Multiple sequence alignment - TraesCS3A01G502100

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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 TraesCS3A01G502100 chr3A 100.000 3345 0 0 1 3345 725604263 725607607 0.000000e+00 6178.0
1 TraesCS3A01G502100 chr3A 99.402 3346 16 3 1 3345 725561934 725565276 0.000000e+00 6065.0
2 TraesCS3A01G502100 chr3A 96.869 1469 16 3 1879 3345 725522062 725523502 0.000000e+00 2431.0
3 TraesCS3A01G502100 chr3A 96.212 396 14 1 799 1193 693551443 693551048 0.000000e+00 647.0
4 TraesCS3A01G502100 chr3A 96.393 305 10 1 1194 1497 175624686 175624382 4.980000e-138 501.0
5 TraesCS3A01G502100 chr3A 95.738 305 12 1 1194 1497 728888995 728889299 1.080000e-134 490.0
6 TraesCS3A01G502100 chr3A 94.677 263 14 0 1617 1879 725518084 725518346 3.110000e-110 409.0
7 TraesCS3A01G502100 chr3A 85.989 364 45 6 1616 1979 725477044 725477401 5.240000e-103 385.0
8 TraesCS3A01G502100 chr3A 94.286 245 14 0 341 585 693551685 693551441 3.150000e-100 375.0
9 TraesCS3A01G502100 chr3A 100.000 122 0 0 1497 1618 693551050 693550929 3.360000e-55 226.0
10 TraesCS3A01G502100 chr3A 93.069 101 7 0 3245 3345 8213864 8213764 7.480000e-32 148.0
11 TraesCS3A01G502100 chr5A 98.474 852 12 1 341 1191 555249104 555248253 0.000000e+00 1500.0
12 TraesCS3A01G502100 chr5A 98.122 852 15 1 341 1191 555234954 555234103 0.000000e+00 1483.0
13 TraesCS3A01G502100 chr5A 93.878 490 24 5 709 1193 536445573 536445085 0.000000e+00 734.0
14 TraesCS3A01G502100 chr5A 95.190 395 18 1 799 1192 641216726 641216332 1.020000e-174 623.0
15 TraesCS3A01G502100 chr5A 94.694 245 13 0 341 585 641216968 641216724 6.770000e-102 381.0
16 TraesCS3A01G502100 chr5A 100.000 120 0 0 1499 1618 555248251 555248132 4.340000e-54 222.0
17 TraesCS3A01G502100 chr5A 97.500 120 3 0 1499 1618 555234101 555233982 4.370000e-49 206.0
18 TraesCS3A01G502100 chr5A 97.500 120 3 0 1500 1619 641216330 641216211 4.370000e-49 206.0
19 TraesCS3A01G502100 chr5A 93.137 102 7 0 3244 3345 617354986 617355087 2.080000e-32 150.0
20 TraesCS3A01G502100 chr5A 96.774 62 2 0 1558 1619 536439050 536438989 1.640000e-18 104.0
21 TraesCS3A01G502100 chrUn 98.357 852 13 1 341 1191 300564129 300563278 0.000000e+00 1495.0
22 TraesCS3A01G502100 chrUn 93.833 227 12 2 582 807 239743999 239743774 1.150000e-89 340.0
23 TraesCS3A01G502100 chrUn 100.000 120 0 0 1499 1618 300563276 300563157 4.340000e-54 222.0
24 TraesCS3A01G502100 chrUn 92.000 100 8 0 3246 3345 103351555 103351654 1.250000e-29 141.0
25 TraesCS3A01G502100 chr3D 85.855 912 88 26 2353 3247 594801203 594802090 0.000000e+00 931.0
26 TraesCS3A01G502100 chr3D 88.360 378 34 6 1622 1995 594800563 594800934 2.370000e-121 446.0
27 TraesCS3A01G502100 chr3D 93.069 101 7 0 3245 3345 279935402 279935302 7.480000e-32 148.0
28 TraesCS3A01G502100 chr3D 95.652 92 4 0 3246 3337 523208197 523208106 7.480000e-32 148.0
