Multiple sequence alignment - TraesCS2D01G435700

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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 TraesCS2D01G435700 chr2D 100.000 2507 0 0 1 2507 546732421 546734927 0.000000e+00 4630.0
1 TraesCS2D01G435700 chr2D 89.911 1903 101 31 1 1874 546636677 546638517 0.000000e+00 2366.0
2 TraesCS2D01G435700 chr2D 89.929 1132 80 17 846 1952 546682280 546683402 0.000000e+00 1428.0
3 TraesCS2D01G435700 chr2D 87.781 1113 84 33 846 1933 546806358 546807443 0.000000e+00 1254.0
4 TraesCS2D01G435700 chr2D 86.429 140 5 4 2206 2331 546807447 546807586 9.350000e-30 141.0
5 TraesCS2D01G435700 chr2B 86.462 1566 154 24 1 1556 653414782 653416299 0.000000e+00 1664.0
6 TraesCS2D01G435700 chr2B 88.450 1039 89 16 1 1033 653402820 653403833 0.000000e+00 1225.0
7 TraesCS2D01G435700 chr2B 93.664 726 43 2 846 1569 653592163 653592887 0.000000e+00 1083.0
8 TraesCS2D01G435700 chr2B 87.255 612 49 7 1911 2507 653446371 653446968 0.000000e+00 671.0
9 TraesCS2D01G435700 chr2B 84.900 351 22 13 1564 1913 653445334 653445654 2.400000e-85 326.0
10 TraesCS2D01G435700 chr2B 83.886 211 15 12 1716 1912 653592967 653593172 1.530000e-42 183.0
11 TraesCS2D01G435700 chr5A 91.930 1202 54 11 558 1739 377361529 377362707 0.000000e+00 1642.0
12 TraesCS2D01G435700 chr5A 89.848 591 32 10 1927 2507 377398296 377398868 0.000000e+00 734.0
13 TraesCS2D01G435700 chr5A 95.833 192 4 2 1748 1935 377363029 377363220 8.710000e-80 307.0
14 TraesCS2D01G435700 chr5A 97.619 42 0 1 2466 2507 657266978 657266938 1.240000e-08 71.3
15 TraesCS2D01G435700 chr2A 88.860 1158 81 23 930 2074 689769891 689768769 0.000000e+00 1380.0
16 TraesCS2D01G435700 chr2A 85.528 1230 124 38 930 2126 689805204 689803996 0.000000e+00 1236.0
17 TraesCS2D01G435700 chr2A 85.605 1181 84 35 787 1933 689761651 689760523 0.000000e+00 1160.0
18 TraesCS2D01G435700 chr2A 92.229 489 27 6 534 1020 689788385 689787906 0.000000e+00 682.0
19 TraesCS2D01G435700 chr2A 87.420 469 22 11 2066 2507 689765447 689764989 2.880000e-139 505.0
20 TraesCS2D01G435700 chr2A 84.091 132 7 4 2206 2323 689760519 689760388 5.670000e-22 115.0
21 TraesCS2D01G435700 chr2A 72.120 434 96 16 158 586 719318534 719318947 9.480000e-20 108.0
22 TraesCS2D01G435700 chr5D 80.978 368 45 13 114 481 327987568 327987226 4.110000e-68 268.0
23 TraesCS2D01G435700 chr5D 81.579 114 18 3 1 113 314156361 314156472 9.550000e-15 91.6
24 TraesCS2D01G435700 chr4B 80.172 232 28 10 1994 2225 447365624 447365411 9.280000e-35 158.0
