Multiple sequence alignment - TraesCS7D01G379600

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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 TraesCS7D01G379600 chr7D 100.000 3008 0 0 784 3791 491864716 491861709 0.000000e+00 5555.0
1 TraesCS7D01G379600 chr7D 88.287 2715 271 28 935 3627 491791006 491788317 0.000000e+00 3208.0
2 TraesCS7D01G379600 chr7D 87.932 2718 285 28 935 3627 491801058 491798359 0.000000e+00 3162.0
3 TraesCS7D01G379600 chr7D 100.000 577 0 0 1 577 491865499 491864923 0.000000e+00 1066.0
4 TraesCS7D01G379600 chr7D 80.903 288 42 8 3501 3788 491798360 491798086 8.250000e-52 215.0
5 TraesCS7D01G379600 chr7A 95.208 2880 107 13 935 3791 558102226 558099355 0.000000e+00 4525.0
6 TraesCS7D01G379600 chr7A 88.471 2715 266 28 935 3627 558082603 558079914 0.000000e+00 3236.0
7 TraesCS7D01G379600 chr7A 88.859 2208 221 17 1432 3627 558092981 558090787 0.000000e+00 2691.0
8 TraesCS7D01G379600 chr7A 91.050 581 25 7 1 575 558103755 558103196 0.000000e+00 760.0
9 TraesCS7D01G379600 chr7A 83.850 613 70 16 821 1409 558093659 558093052 1.190000e-154 556.0
10 TraesCS7D01G379600 chr7A 79.725 291 41 8 3501 3790 558079915 558079642 1.070000e-45 195.0
11 TraesCS7D01G379600 chr7A 90.132 152 7 1 796 947 558102779 558102636 1.390000e-44 191.0
12 TraesCS7D01G379600 chr7B 95.944 2515 94 4 839 3348 521143010 521140499 0.000000e+00 4072.0
13 TraesCS7D01G379600 chr7B 88.343 2728 272 26 935 3627 521133793 521131077 0.000000e+00 3234.0
14 TraesCS7D01G379600 chr7B 87.629 2716 281 33 935 3627 521123801 521121118 0.000000e+00 3103.0
15 TraesCS7D01G379600 chr7B 87.564 587 38 8 1 577 521143930 521143369 0.000000e+00 647.0
16 TraesCS7D01G379600 chr7B 80.690 290 43 8 3501 3790 521131078 521130802 2.970000e-51 213.0
17 TraesCS7D01G379600 chr7B 87.931 58 7 0 790 847 521134131 521134074 6.800000e-08 69.4
18 TraesCS7D01G379600 chr2B 76.418 1692 326 44 1805 3439 729767415 729769090 0.000000e+00 846.0
19 TraesCS7D01G379600 chr2B 81.848 606 97 6 2852 3446 548619347 548619950 7.310000e-137 497.0
20 TraesCS7D01G379600 chr2B 87.719 57 7 0 1109 1165 548624102 548624158 2.440000e-07 67.6
21 TraesCS7D01G379600 chr5A 93.750 48 3 0 1120 1167 565499016 565498969 5.250000e-09 73.1


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 TraesCS7D01G379600 chr7D 491861709 491865499 3790 True 3310.500000 5555 100.000000 1 3791 2 chr7D.!!$R3 3790
1 TraesCS7D01G379600 chr7D 491788317 491791006 2689 True 3208.000000 3208 88.287000 935 3627 1 chr7D.!!$R1 2692
2 TraesCS7D01G379600 chr7D 491798086 491801058 2972 True 1688.500000 3162 84.417500 935 3788 2 chr7D.!!$R2 2853
