Multiple sequence alignment - TraesCS7D01G002300

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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 TraesCS7D01G002300 chr7D 100.000 3310 0 0 1 3310 1536527 1533218 0.000000e+00 6113.0
1 TraesCS7D01G002300 chr7D 92.683 82 5 1 1939 2020 1533347 1533267 2.090000e-22 117.0
2 TraesCS7D01G002300 chr7D 92.683 82 5 1 3181 3261 1534589 1534508 2.090000e-22 117.0
3 TraesCS7D01G002300 chr7D 81.250 80 13 1 2260 2339 424466857 424466934 2.760000e-06 63.9
4 TraesCS7D01G002300 chr7B 95.816 3322 117 8 1 3305 17350398 17347082 0.000000e+00 5345.0
5 TraesCS7D01G002300 chr7B 93.902 82 5 0 1939 2020 17347206 17347125 1.250000e-24 124.0
6 TraesCS7D01G002300 chr7B 83.099 142 15 4 2025 2157 17346920 17346779 1.610000e-23 121.0
7 TraesCS7D01G002300 chr7B 92.683 82 5 1 3181 3261 17348461 17348380 2.090000e-22 117.0
8 TraesCS7D01G002300 chr7B 89.796 49 5 0 2253 2301 441965433 441965481 2.760000e-06 63.9
9 TraesCS7D01G002300 chr7B 86.000 50 7 0 3261 3310 29600291 29600340 2.000000e-03 54.7
10 TraesCS7D01G002300 chr4A 95.691 1880 64 3 499 2361 743747684 743749563 0.000000e+00 3007.0
11 TraesCS7D01G002300 chr4A 95.437 504 22 1 1 503 743744786 743745289 0.000000e+00 802.0
12 TraesCS7D01G002300 chr4A 71.935 734 142 48 2 700 453301909 453301205 4.420000e-34 156.0
13 TraesCS7D01G002300 chr4A 91.765 85 6 1 3178 3261 743749123 743749207 2.090000e-22 117.0
14 TraesCS7D01G002300 chr4A 79.365 126 25 1 2176 2301 79027990 79028114 1.640000e-13 87.9
15 TraesCS7D01G002300 chr7A 84.632 1425 109 45 969 2348 1008243 1009602 0.000000e+00 1317.0
16 TraesCS7D01G002300 chr7A 81.101 545 67 12 2627 3156 1093416 1093939 1.430000e-108 403.0
17 TraesCS7D01G002300 chr7A 80.952 546 67 16 2627 3156 1108819 1109343 6.660000e-107 398.0
18 TraesCS7D01G002300 chr7A 85.766 274 35 1 2539 2812 1009700 1009969 1.500000e-73 287.0
19 TraesCS7D01G002300 chr7A 86.000 50 7 0 3261 3310 83997944 83997993 2.000000e-03 54.7
20 TraesCS7D01G002300 chr3D 77.859 411 80 10 1 403 43507186 43507593 9.180000e-61 244.0
21 TraesCS7D01G002300 chr3D 89.831 59 6 0 621 679 506207921 506207979 3.540000e-10 76.8
22 TraesCS7D01G002300 chr4D 73.542 703 151 29 1 679 190399904 190400595 5.520000e-58 235.0
23 TraesCS7D01G002300 chr4D 78.378 148 26 4 496 643 147077088 147077229 1.260000e-14 91.6
24 TraesCS7D01G002300 chr6D 87.179 195 24 1 492 686 424634898 424634705 1.550000e-53 220.0
25 TraesCS7D01G002300 chr2A 73.087 732 137 43 2 700 620731284 620730580 4.330000e-49 206.0
26 TraesCS7D01G002300 chr3A 72.329 730 142 39 2 698 270570818 270571520 1.220000e-39 174.0
