Multiple sequence alignment - TraesCS3B01G236800

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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 TraesCS3B01G236800 chr3B 100.000 3274 0 0 1 3274 370212559 370215832 0.000000e+00 6047.0
1 TraesCS3B01G236800 chr3B 93.613 1957 114 8 1323 3274 763485553 763483603 0.000000e+00 2911.0
2 TraesCS3B01G236800 chr5D 94.399 1964 93 9 1321 3274 44511941 44513897 0.000000e+00 3001.0
3 TraesCS3B01G236800 chr5D 77.964 835 132 29 325 1124 517218375 517219192 2.960000e-130 475.0
4 TraesCS3B01G236800 chrUn 94.679 1917 89 8 1366 3274 43407879 43409790 0.000000e+00 2963.0
5 TraesCS3B01G236800 chr2D 94.079 1959 89 14 1326 3274 84780830 84782771 0.000000e+00 2950.0
6 TraesCS3B01G236800 chr2D 93.763 1956 99 13 1326 3272 645082450 645080509 0.000000e+00 2915.0
7 TraesCS3B01G236800 chr4D 93.887 1963 104 11 1320 3274 78732772 78730818 0.000000e+00 2946.0
8 TraesCS3B01G236800 chr6D 93.133 1966 105 12 1325 3274 12108135 12106184 0.000000e+00 2856.0
9 TraesCS3B01G236800 chr5A 92.668 1964 125 12 1320 3274 650703525 650701572 0.000000e+00 2811.0
10 TraesCS3B01G236800 chr5A 92.627 1953 112 19 1321 3259 702815062 702813128 0.000000e+00 2780.0
11 TraesCS3B01G236800 chr3D 91.736 1331 82 11 1 1322 279879626 279878315 0.000000e+00 1823.0
12 TraesCS3B01G236800 chr5B 76.790 922 160 34 291 1179 649509291 649510191 4.950000e-128 468.0
13 TraesCS3B01G236800 chr5B 84.776 335 45 3 289 623 649699563 649699891 6.770000e-87 331.0
14 TraesCS3B01G236800 chr1B 90.196 51 5 0 175 225 456610 456560 2.110000e-07 67.6


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 TraesCS3B01G236800 chr3B 370212559 370215832 3273 False 6047 6047 100.000 1 3274 1 chr3B.!!$F1 3273
1 TraesCS3B01G236800 chr3B 763483603 763485553 1950 True 2911 2911 93.613 1323 3274 1 chr3B.!!$R1 1951
2 TraesCS3B01G236800 chr5D 44511941 44513897 1956 False 3001 3001 94.399 1321 3274 1 chr5D.!!$F1 1953
3 TraesCS3B01G236800 chr5D 517218375 517219192 817 False 475 475 77.964 325 1124 1 chr5D.!!$F2 799
4 TraesCS3B01G236800 chrUn 43407879 43409790 1911 False 2963 2963 94.679 1366 3274 1 chrUn.!!$F1 1908
5 TraesCS3B01G236800 chr2D 84780830 84782771 1941 False 2950 2950 94.079 1326 3274 1 chr2D.!!$F1 1948
6 TraesCS3B01G236800 chr2D 645080509 645082450 1941 True 2915 2915 93.763 1326 3272 1 chr2D.!!$R1 1946
7 TraesCS3B01G236800 chr4D 78730818 78732772 1954 True 2946 2946 93.887 1320 3274 1 chr4D.!!$R1 1954
8 TraesCS3B01G236800 chr6D 12106184 12108135 1951 True 2856 2856 93.133 1325 3274 1 chr6D.!!$R1 1949
9 TraesCS3B01G236800 chr5A 650701572 650703525 1953 True 2811 2811 92.668 1320 3274 1 chr5A.!!$R1 1954
10 TraesCS3B01G236800 chr5A 702813128 702815062 1934 True 2780 2780 92.627 1321 3259 1 chr5A.!!$R2 1938
