Multiple sequence alignment - TraesCS6B01G443200

Loading Multiple Alignment...

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 TraesCS6B01G443200 chr6B 100.000 3053 0 0 1 3053 706444804 706441752 0.000000e+00 5638.0
1 TraesCS6B01G443200 chr6B 96.007 1678 52 5 868 2531 706528982 706527306 0.000000e+00 2713.0
2 TraesCS6B01G443200 chr6B 88.375 1729 147 26 823 2511 706352412 706350698 0.000000e+00 2030.0
3 TraesCS6B01G443200 chr6B 88.286 1733 150 27 823 2516 705758315 705756597 0.000000e+00 2026.0
4 TraesCS6B01G443200 chr6B 88.259 1729 150 24 823 2511 706409398 706407683 0.000000e+00 2019.0
5 TraesCS6B01G443200 chr6B 87.723 1735 153 28 823 2516 705784371 705782656 0.000000e+00 1969.0
6 TraesCS6B01G443200 chr6B 96.325 898 18 4 1 884 706529895 706528999 0.000000e+00 1461.0
7 TraesCS6B01G443200 chr6B 87.015 593 48 15 1957 2530 706522360 706521778 2.570000e-180 641.0
8 TraesCS6B01G443200 chr6B 86.792 583 39 18 2005 2565 706091628 706091062 1.560000e-172 616.0
9 TraesCS6B01G443200 chr6B 96.496 371 13 0 2682 3052 706526807 706526437 5.590000e-172 614.0
10 TraesCS6B01G443200 chr6B 90.496 242 12 7 89 322 706112428 706112190 2.960000e-80 309.0
11 TraesCS6B01G443200 chr6B 89.352 216 16 3 89 298 706352835 706352621 6.490000e-67 265.0
12 TraesCS6B01G443200 chr6B 89.352 216 16 3 89 298 706409821 706409607 6.490000e-67 265.0
13 TraesCS6B01G443200 chr6B 88.837 215 18 2 89 298 705784779 705784566 3.020000e-65 259.0
14 TraesCS6B01G443200 chr6B 88.837 215 18 2 89 298 706523599 706523386 3.020000e-65 259.0
15 TraesCS6B01G443200 chr6B 89.888 178 18 0 462 639 706409566 706409389 2.370000e-56 230.0
16 TraesCS6B01G443200 chr6B 89.326 178 19 0 462 639 706352580 706352403 1.100000e-54 224.0
17 TraesCS6B01G443200 chr6B 91.870 123 10 0 517 639 705784484 705784362 4.050000e-39 172.0
18 TraesCS6B01G443200 chr6B 96.552 87 2 1 2566 2652 706526894 706526809 3.170000e-30 143.0
19 TraesCS6B01G443200 chr6A 93.218 2315 134 10 757 3053 609821541 609819232 0.000000e+00 3384.0
20 TraesCS6B01G443200 chr6A 88.149 1713 150 30 823 2511 609815227 609813544 0.000000e+00 1989.0
21 TraesCS6B01G443200 chr6A 91.643 359 11 6 1 344 609821921 609821567 2.130000e-131 479.0
22 TraesCS6B01G443200 chr6D 93.240 1923 98 11 634 2537 463080178 463078269 0.000000e+00 2802.0
23 TraesCS6B01G443200 chr6D 88.844 1730 142 31 823 2514 463073748 463072032 0.000000e+00 2078.0
24 TraesCS6B01G443200 chr6D 95.161 372 18 0 2682 3053 463077980 463077609 3.390000e-164 588.0
25 TraesCS6B01G443200 chr6D 91.667 336 14 4 1 325 463091869 463091537 1.290000e-123 453.0
26 TraesCS6B01G443200 chr6D 92.715 302 19 2 341 642 463091202 463090904 1.680000e-117 433.0
27 TraesCS6B01G443200 chr6D 89.767 215 16 2 89 298 463074170 463073957 1.400000e-68 270.0
28 TraesCS6B01G443200 chr6D 88.202 178 21 0 462 639 463073916 463073739 2.380000e-51 213.0
