Multiple sequence alignment - TraesCS5B01G208600

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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 TraesCS5B01G208600 chr5B 100.000 4379 0 0 1 4379 378509565 378513943 0.000000e+00 8087.0
1 TraesCS5B01G208600 chr5B 84.826 2781 260 77 922 3637 378068231 378070914 0.000000e+00 2649.0
2 TraesCS5B01G208600 chr5B 82.638 1653 163 61 798 2416 377978009 377979571 0.000000e+00 1349.0
3 TraesCS5B01G208600 chr5B 91.027 691 59 2 2637 3324 377979619 377980309 0.000000e+00 929.0
4 TraesCS5B01G208600 chr5B 83.670 643 64 25 1001 1637 377698587 377699194 6.360000e-158 568.0
5 TraesCS5B01G208600 chr5B 88.479 217 24 1 1987 2202 377844490 377844706 1.210000e-65 261.0
6 TraesCS5B01G208600 chr5B 88.837 215 20 3 417 631 377976204 377976414 1.210000e-65 261.0
7 TraesCS5B01G208600 chr5B 84.416 77 6 3 799 870 378068140 378068215 2.180000e-08 71.3
8 TraesCS5B01G208600 chr5A 94.277 4403 179 31 1 4379 430509439 430505086 0.000000e+00 6667.0
9 TraesCS5B01G208600 chr5A 84.387 1883 202 46 1757 3624 430957990 430956185 0.000000e+00 1764.0
10 TraesCS5B01G208600 chr5A 89.447 995 91 11 2637 3625 431029495 431028509 0.000000e+00 1243.0
11 TraesCS5B01G208600 chr5A 86.852 829 74 20 807 1620 431045269 431044461 0.000000e+00 894.0
12 TraesCS5B01G208600 chr5A 88.356 730 58 9 929 1657 430958691 430957988 0.000000e+00 852.0
13 TraesCS5B01G208600 chr5A 84.038 639 46 24 1615 2249 431030128 431029542 8.220000e-157 564.0
14 TraesCS5B01G208600 chr5A 92.647 136 8 2 3663 3797 427318907 427318773 1.240000e-45 195.0
15 TraesCS5B01G208600 chr5D 95.349 3677 131 18 1 3647 326117107 326120773 0.000000e+00 5806.0
16 TraesCS5B01G208600 chr5D 87.255 1020 105 9 2621 3637 325664861 325665858 0.000000e+00 1140.0
17 TraesCS5B01G208600 chr5D 94.708 718 22 4 3671 4379 326121027 326121737 0.000000e+00 1101.0
18 TraesCS5B01G208600 chr5D 89.791 764 64 9 2531 3285 325648108 325648866 0.000000e+00 966.0
19 TraesCS5B01G208600 chr5D 89.148 728 58 16 933 1655 325646757 325647468 0.000000e+00 887.0
20 TraesCS5B01G208600 chr5D 89.116 735 51 11 941 1672 325663603 325664311 0.000000e+00 887.0
21 TraesCS5B01G208600 chr5D 83.515 643 71 21 1001 1637 325422710 325423323 6.360000e-158 568.0
22 TraesCS5B01G208600 chr5D 84.499 529 44 18 1728 2249 325664330 325664827 5.090000e-134 488.0
23 TraesCS5B01G208600 chr5D 85.393 445 54 7 1967 2405 325647610 325648049 6.680000e-123 451.0
