Multiple sequence alignment - TraesCS2A01G052300

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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 TraesCS2A01G052300 chr2A 100.000 5632 0 0 1 5632 20644941 20650572 0.000000e+00 10401
1 TraesCS2A01G052300 chr3B 95.878 5652 173 37 1 5632 555162727 555157116 0.000000e+00 9092
2 TraesCS2A01G052300 chr3B 92.811 3116 177 17 2448 5556 358593217 358596292 0.000000e+00 4470
3 TraesCS2A01G052300 chr3B 96.829 410 12 1 1 409 555157472 555157063 0.000000e+00 684
4 TraesCS2A01G052300 chr3B 95.062 81 3 1 5552 5632 358597949 358598028 5.920000e-25 126
5 TraesCS2A01G052300 chr5A 95.842 5652 177 35 1 5632 41413578 41419191 0.000000e+00 9082
6 TraesCS2A01G052300 chr1B 94.949 5662 218 49 1 5632 654296329 654301952 0.000000e+00 8809
7 TraesCS2A01G052300 chr1D 93.973 5691 253 48 1 5632 332872560 332866901 0.000000e+00 8527
8 TraesCS2A01G052300 chr4A 93.853 5661 259 50 1 5632 271453054 271458654 0.000000e+00 8444
9 TraesCS2A01G052300 chr1A 93.826 5410 245 48 4 5382 272209932 272204581 0.000000e+00 8058
10 TraesCS2A01G052300 chr6B 94.821 4943 220 20 707 5632 581313309 581318232 0.000000e+00 7677
11 TraesCS2A01G052300 chr7B 95.424 4196 138 31 1 4179 702167262 702163104 0.000000e+00 6636
12 TraesCS2A01G052300 chr7B 96.341 410 14 1 1 409 702161583 702161174 0.000000e+00 673
13 TraesCS2A01G052300 chr4D 94.373 4194 163 43 487 4643 456255161 456259318 0.000000e+00 6370
14 TraesCS2A01G052300 chr7A 90.443 2867 177 57 195 3034 81786028 81788824 0.000000e+00 3687
15 TraesCS2A01G052300 chrUn 90.369 1329 70 33 162 1471 415501103 415499814 0.000000e+00 1692


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 TraesCS2A01G052300 chr2A 20644941 20650572 5631 False 10401.0 10401 100.0000 1 5632 1 chr2A.!!$F1 5631
1 TraesCS2A01G052300 chr3B 555157063 555162727 5664 True 4888.0 9092 96.3535 1 5632 2 chr3B.!!$R1 5631
2 TraesCS2A01G052300 chr3B 358593217 358598028 4811 False 2298.0 4470 93.9365 2448 5632 2 chr3B.!!$F1 3184
3 TraesCS2A01G052300 chr5A 41413578 41419191 5613 False 9082.0 9082 95.8420 1 5632 1 chr5A.!!$F1 5631
4 TraesCS2A01G052300 chr1B 654296329 654301952 5623 False 8809.0 8809 94.9490 1 5632 1 chr1B.!!$F1 5631
5 TraesCS2A01G052300 chr1D 332866901 332872560 5659 True 8527.0 8527 93.9730 1 5632 1 chr1D.!!$R1 5631
6 TraesCS2A01G052300 chr4A 271453054 271458654 5600 False 8444.0 8444 93.8530 1 5632 1 chr4A.!!$F1 5631
7 TraesCS2A01G052300 chr1A 272204581 272209932 5351 True 8058.0 8058 93.8260 4 5382 1 chr1A.!!$R1 5378
8 TraesCS2A01G052300 chr6B 581313309 581318232 4923 False 7677.0 7677 94.8210 707 5632 1 chr6B.!!$F1 4925
9 TraesCS2A01G052300 chr7B 702161174 702167262 6088 True 3654.5 6636 95.8825 1 4179 2 chr7B.!!$R1 4178
10 TraesCS2A01G052300 chr4D 456255161 456259318 4157 False 6370.0 6370 94.3730 487 4643 1 chr4D.!!$F1 4156
