Multiple sequence alignment - TraesCS4B01G256800

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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 TraesCS4B01G256800 chr4B 100.000 4171 0 0 1 4171 522410887 522406717 0.000000e+00 7703.0
1 TraesCS4B01G256800 chr7B 97.538 3452 74 6 1 3447 664945257 664948702 0.000000e+00 5893.0
2 TraesCS4B01G256800 chr7B 97.305 3451 87 3 1 3450 666623102 666619657 0.000000e+00 5853.0
3 TraesCS4B01G256800 chr7B 97.703 3309 69 4 1 3308 379918561 379915259 0.000000e+00 5683.0
4 TraesCS4B01G256800 chr7B 91.790 3374 213 29 1 3326 692404014 692400657 0.000000e+00 4638.0
5 TraesCS4B01G256800 chr7B 96.232 690 12 4 3491 4167 664948788 664949476 0.000000e+00 1118.0
6 TraesCS4B01G256800 chr7B 95.238 693 21 2 3491 4171 666619574 666618882 0.000000e+00 1086.0
7 TraesCS4B01G256800 chr7B 100.000 49 0 0 3445 3493 666619681 666619633 1.600000e-14 91.6
8 TraesCS4B01G256800 chr7B 100.000 46 0 0 3448 3493 664948684 664948729 7.430000e-13 86.1
9 TraesCS4B01G256800 chr5B 97.081 3494 96 3 1 3493 34300383 34296895 0.000000e+00 5882.0
10 TraesCS4B01G256800 chr5B 96.981 3511 61 14 1 3494 123794095 123790613 0.000000e+00 5854.0
11 TraesCS4B01G256800 chr5B 96.790 3458 76 6 1 3447 353923709 353927142 0.000000e+00 5738.0
12 TraesCS4B01G256800 chr5B 96.706 3461 80 5 1 3450 18191139 18187702 0.000000e+00 5729.0
13 TraesCS4B01G256800 chr5B 95.382 693 20 2 3491 4171 353927228 353927920 0.000000e+00 1092.0
14 TraesCS4B01G256800 chr5B 95.238 693 21 2 3491 4171 18187619 18186927 0.000000e+00 1086.0
15 TraesCS4B01G256800 chr5B 95.238 693 21 2 3491 4171 123790555 123789863 0.000000e+00 1086.0
16 TraesCS4B01G256800 chr5B 94.949 693 23 5 3491 4171 514054304 514053612 0.000000e+00 1075.0
17 TraesCS4B01G256800 chr5B 95.966 595 13 1 3491 4074 34296836 34296242 0.000000e+00 955.0
18 TraesCS4B01G256800 chr5B 92.762 525 15 8 2969 3493 514054864 514054363 0.000000e+00 737.0
19 TraesCS4B01G256800 chr5B 100.000 49 0 0 3445 3493 353927121 353927169 1.600000e-14 91.6
20 TraesCS4B01G256800 chr5B 97.959 49 1 0 3445 3493 18187726 18187678 7.430000e-13 86.1
21 TraesCS4B01G256800 chr3B 97.282 3458 77 5 1 3447 734220040 734223491 0.000000e+00 5849.0
22 TraesCS4B01G256800 chr3B 95.238 693 21 2 3491 4171 734223577 734224269 0.000000e+00 1086.0
23 TraesCS4B01G256800 chr3B 100.000 37 0 0 3457 3493 734223482 734223518 7.480000e-08 69.4
24 TraesCS4B01G256800 chr2D 94.049 3092 167 12 1 3081 126682544 126685629 0.000000e+00 4674.0
25 TraesCS4B01G256800 chr4A 93.897 639 27 2 3545 4171 692373579 692374217 0.000000e+00 953.0
26 TraesCS4B01G256800 chr4A 87.376 404 21 12 3046 3443 692372915 692373294 1.780000e-118 436.0
27 TraesCS4B01G256800 chr6B 92.801 639 34 2 3545 4171 77324753 77325391 0.000000e+00 915.0


