Multiple sequence alignment - TraesCS5D01G279500

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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 TraesCS5D01G279500 chr5D 100.000 3158 0 0 1 3158 381563954 381567111 0.000000e+00 5832.0
1 TraesCS5D01G279500 chr5D 93.295 1745 102 10 491 2224 390706960 390708700 0.000000e+00 2560.0
2 TraesCS5D01G279500 chr5D 91.414 1188 100 2 980 2166 393555474 393556660 0.000000e+00 1628.0
3 TraesCS5D01G279500 chr5D 85.017 1188 172 6 980 2167 393814574 393813393 0.000000e+00 1203.0
4 TraesCS5D01G279500 chr5D 85.004 1187 170 7 981 2167 393848899 393847721 0.000000e+00 1199.0
5 TraesCS5D01G279500 chr5D 88.056 360 42 1 596 954 393849317 393848958 2.910000e-115 425.0
6 TraesCS5D01G279500 chr5D 86.111 360 49 1 596 954 393814991 393814632 1.370000e-103 387.0
7 TraesCS5D01G279500 chr5D 91.743 218 14 3 1 217 390706525 390706739 1.840000e-77 300.0
8 TraesCS5D01G279500 chr5D 93.684 95 6 0 274 368 210384624 210384718 3.280000e-30 143.0
9 TraesCS5D01G279500 chr5D 82.517 143 25 0 1834 1976 375407499 375407357 3.310000e-25 126.0
10 TraesCS5D01G279500 chr5D 77.640 161 32 4 1819 1977 404882223 404882381 9.320000e-16 95.3
11 TraesCS5D01G279500 chr5B 96.764 2658 59 17 1 2631 457395479 457398136 0.000000e+00 4407.0
12 TraesCS5D01G279500 chr5B 92.993 1370 86 7 491 1853 471134508 471135874 0.000000e+00 1989.0
13 TraesCS5D01G279500 chr5B 91.345 1190 100 1 980 2166 473193425 473194614 0.000000e+00 1624.0
14 TraesCS5D01G279500 chr5B 93.158 380 25 1 1846 2224 471136608 471136987 9.890000e-155 556.0
15 TraesCS5D01G279500 chr5B 93.294 343 21 1 2816 3158 457399000 457399340 3.640000e-139 505.0
16 TraesCS5D01G279500 chr5B 84.787 493 59 10 477 954 473665175 473664684 6.130000e-132 481.0
17 TraesCS5D01G279500 chr5B 80.912 592 82 17 385 961 473192798 473193373 3.740000e-119 438.0
18 TraesCS5D01G279500 chr5B 92.202 218 13 3 1 217 471134073 471134287 3.960000e-79 305.0
19 TraesCS5D01G279500 chr5B 83.439 314 35 13 2705 3013 101827259 101827560 3.100000e-70 276.0
20 TraesCS5D01G279500 chr5B 95.238 84 4 0 2628 2711 457398746 457398829 1.980000e-27 134.0
21 TraesCS5D01G279500 chr5B 82.517 143 25 0 1834 1976 448274397 448274255 3.310000e-25 126.0
22 TraesCS5D01G279500 chr5A 92.314 1197 91 1 980 2175 495327598 495328794 0.000000e+00 1700.0
23 TraesCS5D01G279500 chr5A 85.533 1182 166 5 986 2167 495879401 495878225 0.000000e+00 1230.0
24 TraesCS5D01G279500 chr5A 85.124 484 66 5 477 954 495879949 495879466 1.020000e-134 490.0
25 TraesCS5D01G279500 chr5A 80.161 620 93 20 385 989 495326970 495327574 1.340000e-118 436.0
26 TraesCS5D01G279500 chr5A 78.644 295 51 11 2725 3013 68970361 68970649 5.380000e-43 185.0
