Multiple sequence alignment - TraesCS3D01G521900

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 TraesCS3D01G521900 chr3D 100.000 3394 0 0 918 4311 603409945 603406552 0.000000e+00 6268.0
1 TraesCS3D01G521900 chr3D 87.858 1293 110 31 1878 3140 603374861 603373586 0.000000e+00 1474.0
2 TraesCS3D01G521900 chr3D 100.000 713 0 0 1 713 603410862 603410150 0.000000e+00 1317.0
3 TraesCS3D01G521900 chr3D 90.000 700 55 8 2846 3544 603372335 603371650 0.000000e+00 891.0
4 TraesCS3D01G521900 chr3D 87.884 619 52 10 1660 2260 603375530 603374917 0.000000e+00 706.0
5 TraesCS3D01G521900 chr3D 88.956 498 45 5 3588 4080 603371648 603371156 1.330000e-169 606.0
6 TraesCS3D01G521900 chr3D 89.165 443 34 6 1180 1621 603375968 603375539 1.360000e-149 540.0
7 TraesCS3D01G521900 chr3D 78.686 563 97 12 2468 3026 603353762 603353219 1.910000e-93 353.0
8 TraesCS3D01G521900 chr3D 82.836 134 10 4 2468 2600 603393977 603393856 1.640000e-19 108.0
9 TraesCS3D01G521900 chr3D 96.774 31 1 0 3669 3699 603374431 603374461 8.000000e-03 52.8
10 TraesCS3D01G521900 chr3A 95.759 2028 62 7 2288 4311 732699728 732701735 0.000000e+00 3247.0
11 TraesCS3D01G521900 chr3A 85.462 1245 83 27 1082 2274 732736897 732738095 0.000000e+00 1206.0
12 TraesCS3D01G521900 chr3A 94.498 727 25 9 918 1632 732697939 732698662 0.000000e+00 1107.0
13 TraesCS3D01G521900 chr3A 90.620 693 52 9 1 688 732696845 732697529 0.000000e+00 907.0
14 TraesCS3D01G521900 chr3A 87.983 724 72 13 3588 4305 732739743 732740457 0.000000e+00 841.0
15 TraesCS3D01G521900 chr3A 88.720 656 67 6 2890 3544 732739092 732739741 0.000000e+00 795.0
16 TraesCS3D01G521900 chr3A 92.294 545 37 5 2358 2900 732729562 732730103 0.000000e+00 769.0
17 TraesCS3D01G521900 chr3A 88.198 627 50 13 1648 2260 732698647 732699263 0.000000e+00 726.0
18 TraesCS3D01G521900 chr3A 88.385 551 38 14 1082 1631 732727961 732728486 1.310000e-179 640.0
19 TraesCS3D01G521900 chr3A 86.323 446 26 13 1841 2261 732728627 732729062 1.830000e-123 453.0
20 TraesCS3D01G521900 chr3A 85.083 181 12 6 2188 2366 732729260 732729427 2.060000e-38 171.0
21 TraesCS3D01G521900 chr3A 93.220 59 3 1 2260 2317 732729087 732729145 7.680000e-13 86.1
22 TraesCS3D01G521900 chr3B 96.653 1703 42 7 2260 3961 810335276 810336964 0.000000e+00 2815.0
23 TraesCS3D01G521900 chr3B 95.532 1298 53 4 2855 4150 810378785 810380079 0.000000e+00 2071.0
24 TraesCS3D01G521900 chr3B 89.092 1366 123 15 2923 4278 810522600 810523949 0.000000e+00 1674.0
25 TraesCS3D01G521900 chr3B 91.566 664 26 16 974 1632 810334043 810334681 0.000000e+00 889.0
26 TraesCS3D01G521900 chr3B 89.390 688 66 6 2846 3532 810411078 810411759 0.000000e+00 859.0
27 TraesCS3D01G521900 chr3B 87.989 716 71 10 3588 4295 810461742 810462450 0.000000e+00 832.0
28 TraesCS3D01G521900 chr3B 87.176 733 50 20 1 713 810332773 810333481 0.000000e+00 793.0