24 TraesCS5B01G208600 chr5D 85.535 318 32 8 3323 3637 325652098 325652404 1.960000e-83 320.0
25 TraesCS5B01G208600 chr5D 86.066 244 25 8 417 654 325646227 325646467 2.020000e-63 254.0
26 TraesCS5B01G208600 chr5D 92.481 133 10 0 3663 3795 497493775 497493643 1.610000e-44 191.0
27 TraesCS5B01G208600 chr5D 83.117 77 7 3 799 870 325646666 325646741 1.020000e-06 65.8
28 TraesCS5B01G208600 chr7D 84.103 780 96 17 1730 2498 50650380 50651142 0.000000e+00 728.0
29 TraesCS5B01G208600 chr4A 82.420 785 111 14 1730 2504 482875610 482874843 0.000000e+00 660.0
30 TraesCS5B01G208600 chr6D 82.308 780 107 19 1730 2498 36220046 36220805 0.000000e+00 647.0
31 TraesCS5B01G208600 chr6D 92.086 139 10 1 3663 3800 427226661 427226799 1.240000e-45 195.0
32 TraesCS5B01G208600 chr7A 83.186 678 86 12 1822 2497 22039262 22039913 2.920000e-166 595.0
33 TraesCS5B01G208600 chr7A 82.275 677 92 13 1822 2497 21616749 21617398 1.060000e-155 560.0
34 TraesCS5B01G208600 chr7B 92.647 136 8 2 3663 3797 450794814 450794948 1.240000e-45 195.0
35 TraesCS5B01G208600 chr6B 92.647 136 8 2 3663 3797 623719534 623719400 1.240000e-45 195.0
36 TraesCS5B01G208600 chr2D 91.852 135 11 0 3663 3797 612337056 612336922 5.780000e-44 189.0
37 TraesCS5B01G208600 chr1A 87.879 165 15 4 3636 3797 554032995 554032833 5.780000e-44 189.0


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 TraesCS5B01G208600 chr5B 378509565 378513943 4378 False 8087.000000 8087 100.000000 1 4379 1 chr5B.!!$F3 4378
1 TraesCS5B01G208600 chr5B 378068140 378070914 2774 False 1360.150000 2649 84.621000 799 3637 2 chr5B.!!$F5 2838
2 TraesCS5B01G208600 chr5B 377976204 377980309 4105 False 846.333333 1349 87.500667 417 3324 3 chr5B.!!$F4 2907
3 TraesCS5B01G208600 chr5B 377698587 377699194 607 False 568.000000 568 83.670000 1001 1637 1 chr5B.!!$F1 636
4 TraesCS5B01G208600 chr5A 430505086 430509439 4353 True 6667.000000 6667 94.277000 1 4379 1 chr5A.!!$R2 4378
5 TraesCS5B01G208600 chr5A 430956185 430958691 2506 True 1308.000000 1764 86.371500 929 3624 2 chr5A.!!$R4 2695
6 TraesCS5B01G208600 chr5A 431028509 431030128 1619 True 903.500000 1243 86.742500 1615 3625 2 chr5A.!!$R5 2010
7 TraesCS5B01G208600 chr5A 431044461 431045269 808 True 894.000000 894 86.852000 807 1620 1 chr5A.!!$R3 813
8 TraesCS5B01G208600 chr5D 326117107 326121737 4630 False 3453.500000 5806 95.028500 1 4379 2 chr5D.!!$F4 4378
