Multiple sequence alignment - TraesCS2B01G622100

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 TraesCS2B01G622100 chr2B 100.000 3417 0 0 1 3417 796163563 796166979 0.000000e+00 6311.0
1 TraesCS2B01G622100 chr2B 82.110 218 34 3 1225 1440 797183223 797183437 7.530000e-42 182.0
2 TraesCS2B01G622100 chr2B 80.531 226 34 10 1225 1444 797240393 797240614 7.590000e-37 165.0
3 TraesCS2B01G622100 chr2B 88.596 114 9 2 2408 2518 794675503 794675391 5.950000e-28 135.0
4 TraesCS2B01G622100 chr2B 96.970 66 2 0 1521 1586 794677691 794677626 1.000000e-20 111.0
5 TraesCS2B01G622100 chr2D 95.818 2415 45 13 1043 3417 600580510 600578112 0.000000e+00 3849.0
6 TraesCS2B01G622100 chr2D 93.418 1018 44 6 40 1045 600587228 600586222 0.000000e+00 1487.0
7 TraesCS2B01G622100 chr2D 86.015 1094 80 28 1223 2257 636923158 636922079 0.000000e+00 1105.0
8 TraesCS2B01G622100 chr2D 82.301 226 30 8 1225 1444 638350811 638350590 1.620000e-43 187.0
9 TraesCS2B01G622100 chr2D 75.592 422 72 25 1680 2080 637385428 637385017 2.710000e-41 180.0
10 TraesCS2B01G622100 chr2D 100.000 38 0 0 3209 3246 600577627 600577590 1.700000e-08 71.3
11 TraesCS2B01G622100 chr2D 89.796 49 0 2 2648 2691 637370047 637370095 1.320000e-04 58.4
12 TraesCS2B01G622100 chr2A 91.330 1165 55 19 1 1131 761602606 761603758 0.000000e+00 1550.0
13 TraesCS2B01G622100 chr2A 92.880 632 40 3 1 627 761807859 761807228 0.000000e+00 913.0
14 TraesCS2B01G622100 chr2A 97.697 521 10 1 2108 2626 761777367 761776847 0.000000e+00 894.0
15 TraesCS2B01G622100 chr2A 83.791 765 67 23 1526 2257 762725798 762726538 0.000000e+00 673.0
16 TraesCS2B01G622100 chr2A 96.567 233 8 0 2788 3020 761776675 761776443 1.490000e-103 387.0
17 TraesCS2B01G622100 chr2A 84.638 345 26 7 1223 1540 762724772 762725116 5.500000e-83 318.0
18 TraesCS2B01G622100 chr2A 88.636 264 6 2 3177 3417 761776444 761776182 1.990000e-77 300.0
19 TraesCS2B01G622100 chr2A 89.431 246 14 9 1802 2044 761777634 761777398 1.990000e-77 300.0
20 TraesCS2B01G622100 chr2A 96.450 169 4 1 2592 2758 761776843 761776675 9.340000e-71 278.0
21 TraesCS2B01G622100 chr2A 95.062 162 5 2 1341 1499 761777858 761777697 5.660000e-63 252.0
22 TraesCS2B01G622100 chr2A 90.303 165 13 3 2696 2859 762867738 762867576 2.670000e-51 213.0
23 TraesCS2B01G622100 chr2A 83.186 226 35 3 1215 1438 762660132 762660356 1.610000e-48 204.0
24 TraesCS2B01G622100 chr2A 79.221 308 46 10 2917 3220 762847952 762847659 7.480000e-47 198.0
25 TraesCS2B01G622100 chr2A 100.000 82 0 0 1043 1124 761777997 761777916 5.910000e-33 152.0
