Multiple sequence alignment - TraesCS7D01G093800

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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 TraesCS7D01G093800 chr7D 100.000 2650 0 0 1 2650 56234024 56236673 0.000000e+00 4894
1 TraesCS7D01G093800 chr7D 77.330 1191 238 18 1094 2273 140321546 140320377 0.000000e+00 675
2 TraesCS7D01G093800 chr7D 74.765 531 121 11 1747 2272 55015414 55015936 2.650000e-55 226
3 TraesCS7D01G093800 chr7D 83.007 153 22 4 916 1066 55555766 55555916 4.600000e-28 135
4 TraesCS7D01G093800 chr7A 93.095 2433 138 16 226 2650 60637682 60640092 0.000000e+00 3535
5 TraesCS7D01G093800 chr7A 92.958 213 10 3 1 211 60637487 60637696 3.310000e-79 305
6 TraesCS7D01G093800 chr4A 92.839 2318 137 22 334 2635 673028366 673030670 0.000000e+00 3334
7 TraesCS7D01G093800 chr4A 76.877 1492 298 35 811 2275 670986240 670984769 0.000000e+00 800
8 TraesCS7D01G093800 chr4A 93.624 298 13 3 1 296 673028070 673028363 8.710000e-120 440
9 TraesCS7D01G093800 chr7B 77.979 1326 253 35 967 2273 105522935 105521630 0.000000e+00 795


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 TraesCS7D01G093800 chr7D 56234024 56236673 2649 False 4894 4894 100.0000 1 2650 1 chr7D.!!$F3 2649
1 TraesCS7D01G093800 chr7D 140320377 140321546 1169 True 675 675 77.3300 1094 2273 1 chr7D.!!$R1 1179
2 TraesCS7D01G093800 chr7D 55015414 55015936 522 False 226 226 74.7650 1747 2272 1 chr7D.!!$F1 525
3 TraesCS7D01G093800 chr7A 60637487 60640092 2605 False 1920 3535 93.0265 1 2650 2 chr7A.!!$F1 2649
4 TraesCS7D01G093800 chr4A 673028070 673030670 2600 False 1887 3334 93.2315 1 2635 2 chr4A.!!$F1 2634
5 TraesCS7D01G093800 chr4A 670984769 670986240 1471 True 800 800 76.8770 811 2275 1 chr4A.!!$R1 1464
6 TraesCS7D01G093800 chr7B 105521630 105522935 1305 True 795 795 77.9790 967 2273 1 chr7B.!!$R1 1306

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
148 149 0.112606 TGCCCCGGAAACAAATGGTA 59.887 50.0 0.73 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1722 0.8951 ATGAAAAGCTGGCCGAAGCA 60.895 50.0 16.78 0.2 46.08 3.91 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
42 43 3.366396 GTTGTCTCCTCCAGTAGATCCA 58.634 50.000 0.00 0.0 0.00 3.41
114 115 4.148825 GCCTCCGATGAGCACCGT 62.149 66.667 0.00 0.0 37.29 4.83
134 135 2.358984 TAAGTTTCGCCGTGCCCC 60.359 61.111 0.00 0.0 0.00 5.80
147 148 1.152440 TGCCCCGGAAACAAATGGT 60.152 52.632 0.73 0.0 0.00 3.55
148 149 0.112606 TGCCCCGGAAACAAATGGTA 59.887 50.000 0.73 0.0 0.00 3.25
149 150 0.815095 GCCCCGGAAACAAATGGTAG 59.185 55.000 0.73 0.0 0.00 3.18
150 151 1.889262 GCCCCGGAAACAAATGGTAGT 60.889 52.381 0.73 0.0 0.00 2.73
