Multiple sequence alignment - TraesCS2A01G502900

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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 TraesCS2A01G502900 chr2A 100.000 4086 0 0 1 4086 732544301 732548386 0.000000e+00 7546.0
1 TraesCS2A01G502900 chr2A 98.766 2107 22 3 1 2106 732506636 732508739 0.000000e+00 3744.0
2 TraesCS2A01G502900 chr2A 98.790 1074 10 1 1033 2106 732519371 732520441 0.000000e+00 1908.0
3 TraesCS2A01G502900 chr2A 79.899 995 165 25 2100 3079 729568253 729569227 0.000000e+00 697.0
4 TraesCS2A01G502900 chr2A 90.566 53 3 2 768 818 761182258 761182206 7.330000e-08 69.4
5 TraesCS2A01G502900 chr2A 97.222 36 1 0 3023 3058 766003288 766003253 1.230000e-05 62.1
6 TraesCS2A01G502900 chr2A 94.737 38 2 0 3023 3060 138517679 138517642 4.410000e-05 60.2
7 TraesCS2A01G502900 chr2D 97.079 2499 45 9 981 3465 598610718 598613202 0.000000e+00 4185.0
8 TraesCS2A01G502900 chr2D 95.140 926 19 10 1 917 598609189 598610097 0.000000e+00 1437.0
9 TraesCS2A01G502900 chr2D 97.826 460 10 0 3627 4086 598613384 598613843 0.000000e+00 795.0
10 TraesCS2A01G502900 chr2D 76.737 1281 242 44 1828 3079 595508346 595509599 0.000000e+00 664.0
11 TraesCS2A01G502900 chr2D 97.973 148 2 1 3482 3629 598613189 598613335 5.240000e-64 255.0
12 TraesCS2A01G502900 chr2D 95.833 48 1 1 902 949 598610611 598610657 4.380000e-10 76.8
13 TraesCS2A01G502900 chr2D 84.746 59 5 4 954 1011 598610650 598610705 5.710000e-04 56.5
14 TraesCS2A01G502900 chr2B 95.685 2132 62 10 1349 3465 726463639 726465755 0.000000e+00 3400.0
15 TraesCS2A01G502900 chr2B 93.991 466 24 3 3624 4086 726465919 726466383 0.000000e+00 702.0
16 TraesCS2A01G502900 chr2B 78.932 1049 180 31 2054 3079 723429673 723430703 0.000000e+00 675.0
17 TraesCS2A01G502900 chr2B 85.948 612 53 24 1 598 726462242 726462834 1.250000e-174 623.0
18 TraesCS2A01G502900 chr2B 96.633 297 10 0 981 1277 726463337 726463633 1.020000e-135 494.0
19 TraesCS2A01G502900 chr2B 90.233 215 16 4 409 619 726462687 726462900 4.020000e-70 276.0
20 TraesCS2A01G502900 chr2B 97.516 161 4 0 815 975 726463124 726463284 4.020000e-70 276.0
21 TraesCS2A01G502900 chr2B 84.524 252 23 14 485 727 726462805 726463049 6.830000e-58 235.0
22 TraesCS2A01G502900 chr2B 90.345 145 6 2 3482 3626 726465742 726465878 2.510000e-42 183.0
23 TraesCS2A01G502900 chr2B 97.778 45 1 0 766 810 726463054 726463098 1.220000e-10 78.7
