Multiple sequence alignment - TraesCS4B01G250300

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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 TraesCS4B01G250300 chr4B 100.000 2351 0 0 1 2351 516865853 516868203 0.000000e+00 4342
1 TraesCS4B01G250300 chr2B 88.126 2375 217 21 1 2351 424515206 424512873 0.000000e+00 2763
2 TraesCS4B01G250300 chr2B 86.394 2374 262 29 6 2350 243358847 243361188 0.000000e+00 2538
3 TraesCS4B01G250300 chr6B 87.811 2371 228 23 6 2351 365734876 365737210 0.000000e+00 2721
4 TraesCS4B01G250300 chr6B 90.176 1934 180 8 1 1929 593622101 593624029 0.000000e+00 2510
5 TraesCS4B01G250300 chr6B 85.484 186 27 0 1 186 484602226 484602041 6.630000e-46 195
6 TraesCS4B01G250300 chr3B 87.826 2374 219 22 1 2350 708915701 708913374 0.000000e+00 2719
7 TraesCS4B01G250300 chr3B 87.270 652 37 12 1722 2351 592829749 592829122 0.000000e+00 702
8 TraesCS4B01G250300 chr3B 85.987 314 32 6 16 320 566828720 566829030 2.250000e-85 326
9 TraesCS4B01G250300 chr3B 93.038 158 10 1 2194 2351 36028143 36028299 1.820000e-56 230
10 TraesCS4B01G250300 chr3D 87.881 2360 197 31 16 2350 422945034 422942739 0.000000e+00 2691
11 TraesCS4B01G250300 chr3D 87.595 2362 228 25 16 2351 126392448 126394770 0.000000e+00 2678
12 TraesCS4B01G250300 chr3D 89.223 1661 132 8 713 2351 47209773 47208138 0.000000e+00 2032
13 TraesCS4B01G250300 chr3D 87.927 381 21 9 1993 2350 216460699 216461077 2.160000e-115 425
14 TraesCS4B01G250300 chr5A 86.966 2363 249 24 16 2351 505340207 505342537 0.000000e+00 2603
15 TraesCS4B01G250300 chr7D 86.458 2363 261 26 16 2351 558450789 558453119 0.000000e+00 2536
16 TraesCS4B01G250300 chr7D 88.163 2129 210 22 6 2129 616482463 616484554 0.000000e+00 2497
17 TraesCS4B01G250300 chr7D 85.352 2369 233 43 6 2325 412230173 412232476 0.000000e+00 2348
18 TraesCS4B01G250300 chr7D 88.199 1788 165 23 604 2350 393582796 393581014 0.000000e+00 2091
19 TraesCS4B01G250300 chr7D 86.041 788 58 22 1553 2312 33811040 33810277 0.000000e+00 798
20 TraesCS4B01G250300 chr7D 83.843 458 45 18 1912 2346 511939412 511939863 2.170000e-110 409
21 TraesCS4B01G250300 chr4D 88.347 2154 185 18 221 2349 75774926 75772814 0.000000e+00 2527
22 TraesCS4B01G250300 chr5D 85.914 2364 255 37 16 2346 108339491 108341809 0.000000e+00 2449
23 TraesCS4B01G250300 chr5D 86.994 1607 156 20 769 2351 217059791 217061368 0.000000e+00 1760
