Multiple sequence alignment - TraesCS1D01G131700

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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 TraesCS1D01G131700 chr1D 100.000 4389 0 0 1 4389 155347584 155343196 0.000000e+00 8106.0
1 TraesCS1D01G131700 chr1D 88.754 578 52 10 1 569 343261975 343262548 0.000000e+00 695.0
2 TraesCS1D01G131700 chr1B 96.764 2287 41 10 1406 3683 220751288 220753550 0.000000e+00 3783.0
3 TraesCS1D01G131700 chr1B 98.165 763 12 1 3627 4389 220753566 220754326 0.000000e+00 1330.0
4 TraesCS1D01G131700 chr1B 88.042 761 76 9 404 1154 220740205 220740960 0.000000e+00 887.0
5 TraesCS1D01G131700 chr1B 86.667 180 21 2 1148 1326 220741010 220741187 3.460000e-46 196.0
6 TraesCS1D01G131700 chr1A 97.542 1261 20 2 1392 2650 204826199 204827450 0.000000e+00 2146.0
7 TraesCS1D01G131700 chr1A 95.837 1273 25 9 2615 3884 204827555 204828802 0.000000e+00 2032.0
8 TraesCS1D01G131700 chr1A 93.667 679 38 3 1 678 204801934 204802608 0.000000e+00 1011.0
9 TraesCS1D01G131700 chr1A 96.450 507 10 4 3883 4389 204829062 204829560 0.000000e+00 830.0
10 TraesCS1D01G131700 chr1A 92.601 419 26 4 736 1154 204802608 204803021 8.120000e-167 597.0
11 TraesCS1D01G131700 chr1A 90.476 126 12 0 1222 1347 204824905 204825030 2.720000e-37 167.0
12 TraesCS1D01G131700 chr1A 97.778 45 1 0 1333 1377 204826170 204826214 1.310000e-10 78.7
13 TraesCS1D01G131700 chr2A 89.721 574 53 6 1 569 161846276 161845704 0.000000e+00 728.0
14 TraesCS1D01G131700 chr5B 89.721 574 48 10 1 566 351104535 351105105 0.000000e+00 723.0
15 TraesCS1D01G131700 chr5B 88.368 576 59 7 1 569 436104172 436103598 0.000000e+00 686.0
16 TraesCS1D01G131700 chr5B 92.793 111 7 1 794 904 48848786 48848677 4.540000e-35 159.0
17 TraesCS1D01G131700 chr5B 94.000 50 2 1 742 790 678738456 678738505 1.690000e-09 75.0
18 TraesCS1D01G131700 chr5D 88.715 576 57 6 1 569 215872969 215872395 0.000000e+00 697.0
19 TraesCS1D01G131700 chr5D 89.065 567 52 9 1 560 373201381 373201944 0.000000e+00 695.0
20 TraesCS1D01G131700 chr5D 84.000 75 8 3 730 803 389412808 389412879 7.880000e-08 69.4
21 TraesCS1D01G131700 chr4D 88.850 574 51 8 1 569 32782586 32783151 0.000000e+00 693.0
22 TraesCS1D01G131700 chr4D 92.157 51 3 1 743 792 9557211 9557261 2.190000e-08 71.3
23 TraesCS1D01G131700 chr3A 88.482 573 61 5 1 569 586908253 586907682 0.000000e+00 688.0
24 TraesCS1D01G131700 chr3A 94.495 109 6 0 794 902 36388887 36388779 7.550000e-38 169.0
25 TraesCS1D01G131700 chrUn 87.666 527 48 11 1537 2060 76000745 76000233 8.120000e-167 597.0
26 TraesCS1D01G131700 chrUn 84.431 334 51 1 3094 3426 76000221 75999888 1.180000e-85 327.0
27 TraesCS1D01G131700 chr6D 87.643 526 50 4 1537 2060 5838544 5839056 8.120000e-167 597.0
28 TraesCS1D01G131700 chr6D 86.527 334 45 0 3093 3426 5839064 5839397 6.930000e-98 368.0
