Multiple sequence alignment - TraesCS2A01G231700

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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 TraesCS2A01G231700 chr2A 100.000 5511 0 0 1 5511 272930988 272925478 0.000000e+00 10178.0
1 TraesCS2A01G231700 chr2A 98.655 669 9 0 4843 5511 272916872 272916204 0.000000e+00 1186.0
2 TraesCS2A01G231700 chr2A 98.655 669 9 0 4843 5511 481064599 481063931 0.000000e+00 1186.0
3 TraesCS2A01G231700 chr2A 98.358 670 10 1 4843 5511 38417443 38416774 0.000000e+00 1175.0
4 TraesCS2A01G231700 chr2A 89.080 522 43 6 569 1085 475920975 475921487 2.170000e-178 636.0
5 TraesCS2A01G231700 chr2A 84.615 91 13 1 1386 1476 192584223 192584312 7.600000e-14 89.8
6 TraesCS2A01G231700 chr3A 93.660 2508 145 9 568 3069 560177655 560175156 0.000000e+00 3738.0
7 TraesCS2A01G231700 chr3A 95.254 1791 77 5 1688 3471 267365032 267363243 0.000000e+00 2830.0
8 TraesCS2A01G231700 chr3A 95.467 353 15 1 3119 3471 560175158 560174807 3.730000e-156 562.0
9 TraesCS2A01G231700 chr3A 86.943 314 29 9 275 579 374459225 374458915 5.290000e-90 342.0
10 TraesCS2A01G231700 chr2B 92.886 2263 117 21 1236 3470 654445955 654443709 0.000000e+00 3247.0
11 TraesCS2A01G231700 chr2B 99.103 669 6 0 4843 5511 442557100 442556432 0.000000e+00 1203.0
12 TraesCS2A01G231700 chr2B 98.356 669 11 0 4843 5511 442565555 442564887 0.000000e+00 1175.0
13 TraesCS2A01G231700 chr2B 94.090 423 24 1 823 1245 654447496 654447075 4.650000e-180 641.0
14 TraesCS2A01G231700 chr2B 84.426 610 49 21 4 570 277325149 277325755 4.820000e-155 558.0
15 TraesCS2A01G231700 chr2B 88.424 311 29 2 273 576 404120731 404120421 8.720000e-98 368.0
16 TraesCS2A01G231700 chr4D 94.246 2068 104 8 614 2673 460232805 460234865 0.000000e+00 3145.0
17 TraesCS2A01G231700 chr4D 86.275 306 32 5 273 570 423374866 423374563 1.910000e-84 324.0
18 TraesCS2A01G231700 chr4D 86.230 305 30 8 275 570 218961083 218961384 2.480000e-83 320.0
19 TraesCS2A01G231700 chr4D 85.350 314 37 4 273 579 140885821 140885510 3.200000e-82 316.0
20 TraesCS2A01G231700 chr4D 91.096 146 11 1 1839 1984 369094065 369094208 4.360000e-46 196.0
21 TraesCS2A01G231700 chr4D 87.500 96 11 1 1382 1476 357306220 357306315 5.840000e-20 110.0
22 TraesCS2A01G231700 chr4D 96.923 65 2 0 3407 3471 460237360 460237424 5.840000e-20 110.0
23 TraesCS2A01G231700 chr4D 96.923 65 2 0 3407 3471 460246660 460246724 5.840000e-20 110.0
24 TraesCS2A01G231700 chr3B 92.396 1828 122 11 569 2394 276821949 276820137 0.000000e+00 2590.0
25 TraesCS2A01G231700 chr3B 94.227 1611 79 5 1867 3471 368904030 368905632 0.000000e+00 2447.0
26 TraesCS2A01G231700 chr3B 92.277 1269 83 9 566 1832 368902777 368904032 0.000000e+00 1786.0
27 TraesCS2A01G231700 chr3B 94.605 797 43 0 1595 2391 158637807 158638603 0.000000e+00 1234.0
28 TraesCS2A01G231700 chr3B 94.730 797 30 2 1595 2391 366554138 366554922 0.000000e+00 1229.0
29 TraesCS2A01G231700 chr3B 94.213 553 31 1 2919 3471 530705605 530706156 0.000000e+00 843.0
30 TraesCS2A01G231700 chr3B 85.519 511 47 4 581 1083 639282305 639281814 4.930000e-140 508.0
31 TraesCS2A01G231700 chr3B 82.222 90 16 0 1387 1476 545830960 545831049 1.650000e-10 78.7
32 TraesCS2A01G231700 chr3D 96.589 1378 46 1 3471 4847 333108437 333109814 0.000000e+00 2283.0
33 TraesCS2A01G231700 chr3D 96.517 1378 47 1 3471 4847 364354952 364356329 0.000000e+00 2278.0
34 TraesCS2A01G231700 chr3D 88.296 487 44 5 568 1049 306837900 306837422 6.190000e-159 571.0
35 TraesCS2A01G231700 chr3D 86.901 313 30 5 273 576 496724457 496724767 1.900000e-89 340.0
36 TraesCS2A01G231700 chr3D 86.495 311 34 4 273 576 424223838 424224147 8.850000e-88 335.0
37 TraesCS2A01G231700 chr3D 82.659 173 29 1 569 741 256151617 256151446 9.560000e-33 152.0
38 TraesCS2A01G231700 chr7D 96.522 1380 45 2 3471 4847 124117208 124115829 0.000000e+00 2279.0
39 TraesCS2A01G231700 chr7D 87.500 304 32 1 273 570 269384722 269384419 4.090000e-91 346.0
40 TraesCS2A01G231700 chr5D 96.517 1378 46 2 3471 4847 381682811 381681435 0.000000e+00 2278.0
41 TraesCS2A01G231700 chr5D 88.779 303 27 2 275 570 101777869 101778171 1.130000e-96 364.0
