Multiple sequence alignment - TraesCS2B01G181200

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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 TraesCS2B01G181200 chr2B 100.000 2848 0 0 1 2848 155819013 155821860 0.000000e+00 5260.0
1 TraesCS2B01G181200 chr2B 83.248 585 71 15 1267 1829 87775811 87775232 1.960000e-141 512.0
2 TraesCS2B01G181200 chr2B 81.981 616 85 18 1467 2069 87742513 87743115 1.520000e-137 499.0
3 TraesCS2B01G181200 chr2B 82.305 243 37 6 1566 1805 87529836 87529597 3.720000e-49 206.0
4 TraesCS2B01G181200 chr2B 80.812 271 29 14 993 1254 87775984 87775728 1.040000e-44 191.0
5 TraesCS2B01G181200 chr2B 96.429 56 2 0 993 1048 77804579 77804634 3.020000e-15 93.5
6 TraesCS2B01G181200 chr2D 97.745 1907 37 3 945 2848 105671528 105669625 0.000000e+00 3278.0
7 TraesCS2B01G181200 chr2D 97.689 1904 33 5 945 2848 91786550 91788442 0.000000e+00 3262.0
8 TraesCS2B01G181200 chr2D 82.700 237 41 0 1569 1805 55249118 55248882 7.990000e-51 211.0
9 TraesCS2B01G181200 chr2D 82.305 243 43 0 1563 1805 58639618 58639860 7.990000e-51 211.0
10 TraesCS2B01G181200 chr2D 92.079 101 8 0 997 1097 55265549 55265449 2.960000e-30 143.0
11 TraesCS2B01G181200 chr2A 94.654 1646 72 7 945 2577 109325261 109323619 0.000000e+00 2538.0
12 TraesCS2B01G181200 chr2A 88.396 879 76 14 91 948 154507383 154508256 0.000000e+00 1035.0
13 TraesCS2B01G181200 chr2A 83.513 279 36 6 2576 2848 109323579 109323305 4.710000e-63 252.0
14 TraesCS2B01G181200 chr2A 96.970 66 2 0 1 66 154507320 154507385 8.340000e-21 111.0
15 TraesCS2B01G181200 chrUn 99.052 949 7 2 1 948 232880317 232881264 0.000000e+00 1701.0
16 TraesCS2B01G181200 chrUn 83.598 189 31 0 1567 1755 293132589 293132777 8.110000e-41 178.0
17 TraesCS2B01G181200 chrUn 96.429 56 2 0 993 1048 293131988 293132043 3.020000e-15 93.5
18 TraesCS2B01G181200 chr7D 92.611 988 32 12 1 948 430381427 430382413 0.000000e+00 1382.0
19 TraesCS2B01G181200 chr3B 92.449 980 33 17 1 948 564029815 564030785 0.000000e+00 1362.0
20 TraesCS2B01G181200 chr1A 90.891 988 48 14 1 948 519894716 519895701 0.000000e+00 1288.0
21 TraesCS2B01G181200 chr3A 87.334 979 88 17 1 948 498625464 498624491 0.000000e+00 1088.0
22 TraesCS2B01G181200 chr3A 90.110 91 9 0 961 1051 561247792 561247702 4.980000e-23 119.0
23 TraesCS2B01G181200 chr3A 87.912 91 11 0 961 1051 561290984 561290894 1.080000e-19 108.0
24 TraesCS2B01G181200 chr3A 77.848 158 28 5 797 947 461166912 461166755 1.090000e-14 91.6
25 TraesCS2B01G181200 chr6B 89.789 568 42 9 1 555 451460746 451461310 0.000000e+00 713.0
26 TraesCS2B01G181200 chr1B 75.132 567 88 39 406 948 503875370 503875907 1.720000e-52 217.0
