Multiple sequence alignment - TraesCS4A01G060500

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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 TraesCS4A01G060500 chr4A 100.000 4039 0 0 1 4039 57406998 57411036 0 7459
1 TraesCS4A01G060500 chr5A 93.782 4085 200 31 1 4036 169172092 169176171 0 6087
2 TraesCS4A01G060500 chr5A 92.230 4080 236 41 1 4035 49880404 49884447 0 5703
3 TraesCS4A01G060500 chr5A 94.157 2550 129 17 428 2959 33916758 33914211 0 3866
4 TraesCS4A01G060500 chr2A 93.252 4090 208 32 1 4039 614230006 614225934 0 5962
5 TraesCS4A01G060500 chr2A 92.664 3067 162 39 1 3011 687278320 687275261 0 4359
6 TraesCS4A01G060500 chr2A 92.560 3078 165 45 21 3043 389215413 389212345 0 4357
7 TraesCS4A01G060500 chr3A 93.445 4058 200 42 42 4039 32217081 32213030 0 5960
8 TraesCS4A01G060500 chr7A 93.264 4053 204 43 42 4039 299375323 299371285 0 5908
9 TraesCS4A01G060500 chr7A 93.672 806 35 8 22 813 701318844 701319647 0 1192
10 TraesCS4A01G060500 chr7A 89.940 666 26 19 1 629 624765116 624764455 0 821
11 TraesCS4A01G060500 chr2B 92.836 4104 220 38 1 4036 608466077 608461980 0 5882
12 TraesCS4A01G060500 chr2B 91.142 4064 284 41 21 4036 67257737 67261772 0 5441
13 TraesCS4A01G060500 chr2B 92.762 3081 157 44 21 3043 772243289 772246361 0 4394
14 TraesCS4A01G060500 chr5B 92.628 4083 227 34 1 4039 12567836 12563784 0 5805
15 TraesCS4A01G060500 chr5B 92.255 3796 221 47 22 3746 62149401 62153194 0 5313
16 TraesCS4A01G060500 chr7B 91.109 4083 268 40 22 4039 475377693 475373641 0 5441
17 TraesCS4A01G060500 chr7B 92.535 576 25 9 1 562 194121723 194122294 0 809
18 TraesCS4A01G060500 chr5D 94.936 1086 49 2 2956 4035 424145698 424144613 0 1696
19 TraesCS4A01G060500 chr6A 93.478 460 22 4 22 474 184593916 184594374 0 676


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 TraesCS4A01G060500 chr4A 57406998 57411036 4038 False 7459 7459 100.000 1 4039 1 chr4A.!!$F1 4038
1 TraesCS4A01G060500 chr5A 169172092 169176171 4079 False 6087 6087 93.782 1 4036 1 chr5A.!!$F2 4035
2 TraesCS4A01G060500 chr5A 49880404 49884447 4043 False 5703 5703 92.230 1 4035 1 chr5A.!!$F1 4034
3 TraesCS4A01G060500 chr5A 33914211 33916758 2547 True 3866 3866 94.157 428 2959 1 chr5A.!!$R1 2531
4 TraesCS4A01G060500 chr2A 614225934 614230006 4072 True 5962 5962 93.252 1 4039 1 chr2A.!!$R2 4038
5 TraesCS4A01G060500 chr2A 687275261 687278320 3059 True 4359 4359 92.664 1 3011 1 chr2A.!!$R3 3010
6 TraesCS4A01G060500 chr2A 389212345 389215413 3068 True 4357 4357 92.560 21 3043 1 chr2A.!!$R1 3022
