Multiple sequence alignment - TraesCS7B01G220600

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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 TraesCS7B01G220600 chr7B 100.000 4019 0 0 1 4019 411748774 411752792 0 7422
1 TraesCS7B01G220600 chr7D 95.999 4074 100 24 1 4019 402148481 402152546 0 6562
2 TraesCS7B01G220600 chr7A 95.534 4053 126 23 2 4019 460116240 460120272 0 6431


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 TraesCS7B01G220600 chr7B 411748774 411752792 4018 False 7422 7422 100.000 1 4019 1 chr7B.!!$F1 4018
1 TraesCS7B01G220600 chr7D 402148481 402152546 4065 False 6562 6562 95.999 1 4019 1 chr7D.!!$F1 4018
2 TraesCS7B01G220600 chr7A 460116240 460120272 4032 False 6431 6431 95.534 2 4019 1 chr7A.!!$F1 4017

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
504 505 0.178992 CTGGTGGTTCCTGGCAAGAA 60.179 55.000 0.0 0.0 37.07 2.52 F
505 506 0.178992 TGGTGGTTCCTGGCAAGAAG 60.179 55.000 0.0 0.0 37.07 2.85 F
1412 1464 0.459585 GACGTGGTCATGGCGTATGT 60.460 55.000 0.0 0.0 39.06 2.29 F
1862 1914 1.134075 CTGTGAGCGTGCTGATTGC 59.866 57.895 0.0 0.0 43.25 3.56 F
1869 1921 1.865788 GCGTGCTGATTGCCCTGAAA 61.866 55.000 0.0 0.0 42.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 1544 1.033746 ATCTTGCGGCCAATGGTGAG 61.034 55.000 2.24 0.00 0.00 3.51 R
1599 1651 2.685017 ACCCTCTGCGCATCCTCA 60.685 61.111 12.24 0.00 0.00 3.86 R
2731 2783 1.340889 GTTTGTCCTCATTGCCAGCAA 59.659 47.619 7.64 7.64 40.47 3.91 R
2988 3040 1.952263 AGCTTCACTGCTTTTCGCC 59.048 52.632 0.00 0.00 40.93 5.54 R
3408 3469 2.239654 TCTAGCAAGGAATGACTTGGGG 59.760 50.000 10.57 0.00 46.10 4.96 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
137 138 7.279536 ACATGCTGATAATTTCTCGCCTATATG 59.720 37.037 0.00 0.00 0.00 1.78
200 201 0.466922 CAGGACCATTGATGCCTCCC 60.467 60.000 0.00 0.00 0.00 4.30
215 216 0.180406 CTCCCGGGGTAAACATGGAG 59.820 60.000 23.50 1.70 34.02 3.86
248 249 2.125552 CACGAGCGGCAGATCCAA 60.126 61.111 1.45 0.00 34.01 3.53
501 502 1.150536 GACTGGTGGTTCCTGGCAA 59.849 57.895 0.00 0.00 41.99 4.52
502 503 0.890996 GACTGGTGGTTCCTGGCAAG 60.891 60.000 0.00 0.00 41.99 4.01
503 504 1.352622 ACTGGTGGTTCCTGGCAAGA 61.353 55.000 0.00 0.00 39.12 3.02
504 505 0.178992 CTGGTGGTTCCTGGCAAGAA 60.179 55.000 0.00 0.00 37.07 2.52
505 506 0.178992 TGGTGGTTCCTGGCAAGAAG 60.179 55.000 0.00 0.00 37.07 2.85
736 742 1.133482 CCTCTCTCTCTCTCCCTTCCC 60.133 61.905 0.00 0.00 0.00 3.97
