Multiple sequence alignment - TraesCS7D01G392800

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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 TraesCS7D01G392800 chr7D 100.000 3816 0 0 1 3816 507820799 507816984 0.000000e+00 7047.0
1 TraesCS7D01G392800 chr7D 84.706 170 24 2 489 657 37116840 37116672 6.560000e-38 169.0
2 TraesCS7D01G392800 chr7D 87.075 147 18 1 489 634 187306771 187306917 8.480000e-37 165.0
3 TraesCS7D01G392800 chr7D 82.955 176 24 6 483 655 122878015 122878187 1.840000e-33 154.0
4 TraesCS7D01G392800 chr7D 80.899 178 29 4 302 477 635027243 635027417 6.650000e-28 135.0
5 TraesCS7D01G392800 chr7A 95.203 2314 71 16 705 2991 577445297 577442997 0.000000e+00 3622.0
6 TraesCS7D01G392800 chr7A 92.365 668 43 6 1 667 577448275 577447615 0.000000e+00 944.0
7 TraesCS7D01G392800 chr7A 92.857 378 22 3 3443 3816 577442468 577442092 9.320000e-151 544.0
8 TraesCS7D01G392800 chr7A 90.333 300 15 7 3119 3415 577442840 577442552 7.740000e-102 381.0
9 TraesCS7D01G392800 chr7A 95.625 160 3 1 3026 3181 577442999 577442840 1.760000e-63 254.0
10 TraesCS7D01G392800 chr7A 85.393 178 25 1 301 478 32776508 32776684 2.340000e-42 183.0
11 TraesCS7D01G392800 chr7A 85.965 171 23 1 488 657 197136295 197136125 8.420000e-42 182.0
12 TraesCS7D01G392800 chr7A 85.882 170 20 2 313 478 681095249 681095080 1.090000e-40 178.0
13 TraesCS7D01G392800 chr7A 83.721 172 25 3 489 658 46194516 46194346 3.950000e-35 159.0
14 TraesCS7D01G392800 chr7A 97.059 34 1 0 3415 3448 577442534 577442501 1.480000e-04 58.4
15 TraesCS7D01G392800 chr7B 95.847 1228 37 8 1781 3004 536006213 536004996 0.000000e+00 1973.0
16 TraesCS7D01G392800 chr7B 95.311 1109 41 7 682 1784 536007438 536006335 0.000000e+00 1749.0
17 TraesCS7D01G392800 chr7B 91.270 504 37 4 165 667 536007921 536007424 0.000000e+00 680.0
18 TraesCS7D01G392800 chr7B 94.385 374 17 2 3444 3813 536004578 536004205 4.280000e-159 571.0
19 TraesCS7D01G392800 chr7B 86.595 373 26 10 3086 3448 536004970 536004612 1.290000e-104 390.0
20 TraesCS7D01G392800 chr7B 91.463 164 14 0 302 465 382332091 382331928 3.840000e-55 226.0
21 TraesCS7D01G392800 chr7B 88.950 181 19 1 301 480 626602343 626602523 4.960000e-54 222.0
22 TraesCS7D01G392800 chr7B 94.444 126 5 2 43 168 536010558 536010435 3.890000e-45 193.0
23 TraesCS7D01G392800 chr7B 83.237 173 24 5 489 658 11668534 11668364 1.840000e-33 154.0
24 TraesCS7D01G392800 chr3D 91.860 172 12 2 298 468 87926164 87925994 4.930000e-59 239.0
25 TraesCS7D01G392800 chr2D 92.216 167 10 3 299 464 296364046 296364210 2.290000e-57 233.0
26 TraesCS7D01G392800 chr2D 84.211 171 26 1 489 658 585134258 585134428 8.480000e-37 165.0
27 TraesCS7D01G392800 chr2D 94.737 38 2 0 441 478 602733434 602733397 4.120000e-05 60.2