24 TraesCS4B01G250300 chr5D 85.152 330 23 13 2047 2351 344690636 344690308 4.880000e-82 315
25 TraesCS4B01G250300 chr5B 86.187 847 50 18 1472 2292 595076397 595077202 0.000000e+00 854
26 TraesCS4B01G250300 chr1D 84.786 585 72 12 1775 2346 257425365 257424785 2.620000e-159 571
27 TraesCS4B01G250300 chr1D 88.041 485 43 10 1722 2193 106233403 106233885 5.670000e-156 560
28 TraesCS4B01G250300 chr7B 84.342 562 41 14 1813 2351 6063963 6063426 7.500000e-140 507


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 TraesCS4B01G250300 chr4B 516865853 516868203 2350 False 4342 4342 100.000 1 2351 1 chr4B.!!$F1 2350
1 TraesCS4B01G250300 chr2B 424512873 424515206 2333 True 2763 2763 88.126 1 2351 1 chr2B.!!$R1 2350
2 TraesCS4B01G250300 chr2B 243358847 243361188 2341 False 2538 2538 86.394 6 2350 1 chr2B.!!$F1 2344
3 TraesCS4B01G250300 chr6B 365734876 365737210 2334 False 2721 2721 87.811 6 2351 1 chr6B.!!$F1 2345
4 TraesCS4B01G250300 chr6B 593622101 593624029 1928 False 2510 2510 90.176 1 1929 1 chr6B.!!$F2 1928
5 TraesCS4B01G250300 chr3B 708913374 708915701 2327 True 2719 2719 87.826 1 2350 1 chr3B.!!$R2 2349
6 TraesCS4B01G250300 chr3B 592829122 592829749 627 True 702 702 87.270 1722 2351 1 chr3B.!!$R1 629
7 TraesCS4B01G250300 chr3D 422942739 422945034 2295 True 2691 2691 87.881 16 2350 1 chr3D.!!$R2 2334
8 TraesCS4B01G250300 chr3D 126392448 126394770 2322 False 2678 2678 87.595 16 2351 1 chr3D.!!$F1 2335
9 TraesCS4B01G250300 chr3D 47208138 47209773 1635 True 2032 2032 89.223 713 2351 1 chr3D.!!$R1 1638
10 TraesCS4B01G250300 chr5A 505340207 505342537 2330 False 2603 2603 86.966 16 2351 1 chr5A.!!$F1 2335
11 TraesCS4B01G250300 chr7D 558450789 558453119 2330 False 2536 2536 86.458 16 2351 1 chr7D.!!$F3 2335
12 TraesCS4B01G250300 chr7D 616482463 616484554 2091 False 2497 2497 88.163 6 2129 1 chr7D.!!$F4 2123
13 TraesCS4B01G250300 chr7D 412230173 412232476 2303 False 2348 2348 85.352 6 2325 1 chr7D.!!$F1 2319
14 TraesCS4B01G250300 chr7D 393581014 393582796 1782 True 2091 2091 88.199 604 2350 1 chr7D.!!$R2 1746
15 TraesCS4B01G250300 chr7D 33810277 33811040 763 True 798 798 86.041 1553 2312 1 chr7D.!!$R1 759
16 TraesCS4B01G250300 chr4D 75772814 75774926 2112 True 2527 2527 88.347 221 2349 1 chr4D.!!$R1 2128
17 TraesCS4B01G250300 chr5D 108339491 108341809 2318 False 2449 2449 85.914 16 2346 1 chr5D.!!$F1 2330
18 TraesCS4B01G250300 chr5D 217059791 217061368 1577 False 1760 1760 86.994 769 2351 1 chr5D.!!$F2 1582
