Multiple sequence alignment - TraesCS4D01G228800

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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 TraesCS4D01G228800 chr4D 100.000 2941 0 0 1 2941 388251821 388248881 0.000000e+00 5432
1 TraesCS4D01G228800 chr4A 94.633 2944 152 5 1 2941 69512092 69509152 0.000000e+00 4556
2 TraesCS4D01G228800 chr4A 93.954 2944 172 5 1 2941 69524795 69521855 0.000000e+00 4446
3 TraesCS4D01G228800 chr4B 95.241 1597 74 2 910 2506 476571614 476570020 0.000000e+00 2527
4 TraesCS4D01G228800 chr4B 89.323 871 88 5 1 871 476572480 476571615 0.000000e+00 1088
5 TraesCS4D01G228800 chr4B 96.154 130 5 0 2812 2941 476570017 476569888 2.300000e-51 213
6 TraesCS4D01G228800 chr3D 89.695 1572 135 7 947 2506 78096968 78098524 0.000000e+00 1980
7 TraesCS4D01G228800 chr3D 89.249 1572 141 10 947 2506 77999275 78000830 0.000000e+00 1941
8 TraesCS4D01G228800 chr3A 90.334 1438 120 9 956 2379 91285685 91284253 0.000000e+00 1868
9 TraesCS4D01G228800 chr7D 91.170 1359 95 10 910 2255 177169127 177170473 0.000000e+00 1821
10 TraesCS4D01G228800 chr7D 96.764 309 9 1 2506 2813 381970753 381970445 5.620000e-142 514
11 TraesCS4D01G228800 chr7D 96.753 308 10 0 2506 2813 382053091 382053398 5.620000e-142 514
12 TraesCS4D01G228800 chr7A 90.401 1323 113 4 947 2256 181169024 181170345 0.000000e+00 1727
13 TraesCS4D01G228800 chr7A 90.166 1322 116 5 947 2255 181014945 181016265 0.000000e+00 1709
14 TraesCS4D01G228800 chr7A 90.098 1323 116 7 947 2255 181050507 181051828 0.000000e+00 1703
15 TraesCS4D01G228800 chr7A 77.273 572 108 17 100 658 681739035 681738473 1.700000e-82 316
16 TraesCS4D01G228800 chr7A 74.068 617 122 31 65 659 21615800 21616400 4.940000e-53 219
17 TraesCS4D01G228800 chr2B 96.785 311 9 1 2504 2813 112844208 112844518 4.350000e-143 518
18 TraesCS4D01G228800 chr7B 96.764 309 9 1 2506 2813 742992453 742992761 5.620000e-142 514
19 TraesCS4D01G228800 chr6D 96.764 309 9 1 2506 2813 124520535 124520843 5.620000e-142 514
20 TraesCS4D01G228800 chr5A 96.753 308 10 0 2506 2813 238819796 238819489 5.620000e-142 514
21 TraesCS4D01G228800 chr1A 96.764 309 9 1 2506 2813 498688220 498687912 5.620000e-142 514
22 TraesCS4D01G228800 chr1A 74.637 619 116 33 65 659 557866244 557865643 4.900000e-58 235
23 TraesCS4D01G228800 chr1B 77.720 386 73 10 287 663 38589177 38588796 1.060000e-54 224
24 TraesCS4D01G228800 chr2D 77.638 398 64 23 287 669 5432674 5432287 4.940000e-53 219
25 TraesCS4D01G228800 chr6B 77.387 398 66 19 286 669 571760589 571760976 6.380000e-52 215