28 TraesCS7D01G392800 chr2B 92.216 167 10 3 299 464 366017682 366017518 2.290000e-57 233.0
29 TraesCS7D01G392800 chr2B 87.151 179 20 3 302 477 578597865 578597687 2.320000e-47 200.0
30 TraesCS7D01G392800 chrUn 91.515 165 14 0 299 463 141680743 141680907 1.070000e-55 228.0
31 TraesCS7D01G392800 chr4D 89.714 175 18 0 301 475 117421353 117421179 1.380000e-54 224.0
32 TraesCS7D01G392800 chr3B 78.107 169 33 4 486 652 53476553 53476387 1.880000e-18 104.0


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 TraesCS7D01G392800 chr7D 507816984 507820799 3815 True 7047.000000 7047 100.000000 1 3816 1 chr7D.!!$R2 3815
1 TraesCS7D01G392800 chr7A 577442092 577448275 6183 True 967.233333 3622 93.907000 1 3816 6 chr7A.!!$R4 3815
2 TraesCS7D01G392800 chr7B 536004205 536010558 6353 True 926.000000 1973 92.975333 43 3813 6 chr7B.!!$R3 3770


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
897 5726 0.462789 ACCGTCAACTTCCACGAACT 59.537 50.0 0.0 0.0 38.32 3.01 F
1246 6076 0.031585 CGTGGACGAGTTCTTGGACA 59.968 55.0 0.0 0.0 43.02 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2676 7666 1.069765 CCGGCTACCATTGCGAGAT 59.93 57.895 0.0 0.0 0.0 2.75 R
3007 7998 1.009829 CAGAGTGCCCGAACTTATGC 58.99 55.000 0.0 0.0 0.0 3.14 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
42 43 9.338622 ACGAAAATTAAAGGAGAAAGAGAAAGA 57.661 29.630 0.00 0.00 0.00 2.52
52 53 9.634021 AAGGAGAAAGAGAAAGAAAAGTTGTAT 57.366 29.630 0.00 0.00 0.00 2.29
232 2751 9.703892 AGATACAACACTTATGAGATAATGCTC 57.296 33.333 0.00 0.00 35.46 4.26
251 2770 4.021544 TGCTCGGGCAATTGTCTTTAAAAT 60.022 37.500 8.00 0.00 46.36 1.82
311 2830 9.352191 GTATGTTTAGTCTATCTACTCCTTCCA 57.648 37.037 0.00 0.00 0.00 3.53
395 2914 9.534565 GACATATTTTAGAGTGCAGATTCACTA 57.465 33.333 0.00 0.00 46.40 2.74
423 2942 3.819337 GCTCCGTATGTAGTCCATAGTGA 59.181 47.826 0.00 0.00 36.71 3.41
525 3044 6.307077 ACCTCGCGAAACTTTTTATTAATTGC 59.693 34.615 11.33 0.00 0.00 3.56
549 3068 5.009631 CACAATGTTTACAGGGATGAAGGA 58.990 41.667 0.00 0.00 0.00 3.36
635 3154 8.079203 TCGCTAAATTGTGAGCTTCAAAATTTA 58.921 29.630 20.86 20.86 46.72 1.40
725 5553 7.905604 ATAAAACGTTGAGAGTCATGAATCA 57.094 32.000 23.84 13.13 0.00 2.57
728 5556 6.414408 AACGTTGAGAGTCATGAATCATTC 57.586 37.500 23.84 14.33 0.00 2.67
897 5726 0.462789 ACCGTCAACTTCCACGAACT 59.537 50.000 0.00 0.00 38.32 3.01
904 5733 2.150397 ACTTCCACGAACTTTCCTCG 57.850 50.000 0.00 0.00 42.06 4.63
947 5777 1.664965 GAAGCACACGAGTCCGCTT 60.665 57.895 9.69 9.69 46.90 4.68
961 5791 3.385755 AGTCCGCTTATATAACAACCGGT 59.614 43.478 0.00 0.00 35.95 5.28
1246 6076 0.031585 CGTGGACGAGTTCTTGGACA 59.968 55.000 0.00 0.00 43.02 4.02
1553 6383 9.396022 CTTAGAATTTACATCCAGCTTAAGGAA 57.604 33.333 4.29 0.00 38.93 3.36
