Multiple sequence alignment - TraesCS1A01G440500

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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 TraesCS1A01G440500 chr1A 100.000 4828 0 0 1 4828 589458886 589463713 0.000000e+00 8916.0
1 TraesCS1A01G440500 chr1A 95.042 2481 85 13 1774 4232 514560949 514563413 0.000000e+00 3866.0
2 TraesCS1A01G440500 chr1A 93.095 1202 61 10 62 1246 514559759 514560955 0.000000e+00 1740.0
3 TraesCS1A01G440500 chr1A 94.702 151 7 1 4423 4572 533292979 533292829 2.910000e-57 233.0
4 TraesCS1A01G440500 chr1A 91.018 167 9 6 4409 4573 514563671 514563833 2.260000e-53 220.0
5 TraesCS1A01G440500 chr1A 89.916 119 12 0 1441 1559 541898239 541898121 2.330000e-33 154.0
6 TraesCS1A01G440500 chr1A 91.667 96 8 0 1434 1529 19492300 19492205 3.030000e-27 134.0
7 TraesCS1A01G440500 chr4A 98.537 4444 53 9 1 4437 621505612 621510050 0.000000e+00 7836.0
8 TraesCS1A01G440500 chr4A 89.983 1208 68 18 62 1246 578170668 578169491 0.000000e+00 1511.0
9 TraesCS1A01G440500 chr3B 98.109 4442 48 7 1 4440 756246486 756242079 0.000000e+00 7705.0
10 TraesCS1A01G440500 chr3B 91.332 1419 88 18 1872 3263 800810427 800809017 0.000000e+00 1906.0
11 TraesCS1A01G440500 chr3B 87.179 624 53 14 2722 3339 173133457 173132855 0.000000e+00 684.0
12 TraesCS1A01G440500 chr3B 91.566 166 10 4 4409 4573 727792577 727792415 4.860000e-55 226.0
13 TraesCS1A01G440500 chr3B 90.476 168 10 6 4409 4574 756242054 756241891 2.930000e-52 217.0
14 TraesCS1A01G440500 chr3B 81.857 237 20 20 1552 1773 773480462 773480690 1.380000e-40 178.0
15 TraesCS1A01G440500 chr3B 80.833 240 19 23 1552 1774 585607784 585608013 3.870000e-36 163.0
16 TraesCS1A01G440500 chr3B 80.247 243 19 22 1552 1773 773472051 773472285 6.470000e-34 156.0
17 TraesCS1A01G440500 chr3B 93.750 96 6 0 1434 1529 782348773 782348868 1.400000e-30 145.0
18 TraesCS1A01G440500 chr3B 79.116 249 22 20 1552 1777 782348943 782349184 1.400000e-30 145.0
19 TraesCS1A01G440500 chr3B 93.750 64 4 0 1 64 800824960 800824897 3.980000e-16 97.1
20 TraesCS1A01G440500 chr6B 98.410 2578 35 6 1862 4435 696366732 696364157 0.000000e+00 4529.0
21 TraesCS1A01G440500 chr6B 96.712 2676 72 6 1774 4435 68671435 68674108 0.000000e+00 4440.0
22 TraesCS1A01G440500 chr6B 97.429 2373 53 6 1774 4143 49672954 49670587 0.000000e+00 4037.0
23 TraesCS1A01G440500 chr6B 97.765 1879 40 2 2559 4435 692809074 692810952 0.000000e+00 3236.0
24 TraesCS1A01G440500 chr6B 97.899 1761 30 5 62 1819 696368497 696366741 0.000000e+00 3040.0
25 TraesCS1A01G440500 chr6B 96.659 1646 39 5 2792 4435 38965005 38966636 0.000000e+00 2721.0
26 TraesCS1A01G440500 chr6B 97.727 1144 25 1 62 1204 692807125 692808268 0.000000e+00 1967.0
27 TraesCS1A01G440500 chr6B 95.105 1185 42 4 62 1246 68670273 68671441 0.000000e+00 1853.0
28 TraesCS1A01G440500 chr6B 94.370 1190 46 13 62 1246 38963243 38964416 0.000000e+00 1807.0
