Multiple sequence alignment - TraesCS2B01G016500

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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 TraesCS2B01G016500 chr2B 100.000 3632 0 0 1 3632 7774402 7770771 0.000000e+00 6708.0
1 TraesCS2B01G016500 chr2B 94.806 1367 58 5 1693 3059 7881704 7880351 0.000000e+00 2119.0
2 TraesCS2B01G016500 chr2B 92.161 523 35 2 3108 3630 7880241 7879725 0.000000e+00 734.0
3 TraesCS2B01G016500 chr2B 88.060 67 5 3 2990 3054 7880720 7880655 3.890000e-10 76.8
4 TraesCS2B01G016500 chr2B 86.957 69 6 3 2686 2753 7771417 7771351 1.400000e-09 75.0
5 TraesCS2B01G016500 chr2B 86.957 69 6 3 2986 3052 7771717 7771650 1.400000e-09 75.0
6 TraesCS2B01G016500 chr2B 85.333 75 8 3 2686 2759 7880424 7880352 1.400000e-09 75.0
7 TraesCS2B01G016500 chr6D 90.570 3086 252 23 1 3066 18095183 18092117 0.000000e+00 4050.0
8 TraesCS2B01G016500 chr6D 90.800 250 20 2 3063 3312 18092085 18091839 7.520000e-87 331.0
9 TraesCS2B01G016500 chr6D 88.732 71 5 3 2986 3053 18092501 18092431 2.320000e-12 84.2
10 TraesCS2B01G016500 chr6D 86.957 69 6 3 2686 2753 18092200 18092134 1.400000e-09 75.0
11 TraesCS2B01G016500 chr2D 92.803 1862 105 11 891 2750 2908795 2910629 0.000000e+00 2669.0
12 TraesCS2B01G016500 chr2D 84.790 1499 161 40 352 1816 2823287 2824752 0.000000e+00 1443.0
13 TraesCS2B01G016500 chr2D 88.902 874 58 14 1 866 2907988 2908830 0.000000e+00 1040.0
14 TraesCS2B01G016500 chr2D 92.803 528 32 2 3103 3630 2912333 2912854 0.000000e+00 760.0
15 TraesCS2B01G016500 chr2D 94.562 331 11 4 2743 3066 2911907 2912237 4.190000e-139 505.0
16 TraesCS2B01G016500 chr2D 89.394 66 5 2 2987 3050 2910566 2910631 8.360000e-12 82.4
17 TraesCS2B01G016500 chr2D 85.507 69 7 3 2686 2753 2912156 2912222 6.510000e-08 69.4
18 TraesCS2B01G016500 chr2A 89.428 1731 162 8 960 2671 2760512 2758784 0.000000e+00 2163.0
19 TraesCS2B01G016500 chr2A 90.402 448 28 7 3058 3501 2758430 2757994 3.150000e-160 575.0
20 TraesCS2B01G016500 chr2A 91.860 344 25 2 2726 3066 2758800 2758457 9.120000e-131 477.0
21 TraesCS2B01G016500 chr2A 93.846 130 8 0 3503 3632 2757859 2757730 2.860000e-46 196.0
22 TraesCS2B01G016500 chr2A 79.630 108 19 3 6 111 392463301 392463407 1.400000e-09 75.0
23 TraesCS2B01G016500 chr6B 91.667 60 5 0 523 582 129445196 129445255 2.320000e-12 84.2
24 TraesCS2B01G016500 chr5B 82.796 93 14 2 2 92 59912852 59912944 8.360000e-12 82.4
