Multiple sequence alignment - TraesCS5B01G141400

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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 TraesCS5B01G141400 chr5B 100.000 2285 0 0 1 2285 267114732 267112448 0.000000e+00 4220.0
1 TraesCS5B01G141400 chr5D 92.823 2299 127 20 1 2285 238382005 238384279 0.000000e+00 3297.0
2 TraesCS5B01G141400 chr5D 76.000 325 57 10 233 537 408775474 408775151 5.090000e-32 148.0
3 TraesCS5B01G141400 chr5D 79.000 200 39 2 224 422 404251848 404251651 1.420000e-27 134.0
4 TraesCS5B01G141400 chr5A 91.735 1706 72 24 617 2278 316351776 316350096 0.000000e+00 2305.0
5 TraesCS5B01G141400 chr5A 86.022 651 87 4 9 655 316352540 316351890 0.000000e+00 695.0
6 TraesCS5B01G141400 chr5A 81.714 175 29 3 246 419 31284842 31285014 2.370000e-30 143.0
7 TraesCS5B01G141400 chr4D 80.829 193 31 5 223 413 483611314 483611126 1.830000e-31 147.0
8 TraesCS5B01G141400 chr4D 80.513 195 30 8 232 421 133480993 133480802 2.370000e-30 143.0
9 TraesCS5B01G141400 chr3D 79.167 192 36 4 223 412 572435176 572435365 1.840000e-26 130.0
10 TraesCS5B01G141400 chr4A 80.263 152 27 3 232 381 428145781 428145931 6.670000e-21 111.0
11 TraesCS5B01G141400 chr2A 88.235 51 6 0 508 558 719725746 719725796 6.820000e-06 62.1
12 TraesCS5B01G141400 chr2A 100.000 28 0 0 395 422 756942831 756942804 4.000000e-03 52.8


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 TraesCS5B01G141400 chr5B 267112448 267114732 2284 True 4220 4220 100.0000 1 2285 1 chr5B.!!$R1 2284
1 TraesCS5B01G141400 chr5D 238382005 238384279 2274 False 3297 3297 92.8230 1 2285 1 chr5D.!!$F1 2284
2 TraesCS5B01G141400 chr5A 316350096 316352540 2444 True 1500 2305 88.8785 9 2278 2 chr5A.!!$R1 2269

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
380 384 0.107654 GTAGCCTCATCAAACCGCCT 60.108 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 2062 0.458025 GGAACCAGTCACGACGATCC 60.458 60.0 0.0 0.0 36.2 3.36 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
90 92 3.362706 ACGTCTAGCAATCAACTCCCTA 58.637 45.455 0.00 0.00 0.00 3.53
91 93 3.767673 ACGTCTAGCAATCAACTCCCTAA 59.232 43.478 0.00 0.00 0.00 2.69
92 94 4.406003 ACGTCTAGCAATCAACTCCCTAAT 59.594 41.667 0.00 0.00 0.00 1.73
93 95 4.985409 CGTCTAGCAATCAACTCCCTAATC 59.015 45.833 0.00 0.00 0.00 1.75
94 96 4.985409 GTCTAGCAATCAACTCCCTAATCG 59.015 45.833 0.00 0.00 0.00 3.34
106 109 2.296752 TCCCTAATCGACGACAAACACA 59.703 45.455 0.00 0.00 0.00 3.72
123 126 0.686224 ACATGTTTGGGCATTGGTGG 59.314 50.000 0.00 0.00 0.00 4.61
158 161 2.276732 TGAAGGGGAAAAGTGAGCAG 57.723 50.000 0.00 0.00 0.00 4.24
163 166 1.882623 GGGGAAAAGTGAGCAGAGTTG 59.117 52.381 0.00 0.00 0.00 3.16
