Multiple sequence alignment - TraesCS2B01G510900

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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 TraesCS2B01G510900 chr2B 100.000 5229 0 0 1 5229 706734350 706729122 0.000000e+00 9657.0
1 TraesCS2B01G510900 chr2B 97.133 2686 72 5 2346 5029 706923939 706921257 0.000000e+00 4529.0
2 TraesCS2B01G510900 chr2B 95.947 2023 56 11 277 2299 706926075 706924079 0.000000e+00 3258.0
3 TraesCS2B01G510900 chr2B 82.632 2044 275 49 2328 4319 759440392 759442407 0.000000e+00 1735.0
4 TraesCS2B01G510900 chr2B 82.655 1989 259 60 2342 4273 759346157 759348116 0.000000e+00 1683.0
5 TraesCS2B01G510900 chr2B 82.690 1398 214 17 906 2281 759438997 759440388 0.000000e+00 1216.0
6 TraesCS2B01G510900 chr2B 97.030 202 0 2 5034 5229 706920930 706920729 8.390000e-88 335.0
7 TraesCS2B01G510900 chr2A 93.641 3837 182 32 649 4441 719732435 719728617 0.000000e+00 5677.0
8 TraesCS2B01G510900 chr2A 82.328 2156 294 54 2337 4441 751268507 751270626 0.000000e+00 1790.0
9 TraesCS2B01G510900 chr2A 82.197 2157 296 54 2337 4441 751238120 751240240 0.000000e+00 1775.0
10 TraesCS2B01G510900 chr2A 82.906 1989 250 59 2342 4273 751208743 751210698 0.000000e+00 1707.0
11 TraesCS2B01G510900 chr2A 82.158 2057 254 67 2553 4556 751233149 751235145 0.000000e+00 1661.0
12 TraesCS2B01G510900 chr2A 81.597 1641 242 35 702 2299 751236496 751238119 0.000000e+00 1303.0
13 TraesCS2B01G510900 chr2A 84.003 1294 199 7 1008 2299 751267219 751268506 0.000000e+00 1236.0
14 TraesCS2B01G510900 chr2A 84.003 1294 200 6 1008 2299 751288144 751289432 0.000000e+00 1236.0
15 TraesCS2B01G510900 chr2A 85.561 561 58 14 4485 5028 719728612 719728058 2.730000e-157 566.0
16 TraesCS2B01G510900 chr2A 82.799 686 55 28 1 633 719735155 719734480 5.920000e-154 555.0
17 TraesCS2B01G510900 chr2A 87.413 143 17 1 2531 2673 751268538 751268679 4.190000e-36 163.0
18 TraesCS2B01G510900 chr2A 87.413 143 17 1 2531 2673 751289464 751289605 4.190000e-36 163.0
19 TraesCS2B01G510900 chr2D 93.945 2494 113 20 2550 5029 585687840 585685371 0.000000e+00 3735.0
20 TraesCS2B01G510900 chr2D 89.401 2453 150 37 161 2556 585691147 585688748 0.000000e+00 2988.0
21 TraesCS2B01G510900 chr2D 81.629 2553 338 81 2342 4826 619702235 619704724 0.000000e+00 1995.0
22 TraesCS2B01G510900 chr2D 82.957 1772 230 51 2545 4268 619664418 619666165 0.000000e+00 1533.0
23 TraesCS2B01G510900 chr2D 82.133 1416 225 16 906 2299 619700822 619702231 0.000000e+00 1188.0
24 TraesCS2B01G510900 chr2D 93.789 161 7 3 1 158 585691343 585691183 6.770000e-59 239.0