25 TraesCS2B01G016500 chr4D 84.000 75 10 2 13 85 434454511 434454437 1.810000e-08 71.3
26 TraesCS2B01G016500 chr6A 90.909 44 4 0 6 49 109681010 109680967 3.920000e-05 60.2
27 TraesCS2B01G016500 chr5D 100.000 29 0 0 2183 2211 549325062 549325090 2.000000e-03 54.7
28 TraesCS2B01G016500 chr4A 100.000 29 0 0 2183 2211 620952034 620952062 2.000000e-03 54.7
29 TraesCS2B01G016500 chr7A 100.000 28 0 0 225 252 57607204 57607177 7.000000e-03 52.8


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 TraesCS2B01G016500 chr2B 7770771 7774402 3631 True 2286.00 6708 91.304667 1 3632 3 chr2B.!!$R1 3631
1 TraesCS2B01G016500 chr2B 7879725 7881704 1979 True 751.20 2119 90.090000 1693 3630 4 chr2B.!!$R2 1937
2 TraesCS2B01G016500 chr6D 18091839 18095183 3344 True 1135.05 4050 89.264750 1 3312 4 chr6D.!!$R1 3311
3 TraesCS2B01G016500 chr2D 2823287 2824752 1465 False 1443.00 1443 84.790000 352 1816 1 chr2D.!!$F1 1464
4 TraesCS2B01G016500 chr2D 2907988 2912854 4866 False 854.30 2669 90.661833 1 3630 6 chr2D.!!$F2 3629
5 TraesCS2B01G016500 chr2A 2757730 2760512 2782 True 852.75 2163 91.384000 960 3632 4 chr2A.!!$R1 2672

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
219 222 0.448197 TTTCACGCGAGCAACACAAA 59.552 45.0 15.93 0.0 0.00 2.83 F
1065 1206 0.179059 TCACCATTCATACGCGGCAT 60.179 50.0 12.47 0.0 0.00 4.40 F
1081 1222 0.589729 GCATATCCTGCGCAAACACG 60.590 55.0 13.05 0.0 41.97 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1144 1285 0.320247 GGGCCGATGACATAGAGCAG 60.320 60.000 0.0 0.0 0.0 4.24 R
2606 2761 0.960364 GGTGGACAATGGCACGACAT 60.960 55.000 0.0 0.0 0.0 3.06 R
2928 4374 3.884037 ACCTGGGACATTCAGTTTCTT 57.116 42.857 0.0 0.0 38.2 2.52 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
57 58 3.066064 CGTTTTCACCATTGTGTTCCTCA 59.934 43.478 0.00 0.00 43.26 3.86
213 216 4.391830 AGATCTAATTTTTCACGCGAGCAA 59.608 37.500 15.93 0.00 0.00 3.91
219 222 0.448197 TTTCACGCGAGCAACACAAA 59.552 45.000 15.93 0.00 0.00 2.83
432 437 2.129607 GCACCAAAATGTTGCACTCAG 58.870 47.619 0.00 0.00 33.01 3.35
437 442 5.459762 CACCAAAATGTTGCACTCAGTTTAG 59.540 40.000 13.46 10.36 32.67 1.85
443 448 3.065233 TGTTGCACTCAGTTTAGTTGCAG 59.935 43.478 0.00 0.00 36.01 4.41
445 450 2.613595 TGCACTCAGTTTAGTTGCAGTG 59.386 45.455 0.00 0.00 33.04 3.66
464 493 6.426633 TGCAGTGATATTTTCCATATGTACCG 59.573 38.462 1.24 0.00 0.00 4.02
