Multiple sequence alignment - TraesCS4A01G148100

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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 TraesCS4A01G148100 chr4A 100.000 3394 0 0 1 3394 275495391 275498784 0 6268
1 TraesCS4A01G148100 chr1A 97.294 3400 81 5 1 3394 94765604 94762210 0 5758
2 TraesCS4A01G148100 chr5D 97.265 3400 86 5 1 3394 562925173 562928571 0 5757
3 TraesCS4A01G148100 chr7A 97.206 3400 89 4 1 3394 211308106 211311505 0 5747
4 TraesCS4A01G148100 chr7A 96.971 3400 97 4 1 3394 563544631 563548030 0 5703
5 TraesCS4A01G148100 chr2D 97.118 3400 92 4 1 3394 200934934 200938333 0 5731
6 TraesCS4A01G148100 chr2D 96.382 3400 115 6 1 3394 604416905 604420302 0 5590
7 TraesCS4A01G148100 chr1D 96.882 3400 98 5 1 3394 185786578 185783181 0 5685
8 TraesCS4A01G148100 chr6D 97.236 3329 86 4 72 3394 458889921 458893249 0 5633
9 TraesCS4A01G148100 chr7D 96.294 3400 120 4 1 3394 307118246 307114847 0 5576


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 TraesCS4A01G148100 chr4A 275495391 275498784 3393 False 6268 6268 100.000 1 3394 1 chr4A.!!$F1 3393
1 TraesCS4A01G148100 chr1A 94762210 94765604 3394 True 5758 5758 97.294 1 3394 1 chr1A.!!$R1 3393
2 TraesCS4A01G148100 chr5D 562925173 562928571 3398 False 5757 5757 97.265 1 3394 1 chr5D.!!$F1 3393
3 TraesCS4A01G148100 chr7A 211308106 211311505 3399 False 5747 5747 97.206 1 3394 1 chr7A.!!$F1 3393
4 TraesCS4A01G148100 chr7A 563544631 563548030 3399 False 5703 5703 96.971 1 3394 1 chr7A.!!$F2 3393
5 TraesCS4A01G148100 chr2D 200934934 200938333 3399 False 5731 5731 97.118 1 3394 1 chr2D.!!$F1 3393
6 TraesCS4A01G148100 chr2D 604416905 604420302 3397 False 5590 5590 96.382 1 3394 1 chr2D.!!$F2 3393
7 TraesCS4A01G148100 chr1D 185783181 185786578 3397 True 5685 5685 96.882 1 3394 1 chr1D.!!$R1 3393
8 TraesCS4A01G148100 chr6D 458889921 458893249 3328 False 5633 5633 97.236 72 3394 1 chr6D.!!$F1 3322
9 TraesCS4A01G148100 chr7D 307114847 307118246 3399 True 5576 5576 96.294 1 3394 1 chr7D.!!$R1 3393

