Multiple sequence alignment - TraesCS2B01G498000

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 TraesCS2B01G498000 chr2B 100.000 6323 0 0 1 6323 694446338 694440016 0.000000e+00 11677.0
1 TraesCS2B01G498000 chr2B 98.209 5919 85 11 1 5903 694425561 694419648 0.000000e+00 10323.0
2 TraesCS2B01G498000 chr2B 97.251 2874 74 4 598 3467 694477009 694474137 0.000000e+00 4865.0
3 TraesCS2B01G498000 chr2B 97.972 2170 40 3 3736 5903 694473880 694471713 0.000000e+00 3760.0
4 TraesCS2B01G498000 chr2B 98.095 420 7 1 5904 6323 694471659 694471241 0.000000e+00 730.0
5 TraesCS2B01G498000 chr2B 95.683 417 16 2 5907 6323 694419591 694419177 0.000000e+00 669.0
6 TraesCS2B01G498000 chr2B 95.686 255 7 2 3451 3701 694474119 694473865 2.120000e-109 407.0
7 TraesCS2B01G498000 chr2B 88.889 261 13 7 3081 3330 694421713 694421458 2.210000e-79 307.0
8 TraesCS2B01G498000 chr2B 88.550 262 13 8 3847 4102 694422478 694422228 1.030000e-77 302.0
9 TraesCS2B01G498000 chr2B 88.506 261 14 8 3081 3330 694442492 694442237 1.030000e-77 302.0
10 TraesCS2B01G498000 chr2B 88.506 261 14 8 3847 4102 694443258 694443009 1.030000e-77 302.0
11 TraesCS2B01G498000 chr2B 88.123 261 15 8 3081 3330 694473769 694473514 4.790000e-76 296.0
12 TraesCS2B01G498000 chr2B 87.405 262 16 9 3847 4102 694474524 694474274 1.040000e-72 285.0
13 TraesCS2B01G498000 chr2B 93.793 145 8 1 139 283 761962482 761962339 3.840000e-52 217.0
14 TraesCS2B01G498000 chr2B 93.525 139 9 0 1 139 694477218 694477080 2.310000e-49 207.0
15 TraesCS2B01G498000 chr2B 83.851 161 23 3 402 560 29705901 29705742 3.950000e-32 150.0
16 TraesCS2B01G498000 chr2B 95.918 49 2 0 557 605 694477087 694477039 5.250000e-11 80.5
17 TraesCS2B01G498000 chr2D 91.444 3144 194 27 604 3713 577346203 577343101 0.000000e+00 4246.0
18 TraesCS2B01G498000 chr2D 95.826 2180 79 9 3731 5903 577343121 577340947 0.000000e+00 3511.0
19 TraesCS2B01G498000 chr2D 80.642 1059 155 34 1202 2234 551704573 551703539 0.000000e+00 774.0
20 TraesCS2B01G498000 chr2D 94.062 421 22 3 5904 6323 577340900 577340482 2.490000e-178 636.0
21 TraesCS2B01G498000 chr2D 80.242 496 80 9 2305 2785 551821810 551821318 2.170000e-94 357.0
22 TraesCS2B01G498000 chr2D 78.418 607 71 32 752 1315 551705145 551704556 2.180000e-89 340.0
23 TraesCS2B01G498000 chr2D 86.709 316 31 6 4130 4437 577343488 577343176 2.180000e-89 340.0
24 TraesCS2B01G498000 chr2D 87.259 259 24 4 3847 4102 577343738 577343486 2.880000e-73 287.0
25 TraesCS2B01G498000 chr2D 87.259 259 22 5 3081 3330 577343005 577342749 1.040000e-72 285.0
26 TraesCS2B01G498000 chr2D 92.453 53 4 0 557 609 577346278 577346226 6.800000e-10 76.8
