Multiple sequence alignment - TraesCS7D01G296200

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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 TraesCS7D01G296200 chr7D 100.000 2549 0 0 1 2549 372082217 372084765 0.000000e+00 4708
1 TraesCS7D01G296200 chr3D 94.622 1971 85 12 582 2549 546485995 546487947 0.000000e+00 3033
2 TraesCS7D01G296200 chr2B 93.337 1981 114 14 582 2549 173503419 173501444 0.000000e+00 2911
3 TraesCS7D01G296200 chrUn 93.323 1977 108 15 578 2549 20573297 20575254 0.000000e+00 2898
4 TraesCS7D01G296200 chr7A 93.219 1976 102 21 582 2549 12744485 12742534 0.000000e+00 2878
5 TraesCS7D01G296200 chr6D 93.144 1969 108 14 584 2549 12108135 12106191 0.000000e+00 2863
6 TraesCS7D01G296200 chr6D 91.903 1976 109 22 582 2549 312544302 312542370 0.000000e+00 2715
7 TraesCS7D01G296200 chr6D 92.943 581 40 1 1 580 402232549 402233129 0.000000e+00 845
8 TraesCS7D01G296200 chr7B 92.128 1969 141 12 582 2549 101862225 101864180 0.000000e+00 2765
9 TraesCS7D01G296200 chr4D 92.354 1975 88 21 582 2549 50776934 50778852 0.000000e+00 2752
10 TraesCS7D01G296200 chr4D 93.276 580 39 0 1 580 416152790 416152211 0.000000e+00 856
11 TraesCS7D01G296200 chr4D 88.966 580 64 0 1 580 81958257 81957678 0.000000e+00 717
12 TraesCS7D01G296200 chr1A 90.638 1976 133 21 582 2549 556201763 556203694 0.000000e+00 2577
13 TraesCS7D01G296200 chr5B 91.393 1859 141 15 582 2435 548612963 548611119 0.000000e+00 2529
14 TraesCS7D01G296200 chr5D 91.349 578 49 1 4 580 492809484 492810061 0.000000e+00 789
15 TraesCS7D01G296200 chr5D 91.304 575 49 1 7 580 463626866 463627440 0.000000e+00 784
16 TraesCS7D01G296200 chr5D 91.932 533 42 1 4 535 197356728 197356196 0.000000e+00 745
17 TraesCS7D01G296200 chr5D 89.446 578 59 2 4 580 161499869 161499293 0.000000e+00 728
18 TraesCS7D01G296200 chr4A 89.932 586 53 4 1 580 36250627 36250042 0.000000e+00 750
19 TraesCS7D01G296200 chr4A 89.845 581 58 1 1 580 357348288 357347708 0.000000e+00 745
20 TraesCS7D01G296200 chr4A 76.937 555 98 17 27 580 291215829 291215304 3.210000e-74 289


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 TraesCS7D01G296200 chr7D 372082217 372084765 2548 False 4708 4708 100.000 1 2549 1 chr7D.!!$F1 2548
1 TraesCS7D01G296200 chr3D 546485995 546487947 1952 False 3033 3033 94.622 582 2549 1 chr3D.!!$F1 1967
2 TraesCS7D01G296200 chr2B 173501444 173503419 1975 True 2911 2911 93.337 582 2549 1 chr2B.!!$R1 1967
3 TraesCS7D01G296200 chrUn 20573297 20575254 1957 False 2898 2898 93.323 578 2549 1 chrUn.!!$F1 1971
