Multiple sequence alignment - TraesCS2A01G446600

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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 TraesCS2A01G446600 chr2A 100.000 2599 0 0 1 2599 695521748 695519150 0.000000e+00 4800
1 TraesCS2A01G446600 chr2A 82.799 343 48 9 1 334 695820447 695820107 1.960000e-76 296
2 TraesCS2A01G446600 chr2A 83.934 305 43 5 1 301 695978319 695978017 1.180000e-73 287
3 TraesCS2A01G446600 chr2D 94.336 1836 57 13 807 2599 556069667 556067836 0.000000e+00 2771
4 TraesCS2A01G446600 chr2D 88.164 828 53 13 1 798 556070458 556069646 0.000000e+00 944
5 TraesCS2A01G446600 chr2D 83.284 341 50 4 1 334 556224608 556224268 9.030000e-80 307
6 TraesCS2A01G446600 chr2B 96.296 756 27 1 858 1613 663139185 663138431 0.000000e+00 1240
7 TraesCS2A01G446600 chr2B 91.502 506 33 4 144 645 663139812 663139313 0.000000e+00 688
8 TraesCS2A01G446600 chr2B 87.264 424 42 7 1655 2068 663138417 663137996 8.420000e-130 473
9 TraesCS2A01G446600 chr2B 87.898 314 21 8 2288 2599 663137941 663137643 1.140000e-93 353
10 TraesCS2A01G446600 chr2B 79.218 486 63 19 1 474 663332742 663333201 1.170000e-78 303
11 TraesCS2A01G446600 chr2B 96.552 145 5 0 1 145 663140000 663139856 9.290000e-60 241
12 TraesCS2A01G446600 chr2B 88.983 118 9 2 682 799 663139307 663139194 2.700000e-30 143


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 TraesCS2A01G446600 chr2A 695519150 695521748 2598 True 4800.0 4800 100.000000 1 2599 1 chr2A.!!$R1 2598
1 TraesCS2A01G446600 chr2D 556067836 556070458 2622 True 1857.5 2771 91.250000 1 2599 2 chr2D.!!$R2 2598
2 TraesCS2A01G446600 chr2B 663137643 663140000 2357 True 523.0 1240 91.415833 1 2599 6 chr2B.!!$R1 2598

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
821 897 0.538287 GAAAGCAGACCTGGCACCTT 60.538 55.0 0.0 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2203 0.737804 TGCTCTTGACGCAAAAAGCA 59.262 45.0 17.31 17.31 46.13 3.91 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
170 221 6.813293 TTGAGTATGAGATTGATGAAGGGA 57.187 37.500 0.00 0.00 0.00 4.20
186 237 3.256281 GGAACCCTGAGCTTGAAGG 57.744 57.895 0.00 4.47 0.00 3.46
193 244 2.025887 CCCTGAGCTTGAAGGTATGGTT 60.026 50.000 0.00 0.00 0.00 3.67
197 248 4.832248 TGAGCTTGAAGGTATGGTTAGTG 58.168 43.478 0.00 0.00 0.00 2.74
295 346 4.926244 TCTTGCAATAACTCAACGCAAAA 58.074 34.783 0.00 0.00 41.63 2.44
