Multiple sequence alignment - TraesCS4D01G169600

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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 TraesCS4D01G169600 chr4D 100.000 3510 0 0 1 3510 294703239 294699730 0.000000e+00 6482
1 TraesCS4D01G169600 chr4A 95.970 3027 81 19 497 3510 214311363 214314361 0.000000e+00 4876
2 TraesCS4D01G169600 chr4B 97.718 2717 42 7 804 3510 365622218 365624924 0.000000e+00 4656
3 TraesCS4D01G169600 chr4B 90.441 272 20 5 491 761 365617924 365618190 1.550000e-93 353
4 TraesCS4D01G169600 chr5D 95.219 502 22 2 1 500 342615903 342615402 0.000000e+00 793
5 TraesCS4D01G169600 chr5D 95.723 491 21 0 1 491 516478509 516478019 0.000000e+00 791
6 TraesCS4D01G169600 chr5D 95.335 493 22 1 2 494 350514114 350514605 0.000000e+00 782
7 TraesCS4D01G169600 chr7D 95.723 491 21 0 1 491 204739006 204738516 0.000000e+00 791
8 TraesCS4D01G169600 chr7D 95.723 491 17 4 1 490 75754296 75753809 0.000000e+00 787
9 TraesCS4D01G169600 chr7D 95.519 491 22 0 1 491 507342751 507342261 0.000000e+00 785
10 TraesCS4D01G169600 chr7D 95.706 489 20 1 2 490 600962191 600962678 0.000000e+00 785
11 TraesCS4D01G169600 chr2D 95.706 489 21 0 2 490 598908130 598908618 0.000000e+00 787
12 TraesCS4D01G169600 chr3D 94.990 499 23 2 1 498 281655503 281655006 0.000000e+00 782


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 TraesCS4D01G169600 chr4D 294699730 294703239 3509 True 6482 6482 100.000 1 3510 1 chr4D.!!$R1 3509
1 TraesCS4D01G169600 chr4A 214311363 214314361 2998 False 4876 4876 95.970 497 3510 1 chr4A.!!$F1 3013
2 TraesCS4D01G169600 chr4B 365622218 365624924 2706 False 4656 4656 97.718 804 3510 1 chr4B.!!$F2 2706
3 TraesCS4D01G169600 chr5D 342615402 342615903 501 True 793 793 95.219 1 500 1 chr5D.!!$R1 499

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
895 900 0.250901 ACCGCAGCTTCCACTGAAAT 60.251 50.0 0.00 0.0 40.25 2.17 F
1697 1704 1.444917 GGTTCGGCCAAATCGGATCC 61.445 60.0 2.24 0.0 36.56 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 1704 0.109781 CTGAAACACGCCAAATCCCG 60.110 55.0 0.00 0.0 0.00 5.14 R
2886 2895 0.806102 GACAAGGCGCGCAAGAGATA 60.806 55.0 34.42 0.0 40.82 1.98 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
62 63 2.149521 TTCTCCCTCTTTTCCCCCTT 57.850 50.000 0.00 0.00 0.00 3.95
143 144 0.649475 CGACGACTCCTACTACACCG 59.351 60.000 0.00 0.00 0.00 4.94
