Multiple sequence alignment - TraesCS2D01G089900

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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 TraesCS2D01G089900 chr2D 100.000 3416 0 0 1 3416 39654661 39658076 0.000000e+00 6309
1 TraesCS2D01G089900 chr2D 94.543 3280 142 12 12 3258 291771636 291774911 0.000000e+00 5031
2 TraesCS2D01G089900 chr2D 94.464 560 29 2 2702 3261 291679986 291679429 0.000000e+00 861
3 TraesCS2D01G089900 chr4D 95.954 3460 95 10 1 3416 123348128 123351586 0.000000e+00 5572
4 TraesCS2D01G089900 chr4D 95.581 3462 106 7 1 3416 134977427 134980887 0.000000e+00 5502
5 TraesCS2D01G089900 chr4D 92.014 864 26 4 2595 3416 123561662 123562524 0.000000e+00 1173
6 TraesCS2D01G089900 chr7B 96.457 3302 72 7 4 3261 742950729 742947429 0.000000e+00 5408
7 TraesCS2D01G089900 chr6D 95.059 3461 108 16 1 3416 370020526 370023968 0.000000e+00 5385
8 TraesCS2D01G089900 chr5D 95.106 3433 139 8 4 3416 80020425 80017002 0.000000e+00 5382
9 TraesCS2D01G089900 chr2A 96.276 3303 77 7 1 3258 755478554 755481855 0.000000e+00 5376
10 TraesCS2D01G089900 chr7A 96.275 3302 78 7 4 3261 60170758 60167458 0.000000e+00 5374
11 TraesCS2D01G089900 chr5A 96.214 3302 79 8 1 3258 420183709 420187008 0.000000e+00 5363
12 TraesCS2D01G089900 chr1B 96.256 3285 90 15 4 3261 583563539 583560261 0.000000e+00 5354
13 TraesCS2D01G089900 chr6A 95.804 3313 93 17 1 3268 155855305 155858616 0.000000e+00 5306
14 TraesCS2D01G089900 chr6A 94.444 3438 145 23 1 3416 79193971 79197384 0.000000e+00 5249
15 TraesCS2D01G089900 chr1D 95.797 3236 91 7 4 3195 185745752 185742518 0.000000e+00 5180
16 TraesCS2D01G089900 chr1D 95.077 2844 80 10 615 3416 269428127 269425302 0.000000e+00 4421
17 TraesCS2D01G089900 chr1D 95.738 1009 25 2 2205 3195 185797629 185796621 0.000000e+00 1609
18 TraesCS2D01G089900 chrUn 93.448 870 15 4 2430 3258 417899046 417899914 0.000000e+00 1253
19 TraesCS2D01G089900 chrUn 94.487 653 19 1 2560 3195 422736166 422735514 0.000000e+00 990
20 TraesCS2D01G089900 chr7D 96.386 415 13 2 3002 3416 382029145 382028733 0.000000e+00 682
21 TraesCS2D01G089900 chr6B 89.542 306 29 3 2965 3269 401858376 401858679 5.350000e-103 385


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 TraesCS2D01G089900 chr2D 39654661 39658076 3415 False 6309 6309 100.000 1 3416 1 chr2D.!!$F1 3415
1 TraesCS2D01G089900 chr2D 291771636 291774911 3275 False 5031 5031 94.543 12 3258 1 chr2D.!!$F2 3246
2 TraesCS2D01G089900 chr2D 291679429 291679986 557 True 861 861 94.464 2702 3261 1 chr2D.!!$R1 559
3 TraesCS2D01G089900 chr4D 123348128 123351586 3458 False 5572 5572 95.954 1 3416 1 chr4D.!!$F1 3415
