Multiple sequence alignment - TraesCS6D01G233500

Loading Multiple Alignment...

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 TraesCS6D01G233500 chr6D 100.000 2699 0 0 1 2699 327373914 327371216 0.000000e+00 4985
1 TraesCS6D01G233500 chr6B 89.588 1940 91 37 1 1864 493983224 493985128 0.000000e+00 2361
2 TraesCS6D01G233500 chr6B 93.294 850 41 11 1858 2699 493985474 493986315 0.000000e+00 1240
3 TraesCS6D01G233500 chr6A 93.228 1137 43 14 798 1905 466484211 466483080 0.000000e+00 1642
4 TraesCS6D01G233500 chr6A 86.550 803 60 25 1 770 466484993 466484206 0.000000e+00 841
5 TraesCS6D01G233500 chr6A 89.773 528 30 15 1861 2371 466483083 466482563 0.000000e+00 654
6 TraesCS6D01G233500 chr6A 90.286 175 14 3 2371 2545 466482505 466482334 2.700000e-55 226
7 TraesCS6D01G233500 chr6A 93.836 146 4 1 2554 2699 466482353 466482213 5.850000e-52 215


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 TraesCS6D01G233500 chr6D 327371216 327373914 2698 True 4985.0 4985 100.0000 1 2699 1 chr6D.!!$R1 2698
1 TraesCS6D01G233500 chr6B 493983224 493986315 3091 False 1800.5 2361 91.4410 1 2699 2 chr6B.!!$F1 2698
2 TraesCS6D01G233500 chr6A 466482213 466484993 2780 True 715.6 1642 90.7346 1 2699 5 chr6A.!!$R1 2698

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
352 371 0.037326 CTGCTAACTCGCACCTCCAA 60.037 55.0 0.0 0.0 35.74 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2410 1.069765 CACAGTCCAGCCACGAACT 59.93 57.895 0.0 0.0 0.0 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
19 20 0.885150 TTCAATTGCGGCCACGTACA 60.885 50.000 2.24 0.00 43.45 2.90
95 99 5.515626 GCTAACTAACTGACGGTTATGAGTG 59.484 44.000 7.33 0.00 39.36 3.51
114 118 4.010349 AGTGGTAGTTAGCTTGAAATGCC 58.990 43.478 0.00 0.00 37.80 4.40
116 120 5.045869 AGTGGTAGTTAGCTTGAAATGCCTA 60.046 40.000 5.58 0.00 37.80 3.93
119 123 6.126768 TGGTAGTTAGCTTGAAATGCCTAGAT 60.127 38.462 5.58 0.00 37.80 1.98
143 147 8.994429 ATGATGTTATATTCAGATCGAGTTCC 57.006 34.615 0.00 0.00 0.00 3.62
162 175 8.706936 CGAGTTCCAGAAAATCATATGTATCAG 58.293 37.037 1.90 0.00 31.40 2.90
310 329 2.183046 GAGTCGAGCCTCCTGCAC 59.817 66.667 0.00 0.00 44.83 4.57
326 345 1.479730 TGCACTTCAAAACCATGCACA 59.520 42.857 0.00 0.00 41.18 4.57
328 347 2.223782 GCACTTCAAAACCATGCACAGA 60.224 45.455 0.00 0.00 36.30 3.41
330 349 3.985279 CACTTCAAAACCATGCACAGATG 59.015 43.478 0.00 0.00 0.00 2.90
352 371 0.037326 CTGCTAACTCGCACCTCCAA 60.037 55.000 0.00 0.00 35.74 3.53
361 380 1.070786 GCACCTCCAAACTCCGTGA 59.929 57.895 0.00 0.00 0.00 4.35
392 415 4.893524 TCATACATCCCTACACTACACAGG 59.106 45.833 0.00 0.00 0.00 4.00
