Multiple sequence alignment - TraesCS1D01G076500

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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 TraesCS1D01G076500 chr1D 100.000 3995 0 0 1 3995 58629316 58625322 0 7378
1 TraesCS1D01G076500 chr1D 89.659 2466 226 18 584 3037 58764233 58761785 0 3114
2 TraesCS1D01G076500 chr1D 94.653 1066 26 8 2961 3995 58438868 58439933 0 1624
3 TraesCS1D01G076500 chr1D 83.075 1483 233 16 1507 2980 38367077 38365604 0 1332
4 TraesCS1D01G076500 chr1D 83.096 1473 237 12 1507 2973 38559351 38557885 0 1330
5 TraesCS1D01G076500 chr1D 82.550 1490 246 11 1507 2992 49425366 49423887 0 1299
6 TraesCS1D01G076500 chr1D 80.917 1635 280 25 1507 3121 50023566 50025188 0 1262
7 TraesCS1D01G076500 chr1D 83.726 891 137 8 630 1514 50059217 50060105 0 835
8 TraesCS1D01G076500 chr1D 83.834 866 131 9 657 1517 36618200 36617339 0 815
9 TraesCS1D01G076500 chr1A 97.315 3315 78 6 688 3995 57405804 57402494 0 5618
10 TraesCS1D01G076500 chr1A 91.611 1645 114 10 584 2223 57640249 57638624 0 2252
11 TraesCS1D01G076500 chr1A 94.068 590 25 6 1 586 57406907 57406324 0 887
12 TraesCS1D01G076500 chr1A 84.032 883 131 9 644 1517 36188345 36187464 0 841
13 TraesCS1D01G076500 chr1B 89.052 2457 239 14 592 3037 94233311 94230874 0 3020
14 TraesCS1D01G076500 chr1B 80.506 2806 469 55 630 3406 94327275 94324519 0 2080
15 TraesCS1D01G076500 chr1B 83.778 900 132 12 629 1517 56501839 56500943 0 841
16 TraesCS1D01G076500 chr6A 83.084 1472 240 9 1507 2974 547816112 547817578 0 1330
17 TraesCS1D01G076500 chr6B 82.647 1481 246 11 1515 2991 601866823 601868296 0 1301


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 TraesCS1D01G076500 chr1D 58625322 58629316 3994 True 7378.0 7378 100.0000 1 3995 1 chr1D.!!$R5 3994
1 TraesCS1D01G076500 chr1D 58761785 58764233 2448 True 3114.0 3114 89.6590 584 3037 1 chr1D.!!$R6 2453
2 TraesCS1D01G076500 chr1D 58438868 58439933 1065 False 1624.0 1624 94.6530 2961 3995 1 chr1D.!!$F3 1034
3 TraesCS1D01G076500 chr1D 38365604 38367077 1473 True 1332.0 1332 83.0750 1507 2980 1 chr1D.!!$R2 1473
4 TraesCS1D01G076500 chr1D 38557885 38559351 1466 True 1330.0 1330 83.0960 1507 2973 1 chr1D.!!$R3 1466
5 TraesCS1D01G076500 chr1D 49423887 49425366 1479 True 1299.0 1299 82.5500 1507 2992 1 chr1D.!!$R4 1485
6 TraesCS1D01G076500 chr1D 50023566 50025188 1622 False 1262.0 1262 80.9170 1507 3121 1 chr1D.!!$F1 1614
7 TraesCS1D01G076500 chr1D 50059217 50060105 888 False 835.0 835 83.7260 630 1514 1 chr1D.!!$F2 884
8 TraesCS1D01G076500 chr1D 36617339 36618200 861 True 815.0 815 83.8340 657 1517 1 chr1D.!!$R1 860
9 TraesCS1D01G076500 chr1A 57402494 57406907 4413 True 3252.5 5618 95.6915 1 3995 2 chr1A.!!$R3 3994
10 TraesCS1D01G076500 chr1A 57638624 57640249 1625 True 2252.0 2252 91.6110 584 2223 1 chr1A.!!$R2 1639
11 TraesCS1D01G076500 chr1A 36187464 36188345 881 True 841.0 841 84.0320 644 1517 1 chr1A.!!$R1 873
12 TraesCS1D01G076500 chr1B 94230874 94233311 2437 True 3020.0 3020 89.0520 592 3037 1 chr1B.!!$R2 2445
13 TraesCS1D01G076500 chr1B 94324519 94327275 2756 True 2080.0 2080 80.5060 630 3406 1 chr1B.!!$R3 2776
14 TraesCS1D01G076500 chr1B 56500943 56501839 896 True 841.0 841 83.7780 629 1517 1 chr1B.!!$R1 888
15 TraesCS1D01G076500 chr6A 547816112 547817578 1466 False 1330.0 1330 83.0840 1507 2974 1 chr6A.!!$F1 1467
16 TraesCS1D01G076500 chr6B 601866823 601868296 1473 False 1301.0 1301 82.6470 1515 2991 1 chr6B.!!$F1 1476