29 TraesCS3D01G521900 chr3B 87.500 656 75 6 2890 3544 810461091 810461740 0.000000e+00 750.0
30 TraesCS3D01G521900 chr3B 87.477 551 53 8 1082 1631 810399365 810399900 4.730000e-174 621.0
31 TraesCS3D01G521900 chr3B 84.124 548 63 12 1086 1631 810370159 810370684 3.850000e-140 508.0
32 TraesCS3D01G521900 chr3B 85.301 415 34 11 1874 2261 810400055 810400469 1.870000e-108 403.0
33 TraesCS3D01G521900 chr3B 88.339 283 24 5 3588 3867 810411777 810412053 8.940000e-87 331.0
34 TraesCS3D01G521900 chr3B 78.053 565 97 16 2465 3023 810506503 810507046 8.940000e-87 331.0
35 TraesCS3D01G521900 chr3B 77.548 628 79 28 1648 2260 810334666 810335246 5.380000e-84 322.0
36 TraesCS3D01G521900 chr3B 92.611 203 5 5 4000 4201 810336961 810337154 2.540000e-72 283.0
37 TraesCS3D01G521900 chr3B 81.977 344 25 17 1725 2055 810370736 810371055 1.540000e-64 257.0
38 TraesCS3D01G521900 chr3B 86.070 201 12 8 2050 2235 810378121 810378320 7.310000e-48 202.0
39 TraesCS3D01G521900 chr3B 86.076 79 8 3 206 281 810333089 810333167 9.940000e-12 82.4
40 TraesCS3D01G521900 chr3B 97.619 42 1 0 2851 2892 810460828 810460869 5.980000e-09 73.1


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 TraesCS3D01G521900 chr3D 603406552 603410862 4310 True 3792.500000 6268 100.000000 1 4311 2 chr3D.!!$R4 4310
1 TraesCS3D01G521900 chr3D 603371156 603375968 4812 True 843.400000 1474 88.772600 1180 4080 5 chr3D.!!$R3 2900
2 TraesCS3D01G521900 chr3D 603353219 603353762 543 True 353.000000 353 78.686000 2468 3026 1 chr3D.!!$R1 558
3 TraesCS3D01G521900 chr3A 732696845 732701735 4890 False 1496.750000 3247 92.268750 1 4311 4 chr3A.!!$F1 4310
4 TraesCS3D01G521900 chr3A 732736897 732740457 3560 False 947.333333 1206 87.388333 1082 4305 3 chr3A.!!$F3 3223
5 TraesCS3D01G521900 chr3A 732727961 732730103 2142 False 423.820000 769 89.061000 1082 2900 5 chr3A.!!$F2 1818
6 TraesCS3D01G521900 chr3B 810522600 810523949 1349 False 1674.000000 1674 89.092000 2923 4278 1 chr3B.!!$F2 1355
7 TraesCS3D01G521900 chr3B 810378121 810380079 1958 False 1136.500000 2071 90.801000 2050 4150 2 chr3B.!!$F5 2100
8 TraesCS3D01G521900 chr3B 810332773 810337154 4381 False 864.066667 2815 88.605000 1 4201 6 chr3B.!!$F3 4200
9 TraesCS3D01G521900 chr3B 810411078 810412053 975 False 595.000000 859 88.864500 2846 3867 2 chr3B.!!$F7 1021
10 TraesCS3D01G521900 chr3B 810460828 810462450 1622 False 551.700000 832 91.036000 2851 4295 3 chr3B.!!$F8 1444
11 TraesCS3D01G521900 chr3B 810399365 810400469 1104 False 512.000000 621 86.389000 1082 2261 2 chr3B.!!$F6 1179
12 TraesCS3D01G521900 chr3B 810370159 810371055 896 False 382.500000 508 83.050500 1086 2055 2 chr3B.!!$F4 969
13 TraesCS3D01G521900 chr3B 810506503 810507046 543 False 331.000000 331 78.053000 2465 3023 1 chr3B.!!$F1 558

