Multiple sequence alignment - TraesCS2D01G127100

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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 TraesCS2D01G127100 chr2D 100.000 3305 0 0 1 3305 73856250 73852946 0 6104
1 TraesCS2D01G127100 chr2B 94.153 2514 102 18 811 3305 111690448 111687961 0 3786
2 TraesCS2D01G127100 chr2B 88.688 831 53 12 1 819 111861430 111860629 0 976
3 TraesCS2D01G127100 chr2A 93.155 2542 102 24 802 3305 73201346 73198839 0 3664
4 TraesCS2D01G127100 chr2A 88.303 778 57 16 1 770 73203707 73202956 0 902
5 TraesCS2D01G127100 chr1D 91.508 895 63 8 1077 1969 404760036 404759153 0 1219


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 TraesCS2D01G127100 chr2D 73852946 73856250 3304 True 6104 6104 100.000 1 3305 1 chr2D.!!$R1 3304
1 TraesCS2D01G127100 chr2B 111687961 111690448 2487 True 3786 3786 94.153 811 3305 1 chr2B.!!$R1 2494
2 TraesCS2D01G127100 chr2B 111860629 111861430 801 True 976 976 88.688 1 819 1 chr2B.!!$R2 818
3 TraesCS2D01G127100 chr2A 73198839 73203707 4868 True 2283 3664 90.729 1 3305 2 chr2A.!!$R1 3304
4 TraesCS2D01G127100 chr1D 404759153 404760036 883 True 1219 1219 91.508 1077 1969 1 chr1D.!!$R1 892

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
573 586 0.470766 ACGGGTTTGCCTGACAGTTA 59.529 50.0 0.93 0.0 43.97 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 4169 0.331278 TCGGGCCAAACATCAAGGAT 59.669 50.0 4.39 0.0 0.0 3.24 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
142 147 7.928873 TGACCTCTCTTCCCTTACAAAATAAT 58.071 34.615 0.00 0.00 0.00 1.28
143 148 8.390921 TGACCTCTCTTCCCTTACAAAATAATT 58.609 33.333 0.00 0.00 0.00 1.40
144 149 9.901172 GACCTCTCTTCCCTTACAAAATAATTA 57.099 33.333 0.00 0.00 0.00 1.40
145 150 9.682465 ACCTCTCTTCCCTTACAAAATAATTAC 57.318 33.333 0.00 0.00 0.00 1.89
146 151 9.681062 CCTCTCTTCCCTTACAAAATAATTACA 57.319 33.333 0.00 0.00 0.00 2.41
205 210 3.413327 TGCATTGCATGGCTTTGAAAAT 58.587 36.364 7.38 0.00 31.71 1.82
215 220 9.092338 TGCATGGCTTTGAAAATATAGGAATAT 57.908 29.630 0.00 0.00 0.00 1.28
216 221 9.578439 GCATGGCTTTGAAAATATAGGAATATC 57.422 33.333 0.00 0.00 0.00 1.63
218 223 8.650143 TGGCTTTGAAAATATAGGAATATCCC 57.350 34.615 0.00 0.00 37.19 3.85
219 224 8.456124 TGGCTTTGAAAATATAGGAATATCCCT 58.544 33.333 0.00 0.00 37.19 4.20
220 225 9.975218 GGCTTTGAAAATATAGGAATATCCCTA 57.025 33.333 0.00 0.00 42.51 3.53
466 479 7.707624 TGATGCAAAGAGACCATTAGAATTT 57.292 32.000 0.00 0.00 0.00 1.82
