Multiple sequence alignment - TraesCS5D01G110600

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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 TraesCS5D01G110600 chr5D 100.000 2511 0 0 1 2511 125738964 125736454 0.000000e+00 4638.0
1 TraesCS5D01G110600 chr5D 81.441 555 67 19 16 541 13324196 13323649 2.990000e-114 422.0
2 TraesCS5D01G110600 chr5D 95.337 193 8 1 350 541 125678522 125678330 3.140000e-79 305.0
3 TraesCS5D01G110600 chr5D 85.874 269 35 3 276 541 13329930 13330198 1.470000e-72 283.0
4 TraesCS5D01G110600 chr5D 100.000 33 0 0 304 336 125678550 125678518 7.500000e-06 62.1
5 TraesCS5D01G110600 chr5B 94.501 1382 57 12 542 1915 138345665 138347035 0.000000e+00 2113.0
6 TraesCS5D01G110600 chr5B 96.680 241 6 1 2235 2473 138349215 138349455 1.400000e-107 399.0
7 TraesCS5D01G110600 chr5B 97.283 184 3 2 2090 2271 138347290 138347473 6.740000e-81 311.0
8 TraesCS5D01G110600 chr5B 96.262 107 3 1 1943 2048 138347178 138347284 9.230000e-40 174.0
9 TraesCS5D01G110600 chr5B 97.619 42 1 0 2470 2511 368695718 368695677 3.460000e-09 73.1
10 TraesCS5D01G110600 chr5A 95.820 909 36 2 620 1528 139681566 139682472 0.000000e+00 1467.0
11 TraesCS5D01G110600 chr5A 96.060 533 19 1 1943 2473 139682726 139683258 0.000000e+00 867.0
12 TraesCS5D01G110600 chr5A 92.920 113 8 0 1661 1773 139682500 139682612 5.560000e-37 165.0
13 TraesCS5D01G110600 chr5A 97.619 42 1 0 2470 2511 27541676 27541717 3.460000e-09 73.1
14 TraesCS5D01G110600 chr4D 99.076 541 5 0 1 541 95522322 95521782 0.000000e+00 972.0
15 TraesCS5D01G110600 chr4D 95.855 193 7 1 350 541 95528118 95528310 6.740000e-81 311.0
16 TraesCS5D01G110600 chr4D 100.000 33 0 0 304 336 95528090 95528122 7.500000e-06 62.1
17 TraesCS5D01G110600 chr1D 97.597 541 10 1 1 541 489250371 489249834 0.000000e+00 924.0
18 TraesCS5D01G110600 chr1D 97.059 238 7 0 304 541 489256137 489256374 3.890000e-108 401.0
19 TraesCS5D01G110600 chr7A 81.070 729 93 30 809 1512 690918695 690917987 7.900000e-150 540.0
20 TraesCS5D01G110600 chr7A 86.047 473 45 13 1044 1512 690930212 690929757 2.900000e-134 488.0
21 TraesCS5D01G110600 chr7D 80.521 729 107 26 810 1512 598485845 598485126 6.150000e-146 527.0
22 TraesCS5D01G110600 chr7D 79.612 721 106 35 814 1512 598497252 598496551 1.750000e-131 479.0
23 TraesCS5D01G110600 chr7B 80.187 747 92 35 811 1512 677538959 677538224 2.230000e-140 508.0
24 TraesCS5D01G110600 chr7B 79.972 719 97 32 813 1512 677668124 677667434 1.040000e-133 486.0
