Multiple sequence alignment - TraesCS2D01G268000

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 TraesCS2D01G268000 chr2D 100.000 9682 0 0 1 9682 327966815 327957134 0.000000e+00 17880.0
1 TraesCS2D01G268000 chr2D 83.895 801 84 24 8916 9682 296388485 296387696 0.000000e+00 723.0
2 TraesCS2D01G268000 chr2D 87.688 333 18 9 8916 9225 327939624 327939292 5.530000e-97 366.0
3 TraesCS2D01G268000 chr2D 94.000 50 3 0 1881 1930 327964845 327964796 1.040000e-09 76.8
4 TraesCS2D01G268000 chr2D 94.000 50 3 0 1971 2020 327964935 327964886 1.040000e-09 76.8
5 TraesCS2D01G268000 chr2B 95.729 3793 101 22 4597 8375 397248684 397244939 0.000000e+00 6050.0
6 TraesCS2D01G268000 chr2B 97.660 1111 15 4 3304 4414 397249774 397248675 0.000000e+00 1897.0
7 TraesCS2D01G268000 chr2B 95.402 1131 24 8 848 1973 397251633 397250526 0.000000e+00 1775.0
8 TraesCS2D01G268000 chr2B 97.622 757 18 0 2519 3275 397250527 397249771 0.000000e+00 1299.0
9 TraesCS2D01G268000 chr2B 83.503 788 93 20 8916 9679 365990952 365991726 0.000000e+00 701.0
10 TraesCS2D01G268000 chr2B 80.538 781 96 21 8916 9682 137796274 137795536 5.110000e-152 549.0
11 TraesCS2D01G268000 chr2B 96.063 254 10 0 8441 8694 397244940 397244687 1.950000e-111 414.0
12 TraesCS2D01G268000 chr2B 91.057 246 21 1 1 246 397268627 397268383 2.020000e-86 331.0
13 TraesCS2D01G268000 chr2B 97.382 191 5 0 4411 4601 314778884 314779074 9.380000e-85 326.0
14 TraesCS2D01G268000 chr2B 89.552 134 2 1 8782 8915 397244688 397244567 1.010000e-34 159.0
15 TraesCS2D01G268000 chr2B 92.593 108 6 2 758 864 397251889 397251783 4.680000e-33 154.0
16 TraesCS2D01G268000 chr2B 96.000 50 2 0 1971 2020 397250618 397250569 2.240000e-11 82.4
17 TraesCS2D01G268000 chr2A 96.824 2613 66 9 4597 7199 433626628 433624023 0.000000e+00 4349.0
18 TraesCS2D01G268000 chr2A 97.521 1896 42 4 2519 4414 433628509 433626619 0.000000e+00 3236.0
19 TraesCS2D01G268000 chr2A 94.676 1465 42 13 7237 8694 433624024 433622589 0.000000e+00 2241.0
20 TraesCS2D01G268000 chr2A 94.557 1286 41 12 690 1963 433629792 433628524 0.000000e+00 1960.0
21 TraesCS2D01G268000 chr2A 94.542 513 26 2 2012 2523 101855369 101854858 0.000000e+00 791.0
22 TraesCS2D01G268000 chr2A 94.358 514 27 2 2012 2524 421218769 421219281 0.000000e+00 787.0
23 TraesCS2D01G268000 chr2A 90.040 251 19 3 1 246 433630154 433629905 4.360000e-83 320.0
24 TraesCS2D01G268000 chr2A 92.377 223 13 4 4382 4601 569281634 569281855 2.030000e-81 315.0
25 TraesCS2D01G268000 chr2A 96.350 137 5 0 8782 8918 433622590 433622454 9.780000e-55 226.0
26 TraesCS2D01G268000 chr2A 93.878 98 4 2 612 707 433629915 433629818 7.840000e-31 147.0
27 TraesCS2D01G268000 chr3D 94.882 508 25 1 2012 2518 262995159 262995666 0.000000e+00 793.0
