Multiple sequence alignment - TraesCS7B01G180100

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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 TraesCS7B01G180100 chr7B 100.000 2955 0 0 1 2955 268453131 268456085 0.000000e+00 5457.0
1 TraesCS7B01G180100 chr7B 75.709 247 35 15 1379 1623 533570540 533570317 1.870000e-17 100.0
2 TraesCS7B01G180100 chr7D 92.936 3001 55 39 1 2937 271508316 271505409 0.000000e+00 4222.0
3 TraesCS7B01G180100 chr7D 75.686 255 36 16 1379 1631 505603597 505603367 1.450000e-18 104.0
4 TraesCS7B01G180100 chr7A 92.923 2586 54 34 429 2937 303103093 303100560 0.000000e+00 3642.0
5 TraesCS7B01G180100 chr7A 94.138 290 9 1 16 297 303103951 303103662 4.520000e-118 435.0
6 TraesCS7B01G180100 chr7A 95.161 124 5 1 276 398 303103590 303103467 8.360000e-46 195.0
7 TraesCS7B01G180100 chr7A 75.918 245 34 15 1379 1621 573097002 573096781 5.210000e-18 102.0
8 TraesCS7B01G180100 chr2A 77.236 246 33 15 1379 1623 697290074 697290297 4.000000e-24 122.0
9 TraesCS7B01G180100 chr2B 76.829 246 34 15 1379 1623 664933892 664934115 1.860000e-22 117.0
10 TraesCS7B01G180100 chr2D 76.423 246 35 15 1379 1623 557258876 557259099 8.660000e-21 111.0
11 TraesCS7B01G180100 chr6A 74.797 246 39 13 1378 1622 488062704 488062481 4.060000e-14 89.8


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 TraesCS7B01G180100 chr7B 268453131 268456085 2954 False 5457 5457 100.000 1 2955 1 chr7B.!!$F1 2954
1 TraesCS7B01G180100 chr7D 271505409 271508316 2907 True 4222 4222 92.936 1 2937 1 chr7D.!!$R1 2936
2 TraesCS7B01G180100 chr7A 303100560 303103951 3391 True 1424 3642 94.074 16 2937 3 chr7A.!!$R2 2921

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
945 1419 0.121197 TCCTCCCATCTCCCCTGTTT 59.879 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 2524 0.329596 GTGCTCTTCCTTCCCATGGT 59.67 55.0 11.73 0.0 0.0 3.55 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
72 73 3.658709 AGTTGTTGAAGAGACAGCTAGC 58.341 45.455 6.62 6.62 36.90 3.42
191 192 6.775142 TGTGGAATGTGATTACTGGAAAGAAA 59.225 34.615 0.00 0.00 0.00 2.52
192 193 7.040478 TGTGGAATGTGATTACTGGAAAGAAAG 60.040 37.037 0.00 0.00 0.00 2.62
193 194 7.174946 GTGGAATGTGATTACTGGAAAGAAAGA 59.825 37.037 0.00 0.00 0.00 2.52
194 195 7.723616 TGGAATGTGATTACTGGAAAGAAAGAA 59.276 33.333 0.00 0.00 0.00 2.52
