Multiple sequence alignment - TraesCS5D01G213100

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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 TraesCS5D01G213100 chr5D 100.000 2688 0 0 1 2688 322185344 322182657 0.000000e+00 4964.0
1 TraesCS5D01G213100 chr5B 93.132 2446 91 32 305 2688 373530824 373528394 0.000000e+00 3515.0
2 TraesCS5D01G213100 chr5A 88.624 2180 156 46 1 2101 417332784 417330618 0.000000e+00 2567.0
3 TraesCS5D01G213100 chr7B 97.500 40 1 0 2130 2169 202113032 202113071 4.800000e-08 69.4


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 TraesCS5D01G213100 chr5D 322182657 322185344 2687 True 4964 4964 100.000 1 2688 1 chr5D.!!$R1 2687
1 TraesCS5D01G213100 chr5B 373528394 373530824 2430 True 3515 3515 93.132 305 2688 1 chr5B.!!$R1 2383
2 TraesCS5D01G213100 chr5A 417330618 417332784 2166 True 2567 2567 88.624 1 2101 1 chr5A.!!$R1 2100

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
605 640 0.408309 TTTCCAGAGACGGAGGGAGA 59.592 55.0 0.0 0.0 36.12 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1781 0.236711 GATGTCCATGCGTATGCTGC 59.763 55.0 8.12 0.0 43.34 5.25 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
23 24 6.616774 AATGGTAAATGTTTTGCCTTGTTG 57.383 33.333 8.28 0.00 0.00 3.33
64 75 5.715434 AATACGTTTTGTAGTTGGGCAAT 57.285 34.783 0.00 0.00 36.25 3.56
126 137 7.476540 AAAACTTGGTAGGAAAGACTTTGTT 57.523 32.000 4.85 0.00 0.00 2.83
132 143 2.039418 AGGAAAGACTTTGTTTGGGCC 58.961 47.619 4.85 0.00 0.00 5.80
138 149 1.677052 GACTTTGTTTGGGCCGTTGTA 59.323 47.619 0.00 0.00 0.00 2.41
142 154 1.816074 TGTTTGGGCCGTTGTATCTC 58.184 50.000 0.00 0.00 0.00 2.75
179 191 3.228749 GTTGTGTCTTGCGTGAATGATG 58.771 45.455 0.00 0.00 0.00 3.07
180 192 1.197492 TGTGTCTTGCGTGAATGATGC 59.803 47.619 0.00 0.00 37.07 3.91
181 193 1.197492 GTGTCTTGCGTGAATGATGCA 59.803 47.619 0.00 0.00 45.27 3.96
205 217 7.010091 GCACAACTGCTTTTGTAAAGTAACAAT 59.990 33.333 3.57 0.00 40.63 2.71
206 218 8.320295 CACAACTGCTTTTGTAAAGTAACAATG 58.680 33.333 3.57 0.00 39.04 2.82
232 244 7.414540 GCGAGATCCAAATGATTCTAAACTTGT 60.415 37.037 0.00 0.00 32.41 3.16
238 250 7.027161 CCAAATGATTCTAAACTTGTTACGGG 58.973 38.462 0.00 0.00 0.00 5.28
249 261 3.506844 ACTTGTTACGGGTGTGTTTTGTT 59.493 39.130 0.00 0.00 0.00 2.83
250 262 4.022155 ACTTGTTACGGGTGTGTTTTGTTT 60.022 37.500 0.00 0.00 0.00 2.83
265 277 2.700722 TGTTTGTGACACTAGCACCA 57.299 45.000 7.20 0.00 35.43 4.17
269 281 4.102649 GTTTGTGACACTAGCACCAAAAC 58.897 43.478 7.20 2.99 35.43 2.43
280 292 2.695147 AGCACCAAAACCCAAAGAGAAG 59.305 45.455 0.00 0.00 0.00 2.85
