Multiple sequence alignment - TraesCS1B01G063900

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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 TraesCS1B01G063900 chr1B 100.000 3169 0 0 1 3169 48529627 48532795 0.000000e+00 5853.0
1 TraesCS1B01G063900 chr1B 95.093 2323 86 4 1 2296 23815817 23818138 0.000000e+00 3633.0
2 TraesCS1B01G063900 chr1B 96.437 1235 34 6 1943 3169 388031584 388032816 0.000000e+00 2028.0
3 TraesCS1B01G063900 chr1B 94.410 1145 39 3 1 1121 388030427 388031570 0.000000e+00 1736.0
4 TraesCS1B01G063900 chr1B 95.000 100 5 0 2804 2903 23818139 23818238 1.180000e-34 158.0
5 TraesCS1B01G063900 chr5B 95.603 2320 74 5 1 2296 701464801 701467116 0.000000e+00 3694.0
6 TraesCS1B01G063900 chr5B 95.000 100 5 0 2804 2903 701467117 701467216 1.180000e-34 158.0
7 TraesCS1B01G063900 chr7A 95.857 2269 68 4 1 2245 206573433 206575699 0.000000e+00 3646.0
8 TraesCS1B01G063900 chr7A 89.231 65 3 2 2280 2340 648434466 648434530 9.420000e-11 78.7
9 TraesCS1B01G063900 chr2B 94.041 2299 97 15 1 2275 142887163 142889445 0.000000e+00 3450.0
10 TraesCS1B01G063900 chr3B 96.225 1563 54 4 1609 3169 607501966 607500407 0.000000e+00 2555.0
11 TraesCS1B01G063900 chr3B 93.617 1645 72 6 1 1614 607523105 607521463 0.000000e+00 2425.0
12 TraesCS1B01G063900 chr5A 93.969 1625 71 5 1 1599 670476793 670475170 0.000000e+00 2433.0
13 TraesCS1B01G063900 chr5A 92.549 1624 94 12 1 1599 696328891 696327270 0.000000e+00 2303.0
14 TraesCS1B01G063900 chr5A 94.265 680 36 2 1596 2275 670475032 670474356 0.000000e+00 1037.0
15 TraesCS1B01G063900 chr2D 93.103 1624 86 4 1 1599 197523429 197521807 0.000000e+00 2355.0
16 TraesCS1B01G063900 chr2D 94.273 681 34 3 1596 2275 197521669 197520993 0.000000e+00 1037.0
17 TraesCS1B01G063900 chr1A 92.862 1625 88 6 1 1599 449450024 449451646 0.000000e+00 2333.0
18 TraesCS1B01G063900 chr1A 92.699 1630 85 8 1 1599 374207737 374209363 0.000000e+00 2320.0
19 TraesCS1B01G063900 chr1A 93.824 680 39 2 1596 2275 449451784 449452460 0.000000e+00 1020.0
20 TraesCS1B01G063900 chr5D 93.087 1027 41 6 1 998 498368569 498369594 0.000000e+00 1476.0
21 TraesCS1B01G063900 chr3A 94.273 681 29 6 1596 2275 1715090 1714419 0.000000e+00 1033.0
22 TraesCS1B01G063900 chr2A 85.094 691 46 20 2503 3169 729535343 729534686 0.000000e+00 652.0
23 TraesCS1B01G063900 chr7B 95.556 45 2 0 2272 2316 612639097 612639141 4.380000e-09 73.1


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 TraesCS1B01G063900 chr1B 48529627 48532795 3168 False 5853.0 5853 100.0000 1 3169 1 chr1B.!!$F1 3168
1 TraesCS1B01G063900 chr1B 23815817 23818238 2421 False 1895.5 3633 95.0465 1 2903 2 chr1B.!!$F2 2902
2 TraesCS1B01G063900 chr1B 388030427 388032816 2389 False 1882.0 2028 95.4235 1 3169 2 chr1B.!!$F3 3168
3 TraesCS1B01G063900 chr5B 701464801 701467216 2415 False 1926.0 3694 95.3015 1 2903 2 chr5B.!!$F1 2902