28 TraesCS2D01G268000 chr3D 95.652 92 3 1 8691 8781 525470233 525470142 7.840000e-31 147.0
29 TraesCS2D01G268000 chr3D 86.765 68 6 3 8853 8917 410671776 410671709 1.350000e-08 73.1
30 TraesCS2D01G268000 chr3A 94.882 508 25 1 2012 2518 77936429 77935922 0.000000e+00 793.0
31 TraesCS2D01G268000 chr3A 86.248 669 57 14 1215 1879 622459199 622459836 0.000000e+00 693.0
32 TraesCS2D01G268000 chr3A 90.133 375 26 5 1215 1587 691208880 691209245 2.450000e-130 477.0
33 TraesCS2D01G268000 chr3A 89.231 130 13 1 1751 1879 691209351 691209480 2.800000e-35 161.0
34 TraesCS2D01G268000 chr7A 94.695 509 26 1 2012 2519 319591483 319591991 0.000000e+00 789.0
35 TraesCS2D01G268000 chr7A 87.168 678 58 12 8916 9579 374548990 374548328 0.000000e+00 743.0
36 TraesCS2D01G268000 chr7A 87.411 564 40 11 8916 9448 492252277 492251714 3.840000e-173 619.0
37 TraesCS2D01G268000 chr7A 87.952 332 17 7 8916 9224 492247143 492246812 4.270000e-98 370.0
38 TraesCS2D01G268000 chr7A 88.983 118 9 2 9566 9682 492251640 492251526 1.010000e-29 143.0
39 TraesCS2D01G268000 chr7A 90.000 80 4 2 9566 9644 374548321 374548245 6.190000e-17 100.0
40 TraesCS2D01G268000 chr4D 94.695 509 26 1 2012 2519 351574469 351573961 0.000000e+00 789.0
41 TraesCS2D01G268000 chr4D 94.521 511 27 1 2012 2521 47532654 47533164 0.000000e+00 787.0
42 TraesCS2D01G268000 chr4D 82.244 811 61 28 8915 9682 105249512 105250282 2.970000e-174 623.0
43 TraesCS2D01G268000 chr4D 87.842 329 20 6 8916 9224 105254996 105255324 1.540000e-97 368.0
44 TraesCS2D01G268000 chr4D 85.311 177 26 0 9386 9562 271212014 271212190 5.970000e-42 183.0
45 TraesCS2D01G268000 chr4D 89.076 119 13 0 9385 9503 274462775 274462893 2.180000e-31 148.0
46 TraesCS2D01G268000 chr4D 95.604 91 3 1 8692 8781 12354795 12354705 2.820000e-30 145.0
47 TraesCS2D01G268000 chr4D 89.899 99 9 1 8684 8781 93339462 93339364 1.020000e-24 126.0
48 TraesCS2D01G268000 chr1D 94.695 509 26 1 2012 2519 223524062 223524570 0.000000e+00 789.0
49 TraesCS2D01G268000 chr1D 83.598 189 28 2 9385 9573 55620445 55620630 3.590000e-39 174.0
50 TraesCS2D01G268000 chr1D 97.778 90 1 1 8693 8781 220408740 220408829 4.680000e-33 154.0
51 TraesCS2D01G268000 chr1D 85.333 150 19 2 9385 9534 98829970 98829824 1.680000e-32 152.0
52 TraesCS2D01G268000 chr1D 93.407 91 5 1 8693 8782 272547650 272547560 6.100000e-27 134.0
53 TraesCS2D01G268000 chr1D 93.333 90 5 1 8693 8781 209519400 209519489 2.190000e-26 132.0
54 TraesCS2D01G268000 chr1D 82.667 150 23 2 9385 9534 98832234 98832088 7.890000e-26 130.0
55 TraesCS2D01G268000 chr1D 83.824 136 21 1 9385 9520 258348215 258348349 2.840000e-25 128.0
56 TraesCS2D01G268000 chr1D 95.122 82 3 1 8693 8773 453108477 453108558 2.840000e-25 128.0
57 TraesCS2D01G268000 chr1D 89.796 98 8 2 8685 8781 415425045 415424949 3.670000e-24 124.0
