Multiple sequence alignment - TraesCS7B01G283700

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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 TraesCS7B01G283700 chr7B 100.000 3451 0 0 1 3451 517902314 517905764 0.000000e+00 6373.0
1 TraesCS7B01G283700 chr7B 95.920 2206 71 5 1 2187 73167755 73169960 0.000000e+00 3557.0
2 TraesCS7B01G283700 chr7B 82.688 491 49 18 2866 3342 504404073 504404541 1.490000e-108 403.0
3 TraesCS7B01G283700 chr7B 80.263 456 53 24 3006 3451 504236929 504237357 3.340000e-80 309.0
4 TraesCS7B01G283700 chr7B 85.417 288 35 3 2736 3016 504235343 504235630 3.370000e-75 292.0
5 TraesCS7B01G283700 chr7B 77.307 401 45 26 2876 3255 73170818 73171193 9.770000e-46 195.0
6 TraesCS7B01G283700 chr7B 80.921 152 23 5 2872 3021 81612577 81612724 7.830000e-22 115.0
7 TraesCS7B01G283700 chr7B 97.297 37 0 1 2703 2739 504234250 504234285 1.030000e-05 62.1
8 TraesCS7B01G283700 chr2B 95.512 2206 78 6 3 2187 419938343 419940548 0.000000e+00 3506.0
9 TraesCS7B01G283700 chr2B 93.177 2213 121 11 1 2187 528809719 528807511 0.000000e+00 3223.0
10 TraesCS7B01G283700 chr2B 78.358 402 57 20 2876 3264 419941400 419941784 2.070000e-57 233.0
11 TraesCS7B01G283700 chr3B 95.283 2205 86 4 1 2187 766341722 766343926 0.000000e+00 3480.0
12 TraesCS7B01G283700 chr3B 93.402 1834 119 2 1618 3451 512390230 512392061 0.000000e+00 2715.0
13 TraesCS7B01G283700 chr3B 83.747 1409 183 26 1 1395 473235676 473237052 0.000000e+00 1291.0
14 TraesCS7B01G283700 chr3B 77.396 407 48 24 2876 3261 766344746 766345129 5.840000e-48 202.0
15 TraesCS7B01G283700 chr6B 94.787 1899 77 5 308 2187 617031452 617033347 0.000000e+00 2939.0
16 TraesCS7B01G283700 chr6B 94.771 1224 47 4 1 1208 676683443 676684665 0.000000e+00 1890.0
17 TraesCS7B01G283700 chr6B 94.254 992 51 3 1202 2187 676703236 676704227 0.000000e+00 1511.0
18 TraesCS7B01G283700 chr6B 82.313 147 19 6 2248 2392 299595211 299595352 1.680000e-23 121.0
19 TraesCS7B01G283700 chr1B 92.626 1885 103 7 322 2187 344040425 344042292 0.000000e+00 2678.0
20 TraesCS7B01G283700 chr1B 87.409 548 53 8 2697 3229 579973084 579973630 1.760000e-172 616.0
21 TraesCS7B01G283700 chr1B 88.128 219 24 2 3231 3448 579973713 579973930 3.420000e-65 259.0
22 TraesCS7B01G283700 chr7D 97.420 1434 22 2 1 1419 83758751 83760184 0.000000e+00 2429.0
23 TraesCS7B01G283700 chr7D 96.707 668 21 1 1521 2187 83760186 83760853 0.000000e+00 1110.0
24 TraesCS7B01G283700 chr7D 86.000 300 36 2 2695 2988 478458235 478458534 2.000000e-82 316.0
25 TraesCS7B01G283700 chr7D 79.259 405 47 22 2876 3264 83761732 83762115 7.400000e-62 248.0
26 TraesCS7B01G283700 chr7D 83.448 145 21 3 2866 3010 120263091 120263232 7.770000e-27 132.0
27 TraesCS7B01G283700 chr4B 93.832 1216 59 4 1 1201 43587873 43586659 0.000000e+00 1816.0
