Multiple sequence alignment - TraesCS1B01G101400

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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 TraesCS1B01G101400 chr1B 100.000 2297 0 0 1 2297 111193115 111190819 0 4242
1 TraesCS1B01G101400 chr1B 95.816 1888 79 0 1 1888 544623636 544625523 0 3049
2 TraesCS1B01G101400 chr1B 95.816 1888 77 1 1 1888 544593697 544595582 0 3048
3 TraesCS1B01G101400 chr1B 96.822 409 13 0 1889 2297 80689414 80689006 0 684
4 TraesCS1B01G101400 chrUn 95.924 1889 76 1 1 1888 274341282 274339394 0 3061
5 TraesCS1B01G101400 chrUn 95.922 1888 76 1 1 1888 245706068 245707954 0 3059
6 TraesCS1B01G101400 chrUn 95.869 1888 78 0 1 1888 229310227 229308340 0 3055
7 TraesCS1B01G101400 chrUn 95.869 1888 78 0 1 1888 291535440 291537327 0 3055
8 TraesCS1B01G101400 chrUn 95.816 1888 79 0 1 1888 67501008 67499121 0 3049
9 TraesCS1B01G101400 chrUn 95.816 1888 79 0 1 1888 199874824 199876711 0 3049
10 TraesCS1B01G101400 chrUn 95.710 1888 81 0 1 1888 3845814 3843927 0 3038
11 TraesCS1B01G101400 chrUn 96.822 409 13 0 1889 2297 199876741 199877149 0 684
12 TraesCS1B01G101400 chrUn 96.822 409 13 0 1889 2297 310328500 310328092 0 684
13 TraesCS1B01G101400 chrUn 96.822 409 13 0 1889 2297 454825310 454825718 0 684
14 TraesCS1B01G101400 chrUn 96.577 409 14 0 1889 2297 245707984 245708392 0 678
15 TraesCS1B01G101400 chrUn 96.577 409 14 0 1889 2297 260638276 260637868 0 678
16 TraesCS1B01G101400 chrUn 96.577 409 14 0 1889 2297 404115061 404114653 0 678
17 TraesCS1B01G101400 chrUn 96.577 409 14 0 1889 2297 421394283 421394691 0 678
18 TraesCS1B01G101400 chr6B 96.577 409 14 0 1889 2297 123757776 123757368 0 678


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 TraesCS1B01G101400 chr1B 111190819 111193115 2296 True 4242.0 4242 100.0000 1 2297 1 chr1B.!!$R2 2296
1 TraesCS1B01G101400 chr1B 544623636 544625523 1887 False 3049.0 3049 95.8160 1 1888 1 chr1B.!!$F2 1887
2 TraesCS1B01G101400 chr1B 544593697 544595582 1885 False 3048.0 3048 95.8160 1 1888 1 chr1B.!!$F1 1887
3 TraesCS1B01G101400 chrUn 274339394 274341282 1888 True 3061.0 3061 95.9240 1 1888 1 chrUn.!!$R5 1887
4 TraesCS1B01G101400 chrUn 229308340 229310227 1887 True 3055.0 3055 95.8690 1 1888 1 chrUn.!!$R3 1887
5 TraesCS1B01G101400 chrUn 291535440 291537327 1887 False 3055.0 3055 95.8690 1 1888 1 chrUn.!!$F1 1887