144 145 1.737029 CGACGACTCCTACTACACCGA 60.737 57.143 0.00 0.00 0.00 4.69
172 174 4.137872 TACTACGTGCAGGCCGCC 62.138 66.667 15.40 0.00 41.33 6.13
308 310 4.401202 TGTACTCAGATATTGTCGCTTCCA 59.599 41.667 0.00 0.00 0.00 3.53
317 319 1.286260 GTCGCTTCCACTGACTCGT 59.714 57.895 0.00 0.00 0.00 4.18
446 448 2.357952 TCCCTGATCTTGATCGTACACG 59.642 50.000 6.19 0.00 41.45 4.49
450 452 5.337554 CCTGATCTTGATCGTACACGTTTA 58.662 41.667 1.19 0.00 40.80 2.01
452 454 5.946298 TGATCTTGATCGTACACGTTTACT 58.054 37.500 9.97 0.00 40.80 2.24
490 492 2.107950 TTGAATTAGGGGCGTCACAG 57.892 50.000 0.00 0.00 0.00 3.66
493 495 1.207329 GAATTAGGGGCGTCACAGACT 59.793 52.381 0.00 0.00 0.00 3.24
494 496 0.537188 ATTAGGGGCGTCACAGACTG 59.463 55.000 0.00 0.00 0.00 3.51
496 498 2.725127 TAGGGGCGTCACAGACTGGT 62.725 60.000 7.51 0.00 0.00 4.00
499 501 1.069090 GGCGTCACAGACTGGTTCA 59.931 57.895 7.51 0.00 0.00 3.18
500 502 0.320771 GGCGTCACAGACTGGTTCAT 60.321 55.000 7.51 0.00 0.00 2.57
501 503 0.792640 GCGTCACAGACTGGTTCATG 59.207 55.000 7.51 0.00 0.00 3.07
544 546 1.656652 GCATACAAGGCGACACAGAT 58.343 50.000 0.00 0.00 0.00 2.90
547 549 1.438651 TACAAGGCGACACAGATTGC 58.561 50.000 0.00 0.00 0.00 3.56
556 558 3.425713 ACAGATTGCGCCGCACAG 61.426 61.111 13.21 4.32 38.71 3.66
568 570 1.973281 CGCACAGGGAAAGCACCAT 60.973 57.895 0.00 0.00 0.00 3.55
579 581 3.503748 GGAAAGCACCATAGTGGATATGC 59.496 47.826 2.45 2.65 44.69 3.14
595 597 6.036953 GTGGATATGCTCACTCTCTTTTCTTG 59.963 42.308 0.00 0.00 0.00 3.02
625 627 7.500992 AGATCTTCTATCTTTATTGGAACGCA 58.499 34.615 0.00 0.00 0.00 5.24
660 662 7.405292 ACATCATCATTTAACCAGAGAGGAAA 58.595 34.615 0.00 0.00 41.22 3.13
667 669 9.807921 TCATTTAACCAGAGAGGAAATAAGTTT 57.192 29.630 0.00 0.00 41.22 2.66
704 706 3.119065 GGTAGGAGTAAGCTCAAGTGGTC 60.119 52.174 0.00 0.00 43.37 4.02
797 802 1.127397 GGTTCACGCGCTTTAACTACC 59.873 52.381 5.73 0.00 0.00 3.18
798 803 2.064014 GTTCACGCGCTTTAACTACCT 58.936 47.619 5.73 0.00 0.00 3.08
799 804 3.244976 GTTCACGCGCTTTAACTACCTA 58.755 45.455 5.73 0.00 0.00 3.08
800 805 2.867429 TCACGCGCTTTAACTACCTAC 58.133 47.619 5.73 0.00 0.00 3.18
801 806 1.922545 CACGCGCTTTAACTACCTACC 59.077 52.381 5.73 0.00 0.00 3.18
802 807 1.821136 ACGCGCTTTAACTACCTACCT 59.179 47.619 5.73 0.00 0.00 3.08
803 808 2.232208 ACGCGCTTTAACTACCTACCTT 59.768 45.455 5.73 0.00 0.00 3.50
804 809 3.443681 ACGCGCTTTAACTACCTACCTTA 59.556 43.478 5.73 0.00 0.00 2.69
