Multiple sequence alignment - TraesCS7D01G272600

Loading Multiple Alignment...

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 TraesCS7D01G272600 chr7D 100.000 5573 0 0 1 5573 263033193 263038765 0.000000e+00 10292.0
1 TraesCS7D01G272600 chr7D 96.667 90 2 1 4846 4935 74395372 74395284 1.250000e-31 148.0
2 TraesCS7D01G272600 chr7D 97.619 84 2 0 4846 4929 633248725 633248808 1.620000e-30 145.0
3 TraesCS7D01G272600 chr7D 92.929 99 4 3 4841 4938 74399242 74399146 2.090000e-29 141.0
4 TraesCS7D01G272600 chr7A 95.786 3892 90 21 1711 5573 285693733 285697579 0.000000e+00 6211.0
5 TraesCS7D01G272600 chr7A 91.945 1738 62 33 1 1712 285691887 285693572 0.000000e+00 2362.0
6 TraesCS7D01G272600 chr7A 85.985 528 67 5 1 528 691517236 691516716 4.880000e-155 558.0
7 TraesCS7D01G272600 chr7A 85.417 528 70 5 1 528 514689052 514688532 4.910000e-150 542.0
8 TraesCS7D01G272600 chr7B 94.690 2128 66 21 2998 5090 240638046 240635931 0.000000e+00 3260.0
9 TraesCS7D01G272600 chr7B 92.036 1758 64 30 1 1722 240641018 240639301 0.000000e+00 2401.0
10 TraesCS7D01G272600 chr7B 95.790 1259 22 10 1745 3000 240639317 240638087 0.000000e+00 2002.0
11 TraesCS7D01G272600 chr7B 92.000 450 16 7 5126 5573 240635926 240635495 1.030000e-171 614.0
12 TraesCS7D01G272600 chr7B 95.745 94 1 3 4842 4935 17611701 17611611 1.250000e-31 148.0
13 TraesCS7D01G272600 chr7B 94.737 95 3 2 4842 4935 17517333 17517240 4.500000e-31 147.0
14 TraesCS7D01G272600 chr7B 98.795 83 0 1 4847 4929 17534347 17534266 4.500000e-31 147.0
15 TraesCS7D01G272600 chr5A 84.628 592 57 16 1162 1722 533480443 533479855 4.880000e-155 558.0
16 TraesCS7D01G272600 chr5A 91.837 98 8 0 919 1016 533480563 533480466 2.710000e-28 137.0
17 TraesCS7D01G272600 chr5A 85.965 57 7 1 5390 5445 526891445 526891501 6.030000e-05 60.2
18 TraesCS7D01G272600 chr2A 85.795 528 68 5 1 528 445577636 445577116 2.270000e-153 553.0
19 TraesCS7D01G272600 chr5D 91.919 99 5 3 4842 4939 404192154 404192250 9.740000e-28 135.0
20 TraesCS7D01G272600 chr5D 84.892 139 11 4 1251 1379 418868763 418868625 1.260000e-26 132.0


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 TraesCS7D01G272600 chr7D 263033193 263038765 5572 False 10292.00 10292 100.0000 1 5573 1 chr7D.!!$F1 5572
1 TraesCS7D01G272600 chr7A 285691887 285697579 5692 False 4286.50 6211 93.8655 1 5573 2 chr7A.!!$F1 5572
2 TraesCS7D01G272600 chr7A 691516716 691517236 520 True 558.00 558 85.9850 1 528 1 chr7A.!!$R2 527
3 TraesCS7D01G272600 chr7A 514688532 514689052 520 True 542.00 542 85.4170 1 528 1 chr7A.!!$R1 527
4 TraesCS7D01G272600 chr7B 240635495 240641018 5523 True 2069.25 3260 93.6290 1 5573 4 chr7B.!!$R4 5572