281 293 2.224042 GCACCAAAACCCAAAGAGAAGG 60.224 50.000 0.00 0.00 0.00 3.46
286 298 5.076873 CCAAAACCCAAAGAGAAGGTCATA 58.923 41.667 0.00 0.00 32.00 2.15
287 299 5.538433 CCAAAACCCAAAGAGAAGGTCATAA 59.462 40.000 0.00 0.00 32.00 1.90
288 300 6.211384 CCAAAACCCAAAGAGAAGGTCATAAT 59.789 38.462 0.00 0.00 32.00 1.28
527 562 8.133024 TCAGATTGTAATTGCTAATGGGTTTT 57.867 30.769 0.00 0.00 0.00 2.43
605 640 0.408309 TTTCCAGAGACGGAGGGAGA 59.592 55.000 0.00 0.00 36.12 3.71
715 754 2.884012 CCAAATGTGCCAGTAACTCACA 59.116 45.455 0.00 0.00 43.72 3.58
967 1027 2.840651 ACCATCACCTTGTCTTCCCTAG 59.159 50.000 0.00 0.00 0.00 3.02
968 1028 2.420687 CCATCACCTTGTCTTCCCTAGC 60.421 54.545 0.00 0.00 0.00 3.42
969 1029 2.327325 TCACCTTGTCTTCCCTAGCT 57.673 50.000 0.00 0.00 0.00 3.32
970 1030 3.468071 TCACCTTGTCTTCCCTAGCTA 57.532 47.619 0.00 0.00 0.00 3.32
971 1031 3.097614 TCACCTTGTCTTCCCTAGCTAC 58.902 50.000 0.00 0.00 0.00 3.58
972 1032 3.100671 CACCTTGTCTTCCCTAGCTACT 58.899 50.000 0.00 0.00 0.00 2.57
973 1033 3.515901 CACCTTGTCTTCCCTAGCTACTT 59.484 47.826 0.00 0.00 0.00 2.24
974 1034 3.515901 ACCTTGTCTTCCCTAGCTACTTG 59.484 47.826 0.00 0.00 0.00 3.16
1099 1159 3.136123 CGACGACGGGGAAGGCTA 61.136 66.667 0.00 0.00 35.72 3.93
1288 1363 3.308595 GTCATGTCACTCACACAACGAAA 59.691 43.478 0.00 0.00 38.04 3.46
1291 1366 5.755861 TCATGTCACTCACACAACGAAATTA 59.244 36.000 0.00 0.00 38.04 1.40
1504 1579 2.970639 GCTATCGCCAGCGGGATA 59.029 61.111 7.23 2.62 41.56 2.59
1706 1781 7.545362 AAGTAGAACTACTGCTTGCATAATG 57.455 36.000 14.07 0.00 46.63 1.90
1707 1782 4.889832 AGAACTACTGCTTGCATAATGC 57.110 40.909 0.00 0.00 45.29 3.56
1784 1861 4.387026 TTGTCCAAGAGACCCATGAAAT 57.613 40.909 0.00 0.00 45.68 2.17
1787 1864 3.871594 GTCCAAGAGACCCATGAAATACG 59.128 47.826 0.00 0.00 39.84 3.06
1963 2064 1.520666 CCCACCCCTATGTCACGTC 59.479 63.158 0.00 0.00 0.00 4.34
2127 2233 0.180406 AGCTTTACCATGGGCTACGG 59.820 55.000 18.09 2.12 32.94 4.02
2156 2262 2.039137 GGTCGGGGTCTTCCTCCT 59.961 66.667 0.00 0.00 35.33 3.69
2253 2359 3.525862 AGGAACTTCCTTCATCTCCACT 58.474 45.455 4.29 0.00 46.91 4.00
2298 2404 1.071699 ACAAGAGTTGCACGGTACCAT 59.928 47.619 13.54 0.00 0.00 3.55
2388 2500 6.509418 TTACAGAAATGTATTGCAAGGGTC 57.491 37.500 4.94 0.00 0.00 4.46
2422 2534 7.976135 AGCTACCTTTATCATGACATTCATC 57.024 36.000 0.00 0.00 34.28 2.92
2439 2551 8.809159 ACATTCATCTATAGACAATCGAACAG 57.191 34.615 4.10 3.49 0.00 3.16
2560 2672 6.830114 ATGCTTATGTCTAGTTTAGTTCGC 57.170 37.500 0.00 0.00 0.00 4.70
2570 2682 1.069227 GTTTAGTTCGCTTGGTGCAGG 60.069 52.381 0.00 0.00 43.06 4.85