19 TraesCS4B01G250300 chr5B 595076397 595077202 805 False 854 854 86.187 1472 2292 1 chr5B.!!$F1 820
20 TraesCS4B01G250300 chr1D 257424785 257425365 580 True 571 571 84.786 1775 2346 1 chr1D.!!$R1 571
21 TraesCS4B01G250300 chr7B 6063426 6063963 537 True 507 507 84.342 1813 2351 1 chr7B.!!$R1 538

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
792 882 1.008424 CGCACGATAGATGCCGACT 60.008 57.895 0.0 0.0 39.06 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 1772 0.8364 TCCTCCACGGCTTTCTTCCT 60.836 55.0 0.0 0.0 0.0 3.36 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
79 84 3.545481 CGAGATGGACGCGTGTGC 61.545 66.667 20.70 14.24 37.06 4.57
131 140 2.278849 TGGCAGCCACCATCATTTG 58.721 52.632 11.22 0.00 33.75 2.32
133 142 1.610554 GGCAGCCACCATCATTTGCT 61.611 55.000 6.55 0.00 0.00 3.91
215 239 1.803366 GACCTCGACCTTGACACCGT 61.803 60.000 0.00 0.00 0.00 4.83
329 374 1.808945 CAAGTCAAAGAAGGCGCTGAT 59.191 47.619 7.64 0.00 0.00 2.90
341 386 2.324330 CGCTGATGCCCGAACAACA 61.324 57.895 0.00 0.00 35.36 3.33
403 448 3.842925 GACGCCAAGGGTGAAGCCA 62.843 63.158 2.32 0.00 39.65 4.75
668 752 1.990614 GCCTCTCGGGGGAGTTCTT 60.991 63.158 0.00 0.00 35.12 2.52
792 882 1.008424 CGCACGATAGATGCCGACT 60.008 57.895 0.00 0.00 39.06 4.18
907 997 3.536917 CCGCTGGCTACGATCCCA 61.537 66.667 0.00 0.00 0.00 4.37
909 999 1.069765 CGCTGGCTACGATCCCAAT 59.930 57.895 0.00 0.00 0.00 3.16
992 1082 1.522355 CGGCCTTCATGCGTGATCT 60.522 57.895 9.96 0.00 33.56 2.75
1056 1146 1.542915 CCAGACGACTACGGGAAAGAA 59.457 52.381 0.00 0.00 44.46 2.52
1071 1161 3.580895 GGAAAGAAGAAGAGGAGGAGTGT 59.419 47.826 0.00 0.00 0.00 3.55
1076 1166 2.243810 AGAAGAGGAGGAGTGTGACAC 58.756 52.381 7.83 7.83 34.10 3.67
1131 1222 2.668212 CAAGCTGTCGGGCCGAAA 60.668 61.111 32.91 26.08 37.72 3.46
1135 1226 2.742372 CTGTCGGGCCGAAACTGG 60.742 66.667 32.91 10.17 37.72 4.00
1139 1230 4.697756 CGGGCCGAAACTGGAGCA 62.698 66.667 24.41 0.00 0.00 4.26
1218 1311 4.141505 TGTTGGAGAGACATTGGACAAGAA 60.142 41.667 0.00 0.00 0.00 2.52
1286 1379 1.004044 CCACTGGGAGTTTCATGAGCT 59.996 52.381 0.00 0.00 35.59 4.09
1302 1395 2.039084 TGAGCTCAAGAAGTTTCCTCCC 59.961 50.000 15.67 0.00 0.00 4.30
1422 1515 2.031465 GTCCGCCCCGTGAGAAAA 59.969 61.111 0.00 0.00 0.00 2.29
1466 1560 0.616371 TAGCAAGCCGCCCTCTTTTA 59.384 50.000 0.00 0.00 44.04 1.52
1498 1592 4.023279 AGTTCATGCTTGCGTGTTCATTTA 60.023 37.500 13.58 0.00 0.00 1.40