26 TraesCS4D01G228800 chr3B 89.062 128 14 0 2813 2940 124118854 124118727 3.030000e-35 159


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 TraesCS4D01G228800 chr4D 388248881 388251821 2940 True 5432 5432 100.000000 1 2941 1 chr4D.!!$R1 2940
1 TraesCS4D01G228800 chr4A 69509152 69512092 2940 True 4556 4556 94.633000 1 2941 1 chr4A.!!$R1 2940
2 TraesCS4D01G228800 chr4A 69521855 69524795 2940 True 4446 4446 93.954000 1 2941 1 chr4A.!!$R2 2940
3 TraesCS4D01G228800 chr4B 476569888 476572480 2592 True 1276 2527 93.572667 1 2941 3 chr4B.!!$R1 2940
4 TraesCS4D01G228800 chr3D 78096968 78098524 1556 False 1980 1980 89.695000 947 2506 1 chr3D.!!$F2 1559
5 TraesCS4D01G228800 chr3D 77999275 78000830 1555 False 1941 1941 89.249000 947 2506 1 chr3D.!!$F1 1559
6 TraesCS4D01G228800 chr3A 91284253 91285685 1432 True 1868 1868 90.334000 956 2379 1 chr3A.!!$R1 1423
7 TraesCS4D01G228800 chr7D 177169127 177170473 1346 False 1821 1821 91.170000 910 2255 1 chr7D.!!$F1 1345
8 TraesCS4D01G228800 chr7A 181169024 181170345 1321 False 1727 1727 90.401000 947 2256 1 chr7A.!!$F4 1309
9 TraesCS4D01G228800 chr7A 181014945 181016265 1320 False 1709 1709 90.166000 947 2255 1 chr7A.!!$F2 1308
10 TraesCS4D01G228800 chr7A 181050507 181051828 1321 False 1703 1703 90.098000 947 2255 1 chr7A.!!$F3 1308
11 TraesCS4D01G228800 chr7A 681738473 681739035 562 True 316 316 77.273000 100 658 1 chr7A.!!$R1 558
12 TraesCS4D01G228800 chr7A 21615800 21616400 600 False 219 219 74.068000 65 659 1 chr7A.!!$F1 594
13 TraesCS4D01G228800 chr1A 557865643 557866244 601 True 235 235 74.637000 65 659 1 chr1A.!!$R2 594

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
283 291 0.24912 TGGCGACGAGGTTGATTCAT 59.751 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2115 0.179166 CATACACACGCAACATGGCC 60.179 55.0 0.0 0.0 0.0 5.36 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
20 21 1.133809 CCTTGGAGGTGGAAGTGGGA 61.134 60.000 0.00 0.00 0.00 4.37
25 26 3.948719 GGTGGAAGTGGGACGGCA 61.949 66.667 0.00 0.00 0.00 5.69
33 34 2.118732 TGGGACGGCAGTGGTCTA 59.881 61.111 0.00 0.00 34.82 2.59
61 62 2.661537 CGACGTTGGCAGCTGACA 60.662 61.111 21.20 21.20 0.00 3.58
141 144 1.876416 GCTCCGTTTGTCCTAGTTGCA 60.876 52.381 0.00 0.00 0.00 4.08
167 171 4.657502 TCGGTTTTCGCATCGACA 57.342 50.000 0.00 0.00 34.89 4.35
194 198 2.409984 TAGTCCCCTCCCACTTGGCA 62.410 60.000 0.00 0.00 0.00 4.92
211 215 1.374631 CAGCGTTGCTACTGCCTCA 60.375 57.895 10.27 0.00 36.40 3.86