7 TraesCS4A01G060500 chr3A 32213030 32217081 4051 True 5960 5960 93.445 42 4039 1 chr3A.!!$R1 3997
8 TraesCS4A01G060500 chr7A 299371285 299375323 4038 True 5908 5908 93.264 42 4039 1 chr7A.!!$R1 3997
9 TraesCS4A01G060500 chr7A 701318844 701319647 803 False 1192 1192 93.672 22 813 1 chr7A.!!$F1 791
10 TraesCS4A01G060500 chr7A 624764455 624765116 661 True 821 821 89.940 1 629 1 chr7A.!!$R2 628
11 TraesCS4A01G060500 chr2B 608461980 608466077 4097 True 5882 5882 92.836 1 4036 1 chr2B.!!$R1 4035
12 TraesCS4A01G060500 chr2B 67257737 67261772 4035 False 5441 5441 91.142 21 4036 1 chr2B.!!$F1 4015
13 TraesCS4A01G060500 chr2B 772243289 772246361 3072 False 4394 4394 92.762 21 3043 1 chr2B.!!$F2 3022
14 TraesCS4A01G060500 chr5B 12563784 12567836 4052 True 5805 5805 92.628 1 4039 1 chr5B.!!$R1 4038
15 TraesCS4A01G060500 chr5B 62149401 62153194 3793 False 5313 5313 92.255 22 3746 1 chr5B.!!$F1 3724
16 TraesCS4A01G060500 chr7B 475373641 475377693 4052 True 5441 5441 91.109 22 4039 1 chr7B.!!$R1 4017
17 TraesCS4A01G060500 chr7B 194121723 194122294 571 False 809 809 92.535 1 562 1 chr7B.!!$F1 561
18 TraesCS4A01G060500 chr5D 424144613 424145698 1085 True 1696 1696 94.936 2956 4035 1 chr5D.!!$R1 1079

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
421 474 1.135094 AGATGCTGAGGTATGTGGGG 58.865 55.0 0.0 0.0 0.00 4.96 F
1211 1309 0.107017 ATGGCTGGAAGAACCGATGG 60.107 55.0 0.0 0.0 42.61 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 1501 0.731417 GTGATACAAGCAGCAGCAGG 59.269 55.0 3.17 0.0 45.49 4.85 R
3112 3361 0.881118 ACTGCCATTAGTTGTTGCGG 59.119 50.0 0.00 0.0 0.00 5.69 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
164 193 7.544566 TCTCGAATATAAGTGTTTTTCTCGCTT 59.455 33.333 0.00 0.00 38.78 4.68
311 361 3.957468 GCATTAGTTGGCATCTTGTAGC 58.043 45.455 2.98 0.61 0.00 3.58
421 474 1.135094 AGATGCTGAGGTATGTGGGG 58.865 55.000 0.00 0.00 0.00 4.96
586 675 1.593196 GTTGCACACTGGCAGTCTTA 58.407 50.000 19.13 1.53 45.88 2.10
598 687 2.329379 GCAGTCTTACAGTTGTCCTCG 58.671 52.381 0.00 0.00 0.00 4.63
907 1004 3.570550 ACAGAAGTCAGAGCTAGTTTCGT 59.429 43.478 0.00 0.00 0.00 3.85
997 1094 1.270907 CTACCAGCCACAGACCTCTT 58.729 55.000 0.00 0.00 0.00 2.85
1095 1193 6.209391 ACAGGGGTCAAAAAGTCAGATATTTG 59.791 38.462 0.00 0.00 34.81 2.32
1122 1220 3.525199 ACAAGGATGCCACTAGGAGATTT 59.475 43.478 0.00 0.00 36.89 2.17
1188 1286 5.587443 CACTACATGGCTCAAGATGATTCAA 59.413 40.000 0.00 0.00 0.00 2.69
1206 1304 4.156455 TCAAGATATGGCTGGAAGAACC 57.844 45.455 0.00 0.00 34.07 3.62
1211 1309 0.107017 ATGGCTGGAAGAACCGATGG 60.107 55.000 0.00 0.00 42.61 3.51