5 TraesCS7D01G272600 chr5A 533479855 533480563 708 True 347.50 558 88.2325 919 1722 2 chr5A.!!$R1 803
6 TraesCS7D01G272600 chr2A 445577116 445577636 520 True 553.00 553 85.7950 1 528 1 chr2A.!!$R1 527

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
365 366 1.523484 GCTCTAGCAGCCAAGGAGC 60.523 63.158 9.64 9.64 43.17 4.70 F
1358 1379 0.755686 GCTCATCGTCCATTCCTCCT 59.244 55.000 0.00 0.00 0.00 3.69 F
1359 1380 1.139853 GCTCATCGTCCATTCCTCCTT 59.860 52.381 0.00 0.00 0.00 3.36 F
1361 1382 1.486310 TCATCGTCCATTCCTCCTTGG 59.514 52.381 0.00 0.00 37.10 3.61 F
3034 3317 2.186903 CCGATTGACCTGACCGGG 59.813 66.667 6.32 0.00 36.81 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1567 0.251354 ACCGTGAATGCAGATCAGCT 59.749 50.000 11.68 0.0 34.99 4.24 R
2926 3163 1.201429 GGGTCCCAAAGAGGAGAGCA 61.201 60.000 1.78 0.0 41.22 4.26 R
3047 3330 2.618045 GCCTGCATACCATACCATACCC 60.618 54.545 0.00 0.0 0.00 3.69 R
3456 3739 4.895225 GCATTCGCATTCGCAAGATACTAC 60.895 45.833 0.00 0.0 42.52 2.73 R
4648 4950 0.027979 CGTATGCACGCATCCCAAAG 59.972 55.000 7.99 0.0 42.05 2.77 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
54 55 9.912634 CTTCTCTAATAAAGCTCTCAATCCTAG 57.087 37.037 0.00 0.00 0.00 3.02
148 149 9.630098 CTGCATTTTGTCATTTCACTACTTTAT 57.370 29.630 0.00 0.00 0.00 1.40
297 298 7.608308 ACAACTCTCAGAGCAAGATAATTTC 57.392 36.000 0.00 0.00 32.04 2.17
365 366 1.523484 GCTCTAGCAGCCAAGGAGC 60.523 63.158 9.64 9.64 43.17 4.70
403 404 3.591023 GGCGGGATTTAAGATAGAGCTC 58.409 50.000 5.27 5.27 0.00 4.09
445 446 8.101419 TCTCATACGCTATTCCAGTAAGATCTA 58.899 37.037 0.00 0.00 0.00 1.98
528 530 1.730501 TCAGCACAAGTAGCATCAGC 58.269 50.000 0.00 0.00 42.56 4.26
580 582 4.828925 GAGCTCCTCCACGCAGGC 62.829 72.222 0.87 0.00 37.29 4.85
583 585 4.767255 CTCCTCCACGCAGGCCAC 62.767 72.222 5.01 0.00 37.29 5.01
604 606 4.166888 GGCGAGCTCCTCCATGCA 62.167 66.667 8.47 0.00 0.00 3.96
605 607 2.588314 GCGAGCTCCTCCATGCAG 60.588 66.667 8.47 0.00 0.00 4.41
672 680 4.640855 ACTGTGACGGCGTGACGG 62.641 66.667 31.80 31.80 38.39 4.79
783 795 2.035449 GCCTAAAACCACCACCAAGAAC 59.965 50.000 0.00 0.00 0.00 3.01
1358 1379 0.755686 GCTCATCGTCCATTCCTCCT 59.244 55.000 0.00 0.00 0.00 3.69
1359 1380 1.139853 GCTCATCGTCCATTCCTCCTT 59.860 52.381 0.00 0.00 0.00 3.36
1360 1381 2.831333 CTCATCGTCCATTCCTCCTTG 58.169 52.381 0.00 0.00 0.00 3.61
1361 1382 1.486310 TCATCGTCCATTCCTCCTTGG 59.514 52.381 0.00 0.00 37.10 3.61
1362 1383 1.486310 CATCGTCCATTCCTCCTTGGA 59.514 52.381 0.00 0.00 44.51 3.53
1536 1566 5.802465 TCTTTGCTTCACATCTCAATCTCT 58.198 37.500 0.00 0.00 0.00 3.10
1537 1567 6.939622 TCTTTGCTTCACATCTCAATCTCTA 58.060 36.000 0.00 0.00 0.00 2.43
1676 1730 5.191426 AGGTGATCAATCAGACCATCAAAG 58.809 41.667 0.00 0.00 37.51 2.77
