Multiple sequence alignment - TraesCS4D01G353400

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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 TraesCS4D01G353400 chr4D 100.000 3186 0 0 746 3931 503999674 503996489 0.000000e+00 5884.0
1 TraesCS4D01G353400 chr4D 100.000 500 0 0 1 500 504000419 503999920 0.000000e+00 924.0
2 TraesCS4D01G353400 chr4B 97.372 2511 55 2 772 3281 650409596 650407096 0.000000e+00 4261.0
3 TraesCS4D01G353400 chr4B 97.331 2510 56 2 773 3281 650529779 650527280 0.000000e+00 4253.0
4 TraesCS4D01G353400 chr4B 96.239 2313 65 6 1618 3930 650456939 650454649 0.000000e+00 3770.0
5 TraesCS4D01G353400 chr4B 97.112 2216 51 3 1069 3281 650504348 650502143 0.000000e+00 3740.0
6 TraesCS4D01G353400 chr4B 97.887 1609 23 2 1538 3145 650489208 650487610 0.000000e+00 2772.0
7 TraesCS4D01G353400 chr4B 95.173 808 37 2 746 1552 650457750 650456944 0.000000e+00 1275.0
8 TraesCS4D01G353400 chr4B 94.548 697 27 5 3234 3930 650442466 650441781 0.000000e+00 1066.0
9 TraesCS4D01G353400 chr4B 96.032 504 13 4 1 500 650491065 650490565 0.000000e+00 813.0
10 TraesCS4D01G353400 chr4B 96.032 504 13 4 1 500 650504889 650504389 0.000000e+00 813.0
11 TraesCS4D01G353400 chr4B 95.335 493 16 4 1 489 650530279 650529790 0.000000e+00 776.0
12 TraesCS4D01G353400 chr4B 95.132 493 17 4 1 489 650410146 650409657 0.000000e+00 771.0
13 TraesCS4D01G353400 chr4B 94.778 383 16 2 3359 3741 650484674 650484296 9.400000e-166 593.0
14 TraesCS4D01G353400 chr4B 94.595 370 14 3 1 364 650458237 650457868 5.700000e-158 568.0
15 TraesCS4D01G353400 chr4B 94.550 367 16 2 3375 3741 650523647 650523285 7.370000e-157 564.0
16 TraesCS4D01G353400 chr4B 93.939 264 15 1 3478 3741 650403816 650403554 7.910000e-107 398.0
17 TraesCS4D01G353400 chr4B 96.970 198 6 0 3727 3924 650482886 650482689 2.260000e-87 333.0
18 TraesCS4D01G353400 chr4B 96.465 198 7 0 3727 3924 650521873 650521676 1.050000e-85 327.0
19 TraesCS4D01G353400 chrUn 82.524 2409 328 54 910 3267 110472031 110474397 0.000000e+00 2030.0
20 TraesCS4D01G353400 chrUn 95.166 662 21 2 2621 3281 264767441 264766790 0.000000e+00 1035.0
21 TraesCS4D01G353400 chrUn 93.421 456 17 4 3295 3741 264763233 264762782 0.000000e+00 664.0
22 TraesCS4D01G353400 chrUn 96.970 198 6 0 3727 3924 264761370 264761173 2.260000e-87 333.0
23 TraesCS4D01G353400 chr5D 89.677 1114 113 2 1799 2911 5275057 5273945 0.000000e+00 1419.0
24 TraesCS4D01G353400 chr5D 84.123 907 121 14 759 1645 5275957 5275054 0.000000e+00 856.0
