Multiple sequence alignment - TraesCS3D01G240600

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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 TraesCS3D01G240600 chr3D 100.000 2586 0 0 1 2586 333013657 333011072 0.000000e+00 4776.0
1 TraesCS3D01G240600 chr3D 78.419 1075 175 27 1164 2204 45766386 45765335 0.000000e+00 647.0
2 TraesCS3D01G240600 chr3D 100.000 328 0 0 2729 3056 333010929 333010602 9.370000e-170 606.0
3 TraesCS3D01G240600 chr3D 76.850 838 154 27 999 1808 418383290 418382465 1.300000e-118 436.0
4 TraesCS3D01G240600 chr3A 95.455 1914 70 2 536 2449 450713383 450711487 0.000000e+00 3037.0
5 TraesCS3D01G240600 chr3A 95.833 264 10 1 2784 3047 450711402 450711140 2.820000e-115 425.0
6 TraesCS3D01G240600 chr3A 89.627 241 23 2 1 241 450768892 450768654 3.830000e-79 305.0
7 TraesCS3D01G240600 chr3A 81.250 384 62 7 980 1355 57288398 57288017 4.950000e-78 302.0
8 TraesCS3D01G240600 chr3A 80.620 387 59 10 1837 2211 57288017 57287635 4.990000e-73 285.0
9 TraesCS3D01G240600 chr6D 90.335 1614 98 27 978 2586 94764560 94766120 0.000000e+00 2063.0
10 TraesCS3D01G240600 chr6D 94.139 273 13 3 2784 3056 94766254 94766523 2.190000e-111 412.0
11 TraesCS3D01G240600 chr6D 88.557 201 14 1 560 760 94758704 94758895 5.090000e-58 235.0
12 TraesCS3D01G240600 chr6D 82.759 203 22 7 780 970 94764320 94764521 5.240000e-38 169.0
13 TraesCS3D01G240600 chr3B 93.737 958 42 8 1631 2586 432261900 432260959 0.000000e+00 1421.0
14 TraesCS3D01G240600 chr3B 96.629 623 9 2 575 1195 432262511 432261899 0.000000e+00 1024.0
15 TraesCS3D01G240600 chr3B 78.972 1284 209 33 978 2211 71430522 71429250 0.000000e+00 819.0
16 TraesCS3D01G240600 chr3B 87.110 481 18 11 1 439 432263454 432262976 3.520000e-139 505.0
17 TraesCS3D01G240600 chr3B 77.025 827 156 29 999 1808 151116107 151115298 7.780000e-121 444.0
18 TraesCS3D01G240600 chr3B 76.812 828 156 26 999 1808 154422005 154421196 1.680000e-117 433.0
19 TraesCS3D01G240600 chr3B 94.872 273 12 2 2785 3056 432260826 432260555 2.820000e-115 425.0
20 TraesCS3D01G240600 chr3B 91.852 135 10 1 437 571 432262615 432262482 1.450000e-43 187.0
21 TraesCS3D01G240600 chr6B 92.848 741 53 0 1341 2081 178019329 178018589 0.000000e+00 1075.0
22 TraesCS3D01G240600 chr6B 87.352 506 21 11 2045 2549 178018587 178018124 9.640000e-150 540.0
23 TraesCS3D01G240600 chr6B 77.073 820 154 28 999 1801 678841790 678842592 2.800000e-120 442.0
24 TraesCS3D01G240600 chr6B 94.372 231 11 2 2784 3014 178018090 178017862 1.350000e-93 353.0
25 TraesCS3D01G240600 chr2A 93.168 161 10 1 1 161 563763852 563764011 5.090000e-58 235.0
26 TraesCS3D01G240600 chr4D 82.105 285 36 7 1 274 268085058 268085338 2.370000e-56 230.0
27 TraesCS3D01G240600 chr5D 82.042 284 36 8 1 271 222784447 222784728 8.520000e-56 228.0
28 TraesCS3D01G240600 chr1B 81.915 282 38 5 3 272 305296158 305296438 3.070000e-55 226.0
29 TraesCS3D01G240600 chr1A 86.127 173 22 2 1 171 514776976 514776804 5.200000e-43 185.0