25 TraesCS2D01G435700 chr7A 96.053 76 3 0 149 224 115265274 115265199 9.420000e-25 124.0
26 TraesCS2D01G435700 chr6D 84.874 119 15 3 1 118 194113442 194113558 1.580000e-22 117.0
27 TraesCS2D01G435700 chr6D 93.182 44 3 0 2464 2507 457628237 457628280 5.790000e-07 65.8
28 TraesCS2D01G435700 chr7B 94.737 38 2 0 2464 2501 559947668 559947705 2.690000e-05 60.2


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 TraesCS2D01G435700 chr2D 546732421 546734927 2506 False 4630.0 4630 100.0000 1 2507 1 chr2D.!!$F3 2506
1 TraesCS2D01G435700 chr2D 546636677 546638517 1840 False 2366.0 2366 89.9110 1 1874 1 chr2D.!!$F1 1873
2 TraesCS2D01G435700 chr2D 546682280 546683402 1122 False 1428.0 1428 89.9290 846 1952 1 chr2D.!!$F2 1106
3 TraesCS2D01G435700 chr2D 546806358 546807586 1228 False 697.5 1254 87.1050 846 2331 2 chr2D.!!$F4 1485
4 TraesCS2D01G435700 chr2B 653414782 653416299 1517 False 1664.0 1664 86.4620 1 1556 1 chr2B.!!$F2 1555
5 TraesCS2D01G435700 chr2B 653402820 653403833 1013 False 1225.0 1225 88.4500 1 1033 1 chr2B.!!$F1 1032
6 TraesCS2D01G435700 chr2B 653592163 653593172 1009 False 633.0 1083 88.7750 846 1912 2 chr2B.!!$F4 1066
7 TraesCS2D01G435700 chr2B 653445334 653446968 1634 False 498.5 671 86.0775 1564 2507 2 chr2B.!!$F3 943
8 TraesCS2D01G435700 chr5A 377361529 377363220 1691 False 974.5 1642 93.8815 558 1935 2 chr5A.!!$F2 1377
9 TraesCS2D01G435700 chr5A 377398296 377398868 572 False 734.0 734 89.8480 1927 2507 1 chr5A.!!$F1 580
10 TraesCS2D01G435700 chr2A 689803996 689805204 1208 True 1236.0 1236 85.5280 930 2126 1 chr2A.!!$R2 1196
11 TraesCS2D01G435700 chr2A 689760388 689769891 9503 True 790.0 1380 86.4940 787 2507 4 chr2A.!!$R3 1720

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
359 362 0.320771 GCTTGAGGAGAGGAAACGCA 60.321 55.0 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 11859 0.039764 TCTCCGTCTCCACATCCTGT 59.96 55.0 0.0 0.0 0.0 4.0 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
122 125 4.717629 CACCTTCAGACCGCGCGA 62.718 66.667 34.63 7.97 0.00 5.87
196 199 2.363018 CTCCCAGCCTCCTCGTCA 60.363 66.667 0.00 0.00 0.00 4.35
260 263 1.987855 CCCTCGGCCACCTTGACTA 60.988 63.158 2.24 0.00 0.00 2.59
284 287 3.823330 GCCGACGACATCTCCGGT 61.823 66.667 0.00 0.00 43.51 5.28
332 335 0.884704 TTGAGGCAGAAGTTCACGGC 60.885 55.000 5.50 8.11 0.00 5.68
339 342 2.030805 GCAGAAGTTCACGGCATTTCTT 60.031 45.455 5.50 0.00 0.00 2.52
359 362 0.320771 GCTTGAGGAGAGGAAACGCA 60.321 55.000 0.00 0.00 0.00 5.24
