Multiple sequence alignment - TraesCS1D01G173900

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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 TraesCS1D01G173900 chr1D 100.000 2594 0 0 1 2594 247508648 247506055 0.000000e+00 4791.0
1 TraesCS1D01G173900 chr1D 95.161 62 3 0 2072 2133 59876028 59875967 5.910000e-17 99.0
2 TraesCS1D01G173900 chr1B 94.625 2307 81 11 58 2331 330230637 330232933 0.000000e+00 3533.0
3 TraesCS1D01G173900 chr1B 89.434 265 24 2 2330 2594 330233050 330233310 5.350000e-87 331.0
4 TraesCS1D01G173900 chr1B 95.714 70 3 0 1 70 330230549 330230618 2.110000e-21 113.0
5 TraesCS1D01G173900 chr1A 93.988 2129 68 17 1 2094 299718203 299720306 0.000000e+00 3168.0
6 TraesCS1D01G173900 chr1A 94.801 327 15 1 2268 2594 299720320 299720644 2.300000e-140 508.0
7 TraesCS1D01G173900 chr7B 82.536 481 80 4 1118 1596 584185897 584185419 1.110000e-113 420.0
8 TraesCS1D01G173900 chr7B 92.500 40 2 1 2075 2114 619589037 619589075 3.610000e-04 56.5
9 TraesCS1D01G173900 chr7A 81.980 505 82 7 1098 1596 622742096 622741595 1.110000e-113 420.0
10 TraesCS1D01G173900 chr7A 81.920 448 72 8 1153 1597 624772639 624773080 1.130000e-98 370.0
11 TraesCS1D01G173900 chr7A 94.737 38 2 0 2072 2109 653619550 653619513 2.790000e-05 60.2
12 TraesCS1D01G173900 chr7A 94.737 38 2 0 2072 2109 653636048 653636011 2.790000e-05 60.2
13 TraesCS1D01G173900 chr7A 94.737 38 2 0 2072 2109 653652085 653652048 2.790000e-05 60.2
14 TraesCS1D01G173900 chr5B 79.880 502 99 2 1101 1600 609484550 609485051 1.470000e-97 366.0
15 TraesCS1D01G173900 chr5B 79.518 498 101 1 1101 1597 609481805 609482302 1.140000e-93 353.0
16 TraesCS1D01G173900 chr5B 79.518 498 101 1 1101 1597 609494605 609495102 1.140000e-93 353.0
17 TraesCS1D01G173900 chr5D 79.835 486 98 0 1112 1597 493777645 493778130 3.170000e-94 355.0
18 TraesCS1D01G173900 chr5A 89.394 66 7 0 2068 2133 27727913 27727978 1.650000e-12 84.2
19 TraesCS1D01G173900 chr2A 100.000 31 0 0 2072 2102 194466493 194466463 1.000000e-04 58.4


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 TraesCS1D01G173900 chr1D 247506055 247508648 2593 True 4791.000000 4791 100.000000 1 2594 1 chr1D.!!$R2 2593
1 TraesCS1D01G173900 chr1B 330230549 330233310 2761 False 1325.666667 3533 93.257667 1 2594 3 chr1B.!!$F1 2593
2 TraesCS1D01G173900 chr1A 299718203 299720644 2441 False 1838.000000 3168 94.394500 1 2594 2 chr1A.!!$F1 2593
3 TraesCS1D01G173900 chr7A 622741595 622742096 501 True 420.000000 420 81.980000 1098 1596 1 chr7A.!!$R1 498
4 TraesCS1D01G173900 chr5B 609481805 609485051 3246 False 359.500000 366 79.699000 1101 1600 2 chr5B.!!$F2 499

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
