Multiple sequence alignment - TraesCS6D01G212500

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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 TraesCS6D01G212500 chr6D 100.000 4470 0 0 1 4470 300900169 300895700 0.000000e+00 8255.0
1 TraesCS6D01G212500 chr6D 85.275 455 63 4 3779 4230 187022938 187023391 2.440000e-127 466.0
2 TraesCS6D01G212500 chr6D 94.158 291 15 2 891 1180 50734161 50733872 4.100000e-120 442.0
3 TraesCS6D01G212500 chr6D 97.143 210 6 0 1 210 50735282 50735073 5.500000e-94 355.0
4 TraesCS6D01G212500 chr6D 86.667 105 14 0 3606 3710 34019220 34019116 2.830000e-22 117.0
5 TraesCS6D01G212500 chr6D 83.486 109 13 5 3598 3702 143405024 143404917 3.680000e-16 97.1
6 TraesCS6D01G212500 chr6D 100.000 49 0 0 862 910 50734753 50734705 1.710000e-14 91.6
7 TraesCS6D01G212500 chr6B 96.012 2583 82 9 1191 3764 465685340 465682770 0.000000e+00 4180.0
8 TraesCS6D01G212500 chr6B 87.482 695 83 3 3779 4470 298372048 298372741 0.000000e+00 798.0
9 TraesCS6D01G212500 chr6B 95.614 456 20 0 4015 4470 465682502 465682047 0.000000e+00 732.0
10 TraesCS6D01G212500 chr6B 95.089 224 11 0 3766 3989 465682718 465682495 1.980000e-93 353.0
11 TraesCS6D01G212500 chr6A 95.727 2598 96 4 1180 3764 416648462 416651057 0.000000e+00 4169.0
12 TraesCS6D01G212500 chr6A 95.615 707 30 1 3762 4467 416651105 416651811 0.000000e+00 1133.0
13 TraesCS6D01G212500 chr7D 96.870 1214 15 7 1 1193 127282388 127281177 0.000000e+00 2010.0
14 TraesCS6D01G212500 chr7D 95.238 210 10 0 1 210 458775648 458775439 2.580000e-87 333.0
15 TraesCS6D01G212500 chr7D 85.714 98 14 0 3606 3703 36670940 36671037 2.200000e-18 104.0
16 TraesCS6D01G212500 chr2D 79.942 2079 413 4 1253 3329 156707518 156709594 0.000000e+00 1526.0
17 TraesCS6D01G212500 chr2D 79.519 2080 420 6 1253 3329 156592507 156594583 0.000000e+00 1476.0
18 TraesCS6D01G212500 chr2D 80.318 1763 325 18 1579 3330 481689155 481690906 0.000000e+00 1314.0
19 TraesCS6D01G212500 chr2D 79.863 1758 342 10 1579 3330 481656600 481658351 0.000000e+00 1275.0
20 TraesCS6D01G212500 chr2D 93.103 319 21 1 862 1179 592034946 592035264 2.440000e-127 466.0
21 TraesCS6D01G212500 chr2D 86.139 101 13 1 3606 3705 317345732 317345632 1.700000e-19 108.0
22 TraesCS6D01G212500 chr1D 79.875 2082 409 10 1253 3329 93105116 93103040 0.000000e+00 1515.0
23 TraesCS6D01G212500 chr1D 98.271 347 6 0 209 555 433924268 433924614 3.820000e-170 608.0
24 TraesCS6D01G212500 chr1D 97.342 301 8 0 555 855 433924940 433924640 3.080000e-141 512.0
25 TraesCS6D01G212500 chr1B 79.587 2082 415 10 1253 3329 148416235 148414159 0.000000e+00 1482.0
26 TraesCS6D01G212500 chr1B 91.579 95 8 0 287 381 35031103 35031009 1.010000e-26 132.0