42 TraesCS2A01G231700 chr5D 87.213 305 31 3 273 570 129701830 129701527 1.900000e-89 340.0
43 TraesCS2A01G231700 chr5D 86.581 313 30 7 273 575 154519817 154519507 8.850000e-88 335.0
44 TraesCS2A01G231700 chr5D 86.262 313 32 6 273 576 268466511 268466201 4.120000e-86 329.0
45 TraesCS2A01G231700 chr5D 86.218 312 33 4 273 576 386762138 386762447 4.120000e-86 329.0
46 TraesCS2A01G231700 chr2D 96.519 1379 45 3 3471 4847 292997228 292998605 0.000000e+00 2278.0
47 TraesCS2A01G231700 chr2D 89.492 590 43 5 1 571 236017593 236017004 0.000000e+00 728.0
48 TraesCS2A01G231700 chr2D 87.859 313 31 4 274 579 247787746 247787434 1.460000e-95 361.0
49 TraesCS2A01G231700 chr2D 86.932 176 15 2 3304 3471 180527884 180527709 2.030000e-44 191.0
50 TraesCS2A01G231700 chr1D 96.517 1378 47 1 3471 4847 381133428 381134805 0.000000e+00 2278.0
51 TraesCS2A01G231700 chr1D 96.517 1378 46 2 3471 4847 427559457 427560833 0.000000e+00 2278.0
52 TraesCS2A01G231700 chr1D 96.444 1378 48 1 3471 4847 28459657 28458280 0.000000e+00 2272.0
53 TraesCS2A01G231700 chr1D 96.444 1378 48 1 3471 4847 80485487 80484110 0.000000e+00 2272.0
54 TraesCS2A01G231700 chr1D 86.084 309 32 7 275 575 212846522 212846217 6.890000e-84 322.0
55 TraesCS2A01G231700 chr1D 85.623 313 35 4 273 576 370617982 370617671 2.480000e-83 320.0
56 TraesCS2A01G231700 chr1D 85.266 319 35 4 270 576 362060927 362061245 8.910000e-83 318.0
57 TraesCS2A01G231700 chr1D 85.531 311 34 4 273 576 362075595 362075901 1.150000e-81 315.0
58 TraesCS2A01G231700 chr1D 85.809 303 34 3 275 570 434341391 434341691 4.140000e-81 313.0
59 TraesCS2A01G231700 chr1D 84.936 312 37 7 273 576 31922719 31923028 1.930000e-79 307.0
60 TraesCS2A01G231700 chr1D 85.246 305 37 4 273 570 332705490 332705793 1.930000e-79 307.0
61 TraesCS2A01G231700 chr1D 84.395 314 36 9 273 575 32194871 32194560 4.170000e-76 296.0
62 TraesCS2A01G231700 chr1D 84.395 314 36 7 273 576 340324239 340324549 4.170000e-76 296.0
63 TraesCS2A01G231700 chr1D 84.076 314 40 5 265 570 358823202 358822891 1.500000e-75 294.0
64 TraesCS2A01G231700 chr1D 78.682 258 48 7 569 822 304631438 304631184 1.230000e-36 165.0
65 TraesCS2A01G231700 chr1D 94.872 39 2 0 1118 1156 439885381 439885419 1.660000e-05 62.1
66 TraesCS2A01G231700 chr5A 95.428 1378 46 4 1688 3059 166881975 166880609 0.000000e+00 2180.0
67 TraesCS2A01G231700 chr5A 94.756 553 25 4 2919 3471 216120166 216120714 0.000000e+00 857.0
68 TraesCS2A01G231700 chr5A 88.506 522 48 4 568 1085 310426339 310425826 6.060000e-174 621.0
69 TraesCS2A01G231700 chr5A 95.879 364 14 1 3108 3471 166880605 166880243 6.150000e-164 588.0
70 TraesCS2A01G231700 chr5A 85.714 91 13 0 1386 1476 343200692 343200782 4.540000e-16 97.1
71 TraesCS2A01G231700 chr7A 98.356 669 11 0 4843 5511 499818780 499818112 0.000000e+00 1175.0
72 TraesCS2A01G231700 chr7A 98.214 672 10 2 4841 5511 107569394 107568724 0.000000e+00 1173.0
73 TraesCS2A01G231700 chr7A 97.791 679 13 2 4834 5511 270099421 270100098 0.000000e+00 1170.0
74 TraesCS2A01G231700 chr7A 87.066 317 23 12 273 576 227307171 227307482 5.290000e-90 342.0
75 TraesCS2A01G231700 chr4B 98.356 669 11 0 4843 5511 220286478 220287146 0.000000e+00 1175.0
76 TraesCS2A01G231700 chr4B 85.687 524 60 7 567 1084 279025676 279025162 6.280000e-149 538.0
77 TraesCS2A01G231700 chr4B 85.988 521 47 3 567 1079 361102495 361101993 8.130000e-148 534.0
78 TraesCS2A01G231700 chr4B 85.385 520 45 4 572 1083 403436313 403436809 1.370000e-140 510.0
79 TraesCS2A01G231700 chr4B 90.909 198 18 0 567 764 609109806 609109609 3.270000e-67 267.0
80 TraesCS2A01G231700 chr4B 87.500 160 17 3 3314 3471 645631359 645631201 1.220000e-41 182.0
81 TraesCS2A01G231700 chr4B 87.500 160 17 3 3314 3471 645710433 645710275 1.220000e-41 182.0
82 TraesCS2A01G231700 chr4B 89.706 136 7 2 1849 1984 454353510 454353638 3.410000e-37 167.0
83 TraesCS2A01G231700 chr4A 95.479 553 25 0 2919 3471 371043353 371042801 0.000000e+00 883.0
84 TraesCS2A01G231700 chr4A 89.362 517 43 4 569 1081 33797030 33796522 1.670000e-179 640.0
