Multiple sequence alignment - TraesCS5A01G148000

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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 TraesCS5A01G148000 chr5A 100.000 3446 0 0 1 3446 325930830 325934275 0.000000e+00 6364.0
1 TraesCS5A01G148000 chr5A 94.000 50 3 0 2434 2483 590212365 590212316 3.690000e-10 76.8
2 TraesCS5A01G148000 chr5D 95.075 2457 80 22 55 2486 231353506 231351066 0.000000e+00 3829.0
3 TraesCS5A01G148000 chr5D 88.108 967 109 5 2483 3446 399810880 399811843 0.000000e+00 1144.0
4 TraesCS5A01G148000 chr5B 95.256 1855 54 9 642 2486 275033176 275035006 0.000000e+00 2907.0
5 TraesCS5A01G148000 chr5B 88.218 662 48 15 1 640 275032260 275032913 0.000000e+00 763.0
6 TraesCS5A01G148000 chr5B 95.918 49 2 0 2436 2484 619532105 619532153 2.850000e-11 80.5
7 TraesCS5A01G148000 chr4A 81.867 1671 249 37 686 2321 476978720 476980371 0.000000e+00 1358.0
8 TraesCS5A01G148000 chr4A 96.078 51 2 0 2434 2484 579991650 579991600 2.200000e-12 84.2
9 TraesCS5A01G148000 chr4A 94.118 51 3 0 2434 2484 395644582 395644532 1.030000e-10 78.7
10 TraesCS5A01G148000 chr4B 81.840 1652 254 28 700 2321 141429239 141427604 0.000000e+00 1347.0
11 TraesCS5A01G148000 chr4B 88.454 485 56 0 2962 3446 400387381 400386897 1.380000e-163 586.0
12 TraesCS5A01G148000 chr4B 86.925 413 33 7 2483 2892 400388586 400388192 8.780000e-121 444.0
13 TraesCS5A01G148000 chr4D 81.549 1653 257 30 700 2321 99163017 99161382 0.000000e+00 1319.0
14 TraesCS5A01G148000 chr3A 90.900 967 85 2 2483 3446 691482555 691483521 0.000000e+00 1295.0
15 TraesCS5A01G148000 chr3A 74.569 464 106 11 2944 3401 729418637 729419094 3.510000e-45 193.0
16 TraesCS5A01G148000 chr3A 95.745 47 2 0 2434 2480 591286886 591286840 3.690000e-10 76.8
17 TraesCS5A01G148000 chr2A 86.481 969 126 4 2482 3446 679944492 679945459 0.000000e+00 1059.0
18 TraesCS5A01G148000 chr7A 84.281 967 144 7 2486 3446 17877719 17876755 0.000000e+00 937.0
19 TraesCS5A01G148000 chr1D 83.938 965 146 7 2487 3446 374458399 374457439 0.000000e+00 915.0
20 TraesCS5A01G148000 chr1D 80.777 952 176 7 2487 3433 247501027 247501976 0.000000e+00 737.0
21 TraesCS5A01G148000 chr3B 72.231 641 160 18 2815 3446 145373542 145372911 7.600000e-42 182.0
22 TraesCS5A01G148000 chr6B 71.722 633 164 15 2815 3440 676213011 676212387 2.750000e-36 163.0
23 TraesCS5A01G148000 chr7B 94.118 51 3 0 2434 2484 461082261 461082211 1.030000e-10 78.7
24 TraesCS5A01G148000 chr1A 95.745 47 2 0 2434 2480 33945698 33945652 3.690000e-10 76.8


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 TraesCS5A01G148000 chr5A 325930830 325934275 3445 False 6364 6364 100.0000 1 3446 1 chr5A.!!$F1 3445
