Multiple sequence alignment - TraesCS7B01G153000

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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 TraesCS7B01G153000 chr7B 100.000 3380 0 0 1 3380 203281922 203285301 0.000000e+00 6242
1 TraesCS7B01G153000 chr7B 78.763 372 57 13 491 852 202506025 202505666 2.620000e-56 230
2 TraesCS7B01G153000 chr7D 94.697 3394 123 22 1 3380 232498050 232501400 0.000000e+00 5217
3 TraesCS7B01G153000 chr7D 79.016 386 66 11 491 867 230993156 230992777 2.010000e-62 250
4 TraesCS7B01G153000 chr7A 97.203 2395 61 3 986 3380 244672582 244674970 0.000000e+00 4047
5 TraesCS7B01G153000 chr7A 91.462 937 76 3 1 936 244671648 244672581 0.000000e+00 1284
6 TraesCS7B01G153000 chr7A 82.353 476 63 8 2833 3302 244673951 244674411 8.790000e-106 394
7 TraesCS7B01G153000 chr7A 80.260 385 60 12 491 867 243852607 243852231 3.320000e-70 276


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 TraesCS7B01G153000 chr7B 203281922 203285301 3379 False 6242.000000 6242 100.000000 1 3380 1 chr7B.!!$F1 3379
1 TraesCS7B01G153000 chr7D 232498050 232501400 3350 False 5217.000000 5217 94.697000 1 3380 1 chr7D.!!$F1 3379
2 TraesCS7B01G153000 chr7A 244671648 244674970 3322 False 1908.333333 4047 90.339333 1 3380 3 chr7A.!!$F1 3379

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
520 536 0.249911 AAAGTCTTGCGCGAGAGGTT 60.250 50.0 27.72 19.97 0.0 3.5 F
637 653 0.871722 TTGATCTGTCGGGCAAAACG 59.128 50.0 0.00 0.00 0.0 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 2347 1.153989 CTCCATCCTCCGGGCTAGA 59.846 63.158 0.0 0.0 0.00 2.43 R
2430 2446 6.128145 GCTCTACCTGGAAATTCAGAAACTTC 60.128 42.308 0.0 0.0 36.93 3.01 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
53 54 8.547069 GCTAAGTGTCTGCTATAATCTTTCAAG 58.453 37.037 0.00 0.00 0.00 3.02
74 75 6.814644 TCAAGCCAATGTTCATTGATGATTTC 59.185 34.615 22.17 6.55 36.56 2.17
80 81 9.589111 CCAATGTTCATTGATGATTTCATGTAA 57.411 29.630 22.17 0.00 36.57 2.41
87 88 9.844790 TCATTGATGATTTCATGTAAAAGTGTC 57.155 29.630 0.00 0.00 36.57 3.67
93 94 9.985730 ATGATTTCATGTAAAAGTGTCACAAAT 57.014 25.926 5.62 0.00 34.83 2.32
146 147 8.936864 AGTTATCTACTTTGTGCTTGTTCATAC 58.063 33.333 0.00 0.00 31.29 2.39
153 154 5.699097 TTGTGCTTGTTCATACCCTAAAC 57.301 39.130 0.00 0.00 0.00 2.01
190 191 9.698309 TTCAGAAAACACAACAAATTTCTACAA 57.302 25.926 0.00 0.00 39.43 2.41
197 198 8.770438 ACACAACAAATTTCTACAACAACATT 57.230 26.923 0.00 0.00 0.00 2.71
198 199 9.862371 ACACAACAAATTTCTACAACAACATTA 57.138 25.926 0.00 0.00 0.00 1.90
208 209 9.727859 TTTCTACAACAACATTAGCTAATACCA 57.272 29.630 18.45 0.00 0.00 3.25
238 239 4.700692 ACTCTAGTGCTGAATCAACGACTA 59.299 41.667 0.00 0.00 0.00 2.59
246 247 4.211374 GCTGAATCAACGACTACAACACTT 59.789 41.667 0.00 0.00 0.00 3.16
317 319 2.984471 GCGACTACGAATCACAAGTGAA 59.016 45.455 7.02 0.00 41.65 3.18
