Multiple sequence alignment - TraesCS6D01G137100

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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 TraesCS6D01G137100 chr6D 100.000 4406 0 0 1 4406 105816189 105820594 0.000000e+00 8137
1 TraesCS6D01G137100 chr6A 96.010 3283 85 24 257 3507 128437601 128440869 0.000000e+00 5295
2 TraesCS6D01G137100 chr6A 95.969 769 23 6 3646 4406 128442738 128443506 0.000000e+00 1242
3 TraesCS6D01G137100 chr6A 92.424 264 15 4 1 262 128423229 128423489 5.380000e-99 372
4 TraesCS6D01G137100 chr6A 90.351 114 9 1 3533 3646 128440862 128440973 9.870000e-32 148
5 TraesCS6D01G137100 chr6B 96.623 1836 34 9 2027 3857 192347729 192349541 0.000000e+00 3022
6 TraesCS6D01G137100 chr6B 92.333 2087 91 35 3 2026 192344122 192346202 0.000000e+00 2904
7 TraesCS6D01G137100 chr6B 95.659 645 16 5 3767 4406 192349542 192350179 0.000000e+00 1026
8 TraesCS6D01G137100 chr5D 97.436 156 4 0 1308 1463 67584606 67584761 2.610000e-67 267
9 TraesCS6D01G137100 chr5D 96.178 157 6 0 1308 1464 292148046 292147890 1.570000e-64 257
10 TraesCS6D01G137100 chr5B 96.795 156 5 0 1308 1463 274350683 274350838 1.220000e-65 261
11 TraesCS6D01G137100 chr1A 96.774 155 5 0 1308 1462 530734873 530735027 4.370000e-65 259
12 TraesCS6D01G137100 chr5A 96.154 156 6 0 1308 1463 255614578 255614423 5.660000e-64 255
13 TraesCS6D01G137100 chr2B 94.545 165 6 3 1309 1473 726694619 726694780 7.320000e-63 252
14 TraesCS6D01G137100 chr7D 93.976 166 8 2 1308 1473 437409626 437409463 2.630000e-62 250
15 TraesCS6D01G137100 chr7D 76.577 222 34 8 46 253 501912816 501912599 6.030000e-19 106
16 TraesCS6D01G137100 chr2D 93.878 49 3 0 184 232 606701128 606701080 1.700000e-09 75


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 TraesCS6D01G137100 chr6D 105816189 105820594 4405 False 8137.000000 8137 100.000000 1 4406 1 chr6D.!!$F1 4405
1 TraesCS6D01G137100 chr6A 128437601 128443506 5905 False 2228.333333 5295 94.110000 257 4406 3 chr6A.!!$F2 4149
2 TraesCS6D01G137100 chr6B 192344122 192350179 6057 False 2317.333333 3022 94.871667 3 4406 3 chr6B.!!$F1 4403

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
77 90 0.593773 AAAAACCGCACACACGCATC 60.594 50.000 0.00 0.0 0.00 3.91 F
346 380 1.425694 GCCCCCTTTAGGAGTAGAGG 58.574 60.000 0.00 0.0 38.24 3.69 F
636 677 1.754803 TCAAATATCTGCCGTCCGTCT 59.245 47.619 0.00 0.0 0.00 4.18 F