27 TraesCS6D01G212500 chr1B 87.179 78 10 0 749 826 35014812 35014889 6.160000e-14 89.8
28 TraesCS6D01G212500 chr1B 92.453 53 4 0 288 340 609432753 609432805 4.790000e-10 76.8
29 TraesCS6D01G212500 chr1B 100.000 32 0 0 427 458 35030826 35030795 4.830000e-05 60.2
30 TraesCS6D01G212500 chr2A 80.023 1762 332 16 1579 3330 624394846 624396597 0.000000e+00 1286.0
31 TraesCS6D01G212500 chr2A 91.483 317 26 1 864 1179 766716568 766716884 6.870000e-118 435.0
32 TraesCS6D01G212500 chr2A 83.166 398 64 2 1190 1584 624359567 624359964 1.180000e-95 361.0
33 TraesCS6D01G212500 chr2A 82.161 398 68 2 1190 1584 624394332 624394729 5.540000e-89 339.0
34 TraesCS6D01G212500 chr2A 82.161 398 68 2 1190 1584 624447153 624447550 5.540000e-89 339.0
35 TraesCS6D01G212500 chr2A 95.714 210 9 0 1 210 766715820 766716029 5.540000e-89 339.0
36 TraesCS6D01G212500 chr2A 85.274 292 32 8 891 1180 20799494 20799212 1.570000e-74 291.0
37 TraesCS6D01G212500 chr2A 73.700 654 153 17 3795 4435 775193483 775192836 2.080000e-58 237.0
38 TraesCS6D01G212500 chr2A 86.250 160 22 0 690 849 25359891 25360050 1.650000e-39 174.0
39 TraesCS6D01G212500 chr2A 77.517 298 33 15 208 486 686831200 686831482 1.000000e-31 148.0
40 TraesCS6D01G212500 chr2A 93.407 91 6 0 287 377 25360430 25360340 7.800000e-28 135.0
41 TraesCS6D01G212500 chr2A 81.818 121 6 4 383 497 25360268 25360158 2.220000e-13 87.9
42 TraesCS6D01G212500 chr5A 86.601 709 93 2 3763 4470 94475419 94474712 0.000000e+00 782.0
43 TraesCS6D01G212500 chr5A 85.243 637 81 11 3824 4455 311516216 311516844 1.050000e-180 643.0
44 TraesCS6D01G212500 chr3D 95.517 290 12 1 891 1180 1348035 1347747 3.150000e-126 462.0
45 TraesCS6D01G212500 chr3D 97.619 210 5 0 1 210 1348917 1348708 1.180000e-95 361.0
46 TraesCS6D01G212500 chr3D 95.238 210 10 0 1 210 272101042 272101251 2.580000e-87 333.0
47 TraesCS6D01G212500 chr3D 100.000 49 0 0 862 910 1348083 1348035 1.710000e-14 91.6
48 TraesCS6D01G212500 chr3D 100.000 49 0 0 862 910 1348388 1348340 1.710000e-14 91.6
49 TraesCS6D01G212500 chr4D 95.486 288 12 1 891 1178 62735380 62735094 4.070000e-125 459.0
50 TraesCS6D01G212500 chr4D 99.048 210 2 0 1 210 62736042 62735833 1.170000e-100 377.0
51 TraesCS6D01G212500 chr4D 90.566 106 8 2 748 851 471505584 471505479 6.030000e-29 139.0
52 TraesCS6D01G212500 chr4D 100.000 49 0 0 862 910 62735515 62735467 1.710000e-14 91.6
53 TraesCS6D01G212500 chr7A 90.596 319 29 1 864 1181 717412434 717412752 5.350000e-114 422.0
54 TraesCS6D01G212500 chr7A 90.221 317 29 2 865 1179 707978969 707979285 3.220000e-111 412.0
55 TraesCS6D01G212500 chr7A 87.255 102 13 0 3602 3703 205167760 205167861 2.830000e-22 117.0
56 TraesCS6D01G212500 chr5D 81.346 520 78 7 3763 4281 10777444 10777945 5.380000e-109 405.0
