Multiple sequence alignment - TraesCS7D01G328800

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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 TraesCS7D01G328800 chr7D 100.000 3914 0 0 1 3914 420625554 420629467 0.000000e+00 7228.0
1 TraesCS7D01G328800 chr7D 92.683 41 3 0 432 472 169993032 169992992 4.220000e-05 60.2
2 TraesCS7D01G328800 chr7B 95.032 2979 125 12 954 3914 436701568 436704541 0.000000e+00 4660.0
3 TraesCS7D01G328800 chr7B 84.211 703 53 27 1 677 436698244 436698914 7.140000e-177 630.0
4 TraesCS7D01G328800 chr7B 90.441 272 18 7 675 940 436701255 436701524 6.220000e-93 351.0
5 TraesCS7D01G328800 chr7B 72.131 549 123 25 132 659 555659172 555659711 5.270000e-29 139.0
6 TraesCS7D01G328800 chr7B 81.333 150 22 6 336 483 708439269 708439124 2.470000e-22 117.0
7 TraesCS7D01G328800 chr7A 94.822 2781 104 17 976 3741 512443174 512440419 0.000000e+00 4301.0
8 TraesCS7D01G328800 chr7A 97.714 175 4 0 3740 3914 512440337 512440163 6.360000e-78 302.0
9 TraesCS7D01G328800 chr7A 73.777 511 78 35 132 603 566005603 566006096 2.440000e-32 150.0
10 TraesCS7D01G328800 chr3D 74.110 730 134 41 117 819 48538769 48539470 2.330000e-62 250.0
11 TraesCS7D01G328800 chr6B 78.738 301 48 13 527 821 711696980 711697270 1.860000e-43 187.0
12 TraesCS7D01G328800 chr4B 82.199 191 28 6 633 821 651759590 651759404 4.050000e-35 159.0
13 TraesCS7D01G328800 chr4B 75.219 343 72 10 117 449 651760226 651759887 2.440000e-32 150.0
14 TraesCS7D01G328800 chr4B 74.352 347 66 17 132 465 651093458 651093794 4.110000e-25 126.0
15 TraesCS7D01G328800 chr4B 74.370 238 41 17 578 804 659967617 659967845 2.510000e-12 84.2
16 TraesCS7D01G328800 chr2B 76.289 291 53 13 119 399 794416434 794416150 1.470000e-29 141.0
17 TraesCS7D01G328800 chr2B 74.164 329 57 20 135 458 572786528 572786223 1.150000e-20 111.0
18 TraesCS7D01G328800 chr1B 83.099 142 19 5 682 821 475282712 475282850 1.480000e-24 124.0
19 TraesCS7D01G328800 chr1D 74.497 298 51 18 411 699 433206886 433207167 5.350000e-19 106.0
20 TraesCS7D01G328800 chr2D 80.769 130 21 3 82 207 434341321 434341450 8.950000e-17 99.0
21 TraesCS7D01G328800 chr5A 80.000 140 18 9 88 222 448575394 448575528 1.160000e-15 95.3
22 TraesCS7D01G328800 chr6A 74.206 252 45 15 557 804 529640738 529640503 1.940000e-13 87.9
23 TraesCS7D01G328800 chr2A 78.014 141 24 6 117 250 735313418 735313278 9.010000e-12 82.4
24 TraesCS7D01G328800 chr1A 78.571 112 18 5 704 813 511246735 511246628 7.020000e-08 69.4


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 TraesCS7D01G328800 chr7D 420625554 420629467 3913 False 7228.000000 7228 100.000000 1 3914 1 chr7D.!!$F1 3913
1 TraesCS7D01G328800 chr7B 436698244 436704541 6297 False 1880.333333 4660 89.894667 1 3914 3 chr7B.!!$F2 3913
