Multiple sequence alignment - TraesCS2B01G073700

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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 TraesCS2B01G073700 chr2B 100.000 2798 0 0 1 2798 39940664 39943461 0.000000e+00 5168.0
1 TraesCS2B01G073700 chr2A 95.297 2828 87 26 1 2798 26865045 26867856 0.000000e+00 4444.0
2 TraesCS2B01G073700 chr2A 90.030 1344 78 23 982 2297 770397470 770398785 0.000000e+00 1688.0
3 TraesCS2B01G073700 chr2D 94.811 2833 81 35 1 2798 24487171 24489972 0.000000e+00 4357.0
4 TraesCS2B01G073700 chr7A 90.296 1350 79 25 982 2297 40374656 40375987 0.000000e+00 1720.0
5 TraesCS2B01G073700 chr3A 90.058 1368 71 30 982 2297 588540056 588538702 0.000000e+00 1712.0
6 TraesCS2B01G073700 chr3A 77.471 1558 322 20 550 2094 127856891 127858432 0.000000e+00 905.0
7 TraesCS2B01G073700 chr3A 76.893 1532 338 15 436 1962 127820536 127822056 0.000000e+00 854.0
8 TraesCS2B01G073700 chr3B 77.346 1673 354 23 436 2097 172172664 172171006 0.000000e+00 966.0
9 TraesCS2B01G073700 chr3B 77.047 1673 359 23 436 2097 172054304 172052646 0.000000e+00 939.0
10 TraesCS2B01G073700 chr3B 76.905 1667 366 17 436 2094 173005680 173007335 0.000000e+00 928.0
11 TraesCS2B01G073700 chr3B 76.005 1667 362 30 436 2086 172213956 172212312 0.000000e+00 828.0
12 TraesCS2B01G073700 chr6D 76.867 1660 362 18 436 2086 452125850 452127496 0.000000e+00 918.0
13 TraesCS2B01G073700 chr1B 76.868 1673 356 27 436 2094 456712105 456713760 0.000000e+00 917.0
14 TraesCS2B01G073700 chr1B 85.169 472 52 9 1631 2095 668777649 668778109 4.220000e-128 468.0
15 TraesCS2B01G073700 chr1B 84.163 221 12 7 238 449 668764993 668765199 2.840000e-45 193.0
16 TraesCS2B01G073700 chr3D 76.725 1667 369 17 436 2094 121339821 121341476 0.000000e+00 911.0
17 TraesCS2B01G073700 chr3D 76.583 1674 364 25 436 2097 120144632 120142975 0.000000e+00 894.0
18 TraesCS2B01G073700 chr1A 86.723 354 25 6 1088 1430 576784525 576784867 9.460000e-100 374.0
19 TraesCS2B01G073700 chr1D 96.364 55 2 0 339 393 480439046 480439100 1.070000e-14 91.6


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 TraesCS2B01G073700 chr2B 39940664 39943461 2797 False 5168 5168 100.000 1 2798 1 chr2B.!!$F1 2797
1 TraesCS2B01G073700 chr2A 26865045 26867856 2811 False 4444 4444 95.297 1 2798 1 chr2A.!!$F1 2797
2 TraesCS2B01G073700 chr2A 770397470 770398785 1315 False 1688 1688 90.030 982 2297 1 chr2A.!!$F2 1315
3 TraesCS2B01G073700 chr2D 24487171 24489972 2801 False 4357 4357 94.811 1 2798 1 chr2D.!!$F1 2797