489 519 7.008266 CGTTTTCATTGTTTCTACCACATATGC 59.992 37.037 1.58 0.00 0.00 3.14
514 544 8.715998 GCGTCATAATCTAAAGTGATGATCATT 58.284 33.333 10.14 0.00 30.97 2.57
648 690 1.160329 CGGGAGAATTTGCCCTAGCG 61.160 60.000 12.97 0.00 44.31 4.26
653 695 1.212935 AGAATTTGCCCTAGCGGACAT 59.787 47.619 1.75 0.00 44.31 3.06
712 754 6.145048 CACTAATATTTTCCATACCGGTCGTC 59.855 42.308 12.40 0.00 35.57 4.20
839 897 7.504922 TGAAATTAAAATATGTGAAGCGTGC 57.495 32.000 0.00 0.00 0.00 5.34
864 922 3.272925 TGGTGTGCCAACTTGTCAA 57.727 47.368 0.00 0.00 42.83 3.18
872 935 3.088532 TGCCAACTTGTCAAGAGTGTTT 58.911 40.909 19.53 0.00 0.00 2.83
882 945 5.253330 TGTCAAGAGTGTTTTGAGAAAGGT 58.747 37.500 0.00 0.00 35.39 3.50
894 957 2.301870 TGAGAAAGGTAGTGGCGTGAAT 59.698 45.455 0.00 0.00 0.00 2.57
897 960 0.606604 AAGGTAGTGGCGTGAATCGT 59.393 50.000 0.00 0.00 42.13 3.73
927 990 1.522806 TGCGCCGACTTGTCAAGTT 60.523 52.632 19.09 3.72 43.03 2.66
938 1070 2.605094 GTCAAGTTGACAGCGCAGA 58.395 52.632 27.37 0.00 46.22 4.26
939 1071 1.151668 GTCAAGTTGACAGCGCAGAT 58.848 50.000 27.37 0.00 46.22 2.90
940 1072 1.127582 GTCAAGTTGACAGCGCAGATC 59.872 52.381 27.37 4.15 46.22 2.75
941 1073 1.150827 CAAGTTGACAGCGCAGATCA 58.849 50.000 11.47 7.22 0.00 2.92
946 1078 1.861971 TGACAGCGCAGATCATCATC 58.138 50.000 11.47 0.00 0.00 2.92
1029 1170 1.813753 GGCATTGCTGGCTTGCATG 60.814 57.895 8.82 0.00 44.27 4.06
1058 1199 2.472861 CGACGCTGATCACCATTCATAC 59.527 50.000 0.00 0.00 0.00 2.39
1060 1201 1.193203 CGCTGATCACCATTCATACGC 59.807 52.381 0.00 0.00 0.00 4.42
1061 1202 1.193203 GCTGATCACCATTCATACGCG 59.807 52.381 3.53 3.53 0.00 6.01
1065 1206 0.179059 TCACCATTCATACGCGGCAT 60.179 50.000 12.47 0.00 0.00 4.40
1081 1222 0.589729 GCATATCCTGCGCAAACACG 60.590 55.000 13.05 0.00 41.97 4.49
1144 1285 2.046285 CACCCCATTCTCGGCAACC 61.046 63.158 0.00 0.00 0.00 3.77
1188 1329 2.118404 CAACAACCCACACACCGCT 61.118 57.895 0.00 0.00 0.00 5.52
1221 1362 3.119319 TGCTCAAACCTATGGACCCATA 58.881 45.455 8.35 8.35 37.82 2.74
1473 1614 0.916086 ACACAATCCGGCCCATCTTA 59.084 50.000 0.00 0.00 0.00 2.10
1519 1660 2.695666 GAGTACTTGAGGGCATGCTCTA 59.304 50.000 22.88 4.67 0.00 2.43
1542 1683 3.556213 GCACCGGTATGCCAGTCATAATA 60.556 47.826 6.87 0.00 39.22 0.98
1816 1957 1.755179 ACGCCGGTTAGCTAGAACTA 58.245 50.000 1.90 0.00 0.00 2.24
1830 1974 2.245582 AGAACTAGCACTAACACCGGT 58.754 47.619 0.00 0.00 0.00 5.28
1849 1993 4.556233 CGGTAGTGAGAAGAACAATGACA 58.444 43.478 0.00 0.00 0.00 3.58