224 227 2.315925 TTTTTGCGGGTGAAATTGCA 57.684 40.000 0.00 0.0 35.15 4.08
257 260 9.941325 TTTCGTTTGGTAGATTTATTACACCTA 57.059 29.630 0.00 0.0 0.00 3.08
304 307 3.530265 ACTTGTTTGAGACGTACACCA 57.470 42.857 0.00 0.0 0.00 4.17
305 308 3.454375 ACTTGTTTGAGACGTACACCAG 58.546 45.455 0.00 0.0 0.00 4.00
310 313 1.977056 TGAGACGTACACCAGTCACT 58.023 50.000 0.00 0.0 39.67 3.41
345 348 4.262420 GCACCCCTCTTTTTCAAATTGCTA 60.262 41.667 0.00 0.0 0.00 3.49
370 373 4.301637 ACCTGACCGACATTTGTTTTTC 57.698 40.909 0.00 0.0 0.00 2.29
371 374 3.242936 ACCTGACCGACATTTGTTTTTCG 60.243 43.478 0.00 0.0 0.00 3.46
392 398 3.303495 CGGTTGATCTACACTTGCTAACG 59.697 47.826 9.51 0.0 0.00 3.18
418 424 9.436957 GGAGTCTTGATCTGATGTAAAGTAAAA 57.563 33.333 0.00 0.0 0.00 1.52
454 460 7.449395 TGATCTAATTTGCTCCTAATGGAATGG 59.551 37.037 0.00 0.0 42.66 3.16
458 464 1.287442 TGCTCCTAATGGAATGGGCAA 59.713 47.619 0.00 0.0 42.66 4.52
459 465 1.683385 GCTCCTAATGGAATGGGCAAC 59.317 52.381 0.00 0.0 42.66 4.17
477 483 3.308530 CAACCATTTCTTCGGTTTCAGC 58.691 45.455 0.00 0.0 42.99 4.26
480 486 2.558359 CCATTTCTTCGGTTTCAGCCTT 59.442 45.455 0.00 0.0 0.00 4.35
483 489 4.823790 TTTCTTCGGTTTCAGCCTTTAC 57.176 40.909 0.00 0.0 0.00 2.01
499 505 8.494433 TCAGCCTTTACTTGAATAAGATGGTAT 58.506 33.333 0.00 0.0 37.36 2.73
536 542 7.944729 ACATATTTTACTTGACAGAATGCCT 57.055 32.000 0.00 0.0 42.53 4.75
550 556 4.460382 CAGAATGCCTTCCTCTGCTTTTTA 59.540 41.667 0.00 0.0 30.91 1.52
591 597 5.627499 AATGTAATGTGTGCTGTAACTGG 57.373 39.130 0.00 0.0 0.00 4.00
627 634 6.785076 TGGGACATTGTACTTAGAAATTGGA 58.215 36.000 0.00 0.0 0.00 3.53
670 678 2.672307 GCTCAGGCTGCTGCTGTT 60.672 61.111 19.85 0.0 39.59 3.16
739 749 5.163374 TGTCAGTCATCCACCTCATTATCAG 60.163 44.000 0.00 0.0 0.00 2.90
828 839 6.649557 ACAAGTAAATGGTGCTTAGTGTACTC 59.350 38.462 0.00 0.0 29.98 2.59
840 851 2.096248 AGTGTACTCTCTACTGCAGCC 58.904 52.381 15.27 0.0 0.00 4.85
1092 1110 3.190874 CGAACCCTATGTCTTCTCTTGC 58.809 50.000 0.00 0.0 0.00 4.01
1125 1143 0.533755 GGAGGCTGCAATGTATCGCT 60.534 55.000 0.00 0.0 0.00 4.93
1247 1265 3.430218 GCTCTAATAGTATGTTGCAGCCG 59.570 47.826 0.00 0.0 0.00 5.52
1355 1373 0.687427 AAGGTGCTTGTTGCCAAGGT 60.687 50.000 5.08 0.0 46.72 3.50
1496 1517 0.316204 ACCACTCTGACCGTAAACCG 59.684 55.000 0.00 0.0 0.00 4.44
1701 1722 1.530323 GAAGTTGTACGCATGGGGTT 58.470 50.000 14.94 0.0 0.00 4.11
1724 1745 1.019278 TCGGCCAGCTTTTCATCGTC 61.019 55.000 2.24 0.0 0.00 4.20
1736 1757 4.398549 TTTCATCGTCGATTTGGACAAC 57.601 40.909 4.63 0.0 36.73 3.32
1858 1882 1.940613 GTATCTCGTTGAATGTGGGGC 59.059 52.381 0.00 0.0 0.00 5.80
1889 1913 0.109532 TGGTGGCAAGATGGTTTCGA 59.890 50.000 0.00 0.0 0.00 3.71