308 359 6.128553 ACTCAACGCAAAATGTGTCTATACTG 60.129 38.462 0.00 0.00 40.68 2.74
330 385 7.628234 ACTGACAGATAAAAGTCTGATTCCAT 58.372 34.615 10.08 0.00 46.77 3.41
477 532 4.403432 CGGTCCATGTACCTTAACTTCCTA 59.597 45.833 5.85 0.00 37.39 2.94
492 547 9.745880 CTTAACTTCCTATCGTTAATGAAGCTA 57.254 33.333 0.55 0.00 36.71 3.32
569 624 6.473778 CACATACTAGGAAACGAGTCTCATTG 59.526 42.308 0.00 0.00 43.30 2.82
570 625 6.377429 ACATACTAGGAAACGAGTCTCATTGA 59.623 38.462 0.00 0.00 43.30 2.57
571 626 5.061920 ACTAGGAAACGAGTCTCATTGAC 57.938 43.478 0.00 0.00 43.30 3.18
572 627 4.523173 ACTAGGAAACGAGTCTCATTGACA 59.477 41.667 0.00 0.00 43.30 3.58
573 628 5.186021 ACTAGGAAACGAGTCTCATTGACAT 59.814 40.000 0.00 0.00 43.30 3.06
574 629 6.295349 ACTAGGAAACGAGTCTCATTGACATT 60.295 38.462 0.00 0.00 43.30 2.71
668 744 9.618890 ACACATCATATAGACAATTAAAGCAGT 57.381 29.630 0.00 0.00 0.00 4.40
671 747 8.562052 CATCATATAGACAATTAAAGCAGTGCA 58.438 33.333 19.20 0.00 0.00 4.57
698 774 4.033014 GCCTTTCCTCGAAAAAGATACTCG 59.967 45.833 17.30 5.07 36.09 4.18
760 836 8.768955 GCCAAATACAGATAAGATGTAACTCAG 58.231 37.037 0.00 0.00 36.75 3.35
793 869 2.919328 GCAGGCCTGGCACCTTTT 60.919 61.111 33.46 0.00 34.42 2.27
794 870 2.510551 GCAGGCCTGGCACCTTTTT 61.511 57.895 33.46 0.00 34.42 1.94
818 894 3.257933 CGAAAGCAGACCTGGCAC 58.742 61.111 0.00 0.00 0.00 5.01
819 895 2.328099 CGAAAGCAGACCTGGCACC 61.328 63.158 0.00 0.00 0.00 5.01
820 896 1.073897 GAAAGCAGACCTGGCACCT 59.926 57.895 0.00 0.00 0.00 4.00
821 897 0.538287 GAAAGCAGACCTGGCACCTT 60.538 55.000 0.00 0.00 0.00 3.50
825 901 1.355720 AGCAGACCTGGCACCTTATTT 59.644 47.619 0.00 0.00 0.00 1.40
1089 1165 1.761198 GGTCTCCGTATTAGCCAGGTT 59.239 52.381 0.00 0.00 0.00 3.50
1152 1228 0.400213 TTGAAGGAGATGGCGGTGTT 59.600 50.000 0.00 0.00 0.00 3.32
1222 1298 4.935352 TGCACTTCAGTTATGCCTTTTT 57.065 36.364 0.00 0.00 38.63 1.94
1275 1351 3.569250 AATTTCAATTTCCGTGGTCCG 57.431 42.857 0.00 0.00 0.00 4.79
1481 1557 6.128982 CCATCGAATATGAAGTTGATGACGAG 60.129 42.308 4.97 0.00 36.25 4.18
1557 1633 6.324770 TGAGGCAATCACAGAGTATATCAAGA 59.675 38.462 0.00 0.00 31.12 3.02
1574 1651 1.953559 AGACACAGAAAAGCGCTGAA 58.046 45.000 12.58 0.00 36.86 3.02
1627 1704 2.533232 CCCCCACCCCCAAGTGTA 60.533 66.667 0.00 0.00 35.93 2.90
1642 1719 5.273944 CCAAGTGTAAAACAAGTTCAGAGC 58.726 41.667 0.00 0.00 0.00 4.09
1767 1849 7.109501 TGATTTCGATGGTTCTCAAAAGGATA 58.890 34.615 0.00 0.00 0.00 2.59