29 TraesCS1A01G440500 chr6B 94.096 830 28 11 417 1246 49673756 49672948 0.000000e+00 1242.0
30 TraesCS1A01G440500 chr6B 97.107 726 11 3 1271 1988 692808352 692809075 0.000000e+00 1216.0
31 TraesCS1A01G440500 chr6B 97.784 361 8 0 62 422 49693581 49693221 1.480000e-174 623.0
32 TraesCS1A01G440500 chr6B 97.315 149 4 0 4423 4571 696364130 696363982 2.230000e-63 254.0
33 TraesCS1A01G440500 chr6B 88.398 181 13 8 4409 4587 38966666 38966840 1.360000e-50 211.0
34 TraesCS1A01G440500 chr6B 98.438 64 1 0 1 64 38963044 38963107 3.950000e-21 113.0
35 TraesCS1A01G440500 chr6B 96.923 65 2 0 1 65 49693781 49693717 5.110000e-20 110.0
36 TraesCS1A01G440500 chr6B 96.923 65 2 0 1 65 68670077 68670141 5.110000e-20 110.0
37 TraesCS1A01G440500 chr6B 96.923 65 2 0 1 65 692806925 692806989 5.110000e-20 110.0
38 TraesCS1A01G440500 chr7B 96.167 2583 60 12 1774 4350 707279219 707276670 0.000000e+00 4185.0
39 TraesCS1A01G440500 chr7B 85.818 550 46 14 397 936 656310061 656309534 5.460000e-154 555.0
40 TraesCS1A01G440500 chr7B 97.059 272 8 0 975 1246 707279484 707279213 4.400000e-125 459.0
41 TraesCS1A01G440500 chr7B 91.930 285 21 2 964 1246 656309537 656309253 9.740000e-107 398.0
42 TraesCS1A01G440500 chr2A 94.382 2688 102 16 1774 4435 707273250 707270586 0.000000e+00 4082.0
43 TraesCS1A01G440500 chr2A 77.863 393 29 34 1434 1776 774919117 774918733 1.770000e-44 191.0
44 TraesCS1A01G440500 chr2A 94.792 96 5 0 1434 1529 7746052 7745957 3.010000e-32 150.0
45 TraesCS1A01G440500 chr5B 98.504 2272 30 3 1 2270 649834983 649832714 0.000000e+00 4004.0
46 TraesCS1A01G440500 chr5B 98.380 1790 26 2 2653 4440 649832719 649830931 0.000000e+00 3142.0
47 TraesCS1A01G440500 chr5B 99.207 1388 11 0 3050 4437 684053714 684055101 0.000000e+00 2503.0
48 TraesCS1A01G440500 chr5B 92.708 96 6 1 1434 1529 471283178 471283084 2.340000e-28 137.0
49 TraesCS1A01G440500 chr6A 93.813 2683 100 23 1774 4433 537821450 537824089 0.000000e+00 3975.0
50 TraesCS1A01G440500 chr6A 94.600 2426 85 17 1774 4177 115972651 115970250 0.000000e+00 3712.0
51 TraesCS1A01G440500 chr6A 92.839 1201 64 8 62 1246 537820262 537821456 0.000000e+00 1722.0
52 TraesCS1A01G440500 chr6A 91.457 1194 76 17 62 1246 115973821 115972645 0.000000e+00 1616.0
53 TraesCS1A01G440500 chr6A 84.921 252 32 5 4324 4573 32237128 32237375 2.890000e-62 250.0
54 TraesCS1A01G440500 chr6A 84.082 245 33 5 62 303 49808997 49809238 1.050000e-56 231.0
55 TraesCS1A01G440500 chr7A 96.957 1873 31 4 2565 4435 552980325 552978477 0.000000e+00 3120.0
56 TraesCS1A01G440500 chr7A 97.378 1144 28 2 62 1204 552982280 552981138 0.000000e+00 1945.0
57 TraesCS1A01G440500 chr7A 97.383 726 10 3 1271 1988 552981054 552980330 0.000000e+00 1227.0
58 TraesCS1A01G440500 chr7A 94.488 254 13 1 4574 4827 730068801 730068549 1.630000e-104 390.0
59 TraesCS1A01G440500 chr7A 86.603 209 26 2 4366 4573 20831004 20830797 3.760000e-56 230.0