26 TraesCS2B01G622100 chr2A 80.625 160 28 3 1443 1600 763862582 763862424 1.670000e-23 121.0
27 TraesCS2B01G622100 chr2A 93.939 66 4 0 1521 1586 762720706 762720771 2.170000e-17 100.0
28 TraesCS2B01G622100 chr2A 89.333 75 7 1 1184 1258 761603757 761603830 3.630000e-15 93.5
29 TraesCS2B01G622100 chr2A 95.238 42 2 0 2990 3031 762868062 762868021 2.200000e-07 67.6
30 TraesCS2B01G622100 chr2A 88.679 53 6 0 2990 3042 762695936 762695884 7.910000e-07 65.8
31 TraesCS2B01G622100 chr7A 83.569 1345 133 44 1223 2520 30271557 30272860 0.000000e+00 1179.0
32 TraesCS2B01G622100 chr7A 82.116 1068 88 49 1223 2252 30240689 30241691 0.000000e+00 819.0
33 TraesCS2B01G622100 chr7A 81.313 396 61 11 539 930 609380769 609380383 3.310000e-80 309.0
34 TraesCS2B01G622100 chr7A 93.564 202 13 0 2319 2520 30241696 30241897 5.540000e-78 302.0
35 TraesCS2B01G622100 chr7A 93.258 89 6 0 1121 1209 30271414 30271502 7.690000e-27 132.0
36 TraesCS2B01G622100 chr4A 85.277 1046 84 24 1305 2288 699189121 699188084 0.000000e+00 1014.0
37 TraesCS2B01G622100 chr4A 82.677 381 57 6 552 929 461709893 461710267 2.540000e-86 329.0
38 TraesCS2B01G622100 chr7D 83.598 1134 95 29 1223 2300 29984547 29985645 0.000000e+00 979.0
39 TraesCS2B01G622100 chr7D 84.197 386 41 11 551 930 386363147 386362776 1.170000e-94 357.0
40 TraesCS2B01G622100 chr7D 91.765 85 3 2 2779 2859 133938665 133938581 7.750000e-22 115.0
41 TraesCS2B01G622100 chr7D 100.000 32 0 0 2319 2350 29985643 29985674 3.680000e-05 60.2
42 TraesCS2B01G622100 chr5D 82.576 396 55 11 545 934 487173576 487173189 1.520000e-88 337.0
43 TraesCS2B01G622100 chr5D 87.111 225 18 5 1706 1926 440114468 440114685 9.470000e-61 244.0
44 TraesCS2B01G622100 chr5D 86.813 91 11 1 2567 2657 555493662 555493573 2.170000e-17 100.0
45 TraesCS2B01G622100 chr5D 97.143 35 0 1 2414 2448 296933487 296933454 1.320000e-04 58.4
46 TraesCS2B01G622100 chr4D 82.895 380 55 6 554 930 5663362 5662990 1.970000e-87 333.0
47 TraesCS2B01G622100 chr4D 85.714 133 14 5 239 367 81913131 81913262 5.950000e-28 135.0
48 TraesCS2B01G622100 chr4D 92.941 85 2 2 2779 2859 308853867 308853783 1.670000e-23 121.0
49 TraesCS2B01G622100 chr4D 83.333 90 4 3 2414 2493 308854012 308853924 4.730000e-09 73.1
50 TraesCS2B01G622100 chr6B 82.143 392 54 12 541 927 76179240 76179620 4.250000e-84 322.0
51 TraesCS2B01G622100 chr6B 88.608 158 16 2 224 379 644860528 644860685 1.250000e-44 191.0