739 745 2.657459 TCTCTCTCTCTCCCTTCCCTTT 59.343 50.000 0.00 0.00 0.00 3.11
740 746 3.031013 CTCTCTCTCTCCCTTCCCTTTC 58.969 54.545 0.00 0.00 0.00 2.62
741 747 2.383683 TCTCTCTCTCCCTTCCCTTTCA 59.616 50.000 0.00 0.00 0.00 2.69
744 766 3.777522 TCTCTCTCCCTTCCCTTTCATTC 59.222 47.826 0.00 0.00 0.00 2.67
745 770 2.846827 TCTCTCCCTTCCCTTTCATTCC 59.153 50.000 0.00 0.00 0.00 3.01
748 773 3.597868 TCTCCCTTCCCTTTCATTCCAAT 59.402 43.478 0.00 0.00 0.00 3.16
750 775 4.867086 TCCCTTCCCTTTCATTCCAATAC 58.133 43.478 0.00 0.00 0.00 1.89
753 778 5.662657 CCCTTCCCTTTCATTCCAATACAAT 59.337 40.000 0.00 0.00 0.00 2.71
754 779 6.183360 CCCTTCCCTTTCATTCCAATACAATC 60.183 42.308 0.00 0.00 0.00 2.67
760 785 8.139989 CCCTTTCATTCCAATACAATCTCAATC 58.860 37.037 0.00 0.00 0.00 2.67
761 786 8.910944 CCTTTCATTCCAATACAATCTCAATCT 58.089 33.333 0.00 0.00 0.00 2.40
782 810 6.530913 TCTGAGAACGAAATCTTTCACAAG 57.469 37.500 3.77 0.00 37.01 3.16
839 867 0.806102 ATGCGAATCGGACGTTCCAG 60.806 55.000 4.35 0.00 35.91 3.86
884 912 0.774276 TGCACTCATGGTAAACCCCA 59.226 50.000 0.00 0.00 39.27 4.96
1013 1056 1.021390 CGTTTGATGCGCCCTTCTCT 61.021 55.000 4.18 0.00 0.00 3.10
1110 1162 2.203480 GCACCTGCCCAAGAACCA 60.203 61.111 0.00 0.00 34.31 3.67
1113 1165 2.391130 ACCTGCCCAAGAACCACCA 61.391 57.895 0.00 0.00 0.00 4.17
1114 1166 1.903404 CCTGCCCAAGAACCACCAC 60.903 63.158 0.00 0.00 0.00 4.16
1115 1167 1.152777 CTGCCCAAGAACCACCACA 60.153 57.895 0.00 0.00 0.00 4.17
1140 1192 3.839432 GCCTCGTCCTTCTCCCCG 61.839 72.222 0.00 0.00 0.00 5.73
1141 1193 3.148279 CCTCGTCCTTCTCCCCGG 61.148 72.222 0.00 0.00 0.00 5.73
1412 1464 0.459585 GACGTGGTCATGGCGTATGT 60.460 55.000 0.00 0.00 39.06 2.29
1776 1828 1.553706 CAGCAGGGAATTTGAAGGCT 58.446 50.000 0.00 0.00 0.00 4.58
1862 1914 1.134075 CTGTGAGCGTGCTGATTGC 59.866 57.895 0.00 0.00 43.25 3.56
1866 1918 2.749044 AGCGTGCTGATTGCCCTG 60.749 61.111 0.00 0.00 42.00 4.45
1869 1921 1.865788 GCGTGCTGATTGCCCTGAAA 61.866 55.000 0.00 0.00 42.00 2.69
1921 1973 2.162906 AGGGAGTTGCATGGGGTGT 61.163 57.895 0.00 0.00 0.00 4.16
2036 2088 6.631971 TCTGTTTACAATGTGCTCAATTCA 57.368 33.333 0.00 0.00 0.00 2.57
2037 2089 7.036996 TCTGTTTACAATGTGCTCAATTCAA 57.963 32.000 0.00 0.00 0.00 2.69
2046 2098 3.206034 TGCTCAATTCAAAGCATCACG 57.794 42.857 3.23 0.00 43.30 4.35
2324 2376 4.950050 AGAGCTTCACGGATAGTATTTGG 58.050 43.478 0.00 0.00 0.00 3.28
2731 2783 2.479560 GGCAAACGAACTGCAAAGAAGT 60.480 45.455 9.61 0.00 41.78 3.01