2576 2688 1.666553 CGCTTGGTGCAGGACGTAA 60.667 57.895 0.00 0.00 43.06 3.18
2614 2726 2.618794 CTCCAGATCAATAGCCCTCCT 58.381 52.381 0.00 0.00 0.00 3.69
2679 2791 4.443978 GGGATTCCCATCTCTTTGATCA 57.556 45.455 17.36 0.00 44.65 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.873952 TGCAACAAGGCAAAACATTTACC 59.126 39.130 0.00 0.00 41.65 2.85
34 35 8.351461 CCCAACTACAAAACGTATTTAAGGAAA 58.649 33.333 0.00 0.00 0.00 3.13
47 50 9.483916 AGTTAATTAATTGCCCAACTACAAAAC 57.516 29.630 11.05 2.81 0.00 2.43
56 67 5.241662 GTGCCAAGTTAATTAATTGCCCAA 58.758 37.500 11.05 0.00 0.00 4.12
64 75 8.738645 AAAAACATTGGTGCCAAGTTAATTAA 57.261 26.923 9.65 0.00 39.47 1.40
116 127 1.136110 CAACGGCCCAAACAAAGTCTT 59.864 47.619 0.00 0.00 0.00 3.01
119 130 1.765230 TACAACGGCCCAAACAAAGT 58.235 45.000 0.00 0.00 0.00 2.66
126 137 1.448893 GCGAGATACAACGGCCCAA 60.449 57.895 0.00 0.00 0.00 4.12
132 143 3.673338 TCAAACTCTTGCGAGATACAACG 59.327 43.478 3.51 0.00 39.74 4.10
138 149 2.564947 ACCTCTCAAACTCTTGCGAGAT 59.435 45.455 3.51 0.00 43.99 2.75
142 154 2.032549 CACAACCTCTCAAACTCTTGCG 60.033 50.000 0.00 0.00 32.14 4.85
154 166 0.464036 TCACGCAAGACACAACCTCT 59.536 50.000 0.00 0.00 43.62 3.69
179 191 6.309251 TTGTTACTTTACAAAAGCAGTTGTGC 59.691 34.615 13.58 0.00 41.75 4.57
180 192 7.804614 TTGTTACTTTACAAAAGCAGTTGTG 57.195 32.000 13.58 0.00 41.75 3.33
181 193 7.010091 GCATTGTTACTTTACAAAAGCAGTTGT 59.990 33.333 9.62 9.62 43.95 3.32
205 217 6.115446 AGTTTAGAATCATTTGGATCTCGCA 58.885 36.000 0.00 0.00 34.28 5.10
206 218 6.610741 AGTTTAGAATCATTTGGATCTCGC 57.389 37.500 0.00 0.00 34.28 5.03
232 244 3.504906 TCACAAACAAAACACACCCGTAA 59.495 39.130 0.00 0.00 0.00 3.18
234 246 1.887198 TCACAAACAAAACACACCCGT 59.113 42.857 0.00 0.00 0.00 5.28
235 247 2.255316 GTCACAAACAAAACACACCCG 58.745 47.619 0.00 0.00 0.00 5.28
238 250 4.557301 GCTAGTGTCACAAACAAAACACAC 59.443 41.667 5.62 0.00 43.43 3.82
249 261 2.685897 GGTTTTGGTGCTAGTGTCACAA 59.314 45.455 5.62 0.00 36.22 3.33
250 262 2.294074 GGTTTTGGTGCTAGTGTCACA 58.706 47.619 5.62 0.00 36.22 3.58
265 277 7.855784 AATTATGACCTTCTCTTTGGGTTTT 57.144 32.000 0.00 0.00 33.01 2.43
299 311 4.843728 TCTTTGTGGTAACCCATGATCTC 58.156 43.478 0.00 0.00 44.35 2.75
320 332 4.636648 AGTACATCATATCGACCTCGGATC 59.363 45.833 0.00 0.00 40.29 3.36
403 417 8.220755 TGCTACAAACTTCAAACTTAGTCAAT 57.779 30.769 0.00 0.00 0.00 2.57
516 551 7.519032 TCAAGTTTGTAGGAAAACCCATTAG 57.481 36.000 0.00 0.00 40.26 1.73
627 662 3.937814 ACAAGACGGTGCTCAATCATTA 58.062 40.909 0.00 0.00 0.00 1.90
