Multiple sequence alignment - TraesCS4D01G247700

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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 TraesCS4D01G247700 chr4D 100.000 2336 0 0 1 2336 416576916 416579251 0.000000e+00 4314.0
1 TraesCS4D01G247700 chr4D 94.643 1120 39 7 1218 2336 416643072 416644171 0.000000e+00 1716.0
2 TraesCS4D01G247700 chr4D 98.876 890 10 0 1 890 416147446 416146557 0.000000e+00 1589.0
3 TraesCS4D01G247700 chr4D 89.587 1258 86 21 896 2136 416146503 416145274 0.000000e+00 1555.0
4 TraesCS4D01G247700 chr4D 86.015 1237 105 33 896 2102 416429579 416428381 0.000000e+00 1264.0
5 TraesCS4D01G247700 chr4D 93.972 647 35 2 1185 1829 416694183 416694827 0.000000e+00 976.0
6 TraesCS4D01G247700 chr4D 88.863 431 35 9 898 1324 416642490 416642911 3.440000e-143 518.0
7 TraesCS4D01G247700 chr4D 88.863 431 35 9 898 1324 416693817 416694238 3.440000e-143 518.0
8 TraesCS4D01G247700 chr4D 90.698 172 7 5 735 898 416429791 416429621 1.090000e-53 220.0
9 TraesCS4D01G247700 chr4D 94.964 139 7 0 760 898 416642308 416642446 3.910000e-53 219.0
10 TraesCS4D01G247700 chr4D 94.245 139 8 0 760 898 416693635 416693773 1.820000e-51 213.0
11 TraesCS4D01G247700 chr4D 90.845 142 8 5 2076 2214 416694978 416695117 3.960000e-43 185.0
12 TraesCS4D01G247700 chr4D 93.333 45 2 1 1943 1986 416694968 416694924 5.390000e-07 65.8
13 TraesCS4D01G247700 chr4B 89.948 1343 82 23 898 2214 513450770 513452085 0.000000e+00 1683.0
14 TraesCS4D01G247700 chr4B 89.280 1250 88 24 896 2136 512797803 512796591 0.000000e+00 1524.0
15 TraesCS4D01G247700 chr4B 94.007 901 50 2 1 898 513449821 513450720 0.000000e+00 1362.0
16 TraesCS4D01G247700 chr4B 95.804 143 6 0 756 898 513079437 513079295 5.020000e-57 231.0
17 TraesCS4D01G247700 chr4B 93.277 119 8 0 780 898 512797963 512797845 2.390000e-40 176.0
18 TraesCS4D01G247700 chr4B 97.619 42 0 1 597 637 513450376 513450417 1.160000e-08 71.3
19 TraesCS4D01G247700 chr4A 89.963 1335 88 21 896 2214 47455910 47454606 0.000000e+00 1681.0
20 TraesCS4D01G247700 chr4A 89.429 1050 77 17 1182 2210 47709486 47710522 0.000000e+00 1293.0
21 TraesCS4D01G247700 chr4A 92.245 735 47 5 1215 1942 47650126 47650857 0.000000e+00 1033.0
22 TraesCS4D01G247700 chr4A 91.436 724 44 9 1427 2136 47736827 47737546 0.000000e+00 977.0
23 TraesCS4D01G247700 chr4A 94.825 599 29 2 1 598 47708246 47708843 0.000000e+00 933.0
24 TraesCS4D01G247700 chr4A 91.564 569 32 7 89 646 47456723 47456160 0.000000e+00 771.0
25 TraesCS4D01G247700 chr4A 92.558 430 24 3 896 1324 47736191 47736613 5.520000e-171 610.0
26 TraesCS4D01G247700 chr4A 93.366 407 26 1 1 406 609017031 609017437 3.320000e-168 601.0
27 TraesCS4D01G247700 chr4A 91.822 428 30 4 898 1324 47709121 47709544 2.000000e-165 592.0
28 TraesCS4D01G247700 chr4A 94.643 224 9 1 597 817 47708803 47709026 6.180000e-91 344.0
29 TraesCS4D01G247700 chr4A 92.718 206 15 0 693 898 47456164 47455959 4.880000e-77 298.0
30 TraesCS4D01G247700 chr6A 92.006 638 42 2 1 638 26094936 26094308 0.000000e+00 887.0
31 TraesCS4D01G247700 chr6A 90.909 638 49 2 1 638 26028542 26027914 0.000000e+00 848.0
32 TraesCS4D01G247700 chr7A 91.223 638 46 3 1 638 646297827 646298454 0.000000e+00 859.0
33 TraesCS4D01G247700 chr7A 90.000 250 15 3 389 638 660698189 660697950 4.850000e-82 315.0
34 TraesCS4D01G247700 chr3A 93.350 406 27 0 1 406 434195437 434195032 3.320000e-168 601.0
35 TraesCS4D01G247700 chr3A 90.000 250 15 3 389 638 244516570 244516809 4.850000e-82 315.0
36 TraesCS4D01G247700 chr3B 77.294 643 70 29 1480 2102 71316127 71315541 2.250000e-80 309.0
37 TraesCS4D01G247700 chr5D 85.542 83 12 0 2214 2296 556930120 556930038 1.150000e-13 87.9


