Multiple sequence alignment - TraesCS1A01G129600

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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 TraesCS1A01G129600 chr1A 100.000 3698 0 0 1 3698 167149411 167153108 0.000000e+00 6830.0
1 TraesCS1A01G129600 chr1A 100.000 155 0 0 4006 4160 167153416 167153570 1.890000e-73 287.0
2 TraesCS1A01G129600 chr1D 96.122 3507 107 16 196 3693 136953613 136950127 0.000000e+00 5696.0
3 TraesCS1A01G129600 chr1D 90.995 211 10 3 3346 3556 23947883 23947682 4.100000e-70 276.0
4 TraesCS1A01G129600 chr1D 86.385 213 6 12 1 193 136953979 136953770 1.170000e-50 211.0
5 TraesCS1A01G129600 chr1D 96.552 116 4 0 4008 4123 136949836 136949721 4.240000e-45 193.0
6 TraesCS1A01G129600 chr1D 94.667 75 4 0 4049 4123 136950025 136949951 2.630000e-22 117.0
7 TraesCS1A01G129600 chr1D 97.917 48 1 0 4113 4160 136948143 136948096 2.670000e-12 84.2
8 TraesCS1A01G129600 chr1B 95.224 3287 98 19 441 3693 210211799 210208538 0.000000e+00 5145.0
9 TraesCS1A01G129600 chr1B 94.240 434 17 2 1 426 210212354 210211921 0.000000e+00 656.0
10 TraesCS1A01G129600 chr1B 96.732 153 5 0 4008 4160 210208153 210208001 5.340000e-64 255.0
11 TraesCS1A01G129600 chr3D 91.469 211 9 3 3346 3556 402476149 402476350 8.810000e-72 281.0
12 TraesCS1A01G129600 chr5D 90.995 211 10 3 3346 3556 55336716 55336917 4.100000e-70 276.0
13 TraesCS1A01G129600 chr7B 90.521 211 11 3 3346 3556 688014986 688014785 1.910000e-68 270.0
14 TraesCS1A01G129600 chr7B 92.810 153 11 0 4008 4160 91291843 91291995 5.410000e-54 222.0
15 TraesCS1A01G129600 chr7B 92.810 153 11 0 4008 4160 91294629 91294781 5.410000e-54 222.0
16 TraesCS1A01G129600 chr6D 90.521 211 11 3 3346 3556 117040913 117040712 1.910000e-68 270.0
17 TraesCS1A01G129600 chr4D 90.521 211 11 3 3346 3556 200997560 200997761 1.910000e-68 270.0
18 TraesCS1A01G129600 chr2D 90.521 211 11 3 3346 3556 8648027 8648228 1.910000e-68 270.0
19 TraesCS1A01G129600 chr7D 92.810 153 11 0 4008 4160 129973419 129973571 5.410000e-54 222.0
20 TraesCS1A01G129600 chr7A 92.810 153 11 0 4008 4160 129059342 129059494 5.410000e-54 222.0


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 TraesCS1A01G129600 chr1A 167149411 167153570 4159 False 3558.500000 6830 100.000000 1 4160 2 chr1A.!!$F1 4159
1 TraesCS1A01G129600 chr1D 136948096 136953979 5883 True 1260.240000 5696 94.328600 1 4160 5 chr1D.!!$R2 4159
2 TraesCS1A01G129600 chr1B 210208001 210212354 4353 True 2018.666667 5145 95.398667 1 4160 3 chr1B.!!$R1 4159
3 TraesCS1A01G129600 chr7B 91291843 91294781 2938 False 222.000000 222 92.810000 4008 4160 2 chr7B.!!$F1 152