1726 1954 9.643693 CATACCAAACTAGATGCATTTCTTTTT 57.356 29.630 0.00 0.00 0.00 1.94
1736 1964 8.813643 AGATGCATTTCTTTTTCTTTCTCAAG 57.186 30.769 0.00 0.00 0.00 3.02
1745 1973 8.356000 TCTTTTTCTTTCTCAAGGGTAAAACA 57.644 30.769 0.00 0.00 0.00 2.83
1746 1974 8.808092 TCTTTTTCTTTCTCAAGGGTAAAACAA 58.192 29.630 0.00 0.00 0.00 2.83
1747 1975 9.430623 CTTTTTCTTTCTCAAGGGTAAAACAAA 57.569 29.630 0.00 0.00 0.00 2.83
1748 1976 8.766000 TTTTCTTTCTCAAGGGTAAAACAAAC 57.234 30.769 0.00 0.00 0.00 2.93
1898 2126 3.069016 TCGTAGTGAACAAGCTCAAGGAA 59.931 43.478 0.00 0.00 0.00 3.36
2225 2454 9.725019 AGTATGATCTGACATGTTTAAGTTTCA 57.275 29.630 0.00 7.24 0.00 2.69
2413 2642 4.814147 TGCTCAGTGAGTTCAGTTATCAG 58.186 43.478 21.06 0.00 31.39 2.90
2926 3163 2.694628 TGCTTTGAGGTTGTGCAAGAAT 59.305 40.909 0.00 0.00 0.00 2.40
3034 3317 2.186903 CCGATTGACCTGACCGGG 59.813 66.667 6.32 0.00 36.81 5.73
3035 3318 2.656069 CCGATTGACCTGACCGGGT 61.656 63.158 6.32 0.00 43.07 5.28
3450 3733 7.385267 ACGTACATCTCTCCTCTACGTATTAT 58.615 38.462 0.00 0.00 41.09 1.28
3451 3734 8.526978 ACGTACATCTCTCCTCTACGTATTATA 58.473 37.037 0.00 0.00 41.09 0.98
3855 4148 2.124983 CACATCGTGGGCCTGGAG 60.125 66.667 4.53 0.00 0.00 3.86
3996 4289 0.251916 TGGTGATCGACATGAACCCC 59.748 55.000 0.00 0.00 0.00 4.95
4089 4382 4.849329 CGGCCGTCGCAGTACCTC 62.849 72.222 19.50 0.00 36.38 3.85
4648 4950 5.482686 TTTTGCCTTTTTCATGCTTGTTC 57.517 34.783 0.00 0.00 0.00 3.18
4936 5240 1.818674 GACCAAACGCCCTGATTGAAT 59.181 47.619 0.00 0.00 32.44 2.57
4939 5243 2.995258 CCAAACGCCCTGATTGAATTTG 59.005 45.455 0.00 0.00 32.44 2.32
4940 5244 3.305950 CCAAACGCCCTGATTGAATTTGA 60.306 43.478 0.00 0.00 32.44 2.69
4949 5253 6.127647 GCCCTGATTGAATTTGAGTGTCATTA 60.128 38.462 0.00 0.00 0.00 1.90
4951 5255 7.415989 CCCTGATTGAATTTGAGTGTCATTAGG 60.416 40.741 0.00 0.00 0.00 2.69
4992 5297 0.248134 CGATGAACGGACGAGGAGAC 60.248 60.000 0.00 0.00 38.46 3.36
5005 5310 2.481104 CGAGGAGACAAGAGATGAAGGC 60.481 54.545 0.00 0.00 0.00 4.35
5111 5427 6.154021 AGAGCCATTTTGTTTTGCAGATAGAT 59.846 34.615 0.00 0.00 0.00 1.98
5138 5454 9.358872 GGAAGCAAAATCCTATTTTGTTAGAAG 57.641 33.333 20.36 1.33 40.47 2.85
5217 5534 7.967890 AACATTATCGATGCATATCAGTTCA 57.032 32.000 8.54 0.00 39.47 3.18
5291 5609 9.817365 CACAAGTTATAAAAGAAGTCATGTCTG 57.183 33.333 0.00 0.00 0.00 3.51
5425 5743 6.709018 ACACCTTGCTTGTGTTTTATTACT 57.291 33.333 1.42 0.00 44.19 2.24
5429 5747 7.704472 CACCTTGCTTGTGTTTTATTACTTTGA 59.296 33.333 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.589988 AGACTTAACATGGACTGAAGCG 58.410 45.455 0.00 0.00 0.00 4.68
54 55 7.803659 GGATTTCTTGACAAACTAAGCAACTAC 59.196 37.037 0.00 0.00 0.00 2.73