2 TraesCS7D01G328800 chr7A 512440163 512443174 3011 True 2301.500000 4301 96.268000 976 3914 2 chr7A.!!$R1 2938
3 TraesCS7D01G328800 chr3D 48538769 48539470 701 False 250.000000 250 74.110000 117 819 1 chr3D.!!$F1 702

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
948 3398 1.006758 AGTCCGGTCCATAAGGAGACA 59.993 52.381 0.0 0.0 46.92 3.41 F
1164 3644 0.468029 CAAGCACCAACTCCCACCTT 60.468 55.000 0.0 0.0 0.00 3.50 F
1947 4427 0.038744 CCAAGAGTGGGTGGCTTCAT 59.961 55.000 0.0 0.0 41.77 2.57 F
2194 4674 1.066215 TGGTTGATGTGTCCTCCATCG 60.066 52.381 0.0 0.0 41.28 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 4368 0.315251 GTTTTCAGCTTGTCCTGCCC 59.685 55.000 0.00 0.00 32.87 5.36 R
2186 4666 0.742281 CACTGTTGGCTCGATGGAGG 60.742 60.000 6.88 0.00 40.80 4.30 R
2830 5310 1.655484 ATGATGATTTCACGCTGCGA 58.345 45.000 30.47 6.29 37.11 5.10 R
3560 6059 6.704050 TCGAACATGACACAGAAATAAAGACA 59.296 34.615 0.00 0.00 0.00 3.41 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
54 55 9.801873 TTTCATTTTCCGATTTCCATTATCTTC 57.198 29.630 0.00 0.00 0.00 2.87
56 57 8.840321 TCATTTTCCGATTTCCATTATCTTCTC 58.160 33.333 0.00 0.00 0.00 2.87
62 63 8.840321 TCCGATTTCCATTATCTTCTCATTTTC 58.160 33.333 0.00 0.00 0.00 2.29
63 64 8.844244 CCGATTTCCATTATCTTCTCATTTTCT 58.156 33.333 0.00 0.00 0.00 2.52
941 3391 3.316029 GGCCAGTCCGGTCCATAA 58.684 61.111 0.00 0.00 36.97 1.90
946 3396 1.688311 CCAGTCCGGTCCATAAGGAGA 60.688 57.143 0.00 0.00 46.92 3.71
947 3397 1.409427 CAGTCCGGTCCATAAGGAGAC 59.591 57.143 0.00 0.00 46.92 3.36
948 3398 1.006758 AGTCCGGTCCATAAGGAGACA 59.993 52.381 0.00 0.00 46.92 3.41
949 3399 2.040178 GTCCGGTCCATAAGGAGACAT 58.960 52.381 0.00 0.00 46.92 3.06
950 3400 3.117246 AGTCCGGTCCATAAGGAGACATA 60.117 47.826 0.00 0.00 46.92 2.29
951 3401 3.256136 GTCCGGTCCATAAGGAGACATAG 59.744 52.174 0.00 0.00 46.92 2.23
952 3402 3.117246 TCCGGTCCATAAGGAGACATAGT 60.117 47.826 0.00 0.00 46.92 2.12
985 3465 1.451387 CGCCCAGATTAACCGCCTT 60.451 57.895 0.00 0.00 0.00 4.35
1105 3585 2.606519 TCGGCAGGGCTACAACCT 60.607 61.111 0.00 0.00 39.43 3.50
1129 3609 4.054825 CCACCACCGCCATTGCAC 62.055 66.667 0.00 0.00 37.32 4.57
1130 3610 2.985282 CACCACCGCCATTGCACT 60.985 61.111 0.00 0.00 37.32 4.40
1164 3644 0.468029 CAAGCACCAACTCCCACCTT 60.468 55.000 0.00 0.00 0.00 3.50
1190 3670 0.689745 TCCCCTCATTCCTACCACCG 60.690 60.000 0.00 0.00 0.00 4.94
1195 3675 0.742505 TCATTCCTACCACCGCTACG 59.257 55.000 0.00 0.00 0.00 3.51
1413 3893 1.050988 ACGTGCTGATCAGGGCCTAT 61.051 55.000 23.89 0.00 35.01 2.57
1575 4055 2.265739 GAGCACATCTCGGGCACA 59.734 61.111 0.00 0.00 31.20 4.57
1632 4112 1.871039 GTTGACATGTACGCCAAGTGT 59.129 47.619 0.00 0.00 0.00 3.55
1881 4361 1.076727 GTTTGGTTGGAGGAGGGGG 59.923 63.158 0.00 0.00 0.00 5.40
1884 4364 1.432023 TTGGTTGGAGGAGGGGGTTC 61.432 60.000 0.00 0.00 0.00 3.62