573 586 0.470766 ACGGGTTTGCCTGACAGTTA 59.529 50.000 0.93 0.00 43.97 2.24
688 705 5.578005 AAGATGACATGCATTCTGGAAAG 57.422 39.130 0.00 0.00 37.34 2.62
689 706 4.851843 AGATGACATGCATTCTGGAAAGA 58.148 39.130 0.00 0.00 37.34 2.52
701 718 0.602562 TGGAAAGAAAATGCCAGGCG 59.397 50.000 7.03 0.00 0.00 5.52
739 757 2.036098 TCCCCTAGCGACCGTTCA 59.964 61.111 0.00 0.00 0.00 3.18
745 763 1.337821 CTAGCGACCGTTCACTGAAC 58.662 55.000 11.37 11.37 38.97 3.18
751 769 0.951558 ACCGTTCACTGAACATTGGC 59.048 50.000 19.61 0.00 42.05 4.52
769 787 3.541632 TGGCGTCTTTTCTCTTTTGAGT 58.458 40.909 0.00 0.00 46.30 3.41
1160 2801 2.278401 CGCCCTAAGGTACGACGC 60.278 66.667 0.00 0.00 34.57 5.19
1162 2803 2.764314 GCCCTAAGGTACGACGCGA 61.764 63.158 15.93 0.00 34.57 5.87
1165 2806 1.712977 CCTAAGGTACGACGCGAGCT 61.713 60.000 15.93 1.17 0.00 4.09
1169 2810 1.583194 GGTACGACGCGAGCTCTTC 60.583 63.158 15.93 4.54 0.00 2.87
1170 2811 1.424635 GTACGACGCGAGCTCTTCT 59.575 57.895 15.93 0.00 0.00 2.85
1186 2828 4.331443 GCTCTTCTTTTCGGGATTCTTCTC 59.669 45.833 0.00 0.00 0.00 2.87
1193 2835 5.693769 TTTCGGGATTCTTCTCCTGTATT 57.306 39.130 0.00 0.00 41.67 1.89
1202 2844 8.361139 GGATTCTTCTCCTGTATTTTCGATCTA 58.639 37.037 0.00 0.00 32.18 1.98
1210 2852 9.703892 CTCCTGTATTTTCGATCTAGATGAAAT 57.296 33.333 20.96 18.67 32.20 2.17
1222 2864 7.219535 CGATCTAGATGAAATTTTTGGTGCTTG 59.780 37.037 10.74 0.00 0.00 4.01
1227 2872 3.686726 TGAAATTTTTGGTGCTTGCGTTT 59.313 34.783 0.00 0.00 0.00 3.60
1228 2873 4.870426 TGAAATTTTTGGTGCTTGCGTTTA 59.130 33.333 0.00 0.00 0.00 2.01
1229 2874 5.525378 TGAAATTTTTGGTGCTTGCGTTTAT 59.475 32.000 0.00 0.00 0.00 1.40
1418 3063 5.769662 TCCTGCAATGTTTGATTACTTCACT 59.230 36.000 0.00 0.00 32.84 3.41
1419 3064 6.265196 TCCTGCAATGTTTGATTACTTCACTT 59.735 34.615 0.00 0.00 32.84 3.16
1421 3066 7.036996 TGCAATGTTTGATTACTTCACTTCA 57.963 32.000 0.00 0.00 32.84 3.02
1422 3067 6.917477 TGCAATGTTTGATTACTTCACTTCAC 59.083 34.615 0.00 0.00 32.84 3.18
1433 3079 4.315803 ACTTCACTTCACCTATGAAACCG 58.684 43.478 0.00 0.00 44.28 4.44
1462 3108 5.861222 TCGTATATGTGCTATTTGCCATG 57.139 39.130 0.00 0.00 42.00 3.66
1475 3123 1.451028 GCCATGGAGAGTGGTCTGC 60.451 63.158 18.40 0.00 41.47 4.26
1497 3145 4.275936 GCATTTGCTAAGTATCCACCGAAT 59.724 41.667 0.00 0.00 38.21 3.34
1509 3157 1.508632 CACCGAATTCCAAGTCACGT 58.491 50.000 0.00 0.00 0.00 4.49
1519 3167 1.459592 CCAAGTCACGTCCGTTCATTC 59.540 52.381 0.00 0.00 0.00 2.67
1529 3177 6.798476 TCACGTCCGTTCATTCGTAATATATC 59.202 38.462 0.00 0.00 35.13 1.63