57 TraesCS6D01G212500 chr3A 98.551 207 3 0 4 210 130847715 130847509 2.540000e-97 366.0
58 TraesCS6D01G212500 chr3A 95.714 210 9 0 1 210 57209613 57209404 5.540000e-89 339.0
59 TraesCS6D01G212500 chr5B 90.566 106 8 2 748 851 592313603 592313708 6.030000e-29 139.0
60 TraesCS6D01G212500 chr1A 77.174 276 17 15 208 458 1697454 1697200 7.850000e-23 119.0
61 TraesCS6D01G212500 chr3B 87.129 101 12 1 3603 3702 630871665 630871765 3.650000e-21 113.0
62 TraesCS6D01G212500 chr2B 84.848 99 15 0 3606 3704 315079443 315079345 2.850000e-17 100.0
63 TraesCS6D01G212500 chr4A 90.541 74 5 2 780 851 689653116 689653189 3.680000e-16 97.1


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 TraesCS6D01G212500 chr6D 300895700 300900169 4469 True 8255.00 8255 100.000000 1 4470 1 chr6D.!!$R3 4469
1 TraesCS6D01G212500 chr6D 50733872 50735282 1410 True 296.20 442 97.100333 1 1180 3 chr6D.!!$R4 1179
2 TraesCS6D01G212500 chr6B 465682047 465685340 3293 True 1755.00 4180 95.571667 1191 4470 3 chr6B.!!$R1 3279
3 TraesCS6D01G212500 chr6B 298372048 298372741 693 False 798.00 798 87.482000 3779 4470 1 chr6B.!!$F1 691
4 TraesCS6D01G212500 chr6A 416648462 416651811 3349 False 2651.00 4169 95.671000 1180 4467 2 chr6A.!!$F1 3287
5 TraesCS6D01G212500 chr7D 127281177 127282388 1211 True 2010.00 2010 96.870000 1 1193 1 chr7D.!!$R1 1192
6 TraesCS6D01G212500 chr2D 156707518 156709594 2076 False 1526.00 1526 79.942000 1253 3329 1 chr2D.!!$F2 2076
7 TraesCS6D01G212500 chr2D 156592507 156594583 2076 False 1476.00 1476 79.519000 1253 3329 1 chr2D.!!$F1 2076
8 TraesCS6D01G212500 chr2D 481689155 481690906 1751 False 1314.00 1314 80.318000 1579 3330 1 chr2D.!!$F4 1751
9 TraesCS6D01G212500 chr2D 481656600 481658351 1751 False 1275.00 1275 79.863000 1579 3330 1 chr2D.!!$F3 1751
10 TraesCS6D01G212500 chr1D 93103040 93105116 2076 True 1515.00 1515 79.875000 1253 3329 1 chr1D.!!$R1 2076
11 TraesCS6D01G212500 chr1B 148414159 148416235 2076 True 1482.00 1482 79.587000 1253 3329 1 chr1B.!!$R1 2076
12 TraesCS6D01G212500 chr2A 624394332 624396597 2265 False 812.50 1286 81.092000 1190 3330 2 chr2A.!!$F5 2140
13 TraesCS6D01G212500 chr2A 766715820 766716884 1064 False 387.00 435 93.598500 1 1179 2 chr2A.!!$F6 1178
14 TraesCS6D01G212500 chr2A 775192836 775193483 647 True 237.00 237 73.700000 3795 4435 1 chr2A.!!$R2 640
15 TraesCS6D01G212500 chr5A 94474712 94475419 707 True 782.00 782 86.601000 3763 4470 1 chr5A.!!$R1 707
16 TraesCS6D01G212500 chr5A 311516216 311516844 628 False 643.00 643 85.243000 3824 4455 1 chr5A.!!$F1 631
17 TraesCS6D01G212500 chr3D 1347747 1348917 1170 True 251.55 462 98.284000 1 1180 4 chr3D.!!$R1 1179