4 TraesCS2B01G073700 chr7A 40374656 40375987 1331 False 1720 1720 90.296 982 2297 1 chr7A.!!$F1 1315
5 TraesCS2B01G073700 chr3A 588538702 588540056 1354 True 1712 1712 90.058 982 2297 1 chr3A.!!$R1 1315
6 TraesCS2B01G073700 chr3A 127856891 127858432 1541 False 905 905 77.471 550 2094 1 chr3A.!!$F2 1544
7 TraesCS2B01G073700 chr3A 127820536 127822056 1520 False 854 854 76.893 436 1962 1 chr3A.!!$F1 1526
8 TraesCS2B01G073700 chr3B 172171006 172172664 1658 True 966 966 77.346 436 2097 1 chr3B.!!$R2 1661
9 TraesCS2B01G073700 chr3B 172052646 172054304 1658 True 939 939 77.047 436 2097 1 chr3B.!!$R1 1661
10 TraesCS2B01G073700 chr3B 173005680 173007335 1655 False 928 928 76.905 436 2094 1 chr3B.!!$F1 1658
11 TraesCS2B01G073700 chr3B 172212312 172213956 1644 True 828 828 76.005 436 2086 1 chr3B.!!$R3 1650
12 TraesCS2B01G073700 chr6D 452125850 452127496 1646 False 918 918 76.867 436 2086 1 chr6D.!!$F1 1650
13 TraesCS2B01G073700 chr1B 456712105 456713760 1655 False 917 917 76.868 436 2094 1 chr1B.!!$F1 1658
14 TraesCS2B01G073700 chr3D 121339821 121341476 1655 False 911 911 76.725 436 2094 1 chr3D.!!$F1 1658
15 TraesCS2B01G073700 chr3D 120142975 120144632 1657 True 894 894 76.583 436 2097 1 chr3D.!!$R1 1661

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
419 428 0.754957 ACCGAGCTCCTCTGGATGAG 60.755 60.0 8.47 0.0 42.3 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2312 1.469308 CGTCAAGCGTAAGTCCTCTCT 59.531 52.381 0.0 0.0 41.68 3.1 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
18 21 3.052711 GAACAACTAACACGCGTGC 57.947 52.632 37.35 15.17 0.00 5.34
73 76 1.732259 CCGTAGCAAAGTTCTCGCAAT 59.268 47.619 0.00 0.00 0.00 3.56
74 77 2.474526 CCGTAGCAAAGTTCTCGCAATG 60.475 50.000 0.00 0.00 0.00 2.82
132 140 8.213518 TCTGCAAATTACAAATCCTAGATGTC 57.786 34.615 0.00 0.00 0.00 3.06
225 234 4.029809 GGCGGGCCAACTACCTGT 62.030 66.667 4.39 0.00 35.84 4.00
226 235 2.746277 GCGGGCCAACTACCTGTG 60.746 66.667 4.39 0.00 35.84 3.66
227 236 2.746277 CGGGCCAACTACCTGTGC 60.746 66.667 4.39 0.00 0.00 4.57
419 428 0.754957 ACCGAGCTCCTCTGGATGAG 60.755 60.000 8.47 0.00 42.30 2.90
1063 1077 2.363018 CCGTCTCCTGGAGCTCCA 60.363 66.667 33.04 33.04 45.30 3.86
1270 1285 2.268920 GGCGGATGCACTGGAAGA 59.731 61.111 0.00 0.00 45.35 2.87
1272 1287 2.456119 GCGGATGCACTGGAAGACG 61.456 63.158 0.00 0.00 42.15 4.18
2123 2173 1.753073 GCCAATGAAGTAGGCTGCAAT 59.247 47.619 5.14 0.00 44.92 3.56
