Multiple sequence alignment - TraesCS3B01G493300

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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 TraesCS3B01G493300 chr3B 100.000 2431 0 0 1 2431 738758550 738756120 0.000000e+00 4490.0
1 TraesCS3B01G493300 chr3B 87.545 554 34 12 1885 2431 738913587 738913062 2.070000e-170 608.0
2 TraesCS3B01G493300 chr3B 86.343 432 57 2 1754 2183 707027292 707026861 1.020000e-128 470.0
3 TraesCS3B01G493300 chr3B 86.207 435 57 3 1751 2183 778000504 778000937 3.660000e-128 468.0
4 TraesCS3B01G493300 chr3B 86.420 405 40 7 975 1379 738910730 738910341 1.730000e-116 429.0
5 TraesCS3B01G493300 chr3B 82.327 447 56 12 980 1425 738992823 738992399 1.370000e-97 366.0
6 TraesCS3B01G493300 chr3B 93.333 120 7 1 1 119 738910904 738910785 2.480000e-40 176.0
7 TraesCS3B01G493300 chr3B 84.615 117 10 4 448 557 625191980 625192095 2.560000e-20 110.0
8 TraesCS3B01G493300 chr3D 95.736 774 26 6 987 1757 555801374 555800605 0.000000e+00 1240.0
9 TraesCS3B01G493300 chr3D 91.557 687 33 3 1749 2431 555800423 555799758 0.000000e+00 924.0
10 TraesCS3B01G493300 chr3D 81.267 726 71 32 975 1665 555912528 555911833 5.950000e-146 527.0
11 TraesCS3B01G493300 chr3D 87.770 139 12 2 2293 2431 246906455 246906588 9.000000e-35 158.0
12 TraesCS3B01G493300 chr3D 90.164 122 8 3 1 120 555912701 555912582 3.240000e-34 156.0
13 TraesCS3B01G493300 chr3D 94.253 87 0 3 67 153 555801475 555801394 7.060000e-26 128.0
14 TraesCS3B01G493300 chr3D 81.208 149 24 4 158 304 597160333 597160479 1.530000e-22 117.0
15 TraesCS3B01G493300 chr3D 82.308 130 21 2 162 290 347570807 347570935 7.110000e-21 111.0
16 TraesCS3B01G493300 chr3D 84.615 117 10 5 448 557 470713159 470713274 2.560000e-20 110.0
17 TraesCS3B01G493300 chr3D 79.333 150 26 5 158 304 388315056 388315203 1.540000e-17 100.0
18 TraesCS3B01G493300 chr3D 88.889 72 8 0 219 290 138019013 138019084 3.330000e-14 89.8
19 TraesCS3B01G493300 chr3A 93.232 857 13 3 158 970 24436233 24437088 0.000000e+00 1219.0
20 TraesCS3B01G493300 chr3A 94.118 782 34 8 987 1757 692723855 692723075 0.000000e+00 1179.0
21 TraesCS3B01G493300 chr3A 93.198 691 41 3 1745 2431 692722895 692722207 0.000000e+00 1011.0
22 TraesCS3B01G493300 chr3A 78.615 650 76 34 981 1593 692945242 692944619 2.950000e-99 372.0
23 TraesCS3B01G493300 chr3A 94.268 157 3 4 1 156 692724030 692723879 4.040000e-58 235.0
24 TraesCS3B01G493300 chr3A 89.344 122 9 2 1 120 692945420 692945301 1.510000e-32 150.0
25 TraesCS3B01G493300 chr3A 91.228 57 4 1 501 557 612966054 612966109 2.590000e-10 76.8