1843 1926 9.781834 GGGTTGATTTTAAGTTTTTGGAAAAAG 57.218 29.630 0.00 0.00 38.44 2.27
1892 1975 1.387295 GCTACCCATTGCCAGAAGCC 61.387 60.000 0.00 0.00 42.71 4.35
1980 2063 5.593909 CCTAGGCCAATCATTTACATCACAA 59.406 40.000 5.01 0.00 0.00 3.33
1987 2070 8.971321 GCCAATCATTTACATCACAATATTCAC 58.029 33.333 0.00 0.00 0.00 3.18
2036 2121 9.613428 AAGCTTGCAGTGAGTATTACATATTTA 57.387 29.630 0.00 0.00 0.00 1.40
2107 2194 4.476846 ACAAAATTTTGGGGGAAGAAACCT 59.523 37.500 29.37 6.04 42.34 3.50
2109 2196 2.095604 TTTTGGGGGAAGAAACCTGG 57.904 50.000 0.00 0.00 0.00 4.45
2111 2198 1.466858 TTGGGGGAAGAAACCTGGAT 58.533 50.000 0.00 0.00 0.00 3.41
2116 2203 2.460669 GGGAAGAAACCTGGATGCATT 58.539 47.619 0.00 0.00 0.00 3.56
2135 2222 0.737804 TGCTTTTTGCGTCAAGAGCA 59.262 45.000 18.82 18.82 46.63 4.26
2261 2379 5.694910 CCGTGCTATTCTCGGTATAAAACAT 59.305 40.000 0.00 0.00 44.39 2.71
2308 2426 8.593492 AAGGATAAAACACTTCAAAGAAATGC 57.407 30.769 0.00 0.00 0.00 3.56
2316 2434 7.935338 ACACTTCAAAGAAATGCAATACTTG 57.065 32.000 0.00 0.00 0.00 3.16
2435 2553 4.160252 ACTTTGTTTTGGTGCTCAGTCATT 59.840 37.500 0.00 0.00 0.00 2.57
2440 2558 6.472016 TGTTTTGGTGCTCAGTCATTCTATA 58.528 36.000 0.00 0.00 0.00 1.31
2466 2586 6.884295 TCTTGTATAAAAGGAACACCTCATGG 59.116 38.462 2.74 0.00 39.83 3.66
2493 2613 3.892588 TCCCCAATTGGTAAACAAGACAC 59.107 43.478 22.91 0.00 43.48 3.67
2494 2614 3.006430 CCCCAATTGGTAAACAAGACACC 59.994 47.826 22.91 0.00 43.48 4.16
2544 2666 1.565759 ACAGCATCCTTGGAAGGCATA 59.434 47.619 15.61 0.00 46.06 3.14
2565 2687 1.195442 TACCCATCGCCTCCAACACA 61.195 55.000 0.00 0.00 0.00 3.72
2575 2697 1.021202 CTCCAACACAAAACGCCTCA 58.979 50.000 0.00 0.00 0.00 3.86
2576 2698 1.608590 CTCCAACACAAAACGCCTCAT 59.391 47.619 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.626028 AGTTTTCATTGTCGACCTTGC 57.374 42.857 14.12 0.00 0.00 4.01
170 221 2.025887 CCATACCTTCAAGCTCAGGGTT 60.026 50.000 10.52 0.00 34.02 4.11
186 237 0.107848 AGGTGCGGCACTAACCATAC 60.108 55.000 29.92 12.61 34.45 2.39
283 334 5.932303 AGTATAGACACATTTTGCGTTGAGT 59.068 36.000 0.00 0.00 0.00 3.41
288 339 5.234752 TGTCAGTATAGACACATTTTGCGT 58.765 37.500 0.00 0.00 43.18 5.24
308 359 7.856145 ACATGGAATCAGACTTTTATCTGTC 57.144 36.000 0.00 0.00 45.41 3.51
359 414 3.555139 GTCTGATCTGGCTCTCAAATTCG 59.445 47.826 0.00 0.00 0.00 3.34
477 532 6.324254 AGAGTTACCCTAGCTTCATTAACGAT 59.676 38.462 0.00 0.00 0.00 3.73
569 624 9.294030 CTTAAGAACAAAATGCCTATGAATGTC 57.706 33.333 0.00 0.00 0.00 3.06
