Multiple sequence alignment - TraesCS7A01G331000

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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 TraesCS7A01G331000 chr7A 100.000 2446 0 0 1 2446 484194935 484192490 0 4518
1 TraesCS7A01G331000 chr7A 95.140 823 40 0 1 823 668089405 668088583 0 1299
2 TraesCS7A01G331000 chr7A 96.970 396 12 0 1 396 652221509 652221114 0 665
3 TraesCS7A01G331000 chr3B 87.565 2501 233 54 9 2446 9321375 9323860 0 2824
4 TraesCS7A01G331000 chr5B 88.123 2408 216 45 8 2359 450547612 450550005 0 2798
5 TraesCS7A01G331000 chr5A 96.954 1543 42 5 905 2444 610716470 610718010 0 2584
6 TraesCS7A01G331000 chr5A 96.031 907 36 0 1 907 52388229 52387323 0 1476
7 TraesCS7A01G331000 chr5A 95.590 907 40 0 1 907 578685619 578686525 0 1454
8 TraesCS7A01G331000 chr1A 96.893 1545 42 6 905 2446 423683845 423682304 0 2582
9 TraesCS7A01G331000 chr1A 95.921 907 36 1 1 907 423684795 423683890 0 1469
10 TraesCS7A01G331000 chr2A 96.697 1544 47 4 905 2446 651453587 651455128 0 2566
11 TraesCS7A01G331000 chr2A 96.717 396 13 0 1 396 624504980 624505375 0 660
12 TraesCS7A01G331000 chr3A 96.636 1546 47 5 905 2446 446309352 446310896 0 2562
13 TraesCS7A01G331000 chr3A 97.222 396 11 0 1 396 446308365 446308760 0 671
14 TraesCS7A01G331000 chr6B 88.255 2086 201 35 392 2446 258484985 258482913 0 2455
15 TraesCS7A01G331000 chr2B 88.501 2061 195 34 415 2446 50384698 50386745 0 2455
16 TraesCS7A01G331000 chr7B 87.990 2090 205 36 389 2446 111352641 111354716 0 2427
17 TraesCS7A01G331000 chr7B 96.231 398 14 1 1 398 560793802 560794198 0 651
18 TraesCS7A01G331000 chr6A 96.212 396 15 0 1 396 116925371 116924976 0 649


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 TraesCS7A01G331000 chr7A 484192490 484194935 2445 True 4518.0 4518 100.000 1 2446 1 chr7A.!!$R1 2445
1 TraesCS7A01G331000 chr7A 668088583 668089405 822 True 1299.0 1299 95.140 1 823 1 chr7A.!!$R3 822
2 TraesCS7A01G331000 chr3B 9321375 9323860 2485 False 2824.0 2824 87.565 9 2446 1 chr3B.!!$F1 2437
3 TraesCS7A01G331000 chr5B 450547612 450550005 2393 False 2798.0 2798 88.123 8 2359 1 chr5B.!!$F1 2351
4 TraesCS7A01G331000 chr5A 610716470 610718010 1540 False 2584.0 2584 96.954 905 2444 1 chr5A.!!$F2 1539
5 TraesCS7A01G331000 chr5A 52387323 52388229 906 True 1476.0 1476 96.031 1 907 1 chr5A.!!$R1 906
6 TraesCS7A01G331000 chr5A 578685619 578686525 906 False 1454.0 1454 95.590 1 907 1 chr5A.!!$F1 906
7 TraesCS7A01G331000 chr1A 423682304 423684795 2491 True 2025.5 2582 96.407 1 2446 2 chr1A.!!$R1 2445
8 TraesCS7A01G331000 chr2A 651453587 651455128 1541 False 2566.0 2566 96.697 905 2446 1 chr2A.!!$F2 1541
9 TraesCS7A01G331000 chr3A 446308365 446310896 2531 False 1616.5 2562 96.929 1 2446 2 chr3A.!!$F1 2445
10 TraesCS7A01G331000 chr6B 258482913 258484985 2072 True 2455.0 2455 88.255 392 2446 1 chr6B.!!$R1 2054
11 TraesCS7A01G331000 chr2B 50384698 50386745 2047 False 2455.0 2455 88.501 415 2446 1 chr2B.!!$F1 2031
12 TraesCS7A01G331000 chr7B 111352641 111354716 2075 False 2427.0 2427 87.990 389 2446 1 chr7B.!!$F1 2057