181 182 5.105473 CCATTTCCAGCATGTTTCTGATCTT 60.105 40.000 0.00 0.00 33.54 2.40
190 191 1.176527 CGGTCCATTTCCAGCATGTT 58.823 50.000 0.00 0.00 0.00 2.71
297 298 1.667236 TGTTGGCGCAGATCCATAAG 58.333 50.000 10.83 0.00 32.92 1.73
382 383 3.259625 AGAGCTCTATCTTAAATCCCGCC 59.740 47.826 16.50 0.00 0.00 6.13
403 404 7.651304 AGCGTATGAGAACAATGATCTTCTAAG 59.349 37.037 0.00 0.00 0.00 2.18
445 446 9.173021 TCAATACGAAAACAATGATAGGAACAT 57.827 29.630 0.00 0.00 0.00 2.71
587 589 4.166888 TGCATGGAGGAGCTCGCC 62.167 66.667 15.32 15.32 35.75 5.54
588 590 2.588314 CTGCATGGAGGAGCTCGC 60.588 66.667 6.28 4.80 0.00 5.03
589 591 1.521010 CACTGCATGGAGGAGCTCG 60.521 63.158 19.22 0.00 39.69 5.03
590 592 0.461693 GACACTGCATGGAGGAGCTC 60.462 60.000 19.22 4.71 39.69 4.09
591 593 0.908656 AGACACTGCATGGAGGAGCT 60.909 55.000 19.22 8.94 39.69 4.09
592 594 0.035630 AAGACACTGCATGGAGGAGC 60.036 55.000 19.22 6.76 39.69 4.70
593 595 1.406614 GGAAGACACTGCATGGAGGAG 60.407 57.143 19.22 12.71 42.18 3.69
594 596 0.615331 GGAAGACACTGCATGGAGGA 59.385 55.000 19.22 0.00 0.00 3.71
595 597 0.742281 CGGAAGACACTGCATGGAGG 60.742 60.000 19.22 9.87 0.00 4.30
596 598 0.036952 ACGGAAGACACTGCATGGAG 60.037 55.000 13.34 13.34 0.00 3.86
597 599 0.037326 GACGGAAGACACTGCATGGA 60.037 55.000 0.00 0.00 0.00 3.41
598 600 1.354337 CGACGGAAGACACTGCATGG 61.354 60.000 0.00 0.00 0.00 3.66
599 601 1.959899 GCGACGGAAGACACTGCATG 61.960 60.000 0.00 0.00 0.00 4.06
600 602 1.738099 GCGACGGAAGACACTGCAT 60.738 57.895 0.00 0.00 0.00 3.96
601 603 2.355837 GCGACGGAAGACACTGCA 60.356 61.111 0.00 0.00 0.00 4.41
602 604 3.112709 GGCGACGGAAGACACTGC 61.113 66.667 0.00 0.00 0.00 4.40
825 837 1.826921 GCATCAGCATCACCCAGGG 60.827 63.158 2.85 2.85 41.58 4.45
827 839 1.450848 ACGCATCAGCATCACCCAG 60.451 57.895 0.00 0.00 42.27 4.45
1536 1566 1.482182 ACCGTGAATGCAGATCAGCTA 59.518 47.619 11.68 0.00 34.99 3.32
1537 1567 0.251354 ACCGTGAATGCAGATCAGCT 59.749 50.000 11.68 0.00 34.99 4.24
1676 1730 6.024049 GTCTGCAACTAATAATTCTGTGTGC 58.976 40.000 0.00 0.00 0.00 4.57
1726 1954 8.269317 TCTAGTTTGTTTTACCCTTGAGAAAGA 58.731 33.333 0.00 0.00 0.00 2.52
1736 1964 6.526674 CGAAATGCATCTAGTTTGTTTTACCC 59.473 38.462 0.00 0.00 0.00 3.69
1745 1973 7.672983 TTCTTTCTCGAAATGCATCTAGTTT 57.327 32.000 0.00 0.00 0.00 2.66
1746 1974 7.672983 TTTCTTTCTCGAAATGCATCTAGTT 57.327 32.000 0.00 0.00 0.00 2.24
1747 1975 7.672983 TTTTCTTTCTCGAAATGCATCTAGT 57.327 32.000 0.00 0.00 33.33 2.57
1992 2221 9.904198 TTCATTTGAGAAACCATACATGATAGA 57.096 29.630 0.00 0.00 0.00 1.98
2005 2234 4.687483 CAGGGTGCATTTCATTTGAGAAAC 59.313 41.667 0.00 0.00 40.03 2.78
2042 2271 3.701542 TGCTGGTACTCATTCTCGATCTT 59.298 43.478 0.00 0.00 0.00 2.40
