Multiple sequence alignment - TraesCS7A01G296600

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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 TraesCS7A01G296600 chr7A 100.000 4729 0 0 1 4729 395513525 395518253 0.000000e+00 8733
1 TraesCS7A01G296600 chr6A 97.146 4730 132 3 1 4729 307922646 307917919 0.000000e+00 7984
2 TraesCS7A01G296600 chr6A 94.717 1060 50 4 7 1062 592961294 592960237 0.000000e+00 1642
3 TraesCS7A01G296600 chr5A 96.638 4729 131 2 1 4729 213046759 213051459 0.000000e+00 7827
4 TraesCS7A01G296600 chr5A 97.269 3954 108 0 776 4729 631069218 631065265 0.000000e+00 6704
5 TraesCS7A01G296600 chr5A 89.773 1408 114 16 3236 4632 489495713 489494325 0.000000e+00 1775
6 TraesCS7A01G296600 chr5A 91.667 192 9 6 4539 4729 420432966 420432781 4.690000e-65 259
7 TraesCS7A01G296600 chr1A 96.581 4738 126 4 1 4729 236391030 236395740 0.000000e+00 7819
8 TraesCS7A01G296600 chr3B 96.364 4730 169 3 1 4729 817686345 817691072 0.000000e+00 7779
9 TraesCS7A01G296600 chr3B 96.553 3974 136 1 756 4729 817710255 817714227 0.000000e+00 6578
10 TraesCS7A01G296600 chr3B 97.129 3309 91 3 761 4066 745188 748495 0.000000e+00 5581
11 TraesCS7A01G296600 chr3B 95.382 1494 57 3 1 1494 784352508 784351027 0.000000e+00 2366
12 TraesCS7A01G296600 chr7B 95.983 4730 188 2 1 4729 695576177 695571449 0.000000e+00 7681
13 TraesCS7A01G296600 chr6B 95.917 4727 190 3 1 4726 83866046 83870770 0.000000e+00 7657
14 TraesCS7A01G296600 chr2B 87.793 1065 97 10 1 1062 318192684 318193718 0.000000e+00 1216


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 TraesCS7A01G296600 chr7A 395513525 395518253 4728 False 8733 8733 100.000 1 4729 1 chr7A.!!$F1 4728
1 TraesCS7A01G296600 chr6A 307917919 307922646 4727 True 7984 7984 97.146 1 4729 1 chr6A.!!$R1 4728
2 TraesCS7A01G296600 chr6A 592960237 592961294 1057 True 1642 1642 94.717 7 1062 1 chr6A.!!$R2 1055
3 TraesCS7A01G296600 chr5A 213046759 213051459 4700 False 7827 7827 96.638 1 4729 1 chr5A.!!$F1 4728
4 TraesCS7A01G296600 chr5A 631065265 631069218 3953 True 6704 6704 97.269 776 4729 1 chr5A.!!$R3 3953
5 TraesCS7A01G296600 chr5A 489494325 489495713 1388 True 1775 1775 89.773 3236 4632 1 chr5A.!!$R2 1396
6 TraesCS7A01G296600 chr1A 236391030 236395740 4710 False 7819 7819 96.581 1 4729 1 chr1A.!!$F1 4728
7 TraesCS7A01G296600 chr3B 817686345 817691072 4727 False 7779 7779 96.364 1 4729 1 chr3B.!!$F2 4728