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 TraesCS4B01G256800 chr4B 522406717 522410887 4170 True 7703.000000 7703 100.000000 1 4171 1 chr4B.!!$R1 4170
1 TraesCS4B01G256800 chr7B 379915259 379918561 3302 True 5683.000000 5683 97.703000 1 3308 1 chr7B.!!$R1 3307
2 TraesCS4B01G256800 chr7B 692400657 692404014 3357 True 4638.000000 4638 91.790000 1 3326 1 chr7B.!!$R2 3325
3 TraesCS4B01G256800 chr7B 664945257 664949476 4219 False 2365.700000 5893 97.923333 1 4167 3 chr7B.!!$F1 4166
4 TraesCS4B01G256800 chr7B 666618882 666623102 4220 True 2343.533333 5853 97.514333 1 4171 3 chr7B.!!$R3 4170
5 TraesCS4B01G256800 chr5B 123789863 123794095 4232 True 3470.000000 5854 96.109500 1 4171 2 chr5B.!!$R3 4170
6 TraesCS4B01G256800 chr5B 34296242 34300383 4141 True 3418.500000 5882 96.523500 1 4074 2 chr5B.!!$R2 4073
7 TraesCS4B01G256800 chr5B 353923709 353927920 4211 False 2307.200000 5738 97.390667 1 4171 3 chr5B.!!$F1 4170
8 TraesCS4B01G256800 chr5B 18186927 18191139 4212 True 2300.366667 5729 96.634333 1 4171 3 chr5B.!!$R1 4170
9 TraesCS4B01G256800 chr5B 514053612 514054864 1252 True 906.000000 1075 93.855500 2969 4171 2 chr5B.!!$R4 1202
10 TraesCS4B01G256800 chr3B 734220040 734224269 4229 False 2334.800000 5849 97.506667 1 4171 3 chr3B.!!$F1 4170
11 TraesCS4B01G256800 chr2D 126682544 126685629 3085 False 4674.000000 4674 94.049000 1 3081 1 chr2D.!!$F1 3080
12 TraesCS4B01G256800 chr4A 692372915 692374217 1302 False 694.500000 953 90.636500 3046 4171 2 chr4A.!!$F1 1125
13 TraesCS4B01G256800 chr6B 77324753 77325391 638 False 915.000000 915 92.801000 3545 4171 1 chr6B.!!$F1 626