27 TraesCS2B01G498000 chr2A 94.237 2169 92 16 3755 5903 715423406 715421251 0.000000e+00 3282.0
28 TraesCS2B01G498000 chr2A 92.521 1658 91 12 2069 3693 715425063 715423406 0.000000e+00 2344.0
29 TraesCS2B01G498000 chr2A 91.256 1441 109 11 604 2041 715426674 715425248 0.000000e+00 1947.0
30 TraesCS2B01G498000 chr2A 94.299 421 21 3 5904 6323 715421204 715420786 5.340000e-180 641.0
31 TraesCS2B01G498000 chr2A 85.759 316 34 6 4130 4437 715423773 715423461 2.200000e-84 324.0
32 TraesCS2B01G498000 chr2A 86.486 259 26 4 3847 4102 715424023 715423771 6.240000e-70 276.0
33 TraesCS2B01G498000 chr2A 86.100 259 23 7 3081 3330 715423315 715423061 3.760000e-67 267.0
34 TraesCS2B01G498000 chr2A 88.679 53 6 0 557 609 715426749 715426697 1.470000e-06 65.8
35 TraesCS2B01G498000 chr5D 87.611 565 63 5 4713 5276 464114963 464115521 0.000000e+00 649.0
36 TraesCS2B01G498000 chr5D 83.221 596 81 15 4712 5299 464108647 464109231 4.340000e-146 529.0
37 TraesCS2B01G498000 chr5D 80.127 629 79 34 717 1315 464110518 464111130 1.630000e-115 427.0
38 TraesCS2B01G498000 chr5D 83.043 460 74 2 2326 2784 464106921 464107377 1.270000e-111 414.0
39 TraesCS2B01G498000 chr5D 85.122 410 51 6 1382 1784 464111283 464111689 1.640000e-110 411.0
40 TraesCS2B01G498000 chr5D 83.407 452 60 9 2341 2784 474821386 474820942 7.630000e-109 405.0
41 TraesCS2B01G498000 chr5D 87.500 216 22 5 5273 5486 464116982 464117194 1.760000e-60 244.0
42 TraesCS2B01G498000 chr5D 79.934 304 39 12 5328 5630 464117194 464117476 2.990000e-48 204.0
43 TraesCS2B01G498000 chr5B 80.485 866 141 21 4430 5276 57719020 57718164 6.910000e-179 638.0
44 TraesCS2B01G498000 chr5B 82.264 592 79 16 4724 5299 571204229 571204810 7.370000e-134 488.0
45 TraesCS2B01G498000 chr5B 83.299 491 68 6 2305 2784 571202484 571202971 2.090000e-119 440.0
46 TraesCS2B01G498000 chr5B 87.500 216 23 4 5273 5486 57716684 57716471 4.900000e-61 246.0
47 TraesCS2B01G498000 chr5B 86.256 211 22 6 5328 5537 57716471 57716267 8.250000e-54 222.0
48 TraesCS2B01G498000 chr5A 86.195 565 71 5 4713 5276 43656383 43655825 7.010000e-169 604.0
49 TraesCS2B01G498000 chr5A 86.018 565 72 5 4713 5276 43742283 43741725 3.260000e-167 599.0
50 TraesCS2B01G498000 chr5A 85.841 565 73 5 4713 5276 43694752 43694194 1.520000e-165 593.0
51 TraesCS2B01G498000 chr5A 85.122 410 51 6 1382 1784 43699832 43699426 1.640000e-110 411.0
52 TraesCS2B01G498000 chr5A 84.634 410 53 6 1382 1784 43745975 43745569 3.550000e-107 399.0
53 TraesCS2B01G498000 chr5A 84.390 410 54 6 1382 1784 43659919 43659513 1.650000e-105 394.0
54 TraesCS2B01G498000 chr5A 80.583 515 83 12 1282 1784 584554224 584554733 1.290000e-101 381.0
55 TraesCS2B01G498000 chr5A 88.732 213 21 3 5273 5484 43612676 43612466 2.260000e-64 257.0
