Multiple sequence alignment - TraesCS1B01G196100

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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 TraesCS1B01G196100 chr1B 100.000 2198 0 0 1 2198 352529115 352531312 0 4060
1 TraesCS1B01G196100 chr1B 94.048 840 50 0 1359 2198 499142743 499143582 0 1275
2 TraesCS1B01G196100 chr1B 91.299 839 73 0 1360 2198 435375287 435376125 0 1146
3 TraesCS1B01G196100 chr1B 86.765 680 82 8 2 677 388753477 388754152 0 750
4 TraesCS1B01G196100 chr1B 85.125 679 94 7 1 675 663228764 663229439 0 688
5 TraesCS1B01G196100 chr4A 91.093 842 75 0 1357 2198 706572265 706573106 0 1140
6 TraesCS1B01G196100 chr5B 90.595 840 79 0 1359 2198 686406854 686407693 0 1114
7 TraesCS1B01G196100 chr5B 89.141 838 90 1 1361 2198 208683092 208683928 0 1042
8 TraesCS1B01G196100 chr3B 90.403 844 79 2 1356 2198 456679000 456678158 0 1109
9 TraesCS1B01G196100 chr7B 91.347 809 69 1 1391 2198 464537704 464536896 0 1105
10 TraesCS1B01G196100 chr7B 90.357 840 78 3 1360 2198 362138330 362139167 0 1099
11 TraesCS1B01G196100 chr5D 89.480 846 87 2 1354 2198 158162418 158163262 0 1068
12 TraesCS1B01G196100 chr5D 84.942 684 91 10 2 676 504071753 504071073 0 682
13 TraesCS1B01G196100 chr1A 92.163 689 35 7 684 1359 340249331 340250013 0 955
14 TraesCS1B01G196100 chr1D 93.692 539 24 5 827 1359 260402551 260402017 0 798
15 TraesCS1B01G196100 chr6D 86.842 684 81 7 1 677 411224842 411224161 0 756
16 TraesCS1B01G196100 chr4B 86.510 682 89 3 2 681 619333532 619334212 0 747
17 TraesCS1B01G196100 chr2D 85.776 689 86 5 1 677 595152889 595152201 0 719
18 TraesCS1B01G196100 chr7D 85.294 680 88 10 1 672 95115560 95114885 0 691
19 TraesCS1B01G196100 chr4D 84.949 691 88 14 2 683 391050844 391051527 0 686
20 TraesCS1B01G196100 chr7A 84.956 678 95 5 1 672 141301192 141301868 0 680


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 TraesCS1B01G196100 chr1B 352529115 352531312 2197 False 4060 4060 100.000 1 2198 1 chr1B.!!$F1 2197
1 TraesCS1B01G196100 chr1B 499142743 499143582 839 False 1275 1275 94.048 1359 2198 1 chr1B.!!$F4 839
2 TraesCS1B01G196100 chr1B 435375287 435376125 838 False 1146 1146 91.299 1360 2198 1 chr1B.!!$F3 838
3 TraesCS1B01G196100 chr1B 388753477 388754152 675 False 750 750 86.765 2 677 1 chr1B.!!$F2 675
4 TraesCS1B01G196100 chr1B 663228764 663229439 675 False 688 688 85.125 1 675 1 chr1B.!!$F5 674
5 TraesCS1B01G196100 chr4A 706572265 706573106 841 False 1140 1140 91.093 1357 2198 1 chr4A.!!$F1 841
6 TraesCS1B01G196100 chr5B 686406854 686407693 839 False 1114 1114 90.595 1359 2198 1 chr5B.!!$F2 839