58 TraesCS2D01G268000 chr1D 84.874 119 18 0 9385 9503 199329187 199329305 4.750000e-23 121.0
59 TraesCS2D01G268000 chr1D 90.909 88 7 1 8693 8779 211693640 211693727 6.140000e-22 117.0
60 TraesCS2D01G268000 chr1D 90.110 91 8 1 8692 8781 490104161 490104071 6.140000e-22 117.0
61 TraesCS2D01G268000 chr4A 92.593 540 34 6 2012 2546 183141604 183141066 0.000000e+00 771.0
62 TraesCS2D01G268000 chr3B 83.436 809 94 20 8913 9682 338597113 338597920 0.000000e+00 715.0
63 TraesCS2D01G268000 chr3B 81.715 793 95 28 8916 9682 705033970 705034738 4.970000e-172 616.0
64 TraesCS2D01G268000 chr3B 94.634 205 6 5 4389 4593 695591812 695592011 7.300000e-81 313.0
65 TraesCS2D01G268000 chr3B 84.615 286 21 9 8916 9178 67396960 67396675 7.460000e-66 263.0
66 TraesCS2D01G268000 chr3B 95.604 91 3 1 8693 8782 337214583 337214673 2.820000e-30 145.0
67 TraesCS2D01G268000 chr3B 82.051 117 15 5 242 355 15999988 16000101 2.880000e-15 95.3
68 TraesCS2D01G268000 chr3B 91.935 62 5 0 1215 1276 30994999 30995060 4.820000e-13 87.9
69 TraesCS2D01G268000 chr3B 91.935 62 5 0 1215 1276 729710404 729710343 4.820000e-13 87.9
70 TraesCS2D01G268000 chr3B 91.935 62 5 0 1215 1276 773212106 773212167 4.820000e-13 87.9
71 TraesCS2D01G268000 chr6A 83.602 805 84 23 8916 9678 617255324 617256122 0.000000e+00 712.0
72 TraesCS2D01G268000 chr6A 76.757 555 97 23 8961 9503 430583535 430584069 2.060000e-71 281.0
73 TraesCS2D01G268000 chr6A 94.444 90 4 1 8693 8781 155803851 155803762 4.720000e-28 137.0
74 TraesCS2D01G268000 chr5A 80.541 776 106 34 8916 9676 348716578 348715833 1.100000e-153 555.0
75 TraesCS2D01G268000 chr5A 85.259 251 33 4 9324 9573 73953851 73954098 1.250000e-63 255.0
76 TraesCS2D01G268000 chr5A 89.759 166 14 3 8916 9078 525942656 525942491 9.850000e-50 209.0
77 TraesCS2D01G268000 chr4B 82.791 645 80 17 8916 9535 322644529 322643891 1.840000e-151 547.0
78 TraesCS2D01G268000 chr4B 81.803 610 89 11 8980 9570 201588631 201589237 8.740000e-135 492.0
79 TraesCS2D01G268000 chr4B 90.000 250 25 0 245 494 590136399 590136150 3.370000e-84 324.0
80 TraesCS2D01G268000 chr4B 83.030 330 35 8 8916 9224 201643330 201643659 7.400000e-71 279.0
81 TraesCS2D01G268000 chr4B 81.935 310 32 17 8938 9225 322639348 322639041 3.490000e-59 241.0
82 TraesCS2D01G268000 chr4B 79.819 332 42 17 8916 9225 322526061 322525733 1.640000e-52 219.0
83 TraesCS2D01G268000 chr4B 79.310 319 35 18 8916 9207 61321507 61321821 2.760000e-45 195.0
84 TraesCS2D01G268000 chr4B 92.143 140 8 3 486 622 590135012 590134873 2.760000e-45 195.0
85 TraesCS2D01G268000 chr4B 78.931 318 35 19 8916 9206 62047327 62047639 4.620000e-43 187.0
86 TraesCS2D01G268000 chr4B 84.118 170 25 2 9404 9572 322533889 322533721 7.780000e-36 163.0