1 TraesCS5A01G148000 chr5D 231351066 231353506 2440 True 3829 3829 95.0750 55 2486 1 chr5D.!!$R1 2431
2 TraesCS5A01G148000 chr5D 399810880 399811843 963 False 1144 1144 88.1080 2483 3446 1 chr5D.!!$F1 963
3 TraesCS5A01G148000 chr5B 275032260 275035006 2746 False 1835 2907 91.7370 1 2486 2 chr5B.!!$F2 2485
4 TraesCS5A01G148000 chr4A 476978720 476980371 1651 False 1358 1358 81.8670 686 2321 1 chr4A.!!$F1 1635
5 TraesCS5A01G148000 chr4B 141427604 141429239 1635 True 1347 1347 81.8400 700 2321 1 chr4B.!!$R1 1621
6 TraesCS5A01G148000 chr4B 400386897 400388586 1689 True 515 586 87.6895 2483 3446 2 chr4B.!!$R2 963
7 TraesCS5A01G148000 chr4D 99161382 99163017 1635 True 1319 1319 81.5490 700 2321 1 chr4D.!!$R1 1621
8 TraesCS5A01G148000 chr3A 691482555 691483521 966 False 1295 1295 90.9000 2483 3446 1 chr3A.!!$F1 963
9 TraesCS5A01G148000 chr2A 679944492 679945459 967 False 1059 1059 86.4810 2482 3446 1 chr2A.!!$F1 964
10 TraesCS5A01G148000 chr7A 17876755 17877719 964 True 937 937 84.2810 2486 3446 1 chr7A.!!$R1 960
11 TraesCS5A01G148000 chr1D 374457439 374458399 960 True 915 915 83.9380 2487 3446 1 chr1D.!!$R1 959
12 TraesCS5A01G148000 chr1D 247501027 247501976 949 False 737 737 80.7770 2487 3433 1 chr1D.!!$F1 946

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
295 318 0.543883 TCTGGAAGAGTCCTGCTGCT 60.544 55.000 0.00 0.0 45.22 4.24 F
1306 1626 2.147150 GGTGAGCTCTTTGACAAGGTC 58.853 52.381 16.19 0.0 39.79 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1348 1668 1.370609 CACTGATGAGCTGCTGGAAG 58.629 55.0 7.01 1.65 0.0 3.46 R
2642 2974 0.172352 CGTAAATGTGGCGGGCAATT 59.828 50.0 5.57 6.03 0.0 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
102 106 0.798776 AAGAAAATCTCTGGCGTGCG 59.201 50.000 0.00 0.00 33.37 5.34
202 225 2.801111 GTTGTCTGGTTTTCTCTCGGTC 59.199 50.000 0.00 0.00 0.00 4.79
231 254 6.401047 CGGAGGTAGTACATTCTTCCAATA 57.599 41.667 2.06 0.00 0.00 1.90
243 266 0.817634 TTCCAATAATCTGCGCCCCG 60.818 55.000 4.18 0.00 0.00 5.73
294 317 1.978473 TCTGGAAGAGTCCTGCTGC 59.022 57.895 0.00 0.00 45.22 5.25
295 318 0.543883 TCTGGAAGAGTCCTGCTGCT 60.544 55.000 0.00 0.00 45.22 4.24
313 336 4.302455 CTGCTAGGTGTCGAATCATTAGG 58.698 47.826 0.00 0.00 0.00 2.69
379 406 6.347696 GGATCCTAATCTCATCATGTGATCC 58.652 44.000 3.84 0.00 39.05 3.36
398 425 3.849951 TCCCTCTTGCCGGATCGC 61.850 66.667 5.05 0.00 0.00 4.58
442 469 6.016443 CCCGATACCTAGTTTGTTAGAGGTAG 60.016 46.154 5.90 0.00 45.40 3.18
476 503 3.459232 AGTCATAGCAATTCAGCGCTA 57.541 42.857 10.99 0.00 44.40 4.26
498 525 6.541641 GCTACTGATGAAGGAATCACTTGATT 59.458 38.462 4.07 4.07 46.54 2.57