27 TraesCS2B01G181200 chr6D 81.609 261 38 5 1 261 469269969 469269719 1.030000e-49 207.0
28 TraesCS2B01G181200 chr7B 78.914 313 43 16 406 706 52620155 52620456 1.040000e-44 191.0
29 TraesCS2B01G181200 chr4A 82.500 120 15 5 132 248 714949987 714950103 1.810000e-17 100.0


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 TraesCS2B01G181200 chr2B 155819013 155821860 2847 False 5260.0 5260 100.0000 1 2848 1 chr2B.!!$F3 2847
1 TraesCS2B01G181200 chr2B 87742513 87743115 602 False 499.0 499 81.9810 1467 2069 1 chr2B.!!$F2 602
2 TraesCS2B01G181200 chr2B 87775232 87775984 752 True 351.5 512 82.0300 993 1829 2 chr2B.!!$R2 836
3 TraesCS2B01G181200 chr2D 105669625 105671528 1903 True 3278.0 3278 97.7450 945 2848 1 chr2D.!!$R3 1903
4 TraesCS2B01G181200 chr2D 91786550 91788442 1892 False 3262.0 3262 97.6890 945 2848 1 chr2D.!!$F2 1903
5 TraesCS2B01G181200 chr2A 109323305 109325261 1956 True 1395.0 2538 89.0835 945 2848 2 chr2A.!!$R1 1903
6 TraesCS2B01G181200 chr2A 154507320 154508256 936 False 573.0 1035 92.6830 1 948 2 chr2A.!!$F1 947
7 TraesCS2B01G181200 chrUn 232880317 232881264 947 False 1701.0 1701 99.0520 1 948 1 chrUn.!!$F1 947
8 TraesCS2B01G181200 chr7D 430381427 430382413 986 False 1382.0 1382 92.6110 1 948 1 chr7D.!!$F1 947
9 TraesCS2B01G181200 chr3B 564029815 564030785 970 False 1362.0 1362 92.4490 1 948 1 chr3B.!!$F1 947
10 TraesCS2B01G181200 chr1A 519894716 519895701 985 False 1288.0 1288 90.8910 1 948 1 chr1A.!!$F1 947
11 TraesCS2B01G181200 chr3A 498624491 498625464 973 True 1088.0 1088 87.3340 1 948 1 chr3A.!!$R2 947
12 TraesCS2B01G181200 chr6B 451460746 451461310 564 False 713.0 713 89.7890 1 555 1 chr6B.!!$F1 554
13 TraesCS2B01G181200 chr1B 503875370 503875907 537 False 217.0 217 75.1320 406 948 1 chr1B.!!$F1 542

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
143 146 1.444933 TCACTGTTCAGAATGGGGGT 58.555 50.000 6.83 0.0 36.16 4.95 F
1108 1267 2.825264 GGCTCTATCTGGCGGCTT 59.175 61.111 11.43 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1738 0.106419 GGGGAAATATTCGGGGTGCA 60.106 55.0 0.0 0.0 0.0 4.57 R
2417 2645 0.438830 GCTTCAGTGCCTTAACGTCG 59.561 55.0 0.0 0.0 0.0 5.12 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
143 146 1.444933 TCACTGTTCAGAATGGGGGT 58.555 50.000 6.83 0.0 36.16 4.95
979 1132 4.038642 GCACACAAACCCTAATTCCAGAAA 59.961 41.667 0.00 0.0 0.00 2.52
1080 1239 3.731728 GCTGGTGGCATCTCCCCA 61.732 66.667 0.00 0.0 41.35 4.96
1108 1267 2.825264 GGCTCTATCTGGCGGCTT 59.175 61.111 11.43 0.0 0.00 4.35
1522 1707 9.195411 CACAAATCAAATTGTAACTATGTGCTT 57.805 29.630 0.00 0.0 41.44 3.91
1553 1738 1.463674 GCGGTCCCATGTCAAAAGAT 58.536 50.000 0.00 0.0 0.00 2.40