52 TraesCS2B01G622100 chr7B 83.333 306 44 5 625 930 380542072 380541774 3.360000e-70 276.0
53 TraesCS2B01G622100 chr7B 90.090 111 10 1 2408 2518 746125024 746124915 3.550000e-30 143.0
54 TraesCS2B01G622100 chr7B 80.769 156 22 4 2360 2515 746126490 746126343 7.750000e-22 115.0
55 TraesCS2B01G622100 chrUn 85.062 241 20 11 2290 2522 396320461 396320229 7.370000e-57 231.0
56 TraesCS2B01G622100 chrUn 75.561 401 73 21 1677 2062 234390382 234390772 1.260000e-39 174.0
57 TraesCS2B01G622100 chrUn 88.095 126 10 5 2710 2831 396319993 396319869 9.880000e-31 145.0
58 TraesCS2B01G622100 chr6A 85.635 181 23 3 201 379 573269661 573269840 1.620000e-43 187.0
59 TraesCS2B01G622100 chr1D 92.941 85 2 2 2779 2859 255588985 255588901 1.670000e-23 121.0
60 TraesCS2B01G622100 chr1D 97.222 36 1 0 193 228 233306793 233306828 1.020000e-05 62.1
61 TraesCS2B01G622100 chr1B 94.030 67 4 0 2449 2515 7245434 7245368 6.030000e-18 102.0


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 TraesCS2B01G622100 chr2B 796163563 796166979 3416 False 6311.000000 6311 100.000000 1 3417 1 chr2B.!!$F1 3416
1 TraesCS2B01G622100 chr2D 600577590 600580510 2920 True 1960.150000 3849 97.909000 1043 3417 2 chr2D.!!$R5 2374
2 TraesCS2B01G622100 chr2D 600586222 600587228 1006 True 1487.000000 1487 93.418000 40 1045 1 chr2D.!!$R1 1005
3 TraesCS2B01G622100 chr2D 636922079 636923158 1079 True 1105.000000 1105 86.015000 1223 2257 1 chr2D.!!$R2 1034
4 TraesCS2B01G622100 chr2A 761807228 761807859 631 True 913.000000 913 92.880000 1 627 1 chr2A.!!$R1 626
5 TraesCS2B01G622100 chr2A 761602606 761603830 1224 False 821.750000 1550 90.331500 1 1258 2 chr2A.!!$F3 1257
6 TraesCS2B01G622100 chr2A 762724772 762726538 1766 False 495.500000 673 84.214500 1223 2257 2 chr2A.!!$F4 1034
7 TraesCS2B01G622100 chr2A 761776182 761777997 1815 True 366.142857 894 94.834714 1043 3417 7 chr2A.!!$R5 2374
8 TraesCS2B01G622100 chr7A 30271414 30272860 1446 False 655.500000 1179 88.413500 1121 2520 2 chr7A.!!$F2 1399
9 TraesCS2B01G622100 chr7A 30240689 30241897 1208 False 560.500000 819 87.840000 1223 2520 2 chr7A.!!$F1 1297
10 TraesCS2B01G622100 chr4A 699188084 699189121 1037 True 1014.000000 1014 85.277000 1305 2288 1 chr4A.!!$R1 983
11 TraesCS2B01G622100 chr7D 29984547 29985674 1127 False 519.600000 979 91.799000 1223 2350 2 chr7D.!!$F1 1127


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
663 685 1.032114 GGGCCCTCGTTTTCTGATGG 61.032 60.0 17.04 0.0 0.0 3.51 F
