Multiple sequence alignment - TraesCS2A01G282600

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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 TraesCS2A01G282600 chr2A 100.000 2333 0 0 1 2333 473599695 473602027 0.000000e+00 4309
1 TraesCS2A01G282600 chr2B 92.565 1856 74 13 528 2333 421246744 421248585 0.000000e+00 2604
2 TraesCS2A01G282600 chr2B 85.476 420 45 6 11 428 421246092 421246497 7.710000e-115 424
3 TraesCS2A01G282600 chr2D 92.219 1645 50 18 430 2053 354378634 354380221 0.000000e+00 2257
4 TraesCS2A01G282600 chr2D 90.698 430 37 3 1 429 354377935 354378362 9.350000e-159 569
5 TraesCS2A01G282600 chr2D 93.651 252 14 2 2083 2333 354380222 354380472 2.190000e-100 375


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 TraesCS2A01G282600 chr2A 473599695 473602027 2332 False 4309 4309 100.000000 1 2333 1 chr2A.!!$F1 2332
1 TraesCS2A01G282600 chr2B 421246092 421248585 2493 False 1514 2604 89.020500 11 2333 2 chr2B.!!$F1 2322
2 TraesCS2A01G282600 chr2D 354377935 354380472 2537 False 1067 2257 92.189333 1 2333 3 chr2D.!!$F1 2332

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
933 1212 0.329931 TCGCCAACCTCTCTCTCTCT 59.67 55.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2617 0.110486 GCAAGACTTGGTCCCTTCCA 59.89 55.0 16.8 0.0 32.18 3.53 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
60 61 0.746563 GGCGCCAAGTTATACCTGCA 60.747 55.000 24.80 0.00 0.00 4.41
63 64 2.356135 CGCCAAGTTATACCTGCAACT 58.644 47.619 0.00 0.00 36.56 3.16
81 82 0.598562 CTGACTGGTGCTACACTCGT 59.401 55.000 0.00 0.00 34.40 4.18
130 132 5.689383 AGTCATACATGTTGTTGTTGGAC 57.311 39.130 2.30 1.17 34.39 4.02
147 149 1.658994 GACCGAAAGTGGTGTGACAA 58.341 50.000 0.00 0.00 44.01 3.18
151 153 2.813754 CCGAAAGTGGTGTGACAATGAT 59.186 45.455 0.00 0.00 0.00 2.45
156 158 2.108075 AGTGGTGTGACAATGATGGGAA 59.892 45.455 0.00 0.00 0.00 3.97
192 194 4.863548 TCTTTGTCTTCCGGTATCTCCTA 58.136 43.478 0.00 0.00 0.00 2.94
211 213 4.040095 TCCTACAGAGGTAATCGATCGAGA 59.960 45.833 23.84 11.12 44.19 4.04
223 225 1.434622 GATCGAGACGTCGGTAGCCA 61.435 60.000 10.46 0.00 46.80 4.75
276 279 3.331150 ACAAGTTTGCGTAATCCGATGA 58.669 40.909 0.00 0.00 39.56 2.92
302 305 3.058293 CACGAGATCTCTGATCAGGCTAC 60.058 52.174 22.42 11.76 0.00 3.58
315 318 2.100631 GGCTACGTTGATGCGTGCT 61.101 57.895 0.00 0.00 45.33 4.40
320 323 2.252260 GTTGATGCGTGCTTGCGT 59.748 55.556 0.00 0.00 37.81 5.24
336 339 2.250939 CGTCGTGCCCTTGCTGAAA 61.251 57.895 0.00 0.00 38.71 2.69
343 347 1.809567 GCCCTTGCTGAAAGTGGTGG 61.810 60.000 0.00 0.00 35.30 4.61
350 354 1.961793 CTGAAAGTGGTGGACCGAAA 58.038 50.000 0.00 0.00 39.43 3.46
355 359 0.834612 AGTGGTGGACCGAAACTCAA 59.165 50.000 0.00 0.00 39.43 3.02
372 376 6.605471 AACTCAATTTGGGGATAAAAGTCC 57.395 37.500 0.55 0.00 37.56 3.85
433 709 1.372872 GCGGCGTTTTCTTTGGCAT 60.373 52.632 9.37 0.00 0.00 4.40
482 758 6.215121 CAACTCACAATGTTGAAAATAGGCA 58.785 36.000 0.00 0.00 45.27 4.75