28 TraesCS7B01G283700 chr4B 93.750 1216 60 4 1 1201 43574007 43572793 0.000000e+00 1810.0
29 TraesCS7B01G283700 chr4B 94.283 997 51 3 1196 2187 43564379 43563384 0.000000e+00 1520.0
30 TraesCS7B01G283700 chr4B 95.528 492 18 1 1195 1682 43578259 43577768 0.000000e+00 784.0
31 TraesCS7B01G283700 chr2D 79.644 393 43 23 2888 3264 238089621 238089250 7.400000e-62 248.0
32 TraesCS7B01G283700 chr2D 83.539 243 28 6 2842 3076 25204122 25203884 2.090000e-52 217.0
33 TraesCS7B01G283700 chr2D 87.273 165 15 3 2694 2852 25204620 25204456 2.120000e-42 183.0
34 TraesCS7B01G283700 chr6A 85.616 146 16 4 2248 2393 222695823 222695683 7.720000e-32 148.0
35 TraesCS7B01G283700 chr6D 75.463 216 32 15 2888 3095 16252176 16252378 6.140000e-13 86.1


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 TraesCS7B01G283700 chr7B 517902314 517905764 3450 False 6373.000000 6373 100.000000 1 3451 1 chr7B.!!$F3 3450
1 TraesCS7B01G283700 chr7B 73167755 73171193 3438 False 1876.000000 3557 86.613500 1 3255 2 chr7B.!!$F4 3254
2 TraesCS7B01G283700 chr7B 504234250 504237357 3107 False 221.033333 309 87.659000 2703 3451 3 chr7B.!!$F5 748
3 TraesCS7B01G283700 chr2B 528807511 528809719 2208 True 3223.000000 3223 93.177000 1 2187 1 chr2B.!!$R1 2186
4 TraesCS7B01G283700 chr2B 419938343 419941784 3441 False 1869.500000 3506 86.935000 3 3264 2 chr2B.!!$F1 3261
5 TraesCS7B01G283700 chr3B 512390230 512392061 1831 False 2715.000000 2715 93.402000 1618 3451 1 chr3B.!!$F2 1833
6 TraesCS7B01G283700 chr3B 766341722 766345129 3407 False 1841.000000 3480 86.339500 1 3261 2 chr3B.!!$F3 3260
7 TraesCS7B01G283700 chr3B 473235676 473237052 1376 False 1291.000000 1291 83.747000 1 1395 1 chr3B.!!$F1 1394
8 TraesCS7B01G283700 chr6B 617031452 617033347 1895 False 2939.000000 2939 94.787000 308 2187 1 chr6B.!!$F2 1879
9 TraesCS7B01G283700 chr6B 676683443 676684665 1222 False 1890.000000 1890 94.771000 1 1208 1 chr6B.!!$F3 1207
10 TraesCS7B01G283700 chr6B 676703236 676704227 991 False 1511.000000 1511 94.254000 1202 2187 1 chr6B.!!$F4 985
11 TraesCS7B01G283700 chr1B 344040425 344042292 1867 False 2678.000000 2678 92.626000 322 2187 1 chr1B.!!$F1 1865
12 TraesCS7B01G283700 chr1B 579973084 579973930 846 False 437.500000 616 87.768500 2697 3448 2 chr1B.!!$F2 751
13 TraesCS7B01G283700 chr7D 83758751 83762115 3364 False 1262.333333 2429 91.128667 1 3264 3 chr7D.!!$F3 3263
14 TraesCS7B01G283700 chr4B 43586659 43587873 1214 True 1816.000000 1816 93.832000 1 1201 1 chr4B.!!$R2 1200
15 TraesCS7B01G283700 chr4B 43563384 43564379 995 True 1520.000000 1520 94.283000 1196 2187 1 chr4B.!!$R1 991
16 TraesCS7B01G283700 chr4B 43572793 43578259 5466 True 1297.000000 1810 94.639000 1 1682 2 chr4B.!!$R3 1681

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
318 4576 1.515521 GGTTGGGAAGGTTCTGCACG 61.516 60.0 0.00 0.0 0.00 5.34 F
