Multiple sequence alignment - TraesCS2B01G497900

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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 TraesCS2B01G497900 chr2B 100.000 6326 0 0 1 6326 694425561 694419236 0.000000e+00 11683.0
1 TraesCS2B01G497900 chr2B 98.209 5919 85 11 1 5914 694446338 694440436 0.000000e+00 10323.0
2 TraesCS2B01G497900 chr2B 96.906 2877 82 5 598 3471 694477009 694474137 0.000000e+00 4813.0
3 TraesCS2B01G497900 chr2B 96.915 2593 64 9 3738 6326 694473880 694471300 0.000000e+00 4331.0
4 TraesCS2B01G497900 chr2B 94.972 358 16 2 5971 6326 694440432 694440075 1.540000e-155 560.0
5 TraesCS2B01G497900 chr2B 95.294 255 8 2 3455 3705 694474119 694473865 9.880000e-108 401.0
6 TraesCS2B01G497900 chr2B 88.931 262 12 7 3084 3334 694421713 694421458 2.220000e-79 307.0
7 TraesCS2B01G497900 chr2B 88.931 262 12 7 3849 4104 694422478 694422228 2.220000e-79 307.0
8 TraesCS2B01G497900 chr2B 88.889 261 13 7 3849 4104 694443258 694443009 2.220000e-79 307.0
9 TraesCS2B01G497900 chr2B 88.550 262 13 8 3084 3334 694442492 694442237 1.030000e-77 302.0
10 TraesCS2B01G497900 chr2B 88.168 262 14 8 3084 3334 694473769 694473514 4.800000e-76 296.0
11 TraesCS2B01G497900 chr2B 88.168 262 14 9 3849 4104 694474524 694474274 4.800000e-76 296.0
12 TraesCS2B01G497900 chr2B 93.103 145 9 1 139 283 761962482 761962339 1.790000e-50 211.0
13 TraesCS2B01G497900 chr2B 92.806 139 10 0 1 139 694477218 694477080 1.080000e-47 202.0
14 TraesCS2B01G497900 chr2B 86.275 153 19 2 402 553 29705901 29705750 1.410000e-36 165.0
15 TraesCS2B01G497900 chr2B 97.959 49 1 0 557 605 694477087 694477039 1.130000e-12 86.1
16 TraesCS2B01G497900 chr2D 91.386 3146 196 20 604 3717 577346203 577343101 0.000000e+00 4239.0
17 TraesCS2B01G497900 chr2D 94.983 2611 98 17 3726 6326 577343128 577340541 0.000000e+00 4065.0
18 TraesCS2B01G497900 chr2D 81.527 969 140 25 1289 2236 551704489 551703539 0.000000e+00 761.0
19 TraesCS2B01G497900 chr2D 80.795 453 77 5 2343 2788 551821767 551821318 4.690000e-91 346.0
20 TraesCS2B01G497900 chr2D 86.076 316 34 5 4132 4440 577343488 577343176 1.310000e-86 331.0
21 TraesCS2B01G497900 chr2D 87.645 259 23 4 3849 4104 577343738 577343486 6.200000e-75 292.0
22 TraesCS2B01G497900 chr2D 87.308 260 21 5 3084 3334 577343005 577342749 2.890000e-73 287.0
23 TraesCS2B01G497900 chr2D 94.340 53 3 0 557 609 577346278 577346226 1.460000e-11 82.4
24 TraesCS2B01G497900 chr2A 93.714 2593 109 25 3757 6326 715423406 715420845 0.000000e+00 3836.0