195 196 8.576442 GGAATGTGATTACTGGAAAGAAAGAAA 58.424 33.333 0.00 0.00 0.00 2.52
196 197 9.617975 GAATGTGATTACTGGAAAGAAAGAAAG 57.382 33.333 0.00 0.00 0.00 2.62
197 198 8.924511 ATGTGATTACTGGAAAGAAAGAAAGA 57.075 30.769 0.00 0.00 0.00 2.52
198 199 8.383318 TGTGATTACTGGAAAGAAAGAAAGAG 57.617 34.615 0.00 0.00 0.00 2.85
254 271 3.807553 TCGTTCCGTTTCCTTTTAACCT 58.192 40.909 0.00 0.00 0.00 3.50
267 284 5.880332 TCCTTTTAACCTGATCACTGTATGC 59.120 40.000 0.00 0.00 0.00 3.14
309 419 5.126707 GCTGAATGAAGGAATGAATGGAACT 59.873 40.000 0.00 0.00 0.00 3.01
358 468 0.614697 AACTTTGTATGCCTGGGCCC 60.615 55.000 17.59 17.59 41.09 5.80
430 547 3.430218 GTCAGATTGTCACTCGAAACCTG 59.570 47.826 0.00 0.00 0.00 4.00
432 549 3.185188 CAGATTGTCACTCGAAACCTGTG 59.815 47.826 0.00 0.00 0.00 3.66
433 550 2.684001 TTGTCACTCGAAACCTGTGT 57.316 45.000 2.18 0.00 33.82 3.72
434 551 1.934589 TGTCACTCGAAACCTGTGTG 58.065 50.000 2.18 0.00 33.82 3.82
435 552 1.206132 TGTCACTCGAAACCTGTGTGT 59.794 47.619 2.18 0.00 33.71 3.72
436 553 1.593006 GTCACTCGAAACCTGTGTGTG 59.407 52.381 2.18 0.00 33.71 3.82
453 899 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
455 901 0.454285 GTGTGTGTGTGTGTGTGCAC 60.454 55.000 10.75 10.75 45.44 4.57
539 997 2.362369 CCCTCGACCATGACCTGCT 61.362 63.158 0.00 0.00 0.00 4.24
653 1111 1.077005 ACTCTCAGCTTCACCTCCTCT 59.923 52.381 0.00 0.00 0.00 3.69
773 1234 1.078497 GCACGTGACCATCCATCCA 60.078 57.895 22.23 0.00 0.00 3.41
774 1235 0.464373 GCACGTGACCATCCATCCAT 60.464 55.000 22.23 0.00 0.00 3.41
775 1236 1.586422 CACGTGACCATCCATCCATC 58.414 55.000 10.90 0.00 0.00 3.51
796 1257 5.674052 TCCATCCAAGAAAGAGAGAGAAG 57.326 43.478 0.00 0.00 0.00 2.85
798 1259 3.584406 TCCAAGAAAGAGAGAGAAGCG 57.416 47.619 0.00 0.00 0.00 4.68
912 1386 1.551452 AACGCTACTCCTGCTTCTCT 58.449 50.000 0.00 0.00 0.00 3.10
913 1387 1.551452 ACGCTACTCCTGCTTCTCTT 58.449 50.000 0.00 0.00 0.00 2.85
914 1388 1.896465 ACGCTACTCCTGCTTCTCTTT 59.104 47.619 0.00 0.00 0.00 2.52
915 1389 2.094442 ACGCTACTCCTGCTTCTCTTTC 60.094 50.000 0.00 0.00 0.00 2.62
916 1390 2.165437 CGCTACTCCTGCTTCTCTTTCT 59.835 50.000 0.00 0.00 0.00 2.52
945 1419 0.121197 TCCTCCCATCTCCCCTGTTT 59.879 55.000 0.00 0.00 0.00 2.83
1251 1731 0.322816 TGCCAATGCCACTCCTTCTC 60.323 55.000 0.00 0.00 36.33 2.87
1252 1732 0.034670 GCCAATGCCACTCCTTCTCT 60.035 55.000 0.00 0.00 0.00 3.10