1867 6154 0.188342 AAGGAGCCAAGGCCAAAGAA 59.812 50.0 5.01 0.0 43.17 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 6206 0.107897 TGTCACGTTGTTCAGCTGGT 60.108 50.0 15.13 0.0 0.00 4.00 R
3279 10688 0.313043 AGCACAGCTTCACATGCAAC 59.687 50.0 0.00 0.0 40.63 4.17 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
36 4289 3.641906 CTGAACCTATACCCGAGGATTGT 59.358 47.826 0.00 0.00 37.53 2.71
229 4487 4.442706 TGAAAGGAAGGTATCGATCAAGC 58.557 43.478 0.00 0.00 0.00 4.01
318 4576 1.515521 GGTTGGGAAGGTTCTGCACG 61.516 60.000 0.00 0.00 0.00 5.34
820 5093 5.667626 AGGGCATGTATAATAGACATAGGGG 59.332 44.000 0.00 0.00 35.75 4.79
825 5098 7.624549 CATGTATAATAGACATAGGGGTGCTT 58.375 38.462 0.00 0.00 35.75 3.91
918 5193 9.698309 TTGTTTCCTTTCAATTATATTTGCGAA 57.302 25.926 3.01 0.00 0.00 4.70
1019 5295 1.204146 ATGGACCGTGTGGATAGCTT 58.796 50.000 0.00 0.00 39.21 3.74
1027 5303 0.894835 TGTGGATAGCTTGAGCACGA 59.105 50.000 5.70 0.00 45.16 4.35
1231 5507 3.877559 TCTCCGCACATTGAATCAAGAT 58.122 40.909 1.10 0.00 0.00 2.40
1307 5583 3.562176 GGTTTCACATGGGATGGAAGTCT 60.562 47.826 0.00 0.00 33.60 3.24
1451 5727 9.624373 TTGGTTACCTGTTATTGTAGTGTTTTA 57.376 29.630 2.07 0.00 0.00 1.52
1631 5918 3.527665 AGGCTAAGGGATTGTATGGTGTT 59.472 43.478 0.00 0.00 0.00 3.32
1659 5946 6.418057 TTCCATACTTTGAACAATTGGCTT 57.582 33.333 10.83 0.00 0.00 4.35
1714 6001 1.983224 CGGAAGGCTTTGGAGAGGA 59.017 57.895 0.00 0.00 0.00 3.71
1867 6154 0.188342 AAGGAGCCAAGGCCAAAGAA 59.812 50.000 5.01 0.00 43.17 2.52
1918 6206 6.798482 CAGCCATGCTTCAAGATGTTAATAA 58.202 36.000 0.00 0.00 36.40 1.40
1954 6242 3.271142 CACAACATGTGGGTGCAAC 57.729 52.632 15.45 0.00 44.27 4.17
2061 6349 7.065803 GTGAATTGTCTAGGCTTGCATTTACTA 59.934 37.037 0.00 0.00 0.00 1.82
2094 6382 8.634444 AGATCGTTGAAGCTACAACTATATTCT 58.366 33.333 0.00 0.00 45.19 2.40
2329 6961 6.620678 ACATGATTGTATGCCTTGTTGTTAC 58.379 36.000 0.00 0.00 33.16 2.50
2408 7159 5.009631 CCATGTTCACCCTGAAAACATCTA 58.990 41.667 0.00 0.00 40.63 1.98
2657 7573 6.374053 TGAATCGGTTCATTTGAATAAGCTCA 59.626 34.615 7.11 0.00 39.36 4.26
2681 7597 9.414295 TCATCTAATGCAATGAACAAAAGAAAG 57.586 29.630 0.00 0.00 0.00 2.62
2848 8835 6.347644 GGCTTGGTCAAGTAATTTTGCAATTC 60.348 38.462 0.00 0.00 40.45 2.17
2854 8841 8.063630 GGTCAAGTAATTTTGCAATTCAACAAG 58.936 33.333 0.00 0.00 34.29 3.16
2982 8983 8.578151 AGTTTGAGTAGAAGAGAAGATAAACGT 58.422 33.333 0.00 0.00 31.65 3.99
3037 10352 1.209128 CAAGATTCCGAATCGTCCCG 58.791 55.000 14.16 0.00 42.75 5.14
3146 10471 8.621532 TGTATCCAGAGGTTAATATGCATTTC 57.378 34.615 3.54 0.00 0.00 2.17
3164 10489 8.429493 TGCATTTCAAAAATGTGTAATGTTGA 57.571 26.923 12.53 0.00 38.10 3.18
3265 10674 7.465353 TTGATGAATTTGAAGCTATGTTGGA 57.535 32.000 0.00 0.00 0.00 3.53
3279 10688 2.771089 TGTTGGAGAAGCACTAGCAAG 58.229 47.619 0.00 0.00 45.49 4.01
3343 10754 2.078849 TGTGCTCTGTACGTGGAATG 57.921 50.000 0.00 0.00 0.00 2.67