29 TraesCS6B01G443200 chr6D 85.401 137 13 6 329 462 224773026 224772894 5.310000e-28 135.0
30 TraesCS6B01G443200 chr4B 89.560 182 18 1 642 822 58065506 58065325 2.370000e-56 230.0
31 TraesCS6B01G443200 chr1D 88.268 179 20 1 642 819 460436464 460436642 2.380000e-51 213.0
32 TraesCS6B01G443200 chr1D 86.188 181 23 2 642 821 69525124 69524945 8.640000e-46 195.0
33 TraesCS6B01G443200 chr2D 92.241 116 9 0 348 463 15520399 15520514 6.770000e-37 165.0
34 TraesCS6B01G443200 chr1B 88.971 136 11 4 329 462 458013792 458013925 6.770000e-37 165.0
35 TraesCS6B01G443200 chr5A 92.661 109 8 0 352 460 616354941 616354833 1.130000e-34 158.0
36 TraesCS6B01G443200 chr5A 84.507 142 15 5 329 464 8016408 8016548 1.910000e-27 134.0
37 TraesCS6B01G443200 chr7D 90.435 115 11 0 348 462 115138377 115138491 5.270000e-33 152.0
38 TraesCS6B01G443200 chr3D 90.826 109 7 2 352 460 64866605 64866710 3.170000e-30 143.0
39 TraesCS6B01G443200 chr2B 95.385 65 2 1 756 820 470524113 470524176 5.390000e-18 102.0
40 TraesCS6B01G443200 chr2B 100.000 34 0 0 775 808 17596634 17596667 2.540000e-06 63.9
41 TraesCS6B01G443200 chr2B 90.000 40 4 0 782 821 177600452 177600413 6.000000e-03 52.8
42 TraesCS6B01G443200 chr2A 97.561 41 1 0 779 819 777622221 777622261 1.520000e-08 71.3
43 TraesCS6B01G443200 chr2A 90.244 41 4 0 781 821 130799658 130799618 2.000000e-03 54.7


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 TraesCS6B01G443200 chr6B 706441752 706444804 3052 True 5638.000000 5638 100.000000 1 3053 1 chr6B.!!$R4 3052
1 TraesCS6B01G443200 chr6B 705756597 705758315 1718 True 2026.000000 2026 88.286000 823 2516 1 chr6B.!!$R1 1693
2 TraesCS6B01G443200 chr6B 706521778 706529895 8117 True 971.833333 2713 93.538667 1 3052 6 chr6B.!!$R8 3051
3 TraesCS6B01G443200 chr6B 706350698 706352835 2137 True 839.666667 2030 89.017667 89 2511 3 chr6B.!!$R6 2422
4 TraesCS6B01G443200 chr6B 706407683 706409821 2138 True 838.000000 2019 89.166333 89 2511 3 chr6B.!!$R7 2422
5 TraesCS6B01G443200 chr6B 705782656 705784779 2123 True 800.000000 1969 89.476667 89 2516 3 chr6B.!!$R5 2427
6 TraesCS6B01G443200 chr6B 706091062 706091628 566 True 616.000000 616 86.792000 2005 2565 1 chr6B.!!$R2 560
7 TraesCS6B01G443200 chr6A 609813544 609815227 1683 True 1989.000000 1989 88.149000 823 2511 1 chr6A.!!$R1 1688
8 TraesCS6B01G443200 chr6A 609819232 609821921 2689 True 1931.500000 3384 92.430500 1 3053 2 chr6A.!!$R2 3052
9 TraesCS6B01G443200 chr6D 463072032 463080178 8146 True 1190.200000 2802 91.042800 89 3053 5 chr6D.!!$R2 2964
10 TraesCS6B01G443200 chr6D 463090904 463091869 965 True 443.000000 453 92.191000 1 642 2 chr6D.!!$R3 641

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
289 6220 1.072965 CTCTCTCTTGGGCAAAGGTGT 59.927 52.381 0.88 0.0 36.46 4.16 F