85 TraesCS2A01G231700 chr5B 94.909 550 27 1 2922 3471 205582554 205582006 0.000000e+00 859.0
86 TraesCS2A01G231700 chr5B 89.922 516 50 2 569 1083 71983801 71983287 0.000000e+00 664.0
87 TraesCS2A01G231700 chr5B 95.806 310 12 1 3165 3474 297124796 297124488 2.960000e-137 499.0
88 TraesCS2A01G231700 chr5B 81.574 521 73 10 566 1083 274090884 274091384 5.140000e-110 409.0
89 TraesCS2A01G231700 chr5B 95.082 244 12 0 2922 3165 297128263 297128020 8.660000e-103 385.0
90 TraesCS2A01G231700 chr5B 93.852 244 15 0 3228 3471 71969753 71969510 8.720000e-98 368.0
91 TraesCS2A01G231700 chr5B 87.500 304 32 1 273 570 110633919 110634222 4.090000e-91 346.0
92 TraesCS2A01G231700 chr5B 87.748 302 29 3 273 568 464643101 464643400 4.090000e-91 346.0
93 TraesCS2A01G231700 chr5B 100.000 32 0 0 3304 3335 37811248 37811279 5.960000e-05 60.2
94 TraesCS2A01G231700 chr1B 91.264 538 36 8 2140 2676 102631266 102630739 0.000000e+00 723.0
95 TraesCS2A01G231700 chr1B 91.215 535 38 6 2140 2673 133699267 133699793 0.000000e+00 719.0
96 TraesCS2A01G231700 chr1B 93.885 278 15 2 2140 2417 163667126 163666851 8.540000e-113 418.0
97 TraesCS2A01G231700 chr1B 81.574 521 74 15 569 1083 281031854 281032358 1.430000e-110 411.0
98 TraesCS2A01G231700 chr1B 95.492 244 11 0 3228 3471 281038692 281038935 1.860000e-104 390.0
99 TraesCS2A01G231700 chr1B 88.593 263 22 4 2415 2676 163666750 163666495 4.140000e-81 313.0
100 TraesCS2A01G231700 chr1B 87.500 176 16 5 568 741 372911174 372911345 1.210000e-46 198.0
101 TraesCS2A01G231700 chr1B 82.514 183 30 2 566 747 435078808 435078989 5.710000e-35 159.0
102 TraesCS2A01G231700 chr6B 89.237 511 48 7 570 1077 214170089 214170595 2.800000e-177 632.0
103 TraesCS2A01G231700 chr6B 85.549 519 62 7 569 1084 335174502 335173994 1.050000e-146 531.0
104 TraesCS2A01G231700 chr6B 95.082 244 12 0 3228 3471 715735468 715735225 8.660000e-103 385.0
105 TraesCS2A01G231700 chr6B 93.443 244 16 0 3228 3471 214184053 214184296 4.060000e-96 363.0
106 TraesCS2A01G231700 chr6B 94.118 204 12 0 2943 3146 514606939 514606736 1.490000e-80 311.0
107 TraesCS2A01G231700 chr7B 87.238 525 54 4 565 1085 474554246 474553731 2.210000e-163 586.0
108 TraesCS2A01G231700 chr7B 83.764 542 60 13 568 1084 361208752 361208214 6.420000e-134 488.0
109 TraesCS2A01G231700 chr7B 91.239 331 25 4 567 896 192371988 192371661 1.090000e-121 448.0
110 TraesCS2A01G231700 chr7B 86.817 311 33 4 273 576 59726390 59726699 1.900000e-89 340.0
111 TraesCS2A01G231700 chr7B 95.181 166 8 0 3228 3393 192368045 192367880 4.230000e-66 263.0
112 TraesCS2A01G231700 chr7B 92.941 170 12 0 916 1085 192371671 192371502 1.190000e-61 248.0
113 TraesCS2A01G231700 chr6D 85.249 522 62 7 569 1085 259466147 259465636 1.760000e-144 523.0
114 TraesCS2A01G231700 chr6D 84.909 497 62 5 593 1085 259463701 259463214 1.780000e-134 490.0
115 TraesCS2A01G231700 chr6D 87.500 304 31 3 273 570 174897457 174897155 1.470000e-90 344.0
116 TraesCS2A01G231700 chr6D 86.349 315 34 4 273 579 444609829 444609516 8.850000e-88 335.0
117 TraesCS2A01G231700 chr6D 86.645 307 28 8 273 570 158798960 158799262 1.480000e-85 327.0
118 TraesCS2A01G231700 chr6D 79.191 173 34 2 567 738 178676817 178676988 9.700000e-23 119.0
119 TraesCS2A01G231700 chrUn 83.280 311 38 6 271 571 336337789 336338095 1.960000e-69 274.0
120 TraesCS2A01G231700 chrUn 83.168 303 42 4 272 567 305426721 305426421 9.100000e-68 268.0
121 TraesCS2A01G231700 chrUn 81.940 299 41 9 267 555 31628824 31629119 1.980000e-59 241.0
122 TraesCS2A01G231700 chrUn 80.564 319 48 12 270 579 55412385 55412072 3.320000e-57 233.0
123 TraesCS2A01G231700 chrUn 80.984 305 45 10 273 570 56336195 56336493 4.290000e-56 230.0
124 TraesCS2A01G231700 chrUn 80.719 306 47 8 272 570 346647788 346648088 1.540000e-55 228.0
125 TraesCS2A01G231700 chrUn 80.645 310 46 9 275 575 349657860 349657556 1.540000e-55 228.0
126 TraesCS2A01G231700 chrUn 80.645 310 46 9 275 575 349685448 349685144 1.540000e-55 228.0
127 TraesCS2A01G231700 chrUn 85.549 173 22 3 400 570 92487401 92487572 1.580000e-40 178.0