25 TraesCS4D01G353400 chr5B 89.346 1117 117 2 1796 2911 6624778 6625893 0.000000e+00 1402.0
26 TraesCS4D01G353400 chr5B 85.352 867 113 12 751 1607 6623874 6624736 0.000000e+00 885.0
27 TraesCS4D01G353400 chr5B 81.142 928 142 23 751 1656 6473716 6474632 0.000000e+00 713.0
28 TraesCS4D01G353400 chr5B 85.135 148 19 2 3111 3256 6475854 6476000 8.800000e-32 148.0
29 TraesCS4D01G353400 chr5A 89.078 1117 120 2 1796 2911 3515100 3516215 0.000000e+00 1386.0
30 TraesCS4D01G353400 chr5A 84.828 870 118 11 751 1609 3505668 3506534 0.000000e+00 863.0
31 TraesCS4D01G353400 chr5A 89.130 138 11 3 3118 3255 700175657 700175524 6.760000e-38 169.0
32 TraesCS4D01G353400 chr5A 86.755 151 17 2 3120 3268 3614996 3614847 8.740000e-37 165.0
33 TraesCS4D01G353400 chr5A 77.202 193 39 5 3459 3650 3518300 3518488 1.490000e-19 108.0
34 TraesCS4D01G353400 chr5A 83.871 93 10 4 139 229 3620750 3620661 2.520000e-12 84.2
35 TraesCS4D01G353400 chr6A 91.489 47 2 1 243 287 158408207 158408253 3.280000e-06 63.9
36 TraesCS4D01G353400 chr3A 90.909 44 3 1 244 286 589821903 589821946 1.530000e-04 58.4
37 TraesCS4D01G353400 chr3B 90.244 41 3 1 244 283 588489365 588489405 7.000000e-03 52.8


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 TraesCS4D01G353400 chr4D 503996489 504000419 3930 True 3404.000000 5884 100.000000 1 3931 2 chr4D.!!$R1 3930
1 TraesCS4D01G353400 chr4B 650502143 650504889 2746 True 2276.500000 3740 96.572000 1 3281 2 chr4B.!!$R5 3280
2 TraesCS4D01G353400 chr4B 650454649 650458237 3588 True 1871.000000 3770 95.335667 1 3930 3 chr4B.!!$R3 3929
3 TraesCS4D01G353400 chr4B 650403554 650410146 6592 True 1810.000000 4261 95.481000 1 3741 3 chr4B.!!$R2 3740
4 TraesCS4D01G353400 chr4B 650521676 650530279 8603 True 1480.000000 4253 95.920250 1 3924 4 chr4B.!!$R6 3923
5 TraesCS4D01G353400 chr4B 650482689 650491065 8376 True 1127.750000 2772 96.416750 1 3924 4 chr4B.!!$R4 3923
6 TraesCS4D01G353400 chr4B 650441781 650442466 685 True 1066.000000 1066 94.548000 3234 3930 1 chr4B.!!$R1 696
7 TraesCS4D01G353400 chrUn 110472031 110474397 2366 False 2030.000000 2030 82.524000 910 3267 1 chrUn.!!$F1 2357
8 TraesCS4D01G353400 chrUn 264761173 264767441 6268 True 677.333333 1035 95.185667 2621 3924 3 chrUn.!!$R1 1303
9 TraesCS4D01G353400 chr5D 5273945 5275957 2012 True 1137.500000 1419 86.900000 759 2911 2 chr5D.!!$R1 2152
10 TraesCS4D01G353400 chr5B 6623874 6625893 2019 False 1143.500000 1402 87.349000 751 2911 2 chr5B.!!$F2 2160
11 TraesCS4D01G353400 chr5B 6473716 6476000 2284 False 430.500000 713 83.138500 751 3256 2 chr5B.!!$F1 2505