25 TraesCS5D01G110600 chr7B 89.912 228 23 0 1285 1512 677522636 677522409 6.790000e-76 294.0
26 TraesCS5D01G110600 chr7B 86.415 265 32 4 289 550 651487669 651487406 1.140000e-73 287.0
27 TraesCS5D01G110600 chr7B 88.626 211 21 3 333 541 651491341 651491550 1.150000e-63 254.0
28 TraesCS5D01G110600 chr4A 91.875 160 12 1 1044 1203 574385232 574385074 3.250000e-54 222.0
29 TraesCS5D01G110600 chr4B 92.258 155 12 0 1044 1198 41743710 41743864 1.170000e-53 220.0
30 TraesCS5D01G110600 chr4B 97.619 42 1 0 2470 2511 479402211 479402170 3.460000e-09 73.1
31 TraesCS5D01G110600 chr4B 97.436 39 1 0 2470 2508 376257049 376257087 1.610000e-07 67.6
32 TraesCS5D01G110600 chr3D 100.000 42 0 0 2470 2511 557960211 557960170 7.450000e-11 78.7
33 TraesCS5D01G110600 chr1B 100.000 42 0 0 2470 2511 668914452 668914411 7.450000e-11 78.7
34 TraesCS5D01G110600 chr1A 100.000 42 0 0 2470 2511 280490955 280490996 7.450000e-11 78.7
35 TraesCS5D01G110600 chr2B 95.238 42 2 0 2470 2511 429165119 429165078 1.610000e-07 67.6


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 TraesCS5D01G110600 chr5D 125736454 125738964 2510 True 4638.00 4638 100.000000 1 2511 1 chr5D.!!$R2 2510
1 TraesCS5D01G110600 chr5D 13323649 13324196 547 True 422.00 422 81.441000 16 541 1 chr5D.!!$R1 525
2 TraesCS5D01G110600 chr5B 138345665 138349455 3790 False 749.25 2113 96.181500 542 2473 4 chr5B.!!$F1 1931
3 TraesCS5D01G110600 chr5A 139681566 139683258 1692 False 833.00 1467 94.933333 620 2473 3 chr5A.!!$F2 1853
4 TraesCS5D01G110600 chr4D 95521782 95522322 540 True 972.00 972 99.076000 1 541 1 chr4D.!!$R1 540
5 TraesCS5D01G110600 chr1D 489249834 489250371 537 True 924.00 924 97.597000 1 541 1 chr1D.!!$R1 540
6 TraesCS5D01G110600 chr7A 690917987 690918695 708 True 540.00 540 81.070000 809 1512 1 chr7A.!!$R1 703
7 TraesCS5D01G110600 chr7D 598485126 598485845 719 True 527.00 527 80.521000 810 1512 1 chr7D.!!$R1 702
8 TraesCS5D01G110600 chr7D 598496551 598497252 701 True 479.00 479 79.612000 814 1512 1 chr7D.!!$R2 698
9 TraesCS5D01G110600 chr7B 677538224 677538959 735 True 508.00 508 80.187000 811 1512 1 chr7B.!!$R3 701
10 TraesCS5D01G110600 chr7B 677667434 677668124 690 True 486.00 486 79.972000 813 1512 1 chr7B.!!$R4 699

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
919 950 1.283029 CACACCATCTCCACATTCCCT 59.717 52.381 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
2474 4492 1.153549 GCCAAGCGGGAGAGTACAG 60.154 63.158 1.23 0.0 40.01 2.74 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