2097 2250 1.478510 GAGAAGATGGAGAAGGTGCGA 59.521 52.381 0.00 0.00 0.00 5.10
2098 2251 1.205893 AGAAGATGGAGAAGGTGCGAC 59.794 52.381 0.00 0.00 0.00 5.19
2107 2260 2.749110 GAAGGTGCGACACGAGCTCA 62.749 60.000 15.40 0.00 34.83 4.26
2606 2761 2.758423 TGAATCTTGCTACGCCACTCTA 59.242 45.455 0.00 0.00 0.00 2.43
2617 2772 0.179073 GCCACTCTATGTCGTGCCAT 60.179 55.000 0.00 0.00 0.00 4.40
2675 2830 9.143155 ACACCATTATCTGCCGACATATATATA 57.857 33.333 0.00 0.00 0.00 0.86
2676 2831 9.631452 CACCATTATCTGCCGACATATATATAG 57.369 37.037 0.00 0.00 0.00 1.31
2826 4266 8.262933 GCTTCCTACCCTTTAAGTCTTGTAATA 58.737 37.037 0.00 0.00 0.00 0.98
2950 4396 4.287766 AGAAACTGAATGTCCCAGGTAC 57.712 45.455 0.00 0.00 36.03 3.34
3092 4579 5.200483 AGCGAAATTGAATATTTCCCAGGA 58.800 37.500 0.00 0.00 35.27 3.86
3155 4670 7.873739 AAATCATTTCACCATCTTTTTCGAC 57.126 32.000 0.00 0.00 0.00 4.20
3204 4719 9.490663 GATGATTCCGTACAGTTTGATTTTAAG 57.509 33.333 0.00 0.00 0.00 1.85
3210 4725 7.280428 TCCGTACAGTTTGATTTTAAGACAACA 59.720 33.333 0.00 0.00 0.00 3.33
3306 4821 2.612212 AGTTTGTTTACGTCCTGTGCAG 59.388 45.455 0.00 0.00 0.00 4.41
3355 4870 7.145323 TGTTTAGCTTGGAGTTTGCTTTATTC 58.855 34.615 0.00 0.00 38.15 1.75
3377 4892 0.677731 CGGGGAACATGTCTGTGCAT 60.678 55.000 0.00 0.00 35.22 3.96
3410 4925 0.251341 GGAACATGTGTGCTTCCCCT 60.251 55.000 0.00 0.00 33.29 4.79
3411 4926 1.004277 GGAACATGTGTGCTTCCCCTA 59.996 52.381 0.00 0.00 33.29 3.53
3412 4927 2.357154 GGAACATGTGTGCTTCCCCTAT 60.357 50.000 0.00 0.00 33.29 2.57
3413 4928 3.118038 GGAACATGTGTGCTTCCCCTATA 60.118 47.826 0.00 0.00 33.29 1.31
3414 4929 3.560636 ACATGTGTGCTTCCCCTATAC 57.439 47.619 0.00 0.00 0.00 1.47
3605 5258 5.522460 TCAATGTTACCTATGTAAGCTTCGC 59.478 40.000 0.00 0.00 37.62 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.067821 GATTTGGGCACACGGTTCAAA 59.932 47.619 0.00 0.00 0.00 2.69
437 442 8.076178 GGTACATATGGAAAATATCACTGCAAC 58.924 37.037 7.80 0.00 0.00 4.17
443 448 9.659830 GAAAACGGTACATATGGAAAATATCAC 57.340 33.333 7.80 0.00 0.00 3.06
464 493 7.008266 CGCATATGTGGTAGAAACAATGAAAAC 59.992 37.037 8.46 0.00 0.00 2.43
546 576 1.668101 GCCTCCACTCCGGTCAGTAG 61.668 65.000 0.00 0.00 35.57 2.57
606 636 2.202492 CTTCACCTCCGCTCGACG 60.202 66.667 0.00 0.00 43.15 5.12
648 690 2.230130 TCCAACCCCATTTCATGTCC 57.770 50.000 0.00 0.00 0.00 4.02
653 695 2.688477 AGCTTTTCCAACCCCATTTCA 58.312 42.857 0.00 0.00 0.00 2.69