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 TraesCS2A01G231700 chr2A 272925478 272930988 5510 True 10178.000000 10178 100.000000 1 5511 1 chr2A.!!$R3 5510
1 TraesCS2A01G231700 chr2A 272916204 272916872 668 True 1186.000000 1186 98.655000 4843 5511 1 chr2A.!!$R2 668
2 TraesCS2A01G231700 chr2A 481063931 481064599 668 True 1186.000000 1186 98.655000 4843 5511 1 chr2A.!!$R4 668
3 TraesCS2A01G231700 chr2A 38416774 38417443 669 True 1175.000000 1175 98.358000 4843 5511 1 chr2A.!!$R1 668
4 TraesCS2A01G231700 chr2A 475920975 475921487 512 False 636.000000 636 89.080000 569 1085 1 chr2A.!!$F2 516
5 TraesCS2A01G231700 chr3A 267363243 267365032 1789 True 2830.000000 2830 95.254000 1688 3471 1 chr3A.!!$R1 1783
6 TraesCS2A01G231700 chr3A 560174807 560177655 2848 True 2150.000000 3738 94.563500 568 3471 2 chr3A.!!$R3 2903
7 TraesCS2A01G231700 chr2B 654443709 654447496 3787 True 1944.000000 3247 93.488000 823 3470 2 chr2B.!!$R4 2647
8 TraesCS2A01G231700 chr2B 442556432 442557100 668 True 1203.000000 1203 99.103000 4843 5511 1 chr2B.!!$R2 668
9 TraesCS2A01G231700 chr2B 442564887 442565555 668 True 1175.000000 1175 98.356000 4843 5511 1 chr2B.!!$R3 668
10 TraesCS2A01G231700 chr2B 277325149 277325755 606 False 558.000000 558 84.426000 4 570 1 chr2B.!!$F1 566
11 TraesCS2A01G231700 chr4D 460232805 460237424 4619 False 1627.500000 3145 95.584500 614 3471 2 chr4D.!!$F5 2857
12 TraesCS2A01G231700 chr3B 276820137 276821949 1812 True 2590.000000 2590 92.396000 569 2394 1 chr3B.!!$R1 1825
13 TraesCS2A01G231700 chr3B 368902777 368905632 2855 False 2116.500000 2447 93.252000 566 3471 2 chr3B.!!$F5 2905
14 TraesCS2A01G231700 chr3B 158637807 158638603 796 False 1234.000000 1234 94.605000 1595 2391 1 chr3B.!!$F1 796
15 TraesCS2A01G231700 chr3B 366554138 366554922 784 False 1229.000000 1229 94.730000 1595 2391 1 chr3B.!!$F2 796
16 TraesCS2A01G231700 chr3B 530705605 530706156 551 False 843.000000 843 94.213000 2919 3471 1 chr3B.!!$F3 552
17 TraesCS2A01G231700 chr3D 333108437 333109814 1377 False 2283.000000 2283 96.589000 3471 4847 1 chr3D.!!$F1 1376
18 TraesCS2A01G231700 chr3D 364354952 364356329 1377 False 2278.000000 2278 96.517000 3471 4847 1 chr3D.!!$F2 1376
19 TraesCS2A01G231700 chr7D 124115829 124117208 1379 True 2279.000000 2279 96.522000 3471 4847 1 chr7D.!!$R1 1376
20 TraesCS2A01G231700 chr5D 381681435 381682811 1376 True 2278.000000 2278 96.517000 3471 4847 1 chr5D.!!$R4 1376
21 TraesCS2A01G231700 chr2D 292997228 292998605 1377 False 2278.000000 2278 96.519000 3471 4847 1 chr2D.!!$F1 1376
22 TraesCS2A01G231700 chr2D 236017004 236017593 589 True 728.000000 728 89.492000 1 571 1 chr2D.!!$R2 570
23 TraesCS2A01G231700 chr1D 381133428 381134805 1377 False 2278.000000 2278 96.517000 3471 4847 1 chr1D.!!$F6 1376
24 TraesCS2A01G231700 chr1D 427559457 427560833 1376 False 2278.000000 2278 96.517000 3471 4847 1 chr1D.!!$F7 1376
25 TraesCS2A01G231700 chr1D 28458280 28459657 1377 True 2272.000000 2272 96.444000 3471 4847 1 chr1D.!!$R1 1376
26 TraesCS2A01G231700 chr1D 80484110 80485487 1377 True 2272.000000 2272 96.444000 3471 4847 1 chr1D.!!$R3 1376
27 TraesCS2A01G231700 chr5A 166880243 166881975 1732 True 1384.000000 2180 95.653500 1688 3471 2 chr5A.!!$R2 1783
28 TraesCS2A01G231700 chr5A 216120166 216120714 548 False 857.000000 857 94.756000 2919 3471 1 chr5A.!!$F1 552
29 TraesCS2A01G231700 chr5A 310425826 310426339 513 True 621.000000 621 88.506000 568 1085 1 chr5A.!!$R1 517
30 TraesCS2A01G231700 chr7A 499818112 499818780 668 True 1175.000000 1175 98.356000 4843 5511 1 chr7A.!!$R2 668
31 TraesCS2A01G231700 chr7A 107568724 107569394 670 True 1173.000000 1173 98.214000 4841 5511 1 chr7A.!!$R1 670
32 TraesCS2A01G231700 chr7A 270099421 270100098 677 False 1170.000000 1170 97.791000 4834 5511 1 chr7A.!!$F2 677
33 TraesCS2A01G231700 chr4B 220286478 220287146 668 False 1175.000000 1175 98.356000 4843 5511 1 chr4B.!!$F1 668
34 TraesCS2A01G231700 chr4B 279025162 279025676 514 True 538.000000 538 85.687000 567 1084 1 chr4B.!!$R1 517
35 TraesCS2A01G231700 chr4B 361101993 361102495 502 True 534.000000 534 85.988000 567 1079 1 chr4B.!!$R2 512