1377 1440 1.227527 CTATCCATGCGCCCGAACA 60.228 57.895 4.18 0.0 0.00 3.18 F
1521 1593 0.178992 CACCTCAGGAAAGTGCCCAA 60.179 55.000 0.00 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 1431 1.234615 ACCAACTCATTGTTCGGGCG 61.235 55.000 0.00 0.0 36.63 6.13 R
1377 1440 1.478510 AGATCTCGCGACCAACTCATT 59.521 47.619 3.71 0.0 0.00 2.57 R
1512 1584 2.821969 CTGAGCAAATAGTTGGGCACTT 59.178 45.455 4.91 0.0 36.88 3.16 R
3150 4751 3.786656 CCGATTGGCAGAAGGATCA 57.213 52.632 0.00 0.0 0.00 2.92 R
3469 5070 4.082125 CCCATTCAGCTAGGAAACAAAGT 58.918 43.478 0.00 0.0 0.00 2.66 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
28 29 9.967451 TGATCACAAAATAATAGGTTGGTTAGA 57.033 29.630 0.00 0.00 0.00 2.10
75 88 2.878429 AAAAACCGCACACACGCA 59.122 50.000 0.00 0.00 0.00 5.24
77 90 0.593773 AAAAACCGCACACACGCATC 60.594 50.000 0.00 0.00 0.00 3.91
107 120 9.702253 TGGACTGGCCAATTTTTATTATAGTTA 57.298 29.630 7.01 0.00 45.87 2.24
173 186 9.001542 TGGAATGCAAAGAAAATTTGGATTAAG 57.998 29.630 16.61 0.00 45.84 1.85
235 248 2.749621 GGAAAGTGCCGATTGATTGAGT 59.250 45.455 0.00 0.00 0.00 3.41
254 267 1.511147 GTTAATGCGCGCGTTAAATGG 59.489 47.619 43.24 0.04 38.59 3.16
263 276 1.801771 CGCGTTAAATGGGTCAACTCA 59.198 47.619 0.00 0.00 0.00 3.41
346 380 1.425694 GCCCCCTTTAGGAGTAGAGG 58.574 60.000 0.00 0.00 38.24 3.69
352 386 3.447944 CCCTTTAGGAGTAGAGGTGACAC 59.552 52.174 0.00 0.00 38.24 3.67
362 396 5.880901 AGTAGAGGTGACACCATGATTTTT 58.119 37.500 26.30 2.72 41.95 1.94
413 448 9.733556 TGAGTTGAACCACATATATAAAGTGTT 57.266 29.630 14.14 9.98 0.00 3.32
494 529 6.979817 TCACAAACTCATGATTGTTTTTCCTG 59.020 34.615 11.20 4.13 37.13 3.86
495 530 6.979817 CACAAACTCATGATTGTTTTTCCTGA 59.020 34.615 11.20 0.00 37.13 3.86
497 532 8.206189 ACAAACTCATGATTGTTTTTCCTGAAT 58.794 29.630 8.57 0.00 36.04 2.57
498 533 9.695526 CAAACTCATGATTGTTTTTCCTGAATA 57.304 29.630 9.67 0.00 34.60 1.75
543 580 3.459969 AGGCTTCCTTTTCCCTAATCGAT 59.540 43.478 0.00 0.00 0.00 3.59
544 581 4.079730 AGGCTTCCTTTTCCCTAATCGATT 60.080 41.667 16.15 16.15 0.00 3.34
636 677 1.754803 TCAAATATCTGCCGTCCGTCT 59.245 47.619 0.00 0.00 0.00 4.18
638 679 2.225068 AATATCTGCCGTCCGTCTTG 57.775 50.000 0.00 0.00 0.00 3.02
709 750 2.050350 CCTCCACGGCCTCGACTTA 61.050 63.158 0.00 0.00 40.11 2.24
872 933 2.745884 CCCCACGCGCAATCTTGA 60.746 61.111 5.73 0.00 0.00 3.02