30 TraesCS3D01G240600 chr1A 86.127 173 22 2 1 171 515026864 515026692 5.200000e-43 185.0
31 TraesCS3D01G240600 chr4B 79.104 268 35 16 24 276 422531071 422531332 6.780000e-37 165.0
32 TraesCS3D01G240600 chr2D 76.678 283 50 15 1 273 606206736 606207012 3.180000e-30 143.0
33 TraesCS3D01G240600 chr2D 92.982 57 4 0 416 472 134396464 134396520 1.950000e-12 84.2
34 TraesCS3D01G240600 chr7D 76.241 282 44 16 1 264 595786265 595785989 8.890000e-26 128.0
35 TraesCS3D01G240600 chr7A 94.643 56 3 0 417 472 661573683 661573628 1.510000e-13 87.9


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 TraesCS3D01G240600 chr3D 333010602 333013657 3055 True 2691.000000 4776 100.000000 1 3056 2 chr3D.!!$R3 3055
1 TraesCS3D01G240600 chr3D 45765335 45766386 1051 True 647.000000 647 78.419000 1164 2204 1 chr3D.!!$R1 1040
2 TraesCS3D01G240600 chr3D 418382465 418383290 825 True 436.000000 436 76.850000 999 1808 1 chr3D.!!$R2 809
3 TraesCS3D01G240600 chr3A 450711140 450713383 2243 True 1731.000000 3037 95.644000 536 3047 2 chr3A.!!$R3 2511
4 TraesCS3D01G240600 chr3A 57287635 57288398 763 True 293.500000 302 80.935000 980 2211 2 chr3A.!!$R2 1231
5 TraesCS3D01G240600 chr6D 94764320 94766523 2203 False 881.333333 2063 89.077667 780 3056 3 chr6D.!!$F2 2276
6 TraesCS3D01G240600 chr3B 71429250 71430522 1272 True 819.000000 819 78.972000 978 2211 1 chr3B.!!$R1 1233
7 TraesCS3D01G240600 chr3B 432260555 432263454 2899 True 712.400000 1421 92.840000 1 3056 5 chr3B.!!$R4 3055
8 TraesCS3D01G240600 chr3B 151115298 151116107 809 True 444.000000 444 77.025000 999 1808 1 chr3B.!!$R2 809
9 TraesCS3D01G240600 chr3B 154421196 154422005 809 True 433.000000 433 76.812000 999 1808 1 chr3B.!!$R3 809
10 TraesCS3D01G240600 chr6B 178017862 178019329 1467 True 656.000000 1075 91.524000 1341 3014 3 chr6B.!!$R1 1673
11 TraesCS3D01G240600 chr6B 678841790 678842592 802 False 442.000000 442 77.073000 999 1801 1 chr6B.!!$F1 802

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
189 190 0.171231 CTCGCACCATTCTCTCGTGA 59.829 55.0 0.00 0.00 0.00 4.35 F
1260 1727 0.323360 AATATGCTGCCACCGTGGTT 60.323 50.0 18.95 0.56 40.46 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2518 0.240411 ACACGCGACAAGAGGTAGTC 59.76 55.0 15.93 0.0 0.0 2.59 R
2233 2810 1.250154 TGCCTATGCTTTGTGTGGCC 61.25 55.0 0.00 0.0 39.6 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
152 153 7.271438 GTCAAAAACTGGAATTAATTCTCTCGC 59.729 37.037 23.85 10.37 37.00 5.03
154 155 6.817765 AAACTGGAATTAATTCTCTCGCAA 57.182 33.333 23.85 4.84 37.00 4.85
170 171 2.292292 TCGCAAAAGCTTGGTAGAAACC 59.708 45.455 0.00 0.00 46.98 3.27
172 173 3.609409 CGCAAAAGCTTGGTAGAAACCTC 60.609 47.826 0.00 0.00 46.91 3.85
178 179 0.759959 TTGGTAGAAACCTCGCACCA 59.240 50.000 0.00 0.00 46.91 4.17
180 181 1.349688 TGGTAGAAACCTCGCACCATT 59.650 47.619 0.00 0.00 46.91 3.16
189 190 0.171231 CTCGCACCATTCTCTCGTGA 59.829 55.000 0.00 0.00 0.00 4.35
191 192 0.803768 CGCACCATTCTCTCGTGAGG 60.804 60.000 14.12 2.08 40.58 3.86
193 194 1.737363 GCACCATTCTCTCGTGAGGTC 60.737 57.143 14.12 0.00 40.58 3.85
