Multiple sequence alignment - TraesCS2D01G511000

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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 TraesCS2D01G511000 chr2D 100.000 2978 0 0 1 2978 602696291 602699268 0.000000e+00 5500.0
1 TraesCS2D01G511000 chr2D 86.813 91 9 2 1507 1594 601971218 601971128 6.790000e-17 99.0
2 TraesCS2D01G511000 chr2D 85.714 91 10 2 1507 1594 602729580 602729670 3.160000e-15 93.5
3 TraesCS2D01G511000 chr2D 91.935 62 5 0 1883 1944 601970848 601970787 1.470000e-13 87.9
4 TraesCS2D01G511000 chr2D 91.935 62 5 0 1883 1944 602729950 602730011 1.470000e-13 87.9
5 TraesCS2D01G511000 chr2B 93.480 2592 122 20 421 2978 733062245 733064823 0.000000e+00 3807.0
6 TraesCS2D01G511000 chr2B 86.067 445 30 8 1 438 733061808 733062227 1.630000e-122 449.0
7 TraesCS2D01G511000 chr2B 85.714 91 10 2 1507 1594 732056610 732056520 3.160000e-15 93.5
8 TraesCS2D01G511000 chr2B 82.418 91 13 2 1507 1594 733104297 733104387 3.180000e-10 76.8
9 TraesCS2D01G511000 chr2A 94.155 2224 96 16 299 2514 735329320 735331517 0.000000e+00 3356.0
10 TraesCS2D01G511000 chr2A 92.537 469 26 5 2516 2978 735331668 735332133 0.000000e+00 664.0
11 TraesCS2D01G511000 chr2A 85.526 532 37 18 1 504 735328137 735328656 1.220000e-143 520.0
12 TraesCS2D01G511000 chr2A 93.237 207 13 1 299 504 735328896 735329102 1.340000e-78 303.0
13 TraesCS2D01G511000 chr2A 91.414 198 17 0 110 307 735328649 735328846 3.780000e-69 272.0
14 TraesCS2D01G511000 chr2A 90.909 198 18 0 110 307 735329095 735329292 1.760000e-67 267.0
15 TraesCS2D01G511000 chr1B 93.814 97 6 0 2880 2976 117385726 117385822 2.390000e-31 147.0
16 TraesCS2D01G511000 chr6D 81.452 124 14 7 2397 2514 177792723 177792843 3.160000e-15 93.5
17 TraesCS2D01G511000 chr5D 79.798 99 9 6 2493 2582 160068124 160068220 8.910000e-06 62.1


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 TraesCS2D01G511000 chr2D 602696291 602699268 2977 False 5500 5500 100.000000 1 2978 1 chr2D.!!$F1 2977
1 TraesCS2D01G511000 chr2B 733061808 733064823 3015 False 2128 3807 89.773500 1 2978 2 chr2B.!!$F2 2977
2 TraesCS2D01G511000 chr2A 735328137 735332133 3996 False 897 3356 91.296333 1 2978 6 chr2A.!!$F1 2977

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
288 706 0.446222 GGACACACACACACACACAC 59.554 55.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 3055 0.749454 GCACCACTGGATCCATCACC 60.749 60.0 16.63 0.0 0.0 4.02 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 64 2.047844 CACACCGAGTCAGCCCTG 60.048 66.667 0.00 0.00 0.00 4.45