1904 1928 4.147322 CGATGCACGCCACGTTCC 62.147 66.667 0.00 0.0 38.32 3.62
1996 2026 0.179000 CCTGGTCGATGGAGAAAGGG 59.821 60.000 0.00 0.0 0.00 3.95
2076 2106 2.940971 GCTGTGGAATGCAGTGGATACA 60.941 50.000 0.00 0.0 38.23 2.29
2117 2147 0.613260 TGTGTGACTATGTCTGGCCC 59.387 55.000 0.00 0.0 33.15 5.80
2361 2397 0.548682 AAGCTCTGTCATCCCACCCT 60.549 55.000 0.00 0.0 0.00 4.34
2368 2404 3.016971 CATCCCACCCTGCCTGGA 61.017 66.667 0.00 0.0 38.35 3.86
2419 2457 9.926751 CAATCTGCTACTGTGTTATCTTTATTG 57.073 33.333 0.00 0.0 0.00 1.90
2476 2514 9.553064 GGATGATCTTATATGGGATGTGTATTC 57.447 37.037 0.00 0.0 0.00 1.75
2510 2548 4.633126 TCTTCATGATAGCAACTTGTGAGC 59.367 41.667 0.00 0.0 0.00 4.26
2626 2665 5.948992 ACCAAGTTTTGCTCTGAACTATC 57.051 39.130 0.00 0.0 35.17 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 5.960202 AGGTAAAATTTCCATCTCCAAGCAT 59.040 36.000 0.00 0.00 0.00 3.79
114 115 2.023223 GGCACGGCGAAACTTACGA 61.023 57.895 16.62 0.00 0.00 3.43
134 135 7.611213 AAAGAGATACTACCATTTGTTTCCG 57.389 36.000 0.00 0.00 0.00 4.30
136 137 8.296713 TGCAAAAGAGATACTACCATTTGTTTC 58.703 33.333 0.00 0.00 30.10 2.78
147 148 7.624549 AGTGGAAATCTGCAAAAGAGATACTA 58.375 34.615 0.00 0.00 38.67 1.82
148 149 6.479884 AGTGGAAATCTGCAAAAGAGATACT 58.520 36.000 0.00 0.00 38.67 2.12
149 150 6.749923 AGTGGAAATCTGCAAAAGAGATAC 57.250 37.500 0.00 0.00 38.67 2.24
150 151 8.862325 TTAAGTGGAAATCTGCAAAAGAGATA 57.138 30.769 0.00 0.00 38.67 1.98
296 299 2.794910 CTGAAACAGTGACTGGTGTACG 59.205 50.000 17.92 0.00 35.51 3.67
304 307 1.242076 GCCATGCTGAAACAGTGACT 58.758 50.000 0.00 0.00 33.43 3.41
305 308 0.953727 TGCCATGCTGAAACAGTGAC 59.046 50.000 0.00 0.00 33.43 3.67
310 313 1.907807 GGGGTGCCATGCTGAAACA 60.908 57.895 0.00 0.00 0.00 2.83
345 348 6.399639 AAAACAAATGTCGGTCAGGTAAAT 57.600 33.333 0.00 0.00 0.00 1.40
370 373 3.303495 CGTTAGCAAGTGTAGATCAACCG 59.697 47.826 0.00 0.00 0.00 4.44
371 374 3.617263 CCGTTAGCAAGTGTAGATCAACC 59.383 47.826 0.00 0.00 0.00 3.77
372 375 4.491676 TCCGTTAGCAAGTGTAGATCAAC 58.508 43.478 0.00 0.00 0.00 3.18
374 377 3.762288 ACTCCGTTAGCAAGTGTAGATCA 59.238 43.478 0.00 0.00 0.00 2.92
392 398 9.436957 TTTTACTTTACATCAGATCAAGACTCC 57.563 33.333 0.00 0.00 0.00 3.85
432 438 5.279156 GCCCATTCCATTAGGAGCAAATTAG 60.279 44.000 0.00 0.00 46.74 1.73
435 441 2.967887 GCCCATTCCATTAGGAGCAAAT 59.032 45.455 0.00 0.00 46.74 2.32
438 444 0.925558 TGCCCATTCCATTAGGAGCA 59.074 50.000 0.00 0.00 46.74 4.26
442 448 2.157640 TGGTTGCCCATTCCATTAGG 57.842 50.000 0.00 0.00 35.17 2.69
458 464 1.886542 GGCTGAAACCGAAGAAATGGT 59.113 47.619 0.00 0.00 41.20 3.55