318 320 3.612860 GCGACTACGAATCACAAGTGAAT 59.387 43.478 7.02 0.00 41.65 2.57
349 351 2.397413 AAACGCCACAGACCTCCAGG 62.397 60.000 0.00 0.00 42.17 4.45
418 434 3.882288 TGCAAGTTGAAACTACAGCATGA 59.118 39.130 7.16 0.00 36.71 3.07
423 439 7.293745 CAAGTTGAAACTACAGCATGAGTAAG 58.706 38.462 0.00 0.00 36.71 2.34
512 528 2.245096 CACTGCATAAAAGTCTTGCGC 58.755 47.619 0.00 0.00 39.23 6.09
513 529 1.135972 ACTGCATAAAAGTCTTGCGCG 60.136 47.619 0.00 0.00 39.23 6.86
520 536 0.249911 AAAGTCTTGCGCGAGAGGTT 60.250 50.000 27.72 19.97 0.00 3.50
637 653 0.871722 TTGATCTGTCGGGCAAAACG 59.128 50.000 0.00 0.00 0.00 3.60
648 664 0.951558 GGCAAAACGAGCAGAAGGAA 59.048 50.000 0.00 0.00 0.00 3.36
653 669 1.726853 AACGAGCAGAAGGAATTCGG 58.273 50.000 0.00 0.00 35.72 4.30
660 676 3.390639 AGCAGAAGGAATTCGGATCAGAT 59.609 43.478 0.00 0.00 0.00 2.90
668 684 1.032794 TTCGGATCAGATGACGAGGG 58.967 55.000 0.00 0.00 36.65 4.30
679 695 3.517901 AGATGACGAGGGTAAAATCACCA 59.482 43.478 0.00 0.00 40.65 4.17
688 704 4.140782 AGGGTAAAATCACCAGGGAAAACT 60.141 41.667 0.00 0.00 40.65 2.66
759 775 2.418334 CCCTAACCCTAACACGAAGAGC 60.418 54.545 0.00 0.00 0.00 4.09
906 922 3.628487 GCCCGGTACATTGCAATAACTTA 59.372 43.478 12.53 0.00 0.00 2.24
938 954 1.286248 ATGGGCCTCCGTTTCTAAGT 58.714 50.000 4.53 0.00 35.24 2.24
960 976 2.656069 GCTCCACCGTTAGCTCCCA 61.656 63.158 0.00 0.00 35.80 4.37
1524 1540 0.918983 TCTTCAATCGCCTTCCCCAT 59.081 50.000 0.00 0.00 0.00 4.00
1566 1582 0.896226 AGGTCTACAACGCCCTTCTC 59.104 55.000 0.00 0.00 0.00 2.87
1569 1585 1.134560 GTCTACAACGCCCTTCTCGAT 59.865 52.381 0.00 0.00 0.00 3.59
2331 2347 2.026641 CGGCATCTTGGGAAACATGAT 58.973 47.619 0.00 0.00 42.73 2.45
2430 2446 1.798725 CGCTGCGAATTGCTTGGTG 60.799 57.895 18.66 0.00 46.63 4.17
2453 2469 6.710744 GTGAAGTTTCTGAATTTCCAGGTAGA 59.289 38.462 10.68 0.00 32.31 2.59
2522 2538 3.261643 TGCTGTTGGACTGTGACTGATAT 59.738 43.478 0.00 0.00 0.00 1.63
2523 2539 4.466015 TGCTGTTGGACTGTGACTGATATA 59.534 41.667 0.00 0.00 0.00 0.86
2530 2546 5.363580 TGGACTGTGACTGATATATGCTTGA 59.636 40.000 0.00 0.00 0.00 3.02
2533 2549 6.279123 ACTGTGACTGATATATGCTTGACAG 58.721 40.000 0.00 0.00 34.58 3.51
2556 2572 7.446013 ACAGGTGATTTATTTGTTTTCGGTAGA 59.554 33.333 0.00 0.00 0.00 2.59
2586 2602 7.083062 TCAATGAATAAGGCCATCAGATAGT 57.917 36.000 5.01 0.00 0.00 2.12
2640 2656 3.883489 AGGTTCACAAGAAAAGTAGTGGC 59.117 43.478 0.00 0.00 35.08 5.01
2689 2705 6.067263 TGTAAGTTTTGTGGTTGCATAGAC 57.933 37.500 0.00 0.00 0.00 2.59
2761 2777 7.490962 TCACTGTTCAATTTAGTACCAACTG 57.509 36.000 0.00 0.00 36.36 3.16
2805 2821 3.659183 AAAGATTGGAGCCATGCTACT 57.341 42.857 0.00 0.00 40.76 2.57
2809 2825 2.584835 TTGGAGCCATGCTACTTTGT 57.415 45.000 0.00 0.00 40.76 2.83
2810 2826 3.712016 TTGGAGCCATGCTACTTTGTA 57.288 42.857 0.00 0.00 40.76 2.41
2811 2827 2.985896 TGGAGCCATGCTACTTTGTAC 58.014 47.619 0.00 0.00 40.76 2.90