4 TraesCS7D01G296200 chr7A 12742534 12744485 1951 True 2878 2878 93.219 582 2549 1 chr7A.!!$R1 1967
5 TraesCS7D01G296200 chr6D 12106191 12108135 1944 True 2863 2863 93.144 584 2549 1 chr6D.!!$R1 1965
6 TraesCS7D01G296200 chr6D 312542370 312544302 1932 True 2715 2715 91.903 582 2549 1 chr6D.!!$R2 1967
7 TraesCS7D01G296200 chr6D 402232549 402233129 580 False 845 845 92.943 1 580 1 chr6D.!!$F1 579
8 TraesCS7D01G296200 chr7B 101862225 101864180 1955 False 2765 2765 92.128 582 2549 1 chr7B.!!$F1 1967
9 TraesCS7D01G296200 chr4D 50776934 50778852 1918 False 2752 2752 92.354 582 2549 1 chr4D.!!$F1 1967
10 TraesCS7D01G296200 chr4D 416152211 416152790 579 True 856 856 93.276 1 580 1 chr4D.!!$R2 579
11 TraesCS7D01G296200 chr4D 81957678 81958257 579 True 717 717 88.966 1 580 1 chr4D.!!$R1 579
12 TraesCS7D01G296200 chr1A 556201763 556203694 1931 False 2577 2577 90.638 582 2549 1 chr1A.!!$F1 1967
13 TraesCS7D01G296200 chr5B 548611119 548612963 1844 True 2529 2529 91.393 582 2435 1 chr5B.!!$R1 1853
14 TraesCS7D01G296200 chr5D 492809484 492810061 577 False 789 789 91.349 4 580 1 chr5D.!!$F2 576
15 TraesCS7D01G296200 chr5D 463626866 463627440 574 False 784 784 91.304 7 580 1 chr5D.!!$F1 573
16 TraesCS7D01G296200 chr5D 197356196 197356728 532 True 745 745 91.932 4 535 1 chr5D.!!$R2 531
17 TraesCS7D01G296200 chr5D 161499293 161499869 576 True 728 728 89.446 4 580 1 chr5D.!!$R1 576
18 TraesCS7D01G296200 chr4A 36250042 36250627 585 True 750 750 89.932 1 580 1 chr4A.!!$R1 579
19 TraesCS7D01G296200 chr4A 357347708 357348288 580 True 745 745 89.845 1 580 1 chr4A.!!$R3 579
20 TraesCS7D01G296200 chr4A 291215304 291215829 525 True 289 289 76.937 27 580 1 chr4A.!!$R2 553

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
574 585 0.036765 AGCGCTCCGTGTTTCCATTA 60.037 50.0 2.64 0.0 0.0 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 2379 0.393267 TTACCAGCGCGGCCTTAAAT 60.393 50.0 16.48 0.47 39.03 1.4 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
87 90 4.937620 TCTTGAAGATCCTTTGGACATTCG 59.062 41.667 0.00 0.00 34.29 3.34
196 201 5.437060 GGCCCTTGTTATCATCAGAAAGTA 58.563 41.667 0.00 0.00 0.00 2.24
320 326 2.677228 CCTCCGTCCTTGCCCATT 59.323 61.111 0.00 0.00 0.00 3.16
417 428 5.811796 TCCTAATCTAGCTCTAGACGAGT 57.188 43.478 8.64 0.00 44.11 4.18
475 486 4.717313 GTGTCCGGGGGCTTGACC 62.717 72.222 0.00 0.00 37.93 4.02
545 556 1.227380 GCCACGGTATGCTCCTCAG 60.227 63.158 0.00 0.00 0.00 3.35
