Multiple sequence alignment - TraesCS4B01G163900

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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 TraesCS4B01G163900 chr4B 100.000 2336 0 0 1 2336 339264493 339262158 0.000000e+00 4314.0
1 TraesCS4B01G163900 chr4B 85.912 433 40 11 1728 2139 480059723 480060155 2.130000e-120 442.0
2 TraesCS4B01G163900 chr4B 90.588 170 12 2 1511 1677 480059467 480059635 3.020000e-54 222.0
3 TraesCS4B01G163900 chr1D 94.744 2340 85 12 1 2336 239622685 239620380 0.000000e+00 3605.0
4 TraesCS4B01G163900 chr1D 92.520 1484 64 13 853 2336 212525835 212527271 0.000000e+00 2082.0
5 TraesCS4B01G163900 chr2D 94.545 2328 90 13 4 2327 118532905 118535199 0.000000e+00 3561.0
6 TraesCS4B01G163900 chr2D 80.342 117 19 4 3 117 11559695 11559809 4.140000e-13 86.1
7 TraesCS4B01G163900 chr4D 94.366 2343 93 16 1 2336 93450271 93447961 0.000000e+00 3559.0
8 TraesCS4B01G163900 chr4D 83.458 671 59 18 1521 2139 390273572 390274242 5.600000e-161 577.0
9 TraesCS4B01G163900 chr3B 96.064 1194 42 4 1 1189 809806077 809807270 0.000000e+00 1940.0
10 TraesCS4B01G163900 chr3B 94.516 310 16 1 2027 2336 809807372 809807680 5.840000e-131 477.0
11 TraesCS4B01G163900 chr3A 96.839 1044 31 2 218 1259 431134968 431136011 0.000000e+00 1744.0
12 TraesCS4B01G163900 chr3A 93.678 1044 50 5 1293 2336 431136012 431137039 0.000000e+00 1548.0
13 TraesCS4B01G163900 chr3A 91.875 160 10 2 1 158 431134799 431134957 1.090000e-53 220.0
14 TraesCS4B01G163900 chr5B 87.707 1391 118 22 154 1496 537784761 537783376 0.000000e+00 1572.0
15 TraesCS4B01G163900 chr5A 87.661 1394 116 23 155 1496 558176224 558174835 0.000000e+00 1570.0
16 TraesCS4B01G163900 chr5D 87.563 1391 119 25 155 1496 441405476 441404091 0.000000e+00 1561.0
17 TraesCS4B01G163900 chr7B 92.432 1110 54 7 1235 2336 375392208 375393295 0.000000e+00 1557.0
18 TraesCS4B01G163900 chr4A 82.684 693 59 28 1505 2139 72026450 72027139 2.030000e-155 558.0
19 TraesCS4B01G163900 chr1A 85.849 106 13 2 3 107 33018986 33018882 6.820000e-21 111.0