29 TraesCS3A01G502100 chr3B 85.868 651 72 11 2510 3156 798282644 798283278 0.000000e+00 675.0
30 TraesCS3A01G502100 chr3B 93.895 344 21 0 1 344 787404501 787404158 1.380000e-143 520.0
31 TraesCS3A01G502100 chr3B 89.922 258 20 2 1738 1995 798251994 798252245 8.950000e-86 327.0
32 TraesCS3A01G502100 chr3B 94.118 102 6 0 3244 3345 68254479 68254378 4.470000e-34 156.0
33 TraesCS3A01G502100 chr3B 94.898 98 5 0 3246 3343 772004245 772004148 1.610000e-33 154.0
34 TraesCS3A01G502100 chr3B 95.000 80 3 1 3153 3231 798283897 798283976 1.260000e-24 124.0
35 TraesCS3A01G502100 chr3B 91.304 46 4 0 1617 1662 798251935 798251980 2.790000e-06 63.9
36 TraesCS3A01G502100 chr6D 93.939 396 13 4 799 1193 468855135 468854750 3.720000e-164 588.0
37 TraesCS3A01G502100 chr6D 94.186 344 20 0 1 344 143962804 143963147 2.960000e-145 525.0
38 TraesCS3A01G502100 chr6D 95.968 248 10 0 341 588 468855380 468855133 1.450000e-108 403.0
39 TraesCS3A01G502100 chr6D 98.361 122 2 0 1497 1618 468854752 468854631 7.270000e-52 215.0
40 TraesCS3A01G502100 chr6D 90.722 97 8 1 3241 3337 31271726 31271821 9.740000e-26 128.0
41 TraesCS3A01G502100 chr6D 85.047 107 12 4 3241 3344 291144675 291144570 4.560000e-19 106.0
42 TraesCS3A01G502100 chr6D 87.097 93 11 1 3245 3337 172117814 172117905 1.640000e-18 104.0
43 TraesCS3A01G502100 chr4A 97.384 344 9 0 1 344 603120255 603120598 1.340000e-163 586.0
44 TraesCS3A01G502100 chr4A 96.417 307 8 2 1194 1497 182894393 182894087 1.390000e-138 503.0
45 TraesCS3A01G502100 chr2D 96.812 345 10 1 1 344 597841376 597841032 2.890000e-160 575.0
46 TraesCS3A01G502100 chr2D 95.930 344 14 0 1 344 641886592 641886249 2.910000e-155 558.0
47 TraesCS3A01G502100 chr2D 95.918 98 4 0 3245 3342 604025634 604025731 3.450000e-35 159.0
48 TraesCS3A01G502100 chr2D 93.069 101 7 0 3245 3345 138887358 138887458 7.480000e-32 148.0
49 TraesCS3A01G502100 chr2B 96.221 344 13 0 1 344 727677554 727677211 6.270000e-157 564.0
50 TraesCS3A01G502100 chr1D 95.349 344 16 0 1 344 441063416 441063073 6.310000e-152 547.0
51 TraesCS3A01G502100 chr1D 93.000 100 7 0 3246 3345 468265253 468265154 2.690000e-31 147.0
52 TraesCS3A01G502100 chr1D 91.089 101 9 0 3245 3345 315509546 315509646 1.620000e-28 137.0
53 TraesCS3A01G502100 chr1D 92.473 93 7 0 3245 3337 468861450 468861358 2.090000e-27 134.0
54 TraesCS3A01G502100 chr1D 81.000 100 19 0 3245 3344 342128161 342128062 2.770000e-11 80.5
55 TraesCS3A01G502100 chr2A 92.092 392 23 7 799 1188 773286267 773286652 2.270000e-151 545.0
56 TraesCS3A01G502100 chr2A 95.023 221 10 1 582 801 177665807 177665587 2.470000e-91 346.0
57 TraesCS3A01G502100 chr2A 95.023 221 10 1 582 801 258346746 258346966 2.470000e-91 346.0
58 TraesCS3A01G502100 chr2A 89.552 201 9 9 397 585 773286069 773286269 9.270000e-61 244.0