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
557 562 1.076995 AGGAGGCCATTTTACCCGC 60.077 57.895 5.01 0.0 0.0 6.13 F
2241 2745 0.957395 CCATGGTATCGGCTGGCATC 60.957 60.000 2.57 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2511 3015 0.723414 ACAGCGTGATTGCTTCATCG 59.277 50.0 0.0 0.0 44.46 3.84 R
3900 4452 5.514204 GCAAATCATTGTGAGCATACTGTTC 59.486 40.0 0.0 0.0 38.85 3.18 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
174 175 4.870123 AGTCATGCCTAAACATTGCAAA 57.130 36.364 1.71 0.00 38.69 3.68
223 224 5.237344 AGTTGCACTTAGACATTTCTCACAC 59.763 40.000 0.00 0.00 32.75 3.82
232 233 6.526566 AGACATTTCTCACACGAAAAGTAC 57.473 37.500 0.00 0.00 35.65 2.73
293 295 7.596749 AATGATAATTAGTACATGCTACGCC 57.403 36.000 0.00 0.00 0.00 5.68
307 309 5.588568 TGCTACGCCAATTCAAAATTTTG 57.411 34.783 22.40 22.40 39.48 2.44
332 334 5.475909 AGTGCTCAAAACAGACATCAATGAT 59.524 36.000 0.00 0.00 0.00 2.45
389 391 6.161855 AGGACTATTATCAGCAATGTCGAA 57.838 37.500 0.00 0.00 0.00 3.71
550 555 3.393426 AATCACATGAGGAGGCCATTT 57.607 42.857 5.01 0.00 0.00 2.32
557 562 1.076995 AGGAGGCCATTTTACCCGC 60.077 57.895 5.01 0.00 0.00 6.13
575 580 1.463056 CGCTTCCGATTTGTTACAGCA 59.537 47.619 0.00 0.00 36.29 4.41
576 581 2.095969 CGCTTCCGATTTGTTACAGCAA 60.096 45.455 0.00 0.00 36.29 3.91
667 1125 4.247380 CCCATGCTCCGCCTCCTC 62.247 72.222 0.00 0.00 0.00 3.71
668 1126 3.160047 CCATGCTCCGCCTCCTCT 61.160 66.667 0.00 0.00 0.00 3.69
669 1127 2.420890 CATGCTCCGCCTCCTCTC 59.579 66.667 0.00 0.00 0.00 3.20
840 1337 4.105553 GCCAACCCGGTCCCCTAC 62.106 72.222 0.00 0.00 36.97 3.18
1998 2502 3.895041 GTGATTTGGGGAAAGTGAAGGAA 59.105 43.478 0.00 0.00 0.00 3.36
2232 2736 3.995199 AGTACTTGATGCCATGGTATCG 58.005 45.455 30.28 21.87 39.55 2.92
2241 2745 0.957395 CCATGGTATCGGCTGGCATC 60.957 60.000 2.57 0.00 0.00 3.91
2365 2869 8.132995 ACAAAATTAAACCTACAACTGCTACAC 58.867 33.333 0.00 0.00 0.00 2.90
2511 3015 5.034797 GGACTTTGTAGAAATAATTGCGCC 58.965 41.667 4.18 0.00 0.00 6.53
2966 3475 6.775594 AAAATTGCTCCCTGTAAAGTATCC 57.224 37.500 0.00 0.00 0.00 2.59
3589 4115 4.180817 TGTTGTAATCTCGTACTGCCATG 58.819 43.478 0.00 0.00 0.00 3.66
3900 4452 3.495100 GGATCAGCATAACCTGTACTGGG 60.495 52.174 21.46 12.77 34.47 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 216 8.885722 ACATTTAAAGTACTTTTCGTGTGAGAA 58.114 29.630 25.07 8.07 34.23 2.87
287 289 6.616260 GCACTCAAAATTTTGAATTGGCGTAG 60.616 38.462 28.49 18.03 45.61 3.51
