Multiple sequence alignment - TraesCS7D01G222400

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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 TraesCS7D01G222400 chr7D 100.000 2399 0 0 1 2399 183740811 183743209 0.000000e+00 4431.0
1 TraesCS7D01G222400 chr2D 94.574 2396 119 6 7 2399 148076899 148079286 0.000000e+00 3694.0
2 TraesCS7D01G222400 chr2D 93.851 2407 138 5 1 2399 32711983 32709579 0.000000e+00 3616.0
3 TraesCS7D01G222400 chr2D 93.231 2408 153 8 1 2399 299071705 299069299 0.000000e+00 3535.0
4 TraesCS7D01G222400 chr2D 92.958 2400 154 11 3 2399 477724012 477721625 0.000000e+00 3482.0
5 TraesCS7D01G222400 chr2D 92.500 2360 159 14 1 2356 222708520 222706175 0.000000e+00 3362.0
6 TraesCS7D01G222400 chr4D 93.497 2399 144 8 1 2399 507928227 507925841 0.000000e+00 3555.0
7 TraesCS7D01G222400 chr6D 93.292 2400 154 7 1 2399 219123764 219121371 0.000000e+00 3533.0
8 TraesCS7D01G222400 chr6D 92.676 2403 158 12 1 2399 67626558 67628946 0.000000e+00 3446.0
9 TraesCS7D01G222400 chr3D 92.512 2404 167 12 1 2399 183527840 183530235 0.000000e+00 3430.0
10 TraesCS7D01G222400 chr3A 87.097 62 8 0 2338 2399 657081819 657081880 1.190000e-08 71.3


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 TraesCS7D01G222400 chr7D 183740811 183743209 2398 False 4431 4431 100.000 1 2399 1 chr7D.!!$F1 2398
1 TraesCS7D01G222400 chr2D 148076899 148079286 2387 False 3694 3694 94.574 7 2399 1 chr2D.!!$F1 2392
2 TraesCS7D01G222400 chr2D 32709579 32711983 2404 True 3616 3616 93.851 1 2399 1 chr2D.!!$R1 2398
3 TraesCS7D01G222400 chr2D 299069299 299071705 2406 True 3535 3535 93.231 1 2399 1 chr2D.!!$R3 2398
4 TraesCS7D01G222400 chr2D 477721625 477724012 2387 True 3482 3482 92.958 3 2399 1 chr2D.!!$R4 2396
5 TraesCS7D01G222400 chr2D 222706175 222708520 2345 True 3362 3362 92.500 1 2356 1 chr2D.!!$R2 2355
6 TraesCS7D01G222400 chr4D 507925841 507928227 2386 True 3555 3555 93.497 1 2399 1 chr4D.!!$R1 2398
7 TraesCS7D01G222400 chr6D 219121371 219123764 2393 True 3533 3533 93.292 1 2399 1 chr6D.!!$R1 2398
8 TraesCS7D01G222400 chr6D 67626558 67628946 2388 False 3446 3446 92.676 1 2399 1 chr6D.!!$F1 2398
9 TraesCS7D01G222400 chr3D 183527840 183530235 2395 False 3430 3430 92.512 1 2399 1 chr3D.!!$F1 2398