83 85 3.706373 GGCAGCCCTCGGAGTCAA 61.706 66.667 0.00 0.00 0.00 3.18
163 165 2.552367 GAGGAAAGAGGGAGGAAGGAA 58.448 52.381 0.00 0.00 0.00 3.36
164 166 2.503765 GAGGAAAGAGGGAGGAAGGAAG 59.496 54.545 0.00 0.00 0.00 3.46
165 167 2.114506 AGGAAAGAGGGAGGAAGGAAGA 59.885 50.000 0.00 0.00 0.00 2.87
166 168 2.503765 GGAAAGAGGGAGGAAGGAAGAG 59.496 54.545 0.00 0.00 0.00 2.85
167 169 2.262266 AAGAGGGAGGAAGGAAGAGG 57.738 55.000 0.00 0.00 0.00 3.69
168 170 1.398799 AGAGGGAGGAAGGAAGAGGA 58.601 55.000 0.00 0.00 0.00 3.71
169 171 1.725182 AGAGGGAGGAAGGAAGAGGAA 59.275 52.381 0.00 0.00 0.00 3.36
170 172 2.115427 GAGGGAGGAAGGAAGAGGAAG 58.885 57.143 0.00 0.00 0.00 3.46
171 173 1.208706 GGGAGGAAGGAAGAGGAAGG 58.791 60.000 0.00 0.00 0.00 3.46
172 174 1.273896 GGGAGGAAGGAAGAGGAAGGA 60.274 57.143 0.00 0.00 0.00 3.36
191 193 3.286751 TGCCTTGCAACCACGAGC 61.287 61.111 0.00 0.00 34.76 5.03
232 234 2.197875 GGGAGGCGGGTAGAGCTA 59.802 66.667 0.00 0.00 34.52 3.32
284 702 1.762222 GAGCGGACACACACACACAC 61.762 60.000 0.00 0.00 0.00 3.82
286 704 1.713246 CGGACACACACACACACAC 59.287 57.895 0.00 0.00 0.00 3.82
288 706 0.446222 GGACACACACACACACACAC 59.554 55.000 0.00 0.00 0.00 3.82
290 708 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
292 710 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
294 712 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
296 714 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
329 803 1.202440 ACGACTAGTCAAAACCGTGCA 60.202 47.619 22.37 0.00 0.00 4.57
521 1420 5.353938 TGTAAACACCTGTGTCAAGTCTAC 58.646 41.667 2.98 1.08 44.13 2.59
539 1438 8.553459 AAGTCTACAACTTGAATCCTAATGTG 57.447 34.615 0.00 0.00 46.61 3.21
548 1447 4.006989 TGAATCCTAATGTGTTGGTTCCG 58.993 43.478 0.00 0.00 0.00 4.30
672 1573 5.767269 TGCAGAGCAATTTATTTCGTTCAA 58.233 33.333 0.00 0.00 34.76 2.69
673 1574 6.212235 TGCAGAGCAATTTATTTCGTTCAAA 58.788 32.000 0.00 0.00 34.76 2.69
674 1575 6.867816 TGCAGAGCAATTTATTTCGTTCAAAT 59.132 30.769 0.00 0.00 35.60 2.32
740 1643 7.867909 TCGAAACAAGCTAATGTATCCTATGAG 59.132 37.037 0.00 0.00 32.02 2.90
748 1651 3.969287 TGTATCCTATGAGCAGCATCC 57.031 47.619 0.00 0.00 38.44 3.51
790 1693 7.662669 CCATCCATCTCCAAAGAAAACAAAAAT 59.337 33.333 0.00 0.00 34.49 1.82
791 1694 8.500773 CATCCATCTCCAAAGAAAACAAAAATG 58.499 33.333 0.00 0.00 34.49 2.32
792 1695 6.482973 TCCATCTCCAAAGAAAACAAAAATGC 59.517 34.615 0.00 0.00 34.49 3.56
793 1696 6.260493 CCATCTCCAAAGAAAACAAAAATGCA 59.740 34.615 0.00 0.00 34.49 3.96
