Multiple sequence alignment - TraesCS4A01G372800

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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 TraesCS4A01G372800 chr4A 100.000 2692 0 0 1 2692 647862453 647865144 0 4972
1 TraesCS4A01G372800 chr4A 94.600 2148 110 6 1 2146 669474923 669477066 0 3319
2 TraesCS4A01G372800 chr4A 92.913 762 49 3 1932 2692 669476971 669477728 0 1103
3 TraesCS4A01G372800 chr4B 94.622 2622 129 10 1 2615 552005326 552007942 0 4050
4 TraesCS4A01G372800 chr4B 94.053 723 38 5 1972 2692 451479658 451478939 0 1092
5 TraesCS4A01G372800 chr2B 91.446 2724 191 21 1 2692 621618632 621615919 0 3701
6 TraesCS4A01G372800 chr2B 91.667 1980 151 14 170 2145 503647114 503649083 0 2730
7 TraesCS4A01G372800 chr2B 91.415 1293 79 15 1 1289 676182498 676181234 0 1744
8 TraesCS4A01G372800 chr6B 94.134 2148 116 10 1 2145 133977712 133975572 0 3260
9 TraesCS4A01G372800 chr6B 92.704 2152 140 17 1 2145 438992506 438990365 0 3088
10 TraesCS4A01G372800 chr6B 92.354 2145 149 15 4 2145 571751927 571749795 0 3038
11 TraesCS4A01G372800 chr6B 95.291 722 32 2 1972 2692 133975674 133974954 0 1144
12 TraesCS4A01G372800 chr6B 92.116 761 55 5 1934 2692 227570320 227569563 0 1068
13 TraesCS4A01G372800 chr6B 91.874 763 57 5 1932 2692 149536426 149537185 0 1061
14 TraesCS4A01G372800 chr5B 91.632 2151 164 16 1 2145 638659162 638661302 0 2961
15 TraesCS4A01G372800 chr1B 92.461 2056 145 10 1 2053 631053290 631051242 0 2929
16 TraesCS4A01G372800 chr1B 92.792 763 50 5 1932 2692 306221734 306222493 0 1099
17 TraesCS4A01G372800 chr1B 92.136 763 55 5 1932 2692 275807890 275807131 0 1072
18 TraesCS4A01G372800 chr3B 92.136 763 54 5 1932 2692 178568754 178569512 0 1072


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 TraesCS4A01G372800 chr4A 647862453 647865144 2691 False 4972 4972 100.0000 1 2692 1 chr4A.!!$F1 2691
1 TraesCS4A01G372800 chr4A 669474923 669477728 2805 False 2211 3319 93.7565 1 2692 2 chr4A.!!$F2 2691
2 TraesCS4A01G372800 chr4B 552005326 552007942 2616 False 4050 4050 94.6220 1 2615 1 chr4B.!!$F1 2614
3 TraesCS4A01G372800 chr4B 451478939 451479658 719 True 1092 1092 94.0530 1972 2692 1 chr4B.!!$R1 720
4 TraesCS4A01G372800 chr2B 621615919 621618632 2713 True 3701 3701 91.4460 1 2692 1 chr2B.!!$R1 2691
5 TraesCS4A01G372800 chr2B 503647114 503649083 1969 False 2730 2730 91.6670 170 2145 1 chr2B.!!$F1 1975