6 TraesCS1B01G101400 chrUn 67499121 67501008 1887 True 3049.0 3049 95.8160 1 1888 1 chrUn.!!$R2 1887
7 TraesCS1B01G101400 chrUn 3843927 3845814 1887 True 3038.0 3038 95.7100 1 1888 1 chrUn.!!$R1 1887
8 TraesCS1B01G101400 chrUn 245706068 245708392 2324 False 1868.5 3059 96.2495 1 2297 2 chrUn.!!$F5 2296
9 TraesCS1B01G101400 chrUn 199874824 199877149 2325 False 1866.5 3049 96.3190 1 2297 2 chrUn.!!$F4 2296

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
846 847 0.779997 ACCCTGGAAATGGTTCAGCT 59.22 50.0 0.0 0.0 35.25 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1708 1.073763 CCAGACAATGTCTTCCACCCA 59.926 52.381 13.99 0.0 41.37 4.51 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
204 205 2.196997 TAGGATGGTGCGGCTGCTTT 62.197 55.000 20.27 0.02 43.34 3.51
215 216 1.671054 GCTGCTTTGGTGAGCCGTA 60.671 57.895 0.00 0.00 42.01 4.02
238 239 2.115291 GGAATCGGGTGCTCCAAGC 61.115 63.158 7.20 0.00 42.82 4.01
280 281 2.203070 GGCGATGCGGGATGAACT 60.203 61.111 0.00 0.00 0.00 3.01
309 310 3.463728 TTACGGTGCCCAACTGCGT 62.464 57.895 0.00 0.00 38.92 5.24
315 316 1.527148 TGCCCAACTGCGTGCTAAA 60.527 52.632 0.00 0.00 0.00 1.85
319 320 2.147958 CCCAACTGCGTGCTAAACTAA 58.852 47.619 0.00 0.00 0.00 2.24
341 342 2.805897 CCACAAAGGGTGTTGCTCA 58.194 52.632 0.00 0.00 46.44 4.26
361 362 3.512329 TCAATTAAGACAGCAGGACGGTA 59.488 43.478 0.00 0.00 0.00 4.02
380 381 4.440250 CGGTAGTCATGGAAGTCGAAATCT 60.440 45.833 0.00 0.00 0.00 2.40
445 446 1.474077 GAAAATGGATGGCGCTGAAGT 59.526 47.619 7.64 0.00 0.00 3.01
469 470 1.229820 ACCCACACCCAGCCATCTA 60.230 57.895 0.00 0.00 0.00 1.98
616 617 1.909302 TGAAGGCCGAAGAGGAGAAAT 59.091 47.619 0.00 0.00 45.00 2.17
729 730 3.805207 AGGGAATCGGGTTAAGATTTCG 58.195 45.455 0.00 0.00 38.32 3.46
730 731 2.876550 GGGAATCGGGTTAAGATTTCGG 59.123 50.000 0.00 0.00 38.32 4.30
734 735 2.181975 TCGGGTTAAGATTTCGGGAGT 58.818 47.619 0.00 0.00 0.00 3.85
811 812 5.163437 GCCTCGGGAAGAGTTATCTTTTCTA 60.163 44.000 4.59 0.00 45.98 2.10
820 821 9.852091 GAAGAGTTATCTTTTCTACTTAACGGA 57.148 33.333 0.00 0.00 45.98 4.69
825 826 9.846248 GTTATCTTTTCTACTTAACGGACTACA 57.154 33.333 0.00 0.00 0.00 2.74
837 838 2.374170 ACGGACTACAAACCCTGGAAAT 59.626 45.455 0.00 0.00 0.00 2.17
846 847 0.779997 ACCCTGGAAATGGTTCAGCT 59.220 50.000 0.00 0.00 35.25 4.24
878 879 4.329545 GTGGCCGGAAGAGCACCA 62.330 66.667 5.05 0.00 0.00 4.17