27 TraesCS5D01G279500 chr5A 85.714 147 19 2 3010 3155 552640956 552641101 1.520000e-33 154.0
28 TraesCS5D01G279500 chr4A 83.807 352 47 9 2669 3013 667055875 667055527 3.040000e-85 326.0
29 TraesCS5D01G279500 chr4A 80.592 304 50 7 2715 3013 700328518 700328817 3.170000e-55 226.0
30 TraesCS5D01G279500 chr6B 83.481 339 48 6 2678 3013 664033433 664033100 3.060000e-80 309.0
31 TraesCS5D01G279500 chrUn 79.587 387 62 9 2630 3012 291834635 291834262 8.690000e-66 261.0
32 TraesCS5D01G279500 chr3B 89.151 212 17 4 2794 3002 794846224 794846432 3.120000e-65 259.0
33 TraesCS5D01G279500 chr3B 84.667 150 21 2 3010 3158 382324401 382324253 7.060000e-32 148.0
34 TraesCS5D01G279500 chr3B 94.186 86 5 0 276 361 265853271 265853356 7.110000e-27 132.0
35 TraesCS5D01G279500 chr7A 79.679 374 52 16 2649 3011 192373951 192373591 6.760000e-62 248.0
36 TraesCS5D01G279500 chr7A 83.230 161 19 6 2997 3155 535465482 535465328 1.180000e-29 141.0
37 TraesCS5D01G279500 chr4D 80.352 341 53 9 2675 3010 319112772 319113103 2.430000e-61 246.0
38 TraesCS5D01G279500 chr6A 86.709 158 17 4 3002 3158 590210705 590210551 4.190000e-39 172.0
39 TraesCS5D01G279500 chr6A 94.318 88 5 0 277 364 97081401 97081314 5.490000e-28 135.0
40 TraesCS5D01G279500 chr6D 86.000 150 19 2 3010 3158 441674586 441674438 3.260000e-35 159.0
41 TraesCS5D01G279500 chr6D 91.667 96 7 1 274 368 291239463 291239558 7.110000e-27 132.0
42 TraesCS5D01G279500 chr6D 91.489 94 8 0 268 361 91566717 91566810 2.560000e-26 130.0
43 TraesCS5D01G279500 chr7B 86.395 147 16 4 3010 3155 489641582 489641725 1.170000e-34 158.0
44 TraesCS5D01G279500 chr7B 91.000 100 8 1 262 361 539785138 539785040 1.980000e-27 134.0
45 TraesCS5D01G279500 chr2A 84.242 165 17 8 2997 3157 502270434 502270275 5.460000e-33 152.0
46 TraesCS5D01G279500 chr3D 85.034 147 20 2 3010 3155 612304140 612304285 7.060000e-32 148.0
47 TraesCS5D01G279500 chr7D 95.294 85 4 0 277 361 411331607 411331691 5.490000e-28 135.0
48 TraesCS5D01G279500 chr1D 92.473 93 7 0 272 364 93124879 93124787 1.980000e-27 134.0
49 TraesCS5D01G279500 chr4B 80.952 126 24 0 1849 1974 638844385 638844510 2.000000e-17 100.0


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 TraesCS5D01G279500 chr5D 381563954 381567111 3157 False 5832 5832 100.000000 1 3158 1 chr5D.!!$F2 3157
1 TraesCS5D01G279500 chr5D 393555474 393556660 1186 False 1628 1628 91.414000 980 2166 1 chr5D.!!$F3 1186
2 TraesCS5D01G279500 chr5D 390706525 390708700 2175 False 1430 2560 92.519000 1 2224 2 chr5D.!!$F5 2223
3 TraesCS5D01G279500 chr5D 393847721 393849317 1596 True 812 1199 86.530000 596 2167 2 chr5D.!!$R3 1571
4 TraesCS5D01G279500 chr5D 393813393 393814991 1598 True 795 1203 85.564000 596 2167 2 chr5D.!!$R2 1571
