Multiple sequence alignment - TraesCS3A01G233600

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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 TraesCS3A01G233600 chr3A 100.000 2808 0 0 1 2808 436275105 436272298 0.000000e+00 5186.0
1 TraesCS3A01G233600 chr3A 79.559 1042 129 52 381 1389 40390702 40389712 0.000000e+00 667.0
2 TraesCS3A01G233600 chr3A 79.637 1046 116 51 381 1389 40556821 40555836 0.000000e+00 662.0
3 TraesCS3A01G233600 chr3A 80.325 493 59 23 1918 2397 40389331 40388864 3.460000e-89 339.0
4 TraesCS3A01G233600 chr3A 83.740 246 17 12 1602 1825 40555665 40555421 7.880000e-51 211.0
5 TraesCS3A01G233600 chr3A 83.688 141 6 8 1469 1593 40555844 40555705 1.770000e-22 117.0
6 TraesCS3A01G233600 chr3D 96.138 2434 75 8 380 2808 299744492 299746911 0.000000e+00 3956.0
7 TraesCS3A01G233600 chr3D 82.381 1033 124 39 384 1389 29813105 29812104 0.000000e+00 846.0
8 TraesCS3A01G233600 chr3D 81.159 1035 109 40 704 1704 29790079 29789097 0.000000e+00 752.0
9 TraesCS3A01G233600 chr3D 79.393 956 102 53 417 1334 29862119 29861221 1.120000e-163 586.0
10 TraesCS3A01G233600 chr3D 92.737 179 12 1 19 196 299743215 299743393 9.980000e-65 257.0
11 TraesCS3A01G233600 chr3D 90.050 201 12 5 193 392 299744119 299744312 1.290000e-63 254.0
12 TraesCS3A01G233600 chr3D 78.571 350 40 25 1819 2147 29811842 29811507 6.140000e-47 198.0
13 TraesCS3A01G233600 chr3D 75.956 366 65 8 2447 2799 432507828 432507473 1.730000e-37 167.0
14 TraesCS3A01G233600 chr3D 94.318 88 2 2 1477 1561 29861192 29861105 6.310000e-27 132.0
15 TraesCS3A01G233600 chr3D 96.970 33 1 0 1357 1389 29861223 29861191 3.910000e-04 56.5
16 TraesCS3A01G233600 chr3B 94.982 2451 96 15 377 2808 421532742 421530300 0.000000e+00 3819.0
17 TraesCS3A01G233600 chr3B 84.908 709 81 16 688 1389 50959678 50958989 0.000000e+00 693.0
18 TraesCS3A01G233600 chr3B 80.519 693 97 26 381 1040 50942477 50943164 5.400000e-137 497.0
19 TraesCS3A01G233600 chr3B 85.852 311 29 9 1090 1389 50943174 50943480 1.620000e-82 316.0
20 TraesCS3A01G233600 chr3B 76.393 377 52 27 1819 2175 50943688 50944047 4.810000e-38 169.0
21 TraesCS3A01G233600 chr3B 75.719 313 43 22 1840 2139 50653534 50653242 2.940000e-25 126.0
22 TraesCS3A01G233600 chr3B 78.000 250 18 18 1509 1746 50653917 50653693 3.800000e-24 122.0
23 TraesCS3A01G233600 chr3B 96.491 57 2 0 321 377 421536137 421536081 8.280000e-16 95.3
24 TraesCS3A01G233600 chr3B 86.905 84 6 2 1746 1825 50653536 50653454 3.850000e-14 89.8
25 TraesCS3A01G233600 chr7B 82.621 702 73 34 704 1389 707946959 707946291 2.430000e-160 575.0
26 TraesCS3A01G233600 chr7B 83.108 296 26 14 1550 1825 707946261 707945970 6.010000e-62 248.0
27 TraesCS3A01G233600 chr7B 78.788 297 34 16 382 655 707947581 707947291 3.720000e-39 172.0
28 TraesCS3A01G233600 chr7B 76.159 302 40 25 1819 2104 707946070 707945785 2.270000e-26 130.0
29 TraesCS3A01G233600 chr7B 79.882 169 28 3 2450 2617 506757891 506758054 4.910000e-23 119.0