1218 1316 3.457542 TGGAAGAACCGATGGCACATTG 61.458 50.000 0.00 0.00 42.94 2.82
1230 1328 1.550072 GGCACATTGTTTATGGCCTGT 59.450 47.619 3.32 0.00 42.56 4.00
1378 1476 2.081462 ACATTAACGAAGCTTTCCGGG 58.919 47.619 11.68 0.00 0.00 5.73
1388 1486 1.077716 CTTTCCGGGACATGGACCC 60.078 63.158 17.02 17.02 43.57 4.46
1403 1501 1.578206 GACCCGGAGAAGCAAACTGC 61.578 60.000 0.73 0.00 45.46 4.40
1476 1579 3.309682 TCTGTTCTTGTTCTTTCTGTGCG 59.690 43.478 0.00 0.00 0.00 5.34
1835 1948 5.041951 TGTAGCTTTAAGTTTGGCAATCG 57.958 39.130 0.00 0.00 0.00 3.34
1860 1973 6.426328 GGCACACATGTTCATTTTAAATTGGA 59.574 34.615 0.00 0.00 0.00 3.53
1908 2021 7.165812 CACAGTTTTACTAATCTTGTTGCACAC 59.834 37.037 0.00 0.00 0.00 3.82
1961 2077 3.293714 TGCCATGTGGGTTGCACG 61.294 61.111 0.54 0.00 39.65 5.34
1986 2103 3.502191 TTGTGTCTTTGTTCAGTTGCC 57.498 42.857 0.00 0.00 0.00 4.52
2155 2281 0.319555 GCACGAAGCAGACACCACTA 60.320 55.000 0.00 0.00 44.79 2.74
2265 2398 8.357402 AGAAATTTGTACCACTTACCAACATTC 58.643 33.333 0.00 0.00 0.00 2.67
2270 2405 6.228258 TGTACCACTTACCAACATTCTTCTC 58.772 40.000 0.00 0.00 0.00 2.87
2314 2449 8.995220 TCAGTTGGACATGTATAACTTTTGTAC 58.005 33.333 19.21 0.00 31.47 2.90
2337 2472 5.578727 ACTTGCGAGAATACAGAATTCAGTC 59.421 40.000 8.31 0.00 45.58 3.51
2362 2497 4.142534 GCTGTGATGTATGTTCAGTTGCAT 60.143 41.667 0.00 0.00 0.00 3.96
2411 2547 5.975693 TCTTTTGGACAGTCAAAGTGTTT 57.024 34.783 11.35 0.00 37.82 2.83
2485 2624 1.545582 ACAATGCATGTGTAGTTGGCC 59.454 47.619 0.00 0.00 41.93 5.36
2555 2697 6.594744 TGCTTATCACATCATGGTCAGTTAT 58.405 36.000 0.00 0.00 0.00 1.89
2772 2927 1.037030 AATGCAAATCGGGGCGTCAT 61.037 50.000 0.00 0.00 0.00 3.06
2914 3070 1.871676 CACAGATGCGGATGAATCAGG 59.128 52.381 0.00 0.00 31.86 3.86
2984 3233 3.716872 AGGAGGACAAACAAGAAGAGGAA 59.283 43.478 0.00 0.00 0.00 3.36
3036 3285 0.341258 TGAGGCAGAGGAGGAGGAAT 59.659 55.000 0.00 0.00 0.00 3.01
3075 3324 1.850755 GGGGACAGGGACAAAGGGA 60.851 63.158 0.00 0.00 0.00 4.20
3093 3342 1.339055 GGACAGCAGTTGATGGCAGTA 60.339 52.381 5.50 0.00 42.25 2.74
3112 3361 2.869101 AAGAGGGGAGAAGACAAAGC 57.131 50.000 0.00 0.00 0.00 3.51
3120 3369 1.333619 GAGAAGACAAAGCCGCAACAA 59.666 47.619 0.00 0.00 0.00 2.83
3123 3372 1.961793 AGACAAAGCCGCAACAACTA 58.038 45.000 0.00 0.00 0.00 2.24
3246 3498 1.053424 TGACAACGCCCCTAGTTCTT 58.947 50.000 0.00 0.00 0.00 2.52
3253 3505 1.485066 CGCCCCTAGTTCTTGTGGTAT 59.515 52.381 0.00 0.00 0.00 2.73
3297 3549 1.133809 TAGCACTTCTGCCACCCCTT 61.134 55.000 0.00 0.00 45.53 3.95
3399 3651 5.728471 TGCCAAAGTCAAAGAAAAATGACA 58.272 33.333 8.43 0.00 46.55 3.58
3405 3657 8.392612 CAAAGTCAAAGAAAAATGACAAAGCAT 58.607 29.630 8.43 0.00 46.55 3.79