925 926 0.969917 CGGTGGCCCATGAAAATCCA 60.970 55.000 0.00 0.00 0.00 3.41
938 939 4.030913 TGAAAATCCAGAGGACCGAGTAT 58.969 43.478 0.00 0.00 32.98 2.12
989 990 2.123589 TCAGGTCTCCAAGGTGAACAA 58.876 47.619 8.73 0.00 0.00 2.83
999 1000 3.139029 GGTGAACAACCTCTAGCCG 57.861 57.895 0.00 0.00 46.55 5.52
1235 1236 1.802960 GTCGACTCAGAACTGGTACGA 59.197 52.381 8.70 7.68 0.00 3.43
1287 1288 1.815421 GCATTGCGATGGTCCTCGT 60.815 57.895 15.85 0.00 40.73 4.18
1288 1289 0.529773 GCATTGCGATGGTCCTCGTA 60.530 55.000 15.85 5.37 40.73 3.43
1316 1317 1.344114 ACGCAATGTGATTTTTGCCCT 59.656 42.857 0.00 0.00 44.14 5.19
1334 1335 2.886523 CCCTGTGCTCTGAATGTCAAAA 59.113 45.455 0.00 0.00 0.00 2.44
1406 1407 3.265737 TCTTAAGGTAGCCAAATGCCTCA 59.734 43.478 1.85 0.00 42.71 3.86
1423 1424 6.484364 TGCCTCATCATCTAATTAGTGACA 57.516 37.500 12.19 6.74 0.00 3.58
1425 1426 6.127083 TGCCTCATCATCTAATTAGTGACACA 60.127 38.462 12.19 5.10 0.00 3.72
1453 1454 8.044574 TGAATGGATTAATGAGATTCCCACTA 57.955 34.615 0.00 0.00 0.00 2.74
1511 1512 2.751436 GGCTTGGCGGAATCAGCA 60.751 61.111 7.78 0.00 36.08 4.41
1521 1522 2.648059 CGGAATCAGCAGGGAAAGAAT 58.352 47.619 0.00 0.00 0.00 2.40
1547 1548 3.230976 TGTTGAGCTTGACTCTAGTCCA 58.769 45.455 7.63 0.00 46.41 4.02
1595 1596 1.204146 GATAAGTGGGAGCCCTCACA 58.796 55.000 0.00 0.00 41.39 3.58
1624 1625 8.234546 CGCAAGTGAAATACCACTACTTTTAAT 58.765 33.333 0.00 0.00 45.82 1.40
1696 1698 0.984230 CTCCAAGGCCCAGTCTTACA 59.016 55.000 0.00 0.00 0.00 2.41
1702 1704 3.820425 CCCAGTCTTACAGGGCCA 58.180 61.111 6.18 0.00 38.13 5.36
1706 1708 1.561542 CCAGTCTTACAGGGCCAATCT 59.438 52.381 6.18 0.00 0.00 2.40
1710 1712 0.625849 CTTACAGGGCCAATCTGGGT 59.374 55.000 6.18 0.00 38.19 4.51
1724 1726 2.338809 TCTGGGTGGAAGACATTGTCT 58.661 47.619 13.61 13.61 45.64 3.41
1767 1769 5.221048 GGCGGCACATCTGTTAAAAGATAAT 60.221 40.000 7.86 0.00 35.09 1.28
1798 1800 4.646945 TCCTAAGATGAGCTCAACGAGAAT 59.353 41.667 22.50 1.08 0.00 2.40
1807 1809 6.634805 TGAGCTCAACGAGAATAGAAATCTT 58.365 36.000 15.67 0.00 0.00 2.40
1832 1834 5.018539 GTGGAACAAAAGGGTAAAAGCTT 57.981 39.130 0.00 0.00 44.16 3.74
1877 1879 0.030504 TACGAACCGTGAAAGCGTGA 59.969 50.000 1.93 0.00 41.39 4.35
1878 1880 1.213094 ACGAACCGTGAAAGCGTGAG 61.213 55.000 0.00 0.00 39.18 3.51
1894 1925 2.538939 CGTGAGCTATCGATCGTGTCAA 60.539 50.000 15.94 0.00 0.00 3.18
1946 1977 0.179073 AGCCAAGCGTTCATAGCGAT 60.179 50.000 0.00 0.00 40.04 4.58