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
173 174 0.249398 CCCTCCGGTAGGTGAACTTG 59.751 60.000 15.95 0.0 44.90 3.16 F
689 711 1.153667 GCGAAGGCCAGACAGAGAG 60.154 63.158 5.01 0.0 0.00 3.20 F
2282 3582 1.977854 TGTTGGGACACATCAGCTACT 59.022 47.619 0.00 0.0 39.29 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2477 0.108992 TGTGACGTATCCCTGCGAAC 60.109 55.000 0.0 0.0 34.31 3.95 R
2640 4102 2.968675 AGTGTATCGTTAGGCACCAAC 58.031 47.619 0.0 0.0 32.75 3.77 R
4213 7767 1.081892 CCTTCAACACATCTCCTGCG 58.918 55.000 0.0 0.0 0.00 5.18 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
72 73 4.280929 AGAATATATTCTTTTTGGCCGGCC 59.719 41.667 39.40 39.40 44.28 6.13
144 145 4.488136 CAGGTGGGCGCTGGCATA 62.488 66.667 7.64 0.00 42.47 3.14
173 174 0.249398 CCCTCCGGTAGGTGAACTTG 59.751 60.000 15.95 0.00 44.90 3.16
311 323 5.568685 TTTTTCACACCGACTTTCAATCA 57.431 34.783 0.00 0.00 0.00 2.57
314 326 1.864711 CACACCGACTTTCAATCACGT 59.135 47.619 0.00 0.00 0.00 4.49
316 328 2.131972 CACCGACTTTCAATCACGTGA 58.868 47.619 22.48 22.48 0.00 4.35
317 329 2.736721 CACCGACTTTCAATCACGTGAT 59.263 45.455 25.18 25.18 36.07 3.06
318 330 3.186409 CACCGACTTTCAATCACGTGATT 59.814 43.478 32.82 32.82 44.93 2.57
319 331 3.432252 ACCGACTTTCAATCACGTGATTC 59.568 43.478 34.94 23.56 42.41 2.52
371 387 4.517815 GCGCATACCCGTTCCCGA 62.518 66.667 0.30 0.00 35.63 5.14
384 400 1.895020 TTCCCGAGCTGTAACCGCAT 61.895 55.000 0.00 0.00 0.00 4.73
422 439 2.251642 GCGTGTAATCGGGCATCCC 61.252 63.158 0.00 0.00 41.09 3.85
432 449 1.754234 GGGCATCCCGCATTTGTCT 60.754 57.895 0.00 0.00 45.17 3.41
482 500 4.961438 AAACAAAATCACCTGGCTTGAT 57.039 36.364 0.00 0.00 35.09 2.57
566 586 4.731313 AAGAGGAAAGAAACTGATGGGT 57.269 40.909 0.00 0.00 0.00 4.51
654 675 3.453353 CCTCCGGGTTTCTCCTATTTACA 59.547 47.826 0.00 0.00 36.25 2.41
688 710 2.973899 GCGAAGGCCAGACAGAGA 59.026 61.111 5.01 0.00 0.00 3.10
689 711 1.153667 GCGAAGGCCAGACAGAGAG 60.154 63.158 5.01 0.00 0.00 3.20
1218 1550 2.919043 GCCCCGACCTCCATCATT 59.081 61.111 0.00 0.00 0.00 2.57
1283 1644 4.452733 CCCCCTTCTCGTGTCCGC 62.453 72.222 0.00 0.00 0.00 5.54
1700 2076 7.607991 CACATCTGGTAGGAGAAAAAGTTGTAT 59.392 37.037 0.00 0.00 0.00 2.29
1702 2078 7.554959 TCTGGTAGGAGAAAAAGTTGTATCT 57.445 36.000 0.00 0.00 0.00 1.98
1703 2079 7.386851 TCTGGTAGGAGAAAAAGTTGTATCTG 58.613 38.462 0.00 0.00 0.00 2.90
1704 2080 7.016268 TCTGGTAGGAGAAAAAGTTGTATCTGT 59.984 37.037 0.00 0.00 0.00 3.41
1736 2128 4.843147 TGTGTGTTGATTCGTTGATTGTC 58.157 39.130 0.00 0.00 0.00 3.18
1766 2160 2.733593 GCTGACCGGTCGACACAC 60.734 66.667 28.70 10.85 0.00 3.82
1773 2167 3.198068 GACCGGTCGACACACTAGTATA 58.802 50.000 20.85 0.00 0.00 1.47
1784 2180 6.578919 CGACACACTAGTATACTGCATATGTG 59.421 42.308 22.14 22.14 40.52 3.21
1915 2312 2.027192 ACCATCACTGCTGGAAATACGT 60.027 45.455 5.90 0.00 37.22 3.57
