Multiple sequence alignment - TraesCS4B01G144000

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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 TraesCS4B01G144000 chr4B 100.000 5014 0 0 1 5014 192117150 192112137 0.000000e+00 9260.0
1 TraesCS4B01G144000 chr4D 94.959 5039 183 37 16 5013 128194471 128189463 0.000000e+00 7832.0
2 TraesCS4B01G144000 chr4D 74.631 406 53 35 4456 4858 477532047 477531689 3.150000e-27 134.0
3 TraesCS4B01G144000 chr4A 96.763 3769 75 18 816 4554 439006793 439010544 0.000000e+00 6240.0
4 TraesCS4B01G144000 chr4A 89.314 758 71 10 5 756 439005880 439006633 0.000000e+00 942.0
5 TraesCS4B01G144000 chr5B 76.817 509 89 20 3029 3527 116893634 116893145 4.980000e-65 259.0
6 TraesCS4B01G144000 chr5B 90.476 126 9 3 998 1123 116896389 116896267 4.020000e-36 163.0
7 TraesCS4B01G144000 chr5A 76.817 509 89 21 3029 3527 110379485 110378996 4.980000e-65 259.0
8 TraesCS4B01G144000 chr5A 90.476 126 10 2 998 1123 110382690 110382567 1.120000e-36 165.0
9 TraesCS4B01G144000 chr5D 76.424 509 91 20 3029 3527 107582702 107582213 1.080000e-61 248.0
10 TraesCS4B01G144000 chr5D 93.269 104 7 0 998 1101 107585474 107585371 2.420000e-33 154.0
11 TraesCS4B01G144000 chr3A 76.630 184 31 10 4721 4899 46678419 46678243 1.920000e-14 91.6
12 TraesCS4B01G144000 chr3B 91.667 60 5 0 4282 4341 658062175 658062116 3.220000e-12 84.2
13 TraesCS4B01G144000 chr3B 81.034 116 13 8 4787 4899 727236842 727236733 3.220000e-12 84.2
14 TraesCS4B01G144000 chr7D 90.000 60 6 0 4282 4341 31395964 31396023 1.500000e-10 78.7


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 TraesCS4B01G144000 chr4B 192112137 192117150 5013 True 9260 9260 100.0000 1 5014 1 chr4B.!!$R1 5013
1 TraesCS4B01G144000 chr4D 128189463 128194471 5008 True 7832 7832 94.9590 16 5013 1 chr4D.!!$R1 4997
2 TraesCS4B01G144000 chr4A 439005880 439010544 4664 False 3591 6240 93.0385 5 4554 2 chr4A.!!$F1 4549
3 TraesCS4B01G144000 chr5B 116893145 116896389 3244 True 211 259 83.6465 998 3527 2 chr5B.!!$R1 2529
4 TraesCS4B01G144000 chr5A 110378996 110382690 3694 True 212 259 83.6465 998 3527 2 chr5A.!!$R1 2529
5 TraesCS4B01G144000 chr5D 107582213 107585474 3261 True 201 248 84.8465 998 3527 2 chr5D.!!$R1 2529

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
884 1003 0.179043 TGCAACCAAGGTCGTGCTAA 60.179 50.000 14.89 0.0 34.16 3.09 F
890 1009 1.204941 CCAAGGTCGTGCTAAGCTACT 59.795 52.381 0.00 0.0 0.00 2.57 F
2561 3324 0.393537 AGCTTTCTCGGCTTCCCATG 60.394 55.000 0.00 0.0 36.56 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2992 1.081892 CAGGTGTCATTGGCTTCTCG 58.918 55.000 0.0 0.0 0.00 4.04 R