546 557 1.961180 GCCACGGTATGCTCCTCAGT 61.961 60.000 0.00 0.00 0.00 3.41
547 558 1.399714 CCACGGTATGCTCCTCAGTA 58.600 55.000 0.00 0.00 0.00 2.74
548 559 1.067212 CCACGGTATGCTCCTCAGTAC 59.933 57.143 0.00 0.00 0.00 2.73
549 560 1.022735 ACGGTATGCTCCTCAGTACG 58.977 55.000 0.00 0.00 0.00 3.67
550 561 0.311165 CGGTATGCTCCTCAGTACGG 59.689 60.000 0.00 0.00 0.00 4.02
551 562 1.688772 GGTATGCTCCTCAGTACGGA 58.311 55.000 0.00 0.00 0.00 4.69
558 569 3.111939 CTCAGTACGGAGGGAGCG 58.888 66.667 14.53 0.00 0.00 5.03
559 570 3.127352 CTCAGTACGGAGGGAGCGC 62.127 68.421 14.53 0.00 0.00 5.92
560 571 3.141488 CAGTACGGAGGGAGCGCT 61.141 66.667 11.27 11.27 0.00 5.92
561 572 2.829458 AGTACGGAGGGAGCGCTC 60.829 66.667 29.38 29.38 0.00 5.03
570 581 3.119096 GGAGCGCTCCGTGTTTCC 61.119 66.667 38.78 16.55 40.36 3.13
571 582 2.357034 GAGCGCTCCGTGTTTCCA 60.357 61.111 27.22 0.00 0.00 3.53
572 583 1.741770 GAGCGCTCCGTGTTTCCAT 60.742 57.895 27.22 0.00 0.00 3.41
573 584 1.298859 GAGCGCTCCGTGTTTCCATT 61.299 55.000 27.22 0.00 0.00 3.16
574 585 0.036765 AGCGCTCCGTGTTTCCATTA 60.037 50.000 2.64 0.00 0.00 1.90
575 586 0.800012 GCGCTCCGTGTTTCCATTAA 59.200 50.000 0.00 0.00 0.00 1.40
576 587 1.465187 GCGCTCCGTGTTTCCATTAAC 60.465 52.381 0.00 0.00 0.00 2.01
610 621 1.440618 TCCTTTTGCCCTCAGTGGTA 58.559 50.000 0.00 0.00 0.00 3.25
644 655 1.097232 TTTGCCCTCAGATGCGAATG 58.903 50.000 0.00 0.00 0.00 2.67
712 723 0.832135 TCTGCCTTCTCCGTCAGGTT 60.832 55.000 0.00 0.00 39.05 3.50
771 782 2.945668 GCAGAGACGGCCAATTCTATTT 59.054 45.455 2.24 0.00 0.00 1.40
784 795 5.123186 CCAATTCTATTTAGACCGTTGCACA 59.877 40.000 0.00 0.00 30.81 4.57
892 903 3.295273 ACGGCGACAGAGAGCACA 61.295 61.111 16.62 0.00 34.54 4.57
931 954 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
1019 1045 1.280133 CATGTCTTCCTCAAGCTCCCA 59.720 52.381 0.00 0.00 0.00 4.37
1075 1101 1.070758 ACATGCCTGTCTTCGTCTGTT 59.929 47.619 0.00 0.00 0.00 3.16
1118 1145 0.472471 TGGAGGGTTTCTCACACACC 59.528 55.000 0.00 0.00 44.19 4.16
1119 1146 0.472471 GGAGGGTTTCTCACACACCA 59.528 55.000 0.00 0.00 44.19 4.17
1125 1152 3.222603 GGTTTCTCACACACCAAGGAAT 58.777 45.455 0.00 0.00 0.00 3.01
1171 1198 4.384647 GCAGTGAGAATGGGGTAAGAATCT 60.385 45.833 0.00 0.00 0.00 2.40
1175 1202 3.459969 GAGAATGGGGTAAGAATCTGGGT 59.540 47.826 0.00 0.00 0.00 4.51
1217 1244 2.421388 CGGGATCTTTGAGCAATGGGTA 60.421 50.000 0.00 0.00 0.00 3.69
1296 1323 6.070251 TGGCCAAGACTCTGATAAATGAACTA 60.070 38.462 0.61 0.00 0.00 2.24
1302 1329 9.868277 AAGACTCTGATAAATGAACTACAAGAG 57.132 33.333 0.00 0.00 34.25 2.85
