Multiple sequence alignment - TraesCS2D01G201900

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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 TraesCS2D01G201900 chr2D 100.000 3914 0 0 1 3914 153804614 153808527 0.000000e+00 7228.0
1 TraesCS2D01G201900 chr2D 84.783 138 12 8 3578 3711 28968373 28968241 3.170000e-26 130.0
2 TraesCS2D01G201900 chr2D 80.925 173 22 10 3545 3711 27972922 27973089 4.110000e-25 126.0
3 TraesCS2D01G201900 chr2A 93.937 3645 137 29 2 3576 147464190 147460560 0.000000e+00 5430.0
4 TraesCS2D01G201900 chr2A 92.058 277 22 0 3636 3912 147460425 147460149 1.320000e-104 390.0
5 TraesCS2D01G201900 chr2A 89.349 169 11 2 5 172 640274201 640274363 5.130000e-49 206.0
6 TraesCS2D01G201900 chr2A 92.553 94 7 0 3569 3662 147460533 147460440 6.820000e-28 135.0
7 TraesCS2D01G201900 chr2A 82.270 141 16 8 3441 3576 279056120 279056256 3.200000e-21 113.0
8 TraesCS2D01G201900 chr2B 92.731 2091 101 12 1859 3914 211378034 211380108 0.000000e+00 2972.0
9 TraesCS2D01G201900 chr2B 90.904 1693 94 25 172 1831 211376382 211378047 0.000000e+00 2218.0
10 TraesCS2D01G201900 chr7B 91.228 171 10 5 5 172 429191979 429192147 1.090000e-55 228.0
11 TraesCS2D01G201900 chr7B 85.612 139 19 1 3574 3711 715716986 715716848 1.130000e-30 145.0
12 TraesCS2D01G201900 chr4A 87.791 172 19 2 3 172 75927038 75927209 2.390000e-47 200.0
13 TraesCS2D01G201900 chr4A 82.963 135 21 2 3578 3711 656709966 656709833 1.910000e-23 121.0
14 TraesCS2D01G201900 chr4A 85.437 103 11 3 3441 3540 539749848 539749747 1.920000e-18 104.0
15 TraesCS2D01G201900 chr4A 79.433 141 21 7 3441 3576 176859818 176859955 4.160000e-15 93.5
16 TraesCS2D01G201900 chr1D 85.465 172 21 4 5 172 452644526 452644355 4.020000e-40 176.0
17 TraesCS2D01G201900 chr3B 84.722 144 20 2 3569 3711 507288502 507288360 4.080000e-30 143.0
18 TraesCS2D01G201900 chr3A 83.824 136 15 6 3579 3710 416138713 416138581 5.310000e-24 122.0
19 TraesCS2D01G201900 chr3A 82.143 140 18 6 3441 3576 102531187 102531051 3.200000e-21 113.0
20 TraesCS2D01G201900 chr1B 83.088 136 21 2 3574 3708 555630360 555630226 5.310000e-24 122.0
21 TraesCS2D01G201900 chr7A 81.429 140 19 6 3441 3576 243645596 243645732 1.490000e-19 108.0
22 TraesCS2D01G201900 chr5A 79.286 140 21 7 3442 3576 647108594 647108458 1.500000e-14 91.6