2572 3335 2.620585 AGTCTGCAAAAGAGGAGCAAAC 59.379 45.455 0.0 0.0 37.89 2.93 R
4284 5774 2.035832 ACACAACAAACCCAATAGCAGC 59.964 45.455 0.0 0.0 0.00 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
18 19 3.088923 AGCACCCATGTAGTGACCT 57.911 52.632 15.32 3.23 37.42 3.85
135 136 3.069586 TGTCAAGGGATTGCGGATAGTAG 59.930 47.826 0.00 0.00 0.00 2.57
141 142 1.656095 GATTGCGGATAGTAGCGCATC 59.344 52.381 11.47 3.08 37.22 3.91
160 161 5.443824 CGCATCGATCTTTTCAATCTATCGG 60.444 44.000 0.00 0.00 39.79 4.18
162 163 5.201713 TCGATCTTTTCAATCTATCGGCT 57.798 39.130 0.00 0.00 39.79 5.52
220 222 6.058553 TCCATCAATCTTCTGAATCACTGT 57.941 37.500 0.00 0.00 0.00 3.55
255 258 4.729227 TGCGTAATCTTATGAGTGGACA 57.271 40.909 0.00 0.00 0.00 4.02
287 290 1.213296 GATAGGTTCAGGGCAGGGAA 58.787 55.000 0.00 0.00 0.00 3.97
320 323 4.920640 TCCCAAAATTTGCACGACTTTA 57.079 36.364 0.00 0.00 0.00 1.85
325 328 6.435428 CCAAAATTTGCACGACTTTAGTAGT 58.565 36.000 0.00 0.00 40.71 2.73
356 359 9.857656 ACATCATCCATATTAAGAGACACAAAT 57.142 29.630 0.00 0.00 0.00 2.32
399 402 6.933514 TTTTTAGGCCAGAGAATTCCAAAT 57.066 33.333 5.01 0.00 0.00 2.32
402 405 7.587037 TTTAGGCCAGAGAATTCCAAATATG 57.413 36.000 5.01 0.00 0.00 1.78
481 485 6.868339 TCAACATATCATCTGCGTATTGTAGG 59.132 38.462 0.00 0.00 0.00 3.18
495 499 5.350640 CGTATTGTAGGACTGGAAAAGGTTC 59.649 44.000 0.00 0.00 0.00 3.62
508 512 1.484038 AAGGTTCTTGGCAGTGCAAA 58.516 45.000 18.61 11.65 0.00 3.68
519 523 2.231964 GGCAGTGCAAAGGATGAATGAA 59.768 45.455 18.61 0.00 0.00 2.57
534 539 7.398047 AGGATGAATGAAAAGTCCATCATGAAA 59.602 33.333 0.00 0.00 36.44 2.69
561 566 2.210116 CTGCACAACCGTTGTAAGACT 58.790 47.619 16.44 0.00 43.23 3.24
562 567 1.937223 TGCACAACCGTTGTAAGACTG 59.063 47.619 16.44 4.93 43.23 3.51
563 568 1.937899 GCACAACCGTTGTAAGACTGT 59.062 47.619 16.44 0.00 43.23 3.55
566 571 4.339429 CACAACCGTTGTAAGACTGTTTG 58.661 43.478 16.44 0.00 43.23 2.93
575 580 6.846283 CGTTGTAAGACTGTTTGTGATTTCTC 59.154 38.462 0.00 0.00 0.00 2.87
692 698 7.257722 ACCAGTTTGTTGACAAATAGTTTCTG 58.742 34.615 11.96 12.10 46.12 3.02
693 699 7.122055 ACCAGTTTGTTGACAAATAGTTTCTGA 59.878 33.333 17.23 0.00 46.12 3.27
697 703 7.962934 TTGTTGACAAATAGTTTCTGAAACG 57.037 32.000 23.24 13.54 38.44 3.60
709 715 9.965824 ATAGTTTCTGAAACGATTTGATTGTTT 57.034 25.926 23.24 6.09 46.70 2.83
710 716 8.702163 AGTTTCTGAAACGATTTGATTGTTTT 57.298 26.923 23.24 2.59 44.68 2.43
711 717 9.796120 AGTTTCTGAAACGATTTGATTGTTTTA 57.204 25.926 23.24 3.77 44.68 1.52
745 751 7.251704 AGATTTTACATTCATAAGAGGTGCG 57.748 36.000 0.00 0.00 0.00 5.34
868 987 7.806409 AACACAAGACATTGCTATATATGCA 57.194 32.000 0.00 0.00 40.27 3.96