546 825 6.325919 TGTTTCGTAGATGGAAAATTGCTT 57.674 33.333 0.00 0.00 35.36 3.91
547 826 6.148948 TGTTTCGTAGATGGAAAATTGCTTG 58.851 36.000 0.00 0.00 35.36 4.01
548 827 5.957842 TTCGTAGATGGAAAATTGCTTGT 57.042 34.783 0.00 0.00 35.04 3.16
647 926 2.355197 GGAAATTTCCGGGCAAAATGG 58.645 47.619 21.15 0.00 37.65 3.16
778 1057 9.950496 AATAATCGCTCTCTAATTAATCACCAT 57.050 29.630 0.00 0.00 0.00 3.55
814 1093 2.700407 TTTGCTTACCCCACCCACCG 62.700 60.000 0.00 0.00 0.00 4.94
919 1198 1.573829 GCTTCGTTCACCAATCGCCA 61.574 55.000 0.00 0.00 0.00 5.69
933 1212 0.329931 TCGCCAACCTCTCTCTCTCT 59.670 55.000 0.00 0.00 0.00 3.10
934 1213 0.738389 CGCCAACCTCTCTCTCTCTC 59.262 60.000 0.00 0.00 0.00 3.20
935 1214 1.681780 CGCCAACCTCTCTCTCTCTCT 60.682 57.143 0.00 0.00 0.00 3.10
936 1215 2.024414 GCCAACCTCTCTCTCTCTCTC 58.976 57.143 0.00 0.00 0.00 3.20
937 1216 2.357154 GCCAACCTCTCTCTCTCTCTCT 60.357 54.545 0.00 0.00 0.00 3.10
938 1217 3.545703 CCAACCTCTCTCTCTCTCTCTC 58.454 54.545 0.00 0.00 0.00 3.20
939 1218 3.200825 CCAACCTCTCTCTCTCTCTCTCT 59.799 52.174 0.00 0.00 0.00 3.10
940 1219 4.446371 CAACCTCTCTCTCTCTCTCTCTC 58.554 52.174 0.00 0.00 0.00 3.20
941 1220 4.000928 ACCTCTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 0.00 3.10
942 1221 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
943 1222 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
944 1223 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
945 1224 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
946 1225 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
947 1226 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
948 1227 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
995 1316 2.355244 GAGGATCTAGCACGCGCC 60.355 66.667 5.73 0.00 39.83 6.53
1380 1701 2.661594 GGCGCTCGATTTTGTTTTCTT 58.338 42.857 7.64 0.00 0.00 2.52
1429 1750 8.773404 AATACAGTGTGTTATAGAACAGAACC 57.227 34.615 5.88 0.00 46.20 3.62
1482 1805 2.543777 TAGTAATGATTCCTGCCGGC 57.456 50.000 22.73 22.73 0.00 6.13
1623 1946 1.878211 TGTGTCCATCCAGGCATCTA 58.122 50.000 0.00 0.00 37.29 1.98
1656 1979 1.148310 GTCAGTTTTGCAGAGCGCTA 58.852 50.000 11.50 0.00 43.06 4.26
1659 1982 1.136141 CAGTTTTGCAGAGCGCTACTG 60.136 52.381 23.93 23.93 43.06 2.74
1677 2000 2.880890 ACTGGTGCTAAAACTTGCAGAG 59.119 45.455 0.00 0.00 40.06 3.35
1766 2114 1.617357 GCTATACGTTCCCCCGAGATT 59.383 52.381 0.00 0.00 0.00 2.40
1799 2147 1.344763 ACTCAGTTCCACCAGTGCTAC 59.655 52.381 0.00 0.00 0.00 3.58
1863 2212 6.348213 GCTTGAATTTTCTCCTTTACTGCGTA 60.348 38.462 0.00 0.00 0.00 4.42
1864 2213 7.626452 GCTTGAATTTTCTCCTTTACTGCGTAT 60.626 37.037 0.00 0.00 0.00 3.06
1865 2214 8.780846 TTGAATTTTCTCCTTTACTGCGTATA 57.219 30.769 0.00 0.00 0.00 1.47
1873 2225 5.585390 TCCTTTACTGCGTATACAAGTAGC 58.415 41.667 12.67 4.66 0.00 3.58
1927 2279 4.101790 GCCGGTGAATGGTGTGCG 62.102 66.667 1.90 0.00 0.00 5.34
2077 2429 0.323816 TCTGCAGAGTCGTCCTCCAT 60.324 55.000 13.74 0.00 41.47 3.41