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
526 565 0.389948 GTGATCTTGCCGAGTCCGTT 60.39 55.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2147 1.136308 CGTAACGTGCATAAACCGCAA 60.136 47.619 0.0 0.0 41.97 4.85 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
59 60 0.716108 CTTGACGAAGCTTACCGCAG 59.284 55.000 0.00 0.00 42.61 5.18
127 128 2.811431 CAATCAAGTTCCAACGTGCCTA 59.189 45.455 0.00 0.00 38.12 3.93
186 187 0.535780 CTGGTTCTGTGAGGCAGCAA 60.536 55.000 0.00 0.00 44.66 3.91
233 234 3.536956 AGAATACGAGCCCGAATTCAA 57.463 42.857 6.22 0.00 39.50 2.69
451 490 9.631257 TTCCATGTCATATCATTTTCATACAGT 57.369 29.630 0.00 0.00 0.00 3.55
526 565 0.389948 GTGATCTTGCCGAGTCCGTT 60.390 55.000 0.00 0.00 0.00 4.44
565 604 5.050644 TGTCGACGAATGTAGTTACATGT 57.949 39.130 11.62 2.69 45.55 3.21
651 690 3.953612 GTGACCTGCAAAATATGGGATGA 59.046 43.478 0.00 0.00 0.00 2.92
665 704 1.561542 GGGATGATGACTTCCACCACT 59.438 52.381 0.00 0.00 40.67 4.00
958 1047 3.402628 TGTCCCTCTGCTGTTCTTTAC 57.597 47.619 0.00 0.00 0.00 2.01
979 1069 3.496130 ACGTGAACTCTGCTTCTCATTTG 59.504 43.478 0.00 0.00 0.00 2.32
1007 1098 4.433186 TTTAAATGCAGGTCATGTTCCG 57.567 40.909 0.00 0.00 35.13 4.30
1095 1186 2.940410 TGACCTGAAGAACCAACGTTTC 59.060 45.455 0.00 0.00 30.30 2.78
1112 1203 3.555518 GTTTCGAGGTGCTTGATTCAAC 58.444 45.455 0.00 0.00 0.00 3.18
1120 1211 1.153353 GCTTGATTCAACCCGTTCGA 58.847 50.000 0.00 0.00 0.00 3.71
1364 1464 5.644636 TCTTTGTTACGACTGTCCTTTTTGT 59.355 36.000 1.55 0.00 0.00 2.83
1370 1470 3.504520 ACGACTGTCCTTTTTGTGTGTTT 59.495 39.130 1.55 0.00 0.00 2.83
1387 1487 5.589050 GTGTGTTTACCTGACTCTTTTCCTT 59.411 40.000 0.00 0.00 0.00 3.36
1395 1495 2.092429 TGACTCTTTTCCTTGTGCAGGT 60.092 45.455 0.00 0.00 44.37 4.00
1443 1543 1.043022 CTTTGCAAAGTGGGAAGGCT 58.957 50.000 27.59 0.00 0.00 4.58
1491 1592 1.223187 GTCGTTGAGCTCCGGAAAAA 58.777 50.000 12.15 0.00 0.00 1.94
1642 1743 2.561478 ACCTTACATTCTGTTGCCGT 57.439 45.000 0.00 0.00 0.00 5.68
1996 2105 2.177394 TTTCATCGCTAACTGCACCA 57.823 45.000 0.00 0.00 43.06 4.17
2036 2147 3.222173 TCATGTAGCCACAACCTTTGT 57.778 42.857 0.00 0.00 46.75 2.83
2102 2216 2.772568 TTGCACACAACACACTATGC 57.227 45.000 0.00 0.00 0.00 3.14
2115 2229 2.490903 ACACTATGCGTCTCTAAACCGT 59.509 45.455 0.00 0.00 0.00 4.83
2130 2245 2.736144 ACCGTGTCGTATTGTCATGT 57.264 45.000 0.00 0.00 0.00 3.21
2193 2308 9.326413 GTATATTTTCAGTACAGCTAACATGGT 57.674 33.333 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.909302 GTGAAATCTCCTCAGGGGTGA 59.091 52.381 0.00 0.00 41.17 4.02