659 701 3.832490 ACATCTTTAGCTTTTCCAACCCC 59.168 43.478 0.00 0.00 0.00 4.95
663 705 7.598493 GTGCAATTACATCTTTAGCTTTTCCAA 59.402 33.333 0.00 0.00 0.00 3.53
664 706 7.039784 AGTGCAATTACATCTTTAGCTTTTCCA 60.040 33.333 0.00 0.00 0.00 3.53
712 754 5.064707 CGTTATGTGGGTAGGAACATTGAAG 59.935 44.000 0.00 0.00 38.05 3.02
862 920 6.238484 CCACTACCTTTCTCAAAACACTCTTG 60.238 42.308 0.00 0.00 0.00 3.02
864 922 5.368989 CCACTACCTTTCTCAAAACACTCT 58.631 41.667 0.00 0.00 0.00 3.24
872 935 1.689813 TCACGCCACTACCTTTCTCAA 59.310 47.619 0.00 0.00 0.00 3.02
882 945 0.319083 AACCACGATTCACGCCACTA 59.681 50.000 0.00 0.00 46.94 2.74
927 990 1.411612 AGATGATGATCTGCGCTGTCA 59.588 47.619 9.73 14.56 37.56 3.58
933 1065 5.443824 GCGTGTTTATAGATGATGATCTGCG 60.444 44.000 4.77 0.31 39.44 5.18
934 1066 5.406477 TGCGTGTTTATAGATGATGATCTGC 59.594 40.000 4.77 0.00 39.44 4.26
935 1067 7.042523 TGTTGCGTGTTTATAGATGATGATCTG 60.043 37.037 4.77 0.00 39.44 2.90
936 1068 6.986231 TGTTGCGTGTTTATAGATGATGATCT 59.014 34.615 0.00 0.00 42.03 2.75
937 1069 7.065894 GTGTTGCGTGTTTATAGATGATGATC 58.934 38.462 0.00 0.00 0.00 2.92
938 1070 6.538381 TGTGTTGCGTGTTTATAGATGATGAT 59.462 34.615 0.00 0.00 0.00 2.45
939 1071 5.872070 TGTGTTGCGTGTTTATAGATGATGA 59.128 36.000 0.00 0.00 0.00 2.92
940 1072 6.105657 TGTGTTGCGTGTTTATAGATGATG 57.894 37.500 0.00 0.00 0.00 3.07
941 1073 6.538381 TCATGTGTTGCGTGTTTATAGATGAT 59.462 34.615 0.00 0.00 35.64 2.45
946 1078 5.227805 GCAATCATGTGTTGCGTGTTTATAG 59.772 40.000 17.95 0.00 42.01 1.31
1029 1170 0.457853 TGATCAGCGTCGTTACTGCC 60.458 55.000 0.00 0.00 33.80 4.85
1065 1206 2.395360 GCCGTGTTTGCGCAGGATA 61.395 57.895 16.15 2.63 0.00 2.59
1073 1214 1.082104 CTCTTTCGGCCGTGTTTGC 60.082 57.895 27.15 0.00 0.00 3.68
1081 1222 1.276705 AGGAGAAACTCTCTTTCGGCC 59.723 52.381 0.00 0.00 42.95 6.13
1144 1285 0.320247 GGGCCGATGACATAGAGCAG 60.320 60.000 0.00 0.00 0.00 4.24
1188 1329 1.480212 TTTGAGCAAGGGAGGCGAGA 61.480 55.000 0.00 0.00 36.08 4.04
1200 1341 1.367346 TGGGTCCATAGGTTTGAGCA 58.633 50.000 0.00 0.00 0.00 4.26
1221 1362 2.198304 GACCAAGGCGGAGGGACAAT 62.198 60.000 0.00 0.00 38.63 2.71
1335 1476 2.574929 GACATGGCGTGGACGGTA 59.425 61.111 12.05 0.00 40.23 4.02
1527 1668 4.019321 GCCTCCCTTATTATGACTGGCATA 60.019 45.833 0.00 0.00 38.44 3.14
1533 1674 2.368875 CACGGCCTCCCTTATTATGACT 59.631 50.000 0.00 0.00 0.00 3.41