24 TraesCS2A01G502900 chr7A 88.400 500 35 11 3600 4086 236860488 236859999 7.610000e-162 580.0
25 TraesCS2A01G502900 chr1A 74.291 1023 213 43 2102 3094 497887781 497886779 1.780000e-103 387.0
26 TraesCS2A01G502900 chr1A 83.962 106 11 5 644 747 72674902 72674801 3.360000e-16 97.1
27 TraesCS2A01G502900 chr6B 84.804 204 16 6 3770 3959 54416604 54416806 1.500000e-44 191.0
28 TraesCS2A01G502900 chr6B 88.889 90 9 1 3997 4086 515433500 515433588 4.320000e-20 110.0
29 TraesCS2A01G502900 chr6B 81.132 106 13 7 518 618 250593649 250593546 1.220000e-10 78.7
30 TraesCS2A01G502900 chr3B 80.435 138 23 3 489 624 750461345 750461210 7.230000e-18 102.0
31 TraesCS2A01G502900 chr7B 80.435 138 19 7 487 618 733542974 733543109 9.350000e-17 99.0
32 TraesCS2A01G502900 chr7B 74.632 272 44 16 488 739 7714978 7715244 3.360000e-16 97.1
33 TraesCS2A01G502900 chr7B 77.528 178 27 12 426 598 713436296 713436127 1.210000e-15 95.3
34 TraesCS2A01G502900 chr4D 75.319 235 42 14 394 618 113935270 113935042 9.350000e-17 99.0
35 TraesCS2A01G502900 chr5A 76.279 215 28 11 623 816 452280591 452280379 4.350000e-15 93.5
36 TraesCS2A01G502900 chr1B 81.651 109 14 3 2974 3079 540338366 540338261 7.280000e-13 86.1
37 TraesCS2A01G502900 chr5D 86.301 73 7 3 671 741 75723993 75724064 4.380000e-10 76.8
38 TraesCS2A01G502900 chr5B 94.737 38 1 1 671 707 84480812 84480849 1.590000e-04 58.4
39 TraesCS2A01G502900 chrUn 100.000 28 0 0 3501 3528 45828162 45828189 7.000000e-03 52.8
40 TraesCS2A01G502900 chrUn 100.000 28 0 0 3501 3528 323578085 323578058 7.000000e-03 52.8
41 TraesCS2A01G502900 chr3D 100.000 28 0 0 3501 3528 599436732 599436759 7.000000e-03 52.8


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 TraesCS2A01G502900 chr2A 732544301 732548386 4085 False 7546.000000 7546 100.000000 1 4086 1 chr2A.!!$F4 4085
1 TraesCS2A01G502900 chr2A 732506636 732508739 2103 False 3744.000000 3744 98.766000 1 2106 1 chr2A.!!$F2 2105
2 TraesCS2A01G502900 chr2A 732519371 732520441 1070 False 1908.000000 1908 98.790000 1033 2106 1 chr2A.!!$F3 1073
3 TraesCS2A01G502900 chr2A 729568253 729569227 974 False 697.000000 697 79.899000 2100 3079 1 chr2A.!!$F1 979
4 TraesCS2A01G502900 chr2D 598609189 598613843 4654 False 1134.216667 4185 94.766167 1 4086 6 chr2D.!!$F2 4085
5 TraesCS2A01G502900 chr2D 595508346 595509599 1253 False 664.000000 664 76.737000 1828 3079 1 chr2D.!!$F1 1251
6 TraesCS2A01G502900 chr2B 726462242 726466383 4141 False 696.411111 3400 92.517000 1 4086 9 chr2B.!!$F2 4085