884 1003 0.179043 TGCAACCAAGGTCGTGCTAA 60.179 50.000 14.89 0.00 34.16 3.09
890 1009 1.204941 CCAAGGTCGTGCTAAGCTACT 59.795 52.381 0.00 0.00 0.00 2.57
1143 1262 7.445402 TGATCTGGAATTTCGAGAAGTTTTTCT 59.555 33.333 14.05 0.00 46.22 2.52
1387 1735 3.255149 GGAACTGTTCTTCGTGAGGTCTA 59.745 47.826 19.05 0.00 0.00 2.59
1644 2208 5.650266 TCTTTTGTTACTTTTGGAGTCTGCA 59.350 36.000 0.00 0.00 39.86 4.41
1754 2438 9.974980 TCTTAAATAATGGTTCTGGTTTGAAAC 57.025 29.630 0.00 0.00 34.47 2.78
1835 2544 6.767524 TGTTTACTGAAAGGTCACACAATT 57.232 33.333 0.00 0.00 39.30 2.32
2119 2842 2.821969 CTGCAAAGCTCCAATTACCACT 59.178 45.455 0.00 0.00 0.00 4.00
2269 2992 3.388345 AAGACAGTCTTTCTTCCGACC 57.612 47.619 10.27 0.00 31.57 4.79
2561 3324 0.393537 AGCTTTCTCGGCTTCCCATG 60.394 55.000 0.00 0.00 36.56 3.66
2572 3335 3.181497 CGGCTTCCCATGTTCACAATAAG 60.181 47.826 0.00 0.00 0.00 1.73
2754 3968 6.741992 TGATTCTCCATGTGATTGTTGTAC 57.258 37.500 0.00 0.00 0.00 2.90
2958 4180 2.172851 TTACCTAGGTTTGCACACGG 57.827 50.000 22.11 0.00 0.00 4.94
3175 4658 6.317391 GCCTGATTCTAAGTTAGCATCTGTTT 59.683 38.462 19.15 0.00 31.06 2.83
3203 4686 7.663081 CCAGAATTGGCTTGTATACATGACTAT 59.337 37.037 21.55 17.45 37.73 2.12
3357 4840 9.023967 GCATTCAAGATAACATTTTATGACACC 57.976 33.333 0.00 0.00 0.00 4.16
3371 4854 3.179443 TGACACCACTCTTCACTTCAC 57.821 47.619 0.00 0.00 0.00 3.18
3581 5071 9.930693 CTAGTGTTGTATTCTCCTTTTACTTCT 57.069 33.333 0.00 0.00 0.00 2.85
3762 5252 7.052873 GGTACTGTTGTAGTCAGTATCTCCTA 58.947 42.308 8.63 0.00 45.78 2.94
3763 5253 7.720515 GGTACTGTTGTAGTCAGTATCTCCTAT 59.279 40.741 8.63 0.00 45.78 2.57
3832 5322 7.873739 ATGAAAAATTCTTCATCGGTTTGTC 57.126 32.000 0.96 0.00 41.21 3.18
3850 5340 6.405397 GGTTTGTCCAACATAAAACACTCACT 60.405 38.462 0.00 0.00 37.07 3.41
4245 5735 1.553248 TCCGTAGCCTGTTACAAGCAT 59.447 47.619 8.73 0.00 0.00 3.79
4257 5747 5.549347 TGTTACAAGCATGGAATTGCAATT 58.451 33.333 24.33 24.33 45.23 2.32
4284 5774 2.768253 TTGGACTGCCTCATACACAG 57.232 50.000 0.00 0.00 37.45 3.66
4360 5850 3.326836 ACTTTCTAGAGAAGCTGCACC 57.673 47.619 1.02 0.00 35.21 5.01
4388 5878 2.496899 ATATGCCTCCTATTTGCCGG 57.503 50.000 0.00 0.00 0.00 6.13
4488 5978 0.101579 CACCGGTTTTGCGAAGGTTT 59.898 50.000 2.97 0.00 32.04 3.27
4579 6069 8.338986 TGTTTTGTTTTTCAGTTTTCCTTTGTC 58.661 29.630 0.00 0.00 0.00 3.18
4669 6159 9.898152 TTTTCTTCTTCTTCTTCTTCTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
4671 6161 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
4673 6163 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
4778 6276 9.596677 AAATCATGAACAATTTGTAAATTTGCG 57.403 25.926 0.00 0.00 39.95 4.85
4921 6441 4.061596 GGAACAATTTCCGGATTTGCAAA 58.938 39.130 21.45 15.44 42.20 3.68