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
955 1010 2.930950 ACTTGTCAGTTTTGCTAGGCA 58.069 42.857 0.0 0.0 36.47 4.75 F
1021 1076 0.679505 GCGCATGAGGGGTCATAGTA 59.320 55.000 0.3 0.0 0.00 1.82 F
2401 2458 0.693049 CAAAGAGTGGCCCTAGTGGT 59.307 55.000 0.0 0.0 36.04 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2180 0.902984 TGGGTAGTGCCACTCGACAT 60.903 55.000 0.00 0.0 39.65 3.06 R
3006 3066 0.240411 GGCTCTTCTTGCAGTTGCTG 59.760 55.000 5.62 0.0 42.66 4.41 R
3255 3405 2.438021 AGTCCAGGTAGCAAAGTTCACA 59.562 45.455 0.00 0.0 0.00 3.58 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
208 216 7.771927 ATTCTCTTCATCAAAAGTGTGGATT 57.228 32.000 0.00 0.0 0.00 3.01
668 723 3.053768 TGACATTGAGATATGTTGCCCCA 60.054 43.478 0.00 0.0 38.80 4.96
841 896 4.462280 GCGGGGGAACGGTGGTAG 62.462 72.222 0.00 0.0 0.00 3.18
952 1007 8.094798 TGGTTATTACTTGTCAGTTTTGCTAG 57.905 34.615 0.00 0.0 34.06 3.42
953 1008 7.174253 TGGTTATTACTTGTCAGTTTTGCTAGG 59.826 37.037 0.00 0.0 34.06 3.02
954 1009 5.629079 ATTACTTGTCAGTTTTGCTAGGC 57.371 39.130 0.00 0.0 34.06 3.93
955 1010 2.930950 ACTTGTCAGTTTTGCTAGGCA 58.069 42.857 0.00 0.0 36.47 4.75
1021 1076 0.679505 GCGCATGAGGGGTCATAGTA 59.320 55.000 0.30 0.0 0.00 1.82
1319 1375 2.547855 GCCAATTGACAGGTGTTTTCCC 60.548 50.000 7.12 0.0 0.00 3.97
1400 1457 2.158445 GGGAGAGAGGAGTAGTATGCCA 60.158 54.545 0.00 0.0 0.00 4.92
1858 1915 1.870055 GACCGTCGCCTACTGTTGGA 61.870 60.000 12.54 0.0 0.00 3.53
1953 2010 7.217200 TGACTCATAAGCAGGTAATGATAACC 58.783 38.462 0.00 0.0 37.27 2.85
2123 2180 3.647590 TGCCCACTGATATGCTTCTATGA 59.352 43.478 0.00 0.0 0.00 2.15
2222 2279 3.428532 AGACAAGCCAATTTCTGCATCT 58.571 40.909 0.00 0.0 0.00 2.90
2401 2458 0.693049 CAAAGAGTGGCCCTAGTGGT 59.307 55.000 0.00 0.0 36.04 4.16
2445 2502 7.511959 AGTGATTCAGTATACGAAGAGCATA 57.488 36.000 13.08 0.0 0.00 3.14
2691 2749 2.494870 GTGATCTTCATTTTGCAGGGCT 59.505 45.455 0.00 0.0 0.00 5.19
3006 3066 1.405105 TGCAACAGGAACAACAAGAGC 59.595 47.619 0.00 0.0 0.00 4.09
3043 3136 4.140599 AGAGCAAGAGGAGGCGCG 62.141 66.667 0.00 0.0 34.87 6.86
3180 3279 8.850007 AGGAAGGAAGAAGTGAATTAGTTAAC 57.150 34.615 0.00 0.0 0.00 2.01
3255 3405 5.607477 TGATTCGTGAACTTTAGAAGTGGT 58.393 37.500 0.00 0.0 41.91 4.16
3366 3522 5.007724 GTGAACTATGGTACCTTATTGCTGC 59.992 44.000 14.36 0.0 0.00 5.25
3407 3593 6.562825 GCTTAGTTTTGCTGTCATTTTTGCTC 60.563 38.462 0.00 0.0 0.00 4.26
3423 3629 8.981647 CATTTTTGCTCTTATGCTTAGTTTTGT 58.018 29.630 0.00 0.0 0.00 2.83
3435 3641 4.681483 GCTTAGTTTTGTTGTCATCCTTGC 59.319 41.667 0.00 0.0 0.00 4.01
3580 3959 8.628882 ATTAGAACAAACTTTTTGGAAACTCG 57.371 30.769 3.82 0.0 0.00 4.18
3656 4046 8.531982 ACATAGTTCAACTGACATACACAGTAT 58.468 33.333 0.00 0.0 46.01 2.12
3749 4139 1.718280 ACCCCTCGAGTTCTTCTTGT 58.282 50.000 12.31 0.0 0.00 3.16
4155 4545 0.753111 GCCCTTTCCATCTCGGCAAT 60.753 55.000 0.00 0.0 39.50 3.56
4158 4549 2.497273 CCCTTTCCATCTCGGCAATTTT 59.503 45.455 0.00 0.0 33.14 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 158 1.203125 GGTTGATTTGGGTGAGGGGAA 60.203 52.381 0.00 0.00 0.00 3.97
208 216 0.253347 AGGAAGATGGGGAGGCTCAA 60.253 55.000 17.69 1.19 0.00 3.02
841 896 3.736126 CGTACCCTTTATGAAGACCGTCC 60.736 52.174 0.00 0.00 34.71 4.79
952 1007 1.338020 GCATTATGGTTAGTGCCTGCC 59.662 52.381 0.00 0.00 35.60 4.85
953 1008 2.023673 TGCATTATGGTTAGTGCCTGC 58.976 47.619 0.00 0.00 39.58 4.85
954 1009 4.613944 CATTGCATTATGGTTAGTGCCTG 58.386 43.478 0.00 0.00 39.58 4.85
955 1010 3.068590 GCATTGCATTATGGTTAGTGCCT 59.931 43.478 3.15 0.00 39.58 4.75
1107 1162 0.460109 CATGGTTGATCGACGGAGCA 60.460 55.000 7.01 0.00 36.65 4.26
1400 1457 1.910580 AACCTCATTGGCGTCCGGAT 61.911 55.000 7.81 0.00 40.22 4.18
1758 1815 1.081442 CTTGTTTTTCTCGGGGCGC 60.081 57.895 0.00 0.00 0.00 6.53
1858 1915 3.002791 CTGTGTACACATTCGCCATCTT 58.997 45.455 28.03 0.00 41.01 2.40
2123 2180 0.902984 TGGGTAGTGCCACTCGACAT 60.903 55.000 0.00 0.00 39.65 3.06
2222 2279 5.738619 TCCAAAGCTACAACTATCTCACA 57.261 39.130 0.00 0.00 0.00 3.58
2401 2458 6.826668 TCACTATGTTGTCTTCTTTCCTTCA 58.173 36.000 0.00 0.00 0.00 3.02
2445 2502 1.675641 GTCCCGCAAGCCACTTCAT 60.676 57.895 0.00 0.00 0.00 2.57
2691 2749 6.017026 TCGTTAACACAATGCAATAACTCCAA 60.017 34.615 6.39 0.00 0.00 3.53
3006 3066 0.240411 GGCTCTTCTTGCAGTTGCTG 59.760 55.000 5.62 0.00 42.66 4.41
3043 3136 3.895232 TGTACTCCTCTTCATCTTGCC 57.105 47.619 0.00 0.00 0.00 4.52
3109 3208 2.045634 GCTGTGATGGCTCAGGCA 60.046 61.111 2.01 2.01 43.52 4.75
3255 3405 2.438021 AGTCCAGGTAGCAAAGTTCACA 59.562 45.455 0.00 0.00 0.00 3.58
3407 3593 7.820648 AGGATGACAACAAAACTAAGCATAAG 58.179 34.615 0.00 0.00 0.00 1.73
3423 3629 4.826733 ACAACATAACAGCAAGGATGACAA 59.173 37.500 0.00 0.00 0.00 3.18
3435 3641 6.721571 AACGTAAGGATGACAACATAACAG 57.278 37.500 0.00 0.00 46.39 3.16
3580 3959 7.476492 GTCACGAATTTGAGACCGTTTATTTAC 59.524 37.037 11.15 0.00 32.50 2.01
3664 4054 7.548967 TGTATGTCATTTGAACTATGTCCGTA 58.451 34.615 0.00 0.00 0.00 4.02
3921 4311 4.085733 CCCTGGACCAAACAATGACATTA 58.914 43.478 0.00 0.00 0.00 1.90
4042 4432 3.350219 GACTTGAATAGGCCTGGACAA 57.650 47.619 17.99 16.49 0.00 3.18


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

AutoCloner maintained by Alex Coulton.