2229 2684 3.701241 TCGTGAATTGTTCTGTTTTGCC 58.299 40.909 0.00 0.00 0.00 4.52
2274 3574 2.746279 TCCTGTTTGTTGGGACACAT 57.254 45.000 0.00 0.00 39.29 3.21
2280 3580 3.146066 GTTTGTTGGGACACATCAGCTA 58.854 45.455 0.00 0.00 39.29 3.32
2281 3581 2.472695 TGTTGGGACACATCAGCTAC 57.527 50.000 0.00 0.00 39.29 3.58
2282 3582 1.977854 TGTTGGGACACATCAGCTACT 59.022 47.619 0.00 0.00 39.29 2.57
2284 3584 2.744202 GTTGGGACACATCAGCTACTTG 59.256 50.000 0.00 0.00 39.29 3.16
2512 3972 4.082787 GCATTGACCTCTTCGAAAATGGAA 60.083 41.667 15.92 4.58 0.00 3.53
2671 4317 6.590357 CCTAACGATACACTTGTTGACTTTG 58.410 40.000 0.00 0.00 33.35 2.77
2683 4329 5.229921 TGTTGACTTTGAAGGTTCTTTCG 57.770 39.130 0.00 0.00 0.00 3.46
3725 7268 6.306987 AGTGGTACATTTGAAACTGGAAGAT 58.693 36.000 0.00 0.00 44.52 2.40
3947 7492 3.910989 ACTTCCTTGCCTTTGTAACCTT 58.089 40.909 0.00 0.00 0.00 3.50
4176 7730 9.793252 AAATGTGTCATGCTATCAATTTAGTTC 57.207 29.630 0.00 0.00 0.00 3.01
4197 7751 7.486647 AGTTCGACAACTAGAAGTTACAAAGA 58.513 34.615 0.00 0.00 41.39 2.52
4223 7780 5.356882 TTTTTCAAACTACGCAGGAGATG 57.643 39.130 0.00 0.00 0.00 2.90
4299 7857 4.395959 TTTGTCGTACACTCCAAGTCTT 57.604 40.909 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 6.374578 GCCAAAAAGAATATATTCTCTCGCC 58.625 40.000 24.75 10.84 45.83 5.54
196 197 1.080093 GTGAGATCGACCGTTGGCA 60.080 57.895 0.00 0.00 0.00 4.92
300 312 7.678194 TTTTTGAATCACGTGATTGAAAGTC 57.322 32.000 36.66 27.11 44.22 3.01
371 387 2.819595 CGGCATGCGGTTACAGCT 60.820 61.111 16.56 0.00 35.28 4.24
395 412 2.124860 ATTACACGCGGGAAGGGC 60.125 61.111 19.19 0.00 36.05 5.19
403 420 2.594962 GGATGCCCGATTACACGCG 61.595 63.158 3.53 3.53 0.00 6.01
404 421 2.251642 GGGATGCCCGATTACACGC 61.252 63.158 0.00 0.00 32.13 5.34
405 422 4.043168 GGGATGCCCGATTACACG 57.957 61.111 0.00 0.00 32.13 4.49
432 449 4.393155 ACCAATGCTGGAGCGCGA 62.393 61.111 12.10 0.00 46.92 5.87
566 586 3.137533 GCTGCCTGCCAAAATTTGTTTA 58.862 40.909 4.92 0.00 35.15 2.01
679 701 1.392589 GCTCCTCTCCTCTCTGTCTG 58.607 60.000 0.00 0.00 0.00 3.51
688 710 4.787280 CCGGTGGGCTCCTCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
1298 1663 1.672881 GAGATGAAATTCACGGCAGGG 59.327 52.381 0.00 0.00 0.00 4.45
1464 1838 5.514204 CCATGCGATTCAAAATTTCAGAGAC 59.486 40.000 0.00 0.00 0.00 3.36
1492 1867 3.313526 AGCTTAAGCCATGCGATAAACAG 59.686 43.478 23.71 0.00 43.38 3.16
1543 1918 4.963953 GCAATGCAGTATGTGTAACGATTC 59.036 41.667 0.00 0.00 42.39 2.52
1647 2022 9.684448 CATCATACTCGTAATCAGTCAAGTATT 57.316 33.333 0.00 0.00 29.78 1.89
1648 2023 7.810282 GCATCATACTCGTAATCAGTCAAGTAT 59.190 37.037 0.00 0.00 31.80 2.12
1649 2024 7.139392 GCATCATACTCGTAATCAGTCAAGTA 58.861 38.462 0.00 0.00 0.00 2.24
1650 2025 5.980116 GCATCATACTCGTAATCAGTCAAGT 59.020 40.000 0.00 0.00 0.00 3.16
1663 2039 3.103447 ACCAGATGTGCATCATACTCG 57.897 47.619 13.79 0.00 40.22 4.18