4922 6442 4.694982 GGAACAATTTCCGGATTTGCAAAT 59.305 37.500 24.33 24.33 42.20 2.32
4926 6446 9.092876 GAACAATTTCCGGATTTGCAAATATTA 57.907 29.630 24.15 8.08 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.107654 GGAGGTCACTACATGGGTGC 60.108 60.000 13.83 9.97 34.97 5.01
18 19 3.737559 AAATGCAAGGAGGTACATGGA 57.262 42.857 0.00 0.00 0.00 3.41
118 119 0.603569 CGCTACTATCCGCAATCCCT 59.396 55.000 0.00 0.00 0.00 4.20
135 136 3.599046 AGATTGAAAAGATCGATGCGC 57.401 42.857 0.54 0.00 31.92 6.09
141 142 5.574830 CCTAGCCGATAGATTGAAAAGATCG 59.425 44.000 0.00 0.00 36.92 3.69
160 161 1.381872 TCTGGCCTCCTGTCCTAGC 60.382 63.158 3.32 0.00 0.00 3.42
162 163 0.339859 ATGTCTGGCCTCCTGTCCTA 59.660 55.000 3.32 0.00 0.00 2.94
255 258 2.579410 ACCTATCGTGTTTGCCCTTT 57.421 45.000 0.00 0.00 0.00 3.11
299 302 3.810310 AAAGTCGTGCAAATTTTGGGA 57.190 38.095 10.96 0.00 0.00 4.37
325 328 8.927411 TGTCTCTTAATATGGATGATGTTCTGA 58.073 33.333 0.00 0.00 0.00 3.27
328 331 8.893219 TGTGTCTCTTAATATGGATGATGTTC 57.107 34.615 0.00 0.00 0.00 3.18
481 485 2.294512 CTGCCAAGAACCTTTTCCAGTC 59.705 50.000 0.00 0.00 31.28 3.51
495 499 1.250328 TCATCCTTTGCACTGCCAAG 58.750 50.000 7.71 7.71 32.16 3.61
508 512 6.429151 TCATGATGGACTTTTCATTCATCCT 58.571 36.000 0.00 0.00 34.87 3.24
540 545 1.263217 GTCTTACAACGGTTGTGCAGG 59.737 52.381 31.05 16.03 45.03 4.85
548 553 3.864243 TCACAAACAGTCTTACAACGGT 58.136 40.909 0.00 0.00 0.00 4.83
551 556 7.693952 TGAGAAATCACAAACAGTCTTACAAC 58.306 34.615 0.00 0.00 0.00 3.32
552 557 7.857734 TGAGAAATCACAAACAGTCTTACAA 57.142 32.000 0.00 0.00 0.00 2.41
561 566 5.244402 AGAATGCCATGAGAAATCACAAACA 59.756 36.000 0.00 0.00 0.00 2.83
562 567 5.717119 AGAATGCCATGAGAAATCACAAAC 58.283 37.500 0.00 0.00 0.00 2.93
563 568 5.392272 CGAGAATGCCATGAGAAATCACAAA 60.392 40.000 0.00 0.00 0.00 2.83
566 571 3.873361 TCGAGAATGCCATGAGAAATCAC 59.127 43.478 0.00 0.00 0.00 3.06
575 580 5.936686 AATTGTATCTCGAGAATGCCATG 57.063 39.130 20.91 0.00 0.00 3.66
607 612 6.961359 TGACATTCGTGGTATTCTTAACAG 57.039 37.500 0.00 0.00 0.00 3.16
806 812 5.472137 GCAACCAACCAATGTAGAAAGAGTA 59.528 40.000 0.00 0.00 0.00 2.59
865 984 0.179043 TTAGCACGACCTTGGTTGCA 60.179 50.000 16.00 0.00 0.00 4.08
866 985 0.517316 CTTAGCACGACCTTGGTTGC 59.483 55.000 6.94 7.54 0.00 4.17
868 987 0.396811 AGCTTAGCACGACCTTGGTT 59.603 50.000 7.07 0.00 0.00 3.67
869 988 1.067071 GTAGCTTAGCACGACCTTGGT 60.067 52.381 7.07 0.00 0.00 3.67
871 990 2.263077 CAGTAGCTTAGCACGACCTTG 58.737 52.381 7.07 0.00 0.00 3.61
872 991 1.204941 CCAGTAGCTTAGCACGACCTT 59.795 52.381 7.07 0.00 0.00 3.50
873 992 0.818296 CCAGTAGCTTAGCACGACCT 59.182 55.000 7.07 0.00 0.00 3.85