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
802 804 1.275856 AGTTGGTAACCAATACGCGGA 59.724 47.619 12.47 0.0 45.8 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2561 2567 0.036388 ACCGCGACCTGTCATGATTT 60.036 50.0 8.23 0.0 0.0 2.17 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
249 251 5.128827 CCTGTGTACCTTCCTATTTGCTCTA 59.871 44.000 0.00 0.00 0.00 2.43
382 384 5.211973 AGCCTGTATCAATGAAGAGTAGGA 58.788 41.667 0.00 0.00 0.00 2.94
770 772 3.454371 AAGCGAGACAAAGGCGTATAT 57.546 42.857 0.00 0.00 0.00 0.86
784 786 4.280174 AGGCGTATATTGTGTTCCGATAGT 59.720 41.667 0.00 0.00 0.00 2.12
802 804 1.275856 AGTTGGTAACCAATACGCGGA 59.724 47.619 12.47 0.00 45.80 5.54
810 812 2.318908 ACCAATACGCGGACCCTATTA 58.681 47.619 12.47 0.00 0.00 0.98
821 823 4.451435 GCGGACCCTATTAATTCTTACAGC 59.549 45.833 0.00 0.00 0.00 4.40
843 845 5.827797 AGCAATCCTGTGAAAAGAAGTGTTA 59.172 36.000 0.00 0.00 0.00 2.41
920 922 6.000891 TGTGTGTTTATGCATCAACTCTTC 57.999 37.500 21.14 15.28 0.00 2.87
1332 1334 5.001874 GGAAAGAAAGAATAGGGTTGTCGT 58.998 41.667 0.00 0.00 0.00 4.34
1496 1498 3.466836 AGCATGAGTTCGTTCAAAGTCA 58.533 40.909 0.00 0.00 41.52 3.41
1521 1523 2.127708 GGGGAATCAGAGAAAGGGCTA 58.872 52.381 0.00 0.00 0.00 3.93
1823 1825 6.365970 AAGAAATCTAGCAGTCTCTTCCAA 57.634 37.500 0.00 0.00 0.00 3.53
1909 1911 0.739561 GAATGTCGACCTACCGCTCT 59.260 55.000 14.12 0.00 0.00 4.09
1987 1989 7.870588 AAAACAGTACTCGATTTCTCACTAC 57.129 36.000 0.00 0.00 0.00 2.73
1990 1992 6.613233 ACAGTACTCGATTTCTCACTACAAG 58.387 40.000 0.00 0.00 0.00 3.16
1999 2001 7.279090 TCGATTTCTCACTACAAGAAACAACAA 59.721 33.333 0.75 0.00 43.46 2.83
2030 2032 4.694982 TGTTGTGTGCATATTAGTCACTGG 59.305 41.667 0.00 0.00 0.00 4.00
2045 2047 9.686683 ATTAGTCACTGGTTATAGCTTTGAATT 57.313 29.630 0.00 0.00 0.00 2.17
2234 2236 4.135306 CTGCCACAATGCTCTTGATAGAT 58.865 43.478 6.59 0.00 0.00 1.98
2250 2252 6.438186 TGATAGATGGAAGCATGAATACCA 57.562 37.500 0.00 0.00 35.09 3.25
2414 2416 1.072965 GAGGCCTTCCATGACCATAGG 59.927 57.143 6.77 0.00 33.74 2.57
2441 2443 5.772393 ACCTATCCCATTTTGACAGTACA 57.228 39.130 0.00 0.00 0.00 2.90
2472 2474 5.184479 AGCTGTTCACGGATTAGTTGTACTA 59.816 40.000 0.00 0.00 0.00 1.82
2499 2505 7.615403 ACAACACATATGAGATTCTGTACACT 58.385 34.615 10.38 0.00 0.00 3.55
2533 2539 2.666508 GACACGACACGCAATCTTATGT 59.333 45.455 0.00 0.00 0.00 2.29
2561 2567 3.726557 ATGGCCTTCATCTTTGACAGA 57.273 42.857 3.32 0.00 35.33 3.41
2574 2580 5.624159 TCTTTGACAGAAATCATGACAGGT 58.376 37.500 0.00 0.00 0.00 4.00
2754 2760 7.982761 ACAACTTTGGGATACGTATTTACAA 57.017 32.000 9.92 11.98 37.60 2.41
2765 2771 7.483691 GGATACGTATTTACAAACTGCAAAAGG 59.516 37.037 9.92 0.00 0.00 3.11
2777 2783 7.230510 ACAAACTGCAAAAGGTAGATACAATGA 59.769 33.333 0.00 0.00 32.90 2.57
2930 2937 6.716173 CCCTCTAGACCAGGATAACTTACTAC 59.284 46.154 0.00 0.00 31.91 2.73
3006 3013 4.063998 AGACGAATTGCTATCATCTGCA 57.936 40.909 0.00 0.00 37.42 4.41
3038 3045 7.255942 CCCTCATTATTGAATTTATCCGCCTTT 60.256 37.037 0.00 0.00 0.00 3.11
3141 3149 6.268847 AGTTGTGAGACATCTTCCTCTTAGTT 59.731 38.462 0.00 0.00 0.00 2.24
3174 3182 8.375493 TGGCTTCTTCCTTAGTTCTTTATAGA 57.625 34.615 0.00 0.00 0.00 1.98