7 TraesCS1B01G196100 chr5B 208683092 208683928 836 False 1042 1042 89.141 1361 2198 1 chr5B.!!$F1 837
8 TraesCS1B01G196100 chr3B 456678158 456679000 842 True 1109 1109 90.403 1356 2198 1 chr3B.!!$R1 842
9 TraesCS1B01G196100 chr7B 464536896 464537704 808 True 1105 1105 91.347 1391 2198 1 chr7B.!!$R1 807
10 TraesCS1B01G196100 chr7B 362138330 362139167 837 False 1099 1099 90.357 1360 2198 1 chr7B.!!$F1 838
11 TraesCS1B01G196100 chr5D 158162418 158163262 844 False 1068 1068 89.480 1354 2198 1 chr5D.!!$F1 844
12 TraesCS1B01G196100 chr5D 504071073 504071753 680 True 682 682 84.942 2 676 1 chr5D.!!$R1 674
13 TraesCS1B01G196100 chr1A 340249331 340250013 682 False 955 955 92.163 684 1359 1 chr1A.!!$F1 675
14 TraesCS1B01G196100 chr1D 260402017 260402551 534 True 798 798 93.692 827 1359 1 chr1D.!!$R1 532
15 TraesCS1B01G196100 chr6D 411224161 411224842 681 True 756 756 86.842 1 677 1 chr6D.!!$R1 676
16 TraesCS1B01G196100 chr4B 619333532 619334212 680 False 747 747 86.510 2 681 1 chr4B.!!$F1 679
17 TraesCS1B01G196100 chr2D 595152201 595152889 688 True 719 719 85.776 1 677 1 chr2D.!!$R1 676
18 TraesCS1B01G196100 chr7D 95114885 95115560 675 True 691 691 85.294 1 672 1 chr7D.!!$R1 671
19 TraesCS1B01G196100 chr4D 391050844 391051527 683 False 686 686 84.949 2 683 1 chr4D.!!$F1 681
20 TraesCS1B01G196100 chr7A 141301192 141301868 676 False 680 680 84.956 1 672 1 chr7A.!!$F1 671

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
419 435 0.179045 GGCGGATGACATGTAAGGCT 60.179 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 1926 1.001974 CGTGGACTGGACCATCAAGAA 59.998 52.381 0.0 0.0 42.17 2.52 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 37 4.473520 CTCCACGGGAGCGGCATT 62.474 66.667 1.45 0.00 43.29 3.56
172 176 3.382832 CGGGCTCCTCCTTCACGT 61.383 66.667 0.00 0.00 34.39 4.49
227 231 2.281484 GTCGTGCTTCCCCTTGCA 60.281 61.111 0.00 0.00 36.79 4.08
330 343 3.966543 CAAGGAGGCCGTGGGGTT 61.967 66.667 0.00 0.00 34.97 4.11
336 350 3.948719 GGCCGTGGGGTTGAGTGA 61.949 66.667 0.00 0.00 34.97 3.41
350 365 1.178276 GAGTGAGGAGTGTGGACGAT 58.822 55.000 0.00 0.00 0.00 3.73
414 430 1.829456 CCTGGGCGGATGACATGTA 59.171 57.895 0.00 0.00 33.16 2.29
419 435 0.179045 GGCGGATGACATGTAAGGCT 60.179 55.000 0.00 0.00 0.00 4.58
466 482 4.326227 TGGGAGGTAGGTGGCCGT 62.326 66.667 0.00 0.00 0.00 5.68
528 544 3.370231 GTCCGCCGCAACCCAAAT 61.370 61.111 0.00 0.00 0.00 2.32
538 554 1.374560 CAACCCAAATCCGACGCATA 58.625 50.000 0.00 0.00 0.00 3.14
564 580 2.495809 TCGAAATGGATCGACCGGA 58.504 52.632 9.46 0.00 46.12 5.14
