Multiple sequence alignment - TraesCS4B01G193100

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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 TraesCS4B01G193100 chr4B 100.000 4210 0 0 1 4210 416167130 416162921 0.000000e+00 7775
1 TraesCS4B01G193100 chr4A 96.917 4216 98 13 1 4210 136232416 136236605 0.000000e+00 7036
2 TraesCS4B01G193100 chr4A 91.045 134 12 0 3565 3698 136236449 136236582 9.300000e-42 182
3 TraesCS4B01G193100 chr4D 96.724 4213 108 16 7 4210 337074701 337070510 0.000000e+00 6988


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 TraesCS4B01G193100 chr4B 416162921 416167130 4209 True 7775 7775 100.000 1 4210 1 chr4B.!!$R1 4209
1 TraesCS4B01G193100 chr4A 136232416 136236605 4189 False 3609 7036 93.981 1 4210 2 chr4A.!!$F1 4209
2 TraesCS4B01G193100 chr4D 337070510 337074701 4191 True 6988 6988 96.724 7 4210 1 chr4D.!!$R1 4203

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
87 89 0.036294 GTTTTCGGGGCTCTGCTACT 60.036 55.000 0.0 0.0 0.0 2.57 F
1074 1078 1.546029 CTGATCGAGAGGAACCACACA 59.454 52.381 0.0 0.0 0.0 3.72 F
1794 1802 2.412870 CGCATGACAGTTACCAGTTCA 58.587 47.619 0.0 0.0 0.0 3.18 F
2800 2808 5.503520 CGTCTTCAACTCCAAACCAACTTAC 60.504 44.000 0.0 0.0 0.0 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 1514 1.148310 TCGCTTTTGCCTTCTCTTCG 58.852 50.000 0.00 0.0 43.93 3.79 R
2194 2202 2.945008 TGCCAGGAAGCTAATGAATTCG 59.055 45.455 0.04 0.0 0.00 3.34 R
3101 3109 3.791973 TTGTTGCAGTTACCTTGGTTG 57.208 42.857 0.00 0.0 0.00 3.77 R
3833 3842 1.757699 ACCCTCTAACAGCGGAATCTC 59.242 52.381 0.00 0.0 0.00 2.75 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
33 34 6.705863 ATAACATTGCCAGAATCTTCCTTC 57.294 37.500 0.00 0.00 0.00 3.46
78 80 4.514066 CCTACTATATGTTGTTTTCGGGGC 59.486 45.833 0.00 0.00 0.00 5.80
87 89 0.036294 GTTTTCGGGGCTCTGCTACT 60.036 55.000 0.00 0.00 0.00 2.57
102 104 4.653801 TCTGCTACTGCCTATATTTGGTGA 59.346 41.667 0.00 0.00 38.71 4.02
422 425 2.704572 GCTTGAGGCAGAAGAAAGCTA 58.295 47.619 0.00 0.00 40.04 3.32
632 636 4.098349 ACTGAACATAGACGGCGGTAAATA 59.902 41.667 13.24 0.00 0.00 1.40
977 981 5.538053 CAGTACCACCATACAGAGAGATCAT 59.462 44.000 0.00 0.00 0.00 2.45
978 982 5.772672 AGTACCACCATACAGAGAGATCATC 59.227 44.000 0.00 0.00 0.00 2.92
979 983 4.550669 ACCACCATACAGAGAGATCATCA 58.449 43.478 0.00 0.00 0.00 3.07
1074 1078 1.546029 CTGATCGAGAGGAACCACACA 59.454 52.381 0.00 0.00 0.00 3.72
1182 1186 5.819991 AGAAAGATAATGTGGAAGAAGCCA 58.180 37.500 0.00 0.00 35.02 4.75
1335 1339 3.817084 CAGTGAAATCAAGAGCACCAAGA 59.183 43.478 0.00 0.00 31.85 3.02
1510 1514 4.870363 TGAGTTGTACCGGTTGTTAGTAC 58.130 43.478 15.04 2.78 37.47 2.73
1694 1698 5.048083 TGTTTACTTAGCTGCCAATTCCTTG 60.048 40.000 0.00 0.00 0.00 3.61
1794 1802 2.412870 CGCATGACAGTTACCAGTTCA 58.587 47.619 0.00 0.00 0.00 3.18
1856 1864 6.985188 TCTTTAAACATCTCTCCCATTTCG 57.015 37.500 0.00 0.00 0.00 3.46