805 810 4.040376 CGCGCTTTAACTACCTACCTTAG 58.960 47.826 5.56 0.00 0.00 2.18
827 832 6.996180 AGCTACCTACCATAAGATAAAGCA 57.004 37.500 0.00 0.00 0.00 3.91
895 900 0.250901 ACCGCAGCTTCCACTGAAAT 60.251 50.000 0.00 0.00 40.25 2.17
1697 1704 1.444917 GGTTCGGCCAAATCGGATCC 61.445 60.000 2.24 0.00 36.56 3.36
1792 1799 0.908198 ATCCAGTGGCTTCCAGAGTC 59.092 55.000 3.51 0.00 32.34 3.36
1819 1826 1.068333 CCACGAAGCCTTCCAATGTTG 60.068 52.381 0.00 0.00 0.00 3.33
2582 2589 6.262273 ACACGGAAACTGTGAGTTATTTCAAT 59.738 34.615 16.07 0.00 37.47 2.57
2585 2592 8.194769 ACGGAAACTGTGAGTTATTTCAATTTT 58.805 29.630 0.00 0.00 37.47 1.82
2642 2649 6.701145 TTACAACTTTGGTGTTATGAAGCA 57.299 33.333 0.00 0.00 0.00 3.91
2643 2650 4.932146 ACAACTTTGGTGTTATGAAGCAC 58.068 39.130 0.00 0.00 35.07 4.40
2644 2651 4.400884 ACAACTTTGGTGTTATGAAGCACA 59.599 37.500 0.00 0.00 37.35 4.57
2645 2652 5.068987 ACAACTTTGGTGTTATGAAGCACAT 59.931 36.000 0.00 2.31 42.39 3.21
2646 2653 5.376854 ACTTTGGTGTTATGAAGCACATC 57.623 39.130 0.00 0.00 40.07 3.06
2647 2654 4.826733 ACTTTGGTGTTATGAAGCACATCA 59.173 37.500 0.00 0.00 40.07 3.07
2648 2655 5.301551 ACTTTGGTGTTATGAAGCACATCAA 59.698 36.000 0.00 0.00 41.29 2.57
2649 2656 5.981088 TTGGTGTTATGAAGCACATCAAT 57.019 34.783 0.00 0.00 38.76 2.57
2847 2856 3.535280 TGGTGATGCTATTTCGCACTA 57.465 42.857 0.00 0.00 43.61 2.74
2897 2906 4.554973 GTGTTTGTTGAATATCTCTTGCGC 59.445 41.667 0.00 0.00 0.00 6.09
2947 2957 4.766891 ACAATTCACAACATAGGTTCTGGG 59.233 41.667 0.00 0.00 34.21 4.45
2965 2975 2.162608 TGGGAACATCGTATTTTTGGCG 59.837 45.455 0.00 0.00 33.40 5.69
3007 3017 3.260632 TGTCAGTGCTGTCTAATTGCCTA 59.739 43.478 0.00 0.00 0.00 3.93
3045 3055 4.510711 TGGCAGTTGTAATGTTGCAAATTG 59.489 37.500 0.00 0.00 38.27 2.32
3142 3152 5.992729 GCATGTTTGAGAAATGCAAATTGT 58.007 33.333 0.00 0.00 44.83 2.71
3273 3284 2.114638 TGGTTGCTTTGCAGTCCAC 58.885 52.632 11.97 0.57 40.61 4.02
3322 3333 5.789574 TCTTCTTAATGGGCTAGGGAAAA 57.210 39.130 0.00 0.00 0.00 2.29
3364 3375 7.449395 TCAGATCAGATTCAATTTTGTGAACCT 59.551 33.333 0.00 0.00 40.22 3.50
3448 3459 4.439968 GCTGTCCACAGGTTTACTATACC 58.560 47.826 8.78 0.00 43.94 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 2.614481 GCGACAACCAGGTAGAATGGAA 60.614 50.000 0.00 0.00 40.51 3.53
107 108 2.028484 GTCAACGGTGGCGTCTGA 59.972 61.111 0.00 0.00 0.00 3.27
121 122 2.341257 GTGTAGTAGGAGTCGTCGTCA 58.659 52.381 0.00 0.00 0.00 4.35