25 TraesCS2B01G497900 chr2A 92.410 1660 93 11 2069 3697 715425063 715423406 0.000000e+00 2337.0
26 TraesCS2B01G497900 chr2A 91.476 1443 102 13 604 2041 715426674 715425248 0.000000e+00 1964.0
27 TraesCS2B01G497900 chr2A 85.127 316 37 5 4132 4440 715423773 715423461 1.320000e-81 315.0
28 TraesCS2B01G497900 chr2A 86.873 259 25 4 3849 4104 715424023 715423771 1.340000e-71 281.0
29 TraesCS2B01G497900 chr2A 86.486 259 23 6 3084 3334 715423315 715423061 2.250000e-69 274.0
30 TraesCS2B01G497900 chr2A 90.566 53 5 0 557 609 715426749 715426697 3.160000e-08 71.3
31 TraesCS2B01G497900 chr5D 87.788 565 62 4 4716 5279 464114963 464115521 0.000000e+00 654.0
32 TraesCS2B01G497900 chr5D 83.557 596 79 15 4715 5302 464108647 464109231 2.010000e-149 540.0
33 TraesCS2B01G497900 chr5D 79.968 629 80 33 717 1315 464110518 464111130 7.580000e-114 422.0
34 TraesCS2B01G497900 chr5D 84.878 410 52 6 1382 1784 464111283 464111689 7.640000e-109 405.0
35 TraesCS2B01G497900 chr5D 82.609 460 77 1 2328 2787 464106921 464107377 2.750000e-108 403.0
36 TraesCS2B01G497900 chr5D 82.965 452 63 8 2343 2787 474821386 474820942 4.600000e-106 396.0
37 TraesCS2B01G497900 chr5D 86.878 221 20 8 5276 5492 464116982 464117197 8.200000e-59 239.0
38 TraesCS2B01G497900 chr5D 80.071 281 35 11 5331 5609 464117194 464117455 8.370000e-44 189.0
39 TraesCS2B01G497900 chr5B 80.667 869 134 25 4433 5279 57719020 57718164 1.490000e-180 643.0
40 TraesCS2B01G497900 chr5B 82.285 604 80 17 4715 5302 571204218 571204810 1.220000e-136 497.0
41 TraesCS2B01G497900 chr5B 86.818 220 23 6 5276 5492 57716684 57716468 2.280000e-59 241.0
42 TraesCS2B01G497900 chr5B 86.124 209 23 6 5331 5537 57716471 57716267 2.970000e-53 220.0
43 TraesCS2B01G497900 chr5A 86.372 565 70 5 4716 5279 43656383 43655825 1.510000e-170 610.0
44 TraesCS2B01G497900 chr5A 86.195 565 71 5 4716 5279 43742283 43741725 7.020000e-169 604.0
45 TraesCS2B01G497900 chr5A 86.018 565 72 5 4716 5279 43694752 43694194 3.260000e-167 599.0
46 TraesCS2B01G497900 chr5A 84.878 410 52 6 1382 1784 43699832 43699426 7.640000e-109 405.0
47 TraesCS2B01G497900 chr5A 84.390 410 54 6 1382 1784 43745975 43745569 1.650000e-105 394.0
48 TraesCS2B01G497900 chr5A 84.146 410 55 6 1382 1784 43659919 43659513 7.690000e-104 388.0
49 TraesCS2B01G497900 chr5A 80.943 509 80 13 1289 1784 584554229 584554733 2.770000e-103 387.0
50 TraesCS2B01G497900 chr5A 79.654 462 61 16 2334 2787 584549942 584550378 1.030000e-77 302.0
51 TraesCS2B01G497900 chr5A 88.263 213 21 4 5276 5486 43612676 43612466 1.050000e-62 252.0