23 TraesCS2D01G201900 chr4B 79.286 140 21 7 3442 3576 86136824 86136960 1.500000e-14 91.6


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 TraesCS2D01G201900 chr2D 153804614 153808527 3913 False 7228 7228 100.000000 1 3914 1 chr2D.!!$F2 3913
1 TraesCS2D01G201900 chr2A 147460149 147464190 4041 True 1985 5430 92.849333 2 3912 3 chr2A.!!$R1 3910
2 TraesCS2D01G201900 chr2B 211376382 211380108 3726 False 2595 2972 91.817500 172 3914 2 chr2B.!!$F1 3742

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
704 737 0.029834 AAACGTGTACTCGTCGCAGT 59.970 50.0 21.78 4.74 43.38 4.4 F
726 764 0.771127 ACCCGGCATACATAAGGCAT 59.229 50.0 0.00 0.00 0.00 4.4 F
1831 1888 0.742281 AGCTGACACGGCTGCTATTG 60.742 55.0 1.95 0.00 45.19 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 1854 0.602638 CCGTGTCAGCTTGCTTACCA 60.603 55.000 4.74 0.0 0.00 3.25 R
2388 2446 1.742880 CGTCTGCAGGATGGTGGTG 60.743 63.158 15.13 0.0 35.86 4.17 R
3803 3975 0.392060 AAAGCGGACATTCGGTACCC 60.392 55.000 6.25 0.0 40.11 3.69 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
60 62 7.696453 ACAAGAACGAAAATACAACTGTTTCAG 59.304 33.333 0.00 0.00 37.52 3.02
74 76 2.886523 TGTTTCAGCAACATTCAGGAGG 59.113 45.455 0.00 0.00 40.71 4.30
96 98 2.025699 AGAGGAAAGAGAGGTAGCGAGT 60.026 50.000 0.00 0.00 0.00 4.18
100 102 1.757682 AAGAGAGGTAGCGAGTCCAG 58.242 55.000 0.00 0.00 0.00 3.86
102 104 1.000771 AGAGGTAGCGAGTCCAGCA 60.001 57.895 0.00 0.00 37.01 4.41
116 118 1.656441 CAGCACACTGCCAGGAAAC 59.344 57.895 0.00 0.00 46.52 2.78
118 120 2.564721 GCACACTGCCAGGAAACCC 61.565 63.158 0.00 0.00 37.42 4.11
121 123 1.903404 CACTGCCAGGAAACCCACC 60.903 63.158 0.00 0.00 0.00 4.61
124 126 4.966787 GCCAGGAAACCCACCGCA 62.967 66.667 0.00 0.00 0.00 5.69
143 145 1.059369 CTTGCTCGCCATCGAAACG 59.941 57.895 0.00 0.00 44.98 3.60
186 188 1.202452 ACAGCAAAAGCACTCAAAGCC 60.202 47.619 0.00 0.00 0.00 4.35
376 392 4.151867 CAGCCGTGAAAGTAGTAAAAGACC 59.848 45.833 0.00 0.00 0.00 3.85
521 548 3.376859 CCTGTGACGGCATTAAAATAGCA 59.623 43.478 0.00 0.00 0.00 3.49
559 589 6.432162 TGTTCGCCTACGGATCTTATTATAGT 59.568 38.462 0.00 0.00 40.63 2.12
560 590 7.607607 TGTTCGCCTACGGATCTTATTATAGTA 59.392 37.037 0.00 0.00 40.63 1.82
593 623 2.165845 GGCCGTACACTGTCTGATTAGT 59.834 50.000 0.00 0.00 0.00 2.24
619 649 6.573664 TTACGTCTGCCTAAACTTGTACTA 57.426 37.500 0.00 0.00 0.00 1.82