1253 1733 1.615384 GCCAATGCCACTCCTTCTCTT 60.615 52.381 0.00 0.00 0.00 2.85
1254 1734 2.363683 CCAATGCCACTCCTTCTCTTC 58.636 52.381 0.00 0.00 0.00 2.87
1255 1735 2.026449 CCAATGCCACTCCTTCTCTTCT 60.026 50.000 0.00 0.00 0.00 2.85
1274 1754 7.391554 TCTCTTCTCTTCTCTTCTCTTCTCTTG 59.608 40.741 0.00 0.00 0.00 3.02
1305 1785 7.330208 GTCTTGTTGATTGATTGATTGGGAAAG 59.670 37.037 0.00 0.00 0.00 2.62
1668 2158 3.316029 CCCGCTCAAGATAAATTGCATGA 59.684 43.478 0.00 0.00 0.00 3.07
1669 2159 4.022589 CCCGCTCAAGATAAATTGCATGAT 60.023 41.667 0.00 0.00 0.00 2.45
1670 2160 5.181811 CCCGCTCAAGATAAATTGCATGATA 59.818 40.000 0.00 0.00 0.00 2.15
1671 2161 6.127814 CCCGCTCAAGATAAATTGCATGATAT 60.128 38.462 0.00 0.00 0.00 1.63
1710 2200 4.858935 TCATTCTTTTCTTTTCGGCACAG 58.141 39.130 0.00 0.00 0.00 3.66
1711 2201 2.774439 TCTTTTCTTTTCGGCACAGC 57.226 45.000 0.00 0.00 0.00 4.40
1712 2202 2.020720 TCTTTTCTTTTCGGCACAGCA 58.979 42.857 0.00 0.00 0.00 4.41
1713 2203 2.119457 CTTTTCTTTTCGGCACAGCAC 58.881 47.619 0.00 0.00 0.00 4.40
1714 2204 1.098869 TTTCTTTTCGGCACAGCACA 58.901 45.000 0.00 0.00 0.00 4.57
1776 2266 0.666577 CGTTTCTCCTCCGTGTCACC 60.667 60.000 0.00 0.00 0.00 4.02
2039 2547 1.743252 GGGAAGGAAGAGCACGCAG 60.743 63.158 0.00 0.00 0.00 5.18
2289 2829 5.448360 GCAGCTAGTCCTAGAAGCATTTTTG 60.448 44.000 5.52 0.00 38.75 2.44
2298 2838 6.664816 TCCTAGAAGCATTTTTGTGATGGATT 59.335 34.615 0.00 0.00 0.00 3.01
2299 2839 6.976925 CCTAGAAGCATTTTTGTGATGGATTC 59.023 38.462 0.00 0.00 0.00 2.52
2305 2847 8.091385 AGCATTTTTGTGATGGATTCTTTTTC 57.909 30.769 0.00 0.00 0.00 2.29
2602 3144 4.025360 TGATTTGACCTAGCCAATGCAAT 58.975 39.130 0.00 0.00 41.13 3.56
2712 3254 2.069273 GTATAATACGCTGGCTGGCTG 58.931 52.381 2.00 2.91 0.00 4.85
2713 3255 0.250467 ATAATACGCTGGCTGGCTGG 60.250 55.000 9.98 3.25 0.00 4.85
2714 3256 2.940890 TAATACGCTGGCTGGCTGGC 62.941 60.000 11.09 11.09 42.18 4.85
2756 3298 8.509690 CGAATATAATGTGCTTTCTTGGATGAT 58.490 33.333 0.00 0.00 0.00 2.45
2802 3344 2.743938 CATTGTGCTAGCTACCCTACG 58.256 52.381 17.23 0.00 0.00 3.51
2860 3428 8.362464 TCAAGCCGGATTCTATTACTATATGT 57.638 34.615 5.05 0.00 0.00 2.29
2938 3506 9.550811 CGTTACCAATAAGTGTTAAATTTCTCC 57.449 33.333 0.00 0.00 0.00 3.71
2939 3507 9.850628 GTTACCAATAAGTGTTAAATTTCTCCC 57.149 33.333 0.00 0.00 0.00 4.30
2940 3508 7.476540 ACCAATAAGTGTTAAATTTCTCCCC 57.523 36.000 0.00 0.00 0.00 4.81
