Multiple sequence alignment - TraesCS6B01G394900

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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 TraesCS6B01G394900 chr6B 100.000 2755 0 0 1 2755 670223097 670220343 0 5088
1 TraesCS6B01G394900 chr6B 87.650 1838 193 25 941 2754 300740496 300742323 0 2106
2 TraesCS6B01G394900 chr2B 92.387 1852 123 12 913 2755 608933461 608935303 0 2623
3 TraesCS6B01G394900 chr2B 88.602 1860 189 18 914 2755 141329674 141327820 0 2239
4 TraesCS6B01G394900 chr1B 92.220 1851 130 12 913 2755 599549959 599548115 0 2608
5 TraesCS6B01G394900 chr3B 90.543 1861 152 14 913 2755 166546822 166544968 0 2440
6 TraesCS6B01G394900 chr3B 88.393 1861 191 19 914 2755 547039426 547041280 0 2217
7 TraesCS6B01G394900 chr3B 87.209 1845 201 27 934 2755 512774640 512776472 0 2067
8 TraesCS6B01G394900 chr7B 92.355 1622 104 14 920 2531 220106838 220105227 0 2290
9 TraesCS6B01G394900 chr4B 88.770 1870 171 25 911 2755 1277032 1278887 0 2254
10 TraesCS6B01G394900 chr4D 95.285 912 43 0 1 912 234467333 234466422 0 1447
11 TraesCS6B01G394900 chr4D 95.259 907 43 0 6 912 421444577 421445483 0 1437
12 TraesCS6B01G394900 chr1D 95.066 912 45 0 1 912 206909175 206910086 0 1435
13 TraesCS6B01G394900 chr2D 95.154 908 43 1 6 912 268813174 268812267 0 1432
14 TraesCS6B01G394900 chr2D 94.962 913 46 0 1 913 604204398 604205310 0 1432
15 TraesCS6B01G394900 chr2D 94.852 913 46 1 1 912 48096366 48097278 0 1424
16 TraesCS6B01G394900 chr3D 94.951 911 46 0 2 912 296017331 296018241 0 1428
17 TraesCS6B01G394900 chr3D 94.409 930 49 3 1 929 101754184 101753257 0 1426
18 TraesCS6B01G394900 chr7D 94.846 912 47 0 1 912 201082075 201082986 0 1424


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 TraesCS6B01G394900 chr6B 670220343 670223097 2754 True 5088 5088 100.000 1 2755 1 chr6B.!!$R1 2754
1 TraesCS6B01G394900 chr6B 300740496 300742323 1827 False 2106 2106 87.650 941 2754 1 chr6B.!!$F1 1813
2 TraesCS6B01G394900 chr2B 608933461 608935303 1842 False 2623 2623 92.387 913 2755 1 chr2B.!!$F1 1842
3 TraesCS6B01G394900 chr2B 141327820 141329674 1854 True 2239 2239 88.602 914 2755 1 chr2B.!!$R1 1841
4 TraesCS6B01G394900 chr1B 599548115 599549959 1844 True 2608 2608 92.220 913 2755 1 chr1B.!!$R1 1842
5 TraesCS6B01G394900 chr3B 166544968 166546822 1854 True 2440 2440 90.543 913 2755 1 chr3B.!!$R1 1842
6 TraesCS6B01G394900 chr3B 547039426 547041280 1854 False 2217 2217 88.393 914 2755 1 chr3B.!!$F2 1841
7 TraesCS6B01G394900 chr3B 512774640 512776472 1832 False 2067 2067 87.209 934 2755 1 chr3B.!!$F1 1821
8 TraesCS6B01G394900 chr7B 220105227 220106838 1611 True 2290 2290 92.355 920 2531 1 chr7B.!!$R1 1611