60 TraesCS1A01G440500 chr7A 91.071 168 8 7 4412 4576 552978444 552978281 2.260000e-53 220.0
61 TraesCS1A01G440500 chr7A 98.462 65 1 0 1 65 552982480 552982416 1.100000e-21 115.0
62 TraesCS1A01G440500 chr2D 91.789 682 50 3 567 1246 72859797 72859120 0.000000e+00 944.0
63 TraesCS1A01G440500 chr4D 90.592 574 40 10 526 1098 294034304 294033744 0.000000e+00 749.0
64 TraesCS1A01G440500 chr4D 90.070 574 40 8 526 1098 294057521 294056964 0.000000e+00 728.0
65 TraesCS1A01G440500 chr4D 92.157 153 7 1 1094 1246 294033264 294033117 1.360000e-50 211.0
66 TraesCS1A01G440500 chr4D 93.333 105 7 0 1774 1878 294033123 294033019 6.470000e-34 156.0
67 TraesCS1A01G440500 chr3A 87.975 632 61 7 2713 3339 693578629 693579250 0.000000e+00 732.0
68 TraesCS1A01G440500 chr6D 85.628 494 38 10 4097 4573 12541114 12541591 5.620000e-134 488.0
69 TraesCS1A01G440500 chrUn 95.276 254 11 1 4574 4827 238607114 238606862 7.530000e-108 401.0
70 TraesCS1A01G440500 chrUn 92.509 267 18 2 4562 4827 83767750 83767485 9.810000e-102 381.0
71 TraesCS1A01G440500 chrUn 92.509 267 18 2 4562 4827 83769212 83768947 9.810000e-102 381.0
72 TraesCS1A01G440500 chrUn 92.509 267 18 2 4562 4827 286440734 286440999 9.810000e-102 381.0
73 TraesCS1A01G440500 chrUn 92.509 267 18 2 4562 4827 286442196 286442461 9.810000e-102 381.0
74 TraesCS1A01G440500 chrUn 92.509 267 18 2 4562 4827 410491973 410492238 9.810000e-102 381.0
75 TraesCS1A01G440500 chr5A 94.882 254 12 1 4574 4827 227623598 227623346 3.500000e-106 396.0
76 TraesCS1A01G440500 chr5A 92.509 267 18 2 4562 4827 227651014 227650749 9.810000e-102 381.0
77 TraesCS1A01G440500 chr5A 89.231 130 3 6 1289 1410 386544815 386544689 8.370000e-33 152.0
78 TraesCS1A01G440500 chr5A 94.792 96 5 0 1434 1529 17477377 17477472 3.010000e-32 150.0
79 TraesCS1A01G440500 chr5A 93.902 82 4 1 1552 1632 17477531 17477612 6.560000e-24 122.0
80 TraesCS1A01G440500 chr5A 87.850 107 7 2 1669 1775 17478475 17478575 2.360000e-23 121.0
81 TraesCS1A01G440500 chr2B 88.462 104 6 3 1669 1772 726596206 726596303 2.360000e-23 121.0


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 TraesCS1A01G440500 chr1A 589458886 589463713 4827 False 8916.000000 8916 100.000000 1 4828 1 chr1A.!!$F1 4827
1 TraesCS1A01G440500 chr1A 514559759 514563833 4074 False 1942.000000 3866 93.051667 62 4573 3 chr1A.!!$F2 4511
2 TraesCS1A01G440500 chr4A 621505612 621510050 4438 False 7836.000000 7836 98.537000 1 4437 1 chr4A.!!$F1 4436
3 TraesCS1A01G440500 chr4A 578169491 578170668 1177 True 1511.000000 1511 89.983000 62 1246 1 chr4A.!!$R1 1184
4 TraesCS1A01G440500 chr3B 756241891 756246486 4595 True 3961.000000 7705 94.292500 1 4574 2 chr3B.!!$R5 4573
5 TraesCS1A01G440500 chr3B 800809017 800810427 1410 True 1906.000000 1906 91.332000 1872 3263 1 chr3B.!!$R3 1391
6 TraesCS1A01G440500 chr3B 173132855 173133457 602 True 684.000000 684 87.179000 2722 3339 1 chr3B.!!$R1 617