11 TraesCS3B01G236800 chr3D 279878315 279879626 1311 True 1823 1823 91.736 1 1322 1 chr3D.!!$R1 1321
12 TraesCS3B01G236800 chr5B 649509291 649510191 900 False 468 468 76.790 291 1179 1 chr5B.!!$F1 888

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
250 251 0.462759 GCTGTAGGACCACATGCTCC 60.463 60.0 0.00 0.0 0.0 4.70 F
1001 1030 0.100682 CGCCTAGTACTGCACACGAT 59.899 55.0 5.39 0.0 0.0 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1678 0.250945 TCTCTCTCGCTGTGGTCACT 60.251 55.0 2.66 0.00 0.00 3.41 R
2882 2954 0.644843 CGCACCAACTTTTTGTGCAC 59.355 50.0 10.75 10.75 38.56 4.57 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
27 28 8.259411 TCCACTTGTACTTGTCTGTAACTAAAA 58.741 33.333 0.00 0.00 0.00 1.52
28 29 8.333186 CCACTTGTACTTGTCTGTAACTAAAAC 58.667 37.037 0.00 0.00 0.00 2.43
85 86 3.839490 TGGGAAGTATCGTTTTAGACCCA 59.161 43.478 0.00 0.00 41.81 4.51
139 140 7.063308 ACAAAATGTCACAGTGTTTGAAATGTC 59.937 33.333 17.09 0.00 34.16 3.06
245 246 1.071699 ACGTTTGCTGTAGGACCACAT 59.928 47.619 0.00 0.00 0.00 3.21
250 251 0.462759 GCTGTAGGACCACATGCTCC 60.463 60.000 0.00 0.00 0.00 4.70
252 253 2.388735 CTGTAGGACCACATGCTCCTA 58.611 52.381 9.39 9.39 38.01 2.94
270 271 5.746245 GCTCCTATTATACAAGCTAGCATCG 59.254 44.000 18.83 7.01 0.00 3.84
309 310 8.324306 TGCAGGCTGCTAAGATATTTTCTATAT 58.676 33.333 36.50 0.00 45.31 0.86
341 342 6.374053 CCCCTTGAAAATTCAAAACAACAGTT 59.626 34.615 9.63 0.00 45.61 3.16
471 474 5.036117 AGGCACACTTTTCAGAACTCTTA 57.964 39.130 0.00 0.00 0.00 2.10
594 597 8.296000 TCATATAATGACAACACACCAAGTTTG 58.704 33.333 0.00 0.00 33.59 2.93
603 606 6.589907 ACAACACACCAAGTTTGAAGAATTTC 59.410 34.615 0.00 0.00 0.00 2.17
681 687 1.402456 GGGTGACACACGCTACTAGTG 60.402 57.143 5.39 0.00 42.71 2.74
732 738 1.161563 ACGTGGTTGGCGTTTGGTAG 61.162 55.000 0.00 0.00 39.79 3.18
762 768 1.323534 CACGTACATTAGCAGCGTTCC 59.676 52.381 0.00 0.00 33.28 3.62
763 769 1.067425 ACGTACATTAGCAGCGTTCCA 60.067 47.619 0.00 0.00 31.37 3.53
765 771 2.222729 CGTACATTAGCAGCGTTCCAAC 60.223 50.000 0.00 0.00 0.00 3.77
784 799 4.158384 CAACATCGCACAAGTTGTTATCC 58.842 43.478 5.57 0.00 38.20 2.59
834 849 4.513406 TTTATTAACTTCCCGCTCCCAT 57.487 40.909 0.00 0.00 0.00 4.00
853 868 4.382901 CCCATGAACTCTCTCTTCTTCCTG 60.383 50.000 0.00 0.00 0.00 3.86
891 906 2.239400 TCTCTCTCTTTCTTCACCGCA 58.761 47.619 0.00 0.00 0.00 5.69
937 952 1.523758 GACCGCTGGACTTTTGACAT 58.476 50.000 1.50 0.00 0.00 3.06
938 953 1.197721 GACCGCTGGACTTTTGACATG 59.802 52.381 1.50 0.00 0.00 3.21
949 965 5.584649 GGACTTTTGACATGGACGATCATTA 59.415 40.000 0.00 0.00 0.00 1.90
967 983 1.884075 TAGTGGCATTCGTGTCCGCT 61.884 55.000 0.00 0.00 42.69 5.52