1542 1683 4.016706 CGGTTCACGGCCTCCCTT 62.017 66.667 0.00 0.00 39.42 3.95
1816 1957 1.544691 CTCACTACCGGTGTTAGTGCT 59.455 52.381 25.04 0.00 45.50 4.40
1823 1964 2.313317 TGTTCTTCTCACTACCGGTGT 58.687 47.619 19.93 10.78 45.50 4.16
1827 1968 4.556233 TGTCATTGTTCTTCTCACTACCG 58.444 43.478 0.00 0.00 0.00 4.02
1830 1974 6.427853 CCAACATGTCATTGTTCTTCTCACTA 59.572 38.462 0.00 0.00 37.73 2.74
2076 2229 1.472376 CGCACCTTCTCCATCTTCTCC 60.472 57.143 0.00 0.00 0.00 3.71
2097 2250 2.256764 CACGCTCTGAGCTCGTGT 59.743 61.111 25.59 14.10 45.75 4.49
2107 2260 1.956170 CAACTCCAACGCACGCTCT 60.956 57.895 0.00 0.00 0.00 4.09
2132 2285 2.300152 TCGCTCTCCTTCACAAAGTCAT 59.700 45.455 0.00 0.00 0.00 3.06
2606 2761 0.960364 GGTGGACAATGGCACGACAT 60.960 55.000 0.00 0.00 0.00 3.06
2700 2855 6.058183 AGCATCTCAATAATTAAACGAGCCT 58.942 36.000 0.00 0.00 0.00 4.58
2826 4266 9.472361 CGCGGGCTAGTATATAACAATAAATAT 57.528 33.333 0.00 0.00 0.00 1.28
2928 4374 3.884037 ACCTGGGACATTCAGTTTCTT 57.116 42.857 0.00 0.00 38.20 2.52
3129 4644 9.405587 GTCGAAAAAGATGGTGAAATGATTTAA 57.594 29.630 0.00 0.00 0.00 1.52
3130 4645 8.026607 GGTCGAAAAAGATGGTGAAATGATTTA 58.973 33.333 0.00 0.00 0.00 1.40
3131 4646 6.868339 GGTCGAAAAAGATGGTGAAATGATTT 59.132 34.615 0.00 0.00 0.00 2.17
3155 4670 2.100197 TCTCTCGTTATCACCACCTGG 58.900 52.381 0.00 0.00 42.17 4.45
3166 4681 3.889538 ACGGAATCATCCATCTCTCGTTA 59.110 43.478 0.00 0.00 46.97 3.18
3204 4719 9.399403 GAATCTCTTGGTTTTCTAATTGTTGTC 57.601 33.333 0.00 0.00 0.00 3.18
3330 4845 6.648879 ATAAAGCAAACTCCAAGCTAAACA 57.351 33.333 0.00 0.00 37.70 2.83
3355 4870 0.955428 CACAGACATGTTCCCCGTGG 60.955 60.000 0.00 0.00 37.65 4.94
3377 4892 3.156293 CATGTTCCAGATGACCCAAACA 58.844 45.455 0.00 0.00 0.00 2.83
3410 4925 9.132923 GCAGCCAAGACAGGTATATATAGTATA 57.867 37.037 0.00 0.00 0.00 1.47
3411 4926 7.070074 GGCAGCCAAGACAGGTATATATAGTAT 59.930 40.741 6.55 0.00 0.00 2.12
3412 4927 6.380274 GGCAGCCAAGACAGGTATATATAGTA 59.620 42.308 6.55 0.00 0.00 1.82
3413 4928 5.187967 GGCAGCCAAGACAGGTATATATAGT 59.812 44.000 6.55 0.00 0.00 2.12
3414 4929 5.187772 TGGCAGCCAAGACAGGTATATATAG 59.812 44.000 13.33 0.00 0.00 1.31
3484 5003 7.574967 GCGGGGTGATTAATATTCAAGTTATGG 60.575 40.741 0.00 0.00 0.00 2.74
3565 5218 4.125703 ACATTGAATGAGCTAGCTACTGC 58.874 43.478 19.38 7.15 40.05 4.40


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

AutoCloner maintained by Alex Coulton.