568 584 2.561569 GAAATGGATCGACCGGAACAT 58.438 47.619 9.46 0.00 42.61 2.71
585 601 5.563085 CGGAACATAAAACGGACAAAATGGA 60.563 40.000 0.00 0.00 0.00 3.41
587 603 6.871492 GGAACATAAAACGGACAAAATGGATT 59.129 34.615 0.00 0.00 0.00 3.01
591 608 2.483014 ACGGACAAAATGGATTCGGA 57.517 45.000 0.00 0.00 0.00 4.55
626 644 3.208594 GCCGACCGGTTTATCCTTTTAT 58.791 45.455 9.42 0.00 37.65 1.40
660 678 4.707768 TGGACGGGATGGGGTCGT 62.708 66.667 0.00 0.00 39.99 4.34
687 705 0.921896 AGTTGGCCTCATGCTACCAT 59.078 50.000 3.32 0.00 40.92 3.55
691 709 1.059913 GGCCTCATGCTACCATAGGT 58.940 55.000 0.00 0.00 40.92 3.08
718 736 0.811616 GGACAAGGCAGCCTATGACG 60.812 60.000 16.56 3.75 44.27 4.35
728 746 2.222678 CAGCCTATGACGCTAAATGCAG 59.777 50.000 0.00 0.00 43.06 4.41
731 749 3.430218 GCCTATGACGCTAAATGCAGTAG 59.570 47.826 0.00 0.00 43.06 2.57
740 758 6.475207 ACGCTAAATGCAGTAGTTAATTTCG 58.525 36.000 8.55 4.98 43.06 3.46
752 770 4.647611 AGTTAATTTCGGATCACACACCA 58.352 39.130 0.00 0.00 0.00 4.17
763 781 0.461163 CACACACCAGTCACCGTCAA 60.461 55.000 0.00 0.00 0.00 3.18
770 788 0.946221 CAGTCACCGTCAAGTGGAGC 60.946 60.000 0.00 0.00 38.34 4.70
796 814 1.685820 GAAACCACCTAGCCTGCCT 59.314 57.895 0.00 0.00 0.00 4.75
797 815 0.393132 GAAACCACCTAGCCTGCCTC 60.393 60.000 0.00 0.00 0.00 4.70
798 816 1.133809 AAACCACCTAGCCTGCCTCA 61.134 55.000 0.00 0.00 0.00 3.86
799 817 1.842381 AACCACCTAGCCTGCCTCAC 61.842 60.000 0.00 0.00 0.00 3.51
800 818 1.992277 CCACCTAGCCTGCCTCACT 60.992 63.158 0.00 0.00 0.00 3.41
801 819 1.220206 CACCTAGCCTGCCTCACTG 59.780 63.158 0.00 0.00 0.00 3.66
820 838 2.495270 CTGTCACTGAGCTAGGACACAT 59.505 50.000 5.44 0.00 34.78 3.21
900 918 0.563173 TGCCCTCCACTAGAGCCTAT 59.437 55.000 0.00 0.00 41.74 2.57
901 919 0.972883 GCCCTCCACTAGAGCCTATG 59.027 60.000 0.00 0.00 41.74 2.23
906 924 2.823154 CTCCACTAGAGCCTATGTAGCC 59.177 54.545 0.00 0.00 35.31 3.93
907 925 2.447429 TCCACTAGAGCCTATGTAGCCT 59.553 50.000 0.00 0.00 0.00 4.58
911 929 1.931635 AGAGCCTATGTAGCCTAGCC 58.068 55.000 0.00 0.00 0.00 3.93
943 961 2.659897 GCATGGAGCTAGCGACCG 60.660 66.667 22.20 13.70 41.15 4.79
944 962 3.120105 CATGGAGCTAGCGACCGA 58.880 61.111 22.20 14.78 0.00 4.69
1009 1030 1.078848 GAAGCGAGGATGCTGGTGT 60.079 57.895 0.00 0.00 46.60 4.16
1015 1036 0.326264 GAGGATGCTGGTGTTGGAGT 59.674 55.000 0.00 0.00 0.00 3.85
1022 1043 1.454847 TGGTGTTGGAGTTGGGCAC 60.455 57.895 0.00 0.00 0.00 5.01
1055 1076 1.228337 TGACCCTCGTCTTCGTCCA 60.228 57.895 0.00 0.00 39.94 4.02
1241 1272 1.415672 TTGCCCCTCTCCTCGTTTGT 61.416 55.000 0.00 0.00 0.00 2.83