143 144 1.674962 CACGTAGTAGTAGGCACCCTC 59.325 57.143 0.00 0.00 41.61 4.30
144 145 1.760192 CACGTAGTAGTAGGCACCCT 58.240 55.000 0.00 0.00 41.61 4.34
172 174 1.299165 CTATTCCTGGTCGTCGGCG 60.299 63.158 1.15 1.15 39.92 6.46
174 176 2.667473 AAACTATTCCTGGTCGTCGG 57.333 50.000 0.00 0.00 0.00 4.79
187 189 3.252351 GCCTGGGATCCTCCTAAACTAT 58.748 50.000 12.58 0.00 36.57 2.12
301 303 0.803117 TAGACGAGTCAGTGGAAGCG 59.197 55.000 5.99 0.00 0.00 4.68
317 319 5.238650 TCGAATACAAGTGCTCGATCATAGA 59.761 40.000 0.00 0.00 35.52 1.98
357 359 7.935755 AGTCATACAAGCATCATAATACAAGCT 59.064 33.333 0.00 0.00 0.00 3.74
396 398 5.245531 GGGAAGATATCACAACACAACTCA 58.754 41.667 5.32 0.00 0.00 3.41
450 452 9.817809 ATTCAATCGTACACTAATCATACAAGT 57.182 29.630 0.00 0.00 0.00 3.16
477 479 1.982395 CCAGTCTGTGACGCCCCTA 60.982 63.158 0.00 0.00 37.67 3.53
478 480 3.314331 CCAGTCTGTGACGCCCCT 61.314 66.667 0.00 0.00 37.67 4.79
490 492 2.229792 TCAACCTTGCATGAACCAGTC 58.770 47.619 0.00 0.00 0.00 3.51
493 495 3.229293 TCATTCAACCTTGCATGAACCA 58.771 40.909 2.68 0.00 37.77 3.67
494 496 3.940209 TCATTCAACCTTGCATGAACC 57.060 42.857 2.68 0.00 37.77 3.62
496 498 6.587206 TGTTATCATTCAACCTTGCATGAA 57.413 33.333 0.00 3.10 42.43 2.57
499 501 6.682113 GCTCATGTTATCATTCAACCTTGCAT 60.682 38.462 0.00 0.00 31.15 3.96
500 502 5.393352 GCTCATGTTATCATTCAACCTTGCA 60.393 40.000 0.00 0.00 31.15 4.08
501 503 5.039333 GCTCATGTTATCATTCAACCTTGC 58.961 41.667 0.00 0.00 31.15 4.01
540 542 4.170062 CCTGTGCGGCGCAATCTG 62.170 66.667 38.05 26.26 41.47 2.90
556 558 2.736670 ATCCACTATGGTGCTTTCCC 57.263 50.000 3.19 0.00 41.75 3.97
568 570 6.609212 AGAAAAGAGAGTGAGCATATCCACTA 59.391 38.462 0.00 0.00 43.02 2.74
579 581 7.656948 AGATCTTTGTCAAGAAAAGAGAGTGAG 59.343 37.037 5.04 0.00 44.52 3.51
632 634 8.717717 TCCTCTCTGGTTAAATGATGATGTAAT 58.282 33.333 0.00 0.00 37.07 1.89
636 638 7.870509 TTTCCTCTCTGGTTAAATGATGATG 57.129 36.000 0.00 0.00 37.07 3.07
638 640 9.618890 CTTATTTCCTCTCTGGTTAAATGATGA 57.381 33.333 0.00 0.00 37.07 2.92
680 682 2.832129 CACTTGAGCTTACTCCTACCCA 59.168 50.000 0.00 0.00 42.74 4.51
729 731 5.861787 GCCGTAAATGCAACTAATTTTCACT 59.138 36.000 0.00 0.00 0.00 3.41
742 744 2.753849 GGCTGGGCCGTAAATGCA 60.754 61.111 0.00 0.00 39.62 3.96
770 772 4.980805 GCGCGTGAACCAGGGTGA 62.981 66.667 8.43 0.00 0.00 4.02
797 802 9.750783 TTATCTTATGGTAGGTAGCTAAGGTAG 57.249 37.037 2.58 0.00 0.00 3.18