393 416 3.185880 ACATCCCTACACTACACAGGT 57.814 47.619 0.00 0.00 0.00 4.00
394 417 4.326600 ACATCCCTACACTACACAGGTA 57.673 45.455 0.00 0.00 0.00 3.08
395 418 4.021916 ACATCCCTACACTACACAGGTAC 58.978 47.826 0.00 0.00 0.00 3.34
396 419 4.264262 ACATCCCTACACTACACAGGTACT 60.264 45.833 0.00 0.00 43.88 2.73
397 420 3.960571 TCCCTACACTACACAGGTACTC 58.039 50.000 0.00 0.00 34.60 2.59
398 421 3.022406 CCCTACACTACACAGGTACTCC 58.978 54.545 0.00 0.00 34.60 3.85
399 422 3.308976 CCCTACACTACACAGGTACTCCT 60.309 52.174 0.00 0.00 46.37 3.69
400 423 4.080129 CCCTACACTACACAGGTACTCCTA 60.080 50.000 0.00 0.00 43.07 2.94
401 424 4.880696 CCTACACTACACAGGTACTCCTAC 59.119 50.000 0.00 0.00 43.07 3.18
402 425 4.377762 ACACTACACAGGTACTCCTACA 57.622 45.455 0.00 0.00 43.07 2.74
404 427 4.705507 ACACTACACAGGTACTCCTACATG 59.294 45.833 0.00 0.00 43.07 3.21
406 429 2.536066 ACACAGGTACTCCTACATGCA 58.464 47.619 0.00 0.00 43.07 3.96
407 430 2.233922 ACACAGGTACTCCTACATGCAC 59.766 50.000 0.00 0.00 43.07 4.57
412 453 2.686915 GGTACTCCTACATGCACGTACT 59.313 50.000 0.00 0.00 0.00 2.73
419 460 2.363788 ACATGCACGTACTACCACAG 57.636 50.000 0.00 0.00 0.00 3.66
426 467 2.097825 ACGTACTACCACAGGATCACC 58.902 52.381 0.00 0.00 0.00 4.02
441 482 2.882927 TCACCATCGAACTTATCCGG 57.117 50.000 0.00 0.00 0.00 5.14
442 483 2.380941 TCACCATCGAACTTATCCGGA 58.619 47.619 6.61 6.61 0.00 5.14
443 484 2.963101 TCACCATCGAACTTATCCGGAT 59.037 45.455 22.95 22.95 0.00 4.18
444 485 4.146564 TCACCATCGAACTTATCCGGATA 58.853 43.478 20.49 20.49 0.00 2.59
445 486 4.217767 TCACCATCGAACTTATCCGGATAG 59.782 45.833 22.88 18.54 0.00 2.08
446 487 3.510360 ACCATCGAACTTATCCGGATAGG 59.490 47.826 27.14 27.14 42.97 2.57
447 488 3.512680 CATCGAACTTATCCGGATAGGC 58.487 50.000 28.30 15.11 40.77 3.93
475 517 0.543749 GAGGGAACATGGGAGGTCAG 59.456 60.000 0.00 0.00 0.00 3.51
496 538 2.694920 TTGTGGCCAAGGGTGTCCA 61.695 57.895 7.24 0.00 34.83 4.02
552 594 4.509737 GTAGGCTCCACGGGTCGC 62.510 72.222 0.00 0.00 0.00 5.19
573 615 2.124695 GTTGGGGTCTCCATCGCC 60.125 66.667 0.00 0.00 46.52 5.54
664 706 2.265367 TGTGAGGCACCCATTTCTCTA 58.735 47.619 0.00 0.00 32.73 2.43
781 823 5.297527 CAGCAGCATTGATCCATGTTAGTAA 59.702 40.000 8.45 0.00 0.00 2.24
782 824 5.530171 AGCAGCATTGATCCATGTTAGTAAG 59.470 40.000 8.45 0.00 0.00 2.34
783 825 5.297776 GCAGCATTGATCCATGTTAGTAAGT 59.702 40.000 8.45 0.00 0.00 2.24
784 826 6.483307 GCAGCATTGATCCATGTTAGTAAGTA 59.517 38.462 8.45 0.00 0.00 2.24
785 827 7.519008 GCAGCATTGATCCATGTTAGTAAGTAC 60.519 40.741 8.45 0.00 0.00 2.73
786 828 6.992715 AGCATTGATCCATGTTAGTAAGTACC 59.007 38.462 8.45 0.00 0.00 3.34