52 TraesCS2B01G497900 chr5A 85.646 209 26 4 5331 5537 43612464 43612258 3.840000e-52 217.0
53 TraesCS2B01G497900 chr7D 82.100 581 85 14 4715 5285 570988463 570989034 4.440000e-131 479.0
54 TraesCS2B01G497900 chr7D 89.600 125 11 2 431 553 541971204 541971328 2.360000e-34 158.0
55 TraesCS2B01G497900 chr7B 82.952 481 67 10 2307 2775 626565899 626565422 2.730000e-113 420.0
56 TraesCS2B01G497900 chr7B 93.865 163 9 1 132 293 109894104 109894266 1.760000e-60 244.0
57 TraesCS2B01G497900 chr7B 89.677 155 15 1 140 293 684441413 684441567 5.000000e-46 196.0
58 TraesCS2B01G497900 chr7B 91.034 145 12 1 139 283 22774451 22774594 1.800000e-45 195.0
59 TraesCS2B01G497900 chr7B 86.928 153 18 2 402 553 64004445 64004294 3.030000e-38 171.0
60 TraesCS2B01G497900 chr7B 79.253 241 43 7 316 553 22792524 22792760 1.830000e-35 161.0
61 TraesCS2B01G497900 chr7B 79.167 240 45 5 316 553 22839246 22839482 1.830000e-35 161.0
62 TraesCS2B01G497900 chr7B 84.416 154 19 5 402 553 22716657 22716807 5.110000e-31 147.0
63 TraesCS2B01G497900 chr4A 83.255 424 53 11 139 553 681609789 681609375 2.150000e-99 374.0
64 TraesCS2B01G497900 chr3D 88.931 262 27 2 294 553 592600596 592600857 7.910000e-84 322.0
65 TraesCS2B01G497900 chr3D 90.968 155 13 1 140 293 592600308 592600462 2.310000e-49 207.0
66 TraesCS2B01G497900 chr7A 94.872 156 6 2 139 293 694372306 694372460 6.340000e-60 243.0
67 TraesCS2B01G497900 chr7A 86.826 167 19 2 4548 4711 660082361 660082527 3.900000e-42 183.0
68 TraesCS2B01G497900 chr6A 94.483 145 7 1 139 283 12634305 12634162 8.250000e-54 222.0
69 TraesCS2B01G497900 chr1D 85.625 160 19 4 404 560 486402902 486403060 1.410000e-36 165.0
70 TraesCS2B01G497900 chr3A 74.148 352 74 15 5654 5999 691485578 691485918 5.150000e-26 130.0


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 TraesCS2B01G497900 chr2B 694419236 694425561 6325 True 11683.000000 11683 100.000000 1 6326 1 chr2B.!!$R2 6325
1 TraesCS2B01G497900 chr2B 694440075 694446338 6263 True 5441.500000 10323 96.590500 1 6326 2 chr2B.!!$R5 6325
2 TraesCS2B01G497900 chr2B 694471300 694477218 5918 True 1489.300000 4813 93.745143 1 6326 7 chr2B.!!$R7 6325
3 TraesCS2B01G497900 chr2B 694421458 694422478 1020 True 307.000000 307 88.931000 3084 4104 2 chr2B.!!$R4 1020
4 TraesCS2B01G497900 chr2B 694442237 694443258 1021 True 304.500000 307 88.719500 3084 4104 2 chr2B.!!$R6 1020
5 TraesCS2B01G497900 chr2D 577340541 577346278 5737 True 1549.400000 4239 90.289667 557 6326 6 chr2D.!!$R3 5769
6 TraesCS2B01G497900 chr2D 551703539 551704489 950 True 761.000000 761 81.527000 1289 2236 1 chr2D.!!$R1 947