9 TraesCS5B01G208600 chr5D 325663603 325665858 2255 False 838.333333 1140 86.956667 941 3637 3 chr5D.!!$F3 2696
10 TraesCS5B01G208600 chr5D 325422710 325423323 613 False 568.000000 568 83.515000 1001 1637 1 chr5D.!!$F1 636
11 TraesCS5B01G208600 chr5D 325646227 325652404 6177 False 490.633333 966 86.508333 417 3637 6 chr5D.!!$F2 3220
12 TraesCS5B01G208600 chr7D 50650380 50651142 762 False 728.000000 728 84.103000 1730 2498 1 chr7D.!!$F1 768
13 TraesCS5B01G208600 chr4A 482874843 482875610 767 True 660.000000 660 82.420000 1730 2504 1 chr4A.!!$R1 774
14 TraesCS5B01G208600 chr6D 36220046 36220805 759 False 647.000000 647 82.308000 1730 2498 1 chr6D.!!$F1 768
15 TraesCS5B01G208600 chr7A 22039262 22039913 651 False 595.000000 595 83.186000 1822 2497 1 chr7A.!!$F2 675
16 TraesCS5B01G208600 chr7A 21616749 21617398 649 False 560.000000 560 82.275000 1822 2497 1 chr7A.!!$F1 675

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
675 2144 0.031178 AAAACCTACGTCGTGTCGCT 59.969 50.000 8.47 0.0 0.00 4.93 F
742 2211 1.152567 CCAACCACCACCACCACAT 60.153 57.895 0.00 0.0 0.00 3.21 F
775 2244 1.243342 TTGCCCTGTTTGCTCCATCG 61.243 55.000 0.00 0.0 0.00 3.84 F
1296 2871 1.294138 CTTCGGCCCGGTCTACAAA 59.706 57.895 1.90 0.0 0.00 2.83 F
1320 2895 2.559840 GTCGACGACAAGCTCCGA 59.440 61.111 22.66 0.0 32.09 4.55 F
1450 3062 2.681848 CCAGCAGATCAATTTCGAAGCT 59.318 45.455 0.00 0.0 0.00 3.74 F
2967 4657 0.898320 AGCGCTCTGACAGGTTGTAT 59.102 50.000 2.64 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 3948 3.131396 GAGGTGTGAAGTTGTGTTCGAT 58.869 45.455 0.0 0.0 0.00 3.59 R
2613 4297 4.041049 TGCGTTACAAGCTGAACAATTTG 58.959 39.130 0.0 0.0 35.28 2.32 R
2645 4330 4.811969 TGTTAGGGAAATAGCACGAAGA 57.188 40.909 0.0 0.0 0.00 2.87 R
2928 4618 1.789523 TGAGGTATGGTCTAGCCCAC 58.210 55.000 0.0 0.0 37.31 4.61 R
2967 4657 2.501723 GAGAGCTGGGTCCATGACTTTA 59.498 50.000 0.0 0.0 32.47 1.85 R
3337 8158 2.553602 TGTAGCTCGACGACCTTTGTTA 59.446 45.455 0.0 0.0 0.00 2.41 R
4093 9221 0.392998 CGGTCCAGCTTGCCAGTATT 60.393 55.000 0.0 0.0 0.00 1.89 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
178 180 1.674221 CCAGGCCGTTCTCTTCTTCTG 60.674 57.143 0.00 0.00 0.00 3.02
209 211 4.844085 TGATCTTGAAACTTCCAGTCCCTA 59.156 41.667 0.00 0.00 0.00 3.53
216 218 1.903183 ACTTCCAGTCCCTAGAGCAAC 59.097 52.381 0.00 0.00 0.00 4.17
260 262 2.545106 GGCTTGCACAAAGTCCAAATTG 59.455 45.455 0.00 0.00 38.25 2.32
317 323 3.914364 CCTGCGCTTTCTGTCAATTTTAC 59.086 43.478 9.73 0.00 0.00 2.01
