Multiple sequence alignment - TraesCS2D01G449600

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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 TraesCS2D01G449600 chr2D 100.000 4470 0 0 1 4470 559213736 559209267 0.000000e+00 8255.0
1 TraesCS2D01G449600 chr2D 87.387 1998 208 19 1763 3739 559304573 559302599 0.000000e+00 2254.0
2 TraesCS2D01G449600 chr2D 85.312 1348 129 26 758 2083 559305709 559304409 0.000000e+00 1328.0
3 TraesCS2D01G449600 chr2D 76.294 734 147 17 2308 3026 559304412 559303691 2.540000e-97 366.0
4 TraesCS2D01G449600 chr2D 81.182 457 53 25 3934 4387 559302490 559302064 1.990000e-88 337.0
5 TraesCS2D01G449600 chr2D 75.273 732 139 22 1924 2629 559211429 559210714 1.210000e-80 311.0
6 TraesCS2D01G449600 chr2D 75.171 729 145 18 2308 3023 559211813 559211108 1.210000e-80 311.0
7 TraesCS2D01G449600 chr2D 84.914 232 35 0 1697 1928 559211494 559211263 7.480000e-58 235.0
8 TraesCS2D01G449600 chr2D 84.914 232 35 0 2243 2474 559212040 559211809 7.480000e-58 235.0
9 TraesCS2D01G449600 chr2D 84.699 183 28 0 2293 2475 559304751 559304569 2.750000e-42 183.0
10 TraesCS2D01G449600 chr2D 79.167 168 30 3 2848 3014 559304256 559304093 1.310000e-20 111.0
11 TraesCS2D01G449600 chr2D 97.436 39 1 0 4257 4295 559209387 559209349 2.890000e-07 67.6
12 TraesCS2D01G449600 chr2D 97.436 39 1 0 4350 4388 559209480 559209442 2.890000e-07 67.6
13 TraesCS2D01G449600 chr2D 100.000 33 0 0 4435 4467 477238943 477238911 1.340000e-05 62.1
14 TraesCS2D01G449600 chr2A 93.297 3103 172 19 681 3765 699800065 699796981 0.000000e+00 4545.0
15 TraesCS2D01G449600 chr2A 85.670 1612 194 13 1998 3596 699852500 699850913 0.000000e+00 1663.0
16 TraesCS2D01G449600 chr2A 85.693 1349 127 18 758 2083 699853990 699852685 0.000000e+00 1362.0
17 TraesCS2D01G449600 chr2A 93.989 549 21 1 3934 4470 699796915 699796367 0.000000e+00 821.0
18 TraesCS2D01G449600 chr2A 86.255 713 57 21 1 692 699801834 699801142 0.000000e+00 736.0
19 TraesCS2D01G449600 chr2A 75.995 729 145 19 2308 3023 699798824 699798113 2.560000e-92 350.0
20 TraesCS2D01G449600 chr2A 74.652 647 136 17 1923 2555 699798435 699797803 1.230000e-65 261.0
21 TraesCS2D01G449600 chr2A 85.345 232 34 0 1697 1928 699798499 699798268 1.610000e-59 241.0
22 TraesCS2D01G449600 chr2A 86.170 188 24 2 1763 1949 699852687 699852501 7.580000e-48 202.0
23 TraesCS2D01G449600 chr2A 81.000 100 15 3 304 400 83709102 83709004 4.790000e-10 76.8
24 TraesCS2D01G449600 chr2A 94.872 39 2 0 4350 4388 699796592 699796554 1.340000e-05 62.1
25 TraesCS2D01G449600 chr2A 85.714 56 6 2 483 536 459448069 459448124 1.740000e-04 58.4
26 TraesCS2D01G449600 chr2A 92.308 39 3 0 4257 4295 699796499 699796461 6.250000e-04 56.5
27 TraesCS2D01G449600 chr2B 84.679 2056 256 24 1007 3023 668183029 668180994 0.000000e+00 1997.0
28 TraesCS2D01G449600 chr2B 93.926 889 52 2 2879 3765 668175004 668174116 0.000000e+00 1341.0