7 TraesCS2A01G502900 chr2B 723429673 723430703 1030 False 675.000000 675 78.932000 2054 3079 1 chr2B.!!$F1 1025
8 TraesCS2A01G502900 chr1A 497886779 497887781 1002 True 387.000000 387 74.291000 2102 3094 1 chr1A.!!$R2 992


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
723 821 0.171455 AACGCAGCACAACCGAAAAA 59.829 45.000 0.00 0.00 0.0 1.94 F
762 860 1.002087 AGCGAAAGTGAACGAAGGGAT 59.998 47.619 0.00 0.00 0.0 3.85 F
817 915 1.153549 CTGTAGGCGCCACTTCTCC 60.154 63.158 31.54 8.08 0.0 3.71 F
818 916 2.187163 GTAGGCGCCACTTCTCCC 59.813 66.667 31.54 2.43 0.0 4.30 F
819 917 3.081409 TAGGCGCCACTTCTCCCC 61.081 66.667 31.54 0.00 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2678 0.882042 AAGAACACGCAGCAGGTGAG 60.882 55.000 3.02 2.10 38.73 3.51 R
2339 3061 6.038271 CAGTTTTTGGCAGTAGTTACTTCTGT 59.962 38.462 17.81 0.00 32.65 3.41 R
2545 3284 6.117488 TGCTTTATCTTCAGATTCTGATGCA 58.883 36.000 16.82 14.09 40.39 3.96 R
3081 3826 3.255149 GCCTCCCATCATCATTCATCAAC 59.745 47.826 0.00 0.00 0.00 3.18 R
3102 3847 3.319122 ACCATCTTTTCAACAAGTCCAGC 59.681 43.478 0.00 0.00 0.00 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
313 323 4.992515 CGGTGTACGGGTGCTTTA 57.007 55.556 0.00 0.00 39.42 1.85
723 821 0.171455 AACGCAGCACAACCGAAAAA 59.829 45.000 0.00 0.00 0.00 1.94
750 848 4.057428 AGCGAGGCGAGCGAAAGT 62.057 61.111 0.00 0.00 40.04 2.66
762 860 1.002087 AGCGAAAGTGAACGAAGGGAT 59.998 47.619 0.00 0.00 0.00 3.85
804 902 2.882777 CGCTGCTGGTCGCTGTAG 60.883 66.667 0.00 0.00 39.51 2.74
805 903 2.510238 GCTGCTGGTCGCTGTAGG 60.510 66.667 0.00 0.00 39.51 3.18
806 904 2.510238 CTGCTGGTCGCTGTAGGC 60.510 66.667 0.00 0.00 40.11 3.93
815 913 2.266055 GCTGTAGGCGCCACTTCT 59.734 61.111 31.54 10.27 0.00 2.85
816 914 1.811679 GCTGTAGGCGCCACTTCTC 60.812 63.158 31.54 12.01 0.00 2.87
817 915 1.153549 CTGTAGGCGCCACTTCTCC 60.154 63.158 31.54 8.08 0.00 3.71
818 916 2.187163 GTAGGCGCCACTTCTCCC 59.813 66.667 31.54 2.43 0.00 4.30
819 917 3.081409 TAGGCGCCACTTCTCCCC 61.081 66.667 31.54 0.00 0.00 4.81
1966 2678 6.500684 TCTGATCATTGTTAGGTTTCTTGC 57.499 37.500 0.00 0.00 0.00 4.01
2339 3061 4.346709 TCATCGCAACCCTATATTCCTTCA 59.653 41.667 0.00 0.00 0.00 3.02
3081 3826 3.706698 TCATTCCGTCGAAGATGCTTAG 58.293 45.455 0.00 0.00 43.31 2.18
3102 3847 4.726583 AGTTGATGAATGATGATGGGAGG 58.273 43.478 0.00 0.00 0.00 4.30
3174 3919 3.195661 GCCTTTCCTGTAGTTATGGTCG 58.804 50.000 0.00 0.00 0.00 4.79
