Multiple sequence alignment - TraesCS7A01G051200

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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 TraesCS7A01G051200 chr7A 100.000 3473 0 0 1 3473 24625899 24629371 0.000000e+00 6414.0
1 TraesCS7A01G051200 chr7A 92.806 2252 123 20 1240 3473 24539727 24537497 0.000000e+00 3225.0
2 TraesCS7A01G051200 chr7A 77.360 1038 187 31 987 1988 25006404 25007429 3.890000e-159 571.0
3 TraesCS7A01G051200 chr7A 87.234 188 24 0 418 605 24621355 24621542 7.550000e-52 215.0
4 TraesCS7A01G051200 chr7A 84.925 199 24 4 3 199 24619959 24620153 2.730000e-46 196.0
5 TraesCS7A01G051200 chr7D 93.043 2645 132 29 874 3473 23509619 23512256 0.000000e+00 3818.0
6 TraesCS7A01G051200 chr7D 85.304 1429 163 31 1246 2651 23999893 24001297 0.000000e+00 1432.0
7 TraesCS7A01G051200 chr7D 84.529 1338 171 17 1246 2570 23541341 23540027 0.000000e+00 1291.0
8 TraesCS7A01G051200 chr7D 84.717 1132 129 24 906 1999 24113990 24115115 0.000000e+00 1092.0
9 TraesCS7A01G051200 chr7D 91.334 577 42 2 2 570 23508626 23509202 0.000000e+00 782.0
10 TraesCS7A01G051200 chr7D 87.310 591 65 7 2067 2651 24115197 24115783 0.000000e+00 667.0
11 TraesCS7A01G051200 chr7D 81.848 617 85 18 1918 2527 23507187 23507783 8.660000e-136 494.0
12 TraesCS7A01G051200 chr7D 93.182 308 15 4 569 872 23509274 23509579 6.840000e-122 448.0
13 TraesCS7A01G051200 chr7D 83.673 343 55 1 1456 1798 23982751 23983092 4.320000e-84 322.0
14 TraesCS7A01G051200 chr7D 84.644 267 36 3 975 1240 23999596 23999858 9.560000e-66 261.0
15 TraesCS7A01G051200 chr7D 85.165 182 25 2 3 182 23503495 23503676 5.920000e-43 185.0
16 TraesCS7A01G051200 chr7D 85.938 64 9 0 1468 1531 23579605 23579542 6.220000e-08 69.4
17 TraesCS7A01G051200 chr7D 95.122 41 2 0 918 958 23541748 23541708 8.050000e-07 65.8
18 TraesCS7A01G051200 chr4A 95.470 2009 52 7 874 2848 708300590 708298587 0.000000e+00 3169.0
19 TraesCS7A01G051200 chr4A 95.069 872 40 2 1 872 708301498 708300630 0.000000e+00 1369.0
20 TraesCS7A01G051200 chr4A 84.211 1045 91 24 2451 3473 708259411 708258419 0.000000e+00 948.0
21 TraesCS7A01G051200 chr4A 93.620 627 31 4 2850 3473 708298503 708297883 0.000000e+00 928.0
22 TraesCS7A01G051200 chr4A 76.537 1057 191 46 987 2003 708916796 708915757 3.070000e-145 525.0
23 TraesCS7A01G051200 chr4A 80.492 569 93 14 1448 2000 710413460 710412894 1.490000e-113 420.0
24 TraesCS7A01G051200 chr4A 94.330 194 11 0 584 777 708291169 708290976 7.290000e-77 298.0
25 TraesCS7A01G051200 chr4A 77.729 458 75 19 2174 2618 708914058 708913615 4.450000e-64 255.0
26 TraesCS7A01G051200 chr4A 79.000 400 57 15 209 605 708310013 708309638 7.440000e-62 248.0