36 TraesCS2A01G231700 chr4A 371042801 371043353 552 True 883.000000 883 95.479000 2919 3471 1 chr4A.!!$R2 552
37 TraesCS2A01G231700 chr4A 33796522 33797030 508 True 640.000000 640 89.362000 569 1081 1 chr4A.!!$R1 512
38 TraesCS2A01G231700 chr5B 205582006 205582554 548 True 859.000000 859 94.909000 2922 3471 1 chr5B.!!$R3 549
39 TraesCS2A01G231700 chr5B 71983287 71983801 514 True 664.000000 664 89.922000 569 1083 1 chr5B.!!$R2 514
40 TraesCS2A01G231700 chr5B 297124488 297128263 3775 True 442.000000 499 95.444000 2922 3474 2 chr5B.!!$R4 552
41 TraesCS2A01G231700 chr5B 274090884 274091384 500 False 409.000000 409 81.574000 566 1083 1 chr5B.!!$F3 517
42 TraesCS2A01G231700 chr1B 102630739 102631266 527 True 723.000000 723 91.264000 2140 2676 1 chr1B.!!$R1 536
43 TraesCS2A01G231700 chr1B 133699267 133699793 526 False 719.000000 719 91.215000 2140 2673 1 chr1B.!!$F1 533
44 TraesCS2A01G231700 chr1B 281031854 281032358 504 False 411.000000 411 81.574000 569 1083 1 chr1B.!!$F2 514
45 TraesCS2A01G231700 chr1B 163666495 163667126 631 True 365.500000 418 91.239000 2140 2676 2 chr1B.!!$R2 536
46 TraesCS2A01G231700 chr6B 214170089 214170595 506 False 632.000000 632 89.237000 570 1077 1 chr6B.!!$F1 507
47 TraesCS2A01G231700 chr6B 335173994 335174502 508 True 531.000000 531 85.549000 569 1084 1 chr6B.!!$R1 515
48 TraesCS2A01G231700 chr7B 474553731 474554246 515 True 586.000000 586 87.238000 565 1085 1 chr7B.!!$R2 520
49 TraesCS2A01G231700 chr7B 361208214 361208752 538 True 488.000000 488 83.764000 568 1084 1 chr7B.!!$R1 516
50 TraesCS2A01G231700 chr7B 192367880 192371988 4108 True 319.666667 448 93.120333 567 3393 3 chr7B.!!$R3 2826
51 TraesCS2A01G231700 chr6D 259463214 259466147 2933 True 506.500000 523 85.079000 569 1085 2 chr6D.!!$R3 516

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
310 353 0.041090 TGGGATTTTCCAGGAAGGGC 59.959 55.000 1.07 0.00 38.64 5.19 F
1184 3706 0.106217 CACTCCTCCCTCCTCCTCTC 60.106 65.000 0.00 0.00 0.00 3.20 F
1574 5238 0.465097 AGCATGGACCATAGCAGCAC 60.465 55.000 22.69 4.18 0.00 4.40 F
1729 5419 1.075212 TGGTGTTGATTGATGGCTGGA 59.925 47.619 0.00 0.00 0.00 3.86 F
3365 14455 1.419762 TCAGAGCTGGGCTTTACACAA 59.580 47.619 0.00 0.00 39.88 3.33 F
3553 14830 2.629051 GCCAGTGAAGTATGGGTACAC 58.371 52.381 0.00 0.00 37.05 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 5194 0.251653 TACTCCTCGTGGTGCTCCTT 60.252 55.000 6.34 0.0 34.23 3.36 R
2713 7728 2.428890 CTCAGGGCGTCTTGATTCTAGT 59.571 50.000 1.00 0.0 0.00 2.57 R
3553 14830 0.895530 TAGGACCGACTCCAGCAAAG 59.104 55.000 2.34 0.0 42.46 2.77 R
3555 14832 1.592400 CGTAGGACCGACTCCAGCAA 61.592 60.000 3.08 0.0 42.46 3.91 R
4207 15485 0.822164 GCCTTTCTAGCCGTACCAGA 59.178 55.000 0.00 0.0 0.00 3.86 R
5152 16435 2.435586 GTGCAGGCTGCTGACGAT 60.436 61.111 36.50 0.0 45.31 3.73 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
32 33 5.888161 AGTGTTGATTCACTTGGTTTTCTCT 59.112 36.000 0.00 0.00 44.92 3.10
67 68 2.364002 TCGGTAATCATCATGGCTCGAA 59.636 45.455 0.00 0.00 0.00 3.71
70 71 3.248602 GGTAATCATCATGGCTCGAACAC 59.751 47.826 0.00 0.00 0.00 3.32
71 72 2.696989 ATCATCATGGCTCGAACACA 57.303 45.000 0.00 0.00 0.00 3.72
75 76 2.014335 TCATGGCTCGAACACAGATG 57.986 50.000 0.00 0.00 0.00 2.90
89 103 0.685131 CAGATGCTGGCCCAATTGGA 60.685 55.000 26.60 4.77 37.39 3.53
153 190 1.103803 GCCGACTGGTAGATGAGTCA 58.896 55.000 0.00 0.00 38.87 3.41
156 193 2.294791 CCGACTGGTAGATGAGTCATCC 59.705 54.545 26.14 14.64 41.36 3.51
164 201 2.650813 GATGAGTCATCCGCCGGCTT 62.651 60.000 26.68 6.18 35.07 4.35
171 208 2.363975 ATCCGCCGGCTTGAAGGTA 61.364 57.895 26.68 8.25 0.00 3.08
245 282 7.069344 TCTCCATGAGTTGTCCTATCAAGATA 58.931 38.462 0.00 0.00 0.00 1.98
266 303 7.310664 AGATATTTTGCATGTCTGACAAGTTG 58.689 34.615 15.31 9.87 0.00 3.16
271 308 2.807967 GCATGTCTGACAAGTTGCTGTA 59.192 45.455 21.48 0.00 0.00 2.74
310 353 0.041090 TGGGATTTTCCAGGAAGGGC 59.959 55.000 1.07 0.00 38.64 5.19
349 392 6.156949 AGCTGATAAGTATTTCCCTCAGTGAA 59.843 38.462 0.00 0.00 34.13 3.18
362 405 4.832823 CCCTCAGTGAAAACCAAGGTTATT 59.167 41.667 4.68 2.46 37.35 1.40