26 TraesCS3B01G493300 chr3A 96.970 33 0 1 971 1002 692723884 692723852 1.000000e-03 54.7
27 TraesCS3B01G493300 chr2B 92.882 857 17 2 158 970 65488600 65489456 0.000000e+00 1205.0
28 TraesCS3B01G493300 chr2B 88.304 171 14 6 2260 2425 400811157 400811326 1.470000e-47 200.0
29 TraesCS3B01G493300 chr2B 78.523 298 57 6 678 971 157047482 157047188 3.190000e-44 189.0
30 TraesCS3B01G493300 chr5B 85.582 867 29 11 158 970 26020334 26019510 0.000000e+00 821.0
31 TraesCS3B01G493300 chr5B 86.111 432 58 2 1754 2183 710236057 710235626 4.730000e-127 464.0
32 TraesCS3B01G493300 chr5B 88.889 72 6 2 501 572 493475878 493475947 1.200000e-13 87.9
33 TraesCS3B01G493300 chr6B 82.578 861 90 21 158 969 600988992 600989841 0.000000e+00 704.0
34 TraesCS3B01G493300 chr6B 86.207 435 58 2 1751 2183 61211754 61212188 1.020000e-128 470.0
35 TraesCS3B01G493300 chr6B 86.301 146 20 0 161 306 588900351 588900206 2.500000e-35 159.0
36 TraesCS3B01G493300 chr6B 84.768 151 19 4 158 306 125497164 125497312 5.420000e-32 148.0
37 TraesCS3B01G493300 chr6B 77.647 170 27 8 651 820 657263308 657263466 2.570000e-15 93.5
38 TraesCS3B01G493300 chr2A 86.207 435 58 2 1751 2183 537233657 537234091 1.020000e-128 470.0
39 TraesCS3B01G493300 chr2A 81.548 336 42 14 647 967 161931975 161932305 2.400000e-65 259.0
40 TraesCS3B01G493300 chr2A 79.835 243 41 8 158 396 161931400 161931638 1.160000e-38 171.0
41 TraesCS3B01G493300 chr2A 87.075 147 18 1 160 306 161932306 161932161 5.380000e-37 165.0
42 TraesCS3B01G493300 chr2A 86.486 148 20 0 158 305 529951251 529951398 1.930000e-36 163.0
43 TraesCS3B01G493300 chr2A 86.897 145 18 1 161 305 740377290 740377147 6.960000e-36 161.0
44 TraesCS3B01G493300 chr2A 100.000 33 0 0 2256 2288 516175211 516175179 7.260000e-06 62.1
45 TraesCS3B01G493300 chr7D 85.977 435 59 2 1751 2183 475154961 475155395 4.730000e-127 464.0
46 TraesCS3B01G493300 chr7D 80.000 605 73 20 971 1554 175443575 175444152 1.050000e-108 403.0
47 TraesCS3B01G493300 chr7D 85.235 149 21 1 158 306 500234860 500234713 4.190000e-33 152.0
48 TraesCS3B01G493300 chr7D 83.893 149 24 0 158 306 500222143 500222291 2.520000e-30 143.0
49 TraesCS3B01G493300 chr7D 82.482 137 24 0 169 305 9829253 9829389 1.180000e-23 121.0
50 TraesCS3B01G493300 chr7D 88.732 71 6 1 654 724 500234280 500234212 4.310000e-13 86.1
51 TraesCS3B01G493300 chr6A 85.747 442 60 3 1745 2183 591940747 591940306 4.730000e-127 464.0
52 TraesCS3B01G493300 chr6A 80.755 530 41 23 1207 1713 14098706 14099197 8.270000e-95 357.0