1732 1917 6.378564 TGGGTTTACAAAATGAACAACTCTGA 59.621 34.615 0.00 0.0 0.00 3.27
1837 2043 7.289549 TGAGGATGATGATGAAGACATAGAAGT 59.710 37.037 0.00 0.0 36.82 3.01
1839 2045 6.147492 GGATGATGATGAAGACATAGAAGTGC 59.853 42.308 0.00 0.0 36.82 4.40
1856 2074 6.006449 AGAAGTGCTGGTATGATTGTTTTCT 58.994 36.000 0.00 0.0 0.00 2.52
1910 2128 2.446435 CAGTTATTGGACCAGGGGTTG 58.554 52.381 0.00 0.0 35.25 3.77
1951 2171 6.719370 ACCACAGGCATTAGTAAGAAAAATCA 59.281 34.615 0.00 0.0 0.00 2.57
2072 2297 4.090138 TGTGCGTTGCTTGGTTATATTG 57.910 40.909 0.00 0.0 0.00 1.90
2186 2411 2.857748 CTGACGGTTTGGTTTTTGCTTC 59.142 45.455 0.00 0.0 0.00 3.86
2246 2471 2.092321 TCTAGAGTCCTGCACTAGACCC 60.092 54.545 6.85 0.0 40.70 4.46
2323 2549 8.370182 TGAGCTGCTTAGATCATCAATATTACA 58.630 33.333 2.53 0.0 0.00 2.41
2417 2645 3.554934 TGTCACATATCCAAATCCAGGC 58.445 45.455 0.00 0.0 0.00 4.85
2813 3082 0.872388 CTACGTTTGTTCAGGTGCCC 59.128 55.000 0.00 0.0 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 146 8.898761 TCAACATTTCTGACAGTTTTAAGCTAA 58.101 29.630 1.59 0.00 0.00 3.09
979 1132 1.233369 CCTAGGTCGGAGGGGATGT 59.767 63.158 0.00 0.00 0.00 3.06
1080 1239 1.427368 AGATAGAGCCGGGAGAGACAT 59.573 52.381 2.18 0.00 0.00 3.06
1108 1267 2.125713 CATGCGACGGCTGGTACA 60.126 61.111 0.00 0.00 40.82 2.90
1135 1294 6.632672 GCTTTCTCAACATAGGGATTACCAGA 60.633 42.308 0.00 0.00 43.89 3.86
1137 1296 5.191722 AGCTTTCTCAACATAGGGATTACCA 59.808 40.000 0.00 0.00 43.89 3.25
1491 1675 9.567848 CATAGTTACAATTTGATTTGTGGTACC 57.432 33.333 4.43 4.43 40.00 3.34
1522 1707 4.373116 GACCGCCTGCCGTTCAGA 62.373 66.667 3.77 0.00 45.72 3.27
1543 1728 0.109532 TCGGGGTGCATCTTTTGACA 59.890 50.000 0.00 0.00 0.00 3.58
1553 1738 0.106419 GGGGAAATATTCGGGGTGCA 60.106 55.000 0.00 0.00 0.00 4.57
1732 1917 1.933853 GTTGAGACACTTGCGAACACT 59.066 47.619 0.00 0.00 0.00 3.55
1837 2043 7.545265 GCAATAAAGAAAACAATCATACCAGCA 59.455 33.333 0.00 0.00 0.00 4.41
1839 2045 8.253113 AGGCAATAAAGAAAACAATCATACCAG 58.747 33.333 0.00 0.00 0.00 4.00
1856 2074 7.466746 AATAGCAGAAAGACAAGGCAATAAA 57.533 32.000 0.00 0.00 0.00 1.40
1910 2128 5.509332 GCCTGTGGTTAAGTAGATAGTAGGC 60.509 48.000 0.00 0.00 38.98 3.93
1951 2171 5.104485 CCTCCTAATGCCTAGTGGTTAACTT 60.104 44.000 5.42 0.00 40.56 2.66
2186 2411 2.059541 GAGAAAGAACCGTCTTCACCG 58.940 52.381 0.00 0.00 43.59 4.94
2246 2471 7.797819 ACACTTTTCTTACAGAATTTAGCGAG 58.202 34.615 0.00 0.00 33.67 5.03
2323 2549 3.818210 TGTTGTTGACGATGCTTAACCAT 59.182 39.130 0.00 0.00 0.00 3.55
2417 2645 0.438830 GCTTCAGTGCCTTAACGTCG 59.561 55.000 0.00 0.00 0.00 5.12
2813 3082 1.315257 CCTGGCCCAAATCTTCACCG 61.315 60.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.