Multiple sequence alignment - TraesCS7B01G055800

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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 TraesCS7B01G055800 chr7B 100.000 2763 0 0 1 2763 59062966 59065728 0.000000e+00 5103
1 TraesCS7B01G055800 chr7B 100.000 1727 0 0 3256 4982 59066221 59067947 0.000000e+00 3190
2 TraesCS7B01G055800 chr7B 82.129 1315 154 42 3429 4694 59072648 59073930 0.000000e+00 1051
3 TraesCS7B01G055800 chr7D 97.042 2772 70 4 1 2763 101729334 101732102 0.000000e+00 4654
4 TraesCS7B01G055800 chr7D 96.653 1733 47 4 3260 4982 101732545 101734276 0.000000e+00 2868
5 TraesCS7B01G055800 chr7D 81.830 1596 203 50 3401 4950 101738384 101739938 0.000000e+00 1260
6 TraesCS7B01G055800 chr7D 89.247 93 9 1 37 129 12622757 12622848 1.130000e-21 115
7 TraesCS7B01G055800 chr7A 92.002 1688 95 14 3308 4982 105503758 105505418 0.000000e+00 2333
8 TraesCS7B01G055800 chr7A 84.744 1973 260 24 806 2752 105501534 105503491 0.000000e+00 1938
9 TraesCS7B01G055800 chr7A 82.125 1600 189 45 3401 4950 105512449 105514001 0.000000e+00 1280
10 TraesCS7B01G055800 chr7A 81.118 1377 238 6 950 2324 105510187 105511543 0.000000e+00 1083
11 TraesCS7B01G055800 chr5B 80.129 1082 167 31 3378 4440 531816960 531818012 0.000000e+00 763
12 TraesCS7B01G055800 chr5B 80.102 985 169 18 3476 4441 532239206 532240182 0.000000e+00 708
13 TraesCS7B01G055800 chr5B 75.837 1374 273 36 974 2308 532237214 532238567 1.170000e-180 643
14 TraesCS7B01G055800 chr5B 77.755 989 175 29 3465 4435 533494124 533493163 2.600000e-157 566
15 TraesCS7B01G055800 chr5B 77.507 1027 171 38 3458 4455 532550103 532551098 3.370000e-156 562
16 TraesCS7B01G055800 chr5B 76.332 976 188 33 3458 4406 533376536 533375577 2.700000e-132 483
17 TraesCS7B01G055800 chr5B 73.008 1330 316 34 1040 2339 533381521 533380205 1.280000e-115 427
18 TraesCS7B01G055800 chr5D 80.135 1037 178 20 3423 4441 437867212 437868238 0.000000e+00 749
19 TraesCS7B01G055800 chr5D 77.756 998 174 32 3458 4435 438589541 438588572 2.010000e-158 569
20 TraesCS7B01G055800 chr5D 76.859 1076 199 35 3677 4721 438443069 438442013 3.370000e-156 562
21 TraesCS7B01G055800 chr5D 77.376 968 166 34 3458 4399 438056831 438057771 4.420000e-145 525
22 TraesCS7B01G055800 chr5D 75.207 1089 225 31 1273 2332 437865199 437866271 1.620000e-129 473
23 TraesCS7B01G055800 chr2A 78.693 995 165 33 3458 4429 14703616 14702646 1.970000e-173 619
24 TraesCS7B01G055800 chr2A 78.419 987 166 34 3466 4429 14721115 14720153 2.570000e-167 599
25 TraesCS7B01G055800 chr2A 77.946 993 168 34 3458 4429 14740577 14739615 1.560000e-159 573
26 TraesCS7B01G055800 chr2A 77.638 957 177 26 3458 4391 52762972 52762030 9.430000e-152 547
27 TraesCS7B01G055800 chr2A 77.241 993 182 28 3457 4429 14730453 14729485 4.390000e-150 542
28 TraesCS7B01G055800 chr2A 77.191 947 172 32 3502 4429 14683500 14682579 3.440000e-141 512