3352 4097 2.409152 GCTACAGCTACGGTCTGATC 57.591 55.000 4.07 0.00 38.21 2.92
3353 4098 1.676529 GCTACAGCTACGGTCTGATCA 59.323 52.381 4.07 0.00 38.21 2.92
3354 4099 2.294791 GCTACAGCTACGGTCTGATCAT 59.705 50.000 0.00 0.00 38.21 2.45
3357 4102 2.497675 ACAGCTACGGTCTGATCATGTT 59.502 45.455 0.00 0.00 35.61 2.71
3358 4103 3.699538 ACAGCTACGGTCTGATCATGTTA 59.300 43.478 0.00 0.00 35.61 2.41
3359 4104 4.045104 CAGCTACGGTCTGATCATGTTAC 58.955 47.826 0.00 0.00 33.54 2.50
3360 4105 3.699538 AGCTACGGTCTGATCATGTTACA 59.300 43.478 0.00 0.00 0.00 2.41
3361 4106 4.342378 AGCTACGGTCTGATCATGTTACAT 59.658 41.667 0.00 0.00 0.00 2.29
3362 4107 4.681942 GCTACGGTCTGATCATGTTACATC 59.318 45.833 0.00 0.00 0.00 3.06
3363 4108 5.508153 GCTACGGTCTGATCATGTTACATCT 60.508 44.000 0.00 0.00 0.00 2.90
3364 4109 4.686972 ACGGTCTGATCATGTTACATCTG 58.313 43.478 0.00 0.00 0.00 2.90
3365 4110 4.160439 ACGGTCTGATCATGTTACATCTGT 59.840 41.667 0.00 0.00 0.00 3.41
3366 4111 5.359860 ACGGTCTGATCATGTTACATCTGTA 59.640 40.000 0.00 0.00 0.00 2.74
3451 4210 8.027524 AGAGATCAATCAAGGCATTTAGTAGA 57.972 34.615 0.00 0.00 0.00 2.59
3452 4211 8.489489 AGAGATCAATCAAGGCATTTAGTAGAA 58.511 33.333 0.00 0.00 0.00 2.10
3453 4212 8.443953 AGATCAATCAAGGCATTTAGTAGAAC 57.556 34.615 0.00 0.00 0.00 3.01
3454 4213 8.270744 AGATCAATCAAGGCATTTAGTAGAACT 58.729 33.333 0.00 0.00 0.00 3.01
3455 4214 9.547753 GATCAATCAAGGCATTTAGTAGAACTA 57.452 33.333 0.00 0.00 0.00 2.24
3457 4216 9.330063 TCAATCAAGGCATTTAGTAGAACTATG 57.670 33.333 0.00 0.00 29.64 2.23
3458 4217 7.736447 ATCAAGGCATTTAGTAGAACTATGC 57.264 36.000 6.34 6.34 38.70 3.14
3459 4218 6.649155 TCAAGGCATTTAGTAGAACTATGCA 58.351 36.000 13.81 0.00 40.29 3.96
3460 4219 7.109501 TCAAGGCATTTAGTAGAACTATGCAA 58.890 34.615 13.81 0.00 40.29 4.08
3461 4220 7.609918 TCAAGGCATTTAGTAGAACTATGCAAA 59.390 33.333 13.81 0.00 40.29 3.68
3462 4221 8.408601 CAAGGCATTTAGTAGAACTATGCAAAT 58.591 33.333 13.81 0.35 40.29 2.32
3463 4222 8.159344 AGGCATTTAGTAGAACTATGCAAATC 57.841 34.615 13.81 0.00 40.29 2.17
3464 4223 7.995488 AGGCATTTAGTAGAACTATGCAAATCT 59.005 33.333 13.81 0.00 40.29 2.40
3465 4224 8.624776 GGCATTTAGTAGAACTATGCAAATCTT 58.375 33.333 13.81 0.00 40.29 2.40
3466 4225 9.443283 GCATTTAGTAGAACTATGCAAATCTTG 57.557 33.333 9.03 0.00 39.06 3.02
3593 4352 3.326880 ACTGTCTTTTCCCGACATAACCT 59.673 43.478 0.00 0.00 40.30 3.50
3604 4363 2.537401 GACATAACCTGCAGTACCGTC 58.463 52.381 13.81 8.67 0.00 4.79