25 TraesCS2B01G510900 chr2D 90.000 180 18 0 5050 5229 585684605 585684426 3.150000e-57 233.0
26 TraesCS2B01G510900 chr2D 86.713 143 18 1 2531 2673 619702263 619702404 1.950000e-34 158.0
27 TraesCS2B01G510900 chrUn 84.031 1290 198 7 1013 2299 337511521 337512805 0.000000e+00 1234.0
28 TraesCS2B01G510900 chrUn 87.413 143 17 1 2531 2673 337512837 337512978 4.190000e-36 163.0
29 TraesCS2B01G510900 chr3B 79.882 169 25 9 452 617 815205482 815205320 1.190000e-21 115.0
30 TraesCS2B01G510900 chr7A 78.519 135 22 6 473 603 700797952 700797821 1.210000e-11 82.4
31 TraesCS2B01G510900 chr7B 80.769 104 12 2 408 503 613866874 613866977 2.020000e-09 75.0
32 TraesCS2B01G510900 chr4B 77.869 122 14 11 470 584 425178670 425178785 4.370000e-06 63.9


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 TraesCS2B01G510900 chr2B 706729122 706734350 5228 True 9657.000000 9657 100.000000 1 5229 1 chr2B.!!$R1 5228
1 TraesCS2B01G510900 chr2B 706920729 706926075 5346 True 2707.333333 4529 96.703333 277 5229 3 chr2B.!!$R2 4952
2 TraesCS2B01G510900 chr2B 759346157 759348116 1959 False 1683.000000 1683 82.655000 2342 4273 1 chr2B.!!$F1 1931
3 TraesCS2B01G510900 chr2B 759438997 759442407 3410 False 1475.500000 1735 82.661000 906 4319 2 chr2B.!!$F2 3413
4 TraesCS2B01G510900 chr2A 719728058 719735155 7097 True 2266.000000 5677 87.333667 1 5028 3 chr2A.!!$R1 5027
5 TraesCS2B01G510900 chr2A 751208743 751210698 1955 False 1707.000000 1707 82.906000 2342 4273 1 chr2A.!!$F1 1931
6 TraesCS2B01G510900 chr2A 751233149 751240240 7091 False 1579.666667 1775 81.984000 702 4556 3 chr2A.!!$F2 3854
7 TraesCS2B01G510900 chr2A 751267219 751270626 3407 False 1063.000000 1790 84.581333 1008 4441 3 chr2A.!!$F3 3433
8 TraesCS2B01G510900 chr2A 751288144 751289605 1461 False 699.500000 1236 85.708000 1008 2673 2 chr2A.!!$F4 1665
9 TraesCS2B01G510900 chr2D 585684426 585691343 6917 True 1798.750000 3735 91.783750 1 5229 4 chr2D.!!$R1 5228
10 TraesCS2B01G510900 chr2D 619664418 619666165 1747 False 1533.000000 1533 82.957000 2545 4268 1 chr2D.!!$F1 1723
11 TraesCS2B01G510900 chr2D 619700822 619704724 3902 False 1113.666667 1995 83.491667 906 4826 3 chr2D.!!$F2 3920
12 TraesCS2B01G510900 chrUn 337511521 337512978 1457 False 698.500000 1234 85.722000 1013 2673 2 chrUn.!!$F1 1660

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
117 120 1.743623 CAAACGTCATGCCCCGCTA 60.744 57.895 0.00 0.0 0.0 4.26 F
1079 3787 1.435577 CGCCTTACTACCGCAAAACT 58.564 50.000 0.00 0.0 0.0 2.66 F
2195 4930 0.741221 GGAGGACTTGTCGACATGGC 60.741 60.000 28.62 27.0 0.0 4.40 F
2224 4959 1.002134 GATGGTGGTGGTGGTGAGG 60.002 63.158 0.00 0.0 0.0 3.86 F
