Multiple sequence alignment - TraesCS3D01G064600

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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 TraesCS3D01G064600 chr3D 100.000 2390 0 0 942 3331 28485516 28487905 0.000000e+00 4414.0
1 TraesCS3D01G064600 chr3D 92.234 1249 76 11 946 2178 27889999 27888756 0.000000e+00 1749.0
2 TraesCS3D01G064600 chr3D 86.088 1222 102 32 2171 3331 27886136 27884922 0.000000e+00 1253.0
3 TraesCS3D01G064600 chr3D 100.000 594 0 0 1 594 28484575 28485168 0.000000e+00 1098.0
4 TraesCS3D01G064600 chr3D 82.048 869 136 16 958 1815 28243153 28244012 0.000000e+00 723.0
5 TraesCS3D01G064600 chr3D 91.150 226 17 2 372 594 27890399 27890174 1.500000e-78 303.0
6 TraesCS3D01G064600 chr3D 87.821 156 19 0 193 348 27890528 27890373 2.040000e-42 183.0
7 TraesCS3D01G064600 chr3D 77.670 206 34 7 3126 3327 28244825 28245022 7.550000e-22 115.0
8 TraesCS3D01G064600 chr3D 83.784 111 13 4 1825 1930 28244348 28244458 2.110000e-17 100.0
9 TraesCS3D01G064600 chr3D 86.364 88 11 1 2354 2441 4853085 4853171 9.840000e-16 95.3
10 TraesCS3D01G064600 chr3A 95.198 2395 91 9 942 3331 38238966 38241341 0.000000e+00 3764.0
11 TraesCS3D01G064600 chr3A 94.482 598 29 2 1 594 38238198 38238795 0.000000e+00 918.0
12 TraesCS3D01G064600 chr3A 88.750 80 9 0 515 594 38197784 38197863 7.610000e-17 99.0
13 TraesCS3D01G064600 chr3A 76.216 185 33 8 2873 3052 11530583 11530761 1.650000e-13 87.9
14 TraesCS3D01G064600 chr3B 82.260 885 137 13 945 1815 47262584 47263462 0.000000e+00 747.0
15 TraesCS3D01G064600 chr3B 81.098 164 17 8 3126 3282 47264276 47264432 5.840000e-23 119.0
16 TraesCS3D01G064600 chr3B 83.784 111 13 4 1825 1930 47263797 47263907 2.110000e-17 100.0
17 TraesCS3D01G064600 chr3B 88.750 80 9 0 515 594 47256429 47256508 7.610000e-17 99.0
18 TraesCS3D01G064600 chrUn 86.517 89 11 1 2353 2441 35484472 35484559 2.740000e-16 97.1
19 TraesCS3D01G064600 chr5B 85.000 80 12 0 515 594 57492121 57492042 7.660000e-12 82.4
20 TraesCS3D01G064600 chr5A 92.000 50 4 0 515 564 42688335 42688286 1.660000e-08 71.3
21 TraesCS3D01G064600 chr1A 90.000 50 5 0 3246 3295 481630788 481630837 7.710000e-07 65.8
22 TraesCS3D01G064600 chr1D 88.000 50 6 0 3246 3295 381007731 381007780 3.590000e-05 60.2
23 TraesCS3D01G064600 chr1B 88.000 50 6 0 3246 3295 510793683 510793732 3.590000e-05 60.2


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 TraesCS3D01G064600 chr3D 28484575 28487905 3330 False 2756.000000 4414 100.000000 1 3331 2 chr3D.!!$F3 3330