12 TraesCS4D01G353400 chr5A 3505668 3506534 866 False 863.000000 863 84.828000 751 1609 1 chr5A.!!$F1 858
13 TraesCS4D01G353400 chr5A 3515100 3518488 3388 False 747.000000 1386 83.140000 1796 3650 2 chr5A.!!$F2 1854

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
820 830 0.511221 ATTGTGCGAACCGAGAAACG 59.489 50.000 0.0 0.0 42.18 3.60 F
827 837 2.472397 GCGAACCGAGAAACGAATGAAG 60.472 50.000 0.0 0.0 45.77 3.02 F
1156 1188 3.646162 TGTCCTTGCTCTCTTACCTTCAA 59.354 43.478 0.0 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 2091 0.454620 GACTGAGTGGACTGCGTACG 60.455 60.000 11.84 11.84 0.00 3.67 R
1854 2293 6.610830 TCAGTACCCATGTCATCTACATCTA 58.389 40.000 0.00 0.00 46.15 1.98 R
3041 3486 1.376683 TCGTTGCTGGTATGTGCCC 60.377 57.895 0.00 0.00 0.00 5.36 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
194 197 6.794374 TGTATTGATATTGTGTTGCATGACC 58.206 36.000 0.00 0.00 0.00 4.02
370 380 6.619329 TCTAATTTTGGCAGGGCTAATTTT 57.381 33.333 10.10 3.06 0.00 1.82
450 460 7.894376 ACAAATGTGAAAATGTCCATGAATC 57.106 32.000 0.00 0.00 0.00 2.52
820 830 0.511221 ATTGTGCGAACCGAGAAACG 59.489 50.000 0.00 0.00 42.18 3.60
827 837 2.472397 GCGAACCGAGAAACGAATGAAG 60.472 50.000 0.00 0.00 45.77 3.02
902 919 9.025020 GTCTCACCATATTTATAGACATATGCG 57.975 37.037 1.58 0.00 33.60 4.73
1156 1188 3.646162 TGTCCTTGCTCTCTTACCTTCAA 59.354 43.478 0.00 0.00 0.00 2.69
1346 1378 4.384427 GGAGGTTACCGTTCCCATATTTGA 60.384 45.833 0.00 0.00 0.00 2.69
1528 1564 5.753921 CCTATGGCTTTTCTTCGGTTACTAG 59.246 44.000 0.00 0.00 0.00 2.57
1534 1570 7.118680 TGGCTTTTCTTCGGTTACTAGTTAATG 59.881 37.037 0.00 0.00 0.00 1.90
2017 2457 4.631813 GCTCATGTTTATCTCAAGTCGGTT 59.368 41.667 0.00 0.00 0.00 4.44
2900 3340 8.226819 AGCCTAAAGGAAAAGTAATGATAAGC 57.773 34.615 0.00 0.00 37.39 3.09
3162 3610 5.650283 AGAATTTGGGTATGGAAAGGTTCA 58.350 37.500 0.00 0.00 0.00 3.18
3282 3730 8.077991 CAGTCAATACAGAAAATCAATGTGTGT 58.922 33.333 0.00 0.00 0.00 3.72
3283 3731 8.077991 AGTCAATACAGAAAATCAATGTGTGTG 58.922 33.333 0.00 0.00 0.00 3.82
3284 3732 7.862372 GTCAATACAGAAAATCAATGTGTGTGT 59.138 33.333 0.00 0.00 0.00 3.72
3285 3733 9.061435 TCAATACAGAAAATCAATGTGTGTGTA 57.939 29.630 0.00 0.00 0.00 2.90
3286 3734 9.844790 CAATACAGAAAATCAATGTGTGTGTAT 57.155 29.630 0.00 0.00 31.52 2.29
3326 7443 2.938798 CTTAGCCCCCACCCCACA 60.939 66.667 0.00 0.00 0.00 4.17
3335 7461 3.722813 CACCCCACACCCCGCATA 61.723 66.667 0.00 0.00 0.00 3.14
3569 7747 0.320421 GCTCCGCACCTTGTAAGTCA 60.320 55.000 0.00 0.00 0.00 3.41