1280 1311 6.966435 TGTTTTTGCTTCTTCTTTTCTTGG 57.034 33.333 0.00 0.00 0.00 3.61
1285 1316 2.630098 GCTTCTTCTTTTCTTGGGCCTT 59.370 45.455 4.53 0.00 0.00 4.35
1286 1317 3.553715 GCTTCTTCTTTTCTTGGGCCTTG 60.554 47.826 4.53 0.00 0.00 3.61
1287 1318 3.312736 TCTTCTTTTCTTGGGCCTTGT 57.687 42.857 4.53 0.00 0.00 3.16
1288 1319 4.447138 TCTTCTTTTCTTGGGCCTTGTA 57.553 40.909 4.53 0.00 0.00 2.41
1434 1472 0.611714 AAAGAGCCCGTCCACGTTAT 59.388 50.000 0.00 0.00 37.74 1.89
1437 1475 3.259751 GCCCGTCCACGTTATCGC 61.260 66.667 0.00 0.00 41.18 4.58
1657 1696 4.386049 GTCAAAGACGATCGAGTTGTGATT 59.614 41.667 24.34 0.00 0.00 2.57
1778 1817 2.860041 ACTCCCAGTAGGTATCCACTCT 59.140 50.000 0.00 0.00 36.75 3.24
1835 1874 4.394941 CGCGCGACAACACACTCG 62.395 66.667 28.94 0.00 0.00 4.18
1886 1926 1.039233 GGTTGCACATAGGGCAGCAT 61.039 55.000 10.16 0.00 43.25 3.79
2009 2049 0.672401 TCCAAGTGAATTCGGCCGTC 60.672 55.000 27.15 16.49 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.341531 CCGCTATTGGGAGACGAGAAT 59.658 52.381 0.00 0.00 0.00 2.40
36 37 1.735376 GCCGCTATTGGGAGACGAGA 61.735 60.000 0.00 0.00 0.00 4.04
70 71 2.488355 CGACCGGCAGTACATCGT 59.512 61.111 0.00 0.00 0.00 3.73
227 231 1.408453 GGGGCTATGGAACTACGGCT 61.408 60.000 0.00 0.00 0.00 5.52
269 273 1.321074 AACCCTAGCCTCGAACTCGG 61.321 60.000 0.00 0.00 40.29 4.63
330 343 0.179001 TCGTCCACACTCCTCACTCA 60.179 55.000 0.00 0.00 0.00 3.41
336 350 1.595993 CGGTCATCGTCCACACTCCT 61.596 60.000 0.00 0.00 0.00 3.69
350 365 2.668632 GAAGCCATGGACCGGTCA 59.331 61.111 34.40 21.15 0.00 4.02
520 536 2.341846 ATATGCGTCGGATTTGGGTT 57.658 45.000 4.04 0.00 0.00 4.11
538 554 4.898829 TCGATCCATTTCGAATGCAAAT 57.101 36.364 0.00 0.00 44.56 2.32
555 571 2.094078 TCCGTTTTATGTTCCGGTCGAT 60.094 45.455 0.00 0.00 41.17 3.59
559 575 2.547299 TGTCCGTTTTATGTTCCGGT 57.453 45.000 0.00 0.00 41.17 5.28
562 578 5.774630 TCCATTTTGTCCGTTTTATGTTCC 58.225 37.500 0.00 0.00 0.00 3.62
564 580 6.584563 CGAATCCATTTTGTCCGTTTTATGTT 59.415 34.615 0.00 0.00 0.00 2.71
568 584 4.760715 TCCGAATCCATTTTGTCCGTTTTA 59.239 37.500 0.00 0.00 0.00 1.52
580 596 1.722011 GTGTGACGTCCGAATCCATT 58.278 50.000 14.12 0.00 0.00 3.16
585 601 1.733041 CAGCGTGTGACGTCCGAAT 60.733 57.895 14.12 0.00 44.73 3.34
587 603 4.337060 CCAGCGTGTGACGTCCGA 62.337 66.667 14.12 0.00 44.73 4.55
626 644 0.685097 CCAGTCTCGTCCTTTTGGGA 59.315 55.000 0.00 0.00 42.77 4.37
660 678 1.426251 ATGAGGCCAACTCCACCACA 61.426 55.000 5.01 0.00 46.01 4.17
687 705 3.244582 TGCCTTGTCCTTTCACTACCTA 58.755 45.455 0.00 0.00 0.00 3.08
691 709 1.271379 GGCTGCCTTGTCCTTTCACTA 60.271 52.381 12.43 0.00 0.00 2.74