1574 6404 5.395990 GGAACAATTATCTGGAGGGTCGTTA 60.396 44.000 0.00 0.00 0.00 3.18
1623 6453 7.953710 CCGTAGTACTACTAAAATGCACAAAAC 59.046 37.037 26.36 1.52 31.62 2.43
1652 6492 7.195839 ACAAACTCTTAAGCTTTCAGATGTC 57.804 36.000 3.20 0.00 0.00 3.06
1655 6495 8.993121 CAAACTCTTAAGCTTTCAGATGTCTTA 58.007 33.333 3.20 0.00 0.00 2.10
1718 6569 6.924111 AGTACATGAGGGCACTAAAATTTTG 58.076 36.000 13.76 6.30 0.00 2.44
1958 6936 5.523916 CGTATAGCCTCTTACAAGTTGCATT 59.476 40.000 1.81 0.00 0.00 3.56
2409 7388 6.721318 ACCCTATTGCACTCAGAAAATCTAA 58.279 36.000 0.00 0.00 0.00 2.10
2415 7394 6.182039 TGCACTCAGAAAATCTAATTTCCG 57.818 37.500 0.00 0.00 39.59 4.30
2486 7476 4.738124 CGAGCTTGATGTCTCAGAACTTA 58.262 43.478 0.00 0.00 31.68 2.24
2533 7523 4.630069 GGATTACTTGCTCGCAGAAACTTA 59.370 41.667 0.00 0.00 34.09 2.24
2652 7642 0.974383 CTACCCAACCGAAGTCTGGT 59.026 55.000 0.00 0.00 42.98 4.00
2676 7666 0.898320 CCAAGGAGAGCCGAAAGAGA 59.102 55.000 0.00 0.00 39.96 3.10
2734 7724 1.066286 CCAGAGACCTTGGAGCTTCTG 60.066 57.143 0.00 0.00 0.00 3.02
2924 7915 7.500559 GTGGCTTTATCCATGACTATCTTTCTT 59.499 37.037 0.00 0.00 38.57 2.52
3004 7995 4.689345 GGCGTTCTGTGTTACTTTATGTCT 59.311 41.667 0.00 0.00 0.00 3.41
3005 7996 5.163982 GGCGTTCTGTGTTACTTTATGTCTC 60.164 44.000 0.00 0.00 0.00 3.36
3007 7998 5.060569 CGTTCTGTGTTACTTTATGTCTCGG 59.939 44.000 0.00 0.00 0.00 4.63
3008 7999 4.491676 TCTGTGTTACTTTATGTCTCGGC 58.508 43.478 0.00 0.00 0.00 5.54
3009 8000 4.021807 TCTGTGTTACTTTATGTCTCGGCA 60.022 41.667 0.00 0.00 0.00 5.69
3011 8002 5.968254 TGTGTTACTTTATGTCTCGGCATA 58.032 37.500 0.00 0.00 0.00 3.14
3012 8003 6.399743 TGTGTTACTTTATGTCTCGGCATAA 58.600 36.000 0.11 0.11 38.94 1.90
3013 8004 6.533723 TGTGTTACTTTATGTCTCGGCATAAG 59.466 38.462 4.40 2.89 40.88 1.73
3014 8005 6.534079 GTGTTACTTTATGTCTCGGCATAAGT 59.466 38.462 4.40 7.46 40.88 2.24
3015 8006 7.064253 GTGTTACTTTATGTCTCGGCATAAGTT 59.936 37.037 4.40 0.00 40.88 2.66
3016 8007 7.277098 TGTTACTTTATGTCTCGGCATAAGTTC 59.723 37.037 4.40 4.31 40.88 3.01
3017 8008 4.804139 ACTTTATGTCTCGGCATAAGTTCG 59.196 41.667 4.40 0.00 40.88 3.95
3018 8009 2.225068 ATGTCTCGGCATAAGTTCGG 57.775 50.000 0.00 0.00 0.00 4.30
3019 8010 0.174845 TGTCTCGGCATAAGTTCGGG 59.825 55.000 0.00 0.00 0.00 5.14
3020 8011 1.143183 TCTCGGCATAAGTTCGGGC 59.857 57.895 0.00 0.00 0.00 6.13
3021 8012 1.153449 CTCGGCATAAGTTCGGGCA 60.153 57.895 0.00 0.00 0.00 5.36
3024 8015 1.429148 CGGCATAAGTTCGGGCACTC 61.429 60.000 0.00 0.00 0.00 3.51
3212 8270 3.909430 GTACAAGTGCAGTACTGTAGCA 58.091 45.455 23.44 13.15 40.26 3.49
3368 8429 9.337396 ACGGCATGTTTATTAGAGATTCATTTA 57.663 29.630 0.00 0.00 0.00 1.40
3399 8460 7.659799 TCGTAATGTTCCTCTTCTCATTCAAAA 59.340 33.333 0.00 0.00 33.48 2.44
3528 8649 4.403734 TCAAACTTCAATGTTCCTACCCC 58.596 43.478 0.00 0.00 0.00 4.95