459 465 2.162681 AGGCTGAAACCGAAGAAATGG 58.837 47.619 0.00 0.00 33.69 3.16
464 470 3.764237 AGTAAAGGCTGAAACCGAAGA 57.236 42.857 0.00 0.00 33.69 2.87
465 471 3.813166 TCAAGTAAAGGCTGAAACCGAAG 59.187 43.478 0.00 0.00 33.69 3.79
469 475 7.448748 TCTTATTCAAGTAAAGGCTGAAACC 57.551 36.000 0.00 0.00 33.20 3.27
536 542 9.733556 TTGTGTATAGAATAAAAAGCAGAGGAA 57.266 29.630 0.00 0.00 0.00 3.36
591 597 4.079253 ACAATGTCCCAGTGTTAATGACC 58.921 43.478 0.00 0.00 39.70 4.02
613 619 9.807921 AGGAATCTTGTTTCCAATTTCTAAGTA 57.192 29.630 11.60 0.00 46.40 2.24
670 678 4.877378 TTTCCTCTAACTAGAAACGCCA 57.123 40.909 0.00 0.00 0.00 5.69
828 839 3.181479 TGGTAATAACGGCTGCAGTAGAG 60.181 47.826 16.64 6.93 0.00 2.43
840 851 4.403453 GCTTCTTGCACTTGGTAATAACG 58.597 43.478 0.00 0.00 42.31 3.18
1069 1087 4.177026 CAAGAGAAGACATAGGGTTCGTG 58.823 47.826 0.00 0.00 0.00 4.35
1092 1110 3.464907 CAGCCTCCATCATACAAGTCTG 58.535 50.000 0.00 0.00 0.00 3.51
1125 1143 2.103094 CCGGCTGAAGATCTGACCAATA 59.897 50.000 0.00 0.00 0.00 1.90
1247 1265 1.821332 CGGGAATGGCAGAGGAAGC 60.821 63.158 0.00 0.00 0.00 3.86
1355 1373 4.016444 GGAATAGCCAGTTGTCAATGGAA 58.984 43.478 14.59 5.61 39.02 3.53
1496 1517 5.891451 GGCACCACCAACTTATAGAAAATC 58.109 41.667 0.00 0.00 38.86 2.17
1701 1722 0.895100 ATGAAAAGCTGGCCGAAGCA 60.895 50.000 16.78 0.20 46.08 3.91
1724 1745 2.410730 GGTACAGTCGTTGTCCAAATCG 59.589 50.000 0.00 0.00 41.29 3.34
1740 1761 4.201657 CAGCTGATGGATGAAATGGTACA 58.798 43.478 8.42 0.00 36.49 2.90
1889 1913 3.353836 GTGGAACGTGGCGTGCAT 61.354 61.111 1.94 0.00 39.99 3.96
1904 1928 4.211164 TGTTCAAAGACATCGTAGCTTGTG 59.789 41.667 0.00 0.00 0.00 3.33
1971 1995 3.147595 CCATCGACCAGGGCTCGA 61.148 66.667 4.71 4.71 43.94 4.04
1973 1997 1.330655 TTCTCCATCGACCAGGGCTC 61.331 60.000 0.00 0.00 0.00 4.70
1996 2026 2.985847 GGCCACCCAACTCACTGC 60.986 66.667 0.00 0.00 0.00 4.40
2117 2147 3.347077 AGAGGATTTGCAGAAGAGGTG 57.653 47.619 0.00 0.00 0.00 4.00
2286 2316 2.613977 CCTCCAACGCAACAGAAGAGAT 60.614 50.000 0.00 0.00 0.00 2.75
2290 2320 1.264288 GAACCTCCAACGCAACAGAAG 59.736 52.381 0.00 0.00 0.00 2.85
2361 2397 0.913924 TCATGAGAAGCATCCAGGCA 59.086 50.000 0.00 0.00 34.15 4.75
2368 2404 6.261826 GCTATGGTAAAAGTCATGAGAAGCAT 59.738 38.462 0.00 4.37 37.85 3.79
2419 2457 4.700268 TTGATGTGTACACAATCATGGC 57.300 40.909 31.01 14.77 45.41 4.40
2476 2514 1.001624 TCATGAAGACTGCGCATTCG 58.998 50.000 20.34 7.84 39.07 3.34
2510 2548 6.785191 AGTTTGTTCAAGTACATGACACAAG 58.215 36.000 18.81 0.00 34.72 3.16
2626 2665 6.879276 ATTTATCTCAGTTGCAGGATGATG 57.121 37.500 0.00 0.00 39.69 3.07


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

AutoCloner maintained by Alex Coulton.