570 625 8.253113 CCTTAAGAACAAAATGCCTATGAATGT 58.747 33.333 3.36 0.00 0.00 2.71
571 626 7.223387 GCCTTAAGAACAAAATGCCTATGAATG 59.777 37.037 3.36 0.00 0.00 2.67
572 627 7.267857 GCCTTAAGAACAAAATGCCTATGAAT 58.732 34.615 3.36 0.00 0.00 2.57
573 628 6.350949 GGCCTTAAGAACAAAATGCCTATGAA 60.351 38.462 3.36 0.00 34.62 2.57
574 629 5.127031 GGCCTTAAGAACAAAATGCCTATGA 59.873 40.000 3.36 0.00 34.62 2.15
648 724 6.854892 GCTGCACTGCTTTAATTGTCTATATG 59.145 38.462 1.98 0.00 0.00 1.78
654 730 3.240069 CAGCTGCACTGCTTTAATTGTC 58.760 45.455 0.00 0.00 41.98 3.18
668 744 2.359107 CGAGGAAAGGCAGCTGCA 60.359 61.111 37.63 0.00 44.36 4.41
671 747 1.882623 CTTTTTCGAGGAAAGGCAGCT 59.117 47.619 12.87 0.00 32.93 4.24
717 793 7.831690 TGTATTTGGCTTGACTGGTCATAATAA 59.168 33.333 4.19 0.00 39.64 1.40
718 794 7.342581 TGTATTTGGCTTGACTGGTCATAATA 58.657 34.615 4.19 2.84 39.64 0.98
719 795 6.186957 TGTATTTGGCTTGACTGGTCATAAT 58.813 36.000 4.19 3.60 39.64 1.28
760 836 0.458669 CTGCCAGGTTGCCATCAATC 59.541 55.000 0.00 0.00 34.29 2.67
799 875 2.669569 GCCAGGTCTGCTTTCGCA 60.670 61.111 0.00 0.00 45.60 5.10
800 876 2.669569 TGCCAGGTCTGCTTTCGC 60.670 61.111 0.00 0.00 0.00 4.70
801 877 2.328099 GGTGCCAGGTCTGCTTTCG 61.328 63.158 0.00 0.00 0.00 3.46
802 878 0.538287 AAGGTGCCAGGTCTGCTTTC 60.538 55.000 0.00 0.00 0.00 2.62
803 879 0.771127 TAAGGTGCCAGGTCTGCTTT 59.229 50.000 0.00 0.00 0.00 3.51
804 880 0.995024 ATAAGGTGCCAGGTCTGCTT 59.005 50.000 0.00 0.00 0.00 3.91
805 881 0.995024 AATAAGGTGCCAGGTCTGCT 59.005 50.000 0.00 0.00 0.00 4.24
806 882 1.839424 AAATAAGGTGCCAGGTCTGC 58.161 50.000 0.00 0.00 0.00 4.26
807 883 5.476945 AGTTAAAAATAAGGTGCCAGGTCTG 59.523 40.000 0.00 0.00 0.00 3.51
808 884 5.641155 AGTTAAAAATAAGGTGCCAGGTCT 58.359 37.500 0.00 0.00 0.00 3.85
809 885 5.977489 AGTTAAAAATAAGGTGCCAGGTC 57.023 39.130 0.00 0.00 0.00 3.85
810 886 9.350951 GATATAGTTAAAAATAAGGTGCCAGGT 57.649 33.333 0.00 0.00 0.00 4.00
811 887 9.349713 TGATATAGTTAAAAATAAGGTGCCAGG 57.650 33.333 0.00 0.00 0.00 4.45
838 914 6.983890 TCTGAATAGACAATGCGCTGTTTATA 59.016 34.615 9.73 1.20 29.15 0.98
839 915 5.817296 TCTGAATAGACAATGCGCTGTTTAT 59.183 36.000 9.73 7.97 30.14 1.40
1089 1165 1.073125 TCGGGAAGCAATTGAGGAACA 59.927 47.619 10.34 0.00 0.00 3.18
1152 1228 2.229792 GTGAGATGCAAAACTGTCCCA 58.770 47.619 0.00 0.00 0.00 4.37
1222 1298 7.503521 TGATGCATATATTACGAAGCCAAAA 57.496 32.000 0.00 0.00 0.00 2.44