27 TraesCS7A01G051200 chr6A 85.507 276 37 3 2231 2506 310681614 310681886 5.670000e-73 285.0


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 TraesCS7A01G051200 chr7A 24625899 24629371 3472 False 6414.0 6414 100.000000 1 3473 1 chr7A.!!$F1 3472
1 TraesCS7A01G051200 chr7A 24537497 24539727 2230 True 3225.0 3225 92.806000 1240 3473 1 chr7A.!!$R1 2233
2 TraesCS7A01G051200 chr7A 25006404 25007429 1025 False 571.0 571 77.360000 987 1988 1 chr7A.!!$F2 1001
3 TraesCS7A01G051200 chr7A 24619959 24621542 1583 False 205.5 215 86.079500 3 605 2 chr7A.!!$F3 602
4 TraesCS7A01G051200 chr7D 23503495 23512256 8761 False 1145.4 3818 88.914400 2 3473 5 chr7D.!!$F2 3471
5 TraesCS7A01G051200 chr7D 24113990 24115783 1793 False 879.5 1092 86.013500 906 2651 2 chr7D.!!$F4 1745
6 TraesCS7A01G051200 chr7D 23999596 24001297 1701 False 846.5 1432 84.974000 975 2651 2 chr7D.!!$F3 1676
7 TraesCS7A01G051200 chr7D 23540027 23541748 1721 True 678.4 1291 89.825500 918 2570 2 chr7D.!!$R2 1652
8 TraesCS7A01G051200 chr4A 708297883 708301498 3615 True 1822.0 3169 94.719667 1 3473 3 chr4A.!!$R5 3472
9 TraesCS7A01G051200 chr4A 708258419 708259411 992 True 948.0 948 84.211000 2451 3473 1 chr4A.!!$R1 1022
10 TraesCS7A01G051200 chr4A 710412894 710413460 566 True 420.0 420 80.492000 1448 2000 1 chr4A.!!$R4 552
11 TraesCS7A01G051200 chr4A 708913615 708916796 3181 True 390.0 525 77.133000 987 2618 2 chr4A.!!$R6 1631

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
380 1457 0.751452 GGCTAGGCGGCTACTAAGTT 59.249 55.000 15.70 0.0 34.85 2.66 F
499 1576 1.935873 CAGTTAGATGCATGGTGACCG 59.064 52.381 2.46 0.0 0.00 4.79 F
1376 7823 1.878088 CATGATGATTGCTTCGAGGGG 59.122 52.381 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 7823 0.104120 AAGTGGCCGCTTGAAAAACC 59.896 50.000 30.37 0.0 0.0 3.27 R
1435 7885 2.612221 CGTACCCCTCAAACTGGAACTC 60.612 54.545 0.00 0.0 0.0 3.01 R
3339 11499 0.669619 TGTGTGCTTGCTGAACCATG 59.330 50.000 0.00 0.0 0.0 3.66 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 5.874810 TCTTGACCAACCGATTAGAAGAATG 59.125 40.000 0.00 0.00 0.00 2.67
184 195 4.218200 TGGGTCTCTTGCAATATTGTTGTG 59.782 41.667 16.61 8.25 0.00 3.33
199 210 8.798859 ATATTGTTGTGAGCTCTAAGTTCATT 57.201 30.769 16.19 6.17 37.76 2.57
232 1309 4.328536 ACACGGTATATTTCAAGTTGGCA 58.671 39.130 2.34 0.00 0.00 4.92
263 1340 2.945668 GCTGCAAGTGGGGAGTATTTAG 59.054 50.000 0.00 0.00 35.30 1.85
274 1351 5.368523 TGGGGAGTATTTAGTGGTAGATTGG 59.631 44.000 0.00 0.00 0.00 3.16
276 1353 6.556116 GGGGAGTATTTAGTGGTAGATTGGTA 59.444 42.308 0.00 0.00 0.00 3.25
303 1380 1.342496 GACCAGATGCATCGATCCTCA 59.658 52.381 20.67 0.00 0.00 3.86