1568 3216 6.923508 GGGTAAAGAGAGACCAAAACAATTTG 59.076 38.462 0.00 0.00 44.50 2.32
1727 3383 4.841443 TGCATAAATAGGAGCTGCAATG 57.159 40.909 8.35 4.29 39.68 2.82
1893 3549 7.559590 AATCAGTTAGATGCATTAAGTGGTC 57.440 36.000 22.45 4.71 36.96 4.02
2001 3657 6.774354 TTAGAGACGCGTTATTGTTTCTTT 57.226 33.333 15.53 0.42 32.50 2.52
2036 3692 2.472695 TGTTACTCGAAGCTGCCATT 57.527 45.000 0.00 0.00 0.00 3.16
2084 3740 7.858052 AAAACTTTGCGATTAGAGACAATTG 57.142 32.000 3.24 3.24 0.00 2.32
2181 3837 9.744468 TTTGGTTTCTTGAAAAACTCTATAAGC 57.256 29.630 0.00 0.00 38.81 3.09
2346 4003 3.307059 GCAGACTAAATCCAGTCACCACT 60.307 47.826 6.08 0.00 46.15 4.00
2379 4036 4.876679 GTCTGGCCAGATTTTAAGTAGGAC 59.123 45.833 37.07 17.06 39.97 3.85
2421 4078 9.829507 CATATATTCTATCAATCTTCCTCCCAC 57.170 37.037 0.00 0.00 0.00 4.61
2494 4151 4.226384 AGACATCTATGACCATGGCTGTA 58.774 43.478 13.04 0.81 36.97 2.74
2495 4152 4.842948 AGACATCTATGACCATGGCTGTAT 59.157 41.667 13.04 3.76 36.97 2.29
2512 4169 5.997746 GGCTGTATGAATCCTGTAATTGCTA 59.002 40.000 0.00 0.00 0.00 3.49
2827 4484 5.670361 ACATCCTTAGCTTATTACCTGGGAA 59.330 40.000 0.00 0.00 0.00 3.97
2828 4485 6.332901 ACATCCTTAGCTTATTACCTGGGAAT 59.667 38.462 9.55 9.55 0.00 3.01
2869 4526 5.564651 GCCGCAATAATACCATGTATGCTTT 60.565 40.000 0.00 0.00 0.00 3.51
3062 4719 4.042062 TGAATGATCTCTTGTTGTGGGAGT 59.958 41.667 0.00 0.00 0.00 3.85
3084 4743 2.760650 CTGGTGTGACTGATGGTAGCTA 59.239 50.000 0.00 0.00 0.00 3.32
3202 4861 2.939460 ATAACAGAATTTGGTGGCGC 57.061 45.000 0.00 0.00 0.00 6.53
3204 4863 1.452145 AACAGAATTTGGTGGCGCGT 61.452 50.000 8.43 0.00 0.00 6.01
3255 4914 4.377943 GGCCGTATTGTTTTGCCATTTTTC 60.378 41.667 0.00 0.00 41.76 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 111 6.846505 AGGGAAGAGAGGTCATGTTATATCAA 59.153 38.462 0.00 0.00 0.00 2.57
151 156 9.981114 CTCTTAAAACACCTTTCCAACATAATT 57.019 29.630 0.00 0.00 0.00 1.40
152 157 8.088365 GCTCTTAAAACACCTTTCCAACATAAT 58.912 33.333 0.00 0.00 0.00 1.28
153 158 7.430441 GCTCTTAAAACACCTTTCCAACATAA 58.570 34.615 0.00 0.00 0.00 1.90
167 172 5.531634 CAATGCAAAGAGGCTCTTAAAACA 58.468 37.500 28.78 22.37 35.27 2.83
216 221 4.100189 AGACGTTTCAATCATCCTCTAGGG 59.900 45.833 0.00 0.00 35.41 3.53
217 222 5.269505 AGACGTTTCAATCATCCTCTAGG 57.730 43.478 0.00 0.00 0.00 3.02
218 223 8.703604 TTTAAGACGTTTCAATCATCCTCTAG 57.296 34.615 0.00 0.00 0.00 2.43
219 224 8.311836 ACTTTAAGACGTTTCAATCATCCTCTA 58.688 33.333 0.00 0.00 0.00 2.43
