Multiple sequence alignment - TraesCS7D01G215000

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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 TraesCS7D01G215000 chr7D 100.000 4028 0 0 1 4028 174448654 174444627 0.000000e+00 7439.0
1 TraesCS7D01G215000 chr7D 100.000 36 0 0 3731 3766 174444890 174444855 2.600000e-07 67.6
2 TraesCS7D01G215000 chr7D 100.000 36 0 0 3765 3800 174444924 174444889 2.600000e-07 67.6
3 TraesCS7D01G215000 chr7A 97.156 3059 76 5 1 3058 176436814 176433766 0.000000e+00 5156.0
4 TraesCS7D01G215000 chr7A 98.025 709 12 2 3058 3766 176433734 176433028 0.000000e+00 1230.0
5 TraesCS7D01G215000 chr7A 98.485 264 4 0 3765 4028 176433063 176432800 2.190000e-127 466.0
6 TraesCS7D01G215000 chr7B 96.520 3075 82 12 1 3058 138884688 138881622 0.000000e+00 5062.0
7 TraesCS7D01G215000 chr7B 98.449 709 10 1 3058 3766 138881590 138880883 0.000000e+00 1247.0
8 TraesCS7D01G215000 chr7B 99.621 264 1 0 3765 4028 138880918 138880655 2.180000e-132 483.0


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 TraesCS7D01G215000 chr7D 174444627 174448654 4027 True 2524.733333 7439 100.000000 1 4028 3 chr7D.!!$R1 4027
1 TraesCS7D01G215000 chr7A 176432800 176436814 4014 True 2284.000000 5156 97.888667 1 4028 3 chr7A.!!$R1 4027
2 TraesCS7D01G215000 chr7B 138880655 138884688 4033 True 2264.000000 5062 98.196667 1 4028 3 chr7B.!!$R1 4027

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
512 523 0.253327 GAGGAGTGAATGGGGGACAC 59.747 60.0 0.0 0.0 35.15 3.67 F
1446 1466 1.204146 GTTCCTCCAGCCCATGTCTA 58.796 55.0 0.0 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 1529 1.304381 AATGCAGCGGGTTGGACAT 60.304 52.632 0.0 0.0 0.0 3.06 R
3108 3160 1.016627 GCAGGCATATTCAACGCTCA 58.983 50.000 0.0 0.0 0.0 4.26 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
147 148 4.874977 GTGTAGCTCGCTCCCGCC 62.875 72.222 0.00 0.00 0.00 6.13
304 314 5.912892 TGTCGAGATGAAATGTAATAGCCA 58.087 37.500 0.00 0.00 0.00 4.75
343 353 3.896648 AAACTGCACGATTGTCGAATT 57.103 38.095 6.34 0.00 43.74 2.17
494 505 6.664816 AGAAAAGGACAAATGCTATTGATGGA 59.335 34.615 8.70 0.00 34.38 3.41
503 514 5.579753 ATGCTATTGATGGAGGAGTGAAT 57.420 39.130 0.00 0.00 0.00 2.57
512 523 0.253327 GAGGAGTGAATGGGGGACAC 59.747 60.000 0.00 0.00 35.15 3.67
564 575 3.989705 TGCATCTATGTTCAACGAACG 57.010 42.857 0.00 0.00 44.55 3.95
699 713 5.446143 TCATGCGAAGTGTTTTGGTTTAT 57.554 34.783 0.00 0.00 0.00 1.40
700 714 6.561737 TCATGCGAAGTGTTTTGGTTTATA 57.438 33.333 0.00 0.00 0.00 0.98
701 715 7.151999 TCATGCGAAGTGTTTTGGTTTATAT 57.848 32.000 0.00 0.00 0.00 0.86
745 759 9.213777 TGAGTTTACCATGAGAATTACCTATCT 57.786 33.333 0.00 0.00 0.00 1.98
748 762 9.274206 GTTTACCATGAGAATTACCTATCTTCC 57.726 37.037 0.00 0.00 0.00 3.46