87 TraesCS2D01G268000 chr4B 95.604 91 3 1 8693 8782 664908604 664908694 2.820000e-30 145.0
88 TraesCS2D01G268000 chr4B 93.617 94 5 1 8689 8781 260038596 260038689 1.310000e-28 139.0
89 TraesCS2D01G268000 chr4B 95.455 88 3 1 8691 8777 627255006 627254919 1.310000e-28 139.0
90 TraesCS2D01G268000 chr4B 87.356 87 10 1 241 327 388718006 388718091 2.230000e-16 99.0
91 TraesCS2D01G268000 chr4B 91.935 62 5 0 1215 1276 592358962 592359023 4.820000e-13 87.9
92 TraesCS2D01G268000 chr4B 91.935 62 4 1 1215 1276 106637352 106637292 1.730000e-12 86.1
93 TraesCS2D01G268000 chr5D 81.481 675 84 22 8913 9579 193513385 193514026 5.180000e-142 516.0
94 TraesCS2D01G268000 chr5D 82.752 545 67 17 9049 9570 213521794 213522334 2.460000e-125 460.0
95 TraesCS2D01G268000 chr5D 86.018 329 23 8 8916 9224 193518805 193519130 2.020000e-86 331.0
96 TraesCS2D01G268000 chr5D 95.652 92 3 1 8691 8781 565059363 565059454 7.840000e-31 147.0
97 TraesCS2D01G268000 chr5D 91.262 103 4 5 8679 8779 211215117 211215018 1.700000e-27 135.0
98 TraesCS2D01G268000 chr5D 89.583 48 4 1 9566 9612 213530893 213530940 1.050000e-04 60.2
99 TraesCS2D01G268000 chr7D 87.688 333 20 7 8975 9298 330820152 330820472 1.540000e-97 368.0
100 TraesCS2D01G268000 chr7D 88.365 318 21 6 8916 9224 330828929 330829239 1.540000e-97 368.0
101 TraesCS2D01G268000 chr7D 87.455 279 23 8 349 620 435509081 435508808 2.630000e-80 311.0
102 TraesCS2D01G268000 chr7D 100.000 28 0 0 242 269 517150325 517150298 1.800000e-02 52.8
103 TraesCS2D01G268000 chr6B 83.416 404 46 8 8916 9298 197694852 197694449 1.200000e-93 355.0
104 TraesCS2D01G268000 chr6B 82.231 242 23 13 9003 9224 197659191 197658950 3.570000e-44 191.0
105 TraesCS2D01G268000 chr6B 78.738 301 52 11 9385 9682 439355812 439355521 3.570000e-44 191.0
106 TraesCS2D01G268000 chr6B 88.710 62 5 2 1215 1276 272818074 272818015 3.750000e-09 75.0
107 TraesCS2D01G268000 chr1A 97.917 192 4 0 4407 4598 82525880 82526071 5.600000e-87 333.0
108 TraesCS2D01G268000 chr1A 82.011 189 31 2 9385 9573 256720539 256720354 3.620000e-34 158.0
109 TraesCS2D01G268000 chr1A 82.486 177 28 2 9385 9561 99900986 99901159 1.680000e-32 152.0
110 TraesCS2D01G268000 chr1A 84.768 151 16 5 9386 9534 292765803 292765948 2.820000e-30 145.0
111 TraesCS2D01G268000 chr1A 95.556 90 3 1 8693 8781 284145608 284145697 1.010000e-29 143.0
112 TraesCS2D01G268000 chr1A 90.323 62 6 0 1215 1276 26547818 26547757 2.240000e-11 82.4
113 TraesCS2D01G268000 chrUn 97.382 191 5 0 4411 4601 277314230 277314040 9.380000e-85 326.0
114 TraesCS2D01G268000 chrUn 77.108 415 60 24 8912 9298 243699040 243698633 3.540000e-49 207.0
115 TraesCS2D01G268000 chrUn 77.108 415 60 24 8912 9298 256323815 256324222 3.540000e-49 207.0