9 TraesCS6B01G394900 chr4B 1277032 1278887 1855 False 2254 2254 88.770 911 2755 1 chr4B.!!$F1 1844
10 TraesCS6B01G394900 chr4D 234466422 234467333 911 True 1447 1447 95.285 1 912 1 chr4D.!!$R1 911
11 TraesCS6B01G394900 chr4D 421444577 421445483 906 False 1437 1437 95.259 6 912 1 chr4D.!!$F1 906
12 TraesCS6B01G394900 chr1D 206909175 206910086 911 False 1435 1435 95.066 1 912 1 chr1D.!!$F1 911
13 TraesCS6B01G394900 chr2D 268812267 268813174 907 True 1432 1432 95.154 6 912 1 chr2D.!!$R1 906
14 TraesCS6B01G394900 chr2D 604204398 604205310 912 False 1432 1432 94.962 1 913 1 chr2D.!!$F2 912
15 TraesCS6B01G394900 chr2D 48096366 48097278 912 False 1424 1424 94.852 1 912 1 chr2D.!!$F1 911
16 TraesCS6B01G394900 chr3D 296017331 296018241 910 False 1428 1428 94.951 2 912 1 chr3D.!!$F1 910
17 TraesCS6B01G394900 chr3D 101753257 101754184 927 True 1426 1426 94.409 1 929 1 chr3D.!!$R1 928
18 TraesCS6B01G394900 chr7D 201082075 201082986 911 False 1424 1424 94.846 1 912 1 chr7D.!!$F1 911

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
647 648 1.060729 TCAGATCCAAAACCCGACCA 58.939 50.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2532 2719 0.698818 AAGAAAGGGACGGGCAATCT 59.301 50.0 0.0 0.0 0.0 2.4 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
48 49 2.159057 GGCTTTTAACGGGTCGGATCTA 60.159 50.000 0.00 0.00 0.00 1.98
273 274 2.029470 CGCAAGAATTTTGTGGGCCTTA 60.029 45.455 4.53 0.00 43.02 2.69
323 324 4.668138 AAATCTTGTGGGCCTTTACCTA 57.332 40.909 4.53 0.00 0.00 3.08
364 365 3.254657 CGTGAAATCTTGTGGGCCTTTAA 59.745 43.478 4.53 0.00 0.00 1.52
367 368 5.475564 GTGAAATCTTGTGGGCCTTTAACTA 59.524 40.000 4.53 0.00 0.00 2.24
580 581 3.620488 GTGTTTCCTCCAGCCAATGATA 58.380 45.455 0.00 0.00 0.00 2.15
586 587 5.857471 TCCTCCAGCCAATGATAATTTTG 57.143 39.130 0.00 0.00 0.00 2.44
598 599 6.704512 ATGATAATTTTGCACGTGGAAAAC 57.295 33.333 38.77 28.65 45.55 2.43
647 648 1.060729 TCAGATCCAAAACCCGACCA 58.939 50.000 0.00 0.00 0.00 4.02
652 653 3.716872 AGATCCAAAACCCGACCAGATAT 59.283 43.478 0.00 0.00 0.00 1.63
659 660 5.687166 AAACCCGACCAGATATCTTAACA 57.313 39.130 1.33 0.00 0.00 2.41
762 763 4.020573 AGTGGACACTTCCGTGATGATAAA 60.021 41.667 0.00 0.00 46.37 1.40
805 806 1.749063 TCTACGACAGCACAGGTATGG 59.251 52.381 0.00 0.00 0.00 2.74
813 814 3.181461 ACAGCACAGGTATGGCTATCTTC 60.181 47.826 0.00 0.00 33.37 2.87
959 961 7.380602 CCATTTTTGTTCTTCATGTGAACTCTC 59.619 37.037 23.68 8.29 42.86 3.20
1028 1030 2.591715 GCTTGCACCACACGACCT 60.592 61.111 0.00 0.00 0.00 3.85
1042 1044 3.570975 ACACGACCTACATGACAAGTGTA 59.429 43.478 0.00 0.00 39.43 2.90
1077 1079 3.679389 GATCTGCCTTGACCTGAAGAAA 58.321 45.455 0.00 0.00 0.00 2.52
1205 1207 3.924114 TGAACACTCAAAGGTCCAGAA 57.076 42.857 0.00 0.00 0.00 3.02