392 436 3.557595 CAGGAGAATCACGCAAATCCTAC 59.442 47.826 0.00 0.00 35.43 3.18
394 438 4.649674 AGGAGAATCACGCAAATCCTACTA 59.350 41.667 0.00 0.00 35.43 1.82
411 455 9.705103 AATCCTACTAAATAGTACCTACACACA 57.295 33.333 0.00 0.00 37.73 3.72
682 731 0.976641 AGCCGTTGGATCTTCACAGA 59.023 50.000 0.00 0.00 0.00 3.41
833 884 1.527034 CACCCAATCACCTGTGTCTG 58.473 55.000 0.00 0.00 0.00 3.51
1029 3550 3.645268 GATCCCACCGCTGGCCTTT 62.645 63.158 3.32 0.00 36.00 3.11
1183 3705 1.589399 CCACTCCTCCCTCCTCCTCT 61.589 65.000 0.00 0.00 0.00 3.69
1184 3706 0.106217 CACTCCTCCCTCCTCCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
1525 5189 1.027357 GTCTCGTGGATAAGGGCGTA 58.973 55.000 0.00 0.00 0.00 4.42
1526 5190 1.001597 GTCTCGTGGATAAGGGCGTAG 60.002 57.143 0.00 0.00 0.00 3.51
1527 5191 1.134007 TCTCGTGGATAAGGGCGTAGA 60.134 52.381 0.00 0.00 0.00 2.59
1529 5193 1.884579 TCGTGGATAAGGGCGTAGATC 59.115 52.381 0.00 0.00 0.00 2.75
1530 5194 1.611977 CGTGGATAAGGGCGTAGATCA 59.388 52.381 0.00 0.00 0.00 2.92
1531 5195 2.035449 CGTGGATAAGGGCGTAGATCAA 59.965 50.000 0.00 0.00 0.00 2.57
1532 5196 3.654414 GTGGATAAGGGCGTAGATCAAG 58.346 50.000 0.00 0.00 0.00 3.02
1533 5197 2.632996 TGGATAAGGGCGTAGATCAAGG 59.367 50.000 0.00 0.00 0.00 3.61
1534 5198 2.897969 GGATAAGGGCGTAGATCAAGGA 59.102 50.000 0.00 0.00 0.00 3.36
1554 5218 1.103803 GCACCACGAGGAGTAGATCA 58.896 55.000 5.68 0.00 38.69 2.92
1574 5238 0.465097 AGCATGGACCATAGCAGCAC 60.465 55.000 22.69 4.18 0.00 4.40
1698 5388 1.298859 GGAGATCGTTGTTTGGCGCT 61.299 55.000 7.64 0.00 0.00 5.92
1729 5419 1.075212 TGGTGTTGATTGATGGCTGGA 59.925 47.619 0.00 0.00 0.00 3.86
1820 5715 3.342719 TGAACTGCCGATTAAGATGCAA 58.657 40.909 0.00 0.00 32.58 4.08
1871 6138 4.910195 TCCTGCTCACTGTGATATTTGTT 58.090 39.130 11.45 0.00 0.00 2.83
1915 6182 9.911138 GGTTTGGTTAAGATATAGAGCTACTAC 57.089 37.037 0.00 0.00 33.62 2.73
2133 6401 7.312154 ACAAAATGCTTATTTCGCTTCACATA 58.688 30.769 0.00 0.00 0.00 2.29
2197 6825 3.389002 AGGACCTTTTTGCTTGCATTCTT 59.611 39.130 0.00 0.00 0.00 2.52
2208 6836 4.142204 TGCTTGCATTCTTGTGTCTTTTGA 60.142 37.500 0.00 0.00 0.00 2.69
2288 6950 3.417101 ACGCAATTGACATACCCTTCAA 58.583 40.909 10.34 0.00 36.21 2.69
2455 7428 8.999431 TCTACTAATGTTTGTTTAGCTTGAAGG 58.001 33.333 0.00 0.00 31.22 3.46
2483 7456 2.265589 TGACGTTTTTCTCTTCCCCC 57.734 50.000 0.00 0.00 0.00 5.40
2529 7503 4.963373 TCCCGTATGTTTTGACAAAGAGA 58.037 39.130 0.10 0.00 0.00 3.10
2713 7728 5.715439 AACCTCCATGATATTTGAGTGGA 57.285 39.130 0.00 0.00 37.41 4.02
2715 7730 4.723789 ACCTCCATGATATTTGAGTGGACT 59.276 41.667 0.00 0.00 35.29 3.85
2975 10073 7.284489 TGAAGTGCTTCTTGGTATTTTACAACT 59.716 33.333 12.44 0.00 40.14 3.16
2993 10091 8.958119 TTACAACTGTTTACTCTGAATTCTGT 57.042 30.769 7.05 5.88 0.00 3.41
3129 10995 9.769093 ACACGAAAAATGATAATACTAACAAGC 57.231 29.630 0.00 0.00 0.00 4.01
3204 14294 1.939934 TCGTGTTCACTCCTGCAAAAG 59.060 47.619 1.53 0.00 0.00 2.27
3207 14297 3.003689 CGTGTTCACTCCTGCAAAAGAAT 59.996 43.478 2.18 0.00 0.00 2.40
3365 14455 1.419762 TCAGAGCTGGGCTTTACACAA 59.580 47.619 0.00 0.00 39.88 3.33
3401 14491 5.037385 GTGAAGTTCCAGTTTTTCTTCTGC 58.963 41.667 0.00 0.00 36.49 4.26
3497 14774 6.619801 ATGAAATCGGTATACCTTTTGCTC 57.380 37.500 19.68 8.95 0.00 4.26
3553 14830 2.629051 GCCAGTGAAGTATGGGTACAC 58.371 52.381 0.00 0.00 37.05 2.90
3555 14832 3.307480 GCCAGTGAAGTATGGGTACACTT 60.307 47.826 0.00 0.00 39.33 3.16
3633 14910 3.755378 GTGTTGTCTGATTTCTCTGGCAT 59.245 43.478 0.00 0.00 35.27 4.40
4016 15294 4.746535 TGGGAGCGTATGAGTTTCATTA 57.253 40.909 0.00 0.00 38.26 1.90
4129 15407 5.350504 AAGCAGCTACACAGATCATAGTT 57.649 39.130 0.00 0.00 0.00 2.24
4207 15485 9.224267 CTTGCTGGAATATATGTGCTAGTATTT 57.776 33.333 0.00 0.00 0.00 1.40
4209 15487 8.597167 TGCTGGAATATATGTGCTAGTATTTCT 58.403 33.333 0.00 0.00 0.00 2.52
4229 15507 1.626825 TGGTACGGCTAGAAAGGCTTT 59.373 47.619 13.25 13.25 45.93 3.51
4232 15510 0.322546 ACGGCTAGAAAGGCTTTGGG 60.323 55.000 18.79 8.01 45.93 4.12
4275 15553 7.333423 GTGAAGGTGCAGTACTGTTAATATCAA 59.667 37.037 23.44 0.85 0.00 2.57