116 TraesCS2D01G268000 chrUn 77.519 387 52 23 8916 9274 287139178 287138799 5.930000e-47 200.0
117 TraesCS2D01G268000 chrUn 77.519 387 52 23 8916 9274 287145347 287144968 5.930000e-47 200.0
118 TraesCS2D01G268000 chrUn 77.519 387 52 23 8916 9274 466024150 466024529 5.930000e-47 200.0
119 TraesCS2D01G268000 chrUn 92.391 92 6 1 8691 8781 362465901 362465810 7.890000e-26 130.0
120 TraesCS2D01G268000 chrUn 92.308 91 6 1 8692 8781 21636771 21636681 2.840000e-25 128.0
121 TraesCS2D01G268000 chrUn 91.111 90 7 1 8693 8781 477580649 477580560 4.750000e-23 121.0
122 TraesCS2D01G268000 chrUn 93.243 74 3 2 8708 8781 50416586 50416657 3.700000e-19 108.0
123 TraesCS2D01G268000 chrUn 82.051 117 15 5 242 355 324785451 324785338 2.880000e-15 95.3
124 TraesCS2D01G268000 chrUn 82.051 117 15 5 242 355 325038642 325038529 2.880000e-15 95.3
125 TraesCS2D01G268000 chrUn 100.000 42 0 0 8740 8781 48471429 48471388 2.900000e-10 78.7
126 TraesCS2D01G268000 chrUn 100.000 42 0 0 8740 8781 48498207 48498166 2.900000e-10 78.7
127 TraesCS2D01G268000 chrUn 100.000 42 0 0 8740 8781 235113530 235113489 2.900000e-10 78.7
128 TraesCS2D01G268000 chrUn 100.000 42 0 0 8740 8781 237211132 237211173 2.900000e-10 78.7
129 TraesCS2D01G268000 chrUn 100.000 42 0 0 8740 8781 346824008 346824049 2.900000e-10 78.7
130 TraesCS2D01G268000 chrUn 86.364 66 6 1 8728 8790 41400600 41400535 1.740000e-07 69.4
131 TraesCS2D01G268000 chr7B 97.396 192 4 1 4407 4597 690699402 690699593 9.380000e-85 326.0
132 TraesCS2D01G268000 chr7B 96.907 194 5 1 4402 4595 699827890 699828082 3.370000e-84 324.0
133 TraesCS2D01G268000 chr7B 95.506 89 3 1 8693 8780 92810615 92810527 3.650000e-29 141.0
134 TraesCS2D01G268000 chr7B 94.565 92 4 1 8691 8781 508189383 508189474 3.650000e-29 141.0
135 TraesCS2D01G268000 chr1B 96.447 197 6 1 4401 4597 225811781 225811976 3.370000e-84 324.0
136 TraesCS2D01G268000 chr1B 96.447 197 5 2 4408 4602 476332672 476332868 3.370000e-84 324.0
137 TraesCS2D01G268000 chr1B 95.604 91 3 1 8693 8782 403400254 403400344 2.820000e-30 145.0
138 TraesCS2D01G268000 chr1B 95.556 90 3 1 8693 8781 325975525 325975614 1.010000e-29 143.0
139 TraesCS2D01G268000 chr1B 93.103 58 4 0 1215 1272 647647703 647647760 1.730000e-12 86.1
140 TraesCS2D01G268000 chr6D 95.556 90 3 1 8693 8781 292393182 292393271 1.010000e-29 143.0
141 TraesCS2D01G268000 chr6D 95.556 90 3 1 8693 8781 361526381 361526292 1.010000e-29 143.0
142 TraesCS2D01G268000 chr6D 92.553 94 5 2 8689 8781 200398711 200398803 6.100000e-27 134.0
143 TraesCS2D01G268000 chr6D 93.333 90 5 1 8693 8781 141924995 141924906 2.190000e-26 132.0
144 TraesCS2D01G268000 chr6D 93.333 90 5 1 8693 8781 291383353 291383442 2.190000e-26 132.0
145 TraesCS2D01G268000 chr6D 93.333 90 4 2 8693 8781 457543832 457543744 2.190000e-26 132.0
