Multiple sequence alignment - TraesCS3B01G527700

Loading Multiple Alignment...

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 TraesCS3B01G527700 chr3B 100.000 2963 0 0 1 2963 769485336 769482374 0.000000e+00 5472.0
1 TraesCS3B01G527700 chr3B 93.677 1977 99 7 1 1952 769306076 769304101 0.000000e+00 2935.0
2 TraesCS3B01G527700 chr3B 93.627 1977 99 8 1 1952 770354374 770352400 0.000000e+00 2928.0
3 TraesCS3B01G527700 chr3B 97.038 1013 9 10 1952 2963 9286075 9285083 0.000000e+00 1685.0
4 TraesCS3B01G527700 chr3B 91.651 1090 68 7 1 1068 769249092 769248004 0.000000e+00 1487.0
5 TraesCS3B01G527700 chr3B 88.562 1154 116 8 805 1950 770310156 770309011 0.000000e+00 1386.0
6 TraesCS3B01G527700 chr3B 94.237 885 48 2 1071 1952 769232625 769231741 0.000000e+00 1349.0
7 TraesCS3B01G527700 chr3B 95.435 701 25 3 1 700 769374878 769374184 0.000000e+00 1110.0
8 TraesCS3B01G527700 chr3B 90.144 832 59 7 1 810 770400804 770399974 0.000000e+00 1061.0
9 TraesCS3B01G527700 chr3B 89.892 831 61 9 1 810 769418815 769417987 0.000000e+00 1048.0
10 TraesCS3B01G527700 chr3B 75.294 935 200 21 992 1905 769906909 769905985 4.570000e-113 418.0
11 TraesCS3B01G527700 chr3B 75.187 935 202 20 992 1905 770208680 770207755 5.910000e-112 414.0
12 TraesCS3B01G527700 chr3B 74.633 954 194 28 992 1906 769404785 769403841 7.750000e-101 377.0
13 TraesCS3B01G527700 chr3B 73.888 1034 218 35 815 1817 770346536 770347548 1.680000e-97 366.0
14 TraesCS3B01G527700 chr3B 91.111 135 11 1 1952 2085 42548675 42548541 6.520000e-42 182.0
15 TraesCS3B01G527700 chr3B 100.000 34 0 0 695 728 769374173 769374140 2.470000e-06 63.9
16 TraesCS3B01G527700 chr6A 99.309 1013 6 1 1952 2963 15467460 15466448 0.000000e+00 1831.0
17 TraesCS3B01G527700 chr6A 87.565 193 23 1 2587 2779 27089654 27089463 3.840000e-54 222.0
18 TraesCS3B01G527700 chr6A 86.667 195 26 0 2585 2779 27094052 27093858 1.790000e-52 217.0
19 TraesCS3B01G527700 chr7A 98.031 1016 7 3 1949 2963 66644441 66645444 0.000000e+00 1753.0
20 TraesCS3B01G527700 chr5A 96.940 1013 11 9 1952 2963 458336308 458335315 0.000000e+00 1681.0
21 TraesCS3B01G527700 chrUn 90.809 1088 71 9 1 1066 298658923 298657843 0.000000e+00 1428.0
22 TraesCS3B01G527700 chrUn 90.809 1088 71 9 1 1066 311034673 311035753 0.000000e+00 1428.0
23 TraesCS3B01G527700 chrUn 90.809 1088 71 9 1 1066 311053680 311052600 0.000000e+00 1428.0
24 TraesCS3B01G527700 chrUn 90.809 1088 71 9 1 1066 344523273 344524353 0.000000e+00 1428.0
25 TraesCS3B01G527700 chrUn 94.949 297 12 3 2669 2963 316937590 316937295 2.080000e-126 462.0
