Multiple sequence alignment - TraesCS7A01G044700

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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 TraesCS7A01G044700 chr7A 100.000 3647 0 0 1 3647 20554131 20557777 0.000000e+00 6735.0
1 TraesCS7A01G044700 chr7A 88.835 3699 307 49 1 3647 20481834 20485478 0.000000e+00 4446.0
2 TraesCS7A01G044700 chr7A 86.086 3694 414 40 1 3640 20587754 20591401 0.000000e+00 3882.0
3 TraesCS7A01G044700 chr7A 89.141 3085 288 23 580 3647 20965898 20968952 0.000000e+00 3797.0
4 TraesCS7A01G044700 chr7A 87.367 2818 306 26 852 3645 20650684 20653475 0.000000e+00 3186.0
5 TraesCS7A01G044700 chr7A 84.066 3025 418 35 648 3640 20980270 20983262 0.000000e+00 2857.0
6 TraesCS7A01G044700 chr7A 83.660 3109 431 47 572 3640 20705454 20708525 0.000000e+00 2856.0
7 TraesCS7A01G044700 chr7A 84.843 2771 382 20 894 3647 20910611 20913360 0.000000e+00 2756.0
8 TraesCS7A01G044700 chr7A 86.165 2566 307 23 1099 3647 20457863 20460397 0.000000e+00 2728.0
9 TraesCS7A01G044700 chr7A 83.428 2806 414 35 872 3647 20676374 20679158 0.000000e+00 2558.0
10 TraesCS7A01G044700 chr7A 88.382 241 16 6 1 240 20643372 20643601 2.770000e-71 279.0
11 TraesCS7A01G044700 chr7A 87.552 241 16 6 1 240 20585746 20585973 2.160000e-67 267.0
12 TraesCS7A01G044700 chr7A 86.364 242 19 5 1 239 20453672 20453902 6.050000e-63 252.0
13 TraesCS7A01G044700 chr7A 81.405 242 27 12 2 240 20699066 20699292 8.040000e-42 182.0
14 TraesCS7A01G044700 chr7A 100.000 41 0 0 527 567 20482396 20482436 3.910000e-10 76.8
15 TraesCS7A01G044700 chr7A 100.000 41 0 0 572 612 20554657 20554697 3.910000e-10 76.8
16 TraesCS7A01G044700 chr7A 100.000 41 0 0 527 567 20554702 20554742 3.910000e-10 76.8
17 TraesCS7A01G044700 chr7A 100.000 39 0 0 572 610 20588301 20588339 5.050000e-09 73.1
18 TraesCS7A01G044700 chr7D 94.370 3659 183 5 1 3647 20309877 20313524 0.000000e+00 5594.0
19 TraesCS7A01G044700 chr7D 87.851 2774 300 18 894 3647 20485536 20488292 0.000000e+00 3221.0
20 TraesCS7A01G044700 chr7D 82.763 2866 442 28 816 3647 20946973 20949820 0.000000e+00 2508.0
21 TraesCS7A01G044700 chr7D 85.732 785 97 9 2540 3320 20522757 20523530 0.000000e+00 815.0
22 TraesCS7A01G044700 chr7D 76.923 247 34 9 25 260 20306282 20306516 6.400000e-23 119.0
23 TraesCS7A01G044700 chr7D 100.000 41 0 0 527 567 20310448 20310488 3.910000e-10 76.8
24 TraesCS7A01G044700 chr7D 100.000 39 0 0 572 610 20310403 20310441 5.050000e-09 73.1