749 763 8.561536 TTACCATGAGAATTACCTATCTTCCA 57.438 34.615 0.00 0.00 0.00 3.53
752 766 8.506083 ACCATGAGAATTACCTATCTTCCATTT 58.494 33.333 0.00 0.00 0.00 2.32
798 812 4.154195 CAGAATCCGTAGTTTGGAAGTTGG 59.846 45.833 0.00 0.00 39.39 3.77
888 908 3.930634 ACCTTCAATTGCTCTTTCTGC 57.069 42.857 0.00 0.00 0.00 4.26
939 959 1.392510 GCTCATCGGGTTTCGTAACAC 59.607 52.381 7.25 1.89 40.32 3.32
947 967 2.553685 GGGTTTCGTAACACCTTCCCAT 60.554 50.000 7.25 0.00 35.92 4.00
987 1007 6.683110 GCTTTCTATCTAACGTGGAAGATGGA 60.683 42.308 14.09 14.09 37.78 3.41
991 1011 3.698289 TCTAACGTGGAAGATGGAGTCT 58.302 45.455 0.00 0.00 39.43 3.24
1040 1060 1.248486 TTCTCGCACTCTAGCACAGT 58.752 50.000 0.00 0.00 0.00 3.55
1112 1132 2.414481 CCATGTCTCGCAACTTGAAGAG 59.586 50.000 0.00 7.85 0.00 2.85
1174 1194 1.869754 CGCTGATCGGTGATTACCCTG 60.870 57.143 9.63 0.00 44.53 4.45
1175 1195 1.871080 CTGATCGGTGATTACCCTGC 58.129 55.000 0.22 0.00 44.53 4.85
1260 1280 4.131596 GGTTTGTACTGCCTGTTCAACTA 58.868 43.478 0.00 0.00 36.04 2.24
1443 1463 1.994463 GAGTTCCTCCAGCCCATGT 59.006 57.895 0.00 0.00 0.00 3.21
1446 1466 1.204146 GTTCCTCCAGCCCATGTCTA 58.796 55.000 0.00 0.00 0.00 2.59
1488 1508 1.829970 GCAGCAAAGGGATAGGGGC 60.830 63.158 0.00 0.00 0.00 5.80
1489 1509 1.614711 CAGCAAAGGGATAGGGGCA 59.385 57.895 0.00 0.00 0.00 5.36
1509 1529 5.475564 GGGCAGTCCAATTGAAGTTTTAGTA 59.524 40.000 7.12 0.00 35.00 1.82
1920 1940 0.388649 GTGATCCGCGAACTGTCAGT 60.389 55.000 8.23 0.00 0.00 3.41
2287 2307 1.271217 GCATGGAGCTGCCTATGATCA 60.271 52.381 9.37 0.00 41.15 2.92
2652 2672 5.486775 AGAAGAGGAAGATGACATTCAGGAA 59.513 40.000 0.00 0.00 0.00 3.36
2908 2928 2.114670 GCCGACATGGGTGTGGATG 61.115 63.158 0.00 0.00 39.09 3.51
3068 3120 4.706842 AGTCAGTTTGGTCAAGGTATGT 57.293 40.909 0.00 0.00 0.00 2.29
3108 3160 5.206905 AGCCATCCTTTACAATAGGGTTT 57.793 39.130 0.00 0.00 33.41 3.27
3182 3234 7.554959 TCCTGTACATAGTTTTCCTTCTTCT 57.445 36.000 0.00 0.00 0.00 2.85
3525 3577 5.265191 TCTTCTGTCTCTGCTAGGTTATGT 58.735 41.667 0.00 0.00 0.00 2.29
3593 3645 6.828273 ACATAAGGTCAGCATGCAGTTTAATA 59.172 34.615 21.98 5.03 34.76 0.98
3594 3646 7.339212 ACATAAGGTCAGCATGCAGTTTAATAA 59.661 33.333 21.98 0.00 34.76 1.40
3701 3753 1.275291 TCCTGCCAAACTCTACCTTCG 59.725 52.381 0.00 0.00 0.00 3.79
3758 3810 4.937201 CCTTCAAAGGCCAAAACTAACT 57.063 40.909 5.01 0.00 39.76 2.24
3759 3811 4.620982 CCTTCAAAGGCCAAAACTAACTG 58.379 43.478 5.01 0.00 39.76 3.16
3760 3812 4.340950 CCTTCAAAGGCCAAAACTAACTGA 59.659 41.667 5.01 0.00 39.76 3.41
3761 3813 5.011023 CCTTCAAAGGCCAAAACTAACTGAT 59.989 40.000 5.01 0.00 39.76 2.90
3762 3814 5.452078 TCAAAGGCCAAAACTAACTGATG 57.548 39.130 5.01 0.00 0.00 3.07
3763 3815 5.136828 TCAAAGGCCAAAACTAACTGATGA 58.863 37.500 5.01 0.00 0.00 2.92