819 861 9.866798 ATTAATTGATTTTCAGAGAAGAAAGGC 57.133 29.630 0.00 0.00 38.60 4.35
833 880 0.550914 AAAGGCTTGGGACAGACACA 59.449 50.000 0.00 0.00 42.39 3.72
1042 1102 2.747396 TGCCATTGCTTTAGCCTTTG 57.253 45.000 0.00 0.00 41.18 2.77
1075 1135 1.249469 AAGGAACGTCGGAGGAGGAC 61.249 60.000 4.48 0.00 0.00 3.85
1348 1422 1.738099 GATCGTGGTCAGCAAGCGT 60.738 57.895 0.00 0.00 0.00 5.07
1725 1811 5.766222 CTCTTGATTTGTTCCTGTTCCTTG 58.234 41.667 0.00 0.00 0.00 3.61
1779 1880 1.078918 TCCTCCATCAGCTTGTGCG 60.079 57.895 0.00 0.00 45.42 5.34
1985 2440 1.160137 GGACTGTGCTACTTTGGCTG 58.840 55.000 0.00 0.00 0.00 4.85
1986 2441 0.519077 GACTGTGCTACTTTGGCTGC 59.481 55.000 0.00 0.00 0.00 5.25
1987 2442 0.890996 ACTGTGCTACTTTGGCTGCC 60.891 55.000 12.87 12.87 0.00 4.85
1988 2443 0.607489 CTGTGCTACTTTGGCTGCCT 60.607 55.000 21.03 1.26 0.00 4.75
1989 2444 0.178992 TGTGCTACTTTGGCTGCCTT 60.179 50.000 21.03 4.14 0.00 4.35
1990 2445 0.961753 GTGCTACTTTGGCTGCCTTT 59.038 50.000 21.03 3.77 0.00 3.11
1991 2446 1.341209 GTGCTACTTTGGCTGCCTTTT 59.659 47.619 21.03 4.13 0.00 2.27
1992 2447 2.038659 TGCTACTTTGGCTGCCTTTTT 58.961 42.857 21.03 4.51 0.00 1.94
1993 2448 3.005367 GTGCTACTTTGGCTGCCTTTTTA 59.995 43.478 21.03 5.46 0.00 1.52
2018 2473 5.232202 GCCTTTTTAGCTGTTGTGTTCTTTC 59.768 40.000 0.00 0.00 0.00 2.62
2111 2578 1.527611 CCATCGCACATGGCCAGAT 60.528 57.895 13.05 4.91 40.31 2.90
2112 2579 1.652563 CATCGCACATGGCCAGATG 59.347 57.895 13.05 14.42 40.31 2.90
2316 2791 3.228453 CCCAGAGCAAAATGGAGCATAT 58.772 45.455 0.00 0.00 39.02 1.78
2330 2805 3.129988 GGAGCATATTTTGTCAAGCAGCT 59.870 43.478 0.00 0.00 0.00 4.24
2357 2832 6.599638 AGTGTAAATCCATACTTTCTTGCTCC 59.400 38.462 0.00 0.00 0.00 4.70
2416 2949 0.733150 TGCTACCGATCGTGACTGAG 59.267 55.000 15.09 0.00 0.00 3.35
2436 2969 2.106857 AGACCATTGGAACGGGTGTTAA 59.893 45.455 10.37 0.00 38.78 2.01
2450 2983 5.182570 ACGGGTGTTAAGGCTTTAATCTTTC 59.817 40.000 4.45 0.00 31.81 2.62
2455 2988 8.789762 GGTGTTAAGGCTTTAATCTTTCTTGTA 58.210 33.333 4.45 0.00 31.81 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 99 5.671493 TCTAGGCATTTCAAGCTAACTACC 58.329 41.667 0.00 0.00 0.00 3.18
116 120 9.853555 GAACTCGATCTGAATATAACATCATCT 57.146 33.333 0.00 0.00 0.00 2.90
119 123 7.951591 TGGAACTCGATCTGAATATAACATCA 58.048 34.615 0.00 0.00 0.00 3.07
143 147 7.649370 AGACGCTGATACATATGATTTTCTG 57.351 36.000 10.38 5.78 0.00 3.02
271 284 1.284657 CAATGCTCGATCGCAGTCTT 58.715 50.000 11.09 4.53 44.10 3.01
326 345 0.247460 TGCGAGTTAGCAGTGCATCT 59.753 50.000 19.20 11.90 42.92 2.90