172 175 1.856265 GAGCAGAGTTGGTTTGCCCG 61.856 60.000 0.00 0.00 38.58 6.13
208 211 1.981256 ACTTTGTAACCAGGGCACAG 58.019 50.000 0.00 0.00 0.00 3.66
219 222 4.677182 ACCAGGGCACAGAAATAGAAAAT 58.323 39.130 0.00 0.00 0.00 1.82
285 289 3.903090 TGATCAACCCAAAGCCATCTTTT 59.097 39.130 0.00 0.00 40.35 2.27
299 303 4.559153 CCATCTTTTTGGCGATCTTTGTT 58.441 39.130 0.00 0.00 0.00 2.83
300 304 4.386652 CCATCTTTTTGGCGATCTTTGTTG 59.613 41.667 0.00 0.00 0.00 3.33
302 306 3.068024 TCTTTTTGGCGATCTTTGTTGCT 59.932 39.130 0.00 0.00 0.00 3.91
304 308 3.552604 TTTGGCGATCTTTGTTGCTAC 57.447 42.857 0.00 0.00 0.00 3.58
305 309 2.472695 TGGCGATCTTTGTTGCTACT 57.527 45.000 0.00 0.00 0.00 2.57
314 318 5.546621 TCTTTGTTGCTACTCCTGTAAGT 57.453 39.130 0.00 0.00 0.00 2.24
326 330 4.697352 ACTCCTGTAAGTTTGATGATGTGC 59.303 41.667 0.00 0.00 0.00 4.57
328 332 3.129287 CCTGTAAGTTTGATGATGTGCCC 59.871 47.826 0.00 0.00 0.00 5.36
358 362 4.319984 CGCATCAACCCACATCATCTAATG 60.320 45.833 0.00 0.00 0.00 1.90
370 374 5.012871 ACATCATCTAATGCAGTAGCCTCAT 59.987 40.000 16.22 1.94 41.13 2.90
374 378 5.357742 TCTAATGCAGTAGCCTCATCAAA 57.642 39.130 16.22 0.00 41.13 2.69
380 384 0.107654 GTAGCCTCATCAAACCGCCT 60.108 55.000 0.00 0.00 0.00 5.52
386 390 0.955428 TCATCAAACCGCCTCACAGC 60.955 55.000 0.00 0.00 0.00 4.40
434 438 1.867363 ACCCTCACCGCTCTAGAATT 58.133 50.000 0.00 0.00 0.00 2.17
449 453 3.701532 AGAATTCGTCGTCTCCATCTC 57.298 47.619 0.00 0.00 0.00 2.75
457 461 1.654954 CGTCTCCATCTCCCGTCGTT 61.655 60.000 0.00 0.00 0.00 3.85
458 462 0.531200 GTCTCCATCTCCCGTCGTTT 59.469 55.000 0.00 0.00 0.00 3.60
470 474 3.439476 TCCCGTCGTTTCAACTTCAAAAA 59.561 39.130 0.00 0.00 0.00 1.94
496 500 1.538047 ACGCATTGATCTTGCCAAGT 58.462 45.000 4.04 5.45 36.75 3.16
504 509 1.880027 GATCTTGCCAAGTCCAACGTT 59.120 47.619 4.04 0.00 0.00 3.99
509 514 1.938861 CCAAGTCCAACGTTGTCGG 59.061 57.895 25.63 11.95 41.85 4.79
537 542 4.235762 ACGCCAGACAACGCCACT 62.236 61.111 0.00 0.00 0.00 4.00
543 548 0.861837 CAGACAACGCCACTGTTCTC 59.138 55.000 0.00 0.00 0.00 2.87
546 551 2.030562 AACGCCACTGTTCTCCGG 59.969 61.111 0.00 0.00 0.00 5.14
559 564 0.757561 TCTCCGGGCGTCCATCATAA 60.758 55.000 6.96 0.00 0.00 1.90
566 571 4.320202 CCGGGCGTCCATCATAAAATTTAG 60.320 45.833 6.96 0.00 0.00 1.85
567 572 4.274950 CGGGCGTCCATCATAAAATTTAGT 59.725 41.667 6.96 0.00 0.00 2.24
572 577 9.821662 GGCGTCCATCATAAAATTTAGTAATAC 57.178 33.333 0.00 0.00 0.00 1.89
600 605 6.538381 AGGAAAAACATGAAAATGTCAACACC 59.462 34.615 0.00 0.00 40.50 4.16
603 608 3.963665 ACATGAAAATGTCAACACCACG 58.036 40.909 0.00 0.00 40.50 4.94
631 636 1.377202 ACGAATCATGGCGCCAACT 60.377 52.632 36.33 16.53 0.00 3.16