1 TraesCS3D01G064600 chr3D 27884922 27890528 5606 True 872.000000 1749 89.323250 193 3331 4 chr3D.!!$R1 3138
2 TraesCS3D01G064600 chr3D 28243153 28245022 1869 False 312.666667 723 81.167333 958 3327 3 chr3D.!!$F2 2369
3 TraesCS3D01G064600 chr3A 38238198 38241341 3143 False 2341.000000 3764 94.840000 1 3331 2 chr3A.!!$F3 3330
4 TraesCS3D01G064600 chr3B 47262584 47264432 1848 False 322.000000 747 82.380667 945 3282 3 chr3B.!!$F2 2337

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
449 451 0.173481 CACGAAGAAGATCTCGCCCA 59.827 55.0 0.0 0.0 0.0 5.36 F
1299 1311 0.039618 TTTCTGGGACCCTCATTGGC 59.960 55.0 13.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1585 0.182299 CTCTTCCAATCTGGGGAGGC 59.818 60.000 7.99 0.0 38.32 4.70 R
2869 5911 1.811266 CCCGGTGAGAACTGCATCG 60.811 63.158 0.00 0.0 39.45 3.84 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
28 29 7.964730 ATATTTTCCCCTATTTGACCCTCTA 57.035 36.000 0.00 0.00 0.00 2.43
67 69 1.061421 GGCATTTCGATCAAACGCGTA 59.939 47.619 14.46 0.00 33.81 4.42
87 89 3.402628 AAAGTGGCACGTGAATAGACT 57.597 42.857 22.23 9.46 0.00 3.24
93 95 4.449743 GTGGCACGTGAATAGACTGTTTTA 59.550 41.667 22.23 0.00 0.00 1.52
106 108 5.265989 AGACTGTTTTACCCTTTGGTTCAA 58.734 37.500 0.00 0.00 44.75 2.69
134 136 4.499188 GCCAAAAACTGTTTGACCCTCTAC 60.499 45.833 6.53 0.00 0.00 2.59
177 179 2.035961 GCCAAACCTCTTCCCTGTTTTC 59.964 50.000 0.00 0.00 30.19 2.29
183 185 3.977326 ACCTCTTCCCTGTTTTCTCTTCT 59.023 43.478 0.00 0.00 0.00 2.85
331 333 1.002087 CGAAGCCTGTTTCCCTACTGT 59.998 52.381 0.00 0.00 0.00 3.55
338 340 4.504340 GCCTGTTTCCCTACTGTACAAAGA 60.504 45.833 0.00 0.00 0.00 2.52
449 451 0.173481 CACGAAGAAGATCTCGCCCA 59.827 55.000 0.00 0.00 0.00 5.36
513 518 2.592308 GCCTCCCCGCTTGAAGAT 59.408 61.111 0.00 0.00 0.00 2.40
548 553 2.519780 GATCCTCCTCCGCCTCGT 60.520 66.667 0.00 0.00 0.00 4.18
565 570 3.329889 TGCCGCAACCATCCTCCT 61.330 61.111 0.00 0.00 0.00 3.69
996 1004 2.769663 TGGCCACGTCCTAGTCAAATAT 59.230 45.455 0.00 0.00 0.00 1.28
1277 1289 3.181477 CCATGTCAGCTTTTTGTTGGTCA 60.181 43.478 0.00 0.00 0.00 4.02
1299 1311 0.039618 TTTCTGGGACCCTCATTGGC 59.960 55.000 13.00 0.00 0.00 4.52
1326 1338 3.194755 CCCTTTATTGGCCGCTTTTTACT 59.805 43.478 0.00 0.00 0.00 2.24
1364 1376 5.635120 ACTGGAGTTTAATTTGGAAGAGCT 58.365 37.500 0.00 0.00 0.00 4.09
1450 1462 1.379044 CAGGCTGGGGATGGTGTTC 60.379 63.158 6.61 0.00 0.00 3.18
1488 1504 7.855784 ATTGTCTTACCCTTTCTTCCAAATT 57.144 32.000 0.00 0.00 0.00 1.82
1522 1538 2.730928 GTCAATTTTCATGGTGTTGCCG 59.269 45.455 0.00 0.00 41.21 5.69
