Multiple sequence alignment - TraesCS4B01G204900

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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 TraesCS4B01G204900 chr4B 100.000 4520 0 0 1 4520 436891086 436895605 0.000000e+00 8347.0
1 TraesCS4B01G204900 chr4B 95.522 67 2 1 4043 4109 436895059 436895124 6.180000e-19 106.0
2 TraesCS4B01G204900 chr4B 95.522 67 2 1 3974 4039 436895128 436895194 6.180000e-19 106.0
3 TraesCS4B01G204900 chr4D 97.877 2214 28 5 2267 4477 353426536 353428733 0.000000e+00 3810.0
4 TraesCS4B01G204900 chr4D 93.069 2020 75 22 1 1984 353424073 353426063 0.000000e+00 2894.0
5 TraesCS4B01G204900 chr4D 95.941 271 9 1 1987 2257 353426100 353426368 5.370000e-119 438.0
6 TraesCS4B01G204900 chr4D 96.552 58 2 0 3974 4031 353428310 353428367 3.720000e-16 97.1
7 TraesCS4B01G204900 chr4A 94.086 2232 86 26 2267 4477 111905358 111903152 0.000000e+00 3349.0
8 TraesCS4B01G204900 chr4A 91.192 2316 112 44 1 2257 111907808 111905526 0.000000e+00 3062.0
9 TraesCS4B01G204900 chr4A 93.939 66 4 0 4044 4109 111903667 111903602 2.880000e-17 100.0
10 TraesCS4B01G204900 chr4A 92.647 68 4 1 3976 4042 111903596 111903529 3.720000e-16 97.1
11 TraesCS4B01G204900 chr6A 96.970 33 1 0 4131 4163 117001412 117001444 6.320000e-04 56.5
12 TraesCS4B01G204900 chr5B 96.875 32 0 1 1442 1473 185205636 185205666 8.000000e-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 TraesCS4B01G204900 chr4B 436891086 436895605 4519 False 2853.000 8347 97.014667 1 4520 3 chr4B.!!$F1 4519
1 TraesCS4B01G204900 chr4D 353424073 353428733 4660 False 1809.775 3810 95.859750 1 4477 4 chr4D.!!$F1 4476
2 TraesCS4B01G204900 chr4A 111903152 111907808 4656 True 1652.025 3349 92.966000 1 4477 4 chr4A.!!$R1 4476

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
807 881 0.033601 AAATTACCGGCCTGCCATCA 60.034 50.000 0.00 0.00 35.37 3.07 F
870 957 1.202545 GGTATTTGACCTCTCCCTCGC 60.203 57.143 0.00 0.00 45.89 5.03 F
2147 2287 0.755686 CCTCTCCCCTCACATGTAGC 59.244 60.000 0.00 0.00 0.00 3.58 F
2360 2658 1.189752 TGTTTGGTGCCAAGCTTGAA 58.810 45.000 28.05 12.66 37.88 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2273 1.556911 ACTTCAGCTACATGTGAGGGG 59.443 52.381 9.11 0.0 0.0 4.79 R
2360 2658 5.178096 TCACATGACCCAAGTATGACATT 57.822 39.130 0.00 0.0 0.0 2.71 R
3372 3673 1.446792 CCACGAATCGCTGCTCTGT 60.447 57.895 1.15 0.0 0.0 3.41 R
3771 4074 5.456921 AGGAATAAAGAATCTGCAGGGAA 57.543 39.130 15.13 0.0 0.0 3.97 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
106 138 1.065709 GTACCATCGGCTTGGGAGAAA 60.066 52.381 8.05 0.00 41.35 2.52