288 290 5.176590 GCACTCAAAATTTTGAATTGGCGTA 59.823 36.000 28.49 8.58 45.61 4.42
289 291 4.024977 GCACTCAAAATTTTGAATTGGCGT 60.025 37.500 28.49 20.31 45.61 5.68
290 292 4.211794 AGCACTCAAAATTTTGAATTGGCG 59.788 37.500 28.49 19.77 45.61 5.69
291 293 5.236911 TGAGCACTCAAAATTTTGAATTGGC 59.763 36.000 28.49 25.84 45.61 4.52
292 294 6.847956 TGAGCACTCAAAATTTTGAATTGG 57.152 33.333 28.49 20.66 45.61 3.16
307 309 4.818534 TTGATGTCTGTTTTGAGCACTC 57.181 40.909 0.00 0.00 0.00 3.51
362 364 8.367911 TCGACATTGCTGATAATAGTCCTTATT 58.632 33.333 0.00 0.00 36.05 1.40
367 369 6.480320 ACTTTCGACATTGCTGATAATAGTCC 59.520 38.462 0.00 0.00 0.00 3.85
368 370 7.470289 ACTTTCGACATTGCTGATAATAGTC 57.530 36.000 0.00 0.00 0.00 2.59
372 374 8.391106 GTTTCTACTTTCGACATTGCTGATAAT 58.609 33.333 0.00 0.00 0.00 1.28
378 380 5.297547 TGAGTTTCTACTTTCGACATTGCT 58.702 37.500 0.00 0.00 33.84 3.91
389 391 6.542821 TGTCATCCCAAATGAGTTTCTACTT 58.457 36.000 0.00 0.00 33.84 2.24
531 536 3.393426 AAAATGGCCTCCTCATGTGAT 57.607 42.857 3.32 0.00 0.00 3.06
537 542 0.254747 CGGGTAAAATGGCCTCCTCA 59.745 55.000 3.32 0.00 0.00 3.86
544 549 1.027792 TCGGAAGCGGGTAAAATGGC 61.028 55.000 0.00 0.00 0.00 4.40
550 555 2.188062 AACAAATCGGAAGCGGGTAA 57.812 45.000 0.00 0.00 0.00 2.85
557 562 5.049405 AGTCTTTGCTGTAACAAATCGGAAG 60.049 40.000 0.00 0.00 38.76 3.46
575 580 2.040412 GGTGGAATGGTGAGGAGTCTTT 59.960 50.000 0.00 0.00 0.00 2.52
576 581 1.630878 GGTGGAATGGTGAGGAGTCTT 59.369 52.381 0.00 0.00 0.00 3.01
689 1147 1.755008 GACGAGGTGGAGGAGGAGG 60.755 68.421 0.00 0.00 0.00 4.30
838 1335 3.766691 GCCGTTGAGGGAGCGGTA 61.767 66.667 4.16 0.00 46.41 4.02
1297 1797 3.631686 GTGCTATATGCCACCACATTGAA 59.368 43.478 0.00 0.00 42.00 2.69
1903 2407 5.290493 TGTAATCCCGTAGCAATCATCTT 57.710 39.130 0.00 0.00 0.00 2.40
1998 2502 6.713762 TTGTTCATCATTTCAGAAACCAGT 57.286 33.333 0.00 0.00 0.00 4.00
2241 2745 9.504710 GTAGTATATGTATAAACATCAGGCTCG 57.495 37.037 0.00 0.00 42.92 5.03
2365 2869 3.631250 ACCCATTTAGTAAGGTGCCATG 58.369 45.455 0.00 0.00 0.00 3.66
2511 3015 0.723414 ACAGCGTGATTGCTTCATCG 59.277 50.000 0.00 0.00 44.46 3.84
3589 4115 8.124808 TGGTGTTACCCAAATAAAAATACTCC 57.875 34.615 0.00 0.00 37.50 3.85
3900 4452 5.514204 GCAAATCATTGTGAGCATACTGTTC 59.486 40.000 0.00 0.00 38.85 3.18


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

AutoCloner maintained by Alex Coulton.