6 TraesCS4A01G372800 chr2B 676181234 676182498 1264 True 1744 1744 91.4150 1 1289 1 chr2B.!!$R2 1288
7 TraesCS4A01G372800 chr6B 438990365 438992506 2141 True 3088 3088 92.7040 1 2145 1 chr6B.!!$R2 2144
8 TraesCS4A01G372800 chr6B 571749795 571751927 2132 True 3038 3038 92.3540 4 2145 1 chr6B.!!$R3 2141
9 TraesCS4A01G372800 chr6B 133974954 133977712 2758 True 2202 3260 94.7125 1 2692 2 chr6B.!!$R4 2691
10 TraesCS4A01G372800 chr6B 227569563 227570320 757 True 1068 1068 92.1160 1934 2692 1 chr6B.!!$R1 758
11 TraesCS4A01G372800 chr6B 149536426 149537185 759 False 1061 1061 91.8740 1932 2692 1 chr6B.!!$F1 760
12 TraesCS4A01G372800 chr5B 638659162 638661302 2140 False 2961 2961 91.6320 1 2145 1 chr5B.!!$F1 2144
13 TraesCS4A01G372800 chr1B 631051242 631053290 2048 True 2929 2929 92.4610 1 2053 1 chr1B.!!$R2 2052
14 TraesCS4A01G372800 chr1B 306221734 306222493 759 False 1099 1099 92.7920 1932 2692 1 chr1B.!!$F1 760
15 TraesCS4A01G372800 chr1B 275807131 275807890 759 True 1072 1072 92.1360 1932 2692 1 chr1B.!!$R1 760
16 TraesCS4A01G372800 chr3B 178568754 178569512 758 False 1072 1072 92.1360 1932 2692 1 chr3B.!!$F1 760

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
567 574 0.02877 ATGTGTGTGCCGACAAAACG 59.971 50.0 0.0 0.0 32.49 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2496 1.843851 AGGAACGGGCAATCCATAAGA 59.156 47.619 5.43 0.0 38.23 2.1 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
27 28 3.295712 AGGAGGTCCTCACGAGGTCAA 62.296 57.143 20.72 0.00 44.77 3.18
133 134 0.546988 GGTAGTTCACCCACCTCCCT 60.547 60.000 0.00 0.00 42.07 4.20
182 183 0.550914 ACAAAGGAACAGACCCAGCA 59.449 50.000 0.00 0.00 0.00 4.41
221 223 0.539438 TTTGGAAATGCGAGGCCAGT 60.539 50.000 5.01 0.00 0.00 4.00
264 266 2.489938 AGCGTAAATGACCACACCAT 57.510 45.000 0.00 0.00 0.00 3.55
318 323 9.887406 TTTTACCATTCATTTTCTTCGTACTTC 57.113 29.630 0.00 0.00 0.00 3.01
392 399 6.112734 AGGCATGATTCTTTCGTGTTACATA 58.887 36.000 0.00 0.00 42.42 2.29
431 438 2.341846 TTGGACAGAACCAAGGTCAC 57.658 50.000 0.00 0.00 43.79 3.67
437 444 4.262894 GGACAGAACCAAGGTCACTCAATA 60.263 45.833 0.00 0.00 33.26 1.90
469 476 1.100510 CGTCGACCTGGGTGATCTTA 58.899 55.000 10.58 0.00 0.00 2.10
567 574 0.028770 ATGTGTGTGCCGACAAAACG 59.971 50.000 0.00 0.00 32.49 3.60
578 585 3.100817 CCGACAAAACGATCATGCATTC 58.899 45.455 0.00 0.00 35.09 2.67
680 688 6.369890 TCAAGCTCACACTGAAGAAATATGTC 59.630 38.462 0.00 0.00 0.00 3.06