7 TraesCS1A01G440500 chr6B 49670587 49673756 3169 True 2639.500000 4037 95.762500 417 4143 2 chr6B.!!$R1 3726
8 TraesCS1A01G440500 chr6B 696363982 696368497 4515 True 2607.666667 4529 97.874667 62 4571 3 chr6B.!!$R3 4509
9 TraesCS1A01G440500 chr6B 68670077 68674108 4031 False 2134.333333 4440 96.246667 1 4435 3 chr6B.!!$F2 4434
10 TraesCS1A01G440500 chr6B 692806925 692810952 4027 False 1632.250000 3236 97.380500 1 4435 4 chr6B.!!$F3 4434
11 TraesCS1A01G440500 chr6B 38963044 38966840 3796 False 1213.000000 2721 94.466250 1 4587 4 chr6B.!!$F1 4586
12 TraesCS1A01G440500 chr6B 49693221 49693781 560 True 366.500000 623 97.353500 1 422 2 chr6B.!!$R2 421
13 TraesCS1A01G440500 chr7B 707276670 707279484 2814 True 2322.000000 4185 96.613000 975 4350 2 chr7B.!!$R2 3375
14 TraesCS1A01G440500 chr7B 656309253 656310061 808 True 476.500000 555 88.874000 397 1246 2 chr7B.!!$R1 849
15 TraesCS1A01G440500 chr2A 707270586 707273250 2664 True 4082.000000 4082 94.382000 1774 4435 1 chr2A.!!$R2 2661
16 TraesCS1A01G440500 chr5B 649830931 649834983 4052 True 3573.000000 4004 98.442000 1 4440 2 chr5B.!!$R2 4439
17 TraesCS1A01G440500 chr5B 684053714 684055101 1387 False 2503.000000 2503 99.207000 3050 4437 1 chr5B.!!$F1 1387
18 TraesCS1A01G440500 chr6A 537820262 537824089 3827 False 2848.500000 3975 93.326000 62 4433 2 chr6A.!!$F3 4371
19 TraesCS1A01G440500 chr6A 115970250 115973821 3571 True 2664.000000 3712 93.028500 62 4177 2 chr6A.!!$R1 4115
20 TraesCS1A01G440500 chr7A 552978281 552982480 4199 True 1325.400000 3120 96.250200 1 4576 5 chr7A.!!$R3 4575
21 TraesCS1A01G440500 chr2D 72859120 72859797 677 True 944.000000 944 91.789000 567 1246 1 chr2D.!!$R1 679
22 TraesCS1A01G440500 chr4D 294056964 294057521 557 True 728.000000 728 90.070000 526 1098 1 chr4D.!!$R1 572
23 TraesCS1A01G440500 chr4D 294033019 294034304 1285 True 372.000000 749 92.027333 526 1878 3 chr4D.!!$R2 1352
24 TraesCS1A01G440500 chr3A 693578629 693579250 621 False 732.000000 732 87.975000 2713 3339 1 chr3A.!!$F1 626
25 TraesCS1A01G440500 chrUn 83767485 83769212 1727 True 381.000000 381 92.509000 4562 4827 2 chrUn.!!$R2 265
26 TraesCS1A01G440500 chrUn 286440734 286442461 1727 False 381.000000 381 92.509000 4562 4827 2 chrUn.!!$F2 265

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
435 586 2.441375 CCTCCCACCCACCAAAATTTTT 59.559 45.455 0.0 0.0 0.00 1.94 F
1375 2078 2.890945 TGACGAGTTGAGATGTTCTGGA 59.109 45.455 0.0 0.0 0.00 3.86 F
2997 4282 1.067212 CACGCCTGTGTCTCCTATACC 59.933 57.143 0.0 0.0 41.34 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 3561 5.065235 CACCCACACATGCATCTATCAATA 58.935 41.667 0.00 0.0 0.00 1.90 R
3039 4324 3.303791 GCTCCGAATCAAACGAACAAGTT 60.304 43.478 0.00 0.0 35.59 2.66 R
4707 7606 0.109723 GGCATTATACCCGGAGCCAA 59.890 55.000 0.73 0.0 41.63 4.52 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