664 823 5.880054 ACAAGAAATAAATCCAGACCACG 57.120 39.130 0.00 0.00 0.00 4.94
710 869 1.953311 GCTCGCCCCAAATTAACCAGA 60.953 52.381 0.00 0.00 0.00 3.86
721 880 1.179152 TTAACCAGATGCTCCGACGA 58.821 50.000 0.00 0.00 0.00 4.20
734 893 4.058817 GCTCCGACGAATGATCCTAAAAT 58.941 43.478 0.00 0.00 0.00 1.82
791 951 3.142174 CCTTGCGAGACTCCTTTTTCTT 58.858 45.455 1.22 0.00 0.00 2.52
793 953 2.767505 TGCGAGACTCCTTTTTCTTCC 58.232 47.619 0.00 0.00 0.00 3.46
796 956 3.753797 GCGAGACTCCTTTTTCTTCCAAT 59.246 43.478 0.00 0.00 0.00 3.16
808 968 5.446143 TTTCTTCCAATGCAATTACACGT 57.554 34.783 0.00 0.00 32.46 4.49
859 1019 1.636003 GGAGAAAACCATCACCCCTCT 59.364 52.381 0.00 0.00 0.00 3.69
924 1084 3.681594 CGATAGCAAAAGCCTTCCCACTA 60.682 47.826 0.00 0.00 0.00 2.74
939 1099 2.482494 CCACTACCTTCCCTTCCATCT 58.518 52.381 0.00 0.00 0.00 2.90
997 1161 4.771356 CGTCGTCCGCACCATCGT 62.771 66.667 0.00 0.00 0.00 3.73
1361 1531 2.590092 GGCATCGGCAGGTAAGGT 59.410 61.111 0.00 0.00 43.71 3.50
1682 1876 6.604795 ACATTATGAGTAGATGCCTTTGCTTT 59.395 34.615 0.00 0.00 38.71 3.51
1698 1892 6.747280 CCTTTGCTTTACTGAATGGAATTACG 59.253 38.462 0.00 0.00 36.07 3.18
1789 1990 4.040952 AGCTAGCATGGGTCATTTAGGTAG 59.959 45.833 18.83 0.00 0.00 3.18
1790 1991 4.202367 GCTAGCATGGGTCATTTAGGTAGT 60.202 45.833 10.63 0.00 31.69 2.73
1791 1992 5.011738 GCTAGCATGGGTCATTTAGGTAGTA 59.988 44.000 10.63 0.00 31.69 1.82
1792 1993 6.295916 GCTAGCATGGGTCATTTAGGTAGTAT 60.296 42.308 10.63 0.00 31.69 2.12
1793 1994 7.093465 GCTAGCATGGGTCATTTAGGTAGTATA 60.093 40.741 10.63 0.00 31.69 1.47
1798 1999 9.436957 CATGGGTCATTTAGGTAGTATATTGTC 57.563 37.037 0.00 0.00 0.00 3.18
1858 2059 3.949031 CGAAGAGAAGTCGGGGATC 57.051 57.895 0.00 0.00 34.85 3.36
1859 2060 0.029567 CGAAGAGAAGTCGGGGATCG 59.970 60.000 0.00 0.00 40.90 3.69
1860 2061 1.390565 GAAGAGAAGTCGGGGATCGA 58.609 55.000 0.00 0.00 46.77 3.59
1967 2168 0.601057 AACCGCTACCCATTTGTTGC 59.399 50.000 0.00 0.00 34.32 4.17
2129 2331 6.040209 AGCTTGAAGAGATATCTAGCCATG 57.960 41.667 17.15 12.21 43.64 3.66
2198 2400 5.004821 CACTGCGCTGTCACTTTACTAATAG 59.995 44.000 17.75 0.00 0.00 1.73
2199 2401 5.105877 ACTGCGCTGTCACTTTACTAATAGA 60.106 40.000 14.78 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.669569 ACAGTCGCCCATGTGTGC 60.670 61.111 0.00 0.00 0.00 4.57
14 15 4.056125 CGCTCTCACAGTCGCCCA 62.056 66.667 0.00 0.00 0.00 5.36
58 60 4.747540 TTGCTAGACGTCGTTGTTACTA 57.252 40.909 10.46 0.00 0.00 1.82
72 74 4.893524 TCGATTAGGGAGTTGATTGCTAGA 59.106 41.667 0.00 0.00 0.00 2.43
90 92 4.545823 AAACATGTGTTTGTCGTCGATT 57.454 36.364 10.11 0.00 45.55 3.34
106 109 1.200092 CCCCACCAATGCCCAAACAT 61.200 55.000 0.00 0.00 0.00 2.71