3323 3331 2.430465 ACAGCTATGCCACAAGTTGAG 58.570 47.619 10.54 0.76 0.00 3.02
3355 3363 7.426606 ACTGGTAAACAAAACCCAAGTTAAT 57.573 32.000 0.00 0.00 34.19 1.40
3379 3387 4.399934 GGATCGACCTAGGAATAGGATGAC 59.600 50.000 17.98 2.69 39.60 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.293677 CAGGATAGTCGCCGTATTCAGT 59.706 50.000 0.00 0.00 0.00 3.41
225 227 4.080863 AGAGCAAATAGGAAGGTACACAGG 60.081 45.833 0.00 0.00 0.00 4.00
382 384 2.736347 ACTATCTTCTGCTGGTACCGT 58.264 47.619 7.57 0.00 0.00 4.83
415 417 0.599991 TGTGAGTGCAGTGGCTAACG 60.600 55.000 0.00 0.00 41.91 3.18
770 772 4.202336 TGGTTACCAACTATCGGAACACAA 60.202 41.667 0.00 0.00 0.00 3.33
802 804 7.721399 CAGGATTGCTGTAAGAATTAATAGGGT 59.279 37.037 0.00 0.00 34.07 4.34
810 812 6.899393 TTTCACAGGATTGCTGTAAGAATT 57.101 33.333 10.71 0.00 34.07 2.17
821 823 8.103948 AGATAACACTTCTTTTCACAGGATTG 57.896 34.615 0.00 0.00 0.00 2.67
843 845 4.389374 TGTTCTTTTCGCTGGAGAAAGAT 58.611 39.130 0.00 0.00 40.66 2.40
901 903 9.534565 GACTATAGAAGAGTTGATGCATAAACA 57.465 33.333 25.68 6.09 0.00 2.83
920 922 3.896272 AGGGCGGGAAAACTAGACTATAG 59.104 47.826 0.00 0.00 0.00 1.31
972 974 8.856153 TGAGCTCTACCAATTTTTGTACATTA 57.144 30.769 16.19 0.00 0.00 1.90
1332 1334 6.112734 ACATCTAATCCAAACAGCGTATCAA 58.887 36.000 0.00 0.00 0.00 2.57
1496 1498 2.025510 CCTTTCTCTGATTCCCCTTGCT 60.026 50.000 0.00 0.00 0.00 3.91
1521 1523 6.097270 CCCATGGTCATGATTGTTGACTAAAT 59.903 38.462 11.73 0.00 42.48 1.40
1871 1873 6.306987 ACATTCCTTCTTCTTTCCAAGCTTA 58.693 36.000 0.00 0.00 0.00 3.09
1909 1911 0.396974 AGCAAGGTTCAAAGCCCACA 60.397 50.000 0.00 0.00 0.00 4.17
2030 2032 9.556030 GTAGTTTGTCCAATTCAAAGCTATAAC 57.444 33.333 0.00 0.00 35.83 1.89
2045 2047 7.288389 TCCAGAGTTACTAAAGTAGTTTGTCCA 59.712 37.037 5.77 0.00 40.14 4.02
2234 2236 2.760092 GCCTTTGGTATTCATGCTTCCA 59.240 45.455 0.00 0.00 0.00 3.53
2250 2252 7.220890 TCCTATTTCAAATAGGTAGGCCTTT 57.779 36.000 28.37 0.00 44.18 3.11
2263 2265 8.934023 ACTTCCATAGTTGTTCCTATTTCAAA 57.066 30.769 0.00 0.00 31.29 2.69
2417 2419 6.548321 TGTACTGTCAAAATGGGATAGGTTT 58.452 36.000 0.00 0.00 0.00 3.27
2441 2443 2.851263 TCCGTGAACAGCTAACCATT 57.149 45.000 0.00 0.00 0.00 3.16
2472 2474 7.761704 GTGTACAGAATCTCATATGTGTTGTCT 59.238 37.037 0.00 2.89 0.00 3.41
2499 2505 5.257864 CGTGTCGTGTCGTTATTCTGTATA 58.742 41.667 0.00 0.00 0.00 1.47
2533 2539 5.425217 TCAAAGATGAAGGCCATACTGTAGA 59.575 40.000 5.01 0.00 35.17 2.59
2561 2567 0.036388 ACCGCGACCTGTCATGATTT 60.036 50.000 8.23 0.00 0.00 2.17
2754 2760 7.394359 ACATCATTGTATCTACCTTTTGCAGTT 59.606 33.333 0.00 0.00 33.16 3.16
2765 2771 6.588204 TGGTGGGTAACATCATTGTATCTAC 58.412 40.000 0.00 0.00 34.61 2.59
2777 2783 1.113788 GCATGCATGGTGGGTAACAT 58.886 50.000 27.34 0.00 39.74 2.71
3006 3013 0.550914 TTCAATAATGAGGGCCGCCT 59.449 50.000 9.86 0.00 36.78 5.52
3038 3045 6.209192 AGTCAATAGTGAATTTGGTTGCATCA 59.791 34.615 0.00 0.00 34.87 3.07
3141 3149 6.374417 ACTAAGGAAGAAGCCATTTGTAGA 57.626 37.500 0.00 0.00 0.00 2.59
3174 3182 7.174080 GCAAAGAGTCTAAAAGAGGTGAAAGAT 59.826 37.037 0.00 0.00 0.00 2.40
3355 3363 4.044191 TCATCCTATTCCTAGGTCGATCCA 59.956 45.833 9.08 0.00 44.40 3.41


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

AutoCloner maintained by Alex Coulton.