25 TraesCS7A01G044700 chr4A 87.984 2555 260 27 1117 3640 669371415 669373953 0.000000e+00 2974.0
26 TraesCS7A01G044700 chr4A 86.657 2698 309 27 975 3647 713032313 713034984 0.000000e+00 2940.0
27 TraesCS7A01G044700 chr4A 85.915 2776 335 27 894 3647 713014728 713017469 0.000000e+00 2909.0
28 TraesCS7A01G044700 chr4A 87.512 1057 78 17 103 1123 669351659 669352697 0.000000e+00 1171.0
29 TraesCS7A01G044700 chr4A 100.000 39 0 0 572 610 669352100 669352138 5.050000e-09 73.1
30 TraesCS7A01G044700 chr2D 82.774 3071 470 32 610 3647 598813706 598816750 0.000000e+00 2686.0


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 TraesCS7A01G044700 chr7A 20554131 20557777 3646 False 2296.200000 6735 100.000000 1 3647 3 chr7A.!!$F11 3646
1 TraesCS7A01G044700 chr7A 20965898 20968952 3054 False 3797.000000 3797 89.141000 580 3647 1 chr7A.!!$F7 3067
2 TraesCS7A01G044700 chr7A 20650684 20653475 2791 False 3186.000000 3186 87.367000 852 3645 1 chr7A.!!$F2 2793
3 TraesCS7A01G044700 chr7A 20980270 20983262 2992 False 2857.000000 2857 84.066000 648 3640 1 chr7A.!!$F8 2992
4 TraesCS7A01G044700 chr7A 20705454 20708525 3071 False 2856.000000 2856 83.660000 572 3640 1 chr7A.!!$F5 3068
5 TraesCS7A01G044700 chr7A 20910611 20913360 2749 False 2756.000000 2756 84.843000 894 3647 1 chr7A.!!$F6 2753
6 TraesCS7A01G044700 chr7A 20676374 20679158 2784 False 2558.000000 2558 83.428000 872 3647 1 chr7A.!!$F3 2775
7 TraesCS7A01G044700 chr7A 20481834 20485478 3644 False 2261.400000 4446 94.417500 1 3647 2 chr7A.!!$F10 3646
8 TraesCS7A01G044700 chr7A 20453672 20460397 6725 False 1490.000000 2728 86.264500 1 3647 2 chr7A.!!$F9 3646
9 TraesCS7A01G044700 chr7A 20585746 20591401 5655 False 1407.366667 3882 91.212667 1 3640 3 chr7A.!!$F12 3639
10 TraesCS7A01G044700 chr7D 20485536 20488292 2756 False 3221.000000 3221 87.851000 894 3647 1 chr7D.!!$F1 2753
11 TraesCS7A01G044700 chr7D 20946973 20949820 2847 False 2508.000000 2508 82.763000 816 3647 1 chr7D.!!$F3 2831
12 TraesCS7A01G044700 chr7D 20306282 20313524 7242 False 1465.725000 5594 92.823250 1 3647 4 chr7D.!!$F4 3646
13 TraesCS7A01G044700 chr7D 20522757 20523530 773 False 815.000000 815 85.732000 2540 3320 1 chr7D.!!$F2 780
14 TraesCS7A01G044700 chr4A 669371415 669373953 2538 False 2974.000000 2974 87.984000 1117 3640 1 chr4A.!!$F1 2523
15 TraesCS7A01G044700 chr4A 713032313 713034984 2671 False 2940.000000 2940 86.657000 975 3647 1 chr4A.!!$F3 2672