29 TraesCS1D01G131700 chr6D 80.583 412 48 15 3128 3538 4928244 4928624 5.550000e-74 289.0
30 TraesCS1D01G131700 chr6A 87.287 527 56 5 1537 2060 5206529 5207047 3.780000e-165 592.0
31 TraesCS1D01G131700 chr6A 87.126 334 43 0 3093 3426 5207055 5207388 3.200000e-101 379.0
32 TraesCS1D01G131700 chr6B 84.228 298 38 6 2326 2618 621310185 621309892 9.290000e-72 281.0
33 TraesCS1D01G131700 chr3D 83.178 214 25 6 2313 2526 576775170 576774968 7.500000e-43 185.0
34 TraesCS1D01G131700 chr3D 92.105 114 8 1 794 907 141779124 141779012 4.540000e-35 159.0
35 TraesCS1D01G131700 chr7D 95.192 104 5 0 794 897 73143586 73143483 9.770000e-37 165.0
36 TraesCS1D01G131700 chr7D 94.444 108 5 1 794 900 507792617 507792724 9.770000e-37 165.0
37 TraesCS1D01G131700 chr7D 96.078 51 2 0 742 792 26560672 26560722 2.810000e-12 84.2
38 TraesCS1D01G131700 chr2D 94.393 107 6 0 794 900 534061377 534061483 9.770000e-37 165.0
39 TraesCS1D01G131700 chr4B 93.578 109 4 3 794 902 619660164 619660059 4.540000e-35 159.0
40 TraesCS1D01G131700 chr5A 97.917 48 1 0 743 790 546261906 546261859 2.810000e-12 84.2
41 TraesCS1D01G131700 chr7B 95.833 48 1 1 743 789 118222192 118222239 4.710000e-10 76.8


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 TraesCS1D01G131700 chr1D 155343196 155347584 4388 True 8106.00 8106 100.0000 1 4389 1 chr1D.!!$R1 4388
1 TraesCS1D01G131700 chr1D 343261975 343262548 573 False 695.00 695 88.7540 1 569 1 chr1D.!!$F1 568
2 TraesCS1D01G131700 chr1B 220751288 220754326 3038 False 2556.50 3783 97.4645 1406 4389 2 chr1B.!!$F2 2983
3 TraesCS1D01G131700 chr1B 220740205 220741187 982 False 541.50 887 87.3545 404 1326 2 chr1B.!!$F1 922
4 TraesCS1D01G131700 chr1A 204824905 204829560 4655 False 1050.74 2146 95.6166 1222 4389 5 chr1A.!!$F2 3167
5 TraesCS1D01G131700 chr1A 204801934 204803021 1087 False 804.00 1011 93.1340 1 1154 2 chr1A.!!$F1 1153
6 TraesCS1D01G131700 chr2A 161845704 161846276 572 True 728.00 728 89.7210 1 569 1 chr2A.!!$R1 568
7 TraesCS1D01G131700 chr5B 351104535 351105105 570 False 723.00 723 89.7210 1 566 1 chr5B.!!$F1 565
8 TraesCS1D01G131700 chr5B 436103598 436104172 574 True 686.00 686 88.3680 1 569 1 chr5B.!!$R2 568
9 TraesCS1D01G131700 chr5D 215872395 215872969 574 True 697.00 697 88.7150 1 569 1 chr5D.!!$R1 568
10 TraesCS1D01G131700 chr5D 373201381 373201944 563 False 695.00 695 89.0650 1 560 1 chr5D.!!$F1 559
11 TraesCS1D01G131700 chr4D 32782586 32783151 565 False 693.00 693 88.8500 1 569 1 chr4D.!!$F2 568
12 TraesCS1D01G131700 chr3A 586907682 586908253 571 True 688.00 688 88.4820 1 569 1 chr3A.!!$R2 568
13 TraesCS1D01G131700 chrUn 75999888 76000745 857 True 462.00 597 86.0485 1537 3426 2 chrUn.!!$R1 1889
14 TraesCS1D01G131700 chr6D 5838544 5839397 853 False 482.50 597 87.0850 1537 3426 2 chr6D.!!$F2 1889
15 TraesCS1D01G131700 chr6A 5206529 5207388 859 False 485.50 592 87.2065 1537 3426 2 chr6A.!!$F1 1889