1797 2647 0.671163 TACCGGCGTGTTCACCAATC 60.671 55.0 6.01 0.0 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2867 0.532862 CCTTCCTTGACACGCACAGT 60.533 55.0 0.0 0.0 0.00 3.55 R
3089 3996 0.469070 GAGTGATGCTCTGCTGGGAT 59.531 55.0 0.0 0.0 40.98 3.85 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
94 96 4.807443 TCGTATGTGGTCGATGTTAAACA 58.193 39.130 0.00 0.00 0.00 2.83
95 97 5.228665 TCGTATGTGGTCGATGTTAAACAA 58.771 37.500 0.00 0.00 0.00 2.83
103 105 7.011950 TGTGGTCGATGTTAAACAATATGGATC 59.988 37.037 0.00 0.00 0.00 3.36
134 136 2.064014 GTTCAAGGTAGTGTGTACGCC 58.936 52.381 3.51 0.00 0.00 5.68
297 306 1.945394 GGCTGTGTGCATCCTGAATAG 59.055 52.381 0.00 0.00 45.15 1.73
304 313 2.103771 GTGCATCCTGAATAGGCAGAGA 59.896 50.000 0.00 0.00 44.22 3.10
508 530 4.389077 CCCTCGTTCATGACAACTAGAAAC 59.611 45.833 0.00 0.00 0.00 2.78
536 558 6.280643 GTTTTAGGGAAGCTTGAACATTGTT 58.719 36.000 2.10 0.63 0.00 2.83
537 559 5.705609 TTAGGGAAGCTTGAACATTGTTC 57.294 39.130 20.27 20.27 0.00 3.18
628 650 9.535878 CTGAGTGAAAAATAGTCTAGAATACCC 57.464 37.037 1.27 0.00 0.00 3.69
663 685 1.032114 GGGCCCTCGTTTTCTGATGG 61.032 60.000 17.04 0.00 0.00 3.51
721 743 5.705400 CCTGGGGTCCAAAAATATCTGTAT 58.295 41.667 0.00 0.00 30.80 2.29
749 771 1.218763 CGAATGGAGCAGATGAGCAG 58.781 55.000 0.00 0.00 36.85 4.24
797 819 5.441500 TGATGCCCTCCGATTTTTACATAA 58.558 37.500 0.00 0.00 0.00 1.90
831 853 2.742372 GACGCAACATGCCGACCT 60.742 61.111 7.83 0.00 41.12 3.85
839 861 3.625764 GCAACATGCCGACCTTATCTAAA 59.374 43.478 0.00 0.00 37.42 1.85
912 934 9.590451 TTGAAAATCTGATATTTTGATGGAAGC 57.410 29.630 0.71 0.00 32.03 3.86
969 991 6.024552 TCGTACAAAGACTTAACCCGTTAT 57.975 37.500 0.00 0.00 0.00 1.89
970 992 7.151999 TCGTACAAAGACTTAACCCGTTATA 57.848 36.000 0.00 0.00 0.00 0.98
971 993 7.598278 TCGTACAAAGACTTAACCCGTTATAA 58.402 34.615 0.00 0.00 0.00 0.98
972 994 8.250332 TCGTACAAAGACTTAACCCGTTATAAT 58.750 33.333 0.00 0.00 0.00 1.28
973 995 8.534778 CGTACAAAGACTTAACCCGTTATAATC 58.465 37.037 0.00 0.00 0.00 1.75
974 996 7.854557 ACAAAGACTTAACCCGTTATAATCC 57.145 36.000 0.00 0.00 0.00 3.01
975 997 7.396418 ACAAAGACTTAACCCGTTATAATCCA 58.604 34.615 0.00 0.00 0.00 3.41
976 998 7.335171 ACAAAGACTTAACCCGTTATAATCCAC 59.665 37.037 0.00 0.00 0.00 4.02
977 999 6.803366 AGACTTAACCCGTTATAATCCACT 57.197 37.500 0.00 0.00 0.00 4.00
978 1000 7.191593 AGACTTAACCCGTTATAATCCACTT 57.808 36.000 0.00 0.00 0.00 3.16
1025 1047 7.004086 AGGATAATGTTGAACTTCACTTTGGA 58.996 34.615 0.00 0.00 0.00 3.53
1208 1252 3.650950 ACATCCAAGCCCGCCTGT 61.651 61.111 0.00 0.00 0.00 4.00