26 TraesCS3B01G527700 chrUn 95.283 106 5 0 2483 2588 316937692 316937587 5.080000e-38 169.0
27 TraesCS3B01G527700 chr2B 91.931 347 28 0 2155 2501 109404726 109404380 1.230000e-133 486.0
28 TraesCS3B01G527700 chr2B 93.069 101 6 1 1952 2051 109405035 109404935 2.380000e-31 147.0
29 TraesCS3B01G527700 chr6B 93.072 332 21 1 2080 2411 11701663 11701992 4.440000e-133 484.0
30 TraesCS3B01G527700 chr3A 76.247 922 197 17 1001 1905 712575792 712574876 1.240000e-128 470.0
31 TraesCS3B01G527700 chr3A 75.855 936 188 23 996 1903 712629542 712628617 2.710000e-120 442.0
32 TraesCS3B01G527700 chr7B 94.613 297 14 2 2669 2963 585478693 585478989 2.690000e-125 459.0
33 TraesCS3B01G527700 chr7B 93.776 241 15 0 2080 2320 585477343 585477583 2.170000e-96 363.0
34 TraesCS3B01G527700 chr7B 96.226 106 4 0 2483 2588 585478591 585478696 1.090000e-39 174.0
35 TraesCS3B01G527700 chr2A 94.613 297 13 3 2669 2963 21216906 21216611 9.680000e-125 457.0
36 TraesCS3B01G527700 chr2A 92.996 257 13 4 2712 2963 620708338 620708082 1.300000e-98 370.0
37 TraesCS3B01G527700 chr2A 92.607 257 14 3 2712 2963 736452851 736453107 6.040000e-97 364.0
38 TraesCS3B01G527700 chr2A 94.340 106 6 0 2483 2588 21217008 21216903 2.360000e-36 163.0
39 TraesCS3B01G527700 chr3D 75.350 929 195 20 1001 1903 577341239 577340319 1.640000e-112 416.0
40 TraesCS3B01G527700 chr1B 94.215 242 14 0 2080 2321 32425070 32424829 1.300000e-98 370.0
41 TraesCS3B01G527700 chr5B 93.802 242 15 0 2080 2321 591685850 591686091 6.040000e-97 364.0
42 TraesCS3B01G527700 chr4D 87.931 116 11 2 1971 2085 337052234 337052347 1.850000e-27 134.0


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 TraesCS3B01G527700 chr3B 769482374 769485336 2962 True 5472.00 5472 100.000000 1 2963 1 chr3B.!!$R8 2962
1 TraesCS3B01G527700 chr3B 769304101 769306076 1975 True 2935.00 2935 93.677000 1 1952 1 chr3B.!!$R5 1951
2 TraesCS3B01G527700 chr3B 770352400 770354374 1974 True 2928.00 2928 93.627000 1 1952 1 chr3B.!!$R12 1951
3 TraesCS3B01G527700 chr3B 9285083 9286075 992 True 1685.00 1685 97.038000 1952 2963 1 chr3B.!!$R1 1011
4 TraesCS3B01G527700 chr3B 769248004 769249092 1088 True 1487.00 1487 91.651000 1 1068 1 chr3B.!!$R4 1067
5 TraesCS3B01G527700 chr3B 770309011 770310156 1145 True 1386.00 1386 88.562000 805 1950 1 chr3B.!!$R11 1145
6 TraesCS3B01G527700 chr3B 769231741 769232625 884 True 1349.00 1349 94.237000 1071 1952 1 chr3B.!!$R3 881
7 TraesCS3B01G527700 chr3B 770399974 770400804 830 True 1061.00 1061 90.144000 1 810 1 chr3B.!!$R13 809
8 TraesCS3B01G527700 chr3B 769417987 769418815 828 True 1048.00 1048 89.892000 1 810 1 chr3B.!!$R7 809
