Multiple sequence alignment - TraesCS1B01G063300

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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 TraesCS1B01G063300 chr1B 100.000 3268 0 0 1 3268 48238574 48241841 0.000000 6035.0
1 TraesCS1B01G063300 chr1B 93.688 1917 114 6 380 2291 400394830 400396744 0.000000 2863.0
2 TraesCS1B01G063300 chr6B 94.861 2296 111 6 1 2291 216894758 216897051 0.000000 3579.0
3 TraesCS1B01G063300 chr6B 100.000 30 0 0 3239 3268 8026202 8026231 0.000456 56.5
4 TraesCS1B01G063300 chr6B 100.000 30 0 0 3239 3268 33334319 33334348 0.000456 56.5
5 TraesCS1B01G063300 chr2B 94.723 2293 114 6 4 2291 791334687 791332397 0.000000 3557.0
6 TraesCS1B01G063300 chr2B 94.243 2293 124 6 1 2288 637162646 637164935 0.000000 3496.0
7 TraesCS1B01G063300 chr2B 95.996 949 36 2 2292 3238 625476667 625477615 0.000000 1541.0
8 TraesCS1B01G063300 chr2B 93.718 589 33 4 5 592 111719648 111720233 0.000000 880.0
9 TraesCS1B01G063300 chr4B 93.761 2292 137 5 4 2291 637699207 637696918 0.000000 3435.0
10 TraesCS1B01G063300 chr4B 95.794 951 36 4 2292 3238 427976667 427977617 0.000000 1531.0
11 TraesCS1B01G063300 chr3B 93.685 2296 136 8 1 2291 729226727 729229018 0.000000 3428.0
12 TraesCS1B01G063300 chr3B 95.794 951 36 4 2292 3238 90227107 90226157 0.000000 1531.0
13 TraesCS1B01G063300 chr3B 95.412 959 39 5 2292 3246 473294098 473295055 0.000000 1522.0
14 TraesCS1B01G063300 chr3B 92.608 487 32 4 4 490 746774796 746774314 0.000000 697.0
15 TraesCS1B01G063300 chr4A 92.723 2295 156 9 1 2289 655846295 655848584 0.000000 3302.0
16 TraesCS1B01G063300 chr4A 92.593 2295 159 9 1 2289 655893446 655895735 0.000000 3286.0
17 TraesCS1B01G063300 chr4A 94.105 1917 106 6 380 2291 656355765 656357679 0.000000 2907.0
18 TraesCS1B01G063300 chr7D 96.017 954 30 8 2292 3239 429075346 429074395 0.000000 1544.0
19 TraesCS1B01G063300 chr5B 95.996 949 34 3 2292 3238 476479354 476480300 0.000000 1539.0
20 TraesCS1B01G063300 chr7B 95.899 951 34 5 2292 3238 483189236 483188287 0.000000 1535.0
21 TraesCS1B01G063300 chr7B 95.798 952 36 4 2292 3239 449026361 449025410 0.000000 1533.0
22 TraesCS1B01G063300 chr7B 95.798 952 32 7 2292 3238 93634177 93633229 0.000000 1530.0
23 TraesCS1B01G063300 chr2D 100.000 30 0 0 3239 3268 23321857 23321828 0.000456 56.5
24 TraesCS1B01G063300 chr1D 100.000 30 0 0 3239 3268 79973504 79973533 0.000456 56.5


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 TraesCS1B01G063300 chr1B 48238574 48241841 3267 False 6035 6035 100.000 1 3268 1 chr1B.!!$F1 3267
1 TraesCS1B01G063300 chr1B 400394830 400396744 1914 False 2863 2863 93.688 380 2291 1 chr1B.!!$F2 1911
2 TraesCS1B01G063300 chr6B 216894758 216897051 2293 False 3579 3579 94.861 1 2291 1 chr6B.!!$F3 2290
3 TraesCS1B01G063300 chr2B 791332397 791334687 2290 True 3557 3557 94.723 4 2291 1 chr2B.!!$R1 2287