2872 6656 1.871039 ACAAACATACACGACAGCACC 59.129 47.619 0.00 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 4240 0.807667 CATGGAGTAGTCGCTGGTGC 60.808 60.000 0.00 0.0 0.0 5.01 R
2317 5061 0.110486 ACCCGTTGAACTGGCAAGAT 59.890 50.000 5.65 0.0 0.0 2.40 R
3487 7305 1.830279 TGCTTGCTTTGAGATCCCTG 58.170 50.000 0.00 0.0 0.0 4.45 R
4142 7965 4.985409 GTCTTCAACCTCATCATATCGTCC 59.015 45.833 0.00 0.0 0.0 4.79 R
4841 8698 2.464796 TCGGGATAAGTTAGGCTGGA 57.535 50.000 0.00 0.0 0.0 3.86 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
20 22 3.926821 TCGGGCTAAAACAAAATGGAC 57.073 42.857 0.00 0.00 0.00 4.02
100 103 2.124942 TCACTGCCACACGTTGCA 60.125 55.556 4.34 4.34 35.86 4.08
117 120 1.743623 CAAACGTCATGCCCCGCTA 60.744 57.895 0.00 0.00 0.00 4.26
207 245 3.022287 CCATGTTCATACGCCGCC 58.978 61.111 0.00 0.00 0.00 6.13
218 256 2.894240 TACGCCGCCGATTCCACTTC 62.894 60.000 0.00 0.00 38.29 3.01
288 349 2.962859 ACCCAATGGCCAATAATCTCC 58.037 47.619 10.96 0.00 33.59 3.71
599 703 9.443323 TCGATATTTTTCTGTAATCTTGGTCAA 57.557 29.630 0.00 0.00 0.00 3.18
656 2789 7.394816 AGTACTATTTGTGCTTGTAAGACCAT 58.605 34.615 0.00 0.00 38.47 3.55
933 3617 3.882444 TCTTCATGCCATTCTCCTTCTG 58.118 45.455 0.00 0.00 0.00 3.02
965 3651 2.547211 CCATATGAAAGCAGCTCCTTCG 59.453 50.000 3.65 0.00 0.00 3.79
1079 3787 1.435577 CGCCTTACTACCGCAAAACT 58.564 50.000 0.00 0.00 0.00 2.66
1620 4328 1.417517 AGACCATATTGGCGCAGATCA 59.582 47.619 10.83 0.00 42.67 2.92
1646 4354 1.133976 GGATGGGTCATTGGTCTCTGG 60.134 57.143 0.00 0.00 0.00 3.86
1685 4393 8.680903 CATTACTGGCTTCATCTTAACTGAAAT 58.319 33.333 0.00 0.00 32.53 2.17
1732 4440 1.066143 ACATGACATTCACCGTCTCCC 60.066 52.381 0.00 0.00 34.37 4.30
1747 4455 2.276309 CTCCCAGGGATCACCAAGCC 62.276 65.000 9.31 0.00 43.89 4.35
1993 4701 7.451731 AAGGAGGATCTGAAATGTGGTAATA 57.548 36.000 0.00 0.00 33.73 0.98
2000 4708 9.436957 GGATCTGAAATGTGGTAATAACGATAT 57.563 33.333 0.00 0.00 0.00 1.63
2192 4927 1.002087 GTTGGGAGGACTTGTCGACAT 59.998 52.381 20.80 4.97 0.00 3.06
2195 4930 0.741221 GGAGGACTTGTCGACATGGC 60.741 60.000 28.62 27.00 0.00 4.40
2224 4959 1.002134 GATGGTGGTGGTGGTGAGG 60.002 63.158 0.00 0.00 0.00 3.86
2271 5006 9.838339 AGTTCAACAGGTATATATCTTTCCTTG 57.162 33.333 0.00 0.00 0.00 3.61
2317 5061 3.668141 TCAACGGTATACCTACCTCCA 57.332 47.619 19.68 0.00 44.63 3.86
2369 5205 9.840427 CTTTATGTCGAATTTTAGATGTGGTTT 57.160 29.630 0.00 0.00 0.00 3.27
2387 5223 7.171653 TGTGGTTTGGATGACATACTAATCAA 58.828 34.615 9.06 0.00 32.43 2.57
2393 5229 9.685276 TTTGGATGACATACTAATCAAGACAAT 57.315 29.630 0.00 0.00 0.00 2.71