2124 2174 2.480759 GCCAATGAAGTAGGCTGCAATG 60.481 50.000 5.14 0.00 44.92 2.82
2126 2176 2.133281 ATGAAGTAGGCTGCAATGCA 57.867 45.000 7.99 7.99 33.17 3.96
2127 2177 2.133281 TGAAGTAGGCTGCAATGCAT 57.867 45.000 8.91 0.00 38.13 3.96
2128 2178 2.019249 TGAAGTAGGCTGCAATGCATC 58.981 47.619 8.91 3.99 38.13 3.91
2130 2180 0.256752 AGTAGGCTGCAATGCATCCA 59.743 50.000 27.08 12.37 45.97 3.41
2131 2181 1.133575 AGTAGGCTGCAATGCATCCAT 60.134 47.619 27.08 15.61 45.97 3.41
2132 2182 1.000607 GTAGGCTGCAATGCATCCATG 60.001 52.381 27.08 8.83 45.97 3.66
2133 2183 1.069090 GGCTGCAATGCATCCATGG 59.931 57.895 21.71 4.97 43.41 3.66
2134 2184 1.682451 GGCTGCAATGCATCCATGGT 61.682 55.000 21.71 0.00 43.41 3.55
2135 2185 0.249322 GCTGCAATGCATCCATGGTC 60.249 55.000 8.91 3.07 38.13 4.02
2136 2186 1.107945 CTGCAATGCATCCATGGTCA 58.892 50.000 8.91 8.98 38.13 4.02
2138 2188 1.341187 TGCAATGCATCCATGGTCAGA 60.341 47.619 12.58 0.00 31.71 3.27
2200 2312 3.194329 TGACGACGGTTACTAGAGAGAGA 59.806 47.826 0.00 0.00 0.00 3.10
2201 2313 3.784338 ACGACGGTTACTAGAGAGAGAG 58.216 50.000 0.00 0.00 0.00 3.20
2202 2314 3.446873 ACGACGGTTACTAGAGAGAGAGA 59.553 47.826 0.00 0.00 0.00 3.10
2203 2315 4.046462 CGACGGTTACTAGAGAGAGAGAG 58.954 52.174 0.00 0.00 0.00 3.20
2204 2316 4.202040 CGACGGTTACTAGAGAGAGAGAGA 60.202 50.000 0.00 0.00 0.00 3.10
2205 2317 5.272283 ACGGTTACTAGAGAGAGAGAGAG 57.728 47.826 0.00 0.00 0.00 3.20
2671 2783 0.873743 CGATCGCTCAAGCTTCCTCC 60.874 60.000 0.26 0.00 39.32 4.30
2722 2834 1.006805 GGATCGAGTCGATGGCTGG 60.007 63.158 31.55 0.00 47.00 4.85
2723 2835 1.663074 GATCGAGTCGATGGCTGGC 60.663 63.158 31.55 12.85 47.00 4.85
2724 2836 2.081425 GATCGAGTCGATGGCTGGCT 62.081 60.000 31.55 6.75 47.00 4.75
2757 2869 0.036306 GTGGATGGAGGTTTCACGGT 59.964 55.000 0.00 0.00 0.00 4.83
2759 2871 1.305930 GGATGGAGGTTTCACGGTGC 61.306 60.000 2.51 0.00 0.00 5.01
2782 2896 2.381911 CGGTGGGGGTATATATAGCGT 58.618 52.381 14.20 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 21 3.068732 TGAGGCAAGTTATCTCGGATGAG 59.931 47.826 0.00 0.00 43.99 2.90
73 76 6.349280 GCATGGTTCTGCTTTACTTTACATCA 60.349 38.462 0.00 0.00 39.12 3.07
74 77 6.030228 GCATGGTTCTGCTTTACTTTACATC 58.970 40.000 0.00 0.00 39.12 3.06
132 140 1.929836 GATTCGCTGTACTGAGGCAAG 59.070 52.381 3.61 0.00 0.00 4.01
187 196 0.396695 CAGGGGCATTTGGAGCTCAT 60.397 55.000 17.19 0.00 32.95 2.90
216 225 4.388499 CCGCCGGCACAGGTAGTT 62.388 66.667 28.98 0.00 0.00 2.24
242 251 4.882396 GGAGCTTCGAGGAGGCGC 62.882 72.222 0.00 0.00 39.66 6.53