1000 1029 1.239296 ACGCCTAGTACTGCACACGA 61.239 55.000 5.39 0.00 0.00 4.35
1001 1030 0.100682 CGCCTAGTACTGCACACGAT 59.899 55.000 5.39 0.00 0.00 3.73
1421 1463 0.673333 CTAGTCCATGCGCACCAACA 60.673 55.000 14.90 0.00 0.00 3.33
1423 1465 2.112928 TCCATGCGCACCAACACT 59.887 55.556 14.90 0.00 0.00 3.55
1518 1560 2.238646 ACGGCCAATTCTATTCAGACCA 59.761 45.455 2.24 0.00 0.00 4.02
1556 1598 1.214062 GACCCAGCAGAGAGTCGTG 59.786 63.158 0.00 0.00 0.00 4.35
1631 1678 2.340078 GTGACAGAGAGCACGGCA 59.660 61.111 0.00 0.00 0.00 5.69
1664 1719 4.863925 GAGAGAGAGCACGGCGGC 62.864 72.222 13.24 12.27 0.00 6.53
1739 1794 2.500910 CTCCATGTCTTCCTCAAGCTCT 59.499 50.000 0.00 0.00 0.00 4.09
1800 1855 0.315568 GCCTGTCTTCGTCTGTCTGT 59.684 55.000 0.00 0.00 0.00 3.41
1808 1863 2.734591 GTCTGTCTGTGGTGCCGA 59.265 61.111 0.00 0.00 0.00 5.54
1840 1895 0.393077 CGGAGGGTTTCTCACACACT 59.607 55.000 0.00 0.00 44.19 3.55
1894 1950 2.223971 GCGAGAATGGGGTAAGAATCGA 60.224 50.000 0.00 0.00 0.00 3.59
1990 2046 2.814336 GCTTCTTTCTTTGGGTCGATGT 59.186 45.455 0.00 0.00 0.00 3.06
2129 2185 0.179113 GCACTGACAGAGAGCTAGCC 60.179 60.000 12.13 2.81 35.53 3.93
2167 2223 4.287766 TGAAGAAGAAGGTTAGGAAGCC 57.712 45.455 0.00 0.00 0.00 4.35
2339 2396 8.472007 TCACCTAGTTTAAATGTTGGTCAAAT 57.528 30.769 0.00 0.00 0.00 2.32
2347 2404 9.833182 GTTTAAATGTTGGTCAAATTTGTTTGT 57.167 25.926 17.47 0.00 33.82 2.83
2349 2406 9.831737 TTAAATGTTGGTCAAATTTGTTTGTTG 57.168 25.926 17.47 0.00 33.82 3.33
2350 2407 7.678947 AATGTTGGTCAAATTTGTTTGTTGA 57.321 28.000 17.47 0.00 33.82 3.18
2453 2517 4.541973 TGAAATGCAACTCTCTGCTCTA 57.458 40.909 0.00 0.00 43.07 2.43
2498 2564 1.425066 TCTGTGGGCCAAATTCAGAGT 59.575 47.619 17.81 0.00 32.49 3.24
2556 2622 2.862541 CATCCAATTAGGCCCATTCGA 58.137 47.619 0.00 0.00 37.29 3.71
2586 2654 5.465935 TCTTGCGTGTTTTTCTGTTTTCTT 58.534 33.333 0.00 0.00 0.00 2.52
2634 2702 6.421801 ACTCATAATGCTGAAACTTTTTGTGC 59.578 34.615 0.00 0.00 0.00 4.57
2678 2746 8.306761 CCAGAGCCAAACAATTAAGTTTAGAAT 58.693 33.333 0.00 0.00 39.55 2.40
2882 2954 6.490040 TGTCTAGAAAAATGAAGGGTGGAAAG 59.510 38.462 0.00 0.00 0.00 2.62
2893 2965 2.168313 AGGGTGGAAAGTGCACAAAAAG 59.832 45.455 21.04 0.00 40.73 2.27
2979 3051 2.119495 ACCGCTAGGACAGATGGAAAT 58.881 47.619 0.00 0.00 41.02 2.17
3079 3151 5.557891 TTGTTTTGCACTGAAATTTTGGG 57.442 34.783 0.00 0.00 0.00 4.12
3203 3279 5.375417 TTGCATGTTAGTTCATGACTTGG 57.625 39.130 10.28 0.00 45.41 3.61
3209 3285 7.306749 GCATGTTAGTTCATGACTTGGTTTTTG 60.307 37.037 10.28 0.00 45.41 2.44
3210 3286 7.164230 TGTTAGTTCATGACTTGGTTTTTGT 57.836 32.000 0.00 0.00 39.86 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 5.082251 AGTGGGTCTAAAACGATACTTCC 57.918 43.478 0.00 0.00 0.00 3.46
66 67 7.599998 TGTAAAGTGGGTCTAAAACGATACTTC 59.400 37.037 0.00 0.00 30.50 3.01