2127 2158 6.600882 AATTCAACCTAGTACGAGAGGAAA 57.399 37.500 15.82 8.79 36.61 3.13
2128 2159 6.793505 ATTCAACCTAGTACGAGAGGAAAT 57.206 37.500 15.82 10.17 36.61 2.17
2167 2198 1.539388 TCATCGCGCTTGGTTGAAAAT 59.461 42.857 5.56 0.00 0.00 1.82
2247 2278 2.963854 CTAGCATGCGACGCCTGG 60.964 66.667 23.53 11.84 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.003689 CCAAGTCAGACAAACGATTTGCT 59.996 43.478 2.66 6.19 44.39 3.91
14 15 2.759355 CCCCTATACCCAAGTCAGACA 58.241 52.381 2.66 0.00 0.00 3.41
215 216 3.310860 GAGCACCCGATTCCGTGGT 62.311 63.158 3.61 3.61 43.04 4.16
238 239 0.605589 TGCTTACCAAAAATGGCCCG 59.394 50.000 0.00 0.00 0.00 6.13
309 310 5.523438 CCTTTGTGGGTTTTAGTTTAGCA 57.477 39.130 0.00 0.00 0.00 3.49
338 339 2.932614 CCGTCCTGCTGTCTTAATTGAG 59.067 50.000 0.00 0.00 0.00 3.02
341 342 3.514309 ACTACCGTCCTGCTGTCTTAATT 59.486 43.478 0.00 0.00 0.00 1.40
361 362 3.055530 AGCAGATTTCGACTTCCATGACT 60.056 43.478 0.00 0.00 0.00 3.41
380 381 4.100344 TGAGTTGTTACACACTCCTTAGCA 59.900 41.667 17.95 4.15 30.51 3.49
693 694 4.794648 CCTTTCGGGGGATGCGCA 62.795 66.667 14.96 14.96 0.00 6.09
729 730 4.530857 CGCCACATCCCGACTCCC 62.531 72.222 0.00 0.00 0.00 4.30
730 731 4.530857 CCGCCACATCCCGACTCC 62.531 72.222 0.00 0.00 0.00 3.85
734 735 3.315140 TCAACCGCCACATCCCGA 61.315 61.111 0.00 0.00 0.00 5.14
754 755 1.749634 CTCCGGACTTCCTAACATCGT 59.250 52.381 0.00 0.00 0.00 3.73
758 759 1.171308 CGTCTCCGGACTTCCTAACA 58.829 55.000 0.00 0.00 40.10 2.41
783 784 2.177529 TAACTCTTCCCGAGGCCCCT 62.178 60.000 0.00 0.00 44.33 4.79
811 812 3.244318 CCAGGGTTTGTAGTCCGTTAAGT 60.244 47.826 0.00 0.00 0.00 2.24
820 821 3.895704 ACCATTTCCAGGGTTTGTAGT 57.104 42.857 0.00 0.00 32.12 2.73
823 824 2.965147 CTGAACCATTTCCAGGGTTTGT 59.035 45.455 0.00 0.00 46.97 2.83
825 826 1.970640 GCTGAACCATTTCCAGGGTTT 59.029 47.619 0.00 0.00 46.97 3.27
837 838 0.909610 CCCTACCTCCAGCTGAACCA 60.910 60.000 17.39 0.00 0.00 3.67
846 847 1.080354 CCACTGGACCCTACCTCCA 59.920 63.158 0.00 0.00 36.34 3.86
909 910 1.342275 CCTCTGGATTTTCATGGGCCA 60.342 52.381 9.61 9.61 0.00 5.36
989 990 1.568504 TTGTTCCATCGGCTAGAGGT 58.431 50.000 0.00 0.00 0.00 3.85
995 996 1.747206 GCCTACATTGTTCCATCGGCT 60.747 52.381 0.00 0.00 33.68 5.52
999 1000 2.689983 CCCTTGCCTACATTGTTCCATC 59.310 50.000 0.00 0.00 0.00 3.51
1162 1163 3.572715 ATTCCCGGTCTGTCCCCCA 62.573 63.158 0.00 0.00 0.00 4.96