260 281 1.539665 GTGGGTTTGGGAACTGGGA 59.460 57.895 0.00 0.00 36.03 4.37
550 578 6.686630 TGGTGTATTTGCCTCAATTGTAAAG 58.313 36.000 5.13 0.00 0.00 1.85
657 686 4.504596 TGACGCATGGGCCCATCC 62.505 66.667 35.42 26.32 36.38 3.51
714 743 3.496331 CTCTCCCCTCCTCTAATCACTC 58.504 54.545 0.00 0.00 0.00 3.51
919 950 1.283029 CACACCATCTCCACATTCCCT 59.717 52.381 0.00 0.00 0.00 4.20
921 952 1.842562 CACCATCTCCACATTCCCTCT 59.157 52.381 0.00 0.00 0.00 3.69
925 956 1.769026 TCTCCACATTCCCTCTCTCG 58.231 55.000 0.00 0.00 0.00 4.04
1011 1054 2.159448 CGACGAGAAGATGAGTTCTGCT 60.159 50.000 0.00 0.00 43.73 4.24
1229 1284 2.478746 CGCGTTTCGTTCCCCATG 59.521 61.111 0.00 0.00 0.00 3.66
1231 1286 1.673009 GCGTTTCGTTCCCCATGGA 60.673 57.895 15.22 0.00 39.54 3.41
1513 1633 1.956159 GCGTCCCAGGAGTTCTAGAGT 60.956 57.143 0.00 0.00 0.00 3.24
1606 1726 7.010275 GCTTTAGGTTGTTAGATTAGTTCTCGG 59.990 40.741 0.00 0.00 35.79 4.63
1613 1733 7.165460 TGTTAGATTAGTTCTCGGTCAATGA 57.835 36.000 0.00 0.00 35.79 2.57
1615 1735 7.921214 TGTTAGATTAGTTCTCGGTCAATGATC 59.079 37.037 0.00 0.00 35.79 2.92
1629 1749 5.185454 GTCAATGATCTGGTTGGTGTATCA 58.815 41.667 0.00 0.00 0.00 2.15
1650 1770 6.459670 TCAATGATGAATCTGGTTGGAATG 57.540 37.500 0.00 0.00 30.99 2.67
1651 1771 6.189133 TCAATGATGAATCTGGTTGGAATGA 58.811 36.000 0.00 0.00 30.99 2.57
1658 1778 9.342308 GATGAATCTGGTTGGAATGAAATACTA 57.658 33.333 0.00 0.00 0.00 1.82
1821 1941 5.936956 CAGAGAGTATTTTCTGGCAGTCTTT 59.063 40.000 15.27 0.34 37.70 2.52
1826 1946 8.540388 AGAGTATTTTCTGGCAGTCTTTATGTA 58.460 33.333 15.27 0.00 0.00 2.29
1834 1954 6.048732 TGGCAGTCTTTATGTATTCAGTCA 57.951 37.500 0.00 0.00 0.00 3.41
1893 2013 5.825593 ACTATTTCTCACCAGTTTCAGGA 57.174 39.130 0.00 0.00 0.00 3.86
1924 2058 0.681243 GATGCCAAGACAACCCCCTC 60.681 60.000 0.00 0.00 0.00 4.30
1931 2065 1.760405 AGACAACCCCCTCCAGAAAT 58.240 50.000 0.00 0.00 0.00 2.17
1938 2072 1.490910 CCCCCTCCAGAAATCCTGTAC 59.509 57.143 0.00 0.00 41.33 2.90
1982 2217 7.044798 AGAATCTTGCAGACTAACAAGGATAC 58.955 38.462 14.32 6.93 42.82 2.24
2062 2298 4.228010 TCATCCCATGATGCCATTTTCAT 58.772 39.130 0.00 0.00 46.60 2.57
2297 4315 1.405526 GCATGAAACGGAGGTGCTAGA 60.406 52.381 0.00 0.00 33.25 2.43
2353 4371 5.934625 ACTGTTGTGATTCTGTGGATTACTC 59.065 40.000 0.00 0.00 0.00 2.59
2456 4474 3.553904 TGGTGTTTACCCCAACAGTAAC 58.446 45.455 0.00 0.00 46.96 2.50
2473 4491 6.647229 ACAGTAACTCATGATGATGTGTGAT 58.353 36.000 0.00 0.00 36.61 3.06