4 TraesCS1B01G063300 chr2B 637162646 637164935 2289 False 3496 3496 94.243 1 2288 1 chr2B.!!$F3 2287
5 TraesCS1B01G063300 chr2B 625476667 625477615 948 False 1541 1541 95.996 2292 3238 1 chr2B.!!$F2 946
6 TraesCS1B01G063300 chr2B 111719648 111720233 585 False 880 880 93.718 5 592 1 chr2B.!!$F1 587
7 TraesCS1B01G063300 chr4B 637696918 637699207 2289 True 3435 3435 93.761 4 2291 1 chr4B.!!$R1 2287
8 TraesCS1B01G063300 chr4B 427976667 427977617 950 False 1531 1531 95.794 2292 3238 1 chr4B.!!$F1 946
9 TraesCS1B01G063300 chr3B 729226727 729229018 2291 False 3428 3428 93.685 1 2291 1 chr3B.!!$F2 2290
10 TraesCS1B01G063300 chr3B 90226157 90227107 950 True 1531 1531 95.794 2292 3238 1 chr3B.!!$R1 946
11 TraesCS1B01G063300 chr3B 473294098 473295055 957 False 1522 1522 95.412 2292 3246 1 chr3B.!!$F1 954
12 TraesCS1B01G063300 chr4A 655846295 655848584 2289 False 3302 3302 92.723 1 2289 1 chr4A.!!$F1 2288
13 TraesCS1B01G063300 chr4A 655893446 655895735 2289 False 3286 3286 92.593 1 2289 1 chr4A.!!$F2 2288
14 TraesCS1B01G063300 chr4A 656355765 656357679 1914 False 2907 2907 94.105 380 2291 1 chr4A.!!$F3 1911
15 TraesCS1B01G063300 chr7D 429074395 429075346 951 True 1544 1544 96.017 2292 3239 1 chr7D.!!$R1 947
16 TraesCS1B01G063300 chr5B 476479354 476480300 946 False 1539 1539 95.996 2292 3238 1 chr5B.!!$F1 946
17 TraesCS1B01G063300 chr7B 483188287 483189236 949 True 1535 1535 95.899 2292 3238 1 chr7B.!!$R3 946
18 TraesCS1B01G063300 chr7B 449025410 449026361 951 True 1533 1533 95.798 2292 3239 1 chr7B.!!$R2 947
19 TraesCS1B01G063300 chr7B 93633229 93634177 948 True 1530 1530 95.798 2292 3238 1 chr7B.!!$R1 946

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
356 358 0.603707 ACACGTGTGAGGCATGGAAG 60.604 55.000 22.71 0.0 38.39 3.46 F
1079 1085 1.002087 GGTTGACGATGTTCAGGTCCT 59.998 52.381 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1253 1259 0.036388 TGGATGTTCGTCTTCCCTGC 60.036 55.0 10.67 0.0 38.96 4.85 R
2358 2368 0.834687 TCTTGCGGTGTCCTTACCCT 60.835 55.0 0.00 0.0 37.44 4.34 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
46 47 3.242291 GACGGGCCCCATAGGAGG 61.242 72.222 18.66 0.96 38.24 4.30
356 358 0.603707 ACACGTGTGAGGCATGGAAG 60.604 55.000 22.71 0.00 38.39 3.46
498 500 5.241064 TGTGAAGTCTTTAGAGTTACGAGCT 59.759 40.000 0.00 0.00 37.79 4.09
551 554 2.042162 TCGGGAAGTTGGTAGTAGAGGT 59.958 50.000 0.00 0.00 0.00 3.85
634 637 2.501723 AGGTGCGAGGAGTTCAACATAT 59.498 45.455 0.00 0.00 0.00 1.78
652 658 8.257306 TCAACATATGTGCTTAGTATCTGAACA 58.743 33.333 9.63 0.00 0.00 3.18
678 684 2.616960 CACACTATCTAAGCGTGCCAA 58.383 47.619 0.00 0.00 31.85 4.52
706 712 2.031157 GTGTGCTTGAATGGTTTACGCT 60.031 45.455 0.00 0.00 0.00 5.07
735 741 8.109705 ACATTTGTTATGTGCTTAATCAGACA 57.890 30.769 0.00 0.00 0.00 3.41
740 746 9.979578 TTGTTATGTGCTTAATCAGACAATTTT 57.020 25.926 0.00 0.00 0.00 1.82
