Multiple sequence alignment - TraesCS1B01G013500

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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 TraesCS1B01G013500 chr1B 100.000 3209 0 0 1 3209 6438561 6435353 0.000000e+00 5927
1 TraesCS1B01G013500 chr1B 93.920 3010 157 7 6 2995 22184650 22187653 0.000000e+00 4521
2 TraesCS1B01G013500 chr1B 88.028 852 71 19 745 1576 5521100 5520260 0.000000e+00 979
3 TraesCS1B01G013500 chr1B 85.287 870 80 29 745 1576 5688036 5687177 0.000000e+00 854
4 TraesCS1B01G013500 chr1B 89.482 656 51 10 745 1383 5585820 5585166 0.000000e+00 813
5 TraesCS1B01G013500 chr1B 88.271 665 60 10 1237 1892 5520557 5519902 0.000000e+00 780
6 TraesCS1B01G013500 chr1B 84.767 709 80 17 1219 1910 5687492 5686795 0.000000e+00 686
7 TraesCS1B01G013500 chr1B 87.595 395 42 6 339 727 5688351 5687958 4.880000e-123 451
8 TraesCS1B01G013500 chr1B 90.991 222 18 2 2984 3203 22187670 22187891 6.730000e-77 298
9 TraesCS1B01G013500 chr1B 86.869 198 19 6 346 536 5586084 5585887 6.970000e-52 215
10 TraesCS1B01G013500 chr1B 89.831 118 8 2 2859 2975 7314355 7314241 7.170000e-32 148
11 TraesCS1B01G013500 chr1D 93.338 2867 140 12 6 2826 7157702 7154841 0.000000e+00 4189
12 TraesCS1B01G013500 chr1D 94.886 1486 75 1 6 1491 4340672 4342156 0.000000e+00 2322
13 TraesCS1B01G013500 chr1D 91.439 1647 123 15 1180 2817 4341908 4343545 0.000000e+00 2244
14 TraesCS1B01G013500 chr1D 85.005 2014 224 48 745 2715 5138787 5140765 0.000000e+00 1975
15 TraesCS1B01G013500 chr1D 84.577 1407 151 37 1329 2715 5356898 5358258 0.000000e+00 1336
16 TraesCS1B01G013500 chr1D 82.888 1385 154 48 1343 2715 3710391 3709078 0.000000e+00 1168
17 TraesCS1B01G013500 chr1D 81.631 1361 162 43 1372 2721 3826135 3824852 0.000000e+00 1048
18 TraesCS1B01G013500 chr1D 88.980 853 60 16 746 1576 99013 99853 0.000000e+00 1024
19 TraesCS1B01G013500 chr1D 81.795 769 90 25 745 1494 84329 85066 1.650000e-167 599
20 TraesCS1B01G013500 chr1D 86.650 397 45 5 339 728 98696 99091 1.770000e-117 433
21 TraesCS1B01G013500 chr1D 86.012 336 44 3 394 728 84075 84408 1.090000e-94 357
22 TraesCS1B01G013500 chr1D 92.105 228 15 2 2984 3209 7154484 7154258 5.170000e-83 318
23 TraesCS1B01G013500 chr1D 92.342 222 15 2 2984 3203 4343954 4344175 6.680000e-82 315
24 TraesCS1B01G013500 chr1D 96.875 128 4 0 2867 2994 4343809 4343936 6.970000e-52 215
25 TraesCS1B01G013500 chr1D 96.460 113 4 0 2882 2994 7154614 7154502 1.520000e-43 187
26 TraesCS1B01G013500 chr1D 90.625 96 8 1 742 836 4341312 4341407 3.360000e-25 126
27 TraesCS1B01G013500 chr1D 90.625 96 8 1 742 836 7157063 7156968 3.360000e-25 126
28 TraesCS1B01G013500 chr1A 84.718 1420 150 39 1308 2715 6517557 6518921 0.000000e+00 1358
29 TraesCS1B01G013500 chr1A 83.380 1083 104 38 1293 2366 6561904 6562919 0.000000e+00 933
30 TraesCS1B01G013500 chr1A 83.751 837 95 15 1920 2745 4095940 4095134 0.000000e+00 754