3652 8773 4.014406 ACAGAAAACGGTGGAAAGAAAGT 58.986 39.130 0.00 0.00 0.00 2.66
3729 8850 7.391148 AGCCAAACACTAACGATGAATTATT 57.609 32.000 0.00 0.00 0.00 1.40
3751 8872 6.426980 TTGTCATCCTCAAGAAATTCATCG 57.573 37.500 0.00 0.00 0.00 3.84
3759 8880 6.758416 TCCTCAAGAAATTCATCGACATACTG 59.242 38.462 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.939460 AATTTTCGTGCCACCTATGC 57.061 45.000 0.00 0.00 0.00 3.14
10 11 3.504520 TCTCCTTTAATTTTCGTGCCACC 59.495 43.478 0.00 0.00 0.00 4.61
52 53 9.679661 TTGCATAGAGAAATATTTCCACTTACA 57.320 29.630 21.86 16.04 37.92 2.41
232 2751 8.472683 TTGATTATTTTAAAGACAATTGCCCG 57.527 30.769 5.05 0.00 0.00 6.13
271 2790 9.911788 AGACTAAACATACTCATTTTGGATGAT 57.088 29.630 0.00 0.00 0.00 2.45
287 2806 9.440761 AATGGAAGGAGTAGATAGACTAAACAT 57.559 33.333 0.00 0.00 32.49 2.71
395 2914 4.839121 TGGACTACATACGGAGCAAAATT 58.161 39.130 0.00 0.00 0.00 1.82
525 3044 4.158394 CCTTCATCCCTGTAAACATTGTGG 59.842 45.833 0.00 0.00 0.00 4.17
549 3068 5.015178 TGATTAGGTCACCCTGGAGATTTTT 59.985 40.000 0.00 0.00 42.67 1.94
576 3095 2.123208 TCGGGGATGGCCGTCATA 60.123 61.111 26.14 5.54 35.97 2.15
580 3099 3.976490 TTCTCTCGGGGATGGCCGT 62.976 63.158 0.00 0.00 33.83 5.68
725 5553 3.618351 CTGCTGAGATGGACTTTGGAAT 58.382 45.455 0.00 0.00 0.00 3.01
728 5556 1.093159 GCTGCTGAGATGGACTTTGG 58.907 55.000 0.00 0.00 0.00 3.28
775 5604 1.956802 CTCGTTGGGTTTTCCTGGC 59.043 57.895 0.00 0.00 40.46 4.85
897 5726 2.754375 GTGGGGAAGGCGAGGAAA 59.246 61.111 0.00 0.00 0.00 3.13
947 5777 3.039743 TCTGGCCACCGGTTGTTATATA 58.960 45.455 2.97 0.00 0.00 0.86
961 5791 1.118965 TTTGTCTCGGTCTCTGGCCA 61.119 55.000 4.71 4.71 0.00 5.36
1344 6174 4.016706 GTCACCACCTCCACCCCG 62.017 72.222 0.00 0.00 0.00 5.73
1553 6383 5.365605 TGATAACGACCCTCCAGATAATTGT 59.634 40.000 0.00 0.00 0.00 2.71
1574 6404 9.310449 ACGGATTAGGTTAAGTATGACTATGAT 57.690 33.333 0.00 0.00 0.00 2.45
1623 6453 8.142994 TCTGAAAGCTTAAGAGTTTGTTACAG 57.857 34.615 6.67 8.28 0.00 2.74
1652 6492 7.709182 TGAGTAACATTCACCATACGGAATAAG 59.291 37.037 0.00 0.00 32.71 1.73
1655 6495 5.984725 TGAGTAACATTCACCATACGGAAT 58.015 37.500 0.00 0.00 34.19 3.01
1718 6569 5.793457 GTCAACCGACAAGTTATGCAATTAC 59.207 40.000 0.00 0.00 42.13 1.89
1899 6877 6.427547 CCAAATAGCCTTGCAATTGAGAAAAA 59.572 34.615 10.34 0.00 0.00 1.94
1958 6936 6.600822 TCATTTGCCTGAAAAATCACCAAAAA 59.399 30.769 0.00 0.00 0.00 1.94
2390 7369 7.094205 ACGGAAATTAGATTTTCTGAGTGCAAT 60.094 33.333 11.57 0.00 42.21 3.56
2409 7388 4.991056 CGATCAGATATCACCAACGGAAAT 59.009 41.667 5.32 0.00 0.00 2.17
2415 7394 7.715265 ATGTAAACGATCAGATATCACCAAC 57.285 36.000 5.32 0.00 0.00 3.77
2533 7523 7.925483 TGAAAACAATTACATTTAGCACAGCTT 59.075 29.630 0.00 0.00 40.44 3.74
2676 7666 1.069765 CCGGCTACCATTGCGAGAT 59.930 57.895 0.00 0.00 0.00 2.75