3411 3663 9.897744 CAAAGAAAAATGACAAAGCATAGTCTA 57.102 29.630 0.00 0.00 35.81 2.59
3536 3788 2.877097 TTGCCATTGACAAGAGCCTA 57.123 45.000 9.13 0.00 0.00 3.93
3778 4033 2.570752 AGAAGATGGTGAGTGCAGATGT 59.429 45.455 0.00 0.00 0.00 3.06
3804 4059 7.175104 TGAAGTAAATATGGTCAAGGAAGCTT 58.825 34.615 0.00 0.00 0.00 3.74
3936 4194 6.547510 ACCTAAGCAGAAGATTGTCAAGTTTT 59.452 34.615 0.00 0.00 0.00 2.43
3982 4240 2.237392 CCACAAAAGGTTTGGGGTTCAA 59.763 45.455 12.92 0.00 38.17 2.69
3996 4254 3.244112 GGGGTTCAAAGACGAGAGAGAAA 60.244 47.826 0.00 0.00 0.00 2.52
4021 4279 1.601419 GCCACAGCCATTGATGCAGT 61.601 55.000 0.00 0.00 0.00 4.40
4022 4280 0.892755 CCACAGCCATTGATGCAGTT 59.107 50.000 0.00 0.00 0.00 3.16
4036 4294 1.024271 GCAGTTGTGCCAAGTTCTGA 58.976 50.000 0.00 0.00 44.72 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 205 5.345741 GTGCGAACTGTTGCATAATTTCATT 59.654 36.000 16.54 0.0 43.96 2.57
190 219 3.630312 ACAAAAATAGTGGTGCGAACTGT 59.370 39.130 0.00 0.0 0.00 3.55
311 361 6.344500 ACTATGAAAGATGCCAACTAGTCAG 58.656 40.000 0.00 0.0 0.00 3.51
399 452 1.590932 CACATACCTCAGCATCTGCC 58.409 55.000 0.00 0.0 43.38 4.85
473 534 5.982465 TGCAAACAAGAAAAATAGCAACC 57.018 34.783 0.00 0.0 0.00 3.77
535 597 0.815734 GTACGAGACCTGGCAGCTAA 59.184 55.000 9.56 0.0 0.00 3.09
586 675 0.753262 AAGCTCACGAGGACAACTGT 59.247 50.000 0.00 0.0 0.00 3.55
598 687 8.020819 TGTATTTGTGCAACTAATAAAGCTCAC 58.979 33.333 0.00 0.0 43.92 3.51
935 1032 0.667792 GTCCGCTGGAAGTGTGTCTC 60.668 60.000 0.00 0.0 44.74 3.36
1095 1193 2.359900 CTAGTGGCATCCTTGTCAACC 58.640 52.381 0.00 0.0 39.65 3.77
1142 1240 4.230272 TGATCTGGGGATGAGAATTTCCAA 59.770 41.667 0.00 0.0 33.43 3.53
1188 1286 2.398588 TCGGTTCTTCCAGCCATATCT 58.601 47.619 0.00 0.0 35.57 1.98
1206 1304 2.462889 GCCATAAACAATGTGCCATCG 58.537 47.619 0.00 0.0 33.34 3.84
1211 1309 2.493278 AGACAGGCCATAAACAATGTGC 59.507 45.455 5.01 0.0 33.34 4.57
1218 1316 0.451783 CCGCAAGACAGGCCATAAAC 59.548 55.000 5.01 0.0 43.02 2.01
1230 1328 2.260869 GCTGAAGGCAACCGCAAGA 61.261 57.895 0.00 0.0 41.24 3.02
1378 1476 1.153349 GCTTCTCCGGGTCCATGTC 60.153 63.158 0.00 0.0 0.00 3.06
1388 1486 1.871772 CAGGCAGTTTGCTTCTCCG 59.128 57.895 0.67 0.0 44.28 4.63
1403 1501 0.731417 GTGATACAAGCAGCAGCAGG 59.269 55.000 3.17 0.0 45.49 4.85
1604 1708 7.805083 ATTAGAGTACTATCCCATGCATTCT 57.195 36.000 0.00 0.0 0.00 2.40
1712 1819 7.712797 TCAAAAGAACATAAAAGGAAGACACC 58.287 34.615 0.00 0.0 0.00 4.16
1835 1948 6.426328 TCCAATTTAAAATGAACATGTGTGCC 59.574 34.615 0.00 0.0 0.00 5.01
1908 2021 3.752747 TCTACCAACTGATGCAACACATG 59.247 43.478 0.00 0.0 39.84 3.21