2198 2550 9.507280 CAGCAGATTGTAGTGGTTATTTTATTG 57.493 33.333 0.00 0.00 0.00 1.90
2204 2556 6.486056 TGTAGTGGTTATTTTATTGCCCTCA 58.514 36.000 0.00 0.00 0.00 3.86
2218 2570 3.295093 TGCCCTCAAAACACAAAGATGA 58.705 40.909 0.00 0.00 0.00 2.92
2222 2574 2.975851 CTCAAAACACAAAGATGAGCGC 59.024 45.455 0.00 0.00 32.05 5.92
2265 2617 5.581126 ACACATGAAACGCAATATCCAAT 57.419 34.783 0.00 0.00 0.00 3.16
2270 2622 5.247507 TGAAACGCAATATCCAATGGAAG 57.752 39.130 5.89 0.00 34.34 3.46
2293 2646 0.676151 CCAAGTCTTGCTGGAGCTCC 60.676 60.000 26.78 26.78 42.66 4.70
2297 2650 0.612744 GTCTTGCTGGAGCTCCTCTT 59.387 55.000 32.28 0.00 42.66 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.908910 ATCGTCCATAGCACCAACCA 59.091 50.000 0.00 0.00 0.00 3.67
51 52 2.354704 GCACCAGTCAGTTGCAGGTATA 60.355 50.000 0.00 0.00 0.00 1.47
60 61 1.000163 CGAGTGTAGCACCAGTCAGTT 60.000 52.381 10.08 0.00 35.00 3.16
63 64 1.037493 AACGAGTGTAGCACCAGTCA 58.963 50.000 10.08 0.00 35.00 3.41
130 132 2.217750 TCATTGTCACACCACTTTCGG 58.782 47.619 0.00 0.00 0.00 4.30
147 149 2.107204 GCTCCATACCACTTCCCATCAT 59.893 50.000 0.00 0.00 0.00 2.45
151 153 1.490490 GATGCTCCATACCACTTCCCA 59.510 52.381 0.00 0.00 0.00 4.37
156 158 3.521126 AGACAAAGATGCTCCATACCACT 59.479 43.478 0.00 0.00 0.00 4.00
192 194 2.544686 CGTCTCGATCGATTACCTCTGT 59.455 50.000 19.78 0.00 0.00 3.41
211 213 1.585006 CTTGACTGGCTACCGACGT 59.415 57.895 0.00 0.00 0.00 4.34
223 225 4.442706 CGCATCTTACATTACCCTTGACT 58.557 43.478 0.00 0.00 0.00 3.41
276 279 4.753233 CCTGATCAGAGATCTCGTGTTTT 58.247 43.478 24.62 0.00 34.09 2.43
302 305 2.866510 CGCAAGCACGCATCAACG 60.867 61.111 0.00 0.00 39.50 4.10
312 315 4.927782 AAGGGCACGACGCAAGCA 62.928 61.111 9.29 0.00 45.17 3.91
315 318 4.927782 AGCAAGGGCACGACGCAA 62.928 61.111 0.00 0.00 45.17 4.85
320 323 1.148273 ACTTTCAGCAAGGGCACGA 59.852 52.632 0.00 0.00 44.61 4.35
336 339 0.834612 TTGAGTTTCGGTCCACCACT 59.165 50.000 0.00 0.00 35.14 4.00
343 347 2.510613 TCCCCAAATTGAGTTTCGGTC 58.489 47.619 0.00 0.00 0.00 4.79
372 376 0.393077 CAACTATAGGCCAGTCCCGG 59.607 60.000 5.01 0.00 34.51 5.73
482 758 5.528043 TGCAAATTGTACAAAGGTGACAT 57.472 34.783 13.23 0.00 0.00 3.06
618 897 3.488553 GCCCGGAAATTTCCTAACAATCG 60.489 47.826 29.85 16.27 45.33 3.34
647 926 1.004560 TCTGCACTGCACTGGCTAC 60.005 57.895 0.00 0.00 41.91 3.58
778 1057 6.916360 AAGCAAAATTGATTAGTGGGAGAA 57.084 33.333 0.00 0.00 34.65 2.87
814 1093 2.778679 GTCAATCAGCGCGGTCAC 59.221 61.111 8.38 0.00 0.00 3.67
919 1198 4.366267 AGAGAGAGAGAGAGAGAGAGGTT 58.634 47.826 0.00 0.00 0.00 3.50
933 1212 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
934 1213 3.005261 CGGAGAGAGAGAGAGAGAGAGAG 59.995 56.522 0.00 0.00 0.00 3.20
935 1214 2.959030 CGGAGAGAGAGAGAGAGAGAGA 59.041 54.545 0.00 0.00 0.00 3.10
936 1215 2.959030 TCGGAGAGAGAGAGAGAGAGAG 59.041 54.545 0.00 0.00 0.00 3.20
937 1216 3.026707 TCGGAGAGAGAGAGAGAGAGA 57.973 52.381 0.00 0.00 0.00 3.10
938 1217 3.576118 AGATCGGAGAGAGAGAGAGAGAG 59.424 52.174 0.00 0.00 43.63 3.20