2986 3002 3.495331 ACCAATGTTATGCTGTTGGACA 58.505 40.909 9.73 0.00 42.88 4.02
3025 3041 7.042119 GGTCAAGTGATTTATTTGTTTTGGGTG 60.042 37.037 0.00 0.00 0.00 4.61
3109 3135 8.474710 AGTGAAGGTTAACAAGAAGAGTAGTA 57.525 34.615 8.10 0.00 0.00 1.82
3187 3213 0.893270 TTGAAACATCCACTGCCCCG 60.893 55.000 0.00 0.00 0.00 5.73
3256 3282 2.238144 ACCAACTCTGTGATCCATGAGG 59.762 50.000 0.00 0.00 0.00 3.86
3305 3331 5.220662 CCATGCTACCTTGTACGATTTGAAG 60.221 44.000 0.00 0.00 0.00 3.02
3338 3364 6.207509 AGAGATAGGGCTGACTACTGATAA 57.792 41.667 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.606401 GCAGACACTTAGCTGGGCAA 60.606 55.000 0.00 0.00 32.83 4.52
53 54 6.537301 ACATGAAATCATCAATGAACATTGGC 59.463 34.615 21.93 8.27 46.08 4.52
74 75 9.689976 TGGAATTATTTGTGACACTTTTACATG 57.310 29.630 7.20 0.00 0.00 3.21
98 99 8.964420 AACTGAACGATACATGTTTAAATTGG 57.036 30.769 2.30 0.00 0.00 3.16
112 113 7.544622 AGCACAAAGTAGATAACTGAACGATA 58.455 34.615 0.00 0.00 38.88 2.92
146 147 2.156917 GAAGGTGGAAACCGTTTAGGG 58.843 52.381 0.00 0.00 46.96 3.53
153 154 2.685897 TGTTTTCTGAAGGTGGAAACCG 59.314 45.455 0.00 0.00 32.20 4.44
218 219 4.733850 TGTAGTCGTTGATTCAGCACTAG 58.266 43.478 10.65 0.00 0.00 2.57
220 221 3.660501 TGTAGTCGTTGATTCAGCACT 57.339 42.857 1.35 6.20 0.00 4.40
238 239 5.650266 TGTTACTGTGAAATGGAAGTGTTGT 59.350 36.000 0.00 0.00 0.00 3.32
246 247 5.435686 AGGCTATGTTACTGTGAAATGGA 57.564 39.130 0.00 0.00 0.00 3.41
317 319 7.440255 GGTCTGTGGCGTTTTGTAGTATTATAT 59.560 37.037 0.00 0.00 0.00 0.86
318 320 6.757947 GGTCTGTGGCGTTTTGTAGTATTATA 59.242 38.462 0.00 0.00 0.00 0.98
352 354 8.880244 TGGCCTGATGTAGTATCTTAATTGTAT 58.120 33.333 3.32 0.00 0.00 2.29
353 355 8.257602 TGGCCTGATGTAGTATCTTAATTGTA 57.742 34.615 3.32 0.00 0.00 2.41
354 356 7.136822 TGGCCTGATGTAGTATCTTAATTGT 57.863 36.000 3.32 0.00 0.00 2.71
355 357 7.879677 TCATGGCCTGATGTAGTATCTTAATTG 59.120 37.037 3.32 0.00 0.00 2.32
356 358 7.977818 TCATGGCCTGATGTAGTATCTTAATT 58.022 34.615 3.32 0.00 0.00 1.40
357 359 7.559335 TCATGGCCTGATGTAGTATCTTAAT 57.441 36.000 3.32 0.00 0.00 1.40
358 360 6.994421 TCATGGCCTGATGTAGTATCTTAA 57.006 37.500 3.32 0.00 0.00 1.85
359 361 6.239600 GGTTCATGGCCTGATGTAGTATCTTA 60.240 42.308 3.32 0.00 32.72 2.10
360 362 5.455326 GGTTCATGGCCTGATGTAGTATCTT 60.455 44.000 3.32 0.00 32.72 2.40
361 363 4.040952 GGTTCATGGCCTGATGTAGTATCT 59.959 45.833 3.32 0.00 32.72 1.98
362 364 4.319177 GGTTCATGGCCTGATGTAGTATC 58.681 47.826 3.32 0.00 32.72 2.24
371 387 4.776322 CCGCGGTTCATGGCCTGA 62.776 66.667 19.50 2.06 0.00 3.86
398 414 5.679734 ACTCATGCTGTAGTTTCAACTTG 57.320 39.130 0.00 0.00 40.37 3.16
418 434 4.519730 CGGTTCTAGATCCCGATTCTTACT 59.480 45.833 21.01 0.00 44.41 2.24
423 439 1.272769 CCCGGTTCTAGATCCCGATTC 59.727 57.143 25.14 0.00 44.41 2.52
501 517 0.249911 AACCTCTCGCGCAAGACTTT 60.250 50.000 8.75 0.00 43.02 2.66