27 TraesCS7D01G002300 chr3A 84.496 129 12 6 787 912 360731937 360731814 1.610000e-23 121.0
28 TraesCS7D01G002300 chr6A 71.956 731 146 39 1 700 46758691 46759393 3.420000e-35 159.0
29 TraesCS7D01G002300 chr6A 81.343 134 17 7 787 915 205774282 205774152 5.840000e-18 102.0
30 TraesCS7D01G002300 chr3B 86.290 124 12 5 576 697 40903528 40903648 2.680000e-26 130.0
31 TraesCS7D01G002300 chr2B 83.453 139 15 7 779 913 115895309 115895175 4.490000e-24 122.0
32 TraesCS7D01G002300 chr2B 81.679 131 17 5 787 913 566445418 566445291 5.840000e-18 102.0
33 TraesCS7D01G002300 chr2B 80.000 140 20 7 779 913 780123056 780122920 2.720000e-16 97.1
34 TraesCS7D01G002300 chr5A 81.955 133 18 5 787 915 510997182 510997052 1.260000e-19 108.0
35 TraesCS7D01G002300 chr6B 81.679 131 17 6 787 913 620873998 620873871 5.840000e-18 102.0
36 TraesCS7D01G002300 chr6B 100.000 32 0 0 3268 3299 702809594 702809563 3.570000e-05 60.2
37 TraesCS7D01G002300 chr5B 75.829 211 28 18 470 673 622330929 622330735 5.890000e-13 86.1
38 TraesCS7D01G002300 chr4B 89.062 64 6 1 610 673 68201501 68201439 9.850000e-11 78.7
39 TraesCS7D01G002300 chr1B 97.674 43 1 0 1887 1929 588139016 588138974 1.270000e-09 75.0
40 TraesCS7D01G002300 chr1A 92.683 41 3 0 3259 3299 344498909 344498949 3.570000e-05 60.2


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 TraesCS7D01G002300 chr7D 1533218 1536527 3309 True 2115.666667 6113 95.122000 1 3310 3 chr7D.!!$R1 3309
1 TraesCS7D01G002300 chr7B 17346779 17350398 3619 True 1426.750000 5345 91.375000 1 3305 4 chr7B.!!$R1 3304
2 TraesCS7D01G002300 chr4A 743744786 743749563 4777 False 1308.666667 3007 94.297667 1 3261 3 chr4A.!!$F2 3260
3 TraesCS7D01G002300 chr7A 1008243 1009969 1726 False 802.000000 1317 85.199000 969 2812 2 chr7A.!!$F4 1843
4 TraesCS7D01G002300 chr7A 1093416 1093939 523 False 403.000000 403 81.101000 2627 3156 1 chr7A.!!$F1 529
5 TraesCS7D01G002300 chr7A 1108819 1109343 524 False 398.000000 398 80.952000 2627 3156 1 chr7A.!!$F2 529
6 TraesCS7D01G002300 chr4D 190399904 190400595 691 False 235.000000 235 73.542000 1 679 1 chr4D.!!$F2 678
7 TraesCS7D01G002300 chr2A 620730580 620731284 704 True 206.000000 206 73.087000 2 700 1 chr2A.!!$R1 698

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
679 3109 0.036858 GTTTCGAAGGCCTGCTCTCT 60.037 55.000 5.69 0.0 0.0 3.10 F
758 3188 1.338484 GCTCACCTCTGCTCATTCACA 60.338 52.381 0.00 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 3939 0.535102 CGTGTTCTTGGGTCCTTGCT 60.535 55.000 0.0 0.0 0.0 3.91 R
2525 5008 2.173143 AGTAGGACCTTAGGACCTCTCG 59.827 54.545 24.4 0.0 43.9 4.04 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