1237 1239 2.066262 CAATTGAGTACGTGGCGACTT 58.934 47.619 0.00 0.00 0.00 3.01
1246 1248 1.626654 CGTGGCGACTTCGAAGCAAT 61.627 55.000 24.86 5.72 43.02 3.56
1252 1254 2.839474 CGACTTCGAAGCAATGAAACC 58.161 47.619 24.86 2.76 43.02 3.27
1253 1255 2.721797 CGACTTCGAAGCAATGAAACCG 60.722 50.000 24.86 10.21 43.02 4.44
1257 1259 2.980568 TCGAAGCAATGAAACCGGTAT 58.019 42.857 8.00 0.00 0.00 2.73
1321 1330 4.168101 ACCCTCTTGTCACCTCTGAATTA 58.832 43.478 0.00 0.00 0.00 1.40
1376 1391 7.939039 TGAGTTCACCTGATTCTTTTCTTGTAT 59.061 33.333 0.00 0.00 0.00 2.29
1380 1395 6.823689 TCACCTGATTCTTTTCTTGTATAGGC 59.176 38.462 0.00 0.00 0.00 3.93
1381 1396 6.599244 CACCTGATTCTTTTCTTGTATAGGCA 59.401 38.462 0.00 0.00 0.00 4.75
1459 1474 2.177531 CGTCACAGCTGCAATGGC 59.822 61.111 15.27 5.38 41.68 4.40
1474 1489 0.682209 ATGGCCATTGAGCTCCACAC 60.682 55.000 14.09 0.00 0.00 3.82
1525 1540 0.589223 GATTTCAACACGCGGTCCAA 59.411 50.000 12.47 0.00 0.00 3.53
1526 1541 0.309612 ATTTCAACACGCGGTCCAAC 59.690 50.000 12.47 0.00 0.00 3.77
1590 1605 2.553602 ACGTACAAGTGATCACGTGGTA 59.446 45.455 34.69 25.89 45.14 3.25
1620 1635 6.321821 ACCAAATGCCTACCTTACATTCTA 57.678 37.500 0.00 0.00 33.01 2.10
1634 1649 2.880890 ACATTCTATTGCCGAGGAATGC 59.119 45.455 12.50 0.00 44.91 3.56
1670 1687 7.978975 CCTTTGTTCTTTTCAAAACTATGTCCA 59.021 33.333 0.00 0.00 34.96 4.02
1673 1690 6.922957 TGTTCTTTTCAAAACTATGTCCATGC 59.077 34.615 0.00 0.00 0.00 4.06
1674 1691 6.647334 TCTTTTCAAAACTATGTCCATGCA 57.353 33.333 0.00 0.00 0.00 3.96
1691 1708 4.517832 CCATGCACTATGTTATGACTGCAT 59.482 41.667 8.65 8.65 41.71 3.96
1698 1718 1.206849 TGTTATGACTGCATCTCCGCA 59.793 47.619 0.00 0.00 40.32 5.69
1738 1758 1.195448 GGTGTGTGAGCGACATTTGAG 59.805 52.381 0.00 0.00 36.78 3.02
1797 1818 3.693807 AGGTGTGACAGGAGATACGTTA 58.306 45.455 0.00 0.00 0.00 3.18
1804 1825 6.932400 TGTGACAGGAGATACGTTAATGTTTT 59.068 34.615 5.48 0.00 0.00 2.43
1851 1873 1.917303 GTCGCACCAGTTTTGTGTTTG 59.083 47.619 0.00 0.00 36.11 2.93
1898 1920 4.400251 ACATGGCAAATGTAGTTCATCAGG 59.600 41.667 2.62 0.00 35.48 3.86
1922 1944 6.238759 GGCATGGTTAGTGAAAGTTATCATCC 60.239 42.308 0.00 0.00 0.00 3.51
1993 2018 4.504461 CGACTAGCATGGTAGTTTGATCAC 59.496 45.833 32.05 19.11 33.18 3.06
2060 2091 3.561143 TGTTTCCCATAGTTTGCACACT 58.439 40.909 10.88 10.88 0.00 3.55
2179 2216 9.797642 ATGGCAGATTCAGTATAAATAACATGA 57.202 29.630 0.00 0.00 0.00 3.07
2257 2363 7.657354 TCAGTATACATAACATGGCAGATTCAC 59.343 37.037 5.50 0.00 33.60 3.18
2306 2414 9.881649 ATATACATAACATGGCAGATTCAGTAG 57.118 33.333 0.00 0.00 33.60 2.57
2344 2522 8.019669 GCAGATTCAGTATAAATAACATGGCAG 58.980 37.037 0.00 0.00 0.00 4.85
2345 2523 9.276590 CAGATTCAGTATAAATAACATGGCAGA 57.723 33.333 0.00 0.00 0.00 4.26
2349 2527 9.625747 TTCAGTATAAATAACATGGCAGATTCA 57.374 29.630 0.00 0.00 0.00 2.57
