Multiple sequence alignment - TraesCS7B01G028800

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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 TraesCS7B01G028800 chr7B 100.000 2264 0 0 1 2264 27326590 27328853 0 4181
1 TraesCS7B01G028800 chr7B 91.572 2290 136 35 1 2264 235458118 235455860 0 3107
2 TraesCS7B01G028800 chr7B 90.807 1610 108 28 657 2264 130334623 130336194 0 2117
3 TraesCS7B01G028800 chr5B 98.435 1981 31 0 1 1981 428831273 428833253 0 3487
4 TraesCS7B01G028800 chr5B 98.464 1953 30 0 1 1953 428825822 428827774 0 3441
5 TraesCS7B01G028800 chr5B 94.307 1985 98 7 1 1983 548566789 548564818 0 3025
6 TraesCS7B01G028800 chr5B 90.000 1730 126 32 536 2264 530940281 530938598 0 2193
7 TraesCS7B01G028800 chr2B 97.479 1983 49 1 1 1983 29754553 29752572 0 3384
8 TraesCS7B01G028800 chr2B 91.886 1935 118 24 1 1926 47387771 47385867 0 2667
9 TraesCS7B01G028800 chr2B 90.231 1689 118 32 579 2264 717652642 717654286 0 2161
10 TraesCS7B01G028800 chr6B 92.575 2276 142 18 1 2264 650646689 650644429 0 3241
11 TraesCS7B01G028800 chr6B 91.707 2267 136 31 1 2264 114144817 114142600 0 3097
12 TraesCS7B01G028800 chr6B 91.387 2264 128 26 1 2262 661051621 661053819 0 3038
13 TraesCS7B01G028800 chr6B 93.602 1985 103 13 1 1983 687514423 687512461 0 2940
14 TraesCS7B01G028800 chr4A 91.659 2302 145 30 1 2264 712877454 712879746 0 3144
15 TraesCS7B01G028800 chr4B 93.835 1979 97 11 1 1977 74251922 74253877 0 2955
16 TraesCS7B01G028800 chr3B 92.800 1861 97 17 1 1861 16203476 16201653 0 2660
17 TraesCS7B01G028800 chr3B 90.636 1463 114 18 814 2264 393329884 393331335 0 1921
18 TraesCS7B01G028800 chr6A 93.659 1782 99 10 1 1780 74992217 74990448 0 2652
19 TraesCS7B01G028800 chr1B 90.403 1688 117 31 579 2264 550439508 550437864 0 2178


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 TraesCS7B01G028800 chr7B 27326590 27328853 2263 False 4181 4181 100.0000 1 2264 1 chr7B.!!$F1 2263
1 TraesCS7B01G028800 chr7B 235455860 235458118 2258 True 3107 3107 91.5720 1 2264 1 chr7B.!!$R1 2263
2 TraesCS7B01G028800 chr7B 130334623 130336194 1571 False 2117 2117 90.8070 657 2264 1 chr7B.!!$F2 1607
3 TraesCS7B01G028800 chr5B 428825822 428833253 7431 False 3464 3487 98.4495 1 1981 2 chr5B.!!$F1 1980
4 TraesCS7B01G028800 chr5B 548564818 548566789 1971 True 3025 3025 94.3070 1 1983 1 chr5B.!!$R2 1982
5 TraesCS7B01G028800 chr5B 530938598 530940281 1683 True 2193 2193 90.0000 536 2264 1 chr5B.!!$R1 1728
6 TraesCS7B01G028800 chr2B 29752572 29754553 1981 True 3384 3384 97.4790 1 1983 1 chr2B.!!$R1 1982
7 TraesCS7B01G028800 chr2B 47385867 47387771 1904 True 2667 2667 91.8860 1 1926 1 chr2B.!!$R2 1925
8 TraesCS7B01G028800 chr2B 717652642 717654286 1644 False 2161 2161 90.2310 579 2264 1 chr2B.!!$F1 1685
9 TraesCS7B01G028800 chr6B 650644429 650646689 2260 True 3241 3241 92.5750 1 2264 1 chr6B.!!$R2 2263
10 TraesCS7B01G028800 chr6B 114142600 114144817 2217 True 3097 3097 91.7070 1 2264 1 chr6B.!!$R1 2263
11 TraesCS7B01G028800 chr6B 661051621 661053819 2198 False 3038 3038 91.3870 1 2262 1 chr6B.!!$F1 2261
12 TraesCS7B01G028800 chr6B 687512461 687514423 1962 True 2940 2940 93.6020 1 1983 1 chr6B.!!$R3 1982
13 TraesCS7B01G028800 chr4A 712877454 712879746 2292 False 3144 3144 91.6590 1 2264 1 chr4A.!!$F1 2263
14 TraesCS7B01G028800 chr4B 74251922 74253877 1955 False 2955 2955 93.8350 1 1977 1 chr4B.!!$F1 1976
15 TraesCS7B01G028800 chr3B 16201653 16203476 1823 True 2660 2660 92.8000 1 1861 1 chr3B.!!$R1 1860
16 TraesCS7B01G028800 chr3B 393329884 393331335 1451 False 1921 1921 90.6360 814 2264 1 chr3B.!!$F1 1450
17 TraesCS7B01G028800 chr6A 74990448 74992217 1769 True 2652 2652 93.6590 1 1780 1 chr6A.!!$R1 1779
18 TraesCS7B01G028800 chr1B 550437864 550439508 1644 True 2178 2178 90.4030 579 2264 1 chr1B.!!$R1 1685