2291 2520 4.079154 TGCAGGTAGGAATCTAGAGAGGAA 60.079 45.833 0.00 0.00 0.00 3.36
2292 2521 3.463704 TGCAGGTAGGAATCTAGAGAGGA 59.536 47.826 0.00 0.00 0.00 3.71
2463 2692 5.439721 ACTCTATATCTGCAAATGCCAACA 58.560 37.500 2.46 0.00 41.18 3.33
2470 2699 7.896811 TCACCGAATACTCTATATCTGCAAAT 58.103 34.615 0.00 0.00 0.00 2.32
2926 3163 1.201429 GGGTCCCAAAGAGGAGAGCA 61.201 60.000 1.78 0.00 41.22 4.26
3034 3317 4.717279 ACCATACCCATACCATACCAAC 57.283 45.455 0.00 0.00 0.00 3.77
3035 3318 5.251932 CCATACCATACCCATACCATACCAA 59.748 44.000 0.00 0.00 0.00 3.67
3042 3325 4.226394 TGCATACCATACCATACCCATACC 59.774 45.833 0.00 0.00 0.00 2.73
3043 3326 5.428253 CTGCATACCATACCATACCCATAC 58.572 45.833 0.00 0.00 0.00 2.39
3044 3327 4.473196 CCTGCATACCATACCATACCCATA 59.527 45.833 0.00 0.00 0.00 2.74
3045 3328 3.266772 CCTGCATACCATACCATACCCAT 59.733 47.826 0.00 0.00 0.00 4.00
3046 3329 2.642311 CCTGCATACCATACCATACCCA 59.358 50.000 0.00 0.00 0.00 4.51
3047 3330 2.618045 GCCTGCATACCATACCATACCC 60.618 54.545 0.00 0.00 0.00 3.69
3456 3739 4.895225 GCATTCGCATTCGCAAGATACTAC 60.895 45.833 0.00 0.00 42.52 2.73
3485 3775 1.991965 CCGTACAAACATTGGCATTGC 59.008 47.619 9.18 0.00 34.12 3.56
3491 3781 1.268352 CACCCACCGTACAAACATTGG 59.732 52.381 0.00 0.00 34.12 3.16
3492 3782 1.268352 CCACCCACCGTACAAACATTG 59.732 52.381 0.00 0.00 0.00 2.82
3493 3783 1.611519 CCACCCACCGTACAAACATT 58.388 50.000 0.00 0.00 0.00 2.71
3494 3784 0.891904 GCCACCCACCGTACAAACAT 60.892 55.000 0.00 0.00 0.00 2.71
3495 3785 1.526455 GCCACCCACCGTACAAACA 60.526 57.895 0.00 0.00 0.00 2.83
3996 4289 2.131709 CAGGATGCCCTTGCCCATG 61.132 63.158 0.00 0.00 42.02 3.66
4542 4835 1.544825 CGGTCCTCTGCCTCTTGGAA 61.545 60.000 0.00 0.00 34.57 3.53
4648 4950 0.027979 CGTATGCACGCATCCCAAAG 59.972 55.000 7.99 0.00 42.05 2.77
4949 5253 9.064706 TCGAGAAAGAACGAAATATATAGTCCT 57.935 33.333 0.00 0.00 35.62 3.85
4992 5297 5.330295 CAAAGAATTCGCCTTCATCTCTTG 58.670 41.667 0.00 0.00 0.00 3.02
5005 5310 3.065925 GGAGAATGGAGCCAAAGAATTCG 59.934 47.826 0.00 0.00 33.47 3.34
5082 5398 2.096762 GCAAAACAAAATGGCTCTTCGC 60.097 45.455 0.00 0.00 38.13 4.70
5111 5427 8.415950 TCTAACAAAATAGGATTTTGCTTCCA 57.584 30.769 19.59 3.44 41.66 3.53
5291 5609 4.746611 CACCAACTTGAGAATTTGCTTTCC 59.253 41.667 0.00 0.00 0.00 3.13
5362 5680 7.938140 TGGAGAGTTAATCTGGGTAAAAATG 57.062 36.000 0.00 0.00 38.84 2.32
5375 5693 7.184753 AGGGTTTTATCTCCTTGGAGAGTTAAT 59.815 37.037 21.92 9.58 35.28 1.40
5425 5743 7.618502 ACATGTACTTTGTACACACTTCAAA 57.381 32.000 11.99 0.00 0.00 2.69
5429 5747 7.492020 TCGTTTACATGTACTTTGTACACACTT 59.508 33.333 4.68 1.62 32.39 3.16
5440 5758 5.924825 GTCTCTTGGTCGTTTACATGTACTT 59.075 40.000 4.68 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.