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
506 523 0.616395 TACCGAGCCAGGGATGACAA 60.616 55.0 0.0 0.0 35.02 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2153 0.252696 TCTGGGGCATAGCGGGATAT 60.253 55.0 0.0 0.0 0.0 1.63 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
44 45 2.061848 TGGGATTGAGTTGGAGGAACA 58.938 47.619 0.00 0.00 36.98 3.18
64 71 6.587608 GGAACATTCTCAATGATGTTTCAACC 59.412 38.462 3.24 0.00 41.46 3.77
105 114 6.753107 AAATCTATTCGTTTGTTGTAGGGG 57.247 37.500 0.00 0.00 0.00 4.79
344 359 5.560722 TGGAGTTGATGGACTCACTTTAA 57.439 39.130 7.27 0.00 46.21 1.52
345 360 5.935945 TGGAGTTGATGGACTCACTTTAAA 58.064 37.500 7.27 0.00 46.21 1.52
377 393 6.073711 GCCTTCCGCTGTTATCTTATTTAGAC 60.074 42.308 0.00 0.00 35.19 2.59
386 402 9.490379 CTGTTATCTTATTTAGACGGCCTTAAT 57.510 33.333 0.00 0.00 35.19 1.40
493 510 1.726791 GTGTGTGTCAGCATTACCGAG 59.273 52.381 0.00 0.00 0.00 4.63
506 523 0.616395 TACCGAGCCAGGGATGACAA 60.616 55.000 0.00 0.00 35.02 3.18
516 533 3.021695 CAGGGATGACAATGAAGCACAT 58.978 45.455 0.00 0.00 41.45 3.21
597 614 3.162666 AGGACACGACCACTAAGATGAA 58.837 45.455 0.00 0.00 0.00 2.57
615 632 4.808414 TGAACCATAGGTCACTCTTCTG 57.192 45.455 0.00 0.00 33.12 3.02
684 701 3.129287 ACTCAAGGAACAAGTTTGCACAG 59.871 43.478 0.00 0.00 0.00 3.66
706 723 2.027561 CCGGATGAAGACACACCCTTTA 60.028 50.000 0.00 0.00 0.00 1.85
713 730 1.268899 AGACACACCCTTTAGACGACG 59.731 52.381 0.00 0.00 0.00 5.12
720 737 2.224113 ACCCTTTAGACGACGCTTGAAA 60.224 45.455 0.00 0.00 0.00 2.69
746 763 3.693085 GTCACTAGGTACCTGAACATCGA 59.307 47.826 25.33 8.11 0.00 3.59
805 823 1.134461 CAGAAGAGGAGCACTGGATGG 60.134 57.143 0.00 0.00 0.00 3.51
820 838 3.815401 CTGGATGGTTCGAGTTCAAGTTT 59.185 43.478 0.00 0.00 0.00 2.66
834 852 5.893824 AGTTCAAGTTTCAGGAAGGACATTT 59.106 36.000 0.00 0.00 0.00 2.32
879 897 3.706086 AGTTTTCCTTTGATGCACCAACT 59.294 39.130 0.00 0.00 0.00 3.16
978 996 6.010850 GGACACTATCTACCAGATATGTGGA 58.989 44.000 24.90 8.16 40.44 4.02
987 1005 0.669077 AGATATGTGGACGCCGAGAC 59.331 55.000 0.00 0.00 0.00 3.36
1011 1029 2.748798 GCAATGGGAGATGATCAGCACT 60.749 50.000 14.38 6.65 0.00 4.40
1035 1053 3.414700 GACAGGTCCGTTGCAGCG 61.415 66.667 16.72 16.72 0.00 5.18
1065 1083 3.573967 AGGAGTTAAACCAGCACATTTGG 59.426 43.478 3.35 0.00 41.60 3.28
1071 1089 2.339348 CAGCACATTTGGCGCCAA 59.661 55.556 37.30 37.30 36.08 4.52
1222 1240 5.914898 TGACGACCTGATAAAGAAGATCA 57.085 39.130 0.00 0.00 0.00 2.92
1341 1359 1.405933 CCCGACAGCAGTGATGATGAA 60.406 52.381 16.72 0.00 0.00 2.57
1351 1369 6.482308 CAGCAGTGATGATGAATATGAAGACA 59.518 38.462 0.98 0.00 0.00 3.41
1427 1447 9.209175 GACCACCATATGATCAAGTAGTATTTC 57.791 37.037 3.65 0.00 0.00 2.17
1441 1461 9.886132 CAAGTAGTATTTCCCCCATGTATATAC 57.114 37.037 5.89 5.89 0.00 1.47
1492 1513 2.722094 TCGATTGTATGCCCTTGCTTT 58.278 42.857 0.00 0.00 38.71 3.51
1493 1514 2.682856 TCGATTGTATGCCCTTGCTTTC 59.317 45.455 0.00 0.00 38.71 2.62
1510 1531 7.148120 CCTTGCTTTCTTGATTGAGTGATATGT 60.148 37.037 0.00 0.00 0.00 2.29
1628 1650 2.858344 GAGACGTGATACCGGATTTGTG 59.142 50.000 9.46 0.00 0.00 3.33
1705 1742 2.301346 AGTTCAGAACCAAGGCAACAG 58.699 47.619 9.85 0.00 41.41 3.16