59 TraesCS3A01G502100 chr2A 95.902 122 5 0 1497 1618 773290303 773290424 7.320000e-47 198.0
60 TraesCS3A01G502100 chr2A 94.059 101 6 0 3245 3345 767480864 767480964 1.610000e-33 154.0
61 TraesCS3A01G502100 chr4D 94.186 344 20 0 1 344 449740628 449740285 2.960000e-145 525.0
62 TraesCS3A01G502100 chr4D 91.176 102 9 0 3244 3345 8196280 8196381 4.500000e-29 139.0
63 TraesCS3A01G502100 chr4D 91.919 99 8 0 3246 3344 503566570 503566668 4.500000e-29 139.0
64 TraesCS3A01G502100 chr4D 90.000 100 10 0 3245 3344 15448776 15448677 2.710000e-26 130.0
65 TraesCS3A01G502100 chr7A 96.721 305 9 1 1194 1497 442273597 442273901 1.070000e-139 507.0
66 TraesCS3A01G502100 chr6A 95.223 314 12 3 1194 1506 569480553 569480242 8.340000e-136 494.0
67 TraesCS3A01G502100 chr6A 91.429 105 8 1 3242 3345 153508895 153508791 3.480000e-30 143.0
68 TraesCS3A01G502100 chr6A 88.596 114 12 1 3233 3345 349942290 349942177 1.620000e-28 137.0
69 TraesCS3A01G502100 chr1A 95.724 304 12 1 1194 1496 68157042 68157345 3.880000e-134 488.0
70 TraesCS3A01G502100 chr1A 93.375 317 15 5 1191 1501 465294751 465295067 6.540000e-127 464.0
71 TraesCS3A01G502100 chr1A 93.443 305 16 2 1194 1497 306144189 306143888 1.830000e-122 449.0
72 TraesCS3A01G502100 chr1A 94.248 226 10 3 577 800 28408670 28408894 3.200000e-90 342.0
73 TraesCS3A01G502100 chr1A 94.118 102 6 0 3244 3345 12309112 12309213 4.470000e-34 156.0
74 TraesCS3A01G502100 chr1A 94.059 101 6 0 3245 3345 359915865 359915765 1.610000e-33 154.0
75 TraesCS3A01G502100 chr1A 93.069 101 7 0 3245 3345 23823021 23823121 7.480000e-32 148.0
76 TraesCS3A01G502100 chr1A 93.000 100 7 0 3246 3345 551013092 551012993 2.690000e-31 147.0
77 TraesCS3A01G502100 chr4B 93.913 230 12 2 583 811 634730533 634730305 2.470000e-91 346.0
78 TraesCS3A01G502100 chr4B 90.323 93 9 0 3245 3337 441086314 441086222 4.530000e-24 122.0
79 TraesCS3A01G502100 chr7B 92.925 212 13 2 341 550 584321372 584321161 1.170000e-79 307.0
80 TraesCS3A01G502100 chr7B 95.050 101 5 0 3245 3345 158390971 158390871 3.450000e-35 159.0
81 TraesCS3A01G502100 chr5D 94.000 100 6 0 3246 3345 350229155 350229056 5.780000e-33 152.0
82 TraesCS3A01G502100 chr5D 92.929 99 7 0 3246 3344 369564635 369564537 9.670000e-31 145.0
83 TraesCS3A01G502100 chr5D 92.079 101 8 0 3245 3345 423490384 423490484 3.480000e-30 143.0


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 TraesCS3A01G502100 chr3A 725604263 725607607 3344 False 6178.000000 6178 100.000000 1 3345 1 chr3A.!!$F3 3344
1 TraesCS3A01G502100 chr3A 725561934 725565276 3342 False 6065.000000 6065 99.402000 1 3345 1 chr3A.!!$F2 3344
2 TraesCS3A01G502100 chr3A 725518084 725523502 5418 False 1420.000000 2431 95.773000 1617 3345 2 chr3A.!!$F5 1728
3 TraesCS3A01G502100 chr3A 693550929 693551685 756 True 416.000000 647 96.832667 341 1618 3 chr3A.!!$R3 1277