2941 3509 6.439375 ACCAATAAGTGTTAAATTTCTCCCCC 59.561 38.462 0.00 0.00 0.00 5.40
2942 3510 6.405397 CCAATAAGTGTTAAATTTCTCCCCCG 60.405 42.308 0.00 0.00 0.00 5.73
2943 3511 2.443416 AGTGTTAAATTTCTCCCCCGC 58.557 47.619 0.00 0.00 0.00 6.13
2944 3512 2.164338 GTGTTAAATTTCTCCCCCGCA 58.836 47.619 0.00 0.00 0.00 5.69
2945 3513 2.559231 GTGTTAAATTTCTCCCCCGCAA 59.441 45.455 0.00 0.00 0.00 4.85
2946 3514 3.006003 GTGTTAAATTTCTCCCCCGCAAA 59.994 43.478 0.00 0.00 0.00 3.68
2947 3515 3.641906 TGTTAAATTTCTCCCCCGCAAAA 59.358 39.130 0.00 0.00 0.00 2.44
2948 3516 4.101119 TGTTAAATTTCTCCCCCGCAAAAA 59.899 37.500 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 6.206438 TCAACAACTTGCATGCTCTAATAACA 59.794 34.615 20.33 0.00 0.00 2.41
72 73 3.804193 GCCTGCCTTCCTTTCGCG 61.804 66.667 0.00 0.00 0.00 5.87
159 160 2.139323 ATCACATTCCACATGCTGCT 57.861 45.000 0.00 0.00 0.00 4.24
191 192 4.417426 TTTGTCGGGTTTCTCTCTTTCT 57.583 40.909 0.00 0.00 0.00 2.52
192 193 4.154375 GGATTTGTCGGGTTTCTCTCTTTC 59.846 45.833 0.00 0.00 0.00 2.62
193 194 4.072839 GGATTTGTCGGGTTTCTCTCTTT 58.927 43.478 0.00 0.00 0.00 2.52
194 195 3.328050 AGGATTTGTCGGGTTTCTCTCTT 59.672 43.478 0.00 0.00 0.00 2.85
195 196 2.907042 AGGATTTGTCGGGTTTCTCTCT 59.093 45.455 0.00 0.00 0.00 3.10
196 197 3.263261 GAGGATTTGTCGGGTTTCTCTC 58.737 50.000 0.00 0.00 0.00 3.20
197 198 2.027100 GGAGGATTTGTCGGGTTTCTCT 60.027 50.000 0.00 0.00 0.00 3.10
198 199 2.027100 AGGAGGATTTGTCGGGTTTCTC 60.027 50.000 0.00 0.00 0.00 2.87
254 271 3.118149 AGCCAAGATGCATACAGTGATCA 60.118 43.478 0.00 0.00 0.00 2.92
267 284 3.192001 TCAGCTAAGCAAAAGCCAAGATG 59.808 43.478 0.00 0.00 41.02 2.90
309 419 1.518572 GCCGTAAAGCGAGCTAGCA 60.519 57.895 21.36 0.00 44.77 3.49
368 478 2.721167 ATGGACCGCTTCGCTGCTA 61.721 57.895 0.00 0.00 0.00 3.49
430 547 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
432 549 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
433 550 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
434 551 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
435 552 0.886490 TGCACACACACACACACACA 60.886 50.000 0.00 0.00 0.00 3.72
436 553 0.454285 GTGCACACACACACACACAC 60.454 55.000 13.17 0.00 46.61 3.82
453 899 3.320610 TCTCCTCCTTCTCCTATGGTG 57.679 52.381 0.00 0.00 0.00 4.17
455 901 4.191804 TCTTCTCCTCCTTCTCCTATGG 57.808 50.000 0.00 0.00 0.00 2.74