7 TraesCS2B01G497900 chr2A 715420845 715426749 5904 True 1296.900000 3836 89.521714 557 6326 7 chr2A.!!$R1 5769
8 TraesCS2B01G497900 chr5D 464106921 464117455 10534 False 407.428571 654 83.678429 717 5609 7 chr5D.!!$F1 4892
9 TraesCS2B01G497900 chr5B 571204218 571204810 592 False 497.000000 497 82.285000 4715 5302 1 chr5B.!!$F1 587
10 TraesCS2B01G497900 chr5B 57716267 57719020 2753 True 368.000000 643 84.536333 4433 5537 3 chr5B.!!$R1 1104
11 TraesCS2B01G497900 chr5A 43694194 43694752 558 True 599.000000 599 86.018000 4716 5279 1 chr5A.!!$R1 563
12 TraesCS2B01G497900 chr5A 43655825 43659919 4094 True 499.000000 610 85.259000 1382 5279 2 chr5A.!!$R4 3897
13 TraesCS2B01G497900 chr5A 43741725 43745975 4250 True 499.000000 604 85.292500 1382 5279 2 chr5A.!!$R5 3897
14 TraesCS2B01G497900 chr5A 584549942 584554733 4791 False 344.500000 387 80.298500 1289 2787 2 chr5A.!!$F1 1498
15 TraesCS2B01G497900 chr7D 570988463 570989034 571 False 479.000000 479 82.100000 4715 5285 1 chr7D.!!$F2 570
16 TraesCS2B01G497900 chr3D 592600308 592600857 549 False 264.500000 322 89.949500 140 553 2 chr3D.!!$F1 413

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
685 859 1.321474 CCACTGCTTGTGTGTCCAAT 58.679 50.000 9.00 0.00 44.81 3.16 F
740 3621 3.425162 TTTCCTTCCCTCAAGAGCTTC 57.575 47.619 0.00 0.00 33.29 3.86 F
2066 5254 1.082756 CCGACAGTCGCTTTGTTGC 60.083 57.895 18.02 0.00 38.82 4.17 F
2493 5722 0.451383 TATGCTTTGCACGTGGATGC 59.549 50.000 22.03 22.03 43.04 3.91 F
4312 9359 7.147863 TGCATATTGATGTAAGCAGAATTGGTT 60.148 33.333 0.00 0.00 39.61 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 5254 0.037882 ACATGGTCAGTGACGAGCAG 60.038 55.000 16.89 9.79 45.79 4.24 R
2103 5308 6.016610 GCATTTAACTTCACCACTTAAGGACA 60.017 38.462 7.53 0.00 0.00 4.02 R
2913 6178 3.903714 TGTCTTGATCCTCCTTCTGTTGA 59.096 43.478 0.00 0.00 0.00 3.18 R
4312 9359 1.111116 ACTTCTTGGGTGGACGACGA 61.111 55.000 0.00 0.00 0.00 4.20 R
5985 14079 0.179029 ACCACCCTTCAAGACGGTTG 60.179 55.000 0.00 0.00 0.00 3.77 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
685 859 1.321474 CCACTGCTTGTGTGTCCAAT 58.679 50.000 9.00 0.00 44.81 3.16
740 3621 3.425162 TTTCCTTCCCTCAAGAGCTTC 57.575 47.619 0.00 0.00 33.29 3.86
799 3680 3.996480 ACAAAGAAGTCTGTAGGAGTGC 58.004 45.455 0.00 0.00 0.00 4.40
1284 4288 6.721208 TGAAGGCACATAAGGAAAGAAAGAAT 59.279 34.615 0.00 0.00 0.00 2.40
1637 4650 4.885325 TGTGGTCTTACTTTGGAAAGGAAC 59.115 41.667 4.23 0.00 40.31 3.62
2066 5254 1.082756 CCGACAGTCGCTTTGTTGC 60.083 57.895 18.02 0.00 38.82 4.17