499 526 7.066766 GCTACTGATGAAGGAATCACTTGATTT 59.933 37.037 5.94 0.00 44.14 2.17
959 1279 5.968387 AGTGTCGTAGCATATTTAAGTGC 57.032 39.130 0.00 2.43 41.57 4.40
1306 1626 2.147150 GGTGAGCTCTTTGACAAGGTC 58.853 52.381 16.19 0.00 39.79 3.85
1348 1668 2.280628 GAGGGTGCTGCACATAAGTAC 58.719 52.381 31.35 13.78 35.86 2.73
1390 1710 1.078426 GGATTACTGCCACAGCCGT 60.078 57.895 0.00 0.00 39.94 5.68
1429 1749 3.007398 ACTTGAAGCCTGAGAACCTACTG 59.993 47.826 0.00 0.00 0.00 2.74
1447 1767 6.888632 ACCTACTGCTTGATGAGAATGAAAAT 59.111 34.615 0.00 0.00 0.00 1.82
1495 1815 3.990469 GTGCACTTTCAGAATCGAAGAGA 59.010 43.478 10.32 0.00 43.63 3.10
1534 1854 1.681666 CACCTGTGGATCACCTGCT 59.318 57.895 0.00 0.00 37.04 4.24
1876 2196 0.679002 ATGCCACCACAGATGCTGTC 60.679 55.000 0.00 0.00 43.43 3.51
1920 2240 1.734465 GAAGAACAGCCATGAAGACGG 59.266 52.381 0.00 0.00 0.00 4.79
2236 2556 2.287547 TGAGATGAAACAAACAAGCGGC 60.288 45.455 0.00 0.00 0.00 6.53
2380 2700 9.372369 GTCTCACTTATTATGTTTAGTTCTGCT 57.628 33.333 0.00 0.00 0.00 4.24
2566 2896 5.855925 CGCTAACACAACTTATTTTCATGCA 59.144 36.000 0.00 0.00 0.00 3.96
2582 2912 2.831685 TGCATATGCTAACGGTAGGG 57.168 50.000 27.13 0.00 42.66 3.53
2690 3022 1.121378 TTGGTCTGTTGGGTACGACA 58.879 50.000 0.00 0.00 38.67 4.35
2925 4021 1.832883 TGTGAATGGGTTTGCGCTAT 58.167 45.000 9.73 0.00 0.00 2.97
2935 4031 1.326548 GTTTGCGCTATGAACGGTAGG 59.673 52.381 9.73 0.00 0.00 3.18
2936 4032 0.808453 TTGCGCTATGAACGGTAGGC 60.808 55.000 9.73 0.00 0.00 3.93
3028 4124 0.873312 CGACCCATCACGCTGATCAG 60.873 60.000 18.84 18.84 34.28 2.90
3061 4157 4.760047 CTGCGCCAAGGCCTACGT 62.760 66.667 20.04 0.00 37.98 3.57
3135 4231 6.350194 GGCTTTTCTCAAAGGACGGAATATTT 60.350 38.462 0.00 0.00 40.03 1.40
3187 4284 6.611381 TCGTCCATGAGCTTAAAATGAAAAG 58.389 36.000 0.00 0.00 0.00 2.27
3258 4357 3.387374 TGTAAACTGGGAGTTTGTACGGA 59.613 43.478 11.19 0.00 46.83 4.69
3264 4363 1.622312 GGGAGTTTGTACGGAAGGTCT 59.378 52.381 0.00 0.00 0.00 3.85
3304 4403 0.589708 GCTGGTTTTGTCCACCGTAC 59.410 55.000 0.00 0.00 37.07 3.67
3335 4434 2.690173 TTAATTGTGGACAAACGGCG 57.310 45.000 4.80 4.80 39.55 6.46
3361 4460 1.244366 ATTAATGGGGAGGTGGGCAT 58.756 50.000 0.00 0.00 0.00 4.40
3433 4533 5.583969 ATCGTTTTTAATTTTGTTGCGGG 57.416 34.783 0.00 0.00 0.00 6.13
3434 4534 3.245519 TCGTTTTTAATTTTGTTGCGGGC 59.754 39.130 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 106 2.158475 TCCAATCAATGTGCCCCTATCC 60.158 50.000 0.00 0.00 0.00 2.59
202 225 0.759436 ATGTACTACCTCCGGGCTGG 60.759 60.000 5.83 5.83 40.09 4.85
243 266 3.417185 GAATTTCGAAATCTGACCGCAC 58.583 45.455 22.93 4.22 0.00 5.34
