Multiple sequence alignment - TraesCS7A01G549600

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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 TraesCS7A01G549600 chr7A 100.000 2398 0 0 1 2398 723636822 723639219 0.000000e+00 4429.0
1 TraesCS7A01G549600 chr7A 96.887 2152 65 1 1 2152 723588806 723590955 0.000000e+00 3602.0
2 TraesCS7A01G549600 chr7A 97.845 232 5 0 2167 2398 140678669 140678900 3.710000e-108 401.0
3 TraesCS7A01G549600 chr7A 97.845 232 5 0 2167 2398 723591228 723591459 3.710000e-108 401.0
4 TraesCS7A01G549600 chr3A 97.398 2152 56 0 1 2152 122114662 122116813 0.000000e+00 3664.0
5 TraesCS7A01G549600 chr3A 96.887 2152 67 0 1 2152 48905001 48907152 0.000000e+00 3603.0
6 TraesCS7A01G549600 chr3A 97.498 1559 39 0 594 2152 171150724 171152282 0.000000e+00 2663.0
7 TraesCS7A01G549600 chr3A 97.434 1559 39 1 594 2152 58077807 58076250 0.000000e+00 2656.0
8 TraesCS7A01G549600 chr3A 97.306 1559 42 0 594 2152 545675829 545674271 0.000000e+00 2647.0
9 TraesCS7A01G549600 chr1A 97.308 1560 41 1 594 2152 359191283 359192842 0.000000e+00 2647.0
10 TraesCS7A01G549600 chr1A 97.242 1559 43 0 594 2152 181970126 181968568 0.000000e+00 2641.0
11 TraesCS7A01G549600 chr1A 97.049 1559 32 2 594 2152 67961651 67960107 0.000000e+00 2612.0
12 TraesCS7A01G549600 chr1A 95.962 1560 46 4 594 2152 579041056 579039513 0.000000e+00 2516.0
13 TraesCS7A01G549600 chr1A 98.246 228 4 0 2166 2393 175605873 175606100 1.340000e-107 399.0
14 TraesCS7A01G549600 chr1A 98.238 227 4 0 2167 2393 69813811 69813585 4.800000e-107 398.0
15 TraesCS7A01G549600 chr1A 98.238 227 4 0 2167 2393 502071580 502071354 4.800000e-107 398.0
16 TraesCS7A01G549600 chr3D 96.900 613 19 0 46 658 134545009 134544397 0.000000e+00 1027.0
17 TraesCS7A01G549600 chr3D 97.917 48 1 0 1 48 134545490 134545443 1.530000e-12 84.2
18 TraesCS7A01G549600 chr3D 95.833 48 2 0 1 48 571342351 571342304 7.110000e-11 78.7
19 TraesCS7A01G549600 chr7B 96.085 613 24 0 46 658 642005089 642005701 0.000000e+00 1000.0
20 TraesCS7A01G549600 chr7B 95.833 48 2 0 1 48 642004602 642004649 7.110000e-11 78.7
21 TraesCS7A01G549600 chr2B 96.085 613 24 0 46 658 141277086 141276474 0.000000e+00 1000.0
22 TraesCS7A01G549600 chr2A 95.595 613 25 2 46 658 37684565 37683955 0.000000e+00 981.0
23 TraesCS7A01G549600 chr5B 95.432 613 28 0 46 658 12740861 12740249 0.000000e+00 977.0
24 TraesCS7A01G549600 chr4B 95.269 613 29 0 46 658 208920103 208919491 0.000000e+00 972.0