872 923 2.089201 TGTGCAGCCAATCATCAAGAG 58.911 47.619 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 1741 0.179227 CACACACACACACACACACG 60.179 55.0 0.0 0.0 0.0 4.49 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
185 222 6.161381 ACTTGCAATGCCTTTATCTGAAAAG 58.839 36.000 1.53 0.00 36.43 2.27
189 228 7.215789 TGCAATGCCTTTATCTGAAAAGAAAA 58.784 30.769 1.53 0.00 38.50 2.29
245 284 3.967326 AGACATATTGAGACAATCCCGGA 59.033 43.478 0.73 0.00 0.00 5.14
407 446 5.719085 TGGGCCAAAATGTTCAGTTATACAT 59.281 36.000 2.13 0.00 36.58 2.29
448 488 9.965902 ATTTTATGTTCCATCTGTTAGTCTCTT 57.034 29.630 0.00 0.00 0.00 2.85
803 854 2.666508 GTGAACACACGGTAGCATAGTG 59.333 50.000 0.00 6.79 41.28 2.74
872 923 2.089201 TGTGCAGCCAATCATCAAGAG 58.911 47.619 0.00 0.00 0.00 2.85
940 991 7.630082 GCTCTATATAAAGTACCCACCCATACG 60.630 44.444 0.00 0.00 0.00 3.06
1198 1252 2.257409 CTGCTGTATTCCCCGCCACT 62.257 60.000 0.00 0.00 0.00 4.00
1335 1389 1.185618 ACCACAAGGACAGCGAGCTA 61.186 55.000 0.00 0.00 38.69 3.32
1404 1458 2.093890 TGCAACAAGATGATCCGCATT 58.906 42.857 0.00 0.00 37.34 3.56
1687 1741 7.281100 GCTCCTCACTTATATAAACCATATGGC 59.719 40.741 22.18 0.00 39.32 4.40
1772 1848 5.351740 GCTATCCCAAGAAAAGTGTGTACTC 59.648 44.000 0.00 0.00 35.69 2.59
1904 2081 9.647797 TGTATGTTACCAAGTTAGTAATGACTG 57.352 33.333 0.00 0.00 36.28 3.51
2003 3052 0.321653 GAGAACCAGACAATGCCGGT 60.322 55.000 1.90 0.00 0.00 5.28
2017 3066 2.156098 TGCCGGTAAATTTCAGGTGTC 58.844 47.619 1.90 0.00 0.00 3.67
2096 3148 3.585862 CCCGTCCCACAATATAAGATCG 58.414 50.000 0.00 0.00 0.00 3.69
2141 3242 4.600012 AAAACGATCTTATGGAACGCAG 57.400 40.909 0.00 0.00 42.68 5.18
2155 3256 2.386661 ACGCAGGGAGTACATCTTTG 57.613 50.000 0.00 0.00 0.00 2.77
2188 3289 7.148222 TGTCCAAAATTGTTCTTCGTCTAACAA 60.148 33.333 12.02 12.02 46.37 2.83
2207 3308 0.749649 AGAGCCAGAGTAGCCAATCG 59.250 55.000 0.00 0.00 0.00 3.34
2213 3314 1.596260 CAGAGTAGCCAATCGCATGTG 59.404 52.381 0.00 0.00 41.38 3.21
2278 3379 0.386476 ACATATGCATTTGGGCGCTG 59.614 50.000 19.43 0.00 36.28 5.18
2327 3428 6.274157 ACCAGTTATTCTACTCACAGTCTG 57.726 41.667 0.00 0.00 0.00 3.51
2339 3558 6.665992 ACTCACAGTCTGATAGGTTAACAA 57.334 37.500 6.91 0.00 0.00 2.83
2390 3609 7.093945 GGTCAATCAACCATACAACTATTTGGT 60.094 37.037 0.00 0.00 44.20 3.67
2403 3622 7.196532 ACAACTATTTGGTCTGGCATCAGAAA 61.197 38.462 0.00 0.00 42.38 2.52
2457 3676 6.166984 TCAAGGCCATCTACTTAATCTGAG 57.833 41.667 5.01 0.00 0.00 3.35
2467 3686 2.076100 CTTAATCTGAGCACCGCAACA 58.924 47.619 0.00 0.00 0.00 3.33
2555 4337 6.717997 TGTCATAACACTAGTCCAGTCAGTAA 59.282 38.462 0.00 0.00 34.26 2.24
2556 4338 7.231925 TGTCATAACACTAGTCCAGTCAGTAAA 59.768 37.037 0.00 0.00 34.26 2.01