3608 4367 2.683933 CCTGCAGTACCGTCCCCT 60.684 66.667 13.81 0.00 0.00 4.79
3887 4698 0.537371 GTCCCAACTGACCTTGGTGG 60.537 60.000 0.00 0.00 39.40 4.61
4057 4868 8.902806 TCTAATGGTTATTCCTGTAGCAATTTG 58.097 33.333 0.00 0.00 37.07 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
762 860 3.623960 CCGTAGCCCATTAAAACAATCGA 59.376 43.478 0.00 0.00 0.00 3.59
1966 2678 0.882042 AAGAACACGCAGCAGGTGAG 60.882 55.000 3.02 2.10 38.73 3.51
2339 3061 6.038271 CAGTTTTTGGCAGTAGTTACTTCTGT 59.962 38.462 17.81 0.00 32.65 3.41
2545 3284 6.117488 TGCTTTATCTTCAGATTCTGATGCA 58.883 36.000 16.82 14.09 40.39 3.96
3081 3826 3.255149 GCCTCCCATCATCATTCATCAAC 59.745 47.826 0.00 0.00 0.00 3.18
3102 3847 3.319122 ACCATCTTTTCAACAAGTCCAGC 59.681 43.478 0.00 0.00 0.00 4.85
3350 4095 6.994496 CAGGGACAATACAGATGTAACATGAT 59.006 38.462 0.00 0.00 33.76 2.45
3351 4096 6.348498 CAGGGACAATACAGATGTAACATGA 58.652 40.000 0.00 0.00 33.76 3.07
3352 4097 5.008019 GCAGGGACAATACAGATGTAACATG 59.992 44.000 0.00 0.00 33.76 3.21
3353 4098 5.104360 AGCAGGGACAATACAGATGTAACAT 60.104 40.000 0.00 0.00 33.76 2.71
3354 4099 4.225042 AGCAGGGACAATACAGATGTAACA 59.775 41.667 0.00 0.00 33.76 2.41
3357 4102 4.769688 CAAGCAGGGACAATACAGATGTA 58.230 43.478 0.00 0.00 34.67 2.29
3358 4103 3.614092 CAAGCAGGGACAATACAGATGT 58.386 45.455 0.00 0.00 0.00 3.06
3359 4104 2.357009 GCAAGCAGGGACAATACAGATG 59.643 50.000 0.00 0.00 0.00 2.90
3360 4105 2.648059 GCAAGCAGGGACAATACAGAT 58.352 47.619 0.00 0.00 0.00 2.90
3361 4106 1.675714 CGCAAGCAGGGACAATACAGA 60.676 52.381 0.00 0.00 0.00 3.41
3362 4107 0.729116 CGCAAGCAGGGACAATACAG 59.271 55.000 0.00 0.00 0.00 2.74
3363 4108 0.323302 TCGCAAGCAGGGACAATACA 59.677 50.000 0.00 0.00 33.78 2.29
3364 4109 3.153024 TCGCAAGCAGGGACAATAC 57.847 52.632 0.00 0.00 33.78 1.89
3480 4239 9.182214 ACATTGTAGATCAGATTTGCATAGTTT 57.818 29.630 0.00 0.00 0.00 2.66
3532 4291 2.126888 AAAATTCACGCTGCGCCG 60.127 55.556 23.51 13.93 0.00 6.46
3593 4352 1.675219 GAAAGGGGACGGTACTGCA 59.325 57.895 0.23 0.00 0.00 4.41
3604 4363 3.023735 CAGGGAGGGGGAAAGGGG 61.024 72.222 0.00 0.00 0.00 4.79
3608 4367 1.165782 ATGGTCAGGGAGGGGGAAA 59.834 57.895 0.00 0.00 0.00 3.13
3741 4552 3.371273 CCATGGAGAAAGAAGGATGAGCA 60.371 47.826 5.56 0.00 0.00 4.26
3887 4698 2.263741 CCCTGAACTGCAGTGCACC 61.264 63.158 24.29 12.01 43.33 5.01



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

AutoCloner maintained by Alex Coulton.