5 TraesCS5D01G279500 chr5B 457395479 457399340 3861 False 1682 4407 95.098667 1 3158 3 chr5B.!!$F2 3157
6 TraesCS5D01G279500 chr5B 473192798 473194614 1816 False 1031 1624 86.128500 385 2166 2 chr5B.!!$F4 1781
7 TraesCS5D01G279500 chr5B 471134073 471136987 2914 False 950 1989 92.784333 1 2224 3 chr5B.!!$F3 2223
8 TraesCS5D01G279500 chr5A 495326970 495328794 1824 False 1068 1700 86.237500 385 2175 2 chr5A.!!$F3 1790
9 TraesCS5D01G279500 chr5A 495878225 495879949 1724 True 860 1230 85.328500 477 2167 2 chr5A.!!$R1 1690

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
783 908 1.272769 GTGTAAGAGAACACGGGCTCT 59.727 52.381 0.0 0.0 43.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2712 4271 0.664166 GCACTGCCAATCCAAACACG 60.664 55.0 0.0 0.0 0.0 4.49 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
217 219 7.750229 ATTATGAACATATCTTTCACCGCAT 57.250 32.000 0.00 0.00 35.82 4.73
236 264 5.163513 CGCATTAACTTTCCAGCAGAAAAT 58.836 37.500 3.85 0.00 43.84 1.82
299 400 7.243824 ACTACTCCTTCCGTCCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
455 556 3.460825 TCCCTTCTGTTTATGCCTACCT 58.539 45.455 0.00 0.00 0.00 3.08
516 617 1.478105 GATTGTGCCATCCTTTCCCAC 59.522 52.381 0.00 0.00 0.00 4.61
783 908 1.272769 GTGTAAGAGAACACGGGCTCT 59.727 52.381 0.00 0.00 43.00 4.09
1254 1412 1.492993 GGCTCAGGTTCCTGGAGGTT 61.493 60.000 17.37 0.00 35.01 3.50
2012 2915 3.498397 CGGTGTTCTGGTGATATATTGGC 59.502 47.826 0.00 0.00 0.00 4.52
2076 2979 7.408756 TGCTTATAAATCAATCTTGGCTGTT 57.591 32.000 0.00 0.00 0.00 3.16
2284 3188 0.798776 CACCTGCCGTGATGAAGAAC 59.201 55.000 0.00 0.00 46.20 3.01
2301 3205 8.992835 ATGAAGAACTTCTGGCAAATTTATTC 57.007 30.769 14.31 1.66 40.14 1.75
2415 3319 7.725251 TGAAAGTAGCCTTTGATTCAAAACAT 58.275 30.769 12.62 4.57 40.98 2.71
2474 3378 1.280421 CAGCTGGAACCTTTAGGCTCT 59.720 52.381 5.57 0.00 39.32 4.09
2479 3383 1.065345 GGAACCTTTAGGCTCTGACCC 60.065 57.143 0.00 0.00 39.32 4.46
2480 3384 1.628846 GAACCTTTAGGCTCTGACCCA 59.371 52.381 0.00 0.00 39.32 4.51
2513 3417 4.025229 CGATTGGTTGTGATATTACACCCG 60.025 45.833 9.25 6.09 39.69 5.28
2531 3435 0.457851 CGGTTTTGGCTGGTGTTGAA 59.542 50.000 0.00 0.00 0.00 2.69
2587 3491 0.179124 CACAGCTCCTAGAAGGTCGC 60.179 60.000 0.00 0.00 36.53 5.19
2597 3501 2.047179 AAGGTCGCCCGCTTCTTC 60.047 61.111 0.00 0.00 35.12 2.87
2613 3517 4.282496 CTTCTTCTGCCCTAGAGAACCTA 58.718 47.826 0.00 0.00 36.61 3.08
2673 4190 3.440173 CCAAACAGACATGCGGTTTATCT 59.560 43.478 14.27 0.00 41.87 1.98
2691 4250 3.749665 TCTGCTTTTTGTCCATTTGGG 57.250 42.857 0.00 0.00 35.41 4.12
2719 4278 2.637025 CGCCCACTTCCGTGTTTG 59.363 61.111 0.00 0.00 39.55 2.93
2721 4280 1.527380 GCCCACTTCCGTGTTTGGA 60.527 57.895 0.00 0.00 39.55 3.53