16 TraesCS7A01G044700 chr4A 713014728 713017469 2741 False 2909.000000 2909 85.915000 894 3647 1 chr4A.!!$F2 2753
17 TraesCS7A01G044700 chr4A 669351659 669352697 1038 False 622.050000 1171 93.756000 103 1123 2 chr4A.!!$F4 1020
18 TraesCS7A01G044700 chr2D 598813706 598816750 3044 False 2686.000000 2686 82.774000 610 3647 1 chr2D.!!$F1 3037

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
216 5263 1.917872 TAGTTGCCGCCCATTCTTTT 58.082 45.000 0.00 0.00 0.00 2.27 F
507 5585 2.514803 CGGATTGGTTCCCTCTTTGTT 58.485 47.619 0.00 0.00 42.06 2.83 F
1128 7306 1.765314 CTGGAGCTACAGGGTAGCATT 59.235 52.381 25.15 9.85 42.68 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 7306 3.164977 TCCCTGGCAACACGACCA 61.165 61.111 0.0 0.0 46.17 4.02 R
1375 7555 3.325135 TCTTTCTCCAGTTCCTTCACTCC 59.675 47.826 0.0 0.0 0.00 3.85 R
2835 9052 1.467678 CCCCGCAAACCCAAATGACA 61.468 55.000 0.0 0.0 0.00 3.58 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
79 85 8.184192 AGTATACTTTGTGACTTAATGCATTGC 58.816 33.333 22.27 0.46 0.00 3.56
80 86 5.199024 ACTTTGTGACTTAATGCATTGCA 57.801 34.783 22.27 14.72 44.86 4.08
124 131 7.402054 TCCTAAGCACAATAAAGATTTCTCCA 58.598 34.615 0.00 0.00 0.00 3.86
129 136 6.376581 AGCACAATAAAGATTTCTCCAGGAAG 59.623 38.462 0.00 0.00 35.16 3.46
130 137 6.405176 GCACAATAAAGATTTCTCCAGGAAGG 60.405 42.308 0.00 0.00 35.16 3.46
131 138 6.660949 CACAATAAAGATTTCTCCAGGAAGGT 59.339 38.462 0.00 0.00 39.02 3.50
132 139 6.887002 ACAATAAAGATTTCTCCAGGAAGGTC 59.113 38.462 0.00 0.00 39.02 3.85
133 140 6.899892 ATAAAGATTTCTCCAGGAAGGTCT 57.100 37.500 0.00 0.00 39.02 3.85
152 159 4.640647 GGTCTGGCCGATCTTCTTAATTTT 59.359 41.667 0.00 0.00 0.00 1.82
187 194 2.426024 GTCTGGCGAGTGTGAAGGTATA 59.574 50.000 0.00 0.00 0.00 1.47
192 199 4.100963 TGGCGAGTGTGAAGGTATATTCAT 59.899 41.667 0.00 0.00 41.05 2.57
216 5263 1.917872 TAGTTGCCGCCCATTCTTTT 58.082 45.000 0.00 0.00 0.00 2.27
431 5509 8.343168 TGGAACTAAGTTACCCATAACATTTG 57.657 34.615 0.44 0.00 42.83 2.32
507 5585 2.514803 CGGATTGGTTCCCTCTTTGTT 58.485 47.619 0.00 0.00 42.06 2.83
565 5643 5.069648 CCTGAGATGTTCCTATACAGAAGCA 59.930 44.000 0.00 0.00 0.00 3.91
837 6102 6.491745 TGCTTACACTTTTCCATTATGGTTGA 59.508 34.615 11.39 0.00 39.03 3.18
1128 7306 1.765314 CTGGAGCTACAGGGTAGCATT 59.235 52.381 25.15 9.85 42.68 3.56
1375 7555 6.653273 TTTGTTTGAATCAGATAGCTCTCG 57.347 37.500 0.00 0.00 0.00 4.04
2024 8213 4.439253 AAGCTTTACCAGAAGACAAGGT 57.561 40.909 0.00 0.00 39.41 3.50