1037 1100 4.627284 TCGAGAATGACCCTGGTAAAAA 57.373 40.909 0.00 0.00 0.00 1.94
1073 1136 7.392766 ACTGAATGGATGGATTATCTGGTAA 57.607 36.000 0.00 0.00 36.03 2.85
1368 1431 2.223340 CGTGGAAGTTTGCTATCCATGC 60.223 50.000 0.71 0.00 44.55 4.06
1377 1440 1.227527 CTATCCATGCGCCCGAACA 60.228 57.895 4.18 0.00 0.00 3.18
1401 1464 3.881089 TGAGTTGGTCGCGAGATCTTATA 59.119 43.478 10.24 0.00 43.23 0.98
1493 1565 3.748083 AGATTGAGACATGTGCAGTGTT 58.252 40.909 1.15 0.00 0.00 3.32
1512 1584 3.073798 TGTTGCCTATTTCACCTCAGGAA 59.926 43.478 0.00 0.00 0.00 3.36
1521 1593 0.178992 CACCTCAGGAAAGTGCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
1641 1713 8.511321 TGCGATTCAAAATTCACAGTACTAATT 58.489 29.630 0.00 0.00 0.00 1.40
1728 1800 5.602978 TCCCCCTCTCTTAACAAGTATCATC 59.397 44.000 0.00 0.00 0.00 2.92
1767 1839 4.721776 ACTGGACTTATCTTCCCAAGCATA 59.278 41.667 0.00 0.00 31.33 3.14
2021 2094 5.928264 GGTAAGAACATTTTTGCATTCAGCT 59.072 36.000 0.00 0.00 45.94 4.24
2030 2103 3.870538 TTGCATTCAGCTCTCCCATAT 57.129 42.857 0.00 0.00 45.94 1.78
2116 3714 5.273208 TCTGGTTGACTTATAGGCTTCTCT 58.727 41.667 0.00 0.00 0.00 3.10
2131 3729 2.550277 TCTCTATTCACCCAGGCTCA 57.450 50.000 0.00 0.00 0.00 4.26
2136 3734 2.610438 ATTCACCCAGGCTCACAAAT 57.390 45.000 0.00 0.00 0.00 2.32
2137 3735 3.737559 ATTCACCCAGGCTCACAAATA 57.262 42.857 0.00 0.00 0.00 1.40
2138 3736 2.489938 TCACCCAGGCTCACAAATAC 57.510 50.000 0.00 0.00 0.00 1.89
2408 4006 0.397535 CCCTGCTGCCCATTACCATT 60.398 55.000 0.00 0.00 0.00 3.16
2429 4030 7.975616 ACCATTAATGTCATTTTTCCTGAATCG 59.024 33.333 14.25 0.00 0.00 3.34
2535 4136 1.746861 CGCCCTGTTATCAAGGATGCA 60.747 52.381 0.00 0.00 0.00 3.96
2633 4234 8.677300 TCTGCATCAGTTTTATAACCAAATCTC 58.323 33.333 0.00 0.00 34.71 2.75
3150 4751 5.501156 GAGAACCTCTTATCACAAATGGGT 58.499 41.667 0.00 0.00 0.00 4.51
3421 5022 4.911514 AAGTGAAACCTGCGTTGTAAAT 57.088 36.364 0.00 0.00 37.80 1.40
3422 5023 4.911514 AGTGAAACCTGCGTTGTAAATT 57.088 36.364 0.00 0.00 37.80 1.82
3469 5070 2.807676 TGTGTAGAGATGGCTGACTGA 58.192 47.619 0.00 0.00 0.00 3.41
3560 5162 7.391148 TGGTTTATTCAGGCAGATCTTAAAC 57.609 36.000 12.49 12.49 31.95 2.01
3620 5222 7.230108 CAGAATTATATGTGCATCAGAGGGTTT 59.770 37.037 0.00 0.00 0.00 3.27
3749 7117 8.345724 ACAATTTCTTGAATACTTGCATCTCT 57.654 30.769 0.00 0.00 36.20 3.10
3818 7279 7.096551 GGCTAGATATTTTCTTGGCAAACAAA 58.903 34.615 0.00 3.68 46.94 2.83
