.000 0.00 0.00 0.00 4.10
170 280 2.193127 TCACTGACCCCGTTGGAATAT 58.807 47.619 0.00 0.00 38.00 1.28
184 294 5.277974 CGTTGGAATATCATTAGCAGTTGGG 60.278 44.000 0.00 0.00 0.00 4.12
188 298 6.064717 GGAATATCATTAGCAGTTGGGAGTT 58.935 40.000 0.00 0.00 0.00 3.01
258 384 7.386851 TGTCAATTACTCCCTCTGTAAAGAAG 58.613 38.462 0.00 0.00 34.20 2.85
541 2226 1.967066 TCCCGGACAAATTTTGCATGT 59.033 42.857 0.73 0.00 0.00 3.21
595 2289 3.020984 TGGGTGGAAGAATTATTTCGCC 58.979 45.455 14.29 14.29 36.93 5.54
648 2768 3.469739 CAAATAATGCTGCCCATTTCCC 58.530 45.455 5.20 0.00 41.29 3.97
649 2769 2.475339 ATAATGCTGCCCATTTCCCA 57.525 45.000 5.20 0.00 41.29 4.37
650 2770 2.475339 TAATGCTGCCCATTTCCCAT 57.525 45.000 5.20 0.00 41.29 4.00
651 2771 0.834612 AATGCTGCCCATTTCCCATG 59.165 50.000 0.00 0.00 41.29 3.66
744 3108 2.555670 CCCTAGCCTACTAGCTACCCAG 60.556 59.091 0.00 0.00 44.00 4.45
745 3109 2.375845 CCTAGCCTACTAGCTACCCAGA 59.624 54.545 0.00 0.00 44.00 3.86
1346 5508 5.300752 ACCAGTTAATCACACTGTCTTCAG 58.699 41.667 0.00 0.00 46.18 3.02
1382 5574 6.916360 ATCAAAAAGCTAGTGGAATGGAAA 57.084 33.333 0.00 0.00 0.00 3.13
2462 7592 6.904626 ACTAAGCCACCAATCTAGAATCAAT 58.095 36.000 0.00 0.00 0.00 2.57
2573 7731 4.907269 AGATGGGGTGTGATGTGATGTATA 59.093 41.667 0.00 0.00 0.00 1.47
2577 7735 5.310331 TGGGGTGTGATGTGATGTATATCAT 59.690 40.000 5.38 0.00 44.62 2.45
2625 7783 5.766150 TTATTATATGCCCAAGTGCACAC 57.234 39.130 21.04 3.26 45.48 3.82
2712 7871 2.221169 CACAACCATGCGGCTATATGT 58.779 47.619 0.00 0.00 34.57 2.29
2822 9226 7.070629 TCAATACCCCTTTAGTTTTCCAAACT 58.929 34.615 7.06 7.06 0.00 2.66
2879 9283 5.962031 TCCTAATAAGTTGGAGGTCTTGCTA 59.038 40.000 0.00 0.00 0.00 3.49
2942 9347 3.895704 AGTTTCCTTCCCTAAAGCCAA 57.104 42.857 0.00 0.00 33.29 4.52
2995 9401 2.359230 GCTCTGGCAAGCCGAGTT 60.359 61.111 23.61 0.00 38.26 3.01
3018 9424 3.112075 CACTGCCTACACACCGCG 61.112 66.667 0.00 0.00 0.00 6.46
3038 9444 3.400599 ATTCCTAGCCCCGCAACCG 62.401 63.158 0.00 0.00 0.00 4.44
3158 9564 0.320697 GGGCACTCGGTAAAGTCACT 59.679 55.000 0.00 0.00 0.00 3.41
3187 9593 1.531149 CTGAGTGCCAGGTAAAACACG 59.469 52.381 0.00 0.00 39.23 4.49
3276 9689 2.325082 GCTCGGCATGTCGGTTGTT 61.325 57.895 21.18 0.00 0.00 2.83
3313 9726 1.915983 GAAGACCCCCTAAGCCTGG 59.084 63.158 0.00 0.00 0.00 4.45
3319 9732 2.072487 CCCCTAAGCCTGGCAGCTA 61.072 63.158 22.65 8.14 44.11 3.32
3409 9822 2.303311 GGTTTTGAGGTAGTCTCCAGCT 59.697 50.000 0.00 0.00 41.76 4.24
3431 9844 1.447099 TTTGCCCCTAGGTACAACCA 58.553 50.000 8.29 0.00 41.95 3.67