67 68 7.444299 TGTAAAGTGGGTCTAAAACGATACTT 58.556 34.615 0.00 0.00 31.45 2.24
68 69 6.996509 TGTAAAGTGGGTCTAAAACGATACT 58.003 36.000 0.00 0.00 0.00 2.12
69 70 7.838771 ATGTAAAGTGGGTCTAAAACGATAC 57.161 36.000 0.00 0.00 0.00 2.24
70 71 8.851541 AAATGTAAAGTGGGTCTAAAACGATA 57.148 30.769 0.00 0.00 0.00 2.92
71 72 7.754851 AAATGTAAAGTGGGTCTAAAACGAT 57.245 32.000 0.00 0.00 0.00 3.73
72 73 7.499895 AGAAAATGTAAAGTGGGTCTAAAACGA 59.500 33.333 0.00 0.00 0.00 3.85
73 74 7.645402 AGAAAATGTAAAGTGGGTCTAAAACG 58.355 34.615 0.00 0.00 0.00 3.60
106 107 8.533965 CAAACACTGTGACATTTTGTATTTCTG 58.466 33.333 15.86 0.00 0.00 3.02
108 109 8.627487 TCAAACACTGTGACATTTTGTATTTC 57.373 30.769 15.86 0.00 0.00 2.17
110 111 8.994429 TTTCAAACACTGTGACATTTTGTATT 57.006 26.923 15.86 0.00 0.00 1.89
112 113 8.031864 ACATTTCAAACACTGTGACATTTTGTA 58.968 29.630 15.86 5.90 0.00 2.41
113 114 6.873076 ACATTTCAAACACTGTGACATTTTGT 59.127 30.769 15.86 6.90 0.00 2.83
114 115 7.276218 AGACATTTCAAACACTGTGACATTTTG 59.724 33.333 15.86 13.92 0.00 2.44
158 159 4.099824 CGTGTTTGGCGTTCTAAACTTTT 58.900 39.130 0.00 0.00 37.60 2.27
162 163 1.598601 TCCGTGTTTGGCGTTCTAAAC 59.401 47.619 0.00 0.00 37.32 2.01
245 246 6.611613 ATGCTAGCTTGTATAATAGGAGCA 57.388 37.500 17.23 0.00 41.26 4.26
250 251 7.875316 AACACGATGCTAGCTTGTATAATAG 57.125 36.000 17.23 2.04 0.00 1.73
252 253 8.244494 CATAACACGATGCTAGCTTGTATAAT 57.756 34.615 17.23 0.00 0.00 1.28
279 280 8.324306 AGAAAATATCTTAGCAGCCTGCATATA 58.676 33.333 20.53 10.56 40.01 0.86
282 283 5.383476 AGAAAATATCTTAGCAGCCTGCAT 58.617 37.500 20.53 5.95 40.01 3.96
309 310 9.686683 TGTTTTGAATTTTCAAGGGGATTTAAA 57.313 25.926 5.92 0.00 46.68 1.52
380 381 6.659745 AGTTTGTTGGCATATCATATGCAT 57.340 33.333 27.28 3.79 46.21 3.96
471 474 3.973206 TGTGTCACCACGAATAATCCT 57.027 42.857 0.00 0.00 44.92 3.24
646 652 0.670162 CACCCAACCAAACTCTGCTG 59.330 55.000 0.00 0.00 0.00 4.41
681 687 2.044123 AATGTGGCTAAGGCTGTAGC 57.956 50.000 15.79 15.79 44.87 3.58
732 738 0.869730 AATGTACGTGGCGGTTTGTC 59.130 50.000 0.00 0.00 0.00 3.18
741 747 1.323534 GAACGCTGCTAATGTACGTGG 59.676 52.381 0.00 0.00 37.01 4.94
762 768 4.158384 GGATAACAACTTGTGCGATGTTG 58.842 43.478 10.86 10.86 42.67 3.33
763 769 3.120338 CGGATAACAACTTGTGCGATGTT 60.120 43.478 0.00 0.00 34.82 2.71
765 771 2.415168 ACGGATAACAACTTGTGCGATG 59.585 45.455 0.00 0.00 36.13 3.84
784 799 1.283736 GGACGGTTTGTATGCCTACG 58.716 55.000 0.00 0.00 0.00 3.51
834 849 3.829601 GGACAGGAAGAAGAGAGAGTTCA 59.170 47.826 0.00 0.00 0.00 3.18
853 868 1.213926 AGATGGCAAAGAGATGGGGAC 59.786 52.381 0.00 0.00 0.00 4.46
891 906 1.153369 CACGATGAGAATGGCGGGT 60.153 57.895 0.00 0.00 0.00 5.28
919 934 1.238439 CATGTCAAAAGTCCAGCGGT 58.762 50.000 0.00 0.00 0.00 5.68