30 TraesCS3A01G233600 chr7D 82.906 234 36 3 2475 2706 439237409 439237178 1.020000e-49 207.0
31 TraesCS3A01G233600 chr6B 80.083 241 36 8 2468 2706 445014139 445013909 4.810000e-38 169.0
32 TraesCS3A01G233600 chr6B 81.410 156 25 4 2563 2718 489718125 489717974 1.060000e-24 124.0
33 TraesCS3A01G233600 chr2B 78.873 284 35 12 2449 2727 765395500 765395237 4.810000e-38 169.0
34 TraesCS3A01G233600 chr4B 83.537 164 20 6 2485 2646 624523119 624522961 2.250000e-31 147.0
35 TraesCS3A01G233600 chr5A 82.424 165 25 3 2485 2646 669982484 669982321 1.050000e-29 141.0
36 TraesCS3A01G233600 chr5B 92.771 83 5 1 2621 2703 245968705 245968786 4.910000e-23 119.0
37 TraesCS3A01G233600 chr1B 89.535 86 9 0 2621 2706 667645310 667645395 2.960000e-20 110.0


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 TraesCS3A01G233600 chr3A 436272298 436275105 2807 True 5186.000000 5186 100.000000 1 2808 1 chr3A.!!$R1 2807
1 TraesCS3A01G233600 chr3A 40388864 40390702 1838 True 503.000000 667 79.942000 381 2397 2 chr3A.!!$R2 2016
2 TraesCS3A01G233600 chr3A 40555421 40556821 1400 True 330.000000 662 82.355000 381 1825 3 chr3A.!!$R3 1444
3 TraesCS3A01G233600 chr3D 299743215 299746911 3696 False 1489.000000 3956 92.975000 19 2808 3 chr3D.!!$F1 2789
4 TraesCS3A01G233600 chr3D 29789097 29790079 982 True 752.000000 752 81.159000 704 1704 1 chr3D.!!$R1 1000
5 TraesCS3A01G233600 chr3D 29811507 29813105 1598 True 522.000000 846 80.476000 384 2147 2 chr3D.!!$R3 1763
6 TraesCS3A01G233600 chr3D 29861105 29862119 1014 True 258.166667 586 90.227000 417 1561 3 chr3D.!!$R4 1144
7 TraesCS3A01G233600 chr3B 421530300 421536137 5837 True 1957.150000 3819 95.736500 321 2808 2 chr3B.!!$R3 2487
8 TraesCS3A01G233600 chr3B 50958989 50959678 689 True 693.000000 693 84.908000 688 1389 1 chr3B.!!$R1 701
9 TraesCS3A01G233600 chr3B 50942477 50944047 1570 False 327.333333 497 80.921333 381 2175 3 chr3B.!!$F1 1794
10 TraesCS3A01G233600 chr7B 707945785 707947581 1796 True 281.250000 575 80.169000 382 2104 4 chr7B.!!$R1 1722

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
22 23 0.686789 GCCTCTTGGTGGCCATTTTT 59.313 50.0 9.72 0.0 44.32 1.94 F
1061 5503 0.477204 ATCAGCCCCATCATCACTGG 59.523 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1172 5642 0.392863 TTGGACGATGTGGCTCATGG 60.393 55.0 6.80 8.36 36.83 3.66 R
2465 7067 0.596082 GTATGCCCTTGTTGCAACGT 59.404 50.0 23.79 3.87 42.92 3.99 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
20 21 4.118584 GCCTCTTGGTGGCCATTT 57.881 55.556 9.72 0.00 44.32 2.32
21 22 2.365410 GCCTCTTGGTGGCCATTTT 58.635 52.632 9.72 0.00 44.32 1.82
22 23 0.686789 GCCTCTTGGTGGCCATTTTT 59.313 50.000 9.72 0.00 44.32 1.94
59 60 1.976898 CATGTGTTGCTGCCCCAAT 59.023 52.632 0.00 0.00 0.00 3.16
84 85 5.270893 TCTATATTGCTTCGGTGCACTTA 57.729 39.130 17.98 1.78 43.20 2.24
96 97 4.034279 TCGGTGCACTTAAACTTGTTGTAC 59.966 41.667 17.98 0.00 0.00 2.90
111 112 4.897140 TGTTGTACGGGTGTTAGCTTTAT 58.103 39.130 0.00 0.00 0.00 1.40
147 148 8.549548 GGACGAAAGCCTATTTTAAGAGTATTC 58.450 37.037 0.00 0.00 0.00 1.75