1793 2643 2.739671 GGTACCGGCGTGTTCACC 60.740 66.667 6.01 5.50 0.00 4.02
1794 2644 2.029369 GTACCGGCGTGTTCACCA 59.971 61.111 6.01 0.00 0.00 4.17
1795 2645 1.594836 GTACCGGCGTGTTCACCAA 60.595 57.895 6.01 0.00 0.00 3.67
1796 2646 0.952010 GTACCGGCGTGTTCACCAAT 60.952 55.000 6.01 0.00 0.00 3.16
1797 2647 0.671163 TACCGGCGTGTTCACCAATC 60.671 55.000 6.01 0.00 0.00 2.67
1798 2648 1.963855 CCGGCGTGTTCACCAATCA 60.964 57.895 6.01 0.00 0.00 2.57
1799 2649 1.206578 CGGCGTGTTCACCAATCAC 59.793 57.895 0.00 0.00 0.00 3.06
2010 2867 0.034380 TTGTTGGGGTGAACGGTTCA 60.034 50.000 19.07 19.07 37.33 3.18
2026 2883 0.176910 TTCACTGTGCGTGTCAAGGA 59.823 50.000 2.12 0.00 44.16 3.36
2162 3022 1.536662 AGAAGGTCGAGGGCCTTGT 60.537 57.895 20.33 4.00 45.51 3.16
2862 3769 7.227873 TCAGACTTGGTATTAATTTGGTCACA 58.772 34.615 0.00 0.00 0.00 3.58
2959 3866 3.958798 TGAGAGGGTACAGTACATTAGCC 59.041 47.826 12.89 12.04 36.30 3.93
3048 3955 2.677337 CCAAACTGTTGTTTTTGCCCAG 59.323 45.455 0.00 0.00 43.13 4.45
3057 3964 2.564947 TGTTTTTGCCCAGTTCTGTTGT 59.435 40.909 0.00 0.00 0.00 3.32
3089 3996 7.224297 AGTAACATCCTCTGCTTTCTTTTACA 58.776 34.615 0.00 0.00 0.00 2.41
3138 4045 7.919690 TGCAGTGCACTTTTATCAAGATATAC 58.080 34.615 18.94 0.00 31.71 1.47
3241 4156 9.455847 GAACATGGAGCATCATAATTTTAAGAC 57.544 33.333 0.00 0.00 36.25 3.01
3363 4301 6.430000 TCCAAGGTTGTTAGCTTCATTTCTAC 59.570 38.462 0.00 0.00 39.98 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.672808 AGAAGAGAGTGTGCCATTGAAG 58.327 45.455 0.00 0.00 0.00 3.02
94 96 2.092429 ACAACGGCTGGTGATCCATATT 60.092 45.455 19.82 0.00 43.43 1.28
95 97 1.490490 ACAACGGCTGGTGATCCATAT 59.510 47.619 19.82 0.00 43.43 1.78
103 105 1.101049 ACCTTGAACAACGGCTGGTG 61.101 55.000 9.65 9.65 0.00 4.17
134 136 0.677288 TGTGACCACCTACTCCAACG 59.323 55.000 0.00 0.00 0.00 4.10
297 306 4.436998 CGACACCCGGTCTCTGCC 62.437 72.222 0.00 0.00 44.68 4.85
415 428 6.969043 TGATGGACTCAAGGGTATAACAAAT 58.031 36.000 0.00 0.00 0.00 2.32
508 530 4.274950 TGTTCAAGCTTCCCTAAAACGAAG 59.725 41.667 0.00 0.00 38.81 3.79
536 558 9.528018 GTGGAATTCACTCAAAAATAAACAAGA 57.472 29.630 7.93 0.00 42.86 3.02
537 559 9.311916 TGTGGAATTCACTCAAAAATAAACAAG 57.688 29.630 7.93 0.00 46.20 3.16
615 637 7.403522 AGCTTCTAAAAAGGGGTATTCTAGACT 59.596 37.037 0.00 0.00 0.00 3.24
628 650 2.028112 GGGCCCAAAGCTTCTAAAAAGG 60.028 50.000 19.95 0.00 43.05 3.11
663 685 5.009010 CCTCACATATTGCCTAATTGACACC 59.991 44.000 0.00 0.00 0.00 4.16
700 722 6.334378 TCATACAGATATTTTTGGACCCCA 57.666 37.500 0.00 0.00 0.00 4.96