3440 9853 5.425630 CCCTAGGTACAACCAACTTATGTC 58.574 45.833 8.29 0.00 41.95 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 229 6.042781 TCCCGGCATCTAAGATGTTTATAAGT 59.957 38.462 0.00 0.0 0.00 2.24
164 274 5.625150 ACTCCCAACTGCTAATGATATTCC 58.375 41.667 0.00 0.0 0.00 3.01
170 280 3.674997 GTCAACTCCCAACTGCTAATGA 58.325 45.455 0.00 0.0 0.00 2.57
184 294 0.577269 GTGCTGTCACACGTCAACTC 59.423 55.000 0.00 0.0 42.66 3.01
346 823 2.666508 CCGTCAGTTAATCGTCCAACAG 59.333 50.000 0.00 0.0 0.00 3.16
465 2150 1.747355 GGAGTGATTGGGATGTGCAAG 59.253 52.381 0.00 0.0 0.00 4.01
541 2226 2.304470 TGTTAACAGGTAGCATGCCAGA 59.696 45.455 15.66 0.0 46.86 3.86
595 2289 1.137086 AGCTAGCATTACTGTGTCCGG 59.863 52.381 18.83 0.0 0.00 5.14
648 2768 5.934043 TCGGAATATTAGTTGGAGATGCATG 59.066 40.000 2.46 0.0 0.00 4.06
649 2769 6.114187 TCGGAATATTAGTTGGAGATGCAT 57.886 37.500 0.00 0.0 0.00 3.96
650 2770 5.545063 TCGGAATATTAGTTGGAGATGCA 57.455 39.130 0.00 0.0 0.00 3.96
651 2771 5.179555 GGTTCGGAATATTAGTTGGAGATGC 59.820 44.000 0.00 0.0 0.00 3.91
744 3108 5.801947 CGACAATGAACAATGGGAAATCTTC 59.198 40.000 0.00 0.0 0.00 2.87
745 3109 5.243730 ACGACAATGAACAATGGGAAATCTT 59.756 36.000 0.00 0.0 0.00 2.40
1076 3622 1.736032 CGTAGAACTGAGGGGAAAGCG 60.736 57.143 0.00 0.0 0.00 4.68
1083 3629 0.608640 ACTTGGCGTAGAACTGAGGG 59.391 55.000 0.00 0.0 0.00 4.30
1346 5508 5.947443 AGCTTTTTGATACTGCAATGACTC 58.053 37.500 0.00 0.0 0.00 3.36
1929 7058 3.479269 GAAAGGCTCGCCGTCGTG 61.479 66.667 1.69 0.0 41.95 4.35
2337 7466 1.810412 GCGAAGTCCCTGTTGAACTGT 60.810 52.381 0.00 0.0 0.00 3.55
2462 7592 2.435938 GTCGCCTTTGATCGCCCA 60.436 61.111 0.00 0.0 0.00 5.36
2573 7731 8.277918 AGCAAAGGGAAATACTTAAGAGATGAT 58.722 33.333 10.09 0.0 0.00 2.45
2577 7735 9.975218 ATTAAGCAAAGGGAAATACTTAAGAGA 57.025 29.630 10.09 0.0 34.25 3.10
2650 7809 4.977741 TGTAGAATTCGTCGGAAACAAC 57.022 40.909 0.00 0.0 35.40 3.32
2712 7871 4.693283 CTCTTAGGCGTGGAAATGATGTA 58.307 43.478 0.00 0.0 0.00 2.29
2879 9283 1.838077 CAGAATTAGGAACGGGGAGGT 59.162 52.381 0.00 0.0 0.00 3.85
3018 9424 2.124320 TTGCGGGGCTAGGAATGC 60.124 61.111 0.00 0.0 0.00 3.56
3038 9444 2.431023 TCTGAAGGCGGAGATAGGC 58.569 57.895 0.00 0.0 0.00 3.93
3158 9564 1.545428 CCTGGCACTCAGTTTTGGCTA 60.545 52.381 0.00 0.0 41.83 3.93
3187 9593 1.896660 TGTGTCCTGCCTTTTCCGC 60.897 57.895 0.00 0.0 0.00 5.54
3313 9726 3.316573 AACGAGGCCCACTAGCTGC 62.317 63.158 0.00 0.0 0.00 5.25
3319 9732 2.600769 AGACGAACGAGGCCCACT 60.601 61.111 0.00 0.0 0.00 4.00
3409 9822 3.592427 TGGTTGTACCTAGGGGCAAATAA 59.408 43.478 14.81 4.3 39.58 1.40


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

AutoCloner maintained by Alex Coulton.