11 TraesCS2A01G052300 chr7A 81786028 81788824 2796 False 3687.0 3687 90.4430 195 3034 1 chr7A.!!$F1 2839
12 TraesCS2A01G052300 chrUn 415499814 415501103 1289 True 1692.0 1692 90.3690 162 1471 1 chrUn.!!$R1 1309

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
360 364 0.948623 CATTGTGAGCGGAACCACGA 60.949 55.000 0.0 0.00 36.15 4.35 F
551 569 1.010419 GCCCCGTACGTACACAACAG 61.010 60.000 24.5 7.69 0.00 3.16 F
660 678 1.077429 GCCTGACCTCCACCAATCC 60.077 63.158 0.0 0.00 0.00 3.01 F
661 679 1.852157 GCCTGACCTCCACCAATCCA 61.852 60.000 0.0 0.00 0.00 3.41 F
1217 1319 1.895131 GCAATGGACCAAGGACAACAT 59.105 47.619 0.0 0.00 0.00 2.71 F
1787 1904 2.677875 GGACAGGGGGCAAAGCAG 60.678 66.667 0.0 0.00 0.00 4.24 F
2838 2959 1.065358 GTGGTGGTGAATACACGTCG 58.935 55.000 0.0 0.00 46.77 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 1515 0.037326 CCGCCAAGACACAGAGCTTA 60.037 55.000 0.00 0.0 0.00 3.09 R
1925 2043 0.395724 GGATTGATTCCCCTTGCGGT 60.396 55.000 0.00 0.0 38.75 5.68 R
2318 2436 2.560542 AGGACATCATGTCTATCGCCTC 59.439 50.000 17.46 0.0 46.19 4.70 R
2336 2454 9.565090 CCATGATGTCATTTAGAAAATAGAGGA 57.435 33.333 0.00 0.0 33.61 3.71 R
2763 2881 3.190535 GCTGATTTTCCACTTCCGCTTTA 59.809 43.478 0.00 0.0 0.00 1.85 R
3720 3843 1.337167 CCTTTAGCAACAAGCCTTGCC 60.337 52.381 3.88 0.0 46.63 4.52 R
4683 5229 3.379452 AGCTCCTCCTGCTAGTGTAAAT 58.621 45.455 0.00 0.0 39.21 1.40 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
112 113 3.026694 GGCTCCATGAATTGGTAAAGCT 58.973 45.455 0.00 0.00 46.52 3.74
360 364 0.948623 CATTGTGAGCGGAACCACGA 60.949 55.000 0.00 0.00 36.15 4.35
372 376 3.007635 GGAACCACGAAAAAGGATCGAT 58.992 45.455 0.00 0.00 42.76 3.59
388 392 4.773149 GGATCGATGAATAGGGGTTAGACT 59.227 45.833 0.54 0.00 0.00 3.24
412 416 6.801575 TGTGTGCGTATATCTCTTACATTGA 58.198 36.000 0.00 0.00 0.00 2.57
499 509 2.413453 CTGCGTACTCTGCTTTTTCCTC 59.587 50.000 0.00 0.00 0.00 3.71
527 544 9.308318 CCCAAAAGAAAAATAGAAACGAGAAAA 57.692 29.630 0.00 0.00 0.00 2.29
551 569 1.010419 GCCCCGTACGTACACAACAG 61.010 60.000 24.50 7.69 0.00 3.16
575 593 3.580458 CTCCACCCCAGATTAGATCGATT 59.420 47.826 0.00 0.00 0.00 3.34
622 640 4.778415 GCTTCGCTCGACTCCGCA 62.778 66.667 0.00 0.00 35.37 5.69
660 678 1.077429 GCCTGACCTCCACCAATCC 60.077 63.158 0.00 0.00 0.00 3.01
661 679 1.852157 GCCTGACCTCCACCAATCCA 61.852 60.000 0.00 0.00 0.00 3.41
771 829 2.283676 GTGACCGACTCCTCCCCA 60.284 66.667 0.00 0.00 0.00 4.96
884 973 2.037136 CAAGCTCGCCCTGACCAAG 61.037 63.158 0.00 0.00 0.00 3.61
969 1070 4.654262 ACAGGAACTTGAAGGTAACAGAGA 59.346 41.667 0.00 0.00 34.60 3.10
974 1075 4.058817 ACTTGAAGGTAACAGAGAAAGCG 58.941 43.478 0.00 0.00 41.41 4.68
981 1082 6.038997 AGGTAACAGAGAAAGCGACTAATT 57.961 37.500 0.00 0.00 41.41 1.40
1173 1275 5.366186 AGAGGATGCTACAGATGAAGACAAT 59.634 40.000 0.00 0.00 0.00 2.71
1217 1319 1.895131 GCAATGGACCAAGGACAACAT 59.105 47.619 0.00 0.00 0.00 2.71
