Multiple sequence alignment - TraesCS7D01G359300

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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 TraesCS7D01G359300 chr7D 100.000 3365 0 0 1 3365 461773108 461776472 0.000000e+00 6215.0
1 TraesCS7D01G359300 chr7D 88.865 467 18 7 2214 2647 421325153 421324688 8.210000e-151 544.0
2 TraesCS7D01G359300 chr7A 92.926 2587 142 25 294 2865 538364461 538361901 0.000000e+00 3725.0
3 TraesCS7D01G359300 chr7A 86.733 505 49 12 2869 3365 538361718 538361224 2.280000e-151 545.0
4 TraesCS7D01G359300 chr7A 90.351 228 22 0 4 231 538364795 538364568 1.960000e-77 300.0
5 TraesCS7D01G359300 chr7B 96.802 2189 49 4 373 2541 484589982 484592169 0.000000e+00 3635.0
6 TraesCS7D01G359300 chr7B 90.366 955 35 19 2458 3365 484592168 484593112 0.000000e+00 1201.0
7 TraesCS7D01G359300 chr7B 96.923 390 9 2 1 388 484589476 484589864 0.000000e+00 651.0
8 TraesCS7D01G359300 chr7B 95.946 74 2 1 2214 2286 741645574 741645501 5.900000e-23 119.0
9 TraesCS7D01G359300 chr5A 89.956 458 21 6 2214 2646 53455351 53455808 4.870000e-158 568.0
10 TraesCS7D01G359300 chr5A 89.520 458 23 6 2214 2646 53374299 53374756 1.050000e-154 556.0
11 TraesCS7D01G359300 chr4B 88.889 459 20 8 2214 2646 670351396 670350943 1.370000e-148 536.0
12 TraesCS7D01G359300 chr4B 84.855 482 20 9 2214 2646 251469299 251468822 1.430000e-118 436.0
13 TraesCS7D01G359300 chr6D 88.710 310 11 5 2361 2646 318448433 318448742 1.150000e-94 357.0
14 TraesCS7D01G359300 chr2D 94.949 198 7 2 2454 2648 445700074 445700271 1.170000e-79 307.0
15 TraesCS7D01G359300 chr2D 89.437 142 9 2 2507 2642 445629535 445629676 1.240000e-39 174.0
16 TraesCS7D01G359300 chr5D 95.455 44 1 1 245 287 537086022 537085979 6.020000e-08 69.4
17 TraesCS7D01G359300 chr3D 95.349 43 2 0 245 287 13652716 13652758 6.020000e-08 69.4


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 TraesCS7D01G359300 chr7D 461773108 461776472 3364 False 6215.000000 6215 100.000000 1 3365 1 chr7D.!!$F1 3364
1 TraesCS7D01G359300 chr7A 538361224 538364795 3571 True 1523.333333 3725 90.003333 4 3365 3 chr7A.!!$R1 3361
2 TraesCS7D01G359300 chr7B 484589476 484593112 3636 False 1829.000000 3635 94.697000 1 3365 3 chr7B.!!$F1 3364