258 279 4.576216 TCTGCTCCTTTACTCGATCATC 57.424 45.455 0.00 0.00 0.00 2.92
298 339 8.359875 TCTTTGTTCATTCTCTCACTCTCTAT 57.640 34.615 0.00 0.00 0.00 1.98
353 394 4.097437 TGTCGGTGGTCTTGATATAGACAC 59.903 45.833 7.73 4.62 45.07 3.67
370 411 3.112075 CGCACACGTTCGCCAGAT 61.112 61.111 0.56 0.00 33.53 2.90
372 413 2.476051 CACACGTTCGCCAGATGC 59.524 61.111 0.00 0.00 0.00 3.91
397 438 4.625311 CCTTTCACAGCGAAACTTTGTTTT 59.375 37.500 0.00 0.00 38.72 2.43
439 482 6.325919 TGCTTTAAGATCCGTGTTTTTCAT 57.674 33.333 0.00 0.00 0.00 2.57
440 483 6.378582 TGCTTTAAGATCCGTGTTTTTCATC 58.621 36.000 0.00 0.00 0.00 2.92
441 484 5.800438 GCTTTAAGATCCGTGTTTTTCATCC 59.200 40.000 0.00 0.00 0.00 3.51
442 485 6.569610 GCTTTAAGATCCGTGTTTTTCATCCA 60.570 38.462 0.00 0.00 0.00 3.41
478 884 2.176273 CGCTGCGAAATCTCCCCTG 61.176 63.158 18.66 0.00 0.00 4.45
480 886 1.604378 CTGCGAAATCTCCCCTGGT 59.396 57.895 0.00 0.00 0.00 4.00
486 892 1.413077 GAAATCTCCCCTGGTAGACGG 59.587 57.143 0.00 0.00 0.00 4.79
513 919 5.929415 GCCGATTAACATTTCCCAAAAGAAA 59.071 36.000 0.00 0.00 39.92 2.52
667 1073 3.174265 GCCTGGATCTGGGGAGGG 61.174 72.222 0.00 0.00 0.00 4.30
684 1090 3.284449 GGGTCGTGGGTTGTGTGC 61.284 66.667 0.00 0.00 0.00 4.57
944 1368 7.073457 TGAGCTCTATATATCTAGATCCGCT 57.927 40.000 16.19 7.60 32.51 5.52
1260 1727 0.323360 AATATGCTGCCACCGTGGTT 60.323 50.000 18.95 0.56 40.46 3.67
1326 1793 1.960040 ATTCACTCCTCGATGCGGCA 61.960 55.000 4.58 4.58 0.00 5.69
1433 1920 2.217750 CACCAAGGACGACATGAACAA 58.782 47.619 0.00 0.00 0.00 2.83
1560 2047 0.885879 TGTCTTCGTACACCAGCGAT 59.114 50.000 0.00 0.00 36.97 4.58
1821 2347 2.058595 GTTGGCTAGAGGGCGAGGA 61.059 63.158 0.00 0.00 44.11 3.71
1931 2457 2.962827 CTTGTGGCTGCGTGCTCAG 61.963 63.158 0.00 0.00 42.39 3.35
1992 2518 7.811713 GGAAATCTGAAAATCAAAGACAGGAAG 59.188 37.037 0.00 0.00 0.00 3.46
2083 2647 0.886563 AAGGAAACTGCTCATGCTGC 59.113 50.000 0.00 0.00 42.68 5.25
2088 2652 3.057315 GGAAACTGCTCATGCTGCTTTTA 60.057 43.478 0.00 0.00 41.07 1.52
2196 2773 4.502431 CCACTTTGTAAATTGGGTCCAACC 60.502 45.833 4.37 0.00 38.88 3.77
2248 2825 4.849518 TGTTATAGGCCACACAAAGCATA 58.150 39.130 5.01 0.00 0.00 3.14
2392 2972 0.472471 TGTGGAACCTTTCGGAGCTT 59.528 50.000 0.00 0.00 34.36 3.74
2536 3117 9.356433 CTTGATGAATATAGCTGAGTGACATAG 57.644 37.037 0.00 0.00 0.00 2.23
2844 3482 0.537188 ACGTACATTCTCCTGCCCAG 59.463 55.000 0.00 0.00 0.00 4.45
2849 3487 1.280421 ACATTCTCCTGCCCAGAAGTC 59.720 52.381 0.00 0.00 33.36 3.01
2981 3619 7.276658 CGGATATGTAAACTCATTAGGATGCTC 59.723 40.741 0.00 0.00 33.14 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.014615 GGGACCATTATGATCTTAATTTGTGCT 59.985 37.037 19.73 2.20 0.00 4.40
170 171 0.171231 TCACGAGAGAATGGTGCGAG 59.829 55.000 0.00 0.00 37.53 5.03
172 173 0.803768 CCTCACGAGAGAATGGTGCG 60.804 60.000 11.76 0.00 44.98 5.34
178 179 4.200874 AGTTATCGACCTCACGAGAGAAT 58.799 43.478 11.76 0.00 44.98 2.40
180 181 3.263489 AGTTATCGACCTCACGAGAGA 57.737 47.619 11.76 0.00 44.98 3.10