846 852 1.216977 CATTACCACGACGAGGCCA 59.783 57.895 11.51 0.00 0.00 5.36
927 933 6.238211 CCATAGCCTCTCAATTACGAAAACAG 60.238 42.308 0.00 0.00 0.00 3.16
933 939 7.360946 GCCTCTCAATTACGAAAACAGTATTGT 60.361 37.037 0.00 0.00 39.87 2.71
1051 1057 2.266627 GGTGAGACGTCCGACCAGT 61.267 63.158 22.73 0.02 0.00 4.00
1079 1085 1.002087 GGTTGACGATGTTCAGGTCCT 59.998 52.381 0.00 0.00 0.00 3.85
1268 1274 3.362706 AGTATAGCAGGGAAGACGAACA 58.637 45.455 0.00 0.00 0.00 3.18
1272 1278 0.036388 GCAGGGAAGACGAACATCCA 60.036 55.000 9.71 0.00 38.03 3.41
1311 1317 2.418197 GCAGTTATGCGTGGAGGAACTA 60.418 50.000 0.00 0.00 43.87 2.24
1316 1322 0.535335 TGCGTGGAGGAACTATGTCC 59.465 55.000 0.00 0.00 41.55 4.02
1334 1340 2.429610 GTCCGGTATACCACATCACTGT 59.570 50.000 21.76 0.00 35.44 3.55
1629 1636 8.589335 TTTGATGTTCTAGTGTAGTTCAGTTC 57.411 34.615 0.00 0.00 0.00 3.01
1644 1651 4.771590 TCAGTTCCTTGAATTGATGTGC 57.228 40.909 0.00 0.00 34.30 4.57
1673 1680 6.148150 CGTGAGTAAGGAGTAGATAGGTCATC 59.852 46.154 0.00 0.00 0.00 2.92
1970 1979 4.998051 AGATCAACCCCAACAAGTACATT 58.002 39.130 0.00 0.00 0.00 2.71
1981 1990 4.019792 ACAAGTACATTGACATCCAGCA 57.980 40.909 10.71 0.00 41.83 4.41
2358 2368 2.023673 CTTGCAACCCTTTCTGTCACA 58.976 47.619 0.00 0.00 0.00 3.58
2402 2412 3.229697 ACCCAAAGCTAAGCACTTCTT 57.770 42.857 0.00 0.00 38.79 2.52
2444 2454 1.328279 AGTAGGCCAAACCAAACTGC 58.672 50.000 5.01 0.00 43.14 4.40
2893 2905 1.069378 GAAGAAGTACGTCGGTGGCG 61.069 60.000 3.05 0.00 0.00 5.69
2972 2986 0.906282 CCTGGCCCCTCATTTGCTTT 60.906 55.000 0.00 0.00 0.00 3.51
3243 3259 9.019656 AGATACATTGGAGACATATCACTAGAC 57.980 37.037 0.00 0.00 42.32 2.59
3245 3261 7.423844 ACATTGGAGACATATCACTAGACAA 57.576 36.000 0.00 0.00 42.32 3.18
3246 3262 8.027524 ACATTGGAGACATATCACTAGACAAT 57.972 34.615 0.00 0.00 42.32 2.71
3247 3263 8.489489 ACATTGGAGACATATCACTAGACAATT 58.511 33.333 0.00 0.00 42.32 2.32
3248 3264 9.334947 CATTGGAGACATATCACTAGACAATTT 57.665 33.333 0.00 0.00 42.32 1.82
3249 3265 8.722480 TTGGAGACATATCACTAGACAATTTG 57.278 34.615 0.00 0.00 42.32 2.32
3250 3266 7.275183 TGGAGACATATCACTAGACAATTTGG 58.725 38.462 0.00 0.00 33.40 3.28
3251 3267 7.092891 TGGAGACATATCACTAGACAATTTGGT 60.093 37.037 0.00 0.00 33.40 3.67
3252 3268 7.225538 GGAGACATATCACTAGACAATTTGGTG 59.774 40.741 0.00 0.00 0.00 4.17
3253 3269 7.624549 AGACATATCACTAGACAATTTGGTGT 58.375 34.615 0.00 0.00 0.00 4.16
3254 3270 8.758829 AGACATATCACTAGACAATTTGGTGTA 58.241 33.333 0.00 0.00 0.00 2.90
3255 3271 9.378551 GACATATCACTAGACAATTTGGTGTAA 57.621 33.333 0.00 0.00 0.00 2.41
3256 3272 9.905713 ACATATCACTAGACAATTTGGTGTAAT 57.094 29.630 0.00 0.00 0.00 1.89
3258 3274 6.494893 TCACTAGACAATTTGGTGTAATGC 57.505 37.500 0.00 0.00 0.00 3.56
3259 3275 6.000840 TCACTAGACAATTTGGTGTAATGCA 58.999 36.000 0.00 0.00 0.00 3.96
3260 3276 6.072728 TCACTAGACAATTTGGTGTAATGCAC 60.073 38.462 0.00 0.00 46.97 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.276846 GTCGTGCCACACCCACAC 61.277 66.667 0.00 0.00 32.85 3.82