4 TraesCS1B01G063900 chr7A 206573433 206575699 2266 False 3646.0 3646 95.8570 1 2245 1 chr7A.!!$F1 2244
5 TraesCS1B01G063900 chr2B 142887163 142889445 2282 False 3450.0 3450 94.0410 1 2275 1 chr2B.!!$F1 2274
6 TraesCS1B01G063900 chr3B 607500407 607501966 1559 True 2555.0 2555 96.2250 1609 3169 1 chr3B.!!$R1 1560
7 TraesCS1B01G063900 chr3B 607521463 607523105 1642 True 2425.0 2425 93.6170 1 1614 1 chr3B.!!$R2 1613
8 TraesCS1B01G063900 chr5A 696327270 696328891 1621 True 2303.0 2303 92.5490 1 1599 1 chr5A.!!$R1 1598
9 TraesCS1B01G063900 chr5A 670474356 670476793 2437 True 1735.0 2433 94.1170 1 2275 2 chr5A.!!$R2 2274
10 TraesCS1B01G063900 chr2D 197520993 197523429 2436 True 1696.0 2355 93.6880 1 2275 2 chr2D.!!$R1 2274
11 TraesCS1B01G063900 chr1A 374207737 374209363 1626 False 2320.0 2320 92.6990 1 1599 1 chr1A.!!$F1 1598
12 TraesCS1B01G063900 chr1A 449450024 449452460 2436 False 1676.5 2333 93.3430 1 2275 2 chr1A.!!$F2 2274
13 TraesCS1B01G063900 chr5D 498368569 498369594 1025 False 1476.0 1476 93.0870 1 998 1 chr5D.!!$F1 997
14 TraesCS1B01G063900 chr3A 1714419 1715090 671 True 1033.0 1033 94.2730 1596 2275 1 chr3A.!!$R1 679
15 TraesCS1B01G063900 chr2A 729534686 729535343 657 True 652.0 652 85.0940 2503 3169 1 chr2A.!!$R1 666

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
389 406 2.602676 ATGTGGGTGGGAAGGGTCG 61.603 63.158 0.0 0.0 0.0 4.79 F
1122 1164 2.237392 GACTGCTGAAGGGTGGACTAAT 59.763 50.000 0.0 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2312 3.075283 TCCTCCTTCAACCAATAAAGCCA 59.925 43.478 0.0 0.0 0.00 4.75 R
3015 3223 0.392461 AGGCGATAAAGCAAGGCGAA 60.392 50.000 0.0 0.0 39.27 4.70 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
42 46 9.981460 AGGATTTTGACTTAATTCCAACTCTAT 57.019 29.630 0.00 0.00 32.50 1.98
55 59 9.768215 AATTCCAACTCTATCCCAAAGATTTAA 57.232 29.630 0.00 0.00 36.33 1.52
125 129 3.157087 CCGCTATTGGCCTTATTTCCAT 58.843 45.455 3.32 0.00 37.74 3.41
248 253 2.620251 ACTGCATTGGCGCTATAGAA 57.380 45.000 7.64 0.00 45.35 2.10
287 296 5.620738 TCACTATTGCTGAAGATAAGGCT 57.379 39.130 0.00 0.00 0.00 4.58
305 322 2.716969 GGCTCCCCCATTTAGGAATAGT 59.283 50.000 0.00 0.00 41.22 2.12
389 406 2.602676 ATGTGGGTGGGAAGGGTCG 61.603 63.158 0.00 0.00 0.00 4.79
461 478 7.243604 TGTGCCAGATGGAAAATTTTATCTT 57.756 32.000 11.79 3.61 37.39 2.40
646 687 5.904362 ACATTTCCCTATCTTGAAAGTGC 57.096 39.130 0.00 0.00 34.26 4.40
685 726 9.159364 CAATAGAGTCACAAATCAAGATTCTGA 57.841 33.333 0.00 0.00 31.87 3.27
709 750 3.303990 GGCATGTGCTGTATTCCATAACG 60.304 47.826 4.84 0.00 41.70 3.18
719 760 6.366332 GCTGTATTCCATAACGTCATTAGAGG 59.634 42.308 0.00 0.00 35.80 3.69
799 840 5.133322 ACATATGTTGATGTTCCAGAGGGAT 59.867 40.000 1.41 0.00 44.48 3.85
896 937 6.717289 TGTGGGCTGATTATAACAACTAGTT 58.283 36.000 1.12 1.12 44.27 2.24
1060 1102 7.495934 ACGAGAAAGGTCTTGTTGATATAATGG 59.504 37.037 0.00 0.00 44.87 3.16