621 651 3.858238 CGTCTGCCTAAACTTGTACTAGC 59.142 47.826 4.10 0.00 0.00 3.42
623 653 5.235516 GTCTGCCTAAACTTGTACTAGCAA 58.764 41.667 4.10 0.00 0.00 3.91
661 694 0.940126 GCAGCCATTCCACTACATCG 59.060 55.000 0.00 0.00 0.00 3.84
694 727 6.549912 AGAAACCCAATAGAAAACGTGTAC 57.450 37.500 0.00 0.00 0.00 2.90
697 730 4.240096 ACCCAATAGAAAACGTGTACTCG 58.760 43.478 15.29 15.29 0.00 4.18
702 735 1.122849 GAAAACGTGTACTCGTCGCA 58.877 50.000 21.78 0.00 43.38 5.10
704 737 0.029834 AAACGTGTACTCGTCGCAGT 59.970 50.000 21.78 4.74 43.38 4.40
708 741 1.526584 CGTGTACTCGTCGCAGTCTAC 60.527 57.143 9.11 2.67 0.00 2.59
726 764 0.771127 ACCCGGCATACATAAGGCAT 59.229 50.000 0.00 0.00 0.00 4.40
749 787 1.135489 CGCCGGCATCGTATATACAGT 60.135 52.381 28.98 0.00 33.95 3.55
772 810 4.112716 TGAGATAATACGCCACGAAACA 57.887 40.909 0.00 0.00 0.00 2.83
774 812 4.110482 GAGATAATACGCCACGAAACAGT 58.890 43.478 0.00 0.00 0.00 3.55
777 815 3.308438 AATACGCCACGAAACAGTAGT 57.692 42.857 0.00 0.00 0.00 2.73
894 938 3.807622 GCCGTTAATCACATAGCTAAGCA 59.192 43.478 0.00 0.00 0.00 3.91
898 942 5.005394 CGTTAATCACATAGCTAAGCAACGT 59.995 40.000 0.00 0.00 32.65 3.99
918 962 6.627690 ACGTCTTATATAAATCGAATGGCG 57.372 37.500 19.02 11.48 42.69 5.69
994 1042 1.079266 AGAGCAGCTCGAGCCAAAG 60.079 57.895 32.94 20.84 43.38 2.77
1012 1060 2.179018 CACAAATGGCGGCGAAGG 59.821 61.111 12.98 0.00 0.00 3.46
1149 1200 3.606662 GAGCCTCTCGCCGCCATA 61.607 66.667 0.00 0.00 38.78 2.74
1263 1314 1.144057 GAGGTACAGGCCCATCGTG 59.856 63.158 0.00 0.00 36.67 4.35
1444 1495 2.034066 CCATGCACGGGTTGGAGT 59.966 61.111 2.91 0.00 31.94 3.85
1536 1587 1.599797 GCCTTTGTACCAGCACCGT 60.600 57.895 0.00 0.00 0.00 4.83
1593 1644 2.202756 GTCGACATCCTGCGGACC 60.203 66.667 11.55 0.00 32.98 4.46
1596 1647 1.592669 CGACATCCTGCGGACCATC 60.593 63.158 0.00 0.00 32.98 3.51
1803 1854 3.518998 CCGGAGATCGACGCACCT 61.519 66.667 0.00 0.00 42.43 4.00
1831 1888 0.742281 AGCTGACACGGCTGCTATTG 60.742 55.000 1.95 0.00 45.19 1.90
1897 1955 1.312371 TTCGGCCCACTAAGCAATGC 61.312 55.000 0.00 0.00 0.00 3.56
1962 2020 2.555199 ACGAGCTAATCTGTTGCCATC 58.445 47.619 0.00 0.00 0.00 3.51
1963 2021 1.524355 CGAGCTAATCTGTTGCCATCG 59.476 52.381 0.00 0.00 0.00 3.84
2451 2509 4.457496 CTGATCGTGCAGGCCGGT 62.457 66.667 1.90 0.00 32.26 5.28
