Multiple sequence alignment - TraesCS6D01G343500

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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 TraesCS6D01G343500 chr6D 100.000 3236 0 0 1 3236 443283566 443280331 0.000000e+00 5976
1 TraesCS6D01G343500 chr6D 97.921 2261 44 3 335 2594 443266463 443264205 0.000000e+00 3912
2 TraesCS6D01G343500 chr6D 89.305 187 16 4 287 471 462051219 462051403 6.980000e-57 231
3 TraesCS6D01G343500 chr4A 93.652 2930 102 19 331 3236 524274191 524271322 0.000000e+00 4303
4 TraesCS6D01G343500 chr4A 90.105 950 87 5 2033 2977 190403299 190404246 0.000000e+00 1227
5 TraesCS6D01G343500 chr4A 86.181 398 43 7 7 402 241017983 241017596 1.390000e-113 420
6 TraesCS6D01G343500 chr4A 89.057 265 23 4 2976 3236 190404572 190404834 1.120000e-84 324
7 TraesCS6D01G343500 chrUn 94.621 2082 71 19 287 2367 101224774 101222733 0.000000e+00 3186
8 TraesCS6D01G343500 chrUn 95.820 622 24 2 2616 3236 101222738 101222118 0.000000e+00 1003
9 TraesCS6D01G343500 chrUn 89.880 415 36 6 1 412 40188200 40187789 2.210000e-146 529
10 TraesCS6D01G343500 chrUn 92.705 329 16 5 1 326 29905175 29904852 4.890000e-128 468
11 TraesCS6D01G343500 chr1D 95.184 1931 83 8 1310 3236 49111144 49109220 0.000000e+00 3042
12 TraesCS6D01G343500 chr7D 96.783 1772 51 6 1468 3236 400201424 400199656 0.000000e+00 2952
13 TraesCS6D01G343500 chr7D 96.597 1734 51 7 1468 3198 488121204 488119476 0.000000e+00 2868
14 TraesCS6D01G343500 chr7D 95.017 1184 46 10 287 1459 493948430 493949611 0.000000e+00 1847
15 TraesCS6D01G343500 chr7D 96.386 830 21 6 492 1312 488122032 488121203 0.000000e+00 1358
16 TraesCS6D01G343500 chr7D 90.569 668 42 15 331 995 400202336 400201687 0.000000e+00 865
17 TraesCS6D01G343500 chr7D 91.358 324 24 3 1 323 439201558 439201878 1.070000e-119 440
18 TraesCS6D01G343500 chr7D 91.358 324 25 2 1 323 439202638 439202959 1.070000e-119 440
19 TraesCS6D01G343500 chr7D 83.679 386 46 11 323 696 59727988 59728368 6.640000e-92 348
20 TraesCS6D01G343500 chr3D 91.003 1156 93 8 697 1851 185654560 185655705 0.000000e+00 1548
21 TraesCS6D01G343500 chr5A 87.408 1358 117 36 697 2023 119024826 119026160 0.000000e+00 1511
22 TraesCS6D01G343500 chr5A 89.600 375 28 9 1 370 219238240 219238608 1.760000e-127 466
23 TraesCS6D01G343500 chr2A 88.998 1218 108 21 812 2026 568235057 568233863 0.000000e+00 1483
24 TraesCS6D01G343500 chr2A 90.798 326 28 2 1 325 646772615 646772291 4.960000e-118 435
25 TraesCS6D01G343500 chr2A 91.954 174 10 3 287 458 409171990 409172161 1.160000e-59 241