1947 4427 0.038744 CCAAGAGTGGGTGGCTTCAT 59.961 55.000 0.00 0.00 41.77 2.57
1950 4430 1.656587 AGAGTGGGTGGCTTCATGTA 58.343 50.000 0.00 0.00 0.00 2.29
2019 4499 6.082228 TGGAATGCCATGATATGTGGATAT 57.918 37.500 7.72 0.01 39.92 1.63
2053 4533 1.790387 GCTGACGAAGCGCTTGAAT 59.210 52.632 30.47 12.57 43.45 2.57
2134 4614 3.699038 GGTTTTATCTGCCTGCAACCATA 59.301 43.478 4.06 0.00 0.00 2.74
2186 4666 3.057969 TGGTCTGATGGTTGATGTGTC 57.942 47.619 0.00 0.00 0.00 3.67
2194 4674 1.066215 TGGTTGATGTGTCCTCCATCG 60.066 52.381 0.00 0.00 41.28 3.84
2457 4937 4.347607 CTCAGTCTGGGAAATGGGAAAAT 58.652 43.478 0.00 0.00 0.00 1.82
2830 5310 8.571461 TGTTATCAAGCTGATTTCAAAGATCT 57.429 30.769 4.35 0.00 38.26 2.75
2831 5311 8.671921 TGTTATCAAGCTGATTTCAAAGATCTC 58.328 33.333 0.00 0.00 38.26 2.75
2951 5432 7.801547 AAACAAGTTGATTTTGCTCATATCG 57.198 32.000 10.54 0.00 0.00 2.92
3197 5683 7.874528 TGATATGGAGCACTTCATGTATGTAAG 59.125 37.037 1.45 0.00 0.00 2.34
3280 5766 7.286775 TGGTCTTGCTTAAATTTAGTCCTTGTT 59.713 33.333 0.00 0.00 0.00 2.83
3294 5780 1.558294 CCTTGTTAGGAGGGGTGTACC 59.442 57.143 0.00 0.00 45.05 3.34
3333 5832 7.344093 TGGCCTTCATGGTTTCAAATATAATGA 59.656 33.333 3.32 0.00 38.35 2.57
3560 6059 2.052468 ACAAGGTAGAGGAACCCGTTT 58.948 47.619 0.00 0.00 40.71 3.60
3561 6060 2.224450 ACAAGGTAGAGGAACCCGTTTG 60.224 50.000 0.00 0.00 40.71 2.93
3659 6158 9.923143 TCCATCCTACTGTTTGTTATATAATCG 57.077 33.333 0.00 0.00 0.00 3.34
3878 6460 4.833390 ACTGGCTTGTCAGTAGTTTATCC 58.167 43.478 6.04 0.00 45.18 2.59
3909 6491 5.990120 AGAAACAAATCTAGCTTTGGCAT 57.010 34.783 20.08 8.15 39.83 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.752005 AGAAGATAATGGAAATCGGAAAATGA 57.248 30.769 0.00 0.00 0.00 2.57
37 38 8.844244 AGAAAATGAGAAGATAATGGAAATCGG 58.156 33.333 0.00 0.00 0.00 4.18
214 225 4.394920 GCAGACCGAGTATTCCAAAAATGA 59.605 41.667 0.00 0.00 0.00 2.57
222 233 4.965119 AAAAATGCAGACCGAGTATTCC 57.035 40.909 0.00 0.00 0.00 3.01
885 3335 5.404366 GGCCTCGTTTCCTTGTTTATTTTTC 59.596 40.000 0.00 0.00 0.00 2.29
927 3377 1.409427 GTCTCCTTATGGACCGGACTG 59.591 57.143 9.46 0.00 37.46 3.51
928 3378 1.006758 TGTCTCCTTATGGACCGGACT 59.993 52.381 9.46 0.00 36.55 3.85
930 3380 2.471815 ATGTCTCCTTATGGACCGGA 57.528 50.000 9.46 0.00 37.46 5.14
940 3390 2.447443 TGTCTCGCACTATGTCTCCTT 58.553 47.619 0.00 0.00 0.00 3.36
941 3391 2.130272 TGTCTCGCACTATGTCTCCT 57.870 50.000 0.00 0.00 0.00 3.69
946 3396 2.623889 GTCCCTATGTCTCGCACTATGT 59.376 50.000 0.00 0.00 0.00 2.29
947 3397 2.350868 CGTCCCTATGTCTCGCACTATG 60.351 54.545 0.00 0.00 0.00 2.23
948 3398 1.880675 CGTCCCTATGTCTCGCACTAT 59.119 52.381 0.00 0.00 0.00 2.12
949 3399 1.306148 CGTCCCTATGTCTCGCACTA 58.694 55.000 0.00 0.00 0.00 2.74
950 3400 2.005960 GCGTCCCTATGTCTCGCACT 62.006 60.000 0.00 0.00 45.01 4.40