757 770 7.821359 CCATCATCTACACTCTATTTATGTGGG 59.179 40.741 0.00 0.00 36.16 4.61
838 852 5.509501 CCCATGCAAACTATGTGTCAACTTT 60.510 40.000 0.00 0.00 0.00 2.66
1070 1086 2.661718 TGGTCACCACTATGCGATCTA 58.338 47.619 0.00 0.00 0.00 1.98
1195 1212 2.230508 GAGACATGGAACCGTCACTACA 59.769 50.000 0.00 0.00 32.97 2.74
1336 1354 7.701539 TCATTGCTATGTATGTCCTTTTTGT 57.298 32.000 8.01 0.00 33.34 2.83
1549 1567 2.289694 GGAGGCAGCTGTCAAGAAAGTA 60.290 50.000 22.50 0.00 0.00 2.24
1592 1610 3.107661 GCGTTACACACCGGACGG 61.108 66.667 9.46 9.56 42.03 4.79
1660 1679 9.698309 TTTGTTTCTTTGTCAAAACTATGTTCA 57.302 25.926 0.00 0.00 36.54 3.18
1798 1820 7.618442 ACAGCAGATACGTTTTATGTTTATCG 58.382 34.615 0.00 0.00 0.00 2.92
1894 1917 8.523915 TGGCAAAATGTAGTTCATCAGATATT 57.476 30.769 0.00 0.00 35.48 1.28
1984 2169 4.194640 CAGTACAGCTAACATGGCAGATT 58.805 43.478 0.00 0.00 0.00 2.40
1988 2173 3.054875 ACAGCTAACATGGCAGATTCAGA 60.055 43.478 0.00 0.00 0.00 3.27
2052 2260 8.166061 AGATCCAGTACAATTAACATGGCATAT 58.834 33.333 0.00 0.00 0.00 1.78
2215 2424 6.317391 CCTCAAGAGTCATTCTCCCAATTTAC 59.683 42.308 0.00 0.00 43.71 2.01
2285 2496 0.033366 GTCACAGCGCCCCAATTTTT 59.967 50.000 2.29 0.00 0.00 1.94
2342 2553 8.412456 TCTTGTGTTTTGCTTGAATCTTCAATA 58.588 29.630 5.86 0.00 45.26 1.90
2383 2594 2.105821 TCTTGGACGACCCTTTGTGATT 59.894 45.455 0.34 0.00 35.38 2.57
2395 2606 2.046700 GTGATTGAACGGGGCGGA 60.047 61.111 0.00 0.00 0.00 5.54
2423 2634 1.317613 CTGGGTTTGTGTGCTTGCTA 58.682 50.000 0.00 0.00 0.00 3.49
2567 2778 3.439440 AGGGCCTTCCTGTGTTTTC 57.561 52.632 0.00 0.00 46.07 2.29
2578 2789 2.689983 CCTGTGTTTTCCTGCAACTCTT 59.310 45.455 0.00 0.00 0.00 2.85
2659 2870 2.042831 GTGCCTCGCAGCTTCCATT 61.043 57.895 0.00 0.00 40.08 3.16
2669 2880 2.490903 GCAGCTTCCATTGTTGACTCAT 59.509 45.455 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.380064 TGTTGGAACTTGATTGCCCT 57.620 45.000 0.00 0.00 0.00 5.19
133 134 2.110967 CGGGCTCGTAGTCTTCCGA 61.111 63.158 0.00 0.00 39.83 4.55
182 183 5.234329 CCAAATCGCTTGACAATATCGTACT 59.766 40.000 0.00 0.00 37.17 2.73
221 223 1.280133 AGCTCCTTCATGTGCTTGCTA 59.720 47.619 0.00 0.00 30.96 3.49
264 266 6.432162 AGAGCAAAGCAAAATGAGAGATTGTA 59.568 34.615 0.00 0.00 0.00 2.41
392 399 7.092716 GTCCAAACATGAGCTGTATGAAAATT 58.907 34.615 13.05 2.42 36.98 1.82
431 438 1.766301 CGTACGTCGCTTCGTATTGAG 59.234 52.381 7.22 3.60 45.61 3.02
469 476 1.407656 TTTGGCCTCACGGACTCAGT 61.408 55.000 3.32 0.00 39.94 3.41