124 156 7.876068 TGGGAGAAATAATTTACGTAGCCATAG 59.124 37.037 0.00 0.00 0.00 2.23
127 159 7.149973 AGAAATAATTTACGTAGCCATAGCGA 58.850 34.615 0.00 0.00 46.67 4.93
163 195 4.373116 TTGTCGCGGCAGACCCTC 62.373 66.667 15.27 0.00 40.26 4.30
229 261 2.806856 CTCCTGCGCGTTCTCATGC 61.807 63.158 8.43 0.00 0.00 4.06
499 558 0.872451 GGGGTCGGTTTTTGTTTGCG 60.872 55.000 0.00 0.00 0.00 4.85
500 559 0.179132 GGGTCGGTTTTTGTTTGCGT 60.179 50.000 0.00 0.00 0.00 5.24
646 709 1.079256 CCTCCTGAGTCCTGACCCA 59.921 63.158 0.00 0.00 0.00 4.51
647 710 1.261238 CCTCCTGAGTCCTGACCCAC 61.261 65.000 0.00 0.00 0.00 4.61
648 711 0.542938 CTCCTGAGTCCTGACCCACA 60.543 60.000 0.00 0.00 0.00 4.17
666 740 2.434359 CAGTTTCCTCGCCCGTCC 60.434 66.667 0.00 0.00 0.00 4.79
667 741 3.703127 AGTTTCCTCGCCCGTCCC 61.703 66.667 0.00 0.00 0.00 4.46
732 806 2.742372 CTGGCTGTTCGGTTCGGG 60.742 66.667 0.00 0.00 0.00 5.14
807 881 0.033601 AAATTACCGGCCTGCCATCA 60.034 50.000 0.00 0.00 35.37 3.07
869 956 2.892784 GGTATTTGACCTCTCCCTCG 57.107 55.000 0.00 0.00 45.89 4.63
870 957 1.202545 GGTATTTGACCTCTCCCTCGC 60.203 57.143 0.00 0.00 45.89 5.03
871 958 1.757699 GTATTTGACCTCTCCCTCGCT 59.242 52.381 0.00 0.00 0.00 4.93
912 999 4.660938 GCCCTCCACCACCACCAC 62.661 72.222 0.00 0.00 0.00 4.16
913 1000 3.966543 CCCTCCACCACCACCACC 61.967 72.222 0.00 0.00 0.00 4.61
914 1001 3.174987 CCTCCACCACCACCACCA 61.175 66.667 0.00 0.00 0.00 4.17
930 1017 1.229984 CCACCTCCTCCTTTCCCCT 60.230 63.158 0.00 0.00 0.00 4.79
1546 1645 4.389576 CGTTTGCTGGCGCTGGAC 62.390 66.667 7.64 0.00 36.97 4.02
1787 1886 3.589881 GGGCGATGTCATGCAGGC 61.590 66.667 0.00 0.00 0.00 4.85
1788 1887 2.515523 GGCGATGTCATGCAGGCT 60.516 61.111 0.00 0.00 32.92 4.58
1911 2015 7.504924 TTTGTGGTTAGAATCAACGAATCTT 57.495 32.000 0.00 0.00 0.00 2.40
1926 2030 4.218417 ACGAATCTTCAAACATTTCCCCAG 59.782 41.667 0.00 0.00 0.00 4.45
1941 2045 3.305720 TCCCCAGTACCTGCAATAGTAG 58.694 50.000 0.00 0.00 0.00 2.57
1954 2058 5.601662 TGCAATAGTAGTGGAAGAGCATAC 58.398 41.667 0.00 0.00 0.00 2.39
1958 2062 7.470147 GCAATAGTAGTGGAAGAGCATACACTA 60.470 40.741 5.44 5.44 43.34 2.74
1968 2072 6.091441 GGAAGAGCATACACTAGTGTTTTCAG 59.909 42.308 32.15 18.02 41.83 3.02
1984 2088 6.199719 GTGTTTTCAGAAAGGAAAATCTGCTG 59.800 38.462 4.61 0.00 45.43 4.41
1998 2136 8.992073 GGAAAATCTGCTGTTTCATAAAATTGT 58.008 29.630 8.33 0.00 35.80 2.71
2057 2195 5.670485 TGGCTATATTGTCACCACTGTTAG 58.330 41.667 0.00 0.00 0.00 2.34
2132 2272 5.388654 ACTTCATTGGATTTGTGAACCTCT 58.611 37.500 0.00 0.00 0.00 3.69
2133 2273 5.474876 ACTTCATTGGATTTGTGAACCTCTC 59.525 40.000 0.00 0.00 0.00 3.20
2147 2287 0.755686 CCTCTCCCCTCACATGTAGC 59.244 60.000 0.00 0.00 0.00 3.58