26 TraesCS6D01G343500 chr2A 88.889 189 21 0 288 476 186422725 186422913 1.940000e-57 233
27 TraesCS6D01G343500 chr4B 86.344 1362 124 31 697 2030 247557756 247556429 0.000000e+00 1428
28 TraesCS6D01G343500 chr2D 91.341 947 75 5 2036 2977 439659486 439658542 0.000000e+00 1288
29 TraesCS6D01G343500 chr2D 91.975 324 25 1 1 323 497056441 497056764 1.370000e-123 453
30 TraesCS6D01G343500 chr2D 90.598 234 16 4 3007 3236 439658226 439657995 4.060000e-79 305
31 TraesCS6D01G343500 chr3A 90.295 948 83 7 2036 2977 686266567 686265623 0.000000e+00 1232
32 TraesCS6D01G343500 chr7B 90.657 685 59 3 2033 2713 104513951 104514634 0.000000e+00 905
33 TraesCS6D01G343500 chr7B 89.734 263 23 2 2976 3236 104515350 104515610 1.860000e-87 333
34 TraesCS6D01G343500 chr7B 86.154 195 14 6 506 696 486718438 486718623 7.080000e-47 198
35 TraesCS6D01G343500 chr6A 90.157 701 59 8 2541 3236 311853274 311853969 0.000000e+00 904
36 TraesCS6D01G343500 chr6A 90.741 324 29 1 1 323 329864952 329864629 6.410000e-117 431
37 TraesCS6D01G343500 chr1A 90.114 263 22 2 2976 3236 244554271 244554011 4.000000e-89 339
38 TraesCS6D01G343500 chr1A 87.685 203 21 2 505 705 98578584 98578384 1.940000e-57 233
39 TraesCS6D01G343500 chr7A 89.552 201 18 3 287 486 378986397 378986199 5.360000e-63 252
40 TraesCS6D01G343500 chr7A 82.836 268 32 10 701 965 56202382 56202126 9.030000e-56 228
41 TraesCS6D01G343500 chr1B 88.265 196 11 6 503 696 136010822 136010637 1.170000e-54 224
42 TraesCS6D01G343500 chr6B 82.879 257 34 7 701 955 168768925 168769173 4.200000e-54 222


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 TraesCS6D01G343500 chr6D 443280331 443283566 3235 True 5976.0 5976 100.0000 1 3236 1 chr6D.!!$R2 3235
1 TraesCS6D01G343500 chr6D 443264205 443266463 2258 True 3912.0 3912 97.9210 335 2594 1 chr6D.!!$R1 2259
2 TraesCS6D01G343500 chr4A 524271322 524274191 2869 True 4303.0 4303 93.6520 331 3236 1 chr4A.!!$R2 2905
3 TraesCS6D01G343500 chr4A 190403299 190404834 1535 False 775.5 1227 89.5810 2033 3236 2 chr4A.!!$F1 1203
4 TraesCS6D01G343500 chrUn 101222118 101224774 2656 True 2094.5 3186 95.2205 287 3236 2 chrUn.!!$R3 2949
5 TraesCS6D01G343500 chr1D 49109220 49111144 1924 True 3042.0 3042 95.1840 1310 3236 1 chr1D.!!$R1 1926
6 TraesCS6D01G343500 chr7D 488119476 488122032 2556 True 2113.0 2868 96.4915 492 3198 2 chr7D.!!$R2 2706
7 TraesCS6D01G343500 chr7D 400199656 400202336 2680 True 1908.5 2952 93.6760 331 3236 2 chr7D.!!$R1 2905
8 TraesCS6D01G343500 chr7D 493948430 493949611 1181 False 1847.0 1847 95.0170 287 1459 1 chr7D.!!$F2 1172