1961 2077 5.389411 GCAACTGAACAAAGACACAAAAACC 60.389 40.000 0.00 0.0 0.00 3.27
2155 2281 3.816523 CAGCTTGCAAAATTCCACCAAAT 59.183 39.130 0.00 0.0 0.00 2.32
2265 2398 3.118112 ACATACATCCCAGCCAAGAGAAG 60.118 47.826 0.00 0.0 0.00 2.85
2270 2405 2.947652 CTGAACATACATCCCAGCCAAG 59.052 50.000 0.00 0.0 0.00 3.61
2314 2449 5.276114 CGACTGAATTCTGTATTCTCGCAAG 60.276 44.000 16.89 0.0 42.63 4.01
2337 2472 2.621338 ACTGAACATACATCACAGCCG 58.379 47.619 0.00 0.0 32.67 5.52
2362 2497 8.204160 ACATGTGCAACTACAGAAGCTTATATA 58.796 33.333 0.00 0.0 38.04 0.86
2411 2547 6.707440 AGTTGATGACAATGGTTGTAAACA 57.293 33.333 0.00 0.0 45.52 2.83
2485 2624 5.782047 TGGCCAACTAAAAACATGATTCTG 58.218 37.500 0.61 0.0 0.00 3.02
2596 2741 6.146601 TCTGCATCAACACAAAAGATTCAA 57.853 33.333 0.00 0.0 0.00 2.69
2694 2849 2.350522 GTCATCGATCTTGGCAACTGT 58.649 47.619 0.00 0.0 37.61 3.55
2772 2927 1.066908 CTTTCTTTTTGGAGCACGGCA 59.933 47.619 0.00 0.0 0.00 5.69
2914 3070 1.127343 CTCATCCTTGTCCTCCTCCC 58.873 60.000 0.00 0.0 0.00 4.30
2984 3233 2.723530 TGTCCTCCTCCTCTCCTTTT 57.276 50.000 0.00 0.0 0.00 2.27
3036 3285 2.305927 CCTCTTTGGCCTCACCTTCTTA 59.694 50.000 3.32 0.0 40.22 2.10
3075 3324 2.038952 TCTTACTGCCATCAACTGCTGT 59.961 45.455 0.00 0.0 41.61 4.40
3093 3342 1.352687 GGCTTTGTCTTCTCCCCTCTT 59.647 52.381 0.00 0.0 0.00 2.85
3112 3361 0.881118 ACTGCCATTAGTTGTTGCGG 59.119 50.000 0.00 0.0 0.00 5.69
3120 3369 2.254152 TCCCTCTCACTGCCATTAGT 57.746 50.000 0.00 0.0 0.00 2.24
3123 3372 1.661463 TCTTCCCTCTCACTGCCATT 58.339 50.000 0.00 0.0 0.00 3.16
3246 3498 0.391927 GTGTTGCCGCCTATACCACA 60.392 55.000 0.00 0.0 0.00 4.17
3253 3505 1.078497 CTGGATGTGTTGCCGCCTA 60.078 57.895 0.00 0.0 0.00 3.93
3297 3549 2.892215 TCAATGAATTGTTGCTGCTGGA 59.108 40.909 0.00 0.0 38.84 3.86
3399 3651 2.239654 TGCTGCCCTTAGACTATGCTTT 59.760 45.455 0.00 0.0 0.00 3.51
3405 3657 5.307976 ACATATCAATGCTGCCCTTAGACTA 59.692 40.000 0.00 0.0 36.50 2.59
3411 3663 3.634504 TGAACATATCAATGCTGCCCTT 58.365 40.909 0.00 0.0 36.50 3.95
3536 3788 8.571461 TCTTTTCAGCATCACTTGATAAGAAT 57.429 30.769 5.35 0.0 32.63 2.40
3778 4033 7.175104 AGCTTCCTTGACCATATTTACTTCAA 58.825 34.615 0.00 0.0 0.00 2.69
3804 4059 4.523943 AGTTGGCATATCAGTTTGAAGCAA 59.476 37.500 0.00 0.0 0.00 3.91
3936 4194 1.928567 CCCCCTTTGTGCCCCTAGA 60.929 63.158 0.00 0.0 0.00 2.43
3982 4240 2.733858 GCTCGCATTTCTCTCTCGTCTT 60.734 50.000 0.00 0.0 0.00 3.01
3996 4254 2.044650 AATGGCTGTGGCTCGCAT 60.045 55.556 5.93 0.0 38.73 4.73


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

AutoCloner maintained by Alex Coulton.