220 225 7.162082 ACTTTAAGACGTTTCAATCATCCTCT 58.838 34.615 0.00 0.00 0.00 3.69
221 226 7.365840 ACTTTAAGACGTTTCAATCATCCTC 57.634 36.000 0.00 0.00 0.00 3.71
222 227 9.449719 AATACTTTAAGACGTTTCAATCATCCT 57.550 29.630 0.00 0.00 0.00 3.24
223 228 9.490663 CAATACTTTAAGACGTTTCAATCATCC 57.509 33.333 0.00 0.00 0.00 3.51
309 318 5.291128 AGGAATCTTAATGTACGCTCAAACG 59.709 40.000 0.00 0.00 39.50 3.60
466 479 1.879380 CACCTCATTCGCCTTGTCAAA 59.121 47.619 0.00 0.00 0.00 2.69
534 547 2.672961 TCGTTTGTCATCTAGCCCAG 57.327 50.000 0.00 0.00 0.00 4.45
535 548 2.695359 GTTCGTTTGTCATCTAGCCCA 58.305 47.619 0.00 0.00 0.00 5.36
596 613 1.880027 GAACGGCCAGAAAACTGTCAT 59.120 47.619 2.24 0.00 0.00 3.06
599 616 1.676006 CAAGAACGGCCAGAAAACTGT 59.324 47.619 2.24 0.00 0.00 3.55
632 649 5.178797 GCATAGCAGTTTCTGTTAGGAAGA 58.821 41.667 8.83 0.00 32.35 2.87
684 701 2.723124 TTCGCCTGGCATTTTCTTTC 57.277 45.000 20.29 0.00 0.00 2.62
688 705 2.368655 ACATTTCGCCTGGCATTTTC 57.631 45.000 20.29 0.00 0.00 2.29
689 706 2.687370 GAACATTTCGCCTGGCATTTT 58.313 42.857 20.29 4.04 0.00 1.82
701 718 3.514645 AGATGGCATTTGCGAACATTTC 58.485 40.909 0.00 0.00 43.26 2.17
739 757 3.214328 AGAAAAGACGCCAATGTTCAGT 58.786 40.909 0.00 0.00 0.00 3.41
745 763 4.858935 TCAAAAGAGAAAAGACGCCAATG 58.141 39.130 0.00 0.00 0.00 2.82
1160 2801 2.301577 ATCCCGAAAAGAAGAGCTCG 57.698 50.000 8.37 0.00 0.00 5.03
1162 2803 3.990959 AGAATCCCGAAAAGAAGAGCT 57.009 42.857 0.00 0.00 0.00 4.09
1165 2806 4.532521 AGGAGAAGAATCCCGAAAAGAAGA 59.467 41.667 0.00 0.00 40.53 2.87
1169 2810 3.944087 ACAGGAGAAGAATCCCGAAAAG 58.056 45.455 0.00 0.00 40.53 2.27
1170 2811 5.693769 ATACAGGAGAAGAATCCCGAAAA 57.306 39.130 0.00 0.00 40.53 2.29
1193 2835 7.754924 GCACCAAAAATTTCATCTAGATCGAAA 59.245 33.333 21.83 21.83 33.48 3.46
1202 2844 3.742369 CGCAAGCACCAAAAATTTCATCT 59.258 39.130 0.00 0.00 0.00 2.90
1210 2852 3.126831 CCATAAACGCAAGCACCAAAAA 58.873 40.909 0.00 0.00 45.62 1.94
1211 2853 2.101582 ACCATAAACGCAAGCACCAAAA 59.898 40.909 0.00 0.00 45.62 2.44
1222 2864 2.870411 GACCTCCATGTACCATAAACGC 59.130 50.000 0.00 0.00 0.00 4.84
1227 2872 1.045407 GGCGACCTCCATGTACCATA 58.955 55.000 0.00 0.00 0.00 2.74
1228 2873 1.830145 GGCGACCTCCATGTACCAT 59.170 57.895 0.00 0.00 0.00 3.55
1229 2874 2.717044 CGGCGACCTCCATGTACCA 61.717 63.158 0.00 0.00 0.00 3.25
1418 3063 3.482436 ACAAAGCGGTTTCATAGGTGAA 58.518 40.909 10.13 0.00 42.41 3.18
1419 3064 3.134574 ACAAAGCGGTTTCATAGGTGA 57.865 42.857 10.13 0.00 0.00 4.02