1700 2076 1.271652 ACACACAACACCCACAACAGA 60.272 47.619 0.00 0.00 0.00 3.41
1702 2078 1.270826 CAACACACAACACCCACAACA 59.729 47.619 0.00 0.00 0.00 3.33
1703 2079 1.542030 TCAACACACAACACCCACAAC 59.458 47.619 0.00 0.00 0.00 3.32
1704 2080 1.911057 TCAACACACAACACCCACAA 58.089 45.000 0.00 0.00 0.00 3.33
1736 2128 1.197721 CGGTCAGCCTAGCAAAACAAG 59.802 52.381 0.00 0.00 0.00 3.16
1766 2160 6.015434 TGACACCCACATATGCAGTATACTAG 60.015 42.308 4.74 1.71 0.00 2.57
1773 2167 2.113860 GTGACACCCACATATGCAGT 57.886 50.000 1.58 0.00 45.03 4.40
1784 2180 1.629043 TCTAGTCCACTGTGACACCC 58.371 55.000 9.86 0.00 37.73 4.61
1967 2393 7.362056 CCAACCTACTTCAATAACACAATCCTG 60.362 40.741 0.00 0.00 0.00 3.86
2038 2476 0.172803 GTGACGTATCCCTGCGAACT 59.827 55.000 0.00 0.00 34.31 3.01
2039 2477 0.108992 TGTGACGTATCCCTGCGAAC 60.109 55.000 0.00 0.00 34.31 3.95
2280 3580 6.996879 AGATATATGCAGTTGAATGCTCAAGT 59.003 34.615 5.00 0.00 46.63 3.16
2281 3581 7.361031 GGAGATATATGCAGTTGAATGCTCAAG 60.361 40.741 5.00 0.00 46.63 3.02
2282 3582 6.429078 GGAGATATATGCAGTTGAATGCTCAA 59.571 38.462 5.00 0.00 46.63 3.02
2284 3584 5.936372 TGGAGATATATGCAGTTGAATGCTC 59.064 40.000 5.00 0.00 46.63 4.26
2512 3972 6.259608 GCACATAAGTCAGCTCATTACTGAAT 59.740 38.462 0.00 0.00 45.32 2.57
2640 4102 2.968675 AGTGTATCGTTAGGCACCAAC 58.031 47.619 0.00 0.00 32.75 3.77
2683 4329 8.841300 AGTTCAATAGTTTCTTTGTCCTCTTTC 58.159 33.333 0.00 0.00 0.00 2.62
3478 7016 3.188048 CCACAGCTGAATGAAGACTGTTC 59.812 47.826 23.35 0.00 39.48 3.18
3582 7124 3.722025 CTCAAGTCGAGCAGGAACTCCT 61.722 54.545 0.00 0.00 38.93 3.69
3725 7268 5.615289 CCAACAAATGGGGTGAAACATTTA 58.385 37.500 0.00 0.00 46.27 1.40
3915 7460 2.489722 GGCAAGGAAGTTCAAGATCACC 59.510 50.000 5.01 0.00 0.00 4.02
4176 7730 9.931210 AAAAATCTTTGTAACTTCTAGTTGTCG 57.069 29.630 2.45 0.00 39.11 4.35
4207 7761 3.067106 CAACACATCTCCTGCGTAGTTT 58.933 45.455 0.00 0.00 0.00 2.66
4210 7764 2.654749 TCAACACATCTCCTGCGTAG 57.345 50.000 0.00 0.00 0.00 3.51
4211 7765 2.353704 CCTTCAACACATCTCCTGCGTA 60.354 50.000 0.00 0.00 0.00 4.42
4212 7766 1.609061 CCTTCAACACATCTCCTGCGT 60.609 52.381 0.00 0.00 0.00 5.24
4213 7767 1.081892 CCTTCAACACATCTCCTGCG 58.918 55.000 0.00 0.00 0.00 5.18
4214 7768 2.079925 GTCCTTCAACACATCTCCTGC 58.920 52.381 0.00 0.00 0.00 4.85
4216 7770 4.163078 CCATAGTCCTTCAACACATCTCCT 59.837 45.833 0.00 0.00 0.00 3.69
4217 7771 4.162320 TCCATAGTCCTTCAACACATCTCC 59.838 45.833 0.00 0.00 0.00 3.71
4218 7772 5.344743 TCCATAGTCCTTCAACACATCTC 57.655 43.478 0.00 0.00 0.00 2.75
4223 7780 8.561738 TTTTCTTATCCATAGTCCTTCAACAC 57.438 34.615 0.00 0.00 0.00 3.32
4278 7836 4.365723 GAAGACTTGGAGTGTACGACAAA 58.634 43.478 0.00 0.00 0.00 2.83
4287 7845 0.995024 ATGGGGGAAGACTTGGAGTG 59.005 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.