59 60 1.030457 CAATGCTGCCTCCTCAATCC 58.970 55.000 0.00 0.00 0.00 3.01
233 234 0.984995 GGTCTGTTCCTTAGTGGCCT 59.015 55.000 3.32 0.00 35.26 5.19
335 336 6.266131 AGCAAAATGAGAGATTATGGGGTA 57.734 37.500 0.00 0.00 0.00 3.69
424 463 9.888878 CTGTATGAAAATGATATGACATGGAAC 57.111 33.333 0.00 0.00 0.00 3.62
479 518 1.371337 ATGTACGTCGCTCCGCACTA 61.371 55.000 0.00 0.00 0.00 2.74
497 536 0.179062 GCAAGATCACCCAGCTCGAT 60.179 55.000 0.00 0.00 0.00 3.59
526 565 4.396790 GTCGACATTTTACCATTTGGCCTA 59.603 41.667 11.55 0.00 39.32 3.93
565 604 4.161377 TGATTGTTGATGTAGTCGATCCCA 59.839 41.667 0.00 0.00 0.00 4.37
651 690 3.370527 CGGGATTTAGTGGTGGAAGTCAT 60.371 47.826 0.00 0.00 0.00 3.06
665 704 5.261216 AGCAAAATTCTTCCTCGGGATTTA 58.739 37.500 0.00 0.00 0.00 1.40
857 896 2.355197 CACATAGTTTGCACGGGATGA 58.645 47.619 0.00 0.00 0.00 2.92
958 1047 3.496130 ACAAATGAGAAGCAGAGTTCACG 59.504 43.478 0.00 0.00 0.00 4.35
979 1069 6.215845 ACATGACCTGCATTTAAAAGTGAAC 58.784 36.000 0.00 0.00 34.15 3.18
1007 1098 1.246056 TGCAAGCTCCTGGAACATGC 61.246 55.000 17.74 17.74 38.20 4.06
1095 1186 0.804989 GGGTTGAATCAAGCACCTCG 59.195 55.000 23.98 0.00 42.72 4.63
1112 1203 1.298157 TGCATCAGCTTTCGAACGGG 61.298 55.000 0.00 0.00 42.74 5.28
1120 1211 3.710209 AGTAAGGTCTGCATCAGCTTT 57.290 42.857 13.67 0.00 42.74 3.51
1176 1267 2.925578 CGTAGTGACGGTTCCATGTA 57.074 50.000 0.00 0.00 45.63 2.29
1364 1464 5.367945 AGGAAAAGAGTCAGGTAAACACA 57.632 39.130 0.00 0.00 0.00 3.72
1370 1470 3.135712 TGCACAAGGAAAAGAGTCAGGTA 59.864 43.478 0.00 0.00 0.00 3.08
1387 1487 2.421314 CACAGTCCGACCTGCACA 59.579 61.111 0.00 0.00 35.83 4.57
1395 1495 1.300620 CGTGAAAGCCACAGTCCGA 60.301 57.895 0.00 0.00 45.98 4.55
1443 1543 2.092429 GCTGTGATAGGGGGACAATTCA 60.092 50.000 0.00 0.00 0.00 2.57
1491 1592 4.908601 TCAACCAGTTCCATGTGTAGAT 57.091 40.909 0.00 0.00 0.00 1.98
1642 1743 8.375493 ACAAAGAGATAGTACCTTACATTCCA 57.625 34.615 0.00 0.00 0.00 3.53
1996 2105 1.879575 TCAACCTACCCATGCTAGCT 58.120 50.000 17.23 0.00 0.00 3.32
2036 2147 1.136308 CGTAACGTGCATAAACCGCAA 60.136 47.619 0.00 0.00 41.97 4.85
2102 2216 2.880822 TACGACACGGTTTAGAGACG 57.119 50.000 0.00 0.00 0.00 4.18
2115 2229 8.931775 GGCATATATTTACATGACAATACGACA 58.068 33.333 0.00 0.00 30.05 4.35
2130 2245 9.166173 GTAATGACTCTGCATGGCATATATTTA 57.834 33.333 8.37 0.00 38.13 1.40
2193 2308 5.046231 TGCCATGTTGGTTGTACTGTATCTA 60.046 40.000 0.00 0.00 40.46 1.98


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

AutoCloner maintained by Alex Coulton.