8 TraesCS7A01G296600 chr3B 817710255 817714227 3972 False 6578 6578 96.553 756 4729 1 chr3B.!!$F3 3973
9 TraesCS7A01G296600 chr3B 745188 748495 3307 False 5581 5581 97.129 761 4066 1 chr3B.!!$F1 3305
10 TraesCS7A01G296600 chr3B 784351027 784352508 1481 True 2366 2366 95.382 1 1494 1 chr3B.!!$R1 1493
11 TraesCS7A01G296600 chr7B 695571449 695576177 4728 True 7681 7681 95.983 1 4729 1 chr7B.!!$R1 4728
12 TraesCS7A01G296600 chr6B 83866046 83870770 4724 False 7657 7657 95.917 1 4726 1 chr6B.!!$F1 4725
13 TraesCS7A01G296600 chr2B 318192684 318193718 1034 False 1216 1216 87.793 1 1062 1 chr2B.!!$F1 1061

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
531 541 1.335964 CGCGGATCGTGGATAATCACT 60.336 52.381 0.00 0.00 35.63 3.41 F
1082 1126 0.623194 TCCAATTTGGCCATCTCCGA 59.377 50.000 6.09 0.00 37.47 4.55 F
1988 2032 1.531365 TACCACCACGTTCTCGGGT 60.531 57.895 0.00 0.00 39.02 5.28 F
3068 3114 1.537202 CTGTTTGTCCTGCAGGTTAGC 59.463 52.381 31.58 19.59 36.34 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 2348 0.316442 CGGCACATATTCTGCAAGCG 60.316 55.0 4.83 0.0 36.27 4.68 R
2963 3009 0.588252 CCAGTTGGTTCTCACAAGCG 59.412 55.0 0.00 0.0 0.00 4.68 R
3447 3521 0.037697 TTGTAGTCGAAGCCGCACAT 60.038 50.0 0.00 0.0 35.37 3.21 R
4118 4199 1.148310 CACGTCTTCGCACTTCCAAT 58.852 50.0 0.00 0.0 41.18 3.16 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
59 60 5.467705 CAAACTACGAGGTAGCTACAGTTT 58.532 41.667 23.45 23.45 39.51 2.66
76 77 3.911964 CAGTTTAAATTTGACCCGCTTCG 59.088 43.478 0.00 0.00 0.00 3.79
337 340 9.665264 GTCTTATTTCGATTTGTGATTATTCCC 57.335 33.333 0.00 0.00 0.00 3.97
361 364 7.042119 CCCGAAAACTAAATTCAAATTTGCTGT 60.042 33.333 13.54 1.33 38.90 4.40
378 383 3.115554 GCTGTCACAATGCGAAGTTTTT 58.884 40.909 0.00 0.00 0.00 1.94
531 541 1.335964 CGCGGATCGTGGATAATCACT 60.336 52.381 0.00 0.00 35.63 3.41
618 628 1.682684 GCACCCTTCTCTCCCTCGA 60.683 63.158 0.00 0.00 0.00 4.04
624 634 2.383855 CCTTCTCTCCCTCGAACTGAT 58.616 52.381 0.00 0.00 0.00 2.90
668 681 3.299503 TCCGATCTGATCTGAATCCACA 58.700 45.455 15.16 0.00 0.00 4.17
840 853 2.271173 CCGCCACCCCTAACTTCC 59.729 66.667 0.00 0.00 0.00 3.46
843 856 1.550130 CGCCACCCCTAACTTCCTCA 61.550 60.000 0.00 0.00 0.00 3.86
992 1036 2.042842 TCAACATGGTTGTGGATGGGAT 59.957 45.455 8.75 0.00 35.83 3.85
1082 1126 0.623194 TCCAATTTGGCCATCTCCGA 59.377 50.000 6.09 0.00 37.47 4.55
1131 1175 4.096003 CCCCTCACCGTCGGCAAT 62.096 66.667 12.28 0.00 0.00 3.56
1234 1278 4.981674 CCATGTATTGTTGCGACTTTGTTT 59.018 37.500 5.50 0.00 0.00 2.83