1334 1419 2.729455 GTTGTGCATGCTGCCACA 59.271 55.556 20.33 11.95 44.23 4.17
1340 1425 2.918345 GCATGCTGCCACAAACGGA 61.918 57.895 11.37 0.00 37.42 4.69
1495 1637 6.705863 TTTGCAAATACTTTTGGGCATTTT 57.294 29.167 8.05 0.00 42.09 1.82
1918 2068 3.553105 GCTGAAACTTTTTGTGGAAGCTG 59.447 43.478 0.00 0.00 0.00 4.24
1940 2090 6.455360 TGATTGAATTATTCCAGAGCCAAC 57.545 37.500 2.22 0.00 0.00 3.77
2165 2328 1.686052 TGAAGGGTGGAAAATGCACAC 59.314 47.619 4.42 0.01 42.88 3.82
2455 2650 6.325286 AGTGGCACTTGGTTTAGGATTTAAAA 59.675 34.615 15.88 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.293535 ACCTATATACAGCTTTCCCTGATTCTT 59.706 37.037 0.00 0.00 36.67 2.52
25 26 4.841246 AGGACCTATATACAGCTTTCCCTG 59.159 45.833 0.00 0.00 38.78 4.45
147 150 6.473429 TGTCTAGGCCCCTTATGTATACTA 57.527 41.667 0.00 0.00 0.00 1.82
196 201 4.798882 TCAGGTTCTTTACAACCCACATT 58.201 39.130 0.00 0.00 46.39 2.71
356 362 1.002888 CCCCAGCTGGATAGTAGCATG 59.997 57.143 34.91 12.69 43.53 4.06
361 367 1.837439 CACAACCCCAGCTGGATAGTA 59.163 52.381 34.91 0.00 37.39 1.82
362 368 0.620556 CACAACCCCAGCTGGATAGT 59.379 55.000 34.91 23.69 37.39 2.12
417 428 1.658114 CCACAGAACGACAGTCCGA 59.342 57.895 0.00 0.00 0.00 4.55
500 511 2.662596 CGAAGCACAGGGTGGCTA 59.337 61.111 0.00 0.00 40.01 3.93
501 512 4.335647 CCGAAGCACAGGGTGGCT 62.336 66.667 0.00 0.00 43.46 4.75
545 556 3.902086 GGAGCGCTCCCTCCGTAC 61.902 72.222 40.99 17.11 43.94 3.67
550 561 3.591254 AAACACGGAGCGCTCCCTC 62.591 63.158 42.80 23.89 46.96 4.30
551 562 3.591254 GAAACACGGAGCGCTCCCT 62.591 63.158 42.80 32.29 46.96 4.20
552 563 3.119096 GAAACACGGAGCGCTCCC 61.119 66.667 42.80 27.60 46.96 4.30
553 564 3.119096 GGAAACACGGAGCGCTCC 61.119 66.667 40.89 40.89 46.18 4.70
554 565 2.357034 TGGAAACACGGAGCGCTC 60.357 61.111 29.38 29.38 33.40 5.03
562 573 9.132385 ATTAACCCCACAGTTAATGGAAACACG 62.132 40.741 8.46 0.00 46.27 4.49
563 574 6.014925 ATTAACCCCACAGTTAATGGAAACAC 60.015 38.462 8.46 0.00 46.27 3.32
564 575 6.078664 ATTAACCCCACAGTTAATGGAAACA 58.921 36.000 8.46 0.00 46.27 2.83
565 576 6.599356 ATTAACCCCACAGTTAATGGAAAC 57.401 37.500 8.46 0.00 46.27 2.78
566 577 8.903059 ATAATTAACCCCACAGTTAATGGAAA 57.097 30.769 9.69 0.00 46.97 3.13
567 578 7.562088 GGATAATTAACCCCACAGTTAATGGAA 59.438 37.037 9.69 1.75 46.97 3.53
568 579 7.064229 GGATAATTAACCCCACAGTTAATGGA 58.936 38.462 9.69 3.52 46.97 3.41
569 580 7.066781 AGGATAATTAACCCCACAGTTAATGG 58.933 38.462 8.09 0.00 46.97 3.16
570 581 8.533569 AAGGATAATTAACCCCACAGTTAATG 57.466 34.615 8.09 0.00 46.97 1.90