53 TraesCS3B01G493300 chr6A 87.671 146 9 5 2292 2431 80691595 80691737 6.960000e-36 161.0
54 TraesCS3B01G493300 chr6A 91.111 90 6 2 976 1065 14073642 14073729 1.180000e-23 121.0
55 TraesCS3B01G493300 chr6A 91.045 67 6 0 1046 1112 14077128 14077194 9.260000e-15 91.6
56 TraesCS3B01G493300 chr4A 80.240 334 39 17 647 967 28599411 28599092 2.430000e-55 226.0
57 TraesCS3B01G493300 chr4A 79.874 318 51 12 651 967 583693725 583694030 1.130000e-53 220.0
58 TraesCS3B01G493300 chr4A 79.167 288 54 5 158 442 583691270 583691554 6.860000e-46 195.0
59 TraesCS3B01G493300 chr1B 82.143 224 38 2 745 967 489991088 489991310 8.870000e-45 191.0
60 TraesCS3B01G493300 chr1B 91.367 139 10 2 2294 2431 334452914 334453051 3.190000e-44 189.0
61 TraesCS3B01G493300 chr1B 84.106 151 20 4 158 306 12326128 12325980 2.520000e-30 143.0
62 TraesCS3B01G493300 chr1B 84.000 150 22 2 158 306 433635834 433635686 2.520000e-30 143.0
63 TraesCS3B01G493300 chr1B 88.462 52 4 2 2238 2288 679324623 679324573 7.260000e-06 62.1
64 TraesCS3B01G493300 chr4D 86.127 173 15 8 2265 2431 430817630 430817799 6.910000e-41 178.0
65 TraesCS3B01G493300 chr4D 82.836 134 17 6 158 288 409317115 409317245 5.490000e-22 115.0
66 TraesCS3B01G493300 chr2D 86.986 146 19 0 161 306 15788270 15788125 5.380000e-37 165.0
67 TraesCS3B01G493300 chr2D 93.478 46 1 2 2243 2288 646737976 646738019 1.560000e-07 67.6
68 TraesCS3B01G493300 chr5A 87.162 148 13 3 2290 2431 666346084 666346231 1.930000e-36 163.0
69 TraesCS3B01G493300 chr7B 86.000 150 21 0 157 306 711049132 711049281 6.960000e-36 161.0
70 TraesCS3B01G493300 chr7B 76.615 325 51 14 647 970 74198944 74198644 3.240000e-34 156.0
71 TraesCS3B01G493300 chr7B 80.899 178 32 2 795 971 28070520 28070696 3.260000e-29 139.0
72 TraesCS3B01G493300 chr1A 89.431 123 8 4 1 120 510457022 510457142 1.510000e-32 150.0
73 TraesCS3B01G493300 chr1A 84.667 150 19 4 158 305 562129801 562129948 1.950000e-31 147.0
74 TraesCS3B01G493300 chr1A 80.405 148 29 0 158 305 562130602 562130455 1.980000e-21 113.0
75 TraesCS3B01G493300 chr5D 84.722 144 22 0 161 304 23120255 23120112 7.010000e-31 145.0
76 TraesCS3B01G493300 chr5D 83.333 150 19 5 158 304 23119243 23119389 1.520000e-27 134.0
77 TraesCS3B01G493300 chr5D 81.699 153 18 10 158 305 288077292 288077439 4.250000e-23 119.0
78 TraesCS3B01G493300 chr5D 81.203 133 25 0 157 289 566055470 566055602 9.190000e-20 108.0
79 TraesCS3B01G493300 chr5D 91.489 47 3 1 2242 2288 513975160 513975115 2.020000e-06 63.9
80 TraesCS3B01G493300 chr4B 84.000 150 20 4 158 305 149720954 149720807 9.060000e-30 141.0