2149 2289 1.411977 CTCTCCCCTCACATGTAGCTG 59.588 57.143 0.00 0.00 0.00 4.24
2291 2589 3.560481 CAGCAGCACTCCTTCAGATTATG 59.440 47.826 0.00 0.00 0.00 1.90
2300 2598 7.201767 GCACTCCTTCAGATTATGTTAGCAAAT 60.202 37.037 0.00 0.00 0.00 2.32
2314 2612 7.155655 TGTTAGCAAATTACATCTGCAATCA 57.844 32.000 2.16 0.00 38.58 2.57
2360 2658 1.189752 TGTTTGGTGCCAAGCTTGAA 58.810 45.000 28.05 12.66 37.88 2.69
2382 2680 4.842531 ATGTCATACTTGGGTCATGTGA 57.157 40.909 0.00 0.00 0.00 3.58
2614 2912 9.362539 GATTTGTGATATGCAAGAGTTGAATTT 57.637 29.630 0.00 0.00 29.73 1.82
2699 2997 9.528018 GATTAAATCTTGTTAGACTCTCCTGAG 57.472 37.037 0.00 0.00 45.43 3.35
2949 3249 8.474577 GCATGCTGAATTTTAGATTATTTGTCG 58.525 33.333 11.37 0.00 0.00 4.35
3372 3673 0.694771 ATGAGCCTGCCAAGACAAGA 59.305 50.000 0.00 0.00 0.00 3.02
3384 3685 0.894141 AGACAAGACAGAGCAGCGAT 59.106 50.000 0.00 0.00 0.00 4.58
3953 4258 1.114722 CCTTTCTGGCCTTTGGTGCA 61.115 55.000 3.32 0.00 0.00 4.57
4479 4798 3.411808 CATGTGCATGCCAACTGAC 57.588 52.632 16.68 5.90 31.39 3.51
4480 4799 0.108992 CATGTGCATGCCAACTGACC 60.109 55.000 16.68 0.00 31.39 4.02
4481 4800 0.540133 ATGTGCATGCCAACTGACCA 60.540 50.000 16.68 0.00 0.00 4.02
4482 4801 0.540133 TGTGCATGCCAACTGACCAT 60.540 50.000 16.68 0.00 0.00 3.55
4483 4802 0.108992 GTGCATGCCAACTGACCATG 60.109 55.000 16.68 0.00 39.38 3.66
4484 4803 0.540133 TGCATGCCAACTGACCATGT 60.540 50.000 16.68 0.00 38.79 3.21
4485 4804 0.108992 GCATGCCAACTGACCATGTG 60.109 55.000 6.36 0.00 38.79 3.21
4486 4805 0.528924 CATGCCAACTGACCATGTGG 59.471 55.000 0.00 0.00 42.17 4.17
4498 4817 2.872408 CATGTGGTCCATGTGGGTC 58.128 57.895 0.00 0.00 44.96 4.46
4499 4818 0.038021 CATGTGGTCCATGTGGGTCA 59.962 55.000 0.00 0.00 44.96 4.02
4500 4819 0.038166 ATGTGGTCCATGTGGGTCAC 59.962 55.000 14.36 14.36 40.07 3.67
4501 4820 1.059584 TGTGGTCCATGTGGGTCACT 61.060 55.000 18.80 0.00 40.21 3.41
4502 4821 0.981183 GTGGTCCATGTGGGTCACTA 59.019 55.000 14.11 0.00 38.19 2.74
4503 4822 1.066143 GTGGTCCATGTGGGTCACTAG 60.066 57.143 14.11 0.00 38.19 2.57
4504 4823 0.107654 GGTCCATGTGGGTCACTAGC 60.108 60.000 0.00 0.00 38.11 3.42
4505 4824 0.905357 GTCCATGTGGGTCACTAGCT 59.095 55.000 0.00 0.00 38.11 3.32
4506 4825 1.279271 GTCCATGTGGGTCACTAGCTT 59.721 52.381 0.00 0.00 38.11 3.74
4507 4826 1.555075 TCCATGTGGGTCACTAGCTTC 59.445 52.381 0.00 0.00 38.11 3.86
4508 4827 1.278985 CCATGTGGGTCACTAGCTTCA 59.721 52.381 0.00 0.00 35.11 3.02
4509 4828 2.290260 CCATGTGGGTCACTAGCTTCAA 60.290 50.000 0.00 0.00 35.11 2.69
4510 4829 2.543777 TGTGGGTCACTAGCTTCAAC 57.456 50.000 0.00 0.00 35.11 3.18