4311 15589 1.228552 ACACAGCTCCCCGCATTTT 60.229 52.632 0.00 0.00 42.61 1.82
4317 15595 1.512694 CTCCCCGCATTTTCTTGCC 59.487 57.895 0.00 0.00 39.52 4.52
4335 15613 7.807977 TCTTGCCATTCTTATAGGATTCAAC 57.192 36.000 0.00 0.00 0.00 3.18
4339 15617 6.126507 TGCCATTCTTATAGGATTCAACTGGA 60.127 38.462 0.00 0.00 0.00 3.86
4342 15620 7.775093 CCATTCTTATAGGATTCAACTGGACAA 59.225 37.037 0.00 0.00 0.00 3.18
4450 15728 0.467844 ACACTGCAAATGTCCCTGCA 60.468 50.000 0.00 0.00 46.01 4.41
4557 15835 7.186570 TGGATCACATACATATGTATCCAGG 57.813 40.000 24.24 16.75 44.57 4.45
4603 15881 5.755375 ACTCATTTTGCTCCATATGTAGTCG 59.245 40.000 1.24 0.00 0.00 4.18
4619 15897 7.962995 ATGTAGTCGATGGTGGAATCTATAT 57.037 36.000 0.00 0.00 0.00 0.86
4791 16071 2.751166 ACCTGTCTCTCGACCATTTG 57.249 50.000 0.00 0.00 39.47 2.32
5152 16435 4.942944 TCCTCCTAAACTACTCATGGTCA 58.057 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.405198 TACCGAGTGTCTACCACCCA 59.595 55.000 0.00 0.00 45.74 4.51
67 68 0.251922 AATTGGGCCAGCATCTGTGT 60.252 50.000 6.23 0.00 0.00 3.72
70 71 0.685131 TCCAATTGGGCCAGCATCTG 60.685 55.000 24.29 0.86 36.21 2.90
71 72 0.685458 GTCCAATTGGGCCAGCATCT 60.685 55.000 24.29 0.00 36.21 2.90
75 76 1.187567 ACTTGTCCAATTGGGCCAGC 61.188 55.000 25.83 11.93 39.61 4.85
89 103 5.758784 GGCTGAGAACTACAAACTAACTTGT 59.241 40.000 0.00 0.00 42.20 3.16
124 138 2.262915 CAGTCGGCTGGTGACTCC 59.737 66.667 9.79 0.00 44.60 3.85
153 190 1.906105 TTACCTTCAAGCCGGCGGAT 61.906 55.000 33.44 24.23 0.00 4.18
156 193 1.359459 GACTTACCTTCAAGCCGGCG 61.359 60.000 23.20 8.11 0.00 6.46
245 282 4.053295 GCAACTTGTCAGACATGCAAAAT 58.947 39.130 18.77 0.00 34.10 1.82
266 303 2.606725 CAGCTCACAAGTAGCATACAGC 59.393 50.000 0.00 0.00 46.26 4.40
271 308 2.414994 ATGCAGCTCACAAGTAGCAT 57.585 45.000 0.00 0.00 42.62 3.79
322 365 7.344612 TCACTGAGGGAAATACTTATCAGCTAA 59.655 37.037 0.00 0.00 38.14 3.09
362 405 2.766313 CGTGATTCTCCTGTTGGTTCA 58.234 47.619 0.00 0.00 34.23 3.18
370 413 2.636830 AGGATTTGCGTGATTCTCCTG 58.363 47.619 0.00 0.00 32.01 3.86
378 421 7.069085 AGGTACTATTTAGTAGGATTTGCGTGA 59.931 37.037 0.00 0.00 39.29 4.35
392 436 7.488471 GCTCTTGTGTGTGTAGGTACTATTTAG 59.512 40.741 0.00 0.00 45.60 1.85
394 438 6.164176 GCTCTTGTGTGTGTAGGTACTATTT 58.836 40.000 0.00 0.00 45.60 1.40
438 482 1.272147 GGATTGACAACCCTCTTGCCT 60.272 52.381 0.00 0.00 0.00 4.75
441 485 1.839424 GGGGATTGACAACCCTCTTG 58.161 55.000 19.17 0.00 44.97 3.02
531 575 6.790285 AAATTACCTTGCTGCAATTTTCTG 57.210 33.333 16.38 2.77 28.70 3.02
682 731 6.362283 CGCGAGGTGAAAATTGATTTTAACTT 59.638 34.615 0.00 8.29 39.82 2.66
833 884 4.995058 TGGGGTGGGAGTGGGGTC 62.995 72.222 0.00 0.00 0.00 4.46
1029 3550 1.557269 GGAGGAGGCAAGCAGAGGAA 61.557 60.000 0.00 0.00 0.00 3.36
1132 3654 4.029809 GGCTAGGGTTGGTGCGGT 62.030 66.667 0.00 0.00 0.00 5.68
1298 4960 0.395173 AAATCCCGCCCGTATTTGCT 60.395 50.000 0.00 0.00 0.00 3.91
1305 4967 3.140141 CATGCAAATCCCGCCCGT 61.140 61.111 0.00 0.00 0.00 5.28
1525 5189 0.534412 CTCGTGGTGCTCCTTGATCT 59.466 55.000 6.34 0.00 34.23 2.75
1526 5190 0.460987 CCTCGTGGTGCTCCTTGATC 60.461 60.000 6.34 0.00 34.23 2.92
1527 5191 0.904865 TCCTCGTGGTGCTCCTTGAT 60.905 55.000 6.34 0.00 34.23 2.57
1529 5193 1.079543 CTCCTCGTGGTGCTCCTTG 60.080 63.158 6.34 0.00 34.23 3.61
1530 5194 0.251653 TACTCCTCGTGGTGCTCCTT 60.252 55.000 6.34 0.00 34.23 3.36
1531 5195 0.681564 CTACTCCTCGTGGTGCTCCT 60.682 60.000 6.34 0.00 34.23 3.69
1532 5196 0.680280 TCTACTCCTCGTGGTGCTCC 60.680 60.000 2.99 0.00 34.23 4.70
1533 5197 1.335496 GATCTACTCCTCGTGGTGCTC 59.665 57.143 2.99 0.00 34.23 4.26
1534 5198 1.341089 TGATCTACTCCTCGTGGTGCT 60.341 52.381 2.99 0.00 34.23 4.40
1554 5218 0.256752 TGCTGCTATGGTCCATGCTT 59.743 50.000 15.10 0.00 0.00 3.91
1574 5238 1.088340 CACCAGCAGCTCCTTGATCG 61.088 60.000 0.00 0.00 0.00 3.69
1607 5297 4.063689 CCAATCCTTCTTGATCATCCTCG 58.936 47.826 0.00 0.00 0.00 4.63
1653 5343 3.327404 GTCCCGCCCTTCTTCCCA 61.327 66.667 0.00 0.00 0.00 4.37
1698 5388 4.395231 TCAATCAACACCAAACACACGTTA 59.605 37.500 0.00 0.00 33.99 3.18
1729 5419 1.079127 GGTAGCACACCGCAGTCAT 60.079 57.895 0.00 0.00 46.13 3.06