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
756 6293 0.108615 CTAGAGGTGCTTGTGGTCGG 60.109 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 7906 1.003355 CATGGACCTTGGCGTCTGT 60.003 57.895 0.0 0.0 33.07 3.41 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
726 6209 0.965866 CTAGAGGTGGTGGTCGAGCA 60.966 60.000 14.39 14.39 0.00 4.26
748 6231 2.175878 CACAAGTGCTAGAGGTGCTT 57.824 50.000 0.00 0.00 0.00 3.91
754 6291 0.321671 TGCTAGAGGTGCTTGTGGTC 59.678 55.000 0.00 0.00 0.00 4.02
756 6293 0.108615 CTAGAGGTGCTTGTGGTCGG 60.109 60.000 0.00 0.00 0.00 4.79
757 6294 0.541063 TAGAGGTGCTTGTGGTCGGA 60.541 55.000 0.00 0.00 0.00 4.55
1028 6611 3.382832 CGGTTCCAGGACGAGGCT 61.383 66.667 0.00 0.00 0.00 4.58
1078 6661 2.187946 CGTGGATGGAGGCCAGTC 59.812 66.667 5.01 0.00 36.75 3.51
1223 6807 3.197265 CCAACTATGCACATGATCGTCA 58.803 45.455 0.00 0.00 0.00 4.35
1516 7100 2.868044 GCAAGAAGCGTGAGGAAGAGAA 60.868 50.000 0.00 0.00 0.00 2.87
1567 7151 3.864789 AGAGAGGGCAAGAAAACTTGA 57.135 42.857 13.09 0.00 36.50 3.02
1744 7387 8.064222 CGTGGTCATGAACTATTTATGTCATTC 58.936 37.037 12.94 0.00 0.00 2.67
1745 7388 8.064222 GTGGTCATGAACTATTTATGTCATTCG 58.936 37.037 12.94 0.00 0.00 3.34
1746 7389 7.072030 GGTCATGAACTATTTATGTCATTCGC 58.928 38.462 2.64 0.00 0.00 4.70
1747 7390 7.072030 GTCATGAACTATTTATGTCATTCGCC 58.928 38.462 0.00 0.00 0.00 5.54
1748 7391 6.765512 TCATGAACTATTTATGTCATTCGCCA 59.234 34.615 0.00 0.00 0.00 5.69
1749 7392 6.358118 TGAACTATTTATGTCATTCGCCAC 57.642 37.500 0.00 0.00 0.00 5.01
1750 7393 5.877564 TGAACTATTTATGTCATTCGCCACA 59.122 36.000 0.00 0.00 0.00 4.17
1751 7394 6.542005 TGAACTATTTATGTCATTCGCCACAT 59.458 34.615 0.00 0.00 37.08 3.21
1752 7395 6.545504 ACTATTTATGTCATTCGCCACATC 57.454 37.500 0.00 0.00 34.92 3.06
1753 7396 3.942539 TTTATGTCATTCGCCACATCG 57.057 42.857 0.00 0.00 34.92 3.84
1754 7397 2.595124 TATGTCATTCGCCACATCGT 57.405 45.000 0.00 0.00 34.92 3.73
1755 7398 1.009078 ATGTCATTCGCCACATCGTG 58.991 50.000 0.00 0.00 0.00 4.35
1756 7399 0.320334 TGTCATTCGCCACATCGTGT 60.320 50.000 0.00 0.00 0.00 4.49
1757 7400 1.067495 TGTCATTCGCCACATCGTGTA 60.067 47.619 0.00 0.00 0.00 2.90
1758 7401 2.201732 GTCATTCGCCACATCGTGTAT 58.798 47.619 0.00 0.00 0.00 2.29
1759 7402 2.033747 GTCATTCGCCACATCGTGTATG 60.034 50.000 0.00 0.00 41.74 2.39
1770 7413 5.810074 CCACATCGTGTATGATGAACTTGTA 59.190 40.000 18.26 0.00 46.98 2.41
1926 7678 8.185003 AGCAAAAACATTAACAAAAGACAGAC 57.815 30.769 0.00 0.00 0.00 3.51
2010 7762 2.433318 GCGCAGGAGACCAGACAC 60.433 66.667 0.30 0.00 0.00 3.67
2011 7763 2.262915 CGCAGGAGACCAGACACC 59.737 66.667 0.00 0.00 0.00 4.16
2084 7836 3.625897 CACACCCAGACGCCAGGA 61.626 66.667 0.00 0.00 0.00 3.86
2128 7880 2.433318 GCGCAGGAGACCAGACAC 60.433 66.667 0.30 0.00 0.00 3.67
2129 7881 2.262915 CGCAGGAGACCAGACACC 59.737 66.667 0.00 0.00 0.00 4.16