619 641 3.074390 TCACTTTGATCCACCCATGTTCT 59.926 43.478 0.00 0.00 0.00 3.01
675 2144 0.031178 AAAACCTACGTCGTGTCGCT 59.969 50.000 8.47 0.00 0.00 4.93
687 2156 1.335597 CGTGTCGCTGGTAGAAACTCA 60.336 52.381 0.00 0.00 0.00 3.41
693 2162 1.404315 GCTGGTAGAAACTCAGGTCCG 60.404 57.143 0.00 0.00 0.00 4.79
694 2163 1.893801 CTGGTAGAAACTCAGGTCCGT 59.106 52.381 0.00 0.00 0.00 4.69
696 2165 2.036733 TGGTAGAAACTCAGGTCCGTTG 59.963 50.000 0.00 0.00 0.00 4.10
738 2207 2.520741 CCACCAACCACCACCACC 60.521 66.667 0.00 0.00 0.00 4.61
739 2208 2.277072 CACCAACCACCACCACCA 59.723 61.111 0.00 0.00 0.00 4.17
740 2209 2.124693 CACCAACCACCACCACCAC 61.125 63.158 0.00 0.00 0.00 4.16
741 2210 2.277072 CCAACCACCACCACCACA 59.723 61.111 0.00 0.00 0.00 4.17
742 2211 1.152567 CCAACCACCACCACCACAT 60.153 57.895 0.00 0.00 0.00 3.21
775 2244 1.243342 TTGCCCTGTTTGCTCCATCG 61.243 55.000 0.00 0.00 0.00 3.84
787 2273 1.379443 TCCATCGCAGTCCTACGGT 60.379 57.895 0.00 0.00 0.00 4.83
857 2401 2.370445 ATCCTCCACCCAAGCCGAG 61.370 63.158 0.00 0.00 0.00 4.63
858 2402 2.822643 ATCCTCCACCCAAGCCGAGA 62.823 60.000 0.00 0.00 0.00 4.04
880 2424 1.404851 CCGCCTTCTCTTTCTCTCCAC 60.405 57.143 0.00 0.00 0.00 4.02
904 2452 1.893786 CTCACCTGACCTTCTCCCG 59.106 63.158 0.00 0.00 0.00 5.14
1040 2600 4.122515 GTTCTCGTGCTGCGTCGC 62.123 66.667 11.10 11.10 42.13 5.19
1269 2844 2.510691 CGCGCCAATTACCTCGGT 60.511 61.111 0.00 0.00 0.00 4.69
1296 2871 1.294138 CTTCGGCCCGGTCTACAAA 59.706 57.895 1.90 0.00 0.00 2.83
1301 2876 2.975536 CCCGGTCTACAAAGGCGA 59.024 61.111 0.00 0.00 0.00 5.54
1320 2895 2.559840 GTCGACGACAAGCTCCGA 59.440 61.111 22.66 0.00 32.09 4.55
1450 3062 2.681848 CCAGCAGATCAATTTCGAAGCT 59.318 45.455 0.00 0.00 0.00 3.74
1473 3088 4.253685 TGGTCAATGAACAGCTAGCTTAC 58.746 43.478 16.46 9.91 0.00 2.34
1481 3097 3.460857 ACAGCTAGCTTACTATGTGGC 57.539 47.619 16.46 0.00 0.00 5.01
1812 3447 5.133941 GTCCCCTGAAGTTTCTTTTCTCTT 58.866 41.667 0.00 0.00 0.00 2.85
2261 3935 5.376756 TTTGGGAACTGTAGTAGTGGTTT 57.623 39.130 0.00 0.00 40.26 3.27
2331 4008 9.797556 AATTACTACAAAAGTGTCTGAAAAACC 57.202 29.630 0.00 0.00 39.39 3.27
2537 4221 6.882610 TTTAGCAATCAATGTCAGTTCACT 57.117 33.333 0.00 0.00 0.00 3.41
2582 4266 6.519353 TTCACGAACAGTAGTACAATTGTG 57.481 37.500 21.42 5.66 0.00 3.33
2645 4330 5.411361 TCAGCTTGTAACGCATTGTATTTCT 59.589 36.000 0.00 0.00 0.00 2.52
2967 4657 0.898320 AGCGCTCTGACAGGTTGTAT 59.102 50.000 2.64 0.00 0.00 2.29