2726 4285 0.958822 ACTTCCGTGTTTGGATTGGC 59.041 50.000 0.00 0.00 38.00 4.52
2732 4291 0.664166 GTGTTTGGATTGGCAGTGCG 60.664 55.000 9.45 0.00 0.00 5.34
2766 4325 3.758554 GACACATATTTGTCCTTGTGGCT 59.241 43.478 10.37 0.00 43.32 4.75
2785 4344 3.005791 GGCTGGTATGTGGCCATTTATTC 59.994 47.826 9.72 2.16 44.69 1.75
2790 4349 5.140454 GGTATGTGGCCATTTATTCCTTCT 58.860 41.667 9.72 0.00 32.29 2.85
2962 4546 2.160615 TCGATACAATTGGTTGCCAACG 59.839 45.455 10.83 1.91 46.95 4.10
2971 4555 2.904866 TTGCCAACGTGAGCCCAC 60.905 61.111 7.53 0.00 39.86 4.61
2983 4567 3.502164 AGCCCACATATGCTCAACC 57.498 52.632 1.58 0.00 30.33 3.77
2988 4572 3.118665 GCCCACATATGCTCAACCAAATT 60.119 43.478 1.58 0.00 0.00 1.82
3024 4608 4.377839 TGCGAGTTTCTGATAAGAGGAG 57.622 45.455 0.00 0.00 0.00 3.69
3036 4620 4.289672 TGATAAGAGGAGAAGCCAACCTTT 59.710 41.667 0.00 0.00 40.02 3.11
3037 4621 2.869101 AGAGGAGAAGCCAACCTTTC 57.131 50.000 0.00 0.00 40.02 2.62
3057 4641 2.679716 AGGGCATCCTCCTTGCAC 59.320 61.111 0.00 0.00 43.98 4.57
3066 4650 3.526931 TCCTCCTTGCACTCGAAATAG 57.473 47.619 0.00 0.00 0.00 1.73
3073 4657 4.804139 CCTTGCACTCGAAATAGTTATCGT 59.196 41.667 0.00 0.00 39.91 3.73
3077 4661 5.740569 TGCACTCGAAATAGTTATCGTACAC 59.259 40.000 0.00 0.00 39.91 2.90
3081 4665 4.037923 TCGAAATAGTTATCGTACACCCCC 59.962 45.833 0.00 0.00 39.91 5.40
3082 4666 4.038402 CGAAATAGTTATCGTACACCCCCT 59.962 45.833 0.00 0.00 34.48 4.79
3116 4700 7.148573 CCTGAATACAGTTGAACACATGTCTAC 60.149 40.741 0.00 0.00 42.05 2.59
3128 4712 3.126858 CACATGTCTACCCATCCAAAACG 59.873 47.826 0.00 0.00 0.00 3.60
3130 4714 1.700739 TGTCTACCCATCCAAAACGGT 59.299 47.619 0.00 0.00 35.57 4.83
3135 4719 1.969064 CCATCCAAAACGGTGCCGA 60.969 57.895 18.16 0.00 42.83 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 219 6.983890 GGAACAATTTTCTGCTGGAAAGTTAA 59.016 34.615 3.28 0.00 43.68 2.01
236 264 7.514721 ACTGGATCTTAAAACTAGTGGAACAA 58.485 34.615 0.00 0.00 44.16 2.83
332 433 6.276806 TCCCTCCATCCCATAATATAAAAGCA 59.723 38.462 0.00 0.00 0.00 3.91
335 436 7.905144 ACTCCCTCCATCCCATAATATAAAA 57.095 36.000 0.00 0.00 0.00 1.52
350 451 3.140519 GGTTCTAGGATCTACTCCCTCCA 59.859 52.174 0.00 0.00 46.27 3.86
455 556 5.031066 AGTACAAGTTGCAACTGGTTCTA 57.969 39.130 37.64 21.72 40.22 2.10
516 617 5.537188 TGCTTTGTAAATGTTGGCTTAAGG 58.463 37.500 4.29 0.00 0.00 2.69
677 800 4.593157 CTTCGAAAGGACTGAGAGATACG 58.407 47.826 0.00 0.00 0.00 3.06
1133 1291 3.181464 GGATAGAAGGCACCCTAACTCAC 60.181 52.174 0.00 0.00 31.13 3.51
1254 1412 3.327757 ACACCTCAAGGCTACATTCAAGA 59.672 43.478 0.00 0.00 39.32 3.02
1686 1844 6.027749 CAGTGACTTACAAACAAGACAAACC 58.972 40.000 0.00 0.00 33.21 3.27
1749 1907 5.750352 AGGCCAAGACATTCAAATTCATT 57.250 34.783 5.01 0.00 0.00 2.57