31 TraesCS1B01G013500 chr1A 84.552 725 97 9 6 723 6516437 6517153 0.000000e+00 704
32 TraesCS1B01G013500 chr1A 85.166 391 49 7 347 731 4097476 4097089 3.000000e-105 392


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 TraesCS1B01G013500 chr1B 6435353 6438561 3208 True 5927.000000 5927 100.0000 1 3209 1 chr1B.!!$R1 3208
1 TraesCS1B01G013500 chr1B 22184650 22187891 3241 False 2409.500000 4521 92.4555 6 3203 2 chr1B.!!$F1 3197
2 TraesCS1B01G013500 chr1B 5519902 5521100 1198 True 879.500000 979 88.1495 745 1892 2 chr1B.!!$R3 1147
3 TraesCS1B01G013500 chr1B 5686795 5688351 1556 True 663.666667 854 85.8830 339 1910 3 chr1B.!!$R5 1571
4 TraesCS1B01G013500 chr1B 5585166 5586084 918 True 514.000000 813 88.1755 346 1383 2 chr1B.!!$R4 1037
5 TraesCS1B01G013500 chr1D 5138787 5140765 1978 False 1975.000000 1975 85.0050 745 2715 1 chr1D.!!$F1 1970
6 TraesCS1B01G013500 chr1D 5356898 5358258 1360 False 1336.000000 1336 84.5770 1329 2715 1 chr1D.!!$F2 1386
7 TraesCS1B01G013500 chr1D 7154258 7157702 3444 True 1205.000000 4189 93.1320 6 3209 4 chr1D.!!$R3 3203
8 TraesCS1B01G013500 chr1D 3709078 3710391 1313 True 1168.000000 1168 82.8880 1343 2715 1 chr1D.!!$R1 1372
9 TraesCS1B01G013500 chr1D 3824852 3826135 1283 True 1048.000000 1048 81.6310 1372 2721 1 chr1D.!!$R2 1349
10 TraesCS1B01G013500 chr1D 4340672 4344175 3503 False 1044.400000 2322 93.2334 6 3203 5 chr1D.!!$F5 3197
11 TraesCS1B01G013500 chr1D 98696 99853 1157 False 728.500000 1024 87.8150 339 1576 2 chr1D.!!$F4 1237
12 TraesCS1B01G013500 chr1D 84075 85066 991 False 478.000000 599 83.9035 394 1494 2 chr1D.!!$F3 1100
13 TraesCS1B01G013500 chr1A 6516437 6518921 2484 False 1031.000000 1358 84.6350 6 2715 2 chr1A.!!$F2 2709
14 TraesCS1B01G013500 chr1A 6561904 6562919 1015 False 933.000000 933 83.3800 1293 2366 1 chr1A.!!$F1 1073
15 TraesCS1B01G013500 chr1A 4095134 4097476 2342 True 573.000000 754 84.4585 347 2745 2 chr1A.!!$R1 2398

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
265 267 4.394712 GAGACCAGGTGCACCCCG 62.395 72.222 32.29 23.62 36.42 5.73 F
1766 2501 0.108520 TCCCCGAACAATCACGCTAC 60.109 55.000 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 2576 0.312102 GTTGCTGCTGAGGTTGGTTC 59.688 55.0 0.00 0.00 0.00 3.62 R
3131 4169 0.037605 ACCTTGGCACGTAGCTACAC 60.038 55.0 23.21 11.68 44.79 2.90 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
84 85 7.506599 TGGGTTGATAAAGTACCTCGATATACA 59.493 37.037 8.46 0.00 0.00 2.29
259 261 6.174049 AGATTTAGTAAAAGAGACCAGGTGC 58.826 40.000 0.00 0.00 0.00 5.01
260 262 4.967084 TTAGTAAAAGAGACCAGGTGCA 57.033 40.909 0.00 0.00 0.00 4.57
265 267 4.394712 GAGACCAGGTGCACCCCG 62.395 72.222 32.29 23.62 36.42 5.73
556 570 7.255590 CCCTCCACATGTAAGGCTTTAATAATG 60.256 40.741 17.33 5.52 0.00 1.90
610 625 6.376018 TGCAACTTAGTCCTACACAAGTTTTT 59.624 34.615 6.93 0.00 35.71 1.94