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
801 1091 0.238289 CGTTTGCGGTCTTGCTGAAT 59.762 50.000 0.00 0.0 35.36 2.57 F
1353 1643 1.478916 GGTCTTCCAGTAGTGAGCTCC 59.521 57.143 12.15 2.4 0.00 4.70 F
2783 3108 2.699846 ACAGAAGGCATGGCAAGAAAAA 59.300 40.909 22.64 0.0 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2499 0.535102 AGAAGGCTGGTGTTTGGTCG 60.535 55.000 0.00 0.0 0.00 4.79 R
3069 3394 1.339151 GGATTCGTCTTGGGTGCTTCT 60.339 52.381 0.00 0.0 0.00 2.85 R
4006 4333 3.716431 ACGGTAGGTTCCTGATCCTAAA 58.284 45.455 5.72 0.0 37.94 1.85 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
231 408 8.512138 ACACAAATTAATAAGAGGGAAACGAAG 58.488 33.333 0.00 0.00 0.00 3.79
233 410 8.947115 ACAAATTAATAAGAGGGAAACGAAGAG 58.053 33.333 0.00 0.00 0.00 2.85
289 466 8.865090 ACTCAGGATCATTACATTAGTTAGAGG 58.135 37.037 0.00 0.00 0.00 3.69
366 549 3.783943 CGTTACGAATGGTAAGCAAATGC 59.216 43.478 0.00 0.00 41.61 3.56
381 564 3.425404 CAAATGCATCGGTCCTTTTACG 58.575 45.455 0.00 0.00 0.00 3.18
485 775 5.567138 AGTGAAGAACAAAAGACACCAAG 57.433 39.130 0.00 0.00 0.00 3.61
494 784 4.580580 ACAAAAGACACCAAGGATTCTCAC 59.419 41.667 0.00 0.00 0.00 3.51
801 1091 0.238289 CGTTTGCGGTCTTGCTGAAT 59.762 50.000 0.00 0.00 35.36 2.57
1079 1369 3.744660 ACTCCAACTAGTTTGCTTCCTG 58.255 45.455 5.07 0.00 33.34 3.86
1086 1376 7.286775 TCCAACTAGTTTGCTTCCTGTTTTAAT 59.713 33.333 5.07 0.00 33.34 1.40
1190 1480 7.938140 ACTCCTATGATCAGCTTAGAGTATC 57.062 40.000 12.37 0.00 0.00 2.24
1353 1643 1.478916 GGTCTTCCAGTAGTGAGCTCC 59.521 57.143 12.15 2.40 0.00 4.70
1469 1759 8.989980 ACGAGAGAAAAAGGTAAGTTATTTCTG 58.010 33.333 11.97 3.77 39.66 3.02
1500 1791 5.711506 TGTGATTCTGTTCCATTAGCATGTT 59.288 36.000 0.00 0.00 0.00 2.71
1516 1807 4.630069 AGCATGTTAGTAACTTTGCGGTAG 59.370 41.667 23.64 6.09 42.25 3.18
1689 2008 3.134458 GCTTCCCTGGACGAAATGATAG 58.866 50.000 0.00 0.00 0.00 2.08
1793 2118 9.507329 AGTGTCAATCAGATACTGTTAATTGTT 57.493 29.630 0.00 0.00 45.64 2.83
1938 2263 3.378427 GGGACCAGATGCTTCATTGTAAC 59.622 47.826 2.07 0.00 0.00 2.50
2174 2499 3.674997 TCTTGCTGAACCATGTAAGGAC 58.325 45.455 0.00 0.00 0.00 3.85
2606 2931 8.253113 ACAGAGAAAAGAACAACATGTTTCATT 58.747 29.630 8.77 3.73 41.28 2.57
2628 2953 8.858186 TCATTATAATGATTTGCAACAACGTTG 58.142 29.630 26.20 26.20 40.32 4.10
2661 2986 3.492421 AATGATCCACAAACGCATGTC 57.508 42.857 0.00 0.00 0.00 3.06
2783 3108 2.699846 ACAGAAGGCATGGCAAGAAAAA 59.300 40.909 22.64 0.00 0.00 1.94
2830 3155 6.766467 AGAAACAAGTTATCAGGACGAAAAGT 59.234 34.615 0.00 0.00 0.00 2.66
2936 3261 5.534207 TCCTTTTCTCACGGTTAGTACAA 57.466 39.130 0.00 0.00 0.00 2.41