4 TraesCS2D01G089900 chr4D 134977427 134980887 3460 False 5502 5502 95.581 1 3416 1 chr4D.!!$F3 3415
5 TraesCS2D01G089900 chr4D 123561662 123562524 862 False 1173 1173 92.014 2595 3416 1 chr4D.!!$F2 821
6 TraesCS2D01G089900 chr7B 742947429 742950729 3300 True 5408 5408 96.457 4 3261 1 chr7B.!!$R1 3257
7 TraesCS2D01G089900 chr6D 370020526 370023968 3442 False 5385 5385 95.059 1 3416 1 chr6D.!!$F1 3415
8 TraesCS2D01G089900 chr5D 80017002 80020425 3423 True 5382 5382 95.106 4 3416 1 chr5D.!!$R1 3412
9 TraesCS2D01G089900 chr2A 755478554 755481855 3301 False 5376 5376 96.276 1 3258 1 chr2A.!!$F1 3257
10 TraesCS2D01G089900 chr7A 60167458 60170758 3300 True 5374 5374 96.275 4 3261 1 chr7A.!!$R1 3257
11 TraesCS2D01G089900 chr5A 420183709 420187008 3299 False 5363 5363 96.214 1 3258 1 chr5A.!!$F1 3257
12 TraesCS2D01G089900 chr1B 583560261 583563539 3278 True 5354 5354 96.256 4 3261 1 chr1B.!!$R1 3257
13 TraesCS2D01G089900 chr6A 155855305 155858616 3311 False 5306 5306 95.804 1 3268 1 chr6A.!!$F2 3267
14 TraesCS2D01G089900 chr6A 79193971 79197384 3413 False 5249 5249 94.444 1 3416 1 chr6A.!!$F1 3415
15 TraesCS2D01G089900 chr1D 185742518 185745752 3234 True 5180 5180 95.797 4 3195 1 chr1D.!!$R1 3191
16 TraesCS2D01G089900 chr1D 269425302 269428127 2825 True 4421 4421 95.077 615 3416 1 chr1D.!!$R3 2801
17 TraesCS2D01G089900 chr1D 185796621 185797629 1008 True 1609 1609 95.738 2205 3195 1 chr1D.!!$R2 990
18 TraesCS2D01G089900 chrUn 417899046 417899914 868 False 1253 1253 93.448 2430 3258 1 chrUn.!!$F1 828
19 TraesCS2D01G089900 chrUn 422735514 422736166 652 True 990 990 94.487 2560 3195 1 chrUn.!!$R1 635

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
613 618 0.324614 CCCTTTGCCAATGGAAACCC 59.675 55.0 10.76 0.0 0.00 4.11 F
1330 1338 0.321210 CATGTTAGGCCGTGTGGTCA 60.321 55.0 0.00 0.0 44.71 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2227 1.286501 GCCACTTCGCGATATTGTGA 58.713 50.0 23.67 1.84 0.0 3.58 R
3316 3446 0.681887 TACTCCCGATCCGAAGCACA 60.682 55.0 0.00 0.00 0.0 4.57 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
37 38 6.798315 ATTAATGATCAGAGAAGCGAATGG 57.202 37.500 0.09 0.00 0.00 3.16
414 417 7.010160 AGGCTGCTATATCTAGAAAGAGAAGT 58.990 38.462 0.00 0.00 34.49 3.01
613 618 0.324614 CCCTTTGCCAATGGAAACCC 59.675 55.000 10.76 0.00 0.00 4.11
623 628 3.100671 CAATGGAAACCCGGGGAAATAA 58.899 45.455 27.92 5.91 0.00 1.40
681 686 9.624697 GTATAAAGTGATTCTTGCAATTTCACA 57.375 29.630 25.64 13.88 39.27 3.58
710 715 1.324736 CGTAGCAATTCTCGCAGGAAC 59.675 52.381 0.00 0.00 0.00 3.62
711 716 2.346803 GTAGCAATTCTCGCAGGAACA 58.653 47.619 0.00 0.00 0.00 3.18
752 757 3.361281 TCCTTAACGAGAGCCTAGTCA 57.639 47.619 0.00 0.00 0.00 3.41
