Multiple sequence alignment - TraesCS4B01G147800

Loading Multiple Alignment...

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 TraesCS4B01G147800 chr4B 100.000 3843 0 0 1 3843 211096330 211092488 0.000000e+00 7097
1 TraesCS4B01G147800 chr4B 92.687 3856 220 30 3 3843 199607617 199611425 0.000000e+00 5502
2 TraesCS4B01G147800 chr6B 96.596 3848 121 9 1 3843 42180189 42176347 0.000000e+00 6372
3 TraesCS4B01G147800 chr3B 96.596 3848 122 7 1 3843 664729674 664725831 0.000000e+00 6372
4 TraesCS4B01G147800 chr3B 93.620 3856 201 26 3 3843 646354848 646358673 0.000000e+00 5716
5 TraesCS4B01G147800 chr3B 93.594 3856 201 28 3 3843 656109216 656105392 0.000000e+00 5710
6 TraesCS4B01G147800 chr1B 95.826 3857 139 11 3 3843 84522042 84518192 0.000000e+00 6211
7 TraesCS4B01G147800 chr1B 93.358 3854 208 26 3 3843 575066985 575063167 0.000000e+00 5655
8 TraesCS4B01G147800 chr1B 88.029 1370 128 20 3 1362 164397327 164395984 0.000000e+00 1589
9 TraesCS4B01G147800 chr2B 95.457 3874 139 21 1 3843 293246415 293250282 0.000000e+00 6144
10 TraesCS4B01G147800 chr2B 93.086 3847 206 34 3 3843 35778784 35774992 0.000000e+00 5576
11 TraesCS4B01G147800 chr2B 88.616 1142 99 14 3 1135 88546394 88545275 0.000000e+00 1360
12 TraesCS4B01G147800 chr2B 84.146 410 59 5 594 999 780360577 780360984 3.600000e-105 392
13 TraesCS4B01G147800 chr5B 93.489 3855 208 26 3 3843 519961558 519957733 0.000000e+00 5688
14 TraesCS4B01G147800 chr3A 89.244 1376 113 17 3 1366 554831156 554832508 0.000000e+00 1688


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 TraesCS4B01G147800 chr4B 211092488 211096330 3842 True 7097 7097 100.000 1 3843 1 chr4B.!!$R1 3842
1 TraesCS4B01G147800 chr4B 199607617 199611425 3808 False 5502 5502 92.687 3 3843 1 chr4B.!!$F1 3840
2 TraesCS4B01G147800 chr6B 42176347 42180189 3842 True 6372 6372 96.596 1 3843 1 chr6B.!!$R1 3842
3 TraesCS4B01G147800 chr3B 664725831 664729674 3843 True 6372 6372 96.596 1 3843 1 chr3B.!!$R2 3842
4 TraesCS4B01G147800 chr3B 646354848 646358673 3825 False 5716 5716 93.620 3 3843 1 chr3B.!!$F1 3840
5 TraesCS4B01G147800 chr3B 656105392 656109216 3824 True 5710 5710 93.594 3 3843 1 chr3B.!!$R1 3840
6 TraesCS4B01G147800 chr1B 84518192 84522042 3850 True 6211 6211 95.826 3 3843 1 chr1B.!!$R1 3840
7 TraesCS4B01G147800 chr1B 575063167 575066985 3818 True 5655 5655 93.358 3 3843 1 chr1B.!!$R3 3840
8 TraesCS4B01G147800 chr1B 164395984 164397327 1343 True 1589 1589 88.029 3 1362 1 chr1B.!!$R2 1359
9 TraesCS4B01G147800 chr2B 293246415 293250282 3867 False 6144 6144 95.457 1 3843 1 chr2B.!!$F1 3842
10 TraesCS4B01G147800 chr2B 35774992 35778784 3792 True 5576 5576 93.086 3 3843 1 chr2B.!!$R1 3840
11 TraesCS4B01G147800 chr2B 88545275 88546394 1119 True 1360 1360 88.616 3 1135 1 chr2B.!!$R2 1132
12 TraesCS4B01G147800 chr5B 519957733 519961558 3825 True 5688 5688 93.489 3 3843 1 chr5B.!!$R1 3840
13 TraesCS4B01G147800 chr3A 554831156 554832508 1352 False 1688 1688 89.244 3 1366 1 chr3A.!!$F1 1363