1978 1986 6.349280 GCAATGCCATGTGTTAGTTTAAGAGA 60.349 38.462 0.00 0.00 0.00 3.10
1983 1991 6.349280 GCCATGTGTTAGTTTAAGAGAATGCA 60.349 38.462 0.00 0.00 0.00 3.96
2141 2149 9.452287 CAATAATTTCCTCACCAATCCAAAAAT 57.548 29.630 0.00 0.00 0.00 1.82
2194 2202 6.705863 AAATCAGATGTAGAAAATCAGGGC 57.294 37.500 0.00 0.00 0.00 5.19
2800 2808 5.503520 CGTCTTCAACTCCAAACCAACTTAC 60.504 44.000 0.00 0.00 0.00 2.34
3101 3109 5.544650 TGAGTTGCTACCTACAAACTAACC 58.455 41.667 0.00 0.00 0.00 2.85
3170 3178 0.539438 ATGAAGGTTGCCGGAAAGCA 60.539 50.000 25.99 6.23 42.17 3.91
3192 3200 4.659111 TTCCAAGAACTCAAGACGTACA 57.341 40.909 0.00 0.00 0.00 2.90
3252 3260 6.267471 GGGTTCAAATAAGCATCATTGGGATA 59.733 38.462 0.00 0.00 33.95 2.59
3296 3304 1.827399 GAGGTTGGCTCCAGGTCGAA 61.827 60.000 0.00 0.00 0.00 3.71
3408 3416 4.163839 AGCCTGAGAATTCTAAGTGCATCT 59.836 41.667 24.15 10.74 0.00 2.90
3414 3422 7.487484 TGAGAATTCTAAGTGCATCTACTCAG 58.513 38.462 8.25 0.00 0.00 3.35
3516 3524 3.139397 ACCCTTTGATTGTTAGGTGGTCA 59.861 43.478 0.00 0.00 0.00 4.02
3563 3571 5.197451 TCTGGAAATGGCATAATTTACGGT 58.803 37.500 0.00 0.00 37.79 4.83
3627 3635 2.159382 AGGTTCACAATTGTTAGGGCG 58.841 47.619 8.77 0.00 0.00 6.13
3708 3717 5.048083 TGGCTGTAAATGCTCAAAAACTAGG 60.048 40.000 0.00 0.00 0.00 3.02
3822 3831 4.202631 ACAAATCCACTTTTACCTAGGGCA 60.203 41.667 14.81 0.00 0.00 5.36
3892 3901 5.869344 TGAATCAACAACATCCTCTACTTCG 59.131 40.000 0.00 0.00 0.00 3.79
3916 3925 3.386402 AGGAGCTCTAATTGTCTGTAGCC 59.614 47.826 14.64 0.00 0.00 3.93
3998 4007 4.383931 AGCCCTATTATACAGAGGACGA 57.616 45.455 0.00 0.00 31.45 4.20
4067 4076 7.966111 CTATACAGATAGGACGACAGTATGTC 58.034 42.308 0.00 0.00 45.24 3.06
4106 4116 8.819643 AAGAGTAAGATTCACAACTGTTACTC 57.180 34.615 10.65 10.65 43.32 2.59
4107 4117 8.184304 AGAGTAAGATTCACAACTGTTACTCT 57.816 34.615 14.06 14.06 46.02 3.24
4108 4118 8.233692 GAGTAAGATTCACAACTGTTACTCTG 57.766 38.462 11.16 0.00 41.31 3.35
4109 4119 7.727181 AGTAAGATTCACAACTGTTACTCTGT 58.273 34.615 0.00 0.00 0.00 3.41
4110 4120 8.204836 AGTAAGATTCACAACTGTTACTCTGTT 58.795 33.333 0.00 0.00 38.43 3.16
4111 4121 9.472361 GTAAGATTCACAACTGTTACTCTGTTA 57.528 33.333 0.00 0.00 36.65 2.41
4126 4136 5.473931 ACTCTGTTAGTGCACACTGAATAG 58.526 41.667 21.04 13.93 42.52 1.73
4189 4199 3.995705 GCAAATTGGCTGTAAATGCTTCA 59.004 39.130 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.814264 AGATTCTGGCAATGTTATAAAGGAG 57.186 36.000 0.00 0.00 0.00 3.69
5 6 7.286316 AGGAAGATTCTGGCAATGTTATAAAGG 59.714 37.037 0.00 0.00 0.00 3.11
33 34 4.934001 GGTTTAGAAAAAGGAGTCCCTACG 59.066 45.833 5.25 0.00 43.48 3.51
67 69 0.321298 GTAGCAGAGCCCCGAAAACA 60.321 55.000 0.00 0.00 0.00 2.83
78 80 4.993584 CACCAAATATAGGCAGTAGCAGAG 59.006 45.833 0.00 0.00 44.61 3.35
87 89 7.342581 TCTGTTTATGTCACCAAATATAGGCA 58.657 34.615 0.00 0.00 0.00 4.75
102 104 3.806625 GCATTGGGCATCTGTTTATGT 57.193 42.857 0.00 0.00 43.97 2.29
422 425 3.077359 GTGACAGCAAAGCCTGAATACT 58.923 45.455 0.00 0.00 36.67 2.12