951 3401 1.589196 GCGTCCCTATGTCTCGCAC 60.589 63.158 0.00 0.00 45.01 5.34
952 3402 2.782222 GGCGTCCCTATGTCTCGCA 61.782 63.158 9.79 0.00 46.98 5.10
992 3472 1.021390 GGAGGGAAGCATCGTGTGTG 61.021 60.000 0.00 0.00 0.00 3.82
993 3473 1.296715 GGAGGGAAGCATCGTGTGT 59.703 57.895 0.00 0.00 0.00 3.72
1061 3541 0.179040 GGAGAGGAGACGACGGAGAT 60.179 60.000 0.00 0.00 0.00 2.75
1129 3609 1.407437 GCTTGGAGGTGGTGGTGATAG 60.407 57.143 0.00 0.00 0.00 2.08
1130 3610 0.618458 GCTTGGAGGTGGTGGTGATA 59.382 55.000 0.00 0.00 0.00 2.15
1164 3644 1.673767 AGGAATGAGGGGAAGAAGCA 58.326 50.000 0.00 0.00 0.00 3.91
1195 3675 0.110104 CAGGATTGGAGGATGGAGGC 59.890 60.000 0.00 0.00 0.00 4.70
1246 3726 2.274760 GAGCCTGCCATGGAGCTT 59.725 61.111 18.40 4.86 35.23 3.74
1482 3962 1.820519 AGCGGGTACGTGAAGTTATCA 59.179 47.619 0.00 0.00 43.45 2.15
1542 4022 4.316823 TCGTGCACCTCCCTCCCT 62.317 66.667 12.15 0.00 0.00 4.20
1562 4042 3.311110 ACCGTGTGCCCGAGATGT 61.311 61.111 0.00 0.00 0.00 3.06
1564 4044 4.082523 CCACCGTGTGCCCGAGAT 62.083 66.667 0.00 0.00 31.34 2.75
1632 4112 2.031919 GCATCGTCCACACACCCA 59.968 61.111 0.00 0.00 0.00 4.51
1689 4169 3.127376 CAGCAATCATCGAATTCCACACA 59.873 43.478 0.00 0.00 0.00 3.72
1830 4310 1.761667 CCCTCTAGGCAGAGCAGCT 60.762 63.158 0.00 0.00 46.08 4.24
1888 4368 0.315251 GTTTTCAGCTTGTCCTGCCC 59.685 55.000 0.00 0.00 32.87 5.36
1896 4376 3.491447 CCACAAGGGAAGTTTTCAGCTTG 60.491 47.826 0.00 0.00 40.01 4.01
1942 4422 4.103365 AGAGAACACGAGCTACATGAAG 57.897 45.455 0.00 0.00 0.00 3.02
1947 4427 3.857383 GCTCAAAGAGAACACGAGCTACA 60.857 47.826 0.00 0.00 44.47 2.74
1950 4430 1.789506 GCTCAAAGAGAACACGAGCT 58.210 50.000 0.00 0.00 44.47 4.09
2053 4533 6.518200 GCATCTCCCCTCATTTTGTTAAACAA 60.518 38.462 0.00 0.00 36.11 2.83
2134 4614 3.121929 TGCTTCTTCTACCATCCCTCT 57.878 47.619 0.00 0.00 0.00 3.69
2186 4666 0.742281 CACTGTTGGCTCGATGGAGG 60.742 60.000 6.88 0.00 40.80 4.30
2194 4674 1.135575 GTAATGCTGCACTGTTGGCTC 60.136 52.381 3.57 0.00 0.00 4.70
2457 4937 1.174712 GCTTTCTCACCCTTGCAGCA 61.175 55.000 0.00 0.00 0.00 4.41
2830 5310 1.655484 ATGATGATTTCACGCTGCGA 58.345 45.000 30.47 6.29 37.11 5.10
2831 5311 3.245990 TCTTATGATGATTTCACGCTGCG 59.754 43.478 21.91 21.91 37.11 5.18
2950 5431 2.877168 AGACTAATACGACTAGCACCCG 59.123 50.000 0.00 0.00 0.00 5.28
2951 5432 3.881688 TGAGACTAATACGACTAGCACCC 59.118 47.826 0.00 0.00 0.00 4.61
3197 5683 7.606858 TCATGTTTCTTCATCTCTGAATGAC 57.393 36.000 0.00 0.00 40.52 3.06
3560 6059 6.704050 TCGAACATGACACAGAAATAAAGACA 59.296 34.615 0.00 0.00 0.00 3.41
3561 6060 7.117241 TCGAACATGACACAGAAATAAAGAC 57.883 36.000 0.00 0.00 0.00 3.01
3878 6460 8.807667 AAGCTAGATTTGTTTCTTCAAATGTG 57.192 30.769 8.96 3.30 44.62 3.21


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

AutoCloner maintained by Alex Coulton.