3699 7877 0.250727 ACAACATGCCACTACGCCTT 60.251 50.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 197 7.234187 TGTTCTGCTTATCTATTACAAAGCG 57.766 36.000 0.00 0.00 45.72 4.68
262 268 0.479378 TAAAAGGCCCAACCCGACTT 59.521 50.000 0.00 0.00 40.58 3.01
370 380 5.637810 GCGTGGATGATCGATATTAGGAAAA 59.362 40.000 0.00 0.00 0.00 2.29
411 421 3.376859 ACATTTGTAGTGTGTGTGTGTGG 59.623 43.478 0.00 0.00 0.00 4.17
412 422 4.094146 TCACATTTGTAGTGTGTGTGTGTG 59.906 41.667 6.20 0.00 45.45 3.82
413 423 4.257731 TCACATTTGTAGTGTGTGTGTGT 58.742 39.130 6.20 0.00 45.45 3.72
423 433 7.523293 TCATGGACATTTTCACATTTGTAGT 57.477 32.000 0.00 0.00 0.00 2.73
450 460 9.770097 ACTAACATAACTGAGATTCCATATGTG 57.230 33.333 1.24 0.00 35.00 3.21
745 755 3.644966 TCCATACAAGACCATGAACCC 57.355 47.619 0.00 0.00 0.00 4.11
746 756 5.527582 GTGTATCCATACAAGACCATGAACC 59.472 44.000 0.85 0.00 44.11 3.62
747 757 6.112734 TGTGTATCCATACAAGACCATGAAC 58.887 40.000 0.85 0.00 44.11 3.18
748 758 6.306643 TGTGTATCCATACAAGACCATGAA 57.693 37.500 0.85 0.00 44.11 2.57
820 830 9.722056 AGTGATTTCGCATTTAATACTTCATTC 57.278 29.630 0.00 0.00 0.00 2.67
876 887 9.025020 CGCATATGTCTATAAATATGGTGAGAC 57.975 37.037 4.29 0.00 37.28 3.36
883 900 9.252962 TCAGATGCGCATATGTCTATAAATATG 57.747 33.333 35.96 14.66 38.99 1.78
902 919 9.579768 CATATATTGAGGTAGTAAGTCAGATGC 57.420 37.037 0.00 0.00 0.00 3.91
1156 1188 5.718801 ACCCCAAAACCCTTGTTAAAAAT 57.281 34.783 0.00 0.00 33.30 1.82
1346 1378 6.597562 TCTACACCATACAAAACTTCTTGGT 58.402 36.000 0.00 0.00 37.96 3.67
1734 2091 0.454620 GACTGAGTGGACTGCGTACG 60.455 60.000 11.84 11.84 0.00 3.67
1774 2131 7.981789 TGCTAATCCAATGTGTTGTTTTACAAA 59.018 29.630 0.00 0.00 40.15 2.83
1854 2293 6.610830 TCAGTACCCATGTCATCTACATCTA 58.389 40.000 0.00 0.00 46.15 1.98
2900 3340 3.066900 ACTGTAGCTGGCGTCTGTTATAG 59.933 47.826 11.52 11.52 0.00 1.31
3039 3484 2.052104 GTTGCTGGTATGTGCCCCC 61.052 63.158 0.00 0.00 0.00 5.40
3040 3485 2.406616 CGTTGCTGGTATGTGCCCC 61.407 63.158 0.00 0.00 0.00 5.80
3041 3486 1.376683 TCGTTGCTGGTATGTGCCC 60.377 57.895 0.00 0.00 0.00 5.36
3042 3487 1.794222 GTCGTTGCTGGTATGTGCC 59.206 57.895 0.00 0.00 0.00 5.01
3043 3488 1.419922 CGTCGTTGCTGGTATGTGC 59.580 57.895 0.00 0.00 0.00 4.57
3162 3610 2.880167 GCAGGAAAACCTTCTTCGGGAT 60.880 50.000 0.00 0.00 0.00 3.85
3699 7877 4.404394 TCCTCACGATTATTCTTACTGCCA 59.596 41.667 0.00 0.00 0.00 4.92
3741 7925 6.746104 TGCGAACATAAAAACATGAAGTTG 57.254 33.333 0.00 0.00 41.19 3.16


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

AutoCloner maintained by Alex Coulton.