2350 2528 9.276590 TCAGTATAAATAACATGGCAGATTCAG 57.723 33.333 0.00 0.00 0.00 3.02
2351 2529 9.060347 CAGTATAAATAACATGGCAGATTCAGT 57.940 33.333 0.00 0.00 0.00 3.41
2361 2539 8.978874 ACATGGCAGATTCAGTATAAAATACA 57.021 30.769 0.00 0.00 0.00 2.29
2362 2540 9.578576 ACATGGCAGATTCAGTATAAAATACAT 57.421 29.630 0.00 0.00 0.00 2.29
2363 2541 9.836076 CATGGCAGATTCAGTATAAAATACATG 57.164 33.333 0.00 0.00 0.00 3.21
2364 2542 8.394971 TGGCAGATTCAGTATAAAATACATGG 57.605 34.615 0.00 0.00 0.00 3.66
2365 2543 7.040478 TGGCAGATTCAGTATAAAATACATGGC 60.040 37.037 0.00 0.00 0.00 4.40
2366 2544 7.040478 GGCAGATTCAGTATAAAATACATGGCA 60.040 37.037 0.00 0.00 0.00 4.92
2532 2719 2.553602 CAGTGCTCCAATGTTGCTTACA 59.446 45.455 0.00 0.00 41.97 2.41
2634 2821 0.893270 CTTTGTGATGGAACGGGGCA 60.893 55.000 0.00 0.00 0.00 5.36
2682 2869 2.752030 CTGTTCCAGATCCTACCTCCA 58.248 52.381 0.00 0.00 32.44 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
364 365 0.773644 CCATAATGGGCTGGCCTAGT 59.226 55.000 21.72 9.25 32.67 2.57
367 368 1.538666 GACCATAATGGGCTGGCCT 59.461 57.895 21.72 4.42 44.12 5.19
417 418 2.223803 TTTTGCGGACCATAATGGGT 57.776 45.000 0.00 0.00 43.37 4.51
468 469 2.877043 GGCATAGCCCATCAAGTTTG 57.123 50.000 0.00 0.00 44.06 2.93
580 581 2.556257 GGGTTTTCCACGTGCAAAATT 58.444 42.857 19.59 0.00 42.91 1.82
586 587 1.468506 AATGGGGGTTTTCCACGTGC 61.469 55.000 10.91 0.00 46.21 5.34
762 763 6.721208 AGAAGTGTTCCATGACATTACCAAAT 59.279 34.615 0.00 0.00 0.00 2.32
813 814 9.244799 CATCCATGACAAATTTATGACAGAATG 57.755 33.333 0.00 0.00 46.00 2.67
860 861 2.166870 ACGTGTTTGTCACAGTAGGTCA 59.833 45.455 0.00 0.00 46.44 4.02
959 961 7.596621 GCAAGTAAAATGAAGGAAAGAAGAAGG 59.403 37.037 0.00 0.00 0.00 3.46
1028 1030 4.587262 AGTGGTGACTACACTTGTCATGTA 59.413 41.667 1.04 0.00 46.38 2.29
1042 1044 0.452184 CAGATCGCGTAGTGGTGACT 59.548 55.000 5.77 0.00 39.32 3.41
1077 1079 2.088423 TCAAGCACCTCAAAACGTTGT 58.912 42.857 0.00 0.00 36.07 3.32
1205 1207 5.763204 ACGTACTCAATTGGAAAATGTCTGT 59.237 36.000 5.42 0.00 0.00 3.41
1237 1239 2.459060 TACCGGTTTCATTGCTTCGA 57.541 45.000 15.04 0.00 0.00 3.71
1246 1248 4.018779 AGAGATGGGAAAATACCGGTTTCA 60.019 41.667 15.04 0.00 36.82 2.69
1252 1254 5.880332 TGAAGAAAGAGATGGGAAAATACCG 59.120 40.000 0.00 0.00 0.00 4.02
1253 1255 7.340487 ACATGAAGAAAGAGATGGGAAAATACC 59.660 37.037 0.00 0.00 0.00 2.73
1257 1259 6.070656 ACACATGAAGAAAGAGATGGGAAAA 58.929 36.000 0.00 0.00 0.00 2.29
1295 1301 2.900546 CAGAGGTGACAAGAGGGTTAGT 59.099 50.000 0.00 0.00 0.00 2.24
1334 1343 7.715265 GTGAACTCACAAGAACAGAGATAAA 57.285 36.000 4.96 0.00 45.75 1.40
1376 1391 0.324943 GAAAGCCACAGTCCTGCCTA 59.675 55.000 0.00 0.00 0.00 3.93