794 1697 7.040961 CCATCTCCAAAGAAAACAAAAATGCAT 60.041 33.333 0.00 0.00 34.49 3.96
795 1698 7.862512 TCTCCAAAGAAAACAAAAATGCATT 57.137 28.000 5.99 5.99 0.00 3.56
796 1699 7.918643 TCTCCAAAGAAAACAAAAATGCATTC 58.081 30.769 13.38 0.00 0.00 2.67
797 1700 7.551974 TCTCCAAAGAAAACAAAAATGCATTCA 59.448 29.630 13.38 0.00 0.00 2.57
798 1701 8.048534 TCCAAAGAAAACAAAAATGCATTCAA 57.951 26.923 13.38 0.00 0.00 2.69
799 1702 8.517878 TCCAAAGAAAACAAAAATGCATTCAAA 58.482 25.926 13.38 0.00 0.00 2.69
800 1703 9.136952 CCAAAGAAAACAAAAATGCATTCAAAA 57.863 25.926 13.38 0.00 0.00 2.44
1008 1915 1.892329 GCCACCAATCCAATGGACACT 60.892 52.381 3.09 0.00 43.54 3.55
1086 1993 3.628646 GATCGCCCTGCCTGGTTGT 62.629 63.158 0.00 0.00 0.00 3.32
1119 2026 0.104304 GCGACATCACCGTTCCCTAT 59.896 55.000 0.00 0.00 0.00 2.57
1166 2073 2.586792 GCAGGGCTTCGACCTCAT 59.413 61.111 0.00 0.00 35.03 2.90
1302 2209 3.388703 GAGCTCCCTCCAGCAGCTG 62.389 68.421 16.23 16.23 43.72 4.24
1637 2544 1.211969 CACTACTAGTGCACGCGGT 59.788 57.895 12.47 13.56 39.62 5.68
1818 2725 1.752198 CGGTGTCTCCCAGTGGAAA 59.248 57.895 11.95 0.00 41.17 3.13
1843 2750 2.088763 ATCAGCGTGAACAGCGTCG 61.089 57.895 0.00 0.00 40.04 5.12
1879 2786 4.518590 TCAATGGAAATGCTTTCGACAGAA 59.481 37.500 1.94 0.00 40.57 3.02
1902 2809 0.250467 GGTGCAACTGCTCAAGAGGA 60.250 55.000 0.00 0.00 42.66 3.71
1947 2854 0.846693 ATGGATGCCAAGGTACCCTC 59.153 55.000 8.74 0.00 36.95 4.30
2013 2921 3.449746 TCATGGTACCTTTTTCCCCAG 57.550 47.619 14.36 0.00 0.00 4.45
2143 3055 5.040635 GCCAATATTATGGGTTTGACAACG 58.959 41.667 0.00 0.00 41.01 4.10
2147 3059 2.932855 TATGGGTTTGACAACGGTGA 57.067 45.000 7.88 0.00 33.13 4.02
2333 3246 2.361610 CAAGCCAAGGTCCGCCAT 60.362 61.111 0.00 0.00 37.19 4.40
2335 3248 0.679640 CAAGCCAAGGTCCGCCATTA 60.680 55.000 0.00 0.00 37.19 1.90
2456 3369 7.560368 TGTAAACTTTGACCAAATTTGTGGAT 58.440 30.769 16.73 0.00 41.65 3.41
2713 3776 9.453572 AAGATCTTGTAAATGAAGCAGACAATA 57.546 29.630 7.30 0.00 30.16 1.90
2734 3797 4.838959 CCGTTCATTGCGGTTCAC 57.161 55.556 0.00 0.00 43.84 3.18
2741 3804 1.167851 CATTGCGGTTCACTGGACAT 58.832 50.000 0.00 0.00 0.00 3.06
2800 3868 7.917730 ATGAATGGATTACATGGGAATTTGA 57.082 32.000 0.00 0.00 40.44 2.69
2806 3874 2.629017 ACATGGGAATTTGAAGGCCT 57.371 45.000 0.00 0.00 0.00 5.19
2840 3908 2.017049 CAAAGGGCTTCCATAGGAACG 58.983 52.381 0.00 0.00 36.71 3.95
2858 3926 4.329392 GAACGGGTTCCTAGGATTCAAAA 58.671 43.478 13.57 0.00 33.64 2.44
2860 3928 3.014623 CGGGTTCCTAGGATTCAAAACC 58.985 50.000 13.57 15.52 36.31 3.27
