Multiple sequence alignment - TraesCS3B01G235800

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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 TraesCS3B01G235800 chr3B 100.000 2690 0 0 1 2690 368726829 368729518 0 4968
1 TraesCS3B01G235800 chr3B 95.765 2692 108 6 3 2690 92201131 92203820 0 4335
2 TraesCS3B01G235800 chrUn 96.251 2694 94 6 3 2690 189394069 189396761 0 4409
3 TraesCS3B01G235800 chr5B 96.211 2692 97 5 3 2690 679660427 679663117 0 4401
4 TraesCS3B01G235800 chr7D 96.102 2694 98 5 3 2690 203554816 203552124 0 4386
5 TraesCS3B01G235800 chr7B 96.100 2692 100 5 3 2690 743087729 743090419 0 4385
6 TraesCS3B01G235800 chr5A 96.062 2692 101 5 3 2690 16601393 16598703 0 4379
7 TraesCS3B01G235800 chr5A 96.024 2691 101 6 3 2688 300074509 300077198 0 4372
8 TraesCS3B01G235800 chr6A 96.025 2692 102 5 3 2690 289130160 289132850 0 4373
9 TraesCS3B01G235800 chr4D 96.024 2691 102 5 3 2690 123414412 123417100 0 4372


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 TraesCS3B01G235800 chr3B 368726829 368729518 2689 False 4968 4968 100.000 1 2690 1 chr3B.!!$F2 2689
1 TraesCS3B01G235800 chr3B 92201131 92203820 2689 False 4335 4335 95.765 3 2690 1 chr3B.!!$F1 2687
2 TraesCS3B01G235800 chrUn 189394069 189396761 2692 False 4409 4409 96.251 3 2690 1 chrUn.!!$F1 2687
3 TraesCS3B01G235800 chr5B 679660427 679663117 2690 False 4401 4401 96.211 3 2690 1 chr5B.!!$F1 2687
4 TraesCS3B01G235800 chr7D 203552124 203554816 2692 True 4386 4386 96.102 3 2690 1 chr7D.!!$R1 2687
5 TraesCS3B01G235800 chr7B 743087729 743090419 2690 False 4385 4385 96.100 3 2690 1 chr7B.!!$F1 2687
6 TraesCS3B01G235800 chr5A 16598703 16601393 2690 True 4379 4379 96.062 3 2690 1 chr5A.!!$R1 2687
7 TraesCS3B01G235800 chr5A 300074509 300077198 2689 False 4372 4372 96.024 3 2688 1 chr5A.!!$F1 2685
8 TraesCS3B01G235800 chr6A 289130160 289132850 2690 False 4373 4373 96.025 3 2690 1 chr6A.!!$F1 2687
9 TraesCS3B01G235800 chr4D 123414412 123417100 2688 False 4372 4372 96.024 3 2690 1 chr4D.!!$F1 2687

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
813 814 0.955178 TCTTTTTCCGAAATGCCGCA 59.045 45.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1806 1.264749 TAAGAGGCAGTGCATCCGGT 61.265 55.0 25.1 13.78 40.43 5.28 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
58 59 5.937975 ACCGATTCATCCAATCCAATTTT 57.062 34.783 0.00 0.00 38.17 1.82