9 TraesCS6D01G343500 chr7D 439201558 439202959 1401 False 440.0 440 91.3580 1 323 2 chr7D.!!$F3 322
10 TraesCS6D01G343500 chr3D 185654560 185655705 1145 False 1548.0 1548 91.0030 697 1851 1 chr3D.!!$F1 1154
11 TraesCS6D01G343500 chr5A 119024826 119026160 1334 False 1511.0 1511 87.4080 697 2023 1 chr5A.!!$F1 1326
12 TraesCS6D01G343500 chr2A 568233863 568235057 1194 True 1483.0 1483 88.9980 812 2026 1 chr2A.!!$R1 1214
13 TraesCS6D01G343500 chr4B 247556429 247557756 1327 True 1428.0 1428 86.3440 697 2030 1 chr4B.!!$R1 1333
14 TraesCS6D01G343500 chr2D 439657995 439659486 1491 True 796.5 1288 90.9695 2036 3236 2 chr2D.!!$R1 1200
15 TraesCS6D01G343500 chr3A 686265623 686266567 944 True 1232.0 1232 90.2950 2036 2977 1 chr3A.!!$R1 941
16 TraesCS6D01G343500 chr7B 104513951 104515610 1659 False 619.0 905 90.1955 2033 3236 2 chr7B.!!$F2 1203
17 TraesCS6D01G343500 chr6A 311853274 311853969 695 False 904.0 904 90.1570 2541 3236 1 chr6A.!!$F1 695

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
877 1070 0.517316 GCGACAAGCGACAAAGGAAT 59.483 50.0 0.0 0.0 44.57 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2584 2925 4.996062 GCTAAAAGCAAATGTTGTGCAT 57.004 36.364 0.0 0.0 44.74 3.96 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
135 136 3.291584 CAAAGGAAAGATAAGGGAGGCC 58.708 50.000 0.00 0.00 0.00 5.19
140 141 2.176247 AAGATAAGGGAGGCCGAAGA 57.824 50.000 0.00 0.00 0.00 2.87
152 153 1.374758 CCGAAGAGGACTGTGCACC 60.375 63.158 15.69 0.00 45.00 5.01
186 187 4.602340 ATCGAGTACCACACAAACTCTT 57.398 40.909 0.00 0.00 37.97 2.85
219 220 8.800370 TTTATAGTATCCATTGCAACACAAGA 57.200 30.769 0.00 0.00 42.87 3.02
252 254 5.106869 GCATGCACAATTTCATGAACAACAT 60.107 36.000 14.21 3.98 41.82 2.71
325 335 1.271379 ACGGGCATTTGTGCTAGTCTT 60.271 47.619 0.07 0.00 34.73 3.01
341 473 9.833917 GTGCTAGTCTTTCCCTAATAATAAAGT 57.166 33.333 0.00 0.00 32.15 2.66
391 524 5.700832 TCACAATACGCTTTCTTTCTGTGAT 59.299 36.000 0.00 0.00 37.58 3.06
402 535 7.043391 GCTTTCTTTCTGTGATTTTACGCTTTT 60.043 33.333 0.00 0.00 0.00 2.27
877 1070 0.517316 GCGACAAGCGACAAAGGAAT 59.483 50.000 0.00 0.00 44.57 3.01
886 1079 1.881925 CGACAAAGGAATGGAGGTGCA 60.882 52.381 0.00 0.00 0.00 4.57
1090 1283 1.070445 GCGGATGCTGCTCCTACAT 59.930 57.895 13.65 0.00 38.39 2.29
1112 1305 3.580319 ACCACCAGCCCAAGGTCC 61.580 66.667 0.00 0.00 37.23 4.46
1624 1827 9.856162 TTAGGTAGTAAAATAAATCATGTCCCC 57.144 33.333 0.00 0.00 0.00 4.81
2584 2925 6.839657 CCTTTTACTCAGTCTTATCCCTAGGA 59.160 42.308 11.48 0.00 35.55 2.94
2720 3189 2.079925 CCTCCAAGCTACTTGTGAAGC 58.920 52.381 6.58 0.00 39.58 3.86