29 TraesCS2D01G449600 chr2B 90.402 969 84 3 1923 2882 668181709 668180741 0.000000e+00 1266.0
30 TraesCS2D01G449600 chr2B 93.578 545 16 8 3934 4465 668174050 668173512 0.000000e+00 795.0
31 TraesCS2D01G449600 chr2B 77.565 731 141 17 2308 3024 668182098 668181377 1.920000e-113 420.0
32 TraesCS2D01G449600 chr2B 84.821 224 34 0 1705 1928 668181765 668181542 4.500000e-55 226.0
33 TraesCS2D01G449600 chr2B 84.120 233 37 0 2243 2475 668182325 668182093 4.500000e-55 226.0
34 TraesCS2D01G449600 chr2B 97.619 42 1 0 4347 4388 668173735 668173694 6.200000e-09 73.1
35 TraesCS2D01G449600 chr2B 80.808 99 11 7 302 396 472907950 472908044 2.230000e-08 71.3
36 TraesCS2D01G449600 chr2B 97.436 39 1 0 4257 4295 668173639 668173601 2.890000e-07 67.6
37 TraesCS2D01G449600 chr5B 91.747 521 34 3 2450 2961 339532876 339532356 0.000000e+00 715.0
38 TraesCS2D01G449600 chr5B 96.992 133 4 0 3809 3941 97292257 97292389 1.620000e-54 224.0
39 TraesCS2D01G449600 chr6D 96.350 137 4 1 3805 3941 160470778 160470643 1.620000e-54 224.0
40 TraesCS2D01G449600 chr6D 96.970 132 4 0 3809 3940 217550874 217550743 5.820000e-54 222.0
41 TraesCS2D01G449600 chr6D 97.674 129 3 0 3809 3937 265045554 265045682 5.820000e-54 222.0
42 TraesCS2D01G449600 chr6D 96.970 132 4 0 3809 3940 401999990 401999859 5.820000e-54 222.0
43 TraesCS2D01G449600 chr6D 80.769 104 13 5 303 400 84309875 84309977 1.720000e-09 75.0
44 TraesCS2D01G449600 chr6D 79.825 114 14 6 291 400 471986760 471986868 1.720000e-09 75.0
45 TraesCS2D01G449600 chr6D 97.143 35 0 1 4435 4469 356727048 356727081 1.740000e-04 58.4
46 TraesCS2D01G449600 chr6D 92.500 40 0 3 491 527 43502518 43502557 2.000000e-03 54.7
47 TraesCS2D01G449600 chr1A 97.692 130 3 0 3808 3937 287275008 287275137 1.620000e-54 224.0
48 TraesCS2D01G449600 chr1A 80.000 90 14 4 441 527 551741080 551740992 3.730000e-06 63.9
49 TraesCS2D01G449600 chr4B 95.070 142 5 2 3805 3944 119338516 119338657 5.820000e-54 222.0
50 TraesCS2D01G449600 chr4B 85.185 81 9 2 298 377 307893505 307893583 3.710000e-11 80.5
51 TraesCS2D01G449600 chr4B 100.000 32 0 0 4434 4465 476365489 476365458 4.830000e-05 60.2
52 TraesCS2D01G449600 chr7A 95.620 137 6 0 3803 3939 173720292 173720156 2.090000e-53 220.0
53 TraesCS2D01G449600 chr7A 97.143 35 1 0 4427 4461 138008563 138008529 4.830000e-05 60.2
54 TraesCS2D01G449600 chr7D 95.588 136 5 1 3811 3946 266214380 266214246 2.710000e-52 217.0
55 TraesCS2D01G449600 chr7B 81.188 101 15 3 304 402 658758611 658758709 1.330000e-10 78.7
56 TraesCS2D01G449600 chr7B 79.439 107 18 3 298 402 677518490 677518386 6.200000e-09 73.1
57 TraesCS2D01G449600 chr4A 100.000 34 0 0 4432 4465 16469320 16469353 3.730000e-06 63.9
58 TraesCS2D01G449600 chr4A 78.431 102 18 4 302 400 661172649 661172549 3.730000e-06 63.9
59 TraesCS2D01G449600 chr4D 94.872 39 2 0 4427 4465 358476943 358476905 1.340000e-05 62.1