2103 5308 6.182627 ACCATGTCAACACTGATGTATGATT 58.817 36.000 0.00 0.00 38.45 2.57
2319 5548 4.479786 TTTTTAGCTTTGGGTTGTGCTT 57.520 36.364 0.00 0.00 37.02 3.91
2493 5722 0.451383 TATGCTTTGCACGTGGATGC 59.549 50.000 22.03 22.03 43.04 3.91
4312 9359 7.147863 TGCATATTGATGTAAGCAGAATTGGTT 60.148 33.333 0.00 0.00 39.61 3.67
4332 9379 0.249741 CGTCGTCCACCCAAGAAGTT 60.250 55.000 0.00 0.00 0.00 2.66
4334 9381 0.395312 TCGTCCACCCAAGAAGTTCC 59.605 55.000 0.00 0.00 0.00 3.62
4685 9748 5.140454 AGAGCAATAGTGAAAACCAACCTT 58.860 37.500 0.00 0.00 0.00 3.50
5587 13591 2.817258 CGGCAGTTTGGTCCAATTAAGA 59.183 45.455 4.80 0.00 0.00 2.10
5610 13614 3.496130 CACATTTCTTCTTGCGTCACTCT 59.504 43.478 0.00 0.00 0.00 3.24
5611 13615 4.024556 CACATTTCTTCTTGCGTCACTCTT 60.025 41.667 0.00 0.00 0.00 2.85
5612 13616 5.177511 CACATTTCTTCTTGCGTCACTCTTA 59.822 40.000 0.00 0.00 0.00 2.10
5613 13617 5.758296 ACATTTCTTCTTGCGTCACTCTTAA 59.242 36.000 0.00 0.00 0.00 1.85
5616 13620 5.652744 TCTTCTTGCGTCACTCTTAAAAC 57.347 39.130 0.00 0.00 0.00 2.43
5617 13621 5.357257 TCTTCTTGCGTCACTCTTAAAACT 58.643 37.500 0.00 0.00 0.00 2.66
5618 13622 5.815740 TCTTCTTGCGTCACTCTTAAAACTT 59.184 36.000 0.00 0.00 0.00 2.66
5620 13624 7.656137 TCTTCTTGCGTCACTCTTAAAACTTAT 59.344 33.333 0.00 0.00 0.00 1.73
5622 13626 8.997621 TCTTGCGTCACTCTTAAAACTTATAT 57.002 30.769 0.00 0.00 0.00 0.86
5730 13741 5.503927 TCTCATTTTCTTAGGCAGCTCAAT 58.496 37.500 0.00 0.00 0.00 2.57
5836 13930 6.394345 AGGGGAATGAGAAAGAATTACACT 57.606 37.500 0.00 0.00 0.00 3.55
5839 13933 6.768381 GGGGAATGAGAAAGAATTACACTAGG 59.232 42.308 0.00 0.00 0.00 3.02
5903 13997 0.895530 CCACGCCTAGAGAGTTTCCA 59.104 55.000 0.00 0.00 0.00 3.53
5969 14063 7.343574 TCAACTAATAGTCTATTGCACCCTACA 59.656 37.037 14.32 0.00 0.00 2.74
5985 14079 1.474077 CTACATTGCCAGCAAGAACCC 59.526 52.381 11.21 0.00 39.47 4.11
6258 14355 3.495729 GGGAGGTTCCAGCTTCCA 58.504 61.111 2.42 0.00 41.11 3.53
6265 14362 1.383523 GTTCCAGCTTCCACCTATGC 58.616 55.000 0.00 0.00 0.00 3.14
6291 14388 1.559219 ACAACATGATGATCCCGGACA 59.441 47.619 10.29 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
408 544 2.897969 GACAGTCTGGTCAAGTAGGGAA 59.102 50.000 4.53 0.00 37.73 3.97
620 794 1.135333 GTCCGACCTCACAGGAGAATC 59.865 57.143 0.00 0.00 44.26 2.52
897 3785 7.116233 CACTTTTGGCAAAGGTAACAATGATAC 59.884 37.037 24.66 0.00 43.47 2.24
1284 4288 7.127801 TCCTCCTTTTCATCATTCTCCTTATCA 59.872 37.037 0.00 0.00 0.00 2.15
1303 4307 2.452505 CTCCTTCGACTTCTCCTCCTT 58.547 52.381 0.00 0.00 0.00 3.36