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
661 683 0.034896 AAAGACCTCGCCGACATGTT 59.965 50.000 0.0 0.0 0.00 2.71 F
1254 1334 0.249398 GGCCAAAGCTTCTACCGAGA 59.751 55.000 0.0 0.0 39.73 4.04 F
1365 2599 1.178276 AACCAAACACGCTCCAAACA 58.822 45.000 0.0 0.0 0.00 2.83 F
2133 3371 4.065789 GGTCTGGTTAGAGTTCCTGTTTG 58.934 47.826 0.0 0.0 32.48 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 3371 1.227853 AGAGCAAACACCACGACCC 60.228 57.895 0.00 0.0 0.00 4.46 R
2968 4357 3.827008 TGGTGGCAGCAAAAATTACAA 57.173 38.095 18.31 0.0 0.00 2.41 R
3022 4411 7.923878 CAGTAAATAGAAAGAGGCCTAGAGAAC 59.076 40.741 4.42 0.0 0.00 3.01 R
3489 4882 3.066380 CAGCTGCACGCCACATATATTA 58.934 45.455 0.00 0.0 40.39 0.98 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
74 77 3.920841 AGGTAGGTTTCAGGGGTTTACAT 59.079 43.478 0.00 0.00 0.00 2.29
132 139 3.618780 GACAGCAGCCACAGAGGGG 62.619 68.421 0.00 0.00 38.09 4.79
210 217 0.825010 CAGCAAGGTTGAGGTTGGCT 60.825 55.000 0.00 0.00 0.00 4.75
423 432 1.372582 CACATACCATGCGAGCAACT 58.627 50.000 0.57 0.00 0.00 3.16
602 624 3.261951 CCCATAACTGTCGCGCCG 61.262 66.667 0.00 0.00 0.00 6.46
612 634 4.063967 TCGCGCCGTGACAAGGAT 62.064 61.111 12.01 0.00 0.00 3.24
657 679 1.301401 CCAAAAGACCTCGCCGACA 60.301 57.895 0.00 0.00 0.00 4.35
661 683 0.034896 AAAGACCTCGCCGACATGTT 59.965 50.000 0.00 0.00 0.00 2.71
686 708 0.305009 TATCGCGCTTCTGACGAGAG 59.695 55.000 5.56 0.00 42.44 3.20
719 741 2.506231 TGTGTCTTGGGTCAAAGGTACA 59.494 45.455 0.00 0.00 0.00 2.90
724 746 2.922740 TGGGTCAAAGGTACACAGTC 57.077 50.000 0.00 0.00 0.00 3.51
792 814 5.800438 CGCTCATACATACGCATATACACTT 59.200 40.000 0.00 0.00 0.00 3.16
841 863 0.951040 GAGCACCAGGACTTGAACCG 60.951 60.000 0.00 0.00 0.00 4.44
984 1006 4.742417 CGCATTTTATTGATGACCCAACA 58.258 39.130 0.00 0.00 0.00 3.33
987 1009 6.397272 GCATTTTATTGATGACCCAACAGAA 58.603 36.000 0.00 0.00 0.00 3.02
1010 1032 8.416329 AGAATTACATCATGGATTACAAAAGGC 58.584 33.333 0.00 0.00 0.00 4.35
1093 1116 3.201353 TGCTAAATTATGCGCCACCTA 57.799 42.857 4.18 0.00 0.00 3.08
1108 1131 2.771943 CCACCTAGTTGGCATTCCTAGA 59.228 50.000 14.44 0.00 40.22 2.43
1109 1132 3.432326 CCACCTAGTTGGCATTCCTAGAC 60.432 52.174 14.44 0.00 40.22 2.59
1165 1245 5.812665 GCTTTTGCAAACAGTATCAACTC 57.187 39.130 12.39 0.00 46.58 3.01
1187 1267 0.898789 ACGAGTCCGATTCCACCACT 60.899 55.000 0.00 0.00 39.50 4.00
1194 1274 1.553248 CCGATTCCACCACTACTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
1210 1290 1.410050 CCAAAGCAGCCCAGGGTTTT 61.410 55.000 7.55 0.58 34.04 2.43
1211 1291 1.337118 CAAAGCAGCCCAGGGTTTTA 58.663 50.000 7.55 0.00 34.04 1.52
1220 1300 4.770010 CAGCCCAGGGTTTTAAGTAAATGA 59.230 41.667 7.55 0.00 0.00 2.57
1229 1309 9.831682 AGGGTTTTAAGTAAATGAAATCCCTTA 57.168 29.630 8.72 0.00 44.59 2.69
1248 1328 5.437060 CCTTAAGTATGGCCAAAGCTTCTA 58.563 41.667 10.96 5.82 39.73 2.10