59 60 5.906073 ACCGATTCATCCAATCCAATTTTC 58.094 37.500 0.00 0.00 38.17 2.29
69 70 5.047802 TCCAATCCAATTTTCTCAGAAGTGC 60.048 40.000 0.00 0.00 0.00 4.40
70 71 5.279106 CCAATCCAATTTTCTCAGAAGTGCA 60.279 40.000 0.00 0.00 0.00 4.57
221 222 5.127194 TGCGATTAGAAACCAGTGACTCTAT 59.873 40.000 0.00 0.00 0.00 1.98
230 231 2.424957 CCAGTGACTCTATAGCCAGGGA 60.425 54.545 0.00 0.00 0.00 4.20
270 271 7.321530 AGATATAAAGAATGGGGAGTTAGGGA 58.678 38.462 0.00 0.00 0.00 4.20
397 398 3.568007 TGGGTGAATCAAGTACAACAAGC 59.432 43.478 0.00 0.00 0.00 4.01
430 431 1.559682 TGTGGTAGAAGATTGGGCTCC 59.440 52.381 0.00 0.00 0.00 4.70
477 478 3.868757 AGAAGTACGCATTGCTGACTA 57.131 42.857 7.12 0.00 0.00 2.59
489 490 5.733091 GCATTGCTGACTAACTGTTTGAACA 60.733 40.000 8.91 7.46 37.37 3.18
495 496 6.566753 GCTGACTAACTGTTTGAACAATCCTC 60.567 42.308 8.91 0.00 38.66 3.71
569 570 1.300853 CCCCCAAAAGCAAAGCACG 60.301 57.895 0.00 0.00 0.00 5.34
588 589 1.676916 CGGACTCTACTCACCCACGTA 60.677 57.143 0.00 0.00 0.00 3.57
602 603 2.094078 CCCACGTATTTTCCACCTACGA 60.094 50.000 8.17 0.00 40.38 3.43
679 680 3.546417 CGAGAGTGGATAGCGTGACTAAC 60.546 52.174 0.00 0.00 33.57 2.34
680 681 3.353557 AGAGTGGATAGCGTGACTAACA 58.646 45.455 0.00 0.00 33.57 2.41
685 686 2.159085 GGATAGCGTGACTAACAAGGCT 60.159 50.000 0.00 0.00 41.31 4.58
689 690 1.993370 GCGTGACTAACAAGGCTGTAG 59.007 52.381 0.00 0.00 33.45 2.74
692 693 3.921021 CGTGACTAACAAGGCTGTAGAAG 59.079 47.826 7.03 0.00 33.45 2.85
753 754 5.075670 CGAGAGCAGCATAATTGTTAGTG 57.924 43.478 0.00 0.00 0.00 2.74
757 758 4.848357 AGCAGCATAATTGTTAGTGAGGT 58.152 39.130 0.00 0.00 0.00 3.85
805 806 7.951591 AGAAATTCAATCCTTCTTTTTCCGAA 58.048 30.769 0.00 0.00 0.00 4.30
813 814 0.955178 TCTTTTTCCGAAATGCCGCA 59.045 45.000 0.00 0.00 0.00 5.69
909 910 5.669357 GCATGCGAAATCCTTTGATTGTTTG 60.669 40.000 0.00 0.00 40.34 2.93
973 974 5.163963 GCAAGGCAAGGAAAATAAATTGTCG 60.164 40.000 0.00 0.00 32.64 4.35
980 981 5.705902 AGGAAAATAAATTGTCGGTTTCGG 58.294 37.500 0.00 0.00 36.95 4.30
982 983 5.921976 GGAAAATAAATTGTCGGTTTCGGTT 59.078 36.000 0.00 0.00 36.95 4.44
1033 1036 4.552797 GCTACGCGCAAATTCTCG 57.447 55.556 5.73 0.00 38.92 4.04
1069 1072 6.811253 TGTTCTTAACAACGATGGCTATTT 57.189 33.333 0.00 0.00 38.72 1.40
1153 1156 2.110967 CATGTTCCTGCAGCTCGGG 61.111 63.158 8.66 0.00 42.90 5.14
1175 1178 9.453572 TCGGGTGAGTATAGTTATTTATATCGT 57.546 33.333 0.00 0.00 0.00 3.73