939 1218 3.321968 CAGATCGGAGAGAGAGAGAGAGA 59.678 52.174 0.00 0.00 43.63 3.10
940 1219 3.070159 ACAGATCGGAGAGAGAGAGAGAG 59.930 52.174 0.00 0.00 43.63 3.20
941 1220 3.038280 ACAGATCGGAGAGAGAGAGAGA 58.962 50.000 0.00 0.00 43.63 3.10
942 1221 3.393800 GACAGATCGGAGAGAGAGAGAG 58.606 54.545 0.00 0.00 43.63 3.20
943 1222 2.223947 CGACAGATCGGAGAGAGAGAGA 60.224 54.545 0.00 0.00 44.99 3.10
944 1223 2.135139 CGACAGATCGGAGAGAGAGAG 58.865 57.143 0.00 0.00 44.99 3.20
945 1224 2.232756 CGACAGATCGGAGAGAGAGA 57.767 55.000 0.00 0.00 44.99 3.10
1056 1377 4.770540 ATGGACCTGTTGGCCATG 57.229 55.556 6.09 0.00 43.57 3.66
1411 1732 7.262772 CCTATTCGGTTCTGTTCTATAACACA 58.737 38.462 0.00 0.00 40.69 3.72
1419 1740 2.547990 ACCCCTATTCGGTTCTGTTCT 58.452 47.619 0.00 0.00 0.00 3.01
1420 1741 3.345508 AACCCCTATTCGGTTCTGTTC 57.654 47.619 0.00 0.00 39.46 3.18
1421 1742 3.073356 TCAAACCCCTATTCGGTTCTGTT 59.927 43.478 0.00 0.00 42.90 3.16
1422 1743 2.640826 TCAAACCCCTATTCGGTTCTGT 59.359 45.455 0.00 0.00 42.90 3.41
1423 1744 3.343941 TCAAACCCCTATTCGGTTCTG 57.656 47.619 0.00 0.00 42.90 3.02
1429 1750 8.258007 TGCTATATTCTATCAAACCCCTATTCG 58.742 37.037 0.00 0.00 0.00 3.34
1482 1805 3.849911 TCGATTCAGTAACAGCAAGAGG 58.150 45.455 0.00 0.00 0.00 3.69
1656 1979 2.880890 CTCTGCAAGTTTTAGCACCAGT 59.119 45.455 0.00 0.00 36.62 4.00
1659 1982 2.504367 TCCTCTGCAAGTTTTAGCACC 58.496 47.619 0.00 0.00 36.62 5.01
1772 2120 1.412710 TGGTGGAACTGAGTCACACTC 59.587 52.381 15.86 9.12 45.26 3.51
1863 2212 6.034591 GTGATGTCGTTAGTGCTACTTGTAT 58.965 40.000 0.00 0.00 0.00 2.29
1864 2213 5.048573 TGTGATGTCGTTAGTGCTACTTGTA 60.049 40.000 0.00 0.00 0.00 2.41
1865 2214 4.235360 GTGATGTCGTTAGTGCTACTTGT 58.765 43.478 0.00 0.00 0.00 3.16
1873 2225 3.614176 CCATGTCTGTGATGTCGTTAGTG 59.386 47.826 0.00 0.00 0.00 2.74
1927 2279 6.354130 TGTGCCACCCTACTTATTAAAGATC 58.646 40.000 0.00 0.00 36.50 2.75
2068 2420 2.620115 CCATTGATTTGGATGGAGGACG 59.380 50.000 0.00 0.00 44.49 4.79
2069 2421 2.363359 GCCATTGATTTGGATGGAGGAC 59.637 50.000 6.56 0.00 44.49 3.85
2071 2423 2.390696 TGCCATTGATTTGGATGGAGG 58.609 47.619 6.56 0.00 44.49 4.30
2077 2429 1.622811 GGGTGTTGCCATTGATTTGGA 59.377 47.619 0.00 0.00 39.25 3.53
2155 2507 2.037902 TGCTGAACAGTCGGGAACATAA 59.962 45.455 3.77 0.00 0.00 1.90
2178 2530 7.617723 TGAGGGCAATAAAATAACCACTACAAT 59.382 33.333 0.00 0.00 0.00 2.71
2179 2531 6.948886 TGAGGGCAATAAAATAACCACTACAA 59.051 34.615 0.00 0.00 0.00 2.41
2198 2550 3.858503 GCTCATCTTTGTGTTTTGAGGGC 60.859 47.826 0.00 0.00 35.47 5.19
2204 2556 2.618241 TCAGCGCTCATCTTTGTGTTTT 59.382 40.909 7.13 0.00 0.00 2.43
2222 2574 5.751028 GTGTTCACCTAATAGCTTAGCTCAG 59.249 44.000 11.09 6.72 40.44 3.35
2265 2617 0.110486 GCAAGACTTGGTCCCTTCCA 59.890 55.000 16.80 0.00 32.18 3.53
2270 2622 0.322008 CTCCAGCAAGACTTGGTCCC 60.322 60.000 16.81 0.00 39.79 4.46


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

AutoCloner maintained by Alex Coulton.