721 743 1.205655 CTGCTCCATTCGTTCTCCTCA 59.794 52.381 0.00 0.00 0.00 3.86
749 771 2.503356 ACCATCATGTCCAGACTTCTCC 59.497 50.000 0.00 0.00 0.00 3.71
839 861 8.513774 CCCAATTTTGCACTTTGCTTATTTATT 58.486 29.630 0.00 0.00 45.31 1.40
853 875 4.151512 CACGATTTTACCCCAATTTTGCAC 59.848 41.667 0.00 0.00 0.00 4.57
969 991 6.216662 TGAGTTCAGGGGATTAAAGTGGATTA 59.783 38.462 0.00 0.00 0.00 1.75
970 992 5.015178 TGAGTTCAGGGGATTAAAGTGGATT 59.985 40.000 0.00 0.00 0.00 3.01
971 993 4.540099 TGAGTTCAGGGGATTAAAGTGGAT 59.460 41.667 0.00 0.00 0.00 3.41
972 994 3.913799 TGAGTTCAGGGGATTAAAGTGGA 59.086 43.478 0.00 0.00 0.00 4.02
973 995 4.010349 GTGAGTTCAGGGGATTAAAGTGG 58.990 47.826 0.00 0.00 0.00 4.00
974 996 4.010349 GGTGAGTTCAGGGGATTAAAGTG 58.990 47.826 0.00 0.00 0.00 3.16
975 997 3.655777 TGGTGAGTTCAGGGGATTAAAGT 59.344 43.478 0.00 0.00 0.00 2.66
976 998 4.301072 TGGTGAGTTCAGGGGATTAAAG 57.699 45.455 0.00 0.00 0.00 1.85
977 999 4.946160 ATGGTGAGTTCAGGGGATTAAA 57.054 40.909 0.00 0.00 0.00 1.52
978 1000 5.104109 CCTTATGGTGAGTTCAGGGGATTAA 60.104 44.000 0.00 0.00 0.00 1.40
1025 1047 6.889177 CCAAATGTTTAAGGGGGCATTTTATT 59.111 34.615 0.00 0.00 38.86 1.40
1176 1220 0.181114 GATGTGGGCTAGCATGTCCA 59.819 55.000 18.24 11.77 39.71 4.02
1602 2446 1.990060 GCACTAGCCTCCCTCCACA 60.990 63.158 0.00 0.00 33.58 4.17
1603 2447 2.904131 GCACTAGCCTCCCTCCAC 59.096 66.667 0.00 0.00 33.58 4.02
1799 2649 2.742372 GCGCTACCACCACACTGG 60.742 66.667 0.00 0.00 45.02 4.00
2010 2867 0.532862 CCTTCCTTGACACGCACAGT 60.533 55.000 0.00 0.00 0.00 3.55
2026 2883 0.908198 CTAAGCTCAGGTGCTCCCTT 59.092 55.000 0.00 0.44 42.73 3.95
2369 3236 5.867903 ACAATCTTGGTTGAAATCACCAA 57.132 34.783 13.24 13.24 40.77 3.67
2874 3781 7.390440 CCTTGATCATCAACCAGTAAACTAACA 59.610 37.037 0.00 0.00 32.21 2.41
3048 3955 3.625764 TGTTACTCCAGCAACAACAGAAC 59.374 43.478 0.00 0.00 31.93 3.01
3057 3964 2.355108 GCAGAGGATGTTACTCCAGCAA 60.355 50.000 0.00 0.00 37.81 3.91
3089 3996 0.469070 GAGTGATGCTCTGCTGGGAT 59.531 55.000 0.00 0.00 40.98 3.85
3138 4045 5.977725 CCGAAACCTCACTATGTAGTATGTG 59.022 44.000 0.00 0.00 34.13 3.21
3207 4122 2.363306 TGCTCCATGTTCCTTGTTGT 57.637 45.000 0.00 0.00 0.00 3.32
3241 4156 1.949525 GGGTGCTATGCTACCAACATG 59.050 52.381 11.19 0.00 38.74 3.21
3363 4301 1.067354 GCCAAAAGCACAGGAGAATGG 60.067 52.381 0.00 0.00 42.97 3.16
3385 4323 2.733218 CCGTCGACAAGCGCTCAA 60.733 61.111 12.06 0.00 40.61 3.02



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

AutoCloner maintained by Alex Coulton.