1236 1240 2.105821 TCCCTTTTTCTTCGCTCTTCCA 59.894 45.455 0.00 0.00 0.00 3.53
1246 1250 0.460311 CGCTCTTCCAGAACCGGTAT 59.540 55.000 8.00 0.00 0.00 2.73
1287 1292 7.919313 TCTACTTTGTTTACGTTAGTGACTG 57.081 36.000 0.00 0.00 0.00 3.51
1349 1354 3.482436 TGTGGGATGCTCGTTTAACTTT 58.518 40.909 0.00 0.00 0.00 2.66
1359 1364 9.982291 GATGCTCGTTTAACTTTTGTATTCATA 57.018 29.630 0.00 0.00 0.00 2.15
1386 1391 5.765576 TCCTTATTTACTTGGGTGCACTA 57.234 39.130 17.98 3.30 0.00 2.74
1405 1410 6.264292 TGCACTATGTTTTCAAAAGCTTCCTA 59.736 34.615 0.00 0.00 0.00 2.94
1425 1430 1.481871 TCGAACCGGCTCCTATTTCT 58.518 50.000 0.00 0.00 0.00 2.52
1435 1440 3.510360 GGCTCCTATTTCTATCCGTGCTA 59.490 47.826 0.00 0.00 0.00 3.49
1446 1451 1.009900 CCGTGCTAGACCGATCGAC 60.010 63.158 18.66 10.37 0.00 4.20
1509 1514 2.684927 GCATCAACCTGGGAGCATTAGT 60.685 50.000 0.00 0.00 0.00 2.24
1547 1552 3.959495 ACATGTTCCTATGCCCATTCT 57.041 42.857 0.00 0.00 0.00 2.40
1679 1684 1.757699 AGCTCGAGAAGGAATACCACC 59.242 52.381 18.75 0.00 38.94 4.61
1686 1691 4.517453 CGAGAAGGAATACCACCAAAAACA 59.483 41.667 0.00 0.00 38.94 2.83
1711 1716 6.635030 AGTTCGCTCTCAAATAAAAACCTT 57.365 33.333 0.00 0.00 0.00 3.50
1719 1724 7.706607 GCTCTCAAATAAAAACCTTGTTCACTT 59.293 33.333 0.00 0.00 0.00 3.16
1723 1728 7.821846 TCAAATAAAAACCTTGTTCACTTGCTT 59.178 29.630 0.00 0.00 0.00 3.91
1795 1800 2.853705 TGGGTCAAAAAGTAGGTTCGG 58.146 47.619 0.00 0.00 0.00 4.30
1801 1806 5.299949 GTCAAAAAGTAGGTTCGGTTCCTA 58.700 41.667 0.00 0.00 36.60 2.94
1834 1839 4.389374 TGCCTCTTAAAGACAGAAACAGG 58.611 43.478 0.00 0.00 0.00 4.00
2005 2011 7.475137 TGGGAACAAAAAGGATACAATTAGG 57.525 36.000 0.00 0.00 37.44 2.69
2101 2109 7.691993 ATCTAGAAATAGGTAAAGGAAGGCA 57.308 36.000 0.00 0.00 0.00 4.75
2178 2187 6.808704 TGAAAACATGAACACAAACGAAATCA 59.191 30.769 0.00 0.00 0.00 2.57
2256 2265 3.262915 GGGAGGAGATGGATCGAATTCAT 59.737 47.826 6.22 0.00 0.00 2.57
2290 2299 7.541091 CCTTTCTTTGATGATCTTCAACACATG 59.459 37.037 20.34 12.16 35.42 3.21
2306 2315 5.920193 ACACATGTATTTGAATTCCCTGG 57.080 39.130 0.00 0.00 0.00 4.45
2498 2507 2.289694 CGAGGTCTGGTTCATTGAGGTT 60.290 50.000 0.00 0.00 0.00 3.50
2637 2646 5.855395 CGCTATTGAACTTCGGTACCTATAC 59.145 44.000 10.90 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.646945 TCTTGTGAGAGAGAGTCACTTGTT 59.353 41.667 4.96 0.00 44.02 2.83
1 2 4.037446 GTCTTGTGAGAGAGAGTCACTTGT 59.963 45.833 4.96 0.00 44.02 3.16