3397 8283 2.468915 AGGACTAAGGTAGGGAAGTGC 58.531 52.381 0.00 0.00 0.00 4.40
3422 8308 7.577046 GCGTAGGACAGAATGGTATGTACATAT 60.577 40.741 18.27 2.65 43.62 1.78
3525 8411 2.502130 GGAAAGGTCTCAGGGGACTTAG 59.498 54.545 0.00 0.00 40.21 2.18
3561 8449 5.003160 TCTTGATAGTGACAATGGGTGTTG 58.997 41.667 0.00 0.00 41.96 3.33
3613 8502 5.972935 ACAAAAGTCCGGTTTTGATTTTCT 58.027 33.333 27.71 9.21 46.19 2.52
3768 8895 7.189079 TCAAAAACCTAAACAAATTGACCCT 57.811 32.000 0.00 0.00 0.00 4.34
3895 9022 9.727627 TTTCATTTGCATAAATTTTGGTTCAAC 57.272 25.926 0.00 0.00 34.34 3.18
3926 9053 8.095792 TCCATTGTTTGCAAATGAAATGAGTAT 58.904 29.630 28.58 7.15 38.21 2.12
4081 9209 6.096141 TGTGACAAGTTAATGTTGATGGTGTT 59.904 34.615 7.35 0.00 32.57 3.32
4164 9292 1.392589 GGGATGGGCAAGTACATGTG 58.607 55.000 9.11 0.00 0.00 3.21
4187 9315 5.221823 TGACCTGACATATTGAAGGTTGACA 60.222 40.000 7.66 1.49 37.82 3.58
4349 9478 3.129462 CGTCCAGCTGAGACAAGAGATAA 59.871 47.826 25.32 0.00 33.70 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 180 6.329496 TGGAAGTTTCAAGATCAACAAACAC 58.671 36.000 13.01 8.17 32.20 3.32
209 211 5.293560 GTGAAAAGTAGAGTGAGTTGCTCT 58.706 41.667 0.00 0.00 44.57 4.09
216 218 4.681942 CGTTCTGGTGAAAAGTAGAGTGAG 59.318 45.833 0.00 0.00 33.52 3.51
260 262 3.173151 ACCATTCACCTTGGGAAATTCC 58.827 45.455 2.79 2.79 38.64 3.01
317 323 0.599558 TGGTCGAACCGTACCTGAAG 59.400 55.000 0.00 0.00 42.58 3.02
340 346 3.003275 TCAATTTGCAGGAACGAGTGAAC 59.997 43.478 0.00 0.00 0.00 3.18
619 641 3.211045 CTCAAACCTTCTTCGTGGGAAA 58.789 45.455 0.00 0.00 0.00 3.13
675 2144 2.005370 ACGGACCTGAGTTTCTACCA 57.995 50.000 0.00 0.00 0.00 3.25
687 2156 2.284699 CTCCCTCCCAACGGACCT 60.285 66.667 0.00 0.00 33.32 3.85
738 2207 1.002857 AAGGGAGGGAAGGGAATGTG 58.997 55.000 0.00 0.00 0.00 3.21
739 2208 1.002857 CAAGGGAGGGAAGGGAATGT 58.997 55.000 0.00 0.00 0.00 2.71
740 2209 0.396278 GCAAGGGAGGGAAGGGAATG 60.396 60.000 0.00 0.00 0.00 2.67
741 2210 1.584717 GGCAAGGGAGGGAAGGGAAT 61.585 60.000 0.00 0.00 0.00 3.01
742 2211 2.238701 GGCAAGGGAGGGAAGGGAA 61.239 63.158 0.00 0.00 0.00 3.97
830 2369 2.592308 GTGGAGGATGGAGTGGCC 59.408 66.667 0.00 0.00 37.10 5.36
857 2401 0.899019 AGAGAAAGAGAAGGCGGGTC 59.101 55.000 0.00 0.00 0.00 4.46
858 2402 0.899019 GAGAGAAAGAGAAGGCGGGT 59.101 55.000 0.00 0.00 0.00 5.28
880 2424 0.248843 GAAGGTCAGGTGAGCAGGAG 59.751 60.000 11.53 0.00 44.42 3.69
995 2555 3.474230 GATTTCGCGGCCATGGCAG 62.474 63.158 36.56 33.25 44.11 4.85