3 TraesCS7D01G379600 chr7A 558099355 558103755 4400 True 1825.333333 4525 92.130000 1 3791 3 chr7A.!!$R3 3790
4 TraesCS7D01G379600 chr7A 558079642 558082603 2961 True 1715.500000 3236 84.098000 935 3790 2 chr7A.!!$R1 2855
5 TraesCS7D01G379600 chr7A 558090787 558093659 2872 True 1623.500000 2691 86.354500 821 3627 2 chr7A.!!$R2 2806
6 TraesCS7D01G379600 chr7B 521121118 521123801 2683 True 3103.000000 3103 87.629000 935 3627 1 chr7B.!!$R1 2692
7 TraesCS7D01G379600 chr7B 521140499 521143930 3431 True 2359.500000 4072 91.754000 1 3348 2 chr7B.!!$R3 3347
8 TraesCS7D01G379600 chr7B 521130802 521134131 3329 True 1172.133333 3234 85.654667 790 3790 3 chr7B.!!$R2 3000
9 TraesCS7D01G379600 chr2B 729767415 729769090 1675 False 846.000000 846 76.418000 1805 3439 1 chr2B.!!$F3 1634
10 TraesCS7D01G379600 chr2B 548619347 548619950 603 False 497.000000 497 81.848000 2852 3446 1 chr2B.!!$F1 594

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
114 116 1.246649 TTCGGCAACAGCAACATGAT 58.753 45.000 0.00 0.0 0.00 2.45 F
1136 2000 0.235926 GACAAGCTCGTTTCCAGCAC 59.764 55.000 0.00 0.0 39.56 4.40 F
1752 2673 1.066422 CCGAGCGCTGCTGAAGATA 59.934 57.895 18.48 0.0 39.88 1.98 F
1787 2708 1.449070 GGTTGGTCGTCCCGGAATC 60.449 63.158 0.73 0.0 35.15 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1397 2264 0.396556 GGTGGAGGTGGTGTTGGTTT 60.397 55.000 0.0 0.0 0.00 3.27 R
2554 3505 0.466555 TTTGTAGCACGGCCCAAGTT 60.467 50.000 0.0 0.0 0.00 2.66 R
2650 3604 2.689983 CACCTTCAAGCCTTTTCACTGT 59.310 45.455 0.0 0.0 0.00 3.55 R
2869 3837 2.965831 TCTAGCAACTCCGATGGCTATT 59.034 45.455 0.0 0.0 38.11 1.73 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
114 116 1.246649 TTCGGCAACAGCAACATGAT 58.753 45.000 0.00 0.00 0.00 2.45
115 117 2.106477 TCGGCAACAGCAACATGATA 57.894 45.000 0.00 0.00 0.00 2.15
116 118 1.737236 TCGGCAACAGCAACATGATAC 59.263 47.619 0.00 0.00 0.00 2.24
122 124 5.220739 GGCAACAGCAACATGATACTAAGAG 60.221 44.000 0.00 0.00 0.00 2.85
224 226 6.643388 TGAAATAATCTTGCTCTGCTCTGTA 58.357 36.000 0.00 0.00 0.00 2.74
225 227 7.278135 TGAAATAATCTTGCTCTGCTCTGTAT 58.722 34.615 0.00 0.00 0.00 2.29
226 228 8.424133 TGAAATAATCTTGCTCTGCTCTGTATA 58.576 33.333 0.00 0.00 0.00 1.47
264 266 5.728637 AAAGAAAAGGAAACAGCTATGGG 57.271 39.130 0.00 0.00 0.00 4.00
267 269 2.834638 AAGGAAACAGCTATGGGCAT 57.165 45.000 0.00 0.00 44.79 4.40
268 270 3.951563 AAGGAAACAGCTATGGGCATA 57.048 42.857 0.00 0.00 44.79 3.14
269 271 3.214696 AGGAAACAGCTATGGGCATAC 57.785 47.619 0.00 0.00 44.79 2.39
290 292 4.161333 ACTAACAAATAAGGTCGTCGTCG 58.839 43.478 0.00 0.00 38.55 5.12