539 997 1.065199 CCATCCTTCCTTGTAGCAGCA 60.065 52.381 0.00 0.00 0.00 4.41
653 1111 7.203218 GTGCTATCTATATATGCAATGTCGGA 58.797 38.462 0.00 0.00 35.34 4.55
773 1234 5.396660 GCTTCTCTCTCTTTCTTGGATGGAT 60.397 44.000 0.00 0.00 0.00 3.41
774 1235 4.081198 GCTTCTCTCTCTTTCTTGGATGGA 60.081 45.833 0.00 0.00 0.00 3.41
775 1236 4.190772 GCTTCTCTCTCTTTCTTGGATGG 58.809 47.826 0.00 0.00 0.00 3.51
933 1407 1.679032 GCGCTAACAAACAGGGGAGAT 60.679 52.381 0.00 0.00 0.00 2.75
945 1419 2.745884 AATGCCGCTGCGCTAACA 60.746 55.556 18.00 11.81 41.78 2.41
1251 1731 7.175641 AGACAAGAGAAGAGAAGAGAAGAGAAG 59.824 40.741 0.00 0.00 0.00 2.85
1252 1732 7.004086 AGACAAGAGAAGAGAAGAGAAGAGAA 58.996 38.462 0.00 0.00 0.00 2.87
1253 1733 6.542821 AGACAAGAGAAGAGAAGAGAAGAGA 58.457 40.000 0.00 0.00 0.00 3.10
1254 1734 6.824305 AGACAAGAGAAGAGAAGAGAAGAG 57.176 41.667 0.00 0.00 0.00 2.85
1255 1735 6.549364 ACAAGACAAGAGAAGAGAAGAGAAGA 59.451 38.462 0.00 0.00 0.00 2.87
1274 1754 7.327761 CCAATCAATCAATCAACAAGACAAGAC 59.672 37.037 0.00 0.00 0.00 3.01
1710 2200 1.353609 GAACGGCATTGGCATTGTGC 61.354 55.000 11.10 10.57 43.71 4.57
1711 2201 1.072116 CGAACGGCATTGGCATTGTG 61.072 55.000 11.10 6.71 43.71 3.33
1712 2202 1.212490 CGAACGGCATTGGCATTGT 59.788 52.632 11.10 0.00 43.71 2.71
1713 2203 0.798009 GACGAACGGCATTGGCATTG 60.798 55.000 11.10 5.04 43.71 2.82
1714 2204 1.506262 GACGAACGGCATTGGCATT 59.494 52.632 11.10 0.26 43.71 3.56
1776 2266 1.968017 ACCAACTGCATGCGTGAGG 60.968 57.895 14.09 18.96 0.00 3.86
2016 2524 0.329596 GTGCTCTTCCTTCCCATGGT 59.670 55.000 11.73 0.00 0.00 3.55
2039 2547 4.098155 AGGAGTAGGGAGTTCTTCCTTTC 58.902 47.826 4.86 4.33 45.98 2.62
2092 2602 8.518702 GGTGCTATCTTTTCTCATTTCTTTTCT 58.481 33.333 0.00 0.00 0.00 2.52
2093 2603 7.483059 CGGTGCTATCTTTTCTCATTTCTTTTC 59.517 37.037 0.00 0.00 0.00 2.29
2518 3060 2.906389 CCTCCTAGGCCTGCATTGTATA 59.094 50.000 17.99 0.00 0.00 1.47
2602 3144 9.788889 AGATGATGAAATGAATCAGTAGCAATA 57.211 29.630 0.00 0.00 37.46 1.90
2656 3198 1.514678 GCAACAACAGCATCGGACCA 61.515 55.000 0.00 0.00 0.00 4.02
2756 3298 3.088532 GCTGGATGTCCCAACAACAATA 58.911 45.455 0.00 0.00 46.07 1.90
2802 3344 1.878953 TTGACGAGGAAGGAACAAGC 58.121 50.000 0.00 0.00 0.00 4.01
2912 3480 9.550811 GGAGAAATTTAACACTTATTGGTAACG 57.449 33.333 0.00 0.00 37.09 3.18


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

AutoCloner maintained by Alex Coulton.