1459 1474 3.947910 AAATTGTGTGGAGCTCAATGG 57.052 42.857 17.19 0.00 40.09 3.16
1474 1489 5.920273 GTCAACCAGTTCCATGTGTAAATTG 59.080 40.000 0.00 0.00 0.00 2.32
1525 1540 1.135373 CCTCTATGAACTCACGTGCGT 60.135 52.381 11.67 8.33 0.00 5.24
1526 1541 1.132453 TCCTCTATGAACTCACGTGCG 59.868 52.381 11.67 7.49 0.00 5.34
1570 1585 2.060326 ACCACGTGATCACTTGTACG 57.940 50.000 25.46 15.57 41.86 3.67
1590 1605 3.123273 AGGTAGGCATTTGGTATGGAGT 58.877 45.455 0.00 0.00 0.00 3.85
1600 1615 6.265422 GGCAATAGAATGTAAGGTAGGCATTT 59.735 38.462 0.00 0.00 33.56 2.32
1673 1690 4.683320 CGGAGATGCAGTCATAACATAGTG 59.317 45.833 0.00 0.00 31.96 2.74
1674 1691 4.797604 GCGGAGATGCAGTCATAACATAGT 60.798 45.833 0.00 0.00 31.96 2.12
1691 1708 3.156288 ACATACTAGGCTATGCGGAGA 57.844 47.619 0.00 0.00 0.00 3.71
1698 1718 4.833380 CACCACCACTACATACTAGGCTAT 59.167 45.833 0.00 0.00 0.00 2.97
1779 1799 5.654603 ACATTAACGTATCTCCTGTCACA 57.345 39.130 0.00 0.00 0.00 3.58
1833 1855 1.135257 TCCAAACACAAAACTGGTGCG 60.135 47.619 0.00 0.00 39.87 5.34
1844 1866 1.795872 CGTAGACGCATTCCAAACACA 59.204 47.619 0.00 0.00 0.00 3.72
1851 1873 2.927477 TCAAACATCGTAGACGCATTCC 59.073 45.455 0.00 0.00 42.51 3.01
1898 1920 6.543831 AGGATGATAACTTTCACTAACCATGC 59.456 38.462 0.00 0.00 0.00 4.06
1969 1994 4.159693 TGATCAAACTACCATGCTAGTCGT 59.840 41.667 1.15 0.00 0.00 4.34
1972 1997 4.081642 ACGTGATCAAACTACCATGCTAGT 60.082 41.667 0.00 0.00 0.00 2.57
1993 2018 2.477189 CCGCAAAAAGGTTATGGCTACG 60.477 50.000 0.00 0.00 0.00 3.51
2203 2263 8.432013 TCTGCCATGTTATGTATACTGAATCTT 58.568 33.333 4.17 0.00 0.00 2.40
2280 2387 9.881649 CTACTGAATCTGCCATGTTATGTATAT 57.118 33.333 0.00 0.00 0.00 0.86
2356 2534 9.415008 TGTATGGTACTTAATTTGCCATGTATT 57.585 29.630 13.84 0.00 39.89 1.89
2357 2535 8.846211 GTGTATGGTACTTAATTTGCCATGTAT 58.154 33.333 13.84 0.00 39.89 2.29
2358 2536 7.011576 CGTGTATGGTACTTAATTTGCCATGTA 59.988 37.037 13.84 3.97 39.89 2.29
2359 2537 6.183360 CGTGTATGGTACTTAATTTGCCATGT 60.183 38.462 13.84 0.00 39.89 3.21
2360 2538 6.183360 ACGTGTATGGTACTTAATTTGCCATG 60.183 38.462 13.84 0.00 39.89 3.66
2361 2539 5.883673 ACGTGTATGGTACTTAATTTGCCAT 59.116 36.000 10.46 10.46 42.05 4.40
2362 2540 5.122554 CACGTGTATGGTACTTAATTTGCCA 59.877 40.000 7.58 0.00 0.00 4.92
2363 2541 5.448089 CCACGTGTATGGTACTTAATTTGCC 60.448 44.000 15.65 0.00 34.77 4.52
2364 2542 5.565695 CCACGTGTATGGTACTTAATTTGC 58.434 41.667 15.65 0.00 34.77 3.68
2365 2543 5.122554 TGCCACGTGTATGGTACTTAATTTG 59.877 40.000 15.65 0.00 42.28 2.32
2366 2544 5.247084 TGCCACGTGTATGGTACTTAATTT 58.753 37.500 15.65 0.00 42.28 1.82
2532 2719 0.698818 AAGAAAGGGACGGGCAATCT 59.301 50.000 0.00 0.00 0.00 2.40
2682 2869 2.460669 GGGGCCATCATCTGAAAACTT 58.539 47.619 4.39 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.