977 981 1.753649 CTTCTTCGCCAGAGGAGATGA 59.246 52.381 2.13 2.13 34.90 2.92
978 982 1.753649 TCTTCTTCGCCAGAGGAGATG 59.246 52.381 0.00 0.00 32.71 2.90
979 983 2.151502 TCTTCTTCGCCAGAGGAGAT 57.848 50.000 0.00 0.00 32.71 2.75
1074 1078 2.050144 TGCTTGTTCTCCTCTTCCAGT 58.950 47.619 0.00 0.00 0.00 4.00
1182 1186 3.566130 GCTGGTGGCAGAATTCTCT 57.434 52.632 4.57 0.00 41.35 3.10
1206 1210 8.361139 TGAACAAACTGTTTTTCCTTGAAGTAA 58.639 29.630 17.43 0.00 41.28 2.24
1335 1339 2.091333 ACTTGGTGGTGGATTTGGAACT 60.091 45.455 0.00 0.00 0.00 3.01
1510 1514 1.148310 TCGCTTTTGCCTTCTCTTCG 58.852 50.000 0.00 0.00 43.93 3.79
1716 1724 4.024048 ACTCTTGTTGCTTATGTTGGTTCG 60.024 41.667 0.00 0.00 0.00 3.95
1894 1902 7.041235 TGTGGTGTATTCGTAAGGTTTTAAAGG 60.041 37.037 0.00 0.00 38.47 3.11
1978 1986 7.929785 AGAAAAATCAGAAGAACATGTTGCATT 59.070 29.630 17.58 7.88 0.00 3.56
1983 1991 9.305925 GAAACAGAAAAATCAGAAGAACATGTT 57.694 29.630 11.78 11.78 0.00 2.71
2141 2149 7.178573 TGTTGGAACACAATCATAAGGGAATA 58.821 34.615 0.00 0.00 41.95 1.75
2194 2202 2.945008 TGCCAGGAAGCTAATGAATTCG 59.055 45.455 0.04 0.00 0.00 3.34
2742 2750 8.715191 AAATGCACTTAACTATCTCTTCTCTG 57.285 34.615 0.00 0.00 0.00 3.35
3101 3109 3.791973 TTGTTGCAGTTACCTTGGTTG 57.208 42.857 0.00 0.00 0.00 3.77
3170 3178 4.989168 GTGTACGTCTTGAGTTCTTGGAAT 59.011 41.667 0.00 0.00 0.00 3.01
3252 3260 6.153756 GGCAAAACTTAATTATGTCCGTTGT 58.846 36.000 4.61 0.00 0.00 3.32
3296 3304 5.782845 GGAATTATCCTGGAGACTAGTGGAT 59.217 44.000 14.28 14.28 42.93 3.41
3563 3571 4.077108 ACATACTGTCGTCCTGTCTGTAA 58.923 43.478 0.00 0.00 32.83 2.41
3708 3717 4.083271 GGTTTGAATACTTGGAGCAGTCAC 60.083 45.833 0.00 0.00 0.00 3.67
3753 3762 7.043961 TGGATGTATCTGATACTCTTGTCAC 57.956 40.000 23.96 9.69 36.70 3.67
3822 3831 2.572104 AGCGGAATCTCAAAAGGTAGGT 59.428 45.455 0.00 0.00 0.00 3.08
3833 3842 1.757699 ACCCTCTAACAGCGGAATCTC 59.242 52.381 0.00 0.00 0.00 2.75
3892 3901 3.258971 ACAGACAATTAGAGCTCCTGC 57.741 47.619 10.93 0.48 40.05 4.85
3916 3925 6.767524 TGGTGCTTAGGTGGTATTTTTATG 57.232 37.500 0.00 0.00 0.00 1.90
4067 4076 6.561519 TCTTACTCTTTAGGAATGAAGGGG 57.438 41.667 0.00 0.00 0.00 4.79
4104 4114 4.867047 CCTATTCAGTGTGCACTAACAGAG 59.133 45.833 19.41 7.20 40.20 3.35
4105 4115 4.322725 CCCTATTCAGTGTGCACTAACAGA 60.323 45.833 19.41 8.33 40.20 3.41
4106 4116 3.935203 CCCTATTCAGTGTGCACTAACAG 59.065 47.826 19.41 5.89 40.20 3.16
4107 4117 3.326588 ACCCTATTCAGTGTGCACTAACA 59.673 43.478 19.41 0.00 40.20 2.41
4108 4118 3.939066 ACCCTATTCAGTGTGCACTAAC 58.061 45.455 19.41 8.91 40.20 2.34
4109 4119 4.634012 AACCCTATTCAGTGTGCACTAA 57.366 40.909 19.41 7.61 40.20 2.24
4110 4120 4.634012 AAACCCTATTCAGTGTGCACTA 57.366 40.909 19.41 1.23 40.20 2.74
4111 4121 3.508845 AAACCCTATTCAGTGTGCACT 57.491 42.857 19.41 0.00 43.61 4.40


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

AutoCloner maintained by Alex Coulton.