2907 3976 0.613777 ACCAAAGAGGCCCTTAGACG 59.386 55.000 0.00 0.00 43.14 4.18
2913 3982 2.180159 GAGGCCCTTAGACGCAACCA 62.180 60.000 0.00 0.00 0.00 3.67
2964 4033 3.366883 GCAATTTGCCGTATGAAGAACCA 60.367 43.478 10.34 0.00 37.42 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.196766 TGTCAGCAGTCCAGCTCCAT 61.197 55.000 0.00 0.00 44.54 3.41
10 11 1.196766 ATGTCAGCAGTCCAGCTCCA 61.197 55.000 0.00 0.00 44.54 3.86
12 14 1.367599 GCATGTCAGCAGTCCAGCTC 61.368 60.000 0.00 0.00 44.54 4.09
15 17 4.707791 TGCATGTCAGCAGTCCAG 57.292 55.556 0.00 0.00 40.11 3.86
83 85 4.373116 ATGTCGCTGCGGTCGGTT 62.373 61.111 23.03 0.00 0.00 4.44
170 172 2.908073 CGTGGTTGCAAGGCACTCC 61.908 63.158 0.00 0.00 38.49 3.85
171 173 1.845809 CTCGTGGTTGCAAGGCACTC 61.846 60.000 0.00 0.00 38.49 3.51
191 193 3.474806 GTCATTGTCGACGCCTGG 58.525 61.111 11.62 0.00 0.00 4.45
261 677 3.106407 GTGTGTGTCCGCTCGAGC 61.106 66.667 27.64 27.64 37.78 5.03
284 702 2.099756 TCTCTCTCTGTGTGTGTGTGTG 59.900 50.000 0.00 0.00 0.00 3.82
286 704 2.861750 GCTCTCTCTCTGTGTGTGTGTG 60.862 54.545 0.00 0.00 0.00 3.82
288 706 1.339291 TGCTCTCTCTCTGTGTGTGTG 59.661 52.381 0.00 0.00 0.00 3.82
290 708 2.402305 GTTGCTCTCTCTCTGTGTGTG 58.598 52.381 0.00 0.00 0.00 3.82
292 710 1.268079 TCGTTGCTCTCTCTCTGTGTG 59.732 52.381 0.00 0.00 0.00 3.82
294 712 1.539388 AGTCGTTGCTCTCTCTCTGTG 59.461 52.381 0.00 0.00 0.00 3.66
296 714 3.006940 ACTAGTCGTTGCTCTCTCTCTG 58.993 50.000 0.00 0.00 0.00 3.35
329 803 1.153249 CGTGGTTCCGCATGGGTAT 60.153 57.895 9.14 0.00 37.00 2.73
348 822 3.728076 TTCTTCCCTCGACGAATATGG 57.272 47.619 0.00 0.00 0.00 2.74
493 1391 6.930731 ACTTGACACAGGTGTTTACATTTTT 58.069 32.000 6.51 0.00 45.05 1.94
503 1402 3.451178 AGTTGTAGACTTGACACAGGTGT 59.549 43.478 4.46 4.46 40.47 4.16
521 1420 6.331369 ACCAACACATTAGGATTCAAGTTG 57.669 37.500 0.00 0.00 35.97 3.16
531 1430 2.773487 TGTCGGAACCAACACATTAGG 58.227 47.619 0.00 0.00 0.00 2.69
672 1573 4.923893 TCGTGTCAACCGTCGAATATATT 58.076 39.130 0.00 0.00 0.00 1.28
673 1574 4.556942 TCGTGTCAACCGTCGAATATAT 57.443 40.909 0.00 0.00 0.00 0.86
674 1575 4.556942 ATCGTGTCAACCGTCGAATATA 57.443 40.909 0.00 0.00 35.99 0.86
740 1643 3.032609 CGATCGACGGGATGCTGC 61.033 66.667 10.26 0.00 34.82 5.25
790 1693 6.566942 GCAGCTGATTTGAAATTTTGAATGCA 60.567 34.615 20.43 0.00 0.00 3.96
791 1694 5.793457 GCAGCTGATTTGAAATTTTGAATGC 59.207 36.000 20.43 0.00 0.00 3.56
792 1695 6.013085 CGCAGCTGATTTGAAATTTTGAATG 58.987 36.000 20.43 0.00 0.00 2.67
793 1696 5.927689 TCGCAGCTGATTTGAAATTTTGAAT 59.072 32.000 20.43 0.00 0.00 2.57