15 16 4.901123 CGTCGTGCCACACCCACA 62.901 66.667 0.00 0.00 32.85 4.17
117 118 0.909133 TGCCTCCTGTACCTGCATCA 60.909 55.000 0.00 0.00 0.00 3.07
315 317 7.411049 CGTGTATTAAGACGCTACATCAAACAA 60.411 37.037 11.64 0.00 35.46 2.83
320 322 5.032220 CACGTGTATTAAGACGCTACATCA 58.968 41.667 7.58 0.00 45.67 3.07
356 358 1.219393 GTGCCTGTAGAGCCTGGTC 59.781 63.158 0.00 0.00 0.00 4.02
434 436 1.229359 CTTCAGATGCATGCCCCCT 59.771 57.895 16.68 6.50 0.00 4.79
435 437 1.105759 GTCTTCAGATGCATGCCCCC 61.106 60.000 16.68 4.00 0.00 5.40
551 554 4.383173 TCTGACTACTATTCGCACCGATA 58.617 43.478 0.00 0.00 35.23 2.92
634 637 5.230182 CACTGTGTTCAGATACTAAGCACA 58.770 41.667 0.00 0.00 43.76 4.57
652 658 2.231478 ACGCTTAGATAGTGTGCACTGT 59.769 45.455 19.41 8.14 45.64 3.55
735 741 4.052608 CGGGAAAAAGCAACCGTAAAATT 58.947 39.130 0.00 0.00 41.34 1.82
740 746 1.517210 GCCGGGAAAAAGCAACCGTA 61.517 55.000 2.18 0.00 44.57 4.02
846 852 3.692406 GAGGAGGCGGTTGGACGT 61.692 66.667 0.00 0.00 35.98 4.34
910 916 7.620600 GCGACAATACTGTTTTCGTAATTGAGA 60.621 37.037 4.68 0.00 35.30 3.27
927 933 3.786635 AGTTGAGATGGAGCGACAATAC 58.213 45.455 0.00 0.00 0.00 1.89
933 939 1.474330 TGCTAGTTGAGATGGAGCGA 58.526 50.000 0.00 0.00 35.88 4.93
992 998 1.327690 TTCCTCCGCCATTACGCTCT 61.328 55.000 0.00 0.00 0.00 4.09
1051 1057 0.179032 ACATCGTCAACCTTGGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
1079 1085 0.520404 GTAGTCGTGCTTCTGACCGA 59.480 55.000 0.00 0.00 35.71 4.69
1113 1119 1.303561 GCTGTGGATGCCAACCTCA 60.304 57.895 0.00 0.00 34.18 3.86
1235 1241 3.243101 CCTGCTATACTCGACATCAACGT 60.243 47.826 0.00 0.00 0.00 3.99
1253 1259 0.036388 TGGATGTTCGTCTTCCCTGC 60.036 55.000 10.67 0.00 38.96 4.85
1268 1274 3.790437 CCGCTGCCCTCTGTGGAT 61.790 66.667 0.00 0.00 42.36 3.41
1272 1278 2.925170 AGAACCGCTGCCCTCTGT 60.925 61.111 0.00 0.00 0.00 3.41
1311 1317 3.069586 CAGTGATGTGGTATACCGGACAT 59.930 47.826 21.85 21.85 35.93 3.06
1334 1340 1.833630 TGGTTCACCATTTTGTTGCCA 59.166 42.857 0.00 0.00 42.01 4.92
1629 1636 4.154015 TCACGTTAGCACATCAATTCAAGG 59.846 41.667 0.00 0.00 0.00 3.61
1644 1651 6.991531 ACCTATCTACTCCTTACTCACGTTAG 59.008 42.308 0.00 0.00 0.00 2.34
1697 1704 6.985645 ACACAAGCACAACATGTCATTTTTAT 59.014 30.769 0.00 0.00 0.00 1.40
1970 1979 2.040145 TCTCCATTTGTGCTGGATGTCA 59.960 45.455 0.00 0.00 41.83 3.58
1981 1990 3.485463 TGAACGGAACTCTCCATTTGT 57.515 42.857 0.00 0.00 42.58 2.83
2358 2368 0.834687 TCTTGCGGTGTCCTTACCCT 60.835 55.000 0.00 0.00 37.44 4.34
2402 2412 4.863548 AGATTGATCTTTCTTGCCATGGA 58.136 39.130 18.40 0.00 31.97 3.41
2972 2986 3.620488 AGAACTTGGAGTGCAAGTCAAA 58.380 40.909 27.54 0.00 41.49 2.69
3232 3248 8.840321 GCATTACACCAAATTGTCTAGTGATAT 58.160 33.333 7.01 0.00 32.76 1.63


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

AutoCloner maintained by Alex Coulton.