688 703 9.851686 AAAAGTGATAATATCCTGATAAGTGCA 57.148 29.630 0.00 0.00 0.00 4.57
701 716 6.122850 TGATAAGTGCATGACATGTAAAGC 57.877 37.500 16.62 3.31 0.00 3.51
715 730 5.183140 ACATGTAAAGCGAATAAGGCAAGTT 59.817 36.000 0.00 0.00 0.00 2.66
783 798 8.031864 AGAAGTGATACTATCCTGATAAATGCG 58.968 37.037 0.00 0.00 0.00 4.73
817 832 6.552445 AGTGAATAAGGCAAGTCATCTACT 57.448 37.500 0.00 0.00 41.49 2.57
1063 1089 4.281688 AGCATCAAAACCAAGCAACACTAT 59.718 37.500 0.00 0.00 0.00 2.12
1161 1187 1.573857 TGGAGACTAGCCACATCCCTA 59.426 52.381 0.00 0.00 0.00 3.53
1361 1844 0.179124 TTTCGCAGCAACAACAACCC 60.179 50.000 0.00 0.00 0.00 4.11
1525 2243 5.127031 AGCAACAACAACAACCAATTCTACT 59.873 36.000 0.00 0.00 0.00 2.57
1585 2306 3.569250 ACCGCAACAACAAATACCATC 57.431 42.857 0.00 0.00 0.00 3.51
1766 2501 0.108520 TCCCCGAACAATCACGCTAC 60.109 55.000 0.00 0.00 0.00 3.58
1829 2576 2.430332 ACAACAACATGGTCAGGGTTTG 59.570 45.455 0.00 0.00 0.00 2.93
1973 2741 2.227194 CCTCAACAACAACAGGTACCC 58.773 52.381 8.74 0.00 0.00 3.69
2036 2804 2.821969 GGTGATGACTTCCATTGCACTT 59.178 45.455 0.00 0.00 35.17 3.16
2332 3107 2.868583 GTGTGGATGTCGATCTGATTGG 59.131 50.000 5.09 0.00 0.00 3.16
2395 3170 3.108144 CGCAAGCTGGTGCATTAATTAC 58.892 45.455 10.83 0.00 45.19 1.89
2467 3242 8.017418 TGTAAAATTTGGGTTGAACAGAAGAT 57.983 30.769 0.00 0.00 0.00 2.40
2510 3285 7.557719 TCTTTAATGGTTGGAGATTTGAGATCC 59.442 37.037 0.00 0.00 0.00 3.36
2556 3336 4.421948 GTTCCGACTACTACCATTGTCTG 58.578 47.826 0.00 0.00 0.00 3.51
2682 3470 6.287107 TCTAGCTTTTTCTTGAACTTCACG 57.713 37.500 0.00 0.00 0.00 4.35
2831 3625 1.066257 GCAGCAGGGTGTTTGTGTG 59.934 57.895 0.07 0.00 0.00 3.82
2840 3634 1.680555 GGTGTTTGTGTGTGTCTGGGA 60.681 52.381 0.00 0.00 0.00 4.37
2845 3639 1.073199 GTGTGTGTCTGGGAAGGGG 59.927 63.158 0.00 0.00 0.00 4.79
2880 3888 3.090952 TGCGCATTACTTTGTTTTGCT 57.909 38.095 5.66 0.00 0.00 3.91
2978 3986 1.451504 CTGAGAGTGTGGGTGCCAA 59.548 57.895 0.00 0.00 34.18 4.52
3004 4040 2.281484 GGCAAAGGACACTCGGCA 60.281 61.111 0.00 0.00 0.00 5.69
3016 4052 0.988832 ACTCGGCATACCCCTTTTCA 59.011 50.000 0.00 0.00 0.00 2.69
3032 4068 5.585844 CCCTTTTCAGCAAACAGAAATTTGT 59.414 36.000 0.00 0.00 40.92 2.83
3131 4169 2.686816 GGGACGACGCAAATGGTGG 61.687 63.158 0.00 0.00 0.00 4.61
3144 4182 0.108329 ATGGTGGTGTAGCTACGTGC 60.108 55.000 18.74 11.14 43.29 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.399639 TTCATCAACAAACCTTTAGAACCC 57.600 37.500 0.00 0.00 0.00 4.11
22 23 9.896263 ATGCCAAACATTTTAACATTTTTCATC 57.104 25.926 0.00 0.00 34.40 2.92
106 107 5.923733 TTGGTTTACTGTGGTTCATGTTT 57.076 34.783 0.00 0.00 0.00 2.83
259 261 5.630661 TTGTGTAAATATTTCACGGGGTG 57.369 39.130 3.39 0.00 35.20 4.61
260 262 8.410141 CAATATTGTGTAAATATTTCACGGGGT 58.590 33.333 3.39 4.07 32.24 4.95
556 570 3.118038 TGTGGGTTGTTAGGATATGCTCC 60.118 47.826 0.00 0.00 45.33 4.70