81 TraesCS3B01G493300 chrUn 93.617 47 2 1 2252 2297 297891270 297891224 4.340000e-08 69.4
82 TraesCS3B01G493300 chr6D 100.000 33 0 0 527 559 780952 780984 7.260000e-06 62.1


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 TraesCS3B01G493300 chr3B 738756120 738758550 2430 True 4490.000000 4490 100.000000 1 2431 1 chr3B.!!$R2 2430
1 TraesCS3B01G493300 chr3B 738910341 738913587 3246 True 404.333333 608 89.099333 1 2431 3 chr3B.!!$R4 2430
2 TraesCS3B01G493300 chr3D 555799758 555801475 1717 True 764.000000 1240 93.848667 67 2431 3 chr3D.!!$R1 2364
3 TraesCS3B01G493300 chr3D 555911833 555912701 868 True 341.500000 527 85.715500 1 1665 2 chr3D.!!$R2 1664
4 TraesCS3B01G493300 chr3A 24436233 24437088 855 False 1219.000000 1219 93.232000 158 970 1 chr3A.!!$F1 812
5 TraesCS3B01G493300 chr3A 692722207 692724030 1823 True 619.925000 1179 94.638500 1 2431 4 chr3A.!!$R1 2430
6 TraesCS3B01G493300 chr3A 692944619 692945420 801 True 261.000000 372 83.979500 1 1593 2 chr3A.!!$R2 1592
7 TraesCS3B01G493300 chr2B 65488600 65489456 856 False 1205.000000 1205 92.882000 158 970 1 chr2B.!!$F1 812
8 TraesCS3B01G493300 chr5B 26019510 26020334 824 True 821.000000 821 85.582000 158 970 1 chr5B.!!$R1 812
9 TraesCS3B01G493300 chr6B 600988992 600989841 849 False 704.000000 704 82.578000 158 969 1 chr6B.!!$F3 811
10 TraesCS3B01G493300 chr2A 161931400 161932305 905 False 215.000000 259 80.691500 158 967 2 chr2A.!!$F3 809
11 TraesCS3B01G493300 chr7D 175443575 175444152 577 False 403.000000 403 80.000000 971 1554 1 chr7D.!!$F2 583
12 TraesCS3B01G493300 chr4A 583691270 583694030 2760 False 207.500000 220 79.520500 158 967 2 chr4A.!!$F1 809

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
120 2806 0.178903 TGCACCTCTGAACCCCTAGT 60.179 55.0 0.00 0.00 0.0 2.57 F
370 3133 0.833409 GGATGGAAATGATGGGCCCC 60.833 60.0 22.27 4.91 0.0 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1184 5989 0.035439 ACCCAGTTGCCACGATTAGG 60.035 55.0 0.0 0.0 0.00 2.69 R
1761 6807 0.400213 AAAGGCATCACCAGAACGGA 59.600 50.0 0.0 0.0 43.14 4.69 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 2713 4.438148 TGACAACGTGTGATTTGAGAAGA 58.562 39.130 0.00 0.00 0.00 2.87
120 2806 0.178903 TGCACCTCTGAACCCCTAGT 60.179 55.000 0.00 0.00 0.00 2.57
122 2808 1.757699 GCACCTCTGAACCCCTAGTAG 59.242 57.143 0.00 0.00 0.00 2.57
370 3133 0.833409 GGATGGAAATGATGGGCCCC 60.833 60.000 22.27 4.91 0.00 5.80
970 5769 6.701400 AGATGGTCTTTTTGGACAAAAATTCG 59.299 34.615 19.60 10.97 45.69 3.34
