Multiple sequence alignment - TraesCS7A01G279900

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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 TraesCS7A01G279900 chr7A 100.000 4010 0 0 1 4010 299375355 299371346 0 7406
1 TraesCS7A01G279900 chr3A 95.926 4026 142 15 1 4008 32217114 32213093 0 6506
2 TraesCS7A01G279900 chr6A 95.184 4028 169 21 1 4008 554926829 554922807 0 6340
3 TraesCS7A01G279900 chr5A 95.041 4033 159 24 1 4008 398469591 398473607 0 6301
4 TraesCS7A01G279900 chr5A 94.934 3849 153 23 184 4008 524687471 524683641 0 5989
5 TraesCS7A01G279900 chr5B 94.796 3805 169 23 1 3781 62149395 62153194 0 5903
6 TraesCS7A01G279900 chr1D 93.352 4031 200 51 1 4006 58456624 58460611 0 5897
7 TraesCS7A01G279900 chr1D 93.388 4023 193 44 1 4005 466334528 466338495 0 5888
8 TraesCS7A01G279900 chrUn 95.374 3718 148 17 311 4008 82551933 82548220 0 5891
9 TraesCS7A01G279900 chr7B 91.785 4029 270 46 1 4008 709380649 709384637 0 5550


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 TraesCS7A01G279900 chr7A 299371346 299375355 4009 True 7406 7406 100.000 1 4010 1 chr7A.!!$R1 4009
1 TraesCS7A01G279900 chr3A 32213093 32217114 4021 True 6506 6506 95.926 1 4008 1 chr3A.!!$R1 4007
2 TraesCS7A01G279900 chr6A 554922807 554926829 4022 True 6340 6340 95.184 1 4008 1 chr6A.!!$R1 4007
3 TraesCS7A01G279900 chr5A 398469591 398473607 4016 False 6301 6301 95.041 1 4008 1 chr5A.!!$F1 4007
4 TraesCS7A01G279900 chr5A 524683641 524687471 3830 True 5989 5989 94.934 184 4008 1 chr5A.!!$R1 3824
5 TraesCS7A01G279900 chr5B 62149395 62153194 3799 False 5903 5903 94.796 1 3781 1 chr5B.!!$F1 3780
6 TraesCS7A01G279900 chr1D 58456624 58460611 3987 False 5897 5897 93.352 1 4006 1 chr1D.!!$F1 4005
7 TraesCS7A01G279900 chr1D 466334528 466338495 3967 False 5888 5888 93.388 1 4005 1 chr1D.!!$F2 4004
8 TraesCS7A01G279900 chrUn 82548220 82551933 3713 True 5891 5891 95.374 311 4008 1 chrUn.!!$R1 3697
9 TraesCS7A01G279900 chr7B 709380649 709384637 3988 False 5550 5550 91.785 1 4008 1 chr7B.!!$F1 4007

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
811 832 0.842030 TGCAGGGGAAGATGTGGAGT 60.842 55.000 0.00 0.0 0.0 3.85 F
1237 1259 1.001517 TTTATGGCCTGGCTTGCGA 60.002 52.632 19.68 0.0 0.0 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2663 2727 2.685897 GTGCCAACCTGTTCAGTTACAA 59.314 45.455 0.0 0.0 0.0 2.41 R
3115 3230 0.033796 CCCCTGTCACTGCCATCAAT 60.034 55.000 0.0 0.0 0.0 2.57 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
73 76 5.179742 TGATTAATTCCGTGTTGTAAAGCGT 59.820 36.000 0.00 0.00 0.00 5.07
111 114 2.551270 TGGTAAGGGAGCTGAGTCATT 58.449 47.619 0.00 0.00 0.00 2.57
126 129 6.981559 GCTGAGTCATTTTCTAGGGTAAGTAG 59.018 42.308 0.00 0.00 0.00 2.57
316 321 6.599356 TCTTGTAGTTGACTAGTTGGCATA 57.401 37.500 0.00 0.00 31.11 3.14
342 348 5.664457 TCATAGTTGACATCAGTGGTCATC 58.336 41.667 3.45 3.55 44.11 2.92
533 546 5.925509 TCCACTAGAACTTTTTGTAGCTGT 58.074 37.500 0.00 0.00 32.83 4.40