293 316 4.051922 CACCTAATGATTCGACACCTAGC 58.948 47.826 0.00 0.00 0.00 3.42
294 317 4.051922 GCACCTAATGATTCGACACCTAG 58.948 47.826 0.00 0.00 0.00 3.02
295 318 3.449377 TGCACCTAATGATTCGACACCTA 59.551 43.478 0.00 0.00 0.00 3.08
379 406 2.107141 GATCCGGCAAGAGGGACG 59.893 66.667 0.00 0.00 39.58 4.79
398 425 4.849329 GACGACGGCGCCTACCAG 62.849 72.222 26.68 11.18 42.48 4.00
413 440 4.732672 AACAAACTAGGTATCGGGAGAC 57.267 45.455 0.00 0.00 44.82 3.36
442 469 3.935828 GCTATGACTTCTGAAACCCTGAC 59.064 47.826 0.00 0.00 0.00 3.51
476 503 7.771927 AAAATCAAGTGATTCCTTCATCAGT 57.228 32.000 6.99 0.00 43.41 3.41
553 581 5.675575 GCATAAGTTGATCAGGAGCAAACAG 60.676 44.000 1.04 0.00 38.53 3.16
554 582 4.156556 GCATAAGTTGATCAGGAGCAAACA 59.843 41.667 1.04 0.00 38.53 2.83
567 595 6.757897 AAATCGAATTCAGGCATAAGTTGA 57.242 33.333 6.22 0.00 0.00 3.18
656 949 9.845305 GCAGTCACAGATTTAATAATACGTAAC 57.155 33.333 0.00 0.00 0.00 2.50
721 1021 8.746052 TCCTTGAGACTTTGATTTCTTGTTTA 57.254 30.769 0.00 0.00 0.00 2.01
1348 1668 1.370609 CACTGATGAGCTGCTGGAAG 58.629 55.000 7.01 1.65 0.00 3.46
1429 1749 6.973474 CCTTCAGATTTTCATTCTCATCAAGC 59.027 38.462 0.00 0.00 0.00 4.01
1447 1767 3.573967 GCCCAAAATCAGAAACCTTCAGA 59.426 43.478 0.00 0.00 0.00 3.27
1534 1854 1.951209 TCACCTCTGGAGCCACATAA 58.049 50.000 0.00 0.00 0.00 1.90
1933 2253 8.729805 TTTCAAAGGCATTTAAATTTGTCACT 57.270 26.923 0.00 0.00 34.88 3.41
2458 2787 8.225107 GCAACAGTTATTACTTGTCGAATACAA 58.775 33.333 0.00 0.00 45.90 2.41
2465 2794 4.846137 GCAAGCAACAGTTATTACTTGTCG 59.154 41.667 14.32 0.00 35.97 4.35
2566 2896 1.544691 CGCTCCCTACCGTTAGCATAT 59.455 52.381 0.00 0.00 34.60 1.78
2582 2912 0.382515 AGGATCGTGCTCTTACGCTC 59.617 55.000 0.00 0.00 43.40 5.03
2607 2939 1.615424 GGAGGCCCTGGTCCAACTA 60.615 63.158 0.00 0.00 32.55 2.24
2611 2943 4.741239 GGAGGAGGCCCTGGTCCA 62.741 72.222 11.14 0.00 44.53 4.02
2642 2974 0.172352 CGTAAATGTGGCGGGCAATT 59.828 50.000 5.57 6.03 0.00 2.32
2777 3109 3.676093 GTCAACTTCTTCCGGGAGAAAT 58.324 45.455 25.44 14.20 35.38 2.17
2966 4062 4.775780 GCCCCTTTAACCTTTGGAATAAGT 59.224 41.667 0.00 0.00 0.00 2.24
3028 4124 0.179179 GCAGATCTTGAAAGGCACGC 60.179 55.000 0.00 0.00 0.00 5.34
3061 4157 3.062466 CGAGGGCCAGACGAGTCA 61.062 66.667 6.18 0.00 0.00 3.41
3088 4184 5.238583 CCGTTTGACTTCTAAGAATGACCT 58.761 41.667 0.00 0.00 0.00 3.85
3227 4326 3.698040 ACTCCCAGTTTACACGATCGTAT 59.302 43.478 22.26 13.37 0.00 3.06
3304 4403 5.418524 TGTCCACAATTAATCAGGTTCATGG 59.581 40.000 0.00 0.00 0.00 3.66
3335 4434 3.328050 CCACCTCCCCATTAATAGAGACC 59.672 52.174 9.71 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.