1058 7381 0.537188 AGCATCCGTTGTTCCTCGAT 59.463 50.000 0.00 0.0 0.00 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 7475 0.178967 TGCAAAGAGGGATGTTGGCA 60.179 50.0 0.0 0.0 0.0 4.92 R
2844 9580 1.442769 ACGGCTTGCACAATAGACTG 58.557 50.0 0.0 0.0 0.0 3.51 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
188 6115 1.956170 CACGGCTGACACACCTCAC 60.956 63.158 0.00 0.00 0.00 3.51
214 6144 4.676586 CGGCGGCGACAAAACCAC 62.677 66.667 29.19 0.00 0.00 4.16
289 6220 1.072965 CTCTCTCTTGGGCAAAGGTGT 59.927 52.381 0.88 0.00 36.46 4.16
345 6290 4.724399 TCCATGTGTGTTTTCCTGTGTAT 58.276 39.130 0.00 0.00 0.00 2.29
346 6610 5.136828 TCCATGTGTGTTTTCCTGTGTATT 58.863 37.500 0.00 0.00 0.00 1.89
457 6721 7.042389 GCCAATAAAATTCACCTTTTGTCGAAA 60.042 33.333 0.00 0.00 31.15 3.46
582 6857 6.151663 TCGTCGGATCATGAAACCTATTAA 57.848 37.500 16.57 0.00 0.00 1.40
639 6914 5.242434 TGGTATTGTTCATGACCTACACAC 58.758 41.667 0.00 0.00 32.87 3.82
640 6915 5.012664 TGGTATTGTTCATGACCTACACACT 59.987 40.000 0.00 0.00 32.87 3.55
922 7237 7.165485 ACCAATCTTGCAGTAAACATAGTACA 58.835 34.615 0.00 0.00 0.00 2.90
967 7287 2.503356 CTCTTTGCAGGTGATAGGGACT 59.497 50.000 0.00 0.00 46.37 3.85
969 7289 4.101114 TCTTTGCAGGTGATAGGGACTTA 58.899 43.478 0.00 0.00 41.75 2.24
1058 7381 0.537188 AGCATCCGTTGTTCCTCGAT 59.463 50.000 0.00 0.00 0.00 3.59
1066 7389 1.067776 GTTGTTCCTCGATGACCGTCT 60.068 52.381 0.00 0.00 39.75 4.18
1152 7475 4.324874 AGACAAGCCTTAAGATCTTGGCAT 60.325 41.667 28.96 19.63 45.71 4.40
1196 7519 2.594592 GGGCGTCCACTGCAACTT 60.595 61.111 0.00 0.00 0.00 2.66
1244 7567 2.693017 ACAAGGGTTGTTGGGCCA 59.307 55.556 0.00 0.00 42.22 5.36
1320 7643 3.423154 GGCTTCACCGGCGAGTTG 61.423 66.667 9.30 2.14 0.00 3.16
1535 7859 4.771114 ATAATCTCACCGGAACAATCCA 57.229 40.909 9.46 0.00 46.97 3.41
1974 8298 3.473923 AACAACTTTTGGGGCTTCATG 57.526 42.857 0.00 0.00 34.12 3.07
2018 8342 1.542108 GCAGCTCACCCATCTGGATAC 60.542 57.143 0.00 0.00 37.39 2.24
2144 8476 1.059006 GGATCTGCTCCCATGTCCCT 61.059 60.000 0.00 0.00 38.19 4.20
2199 8531 6.412362 ACTAGCTACCTGATTATTGGACTG 57.588 41.667 0.00 0.00 0.00 3.51
2211 8544 7.933396 TGATTATTGGACTGCTCATTACAATG 58.067 34.615 7.64 0.00 37.75 2.82
2336 8677 2.885266 GGACCTTCCAAACCTTCACTTC 59.115 50.000 0.00 0.00 36.28 3.01
2351 8692 5.822519 CCTTCACTTCGGGAATAAATGATCA 59.177 40.000 0.00 0.00 0.00 2.92
2446 8802 5.229423 CAACCACTCCCATTGTATTGTTTG 58.771 41.667 0.00 0.00 0.00 2.93
2559 8918 0.883833 AGCAAATCAACAAGCGGAGG 59.116 50.000 0.00 0.00 0.00 4.30
2625 9361 7.396540 AGCTCAATACCCAAAAGTCATTAAG 57.603 36.000 0.00 0.00 0.00 1.85
2740 9476 3.194755 GGTTTACCATTGGATGTTGGACC 59.805 47.826 10.37 3.92 36.79 4.46
2759 9495 5.073428 GGACCTGAGAAGAATGGAACTTTT 58.927 41.667 0.00 0.00 0.00 2.27
2844 9580 1.133761 GGGGCAAAGAGGTCCTAATCC 60.134 57.143 0.00 0.00 31.57 3.01