58 59 4.823442 ACAACAATGAATGCACTTCTGAGA 59.177 37.500 0.00 0.00 34.75 3.27
59 60 5.117355 ACAACAATGAATGCACTTCTGAG 57.883 39.130 0.00 0.00 34.75 3.35
69 70 7.008266 GGTTTCGCTATACAACAACAATGAATG 59.992 37.037 0.00 0.00 0.00 2.67
70 71 7.027161 GGTTTCGCTATACAACAACAATGAAT 58.973 34.615 0.00 0.00 0.00 2.57
131 132 4.045207 ACCCTGATCTGGATAGATAGCTCA 59.955 45.833 19.59 0.00 43.63 4.26
250 251 5.163237 CGAATCCCTAACTCCCCATTCTTTA 60.163 44.000 0.00 0.00 0.00 1.85
270 271 3.081804 CTGGCTACAAAGGAAACCGAAT 58.918 45.455 0.00 0.00 0.00 3.34
397 398 0.976641 TACCACAAGCTCTGACCTGG 59.023 55.000 0.00 0.00 0.00 4.45
477 478 5.820947 AGTAACGAGGATTGTTCAAACAGTT 59.179 36.000 0.00 0.00 38.69 3.16
489 490 8.461249 TTGATTAGCTACTAGTAACGAGGATT 57.539 34.615 3.76 0.00 0.00 3.01
495 496 7.917597 TCTGACTTGATTAGCTACTAGTAACG 58.082 38.462 3.76 0.00 0.00 3.18
569 570 2.119801 TACGTGGGTGAGTAGAGTCC 57.880 55.000 0.00 0.00 0.00 3.85
588 589 3.178865 TCTCCCTTCGTAGGTGGAAAAT 58.821 45.455 7.37 0.00 40.19 1.82
602 603 7.084268 AGGATATTTCGATGATTTCTCCCTT 57.916 36.000 0.00 0.00 0.00 3.95
652 653 1.140452 ACGCTATCCACTCTCGTCCTA 59.860 52.381 0.00 0.00 0.00 2.94
670 671 3.570926 TCTACAGCCTTGTTAGTCACG 57.429 47.619 0.00 0.00 38.76 4.35
679 680 4.865365 GCACTACTAACTTCTACAGCCTTG 59.135 45.833 0.00 0.00 0.00 3.61
680 681 4.527038 TGCACTACTAACTTCTACAGCCTT 59.473 41.667 0.00 0.00 0.00 4.35
685 686 8.896320 TCAAAAATGCACTACTAACTTCTACA 57.104 30.769 0.00 0.00 0.00 2.74
689 690 9.899226 ATCTTTCAAAAATGCACTACTAACTTC 57.101 29.630 0.00 0.00 0.00 3.01
753 754 1.328430 CCCGTCCCCTCTTACACCTC 61.328 65.000 0.00 0.00 0.00 3.85
757 758 2.686106 GGCCCGTCCCCTCTTACA 60.686 66.667 0.00 0.00 0.00 2.41
785 786 5.925969 GCATTTCGGAAAAAGAAGGATTGAA 59.074 36.000 7.33 0.00 0.00 2.69
968 969 3.181502 GGTTGTAAAACCGAAACCGACAA 60.182 43.478 0.00 0.00 33.30 3.18
1033 1036 4.753107 TGTTAAGAACAACCGAGATCCAAC 59.247 41.667 0.00 0.00 38.72 3.77
1057 1060 7.170998 CCGAAGACTTAAATAAATAGCCATCGT 59.829 37.037 0.00 0.00 0.00 3.73
1069 1072 4.467082 TGGTGCTACCCGAAGACTTAAATA 59.533 41.667 3.33 0.00 37.50 1.40
1175 1178 5.865085 ACAAGGAACTGTTTATAGCTGTCA 58.135 37.500 0.00 0.00 40.86 3.58
1236 1240 4.080526 AGCACCAATTTCTATACCGGTTCT 60.081 41.667 15.04 2.94 0.00 3.01
1246 1250 8.691797 ACAAAGTAGAAAAAGCACCAATTTCTA 58.308 29.630 3.73 3.73 41.98 2.10