29 TraesCS7B01G055800 chr2D 78.362 989 161 35 3466 4429 12632441 12631481 4.290000e-165 592
30 TraesCS7B01G055800 chr2D 77.140 993 181 32 3457 4429 12626648 12625682 7.340000e-148 534
31 TraesCS7B01G055800 chr2B 77.508 987 174 33 3458 4421 20146561 20147522 2.620000e-152 549
32 TraesCS7B01G055800 chr2B 76.884 995 169 42 3464 4430 65047562 65048523 1.600000e-139 507
33 TraesCS7B01G055800 chrUn 76.119 1005 196 32 3458 4435 345139380 345138393 2.080000e-133 486
34 TraesCS7B01G055800 chrUn 89.247 93 9 1 37 129 45089567 45089658 1.130000e-21 115
35 TraesCS7B01G055800 chrUn 89.247 93 9 1 37 129 171039854 171039945 1.130000e-21 115
36 TraesCS7B01G055800 chr5A 75.816 980 178 42 3457 4412 554228744 554227800 4.580000e-120 442
37 TraesCS7B01G055800 chr5A 78.947 589 92 20 3861 4433 553491189 553490617 6.090000e-99 372
38 TraesCS7B01G055800 chr3A 90.323 93 8 1 37 129 718987889 718987798 2.440000e-23 121
39 TraesCS7B01G055800 chr6D 89.247 93 9 1 37 129 83969628 83969719 1.130000e-21 115
40 TraesCS7B01G055800 chr4D 89.247 93 9 1 37 129 398045222 398045131 1.130000e-21 115
41 TraesCS7B01G055800 chr4B 89.247 93 9 1 37 129 209316391 209316482 1.130000e-21 115
42 TraesCS7B01G055800 chr1D 89.247 93 9 1 37 129 275766202 275766293 1.130000e-21 115


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 TraesCS7B01G055800 chr7B 59062966 59067947 4981 False 4146.5 5103 100.0000 1 4982 2 chr7B.!!$F2 4981
1 TraesCS7B01G055800 chr7B 59072648 59073930 1282 False 1051.0 1051 82.1290 3429 4694 1 chr7B.!!$F1 1265
2 TraesCS7B01G055800 chr7D 101729334 101734276 4942 False 3761.0 4654 96.8475 1 4982 2 chr7D.!!$F3 4981
3 TraesCS7B01G055800 chr7D 101738384 101739938 1554 False 1260.0 1260 81.8300 3401 4950 1 chr7D.!!$F2 1549
4 TraesCS7B01G055800 chr7A 105501534 105505418 3884 False 2135.5 2333 88.3730 806 4982 2 chr7A.!!$F1 4176
5 TraesCS7B01G055800 chr7A 105510187 105514001 3814 False 1181.5 1280 81.6215 950 4950 2 chr7A.!!$F2 4000
6 TraesCS7B01G055800 chr5B 531816960 531818012 1052 False 763.0 763 80.1290 3378 4440 1 chr5B.!!$F1 1062
7 TraesCS7B01G055800 chr5B 532237214 532240182 2968 False 675.5 708 77.9695 974 4441 2 chr5B.!!$F3 3467
8 TraesCS7B01G055800 chr5B 533493163 533494124 961 True 566.0 566 77.7550 3465 4435 1 chr5B.!!$R1 970
9 TraesCS7B01G055800 chr5B 532550103 532551098 995 False 562.0 562 77.5070 3458 4455 1 chr5B.!!$F2 997
10 TraesCS7B01G055800 chr5B 533375577 533381521 5944 True 455.0 483 74.6700 1040 4406 2 chr5B.!!$R2 3366
11 TraesCS7B01G055800 chr5D 437865199 437868238 3039 False 611.0 749 77.6710 1273 4441 2 chr5D.!!$F2 3168
12 TraesCS7B01G055800 chr5D 438588572 438589541 969 True 569.0 569 77.7560 3458 4435 1 chr5D.!!$R2 977
13 TraesCS7B01G055800 chr5D 438442013 438443069 1056 True 562.0 562 76.8590 3677 4721 1 chr5D.!!$R1 1044
14 TraesCS7B01G055800 chr5D 438056831 438057771 940 False 525.0 525 77.3760 3458 4399 1 chr5D.!!$F1 941