2025 8214 3.744660 AGCTTTACCAGAAGACAAGGTG 58.255 45.455 0.00 0.00 36.87 4.00
2048 8237 6.486993 GTGTGGGATCTCTTTTGTAAGAAAGT 59.513 38.462 0.00 0.00 39.80 2.66
2056 8245 8.438676 TCTCTTTTGTAAGAAAGTCTTTCCAG 57.561 34.615 19.58 6.82 39.80 3.86
2128 8317 0.961753 AGTTAGCAAGTGCAAAGGCC 59.038 50.000 6.00 0.00 45.16 5.19
2215 8404 5.945784 TGGAGAAGAATAAATGACCAACTGG 59.054 40.000 0.00 0.00 42.17 4.00
2256 8445 2.176045 TCAAGGCTGGACGACATAAGA 58.824 47.619 0.00 0.00 0.00 2.10
2322 8511 6.575162 AAAAGTTGTTTCCTATACTGCAGG 57.425 37.500 19.93 0.00 34.20 4.85
2340 8529 3.440522 GCAGGTTATTTCCAGAAGACCAC 59.559 47.826 10.40 2.16 0.00 4.16
2586 8775 6.037610 GCTTTGGTGTTAGTTATGAGGATGAG 59.962 42.308 0.00 0.00 0.00 2.90
2587 8776 6.620877 TTGGTGTTAGTTATGAGGATGAGT 57.379 37.500 0.00 0.00 0.00 3.41
2588 8777 5.977635 TGGTGTTAGTTATGAGGATGAGTG 58.022 41.667 0.00 0.00 0.00 3.51
2589 8778 5.483937 TGGTGTTAGTTATGAGGATGAGTGT 59.516 40.000 0.00 0.00 0.00 3.55
2590 8779 5.812642 GGTGTTAGTTATGAGGATGAGTGTG 59.187 44.000 0.00 0.00 0.00 3.82
2591 8780 5.812642 GTGTTAGTTATGAGGATGAGTGTGG 59.187 44.000 0.00 0.00 0.00 4.17
2592 8781 5.104941 TGTTAGTTATGAGGATGAGTGTGGG 60.105 44.000 0.00 0.00 0.00 4.61
2593 8782 2.774234 AGTTATGAGGATGAGTGTGGGG 59.226 50.000 0.00 0.00 0.00 4.96
2596 8785 3.017581 AGGATGAGTGTGGGGGCC 61.018 66.667 0.00 0.00 0.00 5.80
2749 8966 5.126067 CACCTTACTACCTTTGCTATGCAT 58.874 41.667 3.79 3.79 38.76 3.96
2835 9052 7.586349 TGCTATTGGGGATCTTTTTAATCTCT 58.414 34.615 0.00 0.00 0.00 3.10
3007 9224 5.775686 TGCTCAGAAAACAATTGATCCAAG 58.224 37.500 13.59 8.45 0.00 3.61
3203 9420 6.554334 AGAAGTATCAGCGAATCTCTAGTC 57.446 41.667 0.00 0.00 0.00 2.59
3333 9562 0.467290 AGCGGATGAGTCTCCTCTCC 60.467 60.000 5.28 4.60 38.61 3.71
3423 9652 0.035439 GCCATCCCTTTCTCGGTTGA 60.035 55.000 0.00 0.00 0.00 3.18
3580 9813 1.454479 CCATGGCGAGCCTGGAAAT 60.454 57.895 20.55 3.04 36.89 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 85 3.518590 GAAGCTGGAAGAAATGGCAATG 58.481 45.455 0.00 0.00 34.07 2.82
80 86 2.498885 GGAAGCTGGAAGAAATGGCAAT 59.501 45.455 0.00 0.00 34.07 3.56
81 87 1.895131 GGAAGCTGGAAGAAATGGCAA 59.105 47.619 0.00 0.00 34.07 4.52
82 88 1.076024 AGGAAGCTGGAAGAAATGGCA 59.924 47.619 0.00 0.00 34.07 4.92
83 89 1.844687 AGGAAGCTGGAAGAAATGGC 58.155 50.000 0.00 0.00 34.07 4.40
124 131 0.618968 AAGATCGGCCAGACCTTCCT 60.619 55.000 2.24 0.00 35.61 3.36
129 136 2.981859 TTAAGAAGATCGGCCAGACC 57.018 50.000 2.24 0.00 0.00 3.85