283 291 0.249120 TGGCGACGAGGTTGATTCAT 59.751 50.000 0.00 0.00 0.00 2.57
314 323 2.342650 GCATGTTGGTGGACGGCAT 61.343 57.895 0.00 0.00 0.00 4.40
337 347 1.101635 TAGTGGAGCACTCGGATCGG 61.102 60.000 0.00 0.00 41.21 4.18
506 518 1.871418 AGGACTCATCTAGGCAGCAA 58.129 50.000 0.00 0.00 33.25 3.91
511 523 0.894835 TCATCTAGGCAGCAACGTCA 59.105 50.000 0.00 0.00 0.00 4.35
588 603 2.187946 GCGGTGGGACATCTCCAG 59.812 66.667 0.00 0.00 44.52 3.86
870 885 7.342799 ACATCTGACTAATGTGGGCATAAAAAT 59.657 33.333 0.00 0.00 36.04 1.82
899 914 8.594881 AATGTACTTTGACTTGTAGAGTTCTG 57.405 34.615 0.00 0.00 39.19 3.02
908 923 1.204704 TGTAGAGTTCTGCATGACGGG 59.795 52.381 0.00 0.00 33.67 5.28
1069 1096 1.333619 CAAGCACACACAACCACCTAC 59.666 52.381 0.00 0.00 0.00 3.18
1102 1129 5.153675 ACCATAGTGATGAGATGGATGACT 58.846 41.667 7.12 0.00 42.41 3.41
1519 1547 8.642432 GGGTCAGCTATGATATGCAGTTATATA 58.358 37.037 0.00 0.00 37.87 0.86
1642 1671 7.146648 GGTATCATACTCTGCTAACCACTAAC 58.853 42.308 0.00 0.00 0.00 2.34
2023 2115 6.064060 TGGTTCCTCATCTAGCAAATAATGG 58.936 40.000 0.00 0.00 0.00 3.16
2138 2231 0.473755 ATCATGGCCGCAATGTAGGA 59.526 50.000 7.64 0.00 0.00 2.94
2255 2348 8.474710 AGCAGATGCCAATAAATAGAGAAAAT 57.525 30.769 0.14 0.00 43.38 1.82
2547 2642 6.825213 TCGTTACTACTAGCAATGACTTCCTA 59.175 38.462 0.00 0.00 0.00 2.94
2639 2734 6.134061 TCATATCTGTAAGTTCGTTCGATCG 58.866 40.000 9.36 9.36 33.76 3.69
2660 2755 4.698304 TCGTTGACAAGGTTCAAAGAAAGT 59.302 37.500 7.69 0.00 39.89 2.66
2676 2771 0.540365 AAGTGTGGGCCATTCACCAG 60.540 55.000 20.21 0.00 37.45 4.00
2698 2793 3.394719 GAAGGCTAAAAGCGAGATAGGG 58.605 50.000 0.00 0.00 43.62 3.53
2705 2800 6.462067 GGCTAAAAGCGAGATAGGGTTTACTA 60.462 42.308 0.00 0.00 43.62 1.82
2714 2809 7.494952 GCGAGATAGGGTTTACTAGACATTTTT 59.505 37.037 0.00 0.00 0.00 1.94
2739 2834 1.535462 ACAAAGGCGAAGACAATTCCG 59.465 47.619 0.00 0.00 39.87 4.30
2740 2835 0.521735 AAAGGCGAAGACAATTCCGC 59.478 50.000 0.00 0.00 39.87 5.54
2772 2867 6.030228 CAGCCGATTCTCCAAAATTTAAGAC 58.970 40.000 0.00 0.00 0.00 3.01
2794 2889 7.453393 AGACAATTATCCTCACTCAAACTTCA 58.547 34.615 0.00 0.00 0.00 3.02
2802 2897 6.180472 TCCTCACTCAAACTTCAAAAAGTCT 58.820 36.000 0.00 0.00 45.07 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.031417 GCCCATAGACCACTGCCGT 62.031 63.158 0.00 0.00 0.00 5.68
25 26 3.849951 CGCCGCCCATAGACCACT 61.850 66.667 0.00 0.00 0.00 4.00
125 128 2.210116 ACACTGCAACTAGGACAAACG 58.790 47.619 0.00 0.00 0.00 3.60
141 144 1.300388 CGAAAACCGACCGGACACT 60.300 57.895 16.07 0.00 41.76 3.55