15 TraesCS7B01G055800 chr2A 14702646 14703616 970 True 619.0 619 78.6930 3458 4429 1 chr2A.!!$R2 971
16 TraesCS7B01G055800 chr2A 14720153 14721115 962 True 599.0 599 78.4190 3466 4429 1 chr2A.!!$R3 963
17 TraesCS7B01G055800 chr2A 14739615 14740577 962 True 573.0 573 77.9460 3458 4429 1 chr2A.!!$R5 971
18 TraesCS7B01G055800 chr2A 52762030 52762972 942 True 547.0 547 77.6380 3458 4391 1 chr2A.!!$R6 933
19 TraesCS7B01G055800 chr2A 14729485 14730453 968 True 542.0 542 77.2410 3457 4429 1 chr2A.!!$R4 972
20 TraesCS7B01G055800 chr2A 14682579 14683500 921 True 512.0 512 77.1910 3502 4429 1 chr2A.!!$R1 927
21 TraesCS7B01G055800 chr2D 12631481 12632441 960 True 592.0 592 78.3620 3466 4429 1 chr2D.!!$R2 963
22 TraesCS7B01G055800 chr2D 12625682 12626648 966 True 534.0 534 77.1400 3457 4429 1 chr2D.!!$R1 972
23 TraesCS7B01G055800 chr2B 20146561 20147522 961 False 549.0 549 77.5080 3458 4421 1 chr2B.!!$F1 963
24 TraesCS7B01G055800 chr2B 65047562 65048523 961 False 507.0 507 76.8840 3464 4430 1 chr2B.!!$F2 966
25 TraesCS7B01G055800 chrUn 345138393 345139380 987 True 486.0 486 76.1190 3458 4435 1 chrUn.!!$R1 977
26 TraesCS7B01G055800 chr5A 554227800 554228744 944 True 442.0 442 75.8160 3457 4412 1 chr5A.!!$R2 955
27 TraesCS7B01G055800 chr5A 553490617 553491189 572 True 372.0 372 78.9470 3861 4433 1 chr5A.!!$R1 572

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
191 192 0.181350 ATCTCCTGGTTCCCATTCGC 59.819 55.000 0.00 0.00 30.82 4.70 F
206 207 0.614697 TTCGCATCCCTGGAGTCAGA 60.615 55.000 0.00 0.00 43.49 3.27 F
357 358 0.690192 TACCATATGGGGACGCATGG 59.310 55.000 25.55 9.27 45.26 3.66 F
562 569 1.004277 TGTCAGCCAAGGAACCCATAC 59.996 52.381 0.00 0.00 0.00 2.39 F
2443 4319 0.453793 TGCCGTGAAAGTTGTGTTGG 59.546 50.000 0.00 0.00 0.00 3.77 F
2548 4940 2.821546 TGGAGAAATGCCGATTCTACG 58.178 47.619 0.00 0.00 40.07 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 2225 0.035915 TGCTTAGGTTGGCGTATGCA 60.036 50.000 9.59 0.00 45.35 3.96 R
2181 2240 2.363038 TCTGTTTTCAATGCTGCTGCTT 59.637 40.909 17.00 7.67 40.48 3.91 R
2443 4319 1.923227 GCAGCACCTCCTAAAACCGC 61.923 60.000 0.00 0.00 0.00 5.68 R
2725 6153 3.051581 ACACTGGCTTGAGGATGGATAT 58.948 45.455 0.00 0.00 0.00 1.63 R
3316 6745 3.007398 AGAGCTCTGTTTGACCCTAACTG 59.993 47.826 17.42 0.00 0.00 3.16 R
4703 8656 2.359900 CTCTGTCCCACAAAGTATGCC 58.640 52.381 0.00 0.00 0.00 4.40 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
134 135 2.024464 TCGAATTGGGTTCCATGGGATT 60.024 45.455 13.02 0.00 31.53 3.01
191 192 0.181350 ATCTCCTGGTTCCCATTCGC 59.819 55.000 0.00 0.00 30.82 4.70
206 207 0.614697 TTCGCATCCCTGGAGTCAGA 60.615 55.000 0.00 0.00 43.49 3.27
337 338 9.753674 TGGAATCAAAATCTTTAGTTGGATAGT 57.246 29.630 0.00 0.00 0.00 2.12
357 358 0.690192 TACCATATGGGGACGCATGG 59.310 55.000 25.55 9.27 45.26 3.66
455 462 3.565307 ACAAATGGAAGAAGAAGCACCA 58.435 40.909 0.00 0.00 35.09 4.17