2924 7915 4.227197 AGAACAAAGGGAACAGAGAGAGA 58.773 43.478 0.00 0.00 0.00 3.10
3004 7995 1.448893 GTGCCCGAACTTATGCCGA 60.449 57.895 0.00 0.00 0.00 5.54
3005 7996 1.429148 GAGTGCCCGAACTTATGCCG 61.429 60.000 0.00 0.00 0.00 5.69
3007 7998 1.009829 CAGAGTGCCCGAACTTATGC 58.990 55.000 0.00 0.00 0.00 3.14
3008 7999 2.093973 AGACAGAGTGCCCGAACTTATG 60.094 50.000 0.00 0.00 0.00 1.90
3009 8000 2.180276 AGACAGAGTGCCCGAACTTAT 58.820 47.619 0.00 0.00 0.00 1.73
3011 8002 1.629043 TAGACAGAGTGCCCGAACTT 58.371 50.000 0.00 0.00 0.00 2.66
3012 8003 1.751924 GATAGACAGAGTGCCCGAACT 59.248 52.381 0.00 0.00 0.00 3.01
3013 8004 1.751924 AGATAGACAGAGTGCCCGAAC 59.248 52.381 0.00 0.00 0.00 3.95
3014 8005 2.025155 GAGATAGACAGAGTGCCCGAA 58.975 52.381 0.00 0.00 0.00 4.30
3015 8006 1.213182 AGAGATAGACAGAGTGCCCGA 59.787 52.381 0.00 0.00 0.00 5.14
3016 8007 1.606668 GAGAGATAGACAGAGTGCCCG 59.393 57.143 0.00 0.00 0.00 6.13
3017 8008 2.622942 CAGAGAGATAGACAGAGTGCCC 59.377 54.545 0.00 0.00 0.00 5.36
3018 8009 2.622942 CCAGAGAGATAGACAGAGTGCC 59.377 54.545 0.00 0.00 0.00 5.01
3019 8010 2.622942 CCCAGAGAGATAGACAGAGTGC 59.377 54.545 0.00 0.00 0.00 4.40
3020 8011 3.897239 ACCCAGAGAGATAGACAGAGTG 58.103 50.000 0.00 0.00 0.00 3.51
3021 8012 4.601406 AACCCAGAGAGATAGACAGAGT 57.399 45.455 0.00 0.00 0.00 3.24
3024 8015 6.723298 ACATAAACCCAGAGAGATAGACAG 57.277 41.667 0.00 0.00 0.00 3.51
3211 8269 3.490439 AACCCCAAAAGCAGGAAAATG 57.510 42.857 0.00 0.00 0.00 2.32
3212 8270 3.582647 CCTAACCCCAAAAGCAGGAAAAT 59.417 43.478 0.00 0.00 0.00 1.82
3339 8400 7.693952 TGAATCTCTAATAAACATGCCGTTTC 58.306 34.615 4.75 0.00 44.78 2.78
3359 8420 8.674607 AGGAACATTACGAAAGGTAAATGAATC 58.325 33.333 0.00 0.00 43.93 2.52
3360 8421 8.575649 AGGAACATTACGAAAGGTAAATGAAT 57.424 30.769 0.00 0.00 43.93 2.57
3368 8429 5.011738 TGAGAAGAGGAACATTACGAAAGGT 59.988 40.000 0.00 0.00 0.00 3.50
3374 8435 6.968131 TTGAATGAGAAGAGGAACATTACG 57.032 37.500 0.00 0.00 33.92 3.18
3514 8635 2.577606 TGTGTGGGGTAGGAACATTG 57.422 50.000 0.00 0.00 0.00 2.82
3612 8733 5.321959 TCTGTTTTGTTGCTCATGAACAA 57.678 34.783 7.45 7.45 40.65 2.83
3619 8740 3.057174 ACCGTTTTCTGTTTTGTTGCTCA 60.057 39.130 0.00 0.00 0.00 4.26
3620 8741 3.303229 CACCGTTTTCTGTTTTGTTGCTC 59.697 43.478 0.00 0.00 0.00 4.26
3622 8743 2.347150 CCACCGTTTTCTGTTTTGTTGC 59.653 45.455 0.00 0.00 0.00 4.17
3707 8828 8.233868 TGACAATAATTCATCGTTAGTGTTTGG 58.766 33.333 1.35 0.00 39.55 3.28
3729 8850 5.582269 GTCGATGAATTTCTTGAGGATGACA 59.418 40.000 0.00 0.00 0.00 3.58
3751 8872 2.722094 TCATTGTTGGGGCAGTATGTC 58.278 47.619 0.00 0.00 42.54 3.06
3759 8880 1.851304 TGAGGATTCATTGTTGGGGC 58.149 50.000 0.00 0.00 0.00 5.80



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

AutoCloner maintained by Alex Coulton.