1235 1236 1.064825 ACAGTCGGATTCCCCTTGTT 58.935 50.000 0.00 0.00 0.00 2.83
1316 1317 5.532032 TCTTCATTTTGACATTCAGAGCACA 59.468 36.000 0.00 0.00 0.00 4.57
1334 1335 3.578688 GCGCTTGGTTGAATTTCTTCAT 58.421 40.909 0.00 0.00 40.95 2.57
1406 1407 9.842775 ATTCATGTGTGTCACTAATTAGATGAT 57.157 29.630 19.38 0.00 35.11 2.45
1423 1424 7.232127 GGGAATCTCATTAATCCATTCATGTGT 59.768 37.037 10.56 0.00 33.48 3.72
1425 1426 7.232127 GTGGGAATCTCATTAATCCATTCATGT 59.768 37.037 10.56 0.00 33.48 3.21
1453 1454 2.108425 TCGCTGGATAGTAGACAGGGAT 59.892 50.000 15.33 0.00 45.40 3.85
1521 1522 2.609747 AGAGTCAAGCTCAACAGGGTA 58.390 47.619 0.00 0.00 46.47 3.69
1547 1548 5.888161 ACCTCTCAAGTCATTTCACAAAGTT 59.112 36.000 0.00 0.00 0.00 2.66
1595 1596 1.165270 GTGGTATTTCACTTGCGCCT 58.835 50.000 4.18 0.00 34.98 5.52
1624 1625 6.313411 CGACCCACGGAATAAGTAAAATAACA 59.687 38.462 0.00 0.00 38.46 2.41
1696 1698 1.856873 TTCCACCCAGATTGGCCCT 60.857 57.895 0.00 0.00 35.79 5.19
1702 1704 3.331889 AGACAATGTCTTCCACCCAGATT 59.668 43.478 10.56 0.00 40.28 2.40
1706 1708 1.073763 CCAGACAATGTCTTCCACCCA 59.926 52.381 13.99 0.00 41.37 4.51
1710 1712 1.073763 CCCACCAGACAATGTCTTCCA 59.926 52.381 13.99 0.00 41.37 3.53
1724 1726 2.520458 CAGCCAAACTCCCCACCA 59.480 61.111 0.00 0.00 0.00 4.17
1767 1769 1.208052 GCTCATCTTAGGACACCTGCA 59.792 52.381 0.00 0.00 34.61 4.41
1798 1800 6.040391 CCCTTTTGTTCCACACAAGATTTCTA 59.960 38.462 4.66 0.00 46.37 2.10
1807 1809 4.382147 GCTTTTACCCTTTTGTTCCACACA 60.382 41.667 0.00 0.00 0.00 3.72
1832 1834 6.227522 TCGTACTGGAAATCAGAATCAAACA 58.772 36.000 0.00 0.00 46.18 2.83
1894 1925 6.605995 GCCAGTTATCCCTATGGTAACTTTTT 59.394 38.462 8.34 0.00 36.84 1.94
1906 1937 1.211949 GCCACAAGCCAGTTATCCCTA 59.788 52.381 0.00 0.00 34.35 3.53
1946 1977 4.278170 ACATCGAAGGATCAAAAAGCAACA 59.722 37.500 0.00 0.00 0.00 3.33
2036 2067 1.429930 TGGTCTAAACCCAGCTCACA 58.570 50.000 0.00 0.00 45.83 3.58
2062 2093 6.892658 TCAGTAGGGTAAAACTAACGTGTA 57.107 37.500 0.00 0.00 0.00 2.90
2066 2097 6.392354 TGTCATCAGTAGGGTAAAACTAACG 58.608 40.000 0.00 0.00 0.00 3.18
2127 2158 5.787953 TGACCAATTGTGTGAATCAACAT 57.212 34.783 4.43 0.00 31.49 2.71
2128 2159 5.562501 CGATGACCAATTGTGTGAATCAACA 60.563 40.000 4.43 0.00 0.00 3.33
2167 2198 3.378602 TAGCTTCGCGCCACTGGA 61.379 61.111 0.00 0.00 40.39 3.86
2187 2218 3.206150 GTTCAGTCATAATCCGGCACAT 58.794 45.455 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.