3144 3469 6.331845 TGTAACTAGTCAAGACAACACGAAA 58.668 36.000 0.00 0.00 0.00 3.46
3172 3497 6.825721 ACAAAAGCCATAATCTGAGACCTAAG 59.174 38.462 0.00 0.00 0.00 2.18
3221 3546 2.612212 TCTTTTCGCTGGACAAAGTGTC 59.388 45.455 0.00 0.00 46.23 3.67
3358 3684 3.311106 CATGGTCACACATTGCAGAAAC 58.689 45.455 0.00 0.00 0.00 2.78
3389 3715 4.690748 GCATACACAGCTTGACTTGACTAA 59.309 41.667 3.37 0.00 0.00 2.24
3390 3716 5.389935 GCATACACAGCTTGACTTGACTAAC 60.390 44.000 3.37 0.00 0.00 2.34
3391 3717 4.137116 ACACAGCTTGACTTGACTAACA 57.863 40.909 3.37 0.00 0.00 2.41
3392 3718 4.122776 ACACAGCTTGACTTGACTAACAG 58.877 43.478 3.37 0.00 0.00 3.16
3393 3719 4.141937 ACACAGCTTGACTTGACTAACAGA 60.142 41.667 3.37 0.00 0.00 3.41
3394 3720 4.447054 CACAGCTTGACTTGACTAACAGAG 59.553 45.833 0.00 0.00 0.00 3.35
3395 3721 4.100189 ACAGCTTGACTTGACTAACAGAGT 59.900 41.667 0.00 0.00 42.90 3.24
3396 3722 5.302059 ACAGCTTGACTTGACTAACAGAGTA 59.698 40.000 0.00 0.00 39.06 2.59
3397 3723 6.183360 ACAGCTTGACTTGACTAACAGAGTAA 60.183 38.462 0.00 0.00 39.06 2.24
3553 3880 1.412710 GCCACATACTGCTAGCCACTA 59.587 52.381 13.29 0.00 0.00 2.74
3598 3925 2.868583 CGTAGATAAGCAGCAACAGCAT 59.131 45.455 0.00 0.00 0.00 3.79
3639 3966 6.500910 TCAATGCAGTTTATCTCAATCATGC 58.499 36.000 0.00 0.00 0.00 4.06
3640 3967 6.095720 TCAATGCAGTTTATCTCAATCATGCA 59.904 34.615 0.00 0.00 45.42 3.96
4026 4603 4.748277 TTTTAGGATCAGGAACCTACCG 57.252 45.455 4.95 0.00 38.31 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
366 549 2.389962 TTCCCGTAAAAGGACCGATG 57.610 50.000 0.00 0.00 31.50 3.84
381 564 3.435671 CACGGAACAGTTCTGTTATTCCC 59.564 47.826 23.08 12.66 46.80 3.97
404 587 8.488651 TGATGTATCATGCATCATTATCTGAC 57.511 34.615 13.92 0.00 45.18 3.51
1079 1369 7.099120 AGAAAAGACCATGATGGCATTAAAAC 58.901 34.615 12.25 0.00 42.67 2.43
1086 1376 2.231964 GCAAGAAAAGACCATGATGGCA 59.768 45.455 12.25 0.00 42.67 4.92
1353 1643 1.765314 AGAGTCCAATTCTCCCATCCG 59.235 52.381 0.00 0.00 32.93 4.18
1500 1791 7.496591 CCATATTTTCCTACCGCAAAGTTACTA 59.503 37.037 0.00 0.00 0.00 1.82
1516 1807 2.099756 GACACTGGCAGCCATATTTTCC 59.900 50.000 16.64 0.00 30.82 3.13
1689 2008 7.229506 AGGAGTAAATATGTGCTTATTGCTTCC 59.770 37.037 0.00 0.00 43.37 3.46
1804 2129 7.336931 AGGCCTCAGTACATGTTTTATGTTTAG 59.663 37.037 2.30 0.00 33.76 1.85
1805 2130 7.172342 AGGCCTCAGTACATGTTTTATGTTTA 58.828 34.615 2.30 0.00 33.76 2.01
1807 2132 5.570320 AGGCCTCAGTACATGTTTTATGTT 58.430 37.500 2.30 0.00 33.76 2.71
1809 2134 6.823689 AGTTAGGCCTCAGTACATGTTTTATG 59.176 38.462 9.68 0.00 0.00 1.90
1810 2135 6.958767 AGTTAGGCCTCAGTACATGTTTTAT 58.041 36.000 9.68 0.00 0.00 1.40