180 181 2.030893 CACTTTGCCACACCACATACAG 60.031 50.000 0.00 0.00 0.00 2.74
191 192 7.283580 GCCACACCACATACAGGTTTAATTATA 59.716 37.037 0.00 0.00 37.23 0.98
229 959 2.613026 TCCAACCATACCTACGCATG 57.387 50.000 0.00 0.00 0.00 4.06
234 964 4.502431 CCAACCATACCTACGCATGTATGA 60.502 45.833 16.12 0.00 44.50 2.15
444 4514 4.460382 ACAACAGATCAACCATGAATCCAC 59.540 41.667 0.00 0.00 39.49 4.02
535 4633 1.436195 AAGAAGCAGACGCAACGCAA 61.436 50.000 0.00 0.00 42.27 4.85
598 4711 3.771577 GGGAAATATCACCCGAGATGT 57.228 47.619 2.10 0.00 36.56 3.06
663 4784 1.654105 ACGATGCTAGCTTTTTCGTCG 59.346 47.619 21.35 17.29 38.56 5.12
853 5275 4.694233 CGGCTGCTGAGTGTGCCT 62.694 66.667 1.17 0.00 42.90 4.75
854 5276 3.054503 GGCTGCTGAGTGTGCCTG 61.055 66.667 0.00 0.00 41.92 4.85
1018 5443 3.769739 ATCAGACACCAACACAGCTAA 57.230 42.857 0.00 0.00 0.00 3.09
1055 5497 1.540166 CACCCATCAGCCCCATCAT 59.460 57.895 0.00 0.00 0.00 2.45
1061 5503 0.477204 ATCAGCCCCATCATCACTGG 59.523 55.000 0.00 0.00 0.00 4.00
1108 5565 2.050985 GCAACTGCTTGCGTCCAC 60.051 61.111 0.00 0.00 43.42 4.02
1112 5569 1.160329 AACTGCTTGCGTCCACACTC 61.160 55.000 0.00 0.00 0.00 3.51
1352 5829 1.864725 TTCGTACATGGTCGTCGGCA 61.865 55.000 0.00 0.00 0.00 5.69
1358 5835 1.595929 ATGGTCGTCGGCAAAACGT 60.596 52.632 0.00 0.00 40.86 3.99
1655 6224 5.295787 TGTTTTTGATCGACTTGTTACTGCT 59.704 36.000 0.00 0.00 0.00 4.24
1720 6293 8.194104 TGTTTATGTATTTGTTGTTTGCTCTGT 58.806 29.630 0.00 0.00 0.00 3.41
1971 6563 6.663734 TCAGCAGAGCAGGCTACTATATATA 58.336 40.000 0.00 0.00 40.23 0.86
1972 6564 7.293828 TCAGCAGAGCAGGCTACTATATATAT 58.706 38.462 0.00 0.00 40.23 0.86
2016 6609 7.036220 TCTTTCTGGAAGATACGATCACTTTC 58.964 38.462 0.00 0.00 46.36 2.62
2184 6780 7.540400 GCTGCACTCGATCATATATATACATCC 59.460 40.741 0.00 0.00 0.00 3.51
2307 6908 2.879002 AGTGAGTGTAGATGCATCGG 57.121 50.000 20.67 0.00 0.00 4.18
2324 6925 6.237154 TGCATCGGTCATTGGATATATTCAA 58.763 36.000 8.92 8.92 0.00 2.69
2339 6941 9.670442 GGATATATTCAAGGGGGTATACAGATA 57.330 37.037 5.01 0.00 0.00 1.98
2519 7121 8.154203 TCTAGTGGTTCAACATTAATCTTGTCA 58.846 33.333 3.75 0.18 0.00 3.58
2534 7136 5.023533 TCTTGTCAGACATATACCTTGCC 57.976 43.478 3.45 0.00 0.00 4.52
2624 7226 9.753669 GAAATTTTTGACTTAGTTGTGGTTTTG 57.246 29.630 0.00 0.00 0.00 2.44
2629 7231 6.687081 TGACTTAGTTGTGGTTTTGGTAAG 57.313 37.500 0.00 0.00 0.00 2.34
2630 7232 6.416415 TGACTTAGTTGTGGTTTTGGTAAGA 58.584 36.000 0.00 0.00 0.00 2.10
2631 7233 7.057894 TGACTTAGTTGTGGTTTTGGTAAGAT 58.942 34.615 0.00 0.00 0.00 2.40
2632 7234 7.558444 TGACTTAGTTGTGGTTTTGGTAAGATT 59.442 33.333 0.00 0.00 0.00 2.40
2633 7235 8.301252 ACTTAGTTGTGGTTTTGGTAAGATTT 57.699 30.769 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.985645 ACACATGCATAGAAAGAAAGCAAAAA 59.014 30.769 0.00 0.00 38.85 1.94
59 60 2.698274 TGCACCGAAGCAATATAGAGGA 59.302 45.455 0.00 0.00 42.46 3.71
84 85 3.313249 GCTAACACCCGTACAACAAGTTT 59.687 43.478 0.00 0.00 0.00 2.66