1260 2835 4.745751 CCGCCGCAACCGAGGTAA 62.746 66.667 0.00 0.00 36.29 2.85
1296 2871 3.590443 CTTGTCGTCGACGTCGCCT 62.590 63.158 34.40 0.00 40.80 5.52
1301 2876 2.254651 GGAGCTTGTCGTCGACGT 59.745 61.111 34.40 16.81 40.80 4.34
1450 3062 3.423539 AGCTAGCTGTTCATTGACCAA 57.576 42.857 18.57 0.00 0.00 3.67
1812 3447 3.888323 CAGCTCAGCTATCCTCTTGACTA 59.112 47.826 0.00 0.00 36.40 2.59
2210 3876 6.976934 ATCCTTTTCAAAACTGCCTCTTTA 57.023 33.333 0.00 0.00 0.00 1.85
2274 3948 3.131396 GAGGTGTGAAGTTGTGTTCGAT 58.869 45.455 0.00 0.00 0.00 3.59
2537 4221 9.431887 GTGAATTACTAATCTGTAGGTGTTTCA 57.568 33.333 0.00 0.00 0.00 2.69
2613 4297 4.041049 TGCGTTACAAGCTGAACAATTTG 58.959 39.130 0.00 0.00 35.28 2.32
2645 4330 4.811969 TGTTAGGGAAATAGCACGAAGA 57.188 40.909 0.00 0.00 0.00 2.87
2928 4618 1.789523 TGAGGTATGGTCTAGCCCAC 58.210 55.000 0.00 0.00 37.31 4.61
2967 4657 2.501723 GAGAGCTGGGTCCATGACTTTA 59.498 50.000 0.00 0.00 32.47 1.85
3337 8158 2.553602 TGTAGCTCGACGACCTTTGTTA 59.446 45.455 0.00 0.00 0.00 2.41
3397 8283 5.509716 TGTACATACCATTCTGTCCTACG 57.490 43.478 0.00 0.00 0.00 3.51
3525 8411 2.222227 ATCAAGAAGAAAGGTGGGCC 57.778 50.000 0.00 0.00 0.00 5.80
3561 8449 8.299570 CACTGTTTTGCATCCCTATATTTATCC 58.700 37.037 0.00 0.00 0.00 2.59
3613 8502 6.713762 AACATCTTGAACAACAATCCTTGA 57.286 33.333 0.00 0.00 37.88 3.02
3642 8531 2.366972 CCCCCTCCCGGTGATTCT 60.367 66.667 0.00 0.00 0.00 2.40
3768 8895 2.156098 GCACGGTTTCCCTCATAAACA 58.844 47.619 0.00 0.00 38.34 2.83
3786 8913 0.465705 TGGCATTTTGGTTTTCGGCA 59.534 45.000 0.00 0.00 0.00 5.69
3891 9018 2.620585 TGCAAACAATGGACGATGTTGA 59.379 40.909 0.00 0.00 39.57 3.18
3895 9022 4.236147 TCATTTGCAAACAATGGACGATG 58.764 39.130 15.41 4.89 35.21 3.84
3940 9067 3.700538 AGAATCACAAAAGCCCTGCATA 58.299 40.909 0.00 0.00 0.00 3.14
4030 9157 7.548780 AGTGTAGTTTCATGTTGCATTGTTTTT 59.451 29.630 0.00 0.00 0.00 1.94
4081 9209 9.542462 CAGCTTGCCAGTATTAAGTATTAACTA 57.458 33.333 0.00 0.00 44.35 2.24
4093 9221 0.392998 CGGTCCAGCTTGCCAGTATT 60.393 55.000 0.00 0.00 0.00 1.89
4094 9222 1.221840 CGGTCCAGCTTGCCAGTAT 59.778 57.895 0.00 0.00 0.00 2.12
4164 9292 5.122396 GTGTCAACCTTCAATATGTCAGGTC 59.878 44.000 1.41 0.00 38.80 3.85
4187 9315 5.367945 TGACTTGACCTTAGTCCTTTTGT 57.632 39.130 0.00 0.00 42.81 2.83
4349 9478 2.456577 GTGGTTGCATTCCTATTGGGT 58.543 47.619 9.35 0.00 36.25 4.51


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

AutoCloner maintained by Alex Coulton.