2634 2692 4.547905 ATCGCGTACGGGCTCACG 62.548 66.667 25.81 15.00 40.63 4.35
2910 2968 0.669318 GAATGTGCGACCTGGTTCGA 60.669 55.000 18.44 3.07 41.78 3.71
2988 3049 8.985315 TCTGAGCATTACCTTTCATTCATATT 57.015 30.769 0.00 0.00 0.00 1.28
2989 3050 8.843262 TCTGAGCATTACCTTTCATTCATATTG 58.157 33.333 0.00 0.00 0.00 1.90
3142 3224 1.806542 CAATGCGCAGTTGTACCTTCT 59.193 47.619 18.32 0.00 0.00 2.85
3153 3235 1.271163 TGTACCTTCTTCAAAGCCGGG 60.271 52.381 2.18 0.00 0.00 5.73
3155 3237 1.303643 CCTTCTTCAAAGCCGGGCT 60.304 57.895 17.69 17.69 42.56 5.19
3190 3272 3.319755 CATTCGCCAAATGAGTTGCTTT 58.680 40.909 1.12 0.00 46.54 3.51
3195 3277 3.317150 GCCAAATGAGTTGCTTTGTACC 58.683 45.455 0.00 0.00 35.74 3.34
3197 3279 3.252215 CCAAATGAGTTGCTTTGTACCGA 59.748 43.478 0.00 0.00 35.74 4.69
3244 3326 4.566360 CCAAGTTGTTTGTGTCAATCAACC 59.434 41.667 21.89 11.60 39.05 3.77
3260 3342 4.267349 TCAACCTCTACTTTTTCCTCCG 57.733 45.455 0.00 0.00 0.00 4.63
3274 3367 4.316025 TTCCTCCGGGAATTTCTTCATT 57.684 40.909 0.00 0.00 45.72 2.57
3360 3454 4.216042 TGTTGTGAATGAGATGCGTTTCAT 59.784 37.500 6.13 6.13 38.32 2.57
3664 3836 8.561738 TGTTTTGACCTTCTAATCCTATGTTC 57.438 34.615 0.00 0.00 0.00 3.18
3693 3865 4.310022 TCCCATGTTTTTAGAATCCCGT 57.690 40.909 0.00 0.00 0.00 5.28
3716 3888 2.014010 TCAAAGAGGCCCTTGCAATT 57.986 45.000 0.00 0.00 40.13 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.401239 GTTCTTGTAATGAAAAGGGGTAAGCCC 62.401 44.444 0.52 0.52 41.84 5.19
29 31 8.832521 ACAGTTGTATTTTCGTTCTTGTAATGA 58.167 29.630 0.00 0.00 0.00 2.57
57 59 2.235650 CTCTCCTCCTGAATGTTGCTGA 59.764 50.000 0.00 0.00 0.00 4.26
60 62 1.556911 TCCTCTCCTCCTGAATGTTGC 59.443 52.381 0.00 0.00 0.00 4.17
74 76 2.616842 CTCGCTACCTCTCTTTCCTCTC 59.383 54.545 0.00 0.00 0.00 3.20
96 98 1.993701 TTTCCTGGCAGTGTGCTGGA 61.994 55.000 14.43 0.00 44.28 3.86
100 102 2.564721 GGGTTTCCTGGCAGTGTGC 61.565 63.158 14.43 0.91 44.08 4.57
102 104 1.152756 GTGGGTTTCCTGGCAGTGT 60.153 57.895 14.43 0.00 0.00 3.55
143 145 3.621715 CAGGTTTTCGCCCAATAGTACTC 59.378 47.826 0.00 0.00 0.00 2.59
376 392 0.381801 AAACAGGCACAAACTGAGCG 59.618 50.000 0.00 0.00 39.24 5.03
496 523 2.552599 TTTAATGCCGTCACAGGTGA 57.447 45.000 0.00 0.00 37.24 4.02
521 548 2.490903 AGGCGAACACTATAACACGTCT 59.509 45.455 0.00 0.00 0.00 4.18
559 589 2.696187 TGTACGGCCTGCTGATTGTATA 59.304 45.455 4.70 0.00 0.00 1.47