378 381 3.792736 CGGAGGCGGATGGGGAAA 61.793 66.667 0.00 0.00 0.00 3.13
379 382 2.680965 GGAGGCGGATGGGGAAAA 59.319 61.111 0.00 0.00 0.00 2.29
380 383 1.453928 GGAGGCGGATGGGGAAAAG 60.454 63.158 0.00 0.00 0.00 2.27
381 384 1.303282 GAGGCGGATGGGGAAAAGT 59.697 57.895 0.00 0.00 0.00 2.66
382 385 0.748367 GAGGCGGATGGGGAAAAGTC 60.748 60.000 0.00 0.00 0.00 3.01
451 456 2.831685 ATATACCGAAATCGCAGGCA 57.168 45.000 0.00 0.00 38.18 4.75
508 515 3.625764 GCCGTTTTTACCATATCTGCTCA 59.374 43.478 0.00 0.00 0.00 4.26
608 617 2.814919 CAATTAACCTGGGCACGTTGTA 59.185 45.455 0.00 0.00 0.00 2.41
728 739 1.534385 GCACGCGGTAAAACCAAAACT 60.534 47.619 12.47 0.00 38.47 2.66
752 763 2.202892 GAATCCGACTGGCCGACC 60.203 66.667 0.00 0.00 34.14 4.79
753 764 3.000819 AATCCGACTGGCCGACCA 61.001 61.111 0.00 0.00 46.51 4.02
1518 9899 2.026822 ACTGTGGTAGCTTCCAAGATGG 60.027 50.000 14.36 5.40 39.34 3.51
1531 9912 2.437002 GATGGGGCGCGTACCAAA 60.437 61.111 23.80 12.12 40.73 3.28
1621 10026 2.350964 GCTTCGTCGAGATGGATCTACC 60.351 54.545 0.00 0.00 37.25 3.18
1739 10174 9.798994 ATTTGTCTGTTAATTACCTCGTAGTAG 57.201 33.333 0.00 0.00 0.00 2.57
2003 11506 2.622436 GCTGCAACCTAGAAGACGATT 58.378 47.619 0.00 0.00 0.00 3.34
2084 11587 3.390521 TGGAGGAATGGCGCGTCT 61.391 61.111 13.81 0.00 0.00 4.18
2334 11852 0.467384 CTCTGGAGATCGCCATTGGT 59.533 55.000 19.23 0.00 37.30 3.67
2336 11854 1.412710 TCTGGAGATCGCCATTGGTAC 59.587 52.381 19.23 0.00 37.30 3.34
2337 11855 1.138859 CTGGAGATCGCCATTGGTACA 59.861 52.381 19.23 0.00 37.30 2.90
2338 11856 1.134521 TGGAGATCGCCATTGGTACAC 60.135 52.381 14.91 0.00 31.90 2.90
2339 11857 1.134521 GGAGATCGCCATTGGTACACA 60.135 52.381 11.06 0.00 39.29 3.72
2341 11859 1.277842 AGATCGCCATTGGTACACACA 59.722 47.619 4.26 0.00 39.29 3.72
2342 11860 1.396996 GATCGCCATTGGTACACACAC 59.603 52.381 4.26 0.00 39.29 3.82
2395 11923 2.654404 GATCGTGGACGCGGCTAC 60.654 66.667 19.83 19.83 39.60 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 111 2.507102 ATGTCGCGCGGTCTGAAG 60.507 61.111 31.69 0.00 0.00 3.02
244 247 1.153549 GCTAGTCAAGGTGGCCGAG 60.154 63.158 0.00 0.00 0.00 4.63
254 257 2.992689 TCGGCGGGTGCTAGTCAA 60.993 61.111 7.21 0.00 42.25 3.18
284 287 2.228925 GCGTTTACCCACCCAAACTTA 58.771 47.619 0.00 0.00 33.43 2.24
332 335 3.947868 TCCTCTCCTCAAGCAAGAAATG 58.052 45.455 0.00 0.00 0.00 2.32
339 342 0.320771 GCGTTTCCTCTCCTCAAGCA 60.321 55.000 0.00 0.00 0.00 3.91
368 371 1.680338 CATCCGACTTTTCCCCATCC 58.320 55.000 0.00 0.00 0.00 3.51