1249 1329 5.297029 CCTTAAGTATGGCCAAAGCTTCTAC 59.703 44.000 10.96 5.83 39.73 2.59
1254 1334 0.249398 GGCCAAAGCTTCTACCGAGA 59.751 55.000 0.00 0.00 39.73 4.04
1285 1365 5.163488 CCAGTACACGTGATATTGGGTTAGA 60.163 44.000 25.01 0.00 0.00 2.10
1287 1367 6.420903 CAGTACACGTGATATTGGGTTAGATG 59.579 42.308 25.01 0.00 0.00 2.90
1295 1375 2.895372 GGGTTAGATGCACCCGCG 60.895 66.667 0.00 0.00 44.83 6.46
1365 2599 1.178276 AACCAAACACGCTCCAAACA 58.822 45.000 0.00 0.00 0.00 2.83
2133 3371 4.065789 GGTCTGGTTAGAGTTCCTGTTTG 58.934 47.826 0.00 0.00 32.48 2.93
2542 3786 9.950496 ATTCTGAATATACACCTTAGCCTATTG 57.050 33.333 0.00 0.00 0.00 1.90
2595 3841 5.178809 ACTTTGGTTATCTAAACTCACGTGC 59.821 40.000 11.67 0.00 0.00 5.34
2968 4357 6.862209 TCAAAGTACAGCAATTCAAGTGTTT 58.138 32.000 0.00 0.00 0.00 2.83
3022 4411 3.839051 TGTCTGAGAACGAGTCATCAG 57.161 47.619 9.88 9.88 40.42 2.90
3534 4927 3.630769 GCATGACTGGATGACAACATGAT 59.369 43.478 0.00 0.00 41.87 2.45
3564 4957 6.402222 TGGTTGTCAGTTAACAGCAAATTTT 58.598 32.000 8.61 0.00 32.58 1.82
3565 4958 6.312426 TGGTTGTCAGTTAACAGCAAATTTTG 59.688 34.615 8.61 4.72 32.58 2.44
3993 5706 3.904965 TCCACCTTGTGAAGTATACACCA 59.095 43.478 5.50 0.00 37.45 4.17
4128 5841 3.744940 TCCTGAAGGAGCCATTCAAAT 57.255 42.857 0.00 0.00 39.78 2.32
4269 5982 4.819105 ACGAAAGATGGTCCACATAGAA 57.181 40.909 0.00 0.00 40.72 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 77 3.815856 TTGTTGCAAGCTTCCATGAAA 57.184 38.095 0.00 0.00 0.00 2.69
132 139 0.810426 GCCGCCTGCCTAGTCTTAAC 60.810 60.000 0.00 0.00 0.00 2.01
210 217 1.683943 CCTAACGGACGATCCACCTA 58.316 55.000 0.00 0.00 35.91 3.08
441 451 0.981183 TCCCTTCATGGTAGCAACGT 59.019 50.000 0.00 0.00 0.00 3.99
455 465 1.063183 GCCTGCATATCCTCTCCCTT 58.937 55.000 0.00 0.00 0.00 3.95
569 591 1.461461 GGGCTACCCTAGGGATGCA 60.461 63.158 35.38 14.55 41.34 3.96
602 624 4.074970 ACATGTTTGAGGATCCTTGTCAC 58.925 43.478 17.42 11.08 0.00 3.67
611 633 2.610438 AAGCCCACATGTTTGAGGAT 57.390 45.000 0.00 0.00 35.78 3.24
612 634 2.364970 CAAAAGCCCACATGTTTGAGGA 59.635 45.455 0.00 0.00 35.78 3.71
657 679 2.747446 AGAAGCGCGATACCAAAAACAT 59.253 40.909 12.10 0.00 0.00 2.71
661 683 1.730064 GTCAGAAGCGCGATACCAAAA 59.270 47.619 12.10 0.00 0.00 2.44
719 741 4.297071 CGTCGAACACGTGACTGT 57.703 55.556 25.01 3.87 44.07 3.55
760 782 2.390938 GTATGTATGAGCGCTTGCGTA 58.609 47.619 13.26 2.82 45.69 4.42
841 863 2.595655 GTATCCCCAGCCCACCAC 59.404 66.667 0.00 0.00 0.00 4.16
942 964 0.250234 CCGAGATGGCACTTCCTTCA 59.750 55.000 0.00 0.00 40.48 3.02
943 965 3.071580 CCGAGATGGCACTTCCTTC 57.928 57.895 0.00 0.00 38.84 3.46
984 1006 8.416329 GCCTTTTGTAATCCATGATGTAATTCT 58.584 33.333 0.00 0.00 0.00 2.40
987 1009 7.658525 TGCCTTTTGTAATCCATGATGTAAT 57.341 32.000 0.00 0.00 0.00 1.89
1093 1116 3.624777 CATTGGTCTAGGAATGCCAACT 58.375 45.455 0.00 0.00 42.83 3.16