194 198 1.079543 CTGAGGCAGTAGCAACGCT 60.080 57.895 0.00 0.00 44.61 5.07
203 207 1.696097 AACAACGGACCTGAGGCAGT 61.696 55.000 0.00 0.00 0.00 4.40
211 215 0.685660 GAAGAGGGAACAACGGACCT 59.314 55.000 0.00 0.00 35.67 3.85
314 323 1.847328 TCCGAGTGCTCCACTAATCA 58.153 50.000 0.00 0.00 45.44 2.57
337 347 0.037734 AAAATCCTCACCACCCCGAC 59.962 55.000 0.00 0.00 0.00 4.79
407 417 1.738099 GGAACGACAGCGCTCACAT 60.738 57.895 7.13 0.00 42.48 3.21
494 506 2.283298 CAATGACGTTGCTGCCTAGAT 58.717 47.619 0.00 0.00 0.00 1.98
506 518 2.368875 AGAAGGAAGGTGACAATGACGT 59.631 45.455 0.00 0.00 0.00 4.34
689 704 2.346803 TCTGGCGCTGATTACTTCAAC 58.653 47.619 7.64 0.00 32.78 3.18
899 914 2.365582 ACATAAAAGGACCCGTCATGC 58.634 47.619 0.00 0.00 0.00 4.06
908 923 6.798476 GCAGTTAAAACCGTACATAAAAGGAC 59.202 38.462 0.00 0.00 0.00 3.85
1069 1096 2.768253 TCACTATGGTTGTGCTGGAG 57.232 50.000 0.00 0.00 35.58 3.86
1102 1129 2.362397 CGATAGTAGAGGCTCCAAGCAA 59.638 50.000 11.71 0.00 44.75 3.91
1415 1442 3.094484 TGGAACCAAAACTTGACCTGT 57.906 42.857 0.00 0.00 0.00 4.00
1674 1703 0.393402 CACTGCTGCATCTTGCCCTA 60.393 55.000 1.31 0.00 44.23 3.53
1819 1848 4.141801 CGGTGTATAGGAATTGGAACTCCA 60.142 45.833 0.00 0.00 45.94 3.86
1831 1860 4.705507 GCCTCATATTCTCGGTGTATAGGA 59.294 45.833 0.00 0.00 0.00 2.94
2023 2115 0.179166 CATACACACGCAACATGGCC 60.179 55.000 0.00 0.00 0.00 5.36
2127 2220 1.409064 TCCTACTGCTCCTACATTGCG 59.591 52.381 0.00 0.00 0.00 4.85
2138 2231 1.333636 AAGCCGCTCATCCTACTGCT 61.334 55.000 0.00 0.00 0.00 4.24
2255 2348 6.214191 TCACCTTGCAACTTTTATGTTTGA 57.786 33.333 0.00 0.00 0.00 2.69
2483 2578 0.467384 CCTCCTCATCATGCTCCGTT 59.533 55.000 0.00 0.00 0.00 4.44
2639 2734 5.572896 CACACTTTCTTTGAACCTTGTCAAC 59.427 40.000 0.00 0.00 37.24 3.18
2660 2755 1.724148 TTCCTGGTGAATGGCCCACA 61.724 55.000 12.01 1.62 36.31 4.17
2676 2771 3.394719 CCTATCTCGCTTTTAGCCTTCC 58.605 50.000 0.00 0.00 38.18 3.46
2714 2809 5.048991 GGAATTGTCTTCGCCTTTGTAAGAA 60.049 40.000 0.00 0.00 31.41 2.52
2715 2810 4.454504 GGAATTGTCTTCGCCTTTGTAAGA 59.545 41.667 0.00 0.00 0.00 2.10
2748 2843 6.030228 GTCTTAAATTTTGGAGAATCGGCTG 58.970 40.000 0.00 0.00 34.37 4.85
2772 2867 9.748708 TTTTTGAAGTTTGAGTGAGGATAATTG 57.251 29.630 0.00 0.00 0.00 2.32
2807 2902 7.786030 AGTATTGCACTTCTTATAGCTCAGAA 58.214 34.615 0.00 0.00 31.59 3.02
2809 2904 7.042187 CCAAGTATTGCACTTCTTATAGCTCAG 60.042 40.741 0.00 0.00 44.48 3.35


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

AutoCloner maintained by Alex Coulton.