1341 1443 5.279006 GGATTTTGGAGAAGTTTCCCTTGTC 60.279 44.000 0.00 0.00 41.55 3.18
1413 1515 9.683069 GATAAAACAGTCAATGAACACTTCAAT 57.317 29.630 0.00 0.00 43.95 2.57
1461 1563 6.711645 AGTTAAAAACTGCTGGTTATCCGTTA 59.288 34.615 0.00 0.00 41.01 3.18
1679 1781 5.602978 AGTACAAGAATAGTGGGAATCGGAT 59.397 40.000 0.00 0.00 0.00 4.18
1787 1904 2.677875 GGACAGGGGGCAAAGCAG 60.678 66.667 0.00 0.00 0.00 4.24
1925 2043 8.421249 AGGAATAATTTTCACAAGGATGACAA 57.579 30.769 0.00 0.00 0.00 3.18
1997 2115 9.817809 TTGCACTGAATCCTTATTTACTACTAG 57.182 33.333 0.00 0.00 0.00 2.57
2220 2338 7.283127 GCACTTTATTCACCCAATATGAGAAGA 59.717 37.037 0.00 0.00 0.00 2.87
2678 2796 4.882427 GGGAGGGCAGAAAATCTACTTTAC 59.118 45.833 0.00 0.00 0.00 2.01
2838 2959 1.065358 GTGGTGGTGAATACACGTCG 58.935 55.000 0.00 0.00 46.77 5.12
3235 3356 6.011481 TCTAATGGTTACCGTTTTTGGGATT 58.989 36.000 14.53 0.00 34.27 3.01
3393 3514 7.269477 AGTTCAGGAAAATAATGATGCTAGC 57.731 36.000 8.10 8.10 0.00 3.42
3415 3538 6.217294 AGCCAATCTACTAACTCTATTTCGC 58.783 40.000 0.00 0.00 0.00 4.70
3603 3726 4.158394 GCCATGCAGGAAGAATTAAACTCA 59.842 41.667 0.00 0.00 41.22 3.41
3698 3821 9.305925 GATCTTTAAAAGGAAATTGAATGCGAT 57.694 29.630 0.00 0.00 0.00 4.58
3720 3843 7.148407 GCGATTGGTCAGGTGGATAAATATAAG 60.148 40.741 0.00 0.00 0.00 1.73
3769 3892 7.595819 ACACAAATGGAAGGAGTTGATTTTA 57.404 32.000 0.00 0.00 0.00 1.52
3822 3945 4.156190 ACCTCTATACGGATCATTAGTGCG 59.844 45.833 0.00 0.00 0.00 5.34
4201 4326 9.396022 GGTTATCCTCTAAATTTGACATGAAGA 57.604 33.333 0.00 0.00 0.00 2.87
4487 5033 5.573380 ACAAGACCTGATATATGCCATGT 57.427 39.130 0.00 0.00 0.00 3.21
4488 5034 5.945310 ACAAGACCTGATATATGCCATGTT 58.055 37.500 0.00 0.00 0.00 2.71
4683 5229 6.346096 CCGGAAATCAACTTCTGGTTATCTA 58.654 40.000 0.00 0.00 44.03 1.98
5031 5587 3.265791 GGTTGCTGATCCACTGACTAAG 58.734 50.000 0.00 0.00 0.00 2.18
5151 5708 2.983229 TGTGTGGCTTGCAACATTTTT 58.017 38.095 6.08 0.00 0.00 1.94
5242 5800 7.894753 TGCTTGGAATACATGAATGGAATAA 57.105 32.000 0.00 0.00 0.00 1.40
5388 5946 3.026694 GGCTCCATGAATTGGTAAAGCT 58.973 45.455 0.00 0.00 46.52 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
360 364 5.388599 ACCCCTATTCATCGATCCTTTTT 57.611 39.130 0.00 0.00 0.00 1.94
372 376 3.055385 GCACACAGTCTAACCCCTATTCA 60.055 47.826 0.00 0.00 0.00 2.57
388 392 6.695713 GTCAATGTAAGAGATATACGCACACA 59.304 38.462 0.00 0.00 0.00 3.72
412 416 0.541863 CCCTTAATCGGCTCTGGTGT 59.458 55.000 0.00 0.00 0.00 4.16
499 509 7.871853 TCTCGTTTCTATTTTTCTTTTGGGAG 58.128 34.615 0.00 0.00 0.00 4.30
527 544 1.202627 TGTGTACGTACGGGGCTTTTT 60.203 47.619 21.06 0.00 0.00 1.94
529 546 0.392336 TTGTGTACGTACGGGGCTTT 59.608 50.000 21.06 0.00 0.00 3.51
551 569 1.349357 GATCTAATCTGGGGTGGAGCC 59.651 57.143 0.00 0.00 0.00 4.70
575 593 0.456221 GACCAGAGGAATCGAGCGAA 59.544 55.000 0.00 0.00 0.00 4.70