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
313 360 2.741612 CGAGAGGCAGAATTCAGCTAG 58.258 52.381 20.52 6.11 0.0 3.42 F
778 958 3.009473 AGCTCATAAGTCAACCACCATGT 59.991 43.478 0.00 0.00 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1655 0.946221 AAACTCACCGAAGCAGCTCG 60.946 55.0 0.0 0.96 38.58 5.03 R
2552 2835 1.418334 AATGAGTCGAGGATGGGAGG 58.582 55.0 0.0 0.00 0.00 4.30 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
258 261 7.210718 AGAAATAAAGGAACTAAAACCACGG 57.789 36.000 0.00 0.00 38.49 4.94
273 276 6.478512 AAACCACGGCAATAATTATGGAAT 57.521 33.333 3.86 0.00 0.00 3.01
313 360 2.741612 CGAGAGGCAGAATTCAGCTAG 58.258 52.381 20.52 6.11 0.00 3.42
720 900 5.656416 ACCACCACCATTCACTTTTATATGG 59.344 40.000 0.00 0.00 42.56 2.74
737 917 5.640158 ATATGGAAGTAAAACGGGATGGA 57.360 39.130 0.00 0.00 0.00 3.41
778 958 3.009473 AGCTCATAAGTCAACCACCATGT 59.991 43.478 0.00 0.00 0.00 3.21
930 1127 4.927049 ACCACATCATGTTCTGAAATCCT 58.073 39.130 0.00 0.00 37.44 3.24
948 1145 6.605471 AATCCTGGAAAAAGTATTTCCCAC 57.395 37.500 15.33 0.00 45.59 4.61
983 1180 7.876068 TCTCGGCCATTATAAATACCTAGTTTG 59.124 37.037 2.24 0.00 0.00 2.93
1023 1220 4.997395 TCAACTTGAGAAGGTTAGCACATC 59.003 41.667 0.00 0.00 0.00 3.06
1166 1363 5.326900 TGGGGATTCTTTTGGGTAAGTAAC 58.673 41.667 0.00 0.00 0.00 2.50
1338 1535 5.948162 ACACTATGAGCAAAACATGGAGAAT 59.052 36.000 0.00 0.00 32.13 2.40
1458 1655 7.148373 CCAAAATCAAACATTCATGACATTCCC 60.148 37.037 0.00 0.00 0.00 3.97
1522 1721 4.759693 TCACCATAAACCACAGTTCACATC 59.240 41.667 0.00 0.00 34.19 3.06
1527 1726 0.850100 ACCACAGTTCACATCCCCAA 59.150 50.000 0.00 0.00 0.00 4.12
1599 1798 7.090808 CAGACTAATCAACTGTGCAGTACTAA 58.909 38.462 5.18 0.00 41.58 2.24
1747 1946 0.902516 TGGCAAAATACCCCAGGTGC 60.903 55.000 0.00 0.00 36.19 5.01
1964 2163 2.928334 AGAGCATTTGCCATCAGGTAG 58.072 47.619 0.00 0.00 43.38 3.18
1999 2198 0.321671 GGAGCCGCCTATCTATTGCA 59.678 55.000 0.00 0.00 0.00 4.08
2025 2224 1.416401 CTATAACCCAGGTGCCGATGT 59.584 52.381 0.00 0.00 0.00 3.06
2161 2360 9.167311 ACTACAAAGATGGTATTCAAATGACTC 57.833 33.333 0.00 0.00 0.00 3.36
2419 2620 9.174166 GACAAAATTTATCCCAGAGCTTACTAA 57.826 33.333 0.00 0.00 0.00 2.24
2552 2835 6.801862 GGAAACATGTATGCACTAGAAAACAC 59.198 38.462 0.00 0.00 0.00 3.32
2820 3114 8.724229 CATACATATCACATGAAACCTATGGTG 58.276 37.037 0.00 0.00 35.34 4.17
2933 3428 2.571653 TGGATTTCACGACAATCTCCCT 59.428 45.455 0.00 0.00 32.13 4.20
3038 3541 3.960002 GCGTATATGCATCGTTGTTCAAC 59.040 43.478 12.17 5.70 34.15 3.18
3091 3594 7.469537 TTCAAAAGTCAAAGACAACCCTTAA 57.530 32.000 0.00 0.00 34.60 1.85
3257 3769 5.298276 TCGAACTACAAAAGCTGTCCATTTT 59.702 36.000 0.00 0.00 39.64 1.82
3258 3770 5.977129 CGAACTACAAAAGCTGTCCATTTTT 59.023 36.000 0.00 0.00 39.64 1.94
3259 3771 7.012515 TCGAACTACAAAAGCTGTCCATTTTTA 59.987 33.333 0.00 0.00 39.64 1.52
3260 3772 7.646130 CGAACTACAAAAGCTGTCCATTTTTAA 59.354 33.333 0.00 0.00 39.64 1.52
3261 3773 9.308318 GAACTACAAAAGCTGTCCATTTTTAAA 57.692 29.630 0.00 0.00 39.64 1.52
3262 3774 9.660180 AACTACAAAAGCTGTCCATTTTTAAAA 57.340 25.926 0.00 0.00 39.64 1.52