799 804 9.091220 CTTTATCTTATGGTAGGTAGCTAAGGT 57.909 37.037 2.58 0.00 0.00 3.50
800 805 8.035984 GCTTTATCTTATGGTAGGTAGCTAAGG 58.964 40.741 2.58 0.00 0.00 2.69
801 806 8.585881 TGCTTTATCTTATGGTAGGTAGCTAAG 58.414 37.037 2.58 0.00 0.00 2.18
802 807 8.486942 TGCTTTATCTTATGGTAGGTAGCTAA 57.513 34.615 2.58 0.00 0.00 3.09
803 808 8.486942 TTGCTTTATCTTATGGTAGGTAGCTA 57.513 34.615 0.00 0.00 0.00 3.32
804 809 6.996180 TGCTTTATCTTATGGTAGGTAGCT 57.004 37.500 0.00 0.00 0.00 3.32
805 810 6.651225 CCTTGCTTTATCTTATGGTAGGTAGC 59.349 42.308 0.00 0.00 0.00 3.58
895 900 4.193090 TGTTCTTTTCTGGTGCTTCGTTA 58.807 39.130 0.00 0.00 0.00 3.18
995 1002 2.100197 CGGAGTAGGAGTTCATGGTGA 58.900 52.381 0.00 0.00 0.00 4.02
1697 1704 0.109781 CTGAAACACGCCAAATCCCG 60.110 55.000 0.00 0.00 0.00 5.14
1771 1778 1.202330 CTCTGGAAGCCACTGGATCT 58.798 55.000 0.00 0.00 0.00 2.75
1792 1799 3.850098 AAGGCTTCGTGGCACCAGG 62.850 63.158 12.86 0.00 44.55 4.45
2585 2592 6.209788 CCCCAAAGCCACAAGTATAGTAAAAA 59.790 38.462 0.00 0.00 0.00 1.94
2647 2654 6.151480 TGTGTGTGAAGATGCAATGATGTATT 59.849 34.615 0.00 0.00 31.47 1.89
2648 2655 5.648960 TGTGTGTGAAGATGCAATGATGTAT 59.351 36.000 0.00 0.00 34.28 2.29
2649 2656 5.002516 TGTGTGTGAAGATGCAATGATGTA 58.997 37.500 0.00 0.00 0.00 2.29
2807 2814 5.356190 CACCATCTATGCAAAAGATCTGTGT 59.644 40.000 20.42 11.62 33.09 3.72
2808 2815 5.587443 TCACCATCTATGCAAAAGATCTGTG 59.413 40.000 21.51 21.51 36.01 3.66
2886 2895 0.806102 GACAAGGCGCGCAAGAGATA 60.806 55.000 34.42 0.00 40.82 1.98
2897 2906 8.856490 ATTAAGCATAAAATTAAGACAAGGCG 57.144 30.769 0.00 0.00 0.00 5.52
2947 2957 4.088648 CAGACGCCAAAAATACGATGTTC 58.911 43.478 0.00 0.00 0.00 3.18
3007 3017 3.173965 ACTGCCAGGTACACTTCTACAT 58.826 45.455 0.00 0.00 0.00 2.29
3045 3055 1.459592 CACAACCACACTAGCGTTAGC 59.540 52.381 6.17 0.00 45.58 3.09
3142 3152 9.618890 TCAAAATAAAAATTTCACATTGTGGGA 57.381 25.926 16.46 6.26 33.87 4.37
3273 3284 4.203361 CACGGTAAACAACAACAATGTTCG 59.797 41.667 0.00 0.00 46.78 3.95
3322 3333 7.170965 TCTGATCTGAAATTAGCAAAAGGAGT 58.829 34.615 0.00 0.00 0.00 3.85
3358 3369 6.040391 CCTGAAATTTGTAAGTTCCAGGTTCA 59.960 38.462 0.00 0.00 34.78 3.18
3364 3375 6.350110 GCATAGCCTGAAATTTGTAAGTTCCA 60.350 38.462 0.00 0.00 34.78 3.53
3448 3459 4.847365 ACACACGAAATCAATGATCTCG 57.153 40.909 16.38 16.38 35.68 4.04


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

AutoCloner maintained by Alex Coulton.