3990 7451 9.840427 ACACAAACTATAGCATAACAAAACATC 57.160 29.630 0.00 0.00 0.00 3.06
4246 7709 0.612174 AGAGCCGTAGACCTCAGCAA 60.612 55.000 0.00 0.00 0.00 3.91
4260 7723 0.250640 CAGCAACAGTGGAGCCTTCT 60.251 55.000 5.56 0.00 0.00 2.85
4397 7864 1.080093 GTTGTCGCATCCGTCTCCA 60.080 57.895 0.00 0.00 35.54 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.100458 ACCAACCTATTATTTTGTGATCAGC 57.900 36.000 0.00 0.00 0.00 4.26
2 3 9.967451 TCTAACCAACCTATTATTTTGTGATCA 57.033 29.630 0.00 0.00 0.00 2.92
59 72 1.008995 GATGCGTGTGTGCGGTTTT 60.009 52.632 0.00 0.00 37.81 2.43
63 76 1.066656 CATTTGATGCGTGTGTGCGG 61.067 55.000 0.00 0.00 37.81 5.69
64 77 1.066656 CCATTTGATGCGTGTGTGCG 61.067 55.000 0.00 0.00 37.81 5.34
65 78 0.240678 TCCATTTGATGCGTGTGTGC 59.759 50.000 0.00 0.00 0.00 4.57
66 79 1.536766 AGTCCATTTGATGCGTGTGTG 59.463 47.619 0.00 0.00 0.00 3.82
73 86 0.896923 TTGGCCAGTCCATTTGATGC 59.103 50.000 5.11 0.00 46.04 3.91
75 88 4.914177 AAAATTGGCCAGTCCATTTGAT 57.086 36.364 12.73 0.00 46.04 2.57
77 90 8.735692 ATAATAAAAATTGGCCAGTCCATTTG 57.264 30.769 12.73 0.00 46.04 2.32
135 148 5.189736 TCTTTGCATTCCACTACTCATACCT 59.810 40.000 0.00 0.00 0.00 3.08
146 159 6.806388 ATCCAAATTTTCTTTGCATTCCAC 57.194 33.333 0.00 0.00 0.00 4.02
204 217 3.223435 TCGGCACTTTCCCAAAATAACA 58.777 40.909 0.00 0.00 0.00 2.41
213 226 2.091541 TCAATCAATCGGCACTTTCCC 58.908 47.619 0.00 0.00 0.00 3.97
235 248 1.532090 CCCATTTAACGCGCGCATTAA 60.532 47.619 32.58 29.28 0.00 1.40
254 267 0.961019 TGCAGCCAATTGAGTTGACC 59.039 50.000 7.12 0.00 40.37 4.02
263 276 3.160679 ACTCCTAAAGTGCAGCCAATT 57.839 42.857 0.00 0.00 36.65 2.32
301 335 2.579201 CGTCGCCTCACCTCCATT 59.421 61.111 0.00 0.00 0.00 3.16
328 362 2.023307 TCACCTCTACTCCTAAAGGGGG 60.023 54.545 0.00 0.00 41.02 5.40
362 396 7.595819 ATTATGTTGAGTGAAAACAGGGAAA 57.404 32.000 0.00 0.00 40.64 3.13
365 399 6.980593 TCAATTATGTTGAGTGAAAACAGGG 58.019 36.000 0.00 0.00 40.64 4.45
405 440 5.935789 AGCCTGCGTAGATTTTAACACTTTA 59.064 36.000 0.53 0.00 0.00 1.85
413 448 2.689471 TCGGTAGCCTGCGTAGATTTTA 59.311 45.455 0.53 0.00 0.00 1.52
506 543 7.833285 AAGGAAGCCTGAAGTTTATTTGTAA 57.167 32.000 0.00 0.00 32.13 2.41
578 616 2.270352 AAAAGACTCCATTGGCGACA 57.730 45.000 0.00 0.00 39.83 4.35
636 677 2.121291 TGGCCGAATGACTAATGCAA 57.879 45.000 0.00 0.00 0.00 4.08