1108 1131 6.125029 ACTAGCATATCTTTTCAGCATTGGT 58.875 36.000 0.00 0.00 0.00 3.67
1109 1132 6.630444 ACTAGCATATCTTTTCAGCATTGG 57.370 37.500 0.00 0.00 0.00 3.16
1165 1245 0.739813 GGTGGAATCGGACTCGTTGG 60.740 60.000 0.00 0.00 37.69 3.77
1175 1255 3.262420 CTTTGGAGTAGTGGTGGAATCG 58.738 50.000 0.00 0.00 0.00 3.34
1187 1267 1.685224 CCTGGGCTGCTTTGGAGTA 59.315 57.895 0.00 0.00 0.00 2.59
1194 1274 1.133167 ACTTAAAACCCTGGGCTGCTT 60.133 47.619 14.08 3.56 0.00 3.91
1211 1291 8.914011 GCCATACTTAAGGGATTTCATTTACTT 58.086 33.333 7.53 0.00 0.00 2.24
1220 1300 4.405680 GCTTTGGCCATACTTAAGGGATTT 59.594 41.667 6.09 0.00 0.00 2.17
1229 1309 3.621558 GGTAGAAGCTTTGGCCATACTT 58.378 45.455 6.09 10.96 39.73 2.24
1248 1328 3.907260 TACTGGACGCGGTCTCGGT 62.907 63.158 12.47 10.27 36.79 4.69
1249 1329 3.129502 TACTGGACGCGGTCTCGG 61.130 66.667 12.47 4.26 36.79 4.63
1285 1365 3.521529 GAGGCTATCGCGGGTGCAT 62.522 63.158 6.13 5.55 42.97 3.96
1295 1375 2.866762 CAACAACTTAGGCGAGGCTATC 59.133 50.000 7.21 0.00 0.00 2.08
1400 2634 3.129638 CCGTTTGTTCCACCTGAGAAAAA 59.870 43.478 0.00 0.00 0.00 1.94
1401 2635 2.685897 CCGTTTGTTCCACCTGAGAAAA 59.314 45.455 0.00 0.00 0.00 2.29
1402 2636 2.294074 CCGTTTGTTCCACCTGAGAAA 58.706 47.619 0.00 0.00 0.00 2.52
1403 2637 1.210967 ACCGTTTGTTCCACCTGAGAA 59.789 47.619 0.00 0.00 0.00 2.87
1404 2638 0.834612 ACCGTTTGTTCCACCTGAGA 59.165 50.000 0.00 0.00 0.00 3.27
1409 2643 3.437428 GTGTTTAACCGTTTGTTCCACC 58.563 45.455 0.00 0.00 38.42 4.61
1508 2744 2.610859 GGGCAGGAAGGGAGGACA 60.611 66.667 0.00 0.00 0.00 4.02
1629 2867 1.299976 CCTCCACCTTGGGTACTGC 59.700 63.158 0.00 0.00 38.32 4.40
2133 3371 1.227853 AGAGCAAACACCACGACCC 60.228 57.895 0.00 0.00 0.00 4.46
2517 3761 8.934697 ACAATAGGCTAAGGTGTATATTCAGAA 58.065 33.333 0.00 0.00 0.00 3.02
2679 4068 8.508883 TGGGTACAATTATTTATGTTTAGCGT 57.491 30.769 0.00 0.00 0.00 5.07
2932 4321 6.226052 TGCTGTACTTTGATATAGGAGCATG 58.774 40.000 0.00 0.00 0.00 4.06
2935 4324 7.442364 TGAATTGCTGTACTTTGATATAGGAGC 59.558 37.037 0.00 0.00 0.00 4.70
2968 4357 3.827008 TGGTGGCAGCAAAAATTACAA 57.173 38.095 18.31 0.00 0.00 2.41
3022 4411 7.923878 CAGTAAATAGAAAGAGGCCTAGAGAAC 59.076 40.741 4.42 0.00 0.00 3.01
3489 4882 3.066380 CAGCTGCACGCCACATATATTA 58.934 45.455 0.00 0.00 40.39 0.98
3564 4957 5.810587 GCTCGTTGGATAAACTCTTCATACA 59.189 40.000 0.00 0.00 36.56 2.29
3565 4958 6.043411 AGCTCGTTGGATAAACTCTTCATAC 58.957 40.000 0.00 0.00 36.56 2.39
4127 5840 9.707957 CCATTCTCTCCTCATAGTACCTTATAT 57.292 37.037 0.00 0.00 0.00 0.86
4128 5841 7.616150 GCCATTCTCTCCTCATAGTACCTTATA 59.384 40.741 0.00 0.00 0.00 0.98
4152 5865 6.692681 GTCATAAACATCAACATGTACATGCC 59.307 38.462 31.19 0.00 42.89 4.40
4269 5982 1.209019 CTCATACTGCTTGCAGGGTCT 59.791 52.381 23.98 7.92 0.00 3.85


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

AutoCloner maintained by Alex Coulton.