18 TraesCS6D01G212500 chr4D 62735094 62736042 948 True 309.20 459 98.178000 1 1178 3 chr4D.!!$R2 1177
19 TraesCS6D01G212500 chr5D 10777444 10777945 501 False 405.00 405 81.346000 3763 4281 1 chr5D.!!$F1 518

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
1024 1752 1.045407 AGCACCTTACAACTCGGTCA 58.955 50.0 0.0 0.0 0.0 4.02 F
2425 3279 0.466543 ACAATACCCGCCTCGCAATA 59.533 50.0 0.0 0.0 0.0 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2670 3524 1.548357 GGCCTCTGCAGTCTTCCTGA 61.548 60.000 14.67 0.0 44.49 3.86 R
3608 4468 1.272704 ACTTCTTTTGGGATGGAGGGC 60.273 52.381 0.00 0.0 0.00 5.19 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
1024 1752 1.045407 AGCACCTTACAACTCGGTCA 58.955 50.000 0.00 0.00 0.00 4.02
1098 1827 4.036262 TGCAACGACTTAAGTGATTTTGCT 59.964 37.500 25.33 0.51 0.00 3.91
1102 1831 4.024048 ACGACTTAAGTGATTTTGCTGTGG 60.024 41.667 14.14 0.00 0.00 4.17
1155 1884 4.027674 TCTGCAAACCTAGCCACAAATA 57.972 40.909 0.00 0.00 0.00 1.40
1188 1917 2.229792 GCAATTGACTCCCACAAGTGA 58.770 47.619 10.34 0.00 43.04 3.41
1197 1926 3.099905 CTCCCACAAGTGAGATGGAGTA 58.900 50.000 12.37 0.00 35.33 2.59
1749 2603 2.829720 AGTTGCTCAATGCCAATGTCAT 59.170 40.909 0.00 0.00 42.00 3.06
1823 2677 1.064685 TCTCCTACATCGCTGGACTGA 60.065 52.381 0.00 0.00 0.00 3.41
2425 3279 0.466543 ACAATACCCGCCTCGCAATA 59.533 50.000 0.00 0.00 0.00 1.90
2662 3516 2.036089 GGACGTCAACTCTCTTGGTCTT 59.964 50.000 18.91 0.00 0.00 3.01
2670 3524 6.019748 TCAACTCTCTTGGTCTTATCTCCTT 58.980 40.000 0.00 0.00 0.00 3.36
2837 3691 2.158534 ACACTAAGCACCAATTCCACCA 60.159 45.455 0.00 0.00 0.00 4.17
2932 3786 4.021925 GACGACCCTTGCAGCCCT 62.022 66.667 0.00 0.00 0.00 5.19
3362 4216 5.690464 ACAAGCAGAAGATAAGAGGACAT 57.310 39.130 0.00 0.00 0.00 3.06
3388 4242 4.104738 AGAAGGTGGTTTCTCAGATTTCCA 59.895 41.667 0.00 0.00 31.97 3.53
3507 4363 4.320608 CCTTTTAGGCTGCTGAAACAAA 57.679 40.909 0.00 0.00 0.00 2.83
3548 4404 8.153724 TGAAGTATCGCGAATTATATTACGTG 57.846 34.615 15.24 0.00 37.55 4.49
3558 4414 8.212495 GCGAATTATATTACGTGGTACTTTCAG 58.788 37.037 0.00 0.00 0.00 3.02
3624 4484 0.254747 TACGCCCTCCATCCCAAAAG 59.745 55.000 0.00 0.00 0.00 2.27
3716 4584 4.214993 AGGAGTATAACCCAGGTAGCAT 57.785 45.455 0.00 0.00 0.00 3.79
3834 4752 5.946486 AGGTTCTGATCCTTTCTTTCTTGT 58.054 37.500 1.33 0.00 30.18 3.16
3871 4789 4.124351 CGCTGCCCACATGCCTTG 62.124 66.667 0.00 0.00 0.00 3.61
3917 4835 7.549134 GTGTTCATATGAGGTGTTGTTGATCTA 59.451 37.037 5.39 0.00 0.00 1.98
4261 5188 3.548745 CATGAGGTGCTCCATAGTTGA 57.451 47.619 7.70 0.00 35.89 3.18
4467 5394 5.289083 TGTTGACTGGTATATGCATGCTA 57.711 39.130 20.33 9.18 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.290641 GCGATCAAACGGGCTAAATCAT 59.709 45.455 0.00 0.00 0.00 2.45