1820 5715 5.846203 ACAACATGATAAAAACAGCAGCTT 58.154 33.333 0.00 0.00 0.00 3.74
1871 6138 5.757320 CCAAACCACAGTGCAAATATTTTCA 59.243 36.000 0.00 0.00 0.00 2.69
1915 6182 5.220854 CCCACGAGGTAATGCAGAATAAAAG 60.221 44.000 0.00 0.00 0.00 2.27
2133 6401 3.931907 TGCATCCTGTTACAGCCTTAT 57.068 42.857 6.88 0.00 0.00 1.73
2197 6825 6.773976 ATTTTCTCCTTGTCAAAAGACACA 57.226 33.333 0.00 0.00 34.45 3.72
2208 6836 7.124750 CCCTCCAAATGATAATTTTCTCCTTGT 59.875 37.037 0.00 0.00 0.00 3.16
2268 6930 4.637483 ATTGAAGGGTATGTCAATTGCG 57.363 40.909 0.00 0.00 40.71 4.85
2288 6950 5.704515 CACCACTGAACTCTGATTCAAGAAT 59.295 40.000 0.00 0.00 38.12 2.40
2442 7415 7.244192 GTCATGTAACATCCTTCAAGCTAAAC 58.756 38.462 0.00 0.00 0.00 2.01
2446 7419 3.935203 CGTCATGTAACATCCTTCAAGCT 59.065 43.478 0.00 0.00 0.00 3.74
2455 7428 7.015877 GGAAGAGAAAAACGTCATGTAACATC 58.984 38.462 0.00 0.00 0.00 3.06
2483 7456 8.237267 GGAATGTAAGGAAAAAGTCATACACAG 58.763 37.037 0.00 0.00 34.67 3.66
2561 7535 4.512944 CAGGCTACTACCATGTATGCTTTG 59.487 45.833 0.00 0.00 0.00 2.77
2713 7728 2.428890 CTCAGGGCGTCTTGATTCTAGT 59.571 50.000 1.00 0.00 0.00 2.57
2715 7730 2.735151 TCTCAGGGCGTCTTGATTCTA 58.265 47.619 1.00 0.00 0.00 2.10
2774 7789 9.481340 GAATTCCTATTAGGATTCAAATTTGGC 57.519 33.333 17.90 7.98 45.34 4.52
2975 10073 8.777413 CATGAAGAACAGAATTCAGAGTAAACA 58.223 33.333 8.44 0.00 38.72 2.83
2993 10091 6.040729 TGAAAATTGTCTGAAGGCATGAAGAA 59.959 34.615 0.00 0.00 0.00 2.52
3129 10995 8.028938 AGCAGTACTGGCATTATTAAAAACAAG 58.971 33.333 23.95 0.00 0.00 3.16
3204 14294 8.015658 ACAGCAGAATTAACTGTTACGAAATTC 58.984 33.333 14.34 14.34 41.78 2.17
3207 14297 6.854496 ACAGCAGAATTAACTGTTACGAAA 57.146 33.333 0.00 0.00 41.78 3.46
3365 14455 4.104102 TGGAACTTCACTTACCCACTGAAT 59.896 41.667 0.00 0.00 0.00 2.57
3401 14491 4.207891 ACAACAGAGCAGTAATAGGGTG 57.792 45.455 0.00 0.00 0.00 4.61
3462 14739 3.194116 ACCGATTTCATTTGCTGCATTCT 59.806 39.130 1.84 0.00 0.00 2.40
3497 14774 1.665916 CACACAGGACCTGCACTCG 60.666 63.158 21.95 7.57 34.37 4.18
3553 14830 0.895530 TAGGACCGACTCCAGCAAAG 59.104 55.000 2.34 0.00 42.46 2.77
3555 14832 1.592400 CGTAGGACCGACTCCAGCAA 61.592 60.000 3.08 0.00 42.46 3.91
3633 14910 2.993937 AGTCCTTGAAAAACGTGGTGA 58.006 42.857 0.00 0.00 0.00 4.02
3975 15253 6.310941 TCCCAACCTGTTGATTCTTATTCAA 58.689 36.000 11.47 0.00 42.93 2.69
3980 15258 3.686016 GCTCCCAACCTGTTGATTCTTA 58.314 45.455 11.47 0.00 42.93 2.10
3995 15273 3.627395 AATGAAACTCATACGCTCCCA 57.373 42.857 0.00 0.00 35.76 4.37
4016 15294 2.885135 TTGAGTGCCATTCTGGATGT 57.115 45.000 0.00 0.00 40.96 3.06
4129 15407 8.266473 TGCTTAAGGTTTTCCCGTTATATCTAA 58.734 33.333 4.29 0.00 41.86 2.10
4207 15485 0.822164 GCCTTTCTAGCCGTACCAGA 59.178 55.000 0.00 0.00 0.00 3.86
4209 15487 1.272807 AAGCCTTTCTAGCCGTACCA 58.727 50.000 0.00 0.00 0.00 3.25
4229 15507 1.902508 CTTGAAGAGAGCTGGTACCCA 59.097 52.381 10.07 0.00 0.00 4.51
4232 15510 3.944055 TCACTTGAAGAGAGCTGGTAC 57.056 47.619 0.00 0.00 0.00 3.34
4275 15553 3.244078 TGTGTCGCCTTTGAGAGTTACAT 60.244 43.478 0.00 0.00 0.00 2.29
4311 15589 7.500227 CAGTTGAATCCTATAAGAATGGCAAGA 59.500 37.037 0.00 0.00 0.00 3.02
4317 15595 8.737168 TTGTCCAGTTGAATCCTATAAGAATG 57.263 34.615 0.00 0.00 0.00 2.67
4339 15617 5.044846 AGGAATAGGATTTGTAGTGGCTTGT 60.045 40.000 0.00 0.00 0.00 3.16
4342 15620 6.330250 ACATAGGAATAGGATTTGTAGTGGCT 59.670 38.462 0.00 0.00 0.00 4.75
4371 15649 4.202161 GCCTCTTTGATTCGTAGGATCTGA 60.202 45.833 0.00 0.00 0.00 3.27
4372 15650 4.054671 GCCTCTTTGATTCGTAGGATCTG 58.945 47.826 0.00 0.00 0.00 2.90
4450 15728 7.246171 AGTATGTTCCTTGTACTGAAGATGT 57.754 36.000 10.87 0.00 0.00 3.06
4495 15773 8.533657 TCTACCAAGACTTATATTTTGGAACGA 58.466 33.333 8.93 0.47 42.05 3.85
4619 15897 8.125978 TCTCCGTTCCTAAATACAAGTCTTTA 57.874 34.615 0.00 0.00 0.00 1.85
4814 16094 3.838903 GGAAGAAGAAGGGTTAGGAGACA 59.161 47.826 0.00 0.00 0.00 3.41
5081 16364 3.513912 TCGATCTGTATCCCAGTTTGTGT 59.486 43.478 0.00 0.00 42.19 3.72
5152 16435 2.435586 GTGCAGGCTGCTGACGAT 60.436 61.111 36.50 0.00 45.31 3.73


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

AutoCloner maintained by Alex Coulton.