520 536 3.433598 GCTACATTGGCCTCAAGGTATCA 60.434 47.826 3.32 0.00 45.27 2.15
618 634 0.871722 CGTTTTGCCCGACAGATCAA 59.128 50.000 0.00 0.00 0.00 2.57
637 653 3.129871 CTGATCCGAATTCCTTCTGCTC 58.870 50.000 0.00 0.00 0.00 4.26
648 664 1.615883 CCCTCGTCATCTGATCCGAAT 59.384 52.381 9.40 0.00 0.00 3.34
653 669 5.463724 GTGATTTTACCCTCGTCATCTGATC 59.536 44.000 0.00 0.00 0.00 2.92
660 676 2.027561 CCTGGTGATTTTACCCTCGTCA 60.028 50.000 0.00 0.00 40.09 4.35
668 684 6.008331 ACCTAGTTTTCCCTGGTGATTTTAC 58.992 40.000 0.00 0.00 0.00 2.01
679 695 0.992695 GCTCCCACCTAGTTTTCCCT 59.007 55.000 0.00 0.00 0.00 4.20
688 704 2.052690 GCAGACGAGCTCCCACCTA 61.053 63.158 8.47 0.00 0.00 3.08
759 775 2.202810 GCCGCTCTTCTTCCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
789 805 2.892334 GACTGCGTCGCCTTGCAAA 61.892 57.895 15.88 0.00 41.22 3.68
906 922 4.850193 CCCATTCTGCAACTGGGT 57.150 55.556 16.33 0.00 43.93 4.51
938 954 2.978824 GCTAACGGTGGAGCTGGA 59.021 61.111 0.00 0.00 35.73 3.86
1806 1822 3.595819 GCGAATGCCTTGGCTTCT 58.404 55.556 13.18 0.00 33.71 2.85
2172 2188 1.439353 GCATCACATACACAGGCCGG 61.439 60.000 0.00 0.00 0.00 6.13
2331 2347 1.153989 CTCCATCCTCCGGGCTAGA 59.846 63.158 0.00 0.00 0.00 2.43
2430 2446 6.128145 GCTCTACCTGGAAATTCAGAAACTTC 60.128 42.308 0.00 0.00 36.93 3.01
2522 2538 7.701539 ACAAATAAATCACCTGTCAAGCATA 57.298 32.000 0.00 0.00 0.00 3.14
2523 2539 6.594788 ACAAATAAATCACCTGTCAAGCAT 57.405 33.333 0.00 0.00 0.00 3.79
2530 2546 6.399639 ACCGAAAACAAATAAATCACCTGT 57.600 33.333 0.00 0.00 0.00 4.00
2533 2549 9.124807 CTTTCTACCGAAAACAAATAAATCACC 57.875 33.333 0.00 0.00 38.58 4.02
2556 2572 7.562454 TCTGATGGCCTTATTCATTGATTCTTT 59.438 33.333 3.32 0.00 0.00 2.52
2586 2602 7.140705 CACAATTTTGAGCACATTAGTTGAGA 58.859 34.615 0.00 0.00 0.00 3.27
2640 2656 2.753452 TCTGAACTTAGTGCCTACTCCG 59.247 50.000 0.00 0.00 38.36 4.63
2689 2705 9.081204 TGGACCATGGATATTTCAATAATCTTG 57.919 33.333 21.47 0.00 0.00 3.02
2753 2769 1.696884 TCATGGAGCACACAGTTGGTA 59.303 47.619 0.00 0.00 0.00 3.25
2761 2777 8.607441 TTATACTGAATTATCATGGAGCACAC 57.393 34.615 0.00 0.00 34.37 3.82
2931 2947 7.551974 ACAGAATACAATCAGAAGACAGGAATG 59.448 37.037 0.00 0.00 0.00 2.67
2986 3002 3.264193 TCACTTGACCAGCATATCCAACT 59.736 43.478 0.00 0.00 0.00 3.16
3025 3041 6.179906 TGATCTTATTCACTGATCCTTCCC 57.820 41.667 0.00 0.00 36.65 3.97
3109 3135 4.528596 ACTCAACTTACTGCATACTCCACT 59.471 41.667 0.00 0.00 0.00 4.00
3174 3200 4.838152 CCGACGGGGCAGTGGATG 62.838 72.222 5.81 0.00 0.00 3.51
3256 3282 8.510505 GGCTCCAATCTTTATTCTACATGAATC 58.489 37.037 0.00 0.00 43.69 2.52
3305 3331 1.599916 GCCCTATCTCTACAACGCGAC 60.600 57.143 15.93 0.00 0.00 5.19
3338 3364 2.036346 GCCTTGAGGTTTCAGCAAACAT 59.964 45.455 0.00 0.00 43.41 2.71


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

AutoCloner maintained by Alex Coulton.