2246 7998 2.433318 GCGCAGGAGACCAGACAC 60.433 66.667 0.30 0.00 0.00 3.67
2247 7999 2.262915 CGCAGGAGACCAGACACC 59.737 66.667 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
726 6209 1.879796 GCACCTCTAGCACTTGTGCTT 60.880 52.381 29.37 15.68 46.56 3.91
746 6229 0.390472 GCTTCCTCTCCGACCACAAG 60.390 60.000 0.00 0.00 0.00 3.16
748 6231 1.533033 TGCTTCCTCTCCGACCACA 60.533 57.895 0.00 0.00 0.00 4.17
754 6291 1.294659 GCACTTGTGCTTCCTCTCCG 61.295 60.000 17.36 0.00 0.00 4.63
756 6293 2.232452 TCTAGCACTTGTGCTTCCTCTC 59.768 50.000 29.37 0.00 43.52 3.20
757 6294 2.233431 CTCTAGCACTTGTGCTTCCTCT 59.767 50.000 29.37 10.28 43.52 3.69
970 6553 7.738345 ACAAAAAGAACAATTGTTAGCACAAC 58.262 30.769 23.33 9.51 45.88 3.32
1078 6661 2.235898 CCTTCTCCTTCTCCTTGTCCAG 59.764 54.545 0.00 0.00 0.00 3.86
1223 6807 3.377172 GTCATATGCGTTAGTTGGCCTTT 59.623 43.478 3.32 0.00 0.00 3.11
1516 7100 0.321122 CTCCTTCTCTTTGCGTGCCT 60.321 55.000 0.00 0.00 0.00 4.75
1567 7151 3.127533 GTGCATCGCGAGCCCTTT 61.128 61.111 16.66 0.00 0.00 3.11
1744 7387 1.851658 TCATCATACACGATGTGGCG 58.148 50.000 1.64 0.00 42.82 5.69
1745 7388 3.198068 AGTTCATCATACACGATGTGGC 58.802 45.455 1.64 0.00 42.82 5.01
1746 7389 4.631377 ACAAGTTCATCATACACGATGTGG 59.369 41.667 1.64 0.00 42.82 4.17
1747 7390 5.784750 ACAAGTTCATCATACACGATGTG 57.215 39.130 0.00 0.00 42.82 3.21
1748 7391 8.492673 AATTACAAGTTCATCATACACGATGT 57.507 30.769 0.00 0.00 42.82 3.06
1749 7392 7.789302 CGAATTACAAGTTCATCATACACGATG 59.211 37.037 0.00 0.00 43.50 3.84
1750 7393 7.704899 TCGAATTACAAGTTCATCATACACGAT 59.295 33.333 0.00 0.00 0.00 3.73
1751 7394 7.030768 TCGAATTACAAGTTCATCATACACGA 58.969 34.615 0.00 0.00 0.00 4.35
1752 7395 7.216920 TCGAATTACAAGTTCATCATACACG 57.783 36.000 0.00 0.00 0.00 4.49
1753 7396 8.321716 GTCTCGAATTACAAGTTCATCATACAC 58.678 37.037 0.00 0.00 0.00 2.90
1754 7397 8.251026 AGTCTCGAATTACAAGTTCATCATACA 58.749 33.333 0.00 0.00 0.00 2.29
1755 7398 8.635877 AGTCTCGAATTACAAGTTCATCATAC 57.364 34.615 0.00 0.00 0.00 2.39
1757 7400 9.823647 AATAGTCTCGAATTACAAGTTCATCAT 57.176 29.630 0.00 0.00 0.00 2.45
1758 7401 9.653287 AAATAGTCTCGAATTACAAGTTCATCA 57.347 29.630 0.00 0.00 0.00 3.07
1759 7402 9.907576 CAAATAGTCTCGAATTACAAGTTCATC 57.092 33.333 0.00 0.00 0.00 2.92
1770 7413 8.768955 GCACATAATCTCAAATAGTCTCGAATT 58.231 33.333 0.00 0.00 0.00 2.17
2010 7762 3.055602 TCCATCAGACACATCAGACAAGG 60.056 47.826 0.00 0.00 0.00 3.61
2011 7763 3.931468 GTCCATCAGACACATCAGACAAG 59.069 47.826 0.00 0.00 45.55 3.16
2084 7836 3.570212 AAGCCAGACGCCAGGGTT 61.570 61.111 0.00 0.00 40.54 4.11
2128 7880 2.332104 CATCAGACACGTCAGACAAGG 58.668 52.381 0.41 0.00 0.00 3.61
2129 7881 2.029918 TCCATCAGACACGTCAGACAAG 60.030 50.000 0.41 0.00 0.00 3.16
2154 7906 1.003355 CATGGACCTTGGCGTCTGT 60.003 57.895 0.00 0.00 33.07 3.41


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

AutoCloner maintained by Alex Coulton.