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 TraesCS4D01G247700 chr4D 416576916 416579251 2335 False 4314.000000 4314 100.000000 1 2336 1 chr4D.!!$F1 2335
1 TraesCS4D01G247700 chr4D 416145274 416147446 2172 True 1572.000000 1589 94.231500 1 2136 2 chr4D.!!$R2 2135
2 TraesCS4D01G247700 chr4D 416642308 416644171 1863 False 817.666667 1716 92.823333 760 2336 3 chr4D.!!$F2 1576
3 TraesCS4D01G247700 chr4D 416428381 416429791 1410 True 742.000000 1264 88.356500 735 2102 2 chr4D.!!$R3 1367
4 TraesCS4D01G247700 chr4D 416693635 416695117 1482 False 473.000000 976 91.981250 760 2214 4 chr4D.!!$F3 1454
5 TraesCS4D01G247700 chr4B 513449821 513452085 2264 False 1038.766667 1683 93.858000 1 2214 3 chr4B.!!$F1 2213
6 TraesCS4D01G247700 chr4B 512796591 512797963 1372 True 850.000000 1524 91.278500 780 2136 2 chr4B.!!$R2 1356
7 TraesCS4D01G247700 chr4A 47650126 47650857 731 False 1033.000000 1033 92.245000 1215 1942 1 chr4A.!!$F1 727
8 TraesCS4D01G247700 chr4A 47454606 47456723 2117 True 916.666667 1681 91.415000 89 2214 3 chr4A.!!$R1 2125
9 TraesCS4D01G247700 chr4A 47736191 47737546 1355 False 793.500000 977 91.997000 896 2136 2 chr4A.!!$F4 1240
10 TraesCS4D01G247700 chr4A 47708246 47710522 2276 False 790.500000 1293 92.679750 1 2210 4 chr4A.!!$F3 2209
11 TraesCS4D01G247700 chr6A 26094308 26094936 628 True 887.000000 887 92.006000 1 638 1 chr6A.!!$R2 637
12 TraesCS4D01G247700 chr6A 26027914 26028542 628 True 848.000000 848 90.909000 1 638 1 chr6A.!!$R1 637
13 TraesCS4D01G247700 chr7A 646297827 646298454 627 False 859.000000 859 91.223000 1 638 1 chr7A.!!$F1 637
14 TraesCS4D01G247700 chr3B 71315541 71316127 586 True 309.000000 309 77.294000 1480 2102 1 chr3B.!!$R1 622