638 679 2.479560 GGTTTGGCCGAATGACTAATGC 60.480 50.000 9.15 0.00 0.00 3.56
709 750 2.357154 CGGGATGGTGGAGAGGAAAAAT 60.357 50.000 0.00 0.00 0.00 1.82
872 933 5.374071 AGTTCATACCTCAAAACCGAAGTT 58.626 37.500 0.00 0.00 38.03 2.66
1073 1136 5.934625 CACAGAGCAAACCTAGTTCAACTAT 59.065 40.000 0.00 0.00 29.08 2.12
1296 1359 7.095910 GGTGATACTCCAATCATCTATGACTG 58.904 42.308 0.00 0.00 40.03 3.51
1306 1369 6.126863 AGTTCTTTGGTGATACTCCAATCA 57.873 37.500 6.20 0.00 43.25 2.57
1368 1431 1.234615 ACCAACTCATTGTTCGGGCG 61.235 55.000 0.00 0.00 36.63 6.13
1377 1440 1.478510 AGATCTCGCGACCAACTCATT 59.521 47.619 3.71 0.00 0.00 2.57
1493 1565 3.330701 ACTTTCCTGAGGTGAAATAGGCA 59.669 43.478 0.00 0.00 31.75 4.75
1512 1584 2.821969 CTGAGCAAATAGTTGGGCACTT 59.178 45.455 4.91 0.00 36.88 3.16
1521 1593 6.062095 ACTACAAACAACCTGAGCAAATAGT 58.938 36.000 0.00 0.00 0.00 2.12
1641 1713 5.059161 CCTCTTGACTCACAATGAAGACAA 58.941 41.667 0.00 0.00 37.88 3.18
2116 3714 3.737559 ATTTGTGAGCCTGGGTGAATA 57.262 42.857 1.59 0.00 0.00 1.75
2137 3735 9.946165 GTGCTTCAAAAACATAGTTTTAGTAGT 57.054 29.630 8.14 0.00 0.00 2.73
2138 3736 9.944663 TGTGCTTCAAAAACATAGTTTTAGTAG 57.055 29.630 8.14 7.06 0.00 2.57
2408 4006 7.390440 ACAGTCGATTCAGGAAAAATGACATTA 59.610 33.333 0.00 0.00 0.00 1.90
2429 4030 4.743493 ACACCAATTTGTTTGACACAGTC 58.257 39.130 0.00 0.00 37.53 3.51
2535 4136 3.837355 AGCAAAGAACAGATTTGGGACT 58.163 40.909 1.12 0.00 37.96 3.85
3150 4751 3.786656 CCGATTGGCAGAAGGATCA 57.213 52.632 0.00 0.00 0.00 2.92
3422 5023 6.631962 ACCAAAACAACCAAGACGATAAAAA 58.368 32.000 0.00 0.00 0.00 1.94
3469 5070 4.082125 CCCATTCAGCTAGGAAACAAAGT 58.918 43.478 0.00 0.00 0.00 2.66
3543 5145 5.569355 TGAATGGTTTAAGATCTGCCTGAA 58.431 37.500 0.00 0.00 0.00 3.02
3620 5222 5.592587 TGGGAAGAATTAGACAGGGAAAA 57.407 39.130 0.00 0.00 0.00 2.29
3749 7117 6.857437 TCAAGATAGGTCAGAATCAGTTCA 57.143 37.500 0.00 0.00 36.79 3.18
3888 7349 3.289834 CTGCGGCTGTGGCTGTTT 61.290 61.111 0.00 0.00 45.94 2.83
3943 7404 2.289133 TGTATGCTGTAAACGTGGCTGA 60.289 45.455 0.00 0.00 0.00 4.26
4165 7626 1.832912 CACTCTGGCTGGGGTATCC 59.167 63.158 0.00 0.00 0.00 2.59
4246 7709 2.093973 CGTAATGAGAAGGCTCCACTGT 60.094 50.000 0.00 0.00 40.55 3.55
4260 7723 6.600427 TGAGGTTCAGTGAGTATACGTAATGA 59.400 38.462 0.00 7.98 0.00 2.57


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

AutoCloner maintained by Alex Coulton.