56 TraesCS2B01G498000 chr5A 86.256 211 24 5 5328 5537 43612464 43612258 2.290000e-54 224.0
57 TraesCS2B01G498000 chr7D 82.137 571 80 16 4724 5282 570988474 570989034 2.670000e-128 470.0
58 TraesCS2B01G498000 chr7D 89.600 125 11 2 431 553 541971204 541971328 2.360000e-34 158.0
59 TraesCS2B01G498000 chr7B 83.576 481 63 9 2305 2772 626565899 626565422 2.710000e-118 436.0
60 TraesCS2B01G498000 chr7B 93.865 163 9 1 132 293 109894104 109894266 1.760000e-60 244.0
61 TraesCS2B01G498000 chr7B 90.323 155 14 1 140 293 684441413 684441567 1.070000e-47 202.0
62 TraesCS2B01G498000 chr7B 91.724 145 11 1 139 283 22774451 22774594 3.870000e-47 200.0
63 TraesCS2B01G498000 chr7B 85.629 167 21 3 402 567 64004445 64004281 8.430000e-39 172.0
64 TraesCS2B01G498000 chr7B 79.167 240 45 5 316 553 22792524 22792760 1.820000e-35 161.0
65 TraesCS2B01G498000 chr7B 80.093 216 40 3 339 553 22839269 22839482 2.360000e-34 158.0
66 TraesCS2B01G498000 chr7B 84.314 153 21 3 402 553 22716657 22716807 5.110000e-31 147.0
67 TraesCS2B01G498000 chr4A 83.491 424 52 11 139 553 681609789 681609375 4.630000e-101 379.0
68 TraesCS2B01G498000 chr3D 88.550 262 28 2 294 553 592600596 592600857 3.680000e-82 316.0
69 TraesCS2B01G498000 chr3D 91.613 155 12 1 140 293 592600308 592600462 4.970000e-51 213.0
70 TraesCS2B01G498000 chr7A 95.513 156 5 2 139 293 694372306 694372460 1.360000e-61 248.0
71 TraesCS2B01G498000 chr7A 87.425 167 18 2 4545 4708 660082361 660082527 8.370000e-44 189.0
72 TraesCS2B01G498000 chr6A 95.172 145 6 1 139 283 12634305 12634162 1.770000e-55 228.0
73 TraesCS2B01G498000 chr1D 84.472 161 19 5 404 560 486402902 486403060 3.050000e-33 154.0


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 TraesCS2B01G498000 chr2B 694440016 694446338 6322 True 11677.000000 11677 100.000000 1 6323 1 chr2B.!!$R2 6322
1 TraesCS2B01G498000 chr2B 694419177 694425561 6384 True 5496.000000 10323 96.946000 1 6323 2 chr2B.!!$R4 6322
2 TraesCS2B01G498000 chr2B 694471241 694477218 5977 True 1328.812500 4865 94.246875 1 6323 8 chr2B.!!$R7 6322
3 TraesCS2B01G498000 chr2B 694421458 694422478 1020 True 304.500000 307 88.719500 3081 4102 2 chr2B.!!$R5 1021
4 TraesCS2B01G498000 chr2B 694442237 694443258 1021 True 302.000000 302 88.506000 3081 4102 2 chr2B.!!$R6 1021
5 TraesCS2B01G498000 chr2D 577340482 577346278 5796 True 1340.257143 4246 90.716000 557 6323 7 chr2D.!!$R3 5766
6 TraesCS2B01G498000 chr2D 551703539 551705145 1606 True 557.000000 774 79.530000 752 2234 2 chr2D.!!$R2 1482
7 TraesCS2B01G498000 chr2A 715420786 715426749 5963 True 1143.350000 3282 89.917125 557 6323 8 chr2A.!!$R1 5766