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 TraesCS4B01G163900 chr4B 339262158 339264493 2335 True 4314.000000 4314 100.000000 1 2336 1 chr4B.!!$R1 2335
1 TraesCS4B01G163900 chr4B 480059467 480060155 688 False 332.000000 442 88.250000 1511 2139 2 chr4B.!!$F1 628
2 TraesCS4B01G163900 chr1D 239620380 239622685 2305 True 3605.000000 3605 94.744000 1 2336 1 chr1D.!!$R1 2335
3 TraesCS4B01G163900 chr1D 212525835 212527271 1436 False 2082.000000 2082 92.520000 853 2336 1 chr1D.!!$F1 1483
4 TraesCS4B01G163900 chr2D 118532905 118535199 2294 False 3561.000000 3561 94.545000 4 2327 1 chr2D.!!$F2 2323
5 TraesCS4B01G163900 chr4D 93447961 93450271 2310 True 3559.000000 3559 94.366000 1 2336 1 chr4D.!!$R1 2335
6 TraesCS4B01G163900 chr4D 390273572 390274242 670 False 577.000000 577 83.458000 1521 2139 1 chr4D.!!$F1 618
7 TraesCS4B01G163900 chr3B 809806077 809807680 1603 False 1208.500000 1940 95.290000 1 2336 2 chr3B.!!$F1 2335
8 TraesCS4B01G163900 chr3A 431134799 431137039 2240 False 1170.666667 1744 94.130667 1 2336 3 chr3A.!!$F1 2335
9 TraesCS4B01G163900 chr5B 537783376 537784761 1385 True 1572.000000 1572 87.707000 154 1496 1 chr5B.!!$R1 1342
10 TraesCS4B01G163900 chr5A 558174835 558176224 1389 True 1570.000000 1570 87.661000 155 1496 1 chr5A.!!$R1 1341
11 TraesCS4B01G163900 chr5D 441404091 441405476 1385 True 1561.000000 1561 87.563000 155 1496 1 chr5D.!!$R1 1341
12 TraesCS4B01G163900 chr7B 375392208 375393295 1087 False 1557.000000 1557 92.432000 1235 2336 1 chr7B.!!$F1 1101
13 TraesCS4B01G163900 chr4A 72026450 72027139 689 False 558.000000 558 82.684000 1505 2139 1 chr4A.!!$F1 634