704 743 5.033507 CAGATCGATGAGTGTGAGTTACTG 58.966 45.833 0.54 0.00 0.00 2.74
715 754 5.511031 CCTCATTTGATCCAGATCGATGAGT 60.511 44.000 28.97 8.63 46.24 3.41
761 805 4.766891 AGAATATGACAGGGTGGTGTTTTG 59.233 41.667 0.00 0.00 0.00 2.44
842 887 0.743345 GGCGACGCAGGGAATAAAGT 60.743 55.000 23.09 0.00 0.00 2.66
967 1027 6.474102 GCTTGTCTGTAGTAAGATCAAGTAGC 59.526 42.308 0.00 0.00 37.48 3.58
968 1028 7.539436 TGCTTGTCTGTAGTAAGATCAAGTAG 58.461 38.462 0.00 0.00 37.48 2.57
969 1029 7.462571 TGCTTGTCTGTAGTAAGATCAAGTA 57.537 36.000 0.00 9.07 37.48 2.24
970 1030 6.346477 TGCTTGTCTGTAGTAAGATCAAGT 57.654 37.500 0.00 0.00 37.48 3.16
971 1031 5.290643 GCTGCTTGTCTGTAGTAAGATCAAG 59.709 44.000 0.00 0.00 37.81 3.02
972 1032 5.047021 AGCTGCTTGTCTGTAGTAAGATCAA 60.047 40.000 0.00 0.00 0.00 2.57
973 1033 4.464244 AGCTGCTTGTCTGTAGTAAGATCA 59.536 41.667 0.00 0.00 0.00 2.92
974 1034 4.803088 CAGCTGCTTGTCTGTAGTAAGATC 59.197 45.833 0.00 0.00 0.00 2.75
1140 1200 2.280797 GCACAGCACACGGAGGAA 60.281 61.111 0.00 0.00 0.00 3.36
1218 1278 6.469782 AATAAAGTTATCTTACCGACGGGA 57.530 37.500 20.00 6.83 32.92 5.14
1288 1363 3.629398 GCAGCAGAGCTAACCAACATAAT 59.371 43.478 0.00 0.00 36.40 1.28
1291 1366 1.271543 TGCAGCAGAGCTAACCAACAT 60.272 47.619 0.00 0.00 36.40 2.71
1297 1372 1.746991 GGGGTGCAGCAGAGCTAAC 60.747 63.158 19.06 0.00 36.40 2.34
1490 1565 1.480212 TTGGATATCCCGCTGGCGAT 61.480 55.000 19.34 5.54 42.83 4.58
1503 1578 4.215742 CGGCCGCGTCCTTGGATA 62.216 66.667 14.67 0.00 0.00 2.59
1706 1781 0.236711 GATGTCCATGCGTATGCTGC 59.763 55.000 8.12 0.00 43.34 5.25
1707 1782 1.797046 GAGATGTCCATGCGTATGCTG 59.203 52.381 8.12 4.13 43.34 4.41
1784 1861 8.308931 AGGAACAAAAGTACATATGAAGACGTA 58.691 33.333 10.38 0.00 0.00 3.57
1787 1864 9.654663 AGTAGGAACAAAAGTACATATGAAGAC 57.345 33.333 10.38 4.50 0.00 3.01
1900 1977 9.469807 CACAACAAATACCTTTTTACATAGCAA 57.530 29.630 0.00 0.00 0.00 3.91
2127 2233 2.202987 CCGACCTCTGCATCTGGC 60.203 66.667 0.00 0.00 45.13 4.85
2183 2289 1.410882 CTTCCTCGTGAATCCTCTCCC 59.589 57.143 0.00 0.00 31.06 4.30
2248 2354 5.397360 TCATCTATGGCTATTGAGAGTGGA 58.603 41.667 0.43 0.00 0.00 4.02
2253 2359 8.911965 GTGATATCTCATCTATGGCTATTGAGA 58.088 37.037 13.38 13.38 44.83 3.27
2360 2466 6.322201 CCTTGCAATACATTTCTGTAATCCCT 59.678 38.462 0.00 0.00 41.09 4.20
2495 2607 6.920758 GCAATGTGTTTGGTTATGTACTTTGA 59.079 34.615 0.00 0.00 35.75 2.69
2595 2707 2.803285 AGGAGGGCTATTGATCTGGA 57.197 50.000 0.00 0.00 0.00 3.86
2614 2726 1.436195 GCAATGTCCGGCAGCGAATA 61.436 55.000 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.