1275 1351 0.960861 GGAGCAACCCCTAGCAACAC 60.961 60.000 0.00 0.00 0.00 3.32
1481 1557 2.191128 AGGATGTGTTGCCTGTCTTC 57.809 50.000 0.00 0.00 32.06 2.87
1557 1633 1.378531 TGTTCAGCGCTTTTCTGTGT 58.621 45.000 7.50 0.00 33.48 3.72
1574 1651 2.754552 TGCTGTTTCTTCACAAGCTTGT 59.245 40.909 26.36 26.36 43.36 3.16
1581 1658 6.691754 TTGTTCTTATGCTGTTTCTTCACA 57.308 33.333 0.00 0.00 0.00 3.58
1627 1704 8.552083 AAAGAAAATTGCTCTGAACTTGTTTT 57.448 26.923 0.00 0.00 0.00 2.43
1767 1849 6.310764 TCATTATTGCATCCCCAAAATTGT 57.689 33.333 0.00 0.00 0.00 2.71
1843 1926 7.436376 GGCTTTTGTTTTATCATCTAGCCATTC 59.564 37.037 0.00 0.00 43.84 2.67
1892 1975 5.945784 TCAGATGGAAATTTTGGTACTCTGG 59.054 40.000 0.00 0.00 0.00 3.86
1987 2070 8.663025 GCTTGTGTATGTGATATATTCTGGATG 58.337 37.037 0.00 0.00 0.00 3.51
2002 2086 2.810274 CTCACTGCAAGCTTGTGTATGT 59.190 45.455 26.55 15.03 37.60 2.29
2036 2121 7.243604 TGGATCAAGCCATTTTAGAACAAAT 57.756 32.000 0.00 0.00 31.66 2.32
2107 2194 1.270199 ACGCAAAAAGCAATGCATCCA 60.270 42.857 8.35 0.00 46.13 3.41
2109 2196 2.060284 TGACGCAAAAAGCAATGCATC 58.940 42.857 8.35 0.00 46.13 3.91
2111 2198 1.859703 CTTGACGCAAAAAGCAATGCA 59.140 42.857 8.35 0.00 46.13 3.96
2116 2203 0.737804 TGCTCTTGACGCAAAAAGCA 59.262 45.000 17.31 17.31 46.13 3.91
2135 2222 1.488812 TGCGTATTAGGTGGAGCCATT 59.511 47.619 0.00 0.00 40.61 3.16
2316 2434 8.760569 GTTTCTCTACATTTAGCTTAGCATCTC 58.239 37.037 7.07 0.00 0.00 2.75
2418 2536 7.568349 AGATATAGAATGACTGAGCACCAAAA 58.432 34.615 0.00 0.00 0.00 2.44
2440 2558 7.557719 CCATGAGGTGTTCCTTTTATACAAGAT 59.442 37.037 0.00 0.00 45.24 2.40
2450 2568 1.272147 GCTCCCATGAGGTGTTCCTTT 60.272 52.381 0.00 0.00 45.24 3.11
2453 2571 4.645809 GCTCCCATGAGGTGTTCC 57.354 61.111 0.00 0.00 39.14 3.62
2466 2586 2.100197 GTTTACCAATTGGGGAGCTCC 58.900 52.381 27.89 25.59 42.91 4.70
2493 2613 5.705441 TGAGTATTTGTTTTCTACTGCTGGG 59.295 40.000 0.00 0.00 0.00 4.45
2494 2614 6.621596 GCTGAGTATTTGTTTTCTACTGCTGG 60.622 42.308 0.00 0.00 0.00 4.85
2544 2666 0.916086 TGTTGGAGGCGATGGGTATT 59.084 50.000 0.00 0.00 0.00 1.89
2565 2687 2.744202 CTGCTACTCAATGAGGCGTTTT 59.256 45.455 15.38 0.00 33.35 2.43
2575 2697 3.077359 GCTGGTGAAACTGCTACTCAAT 58.923 45.455 0.00 0.00 36.74 2.57
2576 2698 2.104792 AGCTGGTGAAACTGCTACTCAA 59.895 45.455 0.00 0.00 42.54 3.02


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

AutoCloner maintained by Alex Coulton.