1743 1846 3.403968 GAAGACCAACTCCAAGAAGGAC 58.596 50.000 0.00 0.00 43.07 3.85
1757 1860 1.827399 AAGGACGACAAGCGGGATGT 61.827 55.000 0.00 0.00 46.49 3.06
1809 1912 3.091545 GGGCATGATGAACAAGAAGGAA 58.908 45.455 0.00 0.00 0.00 3.36
1941 2114 2.046892 GAGGCGGAGAAGCAAGCA 60.047 61.111 0.00 0.00 39.27 3.91
1969 2142 4.514577 AGATCGAGGCCGCCAACG 62.515 66.667 13.15 16.49 39.67 4.10
1979 2152 3.283684 CGCCAACGCCAAGACCAA 61.284 61.111 0.00 0.00 0.00 3.67
1980 2153 2.644992 GCCAACGCCAAGACCAAG 59.355 61.111 0.00 0.00 0.00 3.61
1981 2154 2.919494 GCCAACGCCAAGACCAAGG 61.919 63.158 0.00 0.00 0.00 3.61
1987 2160 4.659172 CCAAGACCAAGGCCGCCA 62.659 66.667 13.15 0.00 0.00 5.69
1988 2161 2.597217 CAAGACCAAGGCCGCCAA 60.597 61.111 13.15 0.00 0.00 4.52
1989 2162 1.978617 CAAGACCAAGGCCGCCAAT 60.979 57.895 13.15 0.00 0.00 3.16
2129 2302 0.166814 GACATGCTCAAGTTCACCGC 59.833 55.000 0.00 0.00 0.00 5.68
2200 2403 0.745845 GCTGGCATGACCGAACTCAT 60.746 55.000 0.00 0.00 43.94 2.90
2215 2425 1.503347 ACTCATGTCCCACCCCTTTTT 59.497 47.619 0.00 0.00 0.00 1.94
2216 2426 2.719705 ACTCATGTCCCACCCCTTTTTA 59.280 45.455 0.00 0.00 0.00 1.52
2219 2429 3.917629 TCATGTCCCACCCCTTTTTAGTA 59.082 43.478 0.00 0.00 0.00 1.82
2296 2508 1.863267 TTTTTGAAGCCGGCAATGTG 58.137 45.000 31.54 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 84 2.128507 GGGGAGAGGAGTAGGCGTG 61.129 68.421 0.00 0.00 0.00 5.34
80 85 2.279408 GGGGAGAGGAGTAGGCGT 59.721 66.667 0.00 0.00 0.00 5.68
131 140 2.028112 GGGTTTTGGAGAAAATGGGAGC 60.028 50.000 0.00 0.00 33.63 4.70
133 142 3.506398 GAGGGTTTTGGAGAAAATGGGA 58.494 45.455 0.00 0.00 33.63 4.37
313 358 2.174334 GCATCAGCGCCTTCTTTGA 58.826 52.632 2.29 0.00 0.00 2.69
390 435 2.753966 CGCGATGGCTTCACCCTTG 61.754 63.158 0.00 0.00 37.83 3.61
432 507 1.754745 GTTGGTGACCTCCTGCTGA 59.245 57.895 2.11 0.00 0.00 4.26
517 598 1.589461 CCACGACGGTGTTGACGAA 60.589 57.895 0.00 0.00 42.80 3.85
557 641 0.608130 CATCCGAGGGAACACAGACA 59.392 55.000 0.00 0.00 34.34 3.41
657 741 3.327404 TCGGGCAAGAACTCCCCC 61.327 66.667 0.00 0.00 39.39 5.40
665 749 4.717629 CGCTCACGTCGGGCAAGA 62.718 66.667 9.89 0.00 33.53 3.02
792 882 2.257371 GCGTCAGGTAGCACGTCA 59.743 61.111 6.65 0.00 38.32 4.35
846 936 2.763448 GAGGTTCTGCATGTAGTCCTCT 59.237 50.000 29.60 17.52 37.16 3.69
907 997 2.508526 GTCCTGGCTTTGTGTCTCATT 58.491 47.619 0.00 0.00 0.00 2.57
909 999 0.249868 CGTCCTGGCTTTGTGTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