799 804 1.184431 TTTCGGTATGGGTACGCTGA 58.816 50.000 11.59 0.00 0.00 4.26
908 913 0.455815 GATGCCCGGTTCACCAAATC 59.544 55.000 0.00 0.00 35.14 2.17
1191 1196 1.247567 CCAGCGGTGTGAAAGGAATT 58.752 50.000 14.40 0.00 0.00 2.17
1303 1311 2.094442 TCTATTGTGGATGTTCGTGCGA 60.094 45.455 0.00 0.00 0.00 5.10
1310 1318 1.671850 GGATGTTCGTGCGAGAAAGGA 60.672 52.381 0.00 0.00 0.00 3.36
1330 1338 0.321210 CATGTTAGGCCGTGTGGTCA 60.321 55.000 0.00 0.00 44.71 4.02
1372 1380 1.072266 TGGAAAAGGGGCTCTAAGCA 58.928 50.000 0.86 0.00 44.75 3.91
1583 1619 4.443315 CCAAAAGCAAATGAACTCAAGGGT 60.443 41.667 0.00 0.00 0.00 4.34
1677 1713 9.467258 CAATTAGTTCAAATTCTTTCAGAAGCA 57.533 29.630 0.00 0.00 37.69 3.91
1756 1792 3.905591 CCAATTTCTGGCCCCATATTCAT 59.094 43.478 0.00 0.00 38.76 2.57
1943 1979 4.530710 TCTTAGAAAGAGCCGCTAAACA 57.469 40.909 0.00 0.00 32.71 2.83
1947 1983 3.674997 AGAAAGAGCCGCTAAACAATCA 58.325 40.909 0.00 0.00 0.00 2.57
2037 2073 4.227300 GCCTATATCCCCACCAATGTGATA 59.773 45.833 0.00 0.00 45.76 2.15
2096 2132 5.460419 AGCTCTTTTATCGCAGAATTAGACG 59.540 40.000 0.00 0.00 43.58 4.18
2145 2181 4.148825 GTCGGGTCTGCCGCTCAT 62.149 66.667 0.00 0.00 34.97 2.90
2167 2203 7.370383 TCATTTGAAAGCTATGAAACAAGTCC 58.630 34.615 0.00 0.00 0.00 3.85
2174 2210 1.435577 ATGAAACAAGTCCGCGGTAC 58.564 50.000 27.15 21.07 0.00 3.34
2191 2227 4.261447 GCGGTACTTCAAAACTGGAATTGT 60.261 41.667 0.00 0.00 0.00 2.71
2536 2574 7.968405 CACTTTGCCTTACCTGTGAATTAATAC 59.032 37.037 0.00 0.00 0.00 1.89
3051 3180 5.641209 CGTCCTCAGTTCTTTGATTCATTCT 59.359 40.000 0.00 0.00 0.00 2.40
3058 3187 3.411446 TCTTTGATTCATTCTGTGGCGT 58.589 40.909 0.00 0.00 0.00 5.68
3085 3214 5.581126 TCCATCATTGGCTAAACAATCAC 57.419 39.130 0.00 0.00 43.29 3.06
3161 3290 3.958798 CCAATGATGGCCTTTCTGATCTT 59.041 43.478 3.32 0.00 40.58 2.40
3171 3300 8.137745 TGGCCTTTCTGATCTTATTCATTTTT 57.862 30.769 3.32 0.00 0.00 1.94
3302 3431 6.045318 TGATTTTGACGATTGGATCTCTCTC 58.955 40.000 0.00 0.00 0.00 3.20
3313 3442 6.572182 TTGGATCTCTCTCTGAATGGAAAT 57.428 37.500 0.00 0.00 0.00 2.17
3316 3446 5.163216 GGATCTCTCTCTGAATGGAAATGGT 60.163 44.000 0.00 0.00 0.00 3.55
3356 3486 2.962859 ACCACTTTTGAAAGGGCAGAT 58.037 42.857 8.23 0.00 38.11 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.201127 CATTCGCTTCTCTGATCATTAATAAGA 57.799 33.333 0.00 0.00 0.00 2.10
19 20 1.945387 GCCATTCGCTTCTCTGATCA 58.055 50.000 0.00 0.00 0.00 2.92
37 38 5.509622 GCACTTTTCAATCAATTACGAGAGC 59.490 40.000 0.00 0.00 0.00 4.09
262 265 4.759782 TCTTTATGCTCTCGCTAGCTTTT 58.240 39.130 13.93 0.00 43.19 2.27
414 417 9.487790 CTTTGCTAATAATCCAAAACCTTTCAA 57.512 29.630 0.00 0.00 0.00 2.69
450 453 6.978674 TGTAAGTGCCTAGCTGAGTAATAT 57.021 37.500 0.00 0.00 0.00 1.28