9 TraesCS3B01G527700 chr3B 769374140 769374878 738 True 586.95 1110 97.717500 1 728 2 chr3B.!!$R14 727
10 TraesCS3B01G527700 chr3B 769905985 769906909 924 True 418.00 418 75.294000 992 1905 1 chr3B.!!$R9 913
11 TraesCS3B01G527700 chr3B 770207755 770208680 925 True 414.00 414 75.187000 992 1905 1 chr3B.!!$R10 913
12 TraesCS3B01G527700 chr3B 769403841 769404785 944 True 377.00 377 74.633000 992 1906 1 chr3B.!!$R6 914
13 TraesCS3B01G527700 chr3B 770346536 770347548 1012 False 366.00 366 73.888000 815 1817 1 chr3B.!!$F1 1002
14 TraesCS3B01G527700 chr6A 15466448 15467460 1012 True 1831.00 1831 99.309000 1952 2963 1 chr6A.!!$R1 1011
15 TraesCS3B01G527700 chr7A 66644441 66645444 1003 False 1753.00 1753 98.031000 1949 2963 1 chr7A.!!$F1 1014
16 TraesCS3B01G527700 chr5A 458335315 458336308 993 True 1681.00 1681 96.940000 1952 2963 1 chr5A.!!$R1 1011
17 TraesCS3B01G527700 chrUn 298657843 298658923 1080 True 1428.00 1428 90.809000 1 1066 1 chrUn.!!$R1 1065
18 TraesCS3B01G527700 chrUn 311034673 311035753 1080 False 1428.00 1428 90.809000 1 1066 1 chrUn.!!$F1 1065
19 TraesCS3B01G527700 chrUn 311052600 311053680 1080 True 1428.00 1428 90.809000 1 1066 1 chrUn.!!$R2 1065
20 TraesCS3B01G527700 chrUn 344523273 344524353 1080 False 1428.00 1428 90.809000 1 1066 1 chrUn.!!$F2 1065
21 TraesCS3B01G527700 chr2B 109404380 109405035 655 True 316.50 486 92.500000 1952 2501 2 chr2B.!!$R1 549
22 TraesCS3B01G527700 chr3A 712574876 712575792 916 True 470.00 470 76.247000 1001 1905 1 chr3A.!!$R1 904
23 TraesCS3B01G527700 chr3A 712628617 712629542 925 True 442.00 442 75.855000 996 1903 1 chr3A.!!$R2 907
24 TraesCS3B01G527700 chr7B 585477343 585478989 1646 False 332.00 459 94.871667 2080 2963 3 chr7B.!!$F1 883
25 TraesCS3B01G527700 chr3D 577340319 577341239 920 True 416.00 416 75.350000 1001 1903 1 chr3D.!!$R1 902

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
579 585 0.239347 CTTGGAAGCAGTTTCGCTGG 59.761 55.0 0.0 0.0 42.89 4.85 F
663 676 0.523072 CTGGTTCCAAATGTGCTCCG 59.477 55.0 0.0 0.0 0.00 4.63 F
1068 1129 0.534877 TCTTTTCTGCTCTTGCCGCA 60.535 50.0 0.0 0.0 38.71 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 1607 0.817013 CATAAGTGTTTGGCCGGCAT 59.183 50.000 30.85 6.52 0.00 4.40 R
1672 1758 3.136123 CAGCATCACCCCAAGCCG 61.136 66.667 0.00 0.00 0.00 5.52 R
2090 2218 4.202357 GGCATATGGTTACATCAGAGGTCA 60.202 45.833 4.56 0.00 38.53 4.02 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
32 33 3.947834 CAGAAAGTGGTGAAGGAACAACT 59.052 43.478 0.00 0.00 35.77 3.16