2581 4363 5.427806 GGTACTAAGAATAGGTGGTTTCCCT 59.572 44.000 0.00 0.00 36.04 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 222 9.052759 TCCTGTGTAGTCACTTAATTCTTTTTC 57.947 33.333 0.00 0.00 44.14 2.29
189 228 7.680730 ACATCCTGTGTAGTCACTTAATTCTT 58.319 34.615 0.00 0.00 44.14 2.52
245 284 3.057315 CGTGTTTCTGGATGATTTGGCTT 60.057 43.478 0.00 0.00 0.00 4.35
281 320 6.293845 CCTGGACACTGAAGAATTGAGAAAAG 60.294 42.308 0.00 0.00 31.17 2.27
565 605 8.648557 TTTCGAATAGAATGGTAGTTGATCAG 57.351 34.615 0.00 0.00 38.86 2.90
746 797 5.093849 TGGTTTAACTAGGCATGTACTCC 57.906 43.478 0.00 0.00 0.00 3.85
747 798 5.581085 CACTGGTTTAACTAGGCATGTACTC 59.419 44.000 12.84 0.00 30.19 2.59
748 799 5.488341 CACTGGTTTAACTAGGCATGTACT 58.512 41.667 12.84 0.00 30.19 2.73
749 800 4.634443 CCACTGGTTTAACTAGGCATGTAC 59.366 45.833 12.84 0.00 30.19 2.90
750 801 4.287585 ACCACTGGTTTAACTAGGCATGTA 59.712 41.667 12.84 0.00 30.19 2.29
751 802 3.073946 ACCACTGGTTTAACTAGGCATGT 59.926 43.478 12.84 1.93 30.19 3.21
803 854 3.401182 TGGGCAAAACATTTCAGCAATC 58.599 40.909 0.00 0.00 0.00 2.67
956 1007 4.142838 TGTGCAGCTTTCGATTGAACTATG 60.143 41.667 0.00 0.00 32.71 2.23
1243 1297 2.933878 TTCAGCGTCAAGGTTGCCGT 62.934 55.000 0.00 0.00 31.41 5.68
1335 1389 1.908793 AGTAGACAGCGCCACCACT 60.909 57.895 2.29 0.00 0.00 4.00
1404 1458 3.766691 GACCGCCTGTTCCCGCTA 61.767 66.667 0.00 0.00 0.00 4.26
1687 1741 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
1772 1848 6.861055 AGCACACATAGTTTTGGAAATTAACG 59.139 34.615 0.00 0.00 0.00 3.18
1904 2081 1.555477 CTTTCACCGCACAAAACCAC 58.445 50.000 0.00 0.00 0.00 4.16
2077 3129 6.598753 AAAACGATCTTATATTGTGGGACG 57.401 37.500 0.00 0.00 0.00 4.79
2120 3216 3.374058 CCTGCGTTCCATAAGATCGTTTT 59.626 43.478 0.00 0.00 39.42 2.43
2141 3242 2.572104 AGGTGTCCAAAGATGTACTCCC 59.428 50.000 0.00 0.00 0.00 4.30
2170 3271 4.691216 GGCTCTTGTTAGACGAAGAACAAT 59.309 41.667 11.76 0.00 42.86 2.71
2188 3289 0.749649 CGATTGGCTACTCTGGCTCT 59.250 55.000 0.00 0.00 0.00 4.09
2207 3308 4.720649 TTCTAGTACAGAGGACACATGC 57.279 45.455 0.00 0.00 33.83 4.06
2213 3314 9.088512 CAATTGTTGTATTCTAGTACAGAGGAC 57.911 37.037 0.00 0.00 36.08 3.85
2278 3379 7.893658 ACTGTGGTACTGGTATATATAAGTGC 58.106 38.462 7.17 5.96 0.00 4.40
2312 3413 7.668469 TGTTAACCTATCAGACTGTGAGTAGAA 59.332 37.037 2.48 0.00 39.07 2.10
2339 3558 4.389374 CTCGATGGGCCAATAACAAGTAT 58.611 43.478 11.89 0.00 0.00 2.12
2390 3609 4.005650 GAGTTGTGATTTCTGATGCCAGA 58.994 43.478 0.00 0.00 46.95 3.86
2403 3622 6.947733 TCATAGGGTTTCAAATGAGTTGTGAT 59.052 34.615 0.00 0.00 38.47 3.06
2509 3730 6.128499 TGACATTATTTTTCGAACGGTAGTGG 60.128 38.462 0.00 0.00 0.00 4.00
2555 4337 6.955364 GGAAACCACCTATTCTTAGTACCTT 58.045 40.000 0.00 0.00 0.00 3.50
2556 4338 6.556974 GGAAACCACCTATTCTTAGTACCT 57.443 41.667 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.