1122 1164 2.237392 GACTGCTGAAGGGTGGACTAAT 59.763 50.000 0.00 0.00 0.00 1.73
1162 1205 6.939132 ATCAGAAATTTCCACTAGCTCATG 57.061 37.500 14.61 2.86 0.00 3.07
1194 1237 6.894103 AGCAACAAATCCAAGAGAAGGATAAT 59.106 34.615 0.00 0.00 44.94 1.28
1220 1263 9.816354 TGATTTAAAAGGAAATTATAAGGCAGC 57.184 29.630 0.00 0.00 0.00 5.25
1269 1312 3.490348 GGGATGGGATGATACACTTTGG 58.510 50.000 0.00 0.00 0.00 3.28
1278 1321 6.718454 GGGATGATACACTTTGGATGATCATT 59.282 38.462 10.14 0.00 33.63 2.57
1352 1395 7.975058 TGATATATTGTTTGTTCACTGCCATTG 59.025 33.333 0.00 0.00 0.00 2.82
1398 1441 6.872585 ATTGATCCCAACCATACAATGTTT 57.127 33.333 0.00 0.00 34.72 2.83
1436 1479 7.184753 AGGATAATCCAAGGGTAAAGAAGTTCT 59.815 37.037 0.00 0.00 39.61 3.01
1494 1537 3.807622 ACACTACATGAAGGTGTGTTTCG 59.192 43.478 17.09 0.00 41.75 3.46
1527 1570 4.741321 TTTCCGTCGACCCTACATATTT 57.259 40.909 10.58 0.00 0.00 1.40
1533 1576 5.047519 CCGTCGACCCTACATATTTAATCCT 60.048 44.000 10.58 0.00 0.00 3.24
1616 1802 7.004555 TCCATGTTTCTAAGAGAACTTGCTA 57.995 36.000 0.00 0.00 33.26 3.49
1739 1929 7.609532 CCTATGGATTCCTCTACCAATGATTTC 59.390 40.741 3.95 0.00 37.24 2.17
1770 1960 6.566079 TCTCCTCTACCAATGTTGATGATT 57.434 37.500 0.00 0.00 0.00 2.57
1797 1987 4.219115 GTCCTCATCTGATCTACAAGGGA 58.781 47.826 0.00 0.00 0.00 4.20
1844 2034 5.045578 ACCTGAAGCTACAACATCTACCAAT 60.046 40.000 0.00 0.00 0.00 3.16
1861 2052 4.803452 ACCAATTCTGAACAAAAGGGAGA 58.197 39.130 0.00 0.00 0.00 3.71
2121 2312 7.890127 TCATCAATACCAAGGACTCAAATCTTT 59.110 33.333 0.00 0.00 0.00 2.52
2159 2350 6.097554 TGAAGGAGGAGATTTCTGAGATGTAC 59.902 42.308 0.00 0.00 0.00 2.90
2161 2352 5.598005 AGGAGGAGATTTCTGAGATGTACAG 59.402 44.000 0.33 0.00 36.80 2.74
2206 2400 4.095782 TCACCTTCTTGTTTTGCACTACAC 59.904 41.667 0.00 0.00 0.00 2.90
2277 2471 8.691661 TTATAAGCTTGTTTCCTTCTGTTCTT 57.308 30.769 9.86 0.00 0.00 2.52
2334 2528 8.742125 ATCCTCTGTTCTGGATTATATACCAA 57.258 34.615 0.00 0.00 39.84 3.67
2412 2606 3.857157 TGTGTCAAACTAGGCCTCTTT 57.143 42.857 9.68 5.37 0.00 2.52
2421 2615 8.398665 GTCAAACTAGGCCTCTTTATTATGTTG 58.601 37.037 9.68 0.81 0.00 3.33
2428 2622 8.738645 AGGCCTCTTTATTATGTTGTCTAAAG 57.261 34.615 0.00 0.00 34.15 1.85
2747 2953 7.871973 TCATAAATCCATGTTTGTTTTGTCCTG 59.128 33.333 0.00 0.00 0.00 3.86
2873 3081 8.791675 TCAACAATTCATGCTGTTCATTACTAA 58.208 29.630 5.10 0.00 33.51 2.24
3015 3223 6.552445 AGACCTGATAAGCACTAGTGATTT 57.448 37.500 29.45 21.20 40.05 2.17
3069 3277 7.542890 TGTTATTCAAAAGTGTCTTTGCTTCA 58.457 30.769 0.00 0.00 36.44 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 46 8.933653 ACTTGGAATCTTTTTAAATCTTTGGGA 58.066 29.630 0.00 0.0 0.00 4.37
55 59 4.279420 GCTGGAGTGAACTTGGAATCTTTT 59.721 41.667 0.00 0.0 0.00 2.27
125 129 3.133901 AGATGTGTGTGTAGTGGTTCACA 59.866 43.478 0.00 0.0 41.37 3.58
239 244 5.411781 GGGATATGTGTTCCTTCTATAGCG 58.588 45.833 0.00 0.0 33.53 4.26