95 96 2.165998 GGTGAAAGCAGAATTGGAGCT 58.834 47.619 0.00 0.00 41.03 4.09
119 120 6.983906 AAAGAAGTTTCTTGATGGGACAAT 57.016 33.333 7.82 0.00 46.22 2.71
209 211 8.336801 TGAGGAGAAGAACCTTAAATAAAAGC 57.663 34.615 0.00 0.00 37.93 3.51
217 219 7.004691 AGAACCTTAAATAAAAGCAGGTGTCT 58.995 34.615 0.00 0.00 37.93 3.41
339 343 4.927782 GTGGTGGCACGTGCTCCA 62.928 66.667 35.20 35.20 40.38 3.86
396 400 8.257306 AGAAGACTAAAGCCAACAAATTTGAAA 58.743 29.630 24.64 0.41 0.00 2.69
413 417 1.002792 GAAAACAGACGGACAACAGCC 60.003 52.381 0.00 0.00 0.00 4.85
456 460 6.306199 TGGGTACTACGGATATTAGCTACAA 58.694 40.000 0.00 0.00 0.00 2.41
579 585 0.239347 CTTGGAAGCAGTTTCGCTGG 59.761 55.000 0.00 0.00 42.89 4.85
663 676 0.523072 CTGGTTCCAAATGTGCTCCG 59.477 55.000 0.00 0.00 0.00 4.63
669 682 1.361668 CCAAATGTGCTCCGTCTCCG 61.362 60.000 0.00 0.00 0.00 4.63
728 758 4.022589 GCAAACCAACTCCCCTTAACTAAC 60.023 45.833 0.00 0.00 0.00 2.34
729 759 5.134661 CAAACCAACTCCCCTTAACTAACA 58.865 41.667 0.00 0.00 0.00 2.41
739 769 5.105473 TCCCCTTAACTAACAGAATGAGACG 60.105 44.000 0.00 0.00 39.69 4.18
770 800 6.489700 TGTGTCTCCATTTCAAGAAATAAGCA 59.510 34.615 7.65 8.15 38.84 3.91
790 820 5.923204 AGCAACAGCTAGCATATTTAGAGT 58.077 37.500 18.83 0.00 36.70 3.24
863 897 1.955778 CTTGATTCACCACAGCCAACA 59.044 47.619 0.00 0.00 0.00 3.33
917 970 0.993509 TAGAAATGGGGGCCAGAGGG 60.994 60.000 4.39 0.00 36.75 4.30
999 1059 1.002366 GCTGGCAGTACTCACAATCG 58.998 55.000 17.16 0.00 0.00 3.34
1031 1092 2.295909 TGGTTAGTTCTGCCATTGTTGC 59.704 45.455 0.00 0.00 0.00 4.17
1058 1119 2.352960 CAGTTAGCCGGATCTTTTCTGC 59.647 50.000 5.05 0.00 0.00 4.26
1068 1129 0.534877 TCTTTTCTGCTCTTGCCGCA 60.535 50.000 0.00 0.00 38.71 5.69
1143 1207 1.113517 GGCTGGAGATGGCATGCATT 61.114 55.000 21.36 5.56 0.00 3.56
1180 1244 1.754803 TCAAGACGTCAGACAACTGGT 59.245 47.619 19.50 0.00 43.60 4.00
1241 1305 4.107051 GCGCGCTGCACAGGATTT 62.107 61.111 26.67 0.00 45.45 2.17
1304 1370 2.653726 TGAAGAGGCAAAGCAAGTGAA 58.346 42.857 0.00 0.00 0.00 3.18
1322 1388 3.004315 GTGAAAAGGCAATCCTCGTTTCA 59.996 43.478 6.96 6.96 42.52 2.69
1332 1398 1.887854 TCCTCGTTTCATGGACGTGTA 59.112 47.619 17.76 4.73 41.08 2.90
1413 1497 4.082523 GACGCTGCCTGGGCTGTA 62.083 66.667 17.38 0.00 42.51 2.74
1439 1523 3.268986 CGAGAGGCTCGCCGATAT 58.731 61.111 21.80 0.00 46.75 1.63
1470 1554 5.047590 TGAATTCATGAGATTTGTGCAGCTT 60.048 36.000 3.38 0.00 0.00 3.74
1523 1607 4.021104 CGACCCTCTCATCAGGCATATTTA 60.021 45.833 0.00 0.00 31.23 1.40
1672 1758 3.801114 AGCAACCCAAGAACAGTTTTC 57.199 42.857 0.00 0.00 0.00 2.29