4511 4830 2.047061 TGTGGGTCACTAGCTTCAACT 58.953 47.619 0.00 0.00 35.11 3.16
4512 4831 2.037251 TGTGGGTCACTAGCTTCAACTC 59.963 50.000 0.00 0.00 35.11 3.01
4513 4832 2.300437 GTGGGTCACTAGCTTCAACTCT 59.700 50.000 0.00 0.00 0.00 3.24
4514 4833 2.563179 TGGGTCACTAGCTTCAACTCTC 59.437 50.000 0.00 0.00 0.00 3.20
4515 4834 2.829120 GGGTCACTAGCTTCAACTCTCT 59.171 50.000 0.00 0.00 0.00 3.10
4516 4835 3.259625 GGGTCACTAGCTTCAACTCTCTT 59.740 47.826 0.00 0.00 0.00 2.85
4517 4836 4.262678 GGGTCACTAGCTTCAACTCTCTTT 60.263 45.833 0.00 0.00 0.00 2.52
4518 4837 5.301555 GGTCACTAGCTTCAACTCTCTTTT 58.698 41.667 0.00 0.00 0.00 2.27
4519 4838 5.178438 GGTCACTAGCTTCAACTCTCTTTTG 59.822 44.000 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.703621 GCTGCTGCTTATTTATCTTCAATTTCA 59.296 33.333 8.53 0.00 36.03 2.69
18 19 1.503542 GCGTGTGCTGCTGCTTATT 59.496 52.632 17.00 0.00 40.48 1.40
61 62 3.464907 CACACTGTCTCCATCCATCATC 58.535 50.000 0.00 0.00 0.00 2.92
63 64 1.065926 GCACACTGTCTCCATCCATCA 60.066 52.381 0.00 0.00 0.00 3.07
106 138 5.347907 GCTTCGCTATGGCTACGTAAATTAT 59.652 40.000 0.00 0.00 36.09 1.28
190 222 0.320771 AGCACATCTTCGACGCCTTT 60.321 50.000 0.00 0.00 0.00 3.11
229 261 1.299468 GCTCTACGTGGGCGATCTG 60.299 63.158 0.00 0.00 42.00 2.90
363 404 1.172812 AGACCGATCGATCATGGCGA 61.173 55.000 24.40 12.66 42.48 5.54
394 438 1.597027 CCTAGCAATAACGCCCGGG 60.597 63.158 19.09 19.09 0.00 5.73
591 654 3.419580 TCGGGTCGGGTAGGGCTA 61.420 66.667 0.00 0.00 0.00 3.93
646 709 2.030562 CGGGCGAGGAAACTGTGT 59.969 61.111 0.00 0.00 44.43 3.72
647 710 2.027625 GACGGGCGAGGAAACTGTG 61.028 63.158 0.00 0.00 44.43 3.66
648 711 2.342648 GACGGGCGAGGAAACTGT 59.657 61.111 0.00 0.00 44.43 3.55
710 784 3.454587 AACCGAACAGCCAGCGACA 62.455 57.895 0.00 0.00 0.00 4.35
786 860 0.755327 ATGGCAGGCCGGTAATTTCC 60.755 55.000 1.90 0.00 39.42 3.13
912 999 0.846870 AAGGGGAAAGGAGGAGGTGG 60.847 60.000 0.00 0.00 0.00 4.61
913 1000 0.621082 GAAGGGGAAAGGAGGAGGTG 59.379 60.000 0.00 0.00 0.00 4.00
914 1001 0.550393 GGAAGGGGAAAGGAGGAGGT 60.550 60.000 0.00 0.00 0.00 3.85
1045 1132 2.029964 GCACGTCTTGTTCCCCGA 59.970 61.111 0.00 0.00 0.00 5.14
1467 1560 1.227556 GTCCCAATCGTCCCATCCG 60.228 63.158 0.00 0.00 0.00 4.18
1621 1720 1.852157 AAATCCTCCTTGCTGGCCGA 61.852 55.000 0.00 0.00 35.26 5.54
1926 2030 5.593010 CTCTTCCACTACTATTGCAGGTAC 58.407 45.833 0.00 0.00 0.00 3.34
1941 2045 4.457834 ACACTAGTGTATGCTCTTCCAC 57.542 45.455 26.91 0.00 42.90 4.02
1954 2058 8.624776 AGATTTTCCTTTCTGAAAACACTAGTG 58.375 33.333 21.44 21.44 44.46 2.74
1958 2062 6.097412 AGCAGATTTTCCTTTCTGAAAACACT 59.903 34.615 4.18 2.72 44.46 3.55