1811 2136 6.212791 AGAGTTAGGCCTCAGTACATGTTTTA 59.787 38.462 9.68 0.00 33.75 1.52
1812 2137 5.013183 AGAGTTAGGCCTCAGTACATGTTTT 59.987 40.000 9.68 0.00 33.75 2.43
1938 2263 7.406799 AAATGTTGCTTTTTCCAAATCGTAG 57.593 32.000 0.00 0.00 0.00 3.51
2050 2375 8.989131 AAGTATTCTTGTCCTTAGGCAACTATA 58.011 33.333 0.00 0.00 39.78 1.31
2095 2420 4.040339 TGCTCTTGTCCTTAGTCAATCACA 59.960 41.667 0.00 0.00 0.00 3.58
2174 2499 0.535102 AGAAGGCTGGTGTTTGGTCG 60.535 55.000 0.00 0.00 0.00 4.79
2339 2664 9.043079 GCCAGTTAAGTGTTAGGATTACTAATC 57.957 37.037 9.42 0.61 43.20 1.75
2606 2931 9.335891 CTTACAACGTTGTTGCAAATCATTATA 57.664 29.630 36.26 12.55 42.35 0.98
2628 2953 4.458989 TGTGGATCATTTTGTCAGGCTTAC 59.541 41.667 0.00 0.00 0.00 2.34
2783 3108 9.995003 TTTCTGCAATGTTGGATAAAAAGTTAT 57.005 25.926 0.00 0.00 32.36 1.89
2830 3155 2.957402 AGAAAGGCATGAACTCCACA 57.043 45.000 0.00 0.00 0.00 4.17
3069 3394 1.339151 GGATTCGTCTTGGGTGCTTCT 60.339 52.381 0.00 0.00 0.00 2.85
3144 3469 5.189180 GTCTCAGATTATGGCTTTTGTCCT 58.811 41.667 0.00 0.00 0.00 3.85
3172 3497 9.855021 AATGTATTTGTTACTCAAAATGGTAGC 57.145 29.630 0.00 0.00 46.97 3.58
3321 3647 2.519949 TGGGACATTGCAGCCACA 59.480 55.556 0.00 0.00 0.00 4.17
3358 3684 6.453943 AGTCAAGCTGTGTATGCATATCTAG 58.546 40.000 10.16 9.28 0.00 2.43
3389 3715 4.100963 TGAACACATCCACTGTTACTCTGT 59.899 41.667 0.00 0.00 35.29 3.41
3390 3716 4.449068 GTGAACACATCCACTGTTACTCTG 59.551 45.833 0.00 0.00 35.29 3.35
3391 3717 4.100963 TGTGAACACATCCACTGTTACTCT 59.899 41.667 3.39 0.00 35.29 3.24
3392 3718 4.377021 TGTGAACACATCCACTGTTACTC 58.623 43.478 3.39 0.00 35.29 2.59
3393 3719 4.380531 CTGTGAACACATCCACTGTTACT 58.619 43.478 8.09 0.00 41.01 2.24
3394 3720 3.498397 CCTGTGAACACATCCACTGTTAC 59.502 47.826 8.09 0.00 41.01 2.50
3395 3721 3.495983 CCCTGTGAACACATCCACTGTTA 60.496 47.826 8.09 0.00 41.01 2.41
3396 3722 2.575532 CCTGTGAACACATCCACTGTT 58.424 47.619 8.09 0.00 41.01 3.16
3397 3723 1.202806 CCCTGTGAACACATCCACTGT 60.203 52.381 8.09 0.00 41.01 3.55
3497 3824 9.485591 GTGGTTCATTAATCAACAGTAAATACG 57.514 33.333 4.53 0.00 0.00 3.06
3573 3900 4.034510 GCTGTTGCTGCTTATCTACGAATT 59.965 41.667 0.00 0.00 36.03 2.17
3588 3915 4.000325 TCGTACATAAACATGCTGTTGCT 59.000 39.130 0.00 0.00 40.14 3.91
3598 3925 8.888716 ACTGCATTGAATATTCGTACATAAACA 58.111 29.630 10.80 1.83 0.00 2.83
3617 3944 6.459670 TGCATGATTGAGATAAACTGCATT 57.540 33.333 0.00 0.00 33.80 3.56
4005 4332 4.098894 ACGGTAGGTTCCTGATCCTAAAA 58.901 43.478 5.72 0.00 37.94 1.52
4006 4333 3.716431 ACGGTAGGTTCCTGATCCTAAA 58.284 45.455 5.72 0.00 37.94 1.85


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

AutoCloner maintained by Alex Coulton.