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
610 643 2.997315 CTCACTCCGGTGGCTCCA 60.997 66.667 8.63 0.0 43.17 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 2341 1.142748 CATGTCAGGCTCCTCGTCC 59.857 63.158 0.0 0.0 0.0 4.79 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
86 87 3.803082 CCGGTTCGGTCGTCGCTA 61.803 66.667 0.00 0.00 42.73 4.26
148 151 4.400961 GCCTCGCTCCTTGCCTGT 62.401 66.667 0.00 0.00 38.78 4.00
610 643 2.997315 CTCACTCCGGTGGCTCCA 60.997 66.667 8.63 0.00 43.17 3.86
1046 1081 1.706287 GCGAATCGAAGGGACAAGGC 61.706 60.000 6.91 0.00 0.00 4.35
1085 1120 1.251527 ATGAACCTCGGCTCGACACT 61.252 55.000 0.00 0.00 0.00 3.55
1273 1311 4.467084 GCATCGCCCGGGAGAACA 62.467 66.667 31.54 9.05 0.00 3.18
1634 1721 0.110486 AACGAGGCATCCAACACCTT 59.890 50.000 0.00 0.00 32.67 3.50
1677 1764 2.645567 CTGTCGCTCACCGTCACT 59.354 61.111 0.00 0.00 38.35 3.41
1681 1777 4.662961 CGCTCACCGTCACTGCCA 62.663 66.667 0.00 0.00 0.00 4.92
1713 1812 1.956170 CGCAAAGTCGAGCACCACT 60.956 57.895 0.00 0.00 0.00 4.00
1714 1813 0.666274 CGCAAAGTCGAGCACCACTA 60.666 55.000 0.00 0.00 0.00 2.74
1905 2040 1.961180 GCTCTATGGCTCACCCGTGT 61.961 60.000 0.00 0.00 35.87 4.49
1916 2051 0.250989 CACCCGTGTTGTACCCCATT 60.251 55.000 0.00 0.00 0.00 3.16
2032 2198 2.190578 GTTGCTAGGCCCGATGCT 59.809 61.111 0.00 0.00 40.92 3.79
2048 2214 2.124570 CTGTTCCTCATGGGCGGG 60.125 66.667 0.00 0.00 34.39 6.13
2074 2240 4.021925 GGTCAGCTTCGGGTGCCT 62.022 66.667 0.00 0.00 42.54 4.75
2088 2254 2.125350 GCCTCGACAGCTTCAGGG 60.125 66.667 0.00 0.00 0.00 4.45
2181 2357 3.062466 CGGACGAGGAGCCTGACA 61.062 66.667 0.00 0.00 0.00 3.58
2226 2402 0.459899 CAGCCACGAGGTATACTGCA 59.540 55.000 2.25 0.00 37.19 4.41
2229 2405 1.112113 CCACGAGGTATACTGCAGGT 58.888 55.000 19.93 8.94 0.00 4.00
2232 2408 3.131577 CCACGAGGTATACTGCAGGTTTA 59.868 47.826 19.93 1.28 0.00 2.01
2307 2483 2.673523 GAGCTGGCTCCACATGGT 59.326 61.111 11.14 0.00 37.11 3.55
2314 2490 0.966875 GGCTCCACATGGTTGCATCA 60.967 55.000 16.18 0.00 37.43 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.940883 AAATGGCTAGCGACGACCGA 61.941 55.000 9.00 0.00 41.76 4.69
86 87 1.689258 GGGGGTATCTGCAAAATGGCT 60.689 52.381 0.00 0.00 34.04 4.75
117 118 1.377202 GAGGCCAGCGGTTCATGAA 60.377 57.895 5.01 3.38 0.00 2.57
298 307 1.622312 ACGGAGAACAAGAACCTACCC 59.378 52.381 0.00 0.00 0.00 3.69
610 643 3.632333 TCGTTCAGTACATCCCTGAGAT 58.368 45.455 0.00 0.00 39.91 2.75
679 713 1.417517 TGAGCTGGCTGTTTCTCTTGA 59.582 47.619 0.00 0.00 0.00 3.02
951 986 2.396955 CGGCGTGTAGTCTCGGAGT 61.397 63.158 4.69 0.00 0.00 3.85
1046 1081 3.411351 CGAACACCTTCCGCACCG 61.411 66.667 0.00 0.00 0.00 4.94
1677 1764 4.595538 GTCGTGGTGTCGGTGGCA 62.596 66.667 0.00 0.00 0.00 4.92
1905 2040 2.455557 CTTGATGCCAATGGGGTACAA 58.544 47.619 0.00 0.00 39.65 2.41
1961 2105 3.182590 TTCCTGTTGCTGCCGCTCT 62.183 57.895 0.70 0.00 36.97 4.09
2021 2187 3.011517 AGGAACAGCATCGGGCCT 61.012 61.111 0.84 0.00 46.50 5.19
2032 2198 3.727258 CCCCGCCCATGAGGAACA 61.727 66.667 0.00 0.00 38.24 3.18
2048 2214 1.513622 GAAGCTGACCTCCTCGTCC 59.486 63.158 0.00 0.00 31.35 4.79
2074 2240 2.343758 GTGCCCTGAAGCTGTCGA 59.656 61.111 0.00 0.00 0.00 4.20
2157 2333 4.069232 CTCCTCGTCCGCTTGCCA 62.069 66.667 0.00 0.00 0.00 4.92
2165 2341 1.142748 CATGTCAGGCTCCTCGTCC 59.857 63.158 0.00 0.00 0.00 4.79
2181 2357 2.968574 AGGATATCACCTGAAGCGTCAT 59.031 45.455 1.88 0.00 39.01 3.06
2226 2402 4.394729 TGCCTTCTGTCGATTTTAAACCT 58.605 39.130 0.00 0.00 0.00 3.50
2229 2405 3.756434 CCCTGCCTTCTGTCGATTTTAAA 59.244 43.478 0.00 0.00 0.00 1.52
2232 2408 1.614317 CCCCTGCCTTCTGTCGATTTT 60.614 52.381 0.00 0.00 0.00 1.82
2307 2483 1.554617 TCCTGGACGAATCTGATGCAA 59.445 47.619 0.00 0.00 0.00 4.08
2314 2490 3.721087 AATTTGGTCCTGGACGAATCT 57.279 42.857 22.39 11.91 31.06 2.40


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

AutoCloner maintained by Alex Coulton.