146 TraesCS2D01G268000 chr5B 91.935 62 5 0 1215 1276 711381300 711381361 4.820000e-13 87.9
147 TraesCS2D01G268000 chr5B 90.323 62 6 0 1215 1276 596644151 596644090 2.240000e-11 82.4
148 TraesCS2D01G268000 chr5B 90.323 62 5 1 8852 8912 319909190 319909251 8.060000e-11 80.5


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 TraesCS2D01G268000 chr2D 327957134 327966815 9681 True 6011.200000 17880 96.000000 1 9682 3 chr2D.!!$R3 9681
1 TraesCS2D01G268000 chr2D 296387696 296388485 789 True 723.000000 723 83.895000 8916 9682 1 chr2D.!!$R1 766
2 TraesCS2D01G268000 chr2B 397244567 397251889 7322 True 1478.800000 6050 95.077625 758 8915 8 chr2B.!!$R3 8157
3 TraesCS2D01G268000 chr2B 365990952 365991726 774 False 701.000000 701 83.503000 8916 9679 1 chr2B.!!$F2 763
4 TraesCS2D01G268000 chr2B 137795536 137796274 738 True 549.000000 549 80.538000 8916 9682 1 chr2B.!!$R1 766
5 TraesCS2D01G268000 chr2A 433622454 433630154 7700 True 1782.714286 4349 94.835143 1 8918 7 chr2A.!!$R2 8917
6 TraesCS2D01G268000 chr2A 101854858 101855369 511 True 791.000000 791 94.542000 2012 2523 1 chr2A.!!$R1 511
7 TraesCS2D01G268000 chr2A 421218769 421219281 512 False 787.000000 787 94.358000 2012 2524 1 chr2A.!!$F1 512
8 TraesCS2D01G268000 chr3D 262995159 262995666 507 False 793.000000 793 94.882000 2012 2518 1 chr3D.!!$F1 506
9 TraesCS2D01G268000 chr3A 77935922 77936429 507 True 793.000000 793 94.882000 2012 2518 1 chr3A.!!$R1 506
10 TraesCS2D01G268000 chr3A 622459199 622459836 637 False 693.000000 693 86.248000 1215 1879 1 chr3A.!!$F1 664
11 TraesCS2D01G268000 chr3A 691208880 691209480 600 False 319.000000 477 89.682000 1215 1879 2 chr3A.!!$F2 664
12 TraesCS2D01G268000 chr7A 319591483 319591991 508 False 789.000000 789 94.695000 2012 2519 1 chr7A.!!$F1 507
13 TraesCS2D01G268000 chr7A 374548245 374548990 745 True 421.500000 743 88.584000 8916 9644 2 chr7A.!!$R2 728
14 TraesCS2D01G268000 chr7A 492251526 492252277 751 True 381.000000 619 88.197000 8916 9682 2 chr7A.!!$R3 766
15 TraesCS2D01G268000 chr4D 351573961 351574469 508 True 789.000000 789 94.695000 2012 2519 1 chr4D.!!$R3 507
16 TraesCS2D01G268000 chr4D 47532654 47533164 510 False 787.000000 787 94.521000 2012 2521 1 chr4D.!!$F1 509
17 TraesCS2D01G268000 chr4D 105249512 105250282 770 False 623.000000 623 82.244000 8915 9682 1 chr4D.!!$F2 767
18 TraesCS2D01G268000 chr1D 223524062 223524570 508 False 789.000000 789 94.695000 2012 2519 1 chr1D.!!$F6 507
19 TraesCS2D01G268000 chr4A 183141066 183141604 538 True 771.000000 771 92.593000 2012 2546 1 chr4A.!!$R1 534
20 TraesCS2D01G268000 chr3B 338597113 338597920 807 False 715.000000 715 83.436000 8913 9682 1 chr3B.!!$F4 769
21 TraesCS2D01G268000 chr3B 705033970 705034738 768 False 616.000000 616 81.715000 8916 9682 1 chr3B.!!$F6 766