315 317 8.450964 CGGTACATGAATGAAATGGTATTATCC 58.549 37.037 0.00 0.00 0.00 2.59
345 352 7.545362 ACTTCATGGAGAAATAAGACATTCG 57.455 36.000 8.39 0.00 35.40 3.34
346 353 7.331026 ACTTCATGGAGAAATAAGACATTCGA 58.669 34.615 8.39 0.00 35.40 3.71
347 354 7.493971 ACTTCATGGAGAAATAAGACATTCGAG 59.506 37.037 8.39 0.00 35.40 4.04
395 402 7.144722 TGTAATGATGCCTTGAACAGTTAAG 57.855 36.000 0.00 0.00 0.00 1.85
948 1800 2.177233 CCTGTAGTCCTAGGCCTCCTTA 59.823 54.545 9.68 0.00 34.61 2.69
1066 1930 3.195661 GTGCAAACTATTCCTCCTACCG 58.804 50.000 0.00 0.00 0.00 4.02
1136 2000 0.235926 GACAAGCTCGTTTCCAGCAC 59.764 55.000 0.00 0.00 39.56 4.40
1251 2118 6.710295 TCAATAAGATCAATGTCATTACCCCG 59.290 38.462 0.00 0.00 0.00 5.73
1376 2243 1.972223 AGTCCGTCGTCTGGTCCAG 60.972 63.158 13.21 13.21 0.00 3.86
1397 2264 2.503331 CCACATCACCAGCAGTAACAA 58.497 47.619 0.00 0.00 0.00 2.83
1417 2335 1.576368 AACCAACACCACCTCCACCA 61.576 55.000 0.00 0.00 0.00 4.17
1418 2336 1.228245 CCAACACCACCTCCACCAG 60.228 63.158 0.00 0.00 0.00 4.00
1419 2337 1.898574 CAACACCACCTCCACCAGC 60.899 63.158 0.00 0.00 0.00 4.85
1594 2512 2.427245 ATCTCGTGGAAGAGCCGGG 61.427 63.158 2.18 0.00 40.66 5.73
1752 2673 1.066422 CCGAGCGCTGCTGAAGATA 59.934 57.895 18.48 0.00 39.88 1.98
1787 2708 1.449070 GGTTGGTCGTCCCGGAATC 60.449 63.158 0.73 0.00 35.15 2.52
1791 2712 2.202703 GTCGTCCCGGAATCCGTG 60.203 66.667 21.12 9.72 46.80 4.94
2251 3199 1.469940 CCTGCACTGCTTACTCCTACG 60.470 57.143 1.98 0.00 0.00 3.51
2502 3453 1.893808 CAGCTGGTGTGGTGTGTCC 60.894 63.158 5.57 0.00 0.00 4.02
2650 3604 6.267014 AGCTTTAAGTGACCAGACTAGTGTAA 59.733 38.462 0.00 0.00 0.00 2.41
2738 3692 1.352017 ACTGATCCAGCACATCAACCA 59.648 47.619 0.00 0.00 34.37 3.67
2819 3775 2.237143 TGCAATGGTTCTCTCGATTCCT 59.763 45.455 0.00 0.00 0.00 3.36
2893 3861 1.115467 CCATCGGAGTTGCTAGAGGT 58.885 55.000 0.00 0.00 0.00 3.85
3055 4023 3.522343 GGGTTCTAACTACATTCAGGGGT 59.478 47.826 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 16 2.569059 AGCACGCAATAGATGAGCATT 58.431 42.857 0.00 0.00 31.06 3.56
21 23 1.491670 CGCTGTAGCACGCAATAGAT 58.508 50.000 4.59 0.00 42.21 1.98
72 74 4.017380 GCTGATTGATTCTTGACAGCAG 57.983 45.455 0.00 0.00 46.30 4.24
114 116 4.613944 CACACCGTGTCAAACTCTTAGTA 58.386 43.478 0.00 0.00 0.00 1.82
115 117 3.454375 CACACCGTGTCAAACTCTTAGT 58.546 45.455 0.00 0.00 0.00 2.24
116 118 2.221055 GCACACCGTGTCAAACTCTTAG 59.779 50.000 0.00 0.00 35.75 2.18
122 124 1.525619 GTAGAGCACACCGTGTCAAAC 59.474 52.381 0.00 0.00 35.75 2.93
264 266 5.517770 ACGACGACCTTATTTGTTAGTATGC 59.482 40.000 0.00 0.00 0.00 3.14
267 269 5.323900 CGACGACGACCTTATTTGTTAGTA 58.676 41.667 0.00 0.00 42.66 1.82