25 TraesCS7A01G549600 chr5A 98.678 227 3 0 2167 2393 456424055 456424281 1.030000e-108 403.0
26 TraesCS7A01G549600 chr5A 98.678 227 3 0 2167 2393 706173578 706173804 1.030000e-108 403.0
27 TraesCS7A01G549600 chr6A 98.238 227 4 0 2167 2393 607603620 607603846 4.800000e-107 398.0
28 TraesCS7A01G549600 chr4A 96.250 240 8 1 2155 2393 409230431 409230670 2.230000e-105 392.0
29 TraesCS7A01G549600 chr4A 97.917 48 1 0 1 48 724149153 724149200 1.530000e-12 84.2
30 TraesCS7A01G549600 chr5D 97.917 48 1 0 1 48 45712369 45712416 1.530000e-12 84.2
31 TraesCS7A01G549600 chr5D 100.000 44 0 0 1 44 12007551 12007594 5.490000e-12 82.4


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 TraesCS7A01G549600 chr7A 723636822 723639219 2397 False 4429.00 4429 100.0000 1 2398 1 chr7A.!!$F2 2397
1 TraesCS7A01G549600 chr7A 723588806 723591459 2653 False 2001.50 3602 97.3660 1 2398 2 chr7A.!!$F3 2397
2 TraesCS7A01G549600 chr3A 122114662 122116813 2151 False 3664.00 3664 97.3980 1 2152 1 chr3A.!!$F2 2151
3 TraesCS7A01G549600 chr3A 48905001 48907152 2151 False 3603.00 3603 96.8870 1 2152 1 chr3A.!!$F1 2151
4 TraesCS7A01G549600 chr3A 171150724 171152282 1558 False 2663.00 2663 97.4980 594 2152 1 chr3A.!!$F3 1558
5 TraesCS7A01G549600 chr3A 58076250 58077807 1557 True 2656.00 2656 97.4340 594 2152 1 chr3A.!!$R1 1558
6 TraesCS7A01G549600 chr3A 545674271 545675829 1558 True 2647.00 2647 97.3060 594 2152 1 chr3A.!!$R2 1558
7 TraesCS7A01G549600 chr1A 359191283 359192842 1559 False 2647.00 2647 97.3080 594 2152 1 chr1A.!!$F2 1558
8 TraesCS7A01G549600 chr1A 181968568 181970126 1558 True 2641.00 2641 97.2420 594 2152 1 chr1A.!!$R3 1558
9 TraesCS7A01G549600 chr1A 67960107 67961651 1544 True 2612.00 2612 97.0490 594 2152 1 chr1A.!!$R1 1558
10 TraesCS7A01G549600 chr1A 579039513 579041056 1543 True 2516.00 2516 95.9620 594 2152 1 chr1A.!!$R5 1558
11 TraesCS7A01G549600 chr3D 134544397 134545490 1093 True 555.60 1027 97.4085 1 658 2 chr3D.!!$R2 657
12 TraesCS7A01G549600 chr7B 642004602 642005701 1099 False 539.35 1000 95.9590 1 658 2 chr7B.!!$F1 657
13 TraesCS7A01G549600 chr2B 141276474 141277086 612 True 1000.00 1000 96.0850 46 658 1 chr2B.!!$R1 612
14 TraesCS7A01G549600 chr2A 37683955 37684565 610 True 981.00 981 95.5950 46 658 1 chr2A.!!$R1 612
15 TraesCS7A01G549600 chr5B 12740249 12740861 612 True 977.00 977 95.4320 46 658 1 chr5B.!!$R1 612
16 TraesCS7A01G549600 chr4B 208919491 208920103 612 True 972.00 972 95.2690 46 658 1 chr4B.!!$R1 612

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