1569 1585 7.558161 TGAAATACATAGCATTCTTGGTCTG 57.442 36.000 0.00 0.00 34.60 3.51
1622 1638 8.211629 AGCGAAGAAAACTATAGTGGGATATTT 58.788 33.333 6.06 1.87 0.00 1.40
1665 1681 8.665685 GTTTTTATACTTGTGGGTGATAGTCTG 58.334 37.037 0.00 0.00 0.00 3.51
1668 1684 8.777578 TTATACTTGTGGGTGATAGTCTGTAT 57.222 34.615 0.00 0.00 0.00 2.29
1717 1733 5.592282 TGCAAGAGACTTTGTGAAACCAATA 59.408 36.000 0.00 0.00 34.36 1.90
1718 1734 6.265196 TGCAAGAGACTTTGTGAAACCAATAT 59.735 34.615 0.00 0.00 34.36 1.28
1757 1773 3.880490 CCTCTCACGAGCTTCTATGTACT 59.120 47.826 0.00 0.00 35.90 2.73
1766 1782 6.016943 ACGAGCTTCTATGTACTAGGTGATTC 60.017 42.308 0.00 0.00 0.00 2.52
1770 1786 7.782644 AGCTTCTATGTACTAGGTGATTCTTCT 59.217 37.037 0.00 0.00 0.00 2.85
1964 2312 9.555727 TTTTTCGCTAGAGTTTATAAGCCATAT 57.444 29.630 0.00 0.00 0.00 1.78
2140 2496 8.145122 AGTATCTTGCTAAGCTACATAACCTTC 58.855 37.037 10.43 0.00 33.64 3.46
2181 5168 7.881232 TCCGTTAAAAAGTCTATGGAAAGTGAT 59.119 33.333 0.00 0.00 0.00 3.06
2327 5314 5.471116 TGGATCTAATGGAGAAAATGATGCG 59.529 40.000 0.00 0.00 37.85 4.73
2332 5319 4.627611 ATGGAGAAAATGATGCGTGAAG 57.372 40.909 0.00 0.00 0.00 3.02
2338 5325 6.258727 GGAGAAAATGATGCGTGAAGATAGAA 59.741 38.462 0.00 0.00 0.00 2.10
2342 5329 8.893219 AAAATGATGCGTGAAGATAGAAGATA 57.107 30.769 0.00 0.00 0.00 1.98
2348 5335 8.668510 ATGCGTGAAGATAGAAGATAATTGTT 57.331 30.769 0.00 0.00 0.00 2.83
2367 5354 8.891671 AATTGTTTTCTTTGATGTGCTAATGT 57.108 26.923 0.00 0.00 0.00 2.71
2368 5355 7.697352 TTGTTTTCTTTGATGTGCTAATGTG 57.303 32.000 0.00 0.00 0.00 3.21
2369 5356 5.691305 TGTTTTCTTTGATGTGCTAATGTGC 59.309 36.000 0.00 0.00 0.00 4.57
2370 5357 5.710513 TTTCTTTGATGTGCTAATGTGCT 57.289 34.783 0.00 0.00 0.00 4.40
2371 5358 4.690184 TCTTTGATGTGCTAATGTGCTG 57.310 40.909 0.00 0.00 0.00 4.41
2372 5359 4.325972 TCTTTGATGTGCTAATGTGCTGA 58.674 39.130 0.00 0.00 0.00 4.26
2431 5429 5.771666 AGCTTCTGAGATTTGGATTGTTTGA 59.228 36.000 0.00 0.00 0.00 2.69
2524 5522 7.464358 CATGGGCTTGCGTAATTTATATCTAC 58.536 38.462 0.00 0.00 0.00 2.59
2557 5576 1.812571 GTGTTTGTGTGCCTATCTGGG 59.187 52.381 0.00 0.00 36.00 4.45
2668 5695 1.677217 GCAGTGTGGAGAAGCCTTAGG 60.677 57.143 0.00 0.00 37.63 2.69
2732 5759 0.681243 GCATTCAACTCCTCCACCCC 60.681 60.000 0.00 0.00 0.00 4.95
2733 5760 0.698238 CATTCAACTCCTCCACCCCA 59.302 55.000 0.00 0.00 0.00 4.96
2869 5911 2.774234 TCCTCCAGATGAAGGAATGACC 59.226 50.000 0.00 0.00 34.08 4.02
2913 5955 0.828022 CCATTGCATCAATGTGGCCT 59.172 50.000 15.69 0.00 46.69 5.19