4 TraesCS3A01G502100 chr5A 555248132 555249104 972 True 861.000000 1500 99.237000 341 1618 2 chr5A.!!$R4 1277
5 TraesCS3A01G502100 chr5A 555233982 555234954 972 True 844.500000 1483 97.811000 341 1618 2 chr5A.!!$R3 1277
6 TraesCS3A01G502100 chr5A 641216211 641216968 757 True 403.333333 623 95.794667 341 1619 3 chr5A.!!$R5 1278
7 TraesCS3A01G502100 chrUn 300563157 300564129 972 True 858.500000 1495 99.178500 341 1618 2 chrUn.!!$R2 1277
8 TraesCS3A01G502100 chr3D 594800563 594802090 1527 False 688.500000 931 87.107500 1622 3247 2 chr3D.!!$F1 1625
9 TraesCS3A01G502100 chr3B 798282644 798283976 1332 False 399.500000 675 90.434000 2510 3231 2 chr3B.!!$F2 721
10 TraesCS3A01G502100 chr6D 468854631 468855380 749 True 402.000000 588 96.089333 341 1618 3 chr6D.!!$R2 1277
11 TraesCS3A01G502100 chr2A 773286069 773290424 4355 False 329.000000 545 92.515333 397 1618 3 chr2A.!!$F3 1221

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
180 181 1.759445 TGCCTAATCTGCTCCAGAGTC 59.241 52.381 0.0 0.00 44.08 3.36 F
792 809 4.201783 GAATGACTTATTCACCGAAACGGG 60.202 45.833 14.5 4.11 42.41 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 5482 0.965866 AGCCGATGACGAGGAAGACA 60.966 55.000 0.00 0.00 42.66 3.41 R
2547 9943 1.753463 CTAGGAGGCTCCGGTCGTT 60.753 63.158 27.11 11.78 42.75 3.85 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
180 181 1.759445 TGCCTAATCTGCTCCAGAGTC 59.241 52.381 0.00 0.00 44.08 3.36
792 809 4.201783 GAATGACTTATTCACCGAAACGGG 60.202 45.833 14.50 4.11 42.41 5.28
1438 5106 4.960469 AGGATTCAAGATGACATGCCATTT 59.040 37.500 0.00 0.00 0.00 2.32
1810 5482 0.753479 ACCTCATCCTCATCGTCGCT 60.753 55.000 0.00 0.00 0.00 4.93
1867 5539 2.097466 ACAGTGGCAAGAACAAGAAACG 59.903 45.455 0.00 0.00 0.00 3.60
2502 9898 2.972625 TCGGCAGGTTTCATTCTACTG 58.027 47.619 0.00 0.00 0.00 2.74
2547 9943 3.963476 TCCTTTTCCCTCAACCAAGAA 57.037 42.857 0.00 0.00 0.00 2.52
2864 10265 2.039746 TGGAGTTGATTTGGTCGTCCAT 59.960 45.455 1.21 0.00 43.91 3.41
3339 11373 2.497675 GACCTAGACTGCTCCAATGTCA 59.502 50.000 0.00 0.00 33.56 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 5.888161 AGATTAGGCATCTCGGAAACAATTT 59.112 36.000 0.00 0.00 37.79 1.82
180 181 2.364632 TGATTGTATTCACGCAAGGGG 58.635 47.619 0.00 0.00 44.90 4.79
983 1003 0.246910 TCTGTAAATGTACCGCCGCA 59.753 50.000 0.00 0.00 0.00 5.69
1305 4973 7.756395 AATCTAGTGCAAATGAATCCTATGG 57.244 36.000 0.00 0.00 0.00 2.74
1438 5106 6.821665 CAGGAATAGGAAAAACGTAGGATTGA 59.178 38.462 0.00 0.00 0.00 2.57
1810 5482 0.965866 AGCCGATGACGAGGAAGACA 60.966 55.000 0.00 0.00 42.66 3.41
1867 5539 6.183360 CCTCTCTTCCTTCTTTATACCCTGTC 60.183 46.154 0.00 0.00 0.00 3.51
2547 9943 1.753463 CTAGGAGGCTCCGGTCGTT 60.753 63.158 27.11 11.78 42.75 3.85
2864 10265 1.208535 AGACAAGTCCACGACCACAAA 59.791 47.619 0.00 0.00 32.18 2.83


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

AutoCloner maintained by Alex Coulton.