67 510 0.032267 CCCCTTCTAATCCGCTCGAC 59.968 60.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2422 3.003689 CGAACTTGGATTTGCACTTCACT 59.996 43.478 0.0 0.0 0.0 3.41 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
67 510 0.032267 CCCCTTCTAATCCGCTCGAC 59.968 60.000 0.00 0.00 0.00 4.20
94 537 1.536940 TTGGTCATGTCATGTGCTGG 58.463 50.000 12.54 0.00 0.00 4.85
412 855 7.147549 ACCTAGCTTGCAACTAATATCCTTACA 60.148 37.037 0.00 0.00 0.00 2.41
451 894 7.093322 AGTTTATCTGAACATGGCTGAAATC 57.907 36.000 0.00 0.00 31.94 2.17
625 1068 2.632996 AGGACAAGATCAACGAGGTGAA 59.367 45.455 0.00 0.00 0.00 3.18
647 1090 1.006832 GTGTTATGGCGGCTGTGTAG 58.993 55.000 11.43 0.00 0.00 2.74
839 1282 9.389949 TCCTATCTAGTATAGGACAAGTCAGTA 57.610 37.037 19.14 0.00 43.71 2.74
973 1416 4.666512 ACTATTTCTGACCATGTTTGCCT 58.333 39.130 0.00 0.00 0.00 4.75
1159 1602 5.835280 AGATTTGATGGGTTCAACAACTCTT 59.165 36.000 0.00 0.00 43.99 2.85
1560 2005 5.184864 ACTGTTTGTTGGTGTTGAGAAATCA 59.815 36.000 0.00 0.00 0.00 2.57
1642 2087 7.939039 AGAATGTCTGTTTCATGGTCTTTTCTA 59.061 33.333 0.00 0.00 0.00 2.10
1721 2166 6.183360 CCTTAATTCAAAGCCGAGACACTTAG 60.183 42.308 0.00 0.00 0.00 2.18
2059 2518 2.966516 GCAGTACTAGGCTTATCTGGGT 59.033 50.000 0.00 0.00 0.00 4.51
2152 2611 8.254178 TGGATTGTTTGAAATAATGATTGTGC 57.746 30.769 4.60 0.00 0.00 4.57
2153 2612 7.333921 TGGATTGTTTGAAATAATGATTGTGCC 59.666 33.333 4.60 0.00 0.00 5.01
2154 2613 7.333921 GGATTGTTTGAAATAATGATTGTGCCA 59.666 33.333 4.60 0.00 0.00 4.92
2155 2614 7.418840 TTGTTTGAAATAATGATTGTGCCAC 57.581 32.000 0.00 0.00 0.00 5.01
2156 2615 6.519382 TGTTTGAAATAATGATTGTGCCACA 58.481 32.000 0.00 0.00 0.00 4.17
2157 2616 7.160049 TGTTTGAAATAATGATTGTGCCACAT 58.840 30.769 0.00 0.00 0.00 3.21
2158 2617 7.331440 TGTTTGAAATAATGATTGTGCCACATC 59.669 33.333 0.00 0.00 0.00 3.06
2159 2618 6.527057 TGAAATAATGATTGTGCCACATCA 57.473 33.333 0.00 5.43 0.00 3.07
2160 2619 6.566141 TGAAATAATGATTGTGCCACATCAG 58.434 36.000 0.00 0.00 0.00 2.90
2161 2620 6.377712 TGAAATAATGATTGTGCCACATCAGA 59.622 34.615 0.00 0.00 0.00 3.27
2162 2621 6.778834 AATAATGATTGTGCCACATCAGAA 57.221 33.333 0.00 0.00 0.00 3.02
2163 2622 6.778834 ATAATGATTGTGCCACATCAGAAA 57.221 33.333 0.00 0.00 0.00 2.52
2164 2623 5.471556 AATGATTGTGCCACATCAGAAAA 57.528 34.783 0.00 0.00 0.00 2.29
2198 2915 3.435026 GGCTAGGCCCATGTAGAAAATCA 60.435 47.826 4.61 0.00 44.06 2.57
2227 2944 0.895100 GGGCTGAATCTTGTGCCACA 60.895 55.000 0.00 0.00 46.53 4.17
2292 3009 0.028902 GTGACCAAAACGCCACAGTC 59.971 55.000 0.00 0.00 0.00 3.51