60 TraesCS2D01G449600 chr3A 100.000 33 0 0 4435 4467 632608540 632608572 1.340000e-05 62.1
61 TraesCS2D01G449600 chr3A 100.000 30 0 0 504 533 637365419 637365390 6.250000e-04 56.5
62 TraesCS2D01G449600 chr5A 100.000 32 0 0 504 535 403710085 403710116 4.830000e-05 60.2


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 TraesCS2D01G449600 chr2D 559209267 559213736 4469 True 8255.000000 8255 100.000000 1 4470 1 chr2D.!!$R2 4469
1 TraesCS2D01G449600 chr2D 559302064 559305709 3645 True 763.166667 2254 82.340167 758 4387 6 chr2D.!!$R4 3629
2 TraesCS2D01G449600 chr2D 559209349 559212040 2691 True 204.533333 311 85.857333 1697 4388 6 chr2D.!!$R3 2691
3 TraesCS2D01G449600 chr2A 699850913 699853990 3077 True 1075.666667 1663 85.844333 758 3596 3 chr2A.!!$R3 2838
4 TraesCS2D01G449600 chr2A 699796367 699801834 5467 True 884.075000 4545 87.089125 1 4470 8 chr2A.!!$R2 4469
5 TraesCS2D01G449600 chr2B 668180741 668183029 2288 True 827.000000 1997 84.317400 1007 3024 5 chr2B.!!$R2 2017
6 TraesCS2D01G449600 chr2B 668173512 668175004 1492 True 569.175000 1341 95.639750 2879 4465 4 chr2B.!!$R1 1586
7 TraesCS2D01G449600 chr5B 339532356 339532876 520 True 715.000000 715 91.747000 2450 2961 1 chr5B.!!$R1 511

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
592 612 0.099968 CAATGCTCAACTGATGCCCG 59.90 55.0 0.0 0.0 0.0 6.13 F
1688 2834 0.759959 TTGTAGGAGCACGGTGGAAA 59.24 50.0 10.6 0.0 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 3448 1.492176 CCTATCCAGTTGCAGTCCCAT 59.508 52.381 0.00 0.0 0.00 4.00 R
4414 6463 7.246311 GGAGTAGAACACAATGTGATGAATTG 58.754 38.462 21.34 0.0 40.23 2.32 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
34 35 1.654023 GCCAACACGCCACCCTTATC 61.654 60.000 0.00 0.00 0.00 1.75
40 41 0.469917 ACGCCACCCTTATCTGATGG 59.530 55.000 0.00 0.00 0.00 3.51
59 60 8.383175 TCTGATGGGTTTACTTACATCTTCTTT 58.617 33.333 0.00 0.00 40.18 2.52
174 176 4.635833 TGGAACGGTTTTGTTAGGTTTC 57.364 40.909 0.00 0.00 30.75 2.78
177 179 5.884792 TGGAACGGTTTTGTTAGGTTTCTTA 59.115 36.000 0.00 0.00 30.75 2.10
256 267 5.122869 TGAGCTCTTTTCCAAAATCGATGAG 59.877 40.000 16.19 0.00 0.00 2.90
259 270 5.300969 TCTTTTCCAAAATCGATGAGCTG 57.699 39.130 0.00 0.00 0.00 4.24
265 276 4.518590 TCCAAAATCGATGAGCTGTTTTCA 59.481 37.500 0.00 0.00 0.00 2.69
268 279 6.129009 CCAAAATCGATGAGCTGTTTTCAAAG 60.129 38.462 0.00 0.00 0.00 2.77
282 293 7.653311 GCTGTTTTCAAAGTGGATGAACTATTT 59.347 33.333 0.00 0.00 36.57 1.40
283 294 9.533253 CTGTTTTCAAAGTGGATGAACTATTTT 57.467 29.630 0.00 0.00 36.57 1.82
284 295 9.883142 TGTTTTCAAAGTGGATGAACTATTTTT 57.117 25.926 0.00 0.00 36.57 1.94
589 609 2.490903 AGGTTCAATGCTCAACTGATGC 59.509 45.455 0.00 0.00 0.00 3.91
592 612 0.099968 CAATGCTCAACTGATGCCCG 59.900 55.000 0.00 0.00 0.00 6.13
836 1954 1.314581 CGTAGCGCCAAAACGAAAAG 58.685 50.000 14.62 0.00 38.89 2.27
882 2002 2.568003 CCTTTTTCGGGAGCCCTTC 58.432 57.895 3.70 0.00 0.00 3.46