2012 2915 0.682209 CAGTGGAGGGCATTTCCTGG 60.682 60.000 4.01 0.00 37.25 4.45
2076 2979 6.636454 ACTTTCCCCTCAATGTATGTTCTA 57.364 37.500 0.00 0.00 0.00 2.10
2180 3084 8.044309 AGGCAACCATTTAACAACTAAACTTTT 58.956 29.630 0.00 0.00 31.69 2.27
2181 3085 7.561251 AGGCAACCATTTAACAACTAAACTTT 58.439 30.769 0.00 0.00 31.69 2.66
2284 3188 7.636259 TTGAAACGAATAAATTTGCCAGAAG 57.364 32.000 0.00 0.00 0.00 2.85
2301 3205 6.238211 CCAGGTATTGCTAGAAGATTGAAACG 60.238 42.308 0.00 0.00 0.00 3.60
2415 3319 7.645058 AACTCCACTTCTGAATTTTGAAAGA 57.355 32.000 0.00 0.00 0.00 2.52
2480 3384 2.034558 CACAACCAATCGGCAGTTTTCT 59.965 45.455 0.00 0.00 34.57 2.52
2513 3417 2.675844 GTTTTCAACACCAGCCAAAACC 59.324 45.455 0.00 0.00 32.94 3.27
2531 3435 2.623416 GCCAAAGGCTGTAGAAGTGTTT 59.377 45.455 0.00 0.00 46.69 2.83
2587 3491 1.144936 CTAGGGCAGAAGAAGCGGG 59.855 63.158 0.00 0.00 0.00 6.13
2597 3501 4.730966 TCTGTATAGGTTCTCTAGGGCAG 58.269 47.826 0.00 0.00 0.00 4.85
2673 4190 2.223923 CGACCCAAATGGACAAAAAGCA 60.224 45.455 0.00 0.00 37.39 3.91
2712 4271 0.664166 GCACTGCCAATCCAAACACG 60.664 55.000 0.00 0.00 0.00 4.49
2714 4273 1.659233 CGCACTGCCAATCCAAACA 59.341 52.632 0.00 0.00 0.00 2.83
2726 4285 4.312231 CACACGTTGGGCGCACTG 62.312 66.667 12.74 2.36 46.11 3.66
2744 4303 3.758554 AGCCACAAGGACAAATATGTGTC 59.241 43.478 16.58 16.58 45.99 3.67
2747 4306 3.091545 CCAGCCACAAGGACAAATATGT 58.908 45.455 0.00 0.00 44.25 2.29
2754 4313 1.064003 ACATACCAGCCACAAGGACA 58.936 50.000 0.00 0.00 36.89 4.02
2760 4319 2.354729 GGCCACATACCAGCCACA 59.645 61.111 0.00 0.00 46.34 4.17
2766 4325 4.534647 AGGAATAAATGGCCACATACCA 57.465 40.909 8.16 0.00 42.61 3.25
2894 4478 9.609950 ATTTGCGACAATTTAAATTTCATTTGG 57.390 25.926 10.77 1.21 33.82 3.28
2952 4536 3.670377 GGGCTCACGTTGGCAACC 61.670 66.667 23.68 9.17 0.00 3.77
2954 4538 2.904866 GTGGGCTCACGTTGGCAA 60.905 61.111 0.00 0.00 33.87 4.52
2960 4544 1.907739 AGCATATGTGGGCTCACGT 59.092 52.632 17.22 17.22 46.42 4.49
2971 4555 7.204604 TGCAAGATAATTTGGTTGAGCATATG 58.795 34.615 0.00 0.00 0.00 1.78
2983 4567 5.801444 TCGCATTCAACTGCAAGATAATTTG 59.199 36.000 0.00 0.00 42.40 2.32
2988 4572 3.599343 ACTCGCATTCAACTGCAAGATA 58.401 40.909 0.00 0.00 42.40 1.98
3024 4608 1.539157 CCCTCAGAAAGGTTGGCTTC 58.461 55.000 0.00 0.00 44.56 3.86
3057 4641 5.218139 GGGGTGTACGATAACTATTTCGAG 58.782 45.833 0.00 0.00 38.67 4.04
3066 4650 0.755079 GGGAGGGGGTGTACGATAAC 59.245 60.000 0.00 0.00 0.00 1.89
3116 4700 2.969827 GGCACCGTTTTGGATGGG 59.030 61.111 0.00 0.00 42.00 4.00
3128 4712 1.530323 ACACAACCTATTTCGGCACC 58.470 50.000 0.00 0.00 0.00 5.01
3130 4714 3.215151 TCAAACACAACCTATTTCGGCA 58.785 40.909 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.