370 373 0.258774 CCCATCCGACTTTTCCCCAT 59.741 55.000 0.00 0.00 0.00 4.00
372 375 1.076995 CCCCATCCGACTTTTCCCC 60.077 63.158 0.00 0.00 0.00 4.81
373 376 0.330267 TTCCCCATCCGACTTTTCCC 59.670 55.000 0.00 0.00 0.00 3.97
374 377 2.209690 TTTCCCCATCCGACTTTTCC 57.790 50.000 0.00 0.00 0.00 3.13
375 378 2.094700 GCTTTTCCCCATCCGACTTTTC 60.095 50.000 0.00 0.00 0.00 2.29
376 379 1.893137 GCTTTTCCCCATCCGACTTTT 59.107 47.619 0.00 0.00 0.00 2.27
377 380 1.545841 GCTTTTCCCCATCCGACTTT 58.454 50.000 0.00 0.00 0.00 2.66
378 381 0.323451 GGCTTTTCCCCATCCGACTT 60.323 55.000 0.00 0.00 0.00 3.01
379 382 1.303282 GGCTTTTCCCCATCCGACT 59.697 57.895 0.00 0.00 0.00 4.18
380 383 2.112815 CGGCTTTTCCCCATCCGAC 61.113 63.158 0.00 0.00 42.43 4.79
381 384 2.270850 CGGCTTTTCCCCATCCGA 59.729 61.111 0.00 0.00 42.43 4.55
382 385 2.624674 ATCCGGCTTTTCCCCATCCG 62.625 60.000 0.00 0.00 39.79 4.18
440 445 1.196808 CACGTAAACTGCCTGCGATTT 59.803 47.619 0.00 0.00 0.00 2.17
451 456 2.047560 GCGGGAGGCACGTAAACT 60.048 61.111 0.00 0.00 42.87 2.66
474 479 1.571215 AAAACGGCCGGCTCGTAAAG 61.571 55.000 33.03 16.77 40.18 1.85
523 530 0.038343 CCGACGGTTTTAAGGGACGA 60.038 55.000 5.48 0.00 0.00 4.20
530 539 2.686915 TGCCTTTTTCCGACGGTTTTAA 59.313 40.909 14.79 0.00 0.00 1.52
653 664 2.158959 GTGATTCGGCGTCTCGTGG 61.159 63.158 6.85 0.00 0.00 4.94
654 665 2.497092 CGTGATTCGGCGTCTCGTG 61.497 63.158 6.85 0.00 35.71 4.35
655 666 2.202440 CGTGATTCGGCGTCTCGT 60.202 61.111 6.85 0.00 35.71 4.18
656 667 3.607987 GCGTGATTCGGCGTCTCG 61.608 66.667 14.84 14.84 40.26 4.04
657 668 2.202623 AGCGTGATTCGGCGTCTC 60.203 61.111 6.85 5.63 40.26 3.36
752 763 2.093306 TTTATGGTGCTCGAGGTGTG 57.907 50.000 15.58 0.00 0.00 3.82
753 764 3.270877 GAATTTATGGTGCTCGAGGTGT 58.729 45.455 15.58 0.00 0.00 4.16
1518 9899 2.973316 CTTGGTTTGGTACGCGCCC 61.973 63.158 5.73 7.35 0.00 6.13
1621 10026 2.772691 GGTCGACTCCACGGGCTAG 61.773 68.421 16.46 0.00 0.00 3.42
1739 10174 5.571778 AAACATCGTCTTGAAACGTACTC 57.428 39.130 0.00 0.00 43.08 2.59
2204 11707 3.228017 TGCCTCACGTCCACGGAA 61.228 61.111 3.81 0.00 44.95 4.30
2339 11857 0.541998 TCCGTCTCCACATCCTGTGT 60.542 55.000 6.53 0.00 46.45 3.72
2341 11859 0.039764 TCTCCGTCTCCACATCCTGT 59.960 55.000 0.00 0.00 0.00 4.00
2342 11860 1.135915 CTTCTCCGTCTCCACATCCTG 59.864 57.143 0.00 0.00 0.00 3.86
2395 11923 6.392354 TGGTAAAGTGTACAACCTATTCGAG 58.608 40.000 14.10 0.00 32.99 4.04


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

AutoCloner maintained by Alex Coulton.