2926 2978 5.509716 TGAGCAAGATGATGGCTTAAATG 57.490 39.130 0.00 0.00 38.15 2.32
2988 3040 5.120399 ACTGATTCGTCTAGTAGTGAGGAG 58.880 45.833 0.00 0.00 31.38 3.69
2990 3042 2.328819 TCGTCTAGTAGTGAGGAGGC 57.671 55.000 0.00 0.00 0.00 4.70
3020 3072 3.941483 AGTGAAGCTTTCGGTGGATAATG 59.059 43.478 0.00 0.00 0.00 1.90
3217 3277 3.222603 TCTTTTCCCAGCTTGAAACTCC 58.777 45.455 7.51 0.00 31.78 3.85
3238 3298 7.050377 ACTCCACAATGACTGTATATTTGGAG 58.950 38.462 24.07 24.07 41.29 3.86
3336 3396 8.527810 TCACTAAAAATTGACCTCAAACACTTT 58.472 29.630 0.00 0.00 39.55 2.66
3337 3397 8.807581 CACTAAAAATTGACCTCAAACACTTTC 58.192 33.333 0.00 0.00 39.55 2.62
3350 3410 6.039616 TCAAACACTTTCACATTAGCAAACC 58.960 36.000 0.00 0.00 0.00 3.27
3368 3428 1.635487 ACCTTTTGCCAGAGCCATCTA 59.365 47.619 0.00 0.00 38.69 1.98
3569 3631 2.036346 GTGAAGCTTTTGGTGGATGCTT 59.964 45.455 0.00 0.00 45.15 3.91
3580 3642 2.290577 GGTGGATGCTTTTCTCAGACCT 60.291 50.000 0.00 0.00 0.00 3.85
3604 3669 9.834628 CCTTGTTAACTTAAAGATTTTGCGATA 57.165 29.630 7.22 0.00 0.00 2.92
3630 3695 3.330701 TGGTTTCTTCATAGGCTCCAGTT 59.669 43.478 0.00 0.00 0.00 3.16
3631 3696 4.202567 TGGTTTCTTCATAGGCTCCAGTTT 60.203 41.667 0.00 0.00 0.00 2.66
3744 3809 1.689273 GCCTATGATGGTCGGAAGAGT 59.311 52.381 0.00 0.00 43.49 3.24
3745 3810 2.546795 GCCTATGATGGTCGGAAGAGTG 60.547 54.545 0.00 0.00 43.49 3.51
3847 3912 0.819259 TGCCCTTGAGACTTGCACAC 60.819 55.000 0.00 0.00 0.00 3.82
3903 3976 5.989477 TGGTACTGATGGTCTTTTCTATGG 58.011 41.667 0.00 0.00 0.00 2.74
4004 4077 3.230134 CTGGAGGAGGTAGAGGATCAAG 58.770 54.545 0.00 0.00 37.82 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.463050 AGACCCAATAAGAACCAACCAA 57.537 40.909 0.00 0.00 0.00 3.67
200 201 1.200519 TCTCCTCCATGTTTACCCCG 58.799 55.000 0.00 0.00 0.00 5.73
215 216 3.712187 CTCGTGCTCTTTAAGGATCTCC 58.288 50.000 0.00 0.00 0.00 3.71
501 502 4.597075 AGGCCTTCTTCTTCTTCTTCTTCT 59.403 41.667 0.00 0.00 0.00 2.85
502 503 4.694982 CAGGCCTTCTTCTTCTTCTTCTTC 59.305 45.833 0.00 0.00 0.00 2.87
503 504 4.650734 CAGGCCTTCTTCTTCTTCTTCTT 58.349 43.478 0.00 0.00 0.00 2.52
504 505 3.558958 GCAGGCCTTCTTCTTCTTCTTCT 60.559 47.826 0.00 0.00 0.00 2.85
505 506 2.746904 GCAGGCCTTCTTCTTCTTCTTC 59.253 50.000 0.00 0.00 0.00 2.87
736 742 9.731819 CAGATTGAGATTGTATTGGAATGAAAG 57.268 33.333 0.00 0.00 0.00 2.62
753 778 7.116948 GTGAAAGATTTCGTTCTCAGATTGAGA 59.883 37.037 4.73 4.73 44.23 3.27