189 190 6.870971 GAGATGACTCTAAGTTATCGACCT 57.129 41.667 6.30 0.00 43.52 3.85
214 235 8.502387 CAGAAATGATTCTCGTCTTTTTCTCTT 58.498 33.333 0.00 0.00 44.11 2.85
258 279 7.452880 TGAACAAAGATGATTAGTCCCTTTG 57.547 36.000 19.34 19.34 42.86 2.77
314 355 0.322546 GACAGGTCATTGTCCCCACC 60.323 60.000 0.00 0.00 41.24 4.61
315 356 0.673644 CGACAGGTCATTGTCCCCAC 60.674 60.000 0.00 0.00 43.56 4.61
353 394 3.112075 ATCTGGCGAACGTGTGCG 61.112 61.111 6.23 0.00 44.93 5.34
370 411 2.387125 GTTTCGCTGTGAAAGGCGCA 62.387 55.000 16.03 0.00 46.85 6.09
372 413 0.307760 AAGTTTCGCTGTGAAAGGCG 59.692 50.000 16.03 0.00 46.85 5.52
397 438 2.289694 GCAGCCTCAGGAGACACTAAAA 60.290 50.000 0.00 0.00 0.00 1.52
401 442 0.835543 AAGCAGCCTCAGGAGACACT 60.836 55.000 0.00 0.00 0.00 3.55
439 482 2.990740 ACTACCTTTTGGCCATTGGA 57.009 45.000 21.34 0.00 45.59 3.53
440 483 2.094752 CGAACTACCTTTTGGCCATTGG 60.095 50.000 6.09 12.09 45.59 3.16
441 484 2.671070 GCGAACTACCTTTTGGCCATTG 60.671 50.000 6.09 0.00 45.59 2.82
442 485 1.544246 GCGAACTACCTTTTGGCCATT 59.456 47.619 6.09 0.00 45.59 3.16
486 892 2.011222 TGGGAAATGTTAATCGGCGAC 58.989 47.619 13.76 0.00 0.00 5.19
499 905 5.754782 AGGTTTGCTTTTCTTTTGGGAAAT 58.245 33.333 0.00 0.00 35.51 2.17
513 919 1.971695 GCGGGCACTAGGTTTGCTT 60.972 57.895 4.07 0.00 40.07 3.91
667 1073 3.284449 GCACACAACCCACGACCC 61.284 66.667 0.00 0.00 0.00 4.46
883 1303 2.711922 CGGACGGGAAGGAGACAGG 61.712 68.421 0.00 0.00 0.00 4.00
884 1304 2.885861 CGGACGGGAAGGAGACAG 59.114 66.667 0.00 0.00 0.00 3.51
944 1368 3.319198 GGTCTTGTGGGAGCCGGA 61.319 66.667 5.05 0.00 0.00 5.14
950 1374 1.866015 ATCGATCTGGTCTTGTGGGA 58.134 50.000 0.00 0.00 0.00 4.37
1260 1727 1.492319 CGGCAGTTTCCGTGTCGAAA 61.492 55.000 0.00 0.00 45.93 3.46
1326 1793 1.607251 CCGGCGGTGAGAAAGTAGTTT 60.607 52.381 19.97 0.00 0.00 2.66
1453 1940 0.613012 GGCATGCTTTTCCAGGACCT 60.613 55.000 18.92 0.00 0.00 3.85
1560 2047 1.375908 GAAGGTGCCAGCGATGACA 60.376 57.895 0.06 0.00 0.00 3.58
1744 2250 1.537814 TTCCATTTGGGCTGCTGCAG 61.538 55.000 24.80 24.80 41.91 4.41
1821 2347 2.955461 GCCCATGTAGGTGAGAGTAGGT 60.955 54.545 0.00 0.00 34.66 3.08
1931 2457 0.438830 GAGACGAAACGTGGTCATGC 59.561 55.000 14.60 3.26 41.37 4.06
1992 2518 0.240411 ACACGCGACAAGAGGTAGTC 59.760 55.000 15.93 0.00 0.00 2.59
2196 2773 2.028420 TGCTCAAATCGATGGTCAGG 57.972 50.000 0.00 0.00 0.00 3.86
2233 2810 1.250154 TGCCTATGCTTTGTGTGGCC 61.250 55.000 0.00 0.00 39.60 5.36
2536 3117 5.330455 TGTGGTGACAGATAAGATGAGAC 57.670 43.478 0.00 0.00 44.46 3.36
2776 3357 5.331902 ACCATGAATTAACATTCGCTTTCG 58.668 37.500 0.00 0.00 41.77 3.46
2777 3358 5.452302 CGACCATGAATTAACATTCGCTTTC 59.548 40.000 0.00 0.00 41.77 2.62
2844 3482 8.251026 CCAAATTTAACCTATTCTTGGGACTTC 58.749 37.037 0.00 0.00 0.00 3.01
2849 3487 7.902087 TGTTCCAAATTTAACCTATTCTTGGG 58.098 34.615 0.00 0.00 0.00 4.12
2981 3619 3.656651 TTTATCAGCATTCTTCACGCG 57.343 42.857 3.53 3.53 0.00 6.01


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

AutoCloner maintained by Alex Coulton.