475 482 5.070981 CACCAGTGGGAACATCTATACTGAT 59.929 44.000 15.21 0.00 46.14 2.90
491 498 3.686016 ACTGATGAATTAAACGTGGCCT 58.314 40.909 3.32 0.00 0.00 5.19
544 551 5.115480 GGACATTTCACACCAATTTGTTGT 58.885 37.500 0.00 0.00 0.00 3.32
562 569 1.004277 TGTCAGCCAAGGAACCCATAC 59.996 52.381 0.00 0.00 0.00 2.39
582 589 3.149196 ACTGGTAGCATGTTGTTTCCTG 58.851 45.455 0.00 0.00 0.00 3.86
590 597 1.790755 TGTTGTTTCCTGTCGGATCG 58.209 50.000 0.00 0.00 39.58 3.69
621 628 1.013596 CGCAGTGTTGTTTCCTGTCA 58.986 50.000 0.00 0.00 0.00 3.58
626 633 4.129380 CAGTGTTGTTTCCTGTCAGATCA 58.871 43.478 0.00 0.00 0.00 2.92
783 792 3.297134 TTGACTTGCTCTTTCCCAACT 57.703 42.857 0.00 0.00 0.00 3.16
798 807 4.531854 TCCCAACTTGTGACAAGATGAAA 58.468 39.130 29.54 17.43 0.00 2.69
939 948 6.640499 GTCTTTGCATTATTGTTGCTTGTACA 59.360 34.615 0.00 0.00 40.77 2.90
1698 1733 4.395959 AGACGAGTACCTGTTGACAAAA 57.604 40.909 0.00 0.00 0.00 2.44
1704 1739 4.595986 AGTACCTGTTGACAAAAACCAGT 58.404 39.130 0.00 0.00 0.00 4.00
1873 1908 1.699730 GGTAGTTTTTGGGCAGTGGT 58.300 50.000 0.00 0.00 0.00 4.16
2058 2111 1.371635 GCGTTGCAGCGATGGTTTT 60.372 52.632 27.74 0.00 0.00 2.43
2059 2112 1.608093 GCGTTGCAGCGATGGTTTTG 61.608 55.000 27.74 0.00 0.00 2.44
2166 2225 2.910360 TGCTCCTGCATGGCGTAT 59.090 55.556 0.00 0.00 45.31 3.06
2443 4319 0.453793 TGCCGTGAAAGTTGTGTTGG 59.546 50.000 0.00 0.00 0.00 3.77
2548 4940 2.821546 TGGAGAAATGCCGATTCTACG 58.178 47.619 0.00 0.00 40.07 3.51
2725 6153 4.282496 ACCAAACCAAACCACATTGTCTA 58.718 39.130 0.00 0.00 0.00 2.59
2737 6165 5.846164 ACCACATTGTCTATATCCATCCTCA 59.154 40.000 0.00 0.00 0.00 3.86
3316 6745 3.767131 AGGTATAATGGGCAAACACCAAC 59.233 43.478 0.00 0.00 42.17 3.77
3727 7590 5.428184 AAGTAGGGATTCTCAACAAGGAG 57.572 43.478 0.00 0.00 36.21 3.69
4214 8125 6.508030 TGAACCAATAGCTCATATTACCCA 57.492 37.500 0.00 0.00 32.61 4.51
4545 8497 3.509517 GGCAGAGGAATTGGCTGAT 57.490 52.632 0.00 0.00 38.03 2.90
4597 8549 3.248266 GAGGTGTTGCTTTGCATTCATC 58.752 45.455 0.00 0.00 38.76 2.92
4703 8656 4.760047 CCAACTCCCAGTCGGCCG 62.760 72.222 22.12 22.12 0.00 6.13
4858 8811 2.875933 TGTAAAGAAAGGCTTGTCCACG 59.124 45.455 0.00 0.00 36.80 4.94
4918 8871 0.468226 TTGATCCCATCTACACGGGC 59.532 55.000 0.00 0.00 42.75 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.586648 ACCCAATTCGAGAAAGCCTT 57.413 45.000 0.00 0.00 0.00 4.35
134 135 5.586155 TGGGGGTTAAACAATTAGAGTCA 57.414 39.130 0.00 0.00 0.00 3.41
191 192 2.570752 CCCATATCTGACTCCAGGGATG 59.429 54.545 0.00 0.00 40.76 3.51
206 207 8.717717 TGAGATTTCAGTAGACATTTCCCATAT 58.282 33.333 0.00 0.00 0.00 1.78
233 234 2.869192 GCCGATTCAATGAGAGGACTTC 59.131 50.000 5.20 0.00 0.00 3.01
337 338 1.073125 CCATGCGTCCCCATATGGTAA 59.927 52.381 20.46 5.13 36.25 2.85
386 387 9.340223 CCTACTCCTATCCCTTTATTCCTATTT 57.660 37.037 0.00 0.00 0.00 1.40
387 388 8.698476 TCCTACTCCTATCCCTTTATTCCTATT 58.302 37.037 0.00 0.00 0.00 1.73
388 389 8.258641 TCCTACTCCTATCCCTTTATTCCTAT 57.741 38.462 0.00 0.00 0.00 2.57