1295 1300 1.447643 CACATAGGCCTTCCCCGAG 59.552 63.158 12.58 0.00 0.00 4.63
1327 1332 3.350219 AGTTAAACGAGCATCCCACAT 57.650 42.857 0.00 0.00 0.00 3.21
1359 1364 5.777732 TGCACCCAAGTAAATAAGGAACAAT 59.222 36.000 0.00 0.00 0.00 2.71
1375 1380 5.344743 TTTTGAAAACATAGTGCACCCAA 57.655 34.783 14.63 0.00 0.00 4.12
1386 1391 6.817765 TCGATAGGAAGCTTTTGAAAACAT 57.182 33.333 0.00 0.00 0.00 2.71
1405 1410 2.040178 AGAAATAGGAGCCGGTTCGAT 58.960 47.619 12.54 5.40 0.00 3.59
1425 1430 1.154197 CGATCGGTCTAGCACGGATA 58.846 55.000 7.38 0.00 43.33 2.59
1435 1440 5.723672 ATTATTGGTATGTCGATCGGTCT 57.276 39.130 16.41 2.38 0.00 3.85
1446 1451 9.613428 TTGACTGGAGACTTTATTATTGGTATG 57.387 33.333 0.00 0.00 0.00 2.39
1509 1514 6.405278 ACATGTATTGATGTACCAGATCGA 57.595 37.500 0.00 0.00 34.69 3.59
1547 1552 9.216117 GGAAGTTAGCAAAGTTAGACAAGATTA 57.784 33.333 0.00 0.00 0.00 1.75
1679 1684 8.948853 TTATTTGAGAGCGAACTATGTTTTTG 57.051 30.769 0.00 0.00 0.00 2.44
1686 1691 7.923414 AGGTTTTTATTTGAGAGCGAACTAT 57.077 32.000 0.00 0.00 0.00 2.12
1723 1728 2.091720 ACCATTCAGCCATGGATGCTTA 60.092 45.455 25.40 12.90 46.18 3.09
1770 1775 5.918576 CGAACCTACTTTTTGACCCATTTTC 59.081 40.000 0.00 0.00 0.00 2.29
1801 1806 1.264749 TAAGAGGCAGTGCATCCGGT 61.265 55.000 25.10 13.78 40.43 5.28
1834 1839 3.904965 CCTATACTCCTTCTTTCCCTCCC 59.095 52.174 0.00 0.00 0.00 4.30
1861 1867 6.744537 CACTTTCGATAAGAATCCAAAAGCAG 59.255 38.462 12.35 0.00 38.86 4.24
1946 1952 5.734720 TGCCTAGTGACTAAGGATTTTCAG 58.265 41.667 10.87 0.00 0.00 3.02
2037 2045 2.493675 GGGAAACTTGCCATTCCTTCTC 59.506 50.000 4.70 0.00 43.75 2.87
2101 2109 7.494922 AAAAAGCAAAATACCCCTGTGATAT 57.505 32.000 0.00 0.00 0.00 1.63
2139 2148 9.271828 GTTCATGTTTTCAATTTAGAAACCCAT 57.728 29.630 0.00 0.00 37.24 4.00
2200 2209 3.775316 CCAAGAGCTACTCCTCCCTTTTA 59.225 47.826 0.00 0.00 32.17 1.52
2256 2265 9.971922 GAAGATCATCAAAGAAAGGAAAAAGAA 57.028 29.630 0.00 0.00 0.00 2.52
2290 2299 4.855340 TCACTCCCAGGGAATTCAAATAC 58.145 43.478 10.32 0.00 0.00 1.89
2306 2315 4.099573 TCCATACGAGAAATCCTTCACTCC 59.900 45.833 0.00 0.00 33.64 3.85
2498 2507 5.123820 GTGCTAAAGGTTTCATGTGATGCTA 59.876 40.000 0.00 0.00 0.00 3.49
2563 2572 3.243907 GGCCGATTGACAAGACTAGCTAT 60.244 47.826 0.00 0.00 0.00 2.97
2637 2646 3.760580 AGGTCTGTCTTGTTTCAGGAG 57.239 47.619 0.00 0.00 33.13 3.69


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

AutoCloner maintained by Alex Coulton.