572 583 8.808092 CAAAAGGATAATTAACCCCACAGTTAA 58.192 33.333 8.09 0.00 44.12 2.01
573 584 7.093684 GCAAAAGGATAATTAACCCCACAGTTA 60.094 37.037 8.09 0.00 0.00 2.24
574 585 6.295632 GCAAAAGGATAATTAACCCCACAGTT 60.296 38.462 8.09 0.00 0.00 3.16
575 586 5.186992 GCAAAAGGATAATTAACCCCACAGT 59.813 40.000 8.09 0.00 0.00 3.55
576 587 5.395214 GGCAAAAGGATAATTAACCCCACAG 60.395 44.000 8.09 0.00 0.00 3.66
610 621 0.593128 GCAAAACTGAGCACACGGAT 59.407 50.000 0.00 0.00 0.00 4.18
712 723 0.393820 AGGGCCGAGTCAAAACGTTA 59.606 50.000 0.00 0.00 0.00 3.18
784 795 4.265056 GGGTCCCACAAGCCACGT 62.265 66.667 1.78 0.00 36.78 4.49
828 839 3.502211 GCTTTATATAGCACACCCGCAAT 59.498 43.478 9.97 0.00 40.89 3.56
931 954 1.980772 GCTTCCCACTGCCATGCTT 60.981 57.895 0.00 0.00 0.00 3.91
967 992 0.250513 GAAGGGGATCTCAACGCTGT 59.749 55.000 0.00 0.00 0.00 4.40
1118 1145 5.415415 GAATGGACGATTCTGATTCCTTG 57.585 43.478 3.15 0.00 37.98 3.61
1142 1169 1.499056 CCATTCTCACTGCACACGC 59.501 57.895 0.00 0.00 39.24 5.34
1152 1179 3.459598 CCCAGATTCTTACCCCATTCTCA 59.540 47.826 0.00 0.00 0.00 3.27
1171 1198 2.894126 ACGAAAATGGTGCAATTACCCA 59.106 40.909 0.00 0.00 40.09 4.51
1217 1244 3.489355 TGCATGAACACCAAACAGATCT 58.511 40.909 0.00 0.00 0.00 2.75
1296 1323 3.009916 ACCATTCTTCATGCTCCTCTTGT 59.990 43.478 0.00 0.00 0.00 3.16
1302 1329 2.416431 GCACAACCATTCTTCATGCTCC 60.416 50.000 0.00 0.00 0.00 4.70
1340 1425 2.972505 CTCGTGTTGCGGCCACTT 60.973 61.111 2.24 0.00 41.72 3.16
1495 1637 3.707611 ACCAGTGCGATTACCATACCTAA 59.292 43.478 0.00 0.00 0.00 2.69
1634 1779 9.793259 ATTTAAATGTTGGTCACTTCTTCTCTA 57.207 29.630 0.00 0.00 0.00 2.43
1680 1827 9.889128 TCAAAAGTTTCTGAATTCCTCATTTTT 57.111 25.926 2.27 1.24 32.14 1.94
1837 1987 9.573133 AGAAAACAGAAAAACACACAAGATAAG 57.427 29.630 0.00 0.00 0.00 1.73
1840 1990 7.378181 ACAGAAAACAGAAAAACACACAAGAT 58.622 30.769 0.00 0.00 0.00 2.40
1918 2068 5.360714 TGGTTGGCTCTGGAATAATTCAATC 59.639 40.000 0.00 0.00 0.00 2.67
2031 2183 4.996122 GGCACATTTTCCATGACATTTTGA 59.004 37.500 0.00 0.00 0.00 2.69
2165 2328 1.374505 CCCAGCCGCACCAATTTTG 60.375 57.895 0.00 0.00 0.00 2.44
2216 2379 0.393267 TTACCAGCGCGGCCTTAAAT 60.393 50.000 16.48 0.47 39.03 1.40
2225 2388 0.457853 TTCTAGCAGTTACCAGCGCG 60.458 55.000 0.00 0.00 35.48 6.86
2243 2406 5.242393 CCATGTCAAAGTCTTTCCATCTGTT 59.758 40.000 0.00 0.00 0.00 3.16
2455 2650 9.590451 CATGAACTAACATGCAAATTTATTCCT 57.410 29.630 0.00 0.00 40.54 3.36


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

AutoCloner maintained by Alex Coulton.