926 2046 2.072298 CTCTCCGAGTCCAAAGCAAAG 58.928 52.381 0.00 0.00 0.00 2.77
928 2048 0.889186 TCCGAGTCCAAAGCAAAGCC 60.889 55.000 0.00 0.00 0.00 4.35
929 2049 1.172180 CCGAGTCCAAAGCAAAGCCA 61.172 55.000 0.00 0.00 0.00 4.75
931 2051 1.066908 CGAGTCCAAAGCAAAGCCAAA 59.933 47.619 0.00 0.00 0.00 3.28
932 2052 2.481104 CGAGTCCAAAGCAAAGCCAAAA 60.481 45.455 0.00 0.00 0.00 2.44
934 2054 2.235898 AGTCCAAAGCAAAGCCAAAACA 59.764 40.909 0.00 0.00 0.00 2.83
935 2055 3.006247 GTCCAAAGCAAAGCCAAAACAA 58.994 40.909 0.00 0.00 0.00 2.83
936 2056 3.063861 GTCCAAAGCAAAGCCAAAACAAG 59.936 43.478 0.00 0.00 0.00 3.16
937 2057 3.055530 TCCAAAGCAAAGCCAAAACAAGA 60.056 39.130 0.00 0.00 0.00 3.02
938 2058 3.310501 CCAAAGCAAAGCCAAAACAAGAG 59.689 43.478 0.00 0.00 0.00 2.85
939 2059 3.893326 AAGCAAAGCCAAAACAAGAGT 57.107 38.095 0.00 0.00 0.00 3.24
940 2060 3.443099 AGCAAAGCCAAAACAAGAGTC 57.557 42.857 0.00 0.00 0.00 3.36
941 2061 3.026694 AGCAAAGCCAAAACAAGAGTCT 58.973 40.909 0.00 0.00 0.00 3.24
942 2062 3.067320 AGCAAAGCCAAAACAAGAGTCTC 59.933 43.478 0.00 0.00 0.00 3.36
943 2063 3.067320 GCAAAGCCAAAACAAGAGTCTCT 59.933 43.478 0.00 0.00 0.00 3.10
944 2064 4.440663 GCAAAGCCAAAACAAGAGTCTCTT 60.441 41.667 9.43 9.43 37.14 2.85
945 2065 5.277047 CAAAGCCAAAACAAGAGTCTCTTC 58.723 41.667 12.37 0.00 33.78 2.87
946 2066 3.481453 AGCCAAAACAAGAGTCTCTTCC 58.519 45.455 12.37 0.00 33.78 3.46
947 2067 3.137360 AGCCAAAACAAGAGTCTCTTCCT 59.863 43.478 12.37 0.00 33.78 3.36
1097 2224 1.098712 TTGCTTCTGTTCCGCCGTTT 61.099 50.000 0.00 0.00 0.00 3.60
1106 2233 3.656045 CCGCCGTTTCGTTTGCCT 61.656 61.111 0.00 0.00 0.00 4.75
1110 2237 2.426752 CGTTTCGTTTGCCTGCGG 60.427 61.111 0.00 0.00 0.00 5.69
1112 2239 1.833434 CGTTTCGTTTGCCTGCGGTA 61.833 55.000 0.00 0.00 0.00 4.02
1183 2310 4.838152 CGCGGGTGCAGCCTGTAT 62.838 66.667 30.86 0.00 45.57 2.29
1224 2351 1.331399 GGGTGCACTCTACTCCCCTC 61.331 65.000 17.98 0.00 32.66 4.30
1241 2376 4.594920 TCCCCTCATGAATTACATCCTCTC 59.405 45.833 0.00 0.00 37.07 3.20
1384 2523 2.360475 GCTGTTGACCCTCCTGCC 60.360 66.667 0.00 0.00 0.00 4.85
1426 2565 2.853705 CAAGACCCGTTGGAGGTAAAA 58.146 47.619 0.00 0.00 37.88 1.52
1492 2632 5.129485 TCTTCTCTTGCTACCTTATCCCAAG 59.871 44.000 0.00 0.00 35.44 3.61
1499 2639 7.346175 TCTTGCTACCTTATCCCAAGTGTATTA 59.654 37.037 0.00 0.00 35.58 0.98
1527 2667 6.307800 ACCGATTAAATTTTCTGAATTGTGCG 59.692 34.615 0.00 0.00 0.00 5.34
1573 2713 2.898612 TGGGCATTCATTTCTGAAGCAA 59.101 40.909 10.00 0.00 44.32 3.91
1635 2781 1.073897 GGAGCCAAGCTGAACCTGT 59.926 57.895 0.00 0.00 39.88 4.00
1688 2834 0.759959 TTGTAGGAGCACGGTGGAAA 59.240 50.000 10.60 0.00 0.00 3.13
1695 2841 2.275380 GCACGGTGGAAAAGGGCAT 61.275 57.895 10.60 0.00 0.00 4.40
1978 3448 0.615331 GAAGTGCAGTGGATCCTCCA 59.385 55.000 14.23 0.84 45.98 3.86
4411 6460 0.038166 TTAGCTGTTCAGCAAGGGGG 59.962 55.000 23.69 0.00 37.25 5.40