334 353 0.394938 TTTGGAGGTGCGAGTTAGCA 59.605 50.000 0.00 0.00 45.96 3.49
337 356 1.001633 GGAGTTTGGAGGTGCGAGTTA 59.998 52.381 0.00 0.00 0.00 2.24
339 358 1.371558 GGAGTTTGGAGGTGCGAGT 59.628 57.895 0.00 0.00 0.00 4.18
340 359 1.738099 CGGAGTTTGGAGGTGCGAG 60.738 63.158 0.00 0.00 0.00 5.03
341 360 2.342279 CGGAGTTTGGAGGTGCGA 59.658 61.111 0.00 0.00 0.00 5.10
342 361 2.030562 ACGGAGTTTGGAGGTGCG 59.969 61.111 0.00 0.00 37.78 5.34
352 371 3.667497 ATGATCGCATATCACGGAGTT 57.333 42.857 1.06 0.00 32.03 3.01
361 380 5.658634 AGTGTAGGGATGTATGATCGCATAT 59.341 40.000 0.00 0.00 39.09 1.78
392 415 4.260948 GGTAGTACGTGCATGTAGGAGTAC 60.261 50.000 19.05 15.77 35.88 2.73
393 416 3.879295 GGTAGTACGTGCATGTAGGAGTA 59.121 47.826 19.05 4.99 0.00 2.59
394 417 2.686915 GGTAGTACGTGCATGTAGGAGT 59.313 50.000 19.05 5.98 0.00 3.85
395 418 2.686405 TGGTAGTACGTGCATGTAGGAG 59.314 50.000 19.05 0.00 0.00 3.69
396 419 2.424601 GTGGTAGTACGTGCATGTAGGA 59.575 50.000 19.05 7.34 0.00 2.94
397 420 2.164827 TGTGGTAGTACGTGCATGTAGG 59.835 50.000 19.05 1.70 0.00 3.18
398 421 3.435566 CTGTGGTAGTACGTGCATGTAG 58.564 50.000 19.05 2.97 0.00 2.74
399 422 2.164827 CCTGTGGTAGTACGTGCATGTA 59.835 50.000 14.85 14.85 0.00 2.29
400 423 1.067142 CCTGTGGTAGTACGTGCATGT 60.067 52.381 17.19 17.19 0.00 3.21
401 424 1.203758 TCCTGTGGTAGTACGTGCATG 59.796 52.381 6.38 3.82 0.00 4.06
402 425 1.552578 TCCTGTGGTAGTACGTGCAT 58.447 50.000 6.38 0.00 0.00 3.96
404 427 1.475280 TGATCCTGTGGTAGTACGTGC 59.525 52.381 0.00 0.00 0.00 5.34
406 429 2.097825 GGTGATCCTGTGGTAGTACGT 58.902 52.381 0.00 0.00 0.00 3.57
407 430 2.097036 TGGTGATCCTGTGGTAGTACG 58.903 52.381 0.00 0.00 34.23 3.67
412 453 2.153034 TCGATGGTGATCCTGTGGTA 57.847 50.000 0.00 0.00 34.23 3.25
419 460 3.318017 CGGATAAGTTCGATGGTGATCC 58.682 50.000 0.00 0.00 0.00 3.36
426 467 3.512680 GCCTATCCGGATAAGTTCGATG 58.487 50.000 24.06 10.34 33.16 3.84
441 482 2.171840 TCCCTCTTGCTATCGCCTATC 58.828 52.381 0.00 0.00 34.43 2.08
442 483 2.300437 GTTCCCTCTTGCTATCGCCTAT 59.700 50.000 0.00 0.00 34.43 2.57
443 484 1.687123 GTTCCCTCTTGCTATCGCCTA 59.313 52.381 0.00 0.00 34.43 3.93
444 485 0.466124 GTTCCCTCTTGCTATCGCCT 59.534 55.000 0.00 0.00 34.43 5.52
445 486 0.178068 TGTTCCCTCTTGCTATCGCC 59.822 55.000 0.00 0.00 34.43 5.54
446 487 1.869767 CATGTTCCCTCTTGCTATCGC 59.130 52.381 0.00 0.00 0.00 4.58
447 488 2.487934 CCATGTTCCCTCTTGCTATCG 58.512 52.381 0.00 0.00 0.00 2.92
475 517 1.734388 GACACCCTTGGCCACAACAC 61.734 60.000 3.88 0.00 32.14 3.32
496 538 0.955428 ACGATGGCGCAGTTTGACAT 60.955 50.000 10.83 0.25 42.48 3.06