2462 5305 7.069986 TCCTCTTGCTGGACTATATTTCTAGT 58.930 38.462 0.00 0.00 34.65 2.57
2463 5306 7.565398 TCCTCTTGCTGGACTATATTTCTAGTT 59.435 37.037 0.00 0.00 32.11 2.24
2502 5345 5.230942 CAAGTTGTCGAAGATTGTACTCCT 58.769 41.667 0.00 0.00 40.67 3.69
2509 5353 8.058667 TGTCGAAGATTGTACTCCTTGTAATA 57.941 34.615 0.00 0.00 40.67 0.98
2618 6396 5.638657 GCATCATTCTCTTGCTGGACTATAG 59.361 44.000 0.00 0.00 33.61 1.31
2647 6425 3.777106 TTCTGCAGTTGACAAGGAGAT 57.223 42.857 14.67 0.00 29.78 2.75
2696 6477 3.370104 AGTGGCTAGTCTGCTGATACTT 58.630 45.455 0.00 0.00 0.00 2.24
2741 6523 6.366332 GGATATGCAAGTCAAGAGGTATAACG 59.634 42.308 0.00 0.00 0.00 3.18
2872 6656 1.871039 ACAAACATACACGACAGCACC 59.129 47.619 0.00 0.00 0.00 5.01
3165 6958 2.032071 CAAGGGGCCGACGAGTTT 59.968 61.111 0.00 0.00 0.00 2.66
4022 7845 8.803201 TCATGAAGTTCTACGATGTATTCATC 57.197 34.615 4.17 2.37 44.84 2.92
4142 7965 4.218852 CGAAGGAGCCTCTATACTTTAGGG 59.781 50.000 0.00 0.00 0.00 3.53
4333 8166 9.083422 TGGACAAATAAACAATCCATTGAGTAA 57.917 29.630 6.29 0.00 40.14 2.24
4351 8184 9.747898 ATTGAGTAAATTGTAATCCTGGTTGTA 57.252 29.630 0.00 0.00 0.00 2.41
4585 8419 9.905713 TTAATTATATGTTCTCTTTGAGCTGGT 57.094 29.630 0.00 0.00 0.00 4.00
4841 8698 7.865706 AGTGATCTTCAAGCGGTATAAATTT 57.134 32.000 0.00 0.00 0.00 1.82
5010 8871 1.465689 GCGCGTGCATACTGTCAATTT 60.466 47.619 17.66 0.00 42.15 1.82
5029 8890 4.599047 TTTTGATGGCCTGGTAACTTTG 57.401 40.909 3.32 0.00 37.61 2.77
5032 9621 2.107378 TGATGGCCTGGTAACTTTGTGA 59.893 45.455 3.32 0.00 37.61 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 103 1.449601 CTAGCGGGGCATGACGTTT 60.450 57.895 0.00 0.00 0.00 3.60
154 157 4.242602 GCCTGATACACCTTGGCC 57.757 61.111 0.00 0.00 37.81 5.36
183 221 2.124942 TATGAACATGGCGGCGCA 60.125 55.556 34.36 19.88 0.00 6.09
190 228 2.881266 CGGCGGCGTATGAACATGG 61.881 63.158 24.74 0.00 0.00 3.66
192 230 0.531974 AATCGGCGGCGTATGAACAT 60.532 50.000 31.06 12.51 0.00 2.71
605 709 8.487848 TCCCTCCGTTTCATATTACTTCAATAA 58.512 33.333 0.00 0.00 32.84 1.40
607 711 6.895782 TCCCTCCGTTTCATATTACTTCAAT 58.104 36.000 0.00 0.00 0.00 2.57
608 712 6.070424 ACTCCCTCCGTTTCATATTACTTCAA 60.070 38.462 0.00 0.00 0.00 2.69
609 713 5.424252 ACTCCCTCCGTTTCATATTACTTCA 59.576 40.000 0.00 0.00 0.00 3.02
933 3617 4.098349 TGCTTTCATATGGAGCCAATGAAC 59.902 41.667 21.49 12.54 38.87 3.18
965 3651 7.391833 AGACTTCTTTCACCCTATGATCAAAAC 59.608 37.037 0.00 0.00 37.11 2.43
1532 4240 0.807667 CATGGAGTAGTCGCTGGTGC 60.808 60.000 0.00 0.00 0.00 5.01
1620 4328 1.077501 CAATGACCCATCCCACGCT 60.078 57.895 0.00 0.00 0.00 5.07
1646 4354 3.243201 GCCAGTAATGCTTTGATACAGGC 60.243 47.826 3.38 3.38 42.43 4.85