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
651 667 0.034186 AATGCCATCATCACCACCGT 60.034 50.0 0.0 0.0 31.27 4.83 F
1117 1162 0.036010 CACCAGAATGCTCGAAGGGT 60.036 55.0 0.0 0.0 31.97 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 2550 2.022718 ACCAGACTTCTCCAGCTTCT 57.977 50.000 0.00 0.0 0.0 2.85 R
3012 3069 2.289547 GCTAGCAAACTTGTTGGACGAA 59.710 45.455 10.63 0.0 0.0 3.85 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
392 407 6.519353 TTACAATTCAGTTCACACAGTACG 57.481 37.500 0.00 0.00 0.00 3.67
502 517 2.991540 GCAACAACTCCCAGGGCC 60.992 66.667 0.00 0.00 0.00 5.80
503 518 2.520458 CAACAACTCCCAGGGCCA 59.480 61.111 6.18 0.00 0.00 5.36
505 520 1.077265 AACAACTCCCAGGGCCATG 59.923 57.895 11.33 11.33 0.00 3.66
548 563 7.391148 ACACTGGTGTATAAAGGCTTTAATG 57.609 36.000 22.42 12.65 42.90 1.90
614 630 7.891498 TCCATAAGTACAGCTTGACTATACA 57.109 36.000 0.00 0.00 38.05 2.29
628 644 3.936453 GACTATACAAATCGGTGCCACAA 59.064 43.478 0.00 0.00 0.00 3.33
651 667 0.034186 AATGCCATCATCACCACCGT 60.034 50.000 0.00 0.00 31.27 4.83
690 706 5.012561 GGGATTTAGCAGATCCTCAGTACAT 59.987 44.000 11.33 0.00 42.23 2.29
914 959 1.709578 TCCATCTCTCCCTCATTCCG 58.290 55.000 0.00 0.00 0.00 4.30
921 966 1.974957 TCTCCCTCATTCCGACAAACA 59.025 47.619 0.00 0.00 0.00 2.83
1013 1058 4.424711 GGCCATGGCGGAGGAACA 62.425 66.667 29.90 0.00 43.06 3.18
1039 1084 1.086067 CAAGCGTCATCATGCCGAGT 61.086 55.000 0.00 0.00 34.73 4.18
1106 1151 0.324943 AAGCGCCACTACACCAGAAT 59.675 50.000 2.29 0.00 0.00 2.40
1117 1162 0.036010 CACCAGAATGCTCGAAGGGT 60.036 55.000 0.00 0.00 31.97 4.34
1176 1221 1.302033 CAGCGAACCAGACAAGGCT 60.302 57.895 0.00 0.00 0.00 4.58
1284 1329 2.361610 CCTCCACAAATGGCGGCT 60.362 61.111 11.43 0.00 43.97 5.52
1374 1422 0.107703 TCCTACTCATTTGCCCTGCG 60.108 55.000 0.00 0.00 0.00 5.18
2012 2063 9.516314 GTATTAAAAGATATTTGGTGAAGTGGC 57.484 33.333 0.00 0.00 0.00 5.01
2014 2065 6.418057 AAAAGATATTTGGTGAAGTGGCAA 57.582 33.333 0.00 0.00 0.00 4.52
2493 2550 0.111061 AGCATTGGAGGTGACAAGCA 59.889 50.000 0.00 0.00 0.00 3.91
2904 2961 4.036262 TGTGTGTGTCCTTAGAATTGTTGC 59.964 41.667 0.00 0.00 0.00 4.17
3012 3069 8.818057 GTCTATCAAGTACATCGTTTGCTTATT 58.182 33.333 0.00 0.00 0.00 1.40
3047 3104 7.996098 AGTTTGCTAGCTTCCTATTTTGTTA 57.004 32.000 17.23 0.00 0.00 2.41
3103 3160 2.094494 ACGCAACACTAGTCATGGAGAG 60.094 50.000 0.00 0.00 0.00 3.20
3215 3275 6.600822 AGCTTAGACATGAACGGTAGTACTAA 59.399 38.462 3.61 0.00 0.00 2.24
3224 3285 5.049060 TGAACGGTAGTACTAACACGCTAAA 60.049 40.000 17.91 2.60 0.00 1.85
3525 3588 6.714810 AGAATTAACAGTGGCAATACAACTGA 59.285 34.615 7.20 0.00 33.15 3.41