2988 6031 5.297776 CCCAATTTCTACTGTAGCAAGATGG 59.702 44.000 18.93 18.93 0.00 3.51
3207 6303 4.812091 CGATGTATTTTGTACCGATGGGAA 59.188 41.667 0.00 0.00 36.97 3.97
3220 6316 3.636300 CCGATGGGAATTTCAGCCATAAA 59.364 43.478 7.05 0.00 34.06 1.40
3221 6317 4.281688 CCGATGGGAATTTCAGCCATAAAT 59.718 41.667 7.05 0.00 34.06 1.40
3222 6318 5.476599 CCGATGGGAATTTCAGCCATAAATA 59.523 40.000 7.05 0.00 34.06 1.40
3223 6319 6.153340 CCGATGGGAATTTCAGCCATAAATAT 59.847 38.462 7.05 0.00 34.06 1.28
3300 6396 5.496387 CATGTCATTGCTGTCGATCTTAAC 58.504 41.667 0.00 0.00 0.00 2.01
3302 6398 5.961272 TGTCATTGCTGTCGATCTTAACTA 58.039 37.500 0.00 0.00 0.00 2.24
3318 6414 7.432148 TCTTAACTAGCCATGATCCACTTAA 57.568 36.000 0.00 0.00 0.00 1.85
3319 6415 7.272978 TCTTAACTAGCCATGATCCACTTAAC 58.727 38.462 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.850046 AATGATAGAGGGTCAAATAGGGG 57.150 43.478 0.00 0.00 0.00 4.79
59 61 1.277440 CGTGCCACTTTACGCGTTT 59.723 52.632 20.78 0.00 35.20 3.60
67 69 3.067106 CAGTCTATTCACGTGCCACTTT 58.933 45.455 11.67 0.00 0.00 2.66
106 108 4.457603 GGGTCAAACAGTTTTTGGCTTTTT 59.542 37.500 6.34 0.00 34.67 1.94
156 158 1.704641 AAACAGGGAAGAGGTTTGGC 58.295 50.000 0.00 0.00 33.78 4.52
177 179 3.383185 AGGTTTGGCGAGATCTAGAAGAG 59.617 47.826 7.06 0.00 0.00 2.85
183 185 2.431057 GGAAGAGGTTTGGCGAGATCTA 59.569 50.000 0.00 0.00 0.00 1.98
321 323 5.014858 AGATCGTCTTTGTACAGTAGGGAA 58.985 41.667 0.00 0.00 0.00 3.97
331 333 3.447586 CCCTGAAGGAGATCGTCTTTGTA 59.552 47.826 0.00 0.00 38.24 2.41
476 481 2.176273 AGCGCCATCGATGAAGCAC 61.176 57.895 31.52 20.76 38.10 4.40
548 553 2.819984 GAAGGAGGATGGTTGCGGCA 62.820 60.000 0.00 0.00 0.00 5.69
565 570 4.329545 GGCAGAGGCACGTGGGAA 62.330 66.667 18.88 0.00 43.71 3.97
996 1004 1.602237 GAGGTCTTCCCGCATCCAA 59.398 57.895 0.00 0.00 38.74 3.53
1277 1289 3.444029 CCAATGAGGGTCCCAGAAAAAT 58.556 45.455 11.55 0.00 0.00 1.82
1326 1338 1.008327 TCCAGTATGCCCTTCTCAGGA 59.992 52.381 0.00 0.00 40.67 3.86
1364 1376 1.483827 CCTCAATCACAGCTAGGCTCA 59.516 52.381 0.00 0.00 36.40 4.26
1488 1504 2.397044 AATTGACCTCCCTTTGCCAA 57.603 45.000 0.00 0.00 0.00 4.52
1522 1538 1.202348 GGTCTTTTGCAGTACCCATGC 59.798 52.381 0.00 0.00 44.11 4.06
1569 1585 0.182299 CTCTTCCAATCTGGGGAGGC 59.818 60.000 7.99 0.00 38.32 4.70
1591 1607 5.220491 CCACTATAGTTTTCTTCGCTCTTGC 60.220 44.000 1.56 0.00 0.00 4.01
1622 1638 9.109393 GTATAAAAACTACATCAGCATCCTCAA 57.891 33.333 0.00 0.00 0.00 3.02
1665 1681 8.556194 TGCATCGATTTAAGTTGAACCATATAC 58.444 33.333 0.00 0.00 0.00 1.47