3347 10758 1.404181 GCTCTGTACGTGGAATGCTCA 60.404 52.381 0.00 0.00 0.00 4.26
3375 10786 5.572211 CGCTTGCTGATGTGTTTGTATTAT 58.428 37.500 0.00 0.00 0.00 1.28
3402 10813 4.799255 GCCAAGACAAACATTGTTAAGGGG 60.799 45.833 1.76 2.15 45.52 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 4289 8.014070 TGAAATACTTCCACTTATCATCGGTA 57.986 34.615 0.00 0.00 0.00 4.02
229 4487 8.908786 ACACATTTGTATCTATATCACCCAAG 57.091 34.615 0.00 0.00 32.60 3.61
318 4576 1.134491 CCCTAAGAACCCGACCATCAC 60.134 57.143 0.00 0.00 0.00 3.06
394 4652 1.442769 CGTTTGTGTAGCCAGCATCT 58.557 50.000 0.00 0.00 0.00 2.90
825 5098 1.488812 ACTTATACCTCAATGCGCCCA 59.511 47.619 4.18 0.00 0.00 5.36
916 5191 4.554973 GCAAACGAGATGCAATTGTAGTTC 59.445 41.667 7.40 3.91 43.29 3.01
918 5193 4.083581 GCAAACGAGATGCAATTGTAGT 57.916 40.909 7.40 0.00 43.29 2.73
1027 5303 1.048601 TTCTTGCCTCTTCCACGAGT 58.951 50.000 0.00 0.00 0.00 4.18
1231 5507 3.576078 TTTCTTCCTGAAGTGCCTCAA 57.424 42.857 6.78 0.00 39.38 3.02
1307 5583 5.111989 CCTTCTCGCACTGAATCATCTTTA 58.888 41.667 0.00 0.00 0.00 1.85
1631 5918 7.387397 GCCAATTGTTCAAAGTATGGAAATGAA 59.613 33.333 4.43 0.00 0.00 2.57
1867 6154 4.379243 CGCTTGGTCCTGTCGCCT 62.379 66.667 0.00 0.00 0.00 5.52
1918 6206 0.107897 TGTCACGTTGTTCAGCTGGT 60.108 50.000 15.13 0.00 0.00 4.00
1954 6242 4.782156 TGCTGTTGTAAATGATGTTGTCG 58.218 39.130 0.00 0.00 0.00 4.35
1990 6278 2.703536 TGTTGAGGGTCTTCTTGTGCTA 59.296 45.455 0.00 0.00 0.00 3.49
2061 6349 0.179124 GCTTCAACGATCTCGCTCCT 60.179 55.000 0.00 0.00 44.43 3.69
2165 6453 7.068962 TGTGTAAAAGAGATACCGGACATCATA 59.931 37.037 9.46 0.00 0.00 2.15
2238 6528 7.752695 AGCAATGACAATTTACAGTAGCTAAC 58.247 34.615 0.00 0.00 0.00 2.34
2269 6570 1.283613 ACGCATTCCTGGGTTCCATTA 59.716 47.619 0.00 0.00 45.41 1.90
2408 7159 5.448654 TCTGCCAATCAGTAGCCAATAATT 58.551 37.500 0.00 0.00 43.32 1.40
2539 7455 4.558226 TCTCTACCATGCATTCAACACT 57.442 40.909 0.00 0.00 0.00 3.55
2886 8880 5.751243 ATAAAGAAACACAAGCGACAACT 57.249 34.783 0.00 0.00 0.00 3.16
2980 8981 1.325640 CGATCTTCATCTGCCACAACG 59.674 52.381 0.00 0.00 0.00 4.10
2982 8983 3.200483 CATCGATCTTCATCTGCCACAA 58.800 45.455 0.00 0.00 0.00 3.33
3037 10352 9.525409 TTTATACGACAAATAGAAAGGTAGCTC 57.475 33.333 0.00 0.00 0.00 4.09
3096 10421 6.197364 ACTCGGAATTCTACTACACTTCAG 57.803 41.667 5.23 0.00 0.00 3.02
3164 10489 4.806640 CCAGAATTTGGCACCACTTTAT 57.193 40.909 0.00 0.00 40.87 1.40
3265 10674 2.260844 TGCAACTTGCTAGTGCTTCT 57.739 45.000 14.78 0.00 45.31 2.85
3279 10688 0.313043 AGCACAGCTTCACATGCAAC 59.687 50.000 0.00 0.00 40.63 4.17
3375 10786 3.883830 ACAATGTTTGTCTTGGCACAA 57.116 38.095 0.00 0.00 42.24 3.33
3402 10813 4.253685 TCAGCTATGTAAAGGCAACAGAC 58.746 43.478 0.00 0.00 41.41 3.51


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

AutoCloner maintained by Alex Coulton.