811 832 0.842030 TGCAGGGGAAGATGTGGAGT 60.842 55.000 0.00 0.00 0.00 3.85
886 907 1.429687 ACGCCTCTCTATCCCCACTAT 59.570 52.381 0.00 0.00 0.00 2.12
1012 1033 6.446649 CAGACCTCTGAAATGGTTTTCCCAA 61.447 44.000 0.00 0.00 46.28 4.12
1237 1259 1.001517 TTTATGGCCTGGCTTGCGA 60.002 52.632 19.68 0.00 0.00 5.10
1476 1503 8.908786 TTCATCTATTCTTGTTCTTTCTGTGT 57.091 30.769 0.00 0.00 0.00 3.72
1547 1577 1.561643 TTTGTTTGGGTCTGGTGCAA 58.438 45.000 0.00 0.00 0.00 4.08
2158 2210 1.475034 GGAGCAGACACCACTGTTTGA 60.475 52.381 0.00 0.00 34.99 2.69
2215 2267 7.924541 TCCAAGTTACCAATAACCTACAATCT 58.075 34.615 0.00 0.00 41.54 2.40
2325 2378 5.857822 ACTTTTGTAGTTGCGAGAATACC 57.142 39.130 0.00 0.00 31.29 2.73
2663 2727 1.242076 GTCAATGAGCTGTGCAAGGT 58.758 50.000 0.00 0.00 40.07 3.50
2818 2888 3.583966 ACGGGGGTCAACTATACAAGAAA 59.416 43.478 0.00 0.00 0.00 2.52
2905 2975 0.028902 CGACGAGGACACATATGCGA 59.971 55.000 1.58 0.00 0.00 5.10
2970 3058 0.398381 ATGCAGAGGAGGAGGAGGAC 60.398 60.000 0.00 0.00 0.00 3.85
2986 3095 1.636519 AGGACGAAGAGGAAGAGGAGA 59.363 52.381 0.00 0.00 0.00 3.71
3007 3116 1.367848 AGGAGGAGGAGGAGGACAAAT 59.632 52.381 0.00 0.00 0.00 2.32
3115 3230 4.299796 GGGACAAAGGGGCAGCCA 62.300 66.667 15.19 0.00 0.00 4.75
3372 3488 2.739943 TGAGTAGCAGGAGCACACTAT 58.260 47.619 0.00 0.00 45.49 2.12
3432 3548 6.866248 GGATTTGCCGAAGTCAAAGAAAAATA 59.134 34.615 0.00 0.00 39.23 1.40
3441 3557 7.165154 CGAAGTCAAAGAAAAATAACGAAGCAA 59.835 33.333 0.00 0.00 0.00 3.91
3450 3566 6.861065 AAAATAACGAAGCAAAGTCTCAGA 57.139 33.333 0.00 0.00 0.00 3.27
3544 3660 4.807834 CAGCGACAAAGATATGTGTGAGAT 59.192 41.667 0.00 0.00 32.57 2.75
3725 3843 1.610554 GGCAGCATCCATGGCAAACT 61.611 55.000 6.96 0.00 42.45 2.66
3731 3849 2.439409 CATCCATGGCAAACTCTCACA 58.561 47.619 6.96 0.00 0.00 3.58
3806 3926 3.692257 CCAAGAGAAGATGGTGAGTGT 57.308 47.619 0.00 0.00 31.84 3.55
3842 3962 0.610232 ATGGTCAAGGAAGCTGTGCC 60.610 55.000 0.00 0.00 0.00 5.01
3850 3970 1.699634 AGGAAGCTGTGCCTCAAACTA 59.300 47.619 0.00 0.00 0.00 2.24
3862 3982 4.640201 TGCCTCAAACTAATATGCCAACTC 59.360 41.667 0.00 0.00 0.00 3.01
3893 4015 2.622942 GAGCCAACCAATGTCACAGAAA 59.377 45.455 0.00 0.00 0.00 2.52
3941 4063 3.387699 CCTTTCAACAGTCCCACCAAAAT 59.612 43.478 0.00 0.00 0.00 1.82
4008 4133 2.757894 TAGGCCACAAAAGGTTTGGA 57.242 45.000 5.01 0.00 31.39 3.53
4009 4134 1.413118 AGGCCACAAAAGGTTTGGAG 58.587 50.000 5.01 0.00 31.39 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 56 5.229423 AGTACGCTTTACAACACGGAATTA 58.771 37.500 0.00 0.00 0.00 1.40
55 58 3.656559 AGTACGCTTTACAACACGGAAT 58.343 40.909 0.00 0.00 0.00 3.01
73 76 1.067846 CCAAGTGCTGCACGTCTAGTA 60.068 52.381 25.39 0.00 39.64 1.82
111 114 7.707624 TTCGACATTCTACTTACCCTAGAAA 57.292 36.000 0.00 0.00 34.61 2.52
126 129 9.409949 CGAGAAAAACACTTATATTCGACATTC 57.590 33.333 0.00 0.00 0.00 2.67
181 185 6.767524 AACAAAAATAGTGGTGTGAACTGA 57.232 33.333 0.00 0.00 0.00 3.41