3764 3816 5.774690 TCAAAGGCCAAAACTAACTGATGAT 59.225 36.000 5.01 0.00 0.00 2.45
3765 3817 6.267471 TCAAAGGCCAAAACTAACTGATGATT 59.733 34.615 5.01 0.00 0.00 2.57
3766 3818 7.450014 TCAAAGGCCAAAACTAACTGATGATTA 59.550 33.333 5.01 0.00 0.00 1.75
3767 3819 7.396540 AAGGCCAAAACTAACTGATGATTAG 57.603 36.000 5.01 0.00 36.01 1.73
3768 3820 6.721318 AGGCCAAAACTAACTGATGATTAGA 58.279 36.000 5.01 0.00 34.36 2.10
3769 3821 6.599638 AGGCCAAAACTAACTGATGATTAGAC 59.400 38.462 5.01 0.00 34.36 2.59
3770 3822 6.374333 GGCCAAAACTAACTGATGATTAGACA 59.626 38.462 0.00 0.00 34.36 3.41
3771 3823 7.244192 GCCAAAACTAACTGATGATTAGACAC 58.756 38.462 0.00 0.00 34.36 3.67
3772 3824 7.626452 GCCAAAACTAACTGATGATTAGACACC 60.626 40.741 0.00 0.00 34.36 4.16
3773 3825 7.607991 CCAAAACTAACTGATGATTAGACACCT 59.392 37.037 0.00 0.00 34.36 4.00
3774 3826 9.003658 CAAAACTAACTGATGATTAGACACCTT 57.996 33.333 0.00 0.00 34.36 3.50
3775 3827 8.779354 AAACTAACTGATGATTAGACACCTTC 57.221 34.615 0.00 0.00 34.36 3.46
3776 3828 7.482169 ACTAACTGATGATTAGACACCTTCA 57.518 36.000 0.00 0.00 34.36 3.02
3777 3829 7.907389 ACTAACTGATGATTAGACACCTTCAA 58.093 34.615 0.00 0.00 34.36 2.69
3778 3830 8.375506 ACTAACTGATGATTAGACACCTTCAAA 58.624 33.333 0.00 0.00 34.36 2.69
3779 3831 7.678947 AACTGATGATTAGACACCTTCAAAG 57.321 36.000 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 0.802494 ACGCGTAAGGAAAGGCATTG 59.198 50.000 11.67 0.00 38.28 2.82
147 148 1.150567 GGCACAGTAGATCAGCTGCG 61.151 60.000 9.47 7.92 36.26 5.18
343 353 3.682718 GCCAGCAGCTTAATTACCTCTCA 60.683 47.826 0.00 0.00 38.99 3.27
381 391 0.243636 CAAACCCAAAGCCCACGATC 59.756 55.000 0.00 0.00 0.00 3.69
494 505 1.208165 GGTGTCCCCCATTCACTCCT 61.208 60.000 0.00 0.00 33.30 3.69
503 514 1.537889 AGATTCGTGGTGTCCCCCA 60.538 57.895 0.00 0.00 0.00 4.96
512 523 4.931601 TCAGTTTCATTCAGAGATTCGTGG 59.068 41.667 0.00 0.00 0.00 4.94
564 575 6.503589 AGCCTCGTACAGAAGATATGATAC 57.496 41.667 0.00 0.00 0.00 2.24
699 713 9.802039 AAACTCAACTACCCAGTTAATGAAATA 57.198 29.630 0.00 0.00 43.30 1.40
700 714 8.706322 AAACTCAACTACCCAGTTAATGAAAT 57.294 30.769 0.00 0.00 43.30 2.17
701 715 9.059260 GTAAACTCAACTACCCAGTTAATGAAA 57.941 33.333 0.00 0.00 43.30 2.69
759 773 6.929606 ACGGATTCTGGCTCTGTAATAAATAC 59.070 38.462 0.00 0.00 30.46 1.89
775 789 4.154195 CCAACTTCCAAACTACGGATTCTG 59.846 45.833 0.00 0.00 30.99 3.02
782 796 4.994852 TCTTCATCCAACTTCCAAACTACG 59.005 41.667 0.00 0.00 0.00 3.51
872 891 4.053295 GCAAAAGCAGAAAGAGCAATTGA 58.947 39.130 10.34 0.00 34.06 2.57
888 908 8.139989 CCTTTGGATAATAAGATCCTGCAAAAG 58.860 37.037 4.19 5.38 45.07 2.27
987 1007 2.089980 GCAATCATCAGGCAACAGACT 58.910 47.619 0.00 0.00 33.58 3.24
991 1011 2.368439 GGTAGCAATCATCAGGCAACA 58.632 47.619 0.00 0.00 41.41 3.33