567 574 4.510711 CAGGTCACACTAGAATGCATGATC 59.489 45.833 0.00 0.00 0.00 2.92
578 585 4.336433 CCCATATTTTGCAGGTCACACTAG 59.664 45.833 0.00 0.00 0.00 2.57
618 625 7.071069 AGCAAAATTCTTCCTCAGGATTTTT 57.929 32.000 0.00 0.00 45.28 1.94
680 688 1.068121 AAACAGGGGGAGGAGAACTG 58.932 55.000 0.00 0.00 35.40 3.16
740 751 6.814954 ACATCTCCCACATAAATAGAGTGT 57.185 37.500 0.00 0.00 0.00 3.55
747 760 6.097270 CCACATGAAACATCTCCCACATAAAT 59.903 38.462 0.00 0.00 0.00 1.40
757 770 3.488721 GCTGATGCCACATGAAACATCTC 60.489 47.826 19.62 12.04 39.68 2.75
817 831 8.413229 ACTTTAAAGTTGACACATAGTTTGCAT 58.587 29.630 15.22 0.00 35.21 3.96
946 962 5.068636 AGCAGAGTTCACATGAAGAACAAT 58.931 37.500 25.92 16.48 45.93 2.71
1070 1086 3.403038 CGTTGGTTCTTCAGGTCAAGAT 58.597 45.455 0.00 0.00 32.32 2.40
1195 1212 5.532779 GTCTGATCTGGACCTTTGAGTTTTT 59.467 40.000 0.00 0.00 0.00 1.94
1336 1354 5.359194 AGAAAAAGAGTCAGGTGAACTCA 57.641 39.130 6.10 0.00 33.26 3.41
1386 1404 4.202202 CCCACTTTGCAAAGTATTCCAACA 60.202 41.667 37.19 1.64 46.89 3.33
1533 1551 6.791887 TCTTGATTACTTTCTTGACAGCTG 57.208 37.500 13.48 13.48 0.00 4.24
1549 1567 6.146184 CACGTGATCACTTGTACTTCTTGATT 59.854 38.462 22.95 0.00 0.00 2.57
1660 1679 3.245518 TGCACTCGTAACATAGCACAT 57.754 42.857 0.00 0.00 0.00 3.21
1748 1769 4.141482 ACGCCTAAATAGGTTCACATCCAT 60.141 41.667 8.24 0.00 45.42 3.41
1894 1917 4.233123 ACGACGATGACTTTCACTAACA 57.767 40.909 0.00 0.00 0.00 2.41
1984 2169 5.357878 GGATCTGCCATGTTAATTGTTCTGA 59.642 40.000 0.00 0.00 36.34 3.27
2098 2307 6.259167 TCCGCCATGTTATGTGTAGTTAATTC 59.741 38.462 0.00 0.00 0.00 2.17
2099 2308 6.116806 TCCGCCATGTTATGTGTAGTTAATT 58.883 36.000 0.00 0.00 0.00 1.40
2224 2433 5.818678 TGTTTCTACCCTAGATGTTGTGT 57.181 39.130 0.00 0.00 34.22 3.72
2285 2496 1.843851 AGGAACGGGCAATCCATAAGA 59.156 47.619 5.43 0.00 38.23 2.10
2342 2553 6.407074 CCAAGAGAGATAAGGTACAAATCGGT 60.407 42.308 0.00 0.00 0.00 4.69
2423 2634 4.396357 ACTCGGAGATAGGATCTGGAAT 57.604 45.455 12.86 0.00 40.38 3.01
2578 2789 1.345415 TGCAAGAGTGATGAGACAGCA 59.655 47.619 0.00 0.00 0.00 4.41
2648 2859 1.881973 TGAGTCAACAATGGAAGCTGC 59.118 47.619 0.00 0.00 0.00 5.25
2650 2861 3.755378 GACATGAGTCAACAATGGAAGCT 59.245 43.478 0.00 0.00 44.34 3.74
2669 2880 1.134995 GGATGTGCATGACGAGAGACA 60.135 52.381 0.00 0.00 40.57 3.41


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

AutoCloner maintained by Alex Coulton.