794 1697 5.288015 TCGCAGCTGATTTGAAATTTTGAA 58.712 33.333 20.43 0.00 0.00 2.69
795 1698 4.869215 TCGCAGCTGATTTGAAATTTTGA 58.131 34.783 20.43 0.00 0.00 2.69
796 1699 4.682860 ACTCGCAGCTGATTTGAAATTTTG 59.317 37.500 20.43 0.00 0.00 2.44
797 1700 4.874970 ACTCGCAGCTGATTTGAAATTTT 58.125 34.783 20.43 0.00 0.00 1.82
798 1701 4.217118 AGACTCGCAGCTGATTTGAAATTT 59.783 37.500 20.43 0.00 0.00 1.82
799 1702 3.755378 AGACTCGCAGCTGATTTGAAATT 59.245 39.130 20.43 0.00 0.00 1.82
800 1703 3.341823 AGACTCGCAGCTGATTTGAAAT 58.658 40.909 20.43 0.00 0.00 2.17
801 1704 2.771089 AGACTCGCAGCTGATTTGAAA 58.229 42.857 20.43 0.00 0.00 2.69
802 1705 2.462456 AGACTCGCAGCTGATTTGAA 57.538 45.000 20.43 0.00 0.00 2.69
803 1706 3.592898 TTAGACTCGCAGCTGATTTGA 57.407 42.857 20.43 8.03 0.00 2.69
809 1712 4.266502 GTGTTTAGATTAGACTCGCAGCTG 59.733 45.833 10.11 10.11 0.00 4.24
853 1760 2.939103 GAGGTGACATTTGGAATCTCGG 59.061 50.000 0.00 0.00 0.00 4.63
1008 1915 2.557805 GACACGACCGCGACAGTA 59.442 61.111 8.23 0.00 41.64 2.74
1075 1982 2.046892 CTCCGGACAACCAGGCAG 60.047 66.667 0.00 0.00 35.59 4.85
1113 2020 1.415672 GGGTGCCGAATGGATAGGGA 61.416 60.000 0.00 0.00 37.49 4.20
1149 2056 1.522580 GATGAGGTCGAAGCCCTGC 60.523 63.158 0.00 0.00 0.00 4.85
1188 2095 2.677875 CCCAGGGACAGCTTTGGC 60.678 66.667 0.00 0.00 39.06 4.52
1818 2725 1.736126 CTGTTCACGCTGATGCATCTT 59.264 47.619 26.32 6.56 39.64 2.40
1879 2786 1.439353 CTTGAGCAGTTGCACCGTGT 61.439 55.000 6.90 0.00 45.16 4.49
2143 3055 0.749454 GCACCACTGGATCCATCACC 60.749 60.000 16.63 0.00 0.00 4.02
2147 3059 2.300967 ACGGCACCACTGGATCCAT 61.301 57.895 16.63 2.66 0.00 3.41
2322 3235 5.304686 TCTATCAAATAATGGCGGACCTT 57.695 39.130 0.00 0.00 36.63 3.50
2550 3612 3.247173 TGTGCATTGGTTTTCGCAAAATC 59.753 39.130 0.00 0.00 35.87 2.17
2551 3613 3.002144 GTGTGCATTGGTTTTCGCAAAAT 59.998 39.130 0.00 0.00 35.87 1.82
2590 3652 9.712305 TGGCTGATAGCTTAAAAATATACTCTC 57.288 33.333 0.00 0.00 41.99 3.20
2741 3804 3.172339 CCTGGGAATTTCAACCATTGGA 58.828 45.455 10.37 0.00 33.07 3.53
2800 3868 1.342374 GGACCATTGGATTGAGGCCTT 60.342 52.381 6.77 0.00 0.00 4.35
2806 3874 2.818921 CCCTTTGGACCATTGGATTGA 58.181 47.619 10.37 0.00 0.00 2.57
2840 3908 4.270834 GAGGTTTTGAATCCTAGGAACCC 58.729 47.826 17.30 8.44 37.77 4.11
2878 3946 4.086457 GGGCCTCTTTGGTTTGAAAGATA 58.914 43.478 0.84 0.00 40.38 1.98
2907 3976 3.667360 AGATTTTCTTGCCAATGGTTGC 58.333 40.909 0.00 0.00 0.00 4.17
2913 3982 5.106157 CCGTGTTCTAGATTTTCTTGCCAAT 60.106 40.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.