718 736 7.011828 TCCGAAATTAACTACTGCATTTAGC 57.988 36.000 0.00 0.00 45.96 3.09
728 746 5.640357 TGGTGTGTGATCCGAAATTAACTAC 59.360 40.000 0.00 0.00 0.00 2.73
731 749 4.454504 ACTGGTGTGTGATCCGAAATTAAC 59.545 41.667 0.00 0.00 0.00 2.01
740 758 0.670546 CGGTGACTGGTGTGTGATCC 60.671 60.000 0.00 0.00 0.00 3.36
752 770 1.367840 GCTCCACTTGACGGTGACT 59.632 57.895 0.00 0.00 39.34 3.41
763 781 1.846124 TTTCCCTTCCCGCTCCACT 60.846 57.895 0.00 0.00 0.00 4.00
770 788 0.252197 CTAGGTGGTTTCCCTTCCCG 59.748 60.000 0.00 0.00 33.35 5.14
793 811 0.891373 TAGCTCAGTGACAGTGAGGC 59.109 55.000 31.89 25.05 44.00 4.70
796 814 2.163509 GTCCTAGCTCAGTGACAGTGA 58.836 52.381 12.39 12.39 0.00 3.41
797 815 1.889170 TGTCCTAGCTCAGTGACAGTG 59.111 52.381 3.70 3.70 32.69 3.66
798 816 1.889829 GTGTCCTAGCTCAGTGACAGT 59.110 52.381 7.53 0.00 36.05 3.55
799 817 1.889170 TGTGTCCTAGCTCAGTGACAG 59.111 52.381 7.53 0.00 36.05 3.51
800 818 1.995376 TGTGTCCTAGCTCAGTGACA 58.005 50.000 0.00 0.00 34.21 3.58
801 819 2.493675 TGATGTGTCCTAGCTCAGTGAC 59.506 50.000 0.00 0.00 0.00 3.67
820 838 0.179076 CCATCTACTGCGGCATGTGA 60.179 55.000 1.75 2.17 0.00 3.58
900 918 2.681319 TATAACGGGGCTAGGCTACA 57.319 50.000 16.80 0.00 0.00 2.74
901 919 5.420104 TCTTTATATAACGGGGCTAGGCTAC 59.580 44.000 16.80 8.72 0.00 3.58
906 924 5.401531 TGCTCTTTATATAACGGGGCTAG 57.598 43.478 15.96 2.66 0.00 3.42
907 925 5.338056 CCATGCTCTTTATATAACGGGGCTA 60.338 44.000 15.96 7.22 0.00 3.93
911 929 4.631813 GCTCCATGCTCTTTATATAACGGG 59.368 45.833 0.00 0.00 38.95 5.28
1009 1030 1.228831 CCCATGTGCCCAACTCCAA 60.229 57.895 0.00 0.00 0.00 3.53
1015 1036 1.000233 GGATGACCCATGTGCCCAA 60.000 57.895 0.00 0.00 34.14 4.12
1241 1272 3.791973 AAACAACTTGGCATCGAACAA 57.208 38.095 0.00 0.00 0.00 2.83
1280 1311 7.162082 AGCTTATTACAGATACATACAAGGCC 58.838 38.462 0.00 0.00 0.00 5.19
1285 1316 6.084277 CGCGAGCTTATTACAGATACATACA 58.916 40.000 0.00 0.00 0.00 2.29
1286 1317 5.512082 CCGCGAGCTTATTACAGATACATAC 59.488 44.000 8.23 0.00 0.00 2.39
1287 1318 5.182570 ACCGCGAGCTTATTACAGATACATA 59.817 40.000 8.23 0.00 0.00 2.29
1288 1319 4.022242 ACCGCGAGCTTATTACAGATACAT 60.022 41.667 8.23 0.00 0.00 2.29
1434 1472 9.444600 TCAGTGTATATATGTAATCTGTAGCGA 57.555 33.333 0.00 0.00 0.00 4.93
1657 1696 2.573462 GGGCTATGGCAGATATGGAAGA 59.427 50.000 2.58 0.00 40.87 2.87
1835 1874 4.745649 AGAGCATAAACCACGTTCTACTC 58.254 43.478 0.00 0.00 0.00 2.59
1886 1926 1.001974 CGTGGACTGGACCATCAAGAA 59.998 52.381 0.00 0.00 42.17 2.52


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

AutoCloner maintained by Alex Coulton.