1291 1335 2.184020 CTGATGGAACTGGTGCCCGA 62.184 60.000 0.00 0.00 0.00 5.14
1559 1603 4.365514 TTCAGCCTGAGTATTTTGGTGA 57.634 40.909 0.00 0.00 0.00 4.02
1786 1830 1.661341 CTCCTGGACATGCAGTTAGC 58.339 55.000 0.00 0.00 45.96 3.09
1988 2032 1.531365 TACCACCACGTTCTCGGGT 60.531 57.895 0.00 0.00 39.02 5.28
1999 2043 2.032071 CTCGGGTTTCCAAGGCGT 59.968 61.111 0.00 0.00 0.00 5.68
2302 2348 5.444481 CGTTTGTATTTGCAAATTAGCAGCC 60.444 40.000 28.45 16.22 46.54 4.85
2490 2536 4.481368 ACACTAGTTGAGTTTGACCACA 57.519 40.909 0.00 0.00 35.64 4.17
2656 2702 3.942829 AGTTGATTCTTTGATGGAGCGA 58.057 40.909 0.00 0.00 0.00 4.93
3048 3094 2.891191 TGTTCCTTTACCCATGGTCC 57.109 50.000 11.73 0.00 37.09 4.46
3068 3114 1.537202 CTGTTTGTCCTGCAGGTTAGC 59.463 52.381 31.58 19.59 36.34 3.09
3334 3380 3.146104 ACTTGTATTTGCTCCTGCTGT 57.854 42.857 0.00 0.00 40.48 4.40
3397 3443 2.233922 CCTTGTACCAGATGAGTCCGTT 59.766 50.000 0.00 0.00 0.00 4.44
3800 3874 8.557864 CAATCAATTTTTGGTGTGCTCAAATTA 58.442 29.630 0.00 0.00 34.58 1.40
3888 3962 1.958288 AGTGGCCTCCTGACTTGTAT 58.042 50.000 3.32 0.00 0.00 2.29
4010 4091 9.366216 GAACTTGTTCTAACTGGAAACAATTTT 57.634 29.630 6.28 0.00 42.06 1.82
4118 4199 1.282157 GGAGCTCCAGGCCTAAGAAAA 59.718 52.381 28.43 0.00 43.05 2.29
4171 4252 0.038159 GCCGTGAAGTGCTACTCAGT 60.038 55.000 0.00 0.00 0.00 3.41
4551 4632 3.897505 GCCCATGTAGCCCAATAGAATTT 59.102 43.478 0.00 0.00 0.00 1.82
4642 4724 1.135199 GGCTGAATCTTGTGCCACATG 60.135 52.381 0.00 0.49 44.34 3.21
4665 4747 2.590007 GCCACGCTGGATGCCTAG 60.590 66.667 8.04 0.00 40.96 3.02
4697 4779 3.211045 GAGGTTGCTAGTGACCAAAACA 58.789 45.455 15.96 0.00 38.42 2.83
4698 4780 3.214328 AGGTTGCTAGTGACCAAAACAG 58.786 45.455 15.96 0.00 38.42 3.16
4699 4781 3.118038 AGGTTGCTAGTGACCAAAACAGA 60.118 43.478 15.96 0.00 38.42 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 1.735571 GCTCGAAGCGGGTCAAATTTA 59.264 47.619 0.00 0.00 0.00 1.40
76 77 3.989817 ACAAATTTTTGCCGATTCAGCTC 59.010 39.130 3.00 0.00 41.79 4.09
321 324 9.849166 TTTAGTTTTCGGGAATAATCACAAATC 57.151 29.630 0.00 0.00 0.00 2.17
337 340 8.538856 TGACAGCAAATTTGAATTTAGTTTTCG 58.461 29.630 22.31 0.00 36.52 3.46
618 628 0.043940 AGGAGAGAGGGGCATCAGTT 59.956 55.000 0.00 0.00 0.00 3.16
624 634 2.693017 GGAGAGGAGAGAGGGGCA 59.307 66.667 0.00 0.00 0.00 5.36
840 853 1.590932 CGGATTTGGCAGATCCTGAG 58.409 55.000 28.33 13.87 40.76 3.35
992 1036 2.710902 CCTCCTGCCATCGTCGTCA 61.711 63.158 0.00 0.00 0.00 4.35