1668 1684 6.993786 TGCATCGATTTAAGTTGAACCATA 57.006 33.333 0.00 0.00 0.00 2.74
1717 1733 5.128827 TGAGAGGATAGTAGCAAACCGAAAT 59.871 40.000 0.00 0.00 0.00 2.17
1718 1734 4.464951 TGAGAGGATAGTAGCAAACCGAAA 59.535 41.667 0.00 0.00 0.00 3.46
1757 1773 3.117888 GCCCATGGAAGAAGAATCACCTA 60.118 47.826 15.22 0.00 0.00 3.08
1766 1782 6.906157 ACAATATAATGCCCATGGAAGAAG 57.094 37.500 15.22 0.00 0.00 2.85
1770 1786 6.045459 ACTCCTACAATATAATGCCCATGGAA 59.955 38.462 15.22 0.49 0.00 3.53
1981 2332 6.543465 TCATGTAAACTCATTCCTTGCTATGG 59.457 38.462 0.00 0.00 0.00 2.74
2028 2380 6.892658 AGTAGCTACCTCATGACTCATAAG 57.107 41.667 20.31 0.00 0.00 1.73
2124 2480 5.425539 AGGCAAGAGAAGGTTATGTAGCTTA 59.574 40.000 0.00 0.00 44.30 3.09
2128 2484 5.091261 ACAGGCAAGAGAAGGTTATGTAG 57.909 43.478 0.00 0.00 0.00 2.74
2140 2496 2.457366 ACGGACTTTACAGGCAAGAG 57.543 50.000 0.00 0.00 0.00 2.85
2288 5275 2.157738 GATCCAATGGATGTGCCTAGC 58.842 52.381 21.01 0.00 43.27 3.42
2342 5329 8.767085 CACATTAGCACATCAAAGAAAACAATT 58.233 29.630 0.00 0.00 0.00 2.32
2348 5335 5.241285 TCAGCACATTAGCACATCAAAGAAA 59.759 36.000 0.00 0.00 36.85 2.52
2363 5350 5.536161 ACCTGTTGAATTACTTCAGCACATT 59.464 36.000 8.04 0.00 44.54 2.71
2364 5351 5.072741 ACCTGTTGAATTACTTCAGCACAT 58.927 37.500 8.04 0.00 44.54 3.21
2365 5352 4.460263 ACCTGTTGAATTACTTCAGCACA 58.540 39.130 8.04 4.67 44.54 4.57
2366 5353 6.426937 TCTTACCTGTTGAATTACTTCAGCAC 59.573 38.462 8.04 0.53 44.54 4.40
2367 5354 6.530120 TCTTACCTGTTGAATTACTTCAGCA 58.470 36.000 11.02 11.02 46.38 4.41
2368 5355 7.361286 CCTTCTTACCTGTTGAATTACTTCAGC 60.361 40.741 3.17 3.17 42.19 4.26
2369 5356 7.661847 ACCTTCTTACCTGTTGAATTACTTCAG 59.338 37.037 0.00 0.00 42.19 3.02
2370 5357 7.514721 ACCTTCTTACCTGTTGAATTACTTCA 58.485 34.615 0.00 0.00 39.62 3.02
2371 5358 7.878644 AGACCTTCTTACCTGTTGAATTACTTC 59.121 37.037 0.00 0.00 0.00 3.01
2372 5359 7.746703 AGACCTTCTTACCTGTTGAATTACTT 58.253 34.615 0.00 0.00 0.00 2.24
2524 5522 3.311322 ACACAAACACTGTATTCACCACG 59.689 43.478 0.00 0.00 36.10 4.94
2557 5576 2.231215 ACGGAGAACTCTATGCATGC 57.769 50.000 11.82 11.82 0.00 4.06
2869 5911 1.811266 CCCGGTGAGAACTGCATCG 60.811 63.158 0.00 0.00 39.45 3.84
2988 6031 5.059833 CCTGGATTAGGTATTCAGAAGCAC 58.940 45.833 0.00 0.00 41.76 4.40
3081 6169 3.032017 ACCACACATTGTCGAAGAGAG 57.968 47.619 0.00 0.00 36.95 3.20
3300 6396 4.503991 GGAGGTTAAGTGGATCATGGCTAG 60.504 50.000 0.00 0.00 0.00 3.42
3302 6398 2.173569 GGAGGTTAAGTGGATCATGGCT 59.826 50.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.