884 1003 1.302832 GTGCTTGGTGCCAGTAGCT 60.303 57.895 13.93 0.00 44.23 3.32
1263 1398 2.227194 ACTGTTTCGGCCCTAAACTTG 58.773 47.619 22.33 18.01 37.64 3.16
1317 1536 4.160814 TGCAGATAAATTGCTTCTTGGCAT 59.839 37.500 0.00 0.00 42.09 4.40
1387 1735 2.501316 GCACCTTTGGCTTTATTCCCAT 59.499 45.455 0.00 0.00 0.00 4.00
1644 2208 1.609555 GCCTATCGATTCGGAGTGACT 59.390 52.381 15.34 0.00 0.00 3.41
1835 2544 2.357034 GCTCCGCAAAGTCCGTCA 60.357 61.111 0.00 0.00 0.00 4.35
2119 2842 3.500680 GGACAAACGGCTCAACTATGAAA 59.499 43.478 0.00 0.00 34.49 2.69
2269 2992 1.081892 CAGGTGTCATTGGCTTCTCG 58.918 55.000 0.00 0.00 0.00 4.04
2561 3324 5.948992 AGAGGAGCAAACTTATTGTGAAC 57.051 39.130 0.00 0.00 0.00 3.18
2572 3335 2.620585 AGTCTGCAAAAGAGGAGCAAAC 59.379 45.455 0.00 0.00 37.89 2.93
2754 3968 8.299570 ACCTGCAATTTTATCAGAACTGTTTAG 58.700 33.333 0.00 0.00 0.00 1.85
2958 4180 8.557029 GGTCAGTGCAAGTATTTATATTACACC 58.443 37.037 0.00 0.00 0.00 4.16
3175 4658 6.765989 GTCATGTATACAAGCCAATTCTGGTA 59.234 38.462 10.14 0.00 45.53 3.25
3357 4840 3.644884 ACCTACGTGAAGTGAAGAGTG 57.355 47.619 0.00 0.00 0.00 3.51
3581 5071 2.754552 GTGAGGTGGCAAATTAGATGCA 59.245 45.455 3.19 0.00 45.60 3.96
3762 5252 7.467811 CGTGAGCTTTTTGCATAAGATTCCTAT 60.468 37.037 11.97 0.00 45.94 2.57
3763 5253 6.183360 CGTGAGCTTTTTGCATAAGATTCCTA 60.183 38.462 11.97 0.00 45.94 2.94
3832 5322 6.196353 CGTTTTCAGTGAGTGTTTTATGTTGG 59.804 38.462 0.00 0.00 0.00 3.77
3850 5340 5.588648 AGAAACAGATGGACTTTCGTTTTCA 59.411 36.000 0.00 0.00 0.00 2.69
4155 5645 5.221581 ACAGTACAGGTTCCTTTACGACAAT 60.222 40.000 8.82 0.00 0.00 2.71
4245 5735 7.124599 AGTCCAATCAAGATAATTGCAATTCCA 59.875 33.333 27.28 12.37 33.65 3.53
4257 5747 5.366477 TGTATGAGGCAGTCCAATCAAGATA 59.634 40.000 0.00 0.00 33.74 1.98
4284 5774 2.035832 ACACAACAAACCCAATAGCAGC 59.964 45.455 0.00 0.00 0.00 5.25
4360 5850 5.447778 AATAGGAGGCATATTCTCATGGG 57.552 43.478 0.00 0.00 33.18 4.00
4388 5878 2.506438 GCTACACAGCGACCGACC 60.506 66.667 0.00 0.00 38.22 4.79
4488 5978 4.178956 ACCAGCTCAAGGAAGGTTTTAA 57.821 40.909 0.00 0.00 0.00 1.52
4524 6014 4.824479 AAATAACCAGGCCAAAATGGAG 57.176 40.909 15.38 0.00 40.96 3.86
4554 6044 8.556194 AGACAAAGGAAAACTGAAAAACAAAAC 58.444 29.630 0.00 0.00 0.00 2.43
4559 6049 8.988934 AGAAAAGACAAAGGAAAACTGAAAAAC 58.011 29.630 0.00 0.00 0.00 2.43
4609 6099 7.848223 AAAACATGGAAAAGAAGGAAAACAG 57.152 32.000 0.00 0.00 0.00 3.16
4647 6137 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
4854 6370 9.929722 GTTCACGAATTTGCATAGTATTTATGA 57.070 29.630 0.00 0.00 0.00 2.15
4855 6371 9.715123 TGTTCACGAATTTGCATAGTATTTATG 57.285 29.630 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.