971 5770 5.112686 TGGTCTTTTTGGACAAAAATTCGG 58.887 37.500 19.60 10.69 45.69 4.30
972 5771 4.509970 GGTCTTTTTGGACAAAAATTCGGG 59.490 41.667 19.60 10.39 45.69 5.14
973 5772 4.509970 GTCTTTTTGGACAAAAATTCGGGG 59.490 41.667 19.60 9.83 45.69 5.73
974 5773 3.477210 TTTTGGACAAAAATTCGGGGG 57.523 42.857 7.69 0.00 37.35 5.40
1063 5862 1.202568 TGAAGCTGAGTGTGTGTCTGG 60.203 52.381 0.00 0.00 0.00 3.86
1126 5925 2.031012 TTGCTGAGCACCCTCGTG 59.969 61.111 6.64 0.00 41.13 4.35
1173 5978 8.098220 TCATTCTTTCTTTCGATTGATTGACA 57.902 30.769 0.00 0.00 0.00 3.58
1202 6007 2.780595 CCTAATCGTGGCAACTGGG 58.219 57.895 0.00 0.00 37.61 4.45
1203 6008 0.035439 CCTAATCGTGGCAACTGGGT 60.035 55.000 0.00 0.00 37.61 4.51
1204 6009 1.086696 CTAATCGTGGCAACTGGGTG 58.913 55.000 0.00 0.00 37.61 4.61
1205 6010 0.322098 TAATCGTGGCAACTGGGTGG 60.322 55.000 0.00 0.00 37.61 4.61
1491 6336 7.348201 AGTGAAATAAATCTCATTTCGATCGC 58.652 34.615 11.09 0.00 42.68 4.58
1492 6337 6.298569 GTGAAATAAATCTCATTTCGATCGCG 59.701 38.462 11.09 0.00 42.68 5.87
1558 6411 2.930950 ACTTGTTGGAACTGCTGCTAA 58.069 42.857 0.00 0.00 0.00 3.09
1605 6458 5.820423 GTCCACCAAGTTGCATACATACATA 59.180 40.000 0.00 0.00 0.00 2.29
1616 6469 4.381863 GCATACATACATACCGTCAGTTCG 59.618 45.833 0.00 0.00 0.00 3.95
1648 6501 5.290493 AGTGGATAAGATTATTCGGTGCA 57.710 39.130 0.00 0.00 0.00 4.57
1669 6522 0.039256 CACCCCAACAATTCTGCACG 60.039 55.000 0.00 0.00 0.00 5.34
1743 6596 2.996621 CCTCGTGAAAACTCTCATCCAC 59.003 50.000 0.00 0.00 0.00 4.02
1761 6807 1.299976 CGGTTTTCCTGCCTAGCCT 59.700 57.895 0.00 0.00 37.95 4.58
1771 6817 2.359967 GCCTAGCCTCCGTTCTGGT 61.360 63.158 0.00 0.00 39.52 4.00
1902 6948 7.321153 GTTTGTCTACCTATGTGTGTCTACAT 58.679 38.462 0.00 0.00 43.34 2.29
1914 6960 5.003804 GTGTGTCTACATGTTGGATCCTTT 58.996 41.667 14.23 0.00 39.39 3.11
1923 6969 5.104941 ACATGTTGGATCCTTTCGATCTACA 60.105 40.000 14.23 3.95 45.90 2.74
1943 6989 2.016393 ATTCTCTTCATCGGCGGCGA 62.016 55.000 36.40 36.40 0.00 5.54
1947 6993 3.512287 CTTCATCGGCGGCGATTGC 62.512 63.158 39.85 0.00 41.71 3.56
2012 7058 5.416083 TCCCGACTGTCTAATACAACAATG 58.584 41.667 6.21 0.00 37.74 2.82
2071 7117 4.537433 GCCTTCGGCTCGCTCCAT 62.537 66.667 0.00 0.00 46.69 3.41
2072 7118 2.587194 CCTTCGGCTCGCTCCATG 60.587 66.667 0.00 0.00 0.00 3.66
2083 7129 0.108186 CGCTCCATGGCTTGTAGTCA 60.108 55.000 6.96 0.00 32.55 3.41
2252 7298 6.992123 TGGATCTTTGCATAACCACACTATAG 59.008 38.462 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 2808 9.862371 CCTTCCAATATCCGCATATATATAGTC 57.138 37.037 0.00 0.00 0.00 2.59