1421 3066 2.482721 CGAACAAAGCGGTTTCATAGGT 59.517 45.455 10.13 1.74 0.00 3.08
1422 3067 2.482721 ACGAACAAAGCGGTTTCATAGG 59.517 45.455 10.13 1.05 0.00 2.57
1433 3079 6.140737 GCAAATAGCACATATACGAACAAAGC 59.859 38.462 0.00 0.00 44.79 3.51
1462 3108 0.807496 GCAAATGCAGACCACTCTCC 59.193 55.000 0.00 0.00 41.59 3.71
1475 3123 6.377327 AATTCGGTGGATACTTAGCAAATG 57.623 37.500 0.00 0.00 37.61 2.32
1497 3145 0.460722 TGAACGGACGTGACTTGGAA 59.539 50.000 0.00 0.00 0.00 3.53
1509 3157 6.683715 TGCAGATATATTACGAATGAACGGA 58.316 36.000 0.00 0.00 37.61 4.69
1568 3216 9.256477 TGACCATGACGATAATCTAATAAACAC 57.744 33.333 0.00 0.00 0.00 3.32
1727 3383 7.923414 AGTAATGATTTCCAGGTTGAGTTAC 57.077 36.000 0.00 0.00 0.00 2.50
1973 3629 8.287503 AGAAACAATAACGCGTCTCTAATTTTT 58.712 29.630 14.44 4.98 0.00 1.94
1974 3630 7.803724 AGAAACAATAACGCGTCTCTAATTTT 58.196 30.769 14.44 6.57 0.00 1.82
1975 3631 7.360575 AGAAACAATAACGCGTCTCTAATTT 57.639 32.000 14.44 9.61 0.00 1.82
1976 3632 6.963049 AGAAACAATAACGCGTCTCTAATT 57.037 33.333 14.44 4.42 0.00 1.40
1978 3634 6.774354 AAAGAAACAATAACGCGTCTCTAA 57.226 33.333 14.44 0.00 0.00 2.10
1979 3635 6.774354 AAAAGAAACAATAACGCGTCTCTA 57.226 33.333 14.44 0.72 0.00 2.43
1981 3637 6.515340 CAGTAAAAGAAACAATAACGCGTCTC 59.485 38.462 14.44 0.82 0.00 3.36
1982 3638 6.018507 ACAGTAAAAGAAACAATAACGCGTCT 60.019 34.615 14.44 5.62 0.00 4.18
1983 3639 6.131389 ACAGTAAAAGAAACAATAACGCGTC 58.869 36.000 14.44 0.00 0.00 5.19
2001 3657 5.176774 CGAGTAACATGTCTTGCAACAGTAA 59.823 40.000 0.00 0.00 31.50 2.24
2181 3837 5.399301 CAGAAGCAAACCATCAAAAACTACG 59.601 40.000 0.00 0.00 0.00 3.51
2267 3924 2.890311 CCAGCTGGGTTGTCAATACAAA 59.110 45.455 26.14 0.00 46.84 2.83
2278 3935 1.973281 CGTCATTGCCAGCTGGGTT 60.973 57.895 33.46 2.30 39.65 4.11
2494 4151 7.520798 TCAAGGATAGCAATTACAGGATTCAT 58.479 34.615 0.00 0.00 0.00 2.57
2495 4152 6.899089 TCAAGGATAGCAATTACAGGATTCA 58.101 36.000 0.00 0.00 0.00 2.57
2512 4169 0.331278 TCGGGCCAAACATCAAGGAT 59.669 50.000 4.39 0.00 0.00 3.24
2827 4484 3.305964 CGGCTAACAATCATCGTACGAT 58.694 45.455 24.66 24.66 34.81 3.73
2828 4485 2.723209 CGGCTAACAATCATCGTACGA 58.277 47.619 21.93 21.93 0.00 3.43
3062 4719 1.550524 GCTACCATCAGTCACACCAGA 59.449 52.381 0.00 0.00 0.00 3.86
3084 4743 1.717077 TCAGTGGGAGAGGTCCTTAGT 59.283 52.381 0.00 0.00 43.36 2.24
3255 4914 4.837567 AGTTATACCGTAACGCTAAGACG 58.162 43.478 0.00 0.00 39.50 4.18


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

AutoCloner maintained by Alex Coulton.