248 253 3.397527 AGTGATGGGGATATGTGTTCCT 58.602 45.455 0.00 0.0 33.53 3.36
287 296 6.221850 TCCTTTACTATTCCTAAATGGGGGA 58.778 40.000 0.00 0.0 36.20 4.81
305 322 4.597507 ACATTCTGTGAGAGGGTTCCTTTA 59.402 41.667 0.00 0.0 31.76 1.85
461 478 6.710295 GTGTGTTTGCATATCCACCATCTATA 59.290 38.462 0.00 0.0 0.00 1.31
626 667 3.378427 GCGCACTTTCAAGATAGGGAAAT 59.622 43.478 0.30 0.0 33.00 2.17
646 687 4.051922 GACTCTATTGGGTAGTGATTGCG 58.948 47.826 0.00 0.0 0.00 4.85
685 726 0.035534 TGGAATACAGCACATGCCGT 60.036 50.000 0.00 0.0 43.38 5.68
709 750 4.894784 TCACCACTTTGACCTCTAATGAC 58.105 43.478 0.00 0.0 0.00 3.06
719 760 1.896220 TGCCTCATCACCACTTTGAC 58.104 50.000 0.00 0.0 0.00 3.18
758 799 8.303156 CAACATATGTTTCTGGTGGAATTAACA 58.697 33.333 18.50 0.0 35.83 2.41
1019 1061 1.768275 TCTCGTATGCATGGTCCCAAT 59.232 47.619 10.16 0.0 0.00 3.16
1162 1205 3.068024 TCTTGGATTTGTTGCTTGGTGAC 59.932 43.478 0.00 0.0 0.00 3.67
1194 1237 9.816354 GCTGCCTTATAATTTCCTTTTAAATCA 57.184 29.630 0.00 0.0 0.00 2.57
1269 1312 6.630444 ATTACAGGTTCAGCAATGATCATC 57.370 37.500 9.06 0.0 0.00 2.92
1278 1321 6.508030 TTATCCCATATTACAGGTTCAGCA 57.492 37.500 0.00 0.0 0.00 4.41
1398 1441 7.015487 CCCTTGGATTATCCTATTGAATGCAAA 59.985 37.037 12.91 0.0 39.43 3.68
1436 1479 5.068855 TGAAGAGCATGAATGGTTTTGAACA 59.931 36.000 0.00 0.0 38.85 3.18
1494 1537 4.443394 GGTCGACGGAAATACATGATACAC 59.557 45.833 9.92 0.0 0.00 2.90
1616 1802 7.874528 CCTGCTCCAAAGAAAAAGAAACATATT 59.125 33.333 0.00 0.0 0.00 1.28
1701 1891 4.461781 GGAATCCATAGGAGAAATGGCATG 59.538 45.833 0.00 0.0 43.11 4.06
1739 1929 6.179906 ACATTGGTAGAGGAGATATGGTTG 57.820 41.667 0.00 0.0 0.00 3.77
1770 1960 6.266330 CCTTGTAGATCAGATGAGGACATACA 59.734 42.308 0.00 0.0 36.82 2.29
1797 1987 3.267812 TCATCTCTTCTTGATGCCCCTTT 59.732 43.478 0.00 0.0 40.59 3.11
1844 2034 3.632145 GCAGTTCTCCCTTTTGTTCAGAA 59.368 43.478 0.00 0.0 0.00 3.02
1861 2052 4.460731 GCTTCCTCTTTTTCATAGGCAGTT 59.539 41.667 0.00 0.0 0.00 3.16
1869 2060 5.829924 TCTGACTTTGCTTCCTCTTTTTCAT 59.170 36.000 0.00 0.0 0.00 2.57
2121 2312 3.075283 TCCTCCTTCAACCAATAAAGCCA 59.925 43.478 0.00 0.0 0.00 4.75
2159 2350 3.599343 TGCTTACACACCTTATGCTCTG 58.401 45.455 0.00 0.0 0.00 3.35
2161 2352 3.600388 ACTGCTTACACACCTTATGCTC 58.400 45.455 0.00 0.0 0.00 4.26
2334 2528 3.117131 ACAAGGGGAAAGGTCACAAGATT 60.117 43.478 0.00 0.0 0.00 2.40
2590 2791 5.001232 GGACTGTAGCTGGTATGACAAAAA 58.999 41.667 0.00 0.0 0.00 1.94
2860 3068 8.734386 AGAGCTTGGATTTTTAGTAATGAACAG 58.266 33.333 0.00 0.0 0.00 3.16
2873 3081 6.951971 AGTGTATGACTAGAGCTTGGATTTT 58.048 36.000 0.00 0.0 30.86 1.82
2925 3133 4.336713 GGCTGAACTGTGAAGAAAGAAAGT 59.663 41.667 0.00 0.0 0.00 2.66
2934 3142 2.880268 TCATGTTGGCTGAACTGTGAAG 59.120 45.455 0.00 0.0 35.37 3.02
3015 3223 0.392461 AGGCGATAAAGCAAGGCGAA 60.392 50.000 0.00 0.0 39.27 4.70


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

AutoCloner maintained by Alex Coulton.