754 779 7.095481 TGTGAAAGATTTCGTTCTCAGATTGAG 60.095 37.037 7.56 0.00 41.56 3.02
760 785 6.292389 ACTTGTGAAAGATTTCGTTCTCAG 57.708 37.500 9.67 7.84 38.39 3.35
761 786 6.677781 AACTTGTGAAAGATTTCGTTCTCA 57.322 33.333 7.56 7.18 40.01 3.27
765 790 4.499040 CGCAAACTTGTGAAAGATTTCGTT 59.501 37.500 0.00 0.00 41.01 3.85
782 810 2.639286 CCCAGACAGCACGCAAAC 59.361 61.111 0.00 0.00 0.00 2.93
839 867 4.025647 CCAAGAGAAATCGGTCGCTTATTC 60.026 45.833 1.70 0.00 35.74 1.75
884 912 2.860293 CGCGCCAATGTTTCGTCT 59.140 55.556 0.00 0.00 0.00 4.18
1140 1192 1.385206 AATGGAGGAGAGGGAGGCC 60.385 63.158 0.00 0.00 0.00 5.19
1141 1193 0.399806 AGAATGGAGGAGAGGGAGGC 60.400 60.000 0.00 0.00 0.00 4.70
1327 1379 3.854459 GAAAGCTCGCGCCTTCCG 61.854 66.667 0.00 0.00 40.75 4.30
1492 1544 1.033746 ATCTTGCGGCCAATGGTGAG 61.034 55.000 2.24 0.00 0.00 3.51
1599 1651 2.685017 ACCCTCTGCGCATCCTCA 60.685 61.111 12.24 0.00 0.00 3.86
1731 1783 3.142174 TGCATTCCACGTCACAATGTTA 58.858 40.909 10.71 1.42 31.29 2.41
1776 1828 5.163269 CCTGATCACTTCATCATAGTTCCCA 60.163 44.000 0.00 0.00 32.21 4.37
1921 1973 5.621555 GCCTGTCAAAGTATAGACGAACAGA 60.622 44.000 12.84 0.00 37.58 3.41
2046 2098 4.427312 CTGCTAACAATGAATTCCAAGCC 58.573 43.478 2.27 0.00 0.00 4.35
2324 2376 3.510388 TGTCTCGACATTCCATCTGAC 57.490 47.619 0.00 0.00 36.21 3.51
2731 2783 1.340889 GTTTGTCCTCATTGCCAGCAA 59.659 47.619 7.64 7.64 40.47 3.91
2926 2978 2.294233 ACAAGTCACAATGTGCACCATC 59.706 45.455 15.69 0.00 32.98 3.51
2988 3040 1.952263 AGCTTCACTGCTTTTCGCC 59.048 52.632 0.00 0.00 40.93 5.54
3020 3072 2.358322 TGGTCCAAGAAGAACCAACC 57.642 50.000 0.00 0.00 40.04 3.77
3238 3298 6.510879 CCAAATAAGGGAGTCCACTAAAAC 57.489 41.667 12.30 0.00 34.83 2.43
3336 3396 3.386078 TGGCAAAAGGTTTGCTAATGTGA 59.614 39.130 21.32 0.12 44.36 3.58
3337 3397 3.726607 TGGCAAAAGGTTTGCTAATGTG 58.273 40.909 21.32 0.00 44.36 3.21
3350 3410 4.789012 TTTTAGATGGCTCTGGCAAAAG 57.211 40.909 0.00 0.00 42.43 2.27
3408 3469 2.239654 TCTAGCAAGGAATGACTTGGGG 59.760 50.000 10.57 0.00 46.10 4.96
3569 3631 9.847224 ATCTTTAAGTTAACAAGGTCTGAGAAA 57.153 29.630 8.61 0.00 0.00 2.52
3604 3669 4.721776 TGGAGCCTATGAAGAAACCATACT 59.278 41.667 0.00 0.00 0.00 2.12
3630 3695 7.038302 ACAGTTCATGACATTACTTCTAGGGAA 60.038 37.037 0.00 0.00 0.00 3.97
3631 3696 6.440647 ACAGTTCATGACATTACTTCTAGGGA 59.559 38.462 0.00 0.00 0.00 4.20
3924 3997 3.003480 AGCGAACTTAATCACTGCCTTC 58.997 45.455 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.