645 663 1.676968 CGTGGATTGGTGGAGGTCA 59.323 57.895 0.00 0.00 0.00 4.02
719 777 4.506255 GCCCGAAGTGGATGGGGG 62.506 72.222 0.00 0.00 43.52 5.40
761 819 3.057337 CGAACGTTGGGGAGGAGT 58.943 61.111 5.00 0.00 0.00 3.85
858 916 4.742201 GGCGAGCTTGACGAGGCA 62.742 66.667 4.70 0.00 0.00 4.75
907 996 1.522569 GATGTAGGTCCTTGCCGCT 59.477 57.895 0.00 0.00 0.00 5.52
908 997 1.883084 CGATGTAGGTCCTTGCCGC 60.883 63.158 0.00 0.00 0.00 6.53
969 1070 7.624360 TCAATATCCAACAATTAGTCGCTTT 57.376 32.000 0.00 0.00 0.00 3.51
981 1082 7.185318 AGCCATTGAAATTCAATATCCAACA 57.815 32.000 19.42 0.00 44.60 3.33
1173 1275 6.317140 GCTTCAGTTCATCATTGTATTCCTGA 59.683 38.462 0.00 0.00 0.00 3.86
1217 1319 6.115446 CCAAGAATATAAACTCTGGCAGTCA 58.885 40.000 15.27 0.00 32.30 3.41
1317 1419 4.588951 ACAAGGGAAACTTCTCCAAAATCC 59.411 41.667 0.00 0.00 37.29 3.01
1341 1443 3.876914 TGTTCACAAGACTAAGCACCTTG 59.123 43.478 0.00 0.00 42.04 3.61
1413 1515 0.037326 CCGCCAAGACACAGAGCTTA 60.037 55.000 0.00 0.00 0.00 3.09
1461 1563 2.103153 TGACTTGGACTTCCTCCTGT 57.897 50.000 0.00 0.00 40.26 4.00
1679 1781 4.712337 GTCCTCCTCTCTTATTCCAGTTCA 59.288 45.833 0.00 0.00 0.00 3.18
1787 1904 6.751888 AGTTATGTGAAAAGAGTTGTTGTTGC 59.248 34.615 0.00 0.00 0.00 4.17
1925 2043 0.395724 GGATTGATTCCCCTTGCGGT 60.396 55.000 0.00 0.00 38.75 5.68
1997 2115 9.668497 AATCTACTACCCAACTATTCTGAAAAC 57.332 33.333 0.00 0.00 0.00 2.43
2220 2338 4.646492 AGCTTGGACACTGAAACAAGATTT 59.354 37.500 7.38 0.00 42.07 2.17
2318 2436 2.560542 AGGACATCATGTCTATCGCCTC 59.439 50.000 17.46 0.00 46.19 4.70
2336 2454 9.565090 CCATGATGTCATTTAGAAAATAGAGGA 57.435 33.333 0.00 0.00 33.61 3.71
2337 2455 9.565090 TCCATGATGTCATTTAGAAAATAGAGG 57.435 33.333 0.00 0.00 33.61 3.69
2763 2881 3.190535 GCTGATTTTCCACTTCCGCTTTA 59.809 43.478 0.00 0.00 0.00 1.85
2838 2959 7.716998 TCTTTGCAGAAATCATCTAGTATTCCC 59.283 37.037 0.00 0.00 36.32 3.97
3393 3514 9.347934 CTATGCGAAATAGAGTTAGTAGATTGG 57.652 37.037 0.00 0.00 0.00 3.16
3415 3538 3.556633 CCACTTCTCCTAGGCATGCTATG 60.557 52.174 18.92 7.47 0.00 2.23
3698 3821 6.126332 TGCCTTATATTTATCCACCTGACCAA 60.126 38.462 0.00 0.00 0.00 3.67
3720 3843 1.337167 CCTTTAGCAACAAGCCTTGCC 60.337 52.381 3.88 0.00 46.63 4.52
3769 3892 3.756963 GCAACGGGAGAAAAGGTTTCTAT 59.243 43.478 3.30 0.00 0.00 1.98
3822 3945 7.724305 TTCCAGATCATAATAAGCGGTTAAC 57.276 36.000 11.60 0.00 0.00 2.01
4162 4287 9.871175 TTTAGAGGATAACCAGGTTTTAACTTT 57.129 29.630 11.02 3.15 38.94 2.66
4487 5033 6.774673 TGATATCTACTCAACAAACCCACAA 58.225 36.000 3.98 0.00 0.00 3.33
4488 5034 6.367374 TGATATCTACTCAACAAACCCACA 57.633 37.500 3.98 0.00 0.00 4.17
4683 5229 3.379452 AGCTCCTCCTGCTAGTGTAAAT 58.621 45.455 0.00 0.00 39.21 1.40
5031 5587 6.174049 ACAAAATACTTCCTGACTAAGAGGC 58.826 40.000 0.00 0.00 0.00 4.70
5242 5800 1.349688 TGTACCGGCTTCCATGAACTT 59.650 47.619 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.