2474 4492 6.760298 ACAGTAACTCATGATGATGTGTGATC 59.240 38.462 0.00 0.00 36.61 2.92
2475 4493 6.985059 CAGTAACTCATGATGATGTGTGATCT 59.015 38.462 0.00 0.00 36.61 2.75
2476 4494 6.985059 AGTAACTCATGATGATGTGTGATCTG 59.015 38.462 0.00 0.00 36.61 2.90
2477 4495 5.354842 ACTCATGATGATGTGTGATCTGT 57.645 39.130 0.00 0.00 35.46 3.41
2478 4496 6.475596 ACTCATGATGATGTGTGATCTGTA 57.524 37.500 0.00 0.00 35.46 2.74
2479 4497 6.279123 ACTCATGATGATGTGTGATCTGTAC 58.721 40.000 0.00 0.00 35.46 2.90
2480 4498 6.097981 ACTCATGATGATGTGTGATCTGTACT 59.902 38.462 0.00 0.00 35.46 2.73
2481 4499 6.510536 TCATGATGATGTGTGATCTGTACTC 58.489 40.000 0.00 0.00 0.00 2.59
2482 4500 6.323225 TCATGATGATGTGTGATCTGTACTCT 59.677 38.462 0.00 0.00 0.00 3.24
2483 4501 6.141560 TGATGATGTGTGATCTGTACTCTC 57.858 41.667 0.00 0.00 0.00 3.20
2484 4502 4.991153 TGATGTGTGATCTGTACTCTCC 57.009 45.455 0.00 0.00 0.00 3.71
2485 4503 3.701542 TGATGTGTGATCTGTACTCTCCC 59.298 47.826 0.00 0.00 0.00 4.30
2486 4504 2.092323 TGTGTGATCTGTACTCTCCCG 58.908 52.381 0.00 0.00 0.00 5.14
2487 4505 1.103803 TGTGATCTGTACTCTCCCGC 58.896 55.000 0.00 0.00 0.00 6.13
2488 4506 1.341089 TGTGATCTGTACTCTCCCGCT 60.341 52.381 0.00 0.00 0.00 5.52
2489 4507 1.751924 GTGATCTGTACTCTCCCGCTT 59.248 52.381 0.00 0.00 0.00 4.68
2490 4508 1.751351 TGATCTGTACTCTCCCGCTTG 59.249 52.381 0.00 0.00 0.00 4.01
2491 4509 1.067821 GATCTGTACTCTCCCGCTTGG 59.932 57.143 0.00 0.00 0.00 3.61
2492 4510 1.153549 CTGTACTCTCCCGCTTGGC 60.154 63.158 0.00 0.00 0.00 4.52
2504 4522 3.460648 GCTTGGCGGAACTATGTCT 57.539 52.632 0.00 0.00 0.00 3.41
2505 4523 2.596904 GCTTGGCGGAACTATGTCTA 57.403 50.000 0.00 0.00 0.00 2.59
2506 4524 2.901249 GCTTGGCGGAACTATGTCTAA 58.099 47.619 0.00 0.00 0.00 2.10
2507 4525 3.467803 GCTTGGCGGAACTATGTCTAAT 58.532 45.455 0.00 0.00 0.00 1.73
2508 4526 3.495001 GCTTGGCGGAACTATGTCTAATC 59.505 47.826 0.00 0.00 0.00 1.75
2509 4527 4.740934 GCTTGGCGGAACTATGTCTAATCT 60.741 45.833 0.00 0.00 0.00 2.40
2510 4528 5.353394 TTGGCGGAACTATGTCTAATCTT 57.647 39.130 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 281 0.828022 TCCCCGAAGCACGTTATGAT 59.172 50.000 0.00 0.00 40.78 2.45
281 306 8.506168 TCCTTTTATGTGGATTATCTCAACAC 57.494 34.615 0.00 0.00 40.69 3.32
550 578 3.366985 GGGTTGGAATTCACGGATTTCAC 60.367 47.826 7.93 0.00 0.00 3.18
564 592 3.323403 GGTTCACATCATTTGGGTTGGAA 59.677 43.478 0.00 0.00 0.00 3.53
657 686 0.666374 GTTTGGGGTGTTTCGTCCAG 59.334 55.000 0.00 0.00 0.00 3.86