135 138 1.740025 CTCACTTTTCCCCTTCATCGC 59.260 52.381 0.00 0.00 0.00 4.58
158 161 3.680786 GCCCGGGCAAACCAACTC 61.681 66.667 40.73 6.07 40.22 3.01
172 175 0.746659 AGTTGTGCTCAGTTTTGCCC 59.253 50.000 0.00 0.00 0.00 5.36
245 249 9.450807 GGTTGATCAATATATTTGTTTTCTCGG 57.549 33.333 12.12 0.00 0.00 4.63
252 256 7.986889 GGCTTTGGGTTGATCAATATATTTGTT 59.013 33.333 12.12 0.00 0.00 2.83
260 264 4.870636 AGATGGCTTTGGGTTGATCAATA 58.129 39.130 12.12 0.00 0.00 1.90
263 267 2.905415 AGATGGCTTTGGGTTGATCA 57.095 45.000 0.00 0.00 0.00 2.92
285 289 2.742053 GAGTAGCAACAAAGATCGCCAA 59.258 45.455 0.00 0.00 0.00 4.52
295 299 5.676552 TCAAACTTACAGGAGTAGCAACAA 58.323 37.500 0.00 0.00 0.00 2.83
299 303 5.738619 TCATCAAACTTACAGGAGTAGCA 57.261 39.130 0.00 0.00 0.00 3.49
300 304 6.036517 CACATCATCAAACTTACAGGAGTAGC 59.963 42.308 0.00 0.00 0.00 3.58
302 306 5.874810 GCACATCATCAAACTTACAGGAGTA 59.125 40.000 0.00 0.00 0.00 2.59
304 308 4.095483 GGCACATCATCAAACTTACAGGAG 59.905 45.833 0.00 0.00 0.00 3.69
305 309 4.009675 GGCACATCATCAAACTTACAGGA 58.990 43.478 0.00 0.00 0.00 3.86
314 318 1.355381 AGGTCAGGGCACATCATCAAA 59.645 47.619 0.00 0.00 0.00 2.69
326 330 1.450312 GGTTGATGCGAGGTCAGGG 60.450 63.158 0.00 0.00 0.00 4.45
328 332 1.021390 GTGGGTTGATGCGAGGTCAG 61.021 60.000 0.00 0.00 0.00 3.51
358 362 1.009829 CGGTTTGATGAGGCTACTGC 58.990 55.000 0.00 0.00 38.76 4.40
380 384 4.121669 GCTCTCGGCTCGCTGTGA 62.122 66.667 2.91 2.91 38.06 3.58
386 390 2.811317 GTTGGTGCTCTCGGCTCG 60.811 66.667 0.00 0.00 42.39 5.03
434 438 1.818363 CGGGAGATGGAGACGACGA 60.818 63.158 0.00 0.00 0.00 4.20
449 453 3.408288 TTTTGAAGTTGAAACGACGGG 57.592 42.857 0.00 0.00 0.00 5.28
485 489 1.608590 CAACGTTGGACTTGGCAAGAT 59.391 47.619 32.50 17.01 0.00 2.40
496 500 2.659244 GACGCCGACAACGTTGGA 60.659 61.111 30.34 0.00 45.24 3.53
522 527 2.117941 GAACAGTGGCGTTGTCTGGC 62.118 60.000 0.00 0.00 34.02 4.85
537 542 3.000819 ATGGACGCCCGGAGAACA 61.001 61.111 0.73 1.94 34.29 3.18
543 548 1.604604 ATTTTATGATGGACGCCCGG 58.395 50.000 0.00 0.00 34.29 5.73
546 551 9.821662 GTATTACTAAATTTTATGATGGACGCC 57.178 33.333 0.00 0.00 0.00 5.68
572 577 7.009999 TGTTGACATTTTCATGTTTTTCCTTCG 59.990 33.333 0.00 0.00 44.22 3.79
577 582 7.179410 GTGGTGTTGACATTTTCATGTTTTTC 58.821 34.615 0.00 0.00 44.22 2.29
592 597 1.463444 GTAGCCATTCGTGGTGTTGAC 59.537 52.381 0.00 0.00 0.00 3.18
600 605 2.267426 TGATTCGTGTAGCCATTCGTG 58.733 47.619 0.00 0.00 0.00 4.35
603 608 2.031682 GCCATGATTCGTGTAGCCATTC 60.032 50.000 5.21 0.00 0.00 2.67
631 636 9.064706 TGGATTTATTTCTTGTTTACGTAACCA 57.935 29.630 7.70 4.15 35.81 3.67