1968 2072 8.816640 TTTATGAAACAGCAGATTTTCCTTTC 57.183 30.769 0.00 0.00 31.76 2.62
1984 2088 7.068955 CCCGCAAGAAAACAATTTTATGAAAC 58.931 34.615 4.40 0.00 43.02 2.78
1998 2136 3.662759 AATAGGATCCCCGCAAGAAAA 57.337 42.857 8.55 0.00 43.02 2.29
2057 2195 2.165030 GGGGCAATATGTGATGCATAGC 59.835 50.000 0.00 0.00 44.32 2.97
2132 2272 1.833630 CTTCAGCTACATGTGAGGGGA 59.166 52.381 9.11 0.00 0.00 4.81
2133 2273 1.556911 ACTTCAGCTACATGTGAGGGG 59.443 52.381 9.11 0.00 0.00 4.79
2300 2598 6.778834 ACCAAATGATGATTGCAGATGTAA 57.221 33.333 0.00 0.00 0.00 2.41
2360 2658 5.178096 TCACATGACCCAAGTATGACATT 57.822 39.130 0.00 0.00 0.00 2.71
2614 2912 6.769134 TTTCATGATCAACTAGACTACGGA 57.231 37.500 0.00 0.00 0.00 4.69
2912 3210 3.851458 TTCAGCATGCACTATCCTGAT 57.149 42.857 21.98 0.00 34.76 2.90
2949 3249 7.164858 CGATGTAACACGAGAATAAAGAACAC 58.835 38.462 0.00 0.00 0.00 3.32
3372 3673 1.446792 CCACGAATCGCTGCTCTGT 60.447 57.895 1.15 0.00 0.00 3.41
3767 4070 7.001073 GGAATAAAGAATCTGCAGGGAAGTAT 58.999 38.462 15.13 2.68 0.00 2.12
3771 4074 5.456921 AGGAATAAAGAATCTGCAGGGAA 57.543 39.130 15.13 0.00 0.00 3.97
3953 4258 6.150976 TCAACTATCGAAAGGCAAATCATGTT 59.849 34.615 0.00 0.00 0.00 2.71
4165 4472 7.053316 TGTGGAGATTTGTGATGATGTTTTT 57.947 32.000 0.00 0.00 0.00 1.94
4174 4489 7.959658 TGGATTTTATGTGGAGATTTGTGAT 57.040 32.000 0.00 0.00 0.00 3.06
4481 4800 0.038166 GTGACCCACATGGACCACAT 59.962 55.000 0.00 0.00 41.57 3.21
4482 4801 1.059584 AGTGACCCACATGGACCACA 61.060 55.000 18.44 0.00 40.86 4.17
4483 4802 0.981183 TAGTGACCCACATGGACCAC 59.019 55.000 0.00 6.97 39.67 4.16
4484 4803 1.275666 CTAGTGACCCACATGGACCA 58.724 55.000 0.00 0.00 36.74 4.02
4485 4804 0.107654 GCTAGTGACCCACATGGACC 60.108 60.000 0.00 0.00 36.74 4.46
4486 4805 0.905357 AGCTAGTGACCCACATGGAC 59.095 55.000 0.00 0.00 36.74 4.02
4487 4806 1.555075 GAAGCTAGTGACCCACATGGA 59.445 52.381 0.00 0.00 36.74 3.41
4488 4807 1.278985 TGAAGCTAGTGACCCACATGG 59.721 52.381 0.00 0.00 36.74 3.66
4489 4808 2.744202 GTTGAAGCTAGTGACCCACATG 59.256 50.000 0.00 0.00 36.74 3.21
4490 4809 2.639839 AGTTGAAGCTAGTGACCCACAT 59.360 45.455 0.00 0.00 36.74 3.21
4491 4810 2.037251 GAGTTGAAGCTAGTGACCCACA 59.963 50.000 0.00 0.00 36.74 4.17
4492 4811 2.300437 AGAGTTGAAGCTAGTGACCCAC 59.700 50.000 0.00 0.00 34.10 4.61
4493 4812 2.563179 GAGAGTTGAAGCTAGTGACCCA 59.437 50.000 0.00 0.00 0.00 4.51
4494 4813 2.829120 AGAGAGTTGAAGCTAGTGACCC 59.171 50.000 0.00 0.00 0.00 4.46
4495 4814 4.529109 AAGAGAGTTGAAGCTAGTGACC 57.471 45.455 0.00 0.00 0.00 4.02
4496 4815 6.221858 CAAAAGAGAGTTGAAGCTAGTGAC 57.778 41.667 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.