130 137 5.819825 AAAATTAAGAAGATCGGCCAGAC 57.180 39.130 2.24 0.00 0.00 3.51
131 138 5.943416 TCAAAAATTAAGAAGATCGGCCAGA 59.057 36.000 2.24 0.78 0.00 3.86
132 139 6.030228 GTCAAAAATTAAGAAGATCGGCCAG 58.970 40.000 2.24 0.00 0.00 4.85
133 140 5.475220 TGTCAAAAATTAAGAAGATCGGCCA 59.525 36.000 2.24 0.00 0.00 5.36
152 159 2.051334 CCAGACCTTGGTGTTGTCAA 57.949 50.000 0.00 0.00 42.41 3.18
187 194 2.094234 GGGCGGCAACTAAAACATGAAT 60.094 45.455 12.47 0.00 0.00 2.57
192 199 1.271102 GAATGGGCGGCAACTAAAACA 59.729 47.619 12.47 0.00 0.00 2.83
216 5263 9.177608 CTACAGATTAATTTGTGAATCCAAGGA 57.822 33.333 19.13 0.00 33.34 3.36
286 5364 7.823149 ACTGCAATCAAGAAAATGAATAAGC 57.177 32.000 0.00 0.00 32.06 3.09
399 5477 6.321821 TGGGTAACTTAGTTCCATGCTTAT 57.678 37.500 0.00 0.00 0.00 1.73
431 5509 8.723942 TTCATTTTCAGAGAGTTAGCTAATCC 57.276 34.615 9.88 4.80 0.00 3.01
459 5537 3.934579 CCTGCCAGATTGCCAAAATAAAC 59.065 43.478 0.00 0.00 0.00 2.01
565 5643 4.597075 AGGTTAAAATGCCCCAAACTCAAT 59.403 37.500 0.00 0.00 0.00 2.57
837 6102 5.146010 TGCCAAAACACTTCAAAACTCTT 57.854 34.783 0.00 0.00 0.00 2.85
916 6199 7.232118 TCAGTATCATCAGAAAGTTCACTGA 57.768 36.000 12.79 12.79 45.19 3.41
1128 7306 3.164977 TCCCTGGCAACACGACCA 61.165 61.111 0.00 0.00 46.17 4.02
1375 7555 3.325135 TCTTTCTCCAGTTCCTTCACTCC 59.675 47.826 0.00 0.00 0.00 3.85
2024 8213 6.601332 ACTTTCTTACAAAAGAGATCCCACA 58.399 36.000 3.56 0.00 42.60 4.17
2025 8214 6.937465 AGACTTTCTTACAAAAGAGATCCCAC 59.063 38.462 3.56 0.00 42.60 4.61
2048 8237 7.199167 TCATGATTTGTATCTCCTGGAAAGA 57.801 36.000 0.00 0.00 0.00 2.52
2056 8245 7.933577 TGTAGGACATTCATGATTTGTATCTCC 59.066 37.037 10.78 8.48 0.00 3.71
2215 8404 6.959639 TGAATTGTTAATTATCTCCCAGCC 57.040 37.500 0.00 0.00 0.00 4.85
2256 8445 5.204409 TGAAGCTCAGATGCAAAACATTT 57.796 34.783 0.00 0.00 39.84 2.32
2322 8511 6.590234 AAATGGTGGTCTTCTGGAAATAAC 57.410 37.500 0.00 0.00 0.00 1.89
2340 8529 8.536407 CGTACAAGTTGTTTCCTTTTAAAATGG 58.464 33.333 14.90 5.71 0.00 3.16
2749 8966 7.117285 AGCACTGTCATATATCTTGACTTCA 57.883 36.000 15.78 1.03 43.12 3.02
2835 9052 1.467678 CCCCGCAAACCCAAATGACA 61.468 55.000 0.00 0.00 0.00 3.58
3007 9224 2.399916 ACTTGCAAGCTCTCTCCATC 57.600 50.000 26.27 0.00 0.00 3.51
3203 9420 3.129287 GGTTGGACAAATACTGCATCTGG 59.871 47.826 0.00 0.00 0.00 3.86
3580 9813 7.042335 GCTTCTGAGGTTGCTTAAGACTAATA 58.958 38.462 6.67 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.