561 603 0.179000 ATCACAAGGCGATGGAGACC 59.821 55.000 0.00 0.00 0.00 3.85
573 615 5.337219 TGCAAGTAACGTGTTATCACAAG 57.663 39.130 4.87 0.00 44.02 3.16
653 695 4.272489 TGGCAGTTGAATAGAGAAATGGG 58.728 43.478 0.00 0.00 0.00 4.00
819 861 1.138859 TGAGTGTGTGTCTGTCCCAAG 59.861 52.381 0.00 0.00 0.00 3.61
833 880 1.004560 CGCCACCTGTGATGAGTGT 60.005 57.895 0.00 0.00 0.00 3.55
1042 1102 1.068954 GTTCCTTGCAAGCTACAGCAC 60.069 52.381 21.43 3.90 45.16 4.40
1075 1135 0.028242 CAGTAGTAGCGCTCAGTCCG 59.972 60.000 16.34 0.00 0.00 4.79
1198 1272 1.770324 CCTGGGGAAGAAGCACCTT 59.230 57.895 0.00 0.00 30.67 3.50
1230 1304 2.113139 CCTTGGACTGGTGCCGTT 59.887 61.111 0.00 0.00 0.00 4.44
1348 1422 1.339438 GCCACCATCTTCTTGAGCTCA 60.339 52.381 13.74 13.74 0.00 4.26
1725 1811 5.582665 CAGCAGAAGTTTAACCCTCATAGTC 59.417 44.000 0.00 0.00 0.00 2.59
1792 1894 6.889198 TGTTTCACACAATCCCCAAAATTTA 58.111 32.000 0.00 0.00 29.87 1.40
1802 1904 7.652909 TCATTTTTCATCTGTTTCACACAATCC 59.347 33.333 0.00 0.00 33.87 3.01
1955 2410 1.069765 CACAGTCCAGCCACGAACT 59.930 57.895 0.00 0.00 0.00 3.01
1985 2440 4.883083 ACAGCTAAAAAGGCTAAAAAGGC 58.117 39.130 0.00 0.00 38.03 4.35
1986 2441 6.200854 CACAACAGCTAAAAAGGCTAAAAAGG 59.799 38.462 0.00 0.00 38.03 3.11
1987 2442 6.756542 ACACAACAGCTAAAAAGGCTAAAAAG 59.243 34.615 0.00 0.00 38.03 2.27
1988 2443 6.635755 ACACAACAGCTAAAAAGGCTAAAAA 58.364 32.000 0.00 0.00 38.03 1.94
1989 2444 6.215495 ACACAACAGCTAAAAAGGCTAAAA 57.785 33.333 0.00 0.00 38.03 1.52
1990 2445 5.845391 ACACAACAGCTAAAAAGGCTAAA 57.155 34.783 0.00 0.00 38.03 1.85
1991 2446 5.592688 AGAACACAACAGCTAAAAAGGCTAA 59.407 36.000 0.00 0.00 38.03 3.09
1992 2447 5.130350 AGAACACAACAGCTAAAAAGGCTA 58.870 37.500 0.00 0.00 38.03 3.93
1993 2448 3.954258 AGAACACAACAGCTAAAAAGGCT 59.046 39.130 0.00 0.00 41.07 4.58
2018 2473 4.963276 TTGATTATGTTCCAGAAAGGCG 57.037 40.909 0.00 0.00 37.29 5.52
2316 2791 6.443934 TTTACACTAAGCTGCTTGACAAAA 57.556 33.333 24.35 14.24 0.00 2.44
2330 2805 9.162764 GAGCAAGAAAGTATGGATTTACACTAA 57.837 33.333 0.00 0.00 0.00 2.24
2357 2832 9.541143 AAATACTACACCTCAATTTTGGTTTTG 57.459 29.630 0.00 0.00 33.75 2.44
2402 2935 0.741326 ATGGTCTCAGTCACGATCGG 59.259 55.000 20.98 8.65 0.00 4.18
2416 2949 2.188062 TAACACCCGTTCCAATGGTC 57.812 50.000 0.00 0.00 36.52 4.02
2450 2983 8.322906 TGAGTGTCAGGTTAATTTCATACAAG 57.677 34.615 0.00 0.00 0.00 3.16
2455 2988 5.316167 TGCTGAGTGTCAGGTTAATTTCAT 58.684 37.500 6.09 0.00 44.43 2.57
2545 3081 0.988145 TTCTAGACTGGCCATGGGGG 60.988 60.000 15.13 0.00 40.85 5.40


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

AutoCloner maintained by Alex Coulton.