1082 1126 0.541764 GAGGATCTGGAGGAGGCGAT 60.542 60.000 0.00 0.00 0.00 4.58
1131 1175 0.331278 CCTTGGCATGGTTCCAGGTA 59.669 55.000 11.13 0.00 34.66 3.08
1291 1335 2.931320 GCCAAGCTGTACTACTCGCTTT 60.931 50.000 11.33 0.14 40.43 3.51
1593 1637 4.020928 TGACAACGGACTAAAAGATGCCTA 60.021 41.667 0.00 0.00 0.00 3.93
1786 1830 4.902443 TCTTCGCTAAGACAGATACAGG 57.098 45.455 0.00 0.00 36.80 4.00
1988 2032 3.294493 GCTGGCACGCCTTGGAAA 61.294 61.111 9.92 0.00 36.94 3.13
2071 2115 4.345257 GGGTTGAGATAATAGCAGGAGACA 59.655 45.833 0.00 0.00 0.00 3.41
2302 2348 0.316442 CGGCACATATTCTGCAAGCG 60.316 55.000 4.83 0.00 36.27 4.68
2460 2506 9.419297 GTCAAACTCAACTAGTGTAATGTATCA 57.581 33.333 0.00 0.00 38.88 2.15
2480 2526 1.404035 GGAGTTGGTGTGTGGTCAAAC 59.596 52.381 0.00 0.00 0.00 2.93
2490 2536 2.799126 TCACTTGTTGGAGTTGGTGT 57.201 45.000 0.00 0.00 0.00 4.16
2656 2702 3.510360 ACTACTGTTCCACGCAGTCTTAT 59.490 43.478 0.95 0.00 44.96 1.73
2963 3009 0.588252 CCAGTTGGTTCTCACAAGCG 59.412 55.000 0.00 0.00 0.00 4.68
3048 3094 1.537202 GCTAACCTGCAGGACAAACAG 59.463 52.381 39.19 23.03 38.94 3.16
3068 3114 1.067749 CTCCTCCTGATGCTGCTCG 59.932 63.158 0.00 0.00 0.00 5.03
3270 3316 4.202441 CACTAGGCAATCCAGTAGCAATT 58.798 43.478 0.00 0.00 33.74 2.32
3334 3380 4.216042 ACACTCATGATCATCAAAACGCAA 59.784 37.500 4.86 0.00 0.00 4.85
3397 3443 2.815211 GACGCTGCCGCTTCATCA 60.815 61.111 1.64 0.00 38.22 3.07
3447 3521 0.037697 TTGTAGTCGAAGCCGCACAT 60.038 50.000 0.00 0.00 35.37 3.21
3491 3565 2.645297 TCGGAGATGGAGCTAGAGGTAT 59.355 50.000 0.00 0.00 0.00 2.73
3888 3962 1.271707 GCCAGCACCTACCCAACTAAA 60.272 52.381 0.00 0.00 0.00 1.85
4118 4199 1.148310 CACGTCTTCGCACTTCCAAT 58.852 50.000 0.00 0.00 41.18 3.16
4171 4252 9.261180 CAGTCAAATAGAACAGACAACTCTTTA 57.739 33.333 0.00 0.00 33.56 1.85
4418 4499 5.163343 GCTGGTCCCACTAGTCATGTTAATA 60.163 44.000 0.00 0.00 0.00 0.98
4473 4554 5.641709 GCTTTGGCCTTTTACAGTCTATTC 58.358 41.667 3.32 0.00 0.00 1.75
4500 4581 7.126268 AGCCCAATATTTCAGCCTTTTTATCTT 59.874 33.333 0.00 0.00 0.00 2.40
4642 4724 2.437359 ATCCAGCGTGGCAAGCTC 60.437 61.111 25.00 0.00 44.06 4.09
4665 4747 4.366684 CAACCTCCCCAGGCCACC 62.367 72.222 5.01 0.00 45.05 4.61
4697 4779 4.876107 CGACCAAAATATGCCTACTGTTCT 59.124 41.667 0.00 0.00 0.00 3.01
4698 4780 4.634443 ACGACCAAAATATGCCTACTGTTC 59.366 41.667 0.00 0.00 0.00 3.18
4699 4781 4.585879 ACGACCAAAATATGCCTACTGTT 58.414 39.130 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.