1513 4521 6.007076 TGTCAAATTAGTAAGCACCATTCCA 58.993 36.000 0.00 0.00 0.00 3.53
1637 4650 5.116180 TGCGGATATGTTACCTCTCTTTTG 58.884 41.667 0.00 0.00 0.00 2.44
2066 5254 0.037882 ACATGGTCAGTGACGAGCAG 60.038 55.000 16.89 9.79 45.79 4.24
2103 5308 6.016610 GCATTTAACTTCACCACTTAAGGACA 60.017 38.462 7.53 0.00 0.00 4.02
2184 5394 9.842775 ATCTATGAAGCAAATGTTCTGAATCTA 57.157 29.630 0.00 0.00 0.00 1.98
2913 6178 3.903714 TGTCTTGATCCTCCTTCTGTTGA 59.096 43.478 0.00 0.00 0.00 3.18
4312 9359 1.111116 ACTTCTTGGGTGGACGACGA 61.111 55.000 0.00 0.00 0.00 4.20
4332 9379 3.009115 CTTTCCCCTCAGCCCGGA 61.009 66.667 0.73 0.00 0.00 5.14
4334 9381 4.115199 CCCTTTCCCCTCAGCCCG 62.115 72.222 0.00 0.00 0.00 6.13
4685 9748 6.960542 AGGAAGGAAGAAGATTTACCTCTACA 59.039 38.462 0.00 0.00 0.00 2.74
4766 9883 8.188799 TCTGAACCTTGACGATAACTAAGTATG 58.811 37.037 0.00 0.00 0.00 2.39
5456 12423 3.974871 TTTACCACGACAAGAAAAGCC 57.025 42.857 0.00 0.00 0.00 4.35
5587 13591 3.206150 AGTGACGCAAGAAGAAATGTGT 58.794 40.909 0.00 0.00 42.55 3.72
5612 13616 9.174166 GGCATCCCGTATCAATATATAAGTTTT 57.826 33.333 0.00 0.00 0.00 2.43
5613 13617 8.325787 TGGCATCCCGTATCAATATATAAGTTT 58.674 33.333 0.00 0.00 0.00 2.66
5616 13620 7.272244 TGTGGCATCCCGTATCAATATATAAG 58.728 38.462 0.00 0.00 0.00 1.73
5617 13621 7.189079 TGTGGCATCCCGTATCAATATATAA 57.811 36.000 0.00 0.00 0.00 0.98
5618 13622 6.800072 TGTGGCATCCCGTATCAATATATA 57.200 37.500 0.00 0.00 0.00 0.86
5620 13624 5.692115 ATGTGGCATCCCGTATCAATATA 57.308 39.130 0.00 0.00 0.00 0.86
5622 13626 5.425217 AGATATGTGGCATCCCGTATCAATA 59.575 40.000 14.58 0.00 30.85 1.90
5623 13627 2.957402 ATGTGGCATCCCGTATCAAT 57.043 45.000 0.00 0.00 0.00 2.57
5625 13629 3.173151 AGATATGTGGCATCCCGTATCA 58.827 45.455 14.58 0.00 30.85 2.15
5708 13719 5.356190 TGATTGAGCTGCCTAAGAAAATGAG 59.644 40.000 0.00 0.00 0.00 2.90
5730 13741 4.885907 GCTTGATGATCCTCCTGATTTTGA 59.114 41.667 0.00 0.00 32.41 2.69
5836 13930 6.059484 ACTTTTCTTTGTCACGATTTCCCTA 58.941 36.000 0.00 0.00 0.00 3.53
5839 13933 6.631636 GTGTACTTTTCTTTGTCACGATTTCC 59.368 38.462 0.00 0.00 0.00 3.13
5903 13997 0.405198 TGGAGGTCATGCACAATGGT 59.595 50.000 0.00 0.00 36.86 3.55
5969 14063 0.681175 GTTGGGTTCTTGCTGGCAAT 59.319 50.000 8.49 0.00 35.20 3.56
5985 14079 0.179029 ACCACCCTTCAAGACGGTTG 60.179 55.000 0.00 0.00 0.00 3.77
6109 14205 8.700439 TTCTAGGGTTAAAAATGCTAAACTGT 57.300 30.769 0.00 0.00 0.00 3.55
6265 14362 2.954318 GGGATCATCATGTTGTTCCTGG 59.046 50.000 23.77 0.00 36.26 4.45
6291 14388 3.415212 CTCGGGATGGACATGCATTATT 58.585 45.455 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.