714 743 3.821033 AGACGGAAAAGTTTGGAATGGAG 59.179 43.478 0.00 0.00 0.00 3.86
773 802 1.305887 GGAGGACGAGGAGGGGAAA 60.306 63.158 0.00 0.00 0.00 3.13
925 956 3.330766 CGGAGTCGGACAGATTGTC 57.669 57.895 11.27 0.62 46.23 3.18
1231 1286 1.630878 GGGGACAGAACAGGAGAATGT 59.369 52.381 0.00 0.00 33.96 2.71
1268 1383 6.836007 AGGACCTGAAGAGAAGAAAAACAAAT 59.164 34.615 0.00 0.00 0.00 2.32
1513 1633 0.321346 TGCTGGTTTGATCTGCGAGA 59.679 50.000 0.00 0.00 32.79 4.04
1606 1726 5.185454 TGATACACCAACCAGATCATTGAC 58.815 41.667 0.00 0.00 0.00 3.18
1613 1733 6.005066 TCATCATTGATACACCAACCAGAT 57.995 37.500 0.00 0.00 0.00 2.90
1615 1735 6.544931 AGATTCATCATTGATACACCAACCAG 59.455 38.462 0.00 0.00 0.00 4.00
1629 1749 7.484993 TTTCATTCCAACCAGATTCATCATT 57.515 32.000 0.00 0.00 0.00 2.57
1650 1770 7.617041 ACAAGAACCAGATTGCTAGTATTTC 57.383 36.000 0.00 0.00 0.00 2.17
1651 1771 9.686683 ATAACAAGAACCAGATTGCTAGTATTT 57.313 29.630 0.00 0.00 0.00 1.40
1658 1778 7.168219 TGAGTAATAACAAGAACCAGATTGCT 58.832 34.615 0.00 0.00 0.00 3.91
1725 1845 3.068732 TGTTTTCACCATTCATTCCGCAA 59.931 39.130 0.00 0.00 0.00 4.85
1763 1883 3.181483 GGCCATCAACATTCATTCAGACC 60.181 47.826 0.00 0.00 0.00 3.85
1821 1941 6.368791 GCGAATTAGGCATGACTGAATACATA 59.631 38.462 12.69 0.00 0.00 2.29
1826 1946 2.880890 GGCGAATTAGGCATGACTGAAT 59.119 45.455 12.69 0.00 36.61 2.57
1834 1954 3.554934 TGAATCTTGGCGAATTAGGCAT 58.445 40.909 15.30 0.69 46.15 4.40
1893 2013 4.263905 TGTCTTGGCATCCTGGAAGTTTAT 60.264 41.667 0.00 0.00 0.00 1.40
1931 2065 4.820897 CTTGACTGCTACATTGTACAGGA 58.179 43.478 20.54 6.16 34.40 3.86
1938 2072 3.511699 TCTACGCTTGACTGCTACATTG 58.488 45.455 0.00 0.00 0.00 2.82
2052 2288 5.391312 ACAACTTCCACTATGAAAATGGC 57.609 39.130 0.00 0.00 33.20 4.40
2062 2298 5.526111 GTGCTAGTTGAAACAACTTCCACTA 59.474 40.000 19.55 3.20 39.89 2.74
2297 4315 8.844244 GCCATTCATTAATCAGACTAAACAGAT 58.156 33.333 0.00 0.00 0.00 2.90
2456 4474 6.514063 AGTACAGATCACACATCATCATGAG 58.486 40.000 0.09 0.00 33.72 2.90
2473 4491 1.605058 GCCAAGCGGGAGAGTACAGA 61.605 60.000 1.23 0.00 40.01 3.41
2474 4492 1.153549 GCCAAGCGGGAGAGTACAG 60.154 63.158 1.23 0.00 40.01 2.74
2475 4493 2.978824 GCCAAGCGGGAGAGTACA 59.021 61.111 1.23 0.00 40.01 2.90
2486 4504 2.596904 TAGACATAGTTCCGCCAAGC 57.403 50.000 0.00 0.00 0.00 4.01
2487 4505 4.950050 AGATTAGACATAGTTCCGCCAAG 58.050 43.478 0.00 0.00 0.00 3.61
2488 4506 5.353394 AAGATTAGACATAGTTCCGCCAA 57.647 39.130 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.