937 952 3.466836 GAATGCCACTAATGATCGTCCA 58.533 45.455 0.00 0.00 0.00 4.02
938 953 2.476619 CGAATGCCACTAATGATCGTCC 59.523 50.000 0.00 0.00 0.00 4.79
949 965 2.742372 GCGGACACGAATGCCACT 60.742 61.111 0.00 0.00 44.60 4.00
991 1007 2.821366 GGAGGCCATCGTGTGCAG 60.821 66.667 5.01 0.00 0.00 4.41
1000 1029 1.470996 GCAGATCGAGAGGAGGCCAT 61.471 60.000 5.01 0.00 0.00 4.40
1001 1030 2.130426 GCAGATCGAGAGGAGGCCA 61.130 63.158 5.01 0.00 0.00 5.36
1262 1304 6.892658 AATTGGTTGCATACTCAAGTTGTA 57.107 33.333 2.11 0.00 0.00 2.41
1421 1463 0.600255 CGGCAGAGTTCACGGAAAGT 60.600 55.000 0.00 0.00 0.00 2.66
1423 1465 0.599204 GACGGCAGAGTTCACGGAAA 60.599 55.000 0.00 0.00 0.00 3.13
1518 1560 3.286751 ACAAGCCACGCGTGCAAT 61.287 55.556 33.17 17.72 41.40 3.56
1556 1598 2.817396 GCAACGGCTCTCTGCTCC 60.817 66.667 0.00 0.00 42.39 4.70
1631 1678 0.250945 TCTCTCTCGCTGTGGTCACT 60.251 55.000 2.66 0.00 0.00 3.41
1640 1687 1.089481 CGTGCTCTCTCTCTCTCGCT 61.089 60.000 0.00 0.00 0.00 4.93
1664 1719 0.390860 CCTCCACATCTAGCTTCCCG 59.609 60.000 0.00 0.00 0.00 5.14
1690 1745 1.602237 GAAGGGGATCTCAACGCCA 59.398 57.895 0.00 0.00 41.77 5.69
1840 1895 6.531503 AGAACGAATGATTCTAGTTCCTCA 57.468 37.500 16.88 0.00 41.28 3.86
1848 1903 4.796830 GCACACGTAGAACGAATGATTCTA 59.203 41.667 6.44 0.00 46.05 2.10
1894 1950 1.344114 ACGAAAATGGTGCAATTGCCT 59.656 42.857 26.94 7.00 41.18 4.75
1918 1974 1.358787 ACCCATTGCTCAAAGATCCCA 59.641 47.619 0.00 0.00 0.00 4.37
1990 2046 2.259917 TCATCAGAGTCTTGGCCAGAA 58.740 47.619 5.11 0.00 31.28 3.02
2129 2185 4.245660 TCTTCAACATCCTAAGCTCAACG 58.754 43.478 0.00 0.00 0.00 4.10
2167 2223 5.885230 TGGTATTTGTGCTTGATCTTCAG 57.115 39.130 0.00 0.00 0.00 3.02
2498 2564 1.003355 GCCTGCACTTGGCTCTACA 60.003 57.895 8.16 0.00 46.38 2.74
2556 2622 2.052782 AAAACACGCAAGAGAACCCT 57.947 45.000 0.00 0.00 43.62 4.34
2610 2678 6.421501 TGCACAAAAAGTTTCAGCATTATGAG 59.578 34.615 0.00 0.00 0.00 2.90
2634 2702 7.144000 GGCTCTGGAATAATTCAATTAGCTTG 58.856 38.462 0.00 0.00 36.09 4.01
2733 2802 7.747155 TTGGTCTTTGATTTAAATCACGGTA 57.253 32.000 26.69 12.35 44.54 4.02
2863 2935 4.058124 GCACTTTCCACCCTTCATTTTTC 58.942 43.478 0.00 0.00 0.00 2.29
2882 2954 0.644843 CGCACCAACTTTTTGTGCAC 59.355 50.000 10.75 10.75 38.56 4.57
2979 3051 3.521937 CCTTCCCTACCCATGTCAAAGTA 59.478 47.826 0.00 0.00 0.00 2.24
3079 3151 3.007398 TGCAAACATACATTTCCAACCCC 59.993 43.478 0.00 0.00 0.00 4.95
3203 3279 5.463392 GCCCTCTCTTTCATTCAACAAAAAC 59.537 40.000 0.00 0.00 0.00 2.43
3209 3285 4.331108 AGAAGCCCTCTCTTTCATTCAAC 58.669 43.478 0.00 0.00 0.00 3.18
3210 3286 4.583871 GAGAAGCCCTCTCTTTCATTCAA 58.416 43.478 6.23 0.00 46.32 2.69


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

AutoCloner maintained by Alex Coulton.