4414 6463 1.527433 GCTGTTCAGCAAGGGGGTTC 61.527 60.000 18.26 0.00 34.41 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.294138 GGTGGCGTGTTGGCTACTA 59.706 57.895 0.01 0.00 43.16 1.82
34 35 8.567285 AAAGAAGATGTAAGTAAACCCATCAG 57.433 34.615 0.00 0.00 36.91 2.90
59 60 9.907229 AAGAAAGAGGAAAGAAGAAGAAAAGTA 57.093 29.630 0.00 0.00 0.00 2.24
117 118 9.926158 AAAAAGGAACAAGCAAAAATGAAAAAT 57.074 22.222 0.00 0.00 0.00 1.82
152 154 4.705991 AGAAACCTAACAAAACCGTTCCAA 59.294 37.500 0.00 0.00 0.00 3.53
154 156 4.906065 AGAAACCTAACAAAACCGTTCC 57.094 40.909 0.00 0.00 0.00 3.62
235 245 4.101235 GCTCATCGATTTTGGAAAAGAGC 58.899 43.478 11.34 11.34 35.51 4.09
243 253 4.797471 TGAAAACAGCTCATCGATTTTGG 58.203 39.130 0.00 0.00 0.00 3.28
256 267 4.936891 AGTTCATCCACTTTGAAAACAGC 58.063 39.130 0.00 0.00 35.03 4.40
456 476 7.980099 ACATTCGTCGATATAGGAAAAAGTTCT 59.020 33.333 0.00 0.00 33.92 3.01
466 486 5.294356 TGGGAAAACATTCGTCGATATAGG 58.706 41.667 0.00 0.00 0.00 2.57
476 496 6.595772 TTCACAATTTTGGGAAAACATTCG 57.404 33.333 5.53 0.00 46.74 3.34
527 547 6.314896 TGACCGCATTGACTTTTCAAAAATTT 59.685 30.769 0.00 0.00 45.01 1.82
675 696 4.081420 AGGAACATCGCTATTTGACTCAGT 60.081 41.667 0.00 0.00 0.00 3.41
677 698 4.183865 CAGGAACATCGCTATTTGACTCA 58.816 43.478 0.00 0.00 0.00 3.41
879 1999 0.391263 CCGAAGAACCCGGGAAGAAG 60.391 60.000 32.02 13.41 43.05 2.85
882 2002 0.252197 ATTCCGAAGAACCCGGGAAG 59.748 55.000 32.02 10.93 46.47 3.46
915 2035 3.055530 TCTTGTTTTGGCTTTGCTTTGGA 60.056 39.130 0.00 0.00 0.00 3.53
917 2037 3.934579 ACTCTTGTTTTGGCTTTGCTTTG 59.065 39.130 0.00 0.00 0.00 2.77
921 2041 3.067320 AGAGACTCTTGTTTTGGCTTTGC 59.933 43.478 0.00 0.00 0.00 3.68
926 2046 3.481453 AGGAAGAGACTCTTGTTTTGGC 58.519 45.455 22.39 5.91 36.73 4.52
928 2048 4.683781 CGAGAGGAAGAGACTCTTGTTTTG 59.316 45.833 22.39 5.24 44.89 2.44
929 2049 4.877282 CGAGAGGAAGAGACTCTTGTTTT 58.123 43.478 22.39 5.49 44.89 2.43
1148 2275 2.980233 GGCCTGCAAGAACAGCGT 60.980 61.111 0.00 0.00 36.29 5.07
1178 2305 2.389715 AGGGAACGAGAAGGGATACAG 58.610 52.381 0.00 0.00 39.74 2.74
1179 2306 2.544844 AGGGAACGAGAAGGGATACA 57.455 50.000 0.00 0.00 39.74 2.29
1183 2310 0.908180 GGGAAGGGAACGAGAAGGGA 60.908 60.000 0.00 0.00 0.00 4.20
1224 2351 5.366460 ACAGCAGAGAGGATGTAATTCATG 58.634 41.667 0.00 0.00 35.29 3.07
1241 2376 5.233902 CAGAGATCTAAAATCGGAACAGCAG 59.766 44.000 0.00 0.00 0.00 4.24
1499 2639 9.357652 CACAATTCAGAAAATTTAATCGGTGAT 57.642 29.630 0.00 0.00 0.00 3.06
1635 2781 2.705658 TCTTCTCTGGCAGAAACCTCAA 59.294 45.455 19.29 3.97 40.83 3.02
1688 2834 2.014010 TGCTTCCTTTTCATGCCCTT 57.986 45.000 0.00 0.00 0.00 3.95
1978 3448 1.492176 CCTATCCAGTTGCAGTCCCAT 59.508 52.381 0.00 0.00 0.00 4.00
4411 6460 8.292448 AGTAGAACACAATGTGATGAATTGAAC 58.708 33.333 21.34 4.11 38.21 3.18
4414 6463 7.246311 GGAGTAGAACACAATGTGATGAATTG 58.754 38.462 21.34 0.00 40.23 2.32


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

AutoCloner maintained by Alex Coulton.