268 270 4.161333 CGACGACGACCTTATTTGTTAGT 58.839 43.478 0.00 0.00 42.66 2.24
269 271 3.545078 CCGACGACGACCTTATTTGTTAG 59.455 47.826 9.28 0.00 42.66 2.34
290 292 8.739972 GGGATAATACCATTTCATTCATGTACC 58.260 37.037 0.00 0.00 0.00 3.34
315 317 7.775093 TGTCTTATTTCTCCATGAAGTTATGGG 59.225 37.037 0.00 0.00 46.16 4.00
335 342 4.495422 GCTGACCTTTCTCGAATGTCTTA 58.505 43.478 9.67 0.00 0.00 2.10
345 352 1.014564 CCGAACCGCTGACCTTTCTC 61.015 60.000 0.00 0.00 0.00 2.87
346 353 1.004918 CCGAACCGCTGACCTTTCT 60.005 57.895 0.00 0.00 0.00 2.52
347 354 1.005394 TCCGAACCGCTGACCTTTC 60.005 57.895 0.00 0.00 0.00 2.62
395 402 4.759782 ACAGTATATGGCACTCTGAACAC 58.240 43.478 13.94 0.00 0.00 3.32
400 407 6.344500 AGAAGAAACAGTATATGGCACTCTG 58.656 40.000 0.00 0.00 0.00 3.35
793 804 9.687210 CAGCATTCTATACATGTATGCATTTTT 57.313 29.630 25.48 6.11 42.98 1.94
830 1080 2.523015 CTGCCACGAGAAAAATCATGC 58.477 47.619 0.00 0.00 0.00 4.06
833 1083 1.536766 CTGCTGCCACGAGAAAAATCA 59.463 47.619 0.00 0.00 0.00 2.57
948 1800 1.137872 CCTCGGCTCTGCTATTCAACT 59.862 52.381 0.00 0.00 0.00 3.16
1066 1930 2.076863 AGTATCGTTTTCTGTGGCTGC 58.923 47.619 0.00 0.00 0.00 5.25
1136 2000 4.741781 CAAGCGCGAACTTGCCGG 62.742 66.667 12.10 0.00 40.53 6.13
1180 2044 5.239087 CGGGAGAGGTAGATGACTTACTAAC 59.761 48.000 0.00 0.00 0.00 2.34
1376 2243 0.804989 GTTACTGCTGGTGATGTGGC 59.195 55.000 0.00 0.00 0.00 5.01
1397 2264 0.396556 GGTGGAGGTGGTGTTGGTTT 60.397 55.000 0.00 0.00 0.00 3.27
1604 2522 2.055042 ACGCTGAAGGAGCCGAGAT 61.055 57.895 0.00 0.00 46.01 2.75
1605 2523 2.676822 ACGCTGAAGGAGCCGAGA 60.677 61.111 0.00 0.00 46.01 4.04
1707 2628 1.067084 CATCTGCATCGGCGACTCT 59.933 57.895 13.76 0.00 45.35 3.24
1752 2673 2.155065 CCCTCTGGTCTGTGGGTTT 58.845 57.895 6.78 0.00 36.35 3.27
1787 2708 2.738521 CCTCGCTGTTGTCCACGG 60.739 66.667 0.00 0.00 34.40 4.94
1791 2712 1.216710 CTCCTCCTCGCTGTTGTCC 59.783 63.158 0.00 0.00 0.00 4.02
2502 3453 2.564062 ACCTTCATTGGTGGCATTTGAG 59.436 45.455 0.00 0.00 39.17 3.02
2545 3496 3.509659 GCCCAAGTTGGCGTATCC 58.490 61.111 17.07 0.00 42.54 2.59
2554 3505 0.466555 TTTGTAGCACGGCCCAAGTT 60.467 50.000 0.00 0.00 0.00 2.66
2650 3604 2.689983 CACCTTCAAGCCTTTTCACTGT 59.310 45.455 0.00 0.00 0.00 3.55
2738 3692 3.181466 GCAGAAACCAACCAATTTCACCT 60.181 43.478 0.00 0.00 37.30 4.00
2819 3775 4.401202 TGTACCATTGCTCTCGAACAGATA 59.599 41.667 0.00 0.00 0.00 1.98
2869 3837 2.965831 TCTAGCAACTCCGATGGCTATT 59.034 45.455 0.00 0.00 38.11 1.73
2893 3861 4.623932 ACTCTGATGCAAGTAGGACAAA 57.376 40.909 0.00 0.00 0.00 2.83
3076 4044 2.967946 AACCCCGCTAAGCCACTCC 61.968 63.158 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.