1040 1060 4.321452 GCCTTTCAAATTCTGCAGATGACA 60.321 41.667 19.04 10.60 0.00 3.58
1112 1132 1.997874 ATCTGGGTCTGGACAGGGC 60.998 63.158 3.10 0.00 35.47 5.19
1133 1153 0.520847 GCTGCTCAAGGCTGAAACTC 59.479 55.000 0.00 0.00 41.52 3.01
1155 1175 1.871080 CAGGGTAATCACCGATCAGC 58.129 55.000 0.00 0.00 46.86 4.26
1174 1194 1.087501 CCCTCGCTTCTAGTTTTGGC 58.912 55.000 0.00 0.00 0.00 4.52
1175 1195 1.278127 TCCCCTCGCTTCTAGTTTTGG 59.722 52.381 0.00 0.00 0.00 3.28
1260 1280 2.030185 GTGTACACTGTCACCACGATCT 60.030 50.000 18.92 0.00 0.00 2.75
1443 1463 5.710646 AGATCCTTGCTTGTAGGAGATAGA 58.289 41.667 0.00 0.00 44.63 1.98
1446 1466 3.645687 GGAGATCCTTGCTTGTAGGAGAT 59.354 47.826 0.00 0.00 44.63 2.75
1488 1508 8.237267 GGACATACTAAAACTTCAATTGGACTG 58.763 37.037 5.42 0.00 0.00 3.51
1489 1509 7.942341 TGGACATACTAAAACTTCAATTGGACT 59.058 33.333 5.42 0.00 0.00 3.85
1509 1529 1.304381 AATGCAGCGGGTTGGACAT 60.304 52.632 0.00 0.00 0.00 3.06
1920 1940 4.592942 ACTGCTGAAATGAGGCAATCTTA 58.407 39.130 0.00 0.00 35.49 2.10
2652 2672 3.430042 TCTGCATTGCTTTCTTCCTCT 57.570 42.857 10.49 0.00 0.00 3.69
2889 2909 2.601702 ATCCACACCCATGTCGGCA 61.602 57.895 0.00 0.00 36.72 5.69
2908 2928 2.037847 AAGGAACAGGCCCCATGC 59.962 61.111 0.00 0.00 40.16 4.06
3108 3160 1.016627 GCAGGCATATTCAACGCTCA 58.983 50.000 0.00 0.00 0.00 4.26
3525 3577 8.845227 TGAACTAGACAATAAATTTCACAGCAA 58.155 29.630 0.00 0.00 0.00 3.91
3593 3645 4.569719 AGTGTAAATCGATGAAGGGGTT 57.430 40.909 0.00 0.00 0.00 4.11
3594 3646 4.569719 AAGTGTAAATCGATGAAGGGGT 57.430 40.909 0.00 0.00 0.00 4.95
3701 3753 7.947890 TGGGTTGGAATAGATGTAAATAATCCC 59.052 37.037 0.00 0.00 0.00 3.85
3755 3807 6.656693 CCTTTGAAGGTGTCTAATCATCAGTT 59.343 38.462 1.49 0.00 41.41 3.16
3756 3808 6.176183 CCTTTGAAGGTGTCTAATCATCAGT 58.824 40.000 1.49 0.00 41.41 3.41
3757 3809 6.674694 CCTTTGAAGGTGTCTAATCATCAG 57.325 41.667 1.49 0.00 41.41 2.90
3772 3824 5.514274 TCAGTTAGTTTTGGCCTTTGAAG 57.486 39.130 3.32 0.00 0.00 3.02
3773 3825 5.596361 TCATCAGTTAGTTTTGGCCTTTGAA 59.404 36.000 3.32 0.00 0.00 2.69
3774 3826 5.136828 TCATCAGTTAGTTTTGGCCTTTGA 58.863 37.500 3.32 0.00 0.00 2.69
3775 3827 5.452078 TCATCAGTTAGTTTTGGCCTTTG 57.548 39.130 3.32 0.00 0.00 2.77
3776 3828 6.670695 AATCATCAGTTAGTTTTGGCCTTT 57.329 33.333 3.32 0.00 0.00 3.11
3777 3829 6.267471 TGAAATCATCAGTTAGTTTTGGCCTT 59.733 34.615 3.32 0.00 33.04 4.35
3778 3830 5.774690 TGAAATCATCAGTTAGTTTTGGCCT 59.225 36.000 3.32 0.00 33.04 5.19
3779 3831 6.024552 TGAAATCATCAGTTAGTTTTGGCC 57.975 37.500 0.00 0.00 33.04 5.36
3818 3870 0.684805 CCGGTAGGAGCCTGAAGTCT 60.685 60.000 0.00 0.00 41.02 3.24


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

AutoCloner maintained by Alex Coulton.