8 TraesCS2B01G498000 chr5D 464106921 464117476 10555 False 411.142857 649 83.794000 717 5630 7 chr5D.!!$F1 4913
9 TraesCS2B01G498000 chr5B 571202484 571204810 2326 False 464.000000 488 82.781500 2305 5299 2 chr5B.!!$F1 2994
10 TraesCS2B01G498000 chr5B 57716267 57719020 2753 True 368.666667 638 84.747000 4430 5537 3 chr5B.!!$R1 1107
11 TraesCS2B01G498000 chr5A 43694194 43694752 558 True 593.000000 593 85.841000 4713 5276 1 chr5A.!!$R1 563
12 TraesCS2B01G498000 chr5A 43655825 43659919 4094 True 499.000000 604 85.292500 1382 5276 2 chr5A.!!$R4 3894
13 TraesCS2B01G498000 chr5A 43741725 43745975 4250 True 499.000000 599 85.326000 1382 5276 2 chr5A.!!$R5 3894
14 TraesCS2B01G498000 chr5A 584554224 584554733 509 False 381.000000 381 80.583000 1282 1784 1 chr5A.!!$F1 502
15 TraesCS2B01G498000 chr7D 570988474 570989034 560 False 470.000000 470 82.137000 4724 5282 1 chr7D.!!$F2 558
16 TraesCS2B01G498000 chr3D 592600308 592600857 549 False 264.500000 316 90.081500 140 553 2 chr3D.!!$F1 413

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
564 701 1.602323 CAAAACCCGGGTAGCAGCA 60.602 57.895 30.52 0.0 0.00 4.41 F
1321 4339 1.470051 AGAGGAGGAGAAGTCGAAGC 58.530 55.000 0.00 0.0 0.00 3.86 F
1965 4996 5.776716 AGAATTGATCACTTTTGATGGGTGT 59.223 36.000 0.00 0.0 42.95 4.16 F
2821 6077 2.893637 ACATGAGTGTCGATGCTAACC 58.106 47.619 0.00 0.0 31.41 2.85 F
4104 9129 1.289160 AAGGCCTCAAGCTCCATGTA 58.711 50.000 5.23 0.0 43.05 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 4666 2.502130 TGTTGCGGATATGTTACCTCCA 59.498 45.455 0.00 0.00 0.00 3.86 R
2821 6077 1.669115 CCTCTTGTGGACCAGTGCG 60.669 63.158 0.00 0.00 0.00 5.34 R
4104 9129 1.333636 CCCTCAGACTCCGAATGGCT 61.334 60.000 0.00 0.00 34.14 4.75 R
4534 9575 3.086818 TGAACTATATGCGCGCAAGTA 57.913 42.857 39.68 29.16 41.68 2.24 R
5988 12810 1.143329 TGATAAGGTTGGCACCCCCA 61.143 55.000 0.00 0.00 45.63 4.96 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
135 136 4.975856 AGCCGAAAAGATCAGCTTAGTAGC 60.976 45.833 0.00 0.0 38.70 3.58
438 574 1.734477 CCAGACTGTCGCCGTTGAG 60.734 63.158 1.52 0.0 0.00 3.02
554 691 2.360225 CCCGGTACCCAAAACCCG 60.360 66.667 6.25 0.0 40.12 5.28
564 701 1.602323 CAAAACCCGGGTAGCAGCA 60.602 57.895 30.52 0.0 0.00 4.41
657 831 2.536066 GGCCACCCTGTATTTCCTTTT 58.464 47.619 0.00 0.0 0.00 2.27
727 901 8.490311 TGGGATACATTTTGTTCTTTTTCCTTT 58.510 29.630 0.00 0.0 39.74 3.11
799 3680 4.608948 ACAAAGAAGTCTGTAGGAGTGG 57.391 45.455 0.00 0.0 0.00 4.00
1171 4087 4.775253 AGATGGCTAAGTATAAGGAGGAGC 59.225 45.833 0.00 0.0 0.00 4.70
1321 4339 1.470051 AGAGGAGGAGAAGTCGAAGC 58.530 55.000 0.00 0.0 0.00 3.86
1642 4666 9.374711 TGGTCTTACTTTGGAAAGGAATAAAAT 57.625 29.630 4.23 0.0 38.14 1.82