610 625 5.067283 GTGTCAGCCTTAAACAAGAAAAGGA 59.933 40.000 4.56 0.00 42.01 3.36
688 703 4.881273 TGCCTTATTCGCTTTACATGTCAT 59.119 37.500 0.00 0.00 0.00 3.06
701 716 8.534333 TTGCTATAGATAACTTGCCTTATTCG 57.466 34.615 3.21 0.00 0.00 3.34
745 760 5.661458 AGTATCACTTCTACACCCGATTTG 58.339 41.667 0.00 0.00 0.00 2.32
758 773 7.815068 ACGCATTTATCAGGATAGTATCACTTC 59.185 37.037 12.19 0.00 0.00 3.01
783 798 6.494893 TGCCTTATTCACTTTACATGTCAC 57.505 37.500 0.00 0.00 0.00 3.67
857 872 7.171848 TGGATTGATCATCAAAGTTGCTTTTTG 59.828 33.333 3.63 2.92 40.12 2.44
1063 1089 5.242838 GTCTTCATGGTGGATTGGTGTTAAA 59.757 40.000 0.00 0.00 0.00 1.52
1177 1203 3.027412 AGTGGTAATGGTTGTTGTTGCA 58.973 40.909 0.00 0.00 0.00 4.08
1361 1844 1.199097 GGTGGTTGTTGCGGTAGAATG 59.801 52.381 0.00 0.00 0.00 2.67
1525 2243 2.234661 TGTGAAAATGGTGGTTGTTGCA 59.765 40.909 0.00 0.00 0.00 4.08
1585 2306 3.538591 TGCAAGATAGATGGCTGAACAG 58.461 45.455 0.00 0.00 0.00 3.16
1829 2576 0.312102 GTTGCTGCTGAGGTTGGTTC 59.688 55.000 0.00 0.00 0.00 3.62
1973 2741 1.244019 GCTGCAACAAGGTACCCTGG 61.244 60.000 15.04 4.58 32.13 4.45
2036 2804 1.216977 CATCGTTGGCAGGGTACGA 59.783 57.895 13.75 13.75 46.71 3.43
2166 2937 1.542472 TCCATCGACTAAGCAACGACA 59.458 47.619 0.00 0.00 38.79 4.35
2168 2939 4.037565 ACATATCCATCGACTAAGCAACGA 59.962 41.667 0.00 0.00 40.18 3.85
2342 3117 4.574013 CAGGCAAGATGAACCTATGAACTC 59.426 45.833 0.00 0.00 30.84 3.01
2661 3449 5.007332 GTCCGTGAAGTTCAAGAAAAAGCTA 59.993 40.000 18.87 0.00 0.00 3.32
2682 3470 8.782339 TTAAAATTAACTAGCTAGTGGTGTCC 57.218 34.615 26.70 0.00 36.50 4.02
2778 3572 4.652421 TCCGTACCGAGCACAATAATTA 57.348 40.909 0.00 0.00 0.00 1.40
2791 3585 2.159327 ACAACTCCTTTTCCGTACCG 57.841 50.000 0.00 0.00 0.00 4.02
2810 3604 1.381056 ACAAACACCCTGCTGCCAA 60.381 52.632 0.00 0.00 0.00 4.52
2845 3639 2.494445 GCAAACAATAGCCCGCCC 59.506 61.111 0.00 0.00 0.00 6.13
2848 3642 0.179140 AATGCGCAAACAATAGCCCG 60.179 50.000 17.11 0.00 0.00 6.13
2852 3646 6.689178 AACAAAGTAATGCGCAAACAATAG 57.311 33.333 17.11 5.60 0.00 1.73
2857 3651 3.959385 GCAAAACAAAGTAATGCGCAAAC 59.041 39.130 17.11 16.52 0.00 2.93
2880 3888 8.144478 GTGGTATAGTATGAGAGCATGAAAAGA 58.856 37.037 0.00 0.00 35.94 2.52
2978 3986 1.404035 GTGTCCTTTGCCGAGTGTTTT 59.596 47.619 0.00 0.00 0.00 2.43
3004 4040 4.112634 TCTGTTTGCTGAAAAGGGGTAT 57.887 40.909 0.00 0.00 0.00 2.73
3016 4052 5.335191 GGATCTCGACAAATTTCTGTTTGCT 60.335 40.000 0.00 0.00 41.61 3.91
3032 4068 3.056821 AGTGTTCGACAAATGGATCTCGA 60.057 43.478 0.00 0.00 33.47 4.04
3119 4155 0.250727 AGCTACACCACCATTTGCGT 60.251 50.000 0.00 0.00 0.00 5.24
3131 4169 0.037605 ACCTTGGCACGTAGCTACAC 60.038 55.000 23.21 11.68 44.79 2.90
3144 4182 4.704057 AGTACTCTCGGTAAACTACCTTGG 59.296 45.833 0.00 0.00 46.81 3.61
3167 4205 6.855763 TCTATTTACTCCCTTTACCGAACA 57.144 37.500 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.