560 590 1.484653 TGTACGGCCTGCTGATTGTAT 59.515 47.619 4.70 0.00 0.00 2.29
593 623 4.890088 ACAAGTTTAGGCAGACGTAATCA 58.110 39.130 0.00 0.00 0.00 2.57
619 649 4.467198 ACGGCAGTAGTAGTTTATTGCT 57.533 40.909 0.00 0.00 36.74 3.91
621 651 4.893795 GCAACGGCAGTAGTAGTTTATTG 58.106 43.478 0.00 0.00 40.72 1.90
648 681 3.199071 TGGCCTAAACGATGTAGTGGAAT 59.801 43.478 3.32 0.00 0.00 3.01
661 694 5.014202 TCTATTGGGTTTCTTGGCCTAAAC 58.986 41.667 16.11 16.11 35.34 2.01
694 727 2.403987 CGGGTAGACTGCGACGAG 59.596 66.667 0.00 0.00 0.00 4.18
697 730 1.731433 TATGCCGGGTAGACTGCGAC 61.731 60.000 2.18 0.00 0.00 5.19
702 735 2.897969 CCTTATGTATGCCGGGTAGACT 59.102 50.000 11.14 0.21 0.00 3.24
704 737 1.621814 GCCTTATGTATGCCGGGTAGA 59.378 52.381 2.18 0.00 0.00 2.59
708 741 2.747446 GTTATGCCTTATGTATGCCGGG 59.253 50.000 2.18 0.00 0.00 5.73
726 764 2.487372 TGTATATACGATGCCGGCGTTA 59.513 45.455 24.75 12.88 42.62 3.18
749 787 5.834169 TGTTTCGTGGCGTATTATCTCATA 58.166 37.500 0.00 0.00 0.00 2.15
772 810 5.176958 CGTTCGTCCATTTCTGAAAACTACT 59.823 40.000 6.95 0.00 0.00 2.57
774 812 4.449743 CCGTTCGTCCATTTCTGAAAACTA 59.550 41.667 6.95 0.00 0.00 2.24
777 815 3.207778 ACCGTTCGTCCATTTCTGAAAA 58.792 40.909 6.95 0.00 0.00 2.29
869 913 5.389935 GCTTAGCTATGTGATTAACGGCATC 60.390 44.000 8.30 0.00 0.00 3.91
894 938 6.400727 GCGCCATTCGATTTATATAAGACGTT 60.401 38.462 16.79 8.35 41.67 3.99
898 942 7.333174 TCAATGCGCCATTCGATTTATATAAGA 59.667 33.333 4.18 0.00 41.67 2.10
934 978 0.959553 GCAGATGCCTTGATGGATGG 59.040 55.000 0.00 0.00 38.35 3.51
994 1042 2.504681 CTTCGCCGCCATTTGTGC 60.505 61.111 0.00 0.00 0.00 4.57
1016 1064 2.506438 GGACGACGGCGAGAAAGG 60.506 66.667 22.49 0.00 41.64 3.11
1018 1066 2.257371 CAGGACGACGGCGAGAAA 59.743 61.111 22.49 0.00 41.64 2.52
1028 1076 1.228894 AAGGACAGGAGCAGGACGA 60.229 57.895 0.00 0.00 0.00 4.20
1176 1227 4.078516 CTGTTCCCGGACGTCCCC 62.079 72.222 28.52 11.78 0.00 4.81
1438 1489 1.372997 GCTGCGAGAACGACTCCAA 60.373 57.895 0.00 0.00 42.18 3.53
1536 1587 2.265739 GTGTCGAGCATCAGGCCA 59.734 61.111 5.01 0.00 46.50 5.36
1593 1644 3.576356 GCCGCCATGGTGTCGATG 61.576 66.667 23.44 9.18 41.21 3.84
1692 1743 4.201679 CCGTACGCGCCCATCTCA 62.202 66.667 10.49 0.00 36.67 3.27
1741 1792 2.839438 CGAACTCGACGATGCGCTG 61.839 63.158 9.73 0.34 43.02 5.18
1803 1854 0.602638 CCGTGTCAGCTTGCTTACCA 60.603 55.000 4.74 0.00 0.00 3.25