1809 1849 2.190841 CCGCCGGTGTTTTCCAGTT 61.191 57.895 15.14 0.00 0.00 3.16
2047 2088 3.464907 GAGCTATGAGCATGAAGAAGCA 58.535 45.455 0.00 0.00 45.56 3.91
2112 2153 3.678056 ACGTGGATGAGTTTAGCAAGA 57.322 42.857 0.00 0.00 0.00 3.02
2358 2403 1.080298 CGCTTTACCCCGAACTCGT 60.080 57.895 0.00 0.00 37.74 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.539574 TGGTGGTTGAAACATCATTGAGAAT 59.460 36.000 0.00 0.00 0.00 2.40
86 94 6.563222 TTTTCCCCTACAACAAACGAATAG 57.437 37.500 0.00 0.00 0.00 1.73
92 101 4.062293 GCCAATTTTCCCCTACAACAAAC 58.938 43.478 0.00 0.00 0.00 2.93
493 510 0.743097 GCTTCATTGTCATCCCTGGC 59.257 55.000 0.00 0.00 0.00 4.85
506 523 5.086104 ACGGTTAAGTCTATGTGCTTCAT 57.914 39.130 0.00 0.00 40.25 2.57
597 614 4.936802 AGTACAGAAGAGTGACCTATGGT 58.063 43.478 0.00 0.00 39.44 3.55
615 632 4.707448 TGGAGAGGAGTCAGAAATGAGTAC 59.293 45.833 0.00 0.00 0.00 2.73
684 701 1.745489 GGGTGTGTCTTCATCCGGC 60.745 63.158 0.00 0.00 0.00 6.13
706 723 2.223735 TGACTTCTTTCAAGCGTCGTCT 60.224 45.455 0.00 0.00 32.48 4.18
713 730 4.930405 GGTACCTAGTGACTTCTTTCAAGC 59.070 45.833 4.06 0.00 0.00 4.01
720 737 4.737578 TGTTCAGGTACCTAGTGACTTCT 58.262 43.478 15.80 0.00 0.00 2.85
746 763 1.353022 TCCCGGTGAAGCTTGGTATTT 59.647 47.619 2.10 0.00 0.00 1.40
805 823 4.024809 CCTTCCTGAAACTTGAACTCGAAC 60.025 45.833 0.00 0.00 0.00 3.95
820 838 1.626321 TGGCGTAAATGTCCTTCCTGA 59.374 47.619 0.00 0.00 0.00 3.86
834 852 2.646175 GGGCTCAGTGACTGGCGTA 61.646 63.158 13.33 0.00 31.68 4.42
879 897 2.247699 TACTCTTGCCTAGGCTCCAA 57.752 50.000 33.07 18.84 42.51 3.53
885 903 1.542108 GCTGCCATACTCTTGCCTAGG 60.542 57.143 3.67 3.67 0.00 3.02
978 996 2.507102 CATTGCTCGTCTCGGCGT 60.507 61.111 6.85 0.00 0.00 5.68
987 1005 2.414806 CTGATCATCTCCCATTGCTCG 58.585 52.381 0.00 0.00 0.00 5.03
1027 1045 0.955428 TCCTGGATGAACGCTGCAAC 60.955 55.000 0.00 0.00 0.00 4.17
1035 1053 3.440522 GCTGGTTTAACTCCTGGATGAAC 59.559 47.826 0.00 0.00 0.00 3.18
1065 1083 0.674895 ACATCTGGTTCTCTTGGCGC 60.675 55.000 0.00 0.00 0.00 6.53
1071 1089 0.035317 TTGCGCACATCTGGTTCTCT 59.965 50.000 11.12 0.00 0.00 3.10
1181 1199 8.358148 GGTCGTCATTCTTCTCCAATAGTATTA 58.642 37.037 0.00 0.00 0.00 0.98
1341 1359 3.118629 TCGCTCCAGCTTTGTCTTCATAT 60.119 43.478 0.00 0.00 39.32 1.78
1351 1369 3.144506 CCATGATATTCGCTCCAGCTTT 58.855 45.455 0.00 0.00 39.32 3.51
1383 1401 7.685481 TGGTGGTCTACTAGAAATTTTGATCA 58.315 34.615 0.00 0.00 0.00 2.92
1427 1447 7.231722 GCTCAGACTATAGTATATACATGGGGG 59.768 44.444 15.18 3.11 0.00 5.40
1441 1461 5.736486 TCGTTACAGTGCTCAGACTATAG 57.264 43.478 0.00 0.00 0.00 1.31
1510 1531 6.016443 TGCACATGAGACAAACACAATCATAA 60.016 34.615 0.00 0.00 0.00 1.90
1628 1650 2.047179 GTGAGCTCCGGTGGGAAC 60.047 66.667 12.15 0.00 43.27 3.62
1705 1742 4.207599 GTTGTTGTTGTTGTTGTTGTTGC 58.792 39.130 0.00 0.00 0.00 4.17
1809 1849 1.305219 GCAACTATTGGCTCGGTGCA 61.305 55.000 4.30 0.00 45.15 4.57
2112 2153 0.252696 TCTGGGGCATAGCGGGATAT 60.253 55.000 0.00 0.00 0.00 1.63
2358 2403 4.771114 CATGGTTATGGGTAAGTCCTCA 57.229 45.455 0.00 0.00 36.25 3.86


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

AutoCloner maintained by Alex Coulton.