1675 4383 7.333423 CCCTCTGTCGACAATTATTTCAGTTAA 59.667 37.037 20.49 0.00 0.00 2.01
1685 4393 1.553248 CACCCCCTCTGTCGACAATTA 59.447 52.381 20.49 7.20 0.00 1.40
1732 4440 1.751927 GCAGGCTTGGTGATCCCTG 60.752 63.158 8.60 8.60 45.93 4.45
1993 4701 4.401519 TCTCAGGGTCGAGAAAATATCGTT 59.598 41.667 0.00 0.00 39.09 3.85
2000 4708 2.011122 ACCTCTCAGGGTCGAGAAAA 57.989 50.000 0.00 0.00 41.43 2.29
2130 4838 1.077787 CGCAGCCCCACTTCCATTA 60.078 57.895 0.00 0.00 0.00 1.90
2208 4943 2.040359 TCCTCACCACCACCACCA 60.040 61.111 0.00 0.00 0.00 4.17
2209 4944 2.430367 GTCCTCACCACCACCACC 59.570 66.667 0.00 0.00 0.00 4.61
2210 4945 2.147387 AGGTCCTCACCACCACCAC 61.147 63.158 0.00 0.00 46.68 4.16
2224 4959 1.218316 CAAGGCGGAGGTACAGGTC 59.782 63.158 0.00 0.00 0.00 3.85
2271 5006 5.385509 AACCATACAACCAATAAGTGCAC 57.614 39.130 9.40 9.40 0.00 4.57
2317 5061 0.110486 ACCCGTTGAACTGGCAAGAT 59.890 50.000 5.65 0.00 0.00 2.40
2369 5205 9.112725 CAATTGTCTTGATTAGTATGTCATCCA 57.887 33.333 0.00 0.00 0.00 3.41
2407 5243 7.656542 TGCTTTCAAGATTTAACATGCATTTCA 59.343 29.630 0.00 0.00 0.00 2.69
2502 5345 7.907841 TCCTAACCACATCTAGCTATTACAA 57.092 36.000 0.00 0.00 0.00 2.41
2509 5353 5.763876 AAGTTTCCTAACCACATCTAGCT 57.236 39.130 0.00 0.00 34.71 3.32
2618 6396 1.067516 TCAACTGCAGAAAGCCAAAGC 59.932 47.619 23.35 0.00 44.83 3.51
2741 6523 8.730680 TGCATCCTAAAAAGTGAAGTAAATCTC 58.269 33.333 0.00 0.00 0.00 2.75
2801 6585 4.086457 TGACACTGACAGGCATAACTAGA 58.914 43.478 7.51 0.00 0.00 2.43
2872 6656 5.903764 TCGTTCAATTTGGAATTTTGCAG 57.096 34.783 0.00 0.00 0.00 4.41
3165 6958 8.402798 TGGCAATTAGAACAACTTCATTTCTA 57.597 30.769 0.00 0.00 31.93 2.10
3487 7305 1.830279 TGCTTGCTTTGAGATCCCTG 58.170 50.000 0.00 0.00 0.00 4.45
3996 7819 8.809159 ATGAATACATCGTAGAACTTCATGAG 57.191 34.615 0.00 0.00 43.58 2.90
4142 7965 4.985409 GTCTTCAACCTCATCATATCGTCC 59.015 45.833 0.00 0.00 0.00 4.79
4319 8149 9.740239 CAGGATTACAATTTACTCAATGGATTG 57.260 33.333 0.00 0.00 39.10 2.67
4559 8393 9.905713 ACCAGCTCAAAGAGAACATATAATTAA 57.094 29.630 0.00 0.00 0.00 1.40
4826 8674 3.632145 AGGCTGGAAATTTATACCGCTTG 59.368 43.478 0.00 0.00 0.00 4.01
4841 8698 2.464796 TCGGGATAAGTTAGGCTGGA 57.535 50.000 0.00 0.00 0.00 3.86
5010 8871 2.890311 CACAAAGTTACCAGGCCATCAA 59.110 45.455 5.01 0.00 0.00 2.57
5029 8890 2.359230 GAGTGGCCTGGCACTCAC 60.359 66.667 35.22 23.69 45.11 3.51
5032 9621 3.644606 CCTGAGTGGCCTGGCACT 61.645 66.667 24.25 24.25 0.00 4.40
5048 9637 4.767255 CGGCCTCACTGTCCAGCC 62.767 72.222 0.00 2.23 40.33 4.85


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

AutoCloner maintained by Alex Coulton.