1857 1914 2.818921 TGGGAAAATAGCAGCCATGTT 58.181 42.857 0.00 0.00 0.00 2.71
1897 1955 4.988598 AACTGGGCCGTGTCAGCG 62.989 66.667 6.64 0.00 34.57 5.18
2385 2443 4.720902 TGCAGGATGGTGGTGGCG 62.721 66.667 0.00 0.00 35.86 5.69
2388 2446 1.742880 CGTCTGCAGGATGGTGGTG 60.743 63.158 15.13 0.00 35.86 4.17
2391 2449 1.742880 CCACGTCTGCAGGATGGTG 60.743 63.158 15.13 15.47 35.86 4.17
2451 2509 2.103538 GAGACGATGGCGCGGTAA 59.896 61.111 8.83 0.00 42.48 2.85
2889 2947 1.635663 GAACCAGGTCGCACATTCCG 61.636 60.000 0.00 0.00 0.00 4.30
2910 2968 1.604378 CTTCTTGTCGGGCCCTCAT 59.396 57.895 22.43 0.00 0.00 2.90
3119 3201 1.154035 GTACAACTGCGCATTGGGC 60.154 57.895 25.63 17.98 41.94 5.36
3120 3202 0.960364 AGGTACAACTGCGCATTGGG 60.960 55.000 25.63 13.43 0.00 4.12
3153 3235 2.417243 CGAATGGGTCCCATGAAAAAGC 60.417 50.000 24.76 7.11 44.40 3.51
3155 3237 1.548269 GCGAATGGGTCCCATGAAAAA 59.452 47.619 24.76 0.00 44.40 1.94
3190 3272 3.627395 ATCAAATCAAGCCTCGGTACA 57.373 42.857 0.00 0.00 0.00 2.90
3195 3277 7.166473 GCATTACTTTAATCAAATCAAGCCTCG 59.834 37.037 0.00 0.00 0.00 4.63
3197 3279 7.093377 TGGCATTACTTTAATCAAATCAAGCCT 60.093 33.333 0.00 0.00 35.99 4.58
3274 3367 9.234827 CCATGTGATATCTCCAAATAAGCAATA 57.765 33.333 3.98 0.00 0.00 1.90
3360 3454 0.811219 GCCGATGTCATGCTGCAGTA 60.811 55.000 16.64 12.13 0.00 2.74
3400 3497 1.079127 CCGGCGTTCACTTCATCCT 60.079 57.895 6.01 0.00 0.00 3.24
3403 3500 1.535462 CTTTTCCGGCGTTCACTTCAT 59.465 47.619 6.01 0.00 0.00 2.57
3498 3595 8.263940 TGAATCGAATAACCAACTAGGAAAAG 57.736 34.615 0.00 0.00 41.22 2.27
3576 3673 7.780271 ACATAGGAAAAACAAAGGACTCTTTCT 59.220 33.333 0.00 0.00 40.92 2.52
3577 3674 7.941919 ACATAGGAAAAACAAAGGACTCTTTC 58.058 34.615 0.00 0.00 40.92 2.62
3578 3675 7.898014 ACATAGGAAAAACAAAGGACTCTTT 57.102 32.000 0.00 0.00 43.41 2.52
3579 3676 7.684428 GCAACATAGGAAAAACAAAGGACTCTT 60.684 37.037 0.00 0.00 34.07 2.85
3693 3865 1.203038 TGCAAGGGCCTCTTTGATTCA 60.203 47.619 6.46 0.00 40.13 2.57
3716 3888 1.075542 CGAGTCGCCTTTAACATGCA 58.924 50.000 0.00 0.00 0.00 3.96
3803 3975 0.392060 AAAGCGGACATTCGGTACCC 60.392 55.000 6.25 0.00 40.11 3.69
3838 4010 7.605410 TTGATTGTTTAGAATAGTTCGGGTC 57.395 36.000 0.00 0.00 34.02 4.46


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

AutoCloner maintained by Alex Coulton.