22 TraesCS2D01G268000 chr6A 617255324 617256122 798 False 712.000000 712 83.602000 8916 9678 1 chr6A.!!$F2 762
23 TraesCS2D01G268000 chr6A 430583535 430584069 534 False 281.000000 281 76.757000 8961 9503 1 chr6A.!!$F1 542
24 TraesCS2D01G268000 chr5A 348715833 348716578 745 True 555.000000 555 80.541000 8916 9676 1 chr5A.!!$R1 760
25 TraesCS2D01G268000 chr4B 322643891 322644529 638 True 547.000000 547 82.791000 8916 9535 1 chr4B.!!$R5 619
26 TraesCS2D01G268000 chr4B 201588631 201589237 606 False 492.000000 492 81.803000 8980 9570 1 chr4B.!!$F3 590
27 TraesCS2D01G268000 chr4B 590134873 590136399 1526 True 259.500000 324 91.071500 245 622 2 chr4B.!!$R7 377
28 TraesCS2D01G268000 chr5D 193513385 193514026 641 False 516.000000 516 81.481000 8913 9579 1 chr5D.!!$F1 666
29 TraesCS2D01G268000 chr5D 213521794 213522334 540 False 460.000000 460 82.752000 9049 9570 1 chr5D.!!$F3 521

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
510 516 0.108585 TTGTGTCAGAGCTTGGACCC 59.891 55.0 14.00 5.5 33.09 4.46 F
512 518 0.326264 GTGTCAGAGCTTGGACCCAT 59.674 55.0 14.00 0.0 33.09 4.00 F
2155 2409 0.526524 CACACGAGGAAGGATCGAGC 60.527 60.0 1.94 0.0 42.76 5.03 F
3278 3534 0.670854 GACTTCACCTTCAGTCGGCC 60.671 60.0 0.00 0.0 30.51 6.13 F
4421 4677 0.178861 TCTCTTTGGAAGGGGAGCCT 60.179 55.0 0.00 0.0 0.00 4.58 F
4471 4727 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.0 0.00 0.0 0.00 2.69 F
4480 4736 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.0 0.00 0.0 35.79 3.53 F
4527 4783 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.0 0.00 0.0 0.00 4.51 F
5685 6047 0.179108 GGTGTCATGCTCGGTAGACC 60.179 60.0 0.00 0.0 0.00 3.85 F
6836 7490 0.169672 CAAGAATGGTGCTTGAGCGG 59.830 55.0 0.00 0.0 44.16 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2352 0.601046 CATACGCATCTCCGCCACAT 60.601 55.000 0.00 0.00 0.00 3.21 R
2389 2643 0.762418 CCACGCACCCCTATCCATAA 59.238 55.000 0.00 0.00 0.00 1.90 R
3426 3682 1.776662 ACATAGGAAGTCCGCTGCTA 58.223 50.000 0.00 0.00 42.08 3.49 R
4441 4697 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85 R
5542 5902 1.896220 TTGGTGCTCATGTGAAGACC 58.104 50.000 0.00 2.05 0.00 3.85 R
6319 6969 2.675348 GGTTCTCCAGAAATGAGCTTCG 59.325 50.000 0.00 0.00 35.58 3.79 R
6503 7157 5.689031 GTGGTACATTCCATAACATGGCCTA 60.689 44.000 3.32 0.00 46.56 3.93 R
6742 7396 7.147391 TGGCCATTGAGTAGAATTAGGTATTGA 60.147 37.037 0.00 0.00 0.00 2.57 R
7197 7856 0.104197 GGAGGGAGGGGATGGATCTT 60.104 60.000 0.00 0.00 0.00 2.40 R
8686 9392 0.255318 GGACGGAGGGAGTACTCTGA 59.745 60.000 21.88 0.00 44.83 3.27 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)


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

AutoCloner maintained by Alex Coulton.