368 1445 6.043411 CGGAATAGTTAATCTATGGCTAGGC 58.957 44.000 9.85 9.85 39.10 3.93
374 1451 1.187087 ATCTATGGCTAGGCGGCTAC 58.813 55.000 15.70 11.77 39.32 3.58
380 1457 0.751452 GGCTAGGCGGCTACTAAGTT 59.249 55.000 15.70 0.00 34.85 2.66
384 1461 4.236147 GCTAGGCGGCTACTAAGTTATTC 58.764 47.826 15.70 0.00 0.00 1.75
499 1576 1.935873 CAGTTAGATGCATGGTGACCG 59.064 52.381 2.46 0.00 0.00 4.79
505 1582 3.576356 GCATGGTGACCGGATGCG 61.576 66.667 9.46 0.00 33.67 4.73
699 7020 3.202818 TCCATGCTCTGGTATTTCCACAT 59.797 43.478 5.89 0.00 46.08 3.21
850 7175 3.671716 CTTCATATGCATGAGCTAGCCA 58.328 45.455 12.13 9.78 42.11 4.75
872 7197 6.591062 GCCAAGAAAATGCATGAGATTTAACA 59.409 34.615 0.00 0.00 0.00 2.41
1294 7740 5.879237 TCAAACGTTCATATTCATCTTGCC 58.121 37.500 0.00 0.00 0.00 4.52
1376 7823 1.878088 CATGATGATTGCTTCGAGGGG 59.122 52.381 0.00 0.00 0.00 4.79
1435 7885 0.810031 CAACCTAATCGGCGGTGAGG 60.810 60.000 22.36 22.36 35.61 3.86
1687 8156 4.572389 GGATATTCTGCACAACTTCACGAT 59.428 41.667 0.00 0.00 0.00 3.73
2590 10632 6.571605 TGTTCAACAACACATGTCATTTCAT 58.428 32.000 0.00 0.00 42.99 2.57
2828 10890 1.867919 CGCGTCCCTGAGTCTCTTGT 61.868 60.000 0.00 0.00 0.00 3.16
3018 11164 1.829533 CCATGGCTTGGCGGCTATT 60.830 57.895 11.43 0.00 39.09 1.73
3037 11183 8.961092 CGGCTATTGAGTCATTTTTCATATTTG 58.039 33.333 0.00 0.00 0.00 2.32
3083 11229 1.078918 CTCGGCCATGCTTGTCTCA 60.079 57.895 2.24 0.00 0.00 3.27
3084 11230 0.463295 CTCGGCCATGCTTGTCTCAT 60.463 55.000 2.24 0.00 0.00 2.90
3097 11248 6.853720 TGCTTGTCTCATAGTCAAGTAGTAC 58.146 40.000 13.02 0.00 41.34 2.73
3297 11457 6.260050 ACTGGATATGCACATAACTTAAACGG 59.740 38.462 0.00 0.00 0.00 4.44
3358 11518 0.669619 CATGGTTCAGCAAGCACACA 59.330 50.000 0.00 0.00 42.73 3.72
3402 11563 8.124823 ACATATCAAAACAGAAGACATAATGCG 58.875 33.333 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.912486 GTTGCAGGGGTCAGTCCTAT 59.088 55.000 0.00 0.00 36.25 2.57
70 71 5.066505 GTGGAATGCATTCTTCTAATCGGTT 59.933 40.000 32.48 0.00 37.00 4.44
184 195 2.605366 GCCACGAATGAACTTAGAGCTC 59.395 50.000 5.27 5.27 0.00 4.09
232 1309 4.488790 CTTGCAGCCAAGTGGACT 57.511 55.556 0.18 0.00 42.76 3.85
246 1323 4.569719 ACCACTAAATACTCCCCACTTG 57.430 45.455 0.00 0.00 0.00 3.16
263 1340 5.597182 TGGTCAGTATCTACCAATCTACCAC 59.403 44.000 0.00 0.00 42.74 4.16
274 1351 4.216472 TCGATGCATCTGGTCAGTATCTAC 59.784 45.833 23.73 0.00 0.00 2.59
276 1353 3.225940 TCGATGCATCTGGTCAGTATCT 58.774 45.455 23.73 0.00 0.00 1.98
303 1380 7.202056 CCACCAAAGTAAAATTTACCCTTCCTT 60.202 37.037 11.83 0.00 0.00 3.36
320 1397 8.136800 CCGTAAATTAAAAACTACCACCAAAGT 58.863 33.333 0.00 0.00 0.00 2.66