1643 4667 9.639601 GGTCTTACTTTGGAAAGGAATAAAATG 57.360 33.333 4.23 0.0 38.14 2.32
1965 4996 5.776716 AGAATTGATCACTTTTGATGGGTGT 59.223 36.000 0.00 0.0 42.95 4.16
2821 6077 2.893637 ACATGAGTGTCGATGCTAACC 58.106 47.619 0.00 0.0 31.41 2.85
4104 9129 1.289160 AAGGCCTCAAGCTCCATGTA 58.711 50.000 5.23 0.0 43.05 2.29
4721 9813 5.128827 TCTTCCTTCCTACGCTGATTACAAT 59.871 40.000 0.00 0.0 0.00 2.71
4968 10065 6.283694 TCAAATTCTTCTCTGGATGGATACG 58.716 40.000 0.00 0.0 42.51 3.06
5471 12220 2.293122 TCATTGCTTTTCTTGACGTGGG 59.707 45.455 0.00 0.0 0.00 4.61
5637 12399 3.117888 AGTTCGGGATGCCACATATCTTT 60.118 43.478 3.39 0.0 0.00 2.52
5641 12403 5.441500 TCGGGATGCCACATATCTTTAAAA 58.558 37.500 3.39 0.0 0.00 1.52
5642 12404 5.888724 TCGGGATGCCACATATCTTTAAAAA 59.111 36.000 3.39 0.0 0.00 1.94
5988 12810 1.811359 CGGACCTCGAGTTTGACTACT 59.189 52.381 12.31 0.0 42.43 2.57
6251 13074 0.548031 AATGCATGTCCATCCCGAGT 59.452 50.000 0.00 0.0 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
554 691 2.555199 CACTACTTCATGCTGCTACCC 58.445 52.381 0.00 0.00 0.00 3.69
657 831 0.179020 ACAAGCAGTGGCACAGCTAA 60.179 50.000 33.28 0.00 38.97 3.09
1171 4087 3.447586 TCATTACCCCTCGTTCTCTCTTG 59.552 47.826 0.00 0.00 0.00 3.02
1357 4375 1.621317 TGAACTGGTTATGAGCGACCA 59.379 47.619 0.00 0.00 43.37 4.02
1642 4666 2.502130 TGTTGCGGATATGTTACCTCCA 59.498 45.455 0.00 0.00 0.00 3.86
1643 4667 3.188159 TGTTGCGGATATGTTACCTCC 57.812 47.619 0.00 0.00 0.00 4.30
1965 4996 4.223700 ACAACAGATTAGTGATGAGCCTGA 59.776 41.667 0.00 0.00 0.00 3.86
2821 6077 1.669115 CCTCTTGTGGACCAGTGCG 60.669 63.158 0.00 0.00 0.00 5.34
4104 9129 1.333636 CCCTCAGACTCCGAATGGCT 61.334 60.000 0.00 0.00 34.14 4.75
4534 9575 3.086818 TGAACTATATGCGCGCAAGTA 57.913 42.857 39.68 29.16 41.68 2.24
4968 10065 6.197842 GTGAGCAATGCAGTTTTAGAATATGC 59.802 38.462 8.35 0.00 37.40 3.14
5618 12380 4.698201 TTAAAGATATGTGGCATCCCGA 57.302 40.909 0.00 0.00 0.00 5.14
5641 12403 3.386402 TGACGGCTTTCCTCCAAATTTTT 59.614 39.130 0.00 0.00 0.00 1.94
5642 12404 2.962421 TGACGGCTTTCCTCCAAATTTT 59.038 40.909 0.00 0.00 0.00 1.82
5643 12405 2.593026 TGACGGCTTTCCTCCAAATTT 58.407 42.857 0.00 0.00 0.00 1.82
5644 12406 2.286365 TGACGGCTTTCCTCCAAATT 57.714 45.000 0.00 0.00 0.00 1.82
5645 12407 2.094675 CATGACGGCTTTCCTCCAAAT 58.905 47.619 0.00 0.00 0.00 2.32
5751 12520 3.244981 TGGCAAAGTTTACCGAGGGTAAT 60.245 43.478 7.99 0.00 45.95 1.89
5988 12810 1.143329 TGATAAGGTTGGCACCCCCA 61.143 55.000 0.00 0.00 45.63 4.96
6107 12930 4.283212 TCCCCTCCAAAATGCTAAACTTTG 59.717 41.667 0.00 0.00 0.00 2.77
6251 13074 1.863662 GCCTTCGACGAGGACACTGA 61.864 60.000 8.76 0.00 39.25 3.41


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

AutoCloner maintained by Alex Coulton.