354 498 6.866248 AGAAAAGAAGAAAAAGAAAACGCACA 59.134 30.769 0.00 0.0 0.00 4.57
435 586 2.441375 CCTCCCACCCACCAAAATTTTT 59.559 45.455 0.00 0.0 0.00 1.94
1204 1890 5.750067 ACACATGCTTGACTGAATTTTGAAC 59.250 36.000 6.60 0.0 0.00 3.18
1375 2078 2.890945 TGACGAGTTGAGATGTTCTGGA 59.109 45.455 0.00 0.0 0.00 3.86
1880 3124 9.075519 CGATTGAAACTTGTTTGCATATATTGT 57.924 29.630 3.27 0.0 0.00 2.71
2523 3786 7.250032 TCATACCTGATCCATTCTTAGATGG 57.750 40.000 0.00 0.0 46.49 3.51
2618 3883 5.523916 GTCAGCGTATGTAGTTTGGATGAAT 59.476 40.000 0.00 0.0 0.00 2.57
2997 4282 1.067212 CACGCCTGTGTCTCCTATACC 59.933 57.143 0.00 0.0 41.34 2.73
3039 4324 5.010933 ACTAGCTCAACAACACTAGCTCTA 58.989 41.667 0.00 0.0 43.96 2.43
3598 4901 1.398041 GCTATGCAGTGCGAACATCAA 59.602 47.619 11.20 0.0 0.00 2.57
4186 5510 1.080093 CCTACAGCAAAGCCGTCGA 60.080 57.895 0.00 0.0 0.00 4.20
4379 5705 1.572447 GTTAGCGCTTTTGACGGCA 59.428 52.632 18.68 0.0 0.00 5.69
4529 5965 0.884704 CGACGGGAAATGGCCTATGG 60.885 60.000 3.32 0.0 0.00 2.74
4707 7606 4.065281 GGGTGCGTGCCTAGTCGT 62.065 66.667 0.00 0.0 0.00 4.34
4723 7622 1.069668 GTCGTTGGCTCCGGGTATAAT 59.930 52.381 0.00 0.0 0.00 1.28
4747 7646 1.151777 CGGCGGCTGATCGTTGTAAT 61.152 55.000 7.61 0.0 0.00 1.89
4750 7649 1.651987 CGGCTGATCGTTGTAATGGT 58.348 50.000 0.00 0.0 0.00 3.55
4753 7652 1.267532 GCTGATCGTTGTAATGGTGCG 60.268 52.381 0.00 0.0 0.00 5.34
4792 7691 2.668280 GCTCGTGGAGTTGGCGTTC 61.668 63.158 0.00 0.0 31.39 3.95
4812 7711 3.292159 GCGCCGGGAAAAACCACT 61.292 61.111 2.18 0.0 41.20 4.00
4827 7726 1.138069 ACCACTGTGTCATCGTGTTCA 59.862 47.619 7.08 0.0 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
354 498 6.964908 TCATTTGATTTTGTATCGTGTGTGT 58.035 32.000 0.00 0.0 0.00 3.72
1204 1890 1.738099 GTGACAGCAGTAGCACCCG 60.738 63.158 0.00 0.0 45.49 5.28
1375 2078 6.208994 AGTCGACTAGGTAGACATCAAAGTTT 59.791 38.462 18.46 0.0 39.88 2.66
1880 3124 7.974675 GCTAGTTCACTAGTCATGCAAATTTA 58.025 34.615 14.20 0.0 45.85 1.40
2304 3561 5.065235 CACCCACACATGCATCTATCAATA 58.935 41.667 0.00 0.0 0.00 1.90
2523 3786 7.900782 ACCACATGTCATGTTTACTTACTAC 57.099 36.000 15.98 0.0 42.70 2.73
2844 4123 6.075762 TCAACAGAATCAATCACAAGGTTG 57.924 37.500 0.00 0.0 35.63 3.77
2997 4282 8.034058 AGCTAGTACAGAAATTAAACAAGCTG 57.966 34.615 0.00 0.0 34.36 4.24
3039 4324 3.303791 GCTCCGAATCAAACGAACAAGTT 60.304 43.478 0.00 0.0 35.59 2.66
4186 5510 5.057149 GTCGGCATAGATTTTCACCTATGT 58.943 41.667 0.00 0.0 42.43 2.29
4554 5990 2.282674 ACTACCGGACTCGCCACA 60.283 61.111 9.46 0.0 35.94 4.17
4701 7600 0.396139 ATACCCGGAGCCAACGACTA 60.396 55.000 0.73 0.0 0.00 2.59
4707 7606 0.109723 GGCATTATACCCGGAGCCAA 59.890 55.000 0.73 0.0 41.63 4.52
4800 7699 2.031157 CGATGACACAGTGGTTTTTCCC 60.031 50.000 5.31 0.0 34.77 3.97


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

AutoCloner maintained by Alex Coulton.