3263 3775 9.830975 ACTACAAAAGCTGTCCATTTTTAAAAT 57.169 25.926 0.55 0.00 39.64 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.497473 TGTTTTCATTTCAGCTAACCGG 57.503 40.909 0.00 0.00 0.00 5.28
151 152 8.002984 TCTGATATCTGAACACCGTTACATTA 57.997 34.615 9.65 0.00 0.00 1.90
240 243 2.657143 TGCCGTGGTTTTAGTTCCTTT 58.343 42.857 0.00 0.00 0.00 3.11
258 261 6.012745 ACTCCCTCCATTCCATAATTATTGC 58.987 40.000 0.00 0.00 0.00 3.56
273 276 2.679082 GCCTCACTAATACTCCCTCCA 58.321 52.381 0.00 0.00 0.00 3.86
696 876 5.656416 CCATATAAAAGTGAATGGTGGTGGT 59.344 40.000 0.00 0.00 35.23 4.16
720 900 2.963432 TCGTCCATCCCGTTTTACTTC 58.037 47.619 0.00 0.00 0.00 3.01
730 910 0.250338 GGTGCCTATTCGTCCATCCC 60.250 60.000 0.00 0.00 0.00 3.85
737 917 2.741878 GCTACACATGGTGCCTATTCGT 60.742 50.000 0.00 0.00 36.98 3.85
778 958 7.093333 TGTCTAGCATCCTTCAGAACTAATCAA 60.093 37.037 0.00 0.00 0.00 2.57
930 1127 5.047660 CGAATGGTGGGAAATACTTTTTCCA 60.048 40.000 16.56 5.69 46.41 3.53
948 1145 0.744414 AATGGCCGAGACACGAATGG 60.744 55.000 0.00 0.00 45.77 3.16
989 1186 5.337089 CCTTCTCAAGTTGATCTGCTACAGA 60.337 44.000 5.91 0.00 44.99 3.41
1023 1220 5.163468 ACACTGAGTATGGATGTCTAGCAAG 60.163 44.000 0.00 0.00 0.00 4.01
1458 1655 0.946221 AAACTCACCGAAGCAGCTCG 60.946 55.000 0.00 0.96 38.58 5.03
1522 1721 7.069344 ACCTCTAATTTCCTGATTTATTGGGG 58.931 38.462 0.00 0.00 0.00 4.96
1527 1726 9.753674 TCACAAACCTCTAATTTCCTGATTTAT 57.246 29.630 0.00 0.00 0.00 1.40
1576 1775 7.599245 ACTTTAGTACTGCACAGTTGATTAGTC 59.401 37.037 8.86 0.00 42.54 2.59
1599 1798 6.479884 ACTTCTTCAGCATATTCAGGAACTT 58.520 36.000 0.00 0.00 34.60 2.66
1747 1946 4.442612 CCCATCACTACTTCTGGATGACTG 60.443 50.000 0.00 0.00 39.52 3.51
1999 2198 3.684413 CGGCACCTGGGTTATAGAATGTT 60.684 47.826 0.00 0.00 0.00 2.71
2025 2224 7.147320 TGAGATTTGGAGCTGGGAAGATTATAA 60.147 37.037 0.00 0.00 0.00 0.98
2161 2360 4.749245 ACATAAAGTGGCTTTTGACTCG 57.251 40.909 0.00 0.00 35.21 4.18
2394 2595 8.957466 GTTAGTAAGCTCTGGGATAAATTTTGT 58.043 33.333 0.00 0.00 0.00 2.83
2552 2835 1.418334 AATGAGTCGAGGATGGGAGG 58.582 55.000 0.00 0.00 0.00 4.30
2668 2961 3.732212 TGTCATAGGCACACAGATATGC 58.268 45.455 0.00 0.00 41.29 3.14
2820 3114 5.766174 TCAATTTCAGTTGTACCTACCCAAC 59.234 40.000 0.00 0.00 40.94 3.77
2895 3382 2.187958 TCCAGGATGTCCAGTGTAAGG 58.812 52.381 1.30 0.00 38.89 2.69
2900 3387 3.012518 GTGAAATCCAGGATGTCCAGTG 58.987 50.000 16.22 0.00 38.89 3.66
3038 3541 4.449068 CAGCTTGTGTAGTACCAGAAACAG 59.551 45.833 0.00 0.00 0.00 3.16
3259 3771 8.987890 CGTGGAAGGATTATTTTGTTTGATTTT 58.012 29.630 0.00 0.00 0.00 1.82
3260 3772 7.117667 GCGTGGAAGGATTATTTTGTTTGATTT 59.882 33.333 0.00 0.00 0.00 2.17
3261 3773 6.589907 GCGTGGAAGGATTATTTTGTTTGATT 59.410 34.615 0.00 0.00 0.00 2.57
3262 3774 6.099341 GCGTGGAAGGATTATTTTGTTTGAT 58.901 36.000 0.00 0.00 0.00 2.57
3263 3775 5.010112 TGCGTGGAAGGATTATTTTGTTTGA 59.990 36.000 0.00 0.00 0.00 2.69
3264 3776 5.226396 TGCGTGGAAGGATTATTTTGTTTG 58.774 37.500 0.00 0.00 0.00 2.93
3282 3794 5.849357 TTAACCAAGTATGTAACTGCGTG 57.151 39.130 0.00 0.00 38.88 5.34
3284 3796 6.533723 TCAGATTAACCAAGTATGTAACTGCG 59.466 38.462 0.00 0.00 38.88 5.18


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

AutoCloner maintained by Alex Coulton.