2800 3270 4.744795 AGCTACCTGTACAAGAGAATGG 57.255 45.455 0.00 0.00 0.00 3.16
2930 3403 8.742554 AAGTCAATTTATTCAACCGATGTTTC 57.257 30.769 0.00 0.00 30.42 2.78
2972 3445 3.717400 TTGCGTGGTAGAGATGAGATC 57.283 47.619 0.00 0.00 0.00 2.75
3003 4130 5.525378 GCAGAGGAATCAGTATTACAACAGG 59.475 44.000 0.00 0.00 0.00 4.00
3005 4132 7.504403 CAGAGGAATCAGTATTACAACAGGAT 58.496 38.462 0.00 0.00 0.00 3.24
3014 4141 8.318412 TCAGTATTACAACAGGATTTGAAGCTA 58.682 33.333 0.00 0.00 0.00 3.32
3070 4197 2.722094 TCAGGTGCATATGAACAACCC 58.278 47.619 15.92 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 8.892723 ACGATTTTGATATACATGTGACATTGT 58.107 29.630 9.11 0.64 0.00 2.71
92 93 0.032403 GTGAAACTGCTGGCATGCAA 59.968 50.000 21.36 7.49 42.83 4.08
135 136 0.946221 GTGGTGCACAGTCCTCTTCG 60.946 60.000 20.43 0.00 34.08 3.79
140 141 2.737180 CTCGTGGTGCACAGTCCT 59.263 61.111 20.43 0.00 33.40 3.85
152 153 4.333649 TGGTACTCGATAGTTTACCTCGTG 59.666 45.833 0.00 0.00 41.85 4.35
196 197 7.791029 TCTCTTGTGTTGCAATGGATACTATA 58.209 34.615 0.59 0.00 36.36 1.31
197 198 6.653020 TCTCTTGTGTTGCAATGGATACTAT 58.347 36.000 0.59 0.00 36.36 2.12
198 199 6.048732 TCTCTTGTGTTGCAATGGATACTA 57.951 37.500 0.59 0.00 36.36 1.82
200 201 5.824904 ATCTCTTGTGTTGCAATGGATAC 57.175 39.130 0.59 0.00 36.36 2.24
213 214 5.404096 TGTGCATGCAAAATATCTCTTGTG 58.596 37.500 24.58 0.00 0.00 3.33
219 220 7.766738 TCATGAAATTGTGCATGCAAAATATCT 59.233 29.630 31.44 20.49 41.18 1.98
256 258 6.903419 TGTGTATTCGATTATGTGCAAAACA 58.097 32.000 0.00 0.00 44.79 2.83
441 583 8.200120 CGGACCATATGATCACATGAATAGTAT 58.800 37.037 15.64 0.00 37.87 2.12
640 800 2.747467 GCCTCCCCTCCGGTTTTTATAC 60.747 54.545 0.00 0.00 0.00 1.47
877 1070 1.541310 CCTAGGTCGTTGCACCTCCA 61.541 60.000 0.00 0.00 44.08 3.86
886 1079 1.305381 AGCTCCTGCCTAGGTCGTT 60.305 57.895 11.31 0.00 44.88 3.85
1112 1305 1.451067 AGAACCACGTAGAGGAGACG 58.549 55.000 0.00 0.00 42.26 4.18
2584 2925 4.996062 GCTAAAAGCAAATGTTGTGCAT 57.004 36.364 0.00 0.00 44.74 3.96
2720 3189 9.582431 AATCTTTATCAATGCAGAAATTGACAG 57.418 29.630 2.68 1.21 46.46 3.51
2921 3394 3.838244 TTATCTCCCTGGAAACATCGG 57.162 47.619 0.00 0.00 41.51 4.18
2972 3445 2.719739 ACTGATTCCTCTGCACCAATG 58.280 47.619 0.00 0.00 0.00 2.82
3003 4130 6.319658 TCATCCATCTTTGGTAGCTTCAAATC 59.680 38.462 13.06 0.00 44.06 2.17
3005 4132 5.569355 TCATCCATCTTTGGTAGCTTCAAA 58.431 37.500 12.36 12.36 44.06 2.69
3014 4141 4.419282 ACCAAACATCATCCATCTTTGGT 58.581 39.130 7.19 7.19 45.98 3.67
3070 4197 7.661127 TGAAAAGCAAAAATGGAAGATGATG 57.339 32.000 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.