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
906 988 0.17668 AACTCGCAGGCTGATTCGAT 59.823 50.0 20.86 0.91 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 2931 1.204062 GTGTGACCGAATGTGCACG 59.796 57.895 13.13 0.0 34.12 5.34 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
262 264 2.234908 ACTCAGACATTACAGGTGGAGC 59.765 50.000 0.00 0.00 0.00 4.70
906 988 0.176680 AACTCGCAGGCTGATTCGAT 59.823 50.000 20.86 0.91 0.00 3.59
1183 1285 1.142097 GCGAGCTCCAAGGACTACC 59.858 63.158 8.47 0.00 0.00 3.18
1233 1335 1.681327 GAGCCCCGACTACACTCCA 60.681 63.158 0.00 0.00 0.00 3.86
1324 1861 3.736482 GACTACACTCCGGCGAGCG 62.736 68.421 9.30 0.26 40.03 5.03
1520 2057 0.953471 GATTACACGCCCAGCACACA 60.953 55.000 0.00 0.00 0.00 3.72
1887 2441 6.564328 TCACGAATCGATGGATATTATCTGG 58.436 40.000 10.55 0.00 31.01 3.86
2043 2634 2.559668 AGCAATTGTCATGTTCTGTGGG 59.440 45.455 7.40 0.00 0.00 4.61
2210 2840 3.369147 CCGATAGCTCTTGGATTTATGCG 59.631 47.826 0.00 0.00 0.00 4.73
2256 2886 8.256611 AGTCATATAACTTGTGTCACATGTTC 57.743 34.615 30.03 19.13 42.87 3.18
2266 2896 5.182487 TGTGTCACATGTTCAGTTTAGTGT 58.818 37.500 0.18 0.00 0.00 3.55
2270 2900 6.481976 TGTCACATGTTCAGTTTAGTGTTAGG 59.518 38.462 0.00 0.00 0.00 2.69
2274 2904 8.567948 CACATGTTCAGTTTAGTGTTAGGATTT 58.432 33.333 0.00 0.00 0.00 2.17
2301 2931 1.021968 ACGGTTTTGTGGTCTCAAGC 58.978 50.000 0.00 0.00 0.00 4.01
2310 2940 0.534877 TGGTCTCAAGCGTGCACATT 60.535 50.000 18.64 8.11 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
372 374 7.900782 TCCTAGTAATTCGTTCCTTTTCTTG 57.099 36.000 0.00 0.00 0.00 3.02
906 988 0.832135 AGGTGGAGGAAGACTGCGAA 60.832 55.000 0.00 0.00 41.01 4.70
957 1044 1.610363 CGGGATCTACAGCTAGAGCA 58.390 55.000 4.01 0.00 45.16 4.26
965 1056 4.301027 GGCCGGCGGGATCTACAG 62.301 72.222 29.48 0.00 34.06 2.74
1120 1222 3.182967 CGTACTCCTCGTAGTCGTAGTT 58.817 50.000 0.00 0.00 38.33 2.24
1183 1285 1.153489 CAGGGCTCGATGGAGTGTG 60.153 63.158 6.60 0.00 42.53 3.82
1233 1335 3.450115 GTGTAGTCCGGGCTCGCT 61.450 66.667 14.54 0.00 34.56 4.93
1823 2365 5.279406 CCCAAGGAACAAACAAATGCATAGA 60.279 40.000 0.00 0.00 0.00 1.98
1887 2441 4.084507 CGCATCTTCAACAAAACTCGATC 58.915 43.478 0.00 0.00 0.00 3.69
2043 2634 6.269315 CCTAAGACATCAGTACATCACAGTC 58.731 44.000 0.00 0.00 0.00 3.51
2226 2856 6.090783 GTGACACAAGTTATATGACTCACGA 58.909 40.000 0.00 0.00 0.00 4.35
2228 2858 7.331934 ACATGTGACACAAGTTATATGACTCAC 59.668 37.037 13.23 5.50 35.69 3.51
2229 2859 7.386059 ACATGTGACACAAGTTATATGACTCA 58.614 34.615 13.23 0.00 35.69 3.41
2239 2869 5.643379 AAACTGAACATGTGACACAAGTT 57.357 34.783 24.79 24.79 41.94 2.66
2266 2896 9.250624 CACAAAACCGTATTTTCAAAATCCTAA 57.749 29.630 0.00 0.00 0.00 2.69
2270 2900 7.436970 AGACCACAAAACCGTATTTTCAAAATC 59.563 33.333 0.00 0.00 0.00 2.17
2274 2904 5.357314 TGAGACCACAAAACCGTATTTTCAA 59.643 36.000 0.00 0.00 0.00 2.69
2301 2931 1.204062 GTGTGACCGAATGTGCACG 59.796 57.895 13.13 0.00 34.12 5.34


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

AutoCloner maintained by Alex Coulton.