345 1422 6.043411 CGCCTAGCCATAGATTAACTATTCC 58.957 44.000 0.00 0.00 39.50 3.01
358 1435 2.168496 CTTAGTAGCCGCCTAGCCATA 58.832 52.381 0.00 0.00 0.00 2.74
368 1445 8.516811 AAATATGACGAATAACTTAGTAGCCG 57.483 34.615 0.00 0.00 0.00 5.52
395 1472 9.802039 ACCTATGAACTTTGAGGTAACAAATTA 57.198 29.630 0.00 0.00 40.59 1.40
406 1483 7.390440 TGAAACATACCACCTATGAACTTTGAG 59.610 37.037 0.00 0.00 36.45 3.02
419 1496 2.029380 GGCCAACTTGAAACATACCACC 60.029 50.000 0.00 0.00 0.00 4.61
499 1576 1.160329 CCCAAAGGATCGACGCATCC 61.160 60.000 14.71 14.71 42.68 3.51
520 6768 0.681887 CTTCCCCATGCACATGCTCA 60.682 55.000 5.31 0.00 42.66 4.26
699 7020 7.117812 GCTCTACAACAAGTAATGCAACTTAGA 59.882 37.037 3.51 2.84 33.72 2.10
730 7051 2.478292 ACCAATTCCTCGGGTCAGTAT 58.522 47.619 0.00 0.00 0.00 2.12
769 7090 2.627699 GTGGGAGAGATCTGAGATGGAC 59.372 54.545 0.00 0.00 0.00 4.02
872 7197 9.000486 CAGATTGATACTGCAAATCTGACATAT 58.000 33.333 24.39 5.19 36.55 1.78
913 7276 7.331026 ACAGAAGAATCCGAAATGTATTCTGA 58.669 34.615 16.09 0.00 43.08 3.27
927 7290 4.019231 AGGGAGTACCAAACAGAAGAATCC 60.019 45.833 0.00 0.00 43.89 3.01
1069 7485 1.228228 CCATGTACTGGGCTGGCAT 59.772 57.895 2.88 0.00 41.82 4.40
1294 7740 4.004982 TGCATGCAGGCACATACATATAG 58.995 43.478 24.07 0.00 39.25 1.31
1347 7794 4.341366 AGCAATCATCATGTCGTCCATA 57.659 40.909 0.00 0.00 30.71 2.74
1376 7823 0.104120 AAGTGGCCGCTTGAAAAACC 59.896 50.000 30.37 0.00 0.00 3.27
1435 7885 2.612221 CGTACCCCTCAAACTGGAACTC 60.612 54.545 0.00 0.00 0.00 3.01
1687 8156 2.990284 TCCTTCACTCCCCCACATTTTA 59.010 45.455 0.00 0.00 0.00 1.52
2116 8697 9.775854 AATTTTGATTGTTGTGTTCCATTATGA 57.224 25.926 0.00 0.00 0.00 2.15
2563 10605 6.645700 AATGACATGTGTTGTTGAACAAAC 57.354 33.333 12.89 12.93 43.77 2.93
2659 10703 2.416836 CCAGCAATCCAGCATCACAAAG 60.417 50.000 0.00 0.00 36.85 2.77
2720 10765 3.338249 GTCAGTCAGCTAATTGGCTTGA 58.662 45.455 14.38 12.63 41.00 3.02
2784 10829 7.227512 CGGCTTGAGAGTTTCATAAGGAAATAT 59.772 37.037 0.00 0.00 46.55 1.28
2848 10992 7.148407 CGGATGGCCAACTTGAAATATACTATC 60.148 40.741 10.96 0.00 0.00 2.08
2880 11024 6.071952 CCAGCAAATACTCCACACACTTAAAT 60.072 38.462 0.00 0.00 0.00 1.40
2948 11092 5.335661 CCACCAGAAGAAAATTTACCCTTCG 60.336 44.000 15.87 12.57 39.78 3.79
3037 11183 5.391203 GCATTTGCAAGGTCCATCAAATTTC 60.391 40.000 0.00 5.61 37.12 2.17
3297 11457 7.063308 ACAAATCGTAATGATGTTTTCAATGGC 59.937 33.333 0.00 0.00 38.03 4.40
3339 11499 0.669619 TGTGTGCTTGCTGAACCATG 59.330 50.000 0.00 0.00 0.00 3.66
3358 11518 8.565896 TGATATGTGTTTATCAAGACTGCTTT 57.434 30.769 0.00 0.00 36.03 3.51
3402 11563 4.082354 GCCATATTCAGATCAATTGCCTCC 60.082 45.833 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.