96 97 9.458374 CCATTTTATAAATAAAGCTAACACCCG 57.542 33.333 0.00 0.00 34.13 5.28
119 120 6.415573 ACTCTTAAAATAGGCTTTCGTCCAT 58.584 36.000 0.00 0.00 0.00 3.41
120 121 5.801380 ACTCTTAAAATAGGCTTTCGTCCA 58.199 37.500 0.00 0.00 0.00 4.02
147 148 4.696877 TGTGGCAAAGTGAGACAATCATAG 59.303 41.667 0.00 0.00 40.92 2.23
150 151 2.618241 GTGTGGCAAAGTGAGACAATCA 59.382 45.455 0.00 0.00 34.79 2.57
180 181 7.094506 CGAACTGGGGGCTAATATAATTAAACC 60.095 40.741 0.00 0.00 0.00 3.27
191 192 0.702316 AAACCGAACTGGGGGCTAAT 59.298 50.000 0.00 0.00 44.64 1.73
279 1009 9.304731 CGTGCACTAAGGTGTATAATTTACTTA 57.695 33.333 16.19 0.00 44.65 2.24
293 1023 0.685097 ATGGACACGTGCACTAAGGT 59.315 50.000 17.22 7.26 32.58 3.50
299 1029 0.166597 CATGACATGGACACGTGCAC 59.833 55.000 17.22 6.82 37.10 4.57
309 1039 9.616634 GCACTGTTTATTTATATCATGACATGG 57.383 33.333 15.37 0.00 0.00 3.66
338 1068 8.616076 GTCTTGATTTGGAATTGTACCTCTATG 58.384 37.037 0.00 0.00 0.00 2.23
344 1074 5.016831 AGGGTCTTGATTTGGAATTGTACC 58.983 41.667 0.00 0.00 0.00 3.34
444 4514 6.918569 ACAAAGACGATTAGGTAGATTGATCG 59.081 38.462 0.00 0.00 43.65 3.69
535 4633 4.202060 CGGATATATATTCTGTCGCCTGCT 60.202 45.833 0.00 0.00 0.00 4.24
598 4711 4.225942 AGTGCAGGGAGTCTTTATCAATGA 59.774 41.667 0.00 0.00 0.00 2.57
1018 5443 1.674322 GTGGTGGTGGCGCTAATGT 60.674 57.895 7.64 0.00 0.00 2.71
1104 5555 0.836606 TCACAAGCTTGGAGTGTGGA 59.163 50.000 29.18 12.09 42.35 4.02
1108 5565 2.608752 GGCAAATCACAAGCTTGGAGTG 60.609 50.000 29.18 21.99 34.67 3.51
1112 5569 1.938016 GCAGGCAAATCACAAGCTTGG 60.938 52.381 29.18 18.09 36.08 3.61
1172 5642 0.392863 TTGGACGATGTGGCTCATGG 60.393 55.000 6.80 8.36 36.83 3.66
1352 5829 2.433436 GGCAGGTTCCAGATACGTTTT 58.567 47.619 0.00 0.00 0.00 2.43
1358 5835 2.742116 GGCGGGCAGGTTCCAGATA 61.742 63.158 0.00 0.00 0.00 1.98
1655 6224 8.089597 TGTACTGAACAAGATGTCCGTTTTATA 58.910 33.333 0.00 0.00 34.29 0.98
1711 6284 6.600811 AGCATGAAATGATCGACAGAGCAAA 61.601 40.000 0.00 0.00 39.99 3.68
1971 6563 9.190317 AGAAAGAAAGAAAAACAGTGGTTAGAT 57.810 29.630 0.00 0.00 35.82 1.98
1972 6564 8.458843 CAGAAAGAAAGAAAAACAGTGGTTAGA 58.541 33.333 0.00 0.00 35.82 2.10
2184 6780 1.586422 CAGAAGTATGGATGTGGGCG 58.414 55.000 0.00 0.00 0.00 6.13
2248 6849 1.896660 GTTGTCTGGGGCGCTGAAA 60.897 57.895 7.64 4.95 0.00 2.69
2251 6852 2.743928 GAGTTGTCTGGGGCGCTG 60.744 66.667 7.64 2.10 0.00 5.18
2307 6908 5.892348 ACCCCCTTGAATATATCCAATGAC 58.108 41.667 0.00 0.00 0.00 3.06
2324 6925 7.166167 CGCTTATTTTTATCTGTATACCCCCT 58.834 38.462 0.00 0.00 0.00 4.79
2462 7064 2.186532 TGCCCTTGTTGCAACGTATA 57.813 45.000 23.79 4.07 35.40 1.47
2463 7065 1.544724 ATGCCCTTGTTGCAACGTAT 58.455 45.000 23.79 11.79 42.92 3.06
2465 7067 0.596082 GTATGCCCTTGTTGCAACGT 59.404 50.000 23.79 3.87 42.92 3.99
2519 7121 2.206322 TGGGGGCAAGGTATATGTCT 57.794 50.000 0.00 0.00 0.00 3.41
2532 7134 6.489022 ACGAAAAACTAGAATATAATGGGGGC 59.511 38.462 0.00 0.00 0.00 5.80
2770 7377 2.160208 CGACGCCGCACAAAATAAAAAC 60.160 45.455 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.