710 869 1.043816 AGGATCATTCGTCGGAGCAT 58.956 50.000 0.00 0.00 0.00 3.79
721 880 8.462016 GCACAGTGTTCTTATTTTAGGATCATT 58.538 33.333 1.61 0.00 0.00 2.57
734 893 1.217001 CAGTGCGCACAGTGTTCTTA 58.783 50.000 39.21 0.00 41.53 2.10
791 951 4.457603 AGCTTTACGTGTAATTGCATTGGA 59.542 37.500 0.00 0.00 31.76 3.53
793 953 6.689178 AAAGCTTTACGTGTAATTGCATTG 57.311 33.333 10.72 0.00 31.76 2.82
796 956 4.442733 GCAAAAGCTTTACGTGTAATTGCA 59.557 37.500 13.10 0.00 36.66 4.08
808 968 1.284408 CGGGCACGCAAAAGCTTTA 59.716 52.632 13.10 0.00 0.00 1.85
859 1019 3.071206 GGGCAGGAGCACGAGAGA 61.071 66.667 0.00 0.00 44.61 3.10
924 1084 2.192263 GTCTGAGATGGAAGGGAAGGT 58.808 52.381 0.00 0.00 0.00 3.50
1309 1474 1.004560 CCAGCAAGAGAACAGCGGA 60.005 57.895 0.00 0.00 0.00 5.54
1361 1531 1.044611 TCATCTCAACGTCCACCACA 58.955 50.000 0.00 0.00 0.00 4.17
1519 1699 4.512944 GGATTCTCATCAACACGCATATGT 59.487 41.667 4.29 0.00 0.00 2.29
1589 1773 6.064846 ACAAGAAGCACAAATCTGTACAAG 57.935 37.500 0.00 0.00 33.22 3.16
1656 1840 6.125029 AGCAAAGGCATCTACTCATAATGTT 58.875 36.000 0.00 0.00 44.61 2.71
1682 1876 6.170506 AGTCAAAGCGTAATTCCATTCAGTA 58.829 36.000 0.00 0.00 0.00 2.74
1698 1892 3.060602 AGTAAAGCTCACGAGTCAAAGC 58.939 45.455 0.00 1.19 34.95 3.51
1789 1990 6.363473 GCCGTGCTAATTGAAGACAATATAC 58.637 40.000 0.00 0.00 44.67 1.47
1790 1991 5.468746 GGCCGTGCTAATTGAAGACAATATA 59.531 40.000 0.00 0.00 44.67 0.86
1791 1992 4.275936 GGCCGTGCTAATTGAAGACAATAT 59.724 41.667 0.00 0.00 44.67 1.28
1792 1993 3.625764 GGCCGTGCTAATTGAAGACAATA 59.374 43.478 0.00 0.00 44.67 1.90
1793 1994 2.423538 GGCCGTGCTAATTGAAGACAAT 59.576 45.455 0.00 0.00 46.99 2.71
1798 1999 0.742990 TCCGGCCGTGCTAATTGAAG 60.743 55.000 26.12 3.58 0.00 3.02
1855 2056 0.938713 AGTCACGACGATCCTCGATC 59.061 55.000 18.98 9.43 43.74 3.69
1856 2057 0.658368 CAGTCACGACGATCCTCGAT 59.342 55.000 18.98 2.99 43.74 3.59
1857 2058 1.366854 CCAGTCACGACGATCCTCGA 61.367 60.000 18.98 0.00 43.74 4.04
1858 2059 1.062685 CCAGTCACGACGATCCTCG 59.937 63.158 11.84 11.84 46.93 4.63
1859 2060 0.526662 AACCAGTCACGACGATCCTC 59.473 55.000 0.00 0.00 36.20 3.71
1860 2061 0.526662 GAACCAGTCACGACGATCCT 59.473 55.000 0.00 0.00 36.20 3.24
1861 2062 0.458025 GGAACCAGTCACGACGATCC 60.458 60.000 0.00 0.00 36.20 3.36
1862 2063 0.526662 AGGAACCAGTCACGACGATC 59.473 55.000 0.00 0.00 36.20 3.69
1863 2064 1.830279 TAGGAACCAGTCACGACGAT 58.170 50.000 0.00 0.00 36.20 3.73
1866 2067 2.735762 GCTGATAGGAACCAGTCACGAC 60.736 54.545 0.00 0.00 33.19 4.34
1927 2128 1.876156 AGCTCTCAAACTTTTCTGGCG 59.124 47.619 0.00 0.00 0.00 5.69
2129 2331 2.735134 ACGTACGCTTGATCTGGTTTTC 59.265 45.455 16.72 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.