453 3233 3.000819 ATCCGGTCCGCCTGACAA 61.001 61.111 5.50 0.00 46.38 3.18
487 3314 1.470285 GCCAATGCTTCAATGCGATGT 60.470 47.619 0.00 0.00 35.36 3.06
830 5629 2.584064 CTGCCGCCACATAGGTCA 59.416 61.111 0.00 0.00 40.61 4.02
832 5631 3.009115 ACCTGCCGCCACATAGGT 61.009 61.111 0.00 0.00 40.61 3.08
971 5770 2.422945 CCTATGCTTTGGTTACTCCCCC 60.423 54.545 0.00 0.00 34.77 5.40
972 5771 2.932261 CCTATGCTTTGGTTACTCCCC 58.068 52.381 0.00 0.00 34.77 4.81
973 5772 2.298610 GCCTATGCTTTGGTTACTCCC 58.701 52.381 2.25 0.00 32.45 4.30
974 5773 2.999331 TGCCTATGCTTTGGTTACTCC 58.001 47.619 2.25 0.00 38.71 3.85
978 5777 3.117701 TGCCTATGCCTATGCTTTGGTTA 60.118 43.478 7.79 0.00 38.95 2.85
1184 5989 0.035439 ACCCAGTTGCCACGATTAGG 60.035 55.000 0.00 0.00 0.00 2.69
1202 6007 2.676471 GCACCCCATCACCACCAC 60.676 66.667 0.00 0.00 0.00 4.16
1203 6008 3.181530 TGCACCCCATCACCACCA 61.182 61.111 0.00 0.00 0.00 4.17
1204 6009 2.361610 CTGCACCCCATCACCACC 60.362 66.667 0.00 0.00 0.00 4.61
1205 6010 3.064324 GCTGCACCCCATCACCAC 61.064 66.667 0.00 0.00 0.00 4.16
1437 6251 8.492448 CATGCATGCATCCATACATGGTACAG 62.492 46.154 30.07 9.46 44.26 2.74
1438 6252 6.779053 CATGCATGCATCCATACATGGTACA 61.779 44.000 30.07 0.00 44.26 2.90
1491 6336 0.804364 TAGGTAGGTACACACACGCG 59.196 55.000 3.53 3.53 0.00 6.01
1492 6337 3.879295 TCTATAGGTAGGTACACACACGC 59.121 47.826 0.00 0.00 0.00 5.34
1558 6411 5.163258 ACAGTTCTTCTTGGTCACTGAGAAT 60.163 40.000 4.67 0.00 38.59 2.40
1605 6458 4.639310 ACTAGATTATGACGAACTGACGGT 59.361 41.667 0.00 0.00 37.61 4.83
1648 6501 0.469705 TGCAGAATTGTTGGGGTGCT 60.470 50.000 0.00 0.00 0.00 4.40
1658 6511 1.081242 GCCCACACGTGCAGAATTG 60.081 57.895 17.22 4.93 0.00 2.32
1743 6596 0.744771 GAGGCTAGGCAGGAAAACCG 60.745 60.000 19.70 0.00 0.00 4.44
1761 6807 0.400213 AAAGGCATCACCAGAACGGA 59.600 50.000 0.00 0.00 43.14 4.69
1914 6960 5.763088 CCGATGAAGAGAATTGTAGATCGA 58.237 41.667 0.00 0.00 34.75 3.59
1923 6969 1.154205 CGCCGCCGATGAAGAGAATT 61.154 55.000 0.00 0.00 36.29 2.17
1943 6989 1.003580 CCACCACACTAGGACAGCAAT 59.996 52.381 0.00 0.00 0.00 3.56
1947 6993 0.608640 GGACCACCACACTAGGACAG 59.391 60.000 0.00 0.00 35.97 3.51
2012 7058 2.907897 CTCATCGGAGTCGGGCAACC 62.908 65.000 0.00 0.00 44.83 3.77
2071 7117 1.409064 CCTAGCGATGACTACAAGCCA 59.591 52.381 0.00 0.00 35.47 4.75
2072 7118 1.409427 ACCTAGCGATGACTACAAGCC 59.591 52.381 0.00 0.00 35.47 4.35
2083 7129 2.240279 GTCCATAGACCACCTAGCGAT 58.760 52.381 0.00 0.00 37.00 4.58
2223 7269 4.771577 TGTGGTTATGCAAAGATCCATGTT 59.228 37.500 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.