954 1044 1.205893 GACTGATCGGGATCATAGCCC 59.794 57.143 11.48 0.00 45.74 5.19
1056 1146 2.243810 GTGTCACACTCCTCCTCTTCT 58.756 52.381 0.00 0.00 0.00 2.85
1071 1161 1.407656 AAGGCTCCACTTCGGTGTCA 61.408 55.000 0.00 0.00 43.91 3.58
1076 1166 1.001378 CAAACAAAGGCTCCACTTCGG 60.001 52.381 0.00 0.00 0.00 4.30
1131 1222 0.888285 GCTTGCTCTTGTGCTCCAGT 60.888 55.000 0.00 0.00 0.00 4.00
1135 1226 2.175322 GCGCTTGCTCTTGTGCTC 59.825 61.111 0.00 0.00 36.83 4.26
1139 1230 1.835483 CTTCGTGCGCTTGCTCTTGT 61.835 55.000 9.73 0.00 40.12 3.16
1175 1268 1.229428 CTCGCAAAGAAGCTTGTCCA 58.771 50.000 2.10 0.00 0.00 4.02
1218 1311 2.589157 TTCGATGCCGGTCTTGGGT 61.589 57.895 1.90 0.00 36.24 4.51
1286 1379 3.593942 TGGTAGGGAGGAAACTTCTTGA 58.406 45.455 0.00 0.00 44.43 3.02
1302 1395 1.464023 CGCGTGCTCACAATTTGGTAG 60.464 52.381 0.00 0.00 0.00 3.18
1375 1468 4.380531 CTCTCAAGAGTGGCACAAAACTA 58.619 43.478 21.41 0.00 44.16 2.24
1406 1499 0.250989 AATTTTTCTCACGGGGCGGA 60.251 50.000 0.00 0.00 0.00 5.54
1670 1772 0.836400 TCCTCCACGGCTTTCTTCCT 60.836 55.000 0.00 0.00 0.00 3.36
1743 1846 3.499737 GCCACATCCCGCTTGTCG 61.500 66.667 0.00 0.00 38.08 4.35
1809 1912 1.398958 GGCGCTCCTCCTCTCTTGAT 61.399 60.000 7.64 0.00 0.00 2.57
1970 2143 4.659172 TGGCGGCCTTGGTCTTGG 62.659 66.667 21.46 0.00 0.00 3.61
1971 2144 1.978617 ATTGGCGGCCTTGGTCTTG 60.979 57.895 21.46 0.00 0.00 3.02
1972 2145 1.978617 CATTGGCGGCCTTGGTCTT 60.979 57.895 21.46 0.00 0.00 3.01
1973 2146 2.361610 CATTGGCGGCCTTGGTCT 60.362 61.111 21.46 0.00 0.00 3.85
1974 2147 4.133796 GCATTGGCGGCCTTGGTC 62.134 66.667 21.46 1.94 0.00 4.02
1981 2154 4.133796 GGTCTTGGCATTGGCGGC 62.134 66.667 0.00 0.00 42.47 6.53
1982 2155 2.216750 CTTGGTCTTGGCATTGGCGG 62.217 60.000 5.68 1.50 42.47 6.13
1983 2156 1.213537 CTTGGTCTTGGCATTGGCG 59.786 57.895 5.68 0.00 42.47 5.69
1984 2157 1.593265 CCTTGGTCTTGGCATTGGC 59.407 57.895 2.73 2.73 40.13 4.52
2020 2193 2.280389 CCCGGTCATCATGCTCGG 60.280 66.667 0.00 10.42 40.32 4.63
2129 2302 1.300465 CGGCCATGAGATCACTCGG 60.300 63.158 2.24 0.00 45.25 4.63
2200 2403 3.562609 GCATACTAAAAAGGGGTGGGACA 60.563 47.826 0.00 0.00 0.00 4.02
2215 2425 2.738321 CGACACACATGCCAGCATACTA 60.738 50.000 4.52 0.00 34.91 1.82
2216 2426 1.742761 GACACACATGCCAGCATACT 58.257 50.000 4.52 0.00 34.91 2.12
2219 2429 2.042259 CCGACACACATGCCAGCAT 61.042 57.895 0.00 0.00 37.08 3.79


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

AutoCloner maintained by Alex Coulton.