1723 1809 6.696148 GGAGAGTACAAACATAATCGGTACTG 59.304 42.308 7.42 0.00 43.26 2.74
2090 2218 1.305802 TAGTGCCGTCCATGACCCT 60.306 57.895 0.00 0.00 0.00 4.34
2418 2880 8.229811 GTCAAGCAAAAATTATTTGATTCCCAC 58.770 33.333 13.72 8.27 36.07 4.61
2593 3689 3.131400 TCAAGCACGGTTAAAGCCTTTTT 59.869 39.130 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 8.477419 AATTGTCCCATCAAGAAACTTCTTTA 57.523 30.769 1.87 0.00 44.70 1.85
158 160 8.924511 TCCTTCAGCTTATATATCCCTTTTTG 57.075 34.615 0.00 0.00 0.00 2.44
160 162 8.894592 TCATCCTTCAGCTTATATATCCCTTTT 58.105 33.333 0.00 0.00 0.00 2.27
209 211 2.476619 CTGCGTTTGAACTAGACACCTG 59.523 50.000 0.00 0.00 0.00 4.00
217 219 5.804692 TGTCTTTTTCTGCGTTTGAACTA 57.195 34.783 0.00 0.00 0.00 2.24
339 343 1.029681 GTCGCTCCCAACTGGTTTTT 58.970 50.000 0.00 0.00 34.77 1.94
390 394 3.426963 GCTGTTGTCCGTCTGTTTTCAAA 60.427 43.478 0.00 0.00 0.00 2.69
396 400 0.532862 CAGGCTGTTGTCCGTCTGTT 60.533 55.000 6.28 0.00 0.00 3.16
413 417 3.119245 CCCAATGTCAATTGCCTCTTCAG 60.119 47.826 0.00 0.00 41.66 3.02
428 432 5.778750 AGCTAATATCCGTAGTACCCAATGT 59.221 40.000 0.00 0.00 0.00 2.71
663 676 1.320507 GGGACATACTCCTCGGAGAC 58.679 60.000 19.35 5.46 44.53 3.36
669 682 8.152023 AGAATATATTTGGGGACATACTCCTC 57.848 38.462 0.00 0.00 40.62 3.71
728 758 5.107824 AGACACATGATTCGTCTCATTCTG 58.892 41.667 0.00 2.84 35.02 3.02
729 759 5.336150 AGACACATGATTCGTCTCATTCT 57.664 39.130 0.00 0.33 35.02 2.40
770 800 8.792830 TGAAAACTCTAAATATGCTAGCTGTT 57.207 30.769 17.23 5.18 0.00 3.16
863 897 0.037447 GTCCTTGGCTCCTTGCTTCT 59.963 55.000 0.00 0.00 42.39 2.85
935 988 4.641989 GGGCTGCTATTCTCAAGAAATGAA 59.358 41.667 0.00 0.00 37.67 2.57
936 989 4.202441 GGGCTGCTATTCTCAAGAAATGA 58.798 43.478 0.00 0.00 37.61 2.57
999 1059 4.125703 CAGAACTAACCATCTCAGCCATC 58.874 47.826 0.00 0.00 0.00 3.51
1031 1092 0.876342 GATCCGGCTAACTGCTTCCG 60.876 60.000 0.00 0.00 42.39 4.30
1068 1129 5.337009 CCATTTATCCTTGACTTTGCTGCTT 60.337 40.000 0.00 0.00 0.00 3.91
1143 1207 1.324383 TGAGCGCGACCTCCATATTA 58.676 50.000 12.10 0.00 0.00 0.98
1180 1244 2.865276 GCAGCGATGCATCAGTGATCTA 60.865 50.000 25.70 0.00 34.41 1.98
1439 1523 5.047590 ACAAATCTCATGAATTCAGCAGCAA 60.048 36.000 14.54 0.00 0.00 3.91
1523 1607 0.817013 CATAAGTGTTTGGCCGGCAT 59.183 50.000 30.85 6.52 0.00 4.40
1672 1758 3.136123 CAGCATCACCCCAAGCCG 61.136 66.667 0.00 0.00 0.00 5.52
1723 1809 3.435671 ACCAGACGTAAGCATTTTACTGC 59.564 43.478 0.00 0.00 45.62 4.40
2090 2218 4.202357 GGCATATGGTTACATCAGAGGTCA 60.202 45.833 4.56 0.00 38.53 4.02


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

AutoCloner maintained by Alex Coulton.