488 491 2.304761 GACCAGACCCATGTGGAACTTA 59.695 50.000 7.06 0.00 42.06 2.24
600 605 3.074369 CCCCGGGTTTCCATTGGC 61.074 66.667 21.85 0.00 0.00 4.52
613 618 4.718940 ATTGAGCAACTTTATTTCCCCG 57.281 40.909 0.00 0.00 0.00 5.73
623 628 6.680810 TGAAATCGAATGAATTGAGCAACTT 58.319 32.000 0.00 0.00 0.00 2.66
681 686 1.372087 GAATTGCTACGCTGCCTGCT 61.372 55.000 0.00 0.00 40.11 4.24
710 715 1.883021 GGCCCAAACAAGACCGATG 59.117 57.895 0.00 0.00 0.00 3.84
711 716 1.674322 CGGCCCAAACAAGACCGAT 60.674 57.895 0.00 0.00 46.71 4.18
752 757 5.715434 TTACTCTTTTTATGGGCGCTTTT 57.285 34.783 7.64 0.00 0.00 2.27
814 819 3.100671 CCTGGTCTCTACCTTGCTTACT 58.899 50.000 0.00 0.00 46.91 2.24
908 913 9.218359 CTTCACACAATCTCGATTTGAATTATG 57.782 33.333 13.42 5.25 29.78 1.90
1191 1196 7.613022 ACATTCTCATTCTCAAGATTTAAGGCA 59.387 33.333 0.00 0.00 0.00 4.75
1303 1311 1.628846 ACGGCCTAACATGTCCTTTCT 59.371 47.619 0.00 0.00 0.00 2.52
1310 1318 0.321298 GACCACACGGCCTAACATGT 60.321 55.000 0.00 0.00 34.57 3.21
1330 1338 1.875488 ATAGGTACTCCCAAGGCGTT 58.125 50.000 0.00 0.00 41.75 4.84
1583 1619 9.671279 AATACAATGTATCACTCTCATTTGTGA 57.329 29.630 6.34 0.00 45.56 3.58
1832 1868 3.206150 GACATTTGTCGATATGCCACCT 58.794 45.455 0.00 0.00 35.12 4.00
1894 1930 6.546034 CGGGAATGTAAATAGAAAACATCCCT 59.454 38.462 14.56 0.00 38.03 4.20
1961 1997 1.667724 GTAACGCAGTCGAGCTACCTA 59.332 52.381 0.00 0.00 45.00 3.08
2096 2132 4.150098 CGGATAAGCCAACGTTAATAGCTC 59.850 45.833 0.00 0.00 35.94 4.09
2145 2181 5.757886 CGGACTTGTTTCATAGCTTTCAAA 58.242 37.500 0.00 0.00 0.00 2.69
2167 2203 1.504359 TCCAGTTTTGAAGTACCGCG 58.496 50.000 0.00 0.00 0.00 6.46
2174 2210 9.132521 GATATTGTGACAATTCCAGTTTTGAAG 57.867 33.333 16.75 0.00 0.00 3.02
2191 2227 1.286501 GCCACTTCGCGATATTGTGA 58.713 50.000 23.67 1.84 0.00 3.58
2365 2401 2.120232 GTCTAGTGGCATTCGATCACG 58.880 52.381 0.00 0.00 41.26 4.35
2643 2681 1.269448 CTTGGTTTACGCATGGCACTT 59.731 47.619 0.00 0.00 0.00 3.16
2644 2682 0.881118 CTTGGTTTACGCATGGCACT 59.119 50.000 0.00 0.00 0.00 4.40
2705 2743 2.047830 GGGTGGGGTATCCTGAACTAG 58.952 57.143 0.00 0.00 36.20 2.57
3051 3180 2.127271 ATGATGGATTTCACGCCACA 57.873 45.000 0.00 0.00 36.92 4.17
3058 3187 6.602410 TTGTTTAGCCAATGATGGATTTCA 57.398 33.333 0.00 0.00 44.90 2.69
3161 3290 9.781834 ACTTTTTATGCGATCGAAAAATGAATA 57.218 25.926 21.57 5.78 33.04 1.75
3171 3300 5.348164 TCTCATGACTTTTTATGCGATCGA 58.652 37.500 21.57 4.34 0.00 3.59
3302 3431 3.671433 CGAAGCACACCATTTCCATTCAG 60.671 47.826 0.00 0.00 0.00 3.02
3313 3442 2.264480 CCGATCCGAAGCACACCA 59.736 61.111 0.00 0.00 0.00 4.17
3316 3446 0.681887 TACTCCCGATCCGAAGCACA 60.682 55.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.