2862 9598 0.729116 CCAGTCTATTGTGCAAGCCG 59.271 55.000 0.00 0.00 0.00 5.52
2992 9728 2.242043 GGCATGGGTATCTTGGGATTG 58.758 52.381 0.00 0.00 33.71 2.67
3030 9766 1.643811 ACAGAGGAGGTCTAGGCTTCT 59.356 52.381 6.41 0.00 32.51 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 90 7.120726 GGGTTTAAAAGAAAGAGTGCTGCTATA 59.879 37.037 0.00 0.0 0.00 1.31
198 6128 4.676586 CGTGGTTTTGTCGCCGCC 62.677 66.667 0.00 0.0 31.99 6.13
289 6220 4.592997 TGAGTGAGTAATCAGGAGGAGA 57.407 45.455 0.00 0.0 0.00 3.71
345 6290 1.315981 TGCACACAGCCAACCGAAAA 61.316 50.000 0.00 0.0 44.83 2.29
346 6610 1.106351 ATGCACACAGCCAACCGAAA 61.106 50.000 0.00 0.0 44.83 3.46
457 6721 7.955918 ACAAGATGGAAGAAGCAATACTTTTT 58.044 30.769 0.00 0.0 39.29 1.94
582 6857 5.296283 GTGAGCTTGCTCTCATGAACAATAT 59.704 40.000 21.17 0.0 44.04 1.28
845 7122 5.301805 CCTGTACCCATCTTGTTTTCAAAGT 59.698 40.000 0.00 0.0 39.47 2.66
967 7287 2.413837 GAGCCTTGTCGCTTGACTTAA 58.586 47.619 0.00 0.0 43.29 1.85
969 7289 0.946221 CGAGCCTTGTCGCTTGACTT 60.946 55.000 0.00 0.0 42.08 3.01
995 7315 4.045104 CAGTAGCGACAGTAGCATAAAGG 58.955 47.826 8.50 0.0 37.01 3.11
1058 7381 5.845391 TGTGATGTTATCATAGACGGTCA 57.155 39.130 11.27 0.0 42.04 4.02
1066 7389 8.025445 CGAGATCATGTCTGTGATGTTATCATA 58.975 37.037 0.00 0.0 38.88 2.15
1152 7475 0.178967 TGCAAAGAGGGATGTTGGCA 60.179 50.000 0.00 0.0 0.00 4.92
1159 7482 1.005215 CTCCCAACTGCAAAGAGGGAT 59.995 52.381 14.19 0.0 46.81 3.85
1196 7519 2.656069 GGCTTAGTGACTCGCCCCA 61.656 63.158 13.12 0.0 36.56 4.96
1320 7643 1.513622 GAGACGGTTGAGAGGAGGC 59.486 63.158 0.00 0.0 0.00 4.70
1743 8067 0.400213 TCGATGGCAGTGTTTTCCCT 59.600 50.000 0.00 0.0 0.00 4.20
1984 8308 1.535462 GAGCTGCTTTAAGTCGCCAAA 59.465 47.619 2.53 0.0 0.00 3.28
2018 8342 5.178252 CCACCTTGCAGATTATTATCAGACG 59.822 44.000 0.00 0.0 32.95 4.18
2199 8531 4.559153 ACAAACCAAGCATTGTAATGAGC 58.441 39.130 8.70 0.0 46.99 4.26
2211 8544 5.376854 ACAATATGAGTGACAAACCAAGC 57.623 39.130 0.00 0.0 0.00 4.01
2336 8677 3.999663 GAGAGCCTGATCATTTATTCCCG 59.000 47.826 0.00 0.0 0.00 5.14
2351 8692 2.039480 TGATTTTGAGCACTGAGAGCCT 59.961 45.455 0.00 0.0 0.00 4.58
2545 8904 4.871933 AATTTTTCCTCCGCTTGTTGAT 57.128 36.364 0.00 0.0 0.00 2.57
2546 8905 4.664150 AAATTTTTCCTCCGCTTGTTGA 57.336 36.364 0.00 0.0 0.00 3.18
2740 9476 6.305693 ACGAAAAAGTTCCATTCTTCTCAG 57.694 37.500 0.00 0.0 0.00 3.35
2759 9495 9.875691 CTCCATATCCATTCTTTGATATACGAA 57.124 33.333 0.00 0.0 33.50 3.85
2775 9511 1.783071 TGTACACGCCTCCATATCCA 58.217 50.000 0.00 0.0 0.00 3.41
2844 9580 1.442769 ACGGCTTGCACAATAGACTG 58.557 50.000 0.00 0.0 0.00 3.51
2862 9598 9.722056 GAACATTGACATGGAATATGTAGAAAC 57.278 33.333 0.00 0.0 34.27 2.78
3030 9766 2.622942 GGTTGAAAAGCTCCATGTCACA 59.377 45.455 0.00 0.0 42.05 3.58


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

AutoCloner maintained by Alex Coulton.