754 845 1.391485 CAGATCTGACGGTTTTCTGCG 59.609 52.381 18.34 0.00 0.00 5.18
1024 1752 5.233050 CGTTTGATCGCTTTCTGACAGATAT 59.767 40.000 5.87 0.00 0.00 1.63
1098 1827 2.969628 AATCCGTTGCAAAAACCACA 57.030 40.000 0.00 0.00 0.00 4.17
1102 1831 4.284485 ACTCGTTAATCCGTTGCAAAAAC 58.716 39.130 0.00 0.00 0.00 2.43
1155 1884 3.642848 AGTCAATTGCAAGAAACCACCAT 59.357 39.130 4.94 0.00 0.00 3.55
1188 1917 1.338337 CGCCATTCTCGTACTCCATCT 59.662 52.381 0.00 0.00 0.00 2.90
1197 1926 1.741770 GCAACCTCGCCATTCTCGT 60.742 57.895 0.00 0.00 0.00 4.18
1450 2182 3.123620 CAGTCGCTGCTGGCCTTC 61.124 66.667 3.32 0.00 37.74 3.46
1663 2517 0.036388 GAAGGAGGGTGTTGATGCGA 60.036 55.000 0.00 0.00 0.00 5.10
1823 2677 4.814294 GTTCTCGCGGCCGGTGAT 62.814 66.667 29.38 0.00 33.99 3.06
2088 2942 1.614317 GGTGCTTCAGCTTGTGGGTAT 60.614 52.381 0.00 0.00 42.66 2.73
2425 3279 2.993264 AGCTTGCCAATTGCCGCT 60.993 55.556 0.00 1.76 39.86 5.52
2662 3516 3.703556 CTGCAGTCTTCCTGAAGGAGATA 59.296 47.826 5.25 0.00 46.36 1.98
2670 3524 1.548357 GGCCTCTGCAGTCTTCCTGA 61.548 60.000 14.67 0.00 44.49 3.86
2837 3691 4.796231 CGCTACGTGAAGGCCGCT 62.796 66.667 0.00 0.00 0.00 5.52
2932 3786 6.798427 AGCTTCTTCATCAGTGGATAGTTA 57.202 37.500 0.00 0.00 30.87 2.24
3077 3931 2.033141 AGCACGTGCAGCCTCAAT 59.967 55.556 39.21 15.97 45.16 2.57
3143 3997 0.469331 CGGTAGAGGGGGTATGAGCA 60.469 60.000 0.00 0.00 0.00 4.26
3388 4242 8.547967 AAATGTATCACTATTCACTTGTCGTT 57.452 30.769 0.00 0.00 0.00 3.85
3507 4363 9.341899 GCGATACTTCAAAAATTACAGTCAAAT 57.658 29.630 0.00 0.00 0.00 2.32
3548 4404 8.451908 AAACCATATAGAATGCTGAAAGTACC 57.548 34.615 0.00 0.00 35.30 3.34
3558 4414 8.840321 TGAAAGCTCTTAAACCATATAGAATGC 58.160 33.333 0.00 0.00 0.00 3.56
3578 4438 6.739112 ACTTTTCATTGTCCTACTTGAAAGC 58.261 36.000 0.00 0.00 38.77 3.51
3608 4468 1.272704 ACTTCTTTTGGGATGGAGGGC 60.273 52.381 0.00 0.00 0.00 5.19
3624 4484 8.883954 AAGTTGTACTAAGGTTAAGACACTTC 57.116 34.615 0.00 0.00 0.00 3.01
3689 4549 3.842436 ACCTGGGTTATACTCCTTTCGTT 59.158 43.478 0.00 0.00 0.00 3.85
3693 4553 4.368067 TGCTACCTGGGTTATACTCCTTT 58.632 43.478 0.00 0.00 0.00 3.11
3733 4601 9.620660 GAAAATACCACAAAACGATTGTTCTAT 57.379 29.630 0.00 4.72 37.31 1.98
3787 4705 8.898761 CCTAGATAGCTCAGTACCTGTAATATG 58.101 40.741 0.00 0.00 32.61 1.78
3810 4728 7.079451 ACAAGAAAGAAAGGATCAGAACCTA 57.921 36.000 0.00 0.00 36.67 3.08
3834 4752 2.636830 GGAGCTCAGAGCAAAGCATAA 58.363 47.619 24.64 0.00 45.56 1.90
3871 4789 8.564574 TGAACACATTGAAGTATTACCTCAAAC 58.435 33.333 10.97 2.46 0.00 2.93
3917 4835 7.451255 TGGTCAGTGAGGAATGACAAAATATTT 59.549 33.333 7.54 0.00 46.14 1.40


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

AutoCloner maintained by Alex Coulton.