3533 3596 5.183904 AGTGGCAATACAACTGAAAATCTCC 59.816 40.000 0.00 0.00 0.00 3.71
3594 3657 0.398318 GCCTGGAGAAGAACCACAGT 59.602 55.000 0.00 0.00 33.57 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 203 1.085501 GTTCGTTGTGGTGTGGTCGT 61.086 55.000 0.00 0.00 0.00 4.34
201 204 1.639534 GTTCGTTGTGGTGTGGTCG 59.360 57.895 0.00 0.00 0.00 4.79
203 206 0.179067 ATCGTTCGTTGTGGTGTGGT 60.179 50.000 0.00 0.00 0.00 4.16
279 285 9.151471 AGTACTGATGTTGTATGTATGTTTGAC 57.849 33.333 0.00 0.00 0.00 3.18
574 589 8.946085 GTACTTATGGATCTGTGATGTTTTTCA 58.054 33.333 0.00 0.00 0.00 2.69
614 630 3.932089 GCATTTTATTGTGGCACCGATTT 59.068 39.130 16.26 0.00 0.00 2.17
628 644 3.318839 CGGTGGTGATGATGGCATTTTAT 59.681 43.478 0.00 0.00 34.11 1.40
651 667 1.557099 ATCCCACTTGCACGTCTCTA 58.443 50.000 0.00 0.00 0.00 2.43
690 706 4.570772 GTGCACTGTTTAGTCTTGTCAAGA 59.429 41.667 11.36 11.36 34.07 3.02
769 785 3.172106 TGGAAACCGCCCAGTGGA 61.172 61.111 11.95 0.00 36.58 4.02
914 959 0.031994 AGCGGCAATGGTTGTTTGTC 59.968 50.000 1.45 0.00 0.00 3.18
921 966 0.975887 AAATGGAAGCGGCAATGGTT 59.024 45.000 1.45 0.00 0.00 3.67
1039 1084 1.176619 TTGCTCCTCTTGTCCGACGA 61.177 55.000 0.00 0.00 0.00 4.20
1093 1138 2.654749 TCGAGCATTCTGGTGTAGTG 57.345 50.000 0.00 0.00 0.00 2.74
1117 1162 1.600636 CCTTGCCGTGGAGCTCAAA 60.601 57.895 17.19 0.00 0.00 2.69
1176 1221 2.037381 GAGCCTGCTCATCATCTCATCA 59.963 50.000 14.07 0.00 42.31 3.07
1275 1320 4.349503 TGCAGGACAGCCGCCATT 62.350 61.111 0.00 0.00 39.96 3.16
1522 1570 4.286032 AGGATAACACAGAACCAGTGCTTA 59.714 41.667 0.00 0.00 40.59 3.09
1717 1766 6.066690 AGTGACTAGTACTGGTACAACAGAA 58.933 40.000 12.36 0.00 40.97 3.02
1998 2049 2.365293 GACCTTTGCCACTTCACCAAAT 59.635 45.455 0.00 0.00 0.00 2.32
2012 2063 4.641541 TGTGCATCAAGATATGGACCTTTG 59.358 41.667 6.11 0.00 44.83 2.77
2014 2065 4.508551 TGTGCATCAAGATATGGACCTT 57.491 40.909 6.11 0.00 44.83 3.50
2077 2128 5.072741 ACCAGTGCTTGATACATCTTTGTT 58.927 37.500 0.00 0.00 37.28 2.83
2237 2292 8.445493 AGTCCCGAAATTAAATTTAACTACACG 58.555 33.333 12.74 12.92 31.47 4.49
2320 2375 7.851228 TGTTCTACAAGTGATAATCCATGAGT 58.149 34.615 0.00 0.00 0.00 3.41
2493 2550 2.022718 ACCAGACTTCTCCAGCTTCT 57.977 50.000 0.00 0.00 0.00 2.85
2904 2961 6.430451 ACGAAAGCAAACTACAAATCTGAAG 58.570 36.000 0.00 0.00 0.00 3.02
3012 3069 2.289547 GCTAGCAAACTTGTTGGACGAA 59.710 45.455 10.63 0.00 0.00 3.85
3047 3104 8.423349 TCAAGTTTCAACTTCAAATCATGGATT 58.577 29.630 1.76 0.00 45.65 3.01
3533 3596 5.160699 TGCCGTATAGACTTAGTTGTACG 57.839 43.478 13.92 13.92 35.86 3.67


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

AutoCloner maintained by Alex Coulton.