29 30 2.826128 TGATCACACTTAGAACGGCTCT 59.174 45.455 0.00 0.00 38.28 4.09
180 182 7.497595 ACGCTTAAAGTATGTCCTCATAATCA 58.502 34.615 0.00 0.00 38.13 2.57
187 189 0.759346 GTCCTCATAATCAGGGCCGT 59.241 55.000 0.00 0.00 28.18 5.68
340 346 3.759418 AGCACATACCGATATTCGATCG 58.241 45.455 9.36 9.36 43.74 3.69
371 378 4.574013 ACGTACTAGCACATAGTAGACACC 59.426 45.833 0.00 0.00 45.57 4.16
411 418 7.653767 AGTACAACTAAAATAGCAGACACAC 57.346 36.000 0.00 0.00 0.00 3.82
485 515 2.289694 CCTGATCGGTGGTCTTCTTGTT 60.290 50.000 0.00 0.00 0.00 2.83
548 2977 2.158711 ACATGGTGATGATGAAGGCGAT 60.159 45.455 0.00 0.00 33.36 4.58
553 2982 1.572085 GATGATGAAGGCGATGCGGG 61.572 60.000 0.00 0.00 0.00 6.13
588 3017 2.098607 GTCGATGTAGACGAATGGTGGA 59.901 50.000 0.00 0.00 41.31 4.02
627 3056 3.751518 ACGCTCCACAAAAACCTAATCT 58.248 40.909 0.00 0.00 0.00 2.40
679 3109 0.036858 GTTTCGAAGGCCTGCTCTCT 60.037 55.000 5.69 0.00 0.00 3.10
702 3132 1.798283 ACAACTGTATACGCGGCAAA 58.202 45.000 12.47 0.00 0.00 3.68
703 3133 2.352388 ACAACTGTATACGCGGCAAAT 58.648 42.857 12.47 0.47 0.00 2.32
758 3188 1.338484 GCTCACCTCTGCTCATTCACA 60.338 52.381 0.00 0.00 0.00 3.58
766 3196 4.534168 CTCTGCTCATTCACAAAACACAG 58.466 43.478 0.00 0.00 0.00 3.66
922 3352 4.874199 ACTTTCCACCACCCTTTCTTTTA 58.126 39.130 0.00 0.00 0.00 1.52
958 3388 5.528600 TGTGATTTGGGAGGAAAGGAATA 57.471 39.130 0.00 0.00 0.00 1.75
1044 3474 9.091784 GAGTGGATATACGTACGTGAGATATAA 57.908 37.037 30.25 13.72 0.00 0.98
1357 3787 2.427245 CGCCTCCCTCGACCTCAAT 61.427 63.158 0.00 0.00 0.00 2.57
1420 3850 2.213499 CGAAACTCCAACAGACTGCTT 58.787 47.619 1.25 0.00 0.00 3.91
1426 3856 3.244700 ACTCCAACAGACTGCTTAGCATT 60.245 43.478 7.58 0.86 38.13 3.56
1509 3939 3.327404 GCTCCCGGGTTCCTTCCA 61.327 66.667 22.86 0.00 0.00 3.53
1513 3943 2.434331 CCGGGTTCCTTCCAGCAA 59.566 61.111 0.00 0.00 0.00 3.91
1569 3999 4.344865 GGGCATGGTCACGGTGGT 62.345 66.667 8.50 0.00 0.00 4.16
2392 4875 5.379187 CATGAAATGGGTGTATCATCCTCA 58.621 41.667 0.74 0.00 41.79 3.86
2506 4989 1.066587 GTTCTCGGGAGATGCGAGG 59.933 63.158 0.00 0.00 37.29 4.63
2565 5048 6.938030 TCCTACTTGTTTTTGTACGAATGGAT 59.062 34.615 0.00 0.00 0.00 3.41
2663 5146 7.339466 AGGAAATTTATACGTGCAGGAAGAAAT 59.661 33.333 14.38 11.34 0.00 2.17
2687 5171 9.691362 AATAATGTAGACACACCAAAATTGTTC 57.309 29.630 0.00 0.00 37.54 3.18
2690 5174 5.596361 TGTAGACACACCAAAATTGTTCCAT 59.404 36.000 0.00 0.00 0.00 3.41
2868 5360 3.287222 TCTGGGTGTCTGGTTTTTCTTG 58.713 45.455 0.00 0.00 0.00 3.02
3016 5509 5.483937 TCATCCTCATGTAGGTGTAGTTTGT 59.516 40.000 9.98 0.00 46.62 2.83
3201 5699 1.899142 GTGTCCTCAGCTCTTCTTCCT 59.101 52.381 0.00 0.00 0.00 3.36