389 390 7.674327 TCCTACTCCTATCCCTTTATTCCTA 57.326 40.000 0.00 0.00 0.00 2.94
390 391 6.562845 TCCTACTCCTATCCCTTTATTCCT 57.437 41.667 0.00 0.00 0.00 3.36
449 456 1.656587 TAGATGTTCCCACTGGTGCT 58.343 50.000 0.00 0.00 0.00 4.40
455 462 7.623999 ATTCATCAGTATAGATGTTCCCACT 57.376 36.000 0.00 0.00 44.46 4.00
475 482 5.938710 TGTATTACAGGCCACGTTTAATTCA 59.061 36.000 5.01 1.18 0.00 2.57
544 551 1.281867 CAGTATGGGTTCCTTGGCTGA 59.718 52.381 0.00 0.00 0.00 4.26
562 569 3.149196 ACAGGAAACAACATGCTACCAG 58.851 45.455 0.00 0.00 0.00 4.00
582 589 2.664971 CGCCTAGACAATACGATCCGAC 60.665 54.545 0.00 0.00 0.00 4.79
590 597 2.295253 ACACTGCGCCTAGACAATAC 57.705 50.000 4.18 0.00 0.00 1.89
621 628 3.990318 TGCGACGAGACAATATGATCT 57.010 42.857 0.00 0.00 0.00 2.75
626 633 3.845178 TCAGTTTGCGACGAGACAATAT 58.155 40.909 0.00 0.00 0.00 1.28
658 667 2.238395 GGAGAAGGCTCAACAAGAGGAT 59.762 50.000 0.00 0.00 44.86 3.24
798 807 8.825667 TGCTGTTTACTTTGAACTTTCTTTTT 57.174 26.923 0.00 0.00 0.00 1.94
801 810 8.872845 CAATTGCTGTTTACTTTGAACTTTCTT 58.127 29.630 0.00 0.00 0.00 2.52
834 843 4.039092 GCTGCCCTGGCCAGAAGA 62.039 66.667 34.91 15.26 41.09 2.87
939 948 7.386851 CGGTATATGATTCTGGGAATGTACTT 58.613 38.462 0.00 0.00 0.00 2.24
1154 1166 3.889044 GCGTCGAGCCGGATGAGA 61.889 66.667 5.05 0.00 40.81 3.27
1260 1272 1.982395 CGGTGCAGAGGAGGTACCA 60.982 63.158 15.94 0.00 40.58 3.25
1698 1733 5.824624 CAGGTTTATGATGATAGCACTGGTT 59.175 40.000 0.00 0.00 0.00 3.67
1704 1739 4.712051 AGCCAGGTTTATGATGATAGCA 57.288 40.909 0.00 0.00 0.00 3.49
1842 1877 3.564053 AAAACTACCCACGTGGAAGAA 57.436 42.857 36.07 15.98 37.39 2.52
1873 1908 1.602323 GGTTGCATTCGTGGGGTGA 60.602 57.895 0.00 0.00 0.00 4.02
2059 2112 0.679640 TTCATCCCCGACAATGGCAC 60.680 55.000 0.00 0.00 0.00 5.01
2166 2225 0.035915 TGCTTAGGTTGGCGTATGCA 60.036 50.000 9.59 0.00 45.35 3.96
2181 2240 2.363038 TCTGTTTTCAATGCTGCTGCTT 59.637 40.909 17.00 7.67 40.48 3.91
2443 4319 1.923227 GCAGCACCTCCTAAAACCGC 61.923 60.000 0.00 0.00 0.00 5.68
2725 6153 3.051581 ACACTGGCTTGAGGATGGATAT 58.948 45.455 0.00 0.00 0.00 1.63
3263 6691 5.195001 TGACAAAACCAAAGCAGATAACC 57.805 39.130 0.00 0.00 0.00 2.85
3264 6692 5.831997 ACTGACAAAACCAAAGCAGATAAC 58.168 37.500 0.00 0.00 0.00 1.89
3316 6745 3.007398 AGAGCTCTGTTTGACCCTAACTG 59.993 47.826 17.42 0.00 0.00 3.16
3409 6853 3.127895 TGTGTTTTTCCTGGTTTCTGTCG 59.872 43.478 0.00 0.00 0.00 4.35
3727 7590 8.937634 ATTACTTCATTCCTGAATTCATTTGC 57.062 30.769 8.96 0.00 40.52 3.68
4214 8125 9.386010 CACAAATGGGAATTGAACATAATCATT 57.614 29.630 0.00 0.00 0.00 2.57
4476 8421 5.955488 TGAAACAAACAAAAACATCTCGGA 58.045 33.333 0.00 0.00 0.00 4.55
4563 8515 3.619038 GCAACACCTCATCTAGTAAGCAC 59.381 47.826 0.00 0.00 0.00 4.40
4703 8656 2.359900 CTCTGTCCCACAAAGTATGCC 58.640 52.381 0.00 0.00 0.00 4.40
4858 8811 0.589708 GCTACAAACAACGACCACCC 59.410 55.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.