213 217 8.908903 TGTCAACTACAAAAGGTTGTTATTGAT 58.091 29.630 15.42 0.00 46.01 2.57
264 269 7.120579 CCAACTAATGCCAACTAATGTCAACTA 59.879 37.037 0.00 0.00 0.00 2.24
316 321 6.475504 TGACCACTGATGTCAACTATGAAAT 58.524 36.000 0.00 0.00 39.66 2.17
811 832 0.250858 CTGCCTGGTTGTGATGGTCA 60.251 55.000 0.00 0.00 0.00 4.02
823 844 0.251077 GATGCCCTTATCCTGCCTGG 60.251 60.000 0.00 0.00 37.10 4.45
886 907 4.636648 CCTCGAAACTAGCTCTGACTTCTA 59.363 45.833 0.00 0.00 0.00 2.10
923 944 6.998074 TGGAAGTGTGTCTGATAAGTTCAATT 59.002 34.615 6.93 0.00 32.78 2.32
1012 1033 2.192263 GACACAGATCCTTCCCCTTCT 58.808 52.381 0.00 0.00 0.00 2.85
1027 1048 0.389025 ACACTGTCAGCATCGACACA 59.611 50.000 0.00 0.00 40.94 3.72
1357 1379 5.992829 TGTTCTGGAAAGCTTCGTTAATGTA 59.007 36.000 0.00 0.00 0.00 2.29
1547 1577 4.022242 ACGAGCGCATCAAGGTATAGTATT 60.022 41.667 11.47 0.00 0.00 1.89
2158 2210 3.244284 TGCTTCAGCTTGCAAAATTCCAT 60.244 39.130 0.00 0.00 42.66 3.41
2215 2267 3.885901 TGTATGCAAAACACTAACCTGCA 59.114 39.130 0.00 0.00 46.20 4.41
2284 2337 9.077885 ACAAAAGTTATACATGTCCAACTGAAT 57.922 29.630 20.00 10.69 31.80 2.57
2663 2727 2.685897 GTGCCAACCTGTTCAGTTACAA 59.314 45.455 0.00 0.00 0.00 2.41
2818 2888 6.360618 ACTCATCCTCAACAAACTCTTCTTT 58.639 36.000 0.00 0.00 0.00 2.52
2905 2975 3.729108 TGTCCTCCTCCTCTGATTCATT 58.271 45.455 0.00 0.00 0.00 2.57
2970 3058 2.687935 CTCCTTCTCCTCTTCCTCTTCG 59.312 54.545 0.00 0.00 0.00 3.79
2986 3095 0.793617 TTGTCCTCCTCCTCCTCCTT 59.206 55.000 0.00 0.00 0.00 3.36
3007 3116 5.011982 TCCTCTCCTTTGTCCTCTTCTTA 57.988 43.478 0.00 0.00 0.00 2.10
3114 3229 1.100510 CCCTGTCACTGCCATCAATG 58.899 55.000 0.00 0.00 0.00 2.82
3115 3230 0.033796 CCCCTGTCACTGCCATCAAT 60.034 55.000 0.00 0.00 0.00 2.57
3129 3244 0.674895 CGCCTTTGTCTTCTCCCCTG 60.675 60.000 0.00 0.00 0.00 4.45
3372 3488 8.461222 CCAGCAAGTTTTGTCAATCAATATCTA 58.539 33.333 0.00 0.00 35.84 1.98
3432 3548 2.139118 GCTCTGAGACTTTGCTTCGTT 58.861 47.619 9.28 0.00 0.00 3.85
3441 3557 3.630892 ATCAATGCTGCTCTGAGACTT 57.369 42.857 9.28 0.00 0.00 3.01
3450 3566 3.952323 AGCTTGAACATATCAATGCTGCT 59.048 39.130 0.00 5.89 46.62 4.24
3544 3660 4.583907 TCTTGTCAATGGCAAAGTTGATCA 59.416 37.500 0.79 0.00 36.79 2.92
3674 3792 1.199615 GAGCTTAGGTCTGGGAGCTT 58.800 55.000 3.96 0.00 44.88 3.74
3725 3843 0.247460 CGCTTCTGGACCATGTGAGA 59.753 55.000 0.00 0.00 0.00 3.27
3731 3849 1.003118 TGCTTTACGCTTCTGGACCAT 59.997 47.619 0.00 0.00 40.11 3.55
3806 3926 7.933577 CCTTGACCATATTTACTTCAGCATCTA 59.066 37.037 0.00 0.00 0.00 1.98
3842 3962 5.580691 TCACGAGTTGGCATATTAGTTTGAG 59.419 40.000 0.00 0.00 0.00 3.02
3850 3970 2.093500 TCTGCTCACGAGTTGGCATATT 60.093 45.455 0.00 0.00 32.85 1.28
3862 3982 1.739562 GGTTGGCTCTCTGCTCACG 60.740 63.158 0.00 0.00 42.39 4.35
3893 4015 4.290722 AGTCTTCCCCTTGATCTGTTGAAT 59.709 41.667 0.00 0.00 0.00 2.57
3941 4063 4.890158 TGACAATCTTCTGCTTAGGTGA 57.110 40.909 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.