3235 5734 7.226441 CCCAATCCATTGTATCTCTGAATGTA 58.774 38.462 0.00 0.00 36.06 2.29
3294 5793 6.258068 TGCATTTTAAAACCGAACCGAAAAAT 59.742 30.769 1.97 0.00 0.00 1.82
3301 5800 6.503589 AAACCGAACCGAAAAATCATATCA 57.496 33.333 0.00 0.00 0.00 2.15
3302 5801 5.734855 ACCGAACCGAAAAATCATATCAG 57.265 39.130 0.00 0.00 0.00 2.90
3305 5804 6.037172 ACCGAACCGAAAAATCATATCAGAAG 59.963 38.462 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.007038 GGCACCGTCGTACTTGTCA 60.007 57.895 0.00 0.0 0.00 3.58
180 182 1.978617 CAGCATTGGAAACGGCCCT 60.979 57.895 0.00 0.0 30.48 5.19
340 346 1.135199 TGTGCTAGTACGTGCTTAGGC 60.135 52.381 12.53 14.1 39.26 3.93
403 410 5.221461 GGAGGGTATACAATAGGTGTGTCTG 60.221 48.000 5.01 0.0 41.89 3.51
548 2977 1.378911 TACTTCGTCTAGGCCCGCA 60.379 57.895 0.00 0.0 0.00 5.69
588 3017 1.078356 TCTCCTACGCGACTGCTCT 60.078 57.895 15.93 0.0 39.65 4.09
627 3056 1.143277 GATCCTGTACGAGAGAGGGGA 59.857 57.143 5.66 0.0 39.21 4.81
679 3109 1.531677 GCCGCGTATACAGTTGTACGA 60.532 52.381 17.59 0.0 43.45 3.43
702 3132 5.764686 TCATCCGTGAGCTTGCATTTAATAT 59.235 36.000 0.00 0.0 0.00 1.28
703 3133 5.007626 GTCATCCGTGAGCTTGCATTTAATA 59.992 40.000 0.00 0.0 34.36 0.98
758 3188 1.226267 CACGTGCGTGCTGTGTTTT 60.226 52.632 11.81 0.0 39.39 2.43
922 3352 5.184479 CCCAAATCACATGTTGTCTCTCAAT 59.816 40.000 0.00 0.0 38.38 2.57
1426 3856 1.028330 CACCCACGTCGAGGTAGCTA 61.028 60.000 10.91 0.0 33.52 3.32
1509 3939 0.535102 CGTGTTCTTGGGTCCTTGCT 60.535 55.000 0.00 0.0 0.00 3.91
1513 3943 1.366366 CGTCGTGTTCTTGGGTCCT 59.634 57.895 0.00 0.0 0.00 3.85
1563 3993 2.177580 ACTTGCACGTCAACCACCG 61.178 57.895 0.00 0.0 0.00 4.94
2312 4795 8.902806 TGATACACCCATTTCAAATCACTATTC 58.097 33.333 0.00 0.0 0.00 1.75
2525 5008 2.173143 AGTAGGACCTTAGGACCTCTCG 59.827 54.545 24.40 0.0 43.90 4.04
2536 5019 5.673514 TCGTACAAAAACAAGTAGGACCTT 58.326 37.500 0.00 0.0 32.19 3.50
2663 5146 7.285629 TGGAACAATTTTGGTGTGTCTACATTA 59.714 33.333 0.00 0.0 35.16 1.90
2687 5171 7.857569 TCGAACTCAACTAAACTGTTTTATGG 58.142 34.615 11.48 0.0 0.00 2.74
2690 5174 8.254178 TGTTCGAACTCAACTAAACTGTTTTA 57.746 30.769 27.32 0.0 0.00 1.52
2823 5307 0.176680 TCAAAGAGCGATGGAGAGCC 59.823 55.000 0.00 0.0 0.00 4.70
3016 5509 4.640201 GCTCTTGGCATAGTTCATGGTTAA 59.360 41.667 0.00 0.0 41.35 2.01
3201 5699 3.130450 ACAATGGATTGGGGATACAGGA 58.870 45.455 4.45 0.0 41.96 3.86
3235 5734 3.821033 GTCACCAACCTAGCTCACAAATT 59.179 43.478 0.00 0.0 0.00 1.82
3266 5765 3.984633 CGGTTCGGTTTTAAAATGCACAT 59.015 39.130 3.52 0.0 0.00 3.21


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

AutoCloner maintained by Alex Coulton.