2312 3029 6.128742 ACAGTCGACGTATTTTGGTCATAAAC 60.129 38.462 10.46 0.00 32.74 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 510 5.696822 CACATGACATGACCAAAAGAGAAG 58.303 41.667 22.19 0.00 0.00 2.85
128 571 6.005066 TGGTTGACAACTATGGATCATCAT 57.995 37.500 17.52 0.00 0.00 2.45
225 668 9.118236 GAAATGAAAGACACTAATGTAAGCAAC 57.882 33.333 0.00 0.00 39.95 4.17
412 855 7.639378 TCAGATAAACTTGGGGTAAATTAGCT 58.361 34.615 2.09 0.00 0.00 3.32
451 894 1.081641 CAAGGACTTTGCAGCGCTG 60.082 57.895 32.83 32.83 0.00 5.18
490 933 9.628500 TCAAGTCTATATTCTCAGCTAACTGTA 57.372 33.333 0.00 0.00 44.77 2.74
625 1068 2.435938 CAGCCGCCATAACACCGT 60.436 61.111 0.00 0.00 0.00 4.83
868 1311 7.177568 ACATCTCACAGTGAGTTAACTATCTGT 59.822 37.037 26.65 26.04 44.58 3.41
973 1416 3.994729 GCATAGAACACGCAATGCA 57.005 47.368 5.91 0.00 43.30 3.96
1721 2166 3.604875 TGTACTCCCTCCGATCAAAAC 57.395 47.619 0.00 0.00 0.00 2.43
1963 2422 3.003689 CGAACTTGGATTTGCACTTCACT 59.996 43.478 0.00 0.00 0.00 3.41
2152 2611 5.574055 CCAACAATTCGATTTTCTGATGTGG 59.426 40.000 0.00 0.00 0.00 4.17
2153 2612 5.574055 CCCAACAATTCGATTTTCTGATGTG 59.426 40.000 0.00 0.00 0.00 3.21
2154 2613 5.713025 CCCAACAATTCGATTTTCTGATGT 58.287 37.500 0.00 0.00 0.00 3.06
2155 2614 4.563976 GCCCAACAATTCGATTTTCTGATG 59.436 41.667 0.00 0.00 0.00 3.07
2156 2615 4.463891 AGCCCAACAATTCGATTTTCTGAT 59.536 37.500 0.00 0.00 0.00 2.90
2157 2616 3.826157 AGCCCAACAATTCGATTTTCTGA 59.174 39.130 0.00 0.00 0.00 3.27
2158 2617 4.178545 AGCCCAACAATTCGATTTTCTG 57.821 40.909 0.00 0.00 0.00 3.02
2159 2618 4.399303 CCTAGCCCAACAATTCGATTTTCT 59.601 41.667 0.00 0.00 0.00 2.52
2160 2619 4.672409 CCTAGCCCAACAATTCGATTTTC 58.328 43.478 0.00 0.00 0.00 2.29
2161 2620 3.119137 GCCTAGCCCAACAATTCGATTTT 60.119 43.478 0.00 0.00 0.00 1.82
2162 2621 2.427095 GCCTAGCCCAACAATTCGATTT 59.573 45.455 0.00 0.00 0.00 2.17
2163 2622 2.024414 GCCTAGCCCAACAATTCGATT 58.976 47.619 0.00 0.00 0.00 3.34
2164 2623 1.680338 GCCTAGCCCAACAATTCGAT 58.320 50.000 0.00 0.00 0.00 3.59
2198 2915 1.005924 AGATTCAGCCCGGTCCAATTT 59.994 47.619 0.00 0.00 0.00 1.82
2227 2944 0.182061 ATCCAGCGTGGCAATCTGAT 59.818 50.000 16.08 7.30 37.47 2.90
2262 2979 2.552743 GTTTTGGTCACTAGCAACCTCC 59.447 50.000 13.64 0.00 42.54 4.30
2292 3009 5.194199 ACGTTTATGACCAAAATACGTCG 57.806 39.130 0.00 0.00 36.14 5.12
2312 3029 5.091343 TTTCTTCTGGAATGGTCGAAGACG 61.091 45.833 0.00 0.00 45.76 4.18


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

AutoCloner maintained by Alex Coulton.