244 253 4.214327 CGGGAGCTTCGAGGAGGC 62.214 72.222 0.00 0.00 34.80 4.70
396 405 2.487428 CAGAGGAGCTCGGTCGTG 59.513 66.667 7.83 4.17 35.36 4.35
401 410 2.040330 CTCATCCAGAGGAGCTCGG 58.960 63.158 7.83 3.10 40.84 4.63
545 554 1.005340 GCTGCAGATCTTCAAGTCGG 58.995 55.000 20.43 0.00 0.00 4.79
1063 1077 2.948720 GCCTGGAGGACGTCAAGCT 61.949 63.158 18.91 5.08 37.39 3.74
1461 1491 4.760047 CCCAACAGCCTCGACCCG 62.760 72.222 0.00 0.00 0.00 5.28
1866 1912 2.503061 CAGATCCGGGAGCTGGTG 59.497 66.667 30.01 9.81 41.66 4.17
2123 2173 3.009363 TCTTCTTTCTGACCATGGATGCA 59.991 43.478 21.47 12.33 0.00 3.96
2124 2174 3.376546 GTCTTCTTTCTGACCATGGATGC 59.623 47.826 21.47 7.92 0.00 3.91
2126 2176 3.866651 CGTCTTCTTTCTGACCATGGAT 58.133 45.455 21.47 1.98 0.00 3.41
2127 2177 2.612972 GCGTCTTCTTTCTGACCATGGA 60.613 50.000 21.47 0.00 0.00 3.41
2128 2178 1.734465 GCGTCTTCTTTCTGACCATGG 59.266 52.381 11.19 11.19 0.00 3.66
2130 2180 2.839486 TGCGTCTTCTTTCTGACCAT 57.161 45.000 0.00 0.00 0.00 3.55
2131 2181 2.102420 TCTTGCGTCTTCTTTCTGACCA 59.898 45.455 0.00 0.00 0.00 4.02
2132 2182 2.755650 TCTTGCGTCTTCTTTCTGACC 58.244 47.619 0.00 0.00 0.00 4.02
2133 2183 4.449068 TGATTCTTGCGTCTTCTTTCTGAC 59.551 41.667 0.00 0.00 0.00 3.51
2134 2184 4.631131 TGATTCTTGCGTCTTCTTTCTGA 58.369 39.130 0.00 0.00 0.00 3.27
2135 2185 4.997905 TGATTCTTGCGTCTTCTTTCTG 57.002 40.909 0.00 0.00 0.00 3.02
2136 2186 5.702670 TGATTGATTCTTGCGTCTTCTTTCT 59.297 36.000 0.00 0.00 0.00 2.52
2138 2188 5.947228 TGATTGATTCTTGCGTCTTCTTT 57.053 34.783 0.00 0.00 0.00 2.52
2200 2312 1.469308 CGTCAAGCGTAAGTCCTCTCT 59.531 52.381 0.00 0.00 41.68 3.10
2201 2313 1.897641 CGTCAAGCGTAAGTCCTCTC 58.102 55.000 0.00 0.00 41.68 3.20
2457 2569 0.319555 TCGACCTCTTCAACGGCAAG 60.320 55.000 0.00 0.00 0.00 4.01
2459 2571 1.289066 CTCGACCTCTTCAACGGCA 59.711 57.895 0.00 0.00 0.00 5.69
2658 2770 2.303549 ATCGGCGGAGGAAGCTTGAG 62.304 60.000 2.10 0.00 34.52 3.02
2697 2809 0.891449 ATCGACTCGATCCAGCCGAT 60.891 55.000 5.75 5.75 43.45 4.18
2723 2835 3.726517 CACAACCTCGGCGGCAAG 61.727 66.667 10.53 0.00 35.61 4.01
2733 2845 1.780309 TGAAACCTCCATCCACAACCT 59.220 47.619 0.00 0.00 0.00 3.50
2738 2850 0.036306 ACCGTGAAACCTCCATCCAC 59.964 55.000 0.00 0.00 0.00 4.02
2757 2869 4.885640 TATATATACCCCCACCGCGGCA 62.886 54.545 28.58 1.51 0.00 5.69
2759 2871 1.684983 CTATATATACCCCCACCGCGG 59.315 57.143 26.86 26.86 0.00 6.46


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

AutoCloner maintained by Alex Coulton.